From 99ce45011ca8f7f93ba8ff9a673d3b29e182f6ac Mon Sep 17 00:00:00 2001
From: shawn schwartz <s@shawnts.com>
Date: Fri, 22 Nov 2024 20:13:51 -0800
Subject: [PATCH] update(pkgdown): site config #75

---
 DESCRIPTION                         |  9 +--
 README.Rmd                          |  9 +--
 README.md                           | 86 +++++++++++++++++++++++++++--
 docs/404.html                       |  2 +-
 docs/LICENSE-text.html              |  2 +-
 docs/LICENSE.html                   |  2 +-
 docs/articles/index.html            |  2 +-
 docs/articles/preproc-workflow.html |  4 +-
 docs/authors.html                   | 14 ++---
 docs/index.html                     | 63 ++++++++++++++++-----
 docs/pkgdown.yml                    |  2 +-
 docs/reference/bidsify.html         |  2 +-
 docs/reference/deblink.html         |  2 +-
 docs/reference/detransient.html     |  2 +-
 docs/reference/detrend.html         |  2 +-
 docs/reference/epoch.html           | 21 ++++++-
 docs/reference/eyeris-package.html  | 16 ++++--
 docs/reference/glassbox.html        |  2 +-
 docs/reference/index.html           |  2 +-
 docs/reference/interpolate.html     |  2 +-
 docs/reference/load_asc.html        |  2 +-
 docs/reference/lpfilt.html          |  2 +-
 docs/reference/plot.eyeris.html     |  2 +-
 docs/reference/sticker.html         |  2 +-
 docs/reference/zscore.html          |  2 +-
 docs/search.json                    |  2 +-
 man/epoch.Rd                        | 72 ------------------------
 man/eyeris-package.Rd               | 11 ++--
 28 files changed, 203 insertions(+), 138 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8648b0e..ce664a2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,16 +1,17 @@
 Package: eyeris
 Type: Package
-Title: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines
+Title: eyeris
 Version: 0.0.0.9000
 Authors@R:
   person(
-    given = c("Shawn", "Tyler"),
+    given = c("Shawn", "T."),
     family = "Schwartz",
     role = c("aut", "cre"),
     email = "stschwartz@stanford.edu", 
     comment = c(ORCID = "0000-0001-6444-8451")
   )
-Description: More about what it does (maybe more than one line)
+Description: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines
+    More about what it does (maybe more than one line)
     Use four spaces when indenting paragraphs within the Description.
 Encoding: UTF-8
 Depends:
@@ -42,5 +43,5 @@ VignetteBuilder: knitr
 License: MIT + file LICENSE
 Config/testthat/edition: 3
 LazyData: true
-URL: https://shawnschwartz.com/eyeris
+URL: http://shawnschwartz.com/eyeris
 BugReports: https://github.com/shawntz/eyeris/issues
diff --git a/README.Rmd b/README.Rmd
index 62a05e8..79950e2 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -9,16 +9,17 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   fig.path = "man/figures/README-",
-  out.width = "100%"
+  out.width = "100%",
+  fig.cap = "README FIGURE"
 )
 ```
 
 # `eyeris`: create and run flexible and reproducible pupillometry preprocessing pipelines in R <a href="http://shawnschwartz.com/eyeris/" title="eyeris website"><img src="man/figures/logo.png" align="right" height="139" alt="eyeris website" /></a>
 
 <!-- badges: start -->
-<a href="LICENSE.md" alt="MIT License"><img src="https://badgen.net/static/license/MIT/blue?icon=github" /></a>
-<a href="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" alt="R Package Build Status"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" /></a>
-<a href="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" alt="R Package Linter Status"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" /></a>
+<a href="LICENSE.md" alt="MIT License"><img src="https://badgen.net/static/license/MIT/blue?icon=github" alt="MIT License Badge"/></a>
+<a href="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" alt="R Package Build Status"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" alt="Package Build Status Badge" /></a>
+<a href="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" alt="R Package Linter Status"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" alt="Package Linter Status Badge" /></a>
 <!-- badges: end -->
 
 <!-- The goal of eyeris is to ... -->
diff --git a/README.md b/README.md
index 0486ce5..57fafa7 100644
--- a/README.md
+++ b/README.md
@@ -5,9 +5,9 @@
 
 <!-- badges: start -->
 
-<a href="LICENSE.md" alt="MIT License"><img src="https://badgen.net/static/license/MIT/blue?icon=github" /></a>
-<a href="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" alt="R Package Build Status"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" /></a>
-<a href="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" alt="R Package Linter Status"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" /></a>
+<a href="LICENSE.md" alt="MIT License"><img src="https://badgen.net/static/license/MIT/blue?icon=github" alt="MIT License Badge"/></a>
+<a href="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" alt="R Package Build Status"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" alt="Package Build Status Badge" /></a>
+<a href="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" alt="R Package Linter Status"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" alt="Package Linter Status Badge" /></a>
 <!-- badges: end -->
 
 <!-- The goal of eyeris is to ... -->
@@ -62,7 +62,15 @@ eyeris_preproc <- glassbox(demo_data, detrend_data = F, lpfilt = list(plot_freqz
 #> ✔ [  OK  ] - Running eyeris::zscore()
 ```
 
-<img src="man/figures/README-glassbox-example-1.png" width="100%" />
+<div class="figure">
+
+<img src="man/figures/README-glassbox-example-1.png" alt="README FIGURE" width="100%" />
+<p class="caption">
+
+README FIGURE
+</p>
+
+</div>
 
 ### step-wise correction of pupillary signal
 
@@ -70,7 +78,55 @@ eyeris_preproc <- glassbox(demo_data, detrend_data = F, lpfilt = list(plot_freqz
 plot(eyeris_preproc)
 ```
 
-<img src="man/figures/README-glassbox-plot-1.png" width="100%" /><img src="man/figures/README-glassbox-plot-2.png" width="100%" /><img src="man/figures/README-glassbox-plot-3.png" width="100%" /><img src="man/figures/README-glassbox-plot-4.png" width="100%" /><img src="man/figures/README-glassbox-plot-5.png" width="100%" />
+<div class="figure">
+
+<img src="man/figures/README-glassbox-plot-1.png" alt="README FIGURE" width="100%" />
+<p class="caption">
+
+README FIGURE
+</p>
+
+</div>
+
+<div class="figure">
+
+<img src="man/figures/README-glassbox-plot-2.png" alt="README FIGURE" width="100%" />
+<p class="caption">
+
+README FIGURE
+</p>
+
+</div>
+
+<div class="figure">
+
+<img src="man/figures/README-glassbox-plot-3.png" alt="README FIGURE" width="100%" />
+<p class="caption">
+
+README FIGURE
+</p>
+
+</div>
+
+<div class="figure">
+
+<img src="man/figures/README-glassbox-plot-4.png" alt="README FIGURE" width="100%" />
+<p class="caption">
+
+README FIGURE
+</p>
+
+</div>
+
+<div class="figure">
+
+<img src="man/figures/README-glassbox-plot-5.png" alt="README FIGURE" width="100%" />
+<p class="caption">
+
+README FIGURE
+</p>
+
+</div>
 
 ### final pre-post correction of pupillary signal (raw -\> preprocessed)
 
@@ -78,7 +134,25 @@ plot(eyeris_preproc)
 plot(eyeris_preproc, steps = c(1, 5), preview_window = c(0, 100000))
 ```
 
-<img src="man/figures/README-timeseries-plot-1.png" width="100%" /><img src="man/figures/README-timeseries-plot-2.png" width="100%" />
+<div class="figure">
+
+<img src="man/figures/README-timeseries-plot-1.png" alt="README FIGURE" width="100%" />
+<p class="caption">
+
+README FIGURE
+</p>
+
+</div>
+
+<div class="figure">
+
+<img src="man/figures/README-timeseries-plot-2.png" alt="README FIGURE" width="100%" />
+<p class="caption">
+
+README FIGURE
+</p>
+
+</div>
 
 # Comments, suggestions, questions, issues
 
diff --git a/docs/404.html b/docs/404.html
index aeaf813..824a30e 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -76,7 +76,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index be21824..fff5a80 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -48,7 +48,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
index 2a73c11..d72fd25 100644
--- a/docs/LICENSE.html
+++ b/docs/LICENSE.html
@@ -52,7 +52,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/articles/index.html b/docs/articles/index.html
index d0d4725..25fdefb 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -50,7 +50,7 @@ <h3>All vignettes</h3>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/articles/preproc-workflow.html b/docs/articles/preproc-workflow.html
index d392549..cb08c42 100644
--- a/docs/articles/preproc-workflow.html
+++ b/docs/articles/preproc-workflow.html
@@ -78,7 +78,7 @@
     
     
 <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="http://shawnschwartz.com/eyeris/">eyeris</a></span><span class="op">)</span></span></code></pre></div>
+<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="http://shawnschwartz.com/eyeris">eyeris</a></span><span class="op">)</span></span></code></pre></div>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"hello world"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] "hello world"</span></span></code></pre></div>
@@ -88,7 +88,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/authors.html b/docs/authors.html
index 9a5c6e4..c78a242 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -43,7 +43,7 @@
       <h2>Authors</h2>
 
       <ul class="list-unstyled"><li>
-          <p><strong>Shawn Tyler Schwartz</strong>. Author, maintainer. <a href="https://orcid.org/0000-0001-6444-8451" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
+          <p><strong>Shawn T. Schwartz</strong>. Author, maintainer. <a href="https://orcid.org/0000-0001-6444-8451" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
         </li>
       </ul></div>
@@ -53,15 +53,15 @@ <h2 id="citation">Citation</h2>
       <p><small class="dont-index">Source: <a href="https://github.com/shawntz/eyeris/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
       <p>Schwartz ST (2024).
-<em>eyeris: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines</em>.
-R package version 0.0.0.9000, <a href="https://shawnschwartz.com/eyeris" class="external-link">https://shawnschwartz.com/eyeris</a>.
+<em>eyeris: eyeris</em>.
+R package version 0.0.0.9000, <a href="http://shawnschwartz.com/eyeris">http://shawnschwartz.com/eyeris</a>.
 </p>
       <pre>@Manual{,
-  title = {eyeris: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines},
-  author = {Shawn Tyler Schwartz},
+  title = {eyeris: eyeris},
+  author = {Shawn T. Schwartz},
   year = {2024},
   note = {R package version 0.0.0.9000},
-  url = {https://shawnschwartz.com/eyeris},
+  url = {http://shawnschwartz.com/eyeris},
 }</pre>
     </div>
 
