Title: Power and Sample Size Calculations for SNP Association Studies
with Censored Time to Event Outcomes
Diff between survSNP versions 0.21-5 dated 2012-08-06 and 0.21-6 dated 2013-12-11
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
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
Diff between sealasso versions 0.1-1 dated 2013-09-08 and 0.1-2 dated 2013-12-11
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
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
Diff between SBSA versions 0.2.0 dated 2012-03-16 and 0.2.1 dated 2013-12-11
Description: Simplified Bayesian Sensitivity Analysis
Author: Davor Cubranic and Paul Gustafson
Maintainer: Davor Cubranic
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
Diff between QTLRel versions 0.2-12 dated 2012-11-15 and 0.2-14 dated 2013-12-11
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
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
Diff between mleur versions 1.0-5 dated 2012-09-22 and 1.0-6 dated 2013-12-11
Description: Provides functions for unit root testing using MLE method
Author: A. I. McLeod, Hao Yu and Ying Zhang
Maintainer: Ian McLeod
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
Diff between HistogramTools versions 0.2 dated 2013-10-03 and 0.3 dated 2013-12-11
More information about HistogramTools at CRAN
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
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(-)
Permanent link
Title: Dependency Modeling Toolkit
Diff between dmt versions 0.8.10 dated 2012-05-30 and 0.8.20 dated 2013-12-11
Description: Probabilistic dependency modeling toolkit.
Author: Leo Lahti and Olli-Pekka Huovilainen
Maintainer: Leo Lahti
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
Diff between sphet versions 1.4 dated 2013-06-21 and 1.5 dated 2013-12-11
Description: Generalized Method of Moment estimation of Cliff-Ord-type
spatial autoregressive models with and without heteroskedastic
innovations
Author: Gianfranco Piras
Maintainer: Gianfranco Piras
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
Diff between smfsb versions 1.0 dated 2011-10-26 and 1.1 dated 2013-12-11
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
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
Diff between grImport versions 0.8-4 dated 2012-02-15 and 0.9-0 dated 2013-12-11
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
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
Diff between TInPosition versions 0.10.4 dated 2013-06-15 and 0.13.6 dated 2013-12-11
Description: Non-parametric resampling-based inference tests for TExPosition.
Author: Derek Beaton, Jenny Rieck, Herve Abdi
Maintainer: Derek Beaton
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)
Diff between rspear versions 0.1-1 dated 2013-09-09 and 0.1-2 dated 2013-12-11
Description: Calculate SPEARpesticide in R
(http://www.systemecology.eu/SPEAR/index.php)
Author: Eduard Szoecs
Maintainer: Eduard Szoecs
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
Diff between prob versions 0.9-2 dated 2009-11-02 and 0.9-5 dated 2013-12-11
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
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
Diff between pgs versions 0.3-0 dated 2010-02-09 and 0.4-0 dated 2013-12-11
Description: Computation of mean squared errors of stereological predictors.
Author: Kien Kieu
Maintainer: Kien Kieu
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
Diff between kernelPop versions 1.0.0 dated 2013-11-27 and 1.0.2 dated 2013-12-11
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
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
Diff between genlasso versions 1.0 dated 2012-08-19 and 1.1 dated 2013-12-11
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
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
Diff between etable versions 1.0.8 dated 2013-02-22 and 1.2.0 dated 2013-12-11
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
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
Diff between diffractometry versions 0.1-7 dated 2013-06-17 and 0.1-8 dated 2013-12-11
More information about diffractometry at CRAN
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
DESCRIPTION | 17 +++++++----------
MD5 | 2 +-
2 files changed, 8 insertions(+), 11 deletions(-)
Permanent link
Title: Two-table ExPosition
Diff between TExPosition versions 2.0.2 dated 2013-06-15 and 2.6.10 dated 2013-12-11
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
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
Diff between mvngGrAd versions 0.1.2 dated 2011-10-12 and 0.1.3 dated 2013-12-11
Description: Package for moving grid adjustment
in plant breeding field trials.
