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@emmanuelparadis @cran-robot
emmanuelparadis authored and cran-robot committed Dec 16, 2024
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12 changes: 7 additions & 5 deletions DESCRIPTION
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Package: ape
Version: 5.8
Date: 2024-04-09
Version: 5.8-1
Date: 2024-12-10
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 All @@ -25,6 +25,7 @@ Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email
person("Pierre", "Legendre", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-3838-3305")),
person("Jim", "Lemon", role = c("aut", "cph")),
person("Guillaume", "Louvel", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-7745-0785")),
person("Federico", "Marotta", role = c("aut", "cph")),
person("Eric", "Marcon", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-5249-321X")),
person("Rosemary", "McCloskey", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-9772-8553")),
person("Johan", "Nylander", role = c("aut", "cph")),
Expand All @@ -35,7 +36,7 @@ Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email
person("Korbinian", "Strimmer", role = c("aut", "cph"), comment = c(ORCID = "0000-0001-7917-2056")),
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
Suggests: gee, expm, igraph, phangorn, xml2
Imports: nlme, lattice, graphics, methods, stats, utils, parallel, Rcpp
(>= 0.12.0), digest
LinkingTo: Rcpp
Expand All @@ -46,7 +47,7 @@ URL: https://github.com/emmanuelparadis/ape
BugReports: https://github.com/emmanuelparadis/ape/issues
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-04-09 06:21:27 UTC; paradis
Packaged: 2024-12-10 17:29:50 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 All @@ -71,6 +72,7 @@ Author: Emmanuel Paradis [aut, cre, cph]
Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>),
Jim Lemon [aut, cph],
Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>),
Federico Marotta [aut, cph],
Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>),
Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>),
Johan Nylander [aut, cph],
Expand All @@ -82,4 +84,4 @@ 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: 2024-04-11 12:30:02 UTC
Date/Publication: 2024-12-16 00:00:02 UTC
50 changes: 26 additions & 24 deletions MD5
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eb723b61539feef013de476e68b5c50a *COPYING
cca785d1d819e51907b24ed1560babb5 *DESCRIPTION
02dc3ad0a45fbaeef16bb925a8d12e90 *NAMESPACE
41938138989558c127c99e89e82d8604 *NEWS
eca4e03e403fea54d2a91142a74ec350 *DESCRIPTION
d13f723713b9fb894de8e672c8160501 *NAMESPACE
1f20f68370ca015e28fcf9101465365a *NEWS
4dc75ff83940a80aafe96f6a67eefebf *R/CADM.global.R
4f3a09f6a829d788f273399faaf40285 *R/CADM.post.R
fde32bab7748bc8d1e77a006c08159b2 *R/CDF.birth.death.R
