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TMB (version 1.9.17)

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

43,238

Version

1.9.17

License

GPL-2

Issues

67

Pull Requests

4

Stars

182

Forks

84

Maintainer

Kasper Kristensen

Last Published

March 10th, 2025

Functions in TMB (1.9.17)

GK

Gauss Kronrod configuration
config

Get or set internal configuration variables
sdreport

General sdreport function.
dynlib

Add dynlib extension
gdbsource

Source R-script through gdb to get backtrace.
runSymbolicAnalysis

Run symbolic analysis on sparse Hessian
normalize

Normalize process likelihood using the Laplace approximation.
oneStepPredict

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

Print brief model summary
runExample

Run one of the test examples.
precompile

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

Profile based confidence intervals.
print.checkConsistency

Print output from checkConsistency
template

Create cpp template to get started.
tmbroot

Compute likelihood profile confidence intervals of a TMB object by root-finding
tmbprofile

Adaptive likelihood profiling.
newtonOption

Set newton options for a model object.
newton

Generalized newton optimizer.
summary.checkConsistency

Summarize output from checkConsistency
summary.sdreport

summary tables of model parameters
benchmark

Benchmark parallel templates
as.list.sdreport

Convert estimates to original list format.
Rinterface

Create minimal R-code corresponding to a cpp template.
TMB.Version

Version information on API and ABI.
MakeADFun

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

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

Check consistency and Laplace accuracy
FreeADFun

Free memory allocated on the C++ side by MakeADFun.
SR

Sequential reduction configuration
openmp

Control number of OpenMP threads used by a TMB model.
plot.tmbprofile

Plot likelihood profile.