Title: Specialized, high-performance pipeline operators
Diff between pipeR versions 0.3 dated 2014-06-03 and 0.3-1 dated 2014-06-28
Description: Provides specialized, high-performance operators
for chaining commands with three forward-piping
operations: first-argument piping, free piping,
and lambda piping, making command chaining clear,
fast, readable and flexible.
Author: Kun Ren
Maintainer: Kun Ren
DESCRIPTION | 24 ++++++++++--------
MD5 | 16 ++++++++----
NEWS |only
R/functions.R | 21 +++++++---------
R/pipeR.R | 2 -
README.md | 68 +++++++++++++++++------------------------------------
man/free-piping.Rd | 2 -
tests |only
8 files changed, 58 insertions(+), 75 deletions(-)
Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.4-05 dated 2014-05-05 and 0.4-21 dated 2014-06-28
Description: phytools provides various functions for phylogenetic analysis,
mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
DESCRIPTION | 11 ++--
MD5 | 39 +++++++++-------
NAMESPACE | 12 +++--
R/anc.ML.R | 106 +++++++++++++++++++++++++++++++++-------------
R/contMap.R | 17 +++++--
R/densityMap.R | 32 +++++++++++--
R/fancyTree.R | 4 -
R/locate.yeti.R |only
R/make.simmap.R | 4 -
R/phylomorphospace3d.R | 39 +++++++++++++---
R/plotSimmap.R | 37 ++++++++++++----
R/plotTree.wBars.R |only
R/utilities.R | 81 ++++++++++++++++++++++++++---------
man/anc.ML.Rd | 6 +-
man/anc.trend.Rd | 2
man/contMap.Rd | 6 +-
man/densityMap.Rd | 4 -
man/locate.yeti.Rd |only
man/phylomorphospace3d.Rd | 6 +-
man/plotSimmap.Rd | 9 +++
man/plotTree.wBars.Rd |only
man/rescaleSimmap.Rd | 6 +-
man/setMap.Rd |only
23 files changed, 300 insertions(+), 121 deletions(-)
Title: permPGU: Using GPUs in Statistical Genomics
Diff between permGPU versions 0.14.4 dated 2014-06-20 and 0.14.5 dated 2014-06-28
Description: This R extension package can be used to carry out
permutation resampling inference in the context of RNA
microarray studies
Author: Ivo D. Shterev, Sin-Ho Jung, Stephen L. George and Kouros Owzar
Maintainer: Ivo D. Shterev
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
NEWS | 4 ++++
R/test.permgpu.R | 6 ++++++
man/permGPU-package.Rd | 4 ++--
man/test.permgpu.Rd | 6 ++++++
src/permGPU.cu | 4 ++--
7 files changed, 31 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-09 1.4.7
2013-06-18 1.4.5
2012-08-07 1.4.1
2011-10-23 1.2
Title: Regression with Functional Data
Diff between refund versions 0.1-10 dated 2014-05-08 and 0.1-11 dated 2014-06-28
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Ciprian Crainiceanu [aut], Philip Reiss [aut], Jeff Goldsmith [aut],
Lei Huang [aut, cre], Lan Huo [aut], Fabian Scheipl [aut], Bruce Swihart
[ctb], Sonja Greven [ctb], Jaroslaw Harezlak [ctb], Madan Gopal Kundu
[ctb], Yihong Zhao [ctb], Matt McLean [ctb], Luo Xiao [ctb]
Maintainer: Lei Huang
DESCRIPTION | 8
MD5 | 66 +++---
R/fpca.sc.R | 3
R/pffr-ff.R | 113 ++++++-----
R/pffr-methods.R | 4
R/pffr-sff.R | 82 ++++---
R/pffr-utilities.R | 80 ++++---
R/pffr.R | 70 +++++-
data/datalist | 12 -
man/coef.pffr.Rd | 113 ++++-------
