Author: Achim Zeileis, Gabor Grothendieck
Title: Z's ordered observations
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Diff between zoo versions 1.5-8 dated 2009-07-22 and 1.6-0 dated 2009-11-17
zoo-1.5-8/zoo/man/as.Date.ts.Rd |only zoo-1.6-0/zoo/COPYRIGHTS | 2 zoo-1.6-0/zoo/DESCRIPTION | 12 zoo-1.6-0/zoo/NAMESPACE | 6 zoo-1.6-0/zoo/NEWS | 28 zoo-1.6-0/zoo/R/aggregate.zoo.R | 4 zoo-1.6-0/zoo/R/as.Date.ts.R | 4 zoo-1.6-0/zoo/R/index.R | 2 zoo-1.6-0/zoo/R/merge.zoo.R | 27 zoo-1.6-0/zoo/R/na.locf.R | 2 zoo-1.6-0/zoo/R/plot.zoo.R | 60 zoo-1.6-0/zoo/R/read.zoo.R | 63 zoo-1.6-0/zoo/R/rollapply.R | 12 zoo-1.6-0/zoo/R/window.zoo.R | 20 zoo-1.6-0/zoo/R/xyplot.zoo.R | 8 zoo-1.6-0/zoo/R/yearmon.R | 6 zoo-1.6-0/zoo/R/yearqtr.R | 8 zoo-1.6-0/zoo/R/zoo.R | 13 zoo-1.6-0/zoo/R/zzz.R |only zoo-1.6-0/zoo/THANKS | 3 zoo-1.6-0/zoo/WISHLIST | 4 zoo-1.6-0/zoo/demo |only zoo-1.6-0/zoo/inst/doc/zoo-faq.R |only zoo-1.6-0/zoo/inst/doc/zoo-faq.Rnw | 109 + zoo-1.6-0/zoo/inst/doc/zoo-faq.pdf | 1532 +++++++++++---------- zoo-1.6-0/zoo/inst/doc/zoo-quickref.Rnw | 12 zoo-1.6-0/zoo/inst/doc/zoo-quickref.pdf | 569 ++++--- zoo-1.6-0/zoo/inst/doc/zoo.Rnw | 14 zoo-1.6-0/zoo/inst/doc/zoo.pdf | 2294 ++++++++++++++++---------------- zoo-1.6-0/zoo/man/aggregate.zoo.Rd | 10 zoo-1.6-0/zoo/man/as.zoo.Rd | 8 zoo-1.6-0/zoo/man/index.Rd | 4 zoo-1.6-0/zoo/man/lag.zoo.Rd | 2 zoo-1.6-0/zoo/man/merge.zoo.Rd | 18 zoo-1.6-0/zoo/man/na.locf.Rd | 9 zoo-1.6-0/zoo/man/plot.zoo.Rd | 57 zoo-1.6-0/zoo/man/read.zoo.Rd | 48 zoo-1.6-0/zoo/man/window.zoo.Rd | 13 zoo-1.6-0/zoo/man/xyplot.zoo.Rd | 2 zoo-1.6-0/zoo/man/yearmon.Rd | 2 zoo-1.6-0/zoo/man/zoo.Rd | 51 zoo-1.6-0/zoo/man/zooreg.Rd | 28 42 files changed, 2835 insertions(+), 2231 deletions(-)
Author: Thomas Lumley, Achim Zeileis
Title: Robust Covariance Matrix Estimators
Description: Model-robust standard error estimators for
cross-sectional, time series and longitudinal data.
Diff between sandwich versions 2.2-1 dated 2009-02-05 and 2.2-2 dated 2009-11-17
COPYRIGHTS | 2 +- DESCRIPTION | 12 +++++++----- NEWS | 5 +++++ R/estfun.R | 6 ++++-- inst/CITATION | 2 +- inst/doc/sandwich-OOP.pdf |binary inst/doc/sandwich.pdf |binary man/vcovHAC.Rd | 2 +- man/vcovHC.Rd | 2 +- man/weightsLumley.Rd | 2 +- 10 files changed, 21 insertions(+), 12 deletions(-)
Author: Torsten Hothorn, Achim Zeileis, Giovanni Millo, David Mitchell
Title: Testing Linear Regression Models
Description: A collection of tests, data sets and examples for
diagnostic checking in linear regression models.
Diff between lmtest versions 0.9-24 dated 2009-05-28 and 0.9-25 dated 2009-11-17
DESCRIPTION | 8 ++++---- NEWS | 5 +++++ inst/doc/lmtest-intro.pdf |binary man/Mandible.Rd | 4 ++-- man/USDistLag.Rd | 2 +- man/bondyield.Rd | 4 ++-- man/coeftest.Rd | 2 +- man/currencysubstitution.Rd | 6 +++--- man/hmctest.Rd | 2 +- man/jocci.Rd | 2 +- man/lrtest.Rd | 2 +- man/petest.Rd | 13 +++++++++++++ man/waldtest.Rd | 6 +++--- 13 files changed, 37 insertions(+), 19 deletions(-)
Author: Achim Zeileis, Ajay Shah, Ila Patnaik
Title: Exchange Rate Regime Analysis
Description: Exchange rate regression and structural change tools for
estimating, testing, dating, and monitoring (de facto) exchange
rate regimes.
