[Mattice-commits] r89 - in pkg: DATA man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 17 16:30:23 CET 2008
Author: andrew_hipp
Date: 2008-12-17 16:30:23 +0100 (Wed, 17 Dec 2008)
New Revision: 89
Added:
pkg/DATA/carex
pkg/man/carex.Rd
Log:
data set fixed up (carex) and documentation added
Added: pkg/DATA/carex
===================================================================
--- pkg/DATA/carex (rev 0)
+++ pkg/DATA/carex 2008-12-17 15:30:23 UTC (rev 89)
@@ -0,0 +1,108 @@
+structure(list(tree = structure(list(edge = structure(c(54L,
+55L, 55L, 56L, 56L, 54L, 57L, 58L, 58L, 59L, 59L, 57L, 60L, 61L,
+62L, 63L, 63L, 64L, 64L, 62L, 61L, 65L, 65L, 60L, 66L, 67L, 67L,
+66L, 68L, 68L, 69L, 70L, 71L, 72L, 73L, 73L, 74L, 75L, 75L, 74L,
+76L, 76L, 77L, 77L, 72L, 78L, 79L, 79L, 80L, 80L, 81L, 81L, 82L,
+82L, 83L, 83L, 78L, 84L, 85L, 86L, 86L, 85L, 87L, 88L, 88L, 89L,
+90L, 90L, 89L, 91L, 91L, 87L, 92L, 92L, 93L, 93L, 84L, 94L, 94L,
+71L, 95L, 95L, 70L, 96L, 97L, 98L, 98L, 97L, 99L, 99L, 100L,
+101L, 101L, 100L, 102L, 102L, 96L, 103L, 103L, 104L, 104L, 69L,
+105L, 105L, 55L, 1L, 56L, 2L, 3L, 57L, 58L, 4L, 59L, 5L, 6L,
+60L, 61L, 62L, 63L, 7L, 64L, 8L, 9L, 10L, 65L, 11L, 12L, 66L,
+67L, 13L, 14L, 68L, 15L, 69L, 70L, 71L, 72L, 73L, 16L, 74L, 75L,
+17L, 18L, 76L, 19L, 77L, 20L, 21L, 78L, 79L, 22L, 80L, 23L, 81L,
+24L, 82L, 25L, 83L, 26L, 27L, 84L, 85L, 86L, 28L, 29L, 87L, 88L,
+30L, 89L, 90L, 31L, 32L, 91L, 33L, 34L, 92L, 35L, 93L, 36L, 37L,
+94L, 38L, 39L, 95L, 40L, 41L, 96L, 97L, 98L, 42L, 43L, 99L, 44L,
+100L, 101L, 45L, 46L, 102L, 47L, 48L, 103L, 49L, 104L, 50L, 51L,
+105L, 52L, 53L), .Dim = c(104L, 2L)), edge.length = c(0.131608041,
+0.868391959, 0.4774298606, 0.3909620984, 0.3909620984, 0.0376523746,
+0.0915148608, 0.8708327646, 0.228673604, 0.6421591606, 0.6421591606,
+0.03047094, 0.197188661, 0.3667080933, 0.1187924864, 0.2491874447,
+0.0680851795, 0.1811022651, 0.1811022651, 0.3679799311, 0.2879776585,
+0.4467103659, 0.4467103659, 0.0760667065, 0.2546030817, 0.6012068973,
+0.6012068973, 0.0734898564, 0.7823201225, 0.0354531643, 0.0805067273,
+0.1044180282, 0.1470105274, 0.0657037966, 0.3492278788, 0.119097461,
+0.0354160188, 0.194714399, 0.194714399, 0.0351340264, 0.1949963914,
+0.0734473345, 0.1215490569, 0.1215490569, 0.0370307146, 0.0478702765,
+0.3300306842, 0.1023596238, 0.2276710604, 0.0531080597, 0.1745630008,
+0.0755096136, 0.0990533872, 0.0744081089, 0.0246452783, 0.0246452783,
+0.0339921757, 0.0610205014, 0.1472200431, 0.1356682405, 0.1356682405,
+0.055626089, 0.053885115, 0.1733770795, 0.0401682819, 0.0513531937,
+0.0818556039, 0.0818556039, 0.0352913046, 0.0979174931, 0.0979174931,
+0.0400989858, 0.1871632087, 0.0547825691, 0.1323806396, 0.1323806396,
+0.0591487349, 0.2847600501, 0.2847600501, 0.0421214255, 0.5198207772,
+0.5198207772, 0.0696998161, 0.2044319398, 0.1668478906, 0.2253805845,
+0.2253805845, 0.0732033467, 0.3190251283, 0.1229909423, 0.1015139286,
+0.0945202574, 0.0945202574, 0.034953098, 0.161081088, 0.161081088,
+0.1165220723, 0.4801383425, 0.3700801096, 0.1100582329, 0.1100582329,
+0.0946612554, 0.6522057028, 0.6522057028), Nnode = 52L, tip.label = c("argyrantha",
+"preslii", "phaeocephala", "bohemica", "foenea", "praticola",
+"ebenea", "haydeniana", "microptera", "peucophila", "integra",
+"subfusca", "macloviana", "pachystachya", "adusta", "cumulata",
+"hyalina", "brevior", "reniformis", "molestiformis", "shinnersii",
+"opaca", "crawfordii", "bebbii", "cristatella", "projecta", "tribuloidesVtribuloides",
