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Andreas Gammelgaard Damsbo 2025-10-02 13:40:22 +02:00
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15
CITATION.cff
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@ -8,7 +8,7 @@ message: 'To cite package "FreesearchR" in publications use:'
type: software
license: AGPL-3.0-or-later
title: 'FreesearchR: Easy data analysis for clinicians'
version: 25.9.3
version: 25.10.1
doi: 10.5281/zenodo.14527429
identifiers:
- type: url
@ -1050,6 +1050,19 @@ references:
email: jakub.sobolewski@appsilon.com
year: '2025'
doi: 10.32614/CRAN.package.shiny.i18n
- type: software
title: stRoke
abstract: 'stRoke: Clinical Stroke Research'
notes: Imports
url: https://agdamsbo.github.io/stRoke/
repository: https://CRAN.R-project.org/package=stRoke
authors:
- family-names: Damsbo
given-names: Andreas Gammelgaard
email: agdamsbo@clin.au.dk
orcid: https://orcid.org/0000-0002-7559-1154
year: '2025'
doi: 10.32614/CRAN.package.stRoke
- type: software
title: styler
abstract: 'styler: Non-Invasive Pretty Printing of R Code'

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R/sysdata.rda
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30
SESSION.md
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@ -4,18 +4,18 @@
|setting |value |
|:-----------|:------------------------------------------|
|version |R version 4.4.1 (2024-06-14) |
|os |macOS 15.6.1 |
|os |macOS 15.7 |
|system |aarch64, darwin20 |
|ui |RStudio |
|language |(EN) |
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |Europe/Copenhagen |
|date |2025-09-25 |
|date |2025-10-02 |
|rstudio |2025.05.0+496 Mariposa Orchid (desktop) |
|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
|quarto |1.7.30 @ /usr/local/bin/quarto |
|FreesearchR |25.9.3.250925 |
|FreesearchR |25.10.1.251002 |
--------------------------------------------------------------------------------
@ -26,8 +26,6 @@
|apexcharter |0.4.4 |2024-09-06 |CRAN (R 4.4.1) |
|askpass |1.2.1 |2024-10-04 |CRAN (R 4.4.1) |
|assertthat |0.2.1 |2019-03-21 |CRAN (R 4.4.1) |
|attachment |0.4.5 |2025-03-14 |CRAN (R 4.4.1) |
|attempt |0.3.1 |2020-05-03 |CRAN (R 4.4.1) |
|backports |1.5.0 |2024-05-23 |CRAN (R 4.4.1) |
|base64enc |0.1-3 |2015-07-28 |CRAN (R 4.4.1) |
|bayestestR |0.16.1 |2025-07-01 |CRAN (R 4.4.1) |
@ -41,6 +39,7 @@
|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) |
|calendar |0.2.0 |2024-08-20 |CRAN (R 4.4.1) |
|cards |0.6.1 |2025-07-03 |CRAN (R 4.4.1) |
|cardx |0.2.5 |2025-07-03 |CRAN (R 4.4.1) |
|caTools |1.18.3 |2024-09-04 |CRAN (R 4.4.1) |
@ -55,7 +54,6 @@
|colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) |
|commonmark |2.0.0 |2025-07-07 |CRAN (R 4.4.1) |
|crayon |1.5.3 |2024-06-20 |CRAN (R 4.4.1) |
|credentials |2.0.2 |2024-10-04 |CRAN (R 4.4.1) |
|curl |6.4.0 |2025-06-22 |CRAN (R 4.4.1) |
|data.table |1.17.8 |2025-07-10 |CRAN (R 4.4.1) |
|datamods |1.5.3 |2024-10-02 |CRAN (R 4.4.1) |
@ -65,7 +63,6 @@
|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) |
