Title: Distance Measures for Time Series Data
Description: A set of commonly used distance measures and some additional functions which, although initially not designed for this purpose, can be used to measure the dissimilarity between time series. These measures can be used to perform clustering, classification or other data mining tasks which require the definition of a distance measure between time series.
Author: Usue Mori, Alexander Mendiburu, J.A. Lozano
Maintainer: Usue Mori <usue.mori@ehu.eus>
Diff between TSdist versions 3.2 dated 2016-02-12 and 3.3 dated 2016-05-14
DESCRIPTION | 10 +- MD5 | 74 +++++++++--------- inst/doc/README.pdf |binary man/ACFDistance.Rd | 2 man/ARLPCCepsDistance.Rd | 2 man/ARMahDistance.Rd | 2 man/ARPicDistance.Rd | 2 man/CCorDistance.Rd | 182 +++++++++++++++++++++++----------------------- man/CDMDistance.Rd | 2 man/CIDDistance.Rd | 154 +++++++++++++++++++------------------- man/CorDistance.Rd | 2 man/CortDistance.Rd | 2 man/DTWDistance.Rd | 2 man/DissimDistance.Rd | 2 man/EDRDistance.Rd | 2 man/ERPDistance.Rd | 2 man/EuclideanDistance.Rd | 2 man/FourierDistance.Rd | 2 man/FrechetDistance.Rd | 2 man/InfNormDistance.Rd | 2 man/IntPerDistance.Rd | 2 man/LBKeoghDistance.Rd | 2 man/LCSSDistance.Rd | 2 man/LPDistance.Rd | 2 man/ManhattanDistance.Rd | 2 man/MindistSaxDistance.Rd | 170 +++++++++++++++++++++--------------------- man/MinkowskiDistance.Rd | 2 man/NCDDistance.Rd | 2 man/PACFDistance.Rd | 2 man/PDCDistance.Rd | 2 man/PerDistance.Rd | 2 man/PredDistance.Rd | 2 man/STSDistance.Rd | 2 man/SpecGLKDistance.Rd | 2 man/SpecISDDistance.Rd | 2 man/SpecLLRDistance.Rd | 2 man/TquestDistance.Rd | 2 man/WavDistance.Rd | 2 38 files changed, 327 insertions(+), 327 deletions(-)
Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires
the detection of trends and change-points.
This package provides the Mann-Kendall Trend Test,
seasonal Mann-Kendall Test,
correlated seasonal Mann-Kendall Test,
partial Mann-Kendall Trend test,
(Seasonal) Sen's slope, partial correlation trend test and
change-point test after Pettitt.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between trend versions 0.1.0 dated 2016-01-06 and 0.2.0 dated 2016-05-14
DESCRIPTION | 8 ++++---- MD5 | 14 ++++++++------ NAMESPACE | 2 +- R/ww.test.R |only build/vignette.rds |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/trend.pdf |binary man/trend-package.Rd | 21 +++++++++++++++++++-- man/ww.test.Rd |only 9 files changed, 40 insertions(+), 13 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.4 dated 2016-03-26 and 0.12.5 dated 2016-05-14
Rcpp-0.12.4/Rcpp/man/loadRcppModules.Rd |only Rcpp-0.12.5/Rcpp/ChangeLog | 119 ++++++++ Rcpp-0.12.5/Rcpp/DESCRIPTION | 11 Rcpp-0.12.5/Rcpp/MD5 | 72 ++--- Rcpp-0.12.5/Rcpp/NAMESPACE | 2 Rcpp-0.12.5/Rcpp/R/Attributes.R | 12 Rcpp-0.12.5/Rcpp/R/Module.R | 31 +- Rcpp-0.12.5/Rcpp/R/Rcpp.package.skeleton.R | 266 +++++++++---------- Rcpp-0.12.5/Rcpp/R/compilerCheck.R |only Rcpp-0.12.5/Rcpp/R/loadRcppModules.R | 5 Rcpp-0.12.5/Rcpp/build/Rcpp.pdf |binary Rcpp-0.12.5/Rcpp/build/vignette.rds |binary Rcpp-0.12.5/Rcpp/inst/NEWS.Rd | 33 ++ Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-attributes.pdf |binary Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-extending.pdf |binary Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-introduction.pdf |binary Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-modules.R | 20 - Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-modules.Rnw | 21 + Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-modules.pdf |binary Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-package.pdf |binary Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-quickref.pdf |binary Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-sugar.pdf |binary Rcpp-0.12.5/Rcpp/inst/doc/Rcpp-unitTests.pdf |binary Rcpp-0.12.5/Rcpp/inst/doc/Rcpp.bib | 22 - Rcpp-0.12.5/Rcpp/inst/include/Rcpp/String.h | 23 + Rcpp-0.12.5/Rcpp/inst/include/Rcpp/config.h | 4 Rcpp-0.12.5/Rcpp/inst/skeleton/manual-page-stub.Rd |only Rcpp-0.12.5/Rcpp/inst/unitTests/cpp/Matrix.cpp | 10 Rcpp-0.12.5/Rcpp/inst/unitTests/cpp/misc.cpp | 8 Rcpp-0.12.5/Rcpp/inst/unitTests/runit.environments.R | 6 Rcpp-0.12.5/Rcpp/inst/unitTests/runit.misc.R | 5 Rcpp-0.12.5/Rcpp/man/Rcpp-deprecated.Rd |only Rcpp-0.12.5/Rcpp/man/compilerCheck.Rd |only Rcpp-0.12.5/Rcpp/man/loadModule.Rd | 2 Rcpp-0.12.5/Rcpp/man/loadRcppModules-deprecated.Rd |only Rcpp-0.12.5/Rcpp/src/api.cpp | 5 Rcpp-0.12.5/Rcpp/src/attributes.cpp | 4 Rcpp-0.12.5/Rcpp/vignettes/Rcpp-modules.Rnw | 21 + Rcpp-0.12.5/Rcpp/vignettes/Rcpp.bib | 22 - 40 files changed, 483 insertions(+), 241 deletions(-)
Title: Prediction Error Curves for Risk Prediction Models in Survival
Analysis
Description: Validation of risk predictions obtained from survival models and
competing risk models based on censored data using inverse weighting and
cross-validation.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between pec versions 2.4.7 dated 2015-10-05 and 2.4.9 dated 2016-05-14
pec-2.4.7/pec/R/print.reclassification.R |only pec-2.4.9/pec/DESCRIPTION | 16 +- pec-2.4.9/pec/MD5 | 84 +++++++-------- pec-2.4.9/pec/NAMESPACE | 3 pec-2.4.9/pec/R/cindex.R | 137 ++++++++++++++----------- pec-2.4.9/pec/R/ipcw.R | 2 pec-2.4.9/pec/R/pec-package.R | 36 ++++++ pec-2.4.9/pec/R/pec.R | 2 pec-2.4.9/pec/R/predictEventProb.R | 2 pec-2.4.9/pec/R/predictSurvProb.R | 17 ++- pec-2.4.9/pec/R/print.riskReclassification.R |only pec-2.4.9/pec/R/reclass.R | 105 +++++++++++-------- pec-2.4.9/pec/R/wallyPlot.R | 22 ++-- pec-2.4.9/pec/data/threecity.csv.gz |only pec-2.4.9/pec/man/GBSG2.Rd | 2 pec-2.4.9/pec/man/Pbc3.Rd | 4 pec-2.4.9/pec/man/R2.Rd | 4 pec-2.4.9/pec/man/Special.Rd | 2 pec-2.4.9/pec/man/calPlot.Rd | 5 pec-2.4.9/pec/man/cindex.Rd | 16 +- pec-2.4.9/pec/man/cost.Rd | 2 pec-2.4.9/pec/man/coxboost.Rd | 2 pec-2.4.9/pec/man/crps.Rd | 4 pec-2.4.9/pec/man/ipcw.Rd | 5 pec-2.4.9/pec/man/pec.Rd | 8 - pec-2.4.9/pec/man/pecCforest.Rd | 2 pec-2.4.9/pec/man/pecCtree.Rd | 3 pec-2.4.9/pec/man/pecRpart.Rd | 2 pec-2.4.9/pec/man/plot.calibrationPlot.Rd | 2 pec-2.4.9/pec/man/plot.pec.Rd | 12 +- pec-2.4.9/pec/man/plotPredictEventProb.Rd | 5 pec-2.4.9/pec/man/plotPredictSurvProb.Rd | 6 - pec-2.4.9/pec/man/predictEventProb.Rd | 4 pec-2.4.9/pec/man/predictLifeYearsLost.Rd | 4 pec-2.4.9/pec/man/predictRestrictedMeanTime.Rd | 3 pec-2.4.9/pec/man/predictSurvProb.Rd | 9 + pec-2.4.9/pec/man/print.pec.Rd | 2 pec-2.4.9/pec/man/reclass.Rd | 4 pec-2.4.9/pec/man/resolvesplitMethod.Rd | 7 - pec-2.4.9/pec/man/selectCox.Rd | 4 pec-2.4.9/pec/man/selectFGR.Rd | 10 + pec-2.4.9/pec/man/simCost.Rd | 2 pec-2.4.9/pec/man/threecity.Rd |only pec-2.4.9/pec/man/wallyPlot.Rd | 6 - pec-2.4.9/pec/src/cindex.c | 1 45 files changed, 356 insertions(+), 212 deletions(-)
Title: Different Types of Estimators to Deal with Multicollinearity
