Author: Søren Højsgaard
Diff between doBy versions 3.9 dated 2009-05-13 and 4.0.0 dated 2009-07-31
Title: Groupwise computations of summary statistics, general linear
contrasts and other utilities
Description: Facilities for groupwise computations of summary
statistics and other facilities for working with grouped data.
doBy-3.9/doBy/mknamespace |only
doBy-4.0.0/doBy/ChangeLog | 16
doBy-4.0.0/doBy/DESCRIPTION | 12
doBy-4.0.0/doBy/INDEX | 2
doBy-4.0.0/doBy/NAMESPACE | 28
doBy-4.0.0/doBy/R/HmiscStuff.R | 152 ++--
doBy-4.0.0/doBy/R/esticon.R | 9
doBy-4.0.0/doBy/R/esticoncoxph.R |only
doBy-4.0.0/doBy/R/splitBy.R | 248 +++----
doBy-4.0.0/doBy/R/which.maxn.R |only
doBy-4.0.0/doBy/inst/doc/doBy.Rnw | 16
doBy-4.0.0/doBy/inst/doc/doBy.pdf | 1287 +++++++++++++++++++-------------------
doBy-4.0.0/doBy/man/budworm.Rd | 3
doBy-4.0.0/doBy/man/esticon.Rd | 32
doBy-4.0.0/doBy/man/splitBy.Rd | 8
doBy-4.0.0/doBy/man/which.maxn.Rd |only
16 files changed, 970 insertions(+), 843 deletions(-)
Author: Matthias Kohl, Peter Ruckdeschel
Title: Object orientated implementation of probability models
Description: Object orientated implementation of probability models
based on packages 'distr' and 'distrEx'
Diff between distrMod versions 2.1 dated 2009-04-15 and 2.1.1 dated 2009-07-31
DESCRIPTION | 14 +++++++------- R/L2ParamFamily.R | 6 +++--- man/Estimate-class.Rd | 2 ++ man/InternalReturnClasses-class.Rd | 2 +- man/L2ParamFamily-class.Rd | 2 +- man/asSemivar-class.Rd | 12 ++++++++---- man/confint-methods.Rd | 2 +- man/distrModOptions.Rd | 2 +- man/internalClassUnions-class.Rd | 2 +- man/trafo-methods.Rd | 2 +- man/validParameter-methods.Rd | 2 +- 11 files changed, 27 insertions(+), 21 deletions(-)
Author: Matthias Kohl, Peter Ruckdeschel
Title: Implementation of random variables
Description: Implementation of random variables by means of S4 classes
and methods
Diff between RandVar versions 0.6.8 dated 2009-07-31 and 0.6.9 dated 2009-07-31
DESCRIPTION | 10 +++++----- inst/doc/RandVar.pdf |binary inst/doc/svn-multi.sty |only inst/doc/svnkw.sty |only 4 files changed, 5 insertions(+), 5 deletions(-)
Author: Thomas Scheike with contributions from Torben Martinussen and
Jeremy Silver
Title: timereg package for Flexible regression models for survival
data.
Description: Programs for Martinussen and Scheike (2006), `Dynamic
Regression Models for Survival Data', Springer Verlag. Plus
more recent developments. Additive survival model,
semiparmetric proportional odds model, cumulative residuals,
excess risk models and more. Flexible competing risks
regression including GOF-tests.
Diff between timereg versions 1.2-2 dated 2009-06-14 and 1.2-5 dated 2009-07-31
timereg-1.2-2/timereg/R/two-stage.r |only timereg-1.2-2/timereg/man/two.stage.Rd |only timereg-1.2-2/timereg/src/aalen-des.c |only timereg-1.2-2/timereg/src/two-stage.c |only timereg-1.2-5/timereg/DESCRIPTION | 8 - timereg-1.2-5/timereg/NAMESPACE | 8 - timereg-1.2-5/timereg/R/additive-compSs.r |only timereg-1.2-5/timereg/R/additive-lasso.r | 8 - timereg-1.2-5/timereg/R/plots.r | 3 timereg-1.2-5/timereg/R/pls.cv.r | 8 - timereg-1.2-5/timereg/R/two-stage-reg.r | 125 +++++++++++++++++++++------ timereg-1.2-5/timereg/man/dynreg.Rd | 4 timereg-1.2-5/timereg/man/internal-addreg.Rd | 1 timereg-1.2-5/timereg/man/surv-lars.Rd | 3 timereg-1.2-5/timereg/man/two.stage.reg.Rd | 28 +++--- timereg-1.2-5/timereg/src/aalen-test.c | 6 - timereg-1.2-5/timereg/src/aalen.c | 14 +-- timereg-1.2-5/timereg/src/additive-compSs.c |only timereg-1.2-5/timereg/src/breslow.c | 45 +-------- timereg-1.2-5/timereg/src/comprisk.c | 6 - timereg-1.2-5/timereg/src/comptest-cmprsk.c | 3 timereg-1.2-5/timereg/src/comptest.c | 8 - timereg-1.2-5/timereg/src/dynadd.c | 6 - timereg-1.2-5/timereg/src/matrix.h | 35 +++++++ timereg-1.2-5/timereg/src/smooth2.c | 2 timereg-1.2-5/timereg/src/timecox.c | 27 ----- 26 files changed, 202 insertions(+), 146 deletions(-)
Author: Stefano Maria Iacus
Title: Simulation and Inference for Stochastic Differential Equations
Description: Companion package to the book Simulation and Inference for
Stochastic Differential Equations With R Examples, ISBN
978-0-387-75838-1, Springer, NY.
Diff between sde versions 2.0.8 dated 2009-07-24 and 2.0.9 dated 2009-07-31
sde-2.0.8/sde/inst/doc/sde.errata.aux |only sde-2.0.8/sde/inst/doc/sde.errata.log |only sde-2.0.9/sde/DESCRIPTION | 10 +++++----- sde-2.0.9/sde/R/MOdist.R | 4 ++-- sde-2.0.9/sde/inst/doc/sde.errata.pdf |binary sde-2.0.9/sde/man/MOdist.Rd | 2 +- 6 files changed, 8 insertions(+), 8 deletions(-)
Author: L. Andries van der Ark
Diff between mokken versions 1.4 dated 2008-12-18 and 2.0 dated 2009-07-31
Title: Mokken Scale Analysis in R
Description: mokken contains functions for performing Mokken scale
analysis on test and questionnaire data. It includes an
automated item selection algorithm, and various checks of model
assumptions.
mokken-1.4/mokken/R/zzz.R |only
mokken-1.4/mokken/man/search.normal.Rd |only
mokken-2.0/mokken/CITATION |only
mokken-2.0/mokken/DESCRIPTION | 29 +++++++++++----------
mokken-2.0/mokken/NAMESPACE | 25 +++++++++++++++---
mokken-2.0/mokken/R/aisp.R |only
mokken-2.0/mokken/R/check.iio.R | 11 ++++---
mokken-2.0/mokken/R/search.extended.R |only
mokken-2.0/mokken/R/search.ga.R |only
mokken-2.0/mokken/R/search.normal.R | 28 +++++++++++---------
mokken-2.0/mokken/inst |only
mokken-2.0/mokken/man/aisp.Rd |only
mokken-2.0/mokken/man/check.iio.Rd | 4 --
mokken-2.0/mokken/man/check.monotonicity.Rd | 2 -
mokken-2.0/mokken/man/check.pmatrix.Rd | 2 -
mokken-2.0/mokken/man/check.reliability.Rd | 5 ---
mokken-2.0/mokken/man/check.restscore.Rd | 3 --
mokken-2.0/mokken/man/coefH.Rd | 3 --
mokken-2.0/mokken/man/coefZ.Rd | 2 -
mokken-2.0/mokken/man/mokken-package.Rd | 9 ++----
mokken-2.0/mokken/man/plot.monotonicity.class.Rd | 2 -
mokken-2.0/mokken/man/plot.pmatrix.class.Rd | 2 -
mokken-2.0/mokken/man/plot.restscore.class.Rd | 2 -
mokken-2.0/mokken/man/summary.monotonicity.cass.Rd | 5 ---
mokken-2.0/mokken/man/summary.pmatrix.class.Rd | 8 -----
mokken-2.0/mokken/man/summary.restscore.class.Rd | 4 --
mokken-2.0/mokken/src |only
27 files changed, 64 insertions(+), 82 deletions(-)
Author: Wolfgang Viechtbauer
Diff between metafor versions 0.5-0 dated 2009-06-05 and 0.5-3 dated 2009-07-31
Title: Meta-Analysis Package for R
Description: The metafor package consists of a collection of functions
for conducting meta-analyses in R. Fixed- and random-effects
models (with and without moderators) can be fitted via the
general linear (mixed-effects) model. For 2x2 table data, the
Mantel-Haenszel and Peto's method are also implemented.
DESCRIPTION | 10 ++--
NEWS | 21 +++++++++
R/metafor.R | 105 ++++++++++++++++++++++++++++-------------------
man/escalc.Rd | 5 +-
man/forest.default.Rd | 2
man/forest.rma.Rd | 13 +++--
man/plot.rma.uni.Rd | 3 +
man/plot.rma.uni.infl.Rd | 10 ++--
8 files changed, 110 insertions(+), 59 deletions(-)
Author: Felix Kaminsky
Diff between estout versions 0.4-1 dated 2009-05-28 and 0.5-1 dated 2009-07-31
Title: Estimates Output
Description: The function collection stores the estimates of several
models and formats it to a table of the form estimate starred
and std.err. below. The default output is LaTeX but output to
CSV for later editing in a spreadsheet tool is possible as
well. It works for linear models (lm) and panel models from the
"plm"-package (plm).
DESCRIPTION | 15 +++---
R/eststo.R | 12 ++++
R/esttab.R | 145 +++++++++++++++++++++++++++++++++++++++++-----------------
man/esttab.Rd | 6 +-
4 files changed, 126 insertions(+), 52 deletions(-)
Author: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.9.1.4 dated 2009-07-30 and 2.9.1.5 dated 2009-07-31
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
DESCRIPTION | 8 ++++----
R/epicalc.R | 43 +++++++++++++++++++++++--------------------
man/roc.rd | 28 ++++++++++++++++++++++++++++
man/tableStack.rd | 12 +++++++++++-
4 files changed, 66 insertions(+), 25 deletions(-)
Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas
Stabla
Title: Estimation and Testing classes based on package distr
Description: Evaluation (S4-)classes based on package distr for
evaluating procedures (estimators/tests) at data/simulation in
a unified way.
Diff between distrTEst versions 2.1 dated 2009-04-15 and 2.1.1 dated 2009-07-31
DESCRIPTION | 8 ++++---- man/Evaluation-class.Rd | 3 ++- 2 files changed, 6 insertions(+), 5 deletions(-)
Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas
Stabla
Title: Simulation classes based on package distr
Description: Simulation (S4-)classes based on package distr
Diff between distrSim versions 2.1 dated 2009-04-15 and 2.1.1 dated 2009-07-31
DESCRIPTION | 8 ++++---- man/summary-methods.Rd | 36 ++++++++++++++++++++---------------- 2 files changed, 24 insertions(+), 20 deletions(-)
Author: Peter Ruckdeschel
Title: Utilities for Sweave together with TeX listings package
Description: provides utilities for defining R / Rd as
Tex-package-listings "language" and including R / Rd source
file (sniplets) copied from R-forge in its most recent version
(or another url) thereby avoiding inconsistencies between
vignette and documented source code
Diff between SweaveListingUtils versions 0.3 dated 2009-07-02 and 0.3.3 dated 2009-07-31
DESCRIPTION | 12 +- NAMESPACE | 6 - R/SweaveListingOptions.R | 22 +++- R/SweaveListingUtils.R | 162 ++++++++++++++++++++++++--------- R/keywordsStyle.R | 121 +++++++++++++++++++----- inst/NEWS | 14 ++ inst/doc/ExampleSweaveListingUtils.Rnw | 77 +++++++++++---- inst/doc/ExampleSweaveListingUtils.pdf |binary inst/doc/exam00.tex |only inst/doc/preamble.tex | 10 +- inst/doc/preamble2.tex |only inst/doc/preambleExp.tex | 107 +++++++++++++-------- inst/try |only man/SweaveListingOptions.Rd | 45 ++++++++- man/SweaveListingPreparations.Rd | 30 ++++-- man/isBaseOrRecommended.Rd |only man/lstinputSourceFromRForge.Rd | 4 man/lstset.Rd | 35 +++++-- man/setBaseOrRecommended.Rd |only man/taglist.Rd | 11 +- 20 files changed, 485 insertions(+), 171 deletions(-)
More information about SweaveListingUtils at CRAN
Permanent link
Author: Matthias Kohl, Peter Ruckdeschel
Title: Implementation of random variables
Description: Implementation of random variables by means of S4 classes
and methods
Diff between RandVar versions 0.6.7 dated 2009-02-25 and 0.6.8 dated 2009-07-31
DESCRIPTION | 32 +++++++++++++++++++------------- R/util.R | 5 ++++- inst/doc/RandVar.Rnw | 34 +++++++++++++++++++++++++++++++++- inst/doc/RandVar.pdf |binary man/0RandVar-package.Rd | 4 ++-- man/EuclRandVarList-class.Rd | 4 ++-- man/EuclRandVariable-class.Rd | 2 +- 7 files changed, 61 insertions(+), 20 deletions(-)
Author: Ulrike Groemping
Title: Fractional Factorial designs with 2-level factors
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 currently subject to intensive development. While
much of the intended functionality is already available, some
changes and improvements are still to be expected. Suggestions
are welcome.
Diff between FrF2 versions 0.95 dated 2009-07-18 and 0.96 dated 2009-07-31
DESCRIPTION | 12 +- R/FrF2.R | 19 ++- inst/NEWS | 12 ++ man/FrF2.Rd | 5 tests/FrF2test.Rout.save | 274 +++++++++++++++++++++++++++-------------------- tests/pbtest.Rout.save | 15 ++ 6 files changed, 209 insertions(+), 128 deletions(-)
Author: Øivind Skare
Diff between FEST versions 0.04 dated 2009-07-18 and 0.05 dated 2009-07-31
Title: Identification of Family Relations using linked markers
Description: Identification of Family Relations using linked markers.
DESCRIPTION | 8 ++++----
inst/CITATION | 26 ++++++++++++--------------
inst/doc |only
3 files changed, 16 insertions(+), 18 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.4-1 dated 2009-07-18 and 0.5 dated 2009-07-31
DESCRIPTION | 12 + NAMESPACE | 9 + R/DesignAccessors.r | 289 +++++++++++++++++++++++++++++++++++++++++++-- R/add.response.R |only R/cross.design.R |only R/export.design.R | 30 +++- R/fac.design.R | 8 - R/interleave.R |only R/oa.design.R | 19 ++ R/param.design.R |only R/paramtowide.R |only R/printandsummary.design.R |only R/reptolong.R |only R/reptowide.R |only inst/NEWS | 43 ++++++ man/add.response.Rd |only man/class-design.Rd | 160 +++++++++++++++++++++--- man/contr.FrF2.Rd | 15 +- man/cross.design.Rd |only man/export.design.Rd | 16 +- man/fac.design.Rd | 10 + man/oa.design.Rd | 5 man/param.design.Rd |only man/represhape.Rd |only tests |only 25 files changed, 550 insertions(+), 66 deletions(-)
Author: Tyler Kendall and Erik R. Thomas
Title: Vowel Manipulation, Normalization, and Plotting
Description: vowels is an R package for the manipulation,
normalization, and plotting of phonetic and sociophonetic vowel
formant data. vowels is the backend for the NORM website.
Diff between vowels versions 1.0-2 dated 2009-04-23 and 1.0-3 dated 2009-07-30
DESCRIPTION | 8 ++++---- R/vowels.R | 6 +++++- man/vowels-package.Rd | 4 ++-- 3 files changed, 11 insertions(+), 7 deletions(-)
Author: William Revelle
Diff between psych versions 1.0-77 dated 2009-07-27 and 1.0-78 dated 2009-07-30
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A number of routines for personality, psychometrics and
experimental psychology. Functions are primarily for scale
construction using factor analysis, cluster analysis and
reliability analysis, although others provide basic descriptive
statistics. Functions for simulating particular item and test
structures are included. Several functions serve as a useful
front end for structural equation modeling. For more
information, see the personality-project.org/r webpage.
CHANGES | 12
DESCRIPTION | 8
R/ICLUST.cluster.R | 2
R/fa.R | 1
R/factor.stats.R | 6
R/principal.R | 2
inst/NEWS | 6
inst/doc/overview.pdf |13355 ++++++++++++++++++++++-----------------------
inst/doc/psych_for_sem.pdf | 1747 ++---
man/00.psych-package.Rd | 4
man/principal.Rd | 4
11 files changed, 7687 insertions(+), 7460 deletions(-)
Author: Luis Cayuela and Marcelino de la Cruz
Title: Functions to incorporate taxonomic uncertainty on multivariate
analyses of ecological data
Description: Permutational method to incorporate taxonomic uncertainty
and some functions to assess its effects on parameters of some
widely used multivariate methods in ecology
Diff between betaper versions 1.0-0 dated 2008-06-09 and 1.1-0 dated 2009-07-30
betaper-1.0-0/betaper/NAMESPACE |only betaper-1.0-0/betaper/R/betaper.R |only betaper-1.0-0/betaper/R/plot.betaper.R |only betaper-1.0-0/betaper/R/print.betaper.R |only betaper-1.0-0/betaper/man/betaper.Rd |only betaper-1.0-0/betaper/man/plot.betaper.Rd |only betaper-1.1-0/betaper/DESCRIPTION | 29 +++++++++++++---------- betaper-1.1-0/betaper/R/adonis.pertables.R |only betaper-1.1-0/betaper/R/cca.pertables.R |only betaper-1.1-0/betaper/R/mantel.pertables.R |only betaper-1.1-0/betaper/R/pertables.R |only betaper-1.1-0/betaper/R/plot.adonis.pertables.R |only betaper-1.1-0/betaper/R/plot.cca.pertables.R |only betaper-1.1-0/betaper/R/plot.mantel.pertables.R |only betaper-1.1-0/betaper/R/plot.rda.pertables.R |only betaper-1.1-0/betaper/R/print.adonis.pertables.R |only betaper-1.1-0/betaper/R/print.cca.pertables.R |only betaper-1.1-0/betaper/R/print.mantel.pertables.R |only betaper-1.1-0/betaper/R/print.pertables.R |only betaper-1.1-0/betaper/R/print.rda.pertables.R |only betaper-1.1-0/betaper/R/rda.pertables.R |only betaper-1.1-0/betaper/data/Amazonia.rda |binary betaper-1.1-0/betaper/data/HCP.coords.rda |binary betaper-1.1-0/betaper/data/HCP.rda |binary betaper-1.1-0/betaper/data/soils.rda |binary betaper-1.1-0/betaper/man/adonis.pertables.Rd |only betaper-1.1-0/betaper/man/cca.pertables.Rd |only betaper-1.1-0/betaper/man/mantel.pertables.Rd |only betaper-1.1-0/betaper/man/pertables.Rd |only betaper-1.1-0/betaper/man/rda.pertables.Rd |only 30 files changed, 17 insertions(+), 12 deletions(-)
Author: Kurt Hornik
Title: Harvest Metadata Using OAI-PMH v2.0
Description: Harvest metadata using the Open Archives Initiative
Protocol for Metadata Harvesting (OAI-PMH) version 2.0.
Diff between OAIHarvester versions 0.0-3 dated 2009-03-14 and 0.0-4 dated 2009-07-30
DESCRIPTION | 8 ++++---- R/pmh.R | 3 +++ inst/doc/oaih.Rnw | 13 ++++++++----- inst/doc/oaih.bib | 8 ++++++++ inst/doc/oaih.pdf |binary 5 files changed, 23 insertions(+), 9 deletions(-)
Author: Marie Morfin and David Makowski
Title: Model selection uncertainty and model mixing
Description: Implement different types of model mixing and model
selection methods for linear or logistic models.
Diff between MMIX versions 1.0 dated 2009-07-24 and 1.1 dated 2009-07-30
DESCRIPTION | 10 ++++----- R/aucCV.r | 51 ++++++++++++++++++++++--------------------------- R/bmaBic.r | 37 ++++++++++++++++++----------------- R/mixAic.r | 36 +++++++++++++++++----------------- R/pmseCV.r | 17 +++++++++------- R/print.MMIX.r | 7 ++---- man/MMIX-package.Rd | 6 ++--- man/arms.Rd | 2 - man/bootFreq.Rd | 11 +++------- man/pmseCV.Rd | 5 +++- man/print.MMIXclass.Rd | 6 ++--- man/stepSel.Rd | 6 ++--- man/varSelec.Rd | 2 - 13 files changed, 97 insertions(+), 99 deletions(-)
Author: Jon Wakefield
Diff between HWEBayes versions 1.1 dated 2009-07-22 and 1.2 dated 2009-07-30
Title: Bayesian investigation of Hardy-Weinberg Equilibrium via
estimation and testing.
Description: Estimation and testing of HWE using Bayesian methods.
Three models are currently considered: HWE, a model
parameterized in terms of the allele frequencies and a single
inbreeding coefficient f, and the saturated model. Testing is
based on Bayes factors.
DESCRIPTION | 6 +++---
inst/doc/HWEBayes-Guide.Snw |only
inst/doc/HWEBayes-Guide.pdf |binary
3 files changed, 3 insertions(+), 3 deletions(-)
Author: Brian Ripley
Diff between tree versions 1.0-26 dated 2007-07-28 and 1.0-27 dated 2009-07-30
Title: Classification and regression trees
Description: Classification and Regression Trees.
ChangeLog | 9 +
DESCRIPTION | 11 +-
R/grow.q | 22 ++--
R/plot.tree.sequence.q | 10 +-
R/treefix.R | 50 +++++-----
R/treemisc.R | 163 +++++++++++++++++-----------------
inst/po/en@quot/LC_MESSAGES/R-tree.mo |binary
inst/po/en@quot/LC_MESSAGES/tree.mo |binary
man/na.tree.replace.Rd | 4
man/tile.tree.Rd | 10 +-
man/tree.control.Rd | 6 -
po/R-en@quot.po | 9 +
po/R-tree.pot | 10 +-
po/en@quot.po | 16 +--
po/tree.pot | 8 -
src/treefix.c | 8 +
tests/Examples |only
17 files changed, 179 insertions(+), 157 deletions(-)
Author: Mark Bravington, Karen Martien, Dave Gregovich
Title: Testing of Spatial Structure Methods
Description: Provides a framework under which methods of detecting and
managing genetic spatial structure in populations can be
tested.
Diff between tossm versions 1.2 dated 2009-03-06 and 1.3 dated 2009-07-30
tossm-1.2/tossm/NAMESPACE |only tossm-1.2/tossm/R/sysdata.rda |only tossm-1.3/tossm/DESCRIPTION | 31 ++++++++++-------- tossm-1.3/tossm/R/CLA.R | 13 +++++-- tossm-1.3/tossm/R/TOSSM.utils.R | 27 +++++++++++++++ tossm-1.3/tossm/R/Voronoi.funcs.R |only tossm-1.3/tossm/R/def.depleter.R | 3 + tossm-1.3/tossm/R/def.genetic.sampler.R | 17 ++------- tossm-1.3/tossm/R/get.n.in.ss.R |only tossm-1.3/tossm/R/humpbackism.R | 4 +- tossm-1.3/tossm/R/hyptest.network.BSA.R | 24 +++++++++++--- tossm-1.3/tossm/R/hyptest.seq.BSA.R | 2 - tossm-1.3/tossm/R/new.harvest.R | 32 +++++++++++------- tossm-1.3/tossm/R/run.tossm.R | 41 +++++++++++++----------- tossm-1.3/tossm/R/wombsoft.BSA.R | 12 +++---- tossm-1.3/tossm/R/zzz.R |only tossm-1.3/tossm/data/sysdata.rda |only tossm-1.3/tossm/inst/TOSSM_dataset_handbook.pdf |binary tossm-1.3/tossm/inst/TOSSM_users_guide.pdf |binary tossm-1.3/tossm/man/def.genetic.sampler.Rd | 5 +- tossm-1.3/tossm/man/hyptest.network.BSA.Rd | 12 ++++--- tossm-1.3/tossm/man/run.tossm.Rd | 6 +-- tossm-1.3/tossm/man/tossm-internal.Rd |only tossm-1.3/tossm/src/CLC-D.f | 5 +- tossm-1.3/tossm/src/MANAGE-D.f | 24 ++++++++++---- 25 files changed, 164 insertions(+), 94 deletions(-)
Author: Valentin Todorov
Diff between rrcov versions 0.5-01 dated 2009-03-05 and 0.5-02 dated 2009-07-30
Title: Scalable Robust Estimators with High Breakdown Point
Description: Robust Location and Scatter Estimation and Robust
Multivariate Analysis with High Breakdown Point.
ChangeLog | 6 +
DESCRIPTION | 27 ++--
NAMESPACE | 2
R/AllClasses.R | 117 +++++++++----------
R/CovRobust.R | 32 ++---
R/Pca.R | 196 ++++++++++++++++++++++++--------
R/PcaClassic.R | 36 +++---
R/PcaHubert.R | 262 ++++++++++++++++++++++----------------------
R/Wilks.test.R | 172 +++++++++++++++++-----------
inst/doc/UML.pdf |binary
man/CovControlMcd-class.Rd | 45 ++++---
man/CovControlMest-class.Rd | 29 ++--
man/CovControlMve-class.Rd | 35 +++--
man/CovControlOgk-class.Rd | 43 ++++---
man/CovControlSde-class.Rd | 41 +++---
man/CovControlSest-class.Rd | 43 ++++---
man/CovMcd-class.Rd | 84 ++++++--------
man/CovMcd.Rd | 32 ++---
man/CovMest-class.Rd | 36 ++----
man/CovMve-class.Rd | 81 ++++++-------
man/CovOgk-class.Rd | 50 +++-----
man/CovRobust-class.Rd | 29 ++--
man/CovRobust.Rd | 46 ++++---
man/CovSde-class.Rd | 34 ++---
man/CovSest-class.Rd | 42 ++-----
man/CovSest.Rd | 74 ++++++------
man/Pca-class.Rd | 5
man/PcaCov-class.Rd | 43 ++-----
man/PcaGrid-class.Rd | 39 ++----
man/PcaHubert-class.Rd | 49 +++-----
man/PcaHubert.Rd | 6 -
man/PcaLocantore-class.Rd | 45 ++-----
man/PcaProj-class.Rd | 39 ++----
man/Wilks.test.Rd | 18 ++-
man/biplot.Rd |only
man/estimate-methods.Rd | 10 -
tests/thubert.Rout.save | 4
tests/tlda.Rout.save | 4
tests/tmcd4.Rout.save | 4
tests/tmest.Rout.save | 4
tests/tmest4.Rout.save | 4
tests/tmve4.Rout.save | 4
tests/togk4.Rout.save | 4
tests/tqda.Rout.save | 4
tests/tsde.Rout.save | 4
tests/tsest.Rout.save | 4
46 files changed, 978 insertions(+), 910 deletions(-)
Author: Romain Francois
Diff between parser versions 0.0-2 dated 2009-07-27 and 0.0-3 dated 2009-07-30
Title: Detailed R source code parser
Description: detailed source code parser, based on the standard R
parser but organizing the information differently
parser-0.0-2/parser/data/symbols.txt |only
parser-0.0-3/parser/DESCRIPTION | 11 ++++++-----
parser-0.0-3/parser/NAMESPACE | 2 +-
parser-0.0-3/parser/R/parser.R | 9 ++++-----
parser-0.0-3/parser/R/zzz.R | 2 +-
parser-0.0-3/parser/data/grammar_symbols.txt |only
parser-0.0-3/parser/inst/example |only
parser-0.0-3/parser/man/grammar.symbols.Rd | 7 ++++---
parser-0.0-3/parser/man/parser.Rd | 15 ++++-----------
parser-0.0-3/parser/man/symbols.Rd | 8 ++++----
10 files changed, 24 insertions(+), 30 deletions(-)
Author: Vincent J Carey. Ported to R by Thomas Lumley (versions 3.13
and 4.4) and Brian Ripley
Diff between gee versions 4.13-13 dated 2007-06-19 and 4.13-14 dated 2009-07-30
Title: Generalized Estimation Equation solver
Description: Generalized Estimation Equation solver
ChangeLog |only
DESCRIPTION | 16 ++++++++++------
man/gee.Rd | 4 ++--
tests/Examples |only
4 files changed, 12 insertions(+), 8 deletions(-)
Author: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.9.1.3 dated 2009-07-26 and 2.9.1.4 dated 2009-07-30
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
DESCRIPTION | 8 +--
R/epicalc.R | 130 ++++++++++++++++++++++++++++++++++--------------------------
man/VCT.rd | 4 -
3 files changed, 80 insertions(+), 62 deletions(-)
Author: Antonio Gasparrini and Ben Armstrong
Title: Distributed Lag Non-linear Models
Description: The package dlnm contains functions to specify basis and
cross-basis matrices in order to run distributed lag models and
their non-linear extension, then to predict and graph the
results for a fitted model.
Diff between dlnm versions 0.2.1 dated 2009-07-18 and 0.3.0 dated 2009-07-30
DESCRIPTION | 8 R/crossplot.R | 24 R/mkbasis.R | 47 R/mklagbasis.R | 1 inst/dlnmChangeLog | 34 inst/doc/Rplots.pdf |47088 +++++++++++++++++++++++++++++++------------ inst/doc/dlnmOverview.Rnw | 124 inst/doc/dlnmOverview.pdf |50073 +++++++++++++++++++++++++++++++++------------- man/crossbasis.Rd | 20 man/crossplot.Rd | 14 man/crosspred.Rd | 4 11 files changed, 70948 insertions(+), 26489 deletions(-)
Author: Jun Yan
Diff between copula versions 0.8-9 dated 2009-07-24 and 0.8-10 dated 2009-07-30
Title: Multivariate dependence with copulas
Description: Classes (S4) of commonly used copulas including elliptical
(normal and t), Archimedean (Clayton, Gumbel, Frank, and
Ali-Mikhail-Haq), extreme value (Gumbel, Husler-Reiss,
Galambos, and t-EV), and other families (Plackett and
Farlie-Gumbel-Morgenstern). Methods for density, distribution,
random number generation, bivariate dependence measures,
perspective and contour plots. Functions for fitting copula
models with variance estimate. Independence tests among random
variables and random vectors. Serial independence tests for
univariate and multivariate continuous time series.
Goodness-of-fit tests for copulas based on multipliers and on
the parametric bootstrap.
ChangeLog | 7 +++++++
DESCRIPTION | 8 ++++----
R/claytonCopula.R | 2 +-
3 files changed, 12 insertions(+), 5 deletions(-)
Author: Joshua Ulrich
Title: Technical Trading Rules
Description: Functions and data to construct technical trading rules
with R.
Diff between TTR versions 0.2 dated 2009-02-11 and 0.20-0 dated 2009-07-30
CHANGES | 78 +++++---------------- DESCRIPTION | 17 ++-- NAMESPACE | 2 R/GMMA.R |only R/KST.R | 15 +++- R/MACD.R | 13 ++- R/RSI.R | 7 + R/TRIX.R | 21 +++-- R/WebData.R | 72 +++++-------------- R/adjRatios.R |only R/envelopes.R |only R/runFun.R | 137 ++++++++++++++++++++++--------------- R/stochastics.R | 50 ++++++++++--- R/volatility.R | 45 +++++++++--- R/zzz.R | 6 - man/ADX.Rd | 5 - man/ATR.Rd | 2 man/CCI.Rd | 7 + man/CLV.Rd | 2 man/CMF.Rd | 2 man/CMO.Rd | 2 man/DPO.Rd | 2 man/DonchianChannel.Rd | 2 man/EMV.Rd | 2 man/GMMA.Rd |only man/KST.Rd | 5 + man/MACD.Rd | 5 - man/MFI.Rd | 2 man/MovingAverages.Rd | 2 man/OBV.Rd | 2 man/RSI.Rd | 2 man/SAR.Rd | 2 man/TDI.Rd | 6 - man/TRIX.Rd | 6 + man/TTR.Rd | 8 +- man/TTRtools.Rd | 2 man/VHF.Rd | 9 +- man/WPR.Rd | 2 man/WebData.Rd | 2 man/ZigZag.Rd | 2 man/adjRatios.Rd |only man/aroon.Rd | 5 - man/bollingerBands.Rd | 2 man/chaikinAD.Rd | 2 man/chaikinVolatility.Rd | 2 man/changes.Rd | 2 man/runFun.Rd | 30 ++++---- man/stochastics.Rd | 16 +++- man/volatility.Rd | 28 +++++-- man/williamsAD.Rd | 2 src/adjRatios.c |only src/runFun.f | 37 +++++---- tests/unitTests/runit.TTR.runFun.R | 2 53 files changed, 391 insertions(+), 283 deletions(-)
Author: Markus Loecher
Diff between ReadImages versions 0.1.3 dated 2009-07-27 and 0.1.3.1 dated 2009-07-30
Title: Image Reading Module for R
Description: This package provides functions for reading JPEG and PNG
files. This package requires libjpeg
DESCRIPTION | 6 +++---
man/ReadImages-package.Rd | 2 +-
src/Makevars.win |only
3 files changed, 4 insertions(+), 4 deletions(-)
Author: Douglas Bates
Diff between Matrix versions 0.999375-29 dated 2009-06-11 and 0.999375-30 dated 2009-07-30
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using Lapack and SuiteSparse.
ChangeLog | 92 +++++++
DESCRIPTION | 8
NAMESPACE | 16 -
R/Auxiliaries.R | 20 +
R/CHMfactor.R | 44 +++
R/Csparse.R | 10
R/Matrix.R | 23 +
R/Tsparse.R | 2
R/bind2.R | 2
R/diagMatrix.R | 65 +++--
R/dsCMatrix.R | 4
R/ldenseMatrix.R | 6
R/rankMatrix.R | 2
R/spModels.R |only
R/sparseMatrix.R | 115 +--------
R/zzz.R | 4
TODO | 2
inst/doc/Comparisons.pdf |binary
inst/doc/Design-issues.pdf |binary
inst/doc/Intro2Matrix.pdf | 417 +++++++++++++++++-----------------
inst/doc/Introduction.pdf |binary
inst/doc/fullpage.sty |only
inst/doc/sparseModels.pdf |binary
inst/po/de/LC_MESSAGES/Matrix.mo |binary
inst/po/de/LC_MESSAGES/R-Matrix.mo |binary
inst/po/en@quot/LC_MESSAGES/Matrix.mo |binary
inst/test-tools.R | 60 ++++
man/BunchKaufman-methods.Rd | 8
man/CHMfactor-class.Rd | 34 +-
man/Cholesky-class.Rd | 39 ++-
man/Cholesky.Rd | 18 +
man/contrast.Rd |only
man/diagonalMatrix-class.Rd | 16 -
man/qr-methods.Rd | 8
man/sparse.model.matrix.Rd |only
man/sparseQR-class.Rd | 33 +-
po/Matrix.pot | 61 ++--
po/R-de.po | 5
po/de.po | 130 ++++------
po/en@quot.po | 63 ++---
src/CHMfactor.c | 14 +
src/CHMfactor.h | 1
src/chm_common.c | 25 +-
src/dsCMatrix.c | 37 ++-
src/init.c | 1
tests/Simple.R | 2
tests/factorizing.R | 107 ++++++++
tests/indexing.R | 13 -
tests/indexing.Rout.save | 33 ++
tests/spModel.matrix.R |only
50 files changed, 976 insertions(+), 564 deletions(-)
Author: Andrew D. Martin
Diff between MCMCpack versions 1.0-2 dated 2009-07-18 and 1.0-3 dated 2009-07-30
Title: Markov chain Monte Carlo (MCMC) Package
Description: This package contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.2. All
models return coda mcmc objects that can then be summarized
using the coda package. MCMCpack also contains some useful
utility functions, including some additional density functions
and pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization.
DESCRIPTION | 8 +-
HISTORY | 6 +
NAMESPACE | 1
R/MCMCquantreg.R |only
man/MCMCirtHier1d.Rd | 4 -
man/MCMCquantreg.Rd |only
src/MCMCfcds.h | 172 ++++++++++++++++++++++++++++++++++++++++++++++++++-
src/MCMCmedreg.cc |only
src/MCMCquantreg.cc |only
9 files changed, 180 insertions(+), 11 deletions(-)
Author: Jeff Hallman
Diff between tis versions 1.6 dated 2009-06-24 and 1.7 dated 2009-07-28
Title: Time Indexes and Time Indexed Series
Description: Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.
DESCRIPTION | 6 +++---
NEWS | 8 +++++++-
R/nberShade.ggplot.R | 2 +-
man/fortify.tis.Rd | 3 +--
man/nberShade.Rd | 10 ++++------
man/nberShade.ggplot.Rd | 2 +-
6 files changed, 17 insertions(+), 14 deletions(-)
Author: Han Lin Shang and Rob J Hyndman
Title: Rainbow plots, functional bagplot, functional HDR boxplot
Description: Functions and datasets for functional data display and
outlier detection.
