09bea99accdfa65af9ec5a0fd2dc38e6 *DESCRIPTION
a755beeb691e8ab6cfe9b1215356015d *NAMESPACE
da96bb67dc8d29e50c7052649b52648d *NEWS.md
f3cb17fd9a49ea3080fe3115f5b5c30a *R/AddTip.R
d1c7c5156b801d3bd297b064d9331a75 *R/ArtificialExtinction.R
d41d8cd98f00b204e9800998ecf8427e *R/BigInteger.R
af71aae2d627d0394223198555b9c442 *R/ClusterTable.R
7f2d8a7fffd81e76813aa02f0b5c0972 *R/Combinatorics.R
f72540361d8c0bdb5f1711ca49efbfde *R/Consensus.R
c8b221281ac5e09f1d52874a935c2a60 *R/DropTip.R
fac2960db9fd7c1b1c1081007d032bb8 *R/ImposeConstraint.R
12cd1737c58020612405febc6ab578bd *R/Information.R
5375e7794f341801c1b1fbde68b7f707 *R/KeptPaths.R
20d93e29c3f22ae7fd9af4553bd45649 *R/KeptVerts.R
de2df90a8b21c7f4eb2ef700441a2733 *R/PathLengths.R
1613f51da507a8f05e552767bae8ac53 *R/RcppExports-manual.R
0b1e60bbb9619a35d558fad9481de11b *R/RcppExports.R
952a726215d8a9dd93b3f97f36a37c33 *R/ReadTntTree.R
61ff796e49846f22626178fcc94df470 *R/RoguePlot.R
7e24aa1ca52d4e67dd8aa53ec3ef23f2 *R/SplitFunctions.R
5795a19e18f1ad1848db805b4998d8d4 *R/Splits.R
e8d1a037d346e763456fd6895db20f84 *R/Stemwardness.R
6a39da6aedaf31848700706b0edf258a *R/Support.R
089f4ab6765133f41c58304f04a17ae3 *R/TotalCopheneticIndex.R
9e668388046e6f80bc8cbccade27a450 *R/TreeNumber.R
916e8be725407381b6aec7079c26f269 *R/TreeTools-package.R
96d29b464458b5b394aa5fe875882698 *R/as.matrix.R
d8d6b3198e26180d1e2e7c3e72faf732 *R/as.multiPhylo.R
d54768da4a5633d35e2afbadcb11b3d2 *R/data.R
fdedbb8c32a2590ec9922dc4491c43ba *R/helper_functions.R
52339d78e3aee26446f0e30a71416504 *R/mst.R
6a25554db30d2598a34ccafa4db3616c *R/parse_files.R
06a709ca07d4d34b423ebe32ea406c3a *R/phylo.R
8d88dfd3912cd0fd254d672f05179811 *R/sort.R
6d0990c549633a293af7aa01be801a5f *R/split_analysis.R
9fb234ea6184e32a6cf0f17f6904af71 *R/sysdata.rda
06a3830e69a25017cb819a4932d7f81f *R/tree_comparison.R
75c6d3d0b34466040323ea3d6bba6eee *R/tree_display.R
0a2380fdbac226c274567e8dd0a6b44f *R/tree_generation.R
9dc8601facd00e5029eda0dac6cadd7a *R/tree_information.R
a854c61de05481a7e5a7de826dce834b *R/tree_numbering.R
94551cc8d8f230ab28557afb756f6813 *R/tree_properties.R
4306e4fd7f16877b2ab8c6a330f69542 *R/tree_rearrangement.R
1c756aef6ea7ee2ee3fb2458c8d28914 *R/tree_shape.R
a0920d2b39ff700bdba12f0f2efc5116 *R/tree_write.R
cabab83c282ffcf114cf36c7d2e72e78 *R/zzz.R
c167c35145348b326d34d597a96bbc0e *build/partial.rdb
2019b59a6c2c69ac76221ac2e5191bb8 *build/vignette.rds
4f7f08498760060495a1138f1e456d8f *data/Lobo.RData
7a12bfe34746d63554ed9b3d31a0fb5c *data/brewer.R
bb0b8e0646742b8bbbe06122ab81a938 *data/nRootedShapes.R
405a7443baa6a8b25df8bbb3e7f49fdd *data/nUnrootedShapes.R
806aadf10ac2e0ae477ffce74b720f72 *data/unrootedKeys.rda
