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codyn 2.0.6

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

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

BUG FIXES

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

codyn 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).

codyn 2.0.2

BUG FIXES

• use codyn::Evar rather than codyn::EQ in RAC_difference
• fixes for breaking change in testthat (PR #111)

codyn 2.0.1

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

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

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

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

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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