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Validate PCA parameters #35

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15 changes: 15 additions & 0 deletions R/bidsio.R
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Original file line number Diff line number Diff line change
Expand Up @@ -358,6 +358,14 @@ read_confounds.bids_project <- function(x, subid=".*", task=".*", session=".*",
if (!inherits(x, "bids_project")) {
stop("`x` must be a `bids_project` object.")
}

if (!is.numeric(npcs) || length(npcs) != 1 || npcs < 0 || npcs != as.integer(npcs)) {
stop("`npcs` must be a non-negative integer.")
}

if (!is.numeric(perc_var) || length(perc_var) != 1 || perc_var < 0 || perc_var > 100) {
stop("`perc_var` must be between 0 and 100.")
}

# Check participants
sids <- participants(x)
Expand Down Expand Up @@ -446,6 +454,13 @@ read_confounds.bids_project <- function(x, subid=".*", task=".*", session=".*",

#' @keywords internal
process_confounds <- function(dfx, center=TRUE, scale=TRUE, npcs=-1, perc_var=-1) {
if (!is.numeric(npcs) || length(npcs) != 1 || npcs < 0 || npcs != as.integer(npcs)) {
stop("`npcs` must be a non-negative integer.")
}

if (!is.numeric(perc_var) || length(perc_var) != 1 || perc_var < 0 || perc_var > 100) {
stop("`perc_var` must be between 0 and 100.")
}
m <- as.matrix(dfx)
# Impute NAs
if (anyNA(m)) {
Expand Down
9 changes: 9 additions & 0 deletions tests/testthat/test_read_confounds.R
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Expand Up @@ -72,3 +72,12 @@ test_that("canonical names resolve to dataset columns", {
cols <- names(conf$data[[1]])
expect_true(all(c("CSF", "WhiteMatter", "FramewiseDisplacement", "GlobalSignal") %in% cols))
})

test_that("invalid PCA parameters trigger errors", {
setup <- create_confounds_proj()
on.exit(unlink(setup$path, recursive = TRUE, force = TRUE), add = TRUE)
expect_error(read_confounds(setup$proj, npcs = -1), "npcs")
expect_error(read_confounds(setup$proj, npcs = 1.5), "npcs")
expect_error(read_confounds(setup$proj, perc_var = -10), "perc_var")
expect_error(read_confounds(setup$proj, perc_var = 110), "perc_var")
})