A model of within-host interactions between host resources, macroparasite infection and immune response

This project was designed to mathematically investigate the of different host parasite-mitigation strategies on host condition. The R code herein comprises:

An ODE model of within-host interactions between a macroparasite (e.g. helminth) infection, host resource levels and host immune response, and the consequent effects on host condition. In brief, resources are ingested and utilised by the host, leading to inceased condition. The host is infected by a parasite, which matures and establishes within the host; both age stages cause harm to the host, decreasing host condition. The presence of the parasite stimulates an immune response, which can either target larval or adult parasites (a resistance strategy), or ameliorate the harm they cause (a tolerance strategy). The host can also reduce resource intake in order to also reduce ingestion of parasite infective stages (an avoidance strategy). Resistance responses have an associated immunopathology, in that the immune response also harms ..., A mathematical model of within-host interactions between resources, parasite burden and immune response, and the consequences for host condition, was developed and coded using R. Simulations were carried out over a variety of parameter values to study the effects of different resource availabity, infection pressure, and parasite traits. In particular, the level of host investment in an immune response that maximised host condition was determined using the optim function., , # Resource-worm-immune model

[https://doi.org/10.5061/dryad.59zw3r2gx](https://doi.org/10.5061/dryad.59zw3r2gx)

## Overview

Users will usually:

1. Set parameters in RWI_Parameters.R
2. Use RWI_Dynamics.R to calculate trajectories for various parameters sets and plot them as heat maps (time on x-axis, host investment on y-axis, dependent parameter on z-axis)
3. Use RWI_Compare.R to calculate optimal host investment in different strategies under different parameter values
4. Use RWI_PlotOutput.R to plot results of using RWI_Compare.R

The code uses R packages tidyverse (Wickham et al. 2019) and deSolve (Soetaert et al. 2010).

## Code files (uploaded to Zenodo)

##### RWI\_Parameter.R

Contains default parameter values and mathematical models needed to perform simulations. See the associated article for a model description and derivation.

* The time period over which to carry out simulations can be changed by resetting tmax.
* For some parameters, solutions are required over ...