Title: Unit Testing for R
Description: Software testing is important, but, in part because it is
frustrating and boring, many of us avoid it. 'testthat' is a testing
framework for R that is easy to learn and use, and integrates with
your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb] )
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between testthat versions 3.2.3 dated 2025-01-13 and 3.3.0 dated 2025-11-13
testthat-3.2.3/testthat/R/example.R |only testthat-3.2.3/testthat/R/expect-length.R |only testthat-3.2.3/testthat/R/expectations-matches.R |only testthat-3.2.3/testthat/man/auto_test_package.Rd |only testthat-3.2.3/testthat/src/reassign.c |only testthat-3.2.3/testthat/tests/testthat/_snaps/R4.0 |only testthat-3.2.3/testthat/tests/testthat/test-browser.R |only testthat-3.2.3/testthat/tests/testthat/test-catch.R |only testthat-3.2.3/testthat/tests/testthat/test-colour.R |only testthat-3.2.3/testthat/tests/testthat/test-expect-known-hash.R |only testthat-3.2.3/testthat/tests/testthat/test-expect-length.R |only testthat-3.2.3/testthat/tests/testthat/test-expect_that.R |only testthat-3.2.3/testthat/tests/testthat/test-label.R |only testthat-3.2.3/testthat/tests/testthat/test-source_dir.R |only testthat-3.3.0/testthat/DESCRIPTION | 28 testthat-3.3.0/testthat/MD5 | 644 +++++----- testthat-3.3.0/testthat/NAMESPACE | 25 testthat-3.3.0/testthat/NEWS.md | 69 + testthat-3.3.0/testthat/R/auto-test.R | 54 testthat-3.3.0/testthat/R/colour-text.R | 9 testthat-3.3.0/testthat/R/compare.R | 88 - testthat-3.3.0/testthat/R/deprec-condition.R | 38 testthat-3.3.0/testthat/R/describe.R | 36 testthat-3.3.0/testthat/R/edition.R | 13 testthat-3.3.0/testthat/R/evaluate-promise.R | 4 testthat-3.3.0/testthat/R/examples.R |only testthat-3.3.0/testthat/R/expect-all.R |only testthat-3.3.0/testthat/R/expect-comparison.R | 168 ++ testthat-3.3.0/testthat/R/expect-condition.R | 318 +++- testthat-3.3.0/testthat/R/expect-constant.R | 86 - testthat-3.3.0/testthat/R/expect-equality.R | 194 +-- testthat-3.3.0/testthat/R/expect-inheritance.R | 249 ++- testthat-3.3.0/testthat/R/expect-invisible.R | 26 testthat-3.3.0/testthat/R/expect-known.R | 181 +- testthat-3.3.0/testthat/R/expect-match.R |only testthat-3.3.0/testthat/R/expect-named.R | 66 - testthat-3.3.0/testthat/R/expect-no-condition.R | 105 - testthat-3.3.0/testthat/R/expect-output.R | 48 testthat-3.3.0/testthat/R/expect-reference.R |only testthat-3.3.0/testthat/R/expect-self-test.R | 171 +- testthat-3.3.0/testthat/R/expect-setequal.R | 221 ++- testthat-3.3.0/testthat/R/expect-shape.R |only testthat-3.3.0/testthat/R/expect-silent.R | 15 testthat-3.3.0/testthat/R/expect-that.R | 142 +- testthat-3.3.0/testthat/R/expect-vector.R | 24 testthat-3.3.0/testthat/R/expectation.R | 187 +- testthat-3.3.0/testthat/R/extract.R |only testthat-3.3.0/testthat/R/import-standalone-purrr.R |only testthat-3.3.0/testthat/R/local.R | 46 testthat-3.3.0/testthat/R/mock-oo.R |only testthat-3.3.0/testthat/R/mock.R | 121 - testthat-3.3.0/testthat/R/mock2-helpers.R |only testthat-3.3.0/testthat/R/mock2.R | 29 testthat-3.3.0/testthat/R/old-school.R | 131 +- testthat-3.3.0/testthat/R/parallel-config.R | 18 testthat-3.3.0/testthat/R/parallel-taskq.R | 185 ++ testthat-3.3.0/testthat/R/parallel.R | 220 ++- testthat-3.3.0/testthat/R/praise.R | 6 testthat-3.3.0/testthat/R/quasi-label.R | 63 testthat-3.3.0/testthat/R/reporter-check.R | 73 + testthat-3.3.0/testthat/R/reporter-debug.R | 14 testthat-3.3.0/testthat/R/reporter-fail.R | 7 testthat-3.3.0/testthat/R/reporter-junit.R | 74 - testthat-3.3.0/testthat/R/reporter-list.R | 134 +- testthat-3.3.0/testthat/R/reporter-location.R | 3 testthat-3.3.0/testthat/R/reporter-minimal.R | 5 testthat-3.3.0/testthat/R/reporter-multi.R | 22 testthat-3.3.0/testthat/R/reporter-progress.R | 162 +- testthat-3.3.0/testthat/R/reporter-rstudio.R | 5 testthat-3.3.0/testthat/R/reporter-silent.R | 16 testthat-3.3.0/testthat/R/reporter-slow.R |only testthat-3.3.0/testthat/R/reporter-stop.R | 67 - testthat-3.3.0/testthat/R/reporter-summary.R | 46 testthat-3.3.0/testthat/R/reporter-tap.R | 11 testthat-3.3.0/testthat/R/reporter-teamcity.R | 11 testthat-3.3.0/testthat/R/reporter-timing.R |only testthat-3.3.0/testthat/R/reporter-zzz.R | 33 testthat-3.3.0/testthat/R/reporter.R | 25 testthat-3.3.0/testthat/R/skip.R | 92 + testthat-3.3.0/testthat/R/snapshot-cleanup.R | 36 testthat-3.3.0/testthat/R/snapshot-file-snaps.R | 178 +- testthat-3.3.0/testthat/R/snapshot-file.R | 209 ++- testthat-3.3.0/testthat/R/snapshot-github.R |only testthat-3.3.0/testthat/R/snapshot-manage.R | 96 + testthat-3.3.0/testthat/R/snapshot-reporter-parallel.R | 7 testthat-3.3.0/testthat/R/snapshot-reporter.R | 138 +- testthat-3.3.0/testthat/R/snapshot-serialize.R | 12 testthat-3.3.0/testthat/R/snapshot-value.R | 119 - testthat-3.3.0/testthat/R/snapshot.R | 265 +++- testthat-3.3.0/testthat/R/source.R | 135 +- testthat-3.3.0/testthat/R/srcrefs.R | 14 testthat-3.3.0/testthat/R/stack.R | 6 testthat-3.3.0/testthat/R/teardown.R | 13 testthat-3.3.0/testthat/R/test-compiled-code.R | 144 +- testthat-3.3.0/testthat/R/test-example.R | 15 testthat-3.3.0/testthat/R/test-files.R | 236 ++- testthat-3.3.0/testthat/R/test-package.R | 15 testthat-3.3.0/testthat/R/test-state.R | 21 testthat-3.3.0/testthat/R/test-that.R | 176 +- testthat-3.3.0/testthat/R/testthat-package.R | 6 testthat-3.3.0/testthat/R/try-again.R | 72 - testthat-3.3.0/testthat/R/utils.R | 80 - testthat-3.3.0/testthat/R/verify-output.R | 29 testthat-3.3.0/testthat/R/watcher.R | 29 testthat-3.3.0/testthat/build/vignette.rds |binary testthat-3.3.0/testthat/inst/CITATION | 2 testthat-3.3.0/testthat/inst/doc/challenging-tests.R |only testthat-3.3.0/testthat/inst/doc/challenging-tests.Rmd |only testthat-3.3.0/testthat/inst/doc/challenging-tests.html |only testthat-3.3.0/testthat/inst/doc/custom-expectation.R | 207 ++- testthat-3.3.0/testthat/inst/doc/custom-expectation.Rmd | 304 ++++ testthat-3.3.0/testthat/inst/doc/custom-expectation.html | 449 +++++- testthat-3.3.0/testthat/inst/doc/mocking.R |only testthat-3.3.0/testthat/inst/doc/mocking.Rmd |only testthat-3.3.0/testthat/inst/doc/mocking.html |only testthat-3.3.0/testthat/inst/doc/parallel.Rmd | 8 testthat-3.3.0/testthat/inst/doc/parallel.html | 42 testthat-3.3.0/testthat/inst/doc/skipping.R | 18 testthat-3.3.0/testthat/inst/doc/skipping.Rmd | 63 testthat-3.3.0/testthat/inst/doc/skipping.html | 151 +- testthat-3.3.0/testthat/inst/doc/snapshotting.R | 98 + testthat-3.3.0/testthat/inst/doc/snapshotting.Rmd | 219 ++- testthat-3.3.0/testthat/inst/doc/snapshotting.html | 478 ++++--- testthat-3.3.0/testthat/inst/doc/special-files.html | 5 testthat-3.3.0/testthat/inst/doc/test-fixtures.R | 44 testthat-3.3.0/testthat/inst/doc/test-fixtures.Rmd | 127 + testthat-3.3.0/testthat/inst/doc/test-fixtures.html | 484 ++++--- testthat-3.3.0/testthat/inst/doc/third-edition.R | 10 testthat-3.3.0/testthat/inst/doc/third-edition.Rmd | 13 testthat-3.3.0/testthat/inst/doc/third-edition.html | 54 testthat-3.3.0/testthat/inst/include/testthat/vendor/catch.h | 13 testthat-3.3.0/testthat/man/CheckReporter.Rd | 3 testthat-3.3.0/testthat/man/DebugReporter.Rd | 3 testthat-3.3.0/testthat/man/FailReporter.Rd | 3 testthat-3.3.0/testthat/man/JunitReporter.Rd | 15 testthat-3.3.0/testthat/man/ListReporter.Rd | 4 testthat-3.3.0/testthat/man/LocationReporter.Rd | 1 testthat-3.3.0/testthat/man/MinimalReporter.Rd | 3 testthat-3.3.0/testthat/man/MultiReporter.Rd | 3 testthat-3.3.0/testthat/man/ProgressReporter.Rd | 3 testthat-3.3.0/testthat/man/RStudioReporter.Rd | 3 testthat-3.3.0/testthat/man/Reporter.Rd | 3 testthat-3.3.0/testthat/man/SilentReporter.Rd | 6 testthat-3.3.0/testthat/man/SlowReporter.Rd |only testthat-3.3.0/testthat/man/StopReporter.Rd | 12 testthat-3.3.0/testthat/man/SummaryReporter.Rd | 13 testthat-3.3.0/testthat/man/TapReporter.Rd | 3 testthat-3.3.0/testthat/man/TeamcityReporter.Rd | 3 testthat-3.3.0/testthat/man/auto_test.Rd | 23 testthat-3.3.0/testthat/man/comparison-expectations.Rd | 5 testthat-3.3.0/testthat/man/describe.Rd | 1 testthat-3.3.0/testthat/man/equality-expectations.Rd | 2 testthat-3.3.0/testthat/man/expect.Rd | 39 testthat-3.3.0/testthat/man/expect_all_equal.Rd |only testthat-3.3.0/testthat/man/expect_error.Rd | 2 testthat-3.3.0/testthat/man/expect_invisible.Rd | 2 testthat-3.3.0/testthat/man/expect_is.Rd | 10 testthat-3.3.0/testthat/man/expect_known_output.Rd | 2 testthat-3.3.0/testthat/man/expect_length.Rd | 30 testthat-3.3.0/testthat/man/expect_match.Rd | 24 testthat-3.3.0/testthat/man/expect_named.Rd | 2 testthat-3.3.0/testthat/man/expect_no_error.Rd | 2 testthat-3.3.0/testthat/man/expect_no_success.Rd |only testthat-3.3.0/testthat/man/expect_null.Rd | 2 testthat-3.3.0/testthat/man/expect_output.Rd | 2 testthat-3.3.0/testthat/man/expect_output_file.Rd | 2 testthat-3.3.0/testthat/man/expect_reference.Rd | 4 testthat-3.3.0/testthat/man/expect_setequal.Rd | 14 testthat-3.3.0/testthat/man/expect_silent.Rd | 2 testthat-3.3.0/testthat/man/expect_snapshot.Rd | 9 testthat-3.3.0/testthat/man/expect_snapshot_file.Rd | 50 testthat-3.3.0/testthat/man/expect_snapshot_output.Rd | 7 testthat-3.3.0/testthat/man/expect_snapshot_value.Rd | 9 testthat-3.3.0/testthat/man/expect_success.Rd | 20 testthat-3.3.0/testthat/man/expect_that.Rd | 2 testthat-3.3.0/testthat/man/expect_vector.Rd | 4 testthat-3.3.0/testthat/man/expectation.Rd | 25 testthat-3.3.0/testthat/man/extract_test.Rd |only testthat-3.3.0/testthat/man/fail.Rd | 53 testthat-3.3.0/testthat/man/figures/lifecycle-deprecated.svg | 22 testthat-3.3.0/testthat/man/figures/lifecycle-experimental.svg | 22 testthat-3.3.0/testthat/man/figures/lifecycle-stable.svg | 30 testthat-3.3.0/testthat/man/figures/lifecycle-superseded.svg | 22 testthat-3.3.0/testthat/man/inheritance-expectations.Rd | 43 testthat-3.3.0/testthat/man/local_mocked_bindings.Rd | 24 testthat-3.3.0/testthat/man/local_mocked_r6_class.Rd |only testthat-3.3.0/testthat/man/local_mocked_s3_method.Rd |only testthat-3.3.0/testthat/man/local_snapshotter.Rd | 8 testthat-3.3.0/testthat/man/local_test_context.Rd | 2 testthat-3.3.0/testthat/man/logical-expectations.Rd | 26 testthat-3.3.0/testthat/man/mock_output_sequence.Rd |only testthat-3.3.0/testthat/man/not.Rd | 2 testthat-3.3.0/testthat/man/oldskool.Rd | 12 testthat-3.3.0/testthat/man/quasi_label.Rd | 2 testthat-3.3.0/testthat/man/set_state_inspector.Rd | 17 testthat-3.3.0/testthat/man/skip.Rd | 21 testthat-3.3.0/testthat/man/snapshot_accept.Rd | 10 testthat-3.3.0/testthat/man/snapshot_download_gh.Rd |only testthat-3.3.0/testthat/man/source_file.Rd | 11 testthat-3.3.0/testthat/man/succeed.Rd |only testthat-3.3.0/testthat/man/test_dir.Rd | 9 testthat-3.3.0/testthat/man/test_file.Rd | 4 testthat-3.3.0/testthat/man/test_package.Rd | 11 testthat-3.3.0/testthat/man/testthat_examples.Rd | 2 testthat-3.3.0/testthat/man/topic-name.Rd |only testthat-3.3.0/testthat/man/try_again.Rd | 33 testthat-3.3.0/testthat/man/use_catch.Rd | 27 testthat-3.3.0/testthat/man/watch.Rd | 6 testthat-3.3.0/testthat/man/with_mock.Rd | 14 testthat-3.3.0/testthat/src/init.c | 4 testthat-3.3.0/testthat/tests/test-catch.R | 47 testthat-3.3.0/testthat/tests/testthat/_snaps/R4.5 |only testthat-3.3.0/testthat/tests/testthat/_snaps/R4.6 |only testthat-3.3.0/testthat/tests/testthat/_snaps/describe.md | 26 testthat-3.3.0/testthat/tests/testthat/_snaps/edition.md | 13 testthat-3.3.0/testthat/tests/testthat/_snaps/examples.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expect-all.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expect-comparison.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expect-condition.md | 149 ++ testthat-3.3.0/testthat/tests/testthat/_snaps/expect-constant.md | 50 testthat-3.3.0/testthat/tests/testthat/_snaps/expect-equality.md | 131 +- testthat-3.3.0/testthat/tests/testthat/_snaps/expect-inheritance.md | 170 ++ testthat-3.3.0/testthat/tests/testthat/_snaps/expect-invisible.md | 32 testthat-3.3.0/testthat/tests/testthat/_snaps/expect-match.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expect-named.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expect-no-condition.md | 88 - testthat-3.3.0/testthat/tests/testthat/_snaps/expect-output.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expect-reference.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expect-self-test.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expect-setequal.md | 273 +++- testthat-3.3.0/testthat/tests/testthat/_snaps/expect-shape.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expect-silent.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expect-vector.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/expectation.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/extract.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/mock-oo.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/mock.md | 13 testthat-3.3.0/testthat/tests/testthat/_snaps/mock2-helpers.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/parallel.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/quasi-label.md | 21 testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-check.md | 72 - testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-debug.md | 10 testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-junit.md | 27 testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-list.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-location.md | 12 testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-progress.md | 327 ++--- testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-rstudio.md | 12 testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-slow.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-stop.md | 86 - testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-summary.md | 56 testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-tap.md | 10 testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-teamcity.md | 4 testthat-3.3.0/testthat/tests/testthat/_snaps/reporter-zzz.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/skip.md | 34 testthat-3.3.0/testthat/tests/testthat/_snaps/snapshot-cleanup.md | 4 testthat-3.3.0/testthat/tests/testthat/_snaps/snapshot-file.md | 58 testthat-3.3.0/testthat/tests/testthat/_snaps/snapshot-file/foo-not-binary.csv |only testthat-3.3.0/testthat/tests/testthat/_snaps/snapshot-file/foo.csv | 39 testthat-3.3.0/testthat/tests/testthat/_snaps/snapshot-manage.md | 45 testthat-3.3.0/testthat/tests/testthat/_snaps/snapshot-reporter.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/snapshot-value.md | 22 testthat-3.3.0/testthat/tests/testthat/_snaps/snapshot.md | 79 + testthat-3.3.0/testthat/tests/testthat/_snaps/source.md | 35 testthat-3.3.0/testthat/tests/testthat/_snaps/test-compiled-code.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/test-files.md | 40 testthat-3.3.0/testthat/tests/testthat/_snaps/try-again.md |only testthat-3.3.0/testthat/tests/testthat/_snaps/verify-output.md |only testthat-3.3.0/testthat/tests/testthat/extract |only testthat-3.3.0/testthat/tests/testthat/reporters/backtraces.R | 10 testthat-3.3.0/testthat/tests/testthat/reporters/fail.R | 2 testthat-3.3.0/testthat/tests/testthat/reporters/nested.R |only testthat-3.3.0/testthat/tests/testthat/reporters/tests.R | 8 testthat-3.3.0/testthat/tests/testthat/test-colour-text.R |only testthat-3.3.0/testthat/tests/testthat/test-compare.R | 27 testthat-3.3.0/testthat/tests/testthat/test-context.R | 8 testthat-3.3.0/testthat/tests/testthat/test-describe.R | 82 + testthat-3.3.0/testthat/tests/testthat/test-edition.R | 14 testthat-3.3.0/testthat/tests/testthat/test-examples.R | 4 testthat-3.3.0/testthat/tests/testthat/test-expect-all.R |only testthat-3.3.0/testthat/tests/testthat/test-expect-comparison.R | 78 + testthat-3.3.0/testthat/tests/testthat/test-expect-condition.R | 99 + testthat-3.3.0/testthat/tests/testthat/test-expect-constant.R | 30 testthat-3.3.0/testthat/tests/testthat/test-expect-equality.R | 73 - testthat-3.3.0/testthat/tests/testthat/test-expect-inheritance.R | 92 + testthat-3.3.0/testthat/tests/testthat/test-expect-invisible.R | 6 testthat-3.3.0/testthat/tests/testthat/test-expect-known.R | 42 testthat-3.3.0/testthat/tests/testthat/test-expect-match.R | 102 + testthat-3.3.0/testthat/tests/testthat/test-expect-named.R | 51 testthat-3.3.0/testthat/tests/testthat/test-expect-no-condition.R | 28 testthat-3.3.0/testthat/tests/testthat/test-expect-output.R | 28 testthat-3.3.0/testthat/tests/testthat/test-expect-reference.R | 2 testthat-3.3.0/testthat/tests/testthat/test-expect-self-test.R | 137 +- testthat-3.3.0/testthat/tests/testthat/test-expect-setequal.R | 113 + testthat-3.3.0/testthat/tests/testthat/test-expect-shape.R |only testthat-3.3.0/testthat/tests/testthat/test-expect-silent.R | 9 testthat-3.3.0/testthat/tests/testthat/test-expect-vector.R | 13 testthat-3.3.0/testthat/tests/testthat/test-expectation.R | 31 testthat-3.3.0/testthat/tests/testthat/test-extract.R |only testthat-3.3.0/testthat/tests/testthat/test-local.R | 8 testthat-3.3.0/testthat/tests/testthat/test-make-expectation.R | 1 testthat-3.3.0/testthat/tests/testthat/test-mock-oo.R |only testthat-3.3.0/testthat/tests/testthat/test-mock.R | 8 testthat-3.3.0/testthat/tests/testthat/test-mock2-helpers.R |only testthat-3.3.0/testthat/tests/testthat/test-old-school.R | 31 testthat-3.3.0/testthat/tests/testthat/test-parallel-crash.R | 19 testthat-3.3.0/testthat/tests/testthat/test-parallel-errors.R |only testthat-3.3.0/testthat/tests/testthat/test-parallel-outside.R | 2 testthat-3.3.0/testthat/tests/testthat/test-parallel-setup.R | 3 testthat-3.3.0/testthat/tests/testthat/test-parallel-startup.R | 3 testthat-3.3.0/testthat/tests/testthat/test-parallel-stdout.R |only testthat-3.3.0/testthat/tests/testthat/test-parallel-teardown.R | 15 testthat-3.3.0/testthat/tests/testthat/test-parallel.R | 118 + testthat-3.3.0/testthat/tests/testthat/test-parallel/fail/tests/testthat/test-bad.R | 1 testthat-3.3.0/testthat/tests/testthat/test-parallel/outside/tests/testthat/test-outside-2.R | 1 testthat-3.3.0/testthat/tests/testthat/test-parallel/setup/tests/testthat/setup-bad.R | 1 testthat-3.3.0/testthat/tests/testthat/test-parallel/snap/tests/testthat/test-snap-1.R | 1 testthat-3.3.0/testthat/tests/testthat/test-parallel/snap/tests/testthat/test-snap-2.R | 1 testthat-3.3.0/testthat/tests/testthat/test-parallel/snap/tests/testthat/test-snap-3.R | 1 testthat-3.3.0/testthat/tests/testthat/test-parallel/startup/R/fail.R | 3 testthat-3.3.0/testthat/tests/testthat/test-parallel/stdout |only testthat-3.3.0/testthat/tests/testthat/test-parallel/syntax-error |only testthat-3.3.0/testthat/tests/testthat/test-parallel/teardown/tests/testthat/teardown-bad.R | 1 testthat-3.3.0/testthat/tests/testthat/test-quasi-label.R | 50 testthat-3.3.0/testthat/tests/testthat/test-reporter-check.R | 30 testthat-3.3.0/testthat/tests/testthat/test-reporter-debug.R | 10 testthat-3.3.0/testthat/tests/testthat/test-reporter-junit.R | 35 testthat-3.3.0/testthat/tests/testthat/test-reporter-list.R | 51 testthat-3.3.0/testthat/tests/testthat/test-reporter-progress.R | 11 testthat-3.3.0/testthat/tests/testthat/test-reporter-slow.R |only testthat-3.3.0/testthat/tests/testthat/test-reporter-stop.R | 30 testthat-3.3.0/testthat/tests/testthat/test-reporter-summary.R | 15 testthat-3.3.0/testthat/tests/testthat/test-reporter-zzz.R | 9 testthat-3.3.0/testthat/tests/testthat/test-skip.R | 95 + testthat-3.3.0/testthat/tests/testthat/test-snapshot-file.R | 133 +- testthat-3.3.0/testthat/tests/testthat/test-snapshot-manage.R | 73 + testthat-3.3.0/testthat/tests/testthat/test-snapshot-reporter.R | 72 - testthat-3.3.0/testthat/tests/testthat/test-snapshot-serialize.R | 23 testthat-3.3.0/testthat/tests/testthat/test-snapshot-value.R | 18 testthat-3.3.0/testthat/tests/testthat/test-snapshot.R | 83 + testthat-3.3.0/testthat/tests/testthat/test-source.R | 183 ++ testthat-3.3.0/testthat/tests/testthat/test-srcrefs.R | 1 testthat-3.3.0/testthat/tests/testthat/test-teardown.R | 4 testthat-3.3.0/testthat/tests/testthat/test-test-compiled-code.R |only testthat-3.3.0/testthat/tests/testthat/test-test-env.R | 2 testthat-3.3.0/testthat/tests/testthat/test-test-example.R | 7 testthat-3.3.0/testthat/tests/testthat/test-test-files.R | 22 testthat-3.3.0/testthat/tests/testthat/test-test-path.R | 2 testthat-3.3.0/testthat/tests/testthat/test-test-state.R | 5 testthat-3.3.0/testthat/tests/testthat/test-test-that.R | 111 + testthat-3.3.0/testthat/tests/testthat/test-try-again.R | 20 testthat-3.3.0/testthat/tests/testthat/test-verify-output.R | 18 testthat-3.3.0/testthat/vignettes/challenging-tests.Rmd |only testthat-3.3.0/testthat/vignettes/custom-expectation.Rmd | 304 ++++ testthat-3.3.0/testthat/vignettes/mocking.Rmd |only testthat-3.3.0/testthat/vignettes/parallel.Rmd | 8 testthat-3.3.0/testthat/vignettes/skipping.Rmd | 63 testthat-3.3.0/testthat/vignettes/snapshotting.Rmd | 219 ++- testthat-3.3.0/testthat/vignettes/test-fixtures.Rmd | 127 + testthat-3.3.0/testthat/vignettes/third-edition.Rmd | 13 359 files changed, 10573 insertions(+), 5048 deletions(-)
Title: Enrich Figures and Tables with Custom Headers and Footers and
More
Description: A simple and flexible tool designed to create enriched figures and tables by providing a way to add text
around them through predefined or custom layouts.
Any input which is convertible to 'grob' is supported, like 'ggplot', 'gt' or 'flextable'.
Based on R 'grid' graphics, for more details see Paul Murrell (2018) <doi:10.1201/9780429422768>.
Author: Maciej Nasinski [aut, cre],
Alexandra Wall [aut],
Sarah Robson [aut],
Pritish Dash [aut],
Jennifer Winick-Ng [aut],
Lily Nan [ctb],
Alphonse Kwizera [ctb],
Agota Bodoni [ctb],
Eilis Meldrum-Dolan [ctb],
Gary Cao [ctb],
UCB S.A., Belgium [cph, fnd]
Maintainer: Maciej Nasinski <Maciej.Nasinski@ucb.com>
Diff between gridify versions 0.7.4 dated 2025-08-28 and 0.7.5 dated 2025-11-13
DESCRIPTION | 10 - MD5 | 34 ++-- NAMESPACE | 1 NEWS.md | 6 R/pagination_utils.R |only README.md | 23 ++ inst/WORDLIST | 1 inst/doc/create_custom_layout.html | 5 inst/doc/gridify.Rmd | 9 - inst/doc/gridify.html | 18 +- inst/doc/multi_page_examples.R | 42 +--- inst/doc/multi_page_examples.Rmd | 67 ++----- inst/doc/multi_page_examples.html | 296 ++++++++++++++++------------------- inst/doc/simple_examples.html | 7 inst/doc/transparency.html | 7 man/paginate_table.Rd |only tests/testthat/test_paginate_table.R |only vignettes/gridify.Rmd | 9 - vignettes/multi_page_examples.Rmd | 67 ++----- vignettes/tables |only 20 files changed, 282 insertions(+), 320 deletions(-)
Title: Interface to the Global Biodiversity Information Facility API
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility (GBIF;
<https://www.gbif.org/developer/summary>). GBIF is a database
of species occurrence records from sources all over the globe.
rgbif includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the GBIF
tile map service to make rasters summarizing huge amounts of data.
Author: Scott Chamberlain [aut] ,
Damiano Oldoni [aut] ,
Vijay Barve [ctb] ,
Peter Desmet [ctb] ,
Laurens Geffert [ctb],
Dan Mcglinn [ctb] ,
Karthik Ram [ctb] ,
rOpenSci [fnd] ,
John Waller [aut, cre]
Maintainer: John Waller <jwaller@gbif.org>
Diff between rgbif versions 3.8.3 dated 2025-09-04 and 3.8.4 dated 2025-11-13
DESCRIPTION | 6 MD5 | 226 NEWS.md | 13 R/name_backbone.r | 351 R/name_backbone_checklist.R | 313 R/occ_download_sql.R | 5 R/occ_search.r | 18 R/print_gbif.R | 5 R/zzz.r | 59 man/name_backbone.Rd | 173 man/name_backbone_checklist.Rd | 157 man/occ_download_sql.Rd | 7 man/occ_search.Rd | 5 tests/fixtures/collection_search.yml | 76 tests/fixtures/dataset.yml | 1603 tests/fixtures/dataset_doi.yml | 4 tests/fixtures/dataset_list_funs.yml | 9 tests/fixtures/dataset_search.yml | 7068 - tests/fixtures/dataset_search_facet.yml | 56 tests/fixtures/dataset_suggest.yml | 5231 tests/fixtures/dataset_suggest_description.yml | 2328 tests/fixtures/dataset_uuid_funs.yml |83175 ++++++------ tests/fixtures/installation_search.yml | 81 tests/fixtures/installation_uuid_funs.yml | 16 tests/fixtures/installations.yml | 1714 tests/fixtures/installations_deleted.yml | 39 tests/fixtures/installations_uuid.yml | 2 tests/fixtures/installations_uuid_data.yml | 2 tests/fixtures/institution_search.yml | 130 tests/fixtures/name_backbone.yml | 474 tests/fixtures/name_backbone_verbose_true.yml | 479 tests/fixtures/name_issues.yml | 106 tests/fixtures/name_lookup_constituentKey.yml | 1860 tests/fixtures/name_lookup_habitat.yml | 7952 - tests/fixtures/name_lookup_no_results.yml | 2 tests/fixtures/name_suggest.yml | 738 tests/fixtures/name_suggest_many_args.yml | 12 tests/fixtures/name_usage.yml | 4 tests/fixtures/name_usage_data_children.yml | 4 tests/fixtures/name_usage_data_descriptions.yml | 196 tests/fixtures/name_usage_data_distributions.yml | 468 tests/fixtures/name_usage_data_iucnRedListCategory.yml | 4 tests/fixtures/name_usage_data_media.yml | 4 tests/fixtures/name_usage_data_name.yml | 4 tests/fixtures/name_usage_data_parents.yml | 4 tests/fixtures/name_usage_data_references.yml | 4 tests/fixtures/name_usage_data_related.yml | 908 tests/fixtures/name_usage_data_speciesProfiles.yml | 6 tests/fixtures/name_usage_data_synonyms.yml | 4 tests/fixtures/name_usage_data_typeSpecimens.yml | 4 tests/fixtures/name_usage_data_vernacularNames.yml | 139 tests/fixtures/name_usage_fails_well.yml | 4 tests/fixtures/occ_count.yml | 70 tests/fixtures/occ_count_.yml | 30 tests/fixtures/occ_count_facet.yml | 106 tests/fixtures/occ_count_legacy_params.yml | 48 tests/fixtures/occ_data_args_with_many_inputs.yml | 1282 tests/fixtures/occ_data_catalog_number.yml | 424 tests/fixtures/occ_data_coordinateUncertaintyInMeters.yml | 629 tests/fixtures/occ_data_degreeOfEstablishment.yml | 806 tests/fixtures/occ_data_depth.yml | 70 tests/fixtures/occ_data_distanceFromCentroidInMeters.yml | 591 tests/fixtures/occ_data_dropped_fields.yml | 283 tests/fixtures/occ_data_elevation.yml | 195 tests/fixtures/occ_data_eventId.yml | 1060 tests/fixtures/occ_data_fails_well.yml | 12 tests/fixtures/occ_data_gadmGid.yml | 527 tests/fixtures/occ_data_identifiedBy.yml | 978 tests/fixtures/occ_data_isInCluster.yml | 597 tests/fixtures/occ_data_iucnRedListCategory.yml | 1010 tests/fixtures/occ_data_key_gbifid_character_class.yml | 236 tests/fixtures/occ_data_lifeStage.yml | 878 tests/fixtures/occ_data_networkKey.yml | 1002 tests/fixtures/occ_data_occurrenceId.yml | 909 tests/fixtures/occ_data_occurrencestatus.yml | 613 tests/fixtures/occ_data_organismQuantity.yml | 634 tests/fixtures/occ_data_organismQuantityType.yml | 302 tests/fixtures/occ_data_relativeOrganismQuantity.yml | 597 tests/fixtures/occ_data_scientificname.yml | 964 tests/fixtures/occ_data_speciesKey.yml | 979 tests/fixtures/occ_data_verbatimScientificName.yml | 957 tests/fixtures/occ_download_sql_1.yml | 16 tests/fixtures/occ_search_catalognumber.yml | 6 tests/fixtures/occ_search_coordinateUncertaintyInMeters.yml | 628 tests/fixtures/occ_search_degreeOfEstablishment.yml | 806 tests/fixtures/occ_search_depth.yml | 93 tests/fixtures/occ_search_distanceFromCentroidInMeters.yml | 597 tests/fixtures/occ_search_elevation.yml | 396 tests/fixtures/occ_search_eventId.yml | 1061 tests/fixtures/occ_search_fails_well.yml | 12 tests/fixtures/occ_search_gadmGid.yml | 527 tests/fixtures/occ_search_geoDistance.yml | 169 tests/fixtures/occ_search_hierarchy_data.yml | 190 tests/fixtures/occ_search_identifiedBy.yml | 988 tests/fixtures/occ_search_isInCluster.yml | 585 tests/fixtures/occ_search_iucnRedListCategory.yml | 1019 tests/fixtures/occ_search_key_gbifid_character_class.yml | 238 tests/fixtures/occ_search_lifeStage.yml | 876 tests/fixtures/occ_search_many_inputs.yml | 1285 tests/fixtures/occ_search_networkKey.yml | 1006 tests/fixtures/occ_search_occurrenceId.yml | 891 tests/fixtures/occ_search_occurrencestatus.yml | 619 tests/fixtures/occ_search_organismQuantity.yml | 634 tests/fixtures/occ_search_organismQuantityType.yml | 304 tests/fixtures/occ_search_relativeOrganismQuantity.yml | 555 tests/fixtures/occ_search_scientificname.yml | 972 tests/fixtures/occ_search_speciesKey.yml | 971 tests/fixtures/occ_search_verbatimScientificName.yml | 960 tests/fixtures/organizations_search_country.yml | 2 tests/fixtures/organizations_search_uuid.yml | 4196 tests/testthat/test-dataset_gridded.R | 21 tests/testthat/test-name_backbone.r | 99 tests/testthat/test-name_backbone_checklist.R | 251 tests/testthat/test-occ_search.r | 6 114 files changed, 78182 insertions(+), 75838 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-30 1.4
2022-01-10 1.3
Title: Smooth Survival Models, Including Generalized Survival Models
Description: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth <doi:10.1177/0962280216664760>. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects <doi:10.1002/sim.7451>, and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0 [...truncated...]
Author: Mark Clements [aut, cre],
Xing-Rong Liu [aut],
Benjamin Christoffersen [aut],
Paul Lambert [ctb],
Lasse Hjort Jakobsen [ctb],
Alessandro Gasparini [ctb],
Gordon Smyth [cph],
Patrick Alken [cph],
Simon Wood [cph],
Rhys Ulerich [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between rstpm2 versions 1.7.0 dated 2025-08-27 and 1.7.1 dated 2025-11-13
DESCRIPTION | 10 +++--- MD5 | 18 +++++------ R/multistate.R | 20 ++++++------ R/pm2-3.R | 15 +++++---- inst/doc/Introduction.pdf |binary inst/doc/SimpleGuide.pdf |binary inst/doc/multistate.pdf |binary inst/doc/predictnl.pdf |binary inst/working_code.R | 71 +++++++++++++++++++++++++++++++++++++++++++++ tests/testthat/test_base.R | 15 +++------ 10 files changed, 111 insertions(+), 38 deletions(-)
Title: Interactive Tutorials for R
Description: Create interactive tutorials using R Markdown. Use a
combination of narrative, figures, videos, exercises, and quizzes to
create self-paced tutorials for learning about R and R packages.
Author: Garrick Aden-Buie [aut, cre] ,
Barret Schloerke [aut] ,
JJ Allaire [aut, ccp],
Alexander Rossell Hayes [aut] ,
Nischal Shrestha [ctb] ,
Angela Li [ctb] ,
Posit, PBC [cph, fnd],
Ajax.org B.V. [ctb, cph] ,
Zeno Rocha [ctb, cph] ,
Nick Payne [ctb, cph] [...truncated...]
Maintainer: Garrick Aden-Buie <garrick@posit.co>
Diff between learnr versions 0.11.5 dated 2023-09-28 and 0.11.6 dated 2025-11-13
learnr-0.11.5/learnr/tests/testthat/tutorials/hint-copy/hint-copy.html |only learnr-0.11.5/learnr/tests/testthat/tutorials/hint-div/hint-div.html |only learnr-0.11.5/learnr/tests/testthat/tutorials/hint-next/hint-next.html |only learnr-0.11.6/learnr/DESCRIPTION | 28 learnr-0.11.6/learnr/MD5 | 169 +-- learnr-0.11.6/learnr/NAMESPACE | 7 learnr-0.11.6/learnr/NEWS.md | 10 learnr-0.11.6/learnr/R/ace.R | 47 learnr-0.11.6/learnr/R/auto-complete.R | 57 - learnr-0.11.6/learnr/R/available_tutorials.R | 68 - learnr-0.11.6/learnr/R/debug_exercise_checker.R | 39 learnr-0.11.6/learnr/R/evaluators.R | 327 ++++-- learnr-0.11.6/learnr/R/events.R | 18 learnr-0.11.6/learnr/R/events_default.R | 59 - learnr-0.11.6/learnr/R/events_record.R | 18 learnr-0.11.6/learnr/R/exercise.R | 510 ++++++---- learnr-0.11.6/learnr/R/feedback.R | 40 learnr-0.11.6/learnr/R/html-dependencies.R | 4 learnr-0.11.6/learnr/R/html_selector.R | 33 learnr-0.11.6/learnr/R/http-handlers.R | 245 ++-- learnr-0.11.6/learnr/R/i18n.R | 30 learnr-0.11.6/learnr/R/identifiers.R | 40 learnr-0.11.6/learnr/R/initialize.R | 27 learnr-0.11.6/learnr/R/knitr-hooks.R | 263 +++-- learnr-0.11.6/learnr/R/learnr_messages.R | 7 learnr-0.11.6/learnr/R/mock_exercise.R | 45 learnr-0.11.6/learnr/R/mutate_tags.R | 39 learnr-0.11.6/learnr/R/options.R | 28 learnr-0.11.6/learnr/R/praise.R | 28 learnr-0.11.6/learnr/R/question_answers.R | 26 learnr-0.11.6/learnr/R/question_checkbox.R | 11 learnr-0.11.6/learnr/R/question_methods.R | 8 learnr-0.11.6/learnr/R/question_numeric.R | 33 learnr-0.11.6/learnr/R/question_radio.R | 15 learnr-0.11.6/learnr/R/question_text.R | 30 learnr-0.11.6/learnr/R/quiz.R | 173 ++- learnr-0.11.6/learnr/R/quiz_print.R | 85 + learnr-0.11.6/learnr/R/run.R | 203 ++- learnr-0.11.6/learnr/R/storage.R | 298 +++-- learnr-0.11.6/learnr/R/tutorial-format.R | 88 + learnr-0.11.6/learnr/R/tutorial-state.R | 55 - learnr-0.11.6/learnr/R/tutorial_package_dependencies.R | 24 learnr-0.11.6/learnr/R/utils.R | 22 learnr-0.11.6/learnr/R/zzz.R | 2 learnr-0.11.6/learnr/build/vignette.rds |binary learnr-0.11.6/learnr/inst/doc/multilang.R | 49 learnr-0.11.6/learnr/inst/doc/multilang.Rmd | 7 learnr-0.11.6/learnr/inst/doc/multilang.html | 20 learnr-0.11.6/learnr/inst/doc/shinyapps-publishing.html | 8 learnr-0.11.6/learnr/inst/examples/apparmor/apparmor_evaluator.R | 16 learnr-0.11.6/learnr/inst/internals/i18n_random_phrases.rds |binary learnr-0.11.6/learnr/inst/internals/i18n_translations.rds |binary learnr-0.11.6/learnr/inst/staticexports/knitr_engine_caption.R | 1 learnr-0.11.6/learnr/inst/staticexports/strings.R | 1 learnr-0.11.6/learnr/man/mock_exercise.Rd | 2 learnr-0.11.6/learnr/man/rmd-fragments/badges.Rmd | 6 learnr-0.11.6/learnr/man/tutorial.Rd | 4 learnr-0.11.6/learnr/tests/testthat.R | 1 learnr-0.11.6/learnr/tests/testthat/helpers-shinytest2.R | 89 + learnr-0.11.6/learnr/tests/testthat/helpers.R | 14 learnr-0.11.6/learnr/tests/testthat/test-auto-complete.R | 47 learnr-0.11.6/learnr/tests/testthat/test-available-tutorials.R | 5 learnr-0.11.6/learnr/tests/testthat/test-cookies.R | 11 learnr-0.11.6/learnr/tests/testthat/test-dependency.R | 1 learnr-0.11.6/learnr/tests/testthat/test-duplicate_env.R | 2 learnr-0.11.6/learnr/tests/testthat/test-evaluators.R | 237 ++-- learnr-0.11.6/learnr/tests/testthat/test-events.R | 19 learnr-0.11.6/learnr/tests/testthat/test-exercise.R | 275 +++-- learnr-0.11.6/learnr/tests/testthat/test-feedback.R | 14 learnr-0.11.6/learnr/tests/testthat/test-i18n.R | 22 learnr-0.11.6/learnr/tests/testthat/test-install-dependencies.R | 22 learnr-0.11.6/learnr/tests/testthat/test-knitr-hooks.R | 72 + learnr-0.11.6/learnr/tests/testthat/test-mock_exercise.R | 20 learnr-0.11.6/learnr/tests/testthat/test-mutate_tags.R | 12 learnr-0.11.6/learnr/tests/testthat/test-options-reveal_solution.R | 29 learnr-0.11.6/learnr/tests/testthat/test-options.R | 2 learnr-0.11.6/learnr/tests/testthat/test-praise.R | 20 learnr-0.11.6/learnr/tests/testthat/test-question_answers.R | 88 + learnr-0.11.6/learnr/tests/testthat/test-question_checkbox.R | 3 learnr-0.11.6/learnr/tests/testthat/test-question_radio.R | 8 learnr-0.11.6/learnr/tests/testthat/test-question_text.R | 17 learnr-0.11.6/learnr/tests/testthat/test-quiz.R | 26 learnr-0.11.6/learnr/tests/testthat/test-run.R | 26 learnr-0.11.6/learnr/tests/testthat/test-shinytest2-hints.R | 406 +++---- learnr-0.11.6/learnr/tests/testthat/test-storage.R | 18 learnr-0.11.6/learnr/tests/testthat/test-tutorial-state.R | 38 learnr-0.11.6/learnr/vignettes/multilang.Rmd | 7 87 files changed, 3139 insertions(+), 1785 deletions(-)
Title: Analyse Audio Recordings and Automatically Extract Animal
Vocalizations
Description: Contains all the necessary tools to process audio recordings of
various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files,
display audio signals, detect and extract automatically acoustic
features for further analysis such as classification.
Author: Jean Marchal [aut, cre],
Francois Fabianek [aut],
Christopher Scott [aut],
Chris Corben [ctb, cph] ,
David Riggs [ctb, cph] ,
Peter Wilson [ctb, cph] ,
Wildlife Acoustics, inc. [ctb, cph] ,
Jordan Biserkov [ctb],
WavX, inc. [cph]
Maintainer: Jean Marchal <jean.marchal@wavx.ca>
Diff between bioacoustics versions 0.2.8 dated 2022-02-08 and 0.2.10 dated 2025-11-13
DESCRIPTION | 10 MD5 | 52 NEWS.md | 20 R/bioacoustics.R | 48 R/metadata.R | 4 R/print.R | 26 R/read_audio.R | 6 R/read_zc.R | 1050 ++++++------- R/spectro.R | 414 ++--- R/tools.R | 288 +-- README.md | 46 build/vignette.rds |binary configure | 3501 +++++++++++++++++++++++---------------------- configure.ac | 254 +-- inst/doc/introduction.R | 12 inst/doc/introduction.Rmd | 16 inst/doc/introduction.html | 537 ++---- inst/doc/tutorial.R | 654 ++++---- inst/doc/tutorial.Rmd | 19 inst/doc/tutorial.html | 543 ++---- man/read_audio.Rd | 6 src/Makevars.in | 1 src/Makevars.ucrt | 3 src/Makevars.win | 2 tools/winlibs.R | 68 vignettes/introduction.Rmd | 16 vignettes/tutorial.Rmd | 19 27 files changed, 3756 insertions(+), 3859 deletions(-)
Title: Integrated Interface of Bayesian Single Index Models using
'nimble'
Description: Provides tools for fitting Bayesian single index models with flexible choices of priors for both the index and the link function. The package implements model estimation and posterior inference using efficient MCMC algorithms built on the 'nimble' framework, allowing users to specify, extend, and simulate models in a unified and reproducible manner. The following methods are implemented in the package: Antoniadis et al. (2004) <https://www.jstor.org/stable/24307224>, Wang (2009) <doi:10.1016/j.csda.2008.12.010>, Choi et al. (2011) <doi:10.1080/10485251003768019>, Dhara et al. (2019) <doi:10.1214/19-BA1170>, McGee et al. (2023) <doi:10.1111/biom.13569>.
Author: Seowoo Jung [aut, cre],
Eun-kyung Lee [aut]
Maintainer: Seowoo Jung <jsw1347@ewha.ac.kr>
Diff between BayesSIM versions 0.1.4 dated 2025-10-30 and 0.1.5 dated 2025-11-13
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: German Election Database (GERDA)
Description: Provides tools to download comprehensive datasets of local,
state, and federal election results in Germany from 1990 to 2025. The package
facilitates access to data on turnout, vote shares for major parties, and
demographic information across different levels of government (municipal, state,
and federal). It offers access to geographically harmonized datasets
that account for changes in municipal boundaries over time and incorporate
mail-in voting districts. Users can easily retrieve, clean, and standardize
German electoral data, making it ready for analysis. Data is sourced from
<https://github.com/awiedem/german_election_data>.
Author: Hanno Hilbig [aut, cre]
Maintainer: Hanno Hilbig <hhilbig@ucdavis.edu>
Diff between gerda versions 0.3.0 dated 2025-10-29 and 0.4.0 dated 2025-11-12
DESCRIPTION | 6 +-- MD5 | 20 ++++++------ NEWS.md | 10 ++++++ R/gerda_data_list.R | 24 +++++++-------- R/load_gerda_web.R | 54 ++++++++++++++++++++++++++++------- README.md | 4 +- inst/doc/gerda.R | 2 - inst/doc/gerda.Rmd | 2 - inst/doc/gerda.html | 2 - tests/testthat/test-load_gerda_web.R | 49 +++++++++++++++++++++++++++++++ vignettes/gerda.Rmd | 2 - 11 files changed, 133 insertions(+), 42 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.8 dated 2025-11-06 and 0.1.9 dated 2025-11-12
DESCRIPTION | 8 MD5 | 15 R/helper.R | 896 +++++++++++++++---------------- R/xtdml_data.R | 130 ++-- R/xtdml_main.R | 13 R/xtdml_plr.R | 1081 +++++++++++++++++++------------------- README.md |only man/xtdml_data_from_data_frame.Rd | 2 man/xtdml_plr.Rd | 86 +-- 9 files changed, 1120 insertions(+), 1111 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb],
Zoe Clarke [ctb]
Maintainer: Samuel Marsh <sccustomize@gmail.com>
Diff between scCustomize versions 3.2.1 dated 2025-11-08 and 3.2.2 dated 2025-11-12
scCustomize-3.2.1/scCustomize/R/Read_&_Write_Data.R |only scCustomize-3.2.2/scCustomize/DESCRIPTION | 8 - scCustomize-3.2.2/scCustomize/MD5 | 50 +++++----- scCustomize-3.2.2/scCustomize/NEWS.md | 21 ++++ scCustomize-3.2.2/scCustomize/R/Internal_Utilities.R | 12 -- scCustomize-3.2.2/scCustomize/R/LIGER_Internal_Utilities.R | 11 -- scCustomize-3.2.2/scCustomize/R/LIGER_Utilities.R | 6 - scCustomize-3.2.2/scCustomize/R/Object_Utilities.R | 2 scCustomize-3.2.2/scCustomize/R/Plotting_Seurat.R | 2 scCustomize-3.2.2/scCustomize/R/QC_Utilities_Seurat.R | 8 - scCustomize-3.2.2/scCustomize/R/Read_Write_Data.R |only scCustomize-3.2.2/scCustomize/man/Create_10X_H5.Rd | 2 scCustomize-3.2.2/scCustomize/man/Create_CellBender_Merged_Seurat.Rd | 2 scCustomize-3.2.2/scCustomize/man/ElbowPlot_scCustom.Rd | 1 scCustomize-3.2.2/scCustomize/man/Map_New_Meta.Rd | 1 scCustomize-3.2.2/scCustomize/man/Pull_Directory_List.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read10X_GEO.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read10X_Multi_Directory.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read10X_h5_GEO.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read10X_h5_Multi_Directory.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read_Add_cNMF.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read_CellBender_h5_Mat.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read_CellBender_h5_Multi_Directory.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read_CellBender_h5_Multi_File.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read_GEO_Delim.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read_Metrics_10X.Rd | 2 scCustomize-3.2.2/scCustomize/man/Read_Metrics_CellBender.Rd | 2 27 files changed, 77 insertions(+), 73 deletions(-)
Title: A Multi-Process 'dplyr' Backend
Description: Partition a data frame across multiple worker processes to
provide simple multicore parallelism.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between multidplyr versions 0.1.3 dated 2023-03-22 and 0.1.4 dated 2025-11-12
DESCRIPTION | 15 -- LICENSE | 2 MD5 | 41 ++--- NEWS.md | 4 R/cluster-call.R | 15 +- R/cluster-utils.R | 4 R/cluster.R | 31 ++-- R/dplyr-dual.R | 36 ++++ R/dplyr-single.R | 2 R/partydf.R | 18 +- R/utils.R | 1 README.md | 40 ++--- build/vignette.rds |binary inst/doc/multidplyr.R | 4 inst/doc/multidplyr.html | 267 ++++++++++++++++++------------------ man/party_df.Rd | 2 tests/testthat/_snaps/dplyr-dual.md |only tests/testthat/_snaps/partydf.md | 28 +++ tests/testthat/test-cluster-call.R | 6 tests/testthat/test-dplyr-dual.R | 4 tests/testthat/test-dplyr-single.R | 13 + tests/testthat/test-partydf.R | 20 +- 22 files changed, 316 insertions(+), 237 deletions(-)
Title: Kriging-Based Optimization for Computer Experiments
Description: Efficient Global Optimization (EGO) algorithm as described in "Roustant et al. (2012)" <doi:10.18637/jss.v051.i01> and adaptations for problems with noise ("Picheny and Ginsbourger, 2012") <doi:10.1016/j.csda.2013.03.018>, parallel infill, and problems with constraints.
