Author: Heloise Lavigne and Aurelien Proye and Jean-Pierre Gattuso.
Portions of code and/or corrections were contributed by
Jean-Marie Epitalon, Andreas Hofmann, Bernard Gentili, Jim Orr
and Karline Soetaert
Title: Calculates parameters of the seawater carbonate system
Description: Calculates parameters of the seawater carbonate system
Diff between seacarb versions 2.1.4 dated 2009-07-18 and 2.2 dated 2009-10-07
ChangeLog | 19 ++++++++++++++++++- DESCRIPTION | 8 ++++---- R/K1.R | 17 ++++++++++++----- R/K1p.R | 16 +++++++++++++--- R/K2.R | 14 ++++++++++---- R/K2p.R | 17 +++++++++++++---- R/K3p.R | 18 +++++++++++++----- R/Kb.R | 14 ++++++++++---- R/Kf.R | 20 +++++++++++++++----- R/Kh.R | 2 +- R/Khs.R | 18 ++++++++++++++---- R/Kn.R | 12 +++++++----- R/Ks.R | 2 +- R/Ksi.R | 20 +++++++++++++++----- R/Kw.R | 16 +++++++++++----- R/buffer.R | 2 +- R/carb.R | 2 +- R/kconv.R | 16 +++++++++++----- R/pHconv.R | 2 +- man/K1.Rd | 13 +++++++++---- man/K1p.Rd | 7 +++++-- man/K2.Rd | 8 ++++++-- man/K2p.Rd | 10 +++++++--- man/K3p.Rd | 10 +++++++--- man/Kb.Rd | 10 +++++++--- man/Kf.Rd | 17 ++++++++++------- man/Kh.Rd | 4 ++-- man/Khs.Rd | 6 ++++-- man/Kn.Rd | 8 +++++--- man/Ks.Rd | 8 ++++++-- man/Ksi.Rd | 8 ++++++-- man/Kspa.Rd | 4 ++-- man/Kspc.Rd | 4 ++-- man/Kw.Rd | 9 ++++++--- man/bor.Rd | 2 +- man/buffer.Rd | 4 ++-- man/carb.Rd | 20 +++++++++++++++++--- man/kconv.Rd | 3 ++- man/pCa.Rd | 12 +++++++++++- man/pHconv.Rd | 6 ++++-- man/pHinsi.Rd | 2 +- man/pTA.Rd | 17 ++++++++++++++++- man/pgas.Rd | 21 ++++++++++++++++++--- man/pmix.Rd | 17 ++++++++++++++++- man/ppH.Rd | 18 +++++++++++++++++- man/psi.Rd | 2 +- man/rho.Rd | 2 +- 47 files changed, 362 insertions(+), 125 deletions(-)
Author: Romain Francois
Diff between operators versions 0.1-0 dated 2009-01-26 and 0.1-5 dated 2009-10-07
Title: Additional binary operators for the R language
Description: A set of operators for common tasks such as regex
manipulation.
DESCRIPTION | 9 +++++----
NAMESPACE | 2 ++
R/000.R |only
R/file.R | 4 +++-
R/patternRemoving.R | 8 +++++---
R/zzz.R | 4 +++-
inst/options/options.R | 6 +++---
man/decorator.Rd | 2 +-
man/operators-package.Rd | 6 +++---
man/pattern.Rd | 34 ++++++++++++++++++++++------------
man/patternFilter.Rd | 12 ++++++------
11 files changed, 53 insertions(+), 34 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 1.4.1 dated 2009-10-01 and 1.4.2 dated 2009-10-07
CHANGES | 3 +++ DESCRIPTION | 8 ++++---- R/ezPlot.R | 27 ++++++++++++--------------- 3 files changed, 19 insertions(+), 19 deletions(-)
Author: Stefan Wilhelm
Diff between tmvtnorm versions 0.7-2 dated 2009-08-26 and 0.8-3 dated 2009-10-07
Title: Truncated Multivariate Normal Distribution
Description: Computes truncated multivariate normal probabilities,
quantiles and densities, including one-dimensional and
bivariate marginal densities. Random number generation.
Computes first and second moments (i.e. mean and covariance
matrix) for the double-truncated case.
