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shajoezhu merged 1 commit into from
Aug 8, 2026
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update url #1506

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6 changes: 3 additions & 3 deletions DESCRIPTION
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Expand Up @@ -25,9 +25,9 @@ Authors@R: c(
Description: Table, Listings, and Graphs (TLG) library for common outputs
used in clinical trials.
License: Apache License 2.0
URL: https://insightsengineering.github.io/tern/,
https://github.com/insightsengineering/tern/
BugReports: https://github.com/insightsengineering/tern/issues
URL: https://pharmaverse.github.io/tern/,
https://github.com/pharmaverse/tern/
BugReports: https://github.com/pharmaverse/tern/issues
Depends:
R (>= 4.4.0),
rtables (>= 0.6.15)
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62 changes: 31 additions & 31 deletions README.md
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@@ -1,22 +1,22 @@
# tern <a href='https://github.com/insightsengineering/tern'><img src="man/figures/logo.png" align="right" height="200" width="200"/></a>
# tern <a href='https://github.com/pharmaverse/tern'><img src="man/figures/logo.png" align="right" height="200" width="200"/></a>

<!-- start badges -->
[![Check 🛠](https://github.com/insightsengineering/tern/actions/workflows/check.yaml/badge.svg)](https://insightsengineering.github.io/tern/main/unit-test-report/)
[![Docs 📚](https://github.com/insightsengineering/tern/actions/workflows/docs.yaml/badge.svg)](https://insightsengineering.github.io/tern/)
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<!-- end badges -->

The `tern` R package contains analysis functions to create tables and graphs used for clinical trial reporting.
Expand All @@ -27,24 +27,24 @@ The package provides a large range of functionality, such as:

Data visualizations:

- Line plots ([`g_lineplot`](https://insightsengineering.github.io/tern/latest-tag/reference/g_lineplot.html))
- Kaplan-Meier plots ([`g_km`](https://insightsengineering.github.io/tern/latest-tag/reference/g_km.html))
- Forest plots ([`g_forest`](https://insightsengineering.github.io/tern/latest-tag/reference/g_forest.html))
- STEP graphs ([`g_step`](https://insightsengineering.github.io/tern/latest-tag/reference/g_step.html))
- Individual patient plots ([`g_ipp`](https://insightsengineering.github.io/tern/latest-tag/reference/g_ipp.html))
- Waterfall plots ([`g_waterfall`](https://insightsengineering.github.io/tern/latest-tag/reference/g_waterfall.html))
- Bland-Altman plots ([`g_bland_altman`](https://insightsengineering.github.io/tern/latest-tag/reference/g_bland_altman.html))
- Line plots ([`g_lineplot`](https://pharmaverse.github.io/tern/latest-tag/reference/g_lineplot.html))
- Kaplan-Meier plots ([`g_km`](https://pharmaverse.github.io/tern/latest-tag/reference/g_km.html))
- Forest plots ([`g_forest`](https://pharmaverse.github.io/tern/latest-tag/reference/g_forest.html))
- STEP graphs ([`g_step`](https://pharmaverse.github.io/tern/latest-tag/reference/g_step.html))
- Individual patient plots ([`g_ipp`](https://pharmaverse.github.io/tern/latest-tag/reference/g_ipp.html))
- Waterfall plots ([`g_waterfall`](https://pharmaverse.github.io/tern/latest-tag/reference/g_waterfall.html))
- Bland-Altman plots ([`g_bland_altman`](https://pharmaverse.github.io/tern/latest-tag/reference/g_bland_altman.html))

Statistical model fit summaries:

- Logistic regression ([`summarize_logistic`](https://insightsengineering.github.io/tern/latest-tag/reference/summarize_logistic.html))
- Cox regression ([`summarize_coxreg`](https://insightsengineering.github.io/tern/latest-tag/reference/cox_regression.html))
- Logistic regression ([`summarize_logistic`](https://pharmaverse.github.io/tern/latest-tag/reference/summarize_logistic.html))
- Cox regression ([`summarize_coxreg`](https://pharmaverse.github.io/tern/latest-tag/reference/cox_regression.html))

Analysis tables:

- See a list of all available analyze functions [here](https://insightsengineering.github.io/tern/latest-tag/reference/analyze_functions.html)
- See a list of all available summarize functions [here](https://insightsengineering.github.io/tern/latest-tag/reference/summarize_functions.html)
- See a list of all available column-wise analysis functions [here](https://insightsengineering.github.io/tern/latest-tag/reference/analyze_colvars_functions.html)
- See a list of all available analyze functions [here](https://pharmaverse.github.io/tern/latest-tag/reference/analyze_functions.html)
- See a list of all available summarize functions [here](https://pharmaverse.github.io/tern/latest-tag/reference/summarize_functions.html)
- See a list of all available column-wise analysis functions [here](https://pharmaverse.github.io/tern/latest-tag/reference/analyze_colvars_functions.html)

