Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with
ideas from Gary Churchill and Saunak Sen and contributions from
Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr
Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron
Wolen, and Brian Yandell
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between qtl versions 1.36-6 dated 2015-03-05 and 1.37-11 dated 2015-08-25
DESCRIPTION | 12 +++--- MD5 | 68 +++++++++++++++++++------------------- NAMESPACE | 82 +++++++++++++++++++++++++++++++++++++++++++++- R/add_threshold.R | 2 - R/plot.R | 89 +++++++++++++++----------------------------------- R/read.cross.csv.R | 11 +++--- R/read.cross.csvs.R | 11 +++--- R/read.cross.mm.R | 11 ++++-- R/read.cross.tidy.R | 9 +++-- R/refineqtl.R | 8 ++-- R/scantwo.R | 15 ++++++-- R/scantwopermhk.R | 9 +++++ R/stepwiseqtl.R | 11 +++++- R/summary.cross.R | 5 ++ R/util.R | 11 +++++- R/write.cross.mq.R | 7 ++- build/vignette.rds |binary data/badorder.RData |binary data/bristle3.RData |binary data/bristleX.RData |binary data/fake.4way.RData |binary data/fake.bc.RData |binary data/fake.f2.RData |binary data/hyper.RData |binary data/listeria.RData |binary data/locations.RData |binary data/map10.RData |binary data/mapthis.RData |binary data/multitrait.RData |binary inst/CITATION | 14 +++---- inst/INSTALL_ME.txt | 16 ++++---- inst/README.md | 2 - inst/STATUS.txt | 35 +++++++++++++++++++ inst/doc/rqtltour.pdf |binary man/sim.cross.Rd | 24 ++++++------- 35 files changed, 294 insertions(+), 158 deletions(-)
Title: R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)
Description: Provides a basic set of R functions for querying the Cancer
Genomics Data Server (CGDS), hosted by the Computational Biology Center at
Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen <jacobsen@cbio.mskcc.org>
Maintainer: Augustin Luna <lunaa@cbio.mskcc.org>
Diff between cgdsr versions 1.2.3 dated 2015-08-19 and 1.2.4 dated 2015-08-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/cgdsr-getCaseLists.Rd | 2 +- man/cgdsr-getGeneticProfiles.Rd | 2 +- man/cgdsr-getProfileData.Rd | 6 +++--- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: The Skew-Normal and Skew-t Distributions
Description: Define and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.2-3 dated 2015-07-16 and 1.2-4 dated 2015-08-25
DESCRIPTION | 8 ++--- MD5 | 18 +++++------ NEWS | 19 ++++++++---- R/sn-funct.R | 73 ++++++++++++++++++++++++++++++------------------ man/dst.Rd | 13 +++++--- man/makeSECdistr.Rd | 6 ++- man/plot.SECdistr.Rd | 14 ++++++++- man/selm.Rd | 4 +- man/sn-package.Rd | 1 man/summary.SECdistr.Rd | 10 +++--- 10 files changed, 106 insertions(+), 60 deletions(-)
Title: Optimal Stratification of Sampling Frames for Multipurpose
Sampling Surveys
Description: In the field of stratified sampling design, this package
offers an approach for the determination of the best
stratification of a sampling frame, the one that ensures the
minimum sample cost under the condition to satisfy precision
constraints in a multivariate and multidomain case. This
approach is based on the use of the genetic algorithm: each
solution (i.e. a particular partition in strata of the sampling
frame) is considered as an individual in a population; the
fitness of all individuals is evaluated applying the
Bethel-Chromy algorithm to calculate the sampling size
satisfying precision constraints on the target estimates.
Functions in the package allows to: (a) analyse the obtained
results of the optimisation step; (b) assign the new strata
labels to the sampling frame; (c) select a sample from the new
frame accordingly to the best allocation.
Functions for the execution of the genetic algorithm are a modified
version of the functions in the 'genalg' package.
