Title: Citations for knitr markdown files
Diff between knitcitations versions 0.2-0 dated 2013-01-23 and 0.3-1 dated 2013-02-01
Description: While traditional Sweave documents can take advantage of
LaTeX citation tools, knitr also allows users to combine the
much simpler markdown with R code. This package offers
citation tools to make up for this. This package will also
take advantage of the web-based nature of markdown documents to
allow dynamic citations pulled from the web.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger
knitcitations-0.2-0/knitcitations/README.Rmd |only
knitcitations-0.3-1/knitcitations/DESCRIPTION | 11 -
knitcitations-0.3-1/knitcitations/MD5 | 41 +++--
knitcitations-0.3-1/knitcitations/NAMESPACE | 2
knitcitations-0.3-1/knitcitations/NEWS | 16 ++
knitcitations-0.3-1/knitcitations/R/bibliography.R | 23 ---
knitcitations-0.3-1/knitcitations/R/cite.R | 64 +++++----
knitcitations-0.3-1/knitcitations/R/init_knitbib.R | 32 ++--
knitcitations-0.3-1/knitcitations/R/newbib.R |only
knitcitations-0.3-1/knitcitations/R/print_rdfa.R | 2
knitcitations-0.3-1/knitcitations/R/ref.R | 1
knitcitations-0.3-1/knitcitations/R/write.bibtex.R | 42 +++--
knitcitations-0.3-1/knitcitations/R/write_cache.R |only
knitcitations-0.3-1/knitcitations/R/zzz.R | 1
knitcitations-0.3-1/knitcitations/README.md | 85 ++++++++++--
knitcitations-0.3-1/knitcitations/inst/examples/README.Rmd |only
knitcitations-0.3-1/knitcitations/inst/tests |only
knitcitations-0.3-1/knitcitations/man/bibliography.Rd | 18 --
knitcitations-0.3-1/knitcitations/man/cite.Rd | 9 +
knitcitations-0.3-1/knitcitations/man/knitcitations_data.Rd | 11 +
knitcitations-0.3-1/knitcitations/man/newbib.Rd |only
knitcitations-0.3-1/knitcitations/man/ref.Rd | 1
knitcitations-0.3-1/knitcitations/man/write.bibtex.Rd | 24 +--
knitcitations-0.3-1/knitcitations/man/write_cache.Rd |only
knitcitations-0.3-1/knitcitations/tests |only
25 files changed, 244 insertions(+), 139 deletions(-)
Title: Multiple Class Area under ROC Curve
Diff between HandTill2001 versions 0.2-6 dated 2012-11-12 and 0.2-7 dated 2013-02-01
Description: (nothing but) an S4 implementation of Eq. (3) and Eq. (7)
by Hand and Till (2001).
Author: Andreas Dominik Cullmann [aut, cre], Edgar Kublin [ctb]
Maintainer: Andreas Dominik Cullmann
.Rinstignore | 1
ChangeLog |only
DESCRIPTION | 8 ++---
MD5 | 13 ++++----
R/AllClasses.R | 4 +-
inst/doc/consensus_auc.Rnw | 70 +++++++++++++++++++++++---------------------
inst/doc/consensus_auc.pdf |binary
tests/constructors.R | 35 ++++++++++++++++++++++
vignettes/consensus_auc.Rnw | 70 +++++++++++++++++++++++---------------------
9 files changed, 125 insertions(+), 76 deletions(-)
Title: A Lasso for Hierarchical Interactions
Diff between hierNet versions 1.0 dated 2012-07-10 and 1.01 dated 2013-02-01
Description: Fits sparse interaction models for continuous and binary
responses subject to the strong (or weak) hierarchy restriction
that an interaction between two variables only be included if
both (or at least one of) the variables is included as a main
effect. For more details, see Bien, J., Taylor, J.,
Tibshirani, R., (2012) "A Lasso for Hierarchical Interactions"
accepted for publication in Annals of Statistics.
