Finalising doc tests

docs/source/getting_started/code/3_fitting_models_1.py

@@ -14,6 +14,100 @@
 # Parse!
 args = parser.parse_args()
 
+# Run testing verion of script
+if args.test:
+    # 1
+    import os
+
+    import chi
+    import numpy as np
+    import plotly.graph_objects as go
+
+
+    # Implement the model
+    directory = os.path.dirname(__file__)
+    filename = os.path.join(directory, 'one_compartment_pk_model.xml')
+    model = chi.PKPDModel(sbml_file=filename)
+    model.set_outputs(['global.drug_concentration'])
+
+    # Set administration and dosing regimen
+    model.set_administration(compartment='global', direct=False)
+    model.set_dosing_regimen(dose=2, period=1)
+
+    # Simulate treatment response
+    parameters = [0, 0, 10, 1, 2]
+    times = np.linspace(start=0, stop=3, num=200)
+    conc = model.simulate(parameters=parameters, times=times)[0]
+
+    # Plot results
+    fig = go.Figure()
+    fig.add_trace(go.Scatter(
+        x=times,
+        y=conc,
+        mode='lines',
+    ))
+    fig.update_layout(
+        xaxis_title='Time',
+        yaxis_title='Drug concentration',
+        template='plotly_white'
+    )
+    # fig.show()
+
+    # directory = os.path.dirname(os.path.dirname(__file__))
+    # fig.write_html(directory + '/images/3_fitting_models_1.html')
+
+
+    ### Generate synthetic data
+    directory = os.path.dirname(__file__)
+    filename = os.path.join(directory, 'two_compartment_pk_model.xml')
+    model = chi.PKPDModel(sbml_file=filename)
+    model.set_administration(compartment='central', direct=False)
+    model.set_outputs(['central.drug_concentration'])
+
+    # Synthethise data
+    error_model = chi.LogNormalErrorModel()
+    model = chi.PredictiveModel(
+        mechanistic_model=model, error_models=[error_model])
+    model.set_dosing_regimen(dose=2, period=1)
+
+    parameters = [0, 0, 0, 2, 10, 1, 5, 1, 10, 0.1]
+    times = [0.5, 1, 1.5, 2, 2.5, 3]
+    df = model.sample(
+        parameters=parameters, times=times, seed=1, include_regimen=True)
+
+    # Save data (Only do this once, because I added some units changed names)
+    # directory = os.path.dirname(__file__)
+    # df.to_csv(directory + '/dataset_1.csv', index=False)
+
+
+    # 2
+    import pandas as pd
+
+
+    # Import data
+    directory = os.path.dirname(__file__)
+    data = pd.read_csv(directory + '/dataset_1.csv')
+
+    # Plot data
+    fig = go.Figure()
+    fig.add_trace(go.Scatter(
+        x=data.Time,
+        y=data.Value,
+        mode='markers',
+    ))
+    fig.update_layout(
+        xaxis_title='Time in day',
+        yaxis_title='Drug concentration in ng/mL',
+        template='plotly_white'
+    )
+    # fig.show()
+
+    # directory = os.path.dirname(os.path.dirname(__file__))
+    # fig.write_html(directory + '/images/3_fitting_models_2.html')
+
+    # Exit script
+    exit()
+
 # 1
 import os