Title: Ordinary Differential Equation (ODE) Solvers Written in R Using
S4 Classes
Description: Show physics, math and engineering students how an ODE solver
is made and how effective R classes can be for the construction of
the equations that describe natural phenomena. Inspiration for this work
comes from the book on "Computer Simulations in Physics"
by Harvey Gould, Jan Tobochnik, and Wolfgang Christian.
Book link: <http://www.compadre.org/osp/items/detail.cfm?ID=7375>.
Author: Alfonso R. Reyes [aut, cre]
Maintainer: Alfonso R. Reyes <alfonso.reyes@oilgainsanalytics.com>
Diff between rODE versions 0.99.5 dated 2017-07-13 and 0.99.6 dated 2017-11-09
rODE-0.99.5/rODE/man/AbstractODESolver-ODE-method.Rd |only rODE-0.99.5/rODE/man/AbstractODESolver-missing-method.Rd |only rODE-0.99.5/rODE/man/DormandPrince45.Rd |only rODE-0.99.5/rODE/man/EulerRichardson-ODE-method.Rd |only rODE-0.99.5/rODE/man/createODESolver-method.Rd |only rODE-0.99.5/rODE/man/rODE.Rd |only rODE-0.99.5/rODE/man/setState.Rd |only rODE-0.99.6/rODE/DESCRIPTION | 17 rODE-0.99.6/rODE/MD5 | 289 ++++--- rODE-0.99.6/rODE/NAMESPACE | 9 rODE-0.99.6/rODE/R/AbstractODESolver.R | 102 ++ rODE-0.99.6/rODE/R/DormandPrince45.R | 122 ++- rODE-0.99.6/rODE/R/Euler.R | 62 + rODE-0.99.6/rODE/R/EulerRichardson.R | 72 + rODE-0.99.6/rODE/R/ODE.R | 36 rODE-0.99.6/rODE/R/ODEAdaptiveSolver.R | 71 + rODE-0.99.6/rODE/R/ODESolver.R | 42 - rODE-0.99.6/rODE/R/ODESolverFactory.R | 31 rODE-0.99.6/rODE/R/RK4.R | 34 rODE-0.99.6/rODE/R/RK45.R | 6 rODE-0.99.6/rODE/R/Verlet.R | 26 rODE-0.99.6/rODE/R/ode_generics.R | 193 ++--- rODE-0.99.6/rODE/R/rODE-package.r | 5 rODE-0.99.6/rODE/R/utils.R | 23 rODE-0.99.6/rODE/README.md | 157 ++-- rODE-0.99.6/rODE/build/vignette.rds |binary rODE-0.99.6/rODE/demo |only rODE-0.99.6/rODE/inst/doc/Comparison.R | 88 +- rODE-0.99.6/rODE/inst/doc/Comparison.Rmd | 108 ++ rODE-0.99.6/rODE/inst/doc/Comparison.html | 442 ++++++------ rODE-0.99.6/rODE/inst/doc/ErrorEuler.R |only rODE-0.99.6/rODE/inst/doc/ErrorEuler.Rmd |only rODE-0.99.6/rODE/inst/doc/ErrorEuler.html |only rODE-0.99.6/rODE/inst/doc/FallingParticle.R | 183 ++-- rODE-0.99.6/rODE/inst/doc/FallingParticle.Rmd | 39 - rODE-0.99.6/rODE/inst/doc/FallingParticle.html | 102 +- rODE-0.99.6/rODE/inst/doc/Kepler.R | 8 rODE-0.99.6/rODE/inst/doc/Kepler.Rmd | 14 rODE-0.99.6/rODE/inst/doc/Kepler.html | 93 +- rODE-0.99.6/rODE/inst/doc/Muskat-MBal.R |only rODE-0.99.6/rODE/inst/doc/Muskat-MBal.Rmd |only rODE-0.99.6/rODE/inst/doc/Muskat-MBal.html |only rODE-0.99.6/rODE/inst/doc/Pendulum.R | 5 rODE-0.99.6/rODE/inst/doc/Pendulum.Rmd | 10 rODE-0.99.6/rODE/inst/doc/Pendulum.html | 120 +-- rODE-0.99.6/rODE/inst/doc/Planet.R | 11 rODE-0.99.6/rODE/inst/doc/Planet.Rmd | 22 rODE-0.99.6/rODE/inst/doc/Planet.html | 125 +-- rODE-0.99.6/rODE/inst/doc/Projectile.R | 10 rODE-0.99.6/rODE/inst/doc/Projectile.Rmd | 18 rODE-0.99.6/rODE/inst/doc/Projectile.html | 130 +-- rODE-0.99.6/rODE/inst/doc/Reaction.R | 49 - rODE-0.99.6/rODE/inst/doc/Reaction.Rmd | 55 - rODE-0.99.6/rODE/inst/doc/Reaction.html | 95 +- rODE-0.99.6/rODE/inst/doc/rODE_biblio.bib |only rODE-0.99.6/rODE/inst/examples/AdaptiveStepApp.R | 13 rODE-0.99.6/rODE/inst/examples/ComparisonRK45App.R | 28 rODE-0.99.6/rODE/inst/examples/ComparisonRK45ODEApp.R | 44 - rODE-0.99.6/rODE/inst/examples/FallingParticleODEApp.R | 12 rODE-0.99.6/rODE/inst/examples/KeplerApp.R | 17 rODE-0.99.6/rODE/inst/examples/KeplerDormandPrince45.R | 35 rODE-0.99.6/rODE/inst/examples/KeplerDormandPrince45App.R | 39 - rODE-0.99.6/rODE/inst/examples/KeplerEnergy.R | 8 rODE-0.99.6/rODE/inst/examples/KeplerEnergyApp.R | 27 rODE-0.99.6/rODE/inst/examples/KeplerEuler.R | 10 rODE-0.99.6/rODE/inst/examples/KeplerEulerApp.R | 16 rODE-0.99.6/rODE/inst/examples/Logistic.R | 21 rODE-0.99.6/rODE/inst/examples/LogisticApp.R | 25 rODE-0.99.6/rODE/inst/examples/ODETest.R | 13 rODE-0.99.6/rODE/inst/examples/PendulumApp.R | 11 rODE-0.99.6/rODE/inst/examples/PendulumEulerApp.R | 9 rODE-0.99.6/rODE/inst/examples/PendulumRK4App.R | 17 rODE-0.99.6/rODE/inst/examples/PlanetApp.R | 12 rODE-0.99.6/rODE/inst/examples/ProjectileApp.R | 16 rODE-0.99.6/rODE/inst/examples/ReactionApp.R | 11 rODE-0.99.6/rODE/inst/examples/RigidBodyNXFApp.R | 14 rODE-0.99.6/rODE/inst/examples/SHOApp.R | 25 rODE-0.99.6/rODE/inst/examples/SpringRK4App.R | 11 rODE-0.99.6/rODE/inst/examples/VanderpolApp.R | 12 rODE-0.99.6/rODE/inst/examples/VanderpolMuTimeControlApp.R | 12 