Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts with a suite of web APIs for chemical information.
Author: Eduard Szoecs [aut, cre],
Daniel Muench [ctb]
Maintainer: Eduard Szoecs <eduardszoecs@gmail.com>
Diff between webchem versions 0.0.1 dated 2015-03-06 and 0.0.2 dated 2015-08-14
DESCRIPTION | 23 ++++++++----- MD5 | 40 +++++++++++++++-------- NAMESPACE | 8 +++- NEWS |only R/allanwood.R |only R/chemspider.R | 83 ++++++++++++++++++++++++++---------------------- R/cir.R | 32 ++++++++++++------ R/cts.R | 77 ++++++++++++++++++++++++++++++-------------- R/pan.R |only R/pubchem.R | 66 +++++++++++++++++++++++--------------- man/allanwood.Rd |only man/cid_compinfo.Rd | 16 ++++++--- man/cir_query.Rd | 8 ++++ man/csid_compinfo.Rd | 12 ++++-- man/csid_extcompinfo.Rd | 11 ++++-- man/cts_compinfo.Rd | 17 +++++++-- man/cts_convert.Rd | 12 +++++- man/get_cid.Rd | 9 ++++- man/get_csid.Rd | 4 +- man/pan.Rd |only tests |only 21 files changed, 272 insertions(+), 146 deletions(-)
More information about selectiveInference at CRAN
Permanent link
Title: Least-Squares Bilinear Clustering for Three-Way Data
Description: Functions for performing least-squares bilinear clustering of three-way data. The
method uses the bilinear decomposition (or biadditive model) to model two-way matrix slices
while clustering over the third way. Up to four different types of clusters are included, one
for each term of the bilinear decomposition. In this way, matrices are clustered simultaneously
on (a subset of) their overall means, row margins, column margins and row-column interactions.
The orthogonality of the bilinear model results in separability of the joint clustering problem
into four separate ones. Three of these subproblems are specific k-means problems, while a
special algorithm is implemented for the interactions. Plotting methods are provided, including
biplots for the low-rank approximations of the interactions.
Author: Pieter Schoonees [aut, cre], Patrick Groenen [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between lsbclust versions 1.0.2 dated 2015-03-11 and 1.0.3 dated 2015-08-14
DESCRIPTION | 12 +++---- MD5 | 70 ++++++++++++++++++++++---------------------- NAMESPACE | 5 ++- R/RcppExports.R | 40 +++++++++++++++++++++++++ R/lsbclust.R | 3 + data/dcars.rda |binary data/lov.rda |binary data/supermarkets.rda |binary man/ClustMeans.Rd | 2 - man/KMeansW.Rd |only man/LossMat.Rd | 2 - man/bicomp.Rd | 2 - man/cmat.Rd | 2 - man/dcars.Rd | 2 - man/genproc.Rd | 2 - man/indarr.Rd | 2 - man/int.lsbclust.Rd | 2 - man/lov.Rd | 2 - man/lsbclust-package.Rd | 2 - man/lsbclust.Rd | 2 - man/lsbclusttoclue.Rd | 2 - man/orc.lsbclust.Rd | 2 - man/plot.bicomp.Rd | 2 - man/plot.col.kmeans.Rd | 2 - man/plot.int.lsbclust.Rd | 2 - man/plot.lsbclust.Rd | 2 - man/plot.ovl.kmeans.Rd | 2 - man/plot.row.kmeans.Rd | 2 - man/plot.step.lsbclust.Rd | 2 - man/print.lsbclust.Rd | 2 - man/sim.lsbclust.Rd | 2 - man/step.lsbclust.Rd | 2 - man/summary.int.lsbclust.Rd | 2 - man/summary.lsbclust.Rd | 2 - man/supermarkets.Rd | 2 - src/KMeansW.cpp |only src/RcppExports.cpp | 44 +++++++++++++++++++++++++++ 37 files changed, 159 insertions(+), 67 deletions(-)
Title: Generalized Elastic Nets
Description: Implements several extensions of the elastic net regularization scheme. These extensions include individual feature penalties for the L1 term, feature-feature penalties for the L2 term, as well as translation coefficients for the latter.
