SPELT: SPELT function

In nhcooper123/SPELT: Species Pairs Evolutionary Lag Test (SPELT)

Description

The function fits a model of residuals from lag variable contrasts ~ primary variable contrasts against divergence time for each species pair. The optional argument age.limit allows the user to removes species pairs with branches that are longer (i.e. older) than a user defined age limit. The optional argument cut.off allows users to decide how many species pairs they need to trust the analyses (the default is 3).

Usage

SPELT(phy, data, primary.variable, lag.variable, speciesnames, age.limit = NULL,
  warn.dropped = TRUE, cut.off = 3)

Arguments

phy	phylogeny of class 'phylo'
data	dataframe of class 'data.frame'
primary.variable	column name of the variable thought to drive evolution of the lag variable
lag.variable	column name of the variable thought to lag behind the primary variable
speciesnames	column name of the column containing species names
age.limit	maximum age of branches to retain in SPELT. Default = NULL
warn.dropped	If TRUE the function prints a list of species found in the phylogeny but not the data and vice versa. Default = TRUE
cut.off	number of rows that must remain in the data for SPELT to continue. Default = 3

Value

An object of class 'SPELT' which contains the dataframe for SPELT, the summary of the SPELT model, a list of species dropped because they were not in both the phylogeny and data, the primary variable, lag variable, and age limit entered by the user, and the number of cherries.

Examples

data(shorebird, package = "caper")
SPELT.results <- SPELT(shorebird.tree, shorebird.data,
                         "F.Mass", "Egg.Mass", "Species")
summary(SPELT.results)
plot(SPELT.results)
str(SPELT.results$data)

# With an age limit of 10 million years
SPELT.results10MY <- SPELT(shorebird.tree, shorebird.data,
                         "F.Mass", "Egg.Mass", "Species", age.limit = 10)
summary(SPELT.results10MY)
plot(SPELT.results10MY)
str(SPELT.results10MY$data)

nhcooper123/SPELT documentation built on Dec. 24, 2021, 1:28 a.m.