Title: The GSC Applied Geochemistry EDA Package
Diff between rgr versions 1.1.1 dated 2011-03-01 and 1.1.2 dated 2012-01-20
Description: Geological Survey of Canada (GSC) R functions for
exploratory data analysis with applied geochemical data, with
special application to the estimation of background ranges and
identification of outliers, 'anomalies', to support both
environmental studies and mineral exploration.
Author: Robert G. Garrett
Maintainer: Robert G. Garrett
rgr-1.1.1/rgr/inst/doc/What_is_in_rgr_1-1-1.pdf |only
rgr-1.1.1/rgr/inst/doc/rgr_Overview_1-1-1.pdf |only
rgr-1.1.1/rgr/inst/doc/rgr_func_list_1-1-1.pdf |only
rgr-1.1.2/rgr/DESCRIPTION | 8 -
rgr-1.1.2/rgr/MD5 |only
rgr-1.1.2/rgr/NAMESPACE | 2
rgr-1.1.2/rgr/R/anova1.R | 8 -
rgr-1.1.2/rgr/R/anova2.R | 10 -
rgr-1.1.2/rgr/R/expit.R |only
rgr-1.1.2/rgr/R/fences.R | 118 ++++++++++++++-------
rgr-1.1.2/rgr/R/fences.summary.R | 27 +++-
rgr-1.1.2/rgr/R/framework.stats.R | 2
rgr-1.1.2/rgr/R/gx.2dproj.R | 6 -
rgr-1.1.2/rgr/R/gx.ks.test.R | 4
rgr-1.1.2/rgr/R/gx.rma.R | 4
rgr-1.1.2/rgr/R/gx.stats.R | 133 +++++++++++-------------
rgr-1.1.2/rgr/R/gx.summary.R | 4
rgr-1.1.2/rgr/R/gx.summary.groups.R | 4
rgr-1.1.2/rgr/R/gx.summary.mat.R | 7 -
rgr-1.1.2/rgr/R/gx.summary1.R | 8 -
rgr-1.1.2/rgr/R/gx.summary2.R | 6 -
rgr-1.1.2/rgr/R/gx.triples.aov.R | 6 -
rgr-1.1.2/rgr/R/gx.triples.fgx.R | 6 -
rgr-1.1.2/rgr/R/logit.R |only
rgr-1.1.2/rgr/R/map.eda7.R | 17 ++-
rgr-1.1.2/rgr/R/map.eda8.R | 32 +++++
rgr-1.1.2/rgr/R/map.z.R | 29 ++++-
rgr-1.1.2/rgr/R/remove.na.R | 11 +
rgr-1.1.2/rgr/R/tbplots.R | 6 -
rgr-1.1.2/rgr/R/thplot1.R | 18 +--
rgr-1.1.2/rgr/R/thplot2.R | 4
rgr-1.1.2/rgr/R/xyplot.eda7.R | 22 +++
rgr-1.1.2/rgr/R/xyplot.eda8.R | 32 +++++
rgr-1.1.2/rgr/R/xyplot.z.R | 31 ++++-
rgr-1.1.2/rgr/data/fix.test.asis.rda |only
rgr-1.1.2/rgr/data/fix.test.rda |binary
rgr-1.1.2/rgr/data/ogrady.mat2open.rda |only
rgr-1.1.2/rgr/data/sind.mat2open.rda |only
rgr-1.1.2/rgr/inst/doc/What_is_in_rgr_1-1-2.pdf |only
rgr-1.1.2/rgr/inst/doc/rgr_Overview_1-1-2.pdf |only
rgr-1.1.2/rgr/inst/doc/rgr_func_list_1-1-2.pdf |only
rgr-1.1.2/rgr/man/alr.Rd | 14 +-
rgr-1.1.2/rgr/man/anova1.Rd | 14 +-
rgr-1.1.2/rgr/man/anova2.Rd | 14 +-
rgr-1.1.2/rgr/man/bwplots.Rd | 2
rgr-1.1.2/rgr/man/bwplots.by.var.Rd | 8 -
rgr-1.1.2/rgr/man/bxplot.Rd | 2
rgr-1.1.2/rgr/man/caplot.Rd | 10 -
rgr-1.1.2/rgr/man/clr.Rd | 4
rgr-1.1.2/rgr/man/cnpplt.Rd | 6 -
rgr-1.1.2/rgr/man/cutter.Rd | 4
rgr-1.1.2/rgr/man/df.test.Rd | 8 -
rgr-1.1.2/rgr/man/expit.Rd |only
rgr-1.1.2/rgr/man/fences.Rd | 17 ++-
rgr-1.1.2/rgr/man/fences.summary.Rd | 15 +-
rgr-1.1.2/rgr/man/fix.test.Rd | 5
rgr-1.1.2/rgr/man/fix.test.asis.Rd |only
