plotTraitGramMultiPhylo {ppgm} | R Documentation |
plotTraitGramMultiPhylo
Description
Combine the node estimates based on random or specified fossil placement and plot them on a phylotrait gram in a specified directory.
Usage
plotTraitGramMultiPhylo(treedata_min, treedata_max, node_est,
fossils=FALSE, use.paleoclimate=TRUE, paleoclimateUser=NULL,
layerAge=c(0:20), which.biovars, path="")
Arguments
treedata_min |
tree data object with min estimate of the climate envelope |
treedata_max |
tree data object with max estimate of the climate envelope |
node_est |
the estimate of all the nodes, both min and max. Must be in format [[trees]][[permut]][2,species,trait] |
fossils |
a matrix with four columns of min age, max age, longitude, and latitude, in that order, and rows that are entries for fossil occurrences. |
use.paleoclimate |
if left blank, default North America paleoclimate data is used. If FALSE, user submitted paleoclimate must be provided |
paleoclimateUser |
list of data frames with paleoclimates, must be dataframes with columns: GlobalID, Longitude, Latitude, bio1, bio2,...,bio19. (see |
layerAge |
vector with the ages of the paleoclimate dataframes, if using user submitted paleoclimate data |
which.biovars |
A vector of the numbers of the bioclimate variables that should be returned. The bioclimate variables number correspond to the Hijmans table at (https://www.worldclim.org/data/bioclim.html). |
path |
path to the directory where the results should be saved |
Details
plots a traitgram over multiple phylogenetic trees
Value
a trait gram for minimum and maximum of biovariables over a distribution of phylogenetic trees
Author(s)
A. Michelle Lawing, Alexandra F. C. Howard
See Also
plotTraitGram
Examples
data(sampletrees)
data(occurrences)
bounds <- list(sigsq = c(min = 0, max = 1000000))
sample <-sample(sampletrees,5)
test_ppgm <- ppgm(occurrences = occurrences,trees = sample,
model = "BM", which.biovars = c(1), bounds = bounds,
control = list(niter = 20))
## Not run: plotTraitGramMultiPhylo(test_ppgm$treedata_min,
test_ppgm$treedata_max,test_ppgm$node_est)
## End(Not run)