Title: Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
Diff between SNPRelate versions 0.9.9 dated 2013-01-05 and 0.9.10 dated 2013-01-21
Description: A High-performance computing toolset for relatedness and
principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
SNPRelate-0.9.10/SNPRelate/DESCRIPTION | 14 -
SNPRelate-0.9.10/SNPRelate/MD5 | 30 +--
SNPRelate-0.9.10/SNPRelate/NEWS | 5
SNPRelate-0.9.10/SNPRelate/R/main.r | 105 +++++++++++--
SNPRelate-0.9.10/SNPRelate/data/hapmap_geno.RData |only
SNPRelate-0.9.10/SNPRelate/inst/doc/SNPRelateTutorial.Rnw | 4
SNPRelate-0.9.10/SNPRelate/inst/doc/SNPRelateTutorial.pdf |binary
SNPRelate-0.9.10/SNPRelate/inst/extdata/hapmap_geno.gds |only
SNPRelate-0.9.10/SNPRelate/man/SNPRelate-package.Rd | 4
SNPRelate-0.9.10/SNPRelate/man/hapmap_geno.Rd |only
SNPRelate-0.9.10/SNPRelate/man/snpgdsCreateGeno.Rd | 4
SNPRelate-0.9.10/SNPRelate/man/snpgdsCutTree.Rd | 38 ++++
SNPRelate-0.9.10/SNPRelate/man/snpgdsDrawTree.Rd | 14 +
SNPRelate-0.9.10/SNPRelate/man/snpgdsHCluster.Rd | 10 +
SNPRelate-0.9.10/SNPRelate/src/genIBD.cpp | 37 +++-
SNPRelate-0.9.10/SNPRelate/vignettes/SNPRelateTutorial.Rnw | 4
SNPRelate-0.9.9/SNPRelate/data/hapmap.geno.RData |only
SNPRelate-0.9.9/SNPRelate/inst/extdata/hapmap.geno.gds |only
SNPRelate-0.9.9/SNPRelate/man/hapmap.geno.Rd |only
19 files changed, 210 insertions(+), 59 deletions(-)
Title: Flexible procedures for clustering
Diff between fpc versions 2.1-4 dated 2012-08-30 and 2.1-5 dated 2013-01-21
Description: Various methods for clustering and cluster validation.
Fixed point clustering. Linear regression clustering.
Clustering by merging Gaussian mixture components. Symmetric
and asymmetric discriminant projections for visualisation of
the separation of groupings. Cluster validation statistics for
distance based clustering including corrected Rand index.
Cluster-wise cluster stability assessment. Methods for
estimation of the number of clusters: Calinski-Harabasz,
Tibshirani and Walther's prediction strength, Fang and Wang's
bootstrap stability. Gaussian/multinomial mixture fitting for
mixed continuous/categorical variables. Variable-wise
statistics for cluster interpretation. DBSCAN clustering.
Interface functions for many clustering methods implemented in
R, including estimating the number of clusters with kmeans, pam
and clara. Modality diagnosis for Gaussian mixtures. For an
overview see package?fpc.
Author: Christian Hennig
Maintainer: Christian Hennig
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
R/addclustermethods.R | 2 ++
R/clusterboot.R | 6 +++---
R/fpc.R | 4 ++--
R/lcmixed.R | 1 -
man/cluster.stats.Rd | 12 +++++++++---
man/clusterboot.Rd | 12 ++++++------
man/kmeansruns.Rd | 6 +++++-
man/lcmixed.Rd | 2 +-
tests/Examples/fpc-Ex.Rout.save | 22 +++++++++++-----------
tests/fpctests.Rout.save | 32 ++++++++------------------------
12 files changed, 62 insertions(+), 67 deletions(-)
Title: R companion to "Curve and Surface Fitting with Splines"
Diff between DierckxSpline versions 1.1-5 dated 2012-05-06 and 1.1-8 dated 2013-01-21
Description: This package provides a wrapper to the FITPACK routines
written by Paul Dierckx. The original Fortran is available from
http://www.netlib.org/dierckx 2012.02.15: This package is
broken. Currently, it seems NOT to have any users and is not
worth fixing. These FITPACK routines are over 20 years old and
may be obsolete. If you want to fix it, I will happily make
you the maintainer. Spencer Graves
Author: Sundar Dorai-Raj and Spencer Graves
Maintainer: Spencer Graves
DESCRIPTION | 19 ++++++++++---------
MD5 | 14 +++++++-------
NAMESPACE | 10 ++++++----
R/dierckx2fd.R | 34 +++++++++++++++++-----------------
R/zzz.R | 4 ++--
man/as.dierckx.Rd | 4 +++-
man/controlPolygon.Rd | 14 ++++++++------
man/curfit.free.knot.Rd | 37 ++++++++++++++++++++++---------------
8 files changed, 75 insertions(+), 61 deletions(-)
Title: Functional programming in R
Diff between lambda.r versions 1.0.0 dated 2012-11-19 and 1.1.0-3 dated 2013-01-21
Description: A language extension to efficiently write functional
programs in R. Syntax extensions include multi-part function
definitions, pattern matching, guard statements, built-in
(optional) type safety.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
DESCRIPTION | 10 -
MD5 | 27 ++
R/framework.R | 276 +++++++++++++++++++---------
R/objects.R |only
README.md | 91 +++++++++
inst/unitTests/runit.auto_replace.1.R |only
inst/unitTests/runit.auto_replace.2.R |only
inst/unitTests/runit.auto_replace.3.R |only
inst/unitTests/runit.dispatching.4.R | 28 +-
inst/unitTests/runit.examples.R |only
inst/unitTests/runit.function_args.1.R |only
inst/unitTests/runit.function_type.1.R |only
inst/unitTests/runit.optional_arguments.2.R | 2
inst/unitTests/runit.type_variable.1.R |only
inst/unitTests/runit.type_variable.2.R |only
inst/unitTests/runit.type_variable.3.R |only
inst/unitTests/runit.type_variable.4.R |only
inst/unitTests/runit.type_variable.5.R |only
inst/unitTests/runit.type_variable.6.R |only
man/UseFunction.Rd | 8
man/lambda.r-package.Rd | 4
21 files changed, 333 insertions(+), 113 deletions(-)
Title: Functional programming in R
Diff between lambda.r versions 1.0.0 dated 2012-11-19 and 1.1.0-2 dated 2013-01-21
Description: A language extension to efficiently write functional
programs in R. Syntax extensions include multi-part function
definitions, pattern matching, guard statements, built-in
(optional) type safety.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
lambda.r |only
1 file changed
Title: GeMTC Java binary
Diff between gemtc.jar versions 0.14.2 dated 2012-10-30 and 0.14.3 dated 2013-01-21
Description: An R package providing the Java JAR for the gemtc package
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef
gemtc.jar-0.14.2/gemtc.jar/inst/java/mtc-mcmc-0.14.2.jar |only
gemtc.jar-0.14.3/gemtc.jar/DESCRIPTION | 8 ++++----
gemtc.jar-0.14.3/gemtc.jar/MD5 | 4 ++--
gemtc.jar-0.14.3/gemtc.jar/inst/java/mtc-mcmc-0.14.3.jar |only
4 files changed, 6 insertions(+), 6 deletions(-)
Title: GeMTC network meta-analysis
Diff between gemtc versions 0.1-1 dated 2012-10-30 and 0.1-2 dated 2013-01-21
Description: An R package for performing network meta-analyses (mixed
treatment comparisons).