DESCRIPTION | 8 -
NAMESPACE | 2
R/bivariate-marginal-density.R | 2
R/dmvtnorm-marginal.R | 57 --------------
R/dmvtnorm.R | 2
R/mtmvnorm.R | 4
R/onLoad.R |only
R/ptmvnorm-marginal.R |only
R/rtmvnorm.R | 166 ++++++++++++++++++++++++++++++++++++++---
man/dmvtnorm-marginal.Rd | 10 ++
man/dtmvnorm.marginal2.Rd | 40 ++++++---
man/mtmvnorm.Rd | 2
man/ptmvnorm.Rd | 2
man/ptmvnorm.marginal.Rd |only
man/qtmvnorm-marginal.Rd | 6 -
man/rtmvtnorm.Rd | 20 +++-
release-notes.txt | 16 +++
src |only
18 files changed, 233 insertions(+), 104 deletions(-)
Author: Roger Bivand
Diff between spdep versions 0.4-36 dated 2009-08-19 and 0.4-46 dated 2009-10-07
Title: Spatial dependence: weighting schemes, statistics and models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by
distance and tesselations, for summarising these objects, and
for permitting their use in spatial data analysis, including
regional aggregation by minimum spanning tree; a collection of
tests for spatial autocorrelation, including global Moran's I,
APLE, Geary's C, Hubert/Mantel general cross product statistic,
Empirical Bayes estimates and Assunção/Reis Index, Getis/Ord G
and multicoloured join count statistics, local Moran's I and
Getis/Ord G, saddlepoint approximations and exact tests for
global and local Moran's I; and functions for estimating
spatial simultaneous autoregressive (SAR) lag and error models,
impact measures for lag models, weighted and unweighted SAR and
CAR spatial regression models, semi-parametric and Moran
eigenvector spatial filtering, GM SAR error models, and
generalized spatial two stage least squares models.
ChangeLog | 200 ++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 19 ++--
INDEX | 3
NAMESPACE | 16 ++-
R/error.hessian.R |only
R/error.spsarlm.R | 93 ++++++++++++++++++-
R/impacts.R |only
R/kpgm_new.R | 4
R/lag.hessian.R |only
R/lag.spsarlm.R | 170 +++++++++++++++++++++++++++---------
R/nb2mat.R | 31 ++++++
R/spautolm.R | 17 ++-
R/summary.spsarlm.R | 215 ++++++++++++++++++++++++++++++++++------------
data/house.RData |only
inst/ChangeLog | 200 ++++++++++++++++++++++++++++++++++++++++++
inst/doc/CO69.pdf |binary
inst/doc/sids.pdf |binary
man/GMerrorsar.Rd | 3
man/LR.sarlm.Rd | 17 ++-
man/as_dgRMatrix_listw.Rd | 5 -
man/errorsarlm.Rd | 34 ++++---
man/house.Rd |only
man/impacts.sarlm.Rd |only
man/invIrM.Rd | 35 +++++--
man/lagsarlm.Rd | 79 +++++++++++-----
man/spautolm.Rd | 4
man/summary.sarlm.Rd | 15 ++-
man/trW.Rd |only
28 files changed, 976 insertions(+), 184 deletions(-)
Author: Jelle Goeman
Diff between penalized versions 0.9-26 dated 2009-08-06 and 0.9-27 dated 2009-10-07
Title: L1 (lasso) and L2 (ridge) penalized estimation in GLMs and in
the Cox model
Description: A package for fitting possibly high dimensional penalized
regression models. The penalty structure can be any combination
of an L1 penalty (lasso), an L2 penalty (ridge) and a
positivity constraint on the regression coefficients. The
supported regression models are linear, logistic and poisson
regression and the Cox Proportional Hazards model.
Cross-validation routines allow optimization of the tuning
parameters.
DESCRIPTION | 8
R/checkinput.R | 11
R/cvl.R | 10
R/penalized.R | 2
R/penfit.R | 20
changelog.txt | 8
inst/doc/Rplots.pdf | 6936 ++++++++++++++++++++++++-------------------------
inst/doc/penalized.Rnw | 6
inst/doc/penalized.pdf |binary
man/penfit.Rd | 2
man/predict.Rd | 8
11 files changed, 3498 insertions(+), 3513 deletions(-)
Author: Emmanuel Paradis
Title: Population and Evolutionary Genetics Analysis System
Description: pegas provides functions for reading, writing, plotting,
analysing, and manipulating allelic data, and for the analysis
of population nucleotide sequences including coalescence
analyses.