rgr-1.1.2/rgr/man/framework.summary.Rd | 2
rgr-1.1.2/rgr/man/gx.2dproj.Rd | 21 +--
rgr-1.1.2/rgr/man/gx.2dproj.plot.Rd | 7 -
rgr-1.1.2/rgr/man/gx.cnpplts.Rd | 2
rgr-1.1.2/rgr/man/gx.ecdf.Rd | 2
rgr-1.1.2/rgr/man/gx.hist.Rd | 2
rgr-1.1.2/rgr/man/gx.hypergeom.Rd | 2
rgr-1.1.2/rgr/man/gx.ks.test.Rd | 12 +-
rgr-1.1.2/rgr/man/gx.md.display.Rd | 14 --
rgr-1.1.2/rgr/man/gx.md.gait.Rd | 2
rgr-1.1.2/rgr/man/gx.md.gait.closed.Rd | 14 --
rgr-1.1.2/rgr/man/gx.md.plot.Rd | 15 --
rgr-1.1.2/rgr/man/gx.md.plt0.Rd | 12 --
rgr-1.1.2/rgr/man/gx.md.print.Rd | 14 --
rgr-1.1.2/rgr/man/gx.mva.Rd | 16 --
rgr-1.1.2/rgr/man/gx.mvalloc.Rd | 6 -
rgr-1.1.2/rgr/man/gx.mvalloc.closed.Rd | 2
rgr-1.1.2/rgr/man/gx.mvalloc.print.Rd | 6 -
rgr-1.1.2/rgr/man/gx.pearson.Rd | 22 +--
rgr-1.1.2/rgr/man/gx.rma.Rd | 2
rgr-1.1.2/rgr/man/gx.robmva.Rd | 4
rgr-1.1.2/rgr/man/gx.robmva.closed.Rd | 20 +--
rgr-1.1.2/rgr/man/gx.rotate.Rd | 16 --
rgr-1.1.2/rgr/man/gx.rqpca.loadplot.Rd | 14 --
rgr-1.1.2/rgr/man/gx.rqpca.plot.Rd | 17 +--
rgr-1.1.2/rgr/man/gx.rqpca.print.Rd | 16 --
rgr-1.1.2/rgr/man/gx.rqpca.screeplot.Rd | 17 ---
rgr-1.1.2/rgr/man/gx.sort.Rd | 14 +-
rgr-1.1.2/rgr/man/gx.sort.df.Rd | 6 -
rgr-1.1.2/rgr/man/gx.spearman.Rd | 20 +--
rgr-1.1.2/rgr/man/gx.stats.Rd | 6 -
rgr-1.1.2/rgr/man/gx.subset.Rd | 12 +-
rgr-1.1.2/rgr/man/gx.summary.Rd | 5
rgr-1.1.2/rgr/man/gx.summary.groups.Rd | 6 -
rgr-1.1.2/rgr/man/gx.summary.mat.Rd | 23 ++--
rgr-1.1.2/rgr/man/gx.summary1.Rd | 8 -
rgr-1.1.2/rgr/man/gx.summary2.Rd | 2
rgr-1.1.2/rgr/man/gx.triples.aov.Rd | 8 -
rgr-1.1.2/rgr/man/gx.triples.fgx.Rd | 8 -
rgr-1.1.2/rgr/man/ilr.Rd | 16 +-
rgr-1.1.2/rgr/man/inset.Rd | 6 -
rgr-1.1.2/rgr/man/inset.exporter.Rd | 4
rgr-1.1.2/rgr/man/kola.c.Rd | 2
rgr-1.1.2/rgr/man/kola.o.Rd | 4
rgr-1.1.2/rgr/man/logit.Rd |only
rgr-1.1.2/rgr/man/ltdl.fix.Rd | 4
rgr-1.1.2/rgr/man/ltdl.fix.df.Rd | 8 -
rgr-1.1.2/rgr/man/map.eda7.Rd | 21 ++-
rgr-1.1.2/rgr/man/map.eda8.Rd | 20 ++-
rgr-1.1.2/rgr/man/map.tags.Rd | 14 +-
rgr-1.1.2/rgr/man/map.z.Rd | 56 +++++-----
rgr-1.1.2/rgr/man/ms.data1.Rd | 2
rgr-1.1.2/rgr/man/ms.data2.Rd | 2
rgr-1.1.2/rgr/man/ms.data3.Rd | 2
rgr-1.1.2/rgr/man/ogrady.Rd | 2
rgr-1.1.2/rgr/man/ogrady.mat2open.Rd |only
rgr-1.1.2/rgr/man/orthonorm.Rd | 21 +--
rgr-1.1.2/rgr/man/remove.na.Rd | 8 +
rgr-1.1.2/rgr/man/rgr-package.Rd | 2
rgr-1.1.2/rgr/man/shape.Rd | 2
rgr-1.1.2/rgr/man/sind.Rd | 2
rgr-1.1.2/rgr/man/sind.mat2open.Rd |only
rgr-1.1.2/rgr/man/syms.Rd | 2
rgr-1.1.2/rgr/man/tbplots.Rd | 6 -
rgr-1.1.2/rgr/man/tbplots.by.var.Rd | 8 -
rgr-1.1.2/rgr/man/thplot1.Rd | 42 ++++---
rgr-1.1.2/rgr/man/thplot2.Rd | 42 ++++---
rgr-1.1.2/rgr/man/triples.test1.Rd | 2