Description: When multicollinearity exists among predictor variables of the linear model, least square estimators does not provide a better solution for estimating parameters. To deal with multicollinearity several estimators are proposed in the literature. Some of these estimators are Ordinary Least Square Estimator (OLSE), Ordinary Generalized Ordinary Least Square Estimator (OGOLSE), Ordinary Ridge Regression Estimator (ORRE), Ordinary Generalized Ridge Regression Estimator (OGRRE), Restricted Least Square Estimator (RLSE), Ordinary Generalized Restricted Least Square Estimator (OGRLSE), Ordinary Mixed Regression Estimator (OMRE), Ordinary Generalized Mixed Regression Estimator (OGMRE), Liu Estimator (LE), Ordinary Generalized Liu Estimator (OGLE), Restricted Liu Estimator (RLE), Ordinary Generalized Restricted Liu Estimator (OGRLE), Stochastic Restricted Liu Estimator (SRLE), Ordinary Generalized Stochastic Restricted Liu Estimator (OGSRLE), Type (1),(2),(3) Liu Estimator (Type-1,2,3 LTE), Ordinary Generalized Type (1),(2),(3) Liu Estimator (Type-1,2,3 OGLTE), Type (1),(2),(3) Adjusted Liu Estimator (Type-1,2,3 ALTE), Ordinary Generalized Type (1),(2),(3) Adjusted Liu Estimator (Type-1,2,3 OGALTE), Almost Unbiased Ridge Estimator (AURE), Ordinary Generalized Almost Unbiased Ridge Estimator (OGAURE), Almost Unbiased Liu Estimator (AULE), Ordinary Generalized Almost Unbiased Liu Estimator (OGAULE), Stochastic Restricted Ridge Estimator (SRRE), Ordinary Generalized Stochastic Restricted Ridge Estimator (OGSRRE), Restricted Ridge Regression Estimator (RRRE) and Ordinary Generalized Restricted Ridge Regression Estimator (OGRRRE). To select the best estimator in a practical situation the Mean Square Error (MSE) is used. Using this package scalar MSE value of all the above estimators and Prediction Sum of Square (PRESS) values of some of the estimators can be obtained, and the variation of the MSE and PRESS values for the relevant estimators can be shown graphically.
Author: Ajith Dissanayake [aut, cre],
P. Wijekoon [aut],
R-core [cph]
Maintainer: Ajith Dissanayake <sudeera333@gmail.com>
Diff between lrmest versions 1.0 dated 2013-08-31 and 3.0 dated 2016-05-14
lrmest-1.0/lrmest/R/alte1.R |only lrmest-1.0/lrmest/R/alte2.R |only lrmest-1.0/lrmest/R/alte3.R |only lrmest-1.0/lrmest/R/aul.R |only lrmest-1.0/lrmest/R/aur.R |only lrmest-1.0/lrmest/R/checkm.R |only lrmest-1.0/lrmest/R/liu.R |only lrmest-1.0/lrmest/R/lte1.R |only lrmest-1.0/lrmest/R/lte2.R |only lrmest-1.0/lrmest/R/lte3.R |only lrmest-1.0/lrmest/R/mixe.R |only lrmest-1.0/lrmest/R/ols.R |only lrmest-1.0/lrmest/R/rid.R |only lrmest-1.0/lrmest/R/rliu.R |only lrmest-1.0/lrmest/R/rls.R |only lrmest-1.0/lrmest/R/rrre.R |only lrmest-1.0/lrmest/R/srliu.R |only lrmest-1.0/lrmest/R/srre.R |only lrmest-1.0/lrmest/man/lrmest-package.Rd |only lrmest-3.0/lrmest/DESCRIPTION | 19 +- lrmest-3.0/lrmest/MD5 | 108 ++++++++++----- lrmest-3.0/lrmest/NAMESPACE | 4 lrmest-3.0/lrmest/R/alte1.r |only lrmest-3.0/lrmest/R/alte2.r |only lrmest-3.0/lrmest/R/alte3.r |only lrmest-3.0/lrmest/R/aule.r |only lrmest-3.0/lrmest/R/aure.r |only lrmest-3.0/lrmest/R/checkmt.r |only lrmest-3.0/lrmest/R/goeed.R |only lrmest-3.0/lrmest/R/liue.r |only lrmest-3.0/lrmest/R/lt1.r |only lrmest-3.0/lrmest/R/lt2.r |only lrmest-3.0/lrmest/R/lt3.r |only lrmest-3.0/lrmest/R/mix.r |only lrmest-3.0/lrmest/R/ogalte1.r |only lrmest-3.0/lrmest/R/ogalte2.r |only lrmest-3.0/lrmest/R/ogalte3.r |only