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<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">Confusion about spread_draws</h1>
</div>
<div class="quarto-title-meta">
</div>
</header>
<section id="load-data" class="level2">
<h2 class="anchored" data-anchor-id="load-data">Load data</h2>
<div class="cell">
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(brms)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stderr">
<pre><code>Loading required package: Rcpp</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Loading 'brms' package (version 2.20.15). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>
Attaching package: 'brms'</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>The following object is masked from 'package:stats':
ar</code></pre>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stderr">
<pre><code>── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.5
✔ forcats 1.0.0 ✔ stringr 1.5.1
✔ ggplot2 3.5.0 ✔ tibble 3.2.1
✔ lubridate 1.9.3 ✔ tidyr 1.3.1
✔ purrr 1.0.2 </code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors</code></pre>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidybayes)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stderr">
<pre><code>
Attaching package: 'tidybayes'
The following objects are masked from 'package:brms':
dstudent_t, pstudent_t, qstudent_t, rstudent_t</code></pre>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>data_long_summarised <span class="ot">=</span> <span class="fu">readRDS</span>(<span class="at">file =</span> <span class="fu">file.path</span>(<span class="st">"data"</span>,<span class="st">"osf_hedge_cwzds"</span>,<span class="st">"data_long_summarised.Rds"</span>))</span>
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a>data_long_summarised</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 428 × 7
pps session condition n n_correct n_go condition_contrast
<dbl> <int> <int> <int> <int> <dbl> <dbl>
1 1 1 0 450 450 449 0.5
2 1 1 2 150 88 62 -0.5
3 1 2 0 450 448 448 0.5
4 1 2 2 150 59 91 -0.5
5 2 1 0 450 450 449 0.5
6 2 1 2 150 109 41 -0.5
7 2 2 0 450 450 449 0.5
8 2 2 2 150 87 63 -0.5
9 3 1 0 450 450 449 0.5
10 3 1 2 150 118 32 -0.5
# ℹ 418 more rows</code></pre>
</div>
</div>
</section>
<section id="fit-model" class="level2">
<h2 class="anchored" data-anchor-id="fit-model">Fit model</h2>
<div class="cell">
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>model_time_1 <span class="ot">=</span> brms<span class="sc">::</span><span class="fu">brm</span>(</span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a> n_go <span class="sc">|</span> <span class="fu">trials</span>(n) <span class="sc">~</span> <span class="dv">1</span> <span class="sc">+</span> condition_contrast <span class="sc">+</span> (<span class="dv">1</span> <span class="sc">+</span> condition_contrast <span class="sc">|</span> pps),</span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a> <span class="co"># family = binomial(link = "probit"),</span></span>
<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a> <span class="at">family =</span> <span class="fu">binomial</span>(<span class="at">link =</span> <span class="st">"logit"</span>),</span>
<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> <span class="fu">filter</span>(data_long_summarised, session <span class="sc">==</span> <span class="dv">1</span> ),</span>
<span id="cb13-6"><a href="#cb13-6" aria-hidden="true" tabindex="-1"></a> <span class="at">cores =</span> <span class="dv">2</span>,</span>
<span id="cb13-7"><a href="#cb13-7" aria-hidden="true" tabindex="-1"></a> <span class="at">chains =</span> <span class="dv">2</span>,</span>
<span id="cb13-8"><a href="#cb13-8" aria-hidden="true" tabindex="-1"></a> <span class="at">iter =</span> <span class="dv">10000</span>,</span>
<span id="cb13-9"><a href="#cb13-9" aria-hidden="true" tabindex="-1"></a> <span class="co"># init = .01,</span></span>
<span id="cb13-10"><a href="#cb13-10" aria-hidden="true" tabindex="-1"></a> <span class="at">adapt_delta =</span> .<span class="dv">95</span>,</span>
<span id="cb13-11"><a href="#cb13-11" aria-hidden="true" tabindex="-1"></a> <span class="at">backend =</span> <span class="st">"cmdstanr"</span>,</span>
<span id="cb13-12"><a href="#cb13-12" aria-hidden="true" tabindex="-1"></a> <span class="at">threads =</span> <span class="fu">threading</span>(<span class="dv">4</span>),</span>
<span id="cb13-13"><a href="#cb13-13" aria-hidden="true" tabindex="-1"></a> <span class="at">save_warmup =</span> <span class="cn">FALSE</span>,</span>
<span id="cb13-14"><a href="#cb13-14" aria-hidden="true" tabindex="-1"></a> <span class="at">refresh =</span> <span class="dv">2000</span></span>
<span id="cb13-15"><a href="#cb13-15" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stderr">
<pre><code>Start sampling</code></pre>
</div>
<div class="cell-output cell-output-stdout">
<pre><code>Running MCMC with 2 parallel chains, with 4 thread(s) per chain...
