On-demand Model Validation Built into Infectious Disease Early Warning
Systems: Malaria Forecasts in Ethiopia with R package epidemiar
Teklehaimanot Gebrehiwot
Bahir Dar University, Health, Development, and Anti-Malaria Association, Health, Development, and Anti-Malaria Association, Amhara Public Health Institute, Amhara National Regional State Health Bureau
Author ProfileAbstract
Developing and implementing a malaria early warning system that
integrates public health surveillance with monitoring of related
environmental factors is the goal of the Epidemic Prognosis
Incorporating Disease and Environmental Monitoring for Integrated
Assessment (EPIDEMIA) project. Collaborating with our Ethiopian partners
on requirements, we developed the R package epidemiar to provide a
generalized set of functions for disease forecasting, plus customized
code including a Google Earth Engine script for environmental data and
formatting scripts for distributable reports with maps and graphs. Since
2019, a local team at Bahir Dar University in Ethiopia has been using
EPIDEMIA to produce weekly malaria forecasting reports. Intensive
anti-malarial efforts in the Amhara region of Ethiopia have resulted in
declining malaria incidence, with a 75% decrease in cases between 2013
and 2018 (561,101 to 137,445 cases). In this context of potentially
changing malaria transmission patterns, continual model evaluation past
the initial model development is warranted. We built model validation
and assessment tools into the epidemiar R package for on-demand
evaluation for any historical period. Validation statistics included
Mean Error (ME), Mean Absolute Error (MAE), and proportion of
observations that fell inside the prediction intervals. Evaluation can
be made for one through n-week ahead predictions, and include
comparisons with two naïve models: persistence of last known value, and
average cases from that week of the year. Building validation into the
early warning system provides more opportunities to learn about the
model via the validation results. We can identify locations where the
models perform best with district-level results. With on-demand
implementation and time-range flexibility, we can also investigate how
accuracy changes over time, which is of particular interest in places
like Ethiopia with changing patterns and declining trends due to
anti-malarial programs.