tc13/worm-inference

Models to infer helminth worm burden at the community level

helminth inference model

Code and data to reproduce analysis in "Diagnosis of helminths is dependent on worm fecundity and the distribution of parasites within hosts" by Crellen T et al. 2023 Proc Roy Soc B be run using R and Stan.

This models the relationship between total helminth worm burden within a host and egg output as a power law (PL) function. The code can model seperate relationships for surveys in different populations (Thailand and Laos in this analysis).

Code for the inference model is contained within helminth-inference.stan, which is run using CmdStanR from run-helminth-model.R

The posterior model output in .rds format can then be parsed using Rscripts Figure1.R and Figure2.R to replicate figures in the paper.

The file containing the necessary dataset datasets.csv must be downloaded from Dryad.