Title: Power and Sample Size Calculations for SNP Association Studies
with Censored Time to Event Outcomes
Description: This package can be used to conduct asymptotic and empirical power and sample size calculations for SNP association studies with right censored time to event outcomes
Author: Kouros Owzar, Zhiguo Li, Nancy Cox, Sin-Ho Jung and Chanhee Yi
Maintainer: Kouros Owzar
Diff between survSNP versions 0.21-5 dated 2012-08-06 and 0.21-6 dated 2013-12-11
survSNP-0.21-5/survSNP/inst/doc/survSNP.Rnw |only survSNP-0.21-5/survSNP/inst/doc/survSNP.pdf |only survSNP-0.21-6/survSNP/DESCRIPTION | 16 ++++++++-------- survSNP-0.21-6/survSNP/MD5 | 16 ++++++++++------ survSNP-0.21-6/survSNP/build |only survSNP-0.21-6/survSNP/inst/doc/survSNP-knitr.R |only survSNP-0.21-6/survSNP/inst/doc/survSNP-knitr.Rnw |only survSNP-0.21-6/survSNP/inst/doc/survSNP-knitr.pdf |only survSNP-0.21-6/survSNP/man/sim.snp.expsurv.power.Rd | 6 ++++-- survSNP-0.21-6/survSNP/man/survSNP-package.Rd | 10 ++++++---- survSNP-0.21-6/survSNP/man/survSNP.power.table.Rd | 6 ++++-- survSNP-0.21-6/survSNP/vignettes |only 12 files changed, 32 insertions(+), 22 deletions(-)
Title: Standard Error Adjusted Adaptive Lasso
Description: Standard error adjusted adaptive lasso (SEA-lasso) is a version of the adaptive lasso, which incorporates OLS standard error to the L1 penalty weight. This method is intended for variable selection under linear regression settings (n > p). This new weight assignment strategy is especially useful when the collinearity of the design matrix is a concern.
Author: Wei Qian
Maintainer: Wei Qian
Diff between sealasso versions 0.1-1 dated 2013-09-08 and 0.1-2 dated 2013-12-11
ChangeLog |only DESCRIPTION | 6 +++--- MD5 | 12 +++++++----- inst/doc/sealasso.Rnw | 6 +++--- inst/doc/sealasso.pdf |binary man/sealasso.Rd | 4 ++-- man/summary.sealasso.Rd | 2 +- vignettes |only 8 files changed, 16 insertions(+), 14 deletions(-)
Title: Simplified Bayesian Sensitivity Analysis
Description: Simplified Bayesian Sensitivity Analysis
Author: Davor Cubranic and Paul Gustafson
Maintainer: Davor Cubranic
Diff between SBSA versions 0.2.0 dated 2012-03-16 and 0.2.1 dated 2013-12-11
DESCRIPTION | 9 +++++---- MD5 | 13 ++++++++----- build |only inst/doc/SBSA-introduction.R |only inst/doc/SBSA-introduction.pdf |binary man/fitSBSA.Rd | 4 ++-- src/log_binary_functor.cpp | 2 +- src/log_functor.cpp | 2 +- vignettes |only 9 files changed, 17 insertions(+), 13 deletions(-)
Title: Tools for mapping of quantitative traits of genetically related
individuals and calculating identity coefficients from a
pedigree
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng
Maintainer: Riyan Cheng
Diff between QTLRel versions 0.2-12 dated 2012-11-15 and 0.2-14 dated 2013-12-11
ChangeLog | 2 ++ DESCRIPTION | 21 ++++++--------------- MD5 | 24 ++++++++++++------------ R/hapSim.R | 3 ++- R/ibsFn.R | 9 ++++++--- R/idcoef.R | 21 ++++++++++++++------- R/imFn.R | 3 ++- R/qqPlot.R | 18 ++++++++++++------ R/qtl2rel.R | 14 +++++++------- R/rel2qtl.R | 2 +- R/zzz.R | 9 +++++---- data/miscEx.RData |binary inst/doc/index.html | 2 +- 13 files changed, 70 insertions(+), 58 deletions(-)
Title: Maximum likelihood unit root test
Description: Provides functions for unit root testing using MLE method
Author: A. I. McLeod, Hao Yu and Ying Zhang
Maintainer: Ian McLeod
Diff between mleur versions 1.0-5 dated 2012-09-22 and 1.0-6 dated 2013-12-11
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++--------- man/GetPower.Rd | 8 +++++--- man/ar1est.Rd | 3 ++- man/mctest.Rd | 3 ++- man/mleur-package.Rd | 6 +++--- man/mleur.Rd | 3 ++- man/simar1.Rd | 8 +++++--- man/testStatUM.Rd | 3 ++- man/vel.Rd | 2 +- 10 files changed, 37 insertions(+), 28 deletions(-)
Title: Utility Functions for R Histograms
Description: This package provides a number of utility functions useful for manipulating large histograms. This includes methods to trim, subset, merge buckets, merge histograms, convert to CDF, and calculate information loss due to binning. It also provides a protocol buffer representations of the default R histogram class to allow histograms over large data sets to be computed and manipulated in a MapReduce environment.
Author: Murray Stokely
Maintainer: Murray Stokely
Diff between HistogramTools versions 0.2 dated 2013-10-03 and 0.3 dated 2013-12-11
ChangeLog | 41 + DESCRIPTION | 11 MD5 | 44 +- R/bindist.R |only R/histogram.R | 18 R/plot.R | 12 build/vignette.rds |binary inst/doc/HistogramTools-UnitTests.pdf |binary inst/doc/HistogramTools-quickref.R | 4 inst/doc/HistogramTools-quickref.Rnw | 50 +- inst/doc/HistogramTools-quickref.pdf |binary inst/doc/HistogramTools.Rnw | 740 +++++++++++++++++++--------------- inst/doc/HistogramTools.pdf |binary man/bindist.Rd |only man/binning.Rd |only man/histogram-package.Rd | 7 man/informationloss.Rd | 6 man/intersect.Rd |only man/plot.Rd | 8 man/plothist.Rd |only man/quantiles.Rd | 4 man/scale.Rd |only man/trimsparse.Rd | 4 vignettes/HistogramTools-quickref.Rnw | 50 +- vignettes/HistogramTools.Rnw | 740 +++++++++++++++++++--------------- vignettes/refs.bib | 41 + 26 files changed, 1094 insertions(+), 686 deletions(-)
More information about HistogramTools at CRAN
Permanent link
Title: Dependency Modeling Toolkit
Description: Probabilistic dependency modeling toolkit.
