[med-svn] [permute] branch upstream updated (e4bba3b -> 6808f9c)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository permute.

      from  e4bba3b   Imported Upstream version 0.8-3
       new  6808f9c   Imported Upstream version 0.9-0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 DESCRIPTION                                   |  21 +-
 MD5                                           |  92 +++----
 NAMESPACE                                     |  37 +--
 R/Blocks.R                                    |   6 -
 R/allPerms.R                                  |  14 +-
 R/allStrata.R                                 |  10 +-
 R/as.matrix.allPerms.R                        |   6 +
 R/blocks.R                                    |  40 +++
 R/check.R                                     |  27 +-
 R/fixupCall.R                                 |  10 +-
 R/getFoo-methods.R                            | 129 +--------
 R/how.R                                       |   6 +-
 R/nobs-methods.R                              |   3 +
 R/numPerms.R                                  |  20 +-
 R/permCheck.R                                 |   5 -
 R/permuplot.R                                 | 198 --------------
 R/permute-deprecated.R                        |  43 ---
 R/permute.R                                   |  15 +-
 R/print.how.R                                 |   2 +-
 R/print.permutationMatrix.R                   |   5 +-
 R/setFoo-methods.R                            |  82 +-----
 R/shuffle-utils.R                             |   5 +-
 R/shuffle.R                                   | 146 ++++++----
 R/shuffle2.R                                  | 122 ---------
 R/shuffleSet.R                                | 216 +++++++++++----
 R/shuffleSet2.R                               | 205 --------------
 README.md                                     |  33 +++
 build/vignette.rds                            | Bin 230 -> 226 bytes
 data/jackal.rda                               | Bin 233 -> 233 bytes
 inst/ChangeLog                                |  58 +++-
 inst/NEWS                                     |  97 +++++++
 inst/NEWS.Rd                                  |  86 ------
 inst/doc/permutations.R                       |  10 +-
 inst/doc/permutations.Rnw                     |  12 +-
 inst/doc/permutations.pdf                     | Bin 315861 -> 312060 bytes
 inst/tests/test-allPerms.R                    | 127 ---------
 inst/tests/test-shuffleSet.R                  |  42 ---
 man/allPerms.Rd                               |  10 +
 man/check.Rd                                  | 112 ++++----
 man/how.Rd                                    |  10 +-
 man/permCheck-deprecated.Rd                   |  66 -----
 man/permControl-deprecated.Rd                 |  82 ------
 man/permute-deprecated.Rd                     |  25 --
 man/shuffleSet.Rd                             |  20 +-
 tests/Examples/permute-Ex.Rout.save           | 370 +++++++++++---------------
 tests/{test-all.R => testthat.R}              |   6 +-
 tests/testthat/test-allPerms.R                | 289 ++++++++++++++++++++
 tests/testthat/test-as-methods.R              |  18 ++
 tests/testthat/test-blocks.R                  |  11 +
 {inst/tests => tests/testthat}/test-check.R   |  15 +-
 tests/testthat/test-get-methods.R             |  22 ++
 tests/testthat/test-how.R                     |  14 +
 tests/testthat/test-nobs.R                    |  34 +++
 tests/testthat/test-numPerms.R                |  12 +
 tests/testthat/test-permute-fun.R             |  35 +++
 tests/testthat/test-set-methods.R             | 171 ++++++++++++
 tests/testthat/test-shuffle-utils.R           |  64 +++++
 {inst/tests => tests/testthat}/test-shuffle.R |  14 +-
 tests/testthat/test-shuffleSet.R              |  85 ++++++
 vignettes/Z.cls                               | 247 -----------------
 vignettes/permutations.Rnw                    |  12 +-
 61 files changed, 1711 insertions(+), 1963 deletions(-)
 delete mode 100644 R/Blocks.R
 create mode 100644 R/as.matrix.allPerms.R
 create mode 100644 R/blocks.R
 delete mode 100644 R/permCheck.R
 delete mode 100644 R/permuplot.R
 delete mode 100644 R/permute-deprecated.R
 delete mode 100644 R/shuffle2.R
 delete mode 100644 R/shuffleSet2.R
 create mode 100644 README.md
 create mode 100644 inst/NEWS
 delete mode 100644 inst/NEWS.Rd
 delete mode 100644 inst/tests/test-allPerms.R
 delete mode 100644 inst/tests/test-shuffleSet.R
 delete mode 100644 man/permCheck-deprecated.Rd
 delete mode 100644 man/permControl-deprecated.Rd
 delete mode 100644 man/permute-deprecated.Rd
 rename tests/{test-all.R => testthat.R} (59%)
 create mode 100644 tests/testthat/test-allPerms.R
 create mode 100644 tests/testthat/test-as-methods.R
 create mode 100644 tests/testthat/test-blocks.R
 rename {inst/tests => tests/testthat}/test-check.R (61%)
 create mode 100644 tests/testthat/test-get-methods.R
 create mode 100644 tests/testthat/test-how.R
 create mode 100644 tests/testthat/test-nobs.R
 create mode 100644 tests/testthat/test-numPerms.R
 create mode 100644 tests/testthat/test-permute-fun.R
 create mode 100644 tests/testthat/test-set-methods.R
 create mode 100644 tests/testthat/test-shuffle-utils.R
 rename {inst/tests => tests/testthat}/test-shuffle.R (76%)
 create mode 100644 tests/testthat/test-shuffleSet.R
 delete mode 100644 vignettes/Z.cls

-- 
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