Title: Statistical methods for visual fields
Diff between visualFields versions 0.2-2 dated 2012-07-31 and 0.2-4 dated 2012-09-18
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-0.2-2/visualFields/R/colorMapGraph.R |only
visualFields-0.2-2/visualFields/man/colorMapGraph.Rd |only
visualFields-0.2-4/visualFields/DESCRIPTION | 36 +-
visualFields-0.2-4/visualFields/MD5 | 148 +++++------
visualFields-0.2-4/visualFields/NAMESPACE | 7
visualFields-0.2-4/visualFields/R/bebie.R | 70 +++--
visualFields-0.2-4/visualFields/R/colormapgraph.R |only
visualFields-0.2-4/visualFields/R/createviewport.R | 3
visualFields-0.2-4/visualFields/R/ghpostd.R | 10
visualFields-0.2-4/visualFields/R/gloperc.R | 3
visualFields-0.2-4/visualFields/R/loadvfxml.R | 3
visualFields-0.2-4/visualFields/R/locperc.R | 4
visualFields-0.2-4/visualFields/R/poplr.R | 18 +
visualFields-0.2-4/visualFields/R/poplr_cstat.R | 3
visualFields-0.2-4/visualFields/R/progols.R | 13
visualFields-0.2-4/visualFields/R/quad2Dfit.R | 3
visualFields-0.2-4/visualFields/R/ringmapgraph.R |only
visualFields-0.2-4/visualFields/R/stimLoc.R | 3
visualFields-0.2-4/visualFields/R/tdrankadjperc.R | 3
visualFields-0.2-4/visualFields/R/tdrankperc.R | 3
visualFields-0.2-4/visualFields/R/vfcolormap.R | 18 -
visualFields-0.2-4/visualFields/R/vfgrayscale.R | 1
visualFields-0.2-4/visualFields/R/vfiperc.R | 3
visualFields-0.2-4/visualFields/R/vflayout.R | 7
visualFields-0.2-4/visualFields/R/vflayout_legoplot.R | 27 --
visualFields-0.2-4/visualFields/R/vflayout_poplr.R | 159 ++++++++++--
visualFields-0.2-4/visualFields/R/vfplot.R | 22 +
visualFields-0.2-4/visualFields/R/vfplot_poplr.R | 155 +++++++++++
visualFields-0.2-4/visualFields/R/vfplotloc.R | 55 +++-
visualFields-0.2-4/visualFields/R/vfselectvisit.R |only
visualFields-0.2-4/visualFields/R/vfsort.R |only
visualFields-0.2-4/visualFields/R/xmldevval.R | 4
visualFields-0.2-4/visualFields/data/fdplocmap.rda |binary
visualFields-0.2-4/visualFields/data/nv.rda |binary
visualFields-0.2-4/visualFields/data/saplocmap.rda |binary
visualFields-0.2-4/visualFields/data/sapsunyiunv.rda |binary
visualFields-0.2-4/visualFields/data/vf91016left.rda |binary
visualFields-0.2-4/visualFields/data/vf91016right.rda |binary
visualFields-0.2-4/visualFields/data/vfidefault.rda |binary
visualFields-0.2-4/visualFields/doc/news.txt | 16 +
visualFields-0.2-4/visualFields/man/ageLinearModel.Rd | 1
visualFields-0.2-4/visualFields/man/bebie.Rd | 16 -
visualFields-0.2-4/visualFields/man/colormapgraph.Rd |only
visualFields-0.2-4/visualFields/man/createviewport.Rd | 5
visualFields-0.2-4/visualFields/man/fdplocmap.Rd | 6
visualFields-0.2-4/visualFields/man/getnv.Rd | 8
visualFields-0.2-4/visualFields/man/ghpostd.Rd | 9
visualFields-0.2-4/visualFields/man/gloperc.Rd | 3
visualFields-0.2-4/visualFields/man/loadvfxml.Rd | 3
visualFields-0.2-4/visualFields/man/loadvfxmlbatch.Rd | 2
visualFields-0.2-4/visualFields/man/locperc.Rd | 4
visualFields-0.2-4/visualFields/man/poplr.Rd | 3
visualFields-0.2-4/visualFields/man/poplr_cstat.Rd | 3
visualFields-0.2-4/visualFields/man/progols.Rd | 5
visualFields-0.2-4/visualFields/man/quad2Dfit.Rd | 3
visualFields-0.2-4/visualFields/man/ringmapgraph.Rd |only
visualFields-0.2-4/visualFields/man/saplocmap.Rd | 2
visualFields-0.2-4/visualFields/man/sapsunyiunv.Rd | 4
visualFields-0.2-4/visualFields/man/sdnv.Rd | 4
visualFields-0.2-4/visualFields/man/setnv.Rd | 4
visualFields-0.2-4/visualFields/man/stimLoc.Rd | 3
visualFields-0.2-4/visualFields/man/tdpmap.Rd | 4
visualFields-0.2-4/visualFields/man/tdrankadjperc.Rd | 3
visualFields-0.2-4/visualFields/man/tdrankperc.Rd | 3
visualFields-0.2-4/visualFields/man/vfcolormap.Rd | 3
visualFields-0.2-4/visualFields/man/vfidefault.Rd | 2
visualFields-0.2-4/visualFields/man/vfindex.Rd | 2
visualFields-0.2-4/visualFields/man/vfiperc.Rd | 3
visualFields-0.2-4/visualFields/man/vflayout.Rd | 6
visualFields-0.2-4/visualFields/man/vflayout_legoplot.Rd | 5
visualFields-0.2-4/visualFields/man/vflayout_poplr.Rd | 18 +
visualFields-0.2-4/visualFields/man/vfplot.Rd | 13
visualFields-0.2-4/visualFields/man/vfplot_poplr.Rd | 25 +
visualFields-0.2-4/visualFields/man/vfplotloc.Rd | 12
visualFields-0.2-4/visualFields/man/vfselectvisit.Rd |only
visualFields-0.2-4/visualFields/man/vfsettings.Rd | 2
visualFields-0.2-4/visualFields/man/vfsort.Rd |only
visualFields-0.2-4/visualFields/man/visualFields-package.Rd | 6
visualFields-0.2-4/visualFields/man/xmldevval.Rd | 4
visualFields-0.2-4/visualFields/man/xmlvfxy.Rd | 2
80 files changed, 696 insertions(+), 302 deletions(-)
Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Diff between twang versions 1.2-5 dated 2012-03-08 and 1.2-6 dated 2012-09-18
Description: This package offers functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights. This package was originally developed by Drs.