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef
DESCRIPTION | 10 ++--
MD5 | 8 +--
R/mtc.R | 8 +--
R/mtc.rjava.R | 115 +++++++++++++++++++++++++++++++++++++----------------
man/mtc.network.Rd | 15 +++++-
5 files changed, 106 insertions(+), 50 deletions(-)
Title: Create cryptographic hash digests of R objects
Diff between digest versions 0.6.0 dated 2012-11-25 and 0.6.1 dated 2013-01-21
Description: The digest package provides a function 'digest()' for the
creation of hash digests of arbitrary R objects (using the md5,
sha-1, sha-256 and crc32 algorithms) permitting easy comparison
of R language objects, as well as a function 'hmac()' to create
hash-based message authentication code.
The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 and
sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2,
and the crc32 algorithm is described in
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1, sha-256 and aes, this package uses a small standalone
implementations that were provided by Christophe Devine. For
crc32, code from the zlib library is used. For sha-512, an
implementation by Aaron D. Gifford is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely
tested) libraries such as OpenSSL should be used.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 26 ++++++
DESCRIPTION | 18 ++--
MD5 | 18 +++-
NAMESPACE | 7 +
R/AES.R |only
inst |only
man/AES.Rd |only
src/aes.c |only
src/aes.h |only
src/raes.c |only
tests/AESTest.R |only
tests/AESTest.Rout.save |only
tests/digestTest.R | 182 ++++++++++++++++++++++----------------------
tests/digestTest.Rout.save | 184 ++++++++++++++++++++++-----------------------
14 files changed, 238 insertions(+), 197 deletions(-)
Title: A R Adaptive Multiple Importance Sampling
Diff between ARAMIS versions 1.0 dated 2013-01-17 and 1.0.1 dated 2013-01-21
Description: The ARAMIS package runs the Adaptive Multiple Importance
Sampler (AMIS) algorithm from Jean-Marie Cornuet, Jean-Michel
Marin, Antonietta Mira and Christian Robert (2012), Adaptive
Multiple Importance Sampling, Scandinavian Journal of
Statistics. The Code is flexible enough to accommodate
virtually any specification of the target and proposal
distribution together with any clustering routine for the
adaptation step and any initialization procedure.
Author: Luca Pozzi, Antonietta Mira
Maintainer: Luca Pozzi
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/AMIS.R | 7 +++++--
inst/doc/demoARAMIS.Rnw | 4 ++--
inst/doc/demoARAMIS.pdf |binary
5 files changed, 14 insertions(+), 11 deletions(-)
Title: Demonstrations for teaching and learning
Diff between TeachingDemos versions 2.8 dated 2012-03-16 and 2.9 dated 2013-01-21
Description: This package is a set of demonstration functions that can
be used in a classroom to demonstrate statistical concepts, or
on your own to better understand the concepts or the
programming.
