63 lines
2.1 KiB
R
63 lines
2.1 KiB
R
## Example of scoping problem.
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## Originally from a report by Markus Jantti:
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## https://stat.ethz.ch/pipermail/r-help/2005-November/081382.html
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library(nlme)
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data(Ovary)
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## stolen from example(anova.gls)
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# AR(1) errors within each Mare
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## tolerance increased for flang (was 6e-6)
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fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
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correlation = corAR1(form = ~ 1 | Mare))
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int1 <- intervals(fm1)
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## no longer print attr(,"label"), PR#18196 :
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writeLines(intOut <- capture.output(int1))
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stopifnot({
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length(grep(',"label"', intOut, fixed=TRUE)) == 0
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all.equal(int1$corStruct["Phi",],
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c(lower=0.66842829, est.=0.753207889, upper=0.81866619),
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tol = 1e-5)# 7e-6 needed for flan
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all.equal(as.vector(int1$sigma),
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c(3.9747061, 4.61617157, 5.361161), tol = 1e-5)
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})
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# variance changes with a power of the absolute fitted values?
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fm2 <- update(fm1, weights = varPower())
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(a12 <- anova(fm1, fm2))
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stopifnot(identical(a12, anova(fm1, fm2, type = "seq")))# latter had failed
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## now define a little function
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dummy <- function(obj) anova(obj[[1]], obj[[2]])
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(d12 <- dummy(list(fm1, fm2)))
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## last failed < 3.1-66
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rownames(d12) <- rownames(a12)
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stopifnot(all.equal(a12, d12, tol = 1e-15),
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all.equal(a12[2,"p-value"], 0.111752516, tol = 1e-5)
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)
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## PR#13567
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fm1Orth.gls <- gls(distance ~ Sex * I(age - 11), Orthodont,
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correlation = corSymm(form = ~ 1 | Subject),
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weights = varIdent(form = ~ 1 | age))
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(aOr <- anova(fm1Orth.gls, Terms = "Sex"))
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stopifnot(all.equal(aOr[,"F-value"], 9.4030752449,
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aOr[,"p-value"], 0.0027608643857))
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## anova.gls(.) -- REML & ML
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(a1 <- anova(fm1))
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(a1m <- anova(fm1, type="marginal"))
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##
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fm1M <- update(fm1, method = "ML")
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(a1M <- anova(fm1M))
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(a1Mm <- anova(fm1M, type = "marginal"))
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stopifnot(
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all.equal(a1M[,"F-value"],
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c(378.774471, 19.1105834, 1.71334909),
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tolerance = 1e-7)
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,
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all.equal(summary(fm1M)$tTable[,"t-value"] ^ 2,
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as.matrix(a1Mm)[,"F-value"], tolerance = 1e-14)
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,
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all.equal(summary(fm1 )$tTable[,"t-value"] ^ 2,
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as.matrix(a1m )[,"F-value"], tolerance = 1e-14)
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)
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