From be8b30e2d8630697cd6dec4ea5231c9059741861 Mon Sep 17 00:00:00 2001
From: agdamsbo <43278243+agdamsbo@users.noreply.github.com>
Date: Thu, 12 Mar 2026 10:28:25 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20agdamsbo?=
=?UTF-8?q?/FreesearchR@39db24c9be979588ef50e1873758ff9bd9229ffb=20?=
=?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
SESSION.html | 4 +-
SESSION.md | 4 +-
articles/session.html | 4 +-
articles/session.md | 4 +-
index.html | 106 ++++++++++++++++++++++++++++----------
index.md | 100 ++++++++++++++++++++++++-----------
llms.txt | 100 ++++++++++++++++++++++++-----------
news/index.html | 3 +-
news/index.md | 4 +-
pkgdown.yml | 2 +-
reference/data-plots.html | 2 +-
reference/data-plots.md | 2 +-
reference/getfun.html | 2 +-
reference/getfun.md | 2 +-
search.json | 2 +-
15 files changed, 236 insertions(+), 105 deletions(-)
diff --git a/SESSION.html b/SESSION.html
index 9ca778a9..4cea8288 100644
--- a/SESSION.html
+++ b/SESSION.html
@@ -43,7 +43,7 @@
———————————– packages ———————————–
| FreesearchR |
-26.3.2 |
+26.3.3 |
NA |
NA |
| fs |
diff --git a/SESSION.md b/SESSION.md
index 4836b9fb..f626fe3c 100644
--- a/SESSION.md
+++ b/SESSION.md
@@ -2,7 +2,7 @@
| ——————————– R environment ——————————— |
|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| \|setting \|value \| \|:———–\|:——————————————\| \|version \|R version 4.5.2 (2025-10-31) \| \|os \|macOS Tahoe 26.3 \| \|system \|aarch64, darwin20 \| \|ui \|RStudio \| \|language \|(EN) \| \|collate \|en_US.UTF-8 \| \|ctype \|en_US.UTF-8 \| \|tz \|Europe/Copenhagen \| \|date \|2026-03-11 \| \|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 \|26.3.2.260311 \| |
+| \|setting \|value \| \|:———–\|:——————————————\| \|version \|R version 4.5.2 (2025-10-31) \| \|os \|macOS Tahoe 26.3 \| \|system \|aarch64, darwin20 \| \|ui \|RStudio \| \|language \|(EN) \| \|collate \|en_US.UTF-8 \| \|ctype \|en_US.UTF-8 \| \|tz \|Europe/Copenhagen \| \|date \|2026-03-11 \| \|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 \|26.3.3.260311 \| |
## ———————————– packages ———————————–
@@ -68,7 +68,7 @@
| foreach | 1.5.2 | 2022-02-02 | CRAN (R 4.5.0) |
| foreign | 0.8-90 | 2025-03-31 | CRAN (R 4.5.2) |
| Formula | 1.2-5 | 2023-02-24 | CRAN (R 4.5.0) |
-| FreesearchR | 26.3.2 | NA | NA |
+| FreesearchR | 26.3.3 | NA | NA |
| fs | 1.6.6 | 2025-04-12 | CRAN (R 4.5.0) |
| gdtools | 0.5.0 | 2026-02-09 | CRAN (R 4.5.2) |
| generics | 0.1.4 | 2025-05-09 | CRAN (R 4.5.0) |
diff --git a/articles/session.html b/articles/session.html
index ceaf9493..b488e0e4 100644
--- a/articles/session.html
+++ b/articles/session.html
@@ -149,7 +149,7 @@ packages and the latest build info.
| FreesearchR |
-26.3.2.260311 |
+26.3.3.260311 |
@@ -529,7 +529,7 @@ packages and the latest build info.
| FreesearchR |
-26.3.2 |
+26.3.3 |
NA |
NA |
diff --git a/articles/session.md b/articles/session.md
index ebc2a06e..1b4c1e10 100644
--- a/articles/session.md
+++ b/articles/session.md
@@ -32,7 +32,7 @@ FreesearchR:::session_data$platform |> knitr::kable()
| rstudio | 2026.01.1+403 Apple Blossom (desktop) |
| pandoc | 3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
| quarto | 1.7.30 @ /usr/local/bin/quarto |
-| FreesearchR | 26.3.2.260311 |
+| FreesearchR | 26.3.3.260311 |
## Libraries
@@ -102,7 +102,7 @@ FreesearchR:::session_data$libs|> knitr::kable()
| foreach | 1.5.2 | 2022-02-02 | CRAN (R 4.5.0) |
| foreign | 0.8-90 | 2025-03-31 | CRAN (R 4.5.2) |
| Formula | 1.2-5 | 2023-02-24 | CRAN (R 4.5.0) |
-| FreesearchR | 26.3.2 | NA | NA |
+| FreesearchR | 26.3.3 | NA | NA |
| fs | 1.6.6 | 2025-04-12 | CRAN (R 4.5.0) |
| gdtools | 0.5.0 | 2026-02-09 | CRAN (R 4.5.2) |
| generics | 0.1.4 | 2025-05-09 | CRAN (R 4.5.0) |
diff --git a/index.html b/index.html
index 04a54931..970f36ae 100644
--- a/index.html
+++ b/index.html
@@ -91,41 +91,93 @@
help learners get a good start analysing data and coding in R
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:
-
Run locally on your own machine
+Run Locally on Your Own Machine
-
The FreesearchR app can also run on your own machine with no data transmitted anywhere. Blow are the available options.