da58fd7b83f0c90ef476e5f1bface8ba *inst/CITATION
2ae89b289d043cd70da5534771d7fc63 *inst/REFERENCES.bib
08332bfaa1ea8dbbda0e8f3a7134d478 *inst/WORDLIST
2a33c016808841801938c7c7b2dcb1cb *inst/apa-old-doi-prefix.csl
7be48fe3f97d4e5c515b8fb4b62f5a9c *inst/doc/filesystem-navigation.Rmd
776e341f04eae2c239cdb693f5413f7d *inst/doc/filesystem-navigation.html
bde6ddd47311d0879d826c28a5a2e6ac *inst/doc/load-data.R
4a2973f5f06cf7e67a8f433bf0aad0a9 *inst/doc/load-data.Rmd
8abe91ff44e6b18d0760d79fcd7446b3 *inst/doc/load-data.html
52c48e92a6ab50bff073cf47543193f9 *inst/doc/load-trees.R
68f831f6f5a8fc211b9b183213a0de6c *inst/doc/load-trees.Rmd
68826139303791340746e0d349bd0f4b *inst/doc/load-trees.html
38de4a03e1e8a5f07d46535ffc77277e *inst/extdata/input/dataset.nex
c11d9ad2158675f390443c6b64483931 *inst/extdata/input/notes.nex
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/otherfolder/empty.file
1a0bb364bcad07636e183bb94edd0b0d *inst/extdata/output/named.tre
390c2c6ce5db4839de4ec5aa9bc941e3 *inst/extdata/output/numbered.tre
307bd6e4eb9869f849fa0699a2c9b378 *inst/extdata/tests/ape-tree.nex
aa6feda919c49e2c7089b17745b7a3f3 *inst/extdata/tests/continuous.nex
b54d52cfa42e12c593c83861d0a16d2c *inst/extdata/tests/encoding.nex
a85e9f11ab78ea122572292d012ca2a7 *inst/extdata/tests/parse-nexus.nexus
bff84db6cb62d85a13b4f26365ef83c9 *inst/extdata/tests/taxon-notes.nex
b5255e3a064a164f77244565cce30ee7 *inst/extdata/tests/tnt-bare-tree.tnt
1cd58a078d0dd8b5cd11da4bd3beee09 *inst/extdata/tests/tnt-dna.tnt
2871920befb8138b583a76dfa88ce4c5 *inst/extdata/tests/tnt-matrix.tnt
872071d2ef284e3869ea9cbbd10bc0cd *inst/extdata/tests/tnt-namedtree.tre
2d7a2fcd81cb8267de316af92a8663bb *inst/extdata/tests/tnt-tree.tre
8163b3c6ae3da127459c7fc59017dbee *inst/extdata/tests/tnt-trees-and-matrix.tnt
4b1b614aa8681c314281b29094742ccf *inst/include/TreeTools.h
2e400955ee87b3275281d7ad9f09d31f *inst/include/TreeTools/ClusterTable.h
b0ff646344c367168b252ec8d60c835b *inst/include/TreeTools/SplitList.h
f9026dfd230e7a184d83b0d5be93607f *inst/include/TreeTools/assert.h
5786ef202f211dc0c649b77ad6f3f95c *inst/include/TreeTools/keep_tip.h
725b277c8cd214e085d47cd59853b3a0 *inst/include/TreeTools/renumber_tree.h
ece37aed73d042c072e598b6d36ef800 *inst/include/TreeTools/root_tree.h
b069d910e4931ac22742553c062fbfdc *inst/include/TreeTools/types.h
76034f502d95d421cfb795905b2b9ea6 *man/AddTip.Rd
a246565280bae8a7050034c1eeecd8e0 *man/AncestorEdge.Rd
d146e6ac7bd9616cf702f03990e14b87 *man/ApeTime.Rd
5d7269a77147f8d0df70817fae68991d *man/ArtificialExtinction.Rd
d8a8343da7e707110db3ebe4dd7b1f6b *man/CharacterInformation.Rd
1a7c3f7361becce0fb7b8f6d1d03ba76 *man/CladeSizes.Rd