Diff between pegas versions 0.1 dated 2009-05-13 and 0.2 dated 2009-10-07
ChangeLog | 23 +++++++++++++++++++++-- DESCRIPTION | 14 ++++++++------ R/IO.R | 8 ++++---- R/amova.R | 22 +++++++++++++--------- R/haplotype.R | 9 ++++++--- R/heterozygosity.R |only R/nuc.div.R |only R/site.spectrum.R |only R/summary.loci.R | 32 +++++++++++++++++++++++++++++--- R/theta.R |only man/Fst.Rd | 2 -- man/amova.Rd | 4 +++- man/haplotype.Rd | 4 +++- man/heterozygosity.Rd |only man/nuc.div.Rd |only man/read.gtx.Rd | 9 +++++++-- man/site.spectrum.Rd |only man/summary.loci.Rd | 26 +++++++++++++++++++++++--- man/theta.h.Rd |only man/theta.k.Rd |only man/theta.s.Rd |only man/theta.tree.Rd |only man/utilities.Rd | 4 ++-- man/write.loci.Rd | 12 +++++++++++- 24 files changed, 130 insertions(+), 39 deletions(-)
Author: R-core members, Saikat DebRoy
Diff between foreign versions 0.8-37 dated 2009-08-13 and 0.8-38 dated 2009-10-07
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase,
...
Description: Functions for reading and writing data stored by
statistical packages such as Minitab, S, SAS, SPSS, Stata,
Systat, ..., and for reading and writing .dbf (dBase) files.
ChangeLog | 14 ++++++++++++++
DESCRIPTION | 8 ++++----
R/spss.R | 6 ++++--
man/read.dta.Rd | 2 +-
src/spss.c | 12 +++++++++---
5 files changed, 32 insertions(+), 10 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 1.1.9.2 dated 2009-10-01 and 1.1.9.3 dated 2009-10-07
DESCRIPTION | 8 +++--- R/skel.plot.R | 1 man/ccf.series.rwl.Rd | 56 +++++++++++++++++++++++++------------------- man/corr.rwl.seg.Rd | 50 ++++++++++++++++++++++----------------- man/corr.series.seg.Rd | 62 ++++++++++++++++++++++++------------------------- man/series.rwl.plot.Rd | 36 +++++++++++++++------------- man/skel.plot.Rd | 6 +++- 7 files changed, 120 insertions(+), 99 deletions(-)
Author: S original
Diff between boot versions 1.2-39 dated 2009-09-04 and 1.2-40 dated 2009-10-07
Title: Bootstrap R (S-Plus) Functions (Canty)
Description: functions and datasets for bootstrapping from the book
"Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP).
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
R/bootfuns.q | 1 +
inst/po/de |only
inst/po/en@quot/LC_MESSAGES/R-boot.mo |binary
inst/po/fr/LC_MESSAGES/R-boot.mo |binary
inst/po/ru/LC_MESSAGES/R-boot.mo |binary
po/R-boot.pot | 7 +++++--
po/R-de.po |only
po/R-en@quot.po | 9 ++++++---
po/R-fr.po | 6 +++++-
po/R-ru.po | 6 +++++-
tests/Examples/boot-Ex.Rout.save | 27 +++++++++++++++++++++++++--
13 files changed, 57 insertions(+), 13 deletions(-)
Author: Michael Hoehle, Ulrike Feldmann, Sebastian Meyer
Title: Analysis of Infectious Diseases using Stochastic Epidemic Models
Description: Analysis of infectious disease data using stochastic
Susceptible-Exposed-Infectious-Recovered (SEIR) models. Parts
of the R package wrap functionality of a Java program, i.e. a
java virtual machine has to be installed on your computer.
Furthermore, infectious disease surveillance data can now be
modeled based on a multivariate counting process with
additive-multiplicative conditional intensities.
