TMB: Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'
Version 1.7.10

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.

Browse man pages Browse package API and functions Browse package files

AuthorKasper Kristensen [aut, cre, cph], Brad Bell [cph], Hans Skaug [ctb], Arni Magnusson [ctb], Casper Berg [ctb], Anders Nielsen [ctb], Martin Maechler [ctb], Theo Michelot [ctb], Mollie Brooks [ctb], Alex Forrence [ctb], Christoffer Moesgaard Albertsen [ctb], Cole Monnahan [ctb]
Date of publication2017-05-05 21:27:07 UTC
MaintainerKasper Kristensen <kaskr@dtu.dk>
LicenseGPL-2
Version1.7.10
URL http://tmb-project.org
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("TMB")

Man pages

as.list.sdreport: Convert estimates to original list format.
benchmark: Benchmark parallel templates
compile: Compile a C++ template to DLL suitable for MakeADFun.
config: Get or set internal configuration variables
confint.tmbprofile: Profile based confidence intervals.
dynlib: Add dynlib extension
gdbsource: Source R-script through gdb to get backtrace.
MakeADFun: Construct objective functions with derivatives based on a...
newton: Generalized newton optimizer.
newtonOption: Set newton options for a model object.
oneStepPredict: Calculate one-step-ahead (OSA) residuals for a latent...
openmp: Control number of openmp threads.
plot.tmbprofile: Plot likelihood profile.
precompile: Precompile the TMB library in order to speed up compilation...
print.sdreport: Print brief model summary
Rinterface: Create minimal R-code corresponding to a cpp template.
runExample: Run one of the test examples.
runSymbolicAnalysis: Run symbolic analysis on sparse Hessian
sdreport: General sdreport function.
summary.sdreport: summary tables of model parameters
template: Create cpp template to get started.
tmbprofile: Adaptive likelihood profiling.

Functions

MakeADFun Man page Source code
Rinterface Man page Source code
as.list.sdreport Man page Source code
benchmark Man page Source code
checkMatrixPackageVersion Source code
checkSparseHessian Source code
cleanup Source code
compile Man page Source code
config Man page Source code
confint.tmbprofile Man page Source code
declExtract Source code
dynlib Man page Source code
gdbsource Man page Source code
gdbsource.win Source code
getUserDLL Source code
grepRandomParameters Source code
info Source code
install.contrib Source code
isNullPointer Source code
isParallelTemplate Source code
macroExtract Source code
newton Man page Source code
newtonOption Man page Source code
onAttach Source code
onLoad Source code
oneStepPredict Man page Source code
openmp Man page Source code
parallelBenchmark Source code
plot.parallelBenchmark Man page Source code
plot.tmbprofile Man page Source code
precompSource Source code
precompile Man page Source code
precompileSource Source code
print.backtrace Man page Source code
print.sdreport Man page Source code
removeComments Source code
runExample Man page Source code
runSymbolicAnalysis Man page Source code
sdreport Man page Source code
sparseHessianFun Source code
summary.sdreport Man page Source code
tclassExtract Source code
tclassInstantiate Source code
tclassSpecialize Source code
template Man page Source code
tmbprofile Man page Source code
updateCholesky Source code
updateMap Source code