Diff between rainbow versions 1.1 dated 2009-06-04 and 1.2 dated 2009-07-28
DESCRIPTION | 11 ++--- R/bhdr.R | 13 ++---- R/fbag.R | 4 +- R/fboxplot.R | 7 +-- R/fhdr.R | 73 +++++++++++++++++++------------------- data/Australiafertility.rda |binary data/Australiasmoothfertility.rda |binary data/Francemortality.rda |binary data/Francesmoothmortality.rda |binary data/Simulationdata.rda |binary man/Simulationdata.Rd | 3 + man/fboxplot.Rd | 3 - 12 files changed, 54 insertions(+), 60 deletions(-)
Author: Ported to R by Ted Harding and Fernando Tusell Original by
Joseph L. Schafer
Diff between cat versions 0.0-6 dated 2004-10-13 and 0.0-6.2 dated 2009-07-28
Title: Analysis of categorical-variable datasets with missing values
Description: Analysis of categorical-variable with missing values
DESCRIPTION | 17 ++++++++---------
LICENSE |only
man/belt.Rd | 1 -
man/crime.Rd | 1 -
man/dabipf.Rd | 2 --
man/older.Rd | 1 -
man/prelim.cat.Rd | 1 -
man/slice.index.Rd | 3 ---
8 files changed, 8 insertions(+), 18 deletions(-)
Author: Brian Ripley, and from 1999 to Oct 2002 Michael Lapsley
Title: ODBC Database Access
Description: An ODBC database interface
Diff between RODBC versions 1.2-6 dated 2009-06-24 and 1.3-0 dated 2009-07-28
RODBC-1.2-6/RODBC/INSTALL |only RODBC-1.2-6/RODBC/README |only RODBC-1.2-6/RODBC/inst/README |only RODBC-1.2-6/RODBC/man/odbcErrors.Rd |only RODBC-1.2-6/RODBC/tests/sqlite3.Rout |only RODBC-1.3-0/RODBC/ChangeLog | 81 RODBC-1.3-0/RODBC/DESCRIPTION | 14 RODBC-1.3-0/RODBC/NAMESPACE | 22 RODBC-1.3-0/RODBC/R/RODBC.R | 136 - RODBC-1.3-0/RODBC/R/TypeInfo.R | 39 RODBC-1.3-0/RODBC/R/sql.R | 242 +- RODBC-1.3-0/RODBC/inst/doc |only RODBC-1.3-0/RODBC/inst/po/en@quot/LC_MESSAGES/R-RODBC.mo |binary RODBC-1.3-0/RODBC/inst/po/en@quot/LC_MESSAGES/RODBC.mo |binary RODBC-1.3-0/RODBC/man/RODBC-internal.Rd | 13 RODBC-1.3-0/RODBC/man/RODBC-package.Rd | 111 - RODBC-1.3-0/RODBC/man/odbc.Rd | 57 RODBC-1.3-0/RODBC/man/odbcClose.Rd | 6 RODBC-1.3-0/RODBC/man/odbcConnect.Rd | 141 - RODBC-1.3-0/RODBC/man/odbcDataSources.Rd | 29 RODBC-1.3-0/RODBC/man/odbcGetInfo.Rd | 2 RODBC-1.3-0/RODBC/man/setSqlTypeInfo.Rd | 12 RODBC-1.3-0/RODBC/man/sqlColumns.Rd | 133 + RODBC-1.3-0/RODBC/man/sqlCopy.Rd | 9 RODBC-1.3-0/RODBC/man/sqlDrop.Rd | 60 RODBC-1.3-0/RODBC/man/sqlFetch.Rd | 26 RODBC-1.3-0/RODBC/man/sqlQuery.Rd | 106 - RODBC-1.3-0/RODBC/man/sqlSave.Rd | 55 RODBC-1.3-0/RODBC/man/sqlTables.Rd | 145 + RODBC-1.3-0/RODBC/man/sqlTypeInfo.Rd | 48 RODBC-1.3-0/RODBC/manual |only RODBC-1.3-0/RODBC/po/R-RODBC.pot | 17 RODBC-1.3-0/RODBC/po/R-en@quot.po | 19 RODBC-1.3-0/RODBC/po/RODBC.pot | 99 - RODBC-1.3-0/RODBC/po/en@quot.po | 131 - RODBC-1.3-0/RODBC/src/RODBC.c | 1283 +++++---------- RODBC-1.3-0/RODBC/tests/DB2.RR |only RODBC-1.3-0/RODBC/tests/DB2.Rout.save |only RODBC-1.3-0/RODBC/tests/Master.R | 7 RODBC-1.3-0/RODBC/tests/Notes |only RODBC-1.3-0/RODBC/tests/Oracle.RR |only RODBC-1.3-0/RODBC/tests/Oracle.Rout.save |only RODBC-1.3-0/RODBC/tests/SQLServer.RR | 31 RODBC-1.3-0/RODBC/tests/SQLServer.Rout.save | 171 + RODBC-1.3-0/RODBC/tests/access.RR | 1 RODBC-1.3-0/RODBC/tests/access.Rout.save | 27 RODBC-1.3-0/RODBC/tests/excel.Rout.save | 52 RODBC-1.3-0/RODBC/tests/mimer.RR |only RODBC-1.3-0/RODBC/tests/mimer.Rout.save |only RODBC-1.3-0/RODBC/tests/mysql-win.RR | 7 RODBC-1.3-0/RODBC/tests/mysql-win.Rout.save | 53 RODBC-1.3-0/RODBC/tests/mysql.RR | 8 RODBC-1.3-0/RODBC/tests/mysql.Rout.save | 68 RODBC-1.3-0/RODBC/tests/postgresql.RR | 21 RODBC-1.3-0/RODBC/tests/postgresql.Rout.save | 164 - RODBC-1.3-0/RODBC/tests/sqlite3.RR | 24 RODBC-1.3-0/RODBC/tests/sqlite3.Rout.save | 103 - 57 files changed, 1838 insertions(+), 1935 deletions(-)
Author: Adrian Baddeley
Diff between spatstat versions 1.16-0 dated 2009-07-02 and 1.16-1 dated 2009-07-27
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point
Patterns, including multitype/marked points and spatial
covariates, in any two-dimensional spatial region. Contains
functions for plotting spatial data, exploratory data analysis,
model-fitting, simulation, spatial sampling, model diagnostics,
and formal inference. Data types include point patterns, line
segment patterns, spatial windows, and pixel images. Point
process models can be fitted to point pattern data. Cluster
type models are fitted by the method of minimum contrast. Very
general Gibbs point process models can be fitted to point
pattern data using a function ppm similar to lm or glm. Models
may include dependence on covariates, interpoint interaction
and dependence on marks. Fitted models can be simulated
automatically. Also provides facilities for formal inference
(such as chi-squared tests) and model diagnostics (including
simulation envelopes, residuals, residual plots and Q-Q plots).
spatstat-1.16-0/spatstat/.Rbuildindex.5299 |only
spatstat-1.16-0/spatstat/.Rbuildindex.5904 |only
spatstat-1.16-0/spatstat/.Rbuildindex.6375 |only
spatstat-1.16-0/spatstat/man/closing.owin.Rd |only
spatstat-1.16-0/spatstat/man/dilate.owin.Rd |only
spatstat-1.16-0/spatstat/man/erode.owin.Rd |only
spatstat-1.16-0/spatstat/man/opening.owin.Rd |only
spatstat-1.16-1/spatstat/DESCRIPTION | 8
spatstat-1.16-1/spatstat/INDEX | 16
spatstat-1.16-1/spatstat/R/Fest.S | 10
spatstat-1.16-1/spatstat/R/Gest.S | 10
spatstat-1.16-1/spatstat/R/Gmulti.S | 16
spatstat-1.16-1/spatstat/R/Iest.R | 12
spatstat-1.16-1/spatstat/R/Jest.S | 14
spatstat-1.16-1/spatstat/R/Jmulti.S | 18
spatstat-1.16-1/spatstat/R/Kest.S | 67 +-
spatstat-1.16-1/spatstat/R/Kinhom.S | 12
spatstat-1.16-1/spatstat/R/Kmulti.S | 18
spatstat-1.16-1/spatstat/R/Kmulti.inhom.R | 12
spatstat-1.16-1/spatstat/R/bermantest.R |only
spatstat-1.16-1/spatstat/R/blur.R | 9
spatstat-1.16-1/spatstat/R/defaultwin.R | 6
spatstat-1.16-1/spatstat/R/diagnoseppm.R | 2
spatstat-1.16-1/spatstat/R/distbdry.S | 164 -----
spatstat-1.16-1/spatstat/R/effectfun.R | 18
spatstat-1.16-1/spatstat/R/envelope.R | 71 +-
spatstat-1.16-1/spatstat/R/eval.fv.R | 4
spatstat-1.16-1/spatstat/R/images.R | 13
spatstat-1.16-1/spatstat/R/kppm.R | 43 +
spatstat-1.16-1/spatstat/R/kstest.R | 20
spatstat-1.16-1/spatstat/R/localK.R | 18
spatstat-1.16-1/spatstat/R/markcorr.R | 8
spatstat-1.16-1/spatstat/R/mincontrast.R | 18
spatstat-1.16-1/spatstat/R/morphology.R |only
spatstat-1.16-1/spatstat/R/pcf.R | 10
spatstat-1.16-1/spatstat/R/plot.fv.R | 68 +-
spatstat-1.16-1/spatstat/R/ppp.S | 3
spatstat-1.16-1/spatstat/R/psp.R | 4
spatstat-1.16-1/spatstat/R/quadclass.S | 6
spatstat-1.16-1/spatstat/R/rmh.R | 4
spatstat-1.16-1/spatstat/R/rmh.ppm.R | 31 -
spatstat-1.16-1/spatstat/R/rshift.R | 6
spatstat-1.16-1/spatstat/R/window.S | 103 ++-
spatstat-1.16-1/spatstat/R/wingeom.S | 71 ++
spatstat-1.16-1/spatstat/R/xypolygon.S | 4
spatstat-1.16-1/spatstat/inst/doc/shapefiles.pdf | 703 ++++++++++-------------
spatstat-1.16-1/spatstat/man/00spatstat.Rd | 32 -
spatstat-1.16-1/spatstat/man/Kest.Rd | 21
spatstat-1.16-1/spatstat/man/Replace.im.Rd | 4
spatstat-1.16-1/spatstat/man/alltypes.Rd | 3
spatstat-1.16-1/spatstat/man/area.owin.Rd | 4
spatstat-1.16-1/spatstat/man/as.mask.Rd | 1
spatstat-1.16-1/spatstat/man/as.polygonal.Rd |only
spatstat-1.16-1/spatstat/man/bdist.pixels.Rd | 2
spatstat-1.16-1/spatstat/man/bdist.points.Rd | 2
spatstat-1.16-1/spatstat/man/bermantest.Rd |only
spatstat-1.16-1/spatstat/man/clarkevans.Rd | 2
spatstat-1.16-1/spatstat/man/closing.Rd |only
spatstat-1.16-1/spatstat/man/copper.Rd | 9
spatstat-1.16-1/spatstat/man/diagnose.ppm.Rd | 6
spatstat-1.16-1/spatstat/man/diameter.Rd | 2
spatstat-1.16-1/spatstat/man/dilation.Rd |only
spatstat-1.16-1/spatstat/man/distmap.psp.Rd | 17
spatstat-1.16-1/spatstat/man/envelope.Rd | 54 +
spatstat-1.16-1/spatstat/man/eroded.areas.Rd | 4
spatstat-1.16-1/spatstat/man/erosion.Rd |only
spatstat-1.16-1/spatstat/man/internal.Rd | 22
spatstat-1.16-1/spatstat/man/is.empty.Rd |only
spatstat-1.16-1/spatstat/man/kstest.Rd | 6
spatstat-1.16-1/spatstat/man/lgcp.estK.Rd | 15
spatstat-1.16-1/spatstat/man/matclust.estK.Rd | 15
spatstat-1.16-1/spatstat/man/mincontrast.Rd | 10
spatstat-1.16-1/spatstat/man/murchison.Rd | 2
spatstat-1.16-1/spatstat/man/nearestsegment.Rd | 3
spatstat-1.16-1/spatstat/man/opening.Rd |only
spatstat-1.16-1/spatstat/man/owin.object.Rd | 14
spatstat-1.16-1/spatstat/man/perimeter.Rd |only
spatstat-1.16-1/spatstat/man/plot.kppm.Rd | 21
spatstat-1.16-1/spatstat/man/plot.kstest.Rd |only
spatstat-1.16-1/spatstat/man/plot.owin.Rd | 2
spatstat-1.16-1/spatstat/man/rmh.ppm.Rd | 1
spatstat-1.16-1/spatstat/man/rshift.ppp.Rd | 4
spatstat-1.16-1/spatstat/man/setcov.Rd | 2
spatstat-1.16-1/spatstat/man/simulate.kppm.Rd | 28
spatstat-1.16-1/spatstat/man/simulate.ppm.Rd |only
spatstat-1.16-1/spatstat/man/thomas.estK.Rd | 15
86 files changed, 1135 insertions(+), 808 deletions(-)
Author: Markus Loecher
Diff between ReadImages versions 0.1.2 dated 2009-05-27 and 0.1.3 dated 2009-07-27
Title: Image Reading Module for R
Description: This package provides functions for reading JPEG and PNG
files. This package requires libjpeg
ReadImages-0.1.2/ReadImages/src/Makevars.win |only
ReadImages-0.1.3/ReadImages/DESCRIPTION | 8
ReadImages-0.1.3/ReadImages/README | 8
ReadImages-0.1.3/ReadImages/configure | 5109 ++++++++++--------
ReadImages-0.1.3/ReadImages/man/ReadImages-package.Rd | 4
5 files changed, 3013 insertions(+), 2116 deletions(-)
Author: William Revelle
Diff between psych versions 1.0-76 dated 2009-07-18 and 1.0-77 dated 2009-07-27
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A number of routines for personality, psychometrics and
experimental psychology. Functions are primarily for scale
construction using factor analysis, cluster analysis and
reliability analysis, although others provide basic descriptive
statistics. Functions for simulating particular item and test
structures are included. Several functions serve as a useful
front end for structural equation modeling. For more
information, see the personality-project.org/r webpage.
CHANGES | 7
DESCRIPTION | 8
R/error.bars.R | 21
R/error.bars.by.R | 4
R/factor.rotate.R | 11
R/polar.R | 36
R/print.psych.fa.R | 17
inst/NEWS | 5
inst/doc/overview.pdf | 3033 ++--
inst/doc/psych_for_sem.pdf | 1773 +-
inst/doc/psych_manual.pdf |28870 ++++++++++++++++++++++-----------------------
man/00.psych-package.Rd | 4
man/factor.rotate.Rd | 35
man/r.test.Rd | 8
14 files changed, 17223 insertions(+), 16609 deletions(-)
Author: Patrick Giraudoux
Diff between pgirmess versions 1.3.8 dated 2009-01-26 and 1.3.9 dated 2009-07-27
Title: Data analysis in ecology
Description: Miscellaneous functions for analysis and display of
ecological and spatial data
DESCRIPTION | 28 +++++++++++++++-------------
R/selMod.r | 1 +
man/dirProj.rd | 2 +-
man/dirSeg.rd | 2 +-
man/selMod.Rd | 6 +++---
5 files changed, 21 insertions(+), 18 deletions(-)
Author: Jan de Leeuw, Patrick Mair
Title: Gifi Methods
Description: This package performs a homogeneity analysis and various
extensions. Rank restrictions on the category quantifications
can be imposed (nonlinear PCA). The categories are transformed
by means of optimal scaling with options for nominal, ordinal,
and numerical scale levels (for rank-1 restrictions). Variables
can be grouped into sets, in order to emulate regression
analysis and canonical correlation analysis.
Diff between homals versions 0.9-10 dated 2009-02-23 and 0.9-11 dated 2009-07-27
homals-0.9-10/homals/inst/doc/Rplots.pdf |only homals-0.9-10/homals/inst/doc/homalsR.dvi |only homals-0.9-11/homals/DESCRIPTION | 36 homals-0.9-11/homals/R/homals.R | 43 homals-0.9-11/homals/R/normX.R | 12 homals-0.9-11/homals/R/plot.homals.R | 102 - homals-0.9-11/homals/inst/doc/homalsR.bbl |only homals-0.9-11/homals/inst/doc/homalsR.blg |only homals-0.9-11/homals/inst/doc/homalsR.pdf | 2385 ++++++++++++++---------------- homals-0.9-11/homals/man/plot.homals.Rd | 3 10 files changed, 1285 insertions(+), 1296 deletions(-)
Author: Paul Gilbert
Diff between TShistQuote versions 2009.1-1 dated 2009-02-24 and 2009.7-1 dated 2009-07-27
Title: Time Series Database Interface extensions for get.hist.quote
Description: Provides methods for generics in the TSdbi package to
retrieve data from historical quote URLs.
TShistQuote-2009.1-1/TShistQuote/Rplots.pdf |only
TShistQuote-2009.7-1/TShistQuote/DESCRIPTION | 21 ++++++++-----
TShistQuote-2009.7-1/TShistQuote/NEWS | 22 +++++++++++++-
TShistQuote-2009.7-1/TShistQuote/R/TSdbiMethods.R | 20 +++++++-----
TShistQuote-2009.7-1/TShistQuote/inst/doc/TShistQuote.pdf |binary
TShistQuote-2009.7-1/TShistQuote/man/TSdbiMethods.Rd | 4 +-
6 files changed, 49 insertions(+), 18 deletions(-)
Author: Jonathan P. Weeks
Diff between plink versions 1.1-4 dated 2009-06-19 and 1.1-5 dated 2009-07-26
Title: IRT Separate Calibration Linking Methods
Description: This package uses item response theory methods to compute
linking constants and conduct chain linking of unidimensional
or multidimensional tests for multiple groups under a common
item design. The unidimensional methods include the Mean/Mean,
Mean/Sigma, Haebara, and Stocking-Lord methods for dichotomous
(1PL, 2PL and 3PL) and/or polytomous (graded response, partial
credit/generalized partial credit, nominal, and multiple-choice
model) items. The multidimensional methods include the
Reckase-Martineau method and extensions of the Haebara and
Stocking-Lord method using a single dilation parameter,
multiple dilation parameters, or the Oshima, Davey, & Lee
approach for multidimensional extensions of all the
unidimensional dichotomous and polytomous item response models.
The package also includes functions for importing item and/or
ability parameters from common IRT software and ploting item
characteristic/category curves or surfaces, vector plots, and
comparison plots for examining parameter drift.
DESCRIPTION | 13
NAMESPACE | 4
R/classes.R | 262 ++++++++++-
R/drm.R | 87 +++
R/gpcm.R | 111 ++++
R/grm.R | 120 ++++-
R/irt.pars.R | 145 +++++-
R/link.R | 66 ++
R/mcm.R | 84 +++
R/mixed.R | 107 ++++
R/nrm.R | 82 +++
R/plink.R | 514 +++++++++++++++-------
R/plot.R | 1142 ++++++++++++++++++++++++++++++++++++++-----------
R/read.bilog.R | 475 +++++++++++++++++++-
R/sep.pars.R | 584 ++++++++++++++++++++-----
R/summary.R | 163 ++++++
R/weight.R | 67 ++
inst/CITATION | 4
inst/NEWS | 98 +++-
man/irt.prob-class.Rd | 3
man/link-class.Rd | 4
man/list.poly-class.Rd | 6
man/mixed-methods.Rd | 18
man/plink-methods.Rd | 119 +++--
man/plot.irt.prob.Rd | 41 +
man/read.bilog.Rd | 24 -
man/sep.pars-class.Rd | 2
27 files changed, 3600 insertions(+), 745 deletions(-)
Author: Paul Gilbert
Diff between dse versions 2008.10-1 dated 2008-10-19 and 2009.7-1 dated 2009-07-26
Bundle: dse
Contains: dse1 dse2
dse-2008.10-1/dse/dse1/Rplots.pdf |only
dse-2008.10-1/dse/dse1/Rplots1.pdf |only
dse-2008.10-1/dse/dse2/Rplots.pdf |only
dse-2009.7-1/dse/DESCRIPTION | 23 ++++++++++++-----------
dse-2009.7-1/dse/NEWS | 6 ++++++
dse-2009.7-1/dse/dse1/inst/doc/dse-guide.pdf |binary
dse-2009.7-1/dse/dse1/inst/doc/dse1.pdf |binary
dse-2009.7-1/dse/dse1/man/ARMA.Rd | 5 +++--
dse-2009.7-1/dse/dse1/man/SS.Rd | 7 ++++---
dse-2009.7-1/dse/dse1/man/TSdata.Rd | 15 ++++++++-------
dse-2009.7-1/dse/dse1/man/TSdata.object.Rd | 4 ++--
dse-2009.7-1/dse/dse1/man/TSestModel.Rd | 3 ++-
dse-2009.7-1/dse/dse1/man/TSmodel.Rd | 12 +++++++-----
dse-2009.7-1/dse/dse1/man/l.SS.Rd | 2 +-
dse-2009.7-1/dse/dse2/inst/doc/dse2.pdf |binary
dse-2009.7-1/dse/dse2/man/EstEval.Rd | 10 ++++++----
16 files changed, 51 insertions(+), 36 deletions(-)
Author: Ann Lee, Diana Luca, Bert Klei, Bernie Devlin, Kathryn Roeder
Title: Discovering Genetic Ancestry Using Spectral Graph Theory
Description: Discovering Genetic Ancestry Using Spectral Graph Theory
Diff between SpectralGEM versions 0.2.1 dated 2009-06-02 and 1.0 dated 2009-07-26
SpectralGEM-0.2.1/SpectralGEM/man/installGEMcore.Rd |only SpectralGEM-0.2.1/SpectralGEM/src/RcallOlinux.c |only SpectralGEM-0.2.1/SpectralGEM/src/Rcallexe.c |only SpectralGEM-1.0/SpectralGEM/DESCRIPTION | 8 - SpectralGEM-1.0/SpectralGEM/R/Spectral-GEM.R | 91 +++++-------------- SpectralGEM-1.0/SpectralGEM/man/InFile.Rd | 26 +++-- SpectralGEM-1.0/SpectralGEM/man/MMfile.Rd | 6 - SpectralGEM-1.0/SpectralGEM/man/SpectralGEM.Rd | 28 +++-- SpectralGEM-1.0/SpectralGEM/man/plotLam.Rd |only SpectralGEM-1.0/SpectralGEM/man/updateInputFile.Rd | 3 SpectralGEM-1.0/SpectralGEM/src/GEM_sub.f |only SpectralGEM-1.0/SpectralGEM/src/SpectralGEM_v2.2.f90 |only 12 files changed, 64 insertions(+), 98 deletions(-)
Author: Robert B. Gramacy
Diff between tgp versions 2.2-2 dated 2009-05-29 and 2.2-3 dated 2009-07-26
Title: Bayesian treed Gaussian process models
Description: Bayesian nonstationary, semiparametric nonlinear
regression and design by treed Gaussian processes with jumps to
the limiting linear model (LLM). Special cases also
implemented include Bayesian linear models, CART, treed linear
models, stationary separable and isotropic Gaussian processes.
Provides 1-d and 2-d plotting functions (with projection and
slice capabilities) and tree drawing, designed for
visualization of tgp-class output. Sensitivity analysis and
multi-resolution models are supported. Sequential experimental
design and adaptive sampling functions are also provided,
including ALM, ALC, and expected improvement. The latter
supports derivative-free optimization of noisy black-box
functions.
ChangeLog | 9 +++++++
DESCRIPTION | 6 ++--
R/btgp.R | 6 ++++
R/predict.tgp.R | 2 +
R/tgp.R | 4 ++-
R/tgp.default.params.R | 7 ++++-
R/tgp.postprocess.R | 6 +++-
man/btgp.Rd | 6 +++-
src/all_draws.c | 10 ++++++--
src/base.h | 4 +--
src/gp.cc | 11 ++++----
src/gp.h | 4 +--
src/matrix.c | 60 ++++++++++++++++++++++++++++++++++++++++---------
src/matrix.h | 9 ++++---
src/model.cc | 6 +++-
src/mstructs.cc | 8 +++++-
src/mstructs.h | 2 +
src/params.cc | 10 ++++----
src/predict.c | 21 +++++++++++++----
src/predict.h | 5 +---
src/predict_linear.c | 28 +++++++++++++++++-----
src/predict_linear.h | 6 ++--
src/rand_pdf.c | 5 ++--
src/tgp.cc | 25 ++++++++++++--------
src/tgp.h | 4 +--
src/tree.cc | 20 +++++++++-------
src/tree.h | 4 +--
tgp_2.2-2.tar.gz |only
28 files changed, 204 insertions(+), 84 deletions(-)
Author: Radhakrishnan Nagarajan
Diff between packdep versions 0.1 dated 2009-07-18 and 0.2 dated 2009-07-26
Title: Mapping dependencies among R packages
Description: packdep elucidates the dependencies between
user-contributed R packages and identifies key packages
according to social network analysis metrics.
Changelog |only
DESCRIPTION | 11 +++++------
man/centrality.Rd | 4 ++--
man/dependencies.Rd | 4 ++--
man/packdep-package.Rd | 10 +++++-----
man/plot.packdep.centrality.Rd | 2 +-
man/plot.packdep.dependencies.Rd | 2 +-
man/related.packages.Rd | 4 ++--
8 files changed, 18 insertions(+), 19 deletions(-)
Author: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.9.1.2 dated 2009-07-18 and 2.9.1.3 dated 2009-07-26
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
DESCRIPTION | 8 ++++----
R/epicalc.R | 4 ++++
2 files changed, 8 insertions(+), 4 deletions(-)
Author: Markus Loecher, Sense Networks
Title: Overlays on Google map tiles in R
Description: This package serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling. NOTE:
To do anything but downloading static map tiles, RgoogleMaps
needs EITHER rgdal OR ReadImages OR rimage installed ! Such an
OR dependency is difficult to express in the Depends field, so
I moved those packages to suggested. rgdal is your package if
you prefer png file format and ReadImages or rimage if you
prefer jpg format. In the latter cases, you will also need the
libjpeg library installed.
Diff between RgoogleMaps versions 1.1.4 dated 2009-07-18 and 1.1.5 dated 2009-07-26
RgoogleMaps-1.1.4/RgoogleMaps/Read-and-delete-me |only RgoogleMaps-1.1.5/RgoogleMaps/DESCRIPTION | 24 ++++---- RgoogleMaps-1.1.5/RgoogleMaps/R/GetMap.R | 2 RgoogleMaps-1.1.5/RgoogleMaps/R/GetMap.bbox.R | 23 ++++--- RgoogleMaps-1.1.5/RgoogleMaps/R/MapBackground.R | 33 ++++++----- RgoogleMaps-1.1.5/RgoogleMaps/R/MaxZoom.R | 6 +- RgoogleMaps-1.1.5/RgoogleMaps/R/PlotOnStaticMap.R | 2 RgoogleMaps-1.1.5/RgoogleMaps/R/RGB2GRAY.R | 11 +++ RgoogleMaps-1.1.5/RgoogleMaps/R/SPGDF2matrix.R |only RgoogleMaps-1.1.5/RgoogleMaps/inst/doc/RgoogleMaps-intro.pdf |binary RgoogleMaps-1.1.5/RgoogleMaps/man/PlotOnStaticMap.Rd | 2 RgoogleMaps-1.1.5/RgoogleMaps/man/RgoogleMaps-package.Rd | 6 +- RgoogleMaps-1.1.5/RgoogleMaps/man/SPGDF2matrix.Rd |only 13 files changed, 66 insertions(+), 43 deletions(-)
Author: Stefano Maria Iacus
Title: Simulation and Inference for Stochastic Differential Equations
Description: Companion package to the book Simulation and Inference for
Stochastic Differential Equations With R Examples, ISBN
978-0-387-75838-1, Springer, NY.
Diff between sde versions 2.0.7 dated 2009-06-25 and 2.0.8 dated 2009-07-24
DESCRIPTION | 10 ++- R/rOU.R | 2 inst/doc/changes.txt | 3 + inst/doc/sde.errata.log | 143 ++++++++++++++++++++---------------------------- inst/doc/sde.errata.pdf |binary 5 files changed, 71 insertions(+), 87 deletions(-)
Author: Jichun Xie
Diff between qlspack versions 2.1 dated 2009-06-09 and 2.2 dated 2009-07-24
Title: Quasi Least Square Package
Description: QLS is a two-stage computational approach for estimation
of the correlation parameters within the framework of GEE. It
helps solving parameters in mean, scale, and correlation
structures for longitudinal data.
DESCRIPTION | 8 ++++----
man/qls.rd | 3 +++
2 files changed, 7 insertions(+), 4 deletions(-)
Author: David Rossell
Diff between mombf versions 1.0.3 dated 2009-01-26 and 1.0.4 dated 2009-07-24
Title: Moment and Inverse Moment Bayes factors
Description: This package computes Moment and Inverse Moment Bayes
factors for linear models, and approximate Bayes factors for
GLM and situations having a statistic which is asymptotically
normally distributed and sufficient. Routines to evaluate prior
densities, distribution functions, quantiles and modes are
included.
mombf-1.0.3/mombf/inst/doc/Rplots.pdf |only
mombf-1.0.4/mombf/ChangeLog | 4 ++
mombf-1.0.4/mombf/DESCRIPTION | 15 ++++++--
mombf-1.0.4/mombf/R/dmom.r | 17 +++++++--
mombf-1.0.4/mombf/R/g2mode.r | 5 ++
mombf-1.0.4/mombf/R/mode2g.r | 6 ++-
mombf-1.0.4/mombf/R/mombf.lm.r | 12 +++++-
mombf-1.0.4/mombf/R/mombf.r | 10 +++++
mombf-1.0.4/mombf/R/priorp2g.r | 5 ++
mombf-1.0.4/mombf/inst/doc/makefile | 10 +++--
mombf-1.0.4/mombf/inst/doc/mombf.Rnw | 60 +++++++++++++++++++++++-----------
mombf-1.0.4/mombf/inst/doc/mombf.pdf |binary
mombf-1.0.4/mombf/man/dmom.Rd | 15 ++++++--
mombf-1.0.4/mombf/man/mode2g.Rd | 16 +++++----
mombf-1.0.4/mombf/man/mombf.Rd | 24 +++++++++----
15 files changed, 143 insertions(+), 56 deletions(-)
Author: Andrew Gelman
Diff between mi versions 0.08-03 dated 2009-06-24 and 0.08-04 dated 2009-07-24
Title: Missing Data Imputation and Model Checking
Description: Missing-data imputation and model checking
CHANGELOG | 5 +++
DESCRIPTION | 8 ++---
NAMESPACE | 2 -
R/mi.R | 23 ++++++++++------
R/mi.categorical.R | 2 -
R/mi.info.R | 70 ++++++++++++++++++++++++++++++--------------------
R/mi.pmm.R | 2 -
R/mi.preprocess.R | 14 +++-------
man/mi.info.update.Rd | 4 +-
9 files changed, 77 insertions(+), 53 deletions(-)
Author: Jun Yan
Diff between copula versions 0.8-8 dated 2009-07-18 and 0.8-9 dated 2009-07-24
Title: Multivariate dependence with copulas
Description: Classes (S4) of commonly used copulas including elliptical
(normal and t), Archimedean (Clayton, Gumbel, Frank, and
Ali-Mikhail-Haq), extreme value (Gumbel, Husler-Reiss,
Galambos, and t-EV), and other families (Plackett and
Farlie-Gumbel-Morgenstern). Methods for density, distribution,
random number generation, bivariate dependence measures,
perspective and contour plots. Functions for fitting copula
models with variance estimate. Independence tests among random
variables and random vectors. Serial independence tests for
univariate and multivariate continuous time series.
Goodness-of-fit tests for copulas based on multipliers and on
the parametric bootstrap.
ChangeLog | 4 ++++
DESCRIPTION | 12 ++++++------
R/frankCopula.R | 8 +++++++-
R/schlatherCopula.R |only
man/copula-internal.Rd | 1 +
5 files changed, 18 insertions(+), 7 deletions(-)
Author: Jens Oehlschlägel
Diff between bit versions 1.0-2 dated 2009-04-15 and 1.1.0 dated 2009-07-24
Title: A class for vectors of 1-bit booleans
Description: bitmapped vectors of booleans (no NAs), coercion from and
to logicals, integers and integer subscripts; fast boolean
operators and fast summary statistics. With 'bit' vectors you
can store true binary booleans {FALSE,TRUE} at the expense of 1
bit only, on a 32 bit architecture this means factor 32 less
RAM and factor 32 more speed on boolean operations. With this
speed gain it even pays-off to convert to bit in order to avoid
a single boolean operation on logicals or a single set
operation on (longer) integer subscripts, the pay-off is
dramatic when such components are used more than once. Reading
from and writing to bit is approximately as fast as accessing
standard logicals - mostly due to R's time for memory
allocation. The package allows to work with pre-allocated
memory for return values by calling .Call() directly: when
evaluating the speed of C-access with pre-allocated vector
memory, coping from bit to logical requires only 70% of the
time for copying from logical to logical; and copying from
logical to bit comes at a performance penalty of 150%. the
package now contains further classes for representing logical
selections: 'bitwhich' for very skewed selections and 'ri' for
selecting ranges of values for chunked processing. All three
index classes can be used for subsetting 'ff' objects (ff-2.1.0
and higher).
bit-1.0-2/bit/ANNOUNCEMENT.txt |only
bit-1.0-2/bit/man/Logical.rd |only
bit-1.1.0/bit/CHANGES |only
bit-1.1.0/bit/DESCRIPTION | 49
bit-1.1.0/bit/R/bit.R | 3431 +++++++++++++++++++++----------
bit-1.1.0/bit/R/chunkutil.R |only
bit-1.1.0/bit/R/rle.R |only
bit-1.1.0/bit/R/zzz.R | 31
bit-1.1.0/bit/README_devel.txt | 20
bit-1.1.0/bit/man/Extract.rd | 7
bit-1.1.0/bit/man/LogicBit.rd |only
bit-1.1.0/bit/man/Summary.rd | 54
bit-1.1.0/bit/man/as.bit.rd | 15
bit-1.1.0/bit/man/as.bitwhich.rd |only
bit-1.1.0/bit/man/as.logical.bit.rd | 25
bit-1.1.0/bit/man/as.logical.bitwhich.rd |only
bit-1.1.0/bit/man/bbatch.rd |only
bit-1.1.0/bit/man/bit-package.rd | 107
bit-1.1.0/bit/man/bitwhich.rd |only
bit-1.1.0/bit/man/c.bit.rd |only
bit-1.1.0/bit/man/chunk.rd |only
bit-1.1.0/bit/man/intrle.rd |only
bit-1.1.0/bit/man/is.bit.rd |only
bit-1.1.0/bit/man/length.bit.rd | 9
bit-1.1.0/bit/man/physical.rd |only
bit-1.1.0/bit/man/repfromto.rd |only
bit-1.1.0/bit/man/ri.rd |only
bit-1.1.0/bit/man/rlepack.rd |only
bit-1.1.0/bit/man/vecseq.rd |only
bit-1.1.0/bit/prebuild.sh | 30
bit-1.1.0/bit/src/bit.c | 769 +++++-
bit-1.1.0/bit/src/rle.c |only
32 files changed, 3220 insertions(+), 1327 deletions(-)
More information about DiversitySampler at CRAN
Permanent link
Author: Jairo A. Fuquene P.
Title: Robust Bayesian Priors in Clinical Trials: An R Package for
Practitioners
Description: In a recent paper, Fuquene, Cook, & Pericchi (2008)
(http://www.bepress.com/mdandersonbiostat/paper44 ) make a
comprehensive proposal putting forward robust, heavy-tailed
priors over conjugate, light-tailed priors in Bayesian
analysis. The behavior of Robust Bayesian methods is
qualitative different than Conjugate and short tailed Bayesian
methods and arguably much more reasonable and acceptable to the
practitioner and regulatory agencies. This package is useful to
compute the distributions (prior, likelihood and posterior) and
moments of the robust models: Cauchy/Binomial, Cauchy/Normal
and Berger/Normal. Both, Binomial and Normal Likelihoods can be
handled by the software. Furthermore, the assessment of the
hyperparameters and the posterior analysis can be processed.
Diff between ClinicalRobustPriors versions 1.1-2 dated 2009-05-05 and 2.1-2 dated 2009-07-24
DESCRIPTION | 21 ++++++++++----------- R/Cauchy.Normal.R | 4 ++-- 2 files changed, 12 insertions(+), 13 deletions(-)
More information about ClinicalRobustPriors at CRAN
Permanent link
Author: John Fox, Michael Friendly, and Georges Monette
Title: Visualizing Tests in Multivariate Linear Models
Description: Represents sums-of-squares-and-products matrices for
linear hypotheses and for error using ellipses (in two
dimensions) and ellipsoids (in three dimensions).
Diff between heplots versions 0.8-6 dated 2009-04-19 and 0.8-9 dated 2009-07-23
.project |only DESCRIPTION | 12 ++++++------ NAMESPACE | 4 +++- R/ellipse3d.axes.R |only R/heplot.mlm.R | 3 ++- R/heplot1d.R |only R/heplot3d.mlm.R | 3 ++- R/termMeans.R |only data/Bees.rda |only data/FootHead.rda |only data/RootStock.rda |only demo/00Index | 3 ++- demo/bees.contrasts.R |only inst/CHANGES | 15 +++++++++++++++ man/Bees.Rd |only man/FootHead.Rd |only man/RootStock.Rd |only man/ellipse3d.axes.Rd |only man/heplot-package.Rd | 4 ++-- man/heplot.Rd | 27 +++++++++++++++++++++++---- man/heplot1d.Rd |only man/heplot3d.Rd | 18 +++++++++++++----- man/heplots-internal.Rd | 1 + 23 files changed, 69 insertions(+), 21 deletions(-)
Author: Mathias Drton
Diff between SIN versions 0.3 dated 2006-08-11 and 0.4 dated 2009-07-23
Title: A SINful Approach to Selection of Gaussian Graphical Markov
Models
Description: This package provides routines to perform SIN model
selection as described in Drton & Perlman (2004, 2008). The
selected models are represented in the format of the 'ggm'
package, which allows in particular parameter estimation in the
selected model.
DESCRIPTION | 32 ++++++++++++++++++--------------
INDEX | 4 ++--
man/plotBGpvalues.Rd | 7 +++----
man/plotCGpvalues.Rd | 7 +++----
man/plotDAGpvalues.Rd | 7 +++----
man/plotUGpvalues.Rd | 7 +++----
man/simpvalueMx.Rd | 7 +++----
man/simpvalueVec.Rd | 7 +++----
man/sinBG.Rd | 7 +++----
man/sinCG.Rd | 7 +++----
man/sinDAG.Rd | 7 +++----
man/sinUG.Rd | 7 +++----
12 files changed, 50 insertions(+), 56 deletions(-)
Author: Yurii Aulchenko, Maksim Struchalin
Title: genome-wide SNP association analysis
Description: a package for genome-wide association analysis between
quantitative or binary traits and single-nucleiotide
polymorphisms (SNPs).
Diff between GenABEL versions 1.4-2 dated 2009-01-29 and 1.4-3 dated 2009-07-23
GenABEL-1.4-2/GenABEL/tags |only GenABEL-1.4-3/GenABEL/CHANGES.LOG | 20 GenABEL-1.4-3/GenABEL/DESCRIPTION | 17 GenABEL-1.4-3/GenABEL/GenABEL |only GenABEL-1.4-3/GenABEL/R.save |only GenABEL-1.4-3/GenABEL/R/GASurv.R | 4 GenABEL-1.4-3/GenABEL/R/HWE.show.R | 4 GenABEL-1.4-3/GenABEL/R/Xcheck.R | 2 GenABEL-1.4-3/GenABEL/R/Xfix.R | 6 GenABEL-1.4-3/GenABEL/R/add.phdata.R | 4 GenABEL-1.4-3/GenABEL/R/add.plot.R | 4 GenABEL-1.4-3/GenABEL/R/ases.R | 22 GenABEL-1.4-3/GenABEL/R/autosomal.R | 4 GenABEL-1.4-3/GenABEL/R/catable.R | 4 GenABEL-1.4-3/GenABEL/R/ccfast.R | 2 GenABEL-1.4-3/GenABEL/R/ccfast.new.R | 2 GenABEL-1.4-3/GenABEL/R/check.marker.R | 4 GenABEL-1.4-3/GenABEL/R/check.marker.internal.R | 12 GenABEL-1.4-3/GenABEL/R/check.trait.R | 2 GenABEL-1.4-3/GenABEL/R/checkphengen.R | 2 GenABEL-1.4-3/GenABEL/R/convert.snp.affymetrix.R | 6 GenABEL-1.4-3/GenABEL/R/descriptives.marker.R | 4 GenABEL-1.4-3/GenABEL/R/descriptives.scan.R | 2 GenABEL-1.4-3/GenABEL/R/descriptives.trait.R | 4 GenABEL-1.4-3/GenABEL/R/dprfast.R | 4 GenABEL-1.4-3/GenABEL/R/egscore.R | 9 GenABEL-1.4-3/GenABEL/R/egscore.old.R | 6 GenABEL-1.4-3/GenABEL/R/export.merlin.R | 2 GenABEL-1.4-3/GenABEL/R/fcc.R | 2 GenABEL-1.4-3/GenABEL/R/fcc.new.R | 2 GenABEL-1.4-3/GenABEL/R/formetascore.R | 10 GenABEL-1.4-3/GenABEL/R/grammar.R | 4 GenABEL-1.4-3/GenABEL/R/hom.R | 30 GenABEL-1.4-3/GenABEL/R/hom.old.R | 4 GenABEL-1.4-3/GenABEL/R/ibs.R | 10 GenABEL-1.4-3/GenABEL/R/ibs.old.R | 10 GenABEL-1.4-3/GenABEL/R/imphetcheck.R | 2 GenABEL-1.4-3/GenABEL/R/merge.gwaa.data.R | 8 GenABEL-1.4-3/GenABEL/R/merge.snp.data.R | 4 GenABEL-1.4-3/GenABEL/R/mlreg.R | 6 GenABEL-1.4-3/GenABEL/R/mlreg.p.R | 6 GenABEL-1.4-3/GenABEL/R/mmscore.R | 4 GenABEL-1.4-3/GenABEL/R/perid.summary.R | 8 GenABEL-1.4-3/GenABEL/R/plot.check.marker.R | 2 GenABEL-1.4-3/GenABEL/R/plot.scan.gwaa.R | 2 GenABEL-1.4-3/GenABEL/R/polygenic.R | 6 GenABEL-1.4-3/GenABEL/R/qtscore.R | 21 GenABEL-1.4-3/GenABEL/R/r2fast.R | 4 GenABEL-1.4-3/GenABEL/R/r2fast.old.R | 4 GenABEL-1.4-3/GenABEL/R/redundant.R | 2 GenABEL-1.4-3/GenABEL/R/refresh.gwaa.data.R | 4 GenABEL-1.4-3/GenABEL/R/rhofast.R | 4 GenABEL-1.4-3/GenABEL/R/save.snp.data.R | 4 GenABEL-1.4-3/GenABEL/R/scan.glm.2D.R | 2 GenABEL-1.4-3/GenABEL/R/scan.glm.R | 2 GenABEL-1.4-3/GenABEL/R/scan.haplo.2D.R | 2 GenABEL-1.4-3/GenABEL/R/scan.haplo.R | 2 GenABEL-1.4-3/GenABEL/R/show.ncbi.R | 2 GenABEL-1.4-3/GenABEL/R/snp.names.R | 10 GenABEL-1.4-3/GenABEL/R/snp.subset.R | 4 GenABEL-1.4-3/GenABEL/R/summary.snp.data.R | 2 GenABEL-1.4-3/GenABEL/R/ztransform.R | 10 GenABEL-1.4-3/GenABEL/inst/doc/ABEL-tutorial.pdf |30757 ++++------------------- GenABEL-1.4-3/GenABEL/man/GenABEL-package.Rd | 4 GenABEL-1.4-3/GenABEL/man/check.marker.Rd | 2 GenABEL-1.4-3/GenABEL/man/egscore.Rd | 30 GenABEL-1.4-3/GenABEL/man/hom.Rd | 41 GenABEL-1.4-3/GenABEL/man/hom.old.Rd | 2 GenABEL-1.4-3/GenABEL/man/ibs.Rd | 11 GenABEL-1.4-3/GenABEL/man/snp.data-class.Rd | 2 GenABEL-1.4-3/GenABEL/src/gwaa.c | 51 GenABEL-1.4-3/GenABEL/src/lm_gwaa.cpp | 9 GenABEL-1.4-3/GenABEL/src/reg1.h | 4 GenABEL-1.4-3/GenABEL/src/reg1data.h | 7 GenABEL-1.4-3/GenABEL/tmp |only 75 files changed, 6846 insertions(+), 24425 deletions(-)
Author: James Curran
Diff between Bolstad versions 0.2-14 dated 2008-11-10 and 0.2-15 dated 2009-07-23
Title: Bolstad functions
Description: A set of R functions and data sets for the book
Introduction to Bayesian Statistics, Bolstad, W.M. (2007), John
Wiley & Sons ISBN 0-471-27020-2
DESCRIPTION | 24 ++++++++++++++----------
R/bayes.lin.reg.r | 20 ++++++++++----------
man/binodp.Rd | 2 +-
3 files changed, 25 insertions(+), 21 deletions(-)
Author: Robin K. S. Hankin
Title: Bayesian Analysis of Computer Code Output (BACCO)
Description: The BACCO bundle of packages is replaced by the BACCO
package, which provides a vignette that illustrates the
constituent packages (emulator, approximator, calibrator) in
use.
