Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear models
(see, Piironen, Paasiniemi and Vehtari, 2018, <arXiv:1810.02406>).
The package is compatible with the 'rstanarm' and 'brms' packages, but other
reference models can also be used. See the package vignette for more
information and examples.
Author: Juho Piironen [cre, aut],
Markus Paasiniemi [aut],
Aki Vehtari [aut],
Jonah Gabry [ctb],
Paul-Christian Bürkner [ctb],
Marco Colombo [ctb]
Maintainer: Juho Piironen <juho.t.piironen@gmail.com>
Diff between projpred versions 1.1.2 dated 2019-05-31 and 1.1.4 dated 2019-10-02
projpred-1.1.2/projpred/tests/testthat/test_init_refmodel.R |only projpred-1.1.4/projpred/DESCRIPTION | 20 projpred-1.1.4/projpred/MD5 | 74 - projpred-1.1.4/projpred/NAMESPACE | 2 projpred-1.1.4/projpred/NEWS.md | 8 projpred-1.1.4/projpred/R/cv_varsel.R | 43 projpred-1.1.4/projpred/R/glmfun.R | 2 projpred-1.1.4/projpred/R/methods.R | 133 +- projpred-1.1.4/projpred/R/misc.R | 94 + projpred-1.1.4/projpred/R/project.R | 25 projpred-1.1.4/projpred/R/refmodel.R | 39 projpred-1.1.4/projpred/R/summary_funs.R | 28 projpred-1.1.4/projpred/R/varsel.R | 5 projpred-1.1.4/projpred/build/vignette.rds |binary projpred-1.1.4/projpred/data/df_binom.rda |binary projpred-1.1.4/projpred/data/df_gaussian.rda |binary projpred-1.1.4/projpred/inst/doc/quickstart.html | 544 ++++++---- projpred-1.1.4/projpred/man/cv-indices.Rd | 4 projpred-1.1.4/projpred/man/predict.refmodel.Rd | 2 projpred-1.1.4/projpred/man/print-vsel.Rd |only projpred-1.1.4/projpred/man/projpred.Rd | 2 projpred-1.1.4/projpred/man/varsel-statistics.Rd | 4 projpred-1.1.4/projpred/tests/testthat/test_cvindices.R |only projpred-1.1.4/projpred/tests/testthat/test_datafit.R | 10 projpred-1.1.4/projpred/tests/testthat/test_proj_pred.R | 114 +- projpred-1.1.4/projpred/tests/testthat/test_project.R | 138 +- projpred-1.1.4/projpred/tests/testthat/test_refmodel.R |only projpred-1.1.4/projpred/tests/testthat/test_varsel.R | 358 ++++-- projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-10-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-11-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-13-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-14-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-18-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-21-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-22-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-26-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-27-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-28-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-6-1.png |binary projpred-1.1.4/projpred/vignettes/quickstart_files/figure-html/unnamed-chunk-9-1.png |binary 40 files changed, 1105 insertions(+), 544 deletions(-)
Title: Simulates SPSO and Efftox Phase 12 Trials with Correlated
Outcomes
Description: Simulating and conducting four phase 12 clinical trials with correlated binary bivariate outcomes described. Uses the 'Efftox' (efficacy and toxicity tradeoff, <https://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware/Index/2>) and SPSO (Semi-Parametric Stochastic Ordering) models with Utility and Desirability based objective functions for dose finding.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <achapp@lsuhsc.edu>
Diff between Phase12Compare versions 1.2 dated 2019-09-23 and 1.3 dated 2019-10-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/SPSOCODE.cpp | 3 ++- 3 files changed, 7 insertions(+), 6 deletions(-)
More information about Phase12Compare at CRAN
Permanent link
Title: Helps Grade Assignment Submissions that are R Scripts
Description: After being given the location of your students' submissions and a test file, the function runs each .R file, and evaluates the results from all the given tests. Results are neatly returned in a data frame that has a row for each student, and a column for each test.
Author: Taylor Brown [aut, cre]
Maintainer: Taylor Brown <trb5me@virginia.edu>
Diff between gradeR versions 1.0.2 dated 2019-10-01 and 1.0.3 dated 2019-10-02
DESCRIPTION | 6 - MD5 | 24 ++++-- NEWS.md | 6 + README.md | 55 +++++++-------- inst/doc/gradeR.R | 3 inst/doc/gradeR.Rmd | 176 +++++++++++++++++++++++++++++++++++++++++++++++++++ inst/doc/gradeR.html | 133 ++++++++++++++++++++++++++++++++++++++ vignettes/example |only vignettes/gradeR.Rmd | 176 +++++++++++++++++++++++++++++++++++++++++++++++++++ 9 files changed, 541 insertions(+), 38 deletions(-)
Title: CamelUp Board Game as a Teaching Aid for Introductory Statistics
Description: Implements the board game CamelUp for use in introductory statistics classes using a Shiny app.
Author: Michael Czekanski [aut, cre],
Alex Lyford [aut],
Tom Rahr [aut],
Tina Chen [aut]
Maintainer: Michael Czekanski <middleburystatspackages@gmail.com>
Diff between CamelUp versions 0.1.0 dated 2019-09-27 and 0.1.1 dated 2019-10-02
DESCRIPTION | 9 +-- MD5 | 9 ++- NAMESPACE | 1 NEWS.md |only R/Game_Implementation.R | 109 +++++++++++++++++++++++++++++++++--------------- R/app.R | 10 +++- 6 files changed, 92 insertions(+), 46 deletions(-)
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Functions introduced or changed since R v3.0.0 are re-implemented in this
package. The backports are conditionally exported in order to let R resolve
the function name to either the implemented backport, or the respective base
version, if available. Package developers can make use of new functions or
arguments by selectively importing specific backports to
support older installations.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
R Core Team [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.1.4 dated 2019-04-10 and 1.1.5 dated 2019-10-02
DESCRIPTION | 8 ++++---- MD5 | 11 +++++++---- NAMESPACE | 1 + NEWS.md | 4 ++++ R/isTRUE.R |only man/isTRUE.Rd |only tests/test_isFALSE.R | 2 +- tests/test_isTRUE.R |only 8 files changed, 17 insertions(+), 9 deletions(-)
Title: 'R' 'Markdown' Themes for 'UIUC' Documents and Presentations
Description: A set of custom 'R' 'Markdown' templates for documents and
presentations with the University of Illinois at Urbana-Champaign (UIUC)
color scheme and identity standards.
