ed7daea566d69dd11be7536343969ef9 *DESCRIPTION
065b12816224c061ab868394a1a0dcb6 *NAMESPACE
7c57cd3157abea30a5b5c2aa472aebc3 *NEWS.md
c2d907decb2c62c978d8eb1696ebc1de *R/CompareQuartets.R
41579b10bf150b20608867250a804a46 *R/Metrics.R
ad42f3cb247096f654d6a2794cb69282 *R/PairwiseQuartets.R
409c729c8f5bf5fdb43042b152a422e3 *R/PartitionDistance.R
372a084212349b0baff8cb2d160f1fe7 *R/Quartet-package.R
a3a011895854e0078f2c1be41e883037 *R/QuartetDistance.R
e9631fe453d0396c0141613183ab769b *R/RcppExports.R
c6368543b1306ed72f8c6158bd64a90f *R/ResolvedQuartets.R
b62450a93ba889fa58e7268af79d896f *R/TernaryPoints.R
135d78865a536b9a9e6fd32cc65f3b3e *R/VisualizeQuartets.R
38a30e5d02cad9514bf474fbfaae1f96 *R/cpdt.R
12e73b12b809c51c2d90bbf0da8b6f64 *R/data.R
c8a7f67d7e3c8ad06c10c0e82b169156 *R/tqDist.r
00b847ea523643c71ecb81cceb4a6366 *R/zzz.R
7b78cd3152d6bd0c1f9dec8af8889359 *README.md
6e7047eaf2cf626a187ceeaabf03e913 *build/partial.rdb
581045ddaf37d3446911332d41888924 *build/vignette.rds
4610a2fed56c2bbaec42813f44efea7b *data/sq_trees.rda
05798284ff91341fcc3b4a65e707f4d0 *inst/CITATION
f0d0ec625b88c0b8d5ece7e74cfeaab8 *inst/COPYRIGHTS
2494a08c035d6adde15ab4c588cf9315 *inst/REFERENCES.bib
ad7503c774622a02db02858fcb3138dd *inst/WORDLIST
d09791a9201e9696f653ea42e427625e *inst/apa-old-doi-prefix.csl
85dc0dd429efab7c5147e0aeaff99cbf *inst/doc/Quartet-Distance.R
bc7b0993ed536e73e278deaf56fbd7c1 *inst/doc/Quartet-Distance.Rmd
0da1364a405243be7201665b84f38056 *inst/doc/Quartet-Distance.html
b7a3223794b0fc8087dbd6c8e371b166 *inst/doc/Using-Quartet.R
8843e7aa0ce4675741621a46743a02a0 *inst/doc/Using-Quartet.Rmd
f0823d0da4843c8caf24ddf155b8b126 *inst/doc/Using-Quartet.html
145fa68e8da376b4a6fb6d129550965f *inst/preamble.tex
8cd8d2957f7076b88e668e5cbd30462b *inst/trees/all_quartets.new
c77e7e425ce61ad6f4794aa761a96b58 *inst/trees/five_trees.new
866430511e1922de3d699d2bc8d4312f *inst/trees/none.new
27fcf4d2ce88d537dfc7123af31bd851 *inst/trees/one_quartet_twice.new
b149fb81dd30a3ca2c912a05a735af61 *inst/trees/quartet1.new
1dca61cfcdee4fe1b6bdbd31dbdf302b *inst/trees/quartet2.new
a459cbb218d1a152e7b4b61593781063 *inst/trees/quartet_unresolved.new
94c503ebf10649687ebe687dc809e755 *inst/trees/test_tree1.new
72fab1d3604a4bb1bcaf30828a198bb8 *inst/trees/test_tree2.new
70ba65b7a40de93c0b14b7efa0eb0d31 *inst/trees/test_tree3.new
a33e2325f0f8362f37098fd0cfccdf69 *inst/trees/test_tree4.new
5c9b0117aabf90e69f83dfa6caa0b662 *inst/trees/tree_ab-c.new
24c6536d3c734d1ad27d098177e89376 *inst/trees/tree_ac-b.new
453fc4a3acddba283e8f4630145835a6 *inst/trees/two_quartets.new
68aa19327a16788844c103ccdb30b5c3 *inst/trees/two_trees.new
9a6eaab8ddeca800b66b85a3ed869d6a *inst/trees/unresolved1.new
69374825cf9444769488fb0f2817c357 *inst/trees/unresolved2.new
a546a5f909b41a448e80f09a63b8d010 *inst/trees/unresolved_list.new
d3b521cc9810e70195d7dd0bbc13b39c *man/AllQuartets.Rd
f6e94b6044bc411debb1f4de9a5ef474 *man/CompareQuartets.Rd
6977eecb3535d49232afea7d9173b3e0 *man/CompareQuartetsMulti.Rd
2fe6d38eeeec5f45d37d3eea375208f4 *man/CompareSplits.Rd
cec79d6863603320e4eec2bda3e20dac *man/Distances.Rd
d44e23ad042cc23a55502fbc447c36b9 *man/PairSharedQuartetStatus.Rd
36643987a43e96dce24566b1edcf4153 *man/PairSharedSplitStatus.Rd
