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1
DESCRIPTION
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@ -141,5 +141,6 @@ Collate:
'update-variables-ext.R'
'utils-labels.R'
'validation.R'
'version_check.R'
'visual_summary.R'
'wide2long.R'

2
NEWS.md
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@ -1,6 +1,8 @@
# FreesearchR 26.3.4
*NEW* Added app version check against latest release on GitHub. Only runs if internet connection present. No other polling.
*NEW* Added a "Missing" level to the sankey plot function and adjusted the label font size.
# FreesearchR 26.3.3

2
R/hosted_version.R
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@ -1 +1 @@
hosted_version <- function()'v26.3.4-260312'
hosted_version <- function()'v26.3.4-260323'

6
R/launch_FreesearchR.R
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@ -8,6 +8,8 @@
#' @param data_limit_default default data set observations limit
#' @param data_limit_upper data set observations upper limit
#' @param data_limit_lower data set observations lower limit
#' @param check_app_version always attempt to check app version against latest
#' release on GitHub. Default is FALSE
#' @param ... passed on to `shiny::runApp()`
#'
#' @returns shiny app
@ -22,12 +24,14 @@ launch_FreesearchR <- function(include_globalenv = TRUE,
data_limit_default = 1000,
data_limit_upper = 100000,
data_limit_lower = 1,
check_app_version = FALSE,
...) {
Sys.setenv(
INCLUDE_GLOBALENV = include_globalenv,
DATA_LIMIT_DEFAULT = data_limit_default,
DATA_LIMIT_UPPER = data_limit_upper,
DATA_LIMIT_LOWER = data_limit_lower
DATA_LIMIT_LOWER = data_limit_lower,
CHECK_APP_VERSION = check_app_version
)
appDir <- system.file("apps", "FreesearchR", package = "FreesearchR")

92
R/plot_sankey.R
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@ -33,15 +33,17 @@ sankey_ready <- function(data, pri, sec, numbers = "count", ...) {
dplyr::ungroup()
if (numbers == "count") {
out <- out |> dplyr::mutate(
lx = factor(paste0(!!dplyr::sym(pri), "\n(n=", gx.sum, ")")),
ly = factor(paste0(!!dplyr::sym(sec), "\n(n=", gy.sum, ")"))
)
out <- out |> dplyr::mutate(lx = factor(paste0(
!!dplyr::sym(pri), "\n(n=", gx.sum, ")"
)), ly = factor(paste0(
!!dplyr::sym(sec), "\n(n=", gy.sum, ")"
)))
} else if (numbers == "percentage") {
out <- out |> dplyr::mutate(
lx = factor(paste0(!!dplyr::sym(pri), "\n(", round((gx.sum / sum(n)) * 100, 1), "%)")),
ly = factor(paste0(!!dplyr::sym(sec), "\n(", round((gy.sum / sum(n)) * 100, 1), "%)"))
)
out <- out |> dplyr::mutate(lx = factor(paste0(
!!dplyr::sym(pri), "\n(", round((gx.sum / sum(n)) * 100, 1), "%)"
)), ly = factor(paste0(
!!dplyr::sym(sec), "\n(", round((gy.sum / sum(n)) * 100, 1), "%)"
)))
}
if (is.factor(data[[pri]])) {
@ -83,20 +85,38 @@ str_remove_last <- function(data, pattern = "\n") {
#' mtcars |>
#' default_parsing() |>
#' plot_sankey("cyl", "gear", "vs", color.group = "pri")
plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors = NULL,missing.level="Missing") {
#'
#' # stRoke::trial |> plot_sankey("mrs_1", "mrs_6")
plot_sankey <- function(data,
pri,
sec,
ter = NULL,
color.group = "pri",
colors = NULL,
missing.level = "Missing") {
if (!is.null(ter)) {
ds <- split(data, data[ter])
} else {
ds <- list(data)
}
out <- lapply(ds, \(.ds){
plot_sankey_single(.ds, pri = pri, sec = sec, color.group = color.group, colors = colors,missing.level=missing.level)
out <- lapply(ds, \(.ds) {
plot_sankey_single(
.ds,
pri = pri,
sec = sec,
color.group = color.group,
colors = colors,
missing.level = missing.level
)
})
patchwork::wrap_plots(out)
}
#' Beautiful sankey plot
#'
#' @param color.group set group to colour by. "x" or "y".
