vegan - CRAN release 2.7-3

This release deprecates lattice functions with better ggplot2 alternatives in ggvegan new on CRAN. This release addresses issues #444, #759, #761 and #762 For details, see NEWS.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa 3 months ago

vegan - 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.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa 8 months ago

vegan - 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.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa about 1 year ago

vegan - 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 525dce5b38bc9a113decf6e8c205a8c3c4318d79.

Full Changelog: https://github.com/vegandevs/vegan/compare/v2.6-8...v2.6-10

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 1 year ago

vegan - 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.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa almost 2 years ago

vegan - 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.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa about 2 years ago

vegan - 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.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa about 2 years ago

vegan - 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.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 3 years ago

vegan - 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.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa about 4 years ago

vegan - 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.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 5 years ago

vegan - 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).

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 7 years ago

vegan - CRAN release 2.5-3

• passes CRAN tests more cleanly with alternaltive BLAS/Lapack libraries (issue #282).
• Fixes handling empty data in constrained ordination (issue #291).
• Checks for valid numerical input in several functions (issues #284, #292).
• Fixes handling missing values in envfit.
• Fixes scalilng of rda results in simulate.
• Improved checking of valid input in anosim.
• Refuses to show Broken-stick distribution when there are negative eigenvalues in dbrda.
• print method for betadisper is more configurable.
• Deprecates humpfit which is moved to natto package (issue #289).

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 7 years ago

vegan - CRAN release 2.5-2

vegan 2.5-2 was released on the Norwegian Constitution Day, 2018 (happy syttende mai!). This is a minor maintenance release. See discussion in issue #280 for main features.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa about 8 years ago

vegan - CRAN release 2.5-1

This is a major new release. Nearly 40% of all program files were changed. The most significant changes were that compiled code (with .Call interface) is used much more extensively, constrained ordination methods were refactored to use unified code base, and ecological null models were made made more effective. See the NEWS file in the latest release for detailed changes.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa about 8 years ago

vegan - CRAN 2.4-4 release

This is a minor release that fixes the following issues

• orditkplot passes CRAN tests.
• anova(<cca-object>, by = "axis") ignored partial terms. Function uses now forward testing which is less dangerously biased than previous marginal tests.
• summary and inertcomp for RDA, CCA and frieds failed if constraints had zero rank.
• meandist labels are no longer cropped in plots.
• Canberra distance in vegdist can now handle negative entries in input.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa almost 9 years ago

vegan - CRAN release 2.4-3

• Registers C and Fortran routines: no longer NOTE in checking the package.
• Fixes weighting issues with cca result object: changes in centring of biplot scores, in as.mlm methods, and in intersetcor and spenvcor.
• Allows correlation scaling in biplot.rda.
• Allows using species scores in envfit and ordisurf.
• Allows using non-standard variable names in Condition in constrained ordination method.
• Fixes issues in ordiR2step and only allows forward selection.
• Allows configuration of ordispider plots for WA/LC scores in constrained ordination.
• Fixes several issues in tolerance.cca

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa about 9 years ago

vegan - CRAN release 2.4-2

vegan 2.4-2 was released in CRAN on 17/1/17. The release contains more complete NEWS. The major changes are:

• Fixes permutation tests in distance-based constrained ordination (issue #198, PR #199).
• Fixes internal scaling of scores in some constrained ordination methods.
• Fixes weighting in intersetcor
• Fixes issue #219 in betadisper permutation tests.
• Fixes (invisible) return object of ordicluster.
• Fixes tolerance.cca (issue #216).
• Changes scaling of biplot arrows in constrained ordination plots.
• Adds new argument and improves colour coding of small positive values in tabasco.
• Faster nullmodel generation.
• Faster vegdist.
• More robust handling of formula which also fixes issue #200.
• Updated taxonomy of dune meadow species.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 9 years ago

vegan - CRAN release 2.4-1

vegan_2.4-1 was released to CRAN. This fixes the following github issues:

• issue #187: diversity with NA. Also checks against negative input data.
• issue #189: goodness.cca failed when a component had only one axis. This radiated into fixes in several other functions.
• issue #190: goodness.cca regression of ignoring choices argument.
• issues #192 and #193: more robust handling of factors with missing values. Originally reported as an error for betadisper, but radiated into similar fixes in many other functions. The error report #192 was later rectified by fixing R.
• issue #195: regression in linestack which failed to handle expression. The bug fix part of #195 was fixed here, but the feature request still remains.

Issue #194 discusses other changes.

Most extensive change outside github issues was modernizing Fortran code. This also was the immediate reason for this release: CRAN people asked us to modernize good old Fortran.

More detailed listing of changes can be found in the NEWS file of the release.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa almost 10 years ago

vegan - CRAN release 2.4-0

A new major release of vegan was released and is available on CRAN. This release is directly lifted from the current master branch and closes the gap between development and release versions. The release will start the new 2.4 series, and the master branch will be 2.5-0 for the next major release.