3e6be04e0da93efb901b4ca7a4f1cd3e *man/CladisticInfo.Rd
3d658ed439cb7561998dc4c48778eecb *man/ClusterTable-methods.Rd
22ff53d7518a66157a2ee7ddbb9f3b5b *man/ClusterTable.Rd
8b28357bae4946ce57088129e94bbb10 *man/CollapseNode.Rd
88a35a5dd9798bd1ba4c59ccfeb7657a *man/CompatibleSplits.Rd
bf5f2966aba231987c6074d775fabb3b *man/Consensus.Rd
be2a520aff01825387eb34b981ed42b9 *man/ConsensusWithout.Rd
3cacd05a9dd8eee9716becaec19376af *man/ConstrainedNJ.Rd
cd1fb3d0880767adc4b775db9f1224d4 *man/DescendantEdges.Rd
50027bd13a2ba957cd89dbb9af073196 *man/DoubleFactorial.Rd
5ef6b91f9d49bae60f8beda8f20b99e1 *man/DropTip.Rd
71c67b873933558e07abd286c92a61e2 *man/EdgeAncestry.Rd
8c99ebe42eecb9f2cf3bac8401f831f7 *man/EdgeDistances.Rd
fbf94010b47d02ebc86a1f0cdd643555 *man/EndSentence.Rd
a76cf2982867d46dfe37cc5b44ffd487 *man/EnforceOutgroup.Rd
644ac70b8d4364fa3e655a699f88bcac *man/ExtractTaxa.Rd
12aae8d19082802a60a7c4a739a064c1 *man/GenerateTree.Rd
7dc77937690f76c4df6476270d50aeba *man/Hamming.Rd
c09d3b6905e137671a1573335d573dce *man/ImposeConstraint.Rd
60712ab2b79878e2ec45ab5a8537e4c8 *man/KeptPaths.Rd
1bced8786c7811ee2cad655b371d933c *man/KeptVerts.Rd
5a26c0250f9a6564eae602abce768a4f *man/LabelSplits.Rd
46d680e51926e0faf1045fb1ada77646 *man/LeafLabelInterchange.Rd
3ab29edf040ccf95994c6ceb278edb75 *man/ListAncestors.Rd
735b74809d39a60636b601a18b15c38f *man/Lobo.data.Rd
1e4a5e3ee6dd58c2335f09bab1ba5818 *man/MRCA.Rd
5e13da00de5b338d4d445b3ebbc212cc *man/MSTEdges.Rd
51204574d9dd6a838a3b9a368cd12054 *man/MakeTreeBinary.Rd
db99ef47e2de30e136ba812b272a1d6c *man/MatrixToPhyDat.Rd
4ee602388a9586d1198869075c2d5763 *man/MorphoBankDecode.Rd
df95f75bc3b1e1a094817c5e3dc7c2b3 *man/N1Spr.Rd
2acc324bf05e3add8076fae4909088ac *man/NDescendants.Rd
2c590b2d5e46aea85774945888ebcd42 *man/NJTree.Rd
372b45899f393d5c5516954612ffc1ba *man/NPartitionPairs.Rd
b8f54a6dcdb6f4777306053dfbdc2b7e *man/NRooted.Rd
e759341f229c6a100b74464c301dc3a2 *man/NSplits.Rd
5021dbe0fb3fdddcd1573c0ac01bd383 *man/NTip.Rd
6d8c77e944d714845608303fb092c20e *man/NewickTree.Rd
e17b4121853147b4c6e776834ad6d02f *man/Neworder.Rd
94ec513ecac0113ada3bad974ff589ec *man/NodeDepth.Rd
18c6fa404c17955ccdb5e93e8a140c4d *man/NodeOrder.Rd
b92331d1d9925bde82b3302776731ab3 *man/NonDuplicateRoot.Rd
ad03e65dc53c555600dc367d7261711f *man/PairwiseDistances.Rd
cb0be0a8caf1a5855a4e5f2650086ca3 *man/PathLengths.Rd
1ac552a0429a00a086d76951397ddb8e *man/PhyToString.Rd
433f9bde4e173532283efe544fb21c1d *man/PolarizeSplits.Rd
91854842fa0877626858b995336c3958 *man/ReadCharacters.Rd
43f9e55de82bf17c80b47b657c2cdd07 *man/ReadTntTree.Rd
4a48ce4ab9ecda02e97c05d4634af356 *man/Renumber.Rd
d8fa3933b79614486c9c988dc1be0f38 *man/RenumberTips.Rd