Author: Jacob Bien and Rob Tibshirani
Maintainer: Jacob Bien
DESCRIPTION | 10 -
MD5 | 26 ++--
R/funcs.R | 151 +++++++++++++++-----------
man/hierNet-internal.Rd | 6 -
man/hierNet.Rd | 11 +
man/hierNet.cv.Rd | 4
man/hierNet.logistic.Rd | 13 +-
man/hierNet.logistic.path.Rd | 11 +
man/hierNet.path.Rd | 13 +-
man/hierNet.varimp.Rd | 2
man/predict.hierNet.Rd | 2
man/predict.hierNet.logistic.Rd | 2
man/predict.hierNet.path.Rd | 2
src/hierNet.c | 229 ++++++++++++++++------------------------
14 files changed, 235 insertions(+), 247 deletions(-)
Title: Statistical methods for visual fields
Diff between visualFields versions 0.2-8 dated 2012-11-14 and 0.2-13 dated 2013-02-01
Description: A collection of tools for analyzing the field of vision.
It provides a framework for development and use of innovative
methods for visualization, statistical analysis, and clinical
interpretation of visual-field loss and its change over time.
It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch
Maintainer: Ivan Marin-Franch
visualFields-0.2-13/visualFields/DESCRIPTION | 11 -
visualFields-0.2-13/visualFields/MD5 | 120 ++++++++--------
visualFields-0.2-13/visualFields/R/bebie.R | 16 +-
visualFields-0.2-13/visualFields/R/colormapgraph.R | 2
visualFields-0.2-13/visualFields/R/getnv.R | 2
visualFields-0.2-13/visualFields/R/ghpostd.R | 2
visualFields-0.2-13/visualFields/R/hist_poplr.R | 10 -
visualFields-0.2-13/visualFields/R/locperc.R | 24 ++-
visualFields-0.2-13/visualFields/R/pdpmap.R | 12 -
visualFields-0.2-13/visualFields/R/poplr.R | 18 +-
visualFields-0.2-13/visualFields/R/poplr_cstat.R | 15 +-
visualFields-0.2-13/visualFields/R/poplr_pstat.R | 8 -
visualFields-0.2-13/visualFields/R/quad2Dfit.R | 2
visualFields-0.2-13/visualFields/R/sdnv.R | 8 -
visualFields-0.2-13/visualFields/R/setnv.R | 6
visualFields-0.2-13/visualFields/R/stimLoc.R | 2
visualFields-0.2-13/visualFields/R/tdpmap.R | 12 -
visualFields-0.2-13/visualFields/R/tdrankadjperc.R | 4
visualFields-0.2-13/visualFields/R/tdranknv.R | 3
visualFields-0.2-13/visualFields/R/tdrankperc.R | 4
visualFields-0.2-13/visualFields/R/tdval.R | 6
visualFields-0.2-13/visualFields/R/vfcolormap.R | 2
visualFields-0.2-13/visualFields/R/vfgrayscale.R | 2
visualFields-0.2-13/visualFields/R/vfindex.R | 20 +-
visualFields-0.2-13/visualFields/R/vfindexpmap.R | 16 +-
visualFields-0.2-13/visualFields/R/vflayout.R | 46 +++---
visualFields-0.2-13/visualFields/R/vflayout_legoplot.R | 4
visualFields-0.2-13/visualFields/R/vflayout_poplr.R | 54 +++----
visualFields-0.2-13/visualFields/R/vfplot.R | 18 +-
visualFields-0.2-13/visualFields/R/vfplot_poplr.R | 53 +++----
visualFields-0.2-13/visualFields/R/vfsegmentcoord.R | 2
visualFields-0.2-13/visualFields/R/vfstats.R | 14 +
visualFields-0.2-13/visualFields/R/vfstatspmap.R | 16 +-
visualFields-0.2-13/visualFields/data/csplocmap.rda |only
visualFields-0.2-13/visualFields/data/fdplocmap.rda |binary
visualFields-0.2-13/visualFields/data/nvcspsgalpha.rda |only
visualFields-0.2-13/visualFields/data/nvsapdefault.rda |only
visualFields-0.2-13/visualFields/data/saplocmap.rda |binary
visualFields-0.2-13/visualFields/data/vf91016csp1vf.rda |only
