phylolm-methods {phylolm}

Methods for class 'phylolm'.

Description

These are method functions for class 'phylolm'.

Usage

## S3 method for class 'phylolm'
print(x, digits = max(3, getOption("digits") - 3), ...)
## S3 method for class 'phylolm'
summary(object, ...)
## S3 method for class 'phylolm'
nobs(object, ...)
## S3 method for class 'phylolm'
residuals(object,type = c("response"), ...)
## S3 method for class 'phylolm'
predict(object, newdata = NULL, ...)
## S3 method for class 'phylolm'
vcov(object, ...)
## S3 method for class 'phylolm'
logLik(object, ...)
## S3 method for class 'phylolm'
AIC(object, k=2, ...)
## S3 method for class 'phylolm'
plot(x, ...)

Arguments

x

an object of class "phylolm".

object

an object of class "phylolm".

digits

number of digits to show in summary method.

type

Currently, only the "response" type is implemented. It returns the raw residuals, that is, the differences between the observed responses and the predicted values. They are phylogenetically correlated.

newdata

an optional data frame to provide the predictor values at which predictions should be made. If omitted, the fitted values are used. Currently, predictions are made for new species whose placement in the tree is unknown. Only their covariate information is used. The prediction for the trend model is not currently implemented.

k

numeric, the penalty per parameter to be used; the default k = 2 is the classical AIC.

...

further arguments to methods.

Author(s)

Lam Si Tung Ho

See Also

phylolm

Examples

set.seed(321123)
tre = rcoal(50)
y = rTrait(n=1,phy=tre,model="BM")
fit = phylolm(y~1,phy=tre,model="BM")
summary(fit)
vcov(fit)