Title: Functions for a variety of stylometric analyses
Diff between stylo versions 0.5.1 dated 2013-08-08 and 0.5.2 dated 2013-09-08
Description: A number of functions, supplemented by GUI, to perform various
analyses in the field of computational stylistics, authorship
attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder
stylo-0.5.1/stylo/README.md |only
stylo-0.5.2/stylo/DESCRIPTION | 10 -
stylo-0.5.2/stylo/MD5 | 17 +-
stylo-0.5.2/stylo/NEWS | 7 -
stylo-0.5.2/stylo/R/assign.plot.colors.R | 4
stylo-0.5.2/stylo/R/stylo.R | 155 +++++++++++++++++++------
stylo-0.5.2/stylo/R/stylo.default.settings.R | 40 ++++++
stylo-0.5.2/stylo/man/load.corpus.and.parse.Rd | 4
stylo-0.5.2/stylo/man/make.ngrams.Rd | 2
stylo-0.5.2/stylo/man/rolling.delta.Rd | 2
10 files changed, 183 insertions(+), 58 deletions(-)
Title: MVPARTwrap: Additional features for package mvpart.
Diff between MVPARTwrap versions 0.1-9 dated 2012-05-02 and 0.1-9.1 dated 2013-09-08
Description: The main function of this package, MRT, provides to the following information : the proper cluster membership allocation in the tree, the discriminant species for each cluster, the tree nodes at the proper level of R2 (1-relative error), the total species variance partitioned by species, by the tree, and by the splits of the tree, plus a different graphic representation of the final model in the form of a tree. Moreover, the CascadeMRT function allows a cascade MRT analysis and the CasMRTR2 function allows to illustrate the (unadjusted) variation explained by each wave/drops. Last but not least, the R2aGDF function permits the calculation of an adjusted R^2 for an MRT model.
Author: Marie-Helene Ouellette
Maintainer: Marie-Helene Ouellette
DESCRIPTION | 29 +++++++++--------------------
MD5 | 18 +++++++++---------
NAMESPACE | 9 +++++++--
R/CascadeMRT.R | 2 +-
R/MRTsummaryplot.R | 9 ++++++---
R/R2aGDF.R | 2 +-
R/svaluecol.R | 2 +-
man/help_CasMRTR2.Rd | 2 +-
man/help_CascadeMRT.Rd | 2 +-
man/help_R2aGDF.Rd | 4 ++--
10 files changed, 38 insertions(+), 41 deletions(-)
Title: sybil - Efficient Constrained Based Modelling in R
Diff between sybil versions 1.2.2 dated 2013-07-18 and 1.2.4 dated 2013-09-08
Description: The package sybil is a Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis).
Author: Gabriel Gelius-Dietrich [aut, cre],
C. Jonathan Fritzemeier [ctb],
Rajen Piernikarczyk [ctb],
Marc Andre Daxer [ctb],
Benjamin Braasch [ctb],
Abdelmoneim Desouki [ctb]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 15 ++-
MD5 | 124 +++++++++++++++++---------------
NAMESPACE | 3
R/addReact.R | 2
R/blockedReact.R | 4 -
R/doubleGeneDel.R | 2
R/doubleReact.R | 2
R/editEnvir.R | 2
R/findExchReact.R | 7 +
R/geneDeletion.R | 2
R/generics.R | 25 ++++++
R/getsybilenv.R | 18 ++--
R/mod2irrev.R | 4 -
R/modelorg2text.R | 6 -
R/modelorg2tsv.R | 2
R/modelorgClass.R | 116 ++++++++++++++++++++++++------
R/oneGeneDel.R | 2
R/onlyChangeGPR.R | 4 -
R/optObj_clpAPIClass.R | 3
R/optObj_cplexAPIClass.R | 38 +++++++++-
R/optObj_glpkAPIClass.R | 33 ++++++++
R/optObj_lpSolveAPIClass.R | 55 ++++++++++++++
R/optimizer.R | 99 +++++++++++++++++++++-----
R/optsolClass.R | 10 +-
R/optsol_phppClass.R |only
R/optsol_robAnaClass.R | 7 +
R/phpp.R |only
R/reactIdClass.R | 2
R/reactId_ExchClass.R | 2
R/readTSVmod.R | 70 ++++++++++--------
R/rmReact.R | 2
R/robAna.R | 124 +++++++++-----------------------
R/summaryOptsolClass.R | 11 +-
R/sybilLogClass.R | 12 +--
R/sysBiolAlgClass.R | 6 -
R/sysBiolAlg_fbaClass.R | 6 -
R/sysBiolAlg_fvClass.R | 10 +-
R/sysBiolAlg_lmomaClass.R | 8 +-
R/sysBiolAlg_momaClass.R | 8 +-
R/sysBiolAlg_mtfClass.R | 8 +-
R/sysBiolAlg_roomClass.R | 8 +-
R/validmodelorg.R | 6 -
inst/NEWS.Rd | 28 +++++++
inst/doc/sybil.R | 136 +++++++++++++++++++++---------------
inst/doc/sybil.Rnw | 57 +++++++++++++--
inst/doc/sybil.pdf |binary
man/changeUptake-methods.Rd | 6 +
man/deadEndMetabolites-methods.Rd |only
man/getColsNames-methods.Rd |only
man/getRowsNames-methods.Rd |only
man/optimizer.Rd | 43 ++++++++---
man/optsol-class.Rd | 8 +-
man/optsol_phpp-class.Rd |only
man/optsol_robAna-class.Rd | 3
man/phpp.Rd |only
man/ppProc-class.Rd | 2
man/readTSVmod.Rd | 9 +-
man/robAna.Rd | 34 ++++-----
man/setColsNames-methods.Rd |only
