Show only datasets used #1309

llrs-roche · 2025-01-09T10:11:00Z

Pull Request

Only tm_g_ci and tm_g_barcart_simple didn't have the datanames of the module configurable.
I modified tm_g_ci and tm_g_barcart_simple so that only the datasets used are displayed on the module.

See the examples below where the b dataset is not shown on this PR.

`tm_g_ci` example

devtools::load_all("../teal.modules.clinical")
data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb
  
  # Note that this dataset when using this module from this PR does not appear.
  b <- data.frame(r = runif(50))
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

app <- init(
  data = data,
  modules = modules(
    tm_g_ci(
      label = "Confidence Interval Plot",
      x_var = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = c("ARMCD", "BMRKR2"),
          selected = c("ARMCD"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      y_var = data_extract_spec(
        dataname = "ADLB",
        filter = list(
          filter_spec(
            vars = "PARAMCD",
            choices = levels(ADLB$PARAMCD),
            selected = levels(ADLB$PARAMCD)[1],
            multiple = FALSE,
            label = "Select lab:"
          ),
          filter_spec(
            vars = "AVISIT",
            choices = levels(ADLB$AVISIT),
            selected = levels(ADLB$AVISIT)[1],
            multiple = FALSE,
            label = "Select visit:"
          )
        ),
        select = select_spec(
          label = "Analyzed Value",
          choices = c("AVAL", "CHG"),
          selected = "AVAL",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      color = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Color by variable",
          choices = c("SEX", "STRATA1", "STRATA2"),
          selected = c("STRATA1"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

`tm_g_barchart_simple` example

devtools::load_all("../teal.modules.clinical")
library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl %>%
    mutate(ITTFL = factor("Y") %>%
             with_label("Intent-To-Treat Population Flag"))
  ADAE <- tmc_ex_adae %>%
    filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
  
  # Note that this dataset does not appear on this PR when using this module.
  b <- data.frame(r = runif(50))
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADAE <- data[["ADAE"]]

app <- init(
  data = data,
  modules = modules(
    tm_g_barchart_simple(
      label = "ADAE Analysis",
      x = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = variable_choices(
            ADSL,
            c(
              "ARM", "ACTARM", "SEX",
              "RACE", "ITTFL", "SAFFL", "STRATA2"
            )
          ),
          selected = "ACTARM",
          multiple = FALSE
        )
      ),
      fill = list(
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = "SEX",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = NULL,
            multiple = FALSE
          )
        )
      ),
      x_facet = list(
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = "AETOXGR",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = NULL,
            multiple = FALSE
          )
        )
      ),
      y_facet = list(
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = "AESEV",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = NULL,
            multiple = FALSE
          )
        )
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

I don't think the documentation of these modules needs to be updated. (The only change on the documentation is to fix a typo)

R/tm_g_ci.R

m7pr · 2025-01-14T07:42:00Z

@llrs-roche R CMD CHECKs are failiing. Can you review?

teal.modules.clinical.Rproj

llrs-roche · 2025-01-14T09:20:08Z

Triggering the tests again, as they were mainly dependency setup, then I'll try to fix them locally

github-actions · 2025-01-14T09:29:06Z

Unit Tests Summary

1 files 70 suites 1h 10m 16s ⏱️
727 tests 614 ✅ 113 💤 0 ❌
1 987 runs 1 759 ✅ 228 💤 0 ❌

Results for commit 0d62e91.

♻️ This comment has been updated with latest results.

m7pr · 2025-01-14T09:41:04Z

Stuff like that is visible in the dependency installation for documentation build

  ℹ Creating lockfile '.github/pkg.lock'
  ✖ Creating lockfile '.github/pkg.lock' [6.2s]
  
  Error: 
  ! error in pak subprocess
  Caused by error: 
  ! Could not solve package dependencies:
  * deps::.: dependency conflict
  * any::sessioninfo: dependency conflict
  ---
  Backtrace:
  1. pak::lockfile_create(c(deps, extra_deps), lockfile = ".github/pkg.lock", …
  2. pak:::remote(function(...) { …
  3. err$throw(res$error)
  ---
  Subprocess backtrace:
  1. base::withCallingHandlers(cli_message = function(msg) { …
  2. get("lockfile_create_internal", asNamespace("pak"))(...)
  3. prop$stop_for_solution_error()
  4. private$plan$stop_for_solve_error()
  5. pkgdepends:::pkgplan_stop_for_solve_error(self, private)
  6. base::throw(new_error("Could not solve package dependencies:\n", msg, …
  7. | base::signalCondition(cond)
  8. global (function (e) …
  Execution halted
  Error: Process completed with exit code 1.

