Title: Streamline Bioacoustic Analysis
Description: A tool to streamline the analysis of animal acoustic signal structure. The package offers functions for downloading avian vocalizations from the open-access online repository Xeno-Canto, displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals or importing detected signals from other software, assessing performance of methods that measure acoustic similarity, conducting cross-correlations, dynamic time warping, measuring acoustic parameters and analysing interactive vocal signals, among others. Most functions working iteratively allow parallelization to improve computational efficiency.
Author: Marcelo Araya-Salas & Grace Smith Vidaurre
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>
Diff between warbleR versions 1.1.4 dated 2016-11-15 and 1.1.5 dated 2017-01-20
warbleR-1.1.4/warbleR/NEWS |only warbleR-1.1.4/warbleR/R/manualoc.df-data.R |only warbleR-1.1.4/warbleR/data/manualoc.df.rda |only warbleR-1.1.4/warbleR/man/manualoc.df.Rd |only warbleR-1.1.5/warbleR/DESCRIPTION | 14 - warbleR-1.1.5/warbleR/MD5 | 144 +++++------ warbleR-1.1.5/warbleR/NAMESPACE | 2 warbleR-1.1.5/warbleR/NEWS.md |only warbleR-1.1.5/warbleR/R/Phae.long1-data.R | 4 warbleR-1.1.5/warbleR/R/Phae.long2-data.R | 4 warbleR-1.1.5/warbleR/R/Phae.long3-data.R | 4 warbleR-1.1.5/warbleR/R/Phae.long4-data.R | 4 warbleR-1.1.5/warbleR/R/autodetec.R | 23 + warbleR-1.1.5/warbleR/R/checksels.R | 190 +++++++++----- warbleR-1.1.5/warbleR/R/checkwavs.R | 66 ++++- warbleR-1.1.5/warbleR/R/compare.methods.R | 8 warbleR-1.1.5/warbleR/R/dfDTW.R | 92 +------ warbleR-1.1.5/warbleR/R/dfts.R | 179 +++++-------- warbleR-1.1.5/warbleR/R/ffDTW.R | 84 +----- warbleR-1.1.5/warbleR/R/ffts.R | 184 +++++--------- warbleR-1.1.5/warbleR/R/filtersels.R | 89 ++++-- warbleR-1.1.5/warbleR/R/lspec.R | 8 warbleR-1.1.5/warbleR/R/lspec2pdf.R | 8 warbleR-1.1.5/warbleR/R/manualoc.R | 2 warbleR-1.1.5/warbleR/R/mp32wav.R | 14 - warbleR-1.1.5/warbleR/R/querxc.R | 244 +++++++++---------- warbleR-1.1.5/warbleR/R/selec.table-data.R |only warbleR-1.1.5/warbleR/R/seltailor.R | 32 +- warbleR-1.1.5/warbleR/R/sig2noise.R | 12 warbleR-1.1.5/warbleR/R/snrspecs.R | 40 ++- warbleR-1.1.5/warbleR/R/sp.en.ts.R |only warbleR-1.1.5/warbleR/R/specan.R | 33 +- warbleR-1.1.5/warbleR/R/specreator.R | 19 - warbleR-1.1.5/warbleR/R/trackfreqs.R | 167 ++++++++----- warbleR-1.1.5/warbleR/R/wavdur.R | 2 warbleR-1.1.5/warbleR/R/xcmaps.R | 10 warbleR-1.1.5/warbleR/R/xcorr.R | 6 warbleR-1.1.5/warbleR/R/xcorr.graph.R | 4 warbleR-1.1.5/warbleR/README.md | 17 - warbleR-1.1.5/warbleR/build/vignette.rds |binary warbleR-1.1.5/warbleR/data/Cryp.soui.rda |binary warbleR-1.1.5/warbleR/data/Phae.long1.rda |binary warbleR-1.1.5/warbleR/data/Phae.long2.rda |binary warbleR-1.1.5/warbleR/data/Phae.long3.rda |binary warbleR-1.1.5/warbleR/data/Phae.long4.rda |binary warbleR-1.1.5/warbleR/data/selec.table.rda |only warbleR-1.1.5/warbleR/data/selection.files.rda |binary warbleR-1.1.5/warbleR/data/sim.coor.sing.rda |binary warbleR-1.1.5/warbleR/inst/doc/warbleR_workflow.Rmd | 6 warbleR-1.1.5/warbleR/inst/doc/warbleR_workflow.html | 57 ++-- warbleR-1.1.5/warbleR/man/Phae.long1.Rd | 4 warbleR-1.1.5/warbleR/man/Phae.long2.Rd | 4 warbleR-1.1.5/warbleR/man/Phae.long3.Rd | 4 warbleR-1.1.5/warbleR/man/Phae.long4.Rd | 4 warbleR-1.1.5/warbleR/man/autodetec.Rd | 10 warbleR-1.1.5/warbleR/man/checksels.Rd | 20 + warbleR-1.1.5/warbleR/man/checkwavs.Rd | 16 - warbleR-1.1.5/warbleR/man/compare.methods.Rd | 6 warbleR-1.1.5/warbleR/man/dfDTW.Rd | 86 +----- warbleR-1.1.5/warbleR/man/dfts.Rd | 92 +------ warbleR-1.1.5/warbleR/man/ffDTW.Rd | 89 +----- warbleR-1.1.5/warbleR/man/ffts.Rd | 96 +------ warbleR-1.1.5/warbleR/man/filtersels.Rd | 17 - warbleR-1.1.5/warbleR/man/lspec.Rd | 4 warbleR-1.1.5/warbleR/man/lspec2pdf.Rd | 4 warbleR-1.1.5/warbleR/man/querxc.Rd | 35 ++ warbleR-1.1.5/warbleR/man/selec.table.Rd |only warbleR-1.1.5/warbleR/man/seltailor.Rd | 13 - warbleR-1.1.5/warbleR/man/sig2noise.Rd | 6 warbleR-1.1.5/warbleR/man/snrspecs.Rd | 13 - warbleR-1.1.5/warbleR/man/sp.en.ts.Rd |only warbleR-1.1.5/warbleR/man/specan.Rd | 11 warbleR-1.1.5/warbleR/man/specreator.Rd | 9 warbleR-1.1.5/warbleR/man/trackfreqs.Rd | 18 + warbleR-1.1.5/warbleR/man/xcmaps.Rd | 9 warbleR-1.1.5/warbleR/man/xcorr.Rd | 4 warbleR-1.1.5/warbleR/man/xcorr.graph.Rd | 4 warbleR-1.1.5/warbleR/vignettes/warbleR_workflow.Rmd | 6 78 files changed, 1138 insertions(+), 1218 deletions(-)
Title: Data Exchange Between R and LabKey Server
Description: The LabKey client library for R makes it easy for R users to
load live data from a LabKey Server, <http://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a LabKey Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.1.132 dated 2016-11-30 and 2.1.133 dated 2017-01-20
DESCRIPTION | 12 +++++++----- MD5 | 15 +++++++++------ NAMESPACE | 2 ++ NEWS | 4 ++++ R/RcppExports.R |only R/makeDF.R | 10 +++------- build/vignette.rds |binary man/Rlabkey-package.Rd | 4 ++-- src/RcppExports.cpp |only src/listToMatrix.cpp |only 10 files changed, 27 insertions(+), 20 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF';
<http://www.gbif.org/developer/summary>). 'GBIF' is a database
of species occurrence records from sources all over the globe.
'rgbif' includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, and getting counts of occurrence records.
