mirror of
https://github.com/agdamsbo/FreesearchR.git
synced 2026-06-19 04:27:30 +02:00
new version
This commit is contained in:
parent
fdc0bfed02
commit
fcc9443cea
20 changed files with 159 additions and 141 deletions
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@ -8,7 +8,7 @@ message: 'To cite package "FreesearchR" in publications use:'
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type: software
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license: AGPL-3.0-or-later
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title: 'FreesearchR: Easy data analysis for clinicians'
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version: 26.2.2
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version: 26.3.1
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doi: 10.5281/zenodo.14527429
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identifiers:
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- type: url
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@ -1,6 +1,6 @@
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Package: FreesearchR
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Title: Easy data analysis for clinicians
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Version: 26.2.2
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Version: 26.3.1
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Authors@R: c(
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person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0002-7559-1154")),
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8
NEWS.md
8
NEWS.md
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@ -1,3 +1,11 @@
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# FreesearchR 26.3.1
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*FIX* Include font files for static loading without dependency on Google.
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*NEW* Updated text strings to better reflect environment data availability.
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New strings translated.
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# FreesearchR 26.2.2
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*FIX* Minor addition to the previous update with correct activation of the missingness evaluation button.
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@ -1 +1 @@
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app_version <- function()'26.2.2'
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app_version <- function()'26.3.1'
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@ -1 +1 @@
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hosted_version <- function()'v26.2.2-260223'
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hosted_version <- function()'v26.3.1-260228'
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
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23
SESSION.md
23
SESSION.md
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@ -11,11 +11,11 @@
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|collate |en_US.UTF-8 |
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|ctype |en_US.UTF-8 |
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|tz |Europe/Copenhagen |
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|date |2026-02-23 |
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|date |2026-02-28 |
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|rstudio |2026.01.1+403 Apple Blossom (desktop) |
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|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
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|quarto |1.7.30 @ /usr/local/bin/quarto |
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|FreesearchR |26.2.2.260223 |
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|FreesearchR |26.3.1.260228 |
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--------------------------------------------------------------------------------
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@ -26,8 +26,6 @@
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|apexcharter |0.4.5 |2026-01-07 |CRAN (R 4.5.2) |
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|askpass |1.2.1 |2024-10-04 |CRAN (R 4.5.0) |
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|assertthat |0.2.1 |2019-03-21 |CRAN (R 4.5.0) |
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|attachment |0.4.5 |2025-03-14 |CRAN (R 4.5.0) |
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|attempt |0.3.1 |2020-05-03 |CRAN (R 4.5.0) |
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|backports |1.5.0 |2024-05-23 |CRAN (R 4.5.0) |
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|base64enc |0.1-6 |2026-02-02 |CRAN (R 4.5.2) |
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|bayestestR |0.17.0 |2025-08-29 |CRAN (R 4.5.0) |
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@ -46,7 +44,6 @@
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|cardx |0.3.2 |2026-02-05 |CRAN (R 4.5.2) |
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|caTools |1.18.3 |2024-09-04 |CRAN (R 4.5.0) |
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|cellranger |1.1.0 |2016-07-27 |CRAN (R 4.5.0) |
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|cffr |1.2.1 |2026-01-12 |CRAN (R 4.5.2) |
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|checkmate |2.3.4 |2026-02-03 |CRAN (R 4.5.2) |
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|class |7.3-23 |2025-01-01 |CRAN (R 4.5.2) |
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|classInt |0.4-11 |2025-01-08 |CRAN (R 4.5.0) |
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@ -56,6 +53,7 @@
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|colorspace |2.1-2 |2025-09-22 |CRAN (R 4.5.0) |
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|commonmark |2.0.0 |2025-07-07 |CRAN (R 4.5.0) |
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|crayon |1.5.3 |2024-06-20 |CRAN (R 4.5.0) |
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|crul |1.6.0 |NA |NA |
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|curl |7.0.0 |2025-08-19 |CRAN (R 4.5.0) |
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|data.table |1.18.2.1 |2026-01-27 |CRAN (R 4.5.2) |
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|datamods |1.5.3 |2024-10-02 |CRAN (R 4.5.0) |
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@ -65,7 +63,6 @@
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|devtools |2.4.6 |2025-10-03 |CRAN (R 4.5.0) |
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|DHARMa |0.4.7 |2024-10-18 |CRAN (R 4.5.0) |
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|digest |0.6.39 |2025-11-19 |CRAN (R 4.5.2) |
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|dockerfiler |0.2.5 |2025-05-07 |CRAN (R 4.5.0) |
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|doParallel |1.0.17 |2022-02-07 |CRAN (R 4.5.0) |
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|dplyr |1.2.0 |2026-02-03 |CRAN (R 4.5.2) |
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|DT |0.34.0 |2025-09-02 |CRAN (R 4.5.0) |
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@ -88,10 +85,11 @@
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|foreach |1.5.2 |2022-02-02 |CRAN (R 4.5.0) |
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|foreign |0.8-90 |2025-03-31 |CRAN (R 4.5.2) |
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|Formula |1.2-5 |2023-02-24 |CRAN (R 4.5.0) |
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|FreesearchR |26.2.2 |NA |NA |
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|FreesearchR |26.3.1 |NA |NA |
