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nichetools

{nichetools} is a complementary package to {nicheROVER} and {SIBER} that allows the user to extract Bayesian estimates from data objects created by {nicheROVER} or {SIBER}(e.g., niche size and similarities).

Installation

You can install the development version of {nichetools} using the following:

install.packages("devtools")
devtools::install_github("benjaminhlina/nichetools")

You can install the r-universe version of {nichetools} using the following:

install.packages("nichetools", 
                 repos = c("https://benjaminhlina.r-universe.dev", 
                           "https://cran.r-project.org"))

You can install the CRAN version of {nichetools} using the following:

install.packages("nichetools")

Vignette

Once you have loaded {nichetools} and {nicheROVER} or {SIBER} you can access the vignettes using the following code:

vignette("using-nichetools-with-the-package-nicheROVER")

OR

vignette("using-nichetools-with-the-package-SIBER")

You can also use the following to see both vignettes:

browseVignettes("nichetools")

The vignettes are also available online under the articles section of the website. See the following links, how to use {nichetools} with nicheROVER and how to use {nichetools} with SIBER or on my blog.

I highly suggest going through the vignettes as they will walk you through how to use {nichetools} in tandem with {nicheROVER} or {SIBER}.

Citation

To cite this package please cite the following publications

  • Swanson, H.K., Lysy, M., Power, M., Stasko, A.D., Johnson, J.D., and Reist, J.D. 2015. A new probabilistic method for quantifying n-dimensional ecological niches and niche overlap. Ecology 96(2): 318–324. doi:10.1890/14-0235.1

  • Jackson, A.L., Inger, R., Parnell, A.C., and Bearhop, S. 2011. Comparing isotopic niche widths among and within communities: SIBER – Stable Isotope Bayesian Ellipses in R. Journal of Animal Ecology 80(3): 595–602. doi:10.1111/j.1365-2656.2011.01806.x.

  • Layman, C.A., Arrington, D.A., Montaña, C.G., and Post, D.M. 2007. Can stable isotope ratios provide for community-wide measures of trophic structure? Ecology 88(1): 42–48. link

  • Hlina B.L. 2024. nichetools: Complementary package to nicheROVER and SIBER. R package version 0.3.1. https://benjaminhlina.github.io/nichetools/