Title: Purge Training Data from Models
Description: Enables the removal of training data from fitted R models while
retaining predict functionality. The purged models are more portable as their
memory footprints do not scale with the training sample size.
Author: Marc Maier [cre],
Chaoqun Jia [ctb],
MassMutual Advanced Analytics [aut] (http://datascience.massmutual.com)
Maintainer: Marc Maier <mmaier@massmutual.com>
Diff between purge versions 0.1.0 dated 2015-09-02 and 0.2.0 dated 2015-10-28
DESCRIPTION | 22 +++--- MD5 | 12 +-- NAMESPACE | 7 -- R/purge.R | 29 +++++++- man/purge.Rd | 13 +++ tests/purged.filesizes.R | 15 ++++ tests/testthat/test.purge.R | 148 +++++++++++++++++++++++++++++++------------- 7 files changed, 181 insertions(+), 65 deletions(-)
Title: Wild Scale-Enhanced Bootstrap
Description: Perform the Wild Scale-Enhanced (WiSE) bootstrap. Specifically, the user may supply a single or multiple equally-spaced time series and use the WiSE bootstrap to select a wavelet-smoothed model. Conversely, a pre-selected smooth level may also be specified for the time series. Quantities such as the bootstrap sample of wavelet coefficients, smoothed bootstrap samples, and specific hypothesis testing and confidence region results of the wavelet coefficients may be obtained. Additional functions are available to the user which help format the time series before analysis. This methodology is recommended to aid in model selection and signal extraction.
Note: This package specifically uses wavelet bases in the WiSE bootstrap methodology, but the theoretical construct is much more versatile.
Author: Megan Heyman, Snigdhansu Chatterjee
Maintainer: Megan Heyman <heyma029@umn.edu>
Diff between WiSEBoot versions 1.2.0 dated 2015-09-05 and 1.3.0 dated 2015-10-28
DESCRIPTION | 10 +- MD5 | 44 ++++----- NAMESPACE | 5 - NEWS | 17 +++ R/WiSEBoot.R | 53 ++++++++++- R/WiSEHypothesisTest.R | 52 +++++++++-- R/smoothTimeSeries.R | 7 + inst/doc/WiSEBoot_Examples_Vignette.R | 11 +- inst/doc/WiSEBoot_Examples_Vignette.Rnw | 138 ++++++++++++++++++++++--------- inst/doc/WiSEBoot_Examples_Vignette.pdf |binary man/SimulatedSNR0.5Series.Rd | 2 man/SimulatedSNR1.0Series.Rd | 2 man/SimulatedSNR1.5Series.Rd | 2 man/SimulatedSNR2.0Series.Rd | 2 man/SimulatedSmoothSeries.Rd | 2 man/WiSEBoot-package.Rd | 16 +-- man/WiSEBoot.Rd | 38 +++++--- man/WiSEConfidenceRegion.Rd | 17 ++- man/WiSEHypothesisTest.Rd | 31 ++++-- man/padMatrix.Rd | 2 man/padVector.Rd | 2 man/smoothTimeSeries.Rd | 2 vignettes/WiSEBoot_Examples_Vignette.Rnw | 138 ++++++++++++++++++++++--------- 23 files changed, 416 insertions(+), 177 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.2-1 dated 2015-09-09 and 1.2-2 dated 2015-10-28
DESCRIPTION | 16 +-- MD5 | 124 ++++++++++++------------- R/AAA.R | 2 R/DSC_DBSTREAM.R | 2 R/DSC_DStream.R | 2 R/DSD_Memory.R | 4 R/evaluate.R | 23 +++- inst/NEWS | 9 + inst/doc/stream.R | 203 +++++++++++++++--------------------------- inst/doc/stream.Rnw | 90 +++++++----------- inst/doc/stream.pdf |binary inst/doc/stream_extension.pdf |binary man/DSC.Rd | 5 + man/DSC_DBSCAN.Rd | 4 man/DSC_DBSTREAM.Rd | 25 ++--- man/DSC_DStream.Rd | 4 man/DSC_Hierarchical.Rd | 5 + man/DSC_Kmeans.Rd | 4 man/DSC_Macro.Rd | 5 + man/DSC_Micro.Rd | 5 + man/DSC_Reachability.Rd | 4 man/DSC_Sample.Rd | 13 +- man/DSC_Static.Rd | 4 man/DSC_TwoStage.Rd | 4 man/DSC_Window.Rd | 5 + man/DSClassify.Rd | 5 + man/DSD.Rd | 4 man/DSD_BarsAndGaussians.Rd | 5 + man/DSD_Benchmark.Rd | 5 + man/DSD_Cubes.Rd | 5 + man/DSD_Gaussians.Rd | 6 + man/DSD_MG.Rd | 4 man/DSD_Memory.Rd | 4 man/DSD_ReadCSV.Rd | 4 man/DSD_ReadDB.Rd | 4 man/DSD_ScaleStream.Rd | 4 man/DSD_Target.Rd | 5 + man/DSD_UniformNoise.Rd | 5 + man/DSD_mlbenchData.Rd | 5 + man/DSD_mlbenchGenerator.Rd | 5 + man/DSFP.Rd | 5 + man/DSO.Rd | 5 + man/DSO_Sampling.Rd | 4 man/DSO_Window.Rd | 4 man/DST.Rd | 5 + man/MGC.Rd | 6 + man/animation.Rd | 3 man/evaluate.Rd | 31 +++++- man/get_assignment.Rd | 5 + man/get_centers.Rd | 5 + man/get_copy.Rd | 5 + man/get_points.Rd | 5 + man/get_weights.Rd | 5 + man/microToMacro.Rd | 5 + man/nclusters.Rd | 5 + man/plot.Rd | 5 + man/prune_clusters.Rd | 5 + man/recluster.Rd | 5 + man/reset_stream.Rd | 5 + man/save.Rd | 7 + man/update.Rd | 5 + man/write_stream.Rd | 5 + vignettes/stream.Rnw | 90 +++++++----------- 63 files changed, 511 insertions(+), 346 deletions(-)
Title: Sensitivity Indices with Dependent Inputs
Description: Sensitivity indices with dependent correlated inputs, using a
method based on PLS regression.
