Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder
Maintainer: Peter Langfelder
Diff between WGCNA versions 1.42 dated 2014-12-04 and 1.43 dated 2015-01-15
Changelog | 15 +++ DESCRIPTION | 13 +- MD5 | 18 ++-- NAMESPACE | 2 R/Functions.R | 206 ++++++++++++++++++++++++++++++++++++++++------- R/GOenrichmentAnalysis.R | 12 +- R/heatmapWithLegend.R | 26 ----- man/WGCNA-package.Rd | 4 man/blueWhiteRed.Rd | 8 + man/labeledHeatmap.Rd | 40 ++++++++- 10 files changed, 262 insertions(+), 82 deletions(-)
Title: Random graph clustering
Description: Routines for the analysis (unsupervised clustering) of
networks using MIXtures of Erdos-Renyi random graphs
Author: Christophe Ambroise [aut],
Gilles Grasseau [aut],
Mark Hoebeke [aut],
Pierre Latouche [aut, cre],
Vincent Miele [aut],
Franck Picard [aut],
LAPACK authors [aut] (copyrights apply to src/*.f)
Maintainer: Pierre Latouche
Diff between mixer versions 1.7 dated 2013-07-25 and 1.8 dated 2015-01-15
mixer-1.7/mixer/mixer-Ex.R |only mixer-1.8/mixer/DESCRIPTION | 16 ++++-- mixer-1.8/mixer/MD5 | 45 ++++++++---------- mixer-1.8/mixer/NAMESPACE | 1 mixer-1.8/mixer/NEWS | 7 ++ mixer-1.8/mixer/R/init.R | 8 --- mixer-1.8/mixer/R/mixer.R | 7 +- mixer-1.8/mixer/inst/CITATION | 72 ++++++++++++++--------------- mixer-1.8/mixer/man/a_mixer.Rd | 62 ++++++++++++++---------- mixer-1.8/mixer/man/b_graph.affiliation.Rd | 6 +- mixer-1.8/mixer/man/c_plot.mixer.Rd | 3 - mixer-1.8/mixer/man/d_getModel.Rd | 13 ++++- mixer-1.8/mixer/man/d_getModel.mixer.Rd | 3 + mixer-1.8/mixer/man/t_blog.Rd | 2 mixer-1.8/mixer/src/Ermg.cc | 11 +++- mixer-1.8/mixer/src/Graph.cc | 4 - mixer-1.8/mixer/src/ModelDesigner.cc | 6 ++ mixer-1.8/mixer/src/ModelImprover.cc | 7 ++ mixer-1.8/mixer/src/SOCEm.cc | 8 ++- mixer-1.8/mixer/src/VEstep_R.cc | 5 +- mixer-1.8/mixer/src/ermg_R.cc | 14 ++++- mixer-1.8/mixer/src/ermgo_R.cc | 8 +++ mixer-1.8/mixer/src/init_ermg_R.cc | 8 +++ mixer-1.8/mixer/src/matrix.h | 6 +- 24 files changed, 199 insertions(+), 123 deletions(-)
Title: Expected Maximum Profit Classification Performance Measure
Description: Functions for estimating EMP (Expected Maximum Profit Measure) in Credit Risk Scoring and Customer Churn Prediction, according to Verbraken et al (2013, 2014).
