diff --git a/R/app_version.R b/R/app_version.R index 076f20e3..84fbc45c 100644 --- a/R/app_version.R +++ b/R/app_version.R @@ -1 +1 @@ -app_version <- function()'v25.4.4.250428' +app_version <- function()'v25.4.4.250429' diff --git a/R/launch_FreesearchR.R b/R/launch_FreesearchR.R index 5d22820e..c6bcc301 100644 --- a/R/launch_FreesearchR.R +++ b/R/launch_FreesearchR.R @@ -11,7 +11,7 @@ #' @examples #' \dontrun{ #' data(mtcars) -#' shiny_FreesearchR(launch.browser = TRUE) +#' launch_FreesearchR(launch.browser = TRUE) #' } launch_FreesearchR <- function(...){ appDir <- system.file("apps", "FreesearchR", package = "FreesearchR") @@ -22,3 +22,4 @@ launch_FreesearchR <- function(...){ a <- shiny::runApp(appDir = paste0(appDir,"/app.R"), ...) return(invisible(a)) } + diff --git a/R/sysdata.rda b/R/sysdata.rda index ac4e4747..6531331f 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/README.md b/README.md index eaa07f23..10d809f8 100644 --- a/README.md +++ b/README.md @@ -53,4 +53,6 @@ Like any other project, this project was never possible without the great work o - [easystats](https://easystats.github.io/easystats/): the [`performance::check_model()`](https://easystats.github.io/performance/articles/check_model.html) function was central in sparking the idea to create a data analysis tool. +- [IDEAfilter](https://biogen-inc.github.io/IDEAFilter/): a visually appealing data filter function based on the [{shinyDataFilter}](https://github.com/dgkf/shinyDataFilter). + This project was all written by a human and not by any AI-based tools. diff --git a/SESSION.md b/SESSION.md index 4e681f8a..a01a1881 100644 --- a/SESSION.md +++ b/SESSION.md @@ -1,21 +1,21 @@ -------------------------------------------------------------------------------- -------------------------------- 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 |2025-04-28 | -|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 |25.4.4.250428 | +|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 |2025-04-29 | +|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 |25.4.4.250429 | -------------------------------------------------------------------------------- @@ -23,41 +23,64 @@ -------------------------------------------------------------------------------- |package |loadedversion |date |source | |:-------------|:-------------|:----------|:--------------| +|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) | +|backports |1.5.0 |2024-05-23 |CRAN (R 4.4.1) | +|bayestestR |0.15.2 |2025-04-28 |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 |2025-04-24 |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) | +|callr |3.7.6 |2024-03-25 |CRAN (R 4.4.0) | +|cellranger |1.1.0 |2016-07-27 |CRAN (R 4.4.0) | |cffr |1.2.0 |2025-01-25 |CRAN (R 4.4.1) | |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) | +|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) | -|credentials |2.0.2 |2024-10-04 |CRAN (R 4.4.1) | +|crosstalk |1.2.1 |2023-11-23 |CRAN (R 4.4.0) | |curl |6.2.2 |2025-03-24 |CRAN (R 4.4.1) | |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) | |FreesearchR |25.4.4 |NA |NA | |fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) | |generics |0.1.3 |2022-07-05 |CRAN (R 4.4.1) | -|gert |2.1.5 |2025-03-25 |CRAN (R 4.4.1) | -|gh |1.4.1 |2024-03-28 |CRAN (R 4.4.0) | -|gitcreds |0.1.2 |2022-09-08 |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) | -|httr2 |1.1.2 |2025-03-26 |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) | |jsonvalidate |1.5.0 |2025-02-07 |CRAN (R 4.4.1) | @@ -65,38 +88,65 @@ |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) | +|nlme |3.1-168 |2025-03-31 |CRAN (R 4.4.1) | +|nloptr |2.2.1 |2025-03-17 |CRAN (R 4.4.1) | |openssl |2.3.2 |2025-02-03 |CRAN (R 4.4.1) | -|pak |0.8.0.2 |2025-04-08 |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) | +|pkgdown |2.1.1 |2025-04-28 |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) | |R6 |2.6.1 |2025-02-15 |CRAN (R 4.4.1) | -|rappdirs |0.3.3 |2021-01-31 |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) | +|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 |1.4.0 |2025-04-24 |CRAN (R 4.4.1) | +|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) | -|sys |3.4.3 |2024-10-04 |CRAN (R 4.4.1) | |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) | @@ -106,6 +156,8 @@ |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) | diff --git a/inst/apps/FreesearchR/app.R b/inst/apps/FreesearchR/app.R index d4deb602..082962ba 100644 --- a/inst/apps/FreesearchR/app.R +++ b/inst/apps/FreesearchR/app.R @@ -10,7 +10,7 @@ #### Current file: /Users/au301842/FreesearchR/R//app_version.R ######## -app_version <- function()'v25.4.4.250428' +app_version <- function()'v25.4.4.250429' ######## @@ -4553,7 +4553,7 @@ import_file_demo_app <- function() { #' @examples #' \dontrun{ #' data(mtcars) -#' shiny_FreesearchR(launch.browser = TRUE) +#' launch_FreesearchR(launch.browser = TRUE) #' } launch_FreesearchR <- function(...){ appDir <- system.file("apps", "FreesearchR", package = "FreesearchR") @@ -4566,6 +4566,7 @@ launch_FreesearchR <- function(...){ } + ######## #### Current file: /Users/au301842/FreesearchR/R//plot_box.R ######## @@ -9201,14 +9202,15 @@ ui_elements <- list( shiny::br(), shinyWidgets::radioGroupButtons( inputId = "source", - selected = "env", + selected = "file", choices = c( "File upload" = "file", "REDCap server export" = "redcap", "Local or sample data" = "env" ), - width = "100%" + size = "lg" ), + shiny::tags$script('document.querySelector("#source div").style.width = "100%"'), shiny::helpText("Upload a file from your device, get data directly from REDCap or select a sample data set for testing from the app."), shiny::br(), shiny::br(), @@ -9679,6 +9681,7 @@ ui <- bslib::page_fixed( shiny::tags$head( includeHTML(("www/umami-app.html")), tags$link(rel = "stylesheet", type = "text/css", href = "style.css")), + tags$head(tags$link(rel="shortcut icon", href="favicon.svg")), title = "FreesearchR", theme = light, shiny::useBusyIndicators(), @@ -9702,7 +9705,7 @@ ui <- bslib::page_fixed( ), shiny::p( style = "margin: 1; color: #888;", - shiny::tags$a("AG Damsbo", href = "https://andreas.gdamsbo.dk/", target = "_blank", rel = "noopener noreferrer")," | ", app_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer") + shiny::tags$a("Docs", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer")," | ", app_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer") ), ) ) @@ -10098,6 +10101,7 @@ server <- function(input, output, session) { ######### Data filter # IDEAFilter has the least cluttered UI, but might have a License issue + # Consider using shinyDataFilter, though not on CRAN data_filter <- IDEAFilter::IDEAFilter("data_filter", data = shiny::reactive(rv$data_variables), verbose = TRUE diff --git a/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf b/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf index 77a8c207..fd202e74 100644 --- a/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf +++ b/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf @@ -5,6 +5,6 @@ account: agdamsbo server: shinyapps.io hostUrl: https://api.shinyapps.io/v1 appId: 14600805 -bundleId: 10191506 +bundleId: 10199738 url: https://agdamsbo.shinyapps.io/FreesearchR/ version: 1 diff --git a/inst/apps/FreesearchR/server.R b/inst/apps/FreesearchR/server.R index c16cba09..25fd8384 100644 --- a/inst/apps/FreesearchR/server.R +++ b/inst/apps/FreesearchR/server.R @@ -383,6 +383,7 @@ server <- function(input, output, session) { ######### Data filter # IDEAFilter has the least cluttered UI, but might have a License issue + # Consider using shinyDataFilter, though not on CRAN data_filter <- IDEAFilter::IDEAFilter("data_filter", data = shiny::reactive(rv$data_variables), verbose = TRUE diff --git a/inst/apps/FreesearchR/ui.R b/inst/apps/FreesearchR/ui.R index 4dc60a57..61c773d3 100644 --- a/inst/apps/FreesearchR/ui.R +++ b/inst/apps/FreesearchR/ui.R @@ -35,14 +35,15 @@ ui_elements <- list( shiny::br(), shinyWidgets::radioGroupButtons( inputId = "source", - selected = "env", + selected = "file", choices = c( "File upload" = "file", "REDCap server export" = "redcap", "Local or sample data" = "env" ), - width = "100%" + size = "lg" ), + shiny::tags$script('document.querySelector("#source div").style.width = "100%"'), shiny::helpText("Upload a file from your device, get data directly from REDCap or select a sample data set for testing from the app."), shiny::br(), shiny::br(), @@ -513,6 +514,7 @@ ui <- bslib::page_fixed( shiny::tags$head( includeHTML(("www/umami-app.html")), tags$link(rel = "stylesheet", type = "text/css", href = "style.css")), + tags$head(tags$link(rel="shortcut icon", href="favicon.svg")), title = "FreesearchR", theme = light, shiny::useBusyIndicators(), @@ -536,7 +538,7 @@ ui <- bslib::page_fixed( ), shiny::p( style = "margin: 1; color: #888;", - shiny::tags$a("AG Damsbo", href = "https://andreas.gdamsbo.dk/", target = "_blank", rel = "noopener noreferrer")," | ", app_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer") + shiny::tags$a("Docs", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer")," | ", app_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer") ), ) ) diff --git a/inst/apps/FreesearchR/www/favicon.ico b/inst/apps/FreesearchR/www/favicon.ico old mode 100644 new mode 100755 index 9bd76875..502c95eb Binary files a/inst/apps/FreesearchR/www/favicon.ico and b/inst/apps/FreesearchR/www/favicon.ico differ diff --git a/inst/apps/FreesearchR/www/favicon.svg b/inst/apps/FreesearchR/www/favicon.svg new file mode 100755 index 00000000..5f383ab7 --- /dev/null +++ b/inst/apps/FreesearchR/www/favicon.svg @@ -0,0 +1,3 @@ + diff --git a/inst/apps/FreesearchR/www/intro.md b/inst/apps/FreesearchR/www/intro.md index 0b36c872..d34e6984 100644 --- a/inst/apps/FreesearchR/www/intro.md +++ b/inst/apps/FreesearchR/www/intro.md @@ -4,7 +4,7 @@ This is the ***FreesearchR*** data analysis tool. We intend the ***FreesearchR** By intention, this tool has been designed to be simple to use with a minimum of mandatory options to keep the workflow streamlined, while also including a few options to go even further. -There are some simple steps to go through (see corresponding tabs in the top): +Here is a brief summary of the functions: 1. Import data to get started. This can be a spreadsheet/file on your machine, direct export from a REDCap server, sample data or data from a your local environment if run locally. @@ -12,7 +12,7 @@ There are some simple steps to go through (see corresponding tabs in the top): 1. Evaluate data using descriptive analyses methods and inspect cross-correlations -1. Create simple, clean plots for data overview. +1. Create and export simple, clean plots for data overview and insights. 