Author: A. Bouvier [aut], J.-P. Gauchi [aut, cre], E. Volatier [ctb]
Maintainer: Annie Bouvier <annie.bouvier@jouy.inra.fr>
Diff between sivipm versions 1.0-0 dated 2015-04-14 and 1.1-2 dated 2015-10-28
DESCRIPTION | 13 + MD5 | 59 ++++---- NAMESPACE | 9 - NEWS | 36 +++++ R/allmono.R |only R/class-sivip.R |only R/fastregpls2.R |only R/polynome.R | 165 +++++++++++------------ R/regpls2.R | 310 +++++++++++++++++++++++++++------------------ R/sivipm.R | 236 ++++++++++++++++++++++------------ R/vect2poly.R | 6 inst/doc/Vignette.pdf |binary man/cornell1.Rd | 2 man/crpolyX.Rd | 4 man/crpolyXT.Rd | 4 man/poly-class.Rd | 8 + man/polyX-class.Rd | 8 + man/sivip-class.Rd |only man/sivipboot.Rd | 18 ++ man/sivipm-package.Rd | 6 man/sivipm.Rd | 87 ++++++------ man/vect2polyX.Rd | 2 man/vect2polyXT.Rd | 2 src |only tests/exX18Y14.R | 3 tests/exX18Y14.Rout.save | 65 +++++---- tests/exX18Y2.R | 4 tests/exX18Y2.Rout.save | 115 ++++++++-------- tests/exXY180.R | 6 tests/exXY180.Rout.save | 42 +++--- tests/excornell0.R | 20 ++ tests/excornell0.Rout.save | 211 ++++++++++++++++++++---------- tests/excornell1.Rout.save | 31 ++-- 33 files changed, 896 insertions(+), 576 deletions(-)
Title: Database Preferences and Skyline Computation
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator, and some
generalizations (database preferences).
Author: Patrick Roocks <mail@p-roocks.de>
Maintainer: Patrick Roocks <mail@p-roocks.de>
Diff between rPref versions 0.6 dated 2015-08-23 and 0.7 dated 2015-10-28
DESCRIPTION | 8 ++--- MD5 | 56 ++++++++++++++++++++------------------ NAMESPACE | 9 ++++++ NEWS | 24 ++++++++-------- R/RcppExports.R | 46 +++++++++++++++---------------- R/base-pref-macros.R | 38 +++++++++++++++----------- R/base-pref.r | 28 +++++++++++++------ R/complex-pref.r | 45 ++++++++++++++----------------- R/general-pref.r |only R/pred-succ.r | 26 ++++++++--------- R/pref-classes.r | 35 +++++++++++++++--------- R/pref-eval.r | 68 +++++++++++++++++++++++++++++------------------ R/rPref.r | 18 +++++++----- R/show-pref.r | 56 ++++++++++++++++++++------------------ R/visualize.r | 22 +++++++-------- inst/test/test-pref.r | 21 ++++++++++++++ inst/test/test-psel.R | 13 ++++++++ inst/test/test-strings.R | 3 +- man/base_pref.Rd | 28 ++++++++++++------- man/base_pref_macros.Rd | 38 +++++++++++++++----------- man/complex_pref.Rd | 32 ++++++++-------------- man/general_pref.Rd |only man/get_btg.Rd | 6 ++-- man/get_hasse_diag.Rd | 4 +- man/plot_front.Rd | 6 ++-- man/pred_succ.Rd | 23 ++++++++------- man/psel.Rd | 41 ++++++++++++++++------------ man/rPref.Rd | 17 ++++++----- man/show.pref.Rd | 29 +++++++++----------- man/show.query.Rd | 5 ++- 30 files changed, 428 insertions(+), 317 deletions(-)
Title: Ridge Regression and Other Kernels for Genomic Selection
Description: Software for genomic prediction with the RR-BLUP mixed model. One application is to estimate marker effects by ridge regression; alternatively, BLUPs can be calculated based on an additive relationship matrix or a Gaussian kernel.
Author: Jeffrey Endelman
Maintainer: Jeffrey Endelman <endelman@wisc.edu>
Diff between rrBLUP versions 4.3 dated 2014-03-06 and 4.4 dated 2015-10-28
DESCRIPTION | 8 +++---- MD5 | 18 ++++++++-------- NAMESPACE | 3 ++ NEWS | 5 ++++ R/A.mat.R | 7 ++---- R/GWAS.R | 17 ++++++++------- R/kin.blup.R | 59 +++++++++++++++++++++++++++++++++++-------------------- R/kinship.BLUP.R | 5 +--- man/GWAS.Rd | 6 +++-- man/kin.blup.Rd | 8 +++++-- 10 files changed, 83 insertions(+), 53 deletions(-)
Title: In-Source Documentation for R
Description: A 'Doxygen'-like in-source documentation system
for Rd, collation, and 'NAMESPACE' files.