Expand All @@ -13,7 +13,7 @@ fde32bab7748bc8d1e77a006c08159b2 *R/CDF.birth.death.R
30b1f0782318dc8ec3212edb4f03c89a *R/RcppExports.R
6be0924b9f043abaee0968de5cf62aa6 *R/SDM.R
315ae41ee77b323b07e63ff861359ae2 *R/SlowinskiGuyer.R
32e8c4cebd8ca1b33fb7353751fb3c0a *R/ace.R
7c3d7fb622af580317c7c6068e20b360 *R/ace.R
4ce79cf3f3ff49bef989454d86d0c891 *R/additive.R
1d76af894213570636d36c5a671192b3 *R/alex.R
9fe874382f024a98f62a0ccfcd6d09ac *R/all.equal.phylo.R
Expand Down Expand Up @@ -42,7 +42,7 @@ f916a0df46651d0a6640a735c54c84a1 *R/clustal.R
207154a3a9b9ebbe5d7c29995565dc82 *R/compar.ou.R
be772ef6f74e80bbd9be8dcb0d0516be *R/comparePhylo.R
8d7c71929156744fd0e4fac370bf9456 *R/compute.brtime.R
8d6657e3d947dc25eb3e3bb3e3c59308 *R/cophenetic.phylo.R
561a616ff6b7bc134c3f987a695c3c6a *R/cophenetic.phylo.R
13f2dac84d7b8a1da3df0e0c11b4ab1c *R/cophyloplot.R
d136bcb6eac7ea91811b64b3a4cf7572 *R/corphylo.R
1c3460b48ed1e772c40e5993cd663d43 *R/dbd.R
Expand Down Expand Up @@ -86,7 +86,7 @@ dd95923aac8ab849dd128104355529ce *R/pcoa.R
c2357dbf0ca7198c58d97e08ad3d16c4 *R/phydataplot.R
e71db002c66c277bfb57f6914ca143d4 *R/phymltest.R
615818acb88bc5c6d232b8b052506176 *R/pic.R
b7e499ebc4675dd782a3878c8b7d199e *R/plot.phylo.R
4d3a78fe87c663440dab48d266a66d74 *R/plot.phylo.R
6c744c311f1bc32ff85d639b75ec958f *R/plot.phyloExtra.R
5c12c911fc422f8f8d8e160ef79f312d *R/plot.popsize.R
dd009da9120a99c30ca4169b61e5d195 *R/plotPhyloCoor.R
Expand All @@ -97,7 +97,7 @@ d0e8bd41d5acc217fdee3578adcf635b *R/print.parafit.R
b13dfb8f455b1c9e74a364085f72dbce *R/read.caic.R
0a94085734afd8c8144969745e63e9a2 *R/read.dna.R
23f0c2804b21bc58ca30284f1c920bae *R/read.gff.R
6b9a7befc89a7e8acf8254ef96ec1770 *R/read.nexus.R
b483ce78d4918b0364121dad3235cfb3 *R/read.nexus.R
f32f0efa7f1831327407314d5551223d *R/read.nexus.data.R
8b445387c7c86013b96cd1f9a574cddc *R/read.tree.R
0d5a267466528603ac433a8a52f7ca11 *R/reconstruct.R
Expand All @@ -106,13 +106,13 @@ d74ea5a3fd628874c76f4abd63fc59f1 *R/root.R
f584366b32e7414c669714ba5b84951b *R/rotate.R
d5abeb2b5165f3d9613392d0c8f03802 *R/rtree.R
4f1c0fa161136e96ba30bef34b6787ac *R/rtt.R
7d97fe87a4c5abac659d4a9abaf152e6 *R/scales.R
74b3c054294129b6a5618a0548d3f1a8 *R/scales.R
c73717df856fd5c5d575b28e71071324 *R/skyline.R
71bb3f2dcbb807ace238a6ce2af25fe0 *R/skylineplot.R
9c7b02a4625099f715700fb868226b0f *R/speciesTree.R
97c4c3d7cb1606fe6d5519d817156bde *R/subtreeplot.R
bcc8f1fc8363728caba82129412d9e31 *R/subtrees.R
cb78a9e022a7f0e80ba1594cdc05bca6 *R/summary.phylo.R
dea05c19df9a03075f75bbe49cc1bb76 *R/summary.phylo.R
8fbd1589f5d98d76b1154cffb8d4d1f5 *R/treePop.R
b5081fca8758fe4458183c3e25e3e661 *R/triangMtd.R
aca0e4f1c8aae416e5941adaaf47ba64 *R/unique.multiPhylo.R
Expand All @@ -121,20 +121,21 @@ a40ae9ad30c221d4ed14b90e8b406f93 *R/vcv.phylo.R
31b3bb1feed474692f07fcebe3a61ac7 *R/vcv2phylo.R
