Lung Cancer Incidence and Characterisation - OPTIMA

• Study title: The Worldwide Incidence of Lung Cancer
• Study contents: Incidence, table one characterisation, large scale characterisation
• Study lead(s): Danielle Newby ([email protected]) & Cheryl Tan ([email protected])
• ShinyApp PhenotypeR: https://dpa-pde-oxford.shinyapps.io/PhenotypeR_OPTIMA_lung_cancer/
• ShinyApp Main Study: https://dpa-pde-oxford.shinyapps.io/OPTIMA_lung_cancer_incidence_study/
• Publications:

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Repository organisation

This repo is organized as follows:

• 1_Diagnostics: Please find the folders for the diagnostics of cancer phenotypes related to the study. CohortDefinitions has the code related to developing the initial codelists using codelistgenerator. PhenotypeR contains the code to perform cohort diagnostics for phenotypes and PhenotypeRShiny contains the shiny to review results from PhenotypeR.
• 2_Study: please find there the relevant code to obtain the study results.
• 3_Reporting: please find there the code to visualise the results with the shiny app.

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First steps

1. Download this entire repository (you can download as a zip folder using Code -> Download ZIP, or you can use GitHub Desktop).

Running the cohort diagnostics using PhenotypeR

1. Navigate to PhenotypeR. Open the project PhenotypeR.Rproj in RStudio (when inside the project, you will see its name on the top-right of your RStudio session) in 1_Diagnostics/PhenotypeR
2. Open and work though the CodeToRun.R file which should be the only file that you need to interact with. Run the lines in the file, adding your database specific information and so on (see comments within the file for instructions). The last line of this file will run the study (source(here("RunStudy.R")).
3. After running you should then have a zip folder with results to share in your results folder OR you can use the RData file to review your results locally.

Running main study

1. Open the 2_Study folder and open OPTIMACancerIncidenceCharacterization.Rproj in RStudio (when inside the project, you will see its name on the top-right of your RStudio session)
2. Open and work though the CodeToRun.R file which should be the only file that you need to interact with. Run the lines in the file, adding your database specific information and so on (see comments within the file for instructions). The last line of this file will run the study (source(here("RunStudy.R")).
3. After running you should then have a zip folder with results to share in your results folder.