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.

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], Cole Monnahan [ctb] |

Date of publication | 2017-01-16 00:03:37 |

Maintainer | Kasper Kristensen <kaskr@dtu.dk> |

License | GPL-2 |

Version | 1.7.6 |

http://tmb-project.org |

**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.

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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