plotAnimatedPPGM: plotAnimatedPPGM

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

plotAnimatedPPGM

Description

This function creates an animated gif showing the change in modelled suitable habitat through time in geographic space.

Usage

plotAnimatedPPGM(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	desired 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

Requires ImageMagick or GraphicsMagick to be installed on the operating system. This is easy to do if you have macports. Just type sudo port install ImageMagick into terminal.

Value

An animated gif of species through time

Author(s)

A. Michelle Lawing, Alexandra F. C. Howard, Maria-Aleja Hurtado-Materon

Examples

data(sampletrees)
data(occurrences)
tree <- sampletrees[[25]]
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 <- geiger::treedata(tree,sp_data_min,sort=TRUE,warnings=F)
treedata_max <- geiger::treedata(tree,sp_data_max,sort=TRUE,warnings=F)
## Not run: full_est <- nodeEstimateEnvelopes(treedata_min,treedata_max)
node_est <- full_est$est
example_getEnvelopes <- getEnvelopes(treedata_min, treedata_max, node_est)
animatedplot <- plotAnimatedPPGM(example_getEnvelopes,tree,which.biovars=1,path=tempdir())
## End(Not run)

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