Author: Frank Technow
Maintainer: Frank Technow
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
Diff between mvmeta versions 0.3.4 dated 2013-01-23 and 0.3.5 dated 2013-12-11
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
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
Diff between miscFuncs versions 1.2-2 dated 2013-05-21 and 1.2-3 dated 2013-12-11
Description: LaTeX tables, Kalman filter, web scraping, development tools,
relative risk, odds ratio
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor
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
Diff between MCDA versions 0.0.1 dated 2013-11-29 and 0.0.3 dated 2013-12-11
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
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
Diff between InPosition versions 0.10.4 dated 2013-06-15 and 0.12.7 dated 2013-12-11
Description: Non-parametric resampling-based inference tests for ExPosition.
Author: Derek Beaton, Joseph Dunlop, Herve Abdi
Maintainer: Derek Beaton
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
Diff between ExomeDepth versions 0.9.7 dated 2012-12-11 and 0.9.8 dated 2013-12-11
Description: Calls copy number variants (CNVs) from targeted sequence data
Author: Vincent Plagnol
Maintainer: Vincent Plagnol
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
Diff between dtw versions 1.16 dated 2013-05-28 and 1.17-1 dated 2013-12-11
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
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
Diff between DoE.base versions 0.25-2 dated 2013-08-26 and 0.25-3 dated 2013-12-11
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
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
Diff between clusterCrit versions 1.2.2 dated 2013-06-15 and 1.2.3 dated 2013-12-11
Description: compute clustering validation indices
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes
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
Diff between pvar versions 1.0.6 dated 2012-09-28 and 1.0.9 dated 2013-12-11
Description: The calculation of p-variation of the finite sample data
Author: Vygantas Butkus
Maintainer: Vygantas Butkus
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
Diff between mlogitBMA versions 0.1-5 dated 2012-02-22 and 0.1-6 dated 2013-12-11
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
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
Diff between gmm versions 1.4-5 dated 2013-01-11 and 1.5-0 dated 2013-12-11
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
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
Diff between wle versions 0.9-7 dated 2012-10-16 and 0.9-9 dated 2013-12-11
Description: Approach to the robustness via Weighted Likelihood.
Author: Claudio Agostinelli
Maintainer: Claudio Agostinelli
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
Diff between depmixS4 versions 1.3-0 dated 2013-09-18 and 1.3-1 dated 2013-12-11
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
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
Diff between simPopulation versions 0.4.0 dated 2012-02-12 and 0.4.1 dated 2013-12-11
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
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
Diff between simFrame versions 0.5.0 dated 2012-01-02 and 0.5.1 dated 2013-12-11
Description: A general framework for statistical simulation.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons
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
Diff between selectiongain versions 2.0.28 dated 2013-10-22 and 2.0.29 dated 2013-12-11
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
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
Diff between rhosp versions 1.04 dated 2009-02-10 and 1.05 dated 2013-12-11
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
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
Diff between QCA versions 1.1-0 dated 2013-11-01 and 1.1-1 dated 2013-12-11
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
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
Diff between SOAR versions 0.99-10 dated 2012-01-14 and 0.99-11 dated 2013-12-11
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
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
Diff between random versions 0.2.1 dated 2009-08-13 and 0.2.2 dated 2013-12-11
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
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.
Diff between postCP versions 1.7.0 dated 2013-07-01 and 1.7.2 dated 2013-12-11
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
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
Diff between OUwie versions 1.36 dated 2013-11-22 and 1.37 dated 2013-12-11
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
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
Diff between mugnet versions 1.01.3 dated 2013-02-26 and 1.02.0 dated 2013-12-11
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
DESCRIPTION | 16 +++++++---------
MD5 | 4 ++--
demo/blung.r | 8 ++++----
3 files changed, 13 insertions(+), 15 deletions(-)
Title: Categorical Bayesian Network Inference
Diff between catnet versions 1.14.2 dated 2013-07-31 and 1.14.3 dated 2013-12-11
Description: A package that handles discrete Bayesian network models and provides inference using the frequentist approach
Author: Nikolay Balov, Peter Salzman
Maintainer: Nikolay Balov
DESCRIPTION | 10 +++++-----
MD5 | 3 ++-
build |only
3 files changed, 7 insertions(+), 6 deletions(-)