From: paradis Date: Mon, 28 Jul 2008 14:58:38 +0000 (+0000) Subject: changed some data sets (made lighter) + clarified man page for rcoal() X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=85d300f9ba17580ca69943194b789db70bd0dcab;p=ape.git changed some data sets (made lighter) + clarified man page for rcoal() git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@48 6e262413-ae40-0410-9e79-b911bd7a66b7 --- diff --git a/Changes b/Changes index 2fe5b8d..988dd6f 100644 --- a/Changes +++ b/Changes @@ -13,6 +13,13 @@ BUG FIXES 'check.labels = TRUE'. +OTHER CHANGES + + o The data sets bird.orders and bird.families are now stored as + Newick strings; e.g., the command data(bird.orders) calls + read.tree(). + + CHANGES IN APE VERSION 2.2-1 @@ -241,9 +248,9 @@ BUG FIXES OTHER CHANGES - o The code of mlphylo() has almost entirely rewritten, and should - be much stabler. The options have been also greatly simplified - (see ?mlphylo and ?DNAmodel for details). + o The code of mlphylo() has been almost entirely rewritten, and + should be much stabler. The options have been also greatly + simplified (see ?mlphylo and ?DNAmodel for details). o The internal function nTips has been renamed klastorin_nTips. diff --git a/DESCRIPTION b/DESCRIPTION index 96c7945..7d0413a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ape Version: 2.2-2 -Date: 2008-07-18 +Date: 2008-07-22 Title: Analyses of Phylogenetics and Evolution Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, diff --git a/data/bird.families.R b/data/bird.families.R index 27df856..a806ea3 100644 --- a/data/bird.families.R +++ b/data/bird.families.R @@ -1,97 +1,2 @@ -"bird.families" <- -structure(list(edge = structure(c(138, 139, 140, 141, 142, 142, -141, 143, 143, 140, 139, 144, 145, 146, 146, 145, 147, 148, 148, -147, 144, 149, 150, 150, 149, 151, 151, 138, 152, 152, 153, 154, -155, 155, 154, 156, 156, 157, 157, 153, 158, 159, 160, 160, 159, -161, 162, 163, 163, 162, 164, 164, 165, 165, 161, 166, 166, 167, -168, 168, 167, 169, 169, 170, 170, 171, 171, 172, 172, 173, 173, -158, 174, 174, 175, 176, 177, 178, 178, 177, 176, 179, 179, 180, -180, 175, 181, 181, 182, 183, 184, 185, 185, 184, 183, 186, 186, -187, 188, 188, 187, 189, 189, 190, 191, 191, 190, 192, 193, 193, -192, 194, 194, 182, 195, 196, 196, 197, 198, 199, 199, 200, 200, -201, 202, 203, 203, 202, 201, 201, 198, 197, 204, 205, 205, 206, -207, 208, 209, 209, 208, 207, 210, 210, 206, 211, 212, 212, 213, -213, 211, 214, 214, 204, 215, 216, 217, 217, 216, 215, 218, 218, -219, 219, 220, 221, 222, 222, 221, 220, 223, 223, 224, 224, 225, -225, 226, 