Updates in surface_0.3: addRegime -fixed an error that affected analyses where the "aic_threshold" provided differed from zero. -fixed the working of the "sample_shifts" option, which was not applying the correct filter (that a candidate model had to have a delta-AICc below "aic_threshold" in addition to within "sample_threshold" of the best model). collapseRegimes -fixed an error that affected analyses where the "aic_threshold" provided differed from zero. -fixed the working of the "sample_shifts" option, which was not applying the correct filter (that a candidate model had to have a delta-AICc below "aic_threshold" in addition to within "sample_threshold" of the best model). convertTreeData -unused line designating "onames" deleted. pmcSurface -the "pmc" package is now suggested rather than a dependency; an error will be returned if this function is called and "pmc" is not available. runSurface -fixed an error where supplied values of "aic_threshold" were not passed to the functions "surfaceForward" and "surfaceBackward", resulting in the use of the default value of 0. surfaceAICMultiPlot -new function: plot AICc values for multiple SURFACE runs, potentially analyses of a number of credible trees, or repeated analyses of a tree with stochasticity in the stepwise process (using "sample_shifts"). surfaceAICPlot -new functionality: option to draw multiple lines representing the deviance or "partial AICc" of each trait at each step of the analysis, in addition to the overall AICc. -new functionality: option to scale AICc (and deviance) values to the initial value, allowing values for different traits to be expressed relative to the starting model. surfaceForward -fixed an error that affected analyses where the "aic_threshold" provided differed from zero. surfaceSummary -new functionality: can now take both forward and backward phases of a SURFACE analysis and summarize them together (or summarize either one separately) -now returns a matrix of likelihoods for each trait at each step, as well as the regime structure (k, k', c, etc) at each step (used in surfaceAICPlot and surfaceAICMultiPlot) surfaceTraitPlot -new functionality: option to draw ellipses around inferred optima indicating the stationary standard deviation of the OU process given the inferred alpha and sigma_sq parameters. -new functionality: can plot unidimensional trait data (separates regimes on y-axis) -fixed code that led to an error when obtaining colors if there are no non-convergent regimes (can occur if a lineage shifted back to the ancestral regime) surfaceTreePlot -fixed code on line 5 that led to an error if an object (from surfaceForward, surfaceBackward or surfaceSimulate) was supplied with data for only one trait. -fixed code that led to an error when obtaining colors if there are no non-convergent regimes (can occur if a lineage shifted back to the ancestral regime) Documentation files: -moved surfaceAICPlot from the help file "surfaceTreePlot.Rd" to the new help file "surfaceAICPlot.Rd", combined with surfaceAICMultiPlot. -fixed the description for "shifts" in "surfaceSimulate.Rd" (mistakenly had the same description as "n_shifts". -fixed the description of aic_threshold in "surfaceForward", "surfaceBackward", "addRegime", "collapseRegimes", "runSurface", specifically that more stringent thresholds should be *negative* values. -minor changes to the wording and fixing of typos in all .Rd files. -added a (not run) Example in the "surface-package.Rd" help file showing readers how to access the tutorial.