library(ramp.xds)Dynamic Components
In developing a modular framework for model building, we identified five core processes. In ramp.xds, these are handled in three chunks, called COMPONENTS.
XH – Human / Vertebrate Hosts (see The XH Component)
\(\cal X\) – a state space for infection dynamics, immunity, disease, and related processes;
\(\cal H\) – a set of processes to represent host demographic processes, including births, deaths and aging
MY – Adult mosquitoes (see The MY Component)
\(\cal Y\) – a state space describing infection dynamics
\(\cal M\) – a state space describing mosquito ecology
L – Aquatic mosquitoes (see The L Component)
- \(\cal L\) – a state space describing aquatic mosquito ecology
The first step in setting up a model is to determine what module to use for each component.
Each chunk handles its own tasks, such as setting up and indexing variables, computing the derivatives, and parsing outputs. Each COMPONENT has its own design elements to handle a specific set of challenges associated with model building to serve the needs of malaria analysts. Some of these functions are also useful for research on malaria and other mosquito-transmitted pathogens.
XH Component
The X Component is specified by setting Xname = model_name, where model_name is a string that defines the class for S3 methods.
For example:
sis_mod <- xds_setup(Xname = "SIS")In basic setup, the H component is set to a trivial model with no births and no deaths.
MY Component
The MY Component is specified by setting MYZname = model_name, where model_name is a string that defines the class for S3 methods, or equivalently, a model family in ramp.xds or ramp.library
For example:
macdonald_mod <- xds_setup(MYZname = "macdonald")L Component
The L Component is specified by setting Lname = model_name, where model_name is a string that defines the class for S3 methods.
For example:
aqua_mod <- xds_setup(Lname = "basicL")