ermise

This R package is a set of tools and workflow enhancements for data processing and analysis projects.

Core features:

• Create projects with a folder structure geared toward data processing and analysis using RStudio's New Project wizard (File > New Project...) or ermise::create_project()
• Document package dependencies to facilitate collaboration using ermise::require_packages()
• Start a new R Notebook for an analysis using ermise::new_analysis()
• Start a new R source file to develop a helper function using ermise::new_src()

The template's folder structure is based on one recommended by Emily Riederer.

Create a new project

After installing this package, use Rstudio's New Project wizard (File > New Project...) to create a new "ermise Project". ermise will create some folders in the project directory:

You can also create the project without RStudio by calling ermise::create_project() directly.

The created folders are:

• analysis: RMarkdown files that constitute the final data processing or analysis
• src: R scripts that contain useful helper functions or other set-up tasks (e.g. data pulls)
• data: Raw data - this folder should be considered read only!
• save: Intermediate data objects created during the analysis
• doc: Any long-form documentation or setup instructions
• publish: Any files created by the analysis to be used outside of the project

ermise will also create a file called "required_packages.txt" in the project's root folder.

Document package dependencies

To facilitate collaboration on the project, you can call ermise::require_packages() to update the "required_packages.txt" file with new package names as necessary.

For example, this will add dplyr and tidyr to "required_packages.txt":

ermise::require_packages("dplyr", "tidyr")

This can be a decent start to share dependency information if you aren't at the point of needing more fully-featured environment management tools like renv.

Create new analysis and source files

Create a new R Notebook for an analysis using ermise::new_analysis(). This will create a new .Rmd file in the project's /analysis/ folder with some basic formatting. It will also include library() calls to load any packages it found in "required_packages.txt".

For example, run the following line to create a new analysis R Notebook:

ermise::new_analysis("Summary of hospital totals")

This creates a new file in /analysis/ called "summary_of_hospital_totals.Rmd". Assuming we already ran the code above to add dplyr and tidyr to "required_packages.txt", that new file would look like this:

Create a new R source file for a helper function using ermise::new_src(). This will create a new .R folder in /src/ with a simple code template for the helper function.

For example, run the following line to create a new source file:

ermise::new_src("clean_hospital_names")

This creates a new file in /src/ called "clean_hospital_names.R" that looks like this:

The comment block above the function follows roxygen2 formatting.

Installation

You can install ermise directly from GitHub using the devtools package:

devtools::install_github("szego/ermise")

After installing, create a new "ermise Project" using RStudio's New Project wizard (File > New Project...).

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ermise (c) by Antonio R. Vargas

ermise is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

You should have received a copy of the license along with this work. If not, see https://creativecommons.org/licenses/by-nc-sa/4.0/.