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TMB (version 1.7.16)

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

29,270

Version

1.7.16

License

GPL-2

Maintainer

Kasper Kristensen

Last Published

January 15th, 2020

Functions in TMB (1.7.16)

openmp

Control number of openmp threads.
runSymbolicAnalysis

Run symbolic analysis on sparse Hessian
normalize

Normalize process likelihood using the Laplace approximation.
newton

Generalized newton optimizer.
tmbroot

Compute likelihood profile confidence intervals of a TMB object by root-finding
print.checkConsistency

Print output from checkConsistency
precompile

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

Source R-script through gdb to get backtrace.
oneStepPredict

Calculate one-step-ahead (OSA) residuals for a latent variable model.
print.sdreport

Print brief model summary
sdreport

General sdreport function.
plot.tmbprofile

Plot likelihood profile.
runExample

Run one of the test examples.
newtonOption

Set newton options for a model object.
summary.sdreport

summary tables of model parameters
tmbprofile

Adaptive likelihood profiling.
summary.checkConsistency

Summarize output from checkConsistency
template

Create cpp template to get started.
benchmark

Benchmark parallel templates
as.list.sdreport

Convert estimates to original list format.
checkConsistency

Check consistency and Laplace accuracy
compile

Compile a C++ template to DLL suitable for MakeADFun.
Rinterface

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

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

Profile based confidence intervals.
config

Get or set internal configuration variables
dynlib

Add dynlib extension