Copia - Bias correction for richness in abundance data

Copia Logo by Lauren Fonteyn

Copia is a statistical software package for estimating diversity and richness on the basis of abundance data. The package contains several bias-correcting richness estimators, such as the Chao1 and the Jacknife estimator.

Because this package targets so-called “abundance” data from ecology, it has been named using the corresponding Latin term copia. The artwork for the logo has been kindly contributed by Dr. Lauren Fonteyn (Leiden University, NL). The depicted goat is a mythological reference to the cornucopia or “horn of plenty”, the legendary horn of the goat Amaltheia, who fed the infant Zeus with her milk.

See the quickstart to get started.

Copia is licensed under BSD3. The source is on GitHub.

Currently implemented diversity estimation methods

  • Empirical Richness: empirical species richness of an assemblage;

  • Chao1: Chao1 estimate of bias-corrected species richness;

  • “Improved” iChao1 estimate of bias-corrected species richness;

  • Egghe & Proot: Egghe & Proot estimate of bias-corrected species richness;

  • ACE: ACE estimate of bias-corrected species richness (Chao & Lee 1992);

  • Jacknife: Jackknife estimate of bias-corrected species richness;

  • Minsample: Observed population size added to the minimum additional sampling estimate;

Citation

Copia is developed by Mike Kestemont and Folgert Karsdorp. If you wish to cite Copia, please cite the following paper:

@article{kestemont,
  author = {Mike Kestemont}
}