visualFields-0.2-13/visualFields/data/vf91016left.rda |binary
visualFields-0.2-13/visualFields/data/vf91016right.rda |binary
visualFields-0.2-13/visualFields/data/vfShafi2011.rda |only
visualFields-0.2-13/visualFields/data/vfenv.rda |only
visualFields-0.2-13/visualFields/data/vfidefault.rda |binary
visualFields-0.2-13/visualFields/data/vfsettings.rda |binary
visualFields-0.2-13/visualFields/doc/news.txt | 19 ++
visualFields-0.2-13/visualFields/man/bebie.Rd | 2
visualFields-0.2-13/visualFields/man/colormapgraph.Rd | 4
visualFields-0.2-13/visualFields/man/csplocmap.Rd |only
visualFields-0.2-13/visualFields/man/nvcspsgalpha.Rd |only
visualFields-0.2-13/visualFields/man/nvsapdefault.Rd |only
visualFields-0.2-13/visualFields/man/poplr.Rd | 5
visualFields-0.2-13/visualFields/man/poplr_cstat.Rd | 4
visualFields-0.2-13/visualFields/man/saplocmap.Rd | 4
visualFields-0.2-13/visualFields/man/setnv.Rd | 3
visualFields-0.2-13/visualFields/man/vf91016csp1vf.Rd |only
visualFields-0.2-13/visualFields/man/vf91016left.Rd | 2
visualFields-0.2-13/visualFields/man/vf91016right.Rd | 2
visualFields-0.2-13/visualFields/man/vfShafi2011.Rd |only
visualFields-0.2-13/visualFields/man/vfcolormap.Rd | 2
visualFields-0.2-13/visualFields/man/vfenv.Rd |only
visualFields-0.2-13/visualFields/man/vflayout_poplr.Rd | 10 -
visualFields-0.2-13/visualFields/man/vfobject.Rd | 2
visualFields-0.2-13/visualFields/man/vfplot_poplr.Rd | 7
visualFields-0.2-13/visualFields/man/vfsegmentcoord.Rd | 2
visualFields-0.2-8/visualFields/data/nv.rda |only
visualFields-0.2-8/visualFields/data/sapsunyiunv.rda |only
visualFields-0.2-8/visualFields/man/nv.Rd |only
visualFields-0.2-8/visualFields/man/sapsunyiunv.Rd |only
69 files changed, 318 insertions(+), 284 deletions(-)
Title: Efficiently Read Variant Call Format (VCF) into R
Diff between vcf2geno versions 1.7 dated 2013-01-20 and 1.8 dated 2013-02-01
Description: A handy package to read VCF file
Author: Xiaowei Zhan
Maintainer: Xiaowei Zhan
vcf2geno-1.7/vcf2geno/inst/vcf/refFlat_hg19_uniq_gene.txt.gz |only
vcf2geno-1.8/vcf2geno/ChangeLog | 6 +++
vcf2geno-1.8/vcf2geno/DESCRIPTION | 8 ++--
vcf2geno-1.8/vcf2geno/MD5 | 19 +++++-----
vcf2geno-1.8/vcf2geno/inst/doc |only
vcf2geno-1.8/vcf2geno/inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz |only
vcf2geno-1.8/vcf2geno/inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz.tbi |only
vcf2geno-1.8/vcf2geno/inst/vcf/refFlat_hg19.txt.gz |only
vcf2geno-1.8/vcf2geno/src/PatternMatch.h | 2 -
vcf2geno-1.8/vcf2geno/src/R_CPP_interface.h | 3 +
vcf2geno-1.8/vcf2geno/src/TabixReader.h | 4 ++
vcf2geno-1.8/vcf2geno/src/rvMetaLoader.cpp | 19 +++++++++-
vcf2geno-1.8/vcf2geno/src/vcf2genoLoader.cpp | 4 +-
13 files changed, 48 insertions(+), 17 deletions(-)
Title: Functions for Systems Factorial Technology Analysis of Data
Diff between sft versions 0.0-5 dated 2012-08-10 and 0.1-0 dated 2013-02-01
Description: This package contains a series of tools for analyzing
Systems Factorial Technology data. This includes functions for
plotting and statistically testing capacity coefficient
functions and survivor interaction contrast functions.