@@ -70,7 +70,7 @@ <h2 id="citation">Citation</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/index.html b/docs/index.html
index c76a7e2..24bdfad 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -5,7 +5,7 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<title>Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines • eyeris</title>
+<title>eyeris • eyeris</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
 <link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
 <link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
@@ -16,9 +16,9 @@
 <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
 <script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
 <link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
-<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines">
-<meta name="description" content="More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.">
-<meta property="og:description" content="More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="eyeris">
+<meta name="description" content="Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.">
+<meta property="og:description" content="Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.">
 <meta property="og:image" content="http://shawnschwartz.com/eyeris/logo.png">
 </head>
 <body>
@@ -99,7 +99,7 @@ <h3 id="the-glassbox-prescription-function">the <code>glassbox()</code> “presc
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span></span>
 <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="http://shawnschwartz.com/eyeris/">eyeris</a></span><span class="op">)</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="http://shawnschwartz.com/eyeris">eyeris</a></span><span class="op">)</span></span>
 <span></span>
 <span><span class="va">demo_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"assocret.asc"</span>, package <span class="op">=</span> <span class="st">"eyeris"</span><span class="op">)</span></span>
 <span></span>
@@ -112,21 +112,58 @@ <h3 id="the-glassbox-prescription-function">the <code>glassbox()</code> “presc
 <span><span class="co">#&gt; ✔ [  OK  ] - Running eyeris::lpfilt()</span></span>
 <span><span class="co">#&gt; ✔ [  OK  ] - Skipping eyeris::detrend()</span></span>
 <span><span class="co">#&gt; ✔ [  OK  ] - Running eyeris::zscore()</span></span></code></pre></div>
-<p><img src="reference/figures/README-glassbox-example-1.png" width="100%"></p>
+<div class="figure">
+<img src="reference/figures/README-glassbox-example-1.png" alt="README FIGURE" width="100%"><p class="caption">
+README FIGURE
+</p>
+</div>
 </div>
 <div class="section level3">
 <h3 id="step-wise-correction-of-pupillary-signal">step-wise correction of pupillary signal<a class="anchor" aria-label="anchor" href="#step-wise-correction-of-pupillary-signal"></a>
 </h3>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">eyeris_preproc</span><span class="op">)</span></span></code></pre></div>
-<p><img src="reference/figures/README-glassbox-plot-1.png" width="100%"><img src="reference/figures/README-glassbox-plot-2.png" width="100%"><img src="reference/figures/README-glassbox-plot-3.png" width="100%"><img src="reference/figures/README-glassbox-plot-4.png" width="100%"><img src="reference/figures/README-glassbox-plot-5.png" width="100%"></p>
+<div class="figure">
+<img src="reference/figures/README-glassbox-plot-1.png" alt="README FIGURE" width="100%"><p class="caption">
+README FIGURE
+</p>
+</div>
+<div class="figure">
+<img src="reference/figures/README-glassbox-plot-2.png" alt="README FIGURE" width="100%"><p class="caption">
+README FIGURE
+</p>
+</div>
+<div class="figure">
+<img src="reference/figures/README-glassbox-plot-3.png" alt="README FIGURE" width="100%"><p class="caption">
+README FIGURE
+</p>
+</div>
+<div class="figure">
+<img src="reference/figures/README-glassbox-plot-4.png" alt="README FIGURE" width="100%"><p class="caption">
+README FIGURE
+</p>
+</div>
+<div class="figure">
+<img src="reference/figures/README-glassbox-plot-5.png" alt="README FIGURE" width="100%"><p class="caption">
+README FIGURE
+</p>
+</div>
 </div>
 <div class="section level3">
 <h3 id="final-pre-post-correction-of-pupillary-signal-raw---preprocessed">final pre-post correction of pupillary signal (raw -&gt; preprocessed)<a class="anchor" aria-label="anchor" href="#final-pre-post-correction-of-pupillary-signal-raw---preprocessed"></a>
 </h3>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">eyeris_preproc</span>, steps <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">5</span><span class="op">)</span>, preview_window <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">100000</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
-<p><img src="reference/figures/README-timeseries-plot-1.png" width="100%"><img src="reference/figures/README-timeseries-plot-2.png" width="100%"></p>
+<div class="figure">
+<img src="reference/figures/README-timeseries-plot-1.png" alt="README FIGURE" width="100%"><p class="caption">
+README FIGURE
+</p>
+</div>
+<div class="figure">
+<img src="reference/figures/README-timeseries-plot-2.png" alt="README FIGURE" width="100%"><p class="caption">
+README FIGURE
+</p>
+</div>
 </div>
 </div>
 </div>
@@ -163,16 +200,16 @@ <h2 data-toc-skip>Citation</h2>
 <div class="developers">
 <h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
-<li>Shawn Tyler Schwartz <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-6444-8451" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li>Shawn T. Schwartz <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-6444-8451" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
 </ul>
 </div>
 
 <div class="dev-status">
 <h2 data-toc-skip>Dev status</h2>
 <ul class="list-unstyled">
-<li><a href="LICENSE.html" alt="MIT License"><img src="https://badgen.net/static/license/MIT/blue?icon=github"></a></li>
-<li><a href="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" alt="R Package Build Status" class="external-link"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg"></a></li>
-<li><a href="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" alt="R Package Linter Status" class="external-link"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg"></a></li>
+<li><a href="LICENSE.html" alt="MIT License"><img src="https://badgen.net/static/license/MIT/blue?icon=github" alt="MIT License Badge"></a></li>
+<li><a href="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" alt="R Package Build Status" class="external-link"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/build.yml/badge.svg" alt="Package Build Status Badge"></a></li>
+<li><a href="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" alt="R Package Linter Status" class="external-link"><img src="https://github.com/shawntschwartz/eyeris/actions/workflows/linter.yml/badge.svg" alt="Package Linter Status Badge"></a></li>
 </ul>
 </div>
 
@@ -181,7 +218,7 @@ <h2 data-toc-skip>Dev status</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index e5106b8..aa891e0 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   preproc-workflow: preproc-workflow.html
-last_built: 2024-11-23T00:25Z
+last_built: 2024-11-23T04:10Z
 urls:
   reference: http://shawnschwartz.com/eyeris/reference
   article: http://shawnschwartz.com/eyeris/articles
diff --git a/docs/reference/bidsify.html b/docs/reference/bidsify.html
index b6570d0..5a9b562 100644
--- a/docs/reference/bidsify.html
+++ b/docs/reference/bidsify.html
@@ -183,7 +183,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/deblink.html b/docs/reference/deblink.html
index 1a5af1f..94c6ad6 100644
--- a/docs/reference/deblink.html
+++ b/docs/reference/deblink.html
@@ -156,7 +156,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/detransient.html b/docs/reference/detransient.html
index eb84973..2645ea3 100644
--- a/docs/reference/detransient.html
+++ b/docs/reference/detransient.html
@@ -97,7 +97,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/detrend.html b/docs/reference/detrend.html
index 3297a97..dc3bb0c 100644
--- a/docs/reference/detrend.html
+++ b/docs/reference/detrend.html
@@ -86,7 +86,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/epoch.html b/docs/reference/epoch.html
index 0e2b271..e6fbe55 100644
--- a/docs/reference/epoch.html
+++ b/docs/reference/epoch.html
@@ -181,14 +181,31 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">eye_preproc</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"assocret.asc"</span>, package <span class="op">=</span> <span class="st">"eyeris"</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu">eyeris</span><span class="fu">::</span><span class="fu"><a href="load_asc.html">load_asc</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu">eyeris</span><span class="fu">::</span><span class="fu"><a href="deblink.html">deblink</a></span><span class="op">(</span>extend <span class="op">=</span> <span class="fl">50</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu">eyeris</span><span class="fu">::</span><span class="fu"><a href="detransient.html">detransient</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu">eyeris</span><span class="fu">::</span><span class="fu"><a href="interpolate.html">interpolate</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu">eyeris</span><span class="fu">::</span><span class="fu"><a href="lpfilt.html">lpfilt</a></span><span class="op">(</span>plot_freqz <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu">eyeris</span><span class="fu">::</span><span class="fu"><a href="zscore.html">zscore</a></span><span class="op">(</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in operation(data, prev_operation, ...):</span> No NAs detected in pupil data for interpolation.</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">eye_preproc</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu">eyeris</span><span class="fu">::</span><span class="fu">epoch</span><span class="op">(</span>events <span class="op">=</span> <span class="st">"PROBE*"</span>, limits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'eye_preproc' not found</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">eye_preproc</span> <span class="op">|&gt;</span></span></span>
+<span class="r-in"><span>  <span class="fu">eyeris</span><span class="fu">::</span><span class="fu">epoch</span><span class="op">(</span>events <span class="op">=</span> <span class="st">"TRIALID {trial}"</span><span class="op">)</span> <span class="co"># all samples between each trial</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'eye_preproc' not found</span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/eyeris-package.html b/docs/reference/eyeris-package.html
index 1b2cde0..bd7e79c 100644
--- a/docs/reference/eyeris-package.html
+++ b/docs/reference/eyeris-package.html
@@ -1,5 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>eyeris: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines — eyeris-package • eyeris</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="eyeris: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines — eyeris-package"><meta name="description" content="More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description."><meta property="og:description" content="More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description."><meta property="og:image" content="http://shawnschwartz.com/eyeris/logo.png"></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>eyeris: eyeris — eyeris-package • eyeris</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../lightswitch.js"></script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="eyeris: eyeris — eyeris-package"><meta name="description" content="
+Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description."><meta property="og:description" content="
+Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description."><meta property="og:image" content="http://shawnschwartz.com/eyeris/logo.png"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -36,24 +38,26 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>eyeris: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines</h1>
+      <img src="../logo.png" class="logo" alt=""><h1>eyeris: eyeris</h1>
       <small class="dont-index">Source: <a href="https://github.com/shawntz/eyeris/blob/HEAD/R/eyeris-package.R" class="external-link"><code>R/eyeris-package.R</code></a></small>
       <div class="d-none name"><code>eyeris-package.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.</p>
+    <p></p>
+<p>Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.</p>
     </div>
 
