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.
These instructions will enable you to run the RichnessRarefactionExtrapolation.R script.
- R 3.4.3+
- iNEXT R Package
- ggplot2
- RStudio 1.1.423+
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.
- 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.
- R 3.4.2
- iNEXT R Package
- ggplot2
- RStudio 1.1.423
- Timm Nawrocki - Alaska Center for Conservation Science, University of Alaska Anchorage
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.
This project is provided under the GNU General Public License v3.0. It is free to use and modify in part or in whole.