TipCorrelation: Phylogenetic independent contrasts using tip rates
In hisse: Hidden State Speciation and Extinction
View source: R/tipCorrelation.R
TipCorrelation R Documentation
Phylogenetic independent contrasts using tip rates
Description
Performs linear regression between phylogenetic independent contrasts (PICs) of tip rates and continuous trais
Usage
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 Feb. 16, 2023, 10:26 p.m.
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View source: R/tipCorrelation.R
| TipCorrelation | R Documentation |
Phylogenetic independent contrasts using tip rates
Description
Performs linear regression between phylogenetic independent contrasts (PICs) of tip rates and continuous trais
Usage
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.
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