Chain 1 Iteration: 1 / 10000 [ 0%] (Warmup)
Chain 2 Iteration: 1 / 10000 [ 0%] (Warmup)
Chain 2 Iteration: 2000 / 10000 [ 20%] (Warmup)
Chain 1 Iteration: 2000 / 10000 [ 20%] (Warmup)
Chain 1 Iteration: 4000 / 10000 [ 40%] (Warmup)
Chain 2 Iteration: 4000 / 10000 [ 40%] (Warmup)
Chain 1 Iteration: 5001 / 10000 [ 50%] (Sampling)
Chain 2 Iteration: 5001 / 10000 [ 50%] (Sampling)
Chain 2 Iteration: 7000 / 10000 [ 70%] (Sampling)
Chain 1 Iteration: 7000 / 10000 [ 70%] (Sampling)
Chain 2 Iteration: 9000 / 10000 [ 90%] (Sampling)
Chain 1 Iteration: 9000 / 10000 [ 90%] (Sampling)
Chain 2 Iteration: 10000 / 10000 [100%] (Sampling)
Chain 2 finished in 16.7 seconds.
Chain 1 Iteration: 10000 / 10000 [100%] (Sampling)
Chain 1 finished in 17.9 seconds.
Both chains finished successfully.
Mean chain execution time: 17.3 seconds.
Total execution time: 18.0 seconds.</code></pre>
</div>
</div>
</section>
<section id="model-output" class="level2">
<h2 class="anchored" data-anchor-id="model-output">Model Output</h2>
<div class="cell">
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb16"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>model_time_1</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code> Family: binomial
Links: mu = logit
Formula: n_go | trials(n) ~ 1 + condition_contrast + (1 + condition_contrast | pps)
Data: filter(data_long_summarised, session == 1) (Number of observations: 214)
Draws: 2 chains, each with iter = 10000; warmup = 5000; thin = 1;
total post-warmup draws = 10000
Multilevel Hyperparameters:
~pps (Number of levels: 107)
Estimate Est.Error l-95% CI u-95% CI Rhat
sd(Intercept) 0.58 0.05 0.49 0.68 1.00
sd(condition_contrast) 1.73 0.14 1.48 2.03 1.00
cor(Intercept,condition_contrast) 0.46 0.09 0.27 0.63 1.00
Bulk_ESS Tail_ESS
sd(Intercept) 2247 3730
sd(condition_contrast) 1231 2756
cor(Intercept,condition_contrast) 891 2334
Regression Coefficients:
Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
Intercept 1.76 0.07 1.63 1.89 1.00 2220 3740
condition_contrast 6.58 0.18 6.21 6.94 1.00 1517 2842
Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
and Tail_ESS are effective sample size measures, and Rhat is the potential
scale reduction factor on split chains (at convergence, Rhat = 1).</code></pre>
</div>
</div>
<div class="cell">
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb18"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a>tidybayes<span class="sc">::</span><span class="fu">get_variables</span>(model_time_1)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code> [1] "b_Intercept"
[2] "b_condition_contrast"
[3] "sd_pps__Intercept"
[4] "sd_pps__condition_contrast"
[5] "cor_pps__Intercept__condition_contrast"
[6] "Intercept"
[7] "r_pps[1,Intercept]"
[8] "r_pps[2,Intercept]"
[9] "r_pps[3,Intercept]"
[10] "r_pps[4,Intercept]"
[11] "r_pps[5,Intercept]"
[12] "r_pps[7,Intercept]"
[13] "r_pps[8,Intercept]"
[14] "r_pps[9,Intercept]"
[15] "r_pps[10,Intercept]"
[16] "r_pps[11,Intercept]"
[17] "r_pps[12,Intercept]"
[18] "r_pps[13,Intercept]"
[19] "r_pps[14,Intercept]"
[20] "r_pps[15,Intercept]"
[21] "r_pps[16,Intercept]"
[22] "r_pps[18,Intercept]"
[23] "r_pps[19,Intercept]"
[24] "r_pps[20,Intercept]"
[25] "r_pps[21,Intercept]"
[26] "r_pps[22,Intercept]"
[27] "r_pps[23,Intercept]"
[28] "r_pps[24,Intercept]"
[29] "r_pps[25,Intercept]"
[30] "r_pps[26,Intercept]"
[31] "r_pps[27,Intercept]"
[32] "r_pps[28,Intercept]"
[33] "r_pps[29,Intercept]"
[34] "r_pps[30,Intercept]"
[35] "r_pps[31,Intercept]"
[36] "r_pps[32,Intercept]"
[37] "r_pps[33,Intercept]"
[38] "r_pps[34,Intercept]"
[39] "r_pps[35,Intercept]"
[40] "r_pps[36,Intercept]"
[41] "r_pps[38,Intercept]"
[42] "r_pps[39,Intercept]"
[43] "r_pps[40,Intercept]"
[44] "r_pps[41,Intercept]"
[45] "r_pps[42,Intercept]"
