Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-25 0.1-1
2020-09-18 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-29 1.1.0
2018-01-06 1.0.0
2017-02-28 0.5.0
2016-09-02 0.1.5
2016-06-13 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-18 0.5.0
2019-10-16 0.3.0
2019-08-20 0.2.0
2019-02-03 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-16 0.10-6
Title: Unconditional Exact Test
Description: Performs unconditional exact tests and power calculations for 2x2 contingency tables. Calculates Barnard's test (1945) <doi:10.1038/156177a0> using the original CSM test (Barnard, 1947 <doi:10.1093/biomet/34.1-2.123>), using Fisher's p-value referred to as Boschloo's test (1970) <doi:10.1111/j.1467-9574.1970.tb00104.x>, or using a Z-statistic (Suissa and Shuster, 1985, <doi:10.2307/2981892>). Calculations confidence intervals for the difference in proportion.
Author: Peter Calhoun [aut, cre]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>
Diff between Exact versions 2.0 dated 2019-10-14 and 2.1 dated 2020-10-02
Exact-2.0/Exact/R/confIntTemp.R |only Exact-2.1/Exact/DESCRIPTION | 10 +- Exact-2.1/Exact/MD5 | 55 +++++++-------- Exact-2.1/Exact/NAMESPACE | 5 + Exact-2.1/Exact/R/binomialCode.R | 39 ++++++---- Exact-2.1/Exact/R/chisq_TX.R | 33 ++++----- Exact-2.1/Exact/R/confInt.R | 47 ++++++++---- Exact-2.1/Exact/R/csmApprox_TX.R | 31 +++----- Exact-2.1/Exact/R/csmTemp.R | 31 ++++---- Exact-2.1/Exact/R/csmTemp2sidedDelta.R | 26 ++++--- Exact-2.1/Exact/R/exact.reject.region.R | 54 +++++++++----- Exact-2.1/Exact/R/exact.test.R | 28 ++++--- Exact-2.1/Exact/R/fisher.2x2.R | 47 ++++++------ Exact-2.1/Exact/R/maxPvalue.R | 11 +-- Exact-2.1/Exact/R/maxPvalueLookup.R | 4 - Exact-2.1/Exact/R/moreExtreme.R | 64 +++++++++++------ Exact-2.1/Exact/R/moreExtremeCSM.R | 17 ++-- Exact-2.1/Exact/R/multinomialCode.R | 66 +++++++----------- Exact-2.1/Exact/R/power.exact.test.R | 23 +++--- Exact-2.1/Exact/R/santner_TX.R | 14 +-- Exact-2.1/Exact/R/searchExtreme.R | 7 + Exact-2.1/Exact/R/zpooled_TX.R | 105 ++++++++++++----------------- Exact-2.1/Exact/R/zunpooled_TX.R | 19 +++-- Exact-2.1/Exact/build/partial.rdb |binary Exact-2.1/Exact/inst/NEWS.Rd | 14 +++ Exact-2.1/Exact/man/Exact-package.Rd | 16 +++- Exact-2.1/Exact/man/exact.reject.region.Rd | 27 ++++--- Exact-2.1/Exact/man/exact.test.Rd | 75 ++++++++++---------- Exact-2.1/Exact/man/power.exact.test.Rd | 42 +++++++---- 29 files changed, 497 insertions(+), 413 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web services for chemical information. Sources include: Alan
Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver,
ChEBI, Chemical Translation Service, ChemIDplus, ChemSpider, ETOX,
Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem,
SRS, Wikidata.
Author: Eduard Szöcs [aut],
Robert Allaway [ctb],
Daniel Muench [ctb],
Johannes Ranke [ctb],
Andreas Scharmüller [ctb],
Eric R Scott [ctb],
Jan Stanstrup [ctb],
João Vitor F Cavalcante [ctb],
Gordon Getzinger [ctb],
Tamás Stirling [ctb, cre]
Maintainer: Tamás Stirling <stirling.tamas@gmail.com>
Diff between webchem versions 1.0.0 dated 2020-05-28 and 1.1.0 dated 2020-10-02
webchem-1.0.0/webchem/man/build_aw_idx.Rd |only webchem-1.1.0/webchem/DESCRIPTION | 19 webchem-1.1.0/webchem/MD5 | 155 ++--- webchem-1.1.0/webchem/NAMESPACE | 14 webchem-1.1.0/webchem/NEWS.md | 176 +++--- webchem-1.1.0/webchem/R/alanwood.R | 273 +++++----- webchem-1.1.0/webchem/R/chebi.R | 173 +++--- webchem-1.1.0/webchem/R/chemid.R | 295 +++++----- webchem-1.1.0/webchem/R/chemspider.R | 90 ++- webchem-1.1.0/webchem/R/cir.R | 354 +++++++++++-- webchem-1.1.0/webchem/R/cts.R | 185 +++++- webchem-1.1.0/webchem/R/etox.R | 434 ++++++++-------- webchem-1.1.0/webchem/R/extractors.R | 28 - webchem-1.1.0/webchem/R/flavornet.R | 65 +- webchem-1.1.0/webchem/R/integration.R |only webchem-1.1.0/webchem/R/nist.R | 150 +++-- webchem-1.1.0/webchem/R/opsin.R | 52 + webchem-1.1.0/webchem/R/pan.R | 117 ++-- webchem-1.1.0/webchem/R/ping.R | 93 ++- webchem-1.1.0/webchem/R/pubchem.R | 278 ++++++---- webchem-1.1.0/webchem/R/srs.R | 31 - webchem-1.1.0/webchem/R/utils.R | 266 ++++----- webchem-1.1.0/webchem/R/webchem-package.R | 2 webchem-1.1.0/webchem/R/wikidata.R | 148 +++-- webchem-1.1.0/webchem/R/zzz.R |only webchem-1.1.0/webchem/inst/doc/webchem.html | 70 ++ webchem-1.1.0/webchem/man/as.cas.Rd | 3 webchem-1.1.0/webchem/man/aw_query.Rd | 32 - webchem-1.1.0/webchem/man/chebi_comp_entity.Rd | 3 webchem-1.1.0/webchem/man/ci_query.Rd | 25 webchem-1.1.0/webchem/man/cir_img.Rd |only webchem-1.1.0/webchem/man/cir_query.Rd | 52 - webchem-1.1.0/webchem/man/cs_compinfo.Rd | 3 webchem-1.1.0/webchem/man/cs_control.Rd | 3 webchem-1.1.0/webchem/man/cs_convert.Rd | 5 webchem-1.1.0/webchem/man/cs_datasources.Rd | 3 webchem-1.1.0/webchem/man/cs_extcompinfo.Rd | 3 webchem-1.1.0/webchem/man/cs_img.Rd |only webchem-1.1.0/webchem/man/cts_compinfo.Rd | 11 webchem-1.1.0/webchem/man/cts_convert.Rd | 16 webchem-1.1.0/webchem/man/cts_from.Rd | 3 webchem-1.1.0/webchem/man/cts_to.Rd | 3 webchem-1.1.0/webchem/man/etox_basic.Rd | 7 webchem-1.1.0/webchem/man/etox_targets.Rd | 3 webchem-1.1.0/webchem/man/etox_tests.Rd | 3 webchem-1.1.0/webchem/man/find_db.Rd |only webchem-1.1.0/webchem/man/fn_percept.Rd | 15 webchem-1.1.0/webchem/man/get_chebiid.Rd | 49 - webchem-1.1.0/webchem/man/get_cid.Rd | 5 webchem-1.1.0/webchem/man/get_csid.Rd | 5 webchem-1.1.0/webchem/man/get_etoxid.Rd | 9 webchem-1.1.0/webchem/man/get_wdid.Rd | 3 webchem-1.1.0/webchem/man/is.cas.Rd | 3 webchem-1.1.0/webchem/man/is.inchikey.Rd | 3 webchem-1.1.0/webchem/man/is.inchikey_cs.Rd | 3 webchem-1.1.0/webchem/man/is.inchikey_format.Rd | 3 webchem-1.1.0/webchem/man/is.smiles.Rd | 3 webchem-1.1.0/webchem/man/jagst.Rd | 2 webchem-1.1.0/webchem/man/nist_ri.Rd | 12 webchem-1.1.0/webchem/man/opsin_query.Rd | 4 webchem-1.1.0/webchem/man/pan_query.Rd | 19 webchem-1.1.0/webchem/man/parse_mol.Rd | 5 webchem-1.1.0/webchem/man/pc_prop.Rd | 5 webchem-1.1.0/webchem/man/pc_sect.Rd | 4 webchem-1.1.0/webchem/man/pc_synonyms.Rd | 26 webchem-1.1.0/webchem/man/srs_query.Rd | 14 webchem-1.1.0/webchem/man/wd_ident.Rd | 3 webchem-1.1.0/webchem/man/with_cts.Rd |only webchem-1.1.0/webchem/tests/testthat.R | 2 webchem-1.1.0/webchem/tests/testthat/test-alanwood.R | 6 webchem-1.1.0/webchem/tests/testthat/test-chebi.R | 11 webchem-1.1.0/webchem/tests/testthat/test-chemid.R | 18 webchem-1.1.0/webchem/tests/testthat/test-chemspider.R | 84 ++- webchem-1.1.0/webchem/tests/testthat/test-cir.R | 28 - webchem-1.1.0/webchem/tests/testthat/test-cts.R | 19 webchem-1.1.0/webchem/tests/testthat/test-etox.R | 33 - webchem-1.1.0/webchem/tests/testthat/test-extractors.R | 7 webchem-1.1.0/webchem/tests/testthat/test-flavornet.R | 2 webchem-1.1.0/webchem/tests/testthat/test-integration.R |only webchem-1.1.0/webchem/tests/testthat/test-nist.R | 32 - webchem-1.1.0/webchem/tests/testthat/test-pubchem.R | 35 - webchem-1.1.0/webchem/tests/testthat/test-srs.R |only webchem-1.1.0/webchem/tests/testthat/test-utils.R | 23 83 files changed, 2453 insertions(+), 1688 deletions(-)
Title: Dynamically Generates Documentation from a 'Swagger' Compliant
API
Description: A collection of 'HTML', 'JavaScript', and 'CSS' assets that
dynamically generate beautiful documentation from a 'Swagger' compliant API:
<https://swagger.io/specification/>.
Author: Barret Schloerke [cre, aut],
Javier Luraschi [aut],
RStudio [cph],
SmartBear Software [aut, cph]
Maintainer: Barret Schloerke <barret@rstudio.com>
Diff between swagger versions 3.33.0 dated 2020-09-12 and 3.33.1 dated 2020-10-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/dist3/index.html | 5 +++++ tools/download_swagger_ui.R | 11 +++++++++-- 5 files changed, 25 insertions(+), 9 deletions(-)
Title: Utility Functions for 'MixtComp' Outputs
Description: Mixture Composer <https://github.com/modal-inria/MixtComp> is a project to build mixture models with
heterogeneous data sets and partially missing data management. This package contains graphical, getter and some utility
functions to facilitate the analysis of 'MixtComp' output.
