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/output/tree-diversity-analysis

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


Version 2.7-2 (August 2016)

	* compatible with Rcmdr	2.3-0 (August 2016) and vegan 2.4-0 (June 2016)

	* new function ensemble.threshold to calculate threshold values to differentiate
		between absence and presence suitabilities. This function was used earlier
		only internally in the ensemble.test, ensemble.test.splits and ensemble.batch
		functions, whereas it is now available and documented as separarte function.

	* corrected error in makecommunitydataset (error reported by Pascal Hirsch)

	* Graphical User Interface (GUI) now supports following functions or options from 
	vegan:

		o dispweight function (via Transform community matrix menu)
		o fitspecaccum function (via options of "arrhenius", "gleason", "gitay", 
			"lomolino", "asymp", "gompertz", "michaelis-menten", "logis" and 
			"weibull" in Species accumulation curves menu)
		o specslope function (via options in Species accumulation curves menu)
		o rareslope function (via options in Species accumulation curves menu)
		o rarefy function  (via options in Species accumulation curves menu)
		o tsallis function (via options in Renyi profile menu)
		o tsallisaccum function (via options in Renyi profile menu)	
		o dbrda function (via Constrained ordination menu)
		o monoMDS function (via Unconstrained ordination menu)
		o stressplot function (via unconstrained and constrained ordination menus)
		o betadisper function (via Compare distance matrices menu)
		o designdist function (in Distance matrix calculation menu)
		o Lingoes and Cailliez adjustments for wcmdscale, capscale, dbrda and 
			betadisper
		o sqrt.dist argument for wcmdscale, capscale, dbrda and betadisper
		o descriptive string of "species" in scaling of ordination axes (via
			unconstrained and constrained ordination menus)
		o RsquareAdj function for cca, dbrda and capscale (in summaries of constrained 
			ordination)
		o ordibar function (via plotting functions for unconstrained and constrained
			ordination)
		o plotting factor levels in different colours with ordihull, ordiarrows, 
			ordisegments, ordispider, ordibar and ordiellipse (via plotting 
			functions for unconstrained and contrained ordination)
		o summary and ordiareatest for ordihull and ordiellipse (via plotting 
			functions for unconstrained and contrained ordination)
		o ehull option of ordiellipse ((via plotting functions for unconstrained 
			and contrained ordination))

	* change in calculation for ensemble.threshold function when using thresholds from the
		PresenceAbsence package with ensemble.threshold options of "threshold.mean"
		and "threshold.min": five thresholds from the PresenceAbsence package will
		be used (see Details)

	* new parameter ENSEMBLE.weight.min to set minimum output weight for ensemble.test,
		ensemble.test.splits and ensemble.batch. Note that parameter ENSEMBLE.min
		refers to the minimum input weight (and typically used to exclude algorithms
		with low AUC values).

	* ensemble.plot allows to add country boundaries (via maptools package)

	* ensemble.plot exports breaks and colours if only one suitability map is plotted

	* breaks are forced to be unique in ensemble.plot

	* ensemble.analogue gives warning is variables are very strongly correlated with 
	method 'mahal' (as algorithm my fail)

	* corrected problem in ensemble.novel function when x only has one layer

	* avoid error when launching the GUI when dismo package was not installed

	* corrected error in labeling the y-axis in reyniplot function (error reported by
	Mauricio Carrasquilla)


Version 2.7-1 (April 2016)

	* ensemble.batch: procedure stops when no algorithms retained in the k-fold
	cross-validation procedure

	* new Graphical User Interface (GUI) for renaming layer names of calibration
	and prediction stacks

	* included link to Hijmans RJ and Elith J. 2016. Species distribution modelling with R.	

	* options to set width and height of new graphical device for ensemble.plot,
	evaluation.strip.plot and ensemble.centroids functions. Setting any of these parameters
	to a value < 0 results in no opening of a new device .


Version 2.7-0 (March 2016)

	* new Graphical User Interface (GUI) for ensemble suitability modelling.
	Guidelines for getting started are available from the GUI and in the 'doc'
	folder of BiodiversityR

	* included the ensemble.mean function within ensemble.batch, so that
	ensemble.batch also produces the mean ('_MEAN_') ensemble files when several
	ensembles are calibrated via ensemble.batch

	* new function ensemble.plot, especially to apply a colourscheme that
	differentiates between suitabilities below and above a threshold that
	discriminates between predicted absence-presence of the organism

	* new feature in the evaluation.strip.plot to include a boxplot for the 
	presence locations of a data set used for model calibrations

	* included help buttons in various GUI windows


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 function importancevalue to calculate Importance Value Index, and new
	ifri data set (collaboration with the International Forestry Resources and Institutions 
	[IFRI] research network; http://www.ifriresearch.net)  

	* 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