Files

inst
inst/examples
inst/examples/randomregression.cpp
inst/examples/linreg_parallel.cpp
inst/examples/simple.R
inst/examples/randomregression.R
inst/examples/linreg_parallel.R
inst/examples/simple.cpp
inst/examples/ar1xar1.R
inst/examples/ar1xar1.cpp
inst/CITATION
inst/template.cpp
inst/COPYRIGHTS
inst/include
inst/include/Vectorize.hpp
inst/include/tiny_ad
inst/include/tiny_ad/gamma
inst/include/tiny_ad/gamma/stirlerr.cpp
inst/include/tiny_ad/gamma/gammalims.cpp.not_used
inst/include/tiny_ad/gamma/gamma.cpp
inst/include/tiny_ad/gamma/gamma_cody.cpp
inst/include/tiny_ad/gamma/lgammacor.cpp
inst/include/tiny_ad/gamma/undefs.h
inst/include/tiny_ad/gamma/lgamma.cpp
inst/include/tiny_ad/gamma/gamma.hpp
inst/include/tiny_ad/gamma/chebyshev.cpp
inst/include/tiny_ad/mask.hpp
inst/include/tiny_ad/tiny_ad
inst/include/tiny_ad/tiny_ad/tiny_ad.hpp
inst/include/tiny_ad/tiny_ad/tiny_vec.hpp
inst/include/tiny_ad/tiny_ad/tiny_valarray.hpp
inst/include/tiny_ad/compois
inst/include/tiny_ad/compois/compois.hpp
inst/include/tiny_ad/atomic.hpp
inst/include/tiny_ad/robust
inst/include/tiny_ad/robust/distributions.hpp
inst/include/tiny_ad/beta
inst/include/tiny_ad/beta/toms708.cpp
inst/include/tiny_ad/beta/dpq.h
inst/include/tiny_ad/beta/pbeta.cpp
inst/include/tiny_ad/beta/nmath.h
inst/include/tiny_ad/beta/pbeta.hpp
inst/include/tiny_ad/beta/i1mach.cpp
inst/include/tiny_ad/beta/d1mach.cpp
inst/include/tiny_ad/beta/undefs.h
inst/include/tiny_ad/bessel
inst/include/tiny_ad/bessel/bessel_i.cpp
inst/include/tiny_ad/bessel/bessel.h
inst/include/tiny_ad/bessel/bessel_j.cpp
inst/include/tiny_ad/bessel/undefs.h
inst/include/tiny_ad/bessel/bessel_y.cpp
inst/include/tiny_ad/bessel/bessel.hpp
inst/include/tiny_ad/bessel/bessel_k.cpp
inst/include/tiny_ad/tweedie
inst/include/tiny_ad/tweedie/tweedie.hpp
inst/include/tiny_ad/tweedie/tweedie.cpp
inst/include/tiny_ad/integrate
inst/include/tiny_ad/integrate/integrate.hpp
inst/include/tiny_ad/integrate/integrate.cpp
inst/include/Rstream.hpp
inst/include/convert.hpp
inst/include/atomic_macro.hpp
inst/include/distributions_R.hpp
inst/include/config.hpp
inst/include/atomic_math.hpp
inst/include/TMB.hpp
inst/include/atomic_convolve.hpp
inst/include/precompile.hpp
inst/include/lgamma.hpp
inst/include/tmbutils
inst/include/tmbutils/romberg.hpp
inst/include/tmbutils/matexp.hpp
inst/include/tmbutils/autodiff.hpp
inst/include/tmbutils/spmat.hpp
inst/include/tmbutils/density.hpp
inst/include/tmbutils/array.hpp
inst/include/tmbutils/order.hpp
inst/include/tmbutils/R_inla.hpp
inst/include/tmbutils/tmbutils.hpp
inst/include/tmbutils/vector.hpp
inst/include/tmbutils/tmbutils_extra.hpp
inst/include/tmbutils/splines.hpp
inst/include/tmbutils/kronecker.hpp
inst/include/expm.hpp
inst/include/start_parallel.hpp
inst/include/tmb_core.hpp
inst/include/cppad
inst/include/cppad/check_numeric_type.hpp
inst/include/cppad/CheckSimpleVector.h
inst/include/cppad/COPYING
inst/include/cppad/CheckNumericType.h
