entropart 1.6-8 2021-06-04

Bug correction

  • An error occured when a function was called with entopart:: prefix and CheckArguments = TRUE and entropart was loaded.

entropart 1.6-7 2021-04-16

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)

entropart 1.6-6 2020-11-03

Bug correction

  • argument main in autoplot() was ignored.

entropart 1.6-4 2020-01-22

Improvements

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

entropart 1.6-3 2020-01-08

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 2019-04-11

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 2018-02-05

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 2017-11-22

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 2017-03-29

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 2016-12-09

entropart 1.4-5 2016-02-17

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 2016-01-13

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 2015-12-07

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().

entropart 1.4.1 2015-09-29

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 2015-09-08

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 2014-11-13

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 2014-05-17

Bug Correction

  • ChaoPD() returned an incorrect value when q=0 and some probabilities =0.

entropart 1.2.0 2014-05-17

New Features

  • Full support of similarity-based diversity added

Improvements

  • Default values for arguments added whenever possible.

entropart 1.1.4 Unreleased

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 2014-03-22

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

entropart 1.1.1 2013-09-10

  • First Version.