TODO List

A TODO list for permute - or things I know are broken or needed.

summary.allPerms - is not printing the permutation scheme. Done in 0.7-5
print.permControl - this needs to be updated to new API, and I don't like the *** Foo *** headings I used before. Done in 0.7-3
Need a way to update the permutation scheme, e.g. when a control object already exists and want to tweak it. Example is in ?allPerms where I turn mirroring on via
```
 ctrl$within$mirror <- TRUE
```
But how? Best idea currently is an update.permControl method. The generic is in namespace stats. Or a modify() function, perhaps coupled with specific replacement functions for certain components.

DONE, in part, in 0.7-5 The matched call is now returned by how() and this allows update() to do its work with no further effort from me. What isn't so neat is that currently this means you need to type out in full any specification of within and plots as these take the results of function calls. Hence we have, from ./man/how.Rd
```
 plts <- gl(4,10)
 blks <- gl(2,20)
 h1 <- how(within = Within(type = "series", mirror = TRUE),
           plots = Plots(strata = plts, type = "series"),
           blocks = blks)

 ## The design can be updated...
 ## ... remove the blocking:
 update(h1, blocks = NULL)
 ## ... or switch the type of shuffling at a level:
 update(h1, plots = Plots(strata = plts, type = "none"))
```
Where in the second update() the entire Plots() call needs to repeated to change just one part, the type.

This has been tweaked a bit. The second example can now be done via:
```
 update(h1, plots = update(getPlots(h1), type = "none"))
```
Here getPlots(h1) returns the plots component, which too has a call component and hence can be update()ed, hence the nested calls to update().
permControl - deprecate this in favour of how as in "how to permute"? DONE Completed in 0.7-4
permuplot - this may be fundamentally bust - it only worked in the original API and never got updated. Now the API is 2 versions further on! It is also more complex than the original - not sure it'll be easy without a lot of work to visualise all possible schemes.
check insists on returning all permutations without the observed one.

DONE Completed somewhere, probably when I made observed only work via how()

The following example from shuffleSet() gives same number of permutations via numPerms() for both designs; should be fewer if same permutation within each plot.

 ## 10 random permutations in presence of Plot-level strata
 plotStrata <- Plots(strata = gl(4,5))
 CTRL <- how(plots = plotStrata,
             within = Within(type = "free"))
 shuffleSet(20, 10, control = CTRL)
 ## as above but same random permutation within Plot-level strata
 CTRL <- how(plots = plotStrata,
             within = Within(type = "free", constant = TRUE))
 shuffleSet(20, 10, CTRL)

DONE in 0.8-0

Write an Rd page for the "permutationMatrix" S3 class where I can describe the object returned by shuffleSet() and the methods available for it.

DONE in 0.7-8

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TODO List

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