Title: Vector Helpers
Description: Defines new notions of prototype and size that are
used to provide tools for consistent and well-founded type-coercion
and size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut, cre],
Lionel Henry [aut],
Davis Vaughan [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between vctrs versions 0.2.4 dated 2020-03-10 and 0.3.0 dated 2020-05-11
vctrs-0.2.4/vctrs/man/faq/internal/setup.Rmd |only vctrs-0.2.4/vctrs/man/vec_default_cast.Rd |only vctrs-0.2.4/vctrs/src/type-list-of.c |only vctrs-0.2.4/vctrs/tests/testthat/type-misc.R |only vctrs-0.3.0/vctrs/DESCRIPTION | 15 vctrs-0.3.0/vctrs/MD5 | 432 ++- vctrs-0.3.0/vctrs/NAMESPACE | 185 - vctrs-0.3.0/vctrs/NEWS.md | 310 ++ vctrs-0.3.0/vctrs/R/assert.R | 51 vctrs-0.3.0/vctrs/R/bind.R | 53 vctrs-0.3.0/vctrs/R/c.R | 6 vctrs-0.3.0/vctrs/R/cast-list.R | 11 vctrs-0.3.0/vctrs/R/cast.R | 193 - vctrs-0.3.0/vctrs/R/compare.R | 6 vctrs-0.3.0/vctrs/R/conditions.R | 536 +++- vctrs-0.3.0/vctrs/R/dictionary.R | 20 vctrs-0.3.0/vctrs/R/dim.R | 3 vctrs-0.3.0/vctrs/R/equal.R | 6 vctrs-0.3.0/vctrs/R/faq-developer.R |only vctrs-0.3.0/vctrs/R/faq.R |only vctrs-0.3.0/vctrs/R/names.R | 41 vctrs-0.3.0/vctrs/R/partial-factor.R | 3 vctrs-0.3.0/vctrs/R/partial-frame.R | 3 vctrs-0.3.0/vctrs/R/proxy.R | 178 + vctrs-0.3.0/vctrs/R/ptype-abbr-full.R | 14 vctrs-0.3.0/vctrs/R/recycle.R | 2 vctrs-0.3.0/vctrs/R/register-s3.R | 32 vctrs-0.3.0/vctrs/R/rep.R |only vctrs-0.3.0/vctrs/R/shape.R | 52 vctrs-0.3.0/vctrs/R/size.R | 43 vctrs-0.3.0/vctrs/R/slice.R | 37 vctrs-0.3.0/vctrs/R/subscript-loc.R | 44 vctrs-0.3.0/vctrs/R/subscript.R | 51 vctrs-0.3.0/vctrs/R/type-asis.R |only vctrs-0.3.0/vctrs/R/type-bare.R | 513 ---- vctrs-0.3.0/vctrs/R/type-data-frame.R | 246 +- vctrs-0.3.0/vctrs/R/type-date-time.R | 360 +-- vctrs-0.3.0/vctrs/R/type-dplyr.R |only vctrs-0.3.0/vctrs/R/type-factor.R | 116 vctrs-0.3.0/vctrs/R/type-integer64.R | 41 vctrs-0.3.0/vctrs/R/type-list-of.R | 57 vctrs-0.3.0/vctrs/R/type-misc.R | 44 vctrs-0.3.0/vctrs/R/type-rcrd.R | 22 vctrs-0.3.0/vctrs/R/type-table.R |only vctrs-0.3.0/vctrs/R/type-tibble.R | 51 vctrs-0.3.0/vctrs/R/type-unspecified.R | 41 vctrs-0.3.0/vctrs/R/type-vctr.R | 109 vctrs-0.3.0/vctrs/R/type.R | 24 vctrs-0.3.0/vctrs/R/type2.R | 199 + vctrs-0.3.0/vctrs/R/utils.R | 16 vctrs-0.3.0/vctrs/R/vctrs-deprecated.R | 29 vctrs-0.3.0/vctrs/R/zzz.R | 61 vctrs-0.3.0/vctrs/README.md | 5 vctrs-0.3.0/vctrs/build/vctrs.pdf |binary vctrs-0.3.0/vctrs/build/vignette.rds |binary vctrs-0.3.0/vctrs/inst/doc/pillar.R |only vctrs-0.3.0/vctrs/inst/doc/pillar.Rmd |only vctrs-0.3.0/vctrs/inst/doc/pillar.html |only vctrs-0.3.0/vctrs/inst/doc/s3-vector.R | 113 vctrs-0.3.0/vctrs/inst/doc/s3-vector.Rmd | 341 -- vctrs-0.3.0/vctrs/inst/doc/s3-vector.html | 1186 ++++------ vctrs-0.3.0/vctrs/inst/doc/stability.R | 7 vctrs-0.3.0/vctrs/inst/doc/stability.Rmd | 15 vctrs-0.3.0/vctrs/inst/doc/stability.html | 299 +- vctrs-0.3.0/vctrs/inst/doc/type-size.R | 3 vctrs-0.3.0/vctrs/inst/doc/type-size.Rmd | 5 vctrs-0.3.0/vctrs/inst/doc/type-size.html | 17 vctrs-0.3.0/vctrs/man/as-is.Rd |only vctrs-0.3.0/vctrs/man/df_ptype2.Rd |only vctrs-0.3.0/vctrs/man/faq-error-incompatible-attributes.Rd |only vctrs-0.3.0/vctrs/man/faq/developer |only vctrs-0.3.0/vctrs/man/faq/internal/ptype2-identity.Rmd | 2 vctrs-0.3.0/vctrs/man/faq/setup.Rmd |only vctrs-0.3.0/vctrs/man/howto-faq-coercion-data-frame.Rd |only vctrs-0.3.0/vctrs/man/howto-faq-coercion.Rd |only vctrs-0.3.0/vctrs/man/list_of.Rd | 2 vctrs-0.3.0/vctrs/man/maybe_lossy_cast.Rd |only vctrs-0.3.0/vctrs/man/new_data_frame.Rd | 2 vctrs-0.3.0/vctrs/man/new_date.Rd | 10 vctrs-0.3.0/vctrs/man/new_factor.Rd | 3 vctrs-0.3.0/vctrs/man/new_vctr.Rd | 14 vctrs-0.3.0/vctrs/man/partial_factor.Rd | 1 vctrs-0.3.0/vctrs/man/partial_frame.Rd | 1 vctrs-0.3.0/vctrs/man/table.Rd |only vctrs-0.3.0/vctrs/man/theory-faq-coercion.Rd |only vctrs-0.3.0/vctrs/man/unspecified.Rd | 3 vctrs-0.3.0/vctrs/man/vctrs-conditions.Rd | 111 vctrs-0.3.0/vctrs/man/vctrs-package.Rd | 2 vctrs-0.3.0/vctrs/man/vec-rep.Rd |only vctrs-0.3.0/vctrs/man/vec_as_location.Rd | 2 vctrs-0.3.0/vctrs/man/vec_as_names.Rd | 4 vctrs-0.3.0/vctrs/man/vec_as_subscript.Rd | 2 vctrs-0.3.0/vctrs/man/vec_assert.Rd | 46 vctrs-0.3.0/vctrs/man/vec_bind.Rd | 25 vctrs-0.3.0/vctrs/man/vec_c.Rd | 6 vctrs-0.3.0/vctrs/man/vec_cast.Rd | 117 vctrs-0.3.0/vctrs/man/vec_cbind_frame_ptype.Rd |only vctrs-0.3.0/vctrs/man/vec_chop.Rd | 5 vctrs-0.3.0/vctrs/man/vec_data.Rd | 56 vctrs-0.3.0/vctrs/man/vec_default_ptype2.Rd |only vctrs-0.3.0/vctrs/man/vec_is_list.Rd | 7 vctrs-0.3.0/vctrs/man/vec_match.Rd | 21 vctrs-0.3.0/vctrs/man/vec_proxy.Rd |only vctrs-0.3.0/vctrs/man/vec_ptype.Rd | 12 vctrs-0.3.0/vctrs/man/vec_ptype2.Rd | 75 vctrs-0.3.0/vctrs/man/vec_recycle.Rd | 2 vctrs-0.3.0/vctrs/man/vec_repeat.Rd | 19 vctrs-0.3.0/vctrs/man/vec_size.Rd | 11 vctrs-0.3.0/vctrs/man/vec_slice.Rd | 23 vctrs-0.3.0/vctrs/src/arg-counter.c | 39 vctrs-0.3.0/vctrs/src/arg-counter.h | 3 vctrs-0.3.0/vctrs/src/arg.c | 3 vctrs-0.3.0/vctrs/src/bind.c | 90 vctrs-0.3.0/vctrs/src/c.c | 100 vctrs-0.3.0/vctrs/src/cast-bare.c |only vctrs-0.3.0/vctrs/src/cast-dispatch.c | 163 - vctrs-0.3.0/vctrs/src/cast.c | 639 +---- vctrs-0.3.0/vctrs/src/cast.h |only vctrs-0.3.0/vctrs/src/compare.c | 108 vctrs-0.3.0/vctrs/src/conditions.c | 66 vctrs-0.3.0/vctrs/src/dictionary.c | 61 vctrs-0.3.0/vctrs/src/dim.c |only vctrs-0.3.0/vctrs/src/dim.h |only vctrs-0.3.0/vctrs/src/equal.c | 357 +-- vctrs-0.3.0/vctrs/src/group.c | 27 vctrs-0.3.0/vctrs/src/hash.c | 5 vctrs-0.3.0/vctrs/src/init.c | 99 vctrs-0.3.0/vctrs/src/names.c | 96 vctrs-0.3.0/vctrs/src/names.h | 11 vctrs-0.3.0/vctrs/src/proxy-restore.c | 38 vctrs-0.3.0/vctrs/src/proxy.c | 9 vctrs-0.3.0/vctrs/src/ptype-common.h |only vctrs-0.3.0/vctrs/src/ptype2-dispatch.c | 98 vctrs-0.3.0/vctrs/src/ptype2.h |only vctrs-0.3.0/vctrs/src/rep.c |only vctrs-0.3.0/vctrs/src/shape.c |only vctrs-0.3.0/vctrs/src/shape.h |only vctrs-0.3.0/vctrs/src/size-common.c | 8 vctrs-0.3.0/vctrs/src/size.c | 93 vctrs-0.3.0/vctrs/src/slice-array.c | 461 +-- vctrs-0.3.0/vctrs/src/slice-assign-array.c |only vctrs-0.3.0/vctrs/src/slice-assign.c | 315 ++ vctrs-0.3.0/vctrs/src/slice-assign.h |only vctrs-0.3.0/vctrs/src/slice-chop.c | 136 - vctrs-0.3.0/vctrs/src/slice.c | 4 vctrs-0.3.0/vctrs/src/strides.h |only vctrs-0.3.0/vctrs/src/subscript-loc.c | 173 - vctrs-0.3.0/vctrs/src/subscript-loc.h | 50 vctrs-0.3.0/vctrs/src/subscript.c | 125 - vctrs-0.3.0/vctrs/src/subscript.h | 45 vctrs-0.3.0/vctrs/src/translate.c | 18 vctrs-0.3.0/vctrs/src/type-data-frame.c | 326 ++ vctrs-0.3.0/vctrs/src/type-data-frame.h | 27 vctrs-0.3.0/vctrs/src/type-date-time.c | 481 +++- vctrs-0.3.0/vctrs/src/type-factor.c | 66 vctrs-0.3.0/vctrs/src/type-factor.h |only vctrs-0.3.0/vctrs/src/type-info.c | 65 vctrs-0.3.0/vctrs/src/type-tibble.c | 39 vctrs-0.3.0/vctrs/src/type-tibble.h |only vctrs-0.3.0/vctrs/src/type.c | 145 - vctrs-0.3.0/vctrs/src/type2.c | 248 +- vctrs-0.3.0/vctrs/src/typeof2-s3.c | 2 vctrs-0.3.0/vctrs/src/unspecified.c | 1 vctrs-0.3.0/vctrs/src/utils-dispatch.c | 27 vctrs-0.3.0/vctrs/src/utils.c | 361 ++- vctrs-0.3.0/vctrs/src/utils.h | 100 vctrs-0.3.0/vctrs/src/vctrs.h | 156 - vctrs-0.3.0/vctrs/src/version.c | 2 vctrs-0.3.0/vctrs/tests/testthat/error/test-bind.txt |only vctrs-0.3.0/vctrs/tests/testthat/error/test-c.txt | 40 vctrs-0.3.0/vctrs/tests/testthat/error/test-cast.txt |only vctrs-0.3.0/vctrs/tests/testthat/error/test-conditions.txt | 107 vctrs-0.3.0/vctrs/tests/testthat/error/test-dictionary.txt |only vctrs-0.3.0/vctrs/tests/testthat/error/test-recycle.txt | 9 vctrs-0.3.0/vctrs/tests/testthat/error/test-rep.txt |only vctrs-0.3.0/vctrs/tests/testthat/error/test-shape.txt |only vctrs-0.3.0/vctrs/tests/testthat/error/test-slice-assign.txt | 29 vctrs-0.3.0/vctrs/tests/testthat/error/test-slice.txt | 33 vctrs-0.3.0/vctrs/tests/testthat/error/test-subscript-loc.txt | 212 + vctrs-0.3.0/vctrs/tests/testthat/error/test-subscript.txt | 36 vctrs-0.3.0/vctrs/tests/testthat/error/test-type-asis.txt |only vctrs-0.3.0/vctrs/tests/testthat/error/test-type-data-frame.txt |only vctrs-0.3.0/vctrs/tests/testthat/error/test-type2.txt |only vctrs-0.3.0/vctrs/tests/testthat/error/test-unchop.txt | 63 vctrs-0.3.0/vctrs/tests/testthat/helper-expectations.R | 24 vctrs-0.3.0/vctrs/tests/testthat/helper-memory.R |only vctrs-0.3.0/vctrs/tests/testthat/helper-rational.R | 4 vctrs-0.3.0/vctrs/tests/testthat/helper-s3.R | 50 vctrs-0.3.0/vctrs/tests/testthat/helper-s4.R |only vctrs-0.3.0/vctrs/tests/testthat/helper-shape.R |only vctrs-0.3.0/vctrs/tests/testthat/helper-type-dplyr.R |only vctrs-0.3.0/vctrs/tests/testthat/helper-types.R | 7 vctrs-0.3.0/vctrs/tests/testthat/helper-vctrs.R |only vctrs-0.3.0/vctrs/tests/testthat/output/bind-name-repair.txt | 64 vctrs-0.3.0/vctrs/tests/testthat/output/test-vec-as-names.txt | 6 vctrs-0.3.0/vctrs/tests/testthat/test-assert.R | 21 vctrs-0.3.0/vctrs/tests/testthat/test-bind.R | 213 + vctrs-0.3.0/vctrs/tests/testthat/test-c.R | 184 + vctrs-0.3.0/vctrs/tests/testthat/test-cast-error-nested.txt | 12 vctrs-0.3.0/vctrs/tests/testthat/test-cast.R | 53 vctrs-0.3.0/vctrs/tests/testthat/test-compare.R | 20 vctrs-0.3.0/vctrs/tests/testthat/test-conditions.R | 144 + vctrs-0.3.0/vctrs/tests/testthat/test-dictionary.R | 34 vctrs-0.3.0/vctrs/tests/testthat/test-equal.R | 23 vctrs-0.3.0/vctrs/tests/testthat/test-lifecycle-deprecated.R | 6 vctrs-0.3.0/vctrs/tests/testthat/test-names.R | 65 vctrs-0.3.0/vctrs/tests/testthat/test-partial-frame.R | 19 vctrs-0.3.0/vctrs/tests/testthat/test-proxy-restore.R | 20 vctrs-0.3.0/vctrs/tests/testthat/test-proxy.R | 5 vctrs-0.3.0/vctrs/tests/testthat/test-ptype-abbr-full.R | 16 vctrs-0.3.0/vctrs/tests/testthat/test-rep.R |only vctrs-0.3.0/vctrs/tests/testthat/test-s4.R |only vctrs-0.3.0/vctrs/tests/testthat/test-shape.R | 89 vctrs-0.3.0/vctrs/tests/testthat/test-size.R | 11 vctrs-0.3.0/vctrs/tests/testthat/test-slice-assign.R | 356 ++- vctrs-0.3.0/vctrs/tests/testthat/test-slice-chop.R | 206 + vctrs-0.3.0/vctrs/tests/testthat/test-slice.R | 32 vctrs-0.3.0/vctrs/tests/testthat/test-subscript-loc.R | 28 vctrs-0.3.0/vctrs/tests/testthat/test-subscript.R | 18 vctrs-0.3.0/vctrs/tests/testthat/test-type-asis.R |only vctrs-0.3.0/vctrs/tests/testthat/test-type-bare.R | 194 + vctrs-0.3.0/vctrs/tests/testthat/test-type-data-frame.R | 324 ++ vctrs-0.3.0/vctrs/tests/testthat/test-type-date-time.R | 444 ++- vctrs-0.3.0/vctrs/tests/testthat/test-type-dplyr.R |only vctrs-0.3.0/vctrs/tests/testthat/test-type-factor.R | 85 vctrs-0.3.0/vctrs/tests/testthat/test-type-integer64.R | 23 vctrs-0.3.0/vctrs/tests/testthat/test-type-list-of.R | 25 vctrs-0.3.0/vctrs/tests/testthat/test-type-misc.R |only vctrs-0.3.0/vctrs/tests/testthat/test-type-rcrd.R | 42 vctrs-0.3.0/vctrs/tests/testthat/test-type-sf.R |only vctrs-0.3.0/vctrs/tests/testthat/test-type-table.R |only vctrs-0.3.0/vctrs/tests/testthat/test-type-tibble.R | 27 vctrs-0.3.0/vctrs/tests/testthat/test-type-unspecified.R | 14 vctrs-0.3.0/vctrs/tests/testthat/test-type-vctr.R | 84 vctrs-0.3.0/vctrs/tests/testthat/test-type-vec-c-error.txt | 6 vctrs-0.3.0/vctrs/tests/testthat/test-type-vec-size-common-error.txt | 4 vctrs-0.3.0/vctrs/tests/testthat/test-type-vec-type-common-error.txt | 30 vctrs-0.3.0/vctrs/tests/testthat/test-type.R | 14 vctrs-0.3.0/vctrs/tests/testthat/test-type2-error-messages.txt | 4 vctrs-0.3.0/vctrs/tests/testthat/test-type2.R | 182 + vctrs-0.3.0/vctrs/tests/testthat/test-utils.R | 17 vctrs-0.3.0/vctrs/tests/testthat/test-vctrs.R | 1 vctrs-0.3.0/vctrs/vignettes/pillar.Rmd |only vctrs-0.3.0/vctrs/vignettes/s3-vector.Rmd | 341 -- vctrs-0.3.0/vctrs/vignettes/stability.Rmd | 15 vctrs-0.3.0/vctrs/vignettes/type-size.Rmd | 5 246 files changed, 10365 insertions(+), 6092 deletions(-)
Title: Valence Aware Dictionary and sEntiment Reasoner (VADER)
Description: A lexicon and rule-based sentiment analysis tool that is specifically
attuned to sentiments expressed in social media, and works well on texts from other
domains. Hutto & Gilbert (2014) <https://www.aaai.org/ocs/index.php/ICWSM/ICWSM14/paper/view/8109/8122>.