Author: Vincent Kubicki [aut],
Christophe Biernacki [aut],
Quentin Grimonprez [aut],
Matthieu Marbac-Lourdelle [aut],
Étienne Goffinet [ctb],
Serge Iovleff [ctb],
Julien Vandaele [ctb, cre]
Maintainer: Julien Vandaele <julien.vandaele@inria.fr>
Diff between RMixtCompUtilities versions 4.1.2 dated 2020-06-23 and 4.1.3 dated 2020-10-02
DESCRIPTION | 22 ++++++----- MD5 | 24 ++++++------ NAMESPACE | 2 + NEWS | 9 ++++ R/MIXTCOMP_formatParameter.R | 27 +++++++++----- R/MIXTCOMP_misc.R | 29 +++++++++++++++ R/PLOT_barplot.R | 9 +--- R/PLOT_extractCIbounds.R | 42 ++++++++++++--------- R/PLOT_heatmap.R | 2 - R/PLOT_plotUnivariateBoxplots.R | 22 +++++++---- R/PLOT_plotUnivariateDistributions.R | 54 +++++++++++++++------------- R/RMixtCompUtilities-package.R | 4 +- tests/testthat/test.parameterPretreatment.R | 28 ++++++++++++++ 13 files changed, 186 insertions(+), 88 deletions(-)
More information about RMixtCompUtilities at CRAN
Permanent link
Title: Client for Various 'CrossRef' 'APIs'
Description: Client for various 'CrossRef' 'APIs', including 'metadata' search
with their old and newer search 'APIs', get 'citations' in various formats
(including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs'
to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to
full text of articles when available.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Hao Zhu [aut],
Najko Jahn [aut],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rcrossref versions 1.0.0 dated 2020-03-19 and 1.1.0 dated 2020-10-02
rcrossref-1.0.0/rcrossref/build |only rcrossref-1.0.0/rcrossref/inst/doc |only rcrossref-1.0.0/rcrossref/vignettes |only rcrossref-1.1.0/rcrossref/DESCRIPTION | 15 rcrossref-1.1.0/rcrossref/MD5 | 100 +- rcrossref-1.1.0/rcrossref/NAMESPACE | 3 rcrossref-1.1.0/rcrossref/NEWS.md | 10 rcrossref-1.1.0/rcrossref/R/cr_abstract.R | 15 rcrossref-1.1.0/rcrossref/R/cr_agency.r | 2 rcrossref-1.1.0/rcrossref/R/cr_async.R | 2 rcrossref-1.1.0/rcrossref/R/cr_citation.R | 4 rcrossref-1.1.0/rcrossref/R/cr_citation_count.r | 4 rcrossref-1.1.0/rcrossref/R/cr_cn.r | 9 rcrossref-1.1.0/rcrossref/R/cr_ft_links.R | 4 rcrossref-1.1.0/rcrossref/R/cr_ft_text.R | 16 rcrossref-1.1.0/rcrossref/R/cr_fundref.r | 10 rcrossref-1.1.0/rcrossref/R/cr_journals.r | 12 rcrossref-1.1.0/rcrossref/R/cr_licenses.R | 4 rcrossref-1.1.0/rcrossref/R/cr_members.r | 10 rcrossref-1.1.0/rcrossref/R/cr_prefixes.r | 2 rcrossref-1.1.0/rcrossref/R/cr_search.r | 4 rcrossref-1.1.0/rcrossref/R/cr_search_free.r | 4 rcrossref-1.1.0/rcrossref/R/cr_types.R | 2 rcrossref-1.1.0/rcrossref/R/cr_works.R | 38 rcrossref-1.1.0/rcrossref/R/crosscite.R | 4 rcrossref-1.1.0/rcrossref/R/deprecated_defunct.R | 4 rcrossref-1.1.0/rcrossref/R/extract_pdf.R | 4 rcrossref-1.1.0/rcrossref/R/id_converter.R | 3 rcrossref-1.1.0/rcrossref/R/pmid2doi.R | 8 rcrossref-1.1.0/rcrossref/R/rcrossref-package.R | 16 rcrossref-1.1.0/rcrossref/R/requestor.R | 2 rcrossref-1.1.0/rcrossref/R/tdmurl.R | 4 rcrossref-1.1.0/rcrossref/R/zzz.R | 7 rcrossref-1.1.0/rcrossref/README.md | 407 ---------- rcrossref-1.1.0/rcrossref/man/cr_agency.Rd | 2 rcrossref-1.1.0/rcrossref/man/cr_citation_count.Rd | 4 rcrossref-1.1.0/rcrossref/man/cr_cn.Rd | 6 rcrossref-1.1.0/rcrossref/man/cr_funders.Rd | 2 rcrossref-1.1.0/rcrossref/man/cr_journals.Rd | 2 rcrossref-1.1.0/rcrossref/man/cr_licenses.Rd | 2 rcrossref-1.1.0/rcrossref/man/cr_members.Rd | 2 rcrossref-1.1.0/rcrossref/man/cr_prefixes.Rd | 2 rcrossref-1.1.0/rcrossref/man/cr_types.Rd | 2 rcrossref-1.1.0/rcrossref/man/cr_works.Rd | 2 rcrossref-1.1.0/rcrossref/man/rcrossref-package.Rd | 12 rcrossref-1.1.0/rcrossref/tests/fixtures/cr_abstract.yml |only rcrossref-1.1.0/rcrossref/tests/fixtures/cr_abstract_not_found.yml |only rcrossref-1.1.0/rcrossref/tests/fixtures/id_converter_fails_type_param_bad.yml |only rcrossref-1.1.0/rcrossref/tests/testthat/test-cr_abstract.R |only rcrossref-1.1.0/rcrossref/tests/testthat/test-cr_cn.R | 9 rcrossref-1.1.0/rcrossref/tests/testthat/test-cr_works.R | 18 rcrossref-1.1.0/rcrossref/tests/testthat/test-id_converter.R | 5 52 files changed, 229 insertions(+), 570 deletions(-)
Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.9.1 dated 2020-03-25 and 0.9.4 dated 2020-10-02
DESCRIPTION | 9 MD5 | 411 ++++++++++++++++++++-------------------- NAMESPACE | 6 R/definitions.R | 2 R/init.R | 5 R/likebut.R | 80 ++++++- R/model.R | 31 ++- R/nonmemica.R | 4 R/partab.R | 6 R/path.R | 56 +++++ R/runrecord.R |only inst/doc/parameter-table.html | 103 +++++----- man/absolute.Rd | 32 +-- man/as.best.Rd | 148 +++++++------- man/as.bootstrap.Rd | 156 ++++++++------- man/as.bootstrap.numeric.Rd | 46 ++-- man/as.character.init.Rd | 53 ++--- man/as.character.inits.Rd | 61 +++-- man/as.character.items.Rd | 77 ++++--- man/as.character.model.Rd | 53 ++--- man/as.character.problem.Rd |only man/as.data.frame.halfmatrix.Rd | 63 +++--- man/as.halfmatrix.Rd | 63 +++--- man/as.halfmatrix.default.Rd | 61 +++-- man/as.halfmatrix.halfmatrix.Rd | 63 +++--- man/as.init.Rd | 84 ++++---- man/as.init.numeric.Rd | 57 ++--- man/as.inits.Rd | 123 ++++++----- man/as.inits.numeric.Rd | 54 ++--- man/as.items.Rd | 33 +-- man/as.items.character.Rd | 39 +-- man/as.list.model.Rd | 39 +-- man/as.matrices.Rd | 42 ++-- man/as.matrices.inits.Rd | 50 ++-- man/as.matrices.records.Rd | 42 ++-- man/as.matrix.halfmatrix.Rd | 61 +++-- man/as.model.Rd | 122 ++++++----- man/as.model.numeric.Rd | 48 ++-- man/as.omega.Rd | 40 ++- man/as.omega.model.Rd | 46 ++-- man/as.problem.Rd |only man/as.sigma.Rd | 32 +-- man/as.sigma.model.Rd | 39 +-- man/as.tab.Rd | 40 ++- man/as.tab.model.Rd | 46 ++-- man/as.theta.Rd | 40 ++- man/as.theta.model.Rd | 46 ++-- man/as.xml_document.Rd | 122 ++++++----- man/as.xml_document.numeric.Rd | 50 ++-- man/but.Rd | 40 ++- man/but.default.Rd | 48 ++-- man/cash-.init.Rd | 46 ++-- man/cash-set-.init.Rd | 50 ++-- man/comments.Rd | 161 +++++++-------- man/comwidth.Rd | 50 ++-- man/comwidth.character.Rd | 45 ++-- man/comwidth.inits.Rd | 43 ++-- man/comwidth.items.Rd | 43 ++-- man/comwidthOne.Rd | 40 ++- man/comwidthOne.character.Rd | 46 ++-- man/contains.Rd | 46 ++-- man/datafile.Rd | 58 +++-- man/datafile.character.Rd | 92 ++++---- man/datafile.numeric.Rd | 58 +++-- man/definitions.Rd | 171 ++++++++-------- man/definitions.numeric.Rd | 48 ++-- man/depends.Rd | 40 ++- man/depends.default.Rd | 46 ++-- man/enclose.Rd | 67 +++--- man/errors.Rd | 42 ++-- man/errors.character.Rd | 83 ++++---- man/errors.numeric.Rd | 42 ++-- man/estimates.Rd | 42 ++-- man/estimates.character.Rd | 83 ++++---- man/estimates.numeric.Rd | 42 ++-- man/fixed-set-.init.Rd | 54 ++--- man/fixed-set-.inits.Rd | 54 ++--- man/fixed-set-.model.Rd | 54 ++--- man/fixed-set.Rd | 46 ++-- man/fixed.Rd | 114 ++++++----- man/fixed.model.Rd | 62 +++--- man/format.init.Rd | 49 ++-- man/format.inits.Rd | 49 ++-- man/format.items.Rd | 49 ++-- man/format.model.Rd | 55 ++--- man/generalize.Rd | 67 +++--- man/grapes-contains-grapes.Rd | 68 +++--- man/half.Rd | 64 +++--- man/half.matrix.Rd | 63 +++--- man/initDex.Rd | 40 ++- man/initDex.model.Rd | 48 ++-- man/initSubscripts.Rd | 40 ++- man/initSubscripts.model.Rd | 48 ++-- man/initial-set-.model.Rd | 43 ++-- man/initial-set.Rd | 43 ++-- man/initial.Rd | 43 ++-- man/initial.model.Rd | 53 ++--- man/is.defined.Rd | 40 +-- man/is.square.Rd | 64 +++--- man/is.square.matrix.Rd | 64 +++--- man/like.Rd | 40 ++- man/like.default.Rd | 46 ++-- man/likebut.Rd | 132 +++++++----- man/locf.Rd | 153 ++++++++------ man/lower-set-.model.Rd | 43 ++-- man/lower-set.Rd | 43 ++-- man/lower.Rd | 43 ++-- man/lower.model.Rd | 53 ++--- man/maxWidths.Rd | 40 ++- man/maxWidths.list.Rd | 40 ++- man/meta.Rd | 69 +++--- man/meta.character.Rd | 87 ++++---- man/meta.numeric.Rd | 69 +++--- man/metaplot.character.Rd | 111 +++++----- man/metaplot.numeric.Rd | 68 +++--- man/metaplot_character.Rd | 86 ++++---- man/metasuperset.Rd | 101 +++++---- man/modeldir.Rd | 76 +++---- man/modelfile.Rd | 76 +++---- man/modelpath.Rd | 72 +++---- man/modelpath.character.Rd | 83 ++++---- man/modelpath.numeric.Rd | 64 +++--- man/ninput.Rd | 67 +++--- man/ninput.character.Rd | 72 +++---- man/ninput.numeric.Rd | 66 +++--- man/nms_canonical.Rd | 32 +-- man/nms_canonical.character.Rd | 42 ++-- man/nms_canonical.model.Rd | 44 ++-- man/nms_canonical.numeric.Rd | 32 +-- man/nms_nonmem.Rd | 44 ++-- man/nms_nonmem.character.Rd | 54 ++--- man/nms_nonmem.model.Rd | 54 ++--- man/nms_nonmem.numeric.Rd | 45 ++-- man/nms_psn.Rd | 32 +-- man/nms_psn.character.Rd | 42 ++-- man/nms_psn.model.Rd | 44 ++-- man/nms_psn.numeric.Rd | 32 +-- man/nonmemica.Rd | 347 ++++++++++++++++----------------- man/num_parameters.Rd | 32 +-- man/num_parameters.default.Rd | 58 ++--- man/offdiag.Rd | 64 +++--- man/offdiag.halfmatrix.Rd | 62 +++--- man/ord.Rd | 64 +++--- man/ord.halfmatrix.Rd | 64 +++--- man/ord.inits.Rd | 54 ++--- man/ord.items.Rd | 52 ++--- man/ord.matrix.Rd | 64 +++--- man/padded.Rd | 63 +++--- man/parameters.Rd | 42 ++-- man/parameters.character.Rd | 68 +++--- man/parameters.numeric.Rd | 42 ++-- man/parens.Rd | 59 +++-- man/partab.Rd | 83 ++++---- man/partab.character.Rd | 207 +++++++++++--------- man/partab.numeric.Rd | 50 ++-- man/pool.Rd | 65 +++--- man/prettycom.Rd | 40 ++- man/prettycom.character.Rd | 54 ++--- man/print.halfmatrix.Rd | 64 +++--- man/print.init.Rd | 49 ++-- man/print.inits.Rd | 49 ++-- man/print.items.Rd | 49 ++-- man/print.model.Rd | 55 ++--- man/problem.Rd | 44 ++-- man/problem.character.Rd | 50 ++-- man/problem.numeric.Rd | 46 ++-- man/problem_.Rd | 46 ++-- man/psn_nested.Rd |only man/psn_options.Rd |only man/read.model.Rd | 64 +++--- man/relativizePath.Rd | 50 ++-- man/resolve.Rd | 38 +-- man/row_col.Rd | 61 +++-- man/runhead.Rd | 55 ++--- man/runlog.Rd | 46 ++-- man/runlog.character.Rd | 87 ++++---- man/runlog.numeric.Rd | 42 ++-- man/shuffle.Rd | 81 ++++--- man/specfile.Rd | 58 +++-- man/specfile.character.Rd | 101 +++++---- man/specfile.numeric.Rd | 57 +++-- man/sub-.inits.Rd | 43 ++-- man/sub-.model.Rd | 58 +++-- man/sub-sub-.model.Rd | 58 +++-- man/superset.Rd | 79 ++++--- man/superset.character.Rd | 162 ++++++++------- man/superset.numeric.Rd | 79 ++++--- man/superspec.Rd | 71 +++--- man/superspec.character.Rd | 101 +++++---- man/superspec.numeric.Rd | 67 +++--- man/tad.Rd | 105 +++++----- man/tad1.Rd | 54 ++--- man/text2decimal.Rd | 61 +++-- man/tod.Rd | 66 +++--- man/tweak.Rd | 45 ++-- man/tweak.default.Rd | 85 ++++---- man/tweak.init.Rd | 61 +++-- man/tweak.inits.Rd | 61 +++-- man/tweak.model.Rd | 93 ++++----- man/updated.Rd | 42 ++-- man/updated.character.Rd | 61 +++-- man/updated.numeric.Rd | 42 ++-- man/upper-set-.model.Rd | 43 ++-- man/upper-set.Rd | 43 ++-- man/upper.Rd | 43 ++-- man/upper.model.Rd | 53 ++--- man/val_name.Rd | 61 +++-- man/write.model.Rd | 77 +++---- man/xpath.Rd | 124 ++++++------ 209 files changed, 6926 insertions(+), 5965 deletions(-)
Title: Run GWAS/GWEIS Scans Using Binary Dosage Files
Description: Tools to run genome-wide association study (GWAS) and
genome-wide by environment interaction study (GWEIS) scans using the genetic
data stored in a binary dosage file. The user provides a data frame with
the subject's covariate data and the information about the binary dosage
file returned by the BinaryDosage::getbdinfo() routine.
