nodeEstimateEnvelopes {ppgm}

nodeEstimateEnvelopes

Description

This function estimates climate envelopes at nodes with the optional placement of fossils on randomly assigned or specified edges on a tree.

Usage

nodeEstimateEnvelopes(treedata_min, treedata_max, fossils=FALSE, 
fossils.edges=FALSE, model="BM", bounds=list(), control=list(), 
use.paleoclimate = TRUE, paleoclimateUser = NULL, layerAge = c(0:20), 
which.biovars = which.biovars)

Arguments

treedata_min

tree data object with min estimate of the climate envelope – list where first object is phylogeny, and second object is array of species with climate data variables (species must match)

treedata_max

tree data object with max estimate of the climate envelope

fossils

a matrix with three columns of age, longitude, and latitude, in that order, and rows that are entries for fossil occurrences.

fossils.edges

the edge number that the fossil occurs on

model

the model of evolution to use in the ancestral state reconstruction. Options are "estimate", "BM", "OU", "EB", "lambda", "kappa", "delta".

bounds

bounds used for the model, passes to fitContinuous(), uses default if none specified.

control

setting used for optimization of the model likelihood. Passes to fitContinuous().

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

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).

Details

function adds fossils to trees according to addFossil(), then passes to nodeEstimate().

Value

an object of the class "nodeEstimate".

model if model = "estimate", the best fit model of evolution. If the model was specified, then model is the specified model.

est the ancestral node estimates of the continuous character.

phy the phylogeny used for the estimates, which might be transformed depending on the evolutionary model.

BM if model = "BM", returned values from fitContinuous() where the model is "BM"

OU if model = "OU", returned values from fitContinuous() where the model is "OU"

EB if model = "EB", returned values from fitContinuous() where the model is "EB"

lambda if model = "lambda", returned values from fitContinuous() where the model is "lambda"

kappa if model = "kappa", returned values from fitContinuous() where the model is "kappa"

delta if model = "delta", returned values from fitContinuous() where the model is "delta"

fitted if model = "estimate", returned values from the best fit model of evolution.

Author(s)

A. Michelle Lawing, Alexandra F. C. Howard

See Also

nodeEstimate, fitContinuous

Examples

data(sampletrees)
sampletrees <- sample(sampletrees,5)
data(occurrences)
occu <- getBioclimVars(occurrences, which.biovars=c(1,2))
sp_data_min<-sapply(4:5,function(x) tapply(occu[,x],occu$Species,min))
sp_data_max<-sapply(4:5,function(x) tapply(occu[,x],occu$Species,max))
ex_min <- geiger::treedata(sampletrees[[1]], sp_data_min, sort=TRUE)
ex_max <- geiger::treedata(sampletrees[[1]], sp_data_max, sort=TRUE)
colnames(ex_min$data)<- colnames(ex_max$data)<-c("bio1","bio2")  #labels biovars
nodeest<- nodeEstimateEnvelopes(treedata_min=ex_min,treedata_max=ex_max, 
model="BM",which.biovars=c(1,2),
bounds=list(sigsq = c(min = 0, max = 1000000)))