[46] "r_pps[43,Intercept]"
[47] "r_pps[44,Intercept]"
[48] "r_pps[45,Intercept]"
[49] "r_pps[46,Intercept]"
[50] "r_pps[47,Intercept]"
[51] "r_pps[48,Intercept]"
[52] "r_pps[49,Intercept]"
[53] "r_pps[50,Intercept]"
[54] "r_pps[1001,Intercept]"
[55] "r_pps[1002,Intercept]"
[56] "r_pps[1003,Intercept]"
[57] "r_pps[1004,Intercept]"
[58] "r_pps[1005,Intercept]"
[59] "r_pps[1006,Intercept]"
[60] "r_pps[1007,Intercept]"
[61] "r_pps[1008,Intercept]"
[62] "r_pps[1009,Intercept]"
[63] "r_pps[1010,Intercept]"
[64] "r_pps[1011,Intercept]"
[65] "r_pps[1012,Intercept]"
[66] "r_pps[1013,Intercept]"
[67] "r_pps[1014,Intercept]"
[68] "r_pps[1015,Intercept]"
[69] "r_pps[1016,Intercept]"
[70] "r_pps[1017,Intercept]"
[71] "r_pps[1018,Intercept]"
[72] "r_pps[1019,Intercept]"
[73] "r_pps[1020,Intercept]"
[74] "r_pps[1021,Intercept]"
[75] "r_pps[1022,Intercept]"
[76] "r_pps[1023,Intercept]"
[77] "r_pps[1024,Intercept]"
[78] "r_pps[1025,Intercept]"
[79] "r_pps[1026,Intercept]"
[80] "r_pps[1027,Intercept]"
[81] "r_pps[1029,Intercept]"
[82] "r_pps[1030,Intercept]"
[83] "r_pps[1031,Intercept]"
[84] "r_pps[1032,Intercept]"
[85] "r_pps[1033,Intercept]"
[86] "r_pps[1034,Intercept]"
[87] "r_pps[1035,Intercept]"
[88] "r_pps[1036,Intercept]"
[89] "r_pps[1037,Intercept]"
[90] "r_pps[1038,Intercept]"
[91] "r_pps[1039,Intercept]"
[92] "r_pps[1040,Intercept]"
[93] "r_pps[1041,Intercept]"
[94] "r_pps[1042,Intercept]"
[95] "r_pps[1043,Intercept]"
[96] "r_pps[1044,Intercept]"
[97] "r_pps[1045,Intercept]"
[98] "r_pps[1046,Intercept]"
[99] "r_pps[1047,Intercept]"
[100] "r_pps[1048,Intercept]"
[101] "r_pps[1049,Intercept]"
[102] "r_pps[1050,Intercept]"
[103] "r_pps[1051,Intercept]"
[104] "r_pps[1052,Intercept]"
[105] "r_pps[1053,Intercept]"
[106] "r_pps[1054,Intercept]"
[107] "r_pps[1055,Intercept]"
[108] "r_pps[1057,Intercept]"
[109] "r_pps[1058,Intercept]"
[110] "r_pps[1059,Intercept]"
[111] "r_pps[1060,Intercept]"
[112] "r_pps[1061,Intercept]"
[113] "r_pps[1062,Intercept]"
[114] "r_pps[1,condition_contrast]"
[115] "r_pps[2,condition_contrast]"
[116] "r_pps[3,condition_contrast]"
[117] "r_pps[4,condition_contrast]"
[118] "r_pps[5,condition_contrast]"
[119] "r_pps[7,condition_contrast]"
[120] "r_pps[8,condition_contrast]"
[121] "r_pps[9,condition_contrast]"
[122] "r_pps[10,condition_contrast]"
[123] "r_pps[11,condition_contrast]"
[124] "r_pps[12,condition_contrast]"
[125] "r_pps[13,condition_contrast]"
[126] "r_pps[14,condition_contrast]"
[127] "r_pps[15,condition_contrast]"
[128] "r_pps[16,condition_contrast]"
[129] "r_pps[18,condition_contrast]"
[130] "r_pps[19,condition_contrast]"
[131] "r_pps[20,condition_contrast]"
[132] "r_pps[21,condition_contrast]"
[133] "r_pps[22,condition_contrast]"
[134] "r_pps[23,condition_contrast]"
[135] "r_pps[24,condition_contrast]"
[136] "r_pps[25,condition_contrast]"
[137] "r_pps[26,condition_contrast]"
[138] "r_pps[27,condition_contrast]"
[139] "r_pps[28,condition_contrast]"
[140] "r_pps[29,condition_contrast]"
[141] "r_pps[30,condition_contrast]"
[142] "r_pps[31,condition_contrast]"
[143] "r_pps[32,condition_contrast]"
[144] "r_pps[33,condition_contrast]"
[145] "r_pps[34,condition_contrast]"
[146] "r_pps[35,condition_contrast]"
[147] "r_pps[36,condition_contrast]"
[148] "r_pps[38,condition_contrast]"
[149] "r_pps[39,condition_contrast]"
[150] "r_pps[40,condition_contrast]"
[151] "r_pps[41,condition_contrast]"
[152] "r_pps[42,condition_contrast]"
[153] "r_pps[43,condition_contrast]"
[154] "r_pps[44,condition_contrast]"
[155] "r_pps[45,condition_contrast]"
[156] "r_pps[46,condition_contrast]"
[157] "r_pps[47,condition_contrast]"
[158] "r_pps[48,condition_contrast]"
[159] "r_pps[49,condition_contrast]"
[160] "r_pps[50,condition_contrast]"
[161] "r_pps[1001,condition_contrast]"
