Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between PSCBS versions 0.63.0 dated 2017-06-28 and 0.64.0 dated 2018-08-12
PSCBS-0.63.0/PSCBS/man/append.CBS.Rd |only PSCBS-0.63.0/PSCBS/man/append.PSCBS.Rd |only PSCBS-0.64.0/PSCBS/DESCRIPTION | 7 PSCBS-0.64.0/PSCBS/MD5 | 182 PSCBS-0.64.0/PSCBS/NAMESPACE | 6 PSCBS-0.64.0/PSCBS/NEWS | 28 PSCBS-0.64.0/PSCBS/R/006.fixVarArgs.R | 16 PSCBS-0.64.0/PSCBS/R/999.DEPRECATED.R | 8 PSCBS-0.64.0/PSCBS/R/999.NonDocumentedObjects.R | 6 PSCBS-0.64.0/PSCBS/R/AbstractCBS.HCLUST.R | 498 - PSCBS-0.64.0/PSCBS/R/AbstractCBS.PLOT.R | 33 PSCBS-0.64.0/PSCBS/R/AbstractCBS.PRUNE.R | 487 - PSCBS-0.64.0/PSCBS/R/AbstractCBS.R | 343 - PSCBS-0.64.0/PSCBS/R/AbstractCBS.REPORT.R | 200 PSCBS-0.64.0/PSCBS/R/AbstractCBS.RESTRUCT.R | 287 - PSCBS-0.64.0/PSCBS/R/AbstractCBS.clearCalls.R | 60 PSCBS-0.64.0/PSCBS/R/CBS.CALL.R | 2816 ++++------ PSCBS-0.64.0/PSCBS/R/CBS.EXTS.R | 332 - PSCBS-0.64.0/PSCBS/R/CBS.IO.R | 136 PSCBS-0.64.0/PSCBS/R/CBS.PLOT,many.R | 239 PSCBS-0.64.0/PSCBS/R/CBS.PLOT.R | 367 - PSCBS-0.64.0/PSCBS/R/CBS.PRUNE.R | 175 PSCBS-0.64.0/PSCBS/R/CBS.R | 568 -- PSCBS-0.64.0/PSCBS/R/CBS.RESTRUCT.R | 425 - PSCBS-0.64.0/PSCBS/R/CBS.SMOOTH.R | 48 PSCBS-0.64.0/PSCBS/R/CBS.joinSegments.R | 122 PSCBS-0.64.0/PSCBS/R/CBS.updateMeansTogether.R | 191 PSCBS-0.64.0/PSCBS/R/CNA.EXTS.R | 44 PSCBS-0.64.0/PSCBS/R/DNAcopy.EXTS.R | 524 - PSCBS-0.64.0/PSCBS/R/NonPairedPSCBS.R | 288 - PSCBS-0.64.0/PSCBS/R/PSCBS.IO.R | 82 PSCBS-0.64.0/PSCBS/R/PSCBS.R | 177 PSCBS-0.64.0/PSCBS/R/PSCBS.RESTRUCT.R | 232 PSCBS-0.64.0/PSCBS/R/PSCBS.isLocallyPhased.R | 4 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.BOOT.R | 746 +- PSCBS-0.64.0/PSCBS/R/PairedPSCBS.BOOT.sets.R | 398 - PSCBS-0.64.0/PSCBS/R/PairedPSCBS.CALL.R | 90 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.EXTS.R | 550 - PSCBS-0.64.0/PSCBS/R/PairedPSCBS.EXTS3.R | 181 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.PLOT,many.R | 564 -- PSCBS-0.64.0/PSCBS/R/PairedPSCBS.PLOT.R | 758 +- PSCBS-0.64.0/PSCBS/R/PairedPSCBS.PLOT2.R | 318 - PSCBS-0.64.0/PSCBS/R/PairedPSCBS.PRUNE.R | 10 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.R | 154 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.RESTRUCT.R | 371 - PSCBS-0.64.0/PSCBS/R/PairedPSCBS.applyByRegion.R | 599 +- PSCBS-0.64.0/PSCBS/R/PairedPSCBS.callAB.R | 102 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.callCopyNeutral.R | 368 - PSCBS-0.64.0/PSCBS/R/PairedPSCBS.callGNL.R | 246 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.callLOH.R | 178 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.callROH.R | 90 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.estimateDeltaAB.R | 532 - PSCBS-0.64.0/PSCBS/R/PairedPSCBS.estimateDeltaLOH.R | 160 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.estimateKappa.R | 499 - PSCBS-0.64.0/PSCBS/R/PairedPSCBS.extractSegmentDataByLocus.R | 82 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.unTumorBoost.R | 132 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.updateMeans.R | 192 PSCBS-0.64.0/PSCBS/R/PairedPSCBS.updateMeansTogether.R | 233 PSCBS-0.64.0/PSCBS/R/callSegmentationOutliers.R | 188 PSCBS-0.64.0/PSCBS/R/drawLevels.DNAcopy.R | 20 PSCBS-0.64.0/PSCBS/R/exampleData.R | 19 PSCBS-0.64.0/PSCBS/R/findLargeGaps.R | 77 PSCBS-0.64.0/PSCBS/R/findNeutralCopyNumberState.R | 108 PSCBS-0.64.0/PSCBS/R/gapsToSegments.R | 99 PSCBS-0.64.0/PSCBS/R/installDNAcopy.R | 27 PSCBS-0.64.0/PSCBS/R/prememoize.R | 75 PSCBS-0.64.0/PSCBS/R/randomSeed.R | 2 PSCBS-0.64.0/PSCBS/R/segmentByCBS.R | 797 +- PSCBS-0.64.0/PSCBS/R/segmentByNonPairedPSCBS.R | 191 PSCBS-0.64.0/PSCBS/R/segmentByPairedPSCBS.R | 1022 +-- PSCBS-0.64.0/PSCBS/R/testROH.R | 72 PSCBS-0.64.0/PSCBS/R/utils.R |only PSCBS-0.64.0/PSCBS/R/weightedQuantile.R | 58 PSCBS-0.64.0/PSCBS/R/writeWIG.R | 29 PSCBS-0.64.0/PSCBS/build/vignette.rds |binary PSCBS-0.64.0/PSCBS/inst/doc/CBS.pdf |binary PSCBS-0.64.0/PSCBS/inst/doc/PairedPSCBS.pdf |binary PSCBS-0.64.0/PSCBS/man/CBS.Rd | 2 PSCBS-0.64.0/PSCBS/man/NonPairedPSCBS.Rd | 2 PSCBS-0.64.0/PSCBS/man/PSCBS.Rd | 2 PSCBS-0.64.0/PSCBS/man/PairedPSCBS.Rd | 2 PSCBS-0.64.0/PSCBS/man/append.AbstractCBS.Rd | 2 PSCBS-0.64.0/PSCBS/man/c.CBS.Rd |only PSCBS-0.64.0/PSCBS/man/callOutliers.CBS.Rd | 2 PSCBS-0.64.0/PSCBS/man/pruneByDP.AbstractCBS.Rd | 2 PSCBS-0.64.0/PSCBS/man/pruneByHClust.AbstractCBS.Rd | 2 PSCBS-0.64.0/PSCBS/man/segmentByCBS.Rd | 2 PSCBS-0.64.0/PSCBS/man/segmentByPairedPSCBS.Rd | 8 PSCBS-0.64.0/PSCBS/tests/segmentByCBS,report.R | 2 PSCBS-0.64.0/PSCBS/tests/segmentByCBS,shiftTCN.R | 18 PSCBS-0.64.0/PSCBS/tests/segmentByCBS.R | 2 PSCBS-0.64.0/PSCBS/tests/segmentByPairedPSCBS,report.R | 2 PSCBS-0.64.0/PSCBS/tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R | 36 PSCBS-0.64.0/PSCBS/tests/segmentByPairedPSCBS.R | 4 94 files changed, 8746 insertions(+), 10612 deletions(-)
Title: Simulation of Real and Complex Numbers and Small Programming
Utilities
Description: Simulate real and complex numbers from distributions of their
magnitude and arguments. Optionally, the magnitudes and/or arguments may
be fixed in almost arbitrary ways. Plot density and distribution
functions with automatic selection of suitable regions. Small programming
utilities: check if an object is identical to NA, count positional
arguments in a call, set intersection of more than two sets, check if an
argument is unnamed, compute the graph of S4 classes in packages.
Author: Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between gbutils versions 0.2-1 dated 2017-10-05 and 0.3-0 dated 2018-08-12
gbutils-0.2-1/gbutils/NEWS |only gbutils-0.2-1/gbutils/vignettes/auto |only gbutils-0.3-0/gbutils/DESCRIPTION | 25 +++++++++++++++--------- gbutils-0.3-0/gbutils/MD5 | 21 +++++++++++--------- gbutils-0.3-0/gbutils/NAMESPACE | 3 +- gbutils-0.3-0/gbutils/NEWS.md |only gbutils-0.3-0/gbutils/R/S4utils.R |only gbutils-0.3-0/gbutils/README.md |only gbutils-0.3-0/gbutils/build/partial.rdb |only gbutils-0.3-0/gbutils/build/vignette.rds |binary gbutils-0.3-0/gbutils/inst/doc/Plot_pdf.R | 2 - gbutils-0.3-0/gbutils/inst/doc/Plot_pdf.Rnw | 4 +-- gbutils-0.3-0/gbutils/inst/doc/Plot_pdf.pdf |binary gbutils-0.3-0/gbutils/man/adjacencyOfClasses.Rd |only gbutils-0.3-0/gbutils/vignettes/Plot_pdf.Rnw | 4 +-- 15 files changed, 35 insertions(+), 24 deletions(-)
Title: A Wrapper of the 'JavaScript' Library 'agGrid'
Description: Data objects in 'R' can be rendered as 'HTML' tables using the
'JavaScript' library 'ag-grid' (typically via 'R Markdown' or 'Shiny'). The
'ag-grid' library has been included in this 'R' package. The package name
'RagGrid' is an abbreviation of 'R agGrid'.