Author: Hadley Wickham [aut, cre, cph],
Peter Danenberg [aut, cph],
Manuel Eugster [aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between roxygen2 versions 4.1.1 dated 2015-04-15 and 5.0.0 dated 2015-10-28
roxygen2-4.1.1/roxygen2/R/parse-registry.R |only roxygen2-4.1.1/roxygen2/man/roxygen.Rd |only roxygen2-4.1.1/roxygen2/src/parser.cpp |only roxygen2-4.1.1/roxygen2/src/roxygen.h |only roxygen2-4.1.1/roxygen2/tests/testthat/test-complete.R |only roxygen2-4.1.1/roxygen2/tests/testthat/test-cpp-parser.R |only roxygen2-5.0.0/roxygen2/DESCRIPTION | 35 roxygen2-5.0.0/roxygen2/MD5 | 211 +- roxygen2-5.0.0/roxygen2/NAMESPACE | 22 roxygen2-5.0.0/roxygen2/R/RcppExports.R | 12 roxygen2-5.0.0/roxygen2/R/alias.R | 2 roxygen2-5.0.0/roxygen2/R/default-data-format.R |only roxygen2-5.0.0/roxygen2/R/family.R | 30 roxygen2-5.0.0/roxygen2/R/minidesc.R | 6 roxygen2-5.0.0/roxygen2/R/object-defaults.R | 29 roxygen2-5.0.0/roxygen2/R/object-from-call.R | 32 roxygen2-5.0.0/roxygen2/R/object.R | 8 roxygen2-5.0.0/roxygen2/R/order-params.R | 1 roxygen2-5.0.0/roxygen2/R/parse-preref.R | 233 +- roxygen2-5.0.0/roxygen2/R/parse.R | 37 roxygen2-5.0.0/roxygen2/R/rc.R | 4 roxygen2-5.0.0/roxygen2/R/rd-file-api.R | 9 roxygen2-5.0.0/roxygen2/R/rd-parse.R | 8 roxygen2-5.0.0/roxygen2/R/rd-tag-api.R | 64 roxygen2-5.0.0/roxygen2/R/roclet-collate.R | 25 roxygen2-5.0.0/roxygen2/R/roclet-namespace.R | 58 roxygen2-5.0.0/roxygen2/R/roclet-rd.R | 311 +-- roxygen2-5.0.0/roxygen2/R/roclet-vignette.R | 1 roxygen2-5.0.0/roxygen2/R/roxygen-tag.R |only roxygen2-5.0.0/roxygen2/R/roxygen.R | 11 roxygen2-5.0.0/roxygen2/R/roxygenize.R | 21 roxygen2-5.0.0/roxygen2/R/safety.R | 16 roxygen2-5.0.0/roxygen2/R/source.R | 4 roxygen2-5.0.0/roxygen2/R/tag-registry.R |only roxygen2-5.0.0/roxygen2/R/template.R | 12 roxygen2-5.0.0/roxygen2/R/usage.R | 5 roxygen2-5.0.0/roxygen2/R/utils.R | 14 roxygen2-5.0.0/roxygen2/README.md | 14 roxygen2-5.0.0/roxygen2/build/vignette.rds |binary roxygen2-5.0.0/roxygen2/inst/doc/collate.R | 10 roxygen2-5.0.0/roxygen2/inst/doc/collate.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/collate.html | 251 --- roxygen2-5.0.0/roxygen2/inst/doc/formatting.R | 8 roxygen2-5.0.0/roxygen2/inst/doc/formatting.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/formatting.html | 345 +--- roxygen2-5.0.0/roxygen2/inst/doc/namespace.R | 8 roxygen2-5.0.0/roxygen2/inst/doc/namespace.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/namespace.html | 261 --- roxygen2-5.0.0/roxygen2/inst/doc/rd.R | 29 roxygen2-5.0.0/roxygen2/inst/doc/rd.Rmd | 67 roxygen2-5.0.0/roxygen2/inst/doc/rd.html | 880 +++-------- roxygen2-5.0.0/roxygen2/inst/doc/rdkeywords.R | 8 roxygen2-5.0.0/roxygen2/inst/doc/rdkeywords.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/rdkeywords.html | 428 +---- roxygen2-5.0.0/roxygen2/inst/doc/roxygen2.R | 8 roxygen2-5.0.0/roxygen2/inst/doc/roxygen2.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/roxygen2.html | 221 -- roxygen2-5.0.0/roxygen2/man/default_data_format.Rd |only roxygen2-5.0.0/roxygen2/man/is_s3_generic.Rd | 2 roxygen2-5.0.0/roxygen2/man/load_options.Rd |only roxygen2-5.0.0/roxygen2/man/namespace_roclet.Rd | 5 roxygen2-5.0.0/roxygen2/man/new_roclet.Rd | 2 roxygen2-5.0.0/roxygen2/man/object.Rd | 4 roxygen2-5.0.0/roxygen2/man/rd_roclet.Rd | 11 roxygen2-5.0.0/roxygen2/man/register-parser.Rd | 18 roxygen2-5.0.0/roxygen2/man/roc_proc_text.Rd | 2 roxygen2-5.0.0/roxygen2/man/roxygen2-package.Rd |only roxygen2-5.0.0/roxygen2/man/roxygenize.Rd | 2 roxygen2-5.0.0/roxygen2/man/source_package.Rd | 2 roxygen2-5.0.0/roxygen2/man/update_collate.Rd | 2 roxygen2-5.0.0/roxygen2/man/vignette_roclet.Rd | 6 roxygen2-5.0.0/roxygen2/src/RcppExports.cpp | 29 roxygen2-5.0.0/roxygen2/src/isComplete.cpp | 70 roxygen2-5.0.0/roxygen2/src/parser2.cpp |only roxygen2-5.0.0/roxygen2/src/wrapString.cpp | 41 roxygen2-5.0.0/roxygen2/tests/testthat/collate/belt.R | 5 roxygen2-5.0.0/roxygen2/tests/testthat/helper-pkg.