Author: Leo Lahti and Olli-Pekka Huovilainen
Maintainer: Leo Lahti
Diff between dmt versions 0.8.10 dated 2012-05-30 and 0.8.20 dated 2013-12-11
dmt-0.8.10/dmt/inst/doc/cca2.eps |only dmt-0.8.10/dmt/inst/doc/cca2.png |only dmt-0.8.10/dmt/inst/doc/dmt.bib |only dmt-0.8.20/dmt/DESCRIPTION | 18 ++++----- dmt-0.8.20/dmt/LICENSE | 34 +---------------- dmt-0.8.20/dmt/MD5 | 44 ++++++++++++----------- dmt-0.8.20/dmt/NAMESPACE | 4 ++ dmt-0.8.20/dmt/R/dependency.score.R | 5 +- dmt-0.8.20/dmt/R/drcca-functions.R | 3 - dmt-0.8.20/dmt/R/firstlib.R | 5 +- dmt-0.8.20/dmt/R/fit.dependency.model.R | 2 - dmt-0.8.20/dmt/R/internals.R | 2 - dmt-0.8.20/dmt/R/toydata.R | 5 -- dmt-0.8.20/dmt/R/utilities.R | 4 -- dmt-0.8.20/dmt/build |only dmt-0.8.20/dmt/data/expdata1.rda |binary dmt-0.8.20/dmt/data/expdata2.rda |binary dmt-0.8.20/dmt/data/modelData.RData |binary dmt-0.8.20/dmt/inst/doc/dmt.R |only dmt-0.8.20/dmt/inst/doc/dmt.pdf |binary dmt-0.8.20/dmt/man/compare.estimate.and.truth.Rd | 23 +++++++----- dmt-0.8.20/dmt/man/dependency.score.Rd |only dmt-0.8.20/dmt/man/generate.toydata.Rd | 8 +++- dmt-0.8.20/dmt/man/likelihood.Rd | 3 + dmt-0.8.20/dmt/vignettes |only 25 files changed, 71 insertions(+), 89 deletions(-)
Title: Estimation of spatial autoregressive models with and without
heteroskedastic innovations
Description: Generalized Method of Moment estimation of Cliff-Ord-type
spatial autoregressive models with and without heteroskedastic
innovations
Author: Gianfranco Piras
Maintainer: Gianfranco Piras
Diff between sphet versions 1.4 dated 2013-06-21 and 1.5 dated 2013-12-11
sphet-1.4/sphet/INDEX |only sphet-1.4/sphet/inst/doc/bibconc.bib |only sphet-1.5/sphet/ChangeLog | 30 ++++ sphet-1.5/sphet/DESCRIPTION | 11 - sphet-1.5/sphet/MD5 | 32 ++--- sphet-1.5/sphet/NAMESPACE | 1 sphet-1.5/sphet/R/dist_functions.R | 5 sphet-1.5/sphet/R/distance.R | 5 sphet-1.5/sphet/R/gs2slshet.R | 2 sphet-1.5/sphet/R/ivreg.R | 2 sphet-1.5/sphet/R/spreg.R | 211 +++++++++++----------------------- sphet-1.5/sphet/inst/doc/sphet.R | 1 sphet-1.5/sphet/inst/doc/sphet.Rnw | 1 sphet-1.5/sphet/inst/doc/sphet.pdf |binary sphet-1.5/sphet/man/dist_functions.Rd | 2 sphet-1.5/sphet/man/distance.Rd | 4 sphet-1.5/sphet/man/spreg.Rd | 47 ++++--- sphet-1.5/sphet/vignettes |only 18 files changed, 169 insertions(+), 185 deletions(-)
Title: SMfSB 2e: Stochastic Modelling for Systems Biology, second
edition
Description: This package contains code and data for modelling and simulation of stochastic kinetic biochemical network models. It contains the code and data associated with the second edition of the book Stochastic Modelling for Systems Biology, published by Chapman & Hall/CRC Press, November 2011.
Author: Darren Wilkinson
Maintainer: Darren Wilkinson
Diff between smfsb versions 1.0 dated 2011-10-26 and 1.1 dated 2013-12-11
CHANGES | 6 +++++- DESCRIPTION | 20 +++++++++----------- MD5 | 24 +++++++++++++----------- R/mcmcSummary.R | 2 +- R/normgibbs.R | 1 + build |only data/LVdata.rda |binary data/spnModels.rda |binary demo/PMCMC.R | 2 +- inst/doc/smfsb.pdf |binary man/normgibbs.Rd | 2 +- man/simSample.Rd | 7 +------ man/spnModels.Rd | 4 +++- vignettes |only 14 files changed, 35 insertions(+), 33 deletions(-)
Title: Importing Vector Graphics
Description: Functions for converting, importing, and drawing PostScript
pictures in R plots.
Author: Paul Murrell [aut, cre],
Richard Walton [aut],
Simon Potter [ctb]
Maintainer: Paul Murrell
Diff between grImport versions 0.8-4 dated 2012-02-15 and 0.9-0 dated 2013-12-11
grImport-0.8-4/grImport/R/zzz.R |only grImport-0.8-4/grImport/inst/xsl |only grImport-0.9-0/grImport/DESCRIPTION | 23 ++-- grImport-0.9-0/grImport/MD5 | 34 +++--- grImport-0.9-0/grImport/NAMESPACE | 10 - grImport-0.9-0/grImport/R/AllClasses.R | 5 grImport-0.9-0/grImport/R/PostScript2RGML.R | 99 +++++++++++++----- grImport-0.9-0/grImport/R/RGML2picture.R | 30 +++++ grImport-0.9-0/grImport/R/picture2graphics.R | 6 - grImport-0.9-0/grImport/R/picture2grid.R | 131 +++++++++++++++--------- grImport-0.9-0/grImport/R/picturetext.R | 21 ++- grImport-0.9-0/grImport/build |only grImport-0.9-0/grImport/inst/doc/changes.txt | 51 +++++++++ grImport-0.9-0/grImport/inst/doc/import.R |only grImport-0.9-0/grImport/inst/doc/import.pdf |binary grImport-0.9-0/grImport/inst/doc/importText.R |only grImport-0.9-0/grImport/inst/doc/importText.pdf |binary grImport-0.9-0/grImport/man/PictureOp-class.Rd | 12 +- grImport-0.9-0/grImport/man/PostScriptTrace.Rd | 6 - grImport-0.9-0/grImport/man/grid.picture.Rd | 4 20 files changed, 312 insertions(+), 120 deletions(-)
Title: Inference tests for TExPosition
Description: Non-parametric resampling-based inference tests for TExPosition.
Author: Derek Beaton, Jenny Rieck, Herve Abdi
Maintainer: Derek Beaton
Diff between TInPosition versions 0.10.4 dated 2013-06-15 and 0.13.6 dated 2013-12-11
DESCRIPTION | 16 ++--- MD5 | 15 ++--- R/tepBADA.inference.battery.R | 78 +++++++++++++++----------- R/tepDICA.inference.battery.R | 113 ++++++++++++++++++++------------------- R/tinGraphs.R | 2 inst |only man/TInPosition-package.Rd | 6 +- man/tepBADA.inference.battery.Rd | 3 - man/tepDICA.inference.battery.Rd | 7 -- 9 files changed, 129 insertions(+), 111 deletions(-)
Title: Calculate SPEARpesticide in R
(http://www.systemecology.eu/SPEAR/index.php)
Description: Calculate SPEARpesticide in R
(http://www.systemecology.eu/SPEAR/index.php)
Author: Eduard Szoecs
Maintainer: Eduard Szoecs
Diff between rspear versions 0.1-1 dated 2013-09-09 and 0.1-2 dated 2013-12-11
DESCRIPTION | 8 ++++---- LICENSE | 22 ++-------------------- MD5 | 21 +++++++++++---------- NEWS | 5 +++++ R/get_traits.R | 2 +- R/rspear-package.R | 2 +- R/spear.R | 2 +- build |only inst/doc/rspear.pdf |binary man/get_traits.Rd | 2 +- man/rspear-package.Rd | 2 +- man/spear.Rd | 2 +- 12 files changed, 28 insertions(+), 40 deletions(-)
Title: Elementary Probability on Finite Sample Spaces
Description:
This package provides a framework for performing elementary probability
calculations on finite sample spaces, which may be represented by data frames
or lists. Functionality includes setting up sample spaces, counting tools,
defining probability spaces, performing set algebra, calculating probability
and conditional probability, tools for simulation and checking the law of
large numbers, adding random variables, and finding marginal distributions.
Characteristic functions for all base R distributions are included.
