Merge 6f81614 into 75d9928

insightsengineering · May 11, 2023 · f3251cd · f3251cd
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diff --git a/LICENSE b/LICENSE
@@ -4,7 +4,7 @@ Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
 
-    http://www.apache.org/licenses/LICENSE-2.0
+    https://www.apache.org/licenses/LICENSE-2.0
 
 Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,

diff --git a/README.md b/README.md
@@ -41,11 +41,11 @@ The package provides a large range of functionality, for example:
 
 <!-- markdownlint-enable MD007 MD030 -->
 
-Many of these outputs are available to be added into [`teal`](https://insightsengineering.github.io/teal) applications for interactive exploration of data. These [`teal`](https://insightsengineering.github.io/teal) modules are available in the [`teal.modules.clinical`](https://insightsengineering.github.io/teal.modules.clinical) package.
+Many of these outputs are available to be added into [`teal`](https://insightsengineering.github.io/teal/main/) applications for interactive exploration of data. These `teal` modules are available in the [`teal.modules.clinical`](https://insightsengineering.github.io/teal.modules.clinical/main/) package.
 
 ## Installation
 
-It is recommended that you [create and use a Github PAT](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token) to install the latest version of this package. Once you have the PAT, run the following:
+It is recommended that you [create and use a Github PAT](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token) to install the latest version of this package. Once you have the PAT, run the following:
 
 ```r
 Sys.setenv(GITHUB_PAT = "your_access_token_here")
@@ -59,9 +59,9 @@ See package vignettes `browseVignettes(package = "tern")` for usage of this pack
 
 ## Related
 
-* [`rtables`](https://github.com/insightsengineering/rtables) - table engine used
-* [TLG Catalog](https://github.com/insightsengineering/tlg-catalog) - examples for clinical trials tables and graphs
-* [`teal.modules.clinical`](https://insightsengineering.github.io/teal.modules.clinical) - `teal` modules for interactive data analysis
+* [`rtables`](https://insightsengineering.github.io/rtables/main/) - table engine used
+* [TLG Catalog](https://insightsengineering.github.io/tlg-catalog/) - examples for clinical trials tables and graphs
+* [`teal.modules.clinical`](https://insightsengineering.github.io/teal.modules.clinical/main/) - `teal` modules for interactive data analysis
 
 ## Acknowledgment
 

diff --git a/vignettes/tables.Rmd b/vignettes/tables.Rmd
@@ -27,7 +27,7 @@ knitr::opts_chunk$set(
 
 The `tern` R package provides functions to create common analyses from clinical trials in `R`. 
 The core functionality for tabulation is built on the more general purpose `rtables` package. 
-New users should first begin by reading the ["Introduction to tern"](https://insightsengineering.github.io/tern/articles/tern.html) and ["Introduction to `rtables`"](https://roche.github.io/rtables/articles/introduction.html) vignettes.
+New users should first begin by reading the ["Introduction to tern"](https://insightsengineering.github.io/tern/main/articles/tern.html) and ["Introduction to `rtables`"](https://insightsengineering.github.io/rtables/main/articles/introduction.html) vignettes.
 
 The packages used in this vignette are:
 
@@ -54,7 +54,7 @@ The table layout is materialized with the `rtables::build_table` function and th
 The `tern` analyze functions are wrappers around `rtables::analyze` function, they offer various methods useful from the perspective of clinical trials and other statistical projects.
 
 Examples of the `tern` analyze functions are `tern::count_occurrences`, `tern::summarize_ancova` or  `tern::summarize_vars`. 
-As there is no one prefix to identify all `tern` analyze functions it is recommended to use the [the tern website functions reference](https://insightsengineering.github.io/tern/reference/index.html).
+As there is no one prefix to identify all `tern` analyze functions it is recommended to use the [the tern website functions reference](https://insightsengineering.github.io/tern/main/reference/index.html).
 
 ### Internals of `tern` Analyze Functions 
 

diff --git a/vignettes/tern.Rmd b/vignettes/tern.Rmd
@@ -69,7 +69,7 @@ data visualizations helper functions:
 - ...
 
 
-The reference of `tern` functions is available on [the tern website functions reference](https://insightsengineering.github.io/tern/reference/index.html).
+The reference of `tern` functions is available on [the tern website functions reference](https://insightsengineering.github.io/tern/main/reference/index.html).
 
 ---------
 
@@ -82,7 +82,7 @@ The table layout is materialized with the `rtables::build_table` function and th
 The `tern` analytical functions are wrappers around the `rtables::analyze` function; they offer various methods useful from the perspective of clinical trials and other statistical projects.
 
 Examples of the `tern` analytical functions are `tern::count_occurrences`, `tern::summarize_ancova` and `tern::summarize_vars`. 
-As there is no one prefix to identify all `tern` analytical functions it is recommended to use the reference subsection on [the tern website](https://insightsengineering.github.io/tern/reference/index.html).
+As there is no one prefix to identify all `tern` analytical functions it is recommended to use the reference subsection on [the tern website](https://insightsengineering.github.io/tern/main/reference/index.html).
 
 In the `rtables` code below we first describe the two tables and assign the descriptions to the variables `lyt` and `lyt2`. We then built the tables using the actual data with `rtables::build_table`. The description of a table is called a table **layout**. The **analyze instruction** adds to the layout that the `ARM` variable should be analyzed with the `mean` analysis function and the result should be rounded to 1 decimal place.
 Hence, a **layout** is “pre-data”; that is, it’s a description of **how to build a table once we get data**.
@@ -166,17 +166,17 @@ The first plot is a `ggplot2` object and the second plot is a `gTree` object, as
 The second plot has to be properly resized to get a clear and readable table content.
 
 The `tern` functions used for plot generation are mostly `g_` prefixed.
-All `tern` plot functions are listed on [the tern website functions reference](https://insightsengineering.github.io/tern/reference/index.html).
+All `tern` plot functions are listed on [the tern website functions reference](https://insightsengineering.github.io/tern/main/reference/index.html).
 
 ## Interactive Apps
 
 Most of `tern` outputs could be easily accommodated into `shiny` apps. 
 We recommend applying `tern` outputs into `teal` apps. 
-The [`teal` package](https://insightsengineering.github.io/teal/) is a shiny-based interactive exploration framework for analyzing data.
-`teal` shiny apps with `tern` outputs are available in the [`teal.modules.clinical` package](https://insightsengineering.github.io/teal.modules.clinical/).
+The [`teal` package](https://insightsengineering.github.io/teal/main/) is a shiny-based interactive exploration framework for analyzing data.
+`teal` shiny apps with `tern` outputs are available in the [`teal.modules.clinical` package](https://insightsengineering.github.io/teal.modules.clinical/main/).
 
 ## Summary 
 
 In summary, `tern` contains many additional functions for creating tables, listing and graphs used in clinical trials and other statistical analyses. The design of the package gives users a lot of flexibility to meet the analysis needs in a regulatory or exploratory reporting context.
 
-**For more information please explore [the tern website](https://insightsengineering.github.io/tern/).**
+**For more information please explore [the tern website](https://insightsengineering.github.io/tern/main/).**