Title: seawater carbonate chemistry with R
Diff between seacarb versions 2.4.3 dated 2011-11-15 and 2.4.4 dated 2012-06-29
Description: Calculates parameters of the seawater carbonate system.
Code and/or corrections were contributed by Andreas Andersson,
Jean-Marie Epitalon, Bernard Gentili, Andreas Hofmann, Jim Orr,
Aurelien Proye and Karline Soetaert
Author: Heloise Lavigne, Jean-Pierre Gattuso
Maintainer: Jean-Pierre Gattuso
ChangeLog | 10 +
DESCRIPTION | 8 -
MD5 | 10 -
NAMESPACE | 4
R/Pcorrect.R | 196 +++++++++++++++++-----------------
man/carbm.Rd | 334 +++++++++++++++++++++++++++++------------------------------
6 files changed, 283 insertions(+), 279 deletions(-)
Title: Analysis of geostatistical data
Diff between geoR versions 1.7-2 dated 2012-02-02 and 1.7-3 dated 2012-06-29
Description: Geostatistical analysis including traditional,
likelihood-based and Bayesian methods.
Author: Paulo J. Ribeiro Jr
Maintainer: Paulo J. Ribeiro Jr
DESCRIPTION | 12 +++++-----
MD5 | 62 ++++++++++++++++++++++++++---------------------------
NAMESPACE | 2 -
R/auxiliar.R | 2 -
R/corcov.R | 6 +++--
R/eyefit.R | 2 -
R/geoRmisc.R | 4 +--
data/Ksat.rda |binary
data/SIC.rda |binary
data/ca20.rda |binary
data/camg.rda |binary
data/elevation.rda |binary
data/gambia.rda |binary
data/head.rda |binary
data/hoef.rda |binary
data/isaaks.rda |binary
data/kattegat.rda |binary
data/landim1.rda |binary
data/parana.rda |binary
data/s100.rda |binary
data/s121.rda |binary
data/s256i.rda |binary
data/soil250.rda |binary
data/soja98.rda |binary
data/tce.rda |binary
data/wo.rda |binary
data/wolfcamp.rda |binary
data/wrc.rda |binary
inst/CHANGES | 28 +++++++++++++++++++++++
man/dup.coords.Rd | 3 +-
man/krige.bayes.Rd | 38 ++++++++++++++++----------------
man/likfitBGCCM.Rd | 8 ++----
32 files changed, 98 insertions(+), 69 deletions(-)
Title: Catalogues of resolution IV 128 run 2-level fractional
factorials up to 24 factors that do have 5-letter words
Diff between FrF2.catlg128 versions 1.0-2 dated 2011-02-05 and 1.1 dated 2012-06-29
Description: This package provides catalogues of resolution IV regular
fractional factorial designs in 128 runs for up to 24 2-level
factors. The catalogues are complete, excluding resolution IV
designs without 5-letter words, because these do not add value
for a search for clear designs. The previous package with
complete catalogues of clear designs and a namespace added can
be downloaded from the authors website.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 24 ++++++++++++++----------
MD5 |only
NAMESPACE |only
data/catlg128.16.rda |binary
data/catlg128.17.rda |binary
data/catlg128.18.rda |binary
data/catlg128.19.rda |binary
data/catlg128.20.rda |binary
data/catlg128.21.rda |binary
data/catlg128.22.rda |binary
data/catlg128.23.rda |binary
data/catlg128.24.rda |binary
data/catlg128.8to15.rda |binary
inst/NEWS | 10 ++++++++++
man/Catalogues.Rd | 26 ++++++++++++++++++--------
man/FrF2.catlg128-package.Rd | 27 ++++++++++++++++++++++-----
16 files changed, 64 insertions(+), 23 deletions(-)
Title: Fractional Factorial designs with 2-level factors
Diff between FrF2 versions 1.4-1 dated 2012-05-18 and 1.5 dated 2012-06-29
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 still under development. While much of the intended
functionality is already available, some changes and
improvements are still to be expected. Suggestions are welcome.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 12
FrF2-Ex.R | 13
MD5 | 35
NAMESPACE | 23
R/CIG.R | 3
R/CatalogueAccessors.R | 25
R/aaa.R |only
R/estimable2fis.R | 22
R/myscatterplot3d.R | 8
R/sysdata.rda |binary
inst/NEWS | 17
man/CIG.Rd | 7
man/CatalogueAccessors.Rd | 50
tests/FrF2test.Rout.save | 3413 +++++++++++++--------------
tests/addcentertest.Rout.save | 7
tests/foldtest.Rout.save | 3621 ++++++++++++++---------------
tests/generators.from.designtest.Rout.save | 23
tests/generators.summary.test.Rout.save | 945 +++----
tests/pbtest.Rout.save | 7
19 files changed, 4177 insertions(+), 4054 deletions(-)
Title: Centrality-based pathway enrichment
Diff between CePa versions 0.2 dated 2012-06-11 and 0.3 dated 2012-06-29
Description: Use pathway topology information to assign weight to
pathway nodes.