Author: Artem Sokolov
Maintainer: Artem Sokolov <artem.sokolov@gmail.com>
Diff between gelnet versions 1.1 dated 2015-05-14 and 1.2 dated 2015-08-14
CHANGES | 10 + DESCRIPTION | 8 - MD5 | 31 +++-- NAMESPACE | 4 R/gelnet.R | 254 ++++++++++++++++++++++++++++++++++++++++----- man/L1.ceiling.Rd | 2 man/adj2lapl.Rd | 4 man/adj2nlapl.Rd | 4 man/gelnet.L1bin.Rd | 4 man/gelnet.klr.Rd | 8 - man/gelnet.kor.Rd |only man/gelnet.krr.Rd | 9 + man/gelnet.lin.Rd | 2 man/gelnet.lin.obj.Rd | 10 - man/gelnet.logreg.Rd | 2 man/gelnet.logreg.obj.Rd | 8 - man/gelnet.oneclass.Rd |only man/gelnet.oneclass.obj.Rd |only 18 files changed, 292 insertions(+), 68 deletions(-)
Title: R Interface to X-13-ARIMA-SEATS
Description: Easy-to-use interface to X-13-ARIMA-SEATS, the
seasonal adjustment software by the US Census Bureau. It offers full
access to almost all options and outputs of X-13, including X-11 and SEATS,
automatic ARIMA model search, outlier detection and support for user
defined holiday variables, such as Chinese New Year or Indian Diwali. It
also includes a Shiny-based graphical user interface. Seasonal does not
contain the binaries of X-13, which must be installed separately. See the
README file or the vignette for installation notes.
Author: Christoph Sax
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between seasonal versions 0.90.0 dated 2015-05-08 and 1.0.0 dated 2015-08-14
DESCRIPTION | 8 +- MD5 | 57 ++++++++------- NAMESPACE | 7 + NEWS | 182 +++++++++++++++++++++++++++++++-------------------- R/base.methods.R | 4 - R/checkX13.R | 28 +++++-- R/deparse.R | 4 - R/detect.R | 82 ---------------------- R/extractors.R | 1 R/import.spc.R |only R/inspect-sub.R | 65 ++++++++++++++++++ R/inspect.R | 10 +- R/out.R | 3 R/parse_spc.R |only R/plot.R | 21 +++++ R/read_mdl.R | 40 ----------- R/read_series.R | 25 ++++--- R/read_udg.R | 2 R/seas.R | 128 ++++++++++++++++++++++------------- R/spclist.R | 4 - R/static.R | 12 +-- R/summary.R | 5 - R/x13messages.R |only README.md | 73 +++++++++++++++----- build/vignette.rds |binary inst/doc/seas.pdf |binary man/import.spc.Rd |only man/import.ts.Rd |only man/inspect.Rd | 2 man/seas.Rd | 20 ++++- man/static.Rd | 7 + vignettes/README.tex | 102 ++++++++++++++++++++-------- 32 files changed, 532 insertions(+), 360 deletions(-)
Title: Analysis of Data Acquired Using the Receiver Operating
Characteristic Paradigm and Its Extensions
Description: A common task in medical imaging is assessing whether a new imaging system or device is an improvement over an existing one. Observer performance methodology, such as receiver operating characteristic analysis, is widely used for this purpose. Receiver operating characteristic studies are often required for regulatory approval of new devices. The purpose of this work is to software for the analysis of data acquired using the receiver operating characteristic paradigm and its location specific extensions. It is an enhanced implementation of existing Windows software (http://www.devchakraborty.com). In this paradigm the radiologist rates each image for confidence in presence of disease. The images are typically split equally between actually non-diseased and diseased. A common figure of merit is the area under the receiver operating characteristic curve, which has the physical interpretation as the probability that a diseased image is rated higher than a non-diseased one. In receiver operating characteristic studies a number of radiologists (readers) rate images