Ridgeway, McCaffrey, and Morral. Burgette, Griffin and
McCaffrey updated the package in 2011.
Author: Greg Ridgeway
Maintainer: Lane Burgette
DESCRIPTION | 8 ++++----
MD5 | 29 ++++++++++++++++-------------
NAMESPACE | 2 ++
R/diag.plot.R | 25 +++++++++++++++++++++----
R/get.weights.R | 11 ++++++++---
R/ps.R | 1 +
R/ps.summary.R | 9 +++++++--
R/sensitivity.R | 29 +++++++++++++++++++----------
data/egsingle.RData |binary
data/lalonde.RData |binary
data/lindner.RData |binary
data/raceprofiling.RData |binary
inst/doc/twang.pdf |binary
man/get.weights.Rd | 5 +++--
src |only
15 files changed, 81 insertions(+), 38 deletions(-)
Title: Robust Structural Equation Modeling with Missing Data and
Auxiliary Variables
Diff between rsem versions 0.4.1 dated 2012-08-26 and 0.4.3 dated 2012-09-18
Description: This package estimates means and covariance matrix of
multiple variables with missing data using Huber weight and
then estimates a SEM model using lavaan or EQS.
Author: Ke-Hai Yuan and Zhiyong Zhang
Maintainer: Zhiyong Zhang
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
R/rsem.R | 2 +-
man/rsem-package.Rd | 4 ++--
man/rsem.Rd | 2 ++
5 files changed, 15 insertions(+), 12 deletions(-)
Title: Conditional logistic regression: A two-step estimation method
Diff between TwoStepCLogit versions 1.2 dated 2012-07-18 and 1.2.1 dated 2012-09-18
Description: Conditional logistic regression with longitudinal follow
up and individual-level random coefficients: A stable and
efficient two-step estimation method
Author: Radu V. Craiu, Thierry Duchesne, Daniel Fortin and Sophie
Baillargeon
Maintainer: Thierry Duchesne
TwoStepCLogit-1.2.1/TwoStepCLogit/DESCRIPTION | 8 -
TwoStepCLogit-1.2.1/TwoStepCLogit/MD5 | 27 ++--
TwoStepCLogit-1.2.1/TwoStepCLogit/NAMESPACE | 8 -
TwoStepCLogit-1.2.1/TwoStepCLogit/R/Ts.estim.R | 41 +++---
TwoStepCLogit-1.2.1/TwoStepCLogit/R/TwoStepCLogit.R | 4
TwoStepCLogit-1.2.1/TwoStepCLogit/R/ddim.R | 8 -
TwoStepCLogit-1.2.1/TwoStepCLogit/R/internal.R | 14 +-
TwoStepCLogit-1.2.1/TwoStepCLogit/TwoStepCLogit.Rproj |only
TwoStepCLogit-1.2.1/TwoStepCLogit/inst/NEWS.Rd | 5
TwoStepCLogit-1.2.1/TwoStepCLogit/inst/tests/READMEtest.R |only
TwoStepCLogit-1.2.1/TwoStepCLogit/inst/tests/testPaperResults.R | 1
TwoStepCLogit-1.2.1/TwoStepCLogit/inst/tests/testValidation.R | 66 ++++------
TwoStepCLogit-1.2.1/TwoStepCLogit/man/Ts.estim.Rd | 2
TwoStepCLogit-1.2.1/TwoStepCLogit/man/TwoStepCLogit-package.Rd | 4
TwoStepCLogit-1.2.1/TwoStepCLogit/tests/Examples/TwoStepCLogit-Ex.Rout.save | 28 +++-
TwoStepCLogit-1.2/TwoStepCLogit/inst/tests/testREADME.txt |only
16 files changed, 120 insertions(+), 96 deletions(-)
Title: Smoothing-splines Mixed-effects Models
Diff between sme versions 0.3 dated 2012-06-21 and 0.4 dated 2012-09-18
Description: A package for fitting smoothing-splines mixed-effects
models to replicated functional data sets.
