diff --git a/docs/ExtendedKalmanFilter.md b/docs/ExtendedKalmanFilter.md
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+++ b/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 |  | 
+
+
+
+
diff --git a/docs/MassBalance.md b/docs/MassBalance.md
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+++ b/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 |  | 
+
+
+
+
diff --git a/docs/PCAReport.md b/docs/PCAReport.md
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+++ b/docs/PCAReport.md
@@ -0,0 +1,150 @@
+# PCAReport
+
+
+
+
+## Methods
+
+
+### __init__
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+model |  | 
+X_train |  | 
+y_train |  | 
+X_test |  | None
+y_test |  | None
+wavenumbers |  | None
+
+
+
+
+
+### plot_data
+
+
+Plot spectra with optional color coding.   
+Parameters ---------- color_by : Optional[ArrayLike] Optional array for color coding the points. 
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+color_by |  | None
+title |  | "Spectra"
+x_label |  | "Wavenumber"
+y_label |  | "Intensity"
+
+
+
+
+
+### plot_preprocessed_data
+
+
+Plot preprocessed spectra with optional color coding.   
+Parameters ---------- color_by : Optional[ArrayLike] Optional array for color coding the points. 
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+color_by |  | None
+title |  | "Spectra"
+x_label |  | "Wavenumber"
+y_label |  | "Intensity"
+
+
+
+
+
+### _get_ellipse
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+x |  | 
+y |  | 
+ax |  | 
+n_std |  | 3
+edgecolor |  | "red"
+
+
+
+
+
+### plot_scores
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+color_by |  | None
+title |  | "PCA Scores"
+x_axis |  | 1
+y_axis |  | 2
+n_std |  | 3
+
+
+
+
+
+### plot_loadings
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+title |  | "PCA Loadings"
+
+
+
+
+
+### plot_scree
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+title |  | "Cumulative Explained Variance"
+
+
+
+
+
+### plot_residuals
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+color_by |  | None
+label_by |  | None
+title |  | "Residuals"
+
+
+
+
diff --git a/docs/PLSRegressionReport.md b/docs/PLSRegressionReport.md
new file mode 100644
index 0000000..acd8b55
--- /dev/null
+++ b/docs/PLSRegressionReport.md
@@ -0,0 +1,118 @@
+# PLSRegressionReport
+
+
+
+
+## Methods
+
+
+### __init__
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+model |  | 
+X_train |  | 
+y_train |  | 
+X_test |  | None
+y_test |  | None
+wavenumbers |  | None
+
+
+
+
+
+### plot_data
+
+
+Plot spectra with optional color coding.   
+Parameters ---------- color_by : Optional[ArrayLike] Optional array for color coding the points. 
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+color_by |  | None
+title |  | "Spectra"
+x_label |  | "Wavenumber"
+y_label |  | "Intensity"
+
+
+
+
+
+### plot_preprocessed_data
+
+
+Plot preprocessed spectra with optional color coding.   
+Parameters ---------- color_by : Optional[ArrayLike] Optional array for color coding the points. 
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+color_by |  | None
+title |  | "Spectra"
+x_label |  | "Wavenumber"
+y_label |  | "Intensity"
+
+
+
+
+
+### _get_ellipse
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+x |  | 
+y |  | 
+ax |  | 
+n_std |  | 3
+edgecolor |  | "red"
+
+
+
+
+
+### plot_residuals
+
+
+
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+color_by |  | None
+label_by |  | None
+title |  | "Residuals"
+
+
+
+
+
+### plot_prediction_results
+
+
+Plot prediction results for the PLS regression model.   
+Parameters ---------- None   
+Returns ------- None 
+
+#### Parameters
+name | description | default
+--- | --- | ---
+self |  | 
+color_by |  | None
+
+
+
+
diff --git a/docs/README.md b/docs/README.md
index 0b2fca8..5bafc60 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -2,68 +2,92 @@
 
 ## Classes
 
-**[RangeCut](RangeCut.md)**: Cuts a dataframe selecting the wavenumbers between start and end. 
+**[PCAReport](PCAReport.md)**: 
 
-**[Derivative](Derivative.md)**: Calculates the derivative of a each row in a dataframe using the Savitzky-Golay filter. 
+**[PLSRegressionReport](PLSRegressionReport.md)**: 
 
+**[YeastModel](YeastModel.md)**: 
 
-## Functions
+**[MassBalance](MassBalance.md)**: 
 
-### test_range_cut
+**[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. 
 
-Test the range cut. 
+**[ExtendedKalmanFilter](ExtendedKalmanFilter.md)**: 
 
 
+## Functions
 
+### plot_pls_fermentation
 
-### test_derivate
 
+Plots the predicted concentration and the reference hplc measurements. 
+#### Parameters
+name | description | default
+--- | --- | ---
+prediction | load the predictions. | 
+fermentation_hplc | load the reference hplc measurements. | 
 
-Test the derivative. 
 
 
 
 
-### test_train_loadings
+### plot_pls_training
 
 
-Test the loading of the training 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. | 
 
 
 
 
-### test_fermentation_loadings
 
+### plot_spectra
 
-Test the loading of the fermentation data. 
 
