plotGeoRates: plotGeoRates

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

plotGeoRates

Description

plotGeoRates

Usage

plotGeoRates(geo_center, geo_size, time_int, trees, path="")

Arguments

geo_center	change in geographic center of suitable climate envelope, see
geo_size	change in geographic size of suitable climate envelope
time_int	time intervals to plot
trees	distribution of phylogenies
path	path to the directory where the results to be saved

Details

Creates plot with gray background of all pairwise comparisons of change in geo center and area through time. Blue points on top show the sequential change in geo center and expansion/contraction for all lineages

Value

plots of geo rate

Author(s)

A. Michelle Lawing, Alexandra F. C. Howard

See Also

getGeoRates

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()
geo_center<-array(NA,dim=c(100,53,21,21))
geo_size<-array(NA,dim=c(100,53,21,21))
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$est
  envelope[[tr]] <- getEnvelopes(treedata_min[[tr]], treedata_max[[tr]], node_est[[tr]])
  temp <- getGeoRate(envelope[[tr]], sampletrees[[tr]], which.biovars=1)
  geo_center[tr,,,]<-temp$geo_center
  geo_size[tr,,,]<-temp$geo_size
}

## Not run: plotGeoRates(geo_center, geo_size, temp$time_int, sampletrees, path="tempdir()")

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