Author: Mickael Binois [cre, ctb],
Victor Picheny [aut],
David Ginsbourger [aut],
Olivier Roustant [aut],
Sebastien Marmin [ctb],
Tobias Wagner [ctb]
Maintainer: Mickael Binois <mickael.binois@inria.fr>
This is a re-admission after prior archival of version 2.1.1 dated 2021-02-01
Diff between DiceOptim versions 2.1.1 dated 2021-02-01 and 2.1.2 dated 2025-11-12
DESCRIPTION | 31 +- MD5 | 114 ++++----- NAMESPACE | 18 + R/AEI.R | 207 ++++++++-------- R/AEI.grad.R | 127 +++++----- R/AKG.R | 184 +++++++------- R/AKG.grad.R | 128 +++++----- R/DiceOptim-package.R | 466 ++++++++++++++++++------------------- R/EGO.cst.R | 459 ++++++++++++++++++------------------ R/EGO.nsteps.R | 486 +++++++++++++++++++-------------------- R/EI.R | 158 ++++++------ R/EI.grad.R | 192 +++++++-------- R/EQI.R | 198 +++++++-------- R/EQI.grad.R | 130 +++++----- R/ParrConstraint.R | 30 +- R/TREGO.nsteps.R | 241 +++++++++---------- R/branin2.R | 48 +-- R/checkPredict.R | 38 +-- R/crit_AL.R | 300 ++++++++++++------------ R/crit_EFI.R | 254 ++++++++++---------- R/crit_SUR_cst.R | 266 ++++++++++----------- R/critcst_optimizer.R | 360 ++++++++++++++-------------- R/easyEGO.R | 221 ++++++++--------- R/easyEGO.cst.R | 399 ++++++++++++++++---------------- R/fastEGO.nsteps.R | 224 ++++++++--------- R/fastfun.R | 77 +++--- R/goldsteinprice.R | 52 ++-- R/hartman4.R | 49 +-- R/integration_design_cst.R | 128 +++++----- R/kriging.quantile.R | 182 +++++++------- R/kriging.quantile.grad.R | 164 ++++++------- R/max_AEI.R | 156 ++++++------ R/max_AKG.R | 162 ++++++------- R/max_EI.R | 368 ++++++++++++++--------------- R/max_EQI.R | 158 ++++++------ R/max_crit.R | 126 +++++----- R/max_qEI.R | 350 ++++++++++++++-------------- R/min_quantile.R | 152 ++++++------ R/noisy.optimizer.R | 408 ++++++++++++++++---------------- R/prob.of.feasible.improvement.R | 4 R/qEGO.nsteps.R | 374 +++++++++++++++--------------- R/qEI.R | 236 +++++++++--------- R/rosenbrock4.R | 48 +-- R/sampleFromEI.R | 296 +++++++++++------------ R/sphere6.R | 48 +-- R/test_feas_vec.R | 20 - R/update_km_noisyEGO.R | 68 ++--- man/DiceOptim-package.Rd | 5 man/EGO.cst.Rd | 15 - man/crit_AL.Rd | 12 man/critcst_optimizer.Rd | 4 man/easyEGO.Rd | 42 +-- man/easyEGO.cst.Rd | 23 - man/fastfun-class.Rd | 8 man/integration_design_cst.Rd | 6 man/max_qEI.Rd | 6 man/qEGO.nsteps.Rd | 4 man/sampleFromEI.Rd | 2 58 files changed, 4523 insertions(+), 4509 deletions(-)
Title: Convert and Impute Dates to ISO Standard ("International
Organization for Standardization")
Description: Provides functions to convert and impute date values to the ISO 8601
standard format. The package automatically recognizes date patterns within a
data frame and transforms them into consistent ISO-formatted dates. It also
supports imputing missing month or day components in partial date strings
using user-defined rules. Only one date format can be applied within a single
data frame column.
Author: Lukasz Andrzejewski [aut, cre]
Maintainer: Lukasz Andrzejewski <lukasz.coding@gmail.com>
Diff between datetoiso versions 0.2.0 dated 2023-12-01 and 1.0.0 dated 2025-11-12
DESCRIPTION | 21 ++- MD5 | 19 +-- NAMESPACE | 11 + NEWS.md | 57 +++++---- R/date_to_iso.R | 192 +++++++++++++++--------------- R/dfiso.R | 6 R/impute_date.R |only R/viso.R | 6 man/impute_date.Rd |only man/impute_date_dmy.Rd |only man/impute_date_ymd.Rd |only tests/testthat/test-dfiso.R | 240 +++++++++++++++++++------------------- tests/testthat/test-impute_date.R |only 13 files changed, 293 insertions(+), 259 deletions(-)
Title: Process Text and Compute Linguistic Alignment in Conversation
Transcripts
Description: Imports conversation transcripts into R, concatenates them into a single dataframe appending event identifiers, cleans and formats the text, then yokes user-specified psycholinguistic database values to each word. 'ConversationAlign' then computes alignment indices between two interlocutors across each transcript for >40 possible semantic, lexical, and affective dimensions. In addition to alignment, 'ConversationAlign' also produces a table of analytics (e.g., token count, type-token-ratio) in a summary table describing your particular text corpus.
Author: Jamie Reilly [aut, cre] ,
Virginia Ulichney [aut],
Ben Sacks [aut],
Sarah Weinstein [ctb],
Chelsea Helion [ctb],
Gus Cooney [ctb]
Maintainer: Jamie Reilly <jamie_reilly@temple.edu>
Diff between ConversationAlign versions 0.3.2 dated 2025-07-30 and 0.4.0 dated 2025-11-12
DESCRIPTION | 15 - MD5 | 48 ++-- NAMESPACE | 5 R/compute_auc.R | 254 ++++++++++++++++-------- R/compute_lagcorr.R | 2 R/generate_shams.R |only R/prep_dyads.R | 22 +- R/summarize_dyads.R | 13 - build/vignette.rds |binary inst/NEWS.md | 19 + inst/doc/ConversationAlign_Introduction.Rmd | 6 inst/doc/ConversationAlign_Introduction.html | 17 - inst/doc/ConversationAlign_Step1_Read.html | 4 inst/doc/ConversationAlign_Step2_Prep.Rmd | 3 inst/doc/ConversationAlign_Step2_Prep.html | 9 inst/doc/ConversationAlign_Step3_Summarize.R | 11 - inst/doc/ConversationAlign_Step3_Summarize.Rmd | 17 + inst/doc/ConversationAlign_Step3_Summarize.html | 172 ++++++++++++++-- inst/doc/ConversationAlign_Step4_Analytics.html | 4 man/generate_shams.Rd |only man/prep_dyads.Rd | 3 tests/testthat/test-compute_auc.R | 16 - tests/testthat/test-summarize_dyads.R | 2 vignettes/ConversationAlign_Introduction.Rmd | 6 vignettes/ConversationAlign_Step2_Prep.Rmd | 3 vignettes/ConversationAlign_Step3_Summarize.Rmd | 17 + 26 files changed, 496 insertions(+), 172 deletions(-)
More information about ConversationAlign at CRAN
Permanent link
Title: Your Friendly Solution to Managing Browser Cookies
Description: A convenient tool to store and format browser cookies and use them
in 'HTTP' requests (for example, through 'httr2', 'httr' or 'curl').
Author: Johannes B. Gruber [aut, cre]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between cookiemonster versions 0.0.3 dated 2023-11-30 and 0.0.4 dated 2025-11-12
cookiemonster-0.0.3/cookiemonster/man/figures |only cookiemonster-0.0.4/cookiemonster/DESCRIPTION | 22 - cookiemonster-0.0.4/cookiemonster/MD5 | 47 +- cookiemonster-0.0.4/cookiemonster/NAMESPACE | 3 cookiemonster-0.0.4/cookiemonster/NEWS.md | 6 cookiemonster-0.0.4/cookiemonster/R/browser.r |only cookiemonster-0.0.4/cookiemonster/R/get.r | 16 cookiemonster-0.0.4/cookiemonster/R/req_cookiemoster_set.r |only cookiemonster-0.0.4/cookiemonster/R/set.r | 27 + cookiemonster-0.0.4/cookiemonster/R/sysdata.rda |only cookiemonster-0.0.4/cookiemonster/README.md | 77 +++- cookiemonster-0.0.4/cookiemonster/build/vignette.rds |binary cookiemonster-0.0.4/cookiemonster/inst/WORDLIST | 5 cookiemonster-0.0.4/cookiemonster/inst/doc/cookies.R | 39 +- cookiemonster-0.0.4/cookiemonster/inst/doc/cookies.Rmd | 53 ++ cookiemonster-0.0.4/cookiemonster/inst/doc/cookies.html | 190 ++++++---- cookiemonster-0.0.4/cookiemonster/man/add_cookies.Rd | 5 cookiemonster-0.0.4/cookiemonster/man/get_cookies.Rd | 3 cookiemonster-0.0.4/cookiemonster/man/get_cookies_from_browser.Rd |only cookiemonster-0.0.4/cookiemonster/man/req_cookiemonster_set.Rd |only cookiemonster-0.0.4/cookiemonster/tests/testthat/test-browser.R |only cookiemonster-0.0.4/cookiemonster/tests/testthat/test-get.R | 7 cookiemonster-0.0.4/cookiemonster/tests/testthat/test-req_cookiemonster_set.R |only cookiemonster-0.0.4/cookiemonster/tests/testthat/test-set.R | 2 cookiemonster-0.0.4/cookiemonster/vignettes/cookies.Rmd | 53 ++ 25 files changed, 419 insertions(+), 136 deletions(-)
Title: Kernel Smoothing Tools for Philology and Historical Dialectology
Description: Contains kernel smoothing tools designed for use by historical
dialectologists and philologists for exploring spatial and temporal patterns
in noisy historical language data, such as that obtained from historical texts.
The main way in which these might differ from other implementations of kernel
smoothing is that they assume that the function (linguistic variable) being
explored has the form of the relative frequency of a series of discrete
possibilities (linguistic variants). This package also offers a way of exploring
distributions in 2-dimensional space and in time with separate kernels, and
tools for identifying appropriate bandwidths for these.
Author: Tamsin Blaxter [aut, cre]
Maintainer: Tamsin Blaxter <tamsinblaxter@gmail.com>
This is a re-admission after prior archival of version 0.1 dated 2021-02-25
Diff between kernelPhil versions 0.1 dated 2021-02-25 and 0.2 dated 2025-11-12
DESCRIPTION | 20 +++---- MD5 | 14 ++--- NAMESPACE | 1 R/1d.smooths.r | 6 +- R/2d.smooths.r | 79 ++++++++++++++++++++---------- R/3d.smooths.r | 4 + R/bandwidths.r | 28 ++++++---- man/calculate.bandwidths.by.resolution.Rd | 2 8 files changed, 96 insertions(+), 58 deletions(-)
Title: Add Tests to Examples
Description: Add tests in-line in examples. Provides standalone functions for
facilitating easier test writing in Rd files. However, a more familiar
interface is provided using 'roxygen2' tags. Tools are also provided for
facilitating package configuration and use with 'testthat'.
Author: Doug Kelkhoff [aut, cre]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Diff between testex versions 0.2.0 dated 2024-04-14 and 0.2.1 dated 2025-11-12
DESCRIPTION | 9 MD5 | 25 +- NEWS.md | 7 R/testthat.R | 51 +++-- build/vignette.rds |binary inst/WORDLIST |only inst/doc/configuration.html | 180 +++++++++---------- inst/doc/interface_layers.html | 260 ++++++++++++++-------------- inst/pkg.example/DESCRIPTION | 2 inst/pkg.example/man/fn_roxygen_multiple.Rd | 2 man/test_files.Rd | 4 tests/testthat/setup.R | 6 tests/testthat/test-testex.R | 8 tests/testthat/test-testthat.R | 8 14 files changed, 298 insertions(+), 264 deletions(-)
Title: Spatially Explicit Population Models of Disease Transmission in
Wildlife
Description: This extension of the pattern-oriented modeling framework of the
'poems' package provides a collection of modules and functions customized
for modeling disease transmission on a population scale in a spatiotemporally
explicit manner. This includes seasonal time steps, dispersal functions that
track disease state of dispersers, results objects that store disease states,
and a population simulator that includes disease dynamics.
Author: July Pilowsky [aut, cre] ,
National Science Foundation Biology Integration Institute 2213854 [fnd]
Maintainer: July Pilowsky <pilowskyj@caryinstitute.org>
Diff between epizootic versions 1.0.0 dated 2024-10-02 and 2.0.0 dated 2025-11-12
epizootic-1.0.0/epizootic/R/disease_dispersal.r |only epizootic-1.0.0/epizootic/inst/doc/mycoplasma.R |only epizootic-1.0.0/epizootic/tests/testthat/test_results/sample_1_results.qs |only epizootic-2.0.0/epizootic/DESCRIPTION | 17 epizootic-2.0.0/epizootic/MD5 | 42 epizootic-2.0.0/epizootic/NAMESPACE | 13 epizootic-2.0.0/epizootic/NEWS.md | 11 epizootic-2.0.0/epizootic/R/DiseaseModel.R | 150 +- epizootic-2.0.0/epizootic/R/SimulationHandler.R | 351 ++++-- epizootic-2.0.0/epizootic/R/check_simulator_inputs.R | 536 +++++----- epizootic-2.0.0/epizootic/R/disease_dispersal.R |only epizootic-2.0.0/epizootic/R/disease_simulator.R | 125 +- epizootic-2.0.0/epizootic/R/epizootic-package.R | 5 epizootic-2.0.0/epizootic/build/vignette.rds |binary epizootic-2.0.0/epizootic/inst/doc/mycoplasma.Rmd | 414 ------- epizootic-2.0.0/epizootic/inst/doc/mycoplasma.html | 470 -------- epizootic-2.0.0/epizootic/man/SimulationHandler.Rd | 2 epizootic-2.0.0/epizootic/man/disease_dispersal.Rd | 2 epizootic-2.0.0/epizootic/man/disease_simulator.Rd | 54 - epizootic-2.0.0/epizootic/tests/testthat/test-SimulationHandler.R | 204 ++- epizootic-2.0.0/epizootic/tests/testthat/test-aspatial_siri_seasons.R | 366 ++++++ epizootic-2.0.0/epizootic/tests/testthat/test-disease_simulator.R | 388 +++++++ epizootic-2.0.0/epizootic/tests/testthat/test-disease_transitions.R |only epizootic-2.0.0/epizootic/tests/testthat/test_results/sample_1_results.qs2 |only epizootic-2.0.0/epizootic/vignettes/mycoplasma.Rmd | 414 ------- 25 files changed, 1693 insertions(+), 1871 deletions(-)
Title: Income Polarization Index
Description: Extremely fast and memory efficient computation of the DER (or PaF) income polarization index as proposed by Duclos J. Y., Esteban, J. and Ray D. (2004). "Polarization: concepts, measurement, estimation". Econometrica, 72(6): 1737--1772. <doi:10.1111/j.1468-0262.2004.00552.x>. The index may be computed for a single or for a range of values of the alpha-parameter and bootstrapping is also available.
Author: Michail Tsagris [aut, cre],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between DER versions 1.2 dated 2025-11-05 and 1.3 dated 2025-11-12
DER-1.2/DER/R/colpafs.R |only DER-1.2/DER/R/colpafs2.R |only DER-1.2/DER/R/paf2.R |only DER-1.3/DER/DESCRIPTION | 16 +- DER-1.3/DER/MD5 | 39 +++--- DER-1.3/DER/NAMESPACE | 2 DER-1.3/DER/R/RcppExports.R | 24 ++++ DER-1.3/DER/R/paf.boot.R | 20 --- DER-1.3/DER/R/paf2.boot.R | 23 --- DER-1.3/DER/R/pafF.R | 27 ---- DER-1.3/DER/man/DER-package.Rd | 16 ++ DER-1.3/DER/man/colpafs.Rd | 29 +++- DER-1.3/DER/man/colpafs2.Rd | 30 +++-- DER-1.3/DER/man/kde.Rd |only DER-1.3/DER/man/paf.Rd | 37 ++++-- DER-1.3/DER/man/paf.boot.Rd | 30 +++-- DER-1.3/DER/man/paf2.Rd | 32 ++++- DER-1.3/DER/man/paf2.boot.Rd | 30 +++-- DER-1.3/DER/src/RcppExports.cpp | 88 ++++++++++++++- DER-1.3/DER/src/colpafs.cpp |only DER-1.3/DER/src/colpafs2.cpp |only DER-1.3/DER/src/kde.cpp |only DER-1.3/DER/src/paf.cpp | 233 +++++++++++++++++++++++++++++++--------- DER-1.3/DER/src/paf2.cpp |only DER-1.3/DER/src/pafF_helper.cpp |only 25 files changed, 485 insertions(+), 191 deletions(-)
Title: Base Tools for Semi-Automatic Reporting of Ordinary Surveys
Description: Scaffold an entire web-based report using template chunks, based on a small chapter overview and a dataset.
Highly adaptable with prefixes, suffixes, translations, etc. Also contains tools for password-protecting,
e.g. for each organization's report on a website. Developed for the common case of a survey across multiple organizations/sites
where each organization wants to obtain results for their organization compared with everyone else.
See 'saros' (<https://CRAN.R-project.org/package=saros>) for tools used for authors in the drafted reports.
Author: Stephan Daus [aut, cre, cph] ,
Nordic Institute for The Studies of Innovation, Research and Education
[fnd],
Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>
Diff between saros.base versions 1.1.0 dated 2025-06-01 and 1.2.0 dated 2025-11-12
saros.base-1.1.0/saros.base/R/check_paths.R |only saros.base-1.1.0/saros.base/R/render_full_reports.R |only saros.base-1.1.0/saros.base/man/render_full_reports.Rd |only saros.base-1.2.0/saros.base/DESCRIPTION | 12 saros.base-1.2.0/saros.base/MD5 | 149 +- saros.base-1.2.0/saros.base/NAMESPACE | 4 saros.base-1.2.0/saros.base/NEWS.md | 109 + saros.base-1.2.0/saros.base/R/add_core_info_to_chapter_structure.R | 143 +- saros.base-1.2.0/saros.base/R/add_parsed_vars_to_chapter_structure.R | 8 saros.base-1.2.0/saros.base/R/arrange2.R | 39 saros.base-1.2.0/saros.base/R/attach_new_output_to_output.R | 30 saros.base-1.2.0/saros.base/R/check_variable_labels.R |only saros.base-1.2.0/saros.base/R/copy.R | 26 saros.base-1.2.0/saros.base/R/create_directory_structure.R | 432 +++--- saros.base-1.2.0/saros.base/R/create_email_credentials.R | 38 saros.base-1.2.0/saros.base/R/create_htaccess.R | 91 + saros.base-1.2.0/saros.base/R/create_r_files.R | 6 saros.base-1.2.0/saros.base/R/detect_malformed_quarto_project.R |only saros.base-1.2.0/saros.base/R/draft_report.R | 687 +++++----- saros.base-1.2.0/saros.base/R/find_stat_test.R | 108 - saros.base-1.2.0/saros.base/R/gen_qmd_chapters.R | 318 ++-- saros.base-1.2.0/saros.base/R/gen_qmd_file.R | 70 - saros.base-1.2.0/saros.base/R/initialize_saros_project.R | 8 saros.base-1.2.0/saros.base/R/log_unused_variables.R | 1 saros.base-1.2.0/saros.base/R/look_for_extended.R | 204 +- saros.base-1.2.0/saros.base/R/process_yaml.R | 10 saros.base-1.2.0/saros.base/R/qmd_utils.R |only saros.base-1.2.0/saros.base/R/read_main_password_file.R | 24 saros.base-1.2.0/saros.base/R/refer_main_password_file.R | 70 - saros.base-1.2.0/saros.base/R/refine_chapter_overview.R | 100 + saros.base-1.2.0/saros.base/R/remove_from_chapter_structure_if_all_na.R | 44 saros.base-1.2.0/saros.base/R/remove_from_chapter_structure_if_n_below.R | 32 saros.base-1.2.0/saros.base/R/remove_from_chapter_structure_if_no_overlap.R | 19 saros.base-1.2.0/saros.base/R/remove_from_chapter_structure_if_no_type_match.R | 40 saros.base-1.2.0/saros.base/R/remove_from_chapter_structure_if_non_significant.R | 39 saros.base-1.2.0/saros.base/R/sanitize_character_vector.R |only saros.base-1.2.0/saros.base/R/setup_access_restrictions.R | 96 - saros.base-1.2.0/saros.base/R/setup_mesos.R | 350 +++-- saros.base-1.2.0/saros.base/R/setup_mesos_structure.R |only saros.base-1.2.0/saros.base/R/sysdata.rda |only saros.base-1.2.0/saros.base/R/utils.R | 50 saros.base-1.2.0/saros.base/R/utils_qmd.R | 13 saros.base-1.2.0/saros.base/R/validate_access_folder_paths.R | 12 saros.base-1.2.0/saros.base/R/validate_chapter_structure.R | 100 + saros.base-1.2.0/saros.base/R/validate_draft_report_args.R | 213 +-- saros.base-1.2.0/saros.base/R/validate_refine_chapter_overview_args.R | 182 +- saros.base-1.2.0/saros.base/R/zzz.R | 380 +++++ saros.base-1.2.0/saros.base/build/vignette.rds |binary saros.base-1.2.0/saros.base/inst/WORDLIST | 6 saros.base-1.2.0/saros.base/inst/doc/vig_01_basic_file_system.html | 141 ++ saros.base-1.2.0/saros.base/inst/doc/vig_02_project_setup.html | 141 ++ saros.base-1.2.0/saros.base/inst/doc/vig_03_configure_report_cycle.html | 163 ++ saros.base-1.2.0/saros.base/inst/doc/vig_04_prepare_data.html | 217 ++- saros.base-1.2.0/saros.base/inst/doc/vig_05_standard_variable_names.html | 141 ++ saros.base-1.2.0/saros.base/inst/doc/vig_06_prepare_chapter_overview.html | 141 ++ saros.base-1.2.0/saros.base/inst/doc/vig_07_adjust_report_cycle_settings.html | 141 ++ saros.base-1.2.0/saros.base/inst/doc/vig_31_render.html | 141 ++ saros.base-1.2.0/saros.base/inst/doc/vig_32_render_problems.html | 141 ++ saros.base-1.2.0/saros.base/man/check_variable_labels.Rd |only saros.base-1.2.0/saros.base/man/convert_mesos_groups_to_df.Rd |only saros.base-1.2.0/saros.base/man/detect_malformed_quarto_project.Rd |only saros.base-1.2.0/saros.base/man/draft_report.Rd | 4 saros.base-1.2.0/saros.base/man/handle_numbering_inheritance.Rd | 14 saros.base-1.2.0/saros.base/man/refine_chapter_overview.Rd | 68 saros.base-1.2.0/saros.base/man/sanitize_chr_vec.Rd |only saros.base-1.2.0/saros.base/man/setup_access_restrictions.Rd | 34 saros.base-1.2.0/saros.base/man/setup_mesos.Rd | 21 saros.base-1.2.0/saros.base/man/setup_mesos_structure.Rd |only saros.base-1.2.0/saros.base/tests/testthat/test-arrange2.R | 186 +- saros.base-1.2.0/saros.base/tests/testthat/test-check_variable_labels.R |only saros.base-1.2.0/saros.base/tests/testthat/test-chunk_template_variant_4.R |only saros.base-1.2.0/saros.base/tests/testthat/test-create__headers_file.R |only saros.base-1.2.0/saros.base/tests/testthat/test-create_directory_structure.R |only saros.base-1.2.0/saros.base/tests/testthat/test-create_htaccess.R |only saros.base-1.2.0/saros.base/tests/testthat/test-detect_malformed_quarto_project.R |only saros.base-1.2.0/saros.base/tests/testthat/test-get_organize_by_opts.R |only saros.base-1.2.0/saros.base/tests/testthat/test-log_file_exclusions.R |only saros.base-1.2.0/saros.base/tests/testthat/test-read_main_password_file.R |only saros.base-1.2.0/saros.base/tests/testthat/test-refine_chapter_overview.R | 439 ++++++ saros.base-1.2.0/saros.base/tests/testthat/test-remove_from_chapter_structure_if_no_overlap.R | 6 saros.base-1.2.0/saros.base/tests/testthat/test-remove_from_chapter_structure_if_no_type_match.R | 60 saros.base-1.2.0/saros.base/tests/testthat/test-remove_from_chapter_structure_if_non_significant.R |only saros.base-1.2.0/saros.base/tests/testthat/test-replace_label_groups_with_name_groups.R | 44 saros.base-1.2.0/saros.base/tests/testthat/test-sanitize_chr_vec.R |only saros.base-1.2.0/saros.base/tests/testthat/test-setup_access_restrictions.R | 354 +++++ saros.base-1.2.0/saros.base/tests/testthat/test-setup_mesos.R | 256 +++ saros.base-1.2.0/saros.base/tests/testthat/test-setup_mesos_structure.R |only saros.base-1.2.0/saros.base/tests/testthat/test-utils.R | 126 + saros.base-1.2.0/saros.base/tests/testthat/test-validate_access_folder_paths.R |only 89 files changed, 5301 insertions(+), 1941 deletions(-)
Title: Designing Cluster-Randomized Trials with Two Continuous
Co-Primary Outcomes
Description: Provides methods for powering cluster-randomized trials with two continuous co-primary outcomes using five key design techniques. Includes functions for calculating required sample size and statistical power. For more details on methodology, see Owen et al. (2025) <doi:10.1002/sim.70015>, Yang et al. (2022) <doi:10.1111/biom.13692>, Pocock et al. (1987) <doi:10.2307/2531989>, Vickerstaff et al. (2019) <doi:10.1186/s12874-019-0754-4>, and Li et al. (2020) <doi:10.1111/biom.13212>.
Author: Melody Owen [aut, cre]
Maintainer: Melody Owen <melody.owen@yale.edu>
Diff between crt2power versions 1.2.1 dated 2025-05-07 and 1.2.2 dated 2025-11-12
DESCRIPTION | 6 ++-- MD5 | 16 +++++------ R/calc_pwr_comb_outcome.R | 27 +++++++++++++++++++ R/calc_pwr_conj_test.R | 31 ++++++++++++++++++++-- R/calc_pwr_disj_2dftest.R | 27 +++++++++++++++++++ R/calc_pwr_pval_adj.R | 27 +++++++++++++++++++ R/calc_pwr_single_1dftest.R | 27 +++++++++++++++++++ R/run_crt2_design.R | 10 +++++++ README.md | 61 +++++++++++++++++++++++--------------------- 9 files changed, 190 insertions(+), 42 deletions(-)
Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Oeyvind Langsrud [aut, cre],
Jan Bruusgaard [aut],
Solveig Bjoerkholt [ctb],
Susie Jentoft [ctb]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between PxWebApiData versions 1.1.0 dated 2025-10-08 and 1.1.1 dated 2025-11-12
DESCRIPTION | 8 - MD5 | 22 ++-- NAMESPACE | 2 NEWS.md | 7 + R/ApiData.R | 19 ++- R/fromJSONstatExtra.R | 3 R/info.R |only inst/doc/Introduction.R | 28 +++-- inst/doc/Introduction.Rmd | 30 +++-- inst/doc/Introduction.html | 239 +++++++++++++++++++++++---------------------- man/ApiData.Rd | 21 ++- man/info.Rd |only vignettes/Introduction.Rmd | 30 +++-- 13 files changed, 234 insertions(+), 175 deletions(-)
Title: Tools to Manage a Parametric Function that Describes Phenology
and More
Description: Functions used to fit and test the phenology of species based on counts. Based on Girondot, M. (2010) <doi:10.3354/esr00292> for the phenology function, Girondot, M. (2017) <doi:10.1016/j.ecolind.2017.05.063> for the convolution of negative binomial, Girondot, M. and Rizzo, A. (2015) <doi:10.2993/etbi-35-02-337-353.1> for Bayesian estimate, Pfaller JB, ..., Girondot M (2019) <doi:10.1007/s00227-019-3545-x> for tag-loss estimate, Hancock J, ..., Girondot M (2019) <doi:10.1016/j.ecolmodel.2019.04.013> for nesting history, Laloe J-O, ..., Girondot M, Hays GC (2020) <doi:10.1007/s00227-020-03686-x> for aggregating several seasons.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between phenology versions 10.3 dated 2025-06-17 and 2025.11.12 dated 2025-11-12
DESCRIPTION | 10 +-- MD5 | 18 ++--- NEWS | 10 ++- R/CI.RMU.R | 152 ++++++++++++++++++++++++++--------------------- R/add_phenology.R | 8 +- R/fit_phenology.R | 24 +++---- R/phenology-package.R | 4 - man/CI.RMU.Rd | 14 +++- man/figures/imgfile.png |binary man/phenology-package.Rd | 4 - 10 files changed, 142 insertions(+), 102 deletions(-)
Title: Comprehensive Data Summarization for Statistical Analysis
Description: Summarizes data frames by calculating various statistics including central tendency, dispersion, shape, and normality diagnostics. Handles numeric, character, and factor columns with NA-aware computations.
Author: Immad Ahmad Shah [aut],
Uzair Javid Khan [aut, cre],
Sukhdev Mishra [aut]
Maintainer: Uzair Javid Khan <uzairkhan11w@gmail.com>
Diff between DataSum versions 0.1.0 dated 2024-08-28 and 0.1.1 dated 2025-11-12
DESCRIPTION | 24 ++-- MD5 | 14 +- R/datasum.R | 205 ++++++++++++++++++++++++++---------------- man/DataSumm.Rd | 6 - man/Datum.Rd | 9 + man/getmode.Rd | 17 ++- man/shapiro_normality_test.Rd | 7 - tests |only 8 files changed, 173 insertions(+), 109 deletions(-)
Title: Pattern-Oriented Ensemble Modeling System
Description: A framework of interoperable R6 classes (Chang, 2020, <https://CRAN.R-project.org/package=R6>) for building ensembles of viable models via the pattern-oriented modeling (POM) approach (Grimm et al.,2005, <doi:10.1126/science.1116681>). The package includes classes for encapsulating and generating model parameters, and managing the POM workflow. The workflow includes: model setup; generating model parameters via Latin hyper-cube sampling (Iman & Conover, 1980, <doi:10.1080/03610928008827996>); running multiple sampled model simulations; collating summary results; and validating and selecting an ensemble of models that best match known patterns. By default, model validation and selection utilizes an approximate Bayesian computation (ABC) approach (Beaumont et al., 2002, <doi:10.1093/genetics/162.4.2025>), although alternative user-defined functionality could be employed. The package includes a spatially explicit demographic population model simulation engine, [...truncated...]
Author: Sean Haythorne [aut],
Damien Fordham [aut],
Stuart Brown [aut] ,
Jessie Buettel [aut],
Barry Brook [aut],
July Pilowsky [aut, cre]
Maintainer: July Pilowsky <pilowskyj@caryinstitute.org>
Diff between poems versions 1.3.3 dated 2025-05-07 and 1.4.0 dated 2025-11-12
poems-1.3.3/poems/inst/doc/thylacine_example.R |only poems-1.3.3/poems/inst/doc/translocation_example.R |only poems-1.4.0/poems/DESCRIPTION | 8 poems-1.4.0/poems/MD5 | 24 +- poems-1.4.0/poems/NAMESPACE | 2 poems-1.4.0/poems/NEWS.md | 4 poems-1.4.0/poems/R/Generator.R | 18 - poems-1.4.0/poems/build/partial.rdb |binary poems-1.4.0/poems/build/vignette.rds |binary poems-1.4.0/poems/inst/doc/translocation_example.pdf |binary poems-1.4.0/poems/man/Generator.Rd | 2 poems-1.4.0/poems/tests/testthat/test_generator.R | 130 +++++++++++ poems-1.4.0/poems/tests/testthat/test_inputs/Test_1_2.qs2 |only poems-1.4.0/poems/tests/testthat/test_inputs/Test_1_2_df.qs2 |only poems-1.4.0/poems/vignettes/simple_example.html | 88 +++---- 15 files changed, 206 insertions(+), 70 deletions(-)
Title: Nonparametric Methods for Measuring Efficiency and Productivity
Description: Efficiency and productivity indices are measured using this package. This package contains functions for measuring efficiency and productivity of decision making units (DMUs) under the framework of Data Envelopment Analysis (DEA) and its variations.
Author: Dong-hyun Oh [aut, cre],
Dukrok Suh [aut]
Maintainer: Dong-hyun Oh <oh.donghyun77@gmail.com>
Diff between nonparaeff versions 0.5-13 dated 2022-06-20 and 0.5-15 dated 2025-11-12
nonparaeff-0.5-13/nonparaeff/README.md |only nonparaeff-0.5-15/nonparaeff/DESCRIPTION | 19 +++++++++++++------ nonparaeff-0.5-15/nonparaeff/MD5 | 5 ++--- nonparaeff-0.5-15/nonparaeff/man/lp2.Rd | 5 +++-- 4 files changed, 18 insertions(+), 11 deletions(-)
Title: Automatically Create a 'Shiny' App Based on Interactive 'Loon'
Widgets
Description: Package 'shiny' provides interactive web applications in R. Package 'loon' is an interactive toolkit engaged in open-ended, creative and unscripted data exploration. The 'loon.shiny' package can take 'loon' widgets and display a selfsame 'shiny' app.
Author: Zehao Xu [aut, cre],
R. Wayne Oldford [aut]
Maintainer: Zehao Xu <z267xu@gmail.com>
Diff between loon.shiny versions 1.0.3 dated 2022-10-08 and 1.0.4 dated 2025-11-12
DESCRIPTION | 14 MD5 | 164 +- R/adjust_loon_grobs.R | 7 R/button_values.R | 11 R/get_brushId.R | 11 R/get_deactive_index.R | 285 +-- R/get_grobFromGtable.R | 41 R/get_itemLabel.R | 7 R/get_layers.R | 167 +- R/get_layoutMatrix.R | 69 R/get_loonInfo.R | 15 R/get_loonWidgetsInfo-l_graph.R | 1 R/get_loonWidgetsInfo-l_hist.R | 1 R/get_loonWidgetsInfo-l_plot.R | 1 R/get_loonWidgetsInfo-l_serialaxes.R | 1 R/get_loonWidgets_info.R | 9 R/get_output_info.R | 7 R/get_set_guides.R | 119 - R/get_set_labels.R | 283 +-- R/get_set_scales.R | 143 - R/get_set_viewPort.R | 77 R/get_update_linkingInfo.R | 24 R/loon.shiny.R | 45 R/loonGrob_name.R | 8 R/loonGrob_positions.R | 329 ++-- R/loonWidget_name.R | 12 R/loon_reactive_l_graph.R | 2229 ++++++++++++++-------------- R/loon_reactive_l_hist.R | 1394 ++++++++--------- R/loon_reactive_l_plot.R | 2772 +++++++++++++++++------------------ R/loon_reactive_l_serialaxes.R | 1632 ++++++++++---------- R/loon_sidebarPanel-l_graph.R | 1 R/loon_sidebarPanel-l_hist.R | 1 R/loon_sidebarPanel-l_plot.R | 1 R/loon_sidebarPanel-l_serialaxes.R | 1 R/loon_siderbarPanel.R | 59 R/loon_worldView.R | 7 R/move_grid_grob.R | 119 - R/move_halign_grob.R | 811 +++++----- R/move_hdist_grob.R | 827 +++++----- R/move_jitter_grob.R | 1088 ++++++------- R/move_layer_invisible_grob.R | 368 ++-- R/move_layer_visible_grob.R | 362 ++-- R/move_reset_grob.R | 541 +++--- R/move_valign_grob.R | 799 +++++----- R/move_vdist_grob.R | 823 +++++----- R/reorder_grob.R | 127 - R/set_alpha_grob.R | 6 R/set_boundary_grob.R | 55 R/set_color_grob.R | 570 +++---- R/set_deactive_grob.R | 403 ++--- R/set_glyph_grob.R | 255 +-- R/set_grobFromGtable.R | 8 R/set_linkingInfo-l_graph.R | 1 R/set_linkingInfo-l_hist.R | 1 R/set_linkingInfo-l_plot.R | 2 R/set_linkingInfo-l_serialaxes.R | 1 R/set_reactive_grob.R | 407 ++--- R/set_size_grob.R | 515 +++--- R/swapCoords_grob.R | 489 +++--- R/tagsDivGlyph.R | 3 R/tagsDivLayer.R | 3 R/tagsDivLink.R | 5 R/tagsDivModify-l_graph.R | 1 R/tagsDivModify-l_hist.R | 1 R/tagsDivModify-l_plot.R | 2 R/tagsDivModify-l_serialaxes.R | 1 R/tagsDivPlot-l_graph.R | 1 R/tagsDivPlot-l_hist.R | 1 R/tagsDivPlot-l_plot.R | 4 R/tagsDivPlot-l_serialaxes.R | 1 R/tagsDivSelect-l_serialaxes.R | 1 R/tagsDivSelect.R | 3 R/update_limitSliderInput.R | 9 R/update_sideBarPanel.R | 183 +- R/utils.R | 7 build/vignette.rds |binary inst/doc/introduction.R | 4 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 234 +- man/loon.shiny-package.Rd | 3 man/loon.shiny.Rd | 45 man/shiny.loon-deprecated.Rd | 10 vignettes/introduction.Rmd | 2 83 files changed, 9583 insertions(+), 9469 deletions(-)
Title: The Hyperdirichlet Distribution, Mark 2
Description: A suite of routines for the hyperdirichlet distribution
and reified Bradley-Terry; supersedes the 'hyperdirichlet' package;
uses 'disordR' discipline <doi:10.48550/ARXIV.2210.03856>. To cite
in publications please use Hankin 2017 <doi:10.32614/rj-2017-061>,
and for Generalized Plackett-Luce likelihoods use Hankin 2024
<doi:10.18637/jss.v109.i08>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between hyper2 versions 3.1-0 dated 2024-05-31 and 3.2 dated 2025-11-12
hyper2-3.1-0/hyper2/inst/hyper3.Rmd |only hyper2-3.2/hyper2/DESCRIPTION | 16 - hyper2-3.2/hyper2/MD5 | 206 +++++++------- hyper2-3.2/hyper2/NAMESPACE | 33 +- hyper2-3.2/hyper2/NEWS.md | 4 hyper2-3.2/hyper2/R/hyper2.R | 257 +++++++---------- hyper2-3.2/hyper2/R/hyper3.R | 109 ++++++- hyper2-3.2/hyper2/R/profile.R | 2 hyper2-3.2/hyper2/R/psubs.R | 10 hyper2-3.2/hyper2/R/ranktable.R |only hyper2-3.2/hyper2/R/suppfun.R |only hyper2-3.2/hyper2/README.md | 2 hyper2-3.2/hyper2/build/partial.rdb |binary hyper2-3.2/hyper2/build/vignette.rds |binary hyper2-3.2/hyper2/data/NBA.rda |binary hyper2-3.2/hyper2/data/RCLF.rda |only hyper2-3.2/hyper2/data/T20.rda |binary hyper2-3.2/hyper2/data/baseball.rda |binary hyper2-3.2/hyper2/data/carcinoma.rda |binary hyper2-3.2/hyper2/data/chess.rda |binary hyper2-3.2/hyper2/data/constructor.rda |binary hyper2-3.2/hyper2/data/counterstrike.rda |binary hyper2-3.2/hyper2/data/curling.rda |binary hyper2-3.2/hyper2/data/eurodance.rda |binary hyper2-3.2/hyper2/data/eurovision.rda |binary hyper2-3.2/hyper2/data/formula1.rda |binary hyper2-3.2/hyper2/data/handover.rda |binary hyper2-3.2/hyper2/data/hepatitis.rda |binary hyper2-3.2/hyper2/data/icons.rda |binary hyper2-3.2/hyper2/data/interzonal.rda |binary hyper2-3.2/hyper2/data/javelin.rda |binary hyper2-3.2/hyper2/data/jester.rda |binary hyper2-3.2/hyper2/data/karate.rda |binary hyper2-3.2/hyper2/data/kka.rda |binary hyper2-3.2/hyper2/data/masterchef.rda |binary hyper2-3.2/hyper2/data/moto.rda |binary hyper2-3.2/hyper2/data/pentathlon.rda |binary hyper2-3.2/hyper2/data/powerboat.rda |binary hyper2-3.2/hyper2/data/rowing.rda |binary hyper2-3.2/hyper2/data/skating.rda |binary hyper2-3.2/hyper2/data/soling.rda |binary hyper2-3.2/hyper2/data/surfing.rda |binary hyper2-3.2/hyper2/data/sushi.rda |only hyper2-3.2/hyper2/data/table_tennis.rda |binary hyper2-3.2/hyper2/data/tennis.rda |binary hyper2-3.2/hyper2/data/universities.rda |binary hyper2-3.2/hyper2/data/volleyball.rda |binary hyper2-3.2/hyper2/data/volvo.rda |binary hyper2-3.2/hyper2/inst/cheering.Rmd |only hyper2-3.2/hyper2/inst/cloud9_boston_2018.txt |only hyper2-3.2/hyper2/inst/doc/hyper2.pdf |binary hyper2-3.2/hyper2/inst/doc/hyper3.R |only hyper2-3.2/hyper2/inst/doc/hyper3.Rmd |only hyper2-3.2/hyper2/inst/doc/hyper3.html |only hyper2-3.2/hyper2/inst/doc/hyper3_creation.R |only hyper2-3.2/hyper2/inst/doc/hyper3_creation.Rmd |only hyper2-3.2/hyper2/inst/doc/hyper3_creation.html |only hyper2-3.2/hyper2/inst/doc/icons.R | 34 +- hyper2-3.2/hyper2/inst/doc/icons.Rmd | 5 hyper2-3.2/hyper2/inst/doc/icons.html | 133 ++++----- hyper2-3.2/hyper2/inst/doc/integration.pdf |binary hyper2-3.2/hyper2/inst/doc/ordertrans.R | 42 +- hyper2-3.2/hyper2/inst/doc/ordertrans.Rmd | 5 hyper2-3.2/hyper2/inst/doc/ordertrans.html | 133 +++++---- hyper2-3.2/hyper2/inst/doc/zeropower.R | 17 - hyper2-3.2/hyper2/inst/doc/zeropower.Rmd | 12 hyper2-3.2/hyper2/inst/doc/zeropower.html | 43 +- hyper2-3.2/hyper2/inst/exponential_BT.Rmd |only hyper2-3.2/hyper2/inst/hankin-exponential_BT.tex |only hyper2-3.2/hyper2/inst/jss_hyper3_real.R |only hyper2-3.2/hyper2/inst/jss_hyper3_real.Rnw |only hyper2-3.2/hyper2/inst/oecd.txt |only hyper2-3.2/hyper2/inst/sushi.Rmd |only hyper2-3.2/hyper2/inst/sushi.txt |only hyper2-3.2/hyper2/man/Print.Rd | 22 + hyper2-3.2/hyper2/man/RCLF.Rd |only hyper2-3.2/hyper2/man/balance.Rd | 6 hyper2-3.2/hyper2/man/carcinoma.Rd | 2 hyper2-3.2/hyper2/man/character_to_number.Rd | 8 hyper2-3.2/hyper2/man/dirichlet.Rd | 35 +- hyper2-3.2/hyper2/man/formula1.Rd | 27 + hyper2-3.2/hyper2/man/ggrl.Rd | 42 +- hyper2-3.2/hyper2/man/gradient.Rd | 2 hyper2-3.2/hyper2/man/head.hyper2.Rd | 4 hyper2-3.2/hyper2/man/hyper2-package.Rd | 11 hyper2-3.2/hyper2/man/hyper2.Rd | 5 hyper2-3.2/hyper2/man/hyper3.Rd | 18 - hyper2-3.2/hyper2/man/increment.Rd | 30 +- hyper2-3.2/hyper2/man/loglik.Rd | 15 - hyper2-3.2/hyper2/man/maxp.Rd | 5 hyper2-3.2/hyper2/man/ordertable.Rd | 16 - hyper2-3.2/hyper2/man/ordertable2points.Rd | 1 hyper2-3.2/hyper2/man/ordertable2supp.Rd | 19 - hyper2-3.2/hyper2/man/ordertrans.Rd | 4 hyper2-3.2/hyper2/man/pairwise.Rd | 30 +- hyper2-3.2/hyper2/man/ranktable.Rd | 18 - hyper2-3.2/hyper2/man/rhyper3.Rd | 12 hyper2-3.2/hyper2/man/rrace.Rd | 8 hyper2-3.2/hyper2/man/rrank.Rd | 41 +- hyper2-3.2/hyper2/man/skating.Rd | 2 hyper2-3.2/hyper2/man/suppfun.Rd |only hyper2-3.2/hyper2/man/sushi.Rd |only hyper2-3.2/hyper2/man/tests.Rd | 2 hyper2-3.2/hyper2/man/volleyball.Rd | 5 hyper2-3.2/hyper2/man/volvo.Rd | 3 hyper2-3.2/hyper2/man/zipf.Rd | 6 hyper2-3.2/hyper2/src/RcppExports.cpp | 114 +++---- hyper2-3.2/hyper2/src/hyperdirichlet2.cpp | 26 - hyper2-3.2/hyper2/src/hyperdirichlet3.cpp | 34 +- hyper2-3.2/hyper2/tests/testthat/test_dirichlet.R |only hyper2-3.2/hyper2/tests/testthat/test_hyper3.R | 1 hyper2-3.2/hyper2/vignettes/hyper2.bib | 320 +++++++++++++++++++++- hyper2-3.2/hyper2/vignettes/hyper3.Rmd |only hyper2-3.2/hyper2/vignettes/hyper3_creation.Rmd |only hyper2-3.2/hyper2/vignettes/icons.Rmd | 5 hyper2-3.2/hyper2/vignettes/ordertrans.Rmd | 5 hyper2-3.2/hyper2/vignettes/zeropower.Rmd | 12 117 files changed, 1255 insertions(+), 724 deletions(-)
Title: Explore the Innards of 'ggplot2' Objects
Description: Extensions to 'ggplot2' providing low-level debug tools: statistics
and geometries echoing their data argument. Layer manipulation: deletion,
insertion, extraction and reordering of layers. Deletion of unused variables
from the data object embedded in "ggplot" objects.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between gginnards versions 0.2.0-1 dated 2024-11-13 and 0.2.0-2 dated 2025-11-12
DESCRIPTION | 17 MD5 | 50 - NEWS.md | 8 R/data-manip.R | 5 R/gg-structure.R | 9 R/gginnards.R | 2 R/layer-manip.R | 14 R/stat-debug.R | 4 README.md | 113 +-- build/vignette.rds |binary inst/doc/user-guide-1.R | 6 inst/doc/user-guide-1.Rmd | 38 - inst/doc/user-guide-1.html | 1124 +++++++++++++++++++++++++------ inst/doc/user-guide-2.R | 14 inst/doc/user-guide-2.Rmd | 24 inst/doc/user-guide-2.html | 154 ++-- man/delete_layers.Rd | 14 man/drop_vars.Rd | 5 man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-6-2.png |binary man/gginnards-package.Rd | 2 man/stat_debug_group.Rd | 4 man/str.Rd | 9 vignettes/user-guide-1.Rmd | 38 - vignettes/user-guide-2.Rmd | 24 26 files changed, 1269 insertions(+), 409 deletions(-)
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.12/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.7.1 dated 2025-10-01 and 1.7.2 dated 2025-11-12
CFtime-1.7.1/CFtime/R/deprecated.R |only CFtime-1.7.1/CFtime/man/deprecated_functions.Rd |only CFtime-1.7.2/CFtime/DESCRIPTION | 11 - CFtime-1.7.2/CFtime/MD5 | 25 +- CFtime-1.7.2/CFtime/NAMESPACE | 2 CFtime-1.7.2/CFtime/NEWS.md | 10 + CFtime-1.7.2/CFtime/R/CFCalendar.R | 156 +++++++++++----- CFtime-1.7.2/CFtime/R/CFtime.R | 50 +++-- CFtime-1.7.2/CFtime/R/zzz.R | 7 CFtime-1.7.2/CFtime/man/CFCalendar.Rd | 43 ++-- CFtime-1.7.2/CFtime/man/CFTime.Rd | 4 CFtime-1.7.2/CFtime/man/CFtime-package.Rd | 1 CFtime-1.7.2/CFtime/man/sub-.CFTime.Rd |only CFtime-1.7.2/CFtime/tests/testthat/test-CFClimatology.R | 4 CFtime-1.7.2/CFtime/tests/testthat/test-CFbounds.R | 8 15 files changed, 210 insertions(+), 111 deletions(-)
Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute
distance, correlation, auto correlation, clustering and other tasks.
Contains graph clustering algorithm described in "MetaCell: analysis
of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran,
Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad
Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay,
2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman [aut],
Aviezer Lifshitz [aut, cre]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between tgstat versions 2.3.28 dated 2024-09-23 and 2.3.29 dated 2025-11-12
DESCRIPTION | 6 - MD5 | 8 - NEWS.md | 4 inst/doc/manual.html | 240 ++++++++++++++++++++++++++++++++++++++++++++++++--- src/tgstat.cpp | 6 - 5 files changed, 241 insertions(+), 23 deletions(-)
Title: Simulation, Visualization and Comparison of Tumor Evolution Data
Description: Simulating, visualizing and comparing tumor clonal data by using simple commands. This aims at providing a tool to help researchers to easily simulate tumor data and analyze the results of their approaches for studying the composition and the evolutionary history of tumors.
Author: Aitor Sanchez-Ferrera [cre, aut] ,
Maitena Tellaetxe-Abete [aut] ,
Borja Calvo [aut]
Maintainer: Aitor Sanchez-Ferrera <aitor.sanchezf@ehu.eus>
Diff between GeRnika versions 1.1.0 dated 2025-03-27 and 1.2.0 dated 2025-11-12
DESCRIPTION | 15 - MD5 | 22 - R/generate_instances.R | 9 R/phylotree_class.R | 4 R/tree.R | 8 inst/doc/models.R | 2 inst/doc/models.Rmd | 621 ++++++++++++++++++++++++------------------------- inst/doc/models.html | 10 inst/doc/usage.R | 24 - inst/doc/usage.html | 55 ++-- man/add_noise.Rd | 4 vignettes/models.Rmd | 621 ++++++++++++++++++++++++------------------------- 12 files changed, 701 insertions(+), 694 deletions(-)
Title: Geospatial Semantic Segmentation with Torch and Terra
Description: Provides tools for semantic segmentation of geospatial data using convolutional neural
network-based deep learning. Utility functions allow for creating masks, image chips, data frames listing image
chips in a directory, and DataSets for use within DataLoaders. Additional functions are provided to serve as checks
during the data preparation and training process. A UNet architecture can be defined with 4 blocks in the encoder, a
bottleneck block, and 4 blocks in the decoder. The UNet can accept a variable number of input channels, and the user
can define the number of feature maps produced in each encoder and decoder block and the bottleneck. Users can also
choose to (1) replace all rectified linear unit (ReLU) activation functions with leaky ReLU or swish, (2) implement attention gates along the
skip connections, (3) implement squeeze and excitation modules within the encoder blocks, (4) add residual connections
within all blocks, (5) replace the bottleneck with a modified atrous spati [...truncated...]
