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polish and move to new hosted address

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Andreas Gammelgaard Damsbo 2025-04-24 11:00:56 +02:00
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2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: FreesearchR Package: FreesearchR
Title: Browser Based Data Analysis Title: Browser Based Data Analysis
Version: 25.4.3 Version: 25.4.4
Authors@R: Authors@R:
person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"), person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7559-1154")) comment = c(ORCID = "0000-0002-7559-1154"))

4
NEWS.md
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@ -1,3 +1,7 @@
# FreesearchR 25.4.4
Polishing and moved hosted app to new address to fully reflect name change: [https://agdamsbo.shinyapps.io/FreesearchR/](https://agdamsbo.shinyapps.io/FreesearchR/)
# FreesearchR 25.4.3 # FreesearchR 25.4.3
- *NEW*: Added a variables type filter to easily exclude unwanted types. This also includes having data type rather than data class in the summary table. Will evaluate. Types are a simpler, more practical version of the *R* data class to easy interpretation. - *NEW*: Added a variables type filter to easily exclude unwanted types. This also includes having data type rather than data class in the summary table. Will evaluate. Types are a simpler, more practical version of the *R* data class to easy interpretation.

2
R/app_version.R
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@ -1 +1 @@
app_version <- function()'v25.4.3.250423' app_version <- function()'v25.4.4.250424'

27
R/cut-variable-dates.R
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@ -56,6 +56,7 @@ cut_var.hms <- function(x, breaks, ...) {
#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday") #' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday")
#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "month_only") #' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "month_only")
#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks=NULL,format = "%A-%H") #' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks=NULL,format = "%A-%H")
#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks=NULL,format = "%W")
cut_var.POSIXt <- function(x, breaks, right = FALSE, include.lowest = TRUE, start.on.monday = TRUE, ...) { cut_var.POSIXt <- function(x, breaks, right = FALSE, include.lowest = TRUE, start.on.monday = TRUE, ...) {
breaks_o <- breaks breaks_o <- breaks
args <- list(...) args <- list(...)
@ -126,7 +127,10 @@ cut_var.POSIXct <- cut_var.POSIXt
#' @examples #' @examples
#' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(2) #' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(2)
#' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday") #' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday")
cut_var.Date <- function(x, breaks, start.on.monday = TRUE, ...) { #' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(format = "%W")
cut_var.Date <- function(x, breaks=NULL, start.on.monday = TRUE, ...) {
args <- list(...)
if ("format" %in% names(args)){ if ("format" %in% names(args)){
assertthat::assert_that(is.character(args$format)) assertthat::assert_that(is.character(args$format))
out <- forcats::as_factor(format(x,format=args$format)) out <- forcats::as_factor(format(x,format=args$format))
@ -337,10 +341,11 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
variable <- req(input$variable) variable <- req(input$variable)
choices <- c( choices <- c(
# "fixed",
# "quantile" # "quantile"
) )
if ("hms" %in% class(data[[variable]])) { if (any(c("hms","POSIXct") %in% class(data[[variable]]))) {
choices <- c(choices, "hour") choices <- c(choices, "hour")
} else if (any(c("POSIXt", "Date") %in% class(data[[variable]]))) { } else if (any(c("POSIXt", "Date") %in% class(data[[variable]]))) {
choices <- c( choices <- c(
@ -348,6 +353,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
"day", "day",
"weekday", "weekday",
"week", "week",
# "week_only",
"month", "month",
"month_only", "month_only",
"quarter", "quarter",
@ -372,6 +378,8 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
) )
} }
choices <- unique(choices)
shinyWidgets::virtualSelectInput( shinyWidgets::virtualSelectInput(
inputId = session$ns("method"), inputId = session$ns("method"),
label = i18n("Method:"), label = i18n("Method:"),
@ -389,7 +397,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
req(input$n_breaks, input$method) req(input$n_breaks, input$method)
if (input$method == "fixed") { if (input$method == "fixed") {
req(input$fixed_brks) req(input$fixed_brks)
if (any(c("hms", "POSIXt") %in% class(data[[variable]]))) { if (any(c("hms", "POSIXct") %in% class(data[[variable]]))) {
# cut.POSIXct <- cut.POSIXt # cut.POSIXct <- cut.POSIXt
f <- cut_var(data[[variable]], breaks = input$fixed_brks) f <- cut_var(data[[variable]], breaks = input$fixed_brks)
list(var = f, brks = levels(f)) list(var = f, brks = levels(f))
@ -432,6 +440,11 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
# cut.POSIXct <- cut.POSIXt # cut.POSIXct <- cut.POSIXt
f <- cut_var(data[[variable]], breaks = "hour") f <- cut_var(data[[variable]], breaks = "hour")
list(var = f, brks = levels(f)) list(var = f, brks = levels(f))
# } else if (input$method %in% c("week_only")) {
# # As a proof of concept a single option to use "format" parameter
# # https://www.stat.berkeley.edu/~s133/dates.html
# f <- cut_var(data[[variable]], format = "%W")
# list(var = f, brks = levels(f))
} else { } else {
classInt::classIntervals( classInt::classIntervals(
var = as.numeric(data[[variable]]), var = as.numeric(data[[variable]]),
@ -445,6 +458,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
data <- req(data_r()) data <- req(data_r())
variable <- req(input$variable) variable <- req(input$variable)
plot_histogram(data, variable, breaks = breaks_r()$brks, color = datamods:::get_primary_color()) plot_histogram(data, variable, breaks = breaks_r()$brks, color = datamods:::get_primary_color())
# plot_histogram(data = breaks_r()$var, breaks = breaks_r()$brks, color = datamods:::get_primary_color())
}) })
@ -582,8 +596,13 @@ modal_cut_variable <- function(id,
#' @importFrom graphics abline axis hist par plot.new plot.window #' @importFrom graphics abline axis hist par plot.new plot.window
plot_histogram <- function(data, column, bins = 30, breaks = NULL, color = "#112466") { plot_histogram <- function(data, column=NULL, bins = 30, breaks = NULL, color = "#112466") {
if (is.vector(data)){
x <- data
} else {
x <- data[[column]] x <- data[[column]]
}
x <- as.numeric(x) x <- as.numeric(x)
op <- par(mar = rep(1.5, 4)) op <- par(mar = rep(1.5, 4))
on.exit(par(op)) on.exit(par(op))