Author: Scott Chamberlain [aut, cre],
Vijay Barve [ctb],
Dan Mcglinn [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.9.6 dated 2016-12-06 and 0.9.7 dated 2017-01-20
rgbif-0.9.6/rgbif/R/tbl_df_utils.R |only rgbif-0.9.6/rgbif/man/type_sum.Rd |only rgbif-0.9.7/rgbif/DESCRIPTION | 21 rgbif-0.9.7/rgbif/LICENSE | 2 rgbif-0.9.7/rgbif/MD5 | 84 +-- rgbif-0.9.7/rgbif/NAMESPACE | 12 rgbif-0.9.7/rgbif/NEWS.md | 26 + rgbif-0.9.7/rgbif/R/gbif_citation.R | 11 rgbif-0.9.7/rgbif/R/name_lookup.r | 15 rgbif-0.9.7/rgbif/R/occ_download.R | 192 ++++++- rgbif-0.9.7/rgbif/R/occ_download_cancel.R | 15 rgbif-0.9.7/rgbif/R/occ_download_get.r | 17 rgbif-0.9.7/rgbif/R/occ_download_import.R | 24 rgbif-0.9.7/rgbif/R/occ_download_list.R | 10 rgbif-0.9.7/rgbif/R/occ_download_meta.R | 28 - rgbif-0.9.7/rgbif/R/rgbif-package.r | 2 rgbif-0.9.7/rgbif/R/zzz.r | 10 rgbif-0.9.7/rgbif/README.md | 108 ++-- rgbif-0.9.7/rgbif/inst/assets/img/unnamed-chunk-8-1.png |binary rgbif-0.9.7/rgbif/inst/doc/issues_vignette.Rmd | 122 ++-- rgbif-0.9.7/rgbif/inst/doc/issues_vignette.html | 122 ++-- rgbif-0.9.7/rgbif/inst/doc/rgbif_vignette.Rmd | 366 +++++++------- rgbif-0.9.7/rgbif/inst/doc/rgbif_vignette.html | 368 +++++++-------- rgbif-0.9.7/rgbif/inst/doc/taxonomic_names.Rmd | 8 rgbif-0.9.7/rgbif/inst/doc/taxonomic_names.html | 8 rgbif-0.9.7/rgbif/inst/vign/figure/gbifmap1-1.png |binary rgbif-0.9.7/rgbif/inst/vign/issues_vignette.md | 122 ++-- rgbif-0.9.7/rgbif/inst/vign/rgbif_vignette.md | 366 +++++++------- rgbif-0.9.7/rgbif/inst/vign/taxonomic_names.md | 8 rgbif-0.9.7/rgbif/man/name_lookup.Rd | 3 rgbif-0.9.7/rgbif/man/occ_data.Rd | 4 rgbif-0.9.7/rgbif/man/occ_download.Rd | 113 +++- rgbif-0.9.7/rgbif/man/occ_download_cancel.Rd | 7 rgbif-0.9.7/rgbif/man/occ_download_get.Rd | 14 rgbif-0.9.7/rgbif/man/occ_download_import.Rd | 15 rgbif-0.9.7/rgbif/man/occ_download_meta.Rd | 3 rgbif-0.9.7/rgbif/tests/testthat/test-dataset_suggest.r | 2 rgbif-0.9.7/rgbif/tests/testthat/test-download_parsing.R | 6 rgbif-0.9.7/rgbif/tests/testthat/test-name_lookup.r | 4 rgbif-0.9.7/rgbif/tests/testthat/test-nodes.r | 2 rgbif-0.9.7/rgbif/tests/testthat/test-occ_facet.R | 2 rgbif-0.9.7/rgbif/vignettes/issues_vignette.Rmd | 122 ++-- rgbif-0.9.7/rgbif/vignettes/rgbif_vignette.Rmd | 366 +++++++------- rgbif-0.9.7/rgbif/vignettes/taxonomic_names.Rmd | 8 44 files changed, 1427 insertions(+), 1311 deletions(-)
Title: Verification Routines for Ensemble Forecasts of Weather and
Climate
Description: A collection of new forecast verification routines developed for the SPECS
FP7 project. The emphasis is on comparative verification of ensemble forecasts.
Author: Stefan Siegert [aut, cre],
Jonas Bhend [ctb],
Igor Kroener [ctb],
Matteo De Felice [ctb]
Maintainer: Stefan Siegert <s.siegert@exeter.ac.uk>
Diff between SpecsVerification versions 0.4-1 dated 2015-10-23 and 0.5-0 dated 2017-01-20
SpecsVerification-0.4-1/SpecsVerification/R/BrierScoreDecomposition.R |only SpecsVerification-0.4-1/SpecsVerification/R/DressCrpsDiff.R |only SpecsVerification-0.4-1/SpecsVerification/R/DressCrpss.R |only SpecsVerification-0.4-1/SpecsVerification/R/DressIgnDiff.R |only SpecsVerification-0.4-1/SpecsVerification/R/DressIgnSs.R |only SpecsVerification-0.4-1/SpecsVerification/R/EnsBrierDiff.R |only SpecsVerification-0.4-1/SpecsVerification/R/EnsBrierSs.R |only SpecsVerification-0.4-1/SpecsVerification/R/EnsCrpsDiff.R |only SpecsVerification-0.4-1/SpecsVerification/R/EnsCrpss.R |only SpecsVerification-0.4-1/SpecsVerification/R/EnsRpsDiff.R |only SpecsVerification-0.4-1/SpecsVerification/R/EnsRpss.R |only SpecsVerification-0.4-1/SpecsVerification/R/FairBrier.R |only SpecsVerification-0.4-1/SpecsVerification/R/FairBrierDiff.R |only SpecsVerification-0.4-1/SpecsVerification/R/FairBrierSs.R |only SpecsVerification-0.4-1/SpecsVerification/R/FairCrps.R |only SpecsVerification-0.4-1/SpecsVerification/R/FairCrpsDiff.R |only SpecsVerification-0.4-1/SpecsVerification/R/FairCrpss.R |only SpecsVerification-0.4-1/SpecsVerification/R/FairRps.R |only SpecsVerification-0.4-1/SpecsVerification/R/FairRpsDiff.R |only SpecsVerification-0.4-1/SpecsVerification/R/FairRpss.R |only SpecsVerification-0.4-1/SpecsVerification/R/GaussCrpsDecomposition.R |only SpecsVerification-0.4-1/SpecsVerification/R/GaussCrpsDiff.R |only SpecsVerification-0.4-1/SpecsVerification/R/GaussCrpss.R |only SpecsVerification-0.4-1/SpecsVerification/R/Preprocess.R |only SpecsVerification-0.4-1/SpecsVerification/man/BrierScoreDecomposition.Rd |only SpecsVerification-0.4-1/SpecsVerification/man/DressIgnSs.Rd |only SpecsVerification-0.4-1/SpecsVerification/man/EnsScoreDiff.Rd |only SpecsVerification-0.4-1/SpecsVerification/man/EnsSkillScore.Rd |only SpecsVerification-0.4-1/SpecsVerification/man/FairBrier.Rd |only SpecsVerification-0.4-1/SpecsVerification/man/FairCrps.Rd |only SpecsVerification-0.4-1/SpecsVerification/man/FairRps.Rd |only SpecsVerification-0.4-1/SpecsVerification/man/FairScoreDiff.Rd |only SpecsVerification-0.4-1/SpecsVerification/man/FairSkillScore.Rd |only SpecsVerification-0.4-1/SpecsVerification/man/GaussCrpsDecomposition.Rd |only SpecsVerification-0.4-1/SpecsVerification/man/Preprocess.Rd |only SpecsVerification-0.4-1/SpecsVerification/src/dresscrps.c |only SpecsVerification-0.5-0/SpecsVerification/DESCRIPTION | 33 + SpecsVerification-0.5-0/SpecsVerification/MD5 | 177 +++++---- SpecsVerification-0.5-0/SpecsVerification/NAMESPACE | 64 ++- SpecsVerification-0.5-0/SpecsVerification/R/AbsErr.R |only SpecsVerification-0.5-0/SpecsVerification/R/Auc.R |only SpecsVerification-0.5-0/SpecsVerification/R/AucDiff.R |only SpecsVerification-0.5-0/SpecsVerification/R/BrierDecomp.R |only SpecsVerification-0.5-0/SpecsVerification/R/ClimEns.R | 24 - SpecsVerification-0.5-0/SpecsVerification/R/Corr.R | 86 +++- SpecsVerification-0.5-0/SpecsVerification/R/CorrDiff.R | 146 ++++---- SpecsVerification-0.5-0/SpecsVerification/R/Detrend.R | 14 SpecsVerification-0.5-0/SpecsVerification/R/DressCrps.R | 56 +-- SpecsVerification-0.5-0/SpecsVerification/R/DressEnsemble.R | 42 +- SpecsVerification-0.5-0/SpecsVerification/R/DressIgn.R | 13 SpecsVerification-0.5-0/SpecsVerification/R/EnsBrier.R | 73 ++-- SpecsVerification-0.5-0/SpecsVerification/R/EnsCrps.R | 54 +-- SpecsVerification-0.5-0/SpecsVerification/R/EnsQs.R |only SpecsVerification-0.5-0/SpecsVerification/R/EnsRps.R | 86 +++- SpecsVerification-0.5-0/SpecsVerification/R/FitAkdParameters.R | 50 ++ SpecsVerification-0.5-0/SpecsVerification/R/GaussCrps.R | 71 +-- SpecsVerification-0.5-0/SpecsVerification/R/GenerateToyData.R | 37 ++ SpecsVerification-0.5-0/SpecsVerification/R/GetDensity.R | 47 +- SpecsVerification-0.5-0/SpecsVerification/R/PlotDressedEns.R | 15 SpecsVerification-0.5-0/SpecsVerification/R/PlotRankhist.R | 31 + SpecsVerification-0.5-0/SpecsVerification/R/Rankhist.R | 53 ++ SpecsVerification-0.5-0/SpecsVerification/R/RcppExports.R |only SpecsVerification-0.5-0/SpecsVerification/R/ReliabilityDiagram.R | 179 ++++------ SpecsVerification-0.5-0/SpecsVerification/R/ScoreDiff.R |only SpecsVerification-0.5-0/SpecsVerification/R/SkillScore.R |only SpecsVerification-0.5-0/SpecsVerification/R/SpecsVerification.R |only SpecsVerification-0.5-0/SpecsVerification/R/SqErr.R |only SpecsVerification-0.5-0/SpecsVerification/R/TestRankhist.R | 33 + SpecsVerification-0.5-0/SpecsVerification/R/eurotempforecast.R |only SpecsVerification-0.5-0/SpecsVerification/data |only SpecsVerification-0.5-0/SpecsVerification/man/AbsErr.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/Auc.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/AucDiff.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/BrierDecomp.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/ClimEns.Rd | 24 - SpecsVerification-0.5-0/SpecsVerification/man/Corr.Rd | 37 +- SpecsVerification-0.5-0/SpecsVerification/man/CorrDiff.Rd | 45 +- SpecsVerification-0.5-0/SpecsVerification/man/Detrend.Rd | 27 - SpecsVerification-0.5-0/SpecsVerification/man/DressCrps.Rd | 36 +- SpecsVerification-0.5-0/SpecsVerification/man/DressCrpsDiff.Rd | 46 -- SpecsVerification-0.5-0/SpecsVerification/man/DressCrpss.Rd | 34 - SpecsVerification-0.5-0/SpecsVerification/man/DressEnsemble.Rd | 61 +-- SpecsVerification-0.5-0/SpecsVerification/man/DressIgn.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/DressIgnDiff.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/EnsBrier.Rd | 41 +- SpecsVerification-0.5-0/SpecsVerification/man/EnsBrierDiff.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/EnsBrierSs.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/EnsCrps.Rd | 40 +- SpecsVerification-0.5-0/SpecsVerification/man/EnsCrpsDiff.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/EnsCrpss.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/EnsQs.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/EnsRps.Rd | 42 +- SpecsVerification-0.5-0/SpecsVerification/man/EnsRpsDiff.Rd | 39 -- SpecsVerification-0.5-0/SpecsVerification/man/EnsRpss.Rd | 37 +- SpecsVerification-0.5-0/SpecsVerification/man/FairBrierDiff.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/FairBrierSs.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/FairCrpsDiff.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/FairCrpss.