Allow non-unique units columns (PKNCAconc & PKNCAdose) by Gero1999 · Pull Request #435 · humanpred/pknca

Gero1999 · 2025-06-10T07:48:44Z

Makes PKNCAdata$units table able to include any group variable stratifying the units in PKNCAconc / PKNCAdose .

Implementation Summary:

Added pknca_units_table_from_pknca. Creates a default units table based on a PKNCAconc object (and optionally PKNCAdose as well).
Introduced helper functions ensure_column_unit_exists and select_minimal_grouping_cols to support unit column validation and minimal grouping column selection.
Updated PKNCAdata.default to replace manual unit table construction with the new pknca_units_table_from_pknca function.
Added tests for pknca_units_table_from_pknca to verify its behavior with various scenarios, including:
Added new imports (dplyr, rlang, tidyr, utils) and exported pknca_units_table_from_pknca to make the new functionality accessible.

…ero1999/pknca into 416-custom_units_for_PKNCAdata

…PKNCAdata

Gero1999 · 2025-06-16T09:45:14Z

hey @billdenney I adapted some things we did on aNCA to include it as default behaviour in PKNCAdata. This should flexibilize the reading of unit columns in PKNCAconc (and PKNCAdose) related to #416. I added also tests to make sure this is translated into the results, but let me know if I miss something!

I also added some #TODO comments of the main changes I needed to do to adapt the function to PKNCA

billdenney · 2025-09-12T20:01:44Z

Instead of creating a new pknca_units_table_from_pknca() function, can you please make pknca_units_table() to be S3 generic with something like:

pknca_units_table <- function(concu, ...) {
  UseMethod("pknca_units_table")
}

pknca_units_table.default <- function(concu, doseu, amountu, timeu,
                              concu_pref = NULL, doseu_pref = NULL, amountu_pref = NULL, timeu_pref = NULL,
                              conversions = data.frame(), ...) {
  # the current function
}

pknca_units_table.PKNCAdata <- function(concu, ... conversions = data.frame()) {
  # Your function with conversions handled, too.
}

…ero1999/pknca into 416-custom_units_for_PKNCAdata

R/unit-support.R

billdenney · 2025-11-06T15:53:27Z

R/unit-support.R

+  all_unit_cols <- c(concu_col, amountu_col, timeu_col, doseu_col)
+
+  # Join dose units with concentration group columns and units
+  d_concu <- o_conc$data %>%


Please use base R for readability:

unit_cols <- c(group_conc_cols, concu_col, amountu_col, timeu_col) d_concu <- as.data.frame(o_conc) d_concu <- unique(d_concu[, intersect(names(d_concu), unit_cols)]) unit_cols <- c(group_conc_cols, doseu_col) d_doseu <- as.data.frame(o_dose) d_doseu <- unique(d_doseu[, intersect(names(d_doseu), unit_cols)])

billdenney · 2025-11-06T15:54:33Z

R/unit-support.R

+  groups_units_tbl <- merge(d_concu, d_doseu, all.x = TRUE) %>%
+    dplyr::mutate(dplyr::across(dplyr::everything(), ~ as.character(.))) %>%
+    dplyr::group_by(!!!rlang::syms(group_conc_cols)) %>%
+    tidyr::fill(!!!rlang::syms(all_unit_cols), .direction = "downup") %>%


Why is fill necessary here? It seems like it could go against the user's intent as they don't have units in their source data.

billdenney · 2025-11-06T15:55:19Z

R/unit-support.R

+
+  groups_units_tbl <- merge(d_concu, d_doseu, all.x = TRUE) %>%
+    dplyr::mutate(dplyr::across(dplyr::everything(), ~ as.character(.))) %>%
+    dplyr::group_by(!!!rlang::syms(group_conc_cols)) %>%


Please use dplyr::grouped_df() instead of indirection via rlang::syms().

billdenney · 2025-11-06T15:57:12Z

R/unit-support.R

+    unique()
+
+  groups_units_tbl <- merge(d_concu, d_doseu, all.x = TRUE) %>%
+    dplyr::mutate(dplyr::across(dplyr::everything(), ~ as.character(.))) %>%


Why do we need to convert everything to character? I think that it should all be character from the original input. If it is not (perhaps it's a factor), then we should likely handle factor conversion elsewhere. This seems like it is possibly hiding a data problem from the user (possibly causing a hard-to-trace bug in the future) and should be corrected in source data rather than here.

