High-Performance Open-Source Archive
Geom*$default_aes by their values for
compatibility with ggplot2 3.6.0 (PR #3 by @teunbrand)PhyloApply() sometimes raised an “Error in m[, 1] :
incorrect number of dimensions” due to the automatic conversion of a
single-row matrix to a vector by lapply(). This happened
when the tree’s upper slice contained a single species.Coverage() documentation.phylo with multichotomies
raised an error when they were preprocessed by
Preprocess.Tree().aes_(x=~var) aesthetics in ggplots replaced
by aes(x=.data$var).Coverage2Size raised an error when the distribution had
no singletons.entopart:: prefix and CheckArguments = TRUE
and entropart was loaded.main in autoplot() was
ignored.CommunityProfile() does not recenter simulated
diversity values if simulated community size is not that of the actual
community. $mid can store mean simulated values.col, pch, cex and
lty arguments in autoplots.MetaCommunity() with species names may be characters
instead of factors.MetaCommunity().Metacommunity() and
raise an error with an explicit message rather than returning obscure
error messages when used by DivPart() and others.main in autoplot() was
ignored.JackMax to limit the order of the jacknife
estimator in Richness(), whatever the data.DivAccum() function.autoplot() methods added for
entropart objects.Richness returned 0 instead of 1 for a community with a
single species.HqzBeta() returned erroneous values if a species
probability was equal to zero.phylo, phylog, hclust or
PPtree whatever the function.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.exportPattern("^[[:alpha:]]+")help("entropart").GenSimpson and GenSimpsonD).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.EntropyEstimation::Tsallis.z/Entropy.z
rather than the R code of bcTsallis(). This is much faster
when the number of individual is high. Applies to
ChaoWangJost (Best) estimator too.DivProfile() now allows computing bootstrap confidence
intervals.NA with
ChaoWangJost correction. Reported by Zach Marion. Only
partly corrected in Version 1.4-1. Corrected.DivEst returned incorrect beta diversity if q was not
1. Corrected.Unveiled estimator is more versatile.
Correction = "Unveil" is deprecated and replaced by
UnveilC, UnveiliC or UnveilJ in
functions such as Tsallis() or
Diversity().DivProfile(),
CommunityProfile() and PhyloApply() using the
parallel package mclapply. No effect on Windows, pretty much
faster on other systems.vapply() instead of
sapply() makes some functions faster.AllenH() and ChaoPD() returned
NA if 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.phylog trees in AllenH and
ChaoPD() returned erroneous unnormalized diversity (divided
by two) because of the conVersion of phylog to
htree divides branch lengths by two. Corrected.iChao1 returned NA
if the distibution contained singletons but no doubletons.
Corrected.phylog objects (deprecated in ade4) are
replaced by phylo trees from package ape in the
definition of the PPtree class. Issues caused by
phylog such as replacing . and -
by _ in species names do not occur any longer.
phylog trees are still accepted for compatibility.ChaoPD() and AllenH() now accept
phylo trees.Richness now returns a named value. The name contains
the estimator used.NA with ChaoWangJost correction.
Corrected.NA.?SpeciesDistribution.?Hurlbert.Optimal.Similarity.bcShannon().bcTsallis() and bcDiversity(). New “best”
estimator.?TunedPs.?Richness.?AbdFreqCount.?CommunityProfile.?rCommunity.bcTsallis and similar functions with a
probability vector instead of abundance values could cause errors
depending in the correction. Correction is now forced to
None with a warning..Machine$double.eps. Now set to S times (where S is the
number of species, i.e the vector’s length).bcRao).DqZ() and 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”).PhyloValue objects (summary
added).MetaCommunity.ChaoPD() returned an incorrect value when q=0 and some
probabilities =0.Divest() always calculated neutral diversity of
simulated communities so the confidence interval was erroneous for
phylodiversity. Corrected.Paracou618.dist distance matrix between species of
Paracou618.MC added.EntropyCI function added: Entropy of Monte-Carlo
simulated communities.?MergeMC).SimTest class added to test a value against a simulated
distribution (see ?SimTest).Imports directive rather than Depends for
ade4.mergeandlabel does not return warnings any longer
(column names are better addressed).Hqz() was erroneous for q<>1. Corrected.bcPhyloEntropy() and bcPhyloDiversity()
returned an incorrect $Distribution component.
Corrected.summary.MCentropy() did not return the name of the
tree. Corrected.plot.DivProfile(..., Which="Communities"). Corrected.
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