|dockerfiler |0.2.5 |2025-05-07 |CRAN (R 4.4.1) |
|doParallel |1.0.17 |2022-02-07 |CRAN (R 4.4.0) |
|dplyr |1.1.4 |2023-11-17 |CRAN (R 4.4.0) |
|DT |0.33 |2024-04-04 |CRAN (R 4.4.0) |
@ -88,19 +85,16 @@
|foreach |1.5.2 |2022-02-02 |CRAN (R 4.4.0) |
|foreign |0.8-90 |2025-03-31 |CRAN (R 4.4.1) |
|Formula |1.2-5 |2023-02-24 |CRAN (R 4.4.1) |
|FreesearchR |25.9.3 |NA |NA |
|FreesearchR |25.10.1 |NA |NA |
|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) |
|gdtools |0.4.2 |2025-03-27 |CRAN (R 4.4.1) |
|generics |0.1.4 |2025-05-09 |CRAN (R 4.4.1) |
|gert |2.1.5 |2025-03-25 |CRAN (R 4.4.1) |
|ggalluvial |0.12.5 |2023-02-22 |CRAN (R 4.4.0) |
|ggcorrplot |0.1.4.1 |2023-09-05 |CRAN (R 4.4.0) |
|ggforce |0.5.0 |2025-06-18 |CRAN (R 4.4.1) |
|ggplot2 |3.5.2 |2025-04-09 |CRAN (R 4.4.1) |
|ggridges |0.5.6 |2024-01-23 |CRAN (R 4.4.0) |
|ggstats |0.10.0 |2025-07-02 |CRAN (R 4.4.1) |
|gh |1.5.0 |2025-05-26 |CRAN (R 4.4.1) |
|gitcreds |0.1.2 |2022-09-08 |CRAN (R 4.4.1) |
|glue |1.8.0 |2024-09-30 |CRAN (R 4.4.1) |
|gridExtra |2.3 |2017-09-09 |CRAN (R 4.4.1) |
|gt |1.0.0 |2025-04-05 |CRAN (R 4.4.1) |
@ -114,7 +108,6 @@
|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) |
|httr2 |1.2.1 |2025-07-22 |CRAN (R 4.4.1) |
|IDEAFilter |0.2.1 |2025-07-29 |CRAN (R 4.4.1) |
|insight |1.4.0 |2025-08-18 |CRAN (R 4.4.1) |
|iterators |1.0.14 |2022-02-05 |CRAN (R 4.4.1) |
@ -128,9 +121,11 @@
|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) |
|litedown |0.7 |2025-04-08 |CRAN (R 4.4.1) |
|lme4 |1.1-37 |2025-03-26 |CRAN (R 4.4.1) |
|lubridate |1.9.4 |2024-12-08 |CRAN (R 4.4.1) |
|magrittr |2.0.3 |2022-03-30 |CRAN (R 4.4.1) |
|markdown |2.0 |2025-03-23 |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) |
@ -146,7 +141,6 @@
|opdisDownsampling |1.0.1 |2024-04-15 |CRAN (R 4.4.0) |
|openssl |2.3.3 |2025-05-26 |CRAN (R 4.4.1) |
|openxlsx2 |1.18 |2025-07-29 |CRAN (R 4.4.1) |
|pak |0.9.0 |2025-05-27 |CRAN (R 4.4.1) |
|parameters |0.27.0 |2025-07-09 |CRAN (R 4.4.1) |
|patchwork |1.3.1 |2025-06-21 |CRAN (R 4.4.1) |
|pbmcapply |1.5.1 |2022-04-28 |CRAN (R 4.4.1) |
@ -169,6 +163,10 @@
|qqconf |1.3.2 |2023-04-14 |CRAN (R 4.4.0) |
|qqplotr |0.0.6 |2023-01-25 |CRAN (R 4.4.0) |
|quarto |1.5.0 |2025-07-28 |RSPM (R 4.4.0) |
|R.cache |0.17.0 |2025-05-02 |CRAN (R 4.4.1) |
|R.methodsS3 |1.8.2 |2022-06-13 |CRAN (R 4.4.1) |
|R.oo |1.27.1 |2025-05-02 |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) |
|ragg |1.4.0 |2025-04-10 |CRAN (R 4.4.1) |
|rankinPlot |1.1.0 |2023-01-30 |CRAN (R 4.4.0) |
@ -204,14 +202,14 @@
|sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.4.1) |
|shiny |1.11.1 |2025-07-03 |CRAN (R 4.4.1) |
|shiny.i18n |0.3.0 |2023-01-16 |CRAN (R 4.4.0) |
|shiny2docker |0.0.3 |2025-06-28 |CRAN (R 4.4.1) |
|shinybusy |0.3.3 |2024-03-09 |CRAN (R 4.4.0) |
|shinyjs |2.1.0 |2021-12-23 |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) |
|stringr |1.5.1 |2023-11-14 |CRAN (R 4.4.0) |
|sys |3.4.3 |2024-10-04 |CRAN (R 4.4.1) |