+"buffaloriver", "teneraVechinodes", "missouriensis", "teneraVtenera",
+"tincta", "festucacea", "oronensis", "muskingumensis", "bicknellii",
+"merrittfernaldii", "molesta", "normalis", "ovalis3098", "feta",
+"longii", "vexans", "alata", "scopariaVscoparia", "scopariaVtessellata",
+"albolutescens", "suberecta", "ozarkana", "hormathodes", "straminea",
+"xerantica", "athrostachya")), .Names = c("edge", "edge.length",
+"Nnode", "tip.label"), class = "phylo", origin = "bayes.tre"),
+ dat = structure(c(4.382026635, 4.369447852, 4.430816799,
+ 4.382026635, 4.414856779, 4.336767728, 4.430816799, 4.406719247,
+ 4.384274107, 4.304065093, 4.406719247, 4.430816799, 4.454347296,
+ 4.363862664, 4.356708827, 4.048824047, 4.304065093, 4.085976313,
+ 4.382026635, 4.272630208, 4.099829492, 4.201703081, 4.222151267,
+ 4.229312423, 4.248495242, 4.158883083, 4.25561271, 4.248495242,
+ 4.335982696, 3.947003974, 3.999117712, 4.317488114, 4.243769809,
+ 4.304065093, 4.382026635, 4.33073334, 4.276666119, 4.227855121,
+ 4.236133434, 4.175770928, 4.189654742, 4.107589789, 4.237723145,
+ 4.304065093, 4.159976236, 4.219507705, 4.189654742, 4.276666119,
+ 4.077537444, 4.304065093, 4.304065093, 4.219507705, 4.219507705
+ ), .Names = c("argyrantha", "preslii", "phaeocephala", "bohemica",
+ "foenea", "praticola", "ebenea", "haydeniana", "microptera",
+ "peucophila", "integra", "subfusca", "macloviana", "pachystachya",
+ "adusta", "cumulata", "hyalina", "brevior", "reniformis",
+ "molestiformis", "shinnersii", "opaca", "crawfordii", "bebbii",
+ "cristatella", "projecta", "tribuloidesVtribuloides", "buffaloriver",
+ "teneraVechinodes", "missouriensis", "teneraVtenera", "tincta",
+ "festucacea", "oronensis", "muskingumensis", "bicknellii",
+ "merrittfernaldii", "molesta", "normalis", "ovalis3098",
+ "feta", "longii", "vexans", "alata", "scopariaVscoparia",
+ "scopariaVtessellata", "albolutescens", "suberecta", "ozarkana",
+ "hormathodes", "straminea", "xerantica", "athrostachya")),
+ nodes = list(c("alata", "albolutescens", "bebbii", "bicknellii",
+ "brevior", "buffaloriver", "crawfordii", "cristatella", "cumulata",
+ "festucacea", "feta", "hormathodes", "hyalina", "longii",
+ "merrittfernaldii", "missouriensis", "molesta", "molestiformis",
+ "muskingumensis", "normalis", "opaca", "oronensis", "ovalis3098",
+ "ozarkana", "projecta", "reniformis", "scopariaVscoparia",
+ "scopariaVtessellata", "shinnersii", "straminea", "suberecta",
+ "teneraVechinodes", "teneraVtenera", "tincta", "tribuloidesVtribuloides",
+ "vexans", "adusta", "athrostachya", "pachystachya", "xerantica",
+ "macloviana"), c("alata", "albolutescens", "bebbii", "bicknellii",
+ "brevior", "buffaloriver", "crawfordii", "cristatella", "cumulata",
+ "festucacea", "feta", "hormathodes", "hyalina", "longii",
+ "merrittfernaldii", "missouriensis", "molesta", "molestiformis",
+ "muskingumensis", "normalis", "opaca", "oronensis", "ovalis3098",
+ "ozarkana", "projecta", "reniformis", "scopariaVscoparia",
+ "scopariaVtessellata", "shinnersii", "straminea", "suberecta",
+ "teneraVechinodes", "teneraVtenera", "tincta", "tribuloidesVtribuloides",
+ "vexans"), c("bebbii", "bicknellii", "brevior", "buffaloriver",
+ "crawfordii", "cristatella", "cumulata", "festucacea", "hyalina",
+ "merrittfernaldii", "missouriensis", "molesta", "molestiformis",
+ "muskingumensis", "normalis", "opaca", "oronensis", "projecta",
+ "reniformis", "shinnersii", "teneraVechinodes", "teneraVtenera",
