| carex {maticce} | R Documentation |
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.
data(carex)
A list with four items:
ovales.treephylo format with 53 tips
ovales.dataovales.nodesovales.bayesTreesphylo format, subsampled from the MCMC analysis underlying
carex$ovales.bayesTrees.
Phylogeny (ovales.tree) was estimated for approximately 80 species (Hipp 2006), branch lengths optimized using
penalized likelihood in ape, and then the tree was pruned down to only those taxa for which chromosome counts were
available. Chromosome counts (ovales.data) were averaged by population, and the means log-transformed for
analysis. Nodes were selected for analysis based on clade support and number of taxa in the clade.
Andrew L. Hipp <ahipp@mortonarb.org>
Hipp, A.L. (2007) Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae). Evolution 61:2175-2194.
Hipp, A.L., P.E. Rothrock, A.A. Reznicek, and J.A. Weber (2006) Phylogeny and classification of Carex section Ovales (Cyperaceae). International Journal of Plant Sciences 167:1029-1048.
Hipp, A.L. (2007) Non-uniform processes of chromosome evolution in sedges (Carex: Cyperaceae). Evolution 61:2175-2194.
data(carex) # tree comes in in phylo format, but we need an ouchtree object trees <- lapply(carex$ovales.bayesTrees[1:10], ape2ouch) # for expedience, only tests for changes at up to 2 of the first 4 nodes on 10 trees visited in the MCMC phylogenetic analysis trialBayesTrees <- runBatchHansen(trees, carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2) summary(trialBayesTrees) # summarizes results using summary.hansenBatch and displays the results using print.hansenSummary # same analysis as above, but on a single tree trialBayesConsensus <- runBatchHansen(ape2ouch(carex$ovales.tree), carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2) # compares five different models of character change at node 2 multiModel(carex$ovales.tree, carex$ovales.data, carex$ovales.nodes[[2]]) # simulates the evolution of the chromosome number under the model-averaged values trialSim <- ouSim(trialBayesConsensus, ape2ouch(carex$ovales.tree)) # plots the character simulation, with all branches black plot(trialSim) # plots the character simulation, with branch colors changing at all 8 nodes plot(trialSim, colors = paintBranches(carex$ovales.nodes[1:4], trees[[1]])) # plots the character simulation, with branch colors changing only at node 2 plot(trialSim, colors = paintBranches(list(carex$ovales.nodes[[2]]), trees[[1]]))