Author: Maurice Berk [aut, cre]
Maintainer: Maurice Berk
ChangeLog |only
DESCRIPTION | 8 -
MD5 | 27 +++--
NAMESPACE | 2
R/sme.R | 30 +++++-
inst/doc/Tutorial.Rnw | 10 +-
inst/doc/Tutorial.pdf |binary
man/getRoughnessMatrix.Rd |only
man/sme.list.Rd | 5 -
src/LapackSubset.f |only
src/LinearAlgebra.c | 7 +
src/Makevars | 3
src/NelderMead.c |only
src/NelderMead.h |only
src/SME.c | 227 +++++++++++++---------------------------------
src/SME.h | 2
vignettes/Tutorial.Rnw | 10 +-
17 files changed, 133 insertions(+), 198 deletions(-)
Title: Ridge regression and other kernels for genomic selection
Diff between rrBLUP versions 3.8 dated 2012-05-17 and 4.0 dated 2012-09-18
Description: Software for genomic prediction with the RR-BLUP mixed
model. One application is to estimate marker effects by ridge
regression; alternatively, BLUPs can be calculated based on an
additive relationship matrix or a Gaussian kernel.
Author: Jeffrey Endelman
Maintainer: Jeffrey Endelman
DESCRIPTION | 15 +--
MD5 | 28 ++++---
NAMESPACE | 2
NEWS | 5 +
R/A.mat.R | 188 ++++++++++++++++++++++++++------------------------
R/GWA.R | 36 ++++-----
R/kin.blup.R |only
R/kinship.BLUP.R | 8 +-
R/mixed.solve.R | 8 +-
inst/doc |only
man/A.mat.Rd | 59 ++++++++++-----
man/GWA.Rd | 14 +--
man/kin.blup.Rd |only
man/kinship.BLUP.Rd | 13 +--
man/mixed.solve.Rd | 30 +++++--
man/rrBLUP-package.Rd | 14 +--
16 files changed, 229 insertions(+), 191 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.3.4.0 dated 2012-09-06 and 0.3.4.1 dated 2012-09-18
Description: R and Armadillo integration using Rcpp Armadillo is a
templated C++ linear algebra library (by Conrad Sanderson) that
aims towards a good balance between speed and ease of use.
Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions.
Various matrix decompositions are provided through optional
integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to
combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished
through recursive templates and template meta-programming.
This library is useful if C++ has been decided as the language of
choice (due to speed and/or integration capabilities), rather
than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library (currently version 3.4.1). Thus users do not
need to install Armadillo itself in order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration.
Armadillo is licensed under the GNU LGPL version 3 or later, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licensed under the GNU GPL version 2 or later, as is the rest
of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
ChangeLog | 6
DESCRIPTION | 10
MD5 | 44 -
inst/NEWS.Rd | 12
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/doc/unitTests-results/RcppArmadillo-unitTests.html | 6
inst/doc/unitTests-results/RcppArmadillo-unitTests.txt | 34 -
inst/include/armadillo_bits/arma_version.hpp | 2
inst/include/armadillo_bits/atlas_wrapper.hpp | 6
inst/include/armadillo_bits/blas_wrapper.hpp | 124 +++--
inst/include/armadillo_bits/compiler_setup.hpp | 5
inst/include/armadillo_bits/config.hpp | 16
inst/include/armadillo_bits/fn_dot.hpp | 76 +--
inst/include/armadillo_bits/gemv.hpp | 8
inst/include/armadillo_bits/op_dot_bones.hpp | 39 +
inst/include/armadillo_bits/op_dot_meat.hpp | 380 ++++++++++++----
inst/include/armadillo_bits/operator_schur.hpp | 73 +--
inst/include/armadillo_bits/spglue_minus_meat.hpp | 17
inst/include/armadillo_bits/spglue_plus_meat.hpp | 13
inst/include/armadillo_bits/spglue_times_meat.hpp | 3
inst/include/armadillo_bits/traits.hpp | 10
man/RcppArmadillo-package.Rd | 4
23 files changed, 642 insertions(+), 246 deletions(-)
Title: R Commander Plugin for (industrial) Design of Experiments
Diff between RcmdrPlugin.DoE versions 0.11-6 dated 2012-07-19 and 0.11-7 dated 2012-09-18
More information about RcmdrPlugin.DoE at CRAN
Description: WARNING: This package is currently in beta status! The
package provides a platform-independent GUI for design of
experiments. It is implemented as a plugin to the R-Commander,
which is a more general graphical user interface for statistics
in R based on tcl/tk. DoE functionality can be accessed
through the menu Design that is added to the R-Commander menus.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/Menu.export.R | 6 +++---
inst/NEWS | 4 ++++
4 files changed, 14 insertions(+), 10 deletions(-)
Permanent link
Title: Nonparametric Estimation for Multistate Models
Diff between msSurv versions 1.1-0 dated 2012-04-19 and 1.1-2 dated 2012-09-18
Description: Nonparametric estimation for right censored, left
truncated time to event data in multistate models.
Author: Nicole Ferguson
Maintainer: Guy Brock
ChangeLog | 23 ++++++++++++++--
DESCRIPTION | 12 ++++----
MD5 | 35 ++++++++++++++----------
NAMESPACE | 4 ++
R/msSurv-Classes.R | 4 +-
R/msSurv-Methods.R | 20 +++++++-------
R/msSurv-internal.R | 62 +++++++++++++++++++++----------------------
R/msSurv-user.R | 23 +++++++---------
inst |only
man/EntryExit.rd | 6 ++++
man/LTRCdata.Rd | 7 ++++
man/Pst.Rd | 5 +++
man/RCdata.Rd | 7 ++++
man/SOPt.Rd | 5 +++
man/msSurv-class.Rd | 74 ++++++++++++++++++++++++++++------------------------
man/msSurv.Rd | 48 ++++++++++++++++++---------------
vignettes |only
17 files changed, 202 insertions(+), 133 deletions(-)
Title: Bayesian continuous reassessment method (CRM) designs for Phase
I dose-finding trials.
