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<!DOCTYPE html>
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<title>Overview | NimbleUserManual.knit</title>
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<nav role="navigation">
<ul class="summary">
<img src="./nimble-icon.png"
width=100>
<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.3.0</a></li>
<li><a href="/~https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
<li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
<li class="divider"></li>
<li class="part"><span><b>I Introduction</b></span></li>
<li class="chapter" data-level="1" data-path="cha-welcome-nimble.html"><a href="cha-welcome-nimble.html"><i class="fa fa-check"></i><b>1</b> Welcome to NIMBLE</a>
<ul>
<li class="chapter" data-level="1.1" data-path="cha-welcome-nimble.html"><a href="cha-welcome-nimble.html#sec:what-is-nimble"><i class="fa fa-check"></i><b>1.1</b> What does NIMBLE do?</a></li>
<li class="chapter" data-level="1.2" data-path="cha-welcome-nimble.html"><a href="cha-welcome-nimble.html#how-to-use-this-manual"><i class="fa fa-check"></i><b>1.2</b> How to use this manual</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html"><i class="fa fa-check"></i><b>2</b> Lightning introduction</a>
<ul>
<li class="chapter" data-level="2.1" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:brief-example"><i class="fa fa-check"></i><b>2.1</b> A brief example</a></li>
<li class="chapter" data-level="2.2" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:creating-model"><i class="fa fa-check"></i><b>2.2</b> Creating a model</a></li>
<li class="chapter" data-level="2.3" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:compiling-model"><i class="fa fa-check"></i><b>2.3</b> Compiling the model</a></li>
<li class="chapter" data-level="2.4" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:intro-runMCMC"><i class="fa fa-check"></i><b>2.4</b> One-line invocation of MCMC</a></li>
<li class="chapter" data-level="2.5" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:creating-mcmc"><i class="fa fa-check"></i><b>2.5</b> Creating, compiling and running a basic MCMC configuration</a></li>
<li class="chapter" data-level="2.6" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:customizing-mcmc"><i class="fa fa-check"></i><b>2.6</b> Customizing the MCMC</a></li>
<li class="chapter" data-level="2.7" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:running-mcem"><i class="fa fa-check"></i><b>2.7</b> Running MCEM</a></li>
<li class="chapter" data-level="2.8" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:creating-your-own"><i class="fa fa-check"></i><b>2.8</b> Creating your own functions</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="cha-more-introduction.html"><a href="cha-more-introduction.html"><i class="fa fa-check"></i><b>3</b> More introduction</a>
<ul>
<li class="chapter" data-level="3.1" data-path="cha-more-introduction.html"><a href="cha-more-introduction.html#nimble-adopts-and-extends-the-bugs-language-for-specifying-models"><i class="fa fa-check"></i><b>3.1</b> NIMBLE adopts and extends the BUGS language for specifying models</a></li>
<li class="chapter" data-level="3.2" data-path="cha-more-introduction.html"><a href="cha-more-introduction.html#sec:nimble-lang-writ"><i class="fa fa-check"></i><b>3.2</b> nimbleFunctions for writing algorithms</a></li>
<li class="chapter" data-level="3.3" data-path="cha-more-introduction.html"><a href="cha-more-introduction.html#sec:nimble-algor-libr"><i class="fa fa-check"></i><b>3.3</b> The NIMBLE algorithm library</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html"><i class="fa fa-check"></i><b>4</b> Installing NIMBLE</a>
<ul>
<li class="chapter" data-level="4.1" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#sec:requ-run-nimble"><i class="fa fa-check"></i><b>4.1</b> Requirements to run NIMBLE</a></li>
<li class="chapter" data-level="4.2" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#sec:compiler"><i class="fa fa-check"></i><b>4.2</b> Installing a C++ compiler for NIMBLE to use</a>
<ul>
<li class="chapter" data-level="4.2.1" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#macos"><i class="fa fa-check"></i><b>4.2.1</b> MacOS</a></li>
<li class="chapter" data-level="4.2.2" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#linux"><i class="fa fa-check"></i><b>4.2.2</b> Linux</a></li>
<li class="chapter" data-level="4.2.3" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#windows"><i class="fa fa-check"></i><b>4.2.3</b> Windows</a></li>
</ul></li>
<li class="chapter" data-level="4.3" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#installing-the-nimble-package"><i class="fa fa-check"></i><b>4.3</b> Installing the NIMBLE package</a></li>
<li class="chapter" data-level="4.4" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#troubleshooting-installation-problems"><i class="fa fa-check"></i><b>4.4</b> Troubleshooting installation problems</a></li>
<li class="chapter" data-level="4.5" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#customizing-your-installation"><i class="fa fa-check"></i><b>4.5</b> Customizing your installation</a>
<ul>
<li class="chapter" data-level="4.5.1" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#using-your-own-copy-of-eigen"><i class="fa fa-check"></i><b>4.5.1</b> Using your own copy of Eigen</a></li>
<li class="chapter" data-level="4.5.2" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#using-libnimble"><i class="fa fa-check"></i><b>4.5.2</b> Using libnimble</a></li>
<li class="chapter" data-level="4.5.3" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#sec:blas"><i class="fa fa-check"></i><b>4.5.3</b> BLAS and LAPACK</a></li>