rODE-0.99.6/rODE/inst/notebooks/Comparison_Muskat.Rmd |only rODE-0.99.6/rODE/inst/notebooks/Comparison_Muskat.html |only rODE-0.99.6/rODE/inst/notebooks/Comparison_naode.R |only rODE-0.99.6/rODE/inst/notebooks/Comparison_naode.Rmd |only rODE-0.99.6/rODE/inst/notebooks/Comparison_naode.html |only rODE-0.99.6/rODE/inst/notebooks/Muskat-MBal_1to5.Rmd |only rODE-0.99.6/rODE/inst/notebooks/latex_for_Muskat-MBal.Rmd |only rODE-0.99.6/rODE/inst/notebooks/latex_for_Muskat-MBal.html |only rODE-0.99.6/rODE/inst/test_examples/run_test_applications.R | 97 +- rODE-0.99.6/rODE/man/AbstractODESolver-class.Rd | 42 + rODE-0.99.6/rODE/man/DormandPrince45-class.Rd | 168 +++- rODE-0.99.6/rODE/man/Euler-class.Rd | 94 +- rODE-0.99.6/rODE/man/EulerRichardson-class.Rd | 38 - rODE-0.99.6/rODE/man/ODE-class.Rd | 120 ++- rODE-0.99.6/rODE/man/ODEAdaptiveSolver-class.Rd |only rODE-0.99.6/rODE/man/ODESolver-class.Rd | 31 rODE-0.99.6/rODE/man/ODESolverFactory-class.Rd | 79 +- rODE-0.99.6/rODE/man/RK4-class.Rd | 52 - rODE-0.99.6/rODE/man/RK45-class.Rd | 49 - rODE-0.99.6/rODE/man/Verlet-class.Rd | 211 +++-- rODE-0.99.6/rODE/man/doStep-method.Rd | 39 - rODE-0.99.6/rODE/man/enableRuntimeExceptions-method.Rd |only rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-10-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-11-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-12-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-13-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-14-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-15-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-16-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-17-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-18-1.png |only rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-19-1.png |only rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-3-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-4-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-5-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-6-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-7-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-8-1.png |binary rODE-0.99.6/rODE/man/figures/README-unnamed-chunk-9-1.png |binary rODE-0.99.6/rODE/man/getEnergy-method.Rd | 10 rODE-0.99.6/rODE/man/getErrorCode-method.Rd | 16 rODE-0.99.6/rODE/man/getExactSolution-method.Rd | 43 - rODE-0.99.6/rODE/man/getODE-method.Rd |only rODE-0.99.6/rODE/man/getRate-method.Rd | 88 -- rODE-0.99.6/rODE/man/getRateCounter-method.Rd |only rODE-0.99.6/rODE/man/getRateCounts-method.Rd | 2 rODE-0.99.6/rODE/man/getState-method.Rd | 31 rODE-0.99.6/rODE/man/getStepSize-method.Rd | 61 - rODE-0.99.6/rODE/man/getTime-method.Rd | 35 rODE-0.99.6/rODE/man/getTolerance-method.Rd | 16 rODE-0.99.6/rODE/man/importFromExamples.Rd | 2 rODE-0.99.6/rODE/man/init-method.Rd | 39 - rODE-0.99.6/rODE/man/rODE-package.Rd |only rODE-0.99.6/rODE/man/run_test_applications.Rd | 2 rODE-0.99.6/rODE/man/setSolver-method.Rd |only rODE-0.99.6/rODE/man/setState-method.Rd |only rODE-0.99.6/rODE/man/setStepSize-method.Rd | 70 - rODE-0.99.6/rODE/man/setTolerance-method.Rd | 162 +--- rODE-0.99.6/rODE/man/showMethods2.Rd | 4 rODE-0.99.6/rODE/man/step-method.Rd | 41 - rODE-0.99.6/rODE/tests/testthat/test_AbstractODESolver.R | 6 rODE-0.99.6/rODE/tests/testthat/test_ODEAdaptiveSolver.R | 4 rODE-0.99.6/rODE/tests/testthat/test_ODESolver.R | 2 rODE-0.99.6/rODE/tests/testthat/test_Verlet.R | 1 rODE-0.99.6/rODE/tests/testthat/test_utils.R | 23 rODE-0.99.6/rODE/vignettes/Comparison.Rmd | 108 ++ rODE-0.99.6/rODE/vignettes/ErrorEuler.Rmd |only rODE-0.99.6/rODE/vignettes/FallingParticle.Rmd | 39 - rODE-0.99.6/rODE/vignettes/Kepler.Rmd | 14 rODE-0.99.6/rODE/vignettes/Muskat-MBal.Rmd |only rODE-0.99.6/rODE/vignettes/Pendulum.Rmd | 10 rODE-0.99.6/rODE/vignettes/Planet.Rmd | 22 rODE-0.99.6/rODE/vignettes/Projectile.Rmd | 18 rODE-0.99.6/rODE/vignettes/Reaction.Rmd | 55 - 154 files changed, 3214 insertions(+), 2212 deletions(-)
Title: A Non-Parametric Statistical Test to Compare Clustering
Structures
Description: Provides ANOCVA (ANalysis Of Cluster VAriability), a non-parametric statistical test
to compare clustering structures with applications in functional magnetic resonance imaging
data (fMRI). The ANOCVA allows us to compare the clustering structure of multiple groups
simultaneously and also to identify features that contribute to the differential clustering.
