d4969f3531c039fc126af9ce92a82466 *DESCRIPTION
a21bf021e5f0e852d72ea7fe0d8e8d34 *LICENSE
698b650d0c089f3ea28c5204f9ed7f8d *NAMESPACE
551fd8bd44b8b642d96d6886e32d50ff *R/RcppExports.R
432129a07bb3dee2f1e0fab7945d74d4 *R/data.R
0405073b0bcf42c1848de435df1b7628 *R/findGroves.R
650f4190af062a6e04e11340b85106e8 *R/medTree.R
fc828cf8b42cc03850a0d28703931f3b *R/metrics.R
31d79d1687b33555c2e8fed55d033e6e *R/plotGroves.R
c02893bd47dfc7e5a44803859c541a25 *R/plotTreeDiff.R
d6ccdaaaada97e2705317aa33f35598d *R/servers.R
2b05829a61a33edcf15b786df78cbd5b *R/transmissionTrees.R
68cad6d1a1b3e21170aff792870279c7 *R/treespace.R
742f845cee0504bc9e8e6181ee206f18 *README.md
59629421e86164009e8aac965f71da07 *build/vignette.rds
2f82967b31cf0355fca77cf057da0b00 *data/DengueBEASTMCC.RData
1afe5da1601d5ae111806c08e57fec0c *data/DengueSeqs.RData
f128fb06ac44efd32fb04ecc06896bd2 *data/DengueTrees.RData
e49f82b9d2e4e04959fc1609e3242de7 *data/fluTrees.RData
48df74b1807cc03a99ea9f4d16e0a8e9 *data/woodmiceTrees.RData
d9e7787def1af1d39bf31eef01d16d09 *inst/doc/DengueVignette.R
15414436ce0e779d73bb0b3141761db8 *inst/doc/DengueVignette.Rmd
65414b6b44ff647745533e8c91cfec6b *inst/doc/DengueVignette.html
f2b0e4da3bfb586280fdcaecdb9ea82f *inst/doc/TransmissionTreesVignette.R
9a36726bcbd32300484fd4b60f381387 *inst/doc/TransmissionTreesVignette.Rmd
826badf5edb974638f378428efe1bcb9 *inst/doc/TransmissionTreesVignette.html
2dfdcaadb2d7b5ed5c767cae4f7639d6 *inst/doc/introduction.R
ba59cd34245f7e907d1ca68ac9284661 *inst/doc/introduction.Rmd
d742205ea3cb4730d05906c346e4a33f *inst/doc/introduction.html
68e63f60168743249afd05fa19201cb8 *inst/shiny/server.R
3fe00e71926db4b060e6eb97bc194bb4 *inst/shiny/ui.R
72a52ccb88878f4fbc01b01c956377d3 *inst/shiny/www/bootstrap.simplex.css
6209b93fd0d79a50e31f3e727b5e4e46 *inst/shiny/www/html/help.html
d8684ae68cfdcc9049f1ff417ce3c3eb *inst/shiny/www/img/line.png
c3d0c3d454439e0980a1a2af2b355ca8 *inst/shiny/www/img/logo.png
4c310bde08e114bcc81546201149f9d2 *inst/shiny/www/styles.css
4e3d36d681981aa50aafbb2959c1c5f1 *man/DengueBEASTMCC.Rd
11e299eeacbe8e7405923c18b666237d *man/DengueSeqs.Rd
b2b7838d746662aace4f7f11ab25e43d *man/DengueTrees.Rd
b9ad1b0fc4ec54be76258f2b2c250fee *man/findGroves.Rd
d6913d9b7a748d3d1276dbcbb59fbbe5 *man/findMRCIs.Rd
1cb61eea995ada2384bfa495b572e792 *man/fluTrees.Rd
abd503764d974bd4578b965b0c84a5d7 *man/linearMrca.Rd
a3cb0c98811dbb4a4955699dc2554571 *man/medTree.Rd
ca8475c5a8536f8785dde14085dd264c *man/multiDist.Rd
3a3844fc0d5bc9873a8cddc999bdd8c2 *man/plotGroves.Rd
d93d2f9fdec272921901de931b53a12f *man/plotGrovesD3.Rd
2ff1b81ca3f34415b02e26d24363472b *man/plotTreeDiff.Rd
7ce24272af50fdbada5b55821603b708 *man/refTreeDist.Rd
ad90cb7e09137bf200ea8d99e7a3e298 *man/tipDiff.Rd
68f2c6cfd0cbde813f3cb7b2e19c5455 *man/treeDist.Rd
37245c3358aadaea55afcccc2f006b6c *man/treeVec.Rd
2298186f780bb58f06d0923251974721 *man/treespace.Rd
9401355c4029d2036670dd431219821f *man/treespaceServer.Rd
f57bb6a4f63349792b9239a82b113c41 *man/wiwMedTree.Rd
0069d01134bf866197f2999ba4a641fd *man/wiwTreeDist.Rd
d3d047b9337c322f3a663cc3771b81a9 *man/woodmiceTrees.Rd
9c74c81eeaf5d8af22cd33dab4daffcc *src/CPP_update_combinations.cpp
c6831a805f5342deba06265ad41e1fc8 *src/RcppExports.cpp
c68c5ffb7cee9fd27428a8be387833b1 *tests/testthat.R
50737a54d61f4cd9a8097ebf8bb0dc76 *tests/testthat/testbasics.R
15414436ce0e779d73bb0b3141761db8 *vignettes/DengueVignette.Rmd
