Title: Extension to ggplot2.
Diff between GGally versions 0.3.3 dated 2012-05-31 and 0.3.4 dated 2012-07-08
Description: Package contains templates for different plots to be
combined into a plot matrix, as well as a parallel coordinate
plot function.
Author: Barret Schloerke
Maintainer: Di Cook
GGally-0.3.3/GGally/GGally_0.3.2.tar.gz |only
GGally-0.3.4/GGally/DESCRIPTION | 6 ++--
GGally-0.3.4/GGally/GGally_0.3.3.tar.gz |binary
GGally-0.3.4/GGally/MD5 | 23 +++++++++--------
GGally-0.3.4/GGally/NAMESPACE | 2 +
GGally-0.3.4/GGally/R/gg-plots.r | 40 ++++++++++++++++++++++++++++++
GGally-0.3.4/GGally/R/ggpairs.r | 24 +++++++++---------
GGally-0.3.4/GGally/man/find_plot_type.Rd | 3 --
GGally-0.3.4/GGally/man/get_plot_type.Rd | 5 +--
GGally-0.3.4/GGally/man/ggally_lines.Rd |only
GGally-0.3.4/GGally/man/ggally_path.Rd |only
GGally-0.3.4/GGally/man/ggpairs.Rd | 2 -
GGally-0.3.4/GGally/man/plot_types.Rd | 4 +--
GGally-0.3.4/GGally/roxygenize.R | 2 -
14 files changed, 77 insertions(+), 34 deletions(-)
Title: Numerical Methods and Optimization in Finance
Diff between NMOF versions 0.23-1 dated 2012-03-04 and 0.25-4 dated 2012-07-08
Description: Functions, examples and data from the book 'Numerical
Methods and Optimization in Finance' by M. Gilli, D. Maringer
and E. Schumann. The package contains, in particular,
implementations of several optimisation heuristics (such as
Differential Evolution, Genetic Algorithms and Threshold
Accepting).
Author: Enrico Schumann
Maintainer: Enrico Schumann
NMOF-0.23-1/NMOF/inst/unitTests/unitTests3.R |only
NMOF-0.23-1/NMOF/inst/unitTests/unitTests4.R |only
NMOF-0.23-1/NMOF/inst/unitTests/unitTests5.R |only
NMOF-0.25-4/NMOF/DESCRIPTION | 14
NMOF-0.25-4/NMOF/MD5 | 157 ++++++----
NMOF-0.25-4/NMOF/NAMESPACE | 5
NMOF-0.25-4/NMOF/NEWS | 81 +++++
NMOF-0.25-4/NMOF/R/DEopt.R | 38 +-
NMOF-0.25-4/NMOF/R/LSopt.R | 4
NMOF-0.25-4/NMOF/R/NS.R | 18 -
NMOF-0.25-4/NMOF/R/PSopt.R | 37 +-
NMOF-0.25-4/NMOF/R/TAopt.R | 11
NMOF-0.25-4/NMOF/R/callCF.R | 42 +-
NMOF-0.25-4/NMOF/R/callHestoncf.R | 34 +-
NMOF-0.25-4/NMOF/R/internals.R | 34 ++
NMOF-0.25-4/NMOF/R/resampleC.R |only
NMOF-0.25-4/NMOF/R/restartOpt.R | 23 -
NMOF-0.25-4/NMOF/R/showExample.R |only
NMOF-0.25-4/NMOF/data/bundData.RData |binary
NMOF-0.25-4/NMOF/data/fundData.RData |binary
NMOF-0.25-4/NMOF/data/optionData.RData |binary
NMOF-0.25-4/NMOF/inst/NEWS.Rd | 82 +++++