Author: Cristian Bravo, Seppe vanden Broucke and Thomas Verbraken
Maintainer: Cristian Bravo
Diff between EMP versions 2.0.0 dated 2015-01-08 and 2.0.1 dated 2015-01-15
EMP-2.0.0/EMP/man/empRocInfo.Rd |only EMP-2.0.1/EMP/DESCRIPTION | 11 ++++++----- EMP-2.0.1/EMP/MD5 | 19 +++++++++---------- EMP-2.0.1/EMP/NAMESPACE | 5 +++-- EMP-2.0.1/EMP/NEWS | 6 ++++++ EMP-2.0.1/EMP/R/empChurn.R | 14 +++++++++----- EMP-2.0.1/EMP/R/empCreditScoring.R | 12 +++++++----- EMP-2.0.1/EMP/R/empRocInfo.R | 21 +++++++++++++-------- EMP-2.0.1/EMP/man/EMP-package.Rd | 17 +++++------------ EMP-2.0.1/EMP/man/empChurn.Rd | 14 ++++++-------- EMP-2.0.1/EMP/man/empCreditScoring.Rd | 12 +++++------- 11 files changed, 69 insertions(+), 62 deletions(-)
Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal combining or aggregating, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [cre, aut],
Benedikt Graeler [ctb],
Tom Gottfried [ctb],
Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma
Diff between spacetime versions 1.1-1 dated 2014-08-22 and 1.1-2 dated 2015-01-15
spacetime-1.1-1/spacetime/vignettes/wind.pdf |only spacetime-1.1-1/spacetime/vignettes/windts.pdf |only spacetime-1.1-2/spacetime/DESCRIPTION | 14 spacetime-1.1-2/spacetime/MD5 | 92 +- spacetime-1.1-2/spacetime/NAMESPACE | 3 spacetime-1.1-2/spacetime/R/Class-STFDF.R | 6 spacetime-1.1-2/spacetime/R/ST-methods.R | 6 spacetime-1.1-2/spacetime/R/STFDF-methods.R | 147 ++-- spacetime-1.1-2/spacetime/R/STIDF-methods.R | 45 - spacetime-1.1-2/spacetime/R/STSDF-methods.R | 21 spacetime-1.1-2/spacetime/R/aggregate.R | 9 spacetime-1.1-2/spacetime/R/eof.R | 21 spacetime-1.1-2/spacetime/R/over.R | 73 +- spacetime-1.1-2/spacetime/R/raster.R | 3 spacetime-1.1-2/spacetime/R/stconstruct.R | 4 spacetime-1.1-2/spacetime/R/stinteraction.R | 2 spacetime-1.1-2/spacetime/R/stplot.R | 1 spacetime-1.1-2/spacetime/R/timematch.R | 27 spacetime-1.1-2/spacetime/build/vignette.rds |binary spacetime-1.1-2/spacetime/data/air.rda |binary spacetime-1.1-2/spacetime/data/datalist |only spacetime-1.1-2/spacetime/data/fires.rda |binary spacetime-1.1-2/spacetime/demo/00Index | 1 spacetime-1.1-2/spacetime/demo/CressieWikle.R | 17 spacetime-1.1-2/spacetime/demo/aggregate.R |only spacetime-1.1-2/spacetime/inst/ChangeLog | 66 ++ spacetime-1.1-2/spacetime/inst/doc/jss816.R | 99 +-- spacetime-1.1-2/spacetime/inst/doc/jss816.Rnw | 21 spacetime-1.1-2/spacetime/inst/doc/jss816.pdf |binary spacetime-1.1-2/spacetime/inst/doc/stgvis.R | 113 ++- spacetime-1.1-2/spacetime/inst/doc/stgvis.Rmd | 152 ++-- spacetime-1.1-2/spacetime/inst/doc/stgvis.html | 779 +++++++++++-------------- spacetime-1.1-2/spacetime/inst/doc/sto.pdf |binary spacetime-1.1-2/spacetime/inst/doc/stpg.pdf |binary spacetime-1.1-2/spacetime/inst/doc/stsubs.pdf |binary spacetime-1.1-2/spacetime/man/STFDF-class.Rd | 3 spacetime-1.1-2/spacetime/man/STIDF-class.Rd | 22 spacetime-1.1-2/spacetime/man/STSDF-class.Rd | 3 spacetime-1.1-2/spacetime/man/STTDF-class.Rd | 1 spacetime-1.1-2/spacetime/man/air.Rd | 1 spacetime-1.1-2/spacetime/man/eof.Rd | 27 spacetime-1.1-2/spacetime/man/over.Rd | 5 spacetime-1.1-2/spacetime/man/stplot.Rd | 1 spacetime-1.1-2/spacetime/man/timematch.Rd | 1 spacetime-1.1-2/spacetime/tests/rw.R | 1 spacetime-1.1-2/spacetime/tests/rw.Rout.save | 11 spacetime-1.1-2/spacetime/tests/wind.Rout.save | 14 spacetime-1.1-2/spacetime/vignettes/jss816.Rnw | 21 spacetime-1.1-2/spacetime/vignettes/stgvis.Rmd | 152 ++-- 49 files changed, 1083 insertions(+), 902 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Description: Formating of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown
Maintainer: Patrick Brown
Diff between diseasemapping versions 1.1.4 dated 2015-01-05 and 1.1.5 dated 2015-01-15
DESCRIPTION | 12 ++++++------ MD5 | 3 ++- inst |only 3 files changed, 8 insertions(+), 7 deletions(-)
More information about diseasemapping at CRAN
Permanent link
Title: Bundle Methods for Regularized Risk Minimization Package
Description: Bundle methods for minimization of convex and non-convex risk
under L1 or L2 regularization. Implements the algorithm proposed by Teo et
al. (JMLR 2010) as well as the extension proposed by Do and Artieres (JMLR
2012). The package comes with lot of loss functions for machine learning
which make it powerful for big data analysis. The applications includes:
structured prediction, linear SVM, multi-class SVM, f-beta optimization,
ROC optimization, ordinal regression, quantile regression,
epsilon insensitive regression, least mean square, logistic regression,
least absolute deviation regression (see package examples), etc... all with
L1 and L2 regularization.
