Added new nestedness functions
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).
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.
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
by Eduard Szöcz (Uni Landau, Germany).
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
plot function for constrained ordination, and
anova(<cca.object>, by = "margin").
scores function for
monoMDS did not
choices argument and hence dimensions could not be
scores method failed if the number of
requested axes was higher than the ordination object had. This
was reported as an error in
R-sig-ecology mailing list.
noshare = 0 is now
regarded as a numeric threshold that always triggers extended
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
Implemented adjusted R-squared for partial
RDA. For partial model
rda(Y ~ X1 + Condition(X2)) this
is the same as the component
[a] = X1|X2 in variance
varpart and describes the marginal (unique)
effect of constraining term to adjusted R-squared.
Added Cao dissimilarity (CYd) as a new dissimilarity
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,
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
goodness sometimes failed when
metaMDS was based on
isoMDS (MASS package)
metaMDSdist did not use the same defaults for
step-across (extended) dissimilarities as
engine = "isoMDS"). The change of defaults can also influence
triggering of step-across in
capscale(..., metaMDSdist =
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.
ordisegments gained argument
order.by that gives a variable to sort points within
groups. Earlier the points were assumed to be in order.
ordispider invisibly returns the
coordinates to which the points were connected. Typically these
are class centroids of each point, but for constrained ordination
groups they are the LC scores.
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.
plot method (which
also can add items to existing plots). These are similar as
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
function uses simulation with
oecosimu. The function
follows Chase et al. (2011) Ecosphere 2:art24
and was developed with the consultation of Brian Inouye.
meandist could scramble items and give
wrong results, especially when the
numerical. The problem was reported by Dr Miguel Alvarez
metaMDS did not reset
tries when a new model
was started with a
previous.best solution from a different
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 (
simulate methods for
capscale). The change in R 2.14.0 does not influence the
results but you probably wish to upgrade vegan to avoid
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
S3 methods are not exported which means that you
cannot directly use or see contents of functions like
use these functions you should rely on R delegation and simply
cca and for its result objects use
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
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
monoMDS is faster than
previous alternatives. The function uses
written by Peter Minchin.
MDSrotate a new function to replace
metaMDSrotate. This function can rotate both
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
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
Self-starting non-linear species accumulation models
SSlomolino. These can be used with
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).
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
monoMDS as its default ordination
engine. Function gains new argument
engine that can be used
to alternatively select
MASS::isoMDS. The default is not
monoMDS because its
‘weak’ tie treatment can cope with tied maximum
dissimilarities of one. However,
stepacross is the default
isoMDS because it cannot handle adequately these tied
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
metaMDSrotate was replaced with
that can also handle the results of
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.