diff --git a/dev/CODE_OF_CONDUCT.html b/dev/CODE_OF_CONDUCT.html
index df1b541..fddcb08 100644
--- a/dev/CODE_OF_CONDUCT.html
+++ b/dev/CODE_OF_CONDUCT.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/CONTRIBUTING.html b/dev/CONTRIBUTING.html
index 10dc3f2..bf04ecd 100644
--- a/dev/CONTRIBUTING.html
+++ b/dev/CONTRIBUTING.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/LICENSE-text.html b/dev/LICENSE-text.html
index e31d1bb..5c6afbc 100644
--- a/dev/LICENSE-text.html
+++ b/dev/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/LICENSE.html b/dev/LICENSE.html
index 360a50b..03b6e78 100644
--- a/dev/LICENSE.html
+++ b/dev/LICENSE.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/SUPPORT.html b/dev/SUPPORT.html
index 86316ca..3ca23d1 100644
--- a/dev/SUPPORT.html
+++ b/dev/SUPPORT.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/articles/ecotypes.html b/dev/articles/ecotypes.html
index 58c0fd1..c2748b1 100644
--- a/dev/articles/ecotypes.html
+++ b/dev/articles/ecotypes.html
@@ -30,7 +30,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -70,7 +70,7 @@
                         <h4 data-toc-skip class="author">Joe Thorley and
 Ayla Pearson</h4>
             
-            <h4 data-toc-skip class="date">2025-01-03</h4>
+            <h4 data-toc-skip class="date">2025-01-14</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/poissonconsulting/ypr/blob/main/vignettes/ecotypes.Rmd" class="external-link"><code>vignettes/ecotypes.Rmd</code></a></small>
       <div class="d-none name"><code>ecotypes.Rmd</code></div>
@@ -101,8 +101,6 @@ <h2 id="two-ecotypes">Two Ecotypes<a class="anchor" aria-label="anchor" href="#t
 switch to piscivory which allows it to grow much larger.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://poissonconsulting.github.io/ypr/">ypr</a></span><span class="op">)</span></span>
-<span><span class="co">#&gt; Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
-<span><span class="co">#&gt;   object 'type_sum.accel' not found</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span> <span class="co"># for plotting</span></span>
 <span></span>
 <span><span class="va">ecotypes</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_ecotypes.html">ypr_ecotypes</a></span><span class="op">(</span></span>
diff --git a/dev/articles/index.html b/dev/articles/index.html
index 2dd1da2..97a105b 100644
--- a/dev/articles/index.html
+++ b/dev/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/articles/ypr.html b/dev/articles/ypr.html
index 7e8f042..4e0399c 100644
--- a/dev/articles/ypr.html
+++ b/dev/articles/ypr.html
@@ -30,7 +30,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -70,7 +70,7 @@
                         <h4 data-toc-skip class="author">Joe
 Thorley</h4>
             
-            <h4 data-toc-skip class="date">2025-01-03</h4>
+            <h4 data-toc-skip class="date">2025-01-14</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/poissonconsulting/ypr/blob/main/vignettes/ypr.Rmd" class="external-link"><code>vignettes/ypr.Rmd</code></a></small>
       <div class="d-none name"><code>ypr.Rmd</code></div>
@@ -92,8 +92,6 @@ <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#i
 stock-recruitment relationship. The remaining population processes of
 growth, reproduction and death are captured through a series of
 relatively straight-forward deterministic equations.</p>
-<pre><code><span><span class="co">#&gt; Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
-<span><span class="co">#&gt;   object 'type_sum.accel' not found</span></span></code></pre>
 <table class="table">
 <caption>Table 1. The 32 parameters with their default values and
 descriptions.</caption>
@@ -296,12 +294,12 @@ <h3 id="length">Length<a class="anchor" aria-label="anchor" href="#length"></a>
 growth curve</p>
 <p><span class="math display">L = L_{\infty} \cdot (1 - \exp(-k \cdot
 (t-t_0)))</span></p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">population</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_population.html">ypr_population</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="va">population</span>, <span class="st">"Age"</span>, <span class="st">"Length"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-2-1.png" width="384"></p>
 <p>which can be biphasic</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, L2 <span class="op">=</span> <span class="fl">75</span>, Linf2 <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="st">"Age"</span>, <span class="st">"Length"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; Warning: `ypr_population_update()` was deprecated in ypr 0.5.3.</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Please use `ypr_update()` instead.</span></span>
@@ -316,7 +314,7 @@ <h3 id="weight">Weight<a class="anchor" aria-label="anchor" href="#weight"></a>
 <p>The weight (<span class="math inline">W</span>) at a given length is
 assumed to follow the classic allometric relationship</p>
 <p><span class="math display">W = w_\alpha \cdot L^{w_\beta}</span></p>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">population</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, Wa <span class="op">=</span> <span class="fl">0.01</span>, Wb <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="va">population</span>, <span class="st">"Length"</span>, <span class="st">"Weight"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-4-1.png" width="384"></p>
@@ -336,7 +334,7 @@ <h3 id="fecundity">Fecundity<a class="anchor" aria-label="anchor" href="#fecundi
 <p>The fecundity (<span class="math inline">F</span>) is assumed to
 scale allometrically with the weight according to the equation</p>
 <p><span class="math display">F = f_\alpha \cdot W^{f_\beta}</span></p>
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">population</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, fa <span class="op">=</span> <span class="fl">1</span>, fb <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="va">population</span>, <span class="st">"Weight"</span>, <span class="st">"Fecundity"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-5-1.png" width="384"></p>
@@ -350,7 +348,7 @@ <h3 id="spawning">Spawning<a class="anchor" aria-label="anchor" href="#spawning"
 <p>The probability of spawning at length <span class="math inline">L</span> is determined by the equation</p>
 <p><span class="math display">S = \frac{L^{S_p}}{L_s^{S_p} + L^{S_p}}
 \cdot es</span></p>
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">population</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, Ls <span class="op">=</span> <span class="fl">50</span>, Sp <span class="op">=</span> <span class="fl">10</span>, es <span class="op">=</span> <span class="fl">0.8</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="va">population</span>, <span class="st">"Length"</span>, <span class="st">"Spawning"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-6-1.png" width="384"></p>
@@ -363,16 +361,16 @@ <h2 id="death">Death<a class="anchor" aria-label="anchor" href="#death"></a>
 <h3 id="natural-mortality">Natural Mortality<a class="anchor" aria-label="anchor" href="#natural-mortality"></a>
 </h3>
 <p>By default the natural annual interval mortality rate (<span class="math inline">n</span>) is assumed to be constant</p>
-<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="va">population</span>, <span class="st">"Length"</span>, <span class="st">"NaturalMortality"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-7-1.png" width="384"></p>
 <p>although like growth it can vary biphasically</p>
-<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, nL <span class="op">=</span> <span class="fl">0.15</span>, Ln <span class="op">=</span> <span class="fl">60</span><span class="op">)</span>, <span class="st">"Length"</span>, <span class="st">"NaturalMortality"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-8-1.png" width="384"></p>
 <p>The natural mortality rate can also be affected by spawning
 mortality</p>
-<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">population</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, Sm <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="va">population</span>, <span class="st">"Length"</span>, <span class="st">"NaturalMortality"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-9-1.png" width="384"></p>
@@ -384,7 +382,7 @@ <h3 id="fishing-mortality">Fishing Mortality<a class="anchor" aria-label="anchor
 assumed to vary by length as follows</p>
 <p><span class="math display">V = \frac{L^{V_p}}{L_v^{V_p} +
 L^{V_p}}</span></p>
-<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">population</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, Lv <span class="op">=</span> <span class="fl">50</span>, Vp <span class="op">=</span> <span class="fl">50</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="va">population</span>, <span class="st">"Length"</span>, <span class="st">"Vulnerability"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-10-1.png" width="384"></p>
@@ -392,7 +390,7 @@ <h3 id="fishing-mortality">Fishing Mortality<a class="anchor" aria-label="anchor
 effectively knife-edged.</p>
 <p>The probabilty of being retained if captured (<span class="math inline">R</span>) depends on the release rate (<span class="math inline">\rho</span>), the slot limits (<span class="math inline">L_{lo}</span> and <span class="math inline">L_{up}</span>) and the non-compliance with the
 limits (<span class="math inline">N_c</span>)</p>
-<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">population</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, rho <span class="op">=</span> <span class="fl">0.5</span>, Llo <span class="op">=</span> <span class="fl">40</span>, Lup <span class="op">=</span> <span class="fl">70</span>, Nc <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="va">population</span>, <span class="st">"Length"</span>, <span class="st">"Retention"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-11-1.png" width="384"></p>
@@ -403,7 +401,7 @@ <h3 id="fishing-mortality">Fishing Mortality<a class="anchor" aria-label="anchor
 \cdot (1 - R) \cdot H_m</span></p>
 <p>The calculation assumes that a released fish cannot be recaught in
 the same year.</p>
-<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">population</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, pi <span class="op">=</span> <span class="fl">0.3</span>, Hm <span class="op">=</span> <span class="fl">0.2</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="va">population</span>, <span class="st">"Length"</span>, <span class="st">"FishingMortality"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-12-1.png" width="384"></p>
@@ -421,7 +419,7 @@ <h2 id="recruitment">Recruitment<a class="anchor" aria-label="anchor" href="#rec
 = 1</span>) curve then</p>
 <p><span class="math display">R = \frac{\alpha \cdot E}{(\beta \cdot E +
 1)}</span></p>
-<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">population</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, Rk <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/ypr_plot_sr.html">ypr_plot_sr</a></span><span class="op">(</span><span class="va">population</span>, plot_values <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-13-1.png" width="384"></p>
@@ -432,7 +430,7 @@ <h2 id="recruitment">Recruitment<a class="anchor" aria-label="anchor" href="#rec
 relationship is as follows</p>
 <p><span class="math display">R = \alpha \cdot E \cdot \exp (-\beta
 \cdot E)</span></p>
-<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">population</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ypr_population_update.html">ypr_population_update</a></span><span class="op">(</span><span class="va">population</span>, BH <span class="op">=</span> <span class="fl">0L</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/ypr_plot_sr.html">ypr_plot_sr</a></span><span class="op">(</span><span class="va">population</span>, plot_values <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-14-1.png" width="384"></p>
@@ -442,7 +440,7 @@ <h2 id="recruitment">Recruitment<a class="anchor" aria-label="anchor" href="#rec
 concept of the (unfished) survivorship (<span class="math inline">lx_a</span>) which is the probability of a recruit
 surviving to age <span class="math inline">a</span> in the absence of
 fish mortality.</p>
-<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/ypr_plot_schedule.html">ypr_plot_schedule</a></span><span class="op">(</span><span class="va">population</span>, <span class="st">"Age"</span>, <span class="st">"Survivorship"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-15-1.png" width="384"></p>
 <p>The unfished survivorship (<span class="math inline">lx_a</span>) is
@@ -533,10 +531,10 @@ <h2 id="yield">Yield<a class="anchor" aria-label="anchor" href="#yield"></a>
 \text{if}(La &lt; L_y)\ 0\ \text{else}\ R_{0F} \cdot lx_a^F \cdot \pi
 \cdot V_a \cdot R \cdot W_a/1000</span> where <span class="math inline">L_y</span> is the minimum length of a trophy
 fish.</p>
-<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/ypr_plot_yield.html">ypr_plot_yield</a></span><span class="op">(</span><span class="va">population</span>, harvest <span class="op">=</span> <span class="cn">TRUE</span>, biomass <span class="op">=</span> <span class="cn">TRUE</span>, Ly <span class="op">=</span> <span class="fl">60</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-16-1.png" width="384"></p>
-<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/ypr_tabulate_yield.html">ypr_tabulate_yield</a></span><span class="op">(</span><span class="va">population</span>, harvest <span class="op">=</span> <span class="cn">TRUE</span>, biomass <span class="op">=</span> <span class="cn">TRUE</span>, Ly <span class="op">=</span> <span class="fl">60</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2 × 8</span></span></span>
 <span><span class="co">#&gt;   Type       pi     u  Yield   Age Length Weight Effort</span></span>
@@ -553,10 +551,10 @@ <h2 id="efficiency">Efficiency<a class="anchor" aria-label="anchor" href="#effic
 relationship <span class="math display">\pi = 1 - \exp(\log(1-q)\cdot
 E)</span> which can be rearranged to give <span class="math display">E =
 \frac{\log(1-\pi)}{\log(1-q)}.</span></p>
-<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/ypr_plot_yield.html">ypr_plot_yield</a></span><span class="op">(</span><span class="va">population</span>, y <span class="op">=</span> <span class="st">"Effort"</span>, harvest <span class="op">=</span> <span class="cn">TRUE</span>, biomass <span class="op">=</span> <span class="cn">TRUE</span>, Ly <span class="op">=</span> <span class="fl">60</span><span class="op">)</span></span></code></pre></div>
 <p><img src="ypr_files/figure-html/unnamed-chunk-17-1.png" width="384"></p>
-<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/ypr_plot_yield.html">ypr_plot_yield</a></span><span class="op">(</span><span class="va">population</span>, y <span class="op">=</span> <span class="st">"YPUE"</span>, harvest <span class="op">=</span> <span class="cn">TRUE</span>, biomass <span class="op">=</span> <span class="cn">TRUE</span>, Ly <span class="op">=</span> <span class="fl">60</span><span class="op">)</span></span>
 <span><span class="co">#&gt; Warning: Removed 1 row containing missing values or values outside the scale range</span></span>
 <span><span class="co">#&gt; (`geom_line()`).</span></span></code></pre></div>
diff --git a/dev/authors.html b/dev/authors.html
index bc65510..f806627 100644
--- a/dev/authors.html
+++ b/dev/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -58,14 +58,14 @@ <h2 id="citation">Citation</h2>
 
       <p>Thorley J (2025).
 <em>ypr: Yield Per Recruit</em>.
-R package version 0.6.0.9010,
+R package version 0.6.0.9011,
 https://github.com/poissonconsulting/ypr, <a href="https://poissonconsulting.github.io/ypr/">https://poissonconsulting.github.io/ypr/</a>.
 </p>
       <pre>@Manual{,
   title = {ypr: Yield Per Recruit},
   author = {Joe Thorley},
   year = {2025},
-  note = {R package version 0.6.0.9010,
+  note = {R package version 0.6.0.9011,
     https://github.com/poissonconsulting/ypr},
   url = {https://poissonconsulting.github.io/ypr/},
 }</pre>
diff --git a/dev/index.html b/dev/index.html
index 5ab5f15..debf3e8 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -33,7 +33,7 @@
 
     <a class="navbar-brand me-2" href="index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/news/index.html b/dev/news/index.html
index edb784c..549bd03 100644
--- a/dev/news/index.html
+++ b/dev/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,6 +36,11 @@
       <small>Source: <a href="https://github.com/poissonconsulting/ypr/blob/main/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="0.6.0.9011" id="ypr-0609011">ypr 0.6.0.9011<a class="anchor" aria-label="anchor" href="#ypr-0609011"></a></h2>
+<ul><li><p>Merge branch ‘main’ of github.com:poissonconsulting/ypr.</p></li>
+<li><p>Have parameter description NA if documentation corrupted.</p></li>
+</ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.6.0.9010" id="ypr-0609010">ypr 0.6.0.9010<a class="anchor" aria-label="anchor" href="#ypr-0609010"></a></h2>
 <div class="section level3">
diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml
index caaf599..edfb841 100644
--- a/dev/pkgdown.yml
+++ b/dev/pkgdown.yml
@@ -1,10 +1,10 @@
 pandoc: 3.1.11
 pkgdown: 2.1.1.9000
-pkgdown_sha: 4519ca0ae415b415eb8c1c142a6d4d39d8a5b80d
+pkgdown_sha: 6615322cb2ce15b1effcecf894123c88fa10b9c9
 articles:
   ecotypes: ecotypes.html
   ypr: ypr.html
-last_built: 2025-01-03T22:25Z
+last_built: 2025-01-14T18:09Z
 urls:
   reference: https://poissonconsulting.github.io/ypr/reference
   article: https://poissonconsulting.github.io/ypr/articles
diff --git a/dev/reference/adams_bt_03.html b/dev/reference/adams_bt_03.html
index 5b4c67e..76e6abc 100644
--- a/dev/reference/adams_bt_03.html
+++ b/dev/reference/adams_bt_03.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/as_ypr_ecotypes.html b/dev/reference/as_ypr_ecotypes.html
index 3fbce39..baa078d 100644
--- a/dev/reference/as_ypr_ecotypes.html
+++ b/dev/reference/as_ypr_ecotypes.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/as_ypr_population.html b/dev/reference/as_ypr_population.html
index cb6c583..fb08df9 100644
--- a/dev/reference/as_ypr_population.html
+++ b/dev/reference/as_ypr_population.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/as_ypr_populations.html b/dev/reference/as_ypr_populations.html
index 10b7792..76c4595 100644
--- a/dev/reference/as_ypr_populations.html
+++ b/dev/reference/as_ypr_populations.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/check_ecotypes.html b/dev/reference/check_ecotypes.html
index 9778031..63b4328 100644
--- a/dev/reference/check_ecotypes.html
+++ b/dev/reference/check_ecotypes.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/check_population.html b/dev/reference/check_population.html
index 2eef6f5..baabb98 100644
--- a/dev/reference/check_population.html
+++ b/dev/reference/check_population.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/check_populations.html b/dev/reference/check_populations.html
index f242378..4a14e66 100644
--- a/dev/reference/check_populations.html
+++ b/dev/reference/check_populations.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/chilliwack_bt_05.html b/dev/reference/chilliwack_bt_05.html
index bffc214..165f96e 100644
--- a/dev/reference/chilliwack_bt_05.html
+++ b/dev/reference/chilliwack_bt_05.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/index.html b/dev/reference/index.html
index 0159224..d9e67a1 100644
--- a/dev/reference/index.html
+++ b/dev/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/is.ypr_population.html b/dev/reference/is.ypr_population.html
index 1cd4aa6..054405f 100644
--- a/dev/reference/is.ypr_population.html
+++ b/dev/reference/is.ypr_population.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/kootenay_bt_13.html b/dev/reference/kootenay_bt_13.html
index a2ac4c8..63bc571 100644
--- a/dev/reference/kootenay_bt_13.html
+++ b/dev/reference/kootenay_bt_13.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/kootenay_rb.html b/dev/reference/kootenay_rb.html
index b6aa061..9702179 100644
--- a/dev/reference/kootenay_rb.html
+++ b/dev/reference/kootenay_rb.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/kootenay_rb_13.html b/dev/reference/kootenay_rb_13.html
index fd666ab..058a54d 100644
--- a/dev/reference/kootenay_rb_13.html
+++ b/dev/reference/kootenay_rb_13.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/params.html b/dev/reference/params.html
index 483dec1..5f1b865 100644
--- a/dev/reference/params.html
+++ b/dev/reference/params.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/plot.ypr_population.html b/dev/reference/plot.ypr_population.html
index ab05951..bde85e4 100644
--- a/dev/reference/plot.ypr_population.html
+++ b/dev/reference/plot.ypr_population.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/quesnel_bt.html b/dev/reference/quesnel_bt.html
index 8949dd8..21f7b27 100644
--- a/dev/reference/quesnel_bt.html
+++ b/dev/reference/quesnel_bt.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/quesnel_lt.html b/dev/reference/quesnel_lt.html
index ef32d9f..98164b3 100644
--- a/dev/reference/quesnel_lt.html
+++ b/dev/reference/quesnel_lt.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/quesnel_rb.html b/dev/reference/quesnel_rb.html
index 3e22d65..382907c 100644
--- a/dev/reference/quesnel_rb.html
+++ b/dev/reference/quesnel_rb.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/reexports.html b/dev/reference/reexports.html
index f62a748..d2ef9dc 100644
--- a/dev/reference/reexports.html
+++ b/dev/reference/reexports.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/ypr_update.html b/dev/reference/ypr_update.html
index cd1c632..be06b09 100644
--- a/dev/reference/ypr_update.html
+++ b/dev/reference/ypr_update.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/ypr_yield.html b/dev/reference/ypr_yield.html
index 8420bb4..e4eb7f7 100644
--- a/dev/reference/ypr_yield.html
+++ b/dev/reference/ypr_yield.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/reference/ypr_yields.html b/dev/reference/ypr_yields.html
index 775e703..1691de2 100644
--- a/dev/reference/ypr_yields.html
+++ b/dev/reference/ypr_yields.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">ypr</a>
 
-    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9010</small>
+    <small class="nav-text text-danger me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">0.6.0.9011</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/dev/search.json b/dev/search.json
index 434da6e..65ee112 100644
--- a/dev/search.json
+++ b/dev/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to ypr","title":"Contributing to ypr","text":"outlines propose change ypr.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing to ypr","text":"can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to ypr","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to ypr","text":"Fork package clone onto computer. haven’t done , recommend using usethis::create_from_github(\"\", fork = TRUE). Install development dependences devtools::install_dev_deps(), make sure package passes R CMD check running devtools::check(). R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using usethis::pr_init(\"brief-description--change\"). Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number. Begin commit merge messages - indicate user facing changes included NEWS.md. use fledge automatically generate NEWS.md file.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to ypr","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. use roxygen2, Markdown syntax, documentation. use testthat unit tests. Contributions test cases included easier accept.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing to ypr","text":"Please note ypr project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2020 Poisson Consulting Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/SUPPORT.html","id":null,"dir":"","previous_headings":"","what":"Getting help with ypr","title":"Getting help with ypr","text":"Thanks using ypr! filing issue, places explore pieces put together make process smooth possible.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/SUPPORT.html","id":"make-sure-its-new","dir":"","previous_headings":"","what":"Make sure its new","title":"Getting help with ypr","text":"opening new issue, sure search issues pull requests make sure bug hasn’t reported /already fixed development version. default, search pre-populated :issue :open. can edit qualifiers (e.g. :pr, :closed) needed. example, ’d simply remove :open search issues repo, open closed.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/SUPPORT.html","id":"make-a-reprex","dir":"","previous_headings":"","what":"Make a reprex","title":"Getting help with ypr","text":"Start making minimal reproducible example using reprex package. haven’t heard used reprex , ’re treat! Seriously, reprex make R-question-asking endeavors easier (pretty insane ROI five ten minutes ’ll take learn ’s ). additional reprex pointers, check Get help! section tidyverse site.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ecotypes.html","id":"ecotypes","dir":"Articles","previous_headings":"","what":"Ecotypes","title":"Ecotypes","text":"ypr package population considered group interbreeding fish indistinguishable anglers. Ecotypes groups individuals population different life-history strategies. Consequently, ecotypes must share key fishery (pi, Llo, Lup, Nc, rho, Hm q) stock recruitment (BH, RK, tR Rmax) parameters.y use yield-per-recruit approach also necessary assume relative proportion recruits (RPR) adopting life-history strategy independent size composition parental stock.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ecotypes.html","id":"two-ecotypes","dir":"Articles","previous_headings":"","what":"Two Ecotypes","title":"Ecotypes","text":"Consider population smaller ecotype second larger ecotype delays maturation order achieve sufficient size switch piscivory allows grow much larger.","code":"library(ypr) #> Error in get(paste0(generic, \".\", class), envir = get_method_env()) :  #>   object 'type_sum.accel' not found library(ggplot2) # for plotting  ecotypes <- ypr_ecotypes(   Linf2 = 200,   L2 = c(100, 50),   Ls = c(50, 75),   pi = 0.05,   names = c(\"small\", \"large\"),   RPR = c(0.8, 0.2) )  ypr_plot_schedule(ecotypes) + scale_color_manual(values = c(\"black\", \"blue\")) ypr_plot_schedule(ecotypes, x = \"Age\", y = \"Spawning\") + scale_color_manual(values = c(\"black\", \"blue\"))"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ecotypes.html","id":"fish","dir":"Articles","previous_headings":"Two Ecotypes","what":"Fish","title":"Ecotypes","text":"","code":"ypr_plot_fish(ecotypes, color = \"white\") + scale_fill_manual(values = c(\"black\", \"blue\")) ypr_plot_fish(ecotypes, x = \"Length\", y = \"Caught\", color = \"white\", binwidth = 15) + scale_fill_manual(values = c(\"black\", \"blue\"))"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ecotypes.html","id":"stock-recruitment","dir":"Articles","previous_headings":"Two Ecotypes","what":"Stock-Recruitment","title":"Ecotypes","text":"","code":"ypr_plot_sr(ecotypes, biomass = TRUE) ypr_tabulate_sr(ecotypes, biomass = TRUE) #> # A tibble: 3 × 7 #>   Type         pi      u  Eggs Recruits Spawners Fecundity #>   <chr>     <dbl>  <dbl> <dbl>    <dbl>    <dbl>     <dbl> #> 1 unfished 0      0      4085.    0.667    1.27      6431. #> 2 actual   0.05   0.05   2483.    0.549    0.879     5653. #> 3 optimal  0.0833 0.0833 1705.    0.455    0.656     5200."},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ecotypes.html","id":"yield","dir":"Articles","previous_headings":"Two Ecotypes","what":"Yield","title":"Ecotypes","text":"","code":"ypr_tabulate_yield(ecotypes, biomass = TRUE) #> # A tibble: 2 × 8 #>   Type        pi      u Yield   Age Length Weight Effort #>   <chr>    <dbl>  <dbl> <dbl> <dbl>  <dbl>  <dbl>  <dbl> #> 1 actual  0.05   0.05   0.253  7.97   73.6  5474.  0.487 #> 2 optimal 0.0833 0.0833 0.290  7.64   71.9  5026.  0.825 ypr_plot_yield(ecotypes, biomass = TRUE)"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Get Started with ypr","text":"Fish born, grow, reproduce die – whether natural causes fishing. ’s . Modelers just use complicated (complicated) math iron details. Cooper (2006) Equilibrium based yield per recruit (YPR) methods (Walters Martell 2004) estimate capture rate optimizes yield assumption stochasticity density-dependence captured stock-recruitment relationship. remaining population processes growth, reproduction death captured series relatively straight-forward deterministic equations. Table 1. 32 parameters default values descriptions.","code":"#> Error in get(paste0(generic, \".\", class), envir = get_method_env()) :  #>   object 'type_sum.accel' not found"},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"length","dir":"Articles","previous_headings":"Growth","what":"Length","title":"Get Started with ypr","text":"ypr length (cm) age (t) assumed follow Von Bertalanffy growth curve L = L_{\\infty} \\cdot (1 - \\exp(-k \\cdot (t-t_0)))  can biphasic","code":"population <- ypr_population() ypr_plot_schedule(population, \"Age\", \"Length\") ypr_plot_schedule(ypr_population_update(population, L2 = 75, Linf2 = 200), \"Age\", \"Length\") #> Warning: `ypr_population_update()` was deprecated in ypr 0.5.3. #> ℹ Please use `ypr_update()` instead. #> This warning is displayed once every 8 hours. #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was #> generated."