Defunct Functions in Package vegan
The functions or variables listed here are no longer part of vegan as they are no longer needed.
## 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())
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).
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.
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