Author: Katherine Roehrick [aut, cre]
Maintainer: Katherine Roehrick <kr.gitcode@gmail.com>
Diff between vader versions 0.0.2 dated 2020-05-08 and 0.1.0 dated 2020-05-11
vader-0.0.2/vader/man/getVader.Rd |only vader-0.1.0/vader/DESCRIPTION | 6 +++--- vader-0.1.0/vader/MD5 | 12 +++++++----- vader-0.1.0/vader/NAMESPACE | 3 ++- vader-0.1.0/vader/NEWS.md | 4 ++++ vader-0.1.0/vader/R/vader_df.R |only vader-0.1.0/vader/R/vader_main_call.R | 23 ++++++++++++----------- vader-0.1.0/vader/man/get_vader.Rd |only vader-0.1.0/vader/man/vader_df.Rd |only 9 files changed, 28 insertions(+), 20 deletions(-)
Title: Select from a Set of Strings
Description: A backend for the selecting functions of the 'tidyverse'.
It makes it easy to implement select-like functions in your own
packages in a way that is consistent with other 'tidyverse'
interfaces for selection.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between tidyselect versions 1.0.0 dated 2020-01-27 and 1.1.0 dated 2020-05-11
tidyselect-1.0.0/tidyselect/R/select-helpers.R |only tidyselect-1.0.0/tidyselect/man/select_helpers.Rd |only tidyselect-1.1.0/tidyselect/DESCRIPTION | 10 tidyselect-1.1.0/tidyselect/MD5 | 100 +- tidyselect-1.1.0/tidyselect/NEWS.md | 44 tidyselect-1.1.0/tidyselect/R/eval-bool.R | 14 tidyselect-1.1.0/tidyselect/R/eval-select.R | 32 tidyselect-1.1.0/tidyselect/R/eval-walk.R | 57 + tidyselect-1.1.0/tidyselect/R/helpers-misc.R |only tidyselect-1.1.0/tidyselect/R/helpers-pattern.R |only tidyselect-1.1.0/tidyselect/R/helpers-vector.R |only tidyselect-1.1.0/tidyselect/R/helpers-where.R |only tidyselect-1.1.0/tidyselect/R/helpers.R |only tidyselect-1.1.0/tidyselect/R/lifecycle-deprecated.R | 2 tidyselect-1.1.0/tidyselect/R/sets.R | 1 tidyselect-1.1.0/tidyselect/R/utils.R | 43 tidyselect-1.1.0/tidyselect/R/vars.R | 8 tidyselect-1.1.0/tidyselect/R/zzz.R |only tidyselect-1.1.0/tidyselect/README.md | 7 tidyselect-1.1.0/tidyselect/build/vignette.rds |binary tidyselect-1.1.0/tidyselect/inst/doc/syntax.R | 31 tidyselect-1.1.0/tidyselect/inst/doc/syntax.Rmd | 73 - tidyselect-1.1.0/tidyselect/inst/doc/syntax.html | 461 ++++------ tidyselect-1.1.0/tidyselect/inst/doc/tidyselect.html | 48 - tidyselect-1.1.0/tidyselect/man/all_of.Rd |only tidyselect-1.1.0/tidyselect/man/eval_select.Rd | 28 tidyselect-1.1.0/tidyselect/man/everything.Rd |only tidyselect-1.1.0/tidyselect/man/faq-external-vector.Rd | 13 tidyselect-1.1.0/tidyselect/man/faq/external-vector.Rmd | 4 tidyselect-1.1.0/tidyselect/man/language.Rd |only tidyselect-1.1.0/tidyselect/man/one_of.Rd | 8 tidyselect-1.1.0/tidyselect/man/peek_vars.Rd | 2 tidyselect-1.1.0/tidyselect/man/poke_vars.Rd | 6 tidyselect-1.1.0/tidyselect/man/rmd |only tidyselect-1.1.0/tidyselect/man/starts_with.Rd |only tidyselect-1.1.0/tidyselect/man/vars_select.Rd | 2 tidyselect-1.1.0/tidyselect/man/vars_select_helpers.Rd | 11 tidyselect-1.1.0/tidyselect/man/where.Rd |only tidyselect-1.1.0/tidyselect/tests/testthat/helper-tidyselect.R | 6 tidyselect-1.1.0/tidyselect/tests/testthat/outputs/eval-sym-verbosity.txt |only tidyselect-1.1.0/tidyselect/tests/testthat/outputs/rename-errors.txt | 2 tidyselect-1.1.0/tidyselect/tests/testthat/outputs/rename-strict-errors.txt | 6 tidyselect-1.1.0/tidyselect/tests/testthat/outputs/select-eval-boolean-errors.txt | 6 tidyselect-1.1.0/tidyselect/tests/testthat/outputs/test-helpers-where.txt |only tidyselect-1.1.0/tidyselect/tests/testthat/outputs/vars-pull-input-checking.txt | 34 tidyselect-1.1.0/tidyselect/tests/testthat/outputs/vars-rename-error-rename-to-existing.txt | 7 tidyselect-1.1.0/tidyselect/tests/testthat/outputs/vars-rename-error-rename-to-same.txt | 4 tidyselect-1.1.0/tidyselect/tests/testthat/outputs/vars-rename-type-checking.txt | 6 tidyselect-1.1.0/tidyselect/tests/testthat/outputs/vars-select-context-lookup.txt | 1 tidyselect-1.1.0/tidyselect/tests/testthat/outputs/vars-select-index-type.txt | 6 tidyselect-1.1.0/tidyselect/tests/testthat/outputs/vars-select-oob-errors.txt | 14 tidyselect-1.1.0/tidyselect/tests/testthat/test-eval-bool.R | 2 tidyselect-1.1.0/tidyselect/tests/testthat/test-eval-walk.R | 90 + tidyselect-1.1.0/tidyselect/tests/testthat/test-helpers-where.R |only tidyselect-1.1.0/tidyselect/tests/testthat/test-lifecycle-deprecated.R | 4 tidyselect-1.1.0/tidyselect/tests/testthat/test-select-helpers.R | 14 tidyselect-1.1.0/tidyselect/tests/testthat/test-select.R | 13 tidyselect-1.1.0/tidyselect/tests/testthat/test-sets.R | 4 tidyselect-1.1.0/tidyselect/vignettes/syntax.Rmd | 73 - 59 files changed, 690 insertions(+), 607 deletions(-)
Title: Scale Functions for Visualization
Description: Graphical scales map data to aesthetics, and
provide methods for automatically determining breaks and labels for
axes and legends.
Author: Hadley Wickham [aut, cre],
Dana Seidel [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between scales versions 1.1.0 dated 2019-11-18 and 1.1.1 dated 2020-05-11
scales-1.1.0/scales/man/censor.Rd |only scales-1.1.0/scales/man/discard.Rd |only scales-1.1.0/scales/man/squish.Rd |only scales-1.1.0/scales/man/squish_infinite.Rd |only scales-1.1.0/scales/tests/testthat/test-scale.r |only scales-1.1.1/scales/DESCRIPTION | 15 - scales-1.1.1/scales/MD5 | 134 ++++++------ scales-1.1.1/scales/NAMESPACE | 9 scales-1.1.1/scales/NEWS.md | 20 + scales-1.1.1/scales/R/bounds.r | 142 ++++++++++--- scales-1.1.1/scales/R/breaks.r | 6 scales-1.1.1/scales/R/colour-manip.r | 22 +- scales-1.1.1/scales/R/colour-ramp.R | 3 scales-1.1.1/scales/R/date-time.r | 14 - scales-1.1.1/scales/R/full-seq.r | 20 + scales-1.1.1/scales/R/label-date.R | 2 scales-1.1.1/scales/R/label-expression.R | 2 scales-1.1.1/scales/R/label-number-auto.R | 1 scales-1.1.1/scales/R/label-number.r | 8 scales-1.1.1/scales/R/label-ordinal.R | 17 + scales-1.1.1/scales/R/label-percent.R | 2 scales-1.1.1/scales/R/label-wrap.R | 2 scales-1.1.1/scales/R/pal-hue.r | 13 - scales-1.1.1/scales/R/trans-date.r | 4 scales-1.1.1/scales/R/utils.r | 6 scales-1.1.1/scales/README.md | 4 scales-1.1.1/scales/build/partial.rdb |binary scales-1.1.1/scales/build/scales.pdf |binary scales-1.1.1/scales/man/Range.Rd | 10 scales-1.1.1/scales/man/breaks_log.Rd | 2 scales-1.1.1/scales/man/breaks_width.Rd | 6 scales-1.1.1/scales/man/cbreaks.Rd | 3 scales-1.1.1/scales/man/col2hcl.Rd | 8 scales-1.1.1/scales/man/col_numeric.Rd | 46 +++- scales-1.1.1/scales/man/demo_continuous.Rd | 3 scales-1.1.1/scales/man/div_gradient_pal.Rd | 8 scales-1.1.1/scales/man/figures/README-labels-1.png |binary scales-1.1.1/scales/man/figures/README-labels-2.png |binary scales-1.1.1/scales/man/figures/README-palettes-1.png |binary scales-1.1.1/scales/man/figures/README-transforms-1.png |binary scales-1.1.1/scales/man/hue_pal.Rd | 3 scales-1.1.1/scales/man/label_bytes.Rd | 20 + scales-1.1.1/scales/man/label_date.Rd | 5 scales-1.1.1/scales/man/label_dollar.Rd | 67 ++++-- scales-1.1.1/scales/man/label_number.Rd | 76 +++++- scales-1.1.1/scales/man/label_number_auto.Rd | 15 - scales-1.1.1/scales/man/label_number_si.Rd | 20 + scales-1.1.1/scales/man/label_ordinal.Rd | 49 +++- scales-1.1.1/scales/man/label_parse.Rd | 19 + scales-1.1.1/scales/man/label_percent.Rd | 60 +++-- scales-1.1.1/scales/man/label_pvalue.Rd | 37 ++- scales-1.1.1/scales/man/label_scientific.Rd | 60 +++-- scales-1.1.1/scales/man/label_wrap.Rd | 3 scales-1.1.1/scales/man/number.Rd | 13 + scales-1.1.1/scales/man/number_bytes_format.Rd | 3 scales-1.1.1/scales/man/oob.Rd |only scales-1.1.1/scales/man/rescale.Rd | 18 - scales-1.1.1/scales/man/rescale_mid.Rd | 18 - scales-1.1.1/scales/man/scales-package.Rd | 2 scales-1.1.1/scales/man/seq_gradient_pal.Rd | 3 scales-1.1.1/scales/man/show_col.Rd | 21 + scales-1.1.1/scales/man/trans_new.Rd | 12 - scales-1.1.1/scales/man/unit_format.Rd | 15 + scales-1.1.1/scales/man/viridis_pal.Rd | 3 scales-1.1.1/scales/tests/testthat/test-bounds.r | 23 +- scales-1.1.1/scales/tests/testthat/test-full-seq.r |only scales-1.1.1/scales/tests/testthat/test-label-date.R | 4 scales-1.1.1/scales/tests/testthat/test-label-number.r | 10 scales-1.1.1/scales/tests/testthat/test-label-ordinal.R | 19 - scales-1.1.1/scales/tests/testthat/test-label-ordinal.txt |only scales-1.1.1/scales/tests/testthat/test-pal-hue.r | 6 scales-1.1.1/scales/tests/testthat/test-scale-continuous.r |only scales-1.1.1/scales/tests/testthat/test-scale-discrete.r |only 73 files changed, 768 insertions(+), 368 deletions(-)
Title: IP Address Geolocation
Description: Connectors to online and offline sources for taking IP addresses
and geolocating them to country, city, timezone and other geographic ranges. For
individual connectors, see the package index.
Author: Os Keyes [aut, cre], Drew Schmidt [aut], David Robinson [ctb],
Chris Davis [ctb], Bob Rudis [ctb], Maxmind, Inc. [cph], Pascal Gloor [cph], IP2Location.com [cph]
Maintainer: Os Keyes <ironholds@gmail.com>
Diff between rgeolocate versions 1.2.0 dated 2020-04-22 and 1.3.0 dated 2020-05-11
DESCRIPTION | 8 MD5 | 15 R/maxmind.R | 3 R/zzz.R | 2 inst/doc/Introduction_to_rgeolocate.html | 501 +++++++++++++++++++------------ src/maxmind.cpp | 48 ++ src/maxmind.h | 2 tests/testthat/test_maxmind.R | 2 vignettes/Introduction_to_rgeolocate.md |only 9 files changed, 370 insertions(+), 211 deletions(-)
Title: Automates the Creation of New Statistical Analysis Projects
Description: Provides functions to
automatically build a directory structure for a new R
project. Using this structure, 'ProjectTemplate'
automates data loading, preprocessing, library
importing and unit testing.
Author: Aleksandar Blagotic [ctb],
Diego Valle-Jones [ctb],
Jeffrey Breen [ctb],
Joakim Lundborg [ctb],
John Myles White [aut, cph],
Josh Bode [ctb],
Kenton White [ctb, cre],
Kirill Mueller [ctb],
Matteo Redaelli [ctb],
Noah Lorang [ctb],
Patrick Schalk [ctb],
Dominik Schneider [ctb]
Maintainer: Kenton White <jkentonwhite@gmail.com>
Diff between ProjectTemplate versions 0.9.1 dated 2020-04-15 and 0.9.2 dated 2020-05-11
DESCRIPTION | 7 + MD5 | 48 ++++++------- NEWS.md | 8 +- R/add.config.R | 2 R/clean.variable.name.R | 9 +- R/csv2.reader.R | 2 R/list.data.R | 6 - R/load.project.R | 2 R/project.config.R | 2 build/partial.rdb |binary inst/defaults/config/default.dcf | 1 inst/defaults/config/types.dcf | 1 inst/defaults/templates/full/config/global.dcf | 3 inst/defaults/templates/minimal/config/global.dcf | 3 inst/example_data/example_24.R | 2 inst/example_data/example_25.r | 2 man/add.config.Rd | 2 man/clean.variable.name.Rd | 5 + man/internal.parse.extensions.Rd | 2 man/load.project.Rd | 2 man/preinstalled.readers.Rd | 2 man/project.config.Rd | 2 tests/testthat/test-list.R | 2 tests/testthat/test-readers.R | 80 +++++++++++----------- tests/testthat/test-varnames.R | 27 +++++++ 25 files changed, 133 insertions(+), 89 deletions(-)
More information about ProjectTemplate at CRAN
Permanent link
Title: Parse 'User-Agent' Strings
Description: Despite there being a section in RFC 7231
<https://tools.ietf.org/html/rfc7231#section-5.5.3> defining a suggested
structure for 'User-Agent' headers this data is notoriously difficult
to parse consistently. Tools are provided that will take in user agent
strings and return structured R objects. This is a 'V8'-backed package
based on the 'ua-parser' project <https://github.com/ua-parser>.
Author: Bob Rudis [aut, cre],
Lindsey Simon [aut] (uap-core),
Tobie Langel [aut] (uap-core),
Colman Humphrey [ctb]
Maintainer: Bob Rudis <bob@rud.is>
Diff between uaparserjs versions 0.3.1 dated 2020-04-01 and 0.3.5 dated 2020-05-11
uaparserjs-0.3.1/uaparserjs/tests/agents.txt |only uaparserjs-0.3.1/uaparserjs/tests/test-all.R |only uaparserjs-0.3.1/uaparserjs/tests/testthat |only uaparserjs-0.3.5/uaparserjs/DESCRIPTION | 14 +++++++------- uaparserjs-0.3.5/uaparserjs/MD5 | 18 +++++++++--------- uaparserjs-0.3.5/uaparserjs/NEWS.md | 6 ++++++ uaparserjs-0.3.5/uaparserjs/R/utils-mappers.R | 4 ---- uaparserjs-0.3.5/uaparserjs/README.md | 22 +++++++++++----------- uaparserjs-0.3.5/uaparserjs/inst/extdat |only uaparserjs-0.3.5/uaparserjs/inst/js/bld | 3 +-- uaparserjs-0.3.5/uaparserjs/inst/js/bundle.js | 4 ++-- uaparserjs-0.3.5/uaparserjs/inst/tinytest |only uaparserjs-0.3.5/uaparserjs/tests/tinytest.R |only 13 files changed, 36 insertions(+), 35 deletions(-)
Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions
from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh,
R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton <charlton@usgs.gov>
Diff between phreeqc versions 3.6.0 dated 2019-11-30 and 3.6.3 dated 2020-05-11
DESCRIPTION | 8 +- MD5 | 49 +++++++------ R/phreeqc.R | 69 +++++++++++++++---- data/databases.rda |binary inst/CITATION | 4 - man/Amm.dat.Rd | 4 - man/ColdChem.dat.Rd | 4 - man/Tipping_Hurley.dat.Rd |only man/core10.dat.Rd |only man/ex15.dat.Rd | 12 +-- man/frezchem.dat.Rd |only man/iso.dat.Rd | 12 +-- man/llnl.dat.Rd | 12 +-- man/minteq.dat.Rd | 12 +-- man/minteq.v4.dat.Rd | 12 +-- man/phreeqc-package.Rd | 2 man/phreeqc.dat.Rd | 12 +-- man/pitzer.dat.Rd | 12 +-- man/sit.dat.Rd | 12 +-- man/wateq4f.dat.Rd | 12 +-- src/IPhreeqc.h | 2 src/Version.h | 8 +- src/phreeqcpp/PBasic.cpp | 40 +++++++++++ src/phreeqcpp/PBasic.h | 4 + src/phreeqcpp/Phreeqc.h | 1 src/phreeqcpp/readtr.cpp | 39 +++++++--- src/phreeqcpp/transport.cpp | 157 +++++++++++++++++++++----------------------- 27 files changed, 311 insertions(+), 188 deletions(-)
Title: R Interface to 'TensorFlow'
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>,
an open source software library for numerical computation using data
flow graphs. Nodes in the graph represent mathematical operations,
while the graph edges represent the multidimensional data arrays
(tensors) communicated between them. The flexible architecture allows
you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop,
server, or mobile device with a single 'API'. 'TensorFlow' was originally
developed by researchers and engineers working on the Google Brain Team
within Google's Machine Intelligence research organization for the
purposes of conducting machine learning and deep neural networks research,
but the system is general enough to be applicable in a wide variety
of other domains as well.