Author: Greg Snow
Maintainer: Greg Snow
TeachingDemos-2.8/TeachingDemos/R/limits.g.R |only
TeachingDemos-2.8/TeachingDemos/R/sd.g.R |only
TeachingDemos-2.8/TeachingDemos/R/stats.g.R |only
TeachingDemos-2.8/TeachingDemos/man/limits.g.Rd |only
TeachingDemos-2.9/TeachingDemos/DESCRIPTION | 12 -
TeachingDemos-2.9/TeachingDemos/MD5 | 66 +++---
TeachingDemos-2.9/TeachingDemos/NAMESPACE | 18 -
TeachingDemos-2.9/TeachingDemos/NEWS | 28 ++
TeachingDemos-2.9/TeachingDemos/R/HWidentify.R | 4
TeachingDemos-2.9/TeachingDemos/R/R2txt.R | 193 +++++++++++++++++++
TeachingDemos-2.9/TeachingDemos/R/TkListView.R | 18 -
TeachingDemos-2.9/TeachingDemos/R/correct.R |only
TeachingDemos-2.9/TeachingDemos/R/loess.demo.R | 4
TeachingDemos-2.9/TeachingDemos/R/mysymbols.R | 7
TeachingDemos-2.9/TeachingDemos/R/plot.rgl.coin.R | 2
TeachingDemos-2.9/TeachingDemos/R/plot.rgl.die.R | 2
TeachingDemos-2.9/TeachingDemos/R/simfun.R |only
TeachingDemos-2.9/TeachingDemos/R/squishplot.R | 12 -
TeachingDemos-2.9/TeachingDemos/R/tests.R | 5
TeachingDemos-2.9/TeachingDemos/data/USCrimes.rda |only
TeachingDemos-2.9/TeachingDemos/data/coin.faces.rda |binary
TeachingDemos-2.9/TeachingDemos/data/evap.rda |binary
TeachingDemos-2.9/TeachingDemos/data/gps.rda |binary
TeachingDemos-2.9/TeachingDemos/data/ldsgrowth.rda |binary
TeachingDemos-2.9/TeachingDemos/data/outliers.rda |binary
TeachingDemos-2.9/TeachingDemos/data/stork.rda |binary
TeachingDemos-2.9/TeachingDemos/man/R2txt.Rd | 86 ++++++--
TeachingDemos-2.9/TeachingDemos/man/TkPredict.Rd | 8
TeachingDemos-2.9/TeachingDemos/man/USCrimes.Rd |only
TeachingDemos-2.9/TeachingDemos/man/correct.Rd |only
TeachingDemos-2.9/TeachingDemos/man/cortest.Rd | 4
TeachingDemos-2.9/TeachingDemos/man/loess.demo.Rd | 2
TeachingDemos-2.9/TeachingDemos/man/mysymbols.Rd | 4
TeachingDemos-2.9/TeachingDemos/man/normtest.Rd | 2
TeachingDemos-2.9/TeachingDemos/man/petals.Rd | 3
TeachingDemos-2.9/TeachingDemos/man/plot.rgl.coin.Rd | 22 +-
TeachingDemos-2.9/TeachingDemos/man/simfun.Rd |only
TeachingDemos-2.9/TeachingDemos/man/subplot.Rd | 3
TeachingDemos-2.9/TeachingDemos/man/tkexamp.Rd | 9
39 files changed, 395 insertions(+), 119 deletions(-)
Title: Exemplar data sets for SGP analyses.
Diff between SGPdata versions 4.0-0.0 dated 2013-01-07 and 5.0-0.0 dated 2013-01-21
Description: The package SGPdata contains two data sets utilized by the
SGP Package as exemplars for users to set up their own data for
SGP analyses.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner
DESCRIPTION | 11 ++++++-----
LICENSE | 5 ++---
MD5 | 12 ++++++------
inst/CITATION | 12 ++++++------
inst/NEWS | 4 ++++
man/SGPdata-package.Rd | 4 ++--
man/sgpData_LONG.Rd | 6 +++---
7 files changed, 29 insertions(+), 25 deletions(-)
Title: An R Package for the Calculation and Visualization of Student
Growth Percentiles & Percentile Growth Trajectories.
Diff between SGP versions 1.0-0.0 dated 2013-01-16 and 1.0-3.0 dated 2013-01-21
Description: Functions to calculate student growth percentiles and
percentile growth projections/trajectories for students using
large scale, longitudinal assessment data. Functions use
quantile regression to estimate the conditional density
associated with each student's achievement history. Percentile
growth projections/trajectories are calculated using the
coefficient matrices derived from the quantile regression
analyses and specify what percentile growth is required for
students to reach future achievement targets.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner
DESCRIPTION | 45 ++++++++++-----------
LICENSE | 10 ----
MD5 | 79 +++++++++++++++++++-------------------
NAMESPACE | 63 ++++++++++++------------------
R/analyzeSGP.R | 19 +++++++--
R/checksplineMatrix.R | 2
R/combineSGP.R | 12 ++---
R/createKnotsBoundaries.R | 9 ++++
R/growthAchievementPlot.R | 39 +++++++++++++------
R/outputSGP.R | 2
R/startParallel.R | 82 +++++++++++++++++++++-------------------
R/stopParallel.R | 24 +++++------
R/studentGrowthPercentiles.R | 14 +++++-
R/studentGrowthPlot.R | 3 -
R/studentGrowthProjections.R | 1
R/summarizeSGP.R | 13 ++++--
R/testSGP.R | 4 -
R/visualizeSGP.R | 13 +++---
R/zzz.R | 2
data/SGPstateData.rda |binary
inst/CITATION | 10 ++--
inst/NEWS | 14 ++++++
man/SGP-class.Rd | 2
man/SGP-package.Rd | 16 +++----
man/SGPstateData.Rd | 2
man/abcSGP.Rd | 4 -
man/analyzeSGP.Rd | 62 +++++++-----------------------
man/baselineSGP.Rd | 4 -
man/bubblePlot.Rd | 2
man/bubblePlot_Styles.Rd | 4 -
man/combineSGP.Rd | 4 -
man/createKnotsBoundaries.Rd |only
man/gofSGP.Rd | 2
man/growthAchievementPlot.Rd | 13 ++++--
man/studentGrowthPercentiles.Rd | 16 ++++---
man/studentGrowthPlot.Rd | 2
man/studentGrowthPlot_Styles.Rd | 4 -
man/studentGrowthProjections.Rd | 6 +-
man/summarizeSGP.Rd | 38 +++---------------
man/testSGP.Rd | 6 +-
man/visualizeSGP.Rd | 10 ++--
41 files changed, 335 insertions(+), 322 deletions(-)
Title: Structural Equation Modeling Using Partial Least Squares
Diff between semPLS versions 1.0-9 dated 2012-11-06 and 1.0-10 dated 2013-01-21
Description: Fits structural equation models using partial least
squares (PLS). The PLS approach is referred to as
'soft-modeling' technique requiring no distributional
assumptions on the observed data.
