Author: Spencer Graves, Sundar Dorai-Raj, and Romain Francois
Title: sos
Description: R related Search Engines
Diff between sos versions 1.1-3 dated 2009-09-07 and 1.1-5 dated 2009-10-01
DESCRIPTION | 8 - R/PackageSum2.R | 30 ++++ R/findFn.R | 22 +-- R/findFn2.R | 67 +++++---- R/writeFindFn2xls.R | 24 ++- inst/doc/RJournal.sty | 180 +++++++++++++------------ inst/doc/RSiteSearch.bbl | 82 +++++------ inst/doc/RSiteSearch.blg | 48 ++++++ inst/doc/RSiteSearch.pdf |binary inst/doc/RSiteSearch.tex | 4 inst/doc/RSiteSearch_body.tex | 292 +++++++++++++++++++++++++----------------- inst/doc/sos.pdf |binary man/PackageSum2.Rd | 19 ++ man/findFn.Rd | 8 - man/writeFindFn2xls.Rd | 12 + 15 files changed, 488 insertions(+), 308 deletions(-)
Author: Karl W Broman
Diff between qtl versions 1.13-7 dated 2009-09-10 and 1.14-2 dated 2009-10-01
Title: Tools for analyzing QTL experiments
Description: Analysis of experimental crosses to identify genes (called
quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
DESCRIPTION | 8 ++++----
R/qtlcart_io.R | 6 +++---
R/read.cross.mm.R | 5 ++---
inst/README.txt | 12 ++++++------
inst/STATUS.txt | 12 ++++++++++++
inst/TODO.txt | 2 ++
6 files changed, 29 insertions(+), 16 deletions(-)
Author: Jochen Einbeck, Ross Darnell and John Hinde
Title: Nonparametric maximum likelihood estimation for random effect
models
Description: Nonparametric maximum likelihood estimation or Gaussian
quadrature for overdispersed generalized linear models and
variance component models
Diff between npmlreg versions 0.43 dated 2007-09-04 and 0.44 dated 2009-10-01
npmlreg-0.43/npmlreg/inst/doc/npmlreg-v-008.eps |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v-008.pdf |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v-012.eps |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v-012.pdf |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v-015.eps |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v-015.pdf |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v-035.eps |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v-035.pdf |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v-042.eps |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v-042.pdf |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v.aux |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v.log |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v.tex |only npmlreg-0.43/npmlreg/inst/doc/npmlreg-v.toc |only npmlreg-0.44/npmlreg/DESCRIPTION | 33 +++++++++-------- npmlreg-0.44/npmlreg/R/alldist.R | 35 +++++++++++++----- npmlreg-0.44/npmlreg/R/allvc.R | 28 +++++++++----- npmlreg-0.44/npmlreg/data/fabric.rda |only npmlreg-0.44/npmlreg/inst/doc/npmlreg-v.Stex | 10 ++--- npmlreg-0.44/npmlreg/inst/doc/npmlreg-v.pdf |binary npmlreg-0.44/npmlreg/man/alldist.Rd | 46 ++++++++++++++++-------- npmlreg-0.44/npmlreg/man/fabric.Rd |only npmlreg-0.44/npmlreg/man/gqz.Rd | 2 - npmlreg-0.44/npmlreg/man/hosp.Rd | 2 - npmlreg-0.44/npmlreg/man/npmlreg.package.Rd | 8 ++-- npmlreg-0.44/npmlreg/man/plot.glmmNPML.Rd | 4 +- npmlreg-0.44/npmlreg/man/predict.glmmNPML.Rd | 4 +- npmlreg-0.44/npmlreg/man/summary.glmmNPML.Rd | 15 +++++++ 28 files changed, 122 insertions(+), 65 deletions(-)
Author: Andrew Gelman
Diff between mi versions 0.08-04.01 dated 2009-08-13 and 0.08-04.02 dated 2009-10-01
Title: Missing Data Imputation and Model Checking
Description: Missing-data imputation and model checking
DESCRIPTION | 10 ++++++----
man/write.mi.Rd | 2 +-
2 files changed, 7 insertions(+), 5 deletions(-)
Author: Sinnwell JP, Schaid DJ
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: A suite of S-PLUS/R routines for the analysis of
indirectly measured haplotypes. The statistical methods assume
that all subjects are unrelated and that haplotypes are
ambiguous (due to unknown linkage phase of the genetic
markers). The main functions are: haplo.em, haplo.glm,
haplo.score, haplo.power, and seqhap. Copyright: 2003 Mayo
Foundation for Medical Education and Research.
