Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Check all URLs #909

Merged
merged 3 commits into from
May 11, 2023
+14 −14
Merged

Check all URLs #909

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
8797b2f
Update URLs
edelarua May 10, 2023
bc00be5
Merge branch 'main' into 885_check_urls@main
edelarua May 11, 2023
6f81614
Empty commit
edelarua May 11, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion LICENSE
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
10 changes: 5 additions & 5 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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")
Expand All @@ -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

Expand Down
4 changes: 2 additions & 2 deletions vignettes/tables.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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:

Expand All @@ -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

Expand Down
12 changes: 6 additions & 6 deletions vignettes/tern.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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).

---------

Expand All @@ -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**.
Expand Down Expand Up @@ -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/).**