@ -123,19 +143,31 @@ plot_sankey <- function(data, pri, sec, ter = NULL, color.group = "pri", colors
#' stRoke::trial |>
#' default_parsing() |>
#' plot_sankey_single("diabetes", "hypertension")
plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), colors = NULL,missing.level="Missing", ...) {
plot_sankey_single <- function(data,
pri,
sec,
color.group = c("pri", "sec"),
colors = NULL,
missing.level = "Missing",
...) {
color.group <- match.arg(color.group)
# browser()
# if (is.na(ds[c(pri,sec)]))
# browser()
data_orig <- data
data[c(pri, sec)] <- data[c(pri, sec)] |>
dplyr::mutate(
# dplyr::across(dplyr::where(is.logical), as.factor),
dplyr::across(dplyr::where(is.factor), forcats::fct_drop)#,
# dplyr::across(dplyr::where(is.factor), \(.x){forcats::fct_na_value_to_level(.x,missing.level)})
dplyr::across(dplyr::where(is.logical), as.factor),
dplyr::across(dplyr::where(is.factor), forcats::fct_drop),
dplyr::across(dplyr::where(is.factor), \(.x) {
forcats::fct_na_value_to_level(.x, missing.level)
})
)
data <- data |> sankey_ready(pri = pri, sec = sec, ...)
na.color <- "#2986cc"
@ -148,21 +180,26 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
main.colors <- main.colors[match(levels(data[[sec]]), levels(data_orig[[sec]]))]
secondary.colors <- rep(na.color, length(levels(data[[pri]])))
label.colors <- Reduce(c, lapply(list(secondary.colors, rev(main.colors)), contrast_text))
label.colors <- Reduce(c, lapply(list(
secondary.colors, rev(main.colors)
), contrast_text))
} else {
main.colors <- viridisLite::viridis(n = length(levels(data_orig[[pri]])))
## Only keep colors for included levels
main.colors <- main.colors[match(levels(data[[pri]]), levels(data_orig[[pri]]))]
secondary.colors <- rep(na.color, length(levels(data[[sec]])))
label.colors <- Reduce(c, lapply(list(rev(main.colors), secondary.colors), contrast_text))
label.colors <- Reduce(c, lapply(list(
rev(main.colors), secondary.colors
), contrast_text))
}
colors <- c(na.color, main.colors, secondary.colors)
colors[is.na(colors)] <- "grey80"
} else {
label.colors <- contrast_text(colors)
}
group_labels <- c(get_label(data, pri), get_label(data, sec)) |>
group_labels <- c(get_label(data_orig, pri), get_label(data_orig, sec)) |>
sapply(line_break) |>
unname()
@ -181,9 +218,8 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
knot.pos = 0.4,
curve_type = "sigmoid"
) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(sec)),
size = 2,
width = 1 / 3.4
)
size = 2,
width = 1 / 3.4)
} else {
p <- p +
ggalluvial::geom_alluvium(
@ -196,9 +232,8 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
knot.pos = 0.4,
curve_type = "sigmoid"
) + ggalluvial::geom_stratum(ggplot2::aes(fill = !!dplyr::sym(pri)),
size = 2,
width = 1 / 3.4
)
size = 2,
width = 1 / 3.4)
}
## Will fail to use stat="stratum" if library is not loaded.
@ -208,13 +243,10 @@ plot_sankey_single <- function(data, pri, sec, color.group = c("pri", "sec"), co
stat = "stratum",
ggplot2::aes(label = after_stat(stratum)),
colour = label.colors,
size = 8,
size = 6,
lineheight = 1
) +
ggplot2::scale_x_continuous(
breaks = 1:2,
labels = group_labels
) +
ggplot2::scale_x_continuous(breaks = 1:2, labels = group_labels) +
ggplot2::scale_fill_manual(values = colors[-1], na.value = colors[1]) +
# ggplot2::scale_color_manual(values = main.colors) +
ggplot2::theme_void() +

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R/sysdata.rda
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55
README.md
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@ -1,10 +1,9 @@
# FreesearchR <a href="https://agdamsbo.github.io/FreesearchR/"><img src="man/figures/logo.png" align="right" height="70" alt="FreesearchR website" /></a>
# FreesearchR <a href="https://agdamsbo.github.io/FreesearchR/"><img src="man/figures/logo.png" alt="FreesearchR website" align="right" height="70"/></a>
<!-- badges: start -->
[![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)
[![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/FreesearchR/)
[![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) [![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/FreesearchR/)
<!-- badges: end -->
The [***FreesearchR***](https://app.freesearchr.org) is a simple, clinical health data exploration and analysis tool to democratise clinical research by assisting any researcher to easily evaluate and analyse data and export publication ready results.