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|fs |1.6.6 |2025-04-12 |CRAN (R 4.5.0) |
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|gdtools |0.5.0 |2026-02-09 |CRAN (R 4.5.2) |
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|generics |0.1.4 |2025-05-09 |CRAN (R 4.5.0) |
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|gfonts |0.2.0 |NA |NA |
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|ggalluvial |0.12.5 |2023-02-22 |CRAN (R 4.5.0) |
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|ggcorrplot |0.1.4.1 |2023-09-05 |CRAN (R 4.5.0) |
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|ggforce |0.5.0 |2025-06-18 |CRAN (R 4.5.0) |
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@ -110,24 +108,23 @@
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|htmlTable |2.4.3 |2024-07-21 |CRAN (R 4.5.0) |
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|htmltools |0.5.9 |2025-12-04 |CRAN (R 4.5.2) |
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|htmlwidgets |1.6.4 |2023-12-06 |CRAN (R 4.5.0) |
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|httpcode |0.3.0 |NA |NA |
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|httpuv |1.6.16 |2025-04-16 |CRAN (R 4.5.0) |
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|IDEAFilter |0.2.1 |2025-07-29 |CRAN (R 4.5.0) |
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|insight |1.4.6 |2026-02-04 |CRAN (R 4.5.2) |
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|iterators |1.0.14 |2022-02-05 |CRAN (R 4.5.0) |
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|jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.5.0) |
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|jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.5.0) |
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|jsonvalidate |1.5.0 |2025-02-07 |CRAN (R 4.5.0) |
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|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.5.2) |
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|keyring |1.4.1 |2025-06-15 |CRAN (R 4.5.0) |
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|knitr |1.51 |2025-12-20 |CRAN (R 4.5.2) |
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|labeling |0.4.3 |2023-08-29 |CRAN (R 4.5.0) |
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|later |1.4.6 |2026-02-13 |CRAN (R 4.5.2) |
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|lattice |0.22-7 |2025-04-02 |CRAN (R 4.5.2) |
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|lifecycle |1.0.5 |2026-01-08 |CRAN (R 4.5.2) |
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|litedown |0.9 |2025-12-18 |CRAN (R 4.5.2) |
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|lme4 |1.1-38 |2025-12-02 |CRAN (R 4.5.2) |
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|lubridate |1.9.5 |2026-02-04 |CRAN (R 4.5.2) |
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|magrittr |2.0.4 |2025-09-12 |CRAN (R 4.5.0) |
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|markdown |2.0 |2025-03-23 |CRAN (R 4.5.0) |
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|MASS |7.3-65 |2025-02-28 |CRAN (R 4.5.0) |
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|Matrix |1.7-4 |2025-08-28 |CRAN (R 4.5.2) |
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|memoise |2.0.1 |2021-11-26 |CRAN (R 4.5.0) |
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@ -167,7 +164,6 @@
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|R6 |2.6.1 |2025-02-15 |CRAN (R 4.5.0) |
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|ragg |1.5.0 |2025-09-02 |CRAN (R 4.5.0) |
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|rankinPlot |1.1.0 |2023-01-30 |CRAN (R 4.5.0) |
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|rappdirs |0.3.4 |2026-01-17 |CRAN (R 4.5.2) |
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|rbibutils |2.4.1 |2026-01-21 |CRAN (R 4.5.2) |
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|RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.5.0) |
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|Rcpp |1.1.1 |2026-01-10 |CRAN (R 4.5.2) |
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@ -200,7 +196,6 @@
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|sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.5.0) |
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|shiny |1.13.0 |2026-02-20 |CRAN (R 4.5.2) |
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|shiny.i18n |0.3.0 |2023-01-16 |CRAN (R 4.5.0) |
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|shiny2docker |0.0.3 |2025-06-28 |CRAN (R 4.5.0) |
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|shinybusy |0.3.3 |2024-03-09 |CRAN (R 4.5.0) |
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|shinyjs |2.1.1 |2026-01-15 |CRAN (R 4.5.2) |
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|shinyTime |1.0.3 |2022-08-19 |CRAN (R 4.5.0) |
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@ -218,12 +213,13 @@
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|tidyselect |1.2.1 |2024-03-11 |CRAN (R 4.5.0) |
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|timechange |0.4.0 |2026-01-29 |CRAN (R 4.5.2) |
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|toastui |0.4.0 |2025-04-03 |CRAN (R 4.5.0) |
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|triebeard |0.4.1 |NA |NA |
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|tweenr |2.0.3 |2024-02-26 |CRAN (R 4.5.0) |
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|twosamples |2.0.1 |2023-06-23 |CRAN (R 4.5.0) |
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|tzdb |0.5.0 |2025-03-15 |CRAN (R 4.5.0) |
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|urltools |1.7.3.1 |NA |NA |
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|usethis |3.2.1 |2025-09-06 |CRAN (R 4.5.0) |
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|uuid |1.2-2 |2026-01-23 |CRAN (R 4.5.2) |
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|V8 |8.0.1 |2025-10-10 |CRAN (R 4.5.0) |
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|vctrs |0.7.1 |2026-01-23 |CRAN (R 4.5.2) |
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|viridis |0.6.5 |2024-01-29 |CRAN (R 4.5.0) |
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|viridisLite |0.4.3 |2026-02-04 |CRAN (R 4.5.2) |
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@ -234,5 +230,4 @@
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|xml2 |1.5.2 |2026-01-17 |CRAN (R 4.5.2) |
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|xtable |1.8-4 |2019-04-21 |CRAN (R 4.5.0) |
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|yaml |2.3.12 |2025-12-10 |CRAN (R 4.5.2) |
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|yesno |0.1.3 |2024-07-26 |CRAN (R 4.5.0) |
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|zip |2.3.3 |2025-05-13 |CRAN (R 4.5.0) |
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@ -1,7 +1,7 @@
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########
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#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//Rtmpp0JgLn/file73e17b926733.R
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#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpDLoQCo/file14ced11821c07.R
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########
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i18n_path <- here::here("translations")
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@ -72,7 +72,7 @@ if (!"global_freesearchR" %in% ls(name = globalenv())) {
