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

chore: updated docs and render

Browse source
This commit is contained in:
Andreas Gammelgaard Damsbo 2026-03-23 14:10:06 +01:00
commit b0ecce8c54
No known key found for this signature in database
9 changed files with 114 additions and 64 deletions
Download patch file Download diff file Expand all files Collapse all files

55
README.md
View file

@ -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