Diff between haplo.stats versions 1.4.3 dated 2009-04-28 and 1.4.4 dated 2009-10-01
DESCRIPTION | 8 ++++---- NEWS | 16 ---------------- man/geno1to2.Rd | 24 +++++++++--------------- man/get.hapPair.Rd | 21 ++++++++------------- man/glm.fit.nowarn.Rd | 12 ++---------- man/haplo.cc.Rd | 34 +++++++++++++++++++--------------- man/haplo.design.Rd | 33 ++++++++++++++++++++++++--------- man/haplo.em.Rd | 17 ++++++++--------- man/haplo.model.frame.Rd | 27 +++++++++++---------------- man/haplo.power.cc.Rd | 7 ++----- man/haplo.power.qt.Rd | 7 ++----- man/haplo.scan.Rd | 43 ++++++++++++++++++++++++++----------------- man/internalHaploStats.Rd | 38 +++++++++++--------------------------- man/louis.info.Rd | 32 ++++++++++---------------------- 14 files changed, 136 insertions(+), 183 deletions(-)
Author: Vincent Calcagno
Diff between glmulti versions 0.5-1 dated 2009-06-24 and 0.5-2 dated 2009-10-01
Title: GLM model selection and multimodel inference made easy
Description: Automated model selection for GLMs. Provides a wrapper for
glm and similar functions, automatically generating all
possible models (under constraints set by the user) with the
specified response and explanatory variables, and finding the
best models in terms of some Information Criterion (AIC, AICc
or BIC). Can handle very large numbers of candidate models.
Features a Genetic Algorithm to find the best models when an
exhaustive screening of the candidates is not feasible.
DESCRIPTION | 8 ++++----
R/glmulti.R | 9 +++++----
inst/java/glmulti.jar |binary
inst/java/glmulti/GLMModel.class |binary
inst/java/glmulti/ModelGenerator.class |binary
inst/java/glmulti/Resumator.class |binary
man/glmulti.Rd | 10 +---------
7 files changed, 10 insertions(+), 17 deletions(-)
Author: Michael A. Lawrence
Title: Easy analysis and visualization of factorial experiments.
Description: This package facilitates easy analysis of factorial
experiments, including purely within-Ss designs (a.k.a.
"repeated measures"), purely between-Ss designs, and mixed
within-and-between-Ss designs. The functions in this package
provide easy access to descriptive statistics, ANOVA,
permutation tests, and visualization of results.
Diff between ez versions 1.4 dated 2009-09-09 and 1.4.1 dated 2009-10-01
CHANGES | 3 +++ DESCRIPTION | 8 ++++---- R/ez-internal.R | 3 ++- 3 files changed, 9 insertions(+), 5 deletions(-)
Author: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.9.2.3 dated 2009-09-28 and 2.9.2.5 dated 2009-10-01
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
DESCRIPTION | 8 ++--
R/epicalc.R | 109 +++++++++++++++++++++++++++++++++++++++---------------------
man/use.rd | 3 +
3 files changed, 78 insertions(+), 42 deletions(-)
Author: Andy Bunn
Title: Dendrochronology Program Library in R
Description: This package contains functions for performing some
standard tree-ring analyses.
Diff between dplR versions 1.1.9.1 dated 2009-09-04 and 1.1.9.2 dated 2009-10-01
DESCRIPTION | 12 ++++++------ NAMESPACE | 5 ++++- R/ccf.series.rwl.R |only R/corr.rwl.seg.R |only R/corr.series.seg.R |only R/normalize.xdate.R |only R/plot.series.rwl.R |only R/qa.xdate.R |only man/ccf.series.rwl.Rd |only man/chron.Rd | 4 ++-- man/corr.rwl.seg.Rd |only man/corr.series.seg.Rd |only man/dplR-internal.Rd | 2 ++ man/series.rwl.plot.Rd |only man/skel.plot.Rd | 2 +- 15 files changed, 15 insertions(+), 10 deletions(-)
Author: Andrew Gelman
Diff between arm versions 1.2-9 dated 2009-04-29 and 1.2-9.01 dated 2009-10-01
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Description: R functions for processing lm, glm, mer and polr outputs.
DESCRIPTION | 10 ++++++----
man/coefplot.Rd | 2 +-
2 files changed, 7 insertions(+), 5 deletions(-)
Author: Martin Becker
Title: Pearson Distribution System
Description: Implementation of the Pearson distribution system,
including full support for the (d,p,q,r)-family of functions
for probability distributions and fitting via method of moments
and maximum likelihood method.
