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