},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"weight","dir":"Articles","previous_headings":"Growth","what":"Weight","title":"Get Started with ypr","text":"weight (W) given length assumed follow classic allometric relationship W = w_\\alpha \\cdot L^{w_\\beta}  worth noting w_\\alpha, extrapolated weight (g) 1 cm individual, scaling constant affects estimate yield (calculated terms biomass), ie, affect estimate optimal capture rate.","code":"population <- ypr_population_update(population, Wa = 0.01, Wb = 3) ypr_plot_schedule(population, \"Length\", \"Weight\")"},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"fecundity","dir":"Articles","previous_headings":"Reproduction","what":"Fecundity","title":"Get Started with ypr","text":"fecundity (F) assumed scale allometrically weight according equation F = f_\\alpha \\cdot W^{f_\\beta}  f_\\alpha, extrapolated eggs produced 1 g female, scaling constant effect yield optimal capture rate.","code":"population <- ypr_population_update(population, fa = 1, fb = 1) ypr_plot_schedule(population, \"Weight\", \"Fecundity\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"spawning","dir":"Articles","previous_headings":"Reproduction","what":"Spawning","title":"Get Started with ypr","text":"probability spawning length L determined equation S = \\frac{L^{S_p}}{L_s^{S_p} + L^{S_p}} \\cdot es","code":"population <- ypr_population_update(population, Ls = 50, Sp = 10, es = 0.8) ypr_plot_schedule(population, \"Length\", \"Spawning\")"},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"natural-mortality","dir":"Articles","previous_headings":"Death","what":"Natural Mortality","title":"Get Started with ypr","text":"default natural annual interval mortality rate (n) assumed constant  although like growth can vary biphasically  natural mortality rate can also affected spawning mortality","code":"ypr_plot_schedule(population, \"Length\", \"NaturalMortality\") ypr_plot_schedule(ypr_population_update(population, nL = 0.15, Ln = 60), \"Length\", \"NaturalMortality\") population <- ypr_population_update(population, Sm = 0.5) ypr_plot_schedule(population, \"Length\", \"NaturalMortality\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"fishing-mortality","dir":"Articles","previous_headings":"Death","what":"Fishing Mortality","title":"Get Started with ypr","text":"vulnerability capture (V) assumed vary length follows V = \\frac{L^{V_p}}{L_v^{V_p} + L^{V_p}}  V_p 100 vulnerability effectively knife-edged. probabilty retained captured (R) depends release rate (\\rho), slot limits (L_{lo} L_{}) non-compliance limits (N_c)  fishing mortality (U) depends V, R probability capture fully vulnerable (pi) well hooking mortality (H_m) U =  V \\cdot \\pi \\cdot  R +  V \\cdot \\pi \\cdot (1 - R) \\cdot H_m calculation assumes released fish recaught year.","code":"population <- ypr_population_update(population, Lv = 50, Vp = 50) ypr_plot_schedule(population, \"Length\", \"Vulnerability\") population <- ypr_population_update(population, rho = 0.5, Llo = 40, Lup = 70, Nc = 0.1) ypr_plot_schedule(population, \"Length\", \"Retention\") population <- ypr_population_update(population, pi = 0.3, Hm = 0.2) ypr_plot_schedule(population, \"Length\", \"FishingMortality\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"recruitment","dir":"Articles","previous_headings":"","what":"Recruitment","title":"Get Started with ypr","text":"growth, reproduction death defined, final task estimate recruitment (birth) rate. requires lifetime number spawners per spawner low density (R_k) recruitment age (R_t; default 1) defined. recruitment follows Beverton-Holt (BH = 1) curve R = \\frac{\\alpha \\cdot E}{(\\beta \\cdot E + 1)}  E annual eggs (stock) R annual recruits age R_t. Ricker curve (BH = 0) relationship follows R = \\alpha \\cdot E \\cdot \\exp (-\\beta \\cdot E)  number recruits carrying capacity (R_\\text{max}) scaling constant affects estimate yield. calculating recruitment important introduce concept (unfished) survivorship (lx_a) probability recruit surviving age absence fish mortality.  unfished survivorship (lx_a) defined recursively lx_{R_t} = 1, lx_a = lx_{-1} \\cdot (1-N_{-1}) \\;\\text{}\\; > R_t N_a annual interval natural mortality age . fished survivorship (lx_a^F) lx_{R_t}^F = 1, lx_a^F = lx_{-1}^F \\cdot (1 - (1 - N_{-1}) \\cdot (1 - U_{-1})) \\;\\text{}\\; > R_t lifetime number eggs deposited per (unfished) recruit (\\phi) just \\phi = \\sum_{= R_t}^{t_\\text{max}} lx_a \\cdot F_a/2 \\cdot S_a t_\\text{max} maximum age considered (default 20) F_a fecundity age divided two sex ratio assumed 1:1 S_a probability spawning. fished equivalent denoted \\phi_F. important realize unfished equilibrium annual number recruits (R_0) related annual egg deposition according following equation E_0 = \\phi \\cdot R_0 definition \\alpha = \\frac{R_k \\cdot R_0}{E_0} = \\frac{R_k}{\\phi} \\beta term Beverton-Holt curve can found rearranging following formula R_0 = \\frac{\\alpha \\cdot \\phi \\cdot R_0}{\\beta \\cdot \\phi \\cdot R_0 + 1} \\beta \\cdot \\phi \\cdot R_0 + 1 = \\alpha \\cdot \\phi \\beta = \\frac{\\alpha \\cdot \\phi - 1}{\\phi \\cdot R_0} equivalent equation Ricker curve arrived follows R_0 = \\alpha \\cdot \\phi \\cdot R_0 \\cdot \\exp (-\\beta \\cdot \\phi \\cdot R_0) \\frac{1}{\\exp (-\\beta \\cdot \\phi \\cdot R_0)} = \\alpha \\cdot \\phi \\beta \\cdot \\phi \\cdot R_0 = \\log(\\alpha \\cdot \\phi) \\beta = \\frac{\\log(\\alpha \\cdot \\phi)}{\\phi \\cdot R_0} number recruits fished equilibrium (R_{0F}) can found Beverton-Holt curve follows R_{0F} = \\frac{\\alpha \\cdot \\phi_F \\cdot R_{0F}}{\\beta \\cdot \\phi_F \\cdot R_{0F} + 1} \\beta \\cdot \\phi_F \\cdot R_{0F} + 1 = \\alpha \\cdot \\phi_F R_{0F} = \\frac{\\alpha \\cdot \\phi_F - 1}{\\beta \\cdot \\phi_F} Ricker R_{0F} = \\alpha \\cdot \\phi_F \\cdot R_{0F} \\cdot \\exp (-\\beta \\cdot \\phi_F \\cdot R_{0F}) \\frac{1}{\\exp(-\\beta \\cdot \\phi_F \\cdot R_{0F})} = \\alpha \\cdot \\phi_F \\beta \\cdot \\phi_F \\cdot R_{0F} = \\log(\\alpha \\cdot \\phi_F) R_{0F} = \\frac{\\log(\\alpha \\cdot \\phi_F)}{\\beta \\cdot \\phi_F} Finally estimates rescaled carrying capacity identical R_\\text{max} following transformations \\beta = \\beta \\cdot \\kappa / R_\\text{max}      R_0 = R_0 / \\kappa \\cdot R_\\text{max}      R_{0F} = R_{0F} / \\kappa \\cdot R_\\text{max} \\kappa, carrying capacity original scale, \\alpha/\\beta Beverton-Holt \\alpha/(\\beta \\cdot e) Ricker curve.","code":"population <- ypr_population_update(population, Rk = 3) ypr_plot_sr(population, plot_values = FALSE) population <- ypr_population_update(population, BH = 0L) ypr_plot_sr(population, plot_values = FALSE) ypr_plot_schedule(population, \"Age\", \"Survivorship\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"yield","dir":"Articles","previous_headings":"","what":"Yield","title":"Get Started with ypr","text":"yield simply number fish caught (irrespective weight whether harvested) given Y = \\sum_{= R_t}^{t_\\text{max}} R_{0F} \\cdot lx_a^F \\cdot \\pi \\cdot V_a harvested fish considered becomes Y = \\sum_{= R_t}^{t_\\text{max}} R_{0F} \\cdot lx_a^F \\cdot \\pi \\cdot V_a \\cdot R total weight (kg) important Y = \\sum_{= R_t}^{t_\\text{max}} R_{0F} \\cdot lx_a^F \\cdot \\pi \\cdot V_a \\cdot R \\cdot W_a/1000 trophy fish considered Y = \\sum_{= R_t}^{t_\\text{max}} \\text{}(La < L_y)\\ 0\\ \\text{else}\\ R_{0F} \\cdot lx_a^F \\cdot \\pi \\cdot V_a \\cdot R \\cdot W_a/1000 L_y minimum length trophy fish.","code":"ypr_plot_yield(population, harvest = TRUE, biomass = TRUE, Ly = 60) ypr_tabulate_yield(population, harvest = TRUE, biomass = TRUE, Ly = 60) #> # A tibble: 2 × 8 #>   Type       pi     u  Yield   Age Length Weight Effort #>   <chr>   <dbl> <dbl>  <dbl> <dbl>  <dbl>  <dbl>  <dbl> #> 1 actual  0.3   0.18  0.0505  7.39   66.8  3006.   3.39 #> 2 optimal 0.441 0.265 0.0553  7.35   66.7  2978.   5.53"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"efficiency","dir":"Articles","previous_headings":"","what":"Efficiency","title":"Get Started with ypr","text":"catchability q indicates probability capture unit effort (E). assumed related \\pi according relationship \\pi = 1 - \\exp(\\log(1-q)\\cdot E) can rearranged give E = \\frac{\\log(1-\\pi)}{\\log(1-q)}.","code":"ypr_plot_yield(population, y = \"Effort\", harvest = TRUE, biomass = TRUE, Ly = 60) ypr_plot_yield(population, y = \"YPUE\", harvest = TRUE, biomass = TRUE, Ly = 60) #> Warning: Removed 1 row containing missing values or values outside the scale range #> (`geom_line()`)."},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Joe Thorley. Author, maintainer. Ayla Pearson. Contributor. . Copyright holder, funder.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Thorley J (2025). ypr: Yield Per Recruit. R package version 0.6.0.9010, https://github.com/poissonconsulting/ypr, https://poissonconsulting.github.io/ypr/.","code":"@Manual{,   title = {ypr: Yield Per Recruit},   author = {Joe Thorley},   year = {2025},   note = {R package version 0.6.0.9010,     https://github.com/poissonconsulting/ypr},   url = {https://poissonconsulting.github.io/ypr/}, }"},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Yield Per Recruit","text":"ypr R package implements equilibrium-based yield per recruit methods. Yield per recruit methods can used estimate optimal yield (Walters Martell 2004) fish population one ecotypes. yield can based number fish caught (harvested) biomass fish just large (trophy) individuals. key life history parameters growth coefficient (k) mean maximum length (Linf) Von Bertalanffy growth curve length 50% mature (Ls) length 50% vulnerable harvest (Lv) annual interval natural mortality rate (n) lifetime number spawners per spawner low density (Rk) case ecotypes relative proportion recruits belong ecotype (RPR) calculations account stochasticity, predator-prey dynamics, angler responses density-dependent growth.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"schedule","dir":"","previous_headings":"Demonstration","what":"Schedule","title":"Yield Per Recruit","text":"","code":"library(ypr) population <- ypr_population(Rk = 5, Ls = 50, Rmax = 100, rho = 0.6) ypr_plot_schedule(population, x = \"Length\", y = \"Spawning\") ypr_tabulate_schedule(population) #> # A tibble: 20 × 11 #>      Age Length Weight Fecundity Spawning NaturalMortality Vulnerability #>    <int>  <dbl>  <dbl>     <dbl>    <dbl>            <dbl>         <dbl> #>  1     1   13.9   27.0      27.0 3.13e-56              0.2      3.13e-56 #>  2     2   25.9  174.      174.  2.91e-29              0.2      2.91e-29 #>  3     3   36.2  476.      476.  1.04e-14              0.2      1.04e-14 #>  4     4   45.1  918.      918.  3.46e- 5              0.2      3.46e- 5 #>  5     5   52.8 1469.     1469.  9.95e- 1              0.2      9.95e- 1 #>  6     6   59.3 2090.     2090.  1.00e+ 0              0.2      1.00e+ 0 #>  7     7   65.0 2747.     2747.  1.00e+ 0              0.2      1.00e+ 0 #>  8     8   69.9 3412.     3412.  1.00e+ 0              0.2      1.00e+ 0 #>  9     9   74.1 4065.     4065.  1   e+ 0              0.2      1   e+ 0 #> 10    10   77.7 4689.     4689.  1   e+ 0              0.2      1   e+ 0 #> 11    11   80.8 5274.     5274.  1   e+ 0              0.2      1   e+ 0 #> 12    12   83.5 5816.     5816.  1   e+ 0              0.2      1   e+ 0 #> 13    13   85.8 6310.     6310.  1   e+ 0              0.2      1   e+ 0 #> 14    14   87.8 6758.     6758.  1   e+ 0              0.2      1   e+ 0 #> 15    15   89.5 7160.     7160.  1   e+ 0              0.2      1   e+ 0 #> 16    16   90.9 7518.     7518.  1   e+ 0              0.2      1   e+ 0 #> 17    17   92.2 7836.     7836.  1   e+ 0              0.2      1   e+ 0 #> 18    18   93.3 8116.     8116.  1   e+ 0              0.2      1   e+ 0 #> 19    19   94.2 8363.     8363.  1   e+ 0              0.2      1   e+ 0 #> 20    20   95.0 8580.     8580.  1   e+ 0              0.2      1   e+ 0 #> # ℹ 4 more variables: Retention <dbl>, FishingMortality <dbl>, #> #   Survivorship <dbl>, FishedSurvivorship <dbl>"},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"fish","dir":"","previous_headings":"Demonstration","what":"Fish","title":"Yield Per Recruit","text":"","code":"ypr_plot_fish(population, color = \"white\") ypr_tabulate_fish(population) #> # A tibble: 20 × 8 #>      Age Survivors Spawners   Caught Harvested Released HandlingMortalities #>    <dbl>     <dbl>    <dbl>    <dbl>     <dbl>    <dbl>               <dbl> #>  1     1    70.1   2.19e-54 4.39e-55  1.76e-55 2.63e-55                   0 #>  2     2    56.1   1.63e-27 3.26e-28  1.30e-28 1.96e-28                   0 #>  3     3    44.9   4.68e-13 9.36e-14  3.74e-14 5.62e-14                   0 #>  4     4    35.9   1.24e- 3 2.48e- 4  9.93e- 5 1.49e- 4                   0 #>  5     5    28.7   2.86e+ 1 5.72e+ 0  2.29e+ 0 3.43e+ 0                   0 #>  6     6    21.1   2.11e+ 1 4.23e+ 0  1.69e+ 0 2.54e+ 0                   0 #>  7     7    15.6   1.56e+ 1 3.11e+ 0  1.24e+ 0 1.87e+ 0                   0 #>  8     8    11.5   1.15e+ 1 2.29e+ 0  9.16e- 1 1.37e+ 0                   0 #>  9     9     8.43  8.43e+ 0 1.69e+ 0  6.74e- 1 1.01e+ 0                   0 #> 10    10     6.20  6.20e+ 0 1.24e+ 0  4.96e- 1 7.44e- 1                   0 #> 11    11     4.57  4.57e+ 0 9.13e- 1  3.65e- 1 5.48e- 1                   0 #> 12    12     3.36  3.36e+ 0 6.72e- 1  2.69e- 1 4.03e- 1                   0 #> 13    13     2.47  2.47e+ 0 4.95e- 1  1.98e- 1 2.97e- 1                   0 #> 14    14     1.82  1.82e+ 0 3.64e- 1  1.46e- 1 2.18e- 1                   0 #> 15    15     1.34  1.34e+ 0 2.68e- 1  1.07e- 1 1.61e- 1                   0 #> 16    16     0.986 9.86e- 1 1.97e- 1  7.89e- 2 1.18e- 1                   0 #> 17    17     0.726 7.26e- 1 1.45e- 1  5.81e- 2 8.71e- 2                   0 #> 18    18     0.534 5.34e- 1 1.07e- 1  4.27e- 2 6.41e- 2                   0 #> 19    19     0.393 3.93e- 1 7.86e- 2  3.15e- 2 4.72e- 2                   0 #> 20    20     0.289 2.89e- 1 5.79e- 2  2.31e- 2 3.47e- 2                   0 #> # ℹ 1 more variable: Ecotype <chr>"},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"stock-recruitment","dir":"","previous_headings":"Demonstration","what":"Stock-Recruitment","title":"Yield Per Recruit","text":"","code":"ypr_plot_sr(population) ypr_tabulate_sr(population) #> # A tibble: 3 × 7 #>   Type        pi     u    Eggs Recruits Spawners Fecundity #>   <chr>    <dbl> <dbl>   <dbl>    <dbl>    <dbl>     <dbl> #> 1 unfished 0     0     286350.     80      159.      3600. #> 2 actual   0.2   0.08  167831.     70.1    108.      3112. #> 3 optimal  0.458 0.183  84129.     54.0     63.7     2641."},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"yield","dir":"","previous_headings":"Demonstration","what":"Yield","title":"Yield Per Recruit","text":"","code":"ypr_tabulate_yield(population) #> # A tibble: 2 × 8 #>   Type       pi     u Yield   Age Length Weight Effort #>   <chr>   <dbl> <dbl> <dbl> <dbl>  <dbl>  <dbl>  <dbl> #> 1 actual  0.2   0.08   8.63  7.67   65.8  3112.   2.12 #> 2 optimal 0.458 0.183 11.7   6.87   62.6  2641.   5.82 ypr_plot_yield(population)"},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"information","dir":"","previous_headings":"","what":"Information","title":"Yield Per Recruit","text":"information see Get Started vignette.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"interaction","dir":"","previous_headings":"Information","what":"Interaction","title":"Yield Per Recruit","text":"interactively explore effects altering individual parameters schedule, stock-recruitment yield see ypr shiny app. screenshot yield ypr shiny app","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"release","dir":"","previous_headings":"Installation","what":"Release","title":"Yield Per Recruit","text":"install release version CRAN. website release version https://poissonconsulting.github.io/ypr/.","code":"install.packages(\"ypr\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"development","dir":"","previous_headings":"Installation","what":"Development","title":"Yield Per Recruit","text":"install development version r-universe. GitHub","code":"install.packages(\"ypr\", repos = c(\"https://poissonconsulting.r-universe.dev\", \"https://cloud.r-project.org\")) # install.packages(\"remotes\") remotes::install_github(\"poissonconsulting/ypr\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"creditation","dir":"","previous_headings":"","what":"Creditation","title":"Yield Per Recruit","text":"Development ypr partially supported Habitat Conservation Trust Foundation Ministry Forests, Lands Natural Resource Operations. hex designed Forest.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"contribution","dir":"","previous_headings":"","what":"Contribution","title":"Yield Per Recruit","text":"Please report issues. Pull requests always welcome.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Yield Per Recruit","text":"Please note ypr project released Contributor Code Conduct. contributing project, agree abide terms","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/adams_bt_03.html","id":null,"dir":"Reference","previous_headings":"","what":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","title":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","text":"population parameters Bull Trout Adams Lake Bison et al (2003)","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/adams_bt_03.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","text":"","code":"adams_bt_03"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/adams_bt_03.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/adams_bt_03.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","text":"Bison, R., O’Brien, D., Martell, S.J.D. 2003. Analysis Sustainable Fishing Options Adams Lake Bull Trout Using Life History Telemetry Data. BC Ministry Water Land Air Protection, Kamloops, B.C.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/adams_bt_03.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","text":"","code":"adams_bt_03 #> tmax:  20 #> k:     0.13 #> Linf:  131 #> t0:    0.2 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.4 #> Ls:    40 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3.8 #> n:     0.3 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    5 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.06 #> rho:   0 #> Hm:    0.15 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(adams_bt_03)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to an Ecotypes Object — as_ypr_ecotypes","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"Coerce Ecotypes Object","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"","code":"as_ypr_ecotypes(x, ...)  # S3 method for class 'data.frame' as_ypr_ecotypes(x, ...)  # S3 method for class 'ypr_population' as_ypr_ecotypes(x, ...)  # S3 method for class 'ypr_populations' as_ypr_ecotypes(x, ...)  # S3 method for class 'ypr_ecotypes' as_ypr_ecotypes(x, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"x object coerce. ... Additional arguments.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"object class ypr_ecotypes.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"as_ypr_ecotypes(data.frame): Coerce data.frame Ecotypes Object as_ypr_ecotypes(ypr_population): Coerce Population Object Ecotypes Object as_ypr_ecotypes(ypr_populations): Coerce Populations Object Ecotypes Object as_ypr_ecotypes(ypr_ecotypes): Coerce Ecotypes Object Ecotypes Object","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"","code":"as_ypr_ecotypes(as.data.frame(ypr_ecotypes(Ls = c(10, 15, 20)))) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    10, 15, 20 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Ls_10, Ls_15, Ls_20 as_ypr_ecotypes(ypr_population()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_ecotypes(ypr_populations(Ls = c(10, 15, 20))) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    10, 15, 20 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Ls_10, Ls_15, Ls_20 as_ypr_ecotypes(ypr_ecotypes(Ls = c(10, 15, 20))) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    10, 15, 20 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Ls_10, Ls_15, Ls_20"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to a Population Object — as_ypr_population","title":"Coerce to a Population Object — as_ypr_population","text":"Coerce Population Object","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to a Population Object — as_ypr_population","text":"","code":"as_ypr_population(x, ...)  # S3 method for class 'data.frame' as_ypr_population(x, ...)  # S3 method for class 'ypr_population' as_ypr_population(x, ...)  # S3 method for class 'ypr_populations' as_ypr_population(x, ...)  # S3 method for class 'ypr_ecotypes' as_ypr_population(x, ...)  # S3 method for class 'data.frame' as_ypr_populations(x, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to a Population Object — as_ypr_population","text":"x object coerce. ... Unused.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to a Population Object — as_ypr_population","text":"object class ypr_population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Coerce to a Population Object — as_ypr_population","text":"as_ypr_population(data.frame): Coerce data.frame Population Object as_ypr_population(ypr_population): Coerce Population Object Population Object as_ypr_population(ypr_populations): Coerce Populations Object length 1 Population Object as_ypr_population(ypr_ecotypes): Coerce Ecotypes Object length 1 Population Object","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Coerce to a Population Object — as_ypr_population","text":"as_ypr_populations(data.frame): Coerce data.frame Populations Object","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to a Population Object — as_ypr_population","text":"","code":"as_ypr_population(as.data.frame(ypr_population())) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_population(ypr_populations()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_population(ypr_populations()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_population(ypr_ecotypes()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_populations(as.data.frame(ypr_populations(Rk = c(3, 4)))) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3, 4 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to a Populations Object — as_ypr_populations","title":"Coerce to a Populations Object — as_ypr_populations","text":"Coerce Populations Object","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to a Populations Object — as_ypr_populations","text":"","code":"as_ypr_populations(x, ...)  # S3 method for class 'ypr_population' as_ypr_populations(x, ...)  # S3 method for class 'ypr_populations' as_ypr_populations(x, ...)  # S3 method for class 'ypr_ecotypes' as_ypr_populations(x, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to a Populations Object — as_ypr_populations","text":"x object coerce. ... Unused.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to a Populations Object — as_ypr_populations","text":"object class ypr_ecotypes.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Coerce to a Populations Object — as_ypr_populations","text":"as_ypr_populations(ypr_population): Coerce Population Object Population Object as_ypr_populations(ypr_populations): Coerce Populations Object length 1 Population Object as_ypr_populations(ypr_ecotypes): Coerce Ecotypes Object length 1 Population Object","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to a Populations Object — as_ypr_populations","text":"","code":"as_ypr_populations(ypr_population()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_populations(ypr_populations()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_populations(ypr_ecotypes()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_ecotypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Ecotypes — check_ecotypes","title":"Check Ecotypes — check_ecotypes","text":"Checks ypr_ecotypes object valid parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_ecotypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Ecotypes — check_ecotypes","text":"","code":"check_ecotypes(x, x_name = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_ecotypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Ecotypes — check_ecotypes","text":"x object check. x_name string name object x NULL.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_ecotypes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Ecotypes — check_ecotypes","text":"informative error test fails invisible copy x.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_ecotypes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Ecotypes — check_ecotypes","text":"","code":"check_ecotypes(ypr_ecotypes())"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Population — check_population","title":"Check Population — check_population","text":"Checks ypr_population object valid parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Population — check_population","text":"","code":"check_population(x, x_name = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Population — check_population","text":"x object check. x_name string name object x NULL.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Population — check_population","text":"informative error test fails invisible copy x.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Population — check_population","text":"","code":"check_population(ypr_population())"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_populations.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Populations — check_populations","title":"Check Populations — check_populations","text":"Checks ypr_populations object valid parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_populations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Populations — check_populations","text":"","code":"check_populations(x, x_name = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_populations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Populations — check_populations","text":"x object check. x_name string name object x NULL.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_populations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Populations — check_populations","text":"informative error test fails invisible copy x.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_populations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Populations — check_populations","text":"","code":"check_populations(ypr_populations())"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/chilliwack_bt_05.html","id":null,"dir":"Reference","previous_headings":"","what":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","title":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","text":"populations parameters Bull Trout Chilliwack Lake Taylor (2005)","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/chilliwack_bt_05.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","text":"","code":"chilliwack_bt_05"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/chilliwack_bt_05.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","text":"object class ypr_populations().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/chilliwack_bt_05.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","text":"Taylor, J.L. 2005. Sustainability Chilliwack Lake Char Fishery. Ministry Water, Land Air Protection, Surrey, B.C.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/chilliwack_bt_05.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","text":"","code":"chilliwack_bt_05 #> tmax:  20 #> k:     0.12 #> Linf:  86 #> t0:    0.018 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    2.8 #> Ls:    38.5 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5, 4.6, 2.5, 4.6, 2.5, 4.6, 2.5, 4.6, 2.5, 4.6, 2.5, 4.6 #> n:     0.17 #> nL:    0.2 #> Ln:    1000 #> Lv:    36.5 #> Vp:    11.7 #> Llo:   0, 0, 60, 60, 1000, 1000, 0, 0, 60, 60, 1000, 1000 #> Lup:   1000 #> Nc:    0.15 #> pi:    0.2 #> rho:   0 #> Hm:    0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2 #> Rmax:  250 #> Wa:    0.022 #> fa:    2.29 #> q:     0.1 #> RPR:   1 yield <- ypr_tabulate_yield(chilliwack_bt_05, type = \"optimal\") yield$pi <- round(yield$pi, 2) yield <- yield[c(\"Llo\", \"Hm\", \"Rk\", \"pi\")] yield <- tidyr::spread(yield, Rk, pi) yield <- yield[order(-yield$Hm), ] yield #> # A tibble: 6 × 4 #>     Llo    Hm `2.5` `4.6` #>   <dbl> <dbl> <dbl> <dbl> #> 1     0  0.2   0.08  0.14 #> 2    60  0.2   0.14  0.25 #> 3  1000  0.2   0.25  0.45 #> 4     0  0.05  0.08  0.14 #> 5    60  0.05  0.17  0.37 #> 6  1000  0.05  0.41  0.74 if (FALSE) { # \\dontrun{ ypr_plot_yield(chilliwack_bt_05, plot_values = FALSE) +   ggplot2::facet_grid(Rk ~ Hm) +   ggplot2::aes(group = Llo, linetype = Llo) } # }"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/is.ypr_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","title":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","text":"Tests Population, Populations Ecotypes","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/is.ypr_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","text":"","code":"is.ypr_population(x)  is_ypr_population(x)  is.ypr_populations(x)  is_ypr_populations(x)  is.ypr_ecotypes(x)  is_ypr_ecotypes(x)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/is.ypr_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","text":"x object test.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/is.ypr_population.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","text":"is_ypr_population(): Test Population .ypr_populations(): Test Populations is_ypr_populations(): Test Populations .ypr_ecotypes(): Test Ecotypes is_ypr_ecotypes(): Test Ecotypes","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/is.ypr_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","text":"","code":"is.ypr_population(ypr_population()) #> [1] TRUE is_ypr_population(ypr_population()) #> [1] TRUE is.ypr_populations(ypr_populations()) #> [1] TRUE is_ypr_population(ypr_populations()) #> [1] FALSE is.ypr_ecotypes(ypr_ecotypes()) #> [1] TRUE is_ypr_ecotypes(ypr_ecotypes()) #> [1] TRUE"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":null,"dir":"Reference","previous_headings":"","what":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"population parameters Bull Trout Kootenay Lake Andrusak Thorley (2013)","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"","code":"kootenay_bt_13"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"estimates used management.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"Andrusak, G.F., Thorley, J.L. 2013. Kootenay Lake Exploitation Study: Fishing Natural Mortality Large Rainbow Trout Bull Trout: 2013 Annual Report. Poisson Consulting Ltd. Redfish Consulting Ltd. Report, Habitat Conservation Trust Foundation, Victoria, BC.