c66ff250811bce19e0b3ee1604ae6b9a *man/PairwiseQuartets.Rd
fe518b9602600a955e9927d5a19a333c *man/PlotQuartet.Rd
a4a72699e256c29f5b953da1b578603e *man/Quartet-package.Rd
2e0e43d8f95ebf568dfa76882fd87c73 *man/QuartetPoints.Rd
223dab73744f3635bf42ecb940146b57 *man/QuartetState.Rd
8806b4c4b17c25707d073ae46626c82f *man/QuartetStatus.Rd
eb4a9e6cc886deafb0ce100ec121f36b *man/ResolvedQuartets.Rd
ae8a5e86cf2d533f5edc14bfceef3a96 *man/SimilarityMetrics.Rd
893e6ac138c4d1223bec42672cc3f85d *man/SplitStatus.Rd
e81971d3ccec75bb547a682ba82daa7b *man/SymmetricDifferenceLineEnds.Rd
3774c3dc0dc09accab7a54506941a661 *man/TQDist.Rd
adc9ffb0bb6edd8355005668f969c093 *man/TQFile.Rd
9c540df4611cfe1c2457b9148ace2d86 *man/ValidateQuartetFile.Rd
d9d74c7f984a8dce9e7bdebd00cd4e9a *man/VisualizeQuartets.Rd
9955dd3922a30968b29a4d723ddc101e *man/cpdt_dist_file.Rd
82c2c87a8cba6c852daa9a0356c8f3eb *man/dot-AddSlice.Rd
c0096a3704210129d7feadf59655f0bd *man/dot-AllPairsTripletDist.Rd
9fa56cd91a47b8f0a73fac002c28fda2 *man/dot-CheckSize.Rd
68c21042f4b57ab3e63dcd3ef5af5305 *man/dot-NormalizeStatus.Rd
6c61ca5abb2e1e43044a5125d914283b *man/dot-PairsTripletDist.Rd
74124b649675de877aaa89d13fd2cd7b *man/dot-StatusToMatrix.Rd
b5de1aa47771bb1cdac670412ceb450f *man/sq_trees.Rd
6030db61a76cf0720a307a8d1198c170 *man/tqdist_QuartetDistance.Rd
664dc97d4e0fd6f5135a890f8cac6f78 *src/AbstractDistanceCalculator.cpp
e11330ebbd1295da9af918236f64a9bd *src/AbstractDistanceCalculator.h
77916d9404d16cf28eae42d0a4ccc5d9 *src/AllQuartets.cpp
4c09ead14ed84c9fd4eff59c207b9e04 *src/EdgeParser.cpp
5a445d40d8efad503bca4a21b2e937cc *src/HDT.cpp
183de2c5f83f773dddf06f9dac69552d *src/HDTCountingCCToC.cpp
41cd6e024e3db8a6c12da91001a3380c *src/HDTCountingCTransform.cpp
d261b94353ad5a05c8ce218fac4b54ce *src/HDTCountingG.cpp
9b555232a6976177cd0e7c214b1a3c4d *src/HDTCountingIGToC.cpp
e7ff1c0cd71dadce5a0ac249131e32e9 *src/HDTCountingLeaf.cpp
4771722c28df11fc2083c825c2b5ba60 *src/HDTFactory.cpp
6b00ab7b0d11b892e535e739d3e1f44f *src/HDTListUtils.cpp
d3c78a4af7ab4baa9929080d5fe6a069 *src/Makevars
c4aef01b6b42dbd581dcb799103193df *src/NewickParser.cpp
0a46de8efaff1f5a6d7b29ec24645c97 *src/QuartetDistanceCalculator.cpp
ef7fbbb6f61ed6838285bf9af1d079c8 *src/QuartetDistanceCalculator.h
f23e669406096a111d599f97eb547226 *src/RcppExports.cpp
32ba47800433fab2e1a7d4e95065403b *src/RootedTree.cpp
2997b46256907d7476283f584c2c2fe0 *src/RootedTreeFactory.cpp
3669d2c9b03bde8fdffe97a6f1e14783 *src/TripletDistanceCalculator.cpp
6b7863db62ca71949dd871066822fe2f *src/TripletDistanceCalculator.h
92a6e0fb2a21d4607533406d13a10f6b *src/counting_linked_list.h
47a76b1e6009d170ba4580ed49128fc3 *src/counting_linked_list_num_only.h
55634b1a5bb9f832027e9da3a150d167 *src/cpdt-dist.cpp
470c08642eba53bfb385984800e24bd5 *src/cpdt-dist/bit.h
1dbc112dae1a73760613c3a76b327b0f *src/cpdt-dist/cpdt-dist-bin.h
f21c9bdd478ead1b6d1c00cb24754222 *src/cpdt-dist/cpdt-dist.h
b24ec9c984f25cb5e0cc605c2e3cc016 *src/cpdt-dist/nex_parse.h
08b64c8768dd7c8b5bd312dd3eb0ee0c *src/cpdt-dist/tree.h
173c5c95313587b31e47cb87b07a721c *src/cpdt-dist/tree_parse.h
267afd022595175a019ec50e00208e7d *src/cpdt-dist/treenode.h
394a110bdb792b31fa5699fc8ff780b4 *src/cpdt-dist/utils.h
