## vegan News
### Changes in version 2\.6-8
#### New Features
* Wrappers for the unconstrained ordination methods principal components
analysis (PCA), correspondence anslysis (CA), and principal coordinates
analysis (PCO) are now available via `pca()`, `ca()`, and `pco()`
respectively. The underlying methods used are `rda()`, `cca()` and `dbrda()`
respectively. See
[#655](https://github.com/vegandevs/vegan/issues/655).
* The output from the ordination methods `pca()`, `pco()`, `ca()`,
`rda()`, `cca()`, `capscale`, and `dbrda()` has changed slightly to
better separate the results from notifications to the user about
issues encountered with the data or the model. Related to changes in
[#682](https://github.com/vegandevs/vegan/issues/682).
* The constrained ordination functions are now louder at informing users when
one or more terms in a model are aliased (linearly dependent) and their
effects cannot be estimated. See
[#682](https://github.com/vegandevs/vegan/issues/682).
* `cca` and `rda` return centroids for factor levels even when they
are called without formula, for instance, as `cca(dune, dune.env)`.
* `plot.cca` retains default graphical settings also when only one set
of scores was displayed.
* `ordiplot` did not pass character size (`cex`) to `plot.cca`. Version
2.7-0 has more extensive changes, but this fixes the immediate issue
[#656](https://github.com/vegandevs/vegan/issues/656).
* `adonis2()` now defaults to running an omnibus test of the model
(`by = NULL`) instead of a sequential test of model terms (`by =
"terms"`). This makes `adonis2()` more consistent with the default
for related ordination methods. See
[#677](https://github.com/vegandevs/vegan/issues/677).
* `decorana` checks now that input data are numeric instead of
confusing error message (see
https://stackoverflow.com/questions/78666646/).
* `make.cepnames` no longer splits names by hyphen: _Capsella
bursa-pastoris_ used to be `Capspast` but now is `Capsburs`.
#### Bug Fixes
* `dbrda` failed in rare cases when an ordination component had only
negative eigenvalues. Issue
[#670](https://github.com/vegandevs/vegan/issues/670).
* `plot.cca`: biplot or regression arrows were not nicely scaled and
drew no arrows when displayed as the only item in graph.
* `ordipointlabel` failed with `decorana` result. Bounding box for
text could be wrongly estimated with varying values of `cex`.
* `vegdist` with argument `na.rm = TRUE` still failed with missing
values. Dissimilarity methods `"chisq"` (Chi-square distance) and
`"mahalanobis"` did not implement `na.rm = TRUE`. Even when missing
values are removed in calculation, dissimilarities may contain `NA`
depending on the number and pattern of missing values and
dissimilarity method.
* `decostand` standardization method `"clr"` did not implement
`na.rm = TRUE`
(issue [#661](https://github.com/vegandevs/vegan/issues/661)).
Standardization methods `"rank"` and `"rrank"` did not retain `NA`
values but changed them to 0. Original `NA` values are kept in
`decostand`, but with `na.rm = TRUE` they are ignored when
transforming other data values.
* `metaMDS`: half-change scaling failed when `maxdist` was fixed, but
was not 1.
* `summary.ordihull` (and hence `ordiareatest` for convex hulls)
failed if input had more than two dimensions.
* `simulate.rda` failed with univariate response.
* `vegemite` returned only the last page of multi-page table in its
(invisible) return object.
### Changes in version 2\.6-6\.1
* C function `do_wcentre` (weighted centring) can segfault due to a
protection error. The problem was found in automatic CRAN
checks. `do_wcentre` is an internal function that is called from
`envfit` (`vectorfit`), `wcmdscale` and `varpart` (`simpleCCA`)
Fixes bug [#653](https://github.com/vegandevs/vegan/issues/653).
### Changes in version 2\.6-6
#### INSTALLATION
* **vegan** depends on **R** version 4.1.0.
* It is possible to build **vegan** with webR/wasm Fortran
compiler. Issue [#623](https://github.com/vegandevs/vegan/issues/623).
#### NEW FEATURES
* Permutation tests for CCA were completely redesigned to follow C.J.F
ter Braak & D.E. te Beest: Environ Ecol Stat 29, 849–868 (2022)
(https://doi.org/10.1007/s10651-022-00545-4). The constraints are
now re-weighted for the permuted response data, and in partial model
they are also residualized by conditions (partial terms). In
**vegan** (after release 2.4-6) the tests were identical to Canoco,
but ter Braak & te Beest demonstrated that the results are biased.
In old **vegan** (release 2.4-2 and earlier) the predictors were
re-weighted but not residualized. Re-weighting was sufficient to
remove bias with moderate variation of weights, but residualizing of
predictors is necessary with strongly varying weights. See
discussion in issue
[#542](https://github.com/vegandevs/vegan/issues/542).
The new scheme only concerns CCA which is a weighted method, and RDA
and dbRDA permutation is unchanged.
* `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
`"axis"` and by `"onedf"`. Models by `"terms"` and `"margin"` are only
possible with formula interface.
* Permutation tests for constrained ordination objects (`cca`, `rda`,
`dbrda`) with `by = "axis"` stop permutations of later axis once the
`cutoff` limit is reached. Earlier `cutoff` had to be exceeded. The
default is to stop permutations once _P_-value 1 is reached. The
analysis takes care that _P_-values of axes are non-decreasing
similarly as in Canoco.
* Coefficients of effects in `prc` models are scaled similarly as they
were scaled in **vegan** pre 2\.5-1. The change was suggested by
Cajo ter Braak.
* Handling of negative eigenvalues was changed in the `summary` of
`eigenvals`. Negative eigenvalues are given as negative
"explanation", and the accumulated proportions add up over 1 for the
last non-negative eigenvalue, and 1 for the last negative
eigenvalue.
* The printed output of `capscale` shows proportions for real
components only and ignores imaginary dimensions. This is consistent
to `summary` and other support methods. Issue
[#636](https://github.com/vegandevs/vegan/issues/636).
* `RsquareAdj` of `capscale` is based only on positive eigenvalues,
and imaginary components are ignored.
* `stressplot.dbrda` refuses to handle partial models. Only the first
component of variation can be displayed because `dbrda` internal
("working") data structures are not additive. For unconstrained
model `"CA"`, for constrained `"CCA"` and for partial none.
* `predict` for `dbrda` will return the actual
`type = "working"`. Earlier it returned `"lc"` scores weighted by
eigenvalues. Both generated same distances and eigenvalues, though.
#### BUG FIXES
* Parallel processing was inefficiently implemented and could be
slower than non-parallel in permutation tests for constrained
ordination and `adonis2`.
* `plot` and `scores` for `cca` and `rda` family of methods gave an
error when non-existing axes were requested. Now ignores requests to
axes numbers that are higher than in the result object.
* `summary` of `prc` ignored extra parameters (such as `const`).
* Over-fitted models with high number of aliased variables caused a
rare failure in `adonis2` and permutation tests of constrained
ordination methods (`cca`, `rda`, `dbrda`, `capscale`) with
arguments `by = "margin"` or `by = "axis"`. This also concerned
`vif.cca` and `intersetcor`. Typically this occurred with high-order
interactions of factor variables. See issues
[#452](https://github.com/vegandevs/vegan/issues/452) and
[#622](https://github.com/vegandevs/vegan/issues/622)
* Some methods accept rectangular raw data input as alternative to
distances, but did not pass all arguments to distance
functions. These arguments in `vegdist` could be `binary = TRUE` or
`pseudocount` with Aitchison distance. This concerns `dbrda`,
`capscale` and `bioenv`. See issue
[#631](https://github.com/vegandevs/vegan/issues/631)
* `simper` gave arbitrary *p*-values for species that did not occur in
a subset. Now these are given as `NA`. See
https://stackoverflow.com/questions/77881877/
* `Rsquare.adj` gave arbitrary *p*-values for over-fitted models with
no residual variation. Now returns `NA` when _R_2 cannot
be adjusted. Automatic model building could proceed to such cases,
and this was fixed in `ordiR2step` which returns _R_2 = 0
for overfitted cases. The constrained ordination methods issue a
warning if the model has no residual component. See issue
[#610](https://github.com/vegandevs/vegan/issues/610)
* `inertcomp(..., display = "sites", proportional = TRUE)` gave wrong
values.
#### DATA SETS
* Extended the description of the BCI data sets to avoid
confusion. The complete BCI survey includes all stems of down to
1 cm DBH, but the BCI data set in **vegan** is a subset of stems of
DBH 10 cm that was published in
[Science 295, 666—669, 2002](https://www.science.org/doi/10.1126/science.1066854).
The data set is intended only to demonstrate methods in **vegan** and for
ecological research we suggest contacting the BCI team and using the
complete surveys made available in
[Dryad](https://doi.org/10.15146/5xcp-0d46).
#### DEPRECATED AND DEFUNCT
* `adonis` is deprecated: use `adonis2`. There are several CRAN
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). 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 deprecated: you
should use `scores` to extract scores. This version still allows
extracting scores with `summary`, but this will fail in next
versions. For `summary.cca` see
[instructions](https://github.com/vegandevs/vegan/discussions/644)
to change your package.
* 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
`newobject <- update(ancientobject)` to modernize the result.
* `as.mcmc.oecosimu` and `as.mcmc.permat` are defunct: use `toCoda`.
* Code of defunct functions was completely removed.
### Changes in version 2\.6-4
#### NEW FEATURES
* Support of `scores` for
[**ggplot2**](https://CRAN.R-project.org/package=ggplot2) graphics is
improved and extended for ordination functions. Suitable scores can be
requested with argument `tidy = TRUE`, and in general all available
types of scores are returned in a data frame with variable `score`
labelling the type. The option was implemented in default method of
`scores` and for structured `wcmdscale` objects, and glitches were
fixed for `rda` family and `decorana`. Previously `tidy` scores were
implemented for `cca`, `rda`, `dbrda` family of methods, `metaMDS`,
`envfit` and `rarecurve`.
* `adonis2` and `anova` for constrained ordination results can perform a
sequential test of one-degree-of-freedom effects where multi-level
factors are split to their contrasts. Previously the test was
available only in `permutest`.
* New `summary` function for `varpart` for a brief overview. The summary
shows unique and overall contributed variation for each set of
variables. The fractions shared by several sets of variables are
divided equally with all contributing sets following Lai J, Zou Y,
Zhang J, Peres-Neto P (2022\) *Methods in Ecology and Evolution*, 13:
782–788\.
* `decorana` estimates orthogonalized eigenvalues and the total inertia
(scaled Chi-square). Orthogonalized eigenvalues can add up to the
total inertia. Together these enabled implementing `eigenvals`,
`bstick` and `screeplot` methods for `decorana`.
* Axis lengths are reported for all `decorana` methods.
* Implemented `tolerance` method for `decorana`. This returns the
criterion that was used in rescaling DCA, and can be used to inspect
the success of rescaling: it should be constant 1 over the whole axis.
* New `toCoda` function to transform sequential null model results
from `oecosimu` to an object that can be analysed with
[**coda**](https://CRAN.R-project.org/package=coda) for convergence
and independence as an MCMC model. Function replaces
`as.mcmc.oecosimu` and `as.mcmc.permat`.
* `metaMDS` is more informative about finding similar repeated results
with random starts and uses less confusing language when reporting the
results.
* Hellinger distance is directly available in `vegdist`.
* `vegdist`, `betadiver` and `raupcrick` set attribute `maxdist` giving
the numeric value of theoretical maximum of the dissimilarity index.
For many dissimilarities this is 1, but √2 for Chord and
Hellinger distances, for instance. The attribute is `NA` for open
indices that do not have such a ceiling. `betadiver` has three
similarity indices and these set `maxdist` 0\.
* `metaMDS` defaults to halfchange scaling when the dissimilarities have
a numeric `maxdist` attribute, and adapt the threshold to the ceiling
value. For open indices without ceiling, the threshold will be in the
scale of dissimilarities. `metaMDS` used a simple test to detect index
ceiling 1, but the test is now more robust and can also find other
maximum values. If such inference is made, the function will broadcast
a message of assumed value of the ceiling.
* Mountford index in `vegdist` is now scaled to maximum value log(2).
Earlier Mountford distances were scaled to maximum 1\.
* `hatvalues` of constrained ordination objects can sometimes be
practically 1 or above 1, but now these cases will be exactly 1\. In
those cases `rstandard`, `rstudent` and `cooks.distance` will be
`NaN`. The behaviour is similar as in `stats::lm.influence` functions.
