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

outbreaker2 documentation built on May 23, 2022, 5:06 p.m.