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Andreas Gammelgaard Damsbo 2025-04-24 12:53:47 +02:00
parent 6a43ba7b5b
commit ab780591b1
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8 changed files with 1072 additions and 127 deletions
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13
NAMESPACE
View file

@ -18,6 +18,8 @@ export(clean_sep)
export(columnSelectInput)
export(contrast_text)
export(create_baseline)
export(create_column_server)
export(create_column_ui)
export(create_log_tics)
export(create_overview_datagrid)
export(create_plot)
@ -45,6 +47,7 @@ export(format_writer)
export(get_fun_options)
export(get_label)
export(get_plot_options)
export(get_var_icon)
export(getfun)
export(gg_theme_export)
export(gg_theme_shiny)
@ -67,11 +70,13 @@ export(is_valid_token)
export(launch_FreesearchR)
export(limit_log)
export(line_break)
export(list_allowed_operations)
export(m_redcap_readServer)
export(m_redcap_readUI)
export(merge_expression)
export(merge_long)
export(missing_fraction)
export(modal_create_column)
export(modal_cut_variable)
export(modal_update_factor)
export(modify_qmd)
@ -102,6 +107,7 @@ export(repeated_instruments)
export(sankey_ready)
export(selectInputIcon)
export(set_column_label)
export(show_data)
export(sort_by)
export(specify_qmd_format)
export(subset_types)
@ -117,6 +123,7 @@ export(update_variables_ui)
export(vectorSelectInput)
export(vertical_stacked_bars)
export(wide2long)
export(winbox_create_column)
export(winbox_update_factor)
export(wrap_plot_list)
export(write_quarto)
@ -134,6 +141,7 @@ importFrom(htmltools,css)
importFrom(htmltools,tagList)
importFrom(htmltools,tags)
importFrom(htmltools,validateCssUnit)
importFrom(phosphoricons,ph)
importFrom(rlang,"%||%")
importFrom(rlang,call2)
importFrom(rlang,expr)
@ -152,20 +160,25 @@ importFrom(shiny,isTruthy)
importFrom(shiny,modalDialog)
importFrom(shiny,moduleServer)
importFrom(shiny,numericInput)
importFrom(shiny,observe)
importFrom(shiny,observeEvent)
importFrom(shiny,plotOutput)
importFrom(shiny,reactive)
importFrom(shiny,reactiveValues)
importFrom(shiny,renderPlot)
importFrom(shiny,renderUI)
importFrom(shiny,req)
importFrom(shiny,restoreInput)
importFrom(shiny,selectizeInput)
importFrom(shiny,showModal)
importFrom(shiny,tagList)
importFrom(shiny,textAreaInput)
importFrom(shiny,textInput)
importFrom(shiny,uiOutput)
importFrom(shiny,updateActionButton)
importFrom(shiny,updateTextAreaInput)
importFrom(shinyWidgets,WinBox)
importFrom(shinyWidgets,alert)
importFrom(shinyWidgets,noUiSliderInput)
importFrom(shinyWidgets,prettyCheckbox)
importFrom(shinyWidgets,updateVirtualSelect)

2
R/app_version.R
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@ -1 +1 @@
