  CHANGES IN entropart VERSION 1.4.1
  ==================================

NEW FEATURES 

  o 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.
  o ChaoPD() and AllenH() now accept phylo trees.
  o Richness now returns a named value. The name contains the estimator used.
  o 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 

  o The entropy estimation of a distribution with no singleton returned NA with ChaoWangJost correction. Corrected.
  o Entropy or diversity of a vector of zeros returned 0. It now returns NA.
  
  
  
  CHANGES IN entropart VERSION 1.3.3
  ==================================

NEW FEATURES 

  o Abundance and probability vector objects. See ?SpeciesDistribution
  o Hurlbert diversity. See ?Hurlbert
  o Optimal.Similarity.
  o Miller-Madow estimator of entropy (Miller, 1955) added in bcShannon().
  o Chao and Jost (2015) estimator of diversity added in bcTsallis() and bcDiversity(). New "best" estimator.
  o Chao et al. (2015) probability estimation of observed species. See ?TunedPs
  o Estimators of the number of species. See ?Richness
  o Abundance Frequency Count of species. See ?AbdFreqCount
  o Community profiles can be calculated with confidence intervals. See ?CommunityProfile
  o Random Communities. See ?rCommunity

BUG CORRECTION 

  o 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.
  o 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).



  CHANGES IN entropart VERSION 1.2.1
  ==================================

NEW FEATURES 

  o Zhang and Grabchak (2014) bias correction for Shannon beta entropy added.
  o Unbiased estimator of Rao's entropy added (bcRao).

BUG CORRECTION 

  o DqZ() and Hqz() returned an error if all probability values were 0 except one.

IMPROVEMENTS

  o Improved readability of error messages for bad arguments.
  o Improved formating of summmary.DivPart(). Lines were too long.
  o Improved legend for the x-axis of plot.DivPart ("alpha and gamma" instead of "alpha/gamma").
  o Improved support of PhyloValue objects (summary added).
  o Improved help for MetaCommunity.


  CHANGES IN entropart VERSION 1.2.0
  ==================================

BUG CORRECTION 

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


  CHANGES IN entropart VERSION 1.2.0
  ==================================

NEW FEATURES 

  o Full support of similarity-based diversity added 

IMPROVEMENTS

  o Default values for arguments added whenever possible.


  CHANGES IN entropart VERSION 1.1.4
  ==================================

NEW FEATURES 

  o Zhang(2012) bias correction for Shannon entropy added. 
  o Zhang and Grabchak (2014) bias correction for Tsallis entropy added. 

BUG CORRECTION 

  o Divest() always calculated neutral diversity of simulated communities so the confidence interval was erroneous for phylodiversity. Corrected.

  CHANGES IN entropart VERSION 1.1.3
  ==================================

NEW FEATURES 

  o Paracou618.dist distance matrix between species of Paracou618.MC added. 


IMPROVEMENTS

  o Imports directive rather than Depends for ade4.
  o mergeandlabels does not return warnings any longer (column names are better addressed).


BUG CORRECTION

  o Legend was not displayed in plot.DivProfile(..., Which="Communities"). Corrected.


  CHANGES IN entropart VERSION 1.1.2
  ==================================
  
NEW FEATURES 

  o Chao, Wang and Jost (2013) bias correction for Shannon entropy added.
  o EntropyCI function added: Entropy of Monte-Carlo simulated communities.
  o Tools to manipulate MetaCommunity objects added (see ?MergeMC)
  o SimTest class added to test a value against a simulated distribution (see ?SimTest).
  o Vignette added.


BUG CORRECTION 

  o Hqz() was erroneous for q!=1. Corrected.
  o bcPhyloEntropy() and bcPhyloDiversity() returned an incorrect $Distribution component. Corrected.
  o summary.MCentropy() did not return the name of the tree. Corrected.


CHANGES IN entropart VERSION 1.1.1
==================================
  
OVERVIEW 

	o First version.