|stRoke |25.9.2 |2025-09-30 |CRAN (R 4.4.1) |
|styler |1.10.3 |2024-04-07 |CRAN (R 4.4.0) |
|systemfonts |1.2.3 |2025-04-30 |CRAN (R 4.4.1) |
|testthat |3.2.3 |2025-01-13 |CRAN (R 4.4.1) |
|textshaping |1.0.1 |2025-05-01 |CRAN (R 4.4.1) |
@ -226,6 +224,7 @@
|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) |
|utf8 |1.2.6 |2025-06-08 |CRAN (R 4.4.1) |
|uuid |1.2-1 |2024-07-29 |CRAN (R 4.4.1) |
|V8 |6.0.6 |2025-08-18 |CRAN (R 4.4.1) |
|vctrs |0.6.5 |2023-12-01 |CRAN (R 4.4.0) |
@ -236,5 +235,4 @@
|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) |
|yesno |0.1.3 |2024-07-26 |CRAN (R 4.4.1) |
|zip |2.3.3 |2025-05-13 |CRAN (R 4.4.1) |

4
app_docker/app.R
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@ -1,7 +1,7 @@
########
#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpWiu9wh/file1e994fcc5757.R
#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpWiu9wh/file1e9944acd364.R
########
i18n_path <- here::here("translations")
@ -11361,7 +11361,7 @@ ui <- bslib::page_fixed(
## Code formatting dependencies
prismDependencies,
prismRDependency,
html_dependency_FreesearchR(),
# html_dependency_FreesearchR(),
## Version dependent header
header_include(),
## This adds the actual favicon

83
app_docker/renv.lock
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@ -1588,6 +1588,39 @@
"Maintainer": "Winston Chang <winston@posit.co>",
"Repository": "CRAN"
},
"calendar": {
"Package": "calendar",
"Version": "0.2.0",
"Source": "Repository",
"Title": "Create, Read, Write, and Work with 'iCalendar' Files, Calendars and Scheduling Data",
"Authors@R": "c(person(given = \"Robin\", family = \"Lovelace\", role = c(\"aut\", \"cre\"), email = \"rob00x@gmail.com\", comment = c(ORCID = \"0000-0001-5679-6536\")), person(given = \"Layik\", family = \"Hama\", role = \"aut\", email = \"layik.hama@gmail.com\", comment = c(ORCID = \"0000-0003-1912-4890\")), person(given = \"Ollie\", family = \"Lloyd\", role = \"ctb\", email = \"o.lloyd@doctors.org.uk\", comment = c(ORCID = \"0000-0002-9385-1634\")), person(given = \"Franco\", family = \"Scarafia\", role = \"ctb\", email = \"franco.scarafia@hotmail.com\", comment = c(ORCID = \"0009-0005-9822-169X\")), person(given = \"Serkan\", family = \"Korkmaz\", email = \"serkor1@duck.com\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-5052-0982\")) )",
"Description": "Provides function to create, read, write, and work with 'iCalendar' files (which typically have '.ics' or '.ical' extensions), and the scheduling data, calendars and timelines of people, organisations and other entities that they represent. 'iCalendar' is an open standard for exchanging calendar and scheduling information between users and computers, described at <https://icalendar.org/>.",
"License": "Apache License (>= 2.0)",
"URL": "https://github.com/atfutures/calendar, https://atfutures.github.io/calendar/, https://github.com/ATFutures/calendar",
"BugReports": "https://github.com/ATFutures/calendar/issues",