Author: John Morrison [aut, cre],
NCI [fnd] (CA196559),
NCI [fnd] (CA201407),
NIEHS [fnd] (ES007048),
NHLBI [fnd] (HL115606)
Maintainer: John Morrison <jmorr@usc.edu>
Diff between GxEScanR versions 2.0.1 dated 2020-09-29 and 2.0.2 dated 2020-10-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 +++++- inst/WORDLIST | 1 + src/LSLinReg.cpp | 2 +- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: C3S Quality Control Tools for Historical Climate Data
Description: Quality control and formatting tools developed for the Copernicus Data Rescue Service. The package includes functions to handle the Station Exchange Format (SEF), various statistical tests for climate data at daily and sub-daily resolution, as well as functions to plot the data. For more information and documentation see <https://datarescue.climate.copernicus.eu/st_data-quality-control>.
Author: Yuri Brugnara [aut, cre] (<https://orcid.org/0000-0001-8427-0064>),
Alba Gilabert [aut],
Clara Ventura [aut],
Stefan Hunziker [aut]
Maintainer: Yuri Brugnara <yuri.brugnara@giub.unibe.ch>
Diff between dataresqc versions 1.0.3 dated 2020-03-06 and 1.1.0 dated 2020-10-02
DESCRIPTION | 12 +-- MD5 | 38 ++++----- NAMESPACE | 2 R/decade.R | 26 ++++-- R/era-clim.R | 198 +++++++++++++++++++++++++-------------------------- R/input.R | 45 +++++------ R/output.R | 112 +++++++++++++++++----------- data/Bern.rda |binary data/Meta.rda |binary data/Rosario.rda |binary data/Tests.rda |binary data/Variables.rda |binary man/Bern.Rd | 6 + man/Meta.Rd | 34 ++++---- man/Rosario.Rd | 6 + man/Tests.Rd | 28 +++---- man/Variables.Rd | 28 +++---- man/plot_subdaily.Rd | 19 ++++ man/write_flags.Rd | 11 ++ man/write_sef.Rd | 3 20 files changed, 319 insertions(+), 249 deletions(-)
Title: A Binary Download Manager
Description: Tools and functions for managing the download of binary files.
Binary repositories are defined in 'YAML' format. Defining new
pre-download, download and post-download templates allow additional
repositories to be added.
Author: John Harrison [aut] (original author),
Ju Yeong Kim [cre] (rOpenSci maintainer)
Maintainer: Ju Yeong Kim <jkim2345@fredhutch.org>
Diff between binman versions 0.1.1 dated 2018-07-18 and 0.1.2 dated 2020-10-02
DESCRIPTION | 12 - MD5 | 70 +++++----- NEWS.md | 7 - R/assertions.R | 49 +++---- R/assign_directory.R | 15 +- R/binman-package.r | 9 + R/binman_utils.R | 78 ++++++----- R/download_files.R | 53 ++++--- R/postdl_templates.R | 83 +++++++----- R/predl_templates.R | 69 ++++++---- R/process_yaml.R | 66 ++++++--- R/utils.R | 23 +-- README.md | 54 +++---- build/vignette.rds |binary inst/doc/binman-Basics.html | 227 +++++++++++++++++++++++++++++++-- man/app_dir.Rd | 1 man/assign_directory.Rd | 3 man/binman.Rd | 11 + man/download_files.Rd | 11 + man/list_versions.Rd | 1 man/noproc_dlfiles.Rd | 15 +- man/predl_bitbucket_downloads.Rd | 22 ++- man/predl_github_assets.Rd | 20 ++ man/predl_google_storage.Rd | 22 ++- man/process_yaml.Rd | 15 +- man/rm_platform.Rd | 1 man/rm_version.Rd | 1 man/unziptar_dlfiles.Rd | 15 +- tests/testthat.R | 4 tests/testthat/helper.R | 8 - tests/testthat/test-assign_directory.R | 2 tests/testthat/test-binman_utils.R | 24 ++- tests/testthat/test-download_files.R | 23 ++- tests/testthat/test-postdl_templates.R | 46 +++--- tests/testthat/test-predl_templates.R | 80 +++++++---- tests/testthat/test-process_yaml.R | 6 36 files changed, 770 insertions(+), 376 deletions(-)
Title: 'cpt-city' Colour Gradients
Description: Incorporates colour gradients from the 'cpt-city' web archive available at <http://soliton.vm.bytemark.co.uk/pub/cpt-city/>.
Author: Sergio Ibarra-Espinosa [aut, cre]
(<https://orcid.org/0000-0002-3162-1905>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>
Diff between cptcity versions 1.0.4 dated 2019-03-07 and 1.0.6 dated 2020-10-02
DESCRIPTION | 8 +-- MD5 | 20 +++---- NEWS.md | 88 +++++++++++++++++----------------- R/cpt.R | 111 ++++++++++++++++++++++++-------------------- R/lucky.R | 14 +++-- man/cpt.Rd | 17 +++++- man/cpt_names.Rd | 4 + man/cptcity.Rd | 1 man/lucky.Rd | 13 ++++- tests/testthat/test-cpt.R | 37 ++++++++------ tests/testthat/test-lucky.R | 16 +++++- 11 files changed, 198 insertions(+), 131 deletions(-)
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre],
Matt Dennis [ctb],
Gerard Walsh [ctb],
Antoine Bichat [ctb] (<https://orcid.org/0000-0001-6599-7081>),
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb]
Maintainer: Andrew B. Collier <andrew@exegetic.biz>
Diff between emayili versions 0.4.0 dated 2020-06-03 and 0.4.4 dated 2020-10-02
emayili-0.4.0/emayili/man/message.Rd |only emayili-0.4.4/emayili/DESCRIPTION | 11 +++- emayili-0.4.4/emayili/MD5 | 22 ++++---- emayili-0.4.4/emayili/NAMESPACE | 1 emayili-0.4.4/emayili/R/attachment.R | 14 ++--- emayili-0.4.4/emayili/R/envelope.R | 47 +++++++++++++++++-- emayili-0.4.4/emayili/R/message.R | 20 ++++---- emayili-0.4.4/emayili/R/server.R | 2 emayili-0.4.4/emayili/README.md | 37 +++++++++++--- emayili-0.4.4/emayili/man/as.character.envelope.Rd |only emayili-0.4.4/emayili/man/attachment.Rd | 7 ++ emayili-0.4.4/emayili/man/envelope.Rd | 39 +++++++++++++++ emayili-0.4.4/emayili/tests/testthat/test-envelope.R | 47 +++++++++++++++++++ 13 files changed, 199 insertions(+), 48 deletions(-)
Title: Data Quality Assessment for Process-Oriented Data
Description: Provides a variety of methods to identify data quality issues in process-oriented data, which are useful to verify data quality in a process mining context. Builds on the class for activity logs implemented in the package 'bupaR'. Methods to identify data quality issues either consider each activity log entry independently (e.g. missing values, activity duration outliers,...), or focus on the relation amongst several activity log entries (e.g. batch registrations, violations of the expected activity order,...).
Author: Niels Martin [aut, cre],
Greg Van Houdt [ctb],
Gert Janssenswillen [ctb]
Maintainer: Niels Martin <niels.martin@uhasselt.be>
Diff between daqapo versions 0.3.0 dated 2020-04-08 and 0.3.1 dated 2020-10-02
DESCRIPTION | 10 MD5 | 46 +-- R/detect_duration_outliers.R | 8 inst/doc/Introduction-to-DaQAPO.R | 61 ++--- inst/doc/Introduction-to-DaQAPO.Rmd | 1 inst/doc/Introduction-to-DaQAPO.html | 330 ++++++++++++++-------------- man/daqapo.Rd | 1 man/detect_activity_frequency_violations.Rd | 8 man/detect_activity_order_violations.Rd | 19 + man/detect_attribute_dependencies.Rd | 10 man/detect_conditional_activity_presence.Rd | 9 man/detect_inactive_periods.Rd | 11 man/detect_incorrect_activity_names.Rd | 8 man/detect_missing_values.Rd | 9 man/detect_multiregistration.Rd | 10 man/detect_overlaps.Rd | 3 man/detect_related_activities.Rd | 9 man/detect_similar_labels.Rd | 10 man/detect_time_anomalies.Rd | 8 man/hospital.Rd | 6 man/hospital_actlog.Rd | 6 man/hospital_events.Rd | 6 man/reexports.Rd | 8 vignettes/Introduction-to-DaQAPO.Rmd | 1 24 files changed, 333 insertions(+), 265 deletions(-)
Title: Feature Set Enrichment Analysis for Metabolomics and
Transcriptomics
Description: Methods and feature set definitions for feature or gene set
enrichment analysis in transcriptional and metabolic profiling data.
Package includes tests for enrichment based on ranked lists of features,
functions for visualisation and multivariate functional analysis.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between tmod versions 0.44 dated 2020-06-18 and 0.46.2 dated 2020-10-02
tmod-0.44/tmod/inst/doc/tmod.pdf |only tmod-0.44/tmod/inst/doc/tmod.pdf.asis |only tmod-0.46.2/tmod/DESCRIPTION | 17 +++++------ tmod-0.46.2/tmod/MD5 | 33 ++++++++++++--------- tmod-0.46.2/tmod/NAMESPACE | 1 tmod-0.46.2/tmod/R/Egambia.R | 19 ++++++++++++ tmod-0.46.2/tmod/R/panelplots.R | 4 +- tmod-0.46.2/tmod/R/statisticaltests.R | 13 +++++++- tmod-0.46.2/tmod/R/tmodSummary.R | 2 + tmod-0.46.2/tmod/R/visualizations.R | 8 ++--- tmod-0.46.2/tmod/README.md | 43 ++++++++++++++++++++++++++-- tmod-0.46.2/tmod/build/vignette.rds |binary tmod-0.46.2/tmod/data/datalist | 1 tmod-0.46.2/tmod/data/vaccination.rda |only tmod-0.46.2/tmod/inst/doc/tmod_gallery.R |only tmod-0.46.2/tmod/inst/doc/tmod_gallery.Rmd |only tmod-0.46.2/tmod/inst/doc/tmod_gallery.html |only tmod-0.46.2/tmod/man/tmodSummary.Rd | 2 + tmod-0.46.2/tmod/man/tmodUtest.Rd | 5 ++- tmod-0.46.2/tmod/man/vaccination.Rd |only tmod-0.46.2/tmod/vignettes/tmod.pdf |only tmod-0.46.2/tmod/vignettes/tmod_gallery.Rmd |only 22 files changed, 116 insertions(+), 32 deletions(-)
Title: Three Dimensional PCA Plots
Description: Functions simplifying presentation of PCA models in a 3D interactive representation using 'rgl'.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between pca3d versions 0.10.1 dated 2019-12-14 and 0.10.2 dated 2020-10-02
DESCRIPTION | 14 ++++--- MD5 | 21 +++++----- NAMESPACE | 2 - README.md |only build/vignette.rds |binary inst/doc/pca3d.pdf |binary man/defaultPalettePCA3D.Rd | 3 - man/listShapes.Rd | 3 - man/makeMoviePCA.Rd | 3 - man/metabo.Rd | 7 +-- man/pca3d-package.Rd | 90 +++++++++++++++++++++++++++++++++------------ man/snapshotPCA3d.Rd | 3 - 12 files changed, 94 insertions(+), 52 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi [aut],
Yuan Tang [aut, cre] (<https://orcid.org/0000-0001-5243-233X>),
Austin Dickey [ctb],
Matthias Grenié [ctb],
Ryan Thompson [ctb],
Luciano Selzer [ctb],
Dario Strbenac [ctb],
Kirill Voronin [ctb],
Damir Pulatov [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between ggfortify versions 0.4.10 dated 2020-04-26 and 0.4.11 dated 2020-10-02
DESCRIPTION | 23 +++++++----- MD5 | 26 +++++++------- NAMESPACE | 2 + NEWS.md | 6 +++ R/fortify_cluster.R | 76 +++++++++++++++++++++++++++++++++++++++++ R/fortify_stats_lm.R | 4 ++ inst/doc/plot_map.html | 2 - inst/doc/plot_pca.R | 3 + inst/doc/plot_pca.Rmd | 14 +++++++ inst/doc/plot_pca.html | 29 +++++++++++---- man/autoplot.silhouette.Rd |only man/fortify.silhouette.Rd |only tests/testthat/test-cluster.R | 42 ++++++++++++++++++++++ tests/testthat/test-stats-lm.R | 12 ++++++ vignettes/plot_pca.Rmd | 14 +++++++ 15 files changed, 220 insertions(+), 33 deletions(-)
Title: Satellite Derived Water Quality Detection Algorithms
Description: The main purpose of waterquality is to quickly and easily convert
satellite-based reflectance imagery into one or many well-known water quality
algorithms designed for the detection of harmful algal blooms or the following
pigment proxies: chlorophyll-a, blue-green algae (phycocyanin), and turbidity.
