+# teal: Interactive Exploratory Data Analysis with Shiny Web-Applications
[](https://insightsengineering.github.io/teal/main/unit-test-report/)
@@ -19,7 +19,7 @@
[](https://github.com/insightsengineering/teal/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
-*teal* is a shiny-based interactive exploration framework for analyzing data. `teal` applications require app developers to specify:
+`teal` is a shiny-based interactive exploration framework for analyzing data. `teal` applications require app developers to specify:
- Data, which can be:
@@ -50,21 +50,31 @@ A lot of the functionality of the `teal` framework derives from the following pa
See these packages for more information about how to use the different parts of the `teal` framework.
-Please see [`teal` gallery](https://github.com/insightsengineering/teal.gallery) and [TLG Catalog](https://github.com/insightsengineering/tlg-catalog) to see examples of `teal` apps.
+Please see [`teal` gallery](https://insightsengineering.github.io/teal.gallery/) and [TLG Catalog](https://github.com/insightsengineering/tlg-catalog) to see examples of `teal` apps.
+
+Please start with the ["Getting Started" article](https://insightsengineering.github.io/teal/articles/teal.html) and then other [package vignettes](https://insightsengineering.github.io/teal/articles/index.html) for more detailed guide.
## Installation
-From July 2023 `insightsengineering` packages are available on [r-universe](https://r-universe.dev/).
+```r
+install.packages("teal", repos = c("https://insightsengineering.r-universe.dev", getOption("repos")))
+
+# install.packages("pak")
+pak::pak("insightsengineering/teal@*release")
+```
+
+Alternatively you might also use the development version.
```r
-# stable versions
-install.packages('teal', repos = c('https://insightsengineering.r-universe.dev', 'https://cloud.r-project.org'))
+install.packages("teal", repos = c("https://pharmaverse.r-universe.dev", getOption("repos")))
-# beta versions
-install.packages('teal', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org'))
+# install.packages("pak")
+pak::pak("insightsengineering/teal")
```
-See package vignettes `browseVignettes(package = "teal")` for usage of this package.
+## Getting help
+
+If you encounter a bug or you have a feature request - please file an issue. For questions, discussions and staying up to date, please use the "teal" channel in the [pharmaverse slack workspace](https://pharmaverse.slack.com).
## Acknowledgment
diff --git a/_pkgdown.yml b/_pkgdown.yml
index f2d67c0ef9..bdb543ffa5 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -36,7 +36,7 @@ articles:
- teal-bs-themes
reference:
- - title: Teal Core Functions
+ - title: teal Core Functions
desc: These are the main functions needed to build a teal app.
contents:
- init
diff --git a/man/module_teal.Rd b/man/module_teal.Rd
index 008b24d698..a9a7f7f0ea 100644
--- a/man/module_teal.Rd
+++ b/man/module_teal.Rd
@@ -4,7 +4,7 @@
\alias{module_teal}
\alias{ui_teal}
\alias{srv_teal}
-\title{Teal main app module}
+\title{teal main app module}
\usage{
ui_teal(
id,
diff --git a/vignettes/including-general-data-in-teal.Rmd b/vignettes/including-general-data-in-teal.Rmd
index 25ef349157..1d0e2c5e0b 100644
--- a/vignettes/including-general-data-in-teal.Rmd
+++ b/vignettes/including-general-data-in-teal.Rmd
@@ -11,7 +11,7 @@ vignette: >
## Introduction
-Teal applications are not restricted to `CDISC`-standard data. Although many teal modules included with `NEST` are designed for `CDISC` data, those in the library `teal.modules.general` have been designed to work with non-relational data.
+`teal` applications are not restricted to `CDISC`-standard data. Although many teal modules included with `NEST` are designed for `CDISC` data, those in the library `teal.modules.general` have been designed to work with non-relational data.
