updates for surface v0.4 namespace: changed geiger and igraph to suggests, not depends, and no longer importing them in NAMESPACE. changed ape and ouch to imports, not depends. Added MASS to dependencies. removed pmc (currently archived) from imported packages functions: addRegime: line 44 - changed the fill-in AIC value for any branches that had an error to +9999 instead of +1, to avoid conflicts if error_skip=TRUE and sample_shifts=TRUE and sample_threshold >=1 collapseRegimes: now using :: to load igraph functions without importing package convertBack: deleted a problematic line (line 6) that occasionally changed the identity of the first regime when it shouldn't have pmcSurface: this function has been deleted for the time being, and will be restored when the pmc package is back on CRAN or when we write an alternative function for parametric bootstrap specific to SURFACE Hansen models runSurface: now returns a warning if nodes not named, if nodes not named properly, or if dat not a data frame surfaceBackward: now returns a warning if nodes not named properly surfaceForward: now returns a warning if nodes not named properly surfaceSimulate: now using :: to use updated geiger functions (vcv.phylo and transform.phylo) for simulations with type="BM" rather than importing package help files: surface-package.Rd: updated email address surfaceTreePlot.Rd: fixed error in optellipses stationary distribution surfaceTreePlot.Rd: fixed link to "surfaceAICPlot.Rd" all .Rd files: updated references to Ingram & Mahler, Mahler et al.