Learn R Programming

TMB (version 1.9.15)

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.

Copy Link

Version

Install

install.packages('TMB')

Monthly Downloads

33,610

Version

1.9.15

License

GPL-2

Issues

66

Pull Requests

4

Stars

178

Forks

80

Maintainer

Kasper Kristensen

Last Published

September 9th, 2024

Functions in TMB (1.9.15)

benchmark

Benchmark parallel templates
checkConsistency

Check consistency and Laplace accuracy
config

Get or set internal configuration variables
confint.tmbprofile

Profile based confidence intervals.
precompile

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

Print output from checkConsistency
FreeADFun

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

Create cpp template to get started.
newton

Generalized newton optimizer.
normalize

Normalize process likelihood using the Laplace approximation.
oneStepPredict

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

Adaptive likelihood profiling.
print.sdreport

Print brief model summary
newtonOption

Set newton options for a model object.
summary.checkConsistency

Summarize output from checkConsistency
runExample

Run one of the test examples.
GK

Gauss Kronrod configuration
dynlib

Add dynlib extension
summary.sdreport

summary tables of model parameters
tmbroot

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

Source R-script through gdb to get backtrace.
plot.tmbprofile

Plot likelihood profile.
runSymbolicAnalysis

Run symbolic analysis on sparse Hessian
openmp

Control number of OpenMP threads used by a TMB model.
sdreport

General sdreport function.
MakeADFun

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

Version information on API and ABI.
as.list.sdreport

Convert estimates to original list format.
SR

Sequential reduction configuration
compile

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

Create minimal R-code corresponding to a cpp template.