ca8036d46ad0578e2c67d14b725041bb *DESCRIPTION
e9dc66ec6b593418aa477fc4a01778b0 *NAMESPACE
7707a9cba0268052052e0f98efb5da35 *NEWS.md
c878ee2d093f8b9601b6155885e4636c *R/Bootstrap.R
a0d076e1e3ef0ce757396bccdf5a5f28 *R/Fitch.R
762caa0840c6fddf5156b43e3449eef6 *R/IWScore.R
422140c2fb61bb3ea5d2bddcb6b247a7 *R/Jackknife.R
964a5a815894b94d7b5c3ea065b0c494 *R/NNI.R
49263e683d77206375e2fc26509e895b *R/RandomTreeScore.R
118a61277fa4e3892c812343200180bb *R/Ratchet.R
6079f30e5b89758dde14dc46c4b8ede3 *R/ReleaseQuestions.R
53b1f01117b8fc9a835c296b39fd47b7 *R/SPR.R
c9132051590375a028453309a4f35f11 *R/Sectorial.R
9b4f091b6be03fbd24e657231c3f2585 *R/SuccessiveApproximations.R
106651b52025ee9d2074a6b0514ba87f *R/TBR.R
9ec83bac26cd63b3d066e66f9e212ce1 *R/TreeSearch.R
4a380c46719f1ec69f0564efd0a9b145 *R/data.R
0e88df38fe85288751eddc977e8ccc5d *R/data_manipulation.R
8dafe5fc4aa8bd7de762138f0414ca8f *R/mpl_morphy_objects.R
85cf0503cc29c5ce67242f22f90f8805 *R/mpl_morphyex.R
58fa25d00b0e9bb2231444ac38251ab4 *R/mpl_prepare_data.R
7a1e2a7f7a727c17f4edacea306494f1 *R/mpl_visualise.R
3536445946cf5e1a9dcbe2d0e5cbd992 *R/pp_ProfileScore.R
ad1ef24b83210f3c80e9829a70d7c719 *R/pp_info_extra_step.r
b14d5c770e113d2f022372d599223755 *R/tree_rearrangement.R
10d44771aabf67ad18bc4c0affd9f533 *R/zzz.R
7414d00f7c3d5bcf86ef87f483e938b8 *build/partial.rdb
f8135b904887d5876b48091928affea5 *build/vignette.rds
b03aa71a408c0036eb82f0bd9953b7fe *data/congreveLamsdellMatrices.RData
a13b62dc5c41d740b9dc7826d6e7a144 *data/inapplicable.citations.R
c930731d527c5c10c8ef8ad6f231e5cf *data/inapplicable.datasets.rda
03c7d93169712d4f2726b75795bafeac *data/inapplicable.phyData.rda
17e82c121c556ecb46be829c0dd164b8 *data/referenceTree.RData
de5dbfb6111264955b58b625e43886b8 *inst/CITATION
547118822c86a8a57e39b65bb8d0f643 *inst/REFERENCES.bib
ef431f09f7503a5034a894be0ebc546f *inst/WORDLIST
2a33c016808841801938c7c7b2dcb1cb *inst/apa-old-doi-prefix.csl
45f57e002341a25f0b8b3ae70ee8dd70 *inst/doc/getting-started.Rmd
6ba962886b094443bd13b1ae902d868c *inst/doc/getting-started.html
9ad162879226d4a71b85c38a2cedbb58 *inst/doc/inapplicable.R
3d107fd6a22951abaffe9b02651d0c8b *inst/doc/inapplicable.Rmd
17513a5168a4ea6882bd959ed43973a2 *inst/doc/inapplicable.html
672e34b78bc3f1c1d66c4c58993743c6 *inst/doc/profile-scores.R
683da0c7c9491337d2dce4c95a9bd2ff *inst/doc/profile-scores.Rmd
5ef20e310f4466a95e321e1a832bc9ac *inst/doc/profile-scores.html
2eab91e290339d32a5526f24f259cace *inst/doc/profile.R
7f86768aedec880328e03a0ba4c12d89 *inst/doc/profile.Rmd
423e44aad466e229a31d778f362223d8 *inst/doc/profile.html
145fa68e8da376b4a6fb6d129550965f *inst/preamble.tex
a68b8ef6093b455ad20cc5c76d0a738a *inst/tests/benchmark_timing.R
ae4cdef777903c3a7382fb9d6ba29069 *man/AllSPR.Rd
