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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>R Interface · JuliaBUGS.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><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="../">Introduction</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><a class="tocitem" href="../functions/">Functions</a></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="../graph_plotting/">Plotting</a></li><li class="is-active"><a class="tocitem" href>R Interface</a><ul class="internal"><li><a class="tocitem" href="#Reading-BUGS-data-and-init-from-R-like-lists"><span>Reading BUGS <code>data</code> and <code>init</code> from R like lists</span></a></li></ul></li><li><a class="tocitem" href="../pitfalls/">Pitfalls</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="Integrating-R-in-Julia"><a class="docs-heading-anchor" href="#Integrating-R-in-Julia">Integrating R in Julia</a><a id="Integrating-R-in-Julia-1"></a><a class="docs-heading-anchor-permalink" href="#Integrating-R-in-Julia" title="Permalink"></a></h1><p>Julia offers a seamless interface to the <a href="https://www.r-project.org/about.html"><code>R</code> language</a>. </p><ul><li>The <a href="https://github.com/JuliaInterop/RCall.jl"><code>RCall.jl</code></a> package enables interaction with R functions in Julia.</li><li>The <a href="https://github.com/JuliaData/RData.jl"><code>RData.jl</code></a> package allows interfacing with R data in Julia.</li></ul><h2 id="Reading-BUGS-data-and-init-from-R-like-lists"><a class="docs-heading-anchor" href="#Reading-BUGS-data-and-init-from-R-like-lists">Reading BUGS <code>data</code> and <code>init</code> from R like lists</a><a id="Reading-BUGS-data-and-init-from-R-like-lists-1"></a><a class="docs-heading-anchor-permalink" href="#Reading-BUGS-data-and-init-from-R-like-lists" title="Permalink"></a></h2><blockquote><p><strong>Warning</strong>: The data layout in BUGS assumes that the data is stored in row-major order, while R uses column-major order. This discrepancy can lead to issues. <a href="https://mc-stan.org/"><code>Stan</code></a> developers have transformed the data and initializations of example BUGS models for R, which can be found <a href="https://github.com/stan-dev/example-models/tree/master/bugs_examples">here</a>.</p></blockquote><h3 id="Reading-the-list-data-structure-from-R"><a class="docs-heading-anchor" href="#Reading-the-list-data-structure-from-R">Reading the <code>list</code> data structure from R</a><a id="Reading-the-list-data-structure-from-R-1"></a><a class="docs-heading-anchor-permalink" href="#Reading-the-list-data-structure-from-R" title="Permalink"></a></h3><p>The data for <code>Rats</code> is available <a href="https://chjackson.github.io/openbugsdoc/Examples/Ratsdata.html">here</a>. </p><p>In Julia, we can read this data into a Julia dictionary using the <code>RCall.jl</code> package.</p><pre><code class="language-julia-repl hljs">julia&gt; using RCall

julia&gt; data = R&quot;
list(
x = c(8.0, 15.0, 22.0, 29.0, 36.0), xbar = 22, N = 30, T = 5,
Y = structure(
.Data = c(
151, 199, 246, 283, 320,
145, 199, 249, 293, 354,
147, 214, 263, 312, 328,
155, 200, 237, 272, 297,
135, 188, 230, 280, 323,
159, 210, 252, 298, 331,
141, 189, 231, 275, 305,
159, 201, 248, 297, 338,
177, 236, 285, 350, 376,
134, 182, 220, 260, 296,
160, 208, 261, 313, 352,
143, 188, 220, 273, 314,
154, 200, 244, 289, 325,
171, 221, 270, 326, 358,
163, 216, 242, 281, 312,
160, 207, 248, 288, 324,
142, 187, 234, 280, 316,
156, 203, 243, 283, 317,
157, 212, 259, 307, 336,
152, 203, 246, 286, 321,
154, 205, 253, 298, 334,
139, 190, 225, 267, 302,
146, 191, 229, 272, 302,
157, 211, 250, 285, 323,
132, 185, 237, 286, 331,
160, 207, 257, 303, 345,
169, 216, 261, 295, 333,
157, 205, 248, 289, 316,
137, 180, 219, 258, 291,
153, 200, 244, 286, 324
),
.Dim = c(30, 5)
)
)
&quot;
RObject{VecSxp}
$x
[1] 8 15 22 29 36