d1a9c365430e73b2bd34655933e411cf *src/edge_parser.h
e2861a83ce5e617a44fd7733cc79bc3d *src/hdt.h
e947704ae36b3fe86509311137e433c4 *src/hdt_factory.h
0a869dc1a9de30b7d398b26ea7de412f *src/int_stuff.cpp
99f85bbc800a01299504339c2425f0fb *src/int_stuff.h
0eda7a9a0c76da0b41b42713fca6e2e5 *src/memory_allocator.h
1f6b14d6adb436e90de6c71a44c96a89 *src/newick_parser.h
ce775ecb23b0a9f1eaef305593426685 *src/quartet_calc.h
bde5a6a918a5f676af427a2668edeff2 *src/rQuartetDist.cpp
2987852bb65bc91b06059373c85c7a56 *src/rTripletDist.cpp
bfb78b07911799ac87097c3a02b2f832 *src/rooted_tree.h
09e9e5bf70fde2212aa83d74a1d14f2f *src/rooted_tree_factory.h
36376e6d90437cf1768d906ae187f9ba *src/templated_linked_list.h
b4f38b2477748217cb03d7ceaf8006a7 *src/triplet_calc.h
eb1ccdf5bdf36116623fb9519b471444 *src/unrooted_tree.h
9f004e030d7afdc841db44bbaebc1402 *src/util.h
66380a4702500feef2541d252e7c712f *tests/figs/deps.txt
f61f3d9162631305f001e4d3563199d0 *tests/figs/quartetdistance-r/plotquartet-gain.svg
0d4fab4a9d925812b66067e55183c859 *tests/figs/quartetdistance-r/plotquartet-one-star.svg
f60677d1c56338c330b4b5e2d39f3d7b *tests/figs/quartetdistance-r/plotquartet.svg
8f6554d1297f4aa34d877520321a9b6a *tests/figs/vq-label.svg
3caea4d21798ca4344a5c0013cc7cb51 *tests/figs/vq-size.svg
46a104a9ec4348d3dd7b31b288f5156e *tests/figs/vq-tworow.svg
25657dabe5ea160a5b56d0e5f8cf330f *tests/testthat.R
c1ba9d6652fea70fd93e8441dafe1ee8 *tests/testthat/_snaps/QuartetDistance/plotquartet-gain.svg
5b53f2191884990c3bf5c503c7ea579f *tests/testthat/_snaps/QuartetDistance/plotquartet-one-star.svg
680af48611edc10e0c73838b05f4e336 *tests/testthat/_snaps/QuartetDistance/plotquartet.svg
f5d060b4c096261f0b9022204ce3ec6f *tests/testthat/_snaps/VisualizeQuartet/vq-label.svg
c36137694639c1d192fbc4e08a1fc1bb *tests/testthat/_snaps/VisualizeQuartet/vq-size.svg
d21ac7cdcf53ab7c438922e83c2b46e3 *tests/testthat/_snaps/VisualizeQuartet/vq-tworow.svg
3018b44fe4998d7aa669e30670c222d7 *tests/testthat/test-1-tqdist.R
534a6f705db277d6d41c083f5e92ae2b *tests/testthat/test-AllQuartets.cpp.R
57f00b336824e8d7fb45f18fe1475ba8 *tests/testthat/test-CompareQuartets.R
7836e5e636bf8dd9aee1ac7161a74ae8 *tests/testthat/test-NewickParser.cpp.R
c932340b352aafc0dcfc350ec5164b8b *tests/testthat/test-PairwiseQuartets.R
cbc27b6111b29eace04372f3d6c997fa *tests/testthat/test-PartitionDistance.R
a1443e83c9c8cd8b0e1f7a9b038ef362 *tests/testthat/test-QuartetDistance.R
04fe3001a814a691bb57805ed30f47ea *tests/testthat/test-QuartetStates.R
3f25dac40afcfbac0ae49641b70f4563 *tests/testthat/test-ResolvedQuartets.R
d06dbbc89104e1f17e4d53592c91537a *tests/testthat/test-TernaryPoints.R
b37b6616a8a277da9e772266e83504a3 *tests/testthat/test-VisualizeQuartet.R
32a77dbb8644d1df0ab7b7fdee3c160b *tests/testthat/test-ZZZ-Metrics.R
9992bbdfd584e9745a8ba91c2072626b *tests/testthat/test-cpdt.R
22b74e78057533bdd6555f98f9a7d7e5 *tests/testthat/test-mc.cores.R
b6ad6d3f0e8ab9f95a43884bcc85759d *tests/testthat/test-rQuartetDist.cpp.R
c0d32612b64f068706e0fe54cc2b6e94 *tests/testthat/test-regression-correctness.R
bc7b0993ed536e73e278deaf56fbd7c1 *vignettes/Quartet-Distance.Rmd
8843e7aa0ce4675741621a46743a02a0 *vignettes/Using-Quartet.Rmd
