Isodars | Why abundance-based indices are biased | Pairwise isodars and the n-dimensional isodar | The isodar-adjusted inequality | The niche breadth curve | Indices from isodar parameters (Appendix S1) | Simulating data | References
Package: isoniche 1.1.0
isoniche: Isodar-Adjusted, Abundance-Independent Niche Breadth
Estimates habitat niche breadth corrected for the effects of abundance, using isodars (the relationships between a species' densities in pairs of habitats under density-dependent habitat selection). Fits pairwise and n-dimensional isodars, including data where sites lack some habitats, and computes the isodar-adjusted inequality (IAI) at any total abundance, with density-independent and density-dependent niche breadth, bootstrap confidence intervals and diagnostics. Method described in Granot, Dubiner and Belmaker (in revision, Ecology Letters).
Authors:
isoniche_1.1.0.tar.gz
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isoniche_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
isoniche/json (API)
| # Install 'isoniche' in R: |
| install.packages('isoniche', repos = c('https://itai811.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/itai811/isoniche/issues
Pkgdown/docs site:https://itai811.github.io
Datasets:
- moorea_fish - Reef fishes of Moorea in three habitats
Last updated from:fc4aed430f. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 168 | ||
| source / vignettes | OK | 286 | ||
| linux-release | OK | 157 | ||
| macos-release | OK | 178 | ||
| macos-oldrel | OK | 214 | ||
| windows-devel | OK | 233 | ||
| windows-release | OK | 260 | ||
| windows-oldrel | OK | 224 | ||
| wasm-release | OK | 106 |
Exports:check_coveragecommunity_to_longfit_isodarsgroup_sitesiaiiai_curveisoderrniche_breadthpairwise_nicheradius_sensitivitysimulate_isodars
Dependencies:cligluelifecyclemagrittrpillarpkgconfigrlangtibbleutf8vctrs
The method: isodar-adjusted niche breadth
Last update: 2026-11-01
Started: 2026-11-01
Diagnostics: when to trust an estimate
All species of the Moorea data | The flags | Data | Fit | Extrapolation | Uncertainty | Informational | Is the intercept more than noise? | Looking at a flagged species | A workflow
Last update: 2026-11-01
Started: 2026-11-01
Get started with isoniche
What you need | 1. Your data | 2. Check coverage | 3. Estimate niche breadth | 4. Check the diagnostics | 5. Niche breadth across abundances | 6. Compare species | 7. Reporting | References
Last update: 2026-11-01
Started: 2026-11-01
Preparing your data
Long format | From a community matrix | Effort and the unit of abundance | Replicates: sites or surveys | Which habitats | Absent and undersampled habitats | Incomplete sites | Grouping nearby sites | One species in wide format
Last update: 2026-11-01
Started: 2026-11-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Sampling coverage of each species and habitat | check_coverage |
| Convert a community matrix to long format | community_to_long |
| Fit isodars | fit_isodars |
| Group nearby sites into sampling units | group_sites |
| Isodar-adjusted inequality (IAI) | iai |
| Niche breadth as a function of total abundance | iai_curve |
| Bootstrap uncertainty of the isodar-adjusted inequality | isoderr |
| Reef fishes of Moorea in three habitats | moorea_fish |
| Density-independent and density-dependent niche breadth | niche_breadth |
| Niche breadth indices from pairwise isodar parameters | pairwise_niche |
| Plot niche breadth curves | plot.iai_curve |
| Plot niche breadth against abundance | plot.niche_breadth |
| Sensitivity of niche breadth to the grouping radius | radius_sensitivity |
| Simulate abundances in habitats linked by isodars | simulate_isodars |
| Summarise niche breadth results and their diagnostics | print.summary.niche_breadth summary.niche_breadth |