vegan News

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.