Title: Association between Methylation and a phenotype of interest
Diff between CpGassoc versions 1.00 dated 2012-05-22 and 1.1 dated 2012-05-26
Description: CpGassoc is designed to test for association between
methylation at CpG sites across the genome and a phenotype of
interest, adjusting for any relevant covariates. The package
can perform standard analyses of large datasets very quickly
with no need to impute the data. It can also handle mixed
effects models with chip or batch entering the model as a
random intercept. CpGassoc also includes tools to apply
quality control filters, perform permutation tests, and create
QQ plots, manhattan plots, and scatterplots for individual CpG
sites.
Author: Barfield, R., Conneely, K., Kilaru,V
Maintainer: R Barfield
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/cpg.qc.R | 4 ----
inst/doc/CpGassoc.pdf |binary
man/CpGassoc-package.Rd | 4 ++--
5 files changed, 10 insertions(+), 14 deletions(-)
Title: Univariate GARCH models
Diff between rugarch versions 1.0-8 dated 2012-03-01 and 1.0-9 dated 2012-05-26
Description: ARFIMA, in-mean, external regressors and various GARCH
flavours, with methods for fit, forecast, simulation, inference
and plotting.
Author: Alexios Ghalanos
Maintainer: Alexios Ghalanos
rugarch-1.0-8/rugarch/cleanup |only
rugarch-1.0-8/rugarch/vignettes/Introduction_to_the_rugarch_package.tex |only
rugarch-1.0-8/rugarch/vignettes/Sweave.sty |only
rugarch-1.0-9/rugarch/ChangeLog | 12
rugarch-1.0-9/rugarch/DESCRIPTION | 10
rugarch-1.0-9/rugarch/MD5 | 48 -
rugarch-1.0-9/rugarch/NAMESPACE | 1
rugarch-1.0-9/rugarch/R/arfima-main.R | 293 +++++++++-
rugarch-1.0-9/rugarch/R/arfima-methods.R | 47 +
rugarch-1.0-9/rugarch/R/rugarch-aparch.R | 3
rugarch-1.0-9/rugarch/R/rugarch-bootstrap.R | 8
rugarch-1.0-9/rugarch/R/rugarch-egarch.R | 4
rugarch-1.0-9/rugarch/R/rugarch-fgarch.R | 3
rugarch-1.0-9/rugarch/R/rugarch-gjrgarch.R | 3
rugarch-1.0-9/rugarch/R/rugarch-igarch.R | 6
rugarch-1.0-9/rugarch/R/rugarch-methods.R | 9
rugarch-1.0-9/rugarch/R/rugarch-rolling.R | 27
rugarch-1.0-9/rugarch/R/rugarch-sgarch.R | 3
rugarch-1.0-9/rugarch/R/rugarch-startpars.R | 170 +++++
rugarch-1.0-9/rugarch/R/rugarch-tests.R | 4
rugarch-1.0-9/rugarch/R/rugarch-uncertainty.R | 5
rugarch-1.0-9/rugarch/inst/doc/Introduction_to_the_rugarch_package.pdf |binary
rugarch-1.0-9/rugarch/man/arfimafit-methods.Rd | 3
rugarch-1.0-9/rugarch/man/autoarfima.Rd |only
rugarch-1.0-9/rugarch/man/rugarch-package.Rd | 6
rugarch-1.0-9/rugarch/src/Makevars | 2
rugarch-1.0-9/rugarch/src/filters.c | 20
27 files changed, 605 insertions(+), 82 deletions(-)
Title: Interface allowing R to use OpenCL
Diff between OpenCL versions 0.1-2 dated 2012-03-08 and 0.1-3 dated 2012-05-26
Description: This package provides an interface to OpenCL, allowing R
to leverage computing power of GPUs and other HPC accelerator
devices.
Author: Simon Urbanek
Maintainer: Simon Urbanek
DESCRIPTION | 6 ++--
MD5 | 14 +++++------
NAMESPACE | 5 +++
NEWS | 21 ++++++++++++++++
R/ocl.R | 33 +++++++++++++++++++++++---
man/oclRun.Rd | 62 ++++++++++++++++++++++++++++---------------------
man/oclSimpleKernel.Rd | 19 ++++++++-------
src/ocl.c | 26 +++++++++++++++-----
8 files changed, 133 insertions(+), 53 deletions(-)
Title: Negative Binomial Models for RNA-Sequencing Data
Diff between NBPSeq versions 0.1.4 dated 2011-04-24 and 0.1.6 dated 2012-05-26
Description: Negative Binomial (NB) models for two-group comparisons
and regression inferences from RNA-Sequencing Data.
