Title: Quick and Dirty Estimates for Wildlife Populations
Description: Provides simple, fast functions for maximum likelihood and Bayesian estimates of wildlife population parameters, suitable for use with simulated data or bootstraps. Early versions were indeed quick and dirty, but optional error-checking routines and meaningful error messages have been added. Includes single and multi-season occupancy, closed capture population estimation, survival, species richness and distance measures.
Author: Mike Meredith
Maintainer: Mike Meredith <mmeredith@wcs.org>
Diff between wiqid versions 0.1.2 dated 2017-09-10 and 0.1.3 dated 2017-11-18
wiqid-0.1.2/wiqid/man/survivaRD.Rd |only wiqid-0.1.3/wiqid/DESCRIPTION | 10 wiqid-0.1.3/wiqid/MD5 | 132 ++++++------- wiqid-0.1.3/wiqid/NEWS | 11 + wiqid-0.1.3/wiqid/R/Bnormal.R | 5 wiqid-0.1.3/wiqid/R/Bnormal_2.R | 4 wiqid-0.1.3/wiqid/R/BoccSS.R | 20 - wiqid-0.1.3/wiqid/R/BoccSS0.R | 8 wiqid-0.1.3/wiqid/R/Bsecr.R | 47 +--- wiqid-0.1.3/wiqid/R/BsurvCJS.R | 3 wiqid-0.1.3/wiqid/R/Bwiqid_methods.R | 5 wiqid-0.1.3/wiqid/R/Misc.R | 50 +++- wiqid-0.1.3/wiqid/R/UnderOverflow.R |only wiqid-0.1.3/wiqid/R/ch2mArray.R | 5 wiqid-0.1.3/wiqid/R/checkPriors.R | 6 wiqid-0.1.3/wiqid/R/closedCapM0.R | 7 wiqid-0.1.3/wiqid/R/closedCapMb.R | 10 wiqid-0.1.3/wiqid/R/closedCapMh2.R | 2 wiqid-0.1.3/wiqid/R/closedCapMt.R | 5 wiqid-0.1.3/wiqid/R/closedCapMtcov.R | 9 wiqid-0.1.3/wiqid/R/justRunJags.R | 4 wiqid-0.1.3/wiqid/R/occ2sps.R | 54 +---- wiqid-0.1.3/wiqid/R/occ2sps0.R | 43 +--- wiqid-0.1.3/wiqid/R/occ2sps_utils.R |only wiqid-0.1.3/wiqid/R/occMS.R | 13 - wiqid-0.1.3/wiqid/R/occMScovSite.R | 8 wiqid-0.1.3/wiqid/R/occMStime.R | 6 wiqid-0.1.3/wiqid/R/occSS.R | 25 +- wiqid-0.1.3/wiqid/R/occSS0.R | 13 - wiqid-0.1.3/wiqid/R/occSScovSite.R | 17 + wiqid-0.1.3/wiqid/R/occSSrn.R | 21 +- wiqid-0.1.3/wiqid/R/occSSrnSite.R | 16 - wiqid-0.1.3/wiqid/R/occSStime.R | 19 + wiqid-0.1.3/wiqid/R/plotPost.R | 3 wiqid-0.1.3/wiqid/R/predict.R | 3 wiqid-0.1.3/wiqid/R/survCJS.R | 4 wiqid-0.1.3/wiqid/R/survCJSaj.R | 9 wiqid-0.1.3/wiqid/R/survRD.R | 7 wiqid-0.1.3/wiqid/R/survRDah.R | 12 - wiqid-0.1.3/wiqid/R/verify.R | 5 wiqid-0.1.3/wiqid/README | 6 wiqid-0.1.3/wiqid/data/GrandSkinks.rda |binary wiqid-0.1.3/wiqid/data/KanhaTigers.rda |binary wiqid-0.1.3/wiqid/data/KillarneyBirds.rda |binary wiqid-0.1.3/wiqid/data/MeadowVoles.rda |binary wiqid-0.1.3/wiqid/data/Temburong.rda |binary wiqid-0.1.3/wiqid/data/dippers.rda |binary wiqid-0.1.3/wiqid/data/railSims.rda |binary wiqid-0.1.3/wiqid/data/salamanders.rda |binary wiqid-0.1.3/wiqid/data/seedbank.rda |binary wiqid-0.1.3/wiqid/data/weta.rda |binary wiqid-0.1.3/wiqid/inst/tests/testthat/test-BoccSS.R | 26 +- wiqid-0.1.3/wiqid/inst/tests/testthat/test-closedCap.R | 2 wiqid-0.1.3/wiqid/inst/tests/testthat/test-occMS.R | 76 +++---- wiqid-0.1.3/wiqid/inst/tests/testthat/test-occSS0.R | 5 wiqid-0.1.3/wiqid/inst/tests/testthat/test-occSSrn.R | 18 - wiqid-0.1.3/wiqid/inst/tests/testthat/test-occSStime.R | 6 wiqid-0.1.3/wiqid/inst/tests/testthat/test-predict_occSS.R | 14 - wiqid-0.1.3/wiqid/man/Bsecr.Rd | 7 wiqid-0.1.3/wiqid/man/closedCaptures.Rd | 8 wiqid-0.1.3/wiqid/man/occ2sps.Rd | 2 wiqid-0.1.3/wiqid/man/plotComb.Rd | 4 wiqid-0.1.3/wiqid/man/print_Bwiqid.Rd | 2 wiqid-0.1.3/wiqid/man/richEstimators.Rd | 2 wiqid-0.1.3/wiqid/man/stdPriors.Rd | 2 wiqid-0.1.3/wiqid/man/survivalCJS.Rd | 6 wiqid-0.1.3/wiqid/man/survivalRD.Rd |only wiqid-0.1.3/wiqid/man/weta.Rd | 2 wiqid-0.1.3/wiqid/man/wiqid-package.Rd | 2 69 files changed, 424 insertions(+), 387 deletions(-)
Title: Manly Mixture Modeling and Model-Based Clustering
Description: The utility of this package includes finite mixture modeling and model-based clustering through Manly mixture models by Zhu and Melnykov (2016) <DOI:10.1016/j.csda.2016.01.015>. It also provides capabilities for forward and backward model selection procedures.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Michael Hutt [ctb, cph] (NM optimization in c),
Stephen Moshier [ctb, cph] (eigen calculations in c),
Rouben Rostamian [ctb, cph] (memory allocation in c)
Maintainer: Xuwen Zhu <xuwen.zhu@louisville.edu>
Diff between ManlyMix versions 0.1.9 dated 2017-09-25 and 0.1.11 dated 2017-11-18
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- NEWS | 8 ++++++++ R/main.R | 4 ++-- R/other.R | 21 +++++++++++++++++++-- demo/VarAssess.R | 11 +++-------- man/Manly.model.Rd | 3 ++- man/Manly.var.Rd | 11 ++++++++--- 9 files changed, 55 insertions(+), 29 deletions(-)
Title: Iterator Based Expression Template Expansion of Standard
Operators
Description: Creates an easy way to use expression templates with R
semantics on any iterator based structure.
