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feat: revised docs on running locally

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Andreas Gammelgaard Damsbo 2026-03-12 11:08:14 +01:00
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@ -25,45 +25,71 @@ This app has the following simple goals:
1. ease quick data overview and basic visualisations for any clinical researcher 1. ease quick data overview and basic visualisations for any clinical researcher
## Run locally on your own machine Here’s a polished and restructured version of your README section for clarity, conciseness, and user-friendliness:
The ***FreesearchR*** app can also run on your own machine with no data transmitted anywhere. Blow are the available options. ## Run Locally on Your Own Machine
### Run from R (or RStduio) The **FreesearchR** app can be run locally on your machine, ensuring no data is transmitted externally. Below are the available options for setup and configuration.
Working with data in R, FreesearchR is a quick and easy tool to get overview and perform the first explorative analyses to get you going. ### Configuration & Data Loading
Any data available in the your R session will be available to the FreesearchR app. Just follow the below steps to get going: 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.
1. **Requirement:** You need to have [*R* installed](https://www.r-project.org/) and possibly an editor like [RStudio](https://posit.co/download/rstudio-desktop/).
1. Then open the *R* console and copy/paste the following code, that will install the `{devtools}` package and then the `{FreesearchR}` *R*-package with its dependencies: **Configuration Variables**
``` | Variable | Description | Default |
require("devtools") |-------------------------|-----------------------------------------------------------------------------|-----------|
devtools::install_github("agdamsbo/FreesearchR") | `INCLUDE_GLOBALENV` | Load datasets already present in the global R environment into the app | `FALSE` |
library(FreesearchR) | `DATA_LIMIT_DEFAULT` | Default number of observations for previewing or working with a dataset | `10,000` |
# By loading mtcars to the environment, it will be available | `DATA_LIMIT_UPPER` | Maximum number of observations a user can set for the upper limit | `100,000` |
# in the interface like any other data.frame | `DATA_LIMIT_LOWER` | Minimum number of observations a user can set for the lower limit | `1` |
data(mtcars)
launch_FreesearchR()
```
### Running with docker compose ### Run from R (or RStudio)
For advanced users, wanting to deploy the FreesearchR app to run anywhere, a docker image is available. If you're working with data in R, **FreesearchR** is a quick and easy tool for exploratory analysis.
Below is the minimal `docker_compose.yml` file: 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:
```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)
```
All the variables specified above can also be passed to the app on launch from R.
### Running with Docker Compose
For advanced users, you can deploy **FreesearchR** using Docker. A data folder can be mounted to `/app/data` to automatically load supported file types (`.csv`, `.tsv`, `.txt`, `.xls`, `.xlsx`, `.ods`, `.dta`, `.rds`) at startup.
To mount a local data folder, add a `volumes` entry to your `docker-compose.yml` file:
```yaml
services: services:
freesearchr: shiny:
image: ghcr.io/agdamsbo/freesearchr:latest image: ghcr.io/agdamsbo/freesearchr:latest
ports: volumes:
- ./data:/app/data:ro
environment:
- INCLUDE_GLOBALENV=FALSE
- DATA_LIMIT_DEFAULT=10000
- DATA_LIMIT_UPPER=100000
- DATA_LIMIT_LOWER=1
ports:
- '3838:3838' - '3838:3838'
restart: on-failure restart: on-failure
``` ```
- 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.
## Code of Conduct ## Code of Conduct
Please note that the ***FreesearchR*** project is published with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms. Please note that the ***FreesearchR*** project is published with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.