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#### Current file: /Users/au301842/FreesearchR/R//app_version.R
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########
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app_version <- function()'26.2.2'
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app_version <- function()'26.3.1'
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########
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@ -4524,7 +4524,7 @@ data_types <- function() {
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#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
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########
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hosted_version <- function()'v26.2.2-260223'
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hosted_version <- function()'v26.3.1-260228'
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########
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@ -10469,9 +10469,21 @@ custom_theme <- function(...,
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primary = FreesearchR_colors("primary"),
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secondary = FreesearchR_colors("secondary"),
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bootswatch = "united",
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base_font = bslib::font_google("Montserrat"),
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heading_font = bslib::font_google("Public Sans", wght = "700"),
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code_font = bslib::font_google("Open Sans"),
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# base_font = bslib::font_google("Montserrat"),
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base_font = bslib::font_face(
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family = "Montserrat",
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src = "url('/fonts/Montserrat-Regular.ttf') format('truetype')"
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),
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# heading_font = bslib::font_google("Public Sans", wght = "700"),
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heading_font = bslib::font_face(
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family = "PublicSans",
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src = "url('/fonts/PublicSans-Bold.ttf') format('truetype')"
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),
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# code_font = bslib::font_google("Open Sans"),
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code_font = bslib::font_face(
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family = "OpenSans",
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src = "url('/fonts/OpenSans-Regular.ttf') format('truetype')"
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),
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success = FreesearchR_colors("success"),
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info = FreesearchR_colors("info"),
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warning = FreesearchR_colors("warning"),
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@ -10664,11 +10676,12 @@ ui_elements <- function(selection) {
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),
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# shiny::tags$script('document.querySelector("#source div").style.width = "100%"'),
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## Update this to change depending on run locally or hosted
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shiny::helpText(
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i18n$t(
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"Upload a file, get data directly from REDCap or use local or sample data."
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)
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),
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shiny::uiOutput(outputId = "data_sample_text"),
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# shiny::helpText(
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# i18n$t(
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# "Upload a file, get data directly from REDCap or use local or sample data."
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# )
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# ),
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shiny::br(),
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shiny::br(),
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shiny::conditionalPanel(
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@ -13496,16 +13509,6 @@ ui <- bslib::page_fixed(
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#### Current file: /Users/au301842/FreesearchR/app/server.R
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########
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data("mtcars")
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data("iris")
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# trial <- gtsummary::trial
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# starwars <- dplyr::starwars
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#
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# mtcars_na <- rbind(mtcars,NA,NA)
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# thematic::thematic_shiny()
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load_data <- function() {
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Sys.sleep(1)
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shinyjs::hide("loading_page")
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@ -13544,7 +13547,6 @@ server <- function(input, output, session) {
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# session$setCurrentTheme(bs_theme_update(theme = custom_theme(version = 5, bg = "#000",fg="#fff")))
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# })
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##############################################################################
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#########
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######### Setting reactive values
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@ -13637,16 +13639,33 @@ server <- function(input, output, session) {
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# ),
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# selected = "file"
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# )
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if (isTRUE(global_freesearchR$include_globalenv)) {
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env_label <- i18n$t("Local or sample data")
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output$data_sample_text <- shiny::renderText(shiny::helpText(
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i18n$t(
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"Upload a file, get data directly from REDCap or use local or sample data."
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)
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))
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} else {
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env_label <- i18n$t("Sample data")
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output$data_sample_text <- shiny::renderUI(shiny::helpText(
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i18n$t(
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"Upload a file, get data directly from REDCap or use sample data."
