phylolm-methods: Methods for class 'phylolm'.

In lamho86/phylolm: Phylogenetic Linear Regression

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, se.fit = FALSE, ...)
## 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, ...)
## S3 method for class 'phylolm'
confint(object, parm, level=0.95, ...)
## S3 method for class '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(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)

lamho86/phylolm documentation built on Nov. 11, 2023, 6:17 a.m.