Author: Zuguang Gu
Maintainer: Zuguang Gu
CePa-0.2/CePa/CHANGE |only
CePa-0.2/CePa/R/cepa.R |only
CePa-0.2/CePa/R/plot.cepa.R |only
CePa-0.2/CePa/R/plot.cepa.all.R |only
CePa-0.2/CePa/R/print.cepa.R |only
CePa-0.2/CePa/R/print.cepa.all.R |only
CePa-0.2/CePa/vignettes/CePa-006.pdf |only
CePa-0.2/CePa/vignettes/CePa-008.pdf |only
CePa-0.2/CePa/vignettes/CePa-012.pdf |only
CePa-0.2/CePa/vignettes/CePa-014.pdf |only
CePa-0.2/CePa/vignettes/CePa-016.pdf |only
CePa-0.3/CePa/CHANGES |only
CePa-0.3/CePa/DESCRIPTION | 10
CePa-0.3/CePa/MD5 | 103 +++-
CePa-0.3/CePa/NAMESPACE | 14
CePa-0.3/CePa/R/cepa.all.R | 229 ++++++++---
CePa-0.3/CePa/R/generate.pathway.R | 8
CePa-0.3/CePa/R/get.cepa.R | 2
CePa-0.3/CePa/R/global_variable.R |only
CePa-0.3/CePa/R/label.R |only
CePa-0.3/CePa/R/ora_extension.R |only
CePa-0.3/CePa/R/p.table.R | 13
CePa-0.3/CePa/R/plot_print.R |only
CePa-0.3/CePa/R/read.cls.R |only
CePa-0.3/CePa/R/read.gct.R |only
CePa-0.3/CePa/R/report.R | 82 ++-
CePa-0.3/CePa/R/univariate_extension.R |only
CePa-0.3/CePa/data/PID.db.rda |binary
CePa-0.3/CePa/data/datalist |only
CePa-0.3/CePa/inst/doc/CePa.Rnw | 558 ++++++++++++++++++++-------
CePa-0.3/CePa/inst/doc/CePa.pdf |binary
CePa-0.3/CePa/inst/extdata/bk.genome |only
CePa-0.3/CePa/inst/extdata/cepa.template | 98 ++++
CePa-0.3/CePa/man/CePa-package.Rd | 39 +
CePa-0.3/CePa/man/PID.db.Rd | 25 -
CePa-0.3/CePa/man/cepa.Rd | 108 +----
CePa-0.3/CePa/man/cepa.all.Rd | 63 +--
CePa-0.3/CePa/man/cepa.ora.Rd |only
CePa-0.3/CePa/man/cepa.ora.all.Rd |only
CePa-0.3/CePa/man/cepa.univariate.Rd |only
CePa-0.3/CePa/man/cepa.univariate.all.Rd |only
CePa-0.3/CePa/man/eccentricity.Rd | 6
CePa-0.3/CePa/man/generate.pathway.Rd | 4
CePa-0.3/CePa/man/get.cepa.Rd | 21 -
CePa-0.3/CePa/man/p.table.Rd | 23 -
CePa-0.3/CePa/man/pathway.nodes.Rd | 4
CePa-0.3/CePa/man/plot.cepa.Rd | 64 +--
CePa-0.3/CePa/man/plot.cepa.all.Rd | 35 +
CePa-0.3/CePa/man/plot.pathway.catalogue.Rd |only
CePa-0.3/CePa/man/plotGraph.Rd |only
CePa-0.3/CePa/man/plotNull.Rd |only
CePa-0.3/CePa/man/print.cepa.Rd | 33 -
CePa-0.3/CePa/man/print.cepa.all.Rd | 23 -
CePa-0.3/CePa/man/print.pathway.catalogue.Rd |only
CePa-0.3/CePa/man/radiality.Rd | 10
CePa-0.3/CePa/man/reach.Rd | 14
CePa-0.3/CePa/man/read.cls.Rd |only
CePa-0.3/CePa/man/read.gct.Rd |only
CePa-0.3/CePa/man/report.Rd | 13