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/FairRpsDiff.Rd | 40 +- SpecsVerification-0.5-0/SpecsVerification/man/FairRpss.Rd | 37 +- SpecsVerification-0.5-0/SpecsVerification/man/FitAkdParameters.Rd | 36 -- SpecsVerification-0.5-0/SpecsVerification/man/GaussCrps.Rd | 34 + SpecsVerification-0.5-0/SpecsVerification/man/GaussCrpsDiff.Rd | 43 +- SpecsVerification-0.5-0/SpecsVerification/man/GaussCrpss.Rd | 38 +- SpecsVerification-0.5-0/SpecsVerification/man/GenerateToyData.Rd | 78 ++-- SpecsVerification-0.5-0/SpecsVerification/man/GetDensity.Rd | 59 +-- SpecsVerification-0.5-0/SpecsVerification/man/PlotDressedEns.Rd | 37 +- SpecsVerification-0.5-0/SpecsVerification/man/PlotRankhist.Rd | 34 - SpecsVerification-0.5-0/SpecsVerification/man/Rankhist.Rd | 34 + SpecsVerification-0.5-0/SpecsVerification/man/ReliabilityDiagram.Rd | 59 +-- SpecsVerification-0.5-0/SpecsVerification/man/ScoreDiff.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/SkillScore.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/SpecsVerification.Rd | 14 SpecsVerification-0.5-0/SpecsVerification/man/SqErr.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/TestRankhist.Rd | 26 - SpecsVerification-0.5-0/SpecsVerification/man/auc_cpp.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/aucdiff_cpp.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/dresscrps_cpp.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/enscrps_cpp.Rd |only SpecsVerification-0.5-0/SpecsVerification/man/eurotempforecast.Rd |only SpecsVerification-0.5-0/SpecsVerification/src/Makevars | 1 SpecsVerification-0.5-0/SpecsVerification/src/RcppExports.cpp |only SpecsVerification-0.5-0/SpecsVerification/src/auc.cpp |only SpecsVerification-0.5-0/SpecsVerification/src/auc_diff.cpp |only SpecsVerification-0.5-0/SpecsVerification/src/dresscrps.cpp |only SpecsVerification-0.5-0/SpecsVerification/src/enscrps.cpp |only SpecsVerification-0.5-0/SpecsVerification/tests |only 127 files changed, 1423 insertions(+), 1040 deletions(-)
More information about SpecsVerification at CRAN
Permanent link
Title: Spatial Analysis of Field Trials with Splines
Description: Analysis of field trial experiments by modelling spatial trends using two-dimensional Penalised spline (P-spline) models.
Author: Maria Xose Rodriguez-Alvarez [aut, cre],
Martin Boer [aut],
Paul Eilers [aut],
Fred van Eeuwijk [ctb]
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@bcamath.org>
Diff between SpATS versions 1.0-4 dated 2016-07-29 and 1.0-5 dated 2017-01-20
DESCRIPTION | 12 +-- MD5 | 16 ++-- R/obtain.spatialtrend.R | 38 ++++++++-- R/plot.SpATS.R | 166 +++++++++++++++++++++++---------------------- R/predict.SpATS.R | 2 R/variogram.SpATS.R | 4 - man/SpATS-package.Rd | 4 - man/obtain.spatialtrend.Rd | 11 +- man/plot.SpATS.Rd | 3 9 files changed, 147 insertions(+), 109 deletions(-)
Title: Subgroup Identification Based on Differential Effect Search
Description: Provides function to apply "Subgroup Identification based on Differential Effect Search" (SIDES) method proposed by Lipkovich et al. (2011) <doi:10.1002/sim.4289>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between SIDES versions 1.9 dated 2017-01-06 and 1.10 dated 2017-01-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/SIDES_MAIN.R | 18 +++++++++++++----- R/TEST_STAT_PVAL.R | 5 +++++ man/SIDES-package.Rd | 4 ++-- man/SIDES.Rd | 11 +++++++++++ 6 files changed, 40 insertions(+), 16 deletions(-)
Title: Reading LSD Results (.res) Files
Description: Interfaces R with LSD. Reads object-oriented data in results files (.res) produced by LSD and creates appropriate multi-dimensional arrays in R. Also provides functions to extract basic information and statistics from those files. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente (documentation and downloads available at <http://labsimdev.org>).
Author: Marcelo C. Pereira
Maintainer: Marcelo C. Pereira <marcelocpereira@uol.com.br>
Diff between LSDinterface versions 0.2.2 dated 2016-09-11 and 0.2.3 dated 2017-01-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/LSDinterface.R | 6 ++++-- build/partial.rdb |binary 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Permutation Tests for Nonparametric Statistics
Description: Performs a permutation test on the difference between two location parameters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test, a ratio mean deviance test. Also performs some graphing techniques, such as for confidence intervals, vector addition, and Fourier analysis; and includes functions related to the Laplace (double exponential) and triangular distributions. Performs power calculations for the binomial test.
Author: Steven T. Garren [aut, cre]
Maintainer: Steven T. Garren <GARRENST@JMU.EDU>
Diff between jmuOutlier versions 1.1 dated 2016-03-15 and 1.2 dated 2017-01-20
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/dlaplace.R | 1 + R/plaplace.R | 1 + R/qlaplace.R | 4 +++- build/partial.rdb |binary man/perm.cor.test.Rd | 5 +++-- man/perm.f.test.Rd | 4 ++-- man/qlaplace.Rd | 3 ++- 10 files changed, 26 insertions(+), 20 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; the Daymet gridded estimates of daily weather parameters
for North America, version 3, available from the Oak Ridge National Laboratory's
Distributed Active Archive Center (DAAC); and the International Tree Ring Data Bank.
Additional data sources are in the works, global soils (HWSD),
MODIS satellite data products, the National Atlas (US), Natural Earth, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.3.5 dated 2017-01-06 and 2.4.0 dated 2017-01-20
DESCRIPTION | 9 LICENSE | 2 MD5 | 57 - NEWS.md |only R/DAYMET_FUNCTIONS.R | 310 ++++------ R/GHCN_FUNCTIONS.R | 503 ++++++++-------- R/ITRDB_FUNCTIONS.R | 1293 +++++++++++++++++++++--------------------- R/NED_FUNCTIONS.R | 240 +++---- R/NHD_FUNCTIONS.R | 282 ++++----- R/SSURGO_FUNCTIONS.R | 566 +++++++++--------- R/UTILITY_FUNCTIONS.R | 170 ++--- README.md | 2 man/FedData-package.Rd | 4 man/download_daymet_tile.Rd | 2 man/download_itrdb.Rd | 2 man/download_ned_tile.Rd | 6 man/get_daymet.Rd | 12 man/get_daymet_tile.Rd | 2 man/get_ghcn_daily.Rd | 26 man/get_ghcn_daily_station.Rd | 4 man/get_ghcn_inventory.Rd | 2 man/get_itrdb.Rd | 50 - man/get_ned.Rd | 14 man/get_ned_tile.Rd | 6 man/get_nhd.Rd | 10 man/get_ssurgo.Rd | 24 man/get_ssurgo_study_area.Rd | 4 man/substr_right.Rd | 4 tests/testthat/test.GHCN.R | 2 tests/testthat/test.UTILITY.R | 2 30 files changed, 1807 insertions(+), 1803 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow,Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.8.0 dated 2016-12-08 and 0.8.2 dated 2017-01-20
DESCRIPTION | 12 +- MD5 | 78 ++++++++--------- NAMESPACE | 71 ++++++++++++--- R/domain.R | 4 R/incPercentile.R | 10 +- R/lin.ratio.R | 6 - R/linarpr.R | 30 +++--- R/linarpt.R | 16 +-- R/linarr.R | 28 +++--- R/lingini.R | 16 +-- R/lingini2.R | 15 +-- R/lingpg.R | 18 ++-- R/linpoormed.R | 16 +-- R/linqsr.R | 18 ++-- R/linrmir.R | 16 +-- R/linrmpg.R | 20 ++-- R/residual_est.R | 33 +++---- R/var_srs.R | 5 - R/vardchangannual.R | 190 +++++++++++++++++++----------------------- R/vardchanges.R | 119 +++++++++++--------------- R/vardchangespoor.R | 114 ++++++++++++------------- R/vardcros.R | 153 ++++++++++++++++------------------ R/vardcrosannual.R | 135 ++++++++++++++---------------- R/vardcrospoor.R | 131 ++++++++++++++--------------- R/vardom.R | 191 +++++++++++++++++++++--------------------- R/vardom_othstr.R | 60 +++++-------- R/vardomh.R | 216 +++++++++++++++++++++--------------------------- R/variance_est.R | 31 ++---- R/variance_othstr.R | 61 +++++-------- R/varpoord.R | 201 ++++++++++++++++++++++++-------------------- README | 2 inst/CITATION | 23 ++--- inst/COPYING | 2 inst/DISCLAIMER | 16 +-- inst/NEWS | 7 + man/vardom.Rd | 11 ++ man/vardomh.Rd | 11 ++ man/vardpoor-package.Rd | 6 - man/variance_est.Rd | 9 +- man/varpoord.Rd | 23 +++-- 40 files changed, 1061 insertions(+), 1063 deletions(-)
Title: Fetch Hillary Rodham Clinton's Emails
Description: Fetch and process Hillary Rodham Clinton's "personal" emails.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between rodham versions 0.0.2 dated 2016-05-08 and 0.0.3 dated 2017-01-20
DESCRIPTION | 8 +++++--- LICENSE | 2 +- MD5 | 30 +++++++++++++++--------------- NEWS.md | 11 +++++++++++ R/emails.R | 38 +++++++++++++++++++------------------- R/extractor.R | 7 ++++--- R/get_emails.R | 3 --- R/rodham.R | 2 ++ R/utils.R | 17 +++++++++++++++++ README.md | 12 ++++++++---- build/vignette.rds |binary inst/doc/how-to.Rmd | 2 +- inst/doc/how-to.html | 15 +++++++-------- man/get_xpdf.Rd | 4 ++-- man/rodham.Rd | 1 + tests/testthat.R | 8 ++++---- 16 files changed, 97 insertions(+), 63 deletions(-)
Title: Nonparametric Estimation of Preferential Attachment and Node
Fitness in Temporal Complex Networks
Description: A statistically sound method for estimating jointly the attachment function and node fitness in a temporal complex network by maximizing a suitable penalized log-likelihood function is implemented in this package. Tutorial can be found in the accompanying vignette. For a list of references, please run the command: citation("PAFit").