rgr-1.1.2/rgr/man/triples.test2.Rd | 2
rgr-1.1.2/rgr/man/var2fact.Rd | 8 -
rgr-1.1.2/rgr/man/where.na.Rd | 10 -
rgr-1.1.2/rgr/man/wtd.sums.Rd | 2
rgr-1.1.2/rgr/man/xyplot.eda7.Rd | 17 +--
rgr-1.1.2/rgr/man/xyplot.eda8.Rd | 16 +-
rgr-1.1.2/rgr/man/xyplot.tags.Rd | 6 -
rgr-1.1.2/rgr/man/xyplot.z.Rd | 49 ++++----
133 files changed, 812 insertions(+), 683 deletions(-)
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 2.0.53 dated 2011-11-13 and 2.0.54 dated 2012-01-20
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging
Author: Martin Schlather
Maintainer: Martin Schlather
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
src/Gneiting.cc | 2 +-
src/RandomFields.h | 2 +-
tests/source.R | 7 ++++---
5 files changed, 13 insertions(+), 12 deletions(-)
Title: Multivariate Normal and t Distributions
Diff between mvtnorm versions 0.9-9991 dated 2011-06-15 and 0.9-9992 dated 2012-01-20
Description: Computes multivariate normal and t probabilities,
quantiles, random deviates and densities.
Author: Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich
Leisch, Fabian Scheipl, Bjoern Bornkamp, Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 |only
NEWS | 8 +++++++-
R/mvt.R | 8 ++++++--
inst/CHANGES | 8 +++++++-
inst/doc/MVT_Rnews.pdf |binary
man/algorithms.Rd | 4 +++-
src/miwa.c | 1 +
src/mvt.f | 4 ++--
tests/bugfix-tests.R | 4 ++++
tests/bugfix-tests.Rout.save | 6 +++++-
11 files changed, 39 insertions(+), 12 deletions(-)
Title: Approximate Path for Penalized Likelihood Estimators
Diff between apple versions 0.2 dated 2011-12-25 and 0.3 dated 2012-01-20
Description: Approximate Path for Penalized Likelihood Estimators for
Generalized Linear Models penalized by LASSO or MCP
Author: Yi Yu, Yang Feng
Maintainer: Yi Yu
DESCRIPTION | 9 +++++----
MD5 | 14 +++++++-------
R/apple.R | 15 ++++++++++++---
R/auxiliary.R | 6 +++++-
R/cv.R | 2 +-
man/apple.Rd | 2 +-
man/cv.apple.Rd | 6 +++---
src/cd_mcp1.f | 2 +-
8 files changed, 35 insertions(+), 21 deletions(-)
Title: Model selection and multimodel inference based on (Q)AIC(c)
Diff between AICcmodavg versions 1.21 dated 2011-11-04 and 1.22 dated 2012-01-20
Description: This package includes functions to create model selection
tables based on Akaike's information criterion (AIC) and the
second-order AIC (AICc), as well as their quasi-likelihood
counterparts (QAIC, QAICc). Tables are printed with delta AIC
and Akaike weights. The package also features functions to
conduct classic model averaging (multimodel inference) for a
given parameter of interest or predicted values, as well as a
shrinkage version of model averaging parameter estimates.
