Parametric bootstrap test of a null model of i.i.d., but spatially
autocorrelated species against clustering of the species' occupied
areas (or alternatively nestedness). In spite of the lots of
parameters, a standard execution (for the default test statistics, see
parameter teststat below) will be
prabmatrix <- prabinit(file="path/prabmatrixfile",
neighborhood="path/neighborhoodfile")
test <- prabtest(prabmatrix)
summary(test)
Note: Data formats are described
on the prabinit help page. You may also consider the example datasets
kykladspecreg.dat and nb.dat. Take care of the
parameter rows.are.species of prabinit.
prabtest(prabobject, teststat = "distratio", tuning = switch(teststat,
distratio = 0.25, lcomponent = floor(3 * ncol(prabobject$distmat)/4),
isovertice = ncol(prabobject$distmat), nn = 4, NA), times = 1000,
pd = NULL, prange = c(0, 1), nperp = 4, step = 0.1, step2=0.01,
twostep = TRUE,
sf.sim = FALSE, sf.const = sf.sim, pdfnb = FALSE, ignore.richness=FALSE)
# S3 method for prabtest
summary(object, above.p=object$teststat %in%
c("groups","inclusions","mean"),
group.outmean=FALSE,...)
# S3 method for summary.prabtest
print(x, ...)
prabtest prodices
an object of class prabtest, which is a list with components
vector of test statistic values for all simulated populations.
test statistic value for the original data.'
the p-value.
see above.
see above.
regression coefficients from autoconst.
see above.
the distance measure chosen, see prabinit.
the geco-distance tuning parameter (only informative if
distance="geco"), see prabinit.
see above.
see above.
see above.
summary.prabtest produces an object of class
summary.prabtest, which is a list with components
range of the simulation results (test statistic values)
of object.
mean of the simulation results (test statistic values)
of object.
directly
taken from object, see prabtest and abundtest.
if object$teststat="groups", components
rrangeg (matrix of group-wise ranges of test statistic
value), rmeang (vector of group-wise means of test statistic
value), rrangem (range over simulations of overall mean of
within-group dissimilarities), rmeanm (mean over simulations
of overall mean of within-group dissimilarities) are added to the
list object$groupinfo, and this is given out.
an object of class prab (presence-absence data), as
generated by prabinit.
string, indicating the test statistics. "isovertice":
number of isolated vertices in the graph of tuning
smallest distances
between species. "lcomponent": size of largest connectivity
component in this graph. "distratio": ratio between tuning
smallest and largest distances. "nn": average distance of species to
tuningth nearest neighbor.
"inclusions": number of inclusions between areas of different
species (tests for nestedness structure, not for clustering).
integer or (if teststat="distratio") numerical
between 0 and 1. Tuning constant for test statistics, see
teststat.
integer. Number of simulation runs.
numerical between 0 and 1. The probability that a new
region is drawn from the non-neighborhood of the previous regions
belonging to a species under generation. If NA (the default),
prabtest estimates this by function
autoconst. Otherwise the next five parameters have no effect.
numerical range vector, lower value not smaller than 0, larger
value not larger than 1. Range where pd is to be found. Used
by function autoconst.
integer. Number of simulations per pd-value. Used
by function autoconst.
numerical between 0 and 1. Interval length between
subsequent choices of pd for the first simulation. Used
by function autoconst.
numerical between 0 and 1. Interval length between
subsequent choices of pd for the second simulation (see
parameter twostep). Used
by function autoconst.
logical. If TRUE, a first estimation step for
pd is
carried out in the whole prange, and then the final
estimation is determined between the preliminary estimator
-5*step2 and +5*step2. Else, the first simulation
determines the final estimator. Used
by function autoconst.
logical. Indicates if the range sizes of the species
are held fixed
in the test simulation (TRUE) or generated from their empirical
distribution in x (FALSE). See function randpop.nb.
logical. Same as sf.sim, but for estimation of
pd by autoconst.
logical. If TRUE, the probabilities of the regions
are modified according to the number of neighboring regions in
randpop.nb, see Hennig and Hausdorf (2002), p. 5. This is
usually no improvement.
logical. If TRUE, there is no assumption
of species richnesses to differ between regions in the null model.
Regionwise probabilities don't differ in the generation of null
data.
object of class prabtest.
logical. TRUE means that for output from
abundtest the p-value is
p.above, otherwise p.below.
logical. If TRUE and
object$teststat="groups", statistics concerning the mean of
all dissimilarities are given out by print.summary.prabtest.
object of class summary.prabtest.
no meaning, necessary for print and summary methods.
Christian Hennig christian.hennig@unibo.it https://www.unibo.it/sitoweb/christian.hennig/en
From the original data, the distribution of the
range sizes of the species, the autocorrelation parameter pd
(estimated by autoconst) and the distribution on the regions
induced by the relative species numbers are taken. With these
parameters, times populations according to the null model
implemented in randpop.nb are generated and the test statistic
is evaluated. The resulting p-value is number of simulated statistic
values more extreme than than the value of the original data+1
divided by times+1. "More extreme" means smaller for
"lcomponent", "distratio", "nn", larger for
"inclusions", and
twice the smaller number between the original statistic value and the
"border", i.e., a two-sided test for "isovertice".
If pd=NA was
specified, a diagnostic plot
for the estimation of pd is plotted by autoconst.
For details see Hennig
and Hausdorf (2004) and the help pages of the cited functions.
Hennig, C. and Hausdorf, B. (2004) Distance-based parametric bootstrap tests for clustering of species ranges. Computational Statistics and Data Analysis 45, 875-896. http://stat.ethz.ch/Research-Reports/110.html.
Hausdorf, B. and Hennig, C. (2003) Biotic Element Analysis in Biogeography. Systematic Biology 52, 717-723.
Hausdorf, B. and Hennig, C. (2003) Nestedness of north-west European land snail ranges as a consequence of differential immigration from Pleistocene glacial refuges. Oecologia 135, 102-109.
prabinit generates objects of class prab.
autoconst estimates pd from such objects.
randpop.nb generates populations from the null model.
An alternative model is given by cluspop.nb.
Some more information on the test statistics is given in
homogen.test, lcomponent,
distratio, nn,
incmatrix.
The simulations are computed by pop.sim.
options(digits=4)
data(kykladspecreg)
data(nb)
set.seed(1234)
x <- prabinit(prabmatrix=kykladspecreg, neighborhood=nb)
# If you want to use your own ASCII data files, use
# x <- prabinit(file="path/prabmatrixfile",
# neighborhood="path/neighborhoodfile")
kpt <- prabtest(x, times=5, pd=0.35)
# These settings are chosen to make the example execution
# a bit faster; usually you will use prabtest(kprab).
summary(kpt)
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