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MODY-calculator-clinical-paper

This repository contains the code for

  • Make predictions for new patients.
  • Generating analysis and plots.

Folder structure

  1. data: folder containing the data used for the analysis (empty as data cannot be shared)

  2. figures: folder containing figures used for the manuscript

  3. model_development: R code and model fitting objects (several models are included based on the different models fitted for the article)

  4. model_predictions: Vectors containing MODY probability estimations for all of the datasets used (_full.rds represents the full posterior dataset, its omission represents the summary results (2.5%, mean, 97.5%))

  5. new_data_predictions: R code + data + Excel document for making predictions in new datasets

  6. bootstrap_riley_simulation: R code for a simulation study on stability of model predictions based on bootstrapped datasets.

File explanation

  • discrimination_curves.R: this file contains the R code for calculating and plotting ROC and Precision-recall curves.
  • bootstrap_validation_analysis.R: this file contains the R code for making calibration plots of bootstrapped datasets.
  • model_convergence.R: this file contains the R code for checking model convergence in the main models used for this analysis.
  • calibration_plots.R: this file contains the R code for creating the calibration plots for the datasets used.
  • CPRD_analysis.R: this file contains the R code for plotting density plots for probability of MODY.
  • antibody_sensitivity_analysis.R: this contains the R code for plotting probabilities of MODY based on different antibody information availability.