man/coefboot.pffr.Rd | 51 +---
man/expand.call.Rd | 15 -
man/ff.Rd | 157 ++++++---------
man/ffpc.Rd | 79 ++-----
man/ffpcplot.Rd | 44 +---
man/fgam.Rd | 2
man/fitted.pffr.Rd | 23 +-
man/fpca.sc.Rd | 12 -
man/fpca.ssvd.Rd | 96 +++------
man/model.matrix.pffr.Rd | 6
man/pcre.Rd | 47 +---
man/pffr.Rd | 318 +++++++++++--------------------
man/pffrGLS.Rd | 108 +++-------
man/pffrSim.Rd | 57 ++---
man/plot.lpeer.Rd | 2
man/plot.pffr.Rd | 9
man/predict.pffr.Rd | 85 +++-----
man/print.summary.pffr.Rd | 19 -
man/pwcv.Rd | 2
man/residuals.pffr.Rd | 16 -
man/sff.Rd | 115 +++++------
man/smooth.construct.pcre.smooth.spec.Rd | 26 +-
man/smooth.construct.pss.smooth.spec.Rd | 41 +--
man/summary.pffr.Rd | 17 -
34 files changed, 848 insertions(+), 1050 deletions(-)
Title: Partial least squares Regression for generalized linear models
Diff between plsRglm versions 1.0.0 dated 2014-06-27 and 1.0.1 dated 2014-06-28
Description: This package provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand
Maintainer: Frederic Bertrand
DESCRIPTION | 6 +++---
MD5 | 14 +++++++-------
NEWS | 1 +
R/PLS_glm.R | 6 +++---
R/PLS_glm_formula.R | 6 +++---
R/PLS_lm.R | 2 +-
R/PLS_lm_formula.R | 2 +-
inst/doc/plsRglm.pdf |binary
8 files changed, 19 insertions(+), 18 deletions(-)
Title: Partial least squares Regression for Cox models and related
techniques
Diff between plsRcox versions 0.9.999 dated 2014-03-12 and 1.0 dated 2014-06-28
Description: This packages provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models in high dimensional settings.
Author: Frederic Bertrand
Maintainer: Frederic Bertrand
DESCRIPTION | 6 -
MD5 | 6 -
R/predict.plsRcoxmodel.R | 147 ++++++++++++++++++++++-------------------------
man/coxpls3.Rd | 2
4 files changed, 77 insertions(+), 84 deletions(-)
Title: A multi-platform GUI for drawing customizable graphs in R
Diff between GrapheR versions 1.9-82 dated 2013-03-30 and 1.9-83 dated 2014-06-28
Description: GrapheR is a multi-platform user interface for drawing highly customizable graphs in R. It aims to be a valuable help to quickly draw publishable graphs without any knowledge of R commands. Six kinds of graph are available: histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter plot.
Author: Maxime Hervé
Maintainer: Maxime Hervé
DESCRIPTION | 15 ++-----
MD5 | 11 +++--
NEWS | 6 +++
R/Sources.R | 98 +++++++++++++++++++++++++++++++++++++++----------
R/zzzz.R | 2 -
build |only
man/GrapheR-package.Rd | 4 +-
7 files changed, 99 insertions(+), 37 deletions(-)
Title: Interface between R and Google Charts
Diff between googleVis versions 0.5.2 dated 2014-05-05 and 0.5.3 dated 2014-06-28
Description: The googleVis package provides an interface between R and the
Google Charts API. It allows users to create web pages with
interactive charts based on R data frames, using the Google Charts API and
to display them either via the local R HTTP help server or within their own
sites, without uploading the data to Google. A modern browser with Internet
connection is required and for some charts Flash.