Author: Armin Monecke
Maintainer: Armin Monecke
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 6 ++++++
inst/doc/semPLS-intro.Rnw | 6 ++++--
inst/doc/semPLS-intro.pdf |binary
vignettes/semPLS-intro.Rnw | 6 ++++--
6 files changed, 23 insertions(+), 13 deletions(-)
Title: A general-purpose package for dynamic report generation in R
Diff between knitr versions 1.0 dated 2013-01-14 and 1.0.5 dated 2013-01-21
Description: This package provides a general-purpose tool for dynamic
report generation in R, which can be used to deal with any type
of (plain text) files, including Sweave, HTML, Markdown and
reStructuredText. The patterns of code chunks and inline R
expressions can be customized. R code is evaluated as if it
were copied and pasted in an R terminal thanks to the evaluate
package (e.g. we do not need to explicitly print() plots from
ggplot2 or lattice). R code can be reformatted by the formatR
package so that long lines are automatically wrapped, with
indent and spaces being added, and comments being preserved. A
simple caching mechanism is provided to cache results from
computations for the first time and the computations will be
skipped the next time. Almost all common graphics devices,
including those in base R and add-on packages like Cairo,
cairoDevice and tikzDevice, are built-in with this package and
it is straightforward to switch between devices without writing
any special functions. The width and height as well as
alignment of plots in the output document can be specified in
chunk options (the size of plots for graphics devices is still
supported as usual). Multiple plots can be recorded in a single
code chunk, and it is also allowed to rearrange plots to the
end of a chunk or just keep the last plot. Warnings, messages
and errors are written in the output document by default (can
be turned off). Currently LaTeX, HTML, Markdown and reST are
supported, and other output formats can be supported by hook
functions. The large collection of hooks in this package makes
it possible for the user to control almost everything in the R
code input and output. Hooks can be used either to format the
output or to run a specified R code fragment before or after a
code chunk. The language in code chunks is not restricted to R
only (there is simple support to Python and Awk, etc). Many
features are borrowed from or inspired by Sweave, cacheSweave,
pgfSweave, brew and decumar.
Author: Yihui Xie
Maintainer: Yihui Xie
DESCRIPTION | 15 +++----
MD5 | 35 ++++++++--------
Makefile | 10 ++--
R/block.R | 37 +++++++++--------
R/engine.R | 19 +++++++--
R/output.R | 11 ++---
R/parser.R | 15 ++-----
R/pattern.R | 20 ++++-----
R/template.R | 2
R/utils-base64.R | 2
R/utils-conversion.R |only
R/utils-sweave.R | 13 +++---
R/utils.R | 95 +++------------------------------------------
README.md | 6 ++
inst/doc/knitr-intro.pdf |binary
inst/doc/knitr-refcard.pdf |binary
inst/tests/test-parser.R | 6 ++
inst/tests/test-utils.R | 2
man/knit2html.Rd | 12 +++--
19 files changed, 124 insertions(+), 176 deletions(-)
Title: A Fast Parameter Estimation Method for Evolutionary Biology
Diff between jaatha versions 2.0.1 dated 2013-01-11 and 2.0.2 dated 2013-01-21
Description: Jaatha is a composite likelihood method for inferring
evolutionary parameters using genetic data. Given a model of
the evolutionary history of two biological populations as well
as SNP data from multiple individuals from each population, it
estimates model parameters like the time of separation of both
species.
Author: Lisha Mathew, Paul R. Staab and Dirk Metzler
Maintainer: Paul R. Staab
DESCRIPTION | 8 +-
MD5 | 24 +++---
NEWS | 4 +
inst/doc/jaatha.Rnw | 14 ++-
inst/doc/jaatha.pdf |binary
inst/example_fasta_files/sample.fasta | 59 ++++++---------
vignettes/cache/initialSearch.tex | 36 ++++-----
vignettes/cache/refineSearch.tex | 78 ++++++++------------
vignettes/cache/saved_objects/jaatha-complete.Rsave |binary
vignettes/cache/saved_objects/jaatha.Rsave |binary
vignettes/cache/saved_objects/start-points.Rsave |binary
vignettes/jaatha.Rnw | 14 ++-
vignettes/jaatha.bib | 19 ----
13 files changed, 114 insertions(+), 142 deletions(-)
Title: stellar evolution tracks and isochrones
Diff between stellaR versions 0.3-2 dated 2013-01-11 and 0.3-3 dated 2013-01-21
Description: A package to manage and display stellar tracks and
isochrones from Pisa low-mass database. Includes tools for
isochrones construction and tracks interpolation.
Author: Matteo Dell'Omodarme [aut, cre], Giada Valle [aut]
Maintainer: Matteo Dell'Omodarme
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++------------
man/getHbgrid.Rd | 4 ++--
man/getIso.Rd | 4 ++--
man/getTrk.Rd | 5 +++--
man/getTrkSet.Rd | 3 ++-
man/getZahb.Rd | 4 ++--
man/interpTrk.Rd | 4 ++--
man/keypoints.Rd | 2 ++
man/plot.trk.Rd | 3 ++-
man/plot.trkset.Rd | 4 ++--
man/plotAstro.Rd | 3 ++-
man/print.trk.Rd | 3 ++-
13 files changed, 39 insertions(+), 32 deletions(-)
Title: Adapt numerical records to fit (in)equality restrictions with
the Successive Projection Algorithm
Diff between rspa versions 0.1-0 dated 2012-09-21 and 0.1-1 dated 2013-01-21
Description: Based on (optionally sparse) quadratic optimization with
the main algorithms implemented in C. Includes features for
easy processing of many (smaller) records. The algorithm has
been tested on fairly large optimization problems with up to a
few million variables and several hundred thousand
restrictions.
