Install ramp.func
To install the latest version from GitHub, run the following lines of code in an R session.
library(devtools)
devtools::install_github("dd-harp/ramp.func")Trace Functions
In ramp.func, the term trace function describes any function that sets the value of a parameter, variable, or term in a dynamical system. In models of malaria epidemiology, transmission dynamics, and control, it is often useful to isolate one of the dynamical components to study it in isolation, rather than study it as part of a dynamical system that is coupled to some other complex process. Typically, the trace function holds information from some other process: dynamical terms (e.g. the entomological inoculation rate), variables describing weather or vector control, or perturbations to a system.
The functions defined herein are used by other ramp packages:
These functions are used by
ramp.xdsand its satellite packageramp.forcingto configure forcing in the trivial modules.These functions are used by
ramp.falciparumfor exposure exposure.
Kernels
In ramp.xds, the term kernel describes any function we use to generate a probability mass function to model a spatial process:
Mosquito dispersal among patches in
ramp.xdsMosquito disperssal among points in
ramp.microHuman time spent matrices
Functional Responses
In developing a mathematical framework to model mosquito-transmitted pathogens, the ramp packages draw inspiration from ecology and other disciplines. One idea from ecology is a functional response, the shape of a function describing a consumption rate in response to resource availability. More generally, it is any function describing how a rate or probability varies in relation to some other variable. The functional response library here serves other roles as well:
blood feeding rates or egg laying rates in relation to the availability of blood hosts or aquatic habitats.
mosquito mortality rates in relation to temperature.