Author: James Balamuta [aut, cre] (<https://orcid.org/0000-0003-2826-8458>),
Steven Andrew Culpepper [ctb] (Provided the Minimal Orange Beamer
Theme),
David Dalpiaz [ctb] (Collaborated on the LaTeX Journal Theme),
Jose Luis Rodriguez [ctb] (Provided the Market Information Lab (MIL)
Beamer Theme)
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between uiucthemes versions 0.2.1 dated 2018-10-05 and 0.3.0 dated 2019-10-02
DESCRIPTION | 16 +-- MD5 | 45 +++++++--- NAMESPACE | 2 NEWS.md | 26 +++++- R/beamer_templates.R | 119 +++++++++++++++++++++++++--- R/html_templates.R |only README.md | 21 ++-- build/vignette.rds |binary inst/AUTHORS |only inst/COPYRIGHTS |only inst/doc/pkg-templates.Rmd | 12 ++ inst/doc/pkg-templates.html | 38 +++++++- inst/rmarkdown/templates/beamer_imetropolis |only inst/rmarkdown/templates/html_imetropolis |only man/beamer_illinois.Rd | 11 +- man/beamer_imetropolis.Rd |only man/beamer_mil.Rd | 10 +- man/beamer_orange.Rd | 10 +- man/html_imetropolis.Rd |only man/uiucthemes-package.Rd | 6 - vignettes/beamer_imetropolis.png |only vignettes/html_imetropolis.png |only vignettes/pkg-templates.Rmd | 12 ++ 23 files changed, 264 insertions(+), 64 deletions(-)
Title: Powerful Classes for HTTP Requests and Responses
Description: In order to facilitate parsing of http requests and creating
appropriate responses this package provides two classes to handle a lot of
the housekeeping involved in working with http exchanges. The infrastructure
builds upon the 'rook' specification and is thus well suited to be combined
with 'httpuv' based web servers.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>)
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between reqres versions 0.2.2 dated 2018-11-12 and 0.2.3 dated 2019-10-02
DESCRIPTION | 22 ++++---- MD5 | 20 +++---- NAMESPACE | 2 NEWS.md | 9 +++ R/parsers.R | 2 R/reqres-package.R | 2 R/request.R | 6 +- README.md | 125 ++++++++++++++++++++++++++++++++++++------------- man/default_parsers.Rd | 2 man/parsers.Rd | 2 man/reqres-package.Rd | 4 + 11 files changed, 135 insertions(+), 61 deletions(-)
Title: Generalised Joint Regression Modelling
Description: Routines for fitting various joint (and univariate) regression models, with several types of covariate effects, in the presence of equations' errors association, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <rosalba.radice@city.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between GJRM versions 0.2 dated 2019-03-07 and 0.2-1 dated 2019-10-02
GJRM-0.2-1/GJRM/ChangeLog | 11 GJRM-0.2-1/GJRM/DESCRIPTION | 8 GJRM-0.2-1/GJRM/MD5 | 297 +- GJRM-0.2-1/GJRM/NAMESPACE | 16 GJRM-0.2-1/GJRM/R/AT.r | 21 GJRM-0.2-1/GJRM/R/CopulaCLM.r | 18 GJRM-0.2-1/GJRM/R/LM.bpm.r | 2 GJRM-0.2-1/GJRM/R/OR.r | 2 GJRM-0.2-1/GJRM/R/PDef.R | 4 GJRM-0.2-1/GJRM/R/PE.r | 278 -- GJRM-0.2-1/GJRM/R/RR.r | 2 GJRM-0.2-1/GJRM/R/SemiParBIV.fit.R | 370 +++ GJRM-0.2-1/GJRM/R/SemiParBIV.fit.post.r | 8 GJRM-0.2-1/GJRM/R/SemiParBIV.r | 15 GJRM-0.2-1/GJRM/R/SemiParTRIV.r | 7 GJRM-0.2-1/GJRM/R/adjCov.r | 4 GJRM-0.2-1/GJRM/R/ass.dp.r | 4 GJRM-0.2-1/GJRM/R/ass.ms.r | 8 GJRM-0.2-1/GJRM/R/bCopulaCLMgHsCont.R | 2 GJRM-0.2-1/GJRM/R/bcont.R | 2 GJRM-0.2-1/GJRM/R/bcont23.R | 2 GJRM-0.2-1/GJRM/R/bcont23twoParC.R | 2 GJRM-0.2-1/GJRM/R/bcont32.R | 2 GJRM-0.2-1/GJRM/R/bcont32twoParC.R | 2 GJRM-0.2-1/GJRM/R/bcont3twoParC.R | 2 GJRM-0.2-1/GJRM/R/bcontROB.R | 2 GJRM-0.2-1/GJRM/R/bcontSurv.R | 2 GJRM-0.2-1/GJRM/R/bcontSurvG.R | 6 GJRM-0.2-1/GJRM/R/bcontSurvGDep.R |only GJRM-0.2-1/GJRM/R/bcontSurvGcont2Surv.R | 4 GJRM-0.2-1/GJRM/R/bcontSurvGuniv.R | 2 GJRM-0.2-1/GJRM/R/bcontSurvGunivI.R |only GJRM-0.2-1/GJRM/R/bcontSurvGunivInform.r | 4 GJRM-0.2-1/GJRM/R/bcontSurvGunivL.R |only GJRM-0.2-1/GJRM/R/bcontSurvGunivMIXED.R |only GJRM-0.2-1/GJRM/R/bconttwoParC.R | 2 GJRM-0.2-1/GJRM/R/bcorrec.R | 14 GJRM-0.2-1/GJRM/R/bcorrec2.R | 8 GJRM-0.2-1/GJRM/R/bcorrecDiscr.R | 2 GJRM-0.2-1/GJRM/R/bcorrecFuncs.R | 4 GJRM-0.2-1/GJRM/R/bdiscrcont.R | 2 GJRM-0.2-1/GJRM/R/bdiscrcont12.R | 2 GJRM-0.2-1/GJRM/R/bdiscrcont13.R | 2 GJRM-0.2-1/GJRM/R/bdiscrcont23.R | 2 GJRM-0.2-1/GJRM/R/bdiscrdiscr.R | 2 GJRM-0.2-1/GJRM/R/bdiscrdiscr11.R | 2 GJRM-0.2-1/GJRM/R/bdiscrdiscr12.R | 2 GJRM-0.2-1/GJRM/R/bprobgHs.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsCont.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsCont3.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsCont3SS.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsContSS.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsContUniv.r | 15 GJRM-0.2-1/GJRM/R/bprobgHsContUniv3.r | 8 GJRM-0.2-1/GJRM/R/bprobgHsDiscr1.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsDiscr1SS.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsDiscr2.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsDiscr2SS.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsFixTheta.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsPO.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsPO0.r | 2 GJRM-0.2-1/GJRM/R/bprobgHsSS.r | 2 GJRM-0.2-1/GJRM/R/bprobgHstwoParC.r | 2 GJRM-0.2-1/GJRM/R/copgHs.r | 6 GJRM-0.2-1/GJRM/R/copgHs2.r | 4 GJRM-0.2-1/GJRM/R/copgHs3.r | 2 GJRM-0.2-1/GJRM/R/copgHsAT.r | 4 GJRM-0.2-1/GJRM/R/copgHsCont.r | 4 GJRM-0.2-1/GJRM/R/copulaReg.fit.post.r | 5 GJRM-0.2-1/GJRM/R/copulaSampleSel.fit.post.r | 6 GJRM-0.2-1/GJRM/R/copulaSampleSel.r | 17 GJRM-0.2-1/GJRM/R/cv.inform.r | 6 GJRM-0.2-1/GJRM/R/distrHs.r | 2537 +++++++++------------- GJRM-0.2-1/GJRM/R/distrHsAT.r | 182 + GJRM-0.2-1/GJRM/R/distrHsAT1.r | 238 +- GJRM-0.2-1/GJRM/R/distrHsATDiscr.r | 66 GJRM-0.2-1/GJRM/R/distrHsATDiscr2.r | 30 GJRM-0.2-1/GJRM/R/distrHsDiscr.r | 862 ------- GJRM-0.2-1/GJRM/R/enu.tr.R | 14 GJRM-0.2-1/GJRM/R/esp.tr.R | 25 GJRM-0.2-1/GJRM/R/eta.tr.R | 8 GJRM-0.2-1/GJRM/R/form.eq12.r | 25 GJRM-0.2-1/GJRM/R/func.OPT.r | 5 GJRM-0.2-1/GJRM/R/gamlss.fit.post.r | 9 GJRM-0.2-1/GJRM/R/gamlss.r | 526 ++++ GJRM-0.2-1/GJRM/R/ggm.Deriv.R | 29 GJRM-0.2-1/GJRM/R/ggmtrust.R | 19 GJRM-0.2-1/GJRM/R/ggmtrust.path.R | 2 GJRM-0.2-1/GJRM/R/gjrm.r | 53 GJRM-0.2-1/GJRM/R/hazsurv.plot.r | 14 GJRM-0.2-1/GJRM/R/imputeCounter.r | 29 GJRM-0.2-1/GJRM/R/imputeSS.r | 40 GJRM-0.2-1/GJRM/R/int.postcheck.R | 8 GJRM-0.2-1/GJRM/R/jc.probs.r | 19 GJRM-0.2-1/GJRM/R/jc.probs1.r | 65 GJRM-0.2-1/GJRM/R/jc.probs2.r | 42 GJRM-0.2-1/GJRM/R/jc.probs3.r | 5 GJRM-0.2-1/GJRM/R/jc.probs4.r | 8 GJRM-0.2-1/GJRM/R/jc.probs5.r | 18 GJRM-0.2-1/GJRM/R/jc.probs6.r | 3 GJRM-0.2-1/GJRM/R/jc.probs7.r | 59 GJRM-0.2-1/GJRM/R/mm.r | 2 GJRM-0.2-1/GJRM/R/overall.svG.R | 24 GJRM-0.2-1/GJRM/R/polys.setup.r | 3 GJRM-0.2-1/GJRM/R/post.check.R | 12 GJRM-0.2-1/GJRM/R/postVb.r | 141 - GJRM-0.2-1/GJRM/R/pp.r | 15 GJRM-0.2-1/GJRM/R/pream.wm.r | 85 GJRM-0.2-1/GJRM/R/pred.gp.r |only GJRM-0.2-1/GJRM/R/pred.mvt.r | 108 GJRM-0.2-1/GJRM/R/predict.CopulaCLM.r |only GJRM-0.2-1/GJRM/R/predict.SemiParBIV.r | 2 GJRM-0.2-1/GJRM/R/print.SemiParBIV.r | 14 GJRM-0.2-1/GJRM/R/print.copulaSampleSel.r | 10 GJRM-0.2-1/GJRM/R/print.gamlss.r | 17 GJRM-0.2-1/GJRM/R/print.gjrm.r | 45 GJRM-0.2-1/GJRM/R/print.summary.SemiParBIV.r | 8 GJRM-0.2-1/GJRM/R/print.summary.copulaSampleSel.r | 8 GJRM-0.2-1/GJRM/R/print.summary.gamlss.r | 48 GJRM-0.2-1/GJRM/R/print.summary.gjrm.r | 8 GJRM-0.2-1/GJRM/R/probm.R | 2 GJRM-0.2-1/GJRM/R/probmS.R | 2 GJRM-0.2-1/GJRM/R/pscr.r | 79 GJRM-0.2-1/GJRM/R/pscr0.r | 64 GJRM-0.2-1/GJRM/R/r.resp.R |only GJRM-0.2-1/GJRM/R/rIC.R | 58 GJRM-0.2-1/GJRM/R/regH.r | 2 GJRM-0.2-1/GJRM/R/resp.check.R | 52 GJRM-0.2-1/GJRM/R/rob.const.R | 4 GJRM-0.2-1/GJRM/R/rob.int.R | 12 GJRM-0.2-1/GJRM/R/sim.resp.R | 96 GJRM-0.2-1/GJRM/R/startsn.r | 25 GJRM-0.2-1/GJRM/R/summary.SemiParBIV.r | 8 GJRM-0.2-1/GJRM/R/summary.SemiParTRIV.r | 2 GJRM-0.2-1/GJRM/R/summary.copulaSampleSel.r | 8 GJRM-0.2-1/GJRM/R/summary.gamlss.r | 19 GJRM-0.2-1/GJRM/R/summary.gjrm.r | 6 GJRM-0.2-1/GJRM/R/susutsn.r | 22 GJRM-0.2-1/GJRM/R/teta.tr.R | 4 GJRM-0.2-1/GJRM/R/vis.gam2.r | 1 GJRM-0.2-1/GJRM/R/working.comp.r | 2 GJRM-0.2-1/GJRM/man/GJRM-package.Rd | 2 GJRM-0.2-1/GJRM/man/bprobgHsContUniv.Rd | 6 GJRM-0.2-1/GJRM/man/eta.tr.Rd | 4 GJRM-0.2-1/GJRM/man/gamlss.Rd | 44 GJRM-0.2-1/GJRM/man/gjrm.Rd | 35 GJRM-0.2-1/GJRM/man/jc.probs.Rd | 5 GJRM-0.2-1/GJRM/man/pred.gp.Rd |only GJRM-0.2-1/GJRM/man/predict.CopulaCLM.Rd |only GJRM-0.2-1/GJRM/man/predict.SemiParBIV.Rd | 9 GJRM-0.2-1/GJRM/man/resp.check.Rd | 4 GJRM-0.2-1/GJRM/man/summary.gamlss.Rd | 16 GJRM-0.2-1/GJRM/man/summary.gjrm.Rd | 4 GJRM-0.2/GJRM/R/predict2.CLM.r |only GJRM-0.2/GJRM/R/prediction.CLM.r |only 155 files changed, 3719 insertions(+), 3626 deletions(-)
Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write data from neuroimaging files in 'FreeSurfer' <http://freesurfer.net/> binary formats. This includes the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Author: Tim Schäfer
Maintainer: Tim Schäfer <ts+code@rcmd.org>
Diff between freesurferformats versions 0.1.1 dated 2019-09-13 and 0.1.2 dated 2019-10-02
freesurferformats-0.1.1/freesurferformats/R/fs_atlas_region_agg.R |only freesurferformats-0.1.1/freesurferformats/README.md |only freesurferformats-0.1.1/freesurferformats/man/fs.atlas.region.agg.Rd |only freesurferformats-0.1.1/freesurferformats/man/fs.atlas.region.agg.group.Rd |only freesurferformats-0.1.1/freesurferformats/man/fs.spread.value.over.region.Rd |only freesurferformats-0.1.1/freesurferformats/man/fs.value.list.from.agg.res.Rd |only freesurferformats-0.1.1/freesurferformats/tests/testthat/test-fs-atlas-region_agg.R |only freesurferformats-0.1.2/freesurferformats/DESCRIPTION | 9 - freesurferformats-0.1.2/freesurferformats/MD5 | 56 +++++----- freesurferformats-0.1.2/freesurferformats/NAMESPACE | 4 freesurferformats-0.1.2/freesurferformats/R/read_fs_annot.R | 33 +++++ freesurferformats-0.1.2/freesurferformats/R/read_fs_curv.R | 4 freesurferformats-0.1.2/freesurferformats/R/read_fs_mgh.R | 36 +++--- freesurferformats-0.1.2/freesurferformats/R/read_fs_surface.R |only freesurferformats-0.1.2/freesurferformats/R/write_fs_curv.R | 5 freesurferformats-0.1.2/freesurferformats/R/write_fs_surface.R |only freesurferformats-0.1.2/freesurferformats/build/vignette.rds |binary freesurferformats-0.1.2/freesurferformats/inst/doc/freesurferformats.R | 15 ++ freesurferformats-0.1.2/freesurferformats/inst/doc/freesurferformats.Rmd | 31 +++++ freesurferformats-0.1.2/freesurferformats/inst/doc/freesurferformats.html | 30 ++++- freesurferformats-0.1.2/freesurferformats/inst/doc/freesurferformats_write.R | 6 + freesurferformats-0.1.2/freesurferformats/inst/doc/freesurferformats_write.Rmd | 13 ++ freesurferformats-0.1.2/freesurferformats/inst/doc/freesurferformats_write.html | 15 ++ freesurferformats-0.1.2/freesurferformats/inst/extdata/lh.tinysurface |only freesurferformats-0.1.2/freesurferformats/man/fs.get.morph.file.ext.for.format.Rd | 1 freesurferformats-0.1.2/freesurferformats/man/fs.get.morph.file.format.from.filename.Rd | 1 freesurferformats-0.1.2/freesurferformats/man/read.fs.annot.Rd | 6 - freesurferformats-0.1.2/freesurferformats/man/read.fs.surface.Rd |only freesurferformats-0.1.2/freesurferformats/man/readcolortable.Rd | 4 freesurferformats-0.1.2/freesurferformats/man/write.fs.surface.Rd |only freesurferformats-0.1.2/freesurferformats/tests/testthat/test-read-fs-annot.R | 25 ++++ freesurferformats-0.1.2/freesurferformats/tests/testthat/test-read-fs-mgh.R | 34 +++--- freesurferformats-0.1.2/freesurferformats/tests/testthat/test-read-fs-surface.R |only freesurferformats-0.1.2/freesurferformats/tests/testthat/test-write-fs-surface.R |only freesurferformats-0.1.2/freesurferformats/vignettes/freesurferformats.Rmd | 31 +++++ freesurferformats-0.1.2/freesurferformats/vignettes/freesurferformats_write.Rmd | 13 ++ 36 files changed, 288 insertions(+), 84 deletions(-)
More information about freesurferformats at CRAN
Permanent link
Title: Tools for Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter, ``Practical Tools for Designing and Weighting Survey Samples'' (2nd edition, 2018). Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between PracTools versions 1.2 dated 2019-09-07 and 1.2.1 dated 2019-10-02
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/nContMoe.R | 4 +--- 3 files changed, 7 insertions(+), 9 deletions(-)
Title: Calculates the Test-Statistic for the Drift Burst Hypothesis
Description: Calculates the T-Statistic for the drift burst hypothesis from the working paper Christensen, Oomen and Reno (2018) <DOI:10.2139/ssrn.2842535>. The authors' MATLAB code is available upon request, see: <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=2842535>.