Author: G. Jay Kerns [aut, cre, cph]
Maintainer: G. Jay Kerns
Diff between prob versions 0.9-2 dated 2009-11-02 and 0.9-5 dated 2013-12-11
prob-0.9-2/prob/LICENSE |only prob-0.9-2/prob/inst/doc/charfunc.rnw |only prob-0.9-2/prob/inst/doc/prob.rnw |only prob-0.9-5/prob/DESCRIPTION | 39 +++++++++++-------------- prob-0.9-5/prob/MD5 |only prob-0.9-5/prob/NAMESPACE | 43 ++++++++++++++-------------- prob-0.9-5/prob/R/characteristicfunctions.r | 6 +-- prob-0.9-5/prob/R/misc.r | 2 - prob-0.9-5/prob/R/prob.r | 23 +++++++------- prob-0.9-5/prob/R/utils-events.r | 3 - prob-0.9-5/prob/build |only prob-0.9-5/prob/inst/doc/charfunc.Rnw |only prob-0.9-5/prob/inst/doc/charfunc.pdf |binary prob-0.9-5/prob/inst/doc/prob.R |only prob-0.9-5/prob/inst/doc/prob.Rnw |only prob-0.9-5/prob/inst/doc/prob.pdf |binary prob-0.9-5/prob/man/prob-package.Rd | 11 +++---- prob-0.9-5/prob/man/prob.rd | 19 ++++++------ prob-0.9-5/prob/vignettes |only 19 files changed, 70 insertions(+), 76 deletions(-)
Title: Precision of Geometric Sampling
Description: Computation of mean squared errors of stereological predictors.
Author: Kien Kieu
Maintainer: Kien Kieu
Diff between pgs versions 0.3-0 dated 2010-02-09 and 0.4-0 dated 2013-12-11
pgs-0.3-0/pgs/inst/doc/ex_lafig.pdf |only pgs-0.3-0/pgs/inst/doc/italy_pp_counts.RData |only pgs-0.3-0/pgs/inst/doc/pgs_user.bib |only pgs-0.4-0/pgs/DESCRIPTION | 15 +++++++-------- pgs-0.4-0/pgs/MD5 |only pgs-0.4-0/pgs/NAMESPACE |only pgs-0.4-0/pgs/build |only pgs-0.4-0/pgs/inst/doc/pgs_user.R |only pgs-0.4-0/pgs/inst/doc/pgs_user.pdf |binary pgs-0.4-0/pgs/vignettes |only 10 files changed, 7 insertions(+), 8 deletions(-)
Title: Spatially explicit population genetic simulations
Description: This package creates a individual-based population genetic simulation. Individuals have spatial coordinates, dispersal governed by mixtures of Weibull and normal pdfs. It is discrete-time. It can be arbitrarily complex given enough known or assumed demographic characteristics. Simulates diploid and haploid inheritance. Allows the development of null distributions of genotypes for complex demographic scenarios. This version includes some approximations for pollen (male gamete) dispersal.
Author: Allan Strand and James Niehaus
Maintainer: Allan Strand
Diff between kernelPop versions 1.0.0 dated 2013-11-27 and 1.0.2 dated 2013-12-11
CHANGELOG | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/new.example.landscape.R | 6 +++--- src/Landscape_space.cc | 6 ++---- src/Landscape_space.h | 1 + src/RandLib.cc | 4 ++-- 7 files changed, 20 insertions(+), 19 deletions(-)
Title: Path algorithm for generalized lasso problems
Description: This package computes the solution path for generalized
lasso problems. Important use cases are the fused lasso over an
arbitrary graph, and trend fitting of any given polynomial
order. Specialized implementations for the latter two
subproblems are given to improve stability and speed.
Author: Ryan J. Tibshirani, Taylor B. Arnold
Maintainer: Taylor Arnold
Diff between genlasso versions 1.0 dated 2012-08-19 and 1.1 dated 2013-12-11
genlasso-1.0/genlasso/vignettes/jss.bst |only genlasso-1.0/genlasso/vignettes/jss.cls |only genlasso-1.1/genlasso/DESCRIPTION | 9 +++++---- genlasso-1.1/genlasso/MD5 | 10 +++++----- genlasso-1.1/genlasso/build |only genlasso-1.1/genlasso/inst/doc/article.R |only genlasso-1.1/genlasso/man/plot.genlasso.Rd | 4 ++-- genlasso-1.1/genlasso/man/trendfilter.Rd | 6 +++--- 8 files changed, 15 insertions(+), 14 deletions(-)
Title: Easy Table
Description: A table function for descriptive statistics in tabular format, using variables in a data.frame. You can create simple or highly customized tables.
Author: Andreas Schulz
Maintainer: Andreas Schulz
Diff between etable versions 1.0.8 dated 2013-02-22 and 1.2.0 dated 2013-12-11
DESCRIPTION | 16 +---- MD5 | 15 ++-- R/eventpct_cell.R | 2 build |only inst/doc/etable_vignette.R |only inst/doc/etable_vignette.pdf |binary inst/doc/etable_vignette.rnw | 136 +++++++++++++++++++++++++++---------------- man/etable-package.Rd | 4 - man/eventpct_cell.Rd | 1 vignettes |only 10 files changed, 105 insertions(+), 69 deletions(-)
Title: Baseline identification and peak decomposition for x-ray
diffractograms
Description: Residual-based baseline identification and peak decomposition for x-ray diffractograms as introduced in Davies/Gather/Mergel/Meise/Mildenberger (2008).
Author: P.L. Davies, U. Gather, M. Meise, D.Mergel, T. Mildenberger. Additional Code by T. Bernholt and T. Hofmeister
Maintainer: T. Mildenberger
Diff between diffractometry versions 0.1-7 dated 2013-06-17 and 0.1-8 dated 2013-12-11
DESCRIPTION | 17 +++++++---------- MD5 | 2 +- 2 files changed, 8 insertions(+), 11 deletions(-)
More information about diffractometry at CRAN
Permanent link
Title: Two-table ExPosition
Description: TExPosition is an extension of ExPosition for two table analyses, specifically, discriminant analyses.
Author: Derek Beaton, Jenny Rieck, Cherise R. Chin Fatt, Herve Abdi
Maintainer: Derek Beaton
Diff between TExPosition versions 2.0.2 dated 2013-06-15 and 2.6.10 dated 2013-12-11
DESCRIPTION | 14 - MD5 | 44 ++++-- NAMESPACE | 2 R/calculateLVConstraints.R |only R/computeLVConstraints.R |only R/print.tepBADA.R | 24 +-- R/print.tepDICA.R | 29 ++- R/print.tepGPLS.R |only R/print.tepGraphs.R | 12 + R/print.tepPLS.R |only R/print.tepPLSCA.R |only R/tepBADA.R | 20 +- R/tepDICA.R | 20 +- R/tepGPLS.R |only R/tepGraphs.R | 305 ++++++++++++++++++++++++++++-------------- R/tepPLS.R |only R/tepPLSCA.R |only R/texpoDesignCheck.R | 27 ++- inst |only man/TExPosition-package.Rd | 12 - man/calculateLVConstraints.Rd |only man/print.tepGPLS.Rd |only man/print.tepPLS.Rd |only man/print.tepPLSCA.Rd |only man/tepBADA.Rd | 18 +- man/tepDICA.Rd | 14 - man/tepGPLS.Rd |only man/tepGraphs.Rd | 14 + man/tepPLS.Rd |only man/tepPLSCA.Rd |only man/texpoDesignCheck.Rd | 5 31 files changed, 363 insertions(+), 197 deletions(-)
Title: Software for moving grid adjustment in plant breeding field
trials
Description: Package for moving grid adjustment
in plant breeding field trials.
Author: Frank Technow
Maintainer: Frank Technow
Diff between mvngGrAd versions 0.1.2 dated 2011-10-12 and 0.1.3 dated 2013-12-11
DESCRIPTION | 13 +++++++------ MD5 | 11 +++++++---- build |only inst/doc/mvngGrAd.R |only inst/doc/mvngGrAd.Rnw | 2 +- inst/doc/mvngGrAd.pdf |binary man/mvngGrAd-package.Rd | 4 ++-- vignettes |only 8 files changed, 17 insertions(+), 13 deletions(-)
Title: Multivariate and univariate meta-analysis and meta-regression
Description: The package mvmeta consists of a collection of functions to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression in R.
