removing dependency of R library installations on user (Allen==1)
added apTreeshape library to the package vector (and added call to it in previous commit)
added calculation of maximum root distance in the phylogeny to the regional.calc and xregion.analysis functions
added calculation of beta (tree imbalance) and commented out code for calculating Blomberg's K
modified output filenames to be written
modified specification of timeslices to use for analysis
added option to read in simulation files that have already been unzipped in the event that a zipped file does not exist
deleted all mentions of pre.equil.time which was only used for the now obsolete 'pre-equilibrium' scenario
modified specification of timeslices based on num.of.time.slices, which.time.slices, and time.sequence
tried to tidy up nightmare of indicator variables for specifying time slices to use; probably still needs to be completely revised