@ -19,11 +18,11 @@ All feedback is welcome and can be shared as a GitHub issue. Any suggestions on
This app has the following simple goals:
1. help the health clinician getting an overview of data in quality improvement projects and clinical research
1. help the health clinician getting an overview of data in quality improvement projects and clinical research
1. help learners get a good start analysing data and coding in *R*
2. help learners get a good start analysing data and coding in *R*
1. ease quick data overview and basic visualisations for any clinical researcher
3. ease quick data overview and basic visualisations for any clinical researcher
Here’s a polished and restructured version of your README section for clarity, conciseness, and user-friendliness:
@ -35,32 +34,32 @@ The **FreesearchR** app can be run locally on your machine, ensuring no data is
The app can be configured either by passing a named list to `run_app()` or by setting environment variables in a **Docker Compose** file. The following variables control data access and display behavior. If no values are provided, the app will use the defaults listed below.
**Configuration Variables**
| Variable | Description | Default |
|-------------------------|-----------------------------------------------------------------------------|-----------|
| `INCLUDE_GLOBALENV` | Load datasets already present in the global R environment into the app | `FALSE` |
| `DATA_LIMIT_DEFAULT` | Default number of observations for previewing or working with a dataset | `10,000` |
| `DATA_LIMIT_UPPER` | Maximum number of observations a user can set for the upper limit. If set to 0, no uppper limit is applied. | `100,000` |
| `DATA_LIMIT_LOWER` | Minimum number of observations a user can set for the lower limit | `1` |
| Variable | Description | Default |
|--------------|--------------------------------------------|--------------|
| `INCLUDE_GLOBALENV` | Load datasets already present in the global R environment into the app | `FALSE` |
| `DATA_LIMIT_DEFAULT` | Default number of observations for previewing or working with a dataset | `10,000` |
| `DATA_LIMIT_UPPER` | Maximum number of observations a user can set for the upper limit. If set to 0, no uppper limit is applied. | `100,000` |
| `DATA_LIMIT_LOWER` | Minimum number of observations a user can set for the lower limit | `1` |
| `CHECK_APP_VERSION` | Always print version check results. Checks app version against latest release on GitHub. | `FALSE` |
### Run from R (or RStudio)
If you're working with data in R, **FreesearchR** is a quick and easy tool for exploratory analysis.
1. **Requirement:** Ensure you have [R](https://www.r-project.org/) installed, and optionally an editor like [RStudio](https://posit.co/download/rstudio-desktop/).
1. **Requirement:** Ensure you have [R](https://www.r-project.org/) installed, and optionally an editor like [RStudio](https://posit.co/download/rstudio-desktop/).
2. Open the **R console** and run the following code to install the `{FreesearchR}` package and launch the app:
2. Open the **R console** and run the following code to install the `{FreesearchR}` package and launch the app:
```r
if (!require("devtools")) install.packages("devtools")
devtools::install_github("agdamsbo/FreesearchR")
library(FreesearchR)
# Load sample data (e.g., mtcars) to make it available in the app
data(mtcars)
launch_FreesearchR(INCLUDE_GLOBALENV=TRUE)
```
``` r
if (!require("devtools")) install.packages("devtools")
devtools::install_github("agdamsbo/FreesearchR")
library(FreesearchR)
# Load sample data (e.g., mtcars) to make it available in the app
data(mtcars)
launch_FreesearchR(INCLUDE_GLOBALENV=TRUE,CHECK_APP_VERSION=TRUE)
```
All the variables specified above can also be passed to the app on launch from R. Set DATA_LIMIT_UPPER=0 to remove upper data limit. This limit is set to protect the online app version from choking and crashing on large data sets.
