entropart 1.6-15
Bug correction
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.
User-visible changes
- pkgdown site is now built with the bootstrap 5 template.
entropart 1.6-12
Bug correction
- Corrected
Coverage()
documentation.
- “Marcon” correction of Shannon’s entropy never returned
Grassberger’s estimate. This was very rarely an issue.
- Phylogenetic trees of class
phylo
with multichotomies
raised an error when they were preprocessed by
Preprocess.Tree()
.
entropart 1.6-11
Bug correction
- Corrected NEWS file structure.
entropart 1.6-10
Improvements
- Deprecated
aes_(x=~var)
aesthetics in ggplots replaced
by aes(x=.data$var)
.
- entropart no longer suggests SPECIES.
entropart 1.6-9
Bug correction
Coverage2Size
raised an error when the distribution had
no singletons.
Improvements
- entropart no longer depends on ggplot2.
entropart 1.6-8
Bug correction
- An error occured when a function was called with
entopart::
prefix and CheckArguments = TRUE
and entropart was loaded.
entropart 1.6-7
Bug correction
- argument
main
in autoplot()
was
ignored.
Improvements
- Continuous integration by GitHub Actions.
CommunityProfile()
does not recenter simulated
diversity values if simulated community size is not that of the actual
community. $mid
can store mean simulated values.
- CodeFactor recommendations applied.
col
, pch
, cex
and
lty
arguments in autoplot
s.
- The first column of a dataframe passed to
MetaCommunity()
with species names may be characters
instead of factors.
- tibbles are accepted by
MetaCommunity()
.
- Empty communities are detected by
Metacommunity()
and
raise an error with an explicit message rather than returning obscure
error messages when used by DivPart()
and others.
- Suggests rmarkdown (https://github.com/yihui/knitr/issues/1864)
entropart 1.6-6
Bug correction
- argument
main
in autoplot()
was
ignored.
entropart 1.6-4
Improvements
- No longer imports geiger package (required by CRAN).
entropart 1.6-3
New features
- Argument
JackMax
to limit the order of the jacknife
estimator in Richness()
, whatever the data.
Bug correction
- plot.SpeciesDistribution did not fit the logseries and the broken
stick distributions correctly.
- autoplot.DivProfile did not produce appropriate labels in the local
communities profile.
entropart 1.6-1
New features
- Estimation of diversity at a chosen level (sample size or coverage).
DivAccum()
function.
- Entropy accumulation functions.
- ggplot2 supported.
autoplot()
methods added for
entropart objects.
- The “Best” estimator of diversity is now “UnveilJ” and the default
estimator of richness is “Jackknife”.
- The “ChaoWangJost” estimator is renamed “ChaoJost”.
Improvements
- Unit tests added.
- Vignette by pkgdown.
Bug correction
- The jaccknife estimator of richness returned an error for
communities where all species had the same abundance.
Richness
returned 0 instead of 1 for a community with a
single species.
entropart 1.5-3
Improvements
- On Travis now.
- Reduced package size.
- The rule to calculate the number of individuals of MetaCommunities
has been changed to improve gamma diversity bias correction. See the
user manual vignette.
- Generic function arguments cleaned up.
Bug Correction
- Very large metacommunities returned an integer overflow error.
entropart 1.4-8
Bug Correction
HqzBeta()
returned erroneous values if a species
probability was equal to zero.
Improvements
- On GitHub now.
- Documentation updated: phylogenetic dendrograms can be of class
phylo
, phylog
, hclust
or
PPtree
whatever the function.
- The introduction vignette is HTML now.
- A new vignette is dedicated to phylogenies.
entropart 1.4-7
Bug Correction
- Argument checking (
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.
Improvements
- Explicit export of all non-internal functions instead of
exportPattern("^[[:alpha:]]+")
- Updated references to published articles.
- Updated
help("entropart")
.
- New introduction vignette.
- Vignettes compiled with knitr instead of
Sweave.
entropart 1.4-6
Improvements
- LazyData is used to save memory.
- Better reporting of the argument names in embedded calls of
functions.
Bug Correction
- The simulation of log-series communities was incorrect.
entropart 1.4-5
User-visible changes
- Generalized Simpson’s entropy and diversity added
(
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.
Improvements
- ZhangGrabchak estimator of entropy is now calculated by the C code
of
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.
entropart 1.4-4
User-visible changes
DivProfile()
now allows computing bootstrap confidence
intervals.