Author: Maciel C. Vidal [aut, cre], Andre Fujita [aut]
Maintainer: Maciel C. Vidal <calebe@ime.usp.br>
Diff between anocva versions 0.1.0 dated 2016-12-28 and 0.1.1 dated 2017-11-09
DESCRIPTION | 8 +-- MD5 | 30 +++++------ R/anocva.R | 101 ++++++++++++++++++++++---------------- R/anocvaStats.R | 22 ++++---- R/nClust.R | 108 ++++++++++++++++++++++++----------------- R/spectralClustering.R | 49 +++++++++++------- man/anocva.Rd | 88 +++++++++++++++++++-------------- man/anocvaStats.Rd | 9 +++ man/checkClusteringFunction.Rd | 1 man/checkNClust.Rd | 1 man/checkRange01.Rd | 1 man/nClust.Rd | 33 +++++++----- man/nClustMulti.Rd | 43 +++++++++------- man/optimalSilhouette.Rd | 5 + man/optimalSlope.Rd | 5 + man/spectralClustering.Rd | 37 ++++++++------ 16 files changed, 316 insertions(+), 225 deletions(-)
Title: Genetic Simulation Engine
Description: A shiny interface and supporting tools to guide users in choosing
appropriate simulations, setting parameters, calculating summary genetic
statistics, and organizing data output, all within the R environment. In
addition to supporting existing forward and reverse-time simulators, new
simulators can be integrated into the environment relatively easily.
Author: Eric Archer [aut],
Michelle DePrenger-Levin [aut],
Sean Hoban [aut],
Libby Liggins [aut],
Christian Parobek [aut],
Allan Strand [aut, cre]
Maintainer: Allan Strand <stranda@gmail.com>
Diff between skeleSim versions 0.9.5 dated 2016-09-14 and 0.9.7 dated 2017-11-09
DESCRIPTION | 10 MD5 | 26 - R/analysis.funcs.R | 4 R/fsc.run.R | 6 R/runSim.R | 4 README.md | 17 + build/vignette.rds |binary inst/doc/Forecasting.html | 352 ++++++++++++++++++++------- inst/doc/Installing.html | 273 +++++++++++++++----- inst/doc/SampleSize.Rmd | 2 inst/doc/SampleSize.html | 307 +++++++++++++++++------ inst/doc/Simulating.html | 352 +++++++++++++++++++-------- inst/shiny/skeleSimShinyGUI/simcoal-server.R | 8 vignettes/SampleSize.Rmd | 2 14 files changed, 1006 insertions(+), 357 deletions(-)
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.0.4 dated 2017-10-08 and 1.0.5 dated 2017-11-09
sjlabelled-1.0.4/sjlabelled/R/S3-methods.R |only sjlabelled-1.0.5/sjlabelled/DESCRIPTION | 15 sjlabelled-1.0.5/sjlabelled/MD5 | 21 sjlabelled-1.0.5/sjlabelled/NAMESPACE | 7 sjlabelled-1.0.5/sjlabelled/NEWS.md | 15 sjlabelled-1.0.5/sjlabelled/R/as_factor.R |only sjlabelled-1.0.5/sjlabelled/R/as_labelled.R | 220 ++---- sjlabelled-1.0.5/sjlabelled/R/get_model_labels.R | 412 ++++++------- sjlabelled-1.0.5/sjlabelled/R/lbl_df.R |only sjlabelled-1.0.5/sjlabelled/inst/doc/intro_sjlabelled.html | 56 - sjlabelled-1.0.5/sjlabelled/inst/doc/labelleddata.html | 4 sjlabelled-1.0.5/sjlabelled/man/as_factor.Rd |only sjlabelled-1.0.5/sjlabelled/man/lbl_df.Rd | 11 sjlabelled-1.0.5/sjlabelled/man/type_sum.Rd |only 14 files changed, 375 insertions(+), 386 deletions(-)
Title: Gene-Based Association Analysis for Complex Traits
Description: Gene based association test between a group of SNPs and traits
including familial (both continuous and binary) traits, multivariate
continuous (both independent and familial) traits and longitudinal
continuous traits. Part of methods were previously published in Maity et al
(2012) <doi:10.1002/gepi.21663>, Chen et al (2013)
<doi:10.1002/gepi.21703>, Yan et al (2015) <doi:10.1159/000375409>, Yan et
al (2015) <doi:10.1534/genetics.115.178590> and Yan et al (2015)
<doi:10.1159/000445057>.
Author: Qi Yan
Maintainer: Qi Yan <qiy17@pitt.edu>
Diff between KMgene versions 1.0 dated 2017-09-26 and 1.1 dated 2017-11-09
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- R/FKMO_Null_Model.R | 21 +++++++++++++-------- R/FKM_Null_Model.R | 19 +++++++++++++------ R/FbKMO_Null_Model.R | 24 ++++++++++++++++++------ R/FbKM_Null_Model.R | 24 ++++++++++++++++++------ R/MFKM.R | 13 +++++++++++-- R/MFKMO_Null_Model.R | 32 ++++++++++++++++++++++++++++++-- R/MFKM_Null_Model.R | 32 ++++++++++++++++++++++++++++++-- man/FKMO_Null_Model.Rd | 4 ++-- man/FKM_Null_Model.Rd | 4 ++-- man/FbKMO_Null_Model.Rd | 4 ++-- man/FbKM_Null_Model.Rd | 4 ++-- man/MFKM.Rd | 9 +++++++++ man/MFKMO_Null_Model.Rd | 4 ++-- man/MFKM_Null_Model.Rd | 4 ++-- 16 files changed, 172 insertions(+), 62 deletions(-)
Title: Diffs for R Objects
Description: Generate a colorized diff of two R objects for an intuitive
visualization of their differences.
