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I added the sparse AUMC function along with five AUC-variant PK parameters. When running the tests, I encountered the following error: Failure (test-pk.calc.all.R:789:5): pk.nca can be run for each parameter independently (humanpred#473) all(is.na(param_res$result$PPORRES)) is not FALSE actual: TRUE expected: FALSE The parameter mrt.sparse.last was not being calculated independently. To address this, I added the sparse-related parameters to test-pk.calc.all.R under non_pknca_covered_params: f, time_above, mrt.md.obs, mrt.md.pred, sparse_auclast, sparse_auc_se, sparse_auc_df, sparse_aumclast, sparse_aumc_se, sparse_aumc_df, vss.md.obs, vss.md.pred, ceoi, cl.sparse.last, mrt.sparse.last, vz.sparse.last, vss.sparse.last, kel.sparse.last Please let me know if this approach looks correct. After this update, the test results are: [ FAIL 0 | WARN 4 | SKIP 0 | PASS 2264 ] Remaining warning: Warning (test-PKNCA.options.R:440:3): PKNCA.set.summary input checking reset = TRUE is not intended for general use; summary() may not work after resetting summary instructions.
billdenney
requested changes
Mar 30, 2026
tests/testthat/test-pk.calc.all.R
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| non_pknca_covered_params <- c( | ||
| "f", "time_above", "mrt.md.obs", "mrt.md.pred", "sparse_auclast", "sparse_auc_se", "sparse_auc_df", | ||
| "vss.md.obs", "vss.md.pred", "ceoi" | ||
| "f", "time_above", "mrt.md.obs", "mrt.md.pred", |
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We should ensure that all of these parameters are covered and not add to this list.
| #' pharmacokinetics. Journal of Biopharmaceutical Statistics. 1998;8(2):317-328. | ||
| #' doi:10.1080/10543409808835241 | ||
| #' @export | ||
| var_sparse_auc <- function(sparse_pk) { |
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Why did you remove this function?
R/sparse.R
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| options=options, | ||
| auc.type="AUClast", | ||
| lambda.z=NA | ||
| conc = conc, time = time, subject = subject, ..., |
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There are many whitespace-only changes that make the code harder to review. Please remove the whitespace changes.
| #' doi:10.1080/10543409808835241 | ||
| #' @keywords internal | ||
| #' @export | ||
| var_sparse_aumc <- function(sparse_pk) { |
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It looks like you actually just moved the function down here. Please move it back so that the diff is easier to review.
…ach parameter independently (humanpred#473)") test.
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I added the sparse AUMC function along with five AUC-variant PK parameters. When running the tests, I encountered the following error: Failure (test-pk.calc.all.R:789:5): pk.nca can be run for each parameter independently (#473) all(is.na(param_res$result$PPORRES)) is not FALSE
actual: TRUE
expected: FALSE
The parameter mrt.sparse.last was not being calculated independently. To address this, I added the sparse-related parameters to test-pk.calc.all.R under non_pknca_covered_params: f, time_above, mrt.md.obs, mrt.md.pred,
sparse_auclast, sparse_auc_se, sparse_auc_df,
sparse_aumclast, sparse_aumc_se, sparse_aumc_df,
vss.md.obs, vss.md.pred, ceoi,
cl.sparse.last, mrt.sparse.last, vz.sparse.last,
vss.sparse.last, kel.sparse.last
Please let me know if this approach looks correct. After this update, the test results are:
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 2264 ]
Remaining warning:
Warning (test-PKNCA.options.R:440:3): PKNCA.set.summary input checking reset = TRUE is not intended for general use; summary() may not work after resetting summary instructions.