Author: Mark van der Loo
Maintainer: Mark van der Loo
DESCRIPTION | 6 +++---
MD5 | 20 ++++++++++----------
NEWS | 6 +++++-
R/adjust.R | 14 +++++++++-----
R/adjustRecords.R | 2 +-
inst/doc/getting_started.Rnw | 1 -
inst/doc/getting_started.pdf |binary
man/adjust.Rd | 4 ++--
vignettes/Rplots.pdf |binary
vignettes/figure/unnamed-chunk-11.pdf |binary
vignettes/getting_started.Rnw | 1 -
11 files changed, 30 insertions(+), 24 deletions(-)
Title: Response Probability Functions
Diff between rpf versions 0.5 dated 2012-12-25 and 0.6 dated 2013-01-21
Description: The purpose of this package is to factor out logic and
math common to Item Response Theory fitting, diagnostics, and
analysis. It is envisioned as core support code suitable for
more specialized IRT packages to build upon. Complete access to
optimized C functions are made available with
R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut], Jonathan Weeks [ctb]
Maintainer: Joshua Pritikin
rpf-0.5/rpf/man/rpf.getLocation.Rd |only
rpf-0.5/rpf/man/rpf.logprob.wrapper3.Rd |only
rpf-0.5/rpf/man/rpf.prob.wrapper1.Rd |only
rpf-0.5/rpf/man/rpf.prob.wrapper2.Rd |only
rpf-0.5/rpf/man/rpf.prob.wrapper3.Rd |only
rpf-0.5/rpf/man/rpf.prob.wrapper4.Rd |only
rpf-0.5/rpf/man/rpf.prob.wrapper5.Rd |only
rpf-0.5/rpf/man/rpf.setLocation.Rd |only
rpf-0.5/rpf/man/rpf.startingParam.Rd |only
rpf-0.5/rpf/tests/plink.R |only
rpf-0.5/rpf/tests/sample.R |only
rpf-0.6/rpf/.Rinstignore |only
rpf-0.6/rpf/DESCRIPTION | 20 -
rpf-0.6/rpf/MD5 | 84 +++--
rpf-0.6/rpf/NAMESPACE | 27 -
rpf-0.6/rpf/R/classes.R | 324 ++++++++++++----------
rpf-0.6/rpf/R/diagnose.R |only
rpf-0.6/rpf/R/drm.R | 92 +-----
rpf-0.6/rpf/R/gpcm.R | 31 +-
rpf-0.6/rpf/R/graded.R | 49 ---
rpf-0.6/rpf/R/grm.R | 12
rpf-0.6/rpf/R/mcm.R | 24 -
rpf-0.6/rpf/R/ms.R |only
rpf-0.6/rpf/R/nrm.R | 21 -
rpf-0.6/rpf/R/sample.R | 53 ++-
rpf-0.6/rpf/R/science.R |only
rpf-0.6/rpf/SFIF.txt |only
rpf-0.6/rpf/SFPF.txt |only
rpf-0.6/rpf/SFXF.txt |only
rpf-0.6/rpf/data |only
rpf-0.6/rpf/inst |only
rpf-0.6/rpf/man/mentalsilence.Rd |only
rpf-0.6/rpf/man/rpf.1dim.fit.Rd |only
rpf-0.6/rpf/man/rpf.1dim.moment.Rd |only
rpf-0.6/rpf/man/rpf.1dim.stdresidual.Rd |only
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rpf-0.6/rpf/man/rpf.introduction.Rd | 10
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rpf-0.6/rpf/science-prep.R |only
rpf-0.6/rpf/src/glue.c | 262 +++++++++++++++---
rpf-0.6/rpf/src/libirt-rpf.c | 455 ++++++++++++++++++++++++++++++--
rpf-0.6/rpf/src/libirt-rpf.h | 42 ++
rpf-0.6/rpf/tests/dotest.R |only
55 files changed, 1095 insertions(+), 514 deletions(-)
Title: Easy handling of and access to files organized in structured
directories
Diff between R.filesets versions 1.9.0 dated 2012-12-22 and 2.0.0 dated 2013-01-21
Description: A file set refers to a set of files located in one or more
directories on the file system. This package provides classes
and methods to locate, setup, subset, navigate and iterate such
sets. The API is designed such that these classes can be
extended via inheritance to provide a richer API for special
file formats. Moreover, a specific name format is defined such
that filenames and directories can be considered to have full
names which consists of a name followed by comma-separated
tags. This adds additional flexibility to identify file sets
and individual files. NOTE: This package's API should be
considered to be in an beta stage. Its main purpose is
currently to support the aroma.* packages, where it is one of
the main core components; if you decide to build on top of this
package, please contact the author first.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 16 +--
MD5 | 19 ++--
R/TabularTextFile.R | 93 +++++++++++++++++-----
R/readDataFrame.R |only
incl/999.missingdocs.txt | 2
incl/TabularTextFile.readDataFrame.Rex |only
incl/readDataFrame.Rex |only
inst/NEWS | 11 ++
inst/exData/dataSetA,original/fileA,20130116.datx |only
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man/R.filesets-package.Rd | 2
man/TabularTextFile.Rd | 17 +++-
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13 files changed, 124 insertions(+), 37 deletions(-)
Title: Random name generating function and data set
Diff between randomNames versions 0.0-5 dated 2012-01-28 and 0.0-6 dated 2013-01-21
Description: Function to generate random gender and ethnicity correct
first and/or last names. Names are chosen proportionally based
upon their probability of appearing in a large scale data base
of real names.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner
DESCRIPTION | 12 +++++++-----
MD5 | 10 +++++-----
NAMESPACE | 6 ++----
inst/CITATION | 4 ++--
inst/NEWS | 4 ++++
man/randomNames-package.Rd | 4 ++--
6 files changed, 22 insertions(+), 18 deletions(-)
Title: Additive partitions of integers
Diff between partitions versions 1.9-12 dated 2011-12-27 and 1.9-13 dated 2013-01-21
Description: Additive partitions of integers. Enumerates the
partitions, unequal partitions, and restricted partitions of an
integer; the three corresponding partition functions are also
given. Set partitions are now included.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 14 +++++++-------
MD5 | 10 +++++-----
R/partitions.R | 15 +++++++++++----
inst/doc/partitionspaper.pdf |binary
inst/doc/scrabble.pdf |binary
inst/doc/setpartitions.pdf |binary
6 files changed, 23 insertions(+), 16 deletions(-)
Title: Arrays with arbitrary offsets
Diff between Oarray versions 1.4-4 dated 2012-11-07 and 1.4-5 dated 2013-01-21
Description: Generalise the starting point of the array index
Author: Jonathan Rougier
Maintainer: Robin K. S. Hankin
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NAMESPACE | 2 +-
R/Oarray.R | 4 ++--
