Customization

• Final report
  You have the option to include the code in the final report or not.
  To exclude the code and provide a cleaner view for collaborators, open the file '05_render_report.R' and set params: production: TRUE in the YAML title. This will generate a report without displaying the code.
  Conversely, to include the code for thorough inspection of the entire report, open the file '05_render_report.R' and set params: production: FALSE in the YAML title. This will generate a report with the code included.

• Analysis on the whole dataset or only 55+ years population: There is a config.yml that has been set up to run two versions of the analyses: one for all subjects and one for subjects 55+. To run the analysis for all subjects, type WHICH_CONFIG="default" into the terminal. To run the analysis for subjects 55+, type WHICH_CONFIG="old_age" into the terminal.

How to create the final report

• First, download project files from https://github.com/ruth-ma/Group7_DATA550 onto a local computer and save to desired location

Final report using git bash terminal

• Set the Group7_DATA550 folder as the project directory in the bash terminal using the cd command
• Type make into the terminal to generate the report.html product

Final report using the RStudio console

• Set the working directory to your local folder using the setwd() command
• You can run the files individually starting with '00_custom_code.R', followed by '01_table_YingXu.R', '02_Bingbing_graph.R', '03_Jack_analysis_graph.R', '04_Seana_respiratory.R' and finally '05_render_report.R'.
• Tables and plots will be generated in the 'output' folder, while the final report will be found in the main folder.

About the dataset

• This is a dataset about information regarding COVID-19 cases in Mexico (20% of the full data set).
• Information about the variables included in the dataset can be found in the covid_readme.txt file in the raw_data/ folder -You could download the dataset from https://datos.gob.mx/busca/dataset/informacion-referente-a-casos-covid-19-en-mexico.

Code Description

code/00_custom_code.R

• read data from data_raw/ folder
• add the age group variable
• save data to data_custom/ folder

code/01_table_YingXu.R

• write here

code/02_Bingbing_graph.R

• write here

code/03_Jack_analysis_graph.R

• write here

code/04_Seana_respiratory.R

• clean code to perform logistic regression (exposure: respiratory conditions, outcome: ICU admission, covariates: age, sex, tobacco use, pre-existing conditions)
• create plot of odds ratios for pneumonia, COPD, and asthma from logistic regression
• save plot in output/ folder

code/05_render_report.R

• renders report.Rmd R Markdown file

report.Rmd

• read data, tables, and figures from respective locations
• display results for production report