From c837f7f1912a126d871ab44db8147739fc56352f Mon Sep 17 00:00:00 2001 From: Jari Oksanen Date: Sun, 12 May 2024 14:18:55 +0300 Subject: [PATCH] latest NEWS after checking reverse dependencies (cherry picked from commit cdb1b8a4e3261c12759f1ccbc3d631398585c5f3) --- inst/NEWS.md | 32 +++++++++++++++++++++++++------- 1 file changed, 25 insertions(+), 7 deletions(-) diff --git a/inst/NEWS.md b/inst/NEWS.md index 1048782e9..4acea7485 100644 --- a/inst/NEWS.md +++ b/inst/NEWS.md @@ -27,12 +27,20 @@ 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 @@ -134,7 +142,9 @@ 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 @@ -142,6 +152,14 @@ 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