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-alias.R | 22 roxygen2-5.0.0/roxygen2/tests/testthat/test-collate.R | 22 roxygen2-5.0.0/roxygen2/tests/testthat/test-data.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-describein.R | 3 roxygen2-5.0.0/roxygen2/tests/testthat/test-doctype.R | 12 roxygen2-5.0.0/roxygen2/tests/testthat/test-examples.R | 19 roxygen2-5.0.0/roxygen2/tests/testthat/test-family.R | 36 roxygen2-5.0.0/roxygen2/tests/testthat/test-field.R | 2 roxygen2-5.0.0/roxygen2/tests/testthat/test-format.R | 76 roxygen2-5.0.0/roxygen2/tests/testthat/test-inline.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-introduction.R | 51 roxygen2-5.0.0/roxygen2/tests/testthat/test-keyword.R | 5 roxygen2-5.0.0/roxygen2/tests/testthat/test-merge.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-namespace.R | 51 roxygen2-5.0.0/roxygen2/tests/testthat/test-object.R | 4 roxygen2-5.0.0/roxygen2/tests/testthat/test-package-doc.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-param.R | 30 roxygen2-5.0.0/roxygen2/tests/testthat/test-preref.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-raw.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-rc.R | 12 roxygen2-5.0.0/roxygen2/tests/testthat/test-rd.R | 11 roxygen2-5.0.0/roxygen2/tests/testthat/test-rdComplete.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-reexport.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-slot.R | 5 roxygen2-5.0.0/roxygen2/tests/testthat/test-srcref-comment.R | 6 roxygen2-5.0.0/roxygen2/tests/testthat/test-template.R | 15 roxygen2-5.0.0/roxygen2/tests/testthat/test-tokenize-block.R |only roxygen2-5.0.0/roxygen2/tests/testthat/test-topic-name.R | 17 roxygen2-5.0.0/roxygen2/tests/testthat/test-usage.R | 60 roxygen2-5.0.0/roxygen2/tests/testthat/testCollateOverwrite |only roxygen2-5.0.0/roxygen2/tests/testthat/testEagerData |only roxygen2-5.0.0/roxygen2/tests/testthat/testLazyData |only roxygen2-5.0.0/roxygen2/vignettes/collate.Rmd | 24 roxygen2-5.0.0/roxygen2/vignettes/formatting.Rmd | 24 roxygen2-5.0.0/roxygen2/vignettes/namespace.Rmd | 24 roxygen2-5.0.0/roxygen2/vignettes/rd.Rmd | 67 roxygen2-5.0.0/roxygen2/vignettes/rd.md | 46 roxygen2-5.0.0/roxygen2/vignettes/rdkeywords.Rmd | 24 roxygen2-5.0.0/roxygen2/vignettes/roxygen2.Rmd | 24 116 files changed, 2060 insertions(+), 2712 deletions(-)
Title: Rank-Hazard Plots
Description: Rank-hazard plots (Karvanen and Harrell, Statistics in Medicine 2009) visualize the relative importance of covariates in a proportional hazards model. The key idea is to rank the covariate values and plot the relative hazard as a function of ranks scaled to interval [0,1]. The relative hazard is plotted in respect to the reference hazard, which can bee.g. the hazard related to the median of the covariate.
Author: Juha Karvanen, Nanni Koski
Maintainer: Nanni Koski <nanni.t.koski@student.jyu.fi>
Diff between rankhazard versions 1.0 dated 2014-04-02 and 1.0-2 dated 2015-10-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 2 +- man/rankhazardplot.Rd | 3 ++- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between multicool versions 0.1-8 dated 2015-10-22 and 0.1-9 dated 2015-10-28
DESCRIPTION | 11 ++-- MD5 | 21 ++++---- NAMESPACE | 2 R/RcppExports.R | 12 ---- R/allPerm.R | 18 +++--- R/initMC.r | 20 +++---- R/nextPerm.R | 19 +++---- R/zzz.R |only man/initMC.Rd | 87 ++++++++++++++++----------------- man/nextPerm.Rd | 74 ++++++++++++++-------------- src/RcppExports.cpp | 33 ------------ src/multicool.cpp | 134 +++++++++++++++++++++++----------------------------- 12 files changed, 186 insertions(+), 245 deletions(-)
Title: Matching Algorithms in R and C++
Description: Computes matching algorithms efficiently using Rcpp.
Implements the Gale-Shapley Algorithm to compute the stable
matching for two-sided markets, such as the stable marriage
problem and the college-admissions problem. Implements Irving's
Algorithm for the stable roommate problem. Implements the top
trading cycle algorithm for the indivisible goods trading problem.