app_version <- function()'v25.4.4.250424'
app_version <- function()'v25.4.3.250424'

BIN
R/sysdata.rda
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230
SESSION.md
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@ -1,80 +1,166 @@
--------------------------------------------------------------------------------
-------------------------------- R environment ---------------------------------
--------------------------------------------------------------------------------
|setting |value |
|:-----------|:-------------------------------------|
|version |R version 4.4.1 (2024-06-14) |
|os |macOS 15.3.1 |
|system |aarch64, darwin20 |
|ui |RStudio |
|language |(EN) |
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |Europe/Copenhagen |
|date |2025-04-24 |
|rstudio |2024.12.1+563 Kousa Dogwood (desktop) |
|pandoc |3.6.4 @ /opt/homebrew/bin/pandoc |
|quarto |1.6.40 @ /usr/local/bin/quarto |
|FreesearchR |25.4.4.250424 |
|setting |value |
|:-----------|:------------------------------------------|
|version |R version 4.4.1 (2024-06-14) |
|os |macOS 15.3.1 |
|system |aarch64, darwin20 |
|ui |RStudio |
|language |(EN) |
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |Europe/Copenhagen |
|date |2025-04-24 |
|rstudio |2024.12.1+563 Kousa Dogwood (desktop) |
|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
|quarto |1.6.40 @ /usr/local/bin/quarto |
|FreesearchR |25.4.3.250424 |
--------------------------------------------------------------------------------
----------------------------------- packages -----------------------------------
--------------------------------------------------------------------------------
|package |loadedversion |date |source |
|:-----------|:-------------|:----------|:--------------|
|bit |4.6.0 |2025-03-06 |CRAN (R 4.4.1) |
|bit64 |4.6.0-1 |2025-01-16 |CRAN (R 4.4.1) |
|cachem |1.1.0 |2024-05-16 |CRAN (R 4.4.1) |
|cli |3.6.4 |2025-04-23 |CRAN (R 4.4.1) |
|crayon |1.5.3 |2024-06-20 |CRAN (R 4.4.1) |
|desc |1.4.3 |2023-12-10 |CRAN (R 4.4.1) |
|devtools |2.4.5 |2022-10-11 |CRAN (R 4.4.0) |
|digest |0.6.37 |2024-08-19 |CRAN (R 4.4.1) |
|dplyr |1.1.4 |2023-11-17 |CRAN (R 4.4.0) |
|ellipsis |0.3.2 |2021-04-29 |CRAN (R 4.4.1) |
|evaluate |1.0.3 |2025-01-10 |CRAN (R 4.4.1) |
|fastmap |1.2.0 |2024-05-15 |CRAN (R 4.4.1) |
|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) |
|generics |0.1.3 |2022-07-05 |CRAN (R 4.4.1) |
|glue |1.8.0 |2024-09-30 |CRAN (R 4.4.1) |
|here |1.0.1 |2020-12-13 |CRAN (R 4.4.1) |
|hms |1.1.3 |2023-03-21 |CRAN (R 4.4.0) |
|htmltools |0.5.8.1 |2024-04-04 |CRAN (R 4.4.1) |
|htmlwidgets |1.6.4 |2023-12-06 |CRAN (R 4.4.0) |
|httpuv |1.6.16 |2025-04-16 |CRAN (R 4.4.1) |
