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emmanuelparadis authored and cran-robot committed Feb 16, 2023
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12 changes: 6 additions & 6 deletions DESCRIPTION
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@@ -1,6 +1,6 @@
Package: ape
Version: 5.6-2
Date: 2022-03-02
Version: 5.7
Date: 2023-02-13
Title: Analyses of Phylogenetics and Evolution
Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email = "Emmanuel.Paradis@ird.fr", comment = c(ORCID = "0000-0003-3092-2199")),
person("Simon", "Blomberg", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-1062-0839")),
Expand Down Expand Up @@ -36,16 +36,16 @@ Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email
person("Damien", "de Vienne", role = c("aut", "cph"), comment = c(ORCID = "0000-0001-9532-5251")))
Depends: R (>= 3.2.0)
Suggests: gee, expm, igraph, phangorn
Imports: nlme, lattice, graphics, methods, stats, tools, utils,
parallel, Rcpp (>= 0.12.0)
Imports: nlme, lattice, graphics, methods, stats, utils, parallel, Rcpp
(>= 0.12.0), digest
LinkingTo: Rcpp
ZipData: no
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
License: GPL-2 | GPL-3
URL: http://ape-package.ird.fr/
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-03-02 10:45:23 UTC; paradis
Packaged: 2023-02-13 02:38:10 UTC; paradis
Author: Emmanuel Paradis [aut, cre, cph]
(<https://orcid.org/0000-0003-3092-2199>),
Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>),
Expand Down Expand Up @@ -81,4 +81,4 @@ Author: Emmanuel Paradis [aut, cre, cph]
Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Repository: CRAN
Date/Publication: 2022-03-02 12:30:07 UTC
Date/Publication: 2023-02-16 13:30:02 UTC
76 changes: 38 additions & 38 deletions MD5
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eb723b61539feef013de476e68b5c50a *COPYING
1e117441b417d20a67d3276fe50d89b3 *DESCRIPTION
bd467ef100a8f3bc5ad57975c8c1c9e3 *NAMESPACE
3662dbe23b8526cb4ffbe58bf2244189 *DESCRIPTION
ad2c10dbb7ee6ebda0f5649432e1baec *NAMESPACE
854a025cb7e5da3e4fe230c0be950d08 *NEWS
4dc75ff83940a80aafe96f6a67eefebf *R/CADM.global.R
4f3a09f6a829d788f273399faaf40285 *R/CADM.post.R
fde32bab7748bc8d1e77a006c08159b2 *R/CDF.birth.death.R
fdb9cfa0cbda82bda982b290693e44e3 *R/Cheverud.R
0d70725d781e9997eb280ce7b42fa5a4 *R/DNA.R
e90044c380819386c92f32930b694715 *R/DNA.R
2187a1289b767066d1efe1ebbe7c3b0c *R/MPR.R
74b40c31934a023c64485898b0bd42bb *R/MoranI.R
f2017aff2323d76d3727a09516681380 *R/PGLS.R
4286c596e7b321de071ff04fc90afef9 *R/PGLS.R
30b1f0782318dc8ec3212edb4f03c89a *R/RcppExports.R
6be0924b9f043abaee0968de5cf62aa6 *R/SDM.R
315ae41ee77b323b07e63ff861359ae2 *R/SlowinskiGuyer.R
