fintzij/BDAepimodel
Fit Stochastic Epidemic Models in R via Bayesian Data Augmentation

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Fit Stochastic Epidemic Models in R via Bayesian Data Augmentation

.Rbuildignore
.gitignore
BDAepimodel.Rproj
DESCRIPTION
NAMESPACE
R/DEPRECATED FUNCTIONS/build_fb_mats.R R/DEPRECATED FUNCTIONS/calc_subj_likelihood.R R/DEPRECATED FUNCTIONS/extractRateFunctions.R R/DEPRECATED FUNCTIONS/init_subj_mat (DEPRECATED).R R/DEPRECATED FUNCTIONS/pop_likelihood_R.R R/DEPRECATED FUNCTIONS/sample_DT_skeleton.R R/DEPRECATED FUNCTIONS/sample_path_in_interval.R R/DEPRECATED FUNCTIONS/update_matrices.R R/MH_accept_reject.R R/RcppExports.R R/append_missing.R R/auxilliary functions.R R/build_emission_mat.R R/build_initdist.R R/build_irm.R R/build_new_irms.R R/build_rate_mat.R R/build_tpm.R R/build_tpm_seqs.R R/calc_obs_likelihood.R R/calc_pop_likelihood.R R/check_irm.R R/detect_structure.R R/draw_trajec.R R/est_scale_template.R R/expand_pop_mat.R R/extract_rate_fcns.R R/fit_epimodel.R R/generate_keys.R R/get_tpms_to_build.R R/gibbs_template.R R/hello.R R/init_augmentation.R R/init_config_mat.R R/init_epimodel.R R/init_irm.R R/init_obs_mat.R R/init_rate_map.R R/init_results.R R/init_settings.R R/init_state_lookup.R R/init_trajectories.R R/init_tuning.R R/insert_row.R R/insert_trajectory.R R/irm_decomp.R R/kernel_template.R R/match_row.R R/mh_template.R R/plot_epimodel.R R/plot_latent_posterior.R R/prepare_epimodel.R R/reinsert_path.R R/remove_trajectory.R R/sample_at_event_times.R R/sample_at_obs_times.R R/sample_forward.R R/sample_path.R R/sim_one_event.R R/simulate_SIR.R R/simulate_epimodel.R R/subject_probabilities.R R/traj_to_obs.R R/tune_proposal.R R/update_obs_mat.R R/update_params.R R/update_tpms.R README.Rmd README.md
REFERENCES.bib
inst/pomp_vignettes/SEIR_pomp_simulation.R inst/pomp_vignettes/SEIR_pomp_simulation.Rmd
inst/pomp_vignettes/SEIR_pomp_simulation.html
inst/pomp_vignettes/SIRS_pomp_simulation.R inst/pomp_vignettes/SIRS_pomp_simulation.Rmd
inst/pomp_vignettes/SIRS_pomp_simulation.html
inst/pomp_vignettes/SIR_pomp_simulation.R inst/pomp_vignettes/SIR_pomp_simulation.Rmd
inst/pomp_vignettes/SIR_pomp_simulation.html
inst/pomp_vignettes/bbs_pomp_binom_vignette.R inst/pomp_vignettes/bbs_pomp_binom_vignette.Rmd
inst/pomp_vignettes/bbs_pomp_binom_vignette.html
inst/pomp_vignettes/bbs_pomp_negbinom_vignette.R inst/pomp_vignettes/bbs_pomp_negbinom_vignette.Rmd
inst/pomp_vignettes/bbs_pomp_negbinom_vignette.html
inst/pomp_vignettes/model_misspecification_pomp.R inst/pomp_vignettes/model_misspecification_pomp.Rmd
inst/pomp_vignettes/model_misspecification_pomp.html
man/BDAepimodel-package.Rd man/MH_accept_reject.Rd man/append_missing.Rd man/buildEigenArray.Rd man/buildEigenArray_SEIR.Rd man/buildEigenArray_SIR.Rd man/buildFBMats.Rd man/buildRateArray.Rd man/build_emission_mat.Rd man/build_initdist.Rd man/build_irm.Rd man/build_new_irms.Rd man/build_rate_mat.Rd man/build_tpm.Rd man/build_tpm_seqs.Rd man/calc_obs_likelihood.Rd man/calc_pop_likelihood.Rd man/check_irm.Rd man/complexTPM.Rd man/detect_structure.Rd man/draw_trajec.Rd man/est_scale_template.Rd man/expand_pop_mat.Rd man/expit.Rd man/extract_rate_fcns.Rd man/fit_epimodel.Rd man/generate_keys.Rd