Author: Joe Houpt
Maintainer: Joe Houpt
sft-0.0-5/sft/man/micTest.Rd |only
sft-0.1-0/sft/DESCRIPTION | 13 -
sft-0.1-0/sft/MD5 | 36 ++--
sft-0.1-0/sft/NAMESPACE | 2
sft-0.1-0/sft/R/NA-UCIP.R | 54 +++---
sft-0.1-0/sft/R/sic.R | 272 +++++++++++++++++++++--------------
sft-0.1-0/sft/R/ucipTest.R | 8 -
sft-0.1-0/sft/inst/CITATION | 14 -
sft-0.1-0/sft/man/capacity.and.Rd | 4
sft-0.1-0/sft/man/capacity.or.Rd | 4
sft-0.1-0/sft/man/capacityGroup.Rd | 6
sft-0.1-0/sft/man/estimateNAH.Rd | 10 -
sft-0.1-0/sft/man/estimateNAK.Rd | 14 -
sft-0.1-0/sft/man/estimateUCIPand.Rd | 6
sft-0.1-0/sft/man/estimateUCIPor.Rd | 6
sft-0.1-0/sft/man/mic_test.Rd |only
sft-0.1-0/sft/man/siDominance.Rd |only
sft-0.1-0/sft/man/sic.Rd | 10 -
sft-0.1-0/sft/man/sicGroup.Rd | 23 ++
sft-0.1-0/sft/man/sic_test.Rd |only
sft-0.1-0/sft/man/ucipTest.Rd | 4
21 files changed, 288 insertions(+), 198 deletions(-)
Title: PAC-Bayesian Estimation and Prediction in Sparse Additive
Models.
Diff between pacbpred versions 0.92 dated 2012-12-17 and 0.92.1 dated 2013-02-01
Description: This package is intended to perform estimation and
prediction in high-dimensional additive models, using a sparse
PAC-Bayesian point of view and a MCMC algorithm. The method is
fully described in Guedj and Alquier (2013), 'PAC-Bayesian
Estimation and Prediction in Sparse Additive Models',
Electronic Journal of Statistics, 7, 264--291.
Author: Benjamin Guedj
Maintainer: Benjamin Guedj
DESCRIPTION | 13 +++++++------
MD5 | 10 +++++-----
R/zzz.R | 6 +++---
inst/CITATION | 17 ++++++++---------
man/pacbpred-package.Rd | 12 ++++++++----
man/pacbpred.Rd | 17 ++++++++++++-----
6 files changed, 43 insertions(+), 32 deletions(-)
Title: R Commander Plug-in for MPA Statistics
Diff between RcmdrPlugin.MPAStats versions 1.0.1 dated 2012-07-11 and 1.0.2 dated 2013-02-01
More information about RcmdrPlugin.MPAStats at CRAN
Description: This package provides an R Commander plugin that offers a
unified menu of new and pre-existing statistical functions
related to public management and policy analysis statistics.
Functions and menus have been renamed according to the usage in
PMGT 630 in the Master of Public Administration program at
Brigham Young University.
Author: Andrew Heiss
Maintainer: Andrew Heiss
CHANGELOG | 10 ++++++++++
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/RcmdrPlugin.MPAStats.R | 2 +-
R/bivariate-analysis.R | 3 +--
R/confidence-intervals.R | 4 +---
inst/CHANGELOG | 10 ++++++++++
7 files changed, 34 insertions(+), 17 deletions(-)
Permanent link
Title: An R package for computing the similarity of molecules
Diff between Rchemcpp versions 1.0.5 dated 2012-12-07 and 1.0.6 dated 2013-02-01
Description: The Rchemcpp package implements the marginalized graph
kernel and extensions, Tanimoto kernels, graph kernels,
pharmacophore and 3D kernels suggested for measuring the
similarity of molecules.
