NEWS | R Documentation |
Added new nestedness functions nestedbetasor
and
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).
Added function 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.
Added function 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
GitHub
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
etc). Concerns capscale
, ordistep
, varpart
,
plot
function for constrained ordination, and
anova(<cca.object>, by = "margin")
.
The scores
function for monoMDS
did not
honour choices
argument and hence dimensions could not be
chosen in plot
.
The default scores
method failed if the number of
requested axes was higher than the ordination object had. This
was reported as an error in ordiplot
in
R-sig-ecology mailing list.
metaMDS
argument noshare = 0
is now
regarded as a numeric threshold that always triggers extended
dissimilarities (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
output.
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
partition in varpart
and describes the marginal (unique)
effect of constraining term to adjusted R-squared.
Added Cao dissimilarity (CYd) as a new dissimilarity
method in 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,
USA).
Function 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
message to
R-News
mailing list.
stressplot
and goodness
sometimes failed when
metaMDS
was based on isoMDS
(MASS package)
because 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.
ordiarrows
and ordisegments
gained argument
order.by
that gives a variable to sort points within
groups
. Earlier the points were assumed to be in order.
Function ordispider
invisibly returns the
coordinates to which the points were connected. Typically these
are class centroids of each point, but for constrained ordination
with no 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.
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
could 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.
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.