man/setRowsNames-methods.Rd |only
man/singletonMetabolites-methods.Rd |only
man/summaryOptsol-class.Rd | 14 +--
man/sybil-package.Rd | 4 -
vignettes/optObj-class.pdf |binary
vignettes/optsol-class.pdf |binary
vignettes/sybil.Rnw | 57 +++++++++++++--
vignettes/sybil.bib | 38 +++++++++-
vignettes/sysBiolAlg-class.pdf |binary
68 files changed, 882 insertions(+), 425 deletions(-)
Title: Package allowing R to call Python
Diff between rPython versions 0.0-3 dated 2013-03-26 and 0.0-4 dated 2013-09-08
Description: This package permits calls to Python from R
Author: Carlos J. Gil Bellosta
Maintainer: Carlos J. Gil Bellosta
rPython-0.0-3/rPython/README.REQ |only
rPython-0.0-3/rPython/src/Makevars |only
rPython-0.0-4/rPython/DESCRIPTION | 10 +--
rPython-0.0-4/rPython/INSTALL |only
rPython-0.0-4/rPython/MD5 | 13 +---
rPython-0.0-4/rPython/R/python.call.R | 93 ++++++++++++++---------------
rPython-0.0-4/rPython/man/python.call.Rd | 98 ++++++++++++++++++-------------
rPython-0.0-4/rPython/man/python.exec.Rd | 80 ++++++++++++-------------
rPython-0.0-4/rPython/src/pycall.c | 6 +
9 files changed, 161 insertions(+), 139 deletions(-)
Title: Ordinary Regression Analysis with R
Diff between bstats versions 1.1-8-8 dated 2013-08-07 and 1.1-9-8 dated 2013-09-08
Description: This package collects commonly used procedures or
algorithms for general data analysis. In addition, routines
for linear regression analysis, statistical computing and
graphics, and many others have been implemented in R for
some courses taught at the University of South Alabama.
Author: Bin Wang
Maintainer: Bin Wang
DESCRIPTION | 10 +++----
MD5 | 34 +++++++++++++-------------
PORTING | 8 ++++++
R/whitetest.R | 66 +++++++++++++++++++++++++++++++--------------------
man/Raddons.Rd | 2 -
man/aclm.Rd | 4 ++-
man/birth.Rd | 6 +++-
man/edf.Rd | 2 -
man/influenceplot.Rd | 2 -
man/lmci.Rd | 2 -
man/medtest.Rd | 2 -
man/modelcheck.Rd | 2 -
man/modeltest.Rd | 2 -
man/predicotplot.Rd | 2 -
man/residplot.Rd | 2 -
man/scb.Rd | 2 -
man/whitetest.Rd | 5 +++
man/wls.Rd | 2 -
18 files changed, 94 insertions(+), 61 deletions(-)
Title: Documentation for packages distr, distrEx, distrSim, distrTEst,
distrTeach, distrMod, and distrEllipse
Diff between distrDoc versions 2.4 dated 2013-02-07 and 2.4.1 dated 2013-09-08
Description: provides documentation in form of a common vignette to packages distr, distrEx, distrMod, distrSim, distrTEst, distrTeach, and distrEllipse
Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla
Maintainer: Peter Ruckdeschel
distrDoc-2.4.1/distrDoc/DESCRIPTION | 34 ++++++------
distrDoc-2.4.1/distrDoc/MD5 | 18 +++---
distrDoc-2.4.1/distrDoc/NAMESPACE | 62 +++++++++++++++++++++--
distrDoc-2.4.1/distrDoc/R/distrDoc.R | 2
distrDoc-2.4.1/distrDoc/inst/NEWS | 1
distrDoc-2.4.1/distrDoc/inst/doc/distr.R |only
distrDoc-2.4.1/distrDoc/inst/doc/distr.Rnw | 36 ++++---------
distrDoc-2.4.1/distrDoc/inst/doc/distr.pdf |binary
distrDoc-2.4.1/distrDoc/man/0distrDoc-package.Rd | 2
distrDoc-2.4.1/distrDoc/vignettes/distr.Rnw | 36 ++++---------
distrDoc-2.4/distrDoc/distrDoc-Ex.R |only
11 files changed, 112 insertions(+), 79 deletions(-)
Title: Travel To Work Area.
Diff between ttwa versions 0.8.5 dated 2013-08-12 and 0.8.5.1 dated 2013-09-08
Description: This package makes Travel To Work Area from a commuting flow data frame.
Author: Francois Semecurbe, Joachim Timoteo
Maintainer: Francois Semecurbe
DESCRIPTION | 8 ++++----
MD5 | 13 +++++++------
NEWS |only
R/ttwa-internal.R | 12 +++++++++---
R/ttwa.R | 6 +++---
man/reunion_ttw.Rd | 14 ++++++++++----
man/ttwa-package.Rd | 18 ++++++++++++------
man/ttwa.Rd | 27 +++++++++++++++++++--------
8 files changed, 64 insertions(+), 34 deletions(-)
Title: Thinknum Data Connection
Diff between Thinknum versions 1.1.0 dated 2013-09-02 and 1.2 dated 2013-09-08
Description: This package interacts directly with the Thinknum API to offer data
in a number of formats usable in R
Author: Gregory Ugwi
Maintainer: Gregory Ugwi
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/Thinknum.R | 2 +-
README.md | 4 ++--
4 files changed, 9 insertions(+), 9 deletions(-)
Title: Use multiple feature selection algorithms to derive robust
feature sets for two or multiclass classification problems.