4 files changed, 10 insertions(+), 10 deletions(-)
Title: A multivariate emulator
Diff between multivator versions 1.1-0 dated 2012-02-06 and 1.1-1 dated 2013-01-21
Description: A multivariate generalization of the emulator package
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
data/e3mg.rda |binary
data/mcneall.rda |binary
data/mtoys.rda |binary
inst/doc/cias.pdf |binary
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7 files changed, 10 insertions(+), 10 deletions(-)
Title: multivariate polynomials
Diff between multipol versions 1.0-5 dated 2012-01-05 and 1.0-6 dated 2013-01-21
Description: Various utilities to manipulate multivariate polynomials
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
inst/doc/multipol.pdf |binary
3 files changed, 6 insertions(+), 6 deletions(-)
Title: The multiplicative multinomial distribution
Diff between MM versions 1.6-0 dated 2012-02-28 and 1.6-2 dated 2013-01-21
Description: Description: Various utilities for the Multiplicative
Multinomial distribution
Author: Robin K. S. Hankin and P. M. E. Altham
Maintainer: Robin K. S. Hankin
DESCRIPTION | 10 +++++-----
MD5 | 24 ++++++++++++------------
R/MM.R | 24 +++++++++++++++---------
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data/pollen.rda |binary
data/powell.rda |binary
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inst/doc/Gianfranco.pdf |binary
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Title: create and investigate magic squares
Diff between magic versions 1.5-2 dated 2012-07-03 and 1.5-4 dated 2013-01-21
Description: a collection of efficient, vectorized algorithms for the
creation and investigation of magic squares and hypercubes,
including a variety of functions for the manipulation and
analysis of arbitrarily dimensioned arrays. The package
includes methods for creating normal magic squares of any order
greater than 2. The ultimate intention is for the package to
be a computerized embodiment all magic square knowledge,
including direct numerical verification of properties of magic
squares (such as recent results on the determinant of
odd-ordered semimagic squares). Some antimagic functionality
is included. The package also serves as a rebuttal to the
often-heard comment "I thought R was just for statistics".
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 6 ++--
MD5 | 26 +++++++++---------
R/magic.R | 26 +++++++++---------
data/Frankenstein.rda |binary
data/Ollerenshaw.rda |binary
data/cube2.rda |binary
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data/perfectcube6.rda |binary
inst/doc/magicpaper.pdf |binary
man/allsubhypercubes.Rd | 4 ++
man/allsums.Rd | 3 +-
man/is.magichypercube.Rd | 66 ++++++++++++++++++++++++++++++-----------------
14 files changed, 78 insertions(+), 53 deletions(-)
Title: Diagnostic and prognostic meta analysis (metamisc)
Diff between metamisc versions 0.0.3 dated 2012-09-18 and 0.0.4 dated 2013-01-21
Description: This package provides functions for diagnostic and
prognostic meta-analyses. It estimates univariate, bivariate
and multivariate models, and allows the aggregation of
previously published prediction models with new data.
Author: Thomas Debray
Maintainer: Thomas Debray
DESCRIPTION | 15 +++---
MD5 | 30 ++++++------
NAMESPACE | 3 +
R/riley.r | 2
R/uvmeta.r | 119 +++++++++++++++++++++++++++++-------------------
data/Daniels.rda |binary
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man/metamisc-package.Rd | 10 ++--
man/riley.Rd | 8 +--
man/rileyDA.Rd | 6 +-
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man/summary.uvmeta.Rd | 9 +--
man/uvmeta.Rd | 28 +++++++++--
17 files changed, 144 insertions(+), 90 deletions(-)
Title: elliptic functions
Diff between elliptic versions 1.2-9 dated 2011-12-27 and 1.3-0 dated 2013-01-21
Description: A suite of elliptic and related functions including
Weierstrass and Jacobi forms. Also includes various tools for
manipulating and visualizing complex functions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
elliptic-1.2-9/elliptic/inst/doc/elliptic.bib |only
elliptic-1.3-0/elliptic/DESCRIPTION | 13 ++++++-------
elliptic-1.3-0/elliptic/MD5 | 13 +++++++------
elliptic-1.3-0/elliptic/R/elliptic.R | 4 ++--
elliptic-1.3-0/elliptic/inst/doc/ellipticpaper.pdf |binary
elliptic-1.3-0/elliptic/man/e1e2e3.Rd | 2 +-
elliptic-1.3-0/elliptic/man/eta.Rd | 6 ++----
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8 files changed, 18 insertions(+), 20 deletions(-)
Title: Continued fractions
Diff between contfrac versions 1.1-8 dated 2009-10-16 and 1.1-9 dated 2013-01-21
Description: Various utilities for evaluating continued fractions
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 6 +++---
MD5 |only
R/contfrac.R | 2 +-
src/contfrac.c | 4 ++--
4 files changed, 6 insertions(+), 6 deletions(-)
Title: Very large numbers in R
Diff between Brobdingnag versions 1.2-1 dated 2011-08-15 and 1.2-2 dated 2013-01-21
Description: Handles very large numbers in R. Real numbers are held
using their natural logarithms, plus a logical flag indicating
sign. The package includes a vignette that gives a
step-by-step introduction to using S4 methods.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
Brobdingnag-1.2-1/Brobdingnag/inst/doc/.log |only
Brobdingnag-1.2-2/Brobdingnag/DESCRIPTION | 8 ++++----
Brobdingnag-1.2-2/Brobdingnag/MD5 | 6 +++---
Brobdingnag-1.2-2/Brobdingnag/inst/doc/brob.pdf |binary
Brobdingnag-1.2-2/Brobdingnag/inst/doc/brobpaper.pdf |binary
5 files changed, 7 insertions(+), 7 deletions(-)
Title: A generalization of Fisher's exact test
Diff between aylmer versions 1.0-9 dated 2012-10-02 and 1.0-10 dated 2013-01-21
Description: A generalization of Fisher's exact test that allows for
structural zeros.
