TMB: 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.

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], Cole Monnahan [ctb]
Date of publication2017-02-09 00:47:01
MaintainerKasper Kristensen <kaskr@dtu.dk>
LicenseGPL-2
Version1.7.8
http://tmb-project.org

View on CRAN

Functions

as.list.sdreport Man page
benchmark Man page
compile Man page
config Man page
confint.tmbprofile Man page
dynlib Man page
gdbsource Man page
MakeADFun Man page
newton Man page
newtonOption Man page
oneStepPredict Man page
openmp Man page
plot.parallelBenchmark Man page
plot.tmbprofile Man page
precompile Man page
print.backtrace Man page
print.sdreport Man page
Rinterface Man page
runExample Man page
runSymbolicAnalysis Man page
sdreport Man page
summary.sdreport Man page
template Man page
tmbprofile Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.