Create R script to replicate App outputs (#467) #789

Gero1999 · 2025-11-28T09:10:50Z

Issue

Closes #467

Description

Implemented the script file. It was made in order to eventually also be used using a settings file

Definition of Done

R Script export
Can be run independently and give same results as in app
Using aNCA functions

How to test

Do your choices in the App and export the ZIP folder. In the subfolder find the /code/session_script.R and run it. Compare the script outputs with the result files in the exported ZIP

Contributor checklist

Code passes lintr checks
Code passes all unit tests
New logic covered by unit tests
New logic is documented
App or package changes are reflected in NEWS
Package version is incremented

Notes to reviewer

The tests for the function calculate_ratios_app will be included here Enhancement: Add tests for functions to reach 100% coverage #287 independently
The tests for the function get_session_script_code has probably to be also done as an e2e test. To indeed make sure that both session and script are matching

…atio calculations

Copilot

Pull request overview

This PR implements an R script export feature that allows users to download an executable R script capturing their session configuration. The script can be run independently to reproduce the same NCA analysis results.

Key changes:

Added get_session_script_code() function to generate executable R scripts from templates with session data substitution
Moved and exported calculate_table_ratios_app() function from Shiny-specific code to the package API
Added session data capture in multiple Shiny modules to support script generation

Reviewed changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
`R/get_session_script_code.R`	New function to parse templates and substitute session variables with actual values
`R/ratio_calculations.R`	Added exported `calculate_table_ratios_app()` function (moved from internal Shiny code)
`inst/shiny/www/templates/script_template.R`	Template for generating session-specific R scripts with placeholders for session data
`inst/shiny/modules/tab_nca/nca_results.R`	Integration of script generation into the export ZIP functionality
`inst/shiny/modules/tab_nca.R`	Captures settings, ratio_table, and slope_rules to session userData
`inst/shiny/modules/tab_data/*.R`	Captures mapping, filters, and data paths to session userData
`inst/shiny/modules/tab_nca/setup.R`	Removed duplicate ratio_table assignment
`inst/shiny/functions/ratio_table.R`	Removed `calculate_table_ratios_app()` (moved to R/ratio_calculations.R)
`man/*.Rd`	Documentation files for new and moved functions
`NAMESPACE`	Export declaration for `calculate_table_ratios_app()`
`inst/WORDLIST`	Added technical terms for spell checking
`R/zzz.R`	Added `calculate_ratio_app` to global variables list

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inst/shiny/www/templates/script_template.R

R/get_session_code.R

inst/shiny/modules/tab_nca/nca_results.R

R/ratio_calculations.R

R/get_session_script_code.R

R/ratio_calculations.R

R/get_session_script_code.R

Copilot · 2025-11-28T09:15:24Z

R/ratio_calculations.R

+      warning(
+        "Ratio ", ratio_table$PPTESTCD[i], " not computed.",
+        "No comparable groups found between RefGroups",
+        " (", ratio_table$RefGroups[i], ")",
+        "and TestGroups",
+        " (", ratio_table$TestGroups[i], ")"
+      )


The warning message is missing spacing between sentences. Add a space after "not computed." to improve readability: "Ratio ", ratio_table$PPTESTCD[i], " not computed. No comparable groups found..."

R/get_session_code.R

apply relevant copilot suggestions Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Gero1999 · 2026-01-09T10:25:03Z

@Shaakon35

when there is a duplicate in the app, a pop-up appears and you can exclude one point

I opened a new issue (#886) to address this apart, as it will need to modify further more other files from main

adnca created in cdisc_datasets$adnca is not exactly equal to the one in the zip file.

The differences I saw where DTYPE and the duplicates. So it would be related again with #886

ADPP and PP don't have the correct pk parameters, the selection of pk parameter is not correct in the script

Now it has been corrected in the last commits

@js3110

I am still getting this message every time I checkout your branch:

Warning message:
── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── aNCA conflicts
──
✖ `calculate_table_ratios_app` masks `aNCA::calculate_table_ratios_app()`.
ℹ Did you accidentally source a file rather than using `load_all()`?
  Run `rm(list = c("calculate_table_ratios_app"))` to remove the conflicts.

This is expected to happen when changing between dev-branches. This shouldn't present a problem to the user and neither to us once this change is stabilized.

m-kolomanski · 2026-01-09T13:50:31Z

R/get_session_code.R

Ok, but currently the function needs the session object, so you have to go through the app anyway? I would agree if the function also accepted a settings file and had a more generic name, but currently it does not.

At the very least, if we want to implement it this way right now and then add the functionality of parsing a settings file instead of session object, we should have

more generic name

# TODO comments with link or number of appropriate issue to rely that intent.

m-kolomanski · 2026-01-09T13:52:19Z

R/get_session_code.R

+  if (nrow(obj) == 0) {
+    return("data.frame()")
+  }


nitpick: This is redundant, as it is handled by lines 80-83

if (length(obj) == 0 && !is.null(obj)) { return(paste0(class(obj)[1], "()")) }

m-kolomanski · 2026-01-09T13:55:21Z

R/ratio_calculations.R

+#' AdjustingFactor, TestGroups, RefGroups, PPTESTCD.
+#' @returns The updated PKNCAresult object with added rows in the `result` data.frame.
+#' @export
+calculate_table_ratios_app <- function(res, ratio_table) {


m-kolomanski · 2026-01-09T13:58:28Z

R/ratio_calculations.R

+  ratio_results <- vector("list", nrow(ratio_table))
+
+  # Loop through each row of the ratio_table
+  for (i in seq_len(nrow(ratio_table))) {


suggestion: Use apply instead of a for loop.

m-kolomanski · 2026-01-09T14:00:55Z

R/ratio_calculations.R

+
+  all_ratios <- data.frame()
+
+  for (ix in seq_along(match_cols)) {


suggestion: use apply or some other mapping columns, create a list and then bind all rows at once instead of adding rows to an empty data frame one by one.

