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Migrate plyr::llply to lapply() #136

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Migrate plyr::llply to lapply() #136

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9a7e395
Migrate plyr::llply to lapply()
MichaelChirico Jun 4, 2025
c353909
Merge remote-tracking branch 'upstream/develop' into llply
MichaelChirico Jun 5, 2025
58b131c
drop test expecting a progress bar
MichaelChirico Jun 5, 2025
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4 changes: 2 additions & 2 deletions R/bootstrap.R
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Expand Up @@ -281,10 +281,10 @@ ci_auc_bootstrap <- function(roc, conf.level, boot.n, boot.stratified, progress,
progress <- roc_utils_get_progress_bar(progress, title="AUC confidence interval", label="Bootstrap in progress...", ...)

if (boot.stratified) {
aucs <- unlist(llply(1:boot.n, .fun=stratified.ci.auc, roc=roc, .progress=progress, .parallel=parallel))
aucs <- unlist(lapply(seq_len(boot.n), stratified.ci.auc, roc=roc))
}
else {
aucs <- unlist(llply(1:boot.n, .fun=nonstratified.ci.auc, roc=roc, .progress=progress, .parallel=parallel))
aucs <- unlist(lapply(seq_len(boot.n), nonstratified.ci.auc, roc=roc))
}

if (sum(is.na(aucs)) > 0) {
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4 changes: 2 additions & 2 deletions R/ci.auc.R
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Expand Up @@ -100,10 +100,10 @@ ci.auc.smooth.roc <- function(smooth.roc,
progress <- roc_utils_get_progress_bar(progress, title="AUC confidence interval", label="Bootstrap in progress...", ...)

if (boot.stratified) {
aucs <- unlist(llply(1:boot.n, stratified.ci.smooth.auc, roc=roc, smooth.roc.call=smooth.roc.call, auc.call=auc.call, .progress=progress, .parallel=parallel))
aucs <- unlist(lapply(seq_len(boot.n), stratified.ci.smooth.auc, roc=roc, smooth.roc.call=smooth.roc.call, auc.call=auc.call))
}
else {
aucs <- unlist(llply(1:boot.n, nonstratified.ci.smooth.auc, roc=roc, smooth.roc.call=smooth.roc.call, auc.call=auc.call, .progress=progress, .parallel=parallel))
aucs <- unlist(lapply(seq_len(boot.n), nonstratified.ci.smooth.auc, roc=roc, smooth.roc.call=smooth.roc.call, auc.call=auc.call))
}

if (sum(is.na(aucs)) > 0) {
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8 changes: 4 additions & 4 deletions R/var.R
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Expand Up @@ -132,19 +132,19 @@
auc.call <- as.call(c(utils::getS3method("auc", "smooth.roc"), auc.args))

if (boot.stratified) {
aucs <- unlist(llply(1:boot.n, stratified.ci.smooth.auc, roc=non.smoothed.roc, smooth.roc.call=smooth.roc.call, auc.call=auc.call, .progress=progress, .parallel=parallel))
aucs <- unlist(lapply(seq_len(boot.n), stratified.ci.smooth.auc, roc=non.smoothed.roc, smooth.roc.call=smooth.roc.call, auc.call=auc.call))
}
else {
aucs <- unlist(llply(1:boot.n, nonstratified.ci.smooth.auc, roc=non.smoothed.roc, smooth.roc.call=smooth.roc.call, auc.call=auc.call, .progress=progress, .parallel=parallel))
aucs <- unlist(lapply(seq_len(boot.n), nonstratified.ci.smooth.auc, roc=non.smoothed.roc, smooth.roc.call=smooth.roc.call, auc.call=auc.call))

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}
}
## Non smoothed ROC curves variance
else {
if (boot.stratified) {
aucs <- unlist(llply(1:boot.n, stratified.ci.auc, roc=roc, .progress=progress, .parallel=parallel)) # ci.auc: returns aucs just as we need for var, so re-use it!
aucs <- unlist(lapply(seq_len(boot.n), stratified.ci.auc, roc=roc)) # ci.auc: returns aucs just as we need for var, so re-use it!
}
else {
aucs <- unlist(llply(1:boot.n, nonstratified.ci.auc, roc=roc, .progress=progress, .parallel=parallel))
aucs <- unlist(lapply(seq_len(boot.n), nonstratified.ci.auc, roc=roc))
}
}

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4 changes: 0 additions & 4 deletions tests/testthat/test-progress.R
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Expand Up @@ -7,10 +7,6 @@ test_that("can get bar works", {
expect_equal(names(my_progress), c("init", "step", "term"))
})

test_that("progress = text works", {
expect_output(var(r.wfns, method="bootstrap", boot.n=2, progress="text"))
})

test_that("progress = none works", {
expect_silent(var(r.wfns, method="bootstrap", boot.n=2, progress="none"))
})