Author: Aaron Maxwell [aut, cre, cph],
Sarah Farhadpour [aut],
Srinjoy Das [aut],
Yalin Yang [aut]
Maintainer: Aaron Maxwell <Aaron.Maxwell@mail.wvu.edu>
Diff between geodl versions 0.2.0 dated 2024-08-20 and 0.3.0 dated 2025-11-12
geodl-0.2.0/geodl/R/makeTerrainDerivatives.R |only geodl-0.2.0/geodl/R/unetModels.R |only geodl-0.2.0/geodl/build |only geodl-0.2.0/geodl/inst |only geodl-0.2.0/geodl/man/makeTerrainDerivatives.Rd |only geodl-0.2.0/geodl/vignettes |only geodl-0.3.0/geodl/DESCRIPTION | 23 - geodl-0.3.0/geodl/MD5 | 185 ++++------------ geodl-0.3.0/geodl/NAMESPACE | 22 + geodl-0.3.0/geodl/NEWS.md | 22 + geodl-0.3.0/geodl/R/assessDL.R | 46 ++- geodl-0.3.0/geodl/R/assessPnts.R | 2 geodl-0.3.0/geodl/R/checkDynamicChips.R |only geodl-0.3.0/geodl/R/defineDynamicSegDataSet.R |only geodl-0.3.0/geodl/R/defineSegDataSet.R | 12 + geodl-0.3.0/geodl/R/globals.R | 2 geodl-0.3.0/geodl/R/luzMetrics.R | 136 +++++++---- geodl-0.3.0/geodl/R/makeChips.R | 30 +- geodl-0.3.0/geodl/R/makeChipsMultiClass.R | 14 + geodl-0.3.0/geodl/R/makeDynamicChipsSF.R |only geodl-0.3.0/geodl/R/makeLSPs.R |only geodl-0.3.0/geodl/R/makeMasks.R | 6 geodl-0.3.0/geodl/R/predictSpatial.R | 18 + geodl-0.3.0/geodl/R/saveDynamicChips.R |only geodl-0.3.0/geodl/R/segModels.R |only geodl-0.3.0/geodl/R/terrainSegModel.R |only geodl-0.3.0/geodl/R/unifiedFocalLoss.R | 26 +- geodl-0.3.0/geodl/R/utilities.R |only geodl-0.3.0/geodl/R/viewBatch.R | 29 ++ geodl-0.3.0/geodl/R/viewBatchPreds.R | 122 +++++++--- geodl-0.3.0/geodl/R/viewChips.R | 39 +++ geodl-0.3.0/geodl/README.md | 38 ++- geodl-0.3.0/geodl/man/assessDL.Rd | 27 +- geodl-0.3.0/geodl/man/assessPnts.Rd | 2 geodl-0.3.0/geodl/man/callback_save_model_state_dict.Rd |only geodl-0.3.0/geodl/man/checkDynamicChips.Rd |only geodl-0.3.0/geodl/man/countParams.Rd |only geodl-0.3.0/geodl/man/defineDynmamicSegDataSet.Rd |only geodl-0.3.0/geodl/man/defineMobileUNet.Rd | 52 ++-- geodl-0.3.0/geodl/man/defineSegDataSet.Rd | 5 geodl-0.3.0/geodl/man/defineTerrainSeg.Rd |only geodl-0.3.0/geodl/man/defineUNet.Rd | 55 ++-- geodl-0.3.0/geodl/man/defineUNet3p.Rd |only geodl-0.3.0/geodl/man/defineUnifiedFocalLoss.Rd | 15 + geodl-0.3.0/geodl/man/defineUnifiedFocalLossDS.Rd | 4 geodl-0.3.0/geodl/man/luz_metric_f1score.Rd | 8 geodl-0.3.0/geodl/man/luz_metric_overall_accuracy.Rd | 8 geodl-0.3.0/geodl/man/luz_metric_precision.Rd | 10 geodl-0.3.0/geodl/man/luz_metric_recall.Rd | 10 geodl-0.3.0/geodl/man/makeAspect.Rd |only geodl-0.3.0/geodl/man/makeCrv.Rd |only geodl-0.3.0/geodl/man/makeDynamicChipsSF.Rd |only geodl-0.3.0/geodl/man/makeHillshade.Rd |only geodl-0.3.0/geodl/man/makeSlope.Rd |only geodl-0.3.0/geodl/man/makeTPI.Rd |only geodl-0.3.0/geodl/man/makeTRI.Rd |only geodl-0.3.0/geodl/man/makeTerrainVisTerra.Rd |only geodl-0.3.0/geodl/man/makeTerrainVisTorch.Rd |only geodl-0.3.0/geodl/man/predictSpatial.Rd | 11 geodl-0.3.0/geodl/man/saveDynamicChips.Rd |only geodl-0.3.0/geodl/man/viewBatch.Rd | 18 + geodl-0.3.0/geodl/man/viewBatchPreds.Rd | 3 geodl-0.3.0/geodl/man/viewChips.Rd | 5 63 files changed, 650 insertions(+), 355 deletions(-)
Title: Cohort Generation for the OMOP Common Data Model
Description: Generate cohorts and subsets using an Observational
Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database.
Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or
SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).
Author: Anthony Sena [aut, cre],
Jamie Gilbert [aut],
Gowtham Rao [aut],
Freddy Avila Cruz [aut],
Martijn Schuemie [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Anthony Sena <sena@ohdsi.org>
Diff between CohortGenerator versions 0.12.2 dated 2025-09-11 and 1.0.0 dated 2025-11-12
CohortGenerator-0.12.2/CohortGenerator/man/getRequiredTasks.Rd |only CohortGenerator-0.12.2/CohortGenerator/man/isTaskRequired.Rd |only CohortGenerator-0.12.2/CohortGenerator/man/recordTasksDone.Rd |only CohortGenerator-0.12.2/CohortGenerator/man/saveIncremental.Rd |only CohortGenerator-0.12.2/CohortGenerator/tests/testthat/test-Incremental.R |only CohortGenerator-1.0.0/CohortGenerator/DESCRIPTION | 20 CohortGenerator-1.0.0/CohortGenerator/MD5 | 179 ++-- CohortGenerator-1.0.0/CohortGenerator/NAMESPACE | 25 CohortGenerator-1.0.0/CohortGenerator/NEWS.md | 21 CohortGenerator-1.0.0/CohortGenerator/R/CohortConstruction.R | 413 ++++++---- CohortGenerator-1.0.0/CohortGenerator/R/CohortDefinitionSet.R | 20 CohortGenerator-1.0.0/CohortGenerator/R/CohortSample.R | 74 + CohortGenerator-1.0.0/CohortGenerator/R/CohortTables.R | 9 CohortGenerator-1.0.0/CohortGenerator/R/Export.R | 141 ++- CohortGenerator-1.0.0/CohortGenerator/R/Incremental.R | 181 ---- CohortGenerator-1.0.0/CohortGenerator/R/NegativeControlCohorts.R | 108 +- CohortGenerator-1.0.0/CohortGenerator/R/ResultsDataModel.R | 6 CohortGenerator-1.0.0/CohortGenerator/R/RunCohortGeneration.R | 60 - CohortGenerator-1.0.0/CohortGenerator/R/SubsetDefinitions.R | 48 - CohortGenerator-1.0.0/CohortGenerator/R/SubsetQueryBuilders.R | 26 CohortGenerator-1.0.0/CohortGenerator/R/SubsetRecipeFunctions.R |only CohortGenerator-1.0.0/CohortGenerator/R/Subsets.R | 113 ++ CohortGenerator-1.0.0/CohortGenerator/R/TemplateCohorts.R |only CohortGenerator-1.0.0/CohortGenerator/R/TemplateImplementations.R |only CohortGenerator-1.0.0/CohortGenerator/R/TemplateUnion.R |only CohortGenerator-1.0.0/CohortGenerator/R/ValidateCohort.R |only CohortGenerator-1.0.0/CohortGenerator/README.md | 9 CohortGenerator-1.0.0/CohortGenerator/build/vignette.rds |binary CohortGenerator-1.0.0/CohortGenerator/inst/csv/resultsDataModelSpecification.csv | 11 CohortGenerator-1.0.0/CohortGenerator/inst/doc/CreatingCohortSubsetDefinitions.R | 6 CohortGenerator-1.0.0/CohortGenerator/inst/doc/CreatingCohortSubsetDefinitions.Rmd | 9 CohortGenerator-1.0.0/CohortGenerator/inst/doc/CreatingCohortSubsetDefinitions.html | 12 CohortGenerator-1.0.0/CohortGenerator/inst/doc/GeneratingCohorts.R | 6 CohortGenerator-1.0.0/CohortGenerator/inst/doc/GeneratingCohorts.Rmd | 15 CohortGenerator-1.0.0/CohortGenerator/inst/doc/GeneratingCohorts.pdf |binary CohortGenerator-1.0.0/CohortGenerator/inst/doc/SamplingCohorts.R | 9 CohortGenerator-1.0.0/CohortGenerator/inst/doc/SamplingCohorts.Rmd | 9 CohortGenerator-1.0.0/CohortGenerator/inst/doc/SamplingCohorts.pdf |binary CohortGenerator-1.0.0/CohortGenerator/inst/doc/UsingTemplateCohorts.R |only CohortGenerator-1.0.0/CohortGenerator/inst/doc/UsingTemplateCohorts.Rmd |only CohortGenerator-1.0.0/CohortGenerator/inst/doc/UsingTemplateCohorts.html |only CohortGenerator-1.0.0/CohortGenerator/inst/sql/sql_server/CreateCohortTables.sql | 15 CohortGenerator-1.0.0/CohortGenerator/inst/sql/sql_server/ValidateCohorts.sql |only CohortGenerator-1.0.0/CohortGenerator/inst/sql/sql_server/migrations/Migration_2-v0.12.0.sql | 4 CohortGenerator-1.0.0/CohortGenerator/inst/sql/sql_server/migrations/Migration_3-v1.0.0.sql |only CohortGenerator-1.0.0/CohortGenerator/inst/sql/sql_server/subsets/LimitSubsetOperator.sql | 3 CohortGenerator-1.0.0/CohortGenerator/inst/sql/sql_server/templates |only CohortGenerator-1.0.0/CohortGenerator/inst/testdata/Results_Eunomia.zip |binary CohortGenerator-1.0.0/CohortGenerator/inst/testdata/negativecontrols/negativeControlOutcomes.csv | 18 CohortGenerator-1.0.0/CohortGenerator/man/CohortSubsetDefinition.Rd | 18 CohortGenerator-1.0.0/CohortGenerator/man/CohortSubsetOperator.Rd | 3 CohortGenerator-1.0.0/CohortGenerator/man/CohortTemplateDefinition.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/DemographicSubsetOperator.Rd | 1 CohortGenerator-1.0.0/CohortGenerator/man/LimitSubsetOperator.Rd | 3 CohortGenerator-1.0.0/CohortGenerator/man/SubsetOperator.Rd | 18 CohortGenerator-1.0.0/CohortGenerator/man/addCohortTemplateDefintion.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/addExcludeOnIndexSubsetDefinition.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/addIndicationSubsetDefinition.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/addRestrictionSubsetDefinition.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/addSqlCohortDefinition.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/addUnionCohortDefinition.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/computeChecksum.Rd | 1 CohortGenerator-1.0.0/CohortGenerator/man/createAtcCohortTemplateDefinition.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/createCohortSubset.Rd | 36 CohortGenerator-1.0.0/CohortGenerator/man/createCohortSubsetDefinition.Rd | 10 CohortGenerator-1.0.0/CohortGenerator/man/createCohortSubsetOperator.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/createCohortTemplateDefintion.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/createDemographicSubset.Rd | 29 CohortGenerator-1.0.0/CohortGenerator/man/createDemographicSubsetOperator.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/createLimitSubset.Rd | 38 CohortGenerator-1.0.0/CohortGenerator/man/createLimitSubsetOperator.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/createRxNormCohortTemplateDefinition.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/createSnomedCohortTemplateDefinition.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/createUnionCohortTemplate.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/exportCohortStatsTables.Rd | 2 CohortGenerator-1.0.0/CohortGenerator/man/generateCohortSet.Rd | 2 CohortGenerator-1.0.0/CohortGenerator/man/generateNegativeControlOutcomeCohorts.Rd | 8 CohortGenerator-1.0.0/CohortGenerator/man/getCohortDefinitionSet.Rd | 4 CohortGenerator-1.0.0/CohortGenerator/man/getCohortTableNames.Rd | 5 CohortGenerator-1.0.0/CohortGenerator/man/getCohortValidationCounts.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/getDataMigrator.Rd | 2 CohortGenerator-1.0.0/CohortGenerator/man/getExcludeOnIndexSubsetDefinitionIds.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/getIndicationSubsetDefinitionIds.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/getLastGeneratedCohortChecksums.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/getRestrictionSubsetDefinitionIds.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/getTemplateDefinitions.Rd |only CohortGenerator-1.0.0/CohortGenerator/man/migrateDataModel.Rd | 2 CohortGenerator-1.0.0/CohortGenerator/man/runCohortGeneration.Rd | 2 CohortGenerator-1.0.0/CohortGenerator/man/sampleCohortDefinitionSet.Rd | 2 CohortGenerator-1.0.0/CohortGenerator/man/saveCohortDefinitionSet.Rd | 4 CohortGenerator-1.0.0/CohortGenerator/tests/testthat/errorReportSql.txt |only CohortGenerator-1.0.0/CohortGenerator/tests/testthat/setup.R | 2 CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-ChecksumTable.R |only CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-CohortConstructionAndStats.R | 45 - CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-CohortSample.R | 41 CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-CohortTables.R | 9 CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-Export.R | 29 CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-NegativeControlCohorts.R | 24 CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-ResultsDataModel.R | 157 ++- CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-SubsetOperations.R | 30 CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-SubsetRecipies.R |only CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-Subsets.R | 100 +- CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-TemplateCohorts.R |only CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-TemplateImplementations.R |only CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-ValidateCohorts.R |only CohortGenerator-1.0.0/CohortGenerator/tests/testthat/test-dbms-platforms.R | 6 CohortGenerator-1.0.0/CohortGenerator/vignettes/CreatingCohortSubsetDefinitions.Rmd | 9 CohortGenerator-1.0.0/CohortGenerator/vignettes/GeneratingCohorts.Rmd | 15 CohortGenerator-1.0.0/CohortGenerator/vignettes/SamplingCohorts.Rmd | 9 CohortGenerator-1.0.0/CohortGenerator/vignettes/UsingTemplateCohorts.Rmd |only 110 files changed, 1277 insertions(+), 959 deletions(-)
More information about CohortGenerator at CRAN
Permanent link
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steve@svmiller.com>
Diff between stevedata versions 1.7.0 dated 2025-09-17 and 1.8.0 dated 2025-11-12
DESCRIPTION | 6 +++--- MD5 | 23 +++++++++++++---------- NEWS.md | 11 +++++++++++ R/rd-AJR5.R | 3 +-- R/rd-coffee_imports.R | 30 ++++++++++++++++++++++++------ R/rd-epl_odds.R | 2 +- R/rd-postcol_growth.R |only build/partial.rdb |binary data/coffee_imports.rda |binary data/postcol_growth.rda |only man/AJR5.Rd | 3 +-- man/coffee_imports.Rd | 28 ++++++++++++++++++++++------ man/epl_odds.Rd | 4 +--- man/postcol_growth.Rd |only 14 files changed, 77 insertions(+), 33 deletions(-)
Title: Access to Spanish Meteorological Stations Services
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG,
Meteoclimatic...).
Author: Victor Granda [aut, cre] ,
Miquel de Caceres [ctb] ,
Aitor Ameztegui [ctb] ,
Luis Franco [ctb],
Ruben Fernandez-Casal [ctb]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Diff between meteospain versions 0.2.2 dated 2025-10-01 and 0.3.0 dated 2025-11-12
DESCRIPTION | 16 MD5 | 58 +- NEWS.md | 12 R/aemet_helpers.R | 403 +++++------------- R/get_data.R | 8 R/meteocat_helpers.R | 482 +++++++++------------- R/meteoclimatic_helpers.R | 70 ++- R/meteogalicia_helpers.R | 205 ++++----- R/ria_helpers.R | 250 ++++------- R/services_options.R | 8 R/utils.R | 135 ------ build/vignette.rds |binary inst/doc/aemet.Rmd | 2 inst/doc/aemet.html | 68 +-- inst/doc/api_limits.html | 890 ++++++++++++++++++++++------------------- inst/doc/compatibility.Rmd | 1 inst/doc/compatibility.html | 166 ++++--- inst/doc/meteocat.html | 10 inst/doc/meteoclimatic.html | 44 +- inst/doc/meteogalicia.html | 20 inst/doc/ria.html | 174 +++----- man/get_meteo_from.Rd | 2 man/get_quota_from.Rd | 2 man/get_stations_info_from.Rd | 2 man/services_options.Rd | 8 tests/testthat/test-aemet.R | 7 tests/testthat/test-meteocat.R | 10 tests/testthat/test-riaa.R | 8 vignettes/aemet.Rmd | 2 vignettes/compatibility.Rmd | 1 30 files changed, 1419 insertions(+), 1645 deletions(-)
Title: 'shiny' Application for Statistical Test Assumption Checking and
Guidance
Description: A 'shiny' application to assess statistical assumptions and guide users toward appropriate tests. The app is designed for researchers with minimal statistical training and provides diagnostics, plots, and test recommendations for a wide range of analyses. Many statistical assumptions are implemented using the package 'rstatix' (Kassambara, 2019) <doi:10.32614/CRAN.package.rstatix> and 'performance' (Lüdecke et al., 2021) <doi:10.21105/joss.03139>.
Author: Ahmed Bargheet [aut, cre]
Maintainer: Ahmed Bargheet <ahmed.bargheet@yahoo.com>
Diff between AssumpSure versions 1.1.2 dated 2025-10-19 and 1.1.3 dated 2025-11-12
AssumpSure-1.1.2/AssumpSure/inst/extdata/One-way_ANOVA.csv |only AssumpSure-1.1.2/AssumpSure/inst/extdata/starwar.csv |only AssumpSure-1.1.2/AssumpSure/inst/extdata/t-test_1.csv |only AssumpSure-1.1.3/AssumpSure/DESCRIPTION | 26 AssumpSure-1.1.3/AssumpSure/MD5 | 49 - AssumpSure-1.1.3/AssumpSure/NAMESPACE | 9 AssumpSure-1.1.3/AssumpSure/NEWS.md | 8 AssumpSure-1.1.3/AssumpSure/R/bacteria_for_correlation.R |only AssumpSure-1.1.3/AssumpSure/R/chi_fisher.R |only AssumpSure-1.1.3/AssumpSure/R/correlation.R |only AssumpSure-1.1.3/AssumpSure/R/infants.R |only AssumpSure-1.1.3/AssumpSure/R/launch_app.R | 2 AssumpSure-1.1.3/AssumpSure/R/plantgrowth.R |only AssumpSure-1.1.3/AssumpSure/R/stat_tests.R |only AssumpSure-1.1.3/AssumpSure/R/t-test.R |only AssumpSure-1.1.3/AssumpSure/R/zzz.R | 2 AssumpSure-1.1.3/AssumpSure/inst/CITATION |only AssumpSure-1.1.3/AssumpSure/inst/app/app.R | 313 ++++--- AssumpSure-1.1.3/AssumpSure/inst/app/www/infants.csv |only AssumpSure-1.1.3/AssumpSure/inst/extdata/infants.csv | 500 ++++++------ AssumpSure-1.1.3/AssumpSure/inst/extdata/plantgrowth.csv |only AssumpSure-1.1.3/AssumpSure/inst/extdata/t-test.csv | 100 ++ AssumpSure-1.1.3/AssumpSure/man/bacteria_for_correlation.Rd |only AssumpSure-1.1.3/AssumpSure/man/chi_fisher.Rd |only AssumpSure-1.1.3/AssumpSure/man/correlation.Rd |only AssumpSure-1.1.3/AssumpSure/man/infants.Rd |only AssumpSure-1.1.3/AssumpSure/man/plantgrowth.Rd |only AssumpSure-1.1.3/AssumpSure/man/t-test.Rd |only AssumpSure-1.1.3/AssumpSure/tests |only 29 files changed, 601 insertions(+), 408 deletions(-)
Title: Genotype by Environment (GxE) Analysis
Description: Analysis of multi environment data of plant breeding experiments
following the analyses described in Malosetti, Ribaut,
and van Eeuwijk (2013), <doi:10.3389/fphys.2013.00044>.
One of a series of statistical genetic packages for streamlining the analysis of
typical plant breeding experiments developed by Biometris.
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Bart-Jan van Rossum [aut, cre] ,
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb] ,
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie J Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Willem Kruijer [ctb] ,
Ron Wehrens [ctb] ,
Choazhi [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGxE versions 1.0.10 dated 2025-06-24 and 1.0.11 dated 2025-11-12
DESCRIPTION | 33 ++++++++++++------ MD5 | 24 ++++++------- NEWS.md | 4 ++ R/createVarComp.R | 68 +++++++++++++++++++++++++++++++++------ R/gxeVarComp.R | 1 README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/statgenGxE.html | 35 ++++++++++---------- man/herit.Rd | 21 ++++++++---- man/statgenGxE-package.Rd | 6 ++- tests/testthat/Rplots.pdf |binary tests/testthat/test-gxeVarComp.R | 36 ++++++++++---------- 13 files changed, 154 insertions(+), 76 deletions(-)
Title: Makefile Generator for R Analytical Projects
Description: Creates and maintains a build process for complex analytic tasks in R.
Package allows to easily generate Makefile for the (GNU) 'make' tool, which drives the build process
by (in parallel) executing build commands in order to update results accordingly to given dependencies
on changed data or updated source files.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between rmake versions 1.2.0 dated 2025-08-26 and 1.2.1 dated 2025-11-12
DESCRIPTION | 12 - MD5 | 101 +++++++-------- NAMESPACE | 2 NEWS.md | 9 - R/copyRule.R | 12 - R/depRule.R | 8 - R/expandTemplate.R | 20 +-- R/getParam.R | 10 - R/getters.R | 6 R/inShell.R | 20 +-- R/is.rule.R | 6 R/knitrRule.R | 20 +-- R/make.R | 16 +- R/makefile.R | 48 +++---- R/markdownRule.R | 20 +-- R/offlineRule.R | 14 +- R/pipe.R | 2 R/rRule.R | 22 +-- R/replaceSuffix.R | 6 R/replaceVariables.R | 4 R/rmake.R | 24 +-- R/rmakeSkeleton.R | 2 R/rule.R | 28 ++-- R/subdirRule.R | 12 - inst/doc/rmake-intro.Rnw | 166 ++++++++++++------------- inst/doc/rmake-intro.pdf |binary man/copyRule.Rd | 12 - man/defaultVars.Rd | 6 man/depRule.Rd | 8 - man/expandTemplate.Rd | 20 +-- man/getParam.Rd | 10 - man/grapes-greater-than-greater-than-grapes.Rd | 2 man/inShell.Rd | 8 - man/is.rule.Rd | 6 man/knitrRule.Rd | 20 +-- man/make.Rd | 19 +- man/makefile.Rd | 42 +++--- man/markdownRule.Rd | 20 +-- man/offlineRule.Rd | 14 +- man/prerequisites.Rd | 2 man/rRule.Rd | 22 +-- man/replaceSuffix.Rd | 6 man/replaceVariables.Rd | 4 man/rmake-package.Rd | 24 +-- man/rmakeSkeleton.Rd | 2 man/rule.Rd | 28 ++-- man/subdirRule.Rd | 12 - tests/testthat/test-inShell.R |only tests/testthat/test-run-simple.R | 15 +- tests/testthat/test-run-subdir.R | 8 - tests/testthat/test-run-tasks.R | 10 - vignettes/rmake-intro.Rnw | 166 ++++++++++++------------- 52 files changed, 544 insertions(+), 532 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation of hash
digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32',
'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128'
algorithms) permitting easy comparison of R language objects, as well as functions
such as 'hmac()' to create hash-based message authentication code. Please note that
this package is not meant to be deployed for cryptographic purposes for which more
comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel [aut, cre] ,
Antoine Lucas [ctb] ,
Jarek Tuszynski [ctb],
Henrik Bengtsson [ctb] ,
Simon Urbanek [ctb] ,
Mario Frasca [ctb],
Bryan Lewis [ctb],
Murray Stokely [ctb],
Hannes Muehleisen [ctb] ,
Duncan Murdoch [ctb],
Jim Hester [ctb] , [...truncated...]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.37 dated 2024-08-19 and 0.6.38 dated 2025-11-12
ChangeLog | 146 +++++++++++++++ DESCRIPTION | 97 +++++----- MD5 | 51 ++--- NAMESPACE | 2 R/digest.R | 19 + R/sha1.R | 18 - R/vdigest.R | 6 README.md | 8 build/vignette.rds |binary inst/CITATION |only inst/doc/sha1.html | 4 inst/doc/sha1.md | 2 inst/tinytest/test_digest.R | 11 + inst/tinytest/test_raw.R | 14 + inst/tinytest/test_sha1.R | 21 ++ man/digest.Rd | 14 - man/hmac.Rd | 15 - man/sha1.Rd | 19 + src/blake3.c | 154 ++++++++++----- src/blake3.h | 65 ++++-- src/blake3_dispatch.c | 341 +++++++++++++++++++++-------------- src/blake3_impl.h | 105 +++++++++- src/blake3_portability.h |only src/blake3_portable.c | 8 src/digest.c | 424 ++++++++++++++++++++++++-------------------- src/digest.h |only src/init.c | 1 vignettes/sha1.md | 2 28 files changed, 1006 insertions(+), 541 deletions(-)
Title: Transfer Graph Learning
Description: Transfer learning, aiming to use auxiliary domains to help improve learning of the target domain of interest when multiple heterogeneous datasets are available, has been a hot topic in statistical machine learning. The recent transfer learning methods with statistical guarantees mainly focus on the overall parameter transfer for supervised models in the ideal case with the informative auxiliary domains with overall similarity. In contrast, transfer learning for unsupervised graph learning is in its infancy and largely follows the idea of overall parameter transfer as for supervised learning.
In this package, the transfer learning for several complex graphical models is implemented, including Tensor Gaussian graphical models, non-Gaussian directed acyclic graph (DAG), and Gaussian graphical mixture models. Notably, this package promotes local transfer at node-level and subgroup-level in DAG structural learning and Gaussian graphical mixture models, respectively, which are more flexible [...truncated...]
Author: Mingyang Ren [aut, cre] ,
Ruixuan Zhao [aut],
Xin He [aut],
Junhui Wang [aut]
Maintainer: Mingyang Ren <renmingyang17@mails.ucas.ac.cn>
Diff between TransGraph versions 1.0.0 dated 2023-10-19 and 1.1.0 dated 2025-11-12
TransGraph-1.0.0/TransGraph/R/support_functions_TensorGGM.R |only TransGraph-1.0.0/TransGraph/R/tensor.GGM.trans.R |only TransGraph-1.0.0/TransGraph/build |only TransGraph-1.0.0/TransGraph/inst |only TransGraph-1.0.0/TransGraph/man/tensor.GGM.trans.Rd |only TransGraph-1.0.0/TransGraph/vignettes |only TransGraph-1.1.0/TransGraph/DESCRIPTION | 26 +- TransGraph-1.1.0/TransGraph/MD5 | 34 +-- TransGraph-1.1.0/TransGraph/NAMESPACE | 5 TransGraph-1.1.0/TransGraph/R/TLLiNGAM.R | 2 TransGraph-1.1.0/TransGraph/R/Theta.tuning.R | 2 TransGraph-1.1.0/TransGraph/R/support_functions_GGM.R | 65 ++++- TransGraph-1.1.0/TransGraph/R/support_functions_GGMM.R | 56 ++++- TransGraph-1.1.0/TransGraph/R/trans.local.DAG.R | 22 - TransGraph-1.1.0/TransGraph/R/trans_GGMM.R | 16 + TransGraph-1.1.0/TransGraph/R/trans_precision.R | 133 +++--------- TransGraph-1.1.0/TransGraph/man/TLLiNGAM.Rd | 5 TransGraph-1.1.0/TransGraph/man/trans.local.DAG.Rd | 25 -- TransGraph-1.1.0/TransGraph/man/trans_precision.Rd | 38 --- 19 files changed, 183 insertions(+), 246 deletions(-)
Title: Estimating Hidden Population Size using Respondent Driven
Sampling Data
Description: Estimate the size of a networked population based on
respondent-driven sampling data. The package is part of the "RDS Analyst"
suite of packages for the analysis of respondent-driven sampling data.
See Handcock, Gile and Mar (2014) <doi:10.1214/14-EJS923>,
Handcock, Gile and Mar (2015) <doi:10.1111/biom.12255>,
Kim and Handcock (2021) <doi:10.1093/jssam/smz055>, and
McLaughlin, et. al. (2023) <doi:10.1214/23-AOAS1807>.
Author: Mark S. Handcock [aut, cre, cph] ,
Krista J. Gile [aut, cph],
Brian Kim [ctb],
Katherine R. McLaughlin [ctb]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between sspse versions 1.1.0-4 dated 2025-11-06 and 1.1.0-6 dated 2025-11-12
DESCRIPTION | 8 MD5 | 22 - R/plot.sspse.R | 3 R/poscmp.R | 10 R/poscmpwp.R | 663 +++++++++++++++++++++++------------------------ R/posteriorsize.R | 166 ++++++----- src/posteriorcmp2.c | 171 ++++++------ src/posteriorcmp2.h | 8 src/posteriorcmpwpvis.c | 87 +++--- src/posteriorcmpwpvis.h | 6 src/posteriorcmpwpvis2.c | 365 +++++++++++++++---------- src/posteriorcmpwpvis2.h | 10 12 files changed, 802 insertions(+), 717 deletions(-)
Title: In-Text Resize for Images, Tables and Fancy Resize Containers in
'shiny', 'rmarkdown' and 'quarto' Documents
Description: Offers a suite of tools designed to enhance the responsiveness and interactivity of web-based documents and applications created with R. It provides an automatic, configurable resizing toolbar that can be seamlessly integrated with HTML elements such as containers, images, and tables, allowing end-users to dynamically adjust their dimensions. Beyond the toolbar, the package includes a rich collection of flexible, expandable, and interactive container functionalities, such as highly customizable split-screen layouts (splitCard), versatile sizeable cards (sizeableCard), dynamic window-like elements (windowCard), visually engaging emphasis cards (empahsisCard), and sophisticated flexible and elastic card layouts (flexCard, elastiCard). Furthermore, it offers an elegant image viewer and resizer (shinyExpandImage) perfect for interactive galleries. r2resize is particularly well-suited for developers and data scientists looking to create modern, responsive, and user-friendly 'shiny' applicat [...truncated...]
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between r2resize versions 1.9.2 dated 2024-11-25 and 2.0 dated 2025-11-12
DESCRIPTION | 11 MD5 | 126 NEWS.md | 116 R/addJquery.R | 54 R/containerResizer.R | 489 +-- R/markdownResizer.R | 172 - R/novoImageResizer.R | 134 R/r2resize-package.R | 7 R/sliderCards.R | 279 + README.md | 312 - build/vignette.rds |binary inst/doc/example_frequently_asked_r2resize.R | 24 inst/doc/example_frequently_asked_r2resize.Rmd | 476 +- inst/doc/example_frequently_asked_r2resize.html | 318 - inst/doc/introduction_r2resize.Rmd | 120 inst/doc/introduction_r2resize.html | 32 inst/doc/r2resize-flexible-elastic-cards.R |only inst/doc/r2resize-flexible-elastic-cards.Rmd |only inst/doc/r2resize-flexible-elastic-cards.html |only inst/doc/r2resize-image-and-markdown-resizing.R |only inst/doc/r2resize-image-and-markdown-resizing.Rmd |only inst/doc/r2resize-image-and-markdown-resizing.html |only inst/doc/r2resize-resizable-containers.R |only inst/doc/r2resize-resizable-containers.Rmd |only inst/doc/r2resize-resizable-containers.html |only inst/doc/resizable_containers_split_screen_r2resize.Rmd | 162 - inst/doc/resizable_containers_split_screen_r2resize.html | 44 inst/doc/split_card_html_r2resize.Rmd | 174 - inst/doc/split_card_html_r2resize.html | 86 inst/examples/sample1.Rmd | 336 +- inst/themes/default.css | 2 inst/themes/default_bottom.js | 2 inst/themes/default_top.js | 2 inst/themes/divsplitter.js | 2 inst/themes/empahsisCard.css | 2 inst/themes/expandingAccordian.css | 4 inst/themes/expandingAccordian.js | 6 inst/themes/imgviewer.css | 2 inst/themes/imgviewer.js | 2411 ++++++++++++++- inst/themes/rezcontCard.css | 2 inst/themes/rezcontCard.js | 2 inst/themes/splitCard.css | 2 inst/themes/splitCard2.css | 2 inst/themes/splitCard2.js | 2 inst/themes/windowCard.css | 2 inst/themes/windowCard.js | 2 man/add.JQuery.Rd | 51 man/add.resizer.Rd | 169 - man/elastiCard.Rd | 140 man/empahsisCard.Rd | 72 man/emphasisCard.Rd | 71 man/flexCard.Rd | 108 man/r2resize-package.Rd | 2 man/shinyExpandImage.Rd | 133 man/sizeableCard.Rd | 82 man/splitCard.Rd | 155 man/splitCard2.Rd | 118 man/windowCard.Rd | 99 tests/testthat.R | 8 tests/testthat/test-addJquery.R |only tests/testthat/test-containerResizer.R |only tests/testthat/test-flexCard.R | 34 tests/testthat/test-markdownResizer.R |only tests/testthat/test-novoImageResizer.R |only tests/testthat/test-sample.R |only tests/testthat/test-sliderCards.R |only vignettes/example_frequently_asked_r2resize.Rmd | 476 +- vignettes/introduction_r2resize.Rmd | 120 vignettes/r2resize-flexible-elastic-cards.Rmd |only vignettes/r2resize-image-and-markdown-resizing.Rmd |only vignettes/r2resize-resizable-containers.Rmd |only vignettes/resizable_containers_split_screen_r2resize.Rmd | 162 - vignettes/split_card_html_r2resize.Rmd | 174 - 73 files changed, 5652 insertions(+), 2441 deletions(-)
Title: Multi-Study Multi-Modality Generalized Factor Model
Description: We introduce a generalized factor model designed to jointly analyze high-dimensional multi-modality data from multiple studies by extracting study-shared and specified factors. Our factor models account for heterogeneous noises and overdispersion among modality variables with augmented covariates. We propose an efficient and speedy variational estimation procedure for estimating model parameters, along with a novel criterion for selecting the optimal number of factors. More details can be referred to Liu et al. (2025) <doi:10.48550/arXiv.2507.09889>.
Author: Wei Liu [aut, cre],
Qingzhi Zhong [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between MMGFM versions 1.2.0 dated 2025-07-29 and 1.2.1 dated 2025-11-12
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- R/mmgfm.R | 13 +++++++++++-- README.md | 10 +++++++++- inst/doc/simu2_MMGFM.html | 4 ++-- inst/doc/simu_MMGFM.html | 4 ++-- 6 files changed, 36 insertions(+), 19 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-26 0.2.2
Title: Phylogenetic Tree Statistics
Description: Collection of phylogenetic tree statistics,
collected throughout the literature. All functions have been
written to maximize computation speed. The package includes
umbrella functions to calculate all statistics, all balance
associated statistics, or all branching time related statistics.
Furthermore, the 'treestats' package supports summary statistic
calculations on Ltables, provides speed-improved coding of
branching times, Ltable conversion and includes algorithms to
create intermediately balanced trees. Full description can be
found in Janzen (2024) <doi:10.1016/j.ympev.2024.108168>.
Author: Thijs Janzen [cre, aut]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between treestats versions 1.70.7 dated 2025-09-11 and 1.70.8 dated 2025-11-12
treestats-1.70.7/treestats/inst/doc/Example_abc.R |only treestats-1.70.7/treestats/inst/doc/Example_abc.Rmd |only treestats-1.70.7/treestats/inst/doc/Example_abc.html |only treestats-1.70.7/treestats/vignettes/Example_abc.Rmd |only treestats-1.70.8/treestats/DESCRIPTION | 16 - treestats-1.70.8/treestats/MD5 | 54 +++--- treestats-1.70.8/treestats/NEWS.md | 15 + treestats-1.70.8/treestats/R/J_stat.R | 4 treestats-1.70.8/treestats/R/RcppExports.R | 4 treestats-1.70.8/treestats/R/j_one_stat.R | 4 treestats-1.70.8/treestats/R/rpanda.R | 5 treestats-1.70.8/treestats/build/vignette.rds |binary treestats-1.70.8/treestats/inst/doc/Example_data.html | 82 +++++----- treestats-1.70.8/treestats/inst/doc/Getting_started.R | 4 treestats-1.70.8/treestats/inst/doc/Getting_started.Rmd | 4 treestats-1.70.8/treestats/inst/doc/Getting_started.html | 33 ++-- treestats-1.70.8/treestats/inst/doc/Speed_improvement.html | 4 treestats-1.70.8/treestats/man/entropy_j.Rd | 4 treestats-1.70.8/treestats/man/j_one.Rd | 4 treestats-1.70.8/treestats/src/RcppExports.cpp | 12 - treestats-1.70.8/treestats/src/laplacian.cpp | 27 --- treestats-1.70.8/treestats/tests/testthat/test-blum.R | 5 treestats-1.70.8/treestats/tests/testthat/test-colless.R | 2 treestats-1.70.8/treestats/tests/testthat/test-eigen_centrality.R | 10 + treestats-1.70.8/treestats/tests/testthat/test-make_unbalanced_tree.R | 1 treestats-1.70.8/treestats/tests/testthat/test-mean_i.R | 6 treestats-1.70.8/treestats/tests/testthat/test-minmax_adj.R | 5 treestats-1.70.8/treestats/tests/testthat/test-nltt.R | 71 ++++---- treestats-1.70.8/treestats/tests/testthat/test-pigot_rho.R | 13 + treestats-1.70.8/treestats/vignettes/Getting_started.Rmd | 4 30 files changed, 194 insertions(+), 199 deletions(-)
Title: Flexibly Reshape Data: A Reboot of the Reshape Package
Description: Flexibly restructure and aggregate data using just two
functions: melt and 'dcast' (or 'acast').
Author: Hadley Wickham [aut, cre]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between reshape2 versions 1.4.4 dated 2020-04-09 and 1.4.5 dated 2025-11-12
DESCRIPTION | 17 ++-- MD5 | 35 ++++----- NAMESPACE | 10 ++ NEWS.md | 5 + R/RcppExports.R | 4 - R/cast.r | 8 +- R/formula.r | 2 R/helper-margins.r | 2 R/melt.r | 12 ++- README.md | 8 +- inst/CITATION | 16 +--- man/cast.Rd | 6 - src/RcppExports.cpp | 14 ++- src/melt.cpp | 131 ++++++++++++++++----------------- tests/testthat.R | 8 ++ tests/testthat/test-cast.r | 132 ++++++++++++++++++---------------- tests/testthat/test-helper-colsplit.r |only tests/testthat/test-margins.r | 30 +++---- tests/testthat/test-melt.r | 43 +++++++---- 19 files changed, 264 insertions(+), 219 deletions(-)
Title: Nonparametric Circular Methods
Description: Nonparametric smoothing methods for density and regression estimation involving circular data,
including the estimation of the mean regression function and other conditional characteristics.
Author: Maria Alonso-Pena [aut, cre],
Maria Oliveira [aut],
Jose Ameijeiras-Alonso [aut],
Rosa M. Crujeiras [aut],
Irene Gijbels [aut],
Alberto Rodriguez-Casal [aut],
Felicita Scapini [dtc]
Maintainer: Maria Alonso-Pena <mariaalonso.pena@usc.es>
Diff between NPCirc versions 3.1.1 dated 2022-11-10 and 3.1.2 dated 2025-11-12
NPCirc-3.1.1/NPCirc/data/HumanMotorResonance.txt |only NPCirc-3.1.1/NPCirc/data/flywheels.txt |only NPCirc-3.1.1/NPCirc/data/pm10.txt |only NPCirc-3.1.1/NPCirc/data/spikes.txt |only NPCirc-3.1.1/NPCirc/data/zebrafish.txt |only NPCirc-3.1.2/NPCirc/DESCRIPTION | 46 ++++++++++---- NPCirc-3.1.2/NPCirc/MD5 | 62 +++++++++---------- NPCirc-3.1.2/NPCirc/build/partial.rdb |binary NPCirc-3.1.2/NPCirc/data/HumanMotorResonance.txt.gz |only NPCirc-3.1.2/NPCirc/data/flywheels.txt.gz |only NPCirc-3.1.2/NPCirc/data/pm10.txt.gz |only NPCirc-3.1.2/NPCirc/data/spikes.txt.gz |only NPCirc-3.1.2/NPCirc/data/zebrafish.txt.gz |only NPCirc-3.1.2/NPCirc/inst/CITATION | 53 +++++++++++----- NPCirc-3.1.2/NPCirc/man/ancova.circ.lin.Rd | 4 - NPCirc-3.1.2/NPCirc/man/bw.AA.Rd | 4 - NPCirc-3.1.2/NPCirc/man/bw.CV.Rd | 2 NPCirc-3.1.2/NPCirc/man/bw.boot.Rd | 2 NPCirc-3.1.2/NPCirc/man/bw.circ.local.lik.Rd | 4 - NPCirc-3.1.2/NPCirc/man/bw.pi.Rd | 2 NPCirc-3.1.2/NPCirc/man/bw.reg.circ.lin.Rd | 4 - NPCirc-3.1.2/NPCirc/man/bw.rt.Rd | 2 NPCirc-3.1.2/NPCirc/man/circ.local.lik.Rd | 4 - NPCirc-3.1.2/NPCirc/man/circsizer.density.Rd | 2 NPCirc-3.1.2/NPCirc/man/circsizer.regression.Rd | 2 NPCirc-3.1.2/NPCirc/man/dcircmix.Rd | 2 NPCirc-3.1.2/NPCirc/man/dpreg.circ.Rd | 4 - NPCirc-3.1.2/NPCirc/man/dwsn.Rd | 4 - NPCirc-3.1.2/NPCirc/man/kern.den.circ.Rd | 6 - NPCirc-3.1.2/NPCirc/man/kern.dpreg.circ.Rd | 4 - NPCirc-3.1.2/NPCirc/man/kern.reg.circ.lin.Rd | 6 - NPCirc-3.1.2/NPCirc/man/lines.regression.circular.Rd | 4 - NPCirc-3.1.2/NPCirc/man/modalreg.circ.lin.Rd | 6 - NPCirc-3.1.2/NPCirc/man/noeffect.circ.lin.Rd | 4 - NPCirc-3.1.2/NPCirc/man/plot.regression.circular.Rd | 4 - NPCirc-3.1.2/NPCirc/src/Makevars | 12 --- NPCirc-3.1.2/NPCirc/src/Makevars.win | 12 --- 37 files changed, 140 insertions(+), 121 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and
more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.7-1 dated 2025-10-31 and 1.7-2 dated 2025-11-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/R.R | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 10 ++++++++++ man/R.Rd | 3 ++- 6 files changed, 22 insertions(+), 11 deletions(-)
Title: Calculate Textures from Grey-Level Co-Occurrence Matrices
(GLCMs)
Description: Enables calculation of image textures (Haralick 1973)
<doi:10.1109/TSMC.1973.4309314> from grey-level co-occurrence matrices
(GLCMs). Supports processing images that cannot fit in memory.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff <azvoleff@conservation.org>
Diff between glcm versions 1.6.5 dated 2020-02-26 and 1.6.6 dated 2025-11-11
DESCRIPTION | 14 ++++---- MD5 | 31 +++++++++---------- NAMESPACE | 2 - NEWS | 4 ++ R/glcm-package.R | 60 +++++++++++++++++-------------------- R/glcm.R | 9 ++++- README.md | 9 ++--- data/test_raster.RData |binary man/L5TSR_1986.Rd | 18 +++++------ man/calc_glcm_edge.Rd |only man/expected_textures_3x3_1x1.Rd | 12 +++---- man/expected_textures_5x3_n1xn2.Rd | 12 +++---- man/expected_textures_5x7_2x3.Rd | 12 +++---- man/glcm-package.Rd | 38 ++++++++++++++--------- man/test_raster.Rd | 2 - src/RcppExports.cpp | 5 +++ src/calc_texture.cpp | 7 ++-- 17 files changed, 129 insertions(+), 106 deletions(-)
Title: Interface for Multilevel Regression and Poststratification
Description: Dual interfaces, graphical and programmatic, designed for
intuitive applications of Multilevel Regression and Poststratification (MRP).
Users can apply the method to a variety of datasets, from electronic health records
to sample survey data, through an end-to-end Bayesian data analysis workflow.
The package provides robust tools for data cleaning, exploratory analysis,
flexible model building, and insightful result visualization. For more details, see
Si et al. (2020) <https://www150.statcan.gc.ca/n1/en/pub/12-001-x/2020002/article/00003-eng.pdf?st=iF1_Fbrh>
and Si (2025) <doi:10.1214/24-STS932>.
Author: Toan Tran [cre, aut, cph],
Jonah Gabry [aut, cph],
Yajuan Si [aut, cph]
Maintainer: Toan Tran <trannttoan97@gmail.com>
Diff between shinymrp versions 0.9.0 dated 2025-10-09 and 0.9.1 dated 2025-11-11
shinymrp-0.9.0/shinymrp/vignettes/data/model.qs |only shinymrp-0.9.0/shinymrp/vignettes/data/workflow.qs |only shinymrp-0.9.1/shinymrp/DESCRIPTION | 8 shinymrp-0.9.1/shinymrp/MD5 | 53 ++--- shinymrp-0.9.1/shinymrp/NEWS.md | 11 + shinymrp-0.9.1/shinymrp/R/example.R | 4 shinymrp-0.9.1/shinymrp/R/fct_data.R | 67 ++++-- shinymrp-0.9.1/shinymrp/R/mod_analyze_model.R | 10 - shinymrp-0.9.1/shinymrp/R/mod_analyze_upload.R | 60 +++--- shinymrp-0.9.1/shinymrp/R/model.R | 8 shinymrp-0.9.1/shinymrp/R/utils.R | 2 shinymrp-0.9.1/shinymrp/R/utils_server.R | 1 shinymrp-0.9.1/shinymrp/README.md | 6 shinymrp-0.9.1/shinymrp/build/partial.rdb |binary shinymrp-0.9.1/shinymrp/build/vignette.rds |binary shinymrp-0.9.1/shinymrp/inst/doc/example.R | 4 shinymrp-0.9.1/shinymrp/inst/doc/example.Rmd | 4 shinymrp-0.9.1/shinymrp/inst/doc/example.html | 4 shinymrp-0.9.1/shinymrp/inst/doc/workflow.R | 8 shinymrp-0.9.1/shinymrp/inst/doc/workflow.Rmd | 10 - shinymrp-0.9.1/shinymrp/inst/doc/workflow.html | 100 ++++------ shinymrp-0.9.1/shinymrp/man/MRPModel-method-save.Rd | 4 shinymrp-0.9.1/shinymrp/tests/testthat/test-data-processing.R | 29 ++ shinymrp-0.9.1/shinymrp/tests/testthat/test-example.R | 4 shinymrp-0.9.1/shinymrp/tests/testthat/test-mrp-model.R | 2 shinymrp-0.9.1/shinymrp/vignettes/data/model.qs2 |only shinymrp-0.9.1/shinymrp/vignettes/data/workflow.qs2 |only shinymrp-0.9.1/shinymrp/vignettes/example.Rmd | 4 shinymrp-0.9.1/shinymrp/vignettes/spatial_prior.html |only shinymrp-0.9.1/shinymrp/vignettes/workflow.Rmd | 10 - 30 files changed, 233 insertions(+), 180 deletions(-)
Title: Map Image Classification Efficacy
Description: Map image classification efficacy (MICE) adjusts the accuracy rate relative to a random classification baseline (Shao et al. (2021)<doi:10.1109/ACCESS.2021.3116526> and Tang et al. (2024)<doi:10.1109/TGRS.2024.3446950>). Only the proportions from the reference labels are considered, as opposed to the proportions from the reference and predictions, as is the case for the Kappa statistic. This package offers means to calculate MICE and adjusted versions of class-level user's accuracy (i.e., precision) and producer's accuracy (i.e., recall) and F1-scores. Class-level metrics are aggregated using macro-averaging. Functions are also made available to estimate confidence intervals using bootstrapping and statistically compare two classification results.
Author: Aaron Maxwell [aut, cre, cph],
Sarah Farhadpour [aut]
Maintainer: Aaron Maxwell <Aaron.Maxwell@mail.wvu.edu>
Diff between micer versions 0.2.0 dated 2025-01-20 and 0.2.1 dated 2025-11-11
DESCRIPTION | 13 +-- MD5 | 16 ++-- R/micer.R | 14 +--- inst/doc/micerExamples.R | 5 - inst/doc/micerExamples.Rmd | 7 -- inst/doc/micerExamples.html | 144 +++++++++++++++++++++----------------------- man/miceCI.Rd | 5 - man/miceCompare.Rd | 7 -- vignettes/micerExamples.Rmd | 7 -- 9 files changed, 95 insertions(+), 123 deletions(-)
Title: Feature Selection in R
Description: Feature subset selection algorithms modularized in search algorithms and measure utilities.
Author: Alfonso Jimenez-Vilchez [aut, cre] ,
Francisco Aragon-Royon [aut] ,
Adan M. Rodriguez [aut],
Antonio Arauzo-Azofra [aut] ,
Jose Manuel Benitez [aut]
Maintainer: Alfonso Jimenez-Vilchez <i52jivia@uco.es>
Diff between FSinR versions 2.0.9 dated 2025-10-23 and 2.0.10 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 4 ++++ NEWS.md | 4 ++++ build/partial.rdb |binary inst/REFERENCES.bib | 2 +- inst/doc/FSinR.html | 12 ++++++------ inst/doc/methods.html | 34 ++++++++++++++++++++++------------ 8 files changed, 48 insertions(+), 30 deletions(-)
Title: Coarsened Mixtures of Hierarchical Skew Kernels
Description: Bayesian fit of a Dirichlet Process Mixture with hierarchical multivariate skew normal kernels and coarsened posteriors. For more information, see Gorsky, Chan and Ma (2024) <doi:10.1214/22-BA1356>.
Author: S. Gorsky [aut, cre],
C. Chan [ctb],
L. Ma [ctb]
Maintainer: S. Gorsky <sgorsky@umass.edu>
Diff between COMIX versions 1.0.0 dated 2022-11-23 and 1.0.1 dated 2025-11-11
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- build/vignette.rds |binary src/Makevars | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: A Tool for Semi-Automating the Statistical Disclosure Control of
Research Outputs
Description: A Tool for Semi-Automating the Statistical Disclosure Control of Research Outputs.
Author: Jim Smith [cre, ctb] ,
Maha Albashir [aut, ctb],
Richard John Preen [aut, ctb]
Maintainer: Jim Smith <James.Smith@uwe.ac.uk>
Diff between acro versions 0.1.5 dated 2025-07-03 and 0.1.6 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++++++------ NEWS.md | 6 ++++++ R/create_virtualenv.R | 7 ++++--- README.md | 14 ++++++++++++-- inst/INSTALL.md |only inst/Images/settingpython-rstudio-step0.png |only inst/Images/settingpython-rstudio-step1.png |only inst/Images/settingpython-rstudio-step2.png |only inst/Images/settingpython-rstudio-step3.png |only inst/WORDLIST | 12 ++++++++++++ inst/binder |only tests/testthat/Rplots.pdf |binary 13 files changed, 52 insertions(+), 15 deletions(-)
Title: Proteomics Data Analysis and Modeling Tools
Description: A comprehensive, user-friendly package for label-free proteomics data analysis and machine learning-based modeling. Data generated from 'MaxQuant' can be easily used to conduct differential expression analysis, build predictive models with top protein candidates, and assess model performance. promor includes a suite of tools for quality control, visualization, missing data imputation (Lazar et. al. (2016) <doi:10.1021/acs.jproteome.5b00981>), differential expression analysis (Ritchie et. al. (2015) <doi:10.1093/nar/gkv007>), and machine learning-based modeling (Kuhn (2008) <doi:10.18637/jss.v028.i05>).
Author: Chathurani Ranathunge [aut, cre, cph]
Maintainer: Chathurani Ranathunge <caranathunge86@gmail.com>
This is a re-admission after prior archival of version 0.2.1 dated 2023-07-17
Diff between promor versions 0.2.1 dated 2023-07-17 and 0.2.2 dated 2025-11-11
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/handleNA.R | 23 ++++++----------------- README.md | 2 +- inst/doc/intro_to_promor.R | 4 ++-- man/impute_na.Rd | 20 ++++---------------- man/impute_plot.Rd | 2 +- tests/testthat/test-protein_analysis.R | 19 ------------------- 9 files changed, 34 insertions(+), 70 deletions(-)
Title: Native Access Medical Record Retriever for High Yield Analytics
Description: A toolkit for medical records data analysis. The 'naryn'
package implements an efficient data structure for storing medical
records, and provides a set of functions for data extraction,
manipulation and analysis.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Ben Gilat [aut],
Netta Mendelson-Cohen [ctb],
Rami Jaschek [ctb],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between naryn versions 2.6.30 dated 2024-09-27 and 2.6.31 dated 2025-11-11
DESCRIPTION | 9 MD5 | 16 NEWS.md | 5 R/db.R | 2 R/filter.R | 5 inst/doc/advanced.html | 1199 ++++++++++++++++++++++++++++++++++++++----------- man/emr_db.connect.Rd | 2 src/NRTest.cpp | 2 src/naryn.cpp | 18 9 files changed, 980 insertions(+), 278 deletions(-)
Title: Machine Learning Modelling for Everyone
Description: A minimal library specifically designed to make the estimation of
Machine Learning (ML) techniques as easy and accessible as possible,
particularly within the framework of the Knowledge Discovery in
Databases (KDD) process in data mining. The package provides
essential tools to structure and execute each stage of a predictive
or classification modeling workflow, aligning closely with the
fundamental steps of the KDD methodology, from data selection and
preparation, through model building and tuning, to the
interpretation and evaluation of results using Sensitivity Analysis.
