CommunityProfile()does not recenter simulated diversity values if simulated community size is not that of the actual community.
$midcan store mean simulated values.
MetaCommunity()with species names may be characters instead of factors.
Metacommunity()and raise an error with an explicit message rather than returning obscure error messages when used by
JackMaxto limit the order of the jacknife estimator in
Richness(), whatever the data.
autoplot()methods added for entropart objects.
HqzBeta()returned erroneous values if a species probability was equal to zero.
CheckArguments = TRUE) is not possible when the package is not loaded and a function is called by
entropart::function(). An error was returned. It is replaced by a warning.
Originality.Species()is deprecated because it is pointless.
ade4::originality()allows calculating it for q=2. Leinster (2009) and Leinster and Meckes (2015) showed that
Originality.Species()does not depend on the order of diversity.
DivProfile()now allows computing bootstrap confidence intervals.
PhyloApply()using the parallel package mclapply. No effect on Windows, pretty much faster on other systems.
sapply()makes some functions faster.
NAif the tree contained more species than the probability vector. Now, the tree may be pruned or kept unchanged and extra species considered to have probabilities 0.
ChaoPD()returned erroneous unnormalized diversity (divided by two) because of the conVersion of
htreedivides branch lengths by two. Corrected.
NAif the distibution contained singletons but no doubletons. Corrected.
phylogobjects (deprecated in ade4) are replaced by
phylotrees from package ape in the definition of the
PPtreeclass. Issues caused by
phylogsuch as replacing
_in species names do not occur any longer.
phylogtrees are still accepted for compatibility.
Richnessnow returns a named value. The name contains the estimator used.
bcDiversity(). New “best” estimator.
bcTsallisand similar functions with a probability vector instead of abundance values could cause errors depending in the correction. Correction is now forced to
Nonewith a warning.
.Machine$double.eps. Now set to S times (where S is the number of species, i.e the vector’s length).
Hqz()returned an error if all probability values were 0 except one.
summmary.DivPart(). Lines were too long.
plot.DivPart(“alpha and gamma” instead of “alpha/gamma”).
PhyloValueobjects (summary added).
ChaoPD()returned an incorrect value when q=0 and some probabilities =0.
Paracou618.distdistance matrix between species of
EntropyCIfunction added: Entropy of Monte-Carlo simulated communities.
SimTestclass added to test a value against a simulated distribution (see
Importsdirective rather than
mergeandlabeldoes not return warnings any longer (column names are better addressed).