<li class="chapter" data-level="4.5.4" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#customizing-compilation-of-the-nimble-generated-c"><i class="fa fa-check"></i><b>4.5.4</b> Customizing compilation of the NIMBLE-generated C++</a></li>
</ul></li>
</ul></li>
<li class="part"><span><b>II Models in NIMBLE</b></span></li>
<li class="chapter" data-level="5" data-path="cha-writing-models.html"><a href="cha-writing-models.html"><i class="fa fa-check"></i><b>5</b> Writing models in NIMBLE’s dialect of BUGS</a>
<ul>
<li class="chapter" data-level="5.1" data-path="cha-writing-models.html"><a href="cha-writing-models.html#sec:supp-feat-bugs"><i class="fa fa-check"></i><b>5.1</b> Comparison to BUGS dialects supported by WinBUGS, OpenBUGS and JAGS</a>
<ul>
<li class="chapter" data-level="5.1.1" data-path="cha-writing-models.html"><a href="cha-writing-models.html#supported-features-of-bugs-and-jags"><i class="fa fa-check"></i><b>5.1.1</b> Supported features of BUGS and JAGS</a></li>
<li class="chapter" data-level="5.1.2" data-path="cha-writing-models.html"><a href="cha-writing-models.html#sec:extensions-bugs"><i class="fa fa-check"></i><b>5.1.2</b> NIMBLE’s Extensions to BUGS and JAGS</a></li>
<li class="chapter" data-level="5.1.3" data-path="cha-writing-models.html"><a href="cha-writing-models.html#sec:not-yet-supported"><i class="fa fa-check"></i><b>5.1.3</b> Not-supported features of BUGS and JAGS</a></li>
</ul></li>
<li class="chapter" data-level="5.2" data-path="cha-writing-models.html"><a href="cha-writing-models.html#writing-models"><i class="fa fa-check"></i><b>5.2</b> Writing models</a>
<ul>
<li class="chapter" data-level="5.2.1" data-path="cha-writing-models.html"><a href="cha-writing-models.html#declaring-stochastic-and-deterministic-nodes"><i class="fa fa-check"></i><b>5.2.1</b> Declaring stochastic and deterministic nodes</a></li>
<li class="chapter" data-level="5.2.2" data-path="cha-writing-models.html"><a href="cha-writing-models.html#sec:more-kinds-bugs"><i class="fa fa-check"></i><b>5.2.2</b> More kinds of BUGS declarations</a></li>
<li class="chapter" data-level="5.2.3" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:vectorized-versus-scalar-declarations"><i class="fa fa-check"></i><b>5.2.3</b> Vectorized versus scalar declarations</a></li>
<li class="chapter" data-level="5.2.4" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:dists-and-functions"><i class="fa fa-check"></i><b>5.2.4</b> Available distributions</a></li>
<li class="chapter" data-level="5.2.5" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:BUGS-lang-fxns"><i class="fa fa-check"></i><b>5.2.5</b> Available BUGS language functions</a></li>
<li class="chapter" data-level="5.2.6" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:BUGS-link"><i class="fa fa-check"></i><b>5.2.6</b> Available link functions</a></li>
<li class="chapter" data-level="5.2.7" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:trunc"><i class="fa fa-check"></i><b>5.2.7</b> Truncation, censoring, and constraints</a></li>
<li class="chapter" data-level="5.2.8" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:macros"><i class="fa fa-check"></i><b>5.2.8</b> Model macros</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="cha-building-models.html"><a href="cha-building-models.html"><i class="fa fa-check"></i><b>6</b> Building and using models</a>
<ul>
<li class="chapter" data-level="6.1" data-path="cha-building-models.html"><a href="cha-building-models.html#creating-model-objects"><i class="fa fa-check"></i><b>6.1</b> Creating model objects</a>
<ul>
<li class="chapter" data-level="6.1.1" data-path="cha-building-models.html"><a href="cha-building-models.html#using-nimblemodel-to-create-a-model"><i class="fa fa-check"></i><b>6.1.1</b> Using <em>nimbleModel</em> to create a model</a></li>
<li class="chapter" data-level="6.1.2" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:readBUGSmodel"><i class="fa fa-check"></i><b>6.1.2</b> Creating a model from standard BUGS and JAGS input files</a></li>
<li class="chapter" data-level="6.1.3" data-path="cha-building-models.html"><a href="cha-building-models.html#sub:multiple-instances"><i class="fa fa-check"></i><b>6.1.3</b> Making multiple instances from the same model definition</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:nodes-and-variables"><i class="fa fa-check"></i><b>6.2</b> NIMBLE models are objects you can query and manipulate</a>
<ul>
<li class="chapter" data-level="6.2.1" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:what-are-nodes-and-variables"><i class="fa fa-check"></i><b>6.2.1</b> What are variables and nodes?</a></li>
<li class="chapter" data-level="6.2.2" data-path="cha-building-models.html"><a href="cha-building-models.html#determining-the-nodes-and-variables-in-a-model"><i class="fa fa-check"></i><b>6.2.2</b> Determining the nodes and variables in a model</a></li>
<li class="chapter" data-level="6.2.3" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:accessing-nodes"><i class="fa fa-check"></i><b>6.2.3</b> Accessing nodes</a></li>
<li class="chapter" data-level="6.2.4" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:how-nodes-are"><i class="fa fa-check"></i><b>6.2.4</b> How nodes are named</a></li>
<li class="chapter" data-level="6.2.5" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:why-use-node"><i class="fa fa-check"></i><b>6.2.5</b> Why use node names?</a></li>
<li class="chapter" data-level="6.2.6" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:cdisdata"><i class="fa fa-check"></i><b>6.2.6</b> Checking if a node holds data</a></li>
</ul></li>
