caic-class: The 'caic' S3 object class and methods
In caper: Comparative Analyses of Phylogenetics and Evolution in R

caic-class

R Documentation

The 'caic' S3 object class and methods

Description

The functions 'crunch', 'brunch', 'macrocaic' and 'piclm' all return an object containing an independent contrast model. The structure of the object and the available methods are described here.

Format

A 'caic' object is a list containing the following:

contrast.data

A list of the following:

contr: A list containing matrices of the contrasts in the response variable (contr⁠$⁠response) and explanatory variables (contr⁠$⁠explanatory).
nodalVals: A list containing matrices of the nodal values in the response variable (contr⁠$⁠response) and explanatory variables (contr⁠$⁠explanatory).
contrVar: A numeric vector of the expected variance for each contrast.
nChild: A vector showing the number of nodes descending from each internal node
nodeDepth: A vector showing the maximum number of nodes between each internal node and the tips of the phylogeny (including both the node in question and the tip and hence always >=2)
validNodes: A logical vector showing which internal nodes on the tree have valid contrasts, given the available data and any user constraints.

data

A 'comparative.data' object containing the phylogeny used to calculate contrasts and the original data.

lm

An 'lm' object containing a regression model through the origin for the calculated contrast

In addition, the object may have the following attributes:

contr.method: One of 'crunch', 'brunch' or 'piclm'.
macro: Either 'RRD' or 'PDI' if the response contrasts are calculated as species richness contrasts using macrocaic
stand.cont: A logical value showing whether the contrasts in the object have been standardized.