NMOF-0.25-4/NMOF/inst/NMOFex/NMOFman.R |only
NMOF-0.25-4/NMOF/inst/NMOFex/README | 6
NMOF-0.25-4/NMOF/inst/book |only
NMOF-0.25-4/NMOF/inst/doc/DEnss.Rnw | 14
NMOF-0.25-4/NMOF/inst/doc/DEnss.pdf |binary
NMOF-0.25-4/NMOF/inst/doc/LSselect.Rnw | 28 +
NMOF-0.25-4/NMOF/inst/doc/LSselect.pdf |binary
NMOF-0.25-4/NMOF/inst/doc/PSlms.Rnw | 49 +--
NMOF-0.25-4/NMOF/inst/doc/PSlms.pdf |binary
NMOF-0.25-4/NMOF/inst/doc/TAportfolio.Rnw | 61 ++-
NMOF-0.25-4/NMOF/inst/doc/TAportfolio.pdf |binary
NMOF-0.25-4/NMOF/inst/doc/qTableEx.Rnw | 14
NMOF-0.25-4/NMOF/inst/doc/qTableEx.pdf |binary
NMOF-0.25-4/NMOF/inst/doc/repair.Rnw | 13
NMOF-0.25-4/NMOF/inst/doc/repair.pdf |binary
NMOF-0.25-4/NMOF/inst/doc/vectorise.Rnw | 13
NMOF-0.25-4/NMOF/inst/doc/vectorise.pdf |binary
NMOF-0.25-4/NMOF/inst/unitTests/unitTests1.R | 216 +++----------
NMOF-0.25-4/NMOF/inst/unitTests/unitTests2.R | 6
NMOF-0.25-4/NMOF/inst/unitTests/unitTestsDEopt.R | 21 +
NMOF-0.25-4/NMOF/inst/unitTests/unitTestsGAopt.R | 4
NMOF-0.25-4/NMOF/inst/unitTests/unitTestsInternals.R |only
NMOF-0.25-4/NMOF/inst/unitTests/unitTestsLSopt.R |only
NMOF-0.25-4/NMOF/inst/unitTests/unitTestsPSopt.R |only
NMOF-0.25-4/NMOF/inst/unitTests/unitTestsTAopt.R |only
NMOF-0.25-4/NMOF/inst/unitTests/unitTestscallCF.R |only
NMOF-0.25-4/NMOF/man/DEopt.Rd | 165 ++++++----
NMOF-0.25-4/NMOF/man/GAopt.Rd | 188 ++++++------
NMOF-0.25-4/NMOF/man/LSopt.Rd | 233 +++++++++-----
NMOF-0.25-4/NMOF/man/NMOF-internal.Rd | 8
NMOF-0.25-4/NMOF/man/NMOF-package.Rd | 68 ++--
NMOF-0.25-4/NMOF/man/NS.Rd | 41 +-
NMOF-0.25-4/NMOF/man/NSf.Rd | 39 +-
NMOF-0.25-4/NMOF/man/PSopt.Rd | 262 ++++++++++------
NMOF-0.25-4/NMOF/man/TAopt.Rd | 297 ++++++++++---------
NMOF-0.25-4/NMOF/man/bracketing.Rd | 17 -
NMOF-0.25-4/NMOF/man/callCF.Rd | 98 +++---
NMOF-0.25-4/NMOF/man/resampleC.Rd |only
NMOF-0.25-4/NMOF/man/restartOpt.Rd | 12
NMOF-0.25-4/NMOF/man/showExample.Rd |only
NMOF-0.25-4/NMOF/man/testFunctions.Rd | 66 ++--
NMOF-0.25-4/NMOF/man/xwGauss.Rd | 62 +--
NMOF-0.25-4/NMOF/tests/runitNMOF.R | 2
65 files changed, 1562 insertions(+), 1021 deletions(-)
Title: Univariate GARCH models
Diff between rugarch versions 1.0-9 dated 2012-05-26 and 1.0-10 dated 2012-07-08
Description: ARFIMA, in-mean, external regressors and various GARCH
flavours, with methods for fit, forecast, simulation, inference
and plotting.