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R/sysdata.rda
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4
README.md
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@ -4,12 +4,12 @@
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14527429.svg)](https://doi.org/10.5281/zenodo.14527429) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14527429.svg)](https://doi.org/10.5281/zenodo.14527429)
[![rhub](https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml/badge.svg)](https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml) [![rhub](https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml/badge.svg)](https://github.com/agdamsbo/FreesearchR/actions/workflows/rhub.yaml)
[![FreesearchR](https://img.shields.io/badge/Shiny-shinyapps.io-blue?style=flat&labelColor=white&logo=RStudio&logoColor=blue)](https://agdamsbo.shinyapps.io/freesearcheR/) [![FreesearchR](https://img.shields.io/badge/Shiny-shinyapps.io-blue?style=flat&labelColor=white&logo=RStudio&logoColor=blue)](https://agdamsbo.shinyapps.io/FreesearchR/)
<!-- badges: end --> <!-- badges: end -->
This package is the backbone of the ***FreesearchR***, a free and open-source browser based data exploration and analysis tool intended to democratise clinical research by assisting any researcher to easily evaluate and analyse data and export publication ready results. This package is the backbone of the ***FreesearchR***, a free and open-source browser based data exploration and analysis tool intended to democratise clinical research by assisting any researcher to easily evaluate and analyse data and export publication ready results.
The ***FreesearchR***-tool is online and accessible here: [link to the app freely hosted on shinyapps.io](https://agdamsbo.shinyapps.io/FreesearcheR/). All feedback is welcome and can be shared as a GitHub issue. Any suggestions on collaboration is much welcomed. Please reach out! The ***FreesearchR***-tool is online and accessible here: [link to the app freely hosted on shinyapps.io](https://agdamsbo.shinyapps.io/FreesearchR/). All feedback is welcome and can be shared as a GitHub issue. Any suggestions on collaboration is much welcomed. Please reach out!
## Motivation ## Motivation

