67 lines
2.6 KiB
R
67 lines
2.6 KiB
R
library("nlme")
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## PR#18157
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mygnls <- function (mydata)
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gnls(weight ~ SSlogis(Time, Asym, xmid, scal), data = mydata)
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fm1 <- mygnls(Soybean) # failed in 3.1-153 with
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## Error in stats::nls(formula = weight ~ SSlogis(Time, Asym, xmid, scal), :
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## object 'mydata' not found
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## similarly, each of the following calls of
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## nlme.formula(), nlsList.selfStart(), nlme.nlsList()
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## using a self-starting model with local data would fail in 3.1-153 with
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## Error in is.data.frame(data) : object 'mydata' not found
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local({
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mydata <- subset(Loblolly, Seed < "307")
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fm2 <- nlme(height ~ SSasymp(age, Asym, R0, lrc),
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data = mydata, random = Asym ~ 1)
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fml <- nlsList(SSasymp, data = mydata)
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fm3 <- nlme(fml, random = Asym ~ 1)
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})
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## look for data in the parent frame, not in nlme's namespace
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groupedData <- Orthodont
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m3 <- lme(distance ~ age, data = groupedData, random = ~1 | Subject)
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augPred(m3, length.out = 2)
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## gave Error: data in 'm3' call must evaluate to a data frame
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simulate(m3, m2 = list(random = ~ age | Subject), seed = 42, method = "ML")
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## gave Error: 'data' must be a data.frame, environment, or list
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rm(groupedData)
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## PR#15892: formula.gls and formula.lme evaluated the call (in bad scope)
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## same for predict.lme
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invisible(lapply(list(gls, lme), function (FUN) {
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form <- follicles ~ 1
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model <- FUN(form, Ovary)
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stopifnot(identical(formula(model), form))
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stopifnot(all.equal(predict(model, newdata = Ovary[1,]),
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fitted(model)[1], check.attributes = FALSE))
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}))
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## first gave Error in eval(x$call$model) : object 'form' not found
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## second gave Error in eval(mCall$fixed) : object 'form' not found
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## Subject: [Bug 18559] New: nlme -> anova doesn't handle symbolic formulas nicely
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## Date: Sat, 08 Jul 2023 --- by Ben Bolker
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formula <- height ~ a*exp(-b*age)
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fm1 <- nlme(formula, data = Loblolly,
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fixed = a + b ~ 1,
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random = a ~ 1, start = c(a = 100, b = 1))
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## "same" for gnls:
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fmGnl <- gnls(formula, data = Loblolly, start = c(a = 100, b = 1))
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stopifnot(exprs = {
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identical(formula(fm1), formula) ## was equal to stats::formula (!)
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identical(getResponseFormula(fm1), ~height)
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identical(formula(fmGnl), formula) # was stats::formula
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identical(getResponseFormula(fmGnl), ~height)
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})
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## similarly for self-starting models:
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formula <- height ~ SSasymp(age, Asym, R0, lrc)
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fm2 <- nlme(formula, data = Loblolly, fixed = Asym + R0 + lrc ~ 1, random = Asym ~ 1)
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## nlme <= 3.1-164 failed with Error in x$formula :
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## object of type 'symbol' is not subsettable
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stopifnot(identical(formula(fm2), formula))
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