Johansen et al. (2019) <doi:10.21079/11681/35053>.
Author: Richard Johansen [aut, cre] (<https://orcid.org/0000-0003-4287-9677>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Molly Reif [aut] (<https://orcid.org/0000-0003-4207-1459>),
Erich Emery [aut],
U.S. Army Corps of Engineers [fnd]
Maintainer: Richard Johansen <richard.a.johansen@erdc.dren.mil>
Diff between waterquality versions 0.2.2 dated 2018-12-18 and 0.2.5 dated 2020-10-02
waterquality-0.2.2/waterquality/man/figures/README-example-1.png |only waterquality-0.2.5/waterquality/DESCRIPTION | 27 waterquality-0.2.5/waterquality/LICENSE | 2 waterquality-0.2.5/waterquality/MD5 | 139 - waterquality-0.2.5/waterquality/NAMESPACE | 16 waterquality-0.2.5/waterquality/R/extract_lm_functions.R |only waterquality-0.2.5/waterquality/R/map_wq.R |only waterquality-0.2.5/waterquality/R/utils-pipe.R |only waterquality-0.2.5/waterquality/R/waterquality-package.R | 3 waterquality-0.2.5/waterquality/R/wq_calc.R | 4 waterquality-0.2.5/waterquality/README.md | 74 waterquality-0.2.5/waterquality/build/vignette.rds |binary waterquality-0.2.5/waterquality/data/wq_algorithms.rda |binary waterquality-0.2.5/waterquality/inst/CITATION | 20 waterquality-0.2.5/waterquality/inst/doc/waterquality_vignette.R | 169 - waterquality-0.2.5/waterquality/inst/doc/waterquality_vignette.Rmd | 411 ++-- waterquality-0.2.5/waterquality/inst/doc/waterquality_vignette.html | 956 +++++----- waterquality-0.2.5/waterquality/inst/raster/Harsha_Lake_CRS.gpkg |only waterquality-0.2.5/waterquality/inst/raster/Harsha_Simple_Points_CRS.gpkg |only waterquality-0.2.5/waterquality/inst/raster/waterquality_data.csv |only waterquality-0.2.5/waterquality/man/Al10SABI.Rd | 77 waterquality-0.2.5/waterquality/man/Am092Bsub.Rd | 77 waterquality-0.2.5/waterquality/man/Am09KBBI.Rd | 77 waterquality-0.2.5/waterquality/man/Be162B643sub629.Rd | 77 waterquality-0.2.5/waterquality/man/Be162B700sub601.Rd | 77 waterquality-0.2.5/waterquality/man/Be162BsubPhy.Rd | 77 waterquality-0.2.5/waterquality/man/Be16FLHBlueRedNIR.Rd | 77 waterquality-0.2.5/waterquality/man/Be16FLHGreenRedNIR.Rd | 77 waterquality-0.2.5/waterquality/man/Be16FLHVioletRedNIR.Rd | 77 waterquality-0.2.5/waterquality/man/Be16FLHblue.Rd | 77 waterquality-0.2.5/waterquality/man/Be16FLHviolet.Rd | 77 waterquality-0.2.5/waterquality/man/Be16MPI.Rd | 77 waterquality-0.2.5/waterquality/man/Be16NDPhyI.Rd | 77 waterquality-0.2.5/waterquality/man/Be16NDPhyI644over615.Rd | 77 waterquality-0.2.5/waterquality/man/Be16NDPhyI644over629.Rd | 77 waterquality-0.2.5/waterquality/man/Be16NDTIblue.Rd | 77 waterquality-0.2.5/waterquality/man/Be16NDTIviolet.Rd | 77 waterquality-0.2.5/waterquality/man/Be16Phy2BDA644over629.Rd | 77 waterquality-0.2.5/waterquality/man/Da052BDA.Rd | 78 waterquality-0.2.5/waterquality/man/De933BDA.Rd | 78 waterquality-0.2.5/waterquality/man/Gi033BDA.Rd | 78 waterquality-0.2.5/waterquality/man/Go04MCI.Rd | 78 waterquality-0.2.5/waterquality/man/HU103BDA.Rd | 78 waterquality-0.2.5/waterquality/man/Kn07KIVU.Rd | 78 waterquality-0.2.5/waterquality/man/Ku15PhyCI.Rd | 78 waterquality-0.2.5/waterquality/man/Ku15SLH.Rd | 78 waterquality-0.2.5/waterquality/man/MI092BDA.Rd | 78 waterquality-0.2.5/waterquality/man/MM092BDA.Rd | 78 waterquality-0.2.5/waterquality/man/MM12NDCI.Rd | 78 waterquality-0.2.5/waterquality/man/MM12NDCIalt.Rd | 78 waterquality-0.2.5/waterquality/man/MM143BDAopt.Rd | 78 waterquality-0.2.5/waterquality/man/Map_WQ_basemap.Rd |only waterquality-0.2.5/waterquality/man/Map_WQ_raster.Rd |only waterquality-0.2.5/waterquality/man/SI052BDA.Rd | 78 waterquality-0.2.5/waterquality/man/SM122BDA.Rd | 78 waterquality-0.2.5/waterquality/man/SY002BDA.Rd | 78 waterquality-0.2.5/waterquality/man/TurbBe16GreenPlusRedBothOverViolet.Rd | 77 waterquality-0.2.5/waterquality/man/TurbBe16RedOverViolet.Rd | 77 waterquality-0.2.5/waterquality/man/TurbBow06RedOverGreen.Rd | 77 waterquality-0.2.5/waterquality/man/TurbChip09NIROverGreen.Rd | 77 waterquality-0.2.5/waterquality/man/TurbDox02NIRoverRed.Rd | 77 waterquality-0.2.5/waterquality/man/TurbFrohn09GreenPlusRedBothOverBlue.Rd | 77 waterquality-0.2.5/waterquality/man/TurbHarr92NIR.Rd | 77 waterquality-0.2.5/waterquality/man/TurbLath91RedOverBlue.Rd | 77 waterquality-0.2.5/waterquality/man/TurbMoore80Red.Rd | 77 waterquality-0.2.5/waterquality/man/Wy08CI.Rd | 77 waterquality-0.2.5/waterquality/man/Zh10FLH.Rd | 77 waterquality-0.2.5/waterquality/man/extract_lm.Rd |only waterquality-0.2.5/waterquality/man/extract_lm_cv.Rd |only waterquality-0.2.5/waterquality/man/extract_lm_cv_all.Rd |only waterquality-0.2.5/waterquality/man/extract_lm_cv_multi.Rd |only waterquality-0.2.5/waterquality/man/figures/README-example_output-1.png |only waterquality-0.2.5/waterquality/man/pipe.Rd |only waterquality-0.2.5/waterquality/man/waterquality-package.Rd | 16 waterquality-0.2.5/waterquality/man/wq_algorithms.Rd | 6 waterquality-0.2.5/waterquality/man/wq_calc.Rd | 2 waterquality-0.2.5/waterquality/tests/testthat/test-data.R | 2 waterquality-0.2.5/waterquality/vignettes/waterquality_vignette.Rmd | 411 ++-- 78 files changed, 3197 insertions(+), 2542 deletions(-)
Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with
the 'stringr' or 'stringi' packages. The foremost of these is the
extraction of numbers from strings. 'stringr' and 'stringi' make you
figure out the regular expression for yourself; 'strex' takes care of
this for you. There are many other handy functionalities in 'strex'.
Contributions to this package are encouraged: it is intended as a
miscellany of string manipulation functions that cannot be found in
'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between strex versions 1.3.0 dated 2020-09-25 and 1.3.1 dated 2020-10-02
strex-1.3.0/strex/README.md |only strex-1.3.1/strex/DESCRIPTION | 10 ++---- strex-1.3.1/strex/MD5 | 27 +++++++--------- strex-1.3.1/strex/NEWS.md | 12 +++++++ strex-1.3.1/strex/R/arg-match.R | 17 +++------- strex-1.3.1/strex/R/locate.R | 6 ++- strex-1.3.1/strex/R/utils.R | 4 -- strex-1.3.1/strex/build/partial.rdb |binary strex-1.3.1/strex/inst/doc/alphordering-numbers.html | 4 +- strex-1.3.1/strex/inst/doc/argument-matching.html | 4 +- strex-1.3.1/strex/inst/doc/before-and-after.html | 4 +- strex-1.3.1/strex/inst/doc/important-miscellany.html | 4 +- strex-1.3.1/strex/inst/doc/numbers-in-strings.html | 4 +- strex-1.3.1/strex/src/fullocate.c | 3 - strex-1.3.1/strex/tests/testthat/test-currency.R | 31 ++++++++++++------- 15 files changed, 72 insertions(+), 58 deletions(-)
Title: Shiny Applications Internationalization
Description: It provides easy internationalization of Shiny
applications. It can be used as standalone translation package
to translate reports, interactive visualizations or
graphical elements as well.
Author: Dominik Krzemiński [cre, aut],
Krystian Igras [aut],
Appsilon [cph]
Maintainer: Dominik Krzemiński <dominik@appsilon.com>
Diff between shiny.i18n versions 0.1.0 dated 2018-09-13 and 0.2.0 dated 2020-10-02
shiny.i18n-0.1.0/shiny.i18n/inst/examples |only shiny.i18n-0.1.0/shiny.i18n/inst/prepare_package_cran.sh |only shiny.i18n-0.1.0/shiny.i18n/man/translator.Rd |only shiny.i18n-0.2.0/shiny.i18n/DESCRIPTION | 30 shiny.i18n-0.2.0/shiny.i18n/MD5 | 47 - shiny.i18n-0.2.0/shiny.i18n/NAMESPACE | 16 shiny.i18n-0.2.0/shiny.i18n/R/automatic.R |only shiny.i18n-0.2.0/shiny.i18n/R/preproc.R |only shiny.i18n-0.2.0/shiny.i18n/R/translator.R | 306 +++++++--- shiny.i18n-0.2.0/shiny.i18n/R/ui.R |only shiny.i18n-0.2.0/shiny.i18n/R/utils.R | 16 shiny.i18n-0.2.0/shiny.i18n/README.md | 71 +- shiny.i18n-0.2.0/shiny.i18n/inst/rstudio |only shiny.i18n-0.2.0/shiny.i18n/inst/www |only shiny.i18n-0.2.0/shiny.i18n/man/Translator.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/create_translation_addin.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/create_translation_file.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/dot-i18_config.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/dot-onLoad.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/dot-translator_options.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/extract_key_expressions.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/figures |only shiny.i18n-0.2.0/shiny.i18n/man/i18n_state.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/init_i18n.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/multmerge.Rd | 4 shiny.i18n-0.2.0/shiny.i18n/man/read_and_merge_csvs.Rd | 4 shiny.i18n-0.2.0/shiny.i18n/man/save_to_csv.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/save_to_json.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/translate_with_google_cloud.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/update_lang.Rd |only shiny.i18n-0.2.0/shiny.i18n/man/usei18n.Rd |only shiny.i18n-0.2.0/shiny.i18n/tests/testthat/test_preproc.R |only shiny.i18n-0.2.0/shiny.i18n/tests/testthat/test_translator.R | 13 shiny.i18n-0.2.0/shiny.i18n/tests/testthat/test_ui.R |only 34 files changed, 357 insertions(+), 150 deletions(-)
Title: Epistemic Network Analysis
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016) <https://learning-analytics.info/index.php/JLA/article/view/4329>.