20
SESSION.md
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@ -11,11 +11,11 @@
|collate |en_US.UTF-8 | |collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 | |ctype |en_US.UTF-8 |
|tz |Europe/Copenhagen | |tz |Europe/Copenhagen |
|date |2025-04-23 | |date |2025-04-24 |
|rstudio |2024.12.1+563 Kousa Dogwood (desktop) | |rstudio |2024.12.1+563 Kousa Dogwood (desktop) |
|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) | |pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
|quarto |1.6.40 @ /usr/local/bin/quarto | |quarto |1.6.40 @ /usr/local/bin/quarto |
|FreesearchR |25.4.3.250423 | |FreesearchR |25.4.4.250424 |
-------------------------------------------------------------------------------- --------------------------------------------------------------------------------
@ -40,7 +40,7 @@
|class |7.3-23 |2025-01-01 |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) | |classInt |0.4-11 |2025-01-08 |CRAN (R 4.4.1) |
|cli |3.6.4 |2025-02-13 |CRAN (R 4.4.1) | |cli |3.6.4 |2025-02-13 |CRAN (R 4.4.1) |
|clipr |0.8.0 |2022-02-22 |CRAN (R 4.4.1) | |codetools |0.2-20 |2024-03-31 |CRAN (R 4.4.1) |
|colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) | |colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) |
|commonmark |1.9.5 |2025-03-17 |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) | |correlation |0.8.7 |2025-03-03 |CRAN (R 4.4.1) |
@ -66,9 +66,11 @@
|fastmap |1.2.0 |2024-05-15 |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) | |fontawesome |0.5.3 |2024-11-16 |CRAN (R 4.4.1) |
|forcats |1.0.0 |2023-01-29 |CRAN (R 4.4.0) | |forcats |1.0.0 |2023-01-29 |CRAN (R 4.4.0) |
|foreach |1.5.2 |2022-02-02 |CRAN (R 4.4.0) |
|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) | |fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) |
|generics |0.1.3 |2022-07-05 |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) | |ggplot2 |3.5.2 |2025-04-09 |CRAN (R 4.4.1) |
|glmnet |4.1-8 |NA |NA |
|glue |1.8.0 |2024-09-30 |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) | |gt |1.0.0 |2025-04-05 |CRAN (R 4.4.1) |
|gtable |0.3.6 |2024-10-25 |CRAN (R 4.4.1) | |gtable |0.3.6 |2024-10-25 |CRAN (R 4.4.1) |
@ -81,6 +83,7 @@
|httpuv |1.6.16 |2025-04-16 |CRAN (R 4.4.1) | |httpuv |1.6.16 |2025-04-16 |CRAN (R 4.4.1) |
|IDEAFilter |0.2.0 |2024-04-15 |CRAN (R 4.4.0) | |IDEAFilter |0.2.0 |2024-04-15 |CRAN (R 4.4.0) |
|insight |1.2.0 |2025-04-22 |CRAN (R 4.4.1) | |insight |1.2.0 |2025-04-22 |CRAN (R 4.4.1) |
|iterators |1.0.14 |2022-02-05 |CRAN (R 4.4.1) |
|jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.4.0) | |jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.4.0) |
|jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.4.1) | |jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.4.1) |
|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.4.1) | |KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.4.1) |
@ -90,7 +93,6 @@
|lattice |0.22-7 |2025-04-02 |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) | |lifecycle |1.0.4 |2023-11-07 |CRAN (R 4.4.1) |
|lme4 |1.1-37 |2025-03-26 |CRAN (R 4.4.1) | |lme4 |1.1-37 |2025-03-26 |CRAN (R 4.4.1) |
|magick |2.8.6 |NA |NA |
|magrittr |2.0.3 |2022-03-30 |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) | |MASS |7.3-65 |2025-02-28 |CRAN (R 4.4.1) |