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"","code":"kootenay_bt_13 #> tmax:  20 #> k:     0.19 #> Linf:  100 #> t0:    0.5 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.04 #> Ls:    60 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    5 #> n:     0.29 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    5 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.1 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(kootenay_bt_13)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":null,"dir":"Reference","previous_headings":"","what":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"population parameters Rainbow Trout Kootenay Lake.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"","code":"kootenay_rb"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"estimates liable change used management.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"Thorley, J.L., Andrusak, G.F. 2017. fishing natural mortality large, piscivorous Bull Trout Rainbow Trout Kootenay Lake, British Columbia (2008–2013). PeerJ 5: e2874. doi:10.7717/peerj.2874.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"","code":"kootenay_rb #> tmax:  20 #> k:     0.26 #> Linf:  100 #> t0:    0.5 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.2 #> Ls:    75 #> Sp:    20 #> es:    0.9 #> Sm:    0.53 #> fb:    0.86 #> tR:    1 #> BH:    1 #> Rk:    17.65 #> n:     0.23 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    10 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.14 #> rho:   0.62 #> Hm:    0.25 #> Rmax:  115000 #> Wa:    0.005 #> fa:    3.9 #> q:     0.028 #> RPR:   1 ypr_plot_yield(kootenay_rb)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":null,"dir":"Reference","previous_headings":"","what":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"population parameters Rainbow Trout Kootenay Lake Andrusak Thorley (2013)","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"","code":"kootenay_rb_13"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"estimates used management.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"Andrusak, G.F., Thorley, J.L. 2013. Kootenay Lake Exploitation Study: Fishing Natural Mortality Large Rainbow Trout Bull Trout: 2013 Annual Report. Poisson Consulting Ltd. Redfish Consulting Ltd. Report, Habitat Conservation Trust Foundation, Victoria, BC.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"","code":"kootenay_rb_13 #> tmax:  20 #> k:     0.25 #> Linf:  100 #> t0:    0.75 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.39 #> Ls:    60 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    10 #> n:     0.38 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    5 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.1 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(kootenay_rb_13)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/params.html","id":null,"dir":"Reference","previous_headings":"","what":"Parameter Descriptions for ypr Package — params","title":"Parameter Descriptions for ypr Package — params","text":"Default parameter descriptions may overridden individual functions.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parameter Descriptions for ypr Package — params","text":"... dots future extensions must empty. tmax maximum age (yr). k VB growth coefficient (yr-1). Linf VB mean maximum length (cm). t0 (theoretical) age zero length (yr). k2 VB growth coefficient length L2 (yr-1). Linf2 VB mean maximum length length L2 (cm). L2 length (age negative) growth switches first second phase (cm yr). Wb weight (function length) scaling exponent. Ls length (age negative) 50 % mature (cm yr). Sp maturity (function length) power. es annual probability mature fish spawning. Sm spawning mortality probability. fb fecundity (function weight) scaling exponent. tR age survival density-independent (yr). BH Recruitment follows Beverton-Holt (1) Ricker (0) relationship. Rk lifetime spawners per spawner low density (egg tR survival 0 1). n annual interval natural mortality rate age tR. nL annual interval natural mortality rate length Ln. Ln length  (age negative) annual interval natural mortality rate switches n nL (cm yr). Lv length (age negative) 50 % vulnerable harvest (cm yr). Vp vulnerability harvest (function length) power. Llo lower harvest slot length (cm). Lup upper harvest slot length (cm). Nc slot limits non-compliance probability. pi vector probabilities capture calculate yield . rho release probability. Hm hooking mortality probability. Rmax number recruits carrying capacity (ind). Wa (extrapolated) weight 1 cm individual (g). fa (theoretical) fecundity 1 g female (eggs). q catchability (annual probability capture) unit effort. RPR relative proportion recruits ecotype. flag specifying whether include parameter values. u flag specifying whether plot exploitation rate opposed capture rate. percent flag specifying whether plot number fish percent frequency (default). color string color around bar (NULL). population object class ypr_population(). populations object class ypr_populations(). ecotypes object class ypr_ecotypes(). plot_values flag specifying whether plot actual optimal values. Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. title string report title. date date report date. file string path file (without extension). binwidth positive integer width bins grouping. type string indicating whether include '' just 'actual' 'optimal' yield. object population populations. expand flag specifying whether expand parameter combinations. view flag specifying whether view report (rendering html). ask flag specifying whether ask overwriting creating file. description string describing population. age numeric vector age (yr). length numeric vector length (cm). names character vector unique ecotype names. x object coerce.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/params.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Parameter Descriptions for ypr Package — params","text":"flag non-missing logical scalar. string non-missing character scalar.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/plot.ypr_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Population Schedule — plot.ypr_population","title":"Plot Population Schedule — plot.ypr_population","text":"Plot Population Schedule","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/plot.ypr_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Population Schedule — plot.ypr_population","text":"","code":"# S3 method for class 'ypr_population' plot(x, type = \"b\", ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/plot.ypr_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Population Schedule — plot.ypr_population","text":"x population plot. type string specifying plot type. Possible values include 'b', 'p' 'l'. ... Additional arguments passed graphics::plot function.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/plot.ypr_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Population Schedule — plot.ypr_population","text":"invisible copy original object.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/plot.ypr_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Population Schedule — plot.ypr_population","text":"","code":"if (FALSE) { # \\dontrun{ plot(ypr_population()) } # }"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_bt.html","id":null,"dir":"Reference","previous_headings":"","what":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","title":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","text":"population parameters Bull Trout Quesnel Lake, BC.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_bt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","text":"","code":"quesnel_bt"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_bt.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_bt.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","text":"estimates liable change used management.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_bt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","text":"","code":"quesnel_bt #> tmax:  20 #> k:     0.13 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.4 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3.8 #> n:     0.3 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.06 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(quesnel_bt)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_lt.html","id":null,"dir":"Reference","previous_headings":"","what":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","title":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","text":"population parameters Lake Trout Quesnel Lake, BC.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_lt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","text":"","code":"quesnel_lt"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_lt.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_lt.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","text":"estimates liable change used management.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_lt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","text":"","code":"quesnel_lt #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.1 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5 #> n:     0.15 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.04 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(quesnel_lt)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_rb.html","id":null,"dir":"Reference","previous_headings":"","what":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","title":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","text":"population parameters Rainbow Trout Quesnel Lake, BC.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_rb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","text":"","code":"quesnel_rb"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_rb.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_rb.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","text":"estimates liable change used management.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_rb.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","text":"","code":"quesnel_rb #> tmax:  20 #> k:     0.2 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    6 #> n:     0.5 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.14 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(quesnel_rb)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. tibble as_tibble","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"ypr: Yield Per Recruit — ypr-package","title":"ypr: Yield Per Recruit — ypr-package","text":"implementation equilibrium-based yield per recruit methods. Yield per recruit methods can used estimate optimal yield fish population described Walters Martell (2004) <isbn:0-691-11544-3>. yield can based number fish caught (harvested) biomass caught fish just large (trophy) individuals.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"ypr: Yield Per Recruit — ypr-package","text":"Maintainer: Joe Thorley joe@poissonconsulting.ca (ORCID) contributors: Ayla Pearson (ORCID) [contributor] Poisson Consulting [copyright holder, funder]","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_age_at_length.html","id":null,"dir":"Reference","previous_headings":"","what":"Age At Length — ypr_age_at_length","title":"Age At Length — ypr_age_at_length","text":"Age Length","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_age_at_length.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Age At Length — ypr_age_at_length","text":"","code":"ypr_age_at_length(population, length)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_age_at_length.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Age At Length — ypr_age_at_length","text":"population object class ypr_population(). length numeric vector length (cm).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_age_at_length.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Age At Length — ypr_age_at_length","text":"double vector lengths.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_age_at_length.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Age At Length — ypr_age_at_length","text":"","code":"ypr_age_at_length(ypr_population(), seq(0, 100, by = 10)) #>  [1]  0.0000000  0.7024034  1.4876237  2.3778330  3.4055042  4.6209812 #>  [7]  6.1086049  8.0264854 10.7295861 15.3505673        Inf"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_detabulate_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"Detabulate Population Parameters — ypr_detabulate_parameters","title":"Detabulate Population Parameters — ypr_detabulate_parameters","text":"Detabulate Population Parameters","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_detabulate_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detabulate Population Parameters — ypr_detabulate_parameters","text":"","code":"ypr_detabulate_parameters(x)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_detabulate_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detabulate Population Parameters — ypr_detabulate_parameters","text":"x data frame columns Parameter Value specifying one parameters values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_detabulate_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detabulate Population Parameters — ypr_detabulate_parameters","text":"object class ypr_population()","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_detabulate_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Detabulate Population Parameters — ypr_detabulate_parameters","text":"","code":"ypr_detabulate_parameters(ypr_tabulate_parameters(ypr_population())) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_ecotypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Ecotypes Object — ypr_ecotypes","title":"Create Ecotypes Object — ypr_ecotypes","text":"Creates ypr_ecotypes object.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_ecotypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Ecotypes Object — ypr_ecotypes","text":"","code":"ypr_ecotypes(..., names = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_ecotypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Ecotypes Object — ypr_ecotypes","text":"... dots future extensions must empty. names character vector unique ecotype names.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_ecotypes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Ecotypes Object — ypr_ecotypes","text":"ypr_ecotypes() objects","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_ecotypes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Ecotypes Object — ypr_ecotypes","text":"","code":"ypr_ecotypes(Linf = c(1, 2)) #> tmax:  20 #> k:     0.15 #> Linf:  1, 2 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Linf_1, Linf_2 ypr_ecotypes(Linf = c(1, 2), t0 = c(0, 0.5)) #> tmax:  20 #> k:     0.15 #> Linf:  1, 2 #> t0:    0, 0.5 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Linf_1_t0_0, Linf_2_t0_0_5"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":null,"dir":"Reference","previous_headings":"","what":"Exploitation Probability — ypr_exploitation","title":"Exploitation Probability — ypr_exploitation","text":"Converts capture probabilities exploitation probabilities based release handling mortality probabilities probability exploitation includes handling mortalities. calculation assumes released fish recaught year.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Exploitation Probability — ypr_exploitation","text":"","code":"ypr_exploitation(object, pi = ypr_get_par(object))"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Exploitation Probability — ypr_exploitation","text":"object population populations. pi vector capture probabilities calculate exploitation probabilities .","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Exploitation Probability — ypr_exploitation","text":"vector exploitation probabilities.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Exploitation Probability — ypr_exploitation","text":"case release (100% handling mortalities) exploitation probability identical capture probability. Otherwise less.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Exploitation Probability — ypr_exploitation","text":"","code":"ypr_exploitation(ypr_population(pi = 0.4)) #> [1] 0.4 ypr_exploitation(ypr_population(pi = 0.4, rho = 0.6, Hm = 0.2)) #> [1] 0.208"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_get_par.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Parameter Value — ypr_get_par","title":"Get Parameter Value — ypr_get_par","text":"Get Parameter Value","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_get_par.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Parameter Value — ypr_get_par","text":"","code":"ypr_get_par(object, par = \"pi\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_get_par.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Parameter Value — ypr_get_par","text":"object ypr object. par string parameter.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_get_par.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Parameter Value — ypr_get_par","text":"numeric integer scalar vector parameter value.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_get_par.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Parameter Value — ypr_get_par","text":"","code":"ypr_get_par(ypr_population()) #> [1] 0.2"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_length_at_age.html","id":null,"dir":"Reference","previous_headings":"","what":"Length At Age — ypr_length_at_age","title":"Length At Age — ypr_length_at_age","text":"Length Age","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_length_at_age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Length At Age — ypr_length_at_age","text":"","code":"ypr_length_at_age(population, age)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_length_at_age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Length At Age — ypr_length_at_age","text":"population object class ypr_population(). age numeric vector age (yr).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_length_at_age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Length At Age — ypr_length_at_age","text":"double vector lengths.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_length_at_age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Length At Age — ypr_length_at_age","text":"","code":"ypr_length_at_age(ypr_population(), seq(0, 5, by = 0.5)) #>  [1]  0.000000  7.225651 13.929202 20.148378 25.918178 31.271072 36.237185 #>  [8] 40.844464 45.118836 49.084358 52.763345"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Population(s) or Ecotype Names — ypr_names","title":"Population(s) or Ecotype Names — ypr_names","text":"Generates set unique names based differences parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population(s) or Ecotype Names — ypr_names","text":"","code":"ypr_names(x, ...)  # S3 method for class 'ypr_population' ypr_names(x, ...)  # S3 method for class 'ypr_populations' ypr_names(x, ...)  # S3 method for class 'ypr_ecotypes' ypr_names(x, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Population(s) or Ecotype Names — ypr_names","text":"x object class ypr_population, ypr_populations ypr_ecotypes. ... Unused.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Population(s) or Ecotype Names — ypr_names","text":"character vector unique parameter based names.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Population(s) or Ecotype Names — ypr_names","text":"Parameter RPR ignored irrelevant population(s) distinguish ecotypes.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Population(s) or Ecotype Names — ypr_names","text":"ypr_names(ypr_population): Population Names ypr_names(ypr_populations): Populations Names ypr_names(ypr_ecotypes): Ecotypes Names","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Population(s) or Ecotype Names — ypr_names","text":"","code":"ypr_names(ypr_population()) #> [1] \"Pop_1\" ypr_names(ypr_populations()) #> [1] \"Pop_1\" ypr_names(ypr_populations()) #> [1] \"Pop_1\""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_optimize.html","id":null,"dir":"Reference","previous_headings":"","what":"Optimize Capture — ypr_optimize","title":"Optimize Capture — ypr_optimize","text":"Finds annual interval capture probability (pi) maximises yield given population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_optimize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Optimize Capture — ypr_optimize","text":"","code":"ypr_optimize(object, Ly = 0, harvest = TRUE, biomass = FALSE)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_optimize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Optimize Capture — ypr_optimize","text":"object population populations. Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_optimize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Optimize Capture — ypr_optimize","text":"annual interval capture probability (pi) maximises yield.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_optimize.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Optimize Capture — ypr_optimize","text":"","code":"ypr_optimize(ypr_population()) #> [1] 0.115183"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_biomass.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Biomass — ypr_plot_biomass","title":"Plot Biomass — ypr_plot_biomass","text":"Produces frequency histogram total fish 'Biomass' 'Eggs' deposition 'Age' class.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_biomass.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Biomass — ypr_plot_biomass","text":"","code":"ypr_plot_biomass(population, y = \"Biomass\", color = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_biomass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Biomass — ypr_plot_biomass","text":"population object class ypr_population(). y string term y-axis. color string color around bar (NULL).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_biomass.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Biomass — ypr_plot_biomass","text":"ggplot2 object.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_biomass.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Biomass — ypr_plot_biomass","text":"","code":"ypr_plot_biomass(ypr_population(), color = \"white\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_fish.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Fish — ypr_plot_fish","title":"Plot Fish — ypr_plot_fish","text":"Produces frequency histogram number fish 'Survivors', 'Spawners', 'Caught', 'Harvested' 'Released' categories 'Length', 'Age' 'Weight' class.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_fish.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Fish — ypr_plot_fish","text":"","code":"ypr_plot_fish(   population,   x = \"Age\",   y = \"Survivors\",   percent = FALSE,   binwidth = 1L,   color = NULL )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_fish.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Fish — ypr_plot_fish","text":"population object class ypr_population(). x object coerce. y string term y-axis. percent flag specifying whether plot number fish percent frequency (default). binwidth positive integer width bins grouping. color string color around bar (NULL).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_fish.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Fish — ypr_plot_fish","text":"ggplot2 object.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_fish.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Fish — ypr_plot_fish","text":"","code":"ypr_plot_fish(ypr_population(), color = \"white\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_schedule.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","title":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","text":"Produces bivariate line plot two schedule terms.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_schedule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","text":"","code":"ypr_plot_schedule(population, x = \"Age\", y = \"Length\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_schedule.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","text":"population object class ypr_population(). x string term x-axis. y string term y-axis.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_schedule.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","text":"ggplot2 object.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_schedule.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","text":"","code":"ypr_plot_schedule(ypr_population())"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_sr.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Stock-Recruitment Curve — ypr_plot_sr","title":"Plot Stock-Recruitment Curve — ypr_plot_sr","text":"Plot Stock-Recruitment Curve","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_sr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Stock-Recruitment Curve — ypr_plot_sr","text":"","code":"ypr_plot_sr(   population,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   plot_values = TRUE )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_sr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Stock-Recruitment Curve — ypr_plot_sr","text":"population object class ypr_population(). Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. plot_values flag specifying whether plot actual optimal values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_sr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Stock-Recruitment Curve — ypr_plot_sr","text":"ggplot2 object.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_sr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Stock-Recruitment Curve — ypr_plot_sr","text":"","code":"ypr_plot_sr(ypr_population(Rk = 10))  ypr_plot_sr(ypr_population(Rk = 10, BH = 0L))"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Yield by Capture — ypr_plot_yield","title":"Plot Yield by Capture — ypr_plot_yield","text":"Plots 'Yield', 'Age', 'Length', 'Weight', 'Effort', 'YPUE' annual interval capture/exploitation probability.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Yield by Capture — ypr_plot_yield","text":"","code":"ypr_plot_yield(object, ...)  # Default S3 method ypr_plot_yield(   object,   y = \"Yield\",   pi = seq(0, 1, length.out = 100),   Ly = 0,   harvest = TRUE,   biomass = FALSE,   u = harvest,   plot_values = TRUE,   ... )  # S3 method for class 'ypr_populations' ypr_plot_yield(   object,   y = \"Yield\",   pi = seq(0, 1, length.out = 100),   Ly = 0,   harvest = TRUE,   biomass = FALSE,   u = harvest,   plot_values = TRUE,   ... )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Yield by Capture — ypr_plot_yield","text":"object population populations. ... dots future extensions must empty. y string term y-axis. pi vector probabilities capture calculate yield . Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. u flag specifying whether plot exploitation rate opposed capture rate. plot_values flag specifying whether plot actual optimal values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Yield by Capture — ypr_plot_yield","text":"ggplot2 object.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Plot Yield by Capture — ypr_plot_yield","text":"ypr_plot_yield(default): Plot Yield Capture ypr_plot_yield(ypr_populations): Plot Yield Capture","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Yield by Capture — ypr_plot_yield","text":"","code":"if (FALSE) { # \\dontrun{ ypr_plot_yield(   ypr_populations(     Rk = c(2.5, 4.6),     Llo = c(0, 60)   ),   plot_values = FALSE ) +   ggplot2::facet_wrap(~Llo) +   ggplot2::aes(group = Rk, color = Rk) +   ggplot2::scale_color_manual(values = c(\"black\", \"blue\"))  ypr_plot_yield(ypr_populations(Rk = c(2.5, 4.6), Llo = c(0, 60))) +   ggplot2::facet_grid(Rk ~ Llo) } # }  ypr_plot_yield(ypr_population())"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Population Parameters — ypr_population","title":"Population Parameters — ypr_population","text":"Generates object class ypr_population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population Parameters — ypr_population","text":"","code":"ypr_population(   tmax = 20L,   k = 0.15,   Linf = 100,   t0 = 0,   k2 = 0.15,   Linf2 = 100,   L2 = 1000,   Wb = 3,   Ls = 50,   Sp = 100,   es = 1,   Sm = 0,   fb = 1,   tR = 1L,   BH = 1L,   Rk = 3,   n = 0.2,   nL = 0.2,   Ln = 1000,   Lv = 50,   Vp = 100,   Llo = 0,   Lup = 1000,   Nc = 0,   pi = 0.2,   rho = 0,   Hm = 0,   Rmax = 1,   Wa = 0.01,   fa = 1,   q = 0.1,   RPR = 1 )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Population Parameters — ypr_population","text":"tmax maximum age (yr). k VB growth coefficient (yr-1). Linf VB mean maximum length (cm). t0 (theoretical) age zero length (yr). k2 VB growth coefficient length L2 (yr-1). Linf2 VB mean maximum length length L2 (cm). L2 length (age negative) growth switches first second phase (cm yr). Wb weight (function length) scaling exponent. Ls length (age negative) 50 % mature (cm yr). Sp maturity (function length) power. es annual probability mature fish spawning. Sm spawning mortality probability. fb fecundity (function weight) scaling exponent. tR age survival density-independent (yr). BH Recruitment follows Beverton-Holt (1) Ricker (0) relationship. Rk lifetime spawners per spawner low density (egg tR survival 0 1). n annual interval natural mortality rate age tR. nL annual interval natural mortality rate length Ln. Ln length  (age negative) annual interval natural mortality rate switches n nL (cm yr). Lv length (age negative) 50 % vulnerable harvest (cm yr). Vp vulnerability harvest (function length) power. Llo lower harvest slot length (cm). Lup upper harvest slot length (cm). Nc slot limits non-compliance probability. pi annual capture probability. rho release probability. Hm hooking mortality probability. Rmax number recruits carrying capacity (ind). Wa (extrapolated) weight 1 cm individual (g). fa (theoretical) fecundity 1 g female (eggs). q catchability (annual probability capture) unit effort. RPR relative proportion recruits ecotype.