Input data requirements¶
The data required for an MSLT model depend on the model components. Here, we define the data requirements for each type of component.
In general, rates and values are stored in tables with the following columns:
Note
For convenience, all of these input data can be collected into a single data artifact. For each of the tables described below, we identify the name under which it should be stored in a data artifact.
We will see how to use data artifacts in the MSLT tutorials.
Core MSLT¶
The cohorts and their population sizes are defined in the
population.structure table:
year |
age |
sex |
population |
bau_population |
2011 |
2 |
female |
108970.000 |
108970.000 |
2011 |
2 |
male |
114970.000 |
114970.000 |
2011 |
7 |
female |
105600.000 |
105600.000 |
2011 |
7 |
male |
110470.000 |
110470.000 |
… |
… |
… |
… |
… |
2011 |
102 |
female |
1035.000 |
1035.000 |
2011 |
102 |
male |
433.125 |
433.125 |
2011 |
107 |
female |
207.000 |
207.000 |
2011 |
107 |
male |
86.625 |
86.625 |
The age-specific, sex-specific mortality rates are defined in the
cause.all_causes.mortality table:
year_start |
year_end |
age_start |
age_end |
sex |
rate |
2011 |
2012 |
0 |
1 |
female |
0.003586 |
2011 |
2012 |
0 |
1 |
male |
0.004390 |
2011 |
2012 |
1 |
2 |
female |
0.000330 |
2011 |
2012 |
1 |
2 |
male |
0.000340 |
… |
… |
… |
… |
||
2120 |
2121 |
109 |
110 |
female |
0.524922 |
2120 |
2121 |
109 |
110 |
male |
0.529281 |
Note
Rates and other values that apply to specific cohorts during the simulation (i.e., all input data except for the initial cohort population sizes and initial disease/risk factor prevalence) are indexed by time intervals and age intervals.
In the mortality rate table shown above, the rate in each row applies:
From the time in year_start up to (but not including) the time in year_end; and
To cohorts whose age lies between age_start (inclusive) and age_end (exclusive).
Similarly, the age-specific, sex-specific disability rates are defined in the
cause.all_causes.disability_rate table:
year_start |
year_end |
age_start |
age_end |
sex |
rate |
2011 |
2012 |
0 |
1 |
female |
0.014837 |
2011 |
2012 |
0 |
1 |
male |
0.020674 |
2011 |
2012 |
1 |
2 |
female |
0.022379 |
2011 |
2012 |
1 |
2 |
male |
0.026409 |
… |
… |
… |
… |
||
2120 |
2121 |
109 |
110 |
female |
0.366114 |
2120 |
2121 |
109 |
110 |
male |
0.357842 |
Chronic diseases¶
For each chronic disease, the initial prevalence and disease-specific rates
are stored in the following tables (where the disease name is NAME).
The incidence rate (i) is stored in chronic_disease.NAME.incidence:
year_start |
year_end |
age_start |
age_end |
sex |
NAME_i |
2011 |
2012 |
0 |
1 |
female |
0.0 |
… |
… |
… |
… |
The disability rate (DR) is stored in chronic_disease.NAME.morbidity:
year_start |
year_end |
age_start |
age_end |
sex |
NAME_DR |
2011 |
2012 |
0 |
1 |
female |
0.0 |
… |
… |
… |
… |
The mortality rate (f) is stored in chronic_disease.NAME.mortality:
year_start |
year_end |
age_start |
age_end |
sex |
NAME_f |
2011 |
2012 |
0 |
1 |
female |
0.0 |
… |
… |
… |
… |
The initial prevalence is stored in chronic_disease.NAME.prevalence:
year |
age |
sex |
NAME_prev |
2011 |
0 |
female |
0.0 |
… |
… |
… |
… |
The remission rate (r) is stored in chronic_disease.NAME.remission:
year_start |
year_end |
age_start |
age_end |
sex |
NAME_r |
2011 |
2012 |
0 |
1 |
female |
0.0 |
… |
… |
… |
… |
Note
Note that the column names are different in each table.
Acute diseases and other events¶
For each acute disease/event, the morbidity and mortality rates are stored in
the following tables (where the disease/event names is NAME).
The morbidity rate is stored in acute_disease.NAME.morbidity:
year_start |
year_end |
age_start |
age_end |
sex |
NAME_disability_rate |
2011 |
2012 |
0 |
1 |
female |
0.000301 |
… |
… |
… |
… |
The mortality rate is stored in acute_disease.NAME.mortality:
year_start |
year_end |
age_start |
age_end |
sex |
NAME_excess_mortality |
2011 |
2012 |
0 |
1 |
female |
0.000032 |
… |
… |
… |
… |
Note
Note that the column names are different in each table.
