Adds rmarkdown module

[averissimo]

Pull Request

• Fixes https://github.com/insightsengineering/coredev-tasks/issues/675

Thanks to @StefanThoma's for working on the first prototype

Changes description

• Adds rmarkdown module
• Renders the output to module UI and to Reporter
• Source code is not verified as it adds a comment on how to render it
• Adds download button to get the original Rmd file
  • Option in module to enable or disable this functionality
  • downloaded Rmd has module's data included (data pre-processing + filter)
• Uses extra_transform parameter to add "generic decorators" to the top of the UI
  • name is temporary
• Ensure figures are displayed properly in reporter (PDF output)
• Avoid encoding images to base64 (mayb keep it in raw or equivalent)

To discuss

• Should we render the .R to get all the R code from the report and add it to the code of the qenv?
• [limitation] Use of markdown when rendering doesn't print title nor author
  • Rendering it on the page breaks teal
  • Wrapping in iframe doesn't extend full height and then creates strange reports
• Should we use transformers to add extra input / data manipulation
  • Or keep a parameters that allows to add transforms (for example extra inputs) to the module by the app developer

(topics below added from conversation with @gogonzo )

• should teal_report contain markdown elements?
• should teal_data evaluate rmarkdown::render() and include this to @code
• should markdown be evaluated with rmarkdown::render(envir = <qenv>) instead of params = list()?
  • visibility concern here on developing the Rmd

App (same 2nd one in example, but with download = TRUE)

pkgload::load_all("../teal.modules.general")

data <- teal_data()
data <- within(data, {
  CO2 <- CO2
  CO2[["primary_key"]] <- seq_len(nrow(CO2))
})
join_keys(data) <- join_keys(join_key("CO2", "CO2", "primary_key"))

static_decorator <- teal_transform_module(
  label = "N Cols selector",
  ui = function(id) {
    ns <- NS(id)
    tags$div(
      numericInput(ns("n_rows"), "Show n rows", value = 5, min = 0, max = 200, step = 5)
    )
  },
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      reactive({
        req(data())
        within(data(), {
          n_rows <- n_rows_value
        }, n_rows_value = input$n_rows)
      })
    })
  }
)

app <- init(
  data = data,
  modules = modules(
    tm_rmarkdown(
      label = "RMarkdown Module",
      rmd_content = readLines(system.file(file.path("sample_files", "co2_example.Rmd"), package = "teal.modules.general")),
      allow_download = TRUE,
      extra_transform = list(static_decorator)
    )
  )
) |> shiny::runApp()

[averissimo]

Marked as ready to review to start the discussion

[github-actions]

Code Coverage Summary

Filename                      Stmts    Miss  Cover    Missing
--------------------------  -------  ------  -------  -------------------------------------------
R/tm_a_pca.R                    864     864  0.00%    141-1132
R/tm_a_regression.R             751     751  0.00%    180-1027
R/tm_data_table.R               200     200  0.00%    100-348
R/tm_file_viewer.R              172     172  0.00%    47-254
R/tm_front_page.R               143     132  7.69%    77-246
R/tm_g_association.R            320     320  0.00%    161-547
R/tm_g_bivariate.R              664     406  38.86%   332-786, 827, 932, 949, 967, 978-1000
R/tm_g_distribution.R          1106    1106  0.00%    156-1404
R/tm_g_response.R               345     345  0.00%    179-594
R/tm_g_scatterplot.R            709     709  0.00%    261-1065
R/tm_g_scatterplotmatrix.R      272     253  6.99%    200-501, 562, 576
R/tm_missing_data.R            1080    1080  0.00%    124-1380
R/tm_outliers.R                1029    1029  0.00%    162-1341
R/tm_rmarkdown.R                154      68  55.84%   144-196, 225-240, 284-285, 345-368
R/tm_t_crosstable.R             263     263  0.00%    177-482
R/tm_variable_browser.R         887     881  0.68%    89-1113, 1164-1347
R/utils.R                       185     120  35.14%   87-250, 279-305, 317-326, 331, 345-364, 453
R/zzz.R                           2       2  0.00%    2-3
TOTAL                          9146    8701  4.87%

Diff against main

Filename            Stmts    Miss  Cover
----------------  -------  ------  -------
R/tm_rmarkdown.R     +154     +68  +55.84%
TOTAL                +154     +68  +0.87%

Results for commit: d2df067

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[gogonzo]

Shouldn't both documets be reproducible?

