SPECIES-package(SPECIES)
SPECIES-package()所属R语言包：SPECIES
An R pacakge for species richness estimation
物种丰富度估计的R线路咨询
译者：生物统计家园网 机器人LoveR
描述----------Description----------
SPECIES provides multiple functions to compute popular estimators for species richness.These estimators include: (1) jackknife estimator by Burnham and Overton 1978, 1979; (2) lower-bound estimator by Chao 1984; (3) coverage-base estimators ACE, ACE-1 by Chao and Lee 1992; (4) coverage-duplication estimator from Poisson-Gamma model by Chao and Bunge 2002; (5) unconditional nonparametric maximum likelihood estimator by Norris and Pollock 1996, 1998; (6) penalized nonparametric maximum likelihood estimator by Wang and Lindsay 2005; and (7) Poisson-compound Gamma model with smooth nonparametric maximum likelihood estimation by Wang 2010.
SPECIES提供了多项功能，计算流行的物种richness.These估计估计包括：（1）刀切估计伯纳姆和Overton 1978年，1979年（2）1984年的超下限估计，（3）覆盖基估计ACE，ACE-1超和李，1992（4）覆盖重复泊松-Gamma模型的估计，从2002年超，邦吉（5）无条件的非参数极大似然估计的诺里斯和波洛克1996年，1998，（6）处罚非参数的最大似然估计2005年王和林赛（7）复合泊松Gamma模型的平滑非参数的最大似然估计，2010年由王。
Details
详细信息----------Details----------
</table> functions: chao1984, ChaoBunge, ChaoLee1992, jackknife, pcg ,pnpmle, unpmle; data: butterfly, cottontail,EST, insect, microbial, traffic
</ TABLE>功能：chao1984，ChaoBunge，ChaoLee1992，折刀，PCG，pnpmle，unpmle数据：蝴蝶，棉，EST，昆虫，微生物，交通
（作者）----------Author(s)----------
Ji-Ping Wang, Department of Statistics, Northwestern University
Maintainer: jzwang@northwestern.edu
参考文献----------References----------
Acinas, S., Klepac-Ceraj, V., Hunt, D., Pharino, C., Ceraj, I., Distel, D., and Polz, M. (2004), Fine-scale phylogenetic architecture of a complex bacterial community. Nature, 430, 551-554.
Bohning, D. and Schon, D., Nonparametric maximum likelihood estimation of population size based on the counting distribution, Journal of the Royal Statistical Society, Series C: Applied Statistics, 54, 721-737.
Burnham, K. P., and Overton,W. S. (1978), Estimation of the Size of a Closed Population When Capture Probabilities Vary Among Animals, Biometrika, 65, 625-633.
Burnham, K. P., and Overton,W. S. (1979), Robust Estimation of Population Size When Capture Probabilities Vary Among Animals, Ecology, 60, 927-936.
Chao, A. (1984), Nonparametric Estimation of the Number of Classes in a Population, Scandinavian Journal of Statistics, 11, 265-270.
Chao, A. (1987). Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43, 783-791.
Chao, A., and Lee, S.-M. (1992), Estimating the Number of Classes via Sample Coverage, Journal of the American Statistical Association, 87, 210-217.
Chao, A., and Bunge, J. (2002), Estimating the Number of Species in a Stochastic Abundance Model, Biometrics, 58, 531-539.
Fisher, R. A., Corbet, A. S., and Williams, C. B. ,(1943), The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Animal Population, Journal of Animal Ecology, 12, 42-58.
Hong, S. H., and Bunge, J. and Jeon, S.O. and Epstein, S. (2006), Predicting microbial species richness, Proc. Natl. Acad. Sci, 103, 117-122.
Norris, J. L. I., and Pollock, K. H. (1996), Nonparametric MLE Under Two Closed Capture-Recapture Models With Heterogeneity, Biometrics, 52,639-649.
Norris, J. L. I., and Pollock, K. H.(1998), Non-Parametric MLE for Poisson Species Abundance Models Allowing for Heterogeneity Between Species, Environmental and Ecological Statistics, 5, 391-402.
Simar, L. (1976), Maximum likelihood estimation of a compound Poisson process, Annals of Statistics, 4, 1200-1209.
Wang, J.-P. Z. and Lindsay, B. G. (2005), A penalized nonparametric maximum likelihood approach to species richness estimation. Journal of American Statistical Association, 100(471):942-959.
Wang, J.-P., and Lindsay, B.G. (2008), An exponential partial prior for improving NPML estimation for mixtures, Statistical Methodology, 5:30-45.
Wang, J.-P. (2010), Estimating the species richness by a Poisson-Compound Gamma model, Biometrika, 97(3): 727-740.
Wang, J.-P. (2011), SPECIES: An R Package for Species Richness Estimation, Journal of Statistical Software, 40(9), 1-15, URL: http://www.jstatsoft.org/v40/i09/.
实例----------Examples----------
##load library[＃加载库]
library(SPECIES)
## "butterfly" is the famous butterfly data by Fisher 1943.[“蝴蝶”是1943年由Fisher著名的蝴蝶数据。]
data(butterfly)
##jackknife method[＃刀切法]
jackknife(butterfly,k=5)
##using only 'ACE' coverage method[＃只使用“ACE”覆盖方法]
ChaoLee1992(butterfly,t=10, method="all")
##using chao1984 lower bound estimator[＃chao1984下界估计]
chao1984(butterfly)
##using Chao and Bunge coverage-duplication method[＃超，邦吉覆盖范围的重复数据删除方法]
ChaoBunge(butterfly,t=10)
##penalized NPMLE method[＃处罚NPMLE方法的]
#pnpmle(butterfly,t=15,C=1,b=200)[pnpmle，T = 15，C = 1，B = 200（蝴蝶）]
##unconditonal NPMLE method[＃unconditonal NPMLE方法]
#unpmle(butterfly,t=10,C=1,b=200)[unpmle，T = 10，C = 1，B = 200（蝴蝶）]
##Poisson-compound Gamma method[＃的泊松化合物伽玛方法]
#pcg(butterfly,t=20,C=1,b=200)[PCG（蝴蝶，T = 20，C = 1，B = 200）]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
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发表于 2012-9-30 14:49:09