Diff between bootfs versions 1.2 dated 2013-08-26 and 1.4 dated 2013-09-08
Description: To select a set of features used for successful classification of two or more groups of samples, multiple classification and feature selection algorithms are utilised. By combining the results of all methods and applying a bootstrapping approach a robust set of features with high power to distinguish the sample groups is selected.
Author: Christian Bender
Maintainer: Christian Bender
bootfs-1.2/bootfs/man/rfclass_cv.Rd |only
bootfs-1.4/bootfs/DESCRIPTION | 18
bootfs-1.4/bootfs/MD5 | 108 +++--
bootfs-1.4/bootfs/NAMESPACE | 10
bootfs-1.4/bootfs/R/bsGBM.R | 35 +
bootfs-1.4/bootfs/R/bsPAMR.R | 27 -
bootfs-1.4/bootfs/R/bsRFBORUTA.R | 37 +-
bootfs-1.4/bootfs/R/bsSCAD.R | 41 +-
bootfs-1.4/bootfs/R/bs_methods.R | 25 +
bootfs-1.4/bootfs/R/control_params.R |only
bootfs-1.4/bootfs/R/cvGBM.R | 34 +
bootfs-1.4/bootfs/R/cvPAMR.R | 52 +-
bootfs-1.4/bootfs/R/cvRFBORUTA.R | 85 ++--
bootfs-1.4/bootfs/R/cvSCAD.R | 28 +
bootfs-1.4/bootfs/R/cv_gbmclass.R | 26 +
bootfs-1.4/bootfs/R/cv_pamclass.R | 100 ++---
bootfs-1.4/bootfs/R/cv_penalizedSVM.R | 36 +
bootfs-1.4/bootfs/R/cv_rfclass.R | 367 +++++++++++---------
bootfs-1.4/bootfs/R/doBS.R | 62 ++-
bootfs-1.4/bootfs/R/doCV.R | 116 +++---
bootfs-1.4/bootfs/R/extract_feat_pam.R | 8
bootfs-1.4/bootfs/R/extract_features_rf_boruta.R | 8
bootfs-1.4/bootfs/R/extractsignatures.R | 1
bootfs-1.4/bootfs/R/importance_igraph.R | 150 +++++++-
bootfs-1.4/bootfs/R/makeIG.R | 2
bootfs-1.4/bootfs/R/resultBS.R | 178 +++++----
bootfs-1.4/bootfs/R/resultCV.R |only
bootfs-1.4/bootfs/inst/doc/bootfs.R | 132 ++++++-
bootfs-1.4/bootfs/inst/doc/bootfs.Rnw | 178 ++++++++-
bootfs-1.4/bootfs/inst/doc/bootfs.pdf |binary
bootfs-1.4/bootfs/man/bootfs-package.Rd | 64 +--
bootfs-1.4/bootfs/man/bsGBM.Rd | 2
bootfs-1.4/bootfs/man/bsPAMR.Rd | 2
bootfs-1.4/bootfs/man/bsRFBORUTA.Rd | 2
bootfs-1.4/bootfs/man/bsSCAD.Rd | 5
bootfs-1.4/bootfs/man/control_params.Rd |only
bootfs-1.4/bootfs/man/cvGBM.Rd | 2
bootfs-1.4/bootfs/man/cvPAMR.Rd | 2
bootfs-1.4/bootfs/man/cvRFBORUTA.Rd | 24 -
bootfs-1.4/bootfs/man/cvSCAD.Rd | 2
bootfs-1.4/bootfs/man/cv_rfclass.Rd |only
bootfs-1.4/bootfs/man/doBS.Rd | 50 +-
bootfs-1.4/bootfs/man/doCV.Rd | 56 ++-
bootfs-1.4/bootfs/man/extract_feat_pam.Rd | 7
bootfs-1.4/bootfs/man/extract_features_rf_boruta.Rd | 18
bootfs-1.4/bootfs/man/importance_igraph.Rd | 35 +
bootfs-1.4/bootfs/man/resultBS.Rd | 43 --
bootfs-1.4/bootfs/man/resultCV.Rd |only
bootfs-1.4/bootfs/man/rf_multi.Rd | 29 +
bootfs-1.4/bootfs/vignettes/bootfs.Rnw | 178 ++++++++-
bootfs-1.4/bootfs/vignettes/bootfs.tex | 184 ++++++++--
bootfs-1.4/bootfs/vignettes/impgraph1.pdf |binary
bootfs-1.4/bootfs/vignettes/impgraph2.pdf |binary
bootfs-1.4/bootfs/vignettes/references.bib | 53 ++
bootfs-1.4/bootfs/vignettes/resultbsmulti.pdf |only
bootfs-1.4/bootfs/vignettes/resultcvmulti.pdf |only
bootfs-1.4/bootfs/vignettes/rocpam.pdf |binary
bootfs-1.4/bootfs/vignettes/rocrf.pdf |binary
bootfs-1.4/bootfs/vignettes/rocscad.pdf |binary
59 files changed, 1785 insertions(+), 837 deletions(-)
Title: SBML Integration in Package sybil
Diff between sybilSBML versions 2.0.4 dated 2013-08-02 and 2.0.5 dated 2013-09-08
Description: SBML (Systems Biology Markup Language) integration in sybil
Author: Gabriel Gelius-Dietrich [aut, cre],
Deya Alzoubi [ctb]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 11 ++++++-----
MD5 | 20 ++++++++++----------
NAMESPACE | 1 +
R/readSBMLmod.R | 29 ++++++++++++++++-------------
R/sbmlErrorClass.R | 10 +++++-----
configure | 20 ++++++++++----------
configure.ac | 4 ++--
inst/INSTALL | 2 +-
inst/NEWS.Rd | 10 ++++++++++
inst/doc/sybilSBML.pdf |binary
src/Makevars.win | 2 +-
11 files changed, 62 insertions(+), 47 deletions(-)