[162] "r_pps[1002,condition_contrast]"
[163] "r_pps[1003,condition_contrast]"
[164] "r_pps[1004,condition_contrast]"
[165] "r_pps[1005,condition_contrast]"
[166] "r_pps[1006,condition_contrast]"
[167] "r_pps[1007,condition_contrast]"
[168] "r_pps[1008,condition_contrast]"
[169] "r_pps[1009,condition_contrast]"
[170] "r_pps[1010,condition_contrast]"
[171] "r_pps[1011,condition_contrast]"
[172] "r_pps[1012,condition_contrast]"
[173] "r_pps[1013,condition_contrast]"
[174] "r_pps[1014,condition_contrast]"
[175] "r_pps[1015,condition_contrast]"
[176] "r_pps[1016,condition_contrast]"
[177] "r_pps[1017,condition_contrast]"
[178] "r_pps[1018,condition_contrast]"
[179] "r_pps[1019,condition_contrast]"
[180] "r_pps[1020,condition_contrast]"
[181] "r_pps[1021,condition_contrast]"
[182] "r_pps[1022,condition_contrast]"
[183] "r_pps[1023,condition_contrast]"
[184] "r_pps[1024,condition_contrast]"
[185] "r_pps[1025,condition_contrast]"
[186] "r_pps[1026,condition_contrast]"
[187] "r_pps[1027,condition_contrast]"
[188] "r_pps[1029,condition_contrast]"
[189] "r_pps[1030,condition_contrast]"
[190] "r_pps[1031,condition_contrast]"
[191] "r_pps[1032,condition_contrast]"
[192] "r_pps[1033,condition_contrast]"
[193] "r_pps[1034,condition_contrast]"
[194] "r_pps[1035,condition_contrast]"
[195] "r_pps[1036,condition_contrast]"
[196] "r_pps[1037,condition_contrast]"
[197] "r_pps[1038,condition_contrast]"
[198] "r_pps[1039,condition_contrast]"
[199] "r_pps[1040,condition_contrast]"
[200] "r_pps[1041,condition_contrast]"
[201] "r_pps[1042,condition_contrast]"
[202] "r_pps[1043,condition_contrast]"
[203] "r_pps[1044,condition_contrast]"
[204] "r_pps[1045,condition_contrast]"
[205] "r_pps[1046,condition_contrast]"
[206] "r_pps[1047,condition_contrast]"
[207] "r_pps[1048,condition_contrast]"
[208] "r_pps[1049,condition_contrast]"
[209] "r_pps[1050,condition_contrast]"
[210] "r_pps[1051,condition_contrast]"
[211] "r_pps[1052,condition_contrast]"
[212] "r_pps[1053,condition_contrast]"
[213] "r_pps[1054,condition_contrast]"
[214] "r_pps[1055,condition_contrast]"
[215] "r_pps[1057,condition_contrast]"
[216] "r_pps[1058,condition_contrast]"
[217] "r_pps[1059,condition_contrast]"
[218] "r_pps[1060,condition_contrast]"
[219] "r_pps[1061,condition_contrast]"
[220] "r_pps[1062,condition_contrast]"
[221] "lprior"
[222] "lp__"
[223] "accept_stat__"
[224] "treedepth__"
[225] "stepsize__"
[226] "divergent__"
[227] "n_leapfrog__"
[228] "energy__" </code></pre>
</div>
</div>
</section>
<section id="extract-draws-using-spread_draws" class="level2">
<h2 class="anchored" data-anchor-id="extract-draws-using-spread_draws">Extract draws using spread_draws</h2>
<p>spread_draws to get posterior draws for participant 1 on the condition_contrast coefficient.</p>
<p>Weirdly, its giving me 20,000 draws for each participant. I don’t understand this as</p>
<div class="cell">
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb20"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a>subj_draws_time_1 <span class="ot">=</span> model_time_1 <span class="sc">%>%</span></span>
<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a> tidybayes<span class="sc">::</span><span class="fu">spread_draws</span>(r_pps[pps,condition_contrast]) </span>
<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb20-4"><a href="#cb20-4" aria-hidden="true" tabindex="-1"></a>subj_draws_time_1<span class="sc">$</span>pps <span class="sc">%>%</span> <span class="fu">table</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>.
1 2 3 4 5 7 8 9 10 11 12 13 14
20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000
15 16 18 19 20 21 22 23 24 25 26 27 28
20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000
29 30 31 32 33 34 35 36 38 39 40 41 42
20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000