226, 227, 228, 228, 227, 229, 229, 230, 230, 231, 231, -195, 232, 233, 233, 234, 235, 235, 234, 236, 236, 237, 237, 238, -238, 239, 239, 240, 240, 232, 241, 242, 243, 243, 244, 244, 242, -245, 246, 246, 247, 247, 245, 248, 248, 249, 249, 250, 250, 251, -251, 252, 252, 253, 253, 241, 254, 255, 255, 256, 256, 257, 257, -254, 258, 259, 260, 260, 259, 261, 261, 262, 262, 263, 263, 264, -264, 265, 265, 266, 266, 267, 267, 258, 268, 268, 269, 270, 271, -271, 272, 272, 270, 269, 139, 140, 141, 142, 1, 2, 143, 3, 4, -5, 144, 145, 146, 6, 7, 147, 148, 8, 9, 10, 149, 150, 11, 12, -151, 13, 14, 152, 15, 153, 154, 155, 16, 17, 156, 18, 157, 19, -20, 158, 159, 160, 21, 22, 161, 162, 163, 23, 24, 164, 25, 165, -26, 27, 166, 28, 167, 168, 29, 30, 169, 31, 170, 32, 171, 33, -172, 34, 173, 35, 36, 174, 37, 175, 176, 177, 178, 38, 39, 40, -179, 41, 180, 42, 43, 181, 44, 182, 183, 184, 185, 45, 46, 47, -186, 48, 187, 188, 49, 50, 189, 51, 190, 191, 52, 53, 192, 193, -54, 55, 194, 56, 57, 195, 196, 58, 197, 198, 199, 59, 200, 60, -201, 202, 203, 61, 62, 63, 64, 65, 66, 204, 205, 67, 206, 207, -208, 209, 68, 69, 70, 210, 71, 72, 211, 212, 73, 213, 74, 75, -214, 76, 77, 215, 216, 217, 78, 79, 80, 218, 81, 219, 82, 220, -221, 222, 83, 84, 85, 223, 86, 224, 87, 225, 88, 226, 89, 227, -228, 90, 91, 229, 92, 230, 93, 231, 94, 95, 232, 233, 96, 234, -235, 97, 98, 236, 99, 237, 100, 238, 101, 239, 102, 240, 103, -104, 241, 242, 243, 105, 244, 106, 107, 245, 246, 108, 247, 109, -110, 248, 111, 249, 112, 250, 113, 251, 114, 252, 115, 253, 116, -117, 254, 255, 118, 256, 119, 257, 120, 121, 258, 259, 260, 122, -123, 261, 124, 262, 125, 263, 126, 264, 127, 265, 128, 266, 129, -267, 130, 131, 268, 132, 269, 270, 271, 133, 272, 134, 135, 136, -137), .Dim = c(271, 2)), edge.length = c(2.1, 4.1, 3.9, 0.8, -17.1, 17.1, 8.4, 9.5, 9.5, 21.8, 3, 1.3, 1.8, 19.8, 19.8, 6.5, -2.3, 12.8, 12.8, 15.1, 6.8, 3.7, 12.4, 12.4, 6.3, 9.8, 9.8, 1, -27, 0.7, 9.8, 5.5, 11, 11, 3.7, 12.8, 1.3, 11.5, 11.5, 1.3, 0.6, -6.9, 17.5, 17.5, 1, 2.6, 11.6, 9.2, 9.2, 3.8, 17, 6.8, 10.2, -10.2, 1.3, 22.1, 1.1, 7.1, 13.9, 13.9, 1.3, 19.7, 2, 17.7, 1.2, -16.5, 1, 15.5, 3.5, 12, 12, 0.5, 24.5, 0.8, 6.1, 3.1, 1.5, 13, -13, 14.5, 1.2, 16.4, 1.9, 14.5, 14.5, 0.6, 23.1, 0.6, 0.6, 0.6, -11.8, 9.5, 9.5, 21.3, 1.5, 20.4, 1.3, 5.5, 13.6, 13.6, 0.3, 18.8, -0.9, 7.6, 10.3, 10.3, 1, 1.1, 15.8, 15.8, 4.6, 12.3, 12.3, 0.9, -0.8, 20.8, 0.7, 1, 1.6, 17.5, 0.6, 16.9, 1.9, 2.3, 3.5, 9.2, -9.2, 12.7, 15, 15, 19.1, 1.4, 1.6, 17.1, 1.5, 1.5, 0.8, 3, 10.3, -10.3, 13.3, 1.6, 12.5, 12.5, 2.8, 1.3, 11.5, 0.7, 10.8, 10.8, -4.7, 8.1, 8.1, 2.3, 1.2, 