NEWS.md
Coverage() documentation.phylo with multichotomies raised an error when they were preprocessed by Preprocess.Tree().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.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.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.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.?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.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.