As this is a major release, there are numerous large changes. Most important user visible changes are listed in the NEWS with the package. Largest families of changes are:

• distance-based RDA and associated analyses were redesigned to directly decompose dissimilarities. With semimetric indices (such as Bray-Curtis) this means that the components of inertia include negative eigenvalues. The release has a new function dbrda for distance-based RDA while it also keeps the old capscale but with redefined inertia. In addition, we have a new implementation of permutational anova as adonis2 along side the classic adonis. Variation partition can also be based on dissimilarities with similar tools. We also include tools for euclidifying dissimilarities in all cases where negative eigenvalues may appear. The changes touch functions capscale, adonis, betadisper and varpart and their support functions.
• null models are expanded. We have new "curveball" algorithm for binary matrices, and many other functions are streamlined. It is also possible to bind several null models together with new smbind functions. With this function, null models can be stratified by groups of species or sampling units, or it is possible to run models in pieces. The models can be expanded with new simulations, or null models can be simulated in parallel.
• several ordi* functions that add graphical items to ordination plots are now more flexible and easier to parametrize with colours, line types etc. This also concerns functions like plotting betadisper results. There is also a new function ordibar that can plot SD, SE or CI crosses instead of corresponding ellipses, and ordiellipse can draw ellipsoid hulls that enclose all points in each group.
• metaMDS strategies changed so that it is easier to avoid local optima and to see which stopping criterion should be changed to reach the solutions. The MDSrotate function can now rotate a multidimensional MDS solution to separate groups optimally in first dimensions.
• designdist knows now beta-diversity notation so that, e.g., Whittaker's index can be calculated as designdist(BCI, "gamma/alpha - 1", alphagamma = TRUE).
• permustats support functions were improved for analysing permutation test statistics from various vegan objects. Now several permutations can be combined with new c() function, and summary can be used to evaluate the P-values also for combined results.
• Adjusted R-squared can now be analysed for db-RDA and cca.

Parallel to this 2.4-0 release, we also released a new version 1.0-1 of vegan3d with similar improvements and bug fixes.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa almost 10 years ago

vegan - CRAN release 2.3-5

This release was made to fix problems triggered by changes in R-devel: function prcomp gained a new argument rank., and collateral changes made print summary.eigenvals fail in vegan, and we did not pass all tests in CRAN. The new version of handling eigenvals will work both in R-devel and released R versions.

In addition,we fixed a problem in calibrate.cca which would fail if users specified rank. There are also other small fixes which are mostly not visible to users.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa about 10 years ago

vegan - CRAN release v2.3-4

Main reason for this release was that texi2dvi (an external system software) version 6.1 introduced incompatible features that prevented building vegan (issue #158). This release removes texi2dvi dependence in a vignette. All other vignettes are also built and can be accessed with standard R tools. Other changes:

• linestack failed in some cases when the labels argument was used.
• index 19 had a typo on betadiver.
• vegandocs was deprecated: we use now standard R tools.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 10 years ago

vegan - CRAN release 2.3-3

Bug fixes

• Fix issue #152: monoMDS (and hence metaMDS) failed when some dissimilarities were 1e16 or higher.
• Permutations failed with permute control structures in estaccum, ordiareatest, renyiaccum and tsallisaccum.
• Indices that required at least two sampling units in specpool failed when only one sampling unit was supplied.

New Features

• treeheight, treedist and treedive work (or refuse to work) with anomalous trees with reversed branches or negative heights.
• anosim, bioenv and mrpp have more robust handling of alternative input formats.

More in the NEWS file in the package.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 10 years ago

vegan - CRAN release 2.3-2

• Fix printing details of gridded permutations
• Fix weighting of points in ordicluster
• ordiellipse ignored weights in calculation of standard errors (kind = "se")
• adonis and capscale accept dissimilarities in symmetric square matrix as an alternative to a "dist" object (issue #147)
• mso accepts "dist" objects as an alternative to coordinates of locations
• lines and points of procrustes analysis gained argument truemean to allow adding items to original plots.
• rrarefy returns non-rarefied communities when users ask samples larger than observation (issue #144)

More verbose description in NEWS

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 10 years ago

vegan - CRAN release 2.3-1

Major changes:

• fix values tied with statistics in permutation tests
• fix automatic model building in step, ordistep and ordiR2step with aliased candidate variables in constrained ordinatin
• fix centroids of non-factor classes in cca, rda & capscale
• fix handling very long expression in metaMDS calls
• pass NA dissimilarities to monoMDS
• better checking of inputs in rarecurve
• user-friendly definition of scaling in constrained ordination
• add permustats to anova.cca tests
• add BCI.env data

More verbose description in NEWS.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 10 years ago

vegan - Stable CRAN release

Read Release NEWS.

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa almost 11 years ago

vegan - CRAN v2.2-0

Biosphere - Ecological and Environmental Modeling - R
Published by jarioksa over 11 years ago