andreas/FreesearchR
1
0
Fork 0
mirror of https://github.com/agdamsbo/FreesearchR.git synced 2026-06-19 04:27:30 +02:00
Code Issues Projects Releases Packages Wiki Activity

new version ready

Browse source
This commit is contained in:
Andreas Gammelgaard Damsbo 2026-03-31 20:42:22 +02:00
commit de52a56b1f
No known key found for this signature in database
11 changed files with 27 additions and 147 deletions
Download patch file Download diff file Expand all files Collapse all files

2
CITATION.cff
View file

@ -8,7 +8,7 @@ message: 'To cite package "FreesearchR" in publications use:'
type: software
license: AGPL-3.0-or-later
title: 'FreesearchR: Easy data analysis for clinicians'
version: 26.3.5
version: 26.3.6
doi: 10.5281/zenodo.14527429
identifiers:
- type: url

2
DESCRIPTION
View file

@ -1,6 +1,6 @@
Package: FreesearchR
Title: Easy data analysis for clinicians
Version: 26.3.5
Version: 26.3.6
Authors@R: c(
person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7559-1154")),

6
NEWS.md
View file

@ -1,3 +1,9 @@
# FreesearchR 26.3.6
*FIX* Plot single variable in Likert plot.
*FIX* Horisontal stacked plot crashed. Fixed!
# FreesearchR 26.3.5
*FIX* Labelled categorical variables were not handled correctly importing from REDCap resulting in lost labels. Fixed!

2
R/app_version.R
View file

@ -1 +1 @@
app_version <- function()'26.3.5'
app_version <- function()'26.3.6'

113
R/data_plots.R
View file

@ -117,18 +117,7 @@ data_visuals_ui <- function(id, tab_title = "Plots", ...) {
#' @export
data_visuals_server <- function(id,
data,
palettes = c(
"Perceptual (blue-yellow)" = "viridis",
"Perceptual (fire)" = "plasma",
"Colour-blind friendly" = "Okabe-Ito",
"Qualitative (bold)" = "Dark 2",
"Qualitative (paired)" = "Paired",
"Sequential (blues)" = "Blues",
"Diverging (red-blue)" = "RdBu",
"Tableau style" = "Tableau 10",
"Pastel" = "Pastel 1",
"Rainbow" = "rainbow"
),
palettes,
...) {
shiny::moduleServer(
id = id,
@ -150,100 +139,6 @@ data_visuals_server <- function(id,
title = i18n$t("Download"))
})
# ## --- New attempt
#
# rv$plot.params <- shiny::reactive({
# get_plot_options(input$type) |> purrr::pluck(1)
# })
#
# c(output,
# list(shiny::renderUI({
# columnSelectInput(
# inputId = ns("primary"),
# data = data,
# placeholder = "Select variable",
# label = "Response variable",
# multiple = FALSE
# )
# }),
# shiny::renderUI({
# shiny::req(input$primary)
# # browser()
#
# if (!input$primary %in% names(data())) {
# plot_data <- data()[1]
# } else {
# plot_data <- data()[input$primary]
# }
#
# plots <- possible_plots(
# data = plot_data
# )
#
# plots_named <- get_plot_options(plots) |>
# lapply(\(.x){
# stats::setNames(.x$descr, .x$note)
# })
#
# vectorSelectInput(
# inputId = ns("type"),
# selected = NULL,
# label = shiny::h4("Plot type"),
# choices = Reduce(c, plots_named),
# multiple = FALSE
# )
# }),
# shiny::renderUI({
# shiny::req(input$type)
#
# cols <- c(
# rv$plot.params()[["secondary.extra"]],
# all_but(
# colnames(subset_types(
# data(),
# rv$plot.params()[["secondary.type"]]
# )),
# input$primary
# )
# )
#
# columnSelectInput(
# inputId = ns("secondary"),
# data = data,
# selected = cols[1],
# placeholder = "Please select",
# label = if (isTRUE(rv$plot.params()[["secondary.multi"]])) "Additional variables" else "Secondary variable",
# multiple = rv$plot.params()[["secondary.multi"]],
# maxItems = rv$plot.params()[["secondary.max"]],
# col_subset = cols,
# none_label = "No variable"
# )
# }),
# shiny::renderUI({
# shiny::req(input$type)
# columnSelectInput(
# inputId = ns("tertiary"),
# data = data,
# placeholder = "Please select",
# label = "Grouping variable",
# multiple = FALSE,
# col_subset = c(
# "none",
# all_but(
# colnames(subset_types(
# data(),
# rv$plot.params()[["tertiary.type"]]
# )),
# input$primary,
# input$secondary
# )
# ),
# none_label = "No stratification"
# )
# })
# )|> setNames(c("primary","type","secondary","tertiary")),keep.null = TRUE)
output$primary <- shiny::renderUI({
shiny::req(data())
columnSelectInput(
@ -258,13 +153,12 @@ data_visuals_server <- function(id,
# shiny::observeEvent(data, {
# if (is.null(data()) | NROW(data()) == 0) {
# shiny::updateActionButton(inputId = ns("act_plot"), disabled = TRUE)
# shiny::updateActionButton(inputId = "act_plot", disabled = TRUE)
# } else {
# shiny::updateActionButton(inputId = ns("act_plot"), disabled = FALSE)
# shiny::updateActionButton(inputId = "act_plot", disabled = FALSE)
# }
# })
output$type <- shiny::renderUI({
shiny::req(input$primary)
shiny::req(data())
@ -610,6 +504,7 @@ supported_plots <- function() {
primary.type = c("dichotomous", "categorical"),
secondary.type = c("dichotomous", "categorical"),
secondary.multi = TRUE,
secondary.extra = NULL,
tertiary.type = c("dichotomous", "categorical"),
secondary.extra = NULL
)