Title: Import/Export routines for MALDIquant
Diff between MALDIquantForeign versions 0.4 dated 2013-04-28 and 0.5 dated 2013-09-08
More information about MALDIquantForeign at CRAN
Description: This package allows to read (tab, csv, Bruker fid, Ciphergen XML,
mzXML, mzML, imzML, Analyze 7.5) and write (tab, csv, msd, mzML) different
file formats of mass spectrometry data into/from MALDIquant objects.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb
DESCRIPTION | 23 ++++++--------
MD5 | 44 +++++++++++++--------------
NAMESPACE | 1
NEWS | 8 ++++
R/compression-functions.R | 9 ++---
R/download-function.R | 7 ++--
R/filename-functions.R | 2 -
R/filename-methods.R | 2 -
R/import-functions.R | 20 +++++++++---
R/importAuto-functions.R | 6 ++-
R/importImzMl-functions.R | 6 +--
R/importTab-functions.R | 8 ++--
R/list.files-functions.R | 20 +++++++++---
R/msd-functions.R | 4 +-
R/mzMl-functions.R | 4 +-
R/package.R | 5 +--
R/parseCiphergenXml.R | 12 +++----
R/parseMzMl.R | 4 +-
R/xml-functions.R | 10 +++---
inst/tests/test_exportMzMl-methods.R | 7 ++--
inst/tests/test_importBrukerFlex-functions.R | 2 -
man/MALDIquantForeign-package.Rd | 2 -
man/import-functions.Rd | 13 +++++++
23 files changed, 131 insertions(+), 88 deletions(-)
Permanent link
Title: Quantitative Analysis of Mass Spectrometry Data
Diff between MALDIquant versions 1.7 dated 2013-05-23 and 1.8 dated 2013-09-08
Description: MALDIquant provides a complete analysis pipeline for MALDI-TOF
and other mass spectrometry data. Distinctive features include baseline
subtraction methods such as TopHat or SNIP, peak alignment using warping
functions, handling of replicated measurements as well as allowing spectra
with different resolutions.
Author: Sebastian Gibb [aut, cre],
Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb
MALDIquant-1.7/MALDIquant/R/calibrate-methods.R |only
MALDIquant-1.7/MALDIquant/R/imputeMass-methods.R |only
MALDIquant-1.7/MALDIquant/R/iplot-functions.R |only
MALDIquant-1.7/MALDIquant/R/iplot-methods.R |only
MALDIquant-1.7/MALDIquant/R/replaceNonEmptyMassObjects-functions.R |only
MALDIquant-1.7/MALDIquant/R/standardizeTotalIonCurrent-methods.R |only
MALDIquant-1.7/MALDIquant/inst/tests/test_calibrate-methods.R |only
MALDIquant-1.7/MALDIquant/inst/tests/test_imputeMass-methods.R |only
MALDIquant-1.7/MALDIquant/inst/tests/test_replaceNonEmptyMassObjects-functions.R |only
MALDIquant-1.7/MALDIquant/inst/tests/test_standardizeTotalIonCurrent.R |only
MALDIquant-1.7/MALDIquant/man/calibrate-methods.Rd |only
MALDIquant-1.7/MALDIquant/man/imputeMass-methods.Rd |only
MALDIquant-1.7/MALDIquant/man/iplot-methods.Rd |only
MALDIquant-1.7/MALDIquant/man/merge-functions.Rd |only
MALDIquant-1.7/MALDIquant/man/standardizeTotalIonCurrent-methods.Rd |only
MALDIquant-1.8/MALDIquant/DESCRIPTION | 28 -
MALDIquant-1.8/MALDIquant/MD5 | 248 +++++-----
MALDIquant-1.8/MALDIquant/NAMESPACE | 10
MALDIquant-1.8/MALDIquant/NEWS | 98 +++
MALDIquant-1.8/MALDIquant/R/AllClasses.R | 10
MALDIquant-1.8/MALDIquant/R/AllGenerics.R | 66 +-
MALDIquant-1.8/MALDIquant/R/Deprecated.R |only
MALDIquant-1.8/MALDIquant/R/approxfun-methods.R | 10
MALDIquant-1.8/MALDIquant/R/as.matrix-methods.R | 4
MALDIquant-1.8/MALDIquant/R/averageMassSpectra-functions.R |only
MALDIquant-1.8/MALDIquant/R/binPeaks-functions.R | 40 -
MALDIquant-1.8/MALDIquant/R/calculateLabelPositions-methods.R | 47 -
MALDIquant-1.8/MALDIquant/R/calibrateIntensity-functions.R |only
MALDIquant-1.8/MALDIquant/R/calibrateIntensity-methods.R |only
MALDIquant-1.8/MALDIquant/R/colMedians-functions.R |only
MALDIquant-1.8/MALDIquant/R/constructor-functions.R | 3
MALDIquant-1.8/MALDIquant/R/deprecated-functions.R |only
MALDIquant-1.8/MALDIquant/R/detectPeaks-methods.R | 29 -
