CnimbleFunctionBase-class
Class CnimbleFunctionBase
The CAR-Normal Distribution
Calculate number of islands based on a CAR adjacency matrix.
The CAR-Proper Distribution
Class CmodelBaseClass
Class MCMCconf
The Inverse Gamma Distribution
The Stick Breaking Function
The Wishart Distribution
Placeholder for MCMCsuite
ModifiedRmmParseKeywords2
[[' = 'outputCppArrayIndex2',
Constraint calculations in NIMBLE
The Multinomial Distribution
Interval calculations
Convert weights vector to parameters of dcar_proper
distributio
The Exponential Distribution
The Inverse Wishart Distribution
The Multivariate t Distribution
Turn a numeric vector into a single-row or single-column matrix
The Multivariate Normal Distribution
Calculate bounds for the autocorrelation parameter of the dcar_proper
distribution
The Double Exponential (Laplace) Distribution
Set values of one variable of a modelValues object from an R matrix
The Dirichlet Distribution
Configure Reversible Jump for Variable Selection
Calculate the upper bound for the autocorrelation parameter of the dcar_proper
distribution
Class RmodelBaseClass
Determine if any values in a vector are NA or NaN
Makes the Metropolis-Hastings acceptance decision, based upon the input (log) Metropolis-Hastings ratio
Builds an MCEM algorithm from a given NIMBLE model
Convert CAR structural parameters to adjacency, weights, num format
Placeholder for buildEnsembleKF
Placeholder for buildBootstrapFilter
Placeholder for buildIteratedFilter2
Placeholder for buildAuxiliaryFilter
Automated parameter blocking procedure for efficient MCMC sampling
Placeholder for buildLiuWestFilter
Create an MCMC function from a NIMBLE model, or an MCMC configuration object
Explicitly declare a variable in run-time code of a nimbleFunction
Creates a nimbleFunction for executing the Metropolis-Hastings jumping decision,
and updating values in the model, or in a carbon copy modelValues object, accordingly.
Calculate the lower bound for the autocorrelation parameter of the dcar_proper
distribution
Check for interrupt (e.g. Ctrl-C) during nimbleFunction execution. Part of the NIMBLE language.
Extract named elements from MCMC sampler control list
eigenNimbleList definition
Placeholder for compareMCMCs
Class codeBlockClass
The Improper Uniform Distribution
Get value of a parameter of a stochastic node in a model
Get NIMBLE Option
Get posterior samples for a Dirichlet process measure
compile NIMBLE models and nimbleFunctions
Returns number of rows of modelValues
Get the directory path to one of the classic BUGS examples installed with NIMBLE package
Build the MCMCconf object for construction of an MCMC object
Get nimbleFunction definition
Get value of bound of a stochastic node in a model
Make an object of information about a model-parameter pairing for getParam. Used internally
Make an object of information about a model-bound pairing for getBound. Used internally
Class modelBaseClass
check if a nimbleList
check if a nimbleFunction
Create an Identity matrix (Deprecated)
Performs initialization of nimble model node values and log probabilities
Nimble wrapper around R's builtin optim
. Copying function for NIMBLE
cat function for use in nimbleFunctions
Creates numeric, integer or logical vectors for use in nimbleFunctions
Class for NIMBLE model definition
Remove user-supplied distributions from use in NIMBLE BUGS models
Nimble Derivatives
Executes one or more chains of NIMBLE's default MCMC algorithm, for a model specified using BUGS code
create a nimbleList
samplerAssignmentRules-class
Class samplerAssignmentRules
MCMC Sampling Algorithms
valueInCompiledNimbleFunction
get or set value of member data from a compiled nimbleFunction using a multi-interface
Get information about a distribution
return sizes of an object whether it is a vector, matrix or array
Halt execution of a nimbleFunction function method. Part of the NIMBLE language
Access or set values for a set of nodes in a model
Create a NIMBLE modelValues Object
Singular Value Decomposition of a Matrix
Generates a weighted sample (with replacement) of ranks
Print error messages after failed compilation
Temporarily set some NIMBLE options.
Spectral Decomposition of a Matrix
Creates matrix or array objects for use in nimbleFunctions
modelValuesBaseClass-class
Class modelValuesBaseClass
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.
The t 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.
Tests BUGS examples in the NIMBLE system
Create the confs for a custom NIMBLE modelValues object
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)
.
NIMBLE language functions for R-like vector construction
create a nimbleFunction
Class nimbleFunctionBase
Functions and Classes Internal to NIMBLE
access (call) a member function of a nimbleFunction
Create a NIMBLE model from BUGS code
Access or set a member variable of a nimbleFunction
NIMBLE Options Settings
Creates a deafult control
argument for nimOptim
. Creates a deafult control
argument for optim
(just an empty list). nimble
EXPERIMENTAL Data type for the return value of nimOptim
Mathematical functions for BUGS and nimbleFunction programming
Turn BUGS model code into an object for use in nimbleModel
or readBUGSmodel
Create a nimbleFunction that wraps a call to external compiled code
calculate, calculateDiff, simulate, or get the current log probabilities (densities) a set of nodes in a NIMBLE model
Time execution of NIMBLE code
Resizes a modelValues object
Basic nimbleFunctions for calculate, simulate, and getLogProb with a set of nodes
print function for use in nimbleFunctions
Create a NIMBLE BUGS model from a variety of input formats, including BUGS model files
Create a list of nimbleFunctions
Basic nimbleFunctions for using a NIMBLE model with sets of stored values
singleVarAccessClass-class
Class singleVarAccessClass
Add user-supplied distributions for use in NIMBLE BUGS models
svdNimbleList definition
EXPERIMENTAL Data type for the control
parameter of nimOptim
create a virtual nimbleFunction, a base class for other nimbleFunctions
Make an R function callable from compiled nimbleFunctions (including nimbleModels).
create a nimbleType object
Explicitly declare objects created in setup code to be preserved and compiled as member data
Run one or more chains of an MCMC algorithm and return samples, summary and/or WAIC
set the size of a numeric variable in NIMBLE
Perform k-fold cross-validation on a NIMBLE model fit by MCMC
EXPERIMENTAL Data type for the return value of nimDerivs
BUGSdeclClass contains the information extracted from one BUGS declaration
The Chinese Restaurant Process Distribution
The Categorical Distribution