Author: Daniel Falbel [ctb, cph, cre],
JJ Allaire [aut, cph],
RStudio [cph, fnd],
Yuan Tang [aut, cph] (<https://orcid.org/0000-0001-5243-233X>),
Dirk Eddelbuettel [ctb, cph],
Nick Golding [ctb, cph],
Tomasz Kalinowski [ctb, cph],
Google Inc. [ctb, cph] (Examples and Tutorials)
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between tensorflow versions 2.0.0 dated 2019-10-02 and 2.2.0 dated 2020-05-11
tensorflow-2.0.0/tensorflow/inst |only tensorflow-2.2.0/tensorflow/DESCRIPTION | 12 +- tensorflow-2.2.0/tensorflow/MD5 | 60 ++++------ tensorflow-2.2.0/tensorflow/NAMESPACE | 9 + tensorflow-2.2.0/tensorflow/NEWS.md | 6 + tensorflow-2.2.0/tensorflow/R/eager.R | 20 +++ tensorflow-2.2.0/tensorflow/R/extract.R | 2 tensorflow-2.2.0/tensorflow/R/generics.R | 16 ++ tensorflow-2.2.0/tensorflow/R/install.R | 41 +++++- tensorflow-2.2.0/tensorflow/R/modules.R | 7 - tensorflow-2.2.0/tensorflow/R/package.R | 3 tensorflow-2.2.0/tensorflow/R/seed.R | 3 tensorflow-2.2.0/tensorflow/R/types.R | 22 +++ tensorflow-2.2.0/tensorflow/man/install_tensorflow.Rd | 22 ++- tensorflow-2.2.0/tensorflow/man/parse_arguments.Rd | 2 tensorflow-2.2.0/tensorflow/man/parse_flags.Rd | 9 + tensorflow-2.2.0/tensorflow/man/reexports.Rd | 4 tensorflow-2.2.0/tensorflow/man/sub-.tensorflow.tensor.Rd | 8 + tensorflow-2.2.0/tensorflow/man/tensorboard.Rd | 11 + tensorflow-2.2.0/tensorflow/man/tensorflow.Rd | 1 tensorflow-2.2.0/tensorflow/man/tf.Rd | 7 - tensorflow-2.2.0/tensorflow/man/tf_extract_opts.Rd | 14 +- tensorflow-2.2.0/tensorflow/man/tf_function.Rd | 8 + tensorflow-2.2.0/tensorflow/man/tfe_enable_eager_execution.Rd | 8 - tensorflow-2.2.0/tensorflow/man/use_session_with_seed.Rd | 8 + tensorflow-2.2.0/tensorflow/tests/testthat/test-extract-syntax.R | 7 - tensorflow-2.2.0/tensorflow/tests/testthat/test-generic-methods.R | 8 + tensorflow-2.2.0/tensorflow/tests/testthat/test-seed.R |only tensorflow-2.2.0/tensorflow/tests/testthat/test-types.R |only 29 files changed, 221 insertions(+), 97 deletions(-)
Title: Automated Cleaning of Occurrence Records from Biological
Collections
Description: Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) doi:10.1111/2041-210X.13152.
Author: Alexander Zizka [aut, cre],
Daniele Silvestro [ctb],
Tobias Andermann [ctb],
Josue Azevedo [ctb],
Camila Duarte Ritter [ctb],
Daniel Edler [ctb],
Harith Farooq [ctb],
Andrei Herdean [ctb],
Maria Ariza [ctb],
Ruud Scharn [ctb],
Sten Svanteson [ctb],
Niklas Wengstrom [ctb],
Vera Zizka [ctb],
Alexandre Antonelli [ctb],
Irene Steves [rev] (Irene reviewed the package for ropensci, see
<https://github.com/ropensci/onboarding/issues/210>),
Francisco Rodriguez-Sanchez [rev] (Francisco reviewed the package for
ropensci, see <https://github.com/ropensci/onboarding/issues/210>)
Maintainer: Alexander Zizka <alexander.zizka@idiv.de>
Diff between CoordinateCleaner versions 2.0-11 dated 2019-04-24 and 2.0-15 dated 2020-05-11
CoordinateCleaner-2.0-11/CoordinateCleaner/R/CleanCoordinates.R |only CoordinateCleaner-2.0-11/CoordinateCleaner/R/CleanCoordinatesDS.R |only CoordinateCleaner-2.0-11/CoordinateCleaner/R/CleanCoordinatesFOS.R |only CoordinateCleaner-2.0-11/CoordinateCleaner/data/datalist |only CoordinateCleaner-2.0-11/CoordinateCleaner/man/CoordinateCleaner-deprecated.Rd |only CoordinateCleaner-2.0-11/CoordinateCleaner/tests/testthat/Test_fossillevel_cleaning.R |only CoordinateCleaner-2.0-15/CoordinateCleaner/DESCRIPTION | 11 CoordinateCleaner-2.0-15/CoordinateCleaner/MD5 | 105 +- CoordinateCleaner-2.0-15/CoordinateCleaner/NAMESPACE | 2 CoordinateCleaner-2.0-15/CoordinateCleaner/NEWS.md | 38 CoordinateCleaner-2.0-15/CoordinateCleaner/R/CoordinateCleaner-package.R | 14 CoordinateCleaner-2.0-15/CoordinateCleaner/R/cc_cap.R | 2 CoordinateCleaner-2.0-15/CoordinateCleaner/R/cc_cen.R | 4 CoordinateCleaner-2.0-15/CoordinateCleaner/R/cc_coun.R | 11 CoordinateCleaner-2.0-15/CoordinateCleaner/R/cc_gbif.R | 2 CoordinateCleaner-2.0-15/CoordinateCleaner/R/cc_inst.R | 4 CoordinateCleaner-2.0-15/CoordinateCleaner/R/cc_iucn.R | 8 CoordinateCleaner-2.0-15/CoordinateCleaner/R/cc_outl.R | 419 +++++----- CoordinateCleaner-2.0-15/CoordinateCleaner/R/cc_sea.R | 18 CoordinateCleaner-2.0-15/CoordinateCleaner/R/cc_urb.R | 2 CoordinateCleaner-2.0-15/CoordinateCleaner/R/cf_age.R | 2 CoordinateCleaner-2.0-15/CoordinateCleaner/R/cf_outl.R | 3 CoordinateCleaner-2.0-15/CoordinateCleaner/R/clean_coordinates.R | 22 CoordinateCleaner-2.0-15/CoordinateCleaner/R/defunct_functions.R |only CoordinateCleaner-2.0-15/CoordinateCleaner/R/internal_clean_coordinate.R | 21 CoordinateCleaner-2.0-15/CoordinateCleaner/R/methods.spatialvalid.R | 3 CoordinateCleaner-2.0-15/CoordinateCleaner/README.md | 18 CoordinateCleaner-2.0-15/CoordinateCleaner/inst/CITATION | 4 CoordinateCleaner-2.0-15/CoordinateCleaner/man/CoordinateCleaner-defunct.Rd |only CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_cap.Rd | 35 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_cen.Rd | 36 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_coun.Rd | 42 - CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_dupl.Rd | 32 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_equ.Rd | 30 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_gbif.Rd | 34 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_inst.Rd | 37 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_iucn.Rd | 32 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_outl.Rd | 41 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_sea.Rd | 33 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_urb.Rd | 30 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_val.Rd | 29 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cc_zero.Rd | 30 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cd_ddmm.Rd | 20 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cd_round.Rd | 22 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cf_age.Rd | 27 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cf_equal.Rd | 15 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cf_outl.Rd | 27 CoordinateCleaner-2.0-15/CoordinateCleaner/man/cf_range.Rd | 25 CoordinateCleaner-2.0-15/CoordinateCleaner/man/clean_coordinates.Rd | 60 + CoordinateCleaner-2.0-15/CoordinateCleaner/man/clean_dataset.Rd | 18 CoordinateCleaner-2.0-15/CoordinateCleaner/man/clean_fossils.Rd | 41 CoordinateCleaner-2.0-15/CoordinateCleaner/man/countryref.Rd | 6 CoordinateCleaner-2.0-15/CoordinateCleaner/man/institutions.Rd | 10 CoordinateCleaner-2.0-15/CoordinateCleaner/man/pbdb_example.Rd | 4 CoordinateCleaner-2.0-15/CoordinateCleaner/man/plot.spatialvalid.Rd | 14 CoordinateCleaner-2.0-15/CoordinateCleaner/man/write_pyrate.Rd | 16 CoordinateCleaner-2.0-15/CoordinateCleaner/tests/testthat/test_coordinatelevel_functions.R | 39 CoordinateCleaner-2.0-15/CoordinateCleaner/tests/testthat/test_fossillevel_functions.R |only 58 files changed, 972 insertions(+), 526 deletions(-)
More information about CoordinateCleaner at CRAN
Permanent link
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Namita Gupta [aut],
Susanna Marquez [aut],
Nima Nouri [aut],
Ruoyi Jiang [aut],
Julian Zhou [aut],
Kenneth Hoehn [aut],
Daniel Gadala-Maria [ctb],
Jason Vander Heiden [cre, aut],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Diff between alakazam versions 1.0.0 dated 2020-05-08 and 1.0.1 dated 2020-05-11
DESCRIPTION | 20 ++++++++++---------- MD5 | 14 +++++++------- NEWS.md | 2 +- inst/doc/AminoAcids-Vignette.pdf |binary inst/doc/Diversity-Vignette.pdf |binary inst/doc/GeneUsage-Vignette.pdf |binary inst/doc/Lineage-Vignette.pdf |binary inst/doc/Topology-Vignette.pdf |binary 8 files changed, 18 insertions(+), 18 deletions(-)
Title: Stemming Algorithms for the Portuguese Language
Description: Wraps a collection of stemming algorithms for the Portuguese
Language.
Author: Daniel Falbel [aut, cre]
Maintainer: Daniel Falbel <dfalbel@gmail.com>
Diff between ptstem versions 0.0.4 dated 2019-01-02 and 0.0.6 dated 2020-05-11
DESCRIPTION | 10 +-- MD5 | 48 +++++++------- NEWS.md | 4 + R/stem_hunspell.R | 4 - R/stem_modified_hunspell.R | 2 R/stem_porter.R | 2 R/stem_rslp.R | 2 R/utils.R | 2 build/vignette.rds |binary inst/doc/ptstem.R | 30 ++++----- inst/doc/ptstem.Rmd | 2 inst/doc/ptstem.html | 136 ++++++++++++++++++++++++++---------------- man/complete_stems.Rd | 1 man/extract_words.Rd | 1 man/overstemming_index.Rd | 1 man/performance.Rd | 1 man/pipe.Rd | 1 man/ptstem.Rd | 6 - man/stem_hunspell.Rd | 1 man/stem_modified_hunspell.Rd | 1 man/stem_porter.Rd | 1 man/stem_rslp.Rd | 1 man/understemming_index.Rd | 1 man/unify_stems.Rd | 1 vignettes/ptstem.Rmd | 2 25 files changed, 145 insertions(+), 116 deletions(-)
Title: Probabilities for Bivariate Normal Distribution
Description: Computes probabilities of the bivariate normal distribution
in a vectorized R function (Drezner & Wesolowsky, 1990,
<doi:10.1080/00949659008811236>).
Author: Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>)
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between pbv versions 0.3-19 dated 2019-11-04 and 0.4-22 dated 2020-05-11
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/RcppExports.R | 2 +- build/partial.rdb |binary inst/NEWS | 10 ++++++++++ man/pbvnorm.Rd | 4 ++-- src/RcppExports.cpp | 2 +- src/pbv_rcpp_bvnorm.cpp | 4 ++-- 8 files changed, 27 insertions(+), 17 deletions(-)
Title: Forecastable Component Analysis
Description: Implementation of Forecastable Component Analysis ('ForeCA'),
including main algorithms and auxiliary function (summary, plotting, etc.) to
apply 'ForeCA' to multivariate time series data. 'ForeCA' is a novel dimension
reduction (DR) technique for temporally dependent signals. Contrary to other
popular DR methods, such as 'PCA' or 'ICA', 'ForeCA' takes time dependency
explicitly into account and searches for the most ''forecastable'' signal.
The measure of forecastability is based on the Shannon entropy of the spectral
density of the transformed signal.
Author: Georg M. Goerg [aut, cre]
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between ForeCA versions 0.2.4 dated 2016-03-30 and 0.2.6 dated 2020-05-11
ForeCA-0.2.4/ForeCA/NEWS |only ForeCA-0.2.6/ForeCA/DESCRIPTION | 28 - ForeCA-0.2.6/ForeCA/MD5 | 81 +-- ForeCA-0.2.6/ForeCA/NEWS.md |only ForeCA-0.2.6/ForeCA/R/ForeCA-package.R | 30 - ForeCA-0.2.6/ForeCA/R/Omega.R | 74 +-- ForeCA-0.2.6/ForeCA/R/discrete_entropy.R | 68 +- ForeCA-0.2.6/ForeCA/R/foreca.EM.one_weightvector.R | 78 +-- ForeCA-0.2.6/ForeCA/R/foreca.R | 238 +++++----- ForeCA-0.2.6/ForeCA/R/whiten.R | 112 ++-- ForeCA-0.2.6/ForeCA/build |only ForeCA-0.2.6/ForeCA/inst/doc |only ForeCA-0.2.6/ForeCA/man/ForeCA-package.Rd | 25 - ForeCA-0.2.6/ForeCA/man/Omega.Rd | 37 - ForeCA-0.2.6/ForeCA/man/common-arguments.Rd | 1 ForeCA-0.2.6/ForeCA/man/complete-controls.Rd | 24 - ForeCA-0.2.6/ForeCA/man/continuous_entropy.Rd | 1 ForeCA-0.2.6/ForeCA/man/discrete_entropy.Rd | 36 - ForeCA-0.2.6/ForeCA/man/foreca-utils.Rd | 7 ForeCA-0.2.6/ForeCA/man/foreca.EM-aux.Rd | 23 ForeCA-0.2.6/ForeCA/man/foreca.EM.one_weightvector.Rd | 29 - ForeCA-0.2.6/ForeCA/man/foreca.Rd | 94 ++- ForeCA-0.2.6/ForeCA/man/foreca.one_weightvector-utils.Rd | 6 ForeCA-0.2.6/ForeCA/man/initialize_weightvector.Rd | 13 ForeCA-0.2.6/ForeCA/man/mvspectrum-utils.Rd | 1 ForeCA-0.2.6/ForeCA/man/mvspectrum.Rd | 28 - ForeCA-0.2.6/ForeCA/man/mvspectrum2wcov.Rd | 9 ForeCA-0.2.6/ForeCA/man/quadratic_form.Rd | 3 ForeCA-0.2.6/ForeCA/man/sfa.Rd | 1 ForeCA-0.2.6/ForeCA/man/spectral_entropy.Rd | 10 ForeCA-0.2.6/ForeCA/man/whiten.Rd | 51 +- ForeCA-0.2.6/ForeCA/tests/testthat/test_Omega.R | 50 +- ForeCA-0.2.6/ForeCA/tests/testthat/test_discrete_entropy.R | 8 ForeCA-0.2.6/ForeCA/tests/testthat/test_foreca-utils.R | 20 ForeCA-0.2.6/ForeCA/tests/testthat/test_foreca.EM-aux.R | 20 ForeCA-0.2.6/ForeCA/tests/testthat/test_foreca.R | 7 ForeCA-0.2.6/ForeCA/tests/testthat/test_initialize_weightvector.R | 9 ForeCA-0.2.6/ForeCA/tests/testthat/test_mvspectrum.R | 24 - ForeCA-0.2.6/ForeCA/tests/testthat/test_mvspectrum2wcov.R | 18 ForeCA-0.2.6/ForeCA/tests/testthat/test_quadratic_form.R | 3 ForeCA-0.2.6/ForeCA/tests/testthat/test_spectral_entropy.R | 34 - ForeCA-0.2.6/ForeCA/tests/testthat/test_whiten.R | 2 ForeCA-0.2.6/ForeCA/vignettes |only 43 files changed, 662 insertions(+), 641 deletions(-)
Title: Flexible Bayes Factor Testing of Scientific Expectations
Description: Implementation of various default Bayes factors
for testing statistical hypotheses. The package is
intended for applied quantitative researchers in the
social and behavioral sciences, medical research,
and related fields. The Bayes factor tests can be
executed for statistical models such as
univariate and multivariate normal linear models,
generalized linear models, special cases of
linear mixed models, survival models, relational
event models. Parameters that can be tested are
location parameters (e.g., regression coefficients),
variances (e.g., group variances), and measures of
association (e.g,. bivariate correlations).
The statistical underpinnings are
described in
Mulder, Hoijtink, and Xin (2019) <arXiv:1904.00679>,
Mulder and Gelissen (2019) <arXiv:1807.05819>,
Mulder (2016) <DOI:10.1016/j.jmp.2014.09.004>,
Mulder and Fox (2019) <DOI:10.1214/18-BA1115>,
Mulder and Fox (2013) <DOI:10.1007/s11222-011-9295-3>,
Boeing-Messing, van Assen, Hofman, Hoijtink, and Mulder <DOI:10.1037/met0000116>,
Hoijtink, Mulder, van Lissa, and Gu, (2018) <DOI:10.31234/osf.io/v3shc>,
Gu, Mulder, and Hoijtink, (2018) <DOI:10.1111/bmsp.12110>,
Hoijtink, Gu, and Mulder, (2018) <DOI:10.1111/bmsp.12145>, and
Hoijtink, Gu, Mulder, and Rosseel, (2018) <DOI:10.1037/met0000187>.
