version 5.7-1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ape
-Version: 5.7
-Date: 2023-02-13
+Version: 5.7-1
+Date: 2023-03-13
 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")),
@@ -42,10 +42,11 @@ 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/
+URL: http://ape-package.ird.fr/, https://github.com/emmanuelparadis/ape
+BugReports: https://github.com/emmanuelparadis/ape/issues
 Encoding: UTF-8
 NeedsCompilation: yes
-Packaged: 2023-02-13 02:38:10 UTC; paradis
+Packaged: 2023-03-13 10:22:29 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>),
@@ -81,4 +82,4 @@ 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: 2023-02-16 13:30:02 UTC
+Date/Publication: 2023-03-13 12:20:09 UTC

MD5

@@ -1,7 +1,7 @@
 eb723b61539feef013de476e68b5c50a *COPYING
-3662dbe23b8526cb4ffbe58bf2244189 *DESCRIPTION
+b089cbbf2fd35e662ad3cd7753e1995f *DESCRIPTION
 ad2c10dbb7ee6ebda0f5649432e1baec *NAMESPACE
-854a025cb7e5da3e4fe230c0be950d08 *NEWS
+d3adae46df59163741603a5f8e5492a5 *NEWS
 4dc75ff83940a80aafe96f6a67eefebf *R/CADM.global.R
 4f3a09f6a829d788f273399faaf40285 *R/CADM.post.R
 fde32bab7748bc8d1e77a006c08159b2 *R/CDF.birth.death.R
@@ -105,7 +105,7 @@ d7486ab8ac6d584f04bf1f75ca7f6be3 *R/reorder.phylo.R
 dadb8aa13a8ceecdb9052facf29430ca *R/root.R
 f584366b32e7414c669714ba5b84951b *R/rotate.R
 d5abeb2b5165f3d9613392d0c8f03802 *R/rtree.R
-99f8fa6fb6eab7c929abcd08fb5d5e61 *R/rtt.R
+3a7207e43874c203ded61d49a0c1b303 *R/rtt.R
 7d97fe87a4c5abac659d4a9abaf152e6 *R/scales.R
 c73717df856fd5c5d575b28e71071324 *R/skyline.R
 71bb3f2dcbb807ace238a6ce2af25fe0 *R/skylineplot.R
@@ -150,13 +150,13 @@ e2d1339025ed901009bfed58dc6505ff *data/mat5M3ID.RData
 a20dff855d5d35b8072413bd3c5fd126 *inst/CITATION
 44e0e7e0eb4c9edcdbe731d15ad245d1 *inst/doc/DrawingPhylogenies.R
 fe9b452b3978a7379c50f5294b94badc *inst/doc/DrawingPhylogenies.Rnw
-b112b93581305b05c6555ca812c2e9d9 *inst/doc/DrawingPhylogenies.pdf
+79d417655305b726503c0cd60c902e77 *inst/doc/DrawingPhylogenies.pdf
 ae58e3a830ca118636ac7f12cee14cdd *inst/doc/MoranI.R
 dcd55bda01ae5c227823285f250a5adf *inst/doc/MoranI.Rnw
-ebf628bc70431333ac127a451ae3c5de *inst/doc/MoranI.pdf
+39104e6723445886f9181a6bd6c3f1eb *inst/doc/MoranI.pdf
 6db8a8dd3ff8d7bb64ecb15b3d7e4ac3 *inst/doc/RandomTopologies.R
 be40702621d8c4be5dc87c938df5c0b2 *inst/doc/RandomTopologies.Rnw
-4735f148512b43c8f71824a9f3fcaed1 *inst/doc/RandomTopologies.pdf
+ad11a8f739219e7f739d943164d2e553 *inst/doc/RandomTopologies.pdf
 5c133fd944233aaf92d4317149e5c2ea *man/AAbin.Rd
 7f7b284190c3b52358bd330ea58cdf8e *man/CADM.global.Rd
 1abe36a10c34884230d6779d1c6058dd *man/DNAbin.Rd
@@ -173,11 +173,11 @@ c7866d0fc32be91d9cfb6ab3e3fc1e1a *man/SDM.Rd
 2ff5d30c6fb1c5458643f1b3c09e76da *man/all.equal.DNAbin.Rd
 d69fcc8e2e02aff7cdd0decbbd892e40 *man/all.equal.phylo.Rd
 b9e6f622b239d6ef2614285f3a343ee3 *man/alview.Rd
-939b7b612a00127a0cde328f619c82fb *man/ape-internal.Rd
+46dcfadd6545d4a795833202c01b17ff *man/ape-internal.Rd
 35f531f89254780beb7be3e4ef632ad1 *man/ape-package.Rd
 f52b5e2d34295171a6da2359738c99d5 *man/apetools.Rd
 5bba4ae4bfc66b613855cfc182d9b1bc *man/as.alignment.Rd
-d087bf5c0b9206e276a03a62b72a2252 *man/as.bitsplits.Rd
+78ddabc3586cf66f837b5a274e99dab0 *man/as.bitsplits.Rd
 4f014cf2923e2eab6188acd48e8096fa *man/as.matching.Rd
 84b636fd9928b77de91504121216da61 *man/as.phylo.Rd
 697944c0dca01d11817401e1a57049d2 *man/as.phylo.formula.Rd
@@ -187,7 +187,7 @@ ad514b163e70bfbc11dfd34a450799f8 *man/balance.Rd
