Author: Nicholas J. Lewin-Koh and Roger Bivand, contributions by Edzer
J. Pebesma, Eric Archer, Adrian Baddeley, Hans-Jörg Bibiko,
Stéphane Dray, David Forrest, Patrick Giraudoux, Duncan
Golicher, Virgilio Gómez Rubio, Patrick Hausmann, Thomas
Jagger, Sebastian P. Luque, Don MacQueen, Andrew Niccolai and
Tom Short
Title: Tools for reading and handling spatial objects
Description: Set of tools for manipulating and reading geographic data,
in particular ESRI shapefiles; C code used from shapelib. It
includes binary access to GSHHS shoreline files. The package
also provides interface wrappers for exchanging spatial objects
with packages such as PBSmapping, spatstat, maps, RArcInfo,
Stata tmap, WinBUGS, Mondrian, and others.
Diff between maptools versions 0.7-20 dated 2009-02-18 and 0.7-21 dated 2009-03-29
ChangeLog | 24 ++++++++++++++++++++++-- DESCRIPTION | 22 +++++++++++++++++----- LICENSE | 16 ++++++++++------ R/SpatialLines-methods.R | 2 +- R/SpatialPolys-methods.R | 2 +- R/readSplus.R | 8 ++++++++ inst/ChangeLog | 24 ++++++++++++++++++++++-- inst/LICENSE | 6 +----- 8 files changed, 82 insertions(+), 22 deletions(-)
Author: Uwe Ligges
Diff between tuneR versions 0.2-8 dated 2009-01-09 and 0.2-10 dated 2009-03-29
Title: Analysis of music
Description: Collection of tools to analyze music, handling wave files,
transcription, ...
DESCRIPTION | 27 ++++++++++++++++-----------
inst |only
man/MFCC.Rd | 2 +-
man/MonoStereo.Rd | 2 +-
man/WavPlayer.Rd | 2 +-
man/Wave-class.Rd |only
man/Wave.Rd | 28 ++++++----------------------
man/WaveArith.Rd | 2 +-
man/WaveIO.Rd | 2 +-
man/Waveforms.Rd | 2 +-
man/Wspec.Rd | 2 +-
man/bind.Rd | 2 +-
man/channel.Rd | 2 +-
man/downsample.Rd | 2 +-
man/equalWave.Rd | 2 +-
man/extractWave.Rd | 2 +-
man/noSilence.Rd | 2 +-
man/normalize.Rd | 2 +-
man/panorama.Rd | 2 +-
man/periodogram.Rd | 2 +-
man/play.Rd | 2 +-
man/plot-Wave.Rd | 2 +-
man/prepComb.Rd | 2 +-
man/show.Rd | 2 +-
man/summary.Rd | 2 +-
25 files changed, 43 insertions(+), 54 deletions(-)
Author: Karl W Broman
Diff between qtl versions 1.10-27 dated 2009-01-11 and 1.11-12 dated 2009-03-29
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.
.gitignore |only
DESCRIPTION | 18 +-
R/add.cim.covar.R | 14 +
R/add_threshold.R | 14 +
R/addqtl.R | 22 ++
R/argmax.geno.R | 14 +
R/arithscan.R | 14 +
R/calc.genoprob.R | 14 +
R/calc.pairprob.R | 14 +
R/cim.R | 14 +
R/compareorder.R | 14 +
R/countXO.R | 14 +
R/discan.R | 14 +
R/effectplot.R | 90 +++++++++--
R/effectscan.R | 14 +
R/errorlod.R | 14 +
R/est.map.R | 14 +
R/est.rf.R | 14 +
R/fitqtl.R | 20 ++
R/fitstahl.R | 14 +
R/makeqtl.R | 66 +++++---
R/map_construction.R | 14 +
R/plot.R | 120 +++++++++++----
R/plot.scanone.R | 14 +
R/plot.scantwo.R | 14 +
R/plotModel.R | 14 +
R/plotperm.R | 14 +
R/qtlcart_io.R | 14 +
