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Changelog

Source: NEWS.md

codyn (development version)

DOCUMENTATION

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

codyn 2.0.6

CRAN release: 2026-09-18

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)

codyn 2.0.5

CRAN release: 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

CRAN release: 2020-05-06

BUG FIXES

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

codyn 2.0.3

CRAN release: 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

CRAN release: 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

CRAN release: 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)

codyn 2.0.0

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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