DATA550 Final Project

Looking at effects of purpose in life on risk of cognitive impairment on Health and Retirement Study participants using Cox Proportional Hazards model. This will build a report providing summary statistics, Cox regression results, and a cumulative hazard plot between lower and upper tertiles of Purpose in Life scores.

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Code Description

code/build_table1.R

• creates summary statistics dataframe for table building

code/run_analysis.R

• runs Cox model on data and saves the coxph object

code/build_cumhazplot.R

• builds a ggsurvplot object visualizing cumulative hazard from code/run_analysis.R

code/render_report.R

• creates the HTML report from 'final_project_report.Rmd'

Makefile

• contains rules for building the report, docker image, and running the docker image
• make .reportbuild will generate the objects for compiling the report
• it will also create an empty file called .reportbuild in the project root directory, so that make properly knows when to update outputs
• project_image rule will take Renv files and directory files needed to build Docker image
• pull_image dependency rule for da_dockerhub_report using Dockerhub image
• da_dockerhub_report builds the report using Dockerhub image
• da_local_report builds the report using locally built Docker image

Dockerfile

• contains container structure and commands to run report building in the container

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Build Report Locally:

• run make project_image to build the local Docker image (may take some time).
• run make da_local_report to build the report which will output to /report folder.

Build Report with Dockerhub Image:

• run make da_dockerhub_report to pull Dockerhub image and being report-building.
• Built report will appear in report/ folder.