* `as.rad` can handle multi-row data frames or matrices and return a
list of Rank-Abundance data for each row. Earlier only one site was
handled.
* `decostand` returns attribute `parameters` of settings and variables
used in standardization. New function `decobackstand` can use
`parameters` to reconstruct original non-standardized data.
Back-transformation is not exact but has round-off errors, although
there is an attempt to keep original zeros exact. Back-transformation
is not possible for methods `pa`, `rank` and `rrank` and it is not
implemented for `alr`. Back-transformation queried in
* Rarefaction and rarefaction-based methods make sense only with
original observed counts and give misleading results if data are
multiplied or rare species are removed. Observed counts usually have
singletons (species with count one), and these method issue a
warning if minimum count is higher than one (which may be a false
positive, but inspect your data). Concerns functions `rarefy`,
`drarefy`, `rrarefy`, `rarecurve`,
`specaccum(..., method="rarefy")`, `rareslope` and `avgdist`.
See github
[discussion #537](https://github.com/vegandevs/vegan/discussions/537).
* `avgdist` exposes `as.dist` arguments and can return `"dist"`ance
objects that appear as lower triangles instead of appearing as
symmetric matrices.
* `betadisper` plots accept `col` argument
([PR \#300](https://github.com/vegandevs/vegan/pull/300)).
#### BUG FIXES
* `decorana` returned wrong results when Hill's piecewise transformation
(arguments `before`/`after`) were used, unless downweighting was also
used.
* `scores` failed when `metaMDS` result had no species scores. Bug was
introduced in release 2\.6-2\. Issue raised in
* `tolerance.cca` failed when only one axis (`choice`) was requested.
* `decostand(..., method="alr")` did not accept name as a `reference`,
and could fail in some cases.
* CRAN package **proxy** interfered with `simper` and caused an
obscure error (github issue
[\#528](https://github.com/vegandevs/vegan/issues/528)).
#### DEPRECATED AND DEFUNCT
* `adonis` is on way to deprecation. Use `adonis2` instead.
* `as.mcmc.oecosimu` and `as.mcmc.permat` were deprecated: these could
not be used as S3 methods without depending on **coda** package. Use
`toCoda` instead.
### Changes in version 2\.6-2
#### INSTALLATION
* Compiled code is adapted to the changes in **R** 4\.2\.0\. See issues
[\#447](https://github.com/vegandevs/vegan/issues/447),
[\#507](https://github.com/vegandevs/vegan/issues/507).
* Cross-references to function in other packages were adapted to more
stringent tests in CRAN
#### NEW FEATURES
* Aitchison and robust Aitchison distances were added to `vegdist`.
Similar data transformations were added to `decostand`.
* Several functions can return “tidy” data structures that can be used
in ggplot2 graphics: `rarecurve`, `scores` functions for constrained
ordination (`cca` etc.), `decorana`, `envfit`, `metaMDS`.
* `scores.envfit` gained argument `arrow.mul`. vegan `plot` functions
used this automatically, but now it is easier to use `envfit` in
non-vegan plotting.
* Added function `simpson.unb` for unbiased Simpson diversity that is
more robust to the variation in sample sizes.
* `diversity` gained argument `group` to calculate indices for pooled
data. Discussed in issue
[\#393](https://github.com/vegandevs/vegan/issues/393).
* `simper` is much faster even though parallel processing is not
implemented in the new code.
* `pairs` function was added to plot `permustats` variables against each
other.
* `varpart` accepts dissimilarities given as a symmetric square matrix
instead of `"dist"` object per wish of issue
[\#497](https://github.com/vegandevs/vegan/issues/497).
* `metaMDS` adopted a more user-friendly policy, and `trymax` will
always be the maximum number of tries. See dicussion in
.
* `adonis2` accepts `strata`. `adonis2` is the new main function that
replaces old `adonis`. See issue
[\#427](https://github.com/vegandevs/vegan/issues/427).
* Fisher alpha (`fisherfit`) is badly suited for extreme communities
that do not follow Fisher's model. Now `fisherfit` returns `NA` to
communities that have 0 or 1 species, and issues a warning with
communities consisting of singletons and having extreme Fisher alpha.
* `adipart` and `multipart` formulae will automatically add unique id
and and constant. This will always sandwich the requested grouping
between alpha and gamma diversities, but not change the results for
requested groupings.
#### BUG FIXES
* `anova` function failed in marginal tests when constrained partial
ordination model (`cca`, `rda` etc.) had interaction terms. Issue
[\#463](https://github.com/vegandevs/vegan/issues/463).
* Constrained ordination (`cca` etc.) gave misleading results when all
external variables (constraints, condition) were constant and
explained nothing.
* `decorana` could fail when some axes had zero eigenvalues. Issue
[\#401](https://github.com/vegandevs/vegan/issues/401).
* Species accumulation (`specaccum`) failed when there was only one
species, but several “communities”. Issue
[\#501](https://github.com/vegandevs/vegan/issues/501).
* Parallel processing failed in Windows or with socket clusters in
`permutest` of `betadisper`. Issue
[\#369](https://github.com/vegandevs/vegan/issues/369).
* `orditorp` failed if numeric labels were supplied. Reported in
.
* Argument `summarize` was accidentally dropped from `goodness.cca` in
2017\.
* `taxa2dist` failed if there was only one usable taxonomic level. See
.
#### DEPRECATED AND DEFUNCT
* Function `adonis2` will replace `adonis`.
* `humpfit` functions are defunct and removed. They are available in
non-CRAN package natto at .
* `commisimulator` is defunct. Use `simulate` for `nullmodel` objects.
* `permuted.index` is finally defunct (it was deprecated in vegan
2\.2-0\).
* `as.mlm` is defunct. Use functions documented with `influence.cca`,
such as `hatvalues.cca`, `rstandard.cca`, `rstudent.cca`,
`cooks.distance.cca` and others.
### Changes in version 2\.5-7
#### BUG FIXES
* Several distance-based functions failed if all distances were zero
(`betadisper`, `capscale`, `isomap`, `monoMDS`, `pcnm`, `wcmdscale`).
Reported in github issue
[\#372](https://github.com/vegandevs/vegan/issues/372).
* Non-linear self-starting regression models `SSarrhenius`, `SSgitay`,
`SSgleason` and `SSlomolino` failed in future **R**. The failure was
caused by internal changes in **R**-devel. Github issue
[\#382](https://github.com/vegandevs/vegan/issues/382).
* Arrow labels were in wrong position in `plot.envfit(..., add =
FALSE)`.
* `rarecurve` added unnecessary names to the results. Github issue
[\#352](https://github.com/vegandevs/vegan/issues/352).
* `permutest` for `betadisper` failed in parallel processing in Windows
and in other systems when socket clusters were used. Github issue
[\#369](https://github.com/vegandevs/vegan/issues/369).
#### NEW FEATURES
* Chi-square and Chord distances were added to `vegdist`. Both of these
distances can be calculated as Euclidean distances of transformed
data, and actually were available earlier, but many users did not
notice this.
* `monoMDS` (and hence `metaMDS`) uses stricter convergence criteria.
This improves possibilities to find stable solutions. However, users
may still need to tweak convergence criteria with their data. See
discussion in Github issue
[\#354](https://github.com/vegandevs/vegan/issues/354).
* `text` functions for constrained ordination plots (`cca`, `rda`,
`dbrda`, `capscale`) accept now expression labels. This allows using
subscripts, superscripts and mathematical expressions. New support
function `labels.cca` returns the current text labels so that authors
can change the desired ones. See github issue
[\#374](https://github.com/vegandevs/vegan/issues/374).
* `vegemite` returns invisibly the final formatted table allowing
further processing.
* `ordiplot` passes `cex` argument to `linestack` and `decorana` plots.
### Changes in version 2\.5-6
#### BUG FIXES
* `vegdist` silently accepted missing values (`NA`) and removed them
from the analysis also with option `na.rm = FALSE`. The behaviour was
introduced in vegan version 2\.5-1\. See GitHub issue
[\#319](https://github.com/vegandevs/vegan/issues/319).
* The labels were displaced when the bunch of arrows was not drawn at
the origin of the ordination graph in `envfit`. See GitHub issue
[\#315](https://github.com/vegandevs/vegan/issues/315).
* Hill scale in `coverscale` is open-ended and is not limited to percent
data, unlike most traditional cover class scales which are undefined
above 100% cover.
#### NEW FEATURES
* The results of `as.rad` no longer print the index attribute: the
attribute is still in the object, but printing made the output messy.
### Changes in version 2\.5-5
#### INSTALLATION
* vegan depends on **R** 3\.4\.0 or higher. The next vegan release may
increase the dependence to **R** 3\.6\.0\.
* **R** 3\.6\.0 improved the method to find random indices for permuting
and sampling data. Vegan relies now on the **R** functions in its
ecological null models (functions `nullmodel`, `oecosimu`, `commsim`,
`permatfull`, `permatswap` and others). Technically this change is
compatible with **R** 3\.4\.0 and later, but you can only gain the
benefits of improved code with a current release of **R**. The null
models may change due to this change, and most certainly they change
in **R** 3\.6\.0\. See NEWS for the **R** 3\.6\.0 release and
discussion in github issue
[\#312](https://github.com/vegandevs/vegan/issues/312).
Most vegan permutation routines rely on
[permute](https://CRAN.R-project.org/package=permute), and there you
gain similar benefits of improved randomness when you upgrade **R**.
* Thanks to the new **R** dependence, `sigma` for constrained ordination
results works without workarounds of vegan 2\.5-2\. This fixes
completely the issue discussed in
[\#274](https://github.com/vegandevs/vegan/issues/274).
* Vegan test results cannot be reproduced in older versions than **R**
3\.6\.0\. If you are worried about this, you should upgrade **R**.
#### BUG FIXES
* `metaMDS` failed in scaling results when other `engine` than `monoMDS`
was used. However, we recommend you use `monoMDS`. See github issue
[\#310](https://github.com/vegandevs/vegan/issues/310).
#### NEW FEATURES
* `betadisper` changed interpretation of negative squared distances
which give complex-valued distances. Now they are regarded as
zero-distances whereas earlier we used their modulus. This will change
the results in cases where you had negative squared distances. For
further discussion, see github issue
[\#306](https://github.com/vegandevs/vegan/issues/306).
### Changes in version 2\.5-4
#### INSTALLATION AND TESTING
* The code for interpreting formula will change in **R** 3\.6\.0, and
this makes constrained ordination methods (`cca`, `rda`, `dbrda`,
`capscale`) to fail. See github issue
[\#299](https://github.com/vegandevs/vegan/issues/299).
* **R** 3\.6\.0 introduces a new environment variable
`_R_CHECK_LENGTH_1_LOGIC2_`, and several functions fail if this
variable is set. Changes concern `ordiplot`, `plot` and `summary` for
constrained ordination objects, and `ordixyplot`. See github issue
[\#305](https://github.com/vegandevs/vegan/issues/305).
#### BUG FIXES
* `decorana` gave incorrect results when downweighting was used
(argument `iweigh = 1`). The bug was introduced in vegan 2\.5-1 and
reported as github issue
[\#303](https://github.com/vegandevs/vegan/issues/303).
* `goodness` for constrained ordination methods failed when the
constraints had rank = 1 (only one constraining variable). Reported by
Pierre Legendre.
#### NEW FEATURES
* Adjusted _R_2 is enabled for partial RDA models (functions `rda` and
`dbrda`) and partial CCA models (function `cca`) in function
`RsquareAdj`. The feature was disabled in vegan 2\.5-1 for both. For
RDA, the calculation is similar as in vegan 2\.4-6 and earlier.
Partial CCA is now consistent with RDA and differs from the earlier
implementation. For both methods, the partial models are consistent
with `varpart`. See github issue
[\#295](https://github.com/vegandevs/vegan/issues/295).
### Changes in version 2\.5-3
#### INSTALLATION
* Tests for numerical analysis were written more robustly so that they
give more similar results with alternative platforms and versions of
**R** and BLAS/Lapack libraries. See github issue
[\#282](https://github.com/vegandevs/vegan/issues/282).
#### BUG FIXES
* Constrained ordination gave misleading results when some constraints
or conditions had data with NULL variables. This rarely happens in
normal usage, but could happen in marginal `anova` as reported in
github issue [\#291](https://github.com/vegandevs/vegan/issues/291).