dde2fc743acc212b463335d037e1ef06 *man/AsBinary.Rd
43569178ed5302259d192abb091cae08 *man/CharacterLength.Rd
22260b932b2217ac9b79ef05f09b64f4 *man/DoubleNNI.Rd
7a498ef3b556ff2d88def63396c02c1d *man/Evaluate.Rd
d8f87ab6b526c6c2e91bc93f0dbef472 *man/Fitch.Rd
42f756af246eabb93a845528242ea575 *man/ICPerStep.Rd
defbbce1c4c8a2e24dcbb45b1069337d *man/ICSteps.Rd
3c0fe00cca7a8ac24b96e4978309eced *man/IWScore.Rd
c79925a0fa665655e85e146af28956a2 *man/InfoAmounts.Rd
ba454c5cc606c9ec85c5b0ce23994e64 *man/JackLabels.Rd
3ae1382b199d7b93b6bb8bf9bb928aa9 *man/LogisticPoints.Rd
17d16426f32f32e4a696071b8096aef1 *man/MinimumLength.Rd
93e89b5e86dcb09dc7728476aa557863 *man/MorphyBootstrap.Rd
dd8b2b0c5edff87c69a0759b47500f88 *man/MorphyErrorCheck.Rd
f1d1cb327acaf15f5623235850f8d961 *man/MorphyTreeLength.Rd
8dc6634d77d1fa526289764b677189bd *man/MorphyWeights.Rd
c16973916fd2ef63e39be306df53b1b5 *man/NNI.Rd
e585089c1cdaa4621aed2c4e39ef25f3 *man/PhyDat2Morphy.Rd
0431de60f921a5008f147d7441a24866 *man/PrepareDataProfile.Rd
16c76910fcb4462aa0a2d94b6646d69c *man/ProfileScore.Rd
195664a0ee0cfd211cee3b0e39557019 *man/RandomMorphyTree.Rd
ff3e82d3a724f734e93ede41b449304f *man/RandomTreeScore.Rd
92da4c17c74d28b197271109f4c9f831 *man/Ratchet.Rd
72923fc9d91f986917ee015bb6fcce0f *man/RearrangeEdges.Rd
5a509e85ad17ec9c44e8ca33cd393566 *man/SPR.Rd
5b2f66e53bfab9af5d50b41b3efcc4c4 *man/SetMorphyWeights.Rd
0906cacd5043ab805b967d9f13f211fd *man/SingleCharMorphy.Rd
3e91b6f920ac81cbda86ace53977559e *man/StopUnlessBifurcating.Rd
9bbe0d3372e10dc6870df0185ecf765e *man/Suboptimality.Rd
dded311ca7876f54ee4d3d86ba0f2c6a *man/SuccessiveApproximations.Rd
a5b82eeb0baca960201f6f9b24ff025b *man/SuccessiveWeights.Rd
b2adb662a65501b55f79a7cbb0596951 *man/TBR.Rd
34c03f457664aaa294b4e4fef37c894e *man/TBRWarning.Rd
af2127fe528f885fddeaf1c8881f4c4c *man/TipsAreNames.Rd
161bf7cd555d8617957a93ba8e95f3a8 *man/TreeSearch.Rd
afeddd0544ec5aaea576e7272a99922b *man/UniqueExceptHits.Rd
2a6cb72333f24067f570b4ce6fd5d15b *man/UnloadMorphy.Rd
f0d43da7682220bc8bdf225d025f7724 *man/WithOneExtraStep.Rd
32ef966353a2607a9a3d9f0177850c50 *man/congreveLamsdellMatrices.Rd
c0efa08d20f7626e2291f3543a9db57e *man/inapplicable.citations.Rd
b94b143cc5b4de87ac4e67c9010ecb71 *man/inapplicable.datasets.Rd
36a40d17cbe122545578cfb65a627300 *man/inapplicable.phyData.Rd
e1fea4d390fb0457efc4d7d7f4a6a4c5 *man/mpl_apply_tipdata.Rd
0a23306a8179ec4220e973ba15172ae4 *man/mpl_attach_rawdata.Rd
bbdad59a50020b010db713b17c0c0300 *man/mpl_attach_symbols.Rd
322d2dfe0f4ff940f9c48512fa4c23b5 *man/mpl_delete_Morphy.Rd
f58c51b1bed62674c88b38859a65858e *man/mpl_delete_rawdata.Rd
18b02d513ebe60f376da0defb31a245e *man/mpl_first_down_recon.Rd
f0629427162d617c5946111baf9fe8c0 *man/mpl_first_up_recon.Rd
791119f9f5fd4412a83d8e111f2c7c32 *man/mpl_get_charac_weight.Rd
