| PCMPresentCoordinates {PCMBase} | R Documentation |
Determine which traits are present (active) on each node of the tree
Description
For every node (root, internal or tip) in tree, build a logical vector of length k with TRUE values for every present coordinate. Non-present coordinates arize from NA-values in the trait data. These can occur in two cases:
- Missing measurements for some traits at some tips:
the present coordinates are FALSE for the corresponding tip and trait, but are full for all traits at all internal and root nodes.
- non-existent traits for some species:
the FALSE present coordinates propagate towards the parent nodes - an internal or root node will have a present coordinate set to FALSE for a given trait, if all of its descendants have this coordinate set to FALSE.
These two cases have different effect on the likelihood calculation: missing measurements (NA) are integrated out at the parent nodes; while non-existent traits (NaN) are treated as reduced dimensionality of the vector at the parent node.
Usage
PCMPresentCoordinates(X, tree, metaI)
Arguments
X |
numeric k x N matrix of observed values, with possible NA entries. The columns in X are in the order of tree$tip.label |
tree |
a phylo object |
metaI |
The result of calling PCMInfo. |
Value
a k x M logical matrix. The function fails in case when all traits are NAs for some of the tips. In that case an error message is issued "PCMPresentCoordinates:: Some tips have 0 present coordinates. Consider removing these tips.".