diff --git a/R/app_version.R b/R/app_version.R index 84fbc45c..076f20e3 100644 --- a/R/app_version.R +++ b/R/app_version.R @@ -1 +1 @@ -app_version <- function()'v25.4.4.250429' +app_version <- function()'v25.4.4.250428' diff --git a/R/launch_FreesearchR.R b/R/launch_FreesearchR.R index c6bcc301..5d22820e 100644 --- a/R/launch_FreesearchR.R +++ b/R/launch_FreesearchR.R @@ -11,7 +11,7 @@ #' @examples #' \dontrun{ #' data(mtcars) -#' launch_FreesearchR(launch.browser = TRUE) +#' shiny_FreesearchR(launch.browser = TRUE) #' } launch_FreesearchR <- function(...){ appDir <- system.file("apps", "FreesearchR", package = "FreesearchR") @@ -22,4 +22,3 @@ 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 6531331f..ac4e4747 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/README.md b/README.md index 10d809f8..eaa07f23 100644 --- a/README.md +++ b/README.md @@ -53,6 +53,4 @@ 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 a01a1881..4e681f8a 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 |2025-04-29 | -|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 | +|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 | -------------------------------------------------------------------------------- @@ -23,64 +23,41 @@ -------------------------------------------------------------------------------- |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) | -|crosstalk |1.2.1 |2023-11-23 |CRAN (R 4.4.0) | +|credentials |2.0.2 |2024-10-04 |CRAN (R 4.4.1) | |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) | -|ggplot2 |3.5.2 |2025-04-09 |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) | |glue |1.8.0 |2024-09-30 |CRAN (R 4.4.1) | -|gt |1.0.0 |2025-04-05 |CRAN (R 4.4.1) | -|gtable |0.3.6 |2024-10-25 |CRAN (R 4.4.1) | -|gtsummary |2.2.0 |2025-04-14 |CRAN (R 4.4.1) | -|haven |2.5.4 |2023-11-30 |CRAN (R 4.4.0) | |here |1.0.1 |2020-12-13 |CRAN (R 4.4.1) | |hms |1.1.3 |2023-03-21 |CRAN (R 4.4.0) | |htmltools |0.5.8.1 |2024-04-04 |CRAN (R 4.4.1) | |htmlwidgets |1.6.4 |2023-12-06 |CRAN (R 4.4.0) | |httpuv |1.6.16 |2025-04-16 |CRAN (R 4.4.1) | -|IDEAFilter |0.2.0 |2024-04-15 |CRAN (R 4.4.0) | -|insight |1.2.0 |2025-04-22 |CRAN (R 4.4.1) | +|httr2 |1.1.2 |2025-03-26 |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) | @@ -88,65 +65,38 @@ |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) | -|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) | +|pak |0.8.0.2 |2025-04-08 |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) | -|rbibutils |2.3 |2024-10-04 |CRAN (R 4.4.1) | -|RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.4.1) | +|rappdirs |0.3.3 |2021-01-31 |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) | @@ -156,8 +106,6 @@ |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 082962ba..d4deb602 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()'v25.4.4.250429' +app_version <- function()'v25.4.4.250428' ######## @@ -4553,7 +4553,7 @@ import_file_demo_app <- function() { #' @examples #' \dontrun{ #' data(mtcars) -#' launch_FreesearchR(launch.browser = TRUE) +#' shiny_FreesearchR(launch.browser = TRUE) #' } launch_FreesearchR <- function(...){ appDir <- system.file("apps", "FreesearchR", package = "FreesearchR") @@ -4566,7 +4566,6 @@ launch_FreesearchR <- function(...){ } - ######## #### Current file: /Users/au301842/FreesearchR/R//plot_box.R ######## @@ -9202,15 +9201,14 @@ ui_elements <- list( shiny::br(), shinyWidgets::radioGroupButtons( inputId = "source", - selected = "file", + selected = "env", choices = c( "File upload" = "file", "REDCap server export" = "redcap", "Local or sample data" = "env" ), - size = "lg" + width = "100%" ), - shiny::tags$script('document.querySelector("#source div").style.width = "100%"'), shiny::helpText("Upload a file from your device, get data directly from REDCap or select a sample data set for testing from the app."), shiny::br(), shiny::br(), @@ -9681,7 +9679,6 @@ ui <- bslib::page_fixed( shiny::tags$head( includeHTML(("www/umami-app.html")), tags$link(rel = "stylesheet", type = "text/css", href = "style.css")), - tags$head(tags$link(rel="shortcut icon", href="favicon.svg")), title = "FreesearchR", theme = light, shiny::useBusyIndicators(), @@ -9705,7 +9702,7 @@ ui <- bslib::page_fixed( ), shiny::p( style = "margin: 1; color: #888;", - shiny::tags$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$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer") + shiny::tags$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") ), ) ) @@ -10101,7 +10098,6 @@ 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$data_variables), verbose = TRUE diff --git a/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf b/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf index fd202e74..77a8c207 100644 --- a/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf +++ b/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf @@ -5,6 +5,6 @@ account: agdamsbo server: shinyapps.io hostUrl: https://api.shinyapps.io/v1 appId: 14600805 -bundleId: 10199738 +bundleId: 10191506 url: https://agdamsbo.shinyapps.io/FreesearchR/ version: 1 diff --git a/inst/apps/FreesearchR/server.R b/inst/apps/FreesearchR/server.R index 25fd8384..c16cba09 100644 --- a/inst/apps/FreesearchR/server.R +++ b/inst/apps/FreesearchR/server.R @@ -383,7 +383,6 @@ server <- function(input, output, session) { ######### Data filter # IDEAFilter has the least cluttered UI, but might have a License issue - # Consider using shinyDataFilter, though not on CRAN data_filter <- IDEAFilter::IDEAFilter("data_filter", data = shiny::reactive(rv$data_variables), verbose = TRUE diff --git a/inst/apps/FreesearchR/ui.R b/inst/apps/FreesearchR/ui.R index 61c773d3..4dc60a57 100644 --- a/inst/apps/FreesearchR/ui.R +++ b/inst/apps/FreesearchR/ui.R @@ -35,15 +35,14 @@ ui_elements <- list( shiny::br(), shinyWidgets::radioGroupButtons( inputId = "source", - selected = "file", + selected = "env", choices = c( "File upload" = "file", "REDCap server export" = "redcap", "Local or sample data" = "env" ), - size = "lg" + width = "100%" ), - shiny::tags$script('document.querySelector("#source div").style.width = "100%"'), shiny::helpText("Upload a file from your device, get data directly from REDCap or select a sample data set for testing from the app."), shiny::br(), shiny::br(), @@ -514,7 +513,6 @@ ui <- bslib::page_fixed( shiny::tags$head( includeHTML(("www/umami-app.html")), tags$link(rel = "stylesheet", type = "text/css", href = "style.css")), - tags$head(tags$link(rel="shortcut icon", href="favicon.svg")), title = "FreesearchR", theme = light, shiny::useBusyIndicators(), @@ -538,7 +536,7 @@ ui <- bslib::page_fixed( ), shiny::p( style = "margin: 1; color: #888;", - shiny::tags$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$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer") + shiny::tags$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") ), ) ) diff --git a/inst/apps/FreesearchR/www/favicon.ico b/inst/apps/FreesearchR/www/favicon.ico old mode 100755 new mode 100644 index 502c95eb..9bd76875 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 deleted file mode 100755 index 5f383ab7..00000000 --- a/inst/apps/FreesearchR/www/favicon.svg +++ /dev/null @@ -1,3 +0,0 @@ - diff --git a/inst/apps/FreesearchR/www/intro.md b/inst/apps/FreesearchR/www/intro.md index d34e6984..0b36c872 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. -Here is a brief summary of the functions: +There are some simple steps to go through (see corresponding tabs in the top): 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 @@ Here is a brief summary of the functions: 1. Evaluate data using descriptive analyses methods and inspect cross-correlations -1. Create and export simple, clean plots for data overview and insights. +1. Create simple, clean plots for data overview. 1. Create regression models for even more advanced data analyses @@ -30,4 +30,4 @@ Here is a brief summary of the functions: - Code to recreate all steps locally -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). +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). diff --git a/inst/apps/FreesearchR/www/style.css b/inst/apps/FreesearchR/www/style.css index fedcd1f7..f84cc325 100644 --- a/inst/apps/FreesearchR/www/style.css +++ b/inst/apps/FreesearchR/www/style.css @@ -11,7 +11,6 @@ .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 fedcd1f7..f84cc325 100644 --- a/inst/assets/css/FreesearchR.css +++ b/inst/assets/css/FreesearchR.css @@ -11,7 +11,6 @@ .