nimble

EXPERIMENTAL Data type for the return value of nimDerivs

BUGSdeclClass contains the information extracted from one BUGS declaration

The CAR-Normal Distribution

The CAR-Proper Distribution

Calculate number of islands based on a CAR adjacency matrix.

The Categorical Distribution

The Chinese Restaurant Process Distribution

Class CmodelBaseClass

Class CnimbleFunctionBase

Constraint calculations in NIMBLE

The Dirichlet Distribution

The Double Exponential (Laplace) Distribution

The Exponential Distribution

Interval calculations

The Inverse Gamma Distribution

The Inverse Wishart Distribution

Class MCMCconf

Placeholder for MCMCsuite

The Multinomial Distribution

The Multivariate t Distribution

The Multivariate Normal Distribution

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

Class RmodelBaseClass

The Stick Breaking Function

The Wishart Distribution

Determine if any values in a vector are NA or NaN

Convert CAR structural parameters to adjacency, weights, num format

Convert weights vector to parameters of dcar_proper distributio

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

Automated parameter blocking procedure for efficient MCMC sampling

Placeholder for buildAuxiliaryFilter

Placeholder for buildBootstrapFilter

Placeholder for buildEnsembleKF

Placeholder for buildIteratedFilter2

Placeholder for buildLiuWestFilter

Builds an MCEM algorithm from a given NIMBLE model

Create an MCMC function from a NIMBLE model, or an MCMC configuration object

Calculate bounds for the autocorrelation parameter of the dcar_proper distribution

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

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

Class codeBlockClass

Placeholder for compareMCMCs

compile NIMBLE models and nimbleFunctions

Build the MCMCconf object for construction of an MCMC object

Configure Reversible Jump for Variable Selection

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.

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

Remove user-supplied distributions from use in NIMBLE BUGS models

Get information about a distribution

eigenNimbleList definition

Extract named elements from MCMC sampler control list

The Improper Uniform Distribution

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

Get a list of conditionally independent sets of nodes in a nimble model

Get nimbleFunction definition

Get NIMBLE Option

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

Get posterior samples for a Dirichlet process measure

Returns number of rows of modelValues

Create an Identity matrix (Deprecated)

Performs initialization of nimble model node values and log probabilities

check if a nimbleFunction

check if a nimbleList

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

Class modelBaseClass

Class for NIMBLE model definition

Information on initial values in a NIMBLE model

Create a NIMBLE modelValues Object

Class modelValuesBaseClass

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).

access (call) a member function of a nimbleFunction

Access or set a member variable of a nimbleFunction

cat function for use in nimbleFunctions

Copying function for NIMBLE

Nimble Derivatives

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

Spectral Decomposition of a Matrix

Creates matrix or array objects for use in nimbleFunctions

Creates numeric, integer or logical vectors for use in nimbleFunctions

Nimble wrapper around R's builtin optim.

Creates a deafult control argument for nimOptim.

print function for use in nimbleFunctions

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

Singular Value Decomposition of a Matrix

nimble

NIMBLE language functions for R-like vector construction

Functions and Classes Internal to NIMBLE

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

create a nimbleFunction

Class nimbleFunctionBase

Create a list of nimbleFunctions

create a virtual nimbleFunction, a base class for other nimbleFunctions

create a nimbleList

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

Create a NIMBLE model from BUGS code

NIMBLE Options Settings

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

create a nimbleType object

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

EXPERIMENTAL Data type for the control parameter of nimOptim

Creates a deafult control argument for optim (just an empty list).

EXPERIMENTAL Data type for the return value of nimOptim

Print error messages after failed compilation

Generates a weighted sample (with replacement) of ranks

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

Add user-supplied distributions for use in NIMBLE BUGS models

Resizes a modelValues object

Time execution of NIMBLE code

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

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

MCMC Sampling Algorithms

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.

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

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

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

Class singleVarAccessClass

svdNimbleList definition

The t Distribution

Tests BUGS examples in the NIMBLE system

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

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

Temporarily set some NIMBLE options.