For example this application uses the standard `iris` and `mtcars` datasets:
diff --git a/vignettes/teal-bs-themes.Rmd b/vignettes/teal-bs-themes.Rmd
index 60c9a852f3..e5ea84cc50 100644
--- a/vignettes/teal-bs-themes.Rmd
+++ b/vignettes/teal-bs-themes.Rmd
@@ -1,22 +1,22 @@
---
-title: "Teal and Bootstrap Themes"
+title: "teal and Bootstrap Themes"
author: "NEST CoreDev"
date: "2022-09-08"
output: rmarkdown::html_vignette
vignette: >
- %\VignetteIndexEntry{Teal and Bootstrap Themes}
+ %\VignetteIndexEntry{teal and Bootstrap Themes}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
## Introduction
-We offer the easy application of a custom bootstrap theme to a `teal::init` app.
-Teal is a consumer of the `bslib` R package which provides tools for customizing Bootstrap themes e.g. of Shiny apps.
+We offer the easy application of a custom bootstrap theme to a `teal::init` app.
+`teal` is a consumer of the `bslib` R package which provides tools for customizing Bootstrap themes e.g. of Shiny apps.
## Usage
-Teal users have the benefit of custom bootstrap themes by specifying the `teal.bs_theme` R option, which has to be set to `bslib::bs_theme` object.
+`teal` users have the benefit of custom bootstrap themes by specifying the `teal.bs_theme` R option, which has to be set to `bslib::bs_theme` object.
The `bslib::bs_theme(...)` function creates a Bootstrap theme object, where you should specify the (major) Bootstrap version (default or one of 3, 4 or 5).
Optionally you could choose a **`bootswatch` theme** and **customize the app CSS** with functions like `bslib::bs_add_rules`.
Please read more about custom themes in [the `bslib` getting started vignette](https://rstudio.github.io/bslib/articles/bslib.html).
@@ -39,7 +39,7 @@ options("teal.bs_theme" = bslib::bs_theme("Custom Options"))
The best and recommended ways to **explore** the bootstrap themes are to use `bslib::run_with_themer(shinyApp(app$ui, app$server))` or `bslib::bs_theme_preview()`,
both functions offer an interactive explore mode.
Note that the interactive theming for Bootstrap 3 is not supported.
-The `bslib::bs_theme_preview()` is recommended when the end user does not have any shiny app yet.
+The `bslib::bs_theme_preview()` is recommended when the end user does not have any shiny app yet.
When you already have a shiny app and you want to test different bootstrap themes (and `CSS` styling) then `bslib::run_with_themer(shinyApp(app$ui, app$server))` is recommended.
Available bootstrap versions could be checked with `bslib::versions()` and bootstrap themes (`bootswatch`) with `bslib::bootswatch_themes(version = "5")`.
@@ -103,7 +103,7 @@ remotes::install_github("https://github.com/dreamRs/shinyWidgets@main")
### Regular `shiny::fluidPage`
-If you want to update the theme in the regular `shiny::fluidPage` like app, you do not need the `teal.bs_theme` option. Then simply provide the `bslib::bs_theme` directly to the `shiny::fluidPage(theme = bslib::bs_theme(...), ...)`.
+If you want to update the theme in the regular `shiny::fluidPage` like app, you do not need the `teal.bs_theme` option. Then simply provide the `bslib::bs_theme` directly to the `shiny::fluidPage(theme = bslib::bs_theme(...), ...)`.
### Interactive theming guide
diff --git a/vignettes/teal-options.Rmd b/vignettes/teal-options.Rmd
index 4a835c76a2..284604d84a 100644
--- a/vignettes/teal-options.Rmd
+++ b/vignettes/teal-options.Rmd
@@ -1,10 +1,10 @@
---
-title: "Modifying a Teal application with R options"
+title: "Modifying a teal application with R options"
author: "Paweł Rucki"
date: " 2021-12-23"
output: rmarkdown::html_vignette
vignette: >
- %\VignetteIndexEntry{Modifying a Teal application with R options}
+ %\VignetteIndexEntry{Modifying a teal application with R options}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
editor_options:
@@ -81,7 +81,7 @@ This option allows modifying labels and themes of all `ggplot2` plots in a `teal
Default: `teal.widgets::ggplot2_args()`.
