title: Evaluating faecal egg count reduction using a specifically designed package "eggCounts" in R and a user friendly web interface.
abstract: The seemingly straightforward task of analysing faecal egg counts resulting from laboratory procedures such as the McMaster technique has, in reality, a number of complexities. These include Poisson errors in the counting technique which result from eggs being randomly distributed in well mixed faecal samples. In addition, counts between animals in a single experimental or observational group are nearly always over-dispersed. We describe the R package "eggCounts" that we have developed that incorporates both sampling error and over-dispersion between animals to calculate the true egg counts in samples of faeces, the probability distribution of the true counts and summary statistics such as the 95% uncertainty intervals. Based on a hierarchical Bayesian framework, the software will also rigorously estimate the percentage reduction of faecal egg counts and the 95% uncertainty intervals of data generated by a faecal egg count reduction test. We have also developed a user friendly web interface that can be used by those with limited knowledge of the R statistical computing environment. We illustrate the package with three simulated data sets of faecal egg count reduction experiments.
authors.affiliation: Section of Veterinary Epidemiology, Vetsuisse Faculty, University of Zurich, Switzerland. Electronic address: paul.torgerson@access.uzh.ch.
authors.forename: Paul R
authors.initials: PR
authors.lastname: Torgerson
authors.affiliation: Institute of Mathematics, University of Zurich, Switzerland.
authors.forename: Michaela
authors.initials: M
authors.lastname: Paul
authors.affiliation: Institute of Mathematics, University of Zurich, Switzerland.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Furrer
mesh_terms: D000818:Animals; D003627:Data Interpretation, Statistical; D005243:Feces / Q000469:parasitology*; D020407:Internet; D010270:Parasite Egg Count / Q000379:methods*; D021261:Parasitic Sensitivity Tests / Q000379:methods*; D012984:Software
keywords: Anthelmintic resistance; Bayesian hierarchical model; Faecal egg count reduction test; Mathematical techniques; Statistical analysis