Author: Cody L Marquart [aut, cre] (<https://orcid.org/0000-0002-3387-6792>),
Zachari Swiecki [aut],
Wesley Collier [aut],
Brendan Eagan [aut],
Roman Woodward [aut],
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between rENA versions 0.2.1.0 dated 2020-09-16 and 0.2.1.1 dated 2020-10-02
DESCRIPTION | 8 +-- MD5 | 24 ++++----- NEWS.md | 6 ++ inst/CITATION | 2 inst/doc/getting-started.R | 8 +-- inst/doc/getting-started.Rmd | 8 +-- inst/doc/getting-started.html | 98 +++++++++++++++++++++++++++++++------ inst/doc/means-rotation.R | 2 inst/doc/means-rotation.Rmd | 2 inst/doc/means-rotation.html | 78 +++++++++++++++++++++++++++-- tests/testthat/test.ena.make.set.R | 46 ++++++++--------- vignettes/getting-started.Rmd | 8 +-- vignettes/means-rotation.Rmd | 2 13 files changed, 219 insertions(+), 73 deletions(-)
Title: Colorful Data Frames in R Terminal
Description: Colorful Data Frames in the terminal. The new class does
change the behaviour of any of the objects, but adds a style
definition and a print method. Using ANSI escape codes, it
colors the terminal output of data frames. Some column types
(such as p-values and identifiers) are automatically
recognized.
Author: January Weiner [aut, cre] (<https://orcid.org/0000-0003-1438-7819>)
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between colorDF versions 0.1.2 dated 2020-07-01 and 0.1.4 dated 2020-10-02
colorDF-0.1.2/colorDF/man/as.colorDF.Rd |only colorDF-0.1.2/colorDF/man/summary.colorDF.Rd |only colorDF-0.1.4/colorDF/DESCRIPTION | 14 colorDF-0.1.4/colorDF/MD5 | 66 +- colorDF-0.1.4/colorDF/NAMESPACE | 9 colorDF-0.1.4/colorDF/NEWS.md | 6 colorDF-0.1.4/colorDF/R/boxplot.R |only colorDF-0.1.4/colorDF/R/classes.R | 65 +- colorDF-0.1.4/colorDF/R/colorDF-package.R | 115 +++- colorDF-0.1.4/colorDF/R/print.R | 314 ++++++++--- colorDF-0.1.4/colorDF/R/styles.R | 69 +- colorDF-0.1.4/colorDF/R/summary.R | 211 ++++++- colorDF-0.1.4/colorDF/R/themes.R | 73 +- colorDF-0.1.4/colorDF/R/tools.R | 89 +++ colorDF-0.1.4/colorDF/R/utils.R | 76 +- colorDF-0.1.4/colorDF/README.md | 2 colorDF-0.1.4/colorDF/inst/doc/colorDF.R | 76 +- colorDF-0.1.4/colorDF/inst/doc/colorDF.Rmd | 131 +++- colorDF-0.1.4/colorDF/inst/doc/colorDF.html | 562 ++++++++++++-------- colorDF-0.1.4/colorDF/man/add_colorDF_theme.Rd | 2 colorDF-0.1.4/colorDF/man/col_type.Rd | 30 + colorDF-0.1.4/colorDF/man/colorDF-global-options.Rd |only colorDF-0.1.4/colorDF/man/colorDF-package.Rd | 30 - colorDF-0.1.4/colorDF/man/colorDF.Rd | 46 + colorDF-0.1.4/colorDF/man/colorDF_themes.Rd | 2 colorDF-0.1.4/colorDF/man/colorDF_themes_show.Rd | 12 colorDF-0.1.4/colorDF/man/df_search.Rd |only colorDF-0.1.4/colorDF/man/df_style.Rd | 98 +-- colorDF-0.1.4/colorDF/man/figures |only colorDF-0.1.4/colorDF/man/format_col.Rd | 5 colorDF-0.1.4/colorDF/man/get_colorDF_theme.Rd | 6 colorDF-0.1.4/colorDF/man/highlight.Rd | 2 colorDF-0.1.4/colorDF/man/is.colorDF.Rd |only colorDF-0.1.4/colorDF/man/print_colorDF.Rd | 65 ++ colorDF-0.1.4/colorDF/man/remove_df_style.Rd | 7 colorDF-0.1.4/colorDF/man/summary_colorDF.Rd |only colorDF-0.1.4/colorDF/man/term_boxplot.Rd |only colorDF-0.1.4/colorDF/man/uncolor.Rd |only colorDF-0.1.4/colorDF/vignettes/colorDF.Rmd | 131 +++- 39 files changed, 1725 insertions(+), 589 deletions(-)
Title: Clustering of Datasets
Description: Hierarchical and partitioning algorithms of blocks of variables. The partitioning algorithm includes an option called noise cluster to set aside atypical blocks of variables. The CLUSTATIS method (for quantitative blocks) (Llobell, Cariou, Vigneau, Labenne & Qannari (2020) <doi:10.1016/j.foodqual.2018.05.013>, Llobell, Vigneau & Qannari (2019) <doi:10.1016/j.foodqual.2019.02.017>) and the CLUSCATA method (for Check-All-That-Apply data) (Llobell, Cariou, Vigneau, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2018.09.006>, Llobell, Giacalone, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2019.05.017>) are the core of this package.
Author: Fabien Llobell [aut, cre] (Oniris/XLSTAT),
Evelyne Vigneau [ctb] (Oniris),
Veronique Cariou [ctb] (Oniris),
El Mostafa Qannari [ctb] (Oniris)
Maintainer: Fabien Llobell <fllobell@hotmail.fr>
Diff between ClustBlock versions 2.2.0 dated 2020-04-23 and 2.2.1 dated 2020-10-02
DESCRIPTION | 12 ++++++------ MD5 | 23 ++++++++++++----------- NEWS | 3 +-- R/cluscata.R | 13 ++++++------- R/clustatis.R | 12 ++++++------ R/statis.R | 10 ++++++++++ R/summary.cluscata.R | 2 +- R/summary.clustatis.R | 2 +- inst/CITATION | 4 ++-- man/ClustBlock-package.Rd |only man/cluscata.Rd | 4 ++-- man/clustatis.Rd | 4 ++-- man/statis.Rd | 1 + 13 files changed, 50 insertions(+), 40 deletions(-)
Title: Fetching Tabular Data "Onload" in Compiled R Markdown HTML
Documents
Description: Dynamically retrieve data from the web to render HTML tables
on inspection in R Markdown HTML documents.
Author: Yongfu Liao [aut, cre] (<https://orcid.org/0000-0002-1814-2993>)
Maintainer: Yongfu Liao <liao961120@gmail.com>
Diff between getable versions 1.0.2 dated 2020-08-31 and 1.0.3 dated 2020-10-02
DESCRIPTION | 9 +- MD5 | 12 +-- NAMESPACE | 3 R/render.R | 14 ++-- README.md | 39 ++++++++++-- inst/doc/Introduction.html | 13 ++++ inst/rmarkdown/templates/tablefromweb/skeleton/skeleton.Rmd | 10 +-- 7 files changed, 75 insertions(+), 25 deletions(-)
Title: Multinomial Logit Models
Description: Maximum likelihood estimation of random utility discrete
choice models. The software is described in Croissant (2020)
<doi:10.18637/jss.v095.i11> and the underlying methods in
Train (2009) <doi:10.1017/CBO9780511805271>.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between mlogit versions 1.1-0 dated 2020-05-26 and 1.1-1 dated 2020-10-02
DESCRIPTION | 17 - MD5 | 139 ++++---- NEWS.md | 4 R/datasets.R | 22 - build/partial.rdb |binary build/vignette.rds |binary data/Car.rda |binary data/Catsup.rda |binary data/Cracker.rda |binary data/Electricity.rda |binary data/Fishing.rda |binary data/Game.rda |binary data/Game2.rda |binary data/HC.rda |binary data/Heating.rda |binary data/JapaneseFDI.rda |binary data/Mode.rda |binary data/ModeCanada.rda |binary data/NOx.rda |binary data/RiskyTransport.rda |binary data/Train.rda |binary inst/CITATION |only inst/REFERENCES.bib | 62 +-- inst/doc/c2.formula.data.Rmd | 2 inst/doc/c2.formula.data.html | 41 +- inst/doc/c3.rum.Rmd | 2 inst/doc/c3.rum.html | 268 +++++++++------- inst/doc/c4.relaxiid.Rmd | 2 inst/doc/c4.relaxiid.html | 678 ++++++++++++++++++++++++------------------ inst/doc/c5.mxl.Rmd | 2 inst/doc/c5.mxl.html | 138 ++++---- inst/doc/c6.mprobit.Rmd | 2 inst/doc/c6.mprobit.html | 12 inst/doc/c7.miscmodels.Rmd | 2 inst/doc/c7.miscmodels.html | 12 inst/doc/e1mlogit.Rmd | 2 inst/doc/e1mlogit.html | 14 inst/doc/e2nlogit.Rmd | 2 inst/doc/e2nlogit.html | 8 inst/doc/e3mxlogit.Rmd | 2 inst/doc/e3mxlogit.html | 16 inst/doc/e4mprobit.Rmd | 2 inst/doc/e4mprobit.html | 8 inst/doc/mlogit.Rmd | 1 inst/doc/mlogit.html | 7 man/Car.Rd | 8 man/Catsup.Rd | 6 man/Cracker.Rd | 6 man/Electricity.Rd | 8 man/Fishing.Rd | 6 man/Game.Rd | 8 man/HC.Rd | 8 man/Heating.Rd | 8 man/JapaneseFDI.Rd | 6 man/Mode.Rd | 8 man/ModeCanada.Rd | 6 man/NOx.Rd | 8 man/RiskyTransport.Rd | 8 man/Train.Rd | 8 man/mlogit-package.Rd | 4 vignettes/c2.formula.data.Rmd | 2 vignettes/c3.rum.Rmd | 2 vignettes/c4.relaxiid.Rmd | 2 vignettes/c5.mxl.Rmd | 2 vignettes/c6.mprobit.Rmd | 2 vignettes/c7.miscmodels.Rmd | 2 vignettes/e1mlogit.Rmd | 2 vignettes/e2nlogit.Rmd | 2 vignettes/e3mxlogit.Rmd | 2 vignettes/e4mprobit.Rmd | 2 vignettes/mlogit.Rmd | 1 71 files changed, 918 insertions(+), 676 deletions(-)
Title: Computing P-Values of the K-S Test for (Dis)Continuous Null
Distribution
Description: Computes a p-value of the one-sample two-sided (or one-sided, as a special case) Kolmogorov-Smirnov (KS) statistic, for any fixed critical level, and an arbitrary, possibly large sample size for a pre-specified purely discrete, mixed or continuous cumulative distribution function (cdf) under the null hypothesis. If a data sample is supplied, 'KSgeneral' computes the p-value corresponding to the value of the KS test statistic computed based on the user provided data sample. The package 'KSgeneral' implements a novel, accurate and efficient method named Exact-KS-FFT, expressing the p-value as a double-boundary non-crossing probability for a homogeneous Poisson process, which is then efficiently computed using Fast Fourier Transform (FFT). The package can also be used to compute and plot the complementary cdf of the KS statistic which is known to depend on the hypothesized distribution when the latter is discontinuous (i.e. purely discrete or mixed). To cite this package in publication use: Dimitrina S. Dimitrova, Vladimir K. Kaishev, and Senren Tan. Computing the Kolmogorov-Smirnov Distribution When the Underlying CDF is Purely Discrete, Mixed, or Continuous. Journal of Statistical Software. 2020; 95(10): 1--42. <doi:10.18637/jss.v095.i10>.
Author: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>,
Vladimir K. Kaishev <Vladimir.Kaishev.1@city.ac.uk> and
Senren Tan <senren.tan@cass.city.ac.uk>
Maintainer: Senren Tan <senren.tan@cass.city.ac.uk>
Diff between KSgeneral versions 0.1.2 dated 2020-02-11 and 1.0.0 dated 2020-10-02
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ build/partial.rdb |binary inst/CITATION |only man/Population_Data.Rd | 7 +++---- man/cont_ks_c_cdf.Rd | 11 +++++------ man/cont_ks_distribution.Rd | 11 +++++------ man/cont_ks_test.Rd | 9 ++++----- man/disc_ks_c_cdf.Rd | 18 ++++++++---------- man/disc_ks_test.Rd | 13 ++++++------- man/ks_c_cdf_Rcpp.Rd | 21 ++++++++++----------- man/ksgeneral-package.Rd | 9 ++++----- man/mixed_ks_c_cdf.Rd | 13 ++++++------- man/mixed_ks_test.Rd | 13 ++++++------- 14 files changed, 74 insertions(+), 84 deletions(-)
Title: PARAFAC Analysis of Fluorescence Excitation-Emission Matrices
Description: Perform parallel factor analysis (PARAFAC: Hitchcock, 1927)
<doi:10.1002/sapm192761164> on fluorescence excitation-emission
matrices (FEEMs): handle scattering signal and inner filter
effect, scale the dataset, fit the model; perform split-half
validation or jack-knifing. A modified approach called
"randomised split-half" is also available. The package has a low
dependency footprint (only two direct dependencies not in core
or recommended; four total non-core/recommended dependencies)
and has been tested on a wide range of R versions (including R
as old as 3.3.3 from Debian Stretch).
