Finished major revisions to internal package checks, inputs. Arguments are much easier to specify, and functions are better equipped to deal with outputs of varying sizes. Many functions were changed, and it is possible some things may have broken. Please report any issues on the GitHub site.
Continuing under the hood improvements: almost all downstream functions can now handle outputs from the simulation functions of variable length and dimensions with regards to which spatial simulations, null models and metrics were included. The functions metricPerformance and nullPerformance still need revision.
Major improvements in the way metrics, null models and spatial simulations can be specified. If only a subset of pre-defined options are desired, rather than needing to pass a named list of functions, these functions now accept character vectors corresponding to the options as defined in defineMetrics(), defineNulls(), and defineSimulations(). Can still accommodate new metrics, nulls and simulations defined on the fly.
Added a new null model, synthComm, that creates a synthetic community based on species attributes. It will create synthetic total community niche spaces based on the dispersion in trait space of the input communities. Particularly relevant to looking at niche overlap either between the species from multiple sites, or the individuals from multiple species. This is an experimental null model, so confirm it is working before using it extensively in your analyses. Report any issues on the GitHub site.
Added functional dispersion functions, sensu Laliberte and Legendre (2010). The two new relevant functions are FDis and centers. They take similar inputs to dbFD from the FD package, but can be calculated across a variety of ordination spaces (PCA, PCoA, NMDS, etc), instead of only with a PCoA. These functions and the theoretical background are still experimental, and should be treated as such.
Added prepFieldData, calcField, and sesField. Calculation of phylogenetic and trait fields is now a two-step process, where the data are prepped, then the metrics and nulls of interest are calculated over the prepped object. phyloField, traitField, sesPhyloField, and sesTraitField will be deprecated in future versions of the package.
Added mean root distance (MRD) and mean distance to the most recent common ancestor of a sample (distMRCA). For MRD, added both presence-absence and abundance-weighted forms, and for distMRCA, added ability to calculate both the distance to the overall MRCA of a sample, and the distance to the average of the pairwise MRCAs.