vcov.cauphyfit function

Generic Methods for S3 class cauphyfit.

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

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

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

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

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

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

## S3 method for class 'cauphyfit'
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 cauphyfit.
• 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.

Returns

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;

Examples

# Simulate tree and data
set.seed(1289)
phy <- ape::rphylo(20, 0.1, 0)
dat <- rTraitCauchy(n = 1, phy = phy, model = "cauchy",
                    parameters = list(root.value = 10, disp = 0.1))
# Fit the data
fit <- fitCauchy(phy, dat, model = "cauchy", method = "reml")
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)
# coefficients
coef(fit)

See Also

fitCauchy, vcov, logLik

AIC, confint, coef, predict, predict.phylolm