Author: Daniel C. Dillon
Maintainer: Daniel C. Dillon <dcdillon@gmail.com>
Diff between RcppHoney versions 0.1.6 dated 2016-12-16 and 0.1.7 dated 2017-11-18
RcppHoney-0.1.6/RcppHoney/inst/include/RcppHoney/scalar.hpp |only RcppHoney-0.1.6/RcppHoney/inst/tools/stripper |only RcppHoney-0.1.7/RcppHoney/DESCRIPTION | 8 RcppHoney-0.1.7/RcppHoney/MD5 | 52 RcppHoney-0.1.7/RcppHoney/R/plugin.R | 2 RcppHoney-0.1.7/RcppHoney/build/vignette.rds |binary RcppHoney-0.1.7/RcppHoney/configure | 2 RcppHoney-0.1.7/RcppHoney/inst/doc/functions.html | 202 +-- RcppHoney-0.1.7/RcppHoney/inst/doc/introduction.html | 28 RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/binary_operator.hpp | 62 RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/bind.hpp | 97 + RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/default_hooks.hpp | 33 RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/functions.hpp | 637 +++++----- RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/functors.hpp | 337 +++-- RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/hook.hpp | 20 RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/na.hpp | 12 RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/operand.hpp | 13 RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/operators.hpp | 430 +++--- RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/scalar_operator.hpp | 10 RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/traits/ctype.hpp | 65 - RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/traits/return_type.hpp |only RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/traits/widest_numeric_type.hpp | 3 RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoney/unary_operator.hpp | 46 RcppHoney-0.1.7/RcppHoney/inst/include/RcppHoneyForward.hpp | 3 RcppHoney-0.1.7/RcppHoney/inst/tools/r-stripper |only RcppHoney-0.1.7/RcppHoney/inst/unitTests/cpp/functions.cpp | 60 RcppHoney-0.1.7/RcppHoney/inst/unitTests/cpp/operators.cpp | 32 RcppHoney-0.1.7/RcppHoney/src/Makevars | 4 RcppHoney-0.1.7/RcppHoney/src/annoyance.c |only 29 files changed, 1313 insertions(+), 845 deletions(-)
Title: Extensible Style-Sheet Language Transformations
Description: An extension for the 'xml2' package to transform XML documents
by applying an 'xslt' style-sheet.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between xslt versions 1.2 dated 2017-09-18 and 1.3 dated 2017-11-18
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 3 +++ src/Makevars.in | 1 - src/Makevars.win | 2 -- src/xslt.cpp | 5 +++-- 6 files changed, 14 insertions(+), 13 deletions(-)
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' <http://xeno-canto.org/>, displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals, 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 1.1.8 dated 2017-04-27 and 1.1.9 dated 2017-11-18
warbleR-1.1.8/warbleR/R/imp.raven.R |only warbleR-1.1.8/warbleR/R/imp.syrinx.R |only warbleR-1.1.8/warbleR/R/rectw.R |only warbleR-1.1.8/warbleR/R/selection.files-data.R |only warbleR-1.1.8/warbleR/R/spectro2.R |only warbleR-1.1.8/warbleR/R/spectroW.R |only warbleR-1.1.8/warbleR/data/selection.files.rda |only warbleR-1.1.8/warbleR/inst/doc/warbleR_workflow.R |only warbleR-1.1.8/warbleR/inst/doc/warbleR_workflow.Rmd |only warbleR-1.1.8/warbleR/inst/doc/warbleR_workflow.html |only warbleR-1.1.8/warbleR/man/imp.raven.Rd |only warbleR-1.1.8/warbleR/man/imp.syrinx.Rd |only warbleR-1.1.8/warbleR/man/selection.files.Rd |only warbleR-1.1.8/warbleR/vignettes/Phae.snr.csv |only warbleR-1.1.8/warbleR/vignettes/Phaethornis-longirostris-154161.wav-139-trackfreqs.jpeg |only warbleR-1.1.8/warbleR/vignettes/warbleR_workflow.Rmd |only warbleR-1.1.8/warbleR/vignettes/workflow2.png |only warbleR-1.1.9/warbleR/DESCRIPTION | 16 warbleR-1.1.9/warbleR/MD5 | 224 +- warbleR-1.1.9/warbleR/NAMESPACE | 12 warbleR-1.1.9/warbleR/NEWS.md | 41 warbleR-1.1.9/warbleR/R/autodetec.R | 118 - warbleR-1.1.9/warbleR/R/boxw.INTFUN.R |only warbleR-1.1.9/warbleR/R/catalog.R | 878 ++++++---- warbleR-1.1.9/warbleR/R/catalog2pdf.R | 44 warbleR-1.1.9/warbleR/R/checksels.R | 93 - warbleR-1.1.9/warbleR/R/checkwavs.R | 22 warbleR-1.1.9/warbleR/R/class.selection.table.R |only warbleR-1.1.9/warbleR/R/color.spectro.R |only warbleR-1.1.9/warbleR/R/compare.methods.R | 48 warbleR-1.1.9/warbleR/R/coor.graph.R | 5 warbleR-1.1.9/warbleR/R/coor.test.R | 6 warbleR-1.1.9/warbleR/R/cut_sels.R |only warbleR-1.1.9/warbleR/R/dfDTW.R | 74 warbleR-1.1.9/warbleR/R/dfts.R | 92 - warbleR-1.1.9/warbleR/R/ffDTW.R | 15 warbleR-1.1.9/warbleR/R/ffts.R | 32 warbleR-1.1.9/warbleR/R/filled.contour.INTFUN.R |only warbleR-1.1.9/warbleR/R/filled.contour.color.INTFUN.R |only warbleR-1.1.9/warbleR/R/filtersels.R | 31 warbleR-1.1.9/warbleR/R/fixwavs.R | 41 warbleR-1.1.9/warbleR/R/frange.R |only warbleR-1.1.9/warbleR/R/frange.detec.R |only warbleR-1.1.9/warbleR/R/frd.INTFUN.R |only warbleR-1.1.9/warbleR/R/frd.plot.INTFUN.R |only warbleR-1.1.9/warbleR/R/is.selection.table.R |only warbleR-1.1.9/warbleR/R/lspec.R | 41 warbleR-1.1.9/warbleR/R/lspec2pdf.R | 26 warbleR-1.1.9/warbleR/R/make.selection.table.R |only warbleR-1.1.9/warbleR/R/manualoc.R | 19 warbleR-1.1.9/warbleR/R/move.imgs.R |only warbleR-1.1.9/warbleR/R/mp32wav.R | 30 warbleR-1.1.9/warbleR/R/ovlp_sels.R |only