Author: Jan Tilly, Nick Janetos
Maintainer: Jan Tilly <jtilly@econ.upenn.edu>
Diff between matchingR versions 1.1.1 dated 2015-09-21 and 1.2 dated 2015-10-28
matchingR-1.1.1/matchingR/man/checkPreferenceOrder.Rd |only matchingR-1.1.1/matchingR/man/checkPreferenceOrderOnesided.Rd |only matchingR-1.1.1/matchingR/man/checkStability.Rd |only matchingR-1.1.1/matchingR/man/checkStabilityRoommate.Rd |only matchingR-1.1.1/matchingR/man/checkStabilityTopTradingCycle.Rd |only matchingR-1.1.1/matchingR/man/galeShapleyMatching.Rd |only matchingR-1.1.1/matchingR/man/many2one.Rd |only matchingR-1.1.1/matchingR/man/one2many.Rd |only matchingR-1.1.1/matchingR/man/one2one.Rd |only matchingR-1.1.1/matchingR/man/onesided.Rd |only matchingR-1.1.1/matchingR/man/pkg.env.Rd |only matchingR-1.1.1/matchingR/man/set.column.major.Rd |only matchingR-1.1.1/matchingR/man/set.row.major.Rd |only matchingR-1.1.1/matchingR/man/stableRoommateMatching.Rd |only matchingR-1.1.1/matchingR/man/topTradingCycle.Rd |only matchingR-1.1.1/matchingR/man/validateInputs.Rd |only matchingR-1.1.1/matchingR/man/validateInputsOneSided.Rd |only matchingR-1.2/matchingR/DESCRIPTION | 22 matchingR-1.2/matchingR/MD5 | 107 - matchingR-1.2/matchingR/NEWS.md | 9 matchingR-1.2/matchingR/R/RcppExports.R | 211 +- matchingR-1.2/matchingR/R/deprecated.R |only matchingR-1.2/matchingR/R/galeshapley.R | 740 ++++++---- matchingR-1.2/matchingR/R/matchingR.R | 137 - matchingR-1.2/matchingR/R/roommate.R | 260 ++- matchingR-1.2/matchingR/R/toptradingcycle.R | 117 + matchingR-1.2/matchingR/R/utils.R | 17 matchingR-1.2/matchingR/README.md | 60 matchingR-1.2/matchingR/inst/doc/matchingR-intro.R | 54 matchingR-1.2/matchingR/inst/doc/matchingR-intro.Rmd | 95 - matchingR-1.2/matchingR/inst/doc/matchingR-intro.html | 115 + matchingR-1.2/matchingR/inst/doc/matchingR-performance.R | 28 matchingR-1.2/matchingR/inst/doc/matchingR-performance.Rmd | 28 matchingR-1.2/matchingR/inst/doc/matchingR-performance.html | 84 - matchingR-1.2/matchingR/inst/include/matchingR.h | 17 matchingR-1.2/matchingR/man/cpp_wrapper_galeshapley.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_galeshapley_check_stability.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_irving.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_irving_check_stability.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_ttc.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_ttc_check_stability.Rd |only matchingR-1.2/matchingR/man/galeShapley.checkPreferences.Rd |only matchingR-1.2/matchingR/man/galeShapley.checkStability.Rd |only matchingR-1.2/matchingR/man/galeShapley.collegeAdmissions.Rd |only matchingR-1.2/matchingR/man/galeShapley.marriageMarket.Rd |only matchingR-1.2/matchingR/man/galeShapley.validate.Rd |only matchingR-1.2/matchingR/man/matchingR-deprecated.Rd |only matchingR-1.2/matchingR/man/matchingR-package.Rd | 74 - matchingR-1.2/matchingR/man/rankIndex.Rd | 4 matchingR-1.2/matchingR/man/roommate.Rd |only matchingR-1.2/matchingR/man/roommate.checkPreferences.Rd |only matchingR-1.2/matchingR/man/roommate.checkStability.Rd |only matchingR-1.2/matchingR/man/roommate.validate.Rd |only matchingR-1.2/matchingR/man/sortIndex.Rd | 4 matchingR-1.2/matchingR/man/sortIndexOneSided.Rd | 13 matchingR-1.2/matchingR/man/toptrading.Rd | 62 matchingR-1.2/matchingR/man/toptrading.checkStability.Rd |only matchingR-1.2/matchingR/src/RcppExports.cpp | 48 matchingR-1.2/matchingR/src/galeshapley.cpp | 163 +- matchingR-1.2/matchingR/src/galeshapley.h | 21 matchingR-1.2/matchingR/src/roommate.cpp | 118 + matchingR-1.2/matchingR/src/roommate.h | 23 matchingR-1.2/matchingR/src/toptradingcycle.cpp | 141 + matchingR-1.2/matchingR/src/toptradingcycle.h | 21 matchingR-1.2/matchingR/src/utils.cpp | 47 matchingR-1.2/matchingR/src/utils.h | 17 matchingR-1.2/matchingR/tests/testthat/test_galeshapley.R | 161 +- matchingR-1.2/matchingR/tests/testthat/test_roommate.R | 64 matchingR-1.2/matchingR/tests/testthat/test_toptradingcycle.R | 17 matchingR-1.2/matchingR/vignettes/bibliography.bib | 2 matchingR-1.2/matchingR/vignettes/matchingR-intro.Rmd | 95 - matchingR-1.2/matchingR/vignettes/matchingR-performance.Rmd | 28 72 files changed, 2131 insertions(+), 1093 deletions(-)
Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Jeroen Ooms [ctb],
Yixuan Qiu [ctb],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.0.3 dated 2015-10-22 and 0.0.4 dated 2015-10-28
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS |only R/raster.R | 1 - configure | 11 +++++++++++ man/raster_str.Rd | 1 - 6 files changed, 19 insertions(+), 9 deletions(-)
Title: Learning Algorithms for Dynamic Treatment Regimes
Description: Dynamic treatment regimens (DTRs) are sequential decision rules tailored at each stage by time-varying subject-specific features and intermediate outcomes observed in previous stages. This package implements three methods: O-learning (Zhao et. al. 2012,2014), Q-learning (Murphy et. al. 2007; Zhao et.al. 2009) and P-learning (Liu et. al. 2014, 2015) to estimate the optimal DTRs.