lrmest-3.0/lrmest/R/ogaul.r |only lrmest-3.0/lrmest/R/ogaure.r |only lrmest-3.0/lrmest/R/ogliu.r |only lrmest-3.0/lrmest/R/oglte1.r |only lrmest-3.0/lrmest/R/oglte2.r |only lrmest-3.0/lrmest/R/oglte3.r |only lrmest-3.0/lrmest/R/ogmix.r |only lrmest-3.0/lrmest/R/ogrid.r |only lrmest-3.0/lrmest/R/ogrliu.r |only lrmest-3.0/lrmest/R/ogrls.r |only lrmest-3.0/lrmest/R/ogrrre.r |only lrmest-3.0/lrmest/R/ogsrl.r |only lrmest-3.0/lrmest/R/ogsrre.r |only lrmest-3.0/lrmest/R/olse.r |only lrmest-3.0/lrmest/R/optimum.R | 217 ++++++++++++++++++++++++++++++- lrmest-3.0/lrmest/R/ride.r |only lrmest-3.0/lrmest/R/rliue.r |only lrmest-3.0/lrmest/R/rlse.r |only lrmest-3.0/lrmest/R/rrr.r |only lrmest-3.0/lrmest/R/srliue.r |only lrmest-3.0/lrmest/R/srr.r |only lrmest-3.0/lrmest/man/alte1.Rd | 9 - lrmest-3.0/lrmest/man/alte2.Rd | 9 - lrmest-3.0/lrmest/man/alte3.Rd | 11 - lrmest-3.0/lrmest/man/aul.Rd | 7 - lrmest-3.0/lrmest/man/aur.Rd | 6 lrmest-3.0/lrmest/man/liu.Rd | 8 - lrmest-3.0/lrmest/man/lrmest2-package.Rd |only lrmest-3.0/lrmest/man/lte1.Rd | 9 - lrmest-3.0/lrmest/man/lte2.Rd | 9 - lrmest-3.0/lrmest/man/lte3.Rd | 9 - lrmest-3.0/lrmest/man/ogalt1.Rd |only lrmest-3.0/lrmest/man/ogalt2.Rd |only lrmest-3.0/lrmest/man/ogalt3.Rd |only lrmest-3.0/lrmest/man/ogaul.Rd |only lrmest-3.0/lrmest/man/ogaur.Rd |only lrmest-3.0/lrmest/man/ogliu.Rd |only lrmest-3.0/lrmest/man/oglt1.Rd |only lrmest-3.0/lrmest/man/oglt2.Rd |only lrmest-3.0/lrmest/man/oglt3.Rd |only lrmest-3.0/lrmest/man/ogmix.Rd |only lrmest-3.0/lrmest/man/ogols.Rd |only lrmest-3.0/lrmest/man/ogre.Rd |only lrmest-3.0/lrmest/man/ogrliu.Rd |only lrmest-3.0/lrmest/man/ogrls.Rd |only lrmest-3.0/lrmest/man/ogrrre.Rd |only lrmest-3.0/lrmest/man/ogsrliu.Rd |only lrmest-3.0/lrmest/man/ogsrre.Rd |only lrmest-3.0/lrmest/man/optimum.Rd | 23 ++- lrmest-3.0/lrmest/man/rid.Rd | 6 lrmest-3.0/lrmest/man/rliu.Rd | 8 - lrmest-3.0/lrmest/man/rrre.Rd | 6 lrmest-3.0/lrmest/man/srliu.Rd | 8 - lrmest-3.0/lrmest/man/srre.Rd | 6 91 files changed, 388 insertions(+), 94 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 [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.5.0 dated 2016-02-16 and 0.6.0 dated 2016-05-14
DESCRIPTION | 13 MD5 | 80 ++--- NAMESPACE | 44 +- NEWS.md | 236 ++++++++------- R/RcppExports.R | 154 +++++----- R/bandwidths.R |only R/dprhkdecop.R | 541 ++++++++++++++++++------------------ R/eval_tll.R | 22 - R/eval_tt.R | 96 +++--- R/generics.R | 302 ++++++++++---------- R/helpers.R | 549 +++++-------------------------------- R/kdecop.R | 506 +++++++++++++++++----------------- R/kdecopula-package.R | 268 +++++++++--------- R/plot.kdecopula.R | 426 +++++++++++++++------------- README.md | 370 ++++++++++++------------ build/vignette.rds |binary inst/README-unnamed-chunk-10-1.png |binary inst/README-unnamed-chunk-12-1.png |binary inst/README-unnamed-chunk-3-1.png |binary inst/README-unnamed-chunk-6-1.png |binary inst/README-unnamed-chunk-7-1.png |binary inst/README-unnamed-chunk-8-1.png |binary inst/README-unnamed-chunk-9-1.png |binary inst/doc/kdecopula.pdf |binary inst/doc/kdecopula.pdf.asis | 4 inst/include/evaluators.h | 22 - inst/include/hfunc.h | 64 ++-- inst/include/integrate.h | 28 - inst/include/interp.h | 76 ++--- inst/include/kernels.h | 26 - inst/include/renorm.h | 28 - man/dkdecop.Rd | 166 +++++------ man/hkdecop.Rd |only man/kdecop.Rd | 274 +++++++++--------- man/kdecopula.Rd | 142 ++++----- man/logLik.kdecopula.Rd | 86 ++--- man/plot.kdecopula.Rd | 119 ++++---- man/wdbc.Rd | 136 ++++----- src/RcppExports.cpp | 17 - src/hfunc.cpp | 159 ++++++---- src/interp.cpp | 64 +++- vignettes/kdecopula.pdf.asis | 4 42 files changed, 2389 insertions(+), 2633 deletions(-)
