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dietr: an R package for calculating fractional trophic levels from quantitative and qualitative diet data

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Abstract

This article introduces an R package, dietr, which calculates fractional trophic levels from quantitative diet item and qualitative food item data following the routine implemented in TrophLab within the open source R environment. dietr is easy to use and can quickly calculate trophic levels for many diet records. In addition to calculating trophic levels following the TrophLab routines, users can also specify a taxonomic hierarchy and estimate trophic levels at multiple taxonomic levels in a single call of a function. Additionally, dietr works well with FishBase data obtained in R using rfishbase and comes with pre-made databases of prey trophic levels that users can utilize for estimating trophic levels. dietr can also calculate several prey electivity indices. I provide information on dietr’s performance and provide a use case example of how dietr can be used on an empirical dataset. Trophic levels for hundreds of specimens can be calculated in a few seconds and the flexibility of dietr’s input allows users to easily calculate trophic levels from their own data.

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Data Availability

The code and data used to carry out the analysis are provided on the GitHub repository page for the package and are available here: https://github.com/sborstein/dietr.

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Acknowledgements

I would like to thank B. O’Meara, X. Giam, C. Lash, and the López-Fernández lab for their helpful discussions on the construction of the package and the manuscript. I would also like to thank E. Thanou for beta testing the software. Research was supported by the National Science Foundation DEB-1701913 and the Department of Ecology & Evolutionary Biology at the University of Tennessee.

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  1. Department of Ecology and Evolutionary Biology, University of Michigan, Biological Sciences Building 2020, Ann Arbor, MI, 48109, USA

    Samuel R. Borstein

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  1. Samuel R. Borstein
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Correspondence to Samuel R. Borstein.

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Borstein, S.R. dietr: an R package for calculating fractional trophic levels from quantitative and qualitative diet data. Hydrobiologia 847, 4285–4294 (2020). https://doi.org/10.1007/s10750-020-04417-5

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