warbleR-1.1.9/warbleR/R/querxc.R | 29 warbleR-1.1.9/warbleR/R/rectw.INTFUN.R |only warbleR-1.1.9/warbleR/R/selec.table-data.R | 5 warbleR-1.1.9/warbleR/R/seltailor.R | 331 ++- warbleR-1.1.9/warbleR/R/sig2noise.R | 46 warbleR-1.1.9/warbleR/R/snrspecs.R | 20 warbleR-1.1.9/warbleR/R/sp.en.ts.R | 33 warbleR-1.1.9/warbleR/R/specan.R | 116 - warbleR-1.1.9/warbleR/R/specreator.R | 35 warbleR-1.1.9/warbleR/R/spectro.INTFUN.2.R |only warbleR-1.1.9/warbleR/R/spectro.INTFUN.R |only warbleR-1.1.9/warbleR/R/trackfreqs.R | 279 ++- warbleR-1.1.9/warbleR/R/warbleR-package.R | 57 warbleR-1.1.9/warbleR/R/wavdur.R | 14 warbleR-1.1.9/warbleR/R/xcmaps.R | 8 warbleR-1.1.9/warbleR/R/xcorr.R | 30 warbleR-1.1.9/warbleR/R/xcorr.graph.R | 4 warbleR-1.1.9/warbleR/R/zzz.R | 12 warbleR-1.1.9/warbleR/README.md | 50 warbleR-1.1.9/warbleR/build/vignette.rds |binary warbleR-1.1.9/warbleR/data/selec.table.rda |binary warbleR-1.1.9/warbleR/inst/CITATION | 6 warbleR-1.1.9/warbleR/inst/doc/warbleR_workflow_phase1.R |only warbleR-1.1.9/warbleR/inst/doc/warbleR_workflow_phase1.Rmd |only warbleR-1.1.9/warbleR/inst/doc/warbleR_workflow_phase1.html |only warbleR-1.1.9/warbleR/inst/doc/warbleR_workflow_phase2.R |only warbleR-1.1.9/warbleR/inst/doc/warbleR_workflow_phase2.Rmd |only warbleR-1.1.9/warbleR/inst/doc/warbleR_workflow_phase2.html |only warbleR-1.1.9/warbleR/inst/doc/warbleR_workflow_phase3.R |only warbleR-1.1.9/warbleR/inst/doc/warbleR_workflow_phase3.Rmd |only warbleR-1.1.9/warbleR/inst/doc/warbleR_workflow_phase3.html |only warbleR-1.1.9/warbleR/man/autodetec.Rd | 19 warbleR-1.1.9/warbleR/man/catalog.Rd | 71 warbleR-1.1.9/warbleR/man/catalog2pdf.Rd | 12 warbleR-1.1.9/warbleR/man/checksels.Rd | 6 warbleR-1.1.9/warbleR/man/checkwavs.Rd | 4 warbleR-1.1.9/warbleR/man/color.spectro.Rd |only warbleR-1.1.9/warbleR/man/compare.methods.Rd | 10 warbleR-1.1.9/warbleR/man/coor.graph.Rd | 4 warbleR-1.1.9/warbleR/man/coor.test.Rd | 4 warbleR-1.1.9/warbleR/man/cut_sels.Rd |only warbleR-1.1.9/warbleR/man/dfDTW.Rd | 46 warbleR-1.1.9/warbleR/man/dfts.Rd | 45 warbleR-1.1.9/warbleR/man/ffDTW.Rd | 18 warbleR-1.1.9/warbleR/man/ffts.Rd | 17 warbleR-1.1.9/warbleR/man/filtersels.Rd | 5 warbleR-1.1.9/warbleR/man/fixwavs.Rd | 8 warbleR-1.1.9/warbleR/man/frange.Rd |only warbleR-1.1.9/warbleR/man/frange.detec.Rd |only warbleR-1.1.9/warbleR/man/internals.Rd | 31 warbleR-1.1.9/warbleR/man/is.selection.table.Rd |only warbleR-1.1.9/warbleR/man/lspec.Rd | 11 warbleR-1.1.9/warbleR/man/lspec2pdf.Rd | 8 warbleR-1.1.9/warbleR/man/make.selection.table.Rd |only warbleR-1.1.9/warbleR/man/move.imgs.Rd |only warbleR-1.1.9/warbleR/man/mp32wav.Rd | 6 warbleR-1.1.9/warbleR/man/ovlp_sels.Rd |only warbleR-1.1.9/warbleR/man/querxc.Rd | 12 warbleR-1.1.9/warbleR/man/selec.table.Rd | 5 warbleR-1.1.9/warbleR/man/seltailor.Rd | 61 warbleR-1.1.9/warbleR/man/sig2noise.Rd | 11 warbleR-1.1.9/warbleR/man/snrspecs.Rd | 13 warbleR-1.1.9/warbleR/man/sp.en.ts.Rd | 17 warbleR-1.1.9/warbleR/man/specan.Rd | 36 warbleR-1.1.9/warbleR/man/specreator.Rd | 20 warbleR-1.1.9/warbleR/man/trackfreqs.Rd | 75 warbleR-1.1.9/warbleR/man/warbleR.Rd | 54 warbleR-1.1.9/warbleR/man/wavdur.Rd | 2 warbleR-1.1.9/warbleR/man/xcmaps.Rd | 8 warbleR-1.1.9/warbleR/man/xcorr.Rd | 7 warbleR-1.1.9/warbleR/man/xcorr.graph.Rd | 2 warbleR-1.1.9/warbleR/vignettes/154161-autodetec.th10.jpg |binary warbleR-1.1.9/warbleR/vignettes/154161-autodetec.th15.jpg |binary warbleR-1.1.9/warbleR/vignettes/Catalog_p1_labels.jpeg |only warbleR-1.1.9/warbleR/vignettes/Catalog_p1_nolabels.jpeg |only warbleR-1.1.9/warbleR/vignettes/Phae_hisnr.csv |only warbleR-1.1.9/warbleR/vignettes/Phaethornis-longirostris-154070.wav-13_badend.jpeg |only warbleR-1.1.9/warbleR/vignettes/Phaethornis-longirostris-154072-p1.jpg |binary warbleR-1.1.9/warbleR/vignettes/Phaethornis-longirostris-154072.wav-104-trackfreqs.jpeg |only warbleR-1.1.9/warbleR/vignettes/Phaethornis-longirostris-154072.wav-148-dfDTW.jpeg |only warbleR-1.1.9/warbleR/vignettes/Phaethornis-longirostris-154138.wav-33-sp.en.ts.jpeg |only warbleR-1.1.9/warbleR/vignettes/Phaethornis-longirostris-154161.wav-131_badstart.jpeg |only warbleR-1.1.9/warbleR/vignettes/Raven_sels.csv |only warbleR-1.1.9/warbleR/vignettes/Tinamus-major-154191.wav-6-dfDTW.jpeg |only warbleR-1.1.9/warbleR/vignettes/Tinamus-major-154191.wav-6-frange.jpeg |only warbleR-1.1.9/warbleR/vignettes/acoustic_parameters.csv | 55 warbleR-1.1.9/warbleR/vignettes/comp.meth-XCORR-dfDTW-5-12-15-17.jpeg |only warbleR-1.1.9/warbleR/vignettes/manualoc.jpg |binary warbleR-1.1.9/warbleR/vignettes/seltailor_output.csv |only warbleR-1.1.9/warbleR/vignettes/song_types_spectros.jpg |binary warbleR-1.1.9/warbleR/vignettes/warbleR_workflow_phase1.Rmd |only warbleR-1.1.9/warbleR/vignettes/warbleR_workflow_phase2.Rmd |only warbleR-1.1.9/warbleR/vignettes/warbleR_workflow_phase3.Rmd |only warbleR-1.1.9/warbleR/vignettes/xcorr_graph.jpeg |only 147 files changed, 2400 insertions(+), 1286 deletions(-)
Title: Extract Text from Rich Text Format (RTF) Documents
Description: Wraps the 'unrtf' utility to extract text from RTF files. Supports
document conversion to HTML, LaTeX or plain text. Output in HTML is recommended
because 'unrtf' has limited support for converting between character encodings.
