vegan-defunct: Defunct Functions in Package 'vegan'

Description Usage Details See Also

Description

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

Usage

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## 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

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.index2 with shuffle and getNumObs with its specific nobs-methods.

See Also

Defunct, vegan-deprecated


vegan documentation built on May 17, 2018, 5:03 p.m.