add docu section about recreating results from raw data

docs/source/index.md

@@ -51,8 +51,9 @@ You can also download the latest version from [GitHub](https://github.com/JuBiot
 
 markdown/Preparing_raw_data
 markdown/Peak_model_composition
-markdown/PeakPerformance_validation
 markdown/PeakPerformance_workflow
+markdown/PeakPerformance_validation
+notebook/Recreate_data_from_scratch
 markdown/Diagnostic_plots
 markdown/How_to_adapt_PeakPerformance_to_your_data
 ```

docs/source/markdown/Recreate_data_from_scratch.md

@@ -0,0 +1,26 @@
+# Recreate the presented data in paper and documentation from scratch
+
+## Recreate Figure 2 from the PeakPerformance publication
+
+Navigate to `docs/source/notebooks` and run the `Create_results_in_figure_2.ipynb` notebook.  
+
+It is separated into two sections which work and are structured in an analogous manner.
+The first creates the results figure for the single peak and the second for the double peak.
+Both sections walk through the following sequential steps:  
+  1. open and plot example raw data
+  2. define a model
+  3. perform both sampling and posterior predictive sampling
+  4. display the summary DataFrame containing the results of the peak fitting
+  5. display cumulative plot of the posterior predictive check
+  6. display the posterior predictive check and the peak fit against the raw data points.
+
+## Recreate the validation plot from the documentation
+
+To actually recreate the validation plot, navigate to `docs/source/notebooks` and run the notebook `Create_validation_plot_from_raw_data.ipynb`.  
+
+However, not all data loaded in this notebook is raw data.
+Particularly, the data from the first stage of validation using synthetic data sets is pre-processed based on the results of said test using the notebook `Processing_test_1_raw_data.ipynb`.
+Since all necessary files are present for both notebooks, they can be run in any order.  
+
+Also, the data for the comparison with the commercial software MultiQuant in the third stage of validation is contained in `docs/source/notebooks/test3_df_comparison.xlsx`.
+The `PeakPerformance` results listed in this file have been obtained by executing a batch run with the raw data stored in `docs/source/notebooks/paper raw data` using the settings detailed in the `Template.xlsx` file in the same directory.