swati-rajwal/bmi510final

Submission for BMI 510 Coursework at Emory University

🎯Quick Start: Using the Package

This tutorial describes how to access functionality in the bmi510final R Package. Please note that this work is a submission for the BMI-510 Coursework at Emory University taught by Prof. J Lucas McKay.

1. Open R in your terminal (CMD/Gitbash).

2. Download and install the package repository:

   library(devtools)
   install_github("https://github.com/swati-rajwal/bmi510final")

   or

   devtools::install_github("https://github.com/swati-rajwal/bmi510final")

🏃Running Examples

1. Go to the inst/ folder and it contains the Testing_package.r file with examples.
2. Alternatively, once you install the package on your system, you can run help(package = bmi510final) and follow this short GIF to run sample examples for any function provided by this package:

running.a.sample.example.mp4

🔐Environment Variable and Key

One of the functions requires you to have REDCAP_API_TOKEN. Please follow these steps:

1. Close R sessions if already open.
2. Create a .Renviron file in your home directory (i.e., inside the 'bmi510final' folder)
3. Inside the .Renviron file, define the following environment variable: REDCAP_API_TOKEN=<your_api_token_here>
4. Start your R session and now the R session should be able to load the new environment variables.
5. Run the code.

📌Functions Provided:

This package provides a suite of tools designed to facilitate common tasks in biomedical informatics research. It includes functions for analyzing Bernoulli distributions, computing survival curves, unscaling standardized data, approximating principal components, standardizing variable names in datasets, determining minimum sample sizes for statistical tests, and securely fetching data from RedCap. The primary goal is to create reliable, reusable code that enhances productivity and ensures consistency across data analyses. All functions are well-documented and accessible for easy integration into research workflows.

👩‍💻Working on the Package

1. Open Terminal or iTerm2.

2. Download the repository:

   • git clone https://github.com/swati-rajwal/bmi510final
   • cd bmi510final

3. Make changes in the code as you wish

4. Then run r either in cmd or git bash or RStudio

   library(devtools)
   library(roxygen2)
   document()
   install()

   or

   library(bmi510final)
   help(package="bmi510final")
   devtools::document()
   devtools::install()
   devtools::check()

   Please make sure your system has https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html installed on your local computer while for check() function

5. The output of devtools::check() should be:

6. Push up changes

   • git status
   • git add .
   • git commit –m "added minimumN()"
   • git push