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>
Diff between PAFit versions 0.8.7 dated 2016-10-18 and 0.9.3 dated 2017-01-20
DESCRIPTION | 8 MD5 | 33 +- NAMESPACE | 2 NEWS |only R/CreateDataCV.R | 50 +++- R/GetStatistics.R | 10 R/PAFit.R | 600 +++++++++++++++++++++++++++++++++++++++++++-------- R/RcppExports.R | 4 R/performCV.R | 2 R/plot.pafit.r | 4 build/vignette.rds |binary man/CreateDataCV.Rd | 5 man/GetStatistics.Rd | 2 man/PAFit-package.Rd | 4 man/PAFit.Rd | 21 + man/performCV.Rd | 2 src/Cpp_code.cpp | 11 src/RcppExports.cpp | 7 18 files changed, 623 insertions(+), 142 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using 'LAPACK' and 'SuiteSparse'.
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.2-7.1 dated 2016-09-01 and 1.2-8 dated 2017-01-20
DESCRIPTION | 8 +- MD5 | 82 ++++++++++---------- R/AllClass.R | 25 +++++- R/Auxiliaries.R | 7 + R/Matrix.R | 12 +++ R/Ops.R | 110 +++++++++++++++++++--------- R/Summary.R | 7 + R/diagMatrix.R | 1 R/sparseMatrix.R | 1 R/sparseVector.R | 38 +++++---- TODO | 4 + build/vignette.rds |binary inst/NEWS.Rd | 27 ++++++ inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/include/cholmod.h | 65 +++++++++++----- man/Matrix-class.Rd | 3 man/SparseM-conv.Rd | 2 man/cBind.Rd | 3 man/expm.Rd | 2 man/rankMatrix.Rd | 2 man/sparseMatrix-class.Rd | 1 man/sparseVector-class.Rd | 4 - man/sparseVector.Rd | 2 man/uniqTsparse.Rd | 16 +++- src/AMD/Include/amd_internal.h | 2 src/AMD/Source/amd_2.c | 2 src/COLAMD/Source/colamd.c | 4 - src/Csparse.c | 4 - src/Mutils.c | 8 +- src/SuiteSparse_config/SuiteSparse_config.h | 38 ++++++--- src/cs.c | 20 ++++- src/cs.h | 4 - tests/factorizing.R | 5 + tests/group-methods.R | 51 ++++++++++++ tests/indexing.R | 34 ++++++++ tests/indexing.Rout.save | 42 +++++++++- tests/validObj.R | 9 +- vignettes/Matrix.bib | 4 - 42 files changed, 482 insertions(+), 167 deletions(-)
Title: Lexicons for Text Analysis
Description: A collection of lexical hash tables, dictionaries, and
word lists.
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between lexicon versions 0.0.1 dated 2017-01-08 and 0.1.0 dated 2017-01-20
DESCRIPTION | 10 ++++---- MD5 | 38 ++++++++++++++++++--------------- NEWS | 13 +++++++++++ R/hash_sentiment.R | 2 - R/hash_syllable.R | 2 - R/key_grades.R |only R/key_ratings.R |only R/lexicon-package.R | 3 +- R/nrc_emotions.R | 2 - R/pos_df_pronouns.R | 2 - README.md | 55 +++++++++++++++++++++++++++--------------------- data/datalist | 1 data/hash_sentiment.rda |binary data/key_rating.rda |only inst/CITATION | 8 +++--- man/hash_sentiment.Rd | 2 - man/hash_syllable.Rd | 2 - man/key_grade.Rd | 11 ++++++++- man/key_rating.Rd |only man/lexicon.Rd | 2 - man/nrc_emotions.Rd | 2 - man/pos_df_pronouns.Rd | 2 - 22 files changed, 97 insertions(+), 60 deletions(-)
Title: Dynamic Hazard Models using State Space Models
Description: Contains functions that lets you fit dynamic hazard models with binary
outcomes using state space models. The methods are originally described in
Fahrmeir (1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir (1994)
<doi:10.1093/biomet/81.2.317>. The functions also provide an extension hereof where the
Extended Kalman filter is replaced by an Unscented Kalman filter. Models are
fitted with the regular coxph() like formula.
Author: Benjamin Christoffersen [cre, aut],
Alan Miller [ctb],
Anthony Williams [ctb],
Boost developers [ctb, cph],
R-core [ctb, cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between dynamichazard versions 0.1.0 dated 2016-12-28 and 0.2.0 dated 2017-01-20
dynamichazard-0.1.0/dynamichazard/README.md |only dynamichazard-0.1.0/dynamichazard/man/get_survival_case_weigths_and_data.Rd |only dynamichazard-0.1.0/dynamichazard/vignettes/Sim_study_with_logit.pdf |only dynamichazard-0.2.0/dynamichazard/DESCRIPTION | 15 dynamichazard-0.2.0/dynamichazard/MD5 | 116 ++--- dynamichazard-0.2.0/dynamichazard/NAMESPACE | 11 dynamichazard-0.2.0/dynamichazard/NEWS.md |only dynamichazard-0.2.0/dynamichazard/R/RcppExports.R | 8 dynamichazard-0.2.0/dynamichazard/R/boot_est.R |only dynamichazard-0.2.0/dynamichazard/R/ddhazard.R | 182 ++++--- dynamichazard-0.2.0/dynamichazard/R/get_design_matrix.R | 16 dynamichazard-0.2.0/dynamichazard/R/plot.R | 35 + dynamichazard-0.2.0/dynamichazard/R/predict.R | 16 dynamichazard-0.2.0/dynamichazard/R/print.R |only dynamichazard-0.2.0/dynamichazard/R/residuals.R | 14 dynamichazard-0.2.0/dynamichazard/R/risk_obj.R | 14 dynamichazard-0.2.0/dynamichazard/R/roxygen_tags.R | 5 dynamichazard-0.2.0/dynamichazard/R/static_glm.R | 8 dynamichazard-0.2.0/dynamichazard/R/test_utils.R | 2 dynamichazard-0.2.0/dynamichazard/build/vignette.rds |binary dynamichazard-0.2.0/dynamichazard/inst/doc/Bootstrap_illustration.pdf |only dynamichazard-0.2.0/dynamichazard/inst/doc/Bootstrap_illustration.pdf.asis |only dynamichazard-0.2.0/dynamichazard/inst/doc/Comparing_methods_for_logistic_models.R | 7 dynamichazard-0.2.0/dynamichazard/inst/doc/Comparing_methods_for_logistic_models.Rmd | 14 dynamichazard-0.2.0/dynamichazard/inst/doc/Comparing_methods_for_logistic_models.pdf |binary dynamichazard-0.2.0/dynamichazard/inst/doc/Sim_study_with_logit.pdf |only dynamichazard-0.2.0/dynamichazard/inst/doc/Sim_study_with_logit.pdf.asis |only dynamichazard-0.2.0/dynamichazard/inst/doc/ddhazard.R | 27 - dynamichazard-0.2.0/dynamichazard/inst/doc/ddhazard.Rmd | 231 +++++----- dynamichazard-0.2.0/dynamichazard/inst/doc/ddhazard.pdf |binary dynamichazard-0.2.0/dynamichazard/inst/shiny/app.R | 2 dynamichazard-0.2.0/dynamichazard/man/ddhazard.Rd | 71 +-- dynamichazard-0.2.0/dynamichazard/man/ddhazard_boot.Rd |only dynamichazard-0.2.0/dynamichazard/man/get_risk_obj.Rd | 14 dynamichazard-0.2.0/dynamichazard/man/get_survival_case_weights_and_data.Rd |only dynamichazard-0.2.0/dynamichazard/man/plot.fahrmeier_94.Rd | 4 dynamichazard-0.2.0/dynamichazard/man/predict.fahrmeier_94.Rd | 16 dynamichazard-0.2.0/dynamichazard/man/print.ddhazard_boot.Rd |only dynamichazard-0.2.0/dynamichazard/man/print.fahrmeier_94.Rd |only dynamichazard-0.2.0/dynamichazard/man/residuals.fahrmeier_94.Rd | 14 dynamichazard-0.2.0/dynamichazard/man/static_glm.Rd | 2 dynamichazard-0.2.0/dynamichazard/src/Makevars | 2 dynamichazard-0.2.0/dynamichazard/src/Makevars.win | 2 dynamichazard-0.2.0/dynamichazard/src/RcppExports.cpp | 14 dynamichazard-0.2.0/dynamichazard/src/bigglm_wrapper.cpp | 29 - dynamichazard-0.2.0/dynamichazard/src/ddhazard_fit.cpp | 139 +++--- dynamichazard-0.2.0/dynamichazard/src/dynamichazard.h | 11 dynamichazard-0.2.0/dynamichazard/src/thread_pool.cpp | 7 dynamichazard-0.2.0/dynamichazard/src/thread_pool.h | 32 - dynamichazard-0.2.0/dynamichazard/tests/testthat/testUKF.R | 15 dynamichazard-0.2.0/dynamichazard/tests/testthat/testbigglm_wrapper.R | 51 +- dynamichazard-0.2.0/dynamichazard/tests/testthat/testboot_est.R |only dynamichazard-0.2.0/dynamichazard/tests/testthat/testddhazard.R | 15 dynamichazard-0.2.0/dynamichazard/tests/testthat/testdesign_mat_and_risk_obj.R | 15 dynamichazard-0.2.0/dynamichazard/tests/testthat/testfixed_effects_like_recursive_least_squares.R | 6 dynamichazard-0.2.0/dynamichazard/tests/testthat/testfixed_terms_est_in_M_step.R | 59 ++ dynamichazard-0.2.0/dynamichazard/tests/testthat/testloglike.R | 22 dynamichazard-0.2.0/dynamichazard/tests/testthat/testplot.R | 11 dynamichazard-0.2.0/dynamichazard/tests/testthat/testpredict.R | 10 dynamichazard-0.2.0/dynamichazard/tests/testthat/testprint.R |only dynamichazard-0.2.0/dynamichazard/tests/testthat/testresiduals.R | 6 dynamichazard-0.2.0/dynamichazard/tests/testthat/teststatic_glm.R | 6 dynamichazard-0.2.0/dynamichazard/tests/testthat/testtest_utils.R | 4 dynamichazard-0.2.0/dynamichazard/tests/testthat/testweights.R |only dynamichazard-0.2.0/dynamichazard/vignettes/Bootstrap_illustration.pdf.asis |only dynamichazard-0.2.0/dynamichazard/vignettes/Comparing_methods_for_logistic_models.Rmd | 14 dynamichazard-0.2.0/dynamichazard/vignettes/Sim_study_with_logit.pdf.asis | 2 dynamichazard-0.2.0/dynamichazard/vignettes/ddhazard.Rmd | 231 +++++----- 68 files changed, 932 insertions(+), 615 deletions(-)
Title: 'Webdriver'/'Selenium' Binary Manager
Description: There are a number of binary files associated with the
'Webdriver'/'Selenium' project (see <http://www.seleniumhq.org/download/>,
<https://sites.google.com/a/chromium.org/chromedriver/>,
<https://github.com/mozilla/geckodriver>,
<http://phantomjs.org/download.html> and
<https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver> for
more information). This package provides functions to download these
binaries and to manage processes involving them.
Author: John Harrison [aut, cre] (R package wdman)
Maintainer: John Harrison <johndharrison0@gmail.com>
Diff between wdman versions 0.2.0 dated 2017-01-18 and 0.2.1 dated 2017-01-20
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 7 +++++++ R/chrome.R | 29 ++++++++++++++++++++++------- R/gecko.R | 29 ++++++++++++++++++++++------- R/iedriver.R | 29 ++++++++++++++++++++++------- R/phantom.R | 29 ++++++++++++++++++++++------- R/selenium.R | 31 ++++++++++++++++++++++++------- R/utils.R | 39 +++++++++++++++++++++++++++++++++++---- README.md | 9 +++++++-- inst/doc/basics.Rmd | 11 ++++++----- inst/doc/basics.html | 13 +++++++------ tests/testthat/test-utils.R | 25 +++++++++++++++++++++---- vignettes/basics.Rmd | 11 ++++++----- 14 files changed, 218 insertions(+), 78 deletions(-)
Title: Easily Install and Load 'Tidyverse' Packages
Description: The 'tidyverse' is a set of packages that work in harmony
because they share common data representations and 'API' design. This
package is designed to make it easy to install and load multiple
'tidyverse' packages in a single step. Learn more about the 'tidyverse'
at <https://github.com/hadley/tidyverse>.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyverse versions 1.0.0 dated 2016-09-09 and 1.1.0 dated 2017-01-20
DESCRIPTION | 14 +++++++------- LICENSE |only MD5 | 32 +++++++++++++++++++------------- NAMESPACE | 16 ++++++++++++++++ NEWS.md |only R/conflicts.R | 5 +++-- R/tidyverse.R |only R/update.R | 7 ++++++- R/utils.R | 16 ++++++++++++++-- R/zzz.R | 4 +++- README.md | 8 +++++++- build/vignette.rds |binary inst/doc/manifesto.Rmd | 8 ++++---- inst/doc/manifesto.html | 12 ++++++------ man/tidyverse-package.Rd |only man/tidyverse_conflicts.Rd | 1 - man/tidyverse_deps.Rd |only man/tidyverse_packages.Rd |only man/tidyverse_update.Rd | 1 - vignettes/manifesto.Rmd | 8 ++++---- 20 files changed, 89 insertions(+), 43 deletions(-)
Title: Text Processing for Small or Big Data Files
Description: Processes big text data files in batches efficiently. For this purpose, it offers functions for splitting, parsing, tokenizing and creating a vocabulary. Moreover, it includes functions for building either a document-term matrix or a term-document matrix and extracting information from those (term-associations, most frequent terms). Lastly, it embodies functions for calculating token statistics (collocations, look-up tables, string dissimilarities) and functions to work with sparse matrices. The source code is based on 'C++11' and exported in R through the 'Rcpp', 'RcppArmadillo' and 'BH' packages.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between textTinyR versions 1.0.1 dated 2017-01-10 and 1.0.2 dated 2017-01-20
DESCRIPTION | 11 - MD5 | 20 +-- NEWS.md | 5 README.md | 129 ++++++++++++++++++-- configure | 2 configure.ac | 2 inst/doc/functionality_of_textTinyR_package.html | 4 src/ngram_stemmer.h | 2 src/sort_2dim_vecs.h | 4 src/tokenization.h | 148 +++++++++++++++++------ tests/testthat/test-utf_locale.R | 8 - 11 files changed, 266 insertions(+), 69 deletions(-)
Title: Tools for Reshaping Text
Description: Tools that can be used to reshape and restructure text
data.
Author: Tyler Rinker [aut, cre],
Joran Elias [ctb],
Matthew Flickinger [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between textshape versions 1.0.0 dated 2017-01-10 and 1.0.1 dated 2017-01-20
DESCRIPTION | 19 +++++++---- MD5 | 82 ++++++++++++++++++++++++------------------------ NAMESPACE | 2 + NEWS | 17 +++++++++ R/change_index.R | 3 + R/combine.R | 10 ++++- R/duration.R | 10 ++++- R/from_to.R | 31 ++++++++++++------ R/set_output.R |only R/split_portion.R | 16 +++++++-- R/split_run.R | 10 ++++- R/split_sentence.R | 10 ++++- R/split_speaker.R | 26 +++++++++++++-- R/split_token.R | 10 ++++- R/split_transcript.R | 13 ++++++- R/split_word.R | 11 +++++- R/textshape-package.R | 2 - R/tidy_colo_dtm.R | 40 +++++++++++++++-------- R/tidy_dtm.R | 44 ++++++++++++++++--------- R/tidy_list.R | 16 +++++++-- R/tidy_table.R | 11 +++++- R/tidy_vector.R | 11 +++++- R/utils.R | 16 +++++++++ README.md | 63 ++++++++++++++++++------------------ inst/CITATION | 4 +- man/change_index.Rd | 4 +- man/combine.Rd | 10 +++++ man/duration.Rd | 10 +++++ man/from_to.Rd | 13 ++++++- man/set_output.Rd |only man/split_portion.Rd | 15 +++++++- man/split_run.Rd | 10 +++++ man/split_sentence.Rd | 10 +++++ man/split_speaker.Rd | 12 ++++++- man/split_token.Rd | 10 +++++ man/split_transcript.Rd | 12 ++++++- man/split_word.Rd | 10 +++++ man/textshape.Rd | 2 - man/tidy_colo_dtm.Rd | 15 +++++++- man/tidy_dtm.Rd | 11 +++++- man/tidy_list.Rd | 12 +++++-- man/tidy_table.Rd | 10 +++++ man/tidy_vector.Rd | 10 +++++ 43 files changed, 482 insertions(+), 171 deletions(-)
Title: Dependence Tests for Two Variables
Description: Provides test statistics, p-value, and confidence intervals based on 9 hypothesis tests for dependence.
