The Multinomial Distribution
BUGSdeclClass contains the information extracted from one BUGS declaration
Turn a numeric vector into a single-row or single-column matrix
Get nimbleFunction definition
Convert weights vector to parameters of dcar_proper
distributio
Get value of bound of a stochastic node in a model
Builds an MCEM algorithm from a given NIMBLE model
Create a Liu and West particle filter algorithm.
Class MCMCconf
Executes multiple MCMC algorithms and organizes results.
The Exponential Distribution
Class MCMCsuiteClass
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)
.
The Inverse Gamma Distribution
Calculate bounds for the autocorrelation parameter of the dcar_proper
distribution
The Inverse Wishart Distribution
Create an MCMC function from a NIMBLE model, or an MCMC configuration object
The Dirichlet Distribution
The Double Exponential (Laplace) Distribution
access (call) a member function of a nimbleFunction
combine_MCMC_comparison_results
Combine multiple objects returned by compareMCMCs
Nimble wrapper around R's builtin optim
. Creates a deafult control
argument for nimOptim
. Interval calculations
Get information about a distribution
Run multiple MCMCs (packages or NIMBLE cases) for multiple models and return summary results
Convert CAR structural parameters to adjacency, weights, num format
The Wishart Distribution
eigenNimbleList definition
ModifiedRmmParseKeywords2
[[' = 'outputCppArrayIndex2',
Automated parameter blocking procedure for efficient MCMC sampling
Make an object of information about a model-bound pairing for getBound. Used internally
Make an object of information about a model-parameter pairing for getParam. Used internally
Create an auxiliary particle filter algorithm to estimate log-likelihood.
The Multivariate t Distribution
Explicitly declare a variable in run-time code of a nimbleFunction
Calculate the upper bound for the autocorrelation parameter of the dcar_proper
distribution
Calculate the lower bound for the autocorrelation parameter of the dcar_proper
distribution
compile NIMBLE models and nimbleFunctions
Creates matrix or array objects for use in nimbleFunctions
Remove user-supplied distributions from use in NIMBLE BUGS models
Class RmodelBaseClass
Functions and Classes Internal to NIMBLE
return the namespace in which a nimbleFunction is being loaded
Build the MCMCconf object for construction of an MCMC object
Creates numeric, integer or logical vectors for use in nimbleFunctions
Create a bootstrap particle filter algorithm to estimate log-likelihood.
The Stick Breaking Function
Mathematical functions for BUGS and nimbleFunction programming
Get NIMBLE Option
NIMBLE Options Settings
Make an R function callable from compiled nimbleFunctions (including nimbleModels).
Returns number of rows of modelValues
Create an Ensemble Kalman filter algorithm to sample from latent states.
Generates a weighted sample (with replacement) of ranks
Create an Identity matrix (Deprecated)
Create a nimbleFunction that wraps a call to external compiled code
Create a NIMBLE BUGS model from a variety of input formats, including BUGS model files
The Multivariate Normal Distribution
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.
set the size of a numeric variable in NIMBLE
Copying function for NIMBLE
create a nimbleFunction
Makes the Metropolis-Hastings acceptance decision, based upon the input (log) Metropolis-Hastings ratio
Creates a nimbleFunction for executing the Metropolis-Hastings jumping decision,
and updating values in the model, or in a carbon copy modelValues object, accordingly.
Nimble Derivatives
Set values of one variable of a modelValues object from an R matrix
Check for interrupt (e.g. Ctrl-C) during nimbleFunction execution. Part of the NIMBLE language.
The Improper Uniform Distribution
check if a nimbleFunction
print function for use in nimbleFunctions
check if a nimbleList
Tests BUGS examples in the NIMBLE system
Class codeBlockClass
Executes one or more chains of NIMBLE's default MCMC algorithm, for a model specified using BUGS code
Get the directory path to one of the classic BUGS examples installed with NIMBLE package
Get value of a parameter of a stochastic node in a model
make_MCMC_comparison_pages
Make html pages summarizing results from compareMCMCs
Get posterior samples for a Dirichlet process measure
modelValuesBaseClass-class
Class modelValuesBaseClass
updateMCMCcomparisonWithHighOrderESS
Re-estimate effective sample size from results of compareMCMCs
Create a NIMBLE model from BUGS code
Create the confs for a custom NIMBLE modelValues object
Class modelBaseClass
Singular Value Decomposition of a Matrix
Halt execution of a nimbleFunction function method. Part of the NIMBLE language
reshape_comparison_results
Convert comparison results to a more general format
Class for NIMBLE model definition
Create a NIMBLE modelValues Object
return sizes of an object whether it is a vector, matrix or array
Spectral Decomposition of a Matrix
create a virtual nimbleFunction, a base class for other nimbleFunctions
Class nimbleFunctionBase
Create a list of nimbleFunctions
Resizes a modelValues object
create a nimbleType object
Performs initialization of nimble model node values and log probabilities
calculate, calculateDiff, simulate, or get the current log probabilities (densities) a set of nodes in a NIMBLE model
Determine if any values in a vector are NA or NaN
Time execution of NIMBLE code
Access or set a member variable of a nimbleFunction
create a nimbleList
NIMBLE language functions for R-like vector construction
Add user-supplied distributions for use in NIMBLE BUGS models
Temporarily set some NIMBLE options.
The t Distribution
rename_MCMC_comparison_method
Rename a method in an object returned by compareMCMCs
EXPERIMENTAL Data type for the control
parameter of nimOptim
cat function for use in nimbleFunctions
svdNimbleList definition
Perform k-fold cross-validation on a NIMBLE model fit by MCMC
nimble
Turn BUGS model code into an object for use in nimbleModel
or readBUGSmodel
Print error messages after failed compilation
Explicitly declare objects created in setup code to be preserved and compiled as member data
Creates a deafult control
argument for optim
(just an empty list). EXPERIMENTAL Data type for the return value of nimOptim
Run one or more chains of an MCMC algorithm and return samples, summary and/or WAIC
Basic nimbleFunctions for using a NIMBLE model with sets of stored values
singleVarAccessClass-class
Class singleVarAccessClass
Basic nimbleFunctions for calculate, simulate, and getLogProb with a set of nodes
samplerAssignmentRules-class
Class samplerAssignmentRules
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.
MCMC Sampling Algorithms
Access or set values for a set of nodes in a model
valueInCompiledNimbleFunction
get or set value of member data from a compiled nimbleFunction using a multi-interface
Calculate number of islands based on a CAR adjacency matrix.
The Chinese Restaurant Process Distribution
The Categorical Distribution
Class CmodelBaseClass
EXPERIMENTAL Data type for the return value of nimDerivs
Constraint calculations in NIMBLE
The CAR-Normal Distribution
CnimbleFunctionBase-class
Class CnimbleFunctionBase
The CAR-Proper Distribution