Expand All @@ -22,7 +22,7 @@ f2017aff2323d76d3727a09516681380 *R/PGLS.R
c94018d5e792c72e20ce84085b2df9e7 *R/as.matching.R
95c7e4a4f49bf7f953d6ebf47ac8efc0 *R/as.phylo.R
2a23cd78c653d6c2fdee0839a14bc642 *R/as.phylo.formula.R
844a38494dd34adbe916bb9116cd0bc2 *R/balance.R
6cbe1ddceb9bb766fb411016eb9de8a2 *R/balance.R
607d7d6bc0ec5559ce1de5b1d1aab0c1 *R/binaryPGLMM.R
dca39eb98aad1da417a695d1888e8178 *R/bind.tree.R
62af6b44a6b901ffdea315613dbebe0a *R/biplot.pcoa.R
Expand All @@ -33,10 +33,10 @@ e43b5dec7eae6d4bf9371e50117bf6ed *R/cherry.R
56491406d404355aefeb79db3d6f52cd *R/chronoMPL.R
74e1019810b06458e808a447bb099a91 *R/chronopl.R
66297b92d2a53e8aff81ce935aae6711 *R/chronos.R
ae04ae67a369579a4685581374a38a79 *R/clustal.R
dedf66f0595977a11a7dbc2b0d2f56bb *R/coalescent.intervals.R
f916a0df46651d0a6640a735c54c84a1 *R/clustal.R
97a5676345af66cb619555fff740ecd1 *R/coalescent.intervals.R
5ca572331b7e701c933c1ad9cc56650d *R/collapse.singles.R
338accc0accb8e67f31db5a90c033d2f *R/collapsed.intervals.R
6470157961eb3be476bed7027843833f *R/collapsed.intervals.R
01e979242ba4667e48a80fd32c03f254 *R/compar.gee.R
89ce53eb1bb8c0fb36e95810cf7cd769 *R/compar.lynch.R
207154a3a9b9ebbe5d7c29995565dc82 *R/compar.ou.R
Expand All @@ -49,32 +49,32 @@ dedf66f0595977a11a7dbc2b0d2f56bb *R/coalescent.intervals.R
3822f0bb0a9ed4c8c19654e86ef34359 *R/def.R
93480a5b64e0d37f5450891629557615 *R/delta.plot.R
dfd5bb35f1cb1fd9154d023e0e4cfc2b *R/dist.gene.R
b003a47f120c880b5f056a2bff6d26dc *R/dist.topo.R
630118204f88e89f00eff3108093c185 *R/dist.topo.R
b28ced504fedeb7f991f7eba10ad06df *R/diversi.gof.R
8b2ec4004022afdc7e2cb42f2657b628 *R/diversi.time.R
7014fbfc738cde3c1072cc315f2deb30 *R/drop.tip.R
de33bf20f72fece71feecc6d97b15c72 *R/drop.tip.R
688534ea02b3ef7e0403081a12f150fb *R/evonet.R
fceafc86fae624fd9037403ad301d35a *R/ewLasso.R
aa09abeb90ef891384128f978ffce843 *R/extract.popsize.R
5c29d3ee785da587f4ad5288ec36b76a *R/gammaStat.R
2319b283f703eb1bbef58007f92cc31a *R/howmanytrees.R
35d58d3ebd0f6122e27b7542679923f9 *R/howmanytrees.R
68d848281455c4c91e9b91f16170e2f7 *R/identify.phylo.R
53ef536bafe7d9ee6b55bc26dad9b256 *R/is.binary.tree.R
e3832873f0592f2e9a376a1c29e67093 *R/is.binary.tree.R
36ca87fc7b670608c51146b1d9cc5050 *R/is.compatible.R
20716d4216cea771efd752bd5a49e7b4 *R/is.monophyletic.R
a7bd37de10eb3f5c02096dfb9a492307 *R/is.ultrametric.R
0e1155005d48770be5ee2507fd7c5d59 *R/ladderize.R
6c906b61a1e654e6699979f7f08656d0 *R/ladderize.R
c6536c739750042a7c3b6bf34b6fef71 *R/lmorigin.R
8b04202ee3e37522317935a9aa18b875 *R/ltt.plot.R
b4f6a07ce62b4ce96bf969874ec7f4c0 *R/makeLabel.R
34069210fd7b12dda0979c45822e4d3a *R/makeNodeLabel.R
dee0a0e5c4b55b5eb6bf01c6ab70751b *R/makeNodeLabel.R