2
R/hosted_version.R
View file

@ -1 +1 @@
hosted_version <- function()'v26.3.5-260330'
hosted_version <- function()'v26.3.6-260331'

18
R/plot_bar.R
View file

@ -56,30 +56,12 @@ plot_bar_single <- function(data, pri, sec = NULL, style = c("stack", "dodge", "
if (nrow(p_data) > max_level) {
# browser()
p_data <- sort_by(
p_data,
p_data[["Freq"]],
decreasing = TRUE
) |>
head(max_level)
# if (is.null(sec)){
# p_data <- sort_by(
# p_data,
# p_data[["Freq"]],
# decreasing=TRUE) |>
# head(max_level)
# } else {
# split(p_data,p_data[[sec]]) |>
# lapply(\(.x){
# # browser()
# sort_by(
# .x,
# .x[["Freq"]],
# decreasing=TRUE) |>
# head(max_level)
# }) |> dplyr::bind_rows()
# }
}
## Shortens long level names

BIN
R/sysdata.rda
View file

Binary file not shown.

14
SESSION.md
View file

@ -4,18 +4,18 @@
|setting |value |
|:-----------|:------------------------------------------|
|version |R version 4.5.2 (2025-10-31) |
|os |macOS Tahoe 26.3 |
|os |macOS Tahoe 26.4 |
|system |aarch64, darwin20 |
|ui |RStudio |
|language |(EN) |
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |Europe/Copenhagen |
|date |2026-03-30 |
|date |2026-03-31 |
|rstudio |2026.01.1+403 Apple Blossom (desktop) |
|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
|quarto |1.7.30 @ /usr/local/bin/quarto |
|FreesearchR |26.3.5.260330 |
|FreesearchR |26.3.6.260331 |
--------------------------------------------------------------------------------
@ -84,7 +84,7 @@
|foreach |1.5.2 |2022-02-02 |CRAN (R 4.5.0) |
|foreign |0.8-91 |2026-01-29 |CRAN (R 4.5.2) |
|Formula |1.2-5 |2023-02-24 |CRAN (R 4.5.0) |
|FreesearchR |26.3.5 |NA |NA |
|FreesearchR |26.3.6 |NA |NA |
|fs |1.6.7 |2026-03-06 |CRAN (R 4.5.2) |
|gdtools |0.5.0 |2026-02-09 |CRAN (R 4.5.2) |
|generics |0.1.4 |2025-05-09 |CRAN (R 4.5.0) |
@ -150,6 +150,7 @@
|pkgload |1.5.0 |2026-02-03 |CRAN (R 4.5.2) |
|plyr |1.8.9 |2023-10-02 |CRAN (R 4.5.0) |
|polyclip |1.10-7 |2024-07-23 |CRAN (R 4.5.0) |
|polyglotr |1.7.1 |NA |NA |
|pracma |2.4.6 |2025-10-22 |CRAN (R 4.5.0) |
|processx |3.8.6 |2025-02-21 |CRAN (R 4.5.0) |
|promises |1.5.0 |2025-11-01 |CRAN (R 4.5.0) |
@ -187,10 +188,12 @@
|rprojroot |2.1.1 |2025-08-26 |CRAN (R 4.5.0) |
|rsconnect |1.7.0 |2025-12-06 |CRAN (R 4.5.2) |
|rstudioapi |0.18.0 |2026-01-16 |CRAN (R 4.5.2) |
|rvest |1.0.5 |NA |NA |
