# ChangeLog file put under the \inst folder


BiodiversityR versions

	This ChangeLog provides information on new functions integrated in
	the package and some required updates. Updates related to error
	messages for new versions of the base and loaded packages are
	typically not included here (as these were addressed).

	BiodiversityR details on installation are available from:
	http://www.worldagroforestry.org/resources/databases/tree-diversity-analysis

	The manual accompanying the original version of BiodiversityR is
	available from:
	http://www.worldagroforestry.org/downloads/Publications/PDFS/B13695.pdf

Version 2.6-1 (January 2016)

	* ensemble.centroid and ensemble.zones: New functions to determine centroid 
	locations in principal components space of presence locations of an organism. 
	Mahalanobis distance from centroid locations to map zones based on the
	minimum distance from centroid locations.

	* report information on spatial sorting bias in ensemble.test.

	* CIRLES.at and CIRCLES.d options in ensemble.test function to reduce spatial 
	sorting bias between evaluation presence and absence locations

	* threshold.PresenceAbsence option in ensemble.test to use the PresenceAbsence
	package to calculate absence-presence thresholds.
	
	* ensemble.novel: New function to map novel environmental conditions.
	
	* ensemble.area: New function to calculate areas of suitability raster maps.

	* ensemble.analogue: New function to map environmental (climate) analogues.
	
	* ensemble.ecocrop: New function to map suitability based on temperature 
	and rainfall optimal and absolute ranges.

	* corrected problem in handling probit-transformations in ensemble.raster function

	* started ChangeLog


Version 2.5-4 (September 2015)

	* compatibility with Rcmdr restored (eg qqPlot)

	* menu interface scripts updated	

	* new menu option of Analysis of diversity > Add diversity variables to data set

	* new menu option of silhouette in the Cluster analysis plot options


Version 2.5-3 (July 2015)

	* changes in the CAPdiscrim function to result in same results as PRIMER (problem
	handled by including as.dist() function prior to cmdscale() function).

	* new menu option of replacing NA with 0 in the community data set

	* corrected problem in ensemble.test.splits function in obtain AUC-derived
	weights for submodels when weights are not tuned

	* ensured that subfolder to save models is created (ensemble.test function)
	
	* included package information for function visibility


Version 2-5.2 (April 2015)

	* included droplevels() function in function ensemble.test

	* avoiding loading of libraries in ensemble functions (including gam::s()
	for gam formula)

	* included topography-derived variables in BCI.env data (provided by P. Legendre)


Version 2-5.1 (November 2014)

	* menu option to remove species with zero total abundance

	* handle new 8-character species codes in vegan in examples

	* include options to plot as.phylo() cluster dendrograms

	* option to reorder cluster dendrograms

	* option to plot symbols in cluster diagrams

	* BiodiversityR start up message

	* expand vegan functions from menu interface (vegemite, tabasco, coverscale,
	screeplot, bioenv, betadisper, contribdiv, beals, betadiverr, wcmscale, pcnm,
	polaccum, estaccumR, eventstar, indpower, isomap, meandist, nestedchecker,
	nestedtemp, nestednodf, nestedbetasor, nestedbetajac, RsquareAdj, drarefy,
	simper, treeheight)

	* corrected problems with jackknife of diversity analysis (diversityresult
	function with method='jackknife')


Version 2-4.4 (May 2014)

	* new PROBIT option in ensemble.test function to transform outputs of 
	ensemble submodels with probit transformation (also supported in 
	ensemble.raster function)	

	* new ENSEMBLE.exponent option to modify weights of ensemble submodels
	in ensemble model by using exponent

	* corrected use of persp() for accumulated renyi profiles in menu interface


Version 2-4.1 (January 2014)

	* new functions of ensemble.simplified.categories and ensemble.dummy.variables

	* new function of ensemble.evaluation.strip

	* only allow ensemble calibration in ensemble.test and ensemble.test.splits
	functions

	* include legends in menu-interface generated plots no longer via locator()

Older versions

	* mainly changes related to newer version of R base and loaded packages,
	including changes required to maintain compatility with R-commander