Diff between fxregime versions 0.3-0 dated 2009-08-28 and 0.3-1 dated 2009-11-17
DESCRIPTION | 8 ++++---- NEWS | 5 +++++ inst/doc/CNY.pdf |binary inst/doc/INR.pdf |binary man/confint.fxregimes.Rd | 2 +- man/fxreturns.Rd | 2 +- man/refit.Rd | 12 ++++++------ 7 files changed, 17 insertions(+), 12 deletions(-)
Author: Josef Leydold and Wolfgang H\"ormann
Title: R interface to the UNU.RAN random variate generators
Description: Interface to the UNU.RAN library for Universal Non-Uniform
RANdom variate generators
Diff between Runuran versions 0.10.1 dated 2009-08-06 and 0.11.0 dated 2009-11-17
Runuran-0.10.1/Runuran/man/r-method.Rd |only Runuran-0.10.1/Runuran/man/unuran.distr.deprecated.Rd |only Runuran-0.10.1/Runuran/man/uqhinv.Rd |only Runuran-0.10.1/Runuran/man/urhitro.Rd |only Runuran-0.10.1/Runuran/man/urtdr.Rd |only Runuran-0.10.1/Runuran/src/Runuran_source.h |only Runuran-0.11.0/Runuran/DESCRIPTION | 15 Runuran-0.11.0/Runuran/NAMESPACE | 8 Runuran-0.11.0/Runuran/NEWS | 55 Runuran-0.11.0/Runuran/R/Runuran.R | 19 Runuran-0.11.0/Runuran/R/deprecated.R | 62 Runuran-0.11.0/Runuran/R/distributions.R | 320 Runuran-0.11.0/Runuran/R/universal.R | 109 Runuran-0.11.0/Runuran/R/unuran_cmv.R | 6 Runuran-0.11.0/Runuran/R/unuran_cont.R | 7 Runuran-0.11.0/Runuran/R/unuran_discr.R | 6 Runuran-0.11.0/Runuran/R/unuran_distr.R | 3 Runuran-0.11.0/Runuran/configure | 18 Runuran-0.11.0/Runuran/configure.ac | 13 Runuran-0.11.0/Runuran/inst/doc/Runuran.Rnw | 4 Runuran-0.11.0/Runuran/inst/doc/Runuran.pdf | 3445 +++++----- Runuran-0.11.0/Runuran/inst/doc/arvag.bib | 2 Runuran-0.11.0/Runuran/inst/doc/src/advanced.Rnw | 3 Runuran-0.11.0/Runuran/inst/doc/src/arvag.Rnw | 73 Runuran-0.11.0/Runuran/inst/doc/src/distributions.Rnw | 74 Runuran-0.11.0/Runuran/inst/doc/src/glossary.tex | 26 Runuran-0.11.0/Runuran/inst/doc/src/intro.Rnw | 21 Runuran-0.11.0/Runuran/inst/doc/src/specialgenerators.Rnw |only Runuran-0.11.0/Runuran/inst/doc/src/tab-distributions.tex | 64 Runuran-0.11.0/Runuran/inst/doc/src/tab-generators.tex |only Runuran-0.11.0/Runuran/inst/doc/src/version.tex | 2 Runuran-0.11.0/Runuran/man/Runuran-package.Rd | 202 Runuran-0.11.0/Runuran/man/Runuran.distributions.Rd |only Runuran-0.11.0/Runuran/man/Runuran.special.generators.Rd |only Runuran-0.11.0/Runuran/man/ars.new.Rd | 52 Runuran-0.11.0/Runuran/man/dari.new.Rd | 40 Runuran-0.11.0/Runuran/man/dau.new.Rd | 34 Runuran-0.11.0/Runuran/man/dgt.new.Rd | 33 Runuran-0.11.0/Runuran/man/hitro.new.Rd | 11 Runuran-0.11.0/Runuran/man/itdr.new.Rd | 50 Runuran-0.11.0/Runuran/man/pinv.new.Rd | 50 Runuran-0.11.0/Runuran/man/srou.new.Rd | 44 Runuran-0.11.0/Runuran/man/tdr.new.Rd | 55 Runuran-0.11.0/Runuran/man/ud.Rd |only Runuran-0.11.0/Runuran/man/udbeta.Rd |only Runuran-0.11.0/Runuran/man/udbinom.Rd |only Runuran-0.11.0/Runuran/man/udcauchy.Rd |only Runuran-0.11.0/Runuran/man/udchi.Rd |only Runuran-0.11.0/Runuran/man/udchisq.Rd |only Runuran-0.11.0/Runuran/man/udexp.Rd |only Runuran-0.11.0/Runuran/man/udf.Rd |only Runuran-0.11.0/Runuran/man/udfrechet.Rd |only Runuran-0.11.0/Runuran/man/udgamma.Rd |only Runuran-0.11.0/Runuran/man/udgeom.Rd |only Runuran-0.11.0/Runuran/man/udghyp.Rd |only Runuran-0.11.0/Runuran/man/udgig.Rd |only Runuran-0.11.0/Runuran/man/udgumbel.Rd |only Runuran-0.11.0/Runuran/man/udhyper.Rd |only Runuran-0.11.0/Runuran/man/udhyperbolic.Rd |only Runuran-0.11.0/Runuran/man/udig.Rd |only Runuran-0.11.0/Runuran/man/udlaplace.Rd |only Runuran-0.11.0/Runuran/man/udlnorm.Rd |only Runuran-0.11.0/Runuran/man/udlogarithmic.Rd |only Runuran-0.11.0/Runuran/man/udlogis.Rd |only Runuran-0.11.0/Runuran/man/udlomax.Rd |only Runuran-0.11.0/Runuran/man/udnbinom.Rd |only Runuran-0.11.0/Runuran/man/udnorm.Rd |only Runuran-0.11.0/Runuran/man/udpareto.Rd |only Runuran-0.11.0/Runuran/man/udpois.Rd |only Runuran-0.11.0/Runuran/man/udpowerexp.Rd |only Runuran-0.11.0/Runuran/man/udrayleigh.Rd |only Runuran-0.11.0/Runuran/man/udslash.Rd |only Runuran-0.11.0/Runuran/man/udt.Rd |only Runuran-0.11.0/Runuran/man/udweibull.Rd |only Runuran-0.11.0/Runuran/man/unuran-class.Rd | 10 Runuran-0.11.0/Runuran/man/unuran.cmv-class.Rd | 4 Runuran-0.11.0/Runuran/man/unuran.cmv.new.Rd | 8 Runuran-0.11.0/Runuran/man/unuran.cont-class.Rd | 4 Runuran-0.11.0/Runuran/man/unuran.cont.new.Rd | 15 Runuran-0.11.0/Runuran/man/unuran.details.Rd | 4 Runuran-0.11.0/Runuran/man/unuran.discr-class.Rd | 4 Runuran-0.11.0/Runuran/man/unuran.discr.new.Rd | 7 Runuran-0.11.0/Runuran/man/unuran.distr-class.Rd | 4 Runuran-0.11.0/Runuran/man/unuran.new.Rd | 2 Runuran-0.11.0/Runuran/man/unuran.packed-methods.Rd | 2 Runuran-0.11.0/Runuran/man/uq.Rd | 4 Runuran-0.11.0/Runuran/man/ur.Rd | 3 Runuran-0.11.0/Runuran/man/urbeta.Rd | 15 Runuran-0.11.0/Runuran/man/urbinom.Rd | 14 Runuran-0.11.0/Runuran/man/urburr.Rd | 11 Runuran-0.11.0/Runuran/man/urcauchy.Rd | 12 Runuran-0.11.0/Runuran/man/urchi.Rd | 11 Runuran-0.11.0/Runuran/man/urchisq.Rd | 12 Runuran-0.11.0/Runuran/man/urdgt.Rd | 5 Runuran-0.11.0/Runuran/man/urexp.Rd | 11 Runuran-0.11.0/Runuran/man/urextremeI.Rd | 13 Runuran-0.11.0/Runuran/man/urextremeII.Rd | 15 Runuran-0.11.0/Runuran/man/urf.Rd | 11 Runuran-0.11.0/Runuran/man/urgamma.Rd | 13 Runuran-0.11.0/Runuran/man/urgeom.Rd | 11 Runuran-0.11.0/Runuran/man/urgig.Rd | 11 Runuran-0.11.0/Runuran/man/urhyper.Rd | 13 Runuran-0.11.0/Runuran/man/urhyperbolic.Rd | 11 Runuran-0.11.0/Runuran/man/urlaplace.Rd | 11 Runuran-0.11.0/Runuran/man/urlnorm.Rd | 7 Runuran-0.11.0/Runuran/man/urlogarithmic.Rd | 10 Runuran-0.11.0/Runuran/man/urlogis.Rd | 12 Runuran-0.11.0/Runuran/man/urlomax.Rd | 11 Runuran-0.11.0/Runuran/man/urnbinom.Rd | 11 Runuran-0.11.0/Runuran/man/urnorm.Rd | 13 Runuran-0.11.0/Runuran/man/urpareto.Rd | 11 Runuran-0.11.0/Runuran/man/urplanck.Rd | 11 Runuran-0.11.0/Runuran/man/urpois.Rd | 13 Runuran-0.11.0/Runuran/man/urpowerexp.Rd | 11 Runuran-0.11.0/Runuran/man/urrayleigh.Rd | 11 Runuran-0.11.0/Runuran/man/urt.Rd | 7 Runuran-0.11.0/Runuran/man/urtriang.Rd | 15 Runuran-0.11.0/Runuran/man/urweibull.Rd | 12 Runuran-0.11.0/Runuran/man/vnrou.new.Rd | 10 Runuran-0.11.0/Runuran/src/Makevars.in | 4 Runuran-0.11.0/Runuran/src/README | 2 Runuran-0.11.0/Runuran/src/Runuran.c | 116 Runuran-0.11.0/Runuran/src/Runuran.h | 73 Runuran-0.11.0/Runuran/src/Runuran_distr.c | 195 Runuran-0.11.0/Runuran/src/Runuran_pinv.c | 4 Runuran-0.11.0/Runuran/src/config.h.in | 10 Runuran-0.11.0/Runuran/src/config.w32 | 12 Runuran-0.11.0/Runuran/src/distributions.c |only Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_ghyp.c |only Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_gig.c | 48 Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_gig2.c |only Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_hyperbolic.c |only Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_ig.c |only Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_lognormal.c | 24 Runuran-0.11.0/Runuran/src/unuran-src/distributions/c_slash.c | 14 Runuran-0.11.0/Runuran/src/unuran-src/distributions/unur_distributions.h | 4 Runuran-0.11.0/Runuran/src/unuran-src/distributions/unur_stddistr.h | 4 Runuran-0.11.0/Runuran/src/unuran-src/methods/ars.c | 36 Runuran-0.11.0/Runuran/src/unuran-src/methods/dari.c | 2 Runuran-0.11.0/Runuran/src/unuran-src/methods/hinv.c | 2 Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv.c | 919 -- Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv.h | 5 Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_debug.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_info.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_init.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_newset.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_newton.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_regula.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_sample.ch |only Runuran-0.11.0/Runuran/src/unuran-src/methods/ninv_struct.h | 6 Runuran-0.11.0/Runuran/src/unuran-src/methods/norta.c | 4 Runuran-0.11.0/Runuran/src/unuran-src/methods/pinv_prep.ch | 9 Runuran-0.11.0/Runuran/src/unuran-src/methods/pinv_sample.ch | 2 Runuran-0.11.0/Runuran/src/unuran-src/parser/parser.h | 2 Runuran-0.11.0/Runuran/src/unuran-src/parser/stringparser_lists.ch | 34 Runuran-0.11.0/Runuran/src/unuran-src/specfunct/besselK.c |only Runuran-0.11.0/Runuran/src/unuran-src/specfunct/unur_specfunct_source.h | 5 Runuran-0.11.0/Runuran/src/unuran-src/tests/inverror.c | 12 Runuran-0.11.0/Runuran/src/unuran-src/tests/timing.c | 127 Runuran-0.11.0/Runuran/src/unuran-src/tests/unuran_tests.h | 16 Runuran-0.11.0/Runuran/src/unuran-src/unur_Rmath.h |only Runuran-0.11.0/Runuran/src/unuran-src/unuran.h | 15 Runuran-0.11.0/Runuran/src/unuran-src/utils/stream.c | 7 Runuran-0.11.0/Runuran/src/unuran-src/utils/unur_fp.c | 24 Runuran-0.11.0/Runuran/tests/test_deprecated.R | 74 Runuran-0.11.0/Runuran/tests/test_distributions_cont.R | 8 Runuran-0.11.0/Runuran/tests/test_distributions_discr.R | 13 Runuran-0.11.0/Runuran/tests/test_routines.R | 54 Runuran-0.11.0/Runuran/tests/test_ud.R |only 169 files changed, 3895 insertions(+), 3353 deletions(-)
Author: Josef Leydold
Diff between rstream versions 1.2.3 dated 2009-01-08 and 1.2.4 dated 2009-11-17
Title: Streams of random numbers
Description: Unified object oriented interface for multiple independent
streams of random numbers from different sources.
DESCRIPTION | 11 +++++++----
NEWS | 4 ++++
man/rstream-package.Rd | 4 ++--
man/rstream.RNG.Rd | 2 +-
man/rstream.lecuyer-class.Rd | 2 +-
man/rstream.mrg32k3a-class.Rd | 2 +-
man/rstream.runif-class.Rd | 4 ++--
7 files changed, 18 insertions(+), 11 deletions(-)
Author: Robert B. Gramacy
Diff between monomvn versions 1.7-3 dated 2009-08-19 and 1.7-4 dated 2009-11-17
Title: Estimation for multivariate normal and Student-t data with
monotone missingness
Description: Estimation of multivariate normal and student-t data of
arbitrary dimension where the pattern of missing data is
monotone. Through the use of parsimonious/shrinkage regressions
(plsr, pcr, lasso, ridge, etc.), where standard regressions
fail, the package can handle a nearly arbitrary amount of
missing data. The current version supports maximum likelihood
inference and a full Bayesian approach employing scale-mixtures
for the lasso (double-exponential) prior and Student-t errors.
