plotGeoRates: plotGeoRates

Description

plotGeoRates

Usage

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

Value

plots of geo rate

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

Author

A. Michelle Lawing, Alexandra F. C. Howard

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

Examples

Run this code

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
}

if (FALSE) plotGeoRates(geo_center, geo_size, temp$time_int, sampletrees, path="tempdir()")

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