Author: Jeroen Ooms [aut, cre],
Free Software Foundation, Inc [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between unrtf versions 1.0 dated 2017-06-10 and 1.1 dated 2017-11-18
DESCRIPTION | 12 +++++------- MD5 | 5 +++-- NEWS |only src/libunrtf/convert.c | 2 +- 4 files changed, 9 insertions(+), 10 deletions(-)
Title: Draw Treemaps in 'ggplot2'
Description: Provides 'ggplot2' geoms for drawing treemaps.
Author: David Wilkins <david@wilkox.org>
Maintainer: David Wilkins <david@wilkox.org>
Diff between treemapify versions 2.3.2 dated 2017-08-28 and 2.4.0 dated 2017-11-18
treemapify-2.3.2/treemapify/NEWS.md |only treemapify-2.4.0/treemapify/DESCRIPTION | 12 treemapify-2.4.0/treemapify/MD5 | 15 treemapify-2.4.0/treemapify/R/treemapify.R | 6 treemapify-2.4.0/treemapify/R/treemapify_fixed.R | 6 treemapify-2.4.0/treemapify/README.md | 92 +- treemapify-2.4.0/treemapify/build/vignette.rds |binary treemapify-2.4.0/treemapify/inst/doc/introduction-to-treemapify.html | 401 +++++++--- treemapify-2.4.0/treemapify/tests/testthat/test_geoms.R | 18 9 files changed, 406 insertions(+), 144 deletions(-)
Title: Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header
Files
Description: Provided within is a high quality and fast PPRNG that is able to be used in an 'OpenMP' parallel
environment compiled under either C++98 or C++11. The objective of this package release is to consolidate
the distribution of the 'sitmo' library on CRAN by enabling others to link to the 'sitmo' header file instead
of including a copy of 'sitmo' within their individual package. Lastly, the package contains example
implementations using 'sitmo' and three accompanying vignette that provide additional information.
Author: James Balamuta [aut, cre, cph],
Thijs van den Berg [aut, cph]
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between sitmo versions 1.2.1 dated 2017-07-30 and 1.2.2 dated 2017-11-18
DESCRIPTION | 10 MD5 | 22 NAMESPACE | 1 NEWS.md | 8 R/inline-plugin.R | 3 build/vignette.rds |binary inst/doc/big_crush_test.html | 7840 +++++++++++++++++------------------ inst/doc/sitmo_internals.Rmd | 4 inst/doc/sitmo_internals.html | 940 ++-- inst/doc/uniform_rng_with_sitmo.html | 464 +- man/sitmo-package.Rd | 2 vignettes/sitmo_internals.Rmd | 4 12 files changed, 4951 insertions(+), 4347 deletions(-)
Title: Statistical Shape Analysis
Description: Routines for the statistical analysis of landmark
shapes, including Procrustes analysis, graphical displays, principal
components analysis, permutation and bootstrap tests, thin-plate
spline transformation grids and comparing covariance matrices.
See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis,
with Applications in R (2nd Edition), John Wiley and Sons.
Author: Ian L. Dryden
Maintainer: Ian Dryden <ian.dryden@nottingham.ac.uk>
Diff between shapes versions 1.2.2 dated 2017-11-03 and 1.2.3 dated 2017-11-18
shapes-1.2.2/shapes/INSTALL |only shapes-1.2.2/shapes/man/PED.Rd |only shapes-1.2.3/shapes/CHANGES |only shapes-1.2.3/shapes/DESCRIPTION | 12 shapes-1.2.3/shapes/MD5 | 9 shapes-1.2.3/shapes/R/shapes.R | 47 ++- shapes-1.2.3/shapes/man/shapes-internal.Rd | 357 ++++++++++++++--------------- 7 files changed, 218 insertions(+), 207 deletions(-)
Title: Ordinal Data Clustering, Co-Clustering and Classification
Description: Ordinal data classification, clustering and co-clustering using model-based approach with the Bos distribution for ordinal data (Christophe Biernacki and Julien Jacques (2016) <doi:10.1007/s11222-015-9585-2>).
Author: Margot Selosse, Julien Jacques, Christophe Biernacki
Maintainer: Margot Selosse <margot.selosse@gmail.com>
Diff between ordinalClust versions 1.1 dated 2017-11-17 and 1.2 dated 2017-11-18
ordinalClust-1.1/ordinalClust/vignettes/figures/BOS.PNG |only ordinalClust-1.1/ordinalClust/vignettes/figures/LBM.png |only ordinalClust-1.1/ordinalClust/vignettes/figures/different-m.png |only ordinalClust-1.2/ordinalClust/DESCRIPTION | 6 ordinalClust-1.2/ordinalClust/MD5 | 24 +- ordinalClust-1.2/ordinalClust/NEWS.md |only ordinalClust-1.2/ordinalClust/R/bosclassif.R | 13 - ordinalClust-1.2/ordinalClust/R/bosclassif.kc.R | 91 ++++------ ordinalClust-1.2/ordinalClust/R/bosclassif.no.kc.R | 51 ++--- ordinalClust-1.2/ordinalClust/R/bosclassifMulti.kc.R | 70 +++---- ordinalClust-1.2/ordinalClust/R/boscoclust.R | 30 --- ordinalClust-1.2/ordinalClust/inst/doc/ordinalClust.R | 8 ordinalClust-1.2/ordinalClust/inst/doc/ordinalClust.Rmd | 16 - ordinalClust-1.2/ordinalClust/inst/doc/ordinalClust.html | 14 - ordinalClust-1.2/ordinalClust/vignettes/ordinalClust.Rmd | 6 15 files changed, 135 insertions(+), 194 deletions(-)
Title: Cytometric Diversity Indices from Gated Data
Description: Uses multidimensional contingency tables to calculate ecological diversity indices for gated populations.