Author: Michael Mahr, Guenter Klambauer
Maintainer: Guenter Klambauer
DESCRIPTION | 20 +++++++++-----------
MD5 | 4 ++--
inst/doc/Rchemcpp.pdf |binary
3 files changed, 11 insertions(+), 13 deletions(-)
Title: Kernel Factory: An ensemble of kernel Machines
Diff between kernelFactory versions 0.1.0 dated 2012-12-22 and 0.1.1 dated 2013-02-01
Description: Classification based on an ensemble of kernel machines
Author: Michel Ballings, Dirk Van den Poel
Maintainer: Michel Ballings
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/kernelFactory.R | 29 +++++++++++++++++++++++++++--
R/predict.kernelFactory.R | 19 ++++++++++++++++++-
inst/NEWS | 6 ++++++
man/kernelFactory.Rd | 7 ++++---
man/predict.kernelFactory.Rd | 3 ++-
7 files changed, 68 insertions(+), 18 deletions(-)
Title: Import output from LISREL into R
Diff between lisrelToR versions 0.1.2 dated 2013-01-29 and 0.1.3 dated 2013-02-01
Description: This is an unofficial package aimed at automating the
import of LISREL output in R. This package or its maintainer
is not in any way affiliated with the creators of LISREL and
SSI, Inc.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp
DESCRIPTION | 9 ++++-----
MD5 | 17 +++++++++--------
NAMESPACE | 4 ++--
NEWS | 6 ++++++
R/getMatrix.R | 29 +++++++++++++++++++++++------
R/methods.R | 28 ++++++++++++++--------------
R/readLisrel.R | 10 +++++++---
README.md |only
man/methods.Rd | 12 +++---------
man/readLisrel.Rd | 7 -------
10 files changed, 68 insertions(+), 54 deletions(-)
Title: Analysis of Queueing Networks and Models.
Diff between queueing versions 0.2.0 dated 2012-12-09 and 0.2.1 dated 2013-02-01
Description: It provides a versatile tool for analysis of birth and
death based Markovian Queueing Models and Single and Multiclass
Product-Form Queueing Networks. It implements M/M/1, M/M/c,
M/M/Infinite, M/M/1/K, M/M/c/K, M/M/c/c, M/M/1/K/K, M/M/c/K/K,
M/M/c/K/m, M/M/Infinite/K/K, Multiple Channel Open Jackson
Networks, Multiple Channel Closed Jackson Networks, Single
Channel Multiple Class Open Networks, Single Channel Multiple
Class Closed Networks and Single Channel Multiple Class Mixed
Networks. Also it provides a B-Erlang, C-Erlang and Engset
calculators.
Author: Pedro Canadilla
Maintainer: Pedro Canadilla
ChangeLog | 9 ++++++++-
DESCRIPTION | 8 ++++----
MD5 | 10 ++++++----
inst/doc |only
man/SP.Rd | 2 +-
man/SP.o_MM1KK.Rd | 2 +-
man/queueing-package.Rd |only
7 files changed, 20 insertions(+), 11 deletions(-)
Title: Confidence intervals for two sample comparisons
Diff between pairwiseCI versions 0.1-20 dated 2012-08-14 and 0.1-21 dated 2013-02-01
Description: Calculation of the parametric, nonparametric confidence
intervals for the difference or ratio of location parameters,
nonparametric confidence interval for the Behrens-Fisher
problem and for the difference, ratio and odds-ratio of
binomial proportions for comparison of independent samples. The
package provides common wrapper functions to split data sets
and apply confidence intervals or tests to these subsets. A by
statement allows calculation of CI separately for the levels of
further factors. CI are not adjusted for multiplicity.
Author: Frank Schaarschmidt, Daniel Gerhard
Maintainer: Frank Schaarschmidt
DESCRIPTION | 8
MD5 | 10
R/Prop.ratio.R | 575 +++++++++++++++++++++++++++++++------------
data/Oats.rda |binary
data/behenic.rda |binary
man/pairwiseCImethodsProp.Rd | 132 +++++----
6 files changed, 505 insertions(+), 220 deletions(-)
Title: Distance Between Phylogenetic Histories
Diff between distory versions 1.4 dated 2010-06-08 and 1.4.1 dated 2013-02-01
Description: Geodesic distance between phylogenetic trees and
associated functions.
