score_tree: Helper function to assign bin scores to every tip in a given...

In nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty

Helper function to assign bin scores to every tip in a given tree

Description

Helper function to assign bin scores to every tip in a given tree

Usage

score_tree(tree_data, include_unknown = FALSE)

Arguments

tree_data	a list of two elements (phy and data) resulting from using the function treedata.
include_unknown	(logical) whether or not there are unknown tips.

Value

a list of two elements (phy and data). Data is the median bin scored as present or present + unknown.

Examples

# Simulate data table
dataTable <- cbind("241" = rep("1", 5),
                   "242" = rep("1", 5),
                   "243" = c("1", "1", "0", "0", "0"),
                   "244" = c("1", "1", "0", "0", "0"),
                   "245" = c("1", "?", "0", "0", "0"))
rownames(dataTable) <- c("GadusMorhua", "GadusMacrocephalus",
                         "GadusChalcogrammus", "ArctogadusGlacials",
                         "BoreogadusSaida")

# a simple tree
data("tree5", package = "nichevol")
tree5$tip.label <- c("GadusMorhua", "GadusMacrocephalus",
                     "GadusChalcogrammus", "ArctogadusGlacials",
                     "BoreogadusSaida")

# Unite data
treeWithData <- geiger::treedata(tree5, dataTable)

# Get a new tree with tips scored from median bin scores
score_tree(treeWithData, include_unknown = TRUE)

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