inst/include/cppad/CppAD.h
inst/include/cppad/TrackNewDel.h
inst/include/cppad/pow_int.hpp
inst/include/cppad/PowInt.h
inst/include/cppad/LuFactor.h
inst/include/cppad/RombergOne.h
inst/include/cppad/speed
inst/include/cppad/speed/det_grad_33.hpp
inst/include/cppad/speed/det_by_minor.hpp
inst/include/cppad/speed/det_33.hpp
inst/include/cppad/speed/sparse_hes_fun.hpp
inst/include/cppad/speed/mat_sum_sq.hpp
inst/include/cppad/speed/uniform_01.hpp
inst/include/cppad/speed/ode_evaluate.hpp
inst/include/cppad/speed/det_of_minor.hpp
inst/include/cppad/speed/sparse_jac_fun.hpp
inst/include/cppad/speed/det_by_lu.hpp
inst/include/cppad/CppAD_vector.h
inst/include/cppad/lu_factor.hpp
inst/include/cppad/near_equal.hpp
inst/include/cppad/SpeedTest.h
inst/include/cppad/CMakeLists.txt
inst/include/cppad/OdeGearControl.h
inst/include/cppad/local
inst/include/cppad/local/cppad_assert.hpp
inst/include/cppad/local/discrete_op.hpp
inst/include/cppad/local/ad.hpp
inst/include/cppad/local/asin_op.hpp
inst/include/cppad/local/load_op.hpp
inst/include/cppad/local/forward.hpp
inst/include/cppad/local/prototype_op.hpp
inst/include/cppad/local/atan2.hpp
inst/include/cppad/local/cond_op.hpp
inst/include/cppad/local/limits.hpp
inst/include/cppad/local/atan_op.hpp
inst/include/cppad/local/optimize.hpp
inst/include/cppad/local/cond_exp.hpp
inst/include/cppad/local/kasper.hpp
inst/include/cppad/local/tan_op.hpp
inst/include/cppad/local/cos_op.hpp
inst/include/cppad/local/mul_eq.hpp
inst/include/cppad/local/erf_op.hpp
inst/include/cppad/local/rev_hes_sweep.hpp
inst/include/cppad/local/add.hpp
inst/include/cppad/local/config.h.in
inst/include/cppad/local/test_vector.hpp
inst/include/cppad/local/sparse_hessian.hpp
inst/include/cppad/local/define.hpp
inst/include/cppad/local/ad_io.hpp
inst/include/cppad/local/epsilon.hpp
inst/include/cppad/local/convert.hpp
inst/include/cppad/local/bool_fun.hpp
inst/include/cppad/local/op_code.hpp
inst/include/cppad/local/tape_link.hpp
inst/include/cppad/local/sign.hpp
inst/include/cppad/local/base_cond_exp.hpp
inst/include/cppad/local/base_float.hpp
inst/include/cppad/local/unary_plus.hpp
inst/include/cppad/local/ad_fun.hpp
inst/include/cppad/local/independent.hpp
inst/include/cppad/local/var2par.hpp
inst/include/cppad/local/for_jac_sweep.hpp
inst/include/cppad/local/dependent.hpp
inst/include/cppad/local/jacobian.hpp
inst/include/cppad/local/sign_op.hpp
inst/include/cppad/local/mul.hpp
inst/include/cppad/local/pow.hpp
inst/include/cppad/local/forward1sweep.hpp
inst/include/cppad/local/base_std_math.hpp
inst/include/cppad/local/sub_op.hpp
inst/include/cppad/local/fun_check.hpp
inst/include/cppad/local/reverse_sweep.hpp
inst/include/cppad/local/compare.hpp
inst/include/cppad/local/color_general.hpp
inst/include/cppad/local/for_one.hpp
inst/include/cppad/local/equal_op_seq.hpp
inst/include/cppad/local/near_equal_ext.hpp
inst/include/cppad/local/pow_op.hpp
inst/include/cppad/local/testvector.hpp
