Characterising the pre-clinical phase of inflammatory bowel disease

Read me file for the project: An overview of the code.

The files are ordered by numbers. 
- 1: Code file to prepare helper datasets. These datasets are saved in the "temp" folder
- 2: Code file for matching of cases and controls. Both for the general analysis, for the sensitivity analysis using the 2-diagnoses definition (2 IBD dianoses within a 2-year period) and for generation of Charlson's co-morbidity index. The datasets are saved in the main folder 
- 3: Code file for all statistical analyses for all clinical features (one script per feature). Tables of the results are saved in the "results" folder.
- 4: Generations of plots for visualisation of data and analyses performed so far. Also including the code for making figure 1, S1, S2, S3 and S4.
- 5: Code file for the extended analysis, where several features are combined in prediction model. Includes the selection of number of features, the new matching (cases and controls should have a measure of all features within the same time interval), logisitc regression, Random Forest analyses, SVM analyses and the generation of figure 2 and S5.
- 6: Code for making table 1.