4.8, 10.4, 10.4, 15.2, 1.5, 14.9, 0.9, -14, 0.7, 1.2, 1.1, 11, 11, 12.1, 0.9, 12.4, 0.5, 11.9, 0.4, 11.5, -0.4, 11.1, 0.2, 0.8, 10.1, 10.1, 0.2, 10.7, 0.3, 10.4, 0.4, 10, -10, 1.9, 1.8, 17.9, 2.1, 3.7, 12.1, 12.1, 2, 13.8, 0.3, 13.5, -1.4, 12.1, 0.7, 11.4, 0.7, 10.7, 10.7, 6.9, 1.1, 1.3, 10.4, 0.5, -9.9, 9.9, 0.3, 0.2, 11.2, 2, 9.2, 9.2, 0.8, 10.6, 0.4, 10.2, -0.2, 10, 0.4, 9.6, 0.5, 9.1, 0.3, 8.8, 8.8, 1.1, 1.1, 10.6, 0.9, -9.7, 0.6, 9.1, 9.1, 0.6, 0.3, 0.8, 10, 10, 0.2, 10.6, 0.2, 10.4, -0.3, 10.1, 0.4, 9.7, 0.2, 9.5, 0.1, 9.4, 0.3, 9.1, 9.1, 0.7, -10.4, 0.4, 0.2, 0.2, 9.6, 0.3, 9.3, 9.3, 9.8, 10), tip.label = c("Struthionidae", -"Rheidae", "Casuariidae", "Apterygidae", "Tinamidae", "Cracidae", -"Megapodiidae", "Phasianidae", "Numididae", "Odontophoridae", -"Anhimidae", "Anseranatidae", "Dendrocygnidae", "Anatidae", "Turnicidae", -"Indicatoridae", "Picidae", "Megalaimidae", "Lybiidae", "Ramphastidae", -"Galbulidae", "Bucconidae", "Bucerotidae", "Bucorvidae", "Upupidae", -"Phoeniculidae", "Rhinopomastidae", "Trogonidae", "Coraciidae", -"Leptosomidae", "Meropidae", "Momotidae", "Todidae", "Alcedinidae", -"Dacelonidae", "Cerylidae", "Coliidae", "Cuculidae", "Centropidae", -"Coccyzidae", "Opisthocomidae", "Crotophagidae", "Neomorphidae", -"Psittacidae", "Apodidae", "Hemiprocnidae", "Trochilidae", "Musophagidae", -"Tytonidae", "Strigidae", "Aegothelidae", "Podargidae", "Batrachostomidae", -"Steatornithidae", "Nyctibiidae", "Eurostopodidae", "Caprimulgidae", -"Columbidae", "Eurypygidae", "Otididae", "Gruidae", "Heliornithidae", -"Psophiidae", "Cariamidae", "Rhynochetidae", "Rallidae", "Pteroclidae", -"Thinocoridae", "Pedionomidae", "Scolopacidae", "Rostratulidae", -"Jacanidae", "Chionididae", "Burhinidae", "Charadriidae", "Glareolidae", -"Laridae", "Accipitridae", "Sagittariidae", "Falconidae", "Podicipedidae", -"Phaethontidae", "Sulidae", "Anhingidae", "Phalacrocoracidae", -"Ardeidae", "Scopidae", "Phoenicopteridae", "Threskiornithidae", -"Pelecanidae", "Ciconiidae", "Fregatidae", "Spheniscidae", "Gaviidae", -"Procellariidae", "Acanthisittidae", "Pittidae", "Eurylaimidae", -"Tyrannidae", "Thamnophilidae", "Furnariidae", "Formicariidae", -"Conopophagidae", "Rhinocryptidae", "Climacteridae", "Menuridae", -"Ptilonorhynchidae", "Maluridae", "Meliphagidae", "Pardalotidae", -"Eopsaltriidae", "Irenidae", "Orthonychidae", "Pomatostomidae", -"Laniidae", "Vireonidae", "Corvidae", "Bombycillidae", "Cinclidae", -"Muscicapidae", "Sturnidae", "Sittidae", "Certhiidae", "Paridae", -"Aegithalidae", "Hirundinidae", "Regulidae", "Pycnonotidae", -"Cisticolidae", "Zosteropidae", "Sylviidae", "Alaudidae", "Nectariniidae", -"Melanocharitidae", "Paramythiidae", "Passeridae", "Fringillidae" -), Nnode = 135), .Names = c("edge", "edge.length", "tip.label", -"Nnode"), class = "phylo") +require(ape, quietly = TRUE, save = FALSE) +bird.families <- read.tree("bird.families.tre") diff --git a/data/bird.orders.R b/data/bird.orders.R index 73740d9..f1640e1 100644 --- a/data/bird.orders.R +++ b/data/bird.orders.R @@ -1,19 +1,2 @@ -"bird.orders" <- -structure(list(edge = structure(c(24, 25, 26, 26, 25, 27, 28, -28, 27, 24, 29, 29, 30, 30, 31, 32, 32, 33, 34, 34, 33, 35, 35, -31, 36, 36, 37, 37, 38, 38, 39, 40, 41, 41, 40, 42, 42, 39, 43, -44, 44, 45, 45, 43, 25, 26, 1, 2, 27, 28, 3, 4, 5, 29, 6, 30, -7, 31, 32, 8, 33, 34, 9, 10, 35, 11, 12, 36, 13, 37, 14, 38, -15, 39, 40, 41, 16, 17, 42, 18, 19, 43, 44, 20, 45, 21, 22, 23 -), .Dim = c(44, 2)), edge.length = c(2.1, 4.1, 21.8, 21.8, 3, -1.3, 21.6, 21.6, 22.9, 1, 27, 0.7, 26.3, 1.3, 0.6, 24.4, 1, 2.6, -20.8, 20.8, 1.3, 22.1, 22.1, 0.5, 24.5, 0.8, 23.7, 0.6, 23.1, -0.6, 0.6, 0.6, 21.3, 21.3, 1.5, 20.4, 20.4, 0.9, 0.8, 20.8, 0.7, -20.1, 20.1, 21.6), tip.label = c("Struthioniformes", "Tinamiformes", -"Craciformes", "Galliformes", "Anseriformes", "Turniciformes", -"Piciformes", "Galbuliformes", "Bucerotiformes", "Upupiformes", -"Trogoniformes", "Coraciiformes", "Coliiformes", "Cuculiformes", -"Psittaciformes", "Apodiformes", "Trochiliformes", "Musophagiformes", -"Strigiformes", "Columbiformes", "Gruiformes", "Ciconiiformes", -"Passeriformes"), Nnode = 22), .Names = c("edge", "edge.length", -"tip.label", "Nnode"), class = "phylo") +require(ape, quietly = TRUE, save = FALSE) +bird.orders <- read.tree("bird.orders.tre") diff --git a/data/chiroptera.rda b/data/chiroptera.rda index 4842feb..ff55345 100644 Binary files a/data/chiroptera.rda and b/data/chiroptera.rda differ diff --git a/man/rtree.Rd b/man/rtree.Rd index 264ba5d..48401b5 100644 --- a/man/rtree.Rd +++ b/man/rtree.Rd @@ -14,8 +14,8 @@ rmtree(N, n, rooted = TRUE, tip.label = NULL, br = runif, ...) (the default).} \item{tip.label}{a character vector giving the tip labels; if not specified, the tips "t1", "t2", ..., are given.} - \item{br}{either an R function used to generate the branch lengths - (\code{rtree} or \code{NULL} to give no branch lengths) or the + \item{br}{an R function used to generate the branch lengths + (\code{rtree}; use \code{NULL} to simulate only a topology), or the coalescence times (\code{rcoal}). For the latter, a genuine coalescent tree is simulated by default.} \item{...}{further argument(s) to be passed to \code{br}.}