Package: nichetools 0.3.2

Benjamin L. Hlina

nichetools: Complementary Package to 'nicheROVER' and 'SIBER'

Provides functions complementary to packages 'nicheROVER' and 'SIBER' allowing the user to extract Bayesian estimates from data objects created by the packages 'nicheROVER' and 'SIBER'. Please see the following publications for detailed methods on 'nicheROVER' and 'SIBER' Hansen et al. (2015) <doi:10.1890/14-0235.1>, Jackson et al. (2011) <doi:10.1111/j.1365-2656.2011.01806.x>, and Layman et al. (2007) <doi:10.1890/0012-9658(2007)88[42:CSIRPF]2.0.CO;2>, respectfully.

Authors:Benjamin L. Hlina [aut, cre]

nichetools_0.3.2.tar.gz
nichetools_0.3.2.tar.gz(r-4.5-noble)nichetools_0.3.2.tar.gz(r-4.4-noble)
nichetools_0.3.2.tgz(r-4.4-emscripten)nichetools_0.3.2.tgz(r-4.3-emscripten)
nichetools.pdf |nichetools.html✨
nichetools/json (API)
NEWS

# Install 'nichetools' in R:
install.packages('nichetools', repos = 'https://cloud.r-project.org')

Bug tracker:https://github.com/benjaminhlina/nichetools/issues

Pkgdown site:https://benjaminhlina.github.io

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:
  • mu_est_long - A 'data.frame' containing posterior estimates of mu
  • niw_fish_post - A 'list' of the posterior estimates of mu and Sigma from '{nicheROVER}'
  • over_stat - A 'data.frame' containing the estimates of percentage of overlap among groups
  • post_sam_siber - A 'list' of the posterior estimates of mu and Sigma from '{SIBER}'
  • sigma_est_wide - A 'data.frame' containing posterior estimates of Sigma

On CRAN:

Conda:

jagscpp

3.60 score 209 downloads 9 exports 60 dependencies

Last updated 6 months agofrom:3d3150ae0b. Checks:2 OK, 1 NOTE. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKMar 26 2025
R-4.5-linuxNOTEMar 26 2025
R-4.4-linuxOKMar 26 2025

Exports:create_comparisonsextract_group_metricsextract_laymanextract_muextract_niche_sizeextract_overlapextract_sigmaextract_similaritiesniche_ellipse

Dependencies:ashclicodacolorspacecpp11deldirdplyrellipsefansifarverFNNgenericsggplot2gluegtablehdrcdeisobandkernlabKernSmoothkslabelinglatticelifecyclelocfitmagrittrMASSMatrixmclustmgcvmnormtmulticoolmunsellmvtnormnicheROVERnlmepillarpkgconfigpolyclippracmapurrrR6RColorBrewerRcpprjagsrlangscalesSIBERspatstat.dataspatstat.geomspatstat.univarspatstat.utilsstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Using {nichetools} with nicheROVER

Benjamin L. Hlina

Rendered fromusing-nichetools-with-the-package-nicheROVER.Rmdusingknitr::rmarkdownon Mar 26 2025.

Last update: 2024-10-01
Started: 2024-06-08

Using {nichetools} with SIBER

Benjamin L. Hlina

Rendered fromusing-nichetools-with-the-package-SIBER.Rmdusingknitr::rmarkdownon Mar 26 2025.

Last update: 2024-10-01
Started: 2024-08-27

Citation

Swanson HK, Lysy M, Power M, Stasko AD, Johnson JD, Reist JD (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, https://esajournals.onlinelibrary.wiley.com/doi/full/10.1890/14-0235.1.

Jackson AL, Inger R, Parnell AC, 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, https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.1365-2656.2011.01806.x.

Layman CA, Arrington DA, Montaña CG, Post DM (2007). “Can stable isotope ratios provide for community-wide measures of trophic structure?” Ecology, 88(1), 42-48. doi:10.1890/0012-9658(2007)88[42:CSIRPF]2.0.CO;2.

Hlina BL (2024). nichetools: Complementary Package to 'nicheROVER' and 'SIBER'. R package version 0.3.1, https://benjaminhlina.github.io/nichetools/.

Corresponding BibTeX entries: 

  @Article{,
    title = {A new probabilistic method for quantifying n-dimensional
      ecological niches and niche overlap.},
    author = {Heidi K. Swanson and Martin Lysy and Michael Power and
      Ashley D. Stasko and Jim D. Johnson and James D. Reist},
    journal = {Ecology},
    year = {2015},
    volume = {96},
    number = {2},
    pages = {318-324},
    doi = {10.1890/14-0235.1},
    url =
      {https://esajournals.onlinelibrary.wiley.com/doi/full/10.1890/14-0235.1},
  }

  @Article{,
    title = {Comparing isotopic niche widths among and within
      communities: SIBER – Stable Isotope Bayesian Ellipses in R},
    author = {Andrew L. Jackson and Richard Inger and Andrew C. Parnell
      and Stuart Bearhop},
    journal = {Journal of Animal Ecology},
    year = {2011},
    volume = {80},
    number = {3},
    pages = {595-602},
    doi = {10.1111/j.1365-2656.2011.01806.x},
    url =
      {https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.1365-2656.2011.01806.x},
  }

  @Article{,
    title = {Can stable isotope ratios provide for community-wide
      measures of trophic structure?},
    author = {Craig A. Layman and D. Albrey Arrington and Carman G.
      Montaña and David M. Post},
    journal = {Ecology},
    year = {2007},
    volume = {88},
    number = {1},
    pages = {42-48},
    doi = {10.1890/0012-9658(2007)88[42:CSIRPF]2.0.CO;2},
  }

  @Manual{,
    title = {nichetools: Complementary Package to 'nicheROVER' and
      'SIBER'},
    author = {Benjamin L. Hlina},
    year = {2024},
    note = {R package version 0.3.1},
    url = {https://benjaminhlina.github.io/nichetools/},
  }

Readme and manuals

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/