Files in TheoMichelot/hmmTMB

Fit Hidden Markov Models using Template Model Builder

R/dist.R R/dist_def.R R/hmm.R R/hmmTMB-package.R R/logLik.R R/make_formulas.R R/make_mat.R R/markovchain.R R/observation.R R/update.R R/utility.R README.md inst/case_studies/accelerometry_raptor.R inst/case_studies/cjs_dipper.R inst/case_studies/cjs_js_possums.R inst/case_studies/crossbill_occupancy.R inst/case_studies/epileptic.R inst/case_studies/old_faithful.R inst/case_studies/pinkham.R inst/case_studies/spanish_energy.R inst/case_studies/traffic.R inst/case_studies/vbda_caracara.R inst/devel/driver.R inst/devel/driver2.R inst/devel/driver3.R inst/examples/dists/beta/driver.R inst/examples/dists/binom/driver.R inst/examples/dists/cat/driver.R inst/examples/dists/dir/driver.R inst/examples/dists/exp/driver.R inst/examples/dists/foldednorm/driver.R inst/examples/dists/gamma/driver.R inst/examples/dists/lnorm/driver.R inst/examples/dists/mvnorm/driver.R inst/examples/dists/nbinom/driver.R inst/examples/dists/norm/driver.R inst/examples/dists/pois/driver.R inst/examples/dists/t/driver.R inst/examples/dists/truncnorm/driver.R inst/examples/dists/tweedie/driver.R inst/examples/dists/vm/driver.R inst/examples/dists/weibull/driver.R inst/examples/dists/wrpcauchy/driver.R inst/examples/dists/zib/driver.R inst/examples/dists/zinb/driver.R inst/examples/dists/zip/driver.R inst/examples/dists/ztnb/driver.R inst/examples/dists/ztp/driver.R inst/examples/fixed_covs/simple_fixed_covs/fixed_covs.R inst/examples/fixed_covs/updating_models/fixed_covs.R inst/examples/gams/gam_hmm.R inst/examples/random_effects/individual_random_effects.R inst/examples/simple/simple_example.R inst/examples/stan_simple/stan_simple_example.R inst/simulations/random_effects/individual_random_effects.R inst/simulations/simple/simple_example.R inst/simulations/simple_fixed_covs/fixed_covs.R man/Dist.Rd man/HMM.Rd man/MarkovChain.Rd man/Observation.Rd man/as_character_formula.Rd man/as_sparse.Rd man/bdiag_check.Rd man/cov_grid.Rd man/find_re.Rd man/gdeterminant.Rd man/hmmTMB-package.Rd man/hmmTMB_cols.Rd man/invmlogit.Rd man/is_whole_number.Rd man/logLik.HMM.Rd man/logsumexp.Rd man/make_formulas.Rd man/make_matrices.Rd man/mlogit.Rd man/mvnorm_invlink.Rd man/mvnorm_link.Rd man/na_fill.Rd man/prec_to_cov.Rd man/quad_pos_solve.Rd man/strip_comments.Rd man/update.HMM.Rd tests/testthat.R tests/testthat/test_dist.R tests/testthat/test_hmm_fixedcov.R tests/testthat/test_hmm_fixedcov_updating.R tests/testthat/test_hmm_misc.R tests/testthat/test_hmm_simple.R tests/testthat/test_markovchain.R tests/testthat/test_misc.R tests/testthat/test_observation.R vignettes/hmmTMB_adding_distributions.Rmd vignettes/hmmTMB_adding_distributions.pdf vignettes/hmmTMB_advanced_features.Rmd vignettes/hmmTMB_advanced_features.pdf vignettes/hmmTMB_dist_list.Rmd vignettes/hmmTMB_dist_list.pdf vignettes/hmmTMB_example_categorical.Rmd vignettes/hmmTMB_example_categorical.pdf vignettes/hmmTMB_example_movement.Rmd vignettes/hmmTMB_example_movement.pdf vignettes/hmmTMB_example_mvn.Rmd vignettes/hmmTMB_example_mvn.pdf vignettes/hmmTMB_example_occupancy.Rmd vignettes/hmmTMB_example_occupancy.pdf vignettes/hmmTMB_example_stan.Rmd vignettes/hmmTMB_example_stan.pdf vignettes/hmmTMB_formula_syntax.Rmd vignettes/hmmTMB_formula_syntax.pdf vignettes/hmmTMB_general_structures.Rmd vignettes/hmmTMB_general_structures.pdf vignettes/hmmTMB_list_of_online_resources.Rmd vignettes/hmmTMB_package_comparison.Rmd vignettes/hmmTMB_package_comparison.pdf vignettes/hmmTMB_workflow.Rmd vignettes/hmmTMB_workflow.pdf