Pre-release activities

[donyunardi]

Blocked by

• [CRAN Release]: v0.5.0 teal.transform#171
• [CRAN Release]: v0.4.0 teal.data#226
• [CRAN Release]: v0.15.0 teal#1013
• Decrease dependency #618
• test if current main branch code base is working with tern 0.9.3 #921
• [Bug]: Consistent argument names and defaults #923

Align package versions to

• teal.data (>= 0.4.0),
• teal.transform (>= 0.5.0),
• teal (>= 0.15.0),
• teal.widgets (>= 0.4.2),
• teal.logger (>= 0.1.3),
• teal.code(>= 0.5.0),
• teal.reporter (>= 0.2.1),
• tern.gee (>= 0.1.3),
• tern.mmrm (>= 0.3.0),
• rtables (>= 0.6.6),
• rlistings (>= 0.2.7),
• formatters (>= 0.5.5),
• tern (>= 0.9.3)

Summary

We need to clean up the package in preparation for the CRAN release.
CoreDev and SME will collaborate to complete these tasks:

SME tasks (Sprint 1)

• Review and update all functions:
  • No typos, no wrong formats
  • Make sure there is a meaningful description for every module function @shajoezhu, @khatril, @pawelru - adding here TLG-c general link
  • @example tag, make sure it runs, fix if otherwise
  • Make sure functions have @return tag to document the return value (@edelarua to decide which standard to use, they have all same output in form)
  • no \dontrun tag, replace with if(interactive()) if needed
  • tmc has argument_convention that serves as parameters template, make sure this is utilized correctly (i.e. no repetition of parameters).
  • Adding links to specific templates in TLG-c if already mentioned

• Review and update template and vignette that is related to tm_t_shift_by_arm.R #943
• Review and update template and vignette that is related to tm_a_gee.R #944
• Review and update template and vignette that is related to tm_g_ipp.R #945
• Review and update template and vignette that is related to tm_t_events_patyear.R #946
• Review and update template and vignette that is related to tm_t_abnormality.R #947
• Review and update template and vignette that is related to tm_t_abnormality_by_worst_grade.R #948
• Review and update template and vignette that is related to tm_t_events_by_grade.R #949
• Review and update template and vignette that is related to tm_t_shift_by_arm_by_worst.R #950
• Review and update template and vignette that is related to tm_a_mmrm.R #951
• Review and update template and vignette that is related to tm_g_ci.R #952
• Review and update template and vignette that is related to tm_t_summary.R #953
• Review and update template and vignette that is related to tm_g_barchart_simple.R #954
• Review and update template and vignette that is related to tm_t_exposure.R #955
• Review and update template and vignette that is related to tm_t_logistic.R #956
• Review and update template and vignette that is related to tm_t_coxreg.R #957
• Review and update template and vignette that is related to tm_t_events.R #958
• Review and update template and vignette that is related to tm_t_tte.R #959
• Review and update template and vignette that is related to tm_t_pp_prior_medication.R #960
• Review and update template and vignette that is related to tm_g_pp_adverse_events.R #961
• Review and update template and vignette that is related to tm_g_forest_rsp.R #962
• Review and update template and vignette that is related to tm_g_km.R #963
• Review and update template and vignette that is related to tm_g_pp_vitals.R #964
• Review and update template and vignette that is related to tm_t_pp_basic_info.R #965
• Review and update template and vignette that is related to tm_g_pp_patient_timeline.R #966
• Review and update template and vignette that is related to tm_g_forest_tte.R #967
• Review and update template and vignette that is related to tm_t_binary_outcome.R #968
• Review and update template and vignette that is related to tm_t_smq.R #969
• Review and update template and vignette that is related to tm_t_shift_by_grade.R #970
• Review and update template and vignette that is related to tm_t_pp_laboratory.R #971
• Review and update template and vignette that is related to tm_t_pp_medical_history.R #972
• Review and update template and vignette that is related to tm_t_ancova.R #973
• Review and update template and vignette that is related to tm_t_mult_events.R #974
• Review and update template and vignette that is related to tm_g_pp_therapy.R #975
• Review and update template and vignette that is related to tm_t_events_summary.R #977
• Review and update template and vignette that is related to tm_g_lineplot.R #976
• Review and update template and vignette that is related to tm_t_summary_by.R #978
• Review and update template and vignette that is related to tm_t_pp_laboratory.R #979

After that,

• check all vignette, update title and description in DESCRIPTION #1009, which includes the following

• Sanity check of all vignettes, make sure there is no typo, no wrong format, etc.
• Package Title is not duplicated in Package Description in DESCRIPTION file
• All package names in Title and Description fields of DESCRIPTION file are quoted with '
• Review package level documentation (teal.module.clinical.R)

CoreDev tasks (Sprint 2)

We'll move forward with these tasks once SME is done with their tasks.

• substitute assertthat:: usage with checkmate:: equivalents #1012
• Make sure there are no ::: in examples #1013
• remove examples for non-exported functions #1050
• final prerelease check #1014

@insightsengineering/nest-core-dev

[donyunardi]

cc @shajoezhu
Feel free to rearrange if necessary.

[donyunardi]

@insightsengineering/nest-core-dev

I am seeing warnings when clicking the Show R Code in our teal.gallery example app:

and when adding card to the Reporter Previewer:

This is from the efficacy app in teal.gallery example app (dev) for the Demographic Table module, which is using the tm_t_summary module.

This issue is caused by the verified slot in the teal_data object.
To remove this warning (assuming that we do want to remove it), we need to add a verify() method to the teal_data for the module.

So update for tm_t_summary needs to be done here:

teal.modules.clinical/R/tm_t_summary.R

Line 564 in 588688e

verbatim_content = shiny::reactive(teal.code::get_code(all_q())),

and here:

teal.modules.clinical/R/tm_t_summary.R

Line 583 in 588688e

card$append_src(teal.code::get_code(all_q()))

Could someone please confirm this or provide reasons why we shouldn't be doing this?

[vedhav]

@donyunardi That's a good catch. When I tested it, all the modules were showing me the "code unverified" warning.
Upon further investigation, it turns out that the internal function in teal teal:::.datasets_to_data() which is responsible for converting the FilteredData from the filter panel into teal_data object for the modules to use, always returns an unverified teal_data object.

[m7pr]

@vedhav do you think this can be closed? after #1069 is closed?

[vedhav]

Yeah, The issue that Dony pointed out is fixed as we merged #1069.

[Melkiades]

@donyunardi @shajoezhu, I moved up the additional fixes for single functions as we are going through them one after the other and it is the best way not to forget anything