+ "tincta", "tribuloidesVtribuloides", "feta", "ovalis3098"
+ ), c("bebbii", "bicknellii", "brevior", "buffaloriver", "crawfordii",
+ "cristatella", "cumulata", "festucacea", "hyalina", "merrittfernaldii",
+ "missouriensis", "molesta", "molestiformis", "muskingumensis",
+ "normalis", "opaca", "oronensis", "projecta", "reniformis",
+ "shinnersii", "teneraVechinodes", "teneraVtenera", "tincta",
+ "tribuloidesVtribuloides"), c("brevior", "hyalina", "molestiformis",
+ "reniformis", "shinnersii"), c("suberecta", "albolutescens",
+ "scopariaVscoparia", "scopariaVtessellata", "alata", "vexans",
+ "longii"), c("subfusca", "integra", "peucophila", "microptera",
+ "haydeniana", "ebenea"), c("phaeocephala", "preslii", "argyrantha"
+ ))), .Names = c("tree", "dat", "nodes"))
Added: pkg/man/carex.Rd
===================================================================
--- pkg/man/carex.Rd (rev 0)
+++ pkg/man/carex.Rd 2008-12-17 15:30:23 UTC (rev 89)
@@ -0,0 +1,56 @@
+\name{carex}
+\alias{carex}
+\docType{data}
+\title{Carex section Ovales tree, chromosome data, and nodes}
+\description{
+ This is the Carex dataset used in Hipp (2007). It is a list with three items: a tree of 53 taxa for which chromosome
+ counts are known; a vector of log-transformed mean chromosome counts for all taxa; and a list of eight taxon vectors.
+}
+\usage{data(carex)}
+\format{
+ A list with three items:
+ \describe{
+ \item{tree} An ultrametric tree in \code{phylo} format with 53 tips
+ \item{dat} A named numeric vector of log-transformed mean chromosome counts for all 53 taxa
+ \item{nodes} A list of eight taxon vectors defining the eight nodes studied.
+ }
+}
+\details{
+ \item{phylogeny}{
+ Phylogeny (\code{tree}) was estimated for approximately 80 species (Hipp 2006), branch lengths optimized using penalized likelihood
+ in \code{ape}, and then the tree was pruned down to only those taxa for which chromosome counts were available.
+ }
+ \item{chromosome counts}{
+ Chromosome counts (\code{dat}) were averaged by population, and the means log-transformed for analysis.
+ }
+ \item{nodes}{
+ Eight nodes were selected for analysis based on clade support and number of taxa in the clade.
+ }
+}
+\source{
+ Hipp, A.L. (2007)
+ Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae).
+ Evolution 61:2175-2194.
+}
+\references{
+ Hipp, A.L., P.E. Rothrock, A.A. Reznicek, and J.A. Weber (2006)
+ Phylogeny and classification of Carex section Ovales (Cyperaceae).
+ International Journal of Plant Sciences 167:1029-1048.
+
+ Hipp, A.L. (2007)
+ Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae).
+ Evolution 61:2175-2194.
+}
+
+\examples{
+ data(carex)
+ carex$tree <- ape2ouch(carex$tree) # tree comes in in \code{phylo} format, but we need an \code{ouchtree} object
+ attach(carex)
+ trial <- runBatchHansen(tree, dat, nodes, maxNodes = 3) # for expedience, only allows regime changes at up to 3 nodes
+ summary(trial)
+ trialSim <- ouSim(trial, tree) # simulates the evolution of the chromosome number under the model-averaged values
+ plot(trialSim) # plots the character simulation, with all branches black
+ plot(trialSim, colors = paintBranches(nodes, tree)) # plots the character simulation, with branch colors changing at all 8 nodes
+ plot(trialSim, colors = paintBranches(list(nodes[[2]]), tree)) # plots the character simulation, with branch colors changing only at node 2
+}
+\author{Andrew L. Hipp <ahipp at mortonarb.org>}
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