Other handy functions enable the computation of relative
variable importance, evidence ratios, and confidence sets for
the best model. The present version works with linear models
('lm' class), generalized linear models ('glm' class), linear
models fit by generalized least squares ('gls' class), linear
mixed models ('lme' class), generalized linear mixed models
('mer' class), multinomial and ordinal logistic regressions
('multinom' and 'polr' classes), and nonlinear models ('nls'
class). The package also supports various models incorporating
detection probabilities such as single-season occupancy models
('unmarkedFitOccu' class), multiple-season occupancy models
('unmarkedFitColExt' class), single-season heterogeneity models
('unmarkedFitOccuRN' class), single-season and multiple-season
N-mixture models for repeated counts ('unmarkedFitPCount' and
'unmarkedFitPCO' classes, respectively), and distance sampling
models ('unmarkedFitDS' and 'unmarkedFitGDS' classes).
Author: Marc J. Mazerolle
Maintainer: Marc J. Mazerolle
DESCRIPTION | 37 +++++++++++---
MD5 | 46 ++++++++---------
R/AICc.R | 3 -
R/aictab.R | 3 -
R/importance.R | 49 ++++++++++++++++++
R/modavg.R | 3 -
R/modavg.glm.R | 10 ++-
R/modavg.gls.R | 4 +
R/modavg.lme.R | 6 +-
R/modavg.mer.R | 6 +-
R/modavg.mult.R | 4 +
R/modavg.polr.R | 4 +
R/modavg.shrink.R | 3 -
R/modavg.shrink.unmarked.R | 47 +++++++++++++++++
R/modavg.unmarked.R | 54 +++++++++++++++++++-
R/modavgpred.R | 3 -
R/modavgpred.unmarked.R | 14 ++++-
R/predictSE.mer.r | 118 ++++++++++++++++++++++++++++++++++++++++++---
inst/NEWS | 12 ++++
man/AICcmodavg-package.Rd | 7 +-
man/modavg.Rd | 72 +++++++++++++++++++--------
man/modavg.shrink.Rd | 30 ++++++-----
man/modavgpred.Rd | 63 ++++++++++++++++++------
man/predictSE.mer.Rd | 47 +++++++++++++++++
24 files changed, 540 insertions(+), 105 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Diff between rgeos versions 0.2-1 dated 2012-01-15 and 0.2-2 dated 2012-01-20
Description: Interface to Geometry Engine - Open Source (GEOS) using
the C API for topology operations on geometries.
Author: Roger Bivand and Colin Rundel
Maintainer: Roger Bivand
ChangeLog | 17 +++++++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
inst/ChangeLog | 17 +++++++++++++++++
inst/SVN_VERSION | 2 +-
man/experimental-functions.Rd | 2 +-
src/rgeos_poly2nb.c | 9 +++++----
7 files changed, 51 insertions(+), 16 deletions(-)
Title: Regression Models for Ordinal Data
Diff between ordinal versions 2011.09-14 dated 2011-09-14 and 2012.01-19 dated 2012-01-20
Description: This package implements cumulative link (mixed) models
also known as ordered regression models, proportional odds
models, proportional hazards models for grouped survival times
and ordered logit/probit/... models. Estimation is via maximum
likelihood and mixed models are fitted with the Laplace
approximation and adaptive Gauss-Hermite quadrature. Multiple
random effect terms are allowed and they may be nested, crossed
or partially nested/crossed. Restrictions of symmetry and
equidistance can be imposed on the thresholds (cut-points).
Standard model methods are available (summary, anova,
drop-methods, step, confint, predict etc.) in addition to
profile methods and slice methods for visualizing the
likelihood function and checking convergence.
Author: Rune Haubo B Christensen
Maintainer: Rune Haubo B Christensen
DESCRIPTION | 8 ++---
MD5 | 21 ++++++++-------
NEWS | 4 ++
R/clm.methods.R | 19 ++++++++-----
R/clmm.R | 2 +
R/eclm.R | 30 ++++++++++++++--------
R/simple.clm.R |only
inst/doc/clm_intro.pdf |binary
inst/doc/clm_tutorial.pdf |binary
inst/doc/clmm2_tutorial.pdf |binary
tests/clm.formula.R | 60 +++++++++++++++++++++++++++++++++++++++++++-
tests/testCLM.R | 27 +------------------
12 files changed, 114 insertions(+), 57 deletions(-)
Title: Importing Vector Graphics
Diff between grImport versions 0.8-2 dated 2012-01-11 and 0.8-3 dated 2012-01-20
Description: Functions for converting, importing, and drawing
PostScript pictures in R plots.