Diff between BACCO versions 2.0 dated 2009-07-18 and 2.0-2 dated 2009-07-23
DESCRIPTION | 6 +++--- R |only inst/doc/both_papers.pdf | 14 +++++++------- 3 files changed, 10 insertions(+), 10 deletions(-)
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 1.5-7 dated 2009-07-22 and 1.5-8 dated 2009-07-22
DESCRIPTION | 6 NAMESPACE | 4 NEWS | 5 R/as.zoo.R | 7 R/yearmon.R | 4 R/yearqtr.R | 4 inst/doc/zoo-faq.pdf | 10 - inst/doc/zoo-quickref.pdf | 14 - inst/doc/zoo.pdf | 393 +++++++++++++++++++++++----------------------- 9 files changed, 228 insertions(+), 219 deletions(-)
Author: Achim Zeileis, Kurt Hornik
Title: CRAN Task Views
Description: Server-side and client-side tools for task views to
CRAN-style repositories
Diff between ctv versions 0.5-2 dated 2009-06-03 and 0.5-3 dated 2009-07-22
ctv-0.5-2/ctv/inst/ctv/Distributions.html |only ctv-0.5-3/ctv/DESCRIPTION | 8 ctv-0.5-3/ctv/NEWS | 6 ctv-0.5-3/ctv/R/ctv-server.R | 2 ctv-0.5-3/ctv/inst/ctv/Bayesian.ctv | 295 +++++++++++-------- ctv-0.5-3/ctv/inst/ctv/ChemPhys.ctv | 73 +++- ctv-0.5-3/ctv/inst/ctv/Distributions.ctv | 126 +++++--- ctv-0.5-3/ctv/inst/ctv/Econometrics.ctv | 16 - ctv-0.5-3/ctv/inst/ctv/Environmetrics.ctv | 51 ++- ctv-0.5-3/ctv/inst/ctv/ExperimentalDesign.ctv | 81 +++-- ctv-0.5-3/ctv/inst/ctv/Finance.ctv | 14 ctv-0.5-3/ctv/inst/ctv/HighPerformanceComputing.ctv | 4 ctv-0.5-3/ctv/inst/ctv/MachineLearning.ctv | 8 ctv-0.5-3/ctv/inst/ctv/Multivariate.ctv | 18 - ctv-0.5-3/ctv/inst/ctv/NaturalLanguageProcessing.ctv | 8 ctv-0.5-3/ctv/inst/ctv/Optimization.ctv | 18 - ctv-0.5-3/ctv/inst/ctv/Psychometrics.ctv | 9 ctv-0.5-3/ctv/inst/ctv/SocialSciences.ctv | 6 ctv-0.5-3/ctv/inst/ctv/Spatial.ctv | 7 ctv-0.5-3/ctv/inst/ctv/TimeSeries.ctv | 11 ctv-0.5-3/ctv/inst/doc/ctv-howto.pdf |binary 21 files changed, 486 insertions(+), 275 deletions(-)
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 1.5-6 dated 2009-05-21 and 1.5-7 dated 2009-07-22
zoo-1.5-6/zoo/inst/doc/foo.rda |only zoo-1.5-6/zoo/inst/doc/plot-axes.pdf |only zoo-1.5-6/zoo/inst/doc/plot-axes.tex |only zoo-1.5-7/zoo/DESCRIPTION | 16 - zoo-1.5-7/zoo/NAMESPACE | 39 +++ zoo-1.5-7/zoo/NEWS | 28 ++ zoo-1.5-7/zoo/R/ORDER.R | 4 zoo-1.5-7/zoo/R/aggregate.zoo.R | 13 + zoo-1.5-7/zoo/R/as.zoo.R | 26 +- zoo-1.5-7/zoo/R/as.zoo.tis.R |only zoo-1.5-7/zoo/R/na.trim.R | 10 zoo-1.5-7/zoo/R/window.zoo.R | 9 zoo-1.5-7/zoo/R/xyplot.zoo.R | 67 +++++ zoo-1.5-7/zoo/R/yearmon.R | 40 +++ zoo-1.5-7/zoo/R/yearqtr.R | 33 ++ zoo-1.5-7/zoo/R/zoo.R | 74 +++++- zoo-1.5-7/zoo/inst/doc/zoo-faq.pdf | 10 zoo-1.5-7/zoo/inst/doc/zoo-quickref.pdf | 14 - zoo-1.5-7/zoo/inst/doc/zoo.pdf | 393 +++++++++++++++----------------- zoo-1.5-7/zoo/man/aggregate.zoo.Rd | 2 zoo-1.5-7/zoo/man/as.zoo.Rd | 20 + zoo-1.5-7/zoo/man/na.trim.Rd | 7 zoo-1.5-7/zoo/man/xyplot.zoo.Rd | 20 + zoo-1.5-7/zoo/man/yearmon.Rd | 39 ++- zoo-1.5-7/zoo/man/yearqtr.Rd | 29 ++ zoo-1.5-7/zoo/man/zoo.Rd | 4 26 files changed, 639 insertions(+), 258 deletions(-)
More information about safeBinaryRegression at CRAN
Permanent link
Author: Jeffrey A. Ryan, Josh M. Ulrich
Title: Extensible Time Series
Description: Provide for uniform handling of R's different time-based
data classes by extending zoo, maximizing native format
information preservation and allowing for user level
customization and extension, while simplifying cross-class
interoperability.
Diff between xts versions 0.6-6 dated 2009-06-14 and 0.6-7 dated 2009-07-22
DESCRIPTION | 8 NAMESPACE | 2 R/bind.R | 25 + R/coredata.xts.R | 2 R/endpoints.R | 49 +- R/fts.R | 2 R/origin.fix.R | 7 R/timeSeries.R | 3 R/xts.R | 4 R/xts.methods.R | 46 +- R/zoo.R | 18 - R/zzz.R | 4 inst/api_example/src/checkOrder.c | 6 inst/doc/xts.pdf | 652 +++++++++++++++++++------------------- man/subset.xts.Rd |only src/diff.c | 1 src/leadingNA.c | 15 src/merge.c | 2 src/rbind.c | 1 19 files changed, 460 insertions(+), 387 deletions(-)
Author: Jeffrey A. Ryan
Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial
trading strategies
Diff between quantmod versions 0.3-10 dated 2009-06-14 and 0.3-11 dated 2009-07-22
quantmod-0.3-10/quantmod/svn-commit.2.tmp |only quantmod-0.3-10/quantmod/svn-commit.tmp |only quantmod-0.3-11/quantmod/DESCRIPTION | 10 +++++----- quantmod-0.3-11/quantmod/R/chartSeries.R | 7 ++----- 4 files changed, 7 insertions(+), 10 deletions(-)
Author: Rob J Hyndman
Diff between forecasting versions 1.24 dated 2009-04-15 and 1.25 dated 2009-07-22
Bundle: forecasting
Contains: forecast fma Mcomp expsmooth
DESCRIPTION | 8 ++++----
forecast/R/arima.R | 19 +++++++++++++------
forecast/R/ets.R | 2 +-
forecast/R/forecast.R | 14 +++++++++-----
forecast/R/newarima2.R | 5 +++--
forecast/man/auto.arima.Rd | 4 +++-
forecast/man/forecast.ets.Rd | 2 +-
forecast/man/forecastplot.Rd | 7 +++++--
forecast/man/numberdiffs.Rd | 10 +++++++---
9 files changed, 46 insertions(+), 25 deletions(-)
Author: Jon Wakefield
Diff between HWEBayes versions 1.0 dated 2009-06-25 and 1.1 dated 2009-07-22
Title: Bayesian investigation of Hardy-Weinberg Equilibrium via
estimation and testing.
Description: Estimation and testing of HWE using Bayesian methods.
Three models are currently considered: HWE, a model
parameterized in terms of the allele frequencies and a single
inbreeding coefficient f, and the saturated model. Testing is
based on Bayes factors.
HWEBayes-1.0/HWEBayes/inst/doc/HWEBayes-WorkedExample.pdf |only
HWEBayes-1.1/HWEBayes/DESCRIPTION | 10 +++++-----
HWEBayes-1.1/HWEBayes/R/HWEImportSamp.R | 3 ++-
HWEBayes-1.1/HWEBayes/R/HWEmodelsMLE.R | 3 ++-
HWEBayes-1.1/HWEBayes/R/SinglefReject.R | 3 ++-
HWEBayes-1.1/HWEBayes/inst/doc/HWEBayes-Guide.pdf |only
6 files changed, 11 insertions(+), 8 deletions(-)
Author: Torsten Hothorn, Peter Buhlmann, Thomas Kneib, Matthias Schmid
and Benjamin Hofner
Title: Model-Based Boosting
Description: Functional gradient descent algorithms (boosting) for
optimizing general loss functions utilizing componentwise least
squares, either of parametric linear form or smoothing splines,
or regression trees as base learners for fitting generalized
linear, additive and interaction models to potentially
high-dimensional data.
Diff between mboost versions 1.1-1 dated 2009-04-22 and 1.1-2 dated 2009-07-21
DESCRIPTION | 8 +- NAMESPACE | 2 NEWS |only R/bbs2.R |only R/crossvalidation.R | 23 ++++++- R/glmboost.R | 10 +-- R/xsp.R | 112 ++++++++++++++++++++++++++------------ inst/CHANGES | 15 +++++ inst/doc/SurvivalEnsembles.pdf |binary inst/doc/mboost_illustrations.Rnw | 2 inst/doc/mboost_illustrations.pdf |binary man/FP.Rd | 26 ++++---- man/Family.Rd | 23 ++++--- man/baselearners.Rd | 40 +++++++------ man/blackboost.Rd | 35 ++++++----- man/boost_family-class.Rd | 13 ++-- man/control.Rd | 10 ++- man/cvrisk.Rd | 14 ++++ man/gamboost.Rd | 37 +++++++----- man/glmboost.Rd | 40 +++++++------ man/methods.Rd | 31 +++++----- man/survFit.Rd | 10 ++- tests/mboost_illustrations.R | 2 to_do_list.txt | 13 ++++ 24 files changed, 300 insertions(+), 166 deletions(-)
Author: REvolution Computing
Title: Iterator construct for R
Description: Support for iterators, which allow a programmer to
traverse through all the elements of a vector, list, or other
collection of data.
Diff between iterators versions 1.0.1 dated 2009-06-30 and 1.0.2 dated 2009-07-21
DESCRIPTION | 6 ++-- R/iterators.R | 61 ++++++++++++++++++++++++++++--------------------- inst/doc/iterators.pdf |binary inst/doc/iterators.tex |only 4 files changed, 38 insertions(+), 29 deletions(-)
Author: Marco Scutari
Title: Bayesian network structure learning
Description: Bayesian network structure learning via constraint-based
(also known as 'conditional independence') and score-based
algorithms. This package implements the Grow-Shrink (GS)
algorithm, the Incremental Association (IAMB) algorithm, the
Interleaved-IAMB (Inter-IAMB) algorithm, the Fast-IAMB
(Fast-IAMB) algorithm, the Max-Min Parents and Children (MMPC)
algorithm and the Hill-Climbing (HC) greedy search algorithm
for both discrete and Gaussian networks, along with many score
functions and conditional independence tests. Some utility
functions (model comparison and manipulation, random data
generation, arc orientation testing, simple and advanced plots)
are included, as well as basic parametric and bootstrap
inference functions.
Diff between bnlearn versions 1.4.1 dated 2009-06-14 and 1.5 dated 2009-07-21
bnlearn-1.4.1/bnlearn/man/00.bnlearn-package.Rd |only bnlearn-1.4.1/bnlearn/man/10.gs.Rd |only bnlearn-1.4.1/bnlearn/man/11.iamb.Rd |only bnlearn-1.4.1/bnlearn/man/12.fast.iamb.Rd |only bnlearn-1.4.1/bnlearn/man/13.inter.iamb.Rd |only bnlearn-1.4.1/bnlearn/man/14.mmpc.Rd |only bnlearn-1.4.1/bnlearn/man/15.hc.Rd |only bnlearn-1.4.1/bnlearn/man/20.mb.Rd |only bnlearn-1.4.1/bnlearn/man/21.arcops.Rd |only bnlearn-1.4.1/bnlearn/man/22.modelstring.Rd |only bnlearn-1.4.1/bnlearn/man/23.compare.Rd |only bnlearn-1.4.1/bnlearn/man/24.graphgen.Rd |only bnlearn-1.4.1/bnlearn/man/25.ordering.Rd |only bnlearn-1.4.1/bnlearn/man/30.score.Rd |only bnlearn-1.4.1/bnlearn/man/31.ci.test.Rd |only bnlearn-1.4.1/bnlearn/man/32.choose.direction.Rd |only bnlearn-1.4.1/bnlearn/man/33.arc.strength.Rd |only bnlearn-1.4.1/bnlearn/man/40.rbn.Rd |only bnlearn-1.4.1/bnlearn/man/50.plot.bn.Rd |only bnlearn-1.4.1/bnlearn/man/51.graphviz.plot.Rd |only bnlearn-1.4.1/bnlearn/man/52.strength.plot.Rd |only bnlearn-1.4.1/bnlearn/man/A0.learning-test.Rd |only bnlearn-1.4.1/bnlearn/man/A1.gaussian-test.Rd |only bnlearn-1.4.1/bnlearn/man/A2.asia.Rd |only bnlearn-1.4.1/bnlearn/man/A3.lizards.Rd |only bnlearn-1.4.1/bnlearn/man/A4.alarm.Rd |only bnlearn-1.4.1/bnlearn/man/A5.marks.Rd |only bnlearn-1.4.1/bnlearn/man/B0.bn.class.Rd |only bnlearn-1.4.1/bnlearn/man/B1.bn-strength.Rd |only bnlearn-1.4.1/bnlearn/man/C0.snow.Rd |only bnlearn-1.4.1/bnlearn/man/C1.deal.Rd |only bnlearn-1.5/bnlearn/Changelog | 26 ++ bnlearn-1.5/bnlearn/DESCRIPTION | 15 - bnlearn-1.5/bnlearn/NAMESPACE | 23 ++ bnlearn-1.5/bnlearn/R/arc.strength.R | 62 ++++++ bnlearn-1.5/bnlearn/R/backend-indep.R | 15 - bnlearn-1.5/bnlearn/R/backend-score.R | 23 +- bnlearn-1.5/bnlearn/R/bootstrap.R |only bnlearn-1.5/bnlearn/R/choose.direction.R | 125 +++++++++++++- bnlearn-1.5/bnlearn/R/ci.test.R | 4 bnlearn-1.5/bnlearn/R/cpdag.R |only bnlearn-1.5/bnlearn/R/fit.R |only bnlearn-1.5/bnlearn/R/formula.R | 35 +++ bnlearn-1.5/bnlearn/R/frontend-amat.R | 10 - bnlearn-1.5/bnlearn/R/frontend-arcs.R | 9 - bnlearn-1.5/bnlearn/R/frontend-bootstrap.R |only bnlearn-1.5/bnlearn/R/frontend-fit.R |only bnlearn-1.5/bnlearn/R/frontend-formula.R | 24 +- bnlearn-1.5/bnlearn/R/frontend-graph.R | 14 + bnlearn-1.5/bnlearn/R/frontend-lattice.R |only bnlearn-1.5/bnlearn/R/frontend-learning.R | 10 - bnlearn-1.5/bnlearn/R/frontend-plot.R | 13 - bnlearn-1.5/bnlearn/R/frontend-print.R | 49 +++++ bnlearn-1.5/bnlearn/R/frontend-score.R | 90 ++-------- bnlearn-1.5/bnlearn/R/frontend-strength.R |only bnlearn-1.5/bnlearn/R/globals.R | 31 ++- bnlearn-1.5/bnlearn/R/graphviz.R | 80 ++++++--- bnlearn-1.5/bnlearn/R/grow-shrink.R | 2 bnlearn-1.5/bnlearn/R/hill-climbing.R | 32 --- bnlearn-1.5/bnlearn/R/init.R | 7 bnlearn-1.5/bnlearn/R/inter-iamb.R | 29 +++ bnlearn-1.5/bnlearn/R/lattice.R |only bnlearn-1.5/bnlearn/R/learning-algorithms.R | 41 ++-- bnlearn-1.5/bnlearn/R/maxmin-pc.R | 8 bnlearn-1.5/bnlearn/R/scores.R | 163 ++++++++++-------- bnlearn-1.5/bnlearn/R/utils-arcs.R | 26 +- bnlearn-1.5/bnlearn/R/utils-graph.R | 14 - bnlearn-1.5/bnlearn/R/utils-misc.R | 5 bnlearn-1.5/bnlearn/R/utils-sanitization.R | 204 +++++++++++++++++++++-- bnlearn-1.5/bnlearn/inst/bibtex/bnlearn.bib | 81 ++------- bnlearn-1.5/bnlearn/inst/network.scripts/alarm.R | 6 bnlearn-1.5/bnlearn/man/alarm.Rd |only bnlearn-1.5/bnlearn/man/arc.strength.Rd |only bnlearn-1.5/bnlearn/man/arcops.Rd |only bnlearn-1.5/bnlearn/man/asia.Rd |only bnlearn-1.5/bnlearn/man/bn.class.Rd |only bnlearn-1.5/bnlearn/man/bn.fit.Rd |only bnlearn-1.5/bnlearn/man/bn.fit.class.Rd |only bnlearn-1.5/bnlearn/man/bn.fit.methods.Rd |only bnlearn-1.5/bnlearn/man/bn.fit.plots.Rd |only bnlearn-1.5/bnlearn/man/bn.strength-class.Rd |only bnlearn-1.5/bnlearn/man/bnboot.Rd |only bnlearn-1.5/bnlearn/man/bnlearn-package.Rd |only bnlearn-1.5/bnlearn/man/boot.strength.Rd |only bnlearn-1.5/bnlearn/man/choose.direction.Rd |only bnlearn-1.5/bnlearn/man/ci.test.Rd |only bnlearn-1.5/bnlearn/man/compare.Rd |only bnlearn-1.5/bnlearn/man/constraint.Rd |only bnlearn-1.5/bnlearn/man/cpdag.Rd |only bnlearn-1.5/bnlearn/man/deal.Rd |only bnlearn-1.5/bnlearn/man/gaussian-test.Rd |only bnlearn-1.5/bnlearn/man/graphgen.Rd |only bnlearn-1.5/bnlearn/man/graphviz.plot.Rd |only bnlearn-1.5/bnlearn/man/hc.Rd |only bnlearn-1.5/bnlearn/man/learning-test.Rd |only bnlearn-1.5/bnlearn/man/lizards.Rd |only bnlearn-1.5/bnlearn/man/marks.Rd |only bnlearn-1.5/bnlearn/man/mb.Rd |only bnlearn-1.5/bnlearn/man/mmpc.Rd |only bnlearn-1.5/bnlearn/man/modelstring.Rd |only bnlearn-1.5/bnlearn/man/ordering.Rd |only bnlearn-1.5/bnlearn/man/plot.bn.Rd |only bnlearn-1.5/bnlearn/man/rbn.Rd |only bnlearn-1.5/bnlearn/man/score.Rd |only bnlearn-1.5/bnlearn/man/snow.Rd |only bnlearn-1.5/bnlearn/man/strength.plot.Rd |only bnlearn-1.5/bnlearn/src/Makevars | 2 bnlearn-1.5/bnlearn/src/acyclic.c | 77 ++++++-- bnlearn-1.5/bnlearn/src/arcs2amat.c | 28 +-- bnlearn-1.5/bnlearn/src/bayesian.network.c | 2 bnlearn-1.5/bnlearn/src/bn.recovery.c | 6 bnlearn-1.5/bnlearn/src/bootstrap.c |only bnlearn-1.5/bnlearn/src/common.h | 4 bnlearn-1.5/bnlearn/src/dirichlet.posterior.c |only bnlearn-1.5/bnlearn/src/discrete.loglikelihood.c | 51 +++-- bnlearn-1.5/bnlearn/src/graph.generation.c | 146 ++++++++++------ bnlearn-1.5/bnlearn/src/is.row.equal.c | 111 ++++++++++++ bnlearn-1.5/bnlearn/src/linear.algebra.c | 18 +- bnlearn-1.5/bnlearn/src/monte.carlo.c | 49 +++-- bnlearn-1.5/bnlearn/src/mutual.information.c | 86 ++++++--- bnlearn-1.5/bnlearn/src/path.c | 74 +++++--- bnlearn-1.5/bnlearn/src/pearson.x2.c | 87 ++++++--- bnlearn-1.5/bnlearn/src/score.delta.helper.c |only 123 files changed, 1393 insertions(+), 624 deletions(-)
Author: Aaron A. King
Diff between ouch versions 2.5-4 dated 2009-03-13 and 2.5-6 dated 2009-07-21
Title: Ornstein-Uhlenbeck models for phylogenetic comparative
hypotheses
Description: Fit and compare Ornstein-Uhlenbeck models for evolution
along a phylogenetic tree.
DESCRIPTION | 11 ++++------
R/hansen.R | 2 -
inst/CITATION | 4 +--
inst/ChangeLog | 26 +++++++++++++++++++++++--
inst/SVN-REVISION |only
man/hansen.Rd | 4 +--
man/hansentree-methods.Rd | 4 ---
man/ouch-package.Rd | 47 +++++++++++++++++++++++++++-------------------
8 files changed, 63 insertions(+), 35 deletions(-)
Author: Arne Henningsen
Title: Microeconomic Analysis and Modelling
Description: Tools for microeconomic analysis and microeconomic
modelling
Diff between micEcon versions 0.5-18 dated 2009-05-05 and 0.5-22 dated 2009-07-21
DESCRIPTION | 8 INDEX | 8 R/cesEst.R |only R/print.summary.translogRayEst.R |only R/print.translogRayEst.R |only R/summary.translogRayEst.R |only R/translogProdFuncMargCost.R |only R/translogRayDeriv.R |only R/translogRayEst.R |only man/USMeatConsump.Rd | 2 man/aidsBestA0.Rd | 2 man/aidsCalc.Rd | 2 man/aidsConcav.Rd | 2 man/aidsConsist.Rd | 2 man/aidsElas.Rd | 2 man/aidsEst.Rd | 2 man/aidsMono.Rd | 2 man/aidsUtility.Rd | 2 man/cesEst.Rd |only man/fitted.aidsEst.Rd | 2 man/logLik.aidsEst.Rd | 2 man/lrtest.aidsEst.Rd | 2 man/predict.snqProfitEst.Rd | 2 man/print.snqProfitEst.Rd | 4 man/residuals.snqProfitEst.Rd | 2 man/snqProfitCalc.Rd | 2 man/snqProfitEla.Rd | 2 man/snqProfitEst.Rd | 2 man/snqProfitFixEla.Rd | 2 man/snqProfitHessian.Rd | 2 man/snqProfitHessianDeriv.Rd | 2 man/snqProfitImposeConvexity.Rd | 4 man/snqProfitShadowPrices.Rd | 2 man/snqProfitWeights.Rd | 2 man/summary.aidsElas.Rd | 2 man/summary.aidsEst.Rd | 2 man/summary.translogRayEst.Rd |only man/translogMonoRestr.Rd | 6 man/translogProdFuncMargCost.Rd |only man/translogRayDeriv.Rd |only man/translogRayEst.Rd |only tests/aids.R | 52 +-- tests/aids.Rout.save | 73 ++-- tests/cesTest.R |only tests/cesTest.Rout.save |only tests/cobbDouglasTest.Rout.save | 4 tests/colMediansTest.Rout.save | 4 tests/indices.Rout.save | 4 tests/insertColRow.Rout.save | 4 tests/npregHomTest.Rout.save | 4 tests/quadFunc.Rout.save | 16 - tests/snqProfit.R | 8 tests/snqProfit.Rout.save | 26 + tests/translog.R | 132 +++++++++ tests/translog.Rout.save | 570 ++++++++++++++++++++++++++++++++++++++- tests/translogCost.Rout.save | 4 56 files changed, 832 insertions(+), 147 deletions(-)
Author: Fadoua Balabdaoui, Kaspar Rufibach, Filippo Santambrogio
Title: Compute least squares estimates of one bounded or two ordered
isotonic regression curves
Description: We consider the problem of estimating two isotonic
regression curves g1* and g2* under the constraint that they
are ordered, i.e. g1* <= g2*. Given two sets of n data points
y_1, ..., y_n and z_1, ..., z_n that are observed at (the same)
deterministic design points x_1, ..., x_n, the estimates are
obtained by minimizing the Least Squares criterion L(a, b) =
sum_{i=1}^n (y_i - a_i)^2 w1(x_i) + sum_{i=1}^n (z_i - b_i)^2
w2(x_i) over the class of pairs of vectors (a, b) such that a
and b are isotonic and a_i <= b_i for all i = 1, ..., n. The
estimates are computed with a projected subgradient algorithm
where the projection is calculated using a PAVA.
Diff between OrdMonReg versions 1.0.0 dated 2009-04-15 and 1.0.1 dated 2009-07-21
CHANGES | 5 +++++ DESCRIPTION | 33 ++++++++++++++++----------------- man/LSfunctional.Rd | 8 ++++---- man/MA.Rd | 2 +- man/boundedAntiMeanTwo.Rd | 31 ++++++++++++++++--------------- man/boundedIsoMean.Rd | 24 +++++++++++++----------- man/bstar_n.Rd | 2 +- man/mechIng.Rd | 7 +++---- man/ordMonReg-package.Rd | 22 +++++++++++----------- 9 files changed, 70 insertions(+), 64 deletions(-)
Author: Jarrod Hadfield
Title: ML and MCMC Methods for Pedigree Reconstruction and Analysis
Description: The primary aim of MasterBayes is to use MCMC techniques
to integrate over uncertainty in pedigree configurations
estimated from molecular markers and phenotypic data. Emphasis
is put on the marginal distribution of parameters that relate
the phenotypic data to the pedigree. All simulation is done in
compiled C++ for efficency.
Diff between MasterBayes versions 2.43 dated 2009-04-14 and 2.44 dated 2009-07-21
MasterBayes-2.43/MasterBayes/inst/doc/Figures/Tutorial-050.pdf |only MasterBayes-2.43/MasterBayes/inst/doc/Figures/Tutorial-model.DSconfig.pdf |only MasterBayes-2.44/MasterBayes/DESCRIPTION | 8 MasterBayes-2.44/MasterBayes/R/ErrorCheck.R | 59 MasterBayes-2.44/MasterBayes/R/MCMCped.R | 21 MasterBayes-2.44/MasterBayes/R/MLE.beta.R | 4 MasterBayes-2.44/MasterBayes/R/MLE.ped.R | 56 MasterBayes-2.44/MasterBayes/R/MLE.popsize.R | 2 MasterBayes-2.44/MasterBayes/R/PedClasses.R | 14 MasterBayes-2.44/MasterBayes/R/autocorrP.R | 2 MasterBayes-2.44/MasterBayes/R/beta.loglik.R | 2 MasterBayes-2.44/MasterBayes/R/extractA.R | 2 MasterBayes-2.44/MasterBayes/R/fillX.G.R | 10 MasterBayes-2.44/MasterBayes/R/genotype.list.R | 4 MasterBayes-2.44/MasterBayes/R/getPost.R | 5 MasterBayes-2.44/MasterBayes/R/getXlist.R | 15 MasterBayes-2.44/MasterBayes/R/getsPandtP.R | 55 MasterBayes-2.44/MasterBayes/R/legalG.R | 13 MasterBayes-2.44/MasterBayes/R/mismatches.R | 2 MasterBayes-2.44/MasterBayes/R/modeG.R | 2 MasterBayes-2.44/MasterBayes/R/modeP.R | 14 MasterBayes-2.44/MasterBayes/R/orderPed.R | 2 MasterBayes-2.44/MasterBayes/R/popsize.loglik.R | 2 MasterBayes-2.44/MasterBayes/R/post.pairs.R | 2 MasterBayes-2.44/MasterBayes/R/reordXlist.R | 2 MasterBayes-2.44/MasterBayes/R/simgenotypes.R | 39 MasterBayes-2.44/MasterBayes/R/simpedigree.R | 2 MasterBayes-2.44/MasterBayes/R/varPed.R | 56 MasterBayes-2.44/MasterBayes/inst/doc/Figures/Tutorial.Rnw | 323 MasterBayes-2.44/MasterBayes/inst/doc/Rplots.pdf |1128191 +++------- MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-006.pdf | 4 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-007.pdf | 4 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-008.pdf | 4 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-009.pdf | 4 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-022.eps | 6043 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-022.pdf | 7050 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-023.eps |only MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-023.pdf |only 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6726 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.miss.pdf | 7031 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.miss2.eps | 6021 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.miss2.pdf | 7003 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.miss2US.eps | 5664 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.miss2US.pdf | 6556 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.missTest.eps | 6729 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.missTest.pdf | 7014 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.missUS.eps | 6068 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.missUS.pdf | 6828 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.pedEE2.eps | 6261 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model.pedEE2.pdf | 6560 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model2beta.eps | 6149 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model2beta.pdf | 7062 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model3beta.eps | 5878 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model3beta.pdf | 7057 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model4US.eps | 5641 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model4US.pdf | 6552 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model5.eps |17341 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model5.pdf |20043 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model6US.eps | 6178 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-model6US.pdf | 6544 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-mon1.eps |11137 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-mon1.pdf |13993 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-mon2.eps |19838 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-mon2.pdf |14075 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-ys.eps | 6499 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial-ys.pdf | 7076 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial.Rnw | 618 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial.bbl | 9 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial.blg | 58 MasterBayes-2.44/MasterBayes/inst/doc/Tutorial.pdf |232383 +- MasterBayes-2.44/MasterBayes/inst/doc/Tutorial.tex |only MasterBayes-2.44/MasterBayes/man/GdataPed.Rd | 14 MasterBayes-2.44/MasterBayes/man/MCMCped.Rd | 3 MasterBayes-2.44/MasterBayes/man/MLE.beta.Rd | 5 MasterBayes-2.44/MasterBayes/man/MLE.ped.Rd | 6 MasterBayes-2.44/MasterBayes/man/MLE.popsize.Rd | 3 MasterBayes-2.44/MasterBayes/man/MasterBayes.Rd | 13 MasterBayes-2.44/MasterBayes/man/PdataPed.Rd | 2 MasterBayes-2.44/MasterBayes/man/autocorrP.Rd | 9 MasterBayes-2.44/MasterBayes/man/beta.loglik.Rd | 11 MasterBayes-2.44/MasterBayes/man/extractA.Rd | 5 MasterBayes-2.44/MasterBayes/man/fillX.G.Rd | 18 MasterBayes-2.44/MasterBayes/man/genotype.list.Rd | 10 MasterBayes-2.44/MasterBayes/man/getXlist.Rd | 15 MasterBayes-2.44/MasterBayes/man/legalG.Rd | 14 MasterBayes-2.44/MasterBayes/man/mismatches.Rd | 3 MasterBayes-2.44/MasterBayes/man/modeG.Rd | 3 MasterBayes-2.44/MasterBayes/man/modeP.Rd | 7 MasterBayes-2.44/MasterBayes/man/orderPed.Rd | 3 MasterBayes-2.44/MasterBayes/man/popsize.loglik.Rd | 3 MasterBayes-2.44/MasterBayes/man/post.pairs.Rd | 3 MasterBayes-2.44/MasterBayes/man/priorPed.Rd | 7 MasterBayes-2.44/MasterBayes/man/reordXlist.Rd | 5 MasterBayes-2.44/MasterBayes/man/simgenotypes.Rd | 20 MasterBayes-2.44/MasterBayes/man/simpedigree.Rd | 3 MasterBayes-2.44/MasterBayes/man/startPed.Rd | 22 MasterBayes-2.44/MasterBayes/man/summary.genotypeD.Rd | 2 MasterBayes-2.44/MasterBayes/man/tunePed.Rd | 7 MasterBayes-2.44/MasterBayes/man/varPed.Rd | 5 MasterBayes-2.44/MasterBayes/src/ErrorMat.cc | 63 MasterBayes-2.44/MasterBayes/src/ErrorMat.h | 10 MasterBayes-2.44/MasterBayes/src/LikFunctions.cc | 80 MasterBayes-2.44/MasterBayes/src/LikFunctions.h | 2 MasterBayes-2.44/MasterBayes/src/MCMCped.cc | 58 MasterBayes-2.44/MasterBayes/src/MCMCped.h | 4 MasterBayes-2.44/MasterBayes/src/Read_in_data.cc | 2 MasterBayes-2.44/MasterBayes/src/SampG.cc | 2 MasterBayes-2.44/MasterBayes/src/SampGC.cc |only MasterBayes-2.44/MasterBayes/src/SampGC.h |only MasterBayes-2.44/MasterBayes/src/SampP.cc | 2 MasterBayes-2.44/MasterBayes/src/SampS.cc | 2 MasterBayes-2.44/MasterBayes/src/calcX_G.cc | 12 MasterBayes-2.44/MasterBayes/src/calcX_G.h | 3 MasterBayes-2.44/MasterBayes/src/calcX_GD.cc | 12 MasterBayes-2.44/MasterBayes/src/calcX_GS.cc | 12 MasterBayes-2.44/MasterBayes/src/calcX_Gcervus.cc | 453 MasterBayes-2.44/MasterBayes/src/fillXG.cc | 14 MasterBayes-2.44/MasterBayes/src/legalG.cc | 10 258 files changed, 907997 insertions(+), 1272058 deletions(-)
Author: Campo Elias Pardo
Diff between FactoClass versions 0.7.7 dated 2009-05-06 and 1.0.1 dated 2009-07-21
Title: Combination of Factorial Methods and Cluster Analysis
Description: Multivariate exploration of a data table with factorial
analysis and cluster methods.
DESCRIPTION | 10 +++++-----
R/FactoClass.R | 2 ++
R/centroids.R |only
R/planfac.R | 6 +++---
R/plotFactoClass.R | 8 ++++----
R/stableclus.R |only
R/zzz.R | 8 +-------
man/centroids.Rd |only
man/planfac.Rd | 22 ++++++++++++++--------
man/plotFactoClass.Rd | 4 +++-
man/stableclus.Rd |only
11 files changed, 32 insertions(+), 28 deletions(-)
Author: Andrej-Nikolai Spiess
Diff between qpcR versions 1.1-8 dated 2009-03-27 and 1.2-0 dated 2009-07-21
Title: Modelling and analysis of real-time PCR data
Description: Model fitting, optimal model selection and calculation of
various features that are essential in the analysis of
quantitative real-time polymerase chain reaction (qPCR).
qpcR-1.1-8/qpcR/R/ERBCP.R |only
qpcR-1.1-8/qpcR/R/REST.r |only
qpcR-1.1-8/qpcR/R/calib.R |only
qpcR-1.1-8/qpcR/R/confband.R |only
qpcR-1.1-8/qpcR/R/deriv2.b.R |only
qpcR-1.1-8/qpcR/R/deriv2.l.R |only
qpcR-1.1-8/qpcR/R/drmfit.r |only
qpcR-1.1-8/qpcR/R/expGrowth.R |only
qpcR-1.1-8/qpcR/R/mchoice.R |only
qpcR-1.1-8/qpcR/R/pcrfit.R |only
qpcR-1.1-8/qpcR/R/pcrpred.R |only
qpcR-1.1-8/qpcR/R/ratiocalc.R |only
qpcR-1.1-8/qpcR/R/ratiocalc.modlist.R |only
qpcR-1.1-8/qpcR/R/ratiocalc.pcrbatch.R |only
qpcR-1.1-8/qpcR/R/ratioplot.R |only
qpcR-1.1-8/qpcR/R/repform.R |only
qpcR-1.1-8/qpcR/R/residplot.R |only
qpcR-1.1-8/qpcR/R/studtest.R |only
qpcR-1.1-8/qpcR/R/typeid.R |only
qpcR-1.1-8/qpcR/man/LR.Rd |only
qpcR-1.1-8/qpcR/man/REST.rd |only
qpcR-1.1-8/qpcR/man/confband.Rd |only
qpcR-1.1-8/qpcR/man/drmfit.rd |only
qpcR-1.1-8/qpcR/man/mchoice.Rd |only
qpcR-1.1-8/qpcR/man/pcrpred.Rd |only
qpcR-1.1-8/qpcR/man/ratioplot.Rd |only
qpcR-1.1-8/qpcR/man/repform.Rd |only
qpcR-1.1-8/qpcR/man/residplot.Rd |only
qpcR-1.2-0/qpcR/DESCRIPTION | 10
qpcR-1.2-0/qpcR/NAMESPACE | 45 +++
qpcR-1.2-0/qpcR/R/AICc.R | 10
qpcR-1.2-0/qpcR/R/Cy0.R | 35 +-
qpcR-1.2-0/qpcR/R/LR.r | 3
qpcR-1.2-0/qpcR/R/PRESS.R | 61 ++--
qpcR-1.2-0/qpcR/R/Rsq.R | 7
qpcR-1.2-0/qpcR/R/Rsq.ad.r |only
qpcR-1.2-0/qpcR/R/Rsq.cor.r |only
qpcR-1.2-0/qpcR/R/calib.r |only
qpcR-1.2-0/qpcR/R/calib2.r | 293 +++++++++--------------
qpcR-1.2-0/qpcR/R/curvemean.R | 75 ++---
qpcR-1.2-0/qpcR/R/eff.R | 42 +--
qpcR-1.2-0/qpcR/R/efficiency.R | 220 +++++++++--------
qpcR-1.2-0/qpcR/R/evidence.R | 26 --
qpcR-1.2-0/qpcR/R/expcomp.R | 43 +--
qpcR-1.2-0/qpcR/R/expfit.R | 31 +-
qpcR-1.2-0/qpcR/R/maxRatio.r | 13 -
qpcR-1.2-0/qpcR/R/midpoint.R | 10
qpcR-1.2-0/qpcR/R/modlist.R | 76 +++---
qpcR-1.2-0/qpcR/R/mselect.r |only
qpcR-1.2-0/qpcR/R/outlier.R | 30 +-
qpcR-1.2-0/qpcR/R/pcrGOF.R | 2
qpcR-1.2-0/qpcR/R/pcrbatch.R | 205 ++++++++--------
qpcR-1.2-0/qpcR/R/pcrfit.r |only
qpcR-1.2-0/qpcR/R/pcropt1.R | 92 ++++---
qpcR-1.2-0/qpcR/R/pcropt2.R |only
qpcR-1.2-0/qpcR/R/pcrplot.R | 402 ++------------------------------
qpcR-1.2-0/qpcR/R/pcrpred.r |only
qpcR-1.2-0/qpcR/R/propagate.R | 224 ++++++++++++-----
qpcR-1.2-0/qpcR/R/ratiocalc.r |only
qpcR-1.2-0/qpcR/R/resplot.R |only
qpcR-1.2-0/qpcR/R/rnls.r |only
qpcR-1.2-0/qpcR/R/sliwin.R | 77 +++---
qpcR-1.2-0/qpcR/data/qpcR_functions.rda |only
qpcR-1.2-0/qpcR/man/AICc.Rd | 10
qpcR-1.2-0/qpcR/man/Cy0.rd | 43 +--
qpcR-1.2-0/qpcR/man/LR.rd |only
qpcR-1.2-0/qpcR/man/PRESS.Rd | 43 ---
qpcR-1.2-0/qpcR/man/RMSE.Rd | 12
qpcR-1.2-0/qpcR/man/RSS.Rd | 10
qpcR-1.2-0/qpcR/man/Rsq.Rd | 17 -
qpcR-1.2-0/qpcR/man/Rsq.ad.rd |only
qpcR-1.2-0/qpcR/man/Rsq.cor.rd |only
qpcR-1.2-0/qpcR/man/S27.Rd | 2
qpcR-1.2-0/qpcR/man/akaike.weights.Rd | 12
qpcR-1.2-0/qpcR/man/calib.Rd | 143 ++++++-----
qpcR-1.2-0/qpcR/man/calib2.rd | 100 +++----
qpcR-1.2-0/qpcR/man/curvemean.Rd | 20 -
qpcR-1.2-0/qpcR/man/eff.Rd | 30 +-
qpcR-1.2-0/qpcR/man/efficiency.Rd | 99 ++++---
qpcR-1.2-0/qpcR/man/evidence.Rd | 29 +-
qpcR-1.2-0/qpcR/man/expcomp.Rd | 20 -
qpcR-1.2-0/qpcR/man/expfit.Rd | 46 +--
qpcR-1.2-0/qpcR/man/guescini1.Rd | 11
qpcR-1.2-0/qpcR/man/guescini2.Rd | 17 -
qpcR-1.2-0/qpcR/man/maxRatio.rd | 14 -
qpcR-1.2-0/qpcR/man/midpoint.rd |only
qpcR-1.2-0/qpcR/man/modlist.Rd | 57 ++--
qpcR-1.2-0/qpcR/man/mselect.Rd |only
qpcR-1.2-0/qpcR/man/outlier.rd |only
qpcR-1.2-0/qpcR/man/pcrGOF.Rd | 15 -
qpcR-1.2-0/qpcR/man/pcrbatch.Rd | 40 +--
qpcR-1.2-0/qpcR/man/pcrfit.Rd | 56 ++--
qpcR-1.2-0/qpcR/man/pcrimport.Rd | 13 -
qpcR-1.2-0/qpcR/man/pcropt1.Rd | 42 +--
qpcR-1.2-0/qpcR/man/pcropt2.rd |only
qpcR-1.2-0/qpcR/man/pcrplot.Rd | 95 ++-----
qpcR-1.2-0/qpcR/man/pcrpred.rd |only
qpcR-1.2-0/qpcR/man/propagate.Rd | 199 ++++++++++-----
qpcR-1.2-0/qpcR/man/qpcR_functions.rd |only
qpcR-1.2-0/qpcR/man/ratiocalc.Rd | 243 ++++++++++++-------
qpcR-1.2-0/qpcR/man/reps.Rd | 9
qpcR-1.2-0/qpcR/man/reps2.Rd | 11
qpcR-1.2-0/qpcR/man/reps3.Rd | 10
qpcR-1.2-0/qpcR/man/resVar.Rd | 10
qpcR-1.2-0/qpcR/man/resplot.Rd |only
qpcR-1.2-0/qpcR/man/rutledge.Rd | 6
qpcR-1.2-0/qpcR/man/sliwin.Rd | 20 -
107 files changed, 1711 insertions(+), 1825 deletions(-)
Author: Gaston Sanchez
Diff between plspm versions 0.1-3 dated 2009-05-19 and 0.1-4 dated 2009-07-21
Title: Partial Least Squares data analysis methods
Description: Partial Least Squares (PLS) methods with emphasis on
structural equation models with latent variables.
