Defunct Functions in Package vegan

The functions or variables listed here are no longer part of vegan as they are no longer needed.

Usage

## defunct in vegan 2.7-0 (development 2.6-7)
adonis(formula, data, permutations = 999, method = "bray",
    strata = NULL, contr.unordered = "contr.sum",
    contr.ordered = "contr.poly", parallel = getOption("mc.cores"), ...)

## 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())

Details

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.

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.

Usage

Details

See also