|knitr |1.50 |2025-03-16 |CRAN (R 4.4.1) |
|later |1.4.2 |2025-04-08 |CRAN (R 4.4.1) |
|lifecycle |1.0.4 |2023-11-07 |CRAN (R 4.4.1) |
|magrittr |2.0.3 |2022-03-30 |CRAN (R 4.4.1) |
|memoise |2.0.1 |2021-11-26 |CRAN (R 4.4.0) |
|mime |0.13 |2025-03-17 |CRAN (R 4.4.1) |
|miniUI |0.1.2 |2025-04-17 |CRAN (R 4.4.1) |
|pillar |1.10.2 |2025-04-05 |CRAN (R 4.4.1) |
|pkgbuild |1.4.7 |2025-03-24 |CRAN (R 4.4.1) |
|pkgconfig |2.0.3 |2019-09-22 |CRAN (R 4.4.1) |
|pkgload |1.4.0 |2024-06-28 |CRAN (R 4.4.0) |
|profvis |0.4.0 |2024-09-20 |CRAN (R 4.4.1) |
|promises |1.3.2 |2024-11-28 |CRAN (R 4.4.1) |
|purrr |1.0.4 |2025-02-05 |CRAN (R 4.4.1) |
|R6 |2.6.1 |2025-02-15 |CRAN (R 4.4.1) |
|Rcpp |1.0.14 |2025-01-12 |CRAN (R 4.4.1) |
|readr |2.1.5 |2024-01-10 |CRAN (R 4.4.0) |
|remotes |2.5.0 |2024-03-17 |CRAN (R 4.4.1) |
|renv |1.1.4 |2025-03-20 |CRAN (R 4.4.1) |
|rlang |1.1.6 |2025-04-11 |CRAN (R 4.4.1) |
|rprojroot |2.0.4 |2023-11-05 |CRAN (R 4.4.1) |
|rsconnect |1.3.4 |2025-01-22 |CRAN (R 4.4.1) |
|rstudioapi |0.17.1 |2024-10-22 |CRAN (R 4.4.1) |
|sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.4.1) |
|shiny |1.10.0 |2024-12-14 |CRAN (R 4.4.1) |
|tibble |3.2.1 |2023-03-20 |CRAN (R 4.4.0) |
|tidyselect |1.2.1 |2024-03-11 |CRAN (R 4.4.0) |
|tzdb |0.5.0 |2025-03-15 |CRAN (R 4.4.1) |
|urlchecker |1.0.1 |2021-11-30 |CRAN (R 4.4.1) |
|usethis |3.1.0 |2024-11-26 |CRAN (R 4.4.1) |
|vctrs |0.6.5 |2023-12-01 |CRAN (R 4.4.0) |
|vroom |1.6.5 |2023-12-05 |CRAN (R 4.4.0) |
|withr |3.0.2 |2024-10-28 |CRAN (R 4.4.1) |
|xfun |0.52 |2025-04-02 |CRAN (R 4.4.1) |
|xtable |1.8-4 |2019-04-21 |CRAN (R 4.4.1) |
|package |loadedversion |date |source |
|:-------------|:-------------|:----------|:--------------|
|apexcharter |0.4.4 |2024-09-06 |CRAN (R 4.4.1) |
|assertthat |0.2.1 |2019-03-21 |CRAN (R 4.4.1) |
|backports |1.5.0 |2024-05-23 |CRAN (R 4.4.1) |
|bayestestR |0.15.2 |2025-02-07 |CRAN (R 4.4.1) |
|bit |4.6.0 |2025-03-06 |CRAN (R 4.4.1) |
|bit64 |4.6.0-1 |2025-01-16 |CRAN (R 4.4.1) |
|boot |1.3-31 |2024-08-28 |CRAN (R 4.4.1) |
|broom |1.0.8 |2025-03-28 |CRAN (R 4.4.1) |
|broom.helpers |1.20.0 |2025-03-06 |CRAN (R 4.4.1) |
|bsicons |0.1.2 |2023-11-04 |CRAN (R 4.4.0) |
|bslib |0.9.0 |2025-01-30 |CRAN (R 4.4.1) |
|cachem |1.1.0 |2024-05-16 |CRAN (R 4.4.1) |
|cellranger |1.1.0 |2016-07-27 |CRAN (R 4.4.0) |
|class |7.3-23 |2025-01-01 |CRAN (R 4.4.1) |
|classInt |0.4-11 |2025-01-08 |CRAN (R 4.4.1) |
|cli |3.6.5 |2025-04-23 |CRAN (R 4.4.1) |
|colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) |
|commonmark |1.9.5 |2025-03-17 |CRAN (R 4.4.1) |
|correlation |0.8.7 |2025-03-03 |CRAN (R 4.4.1) |
|crayon |1.5.3 |2024-06-20 |CRAN (R 4.4.1) |
