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Rarefaction-Extrapolation of St. Lawrence Island Flora

R script for producing rarefaction curve and extrapolating estimated species richness using iNEXT R package for the Flora of St. Lawrence Island, Alaska. This script was developed for the following paper:

Carlson, M.L., E.J. Trammell, T.W. Nawrocki, and E. Noongwook. 2018. Additions to the Vascular Plant Flora of St. Lawrence Island, Alaska: New Records, Rare Species, and Phytogeographic Patterns. Rhodora. 120:1-41.

Getting Started

These instructions will enable you to run the RichnessRarefactionExtrapolation.R script.

Prerequisites

  1. R 3.4.3+
  2. iNEXT R Package
  3. ggplot2
  4. RStudio 1.1.423+

Installing

Download this repository and unzip it to a folder on a drive accessible to your computer. Local drives may perform better than network drives.

Open the script in RStudio to run. Although the script will self-install iNEXT and ggplot2, we recommend manually installing both packages prior to running the script.

Usage

Individual-based rarefaction and extrapolation of herbarium record dataset

  • Data must be formatted prior to use in this script. See the example file included in the repository (VoucherCount.csv).
  • Script should be run from RStudio. Future development should allow execution of script as stand-alone executable.

Credits

Built With

Authors

  • Timm Nawrocki - Alaska Center for Conservation Science, University of Alaska Anchorage

Usage Requirements

This script uses the iNEXT R Package, which is also available on CRAN. We encourage potential users of this script to read the documentation of iNEXT.

If you use this script, elements of this script, or a derivative product, please cite the following:

Chao, A., N. Gotelli, T. Hsieh, E. Sander, K. Ma, R. Colwell, and A. Ellison. 2014. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecological Monographs. 84: 45–67.

Hsieh, T., K. Ma, and A. Chao. 2016. iNEXT: An R package for interpolation and extrapolation of species diversity (Hill numbers). Methods in Ecology and Evolution. 7: 1451–1456.

License

This project is provided under the GNU General Public License v3.0. It is free to use and modify in part or in whole.