llrs-roche · 2025-01-14T10:02:37Z

I'll compare the Docs/ Pkgdown docs dependency problems with the check run, that could solve the dependencies: https://github.com/insightsengineering/teal.modules.clinical/actions/runs/12687811698/job/35577032936?pr=1309

github-actions · 2025-01-14T10:39:25Z

Unit Test Performance Difference

Test suite performance difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
shinytest2-tm_a_gee	💔	$127.28$	$+4.18$	$0$	$0$	$0$	$0$
shinytest2-tm_a_mmrm	💔	$739.41$	$+14.22$	$0$	$0$	$0$	$0$
shinytest2-tm_g_barchart_simple	💔	$223.12$	$+2.48$	$0$	$0$	$0$	$0$
shinytest2-tm_g_forest_rsp	💚	$177.71$	$-1.83$	$0$	$0$	$0$	$0$
shinytest2-tm_g_km	💚	$272.22$	$-2.05$	$0$	$0$	$0$	$0$
shinytest2-tm_g_pp_adverse_events	💔	$124.62$	$+2.38$	$0$	$0$	$0$	$0$
shinytest2-tm_g_pp_patient_timeline	💔	$242.21$	$+1.85$	$0$	$0$	$0$	$0$
shinytest2-tm_g_pp_therapy	💔	$197.98$	$+1.01$	$0$	$0$	$0$	$0$
shinytest2-tm_g_pp_vitals	💔	$85.89$	$+2.31$	$0$	$0$	$0$	$0$
shinytest2-tm_t_abnormality_by_worst_grade	💔	$66.69$	$+1.73$	$0$	$0$	$0$	$0$
shinytest2-tm_t_ancova	💔	$93.66$	$+3.46$	$0$	$0$	$0$	$0$
shinytest2-tm_t_binary_outcome	💔	$75.58$	$+2.19$	$0$	$0$	$0$	$0$
shinytest2-tm_t_coxreg	💔	$72.25$	$+1.71$	$0$	$0$	$0$	$0$
shinytest2-tm_t_events	💔	$60.39$	$+1.74$	$0$	$0$	$0$	$0$
shinytest2-tm_t_events_by_grade	💔	$89.13$	$+2.93$	$0$	$0$	$0$	$0$
shinytest2-tm_t_events_patyear	💔	$50.54$	$+1.09$	$0$	$0$	$0$	$0$
shinytest2-tm_t_events_summary	💔	$66.61$	$+1.09$	$0$	$0$	$0$	$0$
shinytest2-tm_t_exposure	💔	$78.17$	$+1.35$	$0$	$0$	$0$	$0$
shinytest2-tm_t_pp_laboratory	💔	$122.92$	$+2.09$	$0$	$0$	$0$	$0$
shinytest2-tm_t_pp_medical_history	💔	$64.68$	$+1.67$	$0$	$0$	$0$	$0$
shinytest2-tm_t_pp_prior_medication	💔	$76.08$	$+3.48$	$0$	$0$	$0$	$0$
shinytest2-tm_t_shift_by_arm	💔	$57.10$	$+1.97$	$0$	$0$	$0$	$0$
shinytest2-tm_t_shift_by_arm_by_worst	💔	$88.41$	$+1.68$	$0$	$0$	$0$	$0$
shinytest2-tm_t_smq	💔	$57.89$	$+1.02$	$0$	$0$	$0$	$0$
shinytest2-tm_t_summary_by	💔	$76.90$	$+1.38$	$0$	$0$	$0$	$0$
shinytest2-tm_t_tte	💔	$65.24$	$+1.42$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
shinytest2-tm_a_mmrm	💔	$48.26$	$+1.09$	e2e_tm_a_mmrm_Validate_output_on_different_selection_on_method_g_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💔	$48.39$	$+1.05$	e2e_tm_a_mmrm_Validate_output_on_different_selection_on_method_t_mmrm_cov.

