CHANGES IN PHYLOCLIM VERSION 0.9-3

BUG FIXES
    o Due to an unconsistent behavior of sapply some data 
      prodeced meaningless p-values in age.range.correlation. 
      It has been replaced by lapply to be robust. 
      (thanks to Dan Warren for bug report)		


      CHANGES IN PHYLOCLIM VERSION 0.9-2

BUG FIXES
    o There was a mistake in the calculation of p-values in
      niche.equivalency.test and the print method for both
      niche.quivalency.test and bg.similarity.test stated the null
      hypothesis instead of the alternative hyposthesis. (thanks to 
      Guarino Colli for bug report)

NEW FEATURES
    o The confidence level for CIs in bg.similarity.test can now be
      set via the option conf.level.
    o niche.equivalency.test and bg.similarity.test are now able to use
      categorical environmental covariates.


		CHANGES IN PHYLOCLIM VERSION 0.9-1

IMPROVED FEATURES
    o Calculation of nonparametric confidence intervals in 
      bg.similarity.test.


		CHANGES IN PHYLOCLIM VERSION 0.9-0

IMPROVED FEATURES
    o The code of functions niche.equivalency.test and bg.similarity.test
      has been completely rewritten to match exactly the definition in 
      Warren et al. (2011). Previous versions had relied entirely on the 
      SWD-format (see MAXENT tutorial), which was quicker and easy to im-
      plement at the cost of altering the definition of the back-
      ground similarity test.
    o niche.equivalency.test and bg.similarity.test now produce output
      objects of class 'ntest'. For class 'ntest' a print and a plot
      method have been included, the latter replacing the former 
      non-generic functions plotNicheEquivalency and 
      plotBackgroundSimilarity.


		CHANGES IN PHYLOCLIM VERSION 0.8-5
      
BUG FIXES

    o Plotting of tiplabels in function plotAncClim has been completey
      reworked and is now robust regarding the scale of the phylogenetic 
      tree. Have a look at ?plotAncClim and note the new arguments tipmode, 
      tipspace, cladespace, and nchar. The functionality of arguments 
      show.tips and xspace has been included in tipmode and cladespace, 
      respectively. Note that cladespace is still in a somewhat 
      experimental state.
    
    		
		CHANGES IN PHYLOCLIM VERSION 0.8-4
      
BUG FIXES

    o Code of function pno was reworked and is now ca. 20 percent faster
      than in version 0.8.3. This is due to the replacement of the 
      dependancy on adehabitat for raster map import by pno's own import 
      device for raster layers.
    o A check for correct path_model argument is included in function pno.


		CHANGES IN PHYLOCLIM VERSION 0.8-3
      
Improved documentation of plotAncClim().


		CHANGES IN PHYLOCLIM VERSION 0.8-2
      
BUG FIXES

    o Some users obtained PNOs containing NA values because the 
      distibution of NODATA values (e.g., -9999) in their bioclimatic data 
      and in their ENM models was different. This problem might arise when
      raster maps differ slightly in their coastlines. The function pno()
      will now issue a warning in these cases and treat the corresponding 
      cells as having zero probability in the ENM (e.g., the MAXENT    
      distribution).	
    o plotPNO() is now capable of handling PNO matrixes with only one 
      species.


		CHANGES IN PHYLOCLIM VERSION 0.8-1
      
Only minor changes in the documentation of PHYLOCLIM.


		CHANGES IN PHYLOCLIM VERSION 0.8
      
BUG FIXES

    o The formula of Fitzpatrick and Turelli (2006) was incorrectly 
      implemented in the function age.range.correlation. First, it 
      used 'n' (instead of n - 1) to weight the overlap statistic 'o'. 
      Second, the function was not summing 'o' correctly over all 
      species in both clades. (thanks to Pedro Abell?n and 
      Ben Fitzpatrick for bug report and suggestions for a fix)
	

		CHANGES IN PHYLOCLIM VERSION 0.6

BUG FIXES

    o There was mistake in the formala for the calculation of 
      Hellingers distance in the original publication of Warren,
      Glor and Turelli (2008, Evolution 62:2868-2883; see also
      http://enmtools.blogspot.com/2010/09/error-in-i-metric-but-
      dont-panic.html). The corrected formula is now implemented
      in getDI. As stressed by Dan Warren the error is only a
      scaling issue and does not affect the p-values of the tests 
      based upon it. (thanks to Pascal Title for bug report)
		
		
		CHANGES IN PHYLOCLIM VERSION 0.5
      
BUG FIXES

    o Function bg.similarity.test was mislead by different 
      choices of column names in the SWD files, e.g. "species" 
      instead of "spec". The function can now handle any column 
      name. (thanks to Pascal Title for bug report)


		CHANGES IN PHYLOCLIM VERSION 0.4

NEW FEATURES

    o The functions niche.equivalency.test and bg.similarity.test have
      a new argument mx, which controls the number of memory that is given
      to JAVA during the calls to MAXENT.
      
BUG FIXES

    o The functions niche.equivalency.test and bg.similarity.test were
      not fully Window compatible. (thanks to Alastirs Potts for the fix)


		CHANGES IN PHYLOCLIM VERSION 0.3

NEW FEATURES

    o The function plotPNO has now an argument legend.pos to control
      the position of the legend. Alternatively, the plotting of
      the legend can now be suppressed.