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add RDarwin and DarwinReporter to docs
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certara-jcraig committed Dec 13, 2023
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62 changes: 48 additions & 14 deletions README.md
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Expand Up @@ -28,6 +28,9 @@ install_certara_packages()
check_certara_package_versions()
```

## Modeling

The `RsNLME` suite of packages use Certara's NLME-Engine for execution. Create, edit, and execute a Phoenix NLME model, directly from R!

### [RsNLME](https://certara.github.io/R-RsNLME/index.html) <a href = "https://certara.github.io/R-RsNLME/index.html"><img src='vignettes/img/RsNLME.png' style = "float:right; height: 150px;" align="right" height="150" /></a>

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<br/>

## Machine Learning Model Development Tools

### [RDarwin](https://certara.github.io/R-Darwin/index.html) <a href = "https://certara.github.io/R-Darwin/index.html"><img src='vignettes/img/RDarwin.png' align="left" height="150" style = "float:left; height:150px; padding-right: 10px;"/></a>

[`Certara.RDarwin`](https://certara.github.io/R-Darwin/index.html) is an R package designed to facilitate the usage of [pyDarwin](https://certara.github.io/pyDarwin/html/index.html) with the Certara NLME pharmacometric modeling engine from the R command line. The Python package, pyDarwin, is a powerful tool for using machine learning algorithms for model selection.

<br/>

---

<br/>

### [DarwinReporter](https://certara.github.io/R-DarwinReporter/index.html) <a href = "https://certara.github.io/R-DarwinReporter/index.html"><img src='vignettes/img/DarwinReporter.png' align="right" height="150" style = "float:right; height:150px; padding-right: 10px;"/></a>

[`Certara.DarwinReporter`](https://certara.github.io/R-DarwinReporter/index.html) is an R package that provides a Shiny application, in addition to various plotting and data summary functions, for analyzing results of a [pyDarwin](https://certara.github.io/pyDarwin/html/index.html) automated machine learning based model search.

<br/>

---

<br/>


## Diagnostic Plots and Tables

### [ModelResults](https://certara.github.io/R-model-results/index.html) <a href = "https://certara.github.io/R-model-results/index.html"><img src='vignettes/img/ModelResults.png' align="left" height="150" style = "float:left; height:150px; padding-right: 10px;"/></a>

[`Certara.ModelResults`](https://certara.github.io/R-model-results/index.html) is an R package and Shiny GUI used to generate, customize, and report model diagnostic plots and tables from NLME or NONMEM runs.
Expand All @@ -83,7 +111,21 @@ Users are not limited by the GUI however, Certara.ModelResults will generate the

<br/>

### [VPCResults](https://certara.github.io/R-VPCResults/index.html) <a href = "https://certara.github.io/R-VPCResults/index.html"><img src='vignettes/img/VPCResults.png' align="left" height="150" style = "float:left; height: 150px; padding-right: 10px;"/></a>
### [coveffectsplot](https://smouksassi.github.io/coveffectsplot/) <a href = "https://smouksassi.github.io/coveffectsplot/"><img src='vignettes/img/coveffectsplot.png' align="left" height="150" style = "float:left; height: 150px;"/></a>

[`coveffectsplot`](https://github.com/smouksassi/coveffectsplot) is an R package that provide the function forest_plot and an accompanying Shiny application that facilitates the production of forest plots to visualize covariate effects as commonly used in pharmacometrics population PK/PD report

Learn more about the package [here](https://github.com/smouksassi/coveffectsplot).

<br/>

---

<br/>

## Visual Predictive Check (VPC)

### [VPCResults](https://certara.github.io/R-VPCResults/index.html) <a href = "https://certara.github.io/R-VPCResults/index.html"><img src='vignettes/img/VPCResults.png' align="right" height="150" style = "float:right; height: 150px; padding-right: 10px;"/></a>

[`Certara.VPCResults`](https://certara.github.io/R-VPCResults/index.html) is an R package and Shiny application used to parameterize and plot a Visual Predictive Check (VPC).

Expand All @@ -97,7 +139,7 @@ Users are not limited by the GUI however, [`Certara.VPCResults`](https://certara

<br/>

### [tidyvpc](https://certara.github.io/tidyvpc/index.html) <a href = "https://certara.github.io/tidyvpc/index.html"><img src='vignettes/img/tidyvpc.png' align="right" height="150" style = "float:right; height: 150px;"/></a>
### [tidyvpc](https://certara.github.io/tidyvpc/index.html) <a href = "https://certara.github.io/tidyvpc/index.html"><img src='vignettes/img/tidyvpc.png' align="left" height="150" style = "float:left; height: 150px;"/></a>

The [`tidyvpc`](https://certara.github.io/tidyvpc/index.html) package is used to perform a Visual Predictive Check (VPC), while accounting for stratification, censoring, and prediction correction.

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<br/>

### [ggquickeda](https://smouksassi.github.io/ggquickeda/) <a href = "https://smouksassi.github.io/ggquickeda/"><img src='vignettes/img/ggquickeda.png' align="left" height="150" style = "float:left; height: 150px; padding-right: 10px;"/></a>
## Exploratory Data Analysis (EDA)

### [ggquickeda](https://smouksassi.github.io/ggquickeda/) <a href = "https://smouksassi.github.io/ggquickeda/"><img src='vignettes/img/ggquickeda.png' align="right" height="150" style = "float:right; height: 150px; padding-right: 10px;"/></a>

[`ggquickeda`](https://github.com/smouksassi/ggquickeda) is an R Shiny app/package providing a graphical user interface (GUI) to `ggplot2` and `table1`.

Expand All @@ -125,17 +169,7 @@ For a quick overview using an older version of the app head to this [YouTube Tut

<br/>

### [coveffectsplot](https://smouksassi.github.io/coveffectsplot/) <a href = "https://smouksassi.github.io/coveffectsplot/"><img src='vignettes/img/coveffectsplot.png' align="right" height="150" style = "float:right; height: 150px;"/></a>

[`coveffectsplot`](https://github.com/smouksassi/coveffectsplot) is an R package that provide the function forest_plot and an accompanying Shiny application that facilitates the production of forest plots to visualize covariate effects as commonly used in pharmacometrics population PK/PD report

Learn more about the package [here](https://github.com/smouksassi/coveffectsplot).

<br/>

---

<br/>
## Other

### [ggcertara](https://github.com/certara/ggcertara)

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