Group 1's Midterm Project for DATA 550
In this project, we will estimate the effect of chronic conditions (specifically: diabetes, COPD, asthma, immune suppression, CVD, and obesity) on hospitalization and death of COVID-19 patients in Mexico.
Source: https://datos.gob.mx/busca/dataset/informacion-referente-a-casos-covid-19-en-mexico
- Pragati Prasad
- Jess Chan
- Kanak Belgaum
- Ariana Parquette
- Sim Fan
code/01_data_cleaning.R
- run with
make data
- inputs raw data from
raw_data/
folderraw_data/covid_sub.csv
- Handle missing data
- Set outcome variables to binary
- Change dependent variables (chronic conditions) to either binary or categorical with reference groups
- outputs cleaned/final dataset to
output/
folderoutput/data_cleaned.rds
code/02_descriptive_stat.R
- run with
make descriptive
- inputs cleaned dataset from
output/
folderoutput/data_cleaned.rds
- Make table 1 describing population data
- Histograms of dependent variables (chronic conditions)
- Scatter plot to visualize distribution of dependent variables (chronic conditions) amongst the patient data
- outputs all plots and tables to
output/
folderoutput/02_table_one.rds
output/02_conditioncount.png
output/02_table2.png
output/02_heatmap.png
code/03_modeling.R
- run with
make regression
- inputs cleaned dataset from
output/
folderoutput/data_cleaned.rds
- runs logistic regression models to estimate the effect of chronic conditions on hospitalization and death of COVID-19 patients in Mexico
- outputs regression models in
output
folderoutput/model_1.rds
output/model_2.rds
output/model_1_results.rds
output/model_2_results.rds
code/04_visualization.R
- run with
make visualize
- inputs regression files from
output/
folderoutput/data_cleaned.rds
output/model_1.rds
output/model_2.rds
- Create regression model table
- Diagnostic plots to evaluate model selection
- Assess linearity assumption
- outputs diagnostic plots to
output/
folderoutput/model_1_effects.rds
output/model_2_effects.rds
report.Rmd
- run with
make report.html
- inputs all plots and tables
- outputs formatted report file