smooth_rec: Smooth character table values resulted from ancestral...

In nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty

Smooth character table values resulted from ancestral character state reconstructions

Description

Smooth character table values resulted from ancestral character state reconstructions

Usage

smooth_rec(whole_rec_table)

Arguments

whole_rec_table

matrix containing all reconstructed characters for all tips and nodes. It results from using the functions bin_par_rec or bin_ml_rec.

Value

The matrix of reconstructed characters with smoothed values.

Examples

# a simple tree
data("tree5", package = "nichevol")

# simple matrix of data
dataTable <- cbind("241" = rep("1", length(tree5$tip.label)),
                   "242" = rep("1", length(tree5$tip.label)),
                   "243" = c("1", "1", "0", "0", "0"),
                   "244" = c("1", "1", "0", "0", "0"),
                   "245" = c("1", "?", "0", "0", "0"))
rownames(dataTable) <- tree5$tip.label
treeWdata <- geiger::treedata(tree5, dataTable)

# ancestral reconstruction
parsimonyReconstruction <- bin_par_rec(treeWdata)

# smoothing reconstructions
smooth_rec(parsimonyReconstruction)

nichevol documentation built on March 31, 2023, 5:38 p.m.