2020-08-31 Version 1.2-4 * Removed '$' from entries in help files following updates to how R processes equations in help-file entries in R >=4.2. 2021-06-14 Version 1.2-3 * PGLMM vignette generates a warning (sometimes) under Linux; used set.seed to remove uncertainty 2020-10-12 Version 1.2-2 * Removed apTreeshape as dependency (and so Colless' index) at CRAN's request 2020-07-26 Version 1.2-1 * DESCRIPTION - formatR added to suggests for vignettes (at CRAN's request) * shape.R - is.binary.tree --> is.binary (at ape's request) 2019-02-26 Version 1.2-0 * assemblage.phylogenies - bug in species dropping (affecting IAC and PAE); hat-tip to Carlos Alberto Arnillas * pez-pglmm-overview - minor (but very important!) correction to site and species factor creation (hat-tip to Andrew Tanentzap) * removed .Random.seed object in laja data * added congeneric.impute; fixed regular expression issues in congeneric.merge - hat-tip to Josep Padulles Cubino 2016-01-15 Version 1.1-1 * eco.scape.R & scape.R - changed return type, stopped crashing bug on certain parameter combinations (hat-tip to Ben Weinstein) * metrics.R - more descriptive documentation for .pd (hat-tip to Max Farrell), IMPORTANT change to calculation of .scheiner * CITATION - updated now manuscript released * pez-pglmm-overview - new overview vignette * pglmm.R - corrected mis-specified documentation/code 2015-07-29 Version 1.1-0 * metric.null.R - added generic metrics, metric null distributions, and changed wrapper naming * scale.R - changed return values * CITATION - added citation file 2015-02-10 Version 1.0-0 * pglmm.R - created, examples added to vignette * comparative.comm.R - added wrappers * shape.R - removed PVR package dependency