Author: Julien Prados
Maintainer: Julien Prados
Diff between bmrm versions 1.8 dated 2014-02-10 and 3.0 dated 2015-01-15
DESCRIPTION | 23 +- MD5 | 54 +++--- NAMESPACE | 12 + NEWS | 17 ++ R/bmrm.R | 185 ++++++++++------------- R/cost.R | 16 +- R/loss.R |only R/nrbm.R |only R/scalarClassificationLosses.R | 253 +++++++++++++------------------- R/scalarRegressionLosses.R | 191 ++++++++---------------- R/vectorialLoss.R | 85 ++++------ build/vignette.rds |binary inst/doc/bmrm.R | 10 - inst/doc/bmrm.Rnw | 12 - inst/doc/bmrm.pdf |binary man/bmrm.Rd | 85 ++++------ man/costMatrix.Rd | 12 - man/epsilonInsensitiveRegressionLoss.Rd | 31 +-- man/fbetaLoss.Rd | 28 +-- man/gradient.Rd |only man/hingeLoss.Rd | 36 +--- man/ladRegressionLoss.Rd | 28 +-- man/lmsRegressionLoss.Rd | 25 +-- man/logisticRegressionLoss.Rd | 25 +-- man/nrbm.Rd |only man/ordinalRegressionLoss.Rd | 37 +--- man/quantileRegressionLoss.Rd | 28 +-- man/rocLoss.Rd | 25 +-- man/softMarginVectorLoss.Rd | 47 ++--- vignettes/bmrm.Rnw | 12 - 30 files changed, 546 insertions(+), 731 deletions(-)
Title: Binary Generalized Extreme Value Additive Models
Description: Routine for fitting regression models for binary rare events with linear and nonlinear covariate effects when using the quantile function of the Generalized Extreme Value random variable.
Author: Giampiero Marra, Raffaella Calabrese and Silvia Angela Osmetti
Maintainer: Giampiero Marra
Diff between bgeva versions 0.2 dated 2013-07-05 and 0.3 dated 2015-01-15
ChangeLog | 3 +++ DESCRIPTION | 13 +++++-------- MD5 | 10 +++++----- NAMESPACE | 4 +++- inst/CITATION | 19 ++++++++----------- man/bgeva.Rd | 3 ++- 6 files changed, 26 insertions(+), 26 deletions(-)
Title: Semiparametric Bivariate Probit Modelling
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra
Maintainer: Giampiero Marra
Diff between SemiParBIVProbit versions 3.2-13.1 dated 2015-01-08 and 3.2-13.2 dated 2015-01-15
ChangeLog | 3 + DESCRIPTION | 6 +-- MD5 | 20 +++++------ R/LM.bpm.r | 6 +-- R/SemiParBIVProbit.r | 2 - R/mb.r | 87 ++++++++++++++++++++++-------------------------- R/print.mb.r | 7 +++ inst/CITATION | 16 +------- man/LM.bpm.Rd | 2 - man/SemiParBIVProbit.Rd | 2 - man/mb.Rd | 11 +++--- 11 files changed, 77 insertions(+), 85 deletions(-)
More information about SemiParBIVProbit at CRAN
Permanent link
Title: Database preferences and Skyline computation
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator, and some
generalizations (database preferences).
Author: Patrick Roocks
Maintainer: Patrick Roocks
Diff between rPref versions 0.3 dated 2014-11-18 and 0.4 dated 2015-01-15
DESCRIPTION | 12 +- MD5 | 57 +++++----- NAMESPACE | 6 + NEWS | 18 --- R/base-pref-macros.R | 5 R/base-pref.r | 8 - R/complex-pref.r | 8 - R/pred-succ.r |only R/pref-classes.r | 135 ++++++++++++++++++++++++-- R/pref-eval.r | 5 R/rPref.r | 9 + R/show-pref.r | 84 ++++++++++++---- R/visualize.r | 4 inst/test/test-hasse.R | 28 +++++ inst/test/test-psel.R | 2 man/base_pref.Rd | 124 +++++++++++------------ man/base_pref_macros.Rd | 115 +++++++++++----------- man/complex_pref.Rd | 220 +++++++++++++++++++++--------------------- man/get_btg.Rd | 122 +++++++++++------------ man/get_hasse_diag.Rd | 56 +++++----- man/plot_front.Rd | 82 +++++++-------- man/pred_succ.Rd |only man/psel.Rd | 249 ++++++++++++++++++++++++------------------------ man/rPref.Rd | 97 ++++++++++-------- man/show.pref.Rd |only man/show.query.Rd | 86 ++++++++-------- src/bnl.cpp | 13 -- src/bnl.h | 9 + src/hasse.cpp | 5 src/scalagon.cpp | 9 - src/scalagon.h | 2 31 files changed, 893 insertions(+), 677 deletions(-)
Title: Record Linkage in R
Description: Provides functions for linking and de-duplicating data sets.
