-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Documentation: Update README (12.11.2024) (#115)
* aesthetics: include new images for dark/light mode * aesthetics: add logo images for dark/light mode * aesthetics: badges and purpose addition * documentation: update installation guidelines * documentation: include contributing and documentation sections * documentation: improve installation guides * aesthetics: change badge colors * aesthetics: general improvement of readability * spellcheck: included reupload and cheatsheet in wordlist * instructions: added image and make text more explicit * Update english * docs: updated installation guidelines * docs: added quickstart guide * fix: updated badges * fix: spellcheck * docs: updated link to contributing guidelines * issue: deleted commented text and added links * spellcheck: added codebase to WORDLIST * text: specify to run in terminal * instructions: mention working directory --------- Co-authored-by: Jana Spinner <[email protected]> Co-authored-by: m-kolomanski <[email protected]>
- Loading branch information
3 people
authored
Nov 15, 2024
1 parent
828a45d
commit 622603c
Showing
4 changed files
with
46 additions
and
124 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,144 +1,61 @@ | ||
| # automated Non-Compartmental Analysis (aNCA) | ||
| <img src='inst/shiny/www/images/aNCA_logo_bbg.png#gh-dark-mode-only' align="right" alt="aNCA logo dark bg" height="200" style="float:right; height:200px;"> | ||
| <img src="inst/shiny/www/images/aNCA_logo_wbg.png#gh-light-mode-only" align="right" alt="aNCA logo light bg" height="200" style="float:right; height:200px;"> | ||
|
|
||
| # automated Non-Compartmental Analysis (aNCA) <img src="inst/shiny/www/images/aNCA_logo.png" align="right" width=140 height=140 alt="icon" /> | ||
|
|
||
| <!-- badges: | ||
| [](https://CRAN.R-project.org/package=shiny) | ||
| [](https://github.com/rstudio/shiny/actions) | ||
| <!-- badges: start --> | ||
| [<img src="https://pharmaverse.org/shields/aNCA.svg">](https://pharmaverse.org) | ||
| [](https://opensource.org/licenses/Apache-2.0) | ||
| [](https://CRAN.R-project.org/package=aNCA) | ||
| [](https://github.com/pharmaverse/aNCA/actions) | ||
| [](https://forum.posit.co/new-topic?category=shiny&tags=shiny) | ||
| <!-- badges: end --> | ||
|
|
||
| --> | ||
|
|
||
|
|
||
| ## Description | ||
|
|
||
| This application enables users to upload their datasets and perform Non-Compartment Analysis (NCA) on both pre-clinical and clinical datasets, with the results being easily visualizable. The NCA | ||
| can be tailored to calculate pharmacokinetic parameters for various dosing regimens and time points, given certain restrictions. It also features manual slope selection, simplifying the process of conducting lambda-z-regression and PK-timepoint exclusions. | ||
| Furthermore, the pharmacokinetic parameters can be dynamically visualized through customized graphics such as line and mean plots. The calculated pharmacokinetic parameters can be compiled in a dynamic table, visualized using boxplots, or exported as a comprehensive report. | ||
| Designed with user-friendliness in mind, this app aims to make NCA accessible and straightforward for all scientists. | ||
|
|
||
| ## Installation | ||
|
|
||
| This repository is private and still in developer mode. To install the package, follow the instructions below: | ||
|
|
||
|
|
||
| ### 1. Create Access Token | ||
|
|
||
| In GitHub click on your icon on the top right and head to: Settings > Developer Settings > Personal access tokens and create a classic access token. | ||
|
|
||
| ### 2. Clone the repository | ||
|
|
||
| Assuming you have git installed: | ||
|
|
||
|
|
||
| In RStudio go to "Create a project" > "Create Project from version control" > GitHub and paste the following together with your personal access token into the field for the Repository URL: | ||
|
|
||
|
|
||
| ``` | ||
| https://<your-token>@github.com/pharmaverse/aNCA.git | ||
| ``` | ||
|
|
||
|
|
||
| You can also switch the the directory you want to clone into and run the following in your terminal: | ||
|
|
||
| ```sh | ||
|
|
||
| git clone https://<your-token>@github.com/pharmaverse/aNCA.git | ||
|
|
||
| ``` | ||
|
|
||
| ### 3. Install the package | ||
| <br/> | ||
|
|
||
| > Our aim is to develop and share an open-source R Shiny application for performing Non-Compartmental Analysis (NCA) on clinical and non-clinical datasets worldwide and across pharmaceutical companies. | ||
| Next make sure you have a package development environment set up. If not, install the `devtools` or a similar package (if it does not work, please use R version 4.3.3): | ||
|
|
||
| ```r | ||
| options(repos = c(CRAN = "https://cloud.r-project.org/")) | ||
| install.packages("devtools") | ||
| ``` | ||
| <br/> | ||
|
|
||
| ## Description | ||
|
|
||
| If not already done, head into the cloned repository and install the package, e.g.: | ||
| This application enables users to upload their datasets and perform Non-Compartment Analysis (NCA) on both pre-clinical and clinical datasets, with the results being easily visualizable. Designed with user-friendliness in mind, this app aims to make NCA accessible and straightforward for all scientists. Among the features it currently possess, the App can: | ||
|
|
||
| * **Customize half life calculation**: Either by rule settings definitions or performing manual in-plot adjustments | ||
| * **Define AUC intervals of interest**: Providing by default last and to-infinite calculations | ||
| * **Visualize data and results** with interactive boxplots, summary statistic tables and scatter plots | ||
| * **Produce PP and ADPP** dataset formats of the resulting parameters | ||