|Matrix |1.7-3 |2025-03-11 |CRAN (R 4.4.1) | |Matrix |1.7-3 |2025-03-11 |CRAN (R 4.4.1) |
@ -104,7 +106,6 @@
|nloptr |2.2.1 |2025-03-17 |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) | |openssl |2.3.2 |2025-02-03 |CRAN (R 4.4.1) |
|openxlsx2 |1.14 |2025-03-20 |CRAN (R 4.4.1) | |openxlsx2 |1.14 |2025-03-20 |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) | |parameters |0.24.2 |2025-03-04 |CRAN (R 4.4.1) |
|patchwork |1.3.0 |2024-09-16 |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) | |performance |0.13.0 |2025-01-15 |CRAN (R 4.4.1) |
@ -112,7 +113,6 @@
|pillar |1.10.2 |2025-04-05 |CRAN (R 4.4.1) | |pillar |1.10.2 |2025-04-05 |CRAN (R 4.4.1) |
|pkgbuild |1.4.7 |2025-03-24 |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) | |pkgconfig |2.0.3 |2019-09-22 |CRAN (R 4.4.1) |
|pkgdown |2.1.1 |2024-09-17 |CRAN (R 4.4.1) |
|pkgload |1.4.0 |2024-06-28 |CRAN (R 4.4.0) | |pkgload |1.4.0 |2024-06-28 |CRAN (R 4.4.0) |
|processx |3.8.6 |2025-02-21 |CRAN (R 4.4.1) | |processx |3.8.6 |2025-02-21 |CRAN (R 4.4.1) |
|profvis |0.4.0 |2024-09-20 |CRAN (R 4.4.1) | |profvis |0.4.0 |2024-09-20 |CRAN (R 4.4.1) |
@ -122,6 +122,7 @@
|purrr |1.0.4 |2025-02-05 |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) | |quarto |1.4.4 |2024-07-20 |CRAN (R 4.4.0) |
|R6 |2.6.1 |2025-02-15 |CRAN (R 4.4.1) | |R6 |2.6.1 |2025-02-15 |CRAN (R 4.4.1) |
|ragg |1.4.0 |2025-04-10 |CRAN (R 4.4.1) |
|rbibutils |2.3 |2024-10-04 |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) | |RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.4.1) |
|Rcpp |1.0.14 |2025-01-12 |CRAN (R 4.4.1) | |Rcpp |1.0.14 |2025-01-12 |CRAN (R 4.4.1) |
@ -130,6 +131,8 @@
|readODS |2.3.2 |2025-01-13 |CRAN (R 4.4.1) | |readODS |2.3.2 |2025-01-13 |CRAN (R 4.4.1) |
|readr |2.1.5 |2024-01-10 |CRAN (R 4.4.0) | |readr |2.1.5 |2024-01-10 |CRAN (R 4.4.0) |
|readxl |1.4.5 |2025-03-07 |CRAN (R 4.4.1) | |readxl |1.4.5 |2025-03-07 |CRAN (R 4.4.1) |
|REDCapCAST |25.3.2 |2025-03-10 |CRAN (R 4.4.1) |
|REDCapR |1.4.0 |2025-01-11 |CRAN (R 4.4.1) |
|reformulas |0.4.0 |2024-11-03 |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) | |remotes |2.5.0 |2024-03-17 |CRAN (R 4.4.1) |
|renv |1.1.4 |2025-03-20 |CRAN (R 4.4.1) | |renv |1.1.4 |2025-03-20 |CRAN (R 4.4.1) |
@ -144,11 +147,16 @@
|scales |1.3.0 |2023-11-28 |CRAN (R 4.4.0) | |scales |1.3.0 |2023-11-28 |CRAN (R 4.4.0) |
|see |0.11.0 |2025-03-11 |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) | |sessioninfo |1.2.3 |2025-02-05 |CRAN (R 4.4.1) |
|shape |1.4.6.1 |NA |NA |
|shiny |1.10.0 |2024-12-14 |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) | |shinybusy |0.3.3 |2024-03-09 |CRAN (R 4.4.0) |
|shinyTime |1.0.3 |2022-08-19 |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) | |shinyWidgets |0.9.0 |2025-02-21 |CRAN (R 4.4.1) |
|stringi |1.8.7 |2025-03-27 |CRAN (R 4.4.1) | |stringi |1.8.7 |2025-03-27 |CRAN (R 4.4.1) |
|stringr |1.5.1 |2023-11-14 |CRAN (R 4.4.0) |
|survival |3.8-3 |2024-12-17 |CRAN (R 4.4.1) |
|systemfonts |1.2.2 |2025-04-04 |CRAN (R 4.4.1) |
|textshaping |1.0.0 |2025-01-20 |CRAN (R 4.4.1) |
|tibble |3.2.1 |2023-03-20 |CRAN (R 4.4.0) | |tibble |3.2.1 |2023-03-20 |CRAN (R 4.4.0) |
|tidyr |1.3.1 |2024-01-24 |CRAN (R 4.4.1) | |tidyr |1.3.1 |2024-01-24 |CRAN (R 4.4.1) |
|tidyselect |1.2.1 |2024-03-11 |CRAN (R 4.4.0) | |tidyselect |1.2.1 |2024-03-11 |CRAN (R 4.4.0) |