$xbar
[1] 22

$N
[1] 30

$T
[1] 5

$Y
[,1] [,2] [,3] [,4] [,5]
[1,] 151 141 154 157 132
[2,] 199 189 200 212 185
[3,] 246 231 244 259 237
[4,] 283 275 289 307 286
[5,] 320 305 325 336 331
[6,] 145 159 171 152 160
[7,] 199 201 221 203 207
[8,] 249 248 270 246 257
[9,] 293 297 326 286 303
[10,] 354 338 358 321 345
[11,] 147 177 163 154 169
[12,] 214 236 216 205 216
[13,] 263 285 242 253 261
[14,] 312 350 281 298 295
[15,] 328 376 312 334 333
[16,] 155 134 160 139 157
[17,] 200 182 207 190 205
[18,] 237 220 248 225 248
[19,] 272 260 288 267 289
[20,] 297 296 324 302 316
[21,] 135 160 142 146 137
[22,] 188 208 187 191 180
[23,] 230 261 234 229 219
[24,] 280 313 280 272 258
[25,] 323 352 316 302 291
[26,] 159 143 156 157 153
[27,] 210 188 203 211 200
[28,] 252 220 243 250 244
[29,] 298 273 283 285 286
[30,] 331 314 317 323 324</code></pre><p>alternatively, <code>reval(s::String)</code> will produce the same result in this case.</p><p>If the data is stores in a file, user can use function (may require customizing the function to fit specific needs)</p><pre><code class="language-julia hljs">function read_rlist_to_dictionary(filepath::String)
r_data = open(filepath) do f
s = read(f, String)
reval(s)
end
return rcopy(r_data)
end</code></pre><p>, and save the result to a Julia variable and access the data as a Julia dictionary</p><pre><code class="language-julia-repl hljs">julia&gt; rcopy(data)
OrderedDict{Symbol, Any} with 5 entries:
:x =&gt; [8.0, 15.0, 22.0, 29.0, 36.0]
:xbar =&gt; 22.0
:N =&gt; 30.0
:T =&gt; 5.0
:Y =&gt; [151.0 141.0 … 157.0 132.0; 199.0 189.0 … 212.0 185.0; … ; 298.0 273.0 … 285.0 286.0; 331.0 314.0 … 323.0 324.0]</code></pre><p>It is worth noting that <code>rcopy</code> will automatically convert data names contains <code>.</code> to <code>_</code> in Julia. E.g.</p><pre><code class="language-julia hljs">julia&gt; rcopy(R&quot;list(a.b = 1)&quot;)
OrderedDict{Symbol, Any} with 1 entry:
:a_b =&gt; 1.0</code></pre><h3 id="Transform-Dta-read-from-R-to-Julia-convention"><a class="docs-heading-anchor" href="#Transform-Dta-read-from-R-to-Julia-convention">Transform Dta read from R to Julia convention</a><a id="Transform-Dta-read-from-R-to-Julia-convention-1"></a><a class="docs-heading-anchor-permalink" href="#Transform-Dta-read-from-R-to-Julia-convention" title="Permalink"></a></h3><p>If you want to load data using the R interface, but the data source is in the same layout as BUGS, you can process the data in Julia, for instance</p><pre><code class="language-julia-repl hljs"># define a row-major reshape function, because Julia&#39;s `reshape` is column-major
julia&gt; function rreshape(v::Vector, dim)
return permutedims(reshape(v, reverse(dim)), length(dim):-1:1)
end
rreshape (generic function with 1 method)

julia&gt; rreshape(vcat(data[:Y]...), (30, 5))
30×5 Matrix{Float64}:
151.0 199.0 246.0 283.0 320.0
145.0 199.0 249.0 293.0 354.0
147.0 214.0 263.0 312.0 328.0
155.0 200.0 237.0 272.0 297.0
135.0 188.0 230.0 280.0 323.0
159.0 210.0 252.0 298.0 331.0
141.0 189.0 231.0 275.0 305.0
159.0 201.0 248.0 297.0 338.0
⋮
146.0 191.0 229.0 272.0 302.0
157.0 211.0 250.0 285.0 323.0
132.0 185.0 237.0 286.0 331.0
160.0 207.0 257.0 303.0 345.0
169.0 216.0 261.0 295.0 333.0
157.0 205.0 248.0 289.0 316.0
137.0 180.0 219.0 258.0 291.0
153.0 200.0 244.0 286.0 324.0</code></pre><p>Please always verify the data before using.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../graph_plotting/">« Plotting</a><a class="docs-footer-nextpage" href="../pitfalls/">Pitfalls »</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="Sunday 3 March 2024 05:43">Sunday 3 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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