 
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p>Useful links:</p><ul><li><p><a href="http://shawnschwartz.com/eyeris/">http://shawnschwartz.com/eyeris/</a></p></li>
+    <div class="dont-index"><p>Useful links:</p><ul><li><p><a href="http://shawnschwartz.com/eyeris">http://shawnschwartz.com/eyeris</a></p></li>
+<li><p>Report bugs at <a href="https://github.com/shawntz/eyeris/issues" class="external-link">https://github.com/shawntz/eyeris/issues</a></p></li>
 </ul></div>
     </div>
     <div class="section level2">
     <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
-    <p><strong>Maintainer</strong>: Shawn Schwartz <a href="mailto:stschwartz@stanford.edu">stschwartz@stanford.edu</a> (<a href="https://orcid.org/0000-0001-6444-8451" class="external-link">ORCID</a>)</p>
+    <p><strong>Maintainer</strong>: Shawn Tyler Schwartz <a href="mailto:stschwartz@stanford.edu">stschwartz@stanford.edu</a> (<a href="https://orcid.org/0000-0001-6444-8451" class="external-link">ORCID</a>)</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
@@ -61,7 +65,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/glassbox.html b/docs/reference/glassbox.html
index 7183bee..ad70519 100644
--- a/docs/reference/glassbox.html
+++ b/docs/reference/glassbox.html
@@ -168,7 +168,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 5243ea9..d3f1124 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -127,7 +127,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/interpolate.html b/docs/reference/interpolate.html
index b5c7f84..d166edf 100644
--- a/docs/reference/interpolate.html
+++ b/docs/reference/interpolate.html
@@ -99,7 +99,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/load_asc.html b/docs/reference/load_asc.html
index 26e0b9a..0fbd3f7 100644
--- a/docs/reference/load_asc.html
+++ b/docs/reference/load_asc.html
@@ -96,7 +96,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/lpfilt.html b/docs/reference/lpfilt.html
index 2b35ba2..874c79d 100644
--- a/docs/reference/lpfilt.html
+++ b/docs/reference/lpfilt.html
@@ -107,7 +107,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/plot.eyeris.html b/docs/reference/plot.eyeris.html
index 5ca41b7..216ff53 100644
--- a/docs/reference/plot.eyeris.html
+++ b/docs/reference/plot.eyeris.html
@@ -144,7 +144,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/sticker.html b/docs/reference/sticker.html
index a2dbee4..26ff98a 100644
--- a/docs/reference/sticker.html
+++ b/docs/reference/sticker.html
@@ -60,7 +60,7 @@ <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/reference/zscore.html b/docs/reference/zscore.html
index 79c635a..5e5e1d8 100644
--- a/docs/reference/zscore.html
+++ b/docs/reference/zscore.html
@@ -128,7 +128,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Shawn Tyler Schwartz.</p>
+  <p>Developed by Shawn T. Schwartz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/docs/search.json b/docs/search.json
index e62ed6d..f2f8922 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"http://shawnschwartz.com/eyeris/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 eyeris authors 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":"http://shawnschwartz.com/eyeris/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Shawn Tyler Schwartz. Author, maintainer.","code":""},{"path":"http://shawnschwartz.com/eyeris/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Schwartz ST (2024). eyeris: Create Run Flexible Reproducible Pupillometry Preprocessing Pipelines. R package version 0.0.0.9000, https://shawnschwartz.com/eyeris.","code":"@Manual{,   title = {eyeris: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines},   author = {Shawn Tyler Schwartz},   year = {2024},   note = {R package version 0.0.0.9000},   url = {https://shawnschwartz.com/eyeris}, }"},{"path":[]},{"path":"http://shawnschwartz.com/eyeris/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines","text":"can install development version eyeris GitHub : ","code":"# install.packages(\"devtools\") devtools::install_github(\"shawntz/eyeris\") # install.packages(\"pak\") pak::pak(\"shawntz/eyeris\")"},{"path":[]},{"path":"http://shawnschwartz.com/eyeris/index.html","id":"the-glassbox-prescription-function","dir":"","previous_headings":"Example","what":"the glassbox() “prescription” function","title":"Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines","text":"basic example use eyeris box opinionated set steps parameters one start preprocessing pupillometry data. Critically, “glassbox” – opposed “blackbox” – since step parameter implemented herein fully open accessible . designed pipeline step / function like legos – intentionally carefully designed way allows flexibly construct compare different pipelines. hope enjoy! -shawn","code":"set.seed(1)  library(eyeris)  demo_data <- system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\")  eyeris_preproc <- glassbox(demo_data, detrend_data = F, lpfilt = list(plot_freqz = T)) #> ✔ [  OK  ] - Running eyeris::load_asc() #> ✔ [  OK  ] - Running eyeris::deblink() #> ✔ [  OK  ] - Running eyeris::detransient() #> ✔ [  OK  ] - Running eyeris::interpolate() #> ℹ [ INFO ] - Skipping eyeris::interpolate(): No NAs detected in pupil data for interpolation. #> ✔ [  OK  ] - Running eyeris::lpfilt() #> ✔ [  OK  ] - Skipping eyeris::detrend() #> ✔ [  OK  ] - Running eyeris::zscore()"},{"path":"http://shawnschwartz.com/eyeris/index.html","id":"step-wise-correction-of-pupillary-signal","dir":"","previous_headings":"Example","what":"step-wise correction of pupillary signal","title":"Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines","text":"","code":"plot(eyeris_preproc)"},{"path":"http://shawnschwartz.com/eyeris/index.html","id":"final-pre-post-correction-of-pupillary-signal-raw---preprocessed","dir":"","previous_headings":"Example","what":"final pre-post correction of pupillary signal (raw -> preprocessed)","title":"Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines","text":"","code":"plot(eyeris_preproc, steps = c(1, 5), preview_window = c(0, 100000))"},{"path":"http://shawnschwartz.com/eyeris/index.html","id":"comments-suggestions-questions-issues","dir":"","previous_headings":"","what":"Comments, suggestions, questions, issues","title":"Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines","text":"Please use issues tab (https://github.com/shawntz/eyeris/issues) make note bugs, comments, suggestions, feedback, etc… welcomed appreciated, thanks!","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/bidsify.html","id":null,"dir":"Reference","previous_headings":"","what":"Save out pupil timeseries data in a BIDS-like structure — bidsify","title":"Save out pupil timeseries data in a BIDS-like structure — bidsify","text":"method provides structured way save pupil data BIDS-like structure. method saves epoched data well raw pupil timeseries, formats directory filename structures based metadata provide.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/bidsify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Save out pupil timeseries data in a BIDS-like structure — bidsify","text":"","code":"bidsify(   eyeris,   save_all = TRUE,   epochs_list = NULL,   merge_epochs = FALSE,   bids_dir = NULL,   participant_id = NULL,   session_num = NULL,   task_name = NULL,   run_num = NULL,   save_raw = TRUE,   render_report = TRUE,   html_report = TRUE,   pdf_report = TRUE,   report_seed = 0 )"},{"path":"http://shawnschwartz.com/eyeris/reference/bidsify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Save out pupil timeseries data in a BIDS-like structure — bidsify","text":"eyeris object class eyeris dervived load(). save_all Logical flag indicating whether epochs saved subset . Defaults TRUE. epochs_list List epochs saved. Defaults NULL. merge_epochs Logical flag indicating whether epochs saved one file separate files. Defaults FLASE (merge). bids_dir Base bids_directory. participant_id BIDS subject ID. session_num BIDS session ID. task_name BIDS task ID. run_num BIDS run ID. save_raw Logical flag indicating whether save_raw pupil data addition epoched data. Defaults TRUE. render_report Logical flag indicating whether save eyeris preprocessing summary report. Defaults TRUE. html_report Logical flag indicating whether save eyeris preprocessing summary report HTML file. Defaults TRUE. pdf_report Logical flag indicating whether save eyeris preprocessing summary report PDF file. Note, valid TeX distribution must already installed. Defaults TRUE. report_seed Random seed plots appear report. Defaults 0. See plot() detailed description.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/bidsify.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Save out pupil timeseries data in a BIDS-like structure — bidsify","text":"future, intend function save data official BIDS format eyetracking data (see proposal currently review ). time, however, function instead takes BIDS-inspired approach organizing output files preprocessed pupil data.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/bidsify.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Save out pupil timeseries data in a BIDS-like structure — bidsify","text":"","code":"# Bleed around blink periods just long enough to remove majority of #  deflections due to eyelid movements if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() |>   eyeris::lpfilt(plot_freqz = TRUE) |>   eyeris::zscore() |>   eyeris::epoch(     events = \"PROBE_{type}_{trial}\",     limits = c(-2, 1), # grab 2 seconds prior to and 1 second post event     label = \"prePostProbe\" # custom epoch label name   ) |>   eyeris::bidsify(     bids_dir = \".\", # make bids dir in current directory     participant_id = \"001\",     session_num = \"01\",     task_name = \"assocret\",     run_num = \"01\"   ) } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/deblink.html","id":null,"dir":"Reference","previous_headings":"","what":"NA-pad blink events / missing data — deblink","title":"NA-pad blink events / missing data — deblink","text":"Deblinking (.k.. NA-padding) time series data. intended use method remove blink-related artifacts surrounding periods missing data. instance, individual blinks, usually rapid decreases followed increases pupil size, chunk data missing -'spike'-looking events. deblinking procedure NA-pad missing data point specified number ms.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/deblink.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"NA-pad blink events / missing data — deblink","text":"","code":"deblink(eyeris, extend = 40)"},{"path":"http://shawnschwartz.com/eyeris/reference/deblink.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"NA-pad blink events / missing data — deblink","text":"eyeris object class eyeris dervived load(). extend Either single number indicating number milliseconds pad forward/backward around missing sample, , vector length two indicating different numbers milliseconds pad forward/backward around missing sample, format c(backward, forward).","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/deblink.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"NA-pad blink events / missing data — deblink","text":"eyeris object new column: pupil_deblink.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/deblink.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"NA-pad blink events / missing data — deblink","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 40) # 40 ms in both directions } # }  system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = c(40, 50)) # 40 ms backward, 50 ms forward #> $file #> [1] \"/opt/homebrew/lib/R/4.4/site-library/eyeris/extdata/assocret.asc\" #>  #> $timeseries #> # A tibble: 22,145 × 8 #>    time_orig eye_x eye_y eye      hz type     pupil_raw pupil_raw_deblink #>        <int> <dbl> <dbl> <chr> <dbl> <chr>        <dbl>             <dbl> #>  1  11242177  949.  646. R      1000 diameter      6174              6174 #>  2  11242178  947.  644. R      1000 diameter      6176              6176 #>  3  11242179  946.  643  R      1000 diameter      6178              6178 #>  4  11242180  945.  642  R      1000 diameter      6179              6179 #>  5  11242181  945.  641. R      1000 diameter      6180              6180 #>  6  11242182  945.  642. R      1000 diameter      6182              6182 #>  7  11242183  945.  644. R      1000 diameter      6187              6187 #>  8  11242184  945.  644. R      1000 diameter      6197              6197 #>  9  11242185  945.  643. R      1000 diameter      6207              6207 #> 10  11242186  945.  642. R      1000 diameter      6203              6203 #> # ℹ 22,135 more rows #>  #> $events #> # A tibble: 67 × 3 #>    block     time text                       #>    <dbl>    <dbl> <chr>                      #>  1     1 11242177 !MODE RECORD CR 1000 2 1 R #>  2     1 11243349 EXP_START                  #>  3     1 11243355 TRIALID 0                  #>  4     1 11243356 START_TRIAL_0              #>  5     1 11243356 CUE_START_0                #>  6     1 11244328 CUE_STOP_0                 #>  7     1 11244329 DELAY_START_0              #>  8     1 11245337 DELAY_STOP_0               #>  9     1 11245338 PROBE_START_0              #> 10     1 11245956 RESPONSE_0                 #> # ℹ 57 more rows #>  #> $blinks #> # A tibble: 0 × 5 #> # ℹ 5 variables: block <int>, stime <dbl>, etime <dbl>, dur <dbl>, eye <fct> #>  #> $info #>                  date        model version sample.rate   cr  left right mono #> 1 2009-01-11 02:40:47 EyeLink 1000   4.594        1000 TRUE FALSE  TRUE TRUE #>   screen.x screen.y                                 mount filter.level #> 1     1920     1080 Desktop / Monocular / Head Stabilized            2 #>   sample.dtype event.dtype pupil.dtype velocity resolution htarg input buttons #> 1         GAZE        GAZE    DIAMETER    FALSE      FALSE FALSE FALSE   FALSE #>  #> $latest #> [1] \"pupil_raw_deblink\" #>  #> attr(,\"class\") #> [1] \"eyeris\""},{"path":"http://shawnschwartz.com/eyeris/reference/detransient.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove pupil samples that are physiologically unlikely — detransient","title":"Remove pupil samples that are physiologically unlikely — detransient","text":"intended use method removing pupil samples emerge quickly physiologically expected. accomplished rejecting samples exceed \"speed\"-based threshold (.e., median absolute deviation sample--sample). threshold computed based constant n, defaults value 16.