Author: Bruno M.S. Wanderley, Maria Victoria Quiroga, Andre M. Amado, Fernando Unrein
Maintainer: Bruno M.S. Wanderley <brunobiomed.ufrn@gmail.com>
Diff between flowDiv versions 1.0 dated 2015-10-20 and 2.0 dated 2017-11-18
flowDiv-1.0/flowDiv/R/flowDiv.R |only flowDiv-2.0/flowDiv/DESCRIPTION | 20 ++++--- flowDiv-2.0/flowDiv/MD5 | 9 +-- flowDiv-2.0/flowDiv/NAMESPACE | 19 +++++-- flowDiv-2.0/flowDiv/R/flowDiv_internals.R |only flowDiv-2.0/flowDiv/R/flowDiv_main.R |only flowDiv-2.0/flowDiv/man/flowDiv.Rd | 77 +++++++++++------------------- 7 files changed, 60 insertions(+), 65 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of the package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for
better understanding complex patterns behind multiple dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.4.1 dated 2017-07-19 and 0.4.2 dated 2017-11-18
circlize-0.4.1/circlize/inst/doc/circlize.Rnw |only circlize-0.4.1/circlize/inst/doc/circlize.pdf |only circlize-0.4.1/circlize/inst/doc/circular_phylogenetic_tree.R |only circlize-0.4.1/circlize/inst/doc/circular_phylogenetic_tree.Rnw |only circlize-0.4.1/circlize/inst/doc/circular_phylogenetic_tree.pdf |only circlize-0.4.1/circlize/inst/doc/genomic_plot.R |only circlize-0.4.1/circlize/inst/doc/genomic_plot.Rnw |only circlize-0.4.1/circlize/inst/doc/genomic_plot.pdf |only circlize-0.4.1/circlize/inst/doc/interesting_graphics.R |only circlize-0.4.1/circlize/inst/doc/interesting_graphics.Rnw |only circlize-0.4.1/circlize/inst/doc/interesting_graphics.pdf |only circlize-0.4.1/circlize/inst/doc/visualize_relations_by_chord_diagram.R |only circlize-0.4.1/circlize/inst/doc/visualize_relations_by_chord_diagram.Rnw |only circlize-0.4.1/circlize/inst/doc/visualize_relations_by_chord_diagram.pdf |only circlize-0.4.1/circlize/vignettes/circlize.Rnw |only circlize-0.4.1/circlize/vignettes/circular_phylogenetic_tree.Rnw |only circlize-0.4.1/circlize/vignettes/genomic_plot.Rnw |only circlize-0.4.1/circlize/vignettes/interesting_graphics.Rnw |only circlize-0.4.1/circlize/vignettes/visualize_relations_by_chord_diagram.Rnw |only circlize-0.4.2/circlize/DESCRIPTION | 8 - circlize-0.4.2/circlize/MD5 | 53 ++----- circlize-0.4.2/circlize/NAMESPACE | 5 circlize-0.4.2/circlize/NEWS | 12 + circlize-0.4.2/circlize/R/chordDiagram.R | 75 +++++++--- circlize-0.4.2/circlize/R/circos.nested.R | 39 ++++- circlize-0.4.2/circlize/R/genomic.R | 32 +++- circlize-0.4.2/circlize/R/global.R | 9 + circlize-0.4.2/circlize/R/link.R | 7 circlize-0.4.2/circlize/R/plot.R | 36 ++++ circlize-0.4.2/circlize/R/zzz.R | 17 ++ circlize-0.4.2/circlize/build/vignette.rds |binary circlize-0.4.2/circlize/inst/doc/circlize.Rmd |only circlize-0.4.2/circlize/inst/doc/circlize.html |only circlize-0.4.2/circlize/man/chordDiagram.rd | 3 circlize-0.4.2/circlize/man/chordDiagramFromDataFrame.rd | 9 - circlize-0.4.2/circlize/man/chordDiagramFromMatrix.rd | 3 circlize-0.4.2/circlize/man/circos.axis.rd | 3 circlize-0.4.2/circlize/man/fontsize.rd |only circlize-0.4.2/circlize/vignettes/circlize.Rmd |only 39 files changed, 223 insertions(+), 88 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889> and Mohammadi et al. (2017) <doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.42 dated 2017-11-06 and 2.43 dated 2017-11-18
BDgraph-2.42/BDgraph/src/init.c |only BDgraph-2.43/BDgraph/DESCRIPTION | 8 ++-- BDgraph-2.43/BDgraph/MD5 | 48 +++++++++++++-------------- BDgraph-2.43/BDgraph/NAMESPACE | 5 ++ BDgraph-2.43/BDgraph/R/bdgraph.sim.R | 8 ++-- BDgraph-2.43/BDgraph/man/BDgraph-internal.Rd | 2 - BDgraph-2.43/BDgraph/man/BDgraph-package.Rd | 4 +- BDgraph-2.43/BDgraph/man/bdgraph.Rd | 2 + BDgraph-2.43/BDgraph/man/bdgraph.mpl.Rd | 8 ++-- BDgraph-2.43/BDgraph/man/bdgraph.sim.Rd | 4 ++ BDgraph-2.43/BDgraph/man/compare.Rd | 2 + BDgraph-2.43/BDgraph/man/pgraph.Rd | 2 + BDgraph-2.43/BDgraph/man/plinks.Rd | 2 + BDgraph-2.43/BDgraph/man/plot.bdgraph.Rd | 2 + BDgraph-2.43/BDgraph/man/plot.sim.Rd | 2 + BDgraph-2.43/BDgraph/man/plotcoda.Rd | 2 + BDgraph-2.43/BDgraph/man/plotroc.Rd | 2 + BDgraph-2.43/BDgraph/man/print.bdgraph.Rd | 2 + BDgraph-2.43/BDgraph/man/print.sim.Rd | 4 +- BDgraph-2.43/BDgraph/man/select.Rd | 2 + BDgraph-2.43/BDgraph/man/summary.bdgraph.Rd | 2 + BDgraph-2.43/BDgraph/man/traceplot.Rd | 2 + BDgraph-2.43/BDgraph/man/trensfer.Rd | 8 +++- BDgraph-2.43/BDgraph/src/BDgraph_init.c |only BDgraph-2.43/BDgraph/src/Makevars.in | 2 - BDgraph-2.43/BDgraph/src/Makevars.win | 3 + 26 files changed, 85 insertions(+), 43 deletions(-)
Title: Phylogenetic Clustering (Phyloclustering)
Description: Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) provides a
convenient implementation of phyloclustering for DNA and SNP data,
capable of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It is
designed in C for performance, interfaced with R for visualization,
and incorporates other popular open source programs including
ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>,
seq-gen (Rambaut and Grassly 1997)
<doi:10.1093/bioinformatics/13.3.235>,
Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and
PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>,
<doi:10.1093/molbev/msm088>,
for simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.