Author: Ivan Krylov [aut, cre],
Timur Labutin [ths]
Maintainer: Ivan Krylov <ikrylov@laser.chem.msu.ru>
Diff between albatross versions 0.1-1 dated 2020-09-25 and 0.1-2 dated 2020-10-02
albatross-0.1-1/albatross/man/plot.feemjackknife.Rd |only albatross-0.1-1/albatross/man/plot.feemparafac.Rd |only albatross-0.1-1/albatross/man/plot.feemsplithalf.Rd |only albatross-0.1-1/albatross/tests/jackknife.R |only albatross-0.1-2/albatross/DESCRIPTION | 37 ++--- albatross-0.1-2/albatross/MD5 | 37 ++--- albatross-0.1-2/albatross/R/bootstrap.R | 28 ++-- albatross-0.1-2/albatross/R/marine.R | 17 +- albatross-0.1-2/albatross/build/partial.rdb |binary albatross-0.1-2/albatross/inst |only albatross-0.1-2/albatross/man/feem.Rd | 5 albatross-0.1-2/albatross/man/feemcube.Rd | 4 albatross-0.1-2/albatross/man/feemife.Rd | 5 albatross-0.1-2/albatross/man/feemjackknife.Rd | 116 ++++++++++++------ albatross-0.1-2/albatross/man/feemparafac.Rd | 74 +++++++++-- albatross-0.1-2/albatross/man/feemsplithalf.Rd | 126 ++++++++++++-------- albatross-0.1-2/albatross/man/marine.colours.Rd | 30 ++-- albatross-0.1-2/albatross/tests/feemcube.R | 3 albatross-0.1-2/albatross/tests/feemife.R | 14 -- albatross-0.1-2/albatross/tests/feemscatter.R | 16 +- albatross-0.1-2/albatross/tests/parafac.R | 8 - albatross-0.1-2/albatross/tests/splithalf.R | 4 22 files changed, 318 insertions(+), 206 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-01 3.0.0.2
2020-09-21 3.0.0
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] (<https://orcid.org/0000-0002-3390-5442>),
Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>),
Veronika Braunisch [aut] (<https://orcid.org/0000-0001-7035-4662>),
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>
Diff between SDMtune versions 1.1.1 dated 2020-07-17 and 1.1.2 dated 2020-10-02
SDMtune-1.1.1/SDMtune/man/get_tunable_args.Rd |only SDMtune-1.1.2/SDMtune/DESCRIPTION | 8 - SDMtune-1.1.2/SDMtune/MD5 | 77 +++++----- SDMtune-1.1.2/SDMtune/NAMESPACE | 1 SDMtune-1.1.2/SDMtune/NEWS.md | 5 SDMtune-1.1.2/SDMtune/R/aicc.R | 8 - SDMtune-1.1.2/SDMtune/R/doJk.R | 8 - SDMtune-1.1.2/SDMtune/R/gridSearch.R | 8 - SDMtune-1.1.2/SDMtune/R/optimizeModel.R | 11 - SDMtune-1.1.2/SDMtune/R/predict-SDMmodel.R | 8 - SDMtune-1.1.2/SDMtune/R/predict-SDMmodelCV.R | 8 - SDMtune-1.1.2/SDMtune/R/randomSearch.R | 8 - SDMtune-1.1.2/SDMtune/R/reduceVar.R | 9 - SDMtune-1.1.2/SDMtune/R/utils.R | 58 ------- SDMtune-1.1.2/SDMtune/R/varSel.R | 10 - SDMtune-1.1.2/SDMtune/README.md | 8 - SDMtune-1.1.2/SDMtune/build/vignette.rds |binary SDMtune-1.1.2/SDMtune/inst/CITATION | 24 +-- SDMtune-1.1.2/SDMtune/inst/doc/basic-use.R | 100 ++++++------- SDMtune-1.1.2/SDMtune/inst/doc/basic-use.Rmd | 4 SDMtune-1.1.2/SDMtune/inst/doc/basic-use.html | 103 ++++++++++++-- SDMtune-1.1.2/SDMtune/inst/doc/hyper-tuning.R | 44 ++--- SDMtune-1.1.2/SDMtune/inst/doc/hyper-tuning.html | 99 ++++++++++++- SDMtune-1.1.2/SDMtune/inst/doc/presence-absence.R | 16 +- SDMtune-1.1.2/SDMtune/inst/doc/presence-absence.html | 99 ++++++++++++- SDMtune-1.1.2/SDMtune/inst/doc/var-selection.R | 52 +++---- SDMtune-1.1.2/SDMtune/inst/doc/var-selection.html | 99 ++++++++++++- SDMtune-1.1.2/SDMtune/man/aicc.Rd | 4 SDMtune-1.1.2/SDMtune/man/doJk.Rd | 3 SDMtune-1.1.2/SDMtune/man/gridSearch.Rd | 12 - SDMtune-1.1.2/SDMtune/man/optimizeModel.Rd | 3 SDMtune-1.1.2/SDMtune/man/predict-SDMmodel-method.Rd | 3 SDMtune-1.1.2/SDMtune/man/predict-SDMmodelCV-method.Rd | 3 SDMtune-1.1.2/SDMtune/man/randomSearch.Rd | 3 SDMtune-1.1.2/SDMtune/man/reduceVar.Rd | 3 SDMtune-1.1.2/SDMtune/man/varSel.Rd | 3 SDMtune-1.1.2/SDMtune/tests/testthat/test-utils.R | 13 - SDMtune-1.1.2/SDMtune/vignettes/articles/prepare-data.Rmd | 4 SDMtune-1.1.2/SDMtune/vignettes/articles/train-model.Rmd | 2 SDMtune-1.1.2/SDMtune/vignettes/basic-use.Rmd | 4 40 files changed, 559 insertions(+), 376 deletions(-)
Title: A Utility Package to Help you Deal with "Pignas"
Description: Pigna [_pìn'n'a_] is the Italian word for pine
cone. In jargon, it is used to identify a task which is boring,
banal, annoying, painful, frustrating and maybe even with a not so
beautiful or rewarding result, just like the obstinate act of trying
to challenge yourself in extracting pine nuts from a pine cone,
provided that, in the end, you will find at least one inside it. Here
you can find a backpack of functions to be used to solve small
everyday problems of coding or analyzing (clinical) data, which would
be normally solved using quick-and-dirty patches. You will be able to
convert 'Hmisc' and 'rms' summary()es into data.frames ready to be
rendered by 'pander' and 'knitr'. You can access easy-to-use wrappers
to activate essential but useful progress bars (from 'progress') into
your loops or functionals. Easy setup and control Telegram's bots
(from 'telegram.bot') to send messages or to divert error messages to
a Telegram's chat. You also have some utilities helping you in the
development of packages, like the activation of the same user
interface of 'usethis' into your package, or call polite functions to
ask a user to install other packages. Finally, you find a set of
thematic sets of packages you may use to set up new environments
quickly, installing them in a single call.
Author: Corrado Lanera [aut, cre, cph]
Maintainer: Corrado Lanera <corrado.lanera@gmail.com>
Diff between depigner versions 0.8.1 dated 2020-06-26 and 0.8.3 dated 2020-10-02
DESCRIPTION | 18 +- MD5 | 47 +++---- NEWS.md | 150 +++++++++-------------- R/adjust_p.R | 7 - R/htypes.R | 18 +- R/paired_test_categorical.R | 44 ++++-- R/summary_interact.R | 14 +- R/tidy_summary.R | 14 -- R/use_ui.R | 18 ++ R/usethis_utils.R | 4 README.md | 169 +++++++++++--------------- inst/WORDLIST | 13 +- inst/bib/doc-pkg.bib | 21 +-- inst/templates |only man/adjust_p.Rd | 7 - man/htype.Rd | 12 - man/paired_test_categorical.Rd | 3 man/summary_interact.Rd | 6 tests/testthat/helper.R | 86 ++++++------- tests/testthat/test-htypes.R | 4 tests/testthat/test-paired_test_categorical.R | 29 ++++ tests/testthat/test-paired_test_continuous.R | 13 ++ tests/testthat/test-summary_interact.R | 3 tests/testthat/test-tidy_summary.R | 21 +++ tests/testthat/test-use_ui.R | 5 25 files changed, 400 insertions(+), 326 deletions(-)
Title: Robust Covariance Matrix Estimators
Description: Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic
robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC)
covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC)
covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators);
clustered covariances (one-way and multi-way); panel and panel-corrected covariances;
outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are
applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted
to other classes through S3 methods. Details can be found in Zeileis et al. (2020) <doi:10.18637/jss.v095.i01>,
Zeileis (2004) <doi:10.18637/jss.v011.i10> and Zeileis (2006) <doi:10.18637/jss.v016.i09>.
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>),
Thomas Lumley [aut],
Nathaniel Graham [ctb],
Susanne Koell [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between sandwich versions 2.5-1 dated 2019-04-06 and 3.0-0 dated 2020-10-02
sandwich-2.5-1/sandwich/NEWS |only sandwich-2.5-1/sandwich/THANKS |only sandwich-3.0-0/sandwich/DESCRIPTION | 32 ++- sandwich-3.0-0/sandwich/MD5 | 87 ++++---- sandwich-3.0-0/sandwich/NEWS.md |only sandwich-3.0-0/sandwich/R/auxiliary.R | 47 +++- sandwich-3.0-0/sandwich/R/bread.R | 18 + sandwich-3.0-0/sandwich/R/vcovBS.R | 6 sandwich-3.0-0/sandwich/R/vcovBS.lm.R | 12 + sandwich-3.0-0/sandwich/R/vcovCL.R | 6 sandwich-3.0-0/sandwich/R/vcovPC.R | 6 sandwich-3.0-0/sandwich/R/vcovPL.R | 6 sandwich-3.0-0/sandwich/README.md |only sandwich-3.0-0/sandwich/build/partial.rdb |binary sandwich-3.0-0/sandwich/build/vignette.rds |binary sandwich-3.0-0/sandwich/data/InstInnovation.rda |binary sandwich-3.0-0/sandwich/data/Investment.rda |binary sandwich-3.0-0/sandwich/data/PetersenCL.rda |binary sandwich-3.0-0/sandwich/data/PublicSchools.rda |binary sandwich-3.0-0/sandwich/inst/CITATION | 37 +-- sandwich-3.0-0/sandwich/inst/doc/sandwich-CL.Rnw | 56 +++-- sandwich-3.0-0/sandwich/inst/doc/sandwich-CL.pdf |binary sandwich-3.0-0/sandwich/inst/doc/sandwich-OOP.pdf |binary sandwich-3.0-0/sandwich/inst/doc/sandwich.pdf |binary sandwich-3.0-0/sandwich/man/Investment.Rd | 4 sandwich-3.0-0/sandwich/man/NeweyWest.Rd | 20 +- sandwich-3.0-0/sandwich/man/PetersenCL.Rd | 2 sandwich-3.0-0/sandwich/man/PublicSchools.Rd | 9 sandwich-3.0-0/sandwich/man/bread.Rd | 11 - sandwich-3.0-0/sandwich/man/estfun.Rd | 14 + sandwich-3.0-0/sandwich/man/figures |only sandwich-3.0-0/sandwich/man/isoacf.Rd | 8 sandwich-3.0-0/sandwich/man/kweights.Rd | 6 sandwich-3.0-0/sandwich/man/meat.Rd | 13 + sandwich-3.0-0/sandwich/man/sandwich.Rd | 18 + sandwich-3.0-0/sandwich/man/vcovBS.Rd | 18 - sandwich-3.0-0/sandwich/man/vcovCL.Rd | 22 +- sandwich-3.0-0/sandwich/man/vcovHAC.Rd | 32 +-- sandwich-3.0-0/sandwich/man/vcovHC.Rd | 44 ++-- sandwich-3.0-0/sandwich/man/vcovOPG.Rd | 6 sandwich-3.0-0/sandwich/man/vcovPC.Rd | 16 - sandwich-3.0-0/sandwich/man/vcovPL.Rd | 13 - sandwich-3.0-0/sandwich/man/weightsAndrews.Rd | 10 - sandwich-3.0-0/sandwich/man/weightsLumley.Rd | 13 - sandwich-3.0-0/sandwich/tests/Examples/sandwich-Ex.Rout.save | 14 - sandwich-3.0-0/sandwich/vignettes/hac.bib | 107 +++++++---- sandwich-3.0-0/sandwich/vignettes/sandwich-CL.Rnw | 56 +++-- 47 files changed, 452 insertions(+), 317 deletions(-)
Title: Informative Procrustean Matrix Correlation
Description: Estimates corrected Procrustean correlation between matrices for removing overfitting effect. Coissac Eric and Gonindard-Melodelima Christelle (2019) <bioarXiv:10.1101/842070>.
