Description Usage Arguments Author(s) See Also Examples
These are method functions for class 'phylolm'.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## 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, ...)
|
x |
an object of class |
object |
an object of class |
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 |
... |
further arguments to methods. |
Lam Si Tung Ho
1 2 3 4 5 6 |
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
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