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
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.
fitspecaccum(..., model = "asymp") fitted
logistic model instead of asymptotic model (or the same as
model = "logis").
nestedtemp() failed with very sparse data (fill
plot function for constrained ordination
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
The result objects of
capscale will no longer have scores
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.
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.
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
multipart() printed wrong information about the
analysis type (but did the analysis correctly). Reported by
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
often draw original axes in a wrong angle. The problem was
reported by Elizabeth Ottesen (MIT).
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.
The output of
capscale() displays the value of the
additive constant when argument
add = TRUE was used.
fitted() functions for
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.
monoMDS() have new default
convergence criteria. Most importantly, scale factor of the
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,
ignore now requests to dimensions beyond those calculated
instead of failing, and
results do not drop dimensions.
legend argument for
positioning the legend.
nestednodf() gained a
ordiR2step() gained new argument
TRUE) which can be used to turn off the criterion
of stopping when the adjusted R-squared 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
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-squared. Both were calculated, but only
the latter was displayed.
Permutation tests are much faster in
of calling repeatedly
procrustes(), the goodness of fit
statistic is evaluated within the function.
wcmdscale() gained methods for
plot etc. of the results. These methods are only used if
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
and in that case the new methods are not used.
anova(<cca_object>, ...) 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.
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
adonis can return several statistics, and it has
densityplot method (based on lattice).
oecosimu already had
densityplot, but they are now similar to other vegan
methods, and also work with
radfit functions got a
predict method that
also accepts arguments
total for new
ranks and site totals for prediction. The functions can also
interpolate to non-integer “ranks”, and in some models
Labels can now be set in the
results. The labels must be given in the same order that the
function uses internally, and new support function
can be used to display the default labels in their correct order.
Mantel tests (functions
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
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
betadisper, and the error occurs in
These errors and warnings were triggered by internal changes in
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(<prc-object>, 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.
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
capscale results which do not need row weights.
Reported by Glenn De'ath.
Functions for diversity partitioning (
multipart) have now
default methods. The
formula method is
identical to the previous functions, but the
method can take two matrices as input.
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
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
plot function for
envfit results gained new
bg that can be used to set background colour for
msoplot is more configurable, and allows, for
instance, setting y-axis limits.
Hulls and ellipses are now filled using semitransparent
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
and the projected location of the
these can be used to add
envfit results to existing
Equal aspect ratio cannot be set exactly in
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.
ordipointlabel gained argument to
select only some of the items for plotting. The
argument can be used only with one set of points.
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 Szöcs (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
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.
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.