CePa-0.3/CePa/man/sampleLabel.Rd |only
CePa-0.3/CePa/man/set.pathway.catalogue.Rd |only
CePa-0.3/CePa/man/spread.Rd | 6
CePa-0.3/CePa/vignettes/CePa.Rnw | 558 ++++++++++++++++++++-------
CePa-0.3/CePa/vignettes/CePa.tex |only
CePa-0.3/CePa/vignettes/bibliography.bib | 69 +++
CePa-0.3/CePa/vignettes/f1.pdf |only
CePa-0.3/CePa/vignettes/f10.pdf |only
CePa-0.3/CePa/vignettes/f2.pdf |only
CePa-0.3/CePa/vignettes/f3.pdf |only
CePa-0.3/CePa/vignettes/f4.pdf |only
CePa-0.3/CePa/vignettes/f5.pdf |only
CePa-0.3/CePa/vignettes/f6.pdf |only
CePa-0.3/CePa/vignettes/f8.pdf |only
CePa-0.3/CePa/vignettes/f9.pdf |only
74 files changed, 1578 insertions(+), 657 deletions(-)
Title: MultiPhen, a package for the genetic association testing of
multiple phenotypes
Diff between MultiPhen versions 0.7 dated 2012-06-26 and 0.8 dated 2012-06-29
Description: Performs genetic association tests between SNPs
(one-at-a-time) and multiple phenotypes (separately or in joint
model)
Author: Lachlan Coin, Paul O'Reilly, Yotsawat Pompyen, Clive Hoggart
and Federico Calboli
Maintainer: Federico Calboli
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/MultiPhen-internal.R | 18 ++++++++++++++----
R/mPhen.R | 3 +++
4 files changed, 24 insertions(+), 11 deletions(-)
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Diff between spatstat versions 1.28-0 dated 2012-06-11 and 1.28-1 dated 2012-06-29
Description: A package for analysing spatial data, mainly Spatial Point
Patterns, including multitype/marked points and spatial
covariates, in any two-dimensional spatial region. Also
supports three-dimensional point patterns, and space-time point
patterns in any number of dimensions. Contains over 1000
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, pixel images and
tessellations. Exploratory methods include K-functions,
nearest neighbour distance and empty space statistics, Fry
plots, pair correlation function, kernel smoothed intensity,
relative risk estimation with cross-validated bandwidth
selection, mark correlation functions, segregation indices,
mark dependence diagnostics etc. Point process models can be
fitted to point pattern data using functions ppm, kppm, slrm
similar to glm. Models may include dependence on covariates,
interpoint interaction, cluster formation 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).
