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