363fcbc6015f10900a90ff483d78c779 *DESCRIPTION
aeb3d3525f92d4b2ae0659a9d9cb593b *LICENSE
fb014fe8e62c7e8509c8f52007d7d3a9 *NAMESPACE
8dceb1e086ad63ec5372ebc103b0e176 *R/RcppExports.R
4d37f548893c52bcb32eaaa096e830ef *R/data.R
5d53b69b4abe1eff03d5ac9917a733a0 *R/findGroves.R
19e5b601fe7bef51c650444dce411532 *R/makeCollapsedTree.R
b5cb61e857fe552beb7d6f1a21deff0c *R/medTree.R
08ae20da899fd944ce18f201462b3db4 *R/metrics.R
76eb5cba87cc53f5570e3b60ea2cc020 *R/plotGroves.R
b03c7007a4efee406163838cc7261ad7 *R/plotTreeDiff.R
11e2391453b92e3a1673a8b7ea5a9860 *R/relatedTreeDist.R
962bc87f2f8956c0fe8c82a609d7c317 *R/servers.R
55315edad60b30d42cea086ed3f86069 *R/simulateIndTree.R
fa5a1612b3314a6a8d184d9a4b68b909 *R/tipsMRCAdepths.R
95ad61b15d4ab4ef1183069b96377f5f *R/transmissionTrees.R
556b3536d56a0be37690a8f361755c9e *R/treeConcordance.R
7cc6a1c393ea681427d452909dd5c4f6 *R/treespace.R
829041fc36b0044afc63b45044c1b0aa *README.md
88a61892f5c083fb375962e7e4d11bfd *build/vignette.rds
b22dd6d8a0aa612718b4cbbd9d4ccf16 *data/DengueBEASTMCC.RData
bbf91b415237e7ab1114fcf7cc54ad6a *data/DengueSeqs.RData
bcb388cef1ad20dbc0fbb98ba3812581 *data/DengueTrees.RData
6e65cb60b2f3d343d8a65a515e7669ec *data/fluTrees.RData
c30fe0c101e1d52f45a2faee4fc7b2de *data/woodmiceTrees.RData
f04f4f963e9642774e6ae96bfa1b86d9 *inst/CITATION
d74fe78eb26fcf140278a71ca36e3d11 *inst/doc/DengueVignette.R
90d735d54479cd4ba58862b09bf4dbe8 *inst/doc/DengueVignette.Rmd
821312c7914242150b5e580b4f784176 *inst/doc/DengueVignette.html
f741f075bbd7ef3c098969024181df79 *inst/doc/TransmissionTreesVignette.R
8e285be54aeb47115b7fe4942c719814 *inst/doc/TransmissionTreesVignette.Rmd
56b8dff51ca8e0c437bf4a6c3ec5b1b3 *inst/doc/TransmissionTreesVignette.html
f243d40c8ccfd13baef018a1df95efd6 *inst/doc/introduction.R
cf0d8785e1868e40d23227ef01faa2f7 *inst/doc/introduction.Rmd
6d686b589b172a0a9ddbd1548ef59b9f *inst/doc/introduction.html
12410ec612207db04759cad25ede8193 *inst/doc/tipCategories.R
a4af07adf372f69ddcf75cbdf780afe5 *inst/doc/tipCategories.Rmd
770bbd355fc3bb76880292ca58ef578e *inst/doc/tipCategories.html
6d890be7cf87406d84b7c855acede2a3 *inst/shiny/server.R
244f3ef75e8f6a1a325d980df84d949e *inst/shiny/ui.R
6c4711607de1791415c5b50511e84ad3 *inst/shiny/www/bootstrap.simplex.css
dc516afa494d9430a94c9fb23fc6aa97 *inst/shiny/www/html/help.html
d8684ae68cfdcc9049f1ff417ce3c3eb *inst/shiny/www/img/line.png
c3d0c3d454439e0980a1a2af2b355ca8 *inst/shiny/www/img/logo.png
96abc4b41da8cafa6f565bf5604b460c *inst/shiny/www/styles.css
095129a1994251eec286d5bc3f3fce98 *man/DengueBEASTMCC.Rd
91697d211ad4230586806881efb444da *man/DengueSeqs.Rd
