The functions or variables listed here are no longer part of vegan as they are no longer needed.
## defunct in vegan 2.7-0
adonis(formula, data, permutations = 999, method = "bray",
strata = NULL, contr.unordered = "contr.sum",
contr.ordered = "contr.poly", parallel = getOption("mc.cores"), ...)
orditkplot(...)## 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 adonis
density(x, ...)
# S3 method for vegandensity
plot(x, main = NULL, xlab = NULL, ylab = "Density",
type = "l", zero.line = TRUE, obs.line = TRUE, ...)
# S3 method for 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())
adonis2 replaces adonis with extended
functionality and completely new internal design. The shared arguments
of adonis are similar as in adonis2, but
arguments contr.unordered and contr.ordered can set the
contrasts within adonis.
orditkplot was moved to CRAN package vegan3d version
1.3-0. Install vegan3d and use the function in the old way.
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