insightsengineering · nikolas-burkoff · Sep 8, 2022 · Sep 8, 2022
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -15,7 +15,7 @@ Authors@R: c(
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")),
     person("Maximilian", "Mordig", role = "ctb")
   )
-Description: teal is a shiny based interactive exploration framework for
+Description: A shiny based interactive exploration framework for
     analyzing clinical trials data. teal currently provides a dynamic
     filtering facility and different data viewers. teal shiny applications
     are built using standard shiny modules.

diff --git a/R/module_tabs_with_filters.R b/R/module_tabs_with_filters.R
@@ -24,8 +24,10 @@
 #' @keywords internal
 #'
 #' @examples
+#'
 #' mods <- teal:::get_dummy_modules()
 #' datasets <- teal:::get_dummy_datasets()
+#'
 #' app <- shinyApp(
 #'   ui = function() {
 #'     tagList(
@@ -54,8 +56,7 @@
 #'
 #'
 #' # An example with two filter panels in two apps side-by-side
-#' mods <- teal:::get_dummy_modules()
-#' datasets1 <- datasets2 <- teal:::get_dummy_datasets()
+#' datasets1 <- datasets2 <- datasets
 #' app <- shinyApp(
 #'   ui = function() {
 #'     tagList(

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# Teal: Interactive Exploratory Data Analysis with Shiny Web-Applications <a href='https://insightsengineering.github.io/teal'><img src="man/figures/teal.png" align="right" height="139" style="max-width: 100%;"/></a  >
+# Teal: Interactive Exploratory Data Analysis with Shiny Web-Applications <a href='https://insightsengineering.github.io/teal/'><img src="man/figures/teal.png" align="right" height="139" style="max-width: 100%;"/></a  >
 
 *teal* is a shiny-based interactive exploration framework for analyzing data. `teal` applications require app developers to specify:
 
@@ -10,22 +10,22 @@
     -    `MultiAssayExperiment` objects which are R data structures for representing and analyzing multi-omics experiments
 -   `teal` modules:
     -   `teal modules` are shiny modules built within the `teal` framework that specify analysis to be performed. For example, it can be a module for exploring outliers in the data, or a module for visualizing the data in line plots. Although these can be created from scratch, lost of `teal` modules have been released and we recommend starting with modules found in the following packages:
-        -   [`teal.modules.general`](https://insightsengineering.github.io/teal.modules.general): general modules for exploring relational/independent/CDISC data
-        -   [`teal.modules.clinical`](https://insightsengineering.github.io/teal.modules.clinical): modules specific to CDISC data and clinical trial reporting
-        -   [`teal.modules.hermes`](https://insightsengineering.github.io/teal.modules.hermes): modules for analyzing `MultiAssayExperiment` objects
+        -   [`teal.modules.general`](https://insightsengineering.github.io/teal.modules.general/): general modules for exploring relational/independent/CDISC data
+        -   [`teal.modules.clinical`](https://insightsengineering.github.io/teal.modules.clinical/): modules specific to CDISC data and clinical trial reporting
+        -   [`teal.modules.hermes`](https://insightsengineering.github.io/teal.modules.hermes/): modules for analyzing `MultiAssayExperiment` objects
 
 <!-- markdownlint-enable MD007 MD030 -->
 
 A lot of the functionality of the `teal` framework derives from the following packages:
 
 <!-- markdownlint-disable MD007 MD030 -->
--   [`teal.data`](https://insightsengineering.github.io/teal.data): creating and loading the data needed for `teal` applications.
--   [`teal.widgets`](https://insightsengineering.github.io/teal.widgets): shiny components used within `teal`.
--   [`teal.slice`](https://insightsengineering.github.io/teal.slice): provides a filtering panel to allow filtering of data.
--   [`teal.code`](https://insightsengineering.github.io/teal.code): handles reproducibility of outputs.
--   [`teal.transform`](https://insightsengineering.github.io/teal.transform): standardizes extracting and merging data.
--   [`teal.logger`](https://insightsengineering.github.io/teal.logger): standardizes logging within `teal` framework.
--   [`teal.reporter`](https://insightsengineering.github.io/teal.reporter): allows `teal` applications to generate reports.
+-   [`teal.data`](https://insightsengineering.github.io/teal.data/): creating and loading the data needed for `teal` applications.
+-   [`teal.widgets`](https://insightsengineering.github.io/teal.widgets/): shiny components used within `teal`.
+-   [`teal.slice`](https://insightsengineering.github.io/teal.slice/): provides a filtering panel to allow filtering of data.
+-   [`teal.code`](https://insightsengineering.github.io/teal.code/): handles reproducibility of outputs.
+-   [`teal.transform`](https://insightsengineering.github.io/teal.transform/): standardizes extracting and merging data.
+-   [`teal.logger`](https://insightsengineering.github.io/teal.logger/): standardizes logging within `teal` framework.
+-   [`teal.reporter`](https://insightsengineering.github.io/teal.reporter/): allows `teal` applications to generate reports.
 
 <!-- markdownlint-enable MD007 MD030 -->
 
@@ -41,7 +41,7 @@ if (!require("remotes")) install.packages("remotes")
 remotes::install_github("insightsengineering/teal@*release")
 ```
 
-In order to run many of the examples you will also need to install the [`scda`](https://insightsengineering.github.io/scda) package.
+In order to run many of the examples you will also need to install the [`scda`](https://insightsengineering.github.io/scda/) package.
 
 A stable release of all `NEST` packages from June 2022 is also available [here](https://github.com/insightsengineering/depository#readme).
 

diff --git a/man/ui_tabs_with_filters.Rd b/man/ui_tabs_with_filters.Rd
diff --git a/vignettes/including-adam-data-in-teal.Rmd b/vignettes/including-adam-data-in-teal.Rmd
@@ -91,4 +91,4 @@ if (interactive()) {
 }
 ```
 
-For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the [`teal.data` package](https://insightsengineering.github.io/teal.data).
+For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the [`teal.data` package](https://insightsengineering.github.io/teal.data/).
diff --git a/vignettes/including-general-data-in-teal.Rmd b/vignettes/including-general-data-in-teal.Rmd
@@ -77,4 +77,4 @@ if (interactive()) {
 }
 ```
 
-For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the [`teal.data` package](https://insightsengineering.github.io/teal.data).
+For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the [`teal.data` package](https://insightsengineering.github.io/teal.data/).
diff --git a/vignettes/including-mae-data-in-teal.Rmd b/vignettes/including-mae-data-in-teal.Rmd
@@ -40,4 +40,4 @@ The filter panel supports `MAE` data out of the box, but `teal` itself does not
 The package [`teal.modules.hermes`](https://insightsengineering.github.io/teal.modules.hermes/) has been specifically developed for the 
 analysis of `MAE` data.
 
-For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the [`teal.data` package](https://insightsengineering.github.io/teal.data).
+For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the [`teal.data` package](https://insightsengineering.github.io/teal.data/).
-Original file line number
+Diff line change
@@ Expand Up / @@ -91,4 +91,4 @@ if (interactive()) { @@
     }
     ```
-    For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the [`teal.data` package](https://insightsengineering.github.io/teal.data).
+    For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the [`teal.data` package](https://insightsengineering.github.io/teal.data/).