Author: Jeffrey C. Miecznikowski, En-shuo Hsu, Yanhua Chen, Albert Vexler
Maintainer: En-shuo Hsu <daviden1013@gmail.com>
Diff between testforDEP versions 0.1.0 dated 2017-01-07 and 0.2.0 dated 2017-01-20
testforDEP-0.1.0/testforDEP/R/hCANOVA.R |only testforDEP-0.1.0/testforDEP/man/CANOVA.Rd |only testforDEP-0.1.0/testforDEP/src/canova.cpp |only testforDEP-0.2.0/testforDEP/DESCRIPTION | 8 ++-- testforDEP-0.2.0/testforDEP/MD5 | 23 +++++-------- testforDEP-0.2.0/testforDEP/R/1testforDEP.R | 14 ++++---- testforDEP-0.2.0/testforDEP/R/KENDALL.R | 2 - testforDEP-0.2.0/testforDEP/R/KPlot.R | 2 - testforDEP-0.2.0/testforDEP/R/PEARSON.R | 2 - testforDEP-0.2.0/testforDEP/R/RcppExports.R | 12 ------- testforDEP-0.2.0/testforDEP/R/SPEARMAN.R | 11 +++++- testforDEP-0.2.0/testforDEP/man/AUK.Rd | 2 - testforDEP-0.2.0/testforDEP/man/testforDEP.Rd | 12 +++---- testforDEP-0.2.0/testforDEP/src/RcppExports.cpp | 41 ------------------------ 14 files changed, 40 insertions(+), 89 deletions(-)
Title: Portable System Utilities
Description: Powerful replacements for base system2 with consistent behavior across
platforms. Supports interruption, background tasks, and full control over
STDOUT / STDERR binary or text streams.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between sys versions 1.0 dated 2017-01-17 and 1.1 dated 2017-01-20
DESCRIPTION | 6 +- LICENSE | 2 MD5 | 9 ++-- NEWS |only src/unix/exec.c | 92 ++++++++++++++++++++++++++++---------------- tests/testthat/test-error.R | 20 +++++---- 6 files changed, 80 insertions(+), 49 deletions(-)
Title: Dynamic String Formatting
Description: Pass named and unnamed character vectors into specified positions
in strings. This represents an attempt to replicate some of python's string
formatting.
Author: Alexander Hoyle
Maintainer: Alexander Hoyle <ahoyle@wesleyan.edu>
Diff between stringformattr versions 0.1.0 dated 2016-12-05 and 0.1.1 dated 2017-01-20
stringformattr-0.1.0/stringformattr/man/contat-two-strings.Rd |only stringformattr-0.1.1/stringformattr/DESCRIPTION | 8 - stringformattr-0.1.1/stringformattr/MD5 | 9 + stringformattr-0.1.1/stringformattr/R/format.R | 46 +++++----- stringformattr-0.1.1/stringformattr/README.md |only stringformattr-0.1.1/stringformattr/man/binary-string-concat.Rd |only stringformattr-0.1.1/stringformattr/man/format-string.Rd | 14 +-- 7 files changed, 43 insertions(+), 34 deletions(-)
More information about stringformattr at CRAN
Permanent link
Title: Importing Data from Loligo Systems Software, Calculating
Metabolic Rates and Critical Tensions
Description: Analysis of oxygen consumption data generated by Loligo (R) Systems respirometry equipment. The package includes a function for loading data output by Loligo's 'AutoResp' software (get.witrox.data()), functions for calculating metabolic rates over user-specified time intervals, extracting critical points from data using broken stick regressions based on Yeager and Ultsch (<DOI:10.1086/physzool.62.4.30157935>), and easy functions for converting between different units of barometric pressure.
Author: Tyler L. Moulton
Maintainer: Tyler L. Moulton <tyler.moulton@mail.mcgill.ca>
Diff between rMR versions 1.0.3 dated 2017-01-06 and 1.0.4 dated 2017-01-20
DESCRIPTION | 10 +++--- MD5 | 14 ++++----- R/rMR.R | 72 +++++++++++++++++++++++++++++++++++-------------- build/partial.rdb |binary man/MR.loops.Rd | 6 +++- man/background.resp.rd | 5 ++- man/get.pcrit.Rd | 18 +++++++----- man/rMR-package.Rd | 6 ++-- 8 files changed, 87 insertions(+), 44 deletions(-)
Title: API for Mixpanel
Description: Provides an interface to many endpoints of Mixpanel's Data Export, Engage and JQL API. The R functions allow for event and profile data export as well as for segmentation, retention, funnel and addiction analysis. Results are always parsed into convenient R objects. Furthermore it is possible to load and update profiles.
Author: Meinhard Ploner [aut, cre, cph],
ProSiebenSat.1 Digital GmbH [cph],
BCG Digital Ventures GmbH [cph]
Maintainer: Meinhard Ploner <meinhard.ploner@gmail.com>
Diff between RMixpanel versions 0.6-0 dated 2017-01-11 and 0.6-1 dated 2017-01-20
DESCRIPTION | 8 +++---- MD5 | 20 +++++++++---------- R/mixpanelGetData.R | 4 ++- R/mixpanelGetEvents.R | 16 +++++++++++---- R/mixpanelGetEventsFromFiles.R | 39 ++++++++++++++++++++++++++------------ R/mixpanelGetFunnel.R | 2 - R/mixpanelGetFunnelList.R | 7 +++--- build/partial.rdb |binary man/mixpanelGetEvents.Rd | 4 ++- man/mixpanelGetEventsFromFiles.Rd | 9 ++++---- man/mixpanelGetFunnelList.Rd | 3 +- 11 files changed, 71 insertions(+), 41 deletions(-)
Title: Solving Ordinary Differential Equations to Understand
Luminescence
Description: A collection of functions to simulate luminescence signals in the
mineral quartz based on published models.
Author: Johannes Friedrich [aut, trl, cre],
Sebastian Kreutzer [aut, ths],
Christoph Schmidt [aut, ths]
Maintainer: Johannes Friedrich <johannes.friedrich@uni-bayreuth.de>
Diff between RLumModel versions 0.1.2 dated 2016-09-02 and 0.2.0 dated 2017-01-20
RLumModel-0.1.2/RLumModel/R/set_ODE.R |only RLumModel-0.1.2/RLumModel/R/set_ODE_LM_OSL.R |only RLumModel-0.2.0/RLumModel/DESCRIPTION | 29 RLumModel-0.2.0/RLumModel/MD5 | 85 +- RLumModel-0.2.0/RLumModel/NAMESPACE | 2 RLumModel-0.2.0/RLumModel/NEWS | 109 ++ RLumModel-0.2.0/RLumModel/R/RLumModel-package.R | 35 RLumModel-0.2.0/RLumModel/R/RcppExports.R |only RLumModel-0.2.0/RLumModel/R/calc_concentrations.R | 13 RLumModel-0.2.0/RLumModel/R/calc_signal.R | 26 RLumModel-0.2.0/RLumModel/R/extract_pars.R |only RLumModel-0.2.0/RLumModel/R/model_LuminescenceSignals.R | 367 +++++++--- RLumModel-0.2.0/RLumModel/R/read_SEQ2R.R | 2 RLumModel-0.2.0/RLumModel/R/set_pars.R | 202 ++--- RLumModel-0.2.0/RLumModel/R/simulate_CW_OSL.R | 22 RLumModel-0.2.0/RLumModel/R/simulate_LM_OSL.R | 21 RLumModel-0.2.0/RLumModel/R/simulate_RF.R | 93 +- RLumModel-0.2.0/RLumModel/R/simulate_RF_and_heating.R |only RLumModel-0.2.0/RLumModel/R/simulate_TL.R | 18 RLumModel-0.2.0/RLumModel/R/simulate_heating.R | 19 RLumModel-0.2.0/RLumModel/R/simulate_illumination.R | 19 RLumModel-0.2.0/RLumModel/R/simulate_irradiation.R | 58 + RLumModel-0.2.0/RLumModel/R/simulate_pause.R | 68 + RLumModel-0.2.0/RLumModel/R/translate_sequence.R | 157 +++- RLumModel-0.2.0/RLumModel/build/vignette.rds |binary RLumModel-0.2.0/RLumModel/data/ExampleData.ModelOutput.RData |binary RLumModel-0.2.0/RLumModel/inst/NEWS.Rd | 101 ++ RLumModel-0.2.0/RLumModel/inst/doc/RLumModel_-_Getting_started_with_RLumModel.pdf |binary RLumModel-0.2.0/RLumModel/inst/doc/RLumModel_-_Using_own_parameter_sets.pdf |only RLumModel-0.2.0/RLumModel/inst/doc/RLumModel_-_Using_own_parameter_sets.pdf.asis |only RLumModel-0.2.0/RLumModel/man/ExampleData.ModelOutput.Rd | 19 RLumModel-0.2.0/RLumModel/man/RLumModel-package.Rd | 14 RLumModel-0.2.0/RLumModel/man/model_LuminescenceSignals.Rd | 288 +++++-- RLumModel-0.2.0/RLumModel/man/read_SEQ2R.Rd | 2 RLumModel-0.2.0/RLumModel/src |only RLumModel-0.2.0/RLumModel/tests/testthat/test-create_DRT.sequence.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-create_SAR.sequence.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-model_LuminescenceSignals.R | 40 - RLumModel-0.2.0/RLumModel/tests/testthat/test-read_SEQ2R.R | 12 RLumModel-0.2.0/RLumModel/tests/testthat/test-set_pars.R | 16 RLumModel-0.2.0/RLumModel/tests/testthat/test-simulate_CW_OSL.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-simulate_LM_OSL.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-simulate_RF.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-simulate_RF_and_heating.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-simulate_TL.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-simulate_heating.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-simulate_illumination.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-simulate_irradiation.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-simulate_pause.R |only RLumModel-0.2.0/RLumModel/tests/testthat/test-translate_sequence.R |only RLumModel-0.2.0/RLumModel/vignettes/RLumModel_-_Getting_started_with_RLumModel.Rmd | 21 RLumModel-0.2.0/RLumModel/vignettes/RLumModel_-_Using_own_parameter_sets.Rmd |only RLumModel-0.2.0/RLumModel/vignettes/RLumModel_-_Using_own_parameter_sets.pdf.asis |only 53 files changed, 1352 insertions(+), 506 deletions(-)
Title: Partially Balanced Incomplete Block Designs
Description: It constructs four series of PBIB designs and also assists in calculating the efficiencies of PBIB Designs with any number of associate classes. This will help the researchers in adopting a PBIB designs and calculating the efficiencies of any PBIB design very quickly and efficiently.
