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:
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 = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/benjaminhlina/nichetools/issues
Pkgdown site:https://benjaminhlina.github.io
- 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
Last updated 4 months agofrom:3d3150ae0b. Checks:1 OK, 1 NOTE. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 29 2025 |
| R-4.5-linux | NOTE | Jan 29 2025 |
Exports:create_comparisonsextract_group_metricsextract_laymanextract_muextract_niche_sizeextract_overlapextract_sigmaextract_similaritiesniche_ellipse
Dependencies:ashclicodacolorspacecpp11deldirdplyrellipsefansifarverFNNgenericsggplot2gluegtablehdrcdeisobandkernlabKernSmoothkslabelinglatticelifecyclelocfitmagrittrMASSMatrixmclustmgcvmnormtmulticoolmunsellmvtnormnicheROVERnlmepillarpkgconfigpolyclippracmapurrrR6RColorBrewerRcpprjagsrlangscalesSIBERspatstat.dataspatstat.geomspatstat.univarspatstat.utilsstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Using {nichetools} with nicheROVER
Rendered fromusing-nichetools-with-the-package-nicheROVER.Rmdusingknitr::rmarkdownon Jan 29 2025.Last update: 2024-10-01
Started: 2024-06-08
Using {nichetools} with SIBER
Rendered fromusing-nichetools-with-the-package-SIBER.Rmdusingknitr::rmarkdownon Jan 29 2025.Last update: 2024-10-01
Started: 2024-08-27
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| create comparisons | create_comparisons |
| extract maximum-likelihood estimates for group metrics | extract_group_metrics |
| extract Layman metrics | extract_layman |
| extract mu | extract_mu |
| extract niche size | extract_niche_size |
| extract overlap | extract_overlap |
| extract Sigma | extract_sigma |
| extract similarities | extract_similarities |
| A 'data.frame' containing posterior estimates of mu | mu_est_long |
| Create ellipses based on Bayesian estimates of mu and Sigma | niche_ellipse |
| A 'list' of the posterior estimates of mu and Sigma from '{nicheROVER}' | niw_fish_post |
| A 'data.frame' containing the estimates of percentage of overlap among groups | over_stat |
| A 'list' of the posterior estimates of mu and Sigma from '{SIBER}' | post_sam_siber |
| A 'data.frame' containing posterior estimates of Sigma | sigma_est_wide |