man/getObsTimeInds.Rd man/get_tpms_to_build.Rd man/gibbs_template.Rd man/hello.Rd man/init_augmentation.Rd man/init_config_mat.Rd man/init_epimodel.Rd man/init_irm.Rd man/init_obs_mat.Rd man/init_rate_map.Rd man/init_results.Rd man/init_settings.Rd man/init_state_lookup.Rd man/init_trajectories.Rd man/init_tuning.Rd man/insertPath.Rd man/insert_row.Rd man/insert_trajectory.Rd man/irm_decomp.Rd man/joinCubes.Rd man/logit.Rd man/match_row.Rd man/mh_template.Rd man/normalize.Rd man/plot_epimodel.Rd man/plot_latent_posterior.Rd man/populationLikelihood.Rd man/prepare_epimodel.Rd man/rcpp_hello.Rd man/reinsert_path.Rd man/remove_trajectory.Rd man/reorderMat.Rd man/resolveSubjContrib.Rd man/retrieveKeys.Rd man/retrieveSubjPath.Rd man/sampleEventSubseq.Rd man/sample_at_event_times.Rd man/sample_at_obs_times.Rd man/sample_forward.Rd man/sample_path.Rd man/sim_one_event.Rd man/simulateSIR.Rd man/simulate_SIR.Rd man/subjectLikelihood.Rd man/subject_probabilities.Rd man/templates.Rd man/tpmProdSeqs.Rd man/tpmSeqs.Rd man/traj_to_obs.Rd man/tune_proposal.Rd man/update_obs_mat.Rd man/update_params.Rd man/update_tpms.Rd packrat/init.R
packrat/packrat.lock
packrat/packrat.opts
packrat/src/BH/BH_1.58.0-1.tar (1).gz
packrat/src/BH/BH_1.58.0-1.tar (2).gz
packrat/src/BH/BH_1.58.0-1.tar.gz
packrat/src/DBI/DBI_0.3.1.tar.gz
packrat/src/GillespieSSA/GillespieSSA_0.5-4.tar.gz
packrat/src/MASS/MASS_7.3-44.tar.gz
packrat/src/R6/R6_2.0.1.tar.gz
packrat/src/R6/R6_2.1.1.tar.gz
packrat/src/RColorBrewer/RColorBrewer_1.1-2.tar.gz
packrat/src/RCurl/RCurl_1.95-4.6.tar.gz
packrat/src/RCurl/RCurl_1.95-4.7.tar.gz
packrat/src/Rcpp/Rcpp_0.11.6.tar.gz
packrat/src/Rcpp/Rcpp_0.12.1.tar.gz
packrat/src/XML/XML_3.98-1.1.tar.gz
packrat/src/assertthat/assertthat_0.1.tar.gz
packrat/src/batch/batch_1.1-4.tar.gz
packrat/src/bibtex/bibtex_0.4.0.tar.gz
packrat/src/bitops/bitops_1.0-6.tar.gz
packrat/src/brew/brew_1.0-6.tar.gz
packrat/src/caTools/caTools_1.17.1.tar.gz
packrat/src/coda/coda_0.17-1.tar.gz
packrat/src/codetools/codetools_0.2-11.tar.gz
packrat/src/codetools/codetools_0.2-14.tar.gz
packrat/src/colorspace/colorspace_1.2-6.tar.gz
packrat/src/crayon/crayon_1.2.1.tar.gz
packrat/src/crayon/crayon_1.3.0.tar.gz
packrat/src/curl/curl_0.9.3.tar.gz
packrat/src/curl/curl_0.9.tar.gz
packrat/src/deSolve/deSolve_1.11.tar.gz
packrat/src/devtools/devtools_1.8.0.tar.gz
packrat/src/dichromat/dichromat_2.0-0.tar.gz
packrat/src/digest/digest_0.6.8.tar.gz
packrat/src/doParallel/doParallel_1.0.8.tar.gz
packrat/src/evaluate/evaluate_0.7.2.tar.gz
packrat/src/evaluate/evaluate_0.7.tar.gz
packrat/src/evaluate/evaluate_0.8.tar.gz
packrat/src/foreach/foreach_1.4.2.tar.gz
packrat/src/formatR/formatR_1.2.tar.gz
packrat/src/ggplot2/ggplot2_1.0.1.tar.gz
packrat/src/git2r/git2r_0.10.1.tar.gz
packrat/src/git2r/git2r_0.11.0.tar.gz
packrat/src/gtable/gtable_0.1.2.tar.gz
packrat/src/gtools/gtools_3.5.0.tar.gz
packrat/src/highr/highr_0.5.tar.gz
packrat/src/htmltools/htmltools_0.2.6.tar.gz
packrat/src/httr/httr_0.6.1.tar.gz
packrat/src/httr/httr_1.0.0.tar.gz
packrat/src/igraph/igraph_0.7.1.tar.gz
packrat/src/iterators/iterators_1.0.7.tar.gz
packrat/src/itertools/itertools_0.1-3.tar.gz
packrat/src/jsonlite/jsonlite_0.9.16.tar.gz