Results for commit 231d18d

♻️ This comment has been updated with latest results.

llrs-roche · 2025-01-14T15:27:06Z

The the initial lock files are identical. but on the Docs run when the DESCRIPTION file is modified I see:

Modify DESCRIPTION file (development)
  ℹ Loading metadata database
  ✔ Loading metadata database ... done
  
  ! Failed to resolve dependencies.
  Error:
  * local::teal.modules.clinical:
    * Can't install dependency teal (>= 0.15.2.9079) (>= 0.5.0.9015) (>= 0.6.10.9004) (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.transform (>= 0.5.0.9015) (>= 0.6.10.9004) (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency rtables (>= 0.6.10.9004) (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.code (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.data (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.reporter (>= 0.3.1.9017)
  End of error
  Failed refs: teal, teal.transform, rtables, teal.code, teal.data, and
  teal.reporter.
  ℹ Adding package teal (ref: "insightsengineering/teal") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.transform (ref: "insightsengineering/teal.transform") to the Config/Needs/DepsDev field.
  ℹ Adding package rtables (ref: "insightsengineering/rtables") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.code (ref: "insightsengineering/teal.code") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.data (ref: "insightsengineering/teal.data") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.reporter (ref: "insightsengineering/teal.reporter") to the Config/Needs/DepsDev field.
  ℹ Trying to resolve dependencies again.
  ---
  ! Failed to resolve dependencies.
  Error:
  * local::teal.modules.clinical:
    * Can't install dependency teal (>= 0.15.2.9079)
    * Can't install dependency insightsengineering/teal * insightsengineering/teal: Can't install dependency teal.slice (>= 0.5.1.9015)
  End of error
  Failed refs: teal, insightsengineering/teal, and teal.slice.
  ℹ Reference for package teal already exists in the Config/Needs/DepsDev field. Skipping.
  ℹ Reference for package teal already exists in the Config/Needs/DepsDev field. Skipping.
  ℹ Adding package teal.slice (ref: "insightsengineering/teal.slice") to the Config/Needs/DepsDev field.
  ℹ Trying to resolve dependencies again.
  ---
  ! Failed to resolve dependencies.
  Error:
  * local::teal.modules.clinical: dependency conflict
  End of error
  Failed refs: .
  ℹ Trying to resolve dependencies again.
  ---
  ! Failed to resolve dependencies.
  Error:
  * local::teal.modules.clinical: dependency conflict
  End of error
  Failed refs: .
  ✖ Failed to resolve dependencies. No progress. Exiting.

teal.slice: main at 0.5.1.9019
teal: main at 0.15.2.9098
So it should be able to find the right version, no sure what is happening here

llrs-roche · 2025-01-14T15:50:24Z

@pawelru there seems to be a problem on the Docs/Pkgdown github actions. The action is failing when the required versions are available on the main branch of their repositories (and it continues beyond the specific Modify DESCRIPTION)

pawelru · 2025-01-14T16:38:56Z

This is quite strange

I'm comparing the outcome of check and docs:

check logs

https://github.com/insightsengineering/teal.modules.clinical/actions/runs/12687811698/job/35577032936#step:18:2334

Modify DESCRIPTION file (development)
  ℹ Loading metadata database
  ✔ Loading metadata database ... done
  
  ! Failed to resolve dependencies.
  Error:
  * local::teal.modules.clinical/:
    * Can't install dependency teal (>= 0.15.2.9079) (>= 0.5.0.9015) (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.transform (>= 0.5.0.9015) (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.code (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.data (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.reporter (>= 0.3.1.9017)
  End of error
  Failed refs: teal, teal.transform, teal.code, teal.data, and teal.reporter.
  ℹ Adding package teal (ref: "insightsengineering/teal") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.transform (ref: "insightsengineering/teal.transform") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.code (ref: "insightsengineering/teal.code") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.data (ref: "insightsengineering/teal.data") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.reporter (ref: "insightsengineering/teal.reporter") to the Config/Needs/DepsDev field.
  ℹ Trying to resolve dependencies again.
  ---
  ! Failed to resolve dependencies.
  Error:
  * local::teal.modules.clinical/:
    * Can't install dependency teal (>= 0.15.2.9079)
    * Can't install dependency insightsengineering/teal * insightsengineering/teal: Can't install dependency teal.slice (>= 0.5.1.9015)
  End of error
  Failed refs: teal, insightsengineering/teal, and teal.slice.
  ℹ Reference for package teal already exists in the Config/Needs/DepsDev field. Skipping.
  ℹ Reference for package teal already exists in the Config/Needs/DepsDev field. Skipping.
  ℹ Adding package teal.slice (ref: "insightsengineering/teal.slice") to the Config/Needs/DepsDev field.
  ℹ Trying to resolve dependencies again.
  ---
  ✔ Dependencies resolved successfully.

docs logs

https://github.com/insightsengineering/teal.modules.clinical/actions/runs/12687811632/job/35363019866#step:11:2195

Modify DESCRIPTION file (development)
  ℹ Loading metadata database
  ✔ Loading metadata database ... done
  
