jack1: First- and second-order jacknife estimators
In fossil: Palaeoecological and Palaeogeographical Analysis Tools

Description Usage Arguments Details Value Author(s) References See Also Examples

Computes the extrapolated species richness of a population using first- or second-order jacknife stimators

1 2	jack1(x, taxa.row = TRUE, abund = TRUE) jack2(x, taxa.row = TRUE, abund = TRUE)

`x`	a vector, matrix or data frame of positive integers or zero of any size
`taxa.row`	whether each row of the matrix is a different taxon; if so, value is set to TRUE
`abund`	If true, data is assumed to be abundance, if false, presence absence is assumed

These functions compute the first and second-order jacknife species richness estimators, respectively. Both functions will accept a vector, matrix or data frame of any size made up of positive integers and zeros. Matrices are by default treated such that each row is a different taxon and each column is a sample or locality, however if they are arranged with the taxa as columns, change the argument taxa.row to FALSE. If the data is abundance based, abund should be set to TRUE. If abund is set to FALSE, the data will be converted to presence/absence if not already in that format. For single vectors/columns, taxa.row and abund are ignored.

The value returned is the Jackknife estimated species diversity of the dataset in question.

Matthew Vavrek

Burnham, K.P. & W.S. Overton. 1978. Estimation of the size of a closed population when capture probabilities vary among animals. Biometrika 65, 623-633.

Burnham, K.P. & W.S. Overton. 1979. Robust estimation of population size when capture probabilities vary among animals. Ecology 60, 927-936.

Heltshe, J. & Forrester, N.E. 1983 . Estimating species richness using the jackknife procedure. Biometrics 39, 1-11.

ACE

## sample vector
a<-c(0,5,1,1,2,0,0,1,0,0,8,45)
jack1(a)

## matrix format
a<-matrix(c(0,5,1,1,2,0,0,1,0,0,8,45),4,3)
jack1(a)
jack2(a)
jack2(a,abund = FALSE)

## presence absence matrix of the above abundance matrix
a<-matrix(c(0,1,1,1,1,0,0,1,0,0,1,1),4,3)
jack1(a)
jack2(a)
jack2(a, abund = FALSE)