d6cafb5f466c3592c9f0f85eb094747b *man/Reorder.Rd
f385ba797e695852a442acc806a0a128 *man/RightmostCharacter.Rd
695d00b30eb1c36fa8d5066e223f6cc3 *man/RoguePlot.Rd
347125c970cf2336fbf5ac4badcc1f54 *man/RootNode.Rd
3a5d29cfbcc2a85746fa0580744809cb *man/RootTree.Rd
e1bc7c2ffae1cac8395bd98c298bd27d *man/SampleOne.Rd
ef1db950d2535ab57c87d50fbb3e26c8 *man/SortTree.Rd
a1178fd8b3c717abcee1c9a7cce3a279 *man/SpectrumLegend.Rd
1c6e144f7e27fbf07ea190e857007c45 *man/SplitFrequency.Rd
9ca3bf25d101beba1bdde4eccfc94710 *man/SplitInformation.Rd
000f139f98ffb33fdee64914a3b32d02 *man/SplitMatchProbability.Rd
cecb7ea213e755577a97b78a58e05a9d *man/Splits.Rd
aa10db61bfc272f25b7cdc499b3a166e *man/SplitsInBinaryTree.Rd
2564644ad5fbdd48988fc20793f6bd5f *man/Stemwardness.Rd
9aba2a41ea9d847eb7a96710a82acfac *man/Subsplit.Rd
faf289d281621e9e978b37311ecc3d9a *man/Subtree.Rd
b400a2a41fcc0c3cb08bdd0cdc3afb26 *man/SupportColour.Rd
96f74a716773075e0b264ea6598d1203 *man/TipLabels.Rd
291cec09e39510ddfd61642907603253 *man/TipsInSplits.Rd
a38f25bf9a7a02ac21597e7abda893aa *man/TotalCopheneticIndex.Rd
e305ff4e1cd26ad3dfa4cd87666f8836 *man/TreeIsRooted.Rd
0cb1bef64c532a4dfa74120c595b1354 *man/TreeNumber.Rd
dbcc0224a06ec082cbd51461d2cbeaa7 *man/TreeShape.Rd
a183780ad4be345afca791bc6df47ee8 *man/TreeTools-package.Rd
5137ca579278e231a2ed45570e3b08c7 *man/TreesMatchingSplit.Rd
24d2d6578a66a24a7a4dca7c31ecdb67 *man/TreesMatchingTree.Rd
834a13425ba18650f6876054167d2c15 *man/TrivialSplits.Rd
7812d45a905b7c756f717bff2fc1a456 *man/TrivialTree.Rd
8a952e7b18a95e7f65f3edf5c17ebf77 *man/Unquote.Rd
394271e9a873fde23598e601f0017beb *man/UnrootedTreesMatchingSplit.Rd
98299ee97f231e0e4de870eaed52a000 *man/UnshiftTree.Rd
04aaf55e9ffbc9fb40ea8f0ad195add2 *man/WriteTntCharacters.Rd
eee6b0d9e36889d3d84abadf8e909936 *man/as.Newick.Rd
3d7954e1852c2fd211e47ab7f73f18cb *man/as.multiPhylo.Rd
5aa93261f4fdcbd40bca5dc5b73fbc6c *man/brewer.Rd
6ca0d2a35474140262fac37ef029f8d4 *man/dot-RandomParent.Rd
c862dedc16085134d115c7693ef26919 *man/doubleFactorials.Rd
70675e745ba0f07b75da8993f83f3b9f *man/edge_to_splits.Rd
b43388c69a1d40377c7169ea9100f637 *man/figures/Stemwardness.png
cb1e46f469cfbbbde29c8b5113e1d789 *man/figures/lifecycle-archived.svg
c0d2e5a54f1fa4ff02bf9533079dd1f7 *man/figures/lifecycle-defunct.svg
a1b8c987c676c16af790f563f96cbb1f *man/figures/lifecycle-deprecated.svg
c3978703d8f40f2679795335715e98f4 *man/figures/lifecycle-experimental.svg
952b59dc07b171b97d5d982924244f61 *man/figures/lifecycle-maturing.svg
27b879bf3677ea76e3991d56ab324081 *man/figures/lifecycle-questioning.svg
53b3f893324260b737b3c46ed2a0e643 *man/figures/lifecycle-stable.svg