MALDIquant-1.8/MALDIquant/R/determineWarpingFunctions-functions.R | 56 +-
MALDIquant-1.8/MALDIquant/R/doByLabels-functions.R | 6
MALDIquant-1.8/MALDIquant/R/estimateBaseline-functions.R | 50 +-
MALDIquant-1.8/MALDIquant/R/estimateBaseline-methods.R | 4
MALDIquant-1.8/MALDIquant/R/estimateNoise-methods.R | 2
MALDIquant-1.8/MALDIquant/R/filterPeaks-functions.R | 31 -
MALDIquant-1.8/MALDIquant/R/findEmptyMassObjects-functions.R | 3
MALDIquant-1.8/MALDIquant/R/findLocalMaxima-methods.R | 6
MALDIquant-1.8/MALDIquant/R/grouper-functions.R | 8
MALDIquant-1.8/MALDIquant/R/irregular-functions.R | 2
MALDIquant-1.8/MALDIquant/R/isEmpty-methods.R | 8
MALDIquant-1.8/MALDIquant/R/isFunctionList-functions.R | 4
MALDIquant-1.8/MALDIquant/R/isMassObject-functions.R | 2
MALDIquant-1.8/MALDIquant/R/isMassObjectList-functions.R | 16
MALDIquant-1.8/MALDIquant/R/isValidHalfWindowSize-functions.R | 6
MALDIquant-1.8/MALDIquant/R/labelPeaks-methods.R | 16
MALDIquant-1.8/MALDIquant/R/lines-methods.R | 6
MALDIquant-1.8/MALDIquant/R/localMaxima-functions.R | 14
MALDIquant-1.8/MALDIquant/R/memoryUsage-functions.R | 4
MALDIquant-1.8/MALDIquant/R/merge-functions.R | 170 +-----
MALDIquant-1.8/MALDIquant/R/plot-methods.R | 10
MALDIquant-1.8/MALDIquant/R/range-functions.R |only
MALDIquant-1.8/MALDIquant/R/referencePeaks-functions.R | 2
MALDIquant-1.8/MALDIquant/R/removeBaseline-methods.R | 28 -
MALDIquant-1.8/MALDIquant/R/removeEmptyMassObjects-functions.R | 2
MALDIquant-1.8/MALDIquant/R/show-functions.R | 5
MALDIquant-1.8/MALDIquant/R/show-methods.R | 15
MALDIquant-1.8/MALDIquant/R/smoothIntensity-methods.R |only
MALDIquant-1.8/MALDIquant/R/smoothingFilters-functions.R | 38 -
MALDIquant-1.8/MALDIquant/R/subset-methods.R | 4
MALDIquant-1.8/MALDIquant/R/textLabelRects-functions.R | 8
MALDIquant-1.8/MALDIquant/R/totalIonCurrent-methods.R | 27 -
MALDIquant-1.8/MALDIquant/R/transformIntensity-methods.R | 60 ++
MALDIquant-1.8/MALDIquant/R/trim-methods.R | 83 ---
MALDIquant-1.8/MALDIquant/R/unlist-functions.R | 1
MALDIquant-1.8/MALDIquant/R/warp-functions.R | 1
MALDIquant-1.8/MALDIquant/R/warpingFunction-functions.R | 42 +
MALDIquant-1.8/MALDIquant/R/which.closest-functions.R | 3
MALDIquant-1.8/MALDIquant/demo/baseline.R | 4
MALDIquant-1.8/MALDIquant/demo/peaks.R | 2
MALDIquant-1.8/MALDIquant/demo/warping.R | 14
MALDIquant-1.8/MALDIquant/demo/workflow.R | 16
MALDIquant-1.8/MALDIquant/inst/tests/test_approxfun-methods.R | 6
MALDIquant-1.8/MALDIquant/inst/tests/test_averageMassSpectra-functions.R |only
MALDIquant-1.8/MALDIquant/inst/tests/test_calibrateIntensity-methods.R |only
MALDIquant-1.8/MALDIquant/inst/tests/test_colMedians-functions.R |only
MALDIquant-1.8/MALDIquant/inst/tests/test_constructor-functions.R | 6
MALDIquant-1.8/MALDIquant/inst/tests/test_deprecated-functons.R |only
MALDIquant-1.8/MALDIquant/inst/tests/test_detectPeaks-methods.R | 21
MALDIquant-1.8/MALDIquant/inst/tests/test_determineWarpingFunctions-functions.R | 10
MALDIquant-1.8/MALDIquant/inst/tests/test_estimateBaseline-methods.R | 4
MALDIquant-1.8/MALDIquant/inst/tests/test_estimateNoise-methods.R | 2
MALDIquant-1.8/MALDIquant/inst/tests/test_filterPeaks-functions.R | 8
MALDIquant-1.8/MALDIquant/inst/tests/test_grouper-functions.R | 2
MALDIquant-1.8/MALDIquant/inst/tests/test_isEmpty-methods.R | 2
MALDIquant-1.8/MALDIquant/inst/tests/test_isMassObject-functions.R | 10
MALDIquant-1.8/MALDIquant/inst/tests/test_isMassObjectList-functions.R | 16
MALDIquant-1.8/MALDIquant/inst/tests/test_merge-functions.R | 65 --
MALDIquant-1.8/MALDIquant/inst/tests/test_range-functions.R |only
MALDIquant-1.8/MALDIquant/inst/tests/test_removeBaseline-methods.R | 21
MALDIquant-1.8/MALDIquant/inst/tests/test_smoothIntensity-methods.R |only
MALDIquant-1.8/MALDIquant/inst/tests/test_smoothingFilters-functions.R | 36 -
