simba/advanced_setup.qmd at main · dd-harp/simba · GitHub

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---
title: "Advanced Setup"
format: html
bibliography: data/refs.bib
csl: data/plos.csl
---

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 [@CooperL2019ParetoRules]:

    + **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.xds`  it 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](time_spent.qmd).

### Mosquito Dispersal

## Exposure

The module for [`Exposure`](exposure.qmd) 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](exposure.qmd) for an overview, and

+ [*Heterogeneous Biting*](heterogeneous_biting.qmd)

+ [*Environmental Heterogeneity*](environmental_heterogeneity.qmd)

+ [*Travel Malaria*](travel_malaria.qmd)

+ [*Pre-Erythrocytic Immunity*](travel_malaria.qmd)

## 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.*

+ [*Travel Malaria*](travel_malaria.qmd)

+ [*Visitors*](visitors.qmd)

## Vector Control

## Malaria Therapeutics

## Weather

## Habitat Dynamics

## Species *vs.* Strata

### Multiple Vector Species

### Multiple Host Species