Title: Fusing R and OpenBugs and Beyond
Diff between rbugs versions 0.5-6 dated 2012-02-28 and 0.5-7 dated 2013-02-13
Description: Functions to prepare files needed for running BUGS in
batch-mode, and running BUGS from R. Support for Linux and
Windows systems with OpenBugs is emphasized.
Author: Jun Yan
Maintainer: Marcos Prates
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 9 ++++++---
R/genOpenBugsScript.R | 2 +-
data/rio.RData |only
inst/bugs/model/dengue.bug |only
man/rio.Rd |only
7 files changed, 15 insertions(+), 8 deletions(-)
Title: Tools for the analysis of air pollution data
Diff between openair versions 0.7-0 dated 2012-09-19 and 0.8-0 dated 2013-02-13
Description: Tools to analyse, interpret and understand air pollution
data. Data are typically hourly time series and both monitoring
data and dispersion model output can be analysed. Many
functions can also be applied to other data, including
meteorological and traffic data.
Author: David Carslaw and Karl Ropkins
Maintainer: David Carslaw
DESCRIPTION | 12
MD5 | 94 +++----
NAMESPACE | 1
NEWS | 57 ++++
R/TheilSen.R | 22 +
R/aqStats.R | 26 +-
R/calendarPlot.R | 30 --
R/checkPrep.R | 3
R/corPlot.R | 31 ++
R/date.breaks.R | 7
R/import.R | 37 +-
R/importAURN.R | 2
R/importKCL.R | 10
R/importTraj.R | 3
R/kernelExceed.R | 8
R/modStats.R | 102 ++++---
R/percentileRose.R | 131 ++++++++--
R/polarCluster.R | 11
R/polarPlot.R | 346 +++++++++++++++-----------
R/quickText.R | 2
R/scatterPlot.R | 647 +++++++++++++++++++++++++-------------------------
R/timeAverage.R | 18 +
R/timePlot.R | 194 ++++++--------
R/timeProp.R |only
R/timeVariation.R | 52 ++--
R/trajCluster.R | 18 +
R/trajPlot.R | 303 ++++++++++++++++++-----
R/utilities.R | 120 ++++++---
R/windRose.R | 28 +-
R/zzz.R | 2
data/mydata.RData |binary
man/TheilSen.Rd | 11
man/corPlot.Rd | 21 +
man/import.Rd | 31 +-
man/importKCL.Rd | 4
man/importTraj.Rd | 65 ++---
man/modStats.Rd | 66 ++---
man/percentileRose.Rd | 34 ++
man/polarCluster.Rd | 5
man/polarPlot.Rd | 58 +++-
man/rollingMean.Rd | 39 ++-
man/scatterPlot.Rd | 21 -
man/selectByDate.Rd | 10
man/timeProp.Rd |only
man/trajCluster.Rd | 17 +
man/trajPlot.Rd | 145 +++++++++--
man/windRose.Rd | 4
src/cluster.cpp | 1
src/rolling.cpp | 143 +++++++++--
49 files changed, 1918 insertions(+), 1074 deletions(-)
Title: Statistical tools for the interpretation of forensic DNA
mixtures
Diff between forensim versions 3.2.2 dated 2013-02-12 and 4.0 dated 2013-02-13
Description: Statistical methods and simulation tools for the
interpretation of forensic DNA mixtures
Author: Hinda Haned
Maintainer: Hinda Haned
forensim-3.2.2/forensim/src/recurs.c |only
forensim-4.0/forensim/DESCRIPTION | 12 -
forensim-4.0/forensim/MD5 | 13 +-
forensim-4.0/forensim/R/LR.R | 198 ++++----------------------------
forensim-4.0/forensim/R/LRmixTK.R | 145 ++++++++++++++++++-----
forensim-4.0/forensim/man/LR.Rd | 10 -
forensim-4.0/forensim/man/likEvid.Rd | 12 +
forensim-4.0/forensim/src/auxilary.c |only
forensim-4.0/forensim/src/recursFinal.c |only
9 files changed, 167 insertions(+), 223 deletions(-)
Title: Amelia II: A Program for Missing Data
Diff between Amelia versions 1.6.4 dated 2012-12-18 and 1.7 dated 2013-02-13
Description: Amelia II "multiply imputes" missing data in a single
cross-section (such as a survey), from a time series (like
variables collected for each year in a country), or from a
time-series-cross-sectional data set (such as collected by
years for each of several countries). Amelia II implements our
bootstrapping-based algorithm that gives essentially the same
answers as the standard IP or EMis approaches, is usually
considerably faster than existing approaches and can handle
many more variables. Unlike Amelia I and other statistically
rigorous imputation software, it virtually never crashes (but
please let us know if you find to the contrary!). The program
also generalizes existing approaches by allowing for trends in
time series across observations within a cross-sectional unit,
as well as priors that allow experts to incorporate beliefs
they have about the values of missing cells in their data.