 524a1163eac56d1fc7f65bcd6c74a8d0 *man/bd.ext.Rd
 5f1e61abe5908708f503cb2626a1b5e6 *man/bd.time.Rd
 f929bc1b6391c57a6b0099c4561fd7be *man/binaryPGLMM.Rd
-bfbc3c952d7af7214fb060076b4c079e *man/bind.tree.Rd
+e999ac6ef275c168aad217dfec402266 *man/bind.tree.Rd
 822558d4f7ee04257b2c903c53ec4344 *man/bionj.Rd
 923169087dca05f046cebcac8946e136 *man/bird.families.Rd
 0e41770e1e6d0b8d90c4cf51049213cb *man/bird.orders.Rd
@@ -210,7 +210,7 @@ b114a09e0cb474323d5398ec4ee83d3c *man/collapse.singles.Rd
 bff5a7826f5a39767601e32ceb776247 *man/collapsed.intervals.Rd
 683bf7d71e50f4ec5cd921073291eddd *man/compar.cheverud.Rd
 4d8ee141d7b6b323ef5ee9446000ae32 *man/compar.gee.Rd
-8b7388332d96b234b274fd3433e0da1f *man/compar.lynch.Rd
+84078c1644fb841b9ed5ac7d17cba59b *man/compar.lynch.Rd
 8b079bc165c375f823c40074ad9106c6 *man/compar.ou.Rd
 a49d26747890cef3b75bcc46b0b8b40b *man/comparePhylo.Rd
 a1d0980f32039aa2ca0a0b1b7a5591f8 *man/compute.brlen.Rd
@@ -238,7 +238,7 @@ fbcd1d4bcf74e21fc93c195c7af3db98 *man/delta.plot.Rd
 c7cc398115be066740ca4fb037394727 *man/diversi.gof.Rd
 d646ea0343999bd0e38e86dcf6c12018 *man/diversi.time.Rd
 da8898476bb15b627b34ee1093b9aeb4 *man/diversity.contrast.test.Rd
-25100a091b190cfc0cc4bac7b209143e *man/dnds.Rd
+cf3e0f6cbbc15a6a213b247e01961a64 *man/dnds.Rd
 d5399a965322e672eb026047855acc4e *man/drop.tip.Rd
 66537062a3d706b200f57791daa86102 *man/edges.Rd
 3eb82a23c0ece8a095c8f472736f33a1 *man/evonet.Rd
@@ -285,10 +285,10 @@ c2e2f35f4e233265c86b7967ec2d0630 *man/parafit.Rd
 6714815a437ddde9e4c155595afe9276 *man/pcoa.Rd
 0089077e3be11d37650331437e4a8a48 *man/phydataplot.Rd
 6dfa52711bab351bbcfe2624690eb730 *man/phymltest.Rd
-468e1d9163304629213d4f2ae5294f4b *man/pic.Rd
+9c769e37126330e8243610d21300f9a8 *man/pic.Rd
 0363aa3fa3e86160934e2359c8ac5323 *man/pic.ortho.Rd
 265527313d479d3625df7680c7479cd1 *man/plot.correlogram.Rd
-8a21a645361d98e109cbbee755e17549 *man/plot.phylo.Rd
+25b7c4ba15c7f9daa89f435268207ba4 *man/plot.phylo.Rd
 896198fa3a0ce916346c8b507bf707bf *man/plot.phyloExtra.Rd
 d39058b543c60b3f2a2c22cd88325bb6 *man/plot.varcomp.Rd
 c6ff668831b791540e543df87d952ad8 *man/plotTreeTime.Rd
@@ -298,12 +298,12 @@ cd98ef01fc72ff6a66cf6d24a5197259 *man/rTraitCont.Rd
 59e81eaae91dc77b4275c9a5b2910dda *man/rTraitDisc.Rd
 81f756fdf2ec4c968095595dece8338f *man/rTraitMult.Rd
 a540f8a85f14d4c4ece1d1a19cb15a6f *man/read.GenBank.Rd
-0b7b51b8947b4ea23ed5d6afd48fbc23 *man/read.caic.Rd
-0dc0899b49abbdd8c8ffbb51328586ec *man/read.dna.Rd
+1317e2519ff9b7c61b7e9c21c3b0b5bb *man/read.caic.Rd
+a9acea121adbfe78274a4398adff8fd5 *man/read.dna.Rd
 4bd8a114f7ab4b9ffffd7fd4d1799b36 *man/read.gff.Rd
 fdc2393e70328ae27034c54bf8a847c7 *man/read.nexus.Rd
 9c1d50a3701690f505a8d702bb5d7d24 *man/read.nexus.data.Rd
-80aaced77530e1d5faf459f8695baea2 *man/read.tree.Rd
+23adfe9ee077e6fbe75575b356581a83 *man/read.tree.Rd
 e9c081ee9bb174f530be5cab9ec954e5 *man/reconstruct.Rd
 29fd18c1d0729228307b82dc3ef70ede *man/reorder.phylo.Rd
 23cb928f62f9c7103244fbd752ff9a81 *man/richness.yule.test.Rd
@@ -378,7 +378,7 @@ cea461f86f87000ed51808282d799600 *src/read_dna.c
 295aeaaa825f6f403fb9d1aa94755c7e *src/reorder_Rcpp.cpp
 77c49127a8c5b23efcfe90a0b29bd7ba *src/reorder_phylo.c
 c73f78b21f3cada4ebb5035ac866d0f3 *src/treePop.c
-9d523dc0a364b0ff40400451829a7433 *src/tree_build.c
+731a1b013f6ccf4ca261a8875da53d32 *src/tree_build.c
 42c108c79f26d1940f94b98fcbe271e1 *src/tree_phylo.c
 b6b0929c7faa1b76a8898f12907aabd5 *src/triangMtd.c
 cca4da03778dfa7c87fa6bfb97aac13c *src/triangMtds.c