* Several functions for numerical analysis wrongly accepted non-numeric
data (for instance, factors) and gave either meaningless results or
confusing error messages. Fixed functions include `beals`,
`designdist`, `diversity`, `gdispweight`, `indpower`, `spantree`,
`specpool`, `tsallis`, `tsallisaccum` and `vegdist`. See github issue
[\#292](https://github.com/vegandevs/vegan/issues/292).
* `envfit` with vectors could fail with missing data.
* The original data were not scaled and centred similarly as simulations
in `simulate.rda` when several simulations were returned as a `simmat`
object (which is compatible with `nullmodel` simulations and can be
used in `oecosimu`).
#### NEW FEATURES
* `anosim` checks its input to avoid confusing error messages like that
reported in [StackOverflow question
52082743](https://stackoverflow.com/questions/52082743/).
* Broken-stick distribution (function `bstick`) is no longer calculated
for distance-based Redundancy Analysis (`dbrda`) with negative
eigenvalues, because it is not clear how this should be done. Now
`dbrda` and `capscale` are similar with this respect.
* `print` function for `betadisper` results gained new argument `neigen`
to select the number of eigenvalues shown. The `print` is more robust
when the number of eigenvalues is lower than the requested `neigen`.
#### DEPRECATED
* Function `humpfit` was moved to the natto package and is still
available from . It is scheduled
for complete removal in vegan 2\.6-0\.
### Changes in version 2\.5-2
#### INSTALLATION AND COMPATIBILITY
* Vegan declares dependence on **R** version 3\.2\.0\. This dependence
was not yet noticed in the previous vegan release. However, the
generic `sigma` function was only defined in **R**-3\.3\.0, and
therefore `sigma.cca` of vegan must be spelt out completely when using
**R**-3\.2\.x. See discussion in issue
[\#274](https://github.com/vegandevs/vegan/issues/274).
* CRAN package [klaR](https://CRAN.R-project.org/package=klaR) has
function `rda`, and when loaded together with vegan this clashes with
vegan `rda` for Redundancy Analysis. Vegan tries to mitigate the
problem. In most cases vegan functions will be used if vegan was
loaded after klaR, and an error message is issued if klaR objects are
handled with vegan functions. klaR is also tricked to print an
informative message if it handles vegan objects. However, vegan
namespace can be attached automatically at the start-up and then klaR
functions will take precedence. This was reported as issue
[\#277](https://github.com/vegandevs/vegan/issues/277).
* Bioconductor package phyloseq has a problem with `vegdist` function
for dissimilarities. The problem can be fixed by re-installing
phyloseq from its *source package*. If you cannot do this, you must
either downgrade to vegan version 2\.4-6 or wait till Bioconductor
binary packages are upgraded. This was reported in
[Stackoverflow](https://stackoverflow.com/questions/49882886/), and as
vegan issue [\#272](https://github.com/vegandevs/vegan/issues/272),
and as phyloseq issues
[\#918](https://github.com/joey711/phyloseq/issues/918) and
[\#921](https://github.com/joey711/phyloseq/issues/921).
#### BUG FIXES
* Plotting `betadisper` failed if any of the `groups` had only one
member. Reported in Stackoverflow as [“Error: Incorrect no.of
dimensions” when plotting multivariate data in
Vegan](https://stackoverflow.com/questions/50267430/).
* Permutation tests for constrained ordination (`anova.cca`,
`permutest.cca`) could fail in parallel processing with socket
clusters. Socket clusters are always used in Windows and they can also
be used in other operating systems when created with `makeCluster`.
See issue [\#276](https://github.com/vegandevs/vegan/issues/276).
### Changes in version 2\.5-1
#### GENERAL
* This is a major new release with changes all over the package: Nearly
40% of program files were changed from the previous release. Please
report regressions and other issues in
.
* Compiled code is used much more extensively, and most compiled
functions use `.Call` interface. This gives smaller memory footprint
and is also faster. In wall clock time, the greatest gains are in
permutation tests for constrained ordination methods (`anova.cca`) and
binary null models (`nullmodel`).
* Constrained ordination functions (`cca`, `rda`, `dbrda`, `capscale`)
are completely rewritten and share most of their code. This makes them
more consistent with each other and more robust. The internal
structure changed in constrained ordination objects, and scripts may
fail if they try to access the result object directly. There never was
a guarantee for unchanged internal structure, and such scripts should
be changed and they should use the provided support functions to
access the result object (see documentation of `cca.object` and github
issue [\#262](https://github.com/vegandevs/vegan/issues/262)). Some
support and analysis functions may no longer work with result objects
created in previous vegan versions. You should use
`update(old.result.object)` to fix these old result objects. See
github issues [\#218](https://github.com/vegandevs/vegan/issues/218),
[\#227](https://github.com/vegandevs/vegan/issues/227).
* vegan includes some tests that are run when checking the package
installation. See github issues
[\#181](https://github.com/vegandevs/vegan/issues/181),
[\#271](https://github.com/vegandevs/vegan/issues/271).
* The informative messages (warnings, notes and error messages) are
cleaned and unified which also makes possible to provide translations.
#### NEW FUNCTIONS
* `avgdist`: new function to find averaged dissimilarities from several
random rarefactions of communities. Code by Geoffrey Hannigan. See
github issues [\#242](https://github.com/vegandevs/vegan/issues/242),
[\#243](https://github.com/vegandevs/vegan/issues/243),
[\#246](https://github.com/vegandevs/vegan/issues/246).
* `chaodist`: new function that is similar to `designdist`, but uses
Chao terms that are supposed to take into account the effects of
unseen species (Chao et al., *Ecology Letters* **8,** 148-159; 2005\).
Earlier we had Jaccard-type Chao dissimilarity in `vegdist`, but the
new code allows defining any kind of Chao dissimilarity.
* New functions to find influence statistics of constrained ordination
objects: `hatvalues`, `sigma`, `rstandard`, `rstudent`,
`cooks.distance`, `SSD`, `vcov`, `df.residual`. Some of these could be
earlier found via `as.mlm` function which is deprecated. See github
issue [\#234](https://github.com/vegandevs/vegan/issues/234).
* `boxplot` was added for `permustats` results to display the
(standardized) effect sizes.
* `sppscores`: new function to add or replace species scores in
distance-based ordination such as `dbrda`, `capscale` and `metaMDS`.
Earlier `dbrda` did not have species scores, and species scores in
`capscale` and `metaMDS` were based on raw input data which may not be
consistent with the used dissimilarity measure. See github issue
[\#254](https://github.com/vegandevs/vegan/issues/254).
* `cutreeord`: new function that is similar to `stats::cutree`, but
numbers the cluster in the order they appear in the dendrogram (left
to right) instead of labelling them in the order they appeared in the
data.
* `sipoo.map`: a new data set of locations and sizes of the islands in
the Sipoo archipelago bird data set `sipoo`.
#### NEW FEATURES IN CONSTRAINED ORDINATION
* The inertia of Correspondence Analysis (`cca`) is called “scaled
Chi-square” instead of using a name of a little known statistic.
* If elements for Constraints and Conditions are data frames in
non-formula call of `rda` or `cca`, these are automatically expanded
to model matrices and can contain factor variables. Earlier they had
to be numerical model matrices and factors could only be used with the
formula interface.
* Regression scores for constraints can be extracted and plotted for
constrained ordination methods. See github issue
[\#226](https://github.com/vegandevs/vegan/issues/226).
* Full model (`model = "full"`) is again enabled in permutations tests
for constrained ordination results in `anova.cca` and `permutest.cca`.
* `permutest.cca` gained a new option `by = "onedf"` to perform tests by
sequential one degree-of-freedom contrasts of factors. This option is
not (yet) enabled in `anova.cca`.
* The permutation tests are more robust, and most scoping issues should
have been fixed.
* Permutation tests use compiled C code and they are much faster. See
github issue [\#211](https://github.com/vegandevs/vegan/issues/211).
* `permutest` printed layout is similar to `anova.cca`.
* `eigenvals` gained a new argument (`model`) to select either
constrained or unconstrained scores. The old argument (`constrained`)
is deprecated. See github issue
[\#207](https://github.com/vegandevs/vegan/issues/207).
* `summary.eigenvals` returns a matrix instead of a list containing only
that matrix.
* Adjusted _R_2 is not calculated for partial ordination, because it is
unclear how this should be done (function `RsquareAdj`).
* `ordiresids` can display standardized and studentized residuals.
* Function to construct `model.frame` and `model.matrix` for constrained
ordination are more robust and fail in fewer cases.
* `goodness` and `inertcomp` for constrained ordination result object no
longer has an option to find distances: only explained variation is
available.
* `inertcomp` gained argument `unity`. This will give “local
contributions to beta-diversity” (LCBD) and “species contribution to
beta-diversity” (SCBD) of Legendre & De Cáceres (*Ecology Letters*
**16,** 951-963; 2012\).
* `goodness` is disabled for `capscale`.
* `prc` gained argument `const` for general scaling of results similarly
as in `rda`.
* `prc` uses regression scores for Canoco-compatibility.
#### NEW FEATURES IN NULL MODEL COMMUNITIES
* The C code for swap-based binary null models was made more efficients,
and the models are all faster. Many of these models selected a 2
times 2 submatrix, and for this they generated four random numbers
(two rows, two columns). Now we skip selecting third or fourth random
number if it is obvious that the matrix cannot be swapped. Since most
of time was used in generating random numbers in these functions, and
most candidates were rejected, this speeds up functions. However, this
also means that random number sequences change from previous vegan
versions, and old binary model results cannot be replicated exactly.
See github issues
[\#197](https://github.com/vegandevs/vegan/issues/197),
[\#255](https://github.com/vegandevs/vegan/issues/255) for details and
timing.
* Ecological null models (`nullmodel`, `simulate`, `make.commsim`,
`oecosimu`) gained new null model `"greedyqswap"` which can radically
speed up quasi-swap models with minimal risk of introducing bias.
* Backtracking is written in C and it is much faster. However,
backtracking models are biased, and they are provided only because
they are classic legacy models.
#### NEW FEATURES IN OTHER FUNCTIONS
* `adonis2` gained a column of _R_2 similarly as old `adonis`.
* Great part of **R** code for `decorana` is written in C which makes it
faster and reduces the memory footprint.
* `metaMDS` results gained new `points` and `text` methods.
* `ordiplot` and other ordination `plot` functions can be chained with
their `points` and `text` functions allowing the use of
[magrittr](https://CRAN.R-project.org/package=magrittr) pipes. The
`points` and `text` functions gained argument to draw arrows allowing
their use in drawing biplots or adding vectors of environmental
variables with `ordiplot`. Since many ordination `plot` methods return
an invisible `"ordiplot"` object, these `points` and `text` methods
also work with them. See github issue
[\#257](https://github.com/vegandevs/vegan/issues/257).
* Lattice graphics (`ordixyplot`) for ordination can add polygons that
enclose all points in the panel and complete data.
* `ordicluster` gained option to suppress drawing in plots so that it
can be more easily embedded in other functions for calculations.
* `as.rad` returns the index of included taxa as an attribute.
* Random rarefaction (function `rrarefy`) uses compiled C code and is
much faster.
* `plot` of `specaccum` can draw short horizontal bars to vertical error
bars. See StackOverflow question
[45378751](https://stackoverflow.com/questions/45378751).
* `decostand` gained new standardization methods `rank` and `rrank`
which replace abundance values by their ranks or relative ranks. See
github issue [\#225](https://github.com/vegandevs/vegan/issues/225).
* Clark dissimilarity was added to `vegdist` (this cannot be calculated
with `designdist`).
* `designdist` evaluates minimum terms in compiled code, and the
function is faster than `vegdist` also for dissimilarities using
minimum terms. Although `designdist` is usually faster than `vegdist`,
it is numerically less stable, in particular with large data sets.
* `swan` passes `type` argument to `beals`.
* `tabasco` can use traditional cover scale values from function
`coverscale`. Function `coverscale` can return scaled values as
integers for numerical analysis instead of returning characters for
printing.
* `varpart` can partition Chi-squared inertia of correspondence
analysis with new argument `chisquare`. The adjusted _R_2
is based on permutation tests, and the replicate analysis will have
random variation.
* The explanatory tables can be data frames with factors or single
factors in `varpart` and these will be automatically expanded to model
matrices. Earlier factors could only be used with one-sided model
formulae. Based on the code suggested by Daniel Borcard, Univ.