• document downloaded from tm_rmarkdown
• document downloaded via reporter

[gogonzo]

Key questions:

1. What app-user should be able to download in tm_markdown

• Should this document be reproducible and contain pre-processing, filter-panel and transformator code? Should this document contain outputs?
• I don't think that app-user should receive the same file as app-developer provides do the tm_markdown. app-developer uses rmd file just as a template to handle data, produce outputs (plots and tables) and produce final document by specifying document: html_document/md_document/etc.. App-user thought receives document which content is controlled by app-developer - this could be markdown file containing/not containing code-chunks, html-file, pdf file etc.

2. What should be added to the teal_card (reporter)

• html/md content as single teal_card element?
• md content converted to teal_card elements (multiple elements)?
• rmarkdown::render() call (this is a joke - markdown::render inside of markdown file would be crazy)
• nothing

[StefanThoma]

Would it be possible to use the reporter function to download a rendered document? Ideally the user would have the choice between html and pdf. What do you think?

…

On Fri, Nov 7, 2025 at 8:38 AM Dawid Kałędkowski ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In R/tm_rmarkdown.R <#944 (comment)> : > + + if (allow_download) { + out_data <- eval_code( + q_r(), + paste( + sep = "\n", + sprintf("## R Markdown contents are generated from file, please download it from the module UI."), + sprintf("# rmarkdown::render(%s, params = params)", shQuote(basename(rmd_file), type = "cmd")) + ) + ) + ***@***.*** <- FALSE # manual change verified status as code is being injected + } + + teal.reporter::teal_card(out_data) <- c( + teal.reporter::teal_card(out_data), + rendered_html_r() We could keep it as a single markdown object I think its good to have a single markdown string because anyway at the end (before download) we will concatenate everything to the single file. Only editor will show one combined text-field for this element (i think it is not a big issue so far) the current approach was meant to reduce duplicate rendering This is a fair reason. I feel (not a strong opinion) that if you render markdown using rmarkdown::render and includeMarkdown the speed should be similar to rmarkdown::render to html. rmarkdown renders in two stages to html, first by converting Rmd -> md and then pandoc renders from md -> html. The biggest issue with including html is that html can't be converted to pdf, otf etc. — Reply to this email directly, view it on GitHub <#944 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJUWWERCKCNM7NA66YG6VVT33REA3AVCNFSM6AAAAACLHVPL3CVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZTIMZSGA3TSNRYGU> . You are receiving this because you were mentioned.Message ID: <insightsengineering/teal.modules.general/pull/944/review/3432079685@ github.com>

[averissimo]

@StefanThoma that's one of our goals with this PR. It's now possible for HTML output, the other formats are a WIP, but I believe we'll make it happen

[github-actions]

Unit Tests Summary

  1 files   24 suites   15m 33s ⏱️
158 tests 150 ✅ 5 💤 2 ❌ 1 🔥
480 runs  471 ✅ 5 💤 3 ❌ 1 🔥

For more details on these failures and errors, see this check.