Author: Giulio Barcaroli, Daniela Pagliuca and Egon Willighagen
Maintainer: Giulio Barcaroli <barcarol@istat.it>
Diff between SamplingStrata versions 1.0-3 dated 2014-10-21 and 1.0-4 dated 2015-08-25
DESCRIPTION | 12 +- MD5 | 28 ++--- NAMESPACE | 4 NEWS | 4 R/buildStrataDF.R | 1 R/evalSolution.r | 188 +++++++++++++++++------------------- R/optimizeStrata.R | 122 ++++++++++++++--------- R/strataGenalg.R | 2 R/updateFrame.R | 1 build/vignette.rds |binary data/swissframe.rda |binary data/swissmunicipalities.rda |binary data/swissstrata.rda |binary inst/doc/SamplingStrataVignette.pdf |binary man/evalSolution.Rd | 19 +-- 15 files changed, 208 insertions(+), 173 deletions(-)
More information about SamplingStrata at CRAN
Permanent link
Title: R Interface to the Protocol Buffers API
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal RPC protocols and file formats. Additional
documentation is available in the arXiv.org preprint "RProtoBuf:
Efficient Cross-Language Data Serialization in R" by Eddelbuettel,
Stokely, and Ooms (2014) at <http://arxiv.org/abs/1401.7372>.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.2 dated 2014-12-11 and 0.4.3 dated 2015-08-25
ChangeLog | 52 ++++++++++++++++++++++++++++++++- DESCRIPTION | 25 ++++++--------- MD5 | 26 ++++++++-------- NAMESPACE | 2 - README.md | 4 -- build/vignette.rds |binary inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-quickref.pdf |binary inst/doc/RProtoBuf-unitTests.pdf |binary inst/unitTests/runit.FieldDescriptor.R | 43 +++++++++++++-------------- inst/unitTests/runit.serialize.R | 9 ++--- man/RProtoBuf-package.Rd | 37 +++-------------------- src/Makevars.win | 32 ++++++++++---------- tools/winlibs.R | 12 +++---- 14 files changed, 130 insertions(+), 112 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RMySQL versions 0.10.4 dated 2015-07-28 and 0.10.5 dated 2015-08-25
DESCRIPTION | 12 +-- MD5 | 7 + configure | 205 ++++++++++++++++++++------------------------------------ src/Makevars.in |only tools/winlibs.R | 2 5 files changed, 86 insertions(+), 140 deletions(-)
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kent Russel [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb],
Peter Ellis [ctb],
Jonathan Owen [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.1.8 dated 2015-07-11 and 0.2.1 dated 2015-08-25
networkD3-0.1.8/networkD3/R/treeNetwork.R |only networkD3-0.1.8/networkD3/inst/htmlwidgets/treeNetwork.js |only networkD3-0.1.8/networkD3/inst/htmlwidgets/treeNetwork.yaml |only networkD3-0.1.8/networkD3/man/as.treeNetwork.Rd |only networkD3-0.1.8/networkD3/man/treeNetwork.Rd |only networkD3-0.2.1/networkD3/DESCRIPTION | 14 +-- networkD3-0.2.1/networkD3/MD5 | 40 +++++---- networkD3-0.2.1/networkD3/NAMESPACE | 16 ++- networkD3-0.2.1/networkD3/NEWS | 24 +++++ networkD3-0.2.1/networkD3/R/dendroNetwork.R |only networkD3-0.2.1/networkD3/R/diagonalNetwork.R |only networkD3-0.2.1/networkD3/R/forceNetwork.R | 2 networkD3-0.2.1/networkD3/R/radialNetwork.R |only networkD3-0.2.1/networkD3/R/sankeyNetwork.R | 7 - networkD3-0.2.1/networkD3/R/simpleNetwork.R | 2 networkD3-0.2.1/networkD3/README.md | 2 networkD3-0.2.1/networkD3/inst/examples/examples.R | 42 +++++----- networkD3-0.2.1/networkD3/inst/examples/examples.Rmd | 17 +++- networkD3-0.2.1/networkD3/inst/htmlwidgets/dendroNetwork.js |only networkD3-0.2.1/networkD3/inst/htmlwidgets/dendroNetwork.yaml |only networkD3-0.2.1/networkD3/inst/htmlwidgets/diagonalNetwork.js |only networkD3-0.2.1/networkD3/inst/htmlwidgets/diagonalNetwork.yaml |only networkD3-0.2.1/networkD3/inst/htmlwidgets/forceNetwork.js | 4 networkD3-0.2.1/networkD3/inst/htmlwidgets/radialNetwork.js |only networkD3-0.2.1/networkD3/inst/htmlwidgets/radialNetwork.yaml |only networkD3-0.2.1/networkD3/man/as.radialNetwork.Rd |only networkD3-0.2.1/networkD3/man/dendroNetwork.Rd |only networkD3-0.2.1/networkD3/man/diagonalNetwork.Rd |only networkD3-0.2.1/networkD3/man/networkD3-shiny.Rd | 28 ++++-- networkD3-0.2.1/networkD3/man/radialNetwork.Rd |only 30 files changed, 133 insertions(+), 65 deletions(-)
Title: Meta-Analysis for Diagnostic Test Studies
Description: Bayesian inference analysis for bivariate meta-analysis of diagnostic test studies using integrated nested Laplace approximation with INLA. A purpose built graphic user interface is available. The installation of R package INLA is compulsory for successful usage. The INLA package can be obtained from <http://www.r-inla.org>. We recommend the testing version, which can be downloaded by running: install.packages("INLA", repos="http://www.math.ntnu.no/inla/R/testing").