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detransient.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove pupil samples that are physiologically unlikely — detransient","text":"","code":"detransient(eyeris, n = 16)"},{"path":"http://shawnschwartz.com/eyeris/reference/detransient.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove pupil samples that are physiologically unlikely — detransient","text":"eyeris object class eyeris dervived load(). n constant used compute median absolute deviation (MAD) threshold.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detransient.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove pupil samples that are physiologically unlikely — detransient","text":"eyeris object new column timeseries: pupil_detransient.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detransient.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove pupil samples that are physiologically unlikely — detransient","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/detrend.html","id":null,"dir":"Reference","previous_headings":"","what":"Detrend the pupil time series — detrend","title":"Detrend the pupil time series — detrend","text":"Linearly detrend_pupil data fitting linear model pupil_data ~ time, return fitted betas residuals (pupil_data - fitted_values).","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detrend.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detrend the pupil time series — detrend","text":"","code":"detrend(eyeris)"},{"path":"http://shawnschwartz.com/eyeris/reference/detrend.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detrend the pupil time series — detrend","text":"eyeris object class eyeris dervived load().","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detrend.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detrend the pupil time series — detrend","text":"eyeris object two new columns timeseries: detrend_fitted_betas, pupil_detrend.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detrend.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Detrend the pupil time series — detrend","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() |>   eyeris::lpfilt(plot_freqz = TRUE) |>   eyeris::detrend() } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/epoch.html","id":null,"dir":"Reference","previous_headings":"","what":"Epoch (and baseline) pupil data based on custom event message structure — epoch","title":"Epoch (and baseline) pupil data based on custom event message structure — epoch","text":"Intended used final preprocessing step. function creates data epochs either fixed dynamic durations respect provided events time limits, also includes intuitive metadata parsing feature additional trial data embedded within event messages can easily identified joined resulting epoched data frames.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/epoch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Epoch (and baseline) pupil data based on custom event message structure — epoch","text":"","code":"epoch(   eyeris,   events,   limits = NULL,   label = NULL,   calc_baseline = FALSE,   apply_baseline = FALSE,   baseline_type = c(\"sub\", \"div\"),   baseline_events = NULL,   baseline_period = NULL,   hz = NULL )"},{"path":"http://shawnschwartz.com/eyeris/reference/epoch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Epoch (and baseline) pupil data based on custom event message structure — epoch","text":"eyeris object class eyeris derived load(). events Either (1) single string representing event message perform trial extraction around, using specified limits center epoch around limits (just grabs data epochs subsequent event string type); (2) vector containing start end event message strings – , limits ignored duration trial epoch number samples matched start end event message pair; (3) list 2 dataframes manually specify start/end event timestamp-message pairs pull raw timeseries data – , required raw timestamp event message provided following format: list(data.frame(time = c(...), msg = c(...)), data.frame(time = c(...), msg = c(...))) first data.frame indicates start event timestamp message string pairs, second data.frame indicates end event timestamp message string pairs. event-modes 1 2, way pass event message string must conform standardized protocol eyeris knows find events (optionally) parse included metadata tidy epoch data outputs. two primary choices: either () specify string followed * wildcard expression (e.g., \"PROBE_START*), match messages \"PROBE_START ...\" (... referring potential metadata, trial number, stim file, etc.); (b) specify string using eyeris syntax: (e.g., \"PROBE_{type}_{trial}\"), match messages follow structure like \"PROBE_START_1\" \"PROBE_STOP_1\", generate two additional metadata columns: type trial, contain following values based two example strings: type: ('START', 'STOP'), trial: (1, 1). limits vector 2 values (start, end) seconds, indicating trial extraction occur centered around given start message string events parameter. label (optional) string can provide customize name resulting eyeris class object containing epoched data frame. left NULL (default), list item called epoch_xyz, xyz sanitized version original start event string provided matching. choose specify label , resulting list object name take form: epoch_label. calc_baseline flag indicated whether perform baseline correction. Note, setting calc_baseline TRUE alone compute baseline period, apply preprocessed timeseries unless apply_baseline also set TRUE. apply_baseline flag indicating whether apply calculated baseline pupil timeseries. baseline correction applied pupil latest preprocessing step. baseline_type Whether perform subtractive (sub) divisive (div) baseline correction. Defaults sub. baseline_events Similar events, baseline_events, can supply either (1) single string representing event message center baseline calculation around, indicated baseline_period; (2) single vector containing start end event message string – , baseline_period ignored duration baseline period mean calculated number samples matched start end event message pair, opposed specified fixed duration (described 1). Please note, providing list trial-level start/end message pairs (like events parameter) manually indicate unique start/end chunks baselining currently unsupported. Though, intend add feature later version eyeris, given likely heavily utilized / demand feature. baseline_period vector 2 values (start, end) seconds, indicating window data used perform baseline correction, centered around single string \"start\" message string provided baseline_events. , baseline_period ignored \"start\" \"end\" message string provided baseline_events argument. hz Data sampling rate. specified, use value contained within tracker's metadata.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/epoch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Epoch (and baseline) pupil data based on custom event message structure — epoch","text":"Updated eyeris object dataframes containing epoched data (epoch_).","code":""},{"path":[]},{"path":"http://shawnschwartz.com/eyeris/reference/eyeris-package.html","id":null,"dir":"Reference","previous_headings":"","what":"eyeris: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines — eyeris-package","title":"eyeris: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines — eyeris-package","text":"(maybe one line) Use four spaces indenting paragraphs within Description.","code":""},{"path":[]},{"path":"http://shawnschwartz.com/eyeris/reference/eyeris-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"eyeris: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines — eyeris-package","text":"Maintainer: Shawn Schwartz stschwartz@stanford.edu (ORCID)","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/glassbox.html","id":null,"dir":"Reference","previous_headings":"","what":"A ","title":"A ","text":"glassbox function (contrast \"blackbox\" function run get result (little) idea got input output) primary benefits calling exported function eyeris separately.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/glassbox.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A ","text":"","code":"glassbox(   file,   confirm = FALSE,   detrend_data = FALSE,   num_previews = 3,   preview_duration = 5,   preview_window = NULL,   ... )"},{"path":"http://shawnschwartz.com/eyeris/reference/glassbox.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A ","text":"file SR Research EyeLink .asc file generated official EyeLink edf2asc command. confirm flag indicate whether run glassbox pipeline autonomously way (set FALSE default), interactively provide visualization pipeline step, must also indicate \"(y)es\" \"(n)o\" either proceed cancel current glassbox pipeline operation (set TRUE). detrend_data flag indicate whether run detrend step (set FALSE default). Detrending pupil timeseries can unintended consequences; thus recommend users understand implications detrending – addition whether detrending appropriate research design question(s) – using function. num_previews Number random example \"epochs\" generate previewing effect preprocessing step pupil timeseries. preview_duration Time seconds randomly selected preview. preview_window start stop raw timestamps used subset preprocessed data step eyeris workflow visualization. Defaults NULL, meaning random epochs defined num_previews preview_duration plotted. override random epochs, set preview_window vector relative start stop times (e.g., c(5000, 6000) indicate raw data 5-6 seconds data recorded 1000 Hz). Note, start/stop time values indicated relate raw index position pupil sample 1 n (need specified manually user depending sampling rate recording; .e., 5000-6000 epoch positioned 5-6 seconds start timeseries, sampled 1000 Hz). ... Additional arguments override default, prescribed settings.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/glassbox.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A ","text":"First, glassbox function provides highly opinionated prescription steps starting parameters believe pupillometry researcher use defaults preprocessing pupillometry data. Second, mutually exclusive first point, using function ideally reduce probability accidental mishaps \"reimplementing\" steps preprocessing pipeline within across projects. hope streamline process way collect pupillometry dataset within minutes assess quality data simultaneously running full preprocessing pipeline 1-ish line code! Third, glassbox provides \"interactive\" framework can evaluate consequences parameters within step data real time, facilitating fairly easy--use workflow parameter optimization particular dataset. process essentially takes opinionated steps provides pre-/post-plot timeseries data step can adjust parameters re-run pipeline satisfied choices paramters consequences pupil timeseries data.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/glassbox.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A ","text":"","code":"if (FALSE) { # \\dontrun{ demo_data <- system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\")  # (1) examples using the default prescribed parameters and pipeline recipe ## (a) run an automated pipeline with no real-time inspection of parameters output <- eyeris::glassbox(demo_data)  ## (b) run a interactive workflow (with confirmation prompts after each step) output <- eyeris::glassbox(demo_data, confirm = TRUE)  # (2) examples overriding the default parameters output <- eyeris::glassbox(demo_data,   confirm = TRUE,   deblink = list(extend = 40),   lpfilt = list(plot_freqz = FALSE) ) } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/interpolate.html","id":null,"dir":"Reference","previous_headings":"","what":"Interpolate missing pupil samples — interpolate","title":"Interpolate missing pupil samples — interpolate","text":"Linear interpolation time series data. intended use method filling missing pupil samples (NAs) time series. method uses \"na.approx()\" function zoo package, implements linear interpolation using \"approx()\" function stats package. Currently, NAs beginning end data replaced values either end, respectively, using \"rule = 2\" argument approx() function.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/interpolate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Interpolate missing pupil samples — interpolate","text":"","code":"interpolate(eyeris)"},{"path":"http://shawnschwartz.com/eyeris/reference/interpolate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Interpolate missing pupil samples — interpolate","text":"eyeris object class eyeris dervived load().","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/interpolate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Interpolate missing pupil samples — interpolate","text":"eyeris object new column timeseries: pupil_interpolate.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/interpolate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Interpolate missing pupil samples — interpolate","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/load_asc.html","id":null,"dir":"Reference","previous_headings":"","what":"Load and parse SR Research EyeLink .asc files — load_asc","title":"Load and parse SR Research EyeLink .asc files — load_asc","text":"function builds upon eyelinker::read.asc() function parse messages metadata within EyeLink .asc file. loading additional processing, function returns S3 eyeris class use subsequent eyeris pipeline steps functions.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/load_asc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load and parse SR Research EyeLink .asc files — load_asc","text":"","code":"load_asc(file)"},{"path":"http://shawnschwartz.com/eyeris/reference/load_asc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load and parse SR Research EyeLink .asc files — load_asc","text":"file SR Research EyeLink .asc file generated official EyeLink edf2asc command.