Author: Antonio Gasparrini
Maintainer: Antonio Gasparrini
Diff between mvmeta versions 0.3.4 dated 2013-01-23 and 0.3.5 dated 2013-12-11
mvmeta-0.3.4/mvmeta/otherR |only mvmeta-0.3.5/mvmeta/DESCRIPTION | 15 mvmeta-0.3.5/mvmeta/MD5 | 60 +- mvmeta-0.3.5/mvmeta/NAMESPACE | 140 +++--- mvmeta-0.3.5/mvmeta/R/internal.R | 10 mvmeta-0.3.5/mvmeta/R/mvmeta.R | 2 mvmeta-0.3.5/mvmeta/R/mvmeta.control.R | 15 mvmeta-0.3.5/mvmeta/R/mvmeta.fit.R | 8 mvmeta-0.3.5/mvmeta/R/mvmeta.igls.R | 2 mvmeta-0.3.5/mvmeta/R/mvmeta.ml.R | 101 ++-- mvmeta-0.3.5/mvmeta/R/mvmeta.ml.fn.R | 62 +- mvmeta-0.3.5/mvmeta/R/mvmeta.mm.R | 8 mvmeta-0.3.5/mvmeta/R/mvmeta.reml.R | 101 ++-- mvmeta-0.3.5/mvmeta/R/mvmeta.vc.R |only mvmeta-0.3.5/mvmeta/R/mvmetaSim.R | 10 mvmeta-0.3.5/mvmeta/R/print.mvmeta.R | 70 +-- mvmeta-0.3.5/mvmeta/R/print.summary.mvmeta.R | 234 +++++----- mvmeta-0.3.5/mvmeta/R/simulate.mvmeta.R | 2 mvmeta-0.3.5/mvmeta/R/summary.mvmeta.R | 129 ++--- mvmeta-0.3.5/mvmeta/inst/changeLog | 419 ++++++++++--------- mvmeta-0.3.5/mvmeta/man/berkey98.Rd | 16 mvmeta-0.3.5/mvmeta/man/mvmeta-package.Rd | 51 +- mvmeta-0.3.5/mvmeta/man/mvmeta.Rd | 302 +++++++------ mvmeta-0.3.5/mvmeta/man/mvmeta.control.Rd | 113 ++--- mvmeta-0.3.5/mvmeta/man/mvmeta.fixed.Rd |only mvmeta-0.3.5/mvmeta/man/mvmeta.ml.Rd | 166 +++---- mvmeta-0.3.5/mvmeta/man/mvmeta.ml.fn.Rd | 4 mvmeta-0.3.5/mvmeta/man/mvmeta.mm.Rd |only mvmeta-0.3.5/mvmeta/man/mvmeta.vc.Rd |only mvmeta-0.3.5/mvmeta/man/mvmetaObject.Rd | 4 mvmeta-0.3.5/mvmeta/man/mvmetaSim.Rd | 11 mvmeta-0.3.5/mvmeta/man/na.omit.data.frame.mvmeta.Rd | 2 32 files changed, 1078 insertions(+), 979 deletions(-)
Title: Miscellaneous Useful Functions
Description: LaTeX tables, Kalman filter, web scraping, development tools,
relative risk, odds ratio
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor
Diff between miscFuncs versions 1.2-2 dated 2013-05-21 and 1.2-3 dated 2013-12-11
miscFuncs-1.2-2/miscFuncs/inst/doc/KFfit.R |only miscFuncs-1.2-2/miscFuncs/inst/doc/KFparest.R |only miscFuncs-1.2-2/miscFuncs/inst/doc/miscFuncs.R |only miscFuncs-1.2-3/miscFuncs/DESCRIPTION | 18 +++++++-------- miscFuncs-1.2-3/miscFuncs/MD5 | 27 +++++++++++++---------- miscFuncs-1.2-3/miscFuncs/NAMESPACE | 13 ++++++----- miscFuncs-1.2-3/miscFuncs/R/22tables.R |only miscFuncs-1.2-3/miscFuncs/R/EKFadvance.R | 2 - miscFuncs-1.2-3/miscFuncs/R/KFadvance.R | 1 miscFuncs-1.2-3/miscFuncs/R/KFadvanceAR2.R | 2 - miscFuncs-1.2-3/miscFuncs/R/KFtemplates.R | 2 - miscFuncs-1.2-3/miscFuncs/R/roxbc.R | 2 - miscFuncs-1.2-3/miscFuncs/build |only miscFuncs-1.2-3/miscFuncs/inst/KFfit.R |only miscFuncs-1.2-3/miscFuncs/inst/KFparest.R |only miscFuncs-1.2-3/miscFuncs/inst/doc/miscFuncs.pdf |binary miscFuncs-1.2-3/miscFuncs/man/latexformat.Rd |only miscFuncs-1.2-3/miscFuncs/man/print22.Rd |only miscFuncs-1.2-3/miscFuncs/man/twotwoinfo.Rd |only miscFuncs-1.2-3/miscFuncs/vignettes |only 20 files changed, 36 insertions(+), 31 deletions(-)
Title: MCDA
Description: The MCDA package for the R statistical software allows you to use MCDA methods and functions in R.
Author: Patrick Meyer, Sébastien Bigaret.
Maintainer: Patrick Meyer
Diff between MCDA versions 0.0.1 dated 2013-11-29 and 0.0.3 dated 2013-12-11
MCDA-0.0.1/MCDA/R/applyValueFunctionsOnPerformanceTable.R |only MCDA-0.0.1/MCDA/man/applyValueFunctionsOnPerformanceTable.Rd |only MCDA-0.0.1/MCDA/tests/applyValueFunctionsOnPerformanceTable.R |only MCDA-0.0.3/MCDA/DESCRIPTION | 9 MCDA-0.0.3/MCDA/MD5 | 28 MCDA-0.0.3/MCDA/NAMESPACE | 2 MCDA-0.0.3/MCDA/R/UTA.R | 754 +++++---- MCDA-0.0.3/MCDA/R/UTASTAR.R | 759 +++++----- MCDA-0.0.3/MCDA/R/additiveValueFunctionElicitation.R | 638 ++++---- MCDA-0.0.3/MCDA/R/applyPiecewiseLinearValueFunctionsOnPerformanceTable.R |only MCDA-0.0.3/MCDA/man/UTA.Rd | 53 MCDA-0.0.3/MCDA/man/UTASTAR.Rd | 48 MCDA-0.0.3/MCDA/man/additiveValueFunctionElicitation.Rd | 14 MCDA-0.0.3/MCDA/man/applyPiecewiseLinearValueFunctionsOnPerformanceTable.Rd |only MCDA-0.0.3/MCDA/tests/UTA.R | 33 MCDA-0.0.3/MCDA/tests/UTASTAR.R | 25 MCDA-0.0.3/MCDA/tests/additiveValueFunctionElicitation.R | 23 MCDA-0.0.3/MCDA/tests/applyPiecewiseLinearValueFunctionsOnPerformanceTable.R |only 18 files changed, 1397 insertions(+), 989 deletions(-)
Title: Inference Tests for ExPosition
Description: Non-parametric resampling-based inference tests for ExPosition.
