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 <div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">JuliaBUGS.jl</a></span></div><form class="docs-search" action="../search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><a class="tocitem" href="../example/">Example</a></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="../api/api/">General</a></li><li><a class="tocitem" href="../api/functions/">Functions</a></li><li><a class="tocitem" href="../api/distributions/">Distributions</a></li><li><a class="tocitem" href="../api/user_defined_functions/">User-Defined Functions and Distributions</a></li></ul></li><li><a class="tocitem" href="../differences/">Differences from Other BUGS Implementations</a></li><li><a class="tocitem" href="../pitfalls/">Pitfalls</a></li><li><a class="tocitem" href="../graph_plotting/">Plotting</a></li><li class="is-active"><a class="tocitem" href>R Interface</a></li><li><span class="tocitem">For Developers</span><ul><li><a class="tocitem" href="../parser/">Parser</a></li><li><a class="tocitem" href="../BUGS_notes/">Notes on BUGS Implementations</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>R Interface</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>R Interface</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/TuringLang/JuliaBUGS.jl/blob/master/docs/src/R_interface.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="R-Interface"><a class="docs-heading-anchor" href="#R-Interface">R Interface</a><a id="R-Interface-1"></a><a class="docs-heading-anchor-permalink" href="#R-Interface" title="Permalink"></a></h1><p>Interoperation between Julia and R is very solid and simple to use.</p><p>Here are some very useful packages:</p><ul><li><a href="https://github.com/JuliaInterop/RCall.jl"><code>RCall.jl</code></a>: interaction with R runtime.</li><li><a href="https://github.com/JuliaData/RData.jl"><code>RData.jl</code></a>: reading and writing R data files.</li><li><a href="https://github.com/JuliaData/DataFrames.jl"><code>DataFrames.jl</code></a>: <code>pandas</code> and <code>dplyr</code> for Julia.</li><li><a href="https://github.com/JuliaData/CSV.jl"><code>CSV.jl</code></a>: CSV file reading and writing.</li><li><a href="https://github.com/JuliaIO/JSON.jl"><code>JSON.jl</code></a>, <a href="https://github.com/quinnj/JSON3.jl"><code>JSON3.jl</code></a>, <a href="https://github.com/bhftbootcamp/Serde.jl"><code>Serde.jl</code></a>: JSON file reading and writing.</li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../graph_plotting/">« Plotting</a><a class="docs-footer-nextpage" href="../parser/">Parser »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 18 November 2024 14:42">Monday 18 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
 

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 @bugs(program::String; replace_period::Bool=true, no_enclosure::Bool=false)</code></pre><p>Constructs a Julia Abstract Syntax Tree (AST) representation of a BUGS program. This macro supports two forms of input: a Julia expression or a string containing the BUGS program code. </p><ul><li>When provided with a string, the macro parses it as a BUGS program, with optional arguments to control parsing behavior.</li><li>When given an expression, it performs syntactic checks to ensure compatibility with BUGS syntax.</li></ul><p><strong>Arguments for String Input</strong></p><p>For the string input variant, the following optional arguments are available:</p><ul><li><code>replace_period::Bool</code>: When set to <code>true</code>, all periods (<code>.</code>) in the BUGS code are replaced. This is enabled by default.</li><li><code>no_enclosure::Bool</code>: When <code>true</code>, the parser does not require the BUGS program to be enclosed within <code>model{ ... }</code> brackets. By default, this is set to <code>false</code>.</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/TuringLang/JuliaBUGS.jl/blob/0b43ad031107d15317e32279eb4e4b7e2613dbc8/src/parser/bugs_macro.jl#L161-L175">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="JuliaBUGS.compile" href="#JuliaBUGS.compile"><code>JuliaBUGS.compile</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">compile(model_def, data[, initial_params])</code></pre><p>Compile the model with model definition and data. Optionally, initializations can be provided.  If initializations are not provided, values will be sampled from the prior distributions. </p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/TuringLang/JuliaBUGS.jl/blob/0b43ad031107d15317e32279eb4e4b7e2613dbc8/src/JuliaBUGS.jl#L147-L152">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="JuliaBUGS.initialize!" href="#JuliaBUGS.initialize!"><code>JuliaBUGS.initialize!</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">initialize!(model::BUGSModel, initial_params::NamedTuple)</code></pre><p>Initialize the model with a NamedTuple of initial values, the values are expected to be in the original space.