The 'MLwrap' workflow is organized into four core steps;
preprocessing(), build_model(), fine_tuning(), and
sensitivity_analysis(). These steps correspond, respectively, to
data preparation and transformation, model construction,
hyperparameter optimization, and sensitivity analysis. The user can
access comprehensive model evaluation results including fit
assessment metrics, plots, predictions, and performance diagn [...truncated...]
Author: Javier Martinez Garcia [aut] ,
Juan Jose Montano Moreno [ctb] ,
Albert Sese [cre, ctb]
Maintainer: Albert Sese <albert.sese@uib.es>
Diff between MLwrap versions 0.2.2 dated 2025-11-05 and 0.2.3 dated 2025-11-11
DESCRIPTION | 12 +- MD5 | 18 +-- R/InterpretableML.R | 6 - R/permutation_feature_importance.R | 218 +++++++++++++++++++++++++++++++------ R/table_utils.R | 47 ++++--- README.md | 2 build/partial.rdb |binary man/sensitivity_analysis.Rd | 6 - man/table_pfi_results.Rd | 26 +--- man/table_shap_results.Rd | 23 ++- 10 files changed, 257 insertions(+), 101 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.3.5 dated 2025-11-07 and 0.3.6 dated 2025-11-11
DESCRIPTION | 14 +++++++------- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 10 ++++++++-- R/cms_download_subset.r | 10 +--------- R/cms_login.r | 3 +-- R/translate.R | 2 +- inst/doc/translate.R | 6 ++++-- inst/doc/translate.Rmd | 6 ++++-- inst/doc/translate.html | 6 ++++-- man/account.Rd | 2 +- man/cms_download_native.Rd | 2 +- man/cms_download_subset.Rd | 12 +----------- man/cms_translate.Rd | 2 +- man/cms_wmts.Rd | 2 +- tests/testthat.R | 1 - tests/testthat/test_subset.r | 1 + vignettes/translate.Rmd | 6 ++++-- 17 files changed, 56 insertions(+), 61 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Grain-Size Statistics and Description of Sediment
Description: Full descriptive statistics, physical description of sediment,
metric or phi sieves. Includes a Shiny web application for
interactive grain size analysis and visualization.
Author: Regis K. Gallon [aut, cre] ,
Jerome Fournier [aut]
Maintainer: Regis K. Gallon <regis.gallon@lecnam.net>
Diff between G2Sd versions 2.1.5 dated 2015-12-07 and 2.2 dated 2025-11-11
G2Sd-2.1.5/G2Sd/data/coord_gran.rda |only G2Sd-2.1.5/G2Sd/inst/extdata/www/R_logo.png |only G2Sd-2.1.5/G2Sd/inst/extdata/www/bootstrap3.css |only G2Sd-2.1.5/G2Sd/inst/extdata/www/cnrs.gif |only G2Sd-2.1.5/G2Sd/inst/extdata/www/mnhn.gif |only G2Sd-2.1.5/G2Sd/man/coord_gran.Rd |only G2Sd-2.2/G2Sd/DESCRIPTION | 33 G2Sd-2.2/G2Sd/MD5 | 41 G2Sd-2.2/G2Sd/NAMESPACE | 44 G2Sd-2.2/G2Sd/NEWS | 18 G2Sd-2.2/G2Sd/R/G2Sd-internal.R | 1068 +++++++++++------------- G2Sd-2.2/G2Sd/R/grandistrib.R | 83 + G2Sd-2.2/G2Sd/R/granplot.R | 292 +++++- G2Sd-2.2/G2Sd/R/granstat.R | 215 ++-- G2Sd-2.2/G2Sd/README.md |only G2Sd-2.2/G2Sd/inst/CITATION | 11 G2Sd-2.2/G2Sd/inst/INDEX | 16 G2Sd-2.2/G2Sd/inst/extdata/server.R | 880 ++++++++++++++++--- G2Sd-2.2/G2Sd/inst/extdata/ui.R | 442 ++++++++- G2Sd-2.2/G2Sd/inst/extdata/www/G2SdLogo.png |only G2Sd-2.2/G2Sd/inst/extdata/www/cnam_logo.png |only G2Sd-2.2/G2Sd/man/G2Sd-package.Rd | 102 +- G2Sd-2.2/G2Sd/man/grandistrib.Rd | 96 +- G2Sd-2.2/G2Sd/man/granplot.Rd | 20 G2Sd-2.2/G2Sd/man/granstat.Rd | 245 ++--- G2Sd-2.2/G2Sd/man/granulo.Rd | 56 - 26 files changed, 2413 insertions(+), 1249 deletions(-)
Title: Test Robustness with Directed Acyclic Graphs
Description: Provides robustness checks to align estimands with the identification
that they require. Given a 'dagitty' object and a model specification,
'DAGassist' classifies variables by causal roles, flags problematic controls,
and generates a report comparing the original model with minimal and canonical
adjustment sets. Exports publication-grade reports in 'LaTeX', 'Word', 'Excel',
'dotwhisker', or plain text/'markdown'. 'DAGassist' is built on 'dagitty', an
'R' package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for
creating and analyzing DAGs. Methods draw on Pearl (2009) <doi:10.1017/CBO9780511803161>
and Textor et al. (2016) <doi:10.1093/ije/dyw341>.
Author: Graham Goff [aut, cre] ,
Michael Denly [aut]
Maintainer: Graham Goff <goffgrahamc@gmail.com>
Diff between DAGassist versions 0.2.4 dated 2025-09-21 and 0.2.7 dated 2025-11-11
DESCRIPTION | 36 - MD5 | 57 +-- NAMESPACE | 1 NEWS.md | 31 + R/assist.R | 817 ++++++++++++++++++++++++++++++++----------- R/assist_helpers.R | 173 ++++++++- R/classify.R | 273 +++++++------- R/dotwhisker.R |only R/export_helpers.R | 18 R/report_excel.R | 33 + R/report_latex.R | 224 ++++++++--- R/report_text.R | 65 ++- R/report_word.R | 36 + R/validate.R | 21 - README.md | 71 ++- inst/doc/get-started.R | 115 +++--- inst/doc/get-started.Rmd | 186 ++++++--- inst/doc/get-started.html | 616 ++++++++++++++++---------------- inst/doc/making-reports.R | 50 ++ inst/doc/making-reports.Rmd | 74 +++ inst/doc/making-reports.html | 406 +++++++++++++++++++-- inst/doc/quick-tour.R | 29 + inst/doc/quick-tour.Rmd | 34 + inst/doc/quick-tour.html | 48 +- man/DAGassist.Rd | 147 +++++-- man/art |only man/classify_nodes.Rd | 61 +-- man/figures/logo.png |only vignettes/get-started.Rmd | 186 ++++++--- vignettes/making-reports.Rmd | 74 +++ vignettes/quick-tour.Rmd | 34 + 31 files changed, 2752 insertions(+), 1164 deletions(-)
Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, rational expectations, endogenous targeting and model renormalization, structural stability, stochastic simulation and forecast, optimal control, by A. Luciani (2022) <doi:10.13140/RG.2.2.31160.83202>.
Author: Andrea Luciani [aut, cre] ,
Roberto Stok [aut],
Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>
Diff between bimets versions 4.1.1 dated 2025-10-30 and 4.1.2 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ R/bimets_ts_functions.R | 2 +- README.md | 10 +++++----- inst/doc/bimets.pdf |binary inst/doc/frb2bimets.pdf |binary man/MDL.Rd | 4 ++-- man/RENORM.Rd | 2 +- man/SIMULATE.Rd | 4 ++-- man/STOCHSIMULATE.Rd | 2 +- man/bimets-package.Rd | 6 ++---- 12 files changed, 35 insertions(+), 31 deletions(-)
Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] ,
Riccardo Corradin [aut],
Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>
Diff between BayesChange versions 2.1.2 dated 2025-11-05 and 2.1.3 dated 2025-11-11
DESCRIPTION | 6 MD5 | 52 ++-- NAMESPACE | 48 ++-- NEWS.md | 2 R/BayesChange-package.R | 24 +- inst/doc/tutorial.html | 209 ++++++++++--------- man/BayesChange-package.Rd | 58 ++--- man/ClustCpObj.Rd | 104 ++++----- man/DetectCpObj.Rd | 116 +++++------ man/clust_cp.Rd | 358 +++++++++++++++++----------------- man/clust_cp_epi.Rd | 186 ++++++++--------- man/clust_cp_multi.Rd | 160 +++++++-------- man/clust_cp_uni.Rd | 128 ++++++------ man/detect_cp.Rd | 288 +++++++++++++-------------- man/detect_cp_multi.Rd | 134 ++++++------ man/detect_cp_uni.Rd | 118 +++++------ man/plot.ClustCpObj.Rd | 174 ++++++++-------- man/plot.DetectCpObj.Rd | 110 +++++----- man/posterior_estimate.ClustCpObj.Rd | 116 +++++------ man/posterior_estimate.DetectCpObj.Rd | 106 +++++----- man/posterior_estimate.Rd | 24 +- man/print.ClustCpObj.Rd | 64 +++--- man/print.DetectCpObj.Rd | 62 ++--- man/sim_epi_data.Rd | 72 +++--- man/summary.ClustCpObj.Rd | 64 +++--- man/summary.DetectCpObj.Rd | 64 +++--- tests/testthat.R | 24 +- 27 files changed, 1444 insertions(+), 1427 deletions(-)
Title: Marginal Structural Models with Latent Class Growth Analysis of
Treatment Trajectories
Description: Implements marginal structural models combined with a latent class growth analysis framework for assessing the causal effect of treatment trajectories. Based on the approach described in "Marginal Structural Models with Latent Class Growth Analysis of Treatment Trajectories" Diop, A., Sirois, C., Guertin, J.R., Schnitzer, M.E., Candas, B., Cossette, B., Poirier, P., Brophy, J., Mésidor, M., Blais, C. and Hamel, D., (2023) <doi:10.1177/09622802231202384>.
Author: Awa Diop [aut, cre],
Denis Talbot [aut]
Maintainer: Awa Diop <awa.diop.2@ulaval.ca>
Diff between trajmsm versions 0.1.4 dated 2025-06-16 and 0.1.5 dated 2025-11-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/trajmsm_ipw.R | 1 - 3 files changed, 5 insertions(+), 6 deletions(-)
Title: A Simulation Framework for Spatiotemporal Population Genetics
Description: A framework for simulating spatially explicit genomic data which
leverages real cartographic information for programmatic and visual encoding
of spatiotemporal population dynamics on real geographic landscapes. Population
genetic models are then automatically executed by the 'SLiM' software by Haller
et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom
built-in simulation 'SLiM' script. Additionally, fully abstract spatial models
not tied to a specific geographic location are supported, and users can also
simulate data from standard, non-spatial, random-mating models. These can be
simulated either with the 'SLiM' built-in back-end script, or using an efficient
coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022)
<doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the
R package. Simulated genomic data is saved in a tree-sequence format and can be
loaded, manipulated, and summarised using tree-sequen [...truncated...]
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>
Diff between slendr versions 1.2.0 dated 2025-07-31 and 1.3.0 dated 2025-11-11
slendr-1.2.0/slendr/inst/extdata/models/introgression/__pycache__/script.cpython-312.pyc |only slendr-1.3.0/slendr/DESCRIPTION | 13 - slendr-1.3.0/slendr/MD5 | 130 +++++----- slendr-1.3.0/slendr/NAMESPACE | 1 slendr-1.3.0/slendr/NEWS.md | 12 slendr-1.3.0/slendr/R/interface.R | 1 slendr-1.3.0/slendr/R/shiny.R | 83 +++--- slendr-1.3.0/slendr/R/tree-sequences.R | 28 +- slendr-1.3.0/slendr/R/visualization.R | 46 +-- slendr-1.3.0/slendr/R/zzz.R | 6 slendr-1.3.0/slendr/build/partial.rdb |binary slendr-1.3.0/slendr/build/vignette.rds |binary slendr-1.3.0/slendr/inst/doc/vignette-01-tutorial.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-01-tutorial.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-01-tutorial.html | 28 +- slendr-1.3.0/slendr/inst/doc/vignette-02-grid-model.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-02-grid-model.Rmd | 4 slendr-1.3.0/slendr/inst/doc/vignette-02-grid-model.html | 16 - slendr-1.3.0/slendr/inst/doc/vignette-03-interactions.R | 6 slendr-1.3.0/slendr/inst/doc/vignette-03-interactions.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-03-interactions.html | 4 slendr-1.3.0/slendr/inst/doc/vignette-04-nonspatial-models.R | 6 slendr-1.3.0/slendr/inst/doc/vignette-04-nonspatial-models.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-04-nonspatial-models.html | 2 slendr-1.3.0/slendr/inst/doc/vignette-05-tree-sequences.R | 12 slendr-1.3.0/slendr/inst/doc/vignette-05-tree-sequences.Rmd | 12 slendr-1.3.0/slendr/inst/doc/vignette-05-tree-sequences.html | 10 slendr-1.3.0/slendr/inst/doc/vignette-06-locations.R | 8 slendr-1.3.0/slendr/inst/doc/vignette-06-locations.Rmd | 10 slendr-1.3.0/slendr/inst/doc/vignette-06-locations.html | 22 - slendr-1.3.0/slendr/inst/doc/vignette-07-engines.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-07-engines.Rmd | 4 slendr-1.3.0/slendr/inst/doc/vignette-07-engines.html | 10 slendr-1.3.0/slendr/inst/doc/vignette-08-nonslendr-tskit.R | 8 slendr-1.3.0/slendr/inst/doc/vignette-08-nonslendr-tskit.Rmd | 8 slendr-1.3.0/slendr/inst/doc/vignette-08-nonslendr-tskit.html | 4 slendr-1.3.0/slendr/inst/doc/vignette-10-tracts.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-10-tracts.Rmd | 4 slendr-1.3.0/slendr/inst/doc/vignette-10-tracts.html | 6 slendr-1.3.0/slendr/inst/doc/vignette-11-extensions.R | 6 slendr-1.3.0/slendr/inst/doc/vignette-11-extensions.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-11-extensions.html | 4 slendr-1.3.0/slendr/inst/extdata/models/introgression/__pycache__/script.cpython-313.pyc |only slendr-1.3.0/slendr/inst/extdata/models/introgression/checksums.tsv | 2 slendr-1.3.0/slendr/inst/extdata/models/introgression/ranges.rds |binary slendr-1.3.0/slendr/inst/extdata/models/introgression/script.py | 4 slendr-1.3.0/slendr/inst/extdata/models/introgression/script.slim | 44 +-- slendr-1.3.0/slendr/inst/extdata/models/introgression_msprime.trees |binary slendr-1.3.0/slendr/inst/extdata/models/introgression_slim.trees |binary slendr-1.3.0/slendr/inst/extdata/models/msprime.trees |binary slendr-1.3.0/slendr/inst/scripts/script.slim | 42 +-- slendr-1.3.0/slendr/man/plot_map.Rd | 5 slendr-1.3.0/slendr/tests/testthat/afs_Linux.tsv.gz |binary slendr-1.3.0/slendr/tests/testthat/distances.tsv.gz |binary slendr-1.3.0/slendr/tests/testthat/test-interaction-changes.R | 2 slendr-1.3.0/slendr/tests/testthat/test-msprime-geneflow.R | 2 slendr-1.3.0/slendr/tests/testthat/test-msprime.R | 2 slendr-1.3.0/slendr/vignettes/vignette-01-tutorial.Rmd | 6 slendr-1.3.0/slendr/vignettes/vignette-02-grid-model.Rmd | 4 slendr-1.3.0/slendr/vignettes/vignette-03-interactions.Rmd | 6 slendr-1.3.0/slendr/vignettes/vignette-04-nonspatial-models.Rmd | 6 slendr-1.3.0/slendr/vignettes/vignette-05-tree-sequences.Rmd | 12 slendr-1.3.0/slendr/vignettes/vignette-06-locations.Rmd | 10 slendr-1.3.0/slendr/vignettes/vignette-07-engines.Rmd | 4 slendr-1.3.0/slendr/vignettes/vignette-08-nonslendr-tskit.Rmd | 8 slendr-1.3.0/slendr/vignettes/vignette-10-tracts.Rmd | 4 slendr-1.3.0/slendr/vignettes/vignette-11-extensions.Rmd | 6 67 files changed, 344 insertions(+), 379 deletions(-)
Title: Plots for the Quantitative Analysis of Textual Data
Description: Plotting functions for visualising textual data. Extends 'quanteda' and
related packages with plot methods designed specifically for text data, textual statistics,
and models fit to textual data. Plot types include word clouds, lexical dispersion plots,
scaling plots, network visualisations, and word 'keyness' plots.
Author: Kenneth Benoit [cre, aut, cph] ,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Adam Obeng [aut] ,
Stefan Mueller [aut] ,
Akitaka Matsuo [aut] ,
Ian Fellows [cph] ),
European Research Council [fnd]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda.textplots versions 0.96 dated 2025-09-03 and 0.96.1 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/textplot_keyness.R | 2 +- R/textplot_xray.R | 10 ++++++---- README.md | 8 +++----- man/textplot_xray.Rd | 7 ++++--- 6 files changed, 23 insertions(+), 22 deletions(-)
More information about quanteda.textplots at CRAN
Permanent link
Title: Access and Analyse Data from the 'CVD Prevent' API
Description: Provides an R interface to the 'CVD Prevent' application
programming interface (API), allowing users to retrieve and analyse
cardiovascular disease prevention data from primary care records
across England. The Cardiovascular Disease Prevention Audit
(CVDPREVENT) automatically extracts routinely held GP health data to
support national reporting and improvement initiatives. See the API
documentation for details:
<https://bmchealthdocs.atlassian.net/wiki/spaces/CP/pages/317882369/CVDPREVENT+API+Documentation>.
Author: Craig Parylo [aut, cre, cph] ,
Cardiovascular Disease Prevention Audit [ant]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between cvdprevent versions 0.2.3 dated 2025-11-05 and 0.2.4 dated 2025-11-11
DESCRIPTION | 6 MD5 | 15 NAMESPACE | 1 NEWS.md | 64 R/cvd_memoise.R | 62 README.md | 20 build/vignette.rds |binary inst/doc/using_cvdprevent.html | 4182 ++++++++++++++++++++--------------------- man/cvd_clear_cache.Rd |only 9 files changed, 2213 insertions(+), 2137 deletions(-)
Title: Statistical Analysis of Contingency Tables
Description: Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.
Author: Morten Wang Fagerland [aut],
Stian Lydersen [ctb],
Petter Laake [ctb],
Waldir Leoncio [cre],
Ole Christian Lingjaerde [trl],
Brad J. Biggerstaff [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between contingencytables versions 3.0.1 dated 2024-08-29 and 3.1.0 dated 2025-11-11
DESCRIPTION | 9 MD5 | 225 ++++++------ NEWS.md | 6 R/Adjusted_inv_sinh_CI_OR_2x2.R | 1 R/Adjusted_inv_sinh_CI_ratio_2x2.R | 1 R/Adjusted_log_CI_2x2.R | 1 R/AgrestiCaffo_CI_2x2.R | 1 R/BaptistaPike_exact_conditional_CI_2x2.R | 1 R/BaptistaPike_midP_CI_2x2.R | 1 R/CochranMantelHaenszel_test_stratified_2x2.R | 1 R/Cornfield_exact_conditional_CI_2x2.R | 1 R/Cornfield_midP_CI_2x2.R | 1 R/Exact_unconditional_test_2x2.R | 23 - R/Fisher_exact_test_2x2.R | 7 R/Fisher_midP_test_2x2.R | 1 R/Gart_adjusted_logit_CI_2x2.R | 1 R/Independence_smoothed_logit_CI_2x2.R | 1 R/Inv_sinh_CI_OR_2x2.R | 1 R/Inv_sinh_CI_ratio_2x2.R | 1 R/Katz_log_CI_2x2.R | 1 R/Koopman_asymptotic_score_CI_2x2.R | 1 R/LR_test_2x2.R | 1 R/MOVER_R_Wilson_CI_OR_2x2.R | 1 R/MOVER_R_Wilson_CI_ratio_2x2.R | 1 R/MantelHaenszel_estimate_stratified_2x2.R | 1 R/McNemar_asymptotic_test_CC_paired_2x2.R | 1 R/McNemar_asymptotic_test_paired_2x2.R | 1 R/Mee_asymptotic_score_CI_2x2.R | 1 R/MiettinenNurminen_asymptotic_score_CI_OR_2x2.R | 1 R/MiettinenNurminen_asymptotic_score_CI_difference_2x2.R | 1 R/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.R | 1 R/Newcombe_hybrid_score_CI_2x2.R | 1 R/Newcombe_square_and_add_CI_paired_2x2.R | 1 R/Pearson_LR_test_common_effect_stratified_2x2.R | 1 R/Pearson_chi_squared_test_2x2.R | 4 R/Pearson_chi_squared_test_CC_2x2.R | 1 R/PriceBonett_approximate_Bayes_CI_2x2.R | 1 R/Transformed_Blaker_exact_CI_paired_2x2.R | 1 R/Transformed_Clopper_Pearson_exact_CI_paired_2x2.R | 1 R/Transformed_Clopper_Pearson_midP_CI_paired_2x2.R | 1 R/Uncorrected_asymptotic_score_CI_2x2.R | 1 R/Wald_CI_2x2.R | 1 R/Wald_CI_AgrestiMin_paired_2x2.R | 1 R/Wald_CI_CC_2x2.R | 1 R/Wald_CI_OR_paired_2x2.R | 1 R/Wald_CI_ratio_paired_2x2.R | 1 R/Wald_test_and_CI_common_diff_stratified_2x2.R | 1 R/Wald_test_and_CI_common_ratio_stratified_2x2.R | 1 R/Woolf_logit_CI_2x2.R | 1 R/Z_unpooled_test_2x2.R | 1 R/chapters.R | 15 R/the_2x2_table_CIs_OR.R | 1 R/the_2x2_table_CIs_difference.R | 1 R/the_2x2_table_CIs_ratio.R | 1 R/the_2x2_table_tests.R | 1 R/the_paired_2x2_table_CIs_OR.R | 1 man/Adjusted_inv_sinh_CI_OR_2x2.Rd | 8 man/Adjusted_inv_sinh_CI_ratio_2x2.Rd | 8 man/Adjusted_log_CI_2x2.Rd | 8 man/AgrestiCaffo_CI_2x2.Rd | 8 man/BaptistaPike_exact_conditional_CI_2x2.Rd | 8 man/BaptistaPike_midP_CI_2x2.Rd | 8 man/CochranMantelHaenszel_test_stratified_2x2.Rd | 8 man/Cornfield_exact_conditional_CI_2x2.Rd | 8 man/Cornfield_midP_CI_2x2.Rd | 8 man/Exact_unconditional_test_2x2.Rd | 8 man/Fisher_exact_test_2x2.Rd | 8 man/Fisher_midP_test_2x2.Rd | 8 man/Gart_adjusted_logit_CI_2x2.Rd | 8 man/Independence_smoothed_logit_CI_2x2.Rd | 8 man/Inv_sinh_CI_OR_2x2.Rd | 8 man/Inv_sinh_CI_ratio_2x2.Rd | 8 man/Katz_log_CI_2x2.Rd | 8 man/Koopman_asymptotic_score_CI_2x2.Rd | 8 man/LR_test_2x2.Rd | 8 man/MOVER_R_Wilson_CI_OR_2x2.Rd | 8 man/MOVER_R_Wilson_CI_ratio_2x2.Rd | 8 man/MantelHaenszel_estimate_stratified_2x2.Rd | 8 man/McNemar_asymptotic_test_CC_paired_2x2.Rd | 8 man/McNemar_asymptotic_test_paired_2x2.Rd | 8 man/Mee_asymptotic_score_CI_2x2.Rd | 8 man/MiettinenNurminen_asymptotic_score_CI_OR_2x2.Rd | 8 man/MiettinenNurminen_asymptotic_score_CI_difference_2x2.Rd | 8 man/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.Rd | 8 man/Newcombe_hybrid_score_CI_2x2.Rd | 8 man/Newcombe_square_and_add_CI_paired_2x2.Rd | 8 man/Pearson_LR_test_common_effect_stratified_2x2.Rd | 8 man/Pearson_chi_squared_test_2x2.Rd | 8 man/Pearson_chi_squared_test_CC_2x2.Rd | 8 man/PriceBonett_approximate_Bayes_CI_2x2.Rd | 8 man/Transformed_Blaker_exact_CI_paired_2x2.Rd | 8 man/Transformed_Clopper_Pearson_exact_CI_paired_2x2.Rd | 8 man/Transformed_Clopper_Pearson_midP_CI_paired_2x2.Rd | 8 man/Uncorrected_asymptotic_score_CI_2x2.Rd | 8 man/Wald_CI_2x2.Rd | 8 man/Wald_CI_AgrestiMin_paired_2x2.Rd | 8 man/Wald_CI_CC_2x2.Rd | 8 man/Wald_CI_OR_paired_2x2.Rd | 8 man/Wald_CI_ratio_paired_2x2.Rd | 8 man/Wald_test_and_CI_common_diff_stratified_2x2.Rd | 8 man/Wald_test_and_CI_common_ratio_stratified_2x2.Rd | 8 man/Woolf_logit_CI_2x2.Rd | 8 man/Z_unpooled_test_2x2.Rd | 8 man/chap10.Rd | 8 man/chap4.Rd | 8 man/chap8.Rd | 8 man/the_2x2_table_CIs_OR.Rd | 8 man/the_2x2_table_CIs_difference.Rd | 8 man/the_2x2_table_CIs_ratio.Rd | 8 man/the_2x2_table_tests.Rd | 8 man/the_paired_2x2_table_CIs_OR.Rd | 8 tests/testthat/Rplots.pdf |only tests/testthat/test-ch4.R | 18 tests/testthat/test-validation.R | 4 114 files changed, 667 insertions(+), 133 deletions(-)
More information about contingencytables at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-15 0.2.4
2018-04-30 0.2.3
2016-04-29 0.2.2
2015-07-17 0.2
2014-01-12 0.1
Title: Power Analysis for Research Experiments
Description: Provides tools for calculating statistical power for experiments
analyzed using linear mixed models. It supports standard designs, including
randomized block, split-plot, and Latin Square designs, while offering flexibility
to accommodate a variety of other complex study designs.
Author: Kai Wang [aut, cre, cph] ,
Mutian Niu [aut, cph]
Maintainer: Kai Wang <kai.wang@usys.ethz.ch>
Diff between pwr4exp versions 1.0.0 dated 2025-03-17 and 1.0.1 dated 2025-11-11
DESCRIPTION | 11 ++-- MD5 | 48 ++++++++++++------- NAMESPACE | 20 ++++++++ NEWS.md | 8 ++- R/corClasses.R |only R/df_utils.R | 6 +- R/mkdesign.R | 22 ++++++-- R/standard_designs.R | 6 +- R/utils.R | 125 ++++++++++++++++++++++++++++++++++---------------- build/vignette.rds |binary inst/CITATION | 14 +++-- inst/doc/pwr4exp.R | 4 - inst/doc/pwr4exp.Rmd | 6 +- inst/doc/pwr4exp.html | 23 ++++----- man/corAR1.Rd |only man/corARMA.Rd |only man/corCAR1.Rd |only man/corClasses.Rd |only man/corCompSymm.Rd |only man/corExp.Rd |only man/corGaus.Rd |only man/corLin.Rd |only man/corRatio.Rd |only man/corSpher.Rd |only man/corSymm.Rd |only man/create_designs.Rd | 4 - man/df.lsd.Rd | 4 - man/mkRTrms.Rd | 6 +- man/mkStruct.Rd | 4 - man/mkdesign.Rd | 9 ++- vignettes/pwr4exp.Rmd | 6 +- 31 files changed, 213 insertions(+), 113 deletions(-)
Title: Evolutionary Transcriptomics
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) <doi:10.1093/bioinformatics/btx835>). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.
Author: Hajk-Georg Drost [aut, cre] ,
Stefan Manolache [aut, ctb] ,
Jaruwatana Sodai Lotharukpong [aut, ctb] ,
Nikola Kalabova [aut, ctb] ,
Filipa Martins Costa [aut, ctb],
Kristian K Ullrich [aut, ctb]
Maintainer: Hajk-Georg Drost <hajk-georg.drost@tuebingen.mpg.de>
Diff between myTAI versions 2.3.3 dated 2025-11-07 and 2.3.4 dated 2025-11-11
DESCRIPTION | 8 - MD5 | 74 +++++++-------- NEWS.md | 10 +- R/plot_contribution.R | 13 ++ R/plot_gene_heatmap.R | 17 --- R/taxid.R | 32 ++++++ README.md | 12 -- inst/doc/myTAI.Rmd | 1 inst/doc/myTAI.html | 2 inst/doc/other-strata.Rmd | 1 inst/doc/other-strata.html | 4 inst/doc/phylo-expression-object.R | 12 +- inst/doc/phylo-expression-object.Rmd | 13 +- inst/doc/phylo-expression-object.html | 160 ++++++++++++---------------------- inst/doc/phylostratigraphy.Rmd | 9 + inst/doc/phylostratigraphy.html | 20 ++-- inst/doc/tai-breaker.Rmd | 1 inst/doc/tai-gallery.Rmd | 1 inst/doc/tai-gallery.html | 72 +++++++-------- inst/doc/tai-stats.Rmd | 1 inst/doc/tai-stats.html | 56 +++++------ inst/doc/tai-transform.Rmd | 3 inst/doc/tai-transform.html | 20 ++-- inst/doc/taxonomy.R | 30 +++--- inst/doc/taxonomy.Rmd | 31 ++++-- inst/doc/taxonomy.html | 52 ++++++----- man/dot-plot_gene_heatmap_impl.Rd | 3 man/plot_gene_heatmap.Rd | 3 tests/testthat/test-plotting.R | 15 +++ vignettes/myTAI.Rmd | 1 vignettes/other-strata.Rmd | 1 vignettes/phylo-expression-object.Rmd | 13 +- vignettes/phylostratigraphy.Rmd | 9 + vignettes/tai-breaker.Rmd | 1 vignettes/tai-gallery.Rmd | 1 vignettes/tai-stats.Rmd | 1 vignettes/tai-transform.Rmd | 3 vignettes/taxonomy.Rmd | 31 ++++-- 38 files changed, 384 insertions(+), 353 deletions(-)
Title: Automatic Processing of Terrestrial-Based Technologies Point
Cloud Data for Forestry Purposes
Description: Process automation of point cloud data derived from terrestrial-based technologies such as Terrestrial Laser Scanner (TLS) or Mobile Laser Scanner. 'FORTLS' enables (i) detection of trees and estimation of tree-level attributes (e.g. diameters and heights), (ii) estimation of stand-level variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories at stand-level, and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2022, <doi:10.1016/j.envsoft.2022.105337>).
Author: Juan Alberto Molina-Valero [aut, cph, cre],
Adela Martinez-Calvo [aut, com],
Maria Jose Ginzo Villamayor [aut, com],
Juan Gabriel Alvarez-Gonzalez [aut, ths],
Fernando Montes [aut],
Cesar Perez-Cruzado [aut, ths]
Maintainer: Juan Alberto Molina-Valero <jamolinavalero@gmail.com>
Diff between FORTLS versions 1.6.0 dated 2025-07-29 and 1.6.1 dated 2025-11-11
FORTLS-1.6.0/FORTLS/R/geometric.features.R |only FORTLS-1.6.0/FORTLS/man/geometric.features.Rd |only FORTLS-1.6.0/FORTLS/man/geometric_features_point.Rd |only FORTLS-1.6.0/FORTLS/man/sort_sublists.Rd |only FORTLS-1.6.0/FORTLS/man/subset_matrix_by_indices.Rd |only FORTLS-1.6.0/FORTLS/src/geometric.features.cpp |only FORTLS-1.6.1/FORTLS/DESCRIPTION | 18 FORTLS-1.6.1/FORTLS/MD5 | 72 - FORTLS-1.6.1/FORTLS/R/RcppExports.R | 8 FORTLS-1.6.1/FORTLS/R/auxiliary.functions.R | 142 +- FORTLS-1.6.1/FORTLS/R/install_fortls_python_deps.R | 3 FORTLS-1.6.1/FORTLS/R/normalize.R | 12 FORTLS-1.6.1/FORTLS/R/tree.detection.multi.scan.R | 216 --- FORTLS-1.6.1/FORTLS/R/tree.detection.several.plots.R | 15 FORTLS-1.6.1/FORTLS/R/tree.detection.single.scan.R | 238 --- FORTLS-1.6.1/FORTLS/README.md | 5 FORTLS-1.6.1/FORTLS/build/partial.rdb |binary FORTLS-1.6.1/FORTLS/build/vignette.rds |binary FORTLS-1.6.1/FORTLS/inst/doc/plot_design_optimization.R | 2 FORTLS-1.6.1/FORTLS/inst/doc/plot_design_optimization.Rmd | 4 FORTLS-1.6.1/FORTLS/inst/doc/plot_design_optimization.html | 8 FORTLS-1.6.1/FORTLS/inst/doc/stand_level.Rmd | 4 FORTLS-1.6.1/FORTLS/inst/doc/stand_level.html | 4 FORTLS-1.6.1/FORTLS/inst/doc/tree_level.R | 78 - FORTLS-1.6.1/FORTLS/inst/doc/tree_level.Rmd | 88 - FORTLS-1.6.1/FORTLS/inst/doc/tree_level.html | 875 +++++++------ FORTLS-1.6.1/FORTLS/man/Rioja.data.Rd | 2 FORTLS-1.6.1/FORTLS/man/Rioja.simulations.Rd | 12 FORTLS-1.6.1/FORTLS/man/geometric_features_dist.Rd |only FORTLS-1.6.1/FORTLS/man/geometric_features_knn.Rd |only FORTLS-1.6.1/FORTLS/man/normalize.Rd | 5 FORTLS-1.6.1/FORTLS/man/tree.detection.multi.scan.Rd | 12 FORTLS-1.6.1/FORTLS/man/tree.detection.several.plots.Rd | 11 FORTLS-1.6.1/FORTLS/man/tree.detection.single.scan.Rd | 8 FORTLS-1.6.1/FORTLS/src/RcppExports.cpp | 88 - FORTLS-1.6.1/FORTLS/src/geometric_features_dist.cpp |only FORTLS-1.6.1/FORTLS/src/geometric_features_knn.cpp |only FORTLS-1.6.1/FORTLS/vignettes/plot_design_optimization.Rmd | 4 FORTLS-1.6.1/FORTLS/vignettes/stand_level.Rmd | 4 FORTLS-1.6.1/FORTLS/vignettes/tree.list.multi.tls.csv | 40 FORTLS-1.6.1/FORTLS/vignettes/tree.list.single.tls.csv | 27 FORTLS-1.6.1/FORTLS/vignettes/tree_level.Rmd | 88 - 42 files changed, 1024 insertions(+), 1069 deletions(-)
Title: Diagnosis of Metabolic Dysfunction Associated Fatty Liver
Disease
Description: The latest guidelines proposed by International Expert Consensus are used for the clinical diagnosis of Metabolic Associated Fatty Liver Disease (MAFLD). The new definition takes hepatic steatosis (determined by elastography or histology or biomarker-based fatty liver index) as a major criterion. In addition, race, gender, body mass index (BMI), waist circumference (WC), fasting plasma glucose (FPG), systolic blood pressure (SBP), diastolic blood pressure (DBP), triglycerides (TG), high-density lipoprotein cholesterol (HDLC), homeostatic model assessment of insulin resistance (HOMAIR), high sensitive c-reactive protein (HsCRP) for the diagnosis of MAFLD. Each parameter has to be interpreted based on the proposed cut-offs, making the diagnosis slightly complex and error-prone. This package is developed by incorporating the latest international expert consensus guidelines, and it will aid in the easy and quick diagnosis of MAFLD based on FibroScan in busy healthcare settings and also for [...truncated...]
Author: Jagadish Ramasamy [aut, cre]
Maintainer: Jagadish Ramasamy <iamjagankmr@gmail.com>
Diff between MAFLD versions 3.0.0 dated 2025-09-14 and 4.0.0 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/MAFLD.R | 11 ++++++++++- R/data.R | 1 + README.md | 8 ++++++-- data/x.rda |binary man/x.Rd | 1 + 8 files changed, 33 insertions(+), 14 deletions(-)
More information about SelectBoost.beta at CRAN
Permanent link
Title: Visualising How Nonlinear Dimension Reduction Warps Your Data
Description: To construct a model in 2-D space from 2-D nonlinear
dimension reduction data and then lift it to the high-dimensional
space. Additionally, provides tools to visualise the model overlay the
data in 2-D and high-dimensional space. Furthermore, provides
summaries and diagnostics to evaluate the nonlinear dimension
reduction layout.
Author: Jayani P. Gamage [aut, cre] ,
Dianne Cook [aut] ,
Paul Harrison [aut] ,
Michael Lydeamore [aut] ,
Thiyanga S. Talagala [aut]
Maintainer: Jayani P. Gamage <jayanilakshika76@gmail.com>
Diff between quollr versions 0.3.13 dated 2025-09-23 and 1.0.1 dated 2025-11-11
quollr-0.3.13/quollr/man/plot_rmse_layouts.Rd |only quollr-1.0.1/quollr/DESCRIPTION | 6 quollr-1.0.1/quollr/MD5 | 52 - quollr-1.0.1/quollr/NAMESPACE | 2 quollr-1.0.1/quollr/NEWS.md | 2 quollr-1.0.1/quollr/R/prediction.R | 28 quollr-1.0.1/quollr/data/scurve_plts.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse2.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse3.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse4.rda |binary quollr-1.0.1/quollr/inst/doc/quollr4algo.html | 321 ++++++---- quollr-1.0.1/quollr/inst/doc/quollr5summary.html | 2 quollr-1.0.1/quollr/inst/doc/quollr6bestbinwidth.R | 8 quollr-1.0.1/quollr/inst/doc/quollr6bestbinwidth.Rmd | 14 quollr-1.0.1/quollr/inst/doc/quollr6bestbinwidth.html | 32 quollr-1.0.1/quollr/inst/doc/quollr7bestfit.R | 4 quollr-1.0.1/quollr/inst/doc/quollr7bestfit.Rmd | 10 quollr-1.0.1/quollr/inst/doc/quollr7bestfit.html | 21 quollr-1.0.1/quollr/man/gen_diffbin1_errors.Rd | 4 quollr-1.0.1/quollr/man/glance.highd_vis_model.Rd | 2 quollr-1.0.1/quollr/man/plot_hbe_layouts.Rd |only quollr-1.0.1/quollr/src/prediction.cpp | 6 quollr-1.0.1/quollr/tests/testthat/_snaps/prediction.md | 54 - quollr-1.0.1/quollr/tests/testthat/test-prediction.R | 4 quollr-1.0.1/quollr/vignettes/quollr6bestbinwidth.Rmd | 14 quollr-1.0.1/quollr/vignettes/quollr7bestfit.Rmd | 10 quollr-1.0.1/quollr/vignettes/quollr7bestfit_files/figure-html/unnamed-chunk-3-1.png |binary 28 files changed, 345 insertions(+), 251 deletions(-)
Title: Efficient Evaluation of Quadratic Forms
Description: A range of quadratic forms are evaluated, using efficient methods.
Unnecessary transposes are not performed. Complex values are handled
consistently.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between quadform versions 0.0-2 dated 2024-05-14 and 0.0-4 dated 2025-11-11
quadform-0.0-2/quadform/build |only quadform-0.0-2/quadform/inst |only quadform-0.0-4/quadform/DESCRIPTION | 12 +-- quadform-0.0-4/quadform/MD5 | 15 +--- quadform-0.0-4/quadform/NAMESPACE | 40 ++++++++++- quadform-0.0-4/quadform/NEWS.md | 12 +++ quadform-0.0-4/quadform/R/quadform.R | 108 +++++++++++++++++++++++-------- quadform-0.0-4/quadform/README.md | 18 ++--- quadform-0.0-4/quadform/man/quad.form.Rd | 106 +++++++++++++++--------------- 9 files changed, 206 insertions(+), 105 deletions(-)
Title: Estimate Bayesian Multilevel Models for Compositional Data
Description: Implement Bayesian multilevel modelling for compositional data.
Compute multilevel compositional data and
perform log-ratio transforms at between and within-person levels,
fit Bayesian multilevel models for compositional predictors and outcomes,
and run post-hoc analyses such as isotemporal substitution models.
References:
Le, Stanford, Dumuid, and Wiley (2025) <doi:10.1037/met0000750>,
Le, Dumuid, Stanford, and Wiley (2025) <doi:10.1080/00273171.2025.2565598>.
Author: Flora Le [aut, cre] ,
Joshua F. Wiley [aut]
Maintainer: Flora Le <floralebui@gmail.com>
This is a re-admission after prior archival of version 1.3.2 dated 2025-05-25
Diff between multilevelcoda versions 1.3.2 dated 2025-05-25 and 1.3.3 dated 2025-11-11
multilevelcoda-1.3.2/multilevelcoda/R/substitution-bsubmargins.R |only multilevelcoda-1.3.2/multilevelcoda/R/substitution-sub-margins.R |only multilevelcoda-1.3.2/multilevelcoda/R/substitution-wsubmargins.R |only multilevelcoda-1.3.2/multilevelcoda/man/bsubmargins.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/build.basesub.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/create_substitution.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/print.summary.complr.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/submargins.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/update.complr.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/wsubmargins.Rd |only multilevelcoda-1.3.3/multilevelcoda/DESCRIPTION | 16 multilevelcoda-1.3.3/multilevelcoda/MD5 | 184 multilevelcoda-1.3.3/multilevelcoda/NAMESPACE | 33 multilevelcoda-1.3.3/multilevelcoda/NEWS.md | 11 multilevelcoda-1.3.3/multilevelcoda/R/brmcoda-methods.R | 91 multilevelcoda-1.3.3/multilevelcoda/R/brmcoda.R | 107 multilevelcoda-1.3.3/multilevelcoda/R/build.R | 338 + multilevelcoda-1.3.3/multilevelcoda/R/complr-methods.R | 144 multilevelcoda-1.3.3/multilevelcoda/R/complr.R | 465 +- multilevelcoda-1.3.3/multilevelcoda/R/get.R |only multilevelcoda-1.3.3/multilevelcoda/R/internal.R | 127 multilevelcoda-1.3.3/multilevelcoda/R/optimise.R |only multilevelcoda-1.3.3/multilevelcoda/R/pivot-coord.R | 371 - multilevelcoda-1.3.3/multilevelcoda/R/plot.R | 169 multilevelcoda-1.3.3/multilevelcoda/R/posterior.R | 397 - multilevelcoda-1.3.3/multilevelcoda/R/shiny.R | 484 +- multilevelcoda-1.3.3/multilevelcoda/R/substitution-bsub.R | 41 multilevelcoda-1.3.3/multilevelcoda/R/substitution-bsubmargin.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution-helpers.R | 2310 +++++----- multilevelcoda-1.3.3/multilevelcoda/R/substitution-sub.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution-submargin.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution-wsub.R | 39 multilevelcoda-1.3.3/multilevelcoda/R/substitution-wsubmargin.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution.R | 438 + multilevelcoda-1.3.3/multilevelcoda/R/summary.R | 373 - multilevelcoda-1.3.3/multilevelcoda/R/update.R | 164 multilevelcoda-1.3.3/multilevelcoda/README.md | 5 multilevelcoda-1.3.3/multilevelcoda/build/vignette.rds |binary multilevelcoda-1.3.3/multilevelcoda/inst/doc/B-composition-MLM.Rmd | 60 multilevelcoda-1.3.3/multilevelcoda/inst/doc/B-composition-MLM.html | 60 multilevelcoda-1.3.3/multilevelcoda/inst/doc/C-composition-MMLM.Rmd | 62 multilevelcoda-1.3.3/multilevelcoda/inst/doc/C-composition-MMLM.html | 60 multilevelcoda-1.3.3/multilevelcoda/inst/doc/D-substitution.Rmd | 24 multilevelcoda-1.3.3/multilevelcoda/inst/doc/D-substitution.html | 24 multilevelcoda-1.3.3/multilevelcoda/man/VarCorr.brmcoda.Rd | 10 multilevelcoda-1.3.3/multilevelcoda/man/as.data.frame.complr.Rd | 5 multilevelcoda-1.3.3/multilevelcoda/man/brmcoda.Rd | 40 multilevelcoda-1.3.3/multilevelcoda/man/bsub.Rd | 60 multilevelcoda-1.3.3/multilevelcoda/man/bsubmargin.Rd |only multilevelcoda-1.3.3/multilevelcoda/man/build.base.Rd |only multilevelcoda-1.3.3/multilevelcoda/man/build.rg.Rd | 16 multilevelcoda-1.3.3/multilevelcoda/man/coef.brmcoda.Rd | 12 multilevelcoda-1.3.3/multilevelcoda/man/compilr.Rd | 14 multilevelcoda-1.3.3/multilevelcoda/man/complr.Rd | 47 multilevelcoda-1.3.3/multilevelcoda/man/fitted.brmcoda.Rd | 30 multilevelcoda-1.3.3/multilevelcoda/man/fixef.brmcoda.Rd | 10 multilevelcoda-1.3.3/multilevelcoda/man/get-substitution.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/get_sbp.Rd |only multilevelcoda-1.3.3/multilevelcoda/man/get_variables.Rd |only multilevelcoda-1.3.3/multilevelcoda/man/mcmc_plot.brmcoda.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/mean.complr.Rd | 12 multilevelcoda-1.3.3/multilevelcoda/man/model.frame.brmcoda.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/nobs.brmcoda.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/pairs.brmcoda.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/pivot_coord.Rd | 35 multilevelcoda-1.3.3/multilevelcoda/man/pivot_coord_refit.Rd | 33 multilevelcoda-1.3.3/multilevelcoda/man/pivot_coord_rotate.Rd | 29 multilevelcoda-1.3.3/multilevelcoda/man/plot.brmcoda.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/plot.substitution.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/predict.brmcoda.Rd | 35 multilevelcoda-1.3.3/multilevelcoda/man/print.brmcoda.Rd | 6 multilevelcoda-1.3.3/multilevelcoda/man/print.complr.Rd | 4 multilevelcoda-1.3.3/multilevelcoda/man/print.substitution.Rd | 6 multilevelcoda-1.3.3/multilevelcoda/man/ranef.brmcoda.Rd | 10 multilevelcoda-1.3.3/multilevelcoda/man/residuals.brmcoda.Rd | 10 multilevelcoda-1.3.3/multilevelcoda/man/sub.Rd | 60 multilevelcoda-1.3.3/multilevelcoda/man/submargin.Rd |only multilevelcoda-1.3.3/multilevelcoda/man/substitution.Rd | 75 multilevelcoda-1.3.3/multilevelcoda/man/summary.brmcoda.Rd | 6 multilevelcoda-1.3.3/multilevelcoda/man/summary.complr.Rd | 18 multilevelcoda-1.3.3/multilevelcoda/man/summary.pivot_coord.Rd | 14 multilevelcoda-1.3.3/multilevelcoda/man/summary.substitution.Rd | 6 multilevelcoda-1.3.3/multilevelcoda/man/update.brmcoda.Rd | 21 multilevelcoda-1.3.3/multilevelcoda/man/var.complr.Rd | 6 multilevelcoda-1.3.3/multilevelcoda/man/vcov.brmcoda.Rd | 10 multilevelcoda-1.3.3/multilevelcoda/man/wsub.Rd | 60 multilevelcoda-1.3.3/multilevelcoda/man/wsubmargin.Rd |only multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-bayesfactors.R | 8 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-brmcoda.R | 12 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-bsub.R | 68 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-bsubmargins.R | 48 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-complr.R | 12 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-plotcoda.R | 4 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-submargins.R | 42 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-substitution.R | 20 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-update.R | 58 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-wsub.R | 100 multilevelcoda-1.3.3/multilevelcoda/tests/testthat/test-wsubmargins.R | 48 multilevelcoda-1.3.3/multilevelcoda/vignettes/B-composition-MLM.Rmd | 60 multilevelcoda-1.3.3/multilevelcoda/vignettes/B-composition-MLM.Rmd.orig | 30 multilevelcoda-1.3.3/multilevelcoda/vignettes/C-composition-MMLM.Rmd | 62 multilevelcoda-1.3.3/multilevelcoda/vignettes/C-composition-MMLM.Rmd.orig | 10 multilevelcoda-1.3.3/multilevelcoda/vignettes/D-substitution.Rmd | 24 multilevelcoda-1.3.3/multilevelcoda/vignettes/D-substitution.Rmd.orig | 6 104 files changed, 4295 insertions(+), 3642 deletions(-)
More information about multilevelcoda at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-10 1.14.6.4
Title: Provides Batch Functions and Visualisation for Basic Statistical
Procedures
Description: Designed to streamline data analysis and statistical testing, reducing the length of R
scripts while generating well-formatted outputs in 'pdf', 'Microsoft Word', and 'Microsoft Excel'
formats. In essence, the package contains functions which are sophisticated wrappers around
existing R functions that are called by using 'f_' (user f_riendly) prefix followed by the normal
function name. This first version of the 'rfriend' package focuses primarily on data exploration,
including tools for creating summary tables, f_summary(), performing data transformations,
f_boxcox() in part based on 'MASS/boxcox' and 'rcompanion', and f_bestNormalize()
which wraps and extends functionality from the 'bestNormalize' package. Furthermore, 'rfriend'
can automatically (or on request) generate visualizations such as boxplots, f_boxplot(),
QQ-plots, f_qqnorm(), histograms f_hist(), and density plots. Additionally, the package includes
four statistical test functions: f_aov(), f_kruskal_test(), f_glm(), f_c [...truncated...]
Author: Sander H. van Delden [aut, cre]
Maintainer: Sander H. van Delden <plantmind@proton.me>
Diff between rfriend versions 1.0.0 dated 2025-07-16 and 2.0.0 dated 2025-11-11
DESCRIPTION | 8 - MD5 | 60 ++++---- NAMESPACE | 2 NEWS.md |only R/faov.R | 306 ++++++++++++++++++++++++++++--------------- R/fbestnormalize.R | 242 +++++++++++++++++++++++----------- R/fboxcox.R | 219 ++++++++++++++++++++---------- R/fboxplot.R | 139 ++++++++++++++----- R/fclear.R | 15 -- R/fcorplot.R | 252 +++++++++++++++++++++++------------ R/ffactors.R | 21 +- R/fglm.R | 183 ++++++++++++++++--------- R/fhist.R | 58 +++----- R/fkruskal_test.R | 204 +++++++++++++++++++--------- R/fmodel_compare.R | 2 R/fqqnorm.R | 57 +++----- R/fsummary.R | 125 ++++++++--------- R/helper_extract_extension.R |only R/helper_get_save_path.R |only R/import.R | 2 README.md |only man/f_aov.Rd | 23 +-- man/f_bestNormalize.Rd | 17 +- man/f_boxcox.Rd | 40 ++--- man/f_boxplot.Rd | 24 ++- man/f_corplot.Rd | 21 +- man/f_factors.Rd | 17 +- man/f_glm.Rd | 20 +- man/f_hist.Rd | 14 + man/f_kruskal_test.Rd | 25 +-- man/f_qqnorm.Rd | 14 + man/f_summary.Rd | 21 +- man/print.f_summary.Rd | 2 33 files changed, 1339 insertions(+), 794 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate and play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive. This package is the successor of 'ProTrackR' providing
better performance.