Monotone data augmentation extends this Bayesian approach to
arbitrary missingness patterns. A fully functional standalone
interface to the Bayesian lasso (from Park & Casella) and ridge
regression with model selection via Reversible Jump, and
student-t errors (from Geweke) is also provided
ChangeLog | 10 ++
DESCRIPTION | 8 -
R/blasso.R | 19 ++-
man/blasso.Rd | 11 +-
man/bmonomvn.Rd | 4
man/monomvn-package.Rd | 2
man/monomvn.Rd | 4
src/blasso.cc | 235 +++++++++++++++++++++++++------------------------
src/blasso.h | 6 -
9 files changed, 165 insertions(+), 134 deletions(-)
Author: Fang Chang
Diff between clues versions 0.3.2 dated 2009-03-17 and 0.3.9 dated 2009-11-17
Title: Clustering Method Based on Local Shrinking
Description: The package contains functions for automatically
estimating the number of clusters and getting the final cluster
partition without any input parameter except the stopping rule
for convergence. The package also provides functions to
evaluate and compare the performances of partitions of a data
set both numerically and graphically.
clues-0.3.2/clues/R/clues.CH.R |only
clues-0.3.2/clues/R/clues.sil.R |only
clues-0.3.2/clues/data/Iris.R |only
clues-0.3.2/clues/data/Ruspini.R |only
clues-0.3.2/clues/data/iris.dat |only
clues-0.3.2/clues/data/ruspini.dat |only
clues-0.3.2/clues/man/Get.CH.Rd |only
clues-0.3.2/clues/man/Get.Silhouette.Rd |only
clues-0.3.2/clues/man/Iris.Rd |only
clues-0.3.2/clues/man/Ruspini.Rd |only
clues-0.3.2/clues/src/CH.f |only
clues-0.3.2/clues/src/chooseK_CH3.f |only
clues-0.3.2/clues/src/chooseK_sil3.f |only
clues-0.3.2/clues/src/clustering2.f |only
clues-0.3.2/clues/src/dmedian.f |only
clues-0.3.2/clues/src/dsort.f |only
clues-0.3.2/clues/src/sharpen2.f |only
clues-0.3.2/clues/src/silhouette3.f |only
clues-0.3.9/clues/DESCRIPTION | 14 -
clues-0.3.9/clues/INDEX | 18 -
clues-0.3.9/clues/NAMESPACE | 13 -
clues-0.3.9/clues/R/adjustedRand.R | 98 ++++----
clues-0.3.9/clues/R/clues.R | 175 +++++++++-----
clues-0.3.9/clues/R/clues_CH.R |only
clues-0.3.9/clues/R/clues_sil.R |only
clues-0.3.9/clues/R/clustering.R | 94 +++----
clues-0.3.9/clues/R/compClust.R | 142 +++++------
clues-0.3.9/clues/R/rankDist.R | 117 +++++----
clues-0.3.9/clues/R/shrinking.R | 69 ++---
clues-0.3.9/clues/R/view.R | 383 ++++++++++++++++++++++----------
clues-0.3.9/clues/data/Curve.R | 8
clues-0.3.9/clues/data/Maronna.R | 8
clues-0.3.9/clues/data/Ring.R | 8
clues-0.3.9/clues/data/Vowel.R | 8
clues-0.3.9/clues/inst |only
clues-0.3.9/clues/man/Curve.Rd | 19 +
clues-0.3.9/clues/man/Maronna.Rd | 23 +
clues-0.3.9/clues/man/Ring.Rd | 21 +
clues-0.3.9/clues/man/Vowel.Rd | 30 +-
clues-0.3.9/clues/man/adjustedRand.Rd | 30 --
clues-0.3.9/clues/man/clues.Rd | 42 +--
clues-0.3.9/clues/man/clustering.Rd | 40 ++-
clues-0.3.9/clues/man/compClust.Rd | 58 ++--
clues-0.3.9/clues/man/get_CH.Rd |only
clues-0.3.9/clues/man/get_Silhouette.Rd |only
clues-0.3.9/clues/man/plot.clues.Rd |only
clues-0.3.9/clues/man/plotAvgCurves.Rd | 54 +++-
clues-0.3.9/clues/man/plotClusters.Rd | 45 ++-
clues-0.3.9/clues/man/plotCurves.Rd | 51 +++-
clues-0.3.9/clues/man/print.clues.Rd |only
clues-0.3.9/clues/man/shrinking.Rd | 21 -
clues-0.3.9/clues/man/summary.clues.Rd |only
clues-0.3.9/clues/src/CH.f95 |only
clues-0.3.9/clues/src/adjustedRand.c | 170 +++++++-------
clues-0.3.9/clues/src/chooseK.f95 |only
clues-0.3.9/clues/src/clustering2.f95 |only
clues-0.3.9/clues/src/dmedian.f95 |only
clues-0.3.9/clues/src/dsort.f95 |only
clues-0.3.9/clues/src/sharpen2.f95 |only
clues-0.3.9/clues/src/silhouette3.f95 |only
60 files changed, 1061 insertions(+), 698 deletions(-)
More information about polySegratioMM at CRAN
Permanent link
Author: Brian Walters
Diff between nnDiag versions 0.0-2 dated 2009-11-16 and 0.0-3 dated 2009-11-17
Title: k-Nearest Neighbor Diagnostic Tools
Description: A suite of graphical diagnostic tools to evaluate kNN
classifications.
