caic-class | R Documentation |

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:

- 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.

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