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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.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.