Amelia II also includes useful diagnostics of the fit of
multiple imputation models. The program works from the R
command line or via a graphical user interface that does not
require users to know R.
Author: James Honaker
Maintainer: Matthew Blackwell
Amelia-1.6.4/Amelia/ChangeLog |only
Amelia-1.6.4/Amelia/INDEX |only
Amelia-1.6.4/Amelia/inst/doc/Makefile |only
Amelia-1.6.4/Amelia/inst/doc/amelia.bib |only
Amelia-1.6.4/Amelia/inst/doc/context-menu.png |only
Amelia-1.6.4/Amelia/inst/doc/diag.png |only
Amelia-1.6.4/Amelia/inst/doc/distpri.png |only
Amelia-1.6.4/Amelia/inst/doc/import.png |only
Amelia-1.6.4/Amelia/inst/doc/index.shtml |only
Amelia-1.6.4/Amelia/inst/doc/main.png |only
Amelia-1.6.4/Amelia/inst/doc/numopts.png |only
Amelia-1.6.4/Amelia/inst/doc/options.png |only
Amelia-1.6.4/Amelia/inst/doc/output-log.png |only
Amelia-1.6.4/Amelia/inst/doc/rangepri.png |only
Amelia-1.6.4/Amelia/inst/doc/splash.png |only
Amelia-1.6.4/Amelia/inst/doc/utf8.def |only
Amelia-1.7/Amelia/DESCRIPTION | 12
Amelia-1.7/Amelia/MD5 | 59 -
Amelia-1.7/Amelia/NAMESPACE | 2
Amelia-1.7/Amelia/NEWS | 7
Amelia-1.7/Amelia/R/ameliagui.r | 26
Amelia-1.7/Amelia/R/diag.r | 107 +--
Amelia-1.7/Amelia/R/emb.r | 840 ++++----------------------
Amelia-1.7/Amelia/R/prep.r | 108 +--
Amelia-1.7/Amelia/README | 6
Amelia-1.7/Amelia/README.md |only
Amelia-1.7/Amelia/inst/doc/amelia.Rnw | 495 ++++++++-------
Amelia-1.7/Amelia/inst/doc/amelia.pdf |binary
Amelia-1.7/Amelia/man/amelia.Rd | 30
Amelia-1.7/Amelia/src |only
Amelia-1.7/Amelia/vignettes |only
31 files changed, 609 insertions(+), 1083 deletions(-)
Title: Bivariate Copula Based Regression Models
Diff between CopulaRegression versions 0.1-1 dated 2013-01-22 and 0.1-2 dated 2013-02-13
More information about CopulaRegression at CRAN
Description: This R-packages presents a bivariate, copula-based model
for the joint distribution of a pair of continuous and discrete
random variables. The two marginal random variables are modeled
via generalized linear models, and their joint distribution
(represented by a parametric copula family) is estimated using
maximum-likelihood techniques.
