Commit 1b4749ab authored by Gilles Kratzer's avatar Gilles Kratzer
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......@@ -25,7 +25,7 @@ summary.mcmcabn <- function(object, quantiles = c(0.025, 0.25, 0.5, 0.75, 0.975)
cat("\n\nGlobal acceptance rate: ", 1-mean(object$rejection),"\n",sep = "")
out2<- matrix(data = table(object$method,object$rejection),ncol = 2,dimnames = list(levels(factor(object$method)),c("Accepted", "Rejected")))
out2 <- matrix(data = table(object$method,object$rejection),ncol = 2,dimnames = list(levels(factor(object$method)),c("Accepted", "Rejected")))
print(out2, ...)
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......@@ -23,12 +23,12 @@ ___
## Quick start
To install `mcmabn` you need essentially two R packages: `abn` and `gRbase` and those packages requires some libraries stored on bioconductor:
To install `mcmabn` you need two R packages: [abn](https://CRAN.R-project.org/package=abn) and [gRbase](https://CRAN.R-project.org/package=gRbase) that requires libraries stored not stored on [CRAN](https://cran.r-project.org/) but on [bioconductor](http://www.bioconductor.org/):
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RBGL","Rgraphviz", version = "3.8")
BiocManager::install(c("RBGL","Rgraphviz","graph"), version = "3.8")
install.packages("mcmcabn", dependencies = TRUE)
```
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......@@ -90,7 +90,7 @@
<h1>mcmcabn: a structural MCMC sampler for DAGs learned from observed systemic datasets</h1>
<h4 class="author">Gilles Kratzer, Reinhard Furrer</h4>
<h4 class="date">2019-02-25</h4>
<h4 class="date">2019-02-26</h4>
<div class="hidden name"><code>mcmcabn.Rmd</code></div>
......@@ -254,7 +254,7 @@ dag &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumen
<span class="co">#&gt; XRay 0.0000 0.1079</span>
<span class="co">#&gt; Dyspnea 0.1508 0.0000</span></code></pre></div>
<p>The <code><a href="../reference/query.html">query()</a></code> function recognize formula statements. So it is possible to explicitly query: <strong>what is the probability of LungCancer node being children of the Smoking node?</strong></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/query.html">query</a></span>(<span class="dt">mcmcabn =</span> mcmc.out.asia, <span class="dt">formula =</span> <span class="op">~</span>LungCancer<span class="op">|</span>Smoking)
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/query.html">query</a></span>(<span class="dt">mcmcabn =</span> mcmc.out.asia, <span class="dt">formula =</span> <span class="op">~</span><span class="st"> </span>LungCancer<span class="op">|</span>Smoking)
<span class="co">#&gt; [1] 0.401</span></code></pre></div>
<p>This means that an arrow from Smoking to LungCancer appears in 40.06% of the sampled DAGs.</p>
<p>One can also ask more complicated structural requests. If want to know <strong>what is the probability of Smoking node being parent of both LungCancer and Bronchitis node?</strong></p>
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......@@ -99,8 +99,12 @@
<div id="quick-start" class="section level2">
<h2 class="hasAnchor">
<a href="#quick-start" class="anchor"></a>Quick start</h2>
<p>You can install <code>mcmabn</code> with:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"mcmcabn"</span>)</code></pre></div>
<p>To install <code>mcmabn</code> you need two R packages: <a href="https://CRAN.R-project.org/package=abn">abn</a> and <a href="https://CRAN.R-project.org/package=gRbase">gRbase</a> that requires libraries stored not stored on <a href="https://cran.r-project.org/">CRAN</a> but on <a href="http://www.bioconductor.org/">bioconductor</a>:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="op">!</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/ns-load">requireNamespace</a></span>(<span class="st">"BiocManager"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>))
<span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"BiocManager"</span>)
BiocManager<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/BiocManager/topics/install">install</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"RBGL"</span>,<span class="st">"Rgraphviz"</span>,<span class="st">"graph"</span>), <span class="dt">version =</span> <span class="st">"3.8"</span>)
<span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"mcmcabn"</span>, <span class="dt">dependencies =</span> <span class="ot">TRUE</span>)</code></pre></div>
<p>The three main problems addressed by this R package are:</p>
<ul>
<li>selecting the most probable structure based on a cache of pre-computed scores.</li>
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