Title: Using R to Install Stuff (Such As: R, Rtools, RStudio, Git, and
More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.17.5 dated 2016-03-20 and 0.17.8 dated 2016-05-14
ChangeLog | 41 +++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NEWS | 21 +++++++++++++++++++++ R/install.R | 26 ++++++++++++++++++++------ R/updateR.R | 22 +++++++++++++--------- R/zzz.R | 2 +- man/install.CMake.Rd | 2 +- man/require2.Rd | 4 ++-- man/updateR.Rd | 2 +- 10 files changed, 115 insertions(+), 35 deletions(-)
Title: Belief Propagation in Genotype-Phenotype Networks
Description: Belief propagation methods in genotype-phenotype networks (Conditional Gaussian and Discrete Bayesian Networks) to propagate phenotypic evidence through the network.
Author: Janhavi Moharil
Maintainer: Janhavi Moharil <janhavim@buffalo.edu>
Diff between geneNetBP versions 1.0.0 dated 2016-03-17 and 2.0.0 dated 2016-05-14
geneNetBP-1.0.0/geneNetBP/R/plot.gnbp.R |only geneNetBP-1.0.0/geneNetBP/man/absorb.gnbp.Rd |only geneNetBP-1.0.0/geneNetBP/man/fit.gnbp.Rd |only geneNetBP-1.0.0/geneNetBP/man/plot.gnbp.Rd |only geneNetBP-1.0.0/geneNetBP/vignettes/mouse_graph.eps |only geneNetBP-1.0.0/geneNetBP/vignettes/toy_graph.eps |only geneNetBP-2.0.0/geneNetBP/DESCRIPTION | 21 geneNetBP-2.0.0/geneNetBP/MD5 | 57 geneNetBP-2.0.0/geneNetBP/NAMESPACE | 10 geneNetBP-2.0.0/geneNetBP/R/absorb.dbn.R |only geneNetBP-2.0.0/geneNetBP/R/absorb.gnbp.R | 123 - geneNetBP-2.0.0/geneNetBP/R/fit.dbn.R |only geneNetBP-2.0.0/geneNetBP/R/fit.gnbp.R | 246 ++- geneNetBP-2.0.0/geneNetBP/R/plot-methods.R |only geneNetBP-2.0.0/geneNetBP/build/vignette.rds |binary geneNetBP-2.0.0/geneNetBP/data/hdl.rda |only geneNetBP-2.0.0/geneNetBP/data/mouse.rda |binary geneNetBP-2.0.0/geneNetBP/data/toy.rda |binary geneNetBP-2.0.0/geneNetBP/data/yeast.rda |binary geneNetBP-2.0.0/geneNetBP/inst/doc/geneNetBPvignette.R | 198 ++- geneNetBP-2.0.0/geneNetBP/inst/doc/geneNetBPvignette.Rnw | 916 +++++++++++--- geneNetBP-2.0.0/geneNetBP/inst/doc/geneNetBPvignette.pdf |binary geneNetBP-2.0.0/geneNetBP/man/absorb-methods.Rd |only geneNetBP-2.0.0/geneNetBP/man/fit-methods.Rd |only geneNetBP-2.0.0/geneNetBP/man/gen.evidence.Rd | 6 geneNetBP-2.0.0/geneNetBP/man/geneNetBP-package.Rd | 23 geneNetBP-2.0.0/geneNetBP/man/hdl.Rd |only geneNetBP-2.0.0/geneNetBP/man/mouse.Rd | 12 geneNetBP-2.0.0/geneNetBP/man/plot-methods.Rd |only geneNetBP-2.0.0/geneNetBP/man/toy.Rd | 11 geneNetBP-2.0.0/geneNetBP/man/yeast.Rd | 15 geneNetBP-2.0.0/geneNetBP/vignettes/geneNetBPvignette.Rnw | 916 +++++++++++--- geneNetBP-2.0.0/geneNetBP/vignettes/hdl_gnbp.eps |only geneNetBP-2.0.0/geneNetBP/vignettes/mouse_cgbn_gpfit.eps |only geneNetBP-2.0.0/geneNetBP/vignettes/newbib02.bib | 11 geneNetBP-2.0.0/geneNetBP/vignettes/toy_graph.png |only geneNetBP-2.0.0/geneNetBP/vignettes/yeast_db_cox10.eps |only geneNetBP-2.0.0/geneNetBP/vignettes/yeast_db_cox10_FC.eps |only geneNetBP-2.0.0/geneNetBP/vignettes/yeast_db_dbnfit.eps |only geneNetBP-2.0.0/geneNetBP/vignettes/yeast_db_gpfit.eps |only 40 files changed, 2052 insertions(+), 513 deletions(-)
Title: Various R Functions from the Kostas Lab
Description: A collection of R functions of common use in
the Kostas Lab for microbial ecology.
