turnover-method: Turnover

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

Description

Returns the degree of turnover in taxa composition along a grandient or transect.

Usage

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turnover(object, ...)

## S4 method for signature 'CountMatrix'
turnover(object, method = c("whittaker", "cody",
  "routledge1", "routledge2", "routledge3", "wilson"), simplify = FALSE,
  ...)

## S4 method for signature 'IncidenceMatrix'
turnover(object, method = c("whittaker",
  "cody", "routledge1", "routledge2", "routledge3", "wilson"),
  simplify = FALSE, ...)

Arguments

object

A m x p matrix of count data.

...

Further arguments passed to other methods.

method

A character string specifiying the method to be used (see details). Any unambiguous substring can be given.

simplify

A logical scalar: should the result be simplified to a matrix? The default value, FALSE, returns a list.

Details

The following methods can be used to acertain the degree of turnover in taxa composition along a gradient (β-diversity) on qualitative (presence/absence) data. This assumes that the order of the matrix rows (from 1 to n) follows the progression along the gradient/transect.

whittaker

Whittaker measure.

cody

Cody measure.

routledge1

Routledge first measure.

routledge2

Routledge second measure.

routledge3

Routledge third measure. This is the exponential form of the second measure.

wilson

Wilson measure.

Value

If simplify is FALSE, returns a list (default), else returns a matrix.

Author(s)

N. Frerebeau

References

Cody, M. L. (1975). Towards a theory of continental species diversity: Bird distributions over Mediterranean habitat gradients. In M. L. Cody & J. M. Diamond (Eds.), Ecology and Evolution of Communities. Cambridge, MA: Harvard University Press, p. 214–257.

Routledge, R. D. (1977). On Whittaker’s Components of Diversity. Ecology, 58(5), 1120-1127. DOI: 10.2307/1936932.

Whittaker, R. H. (1960). Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monographs, 30(3), 279-338. DOI: 10.2307/1943563.

Wilson, M. V., & Shmida, A. (1984). Measuring Beta Diversity with Presence-Absence Data. The Journal of Ecology, 72(3), 1055-1064. DOI: 10.2307/2259551.

See Also

richness rarefaction diversity evenness

Other beta-diversity: similarity

Examples

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# Data from Magurran 1988, p. 162
trees <- IncidenceMatrix(
  data = c(1, 1, 1, 0, 0, 0,
           1, 1, 1, 1, 1, 1,
           0, 0, 1, 0, 1, 0,
           0, 0, 0, 1, 1, 1,
           0, 0, 0, 0, 1, 1,
           0, 0, 0, 1, 0, 1),
  nrow = 6, byrow = FALSE,
  dimnames = list(c("1", "2", "3", "4", "5", "6"),
                  c("Birch", "Oak", "Rowan", "Beech", "Hazel", "Holly"))
)

# Whittaker's measure
turnover(trees, "whittaker") # 1

# Cody's measure
turnover(trees, "cody") # 3

# Routledge's measures
turnover(trees, method = c("routledge1", "routledge2", "routledge3"),
         simplify = TRUE)
# 0.29 0.56 1.75

# Wilson and Shmida's measure
turnover(trees, "wilson") # 1

nfrerebeau/tabula documentation built on Feb. 11, 2019, 9:16 a.m.