1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
|
## varcomp.R (2004-10-29)
## Variance Component of Mixed-Effect Linear Model
## Copyright 2004 Julien Dutheil
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
varcomp <- function(x, scale = FALSE, cum = FALSE)
{
if (!("lme" %in% class(x))) stop("Object \"x\" is not of class \"lme\"")
res <- seq(along = x$modelStruct$reStruct)
var <- vector(length = length(res) + 1)
for(i in res) {
var[length(var) - i] <- attr(summary(x$modelStruct$reStruct[[i]]),"stdDev")[1]*x$sigma
}
var[length(var)] <- x$sigma
var <- var^2
if(scale) var <- var/sum(var)
if(cum) var <- cumsum(var)
names(var) <- c(rev(names(x$modelStruct$reStruct)), "Within")
class(var) <- "varcomp"
return(var)
}
plot.varcomp <- function(x, xlab = "Levels", ylab = "Variance", type = "b", ...) {
if (!("varcomp" %in% class(x))) stop("Object \"x\" is not of class \"varcomp\"")
return(xyplot(x ~ ordered(names(x), levels=rev(names(x))), xlab=xlab, ylab=ylab, type=type, ...))
}
|