1fb6214a402808562b962f6ff0ab9db2 *man/DengueTrees.Rd
1d9df35a4f643fadccd2955e5f601539 *man/dot-render.server.info.Rd
d91fae21ed96eac0a2b4fc01f01aab16 *man/findGroves.Rd
d31450f6795104b1824e3f36d3161d3f *man/findMRCIs.Rd
5368ab087178daccfda6080c2cc7a4f6 *man/fluTrees.Rd
cb81f4960674bf2be0843a85e03e820b *man/linearMrca.Rd
6197f441e80bf95789962d6ea87c9816 *man/makeCollapsedTree.Rd
63f97ae59baabc9b97ac4e0cc6ddbc3c *man/medTree.Rd
a1118fda772a5485bb63b6fc3af803e1 *man/multiDist.Rd
d6a69df165998b9bcd3831e8b892a259 *man/plotGroves.Rd
6157cbc706f868e6e5ad4b49173be489 *man/plotGrovesD3.Rd
94f2d3d8c6ff52a0ba7c206fee01e05f *man/plotTreeDiff.Rd
b271223c4312636d92e9a77b7f79d6c4 *man/refTreeDist.Rd
bf25019135537e42d3aa4af7cbc76dac *man/relatedTreeDist.Rd
058f879513aea54cb1fe8c82887c5d17 *man/simulateIndTree.Rd
6548fe1bf09ef8ddd395dc54e16e2d4f *man/tipDiff.Rd
7325336bf6883e4a6cb6d8045e512fde *man/tipsMRCAdepths.Rd
4109e7caade80c691a4e9f43225a0833 *man/treeConcordance.Rd
e4626a424cc2080ce45d0750fe4d32ba *man/treeDist.Rd
742f57ca11cd2a2503ee368fabd01843 *man/treeVec.Rd
5a3547722e685822472a902660cfc46e *man/treespace.Rd
ec2bc877c94fef4eb173e9a61cd1eb09 *man/treespaceServer.Rd
a77475898bc5833024c09c0dc37869db *man/wiwMedTree.Rd
81d99a24989b6bd9bc217ca56b1e1bb1 *man/wiwTreeDist.Rd
ee53473c06ed9d4d1bba201c55995879 *man/woodmiceTrees.Rd
9c74c81eeaf5d8af22cd33dab4daffcc *src/CPP_update_combinations.cpp
c6831a805f5342deba06265ad41e1fc8 *src/RcppExports.cpp
4328a6f98f7e19fdb142fa67fac002ec *tests/testthat.R
4f499b1668c9b2c7a0008473d97532a5 *tests/testthat/testbasics.R
90d735d54479cd4ba58862b09bf4dbe8 *vignettes/DengueVignette.Rmd
8e285be54aeb47115b7fe4942c719814 *vignettes/TransmissionTreesVignette.Rmd
d7d0f02319a4fcc003bed10e738c9d5f *vignettes/construction.png
cf0d8785e1868e40d23227ef01faa2f7 *vignettes/introduction.Rmd
a4af07adf372f69ddcf75cbdf780afe5 *vignettes/tipCategories.Rmd
dece84f823670ff0e7257cc643bf068b *vignettes/treespace3d.png
3957a3c2207cd065f1d95cc704ebaa7d *vignettes/treespaceDensiTree.png
32257dc64bf2670d28770a4679f063a7 *vignettes/treespaceTree.png
badb94ebf8cc44a29833b4eb658fdf44 *vignettes/vignettes/distances-1.png
a9ebb36ae31cc0fd528260758a3559ea *vignettes/vignettes/distances-2.png
bc804c608b84e309a976bf90fb9460ee *vignettes/vignettes/plotgroves-1.png
95c9438bdf54183e1b5c75cdc664b339 *vignettes/vignettes/woodmiceCluster1-1.png
28d7f5fb542b299c015f55c8286bec6b *vignettes/vignettes/woodmiceMedian-1.png
0d5fc8bb7e4e30e4f7de9a757ad0ab42 *vignettes/vignettes/woodmice_plotTreeDiff-1.png
5d34bb63b56d9884d561de8d11e33625 *vignettes/vignettes/woodmice_plotTreeDiff-2.png
