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UNIX

One can specify the path to where the Eigen header files are located and also whether to link common C++ files into every DSO/DLL we create or whether to treat the files as an extra library with:

R CMD INSTALL --configure-args='--with-eigen=/home/duncan/local --enable-lib' nimble

or, within R

install.packages("nimble", configure.args = c("--with-eigen=/home/duncan/local", "--enable-lib=true"), repos = NULL)

Windows

Typically, you need the R developer tools (i.e., compiler, make, etc.) to use nimble. Accordingly, it is quite straightforward to install the package from source as you will have the necessary tools already installed. These are available from the Rtools page on CRAN.

To install the package from source, from within R,

install.packages("nimble", type = "source", INSTALL_opts = "--merge-multiarch")

or from a local copy of the source package,

install.packages("nimble_0.6-2.tar.gz", repos = NULL, INSTALL_opts = "--merge-multiarch")

Alternatively, use the shell command (in the DOS Command prompt)

R CMD INSTALL --merge-multiarch nimble_0.6-2.tar.gz

Of course, you can also compile directly from a clone of the git repository:

R CMD INSTALL --merge-multiarch nimble

The --merge-multiarch is necessary when using a version of R that supports both 32 and 64 bit. This option to installation will ensure that create both 32 and 64 bit installations.

Creating a Windows Binary

R CMD build nimble
R CMD INSTALL --build --merge-multiarch nimble_0.6-2.tar.gz

We need to create the .tar.gz file first, hence the first command.

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Version

Install

install.packages('nimble')

Monthly Downloads

3,227

Version

0.6-6

License

BSD_3_clause + file LICENSE

Maintainer

Christopher Paciorek

Last Published

July 28th, 2017

Functions in nimble (0.6-6)

ADNimbleList

BUGSdeclClass-class

BUGSdeclClass contains the information extracted from one BUGS declaration
CAR-Normal

The CAR-Normal Distribution
CAR_calcNumIslands

Calculate number of islands (distinct connected groups) of CAR adjacency matrix.
CnimbleFunctionBase-class

Class CnimbleFunctionBase
Constraint

Constraint calculations in NIMBLE
Dirichlet

The Dirichlet Distribution
Exponential

The Exponential Distribution
Categorical

The Categorical Distribution
CmodelBaseClass-class

Class CmodelBaseClass
Interval

Interval calculations
ModifiedRmmParseKeywords2

[[' = 'outputCppArrayIndex2',
Multinomial

The Multinomial Distribution
Wishart

The Wishart Distribution
as.carAdjacency

Convert CAR structural parameters to adjecency, weights, num format
decide

Makes the Metropolis-Hastings acceptance decision, based upon the input (log) Metropolis-Hastings ratio
decideAndJump

Creates a nimbleFunction for executing the Metropolis-Hastings jumping decision, and updating values in the model, or in a carbon copy modelValues object, accordingly.
MCMCsuite

Executes multiple MCMC algorithms and organizes results.
MCMCsuiteClass-class

Class MCMCsuiteClass
buildAuxiliaryFilter

Create an auxiliary particle filter algorithm to estimate log-likelihood.
buildBootstrapFilter

Create a bootstrap particle filter algorithm to estimate log-likelihood.
Inverse-Gamma

The Inverse Gamma Distribution
buildEnsembleKF

Create an Ensemble Kalman filter algorithm to sample from latent states.
buildLiuWestFilter

Create a Liu and West particle filter algorithm.
combine_MCMC_comparison_results

Combine multiple objects returned by compareMCMCs
Multivariate-t

The Multivariate t Distribution
MultivariateNormal

The Multivariate Normal Distribution
Rmatrix2mvOneVar

Set values of one variable of a modelValues object from an R matrix
RmodelBaseClass-class

Class RmodelBaseClass
compareMCMCs

Run multiple MCMCs (packages or NIMBLE cases) for multiple models and return summary results
declare

Explicitly declare a variable in run-time code of a nimbleFunction
deregisterDistributions

Remove user-supplied distributions from use in NIMBLE BUGS models
is.nf

check if a nimbleFunction
distributionInfo

Get information about a distribution
eigenNimbleList

eigenNimbleList definition
identityMatrix

Create an Identity matrix
initializeModel

Performs initialization of nimble model node values and log probabilities
compileNimble

compile NIMBLE models and nimbleFunctions
configureMCMC

Build the MCMCconf object for construction of an MCMC object
flat

The Improper Uniform Distribution
getBUGSexampleDir

Get the directory path to one of the classic BUGS examples installed with NIMBLE package
nimCat

cat function for use in nimbleFunctions
nimCopy

Copying function for NIMBLE
nimOptimDefaultControl

nimPrint

print function for use in nimbleFunctions
make_MCMC_comparison_pages

Make html pages summarizing results from compareMCMCs
modelBaseClass-class

Class modelBaseClass
nfMethod

access (call) a member function of a nimbleFunction
nfVar

Access or set a member variable of a nimbleFunction
Inverse-Wishart

The Inverse Wishart Distribution
MCMCconf-class

Class MCMCconf
asRow

Turn a numeric vector into a single-row or single-column matrix
autoBlock

Automated parameter blocking procedure for efficient MCMC sampling
is.nl

check if a nimbleList
modelValuesBaseClass-class

Class modelValuesBaseClass
modelValuesConf

Create the confs for a custom NIMBLE modelValues object
nimStop

Halt execution of a nimbleFunction function method. Part of the NIMBLE language
checkInterrupt