ddb96055d6308eb4d656f815aac13a02 *R/mantel.test.R
d2c16632492bfafd2ee18f2fe3d3d64a *R/matexpo.R
c87ef5f87d7c2d4d520f1eb86d368791 *R/mcmc.popsize.R
9379468b9db1f4a1ed8a71f9908c3c5f *R/me.R
9f58cc8e04d340f201ed3ab729a1e647 *R/mrca.R
eac60117b8225071d992999cf64965d1 *R/mst.R
68dbc2f78a22c00a5a4f3f1d22ffb8a0 *R/multi2di.R
0fa04f6f06673eee17d1ebe5e75340eb *R/multi2di.R
0850fdd19c01d37ac632fc308632a463 *R/mvr.R
ffc4b4e4586d6ffde3a995e4852b65ef *R/nj.R
e3f22d0f260c43be87a17b0ab091e2bb *R/njs.R
Expand All @@ -100,15 +100,15 @@ b13dfb8f455b1c9e74a364085f72dbce *R/read.caic.R
91fba3c1855093faeaf868ec907bc8e2 *R/read.nexus.R
f32f0efa7f1831327407314d5551223d *R/read.nexus.data.R
50ca28afa7dcdc76b1ebb372707e6163 *R/read.tree.R
df2ac5d3de7185c7e26fc95b35192a40 *R/reconstruct.R
09fc661dcae3dc4cc73091f125275bc8 *R/reconstruct.R
d7486ab8ac6d584f04bf1f75ca7f6be3 *R/reorder.phylo.R
9e19dd1ffa47aa5432b7b34d69258dc9 *R/root.R
dadb8aa13a8ceecdb9052facf29430ca *R/root.R
f584366b32e7414c669714ba5b84951b *R/rotate.R
d5abeb2b5165f3d9613392d0c8f03802 *R/rtree.R
be352a2ab62b61eaf8186a7f9b682798 *R/rtt.R
99f8fa6fb6eab7c929abcd08fb5d5e61 *R/rtt.R
7d97fe87a4c5abac659d4a9abaf152e6 *R/scales.R
d2e06f8288af941a00c46248b586225a *R/skyline.R
1f82059f740388b7430b2359e54a147f *R/skylineplot.R
c73717df856fd5c5d575b28e71071324 *R/skyline.R
71bb3f2dcbb807ace238a6ce2af25fe0 *R/skylineplot.R
9c7b02a4625099f715700fb868226b0f *R/speciesTree.R
97c4c3d7cb1606fe6d5519d817156bde *R/subtreeplot.R
bcc8f1fc8363728caba82129412d9e31 *R/subtrees.R
Expand All @@ -121,16 +121,16 @@ a40ae9ad30c221d4ed14b90e8b406f93 *R/vcv.phylo.R
31b3bb1feed474692f07fcebe3a61ac7 *R/vcv2phylo.R
c9adce0f3d0120434ca22f2bb2a0b0c8 *R/which.edge.R
a091953ea941768033d85494e6457691 *R/write.dna.R
2a9393fed275f1b214c0f4fb264f574a *R/write.nexus.R
a9fe8a5e4fa9afb0f96129ea3ee64655 *R/write.nexus.R
a6d3d8d0fb844c0670d5674a1def2bd0 *R/write.nexus.data.R
56e42817fb5ecb97e114290a655d152b *R/write.tree.R
6a729f9f46ea6d1e16156fb73376a59c *R/write.tree.R
774ce72875903259aade5344f9a70aa4 *R/yule.R
c8d3aa3fe64e75e61af07a1b11c74f3f *R/yule.time.R
1eb44ff9e5a036eb845faa1598ce5009 *R/zoom.R
3387c0d0c1f913f8471e1bb34bd2e516 *R/zzz.R
76745d369c54bcccef80b27be05d4602 *README.md
0d49ad8559ab9511db64fc2607c7b143 *build/partial.rdb
9dba3c68c5bae2b18007a3726426e7c6 *build/vignette.rds
ea124a494ad7922985532ad3b308e4d5 *build/partial.rdb
1288198e27dbf622119dce04a0ff722b *build/vignette.rds
db9083e8750aff839d5ebf3ed982f1f1 *data/HP.links.rda
9d9f9232839665422709ded1e541d038 *data/bird.families.rda
a14a6df0f3a735ebc056065077788c90 *data/bird.orders.rda
Expand All @@ -147,16 +147,16 @@ ce7a56faebdf286fdf5ba6c8c3699a79 *data/mat3.RData