Author: Pepijn de Vries [aut, cre] ,
Olav Soerensen [aut]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR2 versions 0.0.5 dated 2024-11-09 and 0.1.0 dated 2025-11-11
DESCRIPTION | 21 MD5 | 177 +++--- NAMESPACE | 208 ++++--- NEWS.md | 88 +-- R/cell.R | 92 ++- R/command.R | 188 +++--- R/cpp11.R | 56 -- R/data.R | 32 - R/demo.R | 16 R/instrument.R | 131 ++-- R/mod_info.R | 61 ++ R/note.R | 198 +++---- R/pattern.R | 79 +- R/play.R |only R/render.R | 100 ++- R/s3.R | 186 +++--- R/samples.R | 290 +++++++++- R/select_ops.R | 649 ++++++++++++----------- README.md | 137 ++--- build/vignette.rds |binary inst/doc/ProTrackR_vs_ProTrackR2.R | 87 ++- inst/doc/ProTrackR_vs_ProTrackR2.Rmd | 293 ++++++---- inst/doc/ProTrackR_vs_ProTrackR2.html | 472 +++++------------ inst/doc/effect_commands.R | 72 ++ inst/doc/effect_commands.Rmd | 214 +++++-- inst/doc/effect_commands.html | 133 ++++ inst/doc/s3class.R | 2 inst/doc/s3class.Rmd | 607 +++++++++++----------- inst/doc/s3class.html | 110 +--- inst/doc/sel_assign.Rmd | 360 ++++++------- inst/doc/sel_assign.html | 44 - inst/mod.intro |binary man/ProTrackR2-package.Rd | 62 +- man/as_modplug_pattern.Rd | 56 +- man/as_pt2cell.Rd |only man/effect_commands.Rd | 48 - man/figures/logo.svg | 396 +++++++------- man/mod_info.Rd | 159 +++-- man/mod_io.Rd | 68 +- man/play.Rd | 119 ++-- man/pt2_cell.Rd | 68 +- man/pt2_command.Rd | 100 +-- man/pt2_demo.Rd | 36 - man/pt2_duration.Rd | 74 +- man/pt2_instrument.Rd | 98 +-- man/pt2_new_mod.Rd | 50 - man/pt2_new_pattern.Rd | 54 - man/pt2_note.Rd | 112 ++-- man/pt2_note_to_period.Rd | 68 +- man/pt2_pattern.Rd | 60 +- man/pt2_render.Rd | 112 ++-- man/pt2_render_options.Rd | 85 +-- man/pt2_sample.Rd | 60 +- man/pt2_sample_to_audio.Rd |only man/pt2_validate.Rd | 62 +- man/s3methods.Rd | 362 +++++++------ man/samp_io.Rd | 74 +- man/sample_properties.Rd |only man/select_assign.Rd | 160 +++-- src/cpp11.cpp | 140 +---- src/get_mod.cpp | 2 src/get_mod.h | 2 src/mod_header.cpp | 37 - src/mod_header.h | 4 src/mod_io.cpp | 26 src/mod_render.cpp | 29 - src/patterns.cpp | 24 src/pt2-clone.h |only src/pt2-clone/LICENSE.txt | 50 - src/pt2-clone/pt2_audio.c | 870 ++++++++++++++++---------------- src/pt2-clone/pt2_module_loader.c | 84 +-- src/pt2-clone/pt2_module_loader.h | 2 src/pt2-clone/pt2_sampler.c | 566 ++++++++++---------- src/pt2-clone/smploaders/pt2_load_wav.c | 9 src/pt_cell.cpp | 329 +----------- src/pt_cell.h | 5 src/pt_cleanup.cpp | 2 src/pt_init.cpp | 3 src/samp_io.cpp | 44 - src/samples.cpp | 87 +-- src/samples.h | 4 tests |only vignettes/ProTrackR_vs_ProTrackR2.Rmd | 293 ++++++---- vignettes/effect_commands.Rmd | 214 +++++-- vignettes/s3class.Rmd | 607 +++++++++++----------- vignettes/sel_assign.Rmd | 360 ++++++------- 86 files changed, 6044 insertions(+), 5395 deletions(-)
Title: Model Based Phylogenetic Analysis
Description: A collection of functions to do model-based phylogenetic analysis.
It includes functions to calculate community phylogenetic diversity,
to estimate correlations among functional traits while accounting for
phylogenetic relationships, and to fit phylogenetic generalized linear
mixed models. The Bayesian phylogenetic generalized linear mixed models
are fitted with the 'INLA' package (<https://www.r-inla.org>).
Author: Anthony Ives [aut],
Russell Dinnage [aut] ,
Lucas A. Nell [aut] ,
Matthew Helmus [aut],
Daijiang Li [aut, cre]
Maintainer: Daijiang Li <daijianglee@gmail.com>
Diff between phyr versions 1.1.0 dated 2020-12-18 and 1.1.3 dated 2025-11-11
DESCRIPTION | 17 MD5 | 61 +- NAMESPACE | 2 NEWS.md | 8 R/RcppExports.R | 28 + R/cor_phylo.R | 234 ++++++----- R/pglmm-utils.R | 262 ++++++++++-- R/pglmm.R | 25 - R/pglmm_compare.R | 8 R/utils.R | 1 README.md | 81 ++- build/vignette.rds |binary inst/doc/benchmarks.R | 246 +++++------ inst/doc/benchmarks.html | 728 ++++++++++++++++++++++------------ inst/doc/pglmm.html | 375 ++++++++++++++--- inst/doc/plot-re.html | 753 +++++++++++++++++++++++++----------- man/cor_phylo.Rd | 118 ++--- man/figures |only man/nobs.communityPGLMM.Rd | 4 man/pglmm-profile-LRT.Rd | 14 man/refit_boots.Rd | 12 man/simulate.communityPGLMM.Rd | 25 + src/RcppExports.cpp | 76 +++ src/binaryPGLMM.cpp | 2 src/cor_phylo.cpp | 544 +++++++++++++------------- src/cor_phylo.h | 157 ++----- tests/testthat/test-cor_phylo.R | 36 + tests/testthat/test-pcd.R | 16 tests/testthat/test-pglmm.R | 57 +- tests/testthat/test-pglmm_compare.R | 2 tests/testthat/test-psv.R | 6 tests/testthat/test_pglmm_utils.R | 24 - 32 files changed, 2522 insertions(+), 1400 deletions(-)
Title: Convert Addresses to Standard Inputs
Description: Efficient tools for parsing and standardizing Australian
addresses from textual data. It utilizes optimized algorithms to accurately identify and
extract components of addresses, such as street names, types, and postcodes, especially
for large batched data in contexts where sending addresses to internet services may be
slow or inappropriate. The core functionality is built on fast string processing techniques
to handle variations in address formats and abbreviations commonly found in Australian
address data. Designed for data scientists, urban planners, and logistics analysts, the
package facilitates the cleaning and normalization of address information, supporting
better data integration and analysis in urban studies, geography, and related fields.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between healthyAddress versions 0.4.5 dated 2025-01-08 and 0.5.1 dated 2025-11-11
DESCRIPTION | 12 - MD5 | 18 + NEWS.md | 4 R/HashStreetName.R | 94 ++++----- R/download_latlon_data.R | 142 +++++++-------- R/fillPostcodeStreets.R | 63 +++--- R/read_locality_by_postcode.R | 2 inst/extdata/LOCALITY_BY_POSTCODE.qdata |only inst/extdata/POSTCODE-STREET_TYPE_CODE-STREET_NAME.qdata |only man/download_latlon_data.Rd | 7 tests/tinytest.R | 10 - 11 files changed, 179 insertions(+), 173 deletions(-)
More information about healthyAddress at CRAN
Permanent link
Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler/>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects.
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg [aut, cre],
Uku Raudvere [aut]
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>
Diff between gprofiler2 versions 0.2.3 dated 2024-02-23 and 0.2.4 dated 2025-11-11
DESCRIPTION | 14 ++-- MD5 | 24 +++---- NAMESPACE | 1 R/gprofiler2.R | 107 ++++++++++++++++++++++---------- build/vignette.rds |binary inst/doc/gprofiler2.R | 60 +++++++++--------- inst/doc/gprofiler2.Rmd | 6 - inst/doc/gprofiler2.html | 154 ++++++++++++++++++++++++----------------------- inst/extdata |only man/gostplot.Rd | 3 man/gprofiler_request.Rd |only man/publish_gostplot.Rd | 3 man/publish_gosttable.Rd | 3 vignettes/gprofiler2.Rmd | 6 - 14 files changed, 218 insertions(+), 163 deletions(-)
Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Toolbox to process raw data from closed loop flux chamber (or tent)
setups into ecosystem gas fluxes usable for analysis. It goes from a
data frame of gas concentration over time (which can contain several
measurements) and a meta data file indicating which measurement was done
when, to a data frame of ecosystem gas fluxes including quality diagnostics.
Organized with one function per step, maximizing user flexibility and backwards
compatibility. Different models to estimate the fluxes from the raw data are
available: exponential as described in
Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, exponential as described in
Hutchinson and Mosier (1981) <doi:10.2136/sssaj1981.03615995004500020017x>,
quadratic, and linear. Other functions include quality assessment,
plotting for visual check, calculation of fluxes based on the setup
specific parameters (chamber size, plot area, ...), gross primary production
and transpiration rate calculation, and light response curves.
Author: Joseph Gaudard [aut, cre] ,
Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>
Diff between fluxible versions 1.3.3 dated 2025-09-25 and 1.3.4 dated 2025-11-11
DESCRIPTION | 8 MD5 | 88 ++--- NEWS.md | 5 R/flux_fitting.R | 27 - R/flux_fitting_exptz.R | 9 R/flux_fitting_hm.R | 7 R/flux_fitting_lm.R | 7 R/flux_fitting_quadratic.R | 9 R/flux_fitting_zhao18.R | 9 R/flux_fortify.R | 10 R/flux_fortify_exp.R | 7 R/flux_fortify_lin.R | 5 R/flux_fortify_quadratic.R | 5 R/flux_param_exp.R | 12 R/flux_param_kappamax.R | 12 R/flux_param_lm.R | 12 R/flux_param_qua.R | 12 R/flux_plot.R | 2 R/flux_plot_flag.R | 2 README.md | 71 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 9 inst/doc/two-gases.html | 4 man/figures/README-short-example-1.png |binary man/figures/logo.png |binary man/flux_fitting.Rd | 4 man/flux_fitting_exptz.Rd | 4 man/flux_fitting_hm.Rd | 4 man/flux_fitting_lm.Rd | 5 man/flux_fitting_quadratic.Rd | 13 man/flux_fitting_zhao18.Rd | 4 man/flux_fortify_exp.Rd | 4 man/flux_fortify_lin.Rd | 4 man/flux_fortify_quadratic.Rd | 4 man/flux_param_exp.Rd | 4 man/flux_param_kappamax.Rd | 4 man/flux_param_lm.Rd | 4 man/flux_param_qua.Rd | 4 tests/testthat/_snaps/flux_fitting.md | 47 +- tests/testthat/_snaps/flux_plot.md | 32 ++ tests/testthat/_snaps/flux_plot/flux-diff-and-lm.svg |only tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-exp-hm.svg |only tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-exp-tz.svg |only tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-quadratic.svg |only tests/testthat/test-flux_fitting.R | 27 + tests/testthat/test-flux_plot.R | 158 ++++++++++ 47 files changed, 456 insertions(+), 202 deletions(-)
Title: Dynamic ICAR Spatiotemporal Factor Models
Description: Bayesian factor models are effective tools for dimension reduction. This is especially applicable to multivariate large-scale datasets. It allows researchers to understand the latent factors of the data which are the linear or non-linear combination of the variables. Dynamic Intrinsic Conditional Autocorrelative Priors (ICAR) Spatiotemporal Factor Models 'DIFM' package provides function to run Markov Chain Monte Carlo (MCMC), evaluation methods and visual plots from Shin and Ferreira (2023)<doi:10.1016/j.spasta.2023.100763>. Our method is a class of Bayesian factor model which can account for spatial and temporal correlations. By incorporating these correlations, the model can capture specific behaviors and provide predictions.
Author: Hwasoo Shin [aut, cre],
Marco Ferreira [aut]
Maintainer: Hwasoo Shin <hshin2@hfhs.org>
Diff between DIFM versions 1.0 dated 2024-04-12 and 1.0.1 dated 2025-11-11
DESCRIPTION | 15 ++++----- MD5 | 14 ++++---- R/RcppExports.R | 15 ++------- build/partial.rdb |binary inst/doc/DIFMvignette.html | 24 +++++++------- src/marginal.d.cpp | 31 +++++++++---------- src/sigma2.simulation.cpp | 65 ++++++++++++++++++++-------------------- src/tau.simulation.cpp | 73 +++++++++++++++++++++++---------------------- 8 files changed, 117 insertions(+), 120 deletions(-)
Title: General Unified Threshold Model of Survival for Bees using
Bayesian Inference
Description: Tools to calibrate, validate, and make predictions with the
General Unified Threshold model of Survival adapted for Bee species. The
model is presented in the publication from Baas, J., Goussen, B., Miles, M.,
Preuss, T.G., Roessing, I. (2022) <doi:10.1002/etc.5423> and
Baas, J., Goussen, B., Taenzler, V., Roeben, V., Miles, M., Preuss, T.G.,
van den Berg, S., Roessink, I. (2024) <doi:10.1002/etc.5871>, and is based on the
GUTS framework Jager, T., Albert, C., Preuss, T.G. and Ashauer, R. (2011)
<doi:10.1021/es103092a>.
The authors are grateful to Bayer A.G. for its financial support.
Author: Benoit Goussen [aut] ,
Liubov Zakharova [ctb],
Carlo Romoli [aut, cre],
Bayer AG [cph, fnd],
ibacon GmbH [cph]
Maintainer: Carlo Romoli <carlo.romoli@ibacon.com>
Diff between BeeGUTS versions 1.3.0 dated 2024-10-23 and 1.4.0 dated 2025-11-11
DESCRIPTION | 26 +++++++-------- MD5 | 36 +++++++++++----------- NEWS.md | 3 + R/BeeGUTS-package.R | 29 +++++++++++++++++ R/ppc.R | 6 +++ README.md | 44 +++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary data/valBetacyfluthrinChronic.rda |only inst/doc/Tutorial.html | 43 ++++++++++++-------------- man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-example-5.png |binary man/ppc.beeSurvValidation.Rd | 6 +++ man/valBetacyfluthrinChronic.Rd |only vignettes/man/figures/Tutorial-example-2.png |binary vignettes/man/figures/Tutorial-example-3.png |binary vignettes/man/figures/Tutorial-example-4.png |binary vignettes/man/figures/Tutorial-example-5.png |binary 20 files changed, 118 insertions(+), 75 deletions(-)
Title: Value Added Receiver Operating Characteristics Curve
Description: A continuous version of the receiver operating characteristics (ROC) curve to assess both classification and continuity performances of biomarkers, diagnostic tests, or risk prediction models.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between varoc versions 0.4.0 dated 2025-06-21 and 1.0.0 dated 2025-11-11
varoc-0.4.0/varoc/R/tmd.R |only varoc-1.0.0/varoc/DESCRIPTION | 11 +- varoc-1.0.0/varoc/MD5 | 12 +-- varoc-1.0.0/varoc/NAMESPACE | 6 - varoc-1.0.0/varoc/R/tmd_ft.R |only varoc-1.0.0/varoc/R/varoc.R | 152 ++++++++++++++++++--------------------- varoc-1.0.0/varoc/R/varoc3d.R |only varoc-1.0.0/varoc/man/varoc.Rd | 43 ++++------- varoc-1.0.0/varoc/man/varoc3d.Rd |only 9 files changed, 105 insertions(+), 119 deletions(-)
Title: Identify and Measure Tree Rings on X-Ray Micro-Density Profiles
Description: Contains functions to identify tree-ring borders based on X-ray micro-density profiles and a Graphical User Interface (GUI) to visualize density profiles and correct tree-ring borders. Campelo F, Mayer K, Grabner M. (2019) <doi:10.1016/j.dendro.2018.11.002>.
Author: Filipe Campelo [aut, cre, cph],
Konrad Mayer [ctb]
Maintainer: Filipe Campelo <fcampelo@ci.uc.pt>
Diff between xRing versions 0.1.1 dated 2022-04-22 and 0.1.2 dated 2025-11-11
xRing-0.1.1/xRing/man/plot.Rd |only xRing-0.1.1/xRing/man/print.Rd |only xRing-0.1.2/xRing/DESCRIPTION | 28 ++--- xRing-0.1.2/xRing/MD5 | 75 +++++++-------- xRing-0.1.2/xRing/R/calibrateFilm.R | 4 xRing-0.1.2/xRing/R/detectRings.R | 2 xRing-0.1.2/xRing/R/imDisplay.R | 2 xRing-0.1.2/xRing/R/imRead.R | 6 - xRing-0.1.2/xRing/R/plot.R | 34 +++--- xRing-0.1.2/xRing/R/plotRings.R | 2 xRing-0.1.2/xRing/R/print.R | 24 ++-- xRing-0.1.2/xRing/R/toxRing.R | 2 xRing-0.1.2/xRing/R/toxRingList.R | 2 xRing-0.1.2/xRing/inst/img/AFO1046.1200dpi_AFO1046.RData |only xRing-0.1.2/xRing/man/PaPiRaw.Rd | 13 ++ xRing-0.1.2/xRing/man/PaPiSpan.Rd | 10 ++ xRing-0.1.2/xRing/man/addRing.Rd | 2 xRing-0.1.2/xRing/man/calibrateFilm.Rd | 2 xRing-0.1.2/xRing/man/combineFrag.Rd | 2 xRing-0.1.2/xRing/man/correctRings.Rd | 2 xRing-0.1.2/xRing/man/detectEwLw.Rd | 2 xRing-0.1.2/xRing/man/detectRings.Rd | 4 xRing-0.1.2/xRing/man/fitCalibrationModel.Rd | 6 - xRing-0.1.2/xRing/man/getBorders.Rd | 2 xRing-0.1.2/xRing/man/getDensity.Rd | 2 xRing-0.1.2/xRing/man/getRwls.Rd | 2 xRing-0.1.2/xRing/man/getSteps.Rd | 2 xRing-0.1.2/xRing/man/imCrop.Rd | 2 xRing-0.1.2/xRing/man/imDisplay.Rd | 4 xRing-0.1.2/xRing/man/imRead.Rd | 8 + xRing-0.1.2/xRing/man/measureProfiles.Rd | 2 xRing-0.1.2/xRing/man/plot.xRing.Rd |only xRing-0.1.2/xRing/man/plot.xRingList.Rd |only xRing-0.1.2/xRing/man/plotRings.Rd | 4 xRing-0.1.2/xRing/man/print.xRing.Rd |only xRing-0.1.2/xRing/man/print.xRingList.Rd |only xRing-0.1.2/xRing/man/removeRing.Rd | 2 xRing-0.1.2/xRing/man/selectProfiles.Rd | 2 xRing-0.1.2/xRing/man/setLastYear.Rd | 2 xRing-0.1.2/xRing/man/stepIncrease.Rd | 2 xRing-0.1.2/xRing/man/toxRing.Rd | 4 xRing-0.1.2/xRing/man/toxRingList.Rd | 4 42 files changed, 170 insertions(+), 98 deletions(-)
Title: Seamless Access to World Bank International Debt Statistics
(IDS)
Description: Access and analyze the World Bank's International Debt Statistics
(IDS) <https://www.worldbank.org/en/programs/debt-statistics/ids>.
IDS provides creditor-debtor relationships between countries, regions, and
institutions. 'wbids' enables users to download, process and work with IDS
series across multiple geographies, counterparts, and time periods.
Author: Teal Emery [aut, cre],
Teal Insights [cph],
Christoph Scheuch [aut] ,
Christopher Smith [ctb]
Maintainer: Teal Emery <lte@tealinsights.com>
Diff between wbids versions 1.1.0 dated 2025-09-04 and 1.1.1 dated 2025-11-11
DESCRIPTION | 6 LICENSE | 4 MD5 | 98 NAMESPACE | 46 NEWS.md | 5 R/global-variables.R | 24 R/ids_bulk.R | 562 +- R/ids_bulk_files.R | 79 R/ids_bulk_series.R | 82 R/ids_get.R | 1082 ++--- R/ids_list_counterparts.R | 58 R/ids_list_entities.R | 130 R/ids_list_series.R | 56 R/ids_list_series_topics.R | 48 R/perform_request.R | 208 R/read_bulk_info.R | 42 R/sysdata.R | 54 R/wbids-package.R | 26 README.md | 294 - build/vignette.rds |binary inst/doc/data-model.R | 94 inst/doc/data-model.html | 5729 +++++++++++++-------------- inst/doc/data-model.qmd | 250 - man/counterparts.Rd | 32 man/entities.Rd | 32 man/ids_bulk.Rd | 116 man/ids_bulk_files.Rd | 56 man/ids_bulk_series.Rd | 66 man/ids_get.Rd | 288 - man/ids_list_counterparts.Rd | 66 man/ids_list_entities.Rd | 88 man/ids_list_geographies.Rd | 90 man/ids_list_series.Rd | 64 man/ids_list_series_topics.Rd | 56 man/read_bulk_info.Rd | 32 man/series.Rd | 32 man/series_topics.Rd | 32 man/wbids-package.Rd | 70 tests/testthat.R | 24 tests/testthat/test-ids_bulk.R | 812 +-- tests/testthat/test-ids_bulk_files.R | 30 tests/testthat/test-ids_bulk_series.R | 30 tests/testthat/test-ids_get.R | 1292 +++--- tests/testthat/test-ids_list_counterparts.R | 20 tests/testthat/test-ids_list_entities.R | 48 tests/testthat/test-ids_list_series.R | 18 tests/testthat/test-ids_list_series_topics.R | 16 tests/testthat/test-perform_request.R | 230 - tests/testthat/test-read_bulk_info.R | 19 vignettes/data-model.qmd | 250 - 50 files changed, 6532 insertions(+), 6354 deletions(-)
Title: Sorted L1 Penalized Estimation
Description: Efficient implementations for Sorted L-One Penalized Estimation
(SLOPE): generalized linear models regularized with the sorted L1-norm
(Bogdan et al. 2015). Supported models include
ordinary least-squares regression, binomial regression, multinomial
regression, and Poisson regression. Both dense and sparse predictor
matrices are supported. In addition, the package features predictor
screening rules that enable fast and efficient solutions to high-dimensional
problems.
Author: Johan Larsson [aut, cre] ,
Jonas Wallin [aut] ,
Malgorzata Bogdan [aut] ,
Ewout van den Berg [aut],
Chiara Sabatti [aut],
Emmanuel Candes [aut],
Evan Patterson [aut],
Weijie Su [aut],
Jakub Kala [aut],
Krystyna Grzesiak [aut],
Mathurin Massias [aut], [...truncated...]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between SLOPE versions 1.1.0 dated 2025-10-30 and 1.2.0 dated 2025-11-11
DESCRIPTION | 6 - MD5 | 47 +++++++------- NEWS.md | 26 ++++++++ R/plot.R | 2 R/regularization_weights.R | 2 R/slope.R | 4 - README.md | 60 +++++++++++++++--- inst/CITATION | 99 +++++++++++-------------------- inst/WORDLIST | 4 + inst/doc/introduction.html | 6 - inst/doc/solvers.html | 8 +- inst/include/slope/cv.h | 11 ++- inst/include/slope/eigen_compat.h |only inst/include/slope/folds.h | 7 +- inst/include/slope/math.h | 4 - inst/include/slope/ols.h | 4 - inst/include/slope/slope.h | 74 +++++++++++++++++++---- inst/include/slope/solvers/hybrid_cd.h | 3 inst/include/slope/solvers/pgd.h | 4 - inst/include/slope/utils.h | 40 +++++++++++- man/SLOPE.Rd | 2 man/figures/README-unnamed-chunk-5-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/regularizationWeights.Rd | 2 src/rcpp_slope.cpp | 16 ++++- tests/testthat/test-coef.R | 26 ++++++++ 26 files changed, 318 insertions(+), 139 deletions(-)
Title: Tools for Information-Based Feature Selection and Scoring
Description: A toolbox of fast, native and parallel implementations of various information-based importance criteria estimators and feature selection filters based on them, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <https://www.jmlr.org/papers/v13/brown12a.html>.
Contains, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <https://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between praznik versions 11.0.0 dated 2022-05-20 and 12.0.0 dated 2025-11-11
praznik-11.0.0/praznik/R/pure.R |only praznik-11.0.0/praznik/tests/testthat |only praznik-11.0.0/praznik/tests/testthat.R |only praznik-12.0.0/praznik/DESCRIPTION | 16 ++++----- praznik-12.0.0/praznik/MD5 | 50 +++++++++++++++-------------- praznik-12.0.0/praznik/NAMESPACE | 1 praznik-12.0.0/praznik/R/transforms.R | 30 +++++++++++++++++ praznik-12.0.0/praznik/inst/CITATION | 24 ++++--------- praznik-12.0.0/praznik/inst/NEWS | 4 ++ praznik-12.0.0/praznik/inst/tinytest |only praznik-12.0.0/praznik/man/tspTransform.Rd |only praznik-12.0.0/praznik/src/cmis.h | 6 +-- praznik-12.0.0/praznik/src/hs.h | 4 +- praznik-12.0.0/praznik/src/ims.h | 2 - praznik-12.0.0/praznik/src/jmis.h | 4 +- praznik-12.0.0/praznik/src/kt.h | 4 +- praznik-12.0.0/praznik/src/minmaxs.h | 4 +- praznik-12.0.0/praznik/src/mis.h | 4 +- praznik-12.0.0/praznik/src/praznik.c | 5 ++ praznik-12.0.0/praznik/src/shared.h | 4 +- praznik-12.0.0/praznik/src/trips.h | 2 - praznik-12.0.0/praznik/src/tsp.h |only praznik-12.0.0/praznik/tests/tinytest.R |only 23 files changed, 98 insertions(+), 66 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.3.2 dated 2025-10-13 and 1.3.3 dated 2025-11-11
DESCRIPTION | 8 MD5 | 38 - NAMESPACE | 1 NEWS.md | 7 R/OMOPGenerics-package.R | 1 R/assert.R | 5 R/classCdmReference.R | 19 R/classCdmTable.R | 10 R/classConceptSetExpression.R | 32 - R/compute.R | 108 +-- R/exportConceptSetExpression.R | 2 R/exportSummarisedResult.R | 18 R/importConceptSetExpression.R | 17 R/logger.R | 47 - inst/doc/logging.html | 52 - inst/doc/summarised_result.html | 886 +++++++++++++++---------------- man/assertLogical.Rd | 3 man/exportSummarisedResult.Rd | 5 tests/testthat/test-logger.R | 6 tests/testthat/test-methodComputeTable.R | 11 20 files changed, 647 insertions(+), 629 deletions(-)
Title: Modelling of Extreme Values
Description: Various tools for the analysis of univariate, multivariate and functional extremes. Exact simulation from max-stable processes (Dombry, Engelke and Oesting, 2016, <doi:10.1093/biomet/asw008>, R-Pareto processes for various parametric models, including Brown-Resnick (Wadsworth and Tawn, 2014, <doi:10.1093/biomet/ast042>) and Extremal Student (Thibaud and Opitz, 2015, <doi:10.1093/biomet/asv045>). Threshold selection methods, including Wadsworth (2016) <doi:10.1080/00401706.2014.998345>, and Northrop and Coleman (2014) <doi:10.1007/s10687-014-0183-z>. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes, e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>.
Author: Leo Belzile [aut, cre] ,
Jennifer L. Wadsworth [aut],
Paul J. Northrop [aut] ,
Raphael Huser [aut] ,
Scott D. Grimshaw [aut] ,
Jin Zhang [ctb],
Michael A. Stephens [ctb],
Art B. Owen [ctb]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between mev versions 2.0 dated 2025-10-22 and 2.1 dated 2025-11-11
DESCRIPTION | 6 MD5 | 50 ++--- NAMESPACE | 7 NEWS.md | 25 ++ R/NCdiag.R | 2 R/coefvariation.R | 14 - R/extgp.R | 363 ++++++++++++++++++++++++++++++++------ R/infomattest.R | 41 +++- R/penultimate.R | 91 +++++++-- R/pickands.R | 4 R/tailindex.R | 23 +- R/threshold.R | 240 +++++++++++++++---------- R/thselect.R | 114 +++++++++++ R/vartymetric.R | 29 ++- inst/doc/mev-vignette.html | 10 - inst/tinytest/test-distribution.R | 122 ++++++++++++ inst/tinytest/test-egp.R | 268 ++++++++++++++-------------- man/egpdist.Rd | 3 man/smith.penult.Rd | 74 +++++-- man/thselect.cbm.Rd |only man/thselect.egp.Rd |only man/thselect.rbm.Rd | 5 man/thselect.sdinfo.Rd | 4 man/thselect.vmetric.Rd | 17 + man/tstab.cv.Rd | 14 - man/tstab.egp.Rd | 13 + man/tstab.gpd.Rd | 4 27 files changed, 1160 insertions(+), 383 deletions(-)
Title: Ecological Trajectory Analysis
Description: Analysis of temporal changes (i.e. dynamics) of ecological entities, defined as trajectories on a chosen multivariate space, by providing a set of
trajectory metrics and visual representations [De Caceres et al. (2019) <doi:10.1002/ecm.1350>;
and Sturbois et al. (2021) <doi:10.1016/j.ecolmodel.2020.109400>]. Includes functions
to estimate metrics for individual trajectories (length, directionality, angles, ...) as well as
metrics to relate pairs of trajectories (dissimilarity and convergence). Functions are also
provided to estimate the ecological quality of ecosystem with respect to reference conditions
[Sturbois et al. (2023) <doi:10.1002/ecs2.4726>].
Author: Miquel De Caceres [aut, cre] ,
Nicolas Djeghri [aut] ,
Anthony Sturbois [aut] ,
Javier De la Casa [ctb]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between ecotraj versions 1.1.1 dated 2025-08-28 and 1.2.0 dated 2025-11-11
DESCRIPTION | 15 ++-- MD5 | 30 ++++++--- NAMESPACE | 10 ++- NEWS.md | 5 + R/cycleShiftArrows.R |only R/ecotraj-package.R | 5 - R/trajectoryComparison.R | 121 ++++++++++++++++++++++++++++++++------- R/trajectoryConvergencePlot.R |only R/trajectoryCyclical.R | 4 - R/trajectoryCyclicalPlots.R | 6 - R/trajectoryRMA.R |only R/trajectoryRMAPlot.R |only build/partial.rdb |binary man/cycleShiftArrows.Rd |only man/trajectoryComparison.Rd | 25 +++++++- man/trajectoryConvergencePlot.Rd |only man/trajectoryCyclical.Rd | 4 - man/trajectoryCyclicalPlots.Rd | 6 - man/trajectoryRMA.Rd |only man/trajectoryRMAPlot.Rd |only 20 files changed, 176 insertions(+), 55 deletions(-)
Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used
in marketing and micro-econometrics applications.
The package includes:
Bayes Regression (univariate or multivariate dep var),
Bayes Seemingly Unrelated Regression (SUR),
Binary and Ordinal Probit,
Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit,
Negative Binomial (Poisson) Regression,
Multivariate Mixtures of Normals (including clustering),
Dirichlet Process Prior Density Estimation with normal base,
Hierarchical Linear Models with normal prior and covariates,
Hierarchical Linear Models with a mixture of normals prior and covariates,
Hierarchical Multinomial Logits with a mixture of normals prior
and covariates,
Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates,
Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data,
Bayesian treatment of linear instrumental variables models,
Analysis of Multivariate Ordinal survey data with scale
usage heterogeneity (as i [...truncated...]
Author: Peter Rossi [aut, cre],
Robert McCulloch [ctb],
Wayne Taylor [ctb],
Dan Yavorsky [ctb]
Maintainer: Peter Rossi <perossichi@gmail.com>
Diff between bayesm versions 3.1-6 dated 2023-09-23 and 3.1-7 dated 2025-11-11
DESCRIPTION | 21 +- MD5 | 33 ++-- NEWS.md |only build/vignette.rds |binary data/Scotch.rda |binary data/bank.rda |binary data/camera.RData |binary data/cheese.rda |binary data/customerSat.rda |binary data/detailing.rda |binary data/margarine.rda |binary data/orangeJuice.rda |binary data/tuna.rda |binary inst/doc/Constrained_MNL_Vignette.R | 32 ++-- inst/doc/Constrained_MNL_Vignette.html | 249 ++++++++++++++++----------------- inst/doc/bayesm_Overview_Vignette.R | 64 ++++---- inst/doc/bayesm_Overview_Vignette.html | 221 ++++++++++++++--------------- src/clusterMix_rcpp_loop.cpp | 2 18 files changed, 311 insertions(+), 311 deletions(-)
Title: Genetic Relatedness Between Polyclonal Infections
Description: An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results.
Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.
Author: Inna Gerlovina [aut, cre]
Maintainer: Inna Gerlovina <innager@berkeley.edu>
Diff between dcifer versions 1.2.1 dated 2023-12-12 and 1.5.0 dated 2025-11-11
DESCRIPTION | 13 ++-- MD5 | 57 +++++++++--------- NAMESPACE | 1 NEWS.md | 18 +++++ R/data.R | 3 R/ibd.R | 131 ++++++++++++++++++++++++++++--------------- R/plot.R | 99 ++++++++++++++++++++++---------- R/prep.R | 80 +++++++++++++++----------- R/probUxUy.R | 40 ++++--------- build/vignette.rds |binary inst/doc/vignetteDcifer.R | 72 ++++++++++++----------- inst/doc/vignetteDcifer.Rmd | 41 ++++++------- inst/doc/vignetteDcifer.pdf |binary man/dsmp.Rd | 3 man/format.Rd | 14 ++-- man/getCOI.Rd | 2 man/ibdDat.Rd | 10 ++- man/ibdEstM.Rd | 6 + man/ibdPair.Rd | 6 + man/matchAfreq.Rd | 15 +++- man/mixMat.Rd |only man/plotColorbar.Rd | 3 man/plotRel.Rd | 36 ++++++----- src/logr.c | 21 ++++-- src/pUxUy.c | 75 +++++++++++++++++------- src/pUxUy0.c | 42 ++++++++++--- src/pUxUy0M1.c | 82 ++++++++++++++++++++------ src/pUxUyEqr.c | 55 ++++++++++++++---- src/pUxUyM1.c | 105 ++++++++++++++++++++++++---------- vignettes/vignetteDcifer.Rmd | 41 ++++++------- 30 files changed, 691 insertions(+), 380 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-27 0.2.0
2023-08-21 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-12 0.1.1
Title: Creates New Folders and Loads Standard Practices for Monterey
County Office of Education
Description: Basic Setup for Projects in R for Monterey County Office of Education. It contains functions often used in the analysis of education data in the county office including seeing if an item is not in a list, rounding in the manner the general public expects, including logos for districts, switching between district names and their county-district-school codes, accessing the local 'SQL' table and making thematically consistent graphs.
Author: David Dobrowski [aut, cre, cph]
Maintainer: David Dobrowski <ddobrowski@montereycoe.org>
Diff between MCOE versions 0.4.0 dated 2024-02-06 and 0.6.0 dated 2025-11-10
DESCRIPTION | 10 - MD5 | 8 - NEWS.md | 5 R/setup_dir.R | 367 +++++++++++++++++++++++++----------------------------- man/mcoe_theme.Rd | 2 5 files changed, 190 insertions(+), 202 deletions(-)
Title: Extending Base 'R' Lists
Description: Extends the functionality of base 'R' lists and provides
specialized data structures 'deque', 'set', 'dict', and 'dict.table',
the latter to extend the 'data.table' package.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between container versions 1.0.5 dated 2024-12-02 and 1.1.0 dated 2025-11-10
container-1.0.5/container/README.md |only container-1.0.5/container/inst/doc/code-development.R |only container-1.0.5/container/inst/doc/code-development.Rmd |only container-1.0.5/container/inst/doc/code-development.html |only container-1.0.5/container/inst/doc/container.R |only container-1.0.5/container/inst/doc/container.Rmd |only container-1.0.5/container/inst/doc/container.html |only container-1.0.5/container/inst/doc/deque-set-dict.R |only container-1.0.5/container/inst/doc/deque-set-dict.Rmd |only container-1.0.5/container/inst/doc/deque-set-dict.html |only container-1.0.5/container/inst/doc/manage-data-columns.R |only container-1.0.5/container/inst/doc/manage-data-columns.Rmd |only container-1.0.5/container/inst/doc/manage-data-columns.html |only container-1.0.5/container/inst/doc/parameter-list.R |only container-1.0.5/container/inst/doc/parameter-list.Rmd |only container-1.0.5/container/inst/doc/parameter-list.html |only container-1.0.5/container/inst/doc/reference-semantics.R |only container-1.0.5/container/inst/doc/reference-semantics.Rmd |only container-1.0.5/container/inst/doc/reference-semantics.html |only container-1.0.5/container/inst/tinytest |only container-1.0.5/container/man/dequeS3.Rd |only container-1.0.5/container/man/dictS3.Rd |only container-1.0.5/container/tests/tinytest.R |only container-1.0.5/container/vignettes/code-development.Rmd |only container-1.0.5/container/vignettes/container.Rmd |only container-1.0.5/container/vignettes/deque-set-dict.Rmd |only container-1.0.5/container/vignettes/manage-data-columns.Rmd |only container-1.0.5/container/vignettes/manage-data-columns_cache |only container-1.0.5/container/vignettes/parameter-list.Rmd |only container-1.0.5/container/vignettes/reference-semantics.Rmd |only container-1.1.0/container/DESCRIPTION | 39 container-1.1.0/container/MD5 | 287 +++--- container-1.1.0/container/NAMESPACE | 9 container-1.1.0/container/NEWS.md | 53 + container-1.1.0/container/R/0-ContainerR6.R | 65 + container-1.1.0/container/R/0-ContainerS3.R | 97 ++ container-1.1.0/container/R/0-DequeR6.R | 4 container-1.1.0/container/R/0-DequeS3.R | 6 container-1.1.0/container/R/0-DictR6.R | 8 container-1.1.0/container/R/0-DictS3.R | 11 container-1.1.0/container/R/0-IteratorR6.R | 18 container-1.1.0/container/R/0-IteratorS3.R | 19 container-1.1.0/container/R/0-SetR6.R | 13 container-1.1.0/container/R/0-SetS3.R | 4 container-1.1.0/container/R/0-dict.table.R | 8 container-1.1.0/container/R/GroupGenericMath.R | 1 container-1.1.0/container/R/GroupGenericSummary.R | 1 container-1.1.0/container/R/Ops-compare.R | 1 container-1.1.0/container/R/Ops-extract.R | 413 +++++++++- container-1.1.0/container/R/Ops-replace.R | 89 +- container-1.1.0/container/R/add.R | 5 container-1.1.0/container/R/addleft.R | 2 container-1.1.0/container/R/all.equal.R | 1 container-1.1.0/container/R/at.R | 2 container-1.1.0/container/R/at2.R | 2 container-1.1.0/container/R/clear.R | 1 container-1.1.0/container/R/clone.R | 1 container-1.1.0/container/R/container-deprecated.R | 7 container-1.1.0/container/R/container-pkg.R | 1 container-1.1.0/container/R/count.R | 2 container-1.1.0/container/R/delete.R | 2 container-1.1.0/container/R/delete_at.R | 6 container-1.1.0/container/R/discard.R | 1 container-1.1.0/container/R/discard_at.R | 1 container-1.1.0/container/R/format.R | 7 container-1.1.0/container/R/get_label.R | 1 container-1.1.0/container/R/has.R | 1 container-1.1.0/container/R/has_name.R | 6 container-1.1.0/container/R/options.R | 1 container-1.1.0/container/R/peek.R | 1 container-1.1.0/container/R/peek_at.R | 1 container-1.1.0/container/R/peek_at2.R | 2 container-1.1.0/container/R/rename.R | 54 - container-1.1.0/container/R/replace.R | 1 container-1.1.0/container/R/replace_at.R | 1 container-1.1.0/container/R/rotate.R | 1 container-1.1.0/container/R/unpack.R | 1 container-1.1.0/container/R/update.R | 1 container-1.1.0/container/R/utils_index.R | 1 container-1.1.0/container/R/utils_misc.R | 8 container-1.1.0/container/TODO |only container-1.1.0/container/build/vignette.rds |binary container-1.1.0/container/inst/doc/v01-interactive-usage.R |only container-1.1.0/container/inst/doc/v01-interactive-usage.Rmd |only container-1.1.0/container/inst/doc/v01-interactive-usage.html |only container-1.1.0/container/inst/doc/v02-code-development.R |only container-1.1.0/container/inst/doc/v02-code-development.Rmd |only container-1.1.0/container/inst/doc/v02-code-development.html |only container-1.1.0/container/inst/doc/v03-parameter-list.R |only container-1.1.0/container/inst/doc/v03-parameter-list.Rmd |only container-1.1.0/container/inst/doc/v03-parameter-list.html |only container-1.1.0/container/inst/doc/v04-manage-data-columns.R |only container-1.1.0/container/inst/doc/v04-manage-data-columns.Rmd |only container-1.1.0/container/inst/doc/v04-manage-data-columns.html |only container-1.1.0/container/inst/doc/v05-deque-set-dict.R |only container-1.1.0/container/inst/doc/v05-deque-set-dict.Rmd |only container-1.1.0/container/inst/doc/v05-deque-set-dict.html |only container-1.1.0/container/inst/doc/v06-reference-semantics.R |only container-1.1.0/container/inst/doc/v06-reference-semantics.Rmd |only container-1.1.0/container/inst/doc/v06-reference-semantics.html |only container-1.1.0/container/man/Container.Rd | 4 container-1.1.0/container/man/ContainerS3.Rd | 34 container-1.1.0/container/man/ContainerS4.Rd |only container-1.1.0/container/man/DequeS3.Rd |only container-1.1.0/container/man/DictS3.Rd |only container-1.1.0/container/man/Iterator.Rd | 4 container-1.1.0/container/man/OpsExtract.Rd | 107 ++ container-1.1.0/container/man/OpsReplace.Rd | 40 container-1.1.0/container/man/Set.Rd | 3 container-1.1.0/container/man/SetS3.Rd | 231 ++--- container-1.1.0/container/man/deprecated.Rd | 7 container-1.1.0/container/man/dict.table.Rd | 16 container-1.1.0/container/man/iterS3.Rd | 14 container-1.1.0/container/tests/testthat |only container-1.1.0/container/tests/testthat.R |only container-1.1.0/container/vignettes/v01-interactive-usage.Rmd |only container-1.1.0/container/vignettes/v02-code-development.Rmd |only container-1.1.0/container/vignettes/v03-parameter-list.Rmd |only container-1.1.0/container/vignettes/v04-manage-data-columns.Rmd |only container-1.1.0/container/vignettes/v05-deque-set-dict.Rmd |only container-1.1.0/container/vignettes/v06-reference-semantics.Rmd |only 121 files changed, 1186 insertions(+), 542 deletions(-)
Title: 'Targets' Extension for 'SQL' Queries
Description: Provides an extension for 'SQL' queries as separate file
within 'targets' pipelines. The shorthand creates two targets,
the query file and the query result.
Author: David Ranzolin [aut, cre, cph],
Roy Storey [ctb]
Maintainer: David Ranzolin <daranzolin@gmail.com>
Diff between sqltargets versions 0.2.1 dated 2024-10-02 and 0.3.0 dated 2025-11-10
DESCRIPTION | 12 ++-- MD5 | 16 ++--- NEWS.md | 10 +++ R/source_sql_to_dataframe.R | 14 ++++ R/sqltargets-option.R | 2 R/utils.R | 2 README.md | 30 +++++++++- tests/testthat/test-tar-sql-deps.R | 3 - tests/testthat/test-tar-sql.R | 110 +++++++++++++++++++++++++++++++++++++ 9 files changed, 179 insertions(+), 20 deletions(-)
Title: Multivariate Joint Modeling for Longitudinal and Time-to-Event
Outcomes with 'INLA'
Description: Estimation of joint models for multivariate longitudinal markers (with various distributions available) and survival outcomes (possibly accounting for competing risks) with Integrated Nested Laplace Approximations (INLA). The flexible and user friendly function joint() facilitates the use of the fast and reliable inference technique implemented in the 'INLA' package for joint modeling. More details are given in the help page of the joint() function (accessible via ?joint in the R console) and the vignette associated to the joint() function (accessible via vignette("INLAjoint") in the R console).
Author: Denis Rustand [cre, aut] ,
Elias Teixeira Krainski [aut] ,
Haavard Rue [aut] ,
Janet van Niekerk [aut]
Maintainer: Denis Rustand <INLAjoint@gmail.com>
Diff between INLAjoint versions 24.3.25 dated 2024-03-25 and 25.11.10 dated 2025-11-10
DESCRIPTION | 23 MD5 | 34 NAMESPACE | 3 R/joint.R | 1371 +++++++++++++++++++++++------ R/joint.run.R |only R/plot.INLAjoint.R | 327 ++++++- R/predict.INLAjoint.R | 2036 ++++++++++++++++++++++++++++++++++---------- R/print.plot.INLAjoint.R | 8 R/print.summary.INLAjoint.R | 30 R/setupFonctions.R | 109 ++ R/summary.INLAjoint.R | 286 +++++- R/zzz.R | 38 README.md | 8 build/vignette.rds |binary inst/CITATION | 2 man/joint.Rd | 37 man/joint.run.Rd |only man/predict.INLAjoint.Rd | 54 - vignettes/INLAjoint.Rmd | 2 19 files changed, 3547 insertions(+), 821 deletions(-)
Title: Output Results from 'rms' Models for Medical Journals
Description: Provides streamlined functions for summarising and visualising
regression models fitted with the 'rms' package, in the preferred format for medical journals.
The 'modelsummary_rms()' function produces concise summaries for linear, logistic, and
Cox regression models, including automatic handling of models containing restricted
cubic spline (RCS) terms. The resulting summary dataframe can be easily converted into
publication-ready documents using the 'flextable' and 'officer' packages. The 'ggrmsMD()'
function creates clear and customizable plots ('ggplot2' objects) to visualise RCS terms.
Author: Samuel Tingle [aut, cre] ,
Georgios Kourounis [aut]
Maintainer: Samuel Tingle <samjamestingle@gmail.com>
Diff between rmsMD versions 1.0.0 dated 2025-06-17 and 1.0.1 dated 2025-11-10
DESCRIPTION | 12 - MD5 | 26 +- NEWS.md |only R/ggrmsMD.R | 5 R/zzz.R | 10 README.md | 28 ++ build/vignette.rds |binary inst/CITATION |only inst/doc/Further_details_ggrmsMD.html | 22 - inst/doc/Further_details_modelsummary_rms.Rmd | 4 inst/doc/Further_details_modelsummary_rms.html | 6 inst/doc/Standard_workflow_with_restricted_cubic_splines.html | 6 tests/testthat/_snaps/snapshot.md | 111 ++++++++++ tests/testthat/test-snapshot.R | 51 ++++ vignettes/Further_details_modelsummary_rms.Rmd | 4 15 files changed, 245 insertions(+), 40 deletions(-)
Title: Riemannian Metrics for Symmetric Positive Definite Matrices
Description: Implements various Riemannian metrics for symmetric positive definite matrices, including AIRM (Affine Invariant Riemannian Metric, <doi:10.1007/s11263-005-3222-z>), Log-Euclidean (<doi:10.1002/mrm.20965>), Euclidean, Log-Cholesky (<doi:10.1137/18M1221084>), and Bures-Wasserstein metrics (<doi:10.1016/j.exmath.2018.01.002>). Provides functions for computing logarithmic and exponential maps, vectorization, and statistical operations on the manifold of positive definite matrices.
Author: Nicolas Escobar [aut, cre] ,
Jaroslaw Harezlak [ths]
Maintainer: Nicolas Escobar <nescoba@iu.edu>
Diff between riemtan versions 0.1.0 dated 2025-04-23 and 0.2.5 dated 2025-11-10
riemtan-0.1.0/riemtan/man/solve_lyapunov.Rd |only riemtan-0.2.5/riemtan/DESCRIPTION | 23 riemtan-0.2.5/riemtan/LICENSE | 2 riemtan-0.2.5/riemtan/MD5 | 193 + riemtan-0.2.5/riemtan/NAMESPACE | 112 - riemtan-0.2.5/riemtan/NEWS.md | 206 + riemtan-0.2.5/riemtan/R/RcppExports.R |only riemtan-0.2.5/riemtan/R/airm.R | 368 +-- riemtan-0.2.5/riemtan/R/bures-wasserstein.R | 187 - riemtan-0.2.5/riemtan/R/data.R | 60 riemtan-0.2.5/riemtan/R/euclidean.R | 130 - riemtan-0.2.5/riemtan/R/log_cholesky.R | 306 +- riemtan-0.2.5/riemtan/R/log_euclidean.R | 158 - riemtan-0.2.5/riemtan/R/other_utils.R | 1049 +++++---- riemtan-0.2.5/riemtan/R/parallel_config.R |only riemtan-0.2.5/riemtan/R/parquet_backend.R |only riemtan-0.2.5/riemtan/R/parquet_io.R |only riemtan-0.2.5/riemtan/R/progress_utils.R |only riemtan-0.2.5/riemtan/R/riemtan-package.R | 18 riemtan-0.2.5/riemtan/R/sample.R | 762 ++++-- riemtan-0.2.5/riemtan/R/super_sample.R |only riemtan-0.2.5/riemtan/R/tangent_handler.R | 364 ++- riemtan-0.2.5/riemtan/README | 168 - riemtan-0.2.5/riemtan/build/partial.rdb |binary riemtan-0.2.5/riemtan/build/vignette.rds |binary riemtan-0.2.5/riemtan/data/airm.rda |binary riemtan-0.2.5/riemtan/data/bures_wasserstein.rda |binary riemtan-0.2.5/riemtan/data/euclidean.rda |binary riemtan-0.2.5/riemtan/data/log_cholesky.rda |binary riemtan-0.2.5/riemtan/data/log_euclidean.rda |binary riemtan-0.2.5/riemtan/inst/doc/performance-benchmarks.R |only riemtan-0.2.5/riemtan/inst/doc/performance-benchmarks.Rmd |only riemtan-0.2.5/riemtan/inst/doc/performance-benchmarks.html |only riemtan-0.2.5/riemtan/inst/doc/riemtan.R | 12 riemtan-0.2.5/riemtan/inst/doc/riemtan.Rmd | 420 +-- riemtan-0.2.5/riemtan/inst/doc/riemtan.html | 1112 +++++----- riemtan-0.2.5/riemtan/inst/doc/using-parquet.R |only riemtan-0.2.5/riemtan/inst/doc/using-parquet.Rmd |only riemtan-0.2.5/riemtan/inst/doc/using-parquet.html |only riemtan-0.2.5/riemtan/man/CSample.Rd | 695 +++--- riemtan-0.2.5/riemtan/man/CSuperSample.Rd |only riemtan-0.2.5/riemtan/man/DataBackend.Rd |only riemtan-0.2.5/riemtan/man/ListBackend.Rd |only riemtan-0.2.5/riemtan/man/ParquetBackend.Rd |only riemtan-0.2.5/riemtan/man/TangentImageHandler.Rd | 464 ++-- riemtan-0.2.5/riemtan/man/airm_exp.Rd | 66 riemtan-0.2.5/riemtan/man/airm_log.Rd | 68 riemtan-0.2.5/riemtan/man/airm_unvec.Rd | 60 riemtan-0.2.5/riemtan/man/airm_vec.Rd | 64 riemtan-0.2.5/riemtan/man/bures_wasserstein_exp.Rd | 40 riemtan-0.2.5/riemtan/man/bures_wasserstein_log.Rd | 40 riemtan-0.2.5/riemtan/man/bures_wasserstein_unvec.Rd | 38 riemtan-0.2.5/riemtan/man/bures_wasserstein_vec.Rd | 38 riemtan-0.2.5/riemtan/man/compute_frechet_mean.Rd | 99 riemtan-0.2.5/riemtan/man/configure_progress.Rd |only riemtan-0.2.5/riemtan/man/create_parquet_backend.Rd |only riemtan-0.2.5/riemtan/man/create_progressor.Rd |only riemtan-0.2.5/riemtan/man/default_ref_pt.Rd | 34 riemtan-0.2.5/riemtan/man/dexp.Rd | 38 riemtan-0.2.5/riemtan/man/dlog.Rd | 38 riemtan-0.2.5/riemtan/man/euclidean_exp.Rd | 40 riemtan-0.2.5/riemtan/man/euclidean_log.Rd | 40 riemtan-0.2.5/riemtan/man/euclidean_unvec.Rd | 38 riemtan-0.2.5/riemtan/man/euclidean_vec.Rd | 38 riemtan-0.2.5/riemtan/man/get_n_workers.Rd |only riemtan-0.2.5/riemtan/man/half_underscore.Rd | 34 riemtan-0.2.5/riemtan/man/id_matr.Rd | 34 riemtan-0.2.5/riemtan/man/is_parallel_enabled.Rd |only riemtan-0.2.5/riemtan/man/is_progress_available.Rd |only riemtan-0.2.5/riemtan/man/log_cholesky_exp.Rd | 40 riemtan-0.2.5/riemtan/man/log_cholesky_log.Rd | 40 riemtan-0.2.5/riemtan/man/log_cholesky_unvec.Rd | 38 riemtan-0.2.5/riemtan/man/log_cholesky_vec.Rd | 38 riemtan-0.2.5/riemtan/man/log_euclidean_exp.Rd | 40 riemtan-0.2.5/riemtan/man/log_euclidean_log.Rd | 40 riemtan-0.2.5/riemtan/man/log_euclidean_unvec.Rd | 38 riemtan-0.2.5/riemtan/man/log_euclidean_vec.Rd | 38 riemtan-0.2.5/riemtan/man/metric.Rd | 46 riemtan-0.2.5/riemtan/man/metrics.Rd | 92 riemtan-0.2.5/riemtan/man/parallel_config.Rd |only riemtan-0.2.5/riemtan/man/progress_utils.Rd |only riemtan-0.2.5/riemtan/man/relocate.Rd | 92 riemtan-0.2.5/riemtan/man/reset_parallel_plan.Rd |only riemtan-0.2.5/riemtan/man/riemtan-package.Rd | 56 riemtan-0.2.5/riemtan/man/rspdnorm.Rd | 76 riemtan-0.2.5/riemtan/man/safe_logm.Rd | 34 riemtan-0.2.5/riemtan/man/set_parallel_plan.Rd |only riemtan-0.2.5/riemtan/man/should_parallelize.Rd |only riemtan-0.2.5/riemtan/man/spd_isometry_from_identity.Rd | 38 riemtan-0.2.5/riemtan/man/spd_isometry_to_identity.Rd | 38 riemtan-0.2.5/riemtan/man/validate_backend.Rd |only riemtan-0.2.5/riemtan/man/validate_conns.Rd | 46 riemtan-0.2.5/riemtan/man/validate_exp_args.Rd | 44 riemtan-0.2.5/riemtan/man/validate_log_args.Rd | 44 riemtan-0.2.5/riemtan/man/validate_metric.Rd | 34 riemtan-0.2.5/riemtan/man/validate_parquet_dir.Rd |only riemtan-0.2.5/riemtan/man/validate_parquet_directory.Rd |only riemtan-0.2.5/riemtan/man/validate_tan_imgs.Rd | 42 riemtan-0.2.5/riemtan/man/validate_unvec_args.Rd | 44 riemtan-0.2.5/riemtan/man/validate_vec_args.Rd | 44 riemtan-0.2.5/riemtan/man/validate_vec_imgs.Rd | 38 riemtan-0.2.5/riemtan/man/vec_at_id.Rd | 52 riemtan-0.2.5/riemtan/man/with_progress.Rd |only riemtan-0.2.5/riemtan/man/with_progress_signal.Rd |only riemtan-0.2.5/riemtan/man/write_connectomes_to_parquet.Rd |only riemtan-0.2.5/riemtan/src |only riemtan-0.2.5/riemtan/tests/testthat.R | 8 riemtan-0.2.5/riemtan/tests/testthat/test-csupersample.R |only riemtan-0.2.5/riemtan/tests/testthat/test-parallel.R |only riemtan-0.2.5/riemtan/tests/testthat/test-parquet-backend.R |only riemtan-0.2.5/riemtan/tests/testthat/test-parquet-integration.R |only riemtan-0.2.5/riemtan/tests/testthat/test-parquet-io.R |only riemtan-0.2.5/riemtan/tests/testthat/tests.R | 288 +- riemtan-0.2.5/riemtan/vignettes/performance-benchmarks.Rmd |only riemtan-0.2.5/riemtan/vignettes/riemtan.Rmd | 420 +-- riemtan-0.2.5/riemtan/vignettes/using-parquet.Rmd |only 116 files changed, 5146 insertions(+), 4398 deletions(-)
Title: Confidence Interval Post-Selection of Variable
Description: Calculates confidence intervals after variable selection using repeated data splits. The package offers methods to address the challenges of post-selection inference, ensuring more accurate confidence intervals in models involving variable selection. The two main functions are 'lmps', which records the different models selected across multiple data splits as well as the corresponding coefficient estimates, and 'cips', which takes the lmps object as input to select variables and perform inferences using two types of voting.
