afab73aff36eb4caa9d7e782fa783b7d *DESCRIPTION
af6f18d9cc3853ba5812ab067d89eb38 *NAMESPACE
d83073300c48c9def3141623fdba979c *R/RcppExports.R
2e4f44fac76c4f9a6ed07228d2566274 *R/TransPhylo-package.R
0e83528e2716e5ef3e9bd6b20fba070f *R/computeHost.R
1528890683404d3d8ae861bad8e1355a *R/computeMats.R
c7a622e8966dd43da0f8bbfa9ead6a13 *R/consTTree.R
727518954aaa926f312aaf6a62d531bc *R/convergence.R
3a367521f4e9682d0b2d810602adf4f0 *R/extractPTree.R
959cd1630336bab9e3b0e6e8ba69e4f8 *R/extractTTree.R
0215b4fbc4edd991eb927247369bb07e *R/extras/getIncidentCases.R
09f41cb54483c4183280542b3c8e29ea *R/extras/transphylo_extras.R
d871ba3830089bd123f1d29861c59625 *R/glueTrees.R
ae0db7f53f88c673dbc624b7c50cd984 *R/inferTTree.R
0a03bef64cbef05dcb63a22622a737c5 *R/infer_multittree_share_param.R
e5fa6f2cfe7863c953feacca98852dff *R/interpret.R
0b53ccbe9987d80d2a84837f847333dd *R/makeCTreeFromPTree.R
1677c506dbb126da064f7bc40bdd3d36 *R/makeTTree.R
2b87c30409af81473863e02cb6b50dcc *R/medTTree.R
9a04ba8b949da25e224ec49c197d502e *R/methods.R
3986de6cb02cad4faaba4b3063edab6a *R/phyloFromPTree.R
b9e6f8e745f032483f9c0520f9856719 *R/plotCTree.R
f1f31368be8f793c69e894eb670ab99a *R/plotTTree.R
9834d4eba59f8d817c4f37e97f49ead0 *R/plotTTree2.R
bf7d3b9ee31f77adea54a48c43ff0fa8 *R/probPTreeGivenTTree.R
c1a82444eed182e73f204b7a937650e2 *R/probTTree.R
f2d697b28aa3c58c2030fa041b75ff91 *R/proposal.R
587ff5fa2823a0114945b0fc3060fa73 *R/ptreeFromPhylo.R
b4beecab71bb5badca50c9ee1fc3319f *R/selectTTree.R
c44f2df1c900fd1802ee072d801c1e0f *R/simulateOutbreak.R
4f9de1423a161e5023dbc7a9074968f1 *R/withinhost.R
73d1d6f691ae92603b2b5651ec26c02a *README.md
a7af7653408be4a9fcd4f7485ff10896 *build/vignette.rds
13b4bfc2f2b78af732799436e3d2a81b *inst/CITATION
571046b34a005aa1fa3055faf5b1b17d *inst/doc/TransPhylo.R
e1677e4cca89a680c0fd6dca591302d9 *inst/doc/TransPhylo.Rmd
f05b18ab7bad19e32c46513618283952 *inst/doc/TransPhylo.html
b86072129f1ccf473def796e79faf078 *inst/doc/infer.R
bb242c3493463016cd3031381659ca52 *inst/doc/infer.Rmd
82429143b61025a361bafa4d4a8c5394 *inst/doc/infer.html
865699ff6d8d8b85653e8e38fe5f5742 *inst/doc/multitree.R
661923b748311c42f76139856eec5360 *inst/doc/multitree.Rmd
2dca9fdba135b948929f64693c816788 *inst/doc/multitree.html
0fc44902116b2d3b9e93d6e3c4b012ca *inst/doc/simulate.R
88eaa459c1b471543a1c23de3ba0e15d *inst/doc/simulate.html
6401bfd0bd10d7b18ba1a4612de498bd *inst/doc/simulate.rmd
e922c8fa5a9646b14816813382f7c349 *man/TransPhylo-package.Rd
51423d397ff578c1559e019a470efdb6 *man/as.mcmc.resTransPhylo.Rd
f9eefb1058211ab4c87985176038cb5c *man/computeMatTDist.Rd
aa1c59189304af4351e18f6a0262b0ff *man/computeMatWIW.Rd
61687432d63fd03ad5bf90df39452f9b *man/consTTree.Rd
