DATA 550 Midterm Project Description

Group 3

Our group is analyzing the dataset with information regarding COVID-19 cases in Mexico.

File structure

The report is been broken into four subproject child reports. Each coder is responsible one of the child reports.

Table 1: Ketki

• table1/ contains all code and output related to creating a descriptive table 1 for the dataset
  • table1/report.Rmd is the child report that makes a descriptive table for our chosen variables of interest

Regression Model: Nick

• model/ contains all code and output related to creating a regression model for the dataset
  • model/code/ is a folder for scripts associated with making regression model for child report
    • model/code/build_model.R is a script to run the regression analysis
  • model/output/ is a folder to hold output associated with regression model
    • model/output/logistic_model.Rds is created by model/code/build_model.R and knit into child report
  • model/config.yml is a configuration file where users can turn off/on variables to be included in the regression model for the dataset by setting their values to TRUE (include) or FALSE (exclude)
  • model/report.Rmd is the child report for the regression model

Comorbiditiy Figures: Dawa

• comorbidities/ contains all code and output related to creating descriptive figures associated with the comorbidities of interest (Dawa)
  • comorbidities/report.Rmd is the child report that makes figures assoicated with the comorbidities in the dataset
  • comorbidities/output is the folder where output plots from the child report are saved

Sociodemographic Figures: Yuzhou

• sociodemographic/ contains all code and output related to creating descriptive figures for the sociodemographic variables in the dataset (Yuzhou)
  • sociodemographic/code/ is a folder for scripts associated with making figures associated with the sociodemographic variables of interest for child report
    • sociodemographic/code/create_subset.R is a script that subsets the data to the sociodemographic variables of interest
  • sociodemographic/report.Rmd is the child report for the sociodemographic figures

Additional Files: Allison

• combined_report.Rmd is the parent report that combines each child report subproject into the final report

• render_combined_report.R is used for rendering the combined report from the command line

• data/ contains the COVID-19 dataset data/covid_sub.csv and a descriptive README about the dataset data/covid_readme.txt

• Makefile is used to run all necessary scripts in proper order for report building

Build Report

To build the final report, first use the make install command to ensure all required packages are synchronized for the project. Next, use the make combined_report.html command to run the Makefile in the main project directory and build the final parent report.

Customize Report

The report can be customized to include/exclude different covariates in our model through the use of the model/config.yml file. The file lists all covariates included in the model. The user can set each of these covariates to TRUE to include or FALSE to exclude them in the logistic regression model.