Model ensembles with different response variables for base and meta models: malaria disaggregation regression combining prevalence and incidence data

Maps of infection risk are a vital tool for the elimination of malaria. Routine surveillance data of malaria case counts, often aggregated over administrative regions, is becoming more widely available and can better measure low malaria risk than prevalence surveys. However, aggregation of case counts over large, heterogeneous areas means that these data are often underpowered for learning relationships between the environment and malaria risk. A model that combines point surveys and aggregated surveillance data could have the benefits of both but must be able to account for the fact that these two data types are different malariometric units. Here, we train multiple machine learning models on point surveys and then combine the predictions from these with a geostatistical disaggregation model that uses routine surveillance data. We find that, in tests using data from Colombia and Madagascar, using a disaggregation regression model to combine predictions from machine learning models trained on point surveys improves model accuracy relative to using the environmental covariates directly.