in two or more treatments, and the object of the analysis is to determine the significance of the inter-treatment difference between reader-averaged figures of merit. In the free-response paradigm the reader marks the locations of suspicious regions and rates each region for confidence in presence of disease, and credit for detection is only given if a true lesion is correctly localized. In the region of interest paradigm each image is divided into a number of regions and the reader rates each region. Each paradigm requires definition of a valid figure of merit that rewards correct decisions and penalizes incorrect ones and specialized significance testing procedures are applied. The package reads data in all currently used data formats including Excel. Significance testing uses two models in widespread use, a jackknife pseudo-value based model and an analysis of variance model with correlated errors. Included are tools for (1) calculating a variety of free-response figures of merit; (2) sample size estimation for planning a future study based on pilot data; (3) viewing empirical operating characteristics in receiver operating characteristic and free-response paradigms; (4) producing formatted report files; and (5) saving a data file in appropriate format for analysis with alternate software. In addition to open-source access to the functions, the package includes a graphical interface for users already familiar with the Windows software, who simply wish to run the program.
Author: Xuetong Zhai [aut, cre],
Dev Chakraborty [aut, ths]
Maintainer: Xuetong Zhai <xuetong.zhai@gmail.com>
Diff between RJafroc versions 0.1.0 dated 2015-07-30 and 0.1.1 dated 2015-08-14
DESCRIPTION | 10 +- MD5 | 63 ++++++++-------- R/CalculateAFROCPoints.R | 2 R/CalculateAvgAFROCPoints.R | 2 R/CalculateAvgFROCPoints.R | 2 R/CalculateAvgROCPoints.R | 2 R/CalculateFROCPoints.R | 2 R/CalculateROCPoints.R | 2 R/DBMHAnalysis.R | 12 +-- R/EmpiricalOpCharac.R | 6 - R/FigureOfMerit.R | 18 ++-- R/ORHAnalysis.R | 12 +-- R/OutputReport.R | 10 ++ R/PowerGivenJK.R | 2 R/PowerTable.R | 2 R/ReadDataFile.R | 8 +- R/SampleSizeGivenJ.R | 2 R/SaveDataFile.R | 2 inst/doc/RJafroc.R | 4 - inst/doc/RJafroc.Rnw | 168 ++++++++++++++++++++++---------------------- inst/doc/RJafroc.pdf |binary man/DBMHAnalysis.Rd | 4 - man/EmpiricalOpCharac.Rd | 6 - man/FigureOfMerit.Rd | 18 ++-- man/ORHAnalysis.Rd | 4 - man/OutputReport.Rd | 10 ++ man/PowerGivenJK.Rd | 2 man/PowerTable.Rd | 2 man/ReadDataFile.Rd | 8 +- man/SampleSizeGivenJ.Rd | 2 man/SaveDataFile.Rd | 2 vignettes/RJafroc.Rnw | 168 ++++++++++++++++++++++---------------------- vignettes/jsslogo.jpg |only 33 files changed, 285 insertions(+), 272 deletions(-)
Title: Relative Survival
Description: Various functions for relative survival analysis.
Author: Maja Pohar Perme [aut, cre], Klemen Pavlic [ctb]
Maintainer: Maja Pohar Perme <maja.pohar@mf.uni-lj.si>
Diff between relsurv versions 2.0-5 dated 2015-05-28 and 2.0-6 dated 2015-08-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 7 +++++++ R/rformulate.r | 4 +++- R/rsdiff.r | 32 +++++++++++++++++++------------- 5 files changed, 37 insertions(+), 22 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources (rpart, RWeka, PMML) yielding objects that share
functionality for print/plot/predict methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree) and model-based
recursive partitioning (mob) from the party package are provided based
on the new infrastructure.
