TMB v1.7.15
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Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'
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.
Functions in TMB
| Name | Description | |
| newton | Generalized newton optimizer. | |
| newtonOption | Set newton options for a model object. | |
| precompile | Precompile the TMB library in order to speed up compilation of templates. | |
| print.checkConsistency | Print output from checkConsistency | |
| sdreport | General sdreport function. | |
| runSymbolicAnalysis | Run symbolic analysis on sparse Hessian | |
| checkConsistency | Check consistency and Laplace accuracy | |
| tmbroot | Compute likelihood profile confidence intervals of a TMB object by root-finding | |
| oneStepPredict | Calculate one-step-ahead (OSA) residuals for a latent variable model. | |
| normalize | Normalize process likelihood using the Laplace approximation. | |
| compile | Compile a C++ template to DLL suitable for MakeADFun. | |
| gdbsource | Source R-script through gdb to get backtrace. | |
| template | Create cpp template to get started. | |
| tmbprofile | Adaptive likelihood profiling. | |
| print.sdreport | Print brief model summary | |
| runExample | Run one of the test examples. | |
| summary.checkConsistency | Summarize output from checkConsistency | |
| summary.sdreport | summary tables of model parameters | |
| MakeADFun | Construct objective functions with derivatives based on a compiled C++ template. | |
| Rinterface | Create minimal R-code corresponding to a cpp template. | |
| config | Get or set internal configuration variables | |
| confint.tmbprofile | Profile based confidence intervals. | |
| dynlib | Add dynlib extension | |
| as.list.sdreport | Convert estimates to original list format. | |
| benchmark | Benchmark parallel templates | |
| openmp | Control number of openmp threads. | |
| plot.tmbprofile | Plot likelihood profile. | |
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Details
| Type | Package |
| Date | 2018-11-08 |
| Copyright | See the file COPYRIGHTS |
| License | GPL-2 |
| URL | http://tmb-project.org |
| BugReports | https://github.com/kaskr/adcomp/issues |
| LinkingTo | Matrix, RcppEigen |
| RoxygenNote | 6.0.1 |
| NeedsCompilation | yes |
| Packaged | 2018-11-08 21:40:08 UTC; kaskr |
| Repository | CRAN |
| Date/Publication | 2018-11-09 16:40:14 UTC |
| imports | graphics , Matrix (>= 1.0-12) , methods , stats , utils |
| suggests | numDeriv , parallel |
| depends | R (>= 3.0.0) |
| linkingto | RcppEigen |
| Contributors | Theo Michelot, Hans Skaug, Cole Monnahan, Arni Magnusson, Martin Maechler, Brad Bell, Casper Berg, Anders Nielsen, Mollie Brooks, Alex Forrence, Christoffer Moesgaard Albertsen |
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