|S7 |0.2.1 |2025-11-14 |CRAN (R 4.5.2) |
|sass |0.4.10 |2025-04-11 |CRAN (R 4.5.0) |
|scales |1.4.0 |2025-04-24 |CRAN (R 4.5.0) |
|see |0.13.0 |2026-01-30 |CRAN (R 4.5.2) |
|selectr |0.5-1 |NA |NA |
|sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.5.0) |
|shiny |1.13.0 |2026-02-20 |CRAN (R 4.5.2) |
|shiny.i18n |0.3.0 |2023-01-16 |CRAN (R 4.5.0) |
@ -211,10 +214,13 @@
|tidyselect |1.2.1 |2024-03-11 |CRAN (R 4.5.0) |
|timechange |0.4.0 |2026-01-29 |CRAN (R 4.5.2) |
|toastui |0.4.0 |2025-04-03 |CRAN (R 4.5.0) |
|triebeard |0.4.1 |NA |NA |
|tweenr |2.0.3 |2024-02-26 |CRAN (R 4.5.0) |
|twosamples |2.0.1 |2023-06-23 |CRAN (R 4.5.0) |
|tzdb |0.5.0 |2025-03-15 |CRAN (R 4.5.0) |
|urltools |1.7.3.1 |NA |NA |
|usethis |3.2.1 |2025-09-06 |CRAN (R 4.5.0) |
|utf8 |1.2.6 |2025-06-08 |CRAN (R 4.5.0) |
|uuid |1.2-2 |2026-01-23 |CRAN (R 4.5.2) |
|vctrs |0.7.1 |2026-01-23 |CRAN (R 4.5.2) |
|viridis |0.6.5 |2024-01-29 |CRAN (R 4.5.0) |

13
man/data-plots.Rd
View file

@ -21,16 +21,7 @@
\usage{
data_visuals_ui(id, tab_title = "Plots", ...)
data_visuals_server(
id,
data,
palettes = c(`Perceptual (blue-yellow)` = "viridis", `Perceptual (fire)` = "plasma",
`Colour-blind friendly` = "Okabe-Ito", `Qualitative (bold)` = "Dark 2",
`Qualitative (paired)` = "Paired", `Sequential (blues)` = "Blues",
`Diverging (red-blue)` = "RdBu", `Tableau style` = "Tableau 10", Pastel = "Pastel 1",
Rainbow = "rainbow"),
...
)
data_visuals_server(id, data, palettes, ...)
create_plot(data, type, pri, sec, ter = NULL, color.palette = "viridis", ...)
@ -170,7 +161,7 @@ mtcars |> plot_hbars(pri = "carb", sec = "cyl")
mtcars |> plot_hbars(pri = "carb", sec = "cyl", ter="am")
mtcars |> plot_hbars(pri = "carb", sec = NULL,color.palette="Blues")
mtcars |> plot_hbars(pri = "carb", sec = NULL,color.palette="Magma")
mtcars |> plot_hbars(pri = "carb", sec = NULL,color.palette="Viridis")
mtcars |> plot_hbars(pri = "carb", sec = "am",color.palette="Viridis")
mtcars |> plot_likert(pri = "carb", sec = "cyl")
mtcars |> plot_likert(pri = "carb", sec = "cyl", ter="am")
mtcars |> plot_likert(pri = "cyl",color.palette="Blues")

2
man/vertical_stacked_bars.Rd
View file

@ -9,7 +9,7 @@ vertical_stacked_bars(
score = "full_score",
group = "pase_0_q",
strata = NULL,
t.size = 10,
t.size = 8,
l.color = "black",
l.size = 0.5,
draw.lines = TRUE,