+
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.
-
Run from R (or RStduio)
+Configuration & Data Loading
-
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.
-
Any data available in the your R session will be available to the FreesearchR app. Just follow the below steps to get going:
-
-Requirement: You need to have R installed and possibly an editor like RStudio.
--
-
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:
-require("devtools")
-devtools::install_github("agdamsbo/FreesearchR")
-library(FreesearchR)
-# By loading mtcars to the environment, it will be available
-# in the interface like any other data.frame
-data(mtcars)
-launch_FreesearchR()
-
-
+
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
+
+
+
+
+
+
+
+
+
+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 |
+100,000 |
+
+
+DATA_LIMIT_LOWER |
+Minimum number of observations a user can set for the lower limit |
+1 |
+
+
+
-
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.
-
Below is the minimal docker_compose.yml file:
-
services:
- freesearchr:
- image: ghcr.io/agdamsbo/freesearchr:latest
- ports:
- - '3838:3838'
- restart: on-failure
+
If you’re working with data in R, FreesearchR is a quick and easy tool for exploratory analysis.
+
+Requirement: Ensure you have R installed, and optionally an editor like RStudio.
+-
+
Open the R console and run the following code to install the FreesearchR package and launch the app:
+
+
+
+
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:
+
services:
+ shiny:
+ image: ghcr.io/agdamsbo/freesearchr:latest
+ volumes:
+ - ./data:/app/data:ro
+ environment:
+ - INCLUDE_GLOBALENV=FALSE
+ - DATA_LIMIT_DEFAULT=10000
+ - DATA_LIMIT_UPPER=100000
+ - DATA_LIMIT_LOWER=1
+ ports:
+ - '3838:3838'
+ 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.
+
diff --git a/index.md b/index.md
index ccfaaf06..4f5a2f75 100644
--- a/index.md
+++ b/index.md
@@ -29,49 +29,87 @@ This app has the following simple goals:
3. 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
+**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 | `100,000` |
+| `DATA_LIMIT_LOWER` | Minimum number of observations a user can set for the lower limit | `1` |
+
+### 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/).
-2. Then open the *R* console and copy/paste the following code, that
- will install the [devtools](https://devtools.r-lib.org/) package and
- then the [FreesearchR](https://github.com/agdamsbo/FreesearchR)
- *R*-package with its dependencies:
+2. Open the **R console** and run the following code to install the
+ [FreesearchR](https://github.com/agdamsbo/FreesearchR) package and
+ launch the app:
- require("devtools")
- devtools::install_github("agdamsbo/FreesearchR")
- library(FreesearchR)
- # By loading mtcars to the environment, it will be available
- # in the interface like any other data.frame
- data(mtcars)
- launch_FreesearchR()
+ ``` 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)
+ ```
-### Running with docker compose
+All the variables specified above can also be passed to the app on
+launch from R.
-For advanced users, wanting to deploy the FreesearchR app to run
-anywhere, a docker image is available.
+### Running with Docker Compose
-Below is the minimal `docker_compose.yml` file:
+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.
- services:
- freesearchr:
- image: ghcr.io/agdamsbo/freesearchr:latest
- ports:
- - '3838:3838'
- restart: on-failure
+To mount a local data folder, add a `volumes` entry to your
+`docker-compose.yml` file:
+
+``` yaml
+services:
+ shiny:
+ image: ghcr.io/agdamsbo/freesearchr:latest
+ volumes:
+ - ./data:/app/data:ro
+ environment:
+ - INCLUDE_GLOBALENV=FALSE
+ - DATA_LIMIT_DEFAULT=10000
+ - DATA_LIMIT_UPPER=100000
+ - DATA_LIMIT_LOWER=1
+ ports:
+ - '3838:3838'
+ 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
diff --git a/llms.txt b/llms.txt
index 7f65ed50..6611cd97 100644
--- a/llms.txt
+++ b/llms.txt
@@ -29,49 +29,87 @@ This app has the following simple goals:
3. 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
+**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 | `100,000` |
+| `DATA_LIMIT_LOWER` | Minimum number of observations a user can set for the lower limit | `1` |
+
+### 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/).