Author: Jingyi Guo <jingyi.guo@math.ntnu.no> and Andrea Riebler <andrea.riebler@math.ntnu.no>
Maintainer: Jingyi Guo <jingyi.guo@math.ntnu.no>
Diff between meta4diag versions 1.0.19 dated 2015-08-23 and 1.0.20 dated 2015-08-25
DESCRIPTION | 15 +++++++++------ MD5 | 16 ++++++++-------- R/meta4diagGUI.R | 4 ++-- data/Catheter.rda |binary data/Scheidler.rda |binary data/Telomerase.rda |binary data/table_cor.rda |binary data/table_var.rda |binary inst/etc/welcometext.txt | 4 ++-- 9 files changed, 21 insertions(+), 18 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable
drop-in replacements for base url() and download.file() with better performance,
support for encryption (https://, ftps://), 'gzip' compression, authentication,
and other 'libcurl' goodies. The core of the package implements a framework for
performing fully customized requests where data can be processed either in memory,
on disk, or streaming via the callback or connection interfaces. Some knowledge of
'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package
which builds on this package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between curl versions 0.9.2 dated 2015-08-08 and 0.9.3 dated 2015-08-25
curl-0.9.2/curl/src/options.c |only curl-0.9.2/curl/src/options.h |only curl-0.9.3/curl/DESCRIPTION | 6 +- curl-0.9.3/curl/MD5 | 22 ++++----- curl-0.9.3/curl/NAMESPACE | 1 curl-0.9.3/curl/NEWS | 5 ++ curl-0.9.3/curl/R/utilities.R | 11 +--- curl-0.9.3/curl/build/vignette.rds |binary curl-0.9.3/curl/configure | 83 +++++++++++++++++++++++++++--------- curl-0.9.3/curl/man/curl_options.Rd | 5 +- curl-0.9.3/curl/src/Makevars.in |only curl-0.9.3/curl/src/Makevars.win | 3 - curl-0.9.3/curl/tools/options.R |only curl-0.9.3/curl/tools/winlibs.R | 2 14 files changed, 92 insertions(+), 46 deletions(-)
Title: Interface to the 'Handsontable.js' Library
Description: An R interface to the 'Handsontable' JavaScript library, which is a
minimalist Excel-like data grid editor.
Author: Jonathan Owen [aut, cre, cph],
Jeff Allen [ctb],
Yihui Xie [ctb],
Enzo Martoglio [ctb],
Warpechowski Marcin [ctb, cph] (Handsontable.js library),
Handsoncode sp. z o.o. [ctb, cph] (Handsontable.js library),
Aisch Gregor [ctb, cph] (Chroma.js library),
Wood Tim [ctb, cph] (Moment.js library),
Chernev Iskren [ctb, cph] (Moment.js library),
Moment.js contributors [ctb, cph] (Moment.js library),
Bushell David [ctb, cph] (Pikaday.js library),
jQuery Foundation [ctb, cph] (jQuery.js library),
Splunk Inc [ctb, cph] (Sparkline.js library)
Maintainer: Jonathan Owen <jonathanro@gmail.com>
Diff between rhandsontable versions 0.1 dated 2015-06-24 and 0.2 dated 2015-08-25
DESCRIPTION | 20 LICENSE | 2 LICENSE.note | 56 MD5 | 63 NAMESPACE | 1 NEWS | 36 R/misc.R | 32 R/rhandsontable-package.R | 8 R/rhandsontable.R | 107 build/vignette.rds |binary inst/doc/intro_rhandsontable.R | 270 inst/doc/intro_rhandsontable.Rmd | 426 inst/doc/intro_rhandsontable.html | 476 inst/htmlwidgets/lib/handsontable/handsontable.full.css | 358 inst/htmlwidgets/lib/handsontable/handsontable.full.js |46985 ++++++++-------- inst/htmlwidgets/lib/jquery |only inst/htmlwidgets/lib/moment/moment.js | 5036 - inst/htmlwidgets/lib/sparkline |only inst/htmlwidgets/rhandsontable.css | 15 inst/htmlwidgets/rhandsontable.js | 121 inst/htmlwidgets/rhandsontable.yaml | 14 man/hot_cell.Rd | 3 man/hot_col.Rd | 8 man/hot_cols.Rd | 7 man/hot_rows.Rd | 3 man/hot_table.Rd | 19 man/hot_to_r.Rd | 3 man/hot_validate_character.Rd | 5 man/hot_validate_numeric.Rd | 5 man/rHandsontableOutput.Rd | 10 man/renderRHandsontable.Rd | 3 man/rhandsontable-package.Rd |only man/rhandsontable.Rd | 6 vignettes/intro_rhandsontable.Rmd | 426 34 files changed, 29278 insertions(+), 25246 deletions(-)
Title: Approximation of First-Passage-Time Densities for Diffusion
Processes
Diff between fptdApprox versions 2.0 dated 2013-12-27 and 2.1 dated 2015-08-25
Description: Efficient approximation of first-passage-time densities for diffusion processes based on the First-Passage-Time Location (FPTL) function.