packrat/src/jsonlite/jsonlite_0.9.17.tar.gz
packrat/src/knitr/knitr_1.10.5.tar.gz
packrat/src/labeling/labeling_0.3.tar.gz
packrat/src/lazyeval/lazyeval_0.1.10.tar.gz
packrat/src/lintr/lintr_0.2.0.tar.gz
packrat/src/magrittr/magrittr_1.5.tar.gz
packrat/src/markdown/markdown_0.7.7.tar.gz
packrat/src/memoise/memoise_0.2.1.tar.gz
packrat/src/mime/mime_0.3.tar.gz
packrat/src/mime/mime_0.4.tar.gz
packrat/src/miscTools/miscTools_0.6-16.tar.gz
packrat/src/munsell/munsell_0.4.2.tar.gz
packrat/src/mvtnorm/mvtnorm_1.0-2.tar.gz
packrat/src/nloptr/nloptr_1.0.4.tar.gz
packrat/src/packrat/1a91cdb290795c24cc0fda94177588b605525674.tar.gz
packrat/src/packrat/packrat_0.4.4.tar.gz
packrat/src/plyr/plyr_1.8.2.tar.gz
packrat/src/pomp/pomp_0.53-5.tar.gz
packrat/src/proto/proto_0.3-10.tar.gz
packrat/src/pryr/pryr_0.1.1.tar.gz
packrat/src/reshape2/reshape2_1.4.1.tar.gz
packrat/src/rex/rex_1.0.1.tar.gz
packrat/src/rmarkdown/rmarkdown_0.6.1.tar.gz
packrat/src/roxygen2/roxygen2_4.1.1.tar.gz
packrat/src/rstudioapi/rstudioapi_0.3.1.tar.gz
packrat/src/rversions/rversions_1.0.0.tar.gz
packrat/src/rversions/rversions_1.0.1.tar.gz
packrat/src/rversions/rversions_1.0.2.tar.gz
packrat/src/scales/scales_0.2.4.tar.gz
packrat/src/stringdist/stringdist_0.9.0.tar.gz
packrat/src/stringi/stringi_0.4-1.tar.gz
packrat/src/stringi/stringi_0.5-5.tar.gz
packrat/src/stringr/stringr_1.0.0.tar.gz
packrat/src/subplex/subplex_1.1-4.tar.gz
packrat/src/testthat/testthat_0.10.0.tar.gz
packrat/src/whisker/whisker_0.3-2.tar.gz
packrat/src/xml2/xml2_0.1.1.tar.gz
packrat/src/xml2/xml2_0.1.2.tar.gz
packrat/src/yaml/yaml_2.1.13.tar.gz
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/buildEigenAnalytic.cpp
src/buildEigenArray.cpp
src/buildFBMats.cpp
src/buildRateArray.cpp
src/getObsTimeInds.cpp
src/insertPath.cpp
src/joinCubes.cpp
src/populationLikelihood.cpp
src/reorderMat.cpp
src/resolveSubjContrib.cpp
src/retrieveKeys.cpp
src/retrieveSubjPath.cpp
src/sampleEventSubseq.cpp
src/subjectLikelihood.cpp
src/tpmProdSeqs.cpp
src/tpmSeqs.cpp
tests/testthat.R tests/testthat/DEPRECATED TESTS/test_init_subj_mat (DEPRECATED).R tests/testthat/test_build_emission_mat.R tests/testthat/test_build_fb_mats.R tests/testthat/test_build_initdist.R tests/testthat/test_build_irm.R tests/testthat/test_build_tpm_seqs.R tests/testthat/test_calc_likelihoods.R tests/testthat/test_check_irm.R tests/testthat/test_extract_rate_fcns.R tests/testthat/test_init_obs_mat.R tests/testthat/test_reinsert_path.R tests/testthat/test_remove_trajectory.R tests/testthat/test_retrieveKeys.R tests/testthat/test_sim_one_event.R vignettes/BDAepimodel.R vignettes/BDAepimodel.Rmd
vignettes/BDAepimodel.html
vignettes/SIR_SEIR_SIRS.R vignettes/SIR_SEIR_SIRS.Rmd
vignettes/SIR_SEIR_SIRS.html
vignettes/bbs_influenza.R vignettes/bbs_influenza.Rmd
vignettes/bbs_influenza.html
vignettes/model_misspecification.R vignettes/model_misspecification.Rmd
vignettes/model_misspecification.html
vignettes/popsize_misspecification.R vignettes/popsize_misspecification.Rmd
vignettes/popsize_misspecification.html
vignettes/prior_effect.R vignettes/prior_effect.Rmd
vignettes/prior_effect.html
fintzij/BDAepimodel documentation built on Sept. 20, 2020, 1:44 p.m.

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