MALDIquant-1.8/MALDIquant/inst/tests/test_totalIonCurrent-methods.R | 23
MALDIquant-1.8/MALDIquant/inst/tests/test_transformIntensity-methods.R | 39 +
MALDIquant-1.8/MALDIquant/inst/tests/test_trim-methods.R | 24
MALDIquant-1.8/MALDIquant/inst/tests/test_warpingFunctions-functions.R |only
MALDIquant-1.8/MALDIquant/man/AbstractMassObject-class.Rd | 34 -
MALDIquant-1.8/MALDIquant/man/MALDIquant-deprecated.Rd |only
MALDIquant-1.8/MALDIquant/man/MALDIquant-internal.Rd | 24
MALDIquant-1.8/MALDIquant/man/MALDIquant-package.Rd | 4
MALDIquant-1.8/MALDIquant/man/MassPeaks-class.Rd | 2
MALDIquant-1.8/MALDIquant/man/MassSpectrum-class.Rd | 26 -
MALDIquant-1.8/MALDIquant/man/averageMassSpectra-functions.Rd |only
MALDIquant-1.8/MALDIquant/man/binPeaks-functions.Rd | 2
MALDIquant-1.8/MALDIquant/man/calibrateIntensity-methods.Rd |only
MALDIquant-1.8/MALDIquant/man/createMassPeaks-functions.Rd | 5
MALDIquant-1.8/MALDIquant/man/createMassSpectrum-functions.Rd | 2
MALDIquant-1.8/MALDIquant/man/detectPeaks-methods.Rd | 49 -
MALDIquant-1.8/MALDIquant/man/determineWarpingFunctions-functions.Rd | 85 +--
MALDIquant-1.8/MALDIquant/man/estimateBaseline-methods.Rd | 8
MALDIquant-1.8/MALDIquant/man/estimateBaselineConvexHull-functions.Rd | 2
MALDIquant-1.8/MALDIquant/man/estimateBaselineMedian-functions.Rd | 4
MALDIquant-1.8/MALDIquant/man/estimateBaselineSnip-functions.Rd | 2
MALDIquant-1.8/MALDIquant/man/estimateBaselineTopHat-functions.Rd | 2
MALDIquant-1.8/MALDIquant/man/estimateNoise-methods.Rd | 10
MALDIquant-1.8/MALDIquant/man/estimateNoiseMad-functions.Rd | 4
MALDIquant-1.8/MALDIquant/man/estimateNoiseSuperSmoother-functions.Rd | 4
MALDIquant-1.8/MALDIquant/man/filterPeaks-functions.Rd | 2
MALDIquant-1.8/MALDIquant/man/findEmptyMassObjects-functions.Rd | 2
MALDIquant-1.8/MALDIquant/man/intensityMatrix-functions.Rd | 2
MALDIquant-1.8/MALDIquant/man/isMassObject-functions.Rd | 16
MALDIquant-1.8/MALDIquant/man/isMassObjectList-functions.Rd | 16
MALDIquant-1.8/MALDIquant/man/labelPeaks-methods.Rd | 2
MALDIquant-1.8/MALDIquant/man/mergeMassPeaks-functions.Rd |only
MALDIquant-1.8/MALDIquant/man/movingAverage-functions.Rd | 29 -
MALDIquant-1.8/MALDIquant/man/plot-methods.Rd | 2
MALDIquant-1.8/MALDIquant/man/referencePeaks-functions.Rd | 2
MALDIquant-1.8/MALDIquant/man/removeBaseline-methods.Rd | 47 -
MALDIquant-1.8/MALDIquant/man/savitzkyGolay-functions.Rd | 25 -
MALDIquant-1.8/MALDIquant/man/smoothIntensity-methods.Rd |only
MALDIquant-1.8/MALDIquant/man/transformIntensity-methods.Rd | 30 -
MALDIquant-1.8/MALDIquant/man/trim-methods.Rd | 44 -
MALDIquant-1.8/MALDIquant/man/warp-functions.Rd | 5
MALDIquant-1.8/MALDIquant/src/MALDIquant.h | 1
MALDIquant-1.8/MALDIquant/src/colMedians.c |only
MALDIquant-1.8/MALDIquant/src/init.c | 1
MALDIquant-1.8/MALDIquant/src/localMaxima.c | 11
MALDIquant-1.8/MALDIquant/src/lowerConvexHull.c | 4
MALDIquant-1.8/MALDIquant/src/morphologicalFilters.c | 10
MALDIquant-1.8/MALDIquant/src/snip.c | 16
143 files changed, 1069 insertions(+), 1134 deletions(-)
Title: R Interface to C API of COIN-OR Clp
Diff between clpAPI versions 1.2.4 dated 2013-07-17 and 1.2.5 dated 2013-09-08
Description: R Interface to C API of COIN-OR Clp, depends on COIN-OR Clp Version >= 1.12.0
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 11 +-
MD5 | 12 +-
NAMESPACE | 2
configure | 229 ++++++++++++++++++++++++----------------------------
configure.ac | 13 --
inst/NEWS.Rd | 8 +
inst/doc/clpAPI.pdf |binary
7 files changed, 130 insertions(+), 145 deletions(-)
Title: Supplementary Item Response Theory Models
Diff between sirt versions 0.34-36 dated 2013-08-13 and 0.36-30 dated 2013-09-08
Description:
Supplementary item response theory models
to complement existing functions in R.