Author: Emil Sjoerup
Maintainer: Emil Sjoerup <emilsjoerup@live.dk>
Diff between DriftBurstHypothesis versions 0.1.3 dated 2019-06-06 and 0.2.0 dated 2019-10-02
ChangeLog | 33 ++++- DESCRIPTION | 8 - MD5 | 26 ++-- NAMESPACE | 9 - R/ClassMethods.R | 171 +++++++++++++++++---------- R/Driftbursts.R | 178 ++++++++++++++++------------ R/RcppExports.R | 12 + build/partial.rdb |binary man/driftBursts.Rd |only man/drift_bursts.Rd | 182 +++-------------------------- src/DBH.cpp | 288 ++++++++++++++++++++++++++++++++++------------ src/RcppExports.cpp | 56 ++++++++ src/utils.cpp |only src/utils.h |only tests/testthat/Rplots.pdf |only tests/testthat/test_DBH.R | 135 +++++++++++++++++++++ 16 files changed, 706 insertions(+), 392 deletions(-)
More information about DriftBurstHypothesis at CRAN
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Title: R Interface to 'TensorFlow'
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>,
an open source software library for numerical computation using data
flow graphs. Nodes in the graph represent mathematical operations,
while the graph edges represent the multidimensional data arrays
(tensors) communicated between them. The flexible architecture allows
you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop,
server, or mobile device with a single 'API'. 'TensorFlow' was originally
developed by researchers and engineers working on the Google Brain Team
within Google's Machine Intelligence research organization for the
purposes of conducting machine learning and deep neural networks research,
but the system is general enough to be applicable in a wide variety
of other domains as well.
Author: Daniel Falbel [ctb, cph, cre],
JJ Allaire [aut, cph],
RStudio [cph, fnd],
Yuan Tang [aut, cph] (<https://orcid.org/0000-0001-5243-233X>),
Dirk Eddelbuettel [ctb, cph],
Nick Golding [ctb, cph],
Tomasz Kalinowski [ctb, cph],
Google Inc. [ctb, cph] (Examples and Tutorials)
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between tensorflow versions 1.14.0 dated 2019-08-01 and 2.0.0 dated 2019-10-02
DESCRIPTION | 6 - MD5 | 26 ++--- NEWS.md | 14 ++ R/compat.R | 12 -- R/generics.R | 33 ++++-- R/install.R | 15 --- R/package.R | 9 - R/save.R | 31 +++++- R/tensorboard.R | 32 ++++-- man/use_compat.Rd | 4 tests/testthat/test-export-savedmodel.R | 101 +++++++-------------- tests/testthat/test-extract-syntax.R | 28 +++++ tests/testthat/test-generic-methods.R | 153 ++++++++++++++++++++++++++++++++ tests/testthat/utils.R | 10 +- 14 files changed, 332 insertions(+), 142 deletions(-)
Title: Interactively Explore Dimension-Reduced Embeddings
Description: A tool to interactively explore the
embeddings created by dimension reduction methods such as
Principal Components Analysis (PCA), Multidimensional Scaling (MDS),
T-distributed Stochastic Neighbour Embedding (t-SNE),
Uniform Manifold Approximation and Projection (UMAP) or any other.
Author: Svetlana Ovchinnikova [aut, cre],
Simon Anders [aut]
Maintainer: Svetlana Ovchinnikova <s.ovchinnikova@zmbh.uni-heidelberg.de>
Diff between sleepwalk versions 0.2.0 dated 2019-08-26 and 0.2.1 dated 2019-10-02
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 9 +++++++++ R/sleepwalk.R | 12 +++++++++--- inst/sleepwalk_canvas.html | 5 ++--- inst/sleepwalk_svg.html | 8 +++----- man/sleepwalk.Rd | 4 +++- 7 files changed, 37 insertions(+), 23 deletions(-)
Title: Summarizing Distributions of Latent Structures
Description: Summaries of distributions on clusterings and feature allocations are provided. Specifically, point estimates are obtained by the sequentially-allocated latent structure optimization (SALSO) algorithm to minimize squared error loss, absolute error loss, Binder loss, or the lower bound of the variation of information loss. Clustering uncertainty can be assessed with the confidence calculations and the associated plot.
Author: David B. Dahl [aut, cre],
Peter Müller [aut]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between sdols versions 1.7.5 dated 2019-07-03 and 2.0.0 dated 2019-10-02
sdols-1.7.5/sdols/R/USArrests.featureAllocations-data.R |only sdols-1.7.5/sdols/R/graph.R |only sdols-1.7.5/sdols/R/onLoad.R |only sdols-1.7.5/sdols/R/plot.sdols.confidence.R |only sdols-1.7.5/sdols/R/scalaPush.clustering.R |only sdols-1.7.5/sdols/R/scalaPush.featureAllocation.R |only sdols-1.7.5/sdols/data/USArrests.featureAllocations.RData |only sdols-1.7.5/sdols/java/sdols_2.12-1.7.3.5-SNAPSHOT-sources.jar |only sdols-1.7.5/sdols/man/USArrests.featureAllocations.Rd |only sdols-1.7.5/sdols/man/plot.sdols.confidence.Rd |only sdols-2.0.0/sdols/DESCRIPTION | 11 - sdols-2.0.0/sdols/LICENSE | 25 --- sdols-2.0.0/sdols/MD5 | 50 ++---- sdols-2.0.0/sdols/NAMESPACE | 25 --- sdols-2.0.0/sdols/NEWS | 4 sdols-2.0.0/sdols/R/confidence.R | 46 +---- sdols-2.0.0/sdols/R/dlso.R | 71 ++------- sdols-2.0.0/sdols/R/expectedPairwiseAllocationMatrix.R | 78 ++-------- sdols-2.0.0/sdols/R/iris.clusterings-data.R | 2 sdols-2.0.0/sdols/R/latentStructureFit.R | 55 ++----- sdols-2.0.0/sdols/R/salso.R | 74 ++------- sdols-2.0.0/sdols/data/iris.clusterings.RData |binary sdols-2.0.0/sdols/inst/java/scala-2.11/sdols.jar |binary sdols-2.0.0/sdols/inst/java/scala-2.12/sdols.jar |binary sdols-2.0.0/sdols/inst/java/scala-2.13/sdols.jar |binary sdols-2.0.0/sdols/java/sdols-source.jar |binary sdols-2.0.0/sdols/man/confidence.Rd | 9 - sdols-2.0.0/sdols/man/dlso.Rd | 43 +---- sdols-2.0.0/sdols/man/expectedPairwiseAllocationMatrix.Rd | 41 +---- sdols-2.0.0/sdols/man/latentStructureFit.Rd | 30 +-- sdols-2.0.0/sdols/man/salso.Rd | 44 +---- 31 files changed, 182 insertions(+), 426 deletions(-)
Title: Combined Cluster and Discriminant Analysis
Description: Implements the combined cluster and discriminant analysis method for finding homogeneous groups of data with known origin as described in Kovacs et. al (2014): Classification into homogeneous groups using combined cluster and discriminant analysis (CCDA). Environmental Modelling & Software. <doi:10.1016/j.envsoft.2014.01.010>.
