pnpmle: Penalized conditional NPML estimator for species richness

Description Usage Arguments Value Author(s) References Examples

View source: R/pnpmle.R

Description

This function calculate the penalized conditional NPML estimator of the species number by Wang and Lindsay 2005. This estimator was based on the conditional likelihood of a Poisson mixture model. A penalty term was introduced into the model to prevent the boundary problem discussed in Wang and Lindsay 2008. The confidence interval is calculated based on a bootstrap procedure. A Fortran function is called to for the computing.

Usage

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pnpmle(n,t=15,C=0,b=200,seed=NULL,conf=0.95,dis=1)

Arguments

n

a matrix or a numerical data frame of two columns. It is also called the “frequency of frequencies” data in literature. The first column is the frequency j=1, 2…; and the second column is n_j, the number of species observed with j individuals in the sample.

t

a positive integer. t is the cutoff value to define the relatively less abundant species to be used in estimation of the Poisson mixture. The default value is t=15. The recommendation is to use \code{t} ≥ 10.

C

integer either 0 or 1. It specifies whether bootstrap confidence interval should be calculated. “C=1” for YES and “C=0” for NO.The default of C is set as 0.

b

integer. b specifies the number of bootstrap samples to be generated for confidence interval. It is ignored if “C=0”.

conf

a positive number ≤ 1. conf specifies the confidence level for confidence interval. The default is 0.95.

seed

a single value, interpreted as an integer. Seed for random number generation

dis

0 or 1. 1 for on-screen display of the mixture output, and 0 for none.

Value

The function pnpmle returns a list of: Nhat, CI (if “C=1”).

Nhat

Point estimate of N

CI

bootstrap confidence interval

Author(s)

Ji-Ping Wang,Department of Statistics, Northwestern University

References

Wang, J.-P. Z. and Lindsay, B. G. ,2005, A penalized nonparametric maximum likelihood approach to species richness estimation. Journal of American Statistical Association, 2005,100(471):942-959

Wang, J.-P., and Lindsay, B.G., 2008, An exponential partial prior for improving NPML estimation for mixtures, Statistical Methodology, 2008,5:30-45

Examples

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library(SPECIES)

##load data from the package, 
## \dQuote{butterfly} is the famous butterfly data by Fisher 1943.
#data(butterfly)

##output estimate without confidence interval using cutoff t=15
#pnpmle(butterfly,t=15,C=0)

##output estimate with confidence interval using cutoff t=15
#pnpmle(butterfly,t=15,C=1, b=200)

SPECIES documentation built on May 30, 2017, 12:31 a.m.

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