model_introduction.Rmd
malariasimple
is a time-discrete, compartmental
approximation of the individual-based malariasimulation
model. This vignette provides a high level overview of the human model
as it is most different from malariasimulation
. An overview
of mosquito biology can be found here.
A more comprehensive overview can be found in Griffin
et al. 2010 (especially Supplementary Information - Protocol 1).
malariasimple
models the target population as divided
into seven compartments defined by disease status. These are:
Each disease compartment is divided into many subcompartments along three axes according to:
They are not necessarily the same width.
Susceptiblity sub-compartments
Within each human sub-compartment, the population is considered a homogeneous unit. Population is defined as a fraction of the total population such that the sum of all compartments across all disease states at a given timestep will always equal 1.
Note in intervention compartments
The population proportion in each compartment is defined in the input parameters, and will stay constant throughout the simulation. Hence, the proportion in each intervention category does not necessarily represent the proportion receiving an intervention at any given time, but rather the population who will receive the intervention at some point during the simulation. In the case of SMC, treatments are only applied to compartments that are in both SMC intervention types and SMC-eligible age-brackets. Hence compartments in the SMC intervention type that are over the maximum SMC age at the first SMC administration will never receive SMC.
At each timestep, some proportion of the population will move between disease states. Transitions occur between corresponding subcompartments (i.e. S111 –> D111)
New births occur into the susceptible state, across sub-compartments
within the youngest age group. malariasimple
currently
assumes an exponential population distribution and no malaria-caused
deaths. As such, the death rate is equal across all compartments and
sub-compartments. New births equal total deaths in each time step, hence
the population remains constant.