Author: Eric Coissac, Christelle Gonindard-Melodelima
Maintainer: Eric Coissac <eric.coissac@metabarcoding.org>
Diff between ProcMod versions 1.0.6 dated 2020-09-21 and 1.0.7 dated 2020-10-02
DESCRIPTION | 11 +++++------ MD5 | 8 ++++---- NAMESPACE | 1 + R/procmod.R | 1 + build/partial.rdb |binary 5 files changed, 11 insertions(+), 10 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression;
- generalised linear mixed models;
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.15-0 dated 2020-09-29 and 4.15-1 dated 2020-10-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 14 ++++++++------ R/metacr.R | 22 +++++++++++++++++----- R/settings.meta.R | 2 +- 5 files changed, 34 insertions(+), 20 deletions(-)
Title: Study Design and Data Analysis in the Presence of Error-Prone
Diagnostic Tests and Self-Reported Outcomes
Description: We consider studies in which information from error-prone
diagnostic tests or self-reports are gathered sequentially to determine the
occurrence of a silent event. Using a likelihood-based approach
incorporating the proportional hazards assumption, we provide functions to
estimate the survival distribution and covariate effects. We also provide
functions for power and sample size calculations for this setting.
Please refer to Xiangdong Gu, Yunsheng Ma, and Raji Balasubramanian (2015)
<doi: 10.1214/15-AOAS810>, Xiangdong Gu and Raji Balasubramanian (2016)
<doi: 10.1002/sim.6962>, Xiangdong Gu, Mahlet G Tadesse, Andrea S Foulkes,
Yunsheng Ma, and Raji Balasubramanian (2020) <doi: 10.1186/s12911-020-01223-w>.
Author: Xiangdong Gu and Raji Balasubramanian
Maintainer: Xiangdong Gu <ustcgxd@gmail.com>
Diff between icensmis versions 1.3.1 dated 2016-01-03 and 1.4.0 dated 2020-10-02
DESCRIPTION | 17 MD5 | 31 + NAMESPACE | 5 R/HighDimCR.R | 592 +++++++++++++++++---------------- R/RcppExports.R | 125 +++---- R/icmis.R | 68 ++- R/icpower_weibull.R |only README.md | 5 man/bayesmc.Rd |only man/datasim.Rd | 121 +++--- man/fitsurv.Rd |only man/icmis.Rd | 167 +++++---- man/icpower.Rd | 93 ++--- man/icpower.val.Rd | 58 ++- man/icpower_weibull.Rd |only man/icpowerpf.Rd | 37 +- src/HighDimCR.cpp | 734 +++++++++++++++++++++++++----------------- src/RcppExports.cpp | 574 +++++++++++++++++--------------- tests/testthat/test_weibull.R |only 19 files changed, 1456 insertions(+), 1171 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre] (<https://orcid.org/0000-0002-5674-3327>),
Andreas Rappold [ctb]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 4.0.1 dated 2020-08-25 and 4.1.0 dated 2020-10-02
DESCRIPTION | 10 ++-- MD5 | 16 +++--- NEWS | 18 +++++++ R/Deriv.R | 105 ++++++++++++++++++++++++++++++-------------- R/Simplify.R | 41 +++++++++++------ man/Deriv-package.Rd | 4 - man/Deriv.Rd | 45 ++++++++++++++++-- tests/testthat.R | 2 tests/testthat/test_Deriv.R | 29 ++++++++++-- 9 files changed, 199 insertions(+), 71 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-11-20 1.0-16
2009-02-23 1.0-15.1
2008-09-29 1.0-15
2008-05-25 1.0-14
2006-11-23 1.0-13
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-15 1.0.2
2017-05-15 1.0.1
2017-05-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-03 1.0-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-23 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-09 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-11 0.2.1
2015-08-29 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-20 0.1.3
2018-04-27 0.1.2
2018-03-17 0.1.1
2018-02-28 0.1.0
Title: Find Optimal Sampling Locations Based on Spatial Covariate(s)
Description: Create sampling designs using the surface reconstruction algorithm.
Original method by: Olsson, D. 2002. A method to optimize soil sampling from
ancillary data. Poster presenterad at: NJF seminar no. 336,
Implementation of Precision Farming in Practical Agriculture, 10-12
June 2002, Skara, Sweden.
Author: Kristin Piikki, Mats Söderström & John Mutua
Maintainer: Kristin Piikki <kristin.piikki@slu.se>
Diff between SurfaceTortoise versions 1.0.1 dated 2019-05-13 and 1.0.2 dated 2020-10-02
SurfaceTortoise-1.0.1/SurfaceTortoise/R/boundary-data.R |only SurfaceTortoise-1.0.1/SurfaceTortoise/data |only SurfaceTortoise-1.0.1/SurfaceTortoise/man/boundary.Rd |only SurfaceTortoise-1.0.2/SurfaceTortoise/DESCRIPTION | 12 +++-- SurfaceTortoise-1.0.2/SurfaceTortoise/LICENSE | 6 +- SurfaceTortoise-1.0.2/SurfaceTortoise/MD5 | 12 ++--- SurfaceTortoise-1.0.2/SurfaceTortoise/R/tortoise.R | 15 +++++-- SurfaceTortoise-1.0.2/SurfaceTortoise/README.md |only SurfaceTortoise-1.0.2/SurfaceTortoise/man/tortoise.Rd | 34 ++++++++++++---- 9 files changed, 53 insertions(+), 26 deletions(-)
More information about SurfaceTortoise at CRAN
Permanent link
Title: Scaling with Ranked Subsampling
Description: Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is a popular method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. An alternative to rarefying is scaling with ranked subsampling (SRS). SRS consists of two steps. In the first step, the total counts for all OTUs (operational taxonomic units) or species in each sample are divided by a scaling factor chosen in such a way that the sum of the scaled counts Cscaled equals Cmin. In the second step, the non-integer Cscaled values are converted into integers by an algorithm that we dub ranked subsampling. The Cscaled value for each OTU or species is split into the integer part Cint (Cint = floor(Cscaled)) and the fractional part Cfrac (Cfrac = Cscaled - Cints). Since the sum of Cint is smaller or equal to Cmin, additional delta C = Cmin - the sum of Cint counts have to be added to the library to reach the total count of Cmin. This is achieved as follows. OTUs are ranked in the descending order of their Cfrac values. Beginning with the OTU of the highest rank, single count per OTU is added to the normalized library until the total number of added counts reaches delta C and the sum of all counts in the normalized library equals Cmin. When the lowest Cfrag involved in picking delta C counts is shared by several OTUs, the OTUs used for adding a single count to the library are selected in the order of their Cint values. This selection minimizes the effect of normalization on the relative frequencies of OTUs. OTUs with identical Cfrag as well as Cint are sampled randomly without replacement. See Beule & Karlovsky (2020) <doi:10.7717/peerj.9593> for details.
Author: Lukas Beule [aut, cre],
Vitor Heidrich [aut],
Petr Karlovsky [aut]
Maintainer: Lukas Beule <lukas.beule@agr.uni-goettingen.de>
Diff between SRS versions 0.1.0 dated 2020-08-31 and 0.1.1 dated 2020-10-02
DESCRIPTION | 15 ++++++++------- MD5 | 9 ++++++--- NAMESPACE | 6 ++++++ R/SRScurve.R |only inst |only man/SRS.Rd | 2 +- man/SRScurve.Rd |only 7 files changed, 21 insertions(+), 11 deletions(-)
Title: Pseudo-Ranks
Description: Efficient calculation of pseudo-ranks and (pseudo)-rank based test statistics. In case of equal sample sizes, pseudo-ranks and mid-ranks are equal. When used for inference mid-ranks may lead to paradoxical results. Pseudo-ranks are in general not affected by such a problem <doi:10.18637/jss.v095.c01>.
Author: Martin Happ [aut, cre] (<https://orcid.org/0000-0003-0009-2665>),
Georg Zimmermann [aut],
Arne C. Bathke [aut],
Edgar Brunner [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Diff between pseudorank versions 0.3.8 dated 2018-11-27 and 1.0.1 dated 2020-10-02
DESCRIPTION | 16 +-- MD5 | 31 +++--- R/S3method.R | 3 R/data.R | 1 README.md | 17 +-- inst |only man/ParadoxicalRanks.Rd | 95 ++++++++++---------- man/hettmansperger_norton_test.Rd | 134 ++++++++++++++++------------- man/hettmansperger_norton_test_internal.Rd | 103 +++++++++++----------- man/kepner_robinson_test.Rd | 112 +++++++++++++----------- man/kepner_robinson_test_internal.Rd | 89 ++++++++++--------- man/kruskal_wallis_internal.Rd | 88 ++++++++++--------- man/kruskal_wallis_test.Rd | 94 +++++++++----------- man/pseudorank-package.Rd | 3 man/pseudorank.Rd | 114 ++++++++++++------------ man/psrank-deprecated.Rd | 69 +++++++------- man/recursiveCalculation.Rd | 40 ++++---- 17 files changed, 538 insertions(+), 471 deletions(-)
Title: A Wrapper of the JavaScript Library 'jsTree'
Description: Creates interactive trees that can be included in 'Shiny' apps and R markdown documents. A tree allows to represent hierarchical data (e.g. the contents of a directory). Similar to the 'shinyTree' package but offers more features and options, such as the grid extension, restricting the drag-and-drop behavior, and settings for the search functionality. It is possible to attach some data to the nodes of a tree and then to get these data in 'Shiny' when a node is selected. Also provides a 'Shiny' gadget allowing to manipulate one or more folders.
Author: Stéphane Laurent [aut, cre],
jQuery contributors [ctb, cph] (jQuery),
Ivan Bozhanov [ctb, cph] (jsTree),
Vedran Opacic [ctb, cph] (jsTree bootstrap theme),
Avi Deitcher [ctb, cph] (jsTreeGrid),
Philip Hutchison [ctb, cph] (PDFObject),
Terence Eden [ctb, cph] (SuperTinyIcons)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between jsTreeR versions 1.0.0 dated 2020-09-22 and 1.1.0 dated 2020-10-02
DESCRIPTION | 10 LICENSE.note | 26 ++ MD5 | 21 + NAMESPACE | 3 NEWS.md | 9 R/folderGadget.R | 555 +++++++++++++++++++++------------------------ README.md | 1 inst/htmlwidgets/gadget |only inst/htmlwidgets/jstree.js | 21 - man/folderGadget.Rd | 39 +++ 10 files changed, 375 insertions(+), 310 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-07 0.3.3.1
2015-03-24 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-20 1.0.0
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2020-07-16 1.0.1
2020-07-10 1.0.0
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2016-08-03 0.0.3
2016-06-28 0.0.2
2015-11-23 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-12 3.0.0
2017-04-14 2.0.0
2015-04-01 1.2-0
2014-04-16 1.1-2
2014-01-25 1.1-1
2013-04-13 1.1-0
2013-03-27 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-17 0.2.5.2
2016-07-10 0.2.5.1
2016-05-30 0.2.5
2016-04-27 0.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-06 1.5-6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-31 1.0.2
2018-06-20 1.0.1
2017-10-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-14 0.1.0
2019-06-14 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-07 0.31
2016-07-15 0.27
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-29 0.1.4
2020-06-21 0.1.3
2020-06-12 0.1.2
2020-03-23 0.1.1
2019-03-31 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-22 0.2.2
2019-10-17 0.2.0
2019-06-18 0.1.8
2019-01-02 0.1.7
2018-09-20 0.1.6
2018-01-05 0.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-18 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-26 1.9.0
2018-05-06 1.8.0
2018-04-20 1.7.0
2018-03-22 1.6.0
2018-03-02 1.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-22 0.1-4
2014-06-15 0.1-3
2014-02-17 0.1-2
2013-07-12 0.1-1
2013-02-24 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-01 1.1.1
2015-06-19 1.0.1
2015-01-02 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-27 0.2.1
2020-05-25 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-25 1.0.1
2013-02-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-25 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-08 0.3.1
2016-03-01 0.3.0
Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene sets
typically used with the 'Gene Set Enrichment Analysis' (GSEA) software
(Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015
<doi:10.1016/j.cels.2015.12.004>) in a standard R data frame with key-value
pairs. The package includes the original human gene symbols and NCBI/Entrez
IDs as well as the equivalents for frequently studied model organisms such
as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 7.1.1 dated 2020-05-14 and 7.2.1 dated 2020-10-02
DESCRIPTION | 15 +- MD5 | 30 ++-- NAMESPACE | 7 NEWS.md | 7 R/functions.R | 83 +++++++++-- R/sysdata.rda |binary README.md | 69 +-------- build/vignette.rds |binary inst/doc/msigdbr-intro.R | 53 ++++--- inst/doc/msigdbr-intro.Rmd | 145 ++++++++++--------- inst/doc/msigdbr-intro.html | 293 ++++++++++++++++++++++------------------ man/msigdbr.Rd | 12 - man/msigdbr_collections.Rd |only man/msigdbr_show_species.Rd | 5 man/msigdbr_species.Rd |only tests/testthat/test-functions.R | 166 +++++++++++++++------- vignettes/msigdbr-intro.Rmd | 145 ++++++++++--------- 17 files changed, 589 insertions(+), 441 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-05-07 1.0-7.1
2009-11-20 1.0-7
2009-02-23 1.0-6.1
2008-09-29 1.0-6
2008-08-18 1.0-5
2008-08-07 1.0-4
2008-05-25 1.0-3
2006-11-15 1.0-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-02 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-08 0.1.2
2019-07-18 0.1.1
2019-05-04 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-10 3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-13 1.1.0
2016-06-02 1.0.17
2014-05-07 1.0.0
2013-05-16 0.9.11
2013-05-07 0.9.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-26 0.1.1
2013-08-05 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-22 1.0.1
2013-12-12 0.9.1
2013-03-25 0.9.0
2011-09-21 0.8.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-08 0.80
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-10 1.0.1
2015-10-02 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-26 1.0.0
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2018-06-18 0.8.0
2018-02-21 0.7.0
2017-12-17 0.6.0
2017-11-11 0.5.0
2017-10-16 0.3.1
2017-09-26 0.3.0
2017-08-23 0.2.0
2017-07-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-15 1.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-23 0.6.4
2014-12-08 0.6.1
2014-09-29 0.6
2014-05-13 0.3.5
2014-04-08 0.3.4
2014-02-06 0.3.2
2014-02-03 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-30 0.90.95
2020-01-15 0.90.94
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-05 0.1.2
2020-06-21 0.1.1
2020-06-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-01-29 1.0.3
2012-09-05 1.0.2
2012-07-16 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-20 1.0.1
Title: Toolkit for Credit Modeling, Analysis and Visualization
Description: Provides a highly efficient R tool suite for Credit Modeling, Analysis and Visualization. Contains infrastructure functionalities such as data exploration and preparation, missing values treatment, outliers treatment, variable derivation, variable selection, dimensionality reduction, grid search for hyper parameters, data mining and visualization, model evaluation, strategy analysis etc. This package is designed to make the development of binary classification models (machine learning based models as well as credit scorecard) simpler and faster.