Author: Brodie Gaslam [aut, cre],
Michael B. Allen [ctb, cph] (Original C implementation of Myers Diff
Algorithm)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between diffobj versions 0.1.6 dated 2016-11-15 and 0.1.7 dated 2017-11-09
DESCRIPTION | 10 - MD5 | 192 ++++++++++++++++----------------- NEWS.md | 20 +++ R/capt.R | 39 ++++-- R/check.R | 2 R/core.R | 4 R/diff.R | 2 R/finalizer.R | 2 R/get.R | 2 R/guides.R | 88 +++++++++------ R/html.R | 2 R/hunks.R | 8 - R/layout.R | 2 R/misc.R | 2 R/myerssimple.R | 2 R/pager.R | 2 R/rdiff.R | 7 - R/rds.R | 14 +- R/s4.R | 36 ++++-- R/set.R | 2 R/styles.R | 105 +++++++++++++++--- R/subset.R | 2 R/summmary.R | 2 R/system.R | 2 R/text.R | 28 +--- R/tochar.R | 2 R/trim.R | 14 +- R/word.R | 2 README.md | 36 ++++-- build/vignette.rds |binary inst/COPYRIGHTS | 8 - inst/doc/diffobj.Rmd | 9 - inst/doc/diffobj.html | 16 -- inst/doc/metacomp.Rmd | 2 inst/doc/metacomp.html | 6 - man/AlignThreshold-class.Rd | 4 man/Diff-class.Rd | 1 man/Extract_PaletteOfStyles.Rd | 3 man/Pager.Rd | 15 +- man/PaletteOfStyles-class.Rd | 4 man/Rdiff_chr.Rd | 1 man/Style.Rd | 63 +++++++--- man/StyleFuns.Rd | 3 man/StyleSummary.Rd | 4 man/StyleText.Rd | 3 man/any-Diff-method.Rd | 1 man/as.character-DiffSummary-method.Rd | 1 man/as.character-MyersMbaSes-method.Rd | 1 man/auto_context.Rd | 1 man/console_lines.Rd | 1 man/diffChr.Rd | 1 man/diffCsv.Rd | 1 man/diffDeparse.Rd | 1 man/diffFile.Rd | 1 man/diffObj.Rd | 1 man/diffPrint.Rd | 1 man/diffStr.Rd | 1 man/diff_myers.Rd | 1 man/diffobj-package.Rd | 1 man/diffobj_s4method_doc.Rd | 3 man/diffobj_set_def_opts.Rd | 1 man/dimnames-PaletteOfStyles-method.Rd | 1 man/extract-Diff-method.Rd | 1 man/finalizeHtml.Rd | 1 man/gdo.Rd | 1 man/guides.Rd | 16 +- man/has_Rdiff.Rd | 6 - man/make_blocking.Rd | 1 man/nchar_html.Rd | 1 man/pager_is_less.Rd | 1 man/par_frame.Rd | 1 man/ses.Rd | 1 man/show-DiffSummary-method.Rd | 1 man/show-PaletteOfStyles-method.Rd | 1 man/show-Style-method.Rd | 1 man/strip_hz_control.Rd | 1 man/summary-Diff-method.Rd | 1 man/summary-MyersMbaSes-method.Rd | 1 man/summary-PaletteOfStyles-method.Rd | 1 man/tag_f.Rd | 8 - man/trim.Rd | 16 +- man/view_or_browse.Rd | 1 man/webfiles.Rd | 4 src/diff.c | 47 +++++++- src/diff.h | 2 src/diffobj.c | 2 src/diffobj.h | 2 src/init.c | 4 tests/testthat/testthat.diffObj.R | 8 + tests/testthat/testthat.diffPrint.R | 26 ++++ tests/testthat/testthat.diffStr.R | 13 ++ tests/testthat/testthat.guide.R | 67 ++++++++++- tests/testthat/testthat.pager.R | 5 tests/testthat/testthat.rrdiff.R | 10 - tests/testthat/testthat.trim.R | 7 + vignettes/diffobj.Rmd | 9 - vignettes/metacomp.Rmd | 2 97 files changed, 662 insertions(+), 400 deletions(-)
Title: AMCE Estimator for Conjoint Experiments
Description: An R implementation of the Average Marginal Component-specific
Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto
T. (2014) <DOI:10.1093/pan/mpt024> Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional
Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
Author: Soubhik Barari, Elissa Berwick, Jens Hainmueller, Daniel Hopkins, Sean Liu, Anton Strezhnev, Teppei Yamamoto
Maintainer: Anton Strezhnev <astrezhnev@fas.harvard.edu>
Diff between cjoint versions 2.0.5 dated 2017-08-03 and 2.0.6 dated 2017-11-09
DESCRIPTION | 10 MD5 | 12 NAMESPACE | 2 R/cjoint.R | 1364 ++++++++++++++++++++++++++++----------------- man/conjoint_data.Rd |only man/plot.amce.Rd | 20 man/read.qualtrics.Rd | 2 man/read.with.qualtRics.Rd |only 8 files changed, 900 insertions(+), 510 deletions(-)
Title: Simulation of Correlated Data with Multiple Variable Types
Description: Generate continuous (normal or non-normal), binary, ordinal, and count (Poisson or Negative
Binomial) variables with a specified correlation matrix. It can also produce a single continuous
variable. This package can be used to simulate data sets that mimic real-world situations (i.e.
clinical or genetic data sets, plasmodes). All variables are generated from standard normal
variables with an imposed intermediate correlation matrix. Continuous variables are simulated
by specifying mean, variance, skewness, standardized kurtosis, and fifth and sixth standardized
cumulants using either Fleishman's third-order (<DOI:10.1007/BF02293811>) or Headrick's
fifth-order (<DOI:10.1016/S0167-9473(02)00072-5>) polynomial transformation. Binary and
ordinal variables are simulated using a modification of GenOrd's ordsample function. Count
variables are simulated using the inverse cdf method. There are two simulation pathways
which differ primarily according to the calculation of the intermediate correlation matrix. In
Correlation Method 1, the intercorrelations involving count variables are determined using a
simulation based, logarithmic correlation correction (adapting Yahav and Shmueli's 2012 method,
<DOI:10.1002/asmb.901>). In Correlation Method 2, the count variables are treated as ordinal
(adapting Barbiero and Ferrari's 2015 modification of GenOrd, <DOI:10.1002/asmb.2072>).
There is an optional error loop that corrects the final correlation matrix to be within a
user-specified precision value of the target matrix. The package also includes functions to
calculate standardized cumulants for theoretical distributions or from real data sets, check
if a target correlation matrix is within the possible correlation bounds (given the distributions
of the simulated variables), summarize results (numerically or graphically), to verify valid power
method pdfs, and to calculate lower standardized kurtosis bounds.