7b35fcdd923587b07e7722c955cf222f *man/convertToCoda.Rd
cb7d9a70099c18fac395f22821b1acd8 *man/dateLastSample.Rd
cec325dba4514f57dce400c910db8e22 *man/extractCTree.Rd
7e0313f9c2683a5ab6e1522ad5ca1ab5 *man/extractPTree.Rd
2a8f9588bced3754a2213400dbc8d946 *man/extractTTree.Rd
c75c4dac2bd180db95b753fc9cbb8c23 *man/getGenerationTimeDist.Rd
2b9c31cd32208a3682b02b1c3b56cc90 *man/getIncidentCases.Rd
bf030341f6a05252bce1007306e4f5d7 *man/getInfectionTimeDist.Rd
3567cd6f5e319155c284702ffc874dbf *man/getOffspringDist.Rd
3237d2ca346f1baf7df4e3501db2bd6f *man/getSamplingTimeDist.Rd
1a9da0333f8a0d7efb089375e113e65c *man/inferTTree.Rd
717c378d89673374f93b14389e140a50 *man/infer_multittree_share_param.Rd
1f99fbd32a020c4d8fdb9b837d59fa5d *man/makeCTreeFromPTree.Rd
ac6793155cce521968112a9e491c1a94 *man/makeTTree.Rd
e1d647e71d85bf854941dbc622551ce4 *man/medTTree.Rd
3d346950727ebfd1f7d53f8f12f5f63a *man/phyloFromPTree.Rd
82305b8fccad7c4b4ca320d4adac4276 *man/plot.ctree.Rd
1ad2272c490007ff2e1012a683d1b901 *man/plot.ptree.Rd
6ad65811bff3ba27613e84e8716413fc *man/plot.resTransPhylo.Rd
767e776d8989630aa4363ec3bc4e6154 *man/plot.ttree.Rd
c2ed5d950cb8fd822c9aa2cba96443eb *man/plotCTree.Rd
8331cb61cf1bb8033de08c74c0c187e7 *man/plotTTree.Rd
948fc9497f1283821f6edbc72cfe097a *man/plotTTree2.Rd
df41c38b537fef955c3a0d58bd7b1ff0 *man/plotTraces.Rd
962922b5d7aff940254c9ff8843633d3 *man/print.ctree.Rd
1b92533747182602d4fef92b416d3152 *man/print.ptree.Rd
67c5f40e844623d5568bed999016eb17 *man/print.resTransPhylo.Rd
147c5a7a4691bfe9b7a057092f641133 *man/print.ttree.Rd
a72e767f6529c8d30b01872420587e1c *man/probPTreeGivenTTree.Rd
f4c3dfb08d93bda781c301536c839825 *man/probPTreeGivenTTreeR.Rd
75b97724d6ba8cee218eefc8ec9dff9b *man/probTTree.Rd
0f4011f87c085c8dfed45b0ecec0a1c2 *man/probTTreeR.Rd
2aff76c7296203ae6dfd8f804365baa4 *man/ptreeFromPhylo.Rd
51073e16a6c89ce087b981d64060505e *man/selectTTree.Rd
d9b95e69ae21e1896fb23284ea6bc0b7 *man/simulateOutbreak.Rd
6ef715909ffe9344d904f5e926cbfeab *man/summary.resTransPhylo.Rd
c608e2460f861d5842b995b32b4d4465 *src/RcppExports.cpp
2addb12d37eb0c97f5f0aa0a3b6f0edf *src/probPTreeGivenTTree.cpp
dc01828289a20a5ab984ae21a3bdb983 *src/probTTree.cpp
d553acf17e9b8928cf0022f8dd81b538 *tests/testthat.R
ec10f7be503717faa0137644b1a007ba *tests/testthat/Rplots.pdf
6bcf3c6ea32326217ec12ddf9a7bb768 *tests/testthat/test_coal.R
a37787c1c31f383be21e237e55e16df2 *tests/testthat/test_session.R
4e4eb9064aff69c784269cdc976c3f11 *tests/testthat/test_trans.R
e1677e4cca89a680c0fd6dca591302d9 *vignettes/TransPhylo.Rmd
bb242c3493463016cd3031381659ca52 *vignettes/infer.Rmd
661923b748311c42f76139856eec5360 *vignettes/multitree.Rmd
6401bfd0bd10d7b18ba1a4612de498bd *vignettes/simulate.rmd