@ -70,7 +69,7 @@ For advanced users, you can deploy **FreesearchR** using Docker. A data folder c
To mount a local data folder, add a `volumes` entry to your `docker-compose.yml` file:
```yaml
``` yaml
services:
shiny:
image: ghcr.io/agdamsbo/freesearchr:latest
@ -86,9 +85,9 @@ services:
restart: on-failure
```
- The `:ro` flag mounts the folder as **read-only**, preventing the app from modifying your original data files.
- The `:ro` flag mounts the folder as **read-only**, preventing the app from modifying your original data files.
- If no volume is mounted, the app will start without any preloaded datasets.
- If no volume is mounted, the app will start without any preloaded datasets.
## Code of Conduct

18
SESSION.md
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@ -11,11 +11,11 @@
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |Europe/Copenhagen |
|date |2026-03-12 |
|date |2026-03-23 |
|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 |26.3.4.260312 |
|FreesearchR |26.3.4.260323 |
--------------------------------------------------------------------------------
@ -33,6 +33,7 @@
|bit64 |4.6.0-1 |2025-01-16 |CRAN (R 4.5.0) |
|bitops |1.0-9 |2024-10-03 |CRAN (R 4.5.0) |
|boot |1.3-32 |2025-08-29 |CRAN (R 4.5.0) |
|brio |1.1.5 |2024-04-24 |CRAN (R 4.5.0) |
|broom |1.0.12 |2026-01-27 |CRAN (R 4.5.2) |
|broom.helpers |1.22.0 |2025-09-17 |CRAN (R 4.5.0) |
|bsicons |0.1.2 |2023-11-04 |CRAN (R 4.5.0) |
@ -43,6 +44,7 @@
|cardx |0.3.2 |2026-02-05 |CRAN (R 4.5.2) |
|caTools |1.18.3 |2024-09-04 |CRAN (R 4.5.0) |
|cellranger |1.1.0 |2016-07-27 |CRAN (R 4.5.0) |
|cffr |1.2.1 |2026-01-12 |CRAN (R 4.5.2) |
|checkmate |2.3.4 |2026-02-03 |CRAN (R 4.5.2) |
|class |7.3-23 |2025-01-01 |CRAN (R 4.5.0) |
|classInt |0.4-11 |2025-01-08 |CRAN (R 4.5.0) |
@ -52,6 +54,7 @@
|colorspace |2.1-2 |2025-09-22 |CRAN (R 4.5.0) |
|commonmark |2.0.0 |2025-07-07 |CRAN (R 4.5.0) |
|crayon |1.5.3 |2024-06-20 |CRAN (R 4.5.0) |
|curl |7.0.0 |2025-08-19 |CRAN (R 4.5.0) |
|data.table |1.18.2.1 |2026-01-27 |CRAN (R 4.5.2) |
|datamods |1.5.3 |2024-10-02 |CRAN (R 4.5.0) |
|datawizard |1.3.0 |2025-10-11 |CRAN (R 4.5.0) |
@ -66,7 +69,7 @@
|e1071 |1.7-17 |2025-12-18 |CRAN (R 4.5.2) |
|easystats |0.7.5 |2025-07-11 |CRAN (R 4.5.0) |
|ellipsis |0.3.2 |2021-04-29 |CRAN (R 4.5.0) |
|emmeans |2.0.2 |2026-03-05 |CRAN (R 4.5.2) |
|emmeans |2.0.1 |2025-12-16 |CRAN (R 4.5.2) |
|esquisse |2.1.0 |2025-02-21 |CRAN (R 4.5.0) |
|estimability |1.5.1 |2024-05-12 |CRAN (R 4.5.0) |
|eulerr |7.0.4 |2025-09-24 |CRAN (R 4.5.0) |
@ -74,6 +77,7 @@
|farver |2.1.2 |2024-05-13 |CRAN (R 4.5.0) |
|fastmap |1.2.0 |2024-05-15 |CRAN (R 4.5.0) |