NEWS

@@ -1,3 +1,4 @@
 See:
 
 http://ape-package.ird.fr/NEWS
+https://github.com/emmanuelparadis/ape/blob/master/NEWS

R/rtt.R

@@ -34,7 +34,7 @@ rtt <- function (t, tip.dates, ncpu = 1, objective = "correlation",
         objective <- function(x, y) {
             # summary(lm(y ~ x))$r.squared
             X[,2] <- x
-            lm.fit(X, y) |> r.squared()
+            r.squared(lm.fit(X, y))
         }
     else if (objective == "rms"){
         objective <- function(x, y){

man/ape-internal.Rd

@@ -1,4 +1,5 @@
 \name{ape-internal}
+\alias{.PlotPhyloEnv}
 \alias{perm.rowscols}
 \alias{phylogram.plot}
 \alias{cladogram.plot}

man/as.bitsplits.Rd

@@ -42,7 +42,7 @@ as.prop.part(x, ...)
 }
 \details{
   These functions count bipartitions as defined by internal branches, so
-  they not work only with unrooted trees. The structure of the class
+  they work only with unrooted trees. The structure of the class
   \code{"bitsplits"} is described in a separate document on ape's web
   site.
 }

man/bind.tree.Rd

@@ -56,9 +56,11 @@ bind.tree(x, y, where = "root", position = 0, interactive = FALSE)
 }
 \examples{
 ### binds the two clades of bird orders
+treefile1 <- tempfile("tree", fileext = ".tre")
+treefile2 <- tempfile("tree", fileext = ".tre")
 cat("((Struthioniformes:21.8,Tinamiformes:21.8):4.1,",
     "((Craciformes:21.6,Galliformes:21.6):1.3,Anseriformes:22.9):3.0):2.1;",
-    file = "ex1.tre", sep = "\n")
+    file = treefile1, sep = "\n")
 cat("(Turniciformes:27.0,(Piciformes:26.3,((Galbuliformes:24.4,",
     "((Bucerotiformes:20.8,Upupiformes:20.8):2.6,",
     "(Trogoniformes:22.1,Coraciiformes:22.1):1.3):1.0):0.6,",
@@ -67,10 +69,10 @@ cat("(Turniciformes:27.0,(Piciformes:26.3,((Galbuliformes:24.4,",
     "(Musophagiformes:20.4,Strigiformes:20.4):1.5):0.6,",
     "((Columbiformes:20.8,(Gruiformes:20.1,Ciconiiformes:20.1):0.7):0.8,",
     "Passeriformes:21.6):0.9):0.6):0.6):0.8):0.5):1.3):0.7):1.0;",
-    file = "ex2.tre", sep = "\n")
-tree.bird1 <- read.tree("ex1.tre")
-tree.bird2 <- read.tree("ex2.tre")
-unlink(c("ex1.tre", "ex2.tre")) # clean-up
+    file = treefile2, sep = "\n")
+tree.bird1 <- read.tree(treefile1)
+tree.bird2 <- read.tree(treefile2)
+unlink(c(treefile1, treefile2)) # clean-up
 (birds <- tree.bird1 + tree.bird2)
 layout(matrix(c(1, 2, 3, 3), 2, 2))
 plot(tree.bird1)