Author: Derek Beaton, Joseph Dunlop, Herve Abdi
Maintainer: Derek Beaton
Diff between InPosition versions 0.10.4 dated 2013-06-15 and 0.12.7 dated 2013-12-11
DESCRIPTION | 14 +++++++------- MD5 | 19 ++++++++++--------- R/boot.ratio.test.R | 3 ++- R/continueResampling.R | 36 ++++++++++++++++++++---------------- R/epCA.inference.battery.R | 6 +++--- R/epGPCA.inference.battery.R | 4 ++-- R/epMCA.inference.battery.R | 13 +++++++------ R/epPCA.inference.battery.R | 4 ++-- inst |only man/InPosition-package.Rd | 6 +++--- man/continueResampling.Rd | 13 ++++++++----- 11 files changed, 64 insertions(+), 54 deletions(-)
Title: Calls CNV from exome sequence data
Description: Calls copy number variants (CNVs) from targeted sequence data
Author: Vincent Plagnol
Maintainer: Vincent Plagnol
Diff between ExomeDepth versions 0.9.7 dated 2012-12-11 and 0.9.8 dated 2013-12-11
DESCRIPTION | 18 +++----- MD5 | 30 +++++++------- R/class_definition.R | 5 -- R/countBamInGranges.R | 74 +++++++++++++++++++++--------------- R/optimize_reference_set.R | 11 +++-- R/plot_CNVs_method.R | 2 R/tools.R | 4 - data/Conrad.hg19.RData |binary data/ExomeCount.RData |binary data/exons.hg19.RData |binary data/exons.hg19.X.RData |binary inst/doc/ExomeDepth-vignette.R |only inst/doc/ExomeDepth-vignette.Rnw | 23 ++++++++++- inst/doc/ExomeDepth-vignette.pdf |binary man/countBamInGRanges.exomeDepth.Rd | 8 ++- man/getBamCounts.Rd | 12 ++++- vignettes |only 17 files changed, 116 insertions(+), 71 deletions(-)
Title: Dynamic time warping algorithms
Description: A comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on. Provides cumulative distances, alignments, specialized plot styles, etc.
Author: Toni Giorgino
Maintainer: Toni Giorgino
Diff between dtw versions 1.16 dated 2013-05-28 and 1.17-1 dated 2013-12-11
dtw-1.16/dtw/inst/TODO |only dtw-1.16/dtw/inst/doc/alignMVM.pdf |only dtw-1.16/dtw/inst/doc/dtw.bib |only dtw-1.16/dtw/inst/doc/mvmSP.pdf |only dtw-1.16/dtw/inst/doc/object-diagram.pdf |only dtw-1.16/dtw/inst/doc/plot-conventions.pdf |only dtw-1.17-1/dtw/DESCRIPTION | 21 +++-------- dtw-1.17-1/dtw/MD5 | 51 +++++++++++++++-------------- dtw-1.17-1/dtw/NAMESPACE | 4 ++ dtw-1.17-1/dtw/R/countPaths.R |only dtw-1.17-1/dtw/R/dtw.R | 10 ++--- dtw-1.17-1/dtw/R/dtwDist.R | 2 - dtw-1.17-1/dtw/R/globalCostMatrix.R | 4 +- dtw-1.17-1/dtw/R/mvm.R | 2 - dtw-1.17-1/dtw/R/stepPattern.R | 21 +++++++---- dtw-1.17-1/dtw/R/warp.R | 2 - dtw-1.17-1/dtw/R/warpArea.R | 2 - dtw-1.17-1/dtw/build |only dtw-1.17-1/dtw/inst/ChangeLog | 9 +++++ dtw-1.17-1/dtw/inst/doc/dtw.R |only dtw-1.17-1/dtw/inst/doc/dtw.Rnw | 22 +++--------- dtw-1.17-1/dtw/inst/doc/dtw.pdf |binary dtw-1.17-1/dtw/inst/dtw.bib | 35 ++++++++++++++++++- dtw-1.17-1/dtw/man/countPaths.Rd |only dtw-1.17-1/dtw/src/Makevars | 3 + dtw-1.17-1/dtw/src/Makevars.win |only dtw-1.17-1/dtw/src/computeCM.c | 13 +++---- dtw-1.17-1/dtw/tests/dtw_test.R | 9 +++-- dtw-1.17-1/dtw/tests/dtw_test.Rout.save | 36 ++++++++++++++------ dtw-1.17-1/dtw/vignettes |only 30 files changed, 151 insertions(+), 95 deletions(-)
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides some utility functions used also by other DoE packages.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping
Diff between DoE.base versions 0.25-2 dated 2013-08-26 and 0.25-3 dated 2013-12-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/plot.design.R | 6 +++--- R/sysdata.rda |binary inst/NEWS | 4 ++++ 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Clustering Indices
Description: compute clustering validation indices
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes
Diff between clusterCrit versions 1.2.2 dated 2013-06-15 and 1.2.3 dated 2013-12-11
clusterCrit-1.2.2/clusterCrit/inst/doc/clusterCrit.bib |only clusterCrit-1.2.3/clusterCrit/DESCRIPTION | 8 clusterCrit-1.2.3/clusterCrit/MD5 | 23 + clusterCrit-1.2.3/clusterCrit/build/clusterCrit.pdf |binary clusterCrit-1.2.3/clusterCrit/build/partial.rdb |binary clusterCrit-1.2.3/clusterCrit/build/vignette.rds |only clusterCrit-1.2.3/clusterCrit/cleanup | 2 clusterCrit-1.2.3/clusterCrit/configure | 223 +---------------- clusterCrit-1.2.3/clusterCrit/configure.ac | 19 + clusterCrit-1.2.3/clusterCrit/inst/doc/clusterCrit.R |only clusterCrit-1.2.3/clusterCrit/src/Makevars.in | 6 clusterCrit-1.2.3/clusterCrit/src/Makevars.win | 2 clusterCrit-1.2.3/clusterCrit/src/logFile.f95 |only clusterCrit-1.2.3/clusterCrit/src/timer.f95 |only clusterCrit-1.2.3/clusterCrit/vignettes |only 15 files changed, 64 insertions(+), 219 deletions(-)
Title: p-variation, calculation and application
Description: The calculation of p-variation of the finite sample data
Author: Vygantas Butkus
Maintainer: Vygantas Butkus
Diff between pvar versions 1.0.6 dated 2012-09-28 and 1.0.9 dated 2013-12-11
pvar-1.0.6/pvar/Change_log.txt |only pvar-1.0.6/pvar/man/BBT.Rd |only pvar-1.0.6/pvar/man/pvarMon.Rd |only pvar-1.0.9/pvar/DESCRIPTION | 13 +++--- pvar-1.0.9/pvar/MD5 | 35 ++++++++--------- pvar-1.0.9/pvar/NAMESPACE | 6 -- pvar-1.0.9/pvar/R/PvarBreakTest.R | 32 ++++++++------- pvar-1.0.9/pvar/R/p-variation.R | 49 +++++++++--------------- pvar-1.0.9/pvar/man/BridgeT.Rd |only pvar-1.0.9/pvar/man/ConcatenateStrings.Rd | 2 pvar-1.0.9/pvar/man/DataSets.Rd | 2 pvar-1.0.9/pvar/man/FindAnalysingPoints.Rd | 4 - pvar-1.0.9/pvar/man/PvarBreakTest.Rd | 30 +++++++------- pvar-1.0.9/pvar/man/PvarExtraFun.Rd | 8 +-- pvar-1.0.9/pvar/man/PvarExtraFun_dev.Rd | 4 - pvar-1.0.9/pvar/man/PvarQuantile.Rd | 12 ++--- pvar-1.0.9/pvar/man/SplitByExtremum.Rd | 4 - pvar-1.0.9/pvar/man/Sum_p.Rd | 6 +- pvar-1.0.9/pvar/man/pvar-package.Rd | 59 ++++++++++++++--------------- pvar-1.0.9/pvar/man/pvar.Rd | 32 +++++++++++---- pvar-1.0.9/pvar/man/pvarPseudoMonotonic.Rd |only 21 files changed, 153 insertions(+), 145 deletions(-)
Title: Bayesian Model Averaging for Multinomial Logit Models
Description: Provides a modified function bic.glm of the BMA package that can be applied to multinomial logit (MNL) data. The data is converted to binary logit using the Begg & Gray approximation. The package also contains functions for maximum likelihood estimation of MNL.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova
Diff between mlogitBMA versions 0.1-5 dated 2012-02-22 and 0.1-6 dated 2013-12-11
mlogitBMA-0.1-5/mlogitBMA/CHANGELOG |only mlogitBMA-0.1-5/mlogitBMA/data/heating.txt |only mlogitBMA-0.1-6/mlogitBMA/ChangeLog |only mlogitBMA-0.1-6/mlogitBMA/DESCRIPTION | 15 +++++-------- mlogitBMA-0.1-6/mlogitBMA/MD5 | 17 +++++++++------ mlogitBMA-0.1-6/mlogitBMA/NAMESPACE | 2 - mlogitBMA-0.1-6/mlogitBMA/R/bic.glm.bg.R | 23 ++++++++++++++------- mlogitBMA-0.1-6/mlogitBMA/data/heating.txt.gz |only mlogitBMA-0.1-6/mlogitBMA/inst/doc/conversion.R |only mlogitBMA-0.1-6/mlogitBMA/man/mlogitBMA-package.Rd | 5 +--- mlogitBMA-0.1-6/mlogitBMA/src |only mlogitBMA-0.1-6/mlogitBMA/tests/test_functions.R | 3 +- mlogitBMA-0.1-6/mlogitBMA/vignettes |only 13 files changed, 37 insertions(+), 28 deletions(-)
Title: Generalized Method of Moments and Generalized Empirical
Likelihood
Description: It is a complete suite to estimate models based on moment
conditions. It includes the two step Generalized method of
moments (GMM) of Hansen(1982), the iterated GMM and continuous
updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several
methods that belong to the Generalized Empirical Likelihood
(GEL) family of estimators, as presented by Smith(1997),
Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).