Author: Alexios Ghalanos
Maintainer: Alexios Ghalanos
ChangeLog | 8 +++
DESCRIPTION | 10 ++--
MD5 | 32 +++++++--------
R/rugarch-aparch.R | 16 +++----
R/rugarch-bootstrap.R | 46 +++++++++++-----------
R/rugarch-egarch.R | 25 ++++++-----
R/rugarch-fgarch.R | 16 +++----
R/rugarch-gjrgarch.R | 16 +++----
R/rugarch-igarch.R | 16 +++----
R/rugarch-methods.R | 19 +++++----
R/rugarch-rolling.R | 18 ++++----
R/rugarch-sgarch.R | 17 ++++----
inst/doc/Introduction_to_the_rugarch_package.Rnw | 2
inst/doc/Introduction_to_the_rugarch_package.pdf |binary
man/rugarch-package.Rd | 6 +-
src/garchsim.cpp | 5 +-
vignettes/Introduction_to_the_rugarch_package.Rnw | 2
17 files changed, 136 insertions(+), 118 deletions(-)
Title: Rcpp bindings for NumPy files
Diff between RcppCNPy versions 0.0.1 dated 2012-07-05 and 0.1.0 dated 2012-07-08
Description: This package provides access to the cnpy library by Carl
Rogers which provides read and write facilities for files
created with (or for) the NumPY extension for Python. Vectors
and matrices of numeric types can be read or written;
compressed files can be read as well. Support for integer files
is available if the package (and Rcpp) are compiled with
-std=c++11.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 22 +++++++++
DESCRIPTION | 14 ++++--
MD5 | 34 ++++++++++-----
cleanup | 2
demo |only
inst/NEWS.Rd | 13 +++++
inst/doc |only
man/RcppCNPy-package.Rd | 38 ++++++-----------
src/Makevars | 24 ----------
src/Makevars.win | 2
src/cnpy.cpp | 88 ++++++++++++++++++++++++++++++++++-----
src/cnpy.h | 15 ++++--
src/cnpyMod.cpp | 107 +++++++++++++++++++++++++++++++++++++-----------
tests |only
vignettes |only
15 files changed, 255 insertions(+), 104 deletions(-)
Title: Tools for using fonts
Diff between extrafont versions 0.9 dated 2012-06-11 and 0.10 dated 2012-07-08
Description: Tools to using fonts other than the standard PostScript
fonts. This package makes it easy to use system TrueType fonts
and with PDF or PostScript output files, and with bitmap output
files in Windows. extrafont can also be used with fonts
packaged specifically to be used with, such as the fontcm
package, which has Computer Modern PostScript fonts with math
symbols. See https://github.com/wch/extrafont for instructions
and examples.
Author: Winston Chang
Maintainer: Winston Chang
DESCRIPTION | 19 -
MD5 | 19 -
NEWS |only
R/load.r | 161 +++++++------
R/truetype.r | 9
R/utils.r | 2
README.md | 28 +-
extrafont.sublime-workspace | 544 +++-----------------------------------------
fontcm.pdf |binary
fonttest.pdf |binary
man/loadfonts.Rd | 11
11 files changed, 204 insertions(+), 589 deletions(-)
Title: US Census 2000 Suite of R Packages
Diff between UScensus2000 versions 1.01 dated 2011-11-14 and 1.02 dated 2012-07-08
Description: US Census 2000 shape files and additional demographic data
from the SF1 100 percent files. This package contains a number
of helper functions for the UScensus2000blk,
UScensus2000blkgrp, UScensus2000tract, UScensus2000cdp
packages.
Author: Zack W. Almquist
Maintainer: Zack W. Almquist
DESCRIPTION | 14 ++++---
MD5 | 9 ++--
NAMESPACE |only
R/demographics.R | 106 ++++++++++++++++++++++++-------------------------------
R/poly.clipper.R | 2 -
R/zzz.R | 17 +++++---
6 files changed, 72 insertions(+), 76 deletions(-)
Title: The package can implement the graph-based reconstruction and
analyses of the KEGG pathways.