Author: Robin K. S. Hankin (R) and Luke J. West (C++)
Maintainer: Robin K. S. Hankin
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
data/frogs.rda |binary
data/glass.rda |binary
data/iqd.rda |binary
data/purum.rda |binary
inst/doc/fishervig.pdf |binary
7 files changed, 10 insertions(+), 10 deletions(-)
Title: VDA
Diff between VDA versions 1.0 dated 2012-11-27 and 1.01 dated 2013-01-21
Description: Multicategory Vertex Discriminant Analysis
Author: Edward Grant, Xia Li, Kenneth Lange, Tong Tong Wu
Maintainer: Edward Grant
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/cv.VDA_LE.default.R | 2 +-
R/cv.VDA_R.default.R | 2 +-
man/plot.cv.VDA_R.Rd | 2 +-
5 files changed, 12 insertions(+), 12 deletions(-)
Title: A set of tools for residential segregation research
Diff between seg versions 0.2-2 dated 2012-06-24 and 0.2-4 dated 2013-01-21
Description: A package that provides functions to measure the overall
degree of residential segregation. The methods implemented in
this package include Duncan and Duncan's index of dissimilarity
(1955), Morrill (1991) and Wong (1993)'s adjusted indices of
dissimilarity, White's spatial segregation measure (1983), and
Reardon and O'Sullivan's spatial segregation measures (2004).
Author: Seong-Yun Hong, David O'Sullivan
Maintainer: Seong-Yun Hong
seg-0.2-2/seg/LICENSE |only
seg-0.2-2/seg/data/auckpop2006.rda |only
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seg-0.2-4/seg/DESCRIPTION | 14 +++++++++-----
seg-0.2-4/seg/MD5 | 22 ++++++++--------------
seg-0.2-4/seg/R/SegSpatial-methods.R | 4 ++--
seg-0.2-4/seg/R/SegSpatialExt-methods.R | 4 ++--
seg-0.2-4/seg/R/spseg.R | 2 +-
seg-0.2-4/seg/data/segdata.rda |binary
seg-0.2-4/seg/man/seg.Rd | 22 +---------------------
seg-0.2-4/seg/man/spseg.Rd | 26 --------------------------
seg-0.2-4/seg/man/whiteseg.Rd | 22 +---------------------
15 files changed, 24 insertions(+), 92 deletions(-)
Title: orloca Rcmdr Plug-in
Diff between RcmdrPlugin.orloca versions 2.1 dated 2010-04-28 and 4.1 dated 2013-01-21
More information about RcmdrPlugin.orloca at CRAN
Description: This package provides a GUI for the orloca package, it is
developed as an Rcmdr plug-in.
Author: Fernando Fernandez-Palacin
Maintainer: Manuel Munoz-Marquez
DESCRIPTION | 15 +-
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R/RcmdrPlugin.Orloca.R | 105 ++++++++------
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man/RcmdrPlugin.orloca-package.Rd | 6
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po/R-RcmdrPlugin.orloca.pot | 87 ++++++------
10 files changed, 208 insertions(+), 191 deletions(-)
Permanent link
Title: Normalize NanoString miRNA and mRNA data
Diff between NanoStringNorm versions 1.1.12 dated 2013-01-08 and 1.1.13 dated 2013-01-21
More information about NanoStringNorm at CRAN
Description: A set of tools for normalizing, diagnostics and
visualization of NanoString nCounter data
Author: Daryl M. Waggott
Maintainer: Daryl Waggott
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/Plot.NanoStringNorm.gvis.R | 3 ++-
inst/doc/NanoStringNorm_Introduction.pdf |binary
4 files changed, 8 insertions(+), 7 deletions(-)
Permanent link
Title: Analysis of Multivariate Event Times
Diff between mets versions 0.1-12 dated 2012-11-20 and 0.1-13 dated 2013-01-21
Description: Implementation of various statistical models for
multivariate event history data. Including multivariate
cumulative incidence models, and bivariate random effects
probit models (Liability models)
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst
mets-0.1-12/mets/inst/tests/run-all.R |only
mets-0.1-12/mets/inst/tests/sim-cens-ts.r |only
mets-0.1-12/mets/inst/tests/sim-nordic-twin.r |only
mets-0.1-12/mets/inst/tests/twinbmi.R |only
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mets-0.1-13/mets/DESCRIPTION | 12
mets-0.1-13/mets/MD5 | 66 ++--
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mets-0.1-13/mets/R/aalenfrailty.R | 2
mets-0.1-13/mets/R/bicomprisk.R | 67 +++-
mets-0.1-13/mets/R/casewise.R | 112 +++----
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mets-0.1-13/mets/R/methodstwinlm.R | 9
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mets-0.1-13/mets/R/summary.bptwin.R | 11
mets-0.1-13/mets/R/surv.boxarea.R | 6
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mets-0.1-13/mets/man/bicomprisk.Rd | 13
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mets-0.1-13/mets/man/casewise.test.Rd | 11
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Title: fit.models
Diff between fit.models versions 0.5-3 dated 2013-01-03 and 0.5-8 dated 2013-01-21
Description: A framework for comparing fitted models
Author: Kjell Konis
Maintainer: Kjell Konis
fit.models-0.5-3/fit.models/R/design.distance.q |only
fit.models-0.5-3/fit.models/R/get.fit.models.registry.q |only
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fit.models-0.5-8/fit.models/R/coef.lmfm.q | 1
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fit.models-0.5-8/fit.models/man/fit.models.Rd | 60 +++-
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Title: Data sets for econometrics
Diff between Ecdat versions 0.1-6.1 dated 2011-02-06 and 0.2-0 dated 2013-01-21