Gero1999 · 2026-01-12T08:44:47Z

At the very least, if we want to implement it this way right now and then add the functionality of parsing a settings file instead of session object, we should have: more generic name, TODO comments

I created a TODO and the implementation will be developed in #835. The name/refactoring of this function I will be done there just for easiness.

Here, in this PR, I removed the redundant check, renamed calculate_table_ratios_app > calculate_table_ratios & refactored to use apply

js3110 · 2026-01-12T15:13:15Z

LGTM :)

Shaakon35

Here we go!! Congratulations @Gero1999 👍

Shaakon35 · 2026-01-15T18:16:02Z

@Gero1999 Can you add in the README, in the Description bullet list:

reproduce your NCA outside of the app, with the R script created

…erse/aNCA into 467-enhancement/r-script

Merge branch '467-enhancement/r-script' of https://github.com/pharmaverse/aNCA into 467-enhancement/r-script # Conflicts: # DESCRIPTION

Gero1999 · 2026-01-19T11:05:24Z

Issue with flags was partially solved here (de-selection of rules prevent color reporting of rows): #896

Gero1999 · 2026-01-22T10:21:17Z

I will rework on this to properly incorporate the new aspects integrated in main:

BLQ imputation
additional grouping variables in ratios considered when requested
ZIP folder

I will include quick how-to-test for specifically these things to specifically review them

Gero1999 added 15 commits November 27, 2025 09:25

feat: add script template for all operations but slope exclusions & r…

6f54851

…atio calculations

feat: make a function to deparse the fill-in the script template

867957d

improve fun allowing reactives

84207ca

include reactives in template script

27a933f

feat: include in zip folder for code script

8fe876d

save filters and mapping for userData

3b8a051

include in session datapath & final units table

76ebe77

adapt script template for final units

b214e70

feat: add ratio table to the script

3e6ee2c

include slope_rules in userData

07bc425

generalize fun

0dedfca

integrate slope rules

68ef670

refactor: lintr

cf2d74b

man: add docs

2a898fc

update wordlist & global variables

3a2f51d

Copilot AI review requested due to automatic review settings November 28, 2025 09:10

Gero1999 linked an issue Nov 28, 2025 that may be closed by this pull request

Enhancement: R Script output for NCA workflow #467

Open

3 tasks

Copilot started reviewing on behalf of Gero1999 November 28, 2025 09:11 View session

Gero1999 requested a review from m-kolomanski November 28, 2025 09:13

Copilot finished reviewing on behalf of Gero1999 November 28, 2025 09:13

Gero1999 marked this pull request as ready for review November 28, 2025 09:13

Copilot AI reviewed Nov 28, 2025

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Copilot AI review requested due to automatic review settings November 28, 2025 09:28

Copilot started reviewing on behalf of Gero1999 November 28, 2025 09:28 View session

refactor: get_session_script_code

4f49a86

Gero1999 review requested due to automatic review settings November 28, 2025 09:33

Copilot finished reviewing on behalf of Gero1999 November 28, 2025 09:33

Gero1999 marked this pull request as draft November 28, 2025 09:39

refactor: lintr

bc3fb4d

add global vars to zzz.R

1b78da1

Gero1999 marked this pull request as ready for review January 9, 2026 10:25

Gero1999 requested a review from Shaakon35 January 9, 2026 14:21

m-kolomanski reviewed Jan 9, 2026

View reviewed changes

Gero1999 added 4 commits January 9, 2026 17:05

add todo & rm redundant data.frame check

a332b90

rename calculate_table_ratios_app > calculate_table ratios

af3fd7c

use apply instead of a for loop in ratio_calculations.R

7144766

man: roxygenise & refactor lintr

ef71957

Gero1999 requested a review from m-kolomanski January 12, 2026 09:07

Merge branch 'main' into 467-enhancement/r-script

47c2b2f

Merge branch 'main' into 467-enhancement/r-script

1fb2b2a

Shaakon35 approved these changes Jan 15, 2026

View reviewed changes

Gero1999 and others added 4 commits January 16, 2026 09:31

readme: add R script msg

892d4d8

add PR task temporarely until tests are added

b80a389

Merge branch '467-enhancement/r-script' of https://github.com/pharmav…

5b60c53

…erse/aNCA into 467-enhancement/r-script

Merge branch 'main' into 467-enhancement/r-script

cb35e83

Gero1999 linked an issue Jan 19, 2026 that may be closed by this pull request

Enhancement: refactor pivot_wider_pknca_results #813

Open

4 tasks

Gero1999 changed the title ~~467 enhancement/r script~~ #467: Create R script to replicate App outputs Jan 19, 2026

Gero1999 changed the title ~~#467: Create R script to replicate App outputs~~ Create R script to replicate App outputs (#467) Jan 19, 2026

Gero1999 added 2 commits January 19, 2026 12:00

rephrase news & bump pkg version

20c47d4

merge: conflict in pkg version solved using current

3370ca7

Merge branch '467-enhancement/r-script' of https://github.com/pharmaverse/aNCA into 467-enhancement/r-script # Conflicts: # DESCRIPTION

Gero1999 mentioned this pull request Jan 19, 2026

Allow user to customize their exported ZIP using new UX/UI (#638) #905

Merged

8 tasks

Merge remote-tracking branch 'origin/main' into 467-enhancement/r-script

086f66e

Gero1999 marked this pull request as draft January 22, 2026 10:19


		all_ratios <- data.frame()

		for (ix in seq_along(match_cols)) {

Create R script to replicate App outputs (#467) #789

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