"Depends": [
"R (>= 3.4.0)"
],
"Imports": [
"cli",
"lubridate",
"tibble"
],
"Suggests": [
"covr",
"knitr",
"rmarkdown",
"testthat"
],
"VignetteBuilder": "knitr",
"Encoding": "UTF-8",
"LazyData": "true",
"RoxygenNote": "7.3.2",
"NeedsCompilation": "no",
"Author": "Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>), Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>), Ollie Lloyd [ctb] (<https://orcid.org/0000-0002-9385-1634>), Franco Scarafia [ctb] (<https://orcid.org/0009-0005-9822-169X>), Serkan Korkmaz [ctb] (<https://orcid.org/0000-0002-5052-0982>)",
"Maintainer": "Robin Lovelace <rob00x@gmail.com>",
"Repository": "CRAN"
},
"cards": {
"Package": "cards",
"Version": "0.6.1",
@ -8257,6 +8290,56 @@
"NeedsCompilation": "yes",
"Repository": "CRAN"
},
"stRoke": {
"Package": "stRoke",
"Version": "25.9.2",
"Source": "Repository",
"Title": "Clinical Stroke Research",
"Authors@R": "person(\"Andreas Gammelgaard\", \"Damsbo\", , \"agdamsbo@clin.au.dk\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-7559-1154\"))",
"Description": "A collection of tools for clinical trial data management and analysis in research and teaching. The package is mainly collected for personal use, but any use beyond that is encouraged. This package has migrated functions from 'agdamsbo/daDoctoR', and new functions has been added. Version follows months and year. See NEWS/Changelog for release notes. This package includes sampled data from the TALOS trial (Kraglund et al (2018) <doi:10.1161/STROKEAHA.117.020067>). The win_prob() function is based on work by Zou et al (2022) <doi:10.1161/STROKEAHA.121.037744>. The age_calc() function is based on work by Becker (2020) <doi:10.18637/jss.v093.i02>.",
"URL": "https://agdamsbo.github.io/stRoke/, https://github.com/agdamsbo/stRoke",
"BugReports": "https://github.com/agdamsbo/stRoke/issues",
"License": "GPL-3",
"Encoding": "UTF-8",
"RoxygenNote": "7.3.2",
"LazyData": "true",
"Suggests": [
"knitr",
"rmarkdown",
"testthat",
"here",
"spelling",
"usethis",
"pak",
"roxygen2",
"devtools"
],
"Config/testthat/edition": "3",
"Imports": [
"calendar",
"dplyr",
"ggplot2",
"grDevices",
"gtsummary",
"lubridate",
"MASS",
"rankinPlot",
"stats",
"tidyr",
"utils",
"tibble",
"tidyselect"
],
"Depends": [
"R (>= 4.1.0)"
],
"VignetteBuilder": "knitr",
"Language": "en-US",
"NeedsCompilation": "no",
"Author": "Andreas Gammelgaard Damsbo [aut, cre] (ORCID: <https://orcid.org/0000-0002-7559-1154>)",
"Maintainer": "Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>",
"Repository": "CRAN"
},
"stringi": {
"Package": "stringi",
"Version": "1.8.7",

2
renv.lock
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@ -8292,7 +8292,7 @@
},
"stRoke": {
"Package": "stRoke",
"Version": "25.9.1",
"Version": "25.9.2",
"Source": "Repository",
"Title": "Clinical Stroke Research",
"Authors@R": "person(\"Andreas Gammelgaard\", \"Damsbo\", , \"agdamsbo@clin.au.dk\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-7559-1154\"))",