NEWS | R Documentation

## vegan News

### 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], and was developed with the consultation of Brian Inouye.

#### BUG FIXES

- Function `meandist` can 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 2 by 2 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.