<li class="chapter" data-level="6.3" data-path="cha-building-models.html"><a href="cha-building-models.html#using-models-in-parallel"><i class="fa fa-check"></i><b>6.3</b> Using models in parallel</a></li>
</ul></li>
<li class="part"><span><b>III Algorithms in NIMBLE</b></span></li>
<li class="chapter" data-level="7" data-path="cha-mcmc.html"><a href="cha-mcmc.html"><i class="fa fa-check"></i><b>7</b> MCMC</a>
<ul>
<li class="chapter" data-level="7.1" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:nimbleMCMC"><i class="fa fa-check"></i><b>7.1</b> One-line invocation of MCMC: <em>nimbleMCMC</em></a></li>
<li class="chapter" data-level="7.2" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:mcmc-configuration"><i class="fa fa-check"></i><b>7.2</b> The MCMC configuration</a>
<ul>
<li class="chapter" data-level="7.2.1" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:default-mcmc-conf"><i class="fa fa-check"></i><b>7.2.1</b> Default MCMC configuration</a></li>
<li class="chapter" data-level="7.2.2" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:customizing-mcmc-conf"><i class="fa fa-check"></i><b>7.2.2</b> Customizing the MCMC configuration</a></li>
</ul></li>
<li class="chapter" data-level="7.3" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:build-compile-mcmc"><i class="fa fa-check"></i><b>7.3</b> Building and compiling the MCMC</a></li>
<li class="chapter" data-level="7.4" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:initMCMC"><i class="fa fa-check"></i><b>7.4</b> Initializing MCMC</a></li>
<li class="chapter" data-level="7.5" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:runMCMC"><i class="fa fa-check"></i><b>7.5</b> User-friendly execution of MCMC algorithms: <em>runMCMC</em></a></li>
<li class="chapter" data-level="7.6" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:executing-the-mcmc-algorithm"><i class="fa fa-check"></i><b>7.6</b> Running the MCMC</a>
<ul>
<li class="chapter" data-level="7.6.1" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:mcmc-rerun"><i class="fa fa-check"></i><b>7.6.1</b> Rerunning versus restarting an MCMC</a></li>
<li class="chapter" data-level="7.6.2" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:sampler-time"><i class="fa fa-check"></i><b>7.6.2</b> Measuring sampler computation times: <em>getTimes</em></a></li>
<li class="chapter" data-level="7.6.3" data-path="cha-mcmc.html"><a href="cha-mcmc.html#assessing-the-adaption-process-of-rw-and-rw_block-samplers"><i class="fa fa-check"></i><b>7.6.3</b> Assessing the adaption process of <em>RW</em> and <em>RW_block</em> samplers</a></li>
</ul></li>
<li class="chapter" data-level="7.7" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:extracting-samples"><i class="fa fa-check"></i><b>7.7</b> Extracting MCMC samples</a></li>
<li class="chapter" data-level="7.8" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:WAIC"><i class="fa fa-check"></i><b>7.8</b> Calculating WAIC</a></li>
<li class="chapter" data-level="7.9" data-path="cha-mcmc.html"><a href="cha-mcmc.html#k-fold-cross-validation"><i class="fa fa-check"></i><b>7.9</b> k-fold cross-validation</a></li>
<li class="chapter" data-level="7.10" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:rjmcmc"><i class="fa fa-check"></i><b>7.10</b> Variable selection using Reversible Jump MCMC</a>
<ul>
<li class="chapter" data-level="7.10.1" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:rjmcmc-indicator"><i class="fa fa-check"></i><b>7.10.1</b> Using indicator variables</a></li>
<li class="chapter" data-level="7.10.2" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:rjmcmc-no-indicator"><i class="fa fa-check"></i><b>7.10.2</b> Without indicator variables</a></li>
</ul></li>
<li class="chapter" data-level="7.11" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:samplers-provided"><i class="fa fa-check"></i><b>7.11</b> Samplers provided with NIMBLE</a>
<ul>
<li class="chapter" data-level="7.11.1" data-path="cha-mcmc.html"><a href="cha-mcmc.html#conjugate-gibbs-samplers"><i class="fa fa-check"></i><b>7.11.1</b> Conjugate (‘Gibbs’) samplers</a></li>
<li class="chapter" data-level="7.11.2" data-path="cha-mcmc.html"><a href="cha-mcmc.html#subsec:HMC"><i class="fa fa-check"></i><b>7.11.2</b> Hamiltonian Monte Carlo (HMC)</a></li>
<li class="chapter" data-level="7.11.3" data-path="cha-mcmc.html"><a href="cha-mcmc.html#particle-filter-samplers"><i class="fa fa-check"></i><b>7.11.3</b> Particle filter samplers</a></li>
<li class="chapter" data-level="7.11.4" data-path="cha-mcmc.html"><a href="cha-mcmc.html#customized-log-likelihood-evaluations-rw_llfunction-sampler"><i class="fa fa-check"></i><b>7.11.4</b> Customized log-likelihood evaluations: <em>RW_llFunction sampler</em></a></li>
</ul></li>
<li class="chapter" data-level="7.12" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:mcmc-example-litters"><i class="fa fa-check"></i><b>7.12</b> Detailed MCMC example: <em>litters</em></a></li>
<li class="chapter" data-level="7.13" data-path="cha-mcmc.html"><a href="cha-mcmc.html#mcmc-suite-compare-mcmcs"><i class="fa fa-check"></i><b>7.13</b> Comparing different MCMCs with <em>MCMCsuite</em> and <em>compareMCMCs</em></a></li>
<li class="chapter" data-level="7.14" data-path="cha-mcmc.html"><a href="cha-mcmc.html#running-mcmc-chains-in-parallel"><i class="fa fa-check"></i><b>7.14</b> Running MCMC chains in parallel</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html"><i class="fa fa-check"></i><b>8</b> Particle Filters, PMCMC, MCEM, Laplace approximation and quadrature</a>
<ul>
<li class="chapter" data-level="8.1" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#particle-filters-sequential-monte-carlo-and-iterated-filtering"><i class="fa fa-check"></i><b>8.1</b> Particle filters / sequential Monte Carlo and iterated filtering</a>
