Files in donkeyshot/phybreak
Analysis of Outbreaks with Sequence Data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/ESS.R
R/RcppExports.R
R/burnin_phybreak.R
R/c_phybreak.R
R/data_documentation.R
R/get_phybreak.R
R/infectorsets.R
R/logLik_phybreak.R
R/mcmc-environment-functions.R
R/mcmc-rewire_paths_complete_classic.R
R/mcmc-rewire_paths_complete_edgewise.R
R/mcmc-rewire_paths_wide_classic.R
R/mcmc-rewire_paths_wide_edgewise.R
R/mcmc-rewire_subfunctions.R
R/mcmc-sample-minitrees.R
R/mcmc-updatehost-paths.R
R/mcmc-updateparameters.R
R/phybreak-package.R
R/phybreak.R
R/phybreakdata.R
R/phylotree.R
R/plotPhylo.R
R/plotPhyloTrans.R
R/plotTrans.R
R/plot_phybreak.R
R/plot_phybreakdata.R
R/print_phybreak.R
R/quantile_phybreak.R
R/sample_phybreak.R
R/sim_phybreak.R
R/thin_phybreak.R
R/transtree.R
R/treetransformations.R
README.md
cran-comments.md
data/AvianFluH7N7_2003.rda
data/FMD_2001.rda
data/FMD_2007.rda
data/M_tuberculosis_2013.rda
inst/CITATION
man/AvianFluH7N7_2003.Rd
man/ESS.Rd
man/FMD_2001.Rd
man/FMD_2007.Rd
man/M_tuberculosis_2013.Rd
man/burnin_phybreak.Rd
man/c.phybreak.Rd
man/get_phybreak.Rd
man/infectorsets.Rd
man/logLik.phybreak.Rd
man/phybreak.Rd
man/phybreakdata.Rd
man/phylotree.Rd
man/plot.phybreak.Rd
man/plot.phybreakdata.Rd
man/plotPhylo.Rd
man/plotPhyloTrans.Rd
man/plotTrans.Rd
man/print.phybreak.Rd
man/quantile.phybreak.Rd
man/sample_phybreak.Rd
man/sim_phybreak.Rd
man/thin.phybreak.Rd
man/transtree.Rd
phybreak.Rproj
src/CCphylo_support.cpp
src/CCphylo_support.h
src/CCphylotree.cpp
src/CCtrans_support.cpp
src/CCtrans_support.h
src/CCtranstree.cpp
src/RcppExports.cpp
src/likseq.cpp
src/likseqenv.cpp
src/mcctree.cpp
src/mtcctree.cpp
src/ptr.cpp
src/sctwh3.cpp
tests/testthat.R
tests/testthat/test_phybreak.R
tests/testthat/test_phybreakdata.R
vignettes/phybreak_intro.Rmd
vignettes/phybreak_intro_cache/html/__globals
vignettes/phybreak_intro_cache/html/__objects
vignettes/phybreak_intro_cache/html/__packages
vignettes/phybreak_intro_cache/html/burnin_996720ad2025f1d671510c8e2a83f035.RData
vignettes/phybreak_intro_cache/html/ms_e4b914bf3d7b91a4206cec0f69fbd18b.RData
vignettes/phybreak_intro_cache/html/sample_1acabe93221bb8ab1bd8a30c190c5355.RData
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-12-1.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-16-1.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-18-1.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-22-1.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-8-1.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-8-2.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-9-1.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-9-2.png