Author: Wei-Chen Chen [aut, cre],
Karin Dorman [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between phyclust versions 0.1-20 dated 2017-08-26 and 0.1-21 dated 2017-11-18
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/phyclust/phyclust_optim_nmmin.c | 2 +- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre],
Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>),
Artifex Software, Inc. [ctb, cph] (pdf_info.ps taken from GPL
Ghostscript)
Maintainer: Ingo Feinerer <feinerer@logic.at>
Diff between tm versions 0.7-1 dated 2017-03-02 and 0.7-2 dated 2017-11-18
tm-0.7-1/tm/man/readTabular.Rd |only tm-0.7-2/tm/DESCRIPTION | 23 ++--- tm-0.7-2/tm/MD5 | 110 ++++++++++++++------------ tm-0.7-2/tm/NAMESPACE | 13 ++- tm-0.7-2/tm/R/RcppExports.R | 6 + tm-0.7-2/tm/R/corpus.R | 58 +++++++++++--- tm-0.7-2/tm/R/doc.R | 4 tm-0.7-2/tm/R/matrix.R | 17 ++-- tm-0.7-2/tm/R/meta.R | 2 tm-0.7-2/tm/R/reader.R | 143 +++++++++++++++++++---------------- tm-0.7-2/tm/R/source.R | 26 ++++-- tm-0.7-2/tm/R/tokenizer.R | 9 +- tm-0.7-2/tm/R/transform.R | 48 ++++++++--- tm-0.7-2/tm/R/utils.R | 18 ---- tm-0.7-2/tm/build/vignette.rds |binary tm-0.7-2/tm/data/acq.rda |binary tm-0.7-2/tm/data/crude.rda |binary tm-0.7-2/tm/inst/NEWS.Rd | 33 ++++++++ tm-0.7-2/tm/inst/doc/extensions.R | 52 ++++-------- tm-0.7-2/tm/inst/doc/extensions.Rnw | 107 +++++++++----------------- tm-0.7-2/tm/inst/doc/extensions.pdf |binary tm-0.7-2/tm/inst/doc/tm.R | 4 tm-0.7-2/tm/inst/doc/tm.Rnw | 4 tm-0.7-2/tm/inst/doc/tm.pdf |binary tm-0.7-2/tm/man/DataframeSource.Rd | 22 ++++- tm-0.7-2/tm/man/PCorpus.Rd | 4 tm-0.7-2/tm/man/Reader.Rd | 2 tm-0.7-2/tm/man/SimpleCorpus.Rd | 6 - tm-0.7-2/tm/man/Source.Rd | 9 +- tm-0.7-2/tm/man/VCorpus.Rd | 7 - tm-0.7-2/tm/man/XMLSource.Rd | 28 +----- tm-0.7-2/tm/man/XMLTextDocument.Rd | 10 +- tm-0.7-2/tm/man/ZipSource.Rd | 6 - tm-0.7-2/tm/man/foreign.Rd | 2 tm-0.7-2/tm/man/getTokenizers.Rd | 3 tm-0.7-2/tm/man/matrix.Rd | 24 ++--- tm-0.7-2/tm/man/readDOC.Rd | 20 +++- tm-0.7-2/tm/man/readDataframe.Rd |only tm-0.7-2/tm/man/readPDF.Rd | 20 ++-- tm-0.7-2/tm/man/readRCV1.Rd | 5 - tm-0.7-2/tm/man/readTagged.Rd | 10 +- tm-0.7-2/tm/man/readXML.Rd | 31 +------ tm-0.7-2/tm/man/removeNumbers.Rd | 19 +++- tm-0.7-2/tm/man/removePunctuation.Rd | 33 ++++++-- tm-0.7-2/tm/man/stemCompletion.Rd | 4 tm-0.7-2/tm/man/stopwords.Rd | 4 tm-0.7-2/tm/man/termFreq.Rd | 73 +++++++++-------- tm-0.7-2/tm/man/tokenizer.Rd | 12 ++ tm-0.7-2/tm/src/RcppExports.cpp | 13 ++- tm-0.7-2/tm/src/copy.c | 2 tm-0.7-2/tm/src/init.c | 14 ++- tm-0.7-2/tm/src/remove.c |only tm-0.7-2/tm/src/scan.c |only tm-0.7-2/tm/src/tdm.cpp | 5 + tm-0.7-2/tm/src/tokenizer.cpp |only tm-0.7-2/tm/tests |only tm-0.7-2/tm/vignettes/extensions.Rnw | 107 +++++++++----------------- tm-0.7-2/tm/vignettes/tm.Rnw | 4 58 files changed, 645 insertions(+), 531 deletions(-)
Title: Next-Generation Sequencing (NGS) Data Analysis Toolkit
Description: Can be used to facilitate the analysis of NGS data, such as visualization, conversion of data format for WEB service input and other purpose.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between ngstk versions 0.1.0 dated 2017-10-11 and 0.1.1 dated 2017-11-18
ngstk-0.1.0/ngstk/inst/extdata/tools/QualityConfirm/result/depth/APL2.bam.depth |only ngstk-0.1.0/ngstk/inst/extdata/tools/QualityConfirm/result/fig/APL1.bam.countFig.ABCA7.pdf |only ngstk-0.1.0/ngstk/inst/extdata/tools/QualityConfirm/result/fig/APL1.bam.countFig.ARID1A.pdf |only ngstk-0.1.0/ngstk/inst/extdata/tools/QualityConfirm/result/fig/APL1.bam.countFig.ARID1B.pdf |only ngstk-0.1.0/ngstk/inst/extdata/tools/QualityConfirm/result/fig/APL1.bam.countFig.ASXL1.pdf |only ngstk-0.1.0/ngstk/inst/extdata/tools/QualityConfirm/result/fig/APL1.bam.countFig.CEBPA.pdf |only ngstk-0.1.0/ngstk/inst/extdata/tools/QualityConfirm/result/fig/APL1.bam.countFig.DNMT3A.pdf |only ngstk-0.1.0/ngstk/inst/extdata/tools/QualityConfirm/result/fig/APL1.bam.countFig.ETV6.pdf |only ngstk-0.1.0/ngstk/inst/extdata/tools/QualityConfirm/result/fig/APL1.bam.countFig.EZH2.pdf |only ngstk-0.1.0/ngstk/inst/extdata/tools/QualityConfirm/result/fig/APL1.bam.countFig.FANCA.pdf |only 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ngstk-0.1.1/ngstk/README.md | 43 ++- ngstk-0.1.1/ngstk/build |only ngstk-0.1.1/ngstk/inst/doc |only ngstk-0.1.1/ngstk/inst/extdata/config/theme.toml | 5 ngstk-0.1.1/ngstk/inst/extdata/tools/QualityConfirm/README.md | 64 +++++ ngstk-0.1.1/ngstk/inst/extdata/tools/gvmap |only ngstk-0.1.1/ngstk/man/fusions2pp_meta.Rd | 2 ngstk-0.1.1/ngstk/man/get_files_ctime.Rd |only ngstk-0.1.1/ngstk/man/get_files_mtime.Rd |only ngstk-0.1.1/ngstk/man/merge_table_files.Rd |only ngstk-0.1.1/ngstk/man/set_colors.Rd | 2 ngstk-0.1.1/ngstk/man/set_tools.Rd | 2 ngstk-0.1.1/ngstk/tests/testthat/test_g_file.R |only ngstk-0.1.1/ngstk/tests/testthat/test_h_log.R |only ngstk-0.1.1/ngstk/vignettes |only 83 files changed, 309 insertions(+), 210 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling based on 'Boost' and 'Eigen'. The 'rvinecopulib'
package implements the core features of the popular 'VineCopula' package, in
particular inference algorithms for both vine copula and bivariate copula
models. Advantages over 'VineCopula' are a sleeker and more modern API,
improved performances, especially in high dimensions, nonparametric and
multi-parameter families. The 'rvinecopulib' package includes 'vinecopulib' as
header-only C++ library (currently version 0.2.3). Thus
users do not need to install 'vinecopulib' itself in order to use
'rvinecopulib'. Since their initial releases, 'vinecopulib' is licensed under
