diff --git a/docs/source/markdown/Recreate_data_from_scratch.md b/docs/source/markdown/Recreate_data_from_scratch.md index 5f1ffac..20660ad 100644 --- a/docs/source/markdown/Recreate_data_from_scratch.md +++ b/docs/source/markdown/Recreate_data_from_scratch.md @@ -2,11 +2,11 @@ ## Recreate Figure 2 from the PeakPerformance publication -Navigate to `docs/source/notebooks` and run the `Create_results_in_figure_2.ipynb` notebook. - +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: +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 @@ -16,11 +16,11 @@ Both sections walk through the following sequential steps: ## 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`. - +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. - +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.