Author: Joris Mulder [aut, cre],
Caspar van Lissa [aut, ctb],
Xin Gu [aut],
Anton Olsson-Collentine [aut, ctb],
Florian Boeing-Messing [aut, ctb],
Donald R. Williams [aut, ctb],
Jean-Paul Fox [aut, ctb],
Janosch Menke [ctb],
Barry Brown [ctb],
James Lovato [ctb],
Kathy Russell [ctb],
Lapack 3.8 [ctb],
Jack Dongarra [ctb],
Jim Bunch [ctb],
Cleve Moler [ctb],
Gilbert Stewart [ctb],
John Burkandt [ctb],
Ashwith Rego [ctb],
Alexander Godunov [ctb],
Alan Miller [ctb],
Jean-Pierre Moreau [ctb],
The R Core Team [cph]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between BFpack versions 0.1.1 dated 2020-02-19 and 0.2.1 dated 2020-05-11
DESCRIPTION | 8 MD5 | 64 - NAMESPACE | 9 NEWS.md | 9 R/BF.coxph.R | 54 - R/BF.default.R | 19 R/BF.lm.R | 639 ++++---------- R/BF.print.R | 189 +--- R/BF_cortest.R |only R/BF_methods.R | 32 R/BFhetcor.R | 2 R/BFicc.R | 774 ++++++----------- R/BFttest.R | 502 +++++------ R/BFvar.R | 22 R/actors.R |only R/get_estimates_unique_to_BFpack.R | 141 +-- R/relevents.R |only R/same_building.R |only R/same_division.R |only R/same_hierarchy.R |only README.md | 2 data/actors.csv |only data/datalist | 5 data/relevents.csv |only data/same_building.csv |only data/same_division.csv |only data/same_hierarchy.csv |only man/BF.Rd | 33 man/actors.Rd |only man/cor_test.Rd |only man/relevents.Rd |only man/same_building.Rd |only man/same_division.Rd |only man/same_hierarchy.Rd |only tests/testthat/test_BFcortest.R |only tests/testthat/test_BFcoxph2.R | 62 - tests/testthat/test_BFmlm.R | 45 tests/testthat/test_BFregression.R | 90 + tests/testthat/test_application6_BF.mlm_correlations.R | 42 tests/testthat/test_application7_BF.lmerMod.R | 4 tests/testthat/test_ttest.R | 135 +- tests/testthat/test_variances.R | 42 42 files changed, 1263 insertions(+), 1661 deletions(-)
Title: Subtests Using Algorithmic Rummaging Techniques
Description: Construct subtests from a pool of items by using ant-colony-optimization, genetic algorithms, brute force, or random sampling.
Schultze (2017) <doi:10.17169/refubium-622>.
Author: Martin Schultze [aut, cre],
Johanna Schüller [ctb]
Maintainer: Martin Schultze <schultze@psych.uni-frankfurt.de>
Diff between stuart versions 0.8.0 dated 2019-08-05 and 0.9.0 dated 2020-05-11
DESCRIPTION | 18 + MD5 | 65 +++--- R/bf.cycle.R | 29 ++ R/bruteforce.R | 12 - R/combinations.R | 2 R/compute.comparisons.R |only R/crossvalidate.Mplus.R | 25 ++ R/crossvalidate.lavaan.R | 28 +- R/data.prep.R | 71 +++++-- R/fitness.R | 13 - R/gene.R | 65 ++++-- R/heuristics.R | 7 R/holdout.R | 6 R/invariance.implementation.R | 25 -- R/mmas.R | 9 R/objective.preset.R | 19 + R/randomsamples.R | 12 - R/run.Mplus.R | 39 ++- R/run.lavaan.R | 46 ++-- R/sanitycheck.R | 15 + R/software.check.R | 4 R/stuart.bruteforce.R | 5 R/stuart.gene.R | 414 ++++++++++++++++++++++++++++++++++++------ R/stuart.mmas.R | 8 R/stuart.randomsamples.R | 5 man/bruteforce.Rd | 38 +++ man/combinations.Rd | 11 - man/fairplayer.Rd | 4 man/gene.Rd | 100 ++++++++-- man/heuristics.Rd | 13 + man/mmas.Rd | 52 ++++- man/randomsamples.Rd | 42 +++- man/stuart-package.Rd | 5 man/sups.Rd | 4 34 files changed, 917 insertions(+), 294 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Namita Gupta [aut],
Susanna Marquez [aut],
Julian Zhou [aut],
Nima Nouri [aut],
Ang Cui [ctb],
Jason Vander Heiden [aut, cre],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Diff between shazam versions 0.2.3 dated 2020-02-06 and 1.0.0 dated 2020-05-11
DESCRIPTION | 49 ++-- MD5 | 184 ++++++++-------- NAMESPACE | 6 NEWS.md | 53 ++++ R/Baseline.R | 272 ++++++++++++------------ R/Core.R | 2 R/DistToNearest.R | 124 ++++++----- R/MutationDefinitions.R | 2 R/MutationProfiling.R | 338 +++++++++++++++--------------- R/RegionDefinitions.R | 46 ++-- R/Shazam.R | 18 + R/Shmulate.R | 97 +++++--- R/TargetingModels.R | 386 +++++++++++++++++++++++++---------- R/sysdata.rda |binary build/vignette.rds |binary data/CHARGE_MUTATIONS.rda |binary data/HH_S5F.rda |binary data/HKL_S5F.rda |binary data/HYDROPATHY_MUTATIONS.rda |binary data/IMGT_V.rda |binary data/IMGT_V_BY_CODONS.rda |binary data/IMGT_V_BY_REGIONS.rda |binary data/IMGT_V_BY_SEGMENTS.rda |binary data/MK_RS5NF.rda |binary data/POLARITY_MUTATIONS.rda |binary data/VOLUME_MUTATIONS.rda |binary inst/doc/Baseline-Vignette.R | 60 ++--- inst/doc/Baseline-Vignette.Rmd | 92 ++++---- inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.R | 55 ++-- inst/doc/DistToNearest-Vignette.Rmd | 136 ++++++++---- inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Mutation-Vignette.R | 46 ++-- inst/doc/Mutation-Vignette.Rmd | 64 ++--- inst/doc/Mutation-Vignette.pdf |binary inst/doc/Shmulate-Vignette.R | 9 inst/doc/Shmulate-Vignette.Rmd | 11 inst/doc/Shmulate-Vignette.pdf |binary inst/doc/Targeting-Vignette.R | 43 ++- inst/doc/Targeting-Vignette.Rmd | 91 +++++--- inst/doc/Targeting-Vignette.pdf |binary man/Baseline-class.Rd | 6 man/HH_S1F.Rd | 6 man/HH_S5F.Rd | 4 man/HKL_S1F.Rd | 6 man/HKL_S5F.Rd | 4 man/IMGT_SCHEMES.Rd | 6 man/MK_RS1NF.Rd | 6 man/MK_RS5NF.Rd | 4 man/MUTATION_SCHEMES.Rd | 6 man/MutabilityModel-class.Rd |only man/RegionDefinition-class.Rd | 4 man/TargetingMatrix-class.Rd |only man/TargetingModel-class.Rd | 6 man/U5N.Rd | 4 man/calcBaseline.Rd | 17 - man/calcExpectedMutations.Rd | 18 - man/calcObservedMutations.Rd | 32 +- man/calculateMutability.Rd | 4 man/collapseClones.Rd | 55 +++- man/consensusSequence.Rd | 11 man/createBaseline.Rd | 6 man/createMutabilityMatrix.Rd | 53 ++-- man/createSubstitutionMatrix.Rd | 26 +- man/createTargetingMatrix.Rd | 20 + man/createTargetingModel.Rd | 28 +- man/distToNearest.Rd | 36 +-- man/editBaseline.Rd | 8 man/expectedMutations.Rd | 22 - man/extendMutabilityMatrix.Rd | 27 +- man/extendSubstitutionMatrix.Rd | 6 man/findThreshold.Rd | 13 - man/groupBaseline.Rd | 27 +- man/minNumMutationsTune.Rd | 7 man/minNumSeqMutationsTune.Rd | 12 - man/observedMutations.Rd | 34 +-- man/plotBaselineDensity.Rd | 21 - man/plotBaselineSummary.Rd | 21 - man/plotDensityThreshold.Rd | 7 man/plotGmmThreshold.Rd | 9 man/plotTune.Rd | 14 - man/shazam.Rd | 4 man/shmulateSeq.Rd | 20 + man/shmulateTree.Rd | 8 man/slideWindowDb.Rd | 8 man/slideWindowSeq.Rd | 4 man/slideWindowTune.Rd | 8 man/summarizeBaseline.Rd | 13 - man/testBaseline.Rd | 25 +- vignettes/Baseline-Vignette.Rmd | 92 ++++---- vignettes/DistToNearest-Vignette.Rmd | 136 ++++++++---- vignettes/Mutation-Vignette.Rmd | 64 ++--- vignettes/Shmulate-Vignette.Rmd | 11 vignettes/Targeting-Vignette.Rmd | 91 +++++--- 94 files changed, 1964 insertions(+), 1300 deletions(-)
Title: Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
Description: Renders vector-based svg images into high-quality custom-size bitmap
arrays using 'librsvg2'. The resulting bitmap can be written to e.g. png, jpeg
or webp format. In addition, the package can convert images directly to various
formats such as pdf or postscript.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between rsvg versions 1.3 dated 2018-05-10 and 2.0 dated 2020-05-11
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS | 4 ++++ R/rsvg.R | 19 +++++++++++-------- cleanup | 2 +- configure | 21 +++++++++++---------- man/rsvg.Rd | 28 +++++++++++++++------------- src/Makevars.win | 16 +++++++--------- 8 files changed, 61 insertions(+), 53 deletions(-)
Title: Phylogenetic Clustering (Phyloclustering)
Description: Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) provides a
convenient implementation of phyloclustering for DNA and SNP data,
capable of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It is
designed in C for performance, interfaced with R for visualization,
and incorporates other popular open source programs including
ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>,
seq-gen (Rambaut and Grassly 1997)
<doi:10.1093/bioinformatics/13.3.235>,
Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and
PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>,
<doi:10.1093/molbev/msm088>,
for simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.
Author: Wei-Chen Chen [aut, cre],
Karin Dorman [aut],
Yan-Han Chen [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between phyclust versions 0.1-28 dated 2019-12-08 and 0.1-29 dated 2020-05-11
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/paml_baseml/tools.c | 5 +++++ 4 files changed, 16 insertions(+), 7 deletions(-)
Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006,
2014). Includes a function for conveniently defining differential equation
models, model solution based on eigenvalues if possible or using numerical
solvers. If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using automatically generated C functions. Please
note that no warranty is implied for correctness of results or fitness for a
particular purpose.
Author: Johannes Ranke [aut, cre, cph]
(<https://orcid.org/0000-0003-4371-6538>),
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9.49.11 dated 2020-04-20 and 0.9.50.1 dated 2020-05-11
mkin-0.9.49.11/mkin/R/DFOP.solution.R |only mkin-0.9.49.11/mkin/R/FOMC.solution.R |only mkin-0.9.49.11/mkin/R/HS.solution.R |only mkin-0.9.49.11/mkin/R/IORE.solution.R |only mkin-0.9.49.11/mkin/R/SFO.solution.R |only mkin-0.9.49.11/mkin/R/SFORB.solution.R |only mkin-0.9.49.11/mkin/R/logistic.solution.R |only mkin-0.9.50.1/mkin/DESCRIPTION | 8 mkin-0.9.50.1/mkin/MD5 | 137 ++--- mkin-0.9.50.1/mkin/NEWS.md | 10 mkin-0.9.50.1/mkin/R/add_err.R | 2 mkin-0.9.50.1/mkin/R/create_deg_func.R |only mkin-0.9.50.1/mkin/R/mkin_wide_to_long.R | 1 mkin-0.9.50.1/mkin/R/mkinerrmin.R | 28 - mkin-0.9.50.1/mkin/R/mkinfit.R | 104 +--- mkin-0.9.50.1/mkin/R/mkinmod.R | 66 +- mkin-0.9.50.1/mkin/R/mkinpredict.R | 207 +++----- mkin-0.9.50.1/mkin/R/nlme.R | 6 mkin-0.9.50.1/mkin/R/parent_solutions.R |only mkin-0.9.50.1/mkin/R/plot.mkinfit.R | 2 mkin-0.9.50.1/mkin/README.md | 2 mkin-0.9.50.1/mkin/build/vignette.rds |binary mkin-0.9.50.1/mkin/inst/doc/FOCUS_D.html | 116 ++-- mkin-0.9.50.1/mkin/inst/doc/FOCUS_L.html | 109 ++-- mkin-0.9.50.1/mkin/inst/doc/mkin.html | 6 mkin-0.9.50.1/mkin/inst/doc/twa.html | 4 mkin-0.9.50.1/mkin/man/DFOP.solution.Rd | 21 mkin-0.9.50.1/mkin/man/FOMC.solution.Rd | 22 mkin-0.9.50.1/mkin/man/HS.solution.Rd | 21 mkin-0.9.50.1/mkin/man/IORE.solution.Rd | 17 mkin-0.9.50.1/mkin/man/SFO.solution.Rd | 23 mkin-0.9.50.1/mkin/man/SFORB.solution.Rd | 21 mkin-0.9.50.1/mkin/man/create_deg_func.Rd |only mkin-0.9.50.1/mkin/man/logistic.solution.Rd | 21 mkin-0.9.50.1/mkin/man/mkinds.Rd | 2 mkin-0.9.50.1/mkin/man/mkinfit.Rd | 14 mkin-0.9.50.1/mkin/man/mkinmod.Rd | 8 mkin-0.9.50.1/mkin/man/mkinpredict.Rd | 114 ++-- mkin-0.9.50.1/mkin/man/nlme.Rd | 6 mkin-0.9.50.1/mkin/man/plot.mkinfit.Rd | 1 mkin-0.9.50.1/mkin/tests/figs/plotting/plot-err-for-focus-d.svg | 86 +-- mkin-0.9.50.1/mkin/tests/figs/plotting/plot-errmod-with-focus-d-obs-eigen.svg | 88 +-- mkin-0.9.50.1/mkin/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg | 186 +++---- mkin-0.9.50.1/mkin/tests/figs/plotting/plot-errmod-with-sfo-lin-a-tc.svg | 182 +++---- mkin-0.9.50.1/mkin/tests/figs/plotting/plot-res-for-focus-d.svg | 86 +-- mkin-0.9.50.1/mkin/tests/testthat/DFOP_FOCUS_C_messages.txt | 240 ++++----- mkin-0.9.50.1/mkin/tests/testthat/FOCUS_2006_D.csf | 2 mkin-0.9.50.1/mkin/tests/testthat/SFO_SFO_printed.txt | 6 mkin-0.9.50.1/mkin/tests/testthat/setup_script.R | 28 - mkin-0.9.50.1/mkin/tests/testthat/slow/test_parent_only.R | 18 mkin-0.9.50.1/mkin/tests/testthat/slow/test_roundtrip_error_parameters.R | 18 mkin-0.9.50.1/mkin/tests/testthat/summary_DFOP_FOCUS_C.txt | 7 mkin-0.9.50.1/mkin/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt | 7 mkin-0.9.50.1/mkin/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt | 83 +-- mkin-0.9.50.1/mkin/tests/testthat/test_CAKE_export.R | 18 mkin-0.9.50.1/mkin/tests/testthat/test_FOCUS_D_UBA_expertise.R | 39 - mkin-0.9.50.1/mkin/tests/testthat/test_FOCUS_chi2_error_level.R | 18 mkin-0.9.50.1/mkin/tests/testthat/test_SFORB.R | 40 - mkin-0.9.50.1/mkin/tests/testthat/test_analytical.R |only mkin-0.9.50.1/mkin/tests/testthat/test_error_models.R | 18 mkin-0.9.50.1/mkin/tests/testthat/test_from_max_mean.R | 34 - mkin-0.9.50.1/mkin/tests/testthat/test_logistic.R | 18 mkin-0.9.50.1/mkin/tests/testthat/test_mkinds.R | 18 mkin-0.9.50.1/mkin/tests/testthat/test_mkinfit_errors.R | 31 - mkin-0.9.50.1/mkin/tests/testthat/test_mkinmod.R | 22 mkin-0.9.50.1/mkin/tests/testthat/test_mkinpredict_SFO_SFO.R | 46 - mkin-0.9.50.1/mkin/tests/testthat/test_nafta.R | 20 mkin-0.9.50.1/mkin/tests/testthat/test_nlme.R | 12 mkin-0.9.50.1/mkin/tests/testthat/test_plots_summary_twa.R | 29 - mkin-0.9.50.1/mkin/tests/testthat/test_schaefer07_complex_case.R | 18 mkin-0.9.50.1/mkin/tests/testthat/test_summary_old_objects.R | 18 mkin-0.9.50.1/mkin/tests/testthat/test_synthetic_data_for_UBA_2014.R | 18 mkin-0.9.50.1/mkin/tests/testthat/test_tests.R | 2 mkin-0.9.50.1/mkin/vignettes/web_only/benchmarks.Rmd | 14 mkin-0.9.50.1/mkin/vignettes/web_only/benchmarks.html | 243 ++++------ 75 files changed, 1314 insertions(+), 1498 deletions(-)
Title: Meta-Analysis of Generalized Additive Models
Description: Meta-analysis of generalized additive
models and generalized additive mixed models. A typical use case is
when data cannot be shared across locations, and an overall meta-analytic
fit is sought. 'metagam' provides functionality for removing individual
participant data from models computed using the 'mgcv' and 'gamm4' packages such
that the model objects can be shared without exposing individual data.
Furthermore, methods for meta-analysing these fits are provided. The implemented
methods are described in Sorensen et al. (2020), <arXiv:2002.02627>,
extending previous works by Schwartz and Zanobetti (2000)
and Crippa et al. (2018) <doi:10.6000/1929-6029.2018.07.02.1>.