Author: Ying Liu, Yuanjia Wang, Donglin Zeng
Maintainer: Ying Liu <yl2802@cumc.columbia.edu>
Diff between DTRlearn versions 1.0 dated 2015-10-23 and 1.1 dated 2015-10-28
DESCRIPTION | 12 ++++----- MD5 | 30 +++++++++++------------ man/DTRlearn-package.Rd | 22 ++++++++++------- man/Olearning.Rd | 27 ++++++++++----------- man/Olearning_Single.Rd | 43 ++++++++++++++++++++++----------- man/Plearning.Rd | 31 +++++++++++------------- man/Qlearning.Rd | 12 ++++----- man/Qlearning_Single.Rd | 16 +++++------- man/make_2classification.Rd | 16 ++++++------ man/make_classification.Rd | 30 +++++++++++++---------- man/plot.linearcl.Rd | 17 ++++++------- man/plot.qlearn.Rd | 27 ++++++--------------- man/predict.linearcl.Rd | 9 ++----- man/predict.qlearn.Rd | 10 +++---- man/predict.rbfcl.Rd | 8 +++--- man/wsvm.Rd | 56 +++++++++++++++++++++++--------------------- 16 files changed, 186 insertions(+), 180 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 1.5 dated 2015-10-25 and 1.7 dated 2015-10-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/C_CIT_V12.R | 14 ++++++++++++-- man/cit-package.Rd | 4 ++-- 4 files changed, 21 insertions(+), 11 deletions(-)
Title: Multivariate Chebyshev Interpolation
Description: Contains methods for creating multivariate Chebyshev
approximation of functions on a hypercube. Some methods for
non-Chebyshev grids are also provided.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research, Oslo, Norway
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between chebpol versions 1.3-1367 dated 2014-09-01 and 1.3-1789 dated 2015-10-28
DESCRIPTION | 17 +++++++++-------- MD5 | 10 +++++----- NAMESPACE | 1 + R/chebpol.R | 2 ++ build/vignette.rds |binary inst/doc/chebpol.pdf |binary 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Bagging Whole-Genome Regression
Description: Designed for whole-genome regressions using Bayesian models fitted via Gibbs sampling with optional resampling techniques and polygenic term with reduced dimensionality.
Author: Alencar Xavier, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between bWGR versions 1.1 dated 2015-10-21 and 1.2 dated 2015-10-28
DESCRIPTION | 10 +-- MD5 | 23 ++++--- R/RcppExports.R | 4 + R/mgr.R |only R/mkr.R | 156 ++++++++++++++++++++++++---------------------------- R/wgr.R | 116 +++++++++++++++++++++++++++++--------- R/wgr2.R |only inst/CITATION | 2 man/bWGR.Rd | 4 - man/mgr.Rd |only man/mkr.Rd | 25 +++----- man/wgr.Rd | 12 ++-- man/wgr2.Rd |only src/KMUP2.cpp |only src/RcppExports.cpp | 19 ++++++ 15 files changed, 225 insertions(+), 146 deletions(-)
Title: Advanced Analysis of B Cell Receptor Repertoire Data
Description: Methods for advanced analysis of B cell receptor repertoire data, like gene usage, mutations, clones and diversity and their visualisation.
Author: Julia Bischof
Maintainer: Julia Bischof <Julia.Bischof@uksh.de>
Diff between bcRep versions 1.1 dated 2015-10-12 and 1.2.2 dated 2015-10-28
DESCRIPTION | 14 +- MD5 | 79 +++++++++---- NAMESPACE | 6 - R/clones.CDR3Length.R | 4 R/clones.R | 10 + R/clones.filterFunctionality.R |only R/clones.filterJunctionFrame.R |only R/clones.filterSize.R |only R/clones.giniIndex.R |only R/clones.shared.R | 10 + R/clones.shared.summary.R | 2 R/combineIMGT.R |only R/compare.aaDistribution.R |only R/compare.geneUsage.R |only R/compare.trueDiversity.R |only R/geneUsage.R | 34 +++-- R/plotAADistribution.R | 61 ++++++---- R/plotClonesCDR3Length.R | 6 - R/plotClonesCopyNumber.R | 9 + R/plotCompareAADistribution.R |only R/plotCompareGeneUsage.R |only R/plotCompareTrueDiversity.R |only R/plotGeneComb.R | 13 +- R/plotGeneUsage.R | 73 +++++++++--- R/plotTrueDiversity.R | 20 ++- R/sequences.functionality.R | 2 R/sequences.geneComb.R | 43 ++++++- R/sequences.junctionFrame.R | 2 build |only data/aaseqtab2.rda |only inst |only man/aaDistribution.Rd | 7 - man/aaseqtab.Rd | 2 man/aaseqtab2.Rd |only man/bcRep-package.Rd | 198 +++++++++++++++++++--------------- man/clones.Rd | 218 +++++++++++++++++++------------------- man/clones.filterFunctionality.Rd |only man/clones.filterJunctionFrame.Rd |only man/clones.filterSize.Rd |only man/clones.giniIndex.Rd |only man/clones.shared.Rd | 202 +++++++++++++++++------------------ man/combineIMGT.Rd |only man/compare.aaDistribution.Rd |only man/compare.geneUsage.Rd |only man/compare.trueDiversity.Rd |only man/geneUsage.Rd | 10 - man/mutationtab.Rd | 3 man/plotClonesCopyNumber.Rd | 7 - man/sequences.geneComb.Rd | 7 - man/trueDiversity.Rd | 2 vignettes |only 51 files changed, 607 insertions(+), 437 deletions(-)
Title: Diversification Rate Estimation and Fast Simulation of
Reconstructed Phylogenetic Trees under Tree-Wide
Time-Heterogeneous Birth-Death Processes Including
Mass-Extinction Events
Description: Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.