Risk factors¶
The tobacco risk factor (as implemented by the
DelayedRisk component) requires
several data tables.
The incidence rate is stored in risk_factor.tobacco.incidence:
year_start |
year_end |
age_start |
age_end |
sex |
incidence |
2011 |
2012 |
0 |
1 |
female |
0.000301 |
… |
… |
… |
… |
The remission rate is stored in risk_factor.tobacco.remission:
year_start |
year_end |
age_start |
age_end |
sex |
remission |
2011 |
2012 |
0 |
1 |
female |
0.000301 |
… |
… |
… |
… |
The initial prevalence for each exposure category is stored in
risk_factor.tobacco.prevalence:
year |
age |
sex |
tobacco.no |
tobacco.yes |
tobacco.0 |
tobacco.1 |
… |
tobacco.20 |
tobacco.21 |
2011 |
0 |
female |
1.0 |
0.0 |
0.0 |
0.0 |
… |
0.0 |
0.0 |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
The relative risk of mortality for each exposure category (defined separately
for the BAU and intervention scenarios) is stored in
risk_factor.tobacco.mortality_relative_risk:
year_start |
year_end |
age_start |
age_end |
sex |
tobacco.no |
tobacco.yes |
… |
tobacco.21 |
tobacco_intervention.no |
tobacco_intervention.yes |
… |
tobacco_intervention.21 |
2011 |
2012 |
0 |
1 |
female |
1.0 |
1.0 |
… |
1.0 |
1.0 |
1.0 |
… |
1.0 |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
The relative risk of chronic disease incidence for each exposure category is
stored in risk_factor.tobacco.disease_relative_risk, which contains
separate columns for each chronic disease.
Shown here is an example for two chronic diseases, called DiseaseA and
DiseaseB:
year_start |
year_end |
age_start |
age_end |
sex |
DiseaseA_no |
DiseaseA_yes |
… |
DiseaseA_21 |
DiseaseB_no |
DiseaseB_yes |
… |
DiseaseB_21 |
2011 |
2012 |
0 |
1 |
female |
1.0 |
1.0 |
… |
1.0 |
1.0 |
1.0 |
… |
1.0 |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
Interventions¶
The TobaccoEradication
and TobaccoFreeGeneration
interventions don’t have any data requirements.
The tobacco tax intervention, however, is characterised in terms of its effect
on the incidence (i.e., uptake) and remission (i.e., cessation) rates.
The incidence effect is stored in
risk_factor.tobacco.tax_effect_incidence:
year_start |
year_end |
age_start |
age_end |
sex |
incidence_effect |
2011 |
2012 |
0 |
1 |
female |
1.0 |
2011 |
2012 |
0 |
1 |
male |
1.0 |
2011 |
2012 |
1 |
2 |
female |
1.0 |
2011 |
2012 |
1 |
2 |
male |
1.0 |
… |
… |
… |
… |
||
2120 |
2121 |
108 |
109 |
female |
0.866004 |
2120 |
2121 |
108 |
109 |
male |
0.866004 |
2120 |
2121 |
109 |
110 |
female |
0.866004 |
2120 |
2121 |
109 |
110 |
male |
0.866004 |
The remission effect is stored in
risk_factor.tobacco.tax_effect_remission:
year_start |
year_end |
age_start |
age_end |
sex |
remission_effect |
2011 |
2012 |
0 |
1 |
female |
1.0 |
2011 |
2012 |
0 |
1 |
male |
1.0 |
2011 |
2012 |
1 |
2 |
female |
1.0 |
2011 |
2012 |
1 |
2 |
male |
1.0 |
… |
… |
… |
… |
||
2031 |
2032 |
22 |
23 |
female |
0.975724 |
2031 |
2032 |
22 |
23 |
male |
0.975724 |
2031 |
2032 |
23 |
24 |
female |
0.975724 |
2031 |
2032 |
23 |
24 |
male |
0.975724 |
… |
… |
… |
… |
||
2120 |
2121 |
108 |
109 |
female |
1.0 |
2120 |
2121 |
108 |
109 |
male |
1.0 |
2120 |
2121 |
109 |
110 |
female |
1.0 |
2120 |
2121 |
109 |
110 |
male |
1.0 |