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