the MIT License, and 'rvinecopulib' is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.2.0.1.0 dated 2017-10-30 and 0.2.3.1.0 dated 2017-11-18
DESCRIPTION | 8 MD5 | 107 ++++--- NEWS.md | 47 +++ R/bicop_methods.R | 11 R/family_sets.R | 6 R/rvinecopulib.R | 6 R/tools.R | 1 R/vinecop_methods.R | 4 README.md | 8 inst/include/version.hpp | 4 inst/include/vinecopulib/bicop/archimedean.hpp | 4 inst/include/vinecopulib/bicop/bb1.hpp | 3 inst/include/vinecopulib/bicop/bb6.hpp | 3 inst/include/vinecopulib/bicop/bb7.hpp | 3 inst/include/vinecopulib/bicop/bb8.hpp | 3 inst/include/vinecopulib/bicop/clayton.hpp | 3 inst/include/vinecopulib/bicop/frank.hpp | 3 inst/include/vinecopulib/bicop/gumbel.hpp | 3 inst/include/vinecopulib/bicop/implementation/abstract.ipp | 2 inst/include/vinecopulib/bicop/implementation/archimedean.ipp | 38 +- inst/include/vinecopulib/bicop/implementation/bb1.ipp | 44 +++ inst/include/vinecopulib/bicop/implementation/bb6.ipp | 61 ++++ inst/include/vinecopulib/bicop/implementation/bb7.ipp | 46 +++ inst/include/vinecopulib/bicop/implementation/bb8.ipp | 43 +++ inst/include/vinecopulib/bicop/implementation/class.ipp | 95 +++---- inst/include/vinecopulib/bicop/implementation/clayton.ipp | 20 + inst/include/vinecopulib/bicop/implementation/family.ipp | 4 inst/include/vinecopulib/bicop/implementation/fit_controls.ipp | 10 inst/include/vinecopulib/bicop/implementation/frank.ipp | 42 ++- inst/include/vinecopulib/bicop/implementation/gumbel.ipp | 23 + inst/include/vinecopulib/bicop/implementation/joe.ipp | 27 +- inst/include/vinecopulib/bicop/implementation/kernel.ipp | 4 inst/include/vinecopulib/bicop/implementation/parametric.ipp | 4 inst/include/vinecopulib/bicop/implementation/student.ipp | 8 inst/include/vinecopulib/bicop/implementation/tll.ipp | 6 inst/include/vinecopulib/bicop/joe.hpp | 3 inst/include/vinecopulib/misc/implementation/tools_eigen.ipp | 4 inst/include/vinecopulib/misc/implementation/tools_interpolation.ipp | 12 inst/include/vinecopulib/misc/implementation/tools_optimization.ipp | 19 - inst/include/vinecopulib/misc/implementation/tools_stats.ipp | 74 ++--- inst/include/vinecopulib/misc/tools_bobyqa.hpp | 32 +- inst/include/vinecopulib/misc/tools_eigen.hpp | 8 inst/include/vinecopulib/misc/tools_interface.hpp | 23 - inst/include/vinecopulib/misc/tools_parallel.hpp | 135 +--------- inst/include/vinecopulib/misc/tools_serialization.hpp | 6 inst/include/vinecopulib/misc/tools_stats.hpp | 20 - inst/include/vinecopulib/misc/tools_stl.hpp | 4 inst/include/vinecopulib/misc/tools_thread.hpp |only inst/include/vinecopulib/vinecop/implementation/class.ipp | 9 inst/include/vinecopulib/vinecop/implementation/rvine_matrix.ipp | 21 + inst/include/vinecopulib/vinecop/implementation/tools_select.ipp | 123 ++++----- inst/include/vinecopulib/vinecop/rvine_matrix.hpp | 3 inst/include/vinecopulib/vinecop/tools_select.hpp | 2 man/rvinecopulib.Rd | 6 tests/testthat/Rplots.pdf |binary 55 files changed, 732 insertions(+), 476 deletions(-)
Title: Analytic Hierarchy Process (AHP)
Description: Given the scores from decision makers, the analytic hierarchy process can be conducted easily.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between easyAHP versions 0.1.0 dated 2017-07-29 and 0.1.1 dated 2017-11-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- man/easyAHP.Rd | 8 +++++--- 3 files changed, 10 insertions(+), 8 deletions(-)
Title: Hierarchical Multiple Imputation
Description: Runs single level and multilevel imputation models. The user just has to pass the data to the main function and, optionally, his analysis model. Basically the package then translates this analysis model into commands to impute the data according to it with functions from 'mice', 'MCMCglmm' or routines build for this package.
Author: Matthias Speidel [aut, cre] (Institute for Employment Research,
Nuremberg, Germany),
Joerg Drechsler [aut] (Institute for Employment Research, Nuremberg,
Germany),
Shahab Jolani [aut] (Maastricht University, Maastricht, The
Netherlands)
Maintainer: Matthias Speidel <matthias.speidel@googlemail.com>
Diff between hmi versions 0.7.8 dated 2017-09-15 and 0.8.1 dated 2017-11-18
hmi-0.7.8/hmi/R/hmi_imp_binary_multi_2017-04-11.R |only hmi-0.7.8/hmi/R/hmi_imp_cat_multi_2017-07-31.R |only hmi-0.7.8/hmi/R/hmi_imp_catordered_multi_2017-08-10.R |only hmi-0.7.8/hmi/R/hmi_imp_cont_multi_2017-09-03.R |only hmi-0.7.8/hmi/R/hmi_imp_count_multi_2017-04-11.R |only hmi-0.7.8/hmi/R/hmi_imp_count_single_2017-04-11.R |only hmi-0.7.8/hmi/R/hmi_imp_interval_2017-08-31.R |only hmi-0.7.8/hmi/R/hmi_imp_roundedcont_2017-09-01.R |only hmi-0.7.8/hmi/R/hmi_imp_semicont_multi_2017-04-11.R |only hmi-0.7.8/hmi/R/hmi_smallfunctions_2017-09-14.R |only hmi-0.7.8/hmi/R/hmi_wrapper_2017-08-24.R |only hmi-0.7.8/hmi/man/remove_excessives.Rd |only hmi-0.7.8/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-11_29e35746e06bd6b850b6c27e2d56c1d0.RData |only hmi-0.7.8/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-11_29e35746e06bd6b850b6c27e2d56c1d0.rdb |only hmi-0.7.8/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-11_29e35746e06bd6b850b6c27e2d56c1d0.rdx |only hmi-0.7.8/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-14_8570dc1fe667939edcf39cb5bd0479d6.RData |only hmi-0.7.8/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-14_8570dc1fe667939edcf39cb5bd0479d6.rdb |only hmi-0.7.8/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-14_8570dc1fe667939edcf39cb5bd0479d6.rdx |only