Diff between bcrm versions 0.3 dated 2012-05-01 and 0.4 dated 2012-09-18
Description: This package implements a wide variety of one and
two-parameter Bayesian CRM designs. The program can run
interactively, allowing the user to enter outcomes after each
cohort has been recruited, or via simulation to assess
operating characteristics.
Author: Michael Sweeting
Maintainer: Michael Sweeting
bcrm-0.3/bcrm/R/bcrm_0.3.R |only
bcrm-0.4/bcrm/DESCRIPTION | 10 +++++-----
bcrm-0.4/bcrm/MD5 | 19 +++++++++++--------
bcrm-0.4/bcrm/NAMESPACE | 5 ++++-
bcrm-0.4/bcrm/NEWS | 5 +++++
bcrm-0.4/bcrm/R/bcrm_0.4.R |only
bcrm-0.4/bcrm/man/bcrm-package.Rd | 5 +++--
bcrm-0.4/bcrm/man/bcrm.Rd | 18 ++++++++++++++++--
bcrm-0.4/bcrm/man/plot.bcrm.sim.Rd | 8 ++++++--
bcrm-0.4/bcrm/man/plot.threep3.Rd |only
bcrm-0.4/bcrm/man/print.bcrm.Rd | 8 ++++++--
bcrm-0.4/bcrm/man/print.threep3.Rd |only
bcrm-0.4/bcrm/man/threep3.Rd |only
13 files changed, 56 insertions(+), 22 deletions(-)
Title: OCI based Oracle database interface for R
Diff between ROracle versions 1.1-4 dated 2012-08-08 and 1.1-5 dated 2012-09-18
Description: Oracle database interface (DBI) driver for R. This is a
DBI-compliant Oracle driver based on the OCI.
Author: Denis Mukhin, David A. James and Jake Luciani
Maintainer: Denis Mukhin
ROracle-1.1-4/ROracle/src/ocimingw.def |only
ROracle-1.1-5/ROracle/DESCRIPTION | 8
ROracle-1.1-5/ROracle/INSTALL | 14
ROracle-1.1-5/ROracle/MD5 | 31 -
ROracle-1.1-5/ROracle/NEWS | 7
ROracle-1.1-5/ROracle/R/oci.R | 112 +---
ROracle-1.1-5/ROracle/configure.win | 34 -
ROracle-1.1-5/ROracle/inst/doc/man/en/OraConnection-class.Rd | 4
ROracle-1.1-5/ROracle/inst/doc/man/en/dbConnect-methods.Rd | 6
ROracle-1.1-5/ROracle/inst/doc/man/en/dbSendQuery-methods.Rd | 7
ROracle-1.1-5/ROracle/man/OraConnection-class.Rd | 4
ROracle-1.1-5/ROracle/man/dbConnect-methods.Rd | 6
ROracle-1.1-5/ROracle/man/dbSendQuery-methods.Rd | 7
ROracle-1.1-5/ROracle/src/Makevars.win | 6
ROracle-1.1-5/ROracle/src/rodbi.c | 297 +++--------
ROracle-1.1-5/ROracle/src/rooci.c | 283 ++++++----
ROracle-1.1-5/ROracle/src/rooci.h | 29 -
17 files changed, 374 insertions(+), 481 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness
estimation
Diff between mgcv versions 1.7-20 dated 2012-08-24 and 1.7-21 dated 2012-09-18
Description: Routines for GAMs and other generalized ridge regression
with multiple smoothing parameter selection by GCV, REML or
UBRE/AIC. Also GAMMs. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood
DESCRIPTION | 6
MD5 | 28 +-
NAMESPACE | 10
R/plots.r | 16 +
R/smooth.r | 87 --------
R/soap.r |only
changeLog | 19 +
man/Predict.matrix.soap.film.Rd |only
man/fs.test.Rd |only
man/inSide.Rd |only
man/mgcv-package.Rd | 7
man/smooth.construct.so.smooth.spec.Rd |only
man/smooth.terms.Rd | 22 +-
po/R-mgcv.pot | 355 ++++++++++++++++++++++++++++-----
po/R-po.po |only
po/po.po |only
src/init.c | 5
src/mgcv.h | 5
src/soap.c |only
19 files changed, 400 insertions(+), 160 deletions(-)
Title: Bayesian graphical models using MCMC
Diff between rjags versions 3-5 dated 2011-10-12 and 3-7 dated 2012-09-18
Description: Interface to the JAGS MCMC library
Author: Martyn Plummer [aut, cre]
Maintainer: Martyn Plummer
rjags-3-5/rjags/.hgtags |only
rjags-3-5/rjags/man/model.samples.Rd |only
rjags-3-5/rjags/man/read.data.Rd |only
rjags-3-7/rjags/DESCRIPTION | 16 +++++++++-------
rjags-3-7/rjags/MD5 | 15 ++++++++-------
rjags-3-7/rjags/R/jags.R | 21 ++++++++++++++++++++-
rjags-3-7/rjags/man/jags.model.Rd | 23 ++++++++++++-----------
rjags-3-7/rjags/man/jags.object.Rd | 11 ++++++-----
rjags-3-7/rjags/man/jags.samples.Rd |only
rjags-3-7/rjags/man/read.jagsdata.Rd |only
rjags-3-7/rjags/man/rjags-deprecated.Rd | 2 +-
rjags-3-7/rjags/man/rjags-package.Rd |only
12 files changed, 56 insertions(+), 32 deletions(-)
Title: Various plotting functions
Diff between plotrix versions 3.4-4 dated 2012-09-11 and 3.4-5 dated 2012-09-18
Description: Lots of plots, various labeling, axis and color scaling
functions.