Author: Sebastian Hoehna and Michael R. May
Maintainer: Sebastian Hoehna <Sebastian.Hoehna@gmail.com>
Diff between TESS versions 2.0.0 dated 2015-06-18 and 2.1.0 dated 2015-10-28
TESS-2.0.0/TESS/vignettes/Bayesian_Diversification_Rate_Analysis.pdf |only TESS-2.1.0/TESS/DESCRIPTION | 10 TESS-2.1.0/TESS/MD5 | 85 ++++-- TESS-2.1.0/TESS/NAMESPACE | 4 TESS-2.1.0/TESS/R/tess.analysis.R | 124 ---------- TESS-2.1.0/TESS/R/tess.plot.output.R | 4 TESS-2.1.0/TESS/R/tess.process.output.R | 2 TESS-2.1.0/TESS/R/tess.sim.age.R | 4 TESS-2.1.0/TESS/R/tess.sim.taxa.R | 29 +- TESS-2.1.0/TESS/R/tess.sim.taxa.age.R | 15 - TESS-2.1.0/TESS/build |only TESS-2.1.0/TESS/inst/doc |only TESS-2.1.0/TESS/man/TESS-package.Rd | 17 + TESS-2.1.0/TESS/man/cettiidae.Rd | 13 - TESS-2.1.0/TESS/man/conifers.Rd | 13 - TESS-2.1.0/TESS/man/mammalia.Rd | 13 - TESS-2.1.0/TESS/man/tess.PosteriorPrediction.Rd | 8 TESS-2.1.0/TESS/man/tess.analysis.Rd | 68 +++-- TESS-2.1.0/TESS/man/tess.likelihood.Rd | 33 ++ TESS-2.1.0/TESS/man/tess.likelihood.rateshift.Rd | 30 +- TESS-2.1.0/TESS/man/tess.mcmc.Rd | 17 + TESS-2.1.0/TESS/man/tess.nTaxa.expected.Rd | 8 TESS-2.1.0/TESS/man/tess.pathSampling.Rd | 15 - TESS-2.1.0/TESS/man/tess.plot.multichain.diagnostics.Rd | 26 +- TESS-2.1.0/TESS/man/tess.plot.output.Rd | 14 - TESS-2.1.0/TESS/man/tess.plot.singlechain.diagnostics.Rd | 14 - TESS-2.1.0/TESS/man/tess.process.output.Rd | 18 - TESS-2.1.0/TESS/man/tess.sim.age.Rd | 2 TESS-2.1.0/TESS/vignettes/Bayesian_Diversification_Rate_Analysis.Rnw |only TESS-2.1.0/TESS/vignettes/ext_figures |only TESS-2.1.0/TESS/vignettes/literature.bib |only TESS-2.1.0/TESS/vignettes/results |only 32 files changed, 313 insertions(+), 273 deletions(-)
Title: Integrates R and Essentia
Description: Contains three functions that query AuriQ Systems' Essentia Database and return the results in R. 'essQuery' takes a single Essentia command and captures the output in R, where you can save the output to a dataframe or stream it directly into additional analysis. 'read.essentia' takes an Essentia script and captures the output csv data into R, where you can save the output to a dataframe or stream it directly into additional analysis. 'capture.essentia' takes a file containing any number of Essentia commands and captures the output of the specified statements into R dataframes. Essentia can be downloaded for free at http://www.auriq.com/documentation/source/install/index.html.