hmi-0.7.8/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-3_fdb06bd954d64ca8444cfbd148f4ad51.RData |only hmi-0.7.8/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-3_fdb06bd954d64ca8444cfbd148f4ad51.rdb |only hmi-0.7.8/hmi/vignettes/my-vignette_cache/html/unnamed-chunk-3_fdb06bd954d64ca8444cfbd148f4ad51.rdx |only hmi-0.8.1/hmi/DESCRIPTION | 9 hmi-0.8.1/hmi/MD5 | 196 +++++----- hmi-0.8.1/hmi/NAMESPACE | 5 hmi-0.8.1/hmi/R/Gcsemv.R |only hmi-0.8.1/hmi/R/hmi_imp_binary_multi_2017-10-12.R |only hmi-0.8.1/hmi/R/hmi_imp_binary_single_2017-04-11.R | 3 hmi-0.8.1/hmi/R/hmi_imp_cat_multi_2017-11-17.R |only hmi-0.8.1/hmi/R/hmi_imp_cat_single_2017-04-13.R | 4 hmi-0.8.1/hmi/R/hmi_imp_catordered_multi_2017-11-13.R |only hmi-0.8.1/hmi/R/hmi_imp_catordered_single_2017-08-02.R | 4 hmi-0.8.1/hmi/R/hmi_imp_cont_multi_2017-10-25.R |only hmi-0.8.1/hmi/R/hmi_imp_cont_single_2017-04-11.R | 4 hmi-0.8.1/hmi/R/hmi_imp_count_multi_2017-10-12.R |only hmi-0.8.1/hmi/R/hmi_imp_count_single_2017-10-12.R |only hmi-0.8.1/hmi/R/hmi_imp_interval_2017-10-17.R |only hmi-0.8.1/hmi/R/hmi_imp_roundedcont_2017-10-18.R |only hmi-0.8.1/hmi/R/hmi_imp_semicont_multi_2017-10-12.R |only hmi-0.8.1/hmi/R/hmi_imp_semicont_single_2017-04-11.R | 4 hmi-0.8.1/hmi/R/hmi_smallfunctions_2017-11-14.R |only hmi-0.8.1/hmi/R/hmi_wrapper_2017-10-12.R |only hmi-0.8.1/hmi/build/vignette.rds |binary hmi-0.8.1/hmi/data |only hmi-0.8.1/hmi/inst/doc/my-vignette.R | 8 hmi-0.8.1/hmi/inst/doc/my-vignette.Rmd | 8 hmi-0.8.1/hmi/inst/doc/my-vignette.html | 12 hmi-0.8.1/hmi/man/Gcsemv.Rd |only hmi-0.8.1/hmi/man/as.data.frame.interval.Rd | 2 hmi-0.8.1/hmi/man/as.interval.Rd | 6 hmi-0.8.1/hmi/man/center.interval.Rd | 2 hmi-0.8.1/hmi/man/chaincheck.Rd |only hmi-0.8.1/hmi/man/cleanup.Rd |only hmi-0.8.1/hmi/man/components.Rd | 2 hmi-0.8.1/hmi/man/contributions4intervals.Rd | 2 hmi-0.8.1/hmi/man/decompose_interval.Rd | 4 hmi-0.8.1/hmi/man/doubleintegral.Rd | 2 hmi-0.8.1/hmi/man/extract_varnames.Rd | 2 hmi-0.8.1/hmi/man/fixed_intercept_check.Rd | 6 hmi-0.8.1/hmi/man/generate_interval.Rd | 2 hmi-0.8.1/hmi/man/get_type.Rd | 2 hmi-0.8.1/hmi/man/hmi.Rd | 37 + hmi-0.8.1/hmi/man/hmi_pool.Rd | 2 hmi-0.8.1/hmi/man/idf2interval.Rd | 2 hmi-0.8.1/hmi/man/imp_binary_multi.Rd | 18 hmi-0.8.1/hmi/man/imp_cat_multi.Rd | 18 hmi-0.8.1/hmi/man/imp_cont_multi.Rd | 18 hmi-0.8.1/hmi/man/imp_count_multi.Rd | 18 hmi-0.8.1/hmi/man/imp_count_single.Rd | 17 hmi-0.8.1/hmi/man/imp_interval.Rd | 2 hmi-0.8.1/hmi/man/imp_orderedcat_multi.Rd | 18 hmi-0.8.1/hmi/man/imp_roundedcont.Rd | 2 hmi-0.8.1/hmi/man/imp_semicont_multi.Rd | 20 - 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Title: Estimation, Gene Selection, and Survival Prediction Based on the
Compound Covariate Method Under the Cox Model
Description: Estimation, gene selection, and survival prediction based on the compound covariate method under the Cox model with high-dimensional gene expressions.
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627> and
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>. Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.5 dated 2017-11-02 and 3.6 dated 2017-11-18
DESCRIPTION | 11 +++++------ MD5 | 8 ++++---- R/uni.selection.R | 31 ++++++++++++++++++------------- man/compound.Cox-package.Rd | 4 ++-- man/uni.selection.Rd | 7 ++++++- 5 files changed, 35 insertions(+), 26 deletions(-)
Title: A Solver for 'ompr' that Uses the R Optimization Infrastructure
('ROI')
Description: A solver for 'ompr' based on the R Optimization Infrastructure ('ROI').
The package makes all solvers in 'ROI' available to solve 'ompr' models. Please see the
'ompr' website <https://dirkschumacher.github.io/ompr> and package docs for more information
and examples on how to use it.
Author: Dirk Schumacher [aut, cre]
Maintainer: Dirk Schumacher <mail@dirk-schumacher.net>
Diff between ompr.roi versions 0.6.1 dated 2017-10-23 and 0.7.0 dated 2017-11-18
DESCRIPTION | 10 ++--- MD5 | 12 ++++-- NAMESPACE | 2 + NEWS.md | 11 ++++++ R/as-roi-model.R |only R/with-roi.R | 68 --------------------------------------- man/as_ROI_model.Rd |only tests/testthat/test-solver-roi.R | 21 ++++++++++++ 8 files changed, 47 insertions(+), 77 deletions(-)
Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh
(2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller
(2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al.
(2008, <doi:10.1214/07-AOS517>); Jiang et al.
(2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre],
Samuel Mueller [aut],
Alan H Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>
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Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Text mining for word processing and sentiment analysis using
'dplyr', 'ggplot2', and other tidy tools.
Author: Gabriela De Queiroz [ctb],
Oliver Keyes [ctb],
David Robinson [aut],
Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>
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Title: Rapid Implementation of Machine Learning Algorithms for Genomic
Data
Description: Supervised machine learning has an increasingly important role in data
analysis. This package introduces a framework for rapidly implementing supervised
machine learning in a high-throughput manner. This package provides a user-friendly
interface that empowers investigators to execute state-of-the-art binary and
multi-class classification, including deep learning, with minimal programming
experience necessary.
Author: Thomas Quinn [aut, cre],
Daniel Tylee [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
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