├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── dist.R ├── dist_def.R ├── hmm.R ├── hmmTMB-package.R ├── logLik.R ├── make_formulas.R ├── make_mat.R ├── markovchain.R ├── observation.R ├── update.R └── utility.R ├── README.md ├── inst ├── CITATION ├── case_studies │ ├── accelerometry_raptor.R │ ├── cjs_dipper.R │ ├── cjs_js_possums.R │ ├── crossbill_occupancy.R │ ├── epileptic.R │ ├── old_faithful.R │ ├── pinkham.R │ ├── spanish_energy.R │ ├── traffic.R │ └── vbda_caracara.R ├── devel │ ├── driver.R │ ├── driver2.R │ ├── driver3.R │ ├── mod.hmm │ ├── true_mod.hmm │ └── wishlist.txt ├── examples │ ├── dists │ │ ├── beta │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── binom │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── cat │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── dir │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── exp │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── foldednorm │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── gamma │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── lnorm │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── mvnorm │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── nbinom │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── norm │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── pois │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── t │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── truncnorm │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── tweedie │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── vm │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── weibull │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── wrpcauchy │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── zib │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── zinb │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── zip │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ ├── ztnb │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ │ └── ztp │ │ │ ├── driver.R │ │ │ ├── mod.hmm │ │ │ └── true_mod.hmm │ ├── factor_smooth_interaction │ │ └── factor_smooth_interaction.R │ ├── fixed_covs │ │ ├── simple_fixed_covs │ │ │ ├── fixed_covs.R │ │ │ ├── fixedcovs_mod.hmm │ │ │ └── true_fixedcovsmod.hmm │ │ └── updating_models │ │ │ ├── fixed_covs.R │ │ │ ├── fixedcovs_mod.hmm │ │ │ └── true_fixedcovsmod.hmm │ ├── gams │ │ ├── gam_hmm.R │ │ ├── gam_mod.hmm │ │ └── true_gam_mod.hmm │ ├── random_effects │ │ ├── fixed_effects_only_mod.hmm │ │ ├── individual_random_effects.R │ │ ├── individual_random_effects_mod.hmm │ │ └── individual_random_effects_truemod.hmm │ ├── simple │ │ ├── pois_mod.hmm │ │ ├── simple_example.R │ │ └── true_pois_mod.hmm │ └── stan_simple │ │ ├── pois_mod.hmm │ │ ├── stan_simple_example.R │ │ └── true_pois_mod.hmm └── simulations │ ├── random_effects │ ├── individual_random_effects.R │ ├── individual_random_effects_mod.hmm │ └── individual_random_effects_truemod.hmm │ ├── simple │ ├── pois_mod.hmm │ ├── simple_example.R │ └── true_pois_mod.hmm │ └── simple_fixed_covs │ ├── fixed_covs.R │ ├── fixedcovs_mod.hmm │ └── true_fixedcovsmod.hmm ├── man ├── Dist.Rd ├── HMM.Rd ├── MarkovChain.Rd ├── Observation.Rd ├── as_character_formula.Rd ├── as_sparse.Rd ├── bdiag_check.Rd ├── check_contiguous.Rd ├── cov_grid.Rd ├── dvm.Rd ├── dwrpcauchy.Rd ├── find_re.Rd ├── gdeterminant.Rd ├── hmmTMB-package.Rd ├── hmmTMB_cols.Rd ├── invmlogit.Rd ├── is_whole_number.Rd ├── logLik.HMM.Rd ├── logsumexp.Rd ├── make_cov.Rd ├── make_formulas.Rd ├── make_matrices.Rd ├── mlogit.Rd ├── mvnorm_invlink.Rd ├── mvnorm_link.Rd ├── na_fill.Rd ├── prec_to_cov.Rd ├── quad_pos_solve.Rd ├── rvm.Rd ├── rwrpcauchy.Rd ├── strip_comments.Rd └── update.HMM.Rd ├── src ├── Makefile ├── Makefile.win ├── added_dists.hpp ├── dist.hpp ├── dist_def.hpp ├── hmmTMB.cpp └── hmmTMB.hpp ├── tests ├── testthat.R └── testthat │ ├── test_dist.R │ ├── test_hmm_fixedcov.R │ ├── test_hmm_fixedcov_updating.R │ ├── test_hmm_misc.R │ ├── test_hmm_simple.R │ ├── test_markovchain.R │ ├── test_misc.R │ └── test_observation.R └── vignettes ├── data.csv ├── hmmTMB_adding_distributions.Rmd ├── hmmTMB_adding_distributions.pdf ├── hmmTMB_advanced_features.Rmd ├── hmmTMB_advanced_features.pdf ├── hmmTMB_dist_list.Rmd ├── hmmTMB_dist_list.pdf ├── hmmTMB_example_categorical.Rmd ├── hmmTMB_example_categorical.pdf ├── hmmTMB_example_movement.Rmd ├── hmmTMB_example_movement.pdf ├── hmmTMB_example_mvn.Rmd ├── hmmTMB_example_mvn.pdf ├── hmmTMB_example_occupancy.Rmd ├── hmmTMB_example_occupancy.pdf ├── hmmTMB_example_stan.Rmd ├── hmmTMB_example_stan.pdf ├── hmmTMB_formula_syntax.Rmd ├── hmmTMB_formula_syntax.pdf ├── hmmTMB_general_structures.Rmd ├── hmmTMB_general_structures.pdf ├── 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