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 publication2017-01-16 00:03:37
MaintainerKasper Kristensen <kaskr@dtu.dk>
LicenseGPL-2
Version1.7.6
http://tmb-project.org

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Files in this package

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

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