| NEWS | R Documentation |
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.
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
updated 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.
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.
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.
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).
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.
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.
treeheight uses much snappier code. The results
should be unchanged.