Historical Epidemiological Data

Cases and deaths

site_file$cases_deaths

World Malaria Report cases and deaths estimates.

Variables

wmr_cases_l WMR case estimate, lower bound
wmr_cases WMR case point estimate
wmr_cases_u WMR case estimate, upper bound
wmr_deaths_l WMR death estimate, lower bound
wmr_deaths WMR death point estimate
wmr_deaths_u WMR death estimate, upper bound
wmr_par WMR population at risk estimates
wmr_incidence_l WMR case incidence estimate, lower bound
wmr_incidence WMR case incidence point estimate
wmr_incidence_u WMR case incidence estimate, upper bound
wmr_mortality_l WMR malaria mortality rate estimate, lower bound
wmr_mortality WMR malaria mortality rate point estimate
wmr_mortality_u WMR malaria mortality rate estimate, upper bound

Description

Time series take all information from the most recent WMR. Older entries are from previous editions of the WMR.

Sources

⚕️ | WHO

Prevalence

site_file$prevalence

Plasmodium falciparum and Plasmodium vivax prevalence estimates

Variables

pfpr Plasmodium falciparum parasite prevalence in 2-10 year olds
pvpr Plasmodium vivax parasite prevalence in 1-99 year olds

Description

Pixel-level estimates of prevalence indicators are aggregated at the site-level by taking the population at risk weighted average.

Prevalence estimates are used for calibrating the baseline EIR using the cali package.

Sources

🌍 | MAP

Entomological inoculation rate (EIR)

site_file$eir

The calibrated baseline entomological inoculation rate (EIR) for each site.

Variables

sp Malaria species the EIR applies to (pf = Plasmodium falciparum, pv = Plasmodium vivax)
eir Calibrated baseline annual entomological inoculation rate (infectious bites per person per year)

Description

The baseline EIR is the key parameter setting transmission intensity in the model. It is not observed directly: for each site (and species) it is calibrated so that the simulated parasite prevalence matches the MAP prevalence estimates (2010–2024) using the cali package.

Sources

🌍 | MAP

Bias correction

site_file$bias_correction

Annual factors used to reconcile modelled case and death counts with the WHO World Malaria Report estimates.

Variables

year Year
case_bias_correction Multiplicative correction applied to modelled cases
death_bias_correction Multiplicative correction applied to modelled deaths

Description

Modelled clinical case and death counts do not exactly reproduce the country-level totals reported in the World Malaria Report. These annual factors rescale the modelled output so that it aligns with the reported WHO burden.

Sources

⚕️ | WHO