Author: Dongping Fan [aut, cre]
Maintainer: Dongping Fan <fdp@pku.edu.cn>
Diff between creditmodel versions 1.2.5 dated 2020-08-26 and 1.2.6 dated 2020-10-02
DESCRIPTION | 8 MD5 | 14 NEWS.md | 5 R/data_anaylsis.R | 855 ++++++++++++++++++++++++--------------------- R/data_transformation.R | 5 R/variable_binning.R | 120 +++--- inst/doc/introduction.html | 126 +++--- man/cohort_analysis.Rd | 16 8 files changed, 625 insertions(+), 524 deletions(-)
Title: GeoJSON to Simple Feature Converter
Description: Converts Between GeoJSON and simple feature objects.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between geojsonsf versions 2.0.0 dated 2020-06-20 and 2.0.1 dated 2020-10-02
DESCRIPTION | 18 - MD5 | 28 +- NEWS.md | 5 build/vignette.rds |binary inst/doc/geojson-sf-conversions.html | 4 inst/include/geojsonsf/geojson/api/df_api.hpp | 9 inst/include/geojsonsf/geojson/geojson_to_sf.hpp | 31 +- inst/include/geojsonsf/geojson/parse.hpp | 11 inst/include/geojsonsf/geojson/write_geometry.hpp | 12 - inst/include/geojsonsf/geojson/writers/write_geojson.hpp | 54 ++++ inst/include/geojsonsf/geometrycollection/geometrycollection.hpp | 117 ++++------ inst/include/geojsonsf/sf/sfc/geojson_sfc.hpp | 1 inst/include/geojsonsf/sf/sfc/utils/sfc_utils.hpp | 23 + inst/include/geojsonsf/sf/sfg/geojson_sfg.hpp | 72 +++++- src/geojson_to_wkt.cpp | 8 15 files changed, 257 insertions(+), 136 deletions(-)
Title: Model Wrappers for Rule-Based Models
Description: Bindings for additional models for use with the 'parsnip' package.
Models include prediction rule ensembles (Friedman and Popescu, 2008)
<doi:10.1214/07-AOAS148>, C5.0 rules (Quinlan, 1992 ISBN: 1558602380), and
Cubist (Kuhn and Johnson, 2013) <doi:10.1007/978-1-4614-6849-3>.
Author: Max Kuhn [aut, cre] (<https://orcid.org/0000-0003-2402-136X>),
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between rules versions 0.0.2 dated 2020-06-10 and 0.0.3 dated 2020-10-02
DESCRIPTION | 8 +++--- MD5 | 22 +++++++++--------- NEWS.md | 6 ++++ R/C5_rules_data.R | 2 + R/cubist_data.R | 1 R/rule_fit.R | 20 ++++++++++++++-- R/rule_fit_data.R | 1 README.md | 63 ++++++++++++++++++++++++++++++++++++++++++---------- inst/WORDLIST | 5 ++++ man/C5_rules.Rd | 6 ++-- man/cubist_rules.Rd | 6 ++-- man/rule_fit.Rd | 22 +++++++++++++++--- 12 files changed, 124 insertions(+), 38 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Blaise Melly [ctb] (Contributions to preprocessing code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Cleve Moler [ctb] (author of several linpack routines),
Victor Chernozhukov [ctb] (contributions to extreme value inference
code),
Ivan Fernandez-Val [ctb] (contributions to extreme value inference
code),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.70 dated 2020-09-28 and 5.73 dated 2020-10-02
DESCRIPTION | 14 ++++++++++--- MD5 | 20 ++++++++++--------- NAMESPACE | 9 +++++++- R/ParetoTest.R |only R/quantreg.R | 49 +++++++++++++++++++++++++++++++++++++++++++++++- R/table.R | 13 ++++++++---- inst/ChangeLog | 22 +++++++++++++++++++++ man/ParetoTest.Rd |only man/dynrq.Rd | 5 +--- man/plot.summary.rqs.Rd | 12 ++++++++--- man/summary.rq.Rd | 21 ++++++++++++++++++-- man/summary.rqss.Rd | 2 - 12 files changed, 140 insertions(+), 27 deletions(-)
Title: Propensity Score Weighting for Causal Inference with
Observational Studies and Randomized Trials
Description: Supports propensity score weighting analysis of observational studies and randomized trials. Enables the estimation and inference of average causal effects with binary and multiple treatments using overlap weights (ATO), inverse probability of treatment weights (ATE), average treatment effect among the treated weights (ATT), matching weights (ATM) and entropy weights (ATEN), with and without propensity score trimming. These weights are members of the family of balancing weights introduced in Li, Morgan and Zaslavsky (2018) <doi:10.1080/01621459.2016.1260466> and Li and Li (2019) <doi:10.1214/19-AOAS1282>.
Author: Tianhui Zhou [aut, cre],
Guangyu Tong [aut],
Fan Li [aut],
Laine Thomas [aut],
Fan Li [aut]
Maintainer: Tianhui Zhou <tianhui.zhou@duke.edu>
Diff between PSweight versions 1.1.0 dated 2020-09-15 and 1.1.1 dated 2020-10-02
DESCRIPTION | 8 MD5 | 24 +- R/ATENbin.R | 426 +++++++++++++++++++++++++------------------------- R/ATENmul.R | 377 ++++++++++++++++++++++----------------------- R/ATEbin.R | 401 +++++++++++++++++++++++------------------------ R/ATEmul.R | 398 +++++++++++++++++++++++------------------------ R/ATMbin.R | 393 +++++++++++++++++++++++----------------------- R/ATMmul.R | 339 ++++++++++++++++++++-------------------- R/ATObin.R | 400 +++++++++++++++++++++++------------------------ R/ATOmul.R | 369 +++++++++++++++++++++----------------------- R/ATTbin.R | 427 +++++++++++++++++++++++++-------------------------- R/ATTmul.R | 411 ++++++++++++++++++++++++------------------------- R/summary_PSweight.R | 10 - 13 files changed, 1986 insertions(+), 1997 deletions(-)
Title: Convert Data to Memorable Phrases
Description: Convert keys and other values to memorable phrases.
Includes some methods to build lists of words.
Author: Max Candocia
Maintainer: Max Candocia <maxcandocia@gmail.com>
Diff between keyToEnglish versions 0.1.0 dated 2020-09-17 and 0.2.0 dated 2020-10-02
DESCRIPTION | 6 MD5 | 57 ++++- NAMESPACE | 6 NEWS.md | 21 + R/data-documentation.R | 148 +++++++++++++ R/keyToEnglish.R | 344 ++++++++++++++++++++++++++++++-- README.md | 11 - data/wl_adjectives_nonorigin.rda |only data/wl_adjectives_visual.rda |only data/wl_animal.rda |binary data/wl_common.rda |binary data/wl_freq5663.rda |binary data/wl_literature.rda |binary data/wl_nouns_concrete.rda |only data/wl_nouns_concrete_plural.rda |only data/wl_science.rda |binary data/wl_verbs_transitive_gerund.rda |only data/wl_verbs_transitive_infinitive.rda |only data/wl_verbs_transitive_present.rda |only data/wml_animals.rda |only data/wml_cutephysics.rda |only data/wml_long_sentence.rda |only inst/COPYRIGHTS | 3 man/GCD.Rd |only man/LCM.Rd |only man/corpora_to_word_list.Rd | 2 man/generate_random_sentences.Rd |only man/hash_to_sentence.Rd |only man/keyToEnglish.Rd | 21 + man/uniqueness_max_size.Rd |only man/uniqueness_probability.Rd |only man/wl_adjectives_nonorigin.Rd |only man/wl_adjectives_visual.Rd |only man/wl_nouns_concrete.Rd |only man/wl_nouns_concrete_plural.Rd |only man/wl_verbs_transitive_gerund.Rd |only man/wl_verbs_transitive_infinitive.Rd |only man/wl_verbs_transitive_present.Rd |only man/wml_animals.Rd |only man/wml_cutephysics.Rd |only man/wml_long_sentence.Rd |only tests/testthat/test_lcm_gcd.R |only tests/testthat/test_multi.R |only tests/testthat/test_uniqueness.R |only 44 files changed, 580 insertions(+), 39 deletions(-)
Title: From Biological Sequences and Simulations to Correlation
Analysis
Description: Utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation. Examples of sequence covariation analysis are provided in: (1) Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M (2014) <doi:10.1002/prot.24570> and (2) Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M (2018) <doi: 10.1371/journal.pcbi.1006209>. An example of side chain correlated motion analysis is provided in: Taddese B, Garnier A, Abdi H, Henrion D, Chabbert M (2020) <doi: 10.1038/s41598-020-72766-1>. This work was supported by the French National Research Agency (Grant number: ANR-11-BSV2-026) and by GENCI (Grant number: 100567).
Author: Bruck Taddese [aut], Antoine Garnier [aut], Madeline Deniaud [aut], Julien Pele [ctb], Lea Bellenger [ctb], Jean-Michel Becu [ctb], Marie Chabbert [aut,cre]
Maintainer: Marie Chabbert <marie.chabbert@univ-angers.fr>
Diff between Bios2cor versions 2.1 dated 2020-01-30 and 2.2 dated 2020-10-02
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/bios2cor-package.Rd | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Adaptive Weights Smoothing
Description: We provide a collection of R-functions implementing
adaptive smoothing procedures in 1D, 2D and 3D. This includes the
Propagation-Separation Approach to adaptive smoothing,
the Intersecting Confidence Intervals (ICI), variational approaches and a non-local means filter.
The package is described in detail in Polzehl J, Papafitsoros K, Tabelow K (2020).
Patch-Wise Adaptive Weights Smoothing in R. Journal of Statistical Software, 95(6), 1-27.
<doi:10.18637/jss.v095.i06>,
Usage of the package in MR imaging is illustrated in Polzehl and Tabelow (2019),
Magnetic Resonance Brain Imaging, Appendix A, Springer, Use R! Series.
<doi:10.1007/978-3-030-29184-6_6>.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between aws versions 2.4-3 dated 2020-07-21 and 2.5 dated 2020-10-02
DESCRIPTION | 20 +++++++++----------- MD5 | 30 +++++++++++++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 46 ++++++++++++++++++---------------------------- inst/doc/aws-Example.pdf |binary man/ICIcombined.Rd | 3 +++ man/ICIsmooth.Rd | 3 +++ man/TV_denoising.Rd | 3 +++ man/aws-package.Rd | 5 ++--- man/aws.Rd | 5 ++--- man/kernsm.Rd | 5 ++++- man/lpaws.Rd | 6 +++--- man/nlmeans.Rd | 3 +++ man/paws.Rd | 5 ++--- man/vpaws.Rd | 5 ++--- 16 files changed, 69 insertions(+), 70 deletions(-)