man/compar.lynch.Rd

@@ -54,11 +54,8 @@ compar.lynch(x, G, eps = 1e-4)
 }
 \examples{
 ### The example in Lynch (1991)
-cat("((((Homo:0.21,Pongo:0.21):0.28,",
-   "Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);",
-   file = "ex.tre", sep = "\n")
-tree.primates <- read.tree("ex.tre")
-unlink("ex.tre")
+x <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);"
+tree.primates <- read.tree(text = x)
 X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
 Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
 compar.lynch(cbind(X, Y),

man/dnds.Rd

@@ -55,7 +55,8 @@ dnds(x, code = 1, codonstart = 1, quiet = FALSE,
 data(woodmouse)
 res <- dnds(woodmouse, quiet = TRUE) # NOT correct
 res2 <- dnds(woodmouse, code = 2, quiet = TRUE) # using the correct code
-identical(res, res2)
+identical(res, res2) # FALSE...
+cor(res, res2) # ... but very close
 ## There a few N's in the woodmouse data, but this does not affect
 ## greatly the results:
 res3 <- dnds(solveAmbiguousBases(woodmouse), code = 2, quiet = TRUE)
@@ -64,6 +65,6 @@ cor(res, res3)
 ## a simple example showing the usefulness of 'details = TRUE'
 X <- as.DNAbin(matrix(c("C", "A", "G", "G", "T", "T"), 2, 3))
 alview(X)
-dnds(X, quiet = TRUE) # NaN + warnings
+dnds(X, quiet = TRUE) # NaN
 dnds(X, details = TRUE) # only a TV at a nondegenerate site
 }

man/pic.Rd

@@ -54,10 +54,8 @@ pic(x, phy, scaled = TRUE, var.contrasts = FALSE,
 }
 \examples{
 ### The example in Phylip 3.5c (originally from Lynch 1991)
-cat("((((Homo:0.21,Pongo:0.21):0.28,",
-   "Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);",
-   file = "ex.tre", sep = "\n")
-tree.primates <- read.tree("ex.tre")
+x <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);"
+tree.primates <- read.tree(text = x)
 X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
 Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
 names(X) <- names(Y) <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago")
@@ -66,6 +64,5 @@ pic.Y <- pic(Y, tree.primates)
 cor.test(pic.X, pic.Y)
 lm(pic.Y ~ pic.X - 1) # both regressions
 lm(pic.X ~ pic.Y - 1) # through the origin
-unlink("ex.tre") # delete the file "ex.tre"
 }
 \keyword{regression}

man/plot.phylo.Rd

@@ -210,12 +210,9 @@
 }
 \examples{
 ### An extract from Sibley and Ahlquist (1990)
-cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",
-   "Athene_noctua:7.3):6.3,Tyto_alba:13.5);",
-   file = "ex.tre", sep = "\n")
-tree.owls <- read.tree("ex.tre")
+x <- "(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);"
+tree.owls <- read.tree(text= x)
 plot(tree.owls)
-unlink("ex.tre") # delete the file "ex.tre"
 
 ### Show the types of trees.
 layout(matrix(1:6, 3, 2))

man/read.caic.Rd

@@ -30,14 +30,15 @@ read.caic(file, brlen = NULL, skip = 0, comment.char = "#", ...)
 \section{Warning}{The branch length support is still experimental and was not fully tested.}
 \seealso{ \code{\link{read.tree}}, \code{\link{read.nexus}} }
 \examples{
-### The same example than in read.tree, without branch lengths.
-### An extract from Sibley and Ahlquist (1990)
+## The same example than in read.tree, without branch lengths.
+## An extract from Sibley and Ahlquist (1990)
+fl <- tempfile("tree", fileext = ".tre")
 cat("AAA","Strix_aluco","AAB","Asio_otus",
    "AB","Athene_noctua","B","Tyto_alba",
-   file = "ex.tre", sep = "\n")
-tree.owls <- read.caic("ex.tre")
+   file = fl, sep = "\n")
+tree.owls <- read.caic(fl)
 plot(tree.owls)
 tree.owls
-unlink("ex.tre") # delete the file "ex.tre"
+unlink(fl) # delete the file "ex.tre"
 }
 \keyword{hplot}