?check
was made to suppress package startup messages from vegan.shuffleSet()
wasn't returning a matrix if nset = 1
andallPerms
was invoked because of a low set of possible permutations. GitHub Issue #19shuffleSet()
are now printed in amore compact form.check()
allow for more reliable permutations(i.e. fewer duplicate permutations) when the set is small. This hasincreased the minperms
setting. Consequently we generate all possiblepermutations up to ~500,000 more often as we now randomly sample fromthe entirely generated set rather than randomly generate permutations.This provides a small performance hit in some rare cases.shuffleSet()
has a new argument quietly = FALSE
which is passedon to check()
.permControl()
and permuplot()
are defunct and have been removedfrom the package.how()
, a new function to create permutation designs. This replacesthe deprecated function permControl
.Plots()
instead of via the old strata
argument of how()
.Blocks are specified via a new argument blocks
, which takes afactor variable.how(). Extractor functions have names
getFoo(), where
Foo()is a component of the design. Replacement functions have names
setFoo`. The replacementfunction are especially for use by package authors wishing to alterpermutation within their functions. The extractor functions arerecommended for all users wishing to extract features of the permutationdesign.'how'
, 'Plots'
or 'Within'
to allowquick updating of features of the permutation design. This approach isintended for interactive use at the top-level and not within functions,where the new setFoo
replacement functions should be used.shuffleSet()
is enhanced in this version. Firstly, the function nowreturns a classed object which has a print()
method to allow forcompact printing of the design elements used to generate the set ofpermutations. Second, shuffleSet()
will sample nset
permutationsfrom the entire set of permutations should a small number of possiblepermutations trigger generation of the entire set. This avoids thegeneration of a set of non-unique permutations. Finally the random seedthat generated the set is stored as an attribute.allPerms()
no longer assumes that samples are in block and/or plotordering.permuplot()
is broken and effectively defunct given the changes tothe way permutation are defined and the addition of blocks.permuplot()
is no longer exported from the package namespace.