Montréal.
#### BUG FIXES
* Very long `Condition()` statements (\> 500 characters) failed in
partial constrained ordination models (`cca`, `rda`, `dbrda`,
`capscale`). The problem was detected in StackOverflow question
[49249816](https://stackoverflow.com/questions/49249816).
* Labels were not adjusted when arrows were rescaled in `envfit` plots.
See StackOverflow question
[49259747](https://stackoverflow.com/questions/49259747).
* `ordiArrowMul` failed if there was only one arrow to be plotted in
`envfit`.
#### DEPRECATED AND DEFUNCT
* `as.mlm` function for constrained correspondence analysis is
deprecated in favour of new functions that directly give the influence
statistics. See github issue
[\#234](https://github.com/vegandevs/vegan/issues/234).
* `commsimulator` is now defunct: use `simulate` for `nullmodel`
objects.
* [ade4](https://CRAN.R-project.org/package=ade4) `cca` objects are no
longer handled in vegan: ade4 has had no `cca` since version 1\.7-8
(August 9, 2017\).
### Changes in version 2\.4-6
#### INSTALLATION AND BUILDING
* CRAN packages are no longer allowed to use FORTRAN input, but
`read.cep` function used FORTRAN format to read legacy CEP and Canoco
files. To avoid NOTEs and WARNINGs, the function was re-written in
**R**. The new `read.cep` is less powerful and more fragile, and can
only read data in “condensed” format, and it can fail in several cases
that were successful with the old code. The old FORTRAN-based function
is still available in
[cepreader](https://CRAN.R-project.org/package=cepreader). See github
issue [\#263](https://github.com/vegandevs/vegan/issues/263). The
cepreader package is developed in
.
#### BUG FIXES
* Some functions for rarefaction (`rrarefy`), species abundance
distribution (`preston`) and species pool (`estimateR`) need exact
integer data, but the test allowed small fuzz. The functions worked
correctly with original data, but if data were transformed and then
back-transformed, they would pass the integer test with fuzz and give
wrong results. For instance, `sqrt(3)^2` would pass the test as 3, but
was interpreted strictly as integer 2\. See github issue
[\#259](https://github.com/vegandevs/vegan/issues/259).
#### NEW FEATURES
* `ordiresids` uses now weighted residuals for `cca` results.
### Changes in version 2\.4-5
#### BUG FIXES
* Several “Swap & Shuffle” null models generated wrong number of initial
matrices. Usually they generated too many, which was not dangerous,
but it was slow. However, random sequences will change with this fix.
* Lattice graphics for ordination (`ordixyplot` and friends) colour the
arrows by `groups` instead of randomly mixed colours.
* Information on constant or mirrored permutations was omitted when
reporting permutation tests (e.g., in `anova` for constrained
ordination).
#### NEW FEATURES
* `ordistep` has improved interpretation of `scope`: if the lower scope
is missing, the formula of the starting solution is taken as the lower
scope instead of using an empty model. See Stackoverflow question
[46985029](https://stackoverflow.com/questions/46985029/).
* `fitspecaccum` gained new support functions `nobs` and `logLik` which
allow better co-operation with other packages and functions. See
GitHub issue [\#250](https://github.com/vegandevs/vegan/issues/250).
* The “backtracking” null model for community simulation is faster.
However, “backtracking” is a biased legacy model that should not be
used except in comparative studies.
### Changes in version 2\.4-4
#### INSTALLATION AND BUILDING
* `orditkplot` should no longer give warnings in CRAN tests.
#### BUG FIXES
* `anova(..., by = "axis")` for constrained ordination (`cca`, `rda`,
`dbrda`) ignored partial terms in `Condition()`.
* `inertcomp` and `summary.cca` failed if the constrained component was
defined, but explained nothing and had zero rank. See StackOverflow:
[R - Error message in doing RDA analysis - vegan
package](https://stackoverflow.com/questions/43683699/).
* Labels are no longer cropped in the `meandist` plots.
#### NEW FEATURES
* The significance tests for the axes of constrained ordination use now
forward testing strategy. More extensive analysis indicated that the
previous marginal tests were biased. This is in conflict with
Legendre, Oksanen & ter Braak, *Methods Ecol Evol* **2,** 269–277
(2011\) who regarded marginal tests as unbiased.
* Canberra distance in `vegdist` can now handle negative input entries
similarly as latest versions of **R**.
### Changes in version 2\.4-3
#### INSTALLATION AND BUILDING
* vegan registers native **C** and **Fortran** routines. This avoids
warnings in model checking, and may also give a small gain in speed.
* Future versions of vegan will deprecate and remove elements
`pCCA$Fit`, `CCA$Xbar`, and `CA$Xbar` from `cca` result objects. This
release provides a new function `ordiYbar` which is able to construct
these elements both from the current and future releases. Scripts and
functions directly accessing these elements should switch to
`ordiYbar` for smooth transition.
#### BUG FIXES
* `as.mlm` methods for constrained ordination include zero intercept to
give the correct residual degrees of freedom for derived statistics.
* `biplot` method for `rda` passes `correlation` argument to the scaling
algorithm.
* Biplot scores were wrongly centred in `cca` which caused a small error
in their values.
* Weighting and centring were corrected in `intersetcor` and `spenvcor`.
The fix can make a small difference when analysing `cca` results.
Partial models were not correctly handled in `intersetcor`.
* `envfit` and `ordisurf` functions failed when applied to species
scores.
* Non-standard variable names can be used within `Condition()` in
partial ordination. Partial models are used internally within several
functions, and a problem was reported by Albin Meyer (Univ Lorraine,
Metz, France) in `ordiR2step` when using a variable name that
contained a hyphen (which was wrongly interpreted as a minus sign in
partial ordination).
* `ordispider` did not pass graphical arguments when used to show the
difference of LC and WA scores in constrained ordination.
* `ordiR2step` uses only `forward` selection to avoid several problems
in model evaluation.
* `tolerance` function could return `NaN` in some cases when it should
have returned `0`. Partial models were not correctly analysed.
Misleading (non-zero) tolerances were sometimes given for species that
occurred only once or sampling units that had only one species.
### Changes in version 2\.4-2
#### BUG FIXES
* Permutation tests (`permutests`, `anova`) for the first axis failed in
constrained distance-based ordination (`dbrda`, `capscale`). Now
`capscale` will also throw away negative eigenvalues when first
eigenvalues are tested. All permutation tests for the first axis are
now faster. The problem was reported by Cleo Tebby and the fixes are
discussed in GitHub issue
[\#198](https://github.com/vegandevs/vegan/issues/198) and pull
request [\#199](https://github.com/vegandevs/vegan/pull/199).
* Some support functions for `dbrda` or `capscale` gave results or some
of their components in wrong scale. Fixes in `stressplot`, `simulate`,
`predict` and `fitted` functions.
* `intersetcor` did not use correct weighting for `cca` and the results
were slightly off.
* `anova` and `permutest` failed when `betadisper` was fitted with
argument `bias.adjust = TRUE`. Fixes Github issue
[\#219](https://github.com/vegandevs/vegan/issues/219) reported by
Ross Cunning, O'ahu, Hawaii.
* `ordicluster` should return invisibly only the coordinates of internal
points (where clusters or points are joined), but last rows contained
coordinates of external points (ordination scores of points).
* The `cca` method of `tolerance` was returning incorrect values for all
but the second axis for sample heterogeneities and species tolerances.
See issue [\#216](https://github.com/vegandevs/vegan/issues/216) for
details.
#### NEW FEATURES
* Biplot scores are scaled similarly as site scores in constrained
ordination methods `cca`, `rda`, `capscale` and `dbrda`. Earlier they
were unscaled (or more technically, had equal scaling on all axes).
* `tabasco` adds argument to `scale` the colours by rows or columns in
addition to the old equal scale over the whole plot. New arguments
`labRow` and `labCex` can be used to change the column or row labels.
Function also takes care that only above-zero observations are
coloured: earlier tiny observed values were merged to zeros and were
not distinct in the plots.
* Sequential null models are somewhat faster (up to 10%). Non-sequential
null models may be marginally faster. These null models are generated
by function `nullmodel` and also used in `oecosimu`.
* `vegdist` is much faster. It used to be clearly slower than
`stats::dist`, but now it is nearly equally fast for the same
dissimilarity measure.
* Handling of `data=` in formula interface is more robust, and messages
on user errors are improved. This fixes points raised in Github issue
[\#200](https://github.com/vegandevs/vegan/issues/200).
* The families and orders in `dune.taxon` were updated to APG IV (*Bot J
Linnean Soc* **181,** 1–20; 2016\) and a corresponding classification
for higher levels (Chase & Reveal, *Bot J Linnean Soc* **161,**
122-127; 2009\).
### Changes in version 2\.4-1
#### INSTALLATION
* Fortran code was modernized to avoid warnings in latest **R**. The
modernization should have no visible effect in functions. Please
report all suspect cases as [vegan
issues](https://github.com/vegandevs/vegan/issues/).
#### BUG FIXES
* Several support functions for ordination methods failed if the
solution had only one ordination axis, for instance, if there was only
one constraining variable in CCA, RDA and friends. This concerned
`goodness` for constrained ordination, `inertcomp`, `fitted` for
`capscale`, `stressplot` for RDA, CCA (GitHub issue
[\#189](https://github.com/vegandevs/vegan/issues/189)).
* `goodness` for CCA & friends ignored `choices` argument (GitHub issue
[\#190](https://github.com/vegandevs/vegan/issues/190)).
* `goodness` function did not consider negative eigenvalues of db-RDA
(function `dbrda`).
* Function `meandist` failed in some cases when one of the groups had
only one observation.
* `linestack` could not handle expressions in `labels`. This regression
is discussed in GitHub issue
[\#195](https://github.com/vegandevs/vegan/issues/195).
* Nestedness measures `nestedbetajac` and `nestedbetasor` expecting
binary data did not cope with quantitative input in evaluating
Baselga's matrix-wide Jaccard or Sørensen dissimilarity indices.
* Function `as.mcmc` to cast `oecosimu` result to an MCMC object
([coda](https://CRAN.R-project.org/package=coda) package) failed if
there was only one chain.
#### NEW FEATURES
* `diversity` function returns now `NA` if the observation had `NA`
values instead of returning `0`. The function also checks the input
and refuses to handle data with negative values. GitHub issue
[\#187](https://github.com/vegandevs/vegan/issues/187).
* `rarefy` function will work more robustly in marginal case when the
user asks for only one individual which can only be one species with
zero variance.
* Several functions are more robust if their factor arguments contain
missing values (`NA`): `betadisper`, `adipart`, `multipart`,
`hiersimu`, `envfit` and constrained ordination methods `cca`, `rda`,
`capscale` and `dbrda`. GitHub issues
[\#192](https://github.com/vegandevs/vegan/issues/192) and
[\#193](https://github.com/vegandevs/vegan/issues/193).
### Changes in version 2\.4-0
#### DISTANCE-BASED ANALYSIS
* Distance-based methods were redesigned and made consistent for
ordination (`capscale`, new `dbrda`), permutational ANOVA (`adonis`,
new `adonis2`), multivariate dispersion (`betadisper`) and variation
partitioning (`varpart`). These methods can produce negative
eigenvalues with several popular semimetric dissimilarity indices, and
they were not handled similarly by all functions. Now all functions
are designed after McArdle & Anderson (*Ecology* 82, 290–297; 2001\).
* `dbrda` is a new function for distance-based Redundancy Analysis
following McArdle & Anderson (*Ecology* 82, 290–297; 2001\). With
metric dissimilarities, the function is equivalent to old `capscale`,
but negative eigenvalues of semimetric indices are handled
differently. In `dbrda` the dissimilarities are decomposed directly
into conditions, constraints and residuals with their negative
eigenvalues, and any of the components can have imaginary dimensions.
Function is mostly compatible with `capscale` and other constrained
ordination methods, but full compatibility cannot be achieved (see
issue [\#140](https://github.com/vegandevs/vegan/issues/140) in
Github). The function is based on the code by Pierre Legendre.
* The old `capscale` function for constrained ordination is still based
only on real components, but the total inertia of the components is
assessed similarly as in `dbrda`.
The significance tests will differ from the previous version, but
function `oldCapscale` will cast the `capscale` result to a similar
form as previously.