<ul>
<li class="chapter" data-level="8.1.1" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#filtering-algorithms"><i class="fa fa-check"></i><b>8.1.1</b> Filtering algorithms</a></li>
<li class="chapter" data-level="8.1.2" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#sec:particle-mcmc"><i class="fa fa-check"></i><b>8.1.2</b> Particle MCMC (PMCMC)</a></li>
</ul></li>
<li class="chapter" data-level="8.2" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#monte-carlo-expectation-maximization-mcem"><i class="fa fa-check"></i><b>8.2</b> Monte Carlo Expectation Maximization (MCEM)</a>
<ul>
<li class="chapter" data-level="8.2.1" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#sec:estimate-mcem-cov"><i class="fa fa-check"></i><b>8.2.1</b> Estimating the asymptotic covariance From MCEM</a></li>
</ul></li>
<li class="chapter" data-level="8.3" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#laplace-approximation-and-adaptive-gauss-hermite-quadrature"><i class="fa fa-check"></i><b>8.3</b> Laplace approximation and adaptive Gauss-Hermite quadrature</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="cha-spatial.html"><a href="cha-spatial.html"><i class="fa fa-check"></i><b>9</b> Spatial models</a>
<ul>
<li class="chapter" data-level="9.1" data-path="cha-spatial.html"><a href="cha-spatial.html#intrinsic-gaussian-car-model-dcar_normal"><i class="fa fa-check"></i><b>9.1</b> Intrinsic Gaussian CAR model: <em>dcar_normal</em></a>
<ul>
<li class="chapter" data-level="9.1.1" data-path="cha-spatial.html"><a href="cha-spatial.html#specification-and-density"><i class="fa fa-check"></i><b>9.1.1</b> Specification and density</a></li>
<li class="chapter" data-level="9.1.2" data-path="cha-spatial.html"><a href="cha-spatial.html#example"><i class="fa fa-check"></i><b>9.1.2</b> Example</a></li>
</ul></li>
<li class="chapter" data-level="9.2" data-path="cha-spatial.html"><a href="cha-spatial.html#proper-gaussian-car-model-dcar_proper"><i class="fa fa-check"></i><b>9.2</b> Proper Gaussian CAR model: <em>dcar_proper</em></a>
<ul>
<li class="chapter" data-level="9.2.1" data-path="cha-spatial.html"><a href="cha-spatial.html#specification-and-density-1"><i class="fa fa-check"></i><b>9.2.1</b> Specification and density</a></li>
<li class="chapter" data-level="9.2.2" data-path="cha-spatial.html"><a href="cha-spatial.html#example-1"><i class="fa fa-check"></i><b>9.2.2</b> Example</a></li>
</ul></li>
<li class="chapter" data-level="9.3" data-path="cha-spatial.html"><a href="cha-spatial.html#sec:spatial-mcmc-sampling-car"><i class="fa fa-check"></i><b>9.3</b> MCMC Sampling of CAR models</a>
<ul>
<li class="chapter" data-level="9.3.1" data-path="cha-spatial.html"><a href="cha-spatial.html#initial-values"><i class="fa fa-check"></i><b>9.3.1</b> Initial values</a></li>
<li class="chapter" data-level="9.3.2" data-path="cha-spatial.html"><a href="cha-spatial.html#zero-neighbor-regions"><i class="fa fa-check"></i><b>9.3.2</b> Zero-neighbor regions</a></li>
<li class="chapter" data-level="9.3.3" data-path="cha-spatial.html"><a href="cha-spatial.html#zero-mean-constraint"><i class="fa fa-check"></i><b>9.3.3</b> Zero-mean constraint</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="cha-bnp.html"><a href="cha-bnp.html"><i class="fa fa-check"></i><b>10</b> Bayesian nonparametric models</a>
<ul>
<li class="chapter" data-level="10.1" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:bnpmixtures"><i class="fa fa-check"></i><b>10.1</b> Bayesian nonparametric mixture models</a></li>
<li class="chapter" data-level="10.2" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:crp"><i class="fa fa-check"></i><b>10.2</b> Chinese Restaurant Process model</a>
<ul>
<li class="chapter" data-level="10.2.1" data-path="cha-bnp.html"><a href="cha-bnp.html#specification-and-density-2"><i class="fa fa-check"></i><b>10.2.1</b> Specification and density</a></li>
<li class="chapter" data-level="10.2.2" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:excrp"><i class="fa fa-check"></i><b>10.2.2</b> Example</a></li>
<li class="chapter" data-level="10.2.3" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:extensionscrp"><i class="fa fa-check"></i><b>10.2.3</b> Extensions</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:sb"><i class="fa fa-check"></i><b>10.3</b> Stick-breaking model</a>
<ul>
<li class="chapter" data-level="10.3.1" data-path="cha-bnp.html"><a href="cha-bnp.html#specification-and-function"><i class="fa fa-check"></i><b>10.3.1</b> Specification and function</a></li>
<li class="chapter" data-level="10.3.2" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:exsb"><i class="fa fa-check"></i><b>10.3.2</b> Example</a></li>
</ul></li>
<li class="chapter" data-level="10.4" data-path="cha-bnp.html"><a href="cha-bnp.html#mcmc-sampling-of-bnp-models"><i class="fa fa-check"></i><b>10.4</b> MCMC sampling of BNP models</a>
<ul>
<li class="chapter" data-level="10.4.1" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:mcmcdcrp"><i class="fa fa-check"></i><b>10.4.1</b> Sampling CRP models</a></li>
<li class="chapter" data-level="10.4.2" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:mcmcsb"><i class="fa fa-check"></i><b>10.4.2</b> Sampling stick-breaking models</a></li>
</ul></li>
</ul></li>
<li class="part"><span><b>IV Programming with NIMBLE</b></span></li>
<li class="chapter" data-level="" data-path="overview.html"><a href="overview.html"><i class="fa fa-check"></i>Overview</a></li>
<li class="chapter" data-level="11" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html"><i class="fa fa-check"></i><b>11</b> Writing simple nimbleFunctions</a>
