nestedtemp {vegan}R Documentation

Nestedness Indices for Communities of Islands or Patches

Description

Patches or local communities are regarded as nested if they all could be subsets of the same community. In general, species poor communities should be subsets of species rich communities, and rare species should only occur in species rich communities.

Usage

nestedchecker(comm)
nestedn0(comm)
nesteddisc(comm)
nestedtemp(comm, ...)
nestednodf(comm, order = TRUE)
## S3 method for class 'nestedtemp':
plot(x, kind = c("temperature", "incidence"),
    col=rev(heat.colors(100)),  names = FALSE, ...)

Arguments

comm Community data.
x Result object for a plot.
col Colour scheme for matrix temperatures.
kind The kind of plot produced.
names Label columns and rows in the plot using names in comm. If it is a logical vector of length 2, row and column labels are returned accordingly.
order Order rows and columns by frequencies.
... Other arguments to functions.

Details

The nestedness functions evaluate alternative indices of nestedness. The functions are intended to be used together with Null model communities and used as an argument in oecosimu to analyse the nonrandomness of results.

Function netstedchecker gives the number of checkerboard units, or 2x2 submatrices where both species occur once but on different sites (Stone & Roberts 1990).

Function nestedn0 implements nestedness measure N0 which is the number of absences from the sites which are richer than the most pauperate site species occurs (Patterson & Atmar 1986).

Function nesteddisc implements discrepancy index which is the number of ones that should be shifted to fill a row with ones in a table arranged by species frequencies (Brualdi & Sanderson 1999). The original definition arranges species (columns) by their frequencies, but did not have any method of handling tied frequencies.

The nesteddisc function tries to order tied columns to minimize the discrepancy statistic but this is rather slow, and with a large number of tied columns there is no guarantee that the best ordering was found. In that case a warning of tied columns will be issued.

Function nestedtemp finds the matrix temperature which is defined as the sum of “surprises” in arranged matrix. In arranged unsurprising matrix all species within proportion given by matrix fill are in the upper left corner of the matrix, and the surprise of the absence or presences is the diagonal distance from the fill line (Atmar & Patterson 1993). Function tries to pack species and sites to a low temperature (Rodríguez-Gironés & Santamaria 2006), but this is an iterative procedure, and the temperatures usually vary among runs. Function nestedtemp also has a plot method which can display either incidences or temperatures of the surprises. Matrix temperature was rather vaguely described (Atmar & Patterson 1993), but Rodríguez-Gironés & Santamaria (2006) are more explicit and their description is used here. However, the results probably differ from other implementations, and users should be cautious in interpreting the results. The details of calculations are explained in the vignette Design decisions and implementation that you can read using functions vignette or vegandocs. Function nestedness in the bipartite package is a direct port of the BINMATNEST programme of Rodríguez-Gironés & Santamaria (2006).

Function nestednodf implements a nestedness metric based on overlap and decreasing fill (Almeida-Neto et al., 2008). Two basic properties are required for a matrix to have the maximum degree of nestedness according to this metric: (1) complete overlap of 1's from right to left columns and from down to up rows, and (2) decreasing marginal totals between all pairs of columns and all pairs of rows. The nestedness statistic is evaluated separately for columns (N columns) for rows (N rows) and combined for the whole matrix (NODF). If you set order = FALSE, the statistic is evaluated with the current matrix ordering allowing tests of other meaningful hypothesis of matrix structure than ordering by row and column totals (see Almeida-Neto et al. 2008).

Value

The result returned by a nestedness function contains an item called statistic, but the other components differ among functions. The functions are constructed so that they can be handled by oecosimu.

Author(s)

Jari Oksanen and Gustavo Carvalho (nestednodf).

References

Almeida-Neto, M., Gumarães, P., Gumarães, P.R., Loyola, R.D. & Ulrich, W. (2008). A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos 117, 1227–1239.

Atmar, W. & Patterson, B.D. (1993). The measurement of order and disorder in the distribution of species in fragmented habitat. Oecologia 96, 373–382.

Brualdi, R.A. & Sanderson, J.G. (1999). Nested species subsets, gaps, and discrepancy. Oecologia 119, 256–264.

Patterson, B.D. & Atmar, W. (1986). Nested subsets and the structure of insular mammalian faunas and archipelagos. Biol. J. Linnean Soc. 28, 65–82.

Rodríguez-Gironés, M.A. & Santamaria, L. (2006). A new algorithm to calculate the nestedness temperature of presence-absence matrices. J. Biogeogr. 33, 924–935.

Stone, L. & Roberts, A. (1990). The checkerboard score and species distributions. Oecologia 85, 74–79.

Wright, D.H., Patterson, B.D., Mikkelson, G.M., Cutler, A. & Atmar, W. (1998). A comparative analysis of nested subset patterns of species composition. Oecologia 113, 1–20.

See Also

In general, the functions should be used with oecosimu which generates Null model communities to assess the nonrandomness of nestedness patterns.

Examples

data(sipoo)
## Matrix temperature
out <- nestedtemp(sipoo)
out
plot(out)
plot(out, kind="incid")
## Use oecosimu to assess the nonrandomness of checker board units
nestedchecker(sipoo)
oecosimu(sipoo, nestedchecker, "quasiswap")
## Another Null model and standardized checkerboard score
oecosimu(sipoo, nestedchecker, "r00", statistic = "C.score")

[Package vegan version 1.16-32 Index]