Author: Pierre Chausse
Maintainer: Pierre Chausse
Diff between gmm versions 1.4-5 dated 2013-01-11 and 1.5-0 dated 2013-12-11
gmm-1.4-5/gmm/inst/doc/empir.bib |only gmm-1.4-5/gmm/licence |only gmm-1.5-0/gmm/DESCRIPTION | 13 +-- gmm-1.5-0/gmm/MD5 | 38 ++++----- gmm-1.5-0/gmm/NAMESPACE | 7 + gmm-1.5-0/gmm/NEWS | 10 ++ gmm-1.5-0/gmm/R/Methods.gmm.R | 141 +++++++++++++++++++++++++++------- gmm-1.5-0/gmm/R/gel.R | 7 - gmm-1.5-0/gmm/R/getModel.R | 17 +--- gmm-1.5-0/gmm/R/gmm.R | 6 - gmm-1.5-0/gmm/R/momentEstim.R | 18 +++- gmm-1.5-0/gmm/build |only gmm-1.5-0/gmm/inst/doc/gmm_with_R.R |only gmm-1.5-0/gmm/inst/doc/gmm_with_R.pdf |binary gmm-1.5-0/gmm/man/bread.Rd | 33 ++++--- gmm-1.5-0/gmm/man/estfun.Rd | 9 +- gmm-1.5-0/gmm/man/gel.Rd | 11 +- gmm-1.5-0/gmm/man/getLamb.Rd | 4 gmm-1.5-0/gmm/man/gmm.Rd | 28 ++++-- gmm-1.5-0/gmm/man/summary.Rd | 3 gmm-1.5-0/gmm/man/vcov.Rd | 9 ++ gmm-1.5-0/gmm/vignettes |only 22 files changed, 252 insertions(+), 102 deletions(-)
Title: Weighted Likelihood Estimation
Description: Approach to the robustness via Weighted Likelihood.
Author: Claudio Agostinelli
Maintainer: Claudio Agostinelli
Diff between wle versions 0.9-7 dated 2012-10-16 and 0.9-9 dated 2013-12-11
wle-0.9-7/wle/COPYRIGHT |only wle-0.9-7/wle/CREDITS |only wle-0.9-7/wle/Makevars |only wle-0.9-7/wle/R/wle.cv.robust.bootstrap.R |only wle-0.9-7/wle/R/wle.cv.robust.bootstrap.m.R |only wle-0.9-7/wle/R/wle.cv.robust.bootstrap.mc.R |only wle-0.9-7/wle/STATUS |only wle-0.9-9/wle/DESCRIPTION | 16 - wle-0.9-9/wle/MD5 | 68 +++---- wle-0.9-9/wle/NAMESPACE | 90 --------- wle-0.9-9/wle/R/extractRoot.R | 25 ++ wle-0.9-9/wle/R/mde.vonmises.R | 253 +++++++++++++-------------- wle-0.9-9/wle/R/mde.wrappednormal.R | 11 - wle-0.9-9/wle/R/wle.gamma.shape.R | 57 ++++-- wle-0.9-9/wle/R/wle.glm.R | 9 wle-0.9-9/wle/R/wle.normal.high.chisq.R |only wle-0.9-9/wle/R/wle.normal.high.r.R | 22 +- wle-0.9-9/wle/R/wle.vonmises.R | 25 +- wle-0.9-9/wle/R/wle.wrappednormal.R | 56 ++--- wle-0.9-9/wle/R/zzz.R | 6 wle-0.9-9/wle/README | 2 wle-0.9-9/wle/data/artificial.rda |binary wle-0.9-9/wle/data/cavendish.rda |binary wle-0.9-9/wle/data/hald.rda |binary wle-0.9-9/wle/data/rocky.rda |binary wle-0.9-9/wle/data/selection.rda |binary wle-0.9-9/wle/inst |only wle-0.9-9/wle/man/mde.vonmises.Rd | 30 +-- wle-0.9-9/wle/man/mde.wrappednormal.Rd | 32 +-- wle-0.9-9/wle/man/plot.wle.lm.Rd | 3 wle-0.9-9/wle/man/wle.aic.ar.Rd | 14 + wle-0.9-9/wle/man/wle.fracdiff.Rd | 28 +- wle-0.9-9/wle/man/wle.glm.Rd | 5 wle-0.9-9/wle/man/wle.glm.weights.Rd | 13 + wle-0.9-9/wle/man/wle.vonmises.Rd | 13 - wle-0.9-9/wle/man/wle.weights.Rd | 3 wle-0.9-9/wle/man/wle.wrappednormal.Rd | 13 - wle-0.9-9/wle/src/dbetawrapper.c |only wle-0.9-9/wle/src/mle.wrappednormal.f |only wle-0.9-9/wle/src/wlemah.f |only 40 files changed, 378 insertions(+), 416 deletions(-)
Title: Dependent Mixture Models - Hidden Markov Models of GLMs and
Other Distributions in S4
Description: Fit latent (hidden) Markov models on mixed categorical and continuous (timeseries)
data, otherwise known as dependent mixture models
Author: Ingmar Visser
Maintainer: Ingmar Visser
Diff between depmixS4 versions 1.3-0 dated 2013-09-18 and 1.3-1 dated 2013-12-11
depmixS4-1.3-0/depmixS4/build |only depmixS4-1.3-1/depmixS4/DESCRIPTION | 8 +- depmixS4-1.3-1/depmixS4/MD5 | 29 ++++----- depmixS4-1.3-1/depmixS4/NEWS | 63 ++++++++++++++------- depmixS4-1.3-1/depmixS4/R/depmixfit.R | 35 ++++++----- depmixS4-1.3-1/depmixS4/R/nobs.R | 2 depmixS4-1.3-1/depmixS4/data/balance.rda |binary depmixS4-1.3-1/depmixS4/data/sp500.rda |binary depmixS4-1.3-1/depmixS4/data/speed.rda |binary depmixS4-1.3-1/depmixS4/inst/doc/depmixS4.R | 20 +++--- depmixS4-1.3-1/depmixS4/inst/doc/depmixS4.Rnw | 7 +- depmixS4-1.3-1/depmixS4/inst/doc/depmixS4.pdf |binary depmixS4-1.3-1/depmixS4/man/depmix.fit.Rd | 2 depmixS4-1.3-1/depmixS4/tests/test1speed.Rout.save | 2 depmixS4-1.3-1/depmixS4/vignettes/depmixS4.Rnw | 7 +- depmixS4-1.3-1/depmixS4/vignettes/depmixS4.bib | 11 +++ 16 files changed, 113 insertions(+), 73 deletions(-)
Title: Simulation of synthetic populations for surveys based on sample
data
Description: Simulate populations for surveys based on sample data with special application to EU-SILC.