<ul>
<li class="chapter" data-level="11.1" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:RC-intro"><i class="fa fa-check"></i><b>11.1</b> Introduction to simple nimbleFunctions</a></li>
<li class="chapter" data-level="11.2" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:r-fiunctions-implemented"><i class="fa fa-check"></i><b>11.2</b> R functions (or variants) implemented in NIMBLE</a>
<ul>
<li class="chapter" data-level="11.2.1" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#finding-help-for-nimbles-versions-of-r-functions"><i class="fa fa-check"></i><b>11.2.1</b> Finding help for NIMBLE’s versions of R functions</a></li>
<li class="chapter" data-level="11.2.2" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#basic-operations"><i class="fa fa-check"></i><b>11.2.2</b> Basic operations</a></li>
<li class="chapter" data-level="11.2.3" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:basic-math-linear"><i class="fa fa-check"></i><b>11.2.3</b> Math and linear algebra</a></li>
<li class="chapter" data-level="11.2.4" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:nimble-dist-funs"><i class="fa fa-check"></i><b>11.2.4</b> Distribution functions</a></li>
<li class="chapter" data-level="11.2.5" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:basic-flow-control"><i class="fa fa-check"></i><b>11.2.5</b> Flow control: <em>if-then-else</em>, <em>for</em>, <em>while</em>, and <em>stop</em></a></li>
<li class="chapter" data-level="11.2.6" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:print"><i class="fa fa-check"></i><b>11.2.6</b> <em>print</em> and <em>cat</em></a></li>
<li class="chapter" data-level="11.2.7" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:check-user-interr"><i class="fa fa-check"></i><b>11.2.7</b> Checking for user interrupts: <em>checkInterrupt</em></a></li>
<li class="chapter" data-level="11.2.8" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#optimization-optim-and-nimoptim"><i class="fa fa-check"></i><b>11.2.8</b> Optimization: <em>optim</em> and <em>nimOptim</em></a></li>
<li class="chapter" data-level="11.2.9" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#integration-integrate-and-nimintegrate"><i class="fa fa-check"></i><b>11.2.9</b> Integration: <em>integrate</em> and <em>nimIntegrate</em></a></li>
<li class="chapter" data-level="11.2.10" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:altern-keyw-some"><i class="fa fa-check"></i><b>11.2.10</b> ‘nim’ synonyms for some functions</a></li>
</ul></li>
<li class="chapter" data-level="11.3" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:how-nimble-handles"><i class="fa fa-check"></i><b>11.3</b> How NIMBLE handles types of variables</a>
<ul>
<li class="chapter" data-level="11.3.1" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:nimbleList-RCFuns"><i class="fa fa-check"></i><b>11.3.1</b> nimbleList data structures</a></li>
<li class="chapter" data-level="11.3.2" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:how-types-work"><i class="fa fa-check"></i><b>11.3.2</b> How numeric types work</a></li>
</ul></li>
<li class="chapter" data-level="11.4" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:decl-argum-return"><i class="fa fa-check"></i><b>11.4</b> Declaring argument and return types</a></li>
<li class="chapter" data-level="11.5" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:comp-nimbl-pass"><i class="fa fa-check"></i><b>11.5</b> Compiled nimbleFunctions pass arguments by reference</a></li>
<li class="chapter" data-level="11.6" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:calling-external-code"><i class="fa fa-check"></i><b>11.6</b> Calling external compiled code</a></li>
<li class="chapter" data-level="11.7" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:calling-R-code"><i class="fa fa-check"></i><b>11.7</b> Calling uncompiled R functions from compiled nimbleFunctions</a></li>
</ul></li>
<li class="chapter" data-level="12" data-path="cha-user-defined.html"><a href="cha-user-defined.html"><i class="fa fa-check"></i><b>12</b> Creating user-defined distributions and functions for models</a>
<ul>
<li class="chapter" data-level="12.1" data-path="cha-user-defined.html"><a href="cha-user-defined.html#sec:user-functions"><i class="fa fa-check"></i><b>12.1</b> User-defined functions</a></li>
<li class="chapter" data-level="12.2" data-path="cha-user-defined.html"><a href="cha-user-defined.html#sec:user-distributions"><i class="fa fa-check"></i><b>12.2</b> User-defined distributions</a>
<ul>
<li class="chapter" data-level="12.2.1" data-path="cha-user-defined.html"><a href="cha-user-defined.html#sec:registerDistributions"><i class="fa fa-check"></i><b>12.2.1</b> Using <em>registerDistributions</em> for alternative parameterizations and providing other information</a></li>
</ul></li>
<li class="chapter" data-level="12.3" data-path="cha-user-defined.html"><a href="cha-user-defined.html#sec:adv-user-def"><i class="fa fa-check"></i><b>12.3</b> Advanced user-defined functions and distributions</a></li>
<li class="chapter" data-level="12.4" data-path="cha-user-defined.html"><a href="cha-user-defined.html#sec:user-macros"><i class="fa fa-check"></i><b>12.4</b> User-defined model macros</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="cha-using-models.html"><a href="cha-using-models.html"><i class="fa fa-check"></i><b>13</b> Working with NIMBLE models</a>
<ul>
<li class="chapter" data-level="13.1" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:accessing-variables"><i class="fa fa-check"></i><b>13.1</b> The variables and nodes in a NIMBLE model</a>
<ul>