Author: Oystein Sorensen [aut, cre] (<https://orcid.org/0000-0003-0724-3542>),
Andreas M. Brandmaier [aut] (<https://orcid.org/0000-0001-8765-6982>),
Athanasia Mo Mowinckel [aut] (<https://orcid.org/0000-0002-5756-0223>)
Maintainer: Oystein Sorensen <oystein.sorensen@psykologi.uio.no>
Diff between metagam versions 0.1.0 dated 2020-02-20 and 0.1.1 dated 2020-05-11
DESCRIPTION | 12 MD5 | 75 +- NAMESPACE | 66 +- R/metagam.R | 408 +++++++-------- R/metagam_package.R | 40 - R/plot_dominance.R | 150 ++--- R/plot_heterogeneity.R | 274 +++++----- R/plot_metagam.R | 150 ++--- R/print_metagam.R | 106 ++-- R/strip_rawdata.R | 296 +++++------ R/summary_metagam.R | 102 +-- R/summary_strip_rawdata.R | 58 +- R/utils-tidy-eval.R | 94 +-- README.md | 312 ++++++----- build/vignette.rds |binary inst/REFERENCES.bib | 133 ++--- inst/doc/dominance.R | 76 +- inst/doc/dominance.Rmd | 162 +++--- inst/doc/dominance.html | 704 +++++++++++++------------- inst/doc/heterogeneity.R | 90 +-- inst/doc/heterogeneity.Rmd | 192 +++---- inst/doc/heterogeneity.html | 748 ++++++++++++++-------------- inst/doc/introduction.R | 102 +-- inst/doc/introduction.Rmd | 206 +++---- inst/doc/introduction.html | 834 +++++++++++++++---------------- inst/doc/multivariate.R | 92 +-- inst/doc/multivariate.Rmd | 198 +++---- inst/doc/multivariate.html | 952 ++++++++++++++++++------------------ inst/examples/metagam_examples.R | 52 - man/figures |only man/print.metagam.Rd | 2 man/print.striprawdata.Rd | 2 tests/testthat.R | 8 tests/testthat/test-metagam.R | 232 ++++---- tests/testthat/test-strip_rawdata.R | 160 +++--- vignettes/dominance.Rmd | 162 +++--- vignettes/heterogeneity.Rmd | 192 +++---- vignettes/introduction.Rmd | 206 +++---- vignettes/multivariate.Rmd | 198 +++---- 39 files changed, 3925 insertions(+), 3921 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented wing2015 for lassnags),
Bourdon Jean-François [ctb] (Implemented sensor_tracking)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 2.2.4 dated 2020-04-23 and 2.2.5 dated 2020-05-11
DESCRIPTION | 8 MD5 | 14 NEWS.md | 6 R/plot.r | 2 R/utils_threads.r | 3 inst/doc/lidR-computation-speed-LAScatalog.html | 2 tests/testthat/Rplots.pdf |binary vignettes/lidR-LAScatalog-engine.html | 415 +++++++++++------------- 8 files changed, 213 insertions(+), 237 deletions(-)
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut],
David Tschumperle [ctb],
Jan Wijffels [ctb],
Haz Edine Assemlal [ctb],
Shota Ochi [cre]
Maintainer: Shota Ochi <shotaochi1990@gmail.com>
Diff between imager versions 0.42.1 dated 2020-02-17 and 0.42.3 dated 2020-05-11
DESCRIPTION | 8 MD5 | 17 build/vignette.rds |binary inst/doc/gettingstarted.html | 34 inst/doc/pixsets.html | 2 inst/include/CImg.h | 2539 ++++++++++++++++++++++----------- inst/include/NOTE_CImg |only man/boats.Rd | 4 src/hough.cpp | 2 tests/testthat/test_load_save_videos.R | 2 10 files changed, 1740 insertions(+), 868 deletions(-)
Title: Design and Analysis for Factorial Experiments
Description: Provides design-based and model-based estimators for the population average marginal component effects in general factorial experiments, including conjoint analysis. The package also implements a series of recommendations offered in de la Cuesta, Egami, and Imai (2019+), and Egami and Imai (2019) <doi:10.1080/01621459.2018.1476246>.
Author: Naoki Egami, Brandon de la Cuesta, Kosuke Imai
Maintainer: Naoki Egami <naoki.egami5@gmail.com>
Diff between factorEx versions 1.0.0 dated 2019-10-01 and 1.0.1 dated 2020-05-11
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/AME_estimate.R | 3 ++- R/model_pAMCE.R | 2 +- man/design_pAMCE.Rd | 15 ++++++++++++--- man/model_pAMCE.Rd | 24 +++++++++++++++++++----- man/plot.pAMCE.Rd | 14 +++++++++++--- man/plot_diagnose.Rd | 10 ++++++++-- man/summary.pAMCE.Rd | 3 +-- man/weights_pAMCE.Rd | 13 +++++++++++-- 10 files changed, 78 insertions(+), 32 deletions(-)
Title: Create Pivot Tables
Description: Create regular pivot tables with just a few lines of R.
More complex pivot tables can also be created, e.g. pivot tables
with irregular layouts, multiple calculations and/or derived
calculations based on multiple data frames. Pivot tables are
constructed using R only and can be written to a range of
output formats (plain text, 'HTML', 'Latex' and 'Excel'),
including with styling/formatting.
Author: Christopher Bailiss [aut, cre]
Maintainer: Christopher Bailiss <cbailiss@gmail.com>
Diff between pivottabler versions 1.3.1 dated 2020-04-01 and 1.4.0 dated 2020-05-11
pivottabler-1.3.1/pivottabler/R/PivotThemes.R |only pivottabler-1.3.1/pivottabler/README.md |only pivottabler-1.3.1/pivottabler/data/datalist |only pivottabler-1.4.0/pivottabler/DESCRIPTION | 8 pivottabler-1.4.0/pivottabler/MD5 | 199 pivottabler-1.4.0/pivottabler/NAMESPACE | 2 pivottabler-1.4.0/pivottabler/NEWS.md | 59 pivottabler-1.4.0/pivottabler/R/PivotBatch.R | 122 pivottabler-1.4.0/pivottabler/R/PivotBatchCalculator.R | 141 pivottabler-1.4.0/pivottabler/R/PivotBatchStatistics.R | 56 pivottabler-1.4.0/pivottabler/R/PivotCalculation.R | 191 pivottabler-1.4.0/pivottabler/R/PivotCalculationGroup.R | 171 pivottabler-1.4.0/pivottabler/R/PivotCalculationGroups.R | 98 pivottabler-1.4.0/pivottabler/R/PivotCalculator.R | 482 + pivottabler-1.4.0/pivottabler/R/PivotCell.R | 157 pivottabler-1.4.0/pivottabler/R/PivotCells.R | 413 + pivottabler-1.4.0/pivottabler/R/PivotData.R | 178 pivottabler-1.4.0/pivottabler/R/PivotDataGroup.R | 1369 +++- pivottabler-1.4.0/pivottabler/R/PivotFilter.R | 113 pivottabler-1.4.0/pivottabler/R/PivotFilterOverrides.R | 154 pivottabler-1.4.0/pivottabler/R/PivotFilters.R | 241 pivottabler-1.4.0/pivottabler/R/PivotHtmlRenderer.R | 84 pivottabler-1.4.0/pivottabler/R/PivotLatexRenderer.R | 72 pivottabler-1.4.0/pivottabler/R/PivotOpenXlsxRenderer.R | 95 pivottabler-1.4.0/pivottabler/R/PivotOpenXlsxStyle.R | 247 pivottabler-1.4.0/pivottabler/R/PivotOpenXlsxStyles.R | 110 pivottabler-1.4.0/pivottabler/R/PivotStyle.R | 98 pivottabler-1.4.0/pivottabler/R/PivotStyles.R | 164 pivottabler-1.4.0/pivottabler/R/PivotTable.R | 2109 +++++- pivottabler-1.4.0/pivottabler/R/pivotThemes.R |only pivottabler-1.4.0/pivottabler/R/utilities.R | 89 pivottabler-1.4.0/pivottabler/build/vignette.rds |binary pivottabler-1.4.0/pivottabler/inst/doc/v00-vignettes.Rmd | 4 pivottabler-1.4.0/pivottabler/inst/doc/v00-vignettes.html | 13 pivottabler-1.4.0/pivottabler/man/PivotBatch.Rd | 305 pivottabler-1.4.0/pivottabler/man/PivotBatchCalculator.Rd | 350 - pivottabler-1.4.0/pivottabler/man/PivotBatchStatistics.Rd | 201 pivottabler-1.4.0/pivottabler/man/PivotCalculation.Rd | 345 - pivottabler-1.4.0/pivottabler/man/PivotCalculationGroup.Rd | 365 - pivottabler-1.4.0/pivottabler/man/PivotCalculationGroups.Rd | 258 pivottabler-1.4.0/pivottabler/man/PivotCalculator.Rd | 998 ++ pivottabler-1.4.0/pivottabler/man/PivotCell.Rd | 321 pivottabler-1.4.0/pivottabler/man/PivotCells.Rd | 645 + pivottabler-1.4.0/pivottabler/man/PivotData.Rd | 297 pivottabler-1.4.0/pivottabler/man/PivotDataGroup.Rd | 1438 +++- pivottabler-1.4.0/pivottabler/man/PivotFilter.Rd | 296 pivottabler-1.4.0/pivottabler/man/PivotFilterOverrides.Rd | 361 - pivottabler-1.4.0/pivottabler/man/PivotFilters.Rd | 527 + pivottabler-1.4.0/pivottabler/man/PivotHtmlRenderer.Rd | 186 pivottabler-1.4.0/pivottabler/man/PivotLatexRenderer.Rd | 211 pivottabler-1.4.0/pivottabler/man/PivotOpenXlsxRenderer.Rd | 246 pivottabler-1.4.0/pivottabler/man/PivotOpenXlsxStyle.Rd | 525 + pivottabler-1.4.0/pivottabler/man/PivotOpenXlsxStyles.Rd | 279 pivottabler-1.4.0/pivottabler/man/PivotStyle.Rd | 295 pivottabler-1.4.0/pivottabler/man/PivotStyles.Rd | 413 - pivottabler-1.4.0/pivottabler/man/PivotTable.Rd | 3358 +++++++++- pivottabler-1.4.0/pivottabler/man/bhmtraindisruption.Rd | 76 pivottabler-1.4.0/pivottabler/man/bhmtrains.Rd | 86 pivottabler-1.4.0/pivottabler/man/checkArgument.Rd | 148 pivottabler-1.4.0/pivottabler/man/cleanOutlineArg.Rd |only pivottabler-1.4.0/pivottabler/man/convertPvtTblToBasicTbl.Rd | 60 pivottabler-1.4.0/pivottabler/man/exportValueAs.Rd | 56 pivottabler-1.4.0/pivottabler/man/getBlankTheme.Rd | 36 pivottabler-1.4.0/pivottabler/man/getCompactTheme.Rd | 36 pivottabler-1.4.0/pivottabler/man/getDefaultTheme.Rd | 36 pivottabler-1.4.0/pivottabler/man/getLargePlainTheme.Rd | 36 pivottabler-1.4.0/pivottabler/man/getPvtStyleDeclarations.Rd | 34 pivottabler-1.4.0/pivottabler/man/getSimpleColoredTheme.Rd | 55 pivottabler-1.4.0/pivottabler/man/getStandardTableTheme.Rd | 38 pivottabler-1.4.0/pivottabler/man/getTheme.Rd | 36 pivottabler-1.4.0/pivottabler/man/isNumericValue.Rd | 34 pivottabler-1.4.0/pivottabler/man/isTextValue.Rd | 34 pivottabler-1.4.0/pivottabler/man/oneToNULL.Rd | 40 pivottabler-1.4.0/pivottabler/man/pivottabler.Rd | 100 pivottabler-1.4.0/pivottabler/man/pvtperfresults.Rd | 58 pivottabler-1.4.0/pivottabler/man/pvtperfsummary.Rd | 72 pivottabler-1.4.0/pivottabler/man/qhpvt.Rd | 140 pivottabler-1.4.0/pivottabler/man/qlpvt.Rd | 74 pivottabler-1.4.0/pivottabler/man/qpvt.Rd | 132 pivottabler-1.4.0/pivottabler/man/renderBasicTable.Rd | 50 pivottabler-1.4.0/pivottabler/man/trainstations.Rd | 58 pivottabler-1.4.0/pivottabler/tests/testthat/test-02-smokeTests.R | 6 pivottabler-1.4.0/pivottabler/tests/testthat/test-04-quickPivotTests.R | 12 pivottabler-1.4.0/pivottabler/tests/testthat/test-06-dataGroupTests.R | 427 + pivottabler-1.4.0/pivottabler/tests/testthat/test-07-calculationTests.R | 138 pivottabler-1.4.0/pivottabler/tests/testthat/test-08-visualTotalTests.R | 2 pivottabler-1.4.0/pivottabler/tests/testthat/test-11-emptyGroupTests.R | 8 pivottabler-1.4.0/pivottabler/tests/testthat/test-12-exportTests.R | 20 pivottabler-1.4.0/pivottabler/tests/testthat/test-14-exportOptionsTests.R | 2 pivottabler-1.4.0/pivottabler/tests/testthat/test-15-findGrouptests.R | 156 pivottabler-1.4.0/pivottabler/tests/testthat/test-16-getCellsTests.R | 39 pivottabler-1.4.0/pivottabler/tests/testthat/test-17-findCellstests.R | 10 pivottabler-1.4.0/pivottabler/tests/testthat/test-18-irregularLayoutTests.R | 8 pivottabler-1.4.0/pivottabler/tests/testthat/test-20-dataGroupFormatting.R | 6 pivottabler-1.4.0/pivottabler/tests/testthat/test-21-alternativeLayouts.R | 16 pivottabler-1.4.0/pivottabler/tests/testthat/test-22-basicRowGroupHeaderLayouts.R | 4 pivottabler-1.4.0/pivottabler/tests/testthat/test-23-outlineLayouts.R | 198 pivottabler-1.4.0/pivottabler/tests/testthat/test-24-exportTests2.R | 6 pivottabler-1.4.0/pivottabler/tests/testthat/test-25-pivotRowColumns.R |only pivottabler-1.4.0/pivottabler/vignettes/data-group-hierarchy1.png |only pivottabler-1.4.0/pivottabler/vignettes/data-group-hierarchy2.png |only pivottabler-1.4.0/pivottabler/vignettes/intro-32.png |only pivottabler-1.4.0/pivottabler/vignettes/layout1.png |binary pivottabler-1.4.0/pivottabler/vignettes/layout3.png |only pivottabler-1.4.0/pivottabler/vignettes/layout4.png |only pivottabler-1.4.0/pivottabler/vignettes/v00-vignettes.Rmd | 4 106 files changed, 17815 insertions(+), 4231 deletions(-)
Title: Generalized Pathmox Approach Segmentation Tree Analysis
Description: Provides a very interesting solution for
handling segmentation variables in complex statistical methodology. It
contains en extended version of the "Pathmox" algorithm (Lamberti, Sanchez
and Aluja,(2016)<doi:10.1002/asmb.2168>) in the context of
Partial Least Squares Path Modeling including the F-block
test (to detect the responsible latent endogenous equations of the
difference), the F-coefficient (to detect the path coefficients responsible
of the difference) and the "invariance" test (to realize a comparison
between the sub-models' latent variables). Furthermore, the package
contains a generalized version of the "Pathmox" algorithm to approach
different methodologies: linear regression and least absolute regression
models.