Results for commit d2df067.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
shinytest2-tm_a_pca	💔	$137.41$	$+6.73$	$0$	$0$	$0$	$0$
shinytest2-tm_a_regression	💔	$64.61$	$+4.30$	$0$	$0$	$0$	$0$
shinytest2-tm_data_table	💔	$25.80$	$+2.38$	$0$	$0$	$0$	$0$
shinytest2-tm_file_viewer	💚	$31.42$	$-2.79$	$-1$	$0$	$+3$	$+1$
shinytest2-tm_front_page	💔	$24.25$	$+1.78$	$0$	$0$	$0$	$0$
shinytest2-tm_g_bivariate	💔	$87.40$	$+3.67$	$0$	$0$	$0$	$0$
shinytest2-tm_g_distribution	💔	$55.98$	$+3.18$	$0$	$0$	$0$	$0$
shinytest2-tm_g_response	💔	$35.12$	$+2.35$	$0$	$0$	$0$	$0$
shinytest2-tm_g_scatterplot	💔	$70.55$	$+3.97$	$0$	$0$	$0$	$0$
shinytest2-tm_g_scatterplotmatrix	💔	$31.73$	$+2.39$	$0$	$0$	$0$	$0$
shinytest2-tm_misssing_data	💔	$58.57$	$+4.31$	$0$	$0$	$0$	$0$
shinytest2-tm_outliers	💔	$138.01$	$+10.52$	$0$	$0$	$0$	$0$
shinytest2-tm_t_crosstable	💔	$36.78$	$+2.24$	$0$	$0$	$0$	$0$
shinytest2-tm_variable_browser	💔	$78.95$	$+5.61$	$0$	$0$	$0$	$0$
tm_rmarkdown	👶		$+0.32$	$+4$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
examples	👶		$+0.01$	example_dot_markdown_internal.Rd
examples	👶		$+0.01$	example_is_tab_active_js.Rd
examples	👶		$+0.10$	example_tm_rmarkdown.Rd
shinytest2-tm_a_pca	💔	$30.61$	$+1.05$	e2e_tm_a_pca_Changing_output_encodings_of_plot_type_hides_and_shows_options.
shinytest2-tm_file_viewer	💚	$8.29$	$-3.93$	e2e_tm_file_viewer_Shows_selected_image_file
shinytest2-tm_g_bivariate	💔	$34.25$	$+1.51$	e2e_tm_g_bivariate_Setting_encoding_inputs_produces_outputs_without_validation_errors.
shinytest2-tm_g_distribution	💔	$20.05$	$+1.42$	e2e_tm_g_distribution_Histogram_encoding_inputs_produce_output_without_validation_errors.
shinytest2-tm_g_scatterplot	💔	$34.41$	$+1.57$	e2e_tm_g_scatterplot_The_encoding_inputs_are_set_without_validation_errors.
shinytest2-tm_outliers	💔	$12.78$	$+1.22$	e2e_tm_outliers_Data_extract_spec_elements_are_initialized_with_the_default_values_specified_by_outlier_var_and_categorical_var_argument.
shinytest2-tm_outliers	💔	$29.70$	$+1.64$	e2e_tm_outliers_Outlier_definition_text_and_range_are_displayed_properly_depending_on_method.
shinytest2-tm_outliers	💔	$14.42$	$+1.44$	e2e_tm_outliers_Outliers_summary_table_is_displayed_with_proper_content.
shinytest2-tm_outliers	💔	$19.93$	$+1.08$	e2e_tm_outliers_Plot_type_is_hidden_when_Boxplot_tab_is_not_selected.
shinytest2-tm_variable_browser	💔	$12.01$	$+1.05$	e2e_tm_variable_browser_Selecting_treat_variable_as_factor_changes_the_table_headers.
shinytest2-tm_variable_browser	💔	$19.01$	$+1.10$	e2e_tm_variable_browser_changing_plot_setting_encodings_doesn_t_show_errors.
tm_rmarkdown	👶		$+0.09$	srv_rmarkdown_renders_expected_html
tm_rmarkdown	👶		$+0.16$	srv_rmarkdown_renders_number_of_rows_of_my_data_to_markdown_file
tm_rmarkdown	👶		$+0.07$	srv_rmarkdown_returns_a_teal.reporter_reactive

Results for commit 82ed11b

♻️ This comment has been updated with latest results.

[osenan]

Is it possible to create unit tests for srv_markdown? With testServer I think it has complex enough server logic to implement them.
Also check if other exported funcions we can create uni test.
I tested the app, based on examples. It looks ok:

But the markdown text is written by he teal_developr right? Are not the users who can add/remove markdown text

[averissimo]

@osenan I've added tests and I think I addressed your comments.

Let's have a new round of review :-)

[osenan]

Thanks for the tests. I have run them locally and they pass. They do not pass in CI due to e2e tests.
They are also very useful. There is a lintr error, we could ignore the lint for names in that line.