Author: Alexander Robitzsch
Maintainer: Alexander Robitzsch
sirt-0.34-36/sirt/R/rasch.testlet.R |only
sirt-0.34-36/sirt/man/rasch.testlet.glmer.Rd |only
sirt-0.34-36/sirt/src/interval_index_c.cpp |only
sirt-0.34-36/sirt/src/mml2_calcpost_v1.cpp |only
sirt-0.34-36/sirt/src/mml2_raschtype_counts.cpp |only
sirt-0.34-36/sirt/src/rm.arraymult.cpp |only
sirt-0.34-36/sirt/src/rm.probraterfct.cpp |only
sirt-0.34-36/sirt/src/rm_calcpost.cpp |only
sirt-0.34-36/sirt/src/rowcumsums_source.cpp |only
sirt-0.34-36/sirt/src/rowksmallest_c.cpp |only
sirt-0.34-36/sirt/src/rowmaxscpp_source.cpp |only
sirt-0.34-36/sirt/src/smirt_calcpost.cpp |only
sirt-0.34-36/sirt/src/smirt_calcprob_comp.cpp |only
sirt-0.34-36/sirt/src/smirt_calcprob_noncomp.cpp |only
sirt-0.36-30/sirt/DESCRIPTION | 17
sirt-0.36-30/sirt/MD5 | 206 +-
sirt-0.36-30/sirt/NAMESPACE | 24
sirt-0.36-30/sirt/R/detect.R | 15
sirt-0.36-30/sirt/R/dif.logisticregression.R | 49
sirt-0.36-30/sirt/R/dif.variance.R | 9
sirt-0.36-30/sirt/R/f1d.irt.R |only
sirt-0.36-30/sirt/R/fit.logistic.R | 8
sirt-0.36-30/sirt/R/gom.em.alg.R | 9
sirt-0.36-30/sirt/R/linking.haberman.R |only
sirt-0.36-30/sirt/R/linking.haberman.aux.R |only
sirt-0.36-30/sirt/R/matrixfunctions_sirt.R | 27
sirt-0.36-30/sirt/R/mcmc.2pno_alg.R | 9
sirt-0.36-30/sirt/R/mcmc.3pno.testlet.R | 37
sirt-0.36-30/sirt/R/mcmc.3pno.testlet_alg.R | 40
sirt-0.36-30/sirt/R/mcmc.3pno.testlet_output.R | 18
sirt-0.36-30/sirt/R/md.pattern.sirt.R |only
sirt-0.36-30/sirt/R/plot.isop.R | 9
sirt-0.36-30/sirt/R/plot.rasch.mml.R |only
sirt-0.36-30/sirt/R/rasch.copula.R | 13
sirt-0.36-30/sirt/R/rasch.copula2.R | 889 ----------
sirt-0.36-30/sirt/R/rasch.copula2_aux.R |only
sirt-0.36-30/sirt/R/rasch.mirtlc_aux.R | 49
sirt-0.36-30/sirt/R/rasch.mml.R | 28
sirt-0.36-30/sirt/R/rasch.mml.npirt.R | 48
sirt-0.36-30/sirt/R/rasch.mml.raschtype.R | 54
sirt-0.36-30/sirt/R/rasch.mml2.R | 24
sirt-0.36-30/sirt/R/rasch.pairwise.R | 82
sirt-0.36-30/sirt/R/rasch.pairwise.itemcluster.R |only
sirt-0.36-30/sirt/R/smirt.R | 7
sirt-0.36-30/sirt/R/stratified.cronbach.alpha.R | 11
sirt-0.36-30/sirt/R/summary.R2noharm.R | 2
sirt-0.36-30/sirt/R/summary.rasch.copula.R | 9
sirt-0.36-30/sirt/R/summary.smirt.R | 10
sirt-0.36-30/sirt/R/tetrachoric2.R | 13
sirt-0.36-30/sirt/R/wle.rasch.R | 43
sirt-0.36-30/sirt/R/yen.q3.R | 31
sirt-0.36-30/sirt/data/data.big5.rda |binary
sirt-0.36-30/sirt/data/data.long.rda |binary
sirt-0.36-30/sirt/data/data.math.rda |binary
sirt-0.36-30/sirt/data/data.ml1.rda |binary
sirt-0.36-30/sirt/data/data.ml2.rda |binary
sirt-0.36-30/sirt/data/data.noharm.rda |binary
sirt-0.36-30/sirt/data/data.pars1.2pl.rda |only
sirt-0.36-30/sirt/data/data.pars1.rasch.rda |only
sirt-0.36-30/sirt/data/data.pisaMath.rda |binary
sirt-0.36-30/sirt/data/data.pisaPars.rda |binary
sirt-0.36-30/sirt/data/data.pisaRead.rda |binary
sirt-0.36-30/sirt/data/data.ratings1.rda |binary
sirt-0.36-30/sirt/data/data.read.rda |binary
sirt-0.36-30/sirt/data/data.timss.rda |binary
sirt-0.36-30/sirt/inst/NEWS | 77
sirt-0.36-30/sirt/man/R2noharm.Rd | 51
sirt-0.36-30/sirt/man/ccov.np.Rd | 2
sirt-0.36-30/sirt/man/conf.detect.Rd | 2
sirt-0.36-30/sirt/man/data.big5.Rd | 11
sirt-0.36-30/sirt/man/data.long.Rd | 85
sirt-0.36-30/sirt/man/data.ml.Rd | 25
sirt-0.36-30/sirt/man/data.pars1.rasch.Rd |only
sirt-0.36-30/sirt/man/data.ratings1.Rd | 7
sirt-0.36-30/sirt/man/data.read.Rd | 94 +
sirt-0.36-30/sirt/man/dif.logistic.regression.Rd | 44
sirt-0.36-30/sirt/man/eigenvalues.manymatrices.Rd | 4
sirt-0.36-30/sirt/man/equating.rasch.Rd | 4
sirt-0.36-30/sirt/man/expl.detect.Rd | 2
sirt-0.36-30/sirt/man/f1d.irt.Rd |only