<li class="chapter" data-level="13.1.1" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:get-nodes"><i class="fa fa-check"></i><b>13.1.1</b> Determining the nodes in a model</a></li>
<li class="chapter" data-level="13.1.2" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:introduced-nodes"><i class="fa fa-check"></i><b>13.1.2</b> Understanding lifted nodes</a></li>
<li class="chapter" data-level="13.1.3" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:cdgetdependencies"><i class="fa fa-check"></i><b>13.1.3</b> Determining dependencies in a model</a></li>
</ul></li>
<li class="chapter" data-level="13.2" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:nodeInfo"><i class="fa fa-check"></i><b>13.2</b> Accessing information about nodes and variables</a>
<ul>
<li class="chapter" data-level="13.2.1" data-path="cha-using-models.html"><a href="cha-using-models.html#getting-distributional-information-about-a-node"><i class="fa fa-check"></i><b>13.2.1</b> Getting distributional information about a node</a></li>
<li class="chapter" data-level="13.2.2" data-path="cha-using-models.html"><a href="cha-using-models.html#getting-information-about-a-distribution"><i class="fa fa-check"></i><b>13.2.2</b> Getting information about a distribution</a></li>
<li class="chapter" data-level="13.2.3" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:getParam"><i class="fa fa-check"></i><b>13.2.3</b> Getting distribution parameter values for a node</a></li>
<li class="chapter" data-level="13.2.4" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:getBound"><i class="fa fa-check"></i><b>13.2.4</b> Getting distribution bounds for a node</a></li>
</ul></li>
<li class="chapter" data-level="13.3" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:cdcalc-cdsim-cdgetl"><i class="fa fa-check"></i><b>13.3</b> Carrying out model calculations</a>
<ul>
<li class="chapter" data-level="13.3.1" data-path="cha-using-models.html"><a href="cha-using-models.html#core-model-operations-calculation-and-simulation"><i class="fa fa-check"></i><b>13.3.1</b> Core model operations: calculation and simulation</a></li>
<li class="chapter" data-level="13.3.2" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:cdsimn-cdcalcn-cdget"><i class="fa fa-check"></i><b>13.3.2</b> Pre-defined nimbleFunctions for operating on model nodes: <em>simNodes</em>, <em>calcNodes</em>, and <em>getLogProbNodes</em></a></li>
<li class="chapter" data-level="13.3.3" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:access-log-prob"><i class="fa fa-check"></i><b>13.3.3</b> Accessing log probabilities via <em>logProb</em> variables</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="14" data-path="cha-data-structures.html"><a href="cha-data-structures.html"><i class="fa fa-check"></i><b>14</b> Data structures in NIMBLE</a>
<ul>
<li class="chapter" data-level="14.1" data-path="cha-data-structures.html"><a href="cha-data-structures.html#sec:modelValues-struct"><i class="fa fa-check"></i><b>14.1</b> The modelValues data structure</a>
<ul>
<li class="chapter" data-level="14.1.1" data-path="cha-data-structures.html"><a href="cha-data-structures.html#creating-modelvalues-objects"><i class="fa fa-check"></i><b>14.1.1</b> Creating modelValues objects</a></li>
<li class="chapter" data-level="14.1.2" data-path="cha-data-structures.html"><a href="cha-data-structures.html#sec:access-cont-modelv"><i class="fa fa-check"></i><b>14.1.2</b> Accessing contents of modelValues</a></li>
</ul></li>
<li class="chapter" data-level="14.2" data-path="cha-data-structures.html"><a href="cha-data-structures.html#sec:nimbleLists"><i class="fa fa-check"></i><b>14.2</b> The nimbleList data structure</a>
<ul>
<li class="chapter" data-level="14.2.1" data-path="cha-data-structures.html"><a href="cha-data-structures.html#sec:predef-nimbleLists"><i class="fa fa-check"></i><b>14.2.1</b> Pre-defined nimbleList types</a></li>
<li class="chapter" data-level="14.2.2" data-path="cha-data-structures.html"><a href="cha-data-structures.html#sec:eigen-nimFunctions"><i class="fa fa-check"></i><b>14.2.2</b> Using <em>eigen</em> and <em>svd</em> in nimbleFunctions</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="15" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html"><i class="fa fa-check"></i><b>15</b> Writing nimbleFunctions to interact with models</a>
<ul>
<li class="chapter" data-level="15.1" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:writ-nimble-funct"><i class="fa fa-check"></i><b>15.1</b> Overview</a></li>
<li class="chapter" data-level="15.2" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:using-comp-nimbl"><i class="fa fa-check"></i><b>15.2</b> Using and compiling nimbleFunctions</a></li>
<li class="chapter" data-level="15.3" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#writing-setup-code"><i class="fa fa-check"></i><b>15.3</b> Writing setup code</a>
<ul>
<li class="chapter" data-level="15.3.1" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#useful-tools-for-setup-functions"><i class="fa fa-check"></i><b>15.3.1</b> Useful tools for setup functions</a></li>
<li class="chapter" data-level="15.3.2" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:access-modify-numer"><i class="fa fa-check"></i><b>15.3.2</b> Accessing and modifying numeric values from setup</a></li>
<li class="chapter" data-level="15.3.3" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#determining-numeric-types-in-nimblefunctions"><i class="fa fa-check"></i><b>15.3.3</b> Determining numeric types in nimbleFunctions</a></li>
<li class="chapter" data-level="15.3.4" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:determ-pers-texttts"><i class="fa fa-check"></i><b>15.3.4</b> Control of setup outputs</a></li>
</ul></li>
