README

This repository contains the files needed to render midterm_project_report.html. It contains a hierarchically ordered set of code folders, a folder with the raw data set wastewater_feb25.csv.zip, a folder with the clean data set wastewater_clean.csv, a folder with the code output, the RMarkdown file midterm_project_report.Rmd and its associated .html file, a .gitignore file, a Makefile that contains GNU Make commands for rendering the report and its components, and a config file that allows the user to customize the report. Briefly, this analysis provides the descriptive epidemiology of SARS-CoV-2 surveillance in the United States by US region from 2020-2024.

Instructions for generating the report

You will need RStudio, bash, and GNU Make to render this report as intended.

1. Clone the data_550_midterm_project repository from GtiHub to a local directory.
2. Navigate to the cloned repository. Set this as your working directory.
3. Type the command make in the RStudio terminal with a bash shell to create the components of the report and compile midterm_project_report.html in your local final_project directory. Alternatively, open the Makefile to see what make commands are available generating individual components of the report.
   NOTE: remove the rendered .html report and all files in the output folder with the command make clean.

Customization

The config.yml file contains four parameters that correspond to the four US regions that are possible to feature in this report: Midwest, Northeast, South, and West. To include a region in the rendered report, set the associated Boolean value to TRUE. Conversely, set the Boolean value to FALSE to exclude a region.
Additional CDC SArs-CoV-2 surveillance data through April 2024 became available. These data are found at test_raw_data/wastewater_feb25.csv.zip in the GitHub directory. To change the data source from the original data to the updated data in this report, set the associated Boolean value for original_data to FALSE. You will need to run the make clean command after changing any parameters to see the changes reflected in the compiled report.

Code directory

Code for creating the tables and figure are found in the code folder:

• code/coder_1/01_clean_data.R: imports raw data, selects key variables, calculates mean by month, creates US region variable, recodes missing data (i.e., 999 –> NA)
• code/coder_1/02_render.R: renders the html report midterm_project_report.html
• code/coder_2/01_make_desc_table.R: imports clean data, calculates summary statistics, creates kable table, saves kable table object
• code/coder_3/01_bargraph.R: imports clean data, creates ggplot bar graph, saves png
• code/coder_4/01_line_graph.R: imports clean data, calculates summary statistics, creates ggplot bar line graph, saves png
• code/coder_5/01_gis_map.R: imports clean data, calculates summary statistics, creates GIS plot, saves png