e2d1339025ed901009bfed58dc6505ff *data/mat5M3ID.RData
101d0ab2e981b0987cde704a2dee1d8d *data/mat5Mrand.RData
39e4fece2bdc527d7a9d4d83d023a947 *data/woodmouse.rda
a8ae5eb66e5a3936afee2d1a3671761a *inst/CITATION
a20dff855d5d35b8072413bd3c5fd126 *inst/CITATION
44e0e7e0eb4c9edcdbe731d15ad245d1 *inst/doc/DrawingPhylogenies.R
fe9b452b3978a7379c50f5294b94badc *inst/doc/DrawingPhylogenies.Rnw
834ebbd9fcee8589b40dd9cee47e3d69 *inst/doc/DrawingPhylogenies.pdf
b112b93581305b05c6555ca812c2e9d9 *inst/doc/DrawingPhylogenies.pdf
ae58e3a830ca118636ac7f12cee14cdd *inst/doc/MoranI.R
dcd55bda01ae5c227823285f250a5adf *inst/doc/MoranI.Rnw
a1b5cd661882a25d2f3e8d68a721394e *inst/doc/MoranI.pdf
ebf628bc70431333ac127a451ae3c5de *inst/doc/MoranI.pdf
6db8a8dd3ff8d7bb64ecb15b3d7e4ac3 *inst/doc/RandomTopologies.R
be40702621d8c4be5dc87c938df5c0b2 *inst/doc/RandomTopologies.Rnw
7d58b25cd91eca5eb9a2d936e7bbdfc9 *inst/doc/RandomTopologies.pdf
4735f148512b43c8f71824a9f3fcaed1 *inst/doc/RandomTopologies.pdf
5c133fd944233aaf92d4317149e5c2ea *man/AAbin.Rd
7f7b284190c3b52358bd330ea58cdf8e *man/CADM.global.Rd
1abe36a10c34884230d6779d1c6058dd *man/DNAbin.Rd
Expand Down Expand Up @@ -204,7 +204,7 @@ c3f19bb492f50bfb1b4f1928a4671abd *man/checkLabel.Rd
c68be7ff5a08664691df3e2813468490 *man/chronoMPL.Rd
c1f01c6200b2f1e2901d45d40daae404 *man/chronopl.Rd
729046ab372c57773441d466b2f2bd6a *man/chronos.Rd
fb080356b866855ea47948168e7d927c *man/clustal.Rd
8d0fce8a8546e5cc2344ba24d527a791 *man/clustal.Rd
866af6e8d769b3d6972ef8e1ac849a12 *man/coalescent.intervals.Rd
b114a09e0cb474323d5398ec4ee83d3c *man/collapse.singles.Rd
bff5a7826f5a39767601e32ceb776247 *man/collapsed.intervals.Rd
Expand All @@ -215,7 +215,7 @@ bff5a7826f5a39767601e32ceb776247 *man/collapsed.intervals.Rd
a49d26747890cef3b75bcc46b0b8b40b *man/comparePhylo.Rd
a1d0980f32039aa2ca0a0b1b7a5591f8 *man/compute.brlen.Rd
dbb4b5b1d5136bd32660699d9d4cc197 *man/compute.brtime.Rd
6b1a39560c6fab87b6f6265d38a005f5 *man/consensus.Rd
2673588811016427759ca9a1ef56c3e9 *man/consensus.Rd
1e5b635a08fe0e1242801ff0caec9d0d *man/cophenetic.phylo.Rd
1ca9ec0cb824468adc03884c940c7aa3 *man/cophyloplot.Rd
643275d7997dfcd82b1ff08057b3f1a7 *man/corBlomberg.Rd
Expand All @@ -239,15 +239,15 @@ c7cc398115be066740ca4fb037394727 *man/diversi.gof.Rd
d646ea0343999bd0e38e86dcf6c12018 *man/diversi.time.Rd
da8898476bb15b627b34ee1093b9aeb4 *man/diversity.contrast.test.Rd
25100a091b190cfc0cc4bac7b209143e *man/dnds.Rd
7e604b3dee6fc7b073d02654080dd4d1 *man/drop.tip.Rd
d5399a965322e672eb026047855acc4e *man/drop.tip.Rd
66537062a3d706b200f57791daa86102 *man/edges.Rd
3eb82a23c0ece8a095c8f472736f33a1 *man/evonet.Rd
9697317017dd41a68961522fb26b6222 *man/ewLasso.Rd
b81094916d0dda1483e31da6681f3bc2 *man/fastme.Rd