DESCRIPTION | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
Author: Daniel P Gaile
Diff between iGenomicViewer versions 2.4.4 dated 2009-10-29 and 2.4.6 dated 2009-11-17
More information about iGenomicViewer at CRAN
Title: Tool for sending interactive bioinformatic heatmaps with
tool-tip content.
Description: A tool for visualizing data
DESCRIPTION | 9 ++-
R/adfWrapper.R | 8 ++-
R/convertLoc.R | 12 ++---
R/dfWrapper.R | 4 +
R/marrayWrapper.R | 10 ++--
inst/doc/figure02.png |only
inst/doc/figure03.png |only
inst/doc/iGGV.Rnw | 80 ++++++++++++++++++++++++++++++++--
inst/doc/iGGV.dvi |binary
inst/doc/iGGV.pdf |binary
inst/doc/iGenomicViewer.Rnw | 102 ++++++++++++++++++++++++++++++++++++++++++++
inst/doc/iGenomicViewer.dvi |binary
inst/doc/iGenomicViewer.pdf |binary
13 files changed, 203 insertions(+), 22 deletions(-)
Permanent link
Author: Robin K. S. Hankin
Title: ecological drift under the UNTB
Description: A collection of utilities for biodiversity data. Includes
the simulation of ecological drift under Hubbell's Unified
Neutral Theory of Biodiversity, and the calculation of various
diagnostics such as Preston curves. Now includes functionality
provided by Francois Munoz and Andrea Manica.
Diff between untb versions 1.6-1 dated 2009-10-15 and 1.6-2 dated 2009-11-17
DESCRIPTION | 8 R/munoz.R | 2 inst/doc/untbpaper.pdf | 3293 ++++++++++++++++++++++++------------------------- 3 files changed, 1637 insertions(+), 1666 deletions(-)
Author: Nicole Kraemer, Juliane Schaefer
Title: Regularized estimation of partial correlation matrices
Description: The package estimates the matrix of partial correlations
based on different regularized regression methods: lasso,
adaptive lasso, PLS, and Ridge Regression.
Diff between parcor versions 0.2 dated 2009-11-12 and 0.2-1 dated 2009-11-17
DESCRIPTION | 8 ++++---- R/adalasso.R | 12 ++++++++---- R/mylars.R | 6 ++++-- R/ridge.cv.R | 6 ++++-- man/adalasso.Rd | 4 ++++ man/mylars.Rd | 6 +++++- man/parcor-package.Rd | 4 ++-- man/ridge.cv.Rd | 3 ++- 8 files changed, 33 insertions(+), 16 deletions(-)
Author: Paul Hiemstra
Diff between automap versions 1.0-2 dated 2009-07-18 and 1.0-4 dated 2009-11-17
Title: Automatic interpolation package
Description: This package performs an automatic interpolation by
automatically estimating the variogram and then calling gstat.
DESCRIPTION | 8 ++---
R/autoKrige.cv.r | 18 ++++++++++-
R/autoKrige.r | 5 +++
R/autokrige.vgm.panel.r | 8 +++++
SvnLog | 65 +++++++++++++++++++++++++++++++++++++++++++
man/autoKrige.rd | 8 +----
man/autoKrige_cv.rd | 11 +++----
man/autofitVariogram.rd | 8 ++---
man/automapPlot.rd | 4 +-
man/compare.cv.rd | 7 +---
man/plot.autoKrige.rd | 6 +--
man/posPredictionInterval.rd | 2 -
12 files changed, 119 insertions(+), 31 deletions(-)
Author: Peter K Dunn
Diff between tweedie versions 2.0.0 dated 2009-08-10 and 2.0.2 dated 2009-11-17
Title: Tweedie exponential family models
Description: Maximum likelihood computations for Tweedie families.