DESCRIPTION | 12 +-
R/GQI.R |only
R/it.reb.R |only
R/local.models.R |only
R/locals.test.R |only
R/nipals.R | 17 +--
R/plot.plsca.R | 2
R/plot.plspm.groups.R | 3
R/pls.boot.R |only
R/pls.efects.R | 5
R/pls.gof.R |only
R/pls.loads.R | 17 +--
R/pls.paths.R | 6 -
R/pls.unidim.R |only
R/pls.weights.R | 41 ++++---
R/plsca.R | 9 -
R/plspm.R | 241 ++++++++++++----------------------------------
R/plspm.groups.R | 142 ++++++++++++---------------
R/plsr1.R | 6 -
R/plsreg1.R | 9 -
R/plsreg2.R | 7 -
R/print.local.models.R |only
R/print.plspm.R | 7 -
R/print.plspm.groups.R | 6 -
R/print.rebus.R |only
R/print.rebus.test.R |only
R/print.summary.plspm.R | 14 +-
R/rebus.pls.R |only
R/rebus.test.R |only
R/res.clus.R |only
R/summary.plspm.R | 16 +--
data/mobile.rda |only
data/sim.data.rda |only
man/arizona.Rd | 2
man/it.reb.Rd |only
man/local.models.Rd |only
man/mobile.Rd |only
man/plot.plspm.groups.Rd | 6 -
man/plot.plsreg1.Rd | 2
man/plot.plsreg2.Rd | 2
man/plspm-internal.Rd | 5
man/plspm-package.Rd | 12 +-
man/plspm.Rd | 12 +-
man/plspm.groups.Rd | 11 --
man/plsreg1.Rd | 2
man/plsreg2.Rd | 2
man/print.local.models.Rd |only
man/print.plspm.groups.Rd | 2
man/print.plsreg2.Rd | 2
man/print.rebus.Rd |only
man/print.rebus.test.Rd |only
man/rebus.pls.Rd |only
man/rebus.test.Rd |only
man/res.clus.Rd |only
man/sim.data.Rd |only
55 files changed, 261 insertions(+), 359 deletions(-)
Author: Klaus Schliep
Title: Phylogenetic analysis in R
Description: Phylogenetic analysis in R (Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
Distance methods & Hadamard conjugation)
Diff between phangorn versions 0.0-5 dated 2009-01-22 and 0.99-2 dated 2009-07-21
phangorn-0.0-5/phangorn/Changes |only phangorn-0.99-2/phangorn/ChangeLog |only phangorn-0.99-2/phangorn/DESCRIPTION | 28 phangorn-0.99-2/phangorn/NAMESPACE | 74 - phangorn-0.99-2/phangorn/R/phylo.R | 1383 ++++++++++++++++---------- phangorn-0.99-2/phangorn/R/sysdata.rda |only phangorn-0.99-2/phangorn/inst |only phangorn-0.99-2/phangorn/man/NJ.Rd | 2 phangorn-0.99-2/phangorn/man/SH.test.Rd |only phangorn-0.99-2/phangorn/man/allTrees.Rd | 3 phangorn-0.99-2/phangorn/man/bootstrap.pml.Rd |only phangorn-0.99-2/phangorn/man/designTree.Rd | 1 phangorn-0.99-2/phangorn/man/parsimony.Rd | 9 phangorn-0.99-2/phangorn/man/phyDat.Rd | 20 phangorn-0.99-2/phangorn/man/pmlCluster.Rd | 12 phangorn-0.99-2/phangorn/man/read.aa.Rd | 2 phangorn-0.99-2/phangorn/man/simSeq.Rd |only phangorn-0.99-2/phangorn/man/splitsNetwork.Rd | 6 phangorn-0.99-2/phangorn/man/treedist.Rd | 9 phangorn-0.99-2/phangorn/man/upgma.Rd | 2 phangorn-0.99-2/phangorn/src/init.c | 2 phangorn-0.99-2/phangorn/src/phangorn.c | 238 +++- phangorn-0.99-2/phangorn/src/phangorn.h | 5 23 files changed, 1155 insertions(+), 641 deletions(-)
Author: Kimihiro Noguchi
Diff between lawstat versions 2.2 dated 2007-11-14 and 2.3 dated 2009-07-21
Title: An R package for biostatistics, public policy, and law
Description: An R software package on statistical tests widely utilized
in biostatistics, public policy and law. Along with the well
known tests for equality of means and variances, randomness,
measures of relative variability etc, the package contains new
robust tests of symmetry, omnibus and directional tests of
normality, and their graphical counterparts such as Robust QQ
plot; a robust trend tests for variances etc. All implemented
tests and methods are illustrated by simulations and real-life
examples from legal statistics, economics, and biostatistics.
DESCRIPTION | 43 +-
R/bartels.test.R | 2
R/brunner.munzel.test.R | 3
R/cd.R | 3
R/cmh.test.R | 8
R/gini.index.R | 3
R/j.maad.R | 2
R/laplace.test.R |only
R/levene.test.R | 488 ++++++++++++++++++++++++++++--
R/lnested.test.R |only
R/lorenz.curve.R | 3
R/ltrend.test.R | 677 ++++++++++++++++++++++++++++++++++++++----
R/mma.test.R |only
R/neuhauser.hothorn.test.R |only
R/nig.parameter.R |only
R/rjb.test.R | 5
R/rlm.test.R |only
R/robust.mmm.test.R |only
R/rqq.R | 5
R/runs.test.R | 2
R/sj.test.R | 2
R/symmetry.test.R | 5
man/bartels.test.Rd | 6
man/brunner.munzel.test.Rd | 1
man/cd.Rd | 2
man/cmh.test.Rd | 13
man/gini.index.Rd | 4
man/laplace.test.Rd |only
man/levene.test.Rd | 95 ++++-
man/lnested.test.Rd |only
man/lorenz.curve.Rd | 1
man/ltrend.test.Rd | 110 +++++-
man/michigan.Rd | 2
man/mma.test.Rd |only
man/neuhauser.hothorn.test.Rd |only
man/nig.parameter.Rd |only
man/rjb.test.Rd | 6
man/rlm.test.Rd |only
man/robust.mmm.test.Rd |only
man/sj.test.Rd | 6
man/zuni.Rd | 2
41 files changed, 1311 insertions(+), 188 deletions(-)
Author: Mikis Stasinopoulos
Diff between gamlss.tr versions 2.0-0 dated 2009-04-03 and 3.0-0 dated 2009-07-21
Title: Generating and fitting truncated (gamlss.family) distributions
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to defined truncated distributions in
GAMLSS models. The main function gen.trun() generates truncated
version of an existing GAMLSS family distribution.
DESCRIPTION | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
Author: Mikis Stasinopoulos
Diff between gamlss.nl versions 2.0-0 dated 2009-04-03 and 3.0-0 dated 2009-07-21
Title: Fitting non linear parametric GAMLSS models
Description: This is an add on package to GAMLSS. It allows one extra
method for fitting GAMLSS models. The main function nlgamlss()
can fit any parametric (up to four parameter) GAMLSS
distribution.
DESCRIPTION | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
Author: Mikis Stasinopoulos
Diff between gamlss.mx versions 2.0-0 dated 2009-04-03 and 3.0-0 dated 2009-07-21
Title: A GAMLSS add on package for fitting mixture distributions
Description: The main purpose of this package is to allow fitting of
mixture distributions with GAMLSS models.
DESCRIPTION | 8 ++++----
R/gamlssMX-10-11-07.R | 18 ++++++++++++++++--
2 files changed, 20 insertions(+), 6 deletions(-)
Author: Mikis Stasinopoulos
Diff between gamlss.dist versions 2.0-0 dated 2009-04-03 and 3.0-0 dated 2009-07-21
Title: Distributions to be used for GAMLSS modelling.
Description: This package contains the distributions for GAMLSS
modelling.
gamlss.dist-2.0-0/gamlss.dist/data |only
gamlss.dist-2.0-0/gamlss.dist/man/CD4.Rd |only
gamlss.dist-2.0-0/gamlss.dist/man/LGAclaims.Rd |only
gamlss.dist-2.0-0/gamlss.dist/man/alveolar.Rd |only
gamlss.dist-2.0-0/gamlss.dist/man/computer.Rd |only
gamlss.dist-2.0-0/gamlss.dist/man/glass.Rd |only
gamlss.dist-2.0-0/gamlss.dist/man/lice.Rd |only
gamlss.dist-2.0-0/gamlss.dist/man/margolin.Rd |only
gamlss.dist-2.0-0/gamlss.dist/man/parzen.Rd |only
gamlss.dist-2.0-0/gamlss.dist/man/species.Rd |only
gamlss.dist-2.0-0/gamlss.dist/man/stylo.Rd |only
gamlss.dist-2.0-0/gamlss.dist/man/tensile.Rd |only
gamlss.dist-2.0-0/gamlss.dist/tests/checkDist.R |only
gamlss.dist-3.0-0/gamlss.dist/DESCRIPTION | 18 ++---
gamlss.dist-3.0-0/gamlss.dist/NAMESPACE | 50 +++++++++++----
gamlss.dist-3.0-0/gamlss.dist/R/BB.R |only
gamlss.dist-3.0-0/gamlss.dist/R/BCCG.R |only
gamlss.dist-3.0-0/gamlss.dist/R/BCPE.R |only
gamlss.dist-3.0-0/gamlss.dist/R/BCT.R |only
gamlss.dist-3.0-0/gamlss.dist/R/BE.R |only
gamlss.dist-3.0-0/gamlss.dist/R/BEINF.R |only
gamlss.dist-3.0-0/gamlss.dist/R/BEo.R |only
gamlss.dist-3.0-0/gamlss.dist/R/BI.R |only
gamlss.dist-3.0-0/gamlss.dist/R/DELAPORT.R | 16 ++--
gamlss.dist-3.0-0/gamlss.dist/R/GA.R |only
gamlss.dist-3.0-0/gamlss.dist/R/GIG.R | 8 +-
gamlss.dist-3.0-0/gamlss.dist/R/GU.R |only
gamlss.dist-3.0-0/gamlss.dist/R/IG.R |only
gamlss.dist-3.0-0/gamlss.dist/R/JSU.R |only
gamlss.dist-3.0-0/gamlss.dist/R/JSUo.R |only
gamlss.dist-3.0-0/gamlss.dist/R/LNO.R |only
gamlss.dist-3.0-0/gamlss.dist/R/Logistic.R |only
gamlss.dist-3.0-0/gamlss.dist/R/NBI.R |only
gamlss.dist-3.0-0/gamlss.dist/R/NBII.R |only
gamlss.dist-3.0-0/gamlss.dist/R/NET.R |only
gamlss.dist-3.0-0/gamlss.dist/R/NO.r |only
gamlss.dist-3.0-0/gamlss.dist/R/PE.R |only
gamlss.dist-3.0-0/gamlss.dist/R/PE2.R |only
gamlss.dist-3.0-0/gamlss.dist/R/PIG.R |only
gamlss.dist-3.0-0/gamlss.dist/R/RG.R |only
gamlss.dist-3.0-0/gamlss.dist/R/SEP.R |only
gamlss.dist-3.0-0/gamlss.dist/R/SI.R |only
gamlss.dist-3.0-0/gamlss.dist/R/SICHEL.R | 10 +--
gamlss.dist-3.0-0/gamlss.dist/R/ST1.R | 4 -
gamlss.dist-3.0-0/gamlss.dist/R/TF.R |only
gamlss.dist-3.0-0/gamlss.dist/R/WEI.R |only
gamlss.dist-3.0-0/gamlss.dist/R/WEI2.R |only
gamlss.dist-3.0-0/gamlss.dist/R/ZAGA.R |only
gamlss.dist-3.0-0/gamlss.dist/R/ZAIG.R |only
gamlss.dist-3.0-0/gamlss.dist/R/ZIP.R |only
gamlss.dist-3.0-0/gamlss.dist/R/checkBCPE.R |only
gamlss.dist-3.0-0/gamlss.dist/R/gamlss-family.R |only
gamlss.dist-3.0-0/gamlss.dist/R/logNO.R |only
gamlss.dist-3.0-0/gamlss.dist/R/make-link-gamlss-new.R |only
gamlss.dist-3.0-0/gamlss.dist/R/po.r |only
gamlss.dist-3.0-0/gamlss.dist/man/BB.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/BCCG.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/BCPE.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/BCt.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/BE.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/BEINF.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/BEOI.Rd | 17 ++---
gamlss.dist-3.0-0/gamlss.dist/man/BEZI.Rd | 19 +++--
gamlss.dist-3.0-0/gamlss.dist/man/BI.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/DEL.Rd | 7 +-
gamlss.dist-3.0-0/gamlss.dist/man/EGB2.Rd | 5 -
gamlss.dist-3.0-0/gamlss.dist/man/EXP.Rd | 7 +-
gamlss.dist-3.0-0/gamlss.dist/man/GA.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/GB1.Rd | 3
gamlss.dist-3.0-0/gamlss.dist/man/GB2.Rd | 6 -
gamlss.dist-3.0-0/gamlss.dist/man/GG.Rd | 10 +--
gamlss.dist-3.0-0/gamlss.dist/man/GIG.Rd | 4 -
gamlss.dist-3.0-0/gamlss.dist/man/GT.Rd | 6 -
gamlss.dist-3.0-0/gamlss.dist/man/GU.rd |only
gamlss.dist-3.0-0/gamlss.dist/man/IG.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/JSU.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/JSUoriginal.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/LNO.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/LOGISTIC.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/NBI.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/NBII.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/NET.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/NO.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/NO2.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/NOF.Rd | 23 +++---
gamlss.dist-3.0-0/gamlss.dist/man/PE.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/PIG.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/PO.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/RG.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/RGE.Rd | 6 -
gamlss.dist-3.0-0/gamlss.dist/man/SEP.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/SEP1.Rd | 18 ++---
gamlss.dist-3.0-0/gamlss.dist/man/SHASH.Rd | 6 +
gamlss.dist-3.0-0/gamlss.dist/man/SI.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/SICHEL.Rd | 5 -
gamlss.dist-3.0-0/gamlss.dist/man/ST1.Rd | 16 ++--
gamlss.dist-3.0-0/gamlss.dist/man/TF.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/WEI.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/WEI2.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/WEI3.Rd | 5 -
gamlss.dist-3.0-0/gamlss.dist/man/ZAGA.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/ZAIG.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/ZIP.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/ZIP2.Rd | 11 +--
gamlss.dist-3.0-0/gamlss.dist/man/checklink.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/exGAUS.Rd | 10 +--
gamlss.dist-3.0-0/gamlss.dist/man/gamlss.dist.package.Rd | 6 -
gamlss.dist-3.0-0/gamlss.dist/man/gamlss.family.Rd |only
gamlss.dist-3.0-0/gamlss.dist/man/make.link.gamlss.Rd |only
gamlss.dist-3.0-0/gamlss.dist/src/tofy.f |only
gamlss.dist-3.0-0/gamlss.dist/src/tofys.f |only
111 files changed, 171 insertions(+), 125 deletions(-)
Author: Mikis Stasinopoulos
Diff between gamlss.cens versions 2.0.0 dated 2009-04-03 and 3.0.0 dated 2009-07-21
Title: Fitting an interval response variable using gamlss.family
distributions
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to fit interval response variables in
GAMLSS models. The main function gen.cens() generates a
censored version of an existing GAMLSS family distribution.
DESCRIPTION | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
Author: Mikis Stasinopoulos
Diff between gamlss versions 2.0-0 dated 2009-04-03 and 3.0-0 dated 2009-07-21
Title: Generalized Additive Models for Location Scale and Shape.
Description: The library for fitting GAMLSS models.
gamlss-2.0-0/gamlss/R/BB.R |only
gamlss-2.0-0/gamlss/R/BCCG.R |only
gamlss-2.0-0/gamlss/R/BCPE.R |only
gamlss-2.0-0/gamlss/R/BCT.R |only
gamlss-2.0-0/gamlss/R/BE.R |only
gamlss-2.0-0/gamlss/R/BEINF.R |only
gamlss-2.0-0/gamlss/R/BEo.R |only
gamlss-2.0-0/gamlss/R/BI.R |only
gamlss-2.0-0/gamlss/R/GA.R |only
gamlss-2.0-0/gamlss/R/GU.R |only
gamlss-2.0-0/gamlss/R/IG.R |only
gamlss-2.0-0/gamlss/R/JSU.R |only
gamlss-2.0-0/gamlss/R/JSUo.R |only
gamlss-2.0-0/gamlss/R/LNO.R |only
gamlss-2.0-0/gamlss/R/Logistic.R |only
gamlss-2.0-0/gamlss/R/NBI.R |only
gamlss-2.0-0/gamlss/R/NBII.R |only
gamlss-2.0-0/gamlss/R/NET.R |only
gamlss-2.0-0/gamlss/R/NO.r |only
gamlss-2.0-0/gamlss/R/PE.R |only
gamlss-2.0-0/gamlss/R/PE2.R |only
gamlss-2.0-0/gamlss/R/PIG.R |only
gamlss-2.0-0/gamlss/R/RG.R |only
gamlss-2.0-0/gamlss/R/SEP.R |only
gamlss-2.0-0/gamlss/R/SI.R |only
gamlss-2.0-0/gamlss/R/TF.R |only
gamlss-2.0-0/gamlss/R/WEI.R |only
gamlss-2.0-0/gamlss/R/WEI2.R |only
gamlss-2.0-0/gamlss/R/ZAIG.R |only
gamlss-2.0-0/gamlss/R/ZIP.R |only
gamlss-2.0-0/gamlss/R/checkBCPE.R |only
gamlss-2.0-0/gamlss/R/logNO.R |only
gamlss-2.0-0/gamlss/R/make-link-gamlss-new.R |only
gamlss-2.0-0/gamlss/R/po.r |only
gamlss-2.0-0/gamlss/R/predict-gamlss.R |only
gamlss-2.0-0/gamlss/data |only
gamlss-2.0-0/gamlss/man/BB.Rd |only
gamlss-2.0-0/gamlss/man/BCCG.Rd |only
gamlss-2.0-0/gamlss/man/BCPE.Rd |only
gamlss-2.0-0/gamlss/man/BCt.Rd |only
gamlss-2.0-0/gamlss/man/BE.Rd |only
gamlss-2.0-0/gamlss/man/BEINF.Rd |only
gamlss-2.0-0/gamlss/man/BI.Rd |only
gamlss-2.0-0/gamlss/man/GA.Rd |only
gamlss-2.0-0/gamlss/man/GU.rd |only
gamlss-2.0-0/gamlss/man/IG.Rd |only
gamlss-2.0-0/gamlss/man/JSU.Rd |only
gamlss-2.0-0/gamlss/man/JSUoriginal.Rd |only
gamlss-2.0-0/gamlss/man/LNO.Rd |only
gamlss-2.0-0/gamlss/man/LOGISTIC.Rd |only
gamlss-2.0-0/gamlss/man/Mums.Rd |only
gamlss-2.0-0/gamlss/man/NBI.Rd |only
gamlss-2.0-0/gamlss/man/NBII.Rd |only
gamlss-2.0-0/gamlss/man/NET.Rd |only
gamlss-2.0-0/gamlss/man/NO.Rd |only
gamlss-2.0-0/gamlss/man/NO2.Rd |only
gamlss-2.0-0/gamlss/man/PE.Rd |only
gamlss-2.0-0/gamlss/man/PIG.Rd |only
gamlss-2.0-0/gamlss/man/PO.Rd |only
gamlss-2.0-0/gamlss/man/RG.Rd |only
gamlss-2.0-0/gamlss/man/SEP.Rd |only
gamlss-2.0-0/gamlss/man/SI.Rd |only
gamlss-2.0-0/gamlss/man/TF.Rd |only
gamlss-2.0-0/gamlss/man/WEI.Rd |only
gamlss-2.0-0/gamlss/man/WEI2.Rd |only
gamlss-2.0-0/gamlss/man/ZAIG.Rd |only
gamlss-2.0-0/gamlss/man/ZIP.Rd |only
gamlss-2.0-0/gamlss/man/abdom.Rd |only
gamlss-2.0-0/gamlss/man/aep.Rd |only
gamlss-2.0-0/gamlss/man/aids.Rd |only
gamlss-2.0-0/gamlss/man/bd.Rd |only
gamlss-2.0-0/gamlss/man/checklink.Rd |only
gamlss-2.0-0/gamlss/man/fabric.Rd |only
gamlss-2.0-0/gamlss/man/gamlss.family.Rd |only
gamlss-2.0-0/gamlss/man/hodges.Rd |only
gamlss-2.0-0/gamlss/man/make.link.gamlss.Rd |only
gamlss-2.0-0/gamlss/man/rent.Rd |only
gamlss-2.0-0/gamlss/man/usair.Rd |only
gamlss-2.0-0/gamlss/src |only
gamlss-3.0-0/gamlss/DESCRIPTION | 13 +-
gamlss-3.0-0/gamlss/NAMESPACE | 43 -------
gamlss-3.0-0/gamlss/R/add.r | 5
gamlss-3.0-0/gamlss/R/centile-pred.R | 8 -
gamlss-3.0-0/gamlss/R/cs.R | 2
gamlss-3.0-0/gamlss/R/cy.R | 4
gamlss-3.0-0/gamlss/R/extra.R | 160 ---------------------------
gamlss-3.0-0/gamlss/R/gamlss.R | 40 +++---
gamlss-3.0-0/gamlss/R/pb.R | 4
gamlss-3.0-0/gamlss/R/predict.gamlss.R |only
gamlss-3.0-0/gamlss/R/term-plot.R | 1
gamlss-3.0-0/gamlss/inst/CITATION |only
gamlss-3.0-0/gamlss/inst/doc/NEWS.txt | 17 ++
gamlss-3.0-0/gamlss/man/VGD.Rd | 4
gamlss-3.0-0/gamlss/man/bfp.Rd | 2
gamlss-3.0-0/gamlss/man/cs.Rd | 4
gamlss-3.0-0/gamlss/man/deviance.gamlss.Rd | 2
gamlss-3.0-0/gamlss/man/gamlss.Rd | 10 -
gamlss-3.0-0/gamlss/man/gamlss.package.Rd | 2
gamlss-3.0-0/gamlss/man/histDist.Rd | 2
gamlss-3.0-0/gamlss/man/pdf.plot.Rd | 10 -
gamlss-3.0-0/gamlss/man/ps.Rd | 4
101 files changed, 87 insertions(+), 250 deletions(-)
Author: Hsin-ya Lee
Diff between bear versions 2.3.1 dated 2009-04-14 and 2.4.0 dated 2009-07-21
Title: Average bioequivalence and bioavailability data analysis tool
Description: An average bioequivalence (ABE) and bioavailability data
analysis tool including sample size estimation,
noncompartmental analysis (NCA), ANOVA (lm) for a standard
RT/TR 2x2x2 crossover design and linear mixed effect model (lme
of nlme) for a 2-treatment, 2-sequence, with 2 periods or more
(i.e. 2x2x3/2x2x4) replicate design or a 2-treatment,
2-sequence, and 1-period parallel ABE study (2x2x1).
DESCRIPTION | 10
R/ARS.r | 329 +++++++--
R/BANOVA.r | 500 +++++++++++++-
R/BANOVAanalyze.r | 102 ++
R/BANOVAcsv.r | 315 +++++++-
R/BANOVAdata.r | 250 +++++--
R/BANOVAmenu.r | 19
R/BANOVAoutput.r | 86 ++
R/BANOVAplot.r | 119 ++-
R/Multiple1menu.r |only
R/MultipleAIC_BANOVA.r |only
R/MultipleAICdemo.r |only
R/MultipleAICoutput.r |only
R/MultipleARS.BANOVA.r |only
R/MultipleARS.r |only
R/MultipleARSdemo.r |only
R/MultipleARSoutput.r |only
R/MultipleBANOVA.r |only
R/MultipleBANOVAanalyze.r |only
R/MultipleBANOVAcsv.r |only
R/MultipleBANOVAdata.r |only
R/MultipleBANOVAmenu.r |only
R/MultipleBANOVAoutput.r |only
R/MultipleBANOVAplot.r |only
R/MultipleNCA.BANOVA.r |only
R/MultipleNCA.BANOVAanalyze.r |only
R/MultipleNCA.BANOVAcsv.r |only
R/MultipleNCA.BANOVAdata.r |only
R/MultipleNCA.BANOVAmenu.r |only
R/MultipleNCA.r |only
R/MultipleNCAanalyze.r |only
R/MultipleNCAcsv.r |only
R/MultipleNCAdata.r |only
R/MultipleNCAdemo.BANOVA.r |only
R/MultipleNCAdemo.r |only
R/MultipleNCAmenu.r |only
R/MultipleNCAoutput.r |only
R/MultipleNCAplot.r |only
R/MultipleNCAsave.r |only
R/MultipleNCAselect.BANOVA.r |only
R/MultipleNCAselect.r |only
R/MultipleNCAselectdemo.BANOVA.r |only
R/MultipleNCAselectdemo.r |only
R/MultipleNCAselectsave.BANOVA.r |only
R/MultipleNCAselectsave.r |only
R/MultipleParaAIC.MIX.r |only
R/MultipleParaAIC.r |only
R/MultipleParaAICdemo.r |only
R/MultipleParaAICoutput.r |only
R/MultipleParaARS.MIX.r |only
R/MultipleParaARS.r |only
R/MultipleParaARSdemo.r |only
R/MultipleParaARSoutput.r |only
R/MultipleParaMIX.r |only
R/MultipleParaMIXanalyze.r |only
R/MultipleParaMIXcsv.r |only
R/MultipleParaMIXdata.r |only
R/MultipleParaMIXmenu.r |only
R/MultipleParaMIXoutput.r |only
R/MultipleParaNCA.MIX.r |only
R/MultipleParaNCA.MIXanalyze.r |only
R/MultipleParaNCA.MIXcsv.r |only
R/MultipleParaNCA.MIXdata.r |only
R/MultipleParaNCA.MIXmenu.r |only
R/MultipleParaNCA.r |only
R/MultipleParaNCAanalyze.r |only
R/MultipleParaNCAcsv.r |only
R/MultipleParaNCAdata.r |only
R/MultipleParaNCAdemo.MIX.r |only
R/MultipleParaNCAdemo.r |only
R/MultipleParaNCAoutput.r |only
R/MultipleParaNCAplot.r |only
R/MultipleParaNCAsave.r |only
R/MultipleParaNCAselect.MIX.r |only
R/MultipleParaNCAselect.r |only
R/MultipleParaNCAselectdemo.MIX.r |only
R/MultipleParaNCAselectdemo.r |only
R/MultipleParaNCAselectsave.MIX.r |only
R/MultipleParaNCAselectsave.r |only
R/MultipleParaTTT.MIX.r |only
R/MultipleParaTTT.r |only
R/MultipleParaTTTAIC.MIX.r |only
R/MultipleParaTTTAIC.r |only
R/MultipleParaTTTAICdemo.r |only
R/MultipleParaTTTAICoutput.r |only
R/MultipleParaTTTARS.MIX.r |only
R/MultipleParaTTTARS.r |only
R/MultipleParaTTTARSdemo.r |only
R/MultipleParaTTTARSoutput.r |only
R/MultipleParaTTTdemo.r |only
R/MultipleParaTTToutput.r |only
R/MultipleParademoMIX.r |only
R/MultipleParademomenu.r |only
R/MultipleParademomenu1.r |only
R/MultipleParamenu.r |only
R/MultipleTTT.BANOVA.r |only
R/MultipleTTT.r |only
R/MultipleTTTAIC.BANOVA.r |only
R/MultipleTTTAIC.r |only
R/MultipleTTTAICdemo.r |only
R/MultipleTTTAICoutput.r |only
R/MultipleTTTARS.BANOVA.r |only
R/MultipleTTTARS.r |only
R/MultipleTTTARSdemo.r |only
R/MultipleTTTARSoutput.r |only
R/MultipleTTTdemo.r |only
R/MultipleTTToutput.r |only
R/Multipleaic.r |only
R/MultipledemoBANOVA.r |only
R/Multipledemomenu.r |only
R/Multipledemomenu1.r |only
R/Multiplego.r |only
R/Multiplemenu.r | 44 +
R/Multiplentertitle.demo.r |only
R/Multiplentertitle.r |only
R/Multipleplotsingle.para.r |only
R/Multipleplotsingle.r |only
R/Multiplestat1menu.r |only
R/Multiplestatmenu.r | 40 +
R/NCA.BANOVAanalyze.r | 127 +++
R/NCA.BANOVAcsv.r | 125 +++
R/NCA.BANOVAdata.r | 60 +
R/NCA.BANOVAmenu.r | 31
R/NCA.r | 287 +++++++-
R/NCAanalyze.r | 204 +++++
R/NCAcsv.r | 146 +++-
R/NCAdata.r | 60 +
R/NCAmenu.r | 54 +
R/NCAoutput.r | 1229 ++++++++++++++++++++++++++---------
R/NCAplot.r | 382 ++++++++--
R/NCAsave.r | 16
R/NCAselect.r | 162 +++-
R/NCAselectsave.BANOVA.r | 3
R/NCAselectsave.r | 70 +
R/RepMIX.r | 174 ++++
R/RepMIXanalyze.r | 44 +
R/RepMIXmenu.r | 19
R/RepMIXoutput.r | 37 -
R/RepNCA.MIXmenu.r | 23
R/Singlego.r |only
R/TTT.r | 312 +++++++-
R/TTTAIC.r | 277 ++++++-
R/TTTARS.r | 330 ++++++++-
R/aic.r | 260 ++++++-
R/demoBANOVA.r | 58 +
R/demomenu.r | 220 +++++-
R/demomenu1.r | 196 +++++
R/description_Multipledrugcode.r |only
R/description_drugcode.r | 18
R/description_plot.r | 5
R/description_size.r | 4
R/description_version.r | 5
R/entertitle.demo.r | 2
R/entertitle.r | 71 +-
R/go.r | 27
R/plotsingle.para.r | 113 ++-
R/plotsingle.r | 69 +
R/stat1menu.r |only
R/statmenu.r | 40 +
R/zzz.R | 6
data/MultipleParadata.r |only
data/Multipledata.r |only
data/TotalSingledata.r | 2
man/AIC_BANOVA.rd | 2
man/AICdemo.rd | 2
man/AICoutput.rd | 2
man/ARS.BANOVA.rd | 4
man/ARS.rd | 2
man/ARSdemo.BANOVA.rd | 2
man/ARSdemo.rd | 4
man/ARSoutput.rd | 4
man/BANOVA.rd | 2
man/BANOVAanalyze.rd | 2
man/BANOVAcsv.rd | 2
man/BANOVAdata.rd | 2
man/BANOVAmenu.rd | 2
man/BANOVAoutput.rd | 2
man/BANOVAplot.rd | 2
man/Multiple1menu.rd |only
man/MultipleAIC_BANOVA.rd |only
man/MultipleAICdemo.rd |only
man/MultipleAICoutput.rd |only
man/MultipleARS.BANOVA.rd |only
man/MultipleARS.rd |only
man/MultipleARSdemo.rd |only
man/MultipleARSoutput.rd |only
man/MultipleBANOVA.rd |only
man/MultipleBANOVAanalyze.rd |only
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man/MultipleBANOVAdata.rd |only
man/MultipleBANOVAmenu.rd |only
man/MultipleBANOVAoutput.rd |only
man/MultipleBANOVAplot.rd |only
man/MultipleNCA.BANOVA.rd |only
man/MultipleNCA.BANOVAanalyze.rd |only
man/MultipleNCA.BANOVAcsv.rd |only
man/MultipleNCA.BANOVAdata.rd |only
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man/MultipleNCA.rd |only
man/MultipleNCAanalyze.rd |only
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man/MultipleNCAdata.rd |only
man/MultipleNCAdemo.BANOVA.rd |only
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man/MultipleNCAmenu.rd |only
man/MultipleNCAoutput.rd |only
man/MultipleNCAplot.rd |only
man/MultipleNCAsave.rd |only
man/MultipleNCAselect.BANOVA.rd |only
man/MultipleNCAselect.rd |only
man/MultipleNCAselectdemo.BANOVA.rd |only
man/MultipleNCAselectdemo.rd |only
man/MultipleNCAselectsave.BANOVA.rd |only
man/MultipleNCAselectsave.rd |only
man/MultipleParaAIC.MIX.rd |only
man/MultipleParaAIC.rd |only
man/MultipleParaAICdemo.rd |only
man/MultipleParaAICoutput.rd |only
man/MultipleParaARS.MIX.rd |only
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man/MultipleParaMIX.rd |only
man/MultipleParaMIXanalyze.rd |only
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man/MultipleParaMIXdata.rd |only
man/MultipleParaMIXmenu.rd |only
man/MultipleParaMIXoutput.rd |only
man/MultipleParaNCA.MIX.rd |only
man/MultipleParaNCA.MIXanalyze.rd |only
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man/MultipleParaNCA.MIXdata.rd |only
man/MultipleParaNCA.MIXmenu.rd |only
man/MultipleParaNCA.rd |only
man/MultipleParaNCAanalyze.rd |only
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man/MultipleParaNCAdata.rd |only
man/MultipleParaNCAdemo.MIX.rd |only
man/MultipleParaNCAdemo.rd |only
man/MultipleParaNCAoutput.rd |only
man/MultipleParaNCAplot.rd |only
man/MultipleParaNCAsave.rd |only
man/MultipleParaNCAselect.MIX.rd |only
man/MultipleParaNCAselect.rd |only
man/MultipleParaNCAselectdemo.MIX.rd |only
man/MultipleParaNCAselectdemo.rd |only
man/MultipleParaNCAselectsave.MIX.rd |only
man/MultipleParaNCAselectsave.rd |only
man/MultipleParaTTT.MIX.rd |only
man/MultipleParaTTT.rd |only
man/MultipleParaTTTAIC.MIX.rd |only
man/MultipleParaTTTAIC.rd |only
man/MultipleParaTTTAICdemo.rd |only
man/MultipleParaTTTAICoutput.rd |only
man/MultipleParaTTTARS.MIX.rd |only
man/MultipleParaTTTARS.rd |only
man/MultipleParaTTTARSdemo.rd |only
man/MultipleParaTTTARSoutput.rd |only
man/MultipleParaTTTdemo.rd |only
man/MultipleParaTTToutput.rd |only
man/MultipleParadata.rd |only
man/MultipleParademoMIX.rd |only
man/MultipleParademomenu.rd |only
man/MultipleParademomenu1.rd |only
man/MultipleParamenu.rd |only
man/MultipleTTT.BANOVA.rd |only
man/MultipleTTT.rd |only
man/MultipleTTTAIC.BANOVA.rd |only
man/MultipleTTTAIC.rd |only
man/MultipleTTTAICdemo.rd |only
man/MultipleTTTAICoutput.rd |only
man/MultipleTTTARS.BANOVA.rd |only
man/MultipleTTTARS.rd |only
man/MultipleTTTARSdemo.rd |only
man/MultipleTTTARSoutput.rd |only
man/MultipleTTTdemo.rd |only
man/MultipleTTToutput.rd |only
man/Multipleaic.rd |only
man/Multipledata.rd |only
man/MultipledemoBANOVA.rd |only
man/Multipledemomenu.rd |only
man/Multipledemomenu1.rd |only
man/Multiplego.rd |only
man/Multiplemenu.rd | 2
man/Multiplentertitle.demo.rd |only
man/Multiplentertitle.rd |only
man/Multipleplotsingle.para.rd |only
man/Multipleplotsingle.rd |only
man/Multiplestat1menu.rd |only
man/Multiplestatmenu.rd | 2
man/NCA.BANOVA.rd | 2
man/NCA.BANOVAanalyze.rd | 2
man/NCA.BANOVAcsv.rd | 2
man/NCA.BANOVAdata.rd | 2
man/NCA.BANOVAmenu.rd | 2
man/NCA.rd | 2
man/NCAanalyze.rd | 2
man/NCAcsv.rd | 2
man/NCAdata.rd | 2
man/NCAdemo.BANOVA.rd | 2
man/NCAdemo.rd | 2
man/NCAmenu.rd | 2
man/NCAoutput.rd | 2
man/NCAplot.rd | 2
man/NCAsave.rd | 2
man/NCAselect.BANOVA.rd | 2
man/NCAselect.rd | 2
man/NCAselectdemo.BANOVA.rd | 2
man/NCAselectdemo.rd | 2
man/NCAselectsave.BANOVA.rd | 2
man/NCAselectsave.rd | 2
man/ParaAIC.MIX.rd | 2
man/ParaAIC.rd | 2
man/ParaAICdemo.rd | 2
man/ParaAICoutput.rd | 2
man/ParaARS.MIX.rd | 2
man/ParaARS.rd | 2
man/ParaARSdemo.rd | 2
man/ParaARSoutput.rd | 2
man/ParaMIX.rd | 2
man/ParaMIXanalyze.rd | 2
man/ParaMIXcsv.rd | 2
man/ParaMIXdata.rd | 2
man/ParaMIXmenu.rd | 2
man/ParaMIXoutput.rd | 2
man/ParaNCA.MIX.rd | 2
man/ParaNCA.MIXanalyze.rd | 2
man/ParaNCA.MIXcsv.rd | 2
man/ParaNCA.MIXdata.rd | 2
man/ParaNCA.MIXmenu.rd | 2
man/ParaNCA.rd | 2
man/ParaNCAanalyze.rd | 4
man/ParaNCAcsv.rd | 2
man/ParaNCAdata.rd | 2
man/ParaNCAdemo.MIX.rd | 2
man/ParaNCAdemo.rd | 2
man/ParaNCAoutput.rd | 2
man/ParaNCAplot.rd | 2
man/ParaNCAsave.rd | 2
man/ParaNCAselect.MIX.rd | 2
man/ParaNCAselect.rd | 2
man/ParaNCAselectdemo.MIX.rd | 2
man/ParaNCAselectdemo.rd | 2
man/ParaNCAselectsave.MIX.rd | 2
man/ParaNCAselectsave.rd | 2
man/ParaTTT.MIX.rd | 2
man/ParaTTT.rd | 2
man/ParaTTTAIC.MIX.rd | 2
man/ParaTTTAIC.rd | 2
man/ParaTTTAICdemo.rd | 2
man/ParaTTTAICoutput.rd | 2
man/ParaTTTARS.MIX.rd | 2
man/ParaTTTARS.rd | 2
man/ParaTTTARSdemo.rd | 2
man/ParaTTTARSoutput.rd | 2
man/ParaTTTdemo.rd | 2
man/ParaTTToutput.rd | 2
man/Paradata.rd | 2
man/ParademoMIX.rd | 2
man/Parademomenu.rd | 2
man/Parademomenu1.rd | 2
man/Paralleldata.rd | 2
man/Paramenu.rd | 4
man/RepAIC.MIX.rd | 2
man/RepAICdemo.rd | 2
man/RepAICoutput.rd | 2
man/RepARS.MIX.rd | 2
man/RepARS.rd | 2
man/RepARSdemo.rd | 2
man/RepARSoutput.rd | 2
man/RepMIX.rd | 2
man/RepMIXanalyze.rd | 2
man/RepMIXcsv.rd | 2
man/RepMIXdata.rd | 2
man/RepMIXmenu.rd | 2
man/RepMIXoutput.rd | 2
man/RepNCA.MIX.rd | 2
man/RepNCA.MIXanalyze.rd | 2
man/RepNCA.MIXcsv.rd | 2
man/RepNCA.MIXdata.rd | 2
man/RepNCA.MIXmenu.rd | 2
man/RepNCA.rd | 2
man/RepNCAanalyze.rd | 2
man/RepNCAcsv.rd | 2
man/RepNCAdata.rd | 2
man/RepNCAdemo.MIX.rd | 2
man/RepNCAdemo.rd | 2
man/RepNCAoutput.rd | 2
man/RepNCAplot.rd | 2
man/RepNCAsave.rd | 2
man/RepNCAselect.MIX.rd | 2
man/RepNCAselect.rd | 2
man/RepNCAselectdemo.MIX.rd | 2
man/RepNCAselectdemo.rd | 2
man/RepNCAselectsave.MIX.rd | 2
man/RepNCAselectsave.rd | 2
man/RepTTT.MIX.rd | 2
man/RepTTT.rd | 2
man/RepTTTAIC.MIX.rd | 2
man/RepTTTAIC.rd | 2
man/RepTTTAICdemo.rd | 2
man/RepTTTAICoutput.rd | 2
man/RepTTTARS.MIX.rd | 2
man/RepTTTARS.rd | 2
man/RepTTTARSdemo.rd | 2
man/RepTTTARSoutput.rd | 2
man/RepTTTdemo.rd | 2
man/RepTTToutput.rd | 2
man/Repaic.rd | 2
man/RepdemoMIX.rd | 2
man/Repdemomenu.rd | 2
man/Repdemomenu1.rd | 2
man/Replicateddata.rd | 2
man/Repmenu.rd | 2
man/Singlego.rd |only
man/TTT.BANOVA.rd | 2
man/TTT.rd | 2
man/TTTAIC.BANOVA.rd | 2
man/TTTAIC.rd | 2
man/TTTAICdemo.rd | 2
man/TTTAICoutput.rd | 2
man/TTTARS.BANOVA.rd | 2
man/TTTARS.rd | 2
man/TTTARSdemo.rd | 2
man/TTTARSoutput.rd | 2
man/TTTdemo.BANOVA.rd | 2
man/TTTdemo.rd | 2
man/TTToutput.rd | 2
man/TotalSingledata.rd | 2
man/aic.rd | 2
man/bye.rd | 2
man/demoBANOVA.rd | 2
man/demomenu.rd | 2
man/demomenu1.rd | 2
man/demopara.rd | 2
man/demosize.rd | 2
man/description_AIC.rd | 2
man/description_ARS.rd | 2
man/description_BANOVA.rd | 2
man/description_Multipledrugcode.rd |only
man/description_NCA.rd | 2
man/description_NCAcsv.rd | 2
man/description_NCAinput.rd | 2
man/description_ParaMIX.rd | 2
man/description_ParaNCAcsv.rd | 2
man/description_ParaNCAinput.rd | 2
man/description_RepMIX.rd | 2
man/description_RepNCAcsv.rd | 2
man/description_RepNCAinput.rd | 2
man/description_Repdrugcode.rd | 2
man/description_TOST1_lnAUC0INF.rd | 2
man/description_TOST1_lnAUC0t.rd | 2
man/description_TOST1_lnCmax.rd | 2
man/description_TOST_lnAUC0INF.rd | 2
man/description_TOST_lnAUC0t.rd | 2
man/description_TOST_lnCmax.rd | 2
man/description_TTT.rd | 2
man/description_TTTAIC.rd | 2
man/description_TTTARS.rd | 2
man/description_drug.rd | 2
man/description_drugcode.rd | 2
man/description_import.rd | 2
man/description_load.rd | 2
man/description_plot.rd | 2
man/description_size.rd | 2
man/description_size_para.rd | 2
man/description_version.rd | 2
man/entertitle.demo.rd | 2
man/entertitle.rd | 2
man/go.rd | 8
man/logdata.rd | 2
man/plotsingle.para.rd | 2
man/plotsingle.rd | 2
man/plotsingle.rep.rd | 2
man/prdcount.rd | 2
man/sizemenu.rd | 2
man/stat1menu.rd |only
man/statmenu.rd | 2
man/xtick.rd | 2
man/ytick.rd | 5
480 files changed, 6373 insertions(+), 1136 deletions(-)
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort,
Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander,
Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
Title: Analyses of Phylogenetics and Evolution
Description: ape provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, analyses of diversification and
macroevolution, computing distances from allelic and nucleotide
data, reading nucleotide sequences, and several tools such as
Mantel's test, computation of minimum spanning tree, the
population parameter theta based on various approaches,
nucleotide diversity, generalized skyline plots, estimation of
absolute evolutionary rates and clock-like trees using mean
path lengths, non-parametric rate smoothing and penalized
likelihood. Phylogeny estimation can be done with the NJ,
BIONJ, and ME methods.