Author: Parneet Kaur <parneet.nonu93@gmail.com>, Kush Sharma <kush.vashishtha@gmail.com>, Davinder Kumar Garg <dkgarg_stat@yahoo.co.in>
Maintainer: Kush Sharma <kush.vashishtha@gmail.com>
Diff between PBIBD versions 1.1 dated 2016-10-14 and 1.2 dated 2017-01-20
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++++++--------- NAMESPACE | 4 ++++ R/series1.R |only R/series2.R |only R/series3.R |only R/series4.R |only build/partial.rdb |binary man/PBIBD-package.Rd | 6 +++++- man/apbibd.Rd | 3 +-- man/apbibd2.Rd | 3 +-- man/apbibd3.Rd | 3 +-- man/apbibd4.Rd | 1 - man/apbibd5.Rd | 3 +-- man/series1.Rd |only man/series2.Rd |only man/series3.Rd |only man/series4.Rd |only 18 files changed, 35 insertions(+), 24 deletions(-)
Title: Forecasting for Stationary and Non-Stationary Time Series
Description: Methods to compute linear h-step ahead prediction coefficients based
on localised and iterated Yule-Walker estimates and empirical mean squared
prediction errors for the resulting predictors. Also, functions to compute
autocovariances for AR(p) processes, to simulate tvARMA(p,q) time series,
and to verify an assumption from Kley et al. (2017),
Preprint arXiv:1611.04460 <http://arxiv.org/abs/1611.04460>.
Author: Tobias Kley [aut, cre],
Philip Preuss [aut],
Piotr Fryzlewicz [aut]
Maintainer: Tobias Kley <t.kley@lse.ac.uk>
Diff between forecastSNSTS versions 1.1-0 dated 2016-11-17 and 1.1-1 dated 2017-01-20
DESCRIPTION | 9 MD5 | 58 ++--- NAMESPACE | 30 +- NEWS | 33 +-- R/RcppExports.R | 180 ++++++++--------- R/acfARp.R | 174 ++++++++--------- R/f.R | 368 ++++++++++++++++++------------------ R/forecastSNSTS-package.R | 114 +++++------ R/models.R | 110 +++++----- R/mspe.R | 374 ++++++++++++++++++------------------- demo/00Index | 2 demo/tvARMA11.R | 218 ++++++++++----------- inst/examples/computeMSPE.R | 60 ++--- inst/examples/mspe.R | 22 +- inst/examples/tvARMA.R | 106 +++++----- man/MSPE.Rd | 124 ++++++------ man/acfARp.Rd | 80 +++---- man/f.Rd | 20 - man/forecastSNSTS-package.Rd | 10 man/plot.MSPE.Rd | 90 ++++---- man/predCoef.Rd | 166 ++++++++-------- man/ts-models-tvARMA.Rd | 80 +++---- src/predCoef.cpp | 2 tests/testthat.R | 8 tests/testthat/test-MSPE.R | 166 ++++++++-------- tests/testthat/test-acfARp.R | 114 +++++------ tests/testthat/test-coefficients.R | 160 +++++++-------- tests/testthat/test-computeMSPE.R | 76 +++---- tests/testthat/test-f.R | 62 +++--- tests/testthat/test-tvARMA.R | 170 ++++++++-------- 30 files changed, 1597 insertions(+), 1589 deletions(-)
Title: Procedures for Ecological Assessment of Surface Waters
Description: Functions for evaluating and visualizing
ecological assessment procedures for surface waters
containing physical, chemical and biological assessments
in the form of value functions.
Author: Nele Schuwirth <nele.schuwirth@eawag.ch> and Peter Reichert <peter.reichert@eawag.ch>
with contributions by Simone Langhans
Maintainer: Nele Schuwirth <nele.schuwirth@eawag.ch>
Diff between ecoval versions 1.0 dated 2014-10-17 and 1.1 dated 2017-01-20
DESCRIPTION | 8 +-- MD5 | 59 ++++++++++++++----------- NAMESPACE | 10 ++++ R/ecoval.plotsymbols.r | 8 +-- R/lake.morphol.2016.r |only R/msk.fish.2004.r | 2 R/val.heavymetals.r | 6 +- data/ecoval.dictionaries.default.RData |binary man/ecoval-package.Rd | 30 +++++++++--- man/ecoval.plotsymbols.Rd | 18 +++++-- man/ecoval.river.create.Rd | 21 ++++++-- man/figures |only man/lake.morphol.2016.aggregate.val.spatial.Rd |only man/lake.morphol.2016.create.Rd |only man/lake.morphol.2016.plot.val.spatial.Rd |only man/lake.morphol.2016.read.attrib.Rd |only man/msk.create.Rd | 25 ++++++++-- man/msk.diatoms.2007.create.Rd | 31 ++++++++++--- man/msk.fish.2004.create.Rd | 30 ++++++++++-- man/msk.hydrol.2011.aggregate.Rd | 31 ++++++++++--- man/msk.hydrol.2011.create.Rd | 31 ++++++++++--- man/msk.invertebrates.2010.create.Rd | 36 +++++++++++---- man/msk.morphol.1998.aggregate.Rd | 36 +++++++++++---- man/msk.morphol.1998.create.Rd | 30 ++++++++++-- man/msk.nutrients.2010.create.Rd | 31 ++++++++++--- man/msk.physapp.2007.create.Rd | 30 ++++++++++-- man/val.heavymetals.create.Rd | 27 ++++++++--- man/val.invertebrates.create.Rd | 41 +++++++++++++---- man/val.micropoll.create.Rd | 48 +++++++++++++++----- man/val.pesticides.create.Rd | 34 +++++++++++--- man/val.spear.create.Rd | 31 ++++++++++--- 31 files changed, 496 insertions(+), 158 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service <http://crunch.io/> provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>
Diff between crunch versions 1.14.2 dated 2016-11-22 and 1.14.4 dated 2017-01-20
crunch-1.14.2/crunch/tests/testthat/api/datasets-4fd71a.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/1/summary-3eeeae.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/1/variables-4fd71a.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/1/variables/birthyr/values-dbf476.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/1/variables/gender/values-6771b2.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/1/variables/hierarchical-4fd71a.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/1/variables/mymrset/subvariables/subvar1/values-6771b2.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/1/variables/mymrset/values-ad350b.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/1/variables/starttime/values-dbf476.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/1/variables/textVar/values-b72581.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/2/summary-3eeeae.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/2/variables-4fd71a.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/2/variables/hierarchical-4fd71a.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/3/summary-3eeeae.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/3/variables-4fd71a.json |only crunch-1.14.2/crunch/tests/testthat/api/datasets/3/variables/hierarchical-4fd71a.json |only crunch-1.14.4/crunch/DESCRIPTION | 10 crunch-1.14.4/crunch/MD5 | 285 ++++----- crunch-1.14.4/crunch/NAMESPACE | 3 crunch-1.14.4/crunch/R/auth.R | 2 crunch-1.14.4/crunch/R/consent.R |only crunch-1.14.4/crunch/R/context-manager.R | 12 crunch-1.14.4/crunch/R/dataset.R | 4 crunch-1.14.4/crunch/R/filters.R | 39 + crunch-1.14.4/crunch/R/fork-and-merge.R | 6 crunch-1.14.4/crunch/R/get-datasets.R | 9 crunch-1.14.4/crunch/R/misc.R | 49 - crunch-1.14.4/crunch/R/new-dataset.R | 2 crunch-1.14.4/crunch/R/projects.R | 59 +- crunch-1.14.4/crunch/R/teams.R | 4 crunch-1.14.4/crunch/R/tuple.R | 4 crunch-1.14.4/crunch/R/variable-delete.R | 19 crunch-1.14.4/crunch/inst/doc/filters.R | 3 crunch-1.14.4/crunch/inst/doc/filters.Rmd | 6 crunch-1.14.4/crunch/inst/doc/filters.html | 5 crunch-1.14.4/crunch/man/consent.Rd | 23 crunch-1.14.4/crunch/man/delete.Rd | 8 crunch-1.14.4/crunch/man/deleteDataset.Rd | 3 crunch-1.14.4/crunch/man/newFilter.Rd |only crunch-1.14.4/crunch/man/newProject.Rd |only crunch-1.14.4/crunch/tests/testthat.R | 3 crunch-1.14.4/crunch/tests/testthat/api/accounts/account1.json | 4 crunch-1.14.4/crunch/tests/testthat/api/accounts/account1/users.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets-d118fa.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets.json | 14 crunch-1.14.4/crunch/tests/testthat/api/datasets/1.json | 32 - crunch-1.14.4/crunch/tests/testthat/api/datasets/1/batches.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/export.json | 6 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/filters |only crunch-1.14.4/crunch/tests/testthat/api/datasets/1/filters.json | 12 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/permissions.json | 6 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/preferences.json | 2 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/savepoints.json | 10 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/settings.json | 4 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/summary-73a614.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/1/table.json | 2 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables-d118fa.