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/TuringLang/JuliaBUGS.jl/blob/0b43ad031107d15317e32279eb4e4b7e2613dbc8/src/model.jl#L226-L230">source</a></section><section><div><pre><code class="nohighlight hljs">initialize!(model::BUGSModel, initial_params::AbstractVector)</code></pre><p>Initialize the model with a vector of initial values, the values can be in transformed space if <code>model.transformed</code> is set to true.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/TuringLang/JuliaBUGS.jl/blob/0b43ad031107d15317e32279eb4e4b7e2613dbc8/src/model.jl#L265-L269">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../example/">« Example</a><a class="docs-footer-nextpage" href="../functions/">Functions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 18 November 2024 14:42">Monday 18 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
 

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 <div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../../">JuliaBUGS.jl</a></span></div><form class="docs-search" action="../../search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../../">Home</a></li><li><a class="tocitem" href="../../example/">Example</a></li><li><span class="tocitem">API</span><ul><li><a class="tocitem" href="../api/">General</a></li><li class="is-active"><a class="tocitem" href>Functions</a><ul class="internal"><li><a class="tocitem" href="#Function-defined-in-Julia-Standard-Library"><span>Function defined in Julia Standard Library</span></a></li><li><a class="tocitem" href="#Function-defined-in-[LogExpFunctions](https://github.com/JuliaStats/LogExpFunctions.jl)"><span>Function defined in <code>LogExpFunctions</code></span></a></li><li><a class="tocitem" href="#Function-defined-in-JuliaBUGS.BUGSPrimitives"><span>Function defined in <code>JuliaBUGS.BUGSPrimitives</code></span></a></li></ul></li><li><a class="tocitem" href="../distributions/">Distributions</a></li><li><a class="tocitem" href="../user_defined_functions/">User-Defined Functions and Distributions</a></li></ul></li><li><a class="tocitem" href="../../differences/">Differences from Other BUGS Implementations</a></li><li><a class="tocitem" href="../../pitfalls/">Pitfalls</a></li><li><a class="tocitem" href="../../graph_plotting/">Plotting</a></li><li><a class="tocitem" href="../../R_interface/">R Interface</a></li><li><span class="tocitem">For Developers</span><ul><li><a class="tocitem" href="../../parser/">Parser</a></li><li><a class="tocitem" href="../../BUGS_notes/">Notes on BUGS Implementations</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">API</a></li><li class="is-active"><a href>Functions</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Functions</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/TuringLang/JuliaBUGS.jl/blob/master/docs/src/api/functions.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><p>Most of the <a href="https://www.multibugs.org/documentation/latest/Functions.html">functions</a> from BUGS have been implemented. </p><p><code>JuliaBUGS</code> directly utilizes functions from the Julia Standard Library when they share the same names and functionalities. For functions not available in the Julia Standard Library and other popular libraries, we have developed equivalents within <code>JuliaBUGS.BUGSPrimitives</code>.</p><h2 id="Function-defined-in-Julia-Standard-Library"><a class="docs-heading-anchor" href="#Function-defined-in-Julia-Standard-Library">Function defined in Julia Standard Library</a><a id="Function-defined-in-Julia-Standard-Library-1"></a><a class="docs-heading-anchor-permalink" href="#Function-defined-in-Julia-Standard-Library" title="Permalink"></a></h2><div class="admonition is-warning"><header class="admonition-header">No keyword arguments syntax in BUGS</header><div class="admonition-body"><p>Please note that some functions listed may accept additional arguments (e.g. <code>trunc</code>) and/or keyword arguments (e.g. <code>sum</code>, <code>sort</code>, <code>mean</code>). However, at the moment <code>JuliaBUGS</code> only supports function arguments of type <code>Real</code> or <code>AbstractArray{Real}</code>. Furthermore, <code>JuliaBUGS</code> does not accommodate the use of keyword argument syntax. Thus, the default values for any optional or keyword arguments will be automatically applied.</p></div></div><article class="docstring"><header><a class="docstring-binding" id="Base.abs" href="#Base.abs"><code>Base.abs</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">abs(x)</code></pre><p>The absolute value of <code>x</code>.</p><p>When <code>abs</code> is applied to signed integers, overflow may occur, resulting in the return of a negative value. This overflow occurs only when <code>abs</code> is applied to the minimum representable value of a signed integer. That is, when <code>x == typemin(typeof(x))</code>, <code>abs(x) == x &lt; 0</code>, not <code>-x</code> as might be expected.</p><p>See also: <a href="api/@ref"><code>abs2</code></a>, <a href="api/@ref"><code>unsigned</code></a>, <a href="api/@ref"><code>sign</code></a>.</p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; abs(-3)
 3