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8 changes: 4 additions & 4 deletions vignettes/C_API.Rmd
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output:
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highlight: haddock
highlight: tango
toc: yes
toc_depth: 3
params:
Expand Down Expand Up @@ -48,7 +48,7 @@ $$\mathbb{E}\left[X\right]=n\,p\qquad\text{and}\qquad\mathrm{Var}\left[X\right]=
double dmultinom(int m, const double *prob, double *x, int give_log);
```

The **R** C API provides a simulator for the multinomial distribution, `rmultinom`.
The [**R** C API](https://CRAN.R-project.org/doc/manuals/r-release/R-exts.html#The-R-API) provides a [simulator for the multinomial distribution, `rmultinom`](https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Distribution-functions).
See the "Rmath.h" header file for information on this facility.
**pomp** provides an evaluator for the probability mass function (`dmultinom`) for this distribution.

Expand Down Expand Up @@ -83,7 +83,7 @@ Input:

On return, `trans[0]`, ..., `trans[m-1]` will be the numbers of individuals making each of the respective transitions.

See [`?reulermultinom`](https://kingaa.github.io/manuals/pomp/html/distributions.html) and [FAQ 3.6](./FAQ.html#eulermultinomial-approximation) for more on the Euler-multinomial distributions.
See [`?reulermultinom`](https://kingaa.github.io/manuals/pomp/html/eulermultinom.html) and [FAQ 3.6](./FAQ.html#eulermultinomial-approximation) for more on the Euler-multinomial distributions.

**NB:** `reulermultinom` does not call `GetRNGstate()` or `PutRNGstate()` internally.
This must be done by the calling program.
Expand All @@ -110,7 +110,7 @@ Input:

The value returned is the probability or log probability (as requested).

See [`?deulermultinom`](https://kingaa.github.io/manuals/pomp/html/distributions.html) and [FAQ 3.6](./FAQ.html#eulermultinomial-approximation) for more on the Euler-multinomial distributions.
See [`?deulermultinom`](https://kingaa.github.io/manuals/pomp/html/eulermultinom.html) and [FAQ 3.6](./FAQ.html#eulermultinomial-approximation) for more on the Euler-multinomial distributions.


### Gamma white noise
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Expand Down Expand Up @@ -228,7 +232,7 @@ <h3>Beta-binomial distribution</h3>
<div id="multinomial-distribution" class="section level3">
<h3>Multinomial distribution</h3>
<div class="sourceCode" id="cb2"><pre class="sourceCode c"><code class="sourceCode c"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true"></a><span class="dt">double</span> dmultinom(<span class="dt">int</span> m, <span class="dt">const</span> <span class="dt">double</span> *prob, <span class="dt">double</span> *x, <span class="dt">int</span> give_log);</span></code></pre></div>
<p>The <strong>R</strong> C API provides a simulator for the multinomial distribution, <code>rmultinom</code>. See the “Rmath.h” header file for information on this facility. <strong>pomp</strong> provides an evaluator for the probability mass function (<code>dmultinom</code>) for this distribution.</p>
<p>The <a href="https://CRAN.R-project.org/doc/manuals/r-release/R-exts.html#The-R-API"><strong>R</strong> C API</a> provides a <a href="https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Distribution-functions">simulator for the multinomial distribution, <code>rmultinom</code></a>. See the “Rmath.h” header file for information on this facility. <strong>pomp</strong> provides an evaluator for the probability mass function (<code>dmultinom</code>) for this distribution.</p>
<p>Input:</p>
<ul>
<li><code>m</code> is a positive integer, is the dimension of the random variable.</li>
Expand Down Expand Up @@ -257,7 +261,7 @@ <h4>Simulate Euler-multinomial transitions</h4>
<li><code>trans</code> is a pointer to the vector that will hold the random deviate.</li>
</ul>
<p>On return, <code>trans[0]</code>, …, <code>trans[m-1]</code> will be the numbers of individuals making each of the respective transitions.</p>
<p>See <a href="https://kingaa.github.io/manuals/pomp/html/distributions.html"><code>?reulermultinom</code></a> and <a href="./FAQ.html#eulermultinomial-approximation">FAQ 3.6</a> for more on the Euler-multinomial distributions.</p>
<p>See <a href="https://kingaa.github.io/manuals/pomp/html/eulermultinom.html"><code>?reulermultinom</code></a> and <a href="./FAQ.html#eulermultinomial-approximation">FAQ 3.6</a> for more on the Euler-multinomial distributions.</p>
<p><strong>NB:</strong> <code>reulermultinom</code> does not call <code>GetRNGstate()</code> or <code>PutRNGstate()</code> internally. This must be done by the calling program. But note that when <code>reulermultinom</code> is called inside a <strong>pomp</strong> rprocess, there is no need to call either <code>GetRNGState()</code> or <code>PutRNGState()</code>; this is handled by <strong>pomp</strong>.</p>
</div>
<div id="compute-probabilities-of-euler-multinomial-transitions" class="section level4">
Expand All @@ -278,7 +282,7 @@ <h4>Compute probabilities of Euler-multinomial transitions</h4>
</ul></li>
</ul>
<p>The value returned is the probability or log probability (as requested).</p>
<p>See <a href="https://kingaa.github.io/manuals/pomp/html/distributions.html"><code>?deulermultinom</code></a> and <a href="./FAQ.html#eulermultinomial-approximation">FAQ 3.6</a> for more on the Euler-multinomial distributions.</p>
<p>See <a href="https://kingaa.github.io/manuals/pomp/html/eulermultinom.html"><code>?deulermultinom</code></a> and <a href="./FAQ.html#eulermultinomial-approximation">FAQ 3.6</a> for more on the Euler-multinomial distributions.</p>
</div>
</div>
<div id="gamma-white-noise" class="section level3">
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Expand Down Expand Up @@ -273,16 +277,16 @@ <h2>Comparing the implementations</h2>
<p>Using each implementation, we’ll now run a number of simulations and compare the amount of time required.</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true"></a><span class="kw">system.time</span>(<span class="kw">simulate</span>(gompertz,<span class="dt">nsim=</span><span class="dv">10000</span>,<span class="dt">format=</span><span class="st">&quot;arrays&quot;</span>))</span></code></pre></div>
<pre><code>## user system elapsed
## 7.962 0.010 7.972</code></pre>
## 7.787 0.015 7.803</code></pre>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true"></a><span class="kw">system.time</span>(<span class="kw">simulate</span>(Gompertz,<span class="dt">nsim=</span><span class="dv">10000</span>,<span class="dt">format=</span><span class="st">&quot;arrays&quot;</span>))</span></code></pre></div>
<pre><code>## user system elapsed
## 0.175 0.008 0.184</code></pre>
## 0.173 0.004 0.177</code></pre>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true"></a><span class="kw">system.time</span>(<span class="kw">pfilter</span>(gompertz,<span class="dt">Np=</span><span class="dv">10000</span>))</span></code></pre></div>
<pre><code>## user system elapsed
## 6.820 0.012 6.832</code></pre>
## 6.837 0.010 6.847</code></pre>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true"></a><span class="kw">system.time</span>(<span class="kw">pfilter</span>(Gompertz,<span class="dt">Np=</span><span class="dv">10000</span>))</span></code></pre></div>
<pre><code>## user system elapsed
## 0.203 0.004 0.207</code></pre>
## 0.22 0.00 0.22</code></pre>
<hr />
<p>This document was produced using <strong>pomp</strong> version 5.5.2.0 and <strong>R</strong> version 4.3.2.</p>
</div>
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