|crosstalk |1.2.1 |2023-11-23 |CRAN (R 4.4.0) |
|data.table |1.17.0 |2025-02-22 |CRAN (R 4.4.1) |
|datamods |1.5.3 |2024-10-02 |CRAN (R 4.4.1) |
|datawizard |1.0.2 |2025-03-24 |CRAN (R 4.4.1) |
|desc |1.4.3 |2023-12-10 |CRAN (R 4.4.1) |
|devtools |2.4.5 |2022-10-11 |CRAN (R 4.4.0) |
|DHARMa |0.4.7 |2024-10-18 |CRAN (R 4.4.1) |
|digest |0.6.37 |2024-08-19 |CRAN (R 4.4.1) |
|dplyr |1.1.4 |2023-11-17 |CRAN (R 4.4.0) |
|DT |0.33 |2024-04-04 |CRAN (R 4.4.0) |
|e1071 |1.7-16 |2024-09-16 |CRAN (R 4.4.1) |
|easystats |0.7.4 |2025-02-06 |CRAN (R 4.4.1) |
|effectsize |1.0.0 |2024-12-10 |CRAN (R 4.4.1) |
|ellipsis |0.3.2 |2021-04-29 |CRAN (R 4.4.1) |
|evaluate |1.0.3 |2025-01-10 |CRAN (R 4.4.1) |
|farver |2.1.2 |2024-05-13 |CRAN (R 4.4.1) |
|fastmap |1.2.0 |2024-05-15 |CRAN (R 4.4.1) |
|fontawesome |0.5.3 |2024-11-16 |CRAN (R 4.4.1) |
|forcats |1.0.0 |2023-01-29 |CRAN (R 4.4.0) |
|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) |
|generics |0.1.3 |2022-07-05 |CRAN (R 4.4.1) |
|ggplot2 |3.5.2 |2025-04-09 |CRAN (R 4.4.1) |
|glue |1.8.0 |2024-09-30 |CRAN (R 4.4.1) |
|gt |1.0.0 |2025-04-05 |CRAN (R 4.4.1) |
|gtable |0.3.6 |2024-10-25 |CRAN (R 4.4.1) |
|gtsummary |2.2.0 |2025-04-14 |CRAN (R 4.4.1) |
|haven |2.5.4 |2023-11-30 |CRAN (R 4.4.0) |
|here |1.0.1 |2020-12-13 |CRAN (R 4.4.1) |
|hms |1.1.3 |2023-03-21 |CRAN (R 4.4.0) |
|htmltools |0.5.8.1 |2024-04-04 |CRAN (R 4.4.1) |
|htmlwidgets |1.6.4 |2023-12-06 |CRAN (R 4.4.0) |
|httpuv |1.6.16 |2025-04-16 |CRAN (R 4.4.1) |
|IDEAFilter |0.2.0 |2024-04-15 |CRAN (R 4.4.0) |
|insight |1.2.0 |2025-04-22 |CRAN (R 4.4.1) |
|jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.4.0) |
|jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.4.1) |
|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.4.1) |
|keyring |1.3.2 |2023-12-11 |CRAN (R 4.4.0) |
|knitr |1.50 |2025-03-16 |CRAN (R 4.4.1) |
|later |1.4.2 |2025-04-08 |CRAN (R 4.4.1) |
|lattice |0.22-7 |2025-04-02 |CRAN (R 4.4.1) |
|lifecycle |1.0.4 |2023-11-07 |CRAN (R 4.4.1) |
|lme4 |1.1-37 |2025-03-26 |CRAN (R 4.4.1) |
|magrittr |2.0.3 |2022-03-30 |CRAN (R 4.4.1) |
|MASS |7.3-65 |2025-02-28 |CRAN (R 4.4.1) |
|Matrix |1.7-3 |2025-03-11 |CRAN (R 4.4.1) |
|memoise |2.0.1 |2021-11-26 |CRAN (R 4.4.0) |
|mime |0.13 |2025-03-17 |CRAN (R 4.4.1) |
|miniUI |0.1.2 |2025-04-17 |CRAN (R 4.4.1) |
|minqa |1.2.8 |2024-08-17 |CRAN (R 4.4.1) |
|modelbased |0.10.0 |2025-03-10 |CRAN (R 4.4.1) |
|munsell |0.5.1 |2024-04-01 |CRAN (R 4.4.1) |
|nlme |3.1-168 |2025-03-31 |CRAN (R 4.4.1) |
|nloptr |2.2.1 |2025-03-17 |CRAN (R 4.4.1) |
|openxlsx2 |1.14 |2025-03-20 |CRAN (R 4.4.1) |
|parameters |0.24.2 |2025-03-04 |CRAN (R 4.4.1) |
|patchwork |1.3.0 |2024-09-16 |CRAN (R 4.4.1) |