inst/include/cppad/local/log_op.hpp
inst/include/cppad/local/acos_op.hpp
inst/include/cppad/local/user_ad.hpp
inst/include/cppad/local/sparse_pack.hpp
inst/include/cppad/local/sparse_binary_op.hpp
inst/include/cppad/local/ad_valued.hpp
inst/include/cppad/local/print_op.hpp
inst/include/cppad/local/div.hpp
inst/include/cppad/local/op.hpp
inst/include/cppad/local/abs.hpp
inst/include/cppad/local/bender_quad.hpp
inst/include/cppad/local/color_symmetric.hpp
inst/include/cppad/local/arithmetic.hpp
inst/include/cppad/local/hessian.hpp
inst/include/cppad/local/sqrt_op.hpp
inst/include/cppad/local/print_for.hpp
inst/include/cppad/local/num_skip.hpp
inst/include/cppad/local/rev_sparse_hes.hpp
inst/include/cppad/local/declare_ad.hpp
inst/include/cppad/local/omp_max_thread.hpp
inst/include/cppad/local/par_var.hpp
inst/include/cppad/local/for_sparse_jac.hpp
inst/include/cppad/local/recorder.hpp
inst/include/cppad/local/discrete.hpp
inst/include/cppad/local/ad_assign.hpp
inst/include/cppad/local/base_double.hpp
inst/include/cppad/local/opt_val_hes.hpp
inst/include/cppad/local/old_atomic.hpp
inst/include/cppad/local/fun_eval.hpp
inst/include/cppad/local/sparse.hpp
inst/include/cppad/local/for_two.hpp
inst/include/cppad/local/forward2sweep.hpp
inst/include/cppad/local/ad_ctor.hpp
inst/include/cppad/local/capacity_order.hpp
inst/include/cppad/local/drivers.hpp
inst/include/cppad/local/vec_ad.hpp
inst/include/cppad/local/undef.hpp
inst/include/cppad/local/ordered.hpp
inst/include/cppad/local/ad_binary.hpp
inst/include/cppad/local/parameter_op.hpp
inst/include/cppad/local/ad_tape.hpp
inst/include/cppad/local/sinh_op.hpp
inst/include/cppad/local/add_eq.hpp
inst/include/cppad/local/base_complex.hpp
inst/include/cppad/local/rev_two.hpp
inst/include/cppad/local/div_op.hpp
inst/include/cppad/local/cppad_colpack.hpp
inst/include/cppad/local/csum_op.hpp
inst/include/cppad/local/sin_op.hpp
inst/include/cppad/local/tanh_op.hpp
inst/include/cppad/local/sparse_list.hpp
inst/include/cppad/local/sub_eq.hpp
inst/include/cppad/local/rev_sparse_jac.hpp
inst/include/cppad/local/forward0sweep.hpp
inst/include/cppad/local/player.hpp
inst/include/cppad/local/sparse_unary_op.hpp
inst/include/cppad/local/abort_recording.hpp
inst/include/cppad/local/cosh_op.hpp
inst/include/cppad/local/rev_jac_sweep.hpp
inst/include/cppad/local/sparse_pattern.hpp
inst/include/cppad/local/sub.hpp
inst/include/cppad/local/cskip_op.hpp
inst/include/cppad/local/bool_valued.hpp
inst/include/cppad/local/identical.hpp
inst/include/cppad/local/std_set.hpp
inst/include/cppad/local/rev_one.hpp
inst/include/cppad/local/div_eq.hpp
inst/include/cppad/local/parallel_ad.hpp
inst/include/cppad/local/hash_code.hpp
inst/include/cppad/local/comp_op.hpp
inst/include/cppad/local/cppad_colpack.cpp
inst/include/cppad/local/atomic_base.hpp
inst/include/cppad/local/value.hpp
inst/include/cppad/local/sparse_jacobian.hpp
inst/include/cppad/local/math_other.hpp