c9adce0f3d0120434ca22f2bb2a0b0c8 *R/which.edge.R
a091953ea941768033d85494e6457691 *R/write.dna.R
a9fe8a5e4fa9afb0f96129ea3ee64655 *R/write.nexus.R
a6660649caf2e2a28dfbc813f24efc3c *R/write.nexus.R
a6d3d8d0fb844c0670d5674a1def2bd0 *R/write.nexus.data.R
36e073048cf9d8fdf78426065254493f *R/write.tree.R
9c8dd90c5e633a1b97023863f47efd1e *R/write.phyloXML.R
8393ff7c6b124798909b97e60a9af1b2 *R/write.tree.R
774ce72875903259aade5344f9a70aa4 *R/yule.R
c8d3aa3fe64e75e61af07a1b11c74f3f *R/yule.time.R
1eb44ff9e5a036eb845faa1598ce5009 *R/zoom.R
3387c0d0c1f913f8471e1bb34bd2e516 *R/zzz.R
86cc44c74ad6bc4c8f4e623248e99c6c *README.md
20c8d3f97d93e2e318a22508275b5a02 *build/partial.rdb
5f072f67dc323e830769184cff696f98 *build/vignette.rds
76161b65639451c966be75488458b3c3 *build/partial.rdb
c99acb8a85df550093b4d4721b5d4dc6 *build/vignette.rds
db9083e8750aff839d5ebf3ed982f1f1 *data/HP.links.rda
9d9f9232839665422709ded1e541d038 *data/bird.families.rda
a14a6df0f3a735ebc056065077788c90 *data/bird.orders.rda
f74f9ed80c04756021cc093d40ca9ff9 *data/carnivora.csv.gz
100769335d485fc11e54b766753a9204 *data/carnivora.csv.gz
4eaf8cbaefa2e8f8d395a9b482ee9967 *data/chiroptera.rda
1c74c3b99d08b0e17eea3ec1065c12d2 *data/cynipids.rda
7fe760c2f3b4deba0554aae6138cb602 *data/gopher.D.rda
Expand All @@ -150,13 +151,13 @@ e2d1339025ed901009bfed58dc6505ff *data/mat5M3ID.RData
a20dff855d5d35b8072413bd3c5fd126 *inst/CITATION
44e0e7e0eb4c9edcdbe731d15ad245d1 *inst/doc/DrawingPhylogenies.R
9d6935787463e165da55172f2d380fca *inst/doc/DrawingPhylogenies.Rnw
349b41146b1b7d78d8ffea4e47623095 *inst/doc/DrawingPhylogenies.pdf
452ffd2d69a0cad8d0d312b8c61b10df *inst/doc/DrawingPhylogenies.pdf
ae58e3a830ca118636ac7f12cee14cdd *inst/doc/MoranI.R
dcd55bda01ae5c227823285f250a5adf *inst/doc/MoranI.Rnw
80e1180fdb65b752148dc19c596df14b *inst/doc/MoranI.pdf
35de25b03fc3f54930ccaccfdb87fc2f *inst/doc/MoranI.pdf
6db8a8dd3ff8d7bb64ecb15b3d7e4ac3 *inst/doc/RandomTopologies.R
8b4fc32c71458880a760eb9cc4e018fc *inst/doc/RandomTopologies.Rnw
db04166d9dbbec4a114e1b7b80c04a13 *inst/doc/RandomTopologies.pdf
5fcc49f193a4c4e31a6207d43648e498 *inst/doc/RandomTopologies.pdf
96c03e13b985ac39c71a6558fda39aed *man/AAbin.Rd
7f7b284190c3b52358bd330ea58cdf8e *man/CADM.global.Rd
c42fdaf2e7435a197fc9ab1a5824c67a *man/DNAbin.Rd
Expand All @@ -181,7 +182,7 @@ fda9f1e51ff562e28dc79b6c0780ec1a *man/as.bitsplits.Rd
4f014cf2923e2eab6188acd48e8096fa *man/as.matching.Rd
84b636fd9928b77de91504121216da61 *man/as.phylo.Rd
697944c0dca01d11817401e1a57049d2 *man/as.phylo.formula.Rd
c1bb2b36369966cc61f802daa27921a2 *man/axisPhylo.Rd
b485c9432402006594c349a0e5929ec4 *man/axisPhylo.Rd
ad514b163e70bfbc11dfd34a450799f8 *man/balance.Rd
1f7aab487d391940a07950332696915e *man/base.freq.Rd
524a1163eac56d1fc7f65bcd6c74a8d0 *man/bd.ext.Rd
Expand Down Expand Up @@ -216,7 +217,7 @@ a49d26747890cef3b75bcc46b0b8b40b *man/comparePhylo.Rd