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)
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))
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}
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shiny::updateSelectInput(inputId = "source", choices = setNames(c("file", "redcap", "env"), c(
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i18n$t("File upload"),
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i18n$t("REDCap server export"),
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i18n$t("Local or sample data")
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env_label
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# i18n$t("Local or sample data")
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)))
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# output$intro_text <- renderUI(includeHTML(i18n$t("www/intro.html")))
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})
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shiny::observeEvent(input$language_select, {
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bslib::accordion_panel_update(id = "acc_chars",
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title = i18n$t("Settings"),
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@ -13659,12 +13678,10 @@ server <- function(input, output, session) {
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target = "acc_pan_mis")
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})
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output$redcap_warning <- shiny::renderUI({
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rv_alerts$redcap_alert
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})
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##############################################################################
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#########
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######### Data import section
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@ -13798,7 +13815,6 @@ server <- function(input, output, session) {
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rv$data_original <- temp_data |>
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default_parsing()
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}
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},
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ignoreNULL = FALSE
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)
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@ -13861,14 +13877,14 @@ server <- function(input, output, session) {
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shiny::observeEvent(list(rv$data_original, rv$data), {
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if (is.null(rv$data_original) |
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NROW(rv$data_original) == 0 |
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is.null(rv$data) | !any(is_splittable(rv$data))) {
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is.null(rv$data) |
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!any(is_splittable(rv$data))) {
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shiny::updateActionButton(inputId = "modal_string", disabled = TRUE)
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} else if (!is.null(rv$data) && any(is_splittable(rv$data))) {
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shiny::updateActionButton(inputId = "modal_string", disabled = FALSE)
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}
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})
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##############################################################################
|
||||
#########
|
||||
######### Data modification section
|
||||
|
|
@ -13893,7 +13909,6 @@ server <- function(input, output, session) {
|
|||
}
|
||||
}, ignoreNULL = TRUE)
|
||||
|
||||
|
||||
shiny::observeEvent(input$data_reset, {
|
||||
shinyWidgets::ask_confirmation(
|
||||
cancelOnDismiss = TRUE,
|
||||
|
|
@ -14216,7 +14231,6 @@ server <- function(input, output, session) {
|
|||
rv$list$table1 <- NULL
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Code export
|
||||
|
|
@ -14280,19 +14294,18 @@ server <- function(input, output, session) {
|
|||
))
|
||||
})
|
||||
|
||||
|
||||
## Just a note to self
|
||||
## This is a very rewarding couple of lines marking new insights to dynamically rendering code
|
||||
shiny::observe({
|
||||
shiny::req(rv$regression)
|
||||
rv$regression()$regression$models |> purrr::imap(\(.x, .i) {
|
||||
rv$regression()$regression$models |>
|
||||
purrr::imap(\(.x, .i) {
|
||||
output[[paste0("code_", tolower(.i))]] <- shiny::renderUI({
|
||||
prismCodeBlock(paste0(paste("#", .i, "regression model\n"), .x$code_table))
|
||||
})
|
||||
})
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data analyses Inputs
|
||||
|
|
@ -14305,7 +14318,8 @@ server <- function(input, output, session) {
|
|||
selected = "none",
|
||||
label = i18n$t("Select variable to stratify baseline"),
|
||||
data = shiny::reactive(rv$data_filtered)(),
|
||||
col_subset = c("none", names(rv$data_filtered)[unlist(lapply(rv$data_filtered, data_type)) %in% c("dichotomous", "categorical", "ordinal")])
|
||||
col_subset = c("none", names(rv$data_filtered)[unlist(lapply(rv$data_filtered, data_type)) %in%
|
||||
c("dichotomous", "categorical", "ordinal")])
|
||||
)
|
||||
})
|
||||
|
||||
|
|
@ -14324,7 +14338,6 @@ server <- function(input, output, session) {
|
|||
# )
|
||||
# })
|
||||
|
||||
|
||||
output$detail_level <- shiny::renderUI({
|
||||
shiny::radioButtons(
|
||||
inputId = "detail_level",
|
||||
|
|
@ -14336,14 +14349,12 @@ server <- function(input, output, session) {
|
|||
)
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Descriptive evaluations
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
|
||||
output$data_info_nochar <- shiny::renderUI({
|
||||
shiny::req(rv$list$data)
|
||||
data_description(rv$list$data,
|
||||
|
|
@ -14362,14 +14373,12 @@ server <- function(input, output, session) {
|
|||
#
|
||||
# })
|
||||
|
||||
|
||||
shiny::observeEvent(list(input$act_eval), {
|
||||
shiny::req(input$strat_var)
|
||||
# shiny::req(input$baseline_theme)
|
||||
shiny::req(input$detail_level)
|
||||
shiny::req(rv$list$data)
|
||||
|
||||
|
||||
parameters <- list(
|
||||
by.var = input$strat_var,
|
||||
add.p = input$add_p == "yes",
|
||||
|
|
@ -14410,7 +14419,6 @@ server <- function(input, output, session) {
|
|||
# }
|
||||
# )
|
||||
|
||||
|
||||
rv$code$table1 <- glue::glue("FreesearchR::create_baseline(df,{list2str(parameters)})")
|
||||
})
|
||||
|
||||
|
|
@ -14451,12 +14459,9 @@ server <- function(input, output, session) {
|
|||
|
||||
## Missingness evaluation
|
||||
|
||||
|
||||
rv$missings <- data_missings_server(id = "missingness",
|
||||
data = shiny::reactive(rv$data_filtered))
|
||||
|
||||
|
||||
|
||||
# shiny::observe({
|
||||
# req(rv$missings())
|
||||
# browser()
|
||||
|
|
@ -14465,7 +14470,6 @@ server <- function(input, output, session) {
|
|||
# mcar_validate(data=rv$missings()[["_data"]],outcome = input$missings_var)
|
||||
# })
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data visuals
|
||||
|
|
|
|||
|
|
@ -314,16 +314,17 @@
|
|||
"The app contains a selelct number of features and will guide you through key analyses.","Appen indeholder udvalgte funktioner, og guider dig gennem de vigtigste analyser."