43 44 45 46 47 48 49 50 1001 1002 1003 1004 1005
20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000
1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018
20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000
1019 1020 1021 1022 1023 1024 1025 1026 1027 1029 1030 1031 1032
20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000
1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045
20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000
1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1057 1058 1059
20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000 20000
1060 1061 1062
20000 20000 20000 </code></pre>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb22"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a>pps_1_draws <span class="ot">=</span> model_time_1 <span class="sc">%>%</span></span>
<span id="cb22-2"><a href="#cb22-2" aria-hidden="true" tabindex="-1"></a> tidybayes<span class="sc">::</span><span class="fu">spread_draws</span>(r_pps[pps,condition_contrast]) <span class="sc">%>%</span></span>
<span id="cb22-3"><a href="#cb22-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(pps <span class="sc">==</span> <span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
</section>
<section id="brms-to-get-same-posterior-draws" class="level2">
<h2 class="anchored" data-anchor-id="brms-to-get-same-posterior-draws">brms to get same posterior draws</h2>
<div class="cell">
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb23"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a>subj_draws_time_1_brms <span class="ot">=</span> <span class="fu">as_draws_df</span>(model_time_1) <span class="sc">%>%</span></span>
<span id="cb23-2"><a href="#cb23-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(<span class="fu">ends_with</span>(<span class="st">"condition_contrast]"</span>)) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Dropping 'draws_df' class as required metadata was removed.</code></pre>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb25"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a>pps_1_draws_brms <span class="ot">=</span> subj_draws_time_1_brms<span class="sc">$</span><span class="st">`</span><span class="at">r_pps[1,condition_contrast]</span><span class="st">`</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
</section>
<section id="comparison" class="level2">
<h2 class="anchored" data-anchor-id="comparison">Comparison</h2>
<p>In both cases i want to analyse the posterior distribution for participant 1.</p>
<p>The first 10,000 draws from pps_1_draws (spread_draws output) match up to the brms output, but the second 10,000 draws look very different.</p>
<div class="cell">
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb26"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a><span class="fu">hist</span>(pps_1_draws_brms)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="99_spreaddraws_confusion_files/figure-html/unnamed-chunk-7-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb27"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="fu">hist</span>(pps_1_draws<span class="sc">$</span>r_pps[<span class="dv">1</span><span class="sc">:</span><span class="dv">10000</span>])</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="99_spreaddraws_confusion_files/figure-html/unnamed-chunk-7-2.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb28"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a><span class="fu">hist</span>(pps_1_draws<span class="sc">$</span>r_pps[<span class="dv">10001</span><span class="sc">:</span><span class="dv">20000</span>])</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="99_spreaddraws_confusion_files/figure-html/unnamed-chunk-7-3.