-
Notifications
You must be signed in to change notification settings - Fork 52
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Implemented a check within the `perf.mixo_splsda()` function which prevents the method running if any of the classes have a single sample associated with them. Also added to checks (in new file: `test-perf.mixo_splsda.R`) which ensure basic functionality as well as whether the function prevents a class with one sample being used.
- Loading branch information
1 parent
2b6ab06
commit 4540dc7
Showing
2 changed files
with
44 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,37 @@ | ||
context("perf.mixo_splsda") | ||
|
||
test_that("perf.mixo_splsda functions", code = { | ||
data(liver.toxicity) | ||
X <- liver.toxicity$gene | ||
Y <- liver.toxicity$treatment$Dose.Group | ||
# create a class with one sample only | ||
#Y[c(1,2)] <- 'FOO' | ||
|
||
res <- plsda(X, Y, ncomp = 2) | ||
set.seed(12) | ||
out <- perf(res, validation = "Mfold", folds = 3, nrepeat = 3) | ||
expect_is(out, "perf") | ||
|
||
ground.ncomp <- matrix(c(2,1,2,2,1,2), ncol = 3, byrow=T, | ||
dimnames = list(c("overall", "BER"), | ||
c("max.dist", "centroids.dist", "mahalanobis.dist"))) | ||
|
||
expect_true(all(out$choice.ncomp == ground.ncomp)) | ||
}) | ||
|
||
test_that("perf.mixo_splsda does not allow for class with 1 associated sample", code = { | ||
data(liver.toxicity) | ||
X <- liver.toxicity$gene | ||
Y <- liver.toxicity$treatment$Dose.Group | ||
# create a class with one sample only | ||
Y[c(1)] <- 'asdf' | ||
|
||
res <- plsda(X, Y, ncomp = 2) | ||
set.seed(12) | ||
expect_error(perf(res, validation = "Mfold", folds = 3, nrepeat = 3), | ||
paste("Cannot evaluate performance when a class level ('", | ||
names(table(res$Y))[which(table(res$Y) == 1)], | ||
"') has only a single assocaited sample.", | ||
sep = ""), | ||
fixed = T) | ||
}) |