a1d0980f32039aa2ca0a0b1b7a5591f8 *man/compute.brlen.Rd
dbb4b5b1d5136bd32660699d9d4cc197 *man/compute.brtime.Rd
2673588811016427759ca9a1ef56c3e9 *man/consensus.Rd
1e5b635a08fe0e1242801ff0caec9d0d *man/cophenetic.phylo.Rd
cad78cf5a7c43d4aa02bd2506440b8ce *man/cophenetic.phylo.Rd
1ca9ec0cb824468adc03884c940c7aa3 *man/cophyloplot.Rd
643275d7997dfcd82b1ff08057b3f1a7 *man/corBlomberg.Rd
445d8651a1977bb4831df4661a43e3bf *man/corBrownian.Rd
Expand Down Expand Up @@ -245,16 +246,16 @@ cf3e0f6cbbc15a6a213b247e01961a64 *man/dnds.Rd
9697317017dd41a68961522fb26b6222 *man/ewLasso.Rd
b81094916d0dda1483e31da6681f3bc2 *man/fastme.Rd
eea313e8ee32597b4cec120d23113642 *man/gammaStat.Rd
3684afa97b61c1e07f02327a7f2b9acd *man/getAnnotationsGenBank.Rd
f8edffddff0582a7ea357652a1af7aa1 *man/getAnnotationsGenBank.Rd
ccf012737965d0de0b4ca2dd9367d9a6 *man/hivtree.Rd
942b38a17ab6ecfa126118370f59bdf6 *man/howmanytrees.Rd
86c49d080fdffd614d8056021e91cc55 *man/identify.phylo.Rd
1da41a514b48c8488326c251f2ee537a *man/image.DNAbin.Rd
45b9403b6c839a7566b42e216565fbe8 *man/image.DNAbin.Rd
ce6b1d4cabb4e6f246b147e8ab520435 *man/is.binary.tree.Rd
18329c0c629c76de2bd4823aefecdfb5 *man/is.compatible.Rd
d2de8fd9549ef01a1dddeb726dd77fcf *man/is.monophyletic.Rd
ad9e7316219c3238b44b02d55c44b4d3 *man/is.ultrametric.Rd
3f6ff8340b6c9770a1f4d2fed72a295d *man/kronoviz.Rd
17917c9fed877d1c9b2776e56c46e191 *man/kronoviz.Rd
4d8fee8d142528834332038e49bd2e65 *man/label2table.Rd
2afa6305e48e4c47a7d94d46401f85a3 *man/ladderize.Rd
472dc874a45f046c8f6ac7b394b6552f *man/latag2n.Rd
Expand Down Expand Up @@ -337,9 +338,10 @@ f4f11cb67f304e5de80d4768508dd765 *man/where.Rd
ef9658f5343bdcbfc3673c7f936934f5 *man/which.edge.Rd
9b83a148295dcfcb3994fdb6eaab0174 *man/woodmouse.Rd
a0f59b5f53c0e8f5d45380cbaf71fb58 *man/write.dna.Rd
df8657f468307a02b8cde93ff4758f1c *man/write.nexus.Rd
5863d8e9f91a9f8c5723aee5f69bb3e6 *man/write.nexus.Rd
9813a7c7a95bf532ffa1297d8369457c *man/write.nexus.data.Rd
06fcd0c13156f7ccc187595adc414d78 *man/write.tree.Rd
68c0d139b9f014602ba370bd27933710 *man/write.phyloXML.Rd
a549d6c95935c86edecbad3beac8aa1a *man/write.tree.Rd
2568c6529e40fae7effe88b6c73998a1 *man/yule.Rd
7df89ac6996c82b52c4c9b3734807de1 *man/yule.cov.Rd
8612123f3617699a8e29ddf0541dc9ee *man/yule.time.Rd
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -75,6 +75,7 @@ export(.compressTipLabel, .PlotPhyloEnv, .uncompressTipLabel,
varcomp, varCompPhylip, vcv, vcv.corPhyl, vcv.phylo, vcv2phylo,
weight.taxo, weight.taxo2, where, which.edge, write.dna,
write.evonet, write.FASTA, write.nexus, write.nexus.data,
write.phyloXML,
write.tree, Xplor, Xplorefiles, yule, yule.cov, yule.time,
zoom, node_depth, node_depth_edgelength, node_height,
node_height_clado, seq_root2tip)
Expand Down
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