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables.json | 34 - crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/birthyr.json | 10 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/birthyr/values-3d4982.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/catarray.json | 16 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/gender.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/gender/values-51980f.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/hierarchical-d118fa.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/hierarchical.json | 14 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/mymrset.json | 18 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/mymrset/subvariables.json | 2 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/mymrset/subvariables/subvar1.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/mymrset/subvariables/subvar1/values-51980f.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/mymrset/subvariables/subvar2.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/mymrset/subvariables/subvar3.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/mymrset/values-22eae5.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/nested-hierarchical.json | 14 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/relative-hierarchical.json | 2 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/starttime.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/starttime/values-3d4982.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/textVar.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/1/variables/textVar/values-641ef3.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/2.json | 16 crunch-1.14.4/crunch/tests/testthat/api/datasets/2/permissions.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/2/summary-73a614.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/2/table.json | 2 crunch-1.14.4/crunch/tests/testthat/api/datasets/2/variables-d118fa.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/2/variables.json | 14 crunch-1.14.4/crunch/tests/testthat/api/datasets/2/variables/hierarchical-d118fa.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/2/variables/mymrset.json | 12 crunch-1.14.4/crunch/tests/testthat/api/datasets/2/variables/mymrset/subvariables.json | 2 crunch-1.14.4/crunch/tests/testthat/api/datasets/2/variables/mymrset/subvariables/subvar2.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/3.json | 22 crunch-1.14.4/crunch/tests/testthat/api/datasets/3/filters.json | 2 crunch-1.14.4/crunch/tests/testthat/api/datasets/3/permissions.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/3/preferences.json | 4 crunch-1.14.4/crunch/tests/testthat/api/datasets/3/summary-73a614.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/3/variables-d118fa.json |only crunch-1.14.4/crunch/tests/testthat/api/datasets/3/variables.json | 6 crunch-1.14.4/crunch/tests/testthat/api/datasets/3/variables/gender.json | 8 crunch-1.14.4/crunch/tests/testthat/api/datasets/3/variables/hierarchical-d118fa.json |only crunch-1.14.4/crunch/tests/testthat/api/progress/1.json | 2 crunch-1.14.4/crunch/tests/testthat/api/progress/2.json | 2 crunch-1.14.4/crunch/tests/testthat/api/progress2/1.json | 2 crunch-1.14.4/crunch/tests/testthat/api/progress2/2.json | 2 crunch-1.14.4/crunch/tests/testthat/api/projects.json | 6 crunch-1.14.4/crunch/tests/testthat/api/projects/project1.json | 6 crunch-1.14.4/crunch/tests/testthat/api/projects/project1/datasets.json | 8 crunch-1.14.4/crunch/tests/testthat/api/projects/project1/datasets/order.json | 4 crunch-1.14.4/crunch/tests/testthat/api/projects/project1/members.json | 6 crunch-1.14.4/crunch/tests/testthat/api/root.json | 22 crunch-1.14.4/crunch/tests/testthat/api/teams.json | 6 crunch-1.14.4/crunch/tests/testthat/api/teams/team1.json | 8 crunch-1.14.4/crunch/tests/testthat/api/teams/team1/members.json | 6 crunch-1.14.4/crunch/tests/testthat/api/users/user1.json | 6 crunch-1.14.4/crunch/tests/testthat/helper-contexts.R | 90 --- crunch-1.14.4/crunch/tests/testthat/helper-expectations.R | 52 - crunch-1.14.4/crunch/tests/testthat/helper.R | 1 crunch-1.14.4/crunch/tests/testthat/test-active-filter.R | 2 crunch-1.14.4/crunch/tests/testthat/test-add-variable-definition.R | 171 +++-- crunch-1.14.4/crunch/tests/testthat/test-api.R | 10 crunch-1.14.4/crunch/tests/testthat/test-append-debug.R | 2 crunch-1.14.4/crunch/tests/testthat/test-appending.R | 4 crunch-1.14.4/crunch/tests/testthat/test-as-data-frame.R | 2 crunch-1.14.4/crunch/tests/testthat/test-batches.R | 12 crunch-1.14.4/crunch/tests/testthat/test-combine-categories.R | 72 +- crunch-1.14.4/crunch/tests/testthat/test-combine-responses.R | 8 crunch-1.14.4/crunch/tests/testthat/test-consent.R |only crunch-1.14.4/crunch/tests/testthat/test-context-manager.R | 8 crunch-1.14.4/crunch/tests/testthat/test-copy-variable.R | 2 crunch-1.14.4/crunch/tests/testthat/test-crunchbox.R | 32 - crunch-1.14.4/crunch/tests/testthat/test-cubes.R | 6 crunch-1.14.4/crunch/tests/testthat/test-dataset-catalog.R | 44 - crunch-1.14.4/crunch/tests/testthat/test-dataset-entity.R | 112 +-- crunch-1.14.4/crunch/tests/testthat/test-dataset-reference.R | 4 crunch-1.14.4/crunch/tests/testthat/test-derive.R | 59 -- crunch-1.14.4/crunch/tests/testthat/test-drop-rows.R | 4 crunch-1.14.4/crunch/tests/testthat/test-export-dataset.R | 14 crunch-1.14.4/crunch/tests/testthat/test-expressions.R | 293 ++++------ crunch-1.14.4/crunch/tests/testthat/test-filters.R | 63 ++ crunch-1.14.4/crunch/tests/testthat/test-fork.R | 34 - crunch-1.14.4/crunch/tests/testthat/test-get-datasets.R | 40 - crunch-1.14.4/crunch/tests/testthat/test-helper.R | 43 - crunch-1.14.4/crunch/tests/testthat/test-hide-variables.R | 62 +- crunch-1.14.4/crunch/tests/testthat/test-join.R | 12 crunch-1.14.4/crunch/tests/testthat/test-make-array.R | 8 crunch-1.14.4/crunch/tests/testthat/test-merge-datasets.R | 36 - crunch-1.14.4/crunch/tests/testthat/test-misc.R | 16 crunch-1.14.4/crunch/tests/testthat/test-new-dataset.R | 20 crunch-1.14.4/crunch/tests/testthat/test-progress.R | 26 crunch-1.14.4/crunch/tests/testthat/test-projects.R | 81 +- crunch-1.14.4/crunch/tests/testthat/test-share.R | 8 crunch-1.14.4/crunch/tests/testthat/test-shoji.R | 23 crunch-1.14.4/crunch/tests/testthat/test-teams.R | 31 - crunch-1.14.4/crunch/tests/testthat/test-update-with-missing.R | 10 crunch-1.14.4/crunch/tests/testthat/test-update.R | 2 crunch-1.14.4/crunch/tests/testthat/test-user.R | 6 crunch-1.14.4/crunch/tests/testthat/test-variable-catalog.R | 32 - crunch-1.14.4/crunch/tests/testthat/test-variable-delete.R | 36 - crunch-1.14.4/crunch/tests/testthat/test-variable-metadata.R | 6 crunch-1.14.4/crunch/tests/testthat/test-variable-type.R | 4 crunch-1.14.4/crunch/tests/testthat/test-variables.R | 8 crunch-1.14.4/crunch/tests/testthat/test-versioning.R | 219 +++---- crunch-1.14.4/crunch/tests/testthat/test-weighting.R | 6 crunch-1.14.4/crunch/tests/testthat/utftesting.R | 21 crunch-1.14.4/crunch/vignettes/filters.Rmd | 6 162 files changed, 1478 insertions(+), 1407 deletions(-)
Title: A Bayesian Semiparametric Factor Analysis Model for Subtype
Identification (Clustering)
Description: Gene expression profiles are commonly utilized to infer disease
subtypes and many clustering methods can be adopted for this task.
However, existing clustering methods may not perform well when
genes are highly correlated and many uninformative genes are included
for clustering. To deal with these challenges, we develop a novel
clustering method in the Bayesian setting. This method, called BCSub,
adopts an innovative semiparametric Bayesian factor analysis model
to reduce the dimension of the data to a few factor scores for
clustering. Specifically, the factor scores are assumed to follow
the Dirichlet process mixture model in order to induce clustering.
Author: Jiehuan Sun [aut, cre], Joshua L. Warren [aut], and Hongyu Zhao [aut]
Maintainer: Jiehuan Sun <jiehuan.sun@yale.edu>
Diff between BCSub versions 0.2 dated 2016-10-29 and 0.3 dated 2017-01-20
DESCRIPTION | 10 ++++++---- MD5 | 8 +++++++- build |only inst |only vignettes |only 5 files changed, 13 insertions(+), 5 deletions(-)