1c1fe7a759b86dc6dbcbe7797ab8246c *man/figures/lifecycle-superseded.svg
1ada11d02c8c52742fb05690800b694d *man/logDoubleFactorials.Rd
76276d071d78733864d0995128c878f4 *man/match.Splits.Rd
9a4a4181863dc9ab66fa67c54a86d055 *man/nRootedShapes.Rd
5c1affb3cddf3b83333a15298093058c *man/print.TreeNumber.Rd
60af5972f0bf6b138f7f94a266851b37 *man/sapply64.Rd
2083bb233a98301216aae3464c3e3341 *man/sort.multiPhylo.Rd
3b3102f0fa0e314b48933dd08bf19273 *man/xor.Rd
44ff769700b1dc6770d496ed17b22cf9 *src/ClusterTable.cpp
7793381b3bd77467cfd399b0e0e14e34 *src/RcppExports-manual.cpp
07816a9eb4391b3f9e42ea56bed0c5cc *src/RcppExports.cpp
e832887f18bf637415b78a4f0da975d5 *src/TreeTools-init.c
fc222debdfb2750e4802a2dbac85e38c *src/ape_reorder.h
fa227b829dcc449a95ba9f315ff953ae *src/as_newick.cpp
c7e6f6fbabebf08f6a14cfe2970352d7 *src/consensus.cpp
6ea766d64de4214bfebc5cfb8421bbbf *src/int_to_tree.cpp
c8d1884fc20be83cad2a47306de7b8cf *src/kept_vertices.cpp
92818e15b47f09fb9894e7783a5b7a43 *src/minimum_spanning_tree.cpp
180c89bbd56c0e52cf97530865e9241b *src/path_lengths.cpp
20c8f60ac17a1600ca9347c4ddfc2b6a *src/splits.cpp
da00e24fea6eeb69efabecc244fd88c0 *src/splits_to_tree.cpp
c7be10480f04a53853852f1f0d35a44e *src/tips_in_splits.cpp
6aafbe9d0aff06da48c5124991771e13 *src/tree_shape.cpp
dddd680474aa4bb6ced59539a358d904 *tests/figs/rogueplot.svg
473e3d09cce37f127cb654c38271f387 *tests/spelling.R
972084bd7e30302c8eb6d36489a1cc20 *tests/testthat.R
18e8c66aa4ccb9698ff7134272314bbd *tests/testthat/Rplots.pdf
3bc91a5ed6f488fc15ddb01ce7233dfa *tests/testthat/_snaps/RoguePlot/rogueplot-poly.svg
913ceb3883760430d25406496e20a583 *tests/testthat/_snaps/RoguePlot/rogueplot-simple.svg
69f72fbebb042ed59f3be0497a56d6fd *tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg
daede718a12a50289d4eb2fb6ce72b90 *tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg
ff60b3091f5c8e4ac21db1fac0e5b0ef *tests/testthat/_snaps/Support/labelsplits-nameless.svg
c0e4963610d294400ccf74bdd387080a *tests/testthat/_snaps/Support/labelsplits-names.svg
2b8b6f66fa5c20790e0ba4e7cb671a42 *tests/testthat/_snaps/Support/labelsplits.svg
87c8bc7742b21e13f85cb1e280a53dd3 *tests/testthat/_snaps/helper_functions/spectrumlegend.svg
96fe8be9631fd5202772c113bd3daa9e *tests/testthat/_snaps/mst/mst-plotting.svg
d535730367b690bfde4f00d77ba243e4 *tests/testthat/_snaps/tree_display/sorted-tree.svg
44e2dab1dcc47c0ea7ad91ea3a6074c6 *tests/testthat/test-AddTip.R
c17a735843b5bf4797db3b33b3feda80 *tests/testthat/test-ArtificialExtinction.R
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-BigInteger.R
8f369649c5092d430e7770e149cffb66 *tests/testthat/test-ClusterTable.R
df033b02f991f20b59d93abe3e9136c7 *tests/testthat/test-DropTip.R