Author: Markus Gesmann [aut, cre],
Diego de Castillo [aut],
Joe Cheng [ctb]
Maintainer: Markus Gesmann
googleVis-0.5.2/googleVis/vignettes/googleVis.Rmd |only
googleVis-0.5.2/googleVis/vignettes/googleVis.html |only
googleVis-0.5.2/googleVis/vignettes/googleVis.md |only
googleVis-0.5.3/googleVis/DESCRIPTION | 19
googleVis-0.5.3/googleVis/MD5 | 121 -
googleVis-0.5.3/googleVis/NEWS | 26
googleVis-0.5.3/googleVis/R/gvis.R | 47
googleVis-0.5.3/googleVis/R/gvisAnnotatedTimeLine.R | 19
googleVis-0.5.3/googleVis/R/gvisCoreCharts.R | 12
googleVis-0.5.3/googleVis/R/gvisTable.R | 7
googleVis-0.5.3/googleVis/R/zzz.R | 5
googleVis-0.5.3/googleVis/README.md | 4
googleVis-0.5.3/googleVis/THANKS | 3
googleVis-0.5.3/googleVis/build/googleVis.pdf |binary
googleVis-0.5.3/googleVis/build/vignette.rds |binary
googleVis-0.5.3/googleVis/demo/Roles.R | 55
googleVis-0.5.3/googleVis/demo/googleVis.R | 6
googleVis-0.5.3/googleVis/inst/doc/Using_Roles_via_googleVis.R | 139 +
googleVis-0.5.3/googleVis/inst/doc/Using_Roles_via_googleVis.Rmd | 17
googleVis-0.5.3/googleVis/inst/doc/Using_Roles_via_googleVis.html | 822 ++++++--
googleVis-0.5.3/googleVis/inst/doc/Using_Trendlines_with_googleVis.R | 36
googleVis-0.5.3/googleVis/inst/doc/Using_Trendlines_with_googleVis.html | 186 +
googleVis-0.5.3/googleVis/inst/doc/Using_googleVis_with_knitr.R | 6
googleVis-0.5.3/googleVis/inst/doc/Using_googleVis_with_knitr.html | 193 +-
googleVis-0.5.3/googleVis/inst/doc/googleVis.Rnw | 32
googleVis-0.5.3/googleVis/inst/doc/googleVis.pdf |binary
googleVis-0.5.3/googleVis/inst/doc/googleVis_examples.R | 299 ++-
googleVis-0.5.3/googleVis/inst/doc/googleVis_examples.Rmd | 2
googleVis-0.5.3/googleVis/inst/doc/googleVis_examples.html | 965 +++++-----
googleVis-0.5.3/googleVis/man/googleVis-package.Rd | 10
googleVis-0.5.3/googleVis/man/gvisAnnotatedTimeLine.Rd | 160 -
googleVis-0.5.3/googleVis/man/gvisAnnotationChart.Rd | 122 -
googleVis-0.5.3/googleVis/man/gvisAreaChart.Rd | 61
googleVis-0.5.3/googleVis/man/gvisBarChart.Rd | 59
googleVis-0.5.3/googleVis/man/gvisBubbleChart.Rd | 87
googleVis-0.5.3/googleVis/man/gvisCalendar.Rd | 69
googleVis-0.5.3/googleVis/man/gvisCandlestickChart.Rd | 114 -
googleVis-0.5.3/googleVis/man/gvisColumnChart.Rd | 59
googleVis-0.5.3/googleVis/man/gvisComboChart.Rd | 66
googleVis-0.5.3/googleVis/man/gvisGauge.Rd | 58
googleVis-0.5.3/googleVis/man/gvisGeoChart.Rd | 147 -
googleVis-0.5.3/googleVis/man/gvisGeoMap.Rd | 145 -
googleVis-0.5.3/googleVis/man/gvisHistogram.Rd | 52
googleVis-0.5.3/googleVis/man/gvisIntensityMap.Rd | 67
googleVis-0.5.3/googleVis/man/gvisLineChart.Rd | 59
googleVis-0.5.3/googleVis/man/gvisMap.Rd | 85
googleVis-0.5.3/googleVis/man/gvisMotionChart.Rd | 159 -
googleVis-0.5.3/googleVis/man/gvisOrgChart.Rd | 94
googleVis-0.5.3/googleVis/man/gvisPieChart.Rd | 59
googleVis-0.5.3/googleVis/man/gvisSankey.Rd | 66
googleVis-0.5.3/googleVis/man/gvisScatterChart.Rd | 65
googleVis-0.5.3/googleVis/man/gvisSteppedAreaChart.Rd | 62
googleVis-0.5.3/googleVis/man/gvisTable.Rd | 89
googleVis-0.5.3/googleVis/man/gvisTimeline.Rd | 57
googleVis-0.5.3/googleVis/man/gvisTreeMap.Rd | 157 -
googleVis-0.5.3/googleVis/man/renderGvis.Rd | 33
googleVis-0.5.3/googleVis/vignettes/Ideas |only
googleVis-0.5.3/googleVis/vignettes/Using_Roles_via_googleVis.Rmd | 17
googleVis-0.5.3/googleVis/vignettes/figures/MotionChart.png |only
googleVis-0.5.3/googleVis/vignettes/figures/googleVisDemoPlots.png |only
googleVis-0.5.3/googleVis/vignettes/figures/gvisObject.png |only