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Population Parameters — ypr_population","text":"object class ypr_population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Population Parameters — ypr_population","text":"","code":"ypr_population(k = 0.1, Linf = 90) #> tmax:  20 #> k:     0.1 #> Linf:  90 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Population Names — ypr_population_names","title":"Population Names — ypr_population_names","text":"Generates set unique names based differences parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population Names — ypr_population_names","text":"","code":"ypr_population_names(population)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Population Names — ypr_population_names","text":"population object class ypr_population, ypr_populations ypr_ecotypes.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Population Names — ypr_population_names","text":"character vector unique parameter based names.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_update.html","id":null,"dir":"Reference","previous_headings":"","what":"Update a Population Object — ypr_population_update","title":"Update a Population Object — ypr_population_update","text":"ypr_update().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_update.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update a Population Object — ypr_population_update","text":"","code":"ypr_population_update(population, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_update.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update a Population Object — ypr_population_update","text":"population ypr_population object. ... One parameter values ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations.html","id":null,"dir":"Reference","previous_headings":"","what":"Populations — ypr_populations","title":"Populations — ypr_populations","text":"Populations","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Populations — ypr_populations","text":"","code":"ypr_populations(..., expand = TRUE, names = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Populations — ypr_populations","text":"... dots future extensions must empty. expand flag specifying whether expand parameter combinations. names character vector unique ecotype names.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Populations — ypr_populations","text":"list ypr_population() objects","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Populations — ypr_populations","text":"","code":"ypr_populations(Rk = c(2.5, 4.6), Hm = c(0.2, 0.05)) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5, 4.6, 2.5, 4.6 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0.05, 0.05, 0.2, 0.2 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations_expand.html","id":null,"dir":"Reference","previous_headings":"","what":"Expand Populations — ypr_populations_expand","title":"Expand Populations — ypr_populations_expand","text":"object class ypr_population() unique combinations parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations_expand.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expand Populations — ypr_populations_expand","text":"","code":"ypr_populations_expand(populations)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations_expand.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expand Populations — ypr_populations_expand","text":"populations object class ypr_populations().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations_expand.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expand Populations — ypr_populations_expand","text":"object class ypr_population.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations_expand.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expand Populations — ypr_populations_expand","text":"","code":"ypr_populations_expand(   ypr_populations(     Rk = c(2.5, 4, 2.5),     Hm = c(0.1, 0.2, 0.1)   ) ) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5, 4, 2.5, 4 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0.1, 0.1, 0.2, 0.2 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_report.html","id":null,"dir":"Reference","previous_headings":"","what":"Report — ypr_report","title":"Report — ypr_report","text":"Creates Rmd file can used generate report.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_report.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Report — ypr_report","text":"","code":"ypr_report(   population,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   title = \"Population Report\",   description = \"\",   date = Sys.Date(),   file = \"report\",   view = FALSE,   ask = TRUE )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_report.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Report — ypr_report","text":"population object class ypr_population(). Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. title string report title. description string describing population. date date report date. file string path file (without extension). view flag specifying whether view report (rendering html). ask flag specifying whether ask overwriting creating file.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_report.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Report — ypr_report","text":"invisible character vector contents file.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_report.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Report — ypr_report","text":"","code":"if (FALSE) { # \\dontrun{ ypr_report(ypr_population(), file = tempfile(), ask = FALSE) } # }"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_schedule.html","id":null,"dir":"Reference","previous_headings":"","what":"Life-History Schedule — ypr_schedule","title":"Life-History Schedule — ypr_schedule","text":"DEPRECATED: Replace ypr_schedule() ypr_tabulate_schedule()","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_schedule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Life-History Schedule — ypr_schedule","text":"","code":"ypr_schedule(population)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_schedule.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Life-History Schedule — ypr_schedule","text":"Generates life-history schedule age population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_sr.html","id":null,"dir":"Reference","previous_headings":"","what":"Stock-Recruitment Parameters — ypr_sr","title":"Stock-Recruitment Parameters — ypr_sr","text":"Returns single rowed data frame SR parameters: alpha Survival egg age tR low density beta Density-dependence Rk Lifetime spawners per spawner low density phi Lifetime eggs deposited per recruit unfished equilibrium phiF Lifetime eggs deposited per recruit fished equilibrium R0 Age tR recruits unfished equilibrium R0F Age tR recruits fished equilibrium S0 Spawners unfished equilibrium S0F Spawners fished equilibrium","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_sr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stock-Recruitment Parameters — ypr_sr","text":"","code":"ypr_sr(object)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_sr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stock-Recruitment Parameters — ypr_sr","text":"object population populations.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_sr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stock-Recruitment Parameters — ypr_sr","text":"data frame SR parameters.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_sr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stock-Recruitment Parameters — ypr_sr","text":"","code":"ypr_sr(ypr_population()) # Beverton-Holt #> # A tibble: 1 × 9 #>      alpha     beta    Rk   phi  phiF    R0   R0F    S0   S0F #>      <dbl>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 0.000838 0.000838     3 3579. 1465. 0.667 0.186  1.33 0.211 ypr_sr(ypr_population(BH = 0L)) # Ricker #> # A tibble: 1 × 9 #>      alpha     beta    Rk   phi  phiF    R0   R0F    S0   S0F #>      <dbl>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 0.000838 0.000308     3 3579. 1465. 0.995 0.455  1.98 0.517"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_biomass.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","title":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","text":"Produces data frame 'Weight' 'Fecundity' number 'Survivors' 'Spawners' total 'Biomass' 'Eggs' 'Age' class.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_biomass.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","text":"","code":"ypr_tabulate_biomass(population)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_biomass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","text":"population object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_biomass.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","text":"data frame","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_biomass.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","text":"","code":"ypr_tabulate_biomass(ypr_population()) #> # A tibble: 20 × 8 #>      Age Length Weight Fecundity Survivors Spawners Biomass     Eggs #>    <int>  <dbl>  <dbl>     <dbl>     <dbl>    <dbl>   <dbl>    <dbl> #>  1     1   13.9   27.0      27.0 0.186     5.82e-57   5.02  7.86e-56 #>  2     2   25.9  174.      174.  0.149     4.32e-30  25.9   3.76e-28 #>  3     3   36.2  476.      476.  0.119     1.24e-15  56.6   2.95e-13 #>  4     4   45.1  918.      918.  0.0951    3.29e- 6  87.4   1.51e- 3 #>  5     5   52.8 1469.     1469.  0.0761    7.58e- 2 112.    5.56e+ 1 #>  6     6   59.3 2090.     2090.  0.0488    4.88e- 2 102.    5.10e+ 1 #>  7     7   65.0 2747.     2747.  0.0312    3.12e- 2  85.7   4.29e+ 1 #>  8     8   69.9 3412.     3412.  0.0200    2.00e- 2  68.2   3.41e+ 1 #>  9     9   74.1 4065.     4065.  0.0128    1.28e- 2  52.0   2.60e+ 1 #> 10    10   77.7 4689.     4689.  0.00818   8.18e- 3  38.4   1.92e+ 1 #> 11    11   80.8 5274.     5274.  0.00524   5.24e- 3  27.6   1.38e+ 1 #> 12    12   83.5 5816.     5816.  0.00335   3.35e- 3  19.5   9.74e+ 0 #> 13    13   85.8 6310.     6310.  0.00214   2.14e- 3  13.5   6.77e+ 0 #> 14    14   87.8 6758.     6758.  0.00137   1.37e- 3   9.28  4.64e+ 0 #> 15    15   89.5 7160.     7160.  0.000878  8.78e- 4   6.29  3.14e+ 0 #> 16    16   90.9 7518.     7518.  0.000562  5.62e- 4   4.23  2.11e+ 0 #> 17    17   92.2 7836.     7836.  0.000360  3.60e- 4   2.82  1.41e+ 0 #> 18    18   93.3 8116.     8116.  0.000230  2.30e- 4   1.87  9.34e- 1 #> 19    19   94.2 8363.     8363.  0.000147  1.47e- 4   1.23  6.16e- 1 #> 20    20   95.0 8580.     8580.  0.0000943 9.43e- 5   0.809 4.05e- 1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_fish.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Fish Numbers — ypr_tabulate_fish","title":"Tabulate Fish Numbers — ypr_tabulate_fish","text":"Produces data frame number fish 'Survivors', 'Spawners', 'Caught', 'Harvested', 'Released' 'HandlingMortalities' categories 'Length', 'Age' 'Weight' class 'Ecotype' (NA applicable)","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_fish.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Fish Numbers — ypr_tabulate_fish","text":"","code":"ypr_tabulate_fish(population, x = \"Age\", binwidth = 1L)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_fish.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Fish Numbers — ypr_tabulate_fish","text":"population object class ypr_population(). x object coerce. binwidth positive integer width bins grouping.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_fish.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Fish Numbers — ypr_tabulate_fish","text":"data frame","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_fish.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Fish Numbers — ypr_tabulate_fish","text":"","code":"ypr_tabulate_fish(ypr_population()) #> # A tibble: 20 × 8 #>      Age Survivors Spawners   Caught Harvested Released HandlingMortalities #>    <dbl>     <dbl>    <dbl>    <dbl>     <dbl>    <dbl>               <dbl> #>  1     1 0.186     5.82e-57 1.16e-57  1.16e-57        0                   0 #>  2     2 0.149     4.32e-30 8.64e-31  8.64e-31        0                   0 #>  3     3 0.119     1.24e-15 2.48e-16  2.48e-16        0                   0 #>  4     4 0.0951    3.29e- 6 6.58e- 7  6.58e- 7        0                   0 #>  5     5 0.0761    7.58e- 2 1.52e- 2  1.52e- 2        0                   0 #>  6     6 0.0488    4.88e- 2 9.75e- 3  9.75e- 3        0                   0 #>  7     7 0.0312    3.12e- 2 6.24e- 3  6.24e- 3        0                   0 #>  8     8 0.0200    2.00e- 2 3.99e- 3  3.99e- 3        0                   0 #>  9     9 0.0128    1.28e- 2 2.56e- 3  2.56e- 3        0                   0 #> 10    10 0.00818   8.18e- 3 1.64e- 3  1.64e- 3        0                   0 #> 11    11 0.00524   5.24e- 3 1.05e- 3  1.05e- 3        0                   0 #> 12    12 0.00335   3.35e- 3 6.70e- 4  6.70e- 4        0                   0 #> 13    13 0.00214   2.14e- 3 4.29e- 4  4.29e- 4        0                   0 #> 14    14 0.00137   1.37e- 3 2.74e- 4  2.74e- 4        0                   0 #> 15    15 0.000878  8.78e- 4 1.76e- 4  1.76e- 4        0                   0 #> 16    16 0.000562  5.62e- 4 1.12e- 4  1.12e- 4        0                   0 #> 17    17 0.000360  3.60e- 4 7.20e- 5  7.20e- 5        0                   0 #> 18    18 0.000230  2.30e- 4 4.61e- 5  4.61e- 5        0                   0 #> 19    19 0.000147  1.47e- 4 2.95e- 5  2.95e- 5        0                   0 #> 20    20 0.0000943 9.43e- 5 1.89e- 5  1.89e- 5        0                   0 #> # ℹ 1 more variable: Ecotype <chr>"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Population Parameters — ypr_tabulate_parameters","title":"Tabulate Population Parameters — ypr_tabulate_parameters","text":"Tabulate Population Parameters","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Population Parameters — ypr_tabulate_parameters","text":"","code":"ypr_tabulate_parameters(population)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Population Parameters — ypr_tabulate_parameters","text":"population object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Population Parameters — ypr_tabulate_parameters","text":"table population parameters","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Population Parameters — ypr_tabulate_parameters","text":"","code":"if (FALSE) { # \\dontrun{ ypr_tabulate_parameters(ypr_population()) } # }"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":null,"dir":"Reference","previous_headings":"","what":"Life-History Schedule — ypr_tabulate_schedule","title":"Life-History Schedule — ypr_tabulate_schedule","text":"Generates life-history schedule age population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Life-History Schedule — ypr_tabulate_schedule","text":"","code":"ypr_tabulate_schedule(object, ...)  # S3 method for class 'ypr_population' ypr_tabulate_schedule(object, ...)  # S3 method for class 'ypr_ecotypes' ypr_tabulate_schedule(object, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Life-History Schedule — ypr_tabulate_schedule","text":"object population populations. ... dots future extensions must empty.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Life-History Schedule — ypr_tabulate_schedule","text":"tibble life-history schedule age.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Life-History Schedule — ypr_tabulate_schedule","text":"ypr_tabulate_schedule(ypr_population): Tabulate Schedule ypr_tabulate_schedule(ypr_ecotypes): Tabulate Schedule","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Life-History Schedule — ypr_tabulate_schedule","text":"","code":"ypr_tabulate_schedule(ypr_population()) #> # A tibble: 20 × 11 #>      Age Length Weight Fecundity Spawning NaturalMortality Vulnerability #>    <int>  <dbl>  <dbl>     <dbl>    <dbl>            <dbl>         <dbl> #>  1     1   13.9   27.0      27.0 3.13e-56              0.2      3.13e-56 #>  2     2   25.9  174.      174.  2.91e-29              0.2      2.91e-29 #>  3     3   36.2  476.      476.  1.04e-14              0.2      1.04e-14 #>  4     4   45.1  918.      918.  3.46e- 5              0.2      3.46e- 5 #>  5     5   52.8 1469.     1469.  9.95e- 1              0.2      9.95e- 1 #>  6     6   59.3 2090.     2090.  1.00e+ 0              0.2      1.00e+ 0 #>  7     7   65.0 2747.     2747.  1.00e+ 0              0.2      1.00e+ 0 #>  8     8   69.9 3412.     3412.  1.00e+ 0              0.2      1.00e+ 0 #>  9     9   74.1 4065.     4065.  1   e+ 0              0.2      1   e+ 0 #> 10    10   77.7 4689.     4689.  1   e+ 0              0.2      1   e+ 0 #> 11    11   80.8 5274.     5274.  1   e+ 0              0.2      1   e+ 0 #> 12    12   83.5 5816.     5816.  1   e+ 0              0.2      1   e+ 0 #> 13    13   85.8 6310.     6310.  1   e+ 0              0.2      1   e+ 0 #> 14    14   87.8 6758.     6758.  1   e+ 0              0.2      1   e+ 0 #> 15    15   89.5 7160.     7160.  1   e+ 0              0.2      1   e+ 0 #> 16    16   90.9 7518.     7518.  1   e+ 0              0.2      1   e+ 0 #> 17    17   92.2 7836.     7836.  1   e+ 0              0.2      1   e+ 0 #> 18    18   93.3 8116.     8116.  1   e+ 0              0.2      1   e+ 0 #> 19    19   94.2 8363.     8363.  1   e+ 0              0.2      1   e+ 0 #> 20    20   95.0 8580.     8580.  1   e+ 0              0.2      1   e+ 0 #> # ℹ 4 more variables: Retention <dbl>, FishingMortality <dbl>, #> #   Survivorship <dbl>, FishedSurvivorship <dbl> ypr_tabulate_schedule(ypr_ecotypes(Linf = c(10, 20))) #> # A tibble: 40 × 13 #>      Age Length Weight Fecundity  Spawning NaturalMortality Vulnerability #>    <int>  <dbl>  <dbl>     <dbl>     <dbl>            <dbl>         <dbl> #>  1     1   1.39 0.0270    0.0270 3.13e-156              0.2     3.13e-156 #>  2     2   2.59 0.174     0.174  2.91e-129              0.2     2.91e-129 #>  3     3   3.62 0.476     0.476  1.04e-114              0.2     1.04e-114 #>  4     4   4.51 0.918     0.918  3.46e-105              0.2     3.46e-105 #>  5     5   5.28 1.47      1.47   2.17e- 98              0.2     2.17e- 98 #>  6     6   5.93 2.09      2.09   2.75e- 93              0.2     2.75e- 93 #>  7     7   6.50 2.75      2.75   2.50e- 89              0.2     2.50e- 89 #>  8     8   6.99 3.41      3.41   3.46e- 86              0.2     3.46e- 86 #>  9     9   7.41 4.06      4.06   1.18e- 83              0.2     1.18e- 83 #> 10    10   7.77 4.69      4.69   1.37e- 81              0.2     1.37e- 81 #> # ℹ 30 more rows #> # ℹ 6 more variables: Retention <dbl>, FishingMortality <dbl>, #> #   Survivorship <dbl>, FishedSurvivorship <dbl>, Ecotype <chr>, #> #   Proportion <dbl>"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"Tabulate Stock-Recruitment Parameters","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"","code":"ypr_tabulate_sr(object, ...)  # Default S3 method ypr_tabulate_sr(   object,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   all = FALSE,   ... )  # S3 method for class 'ypr_populations' ypr_tabulate_sr(   object,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   all = FALSE,   ... )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"object population populations. ... dots future extensions must empty. Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. flag specifying whether include parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"data.frame stock-recruitment parameters.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"ypr_tabulate_sr(default): Tabulate Stock-Recruitment Parameters ypr_tabulate_sr(ypr_populations): Tabulate Stock-Recruitment Parameters","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"","code":"ypr_tabulate_sr(ypr_population()) # Beverton-Holt #> # A tibble: 3 × 7 #>   Type        pi     u  Eggs Recruits Spawners Fecundity #>   <chr>    <dbl> <dbl> <dbl>    <dbl>    <dbl>     <dbl> #> 1 unfished 0     0     2386.    0.667    1.33      3600. #> 2 actual   0.2   0.2    272.    0.186    0.211     2580. #> 3 optimal  0.115 0.115  853.    0.417    0.582     2933. ypr_tabulate_sr(ypr_population(BH = 0L)) # Ricker #> # A tibble: 3 × 7 #>   Type        pi     u  Eggs Recruits Spawners Fecundity #>   <chr>    <dbl> <dbl> <dbl>    <dbl>    <dbl>     <dbl> #> 1 unfished 0     0     3563.    0.995    1.98      3600. #> 2 actual   0.2   0.2    667.    0.455    0.517     2580. #> 3 optimal  0.135 0.135 1485.    0.787    1.04      2844. ypr_tabulate_sr(ypr_populations(Rk = c(2.5, 4.6))) #> # A tibble: 6 × 8 #>   Type         pi      u   Eggs Recruits Spawners Fecundity    Rk #>   <chr>     <dbl>  <dbl>  <dbl>    <dbl>    <dbl>     <dbl> <dbl> #> 1 unfished 0      0      2148.    0.6      1.19       3600.   2.5 #> 2 actual   0.2    0.2      33.6   0.0230   0.0261     2580.   2.5 #> 3 optimal  0.0936 0.0936  818.    0.364    0.538      3041.   2.5 #> 4 unfished 0      0      2801.    0.783    1.56       3600.   4.6 #> 5 actual   0.2    0.2     687.    0.469    0.533      2580.   4.6 #> 6 optimal  0.171  0.171   851.    0.522    0.633      2688.   4.6"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Yield — ypr_tabulate_yield","title":"Tabulate Yield — ypr_tabulate_yield","text":"Tabulate Yield","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Yield — ypr_tabulate_yield","text":"","code":"ypr_tabulate_yield(object, ...)  # Default S3 method ypr_tabulate_yield(   object,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   type = \"both\",   all = FALSE,   ... )  # S3 method for class 'ypr_populations' ypr_tabulate_yield(   object,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   type = \"both\",   all = FALSE,   ... )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Yield — ypr_tabulate_yield","text":"object population populations. ... dots future extensions must empty. Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. type string indicating whether include '' just 'actual' 'optimal' yield. flag specifying whether include parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Yield — ypr_tabulate_yield","text":"data frame.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Tabulate Yield — ypr_tabulate_yield","text":"ypr_tabulate_yield(default): Tabulate Yield ypr_tabulate_yield(ypr_populations): Tabulate Yield","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Yield — ypr_tabulate_yield","text":"","code":"ypr_tabulate_yield(ypr_population()) #> # A tibble: 2 × 8 #>   Type       pi     u  Yield   Age Length Weight Effort #>   <chr>   <dbl> <dbl>  <dbl> <dbl>  <dbl>  <dbl>  <dbl> #> 1 actual  0.2   0.2   0.0422  6.77   62.1  2580.   2.12 #> 2 optimal 0.115 0.115 0.0670  7.36   64.6  2933.   1.16 ypr_tabulate_yield(ypr_populations(Rk = c(3, 5))) #> # A tibble: 4 × 9 #>   Type       pi     u  Yield   Age Length Weight Effort    Rk #>   <chr>   <dbl> <dbl>  <dbl> <dbl>  <dbl>  <dbl>  <dbl> <dbl> #> 1 actual  0.2   0.2   0.0422  6.77   62.1  2580.   2.12     3 #> 2 optimal 0.115 0.115 0.0670  7.36   64.6  2933.   1.16     3 #> 3 actual  0.2   0.2   0.116   6.77   62.1  2580.   2.12     5 #> 4 optimal 0.183 0.183 0.117   6.87   62.6  2641.   1.92     5"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Yields — ypr_tabulate_yields","title":"Tabulate Yields — ypr_tabulate_yields","text":"Tabulate Yields","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Yields — ypr_tabulate_yields","text":"","code":"ypr_tabulate_yields(object, ...)  # Default S3 method ypr_tabulate_yields(   object,   pi = seq(0, 1, length.out = 100),   Ly = 0,   harvest = TRUE,   biomass = FALSE,   all = FALSE,   ... )  # S3 method for class 'ypr_populations' ypr_tabulate_yields(   object,   pi = seq(0, 1, length.out = 100),   Ly = 0,   harvest = TRUE,   biomass = FALSE,   all = FALSE,   ... )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Yields — ypr_tabulate_yields","text":"object population populations. ... dots future extensions must empty. pi vector probabilities capture calculate yield . Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. flag specifying whether include parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Yields — ypr_tabulate_yields","text":"data frame.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Tabulate Yields — ypr_tabulate_yields","text":"ypr_tabulate_yields(default): Tabulate Yields ypr_tabulate_yields(ypr_populations): Tabulate Yields","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Yields — ypr_tabulate_yields","text":"","code":"ypr_tabulate_yields(ypr_population()) #> # A tibble: 100 × 7 #>        pi      u  Yield   Age Length Weight Effort #>     <dbl>  <dbl>  <dbl> <dbl>  <dbl>  <dbl>  <dbl> #>  1 0      0      0      NA      NA      NA  0      #>  2 0.0101 0.0101 0.0126  8.42   68.5  3532. 0.0964 #>  3 0.0202 0.0202 0.0236  8.30   68.0  3466. 0.194  #>  4 0.0303 0.0303 0.0331  8.18   67.6  3402. 0.292  #>  5 0.0404 0.0404 0.0413  8.07   67.2  3339. 0.391  #>  6 0.0505 0.0505 0.0482  7.96   66.8  3279. 0.492  #>  7 0.0606 0.0606 0.0539  7.86   66.5  3220. 0.593  #>  8 0.0707 0.0707 0.0585  7.76   66.1  3163. 0.696  #>  9 0.0808 0.0808 0.0620  7.66   65.7  3108. 0.800  #> 10 0.0909 0.0909 0.0646  7.57   65.4  3054. 0.905  #> # ℹ 90 more rows ypr_tabulate_yields(   ypr_populations(     Rk = c(3, 5)   ),   pi = seq(0, 1, length.out = 10) ) #> # A tibble: 20 × 8 #>       pi     u   Yield   Age Length Weight Effort    Rk #>    <dbl> <dbl>   <dbl> <dbl>  <dbl>  <dbl>  <dbl> <dbl> #>  1 0     0     0       NA      NA      NA    0        3 #>  2 0.111 0.111 0.0669   7.40   64.7  2953.   1.12     3 #>  3 0.222 0.222 0.0288   6.64   61.6  2504.   2.39     3 #>  4 0.333 0.333 0       NA      NA      NA    3.85     3 #>  5 0.444 0.444 0       NA      NA      NA    5.58     3 #>  6 0.556 0.556 0       NA      NA      NA    7.70     3 #>  7 0.667 0.667 0       NA      NA      NA   10.4      3 #>  8 0.778 0.778 0       NA      NA      NA   14.3      3 #>  9 0.889 0.889 0       NA      NA      NA   20.9      3 #> 10 1     1     0       NA      NA      NA  Inf        3 #> 11 0     0     0       NA      NA      NA    0        5 #> 12 0.111 0.111 0.103    7.40   64.7  2953.   1.12     5 #> 13 0.222 0.222 0.114    6.64   61.6  2504.   2.39     5 #> 14 0.333 0.333 0.0750   6.15   59.3  2196.   3.85     5 #> 15 0.444 0.444 0.00589  5.80   57.5  1979.   5.58     5 #> 16 0.556 0.556 0       NA      NA      NA    7.70     5 #> 17 0.667 0.667 0       NA      NA      NA   10.4      5 #> 18 0.778 0.778 0       NA      NA      NA   14.3      5 #> 19 0.889 0.889 0       NA      NA      NA   20.9      5 #> 20 1     1     0       NA      NA      NA  Inf        5 ypr_tabulate_yields(ypr_ecotypes(Linf = c(10, 20))) #> # A tibble: 100 × 7 #>        pi      u    Yield   Age Length Weight Effort #>     <dbl>  <dbl>    <dbl> <dbl>  <dbl>  <dbl>  <dbl> #>  1 0      0      0         NA     NA     NA   0      #>  2 0.0101 0.0101 9.03e-47  19.2   18.9   67.2 0.0964 #>  3 0.0202 0.0202 1.81e-46  19.2   18.9   67.2 0.194  #>  4 0.0303 0.0303 2.71e-46  19.2   18.9   67.2 0.292  #>  5 0.0404 0.0404 3.61e-46  19.2   18.9   67.2 0.391  #>  6 0.0505 0.0505 4.52e-46  19.2   18.9   67.2 0.492  #>  7 0.0606 0.0606 5.42e-46  19.2   18.9   67.2 0.593  #>  8 0.0707 0.0707 6.32e-46  19.2   18.9   67.2 0.696  #>  9 0.0808 0.0808 7.22e-46  19.2   18.9   67.2 0.800  #> 10 0.0909 0.0909 8.13e-46  19.2   18.9   67.2 0.905  #> # ℹ 90 more rows"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_update.html","id":null,"dir":"Reference","previous_headings":"","what":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","title":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","text":"Update YPR Object Currently just works scalar parameters populations ecotypes.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_update.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","text":"","code":"ypr_update(x, ...)  # S3 method for class 'ypr_population' ypr_update(x, ...)  # S3 method for class 'ypr_populations' ypr_update(x, ...)  # S3 method for class 'ypr_ecotypes' ypr_update(x, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_update.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","text":"x population, populations ecotypes object update. ... One parameter values ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_update.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","text":"ypr_update(ypr_population): Update Population Parameters ypr_update(ypr_populations): Update Populations Parameters ypr_update(ypr_ecotypes): Update Populations Parameters","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_update.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","text":"","code":"ypr_update(ypr_population(), Rk = 2.5) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_update(ypr_populations(Rk = c(2.5, 4)), Rk = 2.5) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_update(ypr_ecotypes(Linf = c(2.5, 4)), k = 1.5) #> tmax:  20 #> k:     1.5 #> Linf:  2.5, 4 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Linf_2_5, Linf_4"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":null,"dir":"Reference","previous_headings":"","what":"Yield — ypr_yield","title":"Yield — ypr_yield","text":"Calculates yield population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Yield — ypr_yield","text":"","code":"ypr_yield(object, Ly = 0, harvest = TRUE, biomass = FALSE, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Yield — ypr_yield","text":"object population populations. Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. ... dots future extensions must empty.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Yield — ypr_yield","text":"yield number fish biomass.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Yield — ypr_yield","text":"default, Rmax = 1 number individuals proportion recruits carrying capacity. yield given terms biomass (kg) scaling also depends value Wa (g).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Yield — ypr_yield","text":"","code":"ypr_yield(ypr_population()) #> [1] 0.04220691 #> attr(,\"Age\") #> [1] 6.7687 #> attr(,\"Length\") #> [1] 62.13068 #> attr(,\"Weight\") #> [1] 2580.272 #> attr(,\"Effort\") #> [1] 2.117905 ypr_yield(ypr_ecotypes(Linf = c(100, 200))) #> [1] 0 #> attr(,\"Age\") #> [1] NA #> attr(,\"Length\") #> [1] NA #> attr(,\"Weight\") #> [1] NA #> attr(,\"Effort\") #> [1] 2.117905"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yields.html","id":null,"dir":"Reference","previous_headings":"","what":"Yields — ypr_yields","title":"Yields — ypr_yields","text":"Calculates yield(s) population based one capture rates.