This README file explains how the code in this repository transforms and analyzes the data retrieved via Clinical Study Data Request (Proposal 11223) from the sponsor (Novartis) of the FREEDOMS and FREEDOMS II randomized clinical trials (RCT) to generate the PhD thesis of Begum Irmak On submitted to LMU Munich.
Folder DataManagement
This folder contains SAS codes to transform the raw data tables, as shared by the sponsor, into datasets required for the analysis. In order to define the outcomes and choose/define the predictors, the data is described in the files named “basicdesc”.
Then, the selected predictors (“predictors”) and outcomes (“outcome”) are defined for the intention to treat (ITT) population, respectively for the FREEDOMS (“N2301”) and FREEDOMS II (“N2309”) trials.
Folder Analysis
This folder contains R codes to describe and analyze the predictors and outcomes tables to meet the objectives of the PhD thesis, namely predicting prognosis and response to fingolimod in relapsing-remitting multiple sclerosis patients.
To run the analysis, one only needs to run the 000_master.R, which sources all the other files. The session info can be found in SessionInfo.txt. The following .R files are sourced by the master, respectively:
- 00_paths_pckgs_functions defines all the paths, calls packages, and defines most of the user-defined functions
- 01_studyparam defines the meta-parameters used in the analysis
- 09_functions_report defines user-defined functions for reporting
- 10_import_convert imports the managed datasets and finalizes any data preprocessing, creating the ready-to-analyze datasets
- 20_describe describes the baseline predictors, outcome and missing data
- 40_select_mdl imputes the missing data, tunes hyperparameters, runs the benchmark study to select the modeling method and fits the best one to generate the final model for each outcome in the FREEDOMS dataset, and reports internal validation measures alongside the important variables
- 45_mdl_dtls reports the details of the finally selected models
- 50_evaluate_mdl_overall externally validates the prognostic aspects of the final models in the FREEDOMS II dataset
- 55_evaluate_mdl_counterfact creates the counterfactual dataset from FREEDOMS II and evaluates the treatment response predicted by the final models.
- 900_report reports the findings as Excel tables or colored and black and white figures
- _Trtsel_debug corrects a debug identified in functions in the Trtsel package.