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
Diff between enveomics.R versions 1.0.1 dated 2016-03-06 and 1.1.0 dated 2016-05-14
DESCRIPTION | 7 MD5 | 25 +- NAMESPACE | 29 +-- R/growthcurve.R |only R/recplot2.R | 335 ++++++++++++++++++++++++-------------- README.md | 30 ++- data/growth.curves.rda |only man/enve.GrowthCurve-class.Rd |only man/enve.RecPlot2.Peak-class.Rd | 21 +- man/enve.col2alpha.Rd |only man/enve.growthcurve.Rd |only man/enve.recplot2.changeCutoff.Rd |only man/enve.recplot2.findPeaks.Rd | 50 +++-- man/growth.curves.Rd |only man/plot.enve.GrowthCurve.Rd |only man/plot.enve.RecPlot2.Rd | 46 +++-- man/summary.enve.GrowthCurve.Rd |only man/z$-methods.Rd | 5 18 files changed, 348 insertions(+), 200 deletions(-)
Title: Analyze Cricketers Based on ESPN Cricinfo Statsguru
Description: Tools for analyzing performances of cricketers based on stats in
ESPN Cricinfo Statsguru. The toolset can be used for analysis of Tests,ODIs
and Twenty20 matches of both batsmen and bowlers.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between cricketr versions 0.0.12 dated 2016-01-01 and 0.0.13 dated 2016-05-14
DESCRIPTION | 8 +++---- MD5 | 32 +++++++++++++++++++++-------- R/batsmanCumulativeAverageRuns.R |only R/batsmanCumulativeStrikeRate.R |only R/bowlerCumulativeAvgEconRate.R |only R/bowlerCumulativeAvgWickets.R |only R/relativeBatsmanCumulativeAvgRuns.R |only R/relativeBatsmanCumulativeStrikeRate.R |only R/relativeBowlerCumulativeAvgWickets.R |only R/relativeBowlerCumulativeEconRate.R |only README.md | 7 ++++-- data/ashwin1.csv | 15 +++++++++++++ data/kohli1.csv | 13 +++++++++++ man/batsmanCumulativeAverageRuns.Rd |only man/batsmanCumulativeStrikeRate.Rd |only man/bowlerCumulativeAvgEconRate.Rd |only man/bowlerCumulativeAvgWickets.Rd |only man/getPlayerData.Rd | 3 -- man/getPlayerDataOD.Rd | 2 - man/getPlayerDataSp.Rd | 2 - man/getPlayerDataTT.Rd | 2 - man/relativeBatsmanCumulativeAvgRuns.Rd |only man/relativeBatsmanCumulativeStrikeRate.Rd |only man/relativeBowlerCumulativeAvgEconRate.Rd |only man/relativeBowlerCumulativeAvgWickets.Rd |only 25 files changed, 65 insertions(+), 19 deletions(-)
Title: Reproduce Statistical Analyses and Meta-Analyses
Description: The reproducer R package includes data analysis functions and data
sets (e.g., related to software defect prediction) to streamline reproducible
research in software engineering.
