More information about wrspathrowData at CRAN
Permanent link
Title: Toolbox for Aquatic Ecosystem Modeling
Diff between ecosim versions 1.01 dated 2013-02-14 and 1.2 dated 2014-02-12
Description: Classes and methods for implementing aquatic ecosystem models,
for running these models, and for visualizing their results.
Author: Peter Reichert
Maintainer: Peter Reichert
DESCRIPTION | 14 +-
MD5 | 14 +-
NAMESPACE | 3
R/ecosim.r | 265 ++++++++++++++++++++++++++++++++++++++------------
man/ecosim-package.Rd | 30 +++--
man/plotres.Rd | 1
man/randnorm.Rd |only
man/randou.Rd |only
man/system-class.Rd | 2
9 files changed, 239 insertions(+), 90 deletions(-)
Title: Exact Binary Sequential Designs and Analysis
Diff between binseqtest versions 0.3 dated 2012-11-05 and 0.4 dated 2014-02-12
Description: For a series of binary responses, create stopping boundary with exact results after stopping, allowing updating for missing assessments.
Author: Jenn Kirk, Michael P. Fay
Maintainer: Michael P. Fay
binseqtest-0.3/binseqtest/demo/designSimon.R |only
binseqtest-0.4/binseqtest/CHANGELOG |only
binseqtest-0.4/binseqtest/DESCRIPTION | 17 ++---
binseqtest-0.4/binseqtest/MD5 | 29 +++++-----
binseqtest-0.4/binseqtest/NAMESPACE | 1
binseqtest-0.4/binseqtest/R/allFuncs.R | 18 ++++--
binseqtest-0.4/binseqtest/build |only
binseqtest-0.4/binseqtest/demo/00Index | 1
binseqtest-0.4/binseqtest/demo/SimonTablesUsingClinfun.R | 4 +
binseqtest-0.4/binseqtest/inst/doc/ExactBinarySequentialDesigns.R |only
binseqtest-0.4/binseqtest/inst/doc/ExactBinarySequentialDesigns.Rnw | 2
binseqtest-0.4/binseqtest/inst/doc/ExactBinarySequentialDesigns.pdf |binary
binseqtest-0.4/binseqtest/man/analyzeBoundNBF.Rd | 8 ++
binseqtest-0.4/binseqtest/man/designOBF.Rd | 28 ++++++---
binseqtest-0.4/binseqtest/man/modify.Rd | 4 +
binseqtest-0.4/binseqtest/man/stopTable.Rd | 3 -
binseqtest-0.4/binseqtest/man/unirootDiscrete.Rd | 4 +
binseqtest-0.4/binseqtest/vignettes |only
18 files changed, 74 insertions(+), 45 deletions(-)
Title: Cross-platform Perl based R function to create Excel 2003 (XLS)
and Excel 2007 (XLSX) files
Diff between WriteXLS versions 3.3.1 dated 2014-01-21 and 3.4.0 dated 2014-02-12
Description: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it contains
or can be specified by the user.
Author: Marc Schwartz
Maintainer: Marc Schwartz
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/WriteXLS.R | 2 +-
R/testPerl.R | 2 +-
man/WriteXLS.Rd | 3 +--
man/testPerl.Rd | 3 +--
6 files changed, 13 insertions(+), 15 deletions(-)
Title: R binder for the Yhat API
Diff between yhatr versions 0.6 dated 2013-12-06 and 0.7 dated 2014-02-12
Description: yhatr lets you deploy, maintain, and invoke models via the Yhat
REST API.
Author: Greg Lamp
Maintainer: Greg Lamp
yhatr-0.6/yhatr/man/documentColumn.Rd |only
yhatr-0.6/yhatr/man/documentData.Rd |only
yhatr-0.6/yhatr/man/yhat.document.Rd |only
yhatr-0.6/yhatr/man/yhat.login.Rd |only
yhatr-0.7/yhatr/DESCRIPTION | 8
yhatr-0.7/yhatr/MD5 | 29 +--
yhatr-0.7/yhatr/NAMESPACE | 3
yhatr-0.7/yhatr/NEWS | 30 +++
yhatr-0.7/yhatr/R/yhatr.R | 243 ++++++++++-------------------
yhatr-0.7/yhatr/README | 3
yhatr-0.7/yhatr/demo/iris-glm.R | 8
yhatr-0.7/yhatr/demo/iris-rf.R | 8
yhatr-0.7/yhatr/man/yhat.deploy.Rd | 5
yhatr-0.7/yhatr/man/yhat.deploy.to.file.Rd |only
yhatr-0.7/yhatr/man/yhat.predict.Rd | 12 -
yhatr-0.7/yhatr/man/yhat.predict_raw.Rd | 9 -
yhatr-0.7/yhatr/man/yhat.show_models.Rd | 5
yhatr-0.7/yhatr/man/yhatR-package.Rd | 13 -
18 files changed, 170 insertions(+), 206 deletions(-)
Title: Help to fit of a parametric distribution to non-censored or
censored data
Diff between fitdistrplus versions 1.0-1 dated 2013-04-10 and 1.0-2 dated 2014-02-12
Description: Extends the fitdistr function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation method the package provides moment matching, quantile matching and maximum goodness-of-fit estimation methods (available only for non-censored data).
