Nothing
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 autoplot
s.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.Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.