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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

5,734

Version

0.6-8

License

BSD_3_clause + file LICENSE | GPL (>= 2)

Maintainer

Christopher Paciorek

Last Published

November 22nd, 2017

Functions in nimble (0.6-8)

Dirichlet

The Dirichlet Distribution
CAR-Normal

The CAR-Normal Distribution
ADNimbleList

CAR-Proper

The CAR-Proper Distribution
CmodelBaseClass-class

Class CmodelBaseClass
CnimbleFunctionBase-class

Class CnimbleFunctionBase
BUGSdeclClass-class

BUGSdeclClass contains the information extracted from one BUGS declaration
MCMCsuiteClass-class

Class MCMCsuiteClass
Constraint

Constraint calculations in NIMBLE
ModifiedRmmParseKeywords2

[[' = 'outputCppArrayIndex2',
MCMCconf-class

Class MCMCconf
CAR_calcNumIslands

Calculate number of islands based on a CAR adjacency matrix.
MCMCsuite

Executes multiple MCMC algorithms and organizes results.
Categorical

The Categorical Distribution
buildAuxiliaryFilter

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

The Inverse Gamma Distribution
buildBootstrapFilter

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

Automated parameter blocking procedure for efficient MCMC sampling
Inverse-Wishart

The Inverse Wishart Distribution
Rmatrix2mvOneVar

Set values of one variable of a modelValues object from an R matrix
Exponential

The Exponential Distribution
Wishart

The Wishart Distribution
Interval

Interval calculations
carMinBound

Calculate the lower bound for the autocorrelation parameter of the dcar_proper distribution
checkInterrupt

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

The Multinomial Distribution
MultivariateNormal

The Multivariate Normal Distribution
Multivariate-t

The Multivariate t Distribution
buildEnsembleKF

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

Create a Liu and West particle filter algorithm.
RmodelBaseClass-class

Class RmodelBaseClass
configureMCMC

Build the MCMCconf object for construction of an MCMC object
asRow

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

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

Get the directory path to one of the classic BUGS examples installed with NIMBLE package
as.carAdjacency

Convert CAR structural parameters to adjacency, weights, num format
getBound

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

Calculate bounds for the autocorrelation parameter of the dcar_proper distribution
as.carCM

Convert weights vector to parameters of dcar_proper distributio
codeBlockClass-class

Class codeBlockClass
carMaxBound

Calculate the upper bound for the autocorrelation parameter of the dcar_proper distribution
combine_MCMC_comparison_results

Combine multiple objects returned by compareMCMCs
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.
compareMCMCs

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

compile NIMBLE models and nimbleFunctions
declare

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

Returns number of rows of modelValues
getDefinition

Get nimbleFunction definition
identityMatrix

Create an Identity matrix
modelValuesConf

Create the confs for a custom NIMBLE modelValues object
makeParamInfo

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

Copying function for NIMBLE
make_MCMC_comparison_pages

Make html pages summarizing results from compareMCMCs
buildMCEM

Builds an MCEM algorithm from a given NIMBLE model
buildMCMC

Create an MCMC function, from an MCMCconf object
modelBaseClass-class

Class modelBaseClass
eigenNimbleList

eigenNimbleList definition
modelDefClass-class

Class for NIMBLE model definition
flat

The Improper Uniform Distribution
nimCat

cat function for use in nimbleFunctions
initializeModel

Performs initialization of nimble model node values and log probabilities
is.nf

check if a nimbleFunction
nimble-math

Mathematical functions for BUGS and nimbleFunction programming
deregisterDistributions

Remove user-supplied distributions from use in NIMBLE BUGS models
nimble

nimble
distributionInfo

Get information about a distribution
getLoadingNamespace

return the namespace in which a nimbleFunction is being loaded
getNimbleOption

Get NIMBLE Option
getParam

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

create a nimbleFunction
nimble-R-functions

NIMBLE language functions for R-like vector construction
nimbleFunctionBase-class

Class nimbleFunctionBase
nimble-internal

Functions and Classes Internal to NIMBLE
model_macro_builder

EXPERIMENTAL: Turn a function into a model macro builder A model macro expands one line of code in a nimbleModel into one or more new lines. This supports compact programming by defining re-usable modules. model_macro_builder takes as input a function that constructs new lines of model code from the original line of code. It returns a function suitable for internal use by nimbleModel that arranges arguments for input function. Macros are an experimental feature and are available only after setting nimbleOptions(enableModelMacros = TRUE).
nimbleFunctionList-class

Create a list of nimbleFunctions
is.nl

check if a nimbleList
nimEigen

Spectral Decomposition of a Matrix
makeBoundInfo

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

Creates matrix or array objects for use in nimbleFunctions
nimNumeric

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

Run one or more chains of an MCMC algorithm and return samples, summary and/or WAIC
nimbleFunctionVirtual

create a virtual nimbleFunction, a base class for other nimbleFunctions
samplerAssignmentRules-class

Class samplerAssignmentRules
registerDistributions

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

Rename a method in an object returned by compareMCMCs
modelValues

Create a NIMBLE modelValues Object
nimOptim

modelValuesBaseClass-class

Class modelValuesBaseClass
nimDerivs

Nimble Derivatives
nimOptimDefaultControl

nimDim

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

print function for use in nimbleFunctions
nimStop

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

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

Singular Value Decomposition of a Matrix
nimbleModel

Create a NIMBLE model from BUGS code
nimbleType-class

create a nimbleType object
withNimbleOptions

Temporarily set some NIMBLE options.
nimbleOptions

NIMBLE Options Settings
updateMCMCcomparisonWithHighOrderESS

Re-estimate effective sample size from results of compareMCMCs
optimDefaultControl

optimResultNimbleList

rankSample

Generates a weighted sample (with replacement) of ranks
run.time

Time execution of NIMBLE code
readBUGSmodel

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

Perform k-fold cross-validation on a NIMBLE model fit by MCMC
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.
reshape_comparison_results

Convert comparison results to a more general format
setSize

set the size of a numeric variable in NIMBLE
resize

Resizes a modelValues object
svdNimbleList

svdNimbleList definition
t

The t Distribution
sampler_BASE

MCMC Sampling Algorithms
nimbleMCMC

Executes one or more chains of NIMBLE's default MCMC algorithm, for a model specified using BUGS code
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.
nodeFunctions

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

testBUGSmodel

Tests BUGS examples in the NIMBLE system
setupOutputs

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

access (call) a member function of a nimbleFunction
simNodes

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

Access or set a member variable of a nimbleFunction
simNodesMV

Basic nimbleFunctions for using a NIMBLE model with sets of stored values
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
nimbleList

create a nimbleList
singleVarAccessClass-class

Class singleVarAccessClass