<li class="chapter" data-level="15.4" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:nimble-lang-comp"><i class="fa fa-check"></i><b>15.4</b> Writing run code</a>
<ul>
<li class="chapter" data-level="15.4.1" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:driv-models:-calc"><i class="fa fa-check"></i><b>15.4.1</b> Driving models: <em>calculate</em>, <em>calculateDiff</em>, <em>simulate</em>, <em>getLogProb</em></a></li>
<li class="chapter" data-level="15.4.2" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#getting-and-setting-variable-and-node-values"><i class="fa fa-check"></i><b>15.4.2</b> Getting and setting variable and node values</a></li>
<li class="chapter" data-level="15.4.3" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#getting-parameter-values-and-node-bounds"><i class="fa fa-check"></i><b>15.4.3</b> Getting parameter values and node bounds</a></li>
<li class="chapter" data-level="15.4.4" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:access-model-modelv"><i class="fa fa-check"></i><b>15.4.4</b> Using modelValues objects</a></li>
<li class="chapter" data-level="15.4.5" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:using-model-variable"><i class="fa fa-check"></i><b>15.4.5</b> Using model variables and modelValues in expressions</a></li>
<li class="chapter" data-level="15.4.6" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:incl-other-meth"><i class="fa fa-check"></i><b>15.4.6</b> Including other methods in a nimbleFunction</a></li>
<li class="chapter" data-level="15.4.7" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:using-other-nimbl"><i class="fa fa-check"></i><b>15.4.7</b> Using other nimbleFunctions</a></li>
<li class="chapter" data-level="15.4.8" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:virt-nimbl-nimbl"><i class="fa fa-check"></i><b>15.4.8</b> Virtual nimbleFunctions and nimbleFunctionLists</a></li>
<li class="chapter" data-level="15.4.9" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#character-objects"><i class="fa fa-check"></i><b>15.4.9</b> Character objects</a></li>
<li class="chapter" data-level="15.4.10" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:user-defined-data"><i class="fa fa-check"></i><b>15.4.10</b> User-defined data structures</a></li>
</ul></li>
<li class="chapter" data-level="15.5" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:user-samplers"><i class="fa fa-check"></i><b>15.5</b> Example: writing user-defined samplers to extend NIMBLE’s MCMC engine</a>
<ul>
<li class="chapter" data-level="15.5.1" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#user-defined-samplers-and-posterior-predictive-nodes"><i class="fa fa-check"></i><b>15.5.1</b> User-defined samplers and posterior predictive nodes</a></li>
</ul></li>
<li class="chapter" data-level="15.6" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#copying-nimblefunctions-and-nimble-models"><i class="fa fa-check"></i><b>15.6</b> Copying nimbleFunctions (and NIMBLE models)</a></li>
<li class="chapter" data-level="15.7" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:debugging"><i class="fa fa-check"></i><b>15.7</b> Debugging nimbleFunctions</a></li>
<li class="chapter" data-level="15.8" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#timing-nimblefunctions-with-run.time"><i class="fa fa-check"></i><b>15.8</b> Timing nimbleFunctions with <em>run.time</em></a></li>
<li class="chapter" data-level="15.9" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#clearing-and-unloading-compiled-objects"><i class="fa fa-check"></i><b>15.9</b> Clearing and unloading compiled objects</a></li>
<li class="chapter" data-level="15.10" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#reducing-memory-usage"><i class="fa fa-check"></i><b>15.10</b> Reducing memory usage</a></li>
</ul></li>
<li class="part"><span><b>V Automatic Derivatives in NIMBLE</b></span></li>
<li class="chapter" data-level="16" data-path="cha-AD.html"><a href="cha-AD.html"><i class="fa fa-check"></i><b>16</b> Automatic Derivatives</a>
<ul>
<li class="chapter" data-level="16.1" data-path="cha-AD.html"><a href="cha-AD.html#sec:use-derivs"><i class="fa fa-check"></i><b>16.1</b> How to turn on derivatives in a model</a>
<ul>
<li class="chapter" data-level="16.1.1" data-path="cha-AD.html"><a href="cha-AD.html#finish-setting-up-the-glmm-example"><i class="fa fa-check"></i><b>16.1.1</b> Finish setting up the GLMM example</a></li>
</ul></li>
<li class="chapter" data-level="16.2" data-path="cha-AD.html"><a href="cha-AD.html#sec:AD-laplace"><i class="fa fa-check"></i><b>16.2</b> How to use Laplace approximation and adaptive Gauss-Hermite quadrature</a>
<ul>
<li class="chapter" data-level="16.2.1" data-path="cha-AD.html"><a href="cha-AD.html#using-the-laplace-approximation-methods-directly"><i class="fa fa-check"></i><b>16.2.1</b> Using the Laplace approximation methods directly</a></li>
<li class="chapter" data-level="16.2.2" data-path="cha-AD.html"><a href="cha-AD.html#changing-the-optimization-methods"><i class="fa fa-check"></i><b>16.2.2</b> Changing the optimization methods</a></li>
</ul></li>
<li class="chapter" data-level="16.3" data-path="cha-AD.html"><a href="cha-AD.html#sec:AD-user-def"><i class="fa fa-check"></i><b>16.3</b> How to support derivatives in user-defined functions and distributions</a></li>
<li class="chapter" data-level="16.4" data-path="cha-AD.html"><a href="cha-AD.html#what-operations-are-and-arent-supported-for-ad"><i class="fa fa-check"></i><b>16.4</b> What operations are and aren’t supported for AD</a></li>
<li class="chapter" data-level="16.5" data-path="cha-AD.html"><a href="cha-AD.html#basics-of-obtaining-derivatives-in-nimblefunctions"><i class="fa fa-check"></i><b>16.5</b> Basics of obtaining derivatives in <code>nimbleFunctions</code></a>