Diff between ape versions 2.3-1 dated 2009-06-24 and 2.3-2 dated 2009-07-21
ChangeLog | 24 ++++ DESCRIPTION | 8 - R/all.equal.phylo.R | 34 +++-- R/chronopl.R | 39 +++--- R/dist.topo.R | 16 +- R/drop.tip.R | 4 R/nj.R | 16 +- R/root.R | 25 ++-- R/vcv.phylo.R | 3 Thanks | 4 inst/doc/MoranI.pdf |binary src/nj.c | 309 ++++++++++++++++++++++------------------------------ 12 files changed, 241 insertions(+), 241 deletions(-)
Author: Patrick T. Brandt
Diff between MSBVAR versions 0.3.2 dated 2008-10-12 and 0.4.0 dated 2009-07-21
Title: Markov-Switching, Bayesian, Vector Autoregression Models
Description: Provides methods for estimating frequentist and Bayesian
Vector Autoregression (VAR) models. Functions for reduced form
and structural VAR models are also available. Includes methods
for the generating posterior inferences for VAR forecasts,
impulse responses (using likelihood-based error bands), and
forecast error decompositions. Also includes utility functions
for plotting forecasts and impulse responses, and generating
draws from Wishart and singular multivariate normal densities.
Current version includes some limited functionality to build
models with Markov switching.
DESCRIPTION | 33 ++++++++++++++++++---------------
INDEX | 21 +++++++++++++++++++++
LICENSE | 6 +++---
NAMESPACE | 28 +++++++++++++++++++++++++---
R/BHLK.filter.R |only
R/SS.R |only
R/bingen.R |only
R/dirichlet.R |only
R/gibbs.msbsvar.R |only
R/gibbs.msbvar.R |only
R/hregime.SS.R |only
R/mc.irf.R | 6 +++---
R/mcmc.szbsvar.R | 2 +-
R/msbsvar.R |only
R/msbvar.R |only
R/szbsvar.R | 4 ++--
R/szbvar.R | 10 ++++++----
R/zzz.R | 15 +++++++++------
README | 39 ++++++++++++++++++++++++++++-----------
man/A02mcmc.Rd | 9 +++++----
man/BCFdata.Rd | 8 ++++++--
man/BHLK.filter.Rd |only
man/SZ.prior.evaluation.Rd | 5 +++--
man/dfev.Rd | 4 ++--
man/forecast.Rd | 31 +++++++++++++++++++++----------
man/gibbs.A0.Rd | 13 +++++++------
man/gibbs.msbsvar.Rd |only
man/gibbs.msbvar.Rd |only
man/hc.forecast.Rd | 7 +++++--
man/irf.Rd | 2 +-
man/irf.msbvar.Rd |only
man/list.print.Rd |only
man/mc.irf.Rd | 14 +++++++++-----
man/mean.SS.Rd |only
man/msbsvar.Rd |only
man/msbvar.Rd |only
man/plot.forecast.Rd | 12 +++++++-----
man/plot.mc.irf.Rd | 4 ++--
man/posterior.fit.Rd | 7 ++++---
man/rdirichlet.Rd |only
man/summary.Rd | 2 +-
man/szbsvar.Rd | 37 +++++++++++++++++++++----------------
man/szbvar.Rd | 8 ++++----
src/MSBVARcpp.h | 37 +++++++++++++++++++++++++------------
src/MSBVARfun.cpp | 40 ++++++++++++++++++++++++----------------
src/Makevars | 8 +++++++-
src/SS.cpp |only
src/SS.h |only
src/init.cpp | 28 ++++++----------------------
src/solution.cpp | 2 +-
src/switchingfunctions.cpp |only
51 files changed, 277 insertions(+), 165 deletions(-)
Author: Hai Liu
Diff between COZIGAM versions 2.0-1 dated 2009-02-25 and 2.0-2 dated 2009-07-21
Title: Constrained and Unconstrained Zero-Inflated Generalized Additive
Models with Model Selection Criterion
Description: Constrained and Unconstrained Zero-Inflated Generalized
Additive Models (ZIGAM) fitting with associated model plotting,
prediction and selection.
DESCRIPTION | 21 +++++++++++++--------
R/cozigam.R | 32 +++++++++++++++++++-------------
man/COZIGAM-package.rd |only
man/alaska.rd | 10 ++++++----
man/eggdata.rd | 17 +++++++++--------
5 files changed, 47 insertions(+), 33 deletions(-)
Author: Edzer J. Pebesma
Diff between sp versions 0.9-37 dated 2009-05-28 and 0.9-43 dated 2009-07-19
Title: classes and methods for spatial data
Description: A package that provides classes and methods for spatial
data. The classes document where the spatial location
information resides, for 2D or 3D data. Utility functions are
provided, e.g. for plotting data as maps, spatial selection, as
well as methods for retrieving coordinates, for subsetting,
print, summary, etc.
sp-0.9-37/sp/rlabs |only
sp-0.9-43/sp/ChangeLog | 72
sp-0.9-43/sp/DESCRIPTION | 8
sp-0.9-43/sp/NAMESPACE | 7
sp-0.9-43/sp/R/Class-Spatial.R | 2
sp-0.9-43/sp/R/SpatialLines-methods.R | 48
sp-0.9-43/sp/R/SpatialLinesDataFrame-methods.R | 12
sp-0.9-43/sp/R/SpatialPoints-methods.R | 4
sp-0.9-43/sp/R/SpatialPointsDataFrame-methods.R | 6
sp-0.9-43/sp/R/SpatialPolygons-methods.R | 8
sp-0.9-43/sp/R/SpatialPolygonsDataFrame-methods.R | 9
sp-0.9-43/sp/R/image.R | 4
sp-0.9-43/sp/R/spdists.R | 2
sp-0.9-43/sp/R/spsample.R | 32
sp-0.9-43/sp/inst/ChangeLog | 72
sp-0.9-43/sp/inst/doc/sp.pdf | 3610 ++++++++++-----------
sp-0.9-43/sp/man/CRS-class.Rd | 5
sp-0.9-43/sp/man/DMS-class.Rd | 1
sp-0.9-43/sp/man/GridTopology-class.Rd | 2
sp-0.9-43/sp/man/Spatial-class.Rd | 2
sp-0.9-43/sp/man/SpatialGridDataFrame-class.Rd | 2
sp-0.9-43/sp/man/SpatialLines-class.Rd | 7
sp-0.9-43/sp/man/SpatialLines.Rd | 8
sp-0.9-43/sp/man/SpatialLinesDataFrame-class.Rd | 1
sp-0.9-43/sp/man/SpatialPixelsDataFrame-class.Rd | 2
sp-0.9-43/sp/man/SpatialPoints-class.Rd | 1
sp-0.9-43/sp/man/SpatialPointsDataFrame-class.Rd | 32
sp-0.9-43/sp/man/SpatialPolygons-class.Rd | 9
sp-0.9-43/sp/man/SpatialPolygonsDataFrame-class.Rd | 4
sp-0.9-43/sp/man/coordinates-methods.Rd | 2
sp-0.9-43/sp/man/image.Rd | 4
sp-0.9-43/sp/man/is.projected.Rd | 2
sp-0.9-43/sp/man/spDistsN1.Rd | 8
sp-0.9-43/sp/man/spsample.Rd | 8
sp-0.9-43/sp/src/gcdist.c | 19
sp-0.9-43/sp/src/init.c | 1
sp-0.9-43/sp/src/sp.h | 1
37 files changed, 2133 insertions(+), 1884 deletions(-)
Author: Jim Lemon,Ben Bolker,Sander Oom, Eduardo Klein,Barry
Rowlingson, Hadley Wickham,Anupam Tyagi, Olivier
Eterradossi,Gabor Grothendieck, Michael Toews,John Kane,Mike
Cheetham, Rolf Turner,Carl Witthoft,Julian Stander, Thomas
Petzoldt,Remko Duursma,Elisa Biancotto, Ofir Levy
Title: Various plotting functions
Description: Lots of plots, various labeling, axis and color scaling
functions.
Diff between plotrix versions 2.6-1 dated 2009-06-14 and 2.6-4 dated 2009-07-19
plotrix-2.6-1/plotrix/R/barhier.R |only plotrix-2.6-1/plotrix/man/barhier.Rd |only plotrix-2.6-1/plotrix/man/brkdnCrawler.Rd |only plotrix-2.6-4/plotrix/CITATION | 21 +- plotrix-2.6-4/plotrix/DESCRIPTION | 8 plotrix-2.6-4/plotrix/INDEX | 2 plotrix-2.6-4/plotrix/NEWS | 14 + plotrix-2.6-4/plotrix/R/gap.plot.R | 52 ++--- plotrix-2.6-4/plotrix/R/hierobarp.R | 292 +++++++++++------------------- plotrix-2.6-4/plotrix/R/sizetree.R |only plotrix-2.6-4/plotrix/R/thigmophobe.R | 8 plotrix-2.6-4/plotrix/demo/plotrix.R | 14 - plotrix-2.6-4/plotrix/hierobarp1.R |only plotrix-2.6-4/plotrix/man/gap.plot.Rd | 5 plotrix-2.6-4/plotrix/man/hierobarp.Rd | 65 +++--- plotrix-2.6-4/plotrix/man/hierobrk.Rd | 22 +- plotrix-2.6-4/plotrix/man/sizetree.Rd |only plotrix-2.6-4/plotrix/man/twoord.plot.Rd | 2 18 files changed, 233 insertions(+), 272 deletions(-)
Author: Christopher Brown
Title: Implements hash/associated arrays/dictionaries
Description: This package implements a data structure using R
environments similar to hashes in Perl and dictionaries in
Python but with a purposefully R flavor.
Diff between hash versions 0.23 dated 2009-04-15 and 0.30 dated 2009-07-19
DESCRIPTION | 9 ++-- R/clear.R | 1 R/del.R | 12 ++--- R/get.R | 2 R/hash.R | 106 +++++++++++++++++++++++++++++++++++++++++--------- R/keys.R | 8 ++- R/set.R | 88 ++++++++++++++++++++++++++++++----------- R/show.R | 18 ++++++-- TODO | 56 ++++++++++++++++---------- hash_0.23.tar.gz |only hash_0.30.tar.gz |only man/clear.Rd | 8 +-- man/del.Rd | 25 ++++++++--- man/get.Rd | 10 +++- man/has-key.Rd | 7 ++- man/hash-accessors.Rd | 27 +++++++----- man/hash-class.Rd | 32 +++++++++++---- man/hash-package.Rd | 27 +++++++----- man/hash.Rd | 80 ++++++++++++++++++++++++++++++++----- man/keys.Rd | 27 ++++++++++-- man/length.Rd | 4 - man/set.Rd | 79 ++++++++++++++++++++++++++----------- man/validate.key.Rd | 14 +++++- man/values.Rd | 29 +++++++------ 24 files changed, 481 insertions(+), 188 deletions(-)
Author: David Hajage
Title: Export R objects to asciidoc or txt2tags
Description: Coerce R object to asciidoc or txt2tags syntax. Package
comes with two drivers for Sweave.
Diff between ascii versions 0.1.3 dated 2009-05-11 and 0.2 dated 2009-07-19
ascii-0.1.3/ascii/R/SweaveSyntaxAscii.r |only ascii-0.1.3/ascii/Rplots.pdf |only ascii-0.1.3/ascii/index-ggplot2.pdf |only ascii-0.2/ascii/DESCRIPTION | 10 ++-- ascii-0.2/ascii/NAMESPACE | 3 - ascii-0.2/ascii/NEWS | 30 ++++++++++-- ascii-0.2/ascii/R/RweaveAsciidoc.r | 5 -- ascii-0.2/ascii/R/RweaveT2t.r | 4 - ascii-0.2/ascii/R/SweaveAscii.r | 2 ascii-0.2/ascii/R/asciiAnova.r | 38 ++++++++++----- ascii-0.2/ascii/R/asciiDataFrame.r | 8 +-- ascii-0.2/ascii/R/asciiDefault.r | 6 +- ascii-0.2/ascii/R/asciiDensity.r | 6 +- ascii-0.2/ascii/R/asciiGlm.r | 12 +++- ascii-0.2/ascii/R/asciiHmisc.r | 78 ++++++++++++++++++-------------- ascii-0.2/ascii/R/asciiHtest.r | 6 +- ascii-0.2/ascii/R/asciiLm.r | 12 +++- ascii-0.2/ascii/R/asciiMatrix.r | 6 +- ascii-0.2/ascii/R/asciiPrcomp.r | 12 +++- ascii-0.2/ascii/R/asciiSurvival.r | 12 +++- ascii-0.2/ascii/R/asciiTable.r | 6 +- ascii-0.2/ascii/R/asciiTs.r | 6 +- ascii-0.2/ascii/R/asciiVector.r | 24 ++++++--- ascii-0.2/ascii/R/generic.r | 8 +-- ascii-0.2/ascii/R/misc.r | 22 +++++++-- ascii-0.2/ascii/R/print.r | 17 +++++- ascii-0.2/ascii/R/show.r | 76 ++++++++++++++++++++++++++----- ascii-0.2/ascii/man/RweaveAsciidoc.Rd | 3 - ascii-0.2/ascii/man/RweaveT2t.Rd | 3 - ascii-0.2/ascii/man/SweaveAscii.Rd | 3 - ascii-0.2/ascii/man/ascii.Rd | 25 +++++++++- ascii-0.2/ascii/man/print.ascii.Rd | 4 + ascii-0.2/ascii/testsyntax.Rnw |only ascii-0.2/ascii/testsyntax.html |only ascii-0.2/ascii/testsyntax.txt |only 35 files changed, 311 insertions(+), 136 deletions(-)
Author: Peter K Dunn
Diff between tweedie versions 1.6.7 dated 2009-06-30 and 1.6.8 dated 2009-07-18
Title: Tweedie exponential family models
Description: Maximum likelihood computations for Tweedie families.
CHANGE.log | 4 +
DESCRIPTION | 8 +--
R/tweedie.R | 18 +++----
man/dtweedie.Rd | 2
man/tweedie-package.Rd | 4 -
src/tweedie.f | 116 ++++++++++++++++++++++++-------------------------
6 files changed, 78 insertions(+), 74 deletions(-)
Author: Antonio Fabio Di Narzo, Jose Luis Aznarte, Matthieu Stigler
Title: Time series analysis based on dynamical systems theory
Description: Time series analysis based on dynamical systems theory
Diff between tsDyn versions 0.6-1 dated 2009-02-24 and 0.7 dated 2009-07-18
tsDyn-0.6-1/tsDyn/inst/doc/.build.timestamp |only tsDyn-0.6-1/tsDyn/inst/doc/tsDyn.R |only tsDyn-0.6-1/tsDyn/inst/doc/tsDyn.tex |only tsDyn-0.7/tsDyn/DESCRIPTION | 14 tsDyn-0.7/tsDyn/NAMESPACE | 46 + tsDyn-0.7/tsDyn/R/BBCtest.R |only tsDyn-0.7/tsDyn/R/HanSeo_TVECM.R |only tsDyn-0.7/tsDyn/R/KapShinTest.R |only tsDyn-0.7/tsDyn/R/TVAR.sim.R |only tsDyn-0.7/tsDyn/R/TVAR_LRtest.R |only tsDyn-0.7/tsDyn/R/TVARestim.R |only tsDyn-0.7/tsDyn/R/TVECM.R |only tsDyn-0.7/tsDyn/R/TVECM.sim.R |only tsDyn-0.7/tsDyn/R/TVECMSeoTest.R |only tsDyn-0.7/tsDyn/R/aar.R | 1 tsDyn-0.7/tsDyn/R/lineVar.R |only tsDyn-0.7/tsDyn/R/linear.R | 56 + tsDyn-0.7/tsDyn/R/lstar.R | 20 tsDyn-0.7/tsDyn/R/misc.R | 213 ++++++ tsDyn-0.7/tsDyn/R/miscSETAR.R |only tsDyn-0.7/tsDyn/R/nlVar-methods.R |only tsDyn-0.7/tsDyn/R/nlar-methods.R | 59 + tsDyn-0.7/tsDyn/R/nnet.R | 1 tsDyn-0.7/tsDyn/R/resVar.R |only tsDyn-0.7/tsDyn/R/selectSETAR.R |only tsDyn-0.7/tsDyn/R/setar.R | 856 ++++++++++++++++++---------- tsDyn-0.7/tsDyn/R/setar.sim.R |only tsDyn-0.7/tsDyn/R/setarTest.R |only tsDyn-0.7/tsDyn/R/star.R | 250 ++++---- tsDyn-0.7/tsDyn/data |only tsDyn-0.7/tsDyn/inst/CITATION | 21 tsDyn-0.7/tsDyn/inst/ChangeLog | 25 tsDyn-0.7/tsDyn/inst/doc/tsDyn.Stex | 11 tsDyn-0.7/tsDyn/inst/doc/tsDyn.pdf |binary tsDyn-0.7/tsDyn/man/.Rd2dvi20266 |only tsDyn-0.7/tsDyn/man/BBCTest.Rd |only tsDyn-0.7/tsDyn/man/BIC.Rd |only tsDyn-0.7/tsDyn/man/DataIIPUs.Rd |only tsDyn-0.7/tsDyn/man/DataUsUnemp.Rd |only tsDyn-0.7/tsDyn/man/KapShinTest.Rd |only tsDyn-0.7/tsDyn/man/MakeThSpec.Rd |only tsDyn-0.7/tsDyn/man/TVAR.LRtest.Rd |only tsDyn-0.7/tsDyn/man/TVAR.Rd |only tsDyn-0.7/tsDyn/man/TVAR.sim.Rd |only tsDyn-0.7/tsDyn/man/TVECM.Rd |only tsDyn-0.7/tsDyn/man/TVECM.SeoTest.Rd |only tsDyn-0.7/tsDyn/man/TVECM.sim.Rd |only tsDyn-0.7/tsDyn/man/addRegime.Rd | 3 tsDyn-0.7/tsDyn/man/extendBoot.Rd |only tsDyn-0.7/tsDyn/man/lineVar.Rd |only tsDyn-0.7/tsDyn/man/linear.Rd | 4 tsDyn-0.7/tsDyn/man/nlar-methods.Rd | 3 tsDyn-0.7/tsDyn/man/nlar.Rd | 5 tsDyn-0.7/tsDyn/man/resVar.Rd |only tsDyn-0.7/tsDyn/man/selectSETAR.Rd | 61 + tsDyn-0.7/tsDyn/man/setar.Rd | 33 - tsDyn-0.7/tsDyn/man/setar.sim.Rd |only tsDyn-0.7/tsDyn/man/setarTest.Rd |only tsDyn-0.7/tsDyn/man/sigmoid.Rd | 1 tsDyn-0.7/tsDyn/man/zeroyld.Rd |only tsDyn-0.7/tsDyn/tests |only 61 files changed, 1199 insertions(+), 484 deletions(-)
Author: Roger Koenker
Diff between quantreg versions 4.30 dated 2009-05-12 and 4.36 dated 2009-07-18
Title: Quantile Regression
Description: Quantile regression and related methods.
DESCRIPTION | 10 +-
R/crq.R | 4 -
R/quantreg.R | 5 +
R/rqss.R | 158 ++++++++++++++++++++++++++++++++---------------
R/tools.R |only
demo/00Index | 2
demo/rqsslasso.R |only
inst/ChangeLog | 36 ++++++++++
inst/doc/Rplots.pdf | 96 ++++++++++++++--------------
inst/doc/rq.pdf |binary
man/FAQ.Rd |only
man/dither.Rd |only
man/latex.summary.rqs.Rd | 2
man/latex.table.Rd | 9 --
man/rqss.Rd | 17 ++++-
man/rqss.object.Rd | 3
16 files changed, 223 insertions(+), 119 deletions(-)
Author: William H. Asquith
Title: L-moments, Trimmed L-moments, L-comoments, and Many
Distributions
Description: The package implements the statistical theory of L-moments
including L-moment estimation, probability-weighted moment
estimation, parameter estimation for numerous familiar and
not-so-familiar distributions, and L-moment estimation for the
same distributions from the parameters. L-moments are derived
from the expectations of order statistics and are linear with
respect to the probability- weighted moments. L-moments are
directly analogous to the well-known product moments; however,
L-moments have many advantages including unbiasedness,
robustness, and consistency with respect to the product
moments. This package is oriented around the FORTRAN algorithms
of J.R.M. Hosking, and the nomenclature for many of the
functions parallels that of the Hosking library. However,
numerous extensions are made to aid in expand of the breadth
and ease of L-moment application. Much theoretical extension of
L-moment theory has occurred in recent years. E.A.H. Elamir and
A.H. Seheult have developed the trimmed L-moments, which are
implemented in this package. Further, recent developments by
Robert Serfling and Peng Xiao have extended L-moments into
multivariate space; the so-called sample L-comoments are
implemented here. The supported distributions with moment type
shown as L (L-moments) or TL (trimmed L-moments) and additional
support for right-tail censoring ([RC]) include: Cauchy(TL),
Exponential(L), Gamma(L), Generalized Extreme Value(L),
Generalized Lambda(L & TL), Generalized Logistic (L),
Generalized Normal(L), Generalized Pareto(L[RC] & TL),
Gumbel(L), Normal(L), Kappa(L), Pearson Type III(L), Reverse
Gumbel(L[RC]), Wakeby(L), and Weibull(L).
Diff between lmomco versions 0.96.3 dated 2009-02-23 and 0.97.1 dated 2009-07-18
lmomco-0.96.3/lmomco/junk.R |only lmomco-0.97.1/lmomco/ChangeLog | 9 +++ lmomco-0.97.1/lmomco/DESCRIPTION | 61 +++++++++++++++------------ lmomco-0.97.1/lmomco/INDEX | 16 +++++++ lmomco-0.97.1/lmomco/R/are.par.valid.R | 3 + lmomco-0.97.1/lmomco/R/are.parln3.valid.R |only lmomco-0.97.1/lmomco/R/cdfln3.R |only lmomco-0.97.1/lmomco/R/is.ln3.R |only lmomco-0.97.1/lmomco/R/lmom.test.ln3.R |only lmomco-0.97.1/lmomco/R/lmomln3.R |only lmomco-0.97.1/lmomco/R/lmomray.R | 2 lmomco-0.97.1/lmomco/R/lmomrevgum.R | 2 lmomco-0.97.1/lmomco/R/par2cdf.R | 3 + lmomco-0.97.1/lmomco/R/par2lmom.R | 3 + lmomco-0.97.1/lmomco/R/par2pdf.R | 3 + lmomco-0.97.1/lmomco/R/par2qua.R | 3 + lmomco-0.97.1/lmomco/R/parln3.R |only lmomco-0.97.1/lmomco/R/parray.R | 8 +-- lmomco-0.97.1/lmomco/R/pdfln3.R |only lmomco-0.97.1/lmomco/R/qualn3.R |only lmomco-0.97.1/lmomco/R/vec2par.R | 7 ++- lmomco-0.97.1/lmomco/man/are.par.valid.Rd | 2 lmomco-0.97.1/lmomco/man/are.parln3.valid.Rd |only lmomco-0.97.1/lmomco/man/are.parray.valid.Rd | 4 - lmomco-0.97.1/lmomco/man/cdfln3.Rd |only lmomco-0.97.1/lmomco/man/is.ln3.Rd |only lmomco-0.97.1/lmomco/man/lmom.test.ln3.Rd |only lmomco-0.97.1/lmomco/man/lmomln3.Rd |only lmomco-0.97.1/lmomco/man/par2lmom.Rd | 2 lmomco-0.97.1/lmomco/man/parln3.Rd |only lmomco-0.97.1/lmomco/man/pdfln3.Rd |only lmomco-0.97.1/lmomco/man/qualn3.Rd |only lmomco-0.97.1/lmomco/man/vec2par.Rd | 4 + 33 files changed, 94 insertions(+), 38 deletions(-)
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 2.1.3 dated 2009-06-28 and 2.1.4 dated 2009-07-18
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- man/bjerrum.Rd | 15 ++++++++------- man/buffer.Rd | 22 +++++++++++++++------- man/carb.Rd | 20 ++++++++++---------- man/pCa.Rd | 9 ++++++--- man/pHconv.Rd | 6 ++++-- man/pHinsi.Rd | 3 ++- man/pTA.Rd | 9 ++++++--- man/pgas.Rd | 6 ++++-- man/pmix.Rd | 6 ++++-- man/ppH.Rd | 9 ++++++--- man/psi.Rd | 6 ++++-- 13 files changed, 79 insertions(+), 46 deletions(-)
Author: Benjamin P. Bryant
Title: Scenario Discovery Tools to Support Robust Decision Making
Description: Implements algorithms to help with scenario discovery -
currently only modified version of the the Patient Rule
Induction Method.
Diff between sdtoolkit versions 2.22 dated 2009-03-06 and 2.3 dated 2009-07-18
DESCRIPTION | 27 ++++++++++++++++----------- R/sd.start.r | 13 ++++++------- R/sdprim.r | 8 ++++++++ R/sdwarranty.r |only R/trajplot.r | 8 +++++--- man/1sdtoolkit-package.Rd | 4 ++-- man/sdprim.Rd | 3 +-- man/undocumented.rd | 4 +++- 8 files changed, 41 insertions(+), 26 deletions(-)
Author: Yves Tillé
Diff between sampling versions 2.1 dated 2008-12-15 and 2.2 dated 2009-07-18
Title: Survey Sampling
Description: Functions for drawing and calibrating samples.
DESCRIPTION | 29 +++--
inst/doc/Rplots.pdf | 231 +++++++++++++++++++++++++----------------------
inst/doc/UPexamples.pdf |binary
inst/doc/calibration.pdf |binary
man/UPbrewer.Rd | 14 +-
man/UPopips.Rd | 11 --
man/calibev.Rd | 28 +++--
man/checkcalibration.Rd | 5 -
man/regest_strata.Rd | 4
man/rhg.Rd | 4
man/rhg_strata.Rd | 2
11 files changed, 175 insertions(+), 153 deletions(-)
Author: Arne Henningsen
Diff between sampleSelection versions 0.6-4 dated 2009-01-26 and 0.6-6 dated 2009-07-18
More information about sampleSelection at CRAN
Title: Sample Selection Models
Description: Estimation of Sample Selection Models
DESCRIPTION | 14
R/coef.probit.R | 2
R/coef.selection.R | 2
R/heckit2fit.R | 15
R/heckit5fit.R | 27
R/print.summary.probit.R | 9
R/probit.R | 4
R/selection.R | 17
R/summary.probit.R | 7
R/summary.selection.R | 14
R/vcov.probit.R | 2
R/vcov.selection.R | 2
inst/doc/selection.pdf | 1826 +++++++++++++++++++++++-----------------------
man/probit.Rd | 12
man/selection.Rd | 5
tests/heckit.Rout.save | 39
tests/probit.Rout.save | 18
tests/selection.Rout.save | 26
18 files changed, 1068 insertions(+), 973 deletions(-)
Permanent link
Author: Timothy H. Keitt
Diff between rgdal versions 0.6-9 dated 2009-06-26 and 0.6-10 dated 2009-07-18
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data
Abstraction Library (GDAL) (>= 1.3.1) and access to
projection/transformation operations from the PROJ.4 library.
The GDAL and PROJ.4 libraries are external to the package, and,
when installing the package from source, must be correctly
installed first. Both GDAL raster and OGR vector map data can
be imported into R, and GDAL raster data and OGR vector data
exported. Use is made of classes defined in the sp package.
ChangeLog | 13 +++++++++++--
DESCRIPTION | 8 ++++----
R/ogr.R | 29 +++++++++++++++++++++++++----
R/ogr_sp.R | 32 +++++++++++++++++++++++++-------
inst/ChangeLog | 13 +++++++++++--
man/readOGR.Rd | 2 ++
src/ogrsource.cpp | 14 ++++++++++----
7 files changed, 88 insertions(+), 23 deletions(-)
Author: Rajarshi Guha
Diff between rcdk versions 2.9.2 dated 2009-02-25 and 2.9.3 dated 2009-07-18
Title: rcdk - Interface to the CDK Libraries
Description: This package allows the user to access functionality in
the CDK, a Java framework for cheminformatics. This allows the
user to load molecules, evaluate fingerprints, calculate
molecular descriptors and so on. In addition the CDK API allows
the user to view structures in 2D.
DESCRIPTION | 23 +-
R/io.R | 4
R/rcdk.R | 15 +
inst/cont/rcdk.jar |binary
inst/doc/rcdk.pdf | 507 ++++++++++++++++++++++++++---------------------------
man/loadmol.Rd | 5
man/ops.Rd | 10 -
man/parsesmiles.Rd | 8
8 files changed, 302 insertions(+), 270 deletions(-)
Author: Charles J. Geyer
Diff between rcdd versions 1.1-2 dated 2009-06-24 and 1.1-3 dated 2009-07-18
Title: rcdd (Computational Geometry)
Description: R interface to (some of) cddlib, see
http://www.ifor.math.ethz.ch/~fukuda/cdd_home/cdd.html converts
back and forth between two representations of a convex
polytope: as solution of a set of linear equalities and
inequalities and as convex hull of set of points and rays, also
does linear programming and redundant generator elimination
(for example, convex hull in n dimensions), all with exact
infinite-precision rational arithmetic.
CHANGES | 2 ++
DESCRIPTION | 8 ++++----
inst/doc/vinny.pdf |binary
inst/doc/vinny.tex | 4 ++--
4 files changed, 8 insertions(+), 6 deletions(-)
Author: Graham Williams
Diff between rattle versions 2.4.79 dated 2009-06-24 and 2.4.83 dated 2009-07-18
Title: A graphical user interface for data mining in R using GTK
Description: Rattle (the R Analytic Tool To Learn Easily) provides a
Gnome (RGtk2) based interface to R functionality for data
mining. The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file (or via
ODBC), transform and explore the data, build and evaluate
models, and export models as PMML (predictive modelling markup
language) or as scores. All of this with knowing little about
R. All R commands are logged and commented through the log tab
and so available to the user as a script file or as an aide to
the user to interact directly with R itself. Rattle also
exports a number of utility functions and the graphical user
interface, invoked as rattle(), does not need to be run to
deploy these.
DESCRIPTION | 8
R/data.R | 7
R/evaluate.R | 6
R/explore.R | 14
R/export.R | 15
R/log.R | 8
R/projects.R | 12
R/rattle.R | 27
R/transform.R | 39 +
R/zzz.R | 12
data/weather.RData |binary
data/weatherCanberra.RData |binary
data/weatherSydney.RData |binary
inst/arff/weather.arff | 10
inst/arff/weatherCanberra.arff | 40 +
inst/arff/weatherSydney.arff | 36 +
inst/csv/weatherCanberra.csv | 1182 +++++++++++++++++++++--------------------
inst/csv/weatherSydney.csv | 1002 +++++++++++++++++-----------------
inst/etc/Rlogo.png |only
inst/etc/rattle.glade | 30 -
inst/etc/textviews.xml | 8
21 files changed, 1332 insertions(+), 1124 deletions(-)
Author: Brian S. Yandell
Diff between qtlbim versions 1.9.3 dated 2009-03-22 and 1.9.4 dated 2009-07-18
Title: QTL Bayesian Interval Mapping
Description: Functions for model selection for genetic architecture.
DESCRIPTION | 8
R/genoprob.R | 3
R/io.R | 18
R/mcmc.R | 12
R/scan.R | 269
R/slice.R | 2
inst/doc/bpPDF/slide-15-6.pdf | 198
inst/doc/bpPDF/slide1hpd.pdf | 36
inst/doc/bpPDF/slide2LOD-1.pdf | 26
inst/doc/prototype.qtl.hyper.slides.pdf | 2307 +-
inst/doc/qtlbim.pdf |binary
inst/doc/qtlbimPDF/FIG-QBBF.pdf | 84
inst/doc/qtlbimPDF/FIG-QBCODA.pdf | 38
inst/doc/qtlbimPDF/FIG-QBDIAG.pdf | 134
inst/doc/qtlbimPDF/FIG-QBEPI.pdf | 6206 ++---
inst/doc/qtlbimPDF/FIG-QBHPD.pdf | 36
inst/doc/qtlbimPDF/FIG-QBLOCI34.pdf | 7480 +++---
inst/doc/qtlbimPDF/FIG-Scanone-HyperLPD.pdf | 32
inst/doc/qtlbimPDF/FIG-Scanone-HyperSubset.pdf | 32
inst/doc/qtlbimPDF/FIG-Scantwo-HyperData.pdf | 32
inst/doc/qtlbimPDF/besthc.pdf | 30
inst/doc/qtlbimPDF/bestmds.pdf | 30
inst/doc/qtlbimPDF/closenqtl.pdf | 26
inst/doc/qtlbimPDF/closepat.pdf | 26
inst/doc/qtlbimPDF/mult.pdf |28828 ++++++++++++-------------
inst/doc/qtlbimPDF/multmerge.pdf |15188 ++++++-------
inst/doc/qtlbimPDF/one.pdf | 32
man/plot.scantwo.Rd | 4
man/qb-internal.Rd | 3
man/scanone.Rd | 2
man/sliceone.Rd | 2
man/summary.scanone.Rd | 7
32 files changed, 30656 insertions(+), 30475 deletions(-)
Author: Andrea Spano'
Title: Variables and Attributes Control Charts
Description: qAnalyst performs: control charts for variables and
attributes according to Douglas C. Montgomery Introduction to
Statistical Quality Control book, Capability analysis for
normal and non - normal distributions and Distributions
Identification
Diff between qAnalyst versions 0.5.4 dated 2008-06-13 and 0.5.5 dated 2009-07-18
DESCRIPTION | 18 ++++-- R/plot.capability.R | 144 ++++++++++++++++++++++++++++------------------------ R/plot.spc.R | 81 ++++++++++++++++------------- README | 6 ++ man/testFun.Rd | 3 - 5 files changed, 145 insertions(+), 107 deletions(-)
Author: William Revelle
Diff between psych versions 1.0-75 dated 2009-07-01 and 1.0-76 dated 2009-07-18
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A number of routines for personality, psychometrics and
experimental psychology. Functions are primarily for scale
construction using factor analysis, cluster analysis and
reliability analysis, although others provide basic descriptive
statistics. Functions for simulating particular item and test
structures are included. Several functions serve as a useful
front end for structural equation modeling. For more
information, see the personality-project.org/r webpage.
CHANGES | 8
DESCRIPTION | 8
R/Promax.R | 2
R/factor.stats.R | 6
R/print.psych.fa.R | 20
R/print.psych.omega.R | 25
R/r.test.R | 2
R/schmid.R | 1
inst/doc/overview.pdf | 3129 +++++++++++++++++++++----------------------
inst/doc/psych_for_sem.pdf | 3239 +++++++++++++++++++++------------------------
man/00.psych-package.Rd | 4
man/VSS.scree.Rd | 3
man/bifactor.Rd | 3
man/fa.Rd | 2
man/omega.Rd | 3
man/poly.mat.Rd | 2
man/polychor.matrix.Rd | 10
man/principal.Rd | 24
man/schmid.Rd | 3
19 files changed, 3243 insertions(+), 3251 deletions(-)
Author: Jelle Goeman
Diff between penalized versions 0.9-24 dated 2009-05-28 and 0.9-25 dated 2009-07-18
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/cox.R | 1
changelog.txt | 3
inst/doc/Rplots.pdf |13556 +++++++++++++++++++++++++------------------------
inst/doc/penalized.Rnw | 2
inst/doc/penalized.pdf |binary
6 files changed, 7071 insertions(+), 6499 deletions(-)
Author: Peter Filzmoser Heinrich Fritz Klaudius Kalcher
Title: Robust PCA by Projection Pursuit
Description: Robust PCA by Projection Pursuit
Diff between pcaPP versions 1.6 dated 2009-01-23 and 1.7 dated 2009-07-18
DESCRIPTION | 14 +++++++------- src/conv.cpp | 3 ++- 2 files changed, 9 insertions(+), 8 deletions(-)
Author: Sven Adler
Title: WA, WA-PLS, MW and POM for paleolimnology
Description: This package contains functions for paleolimnology -
wa-regression (see also package analogue by G. Simpson!),
wa-pls and the mowing-window approch. The function palplot
allows a first plot of the data including a trend analysis. The
pom function is just a first test version.
Diff between paltran versions 1.1 dated 2009-06-26 and 1.2-0 dated 2009-07-18
paltran-1.1/paltran/R/pom.R |only paltran-1.1/paltran/man/pom.Rd |only paltran-1.2-0/paltran/DESCRIPTION | 6 - paltran-1.2-0/paltran/R/mft.R |only paltran-1.2-0/paltran/R/mw.R | 6 - paltran-1.2-0/paltran/R/wa.R | 22 ++-- paltran-1.2-0/paltran/R/wapls.R | 142 ++++++++++++++------------- paltran-1.2-0/paltran/man/mft.Rd |only paltran-1.2-0/paltran/man/mw.Rd | 11 +- paltran-1.2-0/paltran/man/paltran-package.Rd | 2 paltran-1.2-0/paltran/man/wapls.Rd | 5 11 files changed, 107 insertions(+), 87 deletions(-)
Author: Torsten Hothorn, Frank Bretz and Peter Westfall with
contributions by Richard M. Heiberger and Andre
Schuetzenmeister
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals for general
linear hypotheses in parametric models, including linear,
generalized linear, linear mixed effects, and survival models.
Diff between multcomp versions 1.1-0 dated 2009-06-08 and 1.1-1 dated 2009-07-18
DESCRIPTION | 6 NEWS | 5 R/cld.R | 12 inst/CHANGES | 5 inst/doc/chfls1.bbl |only inst/doc/chfls1.blg |only inst/doc/chfls1.pdf |binary inst/doc/generalsiminf.bbl |only inst/doc/generalsiminf.blg |only inst/doc/generalsiminf.pdf | 1016 ++++++++++++++++++++--------------------- inst/doc/multcomp-examples.pdf |binary tests/bugfix.R | 9 tests/bugfix.Rout.save | 16 13 files changed, 555 insertions(+), 514 deletions(-)
Author: Christopher Jackson
Diff between msm versions 0.9.1 dated 2009-06-14 and 0.9.2 dated 2009-07-18
Title: Multi-state Markov and hidden Markov models in continuous time
Description: Functions for fitting general continuous-time Markov and
hidden Markov multi-state models to longitudinal data. Both
Markov transition rates and the hidden Markov output process
can be modelled in terms of covariates. A variety of
observation schemes are supported, including processes observed
at arbitrary times, completely-observed processes, and censored
states.
ChangeLog | 11 +++++++++++
DESCRIPTION | 8 ++++----
R/msm.R | 2 ++
inst/NEWS | 11 +++++++++++
inst/doc/msm-manual.pdf |binary
src/pijt.c | 17 +++++++++++++----
tests/simple.R | 12 ++++++------
7 files changed, 47 insertions(+), 14 deletions(-)
Author: Dai Feng and Luke Tierney
Title: Miscellaneous 3D Plots
Description: A collection of miscellaneous 3d plots, including
isosurfaces.
Diff between misc3d versions 0.6-3 dated 2009-06-17 and 0.7-0 dated 2009-07-18
DESCRIPTION | 6 +++--- R/slices3d.R | 15 ++++++++++----- man/slices3d.Rd | 15 +++++++++++++-- 3 files changed, 26 insertions(+), 10 deletions(-)
Author: Luke Keele
Diff between mediation versions 1.0 dated 2009-06-14 and 2.0 dated 2009-07-18
Title: R Package for Causal Mediation Analysis
Description: mediation is a publicly available R package that allows
both parametric and nonparametric causal mediation analysis.