sirt-0.36-30/sirt/man/fit.isop.Rd | 3
sirt-0.36-30/sirt/man/greenyang.reliability.Rd | 22
sirt-0.36-30/sirt/man/latent.regression.em.raschtype.Rd | 4
sirt-0.36-30/sirt/man/linking.haberman.Rd |only
sirt-0.36-30/sirt/man/lsdm.Rd | 4
sirt-0.36-30/sirt/man/marginal.truescore.reliability.Rd | 16
sirt-0.36-30/sirt/man/matrixfunctions.sirt.Rd | 17
sirt-0.36-30/sirt/man/mcmc.3pno.testlet.Rd | 154 +
sirt-0.36-30/sirt/man/mcmclist2coda.Rd | 2
sirt-0.36-30/sirt/man/md.pattern.sirt.Rd |only
sirt-0.36-30/sirt/man/monoreg.rowwise.Rd | 3
sirt-0.36-30/sirt/man/np.dich.Rd | 2
sirt-0.36-30/sirt/man/personfit.stat.Rd | 2
sirt-0.36-30/sirt/man/plausible.value.imputation.raschtype.Rd | 2
sirt-0.36-30/sirt/man/prmse.subscores.scales.Rd | 2
sirt-0.36-30/sirt/man/prob.guttman.Rd | 2
sirt-0.36-30/sirt/man/rasch.copula.Rd | 2
sirt-0.36-30/sirt/man/rasch.jml.Rd | 2
sirt-0.36-30/sirt/man/rasch.jml.jackknife1.Rd | 2
sirt-0.36-30/sirt/man/rasch.mirtlc.Rd | 2
sirt-0.36-30/sirt/man/rasch.mml.Rd | 86
sirt-0.36-30/sirt/man/rasch.pairwise.Rd | 2
sirt-0.36-30/sirt/man/rasch.pairwise.itemcluster.Rd | 43
sirt-0.36-30/sirt/man/rasch.pml.Rd | 8
sirt-0.36-30/sirt/man/rasch.prox.Rd | 4
sirt-0.36-30/sirt/man/sim.qm.ramsay.Rd | 2
sirt-0.36-30/sirt/man/sim.rasch.dep.Rd | 10
sirt-0.36-30/sirt/man/sirt-package.Rd | 265 +-
sirt-0.36-30/sirt/man/smirt.Rd | 2
sirt-0.36-30/sirt/man/stratified.cronbach.alpha.Rd | 26
sirt-0.36-30/sirt/man/tetrachoric2.Rd | 4
sirt-0.36-30/sirt/man/wle.rasch.Rd | 2
sirt-0.36-30/sirt/man/wle.rasch.jackknife.Rd | 2
sirt-0.36-30/sirt/man/yen.q3.Rd | 12
sirt-0.36-30/sirt/src/matrixfunctions_sirt.cpp |only
sirt-0.36-30/sirt/src/md_pattern_csource.cpp |only
sirt-0.36-30/sirt/src/mml2_raschtype_cppcode.cpp |only
sirt-0.36-30/sirt/src/monoreg_rowwise_c.cpp | 1
sirt-0.36-30/sirt/src/rm_cppcode.cpp |only
sirt-0.36-30/sirt/src/smirt_cppcode.cpp |only
120 files changed, 1264 insertions(+), 1646 deletions(-)
Title: A set of tools for measuring spatial segregation
Diff between seg versions 0.2-4 dated 2013-01-21 and 0.3-2 dated 2013-09-08
Description: A package that provides functions for measuring spatial
segregation. The methods implemented in this package include
White's P index (1983), Morrill's D(adj) (1991), Wong's D(w)
and D(s) (1993), and Reardon and O'Sullivan's set of spatial
segregation measures (2004).
Author: Seong-Yun Hong, David O'Sullivan
Maintainer: Seong-Yun Hong
DESCRIPTION | 28 +++++------
MD5 | 18 +++----
NAMESPACE | 44 +++++++++---------
R/seg.R | 87 +++++++++++++++++++-----------------
R/whiteseg.R | 104 +++++++++++++++++++++++---------------------
data/segdata.rda |binary
man/seg.Rd | 128 ++++++++++++++++++++++++++++--------------------------
man/segdata.Rd | 107 +++++++++++++++++++++++----------------------
man/spseg.Rd | 130 +++++++++++++++++++++++++++----------------------------
man/whiteseg.Rd | 115 ++++++++++++++++++++++++------------------------
10 files changed, 394 insertions(+), 367 deletions(-)
Title: MongoDB Client for R
Diff between RMongo versions 0.0.23 dated 2013-03-08 and 0.0.25 dated 2013-09-08
Description: MongoDB Database interface for R. The interface is provided via Java calls to the mongo-java-driver.
Author: Tommy Chheng
Maintainer: Tommy Chheng
DESCRIPTION | 14 -
MD5 | 16 -
NAMESPACE | 5
R/rmongo.R | 14 +
README | 6
inst/java/r-mongo-scala-1.0-SNAPSHOT.jar |binary
man/dbSetWriteConcern-methods.Rd |only
man/mongoDbReplicaSetConnect.Rd |only
tests/RMongo-Ex.R | 2
tests/RMongo-Ex.Rout.save | 300 ++++++++++++++-----------------
10 files changed, 182 insertions(+), 175 deletions(-)