CRAN release 2.7-2

vegan 2.7-2 is on CRAN. Many files have changed, but most of these changes are small technical tweaks that do not influence most users (but may make vegan marginally faster and more robust in some rare cases). Two most important changes are:

• permutation tests for partial RDA and db-RDA adopt similar pattern as partial CCA in CRAN release 2.6-6, and use "residualized predictors". Non-partial RDA and db-RDA are not influenced. Earlier add1 method and anova(..., by = "axis") internally used partial model, but this does not make sense with residualized permutations, and were redesigned. Now add1 and drop1 are consistent for ordination models, whereas they used different internal models in earlier releases.
• The working with tibbles is more robust. Earlier vegan failes its tests if all example data frames were replaced with tibbles. The main problem was that tibbles often do not have real rownames, but vegan assumed named results. Now tibbles and data frames give similar results also for names.

CRAN release 2.7-1

This is a major release that changes many functions. The most important changes are:

• Conventional graphics for constrained ordination (cca, rda, dbrda, capscale) were completely redesigned. Each score type can be independently configured. The location of text labels can be optimized to avoid over-writing, and text labels can be written on opaque labels which guarantees that at least the uppermost is readable. Alternatively, ordination graphics can be constructed using pipes (|>) that allow adding each score type independently. The changes are most important for constrained ordination that have several different score types, but also apply to all ordination graphics.
• adonis is defunct in favour of adonis2. This can break packages, scripts and code that still uses old function. We have given a message on future deprecation since CRAN release 2.6-2 (2022-04-17), and formally deprecated adonis in CRAN release 2.6-6 (2024-05-21). See announcement #641 for fixing your code.
• New functions include MDSaddpoints to add new points to an existing NMDS ordination with support functions.
• Robust Aitchinson distance with matrix completion for zero entries was added to vegdist and corresponding standardization in decostand.

The detailed user-visible changes are best inspected in NEWS.

CRAN Release 2.6-10

Version 2.6-10 is now on CRAN. See NEWS for user-visible changes. These are not many. The main reason for the release was that 2.6-8 had "undefined behaviour" in one C function. This change was not mentioned in NEWS, because I could not be sure that the issue was fixed. I was personally pretty confident of fixing this but I could not replicate the CRAN test results nor guarantee that they were fixed. Current CRAN tests are OK so presumably the issue was fixed. Although undefined behaviour is undefined the issue seems to be harmless because function did not access the item when it was undefined. The issue is very technical: if you really are interested, the critical bug fix is 525dce5.

Full Changelog: v2.6-8...v2.6-10

CRAN release 2.6-8

Many things change, but most changes are minor bug fixes or improved features. Perhaps the most visible change is adding pca, ca and pco functions for unconstrained ordination. For detailed changes, check NEWS.

Critical Bug Fix 2.6-6.1 on CRAN

Internal C function had a "protection error" which could crash R in unpredictable and non-repeatable ways: Function could run quite normally hundreds of times and then crash. The C function was used in several R functions, and errors could occur, e.g. in envfit (especially vectorfit), wcmdscale, capscale and varpart of Chi-square. The release is identical to 2.6-6 except for this bug fix. You should absolutely upgrade.

vegan 2.6-6 on CRAN

See NEWS for new things. The main thing may be unbiased permutation code for CCA significance tests.

This release will break (or prepare to break) some old things.

• adonis is deprecated in favour of adonis2. We have had a deprecation message from vegan 2.6-2 (April 2022), but now this was turned into a warning. Instructions for changing your code are given in #641.
• We deprecate the use of summary to get ordination scores: use scores() instead. As this is a side effect we do not know if you misused summary for scores and we cannot warn. For this release we still enable this bad habit, but you should change your code. Instructions are given in #644.
• Further changes and planned new features are discussed in #645.

vegan 2.6-4 on CRAN

This version has numerous changes all over the code, but nothing very dramatic. Many people may like improved support for making ggplot2 graphics with scores function optionally producing data frames that can be directly used for flexible graphics. For an extensive and detailed description of changes, see NEWS.

vegan 2.6-2 in CRAN

New CRAN release was based on the current master branch. The old cran-2.5 will no longer be updated. For details of changes, see the NEWS in the package. Use command news(package="vegan") in R session to read the news.

Here a brief summary:

• Compiled code was fixed for upcoming R 4.2.0 release, and you must upgrade vegan with new R.
• Several functions can now return their results in tidy format allowing easier use of ggplot2 graphics.
• adonis2 is the new major function for analysis of dissimilarites. The old adonis is still available, but it will be deprecated in the next minor release.
• Aitchison and robust Aitchison distances and standardization were added.
• Unbiased Simpson diversity was added, and diversity gained a groups argument for pooled diversities.
• Following github issues were addressed: #369, #393, #401, #427, #447, #463, #497, #501, #507.

CRAN release 2.5-7

vegan 2.5-7 was released to CRAN on Nov 28, 2020. See NEWS for most important changes.

This release fixes github issues #352, #354, #369, #372, #374 and #382.

vegan 2.5-4 released

vegan 2.5-4 was released on CRAN. This fixes testing errors in R-devel due to changes in formula (issue #299) and errors with new optional tests in R-devel (issue #305). Bugs were fixed in decorana (issue #303) and goodness.cca and also documentation glitches (issue #304). Adjusted R² is again enabled in rda and cca (issue #295).