Refactoring with checkmate and rlang

[PavanLomati]

No description provided.

[billdenney]

This looks like it will make all of the code more consistent. Thank you!. Please merge in the current origin/main branch and resolve the conflicts.

Also, for many of the checkmate calls, you've added .var.name = "name" or similar where name is the parameter name used. Please omit those as they are not necessary since they are the default that checkmate will provide.

[billdenney]

@PavanLomati

Here are the comprehensive findings:

Additional review findings

These supplement the 6 inline comments already on the diff (non-unique classes, conditionMessage(), paste() in messages, stray #'). They're organized by class, highest-leverage first. All behavioral claims were verified against the base branch.

Severity token missing from some preexisting condition classes — breaks class-based capture

Three internal "report a bug" errors are raised with a pknca_internal_* class instead of pknca_error_*:

• pknca_internal_pk_tss_ret_non_na — R/tss.R
• pknca_internal_dose_scaling — R/superposition.R
• pknca_internal_unknown_nca_units — R/unit-support.R

Their siblings correctly use pknca_error_internal_* (pknca_error_internal_tlast in R/auc.R, pknca_error_internal_clast_na in R/aucint.R). A handler filtering on pknca_error_* will silently miss the three pknca_internal_* ones. Please standardize on pknca_error_internal_*.

Negative-path tests deleted instead of migrated — coverage regression

Please restore the tests to match the previous intent.

Across ~10 test files, the expect_error(..., regexp=) cases that exercised the exact validation being refactored were removed rather than updated to the new message/class:

• test-001-add.interval.col.R — entire ~20-case input-validation block (name/FUN/pretty_name/datatype/desc/depends/formalsmap) deleted
• test-PKNCA.options.R — ~18 scalar/factor/NA/"must be a number" checks across nine options, plus PKNCA.set.summary point/spread/description checks
• test-superpostion.R — additional.times non-numeric/negative/>tau and steady.state.tol checks
• test-set_and_assert_intervals.R — 3 whole test_that blocks
• Same pattern in test-time.above.R, test-pk.calc.c0.R, test-class-PKNCAconc.R, test-class-PKNCAdata.R, test-class-PKNCAdose.R, test-exclude.R, test-assertions.R, test-time.to.steady.state.R

The new behavior is now less tested than the old. Please convert these to expect_error(..., class="pknca_error_...") instead of deleting them.

checkmate semantics quietly differ from the manual checks they replaced

Please add tests for where these tests are stricter:

CI can't catch these because the negative tests (finding 2) were deleted. All verified against base:

• finite=TRUE added where the old code accepted Inf: pk.calc.aucabove now uses assert_number(conc_above, na.ok=TRUE, finite=TRUE); old stopifnot(is.numeric, length==1) allowed Inf. conc_above=Inf now errors.
• all-NA acceptance: assert_character/assert_numeric accept an all-NA logical vector by default, where is.character()/is.numeric() rejected it. In R/exclude.R the old else if (!is.character(reason)) became an unconditional assert_character(reason), so reason=NA now passes the type gate. (add.interval.col intentionally relies on this for FUN=NA, but the relaxation is silent elsewhere.)
• Newly stricter, not in the original: add.interval.col adds min.chars=1 to name (rejects "") and unique=TRUE on formalsmap names; R/impute.R assert_scalar(impute) rejects a length-1 list that length(impute)==1 accepted.

None look dangerous, but they're undocumented behavior changes with no test pinning them.

Please find remaining stop and warning calls

"Replaced all stop() and warning() calls" — but genuine sites remain at the PR head:

• stop() in R/auc_integrate.R (the idx_tlast "must occur exactly once" check — not nocov), R/prepare_data.R:165, R/time.above.R:86
• warning() in R/pk.calc.all.R:143 (re-raises a captured condition)

.Rbuildignore references a file not in the repo

The PR adds ^coverage_check\.R$ and strips the trailing newline, but coverage_check.R is not part of the PR or repo — a leftover local-scratch reference. Please drop the line and restore the trailing newline.

Whitespace / formatting issues

Pervasive enough to be a class:

• ) } — closing brace fused onto an abort()/warn() close paren: ~11 sites (e.g. R/auc.R, R/class-PKNCAdata.R, R/superposition.R, R/tss.monoexponential.R, R/exclude.R, R/class-general.R, R/001-add.interval.col.R)
• Zero/under-indentation: R/pk.calc.c0.R (assert_number + if at column 0), R/PKNCA.options.R (if (default && check)), R/class-summary_PKNCAresults.R (} else if)
• Comments displaced onto code lines: R/PKNCA.options.R (assert_number(...) # Must be between 0 and 1), R/aucint.R (} else if (...) { # If using clast.pred…)
• Inconsistent ){ (no space), stray trailing whitespace, and two new "No newline at end of file" (R/pk.calc.simple.R, .Rbuildignore)

A styler/lintr pass clears all of these.

Commented-out dead code left behind (8 sites)

Beyond the #stop(unit_col, …) already noted: #c("interval", …) (R/001-add.interval.col.R), #checkmate::assert_number(… max.missing) (R/PKNCA.options.R), #checkmate::assertNumeric(x$start …) (R/check.intervals.R), #stopifnot(inherits(… o_conc/o_dose)) ×2 and # stopifnot(…cols…) ×2 (R/prepare_data.R), and the trailing assert_number(tlast)#, finite = TRUE) (R/auc_integrate.R).