eea313e8ee32597b4cec120d23113642 *man/gammaStat.Rd
3684afa97b61c1e07f02327a7f2b9acd *man/getAnnotationsGenBank.Rd
ccf012737965d0de0b4ca2dd9367d9a6 *man/hivtree.Rd
4c2fee931d4a7b8242250197b4cd7ca9 *man/howmanytrees.Rd
942b38a17ab6ecfa126118370f59bdf6 *man/howmanytrees.Rd
86c49d080fdffd614d8056021e91cc55 *man/identify.phylo.Rd
b8ba66426802e3dfe44def33f8ebef03 *man/image.DNAbin.Rd
0ede757d7bed82216980d3c4fd592cb6 *man/is.binary.tree.Rd
Expand Down Expand Up @@ -304,7 +304,7 @@ a540f8a85f14d4c4ece1d1a19cb15a6f *man/read.GenBank.Rd
fdc2393e70328ae27034c54bf8a847c7 *man/read.nexus.Rd
9c1d50a3701690f505a8d702bb5d7d24 *man/read.nexus.data.Rd
80aaced77530e1d5faf459f8695baea2 *man/read.tree.Rd
9224f164351fea4be9f7ce9d827f8e58 *man/reconstruct.Rd
e9c081ee9bb174f530be5cab9ec954e5 *man/reconstruct.Rd
29fd18c1d0729228307b82dc3ef70ede *man/reorder.phylo.Rd
23cb928f62f9c7103244fbd752ff9a81 *man/richness.yule.test.Rd
272d66917985780ed4ba250087765d7d *man/rlineage.Rd
Expand Down Expand Up @@ -357,13 +357,13 @@ dd6795fab58ce72bc7905726d911a441 *src/ape.c
1873b242cd0926effe77daca9a8e9a63 *src/bipartition.c
cc02d4de52a7d231ab8582ed6273befc *src/bitsplits.c
81e4ad60b418966cdd09e608e074bb28 *src/delta_plot.c
58a032e97a56e4c41fb9717484d23df5 *src/dist_dna.c
d044c562d8637b2e61f73b23c7500955 *src/dist_dna.c
2a6a59a3a220eb855a3c48bc73dc54ba *src/dist_nodes.c
005ab69356525fbbc1b69950341308c2 *src/ewLasso.c
afa27403972145d083d7f7f8b2536b98 *src/heap.c
a284dc0d46dd1b091f725aa7c5fe0bf1 *src/mat_expo.c
8690aa3b907ed3f407d2d7b8f2205700 *src/me.c
52c31d588a767b637b5a852fceeeb154 *src/me.h
6a0e35109dbc4fda76817d85e7f65b28 *src/me.c
b2232146644d748cdd68153769619d5b *src/me.h
cc4c695b4b001305b83658df8075850e *src/me_balanced.c
cf2bdcf9eda24eb6b572584c0ab79fb4 *src/me_ols.c
8f25a7d4686c85b25862941c023e5974 *src/mvr.c
Expand All @@ -372,10 +372,10 @@ f9e2d2d972065aa012820f7e191fa97d *src/mvrs.c
c027ccb515c9f76c10ae390e60039a40 *src/njs.c
72e310102d7db22ae9b6794d153889ac *src/pic.c
9643db2c211ee54a978ac50f3909cd43 *src/plot_phylo.c
505bade4a05aa07561d67180a6e020ba *src/prop_part.cpp
e5d31418f365d5a7c2c243cb78d30a3b *src/prop_part.cpp
aa8d9966da3b7e970879a49a40c05a07 *src/rTrait.c
cea461f86f87000ed51808282d799600 *src/read_dna.c
f30c6b59e86ad6e7c357d6f054e12f92 *src/reorder_Rcpp.cpp
295aeaaa825f6f403fb9d1aa94755c7e *src/reorder_Rcpp.cpp
77c49127a8c5b23efcfe90a0b29bd7ba *src/reorder_phylo.c
c73f78b21f3cada4ebb5035ac866d0f3 *src/treePop.c
9d523dc0a364b0ff40400451829a7433 *src/tree_build.c
Expand Down
49 changes: 28 additions & 21 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -30,35 +30,37 @@ export(.compressTipLabel, .PlotPhyloEnv, .uncompressTipLabel,
