# 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

 ```1 2``` ```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.

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.

`jack1`, `bootstrap`

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13``` ```## 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

Attaching package: 'shapefiles'

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

[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.