Author: Solt Kovacs, Jozsef Kovacs, Peter Tanos
Maintainer: Solt Kovacs <ccda@caesar.elte.hu>
Diff between ccda versions 1.1 dated 2014-12-08 and 1.1.1 dated 2019-10-02
ccda-1.1.1/ccda/DESCRIPTION | 9 ++++----- ccda-1.1.1/ccda/MD5 | 5 ++--- ccda-1.1.1/ccda/NAMESPACE | 5 +++++ ccda-1.1/ccda/R/ccda-internal.R |only 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut],
Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 2.0.3 dated 2019-09-20 and 2.0.4 dated 2019-10-02
DESCRIPTION | 8 - MD5 | 32 ++--- NEWS.md | 5 R/class_analysis_stage_results.R | 3 R/class_core_parameter_set.R | 4 R/class_design.R | 4 R/class_design_plan.R | 2 R/class_design_power_and_asn.R | 2 R/class_design_set.R | 2 R/f_design_utilities.R | 93 ++++++++++++----- man/ParameterSet_as.data.frame.Rd | 2 man/PowerAndAverageSampleNumberResult_as.data.frame.Rd | 2 man/StageResults_as.data.frame.Rd | 2 man/TrialDesignCharacteristics_as.data.frame.Rd | 2 man/TrialDesignPlan_as.data.frame.Rd | 2 man/TrialDesignSet_as.data.frame.Rd | 2 man/TrialDesign_as.data.frame.Rd | 2 17 files changed, 110 insertions(+), 59 deletions(-)
Title: Fits Psychometric Functions for Multiple Groups
Description: Quickly fits and plots psychometric functions (normal, logistic,
Weibull or any or any function defined by the user) for multiple groups.
Author: Linares Daniel [aut, cre],
L<U+00F3>pez-Moliner Joan [aut]
Maintainer: Linares Daniel <danilinares@gmail.com>
Diff between quickpsy versions 0.1.5 dated 2018-06-12 and 0.1.5.1 dated 2019-10-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- data/qpdat.rda |binary man/thresholds.Rd | 1 - 4 files changed, 6 insertions(+), 7 deletions(-)
Title: Basic Functions for Drawing Path Diagrams
Description: Implementation of simple functions to draw
basic path diagrams just for visualization purposes.
Author: Gaston Sanchez
Maintainer: Gaston Sanchez <gaston.stat@gmail.com>
Diff between pathdiagram versions 0.1.9 dated 2013-07-28 and 0.1.9.1 dated 2019-10-02
DESCRIPTION | 12 +++--- MD5 | 11 +++-- NAMESPACE | 4 ++ README.md | 4 +- build |only inst/doc/intro-pathdiagram.R | 80 +++++++++++++++-------------------------- inst/doc/intro-pathdiagram.pdf |binary 7 files changed, 48 insertions(+), 63 deletions(-)
Title: Common Multiple Testing Procedures and Gatekeeping Procedures
Description: Implementation of commonly used p-value-based and
parametric multiple testing procedures (computation of adjusted
p-values and simultaneous confidence intervals) and parallel
gatekeeping procedures based on the methodology presented in
the book "Multiple Testing Problems in Pharmaceutical
Statistics" (edited by Alex Dmitrienko, Ajit C. Tamhane and
Frank Bretz) published by Chapman and Hall/CRC Press 2009.
Author: Alex Dmitrienko, Eric Nantz, and Gautier Paux, with
contributions by Thomas Brechenmacher
Maintainer: Eric Nantz <eric.nantz@gmail.com>
Diff between multxpert versions 0.1 dated 2011-01-23 and 0.1.1 dated 2019-10-02
DESCRIPTION | 7 ++++--- MD5 |only NAMESPACE | 6 ++++-- R/zzz.R | 10 +++++----- man/paradjp.Rd | 4 ++-- man/pargateadjp.Rd | 4 ++-- man/pvaladjp.Rd | 4 ++-- 7 files changed, 19 insertions(+), 16 deletions(-)
Title: Plotting and Average Theta Functions for Multiple Class Mixed
Rasch Models
Description: Provides supplemental functions for the 'mixRasch'
package (Willse, 2014), <https://cran.r-project.org/package=mixRasch/mixRasch.pdf> including a
plotting function to compare item parameters for multiple
class models and a function that provides average theta values for each class in
a mixture model.
Author: Pamela Trantham [aut, cre]
Maintainer: Pamela Trantham <pamelapsc@yahoo.com>
Diff between mixRaschTools versions 1.1 dated 2018-12-03 and 1.1.1 dated 2019-10-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- data/fourclass_ex.rda |binary data/threeclass_ex.rda |binary man/fourclass_ex.Rd | 2 +- man/threeclass_ex.Rd | 2 +- 6 files changed, 10 insertions(+), 10 deletions(-)
Title: Meta-Analysis of Correlation Coefficients
Description: Implement the DerSimonian-Laird (DSL) and Olkin-Pratt (OP)
meta-analytical approaches with correlation coefficients as
effect sizes.
Author: Etienne Laliberté
Maintainer: Etienne Laliberté <etiennelaliberte@gmail.com>
Diff between metacor versions 1.0-2 dated 2011-03-21 and 1.0-2.1 dated 2019-10-02
DESCRIPTION | 12 ++++++------ MD5 |only NAMESPACE | 4 ++++ data/lui.rda |binary 4 files changed, 10 insertions(+), 6 deletions(-)
Title: Estimation of the Local False Discovery Rates by Type II Maximum
Likelihood Estimation
Description: Suite of R functions for the estimation of the local false discovery rate (LFDR) using Type II maximum likelihood estimation (MLE).
Author: Ye Yang, Marta Padilla, Alaa Ali, Kyle Leckett, Zhenyu Yang, Zuojing Li, Corey M. Yanofsky and David R. Bickel
Maintainer: M. Padilla <padilla.mpf@gmail.com>
Diff between LFDR.MLE versions 1.0 dated 2015-08-06 and 1.0.1 dated 2019-10-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- man/lfdr.l1o.Rd | 6 +++--- man/lfdr.mdl.Rd | 4 ++-- man/lfdr.mle.Rd | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Data and Functions to Accompany the Book "Learning R"
Description: Crabs in the English channel, deer skulls, English
monarchs, half-caste Manga characters, Jamaican cities,
Shakespeare's The Tempest, drugged up cyclists and sexually
transmitted diseases.
Author: Richie Cotton
Maintainer: Richie Cotton <richierocks@gmail.com>
Diff between learningr versions 0.29 dated 2013-11-06 and 0.29.1 dated 2019-10-02
DESCRIPTION | 11 +++++------ MD5 | 23 ++++++++++++----------- build |only data/alpe_d_huez.rda |binary data/alpe_d_huez2.rda |binary data/crab_tag.rda |binary data/deer_endocranial_volume.rda |binary data/english_monarchs.rda |binary data/gonorrhoea.rda |binary data/hafu.rda |binary data/hafu2.rda |binary data/obama_vs_mccain.rda |binary man/deer_endocranial_volume.Rd | 2 +- 13 files changed, 18 insertions(+), 18 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [aut],
Charles Spanbauer [aut],
Matthew Pratola [aut],
Martyn Plummer [ctb],
Nicky Best [ctb],
Kate Cowles [ctb],
Karen Vines [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 2.5 dated 2019-06-17 and 2.6 dated 2019-10-02
DESCRIPTION | 8 MD5 | 95 NEWS | 3 build/vignette.rds |binary data/ACTG175.rda |binary data/alligator.rda |binary data/arq.rda |binary data/bladder.rda |binary data/leukemia.rda |binary data/lung.rda |binary data/transplant.rda |binary data/xdm20.test.rda |binary data/xdm20.train.rda |binary data/ydm20.test.rda |binary data/ydm20.train.rda |binary demo/bladder.recur.bart.R | 6 demo/boston.R | 36 demo/geweke.lung.surv.bart.R | 1 demo/nhanes.pbart1.R | 113 - demo/nhanes.pbart2.R | 105 demo/replication.R | 6 inst/doc/the-BART-R-package.Rnw | 3288 +++++++++++++++++------------- inst/doc/the-BART-R-package.pdf |binary man/bladder.Rd | 16 man/leukemia.Rd | 2 man/lung.Rd | 8 man/recur.bart.Rd | 2 man/recur.pre.bart.Rd | 8 man/transplant.Rd | 30 vignettes/figures/RI-B6-Pl.pdf |binary vignettes/figures/RI-Th-B6.pdf |binary vignettes/figures/RI-Th-Pl.pdf |binary vignettes/figures/alligator.pdf |binary vignettes/figures/boston1.pdf |binary vignettes/figures/boston2.pdf |binary vignettes/figures/boston3.pdf |binary vignettes/figures/boston4.pdf |binary vignettes/figures/boston5.pdf |binary vignettes/figures/boston6.pdf |binary vignettes/figures/chronic-pain1.pdf |only vignettes/figures/chronic-pain2.pdf |only vignettes/figures/geweke-pbart2-1000.pdf |binary vignettes/figures/geweke-pbart2-10000.pdf |binary vignettes/figures/geweke-pbart2-200.pdf |binary vignettes/figures/liver-BART.pdf |binary vignettes/figures/lung.pdf |binary vignettes/figures/sparse-beta-prime.pdf |only vignettes/figures/sparse-pbart.pdf |binary vignettes/references.bib | 99 vignettes/the-BART-R-package.Rnw | 3288 +++++++++++++++++------------- 50 files changed, 4085 insertions(+), 3029 deletions(-)
Title: Exchange Commands Between R and 'JavaScript'
Description: An 'httpuv' based bridge between R and 'JavaScript'. Provides an easy way to exchange commands and data between a web page and a currently running R session.