Diff between iSubpathwayMiner versions 2.0 dated 2012-02-20 and 3.0 dated 2012-07-08
More information about iSubpathwayMiner at CRAN
Description: The package can implement the graph-based reconstruction
and analysis of the KEGG pathways. (1) Our system provides many
strategies of converting pathways to graph models. Ten
functions related to conversion from pathways to graphs are
developed. Furthermore, the combinations of these functions can
get many combined conversion strategies of pathway graphs (>
20). The system can also support topology-based pathway
analysis of molecule sets. (2) The iSubpathwayMiner can support
the annotation and identification of entire pathways based on
molecule (gene and/or metabolite) sets. (3) The
iSubpathwayMiner provides the k-clique method for
identification of metabolic subpathways based on gene sets. (4)
The iSubpathwayMiner provides the Subpathway-GM method for
identification of metabolic subpathways based on gene and
metabolite sets (new!).
Author: Chunquan Li
Maintainer: Chunquan Li
iSubpathwayMiner-2.0/iSubpathwayMiner/R/subpathway-method.R |only
iSubpathwayMiner-2.0/iSubpathwayMiner/man/sampleComponent.Rd |only
iSubpathwayMiner-3.0/iSubpathwayMiner/DESCRIPTION | 53 -
iSubpathwayMiner-3.0/iSubpathwayMiner/MD5 | 57 -
iSubpathwayMiner-3.0/iSubpathwayMiner/R/SubpathwayGM.R |only
iSubpathwayMiner-3.0/iSubpathwayMiner/R/annotation.R | 58 -
iSubpathwayMiner-3.0/iSubpathwayMiner/R/initialize.R | 2
iSubpathwayMiner-3.0/iSubpathwayMiner/R/k-clique.R |only
iSubpathwayMiner-3.0/iSubpathwayMiner/R/metabolic_non-metabolic.R | 163 +--
iSubpathwayMiner-3.0/iSubpathwayMiner/R/sample.R | 40
iSubpathwayMiner-3.0/iSubpathwayMiner/R/topologicalanalysis.R | 119 +-
iSubpathwayMiner-3.0/iSubpathwayMiner/R/visualize.R | 17
iSubpathwayMiner-3.0/iSubpathwayMiner/data/hsa_ncbi-geneid_k2ri.rda |binary
iSubpathwayMiner-3.0/iSubpathwayMiner/inst/doc/iSubpathwayMiner.Rnw | 471 +++-------
iSubpathwayMiner-3.0/iSubpathwayMiner/inst/doc/iSubpathwayMiner.pdf |binary
iSubpathwayMiner-3.0/iSubpathwayMiner/inst/localdata/crc_diff_gene.txt |only
iSubpathwayMiner-3.0/iSubpathwayMiner/inst/localdata/crc_diff_metabolite.txt |only
iSubpathwayMiner-3.0/iSubpathwayMiner/man/SubpathwayGM.Rd |only
iSubpathwayMiner-3.0/iSubpathwayMiner/man/aaa-iSubpathwayMiner-package.Rd | 5
iSubpathwayMiner-3.0/iSubpathwayMiner/man/expandNode.Rd | 6
iSubpathwayMiner-3.0/iSubpathwayMiner/man/filterNode.Rd | 8
iSubpathwayMiner-3.0/iSubpathwayMiner/man/getBackground.Rd | 4
iSubpathwayMiner-3.0/iSubpathwayMiner/man/getExample.Rd | 12
