getGeoRate {ppgm}

getGeoRate

Description

This function calculates the change in suitable habitat through time in geographic space.

Usage

getGeoRate(envelope, tree, which.biovars, use.paleoclimate=TRUE, 
paleoclimateUser=NULL, layerAge=c(0:20))

Arguments

envelope

the min and max climate envelope of each lineage for each time slice, as outputted by getEnvelopes()

tree

the phylogeny of all species. An object of class phylo

which.biovars

a vector of the numbers of the bioclimate variables to be included. The bioclimate variables number correspond to the table at (https://www.worldclim.org/data/bioclim.html).

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

Details

Calculates rate of geographic change of all lineages. Outputs both the geographic center change, and the geographic size change.

Value

geo_center change in geographic center of suitable climate envelope

geo_size change in geographic size of suitable climate envelope

time_int time intervals

Author(s)

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

See Also

getEnvelopes()

Examples

data(sampletrees)
data(occurrences)
data(paleoclimate)
tree <- sampletrees[[25]]
occu <- getBioclimVars(occurrences, which.biovars=1)
sp_data_min<- tapply(occu[,4],occu$Species,min)
sp_data_max<- tapply(occu[,4],occu$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)
full_est <- nodeEstimateEnvelopes(treedata_min,treedata_max)
node_est <- full_est$est
example_getEnvelopes <- getEnvelopes(treedata_min, treedata_max, node_est)
example_getGeoRate <- getGeoRate(example_getEnvelopes, tree, which.biovars=1)