Anne Chao, T. C. Hsieh, Robin L. Chazdon, Robert K. Colwell, and Nicholas J. Gotelli. 2015. Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory. Ecology 96:11891201. http://dx.doi.org/10.1890/14-0550.1


Supplement

R code for JADE (Joint species-rank Abundance Distribution/Estimation) based on individual-based (abundance) and sampling-unit-based (incidence) data.
Ecological Archives E096-107-S1.

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Authors
File list (downloads)
Description


Author(s)

Anne Chao
Institute of Statistics,
National Tsing Hua University,
Hsin-Chu 30043, Taiwan
E-mail: chao@stat.nthu.edu.tw

T. C. Hsieh
Institute of Statistics,
National Tsing Hua University,
Hsin-Chu 30043, Taiwan

Robin L. Chazdon
Department of Ecology and Evolutionary Biology,
University of Connecticut,
Storrs, CT 06269, USA
Department of Ecology and Evolutionary Biology,
University of Colorado,
Boulder, CO 80309, USA

Robert K. Colwell
Department of Ecology and Evolutionary Biology,
University of Connecticut,
Storrs, CT 06269, USA
University of Colorado Museum of Natural History,
Boulder, CO 80309, USA

Nicholas J. Gotelli
Department of Biology,
University of Vermont,
Burlington, VT 05405, USA


File list

JADE.R (MD5: 31757e7a2d9de9266d235d61d8e48f61)

Description

JADE.R –R code for computing the estimated complete species-rank abundance distribution (RAD) based on individual-based (abundance) and sampling-unit-based (incidence) data. The estimated complete RAD includes two parts: (i) the adjusted relative abundances for the set of species detected in the sample, and (ii) the estimated relative abundances for the set of species undetected in the sample but inferred to be present in the assemblage. Then the two parts are jointly combined to obtain the complete RAD estimator.