<ul>
<li class="chapter" data-level="16.5.1" data-path="cha-AD.html"><a href="cha-AD.html#checking-derivatives-with-uncompiled-execution"><i class="fa fa-check"></i><b>16.5.1</b> Checking derivatives with uncompiled execution</a></li>
<li class="chapter" data-level="16.5.2" data-path="cha-AD.html"><a href="cha-AD.html#sec:AD-holding-out"><i class="fa fa-check"></i><b>16.5.2</b> Holding some local variables out of derivative tracking</a></li>
<li class="chapter" data-level="16.5.3" data-path="cha-AD.html"><a href="cha-AD.html#sec:AD-multiple-NF"><i class="fa fa-check"></i><b>16.5.3</b> Using AD with multiple nimbleFunctions</a></li>
<li class="chapter" data-level="16.5.4" data-path="cha-AD.html"><a href="cha-AD.html#sec:understanding-more-AD"><i class="fa fa-check"></i><b>16.5.4</b> Understanding more about how AD works: <em>taping</em> of operations</a></li>
<li class="chapter" data-level="16.5.5" data-path="cha-AD.html"><a href="cha-AD.html#resetting-a-nimderivs-call"><i class="fa fa-check"></i><b>16.5.5</b> Resetting a <code>nimDerivs</code> call</a></li>
<li class="chapter" data-level="16.5.6" data-path="cha-AD.html"><a href="cha-AD.html#a-note-on-performance-benchmarking"><i class="fa fa-check"></i><b>16.5.6</b> A note on performance benchmarking</a></li>
</ul></li>
<li class="chapter" data-level="16.6" data-path="cha-AD.html"><a href="cha-AD.html#advanced-uses-double-taping"><i class="fa fa-check"></i><b>16.6</b> Advanced uses: double taping</a></li>
<li class="chapter" data-level="16.7" data-path="cha-AD.html"><a href="cha-AD.html#derivatives-involving-model-calculations"><i class="fa fa-check"></i><b>16.7</b> Derivatives involving model calculations</a>
<ul>
<li class="chapter" data-level="16.7.1" data-path="cha-AD.html"><a href="cha-AD.html#method-1-nimderivs-of-modelcalculate"><i class="fa fa-check"></i><b>16.7.1</b> Method 1: <code>nimDerivs</code> of <code>model$calculate</code></a></li>
<li class="chapter" data-level="16.7.2" data-path="cha-AD.html"><a href="cha-AD.html#method-2-nimderivs-of-a-method-that-calls-modelcalculate"><i class="fa fa-check"></i><b>16.7.2</b> Method 2: <code>nimDerivs</code> of a method that calls <code>model$calculate</code></a></li>
</ul></li>
<li class="chapter" data-level="16.8" data-path="cha-AD.html"><a href="cha-AD.html#sec:parameter-transform"><i class="fa fa-check"></i><b>16.8</b> Parameter transformations</a></li>
</ul></li>
<li class="chapter" data-level="17" data-path="example-maximum-likelihood-estimation-using-optim-with-gradients-from-nimderivs..html"><a href="example-maximum-likelihood-estimation-using-optim-with-gradients-from-nimderivs..html"><i class="fa fa-check"></i><b>17</b> Example: maximum likelihood estimation using <code>optim</code> with gradients from <code>nimDerivs</code>.</a></li>
<li class="chapter" data-level="" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i>References</a></li>
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<h1>Overview<a href="overview.html#overview" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<p>Part IV is the programmer’s guide to NIMBLE. At the heart of programming in NIMBLE are nimbleFunctions. These support two principal features: (1) a <em>setup</em> function that is run once for each model, nodes, or other setup arguments, and (2) <em>run</em> functions that will be compiled to C++ and are written in a subset of R enhanced with features to operate models. Formally, what can be compiled comprises the NIMBLE language, which is designed to be R-like.</p>
<p>This part of the manual is organized as follows:</p>
<ul>
<li>Chapter <a href="cha-RCfunctions.html#cha-RCfunctions">11</a> describes how to write simple nimbleFunctions, which have no setup code and hence don’t interact with models, to compile parts of R for fast calculations. This covers the subset of R that is compilable, how to declare argument types and return types, and other information.</li>
<li>Chapter <a href="cha-user-defined.html#cha-user-defined">12</a> explains how to write nimbleFunctions that can be included in BUGS code as user-defined distributions or user-defined functions.</li>
<li>Chapter <a href="cha-using-models.html#cha-using-models">13</a> introduces more features of NIMBLE models that are useful for writing nimbleFunctions to use models, focusing on how to query model structure and carry out model calculations.<br />
</li>
<li>Chapter <a href="cha-data-structures.html#cha-data-structures">14</a> introduces two kinds of data structures: <code>modelValues</code> are used for holding multiple sets of values of model variables; <code>nimbleList</code> data structures are similar to R lists but require fixed element names and types, allowing the NIMBLE compiler to use them.</li>
<li>Chapter <a href="cha-progr-with-models.html#cha-progr-with-models">15</a> draws on the previous chapters to show how to write nimbleFunctions that work with models, or more generally that have a setup function for any purpose. Typically a setup function queries model structure (Chapter <a href="cha-using-models.html#cha-using-models">13</a>) and may establish some <code>modelValues</code> or <code>nimbleList</code> data structures or configurations (Chapter <a href="cha-data-structures.html#cha-data-structures">14</a>). Then <em>run</em> functions written in the same way as simple nimbleFunctions (Chapter <a href="cha-RCfunctions.html#cha-RCfunctions">11</a>) along with model operations (Chapter <a href="cha-using-models.html#cha-using-models">13</a>) define algorithm computations that can be compiled via C++.</li>
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