Author: Adrian Baddeley
Maintainer: Adrian Baddeley
DESCRIPTION | 13 +-
MD5 | 78 +++++++-------
NEWS | 70 ++++++++++++
R/eval.fv.R | 15 ++
R/hardcore.R | 7 +
R/intensity.R |only
R/listof.R | 23 +++-
R/logistic.R |only
R/pairwise.family.R | 13 +-
R/plot.fv.R | 59 ++++++++--
R/plot.im.R | 59 ++++++++--
R/plot.splitppp.R | 261 ++++++++++++++++++++++++++++++-----------------
R/ppm.R | 23 +++-
R/ppmclass.R | 12 +-
R/quadclass.R | 4
R/strauss.R | 8 +
R/strausshard.R | 9 +
R/vcov.ppm.R | 24 ++--
R/wingeom.R | 17 +--
inst/doc/getstart.pdf |binary
inst/doc/shapefiles.pdf |binary
man/Gcom.Rd | 2
man/Gres.Rd | 2
man/Kcom.Rd | 2
man/Kres.Rd | 2
man/LambertW.Rd |only
man/contour.listof.Rd | 3
man/intensity.Rd |only
man/intensity.ppm.Rd |only
man/intensity.ppp.Rd |only
man/plot.im.Rd | 2
man/plot.listof.Rd | 33 +++++
man/plot.splitppp.Rd | 24 +++-
man/psst.Rd | 2
man/psstA.Rd | 2
man/psstG.Rd | 2
man/rho2hat.Rd | 4
man/rhohat.Rd | 13 +-
man/spatstat-internal.Rd | 10 +
man/spatstat-package.Rd | 7 -
man/square.Rd | 11 +
src/nndistX.h | 6 -
tests/alltests.R | 28 +++++
43 files changed, 623 insertions(+), 227 deletions(-)
Title: Model-Independent Particle Swarm Optimisation for Environmental
Models
Diff between hydroPSO versions 0.1-56 dated 2012-06-14 and 0.1-57 dated 2012-06-29
Description: This package implements a state-of-the-art version of the
Particle Swarm Optimisation (PSO) algorithm, with a special
focus on the calibration of environmental models. hydroPSO is
model-independent, allowing the user to easily interface any
model code with the calibration engine (PSO). hydroPSO includes
a series of controlling options and PSO variants to fine-tune
the performance of the calibration engine. An advanced
sensitivity analysis function together with user-friendly
plotting summaries facilitate the interpretation and assessment
of the calibration results. Bugs reports/comments/questions are
very welcomed.
Author: Mauricio Zambrano-Bigiarini [aut, cre] and Rodrigo Rojas [ctb]
Maintainer: Mauricio Zambrano-Bigiarini
DESCRIPTION | 8 -
MD5 | 14 +-
NAMESPACE | 3
NEWS | 25 ++++
R/PSO_v2012.R | 259 +++++++++++++++++++++++++++---------------------
R/plot_out.R | 12 +-
man/hydroPSO-package.Rd | 6 -
man/hydroPSO.Rd | 24 ++--
8 files changed, 213 insertions(+), 138 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Diff between rgeos versions 0.2-6 dated 2012-05-02 and 0.2-7 dated 2012-06-29
Description: Interface to Geometry Engine - Open Source (GEOS) using
the C API for topology operations on geometries. The GEOS
library is external to the package, and, when installing the
package from source, must be correctly installed first. Windows
and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand and Colin Rundel
Maintainer: Roger Bivand
ChangeLog | 13 +++++++++++++
DESCRIPTION | 13 +++++--------
MD5 | 13 +++++++------
inst/ChangeLog | 13 +++++++++++++
inst/SVN_VERSION | 2 +-
src/dummy.cc |only
src/local_stubs.c | 1 +
src/rgeos_misc.c | 6 ++++--
8 files changed, 44 insertions(+), 17 deletions(-)
Title: Routines for fitting kinetic models with one or more state
variables to chemical degradation data
Diff between mkin versions 0.8-11 dated 2011-10-20 and 0.9-05 dated 2012-06-29
Description: Calculation routines based on the FOCUS Kinetics Report
(2006). Includes a function for conveniently defining
differential equation models, model solution based on
eigenvalues if possible or using numerical solvers and a choice
of the optimisation methods made available by the FME package
(default is a Levenberg-Marquardt variant). Please note that
