nodeEstimateEnvelopes: nodeEstimateEnvelopes

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

nodeEstimateEnvelopes

Description

This function estimates nodes with the 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())

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	the estimate of the climate envelope of the 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().

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)
data(scel_fossils)
occu <- getBioclimVars(occurrences, which.biovars=1)
sp_data_min<- tapply(occu[,4],occu$Species,min)
sp_data_max<- tapply(occu[,4],occu$Species,max)
ex_min <- geiger::treedata(sampletrees[[1]], sp_data_min)
ex_max <- geiger::treedata(sampletrees[[1]], sp_data_max)
colnames(ex_min$data)<- colnames(ex_max$data)<-"bio1"  #labels biovars
biofossils <- getBioclimVars(scel_fossils,which.biovars=1)
rownames(biofossils)<-paste("fossil",1:length(biofossils[,1]),sep="")
nodeest<- nodeEstimateEnvelopes(treedata_min=ex_min,treedata_max=ex_max, 
model="BM",fossils=biofossils,
bounds=list(sigsq = c(min = 0, max = 1000000)))

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