Methods based on a stochastic approach are implemented as well as
classification algorithms from the machine learning domain.
Author: Andreas Borg
Maintainer: Andreas Borg
Diff between RecordLinkage versions 0.4-6 dated 2014-12-11 and 0.4-7 dated 2015-01-15
RecordLinkage-0.4-6/RecordLinkage/inst/unitTests |only RecordLinkage-0.4-7/RecordLinkage/DESCRIPTION | 11 - RecordLinkage-0.4-7/RecordLinkage/MD5 | 87 +------------ RecordLinkage-0.4-7/RecordLinkage/NEWS | 4 RecordLinkage-0.4-7/RecordLinkage/data/RLdata10000.rda |binary RecordLinkage-0.4-7/RecordLinkage/data/RLdata500.rda |binary RecordLinkage-0.4-7/RecordLinkage/inst/doc/BigData.pdf |binary RecordLinkage-0.4-7/RecordLinkage/inst/doc/EVT.pdf |binary RecordLinkage-0.4-7/RecordLinkage/inst/doc/Supervised.pdf |binary RecordLinkage-0.4-7/RecordLinkage/inst/doc/WeightBased.pdf |binary RecordLinkage-0.4-7/RecordLinkage/man/epiClassify.Rd | 2 RecordLinkage-0.4-7/RecordLinkage/man/epiWeights.Rd | 2 12 files changed, 20 insertions(+), 86 deletions(-)
Title: Estimating Potential and Actual Evapotranspiration with Multiple
Models
Description: Allows the use of user-defined data and constants to calculate potential evapotranspiration (PET i.e. the amount of evaporation from a surface if sufficient water is available) and actual evapotranspiration (AET i.e. the actual amount of water evaporated from a surface) from 17 different formulations including the Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo
Maintainer: Danlu Guo
Diff between Evapotranspiration versions 1.4 dated 2014-06-12 and 1.5 dated 2015-01-15
Evapotranspiration-1.4/Evapotranspiration/man/ET.Truc.Rd |only Evapotranspiration-1.5/Evapotranspiration/DESCRIPTION | 15 Evapotranspiration-1.5/Evapotranspiration/MD5 | 26 - Evapotranspiration-1.5/Evapotranspiration/NAMESPACE | 2 Evapotranspiration-1.5/Evapotranspiration/NEWS | 30 - Evapotranspiration-1.5/Evapotranspiration/R/Evapotranspiration.R | 162 +++++++--- Evapotranspiration-1.5/Evapotranspiration/R/Plotting.R | 68 +--- Evapotranspiration-1.5/Evapotranspiration/man/ET.BlaneyCriddle.Rd | 3 Evapotranspiration-1.5/Evapotranspiration/man/ET.BrutsaertStrickler.Rd | 9 Evapotranspiration-1.5/Evapotranspiration/man/ET.JensenHaise.Rd | 7 Evapotranspiration-1.5/Evapotranspiration/man/ET.MortonCRAE.Rd | 7 Evapotranspiration-1.5/Evapotranspiration/man/ET.MortonCRWE.Rd | 7 Evapotranspiration-1.5/Evapotranspiration/man/ET.Turc.Rd |only Evapotranspiration-1.5/Evapotranspiration/man/ETComparison.Rd | 7 Evapotranspiration-1.5/Evapotranspiration/man/ETPlot.Rd | 3 15 files changed, 205 insertions(+), 141 deletions(-)
More information about Evapotranspiration at CRAN
Permanent link
Title: Database Interface and MySQL Driver for R
Description: Implements DBI-compliant Interface to MySQL and MariaDB Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms
Diff between RMySQL versions 0.10 dated 2015-01-05 and 0.10.1 dated 2015-01-15
DESCRIPTION | 22 ++++++++++------------ MD5 | 6 +++--- R/table.R | 4 ++-- configure | 15 +++++++++++++-- 4 files changed, 28 insertions(+), 19 deletions(-)
Title: Categorical Marginal Models
Description: Quite extensive package for the estimation of marginal models for categorical data.