|flextable |0.9.11 |2026-02-13 |CRAN (R 4.5.2) |
|fontawesome |0.5.3 |2024-11-16 |CRAN (R 4.5.0) |
|fontBitstreamVera |0.1.1 |2017-02-01 |CRAN (R 4.5.0) |
|fontLiberation |0.1.0 |2016-10-15 |CRAN (R 4.5.0) |
|fontquiver |0.2.1 |2017-02-01 |CRAN (R 4.5.0) |
@ -109,9 +113,11 @@
|iterators |1.0.14 |2022-02-05 |CRAN (R 4.5.0) |
|jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.5.0) |
|jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.5.0) |
|jsonvalidate |1.5.0 |2025-02-07 |CRAN (R 4.5.0) |
|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.5.0) |
|keyring |1.4.1 |2025-06-15 |CRAN (R 4.5.0) |
|knitr |1.51 |2025-12-20 |CRAN (R 4.5.2) |
|labeling |0.4.3 |2023-08-29 |CRAN (R 4.5.0) |
|later |1.4.8 |2026-03-05 |CRAN (R 4.5.2) |
|lattice |0.22-7 |2025-04-02 |CRAN (R 4.5.2) |
|lifecycle |1.0.5 |2026-01-08 |CRAN (R 4.5.2) |
@ -123,7 +129,7 @@
|memoise |2.0.1 |2021-11-26 |CRAN (R 4.5.0) |
|mime |0.13 |2025-03-17 |CRAN (R 4.5.0) |
|minqa |1.2.8 |2024-08-17 |CRAN (R 4.5.0) |
|mvtnorm |1.3-5 |2026-03-11 |CRAN (R 4.5.2) |
|mvtnorm |1.3-2 |2024-11-04 |CRAN (R 4.5.2) |
|NHANES |2.1.0 |2015-07-02 |CRAN (R 4.5.0) |
|nlme |3.1-168 |2025-03-31 |CRAN (R 4.5.0) |
|nloptr |2.2.1 |2025-03-17 |CRAN (R 4.5.0) |
@ -156,6 +162,7 @@
|R6 |2.6.1 |2025-02-15 |CRAN (R 4.5.0) |
|ragg |1.5.1 |2026-03-06 |CRAN (R 4.5.2) |
|rankinPlot |1.1.0 |2023-01-30 |CRAN (R 4.5.0) |
|rappdirs |0.3.4 |2026-01-17 |CRAN (R 4.5.2) |
|rbibutils |2.4.1 |2026-01-21 |CRAN (R 4.5.2) |
|RColorBrewer |1.1-3 |2022-04-03 |CRAN (R 4.5.0) |
|Rcpp |1.1.1 |2026-01-10 |CRAN (R 4.5.2) |
@ -197,6 +204,7 @@
|stringr |1.6.0 |2025-11-04 |CRAN (R 4.5.0) |
|stRoke |25.9.2 |2025-09-30 |CRAN (R 4.5.0) |
|systemfonts |1.3.2 |2026-03-05 |CRAN (R 4.5.2) |
|testthat |3.3.2 |2026-01-11 |CRAN (R 4.5.2) |
|textshaping |1.0.5 |2026-03-06 |CRAN (R 4.5.2) |
|thematic |0.1.8 |2025-09-29 |CRAN (R 4.5.0) |
|tibble |3.3.1 |2026-01-11 |CRAN (R 4.5.2) |
@ -208,7 +216,9 @@
|twosamples |2.0.1 |2023-06-23 |CRAN (R 4.5.0) |
|tzdb |0.5.0 |2025-03-15 |CRAN (R 4.5.0) |
|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) |
|V8 |8.0.1 |2025-10-10 |CRAN (R 4.5.0) |
|vctrs |0.7.1 |2026-01-23 |CRAN (R 4.5.2) |
|viridis |0.6.5 |2024-01-29 |CRAN (R 4.5.0) |
|viridisLite |0.4.3 |2026-02-04 |CRAN (R 4.5.2) |

2
man/data-plots.Rd
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@ -170,6 +170,8 @@ mtcars |>
mtcars |>
default_parsing() |>
plot_sankey("cyl", "gear", "vs", color.group = "pri")
# stRoke::trial |> plot_sankey("mrs_1", "mrs_6")
mtcars |> plot_scatter(pri = "mpg", sec = "wt")
mtcars |> plot_violin(pri = "mpg", sec = "cyl", ter = "gear")
}