Files in outbreaker2
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
LICENSE
R/RcppExports.R
R/ref_priors.R
R/outbreaker_data.R
R/create_config.R
R/outbreaker_find_imports.R
R/palettes.R
R/custom_likelihoods.R
R/custom_priors.R
R/ref_likelihoods.R
R/custom_moves.R
R/doc_data.R
R/bind_moves.R
R/outbreaker_chains_methods.R
R/sim_ctd.R
R/create_param.R
R/outbreaker_mcmc_shape.R
R/bind_to_function.R
R/package.R
R/internals.R
R/outbreaker.R
R/outbreaker_move.R
R/zzz.R
R/outbreaker_init_mcmc.R
R/outbreaker_mcmc_store.R
R/get_cpp_api.R
src/priors.cpp
src/RcppExports.cpp
src/moves.cpp
src/internals.cpp
src/priors.h
src/likelihoods.h
src/likelihoods.cpp
src/internals.h
src/moves.h
inst/CITATION
inst/doc/Rcpp_API.R
inst/doc/Rcpp_API.html
inst/doc/overview.Rmd
inst/doc/customisation.Rmd
inst/doc/overview.html
inst/doc/customisation.R
inst/doc/Rcpp_API.Rmd
inst/doc/introduction.html
inst/doc/customisation.html
inst/doc/overview.R
inst/doc/introduction.R
inst/doc/introduction.Rmd
build/vignette.rds
tests/testthat.R
tests/testthat/test_sim_ctd.R
tests/testthat/test_priors.R
tests/testthat/test_data.R
tests/testthat/test_moves.R
tests/testthat/test_non_exported.R
tests/testthat/test_binding.R
tests/testthat/test_config.R
tests/testthat/test_likelihoods.R
tests/testthat/test_find_imports.R
tests/testthat/test_outbreaker.R
vignettes/overview.Rmd
vignettes/customisation.Rmd
vignettes/Rcpp_API.Rmd
vignettes/introduction.Rmd
vignettes/figs-introduction/traces-2.png
vignettes/figs-introduction/many_plots-2.png
vignettes/figs-introduction/config2-2.png
vignettes/figs-introduction/basic_trace-1.png
vignettes/figs-introduction/config2-1.png
vignettes/figs-introduction/w-1.png
vignettes/figs-introduction/traces-3.png
vignettes/figs-introduction/basic_trace_burn-1.png
vignettes/figs-introduction/many_plots-3.png
vignettes/figs-introduction/many_plots-4.png
vignettes/figs-introduction/many_plots-1.png
vignettes/figs-introduction/traces-1.png
vignettes/figs-introduction/many_plots-5.png
vignettes/figs-customisation/res_null_diag-2.png
vignettes/figs-customisation/res_wt-1.png
vignettes/figs-customisation/null_net-1.png
vignettes/figs-customisation/res_null_priors-2.png
vignettes/figs-customisation/traces_custom_priors-3.png
vignettes/figs-customisation/res_null_model-2.png
vignettes/figs-customisation/res_wt-3.png
vignettes/figs-customisation/wt_net-1.png
vignettes/figs-customisation/res_null_model-1.png
vignettes/figs-customisation/run_custom_move_mu-1.png
vignettes/figs-customisation/f_pi-1.png
vignettes/figs-customisation/res_wt-2.png
vignettes/figs-customisation/traces_custom_priors-1.png
vignettes/figs-customisation/run_custom_move_mu-3.png
vignettes/figs-customisation/res_null_priors-1.png
vignettes/figs-customisation/res_new_move-2.png
vignettes/figs-customisation/traces_custom_priors-5.png
vignettes/figs-customisation/traces_custom_priors-2.png
vignettes/figs-customisation/res_null_diag-1.png
vignettes/figs-customisation/run_custom_move_mu-2.png
vignettes/figs-customisation/res_null_model-3.png
vignettes/figs-customisation/null_trees-1.png
vignettes/figs-customisation/res_new_move-1.png
vignettes/figs-customisation/traces_custom_priors-4.png
vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.rdx
vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.RData
vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.RData
vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.rdb
vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.rdb
vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.rdx
vignettes/customisation_cache/html/__packages
vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.rdb
vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.RData
vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.rdx
vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.rdb
vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.RData
vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.RData
vignettes/introduction_cache/html/__packages
vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.rdb
vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.rdx
vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.rdx
data/fake_outbreak.RData
man/outbreaker_package.Rd
man/custom_priors.Rd
man/create_param.Rd
man/custom_likelihoods.Rd
man/fake_outbreak.Rd
man/palettes.Rd
man/outbreaker_chains.Rd
man/sim_ctd.Rd
man/outbreaker.Rd
man/create_config.Rd
man/custom_moves.Rd
man/get_cpp_api.Rd
man/outbreaker_data.Rd
man/bind_to_function.Rd