iSubpathwayMiner-3.0/iSubpathwayMiner/man/getKcSubiGraph.Rd | 8
iSubpathwayMiner-3.0/iSubpathwayMiner/man/getLocSubGraph.Rd |only
iSubpathwayMiner-3.0/iSubpathwayMiner/man/getPrioBackground.Rd | 4
iSubpathwayMiner-3.0/iSubpathwayMiner/man/iSubpathwayMiner-internal.Rd | 3
iSubpathwayMiner-3.0/iSubpathwayMiner/man/identifyGraph.Rd | 40
iSubpathwayMiner-3.0/iSubpathwayMiner/man/identifyTopo.Rd | 24
iSubpathwayMiner-3.0/iSubpathwayMiner/man/plotAnnGraph.Rd | 2
iSubpathwayMiner-3.0/iSubpathwayMiner/man/printGraph.Rd | 2
iSubpathwayMiner-3.0/iSubpathwayMiner/man/printTopo.Rd | 2
iSubpathwayMiner-3.0/iSubpathwayMiner/man/sampleMolecule.Rd |only
iSubpathwayMiner-3.0/iSubpathwayMiner/vignettes/iSubpathwayMiner.Rnw | 471 +++-------
34 files changed, 685 insertions(+), 886 deletions(-)
Permanent link
Title: High Dimensional Discriminant Analysis
Diff between HiDimDA versions 0.2-0 dated 2012-06-29 and 0.2-1 dated 2012-07-08
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
CHANGELOG | 117 +++++------
DESCRIPTION | 10
MD5 | 41 +--
R/DACrossVal.R | 14 -
R/Mlda.R | 2
R/SelectV.R | 515 ++++++++++++++++++++++++-------------------------
R/rghtsngv.R | 106 +++++-----
man/CovE.Rd | 4
man/DACrossVal.Rd | 13 -
man/Dlda.Rd | 22 +-
man/HiDimDA-package.Rd | 333 +++++++++++++++----------------
man/MatMult.Rd | 8
man/Mlda.Rd | 22 +-
man/MldaInvE.Rd | 3
man/RFlda.Rd | 25 +-
man/SelectV.Rd | 243 +++++++++++------------
man/ShrnkMatInv.Rd | 8
man/ShrnkSigE.Rd | 4
man/Slda.Rd | 28 +-
man/canldaRes.Rd | 16 -
man/clldaRes.Rd | 10
src/rghtsngv.f |only
22 files changed, 795 insertions(+), 749 deletions(-)
Title: A collection of statistical tools for biologists
Diff between asbio versions 0.3-40 dated 2011-11-18 and 0.3-42 dated 2012-07-08
Description: Contains functions from: "Foundational Statistics for
Biologists; A Textbook Using R" (Under contract; CRC Press;
Release: Spring 2013)
Author: Ken Aho; many thanks to V. Winston and D. Roberts
Maintainer: Ken Aho
DESCRIPTION | 16 +-
MD5 | 217 +++++++++++++++++++++++-----------------
NAMESPACE | 4
R/Bayes.disc.r | 8 -
R/Bayes.disc.tck.r | 6 -
R/FR.multi.comp.R | 2
R/KW.multi.comp.R | 2
R/ML.k.r |only
R/MS.test.R | 6 -
R/Mrpp.R | 4
R/Pairw.test.R | 6 -
R/R.hat.r |only
R/Venn.R | 12 +-
R/anm.ExpDesign.r | 79 ++++++++++----
R/anm.ExpDesign.tck.r | 2
R/anm.LV.r | 8 +
R/anm.LVc.tck.r | 2
R/anm.LVe.tck.r | 2
R/anm.TM.tck.r | 2
R/anm.ci.r | 3
R/anm.ci.tck.r | 2
R/anm.coin.r | 6 -
R/anm.coin.tck.r | 3
R/anm.cont.pdf.r |only
R/anm.die.r | 2
R/anm.die.tck.r | 2