billdenney · 2025-11-06T16:05:42Z

R/unit-support.R

+    stop(
+      "Units should be uniform at least across concentration groups. ",
+      "Review the units for the next group(s):\n",
+      paste(utils::capture.output(print(mismatching_units_groups)), collapse = "\n")


Rather than capture.output, please directly generate the desired string like:

do.call(paste, lapply(X = names(d), FUN = function(x) paste(x, d[[x]], sep = "=")))

billdenney · 2025-11-06T16:07:03Z

R/unit-support.R

+  units.are.all.na <- all(is.na(groups_units_tbl[,all_unit_cols]))
+  if (units.are.all.na) return(NULL)
+
+  groups_units_tbl %>%


Please convert this to a loop for readability (it will only likely be called a few times, so it should not be a performance issue).

billdenney · 2025-11-06T16:10:21Z

R/unit-support.R

+#' 2. If a column does not exist, it creates the column and assigns default values.
+#' 3. If not default values are provided, it assigns NA to the new column.
+#' @keywords Internal
+ensure_column_unit_exists <- function(pknca_obj, unit_name) {


I think that this is already handled as part of the pknca_set_units() function. Can this function be eliminated, and if not, can you please explain why not?

billdenney · 2025-11-06T16:11:42Z

R/unit-support.R

+}
+
+# Add globalVariables for NSE/dplyr/rlang/tidyr usage
+utils::globalVariables(c(


Please use double colon notation or rlang::.data rather than globalVariables()

billdenney · 2025-11-24T16:40:55Z

Please also merge the current main branch upon making the above changes.

…PKNCAdata (conflicts with no real issue in unit-support.R & NAMESPACE)

Gero1999 and others added 13 commits June 7, 2025 13:00

draft: default units_table for PKNCAdata

cc4d3c2

test: include tests for the default units table for PKNCAconc &PKNCAdose

eae9cfb

make fun to not need PKNCAdose

5fa7fd5

Merge branch 'humanpred:main' into 416-custom_units_for_PKNCAdata

5786c22

rename: fun to pknca_units_table_from_pknca

ebb0cab

docs: roxygenise funs

9ded111

Merge branch '416-custom_units_for_PKNCAdata' of https://github.com/G…

4b70ac2

…ero1999/pknca into 416-custom_units_for_PKNCAdata

fix: consider case when ret$o_dose = NA

518347f

fix: 1) columns order, 2) NULL if no units specified, 3) ignore NAs

41d8bb5

docs: roxygenise indicating additional dplyr funs

c4c6c69

Merge remote-tracking branch 'origin/main' into 416-custom_units_for_…

72e6d55

…PKNCAdata

fix: error for NA o_dose list & attr in units Xu_pref

64285e2

docs: fix example and update namespace

3b0aa18

Gero1999 marked this pull request as ready for review June 16, 2025 12:34

Gero1999 changed the title ~~Allow custom non-unique units (PPORRESU) based on PKNCAconc & PKNCAdose obj~~ Allow non-unique units columns (PKNCAconc & PKNCAdose) Jun 27, 2025

Gero1999 mentioned this pull request Sep 1, 2025

Collaboration: Things to consider for next PKNCA update pharmaverse/aNCA#481

Open

13 tasks

Gero1999 added 8 commits September 12, 2025 22:58

Merge branch '416-custom_units_for_PKNCAdata' of https://github.com/G…

bcfe407

…ero1999/pknca into 416-custom_units_for_PKNCAdata

feat: make pknca_units_table a method for PKNCAdata

02bff3d

test: adjust tests for PKNCAdata input

1c71730

test: refactor to follow PKNCA structure

04b393c

fix: typpo namespaces and docs

957091b

fix: issue for PKNCAdose not being present

3c7e6fc

fix: warning in test due to left_join

efb9118

fix check: update namespace & rm S3 generic message

1d1983d

billdenney requested changes Nov 6, 2025

View reviewed changes

suggestions: as_PKNCAconc, as_PKNCAdose

877a26e

Gero1999 marked this pull request as draft November 24, 2025 21:31

Merge remote-tracking branch 'origin/main' into 416-custom_units_for_…

67a5501

…PKNCAdata (conflicts with no real issue in unit-support.R & NAMESPACE)

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Allow non-unique units columns (PKNCAconc & PKNCAdose)#435

Allow non-unique units columns (PKNCAconc & PKNCAdose)#435
Gero1999 wants to merge 23 commits intohumanpred:mainfrom
Gero1999:416-custom_units_for_PKNCAdata

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Gero1999 commented Jun 10, 2025 •

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