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yields.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Yields — ypr_yields","text":"","code":"ypr_yields(   object,   pi = seq(0, 1, length.out = 100),   Ly = 0,   harvest = TRUE,   biomass = FALSE )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yields.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Yields — ypr_yields","text":"object population populations. pi vector probabilities capture calculate yield . Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yields.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Yields — ypr_yields","text":"numeric vector yields.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yields.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Yields — ypr_yields","text":"","code":"pi <- seq(0, 1, length.out = 30) plot(pi, ypr_yields(ypr_population(), pi), type = \"l\")"},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9010","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9010","text":"Bump version 0.6.0.9009 (#91).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9009","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9009","text":"Bump version 0.6.0.9008 (#89).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9008","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9008","text":"Bump version 0.6.0.9007 (#87).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9007","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9007","text":"Bump version 0.6.0.9006 (#86).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9006","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9006","text":"Bump version 0.6.0.9005 (#85).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9005","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9005","text":"Bump version 0.6.0.9004 (#84).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9004","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9004","text":"Bump version 0.6.0.9003 (#83).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9003","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9003","text":"Bump version 0.6.0.9002 (#81).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9002","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9002","text":"Bump version 0.6.0.9001 (#80).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"continuous-integration-0-6-0-9001","dir":"Changelog","previous_headings":"","what":"Continuous integration","title":"ypr 0.6.0.9001","text":"Fetch tags fledge workflow avoid unnecessary NEWS entries (#78). Use larger retry count lock-threads workflow (#77). Overwrite actions-sync (#76).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"documentation-0-6-0-9001","dir":"Changelog","previous_headings":"","what":"Documentation","title":"ypr 0.6.0.9001","text":"Register poissontemplate usage (@maelle, #71).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"uncategorized-0-6-0-9001","dir":"Changelog","previous_headings":"","what":"Uncategorized","title":"ypr 0.6.0.9001","text":"Merge pull request #75 poissonconsulting/reqName. replaced requireNamespace() rlang::check_installed() Merge pull request #72 poissonconsulting/.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-0609000","dir":"Changelog","previous_headings":"","what":"ypr 0.6.0.9000","title":"ypr 0.6.0.9000","text":"previous version.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-060","dir":"Changelog","previous_headings":"","what":"ypr 0.6.0","title":"ypr 0.6.0","text":"CRAN release: 2022-08-29 Rk now egg tR survival 0 1.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-052","dir":"Changelog","previous_headings":"","what":"ypr 0.5.2","title":"ypr 0.5.2","text":"CRAN release: 2021-07-03 Internal changes .","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-051","dir":"Changelog","previous_headings":"","what":"ypr 0.5.1","title":"ypr 0.5.1","text":"CRAN release: 2020-07-10 House-keeping.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-050","dir":"Changelog","previous_headings":"","what":"ypr 0.5.0","title":"ypr 0.5.0","text":"CRAN release: 2020-03-18 Pass yield parameters Ly, harvest biomass ypr_report(). Removed suggests dependency checkr.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-040","dir":"Changelog","previous_headings":"","what":"ypr 0.4.0","title":"ypr 0.4.0","text":"CRAN release: 2020-01-13","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"population-parameters-0-4-0","dir":"Changelog","previous_headings":"","what":"Population Parameters","title":"ypr 0.4.0","text":"Replaced parameters M (annual instantaneous natural mortality rate) Mb (annual instantaneous natural mortality rate (function length) scaling exponent) A0 (initial post age tR density independent mortality probability) n (annual natural mortality rate age tR length Ln) nL (annual natural mortality rate length Ln) Ln (length natural mortality rate switches n nA) Added parameters k2, Linf2 L2 allow biphasic growth. Set Lp value 1000 opposed Linf. Set Ls Lv arguments 50 opposed Linf/2. Allow L2, Ln, Ls Lv also take ages (negative values).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"populations-0-4-0","dir":"Changelog","previous_headings":"","what":"Population(s)","title":"ypr 0.4.0","text":"Added expand = TRUE argument ypr_populations() allow control combinations. Added ypr_populations_expand() create combinations parameters. Added ypr_populations_update() (well update.ypr_population() update.ypr_populations()). ypr_populations longer requires names. Added ypr_population_names() allow user generate names. Added as_ypr_populations.data.frame(). Added data.frame.ypr_population() data.frame.ypr_populations(). Added ypr_age_at_length() get ages specific lengths given population. Added ypr_length_at_age() get lengths specific ages given population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"population-reports-0-4-0","dir":"Changelog","previous_headings":"","what":"Population Reports","title":"ypr 0.4.0","text":"Added description = \"\" argument ypr_report() allow user describe report. ypr_report() now starts table parameter values parameter descriptions. Added view = FALSE argument ypr_report() allow user view report browser. Added ask = TRUE argument ypr_report() ask overwriting creating file. Deprecated requirement provide file extension ypr_report(). Soft deprecated ypr_schedule() ypr_tabulate_schedule().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"plots-0-4-0","dir":"Changelog","previous_headings":"","what":"Plots","title":"ypr 0.4.0","text":"Added plot biomass eggs report. Added percent = FALSE argument ypr_plot_fish()","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"tables-0-4-0","dir":"Changelog","previous_headings":"","what":"Tables","title":"ypr 0.4.0","text":"Added ypr_tabulate_biomass() easily calculate total biomass eggs. Renamed column HandlingMortality HandlingMortalities ypr_tabulate_fish() ypr_plot_fish(). Renamed column Spawning Spawners ypr_tabulate_fish() ypr_plot_fish().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"bug-fixes-0-4-0","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"ypr 0.4.0","text":"Improved handling unsustainable populations (longer negative fish numbers).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-031","dir":"Changelog","previous_headings":"","what":"ypr 0.3.1","title":"ypr 0.3.1","text":"CRAN release: 2019-04-26 ypr_populations() now generates names Fixed Quesnel Lake Trout Rainbow Trout mix ","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-030","dir":"Changelog","previous_headings":"","what":"ypr 0.3.0","title":"ypr 0.3.0","text":"CRAN release: 2018-11-26 Now uses q instead Ea Eb effort Parameter Rk now greater >= 1","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-020","dir":"Changelog","previous_headings":"","what":"ypr 0.2.0","title":"ypr 0.2.0","text":"Added ypr_exploitation() convert capture probabilities exploitation probabilities. Added ypr_report() generate Rmd file population. Can now pass Rk egg recruit survival (low density). Set default value Wa 0.01. Added ypr_populations() generate combinations parameters. Made ypr_tabulate_sr(), ypr_tabulate_yield(), ypr_tabulate_yields(), ypr_plot_yield() generic definitions ypr_population ypr_populations objects. Added scaling parameter A0 initial interval mortality recruits. Added scaling parameters Ea Eb allow plots yield per effort. Added Age, Length, Weight Effort ypr_tabulate_yield() added ypr_tabulate_yields() Added y arg ypr_plot_yield() allow plotting mean age, length, weight, effort yield per effort exploitation capture probability. Added ypr_plot_histogram() plot frequency distributions catch, spawners lake age, length weight bins. Added ypr_tabulate_parameters() get table parameters, values descriptions ypr_detabulate_parameters() convert back population object. Added ypr_tabulate_sr() get table eggs recruits unfished, actual optimal rates. Added print.ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-010","dir":"Changelog","previous_headings":"","what":"ypr 0.1.0","title":"ypr 0.1.0","text":"Added Mb scale mortality length BH distinguish Beverton-Holt Ricker curves es probability mature fish spawning Sm spawning mortality probability Sp spawning power vulnerability power Vp slot limit non-complicance parameter Nc scaling parameter R0. Added ypr_population_update() update population parameters. Added ypr_yield_tabulate() tabulate actual optimal yields. Added ypr_sr() get stock recruitment parameters ypr_plot_sr() plot. Added ypr_inst2inter() ypr_inter2instant() convert mortality rates. Switched nu M R0 Rmax. Switched yield parameters harvest biomass FALSE default. Renamed Wa b Wb eta Hm mu pi Rt tR. Removed Capture (covered single value) TotalMortality schedule added Spawning.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-001","dir":"Changelog","previous_headings":"","what":"ypr 0.0.1","title":"ypr 0.0.1","text":"Initial Release","code":""}]
+[{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to ypr","title":"Contributing to ypr","text":"outlines propose change ypr.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing to ypr","text":"can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to ypr","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to ypr","text":"Fork package clone onto computer. haven’t done , recommend using usethis::create_from_github(\"\", fork = TRUE). Install development dependences devtools::install_dev_deps(), make sure package passes R CMD check running devtools::check(). R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using usethis::pr_init(\"brief-description--change\"). Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number. Begin commit merge messages - indicate user facing changes included NEWS.md. use fledge automatically generate NEWS.md file.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to ypr","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. use roxygen2, Markdown syntax, documentation. use testthat unit tests. Contributions test cases included easier accept.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing to ypr","text":"Please note ypr project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2020 Poisson Consulting Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/SUPPORT.html","id":null,"dir":"","previous_headings":"","what":"Getting help with ypr","title":"Getting help with ypr","text":"Thanks using ypr! filing issue, places explore pieces put together make process smooth possible.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/SUPPORT.html","id":"make-sure-its-new","dir":"","previous_headings":"","what":"Make sure its new","title":"Getting help with ypr","text":"opening new issue, sure search issues pull requests make sure bug hasn’t reported /already fixed development version. default, search pre-populated :issue :open. can edit qualifiers (e.g. :pr, :closed) needed. example, ’d simply remove :open search issues repo, open closed.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/SUPPORT.html","id":"make-a-reprex","dir":"","previous_headings":"","what":"Make a reprex","title":"Getting help with ypr","text":"Start making minimal reproducible example using reprex package. haven’t heard used reprex , ’re treat! Seriously, reprex make R-question-asking endeavors easier (pretty insane ROI five ten minutes ’ll take learn ’s ). additional reprex pointers, check Get help! section tidyverse site.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ecotypes.html","id":"ecotypes","dir":"Articles","previous_headings":"","what":"Ecotypes","title":"Ecotypes","text":"ypr package population considered group interbreeding fish indistinguishable anglers. Ecotypes groups individuals population different life-history strategies. Consequently, ecotypes must share key fishery (pi, Llo, Lup, Nc, rho, Hm q) stock recruitment (BH, RK, tR Rmax) parameters.y use yield-per-recruit approach also necessary assume relative proportion recruits (RPR) adopting life-history strategy independent size composition parental stock.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ecotypes.html","id":"two-ecotypes","dir":"Articles","previous_headings":"","what":"Two Ecotypes","title":"Ecotypes","text":"Consider population smaller ecotype second larger ecotype delays maturation order achieve sufficient size switch piscivory allows grow much larger.","code":"library(ypr) library(ggplot2) # for plotting  ecotypes <- ypr_ecotypes(   Linf2 = 200,   L2 = c(100, 50),   Ls = c(50, 75),   pi = 0.05,   names = c(\"small\", \"large\"),   RPR = c(0.8, 0.2) )  ypr_plot_schedule(ecotypes) + scale_color_manual(values = c(\"black\", \"blue\")) ypr_plot_schedule(ecotypes, x = \"Age\", y = \"Spawning\") + scale_color_manual(values = c(\"black\", \"blue\"))"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ecotypes.html","id":"fish","dir":"Articles","previous_headings":"Two Ecotypes","what":"Fish","title":"Ecotypes","text":"","code":"ypr_plot_fish(ecotypes, color = \"white\") + scale_fill_manual(values = c(\"black\", \"blue\")) ypr_plot_fish(ecotypes, x = \"Length\", y = \"Caught\", color = \"white\", binwidth = 15) + scale_fill_manual(values = c(\"black\", \"blue\"))"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ecotypes.html","id":"stock-recruitment","dir":"Articles","previous_headings":"Two Ecotypes","what":"Stock-Recruitment","title":"Ecotypes","text":"","code":"ypr_plot_sr(ecotypes, biomass = TRUE) ypr_tabulate_sr(ecotypes, biomass = TRUE) #> # A tibble: 3 × 7 #>   Type         pi      u  Eggs Recruits Spawners Fecundity #>   <chr>     <dbl>  <dbl> <dbl>    <dbl>    <dbl>     <dbl> #> 1 unfished 0      0      4085.    0.667    1.27      6431. #> 2 actual   0.05   0.05   2483.    0.549    0.879     5653. #> 3 optimal  0.0833 0.0833 1705.    0.455    0.656     5200."},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ecotypes.html","id":"yield","dir":"Articles","previous_headings":"Two Ecotypes","what":"Yield","title":"Ecotypes","text":"","code":"ypr_tabulate_yield(ecotypes, biomass = TRUE) #> # A tibble: 2 × 8 #>   Type        pi      u Yield   Age Length Weight Effort #>   <chr>    <dbl>  <dbl> <dbl> <dbl>  <dbl>  <dbl>  <dbl> #> 1 actual  0.05   0.05   0.253  7.97   73.6  5474.  0.487 #> 2 optimal 0.0833 0.0833 0.290  7.64   71.9  5026.  0.825 ypr_plot_yield(ecotypes, biomass = TRUE)"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Get Started with ypr","text":"Fish born, grow, reproduce die – whether natural causes fishing. ’s . Modelers just use complicated (complicated) math iron details. Cooper (2006) Equilibrium based yield per recruit (YPR) methods (Walters Martell 2004) estimate capture rate optimizes yield assumption stochasticity density-dependence captured stock-recruitment relationship. remaining population processes growth, reproduction death captured series relatively straight-forward deterministic equations. Table 1. 32 parameters default values descriptions.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"length","dir":"Articles","previous_headings":"Growth","what":"Length","title":"Get Started with ypr","text":"ypr length (cm) age (t) assumed follow Von Bertalanffy growth curve L = L_{\\infty} \\cdot (1 - \\exp(-k \\cdot (t-t_0)))  can biphasic","code":"population <- ypr_population() ypr_plot_schedule(population, \"Age\", \"Length\") ypr_plot_schedule(ypr_population_update(population, L2 = 75, Linf2 = 200), \"Age\", \"Length\") #> Warning: `ypr_population_update()` was deprecated in ypr 0.5.3. #> ℹ Please use `ypr_update()` instead. #> This warning is displayed once every 8 hours. #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was #> generated."},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"weight","dir":"Articles","previous_headings":"Growth","what":"Weight","title":"Get Started with ypr","text":"weight (W) given length assumed follow classic allometric relationship W = w_\\alpha \\cdot L^{w_\\beta}  worth noting w_\\alpha, extrapolated weight (g) 1 cm individual, scaling constant affects estimate yield (calculated terms biomass), ie, affect estimate optimal capture rate.","code":"population <- ypr_population_update(population, Wa = 0.01, Wb = 3) ypr_plot_schedule(population, \"Length\", \"Weight\")"},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"fecundity","dir":"Articles","previous_headings":"Reproduction","what":"Fecundity","title":"Get Started with ypr","text":"fecundity (F) assumed scale allometrically weight according equation F = f_\\alpha \\cdot W^{f_\\beta}  f_\\alpha, extrapolated eggs produced 1 g female, scaling constant effect yield optimal capture rate.","code":"population <- ypr_population_update(population, fa = 1, fb = 1) ypr_plot_schedule(population, \"Weight\", \"Fecundity\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"spawning","dir":"Articles","previous_headings":"Reproduction","what":"Spawning","title":"Get Started with ypr","text":"probability spawning length L determined equation S = \\frac{L^{S_p}}{L_s^{S_p} + L^{S_p}} \\cdot es","code":"population <- ypr_population_update(population, Ls = 50, Sp = 10, es = 0.8) ypr_plot_schedule(population, \"Length\", \"Spawning\")"},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"natural-mortality","dir":"Articles","previous_headings":"Death","what":"Natural Mortality","title":"Get Started with ypr","text":"default natural annual interval mortality rate (n) assumed constant  although like growth can vary biphasically  natural mortality rate can also affected spawning mortality","code":"ypr_plot_schedule(population, \"Length\", \"NaturalMortality\") ypr_plot_schedule(ypr_population_update(population, nL = 0.15, Ln = 60), \"Length\", \"NaturalMortality\") population <- ypr_population_update(population, Sm = 0.5) ypr_plot_schedule(population, \"Length\", \"NaturalMortality\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"fishing-mortality","dir":"Articles","previous_headings":"Death","what":"Fishing Mortality","title":"Get Started with ypr","text":"vulnerability capture (V) assumed vary length follows V = \\frac{L^{V_p}}{L_v^{V_p} + L^{V_p}}  V_p 100 vulnerability effectively knife-edged. probabilty retained captured (R) depends release rate (\\rho), slot limits (L_{lo} L_{}) non-compliance limits (N_c)  fishing mortality (U) depends V, R probability capture fully vulnerable (pi) well hooking mortality (H_m) U =  V \\cdot \\pi \\cdot  R +  V \\cdot \\pi \\cdot (1 - R) \\cdot H_m calculation assumes released fish recaught year.","code":"population <- ypr_population_update(population, Lv = 50, Vp = 50) ypr_plot_schedule(population, \"Length\", \"Vulnerability\") population <- ypr_population_update(population, rho = 0.5, Llo = 40, Lup = 70, Nc = 0.1) ypr_plot_schedule(population, \"Length\", \"Retention\") population <- ypr_population_update(population, pi = 0.3, Hm = 0.2) ypr_plot_schedule(population, \"Length\", \"FishingMortality\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"recruitment","dir":"Articles","previous_headings":"","what":"Recruitment","title":"Get Started with ypr","text":"growth, reproduction death defined, final task estimate recruitment (birth) rate. requires lifetime number spawners per spawner low density (R_k) recruitment age (R_t; default 1) defined. recruitment follows Beverton-Holt (BH = 1) curve R = \\frac{\\alpha \\cdot E}{(\\beta \\cdot E + 1)}  E annual eggs (stock) R annual recruits age R_t. Ricker curve (BH = 0) relationship follows R = \\alpha \\cdot E \\cdot \\exp (-\\beta \\cdot E)  number recruits carrying capacity (R_\\text{max}) scaling constant affects estimate yield. calculating recruitment important introduce concept (unfished) survivorship (lx_a) probability recruit surviving age absence fish mortality.  unfished survivorship (lx_a) defined recursively lx_{R_t} = 1, lx_a = lx_{-1} \\cdot (1-N_{-1}) \\;\\text{}\\; > R_t N_a annual interval natural mortality age . fished survivorship (lx_a^F) lx_{R_t}^F = 1, lx_a^F = lx_{-1}^F \\cdot (1 - (1 - N_{-1}) \\cdot (1 - U_{-1})) \\;\\text{}\\; > R_t lifetime number eggs deposited per (unfished) recruit (\\phi) just \\phi = \\sum_{= R_t}^{t_\\text{max}} lx_a \\cdot F_a/2 \\cdot S_a t_\\text{max} maximum age considered (default 20) F_a fecundity age divided two sex ratio assumed 1:1 S_a probability spawning. fished equivalent denoted \\phi_F. important realize unfished equilibrium annual number recruits (R_0) related annual egg deposition according following equation E_0 = \\phi \\cdot R_0 definition \\alpha = \\frac{R_k \\cdot R_0}{E_0} = \\frac{R_k}{\\phi} \\beta term Beverton-Holt curve can found rearranging following formula R_0 = \\frac{\\alpha \\cdot \\phi \\cdot R_0}{\\beta \\cdot \\phi \\cdot R_0 + 1} \\beta \\cdot \\phi \\cdot R_0 + 1 = \\alpha \\cdot \\phi \\beta = \\frac{\\alpha \\cdot \\phi - 1}{\\phi \\cdot R_0} equivalent equation Ricker curve arrived follows R_0 = \\alpha \\cdot \\phi \\cdot R_0 \\cdot \\exp (-\\beta \\cdot \\phi \\cdot R_0) \\frac{1}{\\exp (-\\beta \\cdot \\phi \\cdot R_0)} = \\alpha \\cdot \\phi \\beta \\cdot \\phi \\cdot R_0 = \\log(\\alpha \\cdot \\phi) \\beta = \\frac{\\log(\\alpha \\cdot \\phi)}{\\phi \\cdot R_0} number recruits fished equilibrium (R_{0F}) can found Beverton-Holt curve follows R_{0F} = \\frac{\\alpha \\cdot \\phi_F \\cdot R_{0F}}{\\beta \\cdot \\phi_F \\cdot R_{0F} + 1} \\beta \\cdot \\phi_F \\cdot R_{0F} + 1 = \\alpha \\cdot \\phi_F R_{0F} = \\frac{\\alpha \\cdot \\phi_F - 1}{\\beta \\cdot \\phi_F} Ricker R_{0F} = \\alpha \\cdot \\phi_F \\cdot R_{0F} \\cdot \\exp (-\\beta \\cdot \\phi_F \\cdot R_{0F}) \\frac{1}{\\exp(-\\beta \\cdot \\phi_F \\cdot R_{0F})} = \\alpha \\cdot \\phi_F \\beta \\cdot \\phi_F \\cdot R_{0F} = \\log(\\alpha \\cdot \\phi_F) R_{0F} = \\frac{\\log(\\alpha \\cdot \\phi_F)}{\\beta \\cdot \\phi_F} Finally estimates rescaled carrying capacity identical R_\\text{max} following transformations \\beta = \\beta \\cdot \\kappa / R_\\text{max}      R_0 = R_0 / \\kappa \\cdot R_\\text{max}      R_{0F} = R_{0F} / \\kappa \\cdot R_\\text{max} \\kappa, carrying capacity original scale, \\alpha/\\beta Beverton-Holt \\alpha/(\\beta \\cdot e) Ricker curve.","code":"population <- ypr_population_update(population, Rk = 3) ypr_plot_sr(population, plot_values = FALSE) population <- ypr_population_update(population, BH = 0L) ypr_plot_sr(population, plot_values = FALSE) ypr_plot_schedule(population, \"Age\", \"Survivorship\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"yield","dir":"Articles","previous_headings":"","what":"Yield","title":"Get Started with ypr","text":"yield simply number fish caught (irrespective weight whether harvested) given Y = \\sum_{= R_t}^{t_\\text{max}} R_{0F} \\cdot lx_a^F \\cdot \\pi \\cdot V_a harvested fish considered becomes Y = \\sum_{= R_t}^{t_\\text{max}} R_{0F} \\cdot lx_a^F \\cdot \\pi \\cdot V_a \\cdot R total weight (kg) important Y = \\sum_{= R_t}^{t_\\text{max}} R_{0F} \\cdot lx_a^F \\cdot \\pi \\cdot V_a \\cdot R \\cdot W_a/1000 trophy fish considered Y = \\sum_{= R_t}^{t_\\text{max}} \\text{}(La < L_y)\\ 0\\ \\text{else}\\ R_{0F} \\cdot lx_a^F \\cdot \\pi \\cdot V_a \\cdot R \\cdot W_a/1000 L_y minimum length trophy fish.","code":"ypr_plot_yield(population, harvest = TRUE, biomass = TRUE, Ly = 60) ypr_tabulate_yield(population, harvest = TRUE, biomass = TRUE, Ly = 60) #> # A tibble: 2 × 8 #>   Type       pi     u  Yield   Age Length Weight Effort #>   <chr>   <dbl> <dbl>  <dbl> <dbl>  <dbl>  <dbl>  <dbl> #> 1 actual  0.3   0.18  0.0505  7.39   66.8  3006.   3.39 #> 2 optimal 0.441 0.265 0.0553  7.35   66.7  2978.   5.53"},{"path":"https://poissonconsulting.github.io/ypr/dev/articles/ypr.html","id":"efficiency","dir":"Articles","previous_headings":"","what":"Efficiency","title":"Get Started with ypr","text":"catchability q indicates probability capture unit effort (E). assumed related \\pi according relationship \\pi = 1 - \\exp(\\log(1-q)\\cdot E) can rearranged give E = \\frac{\\log(1-\\pi)}{\\log(1-q)}.","code":"ypr_plot_yield(population, y = \"Effort\", harvest = TRUE, biomass = TRUE, Ly = 60) ypr_plot_yield(population, y = \"YPUE\", harvest = TRUE, biomass = TRUE, Ly = 60) #> Warning: Removed 1 row containing missing values or values outside the scale range #> (`geom_line()`)."},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Joe Thorley. Author, maintainer. Ayla Pearson. Contributor. . Copyright holder, funder.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Thorley J (2025). ypr: Yield Per Recruit. R package version 0.6.0.9011, https://github.com/poissonconsulting/ypr, https://poissonconsulting.github.io/ypr/.","code":"@Manual{,   title = {ypr: Yield Per Recruit},   author = {Joe Thorley},   year = {2025},   note = {R package version 0.6.0.9011,     https://github.com/poissonconsulting/ypr},   url = {https://poissonconsulting.github.io/ypr/}, }"},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Yield Per Recruit","text":"ypr R package implements equilibrium-based yield per recruit methods. Yield per recruit methods can used estimate optimal yield (Walters Martell 2004) fish population one ecotypes. yield can based number fish caught (harvested) biomass fish just large (trophy) individuals. key life history parameters growth coefficient (k) mean maximum length (Linf) Von Bertalanffy growth curve length 50% mature (Ls) length 50% vulnerable harvest (Lv) annual interval natural mortality rate (n) lifetime number spawners per spawner low density (Rk) case ecotypes relative proportion recruits belong ecotype (RPR) calculations account stochasticity, predator-prey dynamics, angler responses density-dependent growth.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"schedule","dir":"","previous_headings":"Demonstration","what":"Schedule","title":"Yield Per Recruit","text":"","code":"library(ypr) population <- ypr_population(Rk = 5, Ls = 50, Rmax = 100, rho = 0.6) ypr_plot_schedule(population, x = \"Length\", y = \"Spawning\") ypr_tabulate_schedule(population) #> # A tibble: 20 × 11 #>      Age Length Weight Fecundity Spawning NaturalMortality Vulnerability #>    <int>  <dbl>  <dbl>     <dbl>    <dbl>            <dbl>         <dbl> #>  1     1   13.9   27.0      27.0 3.13e-56              0.2      3.13e-56 #>  2     2   25.9  174.      174.  2.91e-29              0.2      2.91e-29 #>  3     3   36.2  476.      476.  1.04e-14              0.2      1.04e-14 #>  4     4   45.1  918.      918.  3.46e- 5              0.2      3.46e- 5 #>  5     5   52.8 1469.     1469.  9.95e- 1              0.2      9.95e- 1 #>  6     6   59.3 2090.     2090.  1.00e+ 0              0.2      1.00e+ 0 #>  7     7   65.0 2747.     2747.  1.00e+ 0              0.2      1.00e+ 0 #>  8     8   69.9 3412.     3412.  1.00e+ 0              0.2      1.00e+ 0 #>  9     9   74.1 4065.     4065.  1   e+ 0              0.2      1   e+ 0 #> 10    10   77.7 4689.     4689.  1   e+ 0              0.2      1   e+ 0 #> 11    11   80.8 5274.     5274.  1   e+ 0              0.2      1   e+ 0 #> 12    12   83.5 5816.     5816.  1   e+ 0              0.2      1   e+ 0 #> 13    13   85.8 6310.     6310.  1   e+ 0              0.2      1   e+ 0 #> 14    14   87.8 6758.     6758.  1   e+ 0              0.2      1   e+ 0 #> 15    15   89.5 7160.     7160.  1   e+ 0              0.2      1   e+ 0 #> 16    16   90.9 7518.     7518.  1   e+ 0              0.2      1   e+ 0 #> 17    17   92.2 7836.     7836.  1   e+ 0              0.2      1   e+ 0 #> 18    18   93.3 8116.     8116.  1   e+ 0              0.2      1   e+ 0 #> 19    19   94.2 8363.     8363.  1   e+ 0              0.2      1   e+ 0 #> 20    20   95.0 8580.     8580.  1   e+ 0              0.2      1   e+ 0 #> # ℹ 4 more variables: Retention <dbl>, FishingMortality <dbl>, #> #   Survivorship <dbl>, FishedSurvivorship <dbl>"},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"fish","dir":"","previous_headings":"Demonstration","what":"Fish","title":"Yield Per Recruit","text":"","code":"ypr_plot_fish(population, color = \"white\") ypr_tabulate_fish(population) #> # A tibble: 20 × 8 #>      Age Survivors Spawners   Caught Harvested Released HandlingMortalities #>    <dbl>     <dbl>    <dbl>    <dbl>     <dbl>    <dbl>               <dbl> #>  1     1    70.1   2.19e-54 4.39e-55  1.76e-55 2.63e-55                   0 #>  2     2    56.1   1.63e-27 3.26e-28  1.30e-28 1.96e-28                   0 #>  3     3    44.9   4.68e-13 9.36e-14  3.74e-14 5.62e-14                   0 #>  4     4    35.9   1.24e- 3 2.48e- 4  9.93e- 5 1.49e- 4                   0 #>  5     5    28.7   2.86e+ 1 5.72e+ 0  2.29e+ 0 3.43e+ 0                   0 #>  6     6    21.1   2.11e+ 1 4.23e+ 0  1.69e+ 0 2.54e+ 0                   0 #>  7     7    15.6   1.56e+ 1 3.11e+ 0  1.24e+ 0 1.87e+ 0                   0 #>  8     8    11.5   1.15e+ 1 2.29e+ 0  9.16e- 1 1.37e+ 0                   0 #>  9     9     8.43  8.43e+ 0 1.69e+ 0  6.74e- 1 1.01e+ 0                   0 #> 10    10     6.20  6.20e+ 0 1.24e+ 0  4.96e- 1 7.44e- 1                   0 #> 11    11     4.57  4.57e+ 0 9.13e- 1  3.65e- 1 5.48e- 1                   0 #> 12    12     3.36  3.36e+ 0 6.72e- 1  2.69e- 1 4.03e- 1                   0 #> 13    13     2.47  2.47e+ 0 4.95e- 1  1.98e- 1 2.97e- 1                   0 #> 14    14     1.82  1.82e+ 0 3.64e- 1  1.46e- 1 2.18e- 1                   0 #> 15    15     1.34  1.34e+ 0 2.68e- 1  1.07e- 1 1.61e- 1                   0 #> 16    16     0.986 9.86e- 1 1.97e- 1  7.89e- 2 1.18e- 1                   0 #> 17    17     0.726 7.26e- 1 1.45e- 1  5.81e- 2 8.71e- 2                   0 #> 18    18     0.534 5.34e- 1 1.07e- 1  4.27e- 2 6.41e- 2                   0 #> 19    19     0.393 3.93e- 1 7.86e- 2  3.15e- 2 4.72e- 2                   0 #> 20    20     0.289 2.89e- 1 5.79e- 2  2.31e- 2 3.47e- 2                   0 #> # ℹ 1 more variable: Ecotype <chr>"},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"stock-recruitment","dir":"","previous_headings":"Demonstration","what":"Stock-Recruitment","title":"Yield Per Recruit","text":"","code":"ypr_plot_sr(population) ypr_tabulate_sr(population) #> # A tibble: 3 × 7 #>   Type        pi     u    Eggs Recruits Spawners Fecundity #>   <chr>    <dbl> <dbl>   <dbl>    <dbl>    <dbl>     <dbl> #> 1 unfished 0     0     286350.     