Author: Jim Lemon, Ben Bolker, Sander Oom, Eduardo Klein, Barry
Rowlingson, Hadley Wickham, Anupam Tyagi, Olivier Eterradossi,
Gabor Grothendieck, Michael Toews, John Kane, Rolf Turner, Carl
Witthoft, Julian Stander, Thomas Petzoldt, Remko Duursma, Elisa
Biancotto, Ofir Levy, Christophe Dutang, Peter Solymos, Robby
Engelmann, Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann,Ted Toal
Maintainer: Jim Lemon
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/arctext.R | 2 +-
demo/plotrix.R | 2 +-
man/arctext.Rd | 2 ++
5 files changed, 12 insertions(+), 10 deletions(-)
Title: Nonparametric Analysis of Longitudinal Data in Factorial
Experiments
Diff between nparLD versions 2.0 dated 2012-02-27 and 2.1 dated 2012-09-18
Description: The package "nparLD" is designed to perform nonparametric
analysis of longitudinal data in factorial experiments.
Longitudinal data are those which are collected from the same
subjects over time, and they frequently arise in biological
sciences. Nonparametric methods do not require distributional
assumptions, and are applicable to a variety of data types
(continuous, discrete, purely ordinal, and dichotomous). Such
methods are also robust with respect to outliers and for small
sample sizes.
Author: Kimihiro Noguchi
Maintainer: Kimihiro Noguchi
DESCRIPTION | 12 ++++++------
MD5 | 43 ++++++++++++++++++++++---------------------
inst |only
man/amylase.rd | 7 ++++++-
man/dental.rd | 7 ++++++-
man/edema.rd | 7 ++++++-
man/f1.ld.f1.rd | 6 +++++-
man/f1.ld.f2.rd | 6 +++++-
man/f2.ld.f1.rd | 6 +++++-
man/ld.ci.rd | 6 +++++-
man/ld.f1.rd | 6 +++++-
man/ld.f2.rd | 6 +++++-
man/nparLD.rd | 5 ++++-
man/panic.rd | 7 ++++++-
man/panic2.rd | 7 ++++++-
man/plasma.rd | 7 ++++++-
man/plot.nparLD.rd | 6 +++++-
man/print.nparLD.rd | 6 +++++-
man/rat.rd | 5 +++++
man/respiration.rd | 8 +++++++-
man/shoulder.rd | 7 ++++++-
man/summary.nparLD.rd | 6 +++++-
man/tree.rd | 7 ++++++-
23 files changed, 137 insertions(+), 46 deletions(-)
Title: Rmetrics - Autoregressive Conditional Heteroskedastic Modelling
Diff between fGarch versions 2110.80.1 dated 2012-06-04 and 2150.81 dated 2012-09-18
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz and Yohan Chalabi with contribution from Michal
Miklovic, Chris Boudt, Pierre Chausse and others
Maintainer: Yohan Chalabi
fGarch-2110.80.1/fGarch/R/absMoments.R |only
fGarch-2110.80.1/fGarch/R/dist-snig.R |only
fGarch-2110.80.1/fGarch/data/dem2gbp.csv |only
fGarch-2110.80.1/fGarch/data/sp500dge.csv |only
fGarch-2110.80.1/fGarch/inst/DocCopying.pdf |only
fGarch-2110.80.1/fGarch/man/absMoments.Rd |only
fGarch-2110.80.1/fGarch/man/sged.Rd |only
fGarch-2110.80.1/fGarch/man/snorm.Rd |only
fGarch-2110.80.1/fGarch/man/sstd.Rd |only
fGarch-2150.81/fGarch/ChangeLog | 2717 +--------------
fGarch-2150.81/fGarch/DESCRIPTION | 13
fGarch-2150.81/fGarch/MD5 | 60
fGarch-2150.81/fGarch/NAMESPACE | 77
fGarch-2150.81/fGarch/R/dist-absMoments.R |only
fGarch-2150.81/fGarch/R/dist-ged.R |only
fGarch-2150.81/fGarch/R/dist-gedFit.R |only
fGarch-2150.81/fGarch/R/dist-gedSlider.R |only
fGarch-2150.81/fGarch/R/dist-sged.R | 384 --
fGarch-2150.81/fGarch/R/dist-sgedFit.R |only
fGarch-2150.81/fGarch/R/dist-sgedSlider.R |only
fGarch-2150.81/fGarch/R/dist-snorm.R | 366 --
fGarch-2150.81/fGarch/R/dist-snormFit.R |only
fGarch-2150.81/fGarch/R/dist-snormSlider.R |only
fGarch-2150.81/fGarch/R/dist-sstd.R | 351 -
fGarch-2150.81/fGarch/R/dist-sstdFit.R |only
fGarch-2150.81/fGarch/R/dist-sstdSlider.R |only
fGarch-2150.81/fGarch/R/dist-std.R |only
fGarch-2150.81/fGarch/R/dist-stdFit.R |only
fGarch-2150.81/fGarch/R/dist-stdSlider.R |only
fGarch-2150.81/fGarch/R/garch-Hessian.R | 154
fGarch-2150.81/fGarch/R/loglik-aparch.R | 90
fGarch-2150.81/fGarch/data/dem2gbp.csv.gz |only
fGarch-2150.81/fGarch/data/sp500dge.csv.gz |only
fGarch-2150.81/fGarch/inst/unitTests/runit.garchSolver.R | 34
fGarch-2150.81/fGarch/inst/unitTests/runit.snorm.R | 16
fGarch-2150.81/fGarch/man/dist-absMoments.Rd |only
fGarch-2150.81/fGarch/man/dist-ged.Rd |only
fGarch-2150.81/fGarch/man/dist-gedFit.Rd |only
fGarch-2150.81/fGarch/man/dist-gedSlider.Rd |only
fGarch-2150.81/fGarch/man/dist-sged.Rd |only
fGarch-2150.81/fGarch/man/dist-sgedFit.Rd |only
fGarch-2150.81/fGarch/man/dist-sgedSlider.Rd |only
fGarch-2150.81/fGarch/man/dist-snorm.Rd |only
fGarch-2150.81/fGarch/man/dist-snormFit.Rd |only
fGarch-2150.81/fGarch/man/dist-snormSlider.Rd |only
fGarch-2150.81/fGarch/man/dist-sstd.Rd |only
fGarch-2150.81/fGarch/man/dist-sstdFit.Rd |only
fGarch-2150.81/fGarch/man/dist-sstdSlider.Rd |only
fGarch-2150.81/fGarch/man/dist-std.Rd |only
fGarch-2150.81/fGarch/man/dist-stdFit.Rd |only
fGarch-2150.81/fGarch/man/dist-stdSlider.Rd |only
51 files changed, 576 insertions(+), 3686 deletions(-)
Title: Order Restricted Clustering for Microarray Experiments
Diff between ORCME versions 1.1 dated 2012-02-10 and 1.2 dated 2012-09-18
Description: This package provides clustering of genes with similar
dose response (or time course) profiles. It implements the
method described by Lin et al. (2012).
