The functions or variables listed here are no longer part of vegan as they are no longer needed.
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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())
commsimulator is replaced with
make.commsim which defines the Null models, and
simulate.nullmodel that check the input data and
generate the Null model communities.
densityplot methods are
replaced with similar methods for
permustats offers more powerful analysis tools for
z values (a.k.a. standardized effect sizes, SES), and Q-Q
metaMDSrotate is replaced with
MDSrotate which can handle
results in addition to
The permutation functions were moved to the permute package,
and they are documented there. The permute package replaces
getNumObs with its specific
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