Bug Correction
- The entropy estimation (of order different from 1) of a distribution
with no singleton returned
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.
entropart 1.4-3
User-visible changes
- All scalar values of diversity or entropy are now named. Their name
is the bias correction used to obtain them.
- The
Unveiled
estimator is more versatile.
Correction = "Unveil"
is deprecated and replaced by
UnveilC
, UnveiliC
or UnveilJ
in
functions such as Tsallis()
or
Diversity()
.
Improvements
- Parallelization of
DivProfile()
,
CommunityProfile()
and PhyloApply()
using the
parallel package mclapply. No effect on Windows, pretty much
faster on other systems.
- Extensive use of
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.
Bug Correction
- Using
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.
- The richness estimator
iChao1
returned NA
if the distibution contained singletons but no doubletons.
Corrected.
entropart 1.4.1
New Features
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.
- Updated CITATION: the paper about this package has been
published: Eric Marcon, Bruno Herault (2015). entropart: An R Package to
Measure and Partition Diversity. Journal of Statistical
Software, 67(8), 1-26.
Bug Correction
- The entropy estimation of a distribution with no singleton returned
NA
with ChaoWangJost
correction.
Corrected.
- Entropy or diversity of a vector of zeros returned 0. It now returns
NA
.
entropart 1.3.3
New Features
- Abundance and probability vector objects. See
?SpeciesDistribution
.
- Hurlbert diversity. See
?Hurlbert
.
Optimal.Similarity
.
- Miller-Madow estimator of entropy (Miller, 1955) added in
bcShannon()
.
- Chao and Jost (2015) estimator of diversity added in
bcTsallis()
and bcDiversity()
. New “best”
estimator.
- Chao et al. (2015) probability estimation of observed species. See
?TunedPs
.
- Estimators of the number of species. See
?Richness
.
- Abundance Frequency Count of species. See
?AbdFreqCount
.
- Community profiles can be calculated with confidence intervals. See
?CommunityProfile
.
- Random Communities. See
?rCommunity
.
Bug Correction
- Applying
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.
- Allowed rounding error was too small on some systems (typically
r-patched-solaris-sparc) to recognize probability vectors. The
difference between their sum and 1 had to be less than 3 times
.Machine$double.eps
. Now set to S times (where S is the
number of species, i.e the vector’s length).
entropart 1.2.1
New Features
- Zhang and Grabchak (2014) bias correction for Shannon beta entropy
added.
- Unbiased estimator of Rao’s entropy added (
bcRao
).
Bug Correction
DqZ()
and Hqz()
returned an error if all
probability values were 0 except one.
Improvements
- Improved readability of error messages for bad arguments.
- Improved formating of
summmary.DivPart()
. Lines were
too long.
- Improved legend for the x-axis of
plot.DivPart
(“alpha
and gamma” instead of “alpha/gamma”).
- Improved support of
PhyloValue
objects (summary
added).
- Improved help for
MetaCommunity
.
entropart 1.2.0
Bug Correction
ChaoPD()
returned an incorrect value when q=0 and some
probabilities =0.
entropart 1.2.0
New Features
- Full support of similarity-based diversity added
Improvements
- Default values for arguments added whenever possible.
entropart 1.1.4
New Features
- Zhang(2012) bias correction for Shannon entropy added.
- Zhang and Grabchak (2014) bias correction for Tsallis entropy
added.
Bug Correction
Divest()
always calculated neutral diversity of
simulated communities so the confidence interval was erroneous for
phylodiversity. Corrected.
entropart 1.1.3
New Features
Paracou618.dist
distance matrix between species of
Paracou618.MC
added.
- Chao, Wang and Jost (2013) bias correction for Shannon entropy
added.
EntropyCI
function added: Entropy of Monte-Carlo
simulated communities.
- Tools to manipulate MetaCommunity objects added (see
?MergeMC
).
SimTest
class added to test a value against a simulated
distribution (see ?SimTest
).
- Vignette added.
Improvements
Imports
directive rather than Depends
for
ade4.
mergeandlabel
does not return warnings any longer
(column names are better addressed).
Bug Correction
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.
- Legend was not displayed in
plot.DivProfile(..., Which="Communities")
. Corrected.
entropart 1.1.1