|
||||
"Sort by Levels","Sorter efter niveauer"
|
||||
"Reorder factor levels","Omarranger niveauer"
|
||||
"Modify factor levels","Modify factor levels"
|
||||
"Reorder or rename the levels of factor/categorical variables.","Reorder or rename the levels of factor/categorical variables."
|
||||
"Maximum number of observations:","Maximum number of observations:"
|
||||
"setting to 0 includes all","setting to 0 includes all"
|
||||
"Select a dataset from your environment or sample dataset from a package.","Select a dataset from your environment or sample dataset from a package."
|
||||
"Select a sample dataset from a package.","Select a sample dataset from a package."
|
||||
"Data ready to be imported!","Data ready to be imported!"
|
||||
"Data has %s obs. of %s variables.","Data has %s obs. of %s variables."
|
||||
"Modify factor levels","Ændr kategoriske niveauer"
|
||||
"Reorder or rename the levels of factor/categorical variables.","Ændr navn eller rækkefølge på kategorisk variabel."
|
||||
"Maximum number of observations:","Maximale antal observationer:"
|
||||
"setting to 0 includes all","angiv 0 for at inkludere alle"
|
||||
"Select a dataset from your environment or sample dataset from a package.","Vælg et datasæt fra din kørende session eller vælg træningsdata."
|
||||
"Select a sample dataset from a package.","Vælg et træningsdatasæt."
|
||||
"Data ready to be imported!","Data er klar til at blive importeret!"
|
||||
"Data has %s obs. of %s variables.","Data har %s obs. på %s variabler."
|
||||
"Data successfully imported!","Data successfully imported!"
|
||||
"Click to see data","Click to see data"
|
||||
"No data present.","No data present."
|
||||
"You have provided a complete dataset with no missing values.","You have provided a complete dataset with no missing values."
|
||||
"Start by loading data.","Start by loading data."
|
||||
"Click to see data","Klik for at se data"
|
||||
"No data present.","Ingen data tilstede."
|
||||
"You have provided a complete dataset with no missing values.","Data er uden manglende observationer."
|
||||
"Start by loading data.","Start med at vælge data."
|
||||
"Sample data","Træningsdata"
|
||||
|
|
|
|||
|
|
|
@ -327,3 +327,4 @@
|
|||
"No data present.","No data present."
|
||||
"You have provided a complete dataset with no missing values.","You have provided a complete dataset with no missing values."
|
||||
"Start by loading data.","Start by loading data."
|
||||
"Sample data","Sample data"
|
||||
|
|
|
|||
|
BIN
app_docker/www/fonts/Montserrat-Regular.ttf
Executable file
BIN
app_docker/www/fonts/Montserrat-Regular.ttf
Executable file
Binary file not shown.
BIN
app_docker/www/fonts/OpenSans-Regular.ttf
Executable file
BIN
app_docker/www/fonts/OpenSans-Regular.ttf
Executable file
Binary file not shown.
BIN
app_docker/www/fonts/PublicSans-Bold.ttf
Executable file
BIN
app_docker/www/fonts/PublicSans-Bold.ttf
Executable file
Binary file not shown.