<!-- markdownlint-enable MD007 MD030 -->

Expand All @@ -64,18 +64,18 @@ or you can install the latest development version directly from GitHub by runnin

```r
# install.packages("pak")
pak::pak("insightsengineering/tern")
pak::pak("pharmaverse/tern")
```

## Usage

To understand how to use this package, please refer to the [Introduction to `tern`](https://insightsengineering.github.io/tern/latest-tag/articles/tern.html) article, which provides multiple examples of code implementation.
To understand how to use this package, please refer to the [Introduction to `tern`](https://pharmaverse.github.io/tern/latest-tag/articles/tern.html) article, which provides multiple examples of code implementation.

See package vignettes `browseVignettes(package = "tern")` for usage of this package.

## Related

- [`rtables`](https://insightsengineering.github.io/rtables/) - table engine used
- [`rtables`](https://pharmaverse.github.io/rtables/) - table engine used
- [`tlg-catalog`](https://insightsengineering.github.io/tlg-catalog/) - website showcasing many examples of clinical trial tables, listings, and graphs
- [`teal.modules.clinical`](https://insightsengineering.github.io/teal.modules.clinical/) - `teal` modules for interactive data analysis

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6 changes: 3 additions & 3 deletions man/tern-package.Rd
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4 changes: 2 additions & 2 deletions vignettes/tables.Rmd
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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/latest-tag/articles/tern.html) and ["Introduction to `rtables`"](https://insightsengineering.github.io/rtables/latest-release/articles/rtables.html) vignettes.
New users should first begin by reading the ["Introduction to tern"](https://pharmaverse.github.io/tern/latest-tag/articles/tern.html) and ["Introduction to `rtables`"](https://pharmaverse.github.io/rtables/latest-release/articles/rtables.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 `count_occurrences`, `summarize_ancova` or `analyze_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/latest-tag/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://pharmaverse.github.io/tern/latest-tag/reference/index.html).

### Internals of `tern` Analyze Functions

Expand Down
10 changes: 5 additions & 5 deletions vignettes/tern.Rmd
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Expand Up @@ -28,7 +28,7 @@ The `tern` R package contains analytical functions for creating tables and graph
The main focus is on the clinical trial reporting tables but the graphs related to the clinical trials are also valuable.
The core functionality for tabulation is built on top of the more general purpose `rtables` package.

[**It is strongly recommended that you start by reading the "Introduction to `rtables`" vignette to get familiar with the concept of `rtables`.**](https://insightsengineering.github.io/rtables/latest-tag/articles/rtables.html)
[**It is strongly recommended that you start by reading the "Introduction to `rtables`" vignette to get familiar with the concept of `rtables`.**](https://pharmaverse.github.io/rtables/latest-tag/articles/rtables.html)

---------

Expand Down Expand Up @@ -65,7 +65,7 @@ data visualizations helper functions:
- ...


The reference of `tern` functions is available on [the tern website functions reference](https://insightsengineering.github.io/tern/latest-tag/reference/index.html).
The reference of `tern` functions is available on [the tern website functions reference](https://pharmaverse.github.io/tern/latest-tag/reference/index.html).

---------

Expand All @@ -78,7 +78,7 @@ 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 `count_occurrences`, `summarize_ancova` and `analyze_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/latest-tag/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://pharmaverse.github.io/tern/latest-tag/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 @@ -158,7 +158,7 @@ g_lineplot(
)
```

All `tern` functions used for plot generation are `g_` prefixed and are listed on [the tern website functions reference](https://insightsengineering.github.io/tern/latest-tag/reference/index.html#graphs).
All `tern` functions used for plot generation are `g_` prefixed and are listed on [the tern website functions reference](https://pharmaverse.github.io/tern/latest-tag/reference/index.html#graphs).

## Interactive Apps

Expand All @@ -169,4 +169,4 @@ A variety of pre-made `teal` shiny apps for `tern` outputs are available in the

In summary, `tern` contains many additional functions for creating tables, listings, and graphs used in clinical trials and other statistical analyses. The design of the package gives users the flexibility to meet the analysis needs in both regulatory and exploratory reporting contexts.

**For more information please explore [the tern website](https://insightsengineering.github.io/tern/latest-tag/).**
**For more information please explore [the tern website](https://pharmaverse.github.io/tern/latest-tag/).**
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