It implements the methods and suggestions in Imai, Keele, and
Yamamoto (2008) and Imai, Keele, Tingley (2009). In addition
to the estimation of causal mediation effects, the software
also allows researchers to conduct sensitivity analysis for
certain parametric models.
mediation-1.0/mediation/data/job.RData |only
mediation-1.0/mediation/data/job.Rd |only
mediation-1.0/mediation/man/job.Rd |only
mediation-2.0/mediation/ChangeLog |only
mediation-2.0/mediation/DESCRIPTION | 8
mediation-2.0/mediation/R/mediate.R | 271 +++++-----
mediation-2.0/mediation/R/medsens.R | 653 +++++++++++++++++--------
mediation-2.0/mediation/R/medsensr2.R |only
mediation-2.0/mediation/man/mediate.Rd | 72 +-
mediation-2.0/mediation/man/medsens.Rd | 109 +---
mediation-2.0/mediation/man/plot.medsens.Rd | 44 +
mediation-2.0/mediation/man/summary.mediate.Rd | 14
mediation-2.0/mediation/man/summary.medsens.Rd | 35 -
13 files changed, 737 insertions(+), 469 deletions(-)
Author: Ott Toomet
Diff between maxLik versions 0.5-10 dated 2009-01-26 and 0.5-12 dated 2009-07-18
Title: Maximum Likelihood Estimation
Description: Tools for Maximum Likelihood Estimation
DESCRIPTION | 14
INDEX | 1
NAMESPACE |only
R/maxBHHH.R | 30 +
R/maximType.R | 3
R/print.maxLik.R |only
R/returnMessage.R | 2
R/summary.maxLik.R | 14
man/compareDerivatives.Rd | 1
man/maxLik.Rd | 12
tests/examples.R | 42 +-
tests/examples.Rout.save | 915 +++++++++++++++++++++++++++++++++++++++++++++-
12 files changed, 990 insertions(+), 44 deletions(-)
Author: J. R. M. Hosking
Title: Regional frequency analysis using L-moments
Description: Functions for regional frequency analysis using the
methods of J. R. M. Hosking and J. R. Wallis (1997), "Regional
frequency analysis: an approach based on L-moments".
Diff between lmomRFA versions 2.0 dated 2009-05-04 and 2.1 dated 2009-07-18
DESCRIPTION | 8 ++++---- NAMESPACE | 1 + NEWS | 8 ++++++++ R/lmomRFA.r | 2 +- man/Cascades.Rd | 2 ++ 5 files changed, 16 insertions(+), 5 deletions(-)
Author: J. R. M. Hosking
Title: L-moments
Description: Functions related to L-moments: computation of L-moments
of distributions and data samples; parameter estimation;
L-moment ratio diagram; plot vs. quantiles of an extreme-value
distribution.
Diff between lmom versions 1.3 dated 2009-05-04 and 1.4 dated 2009-07-18
DESCRIPTION | 8 ++++---- NAMESPACE | 3 +++ NEWS | 8 ++++++++ R/lmom.r | 22 ++++++++++++++++++++++ man/lmom-package.Rd | 4 ++++ man/lmrdpoints.Rd |only 6 files changed, 41 insertions(+), 4 deletions(-)
Author: Pavel N. Krivitsky
Diff between latentnet versions 2.1-1 dated 2008-02-29 and 2.2 dated 2009-07-18
Title: Latent position and cluster models for statistical networks
Description: A package to fit and simulate latent position and cluster
models for statistical networks.
latentnet-2.1-1/latentnet/R/ergmm.sample.utils.R |only
latentnet-2.1-1/latentnet/R/labelswitch.R |only
latentnet-2.1-1/latentnet/man/ergmm.par.object.Rd |only
latentnet-2.1-1/latentnet/src/post_utils.c |only
latentnet-2.1-1/latentnet/src/post_utils.h |only
latentnet-2.2/latentnet/ChangeLog |only
latentnet-2.2/latentnet/DESCRIPTION | 25 -
latentnet-2.2/latentnet/LICENSE | 2
latentnet-2.2/latentnet/R/InitErgmm.fixed.R | 34 -
latentnet-2.2/latentnet/R/InitErgmm.latent.R | 23
latentnet-2.2/latentnet/R/InitErgmm.random.R |only
latentnet-2.2/latentnet/R/bayesmbc.MCMC.C.R | 40 -
latentnet-2.2/latentnet/R/bayesmbc.R | 41 +
latentnet-2.2/latentnet/R/ergmm.MCMC.C.R | 188 +++++--
latentnet-2.2/latentnet/R/ergmm.R | 100 +---
latentnet-2.2/latentnet/R/ergmm.defaults.R | 11
latentnet-2.2/latentnet/R/ergmm.families.R | 26 -
latentnet-2.2/latentnet/R/ergmm.geodesicmatrix.R | 6
latentnet-2.2/latentnet/R/ergmm.get.model.R | 50 +-
latentnet-2.2/latentnet/R/ergmm.initvals.R | 155 ++++--
latentnet-2.2/latentnet/R/ergmm.par.R | 24 -
latentnet-2.2/latentnet/R/ergmm.permutation.R | 5
latentnet-2.2/latentnet/R/ergmm.probs.R | 397 +++++++++++-----
latentnet-2.2/latentnet/R/ergmm.statseval.R | 249 ++++++----
latentnet-2.2/latentnet/R/ergmm.tuner.R | 109 +++-
latentnet-2.2/latentnet/R/gof.ergmm.R | 29 -
latentnet-2.2/latentnet/R/label.switching.R |only
latentnet-2.2/latentnet/R/mcmc.diagnostics.ergmm.R | 23
latentnet-2.2/latentnet/R/merge.ergmm.R |only
latentnet-2.2/latentnet/R/plot.ergmm.R | 424 +++++++++++-------
latentnet-2.2/latentnet/R/predict.ergmm.R | 88 +++
latentnet-2.2/latentnet/R/print.ergmm.R |only
latentnet-2.2/latentnet/R/print.ergmm.model.R | 21
latentnet-2.2/latentnet/R/procrustes.R |only
latentnet-2.2/latentnet/R/robust.inverse.R | 12
latentnet-2.2/latentnet/R/simulate.ergmm.R | 62 +-
latentnet-2.2/latentnet/R/summary.ergmm.R | 223 ++++++---
latentnet-2.2/latentnet/R/utilities.R | 45 +
latentnet-2.2/latentnet/R/zzz.R | 6
latentnet-2.2/latentnet/data/tribes.RData |binary
latentnet-2.2/latentnet/inst/CITATION | 45 +
latentnet-2.2/latentnet/man/as.mcmc.list.ergmm.Rd | 2
latentnet-2.2/latentnet/man/davis.Rd | 16
latentnet-2.2/latentnet/man/ergmm.Rd | 37 -
latentnet-2.2/latentnet/man/ergmm.control.Rd | 27 -
latentnet-2.2/latentnet/man/ergmm.object.Rd | 59 +-
latentnet-2.2/latentnet/man/ergmm.par.list.object.Rd | 44 +
latentnet-2.2/latentnet/man/ergmm.prior.Rd | 4
latentnet-2.2/latentnet/man/latentnet-internal.Rd | 31 +
latentnet-2.2/latentnet/man/latentnet.Rd | 36 -
latentnet-2.2/latentnet/man/mcmc.diagnostics.ergmm.Rd | 2
latentnet-2.2/latentnet/man/merge.ergmm.Rd |only
latentnet-2.2/latentnet/man/plot.ergmm.Rd | 86 ++-
latentnet-2.2/latentnet/man/predict.ergmm.Rd | 2
latentnet-2.2/latentnet/man/simulate.ergmm.Rd | 8
latentnet-2.2/latentnet/man/summary.ergmm.Rd | 11
latentnet-2.2/latentnet/man/terms.ergmm.Rd | 83 +++
latentnet-2.2/latentnet/man/tribes.Rd | 16
latentnet-2.2/latentnet/src/ergmm_probs.c | 85 +++
latentnet-2.2/latentnet/src/ergmm_probs.h | 5
latentnet-2.2/latentnet/src/ergmm_sampler.c | 136 +++++
latentnet-2.2/latentnet/src/ergmm_sampler.h | 38 +
latentnet-2.2/latentnet/src/ergmm_structs.h | 18
latentnet-2.2/latentnet/src/ergmm_updaters.c | 149 +++++-
latentnet-2.2/latentnet/src/ergmm_updaters.h | 7
latentnet-2.2/latentnet/src/ergmm_utils.c | 27 +
latentnet-2.2/latentnet/src/ergmm_utils.h | 2
latentnet-2.2/latentnet/src/kl_switch.c |only
latentnet-2.2/latentnet/src/kl_switch.h |only
latentnet-2.2/latentnet/src/matrix_utils.c | 45 +
latentnet-2.2/latentnet/src/matrix_utils.h | 2
latentnet-2.2/latentnet/src/mbc_sampler.c | 20
latentnet-2.2/latentnet/src/post_predict.c |only
latentnet-2.2/latentnet/src/post_predict.h |only
latentnet-2.2/latentnet/src/procrustes.c |only
latentnet-2.2/latentnet/src/procrustes.h |only
latentnet-2.2/latentnet/tests/nolatent.R | 20
latentnet-2.2/latentnet/tests/nomixing.R | 2
latentnet-2.2/latentnet/tests/onlymcmc.R | 2
latentnet-2.2/latentnet/tests/plots.R | 23
80 files changed, 2439 insertions(+), 1069 deletions(-)
Author: Klaus Schliep & Klaus Hechenbichler
Title: Weighted k-Nearest Neighbors
Description: Weighted k-Nearest Neighbors Classification and Regression
Diff between kknn versions 1.0-6 dated 2008-07-20 and 1.0-7 dated 2009-07-18
DESCRIPTION | 22 ++++++++++++---------- man/kknn.Rd | 2 +- man/train.kknn.Rd | 2 +- src/dm.c | 2 +- 4 files changed, 15 insertions(+), 13 deletions(-)
Author: Original S functions by Stuart Coles, R port and R
documentation files by Alec Stephenson.
Title: An Introduction to Statistical Modeling of Extreme Values
Description: Functions to support the computations carried out in `An
Introduction to Statistical Modeling of Extreme Values' by
Stuart Coles. The functions may be divided into the following
groups; maxima/minima, order statistics, peaks over thresholds
and point processes.
Diff between ismev versions 1.33 dated 2009-05-13 and 1.34 dated 2009-07-18
DESCRIPTION | 8 ++++---- R/gev.R | 36 ++++++++++++++++++++++++++++++++---- R/gpd.R | 32 ++++++++++++++++++++++++++++---- man/ismev-internal.Rd | 3 +++ 4 files changed, 67 insertions(+), 12 deletions(-)
Author: Richard Bourgon
Diff between intervals versions 0.12.2 dated 2009-06-28 and 0.13.0 dated 2009-07-18
Title: Tools for working with points and intervals
Description: Tools for working with and comparing sets of points and
intervals.
DESCRIPTION | 10
NAMESPACE | 5
NEWS | 11
R/as.matrix.R |only
R/interval_included-methods.R |only
inst/doc/intervals_overview.pdf | 549 ++++++++++++++----------------
man/Intervals_virtual-class.Rd | 5
man/Intervals_virtual_or_numeric-class.Rd | 8
man/as.matrix.Intervals.Rd |only
man/interval_included-methods.Rd |only
man/intervals-package.Rd | 3
11 files changed, 301 insertions(+), 290 deletions(-)
Author: Sebastien Dejean, Ignacio Gonzalez and Kim-Anh Le Cao
Title: Integrate Omics data project
Description: The package supplies two efficients methodologies:
regularized CCA and sparse PLS to unravel relationships between
two heterogeneous data sets of size (nxp) and (nxq) where the p
and q variables are measured on the same samples or individuals
n. These data may come from high throughput technologies, such
as omics data (e.g. transcriptomics, metabolomics or proteomics
data) that require an integrative or joint analysis. However,
integrOmics can also be applied to any other large data sets
where p+q>>n. rCCA is a regularized version of CCA to deal with
the large number of variables. sPLS allows variable selection
in a one step procedure and two frameworks are proposed:
regression and canonical analysis. Numerous graphical outputs
are provided to help interpreting the results.
Diff between integrOmics versions 2.1 dated 2009-06-26 and 2.3 dated 2009-07-18
integrOmics-2.1/integrOmics/R/rccNet.R |only integrOmics-2.1/integrOmics/man/rccNet.Rd |only integrOmics-2.3/integrOmics/DESCRIPTION | 26 +-- integrOmics-2.3/integrOmics/NAMESPACE | 72 +++++----- integrOmics-2.3/integrOmics/R/network.rcc.R |only integrOmics-2.3/integrOmics/R/network.spls.R |only integrOmics-2.3/integrOmics/R/predict.R | 182 +++++++++++++-------------- integrOmics-2.3/integrOmics/man/network.Rd |only integrOmics-2.3/integrOmics/man/predict.Rd | 1 9 files changed, 142 insertions(+), 139 deletions(-)
Author: Rense Nieuwenhuis, Ben Pelzer, Manfred te Grotenhuis
Title: Tools for detecting influential data in mixed effects models
Description: influence.ME provides a collection of tools for
calculating measures of influential data for mixed effects
models. It analyses models that were estimated using lme4. The
basic rationale behind identifying influential data is that
when iteratively single units are omitted from the data, models
based on these data should not produce substantially different
estimates. To standardize the assessment of how influential a
(single group of) observation(s) is, several measures of
influence are common practice. First, DFBETAS is a standardized
measure of the absolute difference between the estimate with a
particular case included and the estimate without that
particular case. Second, Cook's distance provides an overall
measurement of the change in all parameter estimates, or a
selection thereof.
Diff between influence.ME versions 0.6.1 dated 2009-04-27 and 0.7 dated 2009-07-18
DESCRIPTION | 15 ++++++++------- R/dp.ME.cook.R | 17 ++++++----------- R/estex.R | 6 +++--- R/exclude.influence.R | 12 +++++++++++- man/ME.cook.Rd | 4 ++-- man/ME.dfbetas.Rd | 4 ++-- man/ME.pchange.Rd | 22 +++++++++++----------- man/dp.ME.cook.Rd | 6 +++--- man/dp.ME.pchange.Rd | 2 +- man/estex.Rd | 10 +++++++--- man/exclude.influence.Rd | 8 ++++++-- man/grouping.levels.Rd | 3 --- man/influence.ME-package.Rd | 16 ++++++++-------- 13 files changed, 68 insertions(+), 57 deletions(-)
Author: Edzer J. Pebesma
Diff between gstat versions 0.9-61 dated 2009-07-02 and 0.9-62 dated 2009-07-18
Title: geostatistical modelling, prediction and simulation
Description: variogram modelling; simple, ordinary and universal point
or block (co)kriging, sequential Gaussian or indicator
(co)simulation; variogram and variogram map plotting utility
functions.
DESCRIPTION | 8
R/krigeTg.R | 6
inst/doc/gstat.pdf |29387 +++++++++++++++++++++++++++--------------------------
man/krigeTg.Rd | 11
man/pcb.Rd | 2
5 files changed, 15134 insertions(+), 14280 deletions(-)
Author: Brian Lee Yung Rowe
Title: Futile function utilities
Description: A collection of utility functions to expedite software
development
Diff between futile versions 1.0.2 dated 2009-05-28 and 1.1.1 dated 2009-07-18
futile-1.0.2/futile/R/logLevel.R |only futile-1.0.2/futile/man/logLevel.Rd |only futile-1.1.1/futile/DESCRIPTION | 9 +++++---- futile-1.1.1/futile/NAMESPACE |only futile-1.1.1/futile/R/aptions.R |only futile-1.1.1/futile/R/general.R | 14 ++++++++++++++ futile-1.1.1/futile/R/logger.R |only futile-1.1.1/futile/man/futile-package.Rd | 11 ++++++----- futile-1.1.1/futile/man/logger.Rd |only futile-1.1.1/futile/man/mid.Rd | 25 +++++++++++++++++++------ futile-1.1.1/futile/man/options.manager.Rd |only 11 files changed, 44 insertions(+), 15 deletions(-)
Author: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.9.0.2 dated 2009-06-25 and 2.9.1.2 dated 2009-07-18
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
DESCRIPTION | 8 +++---
R/epicalc.R | 65 ++++++++++++++++++++++++++++++++++--------------------
data/Xerop.rdata |only
man/Xerop.rd |only
man/lagVar.rd | 18 +++++++++-----
man/markVisits.rd | 4 ++-
6 files changed, 61 insertions(+), 34 deletions(-)
Author: Kosuke Imai
Diff between eco versions 3.1-2 dated 2009-02-01 and 3.1-4 dated 2009-07-18
Title: R Package for Ecological Inference in 2x2 Tables
Description: eco is a publicly available R package that implements the
Bayesian and likelihood methods proposed in Imai, Lu, and
Strauss (2008) for ecological inference in $2 \times 2$ tables
as well as the method of bounds introduced by Duncan and Davis
(1953). The package fits both parametric and nonparametric
models using either the Expectation-Maximization algorithms
(for likelihood models) or the Markov chain Monte Carlo
algorithms (for Bayesian models). For all models, the
individual-level data can be directly incorporated into the
estimation whenever such data are available. Along with
in-sample and out-of-sample predictions, the package also
provides a functionality which allows one to quantify the
effect of data aggregation on parameter estimation and
hypothesis testing under the parametric likelihood models.
DESCRIPTION | 42 ++++++++++++++++++++++--------------------
NAMESPACE | 3 ++-
R/Qfun.R |only
man/Qfun.Rd |only
man/eco.Rd | 9 ++++++---
man/ecoML.Rd | 9 ++++++---
man/ecoNP.Rd | 9 ++++++---
man/summary.eco.Rd | 6 ++++--
man/summary.ecoML.Rd | 7 +++++--
man/summary.ecoNP.Rd | 6 ++++--
10 files changed, 55 insertions(+), 36 deletions(-)
Author: Christian Ritz
Diff between drc versions 1.7-0 dated 2009-06-08 and 1.7-2 dated 2009-07-18
Title: Analysis of dose-response curves
Description: Analysis of one or multiple curves with focus on
concentration-response, dose-response and time-response curves
used, for example in biology, environmental sciences, medicine,
pharmacology, toxicology.
DESCRIPTION | 8 ++++----
NAMESPACE | 3 ++-
NEWS | 4 ++++
R/lin.test.R |only
R/mr.test.R |only
R/neill.test.R |only
data/etmotc.rda |only
man/CRS.4a.Rd | 1 +
man/etmotc.Rd |only
man/lin.test.Rd |only
man/mr.test.Rd |only
man/neill.test.Rd |only
man/plot.drc.Rd | 2 +-
13 files changed, 12 insertions(+), 6 deletions(-)
Author: Antonio Gasparrini and Ben Armstrong
Title: Distributed Lag Non-linear Models
Description: The package dlnm contains functions to specify basis and
cross-basis matrices in order to run distributed lag models and
their non-linear extension, then to predict and graph the
results for a fitted model.
Diff between dlnm versions 0.1.0 dated 2009-07-01 and 0.2.1 dated 2009-07-18
DESCRIPTION | 8 ++++---- R/crossbasis.R | 2 +- R/crossplot.R | 8 ++++++-- R/crosspred.R | 2 +- R/mkbasis.R | 24 ++++++++++++++++-------- R/mklagbasis.R | 2 +- inst/CITATION | 2 +- inst/dlnmChangeLog |only inst/doc |only man/crossbasis.Rd | 34 +++++++++++++++++++--------------- man/crossplot.Rd | 8 ++++++-- man/crosspred.Rd | 23 +++++++++++++---------- man/dlnm-internal.Rd | 4 +++- man/dlnm-package.Rd | 8 ++++++-- 14 files changed, 77 insertions(+), 48 deletions(-)
Author: Ingmar Visser
Diff between depmix versions 0.9.4 dated 2008-08-07 and 0.9.6 dated 2009-07-18
Title: Dependent Mixture Models
Description: Fit (multigroup) mixtures of latent Markov models on mixed
categorical and continuous (timeseries) data
CHANGES | 15 +
DESCRIPTION | 15 -
R/depmix-internal.R | 454 ++++++++++++++++++++++++++++++++++
R/depmix.R | 36 +-
R/generate.R | 56 ++++
R/lca.R | 60 ++++
R/markovdata.R | 109 ++++++++
R/mgdmm.R | 217 ++++++++++++++++
R/mixdmm.R | 182 +++++++++++++
README | 76 ++---
man/depmix-internal.Rd | 144 +++++-----
man/discrimination.Rd | 66 ++---
man/dmm.Rd | 506 +++++++++++++++++++-------------------
man/fitdmm.Rd | 644 ++++++++++++++++++++++++-------------------------
man/generate.Rd | 146 +++++------
man/mgdmm.Rd | 210 +++++++--------
man/mixdmm.Rd | 224 ++++++++---------
man/speed.Rd | 60 ++--
18 files changed, 2152 insertions(+), 1068 deletions(-)
Author: Jun Yan
Diff between copula versions 0.8-7 dated 2009-06-10 and 0.8-8 dated 2009-07-18
Title: Multivariate dependence with copulas
Description: Classes (S4) of commonly used copulas including elliptical
(normal and t), Archimedean (Clayton, Gumbel, Frank, and
Ali-Mikhail-Haq), extreme value (Gumbel, Husler-Reiss,
Galambos, and t-EV), and other families (Plackett and
Farlie-Gumbel-Morgenstern). Methods for density, distribution,
random number generation, bivariate dependence measures,
perspective and contour plots. Functions for fitting copula
models with variance estimate. Independence tests among random
variables and random vectors. Serial independence tests for
univariate and multivariate continuous time series.
Goodness-of-fit tests for copulas based on multipliers and on
the parametric bootstrap.
DESCRIPTION | 16 ++++++-------
NAMESPACE | 5 ++++
R/Classes.R | 21 +++++++++++++++++
R/Copula.R | 21 +++++++++++++++++
R/E.R | 2 -
R/amhCopula.R | 2 -
R/archmCopula.R | 21 +++++++++++++++++
R/asymCopula.R | 34 +++++++++++++++++++++++++---
R/claytonCopula.R | 3 --
R/debye.R | 2 -
R/derCdfPdf.R | 3 --
R/ellipCopula.R | 21 +++++++++++++++++
R/evTests.R | 2 +
R/fgmCopula.R | 2 -
R/fitCopula.R | 12 +++++-----
R/fitMvdc.R | 21 +++++++++++++++++
R/frankCopula.R | 4 +--
R/galambosCopula.R | 2 -
R/galambosExpr-math.R | 2 -
R/gofTests.R | 43 ++++++++++++++++++++++--------------
R/graphics.R | 2 -
R/gumbelCopula.R | 2 -
R/huslerReissCopula.R | 9 +++----
R/indepCopula.R | 2 -
R/indepTests.R | 53 ++++++++++++++++++++++++++++++++++++---------
R/logseries.R | 2 -
R/mvdc.R | 3 --
R/normalCopula.R | 2 -
R/plackettCopula.R | 2 -
R/skewNormalCopula.R | 2 -
R/stable.R | 2 -
R/sysdata.rda |binary
R/tCopula.R | 3 --
R/tevCopula.R | 15 +++++++++++-
data |only
man/indepTest.Rd | 17 ++++++++------
man/loss.Rd |only
man/multIndepTest.Rd | 10 +++++---
man/multSerialIndepTest.Rd | 10 +++++---
man/rdj.Rd |only
man/serialIndepTest.Rd | 9 +++++--
man/uranium.Rd |only
src/empcop.stat.c | 2 -
src/empcop.stat.h | 2 -
src/empcopm.test.c | 9 ++++---
src/empcops.test.c | 8 +++---
src/empcopsm.test.c | 9 ++++---
src/empcopu.test.c | 7 ++---
src/evtest.c | 10 ++------
src/fgm.c | 2 -
src/set.utils.c | 2 -
src/set.utils.h | 2 -
52 files changed, 318 insertions(+), 119 deletions(-)
Author: Max Kuhn, contributions from Steve Weston, Jed Wing and James
Forester
Title: A collection of contrast methods
Description: Contrast methods, in the style of the Design package, for
fit objects produced by the lm, glm, gls, and geese functions.
Diff between contrast versions 0.9 dated 2009-01-26 and 0.10 dated 2009-07-18
DESCRIPTION | 15 +++++++++------ R/gets.R | 3 ++- inst/CHANGES |only inst/doc/contrast.pdf |binary 4 files changed, 11 insertions(+), 7 deletions(-)
Author: Venkatraman E. Seshan
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if
not fun.
Diff between clinfun versions 0.8.4 dated 2008-12-04 and 0.8.5 dated 2009-07-18
CHANGES | 6 ++++++ DESCRIPTION | 13 ++++++++----- R/jonkheere.R | 13 ++++++++----- man/permtests.Rd | 5 ++++- 4 files changed, 26 insertions(+), 11 deletions(-)
Author: Daniel Samarov
Diff between calib versions 2.0.0 dated 2009-01-28 and 2.0.1 dated 2009-07-18
Title: Statistical tool for calibration of plate based bioassays
Description: Provides basic S4 data structures and routines for
calibration of bioassays
DESCRIPTION | 33 ++--
R/calibfit-accessors.R | 2
R/calibfit-diagnosticFunctions.R | 277 ++++++++-------------------------------
R/calibfit-functions.R | 10 -
inst/doc/HowTo-calib.pdf |binary
inst/doc/Rplots.pdf | 252 +++++++++++++++++------------------
6 files changed, 212 insertions(+), 362 deletions(-)
Author: Christian Zang
Title: Bootstrapped Response and Correlation Functions
Description: Calculation of Bootstrapped Response and Correlation
Functions for Use in Dendroclimatology
Diff between bootRes versions 0.1 dated 2009-06-24 and 0.2 dated 2009-07-18
Changelog |only DESCRIPTION | 8 ++++---- R/bcf.R | 13 +++++++++---- R/brf.R | 14 +++++++++----- R/dcplot.R | 39 ++++++++++++++++++++++++++++++++------- R/dendroclim.R | 8 ++++---- R/pmat.R | 33 +++++++++++++++++++++------------ man/dcplot.Rd | 3 +++ man/dendroclim.Rd | 12 +++++++++--- 9 files changed, 91 insertions(+), 39 deletions(-)
Author: Lester L. Yuan
Title: Compute biological inferences
Description: Imports benthic count data, reformats this data, and
computes environmental inferences from this data.
Diff between bio.infer versions 1.2-3 dated 2009-03-06 and 1.2-4 dated 2009-07-18
DESCRIPTION | 29 ++++++++++++++++------------- R/trait.stat.R | 4 ++-- chm |only 3 files changed, 18 insertions(+), 15 deletions(-)
Author: Michael J. Kane and John W. Emerson
Title: Manage massive matrices in R using C++, with support for shared
memory and memory-mapped files.
Description: Use C++ to create, store, access, and manipulate massive
matrices. Matrices may optionally be allocated to shared
memory and/or may use memory-mapped files.
Diff between bigmemory versions 3.9 dated 2009-06-24 and 3.10 dated 2009-07-18
COPYING |only DESCRIPTION | 8 NAMESPACE |only R/bigmatrixLib.R | 133 ---- R/bigmemoryAnalytics.R |only configure |only configure.Rout | 2 include/boost/array.hpp |only include/boost/cstdint.hpp |only include/boost/detail |only include/boost/exception |only include/boost/interprocess |only include/boost/io_fwd.hpp |only include/boost/mpl/O1_size.hpp |only include/boost/mpl/advance.hpp |only include/boost/mpl/advance_fwd.hpp |only include/boost/mpl/alias.hpp |only include/boost/mpl/always.hpp |only include/boost/mpl/and.hpp |only include/boost/mpl/apply.hpp |only include/boost/mpl/apply_wrap.hpp |only include/boost/mpl/arg_fwd.hpp |only include/boost/mpl/arithmetic.hpp |only include/boost/mpl/at.hpp |only include/boost/mpl/at_fwd.hpp |only include/boost/mpl/aux_/O1_size_impl.hpp |only include/boost/mpl/aux_/adl_barrier.hpp |only include/boost/mpl/aux_/advance_backward.hpp |only include/boost/mpl/aux_/advance_forward.hpp |only include/boost/mpl/aux_/apply_1st.hpp |only include/boost/mpl/aux_/arg_typedef.hpp |only include/boost/mpl/aux_/arithmetic_op.hpp |only include/boost/mpl/aux_/arity.hpp |only include/boost/mpl/aux_/arity_spec.hpp |only include/boost/mpl/aux_/at_impl.hpp |only include/boost/mpl/aux_/back_impl.hpp |only include/boost/mpl/aux_/basic_bind.hpp |only include/boost/mpl/aux_/begin_end_impl.hpp |only include/boost/mpl/aux_/clear_impl.hpp |only include/boost/mpl/aux_/common_name_wknd.hpp |only include/boost/mpl/aux_/comparison_op.hpp |only include/boost/mpl/aux_/config |only include/boost/mpl/aux_/contains_impl.hpp |only include/boost/mpl/aux_/count_args.hpp |only include/boost/mpl/aux_/count_impl.hpp |only include/boost/mpl/aux_/empty_impl.hpp |only include/boost/mpl/aux_/erase_impl.hpp |only include/boost/mpl/aux_/erase_key_impl.hpp |only include/boost/mpl/aux_/filter_iter.hpp |only include/boost/mpl/aux_/find_if_pred.hpp |only include/boost/mpl/aux_/fold_impl.hpp |only include/boost/mpl/aux_/fold_impl_body.hpp |only include/boost/mpl/aux_/fold_op.hpp |only include/boost/mpl/aux_/fold_pred.hpp |only include/boost/mpl/aux_/front_impl.hpp |only include/boost/mpl/aux_/full_lambda.hpp |only include/boost/mpl/aux_/has_apply.hpp |only include/boost/mpl/aux_/has_begin.hpp |only include/boost/mpl/aux_/has_key_impl.hpp |only include/boost/mpl/aux_/has_rebind.hpp |only include/boost/mpl/aux_/has_size.hpp |only include/boost/mpl/aux_/has_tag.hpp |only include/boost/mpl/aux_/has_type.hpp |only include/boost/mpl/aux_/include_preprocessed.hpp |only include/boost/mpl/aux_/insert_impl.hpp |only include/boost/mpl/aux_/insert_range_impl.hpp |only include/boost/mpl/aux_/inserter_algorithm.hpp |only include/boost/mpl/aux_/integral_wrapper.hpp |only include/boost/mpl/aux_/is_msvc_eti_arg.hpp |only include/boost/mpl/aux_/iter_apply.hpp |only include/boost/mpl/aux_/iter_fold_if_impl.hpp |only include/boost/mpl/aux_/iter_fold_impl.hpp |only include/boost/mpl/aux_/iter_push_front.hpp |only include/boost/mpl/aux_/joint_iter.hpp |only include/boost/mpl/aux_/lambda_arity_param.hpp |only include/boost/mpl/aux_/lambda_no_ctps.hpp |only include/boost/mpl/aux_/lambda_spec.hpp |only include/boost/mpl/aux_/lambda_support.hpp |only include/boost/mpl/aux_/largest_int.hpp |only include/boost/mpl/aux_/logical_op.hpp |only include/boost/mpl/aux_/msvc_dtw.hpp |only include/boost/mpl/aux_/msvc_eti_base.hpp |only include/boost/mpl/aux_/msvc_is_class.hpp |only include/boost/mpl/aux_/msvc_never_true.hpp |only include/boost/mpl/aux_/msvc_type.hpp |only include/boost/mpl/aux_/na.hpp |only include/boost/mpl/aux_/na_assert.hpp |only include/boost/mpl/aux_/na_fwd.hpp |only include/boost/mpl/aux_/na_spec.hpp |only include/boost/mpl/aux_/nested_type_wknd.hpp |only include/boost/mpl/aux_/nttp_decl.hpp |only include/boost/mpl/aux_/numeric_cast_utils.hpp |only include/boost/mpl/aux_/numeric_op.hpp |only include/boost/mpl/aux_/order_impl.hpp |only include/boost/mpl/aux_/overload_names.hpp |only include/boost/mpl/aux_/partition_op.hpp |only include/boost/mpl/aux_/pop_back_impl.hpp |only include/boost/mpl/aux_/pop_front_impl.hpp |only include/boost/mpl/aux_/preprocessed/bcc |only include/boost/mpl/aux_/preprocessed/bcc551 |only include/boost/mpl/aux_/preprocessed/dmc |only include/boost/mpl/aux_/preprocessed/gcc |only include/boost/mpl/aux_/preprocessed/mwcw |only include/boost/mpl/aux_/preprocessed/no_ttp/advance_backward.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/advance_forward.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/and.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/apply.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/apply_wrap.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/basic_bind.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/bind_fwd.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/bitor.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/deque.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/divides.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/equal_to.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/fold_impl.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/full_lambda.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/greater.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/greater_equal.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/inherit.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/iter_fold_impl.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/lambda_no_ctps.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/less.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/list.hpp | 285 +++++++++- include/boost/mpl/aux_/preprocessed/no_ttp/list_c.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/map.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/modulus.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/not_equal_to.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/plus.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/quote.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/reverse_fold_impl.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/set.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/set_c.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/shift_right.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/template_arity.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/vector.hpp |only include/boost/mpl/aux_/preprocessor |only include/boost/mpl/aux_/ptr_to_ref.hpp |only include/boost/mpl/aux_/push_back_impl.hpp |only include/boost/mpl/aux_/push_front_impl.hpp |only include/boost/mpl/aux_/range_c |only include/boost/mpl/aux_/reverse_fold_impl.hpp |only include/boost/mpl/aux_/reverse_fold_impl_body.hpp |only include/boost/mpl/aux_/reverse_iter_fold_impl.hpp |only include/boost/mpl/aux_/sequence_wrapper.hpp |only include/boost/mpl/aux_/shift_op.hpp |only include/boost/mpl/aux_/single_element_iter.hpp |only include/boost/mpl/aux_/size_impl.hpp |only include/boost/mpl/aux_/sort_impl.hpp |only include/boost/mpl/aux_/static_cast.hpp |only include/boost/mpl/aux_/template_arity.hpp |only include/boost/mpl/aux_/template_arity_fwd.hpp |only include/boost/mpl/aux_/test |only include/boost/mpl/aux_/test.hpp |only include/boost/mpl/aux_/traits_lambda_spec.hpp |only include/boost/mpl/aux_/transform_iter.hpp |only include/boost/mpl/aux_/type_wrapper.hpp |only include/boost/mpl/aux_/unwrap.hpp |only include/boost/mpl/aux_/value_wknd.hpp |only include/boost/mpl/aux_/yes_no.hpp |only include/boost/mpl/back.hpp |only include/boost/mpl/back_fwd.hpp |only include/boost/mpl/begin.hpp |only include/boost/mpl/begin_end.hpp |only include/boost/mpl/begin_end_fwd.hpp |only include/boost/mpl/bind_fwd.hpp |only include/boost/mpl/bitand.hpp |only include/boost/mpl/bitor.hpp |only include/boost/mpl/bitwise.hpp |only include/boost/mpl/bool_fwd.hpp |only include/boost/mpl/clear.hpp |only include/boost/mpl/clear_fwd.hpp |only include/boost/mpl/comparison.hpp |only include/boost/mpl/contains.hpp |only include/boost/mpl/contains_fwd.hpp |only include/boost/mpl/copy.hpp |only include/boost/mpl/copy_if.hpp |only include/boost/mpl/count.hpp |only include/boost/mpl/count_fwd.hpp |only include/boost/mpl/count_if.hpp |only include/boost/mpl/deque.hpp |only include/boost/mpl/distance.hpp |only include/boost/mpl/distance_fwd.hpp |only include/boost/mpl/divides.hpp |only include/boost/mpl/empty.hpp |only include/boost/mpl/empty_base.hpp |only include/boost/mpl/empty_fwd.hpp |only include/boost/mpl/end.hpp |only include/boost/mpl/equal.hpp |only include/boost/mpl/equal_to.hpp |only include/boost/mpl/erase.hpp |only include/boost/mpl/erase_key.hpp |only include/boost/mpl/find.hpp |only include/boost/mpl/find_if.hpp |only include/boost/mpl/fold.hpp |only include/boost/mpl/for_each.hpp |only include/boost/mpl/front.hpp |only include/boost/mpl/front_fwd.hpp |only include/boost/mpl/front_inserter.hpp |only include/boost/mpl/greater.hpp |only include/boost/mpl/greater_equal.hpp |only include/boost/mpl/has_key.hpp |only include/boost/mpl/has_key_fwd.hpp |only include/boost/mpl/if.hpp |only include/boost/mpl/index_if.hpp |only include/boost/mpl/index_of.hpp |only include/boost/mpl/inherit.hpp |only include/boost/mpl/insert.hpp |only include/boost/mpl/insert_fwd.hpp |only include/boost/mpl/insert_range.hpp |only include/boost/mpl/inserter.hpp |only include/boost/mpl/integral_c.hpp |only include/boost/mpl/integral_c_fwd.hpp |only include/boost/mpl/is_placeholder.hpp |only include/boost/mpl/is_sequence.hpp |only include/boost/mpl/iter_fold.hpp |only include/boost/mpl/iter_fold_if.hpp |only include/boost/mpl/iterator_category.hpp |only include/boost/mpl/iterator_range.hpp |only include/boost/mpl/iterator_tags.hpp |only include/boost/mpl/key_type.hpp |only include/boost/mpl/key_type_fwd.hpp |only include/boost/mpl/lambda.hpp |only include/boost/mpl/lambda_fwd.hpp |only include/boost/mpl/less.hpp |only include/boost/mpl/limits |only include/boost/mpl/list |only include/boost/mpl/list.hpp |only include/boost/mpl/list_c.hpp |only include/boost/mpl/logical.hpp |only include/boost/mpl/long.hpp |only include/boost/mpl/long_fwd.hpp |only include/boost/mpl/map |only include/boost/mpl/map.hpp |only include/boost/mpl/max.hpp |only include/boost/mpl/min.hpp |only include/boost/mpl/min_element.hpp |only include/boost/mpl/min_max.hpp |only include/boost/mpl/modulus.hpp |only include/boost/mpl/multiplies.hpp |only include/boost/mpl/multiset |only include/boost/mpl/next_prior.hpp |only include/boost/mpl/not.hpp |only include/boost/mpl/not_equal_to.hpp |only include/boost/mpl/numeric_cast.hpp |only include/boost/mpl/order.hpp |only include/boost/mpl/pair.hpp |only include/boost/mpl/partition.hpp |only include/boost/mpl/plus.hpp |only include/boost/mpl/pop_front.hpp |only include/boost/mpl/pop_front_fwd.hpp |only include/boost/mpl/print.hpp |only include/boost/mpl/push_back.hpp |only include/boost/mpl/push_back_fwd.hpp |only include/boost/mpl/push_front_fwd.hpp |only include/boost/mpl/quote.hpp |only include/boost/mpl/range_c.hpp |only include/boost/mpl/remove.hpp |only include/boost/mpl/replace.hpp |only include/boost/mpl/replace_if.hpp |only include/boost/mpl/reverse.hpp |only include/boost/mpl/reverse_fold.hpp |only include/boost/mpl/reverse_iter_fold.hpp |only include/boost/mpl/set |only include/boost/mpl/set.hpp |only include/boost/mpl/set_c.hpp |only include/boost/mpl/shift_right.hpp |only include/boost/mpl/size_t_fwd.hpp |only include/boost/mpl/sizeof.hpp |only include/boost/mpl/stable_partition.hpp |only include/boost/mpl/transform.hpp |only include/boost/mpl/transform_view.hpp |only include/boost/mpl/unique.hpp |only include/boost/mpl/upper_bound.hpp |only include/boost/mpl/value_type.hpp |only include/boost/mpl/value_type_fwd.hpp |only include/boost/mpl/vector |only include/boost/mpl/vector.hpp |only include/boost/mpl/void.hpp |only include/boost/mpl/void_fwd.hpp |only include/boost/noncopyable.hpp |only include/boost/numeric |only include/boost/random |only include/boost/shared_ptr.hpp |only include/boost/static_assert.hpp |only include/boost/throw_exception.hpp |only include/boost/type_traits |only include/boost/uuid |only include/boost/uuid.hpp |only man/biglm.big.matrix.Rd | 24 man/bigmemory-package.Rd | 4 290 files changed, 302 insertions(+), 154 deletions(-)
Author: Paul Hiemstra
Diff between automap versions 1.0-0 dated 2009-03-19 and 1.0-2 dated 2009-07-18
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 | 2 -
R/autoKrige.r | 20 +++++++++--
R/autofitVariogram.r | 2 -
R/plot.posPredictionInterval.r | 3 -
R/summary.autoKrige.r | 2 +
R/summary.autofitVariogram.r | 2 +
README | 6 ++-
SvnLog | 72 +++++++++++++++++++++++++++++++++++++++++
inst/CITATION | 2 -
man/autoKrige.rd | 22 ++++++++++--
man/autofitVariogram.rd | 5 +-
tests/autoKrige.cv.Rout.save | 46 ++++++++++++++++++--------
tests/automap.Rout.save | 8 +++-
14 files changed, 164 insertions(+), 36 deletions(-)
Author: Beatriz Pateiro-Lopez, Alberto Rodriguez-Casal.
Title: Generalization of the convex hull of a sample of points in the
plane
Description: This package computes the alpha-shape and alpha-convex
hull of a given sample of points in the plane. The concepts of
alpha-shape and alpha-convex hull generalize the definition of
the convex hull of a finite set of points. The programming is
based on the duality between the Voronoi diagram and Delaunay
triangulation. The package also includes a function that
returns the Delaunay mesh of a given sample of points and its
dual Voronoi diagram in one single object.