|performance |0.13.0 |2025-01-15 |CRAN (R 4.4.1) |
|phosphoricons |0.2.1 |2024-04-08 |CRAN (R 4.4.0) |
|pillar |1.10.2 |2025-04-05 |CRAN (R 4.4.1) |
|pkgbuild |1.4.7 |2025-03-24 |CRAN (R 4.4.1) |
|pkgconfig |2.0.3 |2019-09-22 |CRAN (R 4.4.1) |
|pkgload |1.4.0 |2024-06-28 |CRAN (R 4.4.0) |
|processx |3.8.6 |2025-02-21 |CRAN (R 4.4.1) |
|profvis |0.4.0 |2024-09-20 |CRAN (R 4.4.1) |
|promises |1.3.2 |2024-11-28 |CRAN (R 4.4.1) |
|proxy |0.4-27 |2022-06-09 |CRAN (R 4.4.1) |
|ps |1.9.1 |2025-04-12 |CRAN (R 4.4.1) |
|purrr |1.0.4 |2025-02-05 |CRAN (R 4.4.1) |
|quarto |1.4.4 |2024-07-20 |CRAN (R 4.4.0) |
|R.cache |0.16.0 |2022-07-21 |CRAN (R 4.4.0) |
|R.methodsS3 |1.8.2 |2022-06-13 |CRAN (R 4.4.1) |
|R.oo |1.27.0 |2024-11-01 |CRAN (R 4.4.1) |
|R.utils |2.13.0 |2025-02-24 |CRAN (R 4.4.1) |
|R6 |2.6.1 |2025-02-15 |CRAN (R 4.4.1) |
|rbibutils |2.3 |2024-10-04 |CRAN (R 4.4.1) |
|RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.4.1) |
|Rcpp |1.0.14 |2025-01-12 |CRAN (R 4.4.1) |
|Rdpack |2.6.4 |2025-04-09 |CRAN (R 4.4.1) |
|reactable |0.4.4 |2023-03-12 |CRAN (R 4.4.0) |
|readODS |2.3.2 |2025-01-13 |CRAN (R 4.4.1) |
|readr |2.1.5 |2024-01-10 |CRAN (R 4.4.0) |
|readxl |1.4.5 |2025-03-07 |CRAN (R 4.4.1) |
|REDCapCAST |25.3.2 |2025-03-10 |CRAN (R 4.4.1) |
|REDCapR |1.4.0 |2025-01-11 |CRAN (R 4.4.1) |
|reformulas |0.4.0 |2024-11-03 |CRAN (R 4.4.1) |
|remotes |2.5.0 |2024-03-17 |CRAN (R 4.4.1) |
|renv |1.1.4 |2025-03-20 |CRAN (R 4.4.1) |
|report |0.6.1 |2025-02-07 |CRAN (R 4.4.1) |
|rio |1.2.3 |2024-09-25 |CRAN (R 4.4.1) |
|rlang |1.1.6 |2025-04-11 |CRAN (R 4.4.1) |
|rmarkdown |2.29 |2024-11-04 |CRAN (R 4.4.1) |
|rprojroot |2.0.4 |2023-11-05 |CRAN (R 4.4.1) |
|rsconnect |1.3.4 |2025-01-22 |CRAN (R 4.4.1) |
|rstudioapi |0.17.1 |2024-10-22 |CRAN (R 4.4.1) |
|sass |0.4.10 |2025-04-11 |CRAN (R 4.4.1) |
|scales |1.3.0 |2023-11-28 |CRAN (R 4.4.0) |
|see |0.11.0 |2025-03-11 |CRAN (R 4.4.1) |
|sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.4.1) |
|shiny |1.10.0 |2024-12-14 |CRAN (R 4.4.1) |
|shinybusy |0.3.3 |2024-03-09 |CRAN (R 4.4.0) |
|shinyTime |1.0.3 |2022-08-19 |CRAN (R 4.4.0) |
|shinyWidgets |0.9.0 |2025-02-21 |CRAN (R 4.4.1) |
|stringi |1.8.7 |2025-03-27 |CRAN (R 4.4.1) |
|styler |1.10.3 |2024-04-07 |CRAN (R 4.4.0) |
|tibble |3.2.1 |2023-03-20 |CRAN (R 4.4.0) |
|tidyr |1.3.1 |2024-01-24 |CRAN (R 4.4.1) |
|tidyselect |1.2.1 |2024-03-11 |CRAN (R 4.4.0) |
|toastui |0.4.0 |2025-04-03 |CRAN (R 4.4.1) |
|tzdb |0.5.0 |2025-03-15 |CRAN (R 4.4.1) |
|urlchecker |1.0.1 |2021-11-30 |CRAN (R 4.4.1) |
|usethis |3.1.0 |2024-11-26 |CRAN (R 4.4.1) |
|vctrs |0.6.5 |2023-12-01 |CRAN (R 4.4.0) |
|vroom |1.6.5 |2023-12-05 |CRAN (R 4.4.0) |