Author: Ben Waxer
Maintainer: Ben Waxer <bwaxer@auriq.com>
Diff between RESS versions 1.2 dated 2015-07-30 and 1.3 dated 2015-10-28
RESS-1.2/RESS/R/essquery.R |only RESS-1.2/RESS/R/readudb.R |only RESS-1.2/RESS/man/read.udb.Rd |only RESS-1.3/RESS/DESCRIPTION | 10 +++++----- RESS-1.3/RESS/MD5 | 16 +++++++++------- RESS-1.3/RESS/NAMESPACE | 1 + RESS-1.3/RESS/R/captureessentia.R |only RESS-1.3/RESS/R/essQuery.R |only RESS-1.3/RESS/R/readessentia.R |only RESS-1.3/RESS/man/RESS-package.Rd | 24 +++++++++++++++--------- RESS-1.3/RESS/man/capture.essentia.Rd |only RESS-1.3/RESS/man/essQuery.Rd | 8 ++++---- RESS-1.3/RESS/man/read.essentia.Rd |only 13 files changed, 34 insertions(+), 25 deletions(-)
More information about randomForest.ddR at CRAN
Permanent link
Title: Bayesian Analysis of qRT-PCR Data
Description: Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: http://bit.ly/1Nwo4CB.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Diff between MCMC.qpcr versions 1.2 dated 2015-05-23 and 1.2.2 dated 2015-10-28
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 8 +++++++- R/HPDsummary.R | 2 +- R/getNormalizedData.R | 11 ++++++++--- R/mcmc.qpcr.R | 13 +++++++++---- R/mcmc.qpcr.lognormal.R | 13 +++++++++---- man/MCMC.qpcr-package.Rd | 6 +++--- man/getNormalizedData.Rd | 5 ++++- 9 files changed, 54 insertions(+), 30 deletions(-)
Title: Citations for 'Knitr' Markdown Files
Description: Provides the ability to create dynamic citations
in which the bibliographic information is pulled from the web rather
than having to be entered into a local database such as 'bibtex' ahead of
time. The package is primarily aimed at authoring in the R 'markdown'
format, and can provide outputs for web-based authoring such as linked
text for inline citations. Cite using a 'DOI', URL, or
'bibtex' file key. See the package URL for details.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between knitcitations versions 1.0.6 dated 2015-05-25 and 1.0.7 dated 2015-10-28
DESCRIPTION | 20 ++++++++++---------- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 ++ NEWS | 6 +++--- R/bibliography.R | 2 +- R/cleanbib.R | 3 ++- R/knitcitations.R | 1 + build/vignette.rds |binary inst/doc/tutorial.pdf |binary man/bibliography.Rd | 2 +- man/cleanbib.Rd | 10 +--------- tests/testthat/test_bib_metadata.R | 1 + tests/testthat/test_cite.R | 14 +++++++++++++- 13 files changed, 47 insertions(+), 38 deletions(-)
Title: Multiple Ordinal Tobit (MOT) Model
Description: Fit right censored Multiple Ordinal Tobit (MOT) model.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>
Diff between lmmot versions 0.1.2 dated 2014-12-16 and 0.1.3 dated 2015-10-28
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 4 +++- R/lmmot.R | 7 +++---- R/motFisher.R | 5 +++-- R/motGradient.R | 5 +++-- R/motHessian.R | 5 +++-- R/motLogLik.R | 6 ++++-- man/lmmot.Rd | 5 +++-- man/motFisher.Rd | 7 ++++--- man/motGradient.Rd | 7 ++++--- man/motHessian.Rd | 7 ++++--- man/motLogLik.Rd | 7 ++++--- man/print.lmmot.Rd | 3 ++- man/summary.lmmot.Rd | 3 ++- 15 files changed, 61 insertions(+), 48 deletions(-)
Title: Platform for EDGAR Filing Management
Description: EDGAR is the Electronic Data Gathering, Analysis, and Retrieval system which performs automated collection, validation, indexing, acceptance, and forwarding of submissions by companies and others who are required by law to file forms with the U.S. Securities and Exchange Commission (SEC). This package downloads EDGAR quarterly master index, daily master index, filings from SEC.org site and do sentiment analysis of 10-K statements.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil <bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Diff between edgar versions 1.0.2 dated 2015-09-24 and 1.0.3 dated 2015-10-28
edgar-1.0.2/edgar/R/downlaod_master_index.R |only edgar-1.0.3/edgar/DESCRIPTION | 10 - edgar-1.0.3/edgar/MD5 | 24 +- edgar-1.0.3/edgar/R/download_filings.R | 2 edgar-1.0.3/edgar/R/download_master_index.R |only edgar-1.0.3/edgar/R/get_wordfrquency.R | 5 edgar-1.0.3/edgar/R/polarity_histogram.R | 87 +++++----- edgar-1.0.3/edgar/R/runEDGAR_shiny.R | 9 - edgar-1.0.3/edgar/inst/shiny-edgar/edgarapp/edgar_shiny_functions.R | 14 + edgar-1.0.3/edgar/inst/shiny-edgar/edgarapp/server.R | 10 - edgar-1.0.3/edgar/inst/shiny-edgar/edgarapp/ui.R | 2 edgar-1.0.3/edgar/man/RunEdgarShiny.Rd | 5 edgar-1.0.3/edgar/man/negwords.Rd | 8 edgar-1.0.3/edgar/man/poswords.Rd | 8 14 files changed, 99 insertions(+), 85 deletions(-)
Title: Bayesian Estimation of DINA Model
Description: Estimate the Deterministic Input, Noisy ``And'' Gate (DINA) cognitive diagnostic model parameters using the Gibbs sampler described by Culpepper (2015) DOI: 10.3102/1076998615595403.
Author: Steven Andrew Culpepper [aut, cph, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between dina versions 1.0 dated 2015-10-27 and 1.0.1 dated 2015-10-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- man/DINA_Gibbs.Rd | 18 +++++++++--------- man/DINAsim.Rd | 8 ++++---- man/dina-package.Rd | 2 +- src/DINAcpp101315.cpp | 12 ++++++------ 6 files changed, 28 insertions(+), 28 deletions(-)