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 matrixvector 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
Author  Kasper 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 publication  20170505 21:27:07 UTC 
Maintainer  Kasper Kristensen <kaskr@dtu.dk> 
License  GPL2 
Version  1.7.10 
URL  http://tmbproject.org 
Package repository  View on CRAN 
Installation  Install the latest version of this package by entering the following in R:

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 
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