ee6103ec0f6396f5e2649123cdc1cd82 *tests/testthat/test-ImposeConstraint.R
857755e3e8bf30b4a87e598491380046 *tests/testthat/test-KeptPaths.R
19f6866f29626a5b46f6e7b5fbfc9213 *tests/testthat/test-KeptVerts.R
2350cc4f148c2371fb74b842b50fcb19 *tests/testthat/test-PathLengths.R
6a9fdba6b2f20bc400c78c28771018d9 *tests/testthat/test-ReadTntTree.R
166f82bf3467bcaa6b1b5263850ffe3c *tests/testthat/test-RoguePlot.R
6253b8b47ab41c47c2fba14d0a6dc1e0 *tests/testthat/test-SplitFunctions.R
2d1c52bc39d0c3301fc5962c7b5d70f2 *tests/testthat/test-Splits.R
82783fd90a1e52dfc9307cb4c121b766 *tests/testthat/test-Stemwardness.R
3f669647edcecf46e376b9b7b97d7621 *tests/testthat/test-Support.R
50f7d41c5e8bab9411c96597abf56b66 *tests/testthat/test-TotalCopheneticIndex.R
cfaa4088bb40cd71d5ab67f94146797a *tests/testthat/test-TreeNumber.R
545daa54b7974efca10aafafe5d10aa3 *tests/testthat/test-as.matrix.R
8f5eb4a1c592407f383866336dff13bc *tests/testthat/test-as.multiPhylo.R
75b9b95d2bf72557dab3c46d714cf16d *tests/testthat/test-combinatorics.R
945bf056182ce789adaf8787263616f3 *tests/testthat/test-consensus.R
3efad1bb277d6d6ed5eecd1168d72a87 *tests/testthat/test-helper_functions.R
ad622b63ce3a724635994804d8fcf4ac *tests/testthat/test-information.R
af54af8ef3794c8b98b547956b911682 *tests/testthat/test-int_to_tree.cpp.R
0c347f63d3a9e76f8102b234d09dccc6 *tests/testthat/test-mst.R
39a8c682defcf946430e8a818d1fa9c6 *tests/testthat/test-parsers.R
86dfd571763b9176b605db20325e1b7c *tests/testthat/test-phylo.R
eae8924e4ff90e6ef893b8c8eb53f29b *tests/testthat/test-root_tree.h.R
e312b5f359f25297b16eece8dba0bf76 *tests/testthat/test-sort.R
56a5f47fc0bd8c18a107f382fd552d71 *tests/testthat/test-split_analysis.R
95278cd7ef5596770bac67b87f0a84da *tests/testthat/test-splits.cpp.R
ddba3ad0a07d4d59f03903e8c56ae144 *tests/testthat/test-tree_comparison.R
4c5a3c6a779e458968818541421d78d2 *tests/testthat/test-tree_display.R
69914dc84ecea34a29b77d5e753e0508 *tests/testthat/test-tree_generation-random.R
c5e79fadd9fa232d2b7922779e4675bd *tests/testthat/test-tree_generation.R
baae5ddd8cbf96cd9d07b2ca892ef6cf *tests/testthat/test-tree_information.R
b55d17cfaa7afbd41118f23711f3c269 *tests/testthat/test-tree_numbering.R
2e9b5abdd3e6f69c06f556de84e32fe6 *tests/testthat/test-tree_properties.R
a52199ab9eb9e2872aa6818f810c57f7 *tests/testthat/test-tree_rearrange.R
4c982d737bc741878b47f2fa9ecf5913 *tests/testthat/test-tree_shape.R
c45176b4032e3a89d879076962122438 *tests/testthat/test-tree_write.R
7be48fe3f97d4e5c515b8fb4b62f5a9c *vignettes/filesystem-navigation.Rmd
4a2973f5f06cf7e67a8f433bf0aad0a9 *vignettes/load-data.Rmd
68f831f6f5a8fc211b9b183213a0de6c *vignettes/load-trees.Rmd
