Interval support functions: add/remove impute (#379) #384

Gero1999 · 2025-02-05T00:07:35Z

Contributes to solve #379

New interval supporting functions acting to add/remove imputations from the impute column in PKNCAdata$intervals

Add imputation

interval_add_impute(data, target_impute, after = Inf, target_params = NULL, target_groups = NULL)

impute is the imputation character string to add, matching the behavior of PKNCAdata()
after follows similar behavior to the after argument of base::append(); 0 indicates it will be added as the first imputation method; Inf (or any number greater than the number of methods currently specified) indicates that it will be added as the last imputation method;
If there is already an imputation:

the imputation will be separated by commas (i.e. strsplit(current_impute, split = "[, ]"))
the new imputation will be added at the correct place (defined by after), and
The final imputation method will be put back together separated by commas (i.e. vapply(X = new_impute, FUN = paste, collapse = ",", FUN.VALUE = ""))

Remove imputation

interval_remove_impute(data, target_impute, target_params = NULL, target_groups = NULL)

split any imputation from the intervals and remove it
warn if the imputation was not found in any of the intervals

Note
For both functions optional arguments can be used to specify on which parameters (target_param, character vector) or at which specific interval rows (target_groups; list of column names and values) the action takes place

billdenney

I've not yet reviewed the tests since I requested some bigger changes in the other code.

billdenney · 2025-02-05T15:26:39Z

R/test-intervals_support_funs.R

Please move this to the test/testthat directory.

billdenney · 2025-02-05T15:27:08Z

R/test-intervals_support_funs.R

@@ -0,0 +1,140 @@
+library(testthat)


Please remove the library() lines as they are not needed in testthat tests.

billdenney · 2025-02-05T17:00:38Z

R/intervals_support_funs.R

@@ -0,0 +1,244 @@
+# Load necessary library
+library(dplyr)


Please remove library() from this file. If we need dplyr functions, please use dplyr::function_name().

billdenney · 2025-02-05T17:01:34Z

R/intervals_support_funs.R

+
+#' Remove specified imputation methods from the intervals in a PKNCAdata object.
+#'
+#' @param data A PKNCAdata object containing the intervals and data components.


Please ensure that it can work either on a data.frame or on a PKNCAdata object. (Other comments will relate to this, too.)

billdenney · 2025-02-05T17:03:31Z

R/intervals_support_funs.R

+#' @param data A PKNCAdata object containing the intervals and data components.
+#' @param target_impute A character string specifying the imputation method to be removed.
+#' @param target_params A character vector specifying the parameters to be targeted (optional). If missing, all TRUE in the intervals are taken.
+#' @param target_groups A named list specifying the intervals to be targeted (optional). If missing, all relevant groups are considered.


I like the concept of how you've implemented this. Please make this into a data.frame so that it can work more simply with the way people are accustomed to working with intervals.

Hey! @DaTa will also be the intervals dataframe. I guess in this case we cannot guess the impute column always, sobwould need another arg

Indeed I think using a dataframe as an input would make a lot of sense also to match the intervals for the target_groups arg, which we can call instead something like target_intervals. Here is then an example:

If this is my initial interval table:

USUBJID ANALYTE cmax tmax aucinf.pred impute

001 Analyte1 TRUE TRUE TRUE start_predose

I would then like to remove only for cmax and tmax the imputation, while keeping it for the other parameters:

interval_remove_impute(PKNCAdata$intervals, target_impute = "start_predose", target_params = c("cmax", "tmax"), target_intervals = data.frame(ANALYTE="Analyte1") )

This produces:

USUBJID ANALYTE cmax tmax aucinf.pred impute

001 Analyte1 FALSE FALSE TRUE start_predose

001 Analyte1 TRUE TRUE FALSE NA

That way we keep it intuitive: target_intervals indicates the rows to be considered (even if it can also contain parameter or impute specifications) while target_params the columns for which the removal applies.

billdenney · 2025-02-05T17:22:34Z

R/intervals_support_funs.R

+#' @param target_impute A character string specifying the imputation method to be added.
+#' @param after Numeric value specifying the position after which the imputation method should be added (optional). First is 0, last Inf. If missing, the imputation method is added at the end (Inf).
+#' @param target_params A character vector specifying the parameters to be targeted (optional). If missing, all TRUE in the intervals are taken.
+#' @param target_groups A named list specifying the intervals to be targeted (optional). If missing, all relevant groups are considered.


Please make this a data.frame and for it to work the same as in the other function.

billdenney · 2025-02-05T17:23:00Z

R/intervals_support_funs.R

+#' print(o_data$intervals)
+#'
+#' @export
+interval_add_impute <- function(data, target_impute, after = Inf, target_params = NULL, target_groups = NULL) {


Please make this S3 generic like the other function.

billdenney · 2025-02-05T17:23:26Z

R/intervals_support_funs.R

+  }
+
+  # Get all parameter column names in the PKNCAdata object
+  all_param_options <- names(sapply(PKNCA.options()$single.dose.aucs, is.logical))


Please use the same way of finding parameter names.

billdenney · 2025-02-05T17:24:09Z

R/intervals_support_funs.R

+  } else if ("impute" %in% colnames(data$intervals)) {
+    "impute"
+  } else {
+    stop("The 'data$intervals' object must contain an impute column either defined in the PKNCAdata object or called `impute`.")


We should add the column for the user rather than giving an error if it doesn't exist.

billdenney · 2025-02-05T17:27:01Z

R/intervals_support_funs.R

+  }
+
+  # Identify the targeted intervals to which the action is applied
+  mask_target_rows <- data$intervals %>%


Please simplify this code similar to the above with inner_join() and anti_join().

Gero1999 added 2 commits February 5, 2025 00:25

feat: add functions to remove and add impute

ddf2683

testing: add tests for interval_remove_impute

b8eb907

Gero1999 changed the title ~~Interval support functions (#379)~~ Interval support functions: add/remove impute (#379) Feb 5, 2025

Gero1999 mentioned this pull request Feb 5, 2025

Interval support functions #379

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Interval support functions: add/remove impute (#379) #384

Interval support functions: add/remove impute (#379) #384

Gero1999 commented Feb 5, 2025

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Gero1999 Feb 6, 2025 •

edited

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USUBJID	ANALYTE	cmax	tmax	aucinf.pred	impute
001	Analyte1	FALSE	FALSE	TRUE	start_predose
001	Analyte1	TRUE	TRUE	FALSE	NA

Interval support functions: add/remove impute (#379) #384

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Interval support functions: add/remove impute (#379) #384

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Gero1999 commented Feb 5, 2025

Add imputation

Remove imputation

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Gero1999 Feb 6, 2025 • edited Loading

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Gero1999 Feb 6, 2025 •

edited

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