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[WIP] Refactor allFit to avoid update() in optimizer refits #13

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[WIP] Refactor allFit to avoid update() in optimizer refits #13

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e8a5e8f
Initial plan
Copilot Mar 18, 2026
0fe65d1
Refactor allFit to use refit path for start_from_mle
Copilot Mar 22, 2026
70d31d6
Preserve allFit start handling while using refit fast path
Copilot Mar 22, 2026
b0e5dae
Remove remaining update usage from allFit refit path
Copilot Mar 23, 2026
e950e49
Restrict nlmer warning to start_from_mle path
Copilot Mar 23, 2026
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37 changes: 5 additions & 32 deletions R/allFit.R
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Original file line number Diff line number Diff line change
Expand Up @@ -165,46 +165,19 @@ allFit <- function(object, meth.tab = NULL,
ctrl$optCtrl <- sanitize(ctrl$optCtrl,
opt.ctrls[[optimizer[..i]]])
ctrl <- do.call(if(isGLMM(object)) glmerControl else lmerControl, ctrl)
## need to stick ctrl in formula env so it can be found ...
form <- formula(object)
env <- environment(form)
tmp_env <- new.env(parent = env)
# temporarily changing the environment
environment(form) <- tmp_env
assign("ctrl", ctrl, envir = tmp_env, inherits = FALSE)
# Using the MLE as a starting point
if (start_from_mle) {
if (isGLMM(object)) {
pars <- getME(object, c("theta", "fixef"))
} else {
pars <- getME(object, "theta")
if(isNLMM(object)){
warning("results are not guaranteed when using nlmer")
fit_once <- function() {
if (start_from_mle && isNLMM(object)) {
warning("results are not guaranteed when using nlmer")
}
}
assign("pars", pars, envir = tmp_env, inherits = FALSE)
refit(object, control = ctrl)
}

fit_call <- if (start_from_mle) {
quote(update(object, start = pars, control = ctrl))
} else {
quote(update(object, control = ctrl))
}

tt <- system.time(
rr <- if (catch.errs) {
tryCatch(eval(fit_call), error = function(e) e)
} else {
eval(fit_call)
}
rr <- if (catch.errs) tryCatch(fit_once(), error = function(e) e) else fit_once()
)

attr(rr, "optCtrl") <- ctrl$optCtrl # contains crucial info here
attr(rr, "time") <- tt # store timing info

## restore original values to environment of the object
on.exit({ environment(form) <- env }, add = TRUE)

if (verbose) {
if (inherits(rr,"error")) {
cat("[failed]\n")
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11 changes: 11 additions & 0 deletions tests/testthat/test-allFit.R
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Expand Up @@ -110,6 +110,17 @@ if (testLevel>1) {
cc <- capture.output(ff <- fit_func(cbpp))
expect_true(all(summary(ff)$which.OK))
})

test_that("allFit does not depend on update() data lookup", {
gm1 <- glmer(
cbind(incidence, size - incidence) ~ period + (1 | herd),
data = cbpp, family = binomial
)
gm1@call$data <- quote(.allFit_missing_data_symbol.)
cc <- capture.output(ff <- allFit(gm1, verbose = FALSE,
catch.errs = FALSE))
expect_true(all(summary(ff)$which.OK))
})

test_that("maxfun works", {
gm_it10 <- suppressWarnings(allFit(fit_cbpp_1, verbose=FALSE, maxfun = 10))
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