di2multi.multiPhylo, di2multi.phylo, dist.aa, dist.dna,
dist.gene, dist.nodes, dist.topo, diversi.gof, diversi.time,
diversity.contrast.test, DNAbin2indel, dnds,
drawSupportOnEdges, drop.fossil, drop.tip, dyule, edgelabels,
edges, editFileExtensions, estimate.dates, estimate.mu, evonet,
ewLasso, extract.clade, extract.popsize, fancyarrows,
fastme.bal, fastme.ols, find.skyline.epsilon, floating.pie.asp,
Ftab, gammaStat, GC.content, getAnnotationsGenBank, getMRCA,
drawSupportOnEdges, drop.fossil, drop.tip, drop.tip.multiPhylo,
drop.tip.phylo, dyule, edgelabels, edges, editFileExtensions,
efastats, estimate.dates, estimate.mu, evonet, ewLasso,
extract.clade, extract.popsize, fancyarrows, fastme.bal,
fastme.ols, find.skyline.epsilon, floating.pie.asp, Ftab,
gammaStat, GC.content, getAnnotationsGenBank, getMRCA,
has.singles, howmanytrees, image.AAbin, image.DNAbin,
is.binary, is.binary.multiPhylo, is.binary.phylo,
is.binary.tree, is.compatible, is.compatible.bitsplits,
is.monophyletic, is.rooted, is.rooted.multiPhylo,
is.rooted.phylo, is.ultrametric, is.ultrametric.multiPhylo,
is.ultrametric.phylo, keep.tip, kronoviz, label2table,
labels.DNAbin, ladderize, LargeNumber, latag2n, lmorigin, LTT,
is.ultrametric.phylo, keep.tip, keep.tip.multiPhylo,
keep.tip.phylo, kronoviz, label2table, labels.DNAbin,
ladderize, LargeNumber, latag2n, letterconf, lmorigin, LTT,
ltt.coplot, ltt.lines, ltt.plot, ltt.plot.coords,
makeChronosCalib, makeLabel, makeLabel.character,
makeNodeLabel, mantel.test, matexpo, mcconwaysims.test,
mcmc.popsize, mixedFontLabel, mltt.plot, Moran.I, MPR, mrca,
mst, multi2di, multi2di.multiPhylo, multi2di.phylo, muscle,
mvr, mvrs, Nedge, Nedge.evonet, Nedge.multiPhylo, Nedge.phylo,
new2old.phylo, nexus2DNAbin, nj, njs, Nnode, Nnode.multiPhylo,
Nnode.phylo, node.depth, node.depth.edgelength, node.height,
nodelabels, nodepath, Ntip, Ntip.multiPhylo, Ntip.phylo,
old2new.phylo, ONEwise, SHORTwise, parafit, pcoa,
perm.rowscols, phydataplot, phylogram.plot, phymltest, pic,
pic.ortho, plot.evonet, plot.multiPhylo, plot.phylo,
plotBreakLongEdges, plotPhyloCoor, plotTreeTime, polar2rect,
postorder, postprocess.prop.part, print.AAbin, print.DNAbin,
print.phylo, prop.clades, prop.part, rbdtree, rbind.DNAbin,
rcoal, rDNAbin, read.caic, read.dna, read.evonet, read.FASTA,
read.fastq, read.GenBank, read.gff, read.nexus,
muscle5, mvr, mvrs, Nedge, Nedge.evonet, Nedge.multiPhylo,
Nedge.phylo, new2old.phylo, nexus2DNAbin, nj, njs, Nnode,
Nnode.multiPhylo, Nnode.phylo, node.depth,
node.depth.edgelength, node.height, nodelabels, nodepath, Ntip,
Ntip.multiPhylo, Ntip.phylo, old2new.phylo, ONEwise, SHORTwise,
parafit, pcoa, perm.rowscols, phydataplot, phylogram.plot,
