plotTraitGram: plotTraitGram

In michellelawing/ppgm: PaleoPhyloGeographic Modeling of Climate Niches and Species Distributions

plotTraitGram

Description

Combine the node estimates based on random or specified fossil placement and plot them on a phylotraitgram in a specified directory.

Usage

plotTraitGram(treedata_min, treedata_max, node_est, fossils=FALSE, 
which.biovars, path="", use.paleoclimate=TRUE, paleoclimateUser=NULL,
layerAge=c(0:20))

Arguments

treedata_min	a tree data object with the min estimate of the climate envelope
treedata_max	a tree data object with the max estimate of the climate envelope
node_est	the estimate of all the nodes, both min and max
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.
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
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 getBioclimvars()).
layerAge	vector with the ages of the paleoclimate dataframes, if using user submitted paleoclimate data

Value

a trait gram for minimum and maximum of biovariables

Author(s)

A. Michelle Lawing, Alexandra F. C. Howard

See Also

plotTraitGramMultiPhylo

Examples

data(sampletrees)
data(occurrences)
bounds <- list(sigsq = c(min = 0, max = 1000000))
ex_mytree <- sampletrees[[3]] #single tree
test_con <- ppgmConsensus(occurrences = occurrences, trees = ex_mytree, 
which.biovars = 1, bounds = bounds, control = list(niter = 20))
## Not run: plotTraitGram(test_con$treedata_min,test_con$treedata_max,test_con$node_est)

michellelawing/ppgm documentation built on Dec. 17, 2024, 9:14 p.m.