plotAnimatedPPGMMultiPhylo: plotAnimatedPPGMMultiPhylo

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

plotAnimatedPPGMMultiPhylo

Description

This function creates an animated gif showing the change in modeled suitable habitat through time in geographic space. It requires ImageMagick or GraphicsMagick to be previously installed in the operating system. This is easy to do if you have macports. Just type sudo port install ImageMagick into terminal.

Usage

plotAnimatedPPGMMultiPhylo(envelope, tree, filename="ppgm.gif", 
which.biovars, path="", use.paleoclimate=TRUE, paleoclimateUser=NULL)

Arguments

envelope	the min and max envelope of each lineage for each time slice
tree	the phylogeny or multiple phylogenies that show the relationship between species
filename	filename of output
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()).

Details

Animated gif of species richness through time

Author(s)

A. Michelle Lawing, Alexandra F. C. Howard

Examples

data(sampletrees)
data(occurrences)
sampletrees <- sample(sampletrees,5)
biooccu <- getBioclimVars(occurrences, which.biovars=1)
sp_data_min<- tapply(biooccu[,4],biooccu$Species,min)
sp_data_max<- tapply(biooccu[,4],biooccu$Species,max)
treedata_min <- treedata_max <- node_est <- envelope <- list()
## Not run: for (tr in 1:length(sampletrees)){
  treedata_min[[tr]] <- geiger::treedata(sampletrees[[tr]],sp_data_min,sort=TRUE,warnings=F)
  treedata_max[[tr]] <- geiger::treedata(sampletrees[[tr]],sp_data_max,sort=TRUE,warnings=F)
  full_est <- nodeEstimateEnvelopes(treedata_min[[tr]],treedata_max[[tr]])
  node_est[[tr]] <- full_est$est
  envelope[[tr]] <- getEnvelopes(treedata_min[[tr]], treedata_max[[tr]], node_est[[tr]])
}
animatedplot <- plotAnimatedPPGMMultiPhylo(envelope,sampletrees,which.biovars=1, path=tempdir())
## End(Not run)

michellelawing/ppgm documentation built on April 24, 2024, 10:17 p.m.