convertTreeData
converts a phylo
-formatted tree and a data frame into formats ready to be analyzed with the ouch
functions called by surface
. convertBack
converts an ouchtree
to a data frame including regime information, and is called internally by surfaceTreePlot
. nameNodes
adds unique node labels to a phylo
tree to ensure reliable conversion between formats
convertTreeData(tree, dat)
convertBack(tree, otree, regshifts)
nameNodes(tree)
convertTreeData
returns a list with components otree
(a phylogenetic tree in ouchtree
format) and odata
(a data frame containing trait data, with rownames corresponding to otree@labels
). convertBack
returns a data frame containing original phenotypic data as well as regime assignments of tip taxa. nameNodes
returns the input tree, with arbitrary node names added (zzz1
, zzz2
, etc) to ensure reliable conversion between formats
Phylogenetic tree in phylo
format: to ensure reliable conversion, should have node labels (e.g. using nameNodes
)
Data frame with row names corresponding to the taxa in tree
and columns consisting of one or more trait measurements
Phylogenetic tree in ouchtree
format
Named character vector of regime shifts indicating branches containing shifts (numbered corresponding to otree@nodes
) and regime identities (usually lower-case letters)
Travis Ingram
Ingram, T. & Mahler, D.L. (2013) SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise AIC. Methods in Ecology and Evolution 4: 416-425.
surfaceBackward
, surfaceForward
, surfaceTreePlot
data(surfaceDemo)
tree<-surfaceDemo$tree
dat<-surfaceDemo$sim$dat
olist<-convertTreeData(tree,dat)
Run the code above in your browser using DataLab