Version 2.0.5 ------------- DOCUMENTATION * Added references to Hallett et al. (2016) and Avolio et al. (2019) to DESCRIPTION and README BUG FIXES * Resolved silent error (no longer silent in R 4.1) from failure to use output of `match.arg` (#122). Version 2.0.4 ------------- BUG FIXES * Adapt to R 4.0 breaking change for string to factor conversion (PR # 118) Version 2.0.3 ------------- BUG FIXES * Allow multivariate_ and abundance_difference to use `reference.treatment` with pooling. * Eliminate superfluous treatment.var argument. * Return NA for inconclusive multivariate_change and _difference results (see also vegandevs/vegan#306). Version 2.0.2 ------------- BUG FIXES * use codyn::Evar rather than codyn::EQ in RAC_difference * fixes for breaking change in testthat (PR #111) Version 2.0.1 ------------- DOCUMENTATION * use `@inheritParams` to reduce redundancy BUG FIXES * elminate unverifiable centroid calculation in vegan::betadisper ([#306](https://github.com/vegandevs/vegan/issues/306)) * better error message (#108) * fix handling of Null arguments (#95) Version 2.0.0 ------------- NEW FUNCTIONS * community_structure: Calculates richness and evenness (using specified metric) for a replicate * community_diversity: Calculates diversity (using specified metric) for a replicate * RAC_change: Calculates changes in species richness, evenness, species' ranks, gain, and losses for a replicate over time * abundance_change: For each species in a replicate, calculates changes in abundance over time * curve_change: Calculates changes in the shape of the RAC curve for each replicate over time * multivariate_change: Calculates changes in community composition and dispersion over time * RAC_difference: Calculates differences in species richness, evenness, species' ranks, shared species between paired samples at a single point in time * abundance_difference: Calculates differences in abundance for each species in paired samples at a single point in time * curve_difference: Calculates differences in the shape of the RAC between paired samples at a single point in time * multivariate_difference: Calculates differences in community composition and dispersion of all replicates between treatments at a single point in time BUG FIXES Previous warnings have been changed to errors. Version 1.1.0 ------------- NEW FEATURES * Add S3 class for cyclic_shift *#66) * add an alias for `temporal_torus_translation` (#65) BUG FIXES * selectively import from stats and assertthat (#64) * adjustments to coding consistency (#63) * import 'stats' and 'permute' package methods (#69) * Improved function and parameter names Version 1.0.1 ------------- BUG FIXES * Fixed bug to ensure data frames are ordered before unlisting (#58) * Fixed bug in temporal_torus_translation to correctly recognize numeric data (#59) * Fixed bug in synchrony (Gross) with only 1 spp in a plot (#60) * Fixed bug in calculating variance ratio if species counts are constant (#61) Version 1.0.0 ------------- NEW FEATURES * Initial version (see help topic for 'codyn', e.g. "?codyn") * Includes functions for temporal community dynamics analysis NEW FUNCTIONS * turnover: Calculates species turnover between time periods * mean_rank_shift: Calculates the mean relative change in species rank abundances * rate_change: Calculates the rate change in a community over time * rate_change_interval: Produces a data frame containing differences in species composition between samples at increasing time intervals * community_stability: Calculates community stability over time * variance_ratio: Computes the ratio of the variance of aggregate species abundances in a community * synchrony: Calculates the degree synchrony in species abundances * temporal_torus_translation: Calculates a null test statistic using a temporal modification of the torus translation * temporal_torus_translation_CI: Returns confidence intervals calculated from a temporal modification of the torus translation