* `adonis2` is a new function for permutational ANOVA of
dissimilarities. It is based on the same algorithm as the `dbrda`. The
function can perform overall tests of all independent variables as
well as sequential and marginal tests of each term. The old `adonis`
is still available, but it can only perform sequential tests. With
same settings, `adonis` and `adonis2` give identical results (but see
Github issue [\#156](https://github.com/vegandevs/vegan/issues/156)
for differences).
* Function `varpart` can partition dissimilarities using the same
algorithm as `dbrda`.
* Argument `sqrt.dist` takes square roots of dissimilarities and these
can change many popular semimetric indices to metric distances in
`capscale`, `dbrda`, `wcmdscale`, `adonis2`, `varpart` and
`betadisper` (issue
[\#179](https://github.com/vegandevs/vegan/issues/179) in Github).
* Lingoes and Cailliez adjustments change any dissimilarity into metric
distance in `capscale`, `dbrda`, `adonis2`, `varpart`, `betadisper`
and `wcmdscale`. Earlier we had only Cailliez adjustment in `capscale`
(issue [\#179](https://github.com/vegandevs/vegan/issues/179) in
Github).
* `RsquareAdj` works with `capscale` and `dbrda` and this allows using
`ordiR2step` in model building.
#### BUG FIXES
* `specaccum`: `plot` failed if line type (`lty`) was given. Reported by
Lila Nath Sharma (Univ Bergen, Norway)
#### NEW FUNCTIONS
* `ordibar` is a new function to draw crosses of standard deviations or
standard errors in ordination diagrams instead of corresponding
ellipses.
* Several `permustats` results can be combined with a new `c()`
function.
* New function `smbind` binds together null models by row, column or
replication. If sequential models are bound together, they can be
treated as parallel chains in subsequent analysis (e.g., after
`as.mcmc`). See issue
[\#164](https://github.com/vegandevs/vegan/issues/164) in Github.
#### NEW FEATURES
* Null model analysis was upgraded:
New `"curveball"` algorithm provides a fast null model with fixed row
and column sums for binary matrices after Strona et al. (*Nature
Commun.* 5: 4114; 2014\).
The `"quasiswap"` algorithm gained argument `thin` which can reduce
the bias of null models.
`"backtracking"` is now much faster, but it is still very slow, and
provided mainly to allow comparison against better and faster methods.
Compiled code can now be interrupted in null model simulations.
* `designdist` can now use beta diversity notation (`gamma`, `alpha`)
for easier definition of beta diversity indices.
* `metaMDS` has new iteration strategy: Argument `try` gives the minimum
number of random starts, and `trymax` the maximum number. Earlier we
only hand `try` which gave the maximum number, but now we run at least
`try` times. This reduces the risk of being trapped in a local optimum
(issue [\#154](https://github.com/vegandevs/vegan/issues/154) in
Github).
If there were no convergent solutions, `metaMDS` will now tabulate
stopping criteria (if `trace = TRUE`). This can help in deciding if
any of the criteria should be made more stringent or the number of
iterations increased. The documentation for `monoMDS` and `metaMDS`
give more detailed information on convergence criteria.
* The `summary` of `permustats` prints now *P*-values, and the test
direction (`alternative`) can be changed.
The `qqmath` function of `permustats` can now plot standardized
statistics. This is a partial solution to issue
[\#172](https://github.com/vegandevs/vegan/issues/172) in Github.
* `MDSrotate` can rotate ordination to show maximum separation of factor
levels (classes) using linear discriminant analysis (`lda` in
[MASS](https://CRAN.R-project.org/package=MASS) package).
* `adipart`, `hiersimu` and `multipart` expose argument `method` to
specify the null model.
* `RsquareAdj` works with `cca` and this allows using `ordiR2step` in
model building. The code was developed by Dan McGlinn (issue
[\#161](https://github.com/vegandevs/vegan/issues/161) in Github).
However, `cca` still cannot be used in `varpart`.
* `ordiellipse` and `ordihull` allow setting colours, line types and
other graphical parameters.
The alpha channel can now be given also as a real number in 0 ... 1 in
addition to integer 0 ... 255\.
* `ordiellipse` can now draw ellipsoid hulls that enclose points in a
group.
* `ordicluster`, `ordisegments`, `ordispider` and `lines` and `plot`
functions for `isomap` and `spantree` can use a mixture of colours of
connected points. Their behaviour is similar as in analogous functions
in the the [vegan3d](https://CRAN.R-project.org/package=vegan3d)
package.
* `plot` of `betadisper` is more configurable. See issues
[\#128](https://github.com/vegandevs/vegan/issues/128) and
[\#166](https://github.com/vegandevs/vegan/issues/166) in Github for
details.
* `text` and `points` methods for `orditkplot` respect stored graphical
parameters.
* Environmental data for the Barro Colorado Island forest plots gained
new variables from Harms et al. (*J. Ecol.* 89, 947–959; 2001\). Issue
[\#178](https://github.com/vegandevs/vegan/issues/178) in Github.
#### DEPRECATED AND DEFUNCT
* Function `metaMDSrotate` was removed and replaced with `MDSrotate`.
* `density` and `densityplot` methods for various vegan objects were
deprecated and replaced with `density` and `densityplot` for
`permustats`. Function `permustats` can extract the permutation and
simulation results of vegan result objects.
### Changes in version 2\.3-5
#### BUG FIXES
* `eigenvals` fails with `prcomp` results in **R**-devel. The next
version of `prcomp` will have an argument to limit the number of
eigenvalues shown (`rank.`), and this breaks `eigenvals` in vegan.
* `calibrate` failed for `cca` and friends if `rank` was given.
### Changes in version 2\.3-4
#### BUG FIXES
* `betadiver` index `19` had wrong sign in one of its terms.
* `linestack` failed when the `labels` were given, but the input scores
had no names. Reported by Jeff Wood (ANU, Canberra, ACT).
#### DEPRECATED
* `vegandocs` is deprecated. Current **R** provides better tools for
seeing extra documentation (`news()` and `browseVignettes()`).
#### VIGNETTES
* All vignettes are built with standard **R** tools and can be browsed
with `browseVignettes`. `FAQ-vegan` and `partitioning` were only
accessible with `vegandocs` function.
#### BUILDING
* Dependence on external software `texi2dvi` was removed. Version 6\.1
of `texi2dvi` was incompatible with **R** and prevented building
vegan. The `FAQ-vegan` that was earlier built with `texi2dvi` uses now
[knitr](https://CRAN.R-project.org/package=knitr). Because of this,
vegan is now dependent on **R**-3\.0\.0\. Fixes issue
[\#158](https://github.com/vegandevs/vegan/issues/158) in Github.
### Changes in version 2\.3-3
#### BUG FIXES
* `metaMDS` and `monoMDS` could fail if input dissimilarities were huge:
in the reported case they were of magnitude 1E85\. Fixes issue
[\#152](https://github.com/vegandevs/vegan/issues/152) in Github.
* Permutations failed if they were defined as
[permute](https://CRAN.R-project.org/package=permute) control
structures in `estaccum`, `ordiareatest`, `renyiaccum` and
`tsallisaccum`. Reported by Dan Gafta (Cluj-Napoca) for `renyiaccum`.
* `rarefy` gave false warnings if input was a vector or a single
sampling unit.
* Some extrapolated richness indices in `specpool` needed the number of
doubletons (= number of species occurring in two sampling units), and
these failed when only one sampling unit was supplied. The
extrapolated richness cannot be estimated from a single sampling unit,
but now such cases are handled smoothly instead of failing: observed
non-extrapolated richness with zero standard error will be reported.
The issue was reported in
[StackOverflow](https://stackoverflow.com/questions/34027496/).
#### NEW FEATURES
* `treedist` and `treedive` refuse to handle trees with reversals, i.e,
higher levels are more homogeneous than lower levels. Function
`treeheight` will estimate their total height with absolute values of
branch lengths. Function `treedive` refuses to handle trees with
negative branch heights indicating negative dissimilarities. Function
`treedive` is faster.
* `gdispweight` works when input data are in a matrix instead of a data
frame.
* Input dissimilarities supplied in symmetric matrices or data frames
are more robustly recognized by `anosim`, `bioenv` and `mrpp`.
### Changes in version 2\.3-2
#### BUG FIXES
* Printing details of a gridded permutation design would fail when the
grid was at the within-plot level.
* `ordicluster` joined the branches at wrong coordinates in some cases.
* `ordiellipse` ignored weights when calculating standard errors (`kind
= "se"`). This influenced plots of `cca`, and also influenced
`ordiareatest`.
#### NEW FEATURES
* `adonis` and `capscale` functions recognize symmetric square matrices
as dissimilarities. Formerly dissimilarities had to be given as
`"dist"` objects such as produced by `dist` or `vegdist` functions,
and data frames and matrices were regarded as observations x variables
data which could confuse users (e.g., issue
[\#147](https://github.com/vegandevs/vegan/issues/147)).
* `mso` accepts `"dist"` objects for the distances among locations as an
alternative to coordinates of locations.
* `text`, `points` and `lines` functions for `procrustes` analysis
gained new argument `truemean` which allows adding `procrustes` items
to the plots of original analysis.
* `rrarefy` returns observed non-rarefied communities (with a warning)
when users request subsamples that are larger than the observed
community instead of failing. Function `drarefy` has been similar and
returned sampling probabilities of 1, but now it also issues a
warning. Fixes issue
[\#144](https://github.com/vegandevs/vegan/issues/144) in Github.
### Changes in version 2\.3-1
#### BUG FIXES
* Permutation tests did not always correctly recognize ties with the
observed statistic and this could result in too low `P`-values. This
would happen in particular when all predictor variables were factors
(classes). The changes concern functions `adonis`, `anosim`, `anova`
and `permutest` functions for `cca`, `rda` and `capscale`, `permutest`
for `betadisper`, `envfit`, `mantel` and `mantel.partial`, `mrpp`,
`mso`, `oecosimu`, `ordiareatest`, `protest` and `simper`. This also
fixes issues [\#120](https://github.com/vegandevs/vegan/issues/120)
and [\#132](https://github.com/vegandevs/vegan/issues/132) in GitHub.
* Automated model building in constrained ordination (`cca`, `rda`,
`capscale`) with `step`, `ordistep` and `ordiR2step` could fail if
there were aliased candidate variables, or constraints that were
completely explained by other variables already in the model. This was
a regression introduced in vegan 2\.2-0\.
* Constrained ordination methods `cca`, `rda` and `capscale` treat
character variables as factors in analysis, but did not return their
centroids for plotting.
* Recovery of original data in `metaMDS` when computing WA scores for
species would fail if the expression supplied to argument `comm` was
long & got deparsed to multiple strings. `metaMDSdist` now returns the
(possibly modified) data frame of community data `comm` as attribute
`"comm"` of the returned `dist` object. `metaMDS` now uses this to
compute the WA species scores for the NMDS. In addition, the deparsed
expression for `comm` is now robust to long expressions. Reported by
Richard Telford.
* `metaMDS` and `monoMDS` rejected dissimilarities with missing values.
* Function `rarecurve` did not check its input and this could cause
confusing error messages. Now function checks that input data are
integers that can be interpreted as counts on individuals and all
sampling units have some species. Unchecked bad inputs were the reason
for problems reported in
[Stackoverflow](https://stackoverflow.com/questions/30856909/).
#### NEW FEATURES AND FUNCTIONS
* Scaling of ordination axes in `cca`, `rda` and `capscale` can now be
expressed with descriptive strings `"none"`, `"sites"`, `"species"` or
`"symmetric"` to tell which kind of scores should be scaled by
eigenvalues. These can be further modified with arguments `hill` in
`cca` and `correlation` in `rda`. The old numeric scaling can still be
used.
* The permutation data can be extracted from `anova` results of
constrained ordination (`cca`, `rda`, `capscale`) and further analysed
with `permustats` function.
* New data set `BCI.env` of site information for the Barro Colorado
Island tree community data. Most useful variables are the UTM
coordinates of sample plots. Other variables are constant or nearly
constant and of little use in normal analysis.
### Changes in version 2\.3-0
#### BUG FIXES
* Constrained ordination functions `cca`, `rda` and `capscale` are now
more robust. Scoping of data set names and variable names is much
improved. This should fix numerous long-standing problems, for
instance those reported by Benedicte Bachelot (in email) and Richard
Telford (in Twitter), as well as issues
[\#16](https://github.com/vegandevs/vegan/issues/16) and
[\#100](https://github.com/vegandevs/vegan/issues/100) in GitHub.
