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latest NEWS after checking reverse dependencies
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jarioksa committed May 12, 2024
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The new scheme only concerns CCA which is a weighted method, and RDA
and dbRDA permutation is unchanged.

* `summary` of constrained ordination methods (RDA, CCA, dbRDA) is
less verbose, and gives only summaries of conditional, constrained
and residual components and of eigenvalues. Ordination scores are no
longer printed, but these can be extracted with `scores`
function. Issue
[#203](https://github.com/vegandevs/vegan/issues/203).
* `summary` of ordination results no longer prints ordination scores
that often are so voluminous that they hide the real summary; see issue
[#203](https://github.com/vegandevs/vegan/issues/203). Ordination
scores should be extracted with `scores` function. This breaks some
CRAN packages that use `summary.cca` to extract scores. These should
switch to use `scores`. The maintainers have been contacted and
patch files are suggested to adapt to this change. See
[instructions](https://github.com/vegandevs/vegan/discussions/644)
to fix the packages.

* `scores` function for constrained ordination (CCA, RDA,dbRDA)
default to return all types of scores (`display = "all"`). Function
can optionally return a single type of scores as a list of one matrix
instead of returning a matrix (new argument `droplist`).

* Constrained ordination objects (`cca`, `rda`, `dbrda`) fitted
without formula interface can have permutation tests (`anova`) by
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packages that still use `adonis` although we have contacted all
their authors in June 2022 and again in April 2024, and printed a
message of forthcoming deprecation since **vegan** 2.6-2. See issue
[#523](https://github.com/vegandevs/vegan/issues/523).
[#523](https://github.com/vegandevs/vegan/issues/523). See
[instructions](https://github.com/vegandevs/vegan/discussions/641)
to adapt your packages and functions to use `adonis2`.

* `orditkplot` was moved to CRAN package **vegan3d** and is deprecated
in **vegan**. See issue
[#585](https://github.com/vegandevs/vegan/issues/585) and
announcement
[#632](https://github.com/vegandevs/vegan/discussions/632)

* The use of `summary` to extract ordination scores is no longer
accepted: you should use `scores` to extract scores. `summary.cca`
has a kluge that allows the use of `summary` to extract scores, but
it does not work in all use cases, and will be removed in the next
release. For `summary.cca` see
[instructions](https://github.com/vegandevs/vegan/discussions/644)
to change your package. `summary.decorana` is deprecated.

* Support was removed from ancient `cca` objects (results of `cca`,
`rda`, `dbrda` or `capscale`) generated before CRAN release 2.5
(2016). If you still have such stray relics, use
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