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.

Install the latest version of this package by entering the following in R:
install.packages("TMB")
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 publication2017-04-12 14:52:58 UTC
MaintainerKasper Kristensen <kaskr@dtu.dk>
LicenseGPL-2
Version1.7.9
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

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

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