Author: Allison Cynthia Fialkowski
Maintainer: Allison Cynthia Fialkowski <allijazz@uab.edu>
Diff between SimMultiCorrData versions 0.2.0 dated 2017-10-25 and 0.2.1 dated 2017-11-09
DESCRIPTION | 8 +++--- MD5 | 56 +++++++++++++++++++++---------------------- NEWS.md | 7 +++++ R/calc_lower_skurt.R | 6 +++- R/calc_theory.R | 2 - R/error_vars.R | 1 R/find_constants.R | 5 ++- R/nonnormvar1.R | 13 ++++++--- R/plot_cdf.R | 7 +++-- R/plot_pdf_theory.R | 4 +-- R/plot_sim_pdf_theory.R | 4 +-- R/plot_sim_theory.R | 13 ++++++--- R/rcorrvar.R | 21 +++++++++++----- R/rcorrvar2.R | 21 +++++++++++----- R/valid_corr.R | 14 ++++++---- R/valid_corr2.R | 14 ++++++---- build/partial.rdb |binary inst/doc/benefits.html | 4 +-- inst/doc/dist_comp.html | 6 ++-- inst/doc/errorloop.Rmd | 2 - inst/doc/errorloop.html | 6 ++-- inst/doc/functions.html | 4 +-- inst/doc/method_comp.html | 4 +-- inst/doc/sixth_validpdf.html | 8 +++--- inst/doc/variable_types.html | 4 +-- inst/doc/workflow.html | 26 +++++++++---------- man/plot_cdf.Rd | 6 +++- man/plot_sim_theory.Rd | 6 +++- vignettes/errorloop.Rmd | 2 - 29 files changed, 163 insertions(+), 111 deletions(-)
More information about SimMultiCorrData at CRAN
Permanent link
Title: ROC for Cross Validation Results
Description: Cross validate large genetic data while specifying clinical variables that should always be in the model using the function cv(). An ROC plot from the cross validation data with AUC can be obtained using rocplot(), which also can be used to compare different models. Framework was built to handle genetic data, but works for any data.
Author: Ben Sherwood [aut, cre]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>
Diff between roccv versions 1.0 dated 2016-06-29 and 1.1 dated 2017-11-09
DESCRIPTION | 12 ++++++------ LICENSE | 2 +- MD5 | 16 ++++++++-------- NEWS | 8 ++++++++ R/mainFunctions.R | 10 +++++----- man/cv.Rd | 2 +- man/fit_pred_fold.Rd | 2 +- man/randomly_assign.Rd | 2 +- man/rocplot.Rd | 5 +++-- 9 files changed, 34 insertions(+), 25 deletions(-)
Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least
Squares. The methods include filter methods, wrapper methods and embedded
methods. Both regression and classification is supported.
Author: Kristian Hovde Liland, Tahir Mehmood, Solve Sæbø
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between plsVarSel versions 0.9.1 dated 2016-10-12 and 0.9.2 dated 2017-11-09
DESCRIPTION | 10 +++++----- MD5 | 47 ++++++++++++++++++++++++----------------------- NEWS |only R/GA.R | 2 +- R/filters.R | 19 ++++++++++--------- inst/CITATION | 4 ++-- man/VIP.Rd | 13 ++++++++----- man/bve_pls.Rd | 7 +++---- man/filterPLSR.Rd | 7 +++---- man/ga_pls.Rd | 9 ++++----- man/ipw_pls.Rd | 7 +++---- man/lda_from_pls.Rd | 1 - man/lda_from_pls_cv.Rd | 1 - man/mcuve_pls.Rd | 7 +++---- man/mvrV.Rd | 1 - man/myImagePlot.Rd | 7 +++---- man/plsVarSel.Rd | 1 - man/rep_pls.Rd | 7 +++---- man/setDA.Rd | 1 - man/shaving.Rd | 9 ++++----- man/simulate_classes.Rd | 7 +++---- man/spa_pls.Rd | 7 +++---- man/stpls.Rd | 7 +++---- man/summary.mvrV.Rd | 1 - man/truncation.Rd | 7 +++---- 25 files changed, 88 insertions(+), 101 deletions(-)
Title: R Client for the 'Civis data science API'
Description: A set of tools around common workflows and a convenient interface to make
requests directly to the 'Civis data science API' <https://www.civisanalytics.com/platform/>.
Author: Patrick Miller [cre, aut],
Keith Ingersoll [aut],
Bill Lattner [ctb],
Anh Le [ctb],
Michelangelo D'Agostino [ctb],
Sam Weiss [ctb],
Danning Chen [ctb]
Maintainer: Patrick Miller <pmiller@civisanalytics.com>
Diff between civis versions 1.0.2 dated 2017-09-21 and 1.1.0 dated 2017-11-09
civis-1.0.2/civis/man/scripts_patch_containers_runs.Rd |only civis-1.0.2/civis/man/scripts_post_containers_runs_heartbeats.Rd |only civis-1.0.2/civis/man/scripts_post_containers_runs_logs.Rd |only civis-1.0.2/civis/man/users_patch.Rd |only civis-1.0.2/civis/man/users_post.Rd |only civis-1.1.0/civis/DESCRIPTION | 25 civis-1.1.0/civis/MD5 | 364 civis-1.1.0/civis/NAMESPACE | 213 civis-1.1.0/civis/R/civis_future.R |only civis-1.1.0/civis/R/civis_ml.R | 164 civis-1.1.0/civis/R/civis_ml_plot.R | 2 civis-1.1.0/civis/R/civis_ml_utils.R | 75 civis-1.1.0/civis/R/client_base.R | 22 civis-1.1.0/civis/R/generate_client.R | 12 civis-1.1.0/civis/R/generated_client.R | 8910 +++++++++- civis-1.1.0/civis/R/io.R | 191 civis-1.1.0/civis/R/reports.R | 67 civis-1.1.0/civis/R/rstudio.R |only civis-1.1.0/civis/R/sysdata.rda |binary civis-1.1.0/civis/R/zzz.R | 26 civis-1.1.0/civis/build/vignette.rds |binary civis-1.1.0/civis/inst/rstudio |only civis-1.1.0/civis/inst/scripts |only civis-1.1.0/civis/man/CIVIS_ML_CLASSIFIERS.Rd | 2 civis-1.1.0/civis/man/CIVIS_ML_REGRESSORS.Rd | 2 civis-1.1.0/civis/man/CivisFuture.Rd |only civis-1.1.0/civis/man/announcements_list.Rd |only civis-1.1.0/civis/man/apps_delete_instances_projects.Rd |only civis-1.1.0/civis/man/apps_delete_instances_shares_groups.Rd |only civis-1.1.0/civis/man/apps_delete_instances_shares_users.Rd |only civis-1.1.0/civis/man/apps_get.Rd |only civis-1.1.0/civis/man/apps_get_instances.Rd |only civis-1.1.0/civis/man/apps_list.Rd |only civis-1.1.0/civis/man/apps_list_instances.Rd |only civis-1.1.0/civis/man/apps_list_instances_projects.Rd |only civis-1.1.0/civis/man/apps_list_instances_shares.Rd |only civis-1.1.0/civis/man/apps_patch_instances.Rd |only civis-1.1.0/civis/man/apps_post_instances.Rd |only civis-1.1.0/civis/man/apps_put_instances_archive.Rd |only civis-1.1.0/civis/man/apps_put_instances_projects.Rd |only civis-1.1.0/civis/man/apps_put_instances_shares_groups.Rd |only civis-1.1.0/civis/man/apps_put_instances_shares_users.Rd |only civis-1.1.0/civis/man/cancel.Rd |only civis-1.1.0/civis/man/civis_ml.Rd | 78 civis-1.1.0/civis/man/civis_ml_extra_trees_classifier.Rd | 14 civis-1.1.0/civis/man/civis_ml_extra_trees_regressor.Rd | 14 civis-1.1.0/civis/man/civis_ml_gradient_boosting_classifier.Rd | 14 civis-1.1.0/civis/man/civis_ml_gradient_boosting_regressor.Rd | 14 civis-1.1.0/civis/man/civis_ml_random_forest_classifier.Rd | 14 civis-1.1.0/civis/man/civis_ml_random_forest_regressor.Rd | 14 civis-1.1.0/civis/man/civis_ml_sparse_linear_regressor.Rd | 14 civis-1.1.0/civis/man/civis_ml_sparse_logistic.Rd | 14 civis-1.1.0/civis/man/civis_ml_sparse_ridge_regressor.Rd | 14 civis-1.1.0/civis/man/civis_platform.Rd |only civis-1.1.0/civis/man/clusters_get_kubernetes.Rd |only civis-1.1.0/civis/man/clusters_get_workers.Rd |only civis-1.1.0/civis/man/clusters_list_kubernetes.Rd |only civis-1.1.0/civis/man/clusters_list_workers.Rd |only civis-1.1.0/civis/man/clusters_list_workers_active_jobs.Rd |only civis-1.1.0/civis/man/clusters_list_workers_queued_jobs.Rd |only civis-1.1.0/civis/man/codes_delete.Rd |only civis-1.1.0/civis/man/codes_get.Rd |only civis-1.1.0/civis/man/codes_list.Rd |only civis-1.1.0/civis/man/codes_patch.Rd |only civis-1.1.0/civis/man/codes_post.Rd |only civis-1.1.0/civis/man/codes_put.Rd |only civis-1.1.0/civis/man/endpoints_list.Rd |only civis-1.1.0/civis/man/enhancements_delete_cass_ncoa_projects.Rd |only civis-1.1.0/civis/man/enhancements_delete_cass_ncoa_runs.Rd |only civis-1.1.0/civis/man/enhancements_delete_cass_ncoa_shares_groups.Rd |only civis-1.1.0/civis/man/enhancements_delete_cass_ncoa_shares_users.Rd |only civis-1.1.0/civis/man/enhancements_get_cass_ncoa.Rd |only civis-1.1.0/civis/man/enhancements_get_cass_ncoa_runs.Rd |only civis-1.1.0/civis/man/enhancements_list.Rd |only civis-1.1.0/civis/man/enhancements_list_cass_ncoa_projects.Rd |only civis-1.1.0/civis/man/enhancements_list_cass_ncoa_runs.Rd |only civis-1.1.0/civis/man/enhancements_list_cass_ncoa_runs_logs.Rd |only civis-1.1.0/civis/man/enhancements_list_cass_ncoa_runs_outputs.Rd |only civis-1.1.0/civis/man/enhancements_list_cass_ncoa_shares.Rd |only civis-1.1.0/civis/man/enhancements_list_types.Rd |only civis-1.1.0/civis/man/enhancements_patch_cass_ncoa.Rd |only civis-1.1.0/civis/man/enhancements_post_cass_ncoa.Rd |only civis-1.1.0/civis/man/enhancements_post_cass_ncoa_cancel.Rd |only civis-1.1.0/civis/man/enhancements_post_cass_ncoa_runs.Rd |only civis-1.1.0/civis/man/enhancements_put_cass_ncoa.Rd |only civis-1.1.0/civis/man/enhancements_put_cass_ncoa_archive.Rd |only civis-1.1.0/civis/man/enhancements_put_cass_ncoa_projects.Rd |only civis-1.1.0/civis/man/enhancements_put_cass_ncoa_shares_groups.Rd |only civis-1.1.0/civis/man/enhancements_put_cass_ncoa_shares_users.Rd |only civis-1.1.0/civis/man/exports_list.Rd |only civis-1.1.0/civis/man/files_post_multipart.Rd |only civis-1.1.0/civis/man/files_post_multipart_complete.Rd |only civis-1.1.0/civis/man/generate_client.Rd | 4 civis-1.1.0/civis/man/groups_list.Rd |only civis-1.1.0/civis/man/match_targets_list.Rd |only civis-1.1.0/civis/man/media_delete_optimizations_runs.Rd |only civis-1.1.0/civis/man/media_delete_optimizations_shares_groups.Rd |only civis-1.1.0/civis/man/media_delete_optimizations_shares_users.Rd |only civis-1.1.0/civis/man/media_delete_spot_orders_shares_groups.Rd |only civis-1.1.0/civis/man/media_delete_spot_orders_shares_users.Rd |only civis-1.1.0/civis/man/media_get_optimizations.Rd |only civis-1.1.0/civis/man/media_get_optimizations_runs.Rd |only civis-1.1.0/civis/man/media_get_spot_orders.Rd |only civis-1.1.0/civis/man/media_list_dmas.Rd |only civis-1.1.0/civis/man/media_list_optimizations.Rd |only civis-1.1.0/civis/man/media_list_optimizations_runs.Rd |only civis-1.1.0/civis/man/media_list_optimizations_runs_logs.Rd |only civis-1.1.0/civis/man/media_list_optimizations_shares.Rd |only civis-1.1.0/civis/man/media_list_ratecards.Rd |only civis-1.1.0/civis/man/media_list_spot_orders.Rd |only civis-1.1.0/civis/man/media_list_spot_orders_shares.Rd |only civis-1.1.0/civis/man/media_list_targets.Rd |only civis-1.1.0/civis/man/media_patch_optimizations.Rd |only civis-1.1.0/civis/man/media_post_optimizations.Rd |only civis-1.1.0/civis/man/media_post_optimizations_clone.Rd |only civis-1.1.0/civis/man/media_post_optimizations_runs.Rd |only civis-1.1.0/civis/man/media_post_spot_orders.Rd |only civis-1.1.0/civis/man/media_put_optimizations_archive.Rd |only civis-1.1.0/civis/man/media_put_optimizations_shares_groups.Rd |only