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TMB (version 1.7.4)

Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'

Description

With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines 'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through 'BLAS' and parallel user templates.

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Version

Install

install.packages('TMB')

Monthly Downloads

34,997

Version

1.7.4

License

GPL-2

Maintainer

Kasper Kristensen

Last Published

September 21st, 2016

Functions in TMB (1.7.4)

newtonOption

Set newton options for a model object.
config

Get or set internal configuration variables
gdbsource

Source R-script through gdb to get backtrace.
dynlib

Add dynlib extension
as.list.sdreport

Convert estimates to original list format.
benchmark

Benchmark parallel templates
MakeADFun

Construct objective functions with derivatives based on a compiled C++ template.
compile

Compile a C++ template to DLL suitable for MakeADFun.
print.sdreport

Print brief model summary
precompile

Precompile the TMB library in order to speed up compilation of templates.
runSymbolicAnalysis

Run symbolic analysis on sparse Hessian
Rinterface

Create minimal R-code corresponding to a cpp template.
run_mcmc

MCMC sampling of TMB models
plot.tmbprofile

Plot likelihood profile.
runExample

Run one of the test examples.
run_mcmc.rwm

[BETA VERSION] Draw MCMC samples from a model posterior using a Random Walk Metropolis (RWM) sampler.
run_mcmc.nuts

[BETA VERSION] Draw MCMC samples from a model posterior using the No-U-Turn (NUTS) sampler with dual averaging.
run_mcmc.hmc

[BETA VERSION] Draw MCMC samples from a model posterior using a Hamiltonian sampler.
summary.sdreport

summary tables of model parameters
template

Create cpp template to get started.
confint.tmbprofile

Profile based confidence intervals.
openmp

Control number of openmp threads.