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pcinereus committed Jul 16, 2024
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90 changes: 45 additions & 45 deletions docs/005_setup.html
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Expand Up @@ -3580,8 +3580,8 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan
<pre><code>
SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9e-06 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
Chain 1: Gradient evaluation took 1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Expand All @@ -3598,15 +3598,15 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan
Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.013 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: Elapsed Time: 0.012 seconds (Warm-up)
Chain 1: 0.014 seconds (Sampling)
Chain 1: 0.026 seconds (Total)
Chain 1:

SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3e-06 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
Chain 2: Gradient evaluation took 4e-06 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Expand All @@ -3623,15 +3623,15 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan
Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.013 seconds (Warm-up)
Chain 2: Elapsed Time: 0.012 seconds (Warm-up)
Chain 2: 0.012 seconds (Sampling)
Chain 2: 0.025 seconds (Total)
Chain 2: 0.024 seconds (Total)
Chain 2:

SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 3e-06 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
Chain 3: Gradient evaluation took 4e-06 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Expand All @@ -3655,8 +3655,8 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan

SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3e-06 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
Chain 4: Gradient evaluation took 4e-06 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Expand Down Expand Up @@ -3688,12 +3688,12 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan

Regression Coefficients:
Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
Intercept 0.57 0.32 -0.09 1.20 1.00 2520 2080
x -0.09 0.35 -0.76 0.60 1.00 2980 2157
Intercept 0.59 0.25 0.10 1.10 1.00 2493 2130
x 0.13 0.28 -0.42 0.70 1.00 2558 1726

Further Distributional Parameters:
Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
sigma 0.98 0.29 0.59 1.73 1.00 2089 2097
sigma 0.76 0.24 0.45 1.33 1.00 2078 2302

Draws were sampled using sampling(NUTS). For each parameter, Bulk_ESS
and Tail_ESS are effective sample size measures, and Rhat is the potential
Expand Down Expand Up @@ -3825,8 +3825,8 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan
<pre><code>
SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9e-06 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
Chain 1: Gradient evaluation took 1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Expand All @@ -3843,15 +3843,15 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan
Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.013 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: Elapsed Time: 0.012 seconds (Warm-up)
Chain 1: 0.014 seconds (Sampling)
Chain 1: 0.026 seconds (Total)
Chain 1:

SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3e-06 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
Chain 2: Gradient evaluation took 4e-06 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Expand All @@ -3868,15 +3868,15 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan
Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.013 seconds (Warm-up)
Chain 2: Elapsed Time: 0.012 seconds (Warm-up)
Chain 2: 0.012 seconds (Sampling)
Chain 2: 0.025 seconds (Total)
Chain 2: 0.024 seconds (Total)
Chain 2:

SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 3e-06 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
Chain 3: Gradient evaluation took 4e-06 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Expand All @@ -3900,8 +3900,8 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan

SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3e-06 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
Chain 4: Gradient evaluation took 4e-06 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Expand Down Expand Up @@ -3933,12 +3933,12 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan

Regression Coefficients:
Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
Intercept 0.57 0.32 -0.09 1.20 1.00 2520 2080
x -0.09 0.35 -0.76 0.60 1.00 2980 2157
Intercept 0.59 0.25 0.10 1.10 1.00 2493 2130
x 0.13 0.28 -0.42 0.70 1.00 2558 1726

Further Distributional Parameters:
Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
sigma 0.98 0.29 0.59 1.73 1.00 2089 2097
sigma 0.76 0.24 0.45 1.33 1.00 2078 2302

Draws were sampled using sampling(NUTS). For each parameter, Bulk_ESS
and Tail_ESS are effective sample size measures, and Rhat is the potential
Expand Down Expand Up @@ -4071,8 +4071,8 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan
<pre><code>
SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9e-06 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
Chain 1: Gradient evaluation took 1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Expand All @@ -4089,15 +4089,15 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan
Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.013 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: Elapsed Time: 0.012 seconds (Warm-up)
Chain 1: 0.014 seconds (Sampling)
Chain 1: 0.026 seconds (Total)
Chain 1:

SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3e-06 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
Chain 2: Gradient evaluation took 4e-06 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Expand All @@ -4114,15 +4114,15 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan
Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.013 seconds (Warm-up)
Chain 2: Elapsed Time: 0.012 seconds (Warm-up)
Chain 2: 0.012 seconds (Sampling)
Chain 2: 0.025 seconds (Total)
Chain 2: 0.024 seconds (Total)
Chain 2:

SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 3e-06 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
Chain 3: Gradient evaluation took 4e-06 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Expand All @@ -4146,8 +4146,8 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan

SAMPLING FOR MODEL &#39;anon_model&#39; NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3e-06 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
Chain 4: Gradient evaluation took 4e-06 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Expand Down Expand Up @@ -4179,12 +4179,12 @@ <h1 data-number="5"><span class="header-section-number">5</span> Installing stan

Regression Coefficients:
Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
Intercept 0.57 0.32 -0.09 1.20 1.00 2520 2080
x -0.09 0.35 -0.76 0.60 1.00 2980 2157
Intercept 0.59 0.25 0.10 1.10 1.00 2493 2130
x 0.13 0.28 -0.42 0.70 1.00 2558 1726

Further Distributional Parameters:
Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
sigma 0.98 0.29 0.59 1.73 1.00 2089 2097
sigma 0.76 0.24 0.45 1.33 1.00 2078 2302

Draws were sampled using sampling(NUTS). For each parameter, Bulk_ESS
and Tail_ESS are effective sample size measures, and Rhat is the potential
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16 changes: 8 additions & 8 deletions docs/01_introduction_to_r.html
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Expand Up @@ -5400,23 +5400,23 @@ <h2 data-number="5.7" class="anchored" data-anchor-id="applying-functions-repeti
<div class="cell">
<div class="sourceCode cell-code" id="cb346"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb346-1"><a href="#cb346-1"></a><span class="fu">rep</span>(<span class="fu">runif</span>(<span class="dv">1</span>), <span class="at">times =</span> <span class="dv">5</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 0.07484445 0.07484445 0.07484445 0.07484445 0.07484445</code></pre>
<pre><code>[1] 0.9458475 0.9458475 0.9458475 0.9458475 0.9458475</code></pre>
</div>
<div class="sourceCode cell-code" id="cb348"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb348-1"><a href="#cb348-1"></a><span class="fu">replicate</span>(<span class="at">n =</span> <span class="dv">5</span>, <span class="fu">runif</span>(<span class="dv">1</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 0.76591179 0.08388928 0.26584640 0.73487695 0.43842582</code></pre>
<pre><code>[1] 0.5250212 0.3685890 0.4576018 0.7022586 0.6725221</code></pre>
</div>
</div>
<p>When the function being run within <code>runif()</code> itself produces a vector of length &gt; 1, the <code>runif()</code> function combines each of the vectors together as separate columns in a matrix:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb350"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb350-1"><a href="#cb350-1"></a><span class="fu">replicate</span>(<span class="at">n =</span> <span class="dv">5</span>, <span class="fu">runif</span>(<span class="dv">5</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> [,1] [,2] [,3] [,4] [,5]
[1,] 0.9283322 0.493842982 0.28009916 0.4310423 0.1795866
[2,] 0.2427380 0.662498249 0.64675709 0.8749086 0.8341290
[3,] 0.4031444 0.017788288 0.14456310 0.6213227 0.8458962
[4,] 0.3471878 0.883100660 0.48036510 0.3344275 0.4450143
[5,] 0.5461777 0.002356233 0.07642568 0.1936368 0.3018650</code></pre>
<pre><code> [,1] [,2] [,3] [,4] [,5]
[1,] 0.47177366 0.7630087 0.1715144 0.2283701 0.5587883
[2,] 0.04830149 0.6914195 0.5059087 0.5695025 0.4756927
[3,] 0.10171678 0.6188929 0.7426900 0.6375667 0.2236168
[4,] 0.18979356 0.4300264 0.1335369 0.2998961 0.4113701
[5,] 0.14693282 0.6505941 0.7233454 0.7895954 0.5415339</code></pre>
</div>
</div>
<section id="apply-functions-along-matrix-margins" class="level3" data-number="5.7.1">
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30 changes: 15 additions & 15 deletions docs/04_data_wrangling.html
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