CHANGE.log | 11 +++++++++--
DESCRIPTION | 8 ++++----
R/tweedie.R | 25 ++++++++++++++++++++++++-
man/AICtweedie.Rd |only
man/tweedie-package.Rd | 4 ++--
man/tweedie.profile.Rd | 2 +-
6 files changed, 40 insertions(+), 10 deletions(-)
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and
Leonor Palmeira and Simon Penel
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for
biological sequence (DNA and protein) data. Include also
utilities for sequence data management under the ACNUC system.
Diff between seqinr versions 2.0-6 dated 2009-10-18 and 2.0-7 dated 2009-11-17
seqinr-2.0-6/seqinr/inst/doc/seqinr_2_0-3.pdf |only seqinr-2.0-7/seqinr/DESCRIPTION | 10 seqinr-2.0-7/seqinr/R/comp.R | 13 seqinr-2.0-7/seqinr/R/trimSpace.R | 4 seqinr-2.0-7/seqinr/R/where.is.this.acc.R |only seqinr-2.0-7/seqinr/R/words.pos.R | 6 seqinr-2.0-7/seqinr/inst/doc/seqinr_2_0-7.pdf |only seqinr-2.0-7/seqinr/inst/doc/src/appendix/FAQ.rnw | 13 seqinr-2.0-7/seqinr/inst/doc/src/appendix/FAQ.tex | 42 +- seqinr-2.0-7/seqinr/inst/doc/src/appendix/releasenotes.rnw | 33 ++ seqinr-2.0-7/seqinr/inst/doc/src/appendix/releasenotes.tex | 76 ++++- seqinr-2.0-7/seqinr/inst/doc/src/config/book.bib | 8 seqinr-2.0-7/seqinr/inst/doc/src/figs/cover.pdf | 26 - seqinr-2.0-7/seqinr/inst/doc/src/frontmatter/cover.tex | 16 - seqinr-2.0-7/seqinr/inst/doc/src/frontmatter/licence.tex | 6 seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/acnucsocket.tex | 59 ++-- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/dealseq.rnw | 65 ++-- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/dealseq.tex | 158 ++++------- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/extractseqs.tex | 60 ++-- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/getseqacnuc.rnw | 2 seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/getseqacnuc.tex | 113 ++++--- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/getseqflat.tex | 31 +- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/introduction.tex | 38 +- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/multivariate.tex | 20 - seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/nonparastats.rnw | 14 seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/nonparastats.tex | 66 ++-- seqinr-2.0-7/seqinr/inst/doc/src/mainmatter/querylang.tex | 28 - seqinr-2.0-7/seqinr/inst/doc/src/tables/aacost.tex | 4 seqinr-2.0-7/seqinr/inst/doc/src/tables/dpqrtable.tex | 4 seqinr-2.0-7/seqinr/inst/doc/src/tables/toyaa.tex | 4 seqinr-2.0-7/seqinr/inst/doc/src/tables/toycodon.tex | 4 seqinr-2.0-7/seqinr/man/choosebank.Rd | 4 seqinr-2.0-7/seqinr/man/comp.Rd | 19 - seqinr-2.0-7/seqinr/man/uco.Rd | 21 + seqinr-2.0-7/seqinr/man/where.is.this.acc.Rd |only seqinr-2.0-7/seqinr/man/words.pos.Rd | 5 36 files changed, 543 insertions(+), 429 deletions(-)
Author: Valentin Rousson
Diff between sca versions 0.8-6 dated 2009-02-09 and 0.8-7 dated 2009-11-17
Title: Simple Component Analysis
Description: Simple Component Analysis often provides much more
interpretable components than Principal Components (PCA)
without losing too much.
ChangeLog | 6 ++++++
DESCRIPTION | 14 +++++++++-----
R/aaa.R | 2 +-
man/sca.Rd | 4 ++--
4 files changed, 18 insertions(+), 8 deletions(-)
Author: Liviu Andronic
Title: Graphically export output to LaTeX or HTML
Description: The package helps users to graphically export Rcmdr output
to LaTeX or HTML code, via xtable() or Hmisc::latex(). The
plug-in was originally intended to facilitate exporting Rcmdr
output to formats other than ASCII text and to provide R
novices with an easy-to-use, easy-to-access reference on
exporting R objects to formats suited for printed output. The
package documentation contains several pointers on creating
reports, either by using conventional word processors or
LaTeX/LyX.
