Supplement 1. R code for JADE (Joint species-rank Abundance Distribution/Estimation) based on individual-based (abundance) and sampling-unit-based (incidence) data.

JADE.R (MD5: 31757e7a2d9de9266d235d61d8e48f61)

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.