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/load_asc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load and parse SR Research EyeLink .asc files — load_asc","text":"object S3 class eyeris following attributes: file: Path original .asc file. timeseries: Dataframe raw timeseries data tracker. events: Dataframe event messages timestamps. blinks: Dataframe blink events. info: Dataframe various metadata parsed file header. latest: eyeris variable tracking pipeline run history.","code":""},{"path":[]},{"path":"http://shawnschwartz.com/eyeris/reference/load_asc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load and parse SR Research EyeLink .asc files — load_asc","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/lpfilt.html","id":null,"dir":"Reference","previous_headings":"","what":"Lowpass filtering of time series data — lpfilt","title":"Lowpass filtering of time series data — lpfilt","text":"intended use method smoothing, although specifying wp ws differently one can achieve highpass bandpass filtering well. However, lowpass filtering done pupillometry data.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/lpfilt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lowpass filtering of time series data — lpfilt","text":"","code":"lpfilt(eyeris, wp = 4, ws = 8, rp = 1, rs = 35, plot_freqz = FALSE)"},{"path":"http://shawnschwartz.com/eyeris/reference/lpfilt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lowpass filtering of time series data — lpfilt","text":"eyeris object class eyeris derived load(). wp end passband frequency Hz (desired lowpass cutoff). ws start stopband frequency Hz (required lowpass cutoff). rp Required maximal ripple within passband dB. rs Required minimal attenuation within stopband dB. plot_freqz Boolean flag displaying filter frequency response.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/lpfilt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lowpass filtering of time series data — lpfilt","text":"eyeris object new column timeseries: pupil_lpfilt.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/lpfilt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lowpass filtering of time series data — lpfilt","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() |>   eyeris::lpfilt(plot_freqz = TRUE) } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/plot.eyeris.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot pre-processed pupil data from eyeris — plot.eyeris","title":"Plot pre-processed pupil data from eyeris — plot.eyeris","text":"S3 plotting method objects class eyeris. Plots single-panel timeseries subset pupil timeseries preprocessing step. intended use function provide simple method qualitatively assessing consequences preprocessing recipe parameters raw pupillary signal.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/plot.eyeris.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot pre-processed pupil data from eyeris — plot.eyeris","text":"","code":"# S3 method for class 'eyeris' plot(   x,   ...,   steps = NULL,   num_previews = NULL,   preview_duration = NULL,   preview_window = NULL,   seed = NULL )"},{"path":"http://shawnschwartz.com/eyeris/reference/plot.eyeris.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot pre-processed pupil data from eyeris — plot.eyeris","text":"x object class eyeris derived load(). ... Additional arguments passed plot. steps steps plot; defaults (.e., plot steps). Otherwise, pass vector containing index step(s) want plot, index 1 original raw pupil timeseries. num_previews Number random example \"epochs\" generate previewing effect preprocessing step pupil timeseries. preview_duration Time seconds randomly selected preview. preview_window start stop raw timestamps used subset preprocessed data step eyeris workflow visualization. Defaults NULL, meaning random epochs defined num_examples example_duration plotted. override random epochs, set example_timelim vector relative start stop times (e.g., c(5000, 6000) indicate raw data 5-6 seconds data recorded 1000 Hz). Note, start/stop time values indicated relate raw index position pupil sample 1 n (need specified manually user depending sampling rate recording; .e., 5000-6000 epoch positioned 5-6 seconds start timeseries, sampled 1000 Hz). seed Random seed current plotting session. Leave NULL select num_previews number random preview \"epochs\" (preview_duration) time. Otherwise, choose seed-integer normally select base::set.seed(), able continue re-plotting random example pupil epochs time – helpful adjusting parameters within across eyeris workflow steps.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/plot.eyeris.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot pre-processed pupil data from eyeris — plot.eyeris","text":"return value; iteratively plots subset pupil timeseries preprocessing step run.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/plot.eyeris.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot pre-processed pupil data from eyeris — plot.eyeris","text":"","code":"if (FALSE) { # \\dontrun{ # using the default 10000 to 20000 ms time subset plot(eyeris_data)  # using a custom time subset (i.e., 1 to 500 ms) plot(eyeris_data, preview_window = c(1, 500)) } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/sticker.html","id":null,"dir":"Reference","previous_headings":"","what":"eyeris package logo (hexagon sticker) — sticker","title":"eyeris package logo (hexagon sticker) — sticker","text":"eyeris package logo (hexagon sticker)","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/sticker.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"eyeris package logo (hexagon sticker) — sticker","text":"","code":"sticker"},{"path":"http://shawnschwartz.com/eyeris/reference/sticker.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"eyeris package logo (hexagon sticker) — sticker","text":"png image file rendered README html reports.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":null,"dir":"Reference","previous_headings":"","what":"Z-Score pupil timeseries data — zscore","title":"Z-Score pupil timeseries data — zscore","text":"intended use method scale arbitrary units pupil size timeseries mean 0 standard deviation 1. accomplished mean centering data points dividing standard deviation (.e., z-scoring data, similar base::scale()). Z-scoring pupil data helpful trial-level -subjects analyses arbitrary units pupil size recorded tracker scale across participants, therefore make analyses depend data one participant difficult interpret.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Z-Score pupil timeseries data — zscore","text":"","code":"zscore(eyeris)"},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Z-Score pupil timeseries data — zscore","text":"eyeris object class eyeris dervived load().","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Z-Score pupil timeseries data — zscore","text":"numeric vector giving number characters (code points) element character vector. Missing string missing length.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Z-Score pupil timeseries data — zscore","text":"general, common z-score pupil data within given participant, furthermore, z-score participant's data function block number (tasks/experiments participants complete one block trials) account potential time--task effects across task/experiment blocks. , use eyeris package intended, need specify groups participant/block-level situations described . eyeris designed preprocess single block pupil data single participant, one time. Therefore, later merge preprocessed data eyeris, individual, preprocessed block data participant already independently scaled others. Additionally, intend compare mean z-scored pupil size across task conditions, memory successes vs. memory failures, set behavioral outcome (.e., success/failure) variable grouping variable within analysis. , consequently obtain mean pupil size 0 standard deviation 1 within group (since scaled pupil size calculated timeseries outcome variable group, separately). Instead, compute z-score entire pupil timeseries (epoching data), split take mean z-scored timeseries function condition variable.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Z-Score pupil timeseries data — zscore","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() |>   eyeris::lpfilt(plot_freqz = TRUE) |>   eyeris::zscore() } # }"}]
+[{"path":"http://shawnschwartz.com/eyeris/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 eyeris authors 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":"http://shawnschwartz.com/eyeris/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Shawn T. Schwartz. Author, maintainer.","code":""},{"path":"http://shawnschwartz.com/eyeris/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Schwartz ST (2024). eyeris: eyeris. R package version 0.0.0.9000, http://shawnschwartz.com/eyeris.","code":"@Manual{,   title = {eyeris: eyeris},   author = {Shawn T. Schwartz},   year = {2024},   note = {R package version 0.0.0.9000},   url = {http://shawnschwartz.com/eyeris}, }"},{"path":[]},{"path":"http://shawnschwartz.com/eyeris/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"eyeris","text":"can install development version eyeris GitHub : ","code":"# install.packages(\"devtools\") devtools::install_github(\"shawntz/eyeris\") # install.packages(\"pak\") pak::pak(\"shawntz/eyeris\")"},{"path":[]},{"path":"http://shawnschwartz.com/eyeris/index.html","id":"the-glassbox-prescription-function","dir":"","previous_headings":"Example","what":"the glassbox() “prescription” function","title":"eyeris","text":"basic example use eyeris box opinionated set steps parameters one start preprocessing pupillometry data. Critically, “glassbox” – opposed “blackbox” – since step parameter implemented herein fully open accessible . designed pipeline step / function like legos – intentionally carefully designed way allows flexibly construct compare different pipelines. hope enjoy! -shawn README FIGURE","code":"set.seed(1)  library(eyeris)  demo_data <- system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\")  eyeris_preproc <- glassbox(demo_data, detrend_data = F, lpfilt = list(plot_freqz = T)) #> ✔ [  OK  ] - Running eyeris::load_asc() #> ✔ [  OK  ] - Running eyeris::deblink() #> ✔ [  OK  ] - Running eyeris::detransient() #> ✔ [  OK  ] - Running eyeris::interpolate() #> ℹ [ INFO ] - Skipping eyeris::interpolate(): No NAs detected in pupil data for interpolation. #> ✔ [  OK  ] - Running eyeris::lpfilt() #> ✔ [  OK  ] - Skipping eyeris::detrend() #> ✔ [  OK  ] - Running eyeris::zscore()"},{"path":"http://shawnschwartz.com/eyeris/index.html","id":"step-wise-correction-of-pupillary-signal","dir":"","previous_headings":"Example","what":"step-wise correction of pupillary signal","title":"eyeris","text":"README FIGURE README FIGURE README FIGURE README FIGURE README FIGURE","code":"plot(eyeris_preproc)"},{"path":"http://shawnschwartz.com/eyeris/index.html","id":"final-pre-post-correction-of-pupillary-signal-raw---preprocessed","dir":"","previous_headings":"Example","what":"final pre-post correction of pupillary signal (raw -> preprocessed)","title":"eyeris","text":"README FIGURE README FIGURE","code":"plot(eyeris_preproc, steps = c(1, 5), preview_window = c(0, 100000))"},{"path":"http://shawnschwartz.com/eyeris/index.html","id":"comments-suggestions-questions-issues","dir":"","previous_headings":"","what":"Comments, suggestions, questions, issues","title":"eyeris","text":"Please use issues tab (https://github.com/shawntz/eyeris/issues) make note bugs, comments, suggestions, feedback, etc… welcomed appreciated, thanks!","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/bidsify.html","id":null,"dir":"Reference","previous_headings":"","what":"Save out pupil timeseries data in a BIDS-like structure — bidsify","title":"Save out pupil timeseries data in a BIDS-like structure — bidsify","text":"method provides structured way save pupil data BIDS-like structure. method saves epoched data well raw pupil timeseries, formats directory filename structures based metadata provide.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/bidsify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Save out pupil timeseries data in a BIDS-like structure — bidsify","text":"","code":"bidsify(   eyeris,   save_all = TRUE,   epochs_list = NULL,   merge_epochs = FALSE,   bids_dir = NULL,   participant_id = NULL,   session_num = NULL,   task_name = NULL,   run_num = NULL,   save_raw = TRUE,   render_report = TRUE,   html_report = TRUE,   pdf_report = TRUE,   report_seed = 0 )"},{"path":"http://shawnschwartz.com/eyeris/reference/bidsify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Save out pupil timeseries data in a BIDS-like structure — bidsify","text":"eyeris object class eyeris dervived load(). save_all Logical flag indicating whether epochs saved subset . Defaults TRUE. epochs_list List epochs saved. Defaults NULL. merge_epochs Logical flag indicating whether epochs saved one file separate files. Defaults FLASE (merge). bids_dir Base bids_directory. participant_id BIDS subject ID. session_num BIDS session ID. task_name BIDS task ID. run_num BIDS run ID. save_raw Logical flag indicating whether save_raw pupil data addition epoched data. Defaults TRUE. render_report Logical flag indicating whether save eyeris preprocessing summary report. Defaults TRUE. html_report Logical flag indicating whether save eyeris preprocessing summary report HTML file. Defaults TRUE. pdf_report Logical flag indicating whether save eyeris preprocessing summary report PDF file. Note, valid TeX distribution must already installed. Defaults TRUE. report_seed Random seed plots appear report. Defaults 0. See plot() detailed description.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/bidsify.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Save out pupil timeseries data in a BIDS-like structure — bidsify","text":"future, intend function save data official BIDS format eyetracking data (see proposal currently review ). time, however, function instead takes BIDS-inspired approach organizing output files preprocessed pupil data.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/bidsify.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Save out pupil timeseries data in a BIDS-like structure — bidsify","text":"","code":"# Bleed around blink periods just long enough to remove majority of #  deflections due to eyelid movements if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() |>   eyeris::lpfilt(plot_freqz = TRUE) |>   eyeris::zscore() |>   eyeris::epoch(     events = \"PROBE_{type}_{trial}\",     limits = c(-2, 1), # grab 2 seconds prior to and 1 second post event     label = \"prePostProbe\" # custom epoch label name   ) |>   eyeris::bidsify(     bids_dir = \".