Author: Nicole Kraemer, Daniel Silvestrini
Maintainer: Nicole Kraemer
DESCRIPTION | 8 +--
MD5 | 14 +++---
R/copreg.R | 92 +++++++++++++++++++++++-----------------
R/vuongtest.R | 9 +++
inst/ChangeLog | 7 ++-
man/CopulaRegression-package.Rd | 4 -
man/copreg.Rd | 4 -
man/vuongtest.Rd | 28 ++++++++++--
8 files changed, 105 insertions(+), 61 deletions(-)
Permanent link
Title: R interface to CPLEX
Diff between Rcplex versions 0.3-0 dated 2011-05-06 and 0.3-1 dated 2013-02-13
Description: R interface to CPLEX solvers for linear, quadratic, and
(linear and quadratic) mixed integer programs. Support for
quadratically constrained programming is available. A working
installation of CPLEX is required for usage of the Rcplex
package. See the file "INSTALL" for details on how to install
the Rcplex package in Linux/Unix-like systems and Windows
systems. Support for sparse matrices is provided by an S3-style
class "simple_triplet_matrix" from package slam and by objects
from the Matrix package class hierarchy.
Author: Hector Corrada Bravo, with contributions from Stefan Theussl
and Kurt Hornik
Maintainer: Hector Corrada Bravo
DESCRIPTION | 8 ++++----
MD5 |only
R/CPX_matrix.R | 2 +-
R/Rcplex.R | 20 ++++++++++----------
4 files changed, 15 insertions(+), 15 deletions(-)
Title: Fractional Factorial designs with 2-level factors
Diff between FrF2 versions 1.6-3 dated 2013-02-12 and 1.6-4 dated 2013-02-13
Description: This package creates regular and non-regular Fractional
Factorial designs. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias). The
package is still under development. While much of the intended
functionality is already available, some changes and
improvements are still to be expected. Suggestions are welcome.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 6 ++--
MD5 | 28 ++++++++++----------
R/aaa.R | 7 ++++-
R/estimable2fis.R | 9 +++---
R/sysdata.rda |binary
R/utilcat.R | 2 -
inst/NEWS | 5 +++
man/blockpick.Rd | 4 ++
man/utilitiesCat.Rd | 3 ++
tests/FrF2test.Rout.save | 23 ++++++-----------
tests/addcentertest.Rout.save | 23 ++++++-----------
tests/foldtest.Rout.save | 23 ++++++-----------
tests/generators.from.designtest.Rout.save | 39 ++++++++++++-----------------
tests/generators.summary.test.Rout.save | 23 ++++++-----------
tests/pbtest.Rout.save | 23 ++++++-----------
15 files changed, 102 insertions(+), 116 deletions(-)
Title: The Fisher-EM algorithm
Diff between FisherEM versions 1.2 dated 2012-07-12 and 1.3 dated 2013-02-13
Description: The FisherEM package provides an efficient algorithm for
the unsupervised classification of high-dimensional data. This
FisherEM algorithm models and clusters the data in a
discriminative and low-dimensional latent subspace. It also
provides a low-dimensional representation of the clustered
data.
Author: Charles Bouveyron and Camille Brunet
Maintainer: Camille Brunet
DESCRIPTION | 10 +++---
MD5 | 37 ++++++++++++-----------
NAMESPACE | 2 -
R/estep.R | 5 +--
R/estep_par.R |only
R/evalEM.R | 6 ++-
R/fem.R | 49 ++++++++++++++++++++----------
R/fem.loglik.R | 1
R/fem_main.R | 9 +++--
R/fem_sparse.R | 5 +--
R/fstep.GramSc.R | 5 +--
R/fstep.fisher.R | 3 -
R/fstep.qiao.R | 9 +++--
R/fstep.sparse.R | 8 ++---
R/mstep.R | 1
R/plot.fem.R | 32 ++++++++++++++++++--
demo/FisherEM.r | 87 ++++++++++++++++++++++++++-----------------------------
man/evalEM.Rd | 4 +-
man/fem.Rd | 12 ++++++-
man/plot.fem.Rd | 4 +-
20 files changed, 170 insertions(+), 119 deletions(-)
Title: Flexible Mixture Modeling
Diff between flexmix versions 2.3-9 dated 2013-02-05 and 2.3-10 dated 2013-02-13
Description: FlexMix implements a general framework for finite mixtures
of regression models using the EM algorithm. FlexMix provides
the E-step and all data handling, while the M-step can be
supplied by the user to easily define new models. Existing
drivers implement mixtures of standard linear models,
generalized linear models and model-based clustering.