Author: John Chakerian and Susan Holmes
Maintainer: Susan Holmes
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/gromov.hyperbolicity.R | 2 +-
R/zzz.R | 2 +-
4 files changed, 8 insertions(+), 8 deletions(-)
Title: An R package for changepoint analysis
Diff between changepoint versions 1.0 dated 2013-01-08 and 1.0.3 dated 2013-02-01
Description: Implements various mainstream and specialised changepoint
methods for finding single and multiple changepoints within
data. Many popular non-parametric and frequentist methods are
included. The cpt.mean, cpt.var, cpt.meanvar functions should
be your first point of call.
Author: Rebecca Killick
Maintainer: Rebecca Killick
DESCRIPTION | 8 ++++----
MD5 | 40 ++++++++++++++++++++--------------------
NEWS | 15 +++++++++++++++
R/cpt.R | 28 ++++++++++++++--------------
R/cpt.class.R | 10 +++++-----
R/decision.R | 2 +-
R/exp.R | 4 ++--
R/gamma.R | 4 ++--
R/multiple.nonparametric.R | 4 ++--
R/multiple.norm.R | 6 +++---
R/poisson.R | 4 ++--
R/single.nonparametric.R | 4 ++--
R/single.norm.R | 6 +++---
R/zzz.R | 2 +-
man/changepoint-package.Rd | 4 ++--
man/cpt.mean.Rd | 10 +++++-----
man/cpt.meanvar.Rd | 14 +++++++-------
man/cpt.var.Rd | 14 +++++++-------
man/likelihood-methods.Rd | 2 +-
man/likelihood.Rd | 2 +-
man/logLik-methods.Rd | 9 ++++++++-
21 files changed, 107 insertions(+), 85 deletions(-)
Title: Futile logger subsystem
Diff between futile.logger versions 1.2.1 dated 2012-02-06 and 1.3.0 dated 2013-02-01
Description: A logging library for R
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
futile.logger-1.2.1/futile.logger/R/config.R |only
futile.logger-1.2.1/futile.logger/man/config.Rd |only
futile.logger-1.3.0/futile.logger/DESCRIPTION | 13
futile.logger-1.3.0/futile.logger/MD5 | 24 -
futile.logger-1.3.0/futile.logger/R/appender.R | 13
futile.logger-1.3.0/futile.logger/R/aptions.R |only
futile.logger-1.3.0/futile.logger/R/layout.R | 8
futile.logger-1.3.0/futile.logger/R/logger.R | 209 ++++------
futile.logger-1.3.0/futile.logger/README.md |only
futile.logger-1.3.0/futile.logger/inst |only
futile.logger-1.3.0/futile.logger/man/appender.Rd | 61 +-
futile.logger-1.3.0/futile.logger/man/futile.logger-package.Rd | 136 ++++--
futile.logger-1.3.0/futile.logger/man/layout.Rd | 53 +-
futile.logger-1.3.0/futile.logger/man/logger.Rd | 105 +++--
futile.logger-1.3.0/futile.logger/tests |only
15 files changed, 343 insertions(+), 279 deletions(-)
Title: R Package for Finding Heterogeneous Treatment Effects
Diff between FindIt versions 0.2 dated 2013-01-25 and 0.3 dated 2013-02-01
Description: FindIt is an R package that implements the heterogeneous
treatment effect estimation procedure proposed by Imai and
Ratkovic (2013). The proposed method is applicable, for
example, when selecting a small number of most (or least)
efficacious treatments from a large number of alternative
treatments as well as when identifying subsets of the
population who benefit (or are harmed by) a treatment of
interest. The method adapts the Support Vector Machine
classifier by placing separate LASSO constraints over the
pre-treatment parameters and causal heterogeneity parameters of
interest. This allows for the qualitative distinction between
causal and other parameters, thereby making the variable
selection suitable for the exploration of causal heterogeneity.
Author: Marc Ratkovic
Maintainer: Marc Ratkovic
ChangeLog | 1 +
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/SVMHet.R | 12 ++++++------
man/FindIt.Rd | 12 ++++++------
5 files changed, 21 insertions(+), 20 deletions(-)