eda2539bbd2f452ef57296f486839a2e *man/mpl_get_num_charac.Rd
ade7089a8fcac1e5eefec842bb34652f *man/mpl_get_num_internal_nodes.Rd
44893459b0d1a7b32eeee70ecbd711e2 *man/mpl_get_numtaxa.Rd
6b52506b1348fc04f4c248c2fbf1fcfa *man/mpl_get_symbols.Rd
4ff07f576bd9211941673f42cd9f6b96 *man/mpl_init_Morphy.Rd
22a3d154fcc7b726969dc402e4204aa1 *man/mpl_new_Morphy.Rd
c72a131ad61f068bc2aa7304fbb5a1c5 *man/mpl_second_down_recon.Rd
3739809240359e1a1d7ee96872d36621 *man/mpl_second_up_recon.Rd
3baca50745020e0d9be8453ac70d9a13 *man/mpl_set_charac_weight.Rd
8493675aff4abdf2b357f9712576336a *man/mpl_set_num_internal_nodes.Rd
707e9dd2b61da01d94f56a995068c9c5 *man/mpl_set_parsim_t.Rd
ef8fe92f0d94fd34e20d80310feff95e *man/mpl_translate_error.Rd
a12c610ea180f1876e8334416021f7ab *man/mpl_update_lower_root.Rd
36fce91e067334ac7df0b556fb4d8e73 *man/mpl_update_tip.Rd
8c863223355995d1590b952b49524103 *man/referenceTree.Rd
060827c1d486fea20f5dbfd674c504e7 *man/summary.morphyPtr.Rd
3075545a2b7aab0c713ac79555a24dc2 *src/RMorphy.c
3b6bf799c2bdd5debb3e69fe7f1b96a5 *src/RMorphy.h
b911120af4907c0186d4b8e20d3a05d6 *src/RMorphyUtils.c
ae77b11ab3b639b5abf4d24af17c914f *src/RMorphyUtils.h
1d0a13ee8b6930cc50e6ed4df84cf40b *src/TreeSearch-init.c
23f8018608051c59aea872296596dccb *src/build_postorder.h
6c77b48c63f2b709c078385c9227c718 *src/fitch.c
a44a841dee000b4e8d9d99fe8a97119a *src/fitch.h
71648da21def7593d41683ca49a2aa51 *src/from_ape.c
0a08969ec268efae29e60167ac3fee6a *src/morphy.c
e9d451b45f55d8dc3b0e36fcba1b310b *src/morphy.h
35f1a23c1d9d1884bfa3a89316c0e66a *src/morphydefs.h
dd06abbdda93e74c21e44dde3e5462f1 *src/mpl.c
04a68d6347e8c4e87c4bce1950b5cd28 *src/mpl.h
e4dfbb86174789a14d455158966dc9bb *src/mplerror.h
3b29a100b735d7299cfc17ddc338856c *src/statedata.c
008f1791e2af1564438d6bb29dc82b42 *src/statedata.h
1f7c1184c8e3348f25b1331f6f81ae6e *src/wagner.c
4fe2d0224cc12d1fdd73112d4737cbfb *src/wagner.h
3700c7666fa24eba68595b7191205cc1 *tests/testthat.R
818c444b0d57b2b1177cac1a0d3b6a42 *tests/testthat/test-Fitch.R
57488ea79f7dcd42465bcb5c74f69cf4 *tests/testthat/test-Jackknife.R
e4d061af22d3dc4cbb7778603a1e0f38 *tests/testthat/test-TreeSearch.R
3409360229b5ca9d8c5f9c4338e4b06c *tests/testthat/test-data-manipulation.R
a55056e452b8eb3701aaee1e17411c39 *tests/testthat/test-pp-ICS.R
a5e4f0c12f8d3844cf5c0a5de49f8f21 *tests/testthat/test-pp-fitch.R
63a5e695d25c905d10e1ad45d24133db *tests/testthat/test-pp-random-tree.R
6e7af3da45379abd1cf244e6041037a6 *tests/testthat/test-zzz-tree-rearrange.R
45f57e002341a25f0b8b3ae70ee8dd70 *vignettes/getting-started.Rmd
3d107fd6a22951abaffe9b02651d0c8b *vignettes/inapplicable.Rmd
683da0c7c9491337d2dce4c95a9bd2ff *vignettes/profile-scores.Rmd
7f86768aedec880328e03a0ba4c12d89 *vignettes/profile.Rmd