Author: Giuseppe Lamberti [aut, cre]
Maintainer: Giuseppe Lamberti <giuseppelamb@hotmail.com>
Diff between genpathmox versions 0.3 dated 2017-05-31 and 0.4 dated 2020-05-11
genpathmox-0.3/genpathmox/R/plot_plot.treemodel.R |only genpathmox-0.3/genpathmox/R/plot_plot.treemodelreg.R |only genpathmox-0.3/genpathmox/R/plot_plot.xtree.pls.R |only genpathmox-0.3/genpathmox/R/plot_plot.xtree.reg.R |only genpathmox-0.3/genpathmox/man/plot.treemodel.Rd |only genpathmox-0.3/genpathmox/man/plot.treemodelreg.Rd |only genpathmox-0.3/genpathmox/man/plot.xtree.pls.Rd |only genpathmox-0.3/genpathmox/man/plot.xtree.reg.Rd |only genpathmox-0.4/genpathmox/DESCRIPTION | 13 genpathmox-0.4/genpathmox/MD5 | 260 ++++++++---- genpathmox-0.4/genpathmox/NAMESPACE | 129 +++++ genpathmox-0.4/genpathmox/R/1_fun_blockdiag.R | 2 genpathmox-0.4/genpathmox/R/27_fun_pls.pathmox.R | 8 genpathmox-0.4/genpathmox/R/29_fun_pls.treemodel.R | 2 genpathmox-0.4/genpathmox/R/43_fun_reg.pathmox.R | 8 genpathmox-0.4/genpathmox/R/44_fun_reg.treemodel.R | 2 genpathmox-0.4/genpathmox/R/get_pls.R |only genpathmox-0.4/genpathmox/R/get_tester.R |only genpathmox-0.4/genpathmox/R/get_turner.R |only genpathmox-0.4/genpathmox/man/F.data.pls.Rd | 22 - genpathmox-0.4/genpathmox/man/F.data.reg.Rd | 4 genpathmox-0.4/genpathmox/man/Fb.test.pls.Rd | 4 genpathmox-0.4/genpathmox/man/Fc.test.pls.Rd | 4 genpathmox-0.4/genpathmox/man/Fc.test.reg.Rd | 4 genpathmox-0.4/genpathmox/man/Fg.test.pls.Rd | 4 genpathmox-0.4/genpathmox/man/Fg.test.reg.Rd | 4 genpathmox-0.4/genpathmox/man/all.part.pls.Rd | 21 genpathmox-0.4/genpathmox/man/all.part.reg.Rd | 8 genpathmox-0.4/genpathmox/man/bin.levels.Rd | 4 genpathmox-0.4/genpathmox/man/blockdiag.Rd | 4 genpathmox-0.4/genpathmox/man/build.block.Rd | 4 genpathmox-0.4/genpathmox/man/candidates.tree.Rd | 4 genpathmox-0.4/genpathmox/man/check_args.Rd |only genpathmox-0.4/genpathmox/man/check_blocks.Rd |only genpathmox-0.4/genpathmox/man/check_boot.Rd |only genpathmox-0.4/genpathmox/man/check_data.Rd |only genpathmox-0.4/genpathmox/man/check_maxiter.Rd |only genpathmox-0.4/genpathmox/man/check_model.Rd |only genpathmox-0.4/genpathmox/man/check_modes.Rd |only genpathmox-0.4/genpathmox/man/check_path.Rd |only genpathmox-0.4/genpathmox/man/check_plscomp.Rd |only genpathmox-0.4/genpathmox/man/check_scaling.Rd |only genpathmox-0.4/genpathmox/man/check_scheme.Rd |only genpathmox-0.4/genpathmox/man/check_specs.Rd |only genpathmox-0.4/genpathmox/man/check_tol.Rd |only genpathmox-0.4/genpathmox/man/comb.Rd | 4 genpathmox-0.4/genpathmox/man/df_to_blocks.Rd |only genpathmox-0.4/genpathmox/man/dummy.G.Rd |only genpathmox-0.4/genpathmox/man/dummy_to_list.Rd |only genpathmox-0.4/genpathmox/man/element.Rd | 4 genpathmox-0.4/genpathmox/man/f.min.Rd | 4 genpathmox-0.4/genpathmox/man/factor_to_dummy.Rd |only genpathmox-0.4/genpathmox/man/fblock.tree.pls.Rd | 4 genpathmox-0.4/genpathmox/man/fcoef.tree.pls.Rd | 4 genpathmox-0.4/genpathmox/man/fcoef.tree.reg.Rd | 4 genpathmox-0.4/genpathmox/man/fglobal.tree.Rd | 4 genpathmox-0.4/genpathmox/man/fglobal.tree.pls.Rd | 4 genpathmox-0.4/genpathmox/man/fibtele.Rd | 46 +- genpathmox-0.4/genpathmox/man/fibtelereg.Rd | 46 +- genpathmox-0.4/genpathmox/man/from_to.Rd |only genpathmox-0.4/genpathmox/man/funlist.Rd |only genpathmox-0.4/genpathmox/man/get_PLSR.Rd |only genpathmox-0.4/genpathmox/man/get_PLSR_NA.Rd |only genpathmox-0.4/genpathmox/man/get_boot_stats.Rd |only genpathmox-0.4/genpathmox/man/get_boots.Rd |only genpathmox-0.4/genpathmox/man/get_dummies.Rd |only genpathmox-0.4/genpathmox/man/get_dummy.Rd |only genpathmox-0.4/genpathmox/man/get_effects.Rd |only genpathmox-0.4/genpathmox/man/get_generals.Rd |only genpathmox-0.4/genpathmox/man/get_gof.Rd |only genpathmox-0.4/genpathmox/man/get_inner_summary.Rd |only genpathmox-0.4/genpathmox/man/get_manifests.Rd |only genpathmox-0.4/genpathmox/man/get_metric.Rd |only genpathmox-0.4/genpathmox/man/get_nom_scale.Rd |only genpathmox-0.4/genpathmox/man/get_num_scale.Rd |only genpathmox-0.4/genpathmox/man/get_numerics.Rd |only genpathmox-0.4/genpathmox/man/get_ord_scale.Rd |only genpathmox-0.4/genpathmox/man/get_path_scheme.Rd |only genpathmox-0.4/genpathmox/man/get_paths.Rd |only genpathmox-0.4/genpathmox/man/get_rank.Rd |only genpathmox-0.4/genpathmox/man/get_scores.Rd |only genpathmox-0.4/genpathmox/man/get_treated_data.Rd |only genpathmox-0.4/genpathmox/man/get_unidim.Rd |only genpathmox-0.4/genpathmox/man/get_weights.Rd |only genpathmox-0.4/genpathmox/man/get_weights_nonmetric.Rd |only genpathmox-0.4/genpathmox/man/has_dimension.Rd |only genpathmox-0.4/genpathmox/man/has_factors.Rd |only genpathmox-0.4/genpathmox/man/has_missing.Rd |only genpathmox-0.4/genpathmox/man/has_names.Rd |only genpathmox-0.4/genpathmox/man/has_rownames.Rd |only genpathmox-0.4/genpathmox/man/indexify.Rd |only genpathmox-0.4/genpathmox/man/info.mox.pls.Rd | 8 genpathmox-0.4/genpathmox/man/info.mox.reg.Rd | 4 genpathmox-0.4/genpathmox/man/info.pls_class.Rd | 4 genpathmox-0.4/genpathmox/man/info.reg_class.Rd | 4 genpathmox-0.4/genpathmox/man/invariance.Rd | 18 genpathmox-0.4/genpathmox/man/invariance_test.Rd | 58 +- genpathmox-0.4/genpathmox/man/is_class.Rd |only genpathmox-0.4/genpathmox/man/is_dataframe.Rd |only genpathmox-0.4/genpathmox/man/is_decimal.Rd |only genpathmox-0.4/genpathmox/man/is_diagonal.Rd |only genpathmox-0.4/genpathmox/man/is_even.Rd |only genpathmox-0.4/genpathmox/man/is_integer.Rd |only genpathmox-0.4/genpathmox/man/is_lower_triangular.Rd |only genpathmox-0.4/genpathmox/man/is_matrix.Rd |only genpathmox-0.4/genpathmox/man/is_missing.Rd |only genpathmox-0.4/genpathmox/man/is_multidim.Rd |only genpathmox-0.4/genpathmox/man/is_multiple.Rd |only genpathmox-0.4/genpathmox/man/is_natural.Rd |only genpathmox-0.4/genpathmox/man/is_negative.Rd |only genpathmox-0.4/genpathmox/man/is_negative_decimal.Rd |only genpathmox-0.4/genpathmox/man/is_negative_integer.Rd |only genpathmox-0.4/genpathmox/man/is_odd.Rd |only genpathmox-0.4/genpathmox/man/is_one_dim.Rd |only genpathmox-0.4/genpathmox/man/is_positive.Rd |only genpathmox-0.4/genpathmox/man/is_positive_decimal.Rd |only genpathmox-0.4/genpathmox/man/is_positive_integer.Rd |only genpathmox-0.4/genpathmox/man/is_rectangular_matrix.Rd |only genpathmox-0.4/genpathmox/man/is_scalar.Rd |only genpathmox-0.4/genpathmox/man/is_single.Rd |only genpathmox-0.4/genpathmox/man/is_single_decimal.Rd |only genpathmox-0.4/genpathmox/man/is_single_even.Rd |only genpathmox-0.4/genpathmox/man/is_single_false.Rd |only genpathmox-0.4/genpathmox/man/is_single_logical.Rd |only genpathmox-0.4/genpathmox/man/is_single_negative.Rd |only genpathmox-0.4/genpathmox/man/is_single_negative_decimal.Rd |only genpathmox-0.4/genpathmox/man/is_single_negative_integer.Rd |only genpathmox-0.4/genpathmox/man/is_single_number.Rd |only genpathmox-0.4/genpathmox/man/is_single_odd.Rd |only genpathmox-0.4/genpathmox/man/is_single_positive.Rd |only genpathmox-0.4/genpathmox/man/is_single_positive_decimal.Rd |only genpathmox-0.4/genpathmox/man/is_single_positive_integer.Rd |only genpathmox-0.4/genpathmox/man/is_single_string.Rd |only genpathmox-0.4/genpathmox/man/is_single_true.Rd |only genpathmox-0.4/genpathmox/man/is_square_matrix.Rd |only genpathmox-0.4/genpathmox/man/is_square_numeric_matrix.Rd |only genpathmox-0.4/genpathmox/man/is_string.Rd |only genpathmox-0.4/genpathmox/man/is_tabular.Rd |only genpathmox-0.4/genpathmox/man/is_vector.Rd |only genpathmox-0.4/genpathmox/man/lengths.Rd |only genpathmox-0.4/genpathmox/man/list_of_vectors.Rd |only genpathmox-0.4/genpathmox/man/list_ones.Rd |only genpathmox-0.4/genpathmox/man/list_to_dummy.Rd |only genpathmox-0.4/genpathmox/man/list_to_matrix.Rd |only genpathmox-0.4/genpathmox/man/list_with_vectors.Rd |only genpathmox-0.4/genpathmox/man/listify.Rd |only genpathmox-0.4/genpathmox/man/listsize.Rd |only genpathmox-0.4/genpathmox/man/matrix_to_blocks.Rd |only genpathmox-0.4/genpathmox/man/maxlist.Rd |only genpathmox-0.4/genpathmox/man/meanlist.Rd |only genpathmox-0.4/genpathmox/man/minlist.Rd |only genpathmox-0.4/genpathmox/man/mox.tree.Rd | 4 genpathmox-0.4/genpathmox/man/mox.tree.pls.Rd | 4 genpathmox-0.4/genpathmox/man/node-class.Rd | 4 genpathmox-0.4/genpathmox/man/node.reg_class.Rd | 4 genpathmox-0.4/genpathmox/man/nodes.tree.Rd | 4 genpathmox-0.4/genpathmox/man/normalize.Rd |only genpathmox-0.4/genpathmox/man/partition.Rd | 4 genpathmox-0.4/genpathmox/man/partopt.pls.Rd | 33 + genpathmox-0.4/genpathmox/man/partopt.reg.Rd | 4 genpathmox-0.4/genpathmox/man/percent.node.Rd | 4 genpathmox-0.4/genpathmox/man/pls.pathmox.Rd | 167 ++++--- genpathmox-0.4/genpathmox/man/pls.treemodel.Rd | 109 ++--- genpathmox-0.4/genpathmox/man/plspm.Rd |only genpathmox-0.4/genpathmox/man/print.xtree.pls.Rd | 86 ++- genpathmox-0.4/genpathmox/man/print.xtree.reg.Rd | 46 +- genpathmox-0.4/genpathmox/man/printTree.Rd | 4 genpathmox-0.4/genpathmox/man/prodlist.Rd |only genpathmox-0.4/genpathmox/man/reg.pathmox.Rd | 84 +-- genpathmox-0.4/genpathmox/man/reg.treemodel.Rd | 61 +- genpathmox-0.4/genpathmox/man/root.tree.Rd | 4 genpathmox-0.4/genpathmox/man/same_class.Rd |only genpathmox-0.4/genpathmox/man/same_dim.Rd |only genpathmox-0.4/genpathmox/man/same_length.Rd |only genpathmox-0.4/genpathmox/man/same_mode.Rd |only genpathmox-0.4/genpathmox/man/same_nrow.Rd |only genpathmox-0.4/genpathmox/man/same_type.Rd |only genpathmox-0.4/genpathmox/man/showDeepth.Rd | 4 genpathmox-0.4/genpathmox/man/splitopt.pls.Rd | 34 + genpathmox-0.4/genpathmox/man/splitopt.reg.Rd | 4 genpathmox-0.4/genpathmox/man/sumlist.Rd |only genpathmox-0.4/genpathmox/man/summary.xtree.pls.Rd | 94 ++-- genpathmox-0.4/genpathmox/man/summary.xtree.reg.Rd | 56 +- genpathmox-0.4/genpathmox/man/terminal.tree.Rd | 4 genpathmox-0.4/genpathmox/man/test.particion.reg.Rd | 8 genpathmox-0.4/genpathmox/man/test.partition.pls.Rd | 37 + genpathmox-0.4/genpathmox/man/test_factors.Rd |only genpathmox-0.4/genpathmox/man/test_manifest_scaling.Rd |only genpathmox-0.4/genpathmox/man/test_null_weights.Rd |only genpathmox-0.4/genpathmox/man/tree-class.Rd | 4 genpathmox-0.4/genpathmox/man/treemodel.Rd | 4 genpathmox-0.4/genpathmox/man/treemodelreg.Rd | 4 genpathmox-0.4/genpathmox/man/vector_to_dummy.Rd |only genpathmox-0.4/genpathmox/man/xtree.pls.Rd | 4 genpathmox-0.4/genpathmox/man/xtree.reg.Rd | 4 195 files changed, 954 insertions(+), 668 deletions(-)
Title: Epidemiological Report
Description: Drafting an epidemiological report in 'Microsoft Word' format for a given disease,
similar to the Annual Epidemiological Reports published by the European Centre
for Disease Prevention and Control. Through standalone functions, it is specifically
designed to generate each disease specific output presented in these reports and includes:
- Table with the distribution of cases by Member State over the last five years;
- Seasonality plot with the distribution of cases at the European Union / European Economic Area level,
by month, over the past five years;
- Trend plot with the trend and number of cases at the European Union / European Economic Area level,
by month, over the past five years;
- Age and gender bar graph with the distribution of cases at the European Union / European Economic Area level.
Two types of datasets can be used:
- The default dataset of salmonella 2012-2016 data;
- Any dataset specified as described in the vignette.
Author: Lore Merdrignac [aut, ctr, cre] (Author of the package and original
code),
Tommi Karki [aut, fnd],
Esther Kissling [aut, ctr],
Joana Gomes Dias [aut, fnd] (Project manager)
Maintainer: Lore Merdrignac <l.merdrignac@epiconcept.fr>
Diff between EpiReport versions 0.1.0 dated 2018-11-14 and 0.1.1 dated 2020-05-11
DESCRIPTION | 10 MD5 | 64 +-- R/AER_age_gender_bar.R | 2 R/AER_report.R | 9 R/AER_trend_graph.R | 2 R/internal_functions.R | 4 build/vignette.rds |binary inst/doc/EpiReport_Vignette.R | 58 +- inst/doc/EpiReport_Vignette.Rmd | 19 inst/doc/EpiReport_Vignette.html | 784 ++++++++++++++++++++++++++++----------- man/AERparams.Rd | 110 ++--- man/MSCode.Rd | 56 +- man/SALM2016.Rd | 102 ++--- man/cleanECDCTable.Rd | 65 +-- man/cleanMeasureCode.Rd | 143 +++---- man/filterDisease.Rd | 60 +- man/getAER.Rd | 158 ++++--- man/getAgeGender.Rd | 146 +++---- man/getMap.Rd | 135 +++--- man/getSeason.Rd | 150 +++---- man/getTableByMS.Rd | 144 +++---- man/getTemplate.Rd | 79 +-- man/getTrend.Rd | 146 +++---- man/includeMap.Rd | 113 +++-- man/orderQuasinum.Rd | 86 ++-- man/plotAge.Rd | 101 ++--- man/plotAgeGender.Rd | 130 +++--- man/plotSeasonality.Rd | 100 ++-- man/plotTS12MAvg.Rd | 74 +-- man/previewMap.Rd | 64 +-- man/shapeECDCFlexTable.Rd | 64 +-- man/toCapTitle.Rd | 44 +- vignettes/EpiReport_Vignette.Rmd | 19 33 files changed, 1854 insertions(+), 1387 deletions(-)
Title: Process and Analyze Agilent Cary 620 FTIR Microscope Images
Description: A set of tools to read, process, and summarize Agilent Cary 620 uFTIR Microscope hyperspectral images
primarily intended for microplastic analysis.
Author: Fabio Corradini [aut, cre] (<https://orcid.org/0000-0001-9696-7643>)
Maintainer: Fabio Corradini <fabio.corradini@inia.cl>
Diff between uFTIR versions 0.1.1 dated 2020-03-11 and 0.1.2 dated 2020-05-11
uFTIR-0.1.1/uFTIR/src/Makevars |only uFTIR-0.1.2/uFTIR/DESCRIPTION | 23 ++-- uFTIR-0.1.2/uFTIR/MD5 | 53 ++++++--- uFTIR-0.1.2/uFTIR/NAMESPACE | 5 uFTIR-0.1.2/uFTIR/NEWS.md |only uFTIR-0.1.2/uFTIR/R/RcppExports.R | 8 + uFTIR-0.1.2/uFTIR/R/mask_sam.r |only uFTIR-0.1.2/uFTIR/R/matrix_sam.r |only uFTIR-0.1.2/uFTIR/R/mosaic_chunk.R | 65 +++++++++-- uFTIR-0.1.2/uFTIR/R/mosaic_compose.R | 2 uFTIR-0.1.2/uFTIR/R/mosaic_sam.R | 2 uFTIR-0.1.2/uFTIR/R/plot_methods.R | 2 uFTIR-0.1.2/uFTIR/R/profile_methods.R | 88 +++++++++++++++- uFTIR-0.1.2/uFTIR/R/sam_load.R |only uFTIR-0.1.2/uFTIR/R/sam_write.r |only uFTIR-0.1.2/uFTIR/R/smooth_sam.R | 2 uFTIR-0.1.2/uFTIR/R/uFTIR.R | 1 uFTIR-0.1.2/uFTIR/README.md | 3 uFTIR-0.1.2/uFTIR/cleanup |only uFTIR-0.1.2/uFTIR/configure |only uFTIR-0.1.2/uFTIR/configure.ac |only uFTIR-0.1.2/uFTIR/man/get_profile.Rd | 14 ++ uFTIR-0.1.2/uFTIR/man/mask_sam.Rd |only uFTIR-0.1.2/uFTIR/man/matrix_sam.Rd |only uFTIR-0.1.2/uFTIR/man/mosaic_chunk.Rd | 14 +- uFTIR-0.1.2/uFTIR/man/primpke.Rd | 6 - uFTIR-0.1.2/uFTIR/man/sam_load.Rd |only uFTIR-0.1.2/uFTIR/man/sam_write.Rd |only uFTIR-0.1.2/uFTIR/man/smooth_sam.Rd | 2 uFTIR-0.1.2/uFTIR/src/Makevars.in |only uFTIR-0.1.2/uFTIR/src/RcppExports.cpp | 25 ++++ uFTIR-0.1.2/uFTIR/src/csam_load.cpp |only uFTIR-0.1.2/uFTIR/src/sam_main.cpp | 1 uFTIR-0.1.2/uFTIR/tests/testthat/Rplots.pdf |binary uFTIR-0.1.2/uFTIR/tests/testthat/shape_out/clusters.dbf |binary 35 files changed, 259 insertions(+), 57 deletions(-)
Title: A Stemming Algorithm for the Portuguese Language
Description: Implements the "Stemming Algorithm for the Portuguese Language" <DOI:10.1109/SPIRE.2001.10024>.
