phylolm-methods: Methods for class 'phylolm'.

In phylolm: Phylogenetic Linear Regression

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)

Example output

Loading required package: ape

Call:
phylolm(formula = y ~ 1, phy = tre, model = "BM")

   AIC logLik 
-3.206  3.603 

Raw residuals:
   Min     1Q Median     3Q    Max 
-2.765 -2.530  1.016  2.050  2.450 

Mean tip height: 2.662381
Parameter estimate(s) using ML:
sigma2: 1.062328 

Coefficients:
            Estimate StdErr t.value p.value
(Intercept)   0.6822 1.0716  0.6366  0.5273

R-squared:     0	Adjusted R-squared:     0 
            (Intercept)
(Intercept)    1.148264

phylolm documentation built on July 2, 2020, 3:44 a.m.