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Evaluating faecal egg count reduction using a specifically designed package "eggCounts" in R and a user friendly web interface


Torgerson, Paul R; Paul, Michaela; Furrer, Reinhard (2014). Evaluating faecal egg count reduction using a specifically designed package "eggCounts" in R and a user friendly web interface. International Journal for Parasitology, 44(5):299-303.

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.

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.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Mathematics
05 Vetsuisse Faculty > Chair in Veterinary Epidemiology
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
510 Mathematics
Uncontrolled Keywords:Anthelmintic resistance; Bayesian hierarchical model; Faecal egg count reduction test; Mathematical techniques; Statistical analysis
Language:English
Date:2014
Deposited On:04 Apr 2014 09:41
Last Modified:04 Sep 2017 16:42
Publisher:Elsevier
ISSN:0020-7519
Publisher DOI:https://doi.org/10.1016/j.ijpara.2014.01.005
PubMed ID:24556564

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