vcov.cauphylm: Generic Methods for S3 class 'cauphylm'.

In cauphy: Trait Evolution on Phylogenies Using the Cauchy Process

Generic Methods for S3 class cauphylm.

Description

Generic Methods for S3 class cauphylm.

Usage

## S3 method for class 'cauphylm'
print(x, digits = max(3, getOption("digits") - 3), ...)

## S3 method for class 'cauphylm'
vcov(object, ...)

## S3 method for class 'cauphylm'
logLik(object, ...)

## S3 method for class 'logLik.cauphylm'
AIC(object, k = 2, ...)

## S3 method for class 'cauphylm'
AIC(object, k = 2, ...)

## S3 method for class 'cauphylm'
predict(object, newdata = NULL, se.fit = FALSE, ...)

## S3 method for class 'cauphylm'
confint(object, parm, level = 0.95, ...)

## S3 method for class 'cauphylm'
coef(object, ...)

Arguments

x	an object of class "phylolm".
digits	number of digits to show in summary method.
...	further arguments to methods.
object	an object of class cauphylm.
k	numeric, the penalty per parameter to be used; the default k = 2 is the classical AIC.
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.
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.

Value

Same value as the associated methods from the stats package:

vcov

an estimated covariance matrix, see compute_vcov;

logLik

an object of class logLik;

AIC

a numeric value;

confint

a matrix (or vector) with columns giving lower and upper confidence limits for each parameter;

coef

coefficients extracted from the model;

predict

a vector of predicted values.

See Also

cauphylm, vcov, logLik AIC, confint, coef, predict, predict.phylolm

Examples

# Simulate tree and data
set.seed(1289)
phy <- ape::rphylo(20, 0.1, 0)
error <- rTraitCauchy(n = 1, phy = phy, model = "cauchy",
                      parameters = list(root.value = 0, disp = 0.1))
x1 <- ape::rTraitCont(phy, model = "BM", sigma = 0.1, root.value = 0)
trait <- 3 + 2*x1 + error
# Fit the data
fit <- cauphylm(trait ~ x1, phy = phy)
fit
# vcov matrix
vcov(fit)
# Approximate confidence intervals
confint(fit)
# log likelihood of the fitted object
logLik(fit)
# AIC of the fitted object
AIC(fit)
# predicted values
predict(fit)
# coefficients
coef(fit)

cauphy documentation built on Oct. 1, 2024, 5:08 p.m.