47
inst/apps/FreesearchR/app.R
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@ -10,7 +10,7 @@
#### Current file: /Users/au301842/FreesearchR/R//app_version.R #### Current file: /Users/au301842/FreesearchR/R//app_version.R
######## ########
app_version <- function()'v25.4.3.250423' app_version <- function()'v25.4.4.250424'
######## ########
@ -556,6 +556,7 @@ cut_var.hms <- function(x, breaks, ...) {
#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday") #' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday")
#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "month_only") #' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "month_only")
#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks=NULL,format = "%A-%H") #' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks=NULL,format = "%A-%H")
#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks=NULL,format = "%W")
cut_var.POSIXt <- function(x, breaks, right = FALSE, include.lowest = TRUE, start.on.monday = TRUE, ...) { cut_var.POSIXt <- function(x, breaks, right = FALSE, include.lowest = TRUE, start.on.monday = TRUE, ...) {
breaks_o <- breaks breaks_o <- breaks
args <- list(...) args <- list(...)
@ -626,7 +627,10 @@ cut_var.POSIXct <- cut_var.POSIXt
#' @examples #' @examples
#' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(2) #' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(2)
#' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday") #' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday")
cut_var.Date <- function(x, breaks, start.on.monday = TRUE, ...) { #' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(format = "%W")
cut_var.Date <- function(x, breaks=NULL, start.on.monday = TRUE, ...) {
args <- list(...)
if ("format" %in% names(args)){ if ("format" %in% names(args)){
assertthat::assert_that(is.character(args$format)) assertthat::assert_that(is.character(args$format))
out <- forcats::as_factor(format(x,format=args$format)) out <- forcats::as_factor(format(x,format=args$format))
@ -837,10 +841,11 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
variable <- req(input$variable) variable <- req(input$variable)
choices <- c( choices <- c(
# "fixed",
# "quantile" # "quantile"
) )
if ("hms" %in% class(data[[variable]])) { if (any(c("hms","POSIXct") %in% class(data[[variable]]))) {
choices <- c(choices, "hour") choices <- c(choices, "hour")
} else if (any(c("POSIXt", "Date") %in% class(data[[variable]]))) { } else if (any(c("POSIXt", "Date") %in% class(data[[variable]]))) {
choices <- c( choices <- c(
@ -848,6 +853,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
"day", "day",
"weekday", "weekday",
"week", "week",
# "week_only",
"month", "month",
"month_only", "month_only",
"quarter", "quarter",
@ -872,6 +878,8 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
) )
} }
choices <- unique(choices)
shinyWidgets::virtualSelectInput( shinyWidgets::virtualSelectInput(
inputId = session$ns("method"), inputId = session$ns("method"),
label = i18n("Method:"), label = i18n("Method:"),
@ -889,7 +897,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
req(input$n_breaks, input$method) req(input$n_breaks, input$method)
if (input$method == "fixed") { if (input$method == "fixed") {
req(input$fixed_brks) req(input$fixed_brks)
if (any(c("hms", "POSIXt") %in% class(data[[variable]]))) { if (any(c("hms", "POSIXct") %in% class(data[[variable]]))) {
# cut.POSIXct <- cut.POSIXt # cut.POSIXct <- cut.POSIXt
f <- cut_var(data[[variable]], breaks = input$fixed_brks) f <- cut_var(data[[variable]], breaks = input$fixed_brks)