Author: Wicher Bergsma and Andries van der Ark
Maintainer: L. A. van der Ark
Diff between cmm versions 0.7 dated 2013-02-23 and 0.8 dated 2015-01-15
DESCRIPTION | 13 ++++----- MD5 | 36 +++++++++++++-------------- R/CMM.R | 2 - inst/CITATION | 5 +-- man/Antisemitism.Rd | 24 +++++++++++------- man/BodySatisfaction.Rd | 60 +++++++++++++++++++++++++++++----------------- man/ConstraintMatrix.Rd | 26 +++++++++++++++---- man/DesignMatrix.Rd | 31 +++++++++++++++++------ man/DutchConcern.Rd | 19 ++++++++------ man/EVS.Rd | 41 ++++++++++++++++++------------- man/GSS93.Rd | 53 +++++++++++++++++++++++++++++----------- man/LaborParticipation.Rd | 27 +++++++++++--------- man/MarginalMatrix.Rd | 12 +++++---- man/MarginalModelFit.Rd | 13 +++++---- man/MarihuanaAlcohol.Rd | 12 ++++++--- man/ModelStatistics.Rd | 26 +++++++++++-------- man/NKPS.Rd | 19 ++++++++------ man/SampleStatistics.Rd | 37 ++++++++++++++++------------ man/Smoking.Rd | 12 +++++---- 19 files changed, 290 insertions(+), 178 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-01-17 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-07-16 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-01-29 0.2
2008-10-29 0.1
2008-09-10 0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-02-24 0.03
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-11-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-13 1.3-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-02-11 1.1.1
2010-10-23 1.1
2010-10-13 1.0
Title: Nested Association Mapping
Description: NAM, biparental and random populations toolbox
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu
Maintainer: Alencar Xavier
Diff between NAM versions 1.0.1 dated 2015-01-05 and 1.0.2 dated 2015-01-15
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- R/reml.R |only man/Internals.Rd | 2 +- man/NAM-package.Rd | 8 ++++---- man/reml.Rd |only 6 files changed, 14 insertions(+), 12 deletions(-)
Title: Tools for processing COPAS large-particle flow cytometer data
Description: A logical workflow for the reading, processing, and visualization
of data obtained from the Union Biometrica Complex Object Parametric
Analyzer and Sorter (COPAS) platform large-particle flow cytometers and a
powerful suite of functions for the rapid processing and analysis of large
high-throughput screening data sets. It combines the speed of dplyr with
the elegance of ggplot2 to make analysis of COPAS data fast and painless.
Author: Tyler Shimko
Maintainer: Erik Andersen
Diff between COPASutils versions 0.1.5 dated 2014-12-10 and 0.1.6 dated 2015-01-15
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/COPASutils_functions.R | 2 +- build/vignette.rds |binary data/BioSorter.RData |binary data/PresentationStyle.RData |binary data/bubbleSVMmodel_noProfiler.RData |binary data/doseData.RData |binary data/plateData1.RData |binary data/plateData2.RData |binary inst/doc/Overview.html | 28 ++++++++++++++-------------- 11 files changed, 28 insertions(+), 28 deletions(-)
Title: Composite-likelihood based Analysis of Random Fields
Description: The aim of this package is to collect a set of procedures for the analysis of Random Fields by Composite Likelihood methods. Spatial analysis often involves dealing with large dataset. Therefore even simple studies may be too computationally demanding. Composite likelihood based methods are emerging as useful tools for mitigating such computational problems and show satisfactory results when compared with other techniques such as, for example the tapering method. Moreover, composite likelihood (and related quantities) have some good properties similar to those of the standard likelihood.
Author: Simone Padoan
Maintainer: Simone Padoan
Diff between CompRandFld versions 1.0.3-1 dated 2014-08-23 and 1.0.3-3 dated 2015-01-15
DESCRIPTION | 11 +++++---- MD5 | 14 +++++------ data/irishwinds.rda |binary data/usrain.rda |binary man/Covariogram.Rd | 56 +++++++++++++++++++++++----------------------- man/Covmatrix.Rd | 19 +++++++-------- man/FitComposite.Rd | 58 ++++++++++++++++++++++++------------------------ man/Kri.Rd | 62 ++++++++++++++++++++++++++-------------------------- 8 files changed, 111 insertions(+), 109 deletions(-)