-2. Then open the *R* console and copy/paste the following code, that
- will install the [devtools](https://devtools.r-lib.org/) package and
- then the [FreesearchR](https://github.com/agdamsbo/FreesearchR)
- *R*-package with its dependencies:
+2. Open the **R console** and run the following code to install the
+ [FreesearchR](https://github.com/agdamsbo/FreesearchR) package and
+ launch the app:
- require("devtools")
- devtools::install_github("agdamsbo/FreesearchR")
- library(FreesearchR)
- # By loading mtcars to the environment, it will be available
- # in the interface like any other data.frame
- data(mtcars)
- launch_FreesearchR()
+ ``` 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)
+ ```
-### Running with docker compose
+All the variables specified above can also be passed to the app on
+launch from R.
-For advanced users, wanting to deploy the FreesearchR app to run
-anywhere, a docker image is available.
+### Running with Docker Compose
-Below is the minimal `docker_compose.yml` file:
+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.
- services:
- freesearchr:
- image: ghcr.io/agdamsbo/freesearchr:latest
- ports:
- - '3838:3838'
- restart: on-failure
+To mount a local data folder, add a `volumes` entry to your
+`docker-compose.yml` file:
+
+``` yaml
+services:
+ shiny:
+ image: ghcr.io/agdamsbo/freesearchr:latest
+ volumes:
+ - ./data:/app/data:ro
+ environment:
+ - INCLUDE_GLOBALENV=FALSE
+ - DATA_LIMIT_DEFAULT=10000
+ - DATA_LIMIT_UPPER=100000
+ - DATA_LIMIT_LOWER=1
+ ports:
+ - '3838:3838'
+ 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
diff --git a/news/index.html b/news/index.html
index bc246f45..b9850336 100644
--- a/news/index.html
+++ b/news/index.html
@@ -43,7 +43,8 @@
FreesearchR 26.3.3
-
NEW option to pass global settings when running as docker or launching from R. Support for INCLUDE_GLOBALENV, DATA_LIMIT_DEFAULT, DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Docs are missing…
+
NEW option to pass global settings when running as docker or launching from R. Support for INCLUDE_GLOBALENV, DATA_LIMIT_DEFAULT, DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Described in the README.
+
FIX faster data description function.
FreesearchR 26.3.2
diff --git a/news/index.md b/news/index.md
index e2b49bac..827d7b84 100644
--- a/news/index.md
+++ b/news/index.md
@@ -4,7 +4,9 @@
*NEW* option to pass global settings when running as docker or launching
from R. Support for INCLUDE_GLOBALENV, DATA_LIMIT_DEFAULT,
-DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Docs are missing…
+DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Described in the README.
+
+*FIX* faster data description function.
## FreesearchR 26.3.2
diff --git a/pkgdown.yml b/pkgdown.yml
index 3484db3d..6766e4e8 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
missingness: missingness.html
session: session.html
visuals: visuals.html
-last_built: 2026-03-11T13:00Z
+last_built: 2026-03-12T10:26Z
urls:
reference: https://agdamsbo.github.io/FreesearchR/reference
article: https://agdamsbo.github.io/FreesearchR/articles
diff --git a/reference/data-plots.html b/reference/data-plots.html
index 4a748426..66c4793d 100644
--- a/reference/data-plots.html
+++ b/reference/data-plots.html
@@ -732,7 +732,7 @@ One of c("stack", "dodge", "fill")
#> list()
#>
#> $plot_env
-
#> <environment: 0x558a2b7351a8>
+
#> <environment: 0x56288e807a28>
#>
#> $code
#> FreesearchR::plot_violin(pri = "mpg", sec = "cyl", ter = NULL)
diff --git a/reference/data-plots.md b/reference/data-plots.md
index 97baf4d2..91b0c861 100644
--- a/reference/data-plots.md
+++ b/reference/data-plots.md
@@ -688,7 +688,7 @@ create_plot(mtcars, "plot_violin", "mpg", "cyl") |> attributes()
#> list()
#>
#> $plot_env
-#>
+#>
#>
#> $code
#> FreesearchR::plot_violin(pri = "mpg", sec = "cyl", ter = NULL)
diff --git a/reference/getfun.html b/reference/getfun.html
index 6c1b520c..7e192c81 100644
--- a/reference/getfun.html
+++ b/reference/getfun.html
@@ -139,7 +139,7 @@
#> z$qr <- NULL
#> z
#> }
-#> <bytecode: 0x558a2eae42c0>
+#> <bytecode: 0x56288c98c808>
#> <environment: namespace:stats>
diff --git a/reference/getfun.md b/reference/getfun.md
index c7dd65f4..9d3b787b 100644
--- a/reference/getfun.md
+++ b/reference/getfun.md
@@ -95,6 +95,6 @@ getfun("stats::lm")
#> z$qr <- NULL
#> z
#> }
-#>