|
|
@ -1,7 +1,7 @@
|
|||
|
||||
|
||||
########
|
||||
#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//Rtmpp0JgLn/file73e17f71b1a4.R
|
||||
#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpDLoQCo/file14ced66223522.R
|
||||
########
|
||||
|
||||
i18n_path <- system.file("translations", package = "FreesearchR")
|
||||
|
|
@ -72,7 +72,7 @@ if (!"global_freesearchR" %in% ls(name = globalenv())) {
|
|||
#### Current file: /Users/au301842/FreesearchR/R//app_version.R
|
||||
########
|
||||
|
||||
app_version <- function()'26.2.2'
|
||||
app_version <- function()'26.3.1'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -4524,7 +4524,7 @@ data_types <- function() {
|
|||
#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
|
||||
########
|
||||
|
||||
hosted_version <- function()'v26.2.2-260223'
|
||||
hosted_version <- function()'v26.3.1-260228'
|
||||
|
||||
|
||||
########
|
||||
|
|
@ -10469,9 +10469,21 @@ custom_theme <- function(...,
|
|||
primary = FreesearchR_colors("primary"),
|
||||
secondary = FreesearchR_colors("secondary"),
|
||||
bootswatch = "united",
|
||||
base_font = bslib::font_google("Montserrat"),
|
||||
heading_font = bslib::font_google("Public Sans", wght = "700"),
|
||||
code_font = bslib::font_google("Open Sans"),
|
||||
# base_font = bslib::font_google("Montserrat"),
|
||||
base_font = bslib::font_face(
|
||||
family = "Montserrat",
|
||||
src = "url('/fonts/Montserrat-Regular.ttf') format('truetype')"
|
||||
),
|
||||
# heading_font = bslib::font_google("Public Sans", wght = "700"),
|
||||
heading_font = bslib::font_face(
|
||||
family = "PublicSans",
|
||||
src = "url('/fonts/PublicSans-Bold.ttf') format('truetype')"
|
||||
),
|
||||
# code_font = bslib::font_google("Open Sans"),
|
||||
code_font = bslib::font_face(
|
||||
family = "OpenSans",
|
||||
src = "url('/fonts/OpenSans-Regular.ttf') format('truetype')"
|
||||
),
|
||||
success = FreesearchR_colors("success"),
|
||||
info = FreesearchR_colors("info"),
|
||||
warning = FreesearchR_colors("warning"),
|
||||
|
|
@ -10664,11 +10676,12 @@ ui_elements <- function(selection) {
|
|||
),
|
||||
# shiny::tags$script('document.querySelector("#source div").style.width = "100%"'),
|
||||
## Update this to change depending on run locally or hosted
|
||||
shiny::helpText(
|
||||
i18n$t(
|
||||
"Upload a file, get data directly from REDCap or use local or sample data."
|
||||
)
|
||||
),
|
||||
shiny::uiOutput(outputId = "data_sample_text"),
|
||||
# shiny::helpText(
|
||||
# i18n$t(
|
||||
# "Upload a file, get data directly from REDCap or use local or sample data."
|
||||
# )
|
||||
# ),
|
||||
shiny::br(),
|
||||
shiny::br(),
|
||||
shiny::conditionalPanel(
|
||||
|
|
@ -13496,16 +13509,6 @@ ui <- bslib::page_fixed(
|
|||
#### Current file: /Users/au301842/FreesearchR/app/server.R
|
||||
########
|
||||
|
||||
data("mtcars")
|
||||
data("iris")
|
||||
|
||||
# trial <- gtsummary::trial
|
||||
# starwars <- dplyr::starwars
|
||||
#
|
||||
# mtcars_na <- rbind(mtcars,NA,NA)
|
||||
|
||||
# thematic::thematic_shiny()
|
||||
|
||||
load_data <- function() {
|
||||
Sys.sleep(1)
|
||||
shinyjs::hide("loading_page")
|
||||
|
|
@ -13544,7 +13547,6 @@ server <- function(input, output, session) {
|
|||
# session$setCurrentTheme(bs_theme_update(theme = custom_theme(version = 5, bg = "#000",fg="#fff")))
|
||||
# })
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Setting reactive values
|
||||
|
|
@ -13637,16 +13639,33 @@ server <- function(input, output, session) {
|
|||
# ),
|
||||
# selected = "file"
|
||||
# )
|
||||
|
||||
if (isTRUE(global_freesearchR$include_globalenv)) {
|
||||
env_label <- i18n$t("Local or sample data")
|
||||
output$data_sample_text <- shiny::renderText(shiny::helpText(
|
||||
i18n$t(
|
||||
"Upload a file, get data directly from REDCap or use local or sample data."
|
||||
)
|
||||
))
|
||||
} else {
|
||||
env_label <- i18n$t("Sample data")
|
||||
output$data_sample_text <- shiny::renderUI(shiny::helpText(
|
||||
i18n$t(
|
||||
"Upload a file, get data directly from REDCap or use sample data."