|withr |3.0.2 |2024-10-28 |CRAN (R 4.4.1) |
|writexl |1.5.4 |2025-04-15 |CRAN (R 4.4.1) |
|xfun |0.52 |2025-04-02 |CRAN (R 4.4.1) |
|xml2 |1.3.8 |2025-03-14 |CRAN (R 4.4.1) |
|xtable |1.8-4 |2019-04-21 |CRAN (R 4.4.1) |
|yaml |2.3.10 |2024-07-26 |CRAN (R 4.4.1) |
|zip |2.3.2 |2025-02-01 |CRAN (R 4.4.1) |

928
inst/apps/FreesearchR/app.R
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2
inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf
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@ -5,6 +5,6 @@ account: agdamsbo
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 14600805
bundleId: 10169675
bundleId: 10170130
url: https://agdamsbo.shinyapps.io/FreesearchR/
version: 1

12
inst/apps/FreesearchR/server.R
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@ -2,7 +2,7 @@ library(readr)
library(MASS)
library(stats)
library(gt)
library(openxlsx2)
# library(openxlsx2)
library(haven)
library(readODS)
require(shiny)
@ -15,16 +15,16 @@ library(broom)
library(broom.helpers)
# library(REDCapCAST)
library(easystats)
library(esquisse)
# library(esquisse)
library(patchwork)
library(DHARMa)
library(apexcharter)
library(toastui)
library(datamods)
library(data.table)
library(IDEAFilter)
library(shinyWidgets)
library(DT)
library(data.table)
library(gtsummary)
# library(FreesearchR)
@ -319,13 +319,13 @@ server <- function(input, output, session) {
shiny::observeEvent(
input$modal_column,
datamods::modal_create_column(
modal_create_column(
id = "modal_column",
footer = "This window is aimed at advanced users and require some R-experience!",
title = "Create new variables"
)
)
data_modal_r <- datamods::create_column_server(
data_modal_r <- create_column_server(
id = "modal_column",
data_r = reactive(rv$data)
)
@ -448,7 +448,7 @@ server <- function(input, output, session) {
)
observeEvent(input$modal_browse, {
datamods::show_data(REDCapCAST::fct_drop(rv$data_filtered), title = "Uploaded data overview", type = "modal")
show_data(REDCapCAST::fct_drop(rv$data_filtered), title = "Uploaded data overview", type = "modal")
})
output$original_str <- renderPrint({

12
inst/apps/FreesearchR/ui.R
View file

@ -507,15 +507,9 @@ dark <- custom_theme(
ui <- bslib::page_fixed(
prismDependencies,
prismRDependency,
shiny::tags$head(includeHTML(("www/umami-app.html"))),
shiny::tags$style(
type = "text/css",
# add the name of the tab you want to use as title in data-value
shiny::HTML(
".container-fluid > .nav > li >
a[data-value='FreesearchR'] {font-size: 28px}"
)
),
shiny::tags$head(
includeHTML(("www/umami-app.html")),
tags$link(rel = "stylesheet", type = "text/css", href = "style.css")),
title = "FreesearchR",
theme = light,
shiny::useBusyIndicators(),