Author: Andreas Alfons [aut, cre],
Stefan Kraft [aut]
Maintainer: Andreas Alfons
Diff between simPopulation versions 0.4.0 dated 2012-02-12 and 0.4.1 dated 2013-12-11
simPopulation-0.4.0/simPopulation/inst/doc/simPopulation.bib |only simPopulation-0.4.1/simPopulation/DESCRIPTION | 20 ++++---- simPopulation-0.4.1/simPopulation/MD5 | 23 +++++----- simPopulation-0.4.1/simPopulation/NAMESPACE | 2 simPopulation-0.4.1/simPopulation/NEWS | 8 +++ simPopulation-0.4.1/simPopulation/build |only simPopulation-0.4.1/simPopulation/data/eusilcS.RData |binary simPopulation-0.4.1/simPopulation/data/ghanaS.RData |binary simPopulation-0.4.1/simPopulation/demo/ghana.R | 12 +++-- simPopulation-0.4.1/simPopulation/inst/doc/simPopulation-eusilc.R |only simPopulation-0.4.1/simPopulation/inst/doc/simPopulation-eusilc.Rnw | 15 +++--- simPopulation-0.4.1/simPopulation/inst/doc/simPopulation-eusilc.pdf |binary simPopulation-0.4.1/simPopulation/man/simPopulation-package.Rd | 10 ++-- simPopulation-0.4.1/simPopulation/vignettes |only 14 files changed, 54 insertions(+), 36 deletions(-)
Title: Simulation framework
Description: A general framework for statistical simulation.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons
Diff between simFrame versions 0.5.0 dated 2012-01-02 and 0.5.1 dated 2013-12-11
simFrame-0.5.0/simFrame/inst/doc/UML.eps |only simFrame-0.5.0/simFrame/inst/doc/UML.pdf |only simFrame-0.5.0/simFrame/inst/doc/jss.bst |only simFrame-0.5.0/simFrame/inst/doc/jss.cls |only simFrame-0.5.0/simFrame/inst/doc/simFrame.bib |only simFrame-0.5.0/simFrame/inst/doc/snippets |only simFrame-0.5.1/simFrame/DESCRIPTION | 17 +++-- simFrame-0.5.1/simFrame/MD5 | 57 ++++++++++--------- simFrame-0.5.1/simFrame/NAMESPACE | 2 simFrame-0.5.1/simFrame/NEWS | 10 +++ simFrame-0.5.1/simFrame/R/cluster.R | 18 +++--- simFrame-0.5.1/simFrame/R/clusterRunSimulation.R | 4 - simFrame-0.5.1/simFrame/R/clusterSetup.R | 2 simFrame-0.5.1/simFrame/build |only simFrame-0.5.1/simFrame/data/eusilcP.RData |binary simFrame-0.5.1/simFrame/demo/model-based.R | 2 simFrame-0.5.1/simFrame/demo/parallel.R | 2 simFrame-0.5.1/simFrame/inst/doc/simFrame-eusilc.R |only simFrame-0.5.1/simFrame/inst/doc/simFrame-eusilc.Rnw | 15 ++--- simFrame-0.5.1/simFrame/inst/doc/simFrame-eusilc.pdf |binary simFrame-0.5.1/simFrame/inst/doc/simFrame-intro.R |only simFrame-0.5.1/simFrame/inst/doc/simFrame-intro.Rnw | 19 +++--- simFrame-0.5.1/simFrame/inst/doc/simFrame-intro.pdf |binary simFrame-0.5.1/simFrame/man/simFrame-package.Rd | 10 +-- simFrame-0.5.1/simFrame/src/Makevars.win | 8 +- simFrame-0.5.1/simFrame/src/simFrame.cpp | 7 -- simFrame-0.5.1/simFrame/vignettes |only 27 files changed, 93 insertions(+), 80 deletions(-)
Title: A tool for calculation and optimization of the expected gain
from multi-stage selection
Description: Multi-stage selection is practiced in numerous fields of life and social sciences and particularly in breeding. A special characteristic of multi-stage selection is that candidates are evaluated in successive stages with increasing intensity and effort, and only a fraction of the superior candidates is selected and promoted to the next stage. For the optimum design of such selection programs, the selection gain plays a crucial role. It can be calculated by integration of a truncated multivariate normal (MVN) distribution. While mathematical formulas for calculating the selection gain and the variance among selected candidates were developed long time ago, solutions for numerical calculation were not available. This package can also be used for optimizing multi-stage selection programs for a given total budget and different costs of evaluating the candidates in each stage.
Author: Xuefei Mi, H. Friedrich Utz, Albrecht E. Melchinger (Project contact person: Melchinger@uni-hohenheim.de )
Maintainer: Xuefei Mi
Diff between selectiongain versions 2.0.28 dated 2013-10-22 and 2.0.29 dated 2013-12-11
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/multistageoptimum.grid.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Side effect risks in hospital : simulation and estimation
Description: Evaluating risk (that a patient arises a side effect) during hospitalization is the main purpose of this package. Several methods (Parametric, non parametric and De Vielder estimation) to estimate the risk constant (R) are implemented in this package. There are also functions to simulate the different models of this issue in order to quantify the previous estimators. It is necessary to read at least the first six pages of the report to understand the topic.
Author: Christophe Dutang and Julie Barthes
Maintainer: Christophe Dutang
Diff between rhosp versions 1.04 dated 2009-02-10 and 1.05 dated 2013-12-11
rhosp-1.04/rhosp/inst/doc/d1000exp_exp.pdf |only rhosp-1.04/rhosp/inst/doc/d1000exp_exp_DV.pdf |only rhosp-1.04/rhosp/inst/doc/d100exp_exp.pdf |only rhosp-1.04/rhosp/inst/doc/d100exp_exp_DV.pdf |only rhosp-1.04/rhosp/inst/doc/image_adequat_exp120_unif020.pdf |only rhosp-1.04/rhosp/inst/doc/image_adequat_exp13_lnorm14_1.pdf |only rhosp-1.04/rhosp/inst/doc/image_mod1_exp13_cst13_1000_1000.pdf |only rhosp-1.04/rhosp/inst/doc/image_mod1_exp13_exp15_1000_1000.pdf |only rhosp-1.04/rhosp/inst/doc/image_mod1_exp13_expcomp13_15_110_1000_1000.pdf |only rhosp-1.04/rhosp/inst/doc/image_mod1_exp13_gamma3_13_1000_1000.pdf |only rhosp-1.04/rhosp/inst/doc/image_mod2_exp13_exp15.pdf |only rhosp-1.04/rhosp/inst/doc/mod1.pdf |only rhosp-1.04/rhosp/inst/doc/mod2.pdf |only rhosp-1.05/rhosp/DESCRIPTION | 20 +++--- rhosp-1.05/rhosp/MD5 |only rhosp-1.05/rhosp/inst/CITATION |only rhosp-1.05/rhosp/inst/doc/rhosp.R |only rhosp-1.05/rhosp/inst/doc/rhosp.Rnw | 30 ++++------ rhosp-1.05/rhosp/inst/doc/rhosp.pdf |binary rhosp-1.05/rhosp/man/DV.Rd | 4 + rhosp-1.05/rhosp/man/Table.Rd | 1 rhosp-1.05/rhosp/man/adequadExp.Rd | 8 ++ rhosp-1.05/rhosp/man/estimParam.Rd | 2 rhosp-1.05/rhosp/man/histo.Rd | 21 +++---- rhosp-1.05/rhosp/man/mainSimul.Rd | 21 +++---- rhosp-1.05/rhosp/man/mainSimul2.Rd | 16 ++--- rhosp-1.05/rhosp/man/simul.Rd | 27 ++++----- rhosp-1.05/rhosp/vignettes |only 28 files changed, 79 insertions(+), 71 deletions(-)
Title: A Package for Qualitative Comparative Analysis
Description: This package provides functions for performing Qualitative Comparative Analysis (csQCA, tQCA, mvQCA and fsQCA).
