getTimeSlice: getTimeSlice

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

getTimeSlice

Description

This function extracts estimated ancestral reconstructions for continuous characters any time specified along a phylogeny for all lineages present at the specified time.

Usage

getTimeSlice(timeSlice, tree, trait, model = "BM", plot.est = FALSE)

Arguments

timeSlice	single numeric or a vector with the time (or times) to extract the estimated ancestor reconstructions.
tree	an object of the class "phylo" that should be dated
trait	a vector of both tip values and node estimates that correspond to tree
model	if model = "estimate", the best fit model of evolution. If the model was specified, then model is the specified model, passes to geiger::fitContinuous(). Model options currently supported are: "BM", "OU", "EB", "lambda", "kappa", "delta"
plot.est	a conditional stating whether or not to plot the results

Details

The estimated reconstruction relies on an interpolation between node or between tip and node estimates of the trait. This method assumes a constant rate of evolution along the lineage where the interpolation is taking place.

Value

edge for each time specified, a vector of edges that are present during that time are returned

est for each time specified, a vector of estimates of the ancestral reconstruction along each edge

Author(s)

A. Michelle Lawing, Alexandra F. C. Howard

See Also

geiger::fitContinuous(), nodeEstimate()

Examples

data(sampletrees)
data(occurrences)
occurrences <- getBioclimVars(occurrences, which.biovars=1)
sp_data_min<- tapply(occurrences[,4],occurrences$Species,min)
treedata_min <- geiger::treedata(sampletrees[[1]], sp_data_min)
ex_est <- nodeEstimate(treedata_min, 1, model = 'BM') #runs BM model
ex_timeSlice <- getTimeSlice(10,treedata_min$phy,c(treedata_min$data[,1],ex_est$est))

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