Check for interrupt (e.g. Ctrl-C) during nimbleFunction execution. Part of the NIMBLE language.
codeBlockClass-class

Class codeBlockClass
getLoadingNamespace

return the namespace in which a nimbleFunction is being loaded
getNimbleOption

Get NIMBLE Option
buildMCEM

Builds an MCEM algorithm from a given NIMBLE model
buildMCMC

Create an MCMC function, from an MCMCconf object
getBound

Get value of bound of a stochastic node in a model
getDefinition

Get nimbleFunction definition
getParam

Get value of a parameter of a stochastic node in a model
getsize

Returns number of rows of modelValues
nimDerivs

Nimble Derivatives
nimble-math

Mathematical functions for BUGS and nimbleFunction programming
nimble

nimble
optimResultNimbleList

nimDim

return sizes of an object whether it is a vector, matrix or array
nimEigen

Spectral Decomposition of a Matrix
nimMatrix

Creates matrix or array objects for use in nimbleFunctions
nimbleFunctionList-class

Create a list of nimbleFunctions
nimSvd

Singular Value Decomposition of a Matrix
nimbleFunction

create a nimbleFunction
nimbleFunctionBase-class

Class nimbleFunctionBase
rankSample

Generates a weighted sample (with replacement) of ranks
setAndCalculateOne

Creates a nimbleFunction for setting the value of a scalar model node, calculating the associated deterministic dependents and logProb values, and returning the total sum log-probability.
setSize

set the size of a numeric variable in NIMBLE
svdNimbleList

svdNimbleList definition
t

The t Distribution
nimble-R-functions

NIMBLE language functions for R-like vector construction
nimble-internal

Functions and Classes Internal to NIMBLE
nimbleCode

Turn BUGS model code into an object for use in nimbleModel or readBUGSmodel
nimbleExternalCall

EXPERIMENTAL Create a nimbleFunction that wraps a call to external compiled code
optimControlNimbleList

optimDefaultControl

resize

Resizes a modelValues object
run.time

Time execution of NIMBLE code
testBUGSmodel

Tests BUGS examples in the NIMBLE system
nimbleOptions

NIMBLE Options Settings
nimbleRcall

EXPERIMENTAL Make an R function callable from compiled nimbleFunctions (including nimbleModels).
rename_MCMC_comparison_method

Rename a method in an object returned by compareMCMCs
reshape_comparison_results

Convert comparison results to a more general format
updateMCMCcomparisonWithHighOrderESS

Re-estimate effective sample size from results of compareMCMCs
valueInCompiledNimbleFunction

get or set value of member data from a compiled nimbleFunction using a multi-interface
values

Access or set values for a set of nodes in a model
nimbleFunctionVirtual

create a virtual nimbleFunction, a base class for other nimbleFunctions
readBUGSmodel

Create a NIMBLE BUGS model from a variety of input formats, including BUGS model files
registerDistributions

Add user-supplied distributions for use in NIMBLE BUGS models
makeBoundInfo

Make an object of information about a model-bound pairing for getBound. Used internally
makeParamInfo

Make an object of information about a model-parameter pairing for getParam. Used internally
modelDefClass-class

Class for NIMBLE model definition
modelValues

Create a NIMBLE modelValues Object
nimNumeric

Creates numeric, integer or logical vectors for use in nimbleFunctions
runMCMC

Run one or more chains of an MCMC algorithm and extract samples
samplerAssignmentRules-class

Class samplerAssignmentRules
simNodesMV

Basic nimbleFunctions for using a NIMBLE model with sets of stored values
singleVarAccessClass-class

Class singleVarAccessClass
nimOptim

nimbleList

create a nimbleList
nimbleModel

Create a NIMBLE model from BUGS code
nimbleType-class

create a nimbleType object
nodeFunctions

calculate, calculateDiff, simulate, or get the current log probabilities (densities) a set of nodes in a NIMBLE model
sampler_BASE

MCMC Sampling Algorithms
setAndCalculate

Creates a nimbleFunction for setting the values of one or more model nodes, calculating the associated deterministic dependents and logProb values, and returning the total sum log-probability.
toEigenCalls

[[' = 'sizeDoubleBracket', ## for nimbleFunctionList, this will always go through chainedCall(nfList[[i]], 'foo')(arg1, arg2) ## NEVER GETS MARKED WITH TOEIGENIZE
setupOutputs

Explicitly declare objects created in setup code to be preserved and compiled as member data
simNodes

Basic nimbleFunctions for calculate, simulate, and getLogProb with a set of nodes