### `teal.plot_dpi` (integer value 24 or larger)
-This option controls the dots per inch of the graphs rendered and downloaded when using `plot_with_settings`.
+This option controls the dots per inch of the graphs rendered and downloaded when using `plot_with_settings`.
Default: 72
diff --git a/vignettes/teal.Rmd b/vignettes/teal.Rmd
index 983eb406ee..36c928172a 100644
--- a/vignettes/teal.Rmd
+++ b/vignettes/teal.Rmd
@@ -1,10 +1,10 @@
---
-title: "Getting Started with Teal"
+title: "Getting Started with teal"
author: "NEST CoreDev"
date: "2022-11-03"
output: rmarkdown::html_vignette
vignette: >
- %\VignetteIndexEntry{Getting Started with Teal}
+ %\VignetteIndexEntry{Getting Started with teal}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
@@ -14,7 +14,7 @@ vignette: >
*teal* is a shiny-based interactive exploration framework for analyzing data, with particular emphasis on
`CDISC` clinical trial data. `teal` applications provide their users with:
-* Ability to "pull" in data from external data sources
+* Ability to "pull" in data from external data sources
* Dynamic filtering of data to be used in the analyses
* Ability to generate reproducible code to regenerate the on-screen analyses
* Ability to create and download reports containing results of analyses (for analysis modules which support reporting)
@@ -75,17 +75,17 @@ For modules which include reproducibility functionality, it often contains a "Sh
## Creating your own applications
-`init` is the key function to use to create your `teal` application and it requires two key arguments: `data` and `modules`.
+`init` is the key function to use to create your `teal` application and it requires two key arguments: `data` and `modules`.
-### Application Data
+### Application Data
The `data` argument to the `init` function specifies the data used by your application. This can contain data currently in your R session,
as in the example above, but also can contain `connectors` which describe where to "pull" data from when the application is run. This can be
used to allow data to be pulled into `teal` applications from external sources which require your application users to enter credentials.
In the example above we call `teal_data` to convert the raw datasets into `teal` specific datasets and to bind them in one `R` object.
-This function can also be used to specify relationships between different datasets.
-In order to use `CDISC` clinical trial data in a `teal` application the `cdisc_data` function is used instead.
+This function can also be used to specify relationships between different datasets.
+In order to use `CDISC` clinical trial data in a `teal` application the `cdisc_data` function is used instead.
For further details we recommend exploring the [`teal.data`](https://insightsengineering.github.io/teal.data/) package documentation.
From ace01e4d56dbbb68949ec6aa032a7993c0e3d8d8 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Fri, 4 Aug 2023 12:42:53 +0200
Subject: [PATCH 02/10] change url to tlg-catalog
---
README.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/README.md b/README.md
index cf9f351b58..49964ddea3 100644
--- a/README.md
+++ b/README.md
@@ -50,7 +50,7 @@ A lot of the functionality of the `teal` framework derives from the following pa
See these packages for more information about how to use the different parts of the `teal` framework.
-Please see [`teal` gallery](https://insightsengineering.github.io/teal.gallery/) and [TLG Catalog](https://github.com/insightsengineering/tlg-catalog) to see examples of `teal` apps.
+Please see [`teal` gallery](https://insightsengineering.github.io/teal.gallery) and [TLG Catalog](https://insightsengineering.github.io/tlg-catalog) to see examples of `teal` apps.
Please start with the ["Getting Started" article](https://insightsengineering.github.io/teal/articles/teal.html) and then other [package vignettes](https://insightsengineering.github.io/teal/articles/index.html) for more detailed guide.