Author: Patricia Román-Román, Juan J. Serrano-Pérez and Francisco Torres-Ruiz.
Maintainer: Juan J. Serrano-Pérez
DESCRIPTION | 20 ++++++++------------
MD5 | 38 +++++++++++++++++++-------------------
NAMESPACE | 13 +++++++++++++
R/is.fptl.R | 2 +-
R/plot.fpt.density.R | 5 ++---
man/Approx.cfpt.density.rd | 8 ++++----
man/Approx.fpt.density.rd | 8 ++++----
man/FPTL.Rd | 8 ++++----
man/Integration.Steps.Rd | 8 ++++----
man/diffproc.Rd | 5 +++++
man/fptdApprox-package.Rd | 12 ++++++------
man/growth.intervals.Rd | 6 ++----
man/is.fpt.density.rd | 5 +++++
man/plot.fpt.density.Rd | 15 ++++++++-------
man/plot.fptl.Rd | 17 +++++++----------
man/print.fpt.density.rd | 9 ++++++---
man/report.Rd | 3 +--
man/report.fpt.density.Rd | 8 ++++++--
man/report.summary.fptl.Rd | 5 +++++
man/summary.fptl.Rd | 8 ++++----
20 files changed, 114 insertions(+), 89 deletions(-)
Title: Contouring of Non-Regular Three-Dimensional Data
Description: Create contour lines for a non regular series of points, potentially from a non-regular canvas.
Author: Nicholas Hamilton
Maintainer: Nicholas Hamilton <n.hamilton@unsw.edu.au>
Diff between contoureR versions 1.0.1 dated 2015-08-22 and 1.0.5 dated 2015-08-25
DESCRIPTION | 6 - MD5 | 38 +++--- NEWS | 6 + R/RcppExports-Doc.R | 29 +++++ R/RcppExports.R | 12 +- R/contourLines.R | 22 ++- R/contoureR-package.R | 1 R/convexHull.R | 32 +++-- README.md |only man/contourLinesR.Rd | 6 - man/contoureR.Rd | 1 man/convexHullAM.Rd |only man/getContourLines.Rd | 7 + man/getConvexHull.Rd | 28 +++- src/Makevars.win |only src/RcppExports.cpp | 34 +++++ src/contourWalker.cpp | 112 ++++++++++++------- src/convexHull_Monotone.cpp |only src/convexHull_Monotone.h |only src/functions.cpp | 39 +++--- src/functions.h | 18 ++- src/structs.h | 253 +++++++++++++++++++++++++------------------- src/templates.h |only 23 files changed, 423 insertions(+), 221 deletions(-)
Title: Comparing Objects for Differences
Description: Functions to compare a model object to a comparison object.
If the objects are not identical, the functions can be instructed to
explore various modifications of the objects (e.g., sorting rows,
dropping names) to see if the modified versions are identical.
Author: Paul Murrell
Maintainer: Paul Murrell <p.murrell@auckland.ac.nz>
Diff between compare versions 0.2-5 dated 2014-12-16 and 0.2-6 dated 2015-08-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/same.R | 8 ++------ build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++++ inst/doc/compare-intro.pdf |binary inst/doc/fundamentals.pdf |binary 7 files changed, 20 insertions(+), 15 deletions(-)
Title: Central Limit Theorem Experiments (Theoretical and Simulation)
Description: Central limit theorem experiments presented by data frames or plots. Functions include generating theoretical sample space, corresponding probability, and simulated results as well.
Author: Simiao Ye, Jingning Mei
Maintainer: Simiao Ye <simiao.ye@gmail.com>
Diff between clttools versions 1.0 dated 2015-08-23 and 1.1 dated 2015-08-25
DESCRIPTION | 6 +-- MD5 | 30 ++++++++--------- R/clttools.R | 86 +++++++++----------------------------------------- man/coin.Rd | 3 - man/coin.plot.Rd | 3 - man/coin.simu.Rd | 3 - man/coin.simu.plot.Rd | 3 - man/dice.Rd | 3 - man/dice.plot.Rd | 3 - man/dice.simu.Rd | 3 - man/dice.simu.plot.Rd | 3 - man/expt.Rd | 3 - man/expt.mse.Rd | 3 - man/expt.plot.Rd | 3 - man/expt.simu.Rd | 3 - man/expt.simu.plot.Rd | 3 - 16 files changed, 47 insertions(+), 114 deletions(-)