R/read.cross.R | 14 +
R/read.cross.csv.R | 14 +
R/read.cross.csvs.R | 14 +
R/read.cross.gary.R | 14 +
R/read.cross.karl.R | 14 +
R/read.cross.mm.R | 14 +
R/read.cross.qtx.R | 14 +
R/refineqtl.R | 14 +
R/replacemap.R | 14 +
R/ripple.R | 14 +
R/scanone.R | 14 +
R/scanoneboot.R | 14 +
R/scanqtl.R | 14 +
R/scantwo.R | 14 +
R/sim.geno.R | 14 +
R/sim_ril.R | 14 +
R/simulate.R | 14 +
R/stepwiseqtl.R | 14 +
R/summary.cross.R | 14 +
R/summary.scanone.R | 14 +
R/summary.scantwo.R | 14 +
R/summary.scantwo.old.R | 14 +
R/tryallpositions.R | 14 +
R/util.R | 128 +++++++++++++++-
R/vbscan.R | 14 +
R/write.cross.R | 24 ++-
R/xchr.R | 14 +
R/zzz.R | 14 +
contrib |only
inst/LICENSE.txt | 384 +-----------------------------------------------
inst/README.txt | 12 -
inst/STATUS.txt | 71 ++++++++
inst/TODO.txt | 9 +
inst/docs/rqtltour.R | 4
inst/docs/rqtltour.pdf |binary
inst/docs/rqtltour.tex | 4
man/effectplot.Rd | 9 +
man/qtl-internal.Rd | 4
man/replaceqtl.Rd | 10 -
src/countXO.c | 13 +
src/countXO.h | 13 +
src/discan.c | 13 +
src/discan.h | 13 +
src/discan_covar.c | 13 +
src/discan_covar.h | 13 +
src/effectscan.c | 13 +
src/effectscan.h | 13 +
src/fitqtl_hk.c | 13 +
src/fitqtl_hk.h | 13 +
src/fitqtl_imp.c | 13 +
src/fitqtl_imp.h | 13 +
src/forwsel.c | 13 +
src/forwsel.h | 13 +
src/hmm_4way.c | 13 +
src/hmm_4way.h | 13 +
src/hmm_bc.c | 13 +
src/hmm_bc.h | 13 +
src/hmm_bci.c | 13 +
src/hmm_bci.h | 13 +
src/hmm_cc.c | 13 +
src/hmm_cc.h | 13 +
src/hmm_f2.c | 13 +
src/hmm_f2.h | 13 +
src/hmm_f2i.c | 13 +
src/hmm_f2i.h | 13 +
src/hmm_main.c | 13 +
src/hmm_main.h | 13 +
src/info.c | 13 +
src/info.h | 13 +
src/lapackutil.c | 13 +
src/lapackutil.h | 13 +
src/ripple.c | 13 +
src/ripple.h | 13 +
src/scanone_ehk.c | 13 +
src/scanone_ehk.h | 13 +
src/scanone_em.c | 13 +
src/scanone_em.h | 13 +
src/scanone_em_covar.c | 13 +
src/scanone_em_covar.h | 13 +
src/scanone_hk.c | 13 +
src/scanone_hk.h | 13 +
src/scanone_imp.c | 13 +
src/scanone_imp.h | 13 +
src/scanone_mr.c | 13 +
src/scanone_mr.h | 13 +
src/scanone_np.c | 13 +
src/scanone_np.h | 13 +
src/scantwo_binary_em.c | 13 +
src/scantwo_binary_em.h | 13 +
src/scantwo_em.c | 13 +
src/scantwo_em.h | 13 +
src/scantwo_hk.c | 13 +
src/scantwo_hk.h | 13 +
src/scantwo_imp.c | 13 +
src/scantwo_imp.h | 13 +
src/scantwo_mr.c | 13 +
src/scantwo_mr.h | 13 +
src/simulate.c | 13 +
src/simulate.h | 13 +
src/simulate_cc.c | 13 +
src/simulate_cc.h | 13 +
src/stahl_mf.c | 13 +
src/stahl_mf.h | 13 +
src/summary_scantwo.c | 13 +
src/summary_scantwo.h | 13 +
src/util.c | 13 +
src/util.h | 13 +
src/vbscan.c | 13 +
src/vbscan.h | 13 +
tests/test_io.R | 14 +
tests/test_io.Rout.save | 14 +
139 files changed, 1983 insertions(+), 608 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 ad advanced plots)
are also included.