Author: Svetlana Ovchinnikova [aut, cre],
Simon Anders [aut]
Maintainer: Svetlana Ovchinnikova <s.ovchinnikova@zmbh.uni-heidelberg.de>
Diff between jrc versions 0.1.1 dated 2019-03-31 and 0.2.0 dated 2019-10-02
DESCRIPTION | 10 - MD5 | 25 +- NAMESPACE | 9 NEWS.md |only R/jrc.R | 477 +++++++++++++++++++++++++++++++++++++++++++++----- inst/http_root/jrc.js | 58 +++++- man/allowFunctions.Rd |only man/allowVariables.Rd |only man/authorize.Rd |only man/callFunction.Rd |only man/closePage.Rd | 5 man/getPage.Rd |only man/limitStorage.Rd |only man/openPage.Rd | 24 ++ man/sendCommand.Rd | 7 man/sendData.Rd | 21 +- man/sendHTML.Rd | 5 17 files changed, 571 insertions(+), 70 deletions(-)
Title: Methods for Closed Testing with Simes Inequality, in Particular
Hommel's Method
Description: Provides methods for closed testing using Simes local tests. In particular, calculates adjusted p-values for Hommel's multiple testing method, and provides lower confidence bounds for true discovery proportions. A robust but more conservative variant of the closed testing procedure that does not require the assumption of Simes inequality is also implemented. The methods have been described in detail in Goeman et al (2016) <arXiv:1611.06739v2>.
Author: Jelle Goeman, Rosa Meijer, Thijmen Krebs
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between hommel versions 1.3 dated 2019-08-19 and 1.4 dated 2019-10-02
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/localtest-function.R | 10 +++++----- 4 files changed, 15 insertions(+), 12 deletions(-)
Title: Random Partition Distribution Indexed by Pairwise Information
Description: Implementations are provided for the models described in the paper D. B. Dahl, R. Day, J. Tsai (2017) <DOI:10.1080/01621459.2016.1165103>. The Ewens, Ewens-Pitman, Ewens attraction, Ewens-Pitman attraction, and ddCRP distributions are available for prior and posterior simulation. Posterior simulation is based on a user-supplied likelihood. Supporting functions for partition estimation and plotting are also provided.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between shallot versions 0.4.6 dated 2019-07-03 and 0.4.7 dated 2019-10-02
shallot-0.4.6/shallot/man/enumerate.partitions.Rd |only shallot-0.4.7/shallot/DESCRIPTION | 10 +-- shallot-0.4.7/shallot/LICENSE | 25 ------- shallot-0.4.7/shallot/MD5 | 36 +++++------ shallot-0.4.7/shallot/NAMESPACE | 5 - shallot-0.4.7/shallot/NEWS | 3 shallot-0.4.7/shallot/R/default.mass.R | 47 +++++++-------- shallot-0.4.7/shallot/R/onLoad.R | 24 ++++++- shallot-0.4.7/shallot/R/scalaPush.clustering.R |only shallot-0.4.7/shallot/R/shallot-package.R | 6 - shallot-0.4.7/shallot/R/shallot.R | 38 +----------- shallot-0.4.7/shallot/inst/java/scala-2.11/shallot.jar |binary shallot-0.4.7/shallot/inst/java/scala-2.12/shallot.jar |binary shallot-0.4.7/shallot/inst/java/scala-2.13/shallot.jar |binary shallot-0.4.7/shallot/java/shallot-source.jar |binary shallot-0.4.7/shallot/man/default.mass.Rd | 11 +-- shallot-0.4.7/shallot/man/partition.confidence.Rd | 9 +- shallot-0.4.7/shallot/man/sample.partitions.posterior.Rd | 6 - shallot-0.4.7/shallot/man/shallot-package.Rd | 6 - shallot-0.4.7/shallot/man/variance.ratio.Rd | 7 +- 20 files changed, 104 insertions(+), 129 deletions(-)
Title: Flexible Identification of Phenotype-Specific Subpathways
Description: A network-based systems biology tool for flexible identification of phenotype-specific subpathways in the cancer gene expression data
with multiple categories (such as multiple subtype or developmental stages of cancer). Subtype Set Enrichment Analysis (SubSEA) and Dynamic Changed
Subpathway Analysis (DCSA) are developed to flexible identify subtype specific and dynamic changed subpathways respectively. The operation modes
include extraction of subpathways from biological pathways, inference of subpathway activities in the context of gene expression data, identification
of subtype specific subpathways with SubSEA, identification of dynamic changed subpathways associated with the cancer developmental stage with DCSA,
and visualization of the activities of resulting subpathways by using box plots and heat maps. Its capabilities render the tool could find the specific
abnormal subpathways in the cancer dataset with multi-phenotype samples.
Author: Xudong Han,
Junwei Han,
Qingfei Kong
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between psSubpathway versions 0.1.0 dated 2019-06-21 and 0.1.1 dated 2019-10-02
psSubpathway-0.1.0/psSubpathway/data/geneentrezid.rda |only psSubpathway-0.1.0/psSubpathway/data/genesymbol.rda |only psSubpathway-0.1.1/psSubpathway/DESCRIPTION | 6 psSubpathway-0.1.1/psSubpathway/MD5 | 54 +-- psSubpathway-0.1.1/psSubpathway/NAMESPACE | 2 psSubpathway-0.1.1/psSubpathway/R/DCSAcs.R | 175 ++++------- psSubpathway-0.1.1/psSubpathway/R/ReadClsFile.R | 2 psSubpathway-0.1.1/psSubpathway/R/SubSEA.R | 234 ++++++---------- psSubpathway-0.1.1/psSubpathway/R/isPackageLoaded.R |only psSubpathway-0.1.1/psSubpathway/R/plotSpwACmap.R | 8 psSubpathway-0.1.1/psSubpathway/R/plotSpwNetmap.R | 4 psSubpathway-0.1.1/psSubpathway/R/plotSpwPSheatmap.R |only psSubpathway-0.1.1/psSubpathway/R/plotSubSEScurve.R | 11 psSubpathway-0.1.1/psSubpathway/R/plotheatmap.R | 44 +-- psSubpathway-0.1.1/psSubpathway/R/ssgsea.R | 53 +++ psSubpathway-0.1.1/psSubpathway/data/datalist | 2 psSubpathway-0.1.1/psSubpathway/inst/doc/vignette.R | 18 + psSubpathway-0.1.1/psSubpathway/inst/doc/vignette.Rmd | 35 +- psSubpathway-0.1.1/psSubpathway/inst/doc/vignette.html | 49 ++- psSubpathway-0.1.1/psSubpathway/man/DCSA.Rd | 16 - psSubpathway-0.1.1/psSubpathway/man/ReadClsFile.Rd | 2 psSubpathway-0.1.1/psSubpathway/man/SubSEA.Rd | 17 - psSubpathway-0.1.1/psSubpathway/man/envData.Rd | 4 psSubpathway-0.1.1/psSubpathway/man/isPackageLoaded.Rd |only psSubpathway-0.1.1/psSubpathway/man/plotSpwACmap.Rd | 8 psSubpathway-0.1.1/psSubpathway/man/plotSpwNetmap.Rd | 6 psSubpathway-0.1.1/psSubpathway/man/plotSpwPSheatmap.Rd |only psSubpathway-0.1.1/psSubpathway/man/plotSubSEScurve.Rd | 10 psSubpathway-0.1.1/psSubpathway/man/plotheatmap.Rd | 20 - psSubpathway-0.1.1/psSubpathway/man/ssgsea.Rd | 5 psSubpathway-0.1.1/psSubpathway/vignettes/vignette.Rmd | 35 +- 31 files changed, 423 insertions(+), 397 deletions(-)
Title: Cumulative Sum (CUSUM) Charts for Monitoring of Hospital
Performance
Description: Provides functions for constructing and evaluating
CUSUM charts and RA-CUSUM charts with focus on false signal probability.
