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 2fe5b8d492ef56e7adbaa934e1a44a729492b162..988dd6f1956c1ff5ea4138980f73348327f6bd73 100644 (file)
--- 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 96c7945a0b8c287b4190bc3c13435d6405f30185..7d0413a0cd7733142072f81a29e877cf222930c7 100644 (file)
--- 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 27df856af25c18abac3b0976a1bcc50afc3507fe..a806ea3d9bce2810e12ddb667f20e320dae87a8b 100644 (file)
--- 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 73740d997b6c8505f543150721415eb66b0e888a..f1640e1fb2183e0cbdb31b2168f675036d5a0448 100644 (file)
--- 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 4842feb8c8946276296afc50fc1ec9cdb70148d2..ff55345e4bfdec035ba70fca5335b16f202b5de8 100644 (file)
Binary files a/data/chiroptera.rda and b/data/chiroptera.rda differ

diff --git a/man/rtree.Rd b/man/rtree.Rd
index 264ba5d93e3879b52b31317d81f8b69463cca6ab..48401b5b8341e8a15b439ecbc0a2f599db763319 100644 (file)
--- 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}.}