Diff between RcmdrPlugin.Export versions 0.2-2 dated 2009-10-14 and 0.3-0 dated 2009-11-17
RcmdrPlugin.Export-0.2-2/RcmdrPlugin.Export/R/xtable.Export.R |only RcmdrPlugin.Export-0.2-2/RcmdrPlugin.Export/inst/CHANGES |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/DESCRIPTION | 28 - RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/R/formatdfExport.R |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/R/latexExport.R |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/R/xtableExport.R |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/inst/ChangeLog |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/inst/LIMITATIONS | 8 RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/inst/etc/menus.txt | 16 - RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/.backups |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/RcmdrPlugin.Export-package.Rd | 160 +++++----- RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/formatdfExport.Rd |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/latexExport.Rd |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/utilities.Rd |only RcmdrPlugin.Export-0.3-0/RcmdrPlugin.Export/man/xtableExport.Rd | 99 ++---- 15 files changed, 153 insertions(+), 158 deletions(-)
More information about RcmdrPlugin.Export at CRAN
Permanent link
Author: Keyan Salari, Robert Tibshirani, Jonathan R. Pollack
Title: DR-Integrator
Description: Integrative analysis of DNA copy number and gene
expression data described in Salari et al 2009
Diff between DRI versions 1.0 dated 2009-08-05 and 1.1 dated 2009-11-17
DRI-1.0/DRI/man/dri.fix.missingvals.Rd |only DRI-1.1/DRI/DESCRIPTION | 11 ++++++----- DRI-1.1/DRI/NAMESPACE | 2 +- DRI-1.1/DRI/R/DRI-internal.R |only DRI-1.1/DRI/R/binary.fdr.search.R | 2 +- DRI-1.1/DRI/R/correlate.R | 2 +- DRI-1.1/DRI/R/drcorrelate.R | 2 +- DRI-1.1/DRI/R/drcorrelate.null.R | 2 +- DRI-1.1/DRI/R/dri.correlation.plot.R | 2 +- DRI-1.1/DRI/R/dri.fdrCutoff.R | 2 +- DRI-1.1/DRI/R/dri.fix.missingvals.R | 2 +- DRI-1.1/DRI/R/dri.heatmap.R | 2 +- DRI-1.1/DRI/R/dri.impute.R | 2 +- DRI-1.1/DRI/R/dri.merge.CNbyRNA.R |only DRI-1.1/DRI/R/dri.sig_genes.R | 6 +++--- DRI-1.1/DRI/R/dri.smooth.cghdata.R |only DRI-1.1/DRI/R/drsam.R | 2 +- DRI-1.1/DRI/R/drsam.null.R | 2 +- DRI-1.1/DRI/R/fdr.fast.R | 2 +- DRI-1.1/DRI/R/get.pi0.R | 2 +- DRI-1.1/DRI/R/observed_t.R | 2 +- DRI-1.1/DRI/R/permute.R | 2 +- DRI-1.1/DRI/R/permute_t.R | 2 +- DRI-1.1/DRI/R/runFusedLasso.R |only DRI-1.1/DRI/R/runningmean.R |only DRI-1.1/DRI/R/scale01.R | 2 +- DRI-1.1/DRI/R/sum.fp.R | 2 +- DRI-1.1/DRI/R/ttest.func.R | 2 +- DRI-1.1/DRI/R/varr.R | 2 +- DRI-1.1/DRI/man/DRI-package.Rd | 32 ++++++++++++++++++++------------ DRI-1.1/DRI/man/drcorrelate.Rd | 14 +++++++++----- DRI-1.1/DRI/man/drcorrelate.null.Rd | 14 +++++++++----- DRI-1.1/DRI/man/dri.correlation.plot.Rd | 17 +++++++++++------ DRI-1.1/DRI/man/dri.fdrCutoff.Rd | 25 ++++++++++++++++--------- DRI-1.1/DRI/man/dri.heatmap.Rd | 20 +++++++++++++------- DRI-1.1/DRI/man/dri.impute.Rd | 9 ++++----- DRI-1.1/DRI/man/dri.merge.CNbyRNA.Rd |only DRI-1.1/DRI/man/dri.sig_genes.Rd | 17 +++++++++++------ DRI-1.1/DRI/man/dri.smooth.cghdata.Rd |only DRI-1.1/DRI/man/drsam.Rd | 19 ++++++++++++------- DRI-1.1/DRI/man/drsam.null.Rd | 19 ++++++++++++------- DRI-1.1/DRI/man/mySampleData.Rd | 18 ++++++------------ DRI-1.1/DRI/man/runFusedLasso.Rd |only 43 files changed, 153 insertions(+), 110 deletions(-)
Author: James Honaker
Diff between Amelia versions 1.2-13 dated 2009-08-13 and 1.2-14 dated 2009-11-17
Title: Amelia II: A Program for Missing Data
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.
ChangeLog | 16
DESCRIPTION | 8
NEWS | 11
R/emb.r | 2
R/prep.r | 1
inst/doc/amelia.Rnw | 2
inst/doc/amelia.pdf | 6991 +++++++++++++++++++++------------------------------
inst/doc/copyRd.Rout | 4
inst/doc/index.shtml | 2
9 files changed, 2920 insertions(+), 4117 deletions(-)