Author: Adrian Dusa [aut, cre], Alrik Thiem [aut]
Maintainer: Adrian Dusa
Diff between QCA versions 1.1-0 dated 2013-11-01 and 1.1-1 dated 2013-12-11
DESCRIPTION | 12 +++---- MD5 | 35 +++++++++++---------- NAMESPACE | 1 R/eqmcc.R | 81 +++++++++++++------------------------------------ R/getSolution.R |only R/is.print.R | 32 ++++++++++++++----- R/rowDominance.R | 3 - R/solveChart.R | 59 +++++++++-------------------------- R/truthTable.R | 9 +++++ inst/CITATION | 11 +++--- inst/ChangeLog | 10 ++++-- inst/TODO | 5 ++- man/QCA-internal.Rd | 1 man/QCA.package.Rd | 21 ++++++------ man/eqmcc.Rd | 55 +++++++++++++++++++++------------ man/pof.Rd | 3 + man/truthTable.Rd | 1 src/allSol.c |only src/removeRedundants.c | 2 - src/solveChart.c |only 20 files changed, 166 insertions(+), 175 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-20 1.1-2
2013-03-19 1.1-0
Title: Memory management in R by delayed assignments
Description: Allows objects to be stored on disc and automatically
recalled into memory, as required, by delayed assignment.
Author: Bill Venables, based on original code by David Brahm
Maintainer: Bill Venables
Diff between SOAR versions 0.99-10 dated 2012-01-14 and 0.99-11 dated 2013-12-11
SOAR-0.99-10/SOAR/inst/doc/Makefile |only SOAR-0.99-10/SOAR/inst/doc/refs.bib |only SOAR-0.99-11/SOAR/DESCRIPTION | 16 +++++++-------- SOAR-0.99-11/SOAR/MD5 | 20 +++++++++++-------- SOAR-0.99-11/SOAR/R/SOAR.R | 2 + SOAR-0.99-11/SOAR/build |only SOAR-0.99-11/SOAR/inst/NEWS | 4 +++ SOAR-0.99-11/SOAR/inst/doc/SOAR.R |only SOAR-0.99-11/SOAR/inst/doc/SOAR.Rnw | 35 +++++++++++++++++++++++----------- SOAR-0.99-11/SOAR/inst/doc/SOAR.pdf |binary SOAR-0.99-11/SOAR/man/NAME.Rd |only SOAR-0.99-11/SOAR/man/SOAR-package.Rd | 5 +--- SOAR-0.99-11/SOAR/vignettes |only 13 files changed, 52 insertions(+), 30 deletions(-)
Title: True random numbers using random.org
Description: This package provides an interface to the true random number
service provided by the random.org website created by Mads Haahr.
The random.org web service samples atmospheric noise via radio
tuned to an unused broadcasting frequency together with a skew
correction algorithm due to John von Neumann. More background is
available in the included vignette based on an essay by Mads Haahr.
In its current form, the package offers functions to retrieve
random integers, randomized sequences and random strings.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
Diff between random versions 0.2.1 dated 2009-08-13 and 0.2.2 dated 2013-12-11
random-0.2.1/random/inst/ChangeLog |only random-0.2.1/random/inst/doc/random-intro.bib |only random-0.2.1/random/inst/doc/random.Rdata |only random-0.2.2/random/ChangeLog |only random-0.2.2/random/DESCRIPTION | 28 +++++++++++++------------- random-0.2.2/random/MD5 |only random-0.2.2/random/R/random.R | 2 - random-0.2.2/random/build |only random-0.2.2/random/inst/doc/random-essay.pdf |binary random-0.2.2/random/inst/doc/random-intro.R |only random-0.2.2/random/inst/doc/random-intro.pdf |binary random-0.2.2/random/man/random.Rd | 3 +- random-0.2.2/random/vignettes |only 13 files changed, 17 insertions(+), 16 deletions(-)
Title: A package to estimate posterior probabilities and perform model
selection in change-point models using constrained HMM.
Description: The functions are used for change-point problems, after an initial set of change-points within the data has already been obtained. The function postCP obtains estimates of posterior probabilities of change-point and hidden states for each observation, and confidence intervals for the positions of the change-point. The function postCPsample obtains random samples of sets of change-points using the output of the postCP function. Model selection may be performed using function postCPmodelsel through criteria obtained from function postCPcrit.
Author: Gregory Nuel and The Minh Luong
Maintainer: The Minh Luong
Diff between postCP versions 1.7.0 dated 2013-07-01 and 1.7.2 dated 2013-12-11
DESCRIPTION | 25 ++++++++----------------- MD5 | 26 +++++++++++++------------- R/postCP.modelsel.r | 50 +++++++++++++++++++++++++++++++++----------------- R/postCP.r | 17 ++++++++++------- man/GreedySegmente.Rd | 4 ++-- man/lesum.Rd | 4 ++-- man/mleNB.Rd | 4 ++-- man/plot.postCP.Rd | 4 ++-- man/postCP.Rd | 4 ++-- man/postCPcrit.Rd | 4 ++-- man/postCPmodelsel.Rd | 7 +++---- man/postCPsample.Rd | 4 ++-- man/viterbi.Rd | 4 ++-- src/postCP.cpp | 2 +- 14 files changed, 84 insertions(+), 75 deletions(-)
Title: Analysis of evolutionary rates in an OU framework
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
Diff between OUwie versions 1.36 dated 2013-11-22 and 1.37 dated 2013-12-11
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/OUwie.sim.R | 33 ++++------------- R/varcov.ou.R | 31 +++------------- R/weight.mat.R | 110 ++++++++++++++++++++++++--------------------------------- 5 files changed, 71 insertions(+), 119 deletions(-)
Title: Mixture of Gaussian Bayesian Network Model
Description: A package that models continuous multivariate data via directional acyclic graphs and provides inference based on the frequentist approach
Author: Nikolay Balov
Maintainer: Nikolay Balov
Diff between mugnet versions 1.01.3 dated 2013-02-26 and 1.02.0 dated 2013-12-11
DESCRIPTION | 16 +++++++--------- MD5 | 4 ++-- demo/blung.r | 8 ++++---- 3 files changed, 13 insertions(+), 15 deletions(-)
Title: Categorical Bayesian Network Inference
Description: A package that handles discrete Bayesian network models and provides inference using the frequentist approach
Author: Nikolay Balov, Peter Salzman
Maintainer: Nikolay Balov
Diff between catnet versions 1.14.2 dated 2013-07-31 and 1.14.3 dated 2013-12-11
DESCRIPTION | 10 +++++----- MD5 | 3 ++- build |only 3 files changed, 7 insertions(+), 6 deletions(-)