new docker

CITATION.cff

@@ -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'

SESSION.md

@@ -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) |

app_docker/app.R

@@ -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

app_docker/renv.lock

@@ -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",

renv.lock

@@ -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\"))",