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rKIN: Kernel-based method for estimating isotopic niche size and overlap.

Carolyn A Eckrich1, Shannon E Albeke2,3, Elizabeth A Flaherty4

  • 1Oregon Department of Fish and Wildlife, La Grande, OR, USA.

The Journal of Animal Ecology
|December 5, 2019
PubMed
Summary

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This summary is machine-generated.

This study introduces the rKIN R package for analyzing isotopic niches, offering new methods like kernel utilization density (KUD) for measuring niche size and overlap in animal ecology. It provides a flexible tool for ecologists to explore resource use patterns.

Area of Science:

  • Ecology
  • Stable Isotope Ecology
  • Spatial Ecology

Background:

  • The isotopic niche provides critical information on consumer resource and habitat utilization.
  • Existing tools for quantifying niche size and overlap have limitations, especially with non-normally distributed data.
  • Spatial ecology methods for home range analysis can be adapted for stable isotope ecology.

Purpose of the Study:

  • To introduce the rKIN R package for quantifying isotopic niche size and overlap.
  • To adapt and apply spatial metrics, including kernel utilization density (KUD), to stable isotope data.
  • To demonstrate the performance of rKIN using empirical and simulated datasets.

Main Methods:

  • Utilized existing spatial metrics: minimum convex polygon (MCP) and standard ellipse area (SEA).
Keywords:
kernel utilization densityniche overlapstable isotope analysistrophic niche

Related Experiment Videos

  • Introduced novel metrics based on kernel utilization density (KUD) estimators for isotopic niche analysis.
  • Applied four bandwidth selection methods (reference, normal scale, plug-in, biased cross-validation) within KUD.

    • Main Results:

    • Niche size estimates from MCP, SEA, and KUD were correlated but showed dataset-specific divergences.
    • KUD yielded larger niche sizes and was more sensitive to isotopic data distribution.
    • Pairwise overlap estimates varied, with MCP and SEA potentially including unused areas.
    • Niche size and overlap estimates were consistent across sample sizes greater than 15.
    • Bandwidth methods produced comparable niche size and overlap estimates.

    Conclusions:

    • The rKIN package offers isotope ecologists a robust tool for quantifying isotopic niche dynamics (shifts, expansions, contractions).
    • It enables assessment of various estimation methods and provides flexibility for analyzing different data types convertible to Cartesian coordinates.
    • KUD is a valuable addition for isotopic niche analysis, particularly for non-normally distributed data.