1. Create regression models for even more advanced data analyses @@ -30,4 +30,4 @@ There are some simple steps to go through (see corresponding tabs in the top): - Code to recreate all steps locally -The full [project documentation is here](https://agdamsbo.github.io/FreesearchR/) and all code used is [freely available to read, copy, modify and improve](https://github.com/agdamsbo/FreesearchR) under an [open source license](https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md)! Contributions are welcome and much appreciated and can be reporting issues, suggesting new functionality, improving code or any other feedback [here](https://github.com/agdamsbo/FreesearchR/issues). +The full [project documentation is here](https://agdamsbo.github.io/FreesearchR/) where you'll find detailed description of the app and link to the source code! If you want to [share feedback, please follow this link to a simple survey](https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8), or share on [GitHub](https://github.com/agdamsbo/FreesearchR/issues). diff --git a/inst/apps/FreesearchR/www/style.css b/inst/apps/FreesearchR/www/style.css index f84cc325..fedcd1f7 100644 --- a/inst/apps/FreesearchR/www/style.css +++ b/inst/apps/FreesearchR/www/style.css @@ -11,6 +11,7 @@ .container-fluid > .nav > li > a[data-value='FreesearchR'] {font-size: 28px} + /* from datamods */ .show-block { display: block !important; diff --git a/inst/assets/css/FreesearchR.css b/inst/assets/css/FreesearchR.css index f84cc325..fedcd1f7 100644 --- a/inst/assets/css/FreesearchR.css +++ b/inst/assets/css/FreesearchR.css @@ -11,6 +11,7 @@ .container-fluid > .nav > li > a[data-value='FreesearchR'] {font-size: 28px} + /* from datamods */ .show-block { display: block !important; diff --git a/man/launch_FreesearchR.Rd b/man/launch_FreesearchR.Rd index 5e1e590c..c456e530 100644 --- a/man/launch_FreesearchR.Rd +++ b/man/launch_FreesearchR.Rd @@ -18,6 +18,6 @@ All data.frames in the global environment will be accessible through the app. \examples{ \dontrun{ data(mtcars) -shiny_FreesearchR(launch.browser = TRUE) +launch_FreesearchR(launch.browser = TRUE) } } diff --git a/pkgdown/favicon/apple-touch-icon.png b/pkgdown/favicon/apple-touch-icon.png new file mode 100755 index 00000000..8938e2fc Binary files /dev/null and b/pkgdown/favicon/apple-touch-icon.png differ diff --git a/pkgdown/favicon/favicon-96x96.png b/pkgdown/favicon/favicon-96x96.png new file mode 100755 index 00000000..8ffa76e1 Binary files /dev/null and b/pkgdown/favicon/favicon-96x96.png differ diff --git a/pkgdown/favicon/favicon.ico b/pkgdown/favicon/favicon.ico new file mode 100755 index 00000000..502c95eb Binary files /dev/null and b/pkgdown/favicon/favicon.ico differ diff --git a/pkgdown/favicon/favicon.svg b/pkgdown/favicon/favicon.svg new file mode 100755 index 00000000..5f383ab7 --- /dev/null +++ b/pkgdown/favicon/favicon.svg @@ -0,0 +1,3 @@ + diff --git a/pkgdown/favicon/site.webmanifest b/pkgdown/favicon/site.webmanifest new file mode 100755 index 00000000..92e36720 --- /dev/null +++ b/pkgdown/favicon/site.webmanifest @@ -0,0 +1,21 @@ +{ + "name": "FreesearchR", + "short_name": "FreesearchR", + "icons": [ + { + "src": "/FreesearchR/web-app-manifest-192x192.png", + "sizes": "192x192", + "type": "image/png", + "purpose": "maskable" + }, + { + "src": "/FreesearchR/web-app-manifest-512x512.png", + "sizes": "512x512", + "type": "image/png", + "purpose": "maskable" + } + ], + "theme_color": "#ffffff", + "background_color": "#ffffff", + "display": "standalone" +} diff --git a/pkgdown/favicon/web-app-manifest-192x192.png b/pkgdown/favicon/web-app-manifest-192x192.png new file mode 100755 index 00000000..ea2309d9 Binary files /dev/null and b/pkgdown/favicon/web-app-manifest-192x192.png differ diff --git a/pkgdown/favicon/web-app-manifest-512x512.png b/pkgdown/favicon/web-app-manifest-512x512.png new file mode 100755 index 00000000..1bdca6f1 Binary files /dev/null and b/pkgdown/favicon/web-app-manifest-512x512.png differ diff --git a/renv.lock b/renv.lock index 5e58e951..500d62b6 100644 --- a/renv.lock +++ b/renv.lock @@ -653,11 +653,11 @@ }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "14.4.1-1", + "Version": "14.4.2-1", "Source": "Repository", "Type": "Package", "Title": "'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library", - "Date": "2025-03-27", + "Date": "2025-04-25", "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Binxiang\", \"Ni\", role = \"aut\"), person(\"Conrad\", \"Sanderson\", role = \"aut\", comment = c(ORCID = \"0000-0002-0049-4501\")))", "Description": "'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", "License": "GPL (>= 2)", @@ -967,19 +967,19 @@ }, "bayestestR": { "Package": "bayestestR", - "Version": "0.15.2", + "Version": "0.15.3", "Source": "Repository", "Type": "Package", "Title": "Understand and Describe Bayesian Models and Posterior Distributions", - "Authors@R": "c(person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"cre\"), email = \"dom.makowski@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Daniel\", family = \"Lüdecke\", role = \"aut\", email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Micah K.\", family = \"Wilson\", role = \"aut\", email = \"micah.k.wilson@curtin.edu.au\", comment = c(ORCID = \"0000-0003-4143-7308\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"aut\", email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Paul-Christian\", family = \"Bürkner\", role = \"rev\", email = \"paul.buerkner@gmail.com\"), person(given = \"Tristan\", family = \"Mahr\", role = \"rev\", email = \"tristan.mahr@wisc.edu\", comment = c(ORCID = \"0000-0002-8890-5116\")), person(given = \"Henrik\", family = \"Singmann\", role = \"ctb\", email = \"singmann@gmail.com\", comment = c(ORCID = \"0000-0002-4842-3657\")), person(given = \"Quentin F.\", family = \"Gronau\", role = \"ctb\", comment = c(ORCID = \"0000-0001-5510-6943\")), person(given = \"Sam\", family = \"Crawley\", role = \"ctb\", email = \"sam@crawley.nz\", comment = c(ORCID = \"0000-0002-7847-0411\")))", - "Maintainer": "Dominique Makowski ", + "Authors@R": "c(person(given = \"Dominique\", family = \"Makowski\", role = c(\"aut\", \"cre\"), email = \"officialeasystats@gmail.com\", comment = c(ORCID = \"0000-0001-5375-9967\")), person(given = \"Daniel\", family = \"Lüdecke\", role = \"aut\", email = \"d.luedecke@uke.de\", comment = c(ORCID = \"0000-0002-8895-3206\")), person(given = \"Mattan S.\", family = \"Ben-Shachar\", role = \"aut\", email = \"matanshm@post.bgu.ac.il\", comment = c(ORCID = \"0000-0002-4287-4801\")), person(given = \"Indrajeet\", family = \"Patil\", role = \"aut\", email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(given = \"Micah K.\", family = \"Wilson\", role = \"aut\", email = \"micah.k.wilson@curtin.edu.au\", comment = c(ORCID = \"0000-0003-4143-7308\")), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"aut\", email = \"brenton@wiernik.org\", comment = c(ORCID = \"0000-0001-9560-6336\")), person(given = \"Paul-Christian\", family = \"Bürkner\", role = \"rev\", email = \"paul.buerkner@gmail.com\"), person(given = \"Tristan\", family = \"Mahr\", role = \"rev\", email = \"tristan.mahr@wisc.edu\", comment = c(ORCID = \"0000-0002-8890-5116\")), person(given = \"Henrik\", family = \"Singmann\", role = \"ctb\", email = \"singmann@gmail.com\", comment = c(ORCID = \"0000-0002-4842-3657\")), person(given = \"Quentin F.