diff --git a/DESCRIPTION b/DESCRIPTION index 3e2cc6ab..5a9d85b9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -141,5 +141,6 @@ Collate: 'update-variables-ext.R' 'utils-labels.R' 'validation.R' + 'version_check.R' 'visual_summary.R' 'wide2long.R' diff --git a/NEWS.md b/NEWS.md index f08ae0b2..3cfed098 100644 --- a/NEWS.md +++ b/NEWS.md @@ -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 diff --git a/R/hosted_version.R b/R/hosted_version.R index f0c656d1..17135440 100644 --- a/R/hosted_version.R +++ b/R/hosted_version.R @@ -1 +1 @@ -hosted_version <- function()'v26.3.4-260312' +hosted_version <- function()'v26.3.4-260323' diff --git a/R/launch_FreesearchR.R b/R/launch_FreesearchR.R index a789f185..92d09a51 100644 --- a/R/launch_FreesearchR.R +++ b/R/launch_FreesearchR.R @@ -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") diff --git a/R/plot_sankey.R b/R/plot_sankey.R index b3aa1b55..baa864dd 100644 --- a/R/plot_sankey.R +++ b/R/plot_sankey.R @@ -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() + diff --git a/R/sysdata.rda b/R/sysdata.rda index f8b0df59..efea72cf 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/README.md b/README.md index 344b8649..b6444c6d 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,9 @@ -# FreesearchR FreesearchR website +# FreesearchR FreesearchR website -[![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/) + 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 diff --git a/SESSION.md b/SESSION.md index 1bd978b0..44778018 100644 --- a/SESSION.md +++ b/SESSION.md @@ -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) | diff --git a/man/data-plots.Rd b/man/data-plots.Rd index e5f94f58..cd9efdfd 100644 --- a/man/data-plots.Rd +++ b/man/data-plots.Rd @@ -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") }