SAMPLE: an R package to estimate sampling effort for species’ occurrence rates

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Species’ occurrence rates are the backbone of many ecological studies. Sampling of species occurrence, however, can come with challenges and might prove more difficult than anticipated. Logistical difficulties, limited funds or time, elusiveness or rarity of species and difficult sampling environments are all examples of scenarios that might contribute to (undesired) small sample sizes. In order to help circumvent some of these difficulties and uncertainties, we present SAMPLE , an R package that aims to inform the user whether the amount of sampling conducted is enough to accurately estimate the occurrence rate of species. We use a simulation approach to help verify the accuracy of the package and to help guide the user in choosing the most appropriate values for the available parameters. Moreover, we provide a real data set where we used SAMPLE to estimate the occurrence rate of various coral-dwelling species on their hosts and the minimum number of samples required for an accurate estimation. This provided example data set includes closely related host species, single or multiple symbionts on a single host coral taxon, and data points obtained from different depths to illustrate how occurrence rates can vary depending on the provided input. Due to its simplicity and easiness of use, this package allows for users to run it whilst in the field to estimate if sampling is sufficient or if the sampling approach needs to be adapted for a particular species. We hope that this package proves itself useful to users that need to estimate occurrence or prevalence rates of species and do not always have the possibility to obtain large sample sizes.

Authors 3

1. Henrique Bravo

   University of Groningen

   Affiliation as printed

   GELIFES, University of Groningen, Groningen, The Netherlands

2. Yacine Ben Chehida

   University of Groningen · University of Sheffield · University of York

   Affiliation as printed

   Department of Biology, University of York, Heslington, UK

   Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK

   GELIFES, University of Groningen, Groningen, The Netherlands

   Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 TN, UK

3. Sancia E. T. van der Meij Aachen Marine Biodiversity Group Naturalis Biodiversity Center

   University of Groningen · Naturalis Biodiversity Center

   Affiliation as printed

   GELIFES, University of Groningen, Groningen, The Netherlands

   Marine Biodiversity Group, Naturalis Biodiversity Center, Leiden, The Netherlands