Chronic heart disease

Intervention: a reduction in CHD incidence

Note

In this example, we will also use components from the vivarium_public_health.mslt.disease module.

Compared to the previous simulation, we will now add a chronic disease component, and replace the all-cause mortality rate intervention with an intervention that affects CHD incidence.

To add CHD as a separate cause of morbidity and mortality, we use the Disease component:

Add a chronic disease.

components:
    vivarium_public_health:
        mslt:
            disease:
                - Disease('CHD')

We then replace the ModifyAllCauseMortality intervention with the ModifyDiseaseIncidence intervention. We give this intervention a name (reduce_chd) and identify the disease that it affects (CHD). In the configuration settings, we identify this intervention by name (reduce_chd) and specify the scaling factor for CHD incidence (CHD_incidence_scale).

Add an intervention that reduces CHD incidence.

components:
    vivarium_public_health:
        mslt:
            intervention:
                - ModifyDiseaseIncidence('reduce_chd', 'CHD')
configuration:
    intervention:
        reduce_chd:
            # Reduce the CHD incidence rate by 5%.
            CHD_incidence_scale: 0.95

Finally, we add an observer to record CHD incidence, prevalence, and deaths, in both the BAU scenario and the intervention scenario. We use the Disease observer, identify the disease of interest by name (CHD), and specify the prefix for output files (mslt_reduce_chd).

Record CHD incidence, prevalence, and deaths.

components:
    vivarium_public_health:
        mslt:
            observer:
                - Disease('CHD')

configuration:
    observer:
        output_prefix: results/mslt_reduce_chd

Putting all of these pieces together, we obtain the following simulation definition:

The simulation definition for the BAU scenario and the intervention.

plugins:
    optional:
        data:
            controller: "vivarium_public_health.dataset_manager.ArtifactManager"
            builder_interface: "vivarium_public_health.dataset_manager.ArtifactManagerInterface"

components:
    vivarium_public_health:
        mslt:
            population:
                - BasePopulation()
                - Mortality()
                - Disability()
            disease:
                - Disease('CHD')
            intervention:
                - ModifyDiseaseIncidence('reduce_chd', 'CHD')
            observer:
                - MorbidityMortality()
                - Disease('CHD')

configuration:
    input_data:
        # Change this to "mslt_tobacco_maori_20-years.hdf" for the Maori
        # population.
        artifact_path: artifacts/mslt_tobacco_non-maori_20-years.hdf
        input_draw_number: 0
    population:
        # The population size here is the number of cohorts.
        # There are 22 age bins (0-4, 5-9, ..., 105-109) for females and for
        # males, making a total of 44 cohorts.
        population_size: 44
    time:
        start:
            year: 2011
        end:
            year: 2120
        step_size: 365  # In days
    intervention:
        reduce_chd:
            # Reduce the CHD incidence rate by 5%.
            CHD_incidence_scale: 0.95
    observer:
        output_prefix: results/mslt_reduce_chd

Running the model simulation

The above simulation is already defined in mslt_reduce_chd.yaml. Run this simulation with the following command:

simulate run model_specifications/mslt_reduce_chd.yaml

When this has completed, the output recorded by the MorbidityMortality observer will be saved in the file mslt_reduce_chd_mm.csv.

We can now plot the survival of this cohort in both the BAU and intervention scenarios, relative to the starting population, and see how the survival rate has increased as a result of this intervention.

The impact of reducing the CHD incidence rate by 5% on survival rate. Results are shown for the cohort of males aged 50-54 in 2010. Compare this to the impact of reducing all-cause mortality rate by 5%.

The output recorded by the Disease observer will be saved in the file reduce_chd_disease.csv. The contents of this file will contain the following results:

An extract of the CHD statistics, showing a subset of rows for the cohort of males aged 50-54 in 2010.

Disease	Year of birth	Sex	Age	Year	BAU Incidence	Incidence	BAU Prevalence	Prevalence	BAU Deaths	Deaths	Change in incidence	Change in prevalence
…
CHD	1959	male	52	2011	0.004984	0.004735	0.03664	0.03664	0.0	0.0	-0.000249	0.0
CHD	1959	male	53	2012	0.005339	0.005072	0.04121	0.040955	0.6	0.6	-0.000267	-0.000254
CHD	1959	male	54	2013	0.005698	0.005413	0.046049	0.04553	1.2	1.2	-0.000285	-0.000519
…
CHD	1959	male	108	2067	0.038684	0.03675	0.185506	0.18575	692.3	674.8	-0.001934	0.000243
CHD	1959	male	109	2068	0.038684	0.03675	0.181912	0.182606	705.3	687.8	-0.001934	0.000695
CHD	1959	male	110	2069	0.038684	0.03675	0.178933	0.180058	717.5	700.1	-0.001934	0.001126
…