phylolm (version 2.6.5)

phylolm-methods: Methods for class 'phylolm'.

Description

These are method functions for class 'phylolm'.

Usage

# S3 method for phylolm
print(x, digits = max(3, getOption("digits") - 3), ...)
# S3 method for phylolm
summary(object, ...)
# S3 method for phylolm
nobs(object, ...)
# S3 method for phylolm
residuals(object,type = c("response"), ...)
# S3 method for phylolm
predict(object, newdata = NULL, se.fit = FALSE, ...)
# S3 method for phylolm
vcov(object, ...)
# S3 method for phylolm
logLik(object, ...)
# S3 method for phylolm
AIC(object, k=2, ...)
# S3 method for phylolm
plot(x, ...)
# S3 method for phylolm
confint(object, parm, level=0.95, ...)
# S3 method for phylolm
model.frame(formula, ...)

Arguments

x

an object of class "phylolm".

object

an object of class "phylolm".

formula

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.

se.fit

A switch indicating if standard errors are required.

k

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

parm

a specification of which parameters are to be given confidence intervals, either a vector of numbers or a vector of names. If missing, all parameters are considered.

level

the confidence level required.

...

further arguments to methods.

Author

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)