9a36726bcbd32300484fd4b60f381387 *vignettes/TransmissionTreesVignette.Rmd
94595bba6f2bb206a2c5110bfd9ad1ce *vignettes/figs/BEASTtree_diffs-1.png
616ea34c397181878e7f7ce0d89e4584 *vignettes/figs/BEASTtree_diffs-2.png
1d796bfc0c84b8f8417a987fd2f46d02 *vignettes/figs/compare_BEAST_to_other_trees-1.png
02bf3b9d958d7cbd6ec13a9683f9a346 *vignettes/figs/compare_BEAST_to_other_trees-2.png
539e9b69463f0b6e772e100e7a93dd6a *vignettes/figs/compare_BEAST_to_other_trees-3.png
a5617f068880bef586cf95b95830bc47 *vignettes/figs/compare_trees_NJ_v_ML-1.png
8408ea563a22c2fa85f7a92e7b946ac5 *vignettes/figs/compare_trees_NJ_v_ML_recoloured-1.png
d7d0f02319a4fcc003bed10e738c9d5f *vignettes/figs/construction.png
a674c967f24e2d75e9636f511bf6e04e *vignettes/figs/distances-1.png
d2765ad3784553d03d5b726778a15045 *vignettes/figs/distances-2.png
9d751543c51335a0aff2a82d32647370 *vignettes/figs/distances_readme-1.png
88b11b6f51e21345be1fd8bafa31a279 *vignettes/figs/distances_readme-2.png
56a8de03d01520574f7f6deb83dc09a8 *vignettes/figs/findgroves-with-emphasis_readme-1.png
25f2477bb49002195ffe945d1f3ca698 *vignettes/figs/igraph_options-1.png
e422eec72fe13f0d3c3b6a9bb92dccbe *vignettes/figs/igraph_tree1-1.png
57f2639fd34387f66999ea287995d794 *vignettes/figs/make_NJ-1.png
213f79420bfded98fcf2d58f4c7fb4f2 *vignettes/figs/plotgroves-1.png
4831761d443daec1832115749111b650 *vignettes/figs/plotgroves2_readme-1.png
3c8d0609fb3927e983acbd0e1ddb2abd *vignettes/figs/plotgroves2_readme-2.png
a53902c75200510cf36550d5fb6548c4 *vignettes/figs/plotgroves2_readme-3.png
81ff60166990b9383c139901aab6d593 *vignettes/figs/plotgroves_readme-1.png
70ca565849b0ac819ce99711192d04ad *vignettes/figs/scree_plot-1.png
1946ffbb0ef3c3e72c070de3485399e4 *vignettes/figs/see_ML_boots-1.png
1c921be416a949af520ad9d1b71147f3 *vignettes/figs/see_NJ_boots-1.png
767dc343776c12e94feadac2260488d6 *vignettes/figs/trees2_and_3-1.png
5ec6e9c6ac914f9fb10731e15402e555 *vignettes/figs/trees2_and_3-2.png
dece84f823670ff0e7257cc643bf068b *vignettes/figs/treespace3d.png
3957a3c2207cd065f1d95cc704ebaa7d *vignettes/figs/treespaceDensiTree.png
32257dc64bf2670d28770a4679f063a7 *vignettes/figs/treespaceTree.png
c1abce94178f4d6133695956c540e576 *vignettes/figs/view_ML-1.png
9a4eee5b2307160a1813d396c5de2b4d *vignettes/figs/wiwMedTreePlot-1.png
dce17860c77390fb06d6cd8a33d625c2 *vignettes/figs/wiw_MDS1000-1.png
7dc88e52020d8238ffb4cdab49626e41 *vignettes/figs/woodmice-tip-emphasis_readme-1.png
573bb13e4cecc78a3e80eae9f4f0610c *vignettes/figs/woodmiceCluster1-1.png
ab0985e8095fb910b2ad1856782b7d14 *vignettes/figs/woodmiceCluster1_readme-1.png
d943b17c1a93896811cf93e306f58918 *vignettes/figs/woodmiceMedian-1.png
ef518521ce15ccccddc92c2823eb1f7b *vignettes/figs/woodmiceMedian_readme-1.png
27f232eb46a71e8d64a7055c14960042 *vignettes/figs/woodmicePlots_readme-1.png
3949e7ccccf70ad2de3326e78231347f *vignettes/figs/woodmicePlots_readme-2.png
77cc6241293a3ae7015c9624320322cd *vignettes/figs/woodmicePlots_readme-3.png
d2550a73b8c72e5a1afa7578fd67f772 *vignettes/figs/woodmice_plotTreeDiff-1.png
19ec1731d3cdeed27b25a7781db12f97 *vignettes/figs/woodmice_plotTreeDiff-2.png
b46dc942c6cddb66410ec6c103c3e041 *vignettes/figs/woodmice_plotTreeDiff_readme-1.png
ce99f8bdce61587038cf9c1e7ffc5135 *vignettes/figs/woodmice_plotTreeDiff_readme-2.png
ba59cd34245f7e907d1ca68ac9284661 *vignettes/introduction.Rmd
