SPECIES: an R package for species richness estimation

SPECIES is an R package integrating jackknife, coverage-based, and NPMLE-based nonparametric methods for species richness estimation. The conventional nonparametric methods include: Chao 1987 lower bound estimatior, Chao and Lee 1992 coverage based estimators, Chao and Bunge 2002 coverage-duplication estimator, Burnham and Overton 1979 Jackknife estimaor. In addition this package integrates several additional estimators that are based on nonparametric maximum likelihood estimation (NPMLE) method including unconditional NPMLE by Norris and Pollock 1998; the penalized conditional NPMLE by Wang and Lindsay 2005; and the Poisson-Compound Gamma with NPMLE estimation by Wang 2010.

SPECIES has seven integrated R functions including: jackknife, chao1984,ChaoLee1992,ChaoBunge, pnpmple,unpmle, pcg, which respectively compute the jackknife estimator, coverage-based estimators, penalized conditional NPMLE, unconditional NPMLE and Poisson-Compound Gamma estimators. For detailed usage of functions, please refer to the help file. e.g. in R console, type "help(jackknife)" to see instruction for the jackknife function.

SPECIES package Blog:

  1. Dec 30, 2009: package SPECIES has been updated on Dec 30, 2009 to fix a few bugs
  2. Aug 20,2010 : package SPECIES has been updated on Aug 20, 2010. Functions are re-organized, in particular the coverage based functions have been re-written. Please refer to the manual below for changes.
  3. Jan 25 2010 : package SPECIES has been updated on Jan 25, 2010.  Function arguments have been renamed, confidence level can be specified by user. Random seed can be spcified for random number generation. Please refer to the manual below for changes.
  4. April 15, 2011: two minor bugs were fixed for the pnpmle and pcg functions. These two bugs could occationally result in different estimates. (Thanks to Chee for reporting this).
 

SPECIES R package manual: SPECIES-manual_1.0.pdf
Source package for all platforms: SPECIES_1.0.tar.gz
Binary package for Mac OS X Leopard: SPECIES_1.0.tgz
Binary package for Windows Xp: SPECIES_1.0.zip

or download it from http://cran.r-project.org/web/packages/SPECIES/index.html

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Reference: Wang, J.P., 2011, SPECIES: An R Package for SPECIES Richness Estimation, Journal of Statistical Software, 40(9),1-15, PDF