[create-pull-request] automated change

Author: paucablop

docs/ExtendedKalmanFilter.md

@@ -0,0 +1,37 @@
+# ExtendedKalmanFilter
+
+
+
+
+## Methods
+
+
+### __init__
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+measurement_covariance |  | 
+model_covariance |  | 
+
+
+
+
+
+### calculate
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+measurements |  | 
+
+
+
+

docs/MassBalance.md

@@ -0,0 +1,40 @@
+# MassBalance
+
+
+
+
+## Methods
+
+
+### __init__
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+microbial_kinetics |  | 
+inlet |  | 
+outlet |  | 
+
+
+
+
+
+### calculate
+
+
+Calculates the mass balance for a given kinetic rate list. 
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+concentrations |  | 
+time |  | 
+
+
+
+

docs/README.md

@@ -2,41 +2,63 @@
 
 ## Classes
 
+**[YeastModel](YeastModel.md)**: 
+
+**[MassBalance](MassBalance.md)**: 
+
 **[RangeCut](RangeCut.md)**: Cuts a dataframe selecting the wavenumbers between start and end. 
 
 **[Derivative](Derivative.md)**: Calculates the derivative of a each row in a dataframe using the Savitzky-Golay filter. 
 
+**[ExtendedKalmanFilter](ExtendedKalmanFilter.md)**: 
+
 
 ## Functions
 
-### test_range_cut
+### test_ir_train_loadings
 
 
-Test the range cut. 
+Test the loading of the training data. 
 
 
 
 
-### test_derivate
+### test_ir_fermentation_loadings
 
 
-Test the derivative. 
+Test the loading of the fermentation data. 
 
 
 
 
-### test_train_loadings
+### test_fluorescence_loadings
 
 
-Test the loading of the training data. 
+Test the loading of the fluorescence data 
 
 
 
 
-### test_fermentation_loadings
+### test_range_cut
+
+
+Test the range cut. 
+
+
+
+
+### test_derivate
+
+
+Test the derivative. 
+
+
+
+
+### load_pls_glucose_model
+
 
 
-Test the loading of the fermentation data. 
 
 
 
@@ -55,31 +77,45 @@ y | dataframe containing the reference hplc measurements. |
 
 
 
-### load_train_data
+### plot_mechanistic_fermentation
 
 
-Loads the train data. 
+Plots the predicted concentration and the reference hplc measurements. 
+#### Parameters
+name | description | default
+--- | --- | ---
+prediction | load the predictions. | 
+fermentation_hplc | load the reference hplc measurements. | 
+time |  | 
+concentrations |  | 
+
 
 
 
 
-### load_fermentation_data
+### plot_pls_fermentation
 
 
-Loads the fermentation data. 
+Plots the predicted concentration and the reference hplc measurements. 
+#### Parameters
+name | description | default
+--- | --- | ---
+prediction | load the predictions. | 
+fermentation_hplc | load the reference hplc measurements. | 
 
 
 
 
-### plot_fermentation
 
+### plot_pls_training
 
-Plots the predicted concentration and the reference hplc measurements. 
+
+Plots the PLS predictions and the reference hplc measurements for the training set. 
 #### Parameters
 name | description | default
 --- | --- | ---
-prediction | load the predictions. | 
-fermentation_hplc | load the reference hplc measurements. | 
+predictions | predicted concentrations. | 
+reference | reference hplc measurements. | 
 
 
 
@@ -101,16 +137,42 @@ ylabel | y-axis label |
 
 
 
-### plot_predictions
+### load_filtered_fluorescence_data
 
 
-Plots the PLS predictions and the reference hplc measurements for the training set. 
-#### Parameters
-name | description | default
---- | --- | ---
-predictions | predicted concentrations. | 
-reference | reference hplc measurements. | 
+returns the emission - excitation matrix for the filtered data 
+
+
+
+
+### load_unfiltered_fluorescence_data
+
 
+returns the emission - excitation matrix for the filtered data 
+
+
+
+
+### load_training_data
+
+
+Loads the training data. 
+
+
+
+
+### load_fermentation_spectra_data
+
+
+Loads the fermentation data. 
+
+
+
+
+### load_fermentation_hplc_data
+
+
+Loads the fermentation data. 
 
 
 

docs/YeastModel.md

@@ -0,0 +1,40 @@
+# YeastModel
+
+
+
+
+## Methods
+
+
+### __init__
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+model_type |  | 
+substrate_biomass_yield |  | 
+substrate_product_yield |  | 
+
+
+
+
+
+### calculate_rates
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+substrate_concentration |  | 
+biomass_concentration |  | 
+
+
+
+