80      159.      3600. #> 2 actual   0.2   0.08  167831.     70.1    108.      3112. #> 3 optimal  0.458 0.183  84129.     54.0     63.7     2641."},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"yield","dir":"","previous_headings":"Demonstration","what":"Yield","title":"Yield Per Recruit","text":"","code":"ypr_tabulate_yield(population) #> # A tibble: 2 × 8 #>   Type       pi     u Yield   Age Length Weight Effort #>   <chr>   <dbl> <dbl> <dbl> <dbl>  <dbl>  <dbl>  <dbl> #> 1 actual  0.2   0.08   8.63  7.67   65.8  3112.   2.12 #> 2 optimal 0.458 0.183 11.7   6.87   62.6  2641.   5.82 ypr_plot_yield(population)"},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"information","dir":"","previous_headings":"","what":"Information","title":"Yield Per Recruit","text":"information see Get Started vignette.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"interaction","dir":"","previous_headings":"Information","what":"Interaction","title":"Yield Per Recruit","text":"interactively explore effects altering individual parameters schedule, stock-recruitment yield see ypr shiny app. screenshot yield ypr shiny app","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"release","dir":"","previous_headings":"Installation","what":"Release","title":"Yield Per Recruit","text":"install release version CRAN. website release version https://poissonconsulting.github.io/ypr/.","code":"install.packages(\"ypr\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"development","dir":"","previous_headings":"Installation","what":"Development","title":"Yield Per Recruit","text":"install development version r-universe. GitHub","code":"install.packages(\"ypr\", repos = c(\"https://poissonconsulting.r-universe.dev\", \"https://cloud.r-project.org\")) # install.packages(\"remotes\") remotes::install_github(\"poissonconsulting/ypr\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"creditation","dir":"","previous_headings":"","what":"Creditation","title":"Yield Per Recruit","text":"Development ypr partially supported Habitat Conservation Trust Foundation Ministry Forests, Lands Natural Resource Operations. hex designed Forest.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"contribution","dir":"","previous_headings":"","what":"Contribution","title":"Yield Per Recruit","text":"Please report issues. Pull requests always welcome.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Yield Per Recruit","text":"Please note ypr project released Contributor Code Conduct. contributing project, agree abide terms","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/adams_bt_03.html","id":null,"dir":"Reference","previous_headings":"","what":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","title":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","text":"population parameters Bull Trout Adams Lake Bison et al (2003)","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/adams_bt_03.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","text":"","code":"adams_bt_03"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/adams_bt_03.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/adams_bt_03.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","text":"Bison, R., O’Brien, D., Martell, S.J.D. 2003. Analysis Sustainable Fishing Options Adams Lake Bull Trout Using Life History Telemetry Data. BC Ministry Water Land Air Protection, Kamloops, B.C.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/adams_bt_03.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adams Lake Bull Trout Population Parameters (2003) — adams_bt_03","text":"","code":"adams_bt_03 #> tmax:  20 #> k:     0.13 #> Linf:  131 #> t0:    0.2 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.4 #> Ls:    40 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3.8 #> n:     0.3 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    5 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.06 #> rho:   0 #> Hm:    0.15 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(adams_bt_03)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to an Ecotypes Object — as_ypr_ecotypes","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"Coerce Ecotypes Object","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"","code":"as_ypr_ecotypes(x, ...)  # S3 method for class 'data.frame' as_ypr_ecotypes(x, ...)  # S3 method for class 'ypr_population' as_ypr_ecotypes(x, ...)  # S3 method for class 'ypr_populations' as_ypr_ecotypes(x, ...)  # S3 method for class 'ypr_ecotypes' as_ypr_ecotypes(x, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"x object coerce. ... Additional arguments.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"object class ypr_ecotypes.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"as_ypr_ecotypes(data.frame): Coerce data.frame Ecotypes Object as_ypr_ecotypes(ypr_population): Coerce Population Object Ecotypes Object as_ypr_ecotypes(ypr_populations): Coerce Populations Object Ecotypes Object as_ypr_ecotypes(ypr_ecotypes): Coerce Ecotypes Object Ecotypes Object","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_ecotypes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to an Ecotypes Object — as_ypr_ecotypes","text":"","code":"as_ypr_ecotypes(as.data.frame(ypr_ecotypes(Ls = c(10, 15, 20)))) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    10, 15, 20 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Ls_10, Ls_15, Ls_20 as_ypr_ecotypes(ypr_population()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_ecotypes(ypr_populations(Ls = c(10, 15, 20))) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    10, 15, 20 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Ls_10, Ls_15, Ls_20 as_ypr_ecotypes(ypr_ecotypes(Ls = c(10, 15, 20))) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    10, 15, 20 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Ls_10, Ls_15, Ls_20"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to a Population Object — as_ypr_population","title":"Coerce to a Population Object — as_ypr_population","text":"Coerce Population Object","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to a Population Object — as_ypr_population","text":"","code":"as_ypr_population(x, ...)  # S3 method for class 'data.frame' as_ypr_population(x, ...)  # S3 method for class 'ypr_population' as_ypr_population(x, ...)  # S3 method for class 'ypr_populations' as_ypr_population(x, ...)  # S3 method for class 'ypr_ecotypes' as_ypr_population(x, ...)  # S3 method for class 'data.frame' as_ypr_populations(x, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to a Population Object — as_ypr_population","text":"x object coerce. ... Unused.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to a Population Object — as_ypr_population","text":"object class ypr_population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Coerce to a Population Object — as_ypr_population","text":"as_ypr_population(data.frame): Coerce data.frame Population Object as_ypr_population(ypr_population): Coerce Population Object Population Object as_ypr_population(ypr_populations): Coerce Populations Object length 1 Population Object as_ypr_population(ypr_ecotypes): Coerce Ecotypes Object length 1 Population Object","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Coerce to a Population Object — as_ypr_population","text":"as_ypr_populations(data.frame): Coerce data.frame Populations Object","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to a Population Object — as_ypr_population","text":"","code":"as_ypr_population(as.data.frame(ypr_population())) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_population(ypr_populations()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_population(ypr_populations()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_population(ypr_ecotypes()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_populations(as.data.frame(ypr_populations(Rk = c(3, 4)))) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3, 4 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to a Populations Object — as_ypr_populations","title":"Coerce to a Populations Object — as_ypr_populations","text":"Coerce Populations Object","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to a Populations Object — as_ypr_populations","text":"","code":"as_ypr_populations(x, ...)  # S3 method for class 'ypr_population' as_ypr_populations(x, ...)  # S3 method for class 'ypr_populations' as_ypr_populations(x, ...)  # S3 method for class 'ypr_ecotypes' as_ypr_populations(x, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to a Populations Object — as_ypr_populations","text":"x object coerce. ... Unused.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to a Populations Object — as_ypr_populations","text":"object class ypr_ecotypes.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Coerce to a Populations Object — as_ypr_populations","text":"as_ypr_populations(ypr_population): Coerce Population Object Population Object as_ypr_populations(ypr_populations): Coerce Populations Object length 1 Population Object as_ypr_populations(ypr_ecotypes): Coerce Ecotypes Object length 1 Population Object","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/as_ypr_populations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to a Populations Object — as_ypr_populations","text":"","code":"as_ypr_populations(ypr_population()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_populations(ypr_populations()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 as_ypr_populations(ypr_ecotypes()) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_ecotypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Ecotypes — check_ecotypes","title":"Check Ecotypes — check_ecotypes","text":"Checks ypr_ecotypes object valid parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_ecotypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Ecotypes — check_ecotypes","text":"","code":"check_ecotypes(x, x_name = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_ecotypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Ecotypes — check_ecotypes","text":"x object check. x_name string name object x NULL.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_ecotypes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Ecotypes — check_ecotypes","text":"informative error test fails invisible copy x.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_ecotypes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Ecotypes — check_ecotypes","text":"","code":"check_ecotypes(ypr_ecotypes())"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Population — check_population","title":"Check Population — check_population","text":"Checks ypr_population object valid parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Population — check_population","text":"","code":"check_population(x, x_name = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Population — check_population","text":"x object check. x_name string name object x NULL.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Population — check_population","text":"informative error test fails invisible copy x.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Population — check_population","text":"","code":"check_population(ypr_population())"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_populations.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Populations — check_populations","title":"Check Populations — check_populations","text":"Checks ypr_populations object valid parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_populations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Populations — check_populations","text":"","code":"check_populations(x, x_name = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_populations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Populations — check_populations","text":"x object check. x_name string name object x NULL.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_populations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Populations — check_populations","text":"informative error test fails invisible copy x.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/check_populations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Populations — check_populations","text":"","code":"check_populations(ypr_populations())"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/chilliwack_bt_05.html","id":null,"dir":"Reference","previous_headings":"","what":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","title":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","text":"populations parameters Bull Trout Chilliwack Lake Taylor (2005)","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/chilliwack_bt_05.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","text":"","code":"chilliwack_bt_05"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/chilliwack_bt_05.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","text":"object class ypr_populations().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/chilliwack_bt_05.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","text":"Taylor, J.L. 2005. Sustainability Chilliwack Lake Char Fishery. Ministry Water, Land Air Protection, Surrey, B.C.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/chilliwack_bt_05.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Chilliwack Lake Bull Trout Populations Parameters (2005) — chilliwack_bt_05","text":"","code":"chilliwack_bt_05 #> tmax:  20 #> k:     0.12 #> Linf:  86 #> t0:    0.018 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    2.8 #> Ls:    38.5 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5, 4.6, 2.5, 4.6, 2.5, 4.6, 2.5, 4.6, 2.5, 4.6, 2.5, 4.6 #> n:     0.17 #> nL:    0.2 #> Ln:    1000 #> Lv:    36.5 #> Vp:    11.7 #> Llo:   0, 0, 60, 60, 1000, 1000, 0, 0, 60, 60, 1000, 1000 #> Lup:   1000 #> Nc:    0.15 #> pi:    0.2 #> rho:   0 #> Hm:    0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2 #> Rmax:  250 #> Wa:    0.022 #> fa:    2.29 #> q:     0.1 #> RPR:   1 yield <- ypr_tabulate_yield(chilliwack_bt_05, type = \"optimal\") yield$pi <- round(yield$pi, 2) yield <- yield[c(\"Llo\", \"Hm\", \"Rk\", \"pi\")] yield <- tidyr::spread(yield, Rk, pi) yield <- yield[order(-yield$Hm), ] yield #> # A tibble: 6 × 4 #>     Llo    Hm `2.5` `4.6` #>   <dbl> <dbl> <dbl> <dbl> #> 1     0  0.2   0.08  0.14 #> 2    60  0.2   0.14  0.25 #> 3  1000  0.2   0.25  0.45 #> 4     0  0.05  0.08  0.14 #> 5    60  0.05  0.17  0.37 #> 6  1000  0.05  0.41  0.74 if (FALSE) { # \\dontrun{ ypr_plot_yield(chilliwack_bt_05, plot_values = FALSE) +   ggplot2::facet_grid(Rk ~ Hm) +   ggplot2::aes(group = Llo, linetype = Llo) } # }"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/is.ypr_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","title":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","text":"Tests Population, Populations Ecotypes","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/is.ypr_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","text":"","code":"is.ypr_population(x)  is_ypr_population(x)  is.ypr_populations(x)  is_ypr_populations(x)  is.ypr_ecotypes(x)  is_ypr_ecotypes(x)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/is.ypr_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","text":"x object test.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/is.ypr_population.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","text":"is_ypr_population(): Test Population .ypr_populations(): Test Populations is_ypr_populations(): Test Populations .ypr_ecotypes(): Test Ecotypes is_ypr_ecotypes(): Test Ecotypes","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/is.ypr_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tests if is a Population, Populations or Ecotypes — is.ypr_population","text":"","code":"is.ypr_population(ypr_population()) #> [1] TRUE is_ypr_population(ypr_population()) #> [1] TRUE is.ypr_populations(ypr_populations()) #> [1] TRUE is_ypr_population(ypr_populations()) #> [1] FALSE is.ypr_ecotypes(ypr_ecotypes()) #> [1] TRUE is_ypr_ecotypes(ypr_ecotypes()) #> [1] TRUE"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":null,"dir":"Reference","previous_headings":"","what":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"population parameters Bull Trout Kootenay Lake Andrusak Thorley (2013)","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"","code":"kootenay_bt_13"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"estimates used management.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"Andrusak, G.F., Thorley, J.L. 2013. Kootenay Lake Exploitation Study: Fishing Natural Mortality Large Rainbow Trout Bull Trout: 2013 Annual Report. Poisson Consulting Ltd. Redfish Consulting Ltd. Report, Habitat Conservation Trust Foundation, Victoria, BC.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_bt_13.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kootenay Lake Bull Trout Population Parameters (2013) — kootenay_bt_13","text":"","code":"kootenay_bt_13 #> tmax:  20 #> k:     0.19 #> Linf:  100 #> t0:    0.5 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.04 #> Ls:    60 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    5 #> n:     0.29 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    5 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.1 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(kootenay_bt_13)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":null,"dir":"Reference","previous_headings":"","what":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"population parameters Rainbow Trout Kootenay Lake.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"","code":"kootenay_rb"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"estimates liable change used management.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"Thorley, J.L., Andrusak, G.F. 2017. fishing natural mortality large, piscivorous Bull Trout Rainbow Trout Kootenay Lake, British Columbia (2008–2013). PeerJ 5: e2874. doi:10.7717/peerj.2874.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kootenay Lake Rainbow Trout Population Parameters — kootenay_rb","text":"","code":"kootenay_rb #> tmax:  20 #> k:     0.26 #> Linf:  100 #> t0:    0.5 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.2 #> Ls:    75 #> Sp:    20 #> es:    0.9 #> Sm:    0.53 #> fb:    0.86 #> tR:    1 #> BH:    1 #> Rk:    17.65 #> n:     0.23 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    10 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.14 #> rho:   0.62 #> Hm:    0.25 #> Rmax:  115000 #> Wa:    0.005 #> fa:    3.9 #> q:     0.028 #> RPR:   1 ypr_plot_yield(kootenay_rb)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":null,"dir":"Reference","previous_headings":"","what":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"population parameters Rainbow Trout Kootenay Lake Andrusak Thorley (2013)","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"","code":"kootenay_rb_13"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"estimates used management.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"Andrusak, G.F., Thorley, J.L. 2013. Kootenay Lake Exploitation Study: Fishing Natural Mortality Large Rainbow Trout Bull Trout: 2013 Annual Report. Poisson Consulting Ltd. Redfish Consulting Ltd. Report, Habitat Conservation Trust Foundation, Victoria, BC.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/kootenay_rb_13.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kootenay Lake Rainbow Trout Population Parameters (2013) — kootenay_rb_13","text":"","code":"kootenay_rb_13 #> tmax:  20 #> k:     0.25 #> Linf:  100 #> t0:    0.75 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.39 #> Ls:    60 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    10 #> n:     0.38 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    5 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.1 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(kootenay_rb_13)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/params.html","id":null,"dir":"Reference","previous_headings":"","what":"Parameter Descriptions for ypr Package — params","title":"Parameter Descriptions for ypr Package — params","text":"Default parameter descriptions may overridden individual functions.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parameter Descriptions for ypr Package — params","text":"... dots future extensions must empty. tmax maximum age (yr). k VB growth coefficient (yr-1). Linf VB mean maximum length (cm). t0 (theoretical) age zero length (yr). k2 VB growth coefficient length L2 (yr-1). Linf2 VB mean maximum length length L2 (cm). L2 length (age negative) growth switches first second phase (cm yr). Wb weight (function length) scaling exponent. Ls length (age negative) 50 % mature (cm yr). Sp maturity (function length) power. es annual probability mature fish spawning. Sm spawning mortality probability. fb fecundity (function weight) scaling exponent. tR age survival density-independent (yr). BH Recruitment follows Beverton-Holt (1) Ricker (0) relationship. Rk lifetime spawners per spawner low density (egg tR survival 0 1). n annual interval natural mortality rate age tR. nL annual interval natural mortality rate length Ln. Ln length  (age negative) annual interval natural mortality rate switches n nL (cm yr). Lv length (age negative) 50 % vulnerable harvest (cm yr). Vp vulnerability harvest (function length) power. Llo lower harvest slot length (cm). Lup upper harvest slot length (cm). Nc slot limits non-compliance probability. pi vector probabilities capture calculate yield . rho release probability. Hm hooking mortality probability. Rmax number recruits carrying capacity (ind). Wa (extrapolated) weight 1 cm individual (g). fa (theoretical) fecundity 1 g female (eggs). q catchability (annual probability capture) unit effort. RPR relative proportion recruits ecotype. flag specifying whether include parameter values. u flag specifying whether plot exploitation rate opposed capture rate. percent flag specifying whether plot number fish percent frequency (default). color string color around bar (NULL). population object class ypr_population(). populations object class ypr_populations(). ecotypes object class ypr_ecotypes(). plot_values flag specifying whether plot actual optimal values. Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. title string report title. date date report date. file string path file (without extension). binwidth positive integer width bins grouping. type string indicating whether include '' just 'actual' 'optimal' yield. object population populations. expand flag specifying whether expand parameter combinations. view flag specifying whether view report (rendering html). ask flag specifying whether ask overwriting creating file. description string describing population. age numeric vector age (yr). length numeric vector length (cm). names character vector unique ecotype names. x object coerce.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/params.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Parameter Descriptions for ypr Package — params","text":"flag non-missing logical scalar. string non-missing character scalar.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/plot.ypr_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Population Schedule — plot.ypr_population","title":"Plot Population Schedule — plot.ypr_population","text":"Plot Population Schedule","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/plot.ypr_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Population Schedule — plot.ypr_population","text":"","code":"# S3 method for class 'ypr_population' plot(x, type = \"b\", ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/plot.ypr_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Population Schedule — plot.ypr_population","text":"x population plot. type string specifying plot type. Possible values include 'b', 'p' 'l'. ... Additional arguments passed graphics::plot function.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/plot.ypr_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Population Schedule — plot.ypr_population","text":"invisible copy original object.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/plot.ypr_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Population Schedule — plot.ypr_population","text":"","code":"if (FALSE) { # \\dontrun{ plot(ypr_population()) } # }"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_bt.html","id":null,"dir":"Reference","previous_headings":"","what":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","title":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","text":"population parameters Bull Trout Quesnel Lake, BC.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_bt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","text":"","code":"quesnel_bt"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_bt.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_bt.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","text":"estimates liable change used management.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_bt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Quesnel Lake Bull Trout Population Parameters — quesnel_bt","text":"","code":"quesnel_bt #> tmax:  20 #> k:     0.13 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.4 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3.8 #> n:     0.3 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.06 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(quesnel_bt)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_lt.html","id":null,"dir":"Reference","previous_headings":"","what":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","title":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","text":"population parameters Lake Trout Quesnel Lake, BC.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_lt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","text":"","code":"quesnel_lt"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_lt.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_lt.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","text":"estimates liable change used management.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_lt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Quesnel Lake Lake Trout Population Parameters — quesnel_lt","text":"","code":"quesnel_lt #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3.1 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5 #> n:     0.15 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.04 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(quesnel_lt)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_rb.html","id":null,"dir":"Reference","previous_headings":"","what":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","title":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","text":"population parameters Rainbow Trout Quesnel Lake, BC.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_rb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","text":"","code":"quesnel_rb"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_rb.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","text":"object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_rb.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","text":"estimates liable change used management.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/quesnel_rb.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Quesnel Lake Rainbow Trout Population Parameters — quesnel_rb","text":"","code":"quesnel_rb #> tmax:  20 #> k:     0.2 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    6 #> n:     0.5 #> nL:    0.2 #> Ln:    1000 #> Lv:    40 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.14 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_plot_yield(quesnel_rb)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. tibble as_tibble","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"ypr: Yield Per Recruit — ypr-package","title":"ypr: Yield Per Recruit — ypr-package","text":"implementation equilibrium-based yield per recruit methods. Yield per recruit methods can used estimate optimal yield fish population described Walters Martell (2004) <isbn:0-691-11544-3>. yield can based number fish caught (harvested) biomass caught fish just large (trophy) individuals.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"ypr: Yield Per Recruit — ypr-package","text":"Maintainer: Joe Thorley joe@poissonconsulting.ca (ORCID) contributors: Ayla Pearson (ORCID) [contributor] Poisson Consulting [copyright holder, funder]","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_age_at_length.html","id":null,"dir":"Reference","previous_headings":"","what":"Age At Length — ypr_age_at_length","title":"Age At Length — ypr_age_at_length","text":"Age Length","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_age_at_length.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Age At Length — ypr_age_at_length","text":"","code":"ypr_age_at_length(population, length)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_age_at_length.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Age At Length — ypr_age_at_length","text":"population object class ypr_population(). length numeric vector length (cm).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_age_at_length.