no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke, Katrin Lindenberger, René Lehmann
Maintainer: Johannes Ranke
mkin-0.8-11/mkin/R/mkinstart.R |only
mkin-0.8-11/mkin/inst/doc/header.tex |only
mkin-0.8-11/mkin/inst/doc/references.bib |only
mkin-0.8-11/mkin/inst/doc/run.bat |only
mkin-0.8-11/mkin/inst/unitTests/runit.mkinmod.R |only
mkin-0.8-11/mkin/man/mkinstart.Rd |only
mkin-0.9-05/mkin/DESCRIPTION | 20
mkin-0.9-05/mkin/MD5 | 67 +-
mkin-0.9-05/mkin/NAMESPACE |only
mkin-0.9-05/mkin/R/endpoints.R |only
mkin-0.9-05/mkin/R/ilr.R |only
mkin-0.9-05/mkin/R/mkin_long_to_wide.R | 2
mkin-0.9-05/mkin/R/mkin_wide_to_long.R | 2
mkin-0.9-05/mkin/R/mkinerrmin.R | 74 ++
mkin-0.9-05/mkin/R/mkinfit.R | 490 +++++--------------
mkin-0.9-05/mkin/R/mkinmod.R | 304 ++++++-----
mkin-0.9-05/mkin/R/mkinplot.R | 86 ---
mkin-0.9-05/mkin/R/mkinpredict.R |only
mkin-0.9-05/mkin/R/mkinresplot.R | 2
mkin-0.9-05/mkin/R/transform_odeparms.R |only
mkin-0.9-05/mkin/TODO |only
mkin-0.9-05/mkin/data/FOCUS_2006_DFOP_ref_A_to_B.rda |only
mkin-0.9-05/mkin/data/FOCUS_2006_FOMC_ref_A_to_F.rda |only
mkin-0.9-05/mkin/data/FOCUS_2006_HS_ref_A_to_F.rda |only
mkin-0.9-05/mkin/data/FOCUS_2006_SFO_ref_A_to_F.rda |only
mkin-0.9-05/mkin/data/FOCUS_2006_datasets.RData |binary
mkin-0.9-05/mkin/data/schaefer07_complex_case.RData |binary
mkin-0.9-05/mkin/inst/GUI/README |only
mkin-0.9-05/mkin/inst/doc/mkin.Rnw | 18
mkin-0.9-05/mkin/inst/doc/mkin.pdf |binary
mkin-0.9-05/mkin/inst/unitTests/Makefile |only
mkin-0.9-05/mkin/inst/unitTests/runit.mkinfit.R | 297 +++++++++++
mkin-0.9-05/mkin/inst/unitTests/runit.mkinpredict.R |only
mkin-0.9-05/mkin/man/FOCUS_2006_DFOP_ref_A_to_B.Rd |only
mkin-0.9-05/mkin/man/FOCUS_2006_FOMC_ref_A_to_F.Rd |only
mkin-0.9-05/mkin/man/FOCUS_2006_HS_ref_A_to_F.Rd |only
mkin-0.9-05/mkin/man/FOCUS_2006_SFO_ref_A_to_F.Rd |only
mkin-0.9-05/mkin/man/endpoints.Rd |only
mkin-0.9-05/mkin/man/ilr.Rd |only
mkin-0.9-05/mkin/man/mkinerrmin.Rd | 25
mkin-0.9-05/mkin/man/mkinfit.Rd | 48 -
mkin-0.9-05/mkin/man/mkinmod.Rd | 33 -
mkin-0.9-05/mkin/man/mkinpredict.Rd |only
mkin-0.9-05/mkin/man/schaefer07_complex_case.Rd | 2
mkin-0.9-05/mkin/man/summary.mkinfit.Rd | 14
mkin-0.9-05/mkin/man/transform_odeparms.Rd |only
mkin-0.9-05/mkin/vignettes |only
47 files changed, 795 insertions(+), 689 deletions(-)
Title: Tools for reading and handling spatial objects
Diff between maptools versions 0.8-14 dated 2012-01-15 and 0.8-16 dated 2012-06-29
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.
Author: Nicholas J. Lewin-Koh and Roger Bivand, contributions by Edzer
J. Pebesma, Eric Archer, Adrian Baddeley, Hans-Jörg Bibiko,
Jonathan Callahan, German Carrillo, Stéphane Dray, David
Forrest, Michael Friendly, Patrick Giraudoux, Duncan Golicher,
Virgilio Gómez Rubio, Patrick Hausmann, Karl Ove Hufthammer,
Thomas Jagger, Sebastian P. Luque, Don MacQueen, Andrew
Niccolai, Tom Short, Greg Snow, Ben Stabler and Rolf Turner
Maintainer: Roger Bivand
ChangeLog | 36 ++++++++++++++++
DESCRIPTION | 18 ++++----
MD5 | 24 ++++++-----
NAMESPACE | 2
R/elide.R | 4 +
R/getKMLcoordinates.R | 5 ++
R/midpoint.R |only
R/point_line_distance.R |only
inst/ChangeLog | 36 ++++++++++++++++
man/Rgshhs.Rd | 4 -
man/SpatialLinesMidPoints.Rd |only
man/nearestPointOnLine.Rd |only
man/nearestPointOnSegment.Rd |only
man/snapPointsToLines.Rd |only
man/unionSpatialPolygons.Rd | 4 -
maptools-Ex.R | 93 +++++++++++++++++++++++++++++++++++++++++++
16 files changed, 203 insertions(+), 23 deletions(-)
Title: A package for statistical analysis in epidemiology.