Author: Adetayo Kasim, Martin Otava, Tobias Verbeke
Maintainer: Martin Otava
DESCRIPTION | 11 ++++++-----
MD5 | 10 +++++-----
NEWS | 2 +-
R/ORCME.R | 9 ++++++++-
data/doseData.rda |binary
data/geneData.rda |binary
6 files changed, 20 insertions(+), 12 deletions(-)
Title: Diagnostic and prognostic meta analysis (metamisc)
Diff between metamisc versions 0.0.2 dated 2012-09-12 and 0.0.3 dated 2012-09-18
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
metamisc-0.0.2/metamisc/man/metamisc-data.Rd |only
metamisc-0.0.3/metamisc/DESCRIPTION | 12
metamisc-0.0.3/metamisc/MD5 | 32 +-
metamisc-0.0.3/metamisc/R/riley.r | 357 ++++++++++++++----------
metamisc-0.0.3/metamisc/R/uvmeta.r | 18 -
metamisc-0.0.3/metamisc/data/Daniels.rda |only
metamisc-0.0.3/metamisc/data/Kertai.rda |only
metamisc-0.0.3/metamisc/man/Daniels.Rd |only
metamisc-0.0.3/metamisc/man/Kertai.Rd |only
metamisc-0.0.3/metamisc/man/Scheidler.Rd |only
metamisc-0.0.3/metamisc/man/logLik.riley.Rd | 12
metamisc-0.0.3/metamisc/man/metamisc-package.Rd | 23 -
metamisc-0.0.3/metamisc/man/plot.riley.Rd | 13
metamisc-0.0.3/metamisc/man/predict.riley.Rd | 20 -
metamisc-0.0.3/metamisc/man/predict.uvmeta.Rd | 3
metamisc-0.0.3/metamisc/man/riley.Rd | 84 ++---
metamisc-0.0.3/metamisc/man/rileyDA.Rd |only
metamisc-0.0.3/metamisc/man/rileyES.Rd |only
metamisc-0.0.3/metamisc/man/summary.riley.Rd | 10
metamisc-0.0.3/metamisc/man/summary.uvmeta.Rd | 15 -
metamisc-0.0.3/metamisc/man/uvmeta.Rd | 15 -
21 files changed, 328 insertions(+), 286 deletions(-)
Title: R Commander
Diff between Rcmdr versions 1.9-0 dated 2012-09-01 and 1.9-1 dated 2012-09-18
Description: A platform-independent basic-statistics GUI (graphical
user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre], Liviu Andronic [ctb], Michael Ash [ctb],
Milan Bouchet-Valat [ctb], Theophilius Boye [ctb], Stefano
Calza [ctb], Andy Chang [ctb], Philippe Grosjean [ctb], Richard
Heiberger [ctb], Kosar Karimi Pour [ctb], G. Jay Kerns [ctb],
Renaud Lancelot [ctb], Matthieu Lesnoff [ctb], Uwe Ligges
[ctb], Samir Messad [ctb], Martin Maechler [ctb], Robert
Muenchen [ctb], Duncan Murdoch [ctb], Erich Neuwirth [ctb], Dan
Putler [ctb], Brian Ripley [ctb], Miroslav Ristic [ctb], Peter
Wolf [ctb]
Maintainer: John Fox
DESCRIPTION | 11
MD5 | 49
NEWS | 24
R/graphs-menu.R | 2
R/model-menu.R | 95
inst/doc/Getting-Started-with-the-Rcmdr-ko.pdf |only
inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary
inst/po/es/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/it/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/ja/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/ko/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/pl/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/ro/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/ru/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/sl/LC_MESSAGES/R-Rcmdr.mo |binary
man/Plugins.Rd | 6
man/Rcmdr-package.Rd | 4
po/R-Rcmdr.pot | 28
po/R-es.po | 8148 ++++++++++++-------------
po/R-it.po | 7928 ++++++++++++------------
po/R-ja.po | 166
po/R-ko.po | 119
po/R-pl.po | 25
po/R-ro.po | 136
po/R-ru.po | 104
po/R-sl_utf-8.po | 443 -
26 files changed, 9034 insertions(+), 8254 deletions(-)
Title: Prediction Error Curves for Survival Models
Diff between pec versions 2.1.9 dated 2012-08-28 and 2.2.2 dated 2012-09-18
Description: Validation of predicted survival probabilities using
inverse weighting and resampling.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds
DESCRIPTION | 6 +--
MD5 | 32 +++++++++---------
R/CindexBootstrapCrossValidation.R | 27 +++++++++++----
R/bootstrapCrossValidation.R | 55 ++++++++++++++++++++++++-------
R/cindexMethods.R | 5 +-
R/pecMethods.R | 18 +---------
R/predictEventProb.R | 1
R/predictSurvProb.randomSurvivalForest.R | 2 -
inst |only
man/cindex.Rd | 4 ++
man/pec.Rd | 11 +++++-
man/pecCforest.Rd | 7 +--
man/plotPredictEventProb.Rd | 6 ++-
man/plotPredictSurvProb.Rd | 6 ++-
man/predictSurvProb.Rd | 6 ++-
man/selectCox.Rd | 6 +--
src/pecResiduals.c | 19 +++++++---
test/test-pec.R |only
18 files changed, 140 insertions(+), 71 deletions(-)
Title: Rbundler manages an application's dependencies systematically
and repeatedly.