  ! Failed to resolve dependencies.
  Error:
  * local::teal.modules.clinical:
    * Can't install dependency teal (>= 0.15.2.9079) (>= 0.5.0.9015) (>= 0.6.10.9004) (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.transform (>= 0.5.0.9015) (>= 0.6.10.9004) (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency rtables (>= 0.6.10.9004) (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.code (>= 0.5.0.9012) (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.data (>= 0.6.0.9015) (>= 0.3.1.9017)
    * Can't install dependency teal.reporter (>= 0.3.1.9017)
  End of error
  Failed refs: teal, teal.transform, rtables, teal.code, teal.data, and
  teal.reporter.
  ℹ Adding package teal (ref: "insightsengineering/teal") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.transform (ref: "insightsengineering/teal.transform") to the Config/Needs/DepsDev field.
  ℹ Adding package rtables (ref: "insightsengineering/rtables") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.code (ref: "insightsengineering/teal.code") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.data (ref: "insightsengineering/teal.data") to the Config/Needs/DepsDev field.
  ℹ Adding package teal.reporter (ref: "insightsengineering/teal.reporter") to the Config/Needs/DepsDev field.
  ℹ Trying to resolve dependencies again.
  ---
  ! Failed to resolve dependencies.
  Error:
  * local::teal.modules.clinical:
    * Can't install dependency teal (>= 0.15.2.9079)
    * Can't install dependency insightsengineering/teal * insightsengineering/teal: Can't install dependency teal.slice (>= 0.5.1.9015)
  End of error
  Failed refs: teal, insightsengineering/teal, and teal.slice.
  ℹ Reference for package teal already exists in the Config/Needs/DepsDev field. Skipping.
  ℹ Reference for package teal already exists in the Config/Needs/DepsDev field. Skipping.
  ℹ Adding package teal.slice (ref: "insightsengineering/teal.slice") to the Config/Needs/DepsDev field.
  ℹ Trying to resolve dependencies again.
  ---
  ! Failed to resolve dependencies.
  Error:
  * local::teal.modules.clinical: dependency conflict
  End of error
  Failed refs: .
  ℹ Trying to resolve dependencies again.
  ---
  ! Failed to resolve dependencies.
  Error:
  * local::teal.modules.clinical: dependency conflict
  End of error
  Failed refs: .
  ✖ Failed to resolve dependencies. No progress. Exiting.

Note that the first two steps are identical. In the first step we do teal, teal.transform, rtables, teal.code, teal.data, and teal.reporter. In the second step we do teal.slice. The third step in check is pass and in docs it is a fail without a meaningful error message. I don't know out of my head what could be a reason. I will have a deeper look tomorrow.

pawelru · 2025-01-15T14:13:01Z

I have rerun this and it just works ¯_(ツ)_/¯. Don't ask me why

https://github.com/insightsengineering/teal.modules.clinical/actions/runs/12687811632

This reverts commit c37422f.

llrs · 2025-01-15T16:22:19Z

@m7pr I removed the Rstudio changes on Rproj, but see the explanation about its implications and behavior.

m7pr · 2025-01-16T09:42:58Z

Just tested examples and non-specified datanames (b) are not shown

llrs-roche added 5 commits January 9, 2025 09:47

Fix typo

88bbe54

Use data extract list to provide flexibility to module's datanames.

8b6e482

Use data extract list to provide flexibility to module's datanames

18eb8a0

Rstudio updates

c37422f

Fix documentation typo on Rd

fd6079a

llrs-roche added the core label Jan 9, 2025

Change style

754dfd0

llrs-roche commented Jan 9, 2025

View reviewed changes

R/tm_g_ci.R Show resolved Hide resolved

llrs-roche mentioned this pull request Jan 9, 2025

upversion dep #1308

Merged

m7pr reviewed Jan 14, 2025

View reviewed changes

teal.modules.clinical.Rproj Outdated Show resolved Hide resolved

m7pr self-assigned this Jan 14, 2025

Merge branch 'main' into 1307_flexible_datanames@main

cc68e19

llrs-roche mentioned this pull request Jan 15, 2025

Add ability to set datanames insightsengineering/teal.modules.general#824

Merged

llrs-roche and others added 2 commits January 15, 2025 16:41

Revert "Rstudio updates"

47704a9

This reverts commit c37422f.

[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

0d62e91

m7pr approved these changes Jan 16, 2025

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llrs-roche merged commit 42135a1 into main Jan 16, 2025
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llrs-roche deleted the 1307_flexible_datanames@main branch January 16, 2025 10:06

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Show only datasets used #1309

Show only datasets used #1309

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Show only datasets used #1309

Show only datasets used #1309

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