list(var = f, brks = levels(f)) list(var = f, brks = levels(f))
@ -932,6 +940,11 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
# cut.POSIXct <- cut.POSIXt # cut.POSIXct <- cut.POSIXt
f <- cut_var(data[[variable]], breaks = "hour") f <- cut_var(data[[variable]], breaks = "hour")
list(var = f, brks = levels(f)) list(var = f, brks = levels(f))
# } else if (input$method %in% c("week_only")) {
# # As a proof of concept a single option to use "format" parameter
# # https://www.stat.berkeley.edu/~s133/dates.html
# f <- cut_var(data[[variable]], format = "%W")
# list(var = f, brks = levels(f))
} else { } else {
classInt::classIntervals( classInt::classIntervals(
var = as.numeric(data[[variable]]), var = as.numeric(data[[variable]]),
@ -945,6 +958,7 @@ cut_variable_server <- function(id, data_r = reactive(NULL)) {
data <- req(data_r()) data <- req(data_r())
variable <- req(input$variable) variable <- req(input$variable)
plot_histogram(data, variable, breaks = breaks_r()$brks, color = datamods:::get_primary_color()) plot_histogram(data, variable, breaks = breaks_r()$brks, color = datamods:::get_primary_color())
# plot_histogram(data = breaks_r()$var, breaks = breaks_r()$brks, color = datamods:::get_primary_color())
}) })
@ -1082,8 +1096,13 @@ modal_cut_variable <- function(id,
#' @importFrom graphics abline axis hist par plot.new plot.window #' @importFrom graphics abline axis hist par plot.new plot.window
plot_histogram <- function(data, column, bins = 30, breaks = NULL, color = "#112466") { plot_histogram <- function(data, column=NULL, bins = 30, breaks = NULL, color = "#112466") {
if (is.vector(data)){
x <- data
} else {
x <- data[[column]] x <- data[[column]]
}
x <- as.numeric(x) x <- as.numeric(x)
op <- par(mar = rep(1.5, 4)) op <- par(mar = rep(1.5, 4))
on.exit(par(op)) on.exit(par(op))
@ -8739,7 +8758,7 @@ ui_elements <- list(
shiny::tagList( shiny::tagList(
lapply( lapply(
paste0("code_", c( paste0("code_", c(
"import", "data", "variables", "filter", "table1", "univariable", "multivariable" "import", "format", "data", "variables", "filter", "table1", "univariable", "multivariable"
)), )),
\(.x)shiny::htmlOutput(outputId = .x) \(.x)shiny::htmlOutput(outputId = .x)
) )
@ -8861,7 +8880,8 @@ library(gtsummary)
data(starwars) data(starwars)
data(mtcars) data(mtcars)
mtcars <- mtcars |> append_column(as.Date(sample(1:365, nrow(mtcars))), "rand_dates") mtcars_date <- mtcars |> append_column(as.Date(sample(1:365, nrow(mtcars))), "rand_dates")
mtcars_date$date <- as.Date(sample(seq_len(365),nrow(mtcars)))
data(trial) data(trial)
@ -9018,8 +9038,11 @@ server <- function(input, output, session) {
rv$data_original <- temp_data |> rv$data_original <- temp_data |>
default_parsing() default_parsing()
rv$code$import_print <- list( rv$code$import <- rv$code$import |>
rv$code$import, expression_string(assign.str = "df <-")
rv$code$format <- list(
"df",
rlang::expr(dplyr::select(dplyr::all_of(!!input$import_var))), rlang::expr(dplyr::select(dplyr::all_of(!!input$import_var))),
rlang::call2(.fn = "default_parsing", .ns = "FreesearchR") rlang::call2(.fn = "default_parsing", .ns = "FreesearchR")
) |> ) |>
@ -9304,7 +9327,11 @@ server <- function(input, output, session) {
# }) # })
output$code_import <- shiny::renderUI({ output$code_import <- shiny::renderUI({
prismCodeBlock(paste0("#Data import\n", rv$code$import_print)) prismCodeBlock(paste0("#Data import\n", rv$code$import))
})
output$code_import <- shiny::renderUI({
prismCodeBlock(paste0("#Data import formatting\n", rv$code$format))
}) })
output$code_data <- shiny::renderUI({ output$code_data <- shiny::renderUI({

