b8fcdc7fe6292062715214795421b59a *DESCRIPTION
ff4ce1700b45f63dc6e8f5b8de9a249b *NAMESPACE
a3e4edc2b50e2dfb0ff66ead78f7f39a *NEWS.md
55acc89d8de74df53c47125d8ae74f62 *R/RcppExports.R
27e81513e7b14f794b7b7ff50b38835f *R/burnin-phybreak.R
807d213d9ac35f09dc55d07ae3a1e130 *R/data_documentation.R
8f4d2b03798447bf1761c4ef7c155d4b *R/get-phybreak.R
2992e6383c7369110586c58b98f4da72 *R/infectorsets.R
ed02ddf4e44ef4028a70c0bcdc093dc6 *R/logLik-phybreak.R
0b6e3d490573b6e5e44835afdd9afb8a *R/make-phyloclass.R
4aab69172d4d4cfc3b20bdb5e0c67d0f *R/mcmc-environment-functions.R
bda755c8e9238616854281690b99c4aa *R/mcmc-updatehost-paths.R
70470fe898d639b68fc497418b5e0aae *R/mcmc-updateparameters.R
bde09899c2302b7722d6c942ddc6369c *R/mcmc-updatetopology.R
a067b11f3ca29a934d7a7938a07373f8 *R/phybreak-package.R
3fa05698ab54bdbec14ce3ac92b70803 *R/phybreak.R
2ac251b40f2ad79a2865bc5ee7949dfa *R/phybreakdata.R
fdff5b6725e77414518fa7c5f554129c *R/phylotree.R
897b30454e58c1650724803906629d1d *R/plot-phybreak.R
3b66a3bc3598a2f1b53814091a821ece *R/plot-simphybreak.R
3a9af7bcdea3bcb519499f3e09591a7b *R/plotPhylo.R
15189f63faef48b75dd9428941543dcc *R/plotTrans.R
254063d1fbda457ba780fccc32a4bf85 *R/sample-minitrees.R
c8ab4fc457fab7373c8b1537ad22cdcc *R/sample-phybreak.R
6d05d670fc00a29f1595713e20769540 *R/sim-phybreak.R
8540c614d0187c6f97a06af6267d471a *R/thin-phybreak.R
7c4c34d278a44dc9e6ab7d160f317ed5 *R/transtree.R
3778270804de16bf9aa0648448e7ca17 *R/treetransformations.R
c9e2be308408ff96bb5041cf57293d10 *README.md
9cef938906f660eb9ee22d74d8b7518f *build/vignette.rds
26ede2a080da64fbdb19bdecd400359e *data/AvianFluH7N7_2003.rda
7ff3bcba31f79129bf073e838be979d8 *data/FMD_2001.rda
716fa19cab5b4a8441b4ce8b0dfe7123 *data/FMD_2007.rda
5d4aedc6d65b093fd93f4176ffd2f101 *data/M_tuberculosis_2013.rda
bd1d23eebcbf61df884e56e2793e72e4 *inst/CITATION
249194d46ce9512bd54ab1b9f3041c83 *inst/doc/phybreak_intro.R
6f2327dc03b4f2e8c57bcb059179b6c2 *inst/doc/phybreak_intro.Rmd
b56af82afeed20b2b590efa55d5ea3b1 *inst/doc/phybreak_intro.html
9275e59cac41df873eead62c4333f519 *man/AvianFluH7N7_2003.Rd
42dfc59c78ad4b9421226b36666cef9a *man/FMD_2001.Rd
49899cad349d1793f05cd2ac2aba3da5 *man/FMD_2007.Rd
cb67c7786bf3a03dc3da5503805158e8 *man/M_tuberculosis_2013.Rd
2a99917e79e0989b2ca4523955fb8242 *man/burnin.phybreak.Rd
04ecc30222cc5cf5c3157a2b2c8f7967 *man/get.phybreak.Rd
11ef59bb307dc4d5fdc3a2462f7eedb0 *man/infectorsets.Rd
09383dfa61a0d79cb4933012b53c274f *man/logLik.phybreak.Rd
0e031330f7fc7debe37fb41a92615e96 *man/phybreak.Rd
a240b88d97aaee71104c7c04da5144e1 *man/phybreakdata.Rd
af670cdfcdc7bf25036ce6b83b876838 *man/phylotree.Rd
f79833e1a988690bcef88895b90304f4 *man/plot.phybreak.Rd
628926c39343e718136c735a9b23b084 *man/plot.phybreakdata.Rd
cfc847703da14e252600d87f51dac73e *man/plotPhylo.Rd
1416d1d0b393519fdcb6cc784f98399e *man/plotTrans.Rd
084fc4d113ea23a72d29a2e7c909a1cf *man/sample.phybreak.Rd
092bfab34584ca3b505446622212d6ea *man/sim.phybreak.Rd
0ab464857e19e98abeed45f73d9ed085 *man/thin_phybreak.Rd
8370da93c0f3b32d9d5c6435bc240d0f *man/transtree.Rd
fa997e3de470c121cbd8d7e9696ebf5e *src/CCphylo_support.cpp
efc114041bfbac6a48eb50c30c51fc86 *src/CCphylo_support.h
0677b5281e91be9f7699f0c5ad187f47 *src/CCphylotree.cpp
7c4084809ef633acf64b308d712576ea *src/CCtrans_support.cpp
c28224601dd5c84fba5c1a11f061b896 *src/CCtrans_support.h
00968a5ed71351b39c8bd7aed3f92194 *src/CCtranstree.cpp
1ddc2d90a1124fc63c3a1ee2d75877cd *src/RcppExports.cpp
661e4aa14b1aaf597eb26bb098d35433 *src/likseq.cpp
236fecdf87d334647fed2a9c58a5df5f *src/likseqenv.cpp
044d956a46af43559b82586dad2d2992 *src/mcctree.cpp
f810f0a051cbccfcd24be9873d8ce5b3 *src/mtcctree.cpp
78b645e4ffe16953411f121c1a28f76c *src/ptr.cpp
56c15c8f7bf476a5c1fd955cd0498a97 *src/sctwh3.cpp
1dafc4dd78e797740f02f98d54d52e01 *tests/testthat.R
b0b79d115104ffdfe8f61b01f1162aea *tests/testthat/test_phybreak.R
808a09de8537777c56275cd103520309 *tests/testthat/test_phybreakdata.R
6f2327dc03b4f2e8c57bcb059179b6c2 *vignettes/phybreak_intro.Rmd
6187d936a8b6369d93de0082da34a83b *vignettes/phybreak_intro_cache/html/__globals
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