Diff between Epi versions 1.1.34 dated 2012-03-29 and 1.1.36 dated 2012-06-29
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data,
including interval censored data and representation of
multistate data. Also some useful functions for tabulation and
plotting. Contains some epidemiological datasets.
Author: Bendix Carstensen [aut, cre], Martyn Plummer [aut], Michael
Hills [aut], Esa Laara [ctb]
Maintainer: Bendix Carstensen
CHANGES | 12 +
DESCRIPTION | 22 +-
MD5 | 64 +++----
R/MS.boxes.R | 9 -
R/ci.lin.R | 2
R/cutLexis.R | 2
R/lexis.R | 12 +
R/stattable.R | 6
data/B.dk.rda |binary
data/DMconv.rda |binary
data/DMlate.rda |binary
data/DMrand.rda |binary
data/M.dk.rda |binary
data/N.dk.rda |binary
data/S.typh.rda |binary
data/Y.dk.rda |binary
data/bdendo.rda |binary
data/bdendo11.rda |binary
data/births.rda |binary
data/blcaIT.rda |binary
data/brv.rda |binary
data/diet.rda |binary
data/ewrates.rda |binary
data/gmortDK.rda |binary
data/hivDK.rda |binary
data/lep.rda |binary
data/lungDK.rda |binary
data/mortDK.rda |binary
data/nickel.rda |binary
data/occup.rda |binary
data/thoro.rda |binary
inst/doc/Follow-up.pdf | 410 +++++++++++++++++++++++--------------------------
man/Lexis.Rd | 4
33 files changed, 279 insertions(+), 264 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.9.12 dated 2012-06-25 and 0.9.13 dated 2012-06-29
Description: The Rcpp package provides R functions as well as a C++
library which facilitate the integration of R and C++.
R data types (SEXP) are matched to C++ objects in a class hierarchy.
All R types are supported (vectors, functions, environment, etc
...) and each type is mapped to a dedicated class. For
example, numeric vectors are represented as instances of the
Rcpp::NumericVector class, environments are represented as
instances of Rcpp::Environment, functions are represented as
Rcpp::Function, etc ... The "Rcpp-introduction" vignette
provides a good entry point to Rcpp.
Conversion from C++ to R and back is driven by the templates Rcpp::wrap
and Rcpp::as which are highly flexible and extensible, as
documented in the "Rcpp-extending" vignette.
Rcpp also provides Rcpp modules, a framework that allows exposing C++
functions and classes to the R level. The "Rcpp-modules"
vignette details the current set of features of Rcpp-modules.
Rcpp includes a concept called Rcpp sugar that brings many R functions
into C++. Sugar takes advantage of lazy evaluation and
expression templates to achieve great performance while
exposing a syntax that is much nicer to use than the equivalent
low-level loop code. The "Rcpp-sugar" vignette gives an
overview of the feature.
Several examples are included, and more than 770 unit tests in over 349
unit test functions provide additional usage examples.
An earlier version of Rcpp, containing what we now call the 'classic
Rcpp API' was written during 2005 and 2006 by Dominick Samperi.