Author: Yanming Di
Maintainer: Yanming Di
DESCRIPTION | 17 ++++++++---------
MD5 |only
NAMESPACE | 3 ++-
R/estimate.disp.mapl.R |only
R/hoa.1d.R |only
R/log.likelihood.R |only
R/nb.glm.R |only
R/nb.glm.main.R |only
R/nbp-classes.R | 11 +++++++++++
R/nbp-main.R | 30 +-----------------------------
R/nbpseq.package.R |only
R/smart.plot.R | 4 ++--
data/arab.rda |binary
man/arab.Rd | 8 ++++----
man/estimate.disp.Rd | 10 +++++-----
man/estimate.dispersion.Rd |only
man/estimate.norm.factors.Rd |only
man/nb.glm.test.Rd |only
man/nbp.test.Rd | 9 +++++----
man/plot.nbp.Rd | 2 +-
man/prepare.nb.data.Rd |only
man/prepare.nbp.Rd | 3 ++-
man/print.nbp.Rd | 2 +-
man/test.coefficient.Rd |only
24 files changed, 42 insertions(+), 57 deletions(-)
Title: Visualizations of Paired Comparisons
Diff between multcompView versions 0.1-3 dated 2011-06-15 and 0.1-5 dated 2012-05-26
Description: Convert a logical vector or a vector of p-values or a
correlation, difference, or distance matrix into a display
identifying the pairs for which the differences were not
significantly different. Designed for use in conjunction with
the output of functions like TukeyHSD, dist{stats}, simint,
simtest, csimint, csimtest{multcomp}, friedmanmc,
kruskalmc{pgirmess}.
Author: Spencer Graves, Hans-Peter Piepho and Luciano Selzer with help
from Sundar Dorai-Raj
Maintainer: Luciano Selzer
DESCRIPTION | 11 --
MD5 |only
NAMESPACE | 3
NEWS |only
R/extract_p.R | 38 ++++---
R/multcompBoxplot.R | 246 +++++++++++++++++++++++++------------------------
R/multcompLetters4.R | 4
man/extract_p.Rd | 10 +
man/multcompBoxplot.Rd | 2
man/multcompLetters.Rd | 3
man/multcompTs.Rd | 12 ++
11 files changed, 180 insertions(+), 149 deletions(-)
Title: COSSO, adaptive COSSO, variable selection for nonparametric
smoothing spline (quantile) regression models.
Diff between cosso versions 2.0-1 dated 2012-05-04 and 2.0-2 dated 2012-05-26
Description: COSSO is the short term for Component Selection and
Smoothing Operator. The new regularization method automatically
selects important function components by a soft-thresholding
penalty in the context of smoothing spline ANOVA models. The
details about the procedures are given in the paper by Lin and
Zhang (2007).
Author: Hao Helen Zhang
Maintainer: Chen-Yen Lin
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
R/R.R | 16 ++++++++--------
man/KQR.rd | 5 +++--
man/KQRwt.rd | 14 +++++++-------
man/SSANOVAwt.rd | 2 +-
man/cosso.Rd | 11 ++++-------
man/cosso.qr.Rd | 20 ++++++++++----------
man/plot.cosso.Rd | 4 ++--
man/predict.cosso.Rd | 4 ++--
man/tune.cosso.Rd | 9 +++++++--
man/tune.cosso.qr.rd | 7 ++++---
12 files changed, 63 insertions(+), 59 deletions(-)
Title: Actuarial functions
Diff between actuar versions 1.1-3 dated 2012-01-19 and 1.1-4 dated 2012-05-26
Description: Additional actuarial science functionality, mostly in the
fields of loss distributions, risk theory (including ruin
theory), simulation of compound hierarchical models and
credibility theory. The package also features 17 new
probability laws commonly used in insurance, most notably heavy
tailed distributions.
Author: Vincent Goulet, Sébastien Auclair, Christophe Dutang, Xavier
Milhaud, Tommy Ouellet, Louis-Philippe Pouliot, Mathieu Pigeon
Maintainer: Vincent Goulet
actuar-1.1-3/actuar/actuar-Ex.R |only
actuar-1.1-4/actuar/DESCRIPTION | 8 ++++----
actuar-1.1-4/actuar/MD5 | 23 +++++++++++------------
actuar-1.1-4/actuar/R/CTE.R | 2 +-
actuar-1.1-4/actuar/R/Extract.grouped.data.R | 4 ++--
actuar-1.1-4/actuar/R/elev.R | 2 +-
actuar-1.1-4/actuar/inst/NEWS.Rd | 10 ++++++++++
actuar-1.1-4/actuar/inst/doc/actuar.pdf |binary
actuar-1.1-4/actuar/inst/doc/coverage.pdf |binary
actuar-1.1-4/actuar/inst/doc/credibility.pdf |binary
actuar-1.1-4/actuar/inst/doc/lossdist.pdf |binary
actuar-1.1-4/actuar/inst/doc/risk.pdf |binary
actuar-1.1-4/actuar/inst/doc/simulation.pdf |binary
13 files changed, 29 insertions(+), 20 deletions(-)