Diff between RLadyBug versions 0.5-0 dated 2009-02-03 and 0.6-0 dated 2009-10-07
RLadyBug-0.5-0/RLadyBug/R/spatialSIR.R |only RLadyBug-0.5-0/RLadyBug/R/spatialSIR_epidata.R |only RLadyBug-0.5-0/RLadyBug/R/spatialSIR_helper.R |only RLadyBug-0.5-0/RLadyBug/R/spatialSIR_intensity.R |only RLadyBug-0.5-0/RLadyBug/R/spatialSIR_methods.R |only RLadyBug-0.5-0/RLadyBug/R/spatialSIR_simulation.R |only RLadyBug-0.5-0/RLadyBug/man/spatialSIR.Rd |only RLadyBug-0.5-0/RLadyBug/man/spatialSIR_AIC.Rd |only RLadyBug-0.5-0/RLadyBug/man/spatialSIR_cox.Rd |only RLadyBug-0.5-0/RLadyBug/man/spatialSIR_epidata.Rd |only RLadyBug-0.5-0/RLadyBug/man/spatialSIR_epidata_animate.Rd |only RLadyBug-0.5-0/RLadyBug/man/spatialSIR_epidata_plot.Rd |only RLadyBug-0.5-0/RLadyBug/man/spatialSIR_exData.Rd |only RLadyBug-0.5-0/RLadyBug/man/spatialSIR_intensityPlot.Rd |only RLadyBug-0.5-0/RLadyBug/man/spatialSIR_profile.Rd |only RLadyBug-0.5-0/RLadyBug/man/spatialSIR_simulation.Rd |only RLadyBug-0.6-0/RLadyBug/DESCRIPTION | 44 +++--- RLadyBug-0.6-0/RLadyBug/NAMESPACE | 35 ++--- RLadyBug-0.6-0/RLadyBug/NEWS | 90 +++++++++++++ RLadyBug-0.6-0/RLadyBug/R/twinSIR.R |only RLadyBug-0.6-0/RLadyBug/R/twinSIR_epidata.R |only RLadyBug-0.6-0/RLadyBug/R/twinSIR_helper.R |only RLadyBug-0.6-0/RLadyBug/R/twinSIR_intensity.R |only RLadyBug-0.6-0/RLadyBug/R/twinSIR_methods.R |only RLadyBug-0.6-0/RLadyBug/R/twinSIR_simulation.R |only RLadyBug-0.6-0/RLadyBug/R/zzz.R | 14 +- RLadyBug-0.6-0/RLadyBug/data/bw.RData |only RLadyBug-0.6-0/RLadyBug/data/fooepidata.RData |binary RLadyBug-0.6-0/RLadyBug/data/foofit.RData |binary RLadyBug-0.6-0/RLadyBug/inst/CITATION | 50 ++++--- RLadyBug-0.6-0/RLadyBug/man/LBExperiment-class.Rd | 1 RLadyBug-0.6-0/RLadyBug/man/RLadyBug-package.Rd | 4 RLadyBug-0.6-0/RLadyBug/man/twinSIR.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_cox.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_epidata.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_epidata_animate.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_epidata_intersperse.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_epidata_plot.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_epidata_summary.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_exData.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_intensityPlot.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_methods.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_profile.Rd |only RLadyBug-0.6-0/RLadyBug/man/twinSIR_simulation.Rd |only 44 files changed, 181 insertions(+), 57 deletions(-)
Author: Didier Leibovici
Diff between PTAk versions 1.1-22 dated 2009-08-26 and 1.2-0 dated 2009-10-07
Title: Principal Tensor Analysis on k modes
Description: A multiway method to decompose a tensor (array) of any
order, as a generalisation of SVD also supporting non-identity
metrics and penalisations. 2-way SVD with these extensions is
also available. The package includes also some other multiway
methods: PCAn (Tucker-n) and PARAFAC/CANDECOMP with these
extensions.
PTAk-1.1-22/PTAk/CITATION |only
PTAk-1.1-22/PTAk/LICENSE |only
PTAk-1.1-22/PTAk/inst/doc/PTAklicence.pdf |only
PTAk-1.2-0/PTAk/DESCRIPTION | 10 +++++-----
PTAk-1.2-0/PTAk/inst/CITATION |only
PTAk-1.2-0/PTAk/inst/doc/PTAkgeneral.pdf |binary
PTAk-1.2-0/PTAk/inst/doc/index.html | 13 +++++++------
PTAk-1.2-0/PTAk/inst/doc/left.jpg |only
PTAk-1.2-0/PTAk/inst/doc/logo.jpg |only
PTAk-1.2-0/PTAk/inst/doc/logosm.jpg |only
PTAk-1.2-0/PTAk/inst/doc/right.jpg |only
PTAk-1.2-0/PTAk/inst/doc/up.jpg |only
12 files changed, 12 insertions(+), 11 deletions(-)
Author: Spencer Graves
Title: Companion to Tsay (2005) Analysis of Financial Time Series
Description: R companion to Tsay (2005) Analysis of Financial Time
Series, 2nd ed. (Wiley). Includes data sets, functions and
script files required to work some of the examples. Version
0.3-x includes R objects for all data files used in the text
and script files to recreate most of the analyses in chapters
1-3 and 9 plus parts of chapters 4 and 11.
Diff between FinTS versions 0.4-2 dated 2009-09-07 and 0.4-3 dated 2009-10-07
DESCRIPTION | 8 ++++---- R/runscript.R | 9 ++++++++- man/runscript.Rd | 44 +++++++++++++++++++++++++------------------- 3 files changed, 37 insertions(+), 24 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 2.0-0 dated 2009-10-01 and 2.0-1 dated 2009-10-07
DESCRIPTION | 6 +++--- src/de4_0.c | 6 ++++++ 2 files changed, 9 insertions(+), 3 deletions(-)