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 c456e530..5e1e590c 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) -launch_FreesearchR(launch.browser = TRUE) +shiny_FreesearchR(launch.browser = TRUE) } } diff --git a/pkgdown/favicon/apple-touch-icon.png b/pkgdown/favicon/apple-touch-icon.png deleted file mode 100755 index 8938e2fc..00000000 Binary files a/pkgdown/favicon/apple-touch-icon.png and /dev/null differ diff --git a/pkgdown/favicon/favicon-96x96.png b/pkgdown/favicon/favicon-96x96.png deleted file mode 100755 index 8ffa76e1..00000000 Binary files a/pkgdown/favicon/favicon-96x96.png and /dev/null differ diff --git a/pkgdown/favicon/favicon.ico b/pkgdown/favicon/favicon.ico deleted file mode 100755 index 502c95eb..00000000 Binary files a/pkgdown/favicon/favicon.ico and /dev/null differ diff --git a/pkgdown/favicon/favicon.svg b/pkgdown/favicon/favicon.svg deleted file mode 100755 index 5f383ab7..00000000 --- a/pkgdown/favicon/favicon.svg +++ /dev/null @@ -1,3 +0,0 @@ - diff --git a/pkgdown/favicon/site.webmanifest b/pkgdown/favicon/site.webmanifest deleted file mode 100755 index 92e36720..00000000 --- a/pkgdown/favicon/site.webmanifest +++ /dev/null @@ -1,21 +0,0 @@ -{ - "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 deleted file mode 100755 index ea2309d9..00000000 Binary files a/pkgdown/favicon/web-app-manifest-192x192.png and /dev/null differ diff --git a/pkgdown/favicon/web-app-manifest-512x512.png b/pkgdown/favicon/web-app-manifest-512x512.png deleted file mode 100755 index 1bdca6f1..00000000 Binary files a/pkgdown/favicon/web-app-manifest-512x512.png and /dev/null differ diff --git a/renv.lock b/renv.lock index 500d62b6..5e58e951 100644 --- a/renv.lock +++ b/renv.lock @@ -653,11 +653,11 @@ }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "14.4.2-1", + "Version": "14.4.1-1", "Source": "Repository", "Type": "Package", "Title": "'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library", - "Date": "2025-04-25", + "Date": "2025-03-27", "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": "0.15.3", + "Version": "0.15.2", "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 = \"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 ", + "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 ", "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 (>= 1.1.0)", - "datawizard (>= 1.0.2)", + "insight (>= 1.0.1)", + "datawizard (>= 1.0.0)", "graphics", "methods", "stats", @@ -1008,7 +1008,7 @@ "lavaan", "lme4", "logspline (>= 2.1.21)", - "marginaleffects (>= 0.25.0)", + "marginaleffects (>= 0.24.0)", "MASS", "mclust", "mediation", @@ -1017,8 +1017,8 @@ "parameters", "patchwork", "performance", - "posterior", "quadprog", + "posterior", "RcppEigen", "rmarkdown", "rstan", @@ -1330,7 +1330,7 @@ }, "broom.helpers": { "Package": "broom.helpers", - "Version": "1.21.0", + "Version": "1.20.0", "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\")) )", @@ -1406,8 +1406,7 @@ "survival", "testthat (>= 3.0.0)", "tidycmprsk", - "VGAM", - "svyVGAM" + "VGAM" ], "VignetteBuilder": "knitr", "RdMacros": "lifecycle", @@ -5407,6 +5406,31 @@ "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", @@ -5606,7 +5630,7 @@ }, "openxlsx2": { "Package": "openxlsx2", - "Version": "1.15", + "Version": "1.14", "Source": "Repository", "Type": "Package", "Title": "Read, Write and Edit 'xlsx' Files", @@ -7638,16 +7662,16 @@ }, "scales": { "Package": "scales", - "Version": "1.4.0", + "Version": "1.3.0", "Source": "Repository", "Title": "Scale Functions for Visualization", - "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\")) )", + "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\")) )", "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 (>= 4.1)" + "R (>= 3.6)" ], "Imports": [ "cli", @@ -7655,9 +7679,10 @@ "glue", "labeling", "lifecycle", + "munsell (>= 0.5)", "R6", "RColorBrewer", - "rlang (>= 1.1.0)", + "rlang (>= 1.0.0)", "viridisLite" ], "Suggests": [ @@ -7671,12 +7696,11 @@ ], "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", - "Config/usethis/last-upkeep": "2025-04-23", "Encoding": "UTF-8", "LazyLoad": "yes", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "no", - "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [cre, aut] (), Dana Seidel [aut], Posit Software, PBC [cph, fnd] (03wc8by49)", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [cre, aut] (), Dana Seidel [aut], Posit, PBC [cph, fnd]", "Maintainer": "Thomas Lin Pedersen ", "Repository": "CRAN" },