TipCorrelation: Phylogenetic independent contrasts using tip rates

Description Usage Arguments Details Value Author(s) References

View source: R/tipCorrelation.R

Description

Performs linear regression between phylogenetic independent contrasts (PICs) of tip rates and continuous trais

Usage

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TipCorrelation(phy, tip.rate, trait, log=TRUE, remove.cherries=TRUE, 
scaled=TRUE, positivise=TRUE, use.lmorigin=TRUE)

Arguments

phy

an ultrametric phylogenetic tree of class 'phylo'.

tip.rate

an object of class 'named numeric' containing tip.rates

trait

an object of class 'named numeric' containing continuous trait data

log

Should tip.rate and trait values be logged before regression? The default is TRUE.

remove.cherries

Should PICs of 'cherries' be pruned before regression? The default is TRUE.

scaled

Should PICs be scaled with their expected variances? The default to TRUE.

positivise

Should PICs be positivised before regression? The default is TRUE.

use.lmorigin

Should a regression-through-origin be performed instead of regular linear model? The default is TRUE.

Details

Tip rates as those obtained with MiSSEGreedy are analogous to a continuous trait evolving in the tree and must also be corrected for phylogenetic non-independence before regression analyses. This function does that by using PICs (Felsenstein, 1985) and gives the additional option of removing PICs from 'cherries' from analyses. Cherries (theoretically) inherit the exact same rate class probabilities in any model that uses just branch lengths to estimate tip rates. For that reason, they may: (1) present identical tip rates, forcing the slope of the regression to be close to 0 since all PICs for cherries will be 0; and (2) constitute pseudoreplicates in the analyses. We suspect that, for that reason, it may make sense to prune them out from any PIC analyses that uses tip-rate correlations from tree-only diversification approaches (see Vasconcelos et al. in prep.).

Value

Returns an object that contains:

$correlation

summary of correlation results.

$tip.rate PIC

tip rate PICs for each node.

$trait PIC

trait PICs for each node.

Author(s)

Thais Vasconcelos and Brian O'Meara

References

Vasconcelos, T, B.C. O'Meara, and J.M. Beaulieu. In prep. Felsenstein, J. (1985). Phylogenies and the comparative method. The American Naturalist, 125, 1-15.


hisse documentation built on Nov. 16, 2021, 9:09 a.m.