Diff between bnlearn versions 1.2 dated 2009-02-05 and 1.3 dated 2009-03-29
Changelog | 10 + DESCRIPTION | 35 +++--- NAMESPACE | 3 R/arc.operations.R | 2 R/arc.strength.R | 76 +++++++++++++ R/backend-indep.R | 125 +++------------------- R/fast-iamb.R | 24 ++-- R/frontend-amat.R | 2 R/frontend-learning.R | 4 R/frontend-plot.R | 25 ++++ R/frontend-score.R | 14 +- R/frontend-simulation.R | 6 - R/globals.R | 11 + R/graph-generation.R | 238 +++++-------------------------------------- R/graphviz.R | 24 ++-- R/grow-shrink.R | 24 ++-- R/hill-climbing.R | 6 - R/incremental-association.R | 24 ++-- R/inter-iamb.R | 24 ++-- R/learning-algorithms.R | 28 ++--- R/maxmin-pc.R | 38 +++--- R/simulation.R | 14 +- R/test.R | 225 +++++++++++++++++++++++++++++++--------- R/utils-amat.R | 16 -- R/utils-graph.R | 2 R/utils-misc.R | 20 --- R/utils-sanitization.R | 46 +++++++- R/utils-tests.R | 11 - man/00.bnlearn-package.Rd | 62 +++++++---- man/10.gs.Rd | 22 +-- man/11.iamb.Rd | 18 +-- man/12.fast.iamb.Rd | 18 +-- man/13.inter.iamb.Rd | 18 +-- man/14.mmpc.Rd | 29 +---- man/15.hc.Rd | 10 - man/20.mb.Rd | 3 man/22.modelstring.Rd | 48 ++++---- man/24.graphgen.Rd | 53 ++++----- man/30.score.Rd | 26 +--- man/31.ci.test.Rd | 15 -- man/32.choose.direction.Rd | 3 man/40.rbn.Rd | 3 man/51.graphviz.plot.Rd | 19 +-- man/52.strength.plot.Rd |only man/A3.lizards.Rd | 40 +++---- man/B0.bn.class.Rd | 29 +---- man/B1.bn-strength.Rd |only src/Makevars |only src/acyclic.c | 43 +++---- src/allocations.c |only src/bayesian.network.c | 4 src/bn.recovery.c |only src/cache.structure.c | 31 ++--- src/common.c | 20 +++ src/common.h | 63 +++++++++++ src/configurations.c | 6 - src/discrete.loglikelihood.c | 28 +---- src/graph.generation.c |only src/hc.cache.lookup.c | 7 - src/is.dag.c | 120 +++------------------ src/linear.algebra.c |only src/linear.correlation.c |only src/monte.carlo.c |only src/mutual.information.c | 69 ++---------- src/path.c | 62 +++++------ src/pearson.x2.c | 67 ++---------- 66 files changed, 914 insertions(+), 1099 deletions(-)
Author: originally written by Andrew Gelman
Diff between R2WinBUGS versions 2.1-12 dated 2009-02-13 and 2.1-13 dated 2009-03-29
Title: Running WinBUGS and OpenBUGS from R / S-PLUS
Description: Using this package, it is possible to call a BUGS model,
summarize inferences and convergence in a table and graph, and
save the simulations in arrays for easy access in R / S-PLUS.
In S-PLUS, the openbugs functionality and the windows emulation
functionality is not yet available.
DESCRIPTION | 49 ++++++++++++++++++++++++++-----------------------
R/as.mcmc.list.bugs.R | 15 +++++++--------
R/bugs.R | 2 +-
inst/NEWS | 6 ++++++
inst/doc/R2WinBUGS.pdf | 6 +++---
man/bugs.Rd | 4 ++--
6 files changed, 45 insertions(+), 37 deletions(-)
Author: Eric Lecoutre
Diff between R2HTML versions 1.59 dated 2008-05-25 and 1.59-1 dated 2009-03-29
Title: HTML exportation for R objects
Description: Includes HTML function and methods to write in an HTML
file. Thus, making HTML reports is easy. Includes a function
that allows redirection on the fly, which appears to be very
usefull for teaching purpose, as the student can keep a copy of
the produced output to keep all that he did during the course.
Package comes with a vignette describing how to write HTML
reports for statistical analysis. Finally, a driver for Sweave
allows to parse HTML flat files containing R code and to
automatically write the corresponding outputs (tables and
graphs).
DESCRIPTION | 30 +
R/HTMLcore.R | 922 ++++++++++++++++++++++++-------------------------
man/HTML.data.frame.Rd | 172 ++++-----
man/HTMLStart.Rd | 161 ++++----
4 files changed, 650 insertions(+), 635 deletions(-)
Author: John Maindonald
Title: Data Sets and Functions, supplementary to DAAG
Description: various data sets used in additonal exercises for the book
Maindonald, J.H. and Braun, W.J. (2nd edn 2007) "Data Analysis
and Graphics Using R", and for a 'Data Mining' course. Note
especially the datasets \code{nassCDS} (airbag and other
influences on US vehicle accident outcomes: 1997-2002),
\code{cricketers} (handedness, British first class cricketers
born before 1961 whose handedness was specified),
\code{nswdemo} and related datasets (US Labor Training
Evaluation Data), \code{rockArt} (multivariate binary data on
Pacific rock art), \code{hotspots} (ages and distance from
Kilauea of larval hotspots; c.f. also \code{hotspots2006}),
\code{nihills} (record times for Northern Ireland mountain
races), \code{worldRecords} (record times for track and road
races), \code{progression} (progression of record times for
track races), \code{edcT} and \code{edcCO2} (temperature and
CO2 estimates from the EPICA Dome C ice core, covering 0 to 800
kyr BP), \code{grog} (Australian and NZ liquor consumption
patterns, 1998-2006), and \code{bomregions} (historical
Australian climate data).
Diff between DAAGxtras versions 0.7-4 dated 2009-01-12 and 0.7-5 dated 2009-03-29
DESCRIPTION | 44 ++++++++++++++++++++++++-------------------- data/SOI.RData |binary data/cricketers.RData |only man/SOI.Rd | 4 ++-- man/cricketers.Rd |only 5 files changed, 26 insertions(+), 22 deletions(-)