From 84f979eb3e04c0a2a9d7e46f3a9ad4b0f3d7ad8a Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Fri, 4 Aug 2023 12:47:05 +0200
Subject: [PATCH 03/10] extend wordlist
---
inst/WORDLIST | 1 +
1 file changed, 1 insertion(+)
diff --git a/inst/WORDLIST b/inst/WORDLIST
index b0b6fa1a0a..24b9e8af9d 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -15,3 +15,4 @@ themer
theming
uncheck
cloneable
+pharmaverse
From b0564eacbc2ef02b3b63960296af69e5b63e0926 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Mon, 7 Aug 2023 13:51:16 +0200
Subject: [PATCH 04/10] Update vignettes/teal-bs-themes.Rmd
Co-authored-by: Aleksander Chlebowski <114988527+chlebowa@users.noreply.github.com>
Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
---
vignettes/teal-bs-themes.Rmd | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/vignettes/teal-bs-themes.Rmd b/vignettes/teal-bs-themes.Rmd
index e5ea84cc50..8d8c2edf02 100644
--- a/vignettes/teal-bs-themes.Rmd
+++ b/vignettes/teal-bs-themes.Rmd
@@ -11,7 +11,7 @@ vignette: >
## Introduction
-We offer the easy application of a custom bootstrap theme to a `teal::init` app.
+We offer easy application of a custom bootstrap theme to a `teal::init` app.
`teal` is a consumer of the `bslib` R package which provides tools for customizing Bootstrap themes e.g. of Shiny apps.
## Usage
From e09663f007410b3d09baf308257d7623656b6d2a Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Tue, 8 Aug 2023 09:13:16 +0200
Subject: [PATCH 05/10] Update README.md
Co-authored-by: kartikeya kirar
+# `teal`: Interactive Exploratory Data Analysis with Shiny Web-Applications
[](https://insightsengineering.github.io/teal/main/unit-test-report/)
@@ -48,12 +48,6 @@ A lot of the functionality of the `teal` framework derives from the following pa
-See these packages for more information about how to use the different parts of the `teal` framework.
-
-Please see [`teal` gallery](https://insightsengineering.github.io/teal.gallery) and [TLG Catalog](https://insightsengineering.github.io/tlg-catalog) to see examples of `teal` apps.
-
-Please start with the ["Getting Started" article](https://insightsengineering.github.io/teal/articles/teal.html) and then other [package vignettes](https://insightsengineering.github.io/teal/articles/index.html) for more detailed guide.
-
## Installation
```r
@@ -72,6 +66,48 @@ install.packages("teal", repos = c("https://pharmaverse.r-universe.dev", getOpti
pak::pak("insightsengineering/teal")
```
+## Usage
+
+```r
+library(teal)
+
+app <- init(
+ data = teal_data(
+ dataset("iris", iris)
+ ),
+ modules = list(
+ module(
+ "iris histogram",
+ server = function(input, output, session, data) {
+ output$hist <- renderPlot(
+ hist(data[["iris"]]()[[input$var]])
+ )
+ },
+ ui = function(id, data, ...) {
+ ns <- NS(id)
+ list(
+ shiny::selectInput(
+ ns("var"),
+ "Column name",
+ names(data[["iris"]]())[1:4]
+ ),
+ plotOutput(ns("hist"))
+ )
+ }
+ )
+ )
+)
+
+shinyApp(app$ui, app$server)
+```
+
+
+
+
+Please see [`teal` gallery](https://insightsengineering.github.io/teal.gallery) and [TLG Catalog](https://insightsengineering.github.io/tlg-catalog) to see examples of `teal` apps.
+
+Please start with the ["Getting Started" article](https://insightsengineering.github.io/teal/articles/teal.html) and then other [package vignettes](https://insightsengineering.github.io/teal/articles/index.html) for more detailed guide.
+
## Getting help
If you encounter a bug or you have a feature request - please file an issue. For questions, discussions and staying up to date, please use the "teal" channel in the [pharmaverse slack workspace](https://pharmaverse.slack.com).
diff --git a/inst/readme_app.gif b/inst/readme_app.gif
new file mode 100644
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