Diff between rbundler versions 0.2 dated 2012-09-17 and 0.2.1 dated 2012-09-18
Description: Specify your dependencies in your project's root
directory, and be able to install and use dependencies in a
repeatable fashion without requiring manual maintenance. Uses
a combination of project-specific R library in
PROJECT_ROOT/.Rbundle and a project-specific R_LIBS_USER, set
in PROJECT_ROOT/.Renviron
Author: Yoni Ben-Meshulam
Maintainer: Yoni Ben-Meshulam
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/bundle.r | 1 +
3 files changed, 6 insertions(+), 5 deletions(-)
Title: Korean NLP Package
Diff between KoNLP versions 0.76 dated 2012-09-10 and 0.76.5 dated 2012-09-18
Description: Korean language processing package. Morphological
analyzer, POS tagger, Keystroke converter, Hangul automata...
Author: Heewon Jeon
Maintainer: Heewon Jeon
DESCRIPTION | 6 ++--
MD5 | 18 +++++++-------
NEWS | 6 ++++
R/hangulUtils.R | 37 +++++++++++++++++++++--------
R/manageDic.R | 63 +++++++++++++++++++++++++++++++++++----------------
R/onLoad.R | 14 +++++------
man/backupUsrDic.Rd | 4 +--
man/mergeUserDic.Rd | 14 +++++++----
man/reloadAllDic.Rd | 4 +--
man/restoreUsrDic.Rd | 4 +--
10 files changed, 110 insertions(+), 60 deletions(-)
Title: Empirical Research in Economics with R
Diff between erer versions 1.2 dated 2012-08-19 and 1.3 dated 2012-09-18
Description: This package contains functions and datasets for the book
of 'Empirical Research in Economics: Growing up with R' by Dr.
Changyou Sun. These functions can calculate marginal effects
for a binary probit or logit model, estimate static and dynamic
Almost Ideal Demand System (AIDS) models, and conduct event
analysis.
Author: Changyou Sun
Maintainer: Changyou Sun
DESCRIPTION | 8 +++---
MD5 | 10 ++++----
R/bsStat.R | 54 ++++++++++++++++++++++++-----------------------
inst/doc/erer-manual.pdf |binary
man/bsStat.Rd | 5 +++-
man/erer-package.Rd | 4 +--
6 files changed, 43 insertions(+), 38 deletions(-)
Title: Statistical Tests for Genetic Association Studies
Diff between AssotesteR versions 0.1-1 dated 2012-03-14 and 0.1-7 dated 2012-09-18
Description: R package with statistical tests and methods for genetic
association studies with emphasis on rare variants and binary
(dichotomous) traits
Author: Gaston Sanchez
Maintainer: Gaston Sanchez
DESCRIPTION | 18
MD5 | 85 +-
NAMESPACE | 79 ++
R/ASCORE.Ord.R | 94 +-
R/ASCORE.R | 156 ++--
R/ASSU.Ord.R | 96 +-
R/ASSU.R | 162 ++--
R/ASSUW.Ord.R | 95 +-
R/ASSUW.R | 161 ++--
R/ASUM.Ord.R | 95 +-
R/ASUM.R | 161 ++--
R/AssotesteR-internal.R | 1699 ++++++++++++++++++++++++----------------------
R/BST.R | 155 ++--
R/CALPHA.R | 208 +++--
R/CARV.R | 301 +++++---
R/CAST.R | 168 +++-
R/CMAT.R | 218 +++--
R/CMC.R | 204 +++--
R/GDBR.R | 222 +++---
R/MULTI.R |only
R/ORWSS.R | 159 ++--
R/RARECOVER.R | 202 +++--
R/RBT.R | 126 ++-
R/RVT1.R | 201 +++--
R/RVT2.R | 203 +++--
R/RWAS.R | 196 +++--
R/SCORE.R | 155 ++--
R/SEQSUM.R | 231 +++---
R/SKAT.R | 297 +++++---
R/SSU.R | 156 ++--
R/SSUW.R | 155 ++--
R/SUM.R | 156 ++--
R/TTEST.R | 240 +++---
R/UMINP.R | 154 ++--
R/VT.R | 144 ++-
R/WSS.R | 131 ++-
R/WST.R | 162 ++--
