Package: nichetools 0.3.3

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) <do i: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_0.3.3.tar.gz
nichetools_0.3.3.zip(r-4.7)nichetools_0.3.3.zip(r-4.6)nichetools_0.3.3.zip(r-4.5)
nichetools_0.3.3.tgz(r-4.6-any)nichetools_0.3.3.tgz(r-4.5-any)
nichetools_0.3.3.tar.gz(r-4.7-any)nichetools_0.3.3.tar.gz(r-4.6-any)
nichetools_0.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nichetools/json (API)

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

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

Pkgdown/docs 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

5.16 score 2 stars 18 scripts 452 downloads 9 exports 52 dependencies

Last updated from:ad51e49f64. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK219
source / vignettesOK266
linux-release-x86_64OK230
macos-release-arm64OK136
macos-oldrel-arm64OK119
windows-develOK190
windows-releaseOK164
windows-oldrelOK174
wasm-releaseOK127

Exports:create_comparisonsextract_group_metricsextract_laymanextract_muextract_niche_sizeextract_overlapextract_sigmaextract_similaritiesniche_ellipse

Dependencies:ashclicodacpp11dplyrellipsefarverFNNgenericsggplot2gluegtablehdrcdeisobandkernlabKernSmoothkslabelinglatticelifecyclelocfitmagrittrMatrixmclustmgcvmnormtmulticoolmvtnormnicheROVERnlmepillarpkgconfigpracmapurrrR6RColorBrewerRcpprjagsrlangS7scalesSIBERspatstat.utilsstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Using {nichetools} with nicheROVER
Our Objectives | Bring in trophic niche data | Estimate posterior distribution with Normal-Inverse-Wishart (NIW) priors. | Extract μ values | Extract Σ values | Plot posterior distrubtion of μ and Σ | Estimate niche ellipse | Plot ellipses, densities of each istope, and isotope biplot | Use {patchwork} to make ellipse, density, and biplots into a paneled figure. | Determine the 95% niche similarties for each species | Estimate overall niche size | Plot niche size
Rendered fromusing-nichetools-with-the-package-nicheROVER.Rmdusingknitr::rmarkdown

Last update: 2024-09-30
Started: 2024-05-31

Using {nichetools} with SIBER
Our Objectives | Bring in trophic data | Convert to {SIBER} object | Bayesian Ellipse Analysis | Extract posterior distributions for μ and Σ | Extract Niche Size | Niche Similarties | Bayesian Estimates of Layman's Community Metrics
Rendered fromusing-nichetools-with-the-package-SIBER.Rmdusingknitr::rmarkdown

Last update: 2024-09-30
Started: 2024-07-17