README.md

In PAHPLabResearch/FLASH: FLASH: Free Living Activity Study for Health

Welcome to the online data repository for the Free Living Activity Study for Health (FLASH). The FLASH is an ongoing study with a 24-hour protocol in which physical activity is concurrently assessed in a variety of ways (e.g. wearable devices, questionnaire, partial direct observation). This repository has a threefold purpose:

1. To provide open access data for use in future studies
2. To provide open source code as an example (if not a template) for future studies
3. To provide an example of how GitHub repositories can enhance communications between developers and end users, particularly through issues, pull requests, and milestones.

Accessing data

Data are stored in the data-raw folder. Access is governed by the green Clone or download button, which offers a few options. The simplest option is “Download ZIP”, which will just download the repository to your computer. Then you can navigate to the data-raw folder and work with the data however you like. “Open in Desktop” will use the GitHub Desktop application to open the repository. Above both of those options, there is a link (https://github.com/PAHPLabResearch/FLASH.git) you can use to make yourself a copy through Git channels. This is especially useful in conjunction with RStudio, where you can select “new project -> version control -> git”, paste the link, and click “create project”, at which point an R project will be set up automatically on your machine.

In general, you should probably use the “Download ZIP” option unless you plan on using Git version control to manage your further work on the data set. If that’s the case, chances are you don’t need a lot of further instruction. If you’re just getting your feet wet, though, here are a few good resources:

• Wickham’s R Packages
• RStudio support
  • Version control with Git and SVN
  • Using projects

Access for Non R Users

A utility is available via convert_to_csv to make .csv copies of the data files for use on another platform. Unfortunately this is an R-based workaround. If you don't want to use R at all, you may need to look into whether your platform can work with .rds files, or whether a different file converter is already available somewhere else for you to use.

Working with rds data

The files in data-raw are in an R native file format (.rds extension). If you are not an R user, your software of choice may have a built-in mechanism for importing rds data. If not, you’ll need to convert the files, probably to csv format. That could potentially be done a number of ways, but going through R is probably the most straightforward. You should be able to convert the files with the following steps:

1. Make sure you have R installed.
2. Ideally install RStudio as well.
3. Open RStudio and run the dependency code given in the following section (copy and paste it into the console, then press enter).
4. Go to the data-raw folder and open the file called convert_to_csv.R
5. Run all the code in the file (to do so, click source in Rstudio)
6. After the code has finished running, go back to data-raw and its subdirectories. You should now see csv files you can use as you see fit.

Dependencies

The code in FLASH relies on many other R packages. To make sure you have them all installed, the easiest thing to do is the following:

# Make sure devtools package is installed
if (!"devtools" %in% installed.packages()) install.packages("devtools")

devtools::install_github("PAHPLabResearch/FLASH")

Overview of repository structure

• The R folder contains useful code for generating/manipulating the data set. The code in this directory can be loaded through the devtools package using the command devtools::load_all().

• The man folder contains documentation of the code contained in R.

• The data-raw folder contains data files (rds extension), as well as sample code to illustrate how raw data files (e.g. csv or xls extension) could be processed. README files in each folder orient the user to the contents.

• The Demo_Manuscript folder contains code used for preparing the paper by Hibbing, Lamoureux, and Welk. The code provides an example of how data could be manipulated in different ways.

PAHPLabResearch/FLASH documentation built on May 15, 2020, 7:08 p.m.