* Ordination functions `cca` and `rda` silently accepted dissimilarities
as input although their analysis makes no sense with these methods.
Dissimilarities should be analysed with distance-based redundancy
analysis (`capscale`).
* The variance of the conditional component was over-estimated in
`goodness` of `rda` results, and results were wrong for partial RDA.
The problems were reported in an
[R-sig-ecology](https://stat.ethz.ch/pipermail/r-sig-ecology/2015-March/004936.html)
message by Christoph von Redwitz.
#### WINDOWS
* `orditkplot` did not add file type identifier to saved graphics in
Windows although that is required. The problem only concerned Windows
OS.
#### NEW FEATURES AND FUNCTIONS
* `goodness` function for constrained ordination (`cca`, `rda`,
`capscale`) was redesigned. Function gained argument `addprevious` to
add the variation explained by previous ordination components to axes
when `statistic = "explained"`. With this option, `model = "CCA"` will
include the variation explained by partialled-out conditions, and
`model = "CA"` will include the accumulated variation explained by
conditions and constraints. The former behaviour was `addprevious =
TRUE` for `model = "CCA"`, and `addprevious = FALSE` for `model =
"CA"`. The argument will have no effect when `statistic = "distance"`,
but this will always show the residual distance after all previous
components. Formerly it displayed the residual distance only for the
currently analysed model.
* Functions `ordiArrowMul` and `ordiArrowTextXY` are exported and can be
used in normal interactive sessions. These functions are used to scale
a bunch arrows to fit ordination graphics, and formerly they were
internal functions used within other vegan functions.
* `orditkplot` can export graphics in SVG format. SVG is a vector
graphics format which can be edited with several external programs,
such as Illustrator and Inkscape.
* Rarefaction curve (`rarecurve`) and species accumulation models
(`specaccum`, `fitspecaccum`) gained new functions to estimate the
slope of curve at given location. Originally this was based on a
response to an
[R-SIG-ecology](https://stat.ethz.ch/pipermail/r-sig-ecology/2015-May/005038.html)
query. For rarefaction curves, the function is `rareslope`, and for
species accumulation models it is `specslope`.
The functions are based on analytic equations, and can also be
evaluated at interpolated non-integer values. In `specaccum` models
the functions can be only evaluated for analytic models `"exact"`,
`"rarefaction"` and `"coleman"`. With `"random"` and `"collector"`
methods you can only use finite differences
(`diff(fitted())`). Analytic functions for slope are
used for all non-linear regression models known to `fitspecaccum`.
* Species accumulation models (`specaccum`) and non-liner regression
models for species accumulation (`fitspecaccum`) work more
consistently with weights. In all cases, the models are defined using
the number of sites as independent variable, which with weights means
that observations can be non-integer numbers of virtual sites. The
`predict` models also use the number of sites with `newdata`, and for
analytic models they can estimate the expected values for non-integer
number of sites, and for non-analytic randomized or collector models
they can interpolate on non-integer values.
* `fitspecaccum` gained support functions `AIC` and `deviance`.
* The `varpart` plots of four-component models were redesigned following
Legendre, Borcard & Roberts *Ecology* 93, 1234–1240 (2012\), and they
use now four ellipses instead of three circles and two rectangles. The
components are now labelled in plots, and the circles and ellipses can
be easily filled with transparent background colour.
### Changes in version 2\.2-1
#### GENERAL
* This is a maintenance release to avoid warning messages caused by
changes in CRAN repository. The namespace usage is also more stringent
to avoid warnings and notes in development versions of **R**.
#### INSTALLATION
* vegan can be installed and loaded without tcltk package. The tcltk
package is needed in `orditkplot` function for interactive editing of
ordination graphics.
#### BUG FIXES
* `ordisurf` failed if [gam](https://CRAN.R-project.org/package=gam)
package was loaded due to namespace issues: some support functions of
gam were used instead of
[mgcv](https://CRAN.R-project.org/package=mgcv) functions.
* `tolerance` function failed for unconstrained correspondence analysis.
#### NEW FEATURES
* `estimateR` uses a more exact variance formula for bias-corrected Chao
estimate of extrapolated number of species. The new formula may be
unpublished, but it was derived following the guidelines of Chiu,
Wang, Walther & Chao, *Biometrics* 70, 671–682 (2014\),
[doi:10\.1111/biom.12200](https://doi.org/10.1111/biom.12200), online
supplementary material.
* Diversity accumulation functions `specaccum`, `renyiaccum`,
`tsallisaccum`, `poolaccum` and `estaccumR` use now
[permute](https://CRAN.R-project.org/package=permute) package for
permutations of the order of sampling sites. Normally these functions
only need simple random permutation of sites, but restricted
permutation of the permute package and user-supplied permutation
matrices can be used.
* `estaccumR` function can use parallel processing.
* `linestack` accepts now expressions as labels. This allows using
mathematical symbols and formula given as mathematical expressions.
### Changes in version 2\.2-0
#### GENERAL
* Several vegan functions can now use parallel processing for slow and
repeating calculations. All these functions have argument `parallel`.
The argument can be an integer giving the number of parallel
processes. In unix-alikes (Mac OS, Linux) this will launch
`"multicore"` processing and in Windows it will set up `"snow"`
clusters as desribed in the documentation of the parallel package. If
`option` `"mc.cores"` is set to an integer \> 1, this will be used to
automatically start parallel processing. Finally, the argument can
also be a previously set up `"snow"` cluster which will be used both
in Windows and in unix-alikes. Vegan vignette on Design decision
explains the implementation (use `vegandocs("decission")`, and
parallel package has more extensive documentation on parallel
processing in **R**.
The following function use parallel processing in analysing
permutation statistics: `adonis`, `anosim`, `anova.cca` (and
`permutest.cca`), `mantel` (and `mantel.partial`), `mrpp`,
`ordiareatest`, `permutest.betadisper` and `simper`. In addition,
`bioenv` can compare several candidate sets of models in paralle,
`metaMDS` can launch several random starts in parallel, and `oecosimu`
can evaluate test statistics for several null models in parallel.
* All permutation tests are based on the
[permute](https://CRAN.R-project.org/package=permute) package which
offers strong tools for restricted permutation. All these functions
have argument `permutations`. The default usage of simple
non-restricted permutations is achieved by giving a single integer
number. Restricted permutations can be defined using the `how`
function of the permute package. Finally, the argument can be a
permutation matrix where rows define permutations. It is possible to
use external or user constructed permutations.
See `help(permutations)` for a brief introduction on permutations in
vegan, and permute package for the full documention. The vignette of
the permute package can be read from vegan with command
`vegandocs("permutations")`.
The following functions use the
[permute](https://CRAN.R-project.org/package=permute) package:
`CCorA`, `adonis`, `anosim`, `anova.cca` (plus associated
`permutest.cca`, `add1.cca`, `drop1.cca`, `ordistep`, `ordiR2step`),
`envfit` (plus associated `factorfit` and `vectorfit`), `mantel` (and
`mantel.partial`), `mrpp`, `mso`, `ordiareatest`,
`permutest.betadisper`, `protest` and `simper`.
* Community null model generation has been completely redesigned and
rewritten. The communities are constructed with new `nullmodel`
function and defined in a low level `commsim` function. The actual
null models are generated with a `simulate` function that builds an
array of null models. The new null models include a wide array of
quantitative models in addition to the old binary models, and users
can plug in their own generating functions. The basic tool invoking
and analysing null models is `oecosimu`. The null models are often
used only for the analysis of nestedness, but the implementation in
`oecosimu` allows analysing any statistic, and null models are better
seen as an alternative to permutation tests.
#### INSTALLATION
* vegan package dependencies and namespace imports were adapted to
changes in **R**, and no more trigger warnings and notes in package
tests.
* Three-dimensional ordination graphics using
[scatterplot3d](https://CRAN.R-project.org/package=scatterplot3d) for
static plots and [rgl](https://CRAN.R-project.org/package=rgl) for
dynamic plots were removed from vegan and moved to a companion package
[vegan3d](https://CRAN.R-project.org/package=vegan3d). The package is
available in CRAN.
#### NEW FUNCTIONS
* Function `dispweight` implements dispersion weighting of Clarke et al.
(*Marine Ecology Progress Series*, 320, 11–27\). In addition, we
implemented a new method for generalized dispersion weighting
`gdispweight`. Both methods downweight species that are significantly
over-dispersed.
* New `hclust` support functions `reorder`, `rev` and `scores`.
Functions `reorder` and `rev` are similar as these functions for
`dendrogram` objects in base **R**. However, `reorder` can use (and
defaults to) weighted mean. In weighted mean the node average is
always the mean of member leaves, whereas the `dendrogram` uses always
unweighted means of joined branches.
* Function `ordiareatest` supplements `ordihull` and `ordiellipse` and
provides a randomization test for the one-sided alternative hypothesis
that convex hulls or ellipses in two-dimensional ordination space have
smaller areas than with randomized groups.
* Function `permustats` extracts and inspects permutation results with
support functions `summary`, `density`, `densityplot`, `qqnorm` and
`qqmath`. The `density` and `qqnorm` are standard **R** tools that
only work with one statistic, and `densityplot` and `qqmath` are
lattice graphics that work with univariate and multivariate
statistics. The results of following functions can be extracted:
`anosim`, `adonis`, `mantel` (and `mantel.partial`), `mrpp`,
`oecosimu`, `permustest.cca` (but not the corresponding `anova`
methods), `permutest.betadisper`, and `protest`.
* `stressplot` functions display the ordination distances at given
number of dimensions against original distances. The method functins
are similar to `stressplot` for `metaMDS`, and always use the inherent
distances of each ordination method. The functions are available for
the results `capscale`, `cca`, `princomp`, `prcomp`, `rda`, and
`wcmdscale`.
#### BUG FIXES
* `cascadeKM` of only one group will be `NA` instead of a random value.
* `ordiellipse` can handle points exactly on a line, including only two
points (with a warning).
* plotting `radfit` results for several species failed if any of the
communities had no species or had only one species.
* `RsquareAdj` for `capscale` with negative eigenvalues will now report
`NA` instead of using biased method of `rda` results.
* `simper` failed when a group had only a single member.
#### NEW FEATURES
* `anova.cca` functions were re-written to use the permute package. Old
results may not be exactly reproduced, and models with missing data
may fail in several cases. There is a new option of analysing a
sequence of models against each other.
* `simulate` functions for `cca` and `rda` can return several
simulations in a `nullmodel` compatible object. The functions can
produce simulations with correlated errors (also for `capscale`) in
parametric simulation with Gaussian error.
* `bioenv` can use Manhattan, Gower and Mahalanobis distances in
addition to the default Euclidean. New helper function `bioenvdist`
can extract the dissimilarities applied in best model or any other
model.
* `metaMDS(..., trace = 2)` will show convergence information with the
default `monoMDS` engine.
* Function `MDSrotate` can rotate a `k`-dimensional ordination to `k-1`
variables. When these variables are correlated (like usually is the
case), the vectors can also be correlated to previously rotated
dimensions, but will be uncorrelated to all later ones.
* vegan 2\.0-10 changed the weighted `nestednodf` so that weighted
analysis of binary data was equivalent to binary analysis. However,
this broke the equivalence to the original method. Now the function
has an argument `wbinary` to select the method of analysis. The
problem was reported and a fix submitted by Vanderlei Debastiani
(Universidade Federal do Rio Grande do Sul, Brasil).
* `ordiellipse`, `ordihull` and `ordiellipse` can handle missing values
in `groups`.
* `ordispider` can now use spatial medians instead of means.
* `rankindex` can use Manhattan, Gower and Mahalanobis distance in
addition to the default Euclidean.
* User can set colours and line types in function `rarecurve` for
plotting rarefaction curves.
* `spantree` gained a support function `as.hclust` to change the minimum
spanning tree into an `hclust` tree.
* `fitspecaccum` can do weighted analysis. Gained `lines` method.
* Functions for extrapolated number of species or for the size of
species pool using Chao method were modified following Chiu et al.,
*Biometrics* 70, 671–682 (2014\).
Incidence based `specpool` can now use (and defaults to) small sample
correction with number of sites as the sample size. Function uses
basic Chao extrapolation based on the ratio of singletons and
doubletons, but switches now to bias corrected Chao extrapolation if
there are no doubletons (species found twice). The variance formula
for bias corrected Chao was derived following the supporting on line
material of
[doi:10\.1111/biom.12200](https://doi.org/10.1111/biom.12200) and
differs slightly from Chiu et al. (2014\).
