ppgm (version 1.1)

plotTraitGram: 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))

Value

a trait gram for minimum and maximum of biovariables

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

Author

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))
if (FALSE) plotTraitGram(test_con$treedata_min,test_con$treedata_max,test_con$node_est)