Author: Torsten Hothorn [aut, cre],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.0-2 dated 2015-07-28 and 1.0-3 dated 2015-08-14
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/ctree.R | 29 ++++++++++++++++------------- build/vignette.rds |binary inst/NEWS.Rd | 17 +++++++++++------ inst/doc/constparty.pdf |binary inst/doc/ctree.pdf |binary inst/doc/mob.pdf |binary inst/doc/partykit.pdf |binary 9 files changed, 41 insertions(+), 33 deletions(-)
Title: Simplify Parameters
Description: An interface to simplify organizing parameters used in a package, using external configuration files.
This attempts to provide a cleaner alternative to options().
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth <me@sahilseth.com>
Diff between params versions 0.2 dated 2015-07-27 and 0.2.4 dated 2015-08-14
params-0.2.4/params/DESCRIPTION | 8 ++-- params-0.2.4/params/MD5 | 21 ++++++---- params-0.2.4/params/NAMESPACE | 6 ++- params-0.2.4/params/NEWS.md |only params-0.2.4/params/R/conf.R | 50 +++++++++++++------------ params-0.2.4/params/R/opts.R | 65 ++++++++++++++------------------ params-0.2.4/params/R/pkg-opts.R |only params-0.2.4/params/R/zzz.R | 2 - params-0.2.4/params/README.md | 16 ++++++-- params-0.2.4/params/build |only params-0.2.4/params/man/opts.Rd |only params-0.2.4/params/man/params.Rd | 68 ++++++++++++++++++++++++++++++---- params-0.2.4/params/man/parse_opts.Rd |only params-0.2/params/man/load_conf.Rd |only params-0.2/params/man/parse_conf.Rd |only 15 files changed, 148 insertions(+), 88 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.0.3 dated 2015-07-21 and 0.0.4 dated 2015-08-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/helpers.R | 2 +- man/kdecopula-package.Rd | 6 +++--- src/interp.cpp | 2 +- src/renorm.cpp | 5 +++-- 6 files changed, 17 insertions(+), 16 deletions(-)
Title: Blind Source Separation Methods Based on Joint Diagonalization
and Some BSS Performance Criteria
Description: Cardoso's JADE algorithm as well as his functions for joint diagonalization are ported to R. Also several other blind source separation (BSS) methods, like AMUSE and SOBI, and some criteria for performance evaluation of BSS algorithms, are given.
Author: Klaus Nordhausen, Jean-Francois Cardoso, Jari Miettinen, Hannu Oja, Esa Ollila, Sara Taskinen
Maintainer: Klaus Nordhausen <klaus.nordhausen@utu.fi>
Diff between JADE versions 1.9-92 dated 2014-10-23 and 1.9-93 dated 2015-08-14
JADE-1.9-92/JADE/src/Fortran_JADE.f |only JADE-1.9-93/JADE/DESCRIPTION | 16 +++---- JADE-1.9-93/JADE/MD5 | 80 +++++++++++++++++++++-------------- JADE-1.9-93/JADE/NAMESPACE | 3 - JADE-1.9-93/JADE/R/AMUSE.R | 10 ++-- JADE-1.9-93/JADE/R/ComonGAP.R | 27 ++++++----- JADE-1.9-93/JADE/R/FG.R | 67 ++++++++++++++++------------- JADE-1.9-93/JADE/R/FOBI.R | 13 +++-- JADE-1.9-93/JADE/R/JADE.R | 75 ++++++++++++++++---------------- JADE-1.9-93/JADE/R/MD.R | 38 ++++++++++------ JADE-1.9-93/JADE/R/NSSJD.R | 8 +-- JADE-1.9-93/JADE/R/NSSSD.R | 8 +-- JADE-1.9-93/JADE/R/NSSTDJD.R | 6 +- JADE-1.9-93/JADE/R/SIR.R | 24 +++++----- JADE-1.9-93/JADE/R/SOBI.R | 18 +++---- JADE-1.9-93/JADE/R/amari.error.R | 8 +-- JADE-1.9-93/JADE/R/cjd.R | 36 +++++++-------- JADE-1.9-93/JADE/R/djd.R | 43 ++++++++++-------- JADE-1.9-93/JADE/R/frjd.R |only JADE-1.9-93/JADE/R/internals.R | 14 +++--- JADE-1.9-93/JADE/R/k_JADE.R | 35 +++++++-------- JADE-1.9-93/JADE/R/multscatter.R | 2 JADE-1.9-93/JADE/R/rjd.R | 72 +++++++++++++++---------------- JADE-1.9-93/JADE/R/rjd.fortran.R | 41 ++--------------- JADE-1.9-93/JADE/build |only JADE-1.9-93/JADE/inst/ChangeLog | 8 +++ JADE-1.9-93/JADE/inst/doc |only JADE-1.9-93/JADE/inst/vignette |only JADE-1.9-93/JADE/man/FG.Rd | 5 +- JADE-1.9-93/JADE/man/JADE-package.Rd | 8 +-- JADE-1.9-93/JADE/man/JADE.Rd | 5 -- JADE-1.9-93/JADE/man/NSS.JD.Rd | 6 +- JADE-1.9-93/JADE/man/NSS.TD.JD.Rd | 6 +- JADE-1.9-93/JADE/man/SOBI.Rd | 4 - JADE-1.9-93/JADE/man/k_JADE.Rd | 6 +- JADE-1.9-93/JADE/man/rjd.Rd | 22 +++++---- JADE-1.9-93/JADE/src/cJADE.cpp |only JADE-1.9-93/JADE/vignettes |only 38 files changed, 369 insertions(+), 345 deletions(-)
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: A suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em, haplo.glm, haplo.score, haplo.power, and seqhap; all of which have detailed examples in doc/manualHaploStats.pdf.
Author: Sinnwell JP, Schaid DJ
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
Diff between haplo.stats versions 1.6.11 dated 2014-09-04 and 1.7.1 dated 2015-08-14
DESCRIPTION | 15 +++++---- MD5 | 66 +++++++++++++++++++++--------------------- NAMESPACE | 9 +++++ R/Ginv.R | 2 - R/geno.count.pairs.q | 2 - R/haplo.design.q | 2 - R/haplo.em.control.q | 2 - R/haplo.em.fitter.q | 2 - R/haplo.em.q | 2 - R/haplo.enum.q | 2 - R/haplo.group.q | 2 - R/haplo.hash.q | 2 - R/haplo.score.glm.q | 2 - R/haplo.score.merge.q | 2 - R/haplo.score.podds.q | 2 - R/haplo.score.q | 4 +- R/haplo.score.slide.q | 2 - R/locator.haplo.q | 2 - R/plot.haplo.score.q | 2 - R/plot.haplo.score.slide.q | 2 - R/plot.seqhap.q | 2 - R/print.haplo.em.q | 2 - R/print.haplo.glm.q | 3 - R/print.haplo.group.q | 2 - R/print.haplo.score.merge.q | 2 - R/print.haplo.score.q | 2 - R/print.haplo.score.slide.q | 2 - R/print.seqhap.q | 2 - R/printBanner.q | 2 - R/score.sim.control.q | 2 - R/seqhap.q | 2 - R/summary.haplo.em.q | 2 - R/summaryGeno.q | 2 - inst/doc/manualHaploStats.pdf |binary 34 files changed, 81 insertions(+), 72 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information System (NWIS) tools. Both EPA and USGS water
quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.3.0 dated 2015-07-07 and 2.3.1 dated 2015-08-14
DESCRIPTION | 9 +++--- MD5 | 28 +++++++++---------- R/importWaterML1.r | 9 +++--- R/readNWISdv.r | 1 R/renameColumns.R | 3 -- R/whatWQPsites.R | 4 +- README.md | 3 ++ inst/doc/dataRetrieval.R | 60 +++++++++++++++++++---------------------- inst/doc/dataRetrieval.Rnw | 34 +++++------------------ inst/doc/dataRetrieval.pdf |binary man/importWaterML1.Rd | 9 +++--- man/readNWISdv.Rd | 1 man/renameNWISColumns.Rd | 3 -- tests/testthat/tests_imports.R | 19 ++++++------ vignettes/dataRetrieval.Rnw | 32 ++++----------------- 15 files changed, 89 insertions(+), 126 deletions(-)
Title: Bootstrap Effect Sizes
Description: Calculate robust measures of effect sizes using the bootstrap.
