NEWS
codyn 2.0.5 (2020-12-01)
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).
codyn 2.0.4 (2020-05-06)
BUG FIXES
- Adapt to R 4.0 breaking change for string to factor conversion (PR # 118)
codyn 2.0.3 (2019-09-17)
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).
codyn 2.0.2 (2019-04-09)
BUG FIXES
- use codyn::Evar rather than codyn::EQ in RAC_difference
- fixes for breaking change in testthat (PR #111)
codyn 2.0.1 (2019-03-08)
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)
codyn 2.0.0 (2018-06-12)
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
codyn 1.1.0 (2016-04-27)
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
codyn 1.0.1 (2016-01-15)
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)
codyn 1.0.0 (2015-10-20)
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