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.tree
phylo
format with 53 tips
ovales.data
ovales.nodes
ovales.bayesTrees
phylo
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]]))