chao1: Chao's Species Estimators

In fossil: Palaeoecological and Palaeogeographical Analysis Tools

Description

Computes the Chao species estimator for abundance or presence-absence data

Usage

chao1(x, taxa.row = TRUE)
chao2(x, taxa.row = TRUE)

Arguments

x	a vector, matrix or data frame with species by samples
taxa.row	a logical argument if the species are the rows or columns

Details

chao1 will return an estimate of species richness based on a vector or matrix of abundance data, while chao2 will return an estimate of species richness based on incidence data. Note that chao1 estimator is for abundance data only. The chao2 estimator can be given abundance data and it will automagically convert it to incidence data, but due to the nature of the estimator, the data must contain more than one sample (ie the data must be arranged in a minimum 2 by 2 matrix).

Value

returns a value for the Chao Species Estimator for a the given data.

Note

While the function will still return a value, if all the species abundances are equal to 1 in the input to chao1, a warning will be raised, and the value returned will be equal to the number of species observed.

Author(s)

Matthew Vavrek

References

Chao, A. 1984. Non-parametric 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.

See Also

jack1, bootstrap

Examples

## sample vector
a<-c(0,5,1,1,2,0,0,1,0,0,8,45)
chao1(a)

## matrix format
a<-matrix(c(0,5,1,1,2,0,0,1,0,0,8,45),4,3)
chao1(a)
chao2(a)

## presence absence matrix
a<-matrix(c(0,1,1,1,1,0,0,1,0,0,1,1),4,3)
chao1(a)
chao2(a)

Example output

Loading required package: sp
Loading required package: maps
Loading required package: shapefiles
Loading required package: foreign

Attaching package: 'shapefiles'

The following objects are masked from 'package:foreign':

    read.dbf, write.dbf

[1] 11.5
[1] 4
[1] 6
[1] 6
Warning message:
In chao1(a) :
  This data appears to be presence/absence based, but this estimator is for abundance data only
[1] 6

fossil documentation built on March 23, 2020, 5:06 p.m.