vegan-defunct | R Documentation |
The functions or variables listed here are no longer part of vegan as they are no longer needed.
## defunct in vegan 2.6-0
as.mlm(x)
humpfit(mass, spno, family = poisson, start)
vegandocs(doc = c("NEWS", "ONEWS", "FAQ-vegan", "intro-vegan",
"diversity-vegan", "decision-vegan", "partitioning", "permutations"))
## defunct in vegan 2.5-0
commsimulator(x, method, thin=1)
## defunct in vegan 2.4-0
## S3 method for class 'adonis'
density(x, ...)
## S3 method for class 'vegandensity'
plot(x, main = NULL, xlab = NULL, ylab = "Density",
type = "l", zero.line = TRUE, obs.line = TRUE, ...)
## S3 method for class 'adonis'
densityplot(x, data, xlab = "Null", ...)
## defunct in vegan 2.2-0
metaMDSrotate(object, vec, na.rm = FALSE, ...)
## defunct in vegan 2.0-0
getNumObs(object, ...)
permuted.index2(n, control = permControl())
as.mlm
function is replaced with a set functions that can
find the same statistics directly from the ordination result object:
see hatvalues.cca
, rstandard.cca
,
rstudent.cca
, cooks.distance.cca
,
vcov.cca
.
Function humpfit
was transferred to the natto package and
is still available from https://github.com/jarioksa/natto/.
R functions news
should be used to read vegan
NEWS (news(package = "vegan")
), and
browseVignettes
is a better tool for reading vignettes
than vegandocs
.
Function commsimulator
is replaced with
make.commsim
which defines the Null models, and
functions nullmodel
and
simulate.nullmodel
that check the input data and
generate the Null model communities.
The deprecated density
and densityplot
methods are
replaced with similar methods for permustats
. The
permustats
offers more powerful analysis tools for
permutations, including summary.permustats
giving
z
values (a.k.a. standardized effect sizes, SES), and Q-Q
plots (qqnorm.permustats
,
qqmath.permustats
).
Function metaMDSrotate
is replaced with
MDSrotate
which can handle monoMDS
results in addition to metaMDS
.
The permutation functions were moved to the permute package,
and they are documented there. The permute package replaces
permuted.index
and permuted.index2
with
shuffle
and getNumObs
with its
specific nobs-methods
.
Defunct
, vegan-deprecated
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