Companion code to "Multiscale Computational Modeling of the Cardiopulmonary Consequences of Postnatal Hyperoxia with Implications for Preterm Born Children"
!Flags to note!:
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line 75 in model_sol: reduces computational time for sensitivity analysis and optimization by bypassing the steady-state algorithm. Comment OUT to allow for the steady-state algorithm to run.
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line 64 and lines 467-470 in model_sol: try-catch is useful when running the sensitivity analysis and optimization. However, try-catch can mask bugs and errors when simply running the model via RUN_Cardiovascular_Mechanics, in which case it should be commented OUT.
RUN_Cardiovascular_Mechanics: runs the selected animals for nominal or optimized parameters. Calls plot_PV_loops to plot the model PV-loop output with the PV-loop data.
RUN_sensitivity: runs the local sensitivity analysis.
RUN_optimization: runs the local and/or global optimization code.
RUN_force_Ca: runs the model and plots the force-calcium curve.
plot_combined_sensitivities: Plots boxplots of the sensitivities for each parameter for all Nx and Hx animals. Corresponds to Figure 2 in the companion manuscript.
plot_optimized_pars: plots boxplot comparisons of the optimized parameters for Nx vs Hx. Corresponds to Figure 5 in the companion manuscript.
plot_figure_6_8: plots myofiber power comparisons as boxplots and scatter plots to understand correlations. Corresponds to Figure 6 and 8 in the companion manuscript.
plot_curvature: plots the septal curvature and the relative shortening for the LV, septum, and RV. Corresponds to Figure 7 in the companion manuscript.
Functions:
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make_data_structure_P21: intakes animal id and excel data and generates a corresponding data structure for use in the model.
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plot_PV_loops: intakes the experimental data and simulation results to output figures with the experimental data and model simulations together. Corresponds to Figure 4 in the companion manuscript.
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plot_pv_timecourse: similar to plot_PV_loops but plots the pressure and volume signals.
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load_outputs: unpacks the outputs data structure.
Data:
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P21_data_input.xlsx: excel table containing the data for parameterizing the model, extracted from the experimental data.
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raw_data (folder): raw data as .txt files, data smoothing code, smoothed data
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data (folder): processed data for use in model calibration
Folders:
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model: contains functions called by RUN_Cardiovascular_Mechanics that run and solve the model.
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opt_pars: stores the optimized parameters results from model calibration in RUN_optimization.
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outputs: stores the simulation results from RUN_Cardiovascular_Mechanics
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parameters: contains functions for nominal estimation of the parameters based on the data from P21_data_input.xlsx.
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sens_results: stores the sensitivity results from the local sensitivity analysis in RUN_sensitivity.
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sensitivity: contains functions used for the local sensitivity analysis in RUN_sensitivity.
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Figures: stores figures.
Environment: MATLAB R2024b