\", # make bids dir in current directory     participant_id = \"001\",     session_num = \"01\",     task_name = \"assocret\",     run_num = \"01\"   ) } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/deblink.html","id":null,"dir":"Reference","previous_headings":"","what":"NA-pad blink events / missing data — deblink","title":"NA-pad blink events / missing data — deblink","text":"Deblinking (.k.. NA-padding) time series data. intended use method remove blink-related artifacts surrounding periods missing data. instance, individual blinks, usually rapid decreases followed increases pupil size, chunk data missing -'spike'-looking events. deblinking procedure NA-pad missing data point specified number ms.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/deblink.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"NA-pad blink events / missing data — deblink","text":"","code":"deblink(eyeris, extend = 40)"},{"path":"http://shawnschwartz.com/eyeris/reference/deblink.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"NA-pad blink events / missing data — deblink","text":"eyeris object class eyeris dervived load(). extend Either single number indicating number milliseconds pad forward/backward around missing sample, , vector length two indicating different numbers milliseconds pad forward/backward around missing sample, format c(backward, forward).","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/deblink.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"NA-pad blink events / missing data — deblink","text":"eyeris object new column: pupil_deblink.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/deblink.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"NA-pad blink events / missing data — deblink","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 40) # 40 ms in both directions } # }  system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = c(40, 50)) # 40 ms backward, 50 ms forward #> $file #> [1] \"/opt/homebrew/lib/R/4.4/site-library/eyeris/extdata/assocret.asc\" #>  #> $timeseries #> # A tibble: 22,145 × 8 #>    time_orig eye_x eye_y eye      hz type     pupil_raw pupil_raw_deblink #>        <int> <dbl> <dbl> <chr> <dbl> <chr>        <dbl>             <dbl> #>  1  11242177  949.  646. R      1000 diameter      6174              6174 #>  2  11242178  947.  644. R      1000 diameter      6176              6176 #>  3  11242179  946.  643  R      1000 diameter      6178              6178 #>  4  11242180  945.  642  R      1000 diameter      6179              6179 #>  5  11242181  945.  641. R      1000 diameter      6180              6180 #>  6  11242182  945.  642. R      1000 diameter      6182              6182 #>  7  11242183  945.  644. R      1000 diameter      6187              6187 #>  8  11242184  945.  644. R      1000 diameter      6197              6197 #>  9  11242185  945.  643. R      1000 diameter      6207              6207 #> 10  11242186  945.  642. R      1000 diameter      6203              6203 #> # ℹ 22,135 more rows #>  #> $events #> # A tibble: 67 × 3 #>    block     time text                       #>    <dbl>    <dbl> <chr>                      #>  1     1 11242177 !MODE RECORD CR 1000 2 1 R #>  2     1 11243349 EXP_START                  #>  3     1 11243355 TRIALID 0                  #>  4     1 11243356 START_TRIAL_0              #>  5     1 11243356 CUE_START_0                #>  6     1 11244328 CUE_STOP_0                 #>  7     1 11244329 DELAY_START_0              #>  8     1 11245337 DELAY_STOP_0               #>  9     1 11245338 PROBE_START_0              #> 10     1 11245956 RESPONSE_0                 #> # ℹ 57 more rows #>  #> $blinks #> # A tibble: 0 × 5 #> # ℹ 5 variables: block <int>, stime <dbl>, etime <dbl>, dur <dbl>, eye <fct> #>  #> $info #>                  date        model version sample.rate   cr  left right mono #> 1 2009-01-11 02:40:47 EyeLink 1000   4.594        1000 TRUE FALSE  TRUE TRUE #>   screen.x screen.y                                 mount filter.level #> 1     1920     1080 Desktop / Monocular / Head Stabilized            2 #>   sample.dtype event.dtype pupil.dtype velocity resolution htarg input buttons #> 1         GAZE        GAZE    DIAMETER    FALSE      FALSE FALSE FALSE   FALSE #>  #> $latest #> [1] \"pupil_raw_deblink\" #>  #> attr(,\"class\") #> [1] \"eyeris\""},{"path":"http://shawnschwartz.com/eyeris/reference/detransient.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove pupil samples that are physiologically unlikely — detransient","title":"Remove pupil samples that are physiologically unlikely — detransient","text":"intended use method removing pupil samples emerge quickly physiologically expected. accomplished rejecting samples exceed \"speed\"-based threshold (.e., median absolute deviation sample--sample). threshold computed based constant n, defaults value 16.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detransient.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove pupil samples that are physiologically unlikely — detransient","text":"","code":"detransient(eyeris, n = 16)"},{"path":"http://shawnschwartz.com/eyeris/reference/detransient.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove pupil samples that are physiologically unlikely — detransient","text":"eyeris object class eyeris dervived load(). n constant used compute median absolute deviation (MAD) threshold.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detransient.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove pupil samples that are physiologically unlikely — detransient","text":"eyeris object new column timeseries: pupil_detransient.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detransient.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove pupil samples that are physiologically unlikely — detransient","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/detrend.html","id":null,"dir":"Reference","previous_headings":"","what":"Detrend the pupil time series — detrend","title":"Detrend the pupil time series — detrend","text":"Linearly detrend_pupil data fitting linear model pupil_data ~ time, return fitted betas residuals (pupil_data - fitted_values).","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detrend.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detrend the pupil time series — detrend","text":"","code":"detrend(eyeris)"},{"path":"http://shawnschwartz.com/eyeris/reference/detrend.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detrend the pupil time series — detrend","text":"eyeris object class eyeris dervived load().","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detrend.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detrend the pupil time series — detrend","text":"eyeris object two new columns timeseries: detrend_fitted_betas, pupil_detrend.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/detrend.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Detrend the pupil time series — detrend","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() |>   eyeris::lpfilt(plot_freqz = TRUE) |>   eyeris::detrend() } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/epoch.html","id":null,"dir":"Reference","previous_headings":"","what":"Epoch (and baseline) pupil data based on custom event message structure — epoch","title":"Epoch (and baseline) pupil data based on custom event message structure — epoch","text":"Intended used final preprocessing step. function creates data epochs either fixed dynamic durations respect provided events time limits, also includes intuitive metadata parsing feature additional trial data embedded within event messages can easily identified joined resulting epoched data frames.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/epoch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Epoch (and baseline) pupil data based on custom event message structure — epoch","text":"","code":"epoch(   eyeris,   events,   limits = NULL,   label = NULL,   calc_baseline = FALSE,   apply_baseline = FALSE,   baseline_type = c(\"sub\", \"div\"),   baseline_events = NULL,   baseline_period = NULL,   hz = NULL )"},{"path":"http://shawnschwartz.com/eyeris/reference/epoch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Epoch (and baseline) pupil data based on custom event message structure — epoch","text":"eyeris object class eyeris derived load(). events Either (1) single string representing event message perform trial extraction around, using specified limits center epoch around limits (just grabs data epochs subsequent event string type); (2) vector containing start end event message strings – , limits ignored duration trial epoch number samples matched start end event message pair; (3) list 2 dataframes manually specify start/end event timestamp-message pairs pull raw timeseries data – , required raw timestamp event message provided following format: list(data.frame(time = c(...), msg = c(...)), data.frame(time = c(...), msg = c(...))) first data.frame indicates start event timestamp message string pairs, second data.frame indicates end event timestamp message string pairs. event-modes 1 2, way pass event message string must conform standardized protocol eyeris knows find events (optionally) parse included metadata tidy epoch data outputs. two primary choices: either () specify string followed * wildcard expression (e.g., \"PROBE_START*), match messages \"PROBE_START ...\" (... referring potential metadata, trial number, stim file, etc.); (b) specify string using eyeris syntax: (e.g., \"PROBE_{type}_{trial}\"), match messages follow structure like \"PROBE_START_1\" \"PROBE_STOP_1\", generate two additional metadata columns: type trial, contain following values based two example strings: type: ('START', 'STOP'), trial: (1, 1). limits vector 2 values (start, end) seconds, indicating trial extraction occur centered around given start message string events parameter. label (optional) string can provide customize name resulting eyeris class object containing epoched data frame. left NULL (default), list item called epoch_xyz, xyz sanitized version original start event string provided matching. choose specify label , resulting list object name take form: epoch_label. calc_baseline flag indicated whether perform baseline correction. Note, setting calc_baseline TRUE alone compute baseline period, apply preprocessed timeseries unless apply_baseline also set TRUE. apply_baseline flag indicating whether apply calculated baseline pupil timeseries. baseline correction applied pupil latest preprocessing step. baseline_type Whether perform subtractive (sub) divisive (div) baseline correction. Defaults sub. baseline_events Similar events, baseline_events, can supply either (1) single string representing event message center baseline calculation around, indicated baseline_period; (2) single vector containing start end event message string – , baseline_period ignored duration baseline period mean calculated number samples matched start end event message pair, opposed specified fixed duration (described 1). Please note, providing list trial-level start/end message pairs (like events parameter) manually indicate unique start/end chunks baselining currently unsupported. Though, intend add feature later version eyeris, given likely heavily utilized / demand feature. baseline_period vector 2 values (start, end) seconds, indicating window data used perform baseline correction, centered around single string \"start\" message string provided baseline_events. , baseline_period ignored \"start\" \"end\" message string provided baseline_events argument. hz Data sampling rate. specified, use value contained within tracker's metadata.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/epoch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Epoch (and baseline) pupil data based on custom event message structure — epoch","text":"Updated eyeris object dataframes containing epoched data (epoch_).","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/epoch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Epoch (and baseline) pupil data based on custom event message structure — epoch","text":"","code":"eye_preproc <- system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() |>   eyeris::lpfilt(plot_freqz = TRUE) |>   eyeris::zscore() #> Error in operation(data, prev_operation, ...): No NAs detected in pupil data for interpolation.  eye_preproc |>   eyeris::epoch(events = \"PROBE*\", limits = c(-1, 1)) #> Error in eval(expr, envir, enclos): object 'eye_preproc' not found  eye_preproc |>   eyeris::epoch(events = \"TRIALID {trial}\") # all samples between each trial #> Error in eval(expr, envir, enclos): object 'eye_preproc' not found"},{"path":"http://shawnschwartz.com/eyeris/reference/eyeris-package.html","id":null,"dir":"Reference","previous_headings":"","what":"eyeris: eyeris — eyeris-package","title":"eyeris: eyeris — eyeris-package","text":"Create Run Flexible Reproducible Pupillometry Preprocessing Pipelines (maybe one line) Use four spaces indenting paragraphs within Description.","code":""},{"path":[]},{"path":"http://shawnschwartz.com/eyeris/reference/eyeris-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"eyeris: eyeris — eyeris-package","text":"Maintainer: Shawn Tyler Schwartz stschwartz@stanford.edu (ORCID)","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/glassbox.html","id":null,"dir":"Reference","previous_headings":"","what":"A ","title":"A ","text":"glassbox function (contrast \"blackbox\" function run get result (little) idea got input output) primary benefits calling exported function eyeris separately.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/glassbox.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A ","text":"","code":"glassbox(   file,   confirm = FALSE,   detrend_data = FALSE,   num_previews = 3,   preview_duration = 5,   preview_window = NULL,   ... )"},{"path":"http://shawnschwartz.com/eyeris/reference/glassbox.