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.
A 'caic' object is a list containing the following:
A list of the following:
A list containing matrices of the contrasts in the response
variable (contr$response) and explanatory variables
(contr$explanatory).
A list containing matrices of the nodal values in the
response variable (contr$response) and explanatory variables
(contr$explanatory).
A numeric vector of the expected variance for each contrast.
A vector showing the number of nodes descending from each internal node
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)
A logical vector showing which internal nodes on the tree have valid contrasts, given the available data and any user constraints.
A 'comparative.data' object containing the phylogeny used to calculate contrasts and the original data.
An 'lm' object containing a regression model through the origin for the calculated contrast
In addition, the object may have the following attributes:
One of 'crunch', 'brunch' or 'piclm'.
Either 'RRD' or 'PDI' if the response contrasts are calculated as species richness contrasts using macrocaic
A logical value showing whether the contrasts in the object have been standardized.