Author: Paul Murrell and Richard Walton.
Maintainer: Paul Murrell
DESCRIPTION | 6 +++---
MD5 | 14 +++++++-------
R/PostScript2RGML.R | 3 ++-
inst/doc/changes.txt | 7 ++++++-
inst/doc/circleRas.pdf |binary
inst/doc/fiddledplot.pdf |binary
inst/doc/import.pdf |binary
inst/doc/importText.pdf |binary
8 files changed, 18 insertions(+), 12 deletions(-)
Title: Functional time series analysis
Diff between ftsa versions 2.9 dated 2012-01-08 and 3.0 dated 2012-01-20
Description: Functions for functional time series
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang
CHANGELOG | 5 +++++
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/plot.ftsf.R | 2 +-
R/plot.ftsm.R | 12 ++----------
man/plot.ftsf.Rd | 2 +-
man/plot.ftsm.Rd | 4 +---
7 files changed, 21 insertions(+), 26 deletions(-)
Title: Entropy and Mutual Information Estimation
Diff between entropy versions 1.1.6 dated 2011-03-21 and 1.1.7 dated 2012-01-20
Description: This package implements various estimators of entropy,
such as the shrinkage estimator by Hausser and Strimmer, the
maximum likelihood and the Millow-Madow estimator, various
Bayesian estimators, and the Chao-Shen estimator. It also
offers an R interface to the NSB estimator. Furthermore, it
provides functions for estimating mutual information.
Author: Jean Hausser and Korbinian Strimmer
Maintainer: Korbinian Strimmer
DESCRIPTION | 10 +++++-----
MD5 |only
NAMESPACE |only
NEWS | 6 ++++++
4 files changed, 11 insertions(+), 5 deletions(-)
Title: Efficient Estimation of Covariance and (Partial) Correlation
Diff between corpcor versions 1.6.0 dated 2011-06-27 and 1.6.1 dated 2012-01-20
Description: This package implements a James-Stein-type shrinkage
estimator for the covariance matrix, with separate shrinkage
for variances and correlations. The details of the method are
explained in Sch\"afer and Strimmer (2005) and Opgen-Rhein and
Strimmer (2007). The approach is both computationally as well
as statistically very efficient, it is applicable to "small n,
large p" data, and always returns a positive definite and
well-conditioned covariance matrix. In addition to inferring
the covariance matrix the package also provides shrinkage
estimators for partial correlations and partial variances. The
inverse of the covariance and correlation matrix can be
efficiently computed, as well as any arbitrary power of the
shrinkage correlation matrix. Furthermore, functions are
available for fast singular value decomposition, for computing
the pseudoinverse, and for checking the rank and positive
definiteness of a matrix.
Author: Juliane Schaefer, Rainer Opgen-Rhein, Verena Zuber, A. Pedro
Duarte Silva, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 14 +++++++-------
MD5 |only
NAMESPACE |only
NEWS | 7 ++++++-
R/crossprod.powcor.shrink.R | 4 ++--
man/cov.shrink.Rd | 8 ++++----
man/powcor.shrink.Rd | 11 ++++++-----
7 files changed, 25 insertions(+), 19 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-11-19 1.1
2009-09-07 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-04-03 1.02
2009-03-28 1.01
2009-03-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-01-10 1.1
2009-12-01 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-06-17 0.2-11
2010-01-21 0.2-10
2009-10-26 0.2-8
2009-09-29 0.2-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-02-11 1.6.5.1
2010-08-04 1.6.5
2010-05-03 1.6.4
2009-12-21 1.6.3
2009-09-12 1.6.2
2009-09-10 1.6.1
2009-05-06 1.4.2
2008-07-14 1.4.1
2008-05-27 1.4
2007-06-20 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-09-10 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-05-17 1.0.7
2011-05-16 1.0.6
2010-11-06 1.0.5
2010-07-30 1.0.4
2009-11-26 1.0.3
2009-07-21 1.0.1
2009-05-06 0.7.7
2008-11-19 0.7.6
2008-11-06 0.7.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-11-22 2.0.0
2011-06-19 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-04-06 2.1
2009-09-07 2.0
2009-02-23 1.2-1
2008-11-04 1.2
2008-10-16 1.1