googleVis-0.5.3/googleVis/vignettes/googleVis.Rnw | 32
googleVis-0.5.3/googleVis/vignettes/googleVis.bib | 10
googleVis-0.5.3/googleVis/vignettes/googleVis_examples.Rmd | 2
64 files changed, 3084 insertions(+), 2259 deletions(-)
Title: Fast and versatile argument checks
Diff between checkmate versions 1.0 dated 2014-06-17 and 1.1 dated 2014-06-28
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang
Maintainer: Michel Lang
checkmate-1.0/checkmate/R/which.first.r |only
checkmate-1.0/checkmate/tests/testthat/test_testInt.r |only
checkmate-1.1/checkmate/DESCRIPTION | 12 -
checkmate-1.1/checkmate/MD5 | 106 +++++------
checkmate-1.1/checkmate/NEWS | 11 +
checkmate-1.1/checkmate/R/assert.r | 4
checkmate-1.1/checkmate/R/checkAccess.r | 3
checkmate-1.1/checkmate/R/checkArray.r | 6
checkmate-1.1/checkmate/R/checkAtomic.r | 5
checkmate-1.1/checkmate/R/checkAtomicVector.r | 5
checkmate-1.1/checkmate/R/checkCharacter.r | 8
checkmate-1.1/checkmate/R/checkChoice.r | 3
checkmate-1.1/checkmate/R/checkClass.r | 3
checkmate-1.1/checkmate/R/checkComplex.r | 5
checkmate-1.1/checkmate/R/checkCount.r | 5
checkmate-1.1/checkmate/R/checkDataFrame.r | 8
checkmate-1.1/checkmate/R/checkDirectory.r | 3
checkmate-1.1/checkmate/R/checkEnvironment.r | 3
checkmate-1.1/checkmate/R/checkFactor.r | 8
checkmate-1.1/checkmate/R/checkFlag.r | 5
checkmate-1.1/checkmate/R/checkFunction.r | 15 +
checkmate-1.1/checkmate/R/checkInt.r | 5
checkmate-1.1/checkmate/R/checkInteger.r | 5
checkmate-1.1/checkmate/R/checkIntegerish.r | 5
checkmate-1.1/checkmate/R/checkList.r | 44 ++--
checkmate-1.1/checkmate/R/checkLogical.r | 5
checkmate-1.1/checkmate/R/checkMatrix.r | 5
checkmate-1.1/checkmate/R/checkNamed.r | 5
checkmate-1.1/checkmate/R/checkNull.r | 5
checkmate-1.1/checkmate/R/checkNumber.r | 5
checkmate-1.1/checkmate/R/checkNumeric.r | 5
checkmate-1.1/checkmate/R/checkPathForOutput.r | 3
checkmate-1.1/checkmate/R/checkScalar.r | 5
checkmate-1.1/checkmate/R/checkScalarNA.r | 5
checkmate-1.1/checkmate/R/checkString.r | 3
checkmate-1.1/checkmate/R/checkSubset.r | 20 +-
checkmate-1.1/checkmate/R/checkVector.r | 5
checkmate-1.1/checkmate/R/helper.r | 1
checkmate-1.1/checkmate/R/wfwl.r |only
checkmate-1.1/checkmate/man/assert.Rd | 4
checkmate-1.1/checkmate/man/checkArray.Rd | 3
checkmate-1.1/checkmate/man/checkDataFrame.Rd | 3
checkmate-1.1/checkmate/man/checkFunction.Rd | 4
checkmate-1.1/checkmate/man/checkList.Rd | 3
checkmate-1.1/checkmate/man/checkSubset.Rd | 10 -
checkmate-1.1/checkmate/src/checks.c | 27 +-
checkmate-1.1/checkmate/tests/testthat/test_assert.r | 8
checkmate-1.1/checkmate/tests/testthat/test_checkArray.r | 4
checkmate-1.1/checkmate/tests/testthat/test_checkCharacter.r | 2
checkmate-1.1/checkmate/tests/testthat/test_checkChoice.R | 1
checkmate-1.1/checkmate/tests/testthat/test_checkComplex.r | 2
checkmate-1.1/checkmate/tests/testthat/test_checkFunction.r | 5
checkmate-1.1/checkmate/tests/testthat/test_checkInt.r |only
checkmate-1.1/checkmate/tests/testthat/test_checkList.r | 2
checkmate-1.1/checkmate/tests/testthat/test_checkMatrix.r | 8
checkmate-1.1/checkmate/tests/testthat/test_checkSubset.r | 6
56 files changed, 244 insertions(+), 197 deletions(-)
Title: Nonparametric kernel smoothing methods for mixed data types
Diff between np versions 0.60-0 dated 2014-06-01 and 0.60-2 dated 2014-06-28
Description: This package provides a variety of nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic Research Computing Network (SHARCNET:www.sharcnet.ca).