Author: Boubacar DIALLO [aut, cre]
Maintainer: Boubacar DIALLO <boubacar.diallo0@yahoo.com>
Diff between CIpostSelect versions 0.2.1 dated 2024-10-22 and 0.2.2 dated 2025-11-10
DESCRIPTION | 8 MD5 | 4 R/uneFonction.R | 761 -------------------------------------------------------- 3 files changed, 13 insertions(+), 760 deletions(-)
Title: Weierstrass and Jacobi Elliptic Functions
Description: A suite of elliptic and related functions including Weierstrass and
Jacobi forms. Also includes various tools for manipulating and
visualizing complex functions.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between elliptic versions 1.5-0 dated 2025-09-18 and 1.5-1 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/elliptic.pdf |binary inst/doc/residuetheorem.R | 10 +++++----- inst/doc/residuetheorem.Rnw | 36 +++++++++++++++++++++--------------- inst/doc/residuetheorem.pdf |binary man/theta.neville.Rd | 2 +- vignettes/residuetheorem.Rnw | 36 +++++++++++++++++++++--------------- 11 files changed, 65 insertions(+), 49 deletions(-)
Title: Effects of External Conditions on Air Quality
Description: Analyzes the impact of external conditions on air quality using counterfactual approaches, featuring methods for data preparation, modeling, and visualization.
Author: Raphael Franke [aut],
Imke Voss [aut, cre]
Maintainer: Imke Voss <imke.voss@uba.de>
Diff between ubair versions 1.1.0 dated 2025-01-27 and 1.1.1 dated 2025-11-10
DESCRIPTION | 6 +-- MD5 | 44 ++++++++++++----------- NEWS.md | 5 ++ R/counterfactual_model.R | 2 - R/data_loading.R | 9 +++- R/sample_data_DESN025.R | 39 ++++---------------- R/utils.R | 2 - R/visualisation.R | 4 +- README.md | 26 ++----------- build/vignette.rds |binary inst/doc/neun_euro_ticket_demonstrator.R |only inst/doc/neun_euro_ticket_demonstrator.Rmd |only inst/doc/neun_euro_ticket_demonstrator.html |only inst/doc/user_sample_1.html | 4 +- inst/doc/user_sample_2.html | 2 - inst/doc/user_sample_3.html | 6 +-- inst/sticker/stickers-ubair-1.png |binary man/figures/README-counterfactual-scenario-1.png |binary man/figures/README-feature_importance-1.png |binary man/figures/README-feature_importance-2.png |binary man/figures/README-plot-meteo-data-1.png |binary man/load_uba_data_from_dir.Rd | 2 + man/run_counterfactual.Rd | 2 - man/sample_data_DESN025.Rd | 35 ++++-------------- vignettes/neun_euro_ticket_demonstrator.Rmd |only 25 files changed, 72 insertions(+), 116 deletions(-)
Title: Build a Docker Image from a Directory or Project
Description: Simple utilities to generate a Dockerfile from a directory or
project, build the corresponding Docker image, push the image to
DockerHub, and publicly share the project via Binder.
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between tugboat versions 0.1.4 dated 2025-10-31 and 0.1.5 dated 2025-11-10
DESCRIPTION | 6 +- MD5 | 14 ++--- NEWS.md | 13 +++++ R/binderize.R | 5 ++ R/build.R | 100 ++++++++++++++++++++++++++++++++-------- R/utils.R | 13 +++++ man/build.Rd | 6 ++ tests/testthat/test-binderize.R | 6 ++ 8 files changed, 132 insertions(+), 31 deletions(-)
Title: A Unified Pipeline for Pupillometry Data
Description: Provides a unified pipeline to clean, prepare, plot,
and run basic analyses on pupillometry experiments.
Author: Samuel Forbes [aut, cre],
David Robinson [ctb]
Maintainer: Samuel Forbes <samuel.h.forbes@gmail.com>
Diff between PupillometryR versions 0.0.5 dated 2023-09-15 and 0.0.6 dated 2025-11-10
DESCRIPTION | 12 +++--- MD5 | 30 +++++++-------- NEWS.md | 5 ++ R/clean_and_downsample.R | 59 ++++++++++++++++++------------- R/functional_data.R | 1 R/make_smoothed_data.R | 17 +++++--- R/plot_pupil_data.R | 1 README.md | 15 ++++--- build/vignette.rds |binary inst/doc/PupillometryR.R | 2 - inst/doc/PupillometryR.Rmd | 4 +- inst/doc/PupillometryR.html | 56 +++++++++++++++-------------- man/clean_missing_data.Rd | 41 ++++++++++++--------- man/figures/README-unnamed-chunk-2-1.png |binary man/interpolate_data.Rd | 5 ++ vignettes/PupillometryR.Rmd | 4 +- 16 files changed, 147 insertions(+), 105 deletions(-)
Title: Estimating Peer Effects Using Partial Network Data
Description: Implements IV-estimator and Bayesian estimator for linear-in-means Spatial Autoregressive (SAR) model (see LeSage, 1997 <doi:10.1177/016001769702000107>; Lee, 2004 <doi:10.1111/j.1468-0262.2004.00558.x>; Bramoullé et al., 2009 <doi:10.1016/j.jeconom.2008.12.021>), while assuming that only a partial information about the network structure is available. Examples are when the adjacency matrix is not fully observed or when only consistent estimation of the network formation model is available (see Boucher and Houndetoungan, 2025 <doi:10.48550/arXiv.2509.08145>).
Author: Vincent Boucher [aut],
Aristide Houndetoungan [cre, aut]
Maintainer: Aristide Houndetoungan <ahoundetoungan@ecn.ulaval.ca>
Diff between PartialNetwork versions 1.1.1 dated 2025-09-24 and 1.1.2 dated 2025-11-10
DESCRIPTION | 12 +-- MD5 | 36 ++++++---- NAMESPACE | 3 NEWS.md | 11 ++- R/RcppExports.R | 4 + R/mcmcSAR.R | 5 - R/simIV.R | 88 +++++++++++++------------- R/simSAR.R |only R/smmSAR.R | 4 - inst/CITATION |only inst/doc/PartialNetwork_vignette.R | 102 +++++++++++++----------------- inst/doc/PartialNetwork_vignette.Rmd | 113 +++++++++++++++------------------- inst/doc/PartialNetwork_vignette.pdf |binary man/mcmcSAR.Rd | 5 - man/sim.IV.Rd | 88 +++++++++++++------------- man/simSAR.Rd |only man/smmSAR.Rd | 4 - src/RcppExports.cpp | 19 +++++ src/simSAR.cpp |only vignettes/PartialNetwork_vignette.Rmd | 113 +++++++++++++++------------------- vignettes/References.bib | 8 +- 21 files changed, 313 insertions(+), 302 deletions(-)
More information about PartialNetwork at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-25 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-10 0.1.1
2020-06-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-23 0.3.3
2018-09-12 0.2.0
2017-02-08 0.1.2
2016-12-29 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-06 0.4.1
2024-11-29 0.3.1
Title: Access to the 'RESOURCECODE' Hindcast Database
Description: Utility functions to download data from the 'RESOURCECODE'
hindcast database of sea-states, time series of sea-state parameters
and time series of 1D and 2D wave spectra. See
<https://resourcecode.ifremer.fr> for more details about the available
data. Also provides facilities to plot and analyse downloaded data,
such as computing the sea-state parameters from both the 1D and 2D
surface elevation variance spectral density.
Author: Nicolas Raillard [aut, cre]
Maintainer: Nicolas Raillard <nicolas.raillard@ifremer.fr>
Diff between resourcecode versions 0.4.0 dated 2025-10-22 and 0.5.0 dated 2025-11-10
DESCRIPTION | 14 - MD5 | 36 +-- NAMESPACE | 1 NEWS.md | 7 R/RcppExports.R | 4 R/download_data.R | 357 ++++++++++++++++++----------------- R/resourcecode-package.R | 22 +- R/spectral_data_download.R | 62 ++++-- R/sysdata.rda |binary R/weather_windows.R |only data/rscd_dir.rda |binary data/rscd_freq.rda |binary man/compute_sea_state_2d_spectrum.Rd | 2 man/get_parameters.Rd | 3 man/weather_windows.Rd |only src/RcppExports.cpp | 15 + src/ww_calc_cpp.cpp |only tests/testthat.R | 24 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-data_download.R | 317 ++++++++++++++++++------------- tests/testthat/test_ww_calc.R |only 21 files changed, 493 insertions(+), 371 deletions(-)
Title: Detecting Extremal Values in a Normal Linear Model
Description: Provides a method to detect values poorly explained by a Gaussian linear model. The procedure is based on the maximum of the absolute value of the studentized residuals, which is a parameter-free statistic. This approach generalizes several procedures used to detect abnormal values during longitudinal monitoring of biological markers. For methodological details, see: Berthelot G., Saulière G., Dedecker J. (2025). "DEViaN-LM An R Package for Detecting Abnormal Values in the Gaussian Linear Model". HAL Id: hal-05230549. <https://hal.science/hal-05230549>.
Author: Guillaume Sauliere [aut, cre] ,
Geoffroy Berthelot [aut],
Jerome Dedecker [aut]
Maintainer: Guillaume Sauliere <guillaumesauliere@hotmail.com>
Diff between devianLM versions 1.0.4 dated 2025-10-05 and 1.0.5 dated 2025-11-10
DESCRIPTION | 8 +-- MD5 | 8 +-- NEWS.md | 8 +++ R/devianlm_stats.R | 4 - man/devianlm_stats.Rd | 126 +++++++++++++++++++++++++------------------------- 5 files changed, 81 insertions(+), 73 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-04 0.5.7
2023-05-10 0.5.6.1
2023-03-28 0.5.5
2023-03-13 0.5.4
2023-02-20 0.5.3
2023-01-30 0.5.1
2023-01-13 0.5.0
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.3.0 dated 2025-11-06 and 1.3.2 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/internal_hazard.R | 2 +- R/internal_misc.R | 33 ++++++++++++++++----------------- R/internal_survival.R | 23 +++++++++++------------ tests/testthat/test_survival.R | 8 ++++++++ 6 files changed, 44 insertions(+), 38 deletions(-)
Title: A Fast Permutation-Based Split-Half Reliability Algorithm
Description: Accurately estimates the reliability of cognitive tasks using a fast and flexible permutation-based split-half reliability algorithm that supports stratified splitting while maintaining equal split sizes. See Kahveci, Bathke, and Blechert (2025) <doi:10.3758/s13423-024-02597-y> for details.
Author: Sercan Kahveci [aut, cre]
Maintainer: Sercan Kahveci <sercan.kahveci@plus.ac.at>
Diff between rapidsplithalf versions 0.5 dated 2025-11-06 and 0.6 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/rapidsplit.R | 29 ++++++++--------------------- inst/doc/rapidsplithalf.html | 14 +++++++------- man/figures/README-iatrel-1.png |binary man/figures/README-plotter-1.png |binary man/figures/README-plotter2-1.png |binary man/rapidsplit.Rd | 27 +++++++-------------------- 8 files changed, 32 insertions(+), 58 deletions(-)
More information about rapidsplithalf at CRAN
Permanent link
Title: 'Canvas' LMS API Integration
Description: Allow R users to interact with the 'Canvas' Learning Management System (LMS) API (see
<https://canvas.instructure.com/doc/api/all_resources.html> for details).
It provides a set of functions to access and manipulate course data, assignments, grades, users,
and other resources available through the 'Canvas' API.
Author: Tomer Iwan [aut, cre],
Niels Smits [ctb] ,
VU Analytics [cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between vvcanvas versions 0.0.6 dated 2025-09-05 and 0.0.7 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 13 +++++++++++-- R/get_assignment_submissions.R | 32 ++++++++++++++++++-------------- README.md | 9 --------- man/get_assignment_submissions.Rd | 18 +++++++----------- 6 files changed, 44 insertions(+), 44 deletions(-)
Title: Provider-Agnostic OAuth Authentication for 'shiny' Applications
Description: Provides a simple, configurable, provider-agnostic 'OAuth 2.0' and
'OpenID Connect' (OIDC) authentication framework for 'shiny' applications
using 'S7' classes. Defines providers, clients, and tokens, as well
as various supporting functions and a 'shiny' module. Features include
cross-site request forgery (CSRF) protection, state encryption,
'Proof Key for Code Exchange' (PKCE) handling, validation of OIDC identity
tokens (nonces, signatures, claims), automatic user info retrieval, asynchronous
flows, and hooks for audit logging.
Author: Luka Koning [aut, cre, cph]
Maintainer: Luka Koning <koningluka@gmail.com>
Diff between shinyOAuth versions 0.1.1 dated 2025-11-09 and 0.1.3 dated 2025-11-10
DESCRIPTION | 6 LICENSE | 2 MD5 | 36 ++-- NAMESPACE | 76 +++++----- NEWS.md | 6 README.md | 14 + build/vignette.rds |binary inst/doc/authentication-flow.Rmd | 162 +++++++++++++-------- inst/doc/authentication-flow.html | 227 +++++++++++++++--------------- man/handle_callback.Rd | 166 ++++++++++----------- man/prepare_call.Rd | 120 +++++++-------- man/state_payload_decrypt_validate.Rd | 48 +++--- man/state_store_get_remove.Rd | 46 +++--- man/use_shinyOAuth.Rd | 66 ++++---- tests/testthat/test-introspect-token.R | 1 tests/testthat/test-module-server-async.R | 3 tests/testthat/test-refresh-races.R | 1 tests/testthat/test-state-fail-delay.R | 3 vignettes/authentication-flow.Rmd | 162 +++++++++++++-------- 19 files changed, 630 insertions(+), 515 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac, uniform or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] ,
Branislav Panic [ctb] ,
Jernej Klemenc [ctb] ,
Simon Oman [ctb]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.17.0 dated 2025-11-06 and 2.17.1 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- R/EMMIX.R | 2 +- R/RCLRMIX.R | 2 +- R/RCLSMIX.R | 4 ++-- R/REBMIX.R | 2 +- R/RNGMIX.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 2 +- inst/doc/rebmix.Rnw | 4 ++-- inst/doc/rebmix.pdf |binary src/init.c | 8 ++++---- src/rebmixf.cpp | 2 +- src/rngmixf.cpp | 2 +- vignettes/rebmix.Rnw | 4 ++-- 16 files changed, 35 insertions(+), 35 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Systematic conservation prioritization using mixed integer linear
programming (MILP). It provides a flexible interface for building and
solving conservation planning problems. Once built, conservation planning
problems can be solved using a variety of commercial and open-source exact
algorithm solvers. By using exact algorithm solvers, solutions can be
generated that are guaranteed to be optimal (or within a pre-specified
optimality gap). Furthermore, conservation problems can be constructed to
optimize the spatial allocation of different management actions or zones,
meaning that conservation practitioners can identify solutions that benefit
multiple stakeholders. To solve large-scale or complex conservation
planning problems, users should install the Gurobi optimization software
(available from <https://www.gurobi.com/>) and the 'gurobi' R package (see
Gurobi Installation Guide vignette for details). Users can also install the
IBM CPLEX software (<https://www.ibm.com/products [...truncated...]
Author: Jeffrey O Hanson [aut] ,
Richard Schuster [aut, cre] ,
Nina Morrell [aut],
Matthew Strimas-Mackey [aut] ,
Brandon P M Edwards [aut] ,
Matthew E Watts [aut],
Peter Arcese [aut] ,
Joseph R Bennett [aut] ,
Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 8.0.6 dated 2025-01-09 and 8.1.0 dated 2025-11-10
prioritizr-8.0.6/prioritizr/R/add_loglinear_targets.R |only prioritizr-8.0.6/prioritizr/R/all_binary.R |only prioritizr-8.0.6/prioritizr/R/all_columns_any_finite.R |only prioritizr-8.0.6/prioritizr/R/all_columns_inherit.R |only prioritizr-8.0.6/prioritizr/R/all_finite.R |only prioritizr-8.0.6/prioritizr/R/all_positive.R |only prioritizr-8.0.6/prioritizr/R/all_proportion.R |only prioritizr-8.0.6/prioritizr/R/any_nonNA.R |only prioritizr-8.0.6/prioritizr/R/any_nonzero.R |only prioritizr-8.0.6/prioritizr/R/as_Matrix.R |only prioritizr-8.0.6/prioritizr/R/assertions.R |only prioritizr-8.0.6/prioritizr/R/assertions_class.R |only prioritizr-8.0.6/prioritizr/R/assertions_misc.R |only prioritizr-8.0.6/prioritizr/R/assertions_raster.R |only prioritizr-8.0.6/prioritizr/R/assertions_sf.R |only prioritizr-8.0.6/prioritizr/R/assertions_vector.R |only prioritizr-8.0.6/prioritizr/R/cli.R |only prioritizr-8.0.6/prioritizr/R/get_crs.R |only prioritizr-8.0.6/prioritizr/R/is_numeric_values.R |only prioritizr-8.0.6/prioritizr/R/is_same_crs.R |only prioritizr-8.0.6/prioritizr/R/is_spatial_extents_overlap.R |only prioritizr-8.0.6/prioritizr/R/list_text.R |only prioritizr-8.0.6/prioritizr/R/repr.R |only prioritizr-8.0.6/prioritizr/R/st_geometry_classes.R |only prioritizr-8.0.6/prioritizr/man/add_loglinear_targets.Rd |only prioritizr-8.0.6/prioritizr/src/rcpp_apply_feature_weights.cpp |only prioritizr-8.0.6/prioritizr/tests/testthat/_snaps/assertions.md |only prioritizr-8.0.6/prioritizr/tests/testthat/test_add_boundary_penalties.R |only prioritizr-8.0.6/prioritizr/tests/testthat/test_add_loglinear_targets.R |only prioritizr-8.0.6/prioritizr/tests/testthat/test_assertions.R |only prioritizr-8.1.0/prioritizr/DESCRIPTION | 141 prioritizr-8.1.0/prioritizr/MD5 | 995 + prioritizr-8.1.0/prioritizr/NAMESPACE | 760 - prioritizr-8.1.0/prioritizr/NEWS.md | 5386 +++++----- prioritizr-8.1.0/prioritizr/R/ConservationModifier-class.R | 232 prioritizr-8.1.0/prioritizr/R/ConservationProblem-class.R | 2136 ++- prioritizr-8.1.0/prioritizr/R/Constraint-class.R | 66 prioritizr-8.1.0/prioritizr/R/Decision-class.R | 66 prioritizr-8.1.0/prioritizr/R/Objective-class.R | 89 prioritizr-8.1.0/prioritizr/R/OptimizationProblem-class.R | 524 prioritizr-8.1.0/prioritizr/R/OptimizationProblem-methods.R | 717 - prioritizr-8.1.0/prioritizr/R/Penalty-class.R | 66 prioritizr-8.1.0/prioritizr/R/Portfolio-class.R | 68 prioritizr-8.1.0/prioritizr/R/RcppExports.R | 442 prioritizr-8.1.0/prioritizr/R/Solver-class.R | 259 prioritizr-8.1.0/prioritizr/R/Target-class.R | 64 prioritizr-8.1.0/prioritizr/R/TargetMethod-class.R |only prioritizr-8.1.0/prioritizr/R/Weight-class.R |only prioritizr-8.1.0/prioritizr/R/add_absolute_targets.R | 635 - prioritizr-8.1.0/prioritizr/R/add_asym_connectivity_penalties.R | 775 - prioritizr-8.1.0/prioritizr/R/add_auto_targets.R |only prioritizr-8.1.0/prioritizr/R/add_binary_decisions.R | 192 prioritizr-8.1.0/prioritizr/R/add_boundary_penalties.R | 959 - prioritizr-8.1.0/prioritizr/R/add_cbc_solver.R | 636 - prioritizr-8.1.0/prioritizr/R/add_compile_solver.R | 112 prioritizr-8.1.0/prioritizr/R/add_connectivity_penalties.R | 1199 +- prioritizr-8.1.0/prioritizr/R/add_contiguity_constraints.R | 760 - prioritizr-8.1.0/prioritizr/R/add_cplex_solver.R | 720 - prioritizr-8.1.0/prioritizr/R/add_cuts_portfolio.R | 280 prioritizr-8.1.0/prioritizr/R/add_default_portfolio.R | 80 prioritizr-8.1.0/prioritizr/R/add_default_solver.R | 186 prioritizr-8.1.0/prioritizr/R/add_extra_portfolio.R | 273 prioritizr-8.1.0/prioritizr/R/add_feature_contiguity_constraints.R | 902 - prioritizr-8.1.0/prioritizr/R/add_feature_weights.R | 682 - prioritizr-8.1.0/prioritizr/R/add_gap_portfolio.R | 363 prioritizr-8.1.0/prioritizr/R/add_group_targets.R |only prioritizr-8.1.0/prioritizr/R/add_gurobi_solver.R | 774 - prioritizr-8.1.0/prioritizr/R/add_highs_solver.R | 471 prioritizr-8.1.0/prioritizr/R/add_linear_constraints.R | 888 - prioritizr-8.1.0/prioritizr/R/add_linear_penalties.R | 864 - prioritizr-8.1.0/prioritizr/R/add_locked_in_constraints.R | 1077 + prioritizr-8.1.0/prioritizr/R/add_locked_out_constraints.R | 926 - prioritizr-8.1.0/prioritizr/R/add_lpsymphony_solver.R | 474 prioritizr-8.1.0/prioritizr/R/add_mandatory_allocation_constraints.R | 206 prioritizr-8.1.0/prioritizr/R/add_manual_bounded_constraints.R | 541 - prioritizr-8.1.0/prioritizr/R/add_manual_locked_constraints.R | 646 - prioritizr-8.1.0/prioritizr/R/add_manual_targets.R | 797 - prioritizr-8.1.0/prioritizr/R/add_max_cover_objective.R | 402 prioritizr-8.1.0/prioritizr/R/add_max_features_objective.R | 334 prioritizr-8.1.0/prioritizr/R/add_max_phylo_div_objective.R | 555 - prioritizr-8.1.0/prioritizr/R/add_max_phylo_end_objective.R | 641 - prioritizr-8.1.0/prioritizr/R/add_max_utility_objective.R | 330 prioritizr-8.1.0/prioritizr/R/add_min_largest_shortfall_objective.R | 325 prioritizr-8.1.0/prioritizr/R/add_min_penalties_objective.R | 321 prioritizr-8.1.0/prioritizr/R/add_min_set_objective.R | 259 prioritizr-8.1.0/prioritizr/R/add_min_shortfall_objective.R | 333 prioritizr-8.1.0/prioritizr/R/add_neighbor_constraints.R | 895 - prioritizr-8.1.0/prioritizr/R/add_neighbor_penalties.R |only prioritizr-8.1.0/prioritizr/R/add_proportion_decisions.R | 178 prioritizr-8.1.0/prioritizr/R/add_relative_targets.R | 462 prioritizr-8.1.0/prioritizr/R/add_rsymphony_solver.R | 441 prioritizr-8.1.0/prioritizr/R/add_semicontinuous_decisions.R | 210 prioritizr-8.1.0/prioritizr/R/add_shuffle_portfolio.R | 484 prioritizr-8.1.0/prioritizr/R/add_top_portfolio.R | 297 prioritizr-8.1.0/prioritizr/R/adjacency_matrix.R | 389 prioritizr-8.1.0/prioritizr/R/as.R | 80 prioritizr-8.1.0/prioritizr/R/as_units.R |only prioritizr-8.1.0/prioritizr/R/binary_stack.R | 186 prioritizr-8.1.0/prioritizr/R/boundary_matrix.R | 479 prioritizr-8.1.0/prioritizr/R/branch_matrix.R | 122 prioritizr-8.1.0/prioritizr/R/calibrate_cohon_penalty.R |only prioritizr-8.1.0/prioritizr/R/category_layer.R | 145 prioritizr-8.1.0/prioritizr/R/category_vector.R | 170 prioritizr-8.1.0/prioritizr/R/compile.R | 592 - prioritizr-8.1.0/prioritizr/R/connectivity_matrix.R | 672 - prioritizr-8.1.0/prioritizr/R/constraints.R | 233 prioritizr-8.1.0/prioritizr/R/data.R | 751 - prioritizr-8.1.0/prioritizr/R/decisions.R | 170 prioritizr-8.1.0/prioritizr/R/deprecated.R | 430 prioritizr-8.1.0/prioritizr/R/eval_asym_connectivity_summary.R | 664 - prioritizr-8.1.0/prioritizr/R/eval_boundary_summary.R | 550 - prioritizr-8.1.0/prioritizr/R/eval_connectivity_summary.R | 656 - prioritizr-8.1.0/prioritizr/R/eval_cost_summary.R | 378 prioritizr-8.1.0/prioritizr/R/eval_feature_representation_summary.R | 577 - prioritizr-8.1.0/prioritizr/R/eval_ferrier_importance.R | 793 - prioritizr-8.1.0/prioritizr/R/eval_n_summary.R | 316 prioritizr-8.1.0/prioritizr/R/eval_rank_importance.R | 2034 +-- prioritizr-8.1.0/prioritizr/R/eval_rare_richness_importance.R | 573 - prioritizr-8.1.0/prioritizr/R/eval_replacement_importance.R | 1015 - prioritizr-8.1.0/prioritizr/R/eval_target_coverage_summary.R | 658 - prioritizr-8.1.0/prioritizr/R/external-classes.R | 54 prioritizr-8.1.0/prioritizr/R/fast_extract.R | 386 prioritizr-8.1.0/prioritizr/R/feature_abundances.R | 384 prioritizr-8.1.0/prioritizr/R/feature_names.R | 142 prioritizr-8.1.0/prioritizr/R/get_target_method.R |only prioritizr-8.1.0/prioritizr/R/importance.R | 300 prioritizr-8.1.0/prioritizr/R/internal.R | 212 prioritizr-8.1.0/prioritizr/R/intersecting_units.R | 461 prioritizr-8.1.0/prioritizr/R/knit_print.R | 102 prioritizr-8.1.0/prioritizr/R/linear_interpolation.R |only prioritizr-8.1.0/prioritizr/R/loglinear_interpolation.R | 230 prioritizr-8.1.0/prioritizr/R/marxan_boundary_data_to_matrix.R | 202 prioritizr-8.1.0/prioritizr/R/marxan_connectivity_data_to_matrix.R | 440 prioritizr-8.1.0/prioritizr/R/marxan_problem.R | 974 - prioritizr-8.1.0/prioritizr/R/memory.R | 88 prioritizr-8.1.0/prioritizr/R/number_of_features.R | 140 prioritizr-8.1.0/prioritizr/R/number_of_planning_units.R | 114 prioritizr-8.1.0/prioritizr/R/number_of_total_units.R | 138 prioritizr-8.1.0/prioritizr/R/number_of_zones.R | 146 prioritizr-8.1.0/prioritizr/R/objectives.R | 252 prioritizr-8.1.0/prioritizr/R/optimization_problem.R | 296 prioritizr-8.1.0/prioritizr/R/package.R | 266 prioritizr-8.1.0/prioritizr/R/penalties.R | 233 prioritizr-8.1.0/prioritizr/R/planning_unit_indices.R | 192 prioritizr-8.1.0/prioritizr/R/planning_unit_solution_format.R |only prioritizr-8.1.0/prioritizr/R/planning_unit_solution_status.R | 1155 +- prioritizr-8.1.0/prioritizr/R/portfolios.R | 254 prioritizr-8.1.0/prioritizr/R/presolve_check.R | 1294 +- prioritizr-8.1.0/prioritizr/R/print.R | 88 prioritizr-8.1.0/prioritizr/R/problem-deprecated.R | 821 - prioritizr-8.1.0/prioritizr/R/problem.R | 2458 ++-- prioritizr-8.1.0/prioritizr/R/proximity_matrix.R | 388 prioritizr-8.1.0/prioritizr/R/read_marxan_data.R |only prioritizr-8.1.0/prioritizr/R/read_marxan_parameters.R |only prioritizr-8.1.0/prioritizr/R/reexports.R | 70 prioritizr-8.1.0/prioritizr/R/rescale_matrix.R | 226 prioritizr-8.1.0/prioritizr/R/rij_matrix.R | 514 prioritizr-8.1.0/prioritizr/R/run_calculations.R | 190 prioritizr-8.1.0/prioritizr/R/show.R | 104 prioritizr-8.1.0/prioritizr/R/simulate.R | 496 prioritizr-8.1.0/prioritizr/R/solve.R | 876 - prioritizr-8.1.0/prioritizr/R/solvers.R | 329 prioritizr-8.1.0/prioritizr/R/spec_absolute_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_area_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_duran_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_interp_absolute_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_interp_area_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_jung_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_max_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_min_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_polak_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_pop_size_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_relative_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_rl_ecosystem_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_rl_species_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_rodrigues_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_rule_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_ward_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_watson_targets.R |only prioritizr-8.1.0/prioritizr/R/spec_wilson_targets.R |only prioritizr-8.1.0/prioritizr/R/standalone-all_binary.R |only prioritizr-8.1.0/prioritizr/R/standalone-all_columns_any_finite.R |only prioritizr-8.1.0/prioritizr/R/standalone-all_columns_inherit.R |only prioritizr-8.1.0/prioritizr/R/standalone-all_finite.R |only prioritizr-8.1.0/prioritizr/R/standalone-all_positive.R |only prioritizr-8.1.0/prioritizr/R/standalone-all_proportion.R |only prioritizr-8.1.0/prioritizr/R/standalone-any_nonNA.R |only prioritizr-8.1.0/prioritizr/R/standalone-any_nonzero.R |only prioritizr-8.1.0/prioritizr/R/standalone-as_Matrix.R |only prioritizr-8.1.0/prioritizr/R/standalone-assertions_ConservationProblem.R |only prioritizr-8.1.0/prioritizr/R/standalone-assertions_class.R |only prioritizr-8.1.0/prioritizr/R/standalone-assertions_functions.R |only prioritizr-8.1.0/prioritizr/R/standalone-assertions_handlers.R |only prioritizr-8.1.0/prioritizr/R/standalone-assertions_misc.R |only prioritizr-8.1.0/prioritizr/R/standalone-assertions_raster.R |only prioritizr-8.1.0/prioritizr/R/standalone-assertions_sf.R |only prioritizr-8.1.0/prioritizr/R/standalone-assertions_solvers.R |only prioritizr-8.1.0/prioritizr/R/standalone-assertions_vector.R |only prioritizr-8.1.0/prioritizr/R/standalone-cli.R |only prioritizr-8.1.0/prioritizr/R/standalone-get_crs.R |only prioritizr-8.1.0/prioritizr/R/standalone-is_numeric_values.R |only prioritizr-8.1.0/prioritizr/R/standalone-is_same_crs.R |only prioritizr-8.1.0/prioritizr/R/standalone-is_spatial_extents_overlap.R |only prioritizr-8.1.0/prioritizr/R/standalone-repr.R |only prioritizr-8.1.0/prioritizr/R/summaries.R | 213 prioritizr-8.1.0/prioritizr/R/summary.R | 18 prioritizr-8.1.0/prioritizr/R/target_optimization_format.R |only prioritizr-8.1.0/prioritizr/R/targets.R | 503 prioritizr-8.1.0/prioritizr/R/tbl_df.R | 140 prioritizr-8.1.0/prioritizr/R/test-helpers.R | 296 prioritizr-8.1.0/prioritizr/R/validate_marxan_data.R |only prioritizr-8.1.0/prioritizr/R/waiver.R | 94 prioritizr-8.1.0/prioritizr/R/write_problem.R | 330 prioritizr-8.1.0/prioritizr/R/zone_names.R | 142 prioritizr-8.1.0/prioritizr/R/zones.R | 550 - prioritizr-8.1.0/prioritizr/R/zzz.R | 120 prioritizr-8.1.0/prioritizr/README.md | 1171 +- prioritizr-8.1.0/prioritizr/build/partial.rdb |binary prioritizr-8.1.0/prioritizr/build/vignette.rds |binary prioritizr-8.1.0/prioritizr/inst/CITATION | 45 prioritizr-8.1.0/prioritizr/inst/doc/calibrating_trade-offs_tutorial.Rmd | 1371 +- prioritizr-8.1.0/prioritizr/inst/doc/calibrating_trade-offs_tutorial.html | 319 prioritizr-8.1.0/prioritizr/inst/doc/connectivity_tutorial.Rmd | 1033 - prioritizr-8.1.0/prioritizr/inst/doc/connectivity_tutorial.html | 33 prioritizr-8.1.0/prioritizr/inst/doc/gurobi_installation_guide.Rmd | 370 prioritizr-8.1.0/prioritizr/inst/doc/gurobi_installation_guide.html | 24 prioritizr-8.1.0/prioritizr/inst/doc/management_zones_tutorial.Rmd | 801 - prioritizr-8.1.0/prioritizr/inst/doc/management_zones_tutorial.html | 139 prioritizr-8.1.0/prioritizr/inst/doc/package_overview.Rmd | 2203 ++-- prioritizr-8.1.0/prioritizr/inst/doc/package_overview.html | 1719 +-- prioritizr-8.1.0/prioritizr/inst/doc/prioritizr.Rmd | 655 - prioritizr-8.1.0/prioritizr/inst/doc/prioritizr.html | 371 prioritizr-8.1.0/prioritizr/inst/doc/publication_record.Rmd | 353 prioritizr-8.1.0/prioritizr/inst/doc/publication_record.html | 95 prioritizr-8.1.0/prioritizr/inst/doc/solver_benchmarks.Rmd | 1163 +- prioritizr-8.1.0/prioritizr/inst/doc/solver_benchmarks.html | 12 prioritizr-8.1.0/prioritizr/inst/extdata/marxan/input.dat | 110 prioritizr-8.1.0/prioritizr/inst/extdata/sim_complex_features.tif |only prioritizr-8.1.0/prioritizr/inst/extdata/sim_complex_historical_features.tif |only prioritizr-8.1.0/prioritizr/inst/extdata/sim_complex_locked_in_raster.tif |only prioritizr-8.1.0/prioritizr/inst/extdata/sim_complex_locked_out_raster.tif |only prioritizr-8.1.0/prioritizr/inst/extdata/sim_complex_pu_raster.tif |only prioritizr-8.1.0/prioritizr/inst/extdata/sim_phylogeny.txt | 46 prioritizr-8.1.0/prioritizr/inst/knitr/print.Rmd | 18 prioritizr-8.1.0/prioritizr/inst/scripts |only prioritizr-8.1.0/prioritizr/man/ConservationModifier-class.Rd | 468 prioritizr-8.1.0/prioritizr/man/ConservationProblem-class.Rd | 1424 +- prioritizr-8.1.0/prioritizr/man/Constraint-class.Rd | 172 prioritizr-8.1.0/prioritizr/man/Decision-class.Rd | 172 prioritizr-8.1.0/prioritizr/man/Objective-class.Rd | 218 prioritizr-8.1.0/prioritizr/man/OptimizationProblem-class.Rd | 870 - prioritizr-8.1.0/prioritizr/man/OptimizationProblem-methods.Rd | 349 prioritizr-8.1.0/prioritizr/man/Penalty-class.Rd | 172 prioritizr-8.1.0/prioritizr/man/Portfolio-class.Rd | 176 prioritizr-8.1.0/prioritizr/man/Solver-class.Rd | 512 prioritizr-8.1.0/prioritizr/man/Target-class.Rd | 158 prioritizr-8.1.0/prioritizr/man/TargetMethod-class.Rd |only prioritizr-8.1.0/prioritizr/man/Weight-class.Rd |only prioritizr-8.1.0/prioritizr/man/add_absolute_targets.Rd | 385 prioritizr-8.1.0/prioritizr/man/add_asym_connectivity_penalties.Rd | 608 - prioritizr-8.1.0/prioritizr/man/add_auto_targets.Rd |only prioritizr-8.1.0/prioritizr/man/add_binary_decisions.Rd | 166 prioritizr-8.1.0/prioritizr/man/add_boundary_penalties.Rd | 557 - prioritizr-8.1.0/prioritizr/man/add_cbc_solver.Rd | 449 prioritizr-8.1.0/prioritizr/man/add_connectivity_penalties.Rd | 856 - prioritizr-8.1.0/prioritizr/man/add_contiguity_constraints.Rd | 478 prioritizr-8.1.0/prioritizr/man/add_cplex_solver.Rd | 258 prioritizr-8.1.0/prioritizr/man/add_cuts_portfolio.Rd | 210 prioritizr-8.1.0/prioritizr/man/add_default_portfolio.Rd | 64 prioritizr-8.1.0/prioritizr/man/add_default_solver.Rd | 90 prioritizr-8.1.0/prioritizr/man/add_extra_portfolio.Rd | 182 prioritizr-8.1.0/prioritizr/man/add_feature_contiguity_constraints.Rd | 508 prioritizr-8.1.0/prioritizr/man/add_feature_weights.Rd | 505 prioritizr-8.1.0/prioritizr/man/add_gap_portfolio.Rd | 220 prioritizr-8.1.0/prioritizr/man/add_group_targets.Rd |only prioritizr-8.1.0/prioritizr/man/add_gurobi_solver.Rd | 499 prioritizr-8.1.0/prioritizr/man/add_highs_solver.Rd | 200 prioritizr-8.1.0/prioritizr/man/add_linear_constraints.Rd | 594 - prioritizr-8.1.0/prioritizr/man/add_linear_penalties.Rd | 501 prioritizr-8.1.0/prioritizr/man/add_locked_in_constraints.Rd | 558 - prioritizr-8.1.0/prioritizr/man/add_locked_out_constraints.Rd | 564 - prioritizr-8.1.0/prioritizr/man/add_lsymphony_solver.Rd | 250 prioritizr-8.1.0/prioritizr/man/add_mandatory_allocation_constraints.Rd | 174 prioritizr-8.1.0/prioritizr/man/add_manual_bounded_constraints.Rd | 348 prioritizr-8.1.0/prioritizr/man/add_manual_locked_constraints.Rd | 345 prioritizr-8.1.0/prioritizr/man/add_manual_targets.Rd | 574 - prioritizr-8.1.0/prioritizr/man/add_max_cover_objective.Rd | 356 prioritizr-8.1.0/prioritizr/man/add_max_features_objective.Rd | 290 prioritizr-8.1.0/prioritizr/man/add_max_phylo_div_objective.Rd | 482 prioritizr-8.1.0/prioritizr/man/add_max_phylo_end_objective.Rd | 488 prioritizr-8.1.0/prioritizr/man/add_max_utility_objective.Rd | 278 prioritizr-8.1.0/prioritizr/man/add_min_largest_shortfall_objective.Rd | 284 prioritizr-8.1.0/prioritizr/man/add_min_penalties_objective.Rd | 280 prioritizr-8.1.0/prioritizr/man/add_min_set_objective.Rd | 228 prioritizr-8.1.0/prioritizr/man/add_min_shortfall_objective.Rd | 282 prioritizr-8.1.0/prioritizr/man/add_neighbor_constraints.Rd | 446 prioritizr-8.1.0/prioritizr/man/add_neighbor_penalties.Rd |only prioritizr-8.1.0/prioritizr/man/add_proportion_decisions.Rd | 164 prioritizr-8.1.0/prioritizr/man/add_relative_targets.Rd | 371 prioritizr-8.1.0/prioritizr/man/add_rsymphony_solver.Rd | 218 prioritizr-8.1.0/prioritizr/man/add_semicontinuous_decisions.Rd | 178 prioritizr-8.1.0/prioritizr/man/add_shuffle_portfolio.Rd | 214 prioritizr-8.1.0/prioritizr/man/add_top_portfolio.Rd | 188 prioritizr-8.1.0/prioritizr/man/adjacency_matrix.Rd | 200 prioritizr-8.1.0/prioritizr/man/as_km2.Rd |only prioritizr-8.1.0/prioritizr/man/as_per_km2.Rd |only prioritizr-8.1.0/prioritizr/man/binary_stack.Rd | 125 prioritizr-8.1.0/prioritizr/man/boundary_matrix.Rd | 216 prioritizr-8.1.0/prioritizr/man/branch_matrix.Rd | 88 prioritizr-8.1.0/prioritizr/man/calibrate_cohon_penalty.Rd |only prioritizr-8.1.0/prioritizr/man/category_layer.Rd | 111 prioritizr-8.1.0/prioritizr/man/category_vector.Rd | 105 prioritizr-8.1.0/prioritizr/man/compile.Rd | 130 prioritizr-8.1.0/prioritizr/man/connectivity_matrix.Rd | 376 prioritizr-8.1.0/prioritizr/man/constraints.Rd | 254 prioritizr-8.1.0/prioritizr/man/decisions.Rd | 189 prioritizr-8.1.0/prioritizr/man/eval_asym_connectivity_summary.Rd | 614 - prioritizr-8.1.0/prioritizr/man/eval_boundary_summary.Rd | 644 - prioritizr-8.1.0/prioritizr/man/eval_connectivity_summary.Rd | 608 - prioritizr-8.1.0/prioritizr/man/eval_cost_summary.Rd | 460 prioritizr-8.1.0/prioritizr/man/eval_feature_representation_summary.Rd | 635 - prioritizr-8.1.0/prioritizr/man/eval_ferrier_importance.Rd | 403 prioritizr-8.1.0/prioritizr/man/eval_n_summary.Rd | 430 prioritizr-8.1.0/prioritizr/man/eval_rank_importance.Rd | 854 - prioritizr-8.1.0/prioritizr/man/eval_rare_richness_importance.Rd | 421 prioritizr-8.1.0/prioritizr/man/eval_replacement_importance.Rd | 584 - prioritizr-8.1.0/prioritizr/man/eval_target_coverage_summary.Rd | 636 - prioritizr-8.1.0/prioritizr/man/fast_extract.Rd | 144 prioritizr-8.1.0/prioritizr/man/feature_abundances.Rd | 332 prioritizr-8.1.0/prioritizr/man/feature_names.Rd | 96 prioritizr-8.1.0/prioritizr/man/figures/README-boundary_penalties-1.png |binary prioritizr-8.1.0/prioritizr/man/figures/README-features-1.png |binary prioritizr-8.1.0/prioritizr/man/figures/README-importance-1.png |binary prioritizr-8.1.0/prioritizr/man/figures/README-locked_in_constraints-1.png |binary prioritizr-8.1.0/prioritizr/man/figures/README-locked_in_constraints-2.png |binary prioritizr-8.1.0/prioritizr/man/figures/README-locked_out_constraints-1.png |binary prioritizr-8.1.0/prioritizr/man/figures/README-locked_out_constraints-2.png |binary prioritizr-8.1.0/prioritizr/man/figures/README-minimal_solution-1.png |binary prioritizr-8.1.0/prioritizr/man/figures/README-planning_units-1.png |binary prioritizr-8.1.0/prioritizr/man/importance.Rd | 318 prioritizr-8.1.0/prioritizr/man/intersecting_units.Rd | 186 prioritizr-8.1.0/prioritizr/man/knit_print.Rd | 58 prioritizr-8.1.0/prioritizr/man/linear_interpolation.Rd |only prioritizr-8.1.0/prioritizr/man/loglinear_interpolation.Rd | 192 prioritizr-8.1.0/prioritizr/man/marxan_boundary_data_to_matrix.Rd | 154 prioritizr-8.1.0/prioritizr/man/marxan_connectivity_data_to_matrix.Rd | 188 prioritizr-8.1.0/prioritizr/man/marxan_problem.Rd | 440 prioritizr-8.1.0/prioritizr/man/new_waiver.Rd | 58 prioritizr-8.1.0/prioritizr/man/number_of_features.Rd | 102 prioritizr-8.1.0/prioritizr/man/number_of_planning_units.Rd | 100 prioritizr-8.1.0/prioritizr/man/number_of_total_units.Rd | 128 prioritizr-8.1.0/prioritizr/man/number_of_zones.Rd | 106 prioritizr-8.1.0/prioritizr/man/objectives.Rd | 270 prioritizr-8.1.0/prioritizr/man/optimization_problem.Rd | 192 prioritizr-8.1.0/prioritizr/man/penalties.Rd | 253 prioritizr-8.1.0/prioritizr/man/portfolios.Rd | 272 prioritizr-8.1.0/prioritizr/man/presolve_check.Rd | 382 prioritizr-8.1.0/prioritizr/man/prioritizr-deprecated.Rd | 242 prioritizr-8.1.0/prioritizr/man/prioritizr.Rd | 256 prioritizr-8.1.0/prioritizr/man/problem.Rd | 1095 +- prioritizr-8.1.0/prioritizr/man/proximity_matrix.Rd | 222 prioritizr-8.1.0/prioritizr/man/reexports.Rd | 34 prioritizr-8.1.0/prioritizr/man/rescale_matrix.Rd | 122 prioritizr-8.1.0/prioritizr/man/rij_matrix.Rd | 196 prioritizr-8.1.0/prioritizr/man/rmd |only prioritizr-8.1.0/prioritizr/man/roxygen |only prioritizr-8.1.0/prioritizr/man/run_calculations.Rd | 178 prioritizr-8.1.0/prioritizr/man/show.Rd | 62 prioritizr-8.1.0/prioritizr/man/sim_data.Rd | 530 prioritizr-8.1.0/prioritizr/man/simulate_cost.Rd | 114 prioritizr-8.1.0/prioritizr/man/simulate_data.Rd | 148 prioritizr-8.1.0/prioritizr/man/simulate_species.Rd | 102 prioritizr-8.1.0/prioritizr/man/solve.Rd | 528 prioritizr-8.1.0/prioritizr/man/solvers.Rd | 348 prioritizr-8.1.0/prioritizr/man/spec_absolute_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_area_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_duran_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_interp_absolute_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_interp_area_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_jung_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_max_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_min_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_polak_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_pop_size_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_relative_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_rl_ecosystem_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_rl_species_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_rodrigues_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_rule_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_ward_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_watson_targets.Rd |only prioritizr-8.1.0/prioritizr/man/spec_wilson_targets.Rd |only prioritizr-8.1.0/prioritizr/man/summaries.Rd | 231 prioritizr-8.1.0/prioritizr/man/targets.Rd | 524 prioritizr-8.1.0/prioritizr/man/tibble-methods.Rd | 104 prioritizr-8.1.0/prioritizr/man/write_problem.Rd | 131 prioritizr-8.1.0/prioritizr/man/zone_names.Rd | 100 prioritizr-8.1.0/prioritizr/man/zones.Rd | 268 prioritizr-8.1.0/prioritizr/src/RcppExports.cpp | 148 prioritizr-8.1.0/prioritizr/src/init.c | 130 prioritizr-8.1.0/prioritizr/src/optimization_problem.cpp | 111 prioritizr-8.1.0/prioritizr/src/rcpp_apply_asym_connectivity_penalties.cpp | 2 prioritizr-8.1.0/prioritizr/src/rcpp_apply_boundary_penalties.cpp | 13 prioritizr-8.1.0/prioritizr/src/rcpp_apply_boundary_penalties2.cpp |only prioritizr-8.1.0/prioritizr/src/rcpp_apply_connectivity_penalties.cpp | 2 prioritizr-8.1.0/prioritizr/src/rcpp_apply_locked_constraints.cpp | 19 prioritizr-8.1.0/prioritizr/src/rcpp_apply_max_cover_objective.cpp | 10 prioritizr-8.1.0/prioritizr/src/rcpp_apply_max_features_objective.cpp | 12 prioritizr-8.1.0/prioritizr/src/rcpp_apply_max_phylo_objective.cpp | 14 prioritizr-8.1.0/prioritizr/src/rcpp_apply_max_utility_objective.cpp | 7 prioritizr-8.1.0/prioritizr/src/rcpp_apply_min_largest_shortfall_objective.cpp | 53 prioritizr-8.1.0/prioritizr/src/rcpp_apply_min_shortfall_objective.cpp | 14 prioritizr-8.1.0/prioritizr/src/rcpp_apply_neighbor_constraints.cpp | 69 prioritizr-8.1.0/prioritizr/tests/testthat.R | 54 prioritizr-8.1.0/prioritizr/tests/testthat/_snaps/assertions_functions.md |only prioritizr-8.1.0/prioritizr/tests/testthat/helper_asym_connectivity.R | 126 prioritizr-8.1.0/prioritizr/tests/testthat/helper_boundary.R | 168 prioritizr-8.1.0/prioritizr/tests/testthat/helper_connectivity.R | 116 prioritizr-8.1.0/prioritizr/tests/testthat/helper_ferrier_scores.R | 456 prioritizr-8.1.0/prioritizr/tests/testthat/helper_marxan.R |only prioritizr-8.1.0/prioritizr/tests/testthat/helper_raster.R | 140 prioritizr-8.1.0/prioritizr/tests/testthat/helper_sf.R | 32 prioritizr-8.1.0/prioritizr/tests/testthat/helper_skip.R | 138 prioritizr-8.1.0/prioritizr/tests/testthat/helper_solve_fixed_seed.R | 42 prioritizr-8.1.0/prioritizr/tests/testthat/helper_zones.R |only prioritizr-8.1.0/prioritizr/tests/testthat/setup.R | 8 prioritizr-8.1.0/prioritizr/tests/testthat/test_ConservationModifier.R | 40 prioritizr-8.1.0/prioritizr/tests/testthat/test_OptimizationProblem.R | 508 prioritizr-8.1.0/prioritizr/tests/testthat/test_TargetMethod.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_Waiver.R | 16 prioritizr-8.1.0/prioritizr/tests/testthat/test_add_absolute_targets.R | 633 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_asym_connectivity_penalties.R | 1180 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_boundary_penalties_knapsack.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_add_boundary_penalties_simple.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_add_cbc_solver.R | 1050 + prioritizr-8.1.0/prioritizr/tests/testthat/test_add_connectivity_penalties.R | 708 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_contiguity_constraints.R | 606 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_cplex_solver.R | 796 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_cuts_portfolio.R | 266 prioritizr-8.1.0/prioritizr/tests/testthat/test_add_default_portfolio.R | 176 prioritizr-8.1.0/prioritizr/tests/testthat/test_add_default_solver.R | 36 prioritizr-8.1.0/prioritizr/tests/testthat/test_add_extra_portfolio.R | 238 prioritizr-8.1.0/prioritizr/tests/testthat/test_add_feature_contiguity_constraints.R | 1024 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_feature_weights.R | 1100 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_gap_portfolio.R | 300 prioritizr-8.1.0/prioritizr/tests/testthat/test_add_group_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_add_gurobi_solver.R | 1027 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_highs_solver.R | 996 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_linear_constraints.R | 1296 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_linear_penalties.R | 1206 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_locked_in_constraints.R | 1540 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_locked_out_constraints.R | 1276 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_lpsymphony_solver.R | 834 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_mandatory_allocation_constraints.R | 416 prioritizr-8.1.0/prioritizr/tests/testthat/test_add_manual_bounded_constraints.R | 768 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_manual_locked_constraints.R | 716 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_manual_targets.R | 619 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_max_cover_objective.R | 1268 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_max_features_objective.R | 1510 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_max_phylo_div_objective.R | 1992 +-- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_max_phylo_end_objective.R | 2110 +-- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_max_utility_objective.R | 1482 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_min_largest_shortfall_objective.R | 1307 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_min_penalties_objective.R | 1404 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_min_set_objective.R | 766 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_min_shortfall_objective.R | 1536 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_add_neighbor_constraints.R | 883 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_neighbor_penalties.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_add_relative_targets.R | 539 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_rsymphony_solver.R | 820 - prioritizr-8.1.0/prioritizr/tests/testthat/test_add_shuffle_portfolio.R | 528 prioritizr-8.1.0/prioritizr/tests/testthat/test_add_top_portfolio.R | 296 prioritizr-8.1.0/prioritizr/tests/testthat/test_adjacency_matrix.R | 290 prioritizr-8.1.0/prioritizr/tests/testthat/test_all_binary.R | 222 prioritizr-8.1.0/prioritizr/tests/testthat/test_all_columns_any_finite.R | 154 prioritizr-8.1.0/prioritizr/tests/testthat/test_all_columns_inherit.R | 128 prioritizr-8.1.0/prioritizr/tests/testthat/test_all_finite.R | 212 prioritizr-8.1.0/prioritizr/tests/testthat/test_all_positive.R | 256 prioritizr-8.1.0/prioritizr/tests/testthat/test_all_proportion.R | 148 prioritizr-8.1.0/prioritizr/tests/testthat/test_any_nonNA.R | 310 prioritizr-8.1.0/prioritizr/tests/testthat/test_any_nonzero.R | 272 prioritizr-8.1.0/prioritizr/tests/testthat/test_as_Matrix.R | 56 prioritizr-8.1.0/prioritizr/tests/testthat/test_as_units.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_assertions_ConservationProblem.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_assertions_class.R | 107 prioritizr-8.1.0/prioritizr/tests/testthat/test_assertions_functions.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_assertions_handlers.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_assertions_misc.R | 93 prioritizr-8.1.0/prioritizr/tests/testthat/test_assertions_raster.R | 128 prioritizr-8.1.0/prioritizr/tests/testthat/test_assertions_sf.R | 24 prioritizr-8.1.0/prioritizr/tests/testthat/test_assertions_vector.R | 87 prioritizr-8.1.0/prioritizr/tests/testthat/test_auto_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_binary_stack.R | 92 prioritizr-8.1.0/prioritizr/tests/testthat/test_boundary_matrix.R | 718 - prioritizr-8.1.0/prioritizr/tests/testthat/test_branch_matrix.R | 96 prioritizr-8.1.0/prioritizr/tests/testthat/test_calibrate_cohon_method.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_category_layer.R | 86 prioritizr-8.1.0/prioritizr/tests/testthat/test_category_vector.R | 117 prioritizr-8.1.0/prioritizr/tests/testthat/test_cli.R | 50 prioritizr-8.1.0/prioritizr/tests/testthat/test_compile.R | 490 prioritizr-8.1.0/prioritizr/tests/testthat/test_connectivity_matrix.R | 362 prioritizr-8.1.0/prioritizr/tests/testthat/test_cplex.R | 298 prioritizr-8.1.0/prioritizr/tests/testthat/test_data.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_decisions.R | 542 - prioritizr-8.1.0/prioritizr/tests/testthat/test_documentation.R | 14 prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_asym_connectivity_summary.R | 612 - prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_boundary_summary.R | 732 - prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_connectivity_summary.R | 616 - prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_cost_summary.R | 254 prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_feature_representation_summary.R | 1272 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_ferrier_importance.R | 697 - prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_n_summary.R | 206 prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_rank_importance.R | 3192 +++-- prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_rare_richness_importance.R | 788 - prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_replacement_importance.R | 1356 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_eval_target_coverage_summary.R | 666 - prioritizr-8.1.0/prioritizr/tests/testthat/test_fast_extract.R | 470 prioritizr-8.1.0/prioritizr/tests/testthat/test_feature_abundances.R | 668 - prioritizr-8.1.0/prioritizr/tests/testthat/test_get_crs.R | 94 prioritizr-8.1.0/prioritizr/tests/testthat/test_get_target_method.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_helper_raster.R | 134 prioritizr-8.1.0/prioritizr/tests/testthat/test_internal.R | 46 prioritizr-8.1.0/prioritizr/tests/testthat/test_intersecting_units.R | 414 prioritizr-8.1.0/prioritizr/tests/testthat/test_is_numeric_values.R | 116 prioritizr-8.1.0/prioritizr/tests/testthat/test_is_spatial_extents_overlap.R | 296 prioritizr-8.1.0/prioritizr/tests/testthat/test_marxan_boundary_data_to_matrix.R | 96 prioritizr-8.1.0/prioritizr/tests/testthat/test_marxan_connectivity_data_to_matrix.R | 420 prioritizr-8.1.0/prioritizr/tests/testthat/test_marxan_problem.R | 1076 + prioritizr-8.1.0/prioritizr/tests/testthat/test_memory.R | 64 prioritizr-8.1.0/prioritizr/tests/testthat/test_miscellaneous.R | 8 prioritizr-8.1.0/prioritizr/tests/testthat/test_planning_unit_indices.R | 256 prioritizr-8.1.0/prioritizr/tests/testthat/test_planning_unit_solution_format.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_planning_unit_solution_status.R | 820 - prioritizr-8.1.0/prioritizr/tests/testthat/test_presolve_check.R | 727 - prioritizr-8.1.0/prioritizr/tests/testthat/test_prioritizrdata.R | 138 prioritizr-8.1.0/prioritizr/tests/testthat/test_problem-deprecated.R | 1827 +-- prioritizr-8.1.0/prioritizr/tests/testthat/test_problem.R | 3333 +++--- prioritizr-8.1.0/prioritizr/tests/testthat/test_problem_negative.R | 2474 ++-- prioritizr-8.1.0/prioritizr/tests/testthat/test_proximity_matrix.R | 676 - prioritizr-8.1.0/prioritizr/tests/testthat/test_repr.R | 294 prioritizr-8.1.0/prioritizr/tests/testthat/test_rescale_matrix.R | 84 prioritizr-8.1.0/prioritizr/tests/testthat/test_rij_matrix.R | 660 - prioritizr-8.1.0/prioritizr/tests/testthat/test_roxygen-documentation.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_run_calculations.R | 50 prioritizr-8.1.0/prioritizr/tests/testthat/test_simulate.R | 228 prioritizr-8.1.0/prioritizr/tests/testthat/test_solve.R | 1237 +- prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_absolute_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_area_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_duran_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_interp_absolute_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_interp_area_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_jung_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_max_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_min_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_polak_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_pop_size_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_relative_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_rl_ecosystem_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_rl_species_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_rodrigues_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_rule_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_ward_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_watson_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_spec_wilson_targets.R |only prioritizr-8.1.0/prioritizr/tests/testthat/test_st_geometry_classes.R | 82 prioritizr-8.1.0/prioritizr/tests/testthat/test_write_problem.R | 346 prioritizr-8.1.0/prioritizr/tests/testthat/test_zones.R | 260 prioritizr-8.1.0/prioritizr/vignettes/calibrating_trade-offs_tutorial.Rmd | 1371 +- prioritizr-8.1.0/prioritizr/vignettes/connectivity_tutorial.Rmd | 1033 - prioritizr-8.1.0/prioritizr/vignettes/gurobi_installation_guide.Rmd | 370 prioritizr-8.1.0/prioritizr/vignettes/management_zones_tutorial.Rmd | 801 - prioritizr-8.1.0/prioritizr/vignettes/package_overview.Rmd | 2203 ++-- prioritizr-8.1.0/prioritizr/vignettes/prioritizr.Rmd | 655 - prioritizr-8.1.0/prioritizr/vignettes/publication_record.Rmd | 353 prioritizr-8.1.0/prioritizr/vignettes/reference-style.csl | 402 prioritizr-8.1.0/prioritizr/vignettes/references.bib | 1396 +- prioritizr-8.1.0/prioritizr/vignettes/solver_benchmarks.Rmd | 1163 +- 577 files changed, 99793 insertions(+), 94958 deletions(-)
Title: Structural Equation Modeling with Deep Neural Network and
Machine Learning Algorithms
Description: Training and validation of a custom (or data-driven) Structural
Equation Models using layer-wise Deep Neural Networks or node-wise
Machine Learning algorithms, which extend the fitting procedures of
the 'SEMgraph' R package <doi:10.32614/CRAN.package.SEMgraph>.
