662ff12f11e8b72935379639d3c9d6bc *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
fbfe07c9a99c527d1290b782a2ebc0fe *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
404452dc504a40d321b52aa60e14d4c6 *R/plotTTree2.R
bf7d3b9ee31f77adea54a48c43ff0fa8 *R/probPTreeGivenTTree.R
46a5f7e2a0455f97f638a3ff63bdd4d3 *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
16d1ae6386e531c173436b593094d5ea *build/vignette.rds
13b4bfc2f2b78af732799436e3d2a81b *inst/CITATION
10237d5a0c32091b742357b6942006bc *inst/doc/TransPhylo.R
e1677e4cca89a680c0fd6dca591302d9 *inst/doc/TransPhylo.Rmd
87c599e58bbd1c11e1eb4d95935a8551 *inst/doc/TransPhylo.html
bd8ae358e34814300b1caca6a784d356 *inst/doc/infer.R
bb242c3493463016cd3031381659ca52 *inst/doc/infer.Rmd
ff04957d113189c3f6555cd97980de8e *inst/doc/infer.html
f3ddac1ce7632eb6e3e742f29f388dc9 *inst/doc/multitree.R
661923b748311c42f76139856eec5360 *inst/doc/multitree.Rmd
b5251bb6707e48e9efe933169176636b *inst/doc/multitree.html
647e2bb2578748d2a07cc7a29cd2a703 *inst/doc/simulate.R
01ac67bf744e7ff28cf92399e153e124 *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
40f3baf4f73f403e4e81bbf88ff5bf1d *man/getGenerationTimeDist.Rd
f442c2dad6416556e9931c2f73ab2f44 *man/getIncidentCases.Rd
c6f5f24901d2a83a3ebf64b788d0db2f *man/getInfectionTimeDist.Rd
3567cd6f5e319155c284702ffc874dbf *man/getOffspringDist.Rd
55a419be216d123ceb7477c3e0689746 *man/getSamplingTimeDist.Rd
c55b2a1756e187d084a45b91eb9525ed *man/inferTTree.Rd
08dfe44aa92df0f3a3a14c5e456badb8 *man/infer_multittree_share_param.Rd
d1caf4a71be2de598f7781b66a8c9179 *man/makeCTreeFromPTree.Rd
af0184016fffbafa210b3b9de927b11a *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
4e66d281bbf69b084f6189537c8b9d93 *man/plot.ttree.Rd
b00e0b749f0c338fb6b5312c673d3f52 *man/plotCTree.Rd
61627ba6e8ee132c229ee0b63dcd1f32 *man/plotTTree.Rd
ad4559a78437ced0a218d756f5b962bb *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
c75f7c0db26575b72276b4494fc99428 *man/probTTree.Rd
685cec4003bd0ae04979d404bb536abd *man/probTTreeR.Rd
2aff76c7296203ae6dfd8f804365baa4 *man/ptreeFromPhylo.Rd
51073e16a6c89ce087b981d64060505e *man/selectTTree.Rd
ec1e66d651dadff57c3734d6c55fc1e7 *man/simulateOutbreak.Rd
6ef715909ffe9344d904f5e926cbfeab *man/summary.resTransPhylo.Rd
c608e2460f861d5842b995b32b4d4465 *src/RcppExports.cpp
2addb12d37eb0c97f5f0aa0a3b6f0edf *src/probPTreeGivenTTree.cpp
dc01828289a20a5ab984ae21a3bdb983 *src/probTTree.cpp
d553acf17e9b8928cf0022f8dd81b538 *tests/testthat.R
8a782298d85c1ca7854188ffbeff2ea5 *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