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A ","text":"file SR Research EyeLink .asc file generated official EyeLink edf2asc command. confirm flag indicate whether run glassbox pipeline autonomously way (set FALSE default), interactively provide visualization pipeline step, must also indicate \"(y)es\" \"(n)o\" either proceed cancel current glassbox pipeline operation (set TRUE). detrend_data flag indicate whether run detrend step (set FALSE default). Detrending pupil timeseries can unintended consequences; thus recommend users understand implications detrending – addition whether detrending appropriate research design question(s) – using function. num_previews Number random example \"epochs\" generate previewing effect preprocessing step pupil timeseries. preview_duration Time seconds randomly selected preview. preview_window start stop raw timestamps used subset preprocessed data step eyeris workflow visualization. Defaults NULL, meaning random epochs defined num_previews preview_duration plotted. override random epochs, set preview_window vector relative start stop times (e.g., c(5000, 6000) indicate raw data 5-6 seconds data recorded 1000 Hz). Note, start/stop time values indicated relate raw index position pupil sample 1 n (need specified manually user depending sampling rate recording; .e., 5000-6000 epoch positioned 5-6 seconds start timeseries, sampled 1000 Hz). ... Additional arguments override default, prescribed settings.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/glassbox.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A ","text":"First, glassbox function provides highly opinionated prescription steps starting parameters believe pupillometry researcher use defaults preprocessing pupillometry data. Second, mutually exclusive first point, using function ideally reduce probability accidental mishaps \"reimplementing\" steps preprocessing pipeline within across projects. hope streamline process way collect pupillometry dataset within minutes assess quality data simultaneously running full preprocessing pipeline 1-ish line code! Third, glassbox provides \"interactive\" framework can evaluate consequences parameters within step data real time, facilitating fairly easy--use workflow parameter optimization particular dataset. process essentially takes opinionated steps provides pre-/post-plot timeseries data step can adjust parameters re-run pipeline satisfied choices paramters consequences pupil timeseries data.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/glassbox.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A ","text":"","code":"if (FALSE) { # \\dontrun{ demo_data <- system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\")  # (1) examples using the default prescribed parameters and pipeline recipe ## (a) run an automated pipeline with no real-time inspection of parameters output <- eyeris::glassbox(demo_data)  ## (b) run a interactive workflow (with confirmation prompts after each step) output <- eyeris::glassbox(demo_data, confirm = TRUE)  # (2) examples overriding the default parameters output <- eyeris::glassbox(demo_data,   confirm = TRUE,   deblink = list(extend = 40),   lpfilt = list(plot_freqz = FALSE) ) } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/interpolate.html","id":null,"dir":"Reference","previous_headings":"","what":"Interpolate missing pupil samples — interpolate","title":"Interpolate missing pupil samples — interpolate","text":"Linear interpolation time series data. intended use method filling missing pupil samples (NAs) time series. method uses \"na.approx()\" function zoo package, implements linear interpolation using \"approx()\" function stats package. Currently, NAs beginning end data replaced values either end, respectively, using \"rule = 2\" argument approx() function.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/interpolate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Interpolate missing pupil samples — interpolate","text":"","code":"interpolate(eyeris)"},{"path":"http://shawnschwartz.com/eyeris/reference/interpolate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Interpolate missing pupil samples — interpolate","text":"eyeris object class eyeris dervived load().","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/interpolate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Interpolate missing pupil samples — interpolate","text":"eyeris object new column timeseries: pupil_interpolate.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/interpolate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Interpolate missing pupil samples — interpolate","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/load_asc.html","id":null,"dir":"Reference","previous_headings":"","what":"Load and parse SR Research EyeLink .asc files — load_asc","title":"Load and parse SR Research EyeLink .asc files — load_asc","text":"function builds upon eyelinker::read.asc() function parse messages metadata within EyeLink .asc file. loading additional processing, function returns S3 eyeris class use subsequent eyeris pipeline steps functions.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/load_asc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load and parse SR Research EyeLink .asc files — load_asc","text":"","code":"load_asc(file)"},{"path":"http://shawnschwartz.com/eyeris/reference/load_asc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load and parse SR Research EyeLink .asc files — load_asc","text":"file SR Research EyeLink .asc file generated official EyeLink edf2asc command.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/load_asc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load and parse SR Research EyeLink .asc files — load_asc","text":"object S3 class eyeris following attributes: file: Path original .asc file. timeseries: Dataframe raw timeseries data tracker. events: Dataframe event messages timestamps. blinks: Dataframe blink events. info: Dataframe various metadata parsed file header. latest: eyeris variable tracking pipeline run history.","code":""},{"path":[]},{"path":"http://shawnschwartz.com/eyeris/reference/load_asc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load and parse SR Research EyeLink .asc files — load_asc","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/lpfilt.html","id":null,"dir":"Reference","previous_headings":"","what":"Lowpass filtering of time series data — lpfilt","title":"Lowpass filtering of time series data — lpfilt","text":"intended use method smoothing, although specifying wp ws differently one can achieve highpass bandpass filtering well. However, lowpass filtering done pupillometry data.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/lpfilt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lowpass filtering of time series data — lpfilt","text":"","code":"lpfilt(eyeris, wp = 4, ws = 8, rp = 1, rs = 35, plot_freqz = FALSE)"},{"path":"http://shawnschwartz.com/eyeris/reference/lpfilt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lowpass filtering of time series data — lpfilt","text":"eyeris object class eyeris derived load(). wp end passband frequency Hz (desired lowpass cutoff). ws start stopband frequency Hz (required lowpass cutoff). rp Required maximal ripple within passband dB. rs Required minimal attenuation within stopband dB. plot_freqz Boolean flag displaying filter frequency response.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/lpfilt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lowpass filtering of time series data — lpfilt","text":"eyeris object new column timeseries: pupil_lpfilt.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/lpfilt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lowpass filtering of time series data — lpfilt","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() |>   eyeris::lpfilt(plot_freqz = TRUE) } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/plot.eyeris.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot pre-processed pupil data from eyeris — plot.eyeris","title":"Plot pre-processed pupil data from eyeris — plot.eyeris","text":"S3 plotting method objects class eyeris. Plots single-panel timeseries subset pupil timeseries preprocessing step. intended use function provide simple method qualitatively assessing consequences preprocessing recipe parameters raw pupillary signal.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/plot.eyeris.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot pre-processed pupil data from eyeris — plot.eyeris","text":"","code":"# S3 method for class 'eyeris' plot(   x,   ...,   steps = NULL,   num_previews = NULL,   preview_duration = NULL,   preview_window = NULL,   seed = NULL )"},{"path":"http://shawnschwartz.com/eyeris/reference/plot.eyeris.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot pre-processed pupil data from eyeris — plot.eyeris","text":"x object class eyeris derived load(). ... Additional arguments passed plot. steps steps plot; defaults (.e., plot steps). Otherwise, pass vector containing index step(s) want plot, index 1 original raw pupil timeseries. num_previews Number random example \"epochs\" generate previewing effect preprocessing step pupil timeseries. preview_duration Time seconds randomly selected preview. preview_window start stop raw timestamps used subset preprocessed data step eyeris workflow visualization. Defaults NULL, meaning random epochs defined num_examples example_duration plotted. override random epochs, set example_timelim vector relative start stop times (e.g., c(5000, 6000) indicate raw data 5-6 seconds data recorded 1000 Hz). Note, start/stop time values indicated relate raw index position pupil sample 1 n (need specified manually user depending sampling rate recording; .e., 5000-6000 epoch positioned 5-6 seconds start timeseries, sampled 1000 Hz). seed Random seed current plotting session. Leave NULL select num_previews number random preview \"epochs\" (preview_duration) time. Otherwise, choose seed-integer normally select base::set.seed(), able continue re-plotting random example pupil epochs time – helpful adjusting parameters within across eyeris workflow steps.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/plot.eyeris.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot pre-processed pupil data from eyeris — plot.eyeris","text":"return value; iteratively plots subset pupil timeseries preprocessing step run.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/plot.eyeris.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot pre-processed pupil data from eyeris — plot.eyeris","text":"","code":"if (FALSE) { # \\dontrun{ # using the default 10000 to 20000 ms time subset plot(eyeris_data)  # using a custom time subset (i.e., 1 to 500 ms) plot(eyeris_data, preview_window = c(1, 500)) } # }"},{"path":"http://shawnschwartz.com/eyeris/reference/sticker.html","id":null,"dir":"Reference","previous_headings":"","what":"eyeris package logo (hexagon sticker) — sticker","title":"eyeris package logo (hexagon sticker) — sticker","text":"eyeris package logo (hexagon sticker)","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/sticker.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"eyeris package logo (hexagon sticker) — sticker","text":"","code":"sticker"},{"path":"http://shawnschwartz.com/eyeris/reference/sticker.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"eyeris package logo (hexagon sticker) — sticker","text":"png image file rendered README html reports.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":null,"dir":"Reference","previous_headings":"","what":"Z-Score pupil timeseries data — zscore","title":"Z-Score pupil timeseries data — zscore","text":"intended use method scale arbitrary units pupil size timeseries mean 0 standard deviation 1. accomplished mean centering data points dividing standard deviation (.e., z-scoring data, similar base::scale()). Z-scoring pupil data helpful trial-level -subjects analyses arbitrary units pupil size recorded tracker scale across participants, therefore make analyses depend data one participant difficult interpret.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Z-Score pupil timeseries data — zscore","text":"","code":"zscore(eyeris)"},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Z-Score pupil timeseries data — zscore","text":"eyeris object class eyeris dervived load().","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Z-Score pupil timeseries data — zscore","text":"numeric vector giving number characters (code points) element character vector. Missing string missing length.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Z-Score pupil timeseries data — zscore","text":"general, common z-score pupil data within given participant, furthermore, z-score participant's data function block number (tasks/experiments participants complete one block trials) account potential time--task effects across task/experiment blocks. , use eyeris package intended, need specify groups participant/block-level situations described . eyeris designed preprocess single block pupil data single participant, one time. Therefore, later merge preprocessed data eyeris, individual, preprocessed block data participant already independently scaled others. Additionally, intend compare mean z-scored pupil size across task conditions, memory successes vs. memory failures, set behavioral outcome (.e., success/failure) variable grouping variable within analysis. , consequently obtain mean pupil size 0 standard deviation 1 within group (since scaled pupil size calculated timeseries outcome variable group, separately). Instead, compute z-score entire pupil timeseries (epoching data), split take mean z-scored timeseries function condition variable.","code":""},{"path":"http://shawnschwartz.com/eyeris/reference/zscore.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Z-Score pupil timeseries data — zscore","text":"","code":"if (FALSE) { # \\dontrun{ system.file(\"extdata\", \"assocret.asc\", package = \"eyeris\") |>   eyeris::load_asc() |>   eyeris::deblink(extend = 50) |>   eyeris::detransient() |>   eyeris::interpolate() |>   eyeris::lpfilt(plot_freqz = TRUE) |>   eyeris::zscore() } # }"}]
diff --git a/man/epoch.Rd b/man/epoch.Rd
index 120dc71..c9abf70 100644
--- a/man/epoch.Rd
+++ b/man/epoch.Rd
@@ -109,7 +109,6 @@ feature where additional trial data embedded within event messages can easily
 be identified and joined into the resulting epoched data frames.
 }
 \examples{
-\dontrun{
 eye_preproc <- system.file("extdata", "assocret.asc", package = "eyeris") |>
   eyeris::load_asc() |>
   eyeris::deblink(extend = 50) |>
@@ -124,75 +123,4 @@ eye_preproc |>
 eye_preproc |>
   eyeris::epoch(events = "TRIALID {trial}") # all samples between each trial
 
