Changes in version 2.0.6 (2026-09-18)                  

DOCUMENTATION

  - Added a pkgdown website with a list of publications that cite codyn,
    compiled monthly from OpenAlex (Issue #136)

BUG FIXES

  - Fixed roxygen documentation errors by switching to RMarkdown syntax
    (Issue #135)
  - Fixed package documentation to use _PACKAGE (Issue #135)
  - Fixed docs for community_stability (Issue #128)

                 Changes in version 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).

                 Changes in version 2.0.4 (2020-05-06)                  

BUG FIXES

  - Adapt to R 4.0 breaking change for string to factor conversion (PR
    # 118)

                 Changes in version 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).

                 Changes in version 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)

                 Changes in version 2.0.1 (2019-03-08)                  

DOCUMENTATION

  - use @inheritParams to reduce redundancy

BUG FIXES

  - eliminate unverifiable centroid calculation in vegan::betadisper
    (#306)
  - better error message (#108)
  - fix handling of Null arguments (#95)

                 Changes in version 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.

                 Changes in version 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

                 Changes in version 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)

                 Changes in version 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