phymltest, pic, pic.ortho, plot.evonet, plot.multiPhylo,
plot.phylo, plotBreakLongEdges, plotPhyloCoor, plotTreeTime,
polar2rect, postorder, postprocess.prop.part, print.AAbin,
print.DNAbin, print.phylo, prop.clades, prop.part, rbdtree,
rbind.DNAbin, rcoal, rDNAbin, read.caic, read.dna, read.evonet,
read.FASTA, read.fastq, read.GenBank, read.gff, read.nexus,
read.nexus.data, read.tree, reconstruct, rect2polar,
reorder.evonet, reorder.multiPhylo, reorder.phylo, reorderRcpp,
richness.yule.test, ring, rlineage, rmtree, root,
Expand Down Expand Up @@ -86,13 +88,13 @@ importFrom(grDevices, col2rgb, dev.cur, dev.new, dev.off, dev.set,
devAskNewPage, deviceIsInteractive, grey, rainbow, rgb,
topo.colors)
importFrom(lattice, xyplot, panel.lines, panel.points)
importFrom(methods, as, show)
importFrom(methods, as, hasArg, show)
importFrom(nlme, corMatrix, Dim, getCovariate, getCovariateFormula,
getGroups, getGroupsFormula, gls, Initialize)
importFrom(stats, AIC, anova, as.dist, as.hclust, biplot, coef, complete.cases,
cophenetic, cor, cor.test, cov, cov2cor, density, dgamma,
dpois, drop1, formula, gaussian, glm, hclust, integrate,
lm, mahalanobis, median, model.frame, model.matrix,
lm, lm.fit, mahalanobis, median, model.frame, model.matrix,
model.response, na.fail, na.omit, nlm, nlminb, optim, optimize,
p.adjust, pchisq, pf, pgamma, pnorm, ppois, printCoefmat, pt,
qbinom, qnorm, qt, quantile, quasibinomial, rbinom, reorder, resid,
Expand All @@ -101,6 +103,7 @@ importFrom(stats, AIC, anova, as.dist, as.hclust, biplot, coef, complete.cases,
importFrom(utils, browseURL, download.file, edit, read.table, str)
importFrom(parallel, mclapply)
importFrom(Rcpp, sourceCpp)
importFrom(digest, digest)

## Methods for the classes defined in ape, including for the generics
## defined in ape (see also below). Some methods are exported above.
Expand Down Expand Up @@ -168,9 +171,11 @@ S3method("$", multiPhylo)
S3method("$<-", multiPhylo)
S3method(c, multiPhylo)
S3method(di2multi, multiPhylo)
S3method(drop.tip, multiPhylo)
S3method(is.binary, multiPhylo)
S3method(is.rooted, multiPhylo)
S3method(is.ultrametric, multiPhylo)
S3method(keep.tip, multiPhylo)
S3method(makeLabel, multiPhylo)
S3method(multi2di, multiPhylo)
S3method(Nedge, multiPhylo)
Expand All @@ -193,10 +198,12 @@ S3method(c, phylo)
S3method(cophenetic, phylo)
S3method(degree, phylo)
S3method(di2multi, phylo)
S3method(drop.tip, phylo)
S3method(identify, phylo)
S3method(is.binary, phylo)
S3method(is.rooted, phylo)
S3method(is.ultrametric, phylo)
S3method(keep.tip, phylo)
S3method(makeLabel, phylo)
S3method(multi2di, phylo)
S3method(Nedge, phylo)
Expand Down
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