Author: Lena Hubig [aut, cre] (<https://orcid.org/0000-0002-9454-1232>)
Maintainer: Lena Hubig <cs@lenahubig.de>
Diff between cusum versions 0.4.0 dated 2019-08-28 and 0.4.1 dated 2019-10-02
DESCRIPTION | 11 ++-- MD5 | 60 ++++++++++++---------- NEWS.md | 7 ++ R/cusum.R | 21 +++++-- R/cusum_alpha_sim.R | 30 ++++++++--- R/cusum_limit_exact.R | 15 ++--- R/cusum_limit_sim.R | 15 +++-- R/racusum.R | 47 ++++++++++------- R/racusum_alpha_sim.R | 30 +++++++---- R/racusum_limit_sim.R | 12 +++- R/weights_t.R | 1 README.md | 8 +++ inst/doc/cusum.html | 23 +++----- inst/doc/gscusum.R | 1 inst/doc/gscusum.Rmd | 1 inst/doc/gscusum.html | 38 +++++++------- man/cusum.Rd | 2 man/racusum.Rd | 2 src/gscusum.cpp | 8 +-- tests/figs |only tests/testthat/Rplots.pdf |binary tests/testthat/test-cusum.R | 85 ++++++++++++++++++++++++++++++-- tests/testthat/test-cusum_alpha_sim.R | 62 +++++++++++++++++++++++ tests/testthat/test-cusum_limit_sim.R | 47 ++++++++++++++++- tests/testthat/test-gscusum.R |only tests/testthat/test-plot_cusum.R |only tests/testthat/test-racusum.R | 56 +++++++++++++++++++-- tests/testthat/test-racusum_alpha_sim.R | 60 +++++++++++++++++++--- tests/testthat/test-racusum_dpcl_sim.R |only tests/testthat/test-ragscusum.R |only tests/testthat/test_cusum_limit_exact.R |only tests/testthat/test_racusum_limit_sim.R | 45 +++++++++++----- vignettes/gscusum.Rmd | 1 33 files changed, 520 insertions(+), 168 deletions(-)
Title: Count Transformation Models
Description: Count transformation models featuring
parameters interpretable as discrete hazard ratios, odds ratios,
reverse-time discrete hazard ratios, or transformed expectations.
An appropriate data transformation for a count outcome and
regression coefficients are simultaneously estimated by maximising
the exact discrete log-likelihood using the computational framework
provided in package 'mlt', technical details are given in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Sandra Siegfried [aut],
Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between cotram versions 0.1-0 dated 2019-08-19 and 0.1-1 dated 2019-10-02
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- build/partial.rdb |binary inst/NEWS.Rd | 7 +++++++ inst/doc/cotram.R | 6 ++++-- inst/doc/cotram.Rnw | 28 +++++++++++++++------------- inst/doc/cotram.pdf |binary vignettes/cotram.Rnw | 28 +++++++++++++++------------- vignettes/count_transformation.pdf |binary vignettes/defs.tex | 7 ++++--- 10 files changed, 58 insertions(+), 44 deletions(-)
Title: High Performance Container Data Types
Description: Provides high performance container data types such as Queue, Stack, Deque, Dict and OrderedDict. Benchmarks <https://randy3k.github.io/collections/articles/benchmark.html> have shown that these containers are asymptotically more efficient than those offered by other packages.
Author: Randy Lai [aut, cre],
Andrea Mazzoleni [cph] (tommy hash table library)
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between collections versions 0.1.6 dated 2019-04-04 and 0.2.0 dated 2019-10-02
collections-0.1.6/collections/R/ordereddict.R |only collections-0.1.6/collections/R/priorityqueue.R |only collections-0.1.6/collections/src/priorityqueue.c |only collections-0.1.6/collections/src/priorityqueue.h |only collections-0.1.6/collections/tests/testthat/test_ordereddict.R |only collections-0.1.6/collections/tests/testthat/test_priorityqueue.R |only collections-0.2.0/collections/DESCRIPTION | 16 collections-0.2.0/collections/LICENSE | 2 collections-0.2.0/collections/MD5 | 112 +- collections-0.2.0/collections/NAMESPACE | 17 collections-0.2.0/collections/R/collections.R | 6 collections-0.2.0/collections/R/deque.R | 394 +++++----- collections-0.2.0/collections/R/dict.R | 324 ++++++-- collections-0.2.0/collections/R/ordered_dict.R |only collections-0.2.0/collections/R/priority_queue.R |only collections-0.2.0/collections/R/queue.R | 212 ++--- collections-0.2.0/collections/R/stack.R | 208 ++--- collections-0.2.0/collections/R/zzz.R |only collections-0.2.0/collections/README.md | 21 collections-0.2.0/collections/man/Deque.Rd | 50 - collections-0.2.0/collections/man/DequeL.Rd | 54 - collections-0.2.0/collections/man/Dict.Rd | 45 - collections-0.2.0/collections/man/DictL.Rd |only collections-0.2.0/collections/man/OrderedDict.Rd | 53 - collections-0.2.0/collections/man/OrderedDictL.Rd | 57 - collections-0.2.0/collections/man/PriorityQueue.Rd | 41 - collections-0.2.0/collections/man/Queue.Rd | 38 collections-0.2.0/collections/man/QueueL.Rd | 42 - collections-0.2.0/collections/man/Stack.Rd | 38 collections-0.2.0/collections/man/StackL.Rd | 44 - collections-0.2.0/collections/man/collections-package.Rd | 5 collections-0.2.0/collections/src/Makevars |only collections-0.2.0/collections/src/collections.c | 13 collections-0.2.0/collections/src/deque.c | 50 - collections-0.2.0/collections/src/deque.h | 10 collections-0.2.0/collections/src/dict.c | 136 +++ collections-0.2.0/collections/src/dict.h | 7 collections-0.2.0/collections/src/priority_queue.c |only collections-0.2.0/collections/src/priority_queue.h |only collections-0.2.0/collections/src/queue.c | 18 collections-0.2.0/collections/src/queue.h | 4 collections-0.2.0/collections/src/stack.c | 14 collections-0.2.0/collections/src/stack.h | 4 collections-0.2.0/collections/src/tommyds |only collections-0.2.0/collections/src/utils.c |only collections-0.2.0/collections/src/utils.h |only collections-0.2.0/collections/tests/testthat/test_deque.R | 30 collections-0.2.0/collections/tests/testthat/test_dict.R | 41 - collections-0.2.0/collections/tests/testthat/test_ordered_dict.R |only collections-0.2.0/collections/tests/testthat/test_priority_queue.R |only collections-0.2.0/collections/tests/testthat/test_queue.R | 11 collections-0.2.0/collections/tests/testthat/test_stack.R | 11 52 files changed, 1252 insertions(+), 876 deletions(-)
Title: Functional Linear Mixed Models for Irregularly or Sparsely
Sampled Data
Description: Estimation of functional linear mixed models for irregularly or
sparsely sampled data based on functional principal component analysis.
Author: Jona Cederbaum
Maintainer: Jona Cederbaum <Jona.Cederbaum@gmail.com>
Diff between sparseFLMM versions 0.2.2 dated 2018-04-01 and 0.3.0 dated 2019-10-02
DESCRIPTION | 13 MD5 | 6 R/call_all_functions.R | 2224 ++++++++++++++++++++++++------------------------- man/sparseFLMM.Rd | 27 4 files changed, 1135 insertions(+), 1135 deletions(-)
Title: Create Interactive Carousels with the JavaScript 'Slick' Library
Description: Create and customize interactive carousels using
the 'Slick' JavaScript library and the 'htmlwidgets' package. The
carousels can contain plots produced in R, images, 'iframes', videos
and other 'htmlwidgets'. These carousels can be used directly from
the R console, from 'RStudio', in Shiny apps and R Markdown documents.