10
inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/FreesearchR.dcf Normal file
View file

@ -0,0 +1,10 @@
name: FreesearchR
title:
username: agdamsbo
account: agdamsbo
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 14600805
bundleId: 10169595
url: https://agdamsbo.shinyapps.io/FreesearchR/
version: 1

2
inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
View file

@ -5,6 +5,6 @@ account: agdamsbo
server: shinyapps.io server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1 hostUrl: https://api.shinyapps.io/v1
appId: 13611288 appId: 13611288
bundleId: 10164419 bundleId: 10164589
url: https://agdamsbo.shinyapps.io/freesearcheR/ url: https://agdamsbo.shinyapps.io/freesearcheR/
version: 1 version: 1

16
inst/apps/FreesearchR/server.R
View file

@ -32,7 +32,8 @@ library(gtsummary)
data(starwars) data(starwars)
data(mtcars) data(mtcars)
mtcars <- mtcars |> append_column(as.Date(sample(1:365, nrow(mtcars))), "rand_dates") mtcars_date <- mtcars |> append_column(as.Date(sample(1:365, nrow(mtcars))), "rand_dates")
mtcars_date$date <- as.Date(sample(seq_len(365),nrow(mtcars)))
data(trial) data(trial)
@ -189,8 +190,11 @@ server <- function(input, output, session) {
rv$data_original <- temp_data |> rv$data_original <- temp_data |>
default_parsing() default_parsing()
rv$code$import_print <- list( rv$code$import <- rv$code$import |>
rv$code$import, expression_string(assign.str = "df <-")
rv$code$format <- list(
"df",
rlang::expr(dplyr::select(dplyr::all_of(!!input$import_var))), rlang::expr(dplyr::select(dplyr::all_of(!!input$import_var))),
rlang::call2(.fn = "default_parsing", .ns = "FreesearchR") rlang::call2(.fn = "default_parsing", .ns = "FreesearchR")
) |> ) |>
@ -475,7 +479,11 @@ server <- function(input, output, session) {
# }) # })
output$code_import <- shiny::renderUI({ output$code_import <- shiny::renderUI({
prismCodeBlock(paste0("#Data import\n", rv$code$import_print)) prismCodeBlock(paste0("#Data import\n", rv$code$import))
})
output$code_import <- shiny::renderUI({
prismCodeBlock(paste0("#Data import formatting\n", rv$code$format))
}) })
output$code_data <- shiny::renderUI({ output$code_data <- shiny::renderUI({

2
inst/apps/FreesearchR/ui.R
View file

@ -462,7 +462,7 @@ ui_elements <- list(
shiny::tagList( shiny::tagList(
lapply( lapply(
paste0("code_", c( paste0("code_", c(
"import", "data", "variables", "filter", "table1", "univariable", "multivariable" "import", "format", "data", "variables", "filter", "table1", "univariable", "multivariable"
)), )),
\(.x)shiny::htmlOutput(outputId = .x) \(.x)shiny::htmlOutput(outputId = .x)
) )

21
inst/apps/FreesearchR/www/references.bib
View file

@ -1,24 +1,11 @@
@book{andreasgammelgaarddamsbo2025, @book{andreasgammelgaarddamsbo2025,
title = {agdamsbo/freesearcheR: freesearcheR 25.3.1}, title = {agdamsbo/FreesearchR: FreesearchR 25.4.3},
author = {Andreas Gammelgaard Damsbo, }, author = {Damsbo, Andreas Gammelgaard},
year = {2025}, year = {2025},
month = {03}, month = {04},
date = {2025-03-06}, date = {2025-04-24},
publisher = {Zenodo}, publisher = {Zenodo},
doi = {10.5281/ZENODO.14527429}, doi = {10.5281/ZENODO.14527429},
url = {https://zenodo.org/doi/10.5281/zenodo.14527429} url = {https://zenodo.org/doi/10.5281/zenodo.14527429}
} }
@article{Aam2020,
title = {Post-stroke Cognitive Impairment{\textemdash}Impact of Follow-Up Time and Stroke Subtype on Severity and Cognitive Profile: The Nor-COAST Study},
author = {Aam, Stina and Einstad, Marte Stine and Munthe-Kaas, Ragnhild and Lydersen, Stian and Ihle-Hansen, Hege and Knapskog, Anne Brita and {Ellekjær}, Hanne and Seljeseth, Yngve and Saltvedt, Ingvild},
year = {2020},
date = {2020},
journal = {Frontiers in Neurology},
pages = {1--10},
volume = {11},
number = {July},
doi = {10.3389/fneur.2020.00699},
note = {Citation Key: Aam2020}
}

2
umami-page.html
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@ -1 +1 @@
<script defer src="https://analytics.gdamsbo.dk/script.js" data-website-id="1f3baf18-29aa-4612-931b-58ea35922ae4"></script> <script defer src="https://analytics.gdamsbo.dk/script.js" data-website-id="e7d4e13a-5824-4778-bbc0-8f92fb08303a"></script>