Author: Srikkanth M [aut, cre],
Praveen N [aut, ctb]
Maintainer: Srikkanth M <srikkanth18@gmail.com>
Diff between RagGrid versions 0.1.1 dated 2018-06-12 and 0.2.0 dated 2018-08-12
RagGrid-0.1.1/RagGrid/inst/htmlwidgets/lib/aggrid-enterprice |only RagGrid-0.1.1/RagGrid/inst/htmlwidgets/lib/aggrid/aggrid.css |only RagGrid-0.1.1/RagGrid/inst/htmlwidgets/lib/aggrid/aggrid.min.js |only RagGrid-0.1.1/RagGrid/inst/htmlwidgets/lib/aggrid/compiled-icons.css |only RagGrid-0.2.0/RagGrid/DESCRIPTION | 6 - RagGrid-0.2.0/RagGrid/MD5 | 35 +++++----- RagGrid-0.2.0/RagGrid/NEWS.md |only RagGrid-0.2.0/RagGrid/R/RagGrid.R | 14 ++-- RagGrid-0.2.0/RagGrid/README.md | 18 ++--- RagGrid-0.2.0/RagGrid/inst/htmlwidgets/RagGrid.js | 2 RagGrid-0.2.0/RagGrid/inst/htmlwidgets/RagGrid.yaml | 20 +++-- RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/aggrid-enterprise |only RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/aggrid/ag-grid.min.js |only RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/css/ag-theme-balham-dark.css | 9 ++ RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/css/ag-theme-balham.css | 9 ++ RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/css/ag-theme-blue.css | 21 +++--- RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/css/ag-theme-bootstrap.css | 17 +++- RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/css/ag-theme-dark.css | 17 +++- RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/css/ag-theme-fresh.css | 17 +++- RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/css/ag-theme-material.css | 13 ++- RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/jquery |only RagGrid-0.2.0/RagGrid/inst/htmlwidgets/lib/sparkline |only RagGrid-0.2.0/RagGrid/man/aggrid.Rd | 8 +- 23 files changed, 127 insertions(+), 79 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi
platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 0.9.1.10 dated 2018-07-28 and 0.9.2.0 dated 2018-08-12
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/themes.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory models can be estimated with quadrature (EM)
or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modeling
item and person covariates. Finally, latent class models such as the DINA,
DINO, multidimensional latent class, and several other discrete latent
variable models, including mixture and zero-inflated response models,
are supported.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.28 dated 2018-05-19 and 1.29 dated 2018-08-12
DESCRIPTION | 8 +- MD5 | 121 ++++++++++++++++++------------------ NAMESPACE | 4 + NEWS.md | 39 +++++++++++ R/02-item_methods.R | 38 ++++++----- R/03-estimation.R | 57 ++++++++++++---- R/DIF.R | 11 ++- R/DRF.R |only R/DTF.R | 4 - R/Discrete-methods.R | 12 ++- R/EMstep.group.R | 5 - R/EMstep.utils.R | 7 -- R/LoadPars.R | 6 + R/M2.R | 2 R/Mixture-methods.R | 3 R/MultipleGroup-methods.R | 2 R/PrepData.R | 11 +-- R/SIBTEST.R | 28 ++++---- R/SingleGroup-methods.R | 68 +++++++++++++++++++- R/bfactor.R | 2 R/createGroup.R | 2 R/createItem.R | 37 +++++++++-- R/empirical_plot.R | 2 R/extract.mirt.R | 1 R/fscores.R | 2 R/fscores.internal.R | 14 +++- R/itemGAM.R | 2 R/itemfit.R | 2 R/itemplot.R | 2 R/itemplot.internal.R | 2 R/mdirt.R | 95 +++++++++++++++++++--------- R/mirt.R | 26 +++---- R/mirt.model.R | 14 ++++ R/model.elements.R | 33 ++++++++- R/multipleGroup.R | 6 - R/simdata.R | 4 - R/utils.R | 69 +++++++++++++++++--- build/partial.rdb |binary man/DIF.Rd | 2 man/DRF.Rd |only man/DTF.Rd | 3 man/SIBTEST.Rd | 26 ++++--- man/createItem.Rd | 29 +++++++- man/draw_parameters.Rd |only man/empirical_plot.Rd | 2 man/itemGAM.Rd | 3 man/itemplot.Rd | 3 man/mdirt.Rd | 95 +++++++++++++++++++--------- man/mirt.Rd | 26 +++---- man/mirt.model.Rd | 14 ++++ man/multipleGroup.Rd | 6 - man/plot-method.Rd | 4 - man/thetaComb.Rd |only man/traditional2mirt.Rd |only src/dpars.cpp | 16 ++-- src/traceLinePts.cpp | 16 ++-- src/traceLinePts.h | 4 - tests/tests/test-01-mirtOne.R | 6 + tests/tests/test-04-multipleGroup.R | 79 ++++++++++------------- tests/tests/test-07-mixedmirt.R | 4 - tests/tests/test-10-extras.R | 12 +-- tests/tests/test-11-discrete.R | 27 +++----- tests/tests/test-14-GGUM.R | 42 ++++++------ tests/tests/test-16-DCIRT.R | 36 +++++----- 64 files changed, 788 insertions(+), 408 deletions(-)
Title: Pipe-Style Interface for 'data.table'
Description: Package provides pipe-style interface for 'data.table'. It preserves all
'data.table' features without significant impact on performance. 'let'
and 'take' functions are simplified interfaces for most common data manipulation
tasks. For example, you can write 'mtcars %>% take(mean(mpg), by = am)' for
aggregation or 'mtcars %>% let(hp_wt = hp/wt, hp_wt_mpg = hp_wt/mpg)' for modification.
Use 'take_if/let_if' for conditional aggregation/modification. 'query_if' function
translates its arguments one-to-one to '[.data.table' method. Additionally there are
some conveniences such as automatic 'data.frame' conversion to 'data.table'.
Author: Gregory Demin [aut, cre]
Maintainer: Gregory Demin <gdemin@gmail.com>
Diff between maditr versions 0.5.2 dated 2018-07-18 and 0.6.0 dated 2018-08-12
DESCRIPTION | 8 MD5 | 19 - NAMESPACE | 6 NEWS | 4 R/join.R |only inst/doc/Introduction.R | 57 +++ inst/doc/Introduction.Rmd | 549 ++++++++++++++++++--------------- inst/doc/Introduction.html | 748 +++++++++++++++++++-------------------------- man/dt_left_join.Rd |only tests/testthat.R | 4 tests/testthat/test_join.R |only vignettes/Introduction.Rmd | 549 ++++++++++++++++++--------------- 12 files changed, 1005 insertions(+), 939 deletions(-)
Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives,
t-tests, ANOVAs, regression, correlation matrices, proportion tests,
contingency tables, and factor analysis. This package is also useable from
the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
information).
Author: Ravi Selker, Jonathon Love, Damian Dropmann
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmv versions 0.8.6.2 dated 2018-04-06 and 0.9.2.0 dated 2018-08-12
DESCRIPTION | 12 - MD5 | 80 ++++---- NAMESPACE | 1 R/ancova.h.R | 22 +- R/anova.h.R | 18 + R/anovanp.h.R | 17 + R/anovarm.b.R | 403 ++++++++++++++++++----------------------- R/anovarm.h.R | 263 +++++++++++++++----------- R/anovarmnp.h.R | 9 R/cfa.b.R | 5 R/cfa.h.R | 8 R/conttables.h.R | 24 +- R/conttablespaired.h.R | 19 + R/corrmatrix.b.R | 2 R/corrmatrix.h.R | 11 - R/descriptives.b.R | 139 ++++++++++++-- R/descriptives.h.R | 42 +++- R/efa.h.R | 9 R/linreg.h.R | 20 +- R/loglinear.h.R | 15 - R/logregbin.h.R | 20 +- R/logregmulti.h.R | 20 +- R/logregord.b.R |only R/logregord.h.R |only R/mancova.h.R | 18 + R/pca.h.R | 9 R/proptest2.h.R | 9 R/proptestn.h.R | 14 - R/reliability.h.R | 10 - R/ttestis.b.R | 62 +++++- R/ttestis.h.R | 66 +++++- R/ttestones.b.R | 53 +++-- R/ttestones.h.R | 128 ++++++++----- R/ttestps.b.R | 42 +++- R/ttestps.h.R | 55 ++++- man/anovaRM.Rd | 38 ++- man/descriptives.Rd | 12 - man/logRegOrd.Rd |only man/ttestIS.Rd | 10 - man/ttestOneS.Rd | 17 + man/ttestPS.Rd | 5 tests/testthat/testlogregord.R |only tests/testthat/testttestones.R | 4 43 files changed, 1097 insertions(+), 614 deletions(-)