ppgmMESS: ppgmMESS

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

ppgmMESS

Description

This creates a MESS map for given time slices, climate envelopes, and paleoclimate models.

Usage

ppgmMESS(cem_min, cem_max, est, tree, fossils=NULL, timeslice, 
which.biovars, path = "", use.paleoclimate=TRUE, paleoclimateUser = NULL, 
layerAge=c(0:20), which.plot = c("all","mess","none"))

Arguments

cem_min	the cem min output from the ppgm function. cbind() if there are multiple variables.
cem_max	the cem max output from the ppgm function. cbind() if there are multiple variables.
est	the node_est output from the ppgm function, in list format. [tree][1][min and max][no.of species]
tree	the phylogeny or multiple phylogenies that show the relationship between species
fossils	a matrix with four columns of age to the closest million year integer, longitude, and latitude, in that order, and rows that are entries for fossil occurrences.
timeslice	the time in million of years ago to project MESS maps (0 to 20). can handle single timeslice or vector of times.
which.biovars	the biovariable number(s) between 1 and 19.
path	directory where plots should be stored
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.
layerAge	vector with the ages of the paleoclimate dataframes, if using user submitted paleoclimate data
which.plot	"all" plots trait maps and MESS, "mess" plots MESS map, "none" does not plot

Details

plots MESS maps of climate envelope model for specific time slices. Can either plot individual biovariables, or combined.

Value

list containing array of MESS scores for bioclimatic variables

Author(s)

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

See Also

ppgm()

Examples

data(sampletrees)
data(occurrences)
sampletrees <- sample(sampletrees,5)
bounds <- list(sigsq = c(min = 0, max = 1000000))
test_ppgm <- ppgm(occurrences = occurrences,trees = sampletrees, 
model = "BM", which.biovars = c(1,4,15), bounds = bounds, 
control = list(niter = 20))
#extract min climate envelope for species
cem_min <- cbind(test_ppgm$cem[, 1], test_ppgm$cem[, 2], test_ppgm$cem[, 3])
cem_max <- cbind(test_ppgm$cem[, 7], test_ppgm$cem[, 8], test_ppgm$cem[, 9])
rownames(cem_min) <- rownames(cem_max) <- rownames(test_ppgm$cem)
mess <- ppgmMESS(cem_min,cem_max,test_ppgm$node_est,tree=sampletrees,timeslice=10,
which.biovars=c(1,4,15), path=tempdir(), which.plot="none")

michellelawing/ppgm documentation built on Dec. 17, 2024, 9:14 p.m.