nestedchecker(comm)
nestedn0(comm)
nesteddisc(comm)
nestedtemp(comm, ...)
## S3 method for class 'nestedtemp':
plot(x, kind = c("temperature", "incidendce"),
col=rev(heat.colors(100)), names = FALSE, ...)
plot
.comm
.statistic
, but the other components differ among functions. The
functions are constructed so that they can be handled by
oecosimu
.oecosimu
to analyse
the nonrdanomness 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). Function nestedtemp
finds the
matrix temperature which is defined as the sum of 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
vignette
Design decisions
and implementation that you can read using functions
vignette
or vegandocs
.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.
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.
oecosimu
which generates Null model communities to assess the nonrandomness of
nestedness patterns.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")
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