Author: Mario Grassi [aut],
Barbara Tarantino [cre]
Maintainer: Barbara Tarantino <barbara.tarantino01@universitadipavia.it>
Diff between SEMdeep versions 1.0.0 dated 2025-01-23 and 1.1.0 dated 2025-11-10
DESCRIPTION | 16 MD5 | 42 - NAMESPACE | 4 NEWS.md | 24 - R/DNNhelp.R |only R/SEMdnn.R | 1005 ++++++++++++++++++++++++++----------------- R/SEMhelp.R | 184 ++++--- R/SEMml.R | 481 ++++++++++++-------- README.md | 12 man/SEMdnn.Rd | 158 ++++-- man/SEMml.Rd | 49 -- man/crossValidation.Rd | 4 man/getConnectionWeight.Rd | 35 - man/getGradientWeight.Rd | 38 - man/getLOCO.Rd |only man/getShapleyR2.Rd | 63 +- man/getSignificanceTest.Rd | 56 +- man/getVariableImportance.Rd | 5 man/mapGraph.Rd | 10 man/nplot.Rd | 28 - man/predict.DNN.Rd | 16 man/predict.ML.Rd | 6 man/predict.SEM.Rd | 15 23 files changed, 1317 insertions(+), 934 deletions(-)
Title: Semi-Automatic Reporting of Ordinary Surveys
Description: Offers a systematic way for conditional reporting of figures and tables for many
(and bivariate combinations of) variables, typically from survey data.
Contains interactive 'ggiraph'-based
(<https://CRAN.R-project.org/package=ggiraph>) plotting functions and
data frame-based summary tables (bivariate significance tests,
frequencies/proportions, unique open ended responses, etc) with
many arguments for customization, and extensions possible. Uses a global
options() system for neatly reducing redundant code.
Also contains tools for immediate saving of objects and returning a hashed link to the object,
useful for creating download links to high resolution images upon rendering in 'Quarto'.
Suitable for highly customized reports, primarily intended for survey
research.
Author: Stephan Daus [aut, cre, cph] ,
Julia Silge [ctb] ,
David Robinson [ctb] ,
Nordic Institute for The Studies of Innovation, Research and Education
[fnd],
Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>
Diff between saros versions 1.5.4 dated 2025-06-04 and 1.6.0 dated 2025-11-10
saros-1.5.4/saros/R/convert_trailing_chars.R |only saros-1.5.4/saros/R/crosstable.R |only saros-1.5.4/saros/R/pretty_tabular.R |only saros-1.5.4/saros/R/ungroup_data.R |only saros-1.6.0/saros/DESCRIPTION | 16 saros-1.6.0/saros/LICENSE | 2 saros-1.6.0/saros/MD5 | 282 +- saros-1.6.0/saros/NAMESPACE | 9 saros-1.6.0/saros/NEWS.md | 81 saros-1.6.0/saros/R/check_multiple_dep_and_one_indep.R | 24 saros-1.6.0/saros/R/check_multiple_indep.R | 19 saros-1.6.0/saros/R/check_no_duplicated_label_suffix.R | 56 saros-1.6.0/saros/R/check_options.R | 10 saros-1.6.0/saros/R/check_sort_by.R | 20 saros-1.6.0/saros/R/checks.R | 138 - saros-1.6.0/saros/R/colour.R | 238 +- saros-1.6.0/saros/R/crosstable.data.frame.R | 267 +- saros-1.6.0/saros/R/crosstable.survey.R | 343 +-- saros-1.6.0/saros/R/crowd_plots_as_tabset.R |only saros-1.6.0/saros/R/deprecated.R | 50 saros-1.6.0/saros/R/err_msg.R | 9 saros-1.6.0/saros/R/fig_height_h_barchart.R | 256 +- saros-1.6.0/saros/R/find_stat_test.R | 284 -- saros-1.6.0/saros/R/get_common_levels.R | 10 saros-1.6.0/saros/R/get_fig_title_suffix_from_ggplot.R |only saros-1.6.0/saros/R/get_main_question.R | 48 saros-1.6.0/saros/R/get_raw_labels.R | 20 saros-1.6.0/saros/R/ggsaver.R | 9 saros-1.6.0/saros/R/girafe-utils.R |only saros-1.6.0/saros/R/girafe.R | 344 +-- saros-1.6.0/saros/R/global_settings.R | 33 saros-1.6.0/saros/R/is_arg_explicit.R | 1 saros-1.6.0/saros/R/keep_cols.R | 68 saros-1.6.0/saros/R/keep_indep_cats.R | 4 saros-1.6.0/saros/R/keep_subitem.R | 32 saros-1.6.0/saros/R/make_content.R | 11 saros-1.6.0/saros/R/make_content.cat_freq_plot_docx.R | 31 saros-1.6.0/saros/R/make_content.cat_plot_html.R | 250 +- saros-1.6.0/saros/R/make_content.cat_prop_plot_docx.R | 107 saros-1.6.0/saros/R/make_content.cat_table_html.R | 142 - saros-1.6.0/saros/R/make_content.chr_table_html.R | 70 saros-1.6.0/saros/R/make_content.int_plot_html.R | 307 +- saros-1.6.0/saros/R/make_content.int_table_html.R |only saros-1.6.0/saros/R/make_content.sigtest_table_html.R | 51 saros-1.6.0/saros/R/make_link.R | 78 saros-1.6.0/saros/R/makeme.R | 555 ++--- saros-1.6.0/saros/R/makeme_helpers.R | 1077 ++++++++-- saros-1.6.0/saros/R/makeme_keep_rows.R | 31 saros-1.6.0/saros/R/n_rng.R | 130 - saros-1.6.0/saros/R/post_process_sarosplot_data.R | 80 saros-1.6.0/saros/R/saros.R | 1 saros-1.6.0/saros/R/scale_x_reordered.R | 11 saros-1.6.0/saros/R/simple_desciptives.R | 136 - saros-1.6.0/saros/R/sorting_utils.R |only saros-1.6.0/saros/R/string_wrap.R | 6 saros-1.6.0/saros/R/summarize_cat_cat_data.R | 468 ++-- saros-1.6.0/saros/R/summarize_int_cat_data.R | 32 saros-1.6.0/saros/R/table_utils.R |only saros-1.6.0/saros/R/tabular_read.R |only saros-1.6.0/saros/R/tabular_write.R |only saros-1.6.0/saros/R/txt_from_cat_mesos_plots.R |only saros-1.6.0/saros/R/utils.R | 282 +- saros-1.6.0/saros/R/utils_office.R | 86 saros-1.6.0/saros/R/validate_makeme_options.R | 166 + saros-1.6.0/saros/R/zzz.R | 118 - saros-1.6.0/saros/build/vignette.rds |binary saros-1.6.0/saros/inst/WORDLIST | 27 saros-1.6.0/saros/inst/doc/for_chapter_author.html | 141 + saros-1.6.0/saros/inst/doc/for_developers.html | 141 + saros-1.6.0/saros/inst/doc/for_readers.html | 141 + saros-1.6.0/saros/inst/doc/saros_name.html | 141 + saros-1.6.0/saros/man/add_category_order.Rd |only saros-1.6.0/saros/man/add_dep_order.Rd |only saros-1.6.0/saros/man/add_indep_order.Rd |only saros-1.6.0/saros/man/add_sorting_order_vars.Rd |only saros-1.6.0/saros/man/apply_final_arrangement.Rd |only saros-1.6.0/saros/man/apply_label_wrapping.Rd |only saros-1.6.0/saros/man/apply_legacy_sorting_adjustments.Rd |only saros-1.6.0/saros/man/arrange_table_data.Rd |only saros-1.6.0/saros/man/arrange_with_order.Rd |only saros-1.6.0/saros/man/calculate_category_order.Rd |only saros-1.6.0/saros/man/calculate_column_order.Rd |only saros-1.6.0/saros/man/calculate_indep_category_order.Rd |only saros-1.6.0/saros/man/calculate_indep_column_order.Rd |only saros-1.6.0/saros/man/calculate_indep_proportion_order.Rd |only saros-1.6.0/saros/man/calculate_indep_sum_value_order.Rd |only saros-1.6.0/saros/man/calculate_multiple_category_order.Rd |only saros-1.6.0/saros/man/calculate_proportion_order.Rd |only saros-1.6.0/saros/man/calculate_sum_value_order.Rd |only saros-1.6.0/saros/man/crowd_plots_as_tabset.Rd |only saros-1.6.0/saros/man/detect_variable_types.Rd |only saros-1.6.0/saros/man/determine_variable_basis.Rd |only saros-1.6.0/saros/man/evaluate_variable_selection.Rd |only saros-1.6.0/saros/man/fig_height_h_barchart2.Rd | 2 saros-1.6.0/saros/man/filter_crowd_data.Rd |only saros-1.6.0/saros/man/generate_crowd_output.Rd |only saros-1.6.0/saros/man/generate_data_summary.Rd |only saros-1.6.0/saros/man/get_data_display_column.Rd |only saros-1.6.0/saros/man/get_dep_display_column.Rd |only saros-1.6.0/saros/man/get_fig_title_suffix_from_ggplot.Rd |only saros-1.6.0/saros/man/get_indep_col_name.Rd |only saros-1.6.0/saros/man/get_indep_labels.Rd |only saros-1.6.0/saros/man/get_standard_column_renamer.Rd |only saros-1.6.0/saros/man/get_target_categories.Rd |only saros-1.6.0/saros/man/girafe.Rd | 3 saros-1.6.0/saros/man/handle_crowd_columns.Rd |only saros-1.6.0/saros/man/hex_bw.Rd | 2 saros-1.6.0/saros/man/initialize_arguments.Rd |only saros-1.6.0/saros/man/initialize_crowd_filtering.Rd |only saros-1.6.0/saros/man/makeme.Rd | 102 saros-1.6.0/saros/man/normalize_makeme_arguments.Rd |only saros-1.6.0/saros/man/post_process_makeme_data.Rd |only saros-1.6.0/saros/man/process_all_crowds.Rd |only saros-1.6.0/saros/man/process_binary_category_colors.Rd |only saros-1.6.0/saros/man/process_categorical_na.Rd |only saros-1.6.0/saros/man/process_crowd_data.Rd |only saros-1.6.0/saros/man/process_crowd_settings.Rd |only saros-1.6.0/saros/man/process_global_indep_categories.Rd |only saros-1.6.0/saros/man/process_indep_factor_levels.Rd |only saros-1.6.0/saros/man/process_main_question_and_suffixes.Rd |only saros-1.6.0/saros/man/process_output_results.Rd |only saros-1.6.0/saros/man/process_table_data.Rd |only saros-1.6.0/saros/man/rename_crowd_outputs.Rd |only saros-1.6.0/saros/man/reorder_crowd_array.Rd |only saros-1.6.0/saros/man/resolve_variable_overlaps.Rd |only saros-1.6.0/saros/man/round_numeric_stats.Rd |only saros-1.6.0/saros/man/set_factor_levels_from_order.Rd |only saros-1.6.0/saros/man/setup_and_validate_makeme_args.Rd |only saros-1.6.0/saros/man/setup_table_data.Rd |only saros-1.6.0/saros/man/shift_labels_always_at.Rd |only saros-1.6.0/saros/man/strip_wrap_var.Rd |only saros-1.6.0/saros/man/summarize_cat_cat_data.Rd | 74 saros-1.6.0/saros/man/summarize_data_by_type.Rd |only saros-1.6.0/saros/man/tabular_read.Rd |only saros-1.6.0/saros/man/tabular_write.Rd |only saros-1.6.0/saros/man/txt_from_cat_mesos_plots.Rd |only saros-1.6.0/saros/man/validate_single_dep_var.Rd |only saros-1.6.0/saros/man/validate_type_specific_constraints.Rd |only saros-1.6.0/saros/tests/spelling.R | 10 saros-1.6.0/saros/tests/testthat/_snaps |only saros-1.6.0/saros/tests/testthat/test-add_n_to_label.R | 106 saros-1.6.0/saros/tests/testthat/test-check_multiple_dep_and_one_indep.R | 3 saros-1.6.0/saros/tests/testthat/test-check_multiple_indep.R | 5 saros-1.6.0/saros/tests/testthat/test-check_options.R | 102 saros-1.6.0/saros/tests/testthat/test-check_sort_by.R | 50 saros-1.6.0/saros/tests/testthat/test-checks.R | 26 saros-1.6.0/saros/tests/testthat/test-compare_and_replace_args.R | 47 saros-1.6.0/saros/tests/testthat/test-crosstable.R | 51 saros-1.6.0/saros/tests/testthat/test-crowd_plots_as_tabset.R |only saros-1.6.0/saros/tests/testthat/test-get_fig_title_suffix_from_ggplot.R |only saros-1.6.0/saros/tests/testthat/test-get_main_question.R | 41 saros-1.6.0/saros/tests/testthat/test-girafe-binary-colors.R |only saros-1.6.0/saros/tests/testthat/test-girafe-custom-palette.R |only saros-1.6.0/saros/tests/testthat/test-is_arg_explicit.R | 85 saros-1.6.0/saros/tests/testthat/test-issue-500.R |only saros-1.6.0/saros/tests/testthat/test-keep_cols.R | 109 - saros-1.6.0/saros/tests/testthat/test-make_content.cat_plot_docx.R | 789 ++++--- saros-1.6.0/saros/tests/testthat/test-make_content.cat_plot_html.R | 30 saros-1.6.0/saros/tests/testthat/test-make_content.cat_table_html.R | 106 saros-1.6.0/saros/tests/testthat/test-make_content.chr_table_html.R |only saros-1.6.0/saros/tests/testthat/test-make_content.int_table_html.R |only saros-1.6.0/saros/tests/testthat/test-make_link.R | 39 saros-1.6.0/saros/tests/testthat/test-makeme-hide-crowd-functionality.R |only saros-1.6.0/saros/tests/testthat/test-makeme-int-plot-html-snapshots.R |only saros-1.6.0/saros/tests/testthat/test-makeme-sort-functionality.R |only saros-1.6.0/saros/tests/testthat/test-makeme-table-types.R |only saros-1.6.0/saros/tests/testthat/test-n_rng.R | 80 saros-1.6.0/saros/tests/testthat/test-ordered-factor-sorting.R |only saros-1.6.0/saros/tests/testthat/test-post_process_sarosplot_data.R | 49 saros-1.6.0/saros/tests/testthat/test-simple_desciptives.R | 183 + saros-1.6.0/saros/tests/testthat/test-summarize_cat_cat_data.R | 515 +++- saros-1.6.0/saros/tests/testthat/test-tabular-read.R |only saros-1.6.0/saros/tests/testthat/test-tabular-write.R |only saros-1.6.0/saros/tests/testthat/test-txt_from_cat_mesos_plots-validation.R |only saros-1.6.0/saros/tests/testthat/test-txt_from_cat_mesos_plots.R |only saros-1.6.0/saros/tests/testthat/test-utils-colour.R |only saros-1.6.0/saros/tests/testthat/test-utils-find_stat_test.R |only saros-1.6.0/saros/tests/testthat/test-utils-get_common_levels.R |only saros-1.6.0/saros/tests/testthat/test-utils-ggsaver.R |only saros-1.6.0/saros/tests/testthat/test-utils-global_settings.R |only saros-1.6.0/saros/tests/testthat/test-utils-globals.R |only saros-1.6.0/saros/tests/testthat/test-utils-keep_subitem.R |only saros-1.6.0/saros/tests/testthat/test-utils-make_content.R |only saros-1.6.0/saros/tests/testthat/test-utils-makeme_helpers.R |only saros-1.6.0/saros/tests/testthat/test-utils-n_rng.R |only saros-1.6.0/saros/tests/testthat/test-utils-office.R |only saros-1.6.0/saros/tests/testthat/test-utils-string_wrap.R |only saros-1.6.0/saros/tests/testthat/test-utils-summarize_int_cat_data.R |only saros-1.6.0/saros/tests/testthat/test-utils-table_utils.R |only saros-1.6.0/saros/tests/testthat/test-validation-check_no_duplicated_label_suffix.R |only saros-1.6.0/saros/tests/testthat/test-validation-check_sort_by.R |only 191 files changed, 6698 insertions(+), 3401 deletions(-)
Title: Wrapper for the Gnu Scientific Library
Description: An R wrapper for some of the functionality of the
Gnu Scientific Library.
Author: Robin K. S. Hankin [aut, cre] ,
Andrew Clausen [ctb] ,
Duncan Murdoch [ctb]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between gsl versions 2.1-8 dated 2023-01-24 and 2.1-9 dated 2025-11-10
DESCRIPTION | 11 ++++++----- INSTALL | 16 +++++++++++++++- MD5 | 26 +++++++++++++------------- NEWS.md | 6 ++++++ README.md | 3 +-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 15 ++++----------- inst/doc/gsl.Rnw | 4 ++-- inst/doc/gsl.pdf |binary man/figures/gsl.png |binary src/qrng.c | 22 +++++++++++----------- src/rng.c | 6 +++--- vignettes/gsl.Rnw | 4 ++-- 14 files changed, 63 insertions(+), 50 deletions(-)
Title: Cancer RADAR Project Tool
Description: Cancer RADAR is a project which aim is to develop an
infrastructure that allows quantifying the risk of cancer by migration
background across Europe. This package contains a set of functions
cancer registries partners should use to reshape 5 year-age group
cancer incidence data into a set of summary statistics (see Boyle &
Parkin (1991, ISBN:978-92-832-1195-2)) in lines with Cancer RADAR data
protections rules.
Author: Nienke Alberts [aut],
Damien Georges [aut, cre] ,
Stefano Rosso [aut],
Iacopo Baussano [aut]
Maintainer: Damien Georges <georgesd@iarc.who.int>
Diff between cancerradarr versions 2.0.0 dated 2025-10-28 and 2.1.0 dated 2025-11-10
DESCRIPTION | 6 +-- MD5 | 28 +++++++-------- R/chop_vector.R | 2 - R/create_static_report.R | 4 +- R/custom_ageg_aggregation.R | 6 +-- R/data.R | 8 ++-- R/proportional_rates.R | 2 - README.md | 4 +- inst/extdata/static_report.Rmd | 72 +++++++++++++++++++++-------------------- man/chop_vector.Rd | 2 - man/chopped.vector.list.Rd | 2 - man/custom_ageg_aggregation.Rd | 2 - man/dat.asr.cat.Rd | 4 +- man/globocan.2022.eu.Rd | 2 - man/proportional_rates.Rd | 2 - 15 files changed, 76 insertions(+), 70 deletions(-)
Title: Client for World Banks's 'Indicators' and 'Poverty and
Inequality Platform (PIP)' APIs
Description: Download and search data from the 'World Bank Indicators
API', which provides access to nearly 16,000 time series indicators.
See
<https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api-documentation>
for further details about the API.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
This is a re-admission after prior archival of version 0.6.1 dated 2025-08-29
Diff between worldbank versions 0.6.1 dated 2025-08-29 and 0.7.0 dated 2025-11-10
worldbank-0.6.1/worldbank/man/wb_country_indicator.Rd |only worldbank-0.7.0/worldbank/DESCRIPTION | 12 +- worldbank-0.7.0/worldbank/MD5 | 58 +++++---- worldbank-0.7.0/worldbank/NAMESPACE | 3 worldbank-0.7.0/worldbank/NEWS.md | 7 + worldbank-0.7.0/worldbank/R/cache.R |only worldbank-0.7.0/worldbank/R/fone.R | 15 +- worldbank-0.7.0/worldbank/R/indicators.R | 96 ++++++++-------- worldbank-0.7.0/worldbank/R/pip.R | 39 ++++-- worldbank-0.7.0/worldbank/R/utils.R | 7 + worldbank-0.7.0/worldbank/R/worldbank-package.R | 1 worldbank-0.7.0/worldbank/README.md | 29 ++++ worldbank-0.7.0/worldbank/man/cache.Rd |only worldbank-0.7.0/worldbank/man/figures/README-demo-1.png |only worldbank-0.7.0/worldbank/man/fone.Rd | 9 + worldbank-0.7.0/worldbank/man/pip_aux.Rd | 11 + worldbank-0.7.0/worldbank/man/pip_citation.Rd | 2 worldbank-0.7.0/worldbank/man/pip_data.Rd | 5 worldbank-0.7.0/worldbank/man/pip_group.Rd | 5 worldbank-0.7.0/worldbank/man/pip_health_check.Rd | 2 worldbank-0.7.0/worldbank/man/pip_info.Rd | 2 worldbank-0.7.0/worldbank/man/pip_valid_params.Rd | 5 worldbank-0.7.0/worldbank/man/pip_versions.Rd | 5 worldbank-0.7.0/worldbank/man/wb_country.Rd | 5 worldbank-0.7.0/worldbank/man/wb_data.Rd |only worldbank-0.7.0/worldbank/man/wb_income_level.Rd | 2 worldbank-0.7.0/worldbank/man/wb_indicator.Rd | 2 worldbank-0.7.0/worldbank/man/wb_language.Rd | 2 worldbank-0.7.0/worldbank/man/wb_lending_type.Rd | 2 worldbank-0.7.0/worldbank/man/wb_region.Rd | 5 worldbank-0.7.0/worldbank/man/wb_source.Rd | 5 worldbank-0.7.0/worldbank/man/wb_topic.Rd | 5 worldbank-0.7.0/worldbank/tests/testthat/setup.R |only 33 files changed, 226 insertions(+), 115 deletions(-)
Title: A Lightweight and Flexible Web Framework
Description: A very flexible framework for building server side logic in
R. The framework is unopinionated when it comes to how HTTP requests
and WebSocket messages are handled and supports all levels of app
complexity; from serving static content to full-blown dynamic
web-apps. Fiery does not hold your hand as much as e.g. the shiny
package does, but instead sets you free to create your web app the way
you want.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between fiery versions 1.3.0 dated 2025-08-20 and 1.4.0 dated 2025-11-10
DESCRIPTION | 18 MD5 | 45 - NAMESPACE | 5 NEWS.md | 10 R/Fire.R | 610 ++++++++++++----- R/HandlerStack.R | 17 R/PromiseStack.R | 55 + R/aaa.R | 13 R/additional_type_checks.R | 34 R/fake_request.R | 42 - R/fiery-package.R | 4 R/loggers.R | 129 +++ R/otel.R |only R/request_store.R | 2 README.md | 2 build/vignette.rds |binary man/loggers.Rd | 3 tests/testthat/_snaps/Fire.md | 8 tests/testthat/helper.R | 20 tests/testthat/test-Fire.R | 1279 ++++++++++++++++++++----------------- tests/testthat/test-HandlerStack.R | 141 ++-- tests/testthat/test-PromiseStack.R | 174 ++--- tests/testthat/test-fake_request.R | 201 +++-- tests/testthat/test-loggers.R | 121 +-- 24 files changed, 1792 insertions(+), 1141 deletions(-)
Title: Brazilian COVID-19 Pandemic Data
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at the country, region, state, and city levels. The package also downloads world-level COVID-19 data from Johns Hopkins University's repository. COVID-19 data is available from the start of follow-up until to May 5, 2023, when the World Health Organization (WHO) declared an end to the Public Health Emergency of International Concern (PHEIC) for COVID-19.
Author: Fabio Demarqui [aut, cre, cph],
Cristiano Santos [aut],
Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
This is a re-admission after prior archival of version 1.0.0 dated 2025-08-18
Diff between covid19br versions 1.0.0 dated 2025-08-18 and 1.0.0.1 dated 2025-11-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/downloadData.R | 1 + tests/testthat/test_covid19br.R | 21 +++++++++++++-------- 5 files changed, 26 insertions(+), 16 deletions(-)
Title: Automatic Time Series Analysis and Forecasting using the Ata
Method
Description: The Ata method (Yapar et al. (2019) <doi:10.15672/hujms.461032>), an alternative to exponential smoothing (described in Yapar (2016) <doi:10.15672/HJMS.201614320580>,
Yapar et al. (2017) <doi:10.15672/HJMS.2017.493>), is a new univariate time series forecasting method which provides innovative solutions to issues faced during the
initialization and optimization stages of existing forecasting methods. Forecasting performance of the Ata method is superior to existing methods both in terms of easy
implementation and accurate forecasting. It can be applied to non-seasonal or seasonal time series which can be decomposed into four components (remainder, level, trend
and seasonal). This methodology performed well on the M3 and M4-competition data. This package was written based on Ali Sabri Taylan’s PhD dissertation.
Author: Ali Sabri Taylan [aut, cre, cph] ,
Hanife Taylan Selamlar [aut, cph] ,
Guckan Yapar [aut, ths, cph]
Maintainer: Ali Sabri Taylan <alisabritaylan@gmail.com>
Diff between ATAforecasting versions 0.0.60 dated 2023-06-12 and 0.0.61 dated 2025-11-10
DESCRIPTION | 25 ++++++----- MD5 | 20 +++++---- R/ATA.R | 7 +-- R/ATA_BoxCoxAttributes.r | 2 R/ATA_Decomposition.r | 31 ++++++++++++-- README.md | 91 +++++++++++++++++++++++++++++++++++++++--- build/partial.rdb |binary inst/COPYRIGHT.md |only man/ATA.BoxCoxAttr.Rd | 2 man/ATA.Decomposition.Rd | 11 ++++- man/ATAforecasting-package.Rd | 21 +++++++-- man/figures |only 12 files changed, 170 insertions(+), 40 deletions(-)
More information about ATAforecasting at CRAN
Permanent link
Title: Weighted Random Sampling without Replacement
Description: A collection of implementations of classical and
novel algorithms for weighted sampling without replacement.
Implementations include the algorithm of Efraimidis and Spirakis (2006)
<doi:10.1016/j.ipl.2005.11.003> and Wong and Easton (1980)
<doi:10.1137/0209009>.
Author: Kirill Mueller [aut, cre]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between wrswoR versions 1.1.1 dated 2020-07-26 and 1.2.0 dated 2025-11-10
.aspell |only DESCRIPTION | 32 ++++-- MD5 | 32 +++--- NAMESPACE | 1 NEWS.md | 17 +++ R/RcppExports.R | 6 + R/sample_int_rank.R | 38 ++++++-- R/sample_int_rej.R | 2 README.md | 4 man/sample_int.Rd | 26 ++++- man/wrswoR-package.Rd | 8 + src/RcppExports.cpp | 19 ++++ src/sample_int_crank.cpp | 192 ++++++++++++++++++++++++++++++++--------- tests/testthat.R | 10 +- tests/testthat/test-corner.R | 2 tests/testthat/test-error.R | 47 +++++++++- tests/testthat/test-harmonic.R | 2 tests/testthat/test-unique.R | 2 18 files changed, 341 insertions(+), 99 deletions(-)
Title: Simple Features for R
Description: Support for simple feature access, a standardized way to
encode and analyze spatial vector data. Binds to 'GDAL'
<doi:10.5281/zenodo.5884351> for reading and writing data, to 'GEOS'
<doi:10.5281/zenodo.11396894> for geometrical operations,
and to 'PROJ' <doi:10.5281/zenodo.5884394> for projection
conversions and datum transformations. Uses by default the 's2'
package for geometry operations on geodetic (long/lat degree)
coordinates.
Author: Edzer Pebesma [aut, cre] ,
Roger Bivand [ctb] ,
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] ,
Kirill Mueller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [c [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 1.0-21 dated 2025-05-15 and 1.0-22 dated 2025-11-10
DESCRIPTION | 8 MD5 | 136 +- NAMESPACE | 1 NEWS.md | 18 R/geom-measures.R | 23 R/geom-transformers.R | 55 R/plot.R | 32 R/sf.R | 19 R/sfc.R | 5 R/sfg.R | 6 R/spatstat.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/sf1.R | 2 inst/doc/sf1.Rmd | 12 inst/doc/sf1.html | 2600 +++++++++++++++++++++++++++++++------------ inst/doc/sf2.R | 2 inst/doc/sf2.Rmd | 12 inst/doc/sf2.html | 1996 ++++++++++++++++++++++++++------- inst/doc/sf3.R | 2 inst/doc/sf3.Rmd | 12 inst/doc/sf3.html | 2412 +++++++++++++++++++++++++++++---------- inst/doc/sf4.R | 2 inst/doc/sf4.Rmd | 12 inst/doc/sf4.html | 2086 +++++++++++++++++++++++++++------- inst/doc/sf5.Rmd | 12 inst/doc/sf5.html | 1883 +++++++++++++++++++++++++------ inst/doc/sf6.R | 2 inst/doc/sf6.Rmd | 12 inst/doc/sf6.html | 1782 ++++++++++++++++++++++++----- inst/doc/sf7.R | 2 inst/doc/sf7.Rmd | 12 inst/doc/sf7.html | 2056 ++++++++++++++++++++++++++-------- inst/docker/gdal/Dockerfile | 67 - inst/nc/ones.zarr.zip |only inst/nc/zarr.py |only man/geos_unary.Rd | 31 man/st_line_project_point.Rd | 6 src/stars.cpp | 5 tests/aggregate.Rout.save | 10 tests/cast.Rout.save | 8 tests/crs.Rout.save | 8 tests/dist.Rout.save | 8 tests/dplyr.Rout.save | 8 tests/empty.Rout.save | 8 tests/full.Rout.save | 8 tests/gdal_geom.Rout.save | 8 tests/geos.Rout.save | 8 tests/graticule.Rout.save | 8 tests/grid.Rout.save | 8 tests/maps.Rout.save | 8 tests/plot.Rout.save | 8 tests/read.Rout.save | 8 tests/roundtrip.Rout.save | 8 tests/s2.Rout.save | 8 tests/sample.Rout.save | 8 tests/sfc.Rout.save | 10 tests/sfg.Rout.save | 8 tests/spatstat.Rout.save | 38 tests/stars.R | 9 tests/stars.Rout.save | 67 + tests/units.Rout.save | 8 tests/wkb.Rout.save | 8 vignettes/sf1.Rmd | 12 vignettes/sf2.Rmd | 12 vignettes/sf3.Rmd | 12 vignettes/sf4.Rmd | 12 vignettes/sf5.Rmd | 12 vignettes/sf6.Rmd | 12 vignettes/sf7.Rmd | 12 70 files changed, 12190 insertions(+), 3506 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine (version 3.51.0) and for various extensions is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 2.4.3 dated 2025-08-20 and 2.4.4 dated 2025-11-10
DESCRIPTION | 12 MD5 | 18 NEWS.md | 13 src/SqliteResultImpl.h | 4 src/vendor/extensions/regexp.c | 118 src/vendor/extensions/series.c | 529 ++- src/vendor/extensions/sqlite3ext.h | 7 src/vendor/sqlite3/sqlite3.c | 5519 ++++++++++++++++++++++++++++--------- src/vendor/sqlite3/sqlite3.h | 413 ++ tests/testthat/test-dbConnect.R | 7 10 files changed, 4968 insertions(+), 1672 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.8.1 dated 2025-10-16 and 0.8.2 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/gsea.R | 2 ++ 3 files changed, 7 insertions(+), 5 deletions(-)
Title: Arbitrary Dimensional Clifford Algebras
Description: A suite of routines for Clifford algebras, using the
'Map' class of the Standard Template Library. Canonical
reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra
to geometric calculus"). Special cases including Lorentz transforms,
quaternion multiplication, and Grassmann algebra, are discussed.
Vignettes presenting conformal geometric algebra, quaternions and
split quaternions, dual numbers, and Lorentz transforms are
included. The package follows 'disordR' discipline.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
This is a re-admission after prior archival of version 1.1-2 dated 2025-10-20
Diff between clifford versions 1.1-2 dated 2025-10-20 and 1.1-3 dated 2025-11-10
clifford-1.1-2/clifford/inst/clifford_arxiv.Rnw |only clifford-1.1-2/clifford/inst/doc/cramer_clifford.R |only clifford-1.1-2/clifford/inst/doc/cramer_clifford.Rmd |only clifford-1.1-2/clifford/inst/doc/cramer_clifford.html |only clifford-1.1-2/clifford/inst/doc/determinants_clifford.R |only clifford-1.1-2/clifford/inst/doc/determinants_clifford.Rmd |only clifford-1.1-2/clifford/inst/doc/determinants_clifford.html |only clifford-1.1-2/clifford/inst/doc/getcoeffs.R |only clifford-1.1-2/clifford/inst/doc/getcoeffs.Rmd |only clifford-1.1-2/clifford/inst/doc/getcoeffs.html |only clifford-1.1-2/clifford/inst/doc/lorentz_clifford.R |only clifford-1.1-2/clifford/inst/doc/lorentz_clifford.Rmd |only clifford-1.1-2/clifford/inst/doc/lorentz_clifford.html |only clifford-1.1-2/clifford/inst/doc/pauli_clifford.R |only clifford-1.1-2/clifford/inst/doc/pauli_clifford.Rmd |only clifford-1.1-2/clifford/inst/doc/pauli_clifford.html |only clifford-1.1-2/clifford/inst/doc/pseudoscalar.R |only clifford-1.1-2/clifford/inst/doc/pseudoscalar.Rmd |only clifford-1.1-2/clifford/inst/doc/pseudoscalar.html |only clifford-1.1-2/clifford/inst/doc/quaternion_clifford.R |only clifford-1.1-2/clifford/inst/doc/quaternion_clifford.Rmd |only clifford-1.1-2/clifford/inst/doc/quaternion_clifford.html |only clifford-1.1-2/clifford/inst/dot.Rmd |only clifford-1.1-2/clifford/inst/hankin_aaca_revision.tex |only clifford-1.1-2/clifford/inst/hankin_aaca_revision2.tex |only clifford-1.1-2/clifford/inst/hankin_aaca_revision3.tex |only clifford-1.1-2/clifford/inst/hankin_aca.Rnw |only clifford-1.1-2/clifford/inst/hitzer.Rmd |only clifford-1.1-2/clifford/inst/nectarines.Rmd |only clifford-1.1-2/clifford/inst/read.me |only clifford-1.1-2/clifford/inst/referee_comments.tex |only clifford-1.1-2/clifford/inst/referee_comments2.tex |only clifford-1.1-2/clifford/inst/spheres.R |only clifford-1.1-2/clifford/vignettes/cramer_clifford.Rmd |only clifford-1.1-2/clifford/vignettes/determinants_clifford.Rmd |only clifford-1.1-2/clifford/vignettes/getcoeffs.Rmd |only clifford-1.1-2/clifford/vignettes/lorentz_clifford.Rmd |only clifford-1.1-2/clifford/vignettes/pauli_clifford.Rmd |only clifford-1.1-2/clifford/vignettes/pseudoscalar.Rmd |only clifford-1.1-2/clifford/vignettes/quaternion_clifford.Rmd |only clifford-1.1-3/clifford/DESCRIPTION | 6 clifford-1.1-3/clifford/MD5 | 78 ++-------- clifford-1.1-3/clifford/README.md | 36 +++- clifford-1.1-3/clifford/build/partial.rdb |binary clifford-1.1-3/clifford/build/vignette.rds |binary clifford-1.1-3/clifford/data/dot.rda |binary clifford-1.1-3/clifford/inst/CITATION | 2 clifford-1.1-3/clifford/inst/doc/clifford.pdf |binary clifford-1.1-3/clifford/inst/doc/complex_clifford.Rmd | 2 clifford-1.1-3/clifford/inst/doc/complex_clifford.html | 6 clifford-1.1-3/clifford/inst/doc/conformal_algebra_clifford.html | 10 - clifford-1.1-3/clifford/inst/doc/signature.R | 22 +- clifford-1.1-3/clifford/inst/doc/signature.Rmd | 1 clifford-1.1-3/clifford/inst/doc/signature.html | 17 +- clifford-1.1-3/clifford/man/Ops.clifford.Rd | 2 clifford-1.1-3/clifford/man/antivector.Rd | 8 - clifford-1.1-3/clifford/man/print.Rd | 12 - clifford-1.1-3/clifford/vignettes/clifford.bib | 4 clifford-1.1-3/clifford/vignettes/complex_clifford.Rmd | 2 clifford-1.1-3/clifford/vignettes/signature.Rmd | 1 60 files changed, 100 insertions(+), 109 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-17 0.2.1
2023-01-17 0.2.0
2022-11-01 0.1.1
2022-07-20 0.1.0
Title: The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
Description: An implementation of the Uniform Manifold Approximation and
Projection dimensionality reduction by McInnes et al. (2018)
<doi:10.48550/arXiv.1802.03426>. It also provides means to transform new data and
to carry out supervised dimensionality reduction. An implementation of
the related LargeVis method of Tang et al. (2016) <doi:10.48550/arXiv.1602.00370>
is also provided. This is a complete re-implementation in R (and C++,
via the 'Rcpp' package): no Python installation is required. See the
uwot website (<https://github.com/jlmelville/uwot>) for more
documentation and examples.
Author: James Melville [aut, cre, cph],
Aaron Lun [ctb],
Mohamed Nadhir Djekidel [ctb],
Yuhan Hao [ctb],
Dirk Eddelbuettel [ctb],
Wouter van der Bijl [ctb],
Hugo Gruson [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between uwot versions 0.2.3 dated 2025-02-24 and 0.2.4 dated 2025-11-10
DESCRIPTION | 14 ++++++++------ MD5 | 16 ++++++++-------- NEWS.md | 21 +++++++++++++++++++++ R/init.R | 2 +- R/util.R | 6 +++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/uwot.html | 5 +++-- tests/testthat/test_output.R | 2 +- 9 files changed, 47 insertions(+), 19 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on copula graphical
models for accomplishing the three interrelated goals in genetics and genomics in an
unified way: (1) linkage map construction, (2) constructing linkage disequilibrium
networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-
phenotype-environment interactions networks.
The 'netgwas' package can deal with biparental inbreeding and outbreeding species with
any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes),
tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where
number of variables p is considerably larger than number of sample sizes (p >> n).
The computations is memory-optimized using the sparse matrix output. The 'netgwas'
implements the methodological developments in Behrouzi and Wit (2017)
<doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <doi:10.1093/bioinformatics/bty777>.
Author: Pariya Behrouzi [aut, cre] ,
Ernst C. Wit [ctb]
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between netgwas versions 1.14.3 dated 2024-03-19 and 1.14.4 dated 2025-11-10
DESCRIPTION | 9 +-- MD5 | 12 ++-- R/selectnet.R | 150 ++++++++++++++++++++++++++-------------------------- inst/CITATION | 5 - man/plot.select.Rd | 24 ++++---- man/print.select.Rd | 64 +++++++++++----------- man/selectnet.Rd | 16 ++--- 7 files changed, 139 insertions(+), 141 deletions(-)
Title: Depth Importance in Precision Medicine (DIPM) Method
Description: An implementation by Chen, Li, and Zhang (2022) <doi: 10.1093/bioadv/vbac041> of the Depth Importance in Precision Medicine (DIPM) method
in Chen and Zhang (2022) <doi:10.1093/biostatistics/kxaa021> and Chen and
Zhang (2020) <doi:10.1007/978-3-030-46161-4_16>. The DIPM method is a classification
tree that searches for subgroups with especially poor or strong performance in a given treatment group.