Author: Daniel Gerlanc <dgerlanc@enplusadvisors.com> and Kris Kirby <kkirby@williams.edu>
Maintainer: Daniel Gerlanc <dgerlanc@enplusadvisors.com>
Diff between bootES versions 1.01 dated 2013-01-02 and 1.2 dated 2015-08-14
ChangeLog |only DESCRIPTION | 16 +++++++------- MD5 | 18 ++++++++++------ NAMESPACE | 7 ++++++ R/bootES.R | 29 ++++++++++++++++++++++++++- R/cohensd.R | 2 + R/univariate.R | 19 ++++++++++++++++- README.md |only inst/robust_d_test.csv |only inst/tests/runit.akpRobustD.R |only inst/tests/runit.bootES.R | 45 ++++++++++++++++++++++++++++++++++++++++-- man/bootES.Rd | 4 +++ 12 files changed, 121 insertions(+), 19 deletions(-)
Title: Model-Based Boosting
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut, cre],
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut],
Fabian Sobotka [ctb],
Fabian Scheipl [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mboost versions 2.4-2 dated 2015-02-12 and 2.5-0 dated 2015-08-14
DESCRIPTION | 17 ++-- MD5 | 59 ++++++++-------- NAMESPACE | 2 R/AAA.R | 29 -------- R/bkronecker.R | 24 +++--- R/bl.R | 132 +++++++++++++++++++++++++++----------- R/bmono.R | 30 ++++---- R/bmrf.R | 8 -- R/crossvalidation.R | 30 ++++++-- R/family.R | 32 +++++---- R/helpers.R | 24 ++++++ R/mboost.R | 6 - R/methods.R | 17 ++-- R/plot.R | 16 +++- build/vignette.rds |binary inst/CITATION | 76 +++++++++++++-------- inst/NEWS.Rd | 66 ++++++++++++++++++- inst/doc/SurvivalEnsembles.pdf |binary inst/doc/mboost.pdf |binary inst/doc/mboost_illustrations.pdf |binary inst/doc/mboost_tutorial.pdf |binary man/Family.Rd | 120 ++++++++++++++++++++++++---------- man/baselearners.Rd | 48 ++++++++++--- man/confint.Rd | 4 + man/cvrisk.Rd | 9 ++ man/glmboost.Rd | 19 +---- man/mboost.Rd | 17 ---- man/mboost_package.Rd | 4 - man/methods.Rd | 16 +++- man/plot.Rd |only man/stabsel.Rd | 7 ++ 31 files changed, 532 insertions(+), 280 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Ashley Manton [ctb],
Ben Baumer [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.10.5 dated 2015-05-06 and 1.11 dated 2015-08-14
DESCRIPTION | 28 ++-- MD5 | 75 ++++++------ NAMESPACE | 9 + R/block.R | 15 -- R/citation.R | 3 R/engine.R | 11 - R/hooks-extra.R | 67 ----------- R/hooks-html.R | 2 R/output.R | 6 R/package.R | 1 R/params.R | 207 +++++++++++++--------------------- R/plot.R | 26 +++- R/table.R | 23 ++- R/template.R | 2 R/utils-conversion.R | 6 R/utils.R | 7 + README.md | 7 - build/knitr.pdf |binary build/vignette.rds |binary inst/CITATION | 9 - inst/doc/docco-classic.html | 2 inst/doc/docco-linear.html | 2 inst/doc/knit_expand.html | 4 inst/doc/knit_print.html | 6 inst/doc/knitr-html.html | 2 inst/doc/knitr-intro.html | 12 - inst/doc/knitr-markdown.html | 4 inst/doc/knitr-refcard.pdf |binary man/chunk_hook.Rd | 30 +--- man/kable.Rd | 8 + man/knit2html.Rd | 6 man/knit_params.Rd | 61 +--------- man/knit_params_yaml.Rd |only man/plot_crop.Rd | 5 man/rst2pdf.Rd | 2 man/write_bib.Rd | 3 tests/testit/test-params.R | 97 +++++++++++---- tests/testit/test-plot.R | 6 vignettes/assets/template-refcard.tex | 2 39 files changed, 364 insertions(+), 392 deletions(-)
Title: Flexible Procedures for Clustering
Description: Various methods for clustering and cluster validation.
Fixed point clustering. Linear regression clustering. Clustering by
merging Gaussian mixture components. Symmetric
and asymmetric discriminant projections for visualisation of the
separation of groupings. Cluster validation statistics
for distance based clustering including corrected Rand index.
Cluster-wise cluster stability assessment. Methods for estimation of
the number of clusters: Calinski-Harabasz, Tibshirani and Walther's
prediction strength, Fang and Wang's bootstrap stability.
Gaussian/multinomial mixture fitting for mixed
continuous/categorical variables. Variable-wise statistics for cluster
interpretation. DBSCAN clustering. Interface functions for many
clustering methods implemented in R, including estimating the number of
clusters with kmeans, pam and clara. Modality diagnosis for Gaussian
mixtures. For an overview see package?fpc.
Author: Christian Hennig <c.hennig@ucl.ac.uk>
Maintainer: Christian Hennig <c.hennig@ucl.ac.uk>
Diff between fpc versions 2.1-9 dated 2014-10-02 and 2.1-10 dated 2015-08-14
DESCRIPTION | 13 +++++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 37 +++++++++++++++++++++++++++++++++++++ R/clusterboot.R | 4 ++-- man/cluster.stats.Rd | 17 ++++++----------- man/distancefactor.Rd | 17 +++++++---------- man/distcritmulti.Rd | 14 +++++--------- man/flexmixedruns.Rd | 12 ++++-------- man/lcmixed.Rd | 12 ++++-------- man/pamk.Rd | 11 ++++++++++- tests/Examples/fpc-Ex.Rout.save | 17 ++++++++--------- tests/fpctests.Rout.save | 22 ++++++++++++---------- 12 files changed, 113 insertions(+), 85 deletions(-)
Title: CRISPR AnalyzeR for Pooled CRISPR Screens
Description: CRISPR-Analyzer for pooled CRISPR screens (caRpools) provides an end-to-end analysis of CRISPR screens including quality control, hit candidate analysis, visualization and automated report generation using R markdown. Needs MAGeCK (http://sourceforge.net/p/mageck/wiki/Home/), bowtie2 for all functions. CRISPR (clustered regularly interspaced short palindromic repeats) is a method to perform genome editing. See <https://en.wikipedia.org/wiki/CRISPR> for more information on
CRISPR.
Author: Jan Winter, Florian Heigwer
Maintainer: Jan Winter <jan.winter@dkfz-heidelberg.de>
Diff between caRpools versions 0.82 dated 2015-08-10 and 0.82.3 dated 2015-08-14
DESCRIPTION | 6 +-- MD5 | 18 +++++----- R/compare.analysis.R | 15 ++++---- R/get.gene.info.R | 82 +++++++++++++++++++++++++----------------------- R/load.packages.R | 2 - inst/doc/CaRpools.R | 2 - inst/doc/CaRpools.Rmd | 2 - inst/doc/CaRpools.html | 10 ++--- man/compare.analysis.Rd | 2 - vignettes/CaRpools.Rmd | 2 - 10 files changed, 71 insertions(+), 70 deletions(-)