Diff between PearsonDS versions 0.90 dated 2009-09-19 and 0.91 dated 2009-10-01
PearsonDS-0.90/PearsonDS/config.guess |only PearsonDS-0.90/PearsonDS/config.sub |only PearsonDS-0.90/PearsonDS/install-sh |only PearsonDS-0.91/PearsonDS/DESCRIPTION | 8 ++--- PearsonDS-0.91/PearsonDS/cleanup |only PearsonDS-0.91/PearsonDS/cleanup.win |only PearsonDS-0.91/PearsonDS/configure | 54 +++++++++++++++++++++++++++------- PearsonDS-0.91/PearsonDS/configure.ac | 13 +++++++- PearsonDS-0.91/PearsonDS/inst/CHANGES | 7 ++++ 9 files changed, 66 insertions(+), 16 deletions(-)
Author: Kenneth Knoblauch and Laurence T. Maloney
Title: Maximum Likelihood Conjoint Measurement
Description: Conjoint measurement is a psychophysical procedure in
which stimulus pairs are presented that vary along 2 or more
dimensions and the observer is required to compare the stimuli
along one of them. This package contains functions to estimate
the contribution of the n scales to the judgment by a maximum
likelihood method under several hypotheses of how the
perceptual dimensions interact.
Diff between MLCM versions 0.0-3 dated 2009-09-22 and 0.0-5 dated 2009-10-01
DESCRIPTION | 8 ++++---- NAMESPACE | 3 ++- R/coef.mlcm.R | 17 +++++++++++++++-- R/logLik.mlcm.R | 9 ++++++--- R/mlcm.default.R | 7 +++++-- R/mlcm.formula.R |only R/print.summary.mlcm.R | 7 ++++++- R/summary.mlcm.R | 5 ++++- R/vcov.mlcm.R | 4 +++- inst/NEWS | 6 +++++- inst/ToDo | 2 +- man/mlcm.Rd | 30 ++++++++++++++++++++++++------ man/plot.mlcm.Rd | 3 ++- 13 files changed, 77 insertions(+), 24 deletions(-)
Author: Jouni Lehtonen
Diff between KFAS versions 0.4.3 dated 2009-09-28 and 0.4.4 dated 2009-10-01
Title: Multivariate Kalman filter and smoother, simulation smoother and
forecasting
Description: Package KFAS provides functions for fast Kalman filtering,
state and disturbance smoothing, forecasting and simulation of
multivariate time-variant state space models. All functions can
use exact diffuse initialisation when distributions of some or
all elements of initial state vector are unknown. Filtering,
state smoothing and simulation functions use sequential
processing algorithm, which is faster than standard approach,
and it also allows singularity of prediction error variance
matrix.
DESCRIPTION | 8 +++----
R/KFAS.R | 38 +++++++--------------------------
src/ks.f90 | 59 ++--------------------------------------------------
src/simsmoother.f90 | 44 +++++++++-----------------------------
4 files changed, 27 insertions(+), 122 deletions(-)
Author: David Ardia and Katharine Mullen
Title: Optimization by Differential Evolution
Description: This package provides the DEoptim function which performs
optimization by Differential Evolution.
Diff between DEoptim versions 1.3-3 dated 2009-05-14 and 2.0-0 dated 2009-10-01
DEoptim-1.3-3/DEoptim/demo |only DEoptim-2.0-0/DEoptim/COPYRIGHTS | 2 DEoptim-2.0-0/DEoptim/DESCRIPTION | 16 - DEoptim-2.0-0/DEoptim/NAMESPACE |only DEoptim-2.0-0/DEoptim/NEWS | 25 + DEoptim-2.0-0/DEoptim/R/DEoptim.R | 396 +++++++-------------------- DEoptim-2.0-0/DEoptim/R/methods.R |only DEoptim-2.0-0/DEoptim/R/zzz.R | 8 DEoptim-2.0-0/DEoptim/README | 11 DEoptim-2.0-0/DEoptim/THANKS | 3 DEoptim-2.0-0/DEoptim/inst/CITATION | 7 DEoptim-2.0-0/DEoptim/man/DEoptim-methods.Rd | 102 +++++- DEoptim-2.0-0/DEoptim/man/DEoptim.Rd | 159 ++++------ DEoptim-2.0-0/DEoptim/man/DEoptim.control.Rd |only DEoptim-2.0-0/DEoptim/src |only 15 files changed, 302 insertions(+), 427 deletions(-)