| * **Save your analysis settings** and reupload them later to keep on analysing! | ||
|
|
||
| ```r | ||
| devtools::install() | ||
| ## Installation | ||
| To install the application, clone the repository and load it locally using the following commands in your terminal: | ||
| ``` sh | ||
| git clone https://github.com/pharmaverse/aNCA.git # Clone the repository | ||
| ``` | ||
|
|
||
|
|
||
| ## Use | ||
|
|
||
| Once correctly installed, the aNCA app can be simply run with the following two lines of code: | ||
|
|
||
|
|
||
| ```r | ||
| library(aNCA) | ||
| devtools::load_all() | ||
| aNCA::run_app() | ||
| You can then run the application from the R console anytime. Just make sure first your working directory is set to the aNCA folder: | ||
| ``` r | ||
| # install devtools if not present | ||
| if (!requireNamespace('devtools', quietly = TRUE)) install.packages('devtools') | ||
| devtools::load_all() # load all dependencies | ||
| aNCA::run_app() # run the application | ||
| ``` | ||
|
|
||
| Have fun running your tailored Non-Compartmental Analysis! | ||
|
|
||
| <!-- | ||
| ## Contribute as developer | ||
| To ensure a clean and informative git version history, please adhere to the [guidelines](man/GUIDELINES.md) of our git workflow. You can find further information on possible ways to use gits full power on our homemade [cheatsheet](man/GIT-CHEATSHEET.md). | ||
| --> | ||
|
|
||
| <!-- | ||
| ## Getting started | ||
| You may have realised this template... doesn't contain an app template. That is | ||
| due to the different tools available, and knowledge that there is a lot of | ||
| diversity in how people make shiny apps. | ||
| We have though applied a RocheMeta file (see `project_metadata.yaml`), which will | ||
| be used to index your app against our database of apps and packages. Please do | ||
| look at that file and fill in the fields. | ||
| ### Shiny frameworks | ||
| The easiest way to get started is via the very simple shiny app built into Rstudio. | ||
| To start that, click new in Rstudio, and select `Shiny Web App`. | ||
| If your app is likely to grow - it is strongly recommended to look at Shiny | ||
| Modules. | ||
| There are two common frameworks for structuring a more advanced app. The | ||
| more familiar would be [`golem`]() which structures a shiny app around the ideas | ||
| that inform an R package. | ||
| [`rhino`](https://appsilon.github.io/rhino/) introduces concepts that might be | ||
| new to many R developers, but can be | ||
| seen as the 'most robust, but also more intensive' way to construct an app. | ||
| ### Shiny tools at Roche | ||
| The following R packages exist to help you develop your shiny apps. | ||
| * RocheLogin: This R package can help you add Roche google authentication to your app | ||
| * RocheData: Do not bundle patient data into your apps - RocheData makes it easy to query Roche databases. | ||
| * ShinyCohortBuilder: Powerful tools to build filter panels that work across relational tables | ||
| * RocheDeploy: This package is optimized to push apps to the Apollo Connect server | ||
| ## Sharing your work | ||
| A `project_metadata.yaml` file has been added by default to your repo to index your | ||
| project and find it through RocheMeta REST API (https://connect.apollo.roche.com/RocheMetaAPI/). | ||
| You can visit [`RocheMeta documentation`](https://go.roche.com/RocheMeta) to learn how to fill correctly the file. | ||
| ## Quick start | ||
| The testing data will be automatically loaded upon application startup. You can provide your own dataset in the **data** tab. Here you can also specify pre-processing filters. | ||
|
|
||
| Some basic tags (`R`, `Shiny`) have been added as default to your `project_metadata.yaml` and the | ||
| lifecycle stages have been set to `experimental` and `active development`. | ||
| In the **NCA** tab, start off by loading the pre-processed data using *Submit* button. You will also need to choose dose number in the *Settings*. Then, you will be able to run the NCA analysis. From there, you can also specify different analysis options, like applying flag rule sets and selecting slopes. | ||
|
|
||
| Tags help to find easily your project through an API. Tag your project with more tags! If you are not sure which other tags to use () you can use `RocheMeta::suggest_tags()` function. | ||
| After the setup is done and analysis is performed, you are free to explore the results in the **Outputs** tab. Application supports various customizable plots, as well as report exporting. | ||
|
|
||
| ## License | ||
| ## Contributing | ||
| ### As developer | ||
| To ensure a clean codebase and smooth cooperation, please adhere to the [contributing guidelines](CONTRIBUTING.md). | ||
|
|
||
| The shiny package as a whole is licensed under the GPLv3. See the [LICENSE](LICENSE) file for more details. | ||
| ### As user | ||
| Feel free to open identified [issues](https://github.com/pharmaverse/aNCA/issues/new/choose), to reach out to us for questions or report in our [google sheet](https://forms.gle/c9ULTTv1s75yRaLj7) for feedback. | ||
|
|
||
| ## R version support | ||
| ## Documentation and references | ||
|
|
||
| This Shiny application is supported on the latest release version of R, as well as the previous four minor release versions of R. For example, if the latest release R version is 4.1, then that version is supported, as well as 4.0, 3.6, 3.5, and 3.4. | ||
| * Please go to [our Website](https://pharmaverse.github.io/aNCA/) for further information on the **aNCA app** (still in development). | ||
| * The main package used by the App is `PKNCA`. You can find more of it on its [GitHub](https://github.com/billdenney/pknca) | ||
|
|
||
| --> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.