-eye_preproc |>
-  eyeris::epoch(
-    events = "PROBE_START_{trial}",
-    limits = c(0, 1) # grab the 1 second following probe onset
-  )
-
-eye_preproc |>
-  eyeris::epoch(
-    events = "PROBE_START_{trial}",
-    limits = c(-2, 1), # 2 seconds prior to and 1 second after probe onset
-    label = "prePostProbe" # custom epoch label name
-  )
-
-# here, the `msg` column of each data frame is optional
-eye_prepoc |>
-  eyeris::epoch(
-    events = list(
-      data.frame(time = c(11243355), msg = c("TRIALID 0")), # start events
-      data.frame(time = c(11245956), msg = c("RESPONSE_0")) # end events
-    )
-  )
-
-# note: set `msg` to NA if you only want to pass in start/end timestamps
-eye_preproc |>
-  eyeris::epoch(
-    events = list(
-      data.frame(time = c(11243355), msg = NA), # start events
-      data.frame(time = c(11245956), msg = NA) # end events
-    )
-  )
-
-# examples with baseline arguments enabled
-
-# example 1: use mean of 1-s preceding "PROBE_START" (i.e. "DELAY_STOP")
-to perform subtractive baselining of the 1-s PROBE epochs.
-eye_preproc |>
-  eyeris::epoch(
-    events = "PROBE_START_{trial}",
-    limits = c(0, 1), # grab 0 seconds prior to and 1 second post PROBE event
-    label = "prePostProbe", # custom epoch label name
-    calc_baseline = TRUE,
-    apply_baseline = TRUE,
-    baseline_type = "sub", # "sub"tractive baseline calculation is default
-    baseline_events = "DELAY_STOP_*",
-    baseline_period = c(-1, 0)
-  )
-
-# example 2: use mean of time period between set start/end event messages
-(i.e. between "DELAY_START" and "DELAY_STOP"). In this case, the
-`baseline_period` argument will be ignored since both a "start" and "end"
-message string are provided to the `baseline_events` argument.
-eye_preproc |>
-  eyeris::epoch(
-    events = "PROBE_START_{trial}",
-    limits = c(0, 1), # grab 0 seconds prior to and 1 second post PROBE event
-    label = "prePostProbe", # custom epoch label name
-    calc_baseline = TRUE,
-    apply_baseline = TRUE,
-    baseline_type = "sub", # "sub"tractive baseline calculation is default
-    baseline_events = c("DELAY_START_*",
-                        "DELAY_STOP_*")
-  )
-
-# additional (potentially helpful) example
- start_events <- data.frame(time = c(11243355, 11247588),
-                            msg = c("TRIALID 0", "TRIALID 1"))
- end_events <- data.frame(time = c(11245956, 11250506),
-                          msg = c("RESPONSE_0", "RESPONSE_1"))
- eye_prepoc |>
-  eyeris::epoch(events = list(start_events, end_events))
-}
 }
diff --git a/man/eyeris-package.Rd b/man/eyeris-package.Rd
index 68245e0..7093cba 100644
--- a/man/eyeris-package.Rd
+++ b/man/eyeris-package.Rd
@@ -4,19 +4,22 @@
 \name{eyeris-package}
 \alias{eyeris}
 \alias{eyeris-package}
-\title{eyeris: Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines}
+\title{eyeris: eyeris}
 \description{
-More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
+\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}}
+
+Create and Run Flexible and Reproducible Pupillometry Preprocessing Pipelines More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
 }
 \seealso{
 Useful links:
 \itemize{
-  \item \url{http://shawnschwartz.com/eyeris/}
+  \item \url{http://shawnschwartz.com/eyeris}
+  \item Report bugs at \url{https://github.com/shawntz/eyeris/issues}
 }
 
 }
 \author{
-\strong{Maintainer}: Shawn Schwartz \email{stschwartz@stanford.edu} (\href{https://orcid.org/0000-0001-6444-8451}{ORCID})
+\strong{Maintainer}: Shawn T. Schwartz \email{stschwartz@stanford.edu} (\href{https://orcid.org/0000-0001-6444-8451}{ORCID})
 
 }
 \keyword{internal}