Author: Bettina Gruen and Friedrich Leisch
Maintainer: Bettina Gruen
DESCRIPTION | 10 +++++-----
MD5 | 36 ++++++++++++++++++------------------
R/allClasses.R | 6 +++---
R/condlogit.R | 4 ++--
R/flexmix.R | 5 +++--
R/flxmcmvpois.R | 3 +--
R/glmFix.R | 6 +++---
R/lmm.R | 1 -
R/mgcv.R | 4 ++--
R/models.R | 6 +-----
R/stepFlexmix.R | 32 ++++++++++++++++----------------
R/utils.R | 15 +--------------
inst/NEWS.Rd | 5 +++++
inst/doc/bootstrapping.pdf |binary
inst/doc/flexmix-intro.pdf |binary
inst/doc/mixture-regressions.pdf |binary
inst/doc/regression-examples.pdf |binary
man/FLXMRlmer.Rd | 4 ++--
man/stepFlexmix.Rd | 8 ++------
19 files changed, 64 insertions(+), 81 deletions(-)
Title: Planning and Analyzing Dose Finding experiments
Diff between DoseFinding versions 0.9-3 dated 2013-01-29 and 0.9-4 dated 2013-02-13
Description: The DoseFinding package provides functions for the design
and analysis of dose-finding experiments (for example
pharmaceutical Phase II clinical trials). It provides functions
for: multiple contrast tests, fitting non-linear dose-response
models, calculating optimal designs and an implementation of
the MCPMod methodology.
Author: Bjoern Bornkamp, Jose Pinheiro, Frank Bretz
Maintainer: Bjoern Bornkamp
ChangeLog | 12 ++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++------------
R/MCPMod.R | 3 ++-
R/MCTtest.R | 6 ++++++
R/Mods.R | 39 ++++++++++++++++++++++++++++++---------
R/bFitMod.R | 25 ++++++++++++++++++-------
R/fitMod.R | 4 ----
R/powMCT.R | 2 +-
man/DoseFinding-package.Rd | 4 ++--
man/MCPMod.Rd | 8 ++++++--
tests/testssamplMod.R | 28 ++++++++++++++++++++++++++++
todo.txt | 4 ++++
13 files changed, 125 insertions(+), 42 deletions(-)
Title: Stepwise covariate selection for the Fine & Gray competing risks
regression model
Diff between crrstep versions 2013-01.21 dated 2013-01-27 and 2013-02.12 dated 2013-02-13
Description: Performs forward and backwards stepwise regression for the
Proportional subdistribution hazards model in competing risks
(Fine & Gray 1999). Procedure uses AIC, BIC and BICcr as
selection criteria. BICcr has a penalty of k = log(n*), where
n* is the number of primary events.
Author: Ravi Varadhan & Deborah Kuk
Maintainer: Ravi Varadhan
crrstep-2013-01.21/crrstep/R/crrfast.r |only
crrstep-2013-02.12/crrstep/DESCRIPTION | 8 ++++----
crrstep-2013-02.12/crrstep/MD5 | 5 ++---
crrstep-2013-02.12/crrstep/R/crrstep.r | 20 ++++++++++----------
4 files changed, 16 insertions(+), 17 deletions(-)
Title: This package contains an implementation of continuous convex
piecewise (linear) functions (quadratic coming soon
Diff between ConConPiWiFun versions 0.2 dated 2013-01-22 and 0.3 dated 2013-02-13
Description: Continuous convex piecewise linear (ccpl) resp. quadratic
(ccpq) functions can be implemented with sorted breakpoints and
slopes. This includes functions that are ccpl (resp. ccpq) on a
convex set (i.e. an interval or a point) and infinite out of
the domain. These functions can be very useful for a large
class of optimisation problems. Efficient manipulation (such as
log(N) insertion) of such data structure is obtained with map
standard template library of C++ (that hides balanced trees).
