Turnover

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

Usage

turnover(object, ...)

index_whittaker(x, ...)

index_cody(x, ...)

index_routledge1(x, ...)

index_routledge2(x, ...)

index_routledge3(x, ...)

index_wilson(x, ...)

# S4 method for matrix
turnover(
  object,
  method = c("whittaker", "cody", "routledge1", "routledge2", "routledge3", "wilson"),
  ...
)

# S4 method for data.frame
turnover(
  object,
  method = c("whittaker", "cody", "routledge1", "routledge2", "routledge3", "wilson"),
  ...
)

# S4 method for matrix
index_whittaker(x)

# S4 method for matrix
index_cody(x)

# S4 method for matrix
index_routledge1(x)

# S4 method for matrix
index_routledge2(x)

# S4 method for matrix
index_routledge3(x)

# S4 method for matrix
index_wilson(x)

Arguments

object, x

A \(m \times p\) matrix of count data or incidence data.

...

Further arguments to be passed to internal methods.

method

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

Value

A numeric vector.

Details

The following methods can be used to ascertain the degree of turnover in taxa composition along a gradient (\(\beta\)-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.

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

Other diversity measures: heterogeneity(), occurrence(), plot_diversity, rarefaction(), richness(), similarity(), simulate()

Author

N. Frerebeau

Examples

## Data from Magurran 1988, p. 162
trees <- matrix(
  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
)
colnames(trees) <- c("Birch", "Oak", "Rowan", "Beech", "Hazel", "Holly")

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

## Cody's measure
turnover(trees, "cody") # 3
#> [1] 3

## Routledge's measures
turnover(trees, "routledge1") # 0.29
#> [1] 0.2857143
turnover(trees, "routledge2") # 0.56
#> [1] 0.5594978
turnover(trees, "routledge3") # 1.75
#> [1] 1.749794

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