R/anm.ls.r | 2
R/anm.ls.reg.r |only
R/anm.ls.reg.tck.r |only
R/anm.ls.tck.r | 2
R/anm.mc.bvn.r |only
R/anm.pop.tck.r | 9 +
R/anm.popgrowth.r | 10 +
R/anm.samp.design.R | 1
R/anm.samp.design.tck.r | 2
R/anm.transM.r | 2
R/bplot.r | 134 ++++++------------------
R/demos.r | 9 +
R/lma.tck.r | 1
R/lmr.tck.r | 1
R/lmu.tck.r | 1
R/loglik.plot.r | 23 ++++
R/loglik.tck.r | 4
R/mcmc.norm.hier.r |only
R/prp.r | 2
R/samp.dist.r | 62 ++++++-----
R/samp.dist.snap.tck.r | 14 +-
R/samp.dist.tck.r | 2
R/see.Fcdf.r | 82 ++++++++-------
R/see.HW.r | 15 +-
R/see.M.r | 32 +++--
R/see.adddel.r | 5
R/see.betacdf.r | 76 +++++++-------
R/see.bincdf.r | 52 +++++----
R/see.chicdf.r | 62 ++++++-----
R/see.expcdf.r | 62 +++++------
R/see.exppower.r | 29 ++---
R/see.gamcdf.r | 76 +++++++-------
R/see.geocdf.r | 68 ++++++------
R/see.hypercdf.r | 60 +++++------
R/see.lnormcdf.r | 75 +++++++------
R/see.logic.r | 1
R/see.logiscdf.r | 75 +++++++------
R/see.nbincdf.r | 71 ++++++-------
R/see.nlm.r | 76 +++++++-------
R/see.normcdf.r | 106 ++++++++++---------
R/see.pdfdriver.r | 1
R/see.poiscdf.r | 103 ++++++++++++------
R/see.power.r | 58 +++++-----
R/see.tcdf.r | 56 +++++-----
R/see.typeI_II.r | 2
R/see.unifcdf.r | 72 +++++++------
R/see.weibcdf.r | 75 +++++++------
R/selftest.conf.r | 10 -
R/selftest.pdfs.r | 6 -
R/selftest.prob.r | 9 +
R/selftest.sampd.r | 6 -
R/selftest.treatsamp.r | 8 -
R/shade.F.tck.r | 7 -
R/shade.bin.tck.r | 3
R/shade.chi.tck.r | 5
R/shade.norm.tck.r | 3
R/shade.poi.tck.r | 3
R/shade.r | 142 +++++++++++++-------------
R/shade.t.tck.r | 2
data/Fbird.rda |only
data/PM2.5.rda |only
data/bats.rda |only
data/cuckoo.rda |only
data/fruit.rda |only
data/garments.rda |only
data/goats.rda |only
data/heart.rda |only
data/portneuf.rda |only
data/veneer.rda |only
inst/doc/SampDistLikelihood.pdf |binary
man/Bayes.disc.rd | 4
man/DH.test.rd | 2
man/Fbird.rd |only
man/ML.k.rd |only
man/PM2.5.Rd |only
man/R.hat.rd |only
man/anm.ExpDesign.Rd | 21 ++-
man/anm.cont.pdf.rd |only
man/anm.ls.reg.rd |only
man/anm.mc.bvn.rd |only
man/asthma.Rd | 2
man/bats.rd |only
man/bplot.rd | 66 +++++-------
man/ci.strat.rd | 2
man/cuckoo.Rd |only
man/demos.rd | 2
man/fruit.rd |only
man/garments.rd |only
man/get.dist.Rd | 21 +--
man/goats.rd |only
man/heart.rd |only
man/lmu.tck.rd | 2
man/mcmc.norm.hier.rd |only
man/portneuf.Rd |only
man/prp.rd | 3
man/rankindex.new.Rd | 11 +-
man/samp.dist.Rd | 28 ++---
man/shade.norm.Rd | 15 +-
man/so2.us.cities.rd | 2
man/veneer.rd |only
126 files changed, 1342 insertions(+), 1110 deletions(-)