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Age At Length — ypr_age_at_length","text":"double vector lengths.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_age_at_length.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Age At Length — ypr_age_at_length","text":"","code":"ypr_age_at_length(ypr_population(), seq(0, 100, by = 10)) #>  [1]  0.0000000  0.7024034  1.4876237  2.3778330  3.4055042  4.6209812 #>  [7]  6.1086049  8.0264854 10.7295861 15.3505673        Inf"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_detabulate_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"Detabulate Population Parameters — ypr_detabulate_parameters","title":"Detabulate Population Parameters — ypr_detabulate_parameters","text":"Detabulate Population Parameters","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_detabulate_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detabulate Population Parameters — ypr_detabulate_parameters","text":"","code":"ypr_detabulate_parameters(x)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_detabulate_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detabulate Population Parameters — ypr_detabulate_parameters","text":"x data frame columns Parameter Value specifying one parameters values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_detabulate_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detabulate Population Parameters — ypr_detabulate_parameters","text":"object class ypr_population()","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_detabulate_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Detabulate Population Parameters — ypr_detabulate_parameters","text":"","code":"ypr_detabulate_parameters(ypr_tabulate_parameters(ypr_population())) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_ecotypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Ecotypes Object — ypr_ecotypes","title":"Create Ecotypes Object — ypr_ecotypes","text":"Creates ypr_ecotypes object.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_ecotypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Ecotypes Object — ypr_ecotypes","text":"","code":"ypr_ecotypes(..., names = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_ecotypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Ecotypes Object — ypr_ecotypes","text":"... dots future extensions must empty. names character vector unique ecotype names.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_ecotypes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Ecotypes Object — ypr_ecotypes","text":"ypr_ecotypes() objects","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_ecotypes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Ecotypes Object — ypr_ecotypes","text":"","code":"ypr_ecotypes(Linf = c(1, 2)) #> tmax:  20 #> k:     0.15 #> Linf:  1, 2 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Linf_1, Linf_2 ypr_ecotypes(Linf = c(1, 2), t0 = c(0, 0.5)) #> tmax:  20 #> k:     0.15 #> Linf:  1, 2 #> t0:    0, 0.5 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Linf_1_t0_0, Linf_2_t0_0_5"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":null,"dir":"Reference","previous_headings":"","what":"Exploitation Probability — ypr_exploitation","title":"Exploitation Probability — ypr_exploitation","text":"Converts capture probabilities exploitation probabilities based release handling mortality probabilities probability exploitation includes handling mortalities. calculation assumes released fish recaught year.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Exploitation Probability — ypr_exploitation","text":"","code":"ypr_exploitation(object, pi = ypr_get_par(object))"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Exploitation Probability — ypr_exploitation","text":"object population populations. pi vector capture probabilities calculate exploitation probabilities .","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Exploitation Probability — ypr_exploitation","text":"vector exploitation probabilities.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Exploitation Probability — ypr_exploitation","text":"case release (100% handling mortalities) exploitation probability identical capture probability. Otherwise less.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_exploitation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Exploitation Probability — ypr_exploitation","text":"","code":"ypr_exploitation(ypr_population(pi = 0.4)) #> [1] 0.4 ypr_exploitation(ypr_population(pi = 0.4, rho = 0.6, Hm = 0.2)) #> [1] 0.208"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_get_par.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Parameter Value — ypr_get_par","title":"Get Parameter Value — ypr_get_par","text":"Get Parameter Value","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_get_par.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Parameter Value — ypr_get_par","text":"","code":"ypr_get_par(object, par = \"pi\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_get_par.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Parameter Value — ypr_get_par","text":"object ypr object. par string parameter.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_get_par.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Parameter Value — ypr_get_par","text":"numeric integer scalar vector parameter value.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_get_par.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Parameter Value — ypr_get_par","text":"","code":"ypr_get_par(ypr_population()) #> [1] 0.2"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_length_at_age.html","id":null,"dir":"Reference","previous_headings":"","what":"Length At Age — ypr_length_at_age","title":"Length At Age — ypr_length_at_age","text":"Length Age","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_length_at_age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Length At Age — ypr_length_at_age","text":"","code":"ypr_length_at_age(population, age)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_length_at_age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Length At Age — ypr_length_at_age","text":"population object class ypr_population(). age numeric vector age (yr).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_length_at_age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Length At Age — ypr_length_at_age","text":"double vector lengths.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_length_at_age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Length At Age — ypr_length_at_age","text":"","code":"ypr_length_at_age(ypr_population(), seq(0, 5, by = 0.5)) #>  [1]  0.000000  7.225651 13.929202 20.148378 25.918178 31.271072 36.237185 #>  [8] 40.844464 45.118836 49.084358 52.763345"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Population(s) or Ecotype Names — ypr_names","title":"Population(s) or Ecotype Names — ypr_names","text":"Generates set unique names based differences parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population(s) or Ecotype Names — ypr_names","text":"","code":"ypr_names(x, ...)  # S3 method for class 'ypr_population' ypr_names(x, ...)  # S3 method for class 'ypr_populations' ypr_names(x, ...)  # S3 method for class 'ypr_ecotypes' ypr_names(x, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Population(s) or Ecotype Names — ypr_names","text":"x object class ypr_population, ypr_populations ypr_ecotypes. ... Unused.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Population(s) or Ecotype Names — ypr_names","text":"character vector unique parameter based names.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Population(s) or Ecotype Names — ypr_names","text":"Parameter RPR ignored irrelevant population(s) distinguish ecotypes.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Population(s) or Ecotype Names — ypr_names","text":"ypr_names(ypr_population): Population Names ypr_names(ypr_populations): Populations Names ypr_names(ypr_ecotypes): Ecotypes Names","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Population(s) or Ecotype Names — ypr_names","text":"","code":"ypr_names(ypr_population()) #> [1] \"Pop_1\" ypr_names(ypr_populations()) #> [1] \"Pop_1\" ypr_names(ypr_populations()) #> [1] \"Pop_1\""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_optimize.html","id":null,"dir":"Reference","previous_headings":"","what":"Optimize Capture — ypr_optimize","title":"Optimize Capture — ypr_optimize","text":"Finds annual interval capture probability (pi) maximises yield given population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_optimize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Optimize Capture — ypr_optimize","text":"","code":"ypr_optimize(object, Ly = 0, harvest = TRUE, biomass = FALSE)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_optimize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Optimize Capture — ypr_optimize","text":"object population populations. Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_optimize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Optimize Capture — ypr_optimize","text":"annual interval capture probability (pi) maximises yield.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_optimize.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Optimize Capture — ypr_optimize","text":"","code":"ypr_optimize(ypr_population()) #> [1] 0.115183"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_biomass.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Biomass — ypr_plot_biomass","title":"Plot Biomass — ypr_plot_biomass","text":"Produces frequency histogram total fish 'Biomass' 'Eggs' deposition 'Age' class.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_biomass.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Biomass — ypr_plot_biomass","text":"","code":"ypr_plot_biomass(population, y = \"Biomass\", color = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_biomass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Biomass — ypr_plot_biomass","text":"population object class ypr_population(). y string term y-axis. color string color around bar (NULL).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_biomass.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Biomass — ypr_plot_biomass","text":"ggplot2 object.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_biomass.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Biomass — ypr_plot_biomass","text":"","code":"ypr_plot_biomass(ypr_population(), color = \"white\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_fish.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Fish — ypr_plot_fish","title":"Plot Fish — ypr_plot_fish","text":"Produces frequency histogram number fish 'Survivors', 'Spawners', 'Caught', 'Harvested' 'Released' categories 'Length', 'Age' 'Weight' class.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_fish.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Fish — ypr_plot_fish","text":"","code":"ypr_plot_fish(   population,   x = \"Age\",   y = \"Survivors\",   percent = FALSE,   binwidth = 1L,   color = NULL )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_fish.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Fish — ypr_plot_fish","text":"population object class ypr_population(). x object coerce. y string term y-axis. percent flag specifying whether plot number fish percent frequency (default). binwidth positive integer width bins grouping. color string color around bar (NULL).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_fish.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Fish — ypr_plot_fish","text":"ggplot2 object.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_fish.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Fish — ypr_plot_fish","text":"","code":"ypr_plot_fish(ypr_population(), color = \"white\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_schedule.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","title":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","text":"Produces bivariate line plot two schedule terms.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_schedule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","text":"","code":"ypr_plot_schedule(population, x = \"Age\", y = \"Length\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_schedule.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","text":"population object class ypr_population(). x string term x-axis. y string term y-axis.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_schedule.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","text":"ggplot2 object.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_schedule.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Population or Ecotypes Schedule Terms — ypr_plot_schedule","text":"","code":"ypr_plot_schedule(ypr_population())"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_sr.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Stock-Recruitment Curve — ypr_plot_sr","title":"Plot Stock-Recruitment Curve — ypr_plot_sr","text":"Plot Stock-Recruitment Curve","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_sr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Stock-Recruitment Curve — ypr_plot_sr","text":"","code":"ypr_plot_sr(   population,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   plot_values = TRUE )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_sr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Stock-Recruitment Curve — ypr_plot_sr","text":"population object class ypr_population(). Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. plot_values flag specifying whether plot actual optimal values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_sr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Stock-Recruitment Curve — ypr_plot_sr","text":"ggplot2 object.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_sr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Stock-Recruitment Curve — ypr_plot_sr","text":"","code":"ypr_plot_sr(ypr_population(Rk = 10))  ypr_plot_sr(ypr_population(Rk = 10, BH = 0L))"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Yield by Capture — ypr_plot_yield","title":"Plot Yield by Capture — ypr_plot_yield","text":"Plots 'Yield', 'Age', 'Length', 'Weight', 'Effort', 'YPUE' annual interval capture/exploitation probability.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Yield by Capture — ypr_plot_yield","text":"","code":"ypr_plot_yield(object, ...)  # Default S3 method ypr_plot_yield(   object,   y = \"Yield\",   pi = seq(0, 1, length.out = 100),   Ly = 0,   harvest = TRUE,   biomass = FALSE,   u = harvest,   plot_values = TRUE,   ... )  # S3 method for class 'ypr_populations' ypr_plot_yield(   object,   y = \"Yield\",   pi = seq(0, 1, length.out = 100),   Ly = 0,   harvest = TRUE,   biomass = FALSE,   u = harvest,   plot_values = TRUE,   ... )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Yield by Capture — ypr_plot_yield","text":"object population populations. ... dots future extensions must empty. y string term y-axis. pi vector probabilities capture calculate yield . Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. u flag specifying whether plot exploitation rate opposed capture rate. plot_values flag specifying whether plot actual optimal values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Yield by Capture — ypr_plot_yield","text":"ggplot2 object.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Plot Yield by Capture — ypr_plot_yield","text":"ypr_plot_yield(default): Plot Yield Capture ypr_plot_yield(ypr_populations): Plot Yield Capture","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_plot_yield.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Yield by Capture — ypr_plot_yield","text":"","code":"if (FALSE) { # \\dontrun{ ypr_plot_yield(   ypr_populations(     Rk = c(2.5, 4.6),     Llo = c(0, 60)   ),   plot_values = FALSE ) +   ggplot2::facet_wrap(~Llo) +   ggplot2::aes(group = Rk, color = Rk) +   ggplot2::scale_color_manual(values = c(\"black\", \"blue\"))  ypr_plot_yield(ypr_populations(Rk = c(2.5, 4.6), Llo = c(0, 60))) +   ggplot2::facet_grid(Rk ~ Llo) } # }  ypr_plot_yield(ypr_population())"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Population Parameters — ypr_population","title":"Population Parameters — ypr_population","text":"Generates object class ypr_population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population Parameters — ypr_population","text":"","code":"ypr_population(   tmax = 20L,   k = 0.15,   Linf = 100,   t0 = 0,   k2 = 0.15,   Linf2 = 100,   L2 = 1000,   Wb = 3,   Ls = 50,   Sp = 100,   es = 1,   Sm = 0,   fb = 1,   tR = 1L,   BH = 1L,   Rk = 3,   n = 0.2,   nL = 0.2,   Ln = 1000,   Lv = 50,   Vp = 100,   Llo = 0,   Lup = 1000,   Nc = 0,   pi = 0.2,   rho = 0,   Hm = 0,   Rmax = 1,   Wa = 0.01,   fa = 1,   q = 0.1,   RPR = 1 )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Population Parameters — ypr_population","text":"tmax maximum age (yr). k VB growth coefficient (yr-1). Linf VB mean maximum length (cm). t0 (theoretical) age zero length (yr). k2 VB growth coefficient length L2 (yr-1). Linf2 VB mean maximum length length L2 (cm). L2 length (age negative) growth switches first second phase (cm yr). Wb weight (function length) scaling exponent. Ls length (age negative) 50 % mature (cm yr). Sp maturity (function length) power. es annual probability mature fish spawning. Sm spawning mortality probability. fb fecundity (function weight) scaling exponent. tR age survival density-independent (yr). BH Recruitment follows Beverton-Holt (1) Ricker (0) relationship. Rk lifetime spawners per spawner low density (egg tR survival 0 1). n annual interval natural mortality rate age tR. nL annual interval natural mortality rate length Ln. Ln length  (age negative) annual interval natural mortality rate switches n nL (cm yr). Lv length (age negative) 50 % vulnerable harvest (cm yr). Vp vulnerability harvest (function length) power. Llo lower harvest slot length (cm). Lup upper harvest slot length (cm). Nc slot limits non-compliance probability. pi annual capture probability. rho release probability. Hm hooking mortality probability. Rmax number recruits carrying capacity (ind). Wa (extrapolated) weight 1 cm individual (g). fa (theoretical) fecundity 1 g female (eggs). q catchability (annual probability capture) unit effort. RPR relative proportion recruits ecotype.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Population Parameters — ypr_population","text":"object class ypr_population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Population Parameters — ypr_population","text":"","code":"ypr_population(k = 0.1, Linf = 90) #> tmax:  20 #> k:     0.1 #> Linf:  90 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Population Names — ypr_population_names","title":"Population Names — ypr_population_names","text":"Generates set unique names based differences parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population Names — ypr_population_names","text":"","code":"ypr_population_names(population)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Population Names — ypr_population_names","text":"population object class ypr_population, ypr_populations ypr_ecotypes.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Population Names — ypr_population_names","text":"character vector unique parameter based names.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_update.html","id":null,"dir":"Reference","previous_headings":"","what":"Update a Population Object — ypr_population_update","title":"Update a Population Object — ypr_population_update","text":"ypr_update().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_update.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update a Population Object — ypr_population_update","text":"","code":"ypr_population_update(population, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_population_update.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update a Population Object — ypr_population_update","text":"population ypr_population object. ... One parameter values ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations.html","id":null,"dir":"Reference","previous_headings":"","what":"Populations — ypr_populations","title":"Populations — ypr_populations","text":"Populations","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Populations — ypr_populations","text":"","code":"ypr_populations(..., expand = TRUE, names = NULL)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Populations — ypr_populations","text":"... dots future extensions must empty. expand flag specifying whether expand parameter combinations. names character vector unique ecotype names.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Populations — ypr_populations","text":"list ypr_population() objects","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Populations — ypr_populations","text":"","code":"ypr_populations(Rk = c(2.5, 4.6), Hm = c(0.2, 0.05)) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5, 4.6, 2.5, 4.6 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0.05, 0.05, 0.2, 0.2 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations_expand.html","id":null,"dir":"Reference","previous_headings":"","what":"Expand Populations — ypr_populations_expand","title":"Expand Populations — ypr_populations_expand","text":"object class ypr_population() unique combinations parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations_expand.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expand Populations — ypr_populations_expand","text":"","code":"ypr_populations_expand(populations)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations_expand.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expand Populations — ypr_populations_expand","text":"populations object class ypr_populations().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations_expand.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expand Populations — ypr_populations_expand","text":"object class ypr_population.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_populations_expand.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expand Populations — ypr_populations_expand","text":"","code":"ypr_populations_expand(   ypr_populations(     Rk = c(2.5, 4, 2.5),     Hm = c(0.1, 0.2, 0.1)   ) ) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5, 4, 2.5, 4 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0.1, 0.1, 0.2, 0.2 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_report.html","id":null,"dir":"Reference","previous_headings":"","what":"Report — ypr_report","title":"Report — ypr_report","text":"Creates Rmd file can used generate report.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_report.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Report — ypr_report","text":"","code":"ypr_report(   population,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   title = \"Population Report\",   description = \"\",   date = Sys.Date(),   file = \"report\",   view = FALSE,   ask = TRUE )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_report.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Report — ypr_report","text":"population object class ypr_population(). Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. title string report title. description string describing population. date date report date. file string path file (without extension). view flag specifying whether view report (rendering html). ask flag specifying whether ask overwriting creating file.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_report.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Report — ypr_report","text":"invisible character vector contents file.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_report.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Report — ypr_report","text":"","code":"if (FALSE) { # \\dontrun{ ypr_report(ypr_population(), file = tempfile(), ask = FALSE) } # }"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_schedule.html","id":null,"dir":"Reference","previous_headings":"","what":"Life-History Schedule — ypr_schedule","title":"Life-History Schedule — ypr_schedule","text":"DEPRECATED: Replace ypr_schedule() ypr_tabulate_schedule()","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_schedule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Life-History Schedule — ypr_schedule","text":"","code":"ypr_schedule(population)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_schedule.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Life-History Schedule — ypr_schedule","text":"Generates life-history schedule age population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_sr.html","id":null,"dir":"Reference","previous_headings":"","what":"Stock-Recruitment Parameters — ypr_sr","title":"Stock-Recruitment Parameters — ypr_sr","text":"Returns single rowed data frame SR parameters: alpha Survival egg age tR low density beta Density-dependence Rk Lifetime spawners per spawner low density phi Lifetime eggs deposited per recruit unfished equilibrium phiF Lifetime eggs deposited per recruit fished equilibrium R0 Age tR recruits unfished equilibrium R0F Age tR recruits fished equilibrium S0 Spawners unfished equilibrium S0F Spawners fished equilibrium","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_sr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stock-Recruitment Parameters — ypr_sr","text":"","code":"ypr_sr(object)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_sr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stock-Recruitment Parameters — ypr_sr","text":"object population populations.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_sr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stock-Recruitment Parameters — ypr_sr","text":"data frame SR parameters.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_sr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stock-Recruitment Parameters — ypr_sr","text":"","code":"ypr_sr(ypr_population()) # Beverton-Holt #> # A tibble: 1 × 9 #>      alpha     beta    Rk   phi  phiF    R0   R0F    S0   S0F #>      <dbl>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 0.000838 0.000838     3 3579. 1465. 0.667 0.186  1.33 0.211 ypr_sr(ypr_population(BH = 0L)) # Ricker #> # A tibble: 1 × 9 #>      alpha     beta    Rk   phi  phiF    R0   R0F    S0   S0F #>      <dbl>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 0.000838 0.000308     3 3579. 1465. 0.995 0.455  1.98 0.517"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_biomass.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","title":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","text":"Produces data frame 'Weight' 'Fecundity' number 'Survivors' 'Spawners' total 'Biomass' 'Eggs' 'Age' class.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_biomass.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","text":"","code":"ypr_tabulate_biomass(population)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_biomass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","text":"population object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_biomass.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","text":"data frame","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_biomass.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Biomass (and Eggs) — ypr_tabulate_biomass","text":"","code":"ypr_tabulate_biomass(ypr_population()) #> # A tibble: 20 × 8 #>      Age Length Weight Fecundity Survivors Spawners Biomass     Eggs #>    <int>  <dbl>  <dbl>     <dbl>     <dbl>    <dbl>   <dbl>    <dbl> #>  1     1   13.9   27.0      27.0 0.186     5.82e-57   5.02  7.86e-56 #>  2     2   25.9  174.      174.  0.149     4.32e-30  25.9   3.76e-28 #>  3     3   36.2  476.      476.  0.119     1.24e-15  56.6   2.95e-13 #>  4     4   45.1  918.      918.  0.0951    3.29e- 6  87.4   1.51e- 3 #>  5     5   52.8 1469.     1469.  0.0761    7.58e- 2 112.    5.56e+ 1 #>  6     6   59.3 2090.     2090.  0.0488    4.88e- 2 102.    5.10e+ 1 #>  7     7   65.0 2747.     2747.  0.0312    3.12e- 2  85.7   4.29e+ 1 #>  8     8   69.9 3412.     3412.  0.0200    2.00e- 2  68.2   3.41e+ 1 #>  9     9   74.1 4065.     4065.  0.0128    1.28e- 2  52.0   2.60e+ 1 #> 10    10   77.7 4689.     4689.  0.00818   8.18e- 3  38.4   1.92e+ 1 #> 11    11   80.8 5274.     5274.  0.00524   5.24e- 3  27.6   1.38e+ 1 #> 12    12   83.5 5816.     5816.  0.00335   3.35e- 3  19.5   9.74e+ 0 #> 13    13   85.8 6310.     6310.  0.00214   2.14e- 3  13.5   6.77e+ 0 #> 14    14   87.8 6758.     6758.  0.00137   1.37e- 3   9.28  4.64e+ 0 #> 15    15   89.5 7160.     7160.  0.000878  8.78e- 4   6.29  3.14e+ 0 #> 16    16   90.9 7518.     7518.  0.000562  5.62e- 4   4.23  2.11e+ 0 #> 17    17   92.2 7836.     7836.  0.000360  3.60e- 4   2.82  1.41e+ 0 #> 18    18   93.3 8116.     8116.  0.000230  2.30e- 4   1.87  9.34e- 1 #> 19    19   94.2 8363.     8363.  0.000147  1.47e- 4   1.23  6.16e- 1 #> 20    20   95.0 8580.     8580.  0.0000943 9.43e- 5   0.809 4.05e- 1"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_fish.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Fish Numbers — ypr_tabulate_fish","title":"Tabulate Fish Numbers — ypr_tabulate_fish","text":"Produces data frame number fish 'Survivors', 'Spawners', 'Caught', 'Harvested', 'Released' 'HandlingMortalities' categories 'Length', 'Age' 'Weight' class 'Ecotype' (NA applicable)","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_fish.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Fish Numbers — ypr_tabulate_fish","text":"","code":"ypr_tabulate_fish(population, x = \"Age\", binwidth = 1L)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_fish.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Fish Numbers — ypr_tabulate_fish","text":"population object class ypr_population(). x object coerce. binwidth positive integer width bins grouping.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_fish.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Fish Numbers — ypr_tabulate_fish","text":"data frame","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_fish.