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docs/ExtendedKalmanFilter.md

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# ExtendedKalmanFilter
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## Methods
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### __init__
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#### Parameters
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name | description | default
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--- | --- | ---
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self | |
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measurement_covariance | |
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model_covariance | |
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### calculate
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#### Parameters
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name | description | default
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--- | --- | ---
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measurements | |
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docs/MassBalance.md

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# MassBalance
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## Methods
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### __init__
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#### Parameters
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name | description | default
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--- | --- | ---
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self | |
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microbial_kinetics | |
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inlet | |
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outlet | |
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### calculate
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Calculates the mass balance for a given kinetic rate list.
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#### Parameters
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name | description | default
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--- | --- | ---
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self | |
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concentrations | |
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time | |
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docs/README.md

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

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# YeastModel
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## Methods
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### __init__
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#### Parameters
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name | description | default
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self | |
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model_type | |
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substrate_biomass_yield | |
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substrate_product_yield | |
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### calculate_rates
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#### Parameters
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name | description | default
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--- | --- | ---
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self | |
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substrate_concentration | |
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biomass_concentration | |
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