The `poolaccum` function was changed similarly, but the small sample
correction is used always.
The abundance based `estimateR` uses bias corrected Chao
extrapolation, but earlier it estimated its variance with classic Chao
model. Now we use the widespread approximate estimate from EstimateS
for variance.
With these changes these functions are more similar to **EstimateS**
* `tabasco` uses now `reorder.hclust` for `hclust` object for better
ordering than previously when it cast trees to `dendrogram` objects.
* `treedive` and `treedist` default now to `match.force = TRUE` and can
be silenced with `verbose = FALSE`.
* `vegdist` gained Mahalanobis distance.
* Nomenclature updated in plant community data with the help of
Taxonstand and taxize packages. The taxonomy of the `dune` data was
adapted to the same sources and APG III. `varespec` and `dune` use
8-character names (4 from genus + 4 from species epithet). New data
set on phylogenetic distances for `dune` was extracted from Zanne et
al. (*Nature* 506, 89–92; 2014\).
* User configurable plots for `rarecurve`.
#### DEPRECATED AND DEFUNCT
* `strata` are deprecated in permutations. It is still accepted but will
be phased out in next releases. Use `how` of permute package.
* `cca`, `rda` and `capscale` do not return scores scaled by
eigenvalues: use `scores` function to extract scaled results.
* `commsimulator` is deprecated. Replace `commsimulator(x, method)` with
`simulate(nullmodel(x, method))`.
* `density` and `densityplot` for permutation results are deprecated:
use `permustats` with its `density` and `densityplot` method.
### Changes in version 2\.0-10
#### GENERAL
* This version is adapted to the changes in permute package version
0\.8-0 and no more triggers NOTEs in package checks. This release may
be the last of the 2\.0 series, and the next vegan release is
scheduled to be a major release with newly designed `oecosimu` and
community pattern simulation, support for parallel processing, and
full support of the permute package. If you are interested in these
developments, you may try the development versions of vegan in
[GitHub](https://github.com/jarioksa/vegan) and report the problems
and user experience to us.
#### BUG FIXES
* `envfit` function assumed that all external variables were either
numeric or factors, and failed if they were, say, character strings.
Now only numeric variables are taken as continuous vectors, and all
other variables (character strings, logical) are coerced to factors if
possible. The function also should work with degenerate data, like
only one level of a factor or a constant value of a continuous
environmental variable. The ties were wrongly in assessing permutation
`P`-values in `vectorfit`.
* `nestednodf` with quantitative data was not consistent with binary
models, and the fill was wrongly calculated with quantitative data.
* `oecosimu` now correctly adapts displayed quantiles of simulated
values to the `alternative` test direction.
* `renyiaccum` plotting failed if only one level of diversity `scale`
was used.
#### NEW FEATURES
* The Kempton and Taylor algorithm was found unreliable in `fisherfit`
and `fisher.alpha`, and now the estimation of Fisher α is only
based on the number of species and the number of individuals. The
estimation of standard errors and profile confidence intervals also
had to be scrapped.
* `renyiaccum`, `specaccum` and `tsallisaccum` functions gained `subset`
argument.
* `renyiaccum` can now add a `collector` curve to to the analysis. The
collector curve is the diversity accumulation in the order of the
sampling units. With an interesting ordering or sampling units this
allows comparing actual species accumulations with the expected
randomized accumulation.
* `specaccum` can now perform weighted accumulation using the sampling
effort as weights.
### Changes in version 2\.0-9
* This version is released due to changes in programming interface and
testing procedures in **R** 3\.0\.2\. If you are using an older
version of **R**, there is no need to upgrade vegan. There are no new
features nor bug fixes. The only user-visible changes are in
documentation and in output messages and formatting. Because of **R**
changes, this version is dependent on **R** version 2\.14\.0 or newer
and on lattice package.
### Changes in version 2\.0-8
#### GENERAL
* This is a maintenance release that fixes some issues raised by changed
in **R** toolset for processing vignettes. In the same we also fix
some typographic issues in the vignettes.
#### NEW FEATURES
* `ordisurf` gained new arguments for more flexible definition of fitted
models to better utilize the mgcv`::gam` function.
The linewidth of contours can now be set with the argument `lwd`.
* Labels to arrows are positioned in a better way in `plot` functions
for the results of `envfit`, `cca`, `rda` and `capscale`. The labels
should no longer overlap the arrow tips.
* The setting test direction is clearer in `oecosimu`.
* `ordipointlabel` gained a `plot` method that can be used to replot the
saved result.
### Changes in version 2\.0-7
#### NEW FUNCTIONS
* `tabasco()` is a new function for graphical display of community data
matrix. Technically it is an interface to **R** `heatmap`, but its use
is closer to vegan function `vegemite`. The function can reorder the
community data matrix similarly as `vegemite`, for instance, by
ordination results. Unlike `heatmap`, it only displays dendrograms if
supplied by the user, and it defaults to re-order the dendrograms by
correspondence analysis. Species are ordered to match site ordering or
like determined by the user.
#### BUG FIXES
* Function `fitspecaccum(..., model = "asymp")` fitted logistic model
instead of asymptotic model (or the same as `model = "logis"`).
* `nestedtemp()` failed with very sparse data (fill `< 0.38`%).
#### NEW FEATURES
* The `plot` function for constrained ordination results (`cca`, `rda`,
`capscale`) gained argument `axis.bp` (defaults `TRUE`) which can be
used to suppress axis scale for biplot arrays.
* Number of iterations in nonmetric multidimensional scaling (NMDS) can
be set with keyword `maxit` (defaults `200`) in `metaMDS`.
#### DEPRECATED
* The result objects of `cca`, `rda` and `capscale` will no longer have
scores `u.eig`, `v.eig` and `wa.eig` in the future versions of vegan.
This change does not influence normal usage, because vegan functions
do not need these items. However, external scripts and packages may
need changes in the future versions of vegan.
### Changes in version 2\.0-6
#### BUG FIXES
* The species scores were scaled wrongly in `capscale()`. They were
scaled correctly only when Euclidean distances were used, but usually
`capscale()` is used with non-Euclidean distances. Most graphics will
change and should be redone. The change of scaling mainly influences
the spread of species scores with respect to the site scores.
* Function `clamtest()` failed to set the minimum abundance threshold in
some cases. In addition, the output was wrong when some of the
possible species groups were missing. Both problems were reported by
Richard Telford (Bergen, Norway).
* Plotting an object fitted by `envfit()` would fail if `p.max` was used
and there were unused levels for one or more factors. The unused
levels could result from deletion of observations with missing values
or simply as the result of supplying a subset of a larger data set to
`envfit()`.
* `multipart()` printed wrong information about the analysis type (but
did the analysis correctly). Reported by Valerie Coudrain.
* `oecosimu()` failed if its `nestedfun` returned a data frame. A more
fundamental fix will be in vegan 2\.2-0, where the structure of the
`oecosimu()` result will change.
* The plot of two-dimensional `procrustes()` solutions often draw
original axes in a wrong angle. The problem was reported by Elizabeth
Ottesen (MIT).
* Function `treedive()` for functional or phylogenetic diversity did not
correctly match the species names between the community data and
species tree when the tree contained species that did not occur in the
data. Related function `treedist()` for phylogenetic distances did not
try to match the names at all.
#### NEW FEATURES
* The output of `capscale()` displays the value of the additive constant
when argument `add = TRUE` was used.
* `fitted()` functions for `cca()`, `rda()` and `capscale()` can now
return conditioned (partial) component of the response: Argument
`model` gained a new alternative `model = "pCCA"`.
* `dispindmorisita()` output gained a new column for Chi-squared based
probabilities that the null hypothesis (random distribution) is true.
* `metaMDS()` and `monoMDS()` have new default convergence criteria.
Most importantly, scale factor of the gradient (`sfgrmin`) is
stricter. The former limit was too slack with large data sets and
iterations stopped early without getting close to the solution. In
addition, `scores()` ignore now requests to dimensions beyond those
calculated instead of failing, and `scores()` for `metaMDS()` results
do not drop dimensions.
* `msoplot()` gained `legend` argument for positioning the legend.
* Nestedness function `nestednodf()` gained a `plot` method.
* `ordiR2step()` gained new argument `R2scope` (defaults `TRUE`) which
can be used to turn off the criterion of stopping when the adjusted
_R_2 of the current model exceeds that of the scope. This option
allows model building when the `scope` would be overdetermined (number
of predictors higher than number of observations).
`ordiR2step()` now handles partial redundancy analysis (pRDA).
* `orditorp()` gained argument `select` to select the rows or columns of
the results to display.
* `protest()` prints the standardized residual statistic squared m12
in addition to the squared Procrustes correlation _R_2. Both
were calculated, but only the latter was displayed.
Permutation tests are much faster in `protest()`. Instead of calling
repeatedly `procrustes()`, the goodness of fit statistic is evaluated
within the function.
* `wcmdscale()` gained methods for `print`, `plot` etc. of the results.
These methods are only used if the full `wcmdscale` result is returned
with, e.g., argument `eig = TRUE`. The default is still to return only
a matrix of scores similarly as the standard **R** function
`cmdscale()`, and in that case the new methods are not used.
### Changes in version 2\.0-5
#### BUG FIXES
* `anova(, ...)` failed with `by = "axis"` and `by =
"term"`. The bug was reported by Dr Sven Neulinger (Christian Albrecht
University, Kiel, Germany).
* `radlattice` did not honour argument `BIC = TRUE`, but always
displayed AIC.
#### NEW FUNCTIONS
* Most vegan functions with permutation tests have now a `density`
method that can be used to find empirical probability distributions of
permutations. There is a new `plot` method for these functions that
displays both the density and the observed statistic. The `density`
function is available for `adonis`, `anosim`, `mantel`,
`mantel.partial`, `mrpp`, `permutest.cca` and `procrustes`.
Function `adonis` can return several statistics, and it has now a
`densityplot` method (based on lattice).
Function `oecosimu` already had `density` and `densityplot`, but they
are now similar to other vegan methods, and also work with `adipart`,
`hiersimu` and `multipart`.
* `radfit` functions got a `predict` method that also accepts arguments
`newdata` and `total` for new ranks and site totals for prediction.
The functions can also interpolate to non-integer “ranks”, and in some
models also extrapolate.
#### NEW FEATURES
* Labels can now be set in the `plot` of `envfit` results. The labels
must be given in the same order that the function uses internally, and
new support function `labels` can be used to display the default
labels in their correct order.
* Mantel tests (functions `mantel` and `mantel.partial`) gained argument
`na.rm` which can be used to remove missing values. This options
should be used with care: Permutation tests can be biased if the
missing values were originally in matching or fixed positions.
* `radfit` results can be consistently accessed with the same methods
whether they were a single model for a single site, all models for a
single site or all models for all sites in the data. All functions now
have methods `AIC`, `coef`, `deviance`, `logLik`, `fitted`, `predict`
and `residuals`.
#### INSTALLATION AND BUILDING
* Building of vegan vignettes failed with the latest version of LaTeX
(TeXLive 2012\).
* **R** versions later than 2\.15-1 (including development version)
report warnings and errors when installing and checking vegan, and you
must upgrade vegan to this version. The warnings concern functions
`cIndexKM` and `betadisper`, and the error occurs in `betadisper`.
These errors and warnings were triggered by internal changes in **R**.
### Changes in version 2\.0-4
#### BUG FIXES
* `adipart` assumed constant gamma diversity in simulations when
assessing the `P`-value. This could give biased results if the null
model produces variable gamma diversities and option `weights =
"prop"` is used. The default null model (`"r2dtable"`) and the default
option (`weights = "unif"`) were analysed correctly.
* `anova(, by = "axis")` and other `by` cases failed due to
‘NAMESPACE’ issues.
* `clamtest` wrongly used frequencies instead of the counts when
calculating sample coverage. No detectable differences were produced
when rerunning examples from Chazdon et al. 2011 and vegan help page.
* `envfit` failed with unused factor levels.
* `predict` for `cca` results with `type = "response"` or `type =
"working"` failed with `newdata` if the number of rows did not match
with the original data. Now the `newdata` is ignored if it has a wrong
number of rows. The number of rows must match because the results in
`cca` must be weighted by original row totals. The problem did not
concern `rda` or `capscale` results which do not need row weights.