Diff between alphahull versions 0.1 dated 2009-03-28 and 0.1-1 dated 2009-07-18
alphahull-0.1-1/alphahull/DESCRIPTION | 10 alphahull-0.1-1/alphahull/R/ahull.R | 373 ++++++++++----------- alphahull-0.1-1/alphahull/R/anglesArc.R | 15 alphahull-0.1-1/alphahull/R/arc.R | 10 alphahull-0.1-1/alphahull/R/ashape.R | 154 +++----- alphahull-0.1-1/alphahull/R/complement.R | 353 +++++++++---------- alphahull-0.1-1/alphahull/R/delvor.R | 107 +++--- alphahull-0.1-1/alphahull/R/dummycoor.R | 42 +- alphahull-0.1-1/alphahull/R/inahull.R | 117 +++--- alphahull-0.1-1/alphahull/R/inter.R | 82 ++-- alphahull-0.1-1/alphahull/R/koch.R |only alphahull-0.1-1/alphahull/R/lengthahull.R | 16 alphahull-0.1-1/alphahull/R/plot.ahull.R | 134 +++---- alphahull-0.1-1/alphahull/R/plot.ashape.R | 112 +++--- alphahull-0.1-1/alphahull/R/plot.delvor.R | 98 ++--- alphahull-0.1-1/alphahull/R/rkoch.R |only alphahull-0.1-1/alphahull/R/rotation.R | 19 - alphahull-0.1-1/alphahull/R/tricircum.R | 42 -- alphahull-0.1-1/alphahull/inst |only alphahull-0.1-1/alphahull/man/ahull.Rd | 16 alphahull-0.1-1/alphahull/man/alphahull-package.Rd | 6 alphahull-0.1-1/alphahull/man/anglesArc.Rd | 4 alphahull-0.1-1/alphahull/man/arc.Rd | 8 alphahull-0.1-1/alphahull/man/ashape.Rd | 31 - alphahull-0.1-1/alphahull/man/complement.Rd | 6 alphahull-0.1-1/alphahull/man/delvor.Rd | 6 alphahull-0.1-1/alphahull/man/inahull.Rd | 10 alphahull-0.1-1/alphahull/man/koch.Rd |only alphahull-0.1-1/alphahull/man/lengthahull.Rd | 6 alphahull-0.1-1/alphahull/man/plot.ahull.Rd | 21 - alphahull-0.1-1/alphahull/man/plot.ashape.Rd | 38 +- alphahull-0.1-1/alphahull/man/plot.delvor.Rd | 4 alphahull-0.1-1/alphahull/man/rkoch.Rd |only alphahull-0.1-1/alphahull/man/rotation.Rd | 2 alphahull-0.1-1/alphahull/man/tricircum.Rd | 6 alphahull-0.1/alphahull/Read-and-delete-me |only 36 files changed, 909 insertions(+), 939 deletions(-)
Author: Juan R González, Lluís Armengol, Elisabet Guinó, Xavier Solé,
and Víctor Moreno
Title: SNPs-based whole genome association studies
Description: This package carries out most common analysis when
performing whole genome association studies. These analyses
include descriptive statistics and exploratory analysis of
missing values, calculation of Hardy-Weinberg equilibrium,
analysis of association based on generalized linear models
(either for quantitative or binary traits), and analysis of
multiple SNPs (haplotype and epistasis analysis). Permutation
test and related tests (sum statistic and truncated product)
are also implemented.
Diff between SNPassoc versions 1.5-8 dated 2009-03-09 and 1.6-0 dated 2009-07-18
DESCRIPTION | 36 +++++++++---- R/GenomicControl.R | 40 ++++++--------- R/intervals.haplo.glm.R | 124 +++++++++++++++++++++++++----------------------- R/plot.WGassociation.R | 79 +++++++++++++++++------------- R/z[.WGassociation.R | 6 +- inst/docs/changelog.txt | 10 +++ man/GenomicControl.Rd | 2 src/SNPassoc.f | 25 +++++---- 8 files changed, 182 insertions(+), 140 deletions(-)
Author: Markus Loecher, Sense Networks
Title: Overlays on Google map tiles in R
Description: This package serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling. NOTE:
To do anything but downloading static map tiles, RgoogleMaps
needs EITHER rgdal OR ReadImages installed ! Such an OR
dependency is difficult to express in the Depends field, so I
moved both packages to suggested. rgdal is your package if you
prefer png file format and ReadImages if you prefer jpg format.
In the latter case, you will also need the libjpeg library
installed.
Diff between RgoogleMaps versions 1.1.3 dated 2009-06-18 and 1.1.4 dated 2009-07-18
DESCRIPTION | 21 ++++++++++++++------- inst/doc/RgoogleMaps-intro.pdf |binary man/RgoogleMaps-package.Rd | 8 ++++---- 3 files changed, 18 insertions(+), 11 deletions(-)
Author: Hector Corrada Bravo, with contributions from Stefan Theussl
Title: R interface to CPLEX
Description: R interface to CPLEX solvers for linear, quadratic, and
(linear and quadratic) mixed integer programs. 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.
Diff between Rcplex versions 0.2-1 dated 2008-10-16 and 0.2-2 dated 2009-07-18
Rcplex-0.2-1/Rcplex/R/sparse.R |only Rcplex-0.2-1/Rcplex/man/simple_triplet_matrix.Rd |only Rcplex-0.2-2/Rcplex/DESCRIPTION | 21 ++++++++++++++++----- Rcplex-0.2-2/Rcplex/NAMESPACE | 11 +---------- Rcplex-0.2-2/Rcplex/R/Rcplex.R | 2 +- Rcplex-0.2-2/Rcplex/inst/INSTALL | 12 ++++++++++-- Rcplex-0.2-2/Rcplex/inst/NEWS | 2 ++ Rcplex-0.2-2/Rcplex/src/Rcplex_utils.c | 4 ++-- 8 files changed, 32 insertions(+), 20 deletions(-)
Author: Jake Bowers
Diff between RItools versions 0.1-7 dated 2009-06-25 and 0.1-8 dated 2009-07-18
Title: Randomization inference tools
Description: Tools for randomization inference.
ChangeLog | 19 ++++++++++++++++
DESCRIPTION | 8 +++---
R/harmonic.R | 2 -
R/plot.xbal.R | 2 +
R/xBalance.R | 2 -
R/xBalance.make.stratwts.R | 10 ++++++--
R/xBalanceEngine.R | 2 -
R/xtable.xbal.R | 3 --
ToDo | 6 -----
man/xtable.xbal.Rd | 44 ++++++++++---------------------------
tests/xBalanceTests.Rout.save | 49 +++++++++++++++++++++---------------------
11 files changed, 74 insertions(+), 73 deletions(-)
Author: Michael Lawrence
Diff between RGtk2 versions 2.12.13 dated 2009-06-14 and 2.12.15 dated 2009-07-18
Title: R bindings for Gtk 2.8.0 and above
Description: Facilities in the R language for programming graphical
interfaces using Gtk, the Gimp Tool Kit.
RGtk2-2.12.13/RGtk2/man/GtkPageSetupUnixDialog.Rd |only
RGtk2-2.12.13/RGtk2/man/GtkPrintJob.Rd |only
RGtk2-2.12.13/RGtk2/man/GtkPrintUnixDialog.Rd |only
RGtk2-2.12.13/RGtk2/man/GtkPrinter.Rd |only
RGtk2-2.12.15/RGtk2/DESCRIPTION | 6 ++---
RGtk2-2.12.15/RGtk2/R/gdkManuals.R | 2 -
RGtk2-2.12.15/RGtk2/demo/appWindow.R | 12 +++++++----
RGtk2-2.12.15/RGtk2/demo/iconView.R | 2 -
RGtk2-2.12.15/RGtk2/src/Rgtk.c | 2 +
RGtk2-2.12.15/RGtk2/src/conversion.c | 3 +-
RGtk2-2.12.15/RGtk2/src/gdkManuals.c | 2 -
RGtk2-2.12.15/RGtk2/src/gobject.c | 23 ++++++++++++++--------
RGtk2-2.12.15/RGtk2/src/gtkManuals.c | 19 +++++++++++-------
13 files changed, 45 insertions(+), 26 deletions(-)
Author: David Harte
Title: Time Dependent Point Process Modelling
Description: This package fits and analyses time dependent marked point
process models with an emphasis on earthquake modelling. For a
more detailed introduction to the package, see the topic
"PtProcess". A list of recent changes can be found in the topic
"Changes".
Diff between PtProcess versions 3.1-3 dated 2009-01-26 and 3.1-4 dated 2009-07-18
DESCRIPTION | 19 +++++++++++++------ man/Changes.Rd | 2 ++ man/Phuket.Rd | 4 +++- 3 files changed, 18 insertions(+), 7 deletions(-)
Author: Andrew D. Martin
Diff between MCMCpack versions 1.0-1 dated 2009-07-01 and 1.0-2 dated 2009-07-18
Title: Markov chain Monte Carlo (MCMC) Package
Description: This package contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.2. All
models return coda mcmc objects that can then be summarized
using the coda package. MCMCpack also contains some useful
utility functions, including some additional density functions
and pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization.
MCMCpack-1.0-1/MCMCpack/R/MCMCpoissonChangepoint.R |only
MCMCpack-1.0-1/MCMCpack/man/MCMCpoissonChangepoint.Rd |only
MCMCpack-1.0-1/MCMCpack/src/MCMCpoissonChangepoint.cc |only
MCMCpack-1.0-2/MCMCpack/DESCRIPTION | 8
MCMCpack-1.0-2/MCMCpack/HISTORY | 10
MCMCpack-1.0-2/MCMCpack/NAMESPACE | 3
MCMCpack-1.0-2/MCMCpack/R/MCMCbinaryChange.R |only
MCMCpack-1.0-2/MCMCpack/R/MCMCpoissonChange.R |only
MCMCpack-1.0-2/MCMCpack/R/btsutil.R | 308 +++++++++++-------
MCMCpack-1.0-2/MCMCpack/man/MCMCbinaryChange.Rd |only
MCMCpack-1.0-2/MCMCpack/man/MCMCpoissonChange.Rd |only
MCMCpack-1.0-2/MCMCpack/man/plotChangepoint.Rd | 14
MCMCpack-1.0-2/MCMCpack/man/plotState.Rd | 11
MCMCpack-1.0-2/MCMCpack/src/MCMCbinaryChange.cc |only
MCMCpack-1.0-2/MCMCpack/src/MCMCpoissonChange.cc |only
15 files changed, 232 insertions(+), 122 deletions(-)
Author: Corneliu Henegar
Diff between FunNet versions 1.00-6 dated 2009-01-18 and 1.00-7 dated 2009-07-18
Title: Integrative Functional Analysis of Transcriptional Networks
Description: FunNet is an integrative tool for analyzing gene
co-expression networks built from microarray expression data.
The analytic model implemented in this library involves two
abstraction layers: transcriptional and functional (biological
roles). A functional profiling technique using Gene Ontology &
KEGG annotations is applied to extract a list of relevant
biological themes from microarray expression profiling data.
Afterwards multiple-instance representations are built to
relate significant themes to their transcriptional instances
(i.e. the two layers of the model). An adapted non-linear
dynamical system model is used to quantify the proximity of
relevant genomic themes based on the similarity of the
expression profiles of their gene instances. Eventually an
unsupervised multiple-instance clustering procedure, relying on
the two abstraction layers, is used to identify the structure
of the co-expression network composed from modules of
functionally related transcripts. Functional and
transcriptional maps of the co-expression network are provided
separately together with detailed information on the network
centrality of related transcripts and genomic themes.
FunNet-1.00-6/FunNet/man/HS.GO.DIR.BP.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/HS.GO.DIR.CC.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/HS.GO.DIR.MF.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/HS.KEGG.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/HS.locus.name.Rd |only
FunNet-1.00-6/FunNet/man/HS.unigene.Rd |only
FunNet-1.00-6/FunNet/man/MM.GO.DIR.BP.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/MM.GO.DIR.CC.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/MM.GO.DIR.MF.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/MM.KEGG.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/MM.locus.name.Rd |only
FunNet-1.00-6/FunNet/man/MM.unigene.Rd |only
FunNet-1.00-6/FunNet/man/RN.GO.DIR.BP.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/RN.GO.DIR.CC.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/RN.GO.DIR.MF.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/RN.KEGG.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/RN.locus.name.Rd |only
FunNet-1.00-6/FunNet/man/RN.unigene.Rd |only
FunNet-1.00-6/FunNet/man/SC.GO.DIR.BP.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/SC.GO.DIR.CC.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/SC.GO.DIR.MF.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/SC.KEGG.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/SC.locus.name.Rd |only
FunNet-1.00-6/FunNet/man/SC.orf.Rd |only
FunNet-1.00-7/FunNet/DESCRIPTION | 51 +--
FunNet-1.00-7/FunNet/R/Annotations.R | 324 ++++++--------------
FunNet-1.00-7/FunNet/R/FunNet.R | 231 ++++++++++----
FunNet-1.00-7/FunNet/R/sysdata.rda |binary
FunNet-1.00-7/FunNet/man/Annotations.Rd | 10
FunNet-1.00-7/FunNet/man/FunNet.Rd | 14
FunNet-1.00-7/FunNet/man/annot.base.Rd |only
FunNet-1.00-7/FunNet/man/species.Rd |only
32 files changed, 322 insertions(+), 308 deletions(-)
Author: Ulrike Groemping
Title: Fractional Factorial designs with 2-level factors
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 currently subject to intensive development. While
much of the intended functionality is already available, some
changes and improvements are still to be expected. Suggestions
are welcome.
Diff between FrF2 versions 0.94 dated 2009-06-28 and 0.95 dated 2009-07-18
DESCRIPTION | 8 R/FrF2.R | 14 R/IAPlot.R | 47 ++ R/MEPlot.R | 2 R/estimable2fis.R | 4 R/pb.R | 32 - R/sysdata.rda |binary inst/NEWS | 19 + man/CatalogueAccessors.Rd | 8 man/FrF2-package.Rd | 11 man/FrF2.Rd | 5 man/IAPlot.Rd | 46 +- man/pb.Rd | 3 tests/FrF2test.Rout.save | 800 +++++++++++++++++++++++++++++++++++++--------- 14 files changed, 788 insertions(+), 211 deletions(-)
Author: David Luethi, Philipp Erb
Title: Fast Kalman Filter
Description: This is a flexible implementation of the Kalman filter. It
is entirely written in C and relies fully on linear algebra
subroutines contained in BLAS and LAPACK. Due to the speed of
the filter, the fitting of high-dimensional linear state space
models to large datasets becomes possible. This package also
contains a plot function for the visualization of the state
vector and graphical diagnostics of the residuals.
Diff between FKF versions 0.0.1 dated 2009-02-12 and 0.0.2 dated 2009-07-18
ChangeLog | 5 +++++ DESCRIPTION | 22 ++++++++++++++++------ Fixme | 2 +- NAMESPACE | 2 +- R/fkf.r | 9 +++++++-- man/fkf.Rd | 4 ++-- src/fkflib.c | 23 +++++++++++++++++------ 7 files changed, 49 insertions(+), 18 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.3 dated 2009-06-28 and 0.4-1 dated 2009-07-18
DESCRIPTION | 10 ++++----- NAMESPACE | 7 ++++-- R/DesignAccessors.r | 11 +++++++++- R/contr.FrF2.R |only R/export.design.R | 48 ++++++++++++++++++++++++++++++-------------- R/fac.design.R | 11 +++++++++- R/fix.R |only R/fix.default.R |only R/fix.design.R |only R/oa.design.R | 29 +++++++++++++++++++++----- R/sysdata.rda |binary inst/NEWS | 20 ++++++++++++++++++ man/arrays.Rd | 6 +++-- man/class-design.Rd | 55 +++++++++++++++++++++++++++++++++++++-------------- man/contr.FrF2.Rd |only man/export.design.Rd | 34 ++++++++++++++++++++----------- man/fac.design.Rd | 13 ++++++++++++ man/fix.design.Rd |only man/oa.design.Rd | 40 ++++++++++++++++++++++++++++--------- man/utitlities.Rd | 1 20 files changed, 217 insertions(+), 68 deletions(-)
Author: Simon Urbanek
Diff between Cairo versions 1.4-4 dated 2008-10-19 and 1.4-5 dated 2009-07-18
Title: R graphics device using cairo graphics library for creating
high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
PostScript) and display (X11 and Win32) output.
Description: This package provides a Cairo graphics device that can be
use to create high-quality vector (PDF, PostScript and SVG) and
bitmap output (PNG,JPEG,TIFF), and high-quality rendering in
displays (X11 and Win32). Since it uses the same back-end for
all output, copying across formats is WYSIWYG. Files are
created without the dependence on X11 or other external
programs. This device supports alpha channel (semi-transparent
drawing) and resulting images can contain transparent and
semi-transparent regions. It is ideal for use in server
environemnts (file output) and as a replacement for other
devices that don't have Cairo's capabilities such as alpha
support or anti-aliasing. Backends are modular such that any
subset of backends is supported.
DESCRIPTION | 27 ++++++++++++++++++++++-----
NEWS | 5 +++++
configure.win | 2 +-
src/cairobem.c | 2 +-
src/cairogd.h | 2 +-
5 files changed, 30 insertions(+), 8 deletions(-)
Author: Alessio Boattini and Federico C. F. Calboli; Vincente Canto
Cassola together with Martin Maechler authored the function
mtx.exp.
Title: Biodemography functions
Description: The Biodem package provides a number of functions for
Biodemographycal analysis.
Diff between Biodem versions 0.1 dated 2005-04-25 and 0.2 dated 2009-07-18
DESCRIPTION | 17 +++++++++++------ R/mal.phi.R | 1 + R/mtx.exp.R | 3 +++ R/rri.R | 3 --- R/sur.freq.R | 14 +++++++------- man/sur.freq.Rd | 4 ++-- 6 files changed, 24 insertions(+), 18 deletions(-)
Author: Thomas Kneib, Felix Heinzl, Andreas Brezger, Daniel Sabanes
Bove
Title: R Utilities Accompanying the Software Package BayesX
Description: This package provides functionality for exploring and
visualising estimation results obtained with the software
package BayesX for structured additive regression. It also
provides functions that allow to read, write and manipulate map
objects that are required in spatial analyses performed with
BayesX, a free software for estimating structured additive
regression models (http://www.stat.uni-muenchen.de/~bayesx).
Diff between BayesX versions 0.2 dated 2009-03-11 and 0.2-3 dated 2009-07-18
BayesX-0.2-3/BayesX/DESCRIPTION | 15 - BayesX-0.2-3/BayesX/R/bnd2gra.R | 132 ++++++++--- BayesX-0.2-3/BayesX/R/createxymap.R | 4 BayesX-0.2-3/BayesX/R/drawmap.R | 17 - BayesX-0.2-3/BayesX/R/extractSamples.R | 17 - BayesX-0.2-3/BayesX/R/get.centroids.R | 26 +- BayesX-0.2-3/BayesX/R/read.bnd.R | 152 +++++++++---- BayesX-0.2-3/BayesX/R/read.gra.R | 5 BayesX-0.2-3/BayesX/R/round.bnd.R | 14 - BayesX-0.2-3/BayesX/R/shp2bnd.R | 304 ++++++++++++++++---------- BayesX-0.2-3/BayesX/R/spAndBndConversion.R | 60 ++--- BayesX-0.2-3/BayesX/R/write.bnd.R | 73 ++++-- BayesX-0.2-3/BayesX/inst/ChangeLog |only BayesX-0.2-3/BayesX/man/BayesX-package.Rd | 2 BayesX-0.2-3/BayesX/man/drawmap.Rd | 9 BayesX-0.2-3/BayesX/man/extractSamples.Rd | 3 BayesX-0.2-3/BayesX/man/plotautocor.Rd | 3 BayesX-0.2-3/BayesX/man/plotnonp.Rd | 16 - BayesX-0.2-3/BayesX/man/plotsurf.Rd | 6 BayesX-0.2-3/BayesX/man/read.bnd.Rd | 4 BayesX-0.2-3/BayesX/man/shp2bnd.Rd | 7 BayesX-0.2-3/BayesX/man/spAndBndConversion.Rd | 16 + BayesX-0.2/BayesX/ChangeLog |only 23 files changed, 571 insertions(+), 314 deletions(-)
Author: Karel Van den Meersche
Diff between BCE versions 1.3 dated 2009-06-03 and 1.4 dated 2009-07-18
Title: Bayesian composition estimator: estimating sample (taxonomic)
composition from biomarker data
Description: Function to estimates taxonomic compositions from
biomarker data, using a Bayesian approach.
DESCRIPTION | 10 ++--
man/BCE.Rd | 126 ++++++++++++++++++++++++++++++++++-------------------
man/bceInput.Rd | 17 +++++--
man/bceOutput.rd | 15 ++++--
man/export.bce.Rd | 18 +++++--
man/pairs.bce.Rd | 30 +++++++++---
man/plot.bce.Rd | 12 +++--
man/rescaleRows.Rd | 19 +++++--
man/summary.bce.Rd | 64 ++++++++++++++++++--------
man/tlsce.Rd | 62 ++++++++++++++++++--------
10 files changed, 255 insertions(+), 118 deletions(-)
Author: Robin K. S. Hankin
Title: Bayesian Analysis of Computer Code Output (BACCO)
Description: The BACCO bundle of packages is replaced by the BACCO
package, which provides a vignette that illustrates the
constituent packages (emulator, approximator, calibrator) in
use.
Diff between BACCO versions 1.1-4 dated 2009-05-05 and 2.0 dated 2009-07-18
BACCO-1.1-4/BACCO/approximator |only BACCO-1.1-4/BACCO/calibrator |only BACCO-1.1-4/BACCO/emulator |only BACCO-2.0/BACCO/DESCRIPTION | 28 +++++++++++++++------------- BACCO-2.0/BACCO/inst |only BACCO-2.0/BACCO/man |only 6 files changed, 15 insertions(+), 13 deletions(-)
Author: James Honaker
Diff between Amelia versions 1.2-9 dated 2009-07-02 and 1.2-12 dated 2009-07-18
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 |only
DESCRIPTION | 8
NEWS |only
R/amcheck.r | 80 -
R/ameliagui.r | 14
R/emb.r | 4
README | 25
inst/doc/amelia.Rnw | 2
inst/doc/amelia.pdf | 2376 +++++++++++++++++++++++++--------------------------
inst/doc/copyRd.Rout | 2
inst/doc/index.shtml | 14
11 files changed, 1246 insertions(+), 1279 deletions(-)
Author: Roeland Kindt
Title: GUI for biodiversity and community ecology analysis
Description: This package provides a GUI (Graphical User Interface, via
the R-Commander) and some utility functions (often based on the
vegan package) for statistical analysis of biodiversity and
ecological communities, including species accumulation curves,
diversity indices, Renyi profiles, GLMs for analysis of species
abundance and presence-absence, distance matrices, Mantel
tests, and cluster, constrained and unconstrained ordination
analysis. A book on biodiversity and community ecology analysis
is available for free download from the website.
Diff between BiodiversityR versions 1.2 dated 2008-05-13 and 1.3 dated 2009-07-03
DESCRIPTION | 40 ++++++++++----- R/caprescale.R | 109 ++++++++++++++++++++++--------------------- R/diversityresult.R | 1 inst/etc/BiodiversityGUI.R | 80 +++++++++++++++---------------- man/BiodiversityR-package.Rd | 8 +-- man/BiodiversityRGUI.Rd | 2 man/caprescale.Rd | 11 ++-- man/diversityresult.Rd | 2 man/rankabundance.Rd | 2 9 files changed, 138 insertions(+), 117 deletions(-)
Author: Philippe Grosjean
Diff between tcltk2 versions 1.0-9 dated 2009-06-28 and 1.1-0 dated 2009-07-03
Title: Tcl/Tk Additions
Description: A series of additional Tcl commands and Tk widgets with
style and various functions (under Windows: DDE exchange,
access to the registry and icon manipulation) to supplement the
tcltk package.
tcltk2-1.0-9/tcltk2/R/zzz.R |only
tcltk2-1.0-9/tcltk2/inst/tklibs/balloon1.2 |only
tcltk2-1.0-9/tcltk2/inst/tklibs/bwidget1.7 |only
tcltk2-1.0-9/tcltk2/inst/tklibs/ctext3.1 |only
tcltk2-1.0-9/tcltk2/inst/tklibs/cursor0.1 |only
tcltk2-1.0-9/tcltk2/inst/tklibs/toolbar1.0 |only
tcltk2-1.1-0/tcltk2/DESCRIPTION | 16
tcltk2-1.1-0/tcltk2/NAMESPACE | 16
tcltk2-1.1-0/tcltk2/NEWS | 23 +
tcltk2-1.1-0/tcltk2/R/tclTask.R |only
tcltk2-1.1-0/tcltk2/R/tcltk2-Internal.R |only
tcltk2-1.1-0/tcltk2/R/tk2commands.R | 141 +------
tcltk2-1.1-0/tcltk2/R/tk2ico.R | 95 ++---
tcltk2-1.1-0/tcltk2/R/tk2tip.R | 9
tcltk2-1.1-0/tcltk2/R/tk2widgets.R | 329 ++++++------------
tcltk2-1.1-0/tcltk2/cleanup.win | 11
tcltk2-1.1-0/tcltk2/inst/tklibs/Diagrams0.2 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/autoscroll1.1 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/ctext3.2 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/cursor0.2 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/datefield0.2 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/getstring0.1 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/history0.1 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/ico1.0 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/ipentry0.3 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/khim1.0 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/ntext0.81 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/snit1.0 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/swaplist0.2 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/tablelist4.10 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/tooltip1.4 |only
tcltk2-1.1-0/tcltk2/inst/tklibs/widget3.0 |only
tcltk2-1.1-0/tcltk2/man/setLanguage.Rd | 6
tcltk2-1.1-0/tcltk2/man/tclTask.Rd |only
tcltk2-1.1-0/tcltk2/man/tk2commands.Rd | 46 --
tcltk2-1.1-0/tcltk2/man/tk2widgets.Rd | 68 +--
tcltk2-1.1-0/tcltk2/test.R |only
tcltk2-1.1-0/tcltk2/win/tklibs/winico0.6/pkgIndex.tcl | 3
38 files changed, 292 insertions(+), 471 deletions(-)
Author: S original by James J. Majure
Diff between sgeostat versions 1.0-21 dated 2007-04-11 and 1.0-22 dated 2009-07-03
Title: An Object-oriented Framework for Geostatistical Modeling in S+
Description: An Object-oriented Framework for Geostatistical Modeling
in S+
ChangeLog | 25 +++++++++++++++++--------
DESCRIPTION | 16 ++++++++++------
LICENSE |only
man/identify.point.Rd | 2 +-
man/plot.point.Rd | 3 ++-
man/plot.variogram.Rd | 2 +-
man/print.pair.Rd | 2 +-
man/print.point.Rd | 2 +-
8 files changed, 33 insertions(+), 19 deletions(-)
Author: Steven Kembel
Diff between picante versions 0.7-0 dated 2009-05-24 and 0.7-1 dated 2009-07-03
Title: R tools for integrating phylogenies and ecology
Description: Phylocom integration, community analyses, null-models,
traits and evolution in R
DESCRIPTION | 8 ++++----
R/phylodiversity.R | 34 ++++++++++++++++++++++++++++++++--
man/pd.Rd | 8 +++++---
man/picante-package.Rd | 4 ++--
man/ses.pd.Rd |only
man/utility.Rd | 5 ++++-
6 files changed, 47 insertions(+), 12 deletions(-)
Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas
Stabla
Title: Documentation for packages distr, distrEx, distrSim, distrTEst
Description: provides documentation in form of a common vignette to
packages distr, distrEx, distrMod, distrSim, distrTEst
Diff between distrDoc versions 2.1 dated 2009-04-15 and 2.1.1 dated 2009-07-03
DESCRIPTION | 8 inst/doc/Rplots.pdf | 3924 ++++----- inst/doc/distr.Rnw | 6 inst/doc/distr.pdf |21622 ++++++++++++++++++++++++++++++++++------------------ 4 files changed, 16438 insertions(+), 9122 deletions(-)
Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas
Stabla
Title: Object orientated implementation of distributions
Description: Object orientated implementation of distributions
Diff between distr versions 2.1.1 dated 2009-06-17 and 2.1.3 dated 2009-07-03
distr-2.1.1/distr/inst/doc/.build.timestamp |only distr-2.1.1/distr/inst/doc/newDistributions-AbscDist.eps |only distr-2.1.1/distr/inst/doc/newDistributions-AbscDist.pdf |only distr-2.1.1/distr/inst/doc/newDistributions-DiscrDist.eps |only distr-2.1.1/distr/inst/doc/newDistributions-DiscrDist.pdf |only distr-2.1.1/distr/inst/doc/newDistributions-exam1.eps |only distr-2.1.1/distr/inst/doc/newDistributions-exam1.pdf |only distr-2.1.1/distr/inst/doc/newDistributions.tex |only distr-2.1.3/distr/DESCRIPTION | 14 +- distr-2.1.3/distr/inst/doc/Rplots.pdf | 72 +++++++------- distr-2.1.3/distr/inst/doc/newDistributions.Rnw | 10 + distr-2.1.3/distr/inst/doc/newDistributions.pdf |binary 12 files changed, 51 insertions(+), 45 deletions(-)
Author: Valerie Obenchain
Title: Data retrieval from a Labkey database
Description: This package imports data from a labkey database into an R
data frame
Diff between Rlabkey versions 0.0.7 dated 2009-04-01 and 0.0.8 dated 2009-07-03
Rlabkey-0.0.7/Rlabkey/license |only Rlabkey-0.0.8/Rlabkey/DESCRIPTION | 10 - Rlabkey-0.0.8/Rlabkey/LICENSE |only Rlabkey-0.0.8/Rlabkey/NEWS | 5 Rlabkey-0.0.8/Rlabkey/R/labkey.executeSql.R | 120 +++++++++---------- Rlabkey-0.0.8/Rlabkey/R/labkey.selectRows.R | 156 ++++++++++++------------- Rlabkey-0.0.8/Rlabkey/R/makeFilter.R | 97 +++++++-------- Rlabkey-0.0.8/Rlabkey/man/Rlabkey-package.Rd | 4 Rlabkey-0.0.8/Rlabkey/man/labkey.executeSql.Rd | 16 +- Rlabkey-0.0.8/Rlabkey/man/makeFilter.Rd | 4 10 files changed, 209 insertions(+), 203 deletions(-)
Author: Douglas Bates and Ana Ines Vazquez
Title: Pedigree-based mixed-effects models
Description: Fit pedigree-based mixed-effects models.
Diff between pedigreemm versions 0.2-2 dated 2009-06-02 and 0.2-3 dated 2009-07-02
DESCRIPTION | 8 ++++---- R/pedigree.R | 15 +++++++++++++++ 2 files changed, 19 insertions(+), 4 deletions(-)
Author: Markus Loecher, Sense Networks
Diff between HTMLUtils versions 0.1.2 dated 2009-06-08 and 0.1.3 dated 2009-07-02
Title: Facilitates automated HTML report creation
Description: Facilitates automated HTML report creation, in particular
framed HTML pages and dynamically sortable tables.
DESCRIPTION | 8 ++++----
R/BasicHTML.R | 21 +++++++++++++++------
R/FramedHTML.R | 38 ++++++++++++++++++++++++++++++--------
R/myHTMLInitFile.R | 15 ++++++++++++++-
man/BasicHTML.Rd | 10 ++++++----
man/FramedHTML.Rd | 13 ++++++++-----
man/HTMLUtils-package.Rd | 4 ++--
man/InstallJSC.Rd | 2 +-
man/myHTMLInitFile.Rd | 3 ++-
9 files changed, 82 insertions(+), 32 deletions(-)
Author: Eva Herrmann
Diff between lokern versions 1.0-7 dated 2009-04-03 and 1.0-8 dated 2009-07-02
Title: Kernel Regression Smoothing with Local or Global Plug-in
Bandwidth
Description: Kernel regression smoothing with adaptive local or global
plug-in bandwidth selection.
ChangeLog | 14 ++
DESCRIPTION | 8 -
R/glkerns.R | 19 ++--
demo |only
man/glkerns.Rd | 2
src/glkerns.f | 15 ++-
tests/glk1.R | 11 ++
tests/glk1.Rout.save | 242 ++++++++++++++++++++++++++++++++++++++++++++++++++-
8 files changed, 293 insertions(+), 18 deletions(-)
Author: Delia Bailey
Diff between pcse versions 1.6 dated 2008-11-16 and 1.7 dated 2009-07-02
Title: Panel-Corrected Standard Error Estimation in R
Description: This package contains a function to estimate
panel-corrected standard errors. Data may contain balanced or
unbalanced panels.
DESCRIPTION | 15 ++++++++++-----
R/pcse.R | 27 +++++++++++++--------------
R/summary.pcse.R | 1 -
R/vcovPC.R |only
demo/pcse.R | 8 ++++++++
inst |only
man/pcse-package.Rd | 4 ++--
man/summary.pcse.Rd | 4 ++--
man/vcovPC.Rd |only
9 files changed, 35 insertions(+), 24 deletions(-)
Author: James Honaker
Diff between Amelia versions 1.2-2 dated 2009-04-27 and 1.2-9 dated 2009-07-02
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.
Amelia-1.2-2/Amelia/inst/doc/amelia.aux |only
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Amelia-1.2-9/Amelia/DESCRIPTION | 10
Amelia-1.2-9/Amelia/R/amcheck.r | 203
Amelia-1.2-9/Amelia/R/ameliagui.r | 14
Amelia-1.2-9/Amelia/R/diag.r | 4
Amelia-1.2-9/Amelia/R/emb.r | 99
Amelia-1.2-9/Amelia/R/missmap.R | 117
Amelia-1.2-9/Amelia/R/prep.r | 38
Amelia-1.2-9/Amelia/R/summary.amelia.R | 4
Amelia-1.2-9/Amelia/R/write.amelia.R | 1
Amelia-1.2-9/Amelia/data/freetrade.RData |only
Amelia-1.2-9/Amelia/inst/doc/Makefile | 27
Amelia-1.2-9/Amelia/inst/doc/amelia.Rnw |only
Amelia-1.2-9/Amelia/inst/doc/amelia.pdf |24997 ++++++++++++++++++++-----
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Amelia-1.2-9/Amelia/inst/doc/index.shtml | 4
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Amelia-1.2-9/Amelia/man/africa.Rd | 2
Amelia-1.2-9/Amelia/man/amelia.Rd | 14
Amelia-1.2-9/Amelia/man/compare.density.Rd | 2
Amelia-1.2-9/Amelia/man/freetrade.Rd |only
Amelia-1.2-9/Amelia/man/missmap.Rd | 11
72 files changed, 20915 insertions(+), 4632 deletions(-)
Author: Adrian Baddeley
Diff between spatstat versions 1.15-4 dated 2009-06-16 and 1.16-0 dated 2009-07-02
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point
Patterns, including multitype/marked points and spatial
covariates, in any two-dimensional spatial region. Contains
functions for plotting spatial data, exploratory data analysis,
model-fitting, simulation, spatial sampling, model diagnostics,
and formal inference. Data types include point patterns, line
segment patterns, spatial windows, and pixel images. Point
process models can be fitted to point pattern data. Cluster
type models are fitted by the method of minimum contrast. Very
general Gibbs point process models can be fitted to point
pattern data using a function ppm similar to lm or glm. Models
may include dependence on covariates, interpoint interaction
and dependence on marks. Fitted models can be simulated
automatically. Also provides facilities for formal inference
(such as chi-squared tests) and model diagnostics (including
simulation envelopes, residuals, residual plots and Q-Q plots).
.Rbuildindex.5904 |only
DESCRIPTION | 10
INDEX | 10
R/Fest.S | 186 ++++++++-----
R/Gest.S | 162 ++++++-----
R/Gmulti.S | 189 ++++++++-----
R/Iest.R | 66 ++--
R/Jest.S | 77 ++++-
R/Jmulti.S | 84 ++++--
R/Kinhom.S | 18 -
R/Kmeasure.R | 223 +++++++++++-----
R/Kmulti.inhom.R | 28 +-
R/alltypes.R | 6
R/blur.R | 4
R/deldir.R | 12
R/density.ppp.R | 43 ++-
R/distbdry.S | 16 -
R/envelope.R | 28 +-
R/fv.R | 47 ++-
R/images.R | 47 +++
R/iplot.R |only
R/istat.R |only
R/plot.fasp.R | 7
R/plot.fv.R | 24 +
R/plot.ppp.S | 75 ++---
R/ripras.S | 2
R/superimpose.R | 5
R/tess.R | 32 ++
R/wingeom.S | 47 +++
demo/spatstat.R | 14 -
inst/doc/shapefiles.pdf | 659 ++++++++++++++++++++++++------------------------
man/00spatstat.Rd | 22 +
man/AreaInter.Rd | 2
man/BadGey.Rd | 8
man/Fest.Rd | 33 +-
man/Gcross.Rd | 17 +
man/Gdot.Rd | 11
man/Gest.Rd | 38 +-
man/Gmulti.Rd | 13
man/Hest.Rd | 2
man/Iest.Rd | 8
man/Jcross.Rd | 12
man/Jdot.Rd | 14 -
man/Jest.Rd | 10
man/Jmulti.Rd | 13
man/Kcross.Rd | 2
man/Kcross.inhom.Rd | 11
man/Kdot.Rd | 2
man/Kdot.inhom.Rd | 8
man/Kest.fft.Rd | 2
man/Lcross.inhom.Rd |only
man/Ldot.inhom.Rd |only
man/LennardJones.Rd | 12
man/Lest.Rd | 1
man/Linhom.Rd | 5
man/MultiStrauss.Rd | 3
man/PairPiece.Rd | 4
man/SatPiece.Rd | 3
man/Strauss.Rd | 7
man/StraussHard.Rd | 5
man/adaptive.density.Rd | 2
man/alltypes.Rd | 64 ++--
man/convexhull.Rd |only
man/convexhull.xy.Rd | 1
man/internal.Rd | 18 +
man/iplot.Rd |only
man/is.convex.Rd |only
man/istat.Rd |only
man/localK.Rd | 2
man/markcorr.Rd | 4
man/plot.fasp.Rd | 6
man/plot.fv.Rd | 23 +
man/plot.ppp.Rd | 1
man/ppm.Rd | 8
man/qqplot.ppm.Rd | 6
tests/rmhBasic.R | 4
tests/rmhErrors.R | 2
tests/rmhMulti.R | 2
78 files changed, 1627 insertions(+), 905 deletions(-)
Author: Jose L. Izquierdo
Diff between Metabonomic versions 3.2 dated 2009-07-01 and 3.2.1 dated 2009-07-02
Title: GUI for Metabonomic Analysis
Description: Graphical User Interface for the Metabonomic Analysis
(Baseline, Normalization, Peak Detection, PCA, PLS, Nearest
Neigbourgt, Neural Network) developed to make easy this data
analysis.
Metabonomic-3.2.1/Metabonomic/DESCRIPTION | 14
Metabonomic-3.2.1/Metabonomic/R/Met.Aligm.R | 36 -
Metabonomic-3.2.1/Metabonomic/R/Met.Order.R | 32 -
Metabonomic-3.2.1/Metabonomic/R/Met.PCA.R | 421 +++++++++++++------
Metabonomic-3.2.1/Metabonomic/R/Met.PLS2.R | 10
Metabonomic-3.2.1/Metabonomic/R/Met.Selection.R | 34 -
Metabonomic-3.2.1/Metabonomic/R/Met.peak.detection.R | 9
Metabonomic-3.2.1/Metabonomic/R/Met.spectrum.2.R | 67 ---
Metabonomic-3.2.1/Metabonomic/R/Metabonomic.R | 2
Metabonomic-3.2.1/Metabonomic/R/TABLE.R | 28 -
Metabonomic-3.2.1/Metabonomic/R/showData2.R | 28 -
Metabonomic-3.2/Metabonomic/R/Met.Outliers.R |only
Metabonomic-3.2/Metabonomic/man/Met.Outliers.Rd |only
13 files changed, 354 insertions(+), 327 deletions(-)
Author: P. Neytchev, P. Filzmoser, R. Patnaik, A. Eisl and R. Boubela
Title: Trimmed Maximum Likelihood Estimation
Description: TLE implements a general framework for robust fitting of
finite mixture models. Parameter estimation is performed using
the EM algorithm.
Diff between tlemix versions 0.0.5 dated 2009-05-06 and 0.0.6 dated 2009-07-02
DESCRIPTION | 10 - inst/doc/tlemix-intro.pdf | 439 ++++++++++++++++++++++------------------------ 2 files changed, 219 insertions(+), 230 deletions(-)
Author: Peter Ruckdeschel
Title: Utilities for Sweave together with TeX listings package
Description: provides utilities for defining R / Rd as
Tex-package-listings "language" and including R / Rd source
file (sniplets) copied from R-forge in its most recent version
(or another url) thereby avoiding inconsistencies between
vignette and documented source code
Diff between SweaveListingUtils versions 0.2 dated 2009-04-15 and 0.3 dated 2009-07-02
DESCRIPTION | 15 ++-- R/SweaveListingOptions.R | 9 ++ R/SweaveListingUtils.R | 75 ++++++++++++++++++++++- R/keywordsStyle.R | 3 inst/MASKING | 15 +++- inst/NEWS | 24 +++++++ inst/TeX/Rdlisting.sty | 15 ++-- inst/doc/ExampleSweaveListingUtils.Rnw | 61 +++++++++++++++---- inst/doc/ExampleSweaveListingUtils.pdf |binary inst/doc/cleanup.tex |only inst/doc/preamble.tex | 2 inst/doc/preambleExp.tex | 104 +++++++++++++++++++++------------ man/0SweaveListingUtils-package.Rd | 7 +- man/SweaveListingOptions.Rd | 8 +- man/SweaveListingPreparations.Rd | 30 +++++++++ man/copySourceFromRForge.Rd | 6 - man/library.Rd | 8 ++ man/lstinputSourceFromRForge.Rd | 10 +-- man/readSourceFromRForge.Rd | 4 - 19 files changed, 306 insertions(+), 90 deletions(-)
More information about SweaveListingUtils at CRAN
Permanent link
Author: Derek Young Tatiana Benaglia Didier Chauveau Ryan Elmore Tom
Hettmansperger David Hunter Hoben Thomas Fengjuan Xuan
Title: Tools for analyzing finite mixture models
Description: A collection of R functions for analyzing finite mixture
models. This package is based upon work supported by the
National Science Foundation under Grant No. SES-0518772.