This code has been factored out of Rcpp into the package
RcppClassic, and it is still available for code relying on the
older interface. New development should always use this Rcpp
package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel
ChangeLog | 53 ++++-
DESCRIPTION | 8
MD5 | 62 ++---
inst/NEWS | 25 +-
inst/doc/Rcpp-FAQ.pdf |binary
inst/doc/Rcpp-extending.pdf |binary
inst/doc/Rcpp-introduction.pdf |binary
inst/doc/Rcpp-modules.pdf |binary
inst/doc/Rcpp-package.pdf |binary
inst/doc/Rcpp-quickref.pdf |binary
inst/doc/Rcpp-sugar.pdf |binary
inst/doc/Rcpp-unitTests.pdf |binary
inst/doc/unitTests-results/Rcpp-unitTests.html | 18 -
inst/doc/unitTests-results/Rcpp-unitTests.txt | 61 ++---
inst/examples/FastLM/benchmark.r | 2
inst/include/Rcpp/Environment.h | 4
inst/include/Rcpp/config.h | 2
inst/include/RcppCommon.h | 10
inst/unitTests/runTests.R | 6
inst/unitTests/runit.Function.R | 7
inst/unitTests/runit.Language.R | 262 ++++++++++++------------
inst/unitTests/runit.Module.client.package.R | 72 +++---
inst/unitTests/runit.environments.R | 264 ++++++++++++-------------
inst/unitTests/runit.macros.R | 28 +-
inst/unitTests/runit.modref.R | 42 ++-
inst/unitTests/runit.rcout.R | 39 ++-
inst/unitTests/runit.support.R | 149 +++++++-------
inst/unitTests/testRcppClass/R/load.R | 7
inst/unitTests/testRcppModule/R/zzz.R | 6
src/Environment.cpp | 2
src/exceptions.cpp | 18 +
tests/doRUnit.R | 86 +++++---
32 files changed, 693 insertions(+), 540 deletions(-)
Title: Toy example of S4 package
Diff between packS4 versions 0.9 dated 2011-11-02 and 0.9.1 dated 2012-06-29
Description: This package comes to illustrate the book "Petit Manuel de
Programmation Orientee Objet sous R"
Author: Christophe Genolini
Maintainer: Christophe Genolini
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
R/classCreator.R | 28 +++++++++++++++++-----------
R/global.R | 1 +
man/packS4-package.Rd | 4 ++--
5 files changed, 30 insertions(+), 22 deletions(-)
Title: An examination of indices for determining the number of clusters
: NbClust Package
Diff between NbClust versions 1.0 dated 2012-05-23 and 1.2 dated 2012-06-29
Description: This package provides most of the popular indices for
cluster validation ready to use for the outputs produced by
functions coming from the same package. It also proposes to
user the best clustering scheme from the different results
obtained by varying all combinations of number of clusters,
distance measures, and clustering methods.
Author: Malika Charrad
Maintainer: Malika Charrad
DESCRIPTION | 10 +-
MD5 | 6 -
R/NbClust.R | 216 ++++++++++++++++++++++++++++++++++++++++-----------------
man/NbClust.Rd | 5 +
4 files changed, 167 insertions(+), 70 deletions(-)
Title: High Dimensional Discriminant Analysis
Diff between HiDimDA versions 0.1-1 dated 2011-06-15 and 0.2-0 dated 2012-06-29
Description: Performs Linear Discriminant Analysis in High Dimensional
problems based on reliable covariance estimators for problems
with(many) more variables than observations. Includes routines
for classifier training, prediction, cross-validation and
