Files in phybreak
Analysis of Outbreaks with Sequence Data
MD5
NEWS.md
DESCRIPTION
README.md
NAMESPACE
inst/CITATION
inst/doc/phybreak_intro.html
inst/doc/phybreak_intro.Rmd
inst/doc/phybreak_intro.R
vignettes/phybreak_intro.Rmd
vignettes/phybreak_intro_cache/html/__packages
vignettes/phybreak_intro_cache/html/burnin_a55d71de0c22cd8aa887b8d13475bfaa.RData
vignettes/phybreak_intro_cache/html/sample_3fa3a795c1f35e7e1b1cdd62e2d3fb9d.RData
vignettes/phybreak_intro_cache/html/__objects
vignettes/phybreak_intro_cache/html/__globals
vignettes/phybreak_intro_cache/html/ms_e4b914bf3d7b91a4206cec0f69fbd18b.RData
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-16-1.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-22-1.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-18-1.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-9-2.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-12-1.png
vignettes/phybreak_intro_files/figure-html/unnamed-chunk-8-1.png
R/phybreakdata.R
R/mcmc-environment-functions.R
R/sample-phybreak.R
R/phylotree.R
R/phybreak-package.R
R/thin-phybreak.R
R/plot-simphybreak.R
R/data_documentation.R
R/RcppExports.R
R/mcmc-updatetopology.R
R/transtree.R
R/sim-phybreak.R
R/phybreak.R
R/plotTrans.R
R/mcmc-updatehost-paths.R
R/infectorsets.R
R/make-phyloclass.R
R/logLik-phybreak.R
R/plotPhylo.R
R/get-phybreak.R
R/plot-phybreak.R
R/sample-minitrees.R
R/mcmc-updateparameters.R
R/treetransformations.R
R/burnin-phybreak.R
src/sctwh3.cpp
src/CCtranstree.cpp
src/ptr.cpp
src/mcctree.cpp
src/CCtrans_support.h
src/CCphylo_support.cpp
src/RcppExports.cpp
src/CCphylo_support.h
src/likseqenv.cpp
src/CCphylotree.cpp
src/mtcctree.cpp
src/likseq.cpp
src/CCtrans_support.cpp
man/plotPhylo.Rd
man/FMD_2007.Rd
man/sample.phybreak.Rd
man/infectorsets.Rd
man/phybreak.Rd
man/sim.phybreak.Rd
man/burnin.phybreak.Rd
man/plotTrans.Rd
man/plot.phybreakdata.Rd
man/AvianFluH7N7_2003.Rd
man/logLik.phybreak.Rd
man/M_tuberculosis_2013.Rd
man/FMD_2001.Rd
man/transtree.Rd
man/thin_phybreak.Rd
man/phybreakdata.Rd
man/plot.phybreak.Rd
man/phylotree.Rd
man/get.phybreak.Rd
build/vignette.rds
tests/testthat.R
tests/testthat/test_phybreakdata.R
tests/testthat/test_phybreak.R
data/M_tuberculosis_2013.rda
data/FMD_2001.rda
data/AvianFluH7N7_2003.rda
data/FMD_2007.rda