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut]
Maintainer: Jeffrey S. Racine
CHANGELOG | 25 ++
DESCRIPTION | 8
MD5 | 138 ++++++------
R/bandwidth.R | 8
R/conbandwidth.R | 11
R/condbandwidth.R | 11
R/dbandwidth.R | 11
R/np.condensity.bw.R | 30 ++
R/np.condistribution.bw.R | 29 ++
R/np.density.bw.R | 46 +++-
R/np.distribution.bw.R | 36 ++-
R/np.plregression.R | 78 +++---
R/np.plregression.bw.R | 70 +++---
R/np.qregression.R | 7
R/np.regression.R | 29 ++
R/np.regression.bw.R | 36 ++-
R/np.singleindex.R | 40 ++-
R/np.singleindex.bw.R | 403 +++++++++++++++++++----------------
R/np.smoothcoef.R | 31 ++
R/np.smoothcoef.bw.R | 484 ++++++++++++++++++++++---------------------
R/plbandwidth.R | 7
R/rbandwidth.R | 10
R/sibandwidth.R | 5
R/smoothbandwidth.R | 9
R/util.R | 5
R/zzz.R | 2
README.md | 34 ++-
cleanup | 2
inst/doc/entropy_np.pdf |binary
inst/doc/np.pdf |binary
inst/doc/np_faq.Rnw | 360 ++++++++++++++++++-------------
inst/doc/np_faq.pdf |binary
man/data-oecd.Rd | 2
man/data-wage1.Rd | 14 -
man/np-package.Rd | 8
man/np.condensity.bw.Rd | 14 -
man/np.condistribution.Rd | 12 -
man/np.condistribution.bw.Rd | 18 -
man/np.copula.Rd | 16 -
man/np.density.Rd | 2
man/np.density.bw.Rd | 14 -
man/np.deptest.Rd | 6
man/np.distribution.Rd | 8
man/np.distribution.bw.Rd | 39 +--
man/np.kernelsum.Rd | 14 -
man/np.plot.Rd | 4
man/np.plregression.Rd | 21 +
man/np.plregression.bw.Rd | 17 -
man/np.qcmstest.Rd | 15 -
man/np.qregression.Rd | 21 -
man/np.quantile.Rd | 4
man/np.regression.Rd | 17 +
man/np.regression.bw.Rd | 7
man/np.regressioniv.Rd | 24 +-
man/np.regressionivderiv.Rd | 22 -
man/np.sdeptest.Rd | 2
man/np.sigtest.Rd | 6
man/np.singleindex.Rd | 15 -
man/np.singleindex.bw.Rd | 18 +
man/np.smoothcoef.Rd | 20 +
man/np.smoothcoef.bw.Rd | 2
man/np.unitest.Rd | 2
man/uocquantile.Rd | 4
src/headers.h | 2
src/jksum.c | 202 +++++++++++------
src/kernelcv.c | 122 +++++++---
src/kernele.c | 139 ++++++------
src/np.c | 190 ++++++++++++----
src/statmods.c | 74 ++++--
vignettes/np_faq.Rnw | 360 ++++++++++++++++++-------------
70 files changed, 2094 insertions(+), 1348 deletions(-)
Title: statistical methods for analysing multivariate abundance data
Diff between mvabund versions 3.8.4 dated 2013-12-09 and 3.9.1 dated 2014-06-28
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
mvabund-package.Rd for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: Yi Wang
DESCRIPTION | 10 +++++-----
MD5 | 21 +++++++++++++--------
NAMESPACE | 9 +++++++--
R/anova.manyany.R |only
R/manyany.R |only
R/predict.manyglm.R | 4 ++--
man/anova.manyany.Rd |only
man/anova.manyglm.Rd | 4 ++--
man/manyany.Rd |only
man/plot.manyany.Rd |only
man/residuals.manyglm.Rd | 5 +++--
man/summary.manyglm.Rd | 2 +-
src/Makevars.in | 2 +-
src/glm.cpp | 14 +++++++-------
14 files changed, 41 insertions(+), 30 deletions(-)