+Plots spectra. 
+#### Parameters
+name | description | default
+--- | --- | ---
+spectra | dataframe containing the spectra with the wavenumbers as columns. | 
+title | title of plot | 
+xlabel | x-axis label | 
+ylabel | y-axis label | 
 
 
 
-### cross_validation
 
 
-Performs cross-validation on the data. By default it performs a leave-one-out cross-validation. 
+### plot_mechanistic_fermentation
+
+
+Plots the predicted concentration and the reference hplc measurements. 
 #### Parameters
 name | description | default
 --- | --- | ---
-X | spectra dataframe containing the spectra with the wavenumbers as columns. | 
-y | dataframe containing the reference hplc measurements. | 
+prediction | load the predictions. | 
+fermentation_hplc | load the reference hplc measurements. | 
+time |  | 
+concentrations |  | 
 
 
 
 
 
-### load_train_data
+### load_training_data
 
 
-Loads the train data. 
+Loads the training data. 
 
 
 
 
-### load_fermentation_data
+### load_fermentation_spectra_data
 
 
 Loads the fermentation data. 
@@ -71,15 +95,62 @@ Loads the fermentation data.
 
 
 
-### plot_fermentation
+### load_fermentation_hplc_data
 
 
-Plots the predicted concentration and the reference hplc measurements. 
+Loads the fermentation data. 
+
+
+
+
+### load_filtered_fluorescence_data
+
+
+returns the emission - excitation matrix for the filtered data 
+
+
+
+
+### load_unfiltered_fluorescence_data
+
+
+returns the emission - excitation matrix for the filtered data 
+
+
+
+
+### extract_and_validate_model
+
+
+Validate and extract a PCA or PLS model, optionally from a pipeline.   
+This function checks whether the provided model or the final step in a pipeline is of the expected type (`PCA` or `PLSRegression`) and whether it has been fitted. It also separates any preceding pipeline steps (transformers) from the estimator.   
+Parameters ---------- model : BaseEstimator or Pipeline A fitted scikit-learn estimator or a Pipeline containing a PCA or PLSRegression model as the final step.   
+model_type : {'pca', 'pls'} The expected type of model. Must be one of 'pca' or 'pls'.   
+Returns ------- transformer : Pipeline or None A pipeline containing all steps before the final estimator if the input is a Pipeline. `None` if the input is not a pipeline.   
+estimator : PCA or PLSRegression The validated and fitted PCA or PLSRegression estimator.   
+Raises ------ ValueError If `model_type` is not 'pca' or 'pls'.   
+TypeError If the final model is not of the expected type.   
+NotFittedError If the estimator has not been fitted yet. 
 #### Parameters
 name | description | default
 --- | --- | ---
-prediction | load the predictions. | 
-fermentation_hplc | load the reference hplc measurements. | 
+model |  | 
+model_type |  | 
+
+
+
+
+
+### get_cut_wavenumbers_from_pipeline
+
+
+Retrieve the `cut_wavenumbers` attribute from a 'rangecut' step in a Pipeline, if present.   
+Parameters ---------- pipeline : Pipeline A scikit-learn Pipeline object.   
+Returns ------- cut_wavenumbers : Any or None The `cut_wavenumbers` attribute from the 'rangecut' step, or None if the step is absent. 
+#### Parameters
+name | description | default
+--- | --- | ---
+pipeline |  | 
 
 
 
@@ -88,29 +159,81 @@ fermentation_hplc | load the reference hplc measurements. |
 ### plot_spectra
 
 
-Plots spectra. 
+Plot spectra with optional color coding based on a scalar array.   
+Parameters ---------- x : ArrayLike The x-axis data (e.g., wavenumbers), shape (n_features,) y : ArrayLike The y-axis data (e.g., intensity values), shape (n_samples, n_features) color_by : Optional[ArrayLike], optional Optional array of shape (n_samples,) for color coding the lines. title : str, optional Title of the plot (default is "Spectra"). x_label : str, optional Label for the x-axis (default is "Wavenumber"). y_label : str, optional Label for the y-axis (default is "Intensity").   
+Returns ------- fig : matplotlib.figure.Figure The figure object. ax : matplotlib.axes._axes.Axes The axes object. 
 #### Parameters
 name | description | default
 --- | --- | ---
-spectra | dataframe containing the spectra with the wavenumbers as columns. | 
-title | title of plot | 
-xlabel | x-axis label | 
-ylabel | y-axis label | 
+x |  | 
+y |  | 
+color_by |  | None
+title |  | "Spectra"
+x_label |  | "Wavenumber"
+y_label |  | "Intensity"
 
 
 
 
 
-### plot_predictions
+### cross_validation
 
 
-Plots the PLS predictions and the reference hplc measurements for the training set. 
+Performs cross-validation on the data. By default it performs a leave-one-out cross-validation. 
 #### Parameters
 name | description | default
 --- | --- | ---
-predictions | predicted concentrations. | 
-reference | reference hplc measurements. | 
+X | spectra dataframe containing the spectra with the wavenumbers as columns. | 
+y | dataframe containing the reference hplc measurements. | 
+
+
+
+
+
+### load_pls_glucose_model
+
+
+
+
+
+
+
+### test_range_cut
+
+
+Test the range cut. 
+
+
+
+
+### test_derivate
+
+
+Test the derivative. 
+
+
+
+
+### test_ir_train_loadings
+
+
+Test the loading of the training data. 
+
+
+
+
+### test_ir_fermentation_loadings
+
+
+Test the loading of the fermentation data. 
+
+
+
+
+### test_fluorescence_loadings
+
 
+Test the loading of the fluorescence data 
 
 
 
diff --git a/docs/YeastModel.md b/docs/YeastModel.md
new file mode 100644
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@@ -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 |  | 
+
+
+
+