variable selection.
Author: Antonio Pedro Duarte Silva
Maintainer: Antonio Pedro Duarte Silva
HiDimDA-0.1-1/HiDimDA/R/miscellanea.R |only
HiDimDA-0.1-1/HiDimDA/data/SinghDS.rda |only
HiDimDA-0.1-1/HiDimDA/man/MatMultSigFq.Rd |only
HiDimDA-0.1-1/HiDimDA/man/SinghDS.Rd |only
HiDimDA-0.1-1/HiDimDA/man/predict.RFlda.Rd |only
HiDimDA-0.1-1/HiDimDA/man/solveFq.Rd |only
HiDimDA-0.1-1/HiDimDA/src/BackUps |only
HiDimDA-0.2-0/HiDimDA/CHANGELOG | 34 ++-
HiDimDA-0.2-0/HiDimDA/DESCRIPTION | 15 -
HiDimDA-0.2-0/HiDimDA/MD5 |only
HiDimDA-0.2-0/HiDimDA/NAMESPACE | 10
HiDimDA-0.2-0/HiDimDA/R/DACrossVal.R | 20 +
HiDimDA-0.2-0/HiDimDA/R/DMat.R |only
HiDimDA-0.2-0/HiDimDA/R/Dlda.R |only
HiDimDA-0.2-0/HiDimDA/R/FrobSigAp1.R | 58 ++---
HiDimDA-0.2-0/HiDimDA/R/Mlda.R |only
HiDimDA-0.2-0/HiDimDA/R/RFlda.R | 152 ++-----------
HiDimDA-0.2-0/HiDimDA/R/RepLOptim.R | 288 +++++++++++++-------------
HiDimDA-0.2-0/HiDimDA/R/SelectV.R | 188 ++++++++++++----
HiDimDA-0.2-0/HiDimDA/R/ShrnkMat.R |only
HiDimDA-0.2-0/HiDimDA/R/ShrnkMatInv.R |only
HiDimDA-0.2-0/HiDimDA/R/SigFq.R | 206 ++++++++++++------
HiDimDA-0.2-0/HiDimDA/R/SigFqInv.R | 191 +++++++++++------
HiDimDA-0.2-0/HiDimDA/R/Slda.R |only
HiDimDA-0.2-0/HiDimDA/R/ldaGeneral.R |only
HiDimDA-0.2-0/HiDimDA/R/mylocfdr.R | 101 +++++----
HiDimDA-0.2-0/HiDimDA/R/mylocmle.R | 48 +++-
HiDimDA-0.2-0/HiDimDA/R/rghtsngv.R |only
HiDimDA-0.2-0/HiDimDA/R/solveRFq.R | 52 ++--
HiDimDA-0.2-0/HiDimDA/R/solveShrnkMat.R |only
HiDimDA-0.2-0/HiDimDA/data/AlonDS.rda |binary
HiDimDA-0.2-0/HiDimDA/man/AlonDS.Rd | 7
HiDimDA-0.2-0/HiDimDA/man/CovE.Rd |only
HiDimDA-0.2-0/HiDimDA/man/DACrossVal.Rd | 24 +-
HiDimDA-0.2-0/HiDimDA/man/DMat.Rd |only
HiDimDA-0.2-0/HiDimDA/man/Dlda.Rd |only
HiDimDA-0.2-0/HiDimDA/man/FrobSigAp.Rd | 13 -
HiDimDA-0.2-0/HiDimDA/man/HiDimDA-internal.Rd | 57 ++---
HiDimDA-0.2-0/HiDimDA/man/HiDimDA-package.Rd | 139 +++++++++++-
HiDimDA-0.2-0/HiDimDA/man/MatMult.Rd |only
HiDimDA-0.2-0/HiDimDA/man/Mlda.Rd |only
HiDimDA-0.2-0/HiDimDA/man/MldaInvE.Rd |only
HiDimDA-0.2-0/HiDimDA/man/RFlda.Rd | 84 ++++---
HiDimDA-0.2-0/HiDimDA/man/SelectV.Rd | 58 +++--
HiDimDA-0.2-0/HiDimDA/man/ShrnkMat.Rd |only
HiDimDA-0.2-0/HiDimDA/man/ShrnkMatInv.Rd |only
HiDimDA-0.2-0/HiDimDA/man/ShrnkSigE.Rd |only
HiDimDA-0.2-0/HiDimDA/man/SigFq.Rd | 5
HiDimDA-0.2-0/HiDimDA/man/SigFqInv.Rd | 4
HiDimDA-0.2-0/HiDimDA/man/Slda.Rd |only
HiDimDA-0.2-0/HiDimDA/man/canldaRes.Rd |only
HiDimDA-0.2-0/HiDimDA/man/clldaRes.Rd |only
HiDimDA-0.2-0/HiDimDA/man/solve.Rd |only
HiDimDA-0.2-0/HiDimDA/src/Makevars |only
54 files changed, 1055 insertions(+), 699 deletions(-)
Title: Censored Regression (Tobit) Models
Diff between censReg versions 0.5-12 dated 2012-06-01 and 0.5-14 dated 2012-06-29
Description: Estimation of censored regression (Tobit) models with
cross-section and panel data
Author: Arne Henningsen
Maintainer: Arne Henningsen
DESCRIPTION | 12
MD5 | 12
NEWS | 11
R/logLikCross.R | 8
inst/doc/censReg.pdf |binary
tests/censRegPanelLargerTest.Rout.save | 2
tests/censRegTest.Rout.save | 448 ++++++++++++++++-----------------
7 files changed, 252 insertions(+), 241 deletions(-)