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

codyn: Community Dynamics Metrics

Version 2.0.2

BUG FIXES

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

codyn 2.0.1

codyn: Community Dynamics Metrics

Version 2.0.0

DOCUMENTATION

• use @inheritParams to reduce redundancy

BUG FIXES

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

codyn 2.0.0

codyn: Community Dynamics Metrics

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.

codyn 1.1.0

codyn: Community Dynamics Metrics

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

codyn 1.0.1

codyn: Community Dynamics Metrics

This is a patch release of codyn, providing bug fixes for several edge cases with specific types of data.

• 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)

codyn 1.0.0

codyn: Community Dynamics Metrics

• 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