oecosimu collects and evaluates the
statistics. The Null model communities are described in
make.commsim and permatfull/
permatswap, the definition of Null models in
nullmodel, and nestedness statistics in
nestednodf (which describes several alternative
statistics, including nestedness temperature, $N0$, checker
board units, nestedness discrepancy and NODF).oecosimu(comm, nestfun, method, nsimul = 99, burnin = 0, thin = 1, statistic = "statistic", alternative = c("two.sided", "less", "greater"), batchsize = NA, parallel = getOption("mc.cores"), ...)
"as.ts"(x, ...)
"as.mcmc"(x)nullmodel or an object of class simmat (array
of permuted matrices from simulate.nullmodel). If
comm is a community data, null model simulation
method must be specified. If comm is a
nullmodel, the simulation method is ignored,
and if comm is a simmat object, all other arguments
are ignored except nestfun, statistic and
alternative.nestedtemp), but any
function can be used if it accepts the community as the first
argument, and returns either a plain number or a vector or the
result in list item with the name defined in argument
statistic. See Examples for defining your own functions.make.commsim or a
commsim function. This argument is ignored if
comm is a nullmodel or a simmat
object. See Details and Examples.comm is a simmat object)."tswap")
(ignored with non-sequential methods or when comm is a
simmat object).comm is a simmat
object).nestfun."two.sided" (default), "greater"
or "less". Please note that the $p$-value of two-sided
test is approximately two times higher than in the corresponding
one-sided test ("greater" or "less" depending on the
sign of the difference).NA the analysis is
not broken into batches. See Details.parallel = 1 uses ordinary, non-parallel
processing. The parallel processing is done with parallel
package. If you define a nestfun in Windows that needs other
R packages than vegan or permute, you must set up a
socket cluster before the call. oecosimu result object.oecosimu returns an object of class
"oecosimu". The result object has items statistic and
oecosimu. The statistic contains the complete object
returned by nestfun for the original data. The
oecosimu component contains the following items:
alternative.method used in nullmodel.TRUE if method was sequential.oecosimu is a wrapper that evaluates a statistic
using function given by nestfun, and then simulates a series
of null models based on nullmodel, and evaluates the
statistic on these null models. The vegan packages contains
some nestedness functions that are described separately
(nestedchecker, nesteddisc,
nestedn0, nestedtemp,
nestednodf), but many other functions can be used as
long as they are meaningful with simulated communities. An
applicable function must return either the statistic as a plain
number or a vector, or as a list element "statistic" (like
chisq.test), or in an item whose name is given in the
argument statistic. The statistic can be a single number
(like typical for a nestedness index), or it can be a vector. The
vector indices can be used to analyse site (row) or species (column)
properties, see treedive for an example. Raup-Crick
index (raupcrick) gives an example of using a
dissimilarities. The Null model type can be given as a name (quoted character string)
that is used to define a Null model in make.commsim.
These include all binary models described by Wright et al. (1998),
Jonsson (2001), Gotelli & Entsminger (2003), Miklós &
Podani (2004), and some others. There are several quantitative Null
models, such those discussed by Hardy (2008), and several that are
unpublished (see make.commsim,
permatfull, permatswap for
discussion). The user can also define her own commsim
function (see Examples).
Function works by first defining a nullmodel with
given commsim, and then generating a series of
simulated communities with simulate.nullmodel. A
shortcut can be used for any of these stages and the input can be
comm), Null model function
(nestfun) and the number of simulations (nsimul).
nullmodel object and the number of
simulations, and argument method is ignored.
simulate.nullmodel, and arguments
method and nsimul are ignored.
The last case allows analysing several statistics with the same simulations.
The function first generates simulations with given
nullmodel and then analyses these using the
nestfun. With large data sets and/or large number of
simulations, the generated objects can be very large, and if the
memory is exhausted, the analysis can become very slow and the
system can become unresponsive. The simulation will be broken into
several smaller batches if the simulated nullmodel
objective will be above the set batchsize to avoid memory
problems (see object.size for estimating the size of
the current data set). The parallel processing still increases the
memory needs. The parallel processing is only used for evaluating
nestfun. The main load may be in simulation of the
nullmodel, and parallel argument does not help
there.
Function as.ts transforms the simulated results of sequential
methods into a time series or a ts object. This allows
using analytic tools for time series in studying the sequences (see
examples). Function as.mcmc transforms the simulated results
of sequential methods into an mcmc object of the
coda package. The coda package provides functions for
the analysis of stationarity, adequacy of sample size,
autocorrelation, need of burn-in and much more for sequential
methods, and summary of the results. Please consult the
documentation of the coda package.
Function permustats provides support to the standard
density, densityplot,
qqnorm and qqmath functions for
the simulated values.
Gotelli, N.J. & Entsminger, N.J. (2003). Swap algorithms in null model analysis. Ecology 84, 532--535.
Jonsson, B.G. (2001) A null model for randomization tests of nestedness in species assemblages. Oecologia 127, 309--313.
Miklós, I. & Podani, J. (2004). Randomization of presence-absence matrices: comments and new algorithms. Ecology 85, 86--92.
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 currently defines null models with
commsim and generates the simulated null model
communities with nullmodel and
simulate.nullmodel. For other applications of
oecosimu, see treedive and
raupcrick. Function rndtaxa
(labdsv package) randomizes a community table. See also
nestedtemp (that also discusses other nestedness
functions) and treedive for another application.
## Use the first eigenvalue of correspondence analysis as an index
## of structure: a model for making your own functions.
data(sipoo)
## Traditional nestedness statistics (number of checkerboard units)
oecosimu(sipoo, nestedchecker, "r0")
## sequential model, one-sided test, a vector statistic
out <- oecosimu(sipoo, decorana, "swap", burnin=100, thin=10,
statistic="evals", alt = "greater")
out
## Inspect the swap sequence as a time series object
plot(as.ts(out))
lag.plot(as.ts(out))
acf(as.ts(out))
## Density plot
densityplot(permustats(out), as.table = TRUE, layout = c(1,4))
## Use quantitative null models to compare
## mean Bray-Curtis dissimilarities
data(dune)
meandist <- function(x) mean(vegdist(x, "bray"))
mbc1 <- oecosimu(dune, meandist, "r2dtable")
mbc1
## Define your own null model as a 'commsim' function: shuffle cells
## in each row
foo <- function(x, n, nr, nc, ...) {
out <- array(0, c(nr, nc, n))
for (k in seq_len(n))
out[,,k] <- apply(x, 2, function(z) sample(z, length(z)))
out
}
cf <- commsim("myshuffle", foo, isSeq = FALSE, binary = FALSE,
mode = "double")
oecosimu(dune, meandist, cf)
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