Advanced Setup
Advanced setup handles a large set of model features to add realism or implement malaria control. This is an overview. The topics are covered in detail in separate vignettes that are also accessible from the sidebar menu.
Heterogeneity
In developing a framework for simulation-based analytics, we were concerned about heterogeneity in traits affect outcomes, especially age, care seeking, and drug taking. We wanted a framework that could handle heterogeneity of all sorts. Unfortunately, there is no simple way of describing heterogeneity nor a single way of handling it.
To paraphrase the opening line of Tolstoy’s novel, Anna Karenina,
All homogeneous models are alike; each heterogeneous model is heterogeneous in its own way.
Heterogeneity for human populations was developed around a set of issues that had been identified in the literature.
Heterogeneous Exposure: In their analysis of data collected from households in Nagongera Subcounty, Tororo District, Uganda, Cooper et al. described three kinds of heterogeneity [1]:
Seasonality describes differences in exposure over a year. This can caused by mosquito populations, but it could also be due to human behavioral differences.
Heterogeneous biting is a difference in the average rate of exposure. It is incorporated into the model as a multiplicative factor modifying exposure. It is a kind of epidemiological heterogeneity. In
ramp.xdsit is handled by stratifying a population.Environmental Heterogeneity describes variability in exposure for a homogeneous population stratum.
Epidemiological Heterogeneity describes differences in traits in a population that affect malaria outcomes, including age, heterogeneous biting, differences in travel habits, care seeking, and drug taking .
Human Demography
The default model is set up with no births and no deaths. Models for human demography can include:
Births & Deaths
Migration
Age Structure
Principled Stratification
Models that stratify a human population are handled through a system called principled stratification, including time spent, heterogeneous biting, age structure, or any other epidemiological traits.
Spatial Dynamics
Any model with nPatches\(>1\) is considered to have spatial dynamics. The patch structure describes mosquito activities, while humans are stratified by time spent.
Time Spent
In spatial models, each population stratum must define a vector that describes the fraction of time spent in every patch. The resulting matrix is called the Time Spent matrix. Functions to construct these matrices are described in Time Spent.
Mosquito Dispersal
Exposure
The module for Exposure in ramp.xds translates the daily local EIR for a set of homogeneous population strata into their daily FoI.
Heterogeneous biting is one part of heterogeneous exposure. It affects heterogeneous mixing – blood feeding and transmission – so it is handled through stratification and the blood feeding interface.
In Exposure, we handle environmental heterogeneity, exposure to malaria during travel, and pre-erythrocytic immunity.
See Exposure for an overview, and
Malaria Importation
Each population stratum can travel away from the spatial domain represented by the model and get exposed to malaria. In addition, malaria can be imported by infectious visitors.