|
||||
)
|
||||
))
|
||||
}
|
||||
|
||||
shiny::updateSelectInput(inputId = "source", choices = setNames(c("file", "redcap", "env"), c(
|
||||
i18n$t("File upload"),
|
||||
i18n$t("REDCap server export"),
|
||||
i18n$t("Local or sample data")
|
||||
env_label
|
||||
# i18n$t("Local or sample data")
|
||||
)))
|
||||
|
||||
# output$intro_text <- renderUI(includeHTML(i18n$t("www/intro.html")))
|
||||
})
|
||||
|
||||
|
||||
shiny::observeEvent(input$language_select, {
|
||||
bslib::accordion_panel_update(id = "acc_chars",
|
||||
title = i18n$t("Settings"),
|
||||
|
|
@ -13659,12 +13678,10 @@ server <- function(input, output, session) {
|
|||
target = "acc_pan_mis")
|
||||
})
|
||||
|
||||
|
||||
output$redcap_warning <- shiny::renderUI({
|
||||
rv_alerts$redcap_alert
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data import section
|
||||
|
|
@ -13798,7 +13815,6 @@ server <- function(input, output, session) {
|
|||
rv$data_original <- temp_data |>
|
||||
default_parsing()
|
||||
}
|
||||
|
||||
},
|
||||
ignoreNULL = FALSE
|
||||
)
|
||||
|
|
@ -13861,14 +13877,14 @@ server <- function(input, output, session) {
|
|||
shiny::observeEvent(list(rv$data_original, rv$data), {
|
||||
if (is.null(rv$data_original) |
|
||||
NROW(rv$data_original) == 0 |
|
||||
is.null(rv$data) | !any(is_splittable(rv$data))) {
|
||||
is.null(rv$data) |
|
||||
!any(is_splittable(rv$data))) {
|
||||
shiny::updateActionButton(inputId = "modal_string", disabled = TRUE)
|
||||
} else if (!is.null(rv$data) && any(is_splittable(rv$data))) {
|
||||
shiny::updateActionButton(inputId = "modal_string", disabled = FALSE)
|
||||
}
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data modification section
|
||||
|
|
@ -13893,7 +13909,6 @@ server <- function(input, output, session) {
|
|||
}
|
||||
}, ignoreNULL = TRUE)
|
||||
|
||||
|
||||
shiny::observeEvent(input$data_reset, {
|
||||
shinyWidgets::ask_confirmation(
|
||||
cancelOnDismiss = TRUE,
|
||||
|
|
@ -14216,7 +14231,6 @@ server <- function(input, output, session) {
|
|||
rv$list$table1 <- NULL
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Code export
|
||||
|
|
@ -14280,19 +14294,18 @@ server <- function(input, output, session) {
|
|||
))
|
||||
})
|
||||
|
||||
|
||||
## Just a note to self
|
||||
## This is a very rewarding couple of lines marking new insights to dynamically rendering code
|
||||
shiny::observe({
|
||||
shiny::req(rv$regression)
|
||||
rv$regression()$regression$models |> purrr::imap(\(.x, .i) {
|
||||
rv$regression()$regression$models |>
|
||||
purrr::imap(\(.x, .i) {
|
||||
output[[paste0("code_", tolower(.i))]] <- shiny::renderUI({
|
||||
prismCodeBlock(paste0(paste("#", .i, "regression model\n"), .x$code_table))
|
||||
})
|
||||
})
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data analyses Inputs
|
||||
|
|
@ -14305,7 +14318,8 @@ server <- function(input, output, session) {
|
|||
selected = "none",
|
||||
label = i18n$t("Select variable to stratify baseline"),
|
||||
data = shiny::reactive(rv$data_filtered)(),
|
||||
col_subset = c("none", names(rv$data_filtered)[unlist(lapply(rv$data_filtered, data_type)) %in% c("dichotomous", "categorical", "ordinal")])
|
||||
col_subset = c("none", names(rv$data_filtered)[unlist(lapply(rv$data_filtered, data_type)) %in%
|
||||
c("dichotomous", "categorical", "ordinal")])
|
||||
)
|
||||
})
|
||||
|
||||
|
|
@ -14324,7 +14338,6 @@ server <- function(input, output, session) {
|
|||
# )
|
||||
# })
|
||||
|
||||
|
||||
output$detail_level <- shiny::renderUI({
|
||||
shiny::radioButtons(
|
||||
inputId = "detail_level",
|
||||
|
|
@ -14336,14 +14349,12 @@ server <- function(input, output, session) {
|
|||
)
|
||||
})
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Descriptive evaluations
|
||||
#########
|
||||
##############################################################################
|
||||
|
||||
|
||||
output$data_info_nochar <- shiny::renderUI({
|
||||
shiny::req(rv$list$data)
|
||||
data_description(rv$list$data,
|
||||
|
|
@ -14362,14 +14373,12 @@ server <- function(input, output, session) {
|
|||
#
|
||||
# })
|
||||
|
||||
|
||||
shiny::observeEvent(list(input$act_eval), {
|
||||
shiny::req(input$strat_var)
|
||||
# shiny::req(input$baseline_theme)
|
||||
shiny::req(input$detail_level)
|
||||
shiny::req(rv$list$data)
|
||||
|
||||
|
||||
parameters <- list(
|
||||
by.var = input$strat_var,
|
||||
add.p = input$add_p == "yes",
|
||||
|
|
@ -14410,7 +14419,6 @@ server <- function(input, output, session) {
|
|||
# }
|
||||
# )
|
||||
|
||||
|
||||
rv$code$table1 <- glue::glue("FreesearchR::create_baseline(df,{list2str(parameters)})")
|
||||
})
|
||||
|
||||
|
|
@ -14451,12 +14459,9 @@ server <- function(input, output, session) {
|
|||
|
||||
## Missingness evaluation
|
||||
|
||||
|
||||
rv$missings <- data_missings_server(id = "missingness",
|
||||
data = shiny::reactive(rv$data_filtered))
|
||||
|
||||
|
||||
|
||||
# shiny::observe({
|
||||
# req(rv$missings())
|
||||
# browser()
|
||||
|
|
@ -14465,7 +14470,6 @@ server <- function(input, output, session) {
|
|||
# mcar_validate(data=rv$missings()[["_data"]],outcome = input$missings_var)
|
||||
# })
|
||||
|
||||
|
||||
##############################################################################
|
||||
#########
|
||||
######### Data visuals
|
||||
|
|
|
|||
BIN
inst/apps/FreesearchR/www/fonts/Montserrat-Regular.ttf
Executable file
BIN
inst/apps/FreesearchR/www/fonts/Montserrat-Regular.ttf
Executable file
Binary file not shown.