Author: Daniel Falbel [aut, cre]
Maintainer: Daniel Falbel <dfalbel@gmail.com>
Diff between rslp versions 0.1.0 dated 2016-08-31 and 0.2.0 dated 2020-05-11
DESCRIPTION | 14 ++++++++------ MD5 | 37 +++++++++++++++++++------------------ NEWS.md | 7 +++++++ R/apply-rules.R | 6 +----- R/parse-rules.R | 2 +- R/rslp.R | 9 ++++----- README.md | 32 +++++++++++++++++++++----------- man/apply_rules.Rd | 8 -------- man/extract_raw_rules.Rd | 1 - man/extract_replacement_rules.Rd | 1 - man/extract_rule_info.Rd | 1 - man/extract_rules.Rd | 3 +-- man/extract_rules_info.Rd | 1 - man/pipe.Rd | 1 - man/remove_accents.Rd | 1 - man/rslp.Rd | 9 +++++---- man/rslp_.Rd | 7 ++++--- man/rslp_doc.Rd | 12 ++++++------ man/verify_sufix.Rd | 1 - tests/testthat/test-rslp_doc.R |only 20 files changed, 77 insertions(+), 76 deletions(-)
Title: Predict Antimicrobial Peptides
Description: A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale.
It incorporates two support vector machine models ("precursor" and "mature") trained on publicly available antimicrobial peptide data using calculated
physico-chemical and compositional sequence properties described in Meher et al. (2017) <doi:10.1038/srep42362>.
In order to support genome-wide analyses, these models are designed to accept any type of protein as input
and calculation of compositional properties has been optimised for high-throughput use. For details see Fingerhut et al. 2020 <doi:10.1101/2020.05.07.082412>.
Author: Legana Fingerhut [aut, cre] (<https://orcid.org/0000-0002-2482-5336>),
Ira Cooke [aut] (<https://orcid.org/0000-0001-6520-1397>),
Jinlong Zhang [ctb] (R/read_faa.R),
Nan Xiao [ctb] (R/calc_pseudo_comp.R)
Maintainer: Legana Fingerhut <legana.fingerhut@my.jcu.edu.au>
Diff between ampir versions 0.1.0 dated 2019-12-06 and 1.0.0 dated 2020-05-11
ampir-0.1.0/ampir/tests/hepcidin_paac.rds |only ampir-0.1.0/ampir/tests/hepcidin_paac_lambda4.rds |only ampir-1.0.0/ampir/DESCRIPTION | 30 +-- ampir-1.0.0/ampir/MD5 | 56 +++--- ampir-1.0.0/ampir/NAMESPACE | 3 ampir-1.0.0/ampir/NEWS.md | 15 + ampir-1.0.0/ampir/R/calc_pseudo_comp.R | 11 - ampir-1.0.0/ampir/R/calculate_features.R | 18 + ampir-1.0.0/ampir/R/chunk_rows.R |only ampir-1.0.0/ampir/R/predict_amps.R | 46 ++++- ampir-1.0.0/ampir/R/remove_nonstandard_aa.R |only ampir-1.0.0/ampir/R/sysdata.rda |binary ampir-1.0.0/ampir/README.md | 99 ++++++---- ampir-1.0.0/ampir/build/vignette.rds |binary ampir-1.0.0/ampir/inst/doc/ampir.R | 8 ampir-1.0.0/ampir/inst/doc/ampir.Rmd | 14 - ampir-1.0.0/ampir/inst/doc/ampir.html | 109 +++++++++--- ampir-1.0.0/ampir/inst/doc/train_model.R |only ampir-1.0.0/ampir/inst/doc/train_model.Rmd |only ampir-1.0.0/ampir/inst/doc/train_model.html |only ampir-1.0.0/ampir/inst/extdata/bat_negative.fasta.gz |only ampir-1.0.0/ampir/inst/extdata/bat_positive.fasta.gz |only ampir-1.0.0/ampir/inst/extdata/little_test.fasta | 60 ++---- ampir-1.0.0/ampir/inst/logo |only ampir-1.0.0/ampir/man/calculate_features.Rd | 13 + ampir-1.0.0/ampir/man/chunk_rows.Rd |only ampir-1.0.0/ampir/man/predict_amps.Rd | 8 ampir-1.0.0/ampir/man/remove_nonstandard_aa.Rd |only ampir-1.0.0/ampir/tests/testdata |only ampir-1.0.0/ampir/tests/testthat/test-calc-pseudo-comp.R | 4 ampir-1.0.0/ampir/tests/testthat/test-chunk-rows.R |only ampir-1.0.0/ampir/tests/testthat/test-df_to_faa.R |only ampir-1.0.0/ampir/tests/testthat/test-predict-amps.R | 77 ++++++++ ampir-1.0.0/ampir/tests/testthat/test-read-faa.R |only ampir-1.0.0/ampir/tests/testthat/test-removenonstandardaa.R |only ampir-1.0.0/ampir/vignettes/ampir.Rmd | 14 - ampir-1.0.0/ampir/vignettes/train_model.Rmd |only 37 files changed, 416 insertions(+), 169 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between RODBC versions 1.3-16 dated 2019-09-03 and 1.3-17 dated 2020-05-11
ChangeLog | 37 +++++++++++++++++-------------------- DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/sql.R | 4 ++-- build/vignette.rds |binary inst/doc/RODBC.pdf |binary man/sqlQuery.Rd | 4 ++-- 7 files changed, 33 insertions(+), 36 deletions(-)
More information about xml2relational at CRAN
Permanent link
Title: Working with 'Sapfluxnet' Project Data
Description: Access, modify, aggregate and plot data from the 'Sapfluxnet' project
(<http://sapfluxnet.creaf.cat>), the first global database of sap flow measurements.
Author: Victor Granda [aut, cre] (<https://orcid.org/0000-0002-0469-1991>),
Rafael Poyatos [aut] (<https://orcid.org/0000-0003-0521-2523>),
Victor Flo [aut] (<https://orcid.org/0000-0003-1908-4577>),
Jacob Nelson [ctb] (<https://orcid.org/0000-0002-4663-2420>),
Sapfluxnet Core Team [cph]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Diff between sapfluxnetr versions 0.0.7 dated 2019-05-01 and 0.1.0 dated 2020-05-11
DESCRIPTION | 13 LICENSE | 2 MD5 | 130 +-- NEWS.md | 8 R/helpers.R | 2 R/metrics.R | 16 README.md | 20 build/vignette.rds |binary data/ARG_MAZ.rda |binary data/ARG_TRE.rda |binary data/AUS_CAN_ST2_MIX.rda |binary data/sfn_metadata_ex.rda |binary inst/doc/custom-aggregation.R | 16 inst/doc/custom-aggregation.Rmd | 37 inst/doc/custom-aggregation.html | 467 ++++++------ inst/doc/data-flags.R | 2 inst/doc/data-flags.html | 32 inst/doc/memory-and-parallelization.R | 12 inst/doc/memory-and-parallelization.Rmd | 2 inst/doc/memory-and-parallelization.html | 225 +++-- inst/doc/metadata-and-data-units.R | 12 inst/doc/metadata-and-data-units.Rmd | 2 inst/doc/metadata-and-data-units.html | 158 ++-- inst/doc/sapfluxnetr-quick-guide.R | 90 +- inst/doc/sapfluxnetr-quick-guide.Rmd | 77 +- inst/doc/sapfluxnetr-quick-guide.html | 1118 ++++++++++++++--------------- inst/doc/sfn-data-classes.R | 32 inst/doc/sfn-data-classes.html | 1141 +++++++++++++++--------------- man/ARG_MAZ.Rd | 4 man/ARG_TRE.Rd | 4 man/AUS_CAN_ST2_MIX.Rd | 4 man/figures/README-example_multi-1.png |binary man/figures/README-example_multi-2.png |binary man/figures/README-example_single-1.png |binary man/figures/README-example_single-2.png |binary man/initialize-sfn_data-method.Rd | 19 man/initialize-sfn_data_multi-method.Rd | 1 man/metrics.Rd | 85 +- man/metrics_tidyfier.Rd | 9 man/sfn_get_methods.Rd | 1 man/sfn_metadata_ex.Rd | 4 man/sfn_metrics.Rd | 16 man/sfn_multi_get_methods.Rd | 1 man/sfn_plot.Rd | 11 man/sfn_replacement_methods.Rd | 1 man/show-sfn_data-method.Rd | 1 man/show-sfn_data_multi-method.Rd | 1 tests/testthat/ARG_MAZ.RData |binary tests/testthat/ARG_TRE.RData |binary tests/testthat/AUS_CAN_ST2_MIX.RData |binary tests/testthat/Data/ARG_MAZ.RData |binary tests/testthat/Data/ARG_TRE.RData |binary tests/testthat/Data/AUS_CAN_ST2_MIX.RData |binary tests/testthat/test-getters.R | 2 tests/testthat/test-helpers.R | 2 tests/testthat/test-metrics.R | 2 tests/testthat/test-sfn_data_classes.R | 2 tests/testthat/test-sfn_dplyr_methods.R | 2 tests/testthat/test-visualizations.R | 2 vignettes/custom-aggregation.Rmd | 37 vignettes/memory-and-parallelization.Rmd | 2 vignettes/metadata-and-data-units.Rmd | 2 vignettes/resources/ARG_MAZ.RData |binary vignettes/resources/ARG_TRE.RData |binary vignettes/resources/AUS_CAN_ST2_MIX.RData |binary vignettes/sapfluxnetr-quick-guide.Rmd | 77 +- 66 files changed, 2042 insertions(+), 1864 deletions(-)
Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm).
Estimation is performed using either Laplace approximation method or variational approximation method implemented via TMB (Kristensen et al., (2016), <doi:10.18637/jss.v070.i05>).
For details see Niku et al. (2019a) <doi:10.1371/journal.pone.0216129> and Niku et al. (2019b) <doi:10.1111/2041-210X.13303>.
Author: Jenni Niku, Wesley Brooks, Riki Herliansyah, Francis K.C. Hui, Sara Taskinen, David I. Warton
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>
Diff between gllvm versions 1.2.1 dated 2020-01-23 and 1.2.2 dated 2020-05-11
DESCRIPTION | 10 - MD5 | 60 ++++----- NAMESPACE | 4 R/TMBtrait.R | 178 +++++++++++++++------------ R/confint.gllvm.R | 30 +++- R/getPredictErr.gllvm.R | 34 ++++- R/getResidualCov.gllvm.R | 3 R/gllvm.R | 44 ++++-- R/gllvm.TMB.R | 141 +++++++++++++-------- R/gllvm.auxiliary.R | 119 +++++++++++++----- R/logLik.gllvm.R | 7 - R/ordiplot.gllvm.R | 284 +++++++++++++++++++++++--------------------- R/predict.gllvm.R | 34 ++++- R/predictLVs.gllvm.R | 33 ++--- R/randomCoefplot.R | 6 R/residuals.gllvm.R | 78 ++++++++---- R/simulate.gllvm.R | 63 ++++++--- R/summary.gllvm.R | 5 inst/doc/vignette1.Rmd | 32 ++++ inst/doc/vignette1.html | 51 ++++++- inst/doc/vignette2.R | 22 +-- inst/doc/vignette2.html | 44 +++--- inst/doc/vignette2.rmd | 28 ++-- man/getPredictErr.gllvm.Rd | 9 + man/getResidualCov.gllvm.Rd | 3 man/gllvm.Rd | 28 ++-- man/predictLVs.gllvm.Rd | 2 man/simulate.gllvm.Rd | 9 - src/gllvm.cpp | 260 ++++++++++++++++++++++++---------------- vignettes/vignette1.Rmd | 32 ++++ vignettes/vignette2.rmd | 28 ++-- 31 files changed, 1067 insertions(+), 614 deletions(-)
Title: Robust Mixture Regression
Description: Finite mixture models are a popular technique for modelling unobserved heterogeneity or to approximate general distribution functions in a semi-parametric way. They are used in a lot of different areas such as astronomy, biology, economics, marketing or medicine.
This package is the implementation of popular robust mixture regression methods based on different algorithms including: fleximix, finite mixture models and latent class regression; CTLERob, component-wise adaptive trimming likelihood estimation; mixbi, bi-square estimation; mixL, Laplacian distribution; mixt, t-distribution; TLE, trimmed likelihood estimation.
The implemented algorithms includes: CTLERob stands for Component-wise adaptive Trimming Likelihood Estimation based mixture regression; mixbi stands for mixture regression based on bi-square estimation; mixLstands for mixture regression based on Laplacian distribution; TLE stands for Trimmed Likelihood Estimation based mixture regression. For more detail of the algorithms, please refer to below references.
Reference: Chun Yu, Weixin Yao, Kun Chen (2017) <doi:10.1002/cjs.11310>.
NeyKov N, Filzmoser P, Dimova R et al. (2007) <doi:10.1016/j.csda.2006.12.024>.
Bai X, Yao W. Boyer JE (2012) <doi:10.1016/j.csda.2012.01.016>.
Wennen Chang, Sha Cao, Chi Zhang (2019) <doi:10.1101/426593>.
Author: Sha Cao [aut, cph, ths],
Wennan Chang [aut, cre],
Chi Zhang [aut, ctb, ths]
Maintainer: Wennan Chang <wnchang@iu.edu>
Diff between RobMixReg versions 0.1.0 dated 2020-03-25 and 0.2.0 dated 2020-05-11
RobMixReg-0.1.0/RobMixReg/R/CTLE.short.R |only RobMixReg-0.1.0/RobMixReg/man/CTLE-methods.Rd |only RobMixReg-0.2.0/RobMixReg/DESCRIPTION | 14 +++++----- RobMixReg-0.2.0/RobMixReg/MD5 | 24 +++++++++--------- RobMixReg-0.2.0/RobMixReg/NAMESPACE | 4 +-- RobMixReg-0.2.0/RobMixReg/NEWS.md | 15 ++++++++++- RobMixReg-0.2.0/RobMixReg/R/CTLE.short.rob.R |only RobMixReg-0.2.0/RobMixReg/R/mixL.short.R | 2 - RobMixReg-0.2.0/RobMixReg/R/outer.R | 12 ++++----- RobMixReg-0.2.0/RobMixReg/README.md | 30 +++++++++++++++++------ RobMixReg-0.2.0/RobMixReg/man/CTLERob-methods.Rd |only RobMixReg-0.2.0/RobMixReg/man/DeOut.Rd | 2 - RobMixReg-0.2.0/RobMixReg/man/RobMixReg-class.Rd | 6 +++- RobMixReg-0.2.0/RobMixReg/man/flexmix_2.Rd | 2 - RobMixReg-0.2.0/RobMixReg/man/rmr.Rd | 4 +-- 15 files changed, 73 insertions(+), 42 deletions(-)
Title: Markov Models for Health Economic Evaluations
Description: An implementation of the modelling and reporting features described
in reference textbook and guidelines (Briggs, Andrew, et al. Decision
Modelling for Health Economic Evaluation. Oxford Univ. Press, 2011;
Siebert, U. et al. State-Transition Modeling. Medical Decision Making
32, 690-700 (2012).): deterministic and probabilistic sensitivity analysis,
heterogeneity analysis, time dependency on state-time and model-time
(semi-Markov and non-homogeneous Markov models), etc.
Author: Kevin Zarca [aut, cre],
Antoine Filipovic-Pierucci [aut],
Matthew Wiener [ctb],
Zdenek Kabat [ctb],
Vojtech Filipec [ctb],
Jordan Amdahl [ctb],
Yonatan Carranza Alarcon [ctb],
Vince Daniels [ctb]
Maintainer: Kevin Zarca <kevin.zarca@gmail.com>
Diff between heemod versions 0.12.0 dated 2020-04-14 and 0.13.0 dated 2020-05-11
DESCRIPTION | 8 +- MD5 | 37 ++++----- NAMESPACE | 2 NEWS.md | 6 + R/heemod.R | 2 R/param_eval.R | 6 - R/strategy_eval.R | 4 - inst/doc/a_introduction.html | 4 - inst/doc/b_time_dependency.html | 4 - inst/doc/c_homogeneous.html | 4 - inst/doc/d_non_homogeneous.html | 4 - inst/doc/e_probabilistic.html | 38 ++++----- inst/doc/f_sensitivity.html | 4 - inst/doc/g_heterogeneity.html | 156 ++++++++++++++++++++-------------------- inst/doc/h_tabular.html | 6 - inst/doc/i_reproduction.html | 4 - inst/doc/j_survival.html | 8 +- inst/doc/k_calibration.html | 4 - tests/testthat/Rplots.pdf |only tests/testthat/test_dmhee.R | 6 + 20 files changed, 158 insertions(+), 149 deletions(-)
Title: Diffs for R Objects
Description: Generate a colorized diff of two R objects for an intuitive
visualization of their differences.
Author: Brodie Gaslam [aut, cre],
Michael B. Allen [ctb, cph] (Original C implementation of Myers Diff
Algorithm)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between diffobj versions 0.2.4 dated 2020-03-20 and 0.3.0 dated 2020-05-11
DESCRIPTION | 8 - MD5 | 147 ++++++++++++++++----------------- NAMESPACE | 2 NEWS.md | 12 ++ R/capt.R | 15 +++ R/check.R | 2 R/core.R | 144 ++++++++++++++++++++++++++++---- R/diff.R | 8 + R/finalizer.R | 2 R/get.R | 2 R/guides.R | 17 ++- R/html.R | 2 R/hunks.R | 2 R/layout.R | 2 R/misc.R | 5 - R/myerssimple.R | 2 R/pager.R | 2 R/rdiff.R | 2 R/rds.R | 2 R/s4.R | 4 R/set.R | 2 R/styles.R | 2 R/subset.R | 2 R/summmary.R | 2 R/system.R | 2 R/text.R | 2 R/tochar.R | 2 R/trim.R | 12 +- R/word.R | 2 README.md | 3 build/vignette.rds |binary inst/COPYRIGHTS | 2 inst/script/diffobj.js | 2 man/Extract_PaletteOfStyles.Rd | 1 man/Pager.Rd | 34 +++++-- man/Rdiff_chr.Rd | 6 - man/Style.Rd | 3 man/any-Diff-method.Rd | 1 man/as.character-DiffSummary-method.Rd | 1 man/as.character-MyersMbaSes-method.Rd | 1 man/auto_context.Rd | 6 - man/diffChr.Rd | 47 +++++++--- man/diffCsv.Rd | 44 ++++++--- man/diffDeparse.Rd | 44 ++++++--- man/diffFile.Rd | 44 ++++++--- man/diffPrint.Rd | 47 +++++++--- man/diffStr.Rd | 44 ++++++--- man/diff_myers.Rd | 15 +++ man/diffobj_s4method_doc.Rd | 1 man/dimnames-PaletteOfStyles-method.Rd | 1 man/extract-Diff-method.Rd | 1 man/finalizeHtml.Rd | 1 man/guides.Rd | 6 - man/make_blocking.Rd | 3 man/ses.Rd | 48 ++++++++++ man/show-DiffSummary-method.Rd | 1 man/show-PaletteOfStyles-method.Rd | 1 man/show-Style-method.Rd | 1 man/summary-Diff-method.Rd | 10 +- man/summary-MyersMbaSes-method.Rd | 1 man/summary-PaletteOfStyles-method.Rd | 1 man/trim.Rd | 1 src/diff.c | 2 src/diff.h | 2 tests/run.R | 1 tests/testthat/helper/diffStr/550.rds |only tests/testthat/helper/html/300.rds |binary tests/testthat/helper/html/350.rds |binary tests/testthat/testthat.capture.R | 9 ++ tests/testthat/testthat.check.R | 2 tests/testthat/testthat.core.R | 6 + tests/testthat/testthat.diffChr.R | 7 + tests/testthat/testthat.diffStr.R | 10 ++ tests/testthat/testthat.html.R | 3 tests/testthat/testthat.ses.R | 26 +++++ 75 files changed, 634 insertions(+), 266 deletions(-)
Title: Compositional Analysis of Differentially Expressed Proteins in
Cancer
Description: Compositional analysis of differentially expressed proteins in
cancer and cell culture proteomics experiments. The data include lists of up-
and down-regulated proteins in different cancer types (breast, colorectal,
liver, lung, pancreatic, prostate) and laboratory conditions (hypoxia,
hyperosmotic stress, high glucose, 3D cell culture, and proteins secreted in
hypoxia), together with amino acid compositions computed for protein sequences
obtained from UniProt. Functions are provided to calculate compositional metrics
including protein length, carbon oxidation state, and stoichiometric hydration
state. In addition, phylostrata (evolutionary ages) of protein-coding genes are
compiled using data from Liebeskind et al. (2016) <doi:10.1093/gbe/evw113> or
Trigos et al. (2017) <doi:10.1073/pnas.1617743114>. The vignettes contain
plots of compositional differences, phylostrata for human proteins, and
references for all datasets.