\", family = \"Gronau\", role = \"ctb\", comment = c(ORCID = \"0000-0001-5510-6943\")), person(given = \"Sam\", family = \"Crawley\", role = \"ctb\", email = \"sam@crawley.nz\", comment = c(ORCID = \"0000-0002-7847-0411\")))", + "Maintainer": "Dominique Makowski ", "Description": "Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 ) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors). References: Makowski et al. (2021) .", "Depends": [ "R (>= 3.6)" ], "Imports": [ - "insight (>= 1.0.1)", - "datawizard (>= 1.0.0)", + "insight (>= 1.1.0)", + "datawizard (>= 1.0.2)", "graphics", "methods", "stats", @@ -1008,7 +1008,7 @@ "lavaan", "lme4", "logspline (>= 2.1.21)", - "marginaleffects (>= 0.24.0)", + "marginaleffects (>= 0.25.0)", "MASS", "mclust", "mediation", @@ -1017,8 +1017,8 @@ "parameters", "patchwork", "performance", - "quadprog", "posterior", + "quadprog", "RcppEigen", "rmarkdown", "rstan", @@ -1330,7 +1330,7 @@ }, "broom.helpers": { "Package": "broom.helpers", - "Version": "1.20.0", + "Version": "1.21.0", "Source": "Repository", "Title": "Helpers for Model Coefficients Tibbles", "Authors@R": "c( person(\"Joseph\", \"Larmarange\", , \"joseph@larmarange.net\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7097-700X\")), person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0003-0862-2018\")) )", @@ -1406,7 +1406,8 @@ "survival", "testthat (>= 3.0.0)", "tidycmprsk", - "VGAM" + "VGAM", + "svyVGAM" ], "VignetteBuilder": "knitr", "RdMacros": "lifecycle", @@ -5406,31 +5407,6 @@ "Author": "Dominique Makowski [aut, cre] (), Daniel Lüdecke [aut] (), Mattan S. Ben-Shachar [aut] (), Indrajeet Patil [aut] (), Rémi Thériault [aut] ()", "Repository": "CRAN" }, - "munsell": { - "Package": "munsell", - "Version": "0.5.1", - "Source": "Repository", - "Type": "Package", - "Title": "Utilities for Using Munsell Colours", - "Author": "Charlotte Wickham ", - "Maintainer": "Charlotte Wickham ", - "Description": "Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Munsell's original notation (e.g. \"5R 5/10\") and hexadecimal strings suitable for use directly in R graphics. Also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes.", - "Suggests": [ - "ggplot2", - "testthat" - ], - "Imports": [ - "colorspace", - "methods" - ], - "License": "MIT + file LICENSE", - "URL": "https://cran.r-project.org/package=munsell, https://github.com/cwickham/munsell/", - "RoxygenNote": "7.3.1", - "Encoding": "UTF-8", - "BugReports": "https://github.com/cwickham/munsell/issues", - "NeedsCompilation": "no", - "Repository": "CRAN" - }, "nlme": { "Package": "nlme", "Version": "3.1-168", @@ -5630,7 +5606,7 @@ }, "openxlsx2": { "Package": "openxlsx2", - "Version": "1.14", + "Version": "1.15", "Source": "Repository", "Type": "Package", "Title": "Read, Write and Edit 'xlsx' Files", @@ -7662,16 +7638,16 @@ }, "scales": { "Package": "scales", - "Version": "1.3.0", + "Version": "1.4.0", "Source": "Repository", "Title": "Scale Functions for Visualization", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Dana\", \"Seidel\", role = \"aut\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Dana\", \"Seidel\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.", "License": "MIT + file LICENSE", "URL": "https://scales.r-lib.org, https://github.com/r-lib/scales", "BugReports": "https://github.com/r-lib/scales/issues", "Depends": [ - "R (>= 3.6)" + "R (>= 4.1)" ], "Imports": [ "cli", @@ -7679,10 +7655,9 @@ "glue", "labeling", "lifecycle", - "munsell (>= 0.5)", "R6", "RColorBrewer", - "rlang (>= 1.0.0)", + "rlang (>= 1.1.0)", "viridisLite" ], "Suggests": [ @@ -7696,11 +7671,12 @@ ], "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-23", "Encoding": "UTF-8", "LazyLoad": "yes", - "RoxygenNote": "7.2.3", - "NeedsCompilation": "yes", - "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [cre, aut] (), Dana Seidel [aut], Posit, PBC [cph, fnd]", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [cre, aut] (), Dana Seidel [aut], Posit Software, PBC [cph, fnd] (03wc8by49)", "Maintainer": "Thomas Lin Pedersen ", "Repository": "CRAN" },