civis-1.1.0/civis/man/media_put_optimizations_shares_users.Rd |only civis-1.1.0/civis/man/media_put_spot_orders.Rd |only civis-1.1.0/civis/man/media_put_spot_orders_archive.Rd |only civis-1.1.0/civis/man/media_put_spot_orders_shares_groups.Rd |only civis-1.1.0/civis/man/media_put_spot_orders_shares_users.Rd |only civis-1.1.0/civis/man/multipart_upload.Rd |only civis-1.1.0/civis/man/notebooks_delete.Rd |only civis-1.1.0/civis/man/notebooks_delete_deployments.Rd |only civis-1.1.0/civis/man/notebooks_delete_projects.Rd |only civis-1.1.0/civis/man/notebooks_delete_shares_groups.Rd |only civis-1.1.0/civis/man/notebooks_delete_shares_users.Rd |only civis-1.1.0/civis/man/notebooks_get.Rd |only civis-1.1.0/civis/man/notebooks_get_deployments.Rd |only civis-1.1.0/civis/man/notebooks_list.Rd |only civis-1.1.0/civis/man/notebooks_list_deployments.Rd |only civis-1.1.0/civis/man/notebooks_list_projects.Rd |only civis-1.1.0/civis/man/notebooks_list_shares.Rd |only civis-1.1.0/civis/man/notebooks_list_update_links.Rd |only civis-1.1.0/civis/man/notebooks_patch.Rd |only civis-1.1.0/civis/man/notebooks_post.Rd |only civis-1.1.0/civis/man/notebooks_post_clone.Rd |only civis-1.1.0/civis/man/notebooks_post_deployments.Rd |only civis-1.1.0/civis/man/notebooks_put.Rd |only civis-1.1.0/civis/man/notebooks_put_archive.Rd |only civis-1.1.0/civis/man/notebooks_put_projects.Rd |only civis-1.1.0/civis/man/notebooks_put_shares_groups.Rd |only civis-1.1.0/civis/man/notebooks_put_shares_users.Rd |only civis-1.1.0/civis/man/notifications_list.Rd |only civis-1.1.0/civis/man/ontology_list.Rd |only civis-1.1.0/civis/man/publish_addin.Rd |only civis-1.1.0/civis/man/publish_html.Rd | 5 civis-1.1.0/civis/man/publish_rmd.Rd | 19 civis-1.1.0/civis/man/remote_hosts_list.Rd |only civis-1.1.0/civis/man/remote_hosts_list_data_sets.Rd |only civis-1.1.0/civis/man/remote_hosts_post.Rd |only civis-1.1.0/civis/man/remote_hosts_post_authenticate.Rd |only civis-1.1.0/civis/man/reports_delete_solutions_shares_groups.Rd |only civis-1.1.0/civis/man/reports_delete_solutions_shares_users.Rd |only civis-1.1.0/civis/man/reports_get_solutions.Rd |only civis-1.1.0/civis/man/reports_list_solutions_shares.Rd |only 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civis-1.1.0/civis/man/scripts_patch_python3.Rd | 4 civis-1.1.0/civis/man/scripts_patch_r.Rd | 4 civis-1.1.0/civis/man/scripts_patch_sql.Rd | 4 civis-1.1.0/civis/man/scripts_post.Rd | 4 civis-1.1.0/civis/man/scripts_post_containers.Rd | 4 civis-1.1.0/civis/man/scripts_post_containers_clone.Rd |only civis-1.1.0/civis/man/scripts_post_custom.Rd | 3 civis-1.1.0/civis/man/scripts_post_custom_clone.Rd |only civis-1.1.0/civis/man/scripts_post_javascript.Rd | 4 civis-1.1.0/civis/man/scripts_post_javascript_clone.Rd |only civis-1.1.0/civis/man/scripts_post_python3.Rd | 4 civis-1.1.0/civis/man/scripts_post_python3_clone.Rd |only civis-1.1.0/civis/man/scripts_post_r.Rd | 4 civis-1.1.0/civis/man/scripts_post_r_clone.Rd |only civis-1.1.0/civis/man/scripts_post_sql.Rd | 4 civis-1.1.0/civis/man/scripts_post_sql_clone.Rd |only civis-1.1.0/civis/man/scripts_put_containers.Rd | 4 civis-1.1.0/civis/man/scripts_put_containers_archive.Rd | 2 civis-1.1.0/civis/man/scripts_put_custom.Rd | 3 civis-1.1.0/civis/man/scripts_put_custom_archive.Rd | 3 civis-1.1.0/civis/man/scripts_put_javascript.Rd | 4 civis-1.1.0/civis/man/scripts_put_javascript_archive.Rd | 2 civis-1.1.0/civis/man/scripts_put_python3.Rd | 4 civis-1.1.0/civis/man/scripts_put_python3_archive.Rd | 2 civis-1.1.0/civis/man/scripts_put_r.Rd | 4 civis-1.1.0/civis/man/scripts_put_r_archive.Rd | 2 civis-1.1.0/civis/man/scripts_put_sql.Rd | 4 civis-1.1.0/civis/man/scripts_put_sql_archive.Rd | 2 civis-1.1.0/civis/man/search_list.Rd |only civis-1.1.0/civis/man/search_list_types.Rd |only civis-1.1.0/civis/man/templates_delete_reports.Rd |only civis-1.1.0/civis/man/templates_delete_reports_shares_groups.Rd |only civis-1.1.0/civis/man/templates_delete_reports_shares_users.Rd |only civis-1.1.0/civis/man/templates_delete_scripts.Rd |only civis-1.1.0/civis/man/templates_delete_scripts_projects.Rd |only civis-1.1.0/civis/man/templates_delete_scripts_shares_groups.Rd |only 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civis-1.1.0/civis/tests/testthat/test_client_base.R | 26 civis-1.1.0/civis/tests/testthat/test_io.R | 107 civis-1.1.0/civis/tests/testthat/test_reports.R | 55 civis-1.1.0/civis/tests/testthat/test_rstudio.R |only civis-1.1.0/civis/tools/generate_civis_ml_test_data.R | 33 civis-1.1.0/civis/tools/generate_default_client.R | 16 civis-1.1.0/civis/tools/integration_tests/smoke_test.R | 47 291 files changed, 10126 insertions(+), 873 deletions(-)
Title: Time-Course Gene Set Analysis for RNA-Seq Data
Description: Analyze RNA-seq data with variance component score test accounting
for data heteroscedasticity through precision weights. Perform both gene-wise and gene set
analyses, and can deal with longitudinal data. Method is detailed in: Agniel D & Hejblum BP (2017)
Variance component score test for time-course gene set analysis of longitudinal RNA-seq data,
Biostatistics, 18(4):589-604.