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb29"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb29-1"><a href="#cb29-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mean</span>(pps_1_draws_brms)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>[1] -0.5908408</code></pre>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb31"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb31-1"><a href="#cb31-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mean</span>(pps_1_draws<span class="sc">$</span>r_pps[<span class="dv">1</span><span class="sc">:</span><span class="dv">10000</span>])</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>[1] -0.5908408</code></pre>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb33"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb33-1"><a href="#cb33-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mean</span>(pps_1_draws<span class="sc">$</span>r_pps[<span class="dv">10001</span><span class="sc">:</span><span class="dv">20000</span>])</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 0.8137379</code></pre>
</div>
</div>
<p>I’ve checked and its not the case that the first 10,000 draws are from chain 1:</p>
<div class="cell">
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb35"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb35-1"><a href="#cb35-1" aria-hidden="true" tabindex="-1"></a><span class="fu">table</span>(pps_1_draws<span class="sc">$</span>.chain[<span class="dv">1</span><span class="sc">:</span><span class="dv">10000</span>])</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>
1 2
5000 5000 </code></pre>
</div>
</div>
<p>Anyway, I’m a little confused if there’s something i’ve done wrong here or if there’s been a strange interaction with brms here.</p>
<p>My setup:</p>
<div class="cell">
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb37"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb37-1"><a href="#cb37-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tidybayes_3.0.6 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[5] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1
[9] tibble_3.2.1 ggplot2_3.5.0 tidyverse_2.0.0 brms_2.20.15
[13] Rcpp_1.0.12
loaded via a namespace (and not attached):
[1] svUnit_1.0.6 tidyselect_1.2.0 loo_2.7.0
[4] fastmap_1.1.1 tensorA_0.36.2.1 shinystan_2.6.0
[7] promises_1.2.1 shinyjs_2.1.0 digest_0.6.34
[10] timechange_0.3.0 mime_0.12 lifecycle_1.0.4
[13] StanHeaders_2.32.6 ellipsis_0.3.2 magrittr_2.0.3
[16] posterior_1.5.0 compiler_4.3.2 rlang_1.1.3
[19] tools_4.3.2 igraph_2.0.2 utf8_1.2.4
[22] yaml_2.3.8 knitr_1.45 bridgesampling_1.1-2
[25] htmlwidgets_1.6.4 pkgbuild_1.4.3 curl_5.2.1
[28] plyr_1.8.9 dygraphs_1.1.1.6 abind_1.4-5
[31] miniUI_0.1.1.1 withr_3.0.0 grid_4.3.2
[34] stats4_4.3.2 fansi_1.0.6 xts_0.13.2
[37] xtable_1.8-4 colorspace_2.1-0 inline_0.3.19
[40] scales_1.3.0 gtools_3.9.5 cli_3.6.2
[43] mvtnorm_1.2-4 rmarkdown_2.25 generics_0.1.3
[46] RcppParallel_5.1.7 rstudioapi_0.15.0 tzdb_0.4.0
[49] reshape2_1.4.4 rstan_2.32.6 shinythemes_1.2.0
[52] bayesplot_1.11.1 parallel_4.3.2 matrixStats_1.2.0
[55] base64enc_0.1-3 vctrs_0.6.5 V8_4.4.2
[58] Matrix_1.6-5 jsonlite_1.8.8 arrayhelpers_1.1-0
[61] hms_1.1.3 crosstalk_1.2.1 ggdist_3.3.1
[64] glue_1.7.0 codetools_0.2-19 DT_0.32
[67] distributional_0.4.0 stringi_1.8.3 gtable_0.3.4
[70] later_1.3.2 QuickJSR_1.1.3 munsell_0.5.0
[73] colourpicker_1.3.0 pillar_1.9.0 htmltools_0.5.7
[76] Brobdingnag_1.2-9 R6_2.5.1 evaluate_0.23
[79] shiny_1.8.0 lattice_0.21-9 markdown_1.12
[82] backports_1.4.1 threejs_0.3.3 httpuv_1.6.14
[85] rstantools_2.4.0 coda_0.19-4.1 gridExtra_2.3
[88] nlme_3.1-163 checkmate_2.3.1 xfun_0.42
[91] zoo_1.8-12 pkgconfig_2.0.3 </code></pre>
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