• Deprecated aes_(x=~var) aesthetics in ggplots replaced by aes(x=.data$var). • entropart no longer suggests SPECIES. ### Bug correction • Coverage2Size raised an error when the distribution had no singletons. ### Improvements • entropart no longer depends on ggplot2. ### Bug correction • An error occured when a function was called with entopart:: prefix and CheckArguments = TRUE and entropart was loaded. ### 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 autoplots.
• 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)

### Bug correction

• argument main in autoplot() was ignored.

### Improvements

• No longer imports geiger package (required by CRAN).

### 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.

### 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

• 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.

### 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.

### 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.

### 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.

### 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.

### 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.

### 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().

### 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.

### 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). ### 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. ### Bug Correction • ChaoPD() returned an incorrect value when q=0 and some probabilities =0. ### New Features • Full support of similarity-based diversity added ### Improvements • Default values for arguments added whenever possible. ### 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. ### 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.
• First Version.