Description: Data sets for econometrics
Author: Yves Croissant
Maintainer: Spencer Graves
DESCRIPTION | 13 +
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data/Accident.rda |binary
data/Airline.rda |binary
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data/Benefits.rda |binary
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data/BudgetFood.rda |binary
data/BudgetItaly.rda |binary
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data/CRSPday.rda |binary
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data/Capm.rda |binary
data/Car.rda |binary
data/Caschool.rda |binary
data/Catsup.rda |binary
data/Cigar.rda |binary
data/Cigarette.rda |binary
data/Clothing.rda |binary
data/Computers.rda |binary
data/Consumption.rda |binary
data/Cracker.rda |binary
data/Crime.rda |binary
data/DM.rda |binary
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data/Doctor.rda |binary
data/DoctorAUS.rda |binary
data/DoctorContacts.rda |binary
data/Earnings.rda |binary
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data/Fair.rda |binary
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data/Garch.rda |binary
data/Gasoline.rda |binary
data/Griliches.rda |binary
data/Grunfeld.rda |binary
data/HC.rda |binary
data/HI.rda |binary
data/Hdma.rda |binary
data/Heating.rda |binary
data/Hedonic.rda |binary
data/Housing.rda |binary
data/Hstarts.rda |binary
data/Icecream.rda |binary
data/IncomeUK.rda |binary
data/Intratesm.rda |binary
data/Intratesq.rda |binary
data/Irates.rda |binary
data/Journals.rda |binary
data/Kakadu.rda |binary
data/Ketchup.rda |binary
data/Klein.rda |binary
data/LT.rda |binary
data/LaborSupply.rda |binary
data/Labour.rda |binary
data/Longley.rda |binary
data/MCAS.rda |binary
data/MW.rda |binary
data/Macrodat.rda |binary
data/Males.rda |binary
data/ManufCost.rda |binary
data/Mathlevel.rda |binary
data/MedExp.rda |binary
data/Metal.rda |binary
data/Mishkin.rda |binary
data/Mode.rda |binary
data/ModeChoice.rda |binary
data/Mofa.rda |binary
data/Money.rda |binary
data/MoneyUS.rda |binary
data/Mpyr.rda |binary
data/Mroz.rda |binary
data/MunExp.rda |binary
data/NaturalPark.rda |binary
data/Nerlove.rda |binary
data/OFP.rda |binary
data/Oil.rda |binary
data/Orange.rda |binary
data/PE.rda |binary
data/PPP.rda |binary
data/PSID.rda |binary
data/Participation.rda |binary
data/PatentsHGH.rda |binary
data/PatentsRD.rda |binary
data/Pound.rda |binary
data/Pricing.rda |binary
data/Produc.rda |binary
data/RetSchool.rda |binary
data/SP500.rda |binary
data/Schooling.rda |binary
data/Solow.rda |binary
data/Somerville.rda |binary
data/Star.rda |binary
data/Strike.rda |binary
data/StrikeDur.rda |binary
data/StrikeNb.rda |binary
data/SumHes.rda |binary
data/Tbrate.rda |binary
data/Tobacco.rda |binary
data/Train.rda |binary
data/TranspEq.rda |binary
data/Treatment.rda |binary
data/Tuna.rda |binary
data/UnempDur.rda |binary
data/Unemployment.rda |binary
data/University.rda |binary
data/VietNamH.rda |binary
data/VietNamI.rda |binary
data/Wages.rda |binary
data/Wages1.rda |binary
data/Workinghours.rda |binary
data/Yen.rda |binary
data/Yogurt.rda |binary
data/datalist | 1
data/incomeInequality.rda |only
inst |only
man/Index.Econometrics.Rd | 222 ++++++++++++++--------------
man/Index.Economics.Rd | 296 +++++++++++++++++++-------------------
man/Index.Observations.Rd | 244 +++++++++++++++----------------
man/Index.Source.Rd | 358 +++++++++++++++++++++++-----------------------
man/Index.Time.Series.Rd | 78 +++++-----
man/asNumericDF.Rd |only
man/incomeInequality.Rd |only
130 files changed, 608 insertions(+), 604 deletions(-)
Title: Distributed Lag Non-linear Models
Diff between dlnm versions 1.6.4 dated 2012-08-22 and 1.6.5 dated 2013-01-21
Description: The package dlnm contains functions to specify and run
distributed lag linear and non-linear models.
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini
DESCRIPTION | 11 -
MD5 | 70 +++----
NAMESPACE | 42 +++-
R/coef.crosspred.R | 7
R/coef.crossreduce.R | 7
R/crossbasis.R | 296 +++++++++++++++---------------
R/crossplot.R | 399 ++++++++++++++++++++--------------------
R/crosspred.R | 434 ++++++++++++++++++++++----------------------
R/crossreduce.R | 337 +++++++++++++++++-----------------
R/internal.R | 24 ++
R/lines.crosspred.R | 243 +++++++++++-------------
R/lines.crossreduce.R | 98 ++++-----
R/mkbasis.R | 9
R/mklagbasis.R | 7
R/onebasis.R | 340 +++++++++++++++++-----------------
R/plot.crosspred.R | 384 ++++++++++++++++++--------------------
R/plot.crossreduce.R | 106 +++++-----
R/points.crosspred.R | 240 +++++++++++-------------
R/points.crossreduce.R | 96 ++++-----
R/summary.crossbasis.R | 11 -
R/summary.crosspred.R | 9
R/summary.crossreduce.R | 14 -
R/summary.onebasis.R | 8
R/vcov.crosspred.R | 7
R/vcov.crossreduce.R | 7
inst/ChangeLog | 17 +
inst/doc/biblioVignette.bib | 11 -
inst/doc/dlnmOverview.Rnw | 144 ++++++++++----
inst/doc/dlnmOverview.pdf |binary
man/crossbasis.Rd | 4
man/crosspred.Rd | 6
man/crossreduce.Rd | 10 -
man/dlnm-internal.Rd | 1
man/dlnm-package.Rd | 10 -
man/onebasis.Rd | 2
man/plot.crosspred.Rd | 4
36 files changed, 1768 insertions(+), 1647 deletions(-)