Reported by Glenn De'ath.
#### NEW FEATURES
* Functions for diversity partitioning (`adipart`, `hiersimu` and
`multipart`) have now `formula` and `default` methods. The `formula`
method is identical to the previous functions, but the `default`
method can take two matrices as input.
Functions `adipart` and `multipart` can be used for fast and easy
overall partitioning to alpha, beta and gamma diversities by omitting
the argument describing the hierarchy.
* The method in `betadisper` is biased with small sample sizes. The
effects of the bias are strongest with unequal sample sizes. A bias
adjusted version was developed by Adrian Stier and Ben Bolker, and can
be invoked with argument `bias.adjust` (defaults to `FALSE`).
* `bioenv` accepts dissimilarities (or square matrices that can be
interpreted as dissimilarities) as an alternative to community data.
This allows using other dissimilarities than those available in
`vegdist`.
* `plot` function for `envfit` results gained new argument `bg` that can
be used to set background colour for plotted labels.
* `msoplot` is more configurable, and allows, for instance, setting
y-axis limits.
* Hulls and ellipses are now filled using semitransparent colours in
`ordihull` and `ordiellipse`, and the user can set the degree of
transparency with a new argument `alpha`. The filled shapes are used
when these functions are called with argument `draw = "polygon"`.
Function `ordihull` puts labels (with argument `label = TRUE`) now in
the real polygon centre.
* `ordiplot3d` returns function `envfit.convert` and the projected
location of the `origin`. Together these can be used to add `envfit`
results to existing `ordiplot3d` plots.
Equal aspect ratio cannot be set exactly in `ordiplot3d` because
underlying core routines do not allow this. Now `ordiplot3d` sets
equal axis ranges, and the documents urge users to verify that the
aspect ratio is reasonably equal and the graph looks like a cube. If
the problems cannot be solved in the future, `ordiplot3d` may be
removed from next releases of vegan.
* Function `ordipointlabel` gained argument to `select` only some of the
items for plotting. The argument can be used only with one set of
points.
### Changes in version 2\.0-3
#### NEW FUNCTIONS
* Added new nestedness functions `nestedbetasor` and `nestedbetajac`
that implement multiple-site dissimilarity indices and their
decomposition into turnover and nestedness components following
Baselga (*Global Ecology and Biogeography* 19, 134–143; 2010\).
* Added function `rarecurve` to draw rarefaction curves for each row
(sampling unit) of the input data, optionally with lines showing
rarefied species richness with given sample size for each curve.
* Added function `simper` that implements “similarity percentages” of
Clarke (*Australian Journal of Ecology* 18, 117–143; 1993\). The
method compares two or more groups and decomposes the average
between-group Bray-Curtis dissimilarity index to contributions by
individual species. The code was developed in
[GitHub](https://github.com/jarioksa/vegan) by Eduard Szöcs (Uni
Landau, Germany).
#### BUG FIXES
* `betadisper()` failed when the `groups` was a factor with empty
levels.
* Some constrained ordination methods and their support functions are
more robust in border cases (completely aliased effects, saturated
models, user requests for non-existng scores etc). Concerns
`capscale`, `ordistep`, `varpart`, `plot` function for constrained
ordination, and `anova(, by = "margin")`.
* The `scores` function for `monoMDS` did not honour `choices` argument
and hence dimensions could not be chosen in `plot`.
* The default `scores` method failed if the number of requested axes was
higher than the ordination object had. This was reported as an error
in `ordiplot` in
[R-sig-ecology](https://stat.ethz.ch/pipermail/r-sig-ecology/2012-February/002768.html)
mailing list.
#### NEW FEATURES
* `metaMDS` argument `noshare = 0` is now regarded as a numeric
threshold that always triggers extended dissimilarities
(`stepacross`), instead of being treated as synonymous with `noshare =
FALSE` which always suppresses extended dissimilarities.
* Nestedness discrepancy index `nesteddisc` gained a new argument that
allows user to set the number of iterations in optimizing the index.
* `oecosimu` displays the mean of simulations and describes alternative
hypothesis more clearly in the printed output.
* Implemented adjusted _R_2 for partial RDA. For partial model `rda(Y ~
X1 + Condition(X2))` this is the same as the component `[a] = X1|X2`
in variance partition in `varpart` and describes the marginal (unique)
effect of constraining term to adjusted _R_2.
* Added Cao dissimilarity (CYd) as a new dissimilarity method in
`vegdist` following Cao et al., *Water Envir Res* 69, 95–106 (1997\).
The index should be good for data with high beta diversity and
variable sampling intensity. Thanks to consultation to Yong Cao (Univ
Illinois, USA).
### Changes in version 2\.0-2
#### BUG FIXES
* Function `capscale` failed if constrained component had zero rank.
This happened most likely in partial models when the conditions
aliased constraints. The problem was observed in `anova(..., by
="margin")` which uses partial models to analyses the marginal
effects, and was reported in an email message to [R-News mailing
list](https://stat.ethz.ch/pipermail/r-help/2011-October/293077.html).
* `stressplot` and `goodness` sometimes failed when `metaMDS` was based
on `isoMDS` (MASS package) because `metaMDSdist` did not use the same
defaults for step-across (extended) dissimilarities as `metaMDS(...,
engine = "isoMDS")`. The change of defaults can also influence
triggering of step-across in `capscale(..., metaMDSdist = TRUE)`.
* `adonis` contained a minor bug resulting from incomplete
implementation of a speed-up that did not affect the results. In
fixing this bug, a further bug was identified in transposing the hat
matrices. This second bug was only active following fixing of the
first bug. In fixing both bugs, a speed-up in the internal f.test()
function is fully realised. Reported by Nicholas Lewin-Koh.
#### NEW FEATURES
* `ordiarrows` and `ordisegments` gained argument `order.by` that gives
a variable to sort points within `groups`. Earlier the points were
assumed to be in order.
* Function `ordispider` invisibly returns the coordinates to which the
points were connected. Typically these are class centroids of each
point, but for constrained ordination with no `groups` they are the LC
scores.
### Changes in version 2\.0-1
#### NEW FUNCTIONS
* `clamtest`: new function to classify species as generalists and
specialists in two distinct habitats (CLAM test of Chazdon et al.,
*Ecology* 92, 1332–1343; 2011\). The test is based on multinomial
distribution of individuals in two habitat types or sampling units,
and it is applicable only to count data with no over-dispersion.
* `as.preston` gained `plot` and `lines` methods, and `as.fisher` gained
`plot` method (which also can add items to existing plots). These are
similar as `plot` and `lines` for `prestonfit` and `fisherfit`, but
display only data without the fitted lines.
* `raupcrick`: new function to implement Raup-Crick dissimilarity as a
probability of number of co-occurring species with occurrence
probabilities proportional to species frequencies. Vegan has
Raup-Crick index as a choice in `vegdist`, but that uses equal
sampling probabilities for species and analytic equations. The new
`raupcrick` function uses simulation with `oecosimu`. The function
follows Chase et al. (2011\) *Ecosphere* 2:art24
\[[doi:10\.1890/ES10-00117\.1](https://doi.org/10.1890/ES10-00117.1)\],
and was developed with the consultation of Brian Inouye.
#### BUG FIXES
* Function `meandist` could scramble items and give wrong results,
especially when the `grouping` was numerical. The problem was reported
by Dr Miguel Alvarez (Univ. Bonn).
* `metaMDS` did not reset `tries` when a new model was started with a
`previous.best` solution from a different model.
* Function `permatswap` for community null models using quantitative
swap never swapped items in a 2x2 submatrix if all cells were
filled.
* The result from `permutest.cca` could not be `update`d because of a
‘NAMESPACE’ issue.
* **R** 2\.14\.0 changed so that it does not accept using `sd()`
function for matrices (which was the behaviour at least since **R**
1\.0-0\), and several vegan functions were changed to adapt to this
change (`rda`, `capscale`, `simulate` methods for `rda`, `cca` and
`capscale`). The change in **R** 2\.14\.0 does not influence the
results but you probably wish to upgrade vegan to avoid annoying
warnings.
#### ANALYSES
* `nesteddisc` is slacker and hence faster when trying to optimize the
statistic for tied column frequencies. Tracing showed that in most
cases an improved ordering was found rather early in tries, and the
results are equally good in most cases.
### Changes in version 2\.0-0
#### GENERAL
* Peter Minchin joins the vegan team.
* vegan implements standard **R** ‘NAMESPACE’. In general, `S3` methods
are not exported which means that you cannot directly use or see
contents of functions like `cca.default`, `plot.cca` or
`anova.ccabyterm`. To use these functions you should rely on **R**
delegation and simply use `cca` and for its result objects use `plot`
and `anova` without suffix `.cca`. To see the contents of the function
you can use `:::`, such as `vegan:::cca.default`. This change may
break packages, documents or scripts that rely on non-exported names.
* vegan depends on the permute package. This package provides powerful
tools for restricted permutation schemes. All vegan permutation will
gradually move to use permute, but currently only `betadisper` uses
the new feature.
#### NEW FUNCTIONS
* `monoMDS`: a new function for non-metric multidimensional scaling
(NMDS). This function replaces `MASS::isoMDS` as the default method in
`metaMDS`. Major advantages of `monoMDS` are that it has ‘weak’
(‘primary’) tie treatment which means that it can split tied
observed dissimilarities. ‘Weak’ tie treatment improves ordination of
heterogeneous data sets, because maximum dissimilarities of `1` can be
split. In addition to global NMDS, `monoMDS` can perform local and
hybrid NMDS and metric MDS. It can also handle missing and zero
dissimilarities. Moreover, `monoMDS` is faster than previous
alternatives. The function uses `Fortran` code written by Peter
Minchin.
* `MDSrotate` a new function to replace `metaMDSrotate`. This function
can rotate both `metaMDS` and `monoMDS` results so that the first axis
is parallel to an environmental vector.
* `eventstar` finds the minimum of the evenness profile on the Tsallis
entropy, and uses this to find the corresponding values of diversity,
evenness and numbers equivalent following Mendes et al. (*Ecography*
31, 450-456; 2008\). The code was contributed by Eduardo Ribeira Cunha
and Heloisa Beatriz Antoniazi Evangelista and adapted to vegan by
Peter Solymos.
* `fitspecaccum` fits non-linear regression models to the species
accumulation results from `specaccum`. The function can use new
self-starting species accumulation models in vegan or other
self-starting non-linear regression models in **R**. The function can
fit Arrhenius, Gleason, Gitay, Lomolino (in vegan), asymptotic,
Gompertz, Michaelis-Menten, logistic and Weibull (in base **R**)
models. The function has `plot` and `predict` methods.
* Self-starting non-linear species accumulation models `SSarrhenius`,
`SSgleason`, `SSgitay` and `SSlomolino`. These can be used with
`fitspecaccum` or directly in non-linear regression with `nls`. These
functions were implemented because they were found good for
species-area models by Dengler (*J. Biogeogr.* 36, 728-744; 2009\).
#### NEW FEATURES
* `adonis`, `anosim`, `meandist` and `mrpp` warn on negative
dissimilarities, and `betadisper` refuses to analyse them. All these
functions expect dissimilarities, and giving something else (like
correlations) probably is a user error.
* `betadisper` uses restricted permutation of the permute package.
* `metaMDS` uses `monoMDS` as its default ordination engine. Function
gains new argument `engine` that can be used to alternatively select
`MASS::isoMDS`. The default is not to use `stepacross` with `monoMDS`
because its ‘weak’ tie treatment can cope with tied maximum
dissimilarities of one. However, `stepacross` is the default with
`isoMDS` because it cannot handle adequately these tied maximum
dissimilarities.
* `specaccum` gained `predict` method which uses either linear or spline
interpolation for data between observed points. Extrapolation is
possible with spline interpolation, but may make little sense.
* `specpool` can handle missing values or empty factor levels in the
grouping factor `pool`. Now also checks that the length of the `pool`
matches the number of observations.
#### DEPRECATED AND DEFUNCT
* `metaMDSrotate` was replaced with `MDSrotate` that can also handle the
results of `monoMDS`.
* `permuted.index2` and other “new” permutation code was removed in
favour of the permute package. This code was not intended for normal
use, but packages depending on that code in vegan should instead
depend on permute.
#### ANALYSES
* `treeheight` uses much snappier code. The results should be unchanged.