R/gdbr_IBS.R | 12
R/gdbr_wIBS.R | 12
R/my_check.R |only
R/print.assoctest.R | 24
man/AssotesteR-package.Rd | 8
man/GDBR.Rd | 5
man/MULTI.Rd |only
man/RWAS.Rd | 12
45 files changed, 4635 insertions(+), 2883 deletions(-)
Title: Inference for QTL Hotspots
Diff between qtlhot versions 0.5.2 dated 2012-05-31 and 0.6.1 dated 2012-09-18
Description: Functions to infer co-mapping trait hotspots and causal
models
Author: Elias Chaibub Neto
Maintainer: Brian S. Yandell
qtlhot-0.5.2/qtlhot/R/perm.R |only
qtlhot-0.5.2/qtlhot/R/plot.R |only
qtlhot-0.5.2/qtlhot/R/sim.R |only
qtlhot-0.5.2/qtlhot/R/util.R |only
qtlhot-0.5.2/qtlhot/R/zero.R |only
qtlhot-0.5.2/qtlhot/man/hotspot.plot.Rd |only
qtlhot-0.5.2/qtlhot/man/lod.quantile.permutation.Rd |only
qtlhot-0.5.2/qtlhot/man/perm.Rd |only
qtlhot-0.5.2/qtlhot/man/pull.highlods.Rd |only
qtlhot-0.5.2/qtlhot/vignettes/.Rhistory |only
qtlhot-0.6.1/qtlhot/DESCRIPTION | 16
qtlhot-0.6.1/qtlhot/MD5 | 69 ++-
qtlhot-0.6.1/qtlhot/NAMESPACE | 61 ++-
qtlhot-0.6.1/qtlhot/R/big.R | 37 +-
qtlhot-0.6.1/qtlhot/R/cmst.R |only
qtlhot-0.6.1/qtlhot/R/diag.R | 84 +++-
qtlhot-0.6.1/qtlhot/R/highlod.R | 347 ++++++--------------
qtlhot-0.6.1/qtlhot/R/hotperm.R |only
qtlhot-0.6.1/qtlhot/R/hotsize.R |only
qtlhot-0.6.1/qtlhot/R/max.R |only
qtlhot-0.6.1/qtlhot/R/neqtl.R | 3
qtlhot-0.6.1/qtlhot/R/parallel.R | 44 +-
qtlhot-0.6.1/qtlhot/R/plotcmst.R |only
qtlhot-0.6.1/qtlhot/R/roc.R |only
qtlhot-0.6.1/qtlhot/R/rug.R | 2
qtlhot-0.6.1/qtlhot/R/simcmst.R |only
qtlhot-0.6.1/qtlhot/R/simhot.R |only
qtlhot-0.6.1/qtlhot/R/study.R | 164 +++------
qtlhot-0.6.1/qtlhot/R/utilcmst.R |only
qtlhot-0.6.1/qtlhot/R/utilhot.R |only
qtlhot-0.6.1/qtlhot/R/westwu.R | 148 ++++++--
qtlhot-0.6.1/qtlhot/data |only
qtlhot-0.6.1/qtlhot/inst/deprecated.R |only
qtlhot-0.6.1/qtlhot/inst/doc/cmst.Rnw |only
qtlhot-0.6.1/qtlhot/inst/doc/cmst.pdf |only
qtlhot-0.6.1/qtlhot/inst/doc/qtlhot.Rnw | 300 +++++------------
qtlhot-0.6.1/qtlhot/inst/doc/qtlhot.pdf |binary
qtlhot-0.6.1/qtlhot/inst/notes/cmst.txt |only
qtlhot-0.6.1/qtlhot/inst/notes/code.txt | 80 ++++
qtlhot-0.6.1/qtlhot/inst/notes/plot.R |only
qtlhot-0.6.1/qtlhot/man/CMSTtests.Rd |only
qtlhot-0.6.1/qtlhot/man/GetCandReg.Rd |only
qtlhot-0.6.1/qtlhot/man/GetCommonQtls.Rd |only
qtlhot-0.6.1/qtlhot/man/PrecTpFpMatrix.Rd |only
qtlhot-0.6.1/qtlhot/man/SimCrossCausal.Rd |only
qtlhot-0.6.1/qtlhot/man/filter.threshold.Rd | 15
qtlhot-0.6.1/qtlhot/man/highlod.Rd |only
qtlhot-0.6.1/qtlhot/man/hotperm.Rd |only
qtlhot-0.6.1/qtlhot/man/hotsize.Rd |only
qtlhot-0.6.1/qtlhot/man/sim.hotspot.Rd | 51 +-
qtlhot-0.6.1/qtlhot/man/westwu.Rd |only
qtlhot-0.6.1/qtlhot/vignettes/cmst.Rnw |only
qtlhot-0.6.1/qtlhot/vignettes/qtlhot.Rnw | 300 +++++------------
qtlhot-0.6.1/qtlhot/vignettes/savedperms.RData |binary
54 files changed, 806 insertions(+), 915 deletions(-)
Title: CorrSieve
Diff between corrsieve versions 1.6-6 dated 2012-02-19 and 1.6-7 dated 2012-09-18
Description: Statistical summary of Structure output.
Author: Michael G. Campana
Maintainer: Michael G. Campana
DESCRIPTION | 8 ++++----
MD5 | 3 ++-
inst |only
3 files changed, 6 insertions(+), 5 deletions(-)