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Fish Numbers — ypr_tabulate_fish","text":"","code":"ypr_tabulate_fish(ypr_population()) #> # A tibble: 20 × 8 #>      Age Survivors Spawners   Caught Harvested Released HandlingMortalities #>    <dbl>     <dbl>    <dbl>    <dbl>     <dbl>    <dbl>               <dbl> #>  1     1 0.186     5.82e-57 1.16e-57  1.16e-57        0                   0 #>  2     2 0.149     4.32e-30 8.64e-31  8.64e-31        0                   0 #>  3     3 0.119     1.24e-15 2.48e-16  2.48e-16        0                   0 #>  4     4 0.0951    3.29e- 6 6.58e- 7  6.58e- 7        0                   0 #>  5     5 0.0761    7.58e- 2 1.52e- 2  1.52e- 2        0                   0 #>  6     6 0.0488    4.88e- 2 9.75e- 3  9.75e- 3        0                   0 #>  7     7 0.0312    3.12e- 2 6.24e- 3  6.24e- 3        0                   0 #>  8     8 0.0200    2.00e- 2 3.99e- 3  3.99e- 3        0                   0 #>  9     9 0.0128    1.28e- 2 2.56e- 3  2.56e- 3        0                   0 #> 10    10 0.00818   8.18e- 3 1.64e- 3  1.64e- 3        0                   0 #> 11    11 0.00524   5.24e- 3 1.05e- 3  1.05e- 3        0                   0 #> 12    12 0.00335   3.35e- 3 6.70e- 4  6.70e- 4        0                   0 #> 13    13 0.00214   2.14e- 3 4.29e- 4  4.29e- 4        0                   0 #> 14    14 0.00137   1.37e- 3 2.74e- 4  2.74e- 4        0                   0 #> 15    15 0.000878  8.78e- 4 1.76e- 4  1.76e- 4        0                   0 #> 16    16 0.000562  5.62e- 4 1.12e- 4  1.12e- 4        0                   0 #> 17    17 0.000360  3.60e- 4 7.20e- 5  7.20e- 5        0                   0 #> 18    18 0.000230  2.30e- 4 4.61e- 5  4.61e- 5        0                   0 #> 19    19 0.000147  1.47e- 4 2.95e- 5  2.95e- 5        0                   0 #> 20    20 0.0000943 9.43e- 5 1.89e- 5  1.89e- 5        0                   0 #> # ℹ 1 more variable: Ecotype <chr>"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Population Parameters — ypr_tabulate_parameters","title":"Tabulate Population Parameters — ypr_tabulate_parameters","text":"Tabulate Population Parameters","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Population Parameters — ypr_tabulate_parameters","text":"","code":"ypr_tabulate_parameters(population)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Population Parameters — ypr_tabulate_parameters","text":"population object class ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Population Parameters — ypr_tabulate_parameters","text":"table population parameters","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_parameters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Population Parameters — ypr_tabulate_parameters","text":"","code":"if (FALSE) { # \\dontrun{ ypr_tabulate_parameters(ypr_population()) } # }"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":null,"dir":"Reference","previous_headings":"","what":"Life-History Schedule — ypr_tabulate_schedule","title":"Life-History Schedule — ypr_tabulate_schedule","text":"Generates life-history schedule age population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Life-History Schedule — ypr_tabulate_schedule","text":"","code":"ypr_tabulate_schedule(object, ...)  # S3 method for class 'ypr_population' ypr_tabulate_schedule(object, ...)  # S3 method for class 'ypr_ecotypes' ypr_tabulate_schedule(object, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Life-History Schedule — ypr_tabulate_schedule","text":"object population populations. ... dots future extensions must empty.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Life-History Schedule — ypr_tabulate_schedule","text":"tibble life-history schedule age.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Life-History Schedule — ypr_tabulate_schedule","text":"ypr_tabulate_schedule(ypr_population): Tabulate Schedule ypr_tabulate_schedule(ypr_ecotypes): Tabulate Schedule","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_schedule.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Life-History Schedule — ypr_tabulate_schedule","text":"","code":"ypr_tabulate_schedule(ypr_population()) #> # A tibble: 20 × 11 #>      Age Length Weight Fecundity Spawning NaturalMortality Vulnerability #>    <int>  <dbl>  <dbl>     <dbl>    <dbl>            <dbl>         <dbl> #>  1     1   13.9   27.0      27.0 3.13e-56              0.2      3.13e-56 #>  2     2   25.9  174.      174.  2.91e-29              0.2      2.91e-29 #>  3     3   36.2  476.      476.  1.04e-14              0.2      1.04e-14 #>  4     4   45.1  918.      918.  3.46e- 5              0.2      3.46e- 5 #>  5     5   52.8 1469.     1469.  9.95e- 1              0.2      9.95e- 1 #>  6     6   59.3 2090.     2090.  1.00e+ 0              0.2      1.00e+ 0 #>  7     7   65.0 2747.     2747.  1.00e+ 0              0.2      1.00e+ 0 #>  8     8   69.9 3412.     3412.  1.00e+ 0              0.2      1.00e+ 0 #>  9     9   74.1 4065.     4065.  1   e+ 0              0.2      1   e+ 0 #> 10    10   77.7 4689.     4689.  1   e+ 0              0.2      1   e+ 0 #> 11    11   80.8 5274.     5274.  1   e+ 0              0.2      1   e+ 0 #> 12    12   83.5 5816.     5816.  1   e+ 0              0.2      1   e+ 0 #> 13    13   85.8 6310.     6310.  1   e+ 0              0.2      1   e+ 0 #> 14    14   87.8 6758.     6758.  1   e+ 0              0.2      1   e+ 0 #> 15    15   89.5 7160.     7160.  1   e+ 0              0.2      1   e+ 0 #> 16    16   90.9 7518.     7518.  1   e+ 0              0.2      1   e+ 0 #> 17    17   92.2 7836.     7836.  1   e+ 0              0.2      1   e+ 0 #> 18    18   93.3 8116.     8116.  1   e+ 0              0.2      1   e+ 0 #> 19    19   94.2 8363.     8363.  1   e+ 0              0.2      1   e+ 0 #> 20    20   95.0 8580.     8580.  1   e+ 0              0.2      1   e+ 0 #> # ℹ 4 more variables: Retention <dbl>, FishingMortality <dbl>, #> #   Survivorship <dbl>, FishedSurvivorship <dbl> ypr_tabulate_schedule(ypr_ecotypes(Linf = c(10, 20))) #> # A tibble: 40 × 13 #>      Age Length Weight Fecundity  Spawning NaturalMortality Vulnerability #>    <int>  <dbl>  <dbl>     <dbl>     <dbl>            <dbl>         <dbl> #>  1     1   1.39 0.0270    0.0270 3.13e-156              0.2     3.13e-156 #>  2     2   2.59 0.174     0.174  2.91e-129              0.2     2.91e-129 #>  3     3   3.62 0.476     0.476  1.04e-114              0.2     1.04e-114 #>  4     4   4.51 0.918     0.918  3.46e-105              0.2     3.46e-105 #>  5     5   5.28 1.47      1.47   2.17e- 98              0.2     2.17e- 98 #>  6     6   5.93 2.09      2.09   2.75e- 93              0.2     2.75e- 93 #>  7     7   6.50 2.75      2.75   2.50e- 89              0.2     2.50e- 89 #>  8     8   6.99 3.41      3.41   3.46e- 86              0.2     3.46e- 86 #>  9     9   7.41 4.06      4.06   1.18e- 83              0.2     1.18e- 83 #> 10    10   7.77 4.69      4.69   1.37e- 81              0.2     1.37e- 81 #> # ℹ 30 more rows #> # ℹ 6 more variables: Retention <dbl>, FishingMortality <dbl>, #> #   Survivorship <dbl>, FishedSurvivorship <dbl>, Ecotype <chr>, #> #   Proportion <dbl>"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"Tabulate Stock-Recruitment Parameters","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"","code":"ypr_tabulate_sr(object, ...)  # Default S3 method ypr_tabulate_sr(   object,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   all = FALSE,   ... )  # S3 method for class 'ypr_populations' ypr_tabulate_sr(   object,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   all = FALSE,   ... )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"object population populations. ... dots future extensions must empty. Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. flag specifying whether include parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"data.frame stock-recruitment parameters.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"ypr_tabulate_sr(default): Tabulate Stock-Recruitment Parameters ypr_tabulate_sr(ypr_populations): Tabulate Stock-Recruitment Parameters","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_sr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Stock-Recruitment Parameters — ypr_tabulate_sr","text":"","code":"ypr_tabulate_sr(ypr_population()) # Beverton-Holt #> # A tibble: 3 × 7 #>   Type        pi     u  Eggs Recruits Spawners Fecundity #>   <chr>    <dbl> <dbl> <dbl>    <dbl>    <dbl>     <dbl> #> 1 unfished 0     0     2386.    0.667    1.33      3600. #> 2 actual   0.2   0.2    272.    0.186    0.211     2580. #> 3 optimal  0.115 0.115  853.    0.417    0.582     2933. ypr_tabulate_sr(ypr_population(BH = 0L)) # Ricker #> # A tibble: 3 × 7 #>   Type        pi     u  Eggs Recruits Spawners Fecundity #>   <chr>    <dbl> <dbl> <dbl>    <dbl>    <dbl>     <dbl> #> 1 unfished 0     0     3563.    0.995    1.98      3600. #> 2 actual   0.2   0.2    667.    0.455    0.517     2580. #> 3 optimal  0.135 0.135 1485.    0.787    1.04      2844. ypr_tabulate_sr(ypr_populations(Rk = c(2.5, 4.6))) #> # A tibble: 6 × 8 #>   Type         pi      u   Eggs Recruits Spawners Fecundity    Rk #>   <chr>     <dbl>  <dbl>  <dbl>    <dbl>    <dbl>     <dbl> <dbl> #> 1 unfished 0      0      2148.    0.6      1.19       3600.   2.5 #> 2 actual   0.2    0.2      33.6   0.0230   0.0261     2580.   2.5 #> 3 optimal  0.0936 0.0936  818.    0.364    0.538      3041.   2.5 #> 4 unfished 0      0      2801.    0.783    1.56       3600.   4.6 #> 5 actual   0.2    0.2     687.    0.469    0.533      2580.   4.6 #> 6 optimal  0.171  0.171   851.    0.522    0.633      2688.   4.6"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Yield — ypr_tabulate_yield","title":"Tabulate Yield — ypr_tabulate_yield","text":"Tabulate Yield","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Yield — ypr_tabulate_yield","text":"","code":"ypr_tabulate_yield(object, ...)  # Default S3 method ypr_tabulate_yield(   object,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   type = \"both\",   all = FALSE,   ... )  # S3 method for class 'ypr_populations' ypr_tabulate_yield(   object,   Ly = 0,   harvest = TRUE,   biomass = FALSE,   type = \"both\",   all = FALSE,   ... )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Yield — ypr_tabulate_yield","text":"object population populations. ... dots future extensions must empty. Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. type string indicating whether include '' just 'actual' 'optimal' yield. flag specifying whether include parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Yield — ypr_tabulate_yield","text":"data frame.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Tabulate Yield — ypr_tabulate_yield","text":"ypr_tabulate_yield(default): Tabulate Yield ypr_tabulate_yield(ypr_populations): Tabulate Yield","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yield.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Yield — ypr_tabulate_yield","text":"","code":"ypr_tabulate_yield(ypr_population()) #> # A tibble: 2 × 8 #>   Type       pi     u  Yield   Age Length Weight Effort #>   <chr>   <dbl> <dbl>  <dbl> <dbl>  <dbl>  <dbl>  <dbl> #> 1 actual  0.2   0.2   0.0422  6.77   62.1  2580.   2.12 #> 2 optimal 0.115 0.115 0.0670  7.36   64.6  2933.   1.16 ypr_tabulate_yield(ypr_populations(Rk = c(3, 5))) #> # A tibble: 4 × 9 #>   Type       pi     u  Yield   Age Length Weight Effort    Rk #>   <chr>   <dbl> <dbl>  <dbl> <dbl>  <dbl>  <dbl>  <dbl> <dbl> #> 1 actual  0.2   0.2   0.0422  6.77   62.1  2580.   2.12     3 #> 2 optimal 0.115 0.115 0.0670  7.36   64.6  2933.   1.16     3 #> 3 actual  0.2   0.2   0.116   6.77   62.1  2580.   2.12     5 #> 4 optimal 0.183 0.183 0.117   6.87   62.6  2641.   1.92     5"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate Yields — ypr_tabulate_yields","title":"Tabulate Yields — ypr_tabulate_yields","text":"Tabulate Yields","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate Yields — ypr_tabulate_yields","text":"","code":"ypr_tabulate_yields(object, ...)  # Default S3 method ypr_tabulate_yields(   object,   pi = seq(0, 1, length.out = 100),   Ly = 0,   harvest = TRUE,   biomass = FALSE,   all = FALSE,   ... )  # S3 method for class 'ypr_populations' ypr_tabulate_yields(   object,   pi = seq(0, 1, length.out = 100),   Ly = 0,   harvest = TRUE,   biomass = FALSE,   all = FALSE,   ... )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate Yields — ypr_tabulate_yields","text":"object population populations. ... dots future extensions must empty. pi vector probabilities capture calculate yield . Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. flag specifying whether include parameter values.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate Yields — ypr_tabulate_yields","text":"data frame.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Tabulate Yields — ypr_tabulate_yields","text":"ypr_tabulate_yields(default): Tabulate Yields ypr_tabulate_yields(ypr_populations): Tabulate Yields","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_tabulate_yields.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate Yields — ypr_tabulate_yields","text":"","code":"ypr_tabulate_yields(ypr_population()) #> # A tibble: 100 × 7 #>        pi      u  Yield   Age Length Weight Effort #>     <dbl>  <dbl>  <dbl> <dbl>  <dbl>  <dbl>  <dbl> #>  1 0      0      0      NA      NA      NA  0      #>  2 0.0101 0.0101 0.0126  8.42   68.5  3532. 0.0964 #>  3 0.0202 0.0202 0.0236  8.30   68.0  3466. 0.194  #>  4 0.0303 0.0303 0.0331  8.18   67.6  3402. 0.292  #>  5 0.0404 0.0404 0.0413  8.07   67.2  3339. 0.391  #>  6 0.0505 0.0505 0.0482  7.96   66.8  3279. 0.492  #>  7 0.0606 0.0606 0.0539  7.86   66.5  3220. 0.593  #>  8 0.0707 0.0707 0.0585  7.76   66.1  3163. 0.696  #>  9 0.0808 0.0808 0.0620  7.66   65.7  3108. 0.800  #> 10 0.0909 0.0909 0.0646  7.57   65.4  3054. 0.905  #> # ℹ 90 more rows ypr_tabulate_yields(   ypr_populations(     Rk = c(3, 5)   ),   pi = seq(0, 1, length.out = 10) ) #> # A tibble: 20 × 8 #>       pi     u   Yield   Age Length Weight Effort    Rk #>    <dbl> <dbl>   <dbl> <dbl>  <dbl>  <dbl>  <dbl> <dbl> #>  1 0     0     0       NA      NA      NA    0        3 #>  2 0.111 0.111 0.0669   7.40   64.7  2953.   1.12     3 #>  3 0.222 0.222 0.0288   6.64   61.6  2504.   2.39     3 #>  4 0.333 0.333 0       NA      NA      NA    3.85     3 #>  5 0.444 0.444 0       NA      NA      NA    5.58     3 #>  6 0.556 0.556 0       NA      NA      NA    7.70     3 #>  7 0.667 0.667 0       NA      NA      NA   10.4      3 #>  8 0.778 0.778 0       NA      NA      NA   14.3      3 #>  9 0.889 0.889 0       NA      NA      NA   20.9      3 #> 10 1     1     0       NA      NA      NA  Inf        3 #> 11 0     0     0       NA      NA      NA    0        5 #> 12 0.111 0.111 0.103    7.40   64.7  2953.   1.12     5 #> 13 0.222 0.222 0.114    6.64   61.6  2504.   2.39     5 #> 14 0.333 0.333 0.0750   6.15   59.3  2196.   3.85     5 #> 15 0.444 0.444 0.00589  5.80   57.5  1979.   5.58     5 #> 16 0.556 0.556 0       NA      NA      NA    7.70     5 #> 17 0.667 0.667 0       NA      NA      NA   10.4      5 #> 18 0.778 0.778 0       NA      NA      NA   14.3      5 #> 19 0.889 0.889 0       NA      NA      NA   20.9      5 #> 20 1     1     0       NA      NA      NA  Inf        5 ypr_tabulate_yields(ypr_ecotypes(Linf = c(10, 20))) #> # A tibble: 100 × 7 #>        pi      u    Yield   Age Length Weight Effort #>     <dbl>  <dbl>    <dbl> <dbl>  <dbl>  <dbl>  <dbl> #>  1 0      0      0         NA     NA     NA   0      #>  2 0.0101 0.0101 9.03e-47  19.2   18.9   67.2 0.0964 #>  3 0.0202 0.0202 1.81e-46  19.2   18.9   67.2 0.194  #>  4 0.0303 0.0303 2.71e-46  19.2   18.9   67.2 0.292  #>  5 0.0404 0.0404 3.61e-46  19.2   18.9   67.2 0.391  #>  6 0.0505 0.0505 4.52e-46  19.2   18.9   67.2 0.492  #>  7 0.0606 0.0606 5.42e-46  19.2   18.9   67.2 0.593  #>  8 0.0707 0.0707 6.32e-46  19.2   18.9   67.2 0.696  #>  9 0.0808 0.0808 7.22e-46  19.2   18.9   67.2 0.800  #> 10 0.0909 0.0909 8.13e-46  19.2   18.9   67.2 0.905  #> # ℹ 90 more rows"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_update.html","id":null,"dir":"Reference","previous_headings":"","what":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","title":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","text":"Update YPR Object Currently just works scalar parameters populations ecotypes.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_update.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","text":"","code":"ypr_update(x, ...)  # S3 method for class 'ypr_population' ypr_update(x, ...)  # S3 method for class 'ypr_populations' ypr_update(x, ...)  # S3 method for class 'ypr_ecotypes' ypr_update(x, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_update.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","text":"x population, populations ecotypes object update. ... One parameter values ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_update.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","text":"ypr_update(ypr_population): Update Population Parameters ypr_update(ypr_populations): Update Populations Parameters ypr_update(ypr_ecotypes): Update Populations Parameters","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_update.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update a YPR Object Currently just works with scalar parameters for populations and ecotypes. — ypr_update","text":"","code":"ypr_update(ypr_population(), Rk = 2.5) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_update(ypr_populations(Rk = c(2.5, 4)), Rk = 2.5) #> tmax:  20 #> k:     0.15 #> Linf:  100 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    2.5 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 ypr_update(ypr_ecotypes(Linf = c(2.5, 4)), k = 1.5) #> tmax:  20 #> k:     1.5 #> Linf:  2.5, 4 #> t0:    0 #> k2:    0.15 #> Linf2: 100 #> L2:    1000 #> Wb:    3 #> Ls:    50 #> Sp:    100 #> es:    1 #> Sm:    0 #> fb:    1 #> tR:    1 #> BH:    1 #> Rk:    3 #> n:     0.2 #> nL:    0.2 #> Ln:    1000 #> Lv:    50 #> Vp:    100 #> Llo:   0 #> Lup:   1000 #> Nc:    0 #> pi:    0.2 #> rho:   0 #> Hm:    0 #> Rmax:  1 #> Wa:    0.01 #> fa:    1 #> q:     0.1 #> RPR:   1 #> Ecotype: Linf_2_5, Linf_4"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":null,"dir":"Reference","previous_headings":"","what":"Yield — ypr_yield","title":"Yield — ypr_yield","text":"Calculates yield population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Yield — ypr_yield","text":"","code":"ypr_yield(object, Ly = 0, harvest = TRUE, biomass = FALSE, ...)"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Yield — ypr_yield","text":"object population populations. Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals. ... dots future extensions must empty.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Yield — ypr_yield","text":"yield number fish biomass.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Yield — ypr_yield","text":"default, Rmax = 1 number individuals proportion recruits carrying capacity. yield given terms biomass (kg) scaling also depends value Wa (g).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yield.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Yield — ypr_yield","text":"","code":"ypr_yield(ypr_population()) #> [1] 0.04220691 #> attr(,\"Age\") #> [1] 6.7687 #> attr(,\"Length\") #> [1] 62.13068 #> attr(,\"Weight\") #> [1] 2580.272 #> attr(,\"Effort\") #> [1] 2.117905 ypr_yield(ypr_ecotypes(Linf = c(100, 200))) #> [1] 0 #> attr(,\"Age\") #> [1] NA #> attr(,\"Length\") #> [1] NA #> attr(,\"Weight\") #> [1] NA #> attr(,\"Effort\") #> [1] 2.117905"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yields.html","id":null,"dir":"Reference","previous_headings":"","what":"Yields — ypr_yields","title":"Yields — ypr_yields","text":"Calculates yield(s) population based one capture rates.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yields.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Yields — ypr_yields","text":"","code":"ypr_yields(   object,   pi = seq(0, 1, length.out = 100),   Ly = 0,   harvest = TRUE,   biomass = FALSE )"},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yields.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Yields — ypr_yields","text":"object population populations. pi vector probabilities capture calculate yield . Ly minimum length (trophy) fish consider calculating yield (cm). harvest flag specifying whether calculate yield harvested fish captures. biomass flag specifying whether calculate yield terms biomass versus number individuals.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yields.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Yields — ypr_yields","text":"numeric vector yields.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/reference/ypr_yields.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Yields — ypr_yields","text":"","code":"pi <- seq(0, 1, length.out = 30) plot(pi, ypr_yields(ypr_population(), pi), type = \"l\")"},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-0609011","dir":"Changelog","previous_headings":"","what":"ypr 0.6.0.9011","title":"ypr 0.6.0.9011","text":"Merge branch ‘main’ github.com:poissonconsulting/ypr. parameter description NA documentation corrupted.","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9010","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9010","text":"Bump version 0.6.0.9009 (#91).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9009","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9009","text":"Bump version 0.6.0.9008 (#89).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9008","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9008","text":"Bump version 0.6.0.9007 (#87).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9007","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9007","text":"Bump version 0.6.0.9006 (#86).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9006","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9006","text":"Bump version 0.6.0.9005 (#85).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9005","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9005","text":"Bump version 0.6.0.9004 (#84).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9004","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9004","text":"Bump version 0.6.0.9003 (#83).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9003","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9003","text":"Bump version 0.6.0.9002 (#81).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"fledge-0-6-0-9002","dir":"Changelog","previous_headings":"","what":"fledge","title":"ypr 0.6.0.9002","text":"Bump version 0.6.0.9001 (#80).","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"continuous-integration-0-6-0-9001","dir":"Changelog","previous_headings":"","what":"Continuous integration","title":"ypr 0.6.0.9001","text":"Fetch tags fledge workflow avoid unnecessary NEWS entries (#78). Use larger retry count lock-threads workflow (#77). Overwrite actions-sync (#76).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"documentation-0-6-0-9001","dir":"Changelog","previous_headings":"","what":"Documentation","title":"ypr 0.6.0.9001","text":"Register poissontemplate usage (@maelle, #71).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"uncategorized-0-6-0-9001","dir":"Changelog","previous_headings":"","what":"Uncategorized","title":"ypr 0.6.0.9001","text":"Merge pull request #75 poissonconsulting/reqName. replaced requireNamespace() rlang::check_installed() Merge pull request #72 poissonconsulting/.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-0609000","dir":"Changelog","previous_headings":"","what":"ypr 0.6.0.9000","title":"ypr 0.6.0.9000","text":"previous version.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-060","dir":"Changelog","previous_headings":"","what":"ypr 0.6.0","title":"ypr 0.6.0","text":"CRAN release: 2022-08-29 Rk now egg tR survival 0 1.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-052","dir":"Changelog","previous_headings":"","what":"ypr 0.5.2","title":"ypr 0.5.2","text":"CRAN release: 2021-07-03 Internal changes .","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-051","dir":"Changelog","previous_headings":"","what":"ypr 0.5.1","title":"ypr 0.5.1","text":"CRAN release: 2020-07-10 House-keeping.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-050","dir":"Changelog","previous_headings":"","what":"ypr 0.5.0","title":"ypr 0.5.0","text":"CRAN release: 2020-03-18 Pass yield parameters Ly, harvest biomass ypr_report(). Removed suggests dependency checkr.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-040","dir":"Changelog","previous_headings":"","what":"ypr 0.4.0","title":"ypr 0.4.0","text":"CRAN release: 2020-01-13","code":""},{"path":[]},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"population-parameters-0-4-0","dir":"Changelog","previous_headings":"","what":"Population Parameters","title":"ypr 0.4.0","text":"Replaced parameters M (annual instantaneous natural mortality rate) Mb (annual instantaneous natural mortality rate (function length) scaling exponent) A0 (initial post age tR density independent mortality probability) n (annual natural mortality rate age tR length Ln) nL (annual natural mortality rate length Ln) Ln (length natural mortality rate switches n nA) Added parameters k2, Linf2 L2 allow biphasic growth. Set Lp value 1000 opposed Linf. Set Ls Lv arguments 50 opposed Linf/2. Allow L2, Ln, Ls Lv also take ages (negative values).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"populations-0-4-0","dir":"Changelog","previous_headings":"","what":"Population(s)","title":"ypr 0.4.0","text":"Added expand = TRUE argument ypr_populations() allow control combinations. Added ypr_populations_expand() create combinations parameters. Added ypr_populations_update() (well update.ypr_population() update.ypr_populations()). ypr_populations longer requires names. Added ypr_population_names() allow user generate names. Added as_ypr_populations.data.frame(). Added data.frame.ypr_population() data.frame.ypr_populations(). Added ypr_age_at_length() get ages specific lengths given population. Added ypr_length_at_age() get lengths specific ages given population.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"population-reports-0-4-0","dir":"Changelog","previous_headings":"","what":"Population Reports","title":"ypr 0.4.0","text":"Added description = \"\" argument ypr_report() allow user describe report. ypr_report() now starts table parameter values parameter descriptions. Added view = FALSE argument ypr_report() allow user view report browser. Added ask = TRUE argument ypr_report() ask overwriting creating file. Deprecated requirement provide file extension ypr_report(). Soft deprecated ypr_schedule() ypr_tabulate_schedule().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"plots-0-4-0","dir":"Changelog","previous_headings":"","what":"Plots","title":"ypr 0.4.0","text":"Added plot biomass eggs report. Added percent = FALSE argument ypr_plot_fish()","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"tables-0-4-0","dir":"Changelog","previous_headings":"","what":"Tables","title":"ypr 0.4.0","text":"Added ypr_tabulate_biomass() easily calculate total biomass eggs. Renamed column HandlingMortality HandlingMortalities ypr_tabulate_fish() ypr_plot_fish(). Renamed column Spawning Spawners ypr_tabulate_fish() ypr_plot_fish().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"bug-fixes-0-4-0","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"ypr 0.4.0","text":"Improved handling unsustainable populations (longer negative fish numbers).","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-031","dir":"Changelog","previous_headings":"","what":"ypr 0.3.1","title":"ypr 0.3.1","text":"CRAN release: 2019-04-26 ypr_populations() now generates names Fixed Quesnel Lake Trout Rainbow Trout mix ","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-030","dir":"Changelog","previous_headings":"","what":"ypr 0.3.0","title":"ypr 0.3.0","text":"CRAN release: 2018-11-26 Now uses q instead Ea Eb effort Parameter Rk now greater >= 1","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-020","dir":"Changelog","previous_headings":"","what":"ypr 0.2.0","title":"ypr 0.2.0","text":"Added ypr_exploitation() convert capture probabilities exploitation probabilities. Added ypr_report() generate Rmd file population. Can now pass Rk egg recruit survival (low density). Set default value Wa 0.01. Added ypr_populations() generate combinations parameters. Made ypr_tabulate_sr(), ypr_tabulate_yield(), ypr_tabulate_yields(), ypr_plot_yield() generic definitions ypr_population ypr_populations objects. Added scaling parameter A0 initial interval mortality recruits. Added scaling parameters Ea Eb allow plots yield per effort. Added Age, Length, Weight Effort ypr_tabulate_yield() added ypr_tabulate_yields() Added y arg ypr_plot_yield() allow plotting mean age, length, weight, effort yield per effort exploitation capture probability. Added ypr_plot_histogram() plot frequency distributions catch, spawners lake age, length weight bins. Added ypr_tabulate_parameters() get table parameters, values descriptions ypr_detabulate_parameters() convert back population object. Added ypr_tabulate_sr() get table eggs recruits unfished, actual optimal rates. Added print.ypr_population().","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-010","dir":"Changelog","previous_headings":"","what":"ypr 0.1.0","title":"ypr 0.1.0","text":"Added Mb scale mortality length BH distinguish Beverton-Holt Ricker curves es probability mature fish spawning Sm spawning mortality probability Sp spawning power vulnerability power Vp slot limit non-complicance parameter Nc scaling parameter R0. Added ypr_population_update() update population parameters. Added ypr_yield_tabulate() tabulate actual optimal yields. Added ypr_sr() get stock recruitment parameters ypr_plot_sr() plot. Added ypr_inst2inter() ypr_inter2instant() convert mortality rates. Switched nu M R0 Rmax. Switched yield parameters harvest biomass FALSE default. Renamed Wa b Wb eta Hm mu pi Rt tR. Removed Capture (covered single value) TotalMortality schedule added Spawning.","code":""},{"path":"https://poissonconsulting.github.io/ypr/dev/news/index.html","id":"ypr-001","dir":"Changelog","previous_headings":"","what":"ypr 0.0.1","title":"ypr 0.0.1","text":"Initial Release","code":""}]