This package is a wrapper on such a class based on Rcpp
modules.
Author: Robin Girard
Maintainer: Robin Girard
ConConPiWiFun-0.2/ConConPiWiFun/src/OptimMargInt.cc |only
ConConPiWiFun-0.3/ConConPiWiFun/DESCRIPTION | 6 -
ConConPiWiFun-0.3/ConConPiWiFun/MD5 | 13 +-
ConConPiWiFun-0.3/ConConPiWiFun/inst |only
ConConPiWiFun-0.3/ConConPiWiFun/man/ConConPiWiFun-package.Rd | 66 -----------
ConConPiWiFun-0.3/ConConPiWiFun/man/cplfunction.Rd |only
ConConPiWiFun-0.3/ConConPiWiFun/man/cplfunctionvec.Rd |only
ConConPiWiFun-0.3/ConConPiWiFun/src/Makevars | 2
ConConPiWiFun-0.3/ConConPiWiFun/src/Makevars.win | 7 -
ConConPiWiFun-0.3/ConConPiWiFun/src/cplfunction.cc |only
10 files changed, 21 insertions(+), 73 deletions(-)
Title: Subdistribution Analysis of Competing Risks
Diff between cmprsk versions 2.2-3 dated 2012-12-11 and 2.2-4 dated 2013-02-13
Description: Estimation, testing and regression modeling of
subdistribution functions in competing risks, as described in
Gray (1988), A class of K-sample tests for comparing the
cumulative incidence of a competing risk, Ann. Stat.
16:1141-1154, and Fine JP and Gray RJ (1999), A proportional
hazards model for the subdistribution of a competing risk,
JASA, 94:496-509.
Author: Bob Gray
Maintainer: Bob Gray
DESCRIPTION | 12 ++++++------
MD5 | 10 +++++-----
R/cmprsk.R | 46 ++++++++++++++++++++++++++++++----------------
man/crr.Rd | 13 ++++++++++++-
src/crr.f | 36 +++++++++++++++++++++---------------
tests/test.Rout.save | 45 ++++++++++++++++++++++++---------------------
6 files changed, 98 insertions(+), 64 deletions(-)
Title: Additive and multiplicative effects modeling of networks and
relational data
Diff between amen versions 0.90 dated 2012-12-19 and 0.91 dated 2013-02-13
Description: This package computes Bayesian estimates for additive and
multiplicative effects (AME) models for networks and relational
data. The basic model includes regression terms, the covariance
structure of the social relations model (Warner, Kenny and
Stoto (1979), Wong (1982)), and multiplicative factor effects
(Hoff(2009)). Four different link functions accommodate
different relational data structures, including binary/network
data (bin), normal relational data (nrm), ordinal relational
data (ord) and data from fixed-rank nomination schemes (frn).
Development of this software was supported in part by NICHD
grant R01HD067509-01A1.
Author: Peter Hoff, Bailey Fosdick, Alex Volfovsky, Kate Stovel
Maintainer: Peter D. Hoff
DESCRIPTION | 8 ++++----
MD5 | 32 ++++++++++++++++----------------
R/ame_bin.R | 7 ++++++-
R/ame_cbin.R | 8 +++++++-
R/ame_frn.R | 8 +++++++-
R/ame_nrm.R | 19 ++++++++-----------
R/ame_ord.R | 6 ++++--
R/ame_rrl.R | 10 +++++-----
R/probit_start.R | 8 +++-----
man/ame_bin.Rd | 2 +-
man/ame_cbin.Rd | 2 +-
man/ame_frn.Rd | 2 +-
man/ame_nrm.Rd | 2 +-
man/ame_ord.Rd | 2 +-
man/ame_rrl.Rd | 2 +-
man/amen-package.Rd | 4 ++--
man/probit_start.Rd | 34 ++++++++++++----------------------
17 files changed, 80 insertions(+), 76 deletions(-)