Author: Lech Madeyski [cre, aut, ctb],
Marian Jureczko [ctb] (Data contributor),
Barbara Kitchenham [ctb] (Data contributor),
David Budgen [ctb] (Data contributor),
Pearl Brereton [ctb] (Data contributor),
Jacky Keung [ctb] (Data contributor),
Stuart Charters [ctb] (Data contributor),
Shirley Gibbs [ctb] (Data contributor),
Amnart Pohthong [ctb] (Data contributor)
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>
Diff between reproducer versions 0.1.4 dated 2016-01-25 and 0.1.5 dated 2016-05-14
DESCRIPTION | 12 ++++---- MD5 | 34 +++++++++++------------ NEWS.md | 8 +++++ R/data.R | 20 ++++++------- R/reproducer.R | 2 - README.md | 8 ++--- data/KitchenhamMadeyskiBudgen16.SubjectData.rda |binary inst/CITATION | 23 +++++++++++++++ man/KitchenhamMadeyskiBudgen16.COCOMO.Rd | 2 - man/KitchenhamMadeyskiBudgen16.DiffInDiffData.Rd | 2 - man/KitchenhamMadeyskiBudgen16.FINNISH.Rd | 2 - man/KitchenhamMadeyskiBudgen16.PolishData.Rd | 2 - man/KitchenhamMadeyskiBudgen16.PolishSubjects.Rd | 2 - man/KitchenhamMadeyskiBudgen16.SubjectData.Rd | 2 - man/Madeyski15EISEJ.OpenProjects.Rd | 2 - man/Madeyski15EISEJ.PropProjects.Rd | 2 - man/Madeyski15EISEJ.StudProjects.Rd | 2 - man/Madeyski15SQJ.NDC.Rd | 2 - 18 files changed, 79 insertions(+), 48 deletions(-)
Title: Visualizing and Analyzing Mass Spectrometry Related Data in
Proteomics
Description: This R package helps with quality checks, visualizations
and analysis of mass spectrometry data, coming from proteomics
experiments. The package is developed, tested and used at the Functional
Genomics Center Zurich. We use this package mainly for prototyping,
teaching, and having fun with proteomics data. But it can also be
used to do data analysis for small scale data sets.
Author: Christian Panse <cp@fgcz.ethz.ch>, Jonas Grossmann <jg@fgcz.ethz.ch>,
Simon Barkow-Oesterreicher <sb@fgcz.ethz.ch>
Maintainer: Christian Panse <cp@fgcz.ethz.ch>
Diff between protViz versions 0.2.9 dated 2014-09-30 and 0.2.15 dated 2016-05-14
protViz-0.2.15/protViz/DESCRIPTION | 14 +++++++------- protViz-0.2.15/protViz/MD5 | 16 +++++++++------- protViz-0.2.15/protViz/NAMESPACE | 15 +++++++++++++++ protViz-0.2.15/protViz/R/fragmentIon.R | 7 ++----- protViz-0.2.15/protViz/README.md |only protViz-0.2.15/protViz/build/vignette.rds |binary protViz-0.2.15/protViz/inst/CITATION |only protViz-0.2.15/protViz/inst/NEWS.Rd |only protViz-0.2.15/protViz/man/fragmentIons.Rd | 7 ++++++- protViz-0.2.15/protViz/vignettes/PTM_MarkerFinder.Rnw | 2 +- protViz-0.2.9/protViz/NEWS |only 11 files changed, 40 insertions(+), 21 deletions(-)
Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control
association tests of highly polymorphic genetic data [e.g., human leukocyte antigen
(HLA) data]. Performs association tests at multiple levels of polymorphism
(haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach
JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a
common class to account for sparse cells in tables as described by Hollenbach JA,
Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill
Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
Diff between BIGDAWG versions 1.3.4 dated 2016-04-09 and 1.4.0 dated 2016-05-14
BIGDAWG-1.3.4/BIGDAWG/data/HLA_sample.RData |only BIGDAWG-1.3.4/BIGDAWG/man/HWEChiSq.Rd |only BIGDAWG-1.4.0/BIGDAWG/DESCRIPTION | 12 BIGDAWG-1.4.0/BIGDAWG/MD5 | 59 - BIGDAWG-1.4.0/BIGDAWG/NEWS | 144 ++-- BIGDAWG-1.4.0/BIGDAWG/R/A_ExonPtnAlign_functions.R | 8 BIGDAWG-1.4.0/BIGDAWG/R/BIGDAWG.R | 57 + BIGDAWG-1.4.0/BIGDAWG/R/CheckRelease.R |only BIGDAWG-1.4.0/BIGDAWG/R/HWE.R | 90 -- BIGDAWG-1.4.0/BIGDAWG/R/HWE_support_functions.R | 86 ++ BIGDAWG-1.4.0/BIGDAWG/R/check_functions.R | 390 +++++------ BIGDAWG-1.4.0/BIGDAWG/R/data.R | 28 BIGDAWG-1.4.0/BIGDAWG/R/general_functions.R | 703 ++++++++++----------- BIGDAWG-1.4.0/BIGDAWG/R/sysdata.rda |binary BIGDAWG-1.4.0/BIGDAWG/R/update_wrapper.R | 177 ++--- BIGDAWG-1.4.0/BIGDAWG/build/vignette.rds |binary BIGDAWG-1.4.0/BIGDAWG/data/HLA_data.RData |only BIGDAWG-1.4.0/BIGDAWG/inst/doc/BIGDAWG.Rmd | 372 ++++++----- BIGDAWG-1.4.0/BIGDAWG/inst/doc/BIGDAWG.html | 454 +++++++------ BIGDAWG-1.4.0/BIGDAWG/man/BIGDAWG.Rd | 108 +-- BIGDAWG-1.4.0/BIGDAWG/man/CheckRelease.Rd |only BIGDAWG-1.4.0/BIGDAWG/man/DRB345.parser.Rd | 36 - BIGDAWG-1.4.0/BIGDAWG/man/DRB345.zygosity.Rd | 36 - BIGDAWG-1.4.0/BIGDAWG/man/Err.Log.Rd | 42 - BIGDAWG-1.4.0/BIGDAWG/man/H.Rd | 40 - BIGDAWG-1.4.0/BIGDAWG/man/HLA_data.Rd | 2 BIGDAWG-1.4.0/BIGDAWG/man/HWE.ChiSq.Rd |only BIGDAWG-1.4.0/BIGDAWG/man/HWE.wrapper.Rd |only BIGDAWG-1.4.0/BIGDAWG/man/UpdateRelease.Rd | 43 - BIGDAWG-1.4.0/BIGDAWG/man/getAllele.Count.Rd | 36 - BIGDAWG-1.4.0/BIGDAWG/man/getCS.Mat.Rd | 48 - BIGDAWG-1.4.0/BIGDAWG/man/getCS.stat.Rd | 40 - BIGDAWG-1.4.0/BIGDAWG/man/getHap.Rd | 40 - BIGDAWG-1.4.0/BIGDAWG/vignettes/BIGDAWG.Rmd | 372 ++++++----- 34 files changed, 1815 insertions(+), 1608 deletions(-)
Title: Research Project Directory Generator
Description: Create a project directory structure, along with typical files
for that project. This allows projects to be quickly and easily created,
as well as for them to be standardized. Designed specifically with scientists
in mind (mainly bio-medical researchers, but likely applies to other fields).
Author: Luke Johnston [aut, cre]
Maintainer: Luke Johnston <lwjohnst@gmail.com>
Diff between prodigenr versions 0.2.6 dated 2016-04-29 and 0.2.7 dated 2016-05-14
DESCRIPTION | 6 ++-- MD5 | 15 ++++++---- NEWS.md |only R/prodigen.R | 5 ++- README.md | 8 ++--- build/vignette.rds |binary inst/doc/introduction.html | 11 +++---- inst/templates/files/Rprofile |only inst/templates/files/rstudio |only tests/testthat/test-projects.R | 58 ++++++++++++++++++++--------------------- 10 files changed, 54 insertions(+), 49 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii)
Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v)
Matrix functions, (vi) Projector and canonical efficiency functions, and (vii)
Miscellaneous functions. A document 'daeDesignRandomization.pdf', available
in the doc subdirectory of the installation directory for 'dae', describes the
use of the package for generating randomized layouts for experiments. The ANOVA
functions facilitate the extraction of information when the 'Error' function has
been used in the call to 'aov'.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between dae versions 2.7-6 dated 2015-11-03 and 2.7-15 dated 2016-05-14
DESCRIPTION | 24 +- MD5 | 75 +++++--- NAMESPACE | 14 + R/design.plot.r | 41 ++-- R/design.r |only R/designPlot.r |only R/fac.functions.r | 18 +- R/fac.matop.r | 5 R/mat.functions.r | 230 +++++++++++++++++++++++++-- R/proj.canon.v4.r | 26 ++- R/proj.r | 33 ++- R/projs.canon.v4.r | 10 - build/partial.rdb |binary inst/NEWS.Rd | 49 +++++ inst/doc/dae-manual.pdf |binary man/Ameasures.Rd |only man/Sensory3Phase.dat.Rd | 1 man/as.numfac.Rd | 4 man/blockboundary.plot.Rd | 6 man/blockboundaryPlot.Rd |only man/dae-package.Rd | 376 ++++++++++++++++++++++++++------------------- man/design.plot.Rd | 14 + man/designLatinSqrSys.Rd |only man/designPlot.Rd |only man/efficiency.criteria.Rd | 21 +- man/fac.divide.Rd | 2 man/fac.layout.Rd | 8 man/fac.recode.Rd | 12 - man/fac.sumop.Rd | 2 man/mat.Vpred.Rd |only man/mat.ar1.Rd | 16 + man/mat.ar2.Rd |only man/mat.ar3.Rd |only man/mat.arma.Rd |only man/mat.banded.Rd | 4 man/mat.exp.Rd | 8 man/mat.ma1.Rd |only man/mat.ma2.Rd |only man/mat.sar2.Rd |only man/proj2.combine.Rd | 14 + man/projs.2canon.Rd | 12 - man/projs.canon.Rd | 20 +- man/projs.structure.Rd | 7 man/summary.p2canon.Rd | 12 - man/summary.pcanon.Rd | 13 - 45 files changed, 742 insertions(+), 335 deletions(-)