Author: Jeffrey Dick [aut, cre] (<https://orcid.org/0000-0002-0687-5890>),
Ben Bolker [ctb] (<https://orcid.org/0000-0002-2127-0443>)
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between canprot versions 0.1.2 dated 2019-02-26 and 1.0.0 dated 2020-05-11
canprot-0.1.2/canprot/R/check_ID.R |only canprot-0.1.2/canprot/R/get_pdat.R |only canprot-0.1.2/canprot/R/lapply_canprot.R |only canprot-0.1.2/canprot/R/pdat_CRC.R |only canprot-0.1.2/canprot/R/remove_entries.R |only canprot-0.1.2/canprot/inst/doc/basis_comparison.R |only canprot-0.1.2/canprot/inst/doc/basis_comparison.Rmd |only canprot-0.1.2/canprot/inst/doc/basis_comparison.html |only canprot-0.1.2/canprot/inst/doc/colorectal.R |only canprot-0.1.2/canprot/inst/doc/colorectal.Rmd |only canprot-0.1.2/canprot/inst/doc/colorectal.html |only canprot-0.1.2/canprot/inst/doc/hyperosmotic.R |only canprot-0.1.2/canprot/inst/doc/hyperosmotic.Rmd |only canprot-0.1.2/canprot/inst/doc/hyperosmotic.html |only canprot-0.1.2/canprot/inst/doc/hypoxia.R |only canprot-0.1.2/canprot/inst/doc/hypoxia.Rmd |only canprot-0.1.2/canprot/inst/doc/hypoxia.html |only canprot-0.1.2/canprot/inst/doc/pancreatic.R |only canprot-0.1.2/canprot/inst/doc/pancreatic.Rmd |only canprot-0.1.2/canprot/inst/doc/pancreatic.html |only canprot-0.1.2/canprot/inst/doc/potential_diagrams.R |only canprot-0.1.2/canprot/inst/doc/potential_diagrams.Rmd |only canprot-0.1.2/canprot/inst/doc/potential_diagrams.html |only canprot-0.1.2/canprot/inst/extdata/aa/bacteria/KKG+12_aa.csv |only canprot-0.1.2/canprot/inst/extdata/aa/bacteria/KLB+15_aa.csv |only canprot-0.1.2/canprot/inst/extdata/aa/fungus |only canprot-0.1.2/canprot/inst/extdata/aa/mouse/KKC+16_aa.csv |only canprot-0.1.2/canprot/inst/extdata/aa/mouse/LAR+12_aa.csv |only canprot-0.1.2/canprot/inst/extdata/aa/mouse/LDB+15_aa.csv |only canprot-0.1.2/canprot/inst/extdata/aa/mouse/WCM+09_aa.csv |only canprot-0.1.2/canprot/inst/extdata/aa/rat/DPL+10_aa.csv |only canprot-0.1.2/canprot/inst/extdata/aa/rat/XCJ+16_aa.csv |only canprot-0.1.2/canprot/inst/extdata/colors |only canprot-0.1.2/canprot/inst/extdata/expression/CRC |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/BMJ+11.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/BRA+10.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/BSA+15.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/CBW+11.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/DPL+10.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/DYL+14.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/FWH+13.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/HWA+16.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/HXS+06.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/LAR+12.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/LCS16.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/MHG+12.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/MVC+12.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/RHD+13.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/RKP+14.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/RSE+16.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/VTMF13.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/WRK+14.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/XCJ+16.csv |only canprot-0.1.2/canprot/inst/extdata/expression/hypoxia/YLW+16.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/CCC+12.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/CCCC13.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/CLG+15.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/GSC14.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/KKG+12.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/KLB+15.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/LDB+15.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/OBBH11.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/PW08.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/RBP+16.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/TSZ+13.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/WCM+09.csv |only canprot-0.1.2/canprot/inst/extdata/expression/osmotic/YDZ+15.csv |only canprot-0.1.2/canprot/inst/extdata/expression/pancreatic/CBP+07.csv |only canprot-0.1.2/canprot/inst/extdata/expression/pancreatic/CGB+05.csv |only canprot-0.1.2/canprot/inst/extdata/expression/pancreatic/CTZ+09.csv |only canprot-0.1.2/canprot/inst/extdata/expression/pancreatic/CYD+05.csv |only canprot-0.1.2/canprot/inst/extdata/expression/pancreatic/ISI+14.csv |only canprot-0.1.2/canprot/inst/extdata/expression/pancreatic/KBK+12.csv |only canprot-0.1.2/canprot/inst/extdata/expression/pancreatic/KHO+13.csv |only canprot-0.1.2/canprot/inst/extdata/expression/pancreatic/KKC+16.csv |only canprot-0.1.2/canprot/inst/extdata/expression/pancreatic/KPC+13.csv |only canprot-0.1.2/canprot/inst/extdata/expression/pancreatic/LHE+04.csv |only 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Title: Biological Analysis and Visualization of Weather Radar Data
Description: Extract, visualize and summarize aerial movements of birds and
insects from weather radar data. See <doi:10.1111/ecog.04028>
for a software paper describing package and methodologies.
Author: Adriaan M. Dokter [aut, cre] (<https://orcid.org/0000-0001-6573-066X>),
Peter Desmet [aut] (<https://orcid.org/0000-0002-8442-8025>),
Stijn Van Hoey [aut] (<https://orcid.org/0000-0001-6413-3185>),
Bart Kranstauber [ctb] (<https://orcid.org/0000-0001-8303-780X>),
Cecilia Nilsson [ctb] (<https://orcid.org/0000-0001-8957-4411>),
Jurriaan Spaaks [ctb],
Lourens Veen [ctb],
Liesbeth Verlinden [ctb] (<https://orcid.org/0000-0003-1744-9325>),
Hidde Leijnse [ctb] (<https://orcid.org/0000-0001-7835-4480>)
Maintainer: Adriaan M. Dokter <amd427@cornell.edu>
Diff between bioRad versions 0.5.1 dated 2020-04-01 and 0.5.2 dated 2020-05-11
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Title: Inferring Developmental Chronologies from Single-Cell RNA
Sequencing Data
Description: An accurate and easy tool for performing linear trajectory inference on
single cells using single-cell RNA sequencing data. In addition, SCORPIUS
provides functions for discovering the most important genes with respect to
the reconstructed trajectory, as well as nice visualisation tools.
Cannoodt et al. (2016) <doi:10.1101/079509>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [ctb] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between SCORPIUS versions 1.0.6 dated 2020-03-16 and 1.0.7 dated 2020-05-11
DESCRIPTION | 12 MD5 | 28 - NAMESPACE | 2 NEWS.md | 8 R/dynwrap_integration.R | 8 R/plotting.R | 4 README.md | 31 - build/vignette.rds |binary inst/doc/ginhoux.html | 48 - inst/doc/seurat.html | 885 +++++++++++++++++++++----------- inst/doc/simulated-data.html | 44 - man/figures/README_moduled_tafs-1.png |binary man/figures/README_visualise_tafs-1.png |binary man/ginhoux.Rd | 4 man/ti_scorpius_run_fun.Rd | 4 15 files changed, 677 insertions(+), 401 deletions(-)
Title: Read, Manipulate, and Write Profiler Data
Description: Defines a data structure for profiler data, and methods to read and
write from the 'Rprof' and 'pprof' file formats.
Author: Kirill Müller [aut, cre],
R Consortium [fnd]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between profile versions 1.0.1 dated 2020-05-01 and 1.0.2 dated 2020-05-11
DESCRIPTION | 12 +++++----- MD5 | 13 ++++++----- NAMESPACE | 2 + NEWS.md | 5 ++++ R/api.R | 55 +++++++++++++++++++++++++++++++++++++++++++++--- inst/WORDLIST |only man/read_rprof.Rd | 6 ++--- man/validate_profile.Rd | 19 ++++++++++++++-- 8 files changed, 92 insertions(+), 20 deletions(-)
Title: A Very Fast 2D Concave Hull Algorithm
Description: The concaveman function ports the 'concaveman' (<https://github.com/mapbox/concaveman>) library from 'mapbox'. It computes the concave polygon(s) for one or several set of points.
Author: Joël Gombin [cre, aut],
Ramnath Vaidyanathan [aut],
Vladimir Agafonkin [aut],
Mapbox [cph]
Maintainer: Joël Gombin <joel.gombin@gmail.com>
Diff between concaveman versions 1.0.0 dated 2017-07-25 and 1.1.0 dated 2020-05-11
DESCRIPTION | 15 ++++++++------- MD5 | 20 +++++++++++--------- NAMESPACE | 2 -- NEWS.md | 7 ++++++- R/concaveman-pkg.R | 2 +- R/concaveman.R | 11 ++--------- data/points.rda |binary man/concaveman.Rd | 14 ++++---------- man/figures |only man/points.Rd | 4 +++- tests/testthat/test_concaveman.R | 2 -- 11 files changed, 35 insertions(+), 42 deletions(-)
Title: K-means clustering with build-in missing data imputation
Description: This clustering algorithm deals with missing data via weights that are imposed on missings and successively increased. See the vignette for details.
Author: Oliver Pfaffel
Maintainer: Oliver Pfaffel <opfaffel@gmail.com>
Diff between ClustImpute versions 0.1.3 dated 2019-08-01 and 0.1.4 dated 2020-05-11
DESCRIPTION | 10 +- MD5 | 21 +++-- NAMESPACE | 2 NEWS.md | 6 + R/ClustImpute.R | 61 ++++++++++++++-- README.md | 13 ++- build/vignette.rds |binary inst/doc/Example_on_simulated_data.R | 50 ++++++------- inst/doc/Example_on_simulated_data.html | 121 +++++++++++++++----------------- man/ClustImpute.Rd | 14 +++ man/check_replace_dups.Rd |only man/figures |only 12 files changed, 185 insertions(+), 113 deletions(-)
Title: R Client for the BAN API
Description: A client for the "Base Adresses Nationale" (BAN) API, which allows to (batch)
geocode and reverse-geocode French addresses. For more information about the BAN and its API, please see <https://adresse.data.gouv.fr/api>.
Author: Joel Gombin [cre, aut],
Paul-Antoine Chevalier [aut]
Maintainer: Joel Gombin <joel.gombin@gmail.com>
Diff between banR versions 0.2.1 dated 2019-12-05 and 0.2.2 dated 2020-05-11
DESCRIPTION | 11 +- MD5 | 16 +-- NEWS.md | 3 README.md | 13 +- build/vignette.rds |binary inst/doc/geocode.html | 183 +++++++++++++++++++-------------------- man/paris2012.Rd | 6 - tests/testthat/test_geocode.R | 6 - tests/testthat/test_geocodetbl.R | 14 +- 9 files changed, 131 insertions(+), 121 deletions(-)
Title: Comprehensive and Easy to Use Quality Control of GWAS Results
Description: When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Author: Alireza Ani [aut, cre],
Peter J. van der Most [aut],
Ahmad Vaez [aut],
Ilja M. Nolte [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between GWASinspector versions 1.4.7 dated 2020-04-22 and 1.4.7.1 dated 2020-05-11
ChangeLog | 4 DESCRIPTION | 8 - MD5 | 38 +++---- NEWS | 4 R/aaa.R | 2 R/compare_GWASs.R | 77 ++++++++++++--- R/excelReportFunctions.R | 151 +++++++++++++++++++------------ R/multiStudyFunctions.R | 14 ++ R/multiStudyPlots.R | 12 +- R/rSQLiteFunctions.R | 2 R/reportRelatedFunctions.R | 10 +- R/run_inspector.R | 62 +++++------- R/studyFunctions.R | 98 ++++++++++++++------ R/variantMatchingFunctions.R | 51 +++++++++- R/zzz.R | 6 - inst/doc/GWASinspector.html | 4 inst/extdata/config.ini | 21 +++- inst/rmd/mainReport_extra.rmd | 34 +++++- inst/rmd/multiFileReport_alone_extra.rmd | 28 +++-- inst/rmd/multiFileReport_extra.rmd | 32 ++++-- 20 files changed, 454 insertions(+), 204 deletions(-)
Title: Enhancements for 'broom' and 'easystats' Package Families
Description: Provides helper functions that assist in data
analysis workflows involving regression analyses. The goal is to
combine the functionality offered by different set of packages
('broom', 'broom.mixed', 'parameters', and 'performance') through a
common syntax to return tidy dataframes containing model parameters
and performance measure summaries. The 'grouped_' variants of the
generics provides a convenient way to execute functions across a
combination of grouping variable(s) in a dataframe.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between broomExtra versions 4.0.0 dated 2020-04-22 and 4.0.2 dated 2020-05-11
broomExtra-4.0.0/broomExtra/build/vignette.rds |only broomExtra-4.0.0/broomExtra/inst/doc |only broomExtra-4.0.0/broomExtra/vignettes |only broomExtra-4.0.2/broomExtra/DESCRIPTION | 11 +++---- broomExtra-4.0.2/broomExtra/MD5 | 33 ++++++++------------- broomExtra-4.0.2/broomExtra/NEWS.md | 7 ++++ broomExtra-4.0.2/broomExtra/R/generics.R | 9 ----- broomExtra-4.0.2/broomExtra/R/generics_easystats.R | 1 broomExtra-4.0.2/broomExtra/R/grouped_generics.R | 14 -------- broomExtra-4.0.2/broomExtra/README.md | 4 +- broomExtra-4.0.2/broomExtra/build/broomExtra.pdf |binary broomExtra-4.0.2/broomExtra/man/augment.Rd | 7 ---- broomExtra-4.0.2/broomExtra/man/glance.Rd | 3 - broomExtra-4.0.2/broomExtra/man/grouped_augment.Rd | 7 ---- broomExtra-4.0.2/broomExtra/man/grouped_glance.Rd | 7 ---- broomExtra-4.0.2/broomExtra/man/grouped_tidy.Rd | 7 ---- broomExtra-4.0.2/broomExtra/man/tidy.Rd | 7 ---- broomExtra-4.0.2/broomExtra/man/tidy_parameters.Rd | 1 18 files changed, 29 insertions(+), 89 deletions(-)
Title: Analysis of Basketball Data
Description: Collection of tools to work with basketball data. Functions available are related to friendly
web scraping and visualization. Data were obtained from <http://www.euroleague.net/>,
<http://www.eurocupbasketball.com/> and <http://www.acb.com>, following the instructions
of their respectives robots.txt files, when available. Tools for visualization include a population pyramid, 2D plots,
circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games
and maps of nationalities. Please see Vinue (2020) <doi:10.1089/big.2018.0124>.
Author: Guillermo Vinue
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between BAwiR versions 1.2.3 dated 2020-04-14 and 1.2.4 dated 2020-05-11
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 4 ++++ R/do_four_factors_df.R | 12 ++++++++++-- build/vignette.rds |binary inst/doc/BAwiR.html | 10 +++++----- man/BAwiR-package.Rd | 4 ++-- man/do_four_factors_df.Rd | 4 ++++ 8 files changed, 36 insertions(+), 20 deletions(-)
Title: Baseline Correction of Spectra
Description: Collection of baseline correction algorithms, along with a framework and a Tcl/Tk enabled GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.
Author: Kristian Hovde Liland [aut, cre],
Bjørn-Helge Mevik [aut],
Roberto Canteri [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between baseline versions 1.2-3 dated 2020-02-03 and 1.3-0 dated 2020-05-11
DESCRIPTION | 12 MD5 | 21 - NEWS | 4 R/baseline.rollingBall.R | 124 ++++---- R/baselineGUI.R | 678 +++++++++++++++++++++++------------------------ R/baselineGUI2.R |only R/globals.R | 8 R/optimWizard.R | 420 +++++++++++++++-------------- R/plotOptim.R | 320 +++++++++++----------- man/baseline-package.Rd | 2 man/baseline.Rd | 2 man/baselineGUI.Rd | 4 12 files changed, 823 insertions(+), 772 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-21 0.2.1
2017-03-31 0.2-0
2013-08-08 0.1-17
2013-05-30 0.1-16
2012-12-28 0.1-15
2012-10-07 0.1-14
2012-09-10 0.1-13
2012-08-08 0.1-12
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-25 3.2.1
2020-04-21 3.2.0
2020-02-10 3.1.1
2020-01-27 3.1.0
2019-12-18 3.0.9
2019-11-07 3.0.8
2019-09-12 3.0.4
2019-09-11 3.0.3
2019-08-23 3.0.1
2019-07-31 3.0.0
2019-05-29 2.9.6
2019-04-13 2.9.0
2019-02-03 2.8.2