Author: Cai Li [aut, cre],
Victoria Chen [aut],
Heping Zhang [aut]
Maintainer: Cai Li <cai.li.stats@gmail.com>
Diff between dipm versions 1.11 dated 2025-06-15 and 1.12 dated 2025-11-10
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 3 ++- R/node_dipm.R | 13 +++++++------ 4 files changed, 18 insertions(+), 15 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre] ,
Hugh Benjamin Zachariae [aut],
Indrajeet Patil [ctb] ,
Daniel Luedecke [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 1.8.1 dated 2025-08-24 and 2.0.0 dated 2025-11-10
DESCRIPTION | 8 MD5 | 202 ++--- NEWS.md | 10 R/baseline.R | 13 R/baseline_binomial.R | 26 R/baseline_gaussian.R | 45 - R/baseline_multinomial.R | 29 R/baseline_wrappers.R | 13 R/call_validate.R | 12 R/choosing_metrics_functions.R | 6 R/combine_predictors.R | 21 R/combine_predictors_prepare_args.R | 16 R/computational_grid.R | 10 R/confusion_matrix.R | 91 +- R/cross_validate.R | 34 R/cross_validate_list.R | 42 - R/data_documentation.R | 22 R/evaluate.R | 195 ++--- R/evaluate_predictions_binomial.R | 25 R/evaluate_predictions_gaussian.R | 45 - R/evaluate_predictions_multinomial.R | 112 +-- R/evaluate_residuals.R | 6 R/extract_model_effects.R | 7 R/extract_probabilities_of.R | 22 R/extract_special_fn_specific_hparams.R | 2 R/fit_model.R | 1 R/fit_predict_model_fn.R | 46 - R/get_nested_model_coefficients.R | 120 +-- R/helpers.R | 168 ++-- R/internal_evaluate_model.R | 1 R/internal_evaluate_predictions.R | 51 - R/metrics.R | 8 R/model_functions.R | 10 R/most_challenging.R | 277 ++++--- R/multiclass_probability_tibble.R | 16 R/nesting_predictions.R | 11 R/plot_confusion_matrix.R | 359 +++++----- R/plot_metric_density.R | 80 +- R/plot_probabilities.R | 131 +-- R/plot_probabilities_ecdf.R | 80 +- R/plot_probability_violins.R | 2 R/plotting_utilities.R | 173 ++-- R/predict_functions.R | 1 R/prepare_evaluation.R | 22 R/prepare_train_test.R | 72 +- R/preprocess_functions.R | 19 R/process_info.R | 110 +-- R/reconstruct_formulas.R | 3 R/run_model_fitting.R | 36 - R/run_prediction_process.R | 35 R/run_quietly.R | 30 R/select_definitions.R | 15 R/select_metrics.R | 10 R/set_info_cols.R | 3 R/set_metrics.R | 25 R/simplify_formula.R | 30 R/softmax.R | 26 R/summarize_metrics.R | 27 R/table_of_content_markdown.R | 4 R/update_hyperparameters.R | 25 R/update_model_specifics.R | 5 R/validate.R | 33 R/validate_fold.R | 4 R/validate_list.R | 45 - build/stage23.rdb |binary inst/doc/Creating_a_confusion_matrix.html | 22 inst/doc/available_metrics.html | 4 inst/doc/cross_validating_custom_functions.html | 10 inst/doc/evaluate_by_id.html | 6 inst/doc/picking_the_number_of_folds_for_cross-validation.html | 8 man/baseline.Rd | 8 man/baseline_binomial.Rd | 2 man/baseline_gaussian.Rd | 2 man/baseline_multinomial.Rd | 4 man/cross_validate.Rd | 11 man/evaluate.Rd | 98 +- man/most_challenging.Rd | 12 man/plot_confusion_matrix.Rd | 42 - man/plot_metric_density.Rd | 12 man/plot_probabilities.Rd | 1 man/plot_probabilities_ecdf.Rd | 1 man/predicted.musicians.Rd | 20 man/preprocess_functions.Rd | 2 man/summarize_metrics.Rd | 8 man/update_hyperparameters.Rd | 3 man/validate.Rd | 9 tests/testthat/test_cross_validate.R | 169 ++++ tests/testthat/test_evaluate.R | 44 - tests/testthat/test_validate.R | 8 vignettes/man/figures/vignette_conf_mat-unnamed-chunk-12-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-13-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-15-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-16-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-16-2.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-17-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-18-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-5-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-6-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-9-1.png |binary vignettes/man/figures/vignette_cv_custom_fn-unnamed-chunk-35-1.png |binary vignettes/man/figures/vignette_pick_k-unnamed-chunk-3-1.png |binary vignettes/man/figures/vignette_pick_k-unnamed-chunk-5-1.png |binary 102 files changed, 1891 insertions(+), 1743 deletions(-)
Title: Brings Seurat to the Tidyverse
Description: It creates an invisible layer that allow to see the 'Seurat' object
as tibble and interact seamlessly with the tidyverse.
Author: Stefano Mangiola [aut, cre],
Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyseurat versions 0.8.4 dated 2025-10-02 and 0.8.7 dated 2025-11-09
DESCRIPTION | 8 +-- MD5 | 40 ++++++++--------- NAMESPACE | 3 - R/methods.R | 30 ++++--------- R/methods_DEPRECATED.R | 6 +- README.md | 26 +++++------ build/stage23.rdb |binary inst/NEWS.rd | 6 ++ inst/doc/figures_article.html | 2 inst/doc/introduction.R | 2 inst/doc/introduction.html | 83 ++++++++++++++++++------------------- man/figures/pc_plot-1.png |binary man/figures/plot1-1.png |binary man/figures/plot2-1.png |binary man/figures/unnamed-chunk-15-1.png |binary man/fragments/intro.Rmd | 4 - man/join_features.Rd | 2 man/join_transcripts.Rd | 2 man/plotly.Rd | 2 man/tidy.Rd | 19 +++----- tests/testthat/test-methods.R | 8 +++ 21 files changed, 121 insertions(+), 122 deletions(-)
Title: Robust Sufficient Dimension Reduction
Description: A novel sufficient-dimension reduction method is robust against outliers using alpha-distance covariance and manifold-learning in dimensionality reduction problems. Please refer Hsin-Hsiung Huang, Feng Yu & Teng Zhang (2024) <doi:10.1080/10485252.2024.2313137> for the details.
Author: Sheau-Chiann Chen [aut, cre] ,
Shilin Zhao [aut],
Hsin-Hsiung Bill Huang [aut]
Maintainer: Sheau-Chiann Chen <sheau-chiann.chen.1@vumc.org>
Diff between rSDR versions 1.0.2.1 dated 2025-10-28 and 1.0.3.0 dated 2025-11-09
DESCRIPTION | 14 +- MD5 | 22 ++-- R/cost_fun_esting.R | 20 ++-- R/optimal_alpha_boot.R | 5 - R/optimal_alpha_cv.R | 2 R/rSDR.R | 38 +++++--- inst/doc/rSDR_vignette.R | 28 ++--- inst/doc/rSDR_vignette.Rmd | 37 +++---- inst/doc/rSDR_vignette.html | 208 +++++++++++++++++++++----------------------- man/optimal_alpha_boot.Rd | 3 man/optimal_alpha_cv.Rd | 2 vignettes/rSDR_vignette.Rmd | 37 +++---- 12 files changed, 211 insertions(+), 205 deletions(-)
Title: Network Representations of Attitudes
Description: A tool for computing network representations of attitudes,
extracted from tabular data such as sociological surveys. Development of
surveygraph software and training materials was initially funded by the
European Union under the ERC Proof-of-concept programme (ERC,
Attitude-Maps-4-All, project number: 101069264). Views and opinions expressed
are however those of the author(s) only and do not necessarily reflect those
of the European Union or the European Research Council Executive Agency.
Neither the European Union nor the granting authority can be held responsible
for them.
Author: Samuel Unicomb [aut, cre],
Ana Jovancevic [aut],
Caoimhe O'Reilly [aut],
Alejandro Dinkelberg [aut],
Padraig MacCarron [aut],
David O'Sullivan [aut],
Paul Maher [aut],
Mike Quayle [aut]
Maintainer: Samuel Unicomb <samuelunicomb@gmail.com>
Diff between surveygraph versions 0.1.2 dated 2024-06-04 and 1.0.0 dated 2025-11-09
surveygraph-0.1.2/surveygraph/R/projection.R |only surveygraph-0.1.2/surveygraph/R/synthetic-data.R |only surveygraph-0.1.2/surveygraph/R/threshold-profile.R |only surveygraph-0.1.2/surveygraph/src/build_graphs.cc |only surveygraph-0.1.2/surveygraph/src/components.cc |only surveygraph-0.1.2/surveygraph/src/graph.h |only surveygraph-0.1.2/surveygraph/src/make_projection.cc |only surveygraph-0.1.2/surveygraph/src/make_projection_agent_pilot.cc |only surveygraph-0.1.2/surveygraph/src/make_projection_symbolic_pilot.cc |only surveygraph-0.1.2/surveygraph/src/make_threshold_profile.cc |only surveygraph-0.1.2/surveygraph/tests/README.md |only surveygraph-0.1.2/surveygraph/tests/testthat/test-projection.R |only surveygraph-0.1.2/surveygraph/tests/testthat/test-synthetic-data.R |only surveygraph-1.0.0/surveygraph/DESCRIPTION | 18 - surveygraph-1.0.0/surveygraph/MD5 | 54 +-- surveygraph-1.0.0/surveygraph/NAMESPACE | 5 surveygraph-1.0.0/surveygraph/NEWS.md | 4 surveygraph-1.0.0/surveygraph/R/data-preprocess.R |only surveygraph-1.0.0/surveygraph/R/make-projection.R |only surveygraph-1.0.0/surveygraph/R/make-synthetic-data.R |only surveygraph-1.0.0/surveygraph/R/make-threshold-profile.R |only surveygraph-1.0.0/surveygraph/R/surveygraph.R | 6 surveygraph-1.0.0/surveygraph/README.md | 33 + surveygraph-1.0.0/surveygraph/build |only surveygraph-1.0.0/surveygraph/inst/doc |only surveygraph-1.0.0/surveygraph/man/data_preprocess.Rd |only surveygraph-1.0.0/surveygraph/man/make_projection.Rd | 77 +++- surveygraph-1.0.0/surveygraph/man/make_synthetic_data.Rd | 20 - surveygraph-1.0.0/surveygraph/man/make_threshold_profile.Rd | 25 + surveygraph-1.0.0/surveygraph/man/surveygraph.Rd | 32 + surveygraph-1.0.0/surveygraph/src/edge.h |only surveygraph-1.0.0/surveygraph/src/init.cc | 70 +--- surveygraph-1.0.0/surveygraph/src/make_projection_pilot.cc |only surveygraph-1.0.0/surveygraph/src/make_threshold_profile_pilot.cc | 175 ++++++---- surveygraph-1.0.0/surveygraph/src/surveygraph.h | 110 +++--- surveygraph-1.0.0/surveygraph/src/surveygraph_edgelist.cc |only surveygraph-1.0.0/surveygraph/src/surveygraph_make_projection.cc |only surveygraph-1.0.0/surveygraph/src/surveygraph_make_threshold_profile.cc |only surveygraph-1.0.0/surveygraph/src/unionfind.h |only surveygraph-1.0.0/surveygraph/tests/testthat/test_make_projection_comparisons.R |only surveygraph-1.0.0/surveygraph/vignettes |only 41 files changed, 400 insertions(+), 229 deletions(-)
Title: Analysis and Manipulation of Data from Minecraft Bedrock Edition
Description: Implements an interface to Minecraft (Bedrock Edition) worlds. Supports the analysis and management of these worlds and game saves.
Author: Reed Cartwright [aut, cre] ,
Rich FitzJohn [ctb],
Christian Stigen Larsen [ctb],
The LevelDB Authors [cph]
Maintainer: Reed Cartwright <racartwright@gmail.com>
Diff between rbedrock versions 0.4.1 dated 2025-08-24 and 0.4.2 dated 2025-11-09
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/finalized_state.R | 2 +- R/legacy-checksums.R | 2 +- data/biome_df.rda |binary data/vanilla_block_list.rda |binary data/vanilla_block_property_type_list.rda |binary data/vanilla_block_states_df.rda |binary man/FinalizedState.Rd | 2 +- tests/testthat/test_legacy-checksums.R | 2 +- 11 files changed, 23 insertions(+), 17 deletions(-)
Title: Plot and Analyse Time-Intensity Data
Description: Plots and analyzes time-intensity curve data, such as data from
(contrast-enhanced) ultrasound. Values such as peak intensity, time to
peak, area under the curve, wash in rate and wash out rate are calculated.
Author: Samuel James Tingle [aut, cre]
Maintainer: Samuel James Tingle <samjamestingle@gmail.com>
Diff between tican versions 1.0.3 dated 2025-05-26 and 1.1.0 dated 2025-11-09
DESCRIPTION | 10 +- MD5 | 32 ++++---- NAMESPACE | 3 NEWS.md | 4 + R/tic_analyse.R | 102 ++++++++++++++++----------- R/tic_auc.R | 22 ----- R/tic_wir.R |only R/tic_wor.R |only R/ttpeak.R | 24 ------ build/vignette.rds |binary inst/doc/tican-vignette.R | 76 ++++++++++++++++---- inst/doc/tican-vignette.Rmd | 105 +++++++++++++++++++++++---- inst/doc/tican-vignette.html | 162 ++++++++++++++++++++++++------------------- man/tic_analyse.Rd | 35 +++------ man/tic_auc.Rd | 21 ----- man/tic_wir.Rd |only man/tic_wor.Rd |only man/ttpeak.Rd | 23 ------ vignettes/tican-vignette.Rmd | 105 +++++++++++++++++++++++---- 19 files changed, 443 insertions(+), 281 deletions(-)
Title: Quantum Computing for Analyzing CD4 Lymphocytes and
Antiretroviral Therapy
Description: Resources, tutorials, and code snippets dedicated to exploring the intersection of quantum computing and artificial intelligence (AI) in the context of analyzing Cluster of Differentiation 4 (CD4) lymphocytes and optimizing antiretroviral therapy (ART) for human immunodeficiency virus (HIV). With the emergence of quantum artificial intelligence and the development of small-scale quantum computers, there's an unprecedented opportunity to revolutionize the understanding of HIV dynamics and treatment strategies. This project leverages the R package 'qsimulatR' (Ostmeyer and Urbach, 2023, <https://CRAN.R-project.org/package=qsimulatR>), a quantum computer simulator, to explore these applications in quantum computing techniques, addressing the challenges in studying CD4 lymphocytes and enhancing ART efficacy.
Author: Juan Pablo Acuna Gonzalez [aut, cre, cph]
Maintainer: Juan Pablo Acuna Gonzalez <22253567@uagro.mx>
Diff between qvirus versions 0.0.4 dated 2025-05-20 and 0.0.5 dated 2025-11-09
DESCRIPTION | 12 MD5 | 74 +-- NAMESPACE | 38 - NEWS.md | 54 ++ R/InteractionClassification.R | 90 ++-- R/cd_diff.R | 70 +-- R/cds_diff.R | 70 +-- R/data.R | 328 ++++++++-------- R/estimate_payoffs.R | 84 ++-- R/mse.InteractionClassification.R | 126 +++--- R/mse.payoffs.R | 116 ++--- R/nearest_payoff.R | 64 +-- R/payoffs_list.R | 112 ++--- R/phen_hiv.R | 132 +++--- R/run_bb84_simulation.R |only R/run_e91_simulation.R |only R/summary.InteractionClassification.R | 116 ++--- R/summary.payoffs.R | 94 ++-- R/vl_diff.R | 72 +-- R/vlog_diff.R | 76 +-- R/vlogs_diff.R | 82 ++-- README.md | 44 +- build/partial.rdb |binary man/run_bb84_simulation.Rd |only man/run_e91_simulation.Rd |only tests/testthat/test-InteractionClassification.R | 24 - tests/testthat/test-cd_diff.R | 14 tests/testthat/test-cds_diff.R | 12 tests/testthat/test-estimate_payoffs.R | 26 - tests/testthat/test-mse.InteractionClassification.R | 24 - tests/testthat/test-mse.payoffs.R | 26 - tests/testthat/test-nearest_payoff.R | 18 tests/testthat/test-payoffs_list.R | 18 tests/testthat/test-phen_hiv.R | 22 - tests/testthat/test-run_bb84_simulation.R |only tests/testthat/test-run_e91_simulation.R |only tests/testthat/test-summary.InteractionClassification.R | 24 - tests/testthat/test-summary.payoffs.R | 28 - tests/testthat/test-vl_diff.R | 16 tests/testthat/test-vlog_diff.R | 14 tests/testthat/test-vlogs_diff.R | 12 41 files changed, 1086 insertions(+), 1046 deletions(-)
Title: Structure Learning with Copula Graphical Model
Description: Statistical tool for learning the structure of direct associations among variables for
continuous data, discrete data and mixed discrete-continuous data. The package is based
on the copula graphical model in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287>.
Author: Pariya Behrouzi [aut, cre]
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between nutriNetwork versions 0.1.2 dated 2023-07-05 and 0.2.0 dated 2025-11-09
DESCRIPTION | 17 +++-- MD5 | 9 +-- R/selectnet.R | 156 ++++++++++++++++++++++++++--------------------------- inst |only man/plot.select.Rd | 21 +++---- man/selectnet.Rd | 32 +++++----- 6 files changed, 120 insertions(+), 115 deletions(-)
Title: Sampling from the von Mises-Fisher Distribution
Description: Provides fast sampling from von Mises-Fisher distribution using the method proposed by Andrew T.A Wood (1994) <doi:10.1080/03610919408813161>.
Author: Aristide Houndetoungan [cre, aut]
Maintainer: Aristide Houndetoungan <ahoundetoungan@ecn.ulaval.ca>
Diff between vMF versions 0.0.3 dated 2024-03-09 and 0.0.4 dated 2025-11-09
vMF-0.0.3/vMF/README.md |only vMF-0.0.4/vMF/DESCRIPTION | 16 ++++++------ vMF-0.0.4/vMF/MD5 | 20 +++++++-------- vMF-0.0.4/vMF/build/partial.rdb |binary vMF-0.0.4/vMF/build/vignette.rds |binary vMF-0.0.4/vMF/inst/doc/vMF.R | 52 +++++++++++++++++++-------------------- vMF-0.0.4/vMF/inst/doc/vMF.Rmd | 12 ++++----- vMF-0.0.4/vMF/inst/doc/vMF.pdf |binary vMF-0.0.4/vMF/man/vMF-package.Rd |only vMF-0.0.4/vMF/src/Makevars | 13 --------- vMF-0.0.4/vMF/src/Makevars.win | 9 ------ vMF-0.0.4/vMF/vignettes/vMF.Rmd | 12 ++++----- 12 files changed, 58 insertions(+), 76 deletions(-)
Title: Test Coverage for Packages
Description: Track and report code coverage for your package and (optionally)
upload the results to a coverage service like 'Codecov' <https://about.codecov.io> or
'Coveralls' <https://coveralls.io>. Code coverage is a measure of the amount of
code being exercised by a set of tests. It is an indirect measure of test
quality and completeness. This package is compatible with any testing
methodology or framework and tracks coverage of both R code and compiled
C/C++/FORTRAN code.
Author: Jim Hester [aut, cre],
Willem Ligtenberg [ctb],
Kirill Mueller [ctb],
Henrik Bengtsson [ctb],
Steve Peak [ctb],
Kirill Sevastyanenko [ctb],
Jon Clayden [ctb],
Robert Flight [ctb],
Eric Brown [ctb],
Brodie Gaslam [ctb],
Will Beasley [ctb],
Robert Krzyz [...truncated...]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between covr versions 3.6.4 dated 2023-11-09 and 3.6.5 dated 2025-11-09
covr-3.6.4/covr/tests/testthat/test-tally_coverage.R |only covr-3.6.5/covr/DESCRIPTION | 18 covr-3.6.5/covr/MD5 | 159 +- covr-3.6.5/covr/NAMESPACE | 6 covr-3.6.5/covr/NEWS.md | 31 covr-3.6.5/covr/R/R6.R | 26 covr-3.6.5/covr/R/S7.R |only covr-3.6.5/covr/R/box.R |only covr-3.6.5/covr/R/cobertura.R | 6 covr-3.6.5/covr/R/codecov.R | 14 covr-3.6.5/covr/R/compiled.R | 47 covr-3.6.5/covr/R/coveralls.R | 6 covr-3.6.5/covr/R/covr.R | 71 - covr-3.6.5/covr/R/exclusions.R | 10 covr-3.6.5/covr/R/gitlab.R | 2 covr-3.6.5/covr/R/icc.R | 2 covr-3.6.5/covr/R/parse_data.R | 20 covr-3.6.5/covr/R/replace.R | 4 covr-3.6.5/covr/R/summary_functions.R | 30 covr-3.6.5/covr/R/trace_calls.R | 24 covr-3.6.5/covr/R/trace_tests.R | 146 +- covr-3.6.5/covr/R/utils.R | 11 covr-3.6.5/covr/README.md | 2 covr-3.6.5/covr/build/vignette.rds |binary covr-3.6.5/covr/inst/doc/how_it_works.R | 2 covr-3.6.5/covr/inst/doc/how_it_works.Rmd | 3 covr-3.6.5/covr/inst/doc/how_it_works.html | 25 covr-3.6.5/covr/man/covr.record_tests.Rd | 27 covr-3.6.5/covr/man/current_test_call_count.Rd |only covr-3.6.5/covr/man/current_test_index.Rd |only covr-3.6.5/covr/man/current_test_key.Rd |only covr-3.6.5/covr/man/gitlab.Rd | 2 covr-3.6.5/covr/src/reassign.c | 132 +- covr-3.6.5/covr/tests/testthat.R | 20 covr-3.6.5/covr/tests/testthat/Test+Char/TestCompiled/src/simple.cc | 2 covr-3.6.5/covr/tests/testthat/Test+Char/TestCompiled/tests/testthat/test-TestCompiled.R | 1 covr-3.6.5/covr/tests/testthat/TestCompiled/src/simple-header.h | 2 covr-3.6.5/covr/tests/testthat/TestCompiled/src/simple.cc | 2 covr-3.6.5/covr/tests/testthat/TestCompiled/tests/testthat/test-TestCompiled.R | 1 covr-3.6.5/covr/tests/testthat/TestCompiledSubdir/src/lib/simple.c | 2 covr-3.6.5/covr/tests/testthat/TestS7 |only covr-3.6.5/covr/tests/testthat/Testbox |only covr-3.6.5/covr/tests/testthat/Testbox_R6 |only covr-3.6.5/covr/tests/testthat/Testbox_attached_modules_functions |only covr-3.6.5/covr/tests/testthat/Testbox_attached_modules_functions_R6 |only covr-3.6.5/covr/tests/testthat/_snaps |only covr-3.6.5/covr/tests/testthat/test-Compiled.R | 30 covr-3.6.5/covr/tests/testthat/test-R6.R | 2 covr-3.6.5/covr/tests/testthat/test-RC.R | 1 covr-3.6.5/covr/tests/testthat/test-S4.R | 1 covr-3.6.5/covr/tests/testthat/test-S7.R |only covr-3.6.5/covr/tests/testthat/test-box-R6.R |only covr-3.6.5/covr/tests/testthat/test-box.R |only covr-3.6.5/covr/tests/testthat/test-box_attached_modules_functions-R6.R |only covr-3.6.5/covr/tests/testthat/test-box_attached_modules_functions.R |only covr-3.6.5/covr/tests/testthat/test-braceless.R | 2 covr-3.6.5/covr/tests/testthat/test-cobertura.R | 2 covr-3.6.5/covr/tests/testthat/test-codecov.R | 649 ++++------ covr-3.6.5/covr/tests/testthat/test-corner-cases.R | 2 covr-3.6.5/covr/tests/testthat/test-coveralls.R | 182 +- covr-3.6.5/covr/tests/testthat/test-covr.R | 3 covr-3.6.5/covr/tests/testthat/test-exclusions.R | 4 covr-3.6.5/covr/tests/testthat/test-file_coverage.R | 1 covr-3.6.5/covr/tests/testthat/test-functions.R | 1 covr-3.6.5/covr/tests/testthat/test-gcov.R | 105 - covr-3.6.5/covr/tests/testthat/test-gitlab.R | 2 covr-3.6.5/covr/tests/testthat/test-memoised.R | 1 covr-3.6.5/covr/tests/testthat/test-null.R | 2 covr-3.6.5/covr/tests/testthat/test-package_coverage.R | 1 covr-3.6.5/covr/tests/testthat/test-parallel.R | 5 covr-3.6.5/covr/tests/testthat/test-print.R | 18 covr-3.6.5/covr/tests/testthat/test-record_tests.R | 24 covr-3.6.5/covr/tests/testthat/test-report.R | 4 covr-3.6.5/covr/tests/testthat/test-sonarqube.R | 2 covr-3.6.5/covr/tests/testthat/test-summary.R | 4 covr-3.6.5/covr/tests/testthat/test-trace_calls.R | 1 covr-3.6.5/covr/tests/testthat/test-utils.R | 66 - covr-3.6.5/covr/tests/testthat/test-vectorized.R | 1 covr-3.6.5/covr/vignettes/how_it_works.Rmd | 3 79 files changed, 1163 insertions(+), 812 deletions(-)
Title: Econometrics of Network Data
Description: Simulating and estimating peer effect models and network formation models. The class of peer effect models includes linear-in-means models (Lee, 2004; <doi:10.1111/j.1468-0262.2004.00558.x>), Tobit models (Xu and Lee, 2015; <doi:10.1016/j.jeconom.2015.05.004>), and discrete numerical data models (Houndetoungan, 2025; <doi:10.48550/arXiv.2405.17290>). The network formation models include pair-wise regressions with degree heterogeneity (Graham, 2017; <doi:10.3982/ECTA12679>) and exponential random graph models (Mele, 2017; <doi:10.3982/ECTA10400>).
Author: Aristide Houndetoungan [cre, aut]
Maintainer: Aristide Houndetoungan <ahoundetoungan@ecn.ulaval.ca>
Diff between CDatanet versions 2.2.1 dated 2025-01-07 and 2.2.2 dated 2025-11-09
DESCRIPTION | 18 MD5 | 40 + NAMESPACE | 9 NEWS.md | 14 R/CDatanet.R | 2 R/RcppExports.R | 52 ++ R/auxfunc.R | 1 R/cdnet.R | 214 +++++----- R/homophily.fe.R | 58 ++ R/homophily.re.R | 15 R/meffects.R |only R/sart.R | 144 +++---- build/partial.rdb |binary man/CDatanet-package.Rd | 4 man/meffects.Rd |only man/simcdnet.Rd | 6 man/simsart.Rd | 16 src/RcppExports.cpp | 261 +++++++++++- src/cdnet.cpp | 987 ++++++++++++++++++++++++++++++++---------------- src/homophily.cpp | 2 src/sartcomplet.cpp | 82 +-- src/sartincomplet.cpp | 421 +++++++++++++++----- 22 files changed, 1638 insertions(+), 708 deletions(-)
Title: Accounting Analysis
Description: Provides methods for processing corporate balance sheets with a focus on the Brazilian reporting format. Includes data standardization, classification by accounting categories, and aggregation of values. Supports accounting and financial analyses of companies, improving efficiency and ensuring reproducibility of empirical studies.
Author: Lissandro Costa de Sousa [cre, aut],
Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Costa de Sousa <lisandrosousa54@gmail.com>
Diff between adcontabil versions 1.1.0 dated 2025-11-08 and 1.1.8 dated 2025-11-09
DESCRIPTION | 6 +- MD5 | 12 ++-- R/AV_AH.R | 136 ++++++++++++++++++++++++++++++------------------- R/indicadores.R | 31 +++++++++++ R/padronizar_balanco.R | 8 +- man/calcular_AV_AH.Rd | 38 ++++++------- man/indicadores.Rd | 32 +++++++++++ 7 files changed, 178 insertions(+), 85 deletions(-)
Title: Broadcasted Array Operations Like 'NumPy'
Description: Implements efficient 'NumPy'-like broadcasted operations for atomic and recursive arrays.
In the context of operations involving 2 (or more) arrays,
“broadcasting” refers to efficiently recycling array dimensions,
without making copies.
Besides linking to 'Rcpp',
'broadcast' does not use any external libraries in any way;
'broadcast' was essentially made from scratch and can be installed out-of-the-box.
The implementations available in 'broadcast' include, but are not limited to, the following.
1) Broadcasted element-wise operations on any 2 arrays;
they support a large set of
relational, arithmetic, Boolean, string, and bit-wise operations.
2) A faster, more memory efficient, and broadcasted abind-like function,
for binding arrays along an arbitrary dimension.
3) Broadcasted ifelse-like, and apply-like functions.
4) Casting functions,
that cast subset-groups of an array to a new dimension, cast nested lists to dimensional lists, and vice-versa.
5) A few linear algebra functions for st [...truncated...]
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>
Diff between broadcast versions 0.1.5.3 dated 2025-10-10 and 0.1.6.1 dated 2025-11-09
broadcast-0.1.5.3/broadcast/R/internal_cast.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/acast/test-acast-bycolumn.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/acast/test-acast-bylayer.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/acast/test-acast-byrow.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/class/test-class.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/internal/test-orthogonal.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/test-bc_dim.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/test-ndim.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/test-rep_dim.R |only broadcast-0.1.5.3/broadcast/src/C_bindhelper_vdims.c |only broadcast-0.1.5.3/broadcast/src/C_dims_all_equal.c |only broadcast-0.1.5.3/broadcast/src/C_dims_all_orthogonal.c |only broadcast-0.1.5.3/broadcast/src/rcpp_bcDist_dec.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_bcDist_str.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_bcFact_int.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_normalize_dims.cpp |only broadcast-0.1.6.1/broadcast/DESCRIPTION | 9 broadcast-0.1.6.1/broadcast/MD5 | 297 +- broadcast-0.1.6.1/broadcast/NAMESPACE | 10 broadcast-0.1.6.1/broadcast/NEWS.md | 20 broadcast-0.1.6.1/broadcast/R/RcppExports.R | 220 +- broadcast-0.1.6.1/broadcast/R/aaa00_broadcast_help.R | 7 broadcast-0.1.6.1/broadcast/R/aaa02_broadcast_casting.R | 10 broadcast-0.1.6.1/broadcast/R/aaa03_broadcast_bind.R | 20 broadcast-0.1.6.1/broadcast/R/aaa04_broadcast_linearalgebra.R | 2 broadcast-0.1.6.1/broadcast/R/acast.R | 45 broadcast-0.1.6.1/broadcast/R/bc_b.R | 16 broadcast-0.1.6.1/broadcast/R/bc_bit.R | 16 broadcast-0.1.6.1/broadcast/R/bc_cplx.R | 16 broadcast-0.1.6.1/broadcast/R/bc_d.R | 49 broadcast-0.1.6.1/broadcast/R/bc_i.R | 40 broadcast-0.1.6.1/broadcast/R/bc_ifelse.R | 16 broadcast-0.1.6.1/broadcast/R/bc_list.R | 15 broadcast-0.1.6.1/broadcast/R/bc_raw.R | 8 broadcast-0.1.6.1/broadcast/R/bc_str.R | 30 broadcast-0.1.6.1/broadcast/R/bc_strrep.R |only broadcast-0.1.6.1/broadcast/R/bcapply.R | 12 broadcast-0.1.6.1/broadcast/R/bind_array.R | 18 broadcast-0.1.6.1/broadcast/R/broadcastWrappers.R | 55 broadcast-0.1.6.1/broadcast/R/broadcaster.R | 85 broadcast-0.1.6.1/broadcast/R/cast_dim2hier.R | 6 broadcast-0.1.6.1/broadcast/R/cast_hier2dim.R | 30 broadcast-0.1.6.1/broadcast/R/cast_shallow2atomic.R |only broadcast-0.1.6.1/broadcast/R/dropnests.R | 2 broadcast-0.1.6.1/broadcast/R/hier2dim.R | 110 - broadcast-0.1.6.1/broadcast/R/internal_acast.R |only broadcast-0.1.6.1/broadcast/R/internal_acast_names.R |only broadcast-0.1.6.1/broadcast/R/internal_binary.R | 104 - broadcast-0.1.6.1/broadcast/R/internal_binary_names.R | 18 broadcast-0.1.6.1/broadcast/R/internal_bind.R | 123 - broadcast-0.1.6.1/broadcast/R/internal_bind_names.R | 4 broadcast-0.1.6.1/broadcast/R/internal_functions.R | 8 broadcast-0.1.6.1/broadcast/R/internal_hiercast.R |only broadcast-0.1.6.1/broadcast/R/internal_opfuns.R | 2 broadcast-0.1.6.1/broadcast/R/internal_typefuns.R | 38 broadcast-0.1.6.1/broadcast/R/linear_algebra_stats.R | 3 broadcast-0.1.6.1/broadcast/R/meta_functions.R | 142 + broadcast-0.1.6.1/broadcast/R/ndim.R | 2 broadcast-0.1.6.1/broadcast/R/overload_ops_math.R | 6 broadcast-0.1.6.1/broadcast/R/overload_relops.R | 8 broadcast-0.1.6.1/broadcast/R/vector2array.R |only broadcast-0.1.6.1/broadcast/inst/examples/bc_strrep.R |only broadcast-0.1.6.1/broadcast/inst/examples/bind_array.R | 8 broadcast-0.1.6.1/broadcast/inst/examples/broadcaster.R | 32 broadcast-0.1.6.1/broadcast/inst/examples/cast_shallow2atomic.R |only broadcast-0.1.6.1/broadcast/inst/examples/vector2array.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/source.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-backtransform.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-bycolumn_named.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-bylayer_named.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-byrow_namedR.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-crashtest.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-edgecases.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-errors.R | 62 broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-simple.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_b/test-bc_b.R | 1026 +--------- broadcast-0.1.6.1/broadcast/inst/tinytest/bc_cplx/test-bc_cplx_math.R | 352 --- broadcast-0.1.6.1/broadcast/inst/tinytest/bc_general/test-bc_strrep.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_general/test-binaryerrors.R | 2 broadcast-0.1.6.1/broadcast/inst/tinytest/bc_list/test-bc_list.R | 2 broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-bc_d_math.R | 662 ------ broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-bc_i_math.R | 791 ------- broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-bc_i_rel.R | 600 ----- broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/source.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-1d.R | 38 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-array.R | 32 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-between.R | 32 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-ortho.R | 39 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-vector.R | 37 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-zerolen.R | 37 broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array-broadcaster.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array-errors.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array_internal.R | 30 broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-partialdimnames.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_3_row/test-rbind_bc.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-cast_hier2dim-nonames.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-cast_hier2dim.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-cast_hier2dim_names.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-hiernames2dimnames-errors.R | 4 broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-hiernames2dimnames-nonames.R | 24 broadcast-0.1.6.1/broadcast/inst/tinytest/class/test-broadcaster_set.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/class/test-mbroadcasters.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/count/count_tests.R | 6 broadcast-0.1.6.1/broadcast/inst/tinytest/helper |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-conformable.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-dimmode.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-dimnames_fit.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-mini.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/overload/test-math_cplx.R | 362 --- broadcast-0.1.6.1/broadcast/inst/tinytest/overload/test-math_cplx_by_other.R | 600 ----- broadcast-0.1.6.1/broadcast/inst/tinytest/overload/test-math_d.R | 535 ----- broadcast-0.1.6.1/broadcast/inst/tinytest/shallow2atomic |only broadcast-0.1.6.1/broadcast/inst/tinytest/source.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/test-S4error-callerenv.R | 3 broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary1d.R | 27 broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_attr_broadcaster.R | 28 broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_errors.R | 109 - broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_zerolen.R | 24 broadcast-0.1.6.1/broadcast/inst/tinytest/test-ellipsis.R | 17 broadcast-0.1.6.1/broadcast/man/aaa00_broadcast_help.Rd | 9 broadcast-0.1.6.1/broadcast/man/aaa01_broadcast_operators.Rd | 32 broadcast-0.1.6.1/broadcast/man/aaa02_broadcast_casting.Rd | 10 broadcast-0.1.6.1/broadcast/man/acast.Rd | 31 broadcast-0.1.6.1/broadcast/man/bc_ifelse.Rd | 4 broadcast-0.1.6.1/broadcast/man/bc_strrep.Rd |only broadcast-0.1.6.1/broadcast/man/bcapply.Rd | 2 broadcast-0.1.6.1/broadcast/man/bind_array.Rd | 27 broadcast-0.1.6.1/broadcast/man/broadcaster.Rd | 69 broadcast-0.1.6.1/broadcast/man/cast_dim2hier.Rd | 2 broadcast-0.1.6.1/broadcast/man/cast_hier2dim.Rd | 8 broadcast-0.1.6.1/broadcast/man/cast_shallow2atomic.Rd |only broadcast-0.1.6.1/broadcast/man/hier2dim.Rd | 5 broadcast-0.1.6.1/broadcast/man/linear_algebra_stats.Rd | 2 broadcast-0.1.6.1/broadcast/man/ndim.Rd | 2 broadcast-0.1.6.1/broadcast/man/vector2array.Rd |only broadcast-0.1.6.1/broadcast/src/C_any_nonarray.c |only broadcast-0.1.6.1/broadcast/src/C_arraysize_overflow.c |only broadcast-0.1.6.1/broadcast/src/C_bindhelper_get_alongdims.c |only broadcast-0.1.6.1/broadcast/src/C_bindhelper_need_coerce.c |only broadcast-0.1.6.1/broadcast/src/C_check_conf_dim.c | 51 broadcast-0.1.6.1/broadcast/src/C_determine_dimmode.c |only broadcast-0.1.6.1/broadcast/src/C_dims_allge.c |only broadcast-0.1.6.1/broadcast/src/C_make_dcp.c | 9 broadcast-0.1.6.1/broadcast/src/C_sd_lc.c | 34 broadcast-0.1.6.1/broadcast/src/C_unlisthelper_maxlen.c |only broadcast-0.1.6.1/broadcast/src/RcppExports.cpp | 687 +++++- broadcast-0.1.6.1/broadcast/src/broadcast.h | 808 +++---- broadcast-0.1.6.1/broadcast/src/rcpp_bcD_dec.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcD_int.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcD_str.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_b.cpp | 43 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_bit.cpp | 48 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_cplx.cpp | 34 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_dec.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_int.cpp | 31 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_raw.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_str.cpp | 34 broadcast-0.1.6.1/broadcast/src/rcpp_bc_b.cpp | 184 + broadcast-0.1.6.1/broadcast/src/rcpp_bc_bind.cpp | 62 broadcast-0.1.6.1/broadcast/src/rcpp_bc_bit.cpp | 48 broadcast-0.1.6.1/broadcast/src/rcpp_bc_cplx.cpp | 44 broadcast-0.1.6.1/broadcast/src/rcpp_bc_dec.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bc_ifelse.cpp | 38 broadcast-0.1.6.1/broadcast/src/rcpp_bc_int.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bc_list.cpp | 29 broadcast-0.1.6.1/broadcast/src/rcpp_bc_raw.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bc_str.cpp | 32 broadcast-0.1.6.1/broadcast/src/rcpp_bc_strrep.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcapply.cpp | 21 broadcast-0.1.6.1/broadcast/src/rcpp_bindhelpers.cpp | 81 broadcast-0.1.6.1/broadcast/src/rcpp_cast_shallow2atomic.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_set_attr.cpp | 44 broadcast-0.1.6.1/broadcast/tests/tinytest.R | 12 173 files changed, 3769 insertions(+), 6105 deletions(-)
Title: Assessing Normality of Stationary Process
Description: Despite that several tests for normality in stationary processes have been proposed in the literature, consistent implementations of these tests in programming languages are limited. Seven normality test are implemented. The asymptotic Lobato & Velasco's, asymptotic Epps, Psaradakis and Vávra, Lobato & Velasco's and Epps sieve bootstrap approximations, El bouch et al., and the random projections tests for univariate stationary process. Some other diagnostics such as, unit root test for stationarity, seasonal tests for seasonality, and arch effect test for volatility; are also performed. Additionally, the El bouch test performs normality tests for bivariate time series. The package also offers residual diagnostic for linear time series models developed in several packages.
Author: Asael Alonzo Matamoros [aut, cre],
Alicia Nieto-Reyes [aut],
Rob Hyndman [ctb],
Mitchell O'Hara-Wild [ctb],
Trapletti A. [ctb]
Maintainer: Asael Alonzo Matamoros <asael.alonzo@gmail.com>
Diff between nortsTest versions 1.1.2 dated 2024-01-25 and 1.1.3 dated 2025-11-09
DESCRIPTION | 10 ++--- MD5 | 17 +++++---- NEWS.md | 15 ++++++++ R/autoplot.R | 4 +- R/epps_test.R | 21 +++++++++--- R/nortsTest-package.R | 60 +++++++++++++++------------------- README.md | 2 - man/autoplot.ts.Rd | 4 +- man/nortsTest-package.Rd | 78 ++++++++++++++++++++++++++++----------------- tests/testthat/test-epps.r |only 10 files changed, 126 insertions(+), 85 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Supports Gaussian and binomial responses. Also implements the randomized permutation whole-model test for SVEM with Gaussian responses (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). Some parts of the package code were drafted with assistance from generative AI tools.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 2.3.1 dated 2025-10-13 and 2.5.4 dated 2025-11-09
SVEMnet-2.3.1/SVEMnet/R/predict_with_ci.R |only SVEMnet-2.3.1/SVEMnet/R/svem_significance_test.R |only SVEMnet-2.3.1/SVEMnet/man/predict_with_ci.Rd |only SVEMnet-2.3.1/SVEMnet/man/svem_significance_test.Rd |only SVEMnet-2.3.1/SVEMnet/vignettes/bic_sim.R |only SVEMnet-2.3.1/SVEMnet/vignettes/bic_sim_v2.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_aicc.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_aicc_c2.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_aicc_cvglm.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_and_objective.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_26AUG25.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_27AUG25_pp.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_27AUG25_second_script_pp.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_28AUG25_script.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svem_vs_lassoCV.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svem_vs_lassoCV_par_v2.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svemnet_sim.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svemnet_sim_identity.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svemnet_sim_mixture_v2.R |only SVEMnet-2.5.4/SVEMnet/DESCRIPTION | 19 SVEMnet-2.5.4/SVEMnet/MD5 | 109 - SVEMnet-2.5.4/SVEMnet/NAMESPACE | 13 SVEMnet-2.5.4/SVEMnet/NEWS | 3 SVEMnet-2.5.4/SVEMnet/R/SVEMnet-package.R | 29 SVEMnet-2.5.4/SVEMnet/R/SVEMnet.R | 539 ++++- SVEMnet-2.5.4/SVEMnet/R/bigexp.R | 702 +++++-- SVEMnet-2.5.4/SVEMnet/R/coef.R | 178 + SVEMnet-2.5.4/SVEMnet/R/glmnet_with_cv.R | 386 +++ SVEMnet-2.5.4/SVEMnet/R/globals.R | 2 SVEMnet-2.5.4/SVEMnet/R/lipid_screen.R | 111 - SVEMnet-2.5.4/SVEMnet/R/plot.svemnet.R | 270 ++ SVEMnet-2.5.4/SVEMnet/R/plot.svemtest.R | 60 SVEMnet-2.5.4/SVEMnet/R/predict.cv.R | 155 + SVEMnet-2.5.4/SVEMnet/R/predict.svem_lasso.R | 405 ++-- SVEMnet-2.5.4/SVEMnet/R/svem_optimize_random.R | 987 +++++++--- SVEMnet-2.5.4/SVEMnet/R/svem_random_table_multi.R | 101 - SVEMnet-2.5.4/SVEMnet/R/svem_significance_test_parallel.R | 249 +- SVEMnet-2.5.4/SVEMnet/data/lipid_screen.rda |binary SVEMnet-2.5.4/SVEMnet/inst/doc/SVEMnet_vignette.R | 89 SVEMnet-2.5.4/SVEMnet/inst/doc/SVEMnet_vignette.Rmd | 158 - SVEMnet-2.5.4/SVEMnet/inst/doc/SVEMnet_vignette.html | 430 +--- SVEMnet-2.5.4/SVEMnet/man/SVEMnet-package.Rd | 34 SVEMnet-2.5.4/SVEMnet/man/SVEMnet.Rd | 171 + SVEMnet-2.5.4/SVEMnet/man/bigexp_formula.Rd | 31 SVEMnet-2.5.4/SVEMnet/man/bigexp_model_matrix.Rd | 30 SVEMnet-2.5.4/SVEMnet/man/bigexp_prepare.Rd | 63 SVEMnet-2.5.4/SVEMnet/man/bigexp_terms.Rd | 138 + SVEMnet-2.5.4/SVEMnet/man/bigexp_train.Rd | 54 SVEMnet-2.5.4/SVEMnet/man/coef.svem_model.Rd | 66 SVEMnet-2.5.4/SVEMnet/man/glmnet_with_cv.Rd | 277 ++ SVEMnet-2.5.4/SVEMnet/man/lipid_screen.Rd | 141 + SVEMnet-2.5.4/SVEMnet/man/plot.svem_binomial.Rd |only SVEMnet-2.5.4/SVEMnet/man/plot.svem_model.Rd | 49 SVEMnet-2.5.4/SVEMnet/man/plot.svem_significance_test.Rd | 21 SVEMnet-2.5.4/SVEMnet/man/predict.svem_model.Rd | 194 + SVEMnet-2.5.4/SVEMnet/man/predict_cv.Rd | 90 SVEMnet-2.5.4/SVEMnet/man/print.bigexp_spec.Rd |only SVEMnet-2.5.4/SVEMnet/man/svem_nonzero.Rd |only SVEMnet-2.5.4/SVEMnet/man/svem_optimize_random.Rd | 384 ++- SVEMnet-2.5.4/SVEMnet/man/svem_random_table_multi.Rd | 81 SVEMnet-2.5.4/SVEMnet/man/svem_significance_test_parallel.Rd | 170 + SVEMnet-2.5.4/SVEMnet/man/with_bigexp_contrasts.Rd | 31 SVEMnet-2.5.4/SVEMnet/tests/testthat/test-fit-and-predict.R | 369 +++ SVEMnet-2.5.4/SVEMnet/tests/testthat/test-optimize-random.R | 109 - SVEMnet-2.5.4/SVEMnet/tests/testthat/test-significance-tests.R | 4 SVEMnet-2.5.4/SVEMnet/vignettes/SVEMnet_vignette.Rmd | 158 - SVEMnet-2.5.4/SVEMnet/vignettes/binary_sim_05NOV25.R |only 67 files changed, 5403 insertions(+), 2257 deletions(-)
Title: Uniformity Tests on the Circle, Sphere, and Hypersphere
Description: Implementation of uniformity tests on the circle and
(hyper)sphere. The main function of the package is unif_test(), which
conveniently collects more than 35 tests for assessing uniformity on
S^{p-1} = {x in R^p : ||x|| = 1}, p >= 2. The test statistics are
implemented in the unif_stat() function, which allows computing several
statistics for different samples within a single call, thus facilitating
Monte Carlo experiments. Furthermore, the unif_stat_MC() function allows
parallelizing them in a simple way. The asymptotic null distributions of
the statistics are available through the function unif_stat_distr(). The
core of 'sphunif' is coded in C++ by relying on the 'Rcpp' package.
The package also provides several novel datasets and gives the replicability
for the data applications/simulations in García-Portugués et al. (2021)
<doi:10.1007/978-3-030-69944-4_12>, García-Portugués et al. (2023)
<doi:10.3150/21-BEJ1454>, Fernández-de-Marcos and
García-Portugués (2024) <d [...truncated...]
Author: Eduardo Garcia-Portugues [aut, cre] ,
Thomas Verdebout [aut] ,
Alberto Fernandez-de-Marcos [ctb],
Paula Navarro [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between sphunif versions 1.4.2 dated 2025-08-18 and 1.4.3 dated 2025-11-09
DESCRIPTION | 10 - MD5 | 78 +++++++------- NEWS.md | 8 + R/Pn.R | 2 R/Sobolev.R | 29 +++-- R/cir_distr.R | 2 R/cir_stat.R | 5 R/data.R | 14 +- R/harmonics.R | 12 +- R/locdev.R | 2 R/sph_distr.R | 1 R/sph_stat.R | 2 R/sphunif-package.R | 20 +-- R/unif_stat.R | 2 R/unif_stat_distr.R | 57 ++++++---- R/unif_test.R | 6 - inst/WORDLIST | 2 inst/doc/sphunif.R | 4 inst/doc/sphunif.Rmd | 21 ++- inst/doc/sphunif.html | 181 ++++++++++++++++++---------------- man/Pn.Rd | 2 man/Sobolev.Rd | 3 man/Sobolev_coefs.Rd | 4 man/avail_tests.Rd | 2 man/cir_stat.Rd | 5 man/cir_stat_distr.Rd | 5 man/comets.Rd | 2 man/craters.Rd | 12 +- man/harmonics.Rd | 12 +- man/locdev.Rd | 2 man/sph_stat.Rd | 2 man/sphunif-package.Rd | 20 +-- man/unif_stat.Rd | 2 man/unif_stat_distr.Rd | 5 man/unif_test.Rd | 4 tests/testthat/test_Sobolev.R | 15 ++ tests/testthat/test_unif_stat.R | 4 tests/testthat/test_unif_stat_distr.R | 66 ++++++++++++ vignettes/sphunif.Rmd | 21 ++- vignettes/sphunif.bib | 15 +- 40 files changed, 398 insertions(+), 263 deletions(-)
Title: Longitudinal Surrogate Marker Analysis
Description: Assess the proportion of treatment effect explained by a longitudinal surrogate marker as described in Agniel D and Parast L (2021) <doi:10.1111/biom.13310>; and estimate the treatment effect on a longitudinal surrogate marker as described in Wang et al. (2025) <doi:10.1093/biomtc/ujaf104>. A tutorial for this package can be found at <https://www.laylaparast.com/longsurr>.
Author: Layla Parast [aut, cre],
Denis Agniel [aut],
Xuan Wang [aut]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between longsurr versions 1.0 dated 2022-09-29 and 1.1 dated 2025-11-09
DESCRIPTION | 16 - MD5 | 12 - NAMESPACE | 8 R/longsurr.functions.R | 416 ++++++++++++++++++++++++++++++++++++++++++++- data/data_sjm.RData |only man/data_sjm.Rd |only man/resam.Rd |only man/resam_nonlinear.Rd |only man/sjm_linear_estimate.Rd |only man/sjm_nl_estimate.Rd |only 10 files changed, 436 insertions(+), 16 deletions(-)
Title: Meta-Analysis of Quantiles and Functions of Quantiles
Description: Implements a novel density-based approach for estimating unknown parameters, distribution visualisations and meta-analyses of quantiles and ther functions.
A detailed vignettes with example datasets and code to prepare data and analyses is available at <https://bookdown.org/a2delivera/metaquant/>.
The methods are described in the pre-print by De Livera, Prendergast and Kumaranathunga (2024, <doi:10.48550/arXiv.2411.10971>).
Author: Udara Kumaranathunga [aut, cre],
Alysha De Livera [aut],
Luke Prendergast [aut]
Maintainer: Udara Kumaranathunga <U.Kumaranathunga@latrobe.edu.au>
Diff between metaquant versions 0.1.2 dated 2025-08-21 and 0.1.3 dated 2025-11-09
metaquant-0.1.2/metaquant/build |only metaquant-0.1.2/metaquant/man/est.density.five.Rd |only metaquant-0.1.2/metaquant/man/est.density.minq2max.Rd |only metaquant-0.1.2/metaquant/man/est.density.q1q2q3.Rd |only metaquant-0.1.3/metaquant/DESCRIPTION | 20 - metaquant-0.1.3/metaquant/MD5 | 29 - metaquant-0.1.3/metaquant/NAMESPACE | 11 metaquant-0.1.3/metaquant/R/est.mean.R | 99 ++--- metaquant-0.1.3/metaquant/R/est.sd.R | 26 - metaquant-0.1.3/metaquant/R/helper.functions.R | 308 +++++++++++++++++- metaquant-0.1.3/metaquant/R/metaquant.R |only metaquant-0.1.3/metaquant/R/plotdist.R | 201 ----------- metaquant-0.1.3/metaquant/man/est.gld.five.Rd |only metaquant-0.1.3/metaquant/man/est.mean.Rd | 18 - metaquant-0.1.3/metaquant/man/est.q.study.level.Rd |only metaquant-0.1.3/metaquant/man/est.r.study.level.Rd |only metaquant-0.1.3/metaquant/man/est.sd.Rd | 8 metaquant-0.1.3/metaquant/man/est.sld.minq2max.Rd |only metaquant-0.1.3/metaquant/man/est.sld.q1q2q3.Rd |only metaquant-0.1.3/metaquant/man/metaquant.Rd |only metaquant-0.1.3/metaquant/man/plotdist.Rd | 10 21 files changed, 413 insertions(+), 317 deletions(-)
Title: Neat Data for Presentation
Description: Utilities for unambiguous, neat and legible
representation of data (date, time stamp, numbers, percentages and strings)
for presentation of analysis , aiming for elegance and consistency.
The purpose of this package is to format data, that is better
for presentation and any automation jobs that reports numbers.
Author: Shivaprakash Suresh [aut, cre, cph]
Maintainer: Shivaprakash Suresh <dswithai@gmail.com>
This is a re-admission after prior archival of version 0.2.0 dated 2023-03-23
Diff between neatR versions 0.2.0 dated 2023-03-23 and 0.2.1 dated 2025-11-09
DESCRIPTION | 8 - MD5 | 28 ++--- R/src.R | 248 +++++++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/neat-data.R | 54 +++++----- inst/doc/neat-data.Rmd | 70 ++++++------- inst/doc/neat-data.html | 213 ++++++++++++++++++++--------------------- man/ndate.Rd | 10 - man/nday.Rd | 8 - man/nnumber.Rd | 8 - man/npercent.Rd | 23 ++-- man/nstring.Rd | 20 +-- man/ntimestamp.Rd | 28 ++--- tests/testthat/tests.R | 32 +++--- vignettes/neat-data.Rmd | 70 ++++++------- 15 files changed, 432 insertions(+), 388 deletions(-)