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 the host. Code to plot model trajectories over
time. Code to plot multiple trajectories as a heat map, in which the
x-axis is time and the y-axis is a parameter representing the host
investment in its parasite-mitigation strategy. Code to calculate the
optimum host investment for each strategy, over various sets of parameter
values, as determined by maximising mean host condition over a given
timeframe, and to plot the output. The same are also provided for an ODE
model in which the total immune response is allocated between the two
resistance responses and tolerance (a combined strategy). The optimisation
code optimises both the total investment in immune repsonse, and how much
is allocated to the three different individual strategies. The model and
results are described in detail in the associated manuscript. We also
provide here the simulated datasets in which the optimum host investments
were calculated over a range of different parameter values, as these take
several hours to run on a standard desktop computer..