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 It has been replaced by lapply to be robust.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.