Author: Jonathan Sidi [aut, cre]
Maintainer: Jonathan Sidi <yonis@metrumrg.com>
Diff between slickR versions 0.2.4 dated 2018-03-06 and 0.4.4 dated 2019-10-02
DESCRIPTION | 35 ++++++----- MD5 | 58 +++++++++++++++--- NAMESPACE | 5 + NEWS.md |only R/getHelp.R | 90 ++++++---------------------- R/nba_player_logo-data.R |only R/nba_team_logo-data.R |only R/slickR.R | 140 ++++++++++++++++++++++++++++++--------------- R/slickpdf.R |only R/style_widget.R | 18 ----- README.md | 15 ++-- build |only data |only inst/doc |only inst/htmlwidgets/slickR.js | 92 ++++++++++++++++++++--------- man/figures |only man/getHelp.Rd | 2 man/nba_player_logo.Rd |only man/nba_team_logo.Rd |only man/slickR.Rd | 75 +++++++++++++++--------- man/slickpdf.Rd |only vignettes |only 22 files changed, 315 insertions(+), 215 deletions(-)
Title: The Complete R6 Probability Distributions Interface
Description: An R6 object oriented distributions package. Unified interface for 42 probability distributions and 11 kernels including functionality for multiple scientific types. Additionally functionality for composite distributions and numerical imputation. Design patterns including wrappers and decorators are described in Gamma et al. (1994, ISBN:0-201-63361-2). For quick reference of probability distributions including d/p/q/r functions and results we refer to McLaughlin, M. P. (2001). Additionally Devroye (1986, ISBN:0-387-96305-7) for sampling the Dirichlet distribution, Gentle (2009) <doi:10.1007/978-0-387-98144-4> for sampling the Multivariate Normal distribution and Michael et al. (1976) <doi:10.2307/2683801> for sampling the Wald distribution.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut],
Peter Ruckdeschel [ctb] (Author of distr),
Matthias Kohl [ctb] (Author of distr),
Shen Chen [ctb],
Jordan Deenichin [ctb],
Chengyang Gao [ctb],
Chloe Zhaoyuan Gu [ctb],
Yunjie He [ctb],
Xiaowen Huang [ctb],
Shuhan Liu [ctb],
Runlong Yu [ctb],
Chijing Zeng [ctb],
Qian Zhou [ctb]
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>
Diff between distr6 versions 1.1.0 dated 2019-08-27 and 1.2.0 dated 2019-10-02
DESCRIPTION | 57 ++--- MD5 | 235 +++++++++++----------- NAMESPACE | 5 NEWS.md | 31 ++ R/Distribution.R | 109 ++++++++-- R/DistributionDecorator_CoreStatistics.R | 6 R/DistributionDecorator_ExoticStatistics.R | 2 R/DistributionDecorator_FunctionImputation.R | 13 - R/Distribution_Kernel.R | 9 R/Distribution_SDistribution.R | 9 R/Kernel_Cosine.R | 2 R/Kernel_Epanechnikov.R | 2 R/Kernel_Logistic.R | 2 R/Kernel_Quartic.R | 2 R/Kernel_Sigmoid.R | 2 R/Kernel_Silverman.R | 2 R/Kernel_Triangular.R | 2 R/Kernel_Tricube.R | 2 R/Kernel_Triweight.R | 2 R/Kernel_Uniform.R | 2 R/RSmisc_helpers.R | 10 R/SDistribution_Arcsine.R | 6 R/SDistribution_Bernoulli.R | 7 R/SDistribution_Beta.R | 13 - R/SDistribution_BetaNoncentral.R |only R/SDistribution_Binomial.R | 6 R/SDistribution_Categorical.R | 6 R/SDistribution_Cauchy.R | 8 R/SDistribution_ChiSquared.R | 12 - R/SDistribution_ChiSquaredNoncentral.R |only R/SDistribution_Degenerate.R | 6 R/SDistribution_Dirichlet.R | 7 R/SDistribution_DiscreteUniform.R | 7 R/SDistribution_Empirical.R | 13 - R/SDistribution_Exponential.R | 6 R/SDistribution_FDistribution.R | 23 +- R/SDistribution_FDistributionNoncentral.R |only R/SDistribution_Frechet.R | 6 R/SDistribution_Gamma.R | 14 - R/SDistribution_Geometric.R | 8 R/SDistribution_Gompertz.R | 7 R/SDistribution_Gumbel.R | 6 R/SDistribution_Hypergeometric.R | 7 R/SDistribution_InverseGamma.R | 5 R/SDistribution_Laplace.R | 6 R/SDistribution_Logarithmic.R | 7 R/SDistribution_Logistic.R | 6 R/SDistribution_Loglogistic.R | 8 R/SDistribution_Lognormal.R | 7 R/SDistribution_Multinomial.R | 7 R/SDistribution_MultivariateNormal.R | 6 R/SDistribution_NegBinomal.R | 7 R/SDistribution_Normal.R | 1 R/SDistribution_Pareto.R | 7 R/SDistribution_Poisson.R | 9 R/SDistribution_Rayleigh.R | 6 R/SDistribution_StudentT.R | 21 + R/SDistribution_StudentTNoncentral.R |only R/SDistribution_Triangular.R | 6 R/SDistribution_Uniform.R | 7 R/SDistribution_Wald.R | 6 R/SDistribution_Weibull.R | 26 +- R/SDistribution_WeightedDiscrete.R |only R/Wrapper.R | 15 + R/Wrapper_Convolution.R | 2 R/Wrapper_HuberizedDistribution.R | 2 R/Wrapper_MixtureDistribution.R | 2 R/Wrapper_ProductDistribution.R | 2 R/Wrapper_TruncatedDistribution.R | 4 R/Wrapper_VectorDistribution.R | 2 R/assertions.R | 45 ++-- R/distr6_globals.R | 7 R/getParameterSet.R | 79 ++++++- R/listDecorators.R | 15 - R/listDistributions.R | 42 --- R/listKernels.R | 27 -- R/listSpecialSets.R | 24 -- R/listWrappers.R | 16 - README.md | 13 - inst/doc/distr6.html | 56 ++--- man/BetaNoncentral.Rd |only man/Cauchy.Rd | 3 man/ChiSquared.Rd | 4 man/ChiSquaredNoncentral.Rd |only man/Distribution.Rd | 21 + man/DistributionWrapper.Rd | 17 + man/Empirical.Rd | 2 man/FDistribution.Rd | 2 man/FDistributionNoncentral.Rd |only man/FunctionImputation.Rd | 7 man/Kernel.Rd | 11 + man/Normal.Rd | 1 man/SDistribution.Rd | 11 + man/StudentT.Rd | 5 man/StudentTNoncentral.Rd |only man/Uniform.Rd | 3 man/Weibull.Rd | 10 man/WeightedDiscrete.Rd |only man/isCdf.Rd |only man/isPdf.Rd |only man/isQuantile.Rd |only man/isRand.Rd |only man/testContinuous.Rd | 11 - man/testDiscrete.Rd | 11 - man/testDistribution.Rd | 11 - man/testDistributionList.Rd | 11 - man/testLeptokurtic.Rd | 11 - man/testMatrixvariate.Rd | 11 - man/testMesokurtic.Rd | 11 - man/testMixture.Rd | 11 - man/testMultivariate.Rd | 11 - man/testNegativeSkew.Rd | 11 - man/testNoSkew.Rd | 10 man/testPlatykurtic.Rd | 11 - man/testPositiveSkew.Rd | 11 - man/testSymmetric.Rd | 11 - man/testUnivariate.Rd | 11 - tests/testthat/test-DistBetaNoncentral.R |only tests/testthat/test-DistChiSquared.R | 86 ++++---- tests/testthat/test-DistChiSquaredNoncentral.R |only tests/testthat/test-DistEmpirical.R | 7 tests/testthat/test-DistFDistributionNoncentral.R |only tests/testthat/test-DistStudentT.R | 2 tests/testthat/test-DistStudentTNoncentral.R |only tests/testthat/test-DistWeibull.R | 14 + tests/testthat/test-DistWeightedDiscrete.R |only tests/testthat/test-Distributions.R | 16 + tests/testthat/test-ParameterSet.R | 3 128 files changed, 1064 insertions(+), 500 deletions(-)