BIN
inst/apps/FreesearchR/www/fonts/OpenSans-Regular.ttf
Executable file
BIN
inst/apps/FreesearchR/www/fonts/OpenSans-Regular.ttf
Executable file
Binary file not shown.
BIN
inst/apps/FreesearchR/www/fonts/PublicSans-Bold.ttf
Executable file
BIN
inst/apps/FreesearchR/www/fonts/PublicSans-Bold.ttf
Executable file
Binary file not shown.
|
|
@ -314,16 +314,17 @@
|
|||
"The app contains a selelct number of features and will guide you through key analyses.","Appen indeholder udvalgte funktioner, og guider dig gennem de vigtigste analyser."
|
||||
"Sort by Levels","Sorter efter niveauer"
|
||||
"Reorder factor levels","Omarranger niveauer"
|
||||
"Modify factor levels","Modify factor levels"
|
||||
"Reorder or rename the levels of factor/categorical variables.","Reorder or rename the levels of factor/categorical variables."
|
||||
"Maximum number of observations:","Maximum number of observations:"
|
||||
"setting to 0 includes all","setting to 0 includes all"
|
||||
"Select a dataset from your environment or sample dataset from a package.","Select a dataset from your environment or sample dataset from a package."
|
||||
"Select a sample dataset from a package.","Select a sample dataset from a package."
|
||||
"Data ready to be imported!","Data ready to be imported!"
|
||||
"Data has %s obs. of %s variables.","Data has %s obs. of %s variables."
|
||||
"Modify factor levels","Ændr kategoriske niveauer"
|
||||
"Reorder or rename the levels of factor/categorical variables.","Ændr navn eller rækkefølge på kategorisk variabel."
|
||||
"Maximum number of observations:","Maximale antal observationer:"
|
||||
"setting to 0 includes all","angiv 0 for at inkludere alle"
|
||||
"Select a dataset from your environment or sample dataset from a package.","Vælg et datasæt fra din kørende session eller vælg træningsdata."
|
||||
"Select a sample dataset from a package.","Vælg et træningsdatasæt."
|
||||
"Data ready to be imported!","Data er klar til at blive importeret!"
|
||||
"Data has %s obs. of %s variables.","Data har %s obs. på %s variabler."
|
||||
"Data successfully imported!","Data successfully imported!"
|
||||
"Click to see data","Click to see data"
|
||||
"No data present.","No data present."
|
||||
"You have provided a complete dataset with no missing values.","You have provided a complete dataset with no missing values."
|
||||
"Start by loading data.","Start by loading data."
|
||||
"Click to see data","Klik for at se data"
|
||||
"No data present.","Ingen data tilstede."
|
||||
"You have provided a complete dataset with no missing values.","Data er uden manglende observationer."
|
||||
"Start by loading data.","Start med at vælge data."
|
||||
"Sample data","Træningsdata"
|
||||
|
|
|
|||
|
|
|
@ -327,3 +327,4 @@
|
|||
"No data present.","No data present."
|
||||
"You have provided a complete dataset with no missing values.","You have provided a complete dataset with no missing values."
|
||||
"Start by loading data.","Start by loading data."
|
||||
"Sample data","Sample data"
|
||||
|
|
|
|||
|
|
|
@ -10,9 +10,12 @@ custom_theme(
|
|||
primary = FreesearchR_colors("primary"),
|
||||
secondary = FreesearchR_colors("secondary"),
|
||||
bootswatch = "united",
|
||||
base_font = bslib::font_google("Montserrat"),
|
||||
heading_font = bslib::font_google("Public Sans", wght = "700"),
|
||||
code_font = bslib::font_google("Open Sans"),
|
||||
base_font = bslib::font_face(family = "Montserrat", src =
|
||||
"url('/fonts/Montserrat-Regular.ttf') format('truetype')"),
|
||||
heading_font = bslib::font_face(family = "PublicSans", src =
|
||||
"url('/fonts/PublicSans-Bold.ttf') format('truetype')"),
|
||||
code_font = bslib::font_face(family = "OpenSans", src =
|
||||
"url('/fonts/OpenSans-Regular.ttf') format('truetype')"),
|
||||
success = FreesearchR_colors("success"),
|
||||
info = FreesearchR_colors("info"),
|
||||
warning = FreesearchR_colors("warning"),
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue