Title: Regularized Linear Models
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between mpath versions 0.1-18 dated 2015-06-10 and 0.1-19 dated 2015-07-23
DESCRIPTION | 6 +++--- MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 2 ++ NEWS | 7 ++++++- build/vignette.rds |binary inst/doc/german.pdf |binary man/breadReg.Rd | 2 +- man/conv2zipath.Rd | 2 +- man/cv.glmreg.Rd | 2 +- man/cv.glmregNB.Rd | 4 ++-- man/cv.glmreg_fit.Rd | 4 ++-- man/cv.zipath.Rd | 7 +++++-- man/glmreg.Rd | 8 ++++---- man/glmregNB.Rd | 11 +++++++---- man/glmreg_fit.Rd | 12 ++++++------ man/meatReg.Rd | 2 +- man/mpath-internal.Rd | 2 +- man/p_zipath.Rd | 4 ++-- man/se.Rd | 2 +- man/tuning_zipath.Rd | 4 ++-- man/vuong.Rd | 6 +++--- man/zipath.Rd | 14 +++++++------- vignettes/mpath.bib | 2 +- 23 files changed, 80 insertions(+), 67 deletions(-)
Title: Wilcox Robust Estimation and Testing
Description: A user-friendly version of Wilcox' robust statistics functions (WRS package on GitHub). It implements robust tests for various ANOVA and ANCOVA techniques as described in R. Wilcox (2012) 'Introduction to Robust Estimation and Hypothesis Testing'.
Author: Patrick Mair [cre, aut],
Felix Schoenbrodt [aut],
Rand Wilcox [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between WRS2 versions 0.3-1 dated 2014-12-03 and 0.3-2 dated 2015-07-23
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- NAMESPACE | 6 ++++-- man/WRS2-package.Rd | 4 ++-- man/spider.Rd | 2 +- 5 files changed, 19 insertions(+), 17 deletions(-)
Title: Bayesian Variable Selection and Model Choice for Generalized
Additive Mixed Models
Description: Bayesian variable selection, model choice, and regularized
estimation for (spatial) generalized additive mixed regression models
via stochastic search variable selection with spike-and-slab priors.
Author: Fabian Scheipl
<fabian.scheipl@stat.uni-muenchen.de>
Maintainer: Fabian Scheipl
<fabian.scheipl@stat.uni-muenchen.de>
Diff between spikeSlabGAM versions 1.1-8 dated 2014-12-04 and 1.1-9 dated 2015-07-23
DESCRIPTION | 21 MD5 | 76 - NAMESPACE | 9 NEWS | 6 R/bugs.R | 84 - R/plot.R | 1307 ++++++++++++----------- R/predict.R | 411 +++---- R/spikeAndSlab.R | 1097 ++++++++++---------- R/spikeSlabGAM.R | 218 ++- R/ssGAMDesign.R | 542 +++++---- R/summary.R | 327 +++-- R/terms.R | 839 ++++++++------- R/utils.R | 1367 ++++++++++++------------- R/zzz.R |only build/vignette.rds |binary inst/CITATION | 16 inst/doc/UsingSpikeSlabGAM.R | 121 +- inst/doc/UsingSpikeSlabGAM.Rnw | 717 ++++++------- inst/doc/UsingSpikeSlabGAM.pdf |binary man/evalTerm.Rd | 30 man/fct.Rd | 6 man/getPosteriorTerm.Rd | 11 man/lin.Rd | 9 man/mrf.Rd | 43 man/plot.spikeSlabGAM.Rd | 97 + man/plotTerm.Rd | 75 - man/predict.spikeSlabGAM.Rd | 50 man/print.summary.spikeSlabGAM.Rd | 17 man/rnd.Rd | 6 man/sm.Rd | 50 man/spikeAndSlab.Rd | 190 +-- man/spikeSlabGAM.Rd | 132 +- man/srf.Rd | 79 - man/ssGAM2Bugs.Rd | 20 man/ssGAMDesign.Rd | 67 - man/summary.spikeSlabGAM.Rd | 30 man/u.Rd | 3 src/Makevars | 2 vignettes/UsingSpikeSlabGAM-plotm1sm2fprep.pdf |only vignettes/UsingSpikeSlabGAM.Rnw | 717 ++++++------- 40 files changed, 4575 insertions(+), 4217 deletions(-)
Title: Rasch Sampler
Description: MCMC based sampling of binary matrices with fixed margins as used in exact Rasch model tests.
Author: Patrick Mair [cre, aut],
Reinhold Hatzinger [aut],
Norman D. Verhelst [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between RaschSampler versions 0.8-7 dated 2014-11-26 and 0.8-8 dated 2015-07-23
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- man/RaschSampler-package.Rd | 10 ++++------ 3 files changed, 12 insertions(+), 14 deletions(-)
Title: Routines for Constructing and Evaluating Self-Organizing Maps
Description: A set of routines which are useful in constructing
and evaluating self-organizing maps (SOMs).
Author: Lutz Hamel [aut, cre],
Benjamin Ott [aut],
Gregory Breard [aut]
Maintainer: Lutz Hamel <hamel@cs.uri.edu>
Diff between popsom versions 2.3 dated 2013-10-09 and 3.0.1 dated 2015-07-23
DESCRIPTION | 16 +-- MD5 | 12 +- NAMESPACE | 4 R/map-utils.R | 236 +++++++++++++++++++++++++++++++++++++++++++----- man/map.accuracy.Rd |only man/map.quality.Rd |only man/map.significance.Rd | 2 man/popsom-internal.Rd | 14 ++ 8 files changed, 244 insertions(+), 40 deletions(-)
Title: Process Improvement using Data
Description: A collection of scripts and data files for the statistics text:
"Process Improvement using Data". The package contains code for designed
experiments, data sets and other convenience functions used in the book.
Author: Kevin Dunn [aut, cre]
Maintainer: Kevin Dunn <kevin.dunn@mcmaster.ca>
Diff between pid versions 0.15 dated 2015-07-12 and 0.32 dated 2015-07-23
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++++++++++++------- NAMESPACE | 21 ++++++++++++++++++--- R/contourPlot.R |only R/grocery.R |only R/manufacture.R |only R/paretoPlot.R | 33 ++++++++++++++++++++++----------- R/popcorn.R |only R/tradeOffTable.R |only R/tradeoff.R |only data/boilingpot.rda |only data/golf.rda |only data/solar.rda |binary inst |only man/boilingpot.Rd |only man/contourPlot.Rd |only man/figures |only man/golf.Rd |only man/grocery.Rd |only man/manfacture.Rd |only man/oildoe.Rd | 2 +- man/pid-package.Rd | 13 +++---------- man/popcorn.Rd |only man/solar.Rd | 2 +- man/tradeOffTable.Rd |only man/tradeoff.Rd |only 26 files changed, 77 insertions(+), 38 deletions(-)
Title: Discover Probable Duplicates in Plant Genetic Resources
Collections
Description: Provides functions to aid the identification of probable/possible
duplicates in Plant Genetic Resources (PGR) collections using
'passport databases' comprising of information records of each constituent
sample. These include methods for cleaning the data, creation of a
searchable Key Word in Context (KWIC) index of keywords associated with
sample records and the identification of nearly identical records with
similar information by fuzzy, phonetic and semantic matching of keywords.
Author: J. Aravind [aut, cre],
J. Radhamani [aut],
Kalyani Srinivasan [aut],
B. Ananda Subhash [aut],
R. K. Tyagi [aut]
Maintainer: J. Aravind <aravindj@nbpgr.ernet.in>
Diff between PGRdup versions 0.2 dated 2015-04-14 and 0.2.1 dated 2015-07-23
DESCRIPTION | 17 MD5 | 70 NAMESPACE | 16 R/AddProbDup.R | 3 R/DisProbDup.R | 5 R/KWCounts.R |only R/KWIC.R | 26 R/MergeKW.R | 12 R/MergeProbDup.R |only R/ParseProbDup.R | 3 R/ProbDup.R | 528 +++--- R/ReconstructProbDup.R | 29 R/ReviewProbDup.R | 11 R/SplitProbDup.R |only R/globals.R | 6 R/print.KWIC.R |only R/print.ProbDup.R |only README.md | 86 build |only inst/CITATION | 6 inst/doc |only inst/extdata/PGRdup.svg | 3969 ++++++++++++++++++++++++++++++++++++++++------ man/AddProbDup.Rd | 5 man/DataClean.Rd | 3 man/DisProbDup.Rd | 5 man/DoubleMetaphone.Rd | 3 man/GN1000.Rd | 3 man/KWCounts.Rd |only man/KWIC.Rd | 9 man/MergeKW.Rd | 3 man/MergeProbDup.Rd |only man/PGRdup-package.Rd | 3 man/ParseProbDup.Rd | 5 man/ProbDup.Rd | 19 man/ReconstructProbDup.Rd | 5 man/ReviewProbDup.Rd | 5 man/SplitProbDup.Rd |only man/ValidatePrimKey.Rd | 3 man/print.KWIC.Rd |only man/print.ProbDup.Rd |only vignettes |only 41 files changed, 4063 insertions(+), 795 deletions(-)
Title: Mixtures of Proportional Hazard Models
Description: Fits multiple variable mixtures of various parametric proportional hazard models using the EM-Algorithm. Proportionality restrictions can be imposed on the latent groups and/or on the variables. Several survival distributions can be specified. Missing values and censored values are allowed. Independence is assumed over the single variables.
Author: Patrick Mair [cre, aut],
Marcus Hudec [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between mixPHM versions 0.7-1 dated 2014-11-26 and 0.7-2 dated 2015-07-23
mixPHM-0.7-1/mixPHM/R/plot.hazard.R |only mixPHM-0.7-1/mixPHM/R/plot.profile.R |only mixPHM-0.7-1/mixPHM/R/plot.survival.R |only mixPHM-0.7-1/mixPHM/man/plot.hazard.Rd |only mixPHM-0.7-2/mixPHM/DESCRIPTION | 16 - mixPHM-0.7-2/mixPHM/MD5 | 16 - mixPHM-0.7-2/mixPHM/NAMESPACE | 6 mixPHM-0.7-2/mixPHM/R/Eclass.R | 298 +++++++++++++++--------------- mixPHM-0.7-2/mixPHM/R/plot_hazard.R |only mixPHM-0.7-2/mixPHM/R/plot_profile.R |only mixPHM-0.7-2/mixPHM/R/plot_survival.R |only mixPHM-0.7-2/mixPHM/man/mixPHM-package.Rd | 4 mixPHM-0.7-2/mixPHM/man/plot_hazard.Rd |only 13 files changed, 170 insertions(+), 170 deletions(-)
Title: Gifi Methods for Optimal Scaling
Description: Performs a homogeneity analysis (multiple correspondence analysis) and various extensions. Rank restrictions on the category quantifications can be imposed (nonlinear PCA). The categories are transformed by means of optimal scaling with options for nominal, ordinal, and numerical scale levels (for rank-1 restrictions). Variables can be grouped into sets, in order to emulate regression analysis and canonical correlation analysis.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between homals versions 1.0-5 dated 2014-03-05 and 1.0-6 dated 2015-07-23
homals-1.0-5/homals/COPYING |only homals-1.0-6/homals/DESCRIPTION | 18 ++++++++---------- homals-1.0-6/homals/MD5 | 9 ++++----- homals-1.0-6/homals/NAMESPACE | 2 ++ homals-1.0-6/homals/man/homals-package.Rd | 2 +- homals-1.0-6/homals/man/plot.homals.Rd | 6 ------ 6 files changed, 15 insertions(+), 22 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.1.2.3 dated 2015-07-03 and 1.1.3 dated 2015-07-23
ddalpha-1.1.2.3/ddalpha/man/ddalpha.getErrorRateJK.Rd |only ddalpha-1.1.3/ddalpha/DESCRIPTION | 8 ddalpha-1.1.3/ddalpha/MD5 | 90 ++++--- ddalpha-1.1.3/ddalpha/NAMESPACE | 8 ddalpha-1.1.3/ddalpha/R/dataf.geneexp.r | 9 ddalpha-1.1.3/ddalpha/R/dataf.growth.r | 8 ddalpha-1.1.3/ddalpha/R/dataf.medflies.r | 9 ddalpha-1.1.3/ddalpha/R/dataf.sim.r | 8 ddalpha-1.1.3/ddalpha/R/dataf.tecator.r | 9 ddalpha-1.1.3/ddalpha/R/ddalpha-internal.r | 125 +++++----- ddalpha-1.1.3/ddalpha/R/ddalpha.classify.r | 10 ddalpha-1.1.3/ddalpha/R/ddalpha.test.r | 4 ddalpha-1.1.3/ddalpha/R/ddalpha.train.r | 161 ++++++++++---- ddalpha-1.1.3/ddalpha/R/depth.contours.r | 16 - ddalpha-1.1.3/ddalpha/R/depth.potential.r |only ddalpha-1.1.3/ddalpha/R/depth.spatial.r | 44 +++ ddalpha-1.1.3/ddalpha/R/draw.ddplot.r |only ddalpha-1.1.3/ddalpha/R/lda.r | 2 ddalpha-1.1.3/ddalpha/R/mahalanobis.scaling.r | 2 ddalpha-1.1.3/ddalpha/man/ddalpha-package.Rd | 6 ddalpha-1.1.3/ddalpha/man/ddalpha.getErrorRateCV.Rd | 29 -- ddalpha-1.1.3/ddalpha/man/ddalpha.getErrorRatePart.Rd |only ddalpha-1.1.3/ddalpha/man/ddalpha.test.Rd | 2 ddalpha-1.1.3/ddalpha/man/ddalpha.train.Rd | 8 ddalpha-1.1.3/ddalpha/man/depth..Rd | 5 ddalpha-1.1.3/ddalpha/man/depth.Mahalanobis.Rd | 1 ddalpha-1.1.3/ddalpha/man/depth.halfspace.Rd | 2 ddalpha-1.1.3/ddalpha/man/depth.potential.Rd |only ddalpha-1.1.3/ddalpha/man/depth.projection.Rd | 2 ddalpha-1.1.3/ddalpha/man/depth.simplicial.Rd | 2 ddalpha-1.1.3/ddalpha/man/depth.simplicialVolume.Rd | 2 ddalpha-1.1.3/ddalpha/man/depth.space..Rd | 3 ddalpha-1.1.3/ddalpha/man/depth.space.Mahalanobis.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.halfspace.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.potential.Rd |only ddalpha-1.1.3/ddalpha/man/depth.space.projection.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.simplicial.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.simplicialVolume.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.spatial.Rd | 4 ddalpha-1.1.3/ddalpha/man/depth.space.zonoid.Rd | 5 ddalpha-1.1.3/ddalpha/man/depth.spatial.Rd | 2 ddalpha-1.1.3/ddalpha/man/depth.zonoid.Rd | 2 ddalpha-1.1.3/ddalpha/man/draw.ddplot.Rd |only ddalpha-1.1.3/ddalpha/man/resetPar.Rd |only ddalpha-1.1.3/ddalpha/src/DataStructures.h | 3 ddalpha-1.1.3/ddalpha/src/Knn.cpp | 2 ddalpha-1.1.3/ddalpha/src/PotentialDepth.cpp |only ddalpha-1.1.3/ddalpha/src/PotentialDepth.h |only ddalpha-1.1.3/ddalpha/src/ZonoidDepth.cpp | 3 ddalpha-1.1.3/ddalpha/src/ddalpha.cpp | 50 ++++ ddalpha-1.1.3/ddalpha/src/stdafx.h | 1 51 files changed, 458 insertions(+), 209 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized linear mixed models using Stan for full Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.3.0 dated 2015-06-29 and 0.4.0 dated 2015-07-23
brms-0.3.0/brms/R/bugs.R |only brms-0.3.0/brms/R/extract.old.R |only brms-0.3.0/brms/R/support.internal.R |only brms-0.3.0/brms/man/brm.plot.Rd |only brms-0.3.0/brms/tests/testthat/tests.support.R |only brms-0.4.0/brms/DESCRIPTION | 20 brms-0.4.0/brms/MD5 | 59 +- brms-0.4.0/brms/NAMESPACE | 4 brms-0.4.0/brms/R/data.docu.R | 3 brms-0.4.0/brms/R/internal.postfit.R |only brms-0.4.0/brms/R/internal.prefit.R |only brms-0.4.0/brms/R/main.R | 132 ++-- brms-0.4.0/brms/R/misc.R |only brms-0.4.0/brms/R/parser.R | 54 + brms-0.4.0/brms/R/s3.generics.R | 92 ++- brms-0.4.0/brms/R/s3.methods.R | 312 +++++----- brms-0.4.0/brms/R/stan.R | 488 +++++++++-------- brms-0.4.0/brms/R/support.export.R | 284 +++++---- brms-0.4.0/brms/README.md | 48 + brms-0.4.0/brms/data/epilepsy.rda |binary brms-0.4.0/brms/man/VarCorr.Rd | 5 brms-0.4.0/brms/man/WAIC.Rd |only brms-0.4.0/brms/man/brm.Rd | 45 + brms-0.4.0/brms/man/brm.data.Rd | 21 brms-0.4.0/brms/man/brm.pars.Rd | 17 brms-0.4.0/brms/man/epilepsy.Rd | 1 brms-0.4.0/brms/man/fixef.Rd | 2 brms-0.4.0/brms/man/hypothesis.Rd | 21 brms-0.4.0/brms/man/kidney.Rd | 2 brms-0.4.0/brms/man/plot.brmsfit.Rd | 4 brms-0.4.0/brms/man/posterior.samples.Rd | 3 brms-0.4.0/brms/man/ranef.Rd | 11 brms-0.4.0/brms/tests/testthat/tests.internal.prefit.R |only brms-0.4.0/brms/tests/testthat/tests.parser.R | 44 + brms-0.4.0/brms/tests/testthat/tests.stan.R | 108 ++- brms-0.4.0/brms/tests/testthat/tests.support.export.R |only 36 files changed, 1049 insertions(+), 731 deletions(-)
Title: Simple and Canonical Correspondence Analysis
Description: Performs simple and canonical CA (covariates on rows/columns) on a two-way frequency table (with missings) by means of SVD. Different scaling methods (standard, centroid, Benzecri, Goodman) as well as various plots including confidence ellipsoids are provided.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between anacor versions 1.0-5 dated 2014-09-08 and 1.0-6 dated 2015-07-23
anacor-1.0-5/anacor/COPYING |only anacor-1.0-6/anacor/DESCRIPTION | 15 ++++++++------- anacor-1.0-6/anacor/MD5 | 9 ++++----- anacor-1.0-6/anacor/NAMESPACE | 7 ++++--- anacor-1.0-6/anacor/man/anacor-package.Rd | 6 +++--- anacor-1.0-6/anacor/man/plot.anacor.Rd | 2 +- 6 files changed, 20 insertions(+), 19 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.5 dated 2015-04-14 and 1.6 dated 2015-07-23
openair-1.5/openair/data/mydata.RData |only openair-1.6/openair/DESCRIPTION | 16 openair-1.6/openair/MD5 | 158 - openair-1.6/openair/NAMESPACE | 42 openair-1.6/openair/R/GoogleMapsPlot.R | 5 openair-1.6/openair/R/TheilSen.R | 39 openair-1.6/openair/R/airbaseStats.R | 11 openair-1.6/openair/R/aqStats.R | 33 openair-1.6/openair/R/calendarPlot.R | 14 openair-1.6/openair/R/cutData.R | 2 openair-1.6/openair/R/importAURN.R | 15 openair-1.6/openair/R/importKCL.R | 18 openair-1.6/openair/R/polarPlot.R | 6 openair-1.6/openair/R/scatterPlot.R | 2282 ++++++++++++------------- openair-1.6/openair/R/selectRunning.R | 2 openair-1.6/openair/R/smoothTrend.R | 4 openair-1.6/openair/R/summaryPlot.R | 2 openair-1.6/openair/R/timeAverage.R | 646 +++---- openair-1.6/openair/R/timePlot.R | 187 +- openair-1.6/openair/R/timeProp.R | 36 openair-1.6/openair/R/timeVariation.R | 6 openair-1.6/openair/R/trajCluster.R | 46 openair-1.6/openair/R/trajLevel.R | 93 - openair-1.6/openair/R/trajPlot.R | 222 +- openair-1.6/openair/R/utilities.R | 14 openair-1.6/openair/R/windRose.R | 244 +- openair-1.6/openair/README.md | 20 openair-1.6/openair/data/mydata.rda |only openair-1.6/openair/man/GoogleMapsPlot.Rd | 2 openair-1.6/openair/man/TaylorDiagram.Rd | 2 openair-1.6/openair/man/TheilSen.Rd | 14 openair-1.6/openair/man/airbaseFindCode.Rd | 2 openair-1.6/openair/man/airbaseInfo.Rd | 2 openair-1.6/openair/man/airbaseSplice.Rd | 2 openair-1.6/openair/man/airbaseStats.Rd | 2 openair-1.6/openair/man/aqStats.Rd | 2 openair-1.6/openair/man/calcFno2.Rd | 2 openair-1.6/openair/man/calcPercentile.Rd | 2 openair-1.6/openair/man/calendarPlot.Rd | 2 openair-1.6/openair/man/conditionalEval.Rd | 2 openair-1.6/openair/man/conditionalQuantile.Rd | 2 openair-1.6/openair/man/corPlot.Rd | 2 openair-1.6/openair/man/cutData.Rd | 2 openair-1.6/openair/man/drawOpenKey.Rd | 2 openair-1.6/openair/man/import.Rd | 2 openair-1.6/openair/man/importADMS.Rd | 2 openair-1.6/openair/man/importAURN.Rd | 2 openair-1.6/openair/man/importAURNCsv.Rd | 2 openair-1.6/openair/man/importAirbase.Rd | 2 openair-1.6/openair/man/importKCL.Rd | 2 openair-1.6/openair/man/importMeta.Rd | 2 openair-1.6/openair/man/importSAQN.Rd | 2 openair-1.6/openair/man/importTraj.Rd | 2 openair-1.6/openair/man/kernelExceed.Rd | 2 openair-1.6/openair/man/linearRelation.Rd | 2 openair-1.6/openair/man/modStats.Rd | 2 openair-1.6/openair/man/mydata.Rd | 2 openair-1.6/openair/man/openColours.Rd | 2 openair-1.6/openair/man/openair.Rd | 2 openair-1.6/openair/man/percentileRose.Rd | 2 openair-1.6/openair/man/polarAnnulus.Rd | 2 openair-1.6/openair/man/polarCluster.Rd | 2 openair-1.6/openair/man/polarFreq.Rd | 2 openair-1.6/openair/man/polarPlot.Rd | 2 openair-1.6/openair/man/quickText.Rd | 2 openair-1.6/openair/man/rollingMean.Rd | 2 openair-1.6/openair/man/scatterPlot.Rd | 35 openair-1.6/openair/man/selectByDate.Rd | 2 openair-1.6/openair/man/selectRunning.Rd | 2 openair-1.6/openair/man/smoothTrend.Rd | 2 openair-1.6/openair/man/splitByDate.Rd | 2 openair-1.6/openair/man/summaryPlot.Rd | 2 openair-1.6/openair/man/timeAverage.Rd | 15 openair-1.6/openair/man/timePlot.Rd | 33 openair-1.6/openair/man/timeProp.Rd | 2 openair-1.6/openair/man/timeVariation.Rd | 2 openair-1.6/openair/man/trajCluster.Rd | 4 openair-1.6/openair/man/trajLevel.Rd | 8 openair-1.6/openair/man/trajPlot.Rd | 84 openair-1.6/openair/man/trendLevel.Rd | 2 openair-1.6/openair/man/windRose.Rd | 24 81 files changed, 2505 insertions(+), 1965 deletions(-)
Title: Cluster Distances Through Trees
Description: Create a measure of inter-point dissimilarity useful
for clustering mixed data, and, optionally, perform the clustering.
Author: Sam Buttrey
Maintainer: Sam Buttrey <buttrey@nps.edu>
Diff between treeClust versions 1.0-0 dated 2015-03-19 and 1.1-1 dated 2015-07-23
DESCRIPTION | 9 +- MD5 | 24 +++-- NAMESPACE | 9 +- R/cramer.R | 2 R/d3.dist.R | 10 +- R/plot.treeClust.R | 35 ++++---- R/rpart.predict.leaves.R | 32 +++---- R/treeClust.R | 196 +++++++++++++++++------------------------------ R/treeClust.control.R | 6 - R/treeClust.rpart.R |only man/plot.treeClust.Rd | 8 + man/treeClust.Rd | 14 +-- man/treeClust.control.Rd | 18 +++- man/treeClust.rpart.Rd |only 14 files changed, 178 insertions(+), 185 deletions(-)
Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the TraMineR package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of TraMineR.
Author: Gilbert Ritschard [aut, cre, ths, cph],
Matthias Studer [aut],
Reto Buergin [aut],
Alexis Gabadinho [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineRextras versions 0.2.3 dated 2015-01-27 and 0.2.4 dated 2015-07-23
DESCRIPTION | 17 ++- MD5 | 15 ++- NAMESPACE | 15 +-- R/seqemlt.R | 185 ++++++++++++++++++++---------------------- R/seqplot-rf.R |only inst/NEWS | 19 +++- inst/NEWS.Rd | 13 ++ man/TraMineRextras-package.Rd |only man/seqemlt.Rd | 48 +++++----- man/seqplot-rf.Rd |only 10 files changed, 173 insertions(+), 139 deletions(-)
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Title: Spanning Trees Used for Network Inference
Description: Bayesian inference of graphical model structures using spanning trees.
Author: Loïc Schwaller
Maintainer: Loïc Schwaller <loic.schwaller@ens-lyon.org>
Diff between saturnin versions 1.0 dated 2015-04-11 and 1.1.1 dated 2015-07-23
DESCRIPTION | 12 +++++++----- MD5 | 11 +++++++---- NAMESPACE | 6 +++++- R/RcppExports.R |only R/edge.prob.R | 30 ++++++++++++------------------ man/edge.prob.Rd | 6 +----- src |only 7 files changed, 32 insertions(+), 33 deletions(-)
Title: Clustering for Business Analytics
Description: Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation.
Author: Christian Buchta and Michael Hahsler
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between cba versions 0.2-14 dated 2014-01-15 and 0.2-15 dated 2015-07-23
DESCRIPTION | 8 +++++--- MD5 | 4 ++-- NAMESPACE | 10 ++++++++++ 3 files changed, 17 insertions(+), 5 deletions(-)
Title: Probability-Scale Residuals and Residual Correlations
Description: Computes probability-scale residuals and residual correlations
for continuous, ordinal, binary, count, and time-to-event data.
Author: Charles Dupont, Jeffrey Horner, Chun Li, Qi Liu, Bryan Shepherd
Maintainer: Charles Dupont <charles.dupont@vanderbilt.edu>
Diff between PResiduals versions 0.2-1 dated 2015-03-03 and 0.2-2 dated 2015-07-23
DESCRIPTION | 14 ++- MD5 | 44 +++++++---- NAMESPACE | 36 ++++++++- R/cobot.R | 23 +++++- R/cocobot.R | 174 ++++------------------------------------------ R/cocobot_orm.R |only R/condis.R |only R/corTS.R |only R/countbot.R | 173 ++------------------------------------------- R/getCI.R |only R/lm.scores.R |only R/megabot.R |only R/nb.scores.R |only R/newPolr.R | 3 R/orm.scores.R |only R/pgumbel.R | 9 ++ R/poisson.scores.R |only R/presid.R | 14 +++ man/GKGamma.Rd | 3 man/PResiduals-package.Rd | 3 man/cobot.Rd | 3 man/cocobot.Rd | 11 +- man/countbot.Rd | 5 - man/diagn.Rd | 3 man/megabot.Rd |only man/presid.Rd | 3 man/print.cobot.Rd | 3 man/print.cocobot.Rd | 3 28 files changed, 160 insertions(+), 367 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC) and the Generalized Adjustment Criterion (GAC)
are implemented.
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut],
Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb],
Antti Hyttinen [ctb], Jonas Peters [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.2-3 dated 2015-07-12 and 2.2-4 dated 2015-07-23
DESCRIPTION | 12 MD5 | 71 +- NAMESPACE | 11 R/AllClasses.R | 149 ++-- R/genRandDAG.R | 623 +++++++++---------- R/gies.R | 79 -- R/lingamFuns.R | 4 R/pcalg.R | 1407 +++++++++++++++++++++---------------------- TODO | 79 +- inst/NEWS.Rd | 28 inst/doc/pcalgDoc.pdf |binary man/GaussParDAG-class.Rd | 68 +- man/LINGAM.Rd | 76 +- man/ParDAG-class.Rd | 8 man/binCItest.Rd | 5 man/dag2pag.Rd | 18 man/disCItest.Rd | 15 man/fciAlgo-class.Rd | 19 man/fciPlus.Rd | 4 man/gAlgo-class.Rd | 10 man/gies.Rd | 6 man/gmD.Rd | 40 - man/mcor.Rd | 23 man/pcAlgo-class.Rd | 176 ++--- man/pcSelect.Rd | 42 - man/r.gauss.pardag.Rd | 56 - man/randDAG.Rd | 246 ++++--- man/randomDAG.Rd | 7 man/unifDAG.Rd | 178 +++-- man/wgtMatrix.Rd | 50 - tests/test_fciPlus.R | 21 tests/test_gSquareDis.R | 171 +++++ tests/test_gies.R | 32 tests/test_pcSelect.R | 172 ++++- tests/test_randDAG.R | 66 +- tests/test_randDAG.Rout.save |only tests/test_rfci.R | 4 37 files changed, 2252 insertions(+), 1724 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between multcomp versions 1.4-0 dated 2015-03-05 and 1.4-1 dated 2015-07-23
DESCRIPTION | 12 +- MD5 | 41 ++++---- NAMESPACE | 8 + R/expressions.R | 2 R/glht.R | 2 R/mcp.R | 2 build/vignette.rds |binary data/cholesterol.rda |binary data/litter.rda |binary inst/NEWS | 6 + inst/doc/chfls1.pdf |binary inst/doc/generalsiminf.pdf |binary inst/doc/multcomp-examples.pdf |binary man/cftest.Rd | 4 tests/Examples/multcomp-Ex.Rout.save | 141 +++++++++++++---------------- tests/bugfix.Rout.save | 11 +- tests/regtest-Tukey.Rout.save | 20 ++-- tests/regtest-anova.Rout.save | 8 - tests/regtest-interface-extended.Rout.save | 6 - tests/regtest-interface.Rout.save | 12 +- tests/regtest-lme.Rout.save | 9 - tests/regtest-mmm.Rout.save |only 22 files changed, 146 insertions(+), 138 deletions(-)
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Title: Monotone Multi-Layer Perceptron Neural Network
Description: Train and make predictions from a multi-layer perceptron neural
network with partial monotonicity constraints.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <acannon@eos.ubc.ca>
Diff between monmlp versions 1.1.2 dated 2012-09-27 and 1.1.3 dated 2015-07-23
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 8 +++++--- man/monmlp-package.Rd | 2 +- 4 files changed, 15 insertions(+), 13 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-6 dated 2015-03-31 and 1.8-7 dated 2015-07-23
mgcv-1.8-6/mgcv/inst/po/po |only mgcv-1.8-6/mgcv/po/R-po.po |only mgcv-1.8-6/mgcv/po/po.po |only mgcv-1.8-7/mgcv/ChangeLog | 49 +++ mgcv-1.8-7/mgcv/DESCRIPTION | 6 mgcv-1.8-7/mgcv/MD5 | 55 +-- mgcv-1.8-7/mgcv/NAMESPACE | 24 + mgcv-1.8-7/mgcv/R/bam.r | 577 +++++++++++++++++++++++++++++++++---- mgcv-1.8-7/mgcv/R/efam.r | 46 +- mgcv-1.8-7/mgcv/R/fast-REML.r | 345 ++++++++++++++++++---- mgcv-1.8-7/mgcv/R/gam.fit3.r | 237 ++++++++++++--- mgcv-1.8-7/mgcv/R/gam.fit4.r | 75 +++- mgcv-1.8-7/mgcv/R/gamm.r | 5 mgcv-1.8-7/mgcv/R/jagam.r | 34 +- mgcv-1.8-7/mgcv/R/mgcv.r | 120 ++++--- mgcv-1.8-7/mgcv/R/misc.r | 88 +++++ mgcv-1.8-7/mgcv/R/smooth.r | 72 +++- mgcv-1.8-7/mgcv/man/bam.Rd | 17 - mgcv-1.8-7/mgcv/man/gam.control.Rd | 4 mgcv-1.8-7/mgcv/man/gam.scale.Rd | 13 mgcv-1.8-7/mgcv/man/initial.sp.Rd | 4 mgcv-1.8-7/mgcv/man/jagam.Rd | 10 mgcv-1.8-7/mgcv/po/R-de.po | 148 ++++----- mgcv-1.8-7/mgcv/po/de.po | 4 mgcv-1.8-7/mgcv/src/discrete.c |only mgcv-1.8-7/mgcv/src/gdi.c | 41 -- mgcv-1.8-7/mgcv/src/init.c | 13 mgcv-1.8-7/mgcv/src/mat.c | 231 +++++++++++++- mgcv-1.8-7/mgcv/src/mgcv.h | 20 + mgcv-1.8-7/mgcv/src/misc.c | 21 - 30 files changed, 1803 insertions(+), 456 deletions(-)
Title: Manipulate, Validate and Resolve IP Addresses
Description: A toolkit for manipulating,
validating and testing IP addresses and ranges, along with
datasets relating to IP addresses. While it primarily has
support for the IPv4 address space, more extensive IPv6 support
is intended.
Author: Bob Rudis <bob@rudis.net> [aut, cre], Oliver Keyes <ironholds@gmail.com> [aut]
Maintainer: Bob Rudis <bob@rudis.net>
Diff between iptools versions 0.2.0 dated 2015-07-01 and 0.2.1 dated 2015-07-23
iptools-0.2.0/iptools/tests/testthat/test_host_resolution.R |only iptools-0.2.1/iptools/DESCRIPTION | 8 +- iptools-0.2.1/iptools/MD5 | 29 ++++--- iptools-0.2.1/iptools/NAMESPACE | 1 iptools-0.2.1/iptools/R/RcppExports.R | 22 +++++ iptools-0.2.1/iptools/build/vignette.rds |binary iptools-0.2.1/iptools/configure | 18 ++-- iptools-0.2.1/iptools/inst/doc/introduction_to_iptools.Rmd | 2 iptools-0.2.1/iptools/inst/doc/introduction_to_iptools.html | 4 - iptools-0.2.1/iptools/inst/doc/iptools_datasets.html | 4 - iptools-0.2.1/iptools/man/xff_extract.Rd |only iptools-0.2.1/iptools/src/RcppExports.cpp | 12 +++ iptools-0.2.1/iptools/src/asio_bindings.cpp | 45 ++++++++++++ iptools-0.2.1/iptools/src/asio_bindings.h | 34 +++++++-- iptools-0.2.1/iptools/src/iptools.cpp | 25 ++++++ iptools-0.2.1/iptools/tests/testthat/text_xff_extraction.R |only iptools-0.2.1/iptools/vignettes/introduction_to_iptools.Rmd | 2 17 files changed, 168 insertions(+), 38 deletions(-)
Title: Plot the Effects of Variables in Interaction Terms
Description: Plots the conditional coefficients ("marginal effects") of variables included in multiplicative interaction terms.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between interplot versions 0.1.0.1 dated 2015-07-01 and 0.1.0.2 dated 2015-07-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/Interplot.R | 2 +- R/Interplot_mi.R | 6 ++---- R/Interplot_mlmmi.R | 7 +++---- 5 files changed, 13 insertions(+), 16 deletions(-)
Title: GEV Conditional Density Estimation Network
Description: Implements a flexible nonlinear modelling framework for nonstationary
generalized extreme value analysis in hydroclimatology.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <acannon@eos.ubc.ca>
Diff between GEVcdn versions 1.1.3 dated 2014-04-15 and 1.1.4 dated 2015-07-23
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 8 +++++--- man/GEVcdn-package.Rd | 2 +- 4 files changed, 14 insertions(+), 12 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN)
Description: A fast reimplementation of the density-based DBSCAN clustering algorithm for spatial data introduced by Ester et al. 'A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise,' 1996. This implementation uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. The implementation is many times faster than the R-based implementation in package fpc.
Author: Michael Hahsler [aut, cre, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 0.9-0 dated 2015-07-16 and 0.9-1 dated 2015-07-23
dbscan-0.9-0/dbscan/src/util.cpp |only dbscan-0.9-0/dbscan/src/util.h |only dbscan-0.9-1/dbscan/DESCRIPTION | 14 +- dbscan-0.9-1/dbscan/MD5 | 29 ++-- dbscan-0.9-1/dbscan/NAMESPACE | 3 dbscan-0.9-1/dbscan/R/RcppExports.R | 8 - dbscan-0.9-1/dbscan/R/dbscan.R | 9 + dbscan-0.9-1/dbscan/R/kNNdistplot.R | 24 +++ dbscan-0.9-1/dbscan/inst/NEWS | 6 dbscan-0.9-1/dbscan/man/dbscan.Rd | 97 +++++++++----- dbscan-0.9-1/dbscan/man/kNNdistplot.Rd | 31 +++- dbscan-0.9-1/dbscan/src/ANN/ANN.h | 173 +++++++++++++------------- dbscan-0.9-1/dbscan/src/RcppExports.cpp | 24 +++ dbscan-0.9-1/dbscan/src/brute.cpp | 27 +++- dbscan-0.9-1/dbscan/src/dbscan.cpp | 100 ++++++++------- dbscan-0.9-1/dbscan/src/kNNdist.cpp |only dbscan-0.9-1/dbscan/src/kd_fix_rad_search.cpp | 3 17 files changed, 343 insertions(+), 205 deletions(-)
Title: Conditional Density Estimation Network Construction and
Evaluation
Description: Parameters of a user-specified probability distribution are modelled by a multi-layer perceptron artificial neural network. This framework can be used to implement probabilistic nonlinear models including mixture density networks, heteroscedastic regression models, zero-inflated models, and the like.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <acannon@eos.ubc.ca>
Diff between CaDENCE versions 1.2.2 dated 2015-02-20 and 1.2.3 dated 2015-07-23
DESCRIPTION | 4 ++-- MD5 | 8 ++++---- NAMESPACE | 22 ++++++++++++++++++++++ man/cadence.fit.Rd | 13 ++++++------- man/gam.style.Rd | 6 +++--- 5 files changed, 37 insertions(+), 16 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.5-2 dated 2015-04-16 and 2.5-3 dated 2015-07-23
DESCRIPTION | 8 +-- MD5 | 77 +++++++++++++++---------------- NAMESPACE | 2 R/CAPdiscrim.R | 28 +++++++---- R/accumcomp.R | 8 +-- R/accumplot.R | 10 ++-- R/distdisplayed.R | 4 - R/ensemble.analogue.R | 2 R/ensemble.habitat.change.R | 2 R/ensemble.mean.R | 12 ++-- R/ensemble.raster.R | 44 ++++++++--------- R/ensemble.simplified.categories.R | 2 R/ensemble.test.R | 91 +++++++++++++++++++------------------ R/ensemble.test.splits.R | 5 +- R/evaluation.strip.plot.R | 14 ++--- R/import.from.Excel.R | 4 - R/loaded.citations.R | 2 R/multiconstrained.R | 2 R/ordibubble.R | 4 - R/ordicoeno.R | 12 ++-- R/ordiequilibriumcircle.R | 14 ++--- R/ordihull.centroids.R | 10 ++-- R/ordinearest.R | 2 R/ordispider.centroids.R | 4 - R/ordisymbol.R | 10 ++-- R/ordivector.R | 10 ++-- R/radfitresult.R | 4 - R/rankabuncomp.R | 16 +++--- R/rankabunplot.R | 16 +++--- R/renyiplot.R | 26 +++++----- R/replaceNAcomm.R |only R/residualssurface.R | 10 ++-- R/spatialsample.R | 24 ++++----- inst/etc/BiodiversityGUI.R | 9 +++ inst/etc/BiodiversityR-menus.txt | 3 - inst/etc/Rcmdr-menus.txt | 7 ++ man/CAPdiscrim.Rd | 15 +++++- man/add.spec.scores.Rd | 22 +++++--- man/ensemble.raster.Rd | 2 man/removeNAcomm.Rd | 3 + 40 files changed, 297 insertions(+), 243 deletions(-)