inst/include/cppad/local/pod_vector.hpp
inst/include/cppad/local/abs_op.hpp
inst/include/cppad/local/reverse.hpp
inst/include/cppad/local/exp_op.hpp
inst/include/cppad/local/sparse_set.hpp
inst/include/cppad/local/unary_minus.hpp
inst/include/cppad/local/compute_assign.hpp
inst/include/cppad/local/mul_op.hpp
inst/include/cppad/local/lu_ratio.hpp
inst/include/cppad/local/checkpoint.hpp
inst/include/cppad/local/add_op.hpp
inst/include/cppad/local/erf.hpp
inst/include/cppad/local/integer.hpp
inst/include/cppad/local/fun_construct.hpp
inst/include/cppad/local/std_math_ad.hpp
inst/include/cppad/local/store_op.hpp
inst/include/cppad/Runge45.h
inst/include/cppad/lu_solve.hpp
inst/include/cppad/ErrorHandler.h
inst/include/cppad/elapsed_seconds.hpp
inst/include/cppad/configure.hpp
inst/include/cppad/index_sort.hpp
inst/include/cppad/OdeGear.h
inst/include/cppad/nan.hpp
inst/include/cppad/memory_leak.hpp
inst/include/cppad/Rosen34.h
inst/include/cppad/error_handler.hpp
inst/include/cppad/runge_45.hpp
inst/include/cppad/ode_err_control.hpp
inst/include/cppad/ode_gear_control.hpp
inst/include/cppad/romberg_one.hpp
inst/include/cppad/ipopt
inst/include/cppad/ipopt/solve.hpp
inst/include/cppad/ipopt/solve_result.hpp
inst/include/cppad/ipopt/solve_callback.hpp
inst/include/cppad/configure.hpp.in
inst/include/cppad/OdeErrControl.h
inst/include/cppad/RombergMul.h
inst/include/cppad/omp_alloc.hpp
inst/include/cppad/rosen_34.hpp
inst/include/cppad/example
inst/include/cppad/example/eigen_plugin.hpp
inst/include/cppad/example/cppad_eigen.hpp
inst/include/cppad/example/base_adolc.hpp
inst/include/cppad/example/matrix_mul.hpp
inst/include/cppad/check_simple_vector.hpp
inst/include/cppad/lu_invert.hpp
inst/include/cppad/vector.hpp
inst/include/cppad/LuSolve.h
inst/include/cppad/track_new_del.hpp
inst/include/cppad/time_test.hpp
inst/include/cppad/NearEqual.h
inst/include/cppad/ode_gear.hpp
inst/include/cppad/LuInvert.h
inst/include/cppad/cppad.hpp
inst/include/cppad/base_require.hpp
inst/include/cppad/thread_alloc.hpp
inst/include/cppad/poly.hpp
inst/include/cppad/Poly.h
inst/include/cppad/speed_test.hpp
inst/include/cppad/romberg_mul.hpp
inst/include/checkpoint_macro.hpp
inst/include/dnorm.hpp
inst/include/convenience.hpp
src
src/local_stubs.c
src/Makevars
src/utils.c
src/external_metis.c
src/solve_subset.c
src/init.c
NAMESPACE
NEWS
R
R/TMB.R
R/validation.R
R/benchmark.R
R/sdreport.R
R/tmbprofile.R
R/config.R
R/header_tool.R
R/examples.R
R/zzz.R
R/gdbsource.R
MD5
DESCRIPTION
man
man/newton.Rd
man/summary.sdreport.Rd
man/Rinterface.Rd
man/oneStepPredict.Rd
man/benchmark.Rd
man/runSymbolicAnalysis.Rd
man/confint.tmbprofile.Rd
man/sdreport.Rd
man/tmbprofile.Rd
man/print.sdreport.Rd
man/newtonOption.Rd
man/dynlib.Rd
man/precompile.Rd
man/compile.Rd
man/as.list.sdreport.Rd
man/gdbsource.Rd
man/plot.tmbprofile.Rd
man/openmp.Rd
man/config.Rd
man/template.Rd
man/MakeADFun.Rd
man/runExample.Rd
TMB documentation built on May 20, 2017, 3:19 a.m.