58 lines
1.8 KiB
R
58 lines
1.8 KiB
R
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library(nlme)
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if (requireNamespace("MASS")) {
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## Example 1 --- was ./update.R ---
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data(petrol, package = 'MASS')
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Petrol <- petrol
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Petrol[, 2:5] <- scale(Petrol[, 2:5], scale = FALSE)
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pet3.lme <- lme(Y ~ SG + VP + V10 + EP,
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random = ~ 1 | No, data = Petrol, method="ML")
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upet3 <- update(pet3.lme, Y ~ SG + VP + V10)
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upet3
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vc3 <- VarCorr(upet3)
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upet2 <- lme(Y ~ SG + VP + V10, random = ~ 1 | No, data = Petrol, method = "ML")
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stopifnot(
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all.equal(upet3, upet2, tol = 1e-15)
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,
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all.equal(fixef(upet3),
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c("(Intercept)" = 19.659375, SG = 0.125045632,
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VP = 2.27818601, V10 = 0.0672413592), tol = 1e-8)# 1e-9
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,
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all.equal(as.numeric(vc3[,"StdDev"]),
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c(0.00029397, 9.69657845), tol=1e-6)
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)
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}
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## Example 2 ---
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data(Assay)
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as1 <- lme(logDens~sample*dilut, data=Assay,
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random=pdBlocked(list(
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pdIdent(~1),
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pdIdent(~sample-1),
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pdIdent(~dilut-1))))
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as1s <- update(as1, random=pdCompSymm(~sample-1))
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(an.1s <- anova(as1, as1s)) # non significant
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stopifnot(
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all.equal(drop(data.matrix(an.1s[2,-1])),
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c(Model = 2, df = 33, AIC = -10.958851, BIC = 35.280663,
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logLik = 38.479425, Test = 2,
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L.Ratio = 0.11370211, `p-value` = 0.73596807), tol=8e-8))
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as1S <- update(as1, . ~ sample+dilut) # dropping FE interaction
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tools::assertWarning(anova(as1, as1S))# REML not ok for different FE.
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as1M <- update(as1, method = "ML")
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as1SM <- update(as1S, method = "ML")
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(anM <- anova(as1M, as1SM)) # anova() OK: comparing MLE fits
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## ==> significant: P ~= 0.0054
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stopifnot(
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all.equal(drop(data.matrix(anM[2,])[,-(1:2)]),
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c(df = 14, AIC = -169.588248, BIC = -140.267424, logLik = 98.7941241,
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Test = 2, L.Ratio = 39.7345188, `p-value` = 0.0053958561),
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tol = 8e-8)
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)
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