Author: Denis Agniel [aut],
Boris P. Hejblum [aut, cre]
Maintainer: Boris P. Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between tcgsaseq versions 1.6.2 dated 2017-08-04 and 1.6.3 dated 2017-11-09
DESCRIPTION | 15 ++--- MD5 | 45 ++++++++------- NEWS.md | 5 + R/TcGSAseq-package.R | 11 ++- R/baduel.R | 13 ++-- R/sp_weights.R | 19 ++++-- R/tcgsa_seq.R | 144 ++++++++++++++++++++++++++++++++++++++------------- R/varseq.R | 13 +++- R/vc_score.R | 24 ++++++-- R/vc_score_h.R | 12 ++-- R/vc_test_asym.R | 72 ++++++++++++++++--------- R/vc_test_perm.R | 14 +++- README.md | 4 - inst/CITATION | 20 +++---- man/baduel_5gs.Rd | 11 ++- man/tcgsa_seq.Rd | 44 ++++++++++----- man/tcgsaseq.Rd | 11 ++- man/varseq.Rd | 12 +++- man/vc_score.Rd | 5 + man/vc_score_h.Rd | 4 + man/vc_test_asym.Rd | 16 +++-- man/vc_test_perm.Rd | 5 + tests |only 23 files changed, 352 insertions(+), 167 deletions(-)
Title: Reduced-Rank Regression
Description: Multivariate regression methodologies including reduced-rank
regression (RRR), reduced-rank ridge regression (RRS), robust reduced-rank
regression (R4), generalized/mixed-response reduced-rank regression (mRRR),
row-sparse reduced-rank regression (SRRR), reduced-rank regression with a
sparse singular value decomposition (RSSVD), and sparse and orthogonal
factor regression (SOFAR).
Author: Kun Chen [aut, cre],
Wenjie Wang [ctb],
Jun Yan [ctb]
Maintainer: Kun Chen <kun.chen@uconn.edu>
Diff between rrpack versions 0.1-5 dated 2017-06-22 and 0.1-6 dated 2017-11-09
DESCRIPTION | 8 +++--- MD5 | 30 ++++++++++++------------ R/RcppExports.R | 28 +++++++++++----------- R/r4.R | 2 - R/sim.R | 7 ++--- R/sofar.R | 41 +++++++++++++++++++++++---------- man/cv.sofar.Rd | 5 +++- man/r4.Rd | 2 - man/rrr.sim2.Rd | 2 - man/rrr.sim4.Rd | 4 --- man/rrr.sim5.Rd | 2 - man/sofar.Rd | 9 ++++--- src/RcppExports.cpp | 32 +++++++++++++------------- src/rrpack_init.c | 64 ++++++++++++++++++++++++++-------------------------- src/srrr.cpp | 22 +++++++++-------- src/surr_fit.cpp | 15 ++++++------ 16 files changed, 148 insertions(+), 125 deletions(-)
Title: Family Sequence Kernel Association Test for Rare and Common
Variants
Description: FamSKAT-RC is a family-based association kernel test for both
rare and common variants. This test is general and several special cases
are known as other methods: famSKAT, which only focuses on rare variants
in family-based data, SKAT, which focuses on rare variants in
population-based data (unrelated individuals), and SKAT-RC, which focuses
on both rare and common variants in population-based data. When one
applies famSKAT-RC and sets the value of phi to 1, famSKAT-RC becomes
famSKAT. When one applies famSKAT-RC and set the value of phi to 1 and the
kinship matrix to the identity matrix, famSKAT-RC becomes SKAT. When one
applies famSKAT-RC and set the kinship matrix (fullkins) to the identity
matrix (and phi is not equal to 1), famSKAT-RC becomes SKAT-RC. We also
include a small sample synthetic pedigree to demonstrate the method with.
For more details see Saad M and Wijsman EM (2014) <doi:10.1002/gepi.21844>.
Author: Khalid B. Kunji [aut, cre], Mohamad Saad [aut]
Maintainer: Khalid B. Kunji <kkunji@hbku.edu.qa>
Diff between famSKATRC versions 1.0.3 dated 2017-10-12 and 1.1.0 dated 2017-11-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/famSKAT_RC.R | 16 +++++++--------- build/partial.rdb |binary 4 files changed, 13 insertions(+), 15 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between devtools versions 1.13.3 dated 2017-08-02 and 1.13.4 dated 2017-11-09
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 1 - NEWS.md | 11 +++++++---- R/utils.r | 4 ++++ R/zzz.r | 2 +- build/vignette.rds |binary inst/doc/dependencies.html | 4 ++-- tests/testthat/test-load.r | 8 ++++---- tests/testthat/testDllRcpp/R/RcppExports.R | 6 +----- tests/testthat/testDllRcpp/src/RcppExports.cpp | 14 +++----------- 11 files changed, 36 insertions(+), 42 deletions(-)