Diff between mixtools versions 0.4.0 dated 2009-04-28 and 0.4.1 dated 2009-07-02
DESCRIPTION | 9 +++--- R/normalmixEM.R | 65 ++++++++++++++++++++++++--------------------- R/parse.constraints.R |only R/tauequivnormalmixEM.R |only R/zzz.R | 1 man/normalmixEM.Rd | 20 +++++++++++++ man/tauequivnormalmixEM.Rd |only 7 files changed, 61 insertions(+), 34 deletions(-)
Author: G. Grothendieck
Title: Utilities for strings and function arguments.
Description: gsubfn is like gsub but can take a replacement function or
certain other objects instead of the replacement string.
Matches and back references are input to the replacement
function and replaced by the function output. gsubfn can be
used to split strings based on content rather than delimiters
and for quasi-perl-style string interpolation. The package also
has facilities for translating formulas to functions and
allowing such formulas in function calls instead of functions.
This can be used with R functions such as apply, sapply,
lapply, optim, integrate, xyplot, Filter and any other function
that expects another function as an input argument or functions
like cat or sql calls that may involve strings where
substitution is desirable.
Diff between gsubfn versions 0.3-8 dated 2008-12-15 and 0.5-0 dated 2009-07-02
DESCRIPTION | 48 +- R/fn.R | 13 R/gsubfn.R | 70 ++++ inst/NEWS | 9 inst/THANKS | 1 inst/doc/Rplots.pdf | 48 +- inst/doc/gsubfn.R | 2 inst/doc/gsubfn.Rnw | 10 inst/doc/gsubfn.pdf | 856 +++++++++++++++++++++++++++------------------------- man/fn.Rd | 1 man/gsubfn.Rd | 2 man/strapply.Rd | 41 ++ 12 files changed, 628 insertions(+), 473 deletions(-)
Author: Edzer J. Pebesma
Diff between gstat versions 0.9-60 dated 2009-05-15 and 0.9-61 dated 2009-07-02
Title: geostatistical modelling, prediction and simulation
Description: variogram modelling; simple, ordinary and universal point
or block (co)kriging, sequential Gaussian or indicator
(co)simulation; variogram and variogram map plotting utility
functions.
DESCRIPTION | 8
INDEX | 1
NAMESPACE | 1
R/krigeTg.R |only
R/predict.gstat.R | 5
inst/ChangeLog | 131
inst/doc/gstat.pdf |29029 ++++++++++++++++++++++++++---------------------------
man/krigeTg.Rd |only
man/pcb.Rd | 2
src/data.c | 10
src/lex.c | 109
src/lex.l | 3
src/random.c | 2
src/version.h | 6
14 files changed, 14536 insertions(+), 14771 deletions(-)
Author: Pierre Chausse
Diff between gmm versions 1.0-6 dated 2009-05-12 and 1.0-7 dated 2009-07-02
Title: Generalized Method of Moments and Generalized Empirical
Likelihood
Description: It is a complete suite to estimate models based on moment
conditions. It includes the two step Generalized method of
moments (GMM) of Hansen(1982), the iterated GMM and continuous
updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several
methods that belong to the Generalized Empirical Likelihood
(GEL) family of estimators, as presented by Smith(1997),
Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).
DESCRIPTION | 10
NEWS | 6
R/gmm_tools.R | 30 +
data/Finance.rda |binary
inst/doc/gmm_with_R.pdf | 800 ++++++++++++++++++++++++------------------------
inst/doc/gmm_with_R.rnw | 10
man/Finance.Rd | 72 +---
man/gmm.Rd | 81 ++--
man/kweights2.Rd |only
man/lintest.Rd | 2
man/rho.Rd | 19 -
11 files changed, 512 insertions(+), 518 deletions(-)
Author: Friedrich Leisch
Title: Flexible Cluster Algorithms
Description: The main function kcca implements a general framework for
k-centroids cluster analysis supporting arbitrary distance
measures and centroid computation. Further cluster methods
include hard competitive learning, neural gas, and QT
clustering. There are numerous visualization methods for
cluster results (neighborhood graphs, convex cluster hulls,
barcharts of centroids, ...), and bootstrap methods for the
analysis of cluster stability.
Diff between flexclust versions 1.2-0 dated 2009-06-19 and 1.2-1 dated 2009-07-02
DESCRIPTION | 8 +-- NEWS | 16 ++++++- R/AAA-classes.R | 9 ++++ R/bootstrap.R | 110 ++++++++++++++++++++++++++++++++++++++++++++++++--- R/utils.R | 6 -- man/bootFlexclust.Rd | 22 +++++++--- man/stepFlexclust.Rd | 4 + 7 files changed, 153 insertions(+), 22 deletions(-)
Author: Ingo Feinerer
Title: Text Mining Package
Description: A framework for text mining applications within R.
Diff between tm versions 0.3-4.1 dated 2009-05-04 and 0.4 dated 2009-07-01
tm-0.3-4.1/tm/R/plaintextdoc.R |only tm-0.3-4.1/tm/R/resolve.R |only tm-0.3-4.1/tm/R/sparse.R |only tm-0.3-4.1/tm/R/textdoccol.R |only tm-0.3-4.1/tm/man/TermDocMatrix.Rd |only tm-0.3-4.1/tm/man/TextDocCol-class.Rd |only tm-0.3-4.1/tm/man/TextDocCol.Rd |only tm-0.3-4.1/tm/man/appendMeta.Rd |only tm-0.3-4.1/tm/man/loadDoc.Rd |only tm-0.3-4.1/tm/man/removeMeta.Rd |only tm-0.3-4.1/tm/man/tmUpdate.Rd |only tm-0.4/tm/DESCRIPTION | 12 - tm-0.4/tm/NAMESPACE | 49 ++---- tm-0.4/tm/R/aobjects.R | 106 +++++-------- tm-0.4/tm/R/chunks.R | 2 tm-0.4/tm/R/corpus.R |only tm-0.4/tm/R/distmeasure.R | 1 tm-0.4/tm/R/doc.R |only tm-0.4/tm/R/filter.R | 26 --- tm-0.4/tm/R/matrix.R | 44 ++++- tm-0.4/tm/R/meta.R | 54 ++++-- tm-0.4/tm/R/reader.R | 205 ++++++++++++++------------ tm-0.4/tm/R/source.R | 69 +++----- tm-0.4/tm/R/stopwords.R | 18 +- tm-0.4/tm/R/textrepo.R | 15 - tm-0.4/tm/R/transform.R | 107 ++++++------- tm-0.4/tm/R/weight.R | 29 --- tm-0.4/tm/data/acq.rda |binary tm-0.4/tm/data/crude.rda |binary tm-0.4/tm/inst/CITATION | 6 tm-0.4/tm/inst/NEWS | 24 +++ tm-0.4/tm/inst/doc/extensions.Rnw | 2 tm-0.4/tm/inst/doc/extensions.pdf |binary tm-0.4/tm/inst/doc/tm.Rnw | 162 ++++++++++---------- tm-0.4/tm/inst/doc/tm.pdf |binary tm-0.4/tm/man/Corpus-class.Rd |only tm-0.4/tm/man/IN-methods.Rd | 3 tm-0.4/tm/man/NewsgroupDocument-class.Rd | 28 ++- tm-0.4/tm/man/PCorpus-class.Rd |only tm-0.4/tm/man/PCorpus.Rd |only tm-0.4/tm/man/PlainTextDocument-class.Rd | 22 ++ tm-0.4/tm/man/StructuredTextDocument-class.Rd | 22 ++ tm-0.4/tm/man/TextRepository-class.Rd | 4 tm-0.4/tm/man/VCorpus-class.Rd |only tm-0.4/tm/man/VCorpus.Rd |only tm-0.4/tm/man/XMLTextDocument-class.Rd | 22 ++ tm-0.4/tm/man/acq.Rd | 5 tm-0.4/tm/man/appendElem.Rd | 11 - tm-0.4/tm/man/asPlain.Rd | 2 tm-0.4/tm/man/convertReut21578XMLPlain.Rd | 7 tm-0.4/tm/man/crude.Rd | 5 tm-0.4/tm/man/inspect.Rd | 6 tm-0.4/tm/man/materialize.Rd | 1 tm-0.4/tm/man/matrix.Rd |only tm-0.4/tm/man/meta.Rd | 1 tm-0.4/tm/man/prescindMeta.Rd | 33 ++-- tm-0.4/tm/man/readDOC.Rd | 4 tm-0.4/tm/man/readGmane.Rd | 4 tm-0.4/tm/man/readHTML.Rd | 5 tm-0.4/tm/man/readNewsgroup.Rd | 5 tm-0.4/tm/man/readPDF.Rd | 8 - tm-0.4/tm/man/readPlain.Rd | 9 - tm-0.4/tm/man/readRCV1.Rd | 4 tm-0.4/tm/man/readReut21578XML.Rd | 9 - tm-0.4/tm/man/readTabular.Rd | 6 tm-0.4/tm/man/readXML.Rd | 10 - tm-0.4/tm/man/removeSignature.Rd | 2 tm-0.4/tm/man/sFilter.Rd | 5 tm-0.4/tm/man/stopwords.Rd | 6 tm-0.4/tm/man/subset-methods.Rd | 26 +-- tm-0.4/tm/man/tmMap-methods.Rd | 11 - tm-0.4/tm/man/weightBin.Rd | 5 tm-0.4/tm/man/weightTf.Rd | 4 tm-0.4/tm/man/weightTfIdf.Rd | 5 74 files changed, 632 insertions(+), 599 deletions(-)
Author: D.J.J. Walvoort, D.J. Brus, and J.J. de Gruijter
Title: Spatial Coverage Sampling
Description: Spatial coverage sampling and random sampling from compact
geographical strata created by k-means.
Diff between spcosa versions 0.1-3 dated 2009-05-17 and 0.1-4 dated 2009-07-01
spcosa-0.1-3/spcosa/tests/runTestSuite.Rout |only spcosa-0.1-4/spcosa/DESCRIPTION | 12 spcosa-0.1-4/spcosa/NEWS | 38 spcosa-0.1-4/spcosa/R/method_getCellSize-CompactStratification.R | 2 spcosa-0.1-4/spcosa/R/method_getNumberOfCells-CompactStratification.R | 2 spcosa-0.1-4/spcosa/R/method_setAs_CompactStratification-SpatialPixels.R | 2 spcosa-0.1-4/spcosa/R/method_setAs_CompactStratification-SpatialPixelsDataFrame.R | 8 spcosa-0.1-4/spcosa/R/method_spsample_CompactStratification-numeric-missing.R | 1 spcosa-0.1-4/spcosa/inst/doc/spcosa.pdf | 2077 ++++------ spcosa-0.1-4/spcosa/man/stratify-methods.Rd | 6 spcosa-0.1-4/spcosa/tests/unitTesting.html | 18 11 files changed, 1019 insertions(+), 1147 deletions(-)
Author: Kurt Hornik, David Meyer, Christian Buchta
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and
matrices, based on index arrays and simple triplet
representations, respectively.
Diff between slam versions 0.1 dated 2009-06-26 and 0.1-1 dated 2009-07-01
DESCRIPTION | 10 +++++----- NAMESPACE | 24 ++++++++++++++++++++++++ R/matrix.R | 12 ++++++++++++ R/stm.R |only man/crossprod.Rd |only man/sums.Rd |only src |only tests |only 8 files changed, 41 insertions(+), 5 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 2.0-3 dated 2009-04-28 and 2.0-4 dated 2009-07-01
DESCRIPTION | 10 R/readBins.R | 9 R/readPanels.R | 7 inst/abif/Prototype_PowerPlex_EP01_Bins.txt |only inst/abif/Prototype_PowerPlex_EP01_Pa.txt |only inst/doc/seqinr_2_0-3.pdf | 8400 ++++++++++++++-------------- inst/doc/src/appendix/releasenotes.rnw | 28 man/readBins.Rd | 8 man/readPanels.Rd | 7 9 files changed, 4268 insertions(+), 4201 deletions(-)
Author: Julien Barnier
Diff between rgrs versions 0.2-10 dated 2009-06-09 and 0.2-11 dated 2009-07-01
Title: Functions to make R usage in social sciences easier (in french)
Description: This package provides functions for beginners and social
sciences students or researchers. Currently it includes
functions for cross-tabulation, weighting, results export, and
maps plotting. The documentation and help pages are written in
french.
DESCRIPTION | 10 +++++-----
R/copie.default.R | 10 ++++++----
data/hdv2003.rda |binary
3 files changed, 11 insertions(+), 9 deletions(-)
Author: Kurt Hornik and David Meyer
Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate
functions, and fitters for consensus relations.
Diff between relations versions 0.5-1 dated 2009-02-20 and 0.5-2 dated 2009-07-01
relations-0.5-1/relations/R/sparse.R |only relations-0.5-2/relations/DESCRIPTION | 20 + relations-0.5-2/relations/NAMESPACE | 23 -- relations-0.5-2/relations/NEWS | 4 relations-0.5-2/relations/R/fitters.R | 6 relations-0.5-2/relations/R/mip.R | 44 ++-- relations-0.5-2/relations/R/relation.R | 5 relations-0.5-2/relations/inst/NEWS | 4 relations-0.5-2/relations/inst/doc/relations.pdf |binary relations-0.5-2/relations/inst/po/en@quot/LC_MESSAGES/R-relations.mo |binary relations-0.5-2/relations/po/R-en@quot.po | 105 ++++++---- relations-0.5-2/relations/po/R-relations.pot | 82 +++++-- 12 files changed, 178 insertions(+), 115 deletions(-)
Author: Karl W Broman
Diff between qtlbook versions 0.17-1 dated 2009-04-28 and 0.17-2 dated 2009-07-01
Title: Datasets for the R/qtl book
Description: Datasets for the book, A Guide to QTL Mapping with R/qtl
DESCRIPTION | 10 +++++-----
inst/CITATION |only
inst/STATUS.txt | 7 +++++++
man/ch3a.Rd | 5 +++++
man/ch3b.Rd | 5 +++++
man/ch3c.Rd | 5 +++++
6 files changed, 27 insertions(+), 5 deletions(-)
Author: Karl W Broman
Diff between qtl versions 1.11-12 dated 2009-03-29 and 1.12-26 dated 2009-07-01
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.
qtl-1.11-12/qtl/src/hmm_cc.c |only
qtl-1.11-12/qtl/src/hmm_cc.h |only
qtl-1.11-12/qtl/src/simulate_cc.c |only
qtl-1.11-12/qtl/src/simulate_cc.h |only
qtl-1.12-26/qtl/DESCRIPTION | 12
qtl-1.12-26/qtl/INDEX | 6
qtl-1.12-26/qtl/R/add.cim.covar.R | 13
qtl-1.12-26/qtl/R/add_threshold.R | 57 +++-
qtl-1.12-26/qtl/R/addqtl.R | 21 +
qtl-1.12-26/qtl/R/argmax.geno.R | 35 +-
qtl-1.12-26/qtl/R/arithscan.R | 31 +-
qtl-1.12-26/qtl/R/calc.genoprob.R | 59 +++-
qtl-1.12-26/qtl/R/calc.pairprob.R | 54 ++--
qtl-1.12-26/qtl/R/cim.R | 19 -
qtl-1.12-26/qtl/R/compareorder.R | 25 -
qtl-1.12-26/qtl/R/countXO.R | 49 ++-
qtl-1.12-26/qtl/R/discan.R | 13
qtl-1.12-26/qtl/R/effectplot.R | 13
qtl-1.12-26/qtl/R/effectscan.R | 13
qtl-1.12-26/qtl/R/errorlod.R | 21 -
qtl-1.12-26/qtl/R/est.map.R | 27 +-
qtl-1.12-26/qtl/R/est.rf.R | 31 +-
qtl-1.12-26/qtl/R/fitqtl.R | 16 -
qtl-1.12-26/qtl/R/fitstahl.R | 13
qtl-1.12-26/qtl/R/makeqtl.R | 13
qtl-1.12-26/qtl/R/map_construction.R | 13
qtl-1.12-26/qtl/R/plot.R | 27 +-
qtl-1.12-26/qtl/R/plot.scanone.R | 19 -
qtl-1.12-26/qtl/R/plot.scantwo.R | 22 -
qtl-1.12-26/qtl/R/plotModel.R | 13
qtl-1.12-26/qtl/R/plotperm.R | 13
qtl-1.12-26/qtl/R/qtlcart_io.R | 13
qtl-1.12-26/qtl/R/read.cross.R | 39 +-
qtl-1.12-26/qtl/R/read.cross.csv.R | 35 --
qtl-1.12-26/qtl/R/read.cross.csvs.R | 24 -
qtl-1.12-26/qtl/R/read.cross.gary.R | 13
qtl-1.12-26/qtl/R/read.cross.karl.R | 13
qtl-1.12-26/qtl/R/read.cross.mm.R | 13
qtl-1.12-26/qtl/R/read.cross.qtx.R | 13
qtl-1.12-26/qtl/R/readMWril.R |only
qtl-1.12-26/qtl/R/refineqtl.R | 13
qtl-1.12-26/qtl/R/replacemap.R | 20 -
qtl-1.12-26/qtl/R/ril48_reorg.R |only
qtl-1.12-26/qtl/R/ripple.R | 33 +-
qtl-1.12-26/qtl/R/scanone.R | 47 ++-
qtl-1.12-26/qtl/R/scanoneboot.R | 13
qtl-1.12-26/qtl/R/scanqtl.R | 13
qtl-1.12-26/qtl/R/scantwo.R | 74 +++--
qtl-1.12-26/qtl/R/sim.geno.R | 38 ++
qtl-1.12-26/qtl/R/sim_ril.R | 244 +++++++++++-------
qtl-1.12-26/qtl/R/simulate.R | 54 +++-
qtl-1.12-26/qtl/R/stepwiseqtl.R | 17 -
qtl-1.12-26/qtl/R/summary.cross.R | 60 ++--
qtl-1.12-26/qtl/R/summary.scanone.R | 47 ++-
qtl-1.12-26/qtl/R/summary.scantwo.R | 67 +++--
qtl-1.12-26/qtl/R/summary.scantwo.old.R | 13
qtl-1.12-26/qtl/R/tryallpositions.R | 27 +-
qtl-1.12-26/qtl/R/util.R | 301 +++++++++++++++++++++-
qtl-1.12-26/qtl/R/vbscan.R | 13
qtl-1.12-26/qtl/R/write.cross.R | 13
qtl-1.12-26/qtl/R/xchr.R | 13
qtl-1.12-26/qtl/R/zzz.R | 13
qtl-1.12-26/qtl/inst/BUGS.txt | 16 +
qtl-1.12-26/qtl/inst/CITATION |only
qtl-1.12-26/qtl/inst/LICENSE.txt | 10
qtl-1.12-26/qtl/inst/README.txt | 12
qtl-1.12-26/qtl/inst/STATUS.txt | 152 ++++++++++-
qtl-1.12-26/qtl/inst/TODO.txt | 32 +-
qtl-1.12-26/qtl/inst/docs/rqtltour.R | 2
qtl-1.12-26/qtl/inst/docs/rqtltour.pdf | 344 ++++++++++++--------------
qtl-1.12-26/qtl/inst/docs/rqtltour.tex | 6
qtl-1.12-26/qtl/man/add.threshold.Rd | 4
qtl-1.12-26/qtl/man/checkAlleles.Rd | 2
qtl-1.12-26/qtl/man/chrnames.Rd |only
qtl-1.12-26/qtl/man/clean.cross.Rd | 3
qtl-1.12-26/qtl/man/clean.scantwo.Rd | 13
qtl-1.12-26/qtl/man/compareorder.Rd | 2
qtl-1.12-26/qtl/man/findDupMarkers.Rd |only
qtl-1.12-26/qtl/man/geno.crosstab.Rd | 5
qtl-1.12-26/qtl/man/listeria.Rd | 2
qtl-1.12-26/qtl/man/max.scanone.Rd | 2
qtl-1.12-26/qtl/man/plot.rf.Rd | 5
qtl-1.12-26/qtl/man/plot.scanone.Rd | 2
qtl-1.12-26/qtl/man/qtl-internal.Rd | 30 +-
qtl-1.12-26/qtl/man/readMWril.Rd |only
qtl-1.12-26/qtl/man/ripple.Rd | 2
qtl-1.12-26/qtl/man/scanone.Rd | 7
qtl-1.12-26/qtl/man/scantwo.Rd | 14 -
qtl-1.12-26/qtl/man/sim.cross.Rd | 88 ++++++
qtl-1.12-26/qtl/man/simFounderSnps.Rd |only
qtl-1.12-26/qtl/man/subset.cross.Rd | 9
qtl-1.12-26/qtl/man/subset.map.Rd |only
qtl-1.12-26/qtl/man/summary.scanone.Rd | 6
qtl-1.12-26/qtl/man/summary.scantwo.Rd | 4
qtl-1.12-26/qtl/man/switch.order.Rd | 2
qtl-1.12-26/qtl/man/tryallpositions.Rd | 8
qtl-1.12-26/qtl/man/xaxisloc.scanone.Rd |only
qtl-1.12-26/qtl/src/countXO.c | 32 +-
qtl-1.12-26/qtl/src/countXO.h | 31 +-
qtl-1.12-26/qtl/src/discan.c | 13
qtl-1.12-26/qtl/src/discan.h | 13
qtl-1.12-26/qtl/src/discan_covar.c | 13
qtl-1.12-26/qtl/src/discan_covar.h | 13
qtl-1.12-26/qtl/src/effectscan.c | 13
qtl-1.12-26/qtl/src/effectscan.h | 13
qtl-1.12-26/qtl/src/findDupMarkers_notexact.c |only
qtl-1.12-26/qtl/src/findDupMarkers_notexact.h |only
qtl-1.12-26/qtl/src/fitqtl_hk.c | 13
qtl-1.12-26/qtl/src/fitqtl_hk.h | 13
qtl-1.12-26/qtl/src/fitqtl_imp.c | 13
qtl-1.12-26/qtl/src/fitqtl_imp.h | 13
qtl-1.12-26/qtl/src/forwsel.c | 13
qtl-1.12-26/qtl/src/forwsel.h | 13
qtl-1.12-26/qtl/src/hmm_4way.c | 23 -
qtl-1.12-26/qtl/src/hmm_4way.h | 13
qtl-1.12-26/qtl/src/hmm_bc.c | 19 -
qtl-1.12-26/qtl/src/hmm_bc.h | 13
qtl-1.12-26/qtl/src/hmm_bci.c | 13
qtl-1.12-26/qtl/src/hmm_bci.h | 13
qtl-1.12-26/qtl/src/hmm_f2.c | 23 -
qtl-1.12-26/qtl/src/hmm_f2.h | 15 -
qtl-1.12-26/qtl/src/hmm_f2i.c | 13
qtl-1.12-26/qtl/src/hmm_f2i.h | 13
qtl-1.12-26/qtl/src/hmm_main.c | 35 +-
qtl-1.12-26/qtl/src/hmm_main.h | 21 -
qtl-1.12-26/qtl/src/hmm_ri4self.c |only
qtl-1.12-26/qtl/src/hmm_ri4self.h |only
qtl-1.12-26/qtl/src/hmm_ri4sib.c |only
qtl-1.12-26/qtl/src/hmm_ri4sib.h |only
qtl-1.12-26/qtl/src/hmm_ri8self.c |only
qtl-1.12-26/qtl/src/hmm_ri8self.h |only
qtl-1.12-26/qtl/src/hmm_ri8sib.c |only
qtl-1.12-26/qtl/src/hmm_ri8sib.h |only
qtl-1.12-26/qtl/src/info.c | 13
qtl-1.12-26/qtl/src/info.h | 13
qtl-1.12-26/qtl/src/lapackutil.c | 13
qtl-1.12-26/qtl/src/lapackutil.h | 13
qtl-1.12-26/qtl/src/ril48_reorg.c |only
qtl-1.12-26/qtl/src/ril48_reorg.h |only
qtl-1.12-26/qtl/src/ripple.c | 75 ++++-
qtl-1.12-26/qtl/src/ripple.h | 46 ++-
qtl-1.12-26/qtl/src/scanone_ehk.c | 13
qtl-1.12-26/qtl/src/scanone_ehk.h | 13
qtl-1.12-26/qtl/src/scanone_em.c | 13
qtl-1.12-26/qtl/src/scanone_em.h | 13
qtl-1.12-26/qtl/src/scanone_em_covar.c | 13
qtl-1.12-26/qtl/src/scanone_em_covar.h | 13
qtl-1.12-26/qtl/src/scanone_hk.c | 13
qtl-1.12-26/qtl/src/scanone_hk.h | 13
qtl-1.12-26/qtl/src/scanone_imp.c | 13
qtl-1.12-26/qtl/src/scanone_imp.h | 13
qtl-1.12-26/qtl/src/scanone_mr.c | 13
qtl-1.12-26/qtl/src/scanone_mr.h | 13
qtl-1.12-26/qtl/src/scanone_np.c | 13
qtl-1.12-26/qtl/src/scanone_np.h | 13
qtl-1.12-26/qtl/src/scantwo_binary_em.c | 13
qtl-1.12-26/qtl/src/scantwo_binary_em.h | 13
qtl-1.12-26/qtl/src/scantwo_em.c | 13
qtl-1.12-26/qtl/src/scantwo_em.h | 13
qtl-1.12-26/qtl/src/scantwo_hk.c | 13
qtl-1.12-26/qtl/src/scantwo_hk.h | 13
qtl-1.12-26/qtl/src/scantwo_imp.c | 13
qtl-1.12-26/qtl/src/scantwo_imp.h | 13
qtl-1.12-26/qtl/src/scantwo_mr.c | 13
qtl-1.12-26/qtl/src/scantwo_mr.h | 13
qtl-1.12-26/qtl/src/simulate.c | 13
qtl-1.12-26/qtl/src/simulate.h | 13
qtl-1.12-26/qtl/src/simulate_ril.c |only
qtl-1.12-26/qtl/src/simulate_ril.h |only
qtl-1.12-26/qtl/src/stahl_mf.c | 13
qtl-1.12-26/qtl/src/stahl_mf.h | 13
qtl-1.12-26/qtl/src/summary_scantwo.c | 13
qtl-1.12-26/qtl/src/summary_scantwo.h | 13
qtl-1.12-26/qtl/src/util.c | 75 ++++-
qtl-1.12-26/qtl/src/util.h | 45 ++-
qtl-1.12-26/qtl/src/vbscan.c | 13
qtl-1.12-26/qtl/src/vbscan.h | 13
qtl-1.12-26/qtl/tests/test_io.R | 13
qtl-1.12-26/qtl/tests/test_io.Rout.save | 29 +-
179 files changed, 2449 insertions(+), 1463 deletions(-)
Author: William Revelle
Diff between psych versions 1.0-74 dated 2009-06-26 and 1.0-75 dated 2009-07-01
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A number of routines for personality, psychometrics and
experimental psychology. Functions are primarily for scale
construction using factor analysis, cluster analysis and
reliability analysis, although others provide basic descriptive
statistics. Functions for simulating particular item and test
structures are included. Several functions serve as a useful
front end for structural equation modeling. For more
information, see the personality-project.org/r webpage.
CHANGES | 6
DESCRIPTION | 8
R/fa.R | 1
R/omega.R | 2
R/principal.R | 2
R/print.psych.fa.R | 6
R/smc.R | 2
data/Harman.rda |only
inst/NEWS | 5
inst/doc/all.bib | 584 +-
inst/doc/overview.Rnw | 45
inst/doc/overview.pdf | 9090 ++++++++++++++++++++--------------------
inst/doc/psych_for_sem.Rnw | 29
inst/doc/psych_for_sem.pdf | 9988 ++++++++++++++++++++++-----------------------
man/00.psych-package.Rd | 12
man/Harman.Rd |only
man/ICLUST.Rd | 1
man/ICLUST.graph.Rd | 1
man/ICLUST.sort.Rd | 1
man/SD.Rd | 1
man/VSS.parallel.Rd | 1
man/VSS.plot.Rd | 1
man/VSS.scree.Rd | 6
man/bifactor.Rd | 1
man/circ.tests.Rd | 2
man/cluster.cor.Rd | 2
man/cluster.fit.Rd | 1
man/cluster.loadings.Rd | 1
man/count.pairwise.Rd | 1
man/describe.Rd | 1
man/describe.by.Rd | 1
man/eigen.loadings.Rd | 1
man/ellipses.Rd | 1
man/error.bars.Rd | 1
man/error.crosses.Rd | 1
man/fa.Rd | 2
man/fa.graph.Rd | 1
man/fa.parallel.Rd | 1
man/factor.congruence.Rd | 1
man/factor.fit.Rd | 1
man/factor.model.Rd | 1
man/factor.residuals.Rd | 1
man/factor.rotate.Rd | 1
man/factor2cluster.Rd | 1
man/geometric.mean.Rd | 1
man/harmonic.mean.Rd | 1
man/irt.item.diff.rasch.Rd | 1
man/irt.person.rasch.Rd | 1
man/mat.regress.Rd | 1
man/matrix.addition.Rd | 1
man/multi.hist.Rd | 1
man/omega.Rd | 3
man/omega.graph.Rd | 1
man/p.rep.Rd | 1
man/pairs.panels.Rd | 1
man/phi.demo.Rd | 1
man/phi2poly.Rd | 1
man/polar.Rd | 1
man/poly.mat.Rd | 5
man/polychor.matrix.Rd | 1
man/principal.Rd | 2
man/r.test.Rd | 1
man/read.clipboard.Rd | 1
man/schmid.Rd | 1
man/score.alpha.Rd | 1
man/score.items.Rd | 1
man/sim.VSS.Rd | 1
man/sim.congeneric.Rd | 1
man/sim.hierarchical.Rd | 1
man/sim.item.Rd | 1
man/simulation.circ.Rd | 1
man/table2matrix.Rd | 1
man/test.psych.Rd | 1
man/thurstone.Rd | 6
74 files changed, 10199 insertions(+), 9659 deletions(-)
Author: Karl W Broman
Diff between negenes versions 0.98-7 dated 2007-10-09 and 0.98-8 dated 2009-07-01
Title: Estimating the number of essential genes in a genome
Description: Estimating the number of essential genes in a genome on
the basis of data from a random transposon mutagenesis
experiment, through the use of a Gibbs sampler.
DESCRIPTION | 14 +++++++++-----
inst/CITATION |only
inst/STATUS.txt | 5 +++++
3 files changed, 14 insertions(+), 5 deletions(-)
Author: Chris Fraley and Adrian Raftery
Title: Model-Based Clustering / Normal Mixture Modeling
Description: Model-based clustering and normal mixture modeling
including Bayesian regularization
Diff between mclust versions 3.2.1 dated 2009-06-19 and 3.3.1 dated 2009-07-01
mclust-3.2.1/mclust/README |only mclust-3.3.1/mclust/CHANGELOG | 23 ++ mclust-3.3.1/mclust/DESCRIPTION | 6 mclust-3.3.1/mclust/R/mclust.R | 262 +++++++++++++++++++++--------- mclust-3.3.1/mclust/core |only mclust-3.3.1/mclust/man/Mclust.Rd | 14 + mclust-3.3.1/mclust/man/decomp2sigma.Rd | 6 mclust-3.3.1/mclust/man/defaultPrior.Rd | 12 - mclust-3.3.1/mclust/man/em.Rd | 12 - mclust-3.3.1/mclust/man/emE.Rd | 12 - mclust-3.3.1/mclust/man/mclustBIC.Rd | 17 + mclust-3.3.1/mclust/man/mclustVariance.Rd | 7 mclust-3.3.1/mclust/man/me.Rd | 17 + mclust-3.3.1/mclust/man/meE.Rd | 17 + mclust-3.3.1/mclust/man/priorControl.Rd | 12 - mclust-3.3.1/mclust/man/sigma2decomp.Rd | 8 mclust-3.3.1/mclust/man/unmap.Rd | 9 - 17 files changed, 307 insertions(+), 127 deletions(-)
Author: Toni Giorgino
Diff between dtw versions 1.12-5 dated 2009-01-07 and 1.13-1 dated 2009-07-01
Title: Dynamic Time Warping algorithms
Description: Comprehensive implementation of Dynamic Time Warping
algorithms in R. DTW finds the optimal (least cumulative
distance) mapping between two time series. All common DTW
variants are covered, including local and global constraints,
arbitrary timeseries lenghts, distance definitions, MVM, etc.
Package computes cumulative distance, warping functions, plots,
normalizations, etc.
DESCRIPTION | 25 +++++++++++++----------
NAMESPACE |only
R/dtw.R | 13 +++++++++++-
R/globalCostMatrix.R | 4 +--
R/plot.dtw.R | 7 +++---
R/window.R | 6 +----
R/zzz.R | 16 +++++----------
inst/ChangeLog | 6 +++++
inst/TODO | 46 ++++++++++----------------------------------
inst/dtw.bib | 49 +++++++++++++++++++++++++++++++++++++++++++++++
man/dtw-package.Rd | 8 +++----
man/dtw.Rd | 2 +
man/dtwPlot.Rd | 13 +++++++-----
man/stepPattern.Rd | 6 ++---
tests/dtw_test.R | 21 ++++++++++++++++----
tests/dtw_test.Rout.save | 25 ++++++++++++++++++-----
16 files changed, 159 insertions(+), 88 deletions(-)
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification
and regression models
Diff between caret versions 4.18 dated 2009-06-18 and 4.19 dated 2009-07-01
DESCRIPTION | 8 R/createModel.R | 185 +++++++++- R/misc.R | 2 R/predict.train.R | 2 R/predictionFunction.R | 1 R/train.default.R | 25 - inst/CHANGES | 11 inst/doc/caretMisc.pdf | 782 ++++++++++++++++++++++---------------------- inst/doc/caretSelection.pdf | 637 +++++++++++++++++------------------ inst/doc/caretTrain.pdf |binary inst/doc/caretVarImp.pdf |binary man/train.Rd | 4 12 files changed, 911 insertions(+), 746 deletions(-)
Author: Tomas William Fitzgerald
Title: Robust spline interpolation for dual color array comparative
genomic hybridisation data
Description: Spline fitting and interpolation
Diff between aCGH.Spline versions 1.0 dated 2009-06-24 and 2.1 dated 2009-07-01
DESCRIPTION | 10 +++++----- R/GenomePlot.R | 1 + R/Jspline.R | 7 ++++--- R/SetJ.R | 1 + R/WriteGFF.R | 2 +- R/fe.write.R | 3 ++- 6 files changed, 14 insertions(+), 10 deletions(-)
Author: Adrian Dusa
Diff between QCA versions 0.5-3 dated 2009-03-28 and 0.5-4 dated 2009-07-01
Title: Qualitative Comparative Analysis
Description: Performs the Quine-McCluskey algorithm for Qualitative
Comparative Analysis, as described in Ragin, Charles C. 1987
"The Comparative Method. Moving beyond qualitative and
quantitative strategies", Berkeley: University of California
Press. In the classical approach it currently handles about 15
conditions and one outcome, but since version 0.4-5 the package
has an enhanced, faster function that obtains the same exact
solutions with a substantially lower memory consumption, and it
handles even more causal conditions. The next versions of this
algorithm will be oriented towards multi-value and fuzzy-set
functions. Also, in the near future the current functions will
deal with missing values in the data
DESCRIPTION | 10 +++++-----
R/eqmcc.R | 18 +++++++++---------
R/qmcc.R | 23 ++++++++++++-----------
R/verifyQCA.R | 2 +-
R/writePrimeimp.R | 6 +++---
inst/CHANGES | 6 +++++-
man/QCA.package.Rd | 4 ++--
7 files changed, 37 insertions(+), 32 deletions(-)
Author: Martin Schlather
Diff between RandomFields versions 1.3.39 dated 2009-06-29 and 1.3.40 dated 2009-07-01
Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging
DESCRIPTION | 6 +++---
src/auxiliary.cc | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
Author: Kurt Hornik, with contributions from Christian Buchta, Torsten
Hothorn, Alexandros Karatzoglou, David Meyer, and Achim Zeileis
Title: R/Weka interface
Description: An R interface to Weka (Version 3.6.1). Weka is a
collection of machine learning algorithms for data mining tasks
written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Both the R interface and Weka itself are
contained in the RWeka package. For more information on Weka
see http://www.cs.waikato.ac.nz/~ml/weka/.
Diff between RWeka versions 0.3-19 dated 2009-06-09 and 0.3-20 dated 2009-07-01
CHANGELOG | 6 +++++- DESCRIPTION | 10 +++++----- R/classifiers.R | 20 +++++++++++++------- R/onLoad.R | 10 ++-------- R/readers.R | 38 +++++++++++++++++++------------------- inst/java/RWeka.jar |binary inst/java/weka.jar |binary java/Makefile | 20 ++++++++++++++++++++ 8 files changed, 64 insertions(+), 40 deletions(-)
Author: Jose L. Izquierdo
Diff between Metabonomic versions 3.1.3.3 dated 2009-05-12 and 3.2 dated 2009-07-01
Title: GUI for Metabonomic Analysis
Description: Graphical User Interface for the Metabonomic Analysis
(Baseline, Normalization, Peak Detection, PCA, PLS, Nearest
Neigbourgt, Neural Network) developed to make easy this data
analysis.
Metabonomic-3.1.3.3/Metabonomic/R/Met.Baseline.R |only
Metabonomic-3.1.3.3/Metabonomic/R/Met.LDA.multi.R |only
Metabonomic-3.1.3.3/Metabonomic/R/Met.LDA.multi2.R |only
Metabonomic-3.1.3.3/Metabonomic/R/Met.PLS2.multi.R |only
Metabonomic-3.1.3.3/Metabonomic/R/Met.PLS2.multi2.R |only
Metabonomic-3.1.3.3/Metabonomic/R/Met.PLS3D.R |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.Baseline.Rd |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.LDA.multi.Rd |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.LDA.multi2.Rd |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.PLS2.multi.Rd |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.PLS2.multi2.Rd |only
Metabonomic-3.1.3.3/Metabonomic/man/Met.PLS3D.Rd |only
Metabonomic-3.2/Metabonomic/DESCRIPTION | 10
Metabonomic-3.2/Metabonomic/R/Import.data.R | 36
Metabonomic-3.2/Metabonomic/R/Met.KNN.R | 168 -
Metabonomic-3.2/Metabonomic/R/Met.LDA.R | 611 ++--
Metabonomic-3.2/Metabonomic/R/Met.Load.Data.R | 2
Metabonomic-3.2/Metabonomic/R/Met.NN1.R | 165 -
Metabonomic-3.2/Metabonomic/R/Met.NN2.R | 239 -
Metabonomic-3.2/Metabonomic/R/Met.PLS1.R | 109
Metabonomic-3.2/Metabonomic/R/Met.PLS2.R | 2223 ++++-------------
Metabonomic-3.2/Metabonomic/R/Met.Selection.R | 319 --
Metabonomic-3.2/Metabonomic/R/Phase.correction.R | 376 +-
Metabonomic-3.2/Metabonomic/inst |only
24 files changed, 1435 insertions(+), 2823 deletions(-)
Author: Andrew D. Martin
Diff between MCMCpack versions 0.9-6 dated 2009-02-17 and 1.0-1 dated 2009-07-01
Title: Markov chain Monte Carlo (MCMC) Package
Description: This package contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.2. All
models return coda mcmc objects that can then be summarized
using the coda package. MCMCpack also contains some useful
utility functions, including some additional density functions
and pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization.
DESCRIPTION | 32 +++++++++++++++++---------------
HISTORY | 1 +
NAMESPACE | 1 +
R/MCMCdynamicIRT1d-b.R |only
R/MCMCdynamicIRT1d.R |only
data/Rehnquist.rda |only
man/MCMCdynamicIRT1d.Rd |only
man/MCMCirtKd.Rd | 2 +-
man/Rehnquist.Rd |only
src/MCMCdynamicIRT1d-b.cc |only
src/MCMCdynamicIRT1d.cc |only
11 files changed, 20 insertions(+), 16 deletions(-)
Author: Klaus Nordhausen, Jean-Francois Cardoso, Hannu Oja, Esa Ollila
Title: JADE and ICA performance criteria
Description: The package ports JF Cardoso's JADE algorithm as well as
his function for joint diagonalization. There are also several
criteria for performance evaluation of ICA algorithms.
Diff between JADE versions 1.0-2 dated 2009-04-22 and 1.0-3 dated 2009-07-01
DESCRIPTION | 8 ++++---- R/JADE.R | 10 ++++++++-- inst/CHANGES | 5 +++++ man/ComonGAP.Rd | 2 +- man/JADE-package.Rd | 4 ++-- man/JADE.Rd | 14 ++++++++++++++ man/rjd.Rd | 3 ++- 7 files changed, 36 insertions(+), 10 deletions(-)
Author: Hadley Wickham
Diff between DescribeDisplay versions 0.2.0 dated 2009-05-15 and 0.2.1 dated 2009-07-01
More information about DescribeDisplay at CRAN
Title: R interface to DescribeDisplay (GGobi plugin)
Description: Produce publication quality graphics from output of
GGobi's describe display plugin
DESCRIPTION | 6 +++---
NAMESPACE |only
R/data.r | 16 +++++++++++-----
R/ggplot-barchart.r | 12 +++++++-----
R/ggplot-parcoords.r | 3 +++
R/ggplot-scatmat.r | 1 +
R/ggplot-timeseries.r | 6 +++++-
R/ggplot.r | 5 ++++-
man/addbrush.Rd | 4 +---
man/ddpanelGrob.Rd | 4 +---
man/ggplot.ddplot.Rd | 3 +--
man/ggplot.parcoords.Rd | 3 +--
man/plot.dd.Rd | 3 +--
man/plot.ddplot.Rd | 4 +---
14 files changed, 40 insertions(+), 30 deletions(-)
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