Author: Marie Laure Delignette-Muller [aut, cre],
Christophe Dutang [aut],
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb]
Maintainer: Marie Laure Delignette-Muller
plotdist.R | 5
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/DESCRIPTION | 36 ++---
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/MD5 | 38 ++---
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/R/bootdistcens.R | 6
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/R/plotdist.R | 69 ++++++++--
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/data/danishmulti.rda |binary
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/data/danishuni.rda |binary
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/data/endosulfan.rda |binary
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/data/fluazinam.rda |binary
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/data/groundbeef.rda |binary
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/data/salinity.rda |binary
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/data/smokedfish.rda |binary
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/data/toxocara.rda |binary
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/inst/CITATION | 6
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/inst/NEWS | 19 ++
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/man/fitdist.Rd | 2
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/man/graphcomp.Rd | 26 ++-
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/man/plotdist.Rd | 19 ++
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/man/qmedist.Rd | 2
tmp/cranberry25f51945a626/fitdistrplus-1.0-2/fitdistrplus/man/quantiles.Rd | 20 +-
20 files changed, 165 insertions(+), 83 deletions(-)
Title: Quality Control of Genome Wide Association Study results
Diff between QCGWAS versions 1.0-7 dated 2013-11-08 and 1.0-8 dated 2014-02-12
Description: Tools for (automated and manual) quality control of
the results of Genome Wide Association Studies
Author: Peter J. van der Most and Ilja M. Nolte
Maintainer: Peter J. van der Most
QCGWAS-1.0-7/QCGWAS/data/header_translations.RData |only
QCGWAS-1.0-7/QCGWAS/inst/doc/QCGWAS-v10-7_manual.pdf |only
QCGWAS-1.0-7/QCGWAS/inst/doc/QCGWAS_v10-7_documentation.doc |only
QCGWAS-1.0-7/QCGWAS/inst/doc/QCGWAS_v10-7_quick_start_guide.doc |only
QCGWAS-1.0-8/QCGWAS/DESCRIPTION | 10 +-
QCGWAS-1.0-8/QCGWAS/MD5 | 30 +++---
QCGWAS-1.0-8/QCGWAS/R/QCGWAS-internal.R | 2
QCGWAS-1.0-8/QCGWAS/R/QC_GWAS.R | 47 +++++++---
QCGWAS-1.0-8/QCGWAS/R/QC_series.R | 2
QCGWAS-1.0-8/QCGWAS/R/filter_GWAS.R | 7 -
QCGWAS-1.0-8/QCGWAS/R/save_log.R | 2
QCGWAS-1.0-8/QCGWAS/data/gwa_sample.rda |binary
QCGWAS-1.0-8/QCGWAS/data/header_translations.rda |only
QCGWAS-1.0-8/QCGWAS/inst/CITATION | 23 +++-
QCGWAS-1.0-8/QCGWAS/inst/doc/QCGWAS_v10-8_documentation.doc |only
QCGWAS-1.0-8/QCGWAS/inst/doc/QCGWAS_v10-8_quick_start_guide.doc |only
QCGWAS-1.0-8/QCGWAS/inst/doc/QCGWAS_v10_8_manual.pdf |only
QCGWAS-1.0-8/QCGWAS/man/QCGWAS-package.Rd | 4
QCGWAS-1.0-8/QCGWAS/man/QC_GWAS.Rd | 19 +++-
QCGWAS-1.0-8/QCGWAS/man/plot_distribution.Rd | 16 ---
20 files changed, 96 insertions(+), 66 deletions(-)
Title: Cubature over Polygonal Domains
Diff between polyCub versions 0.4-1 dated 2013-12-05 and 0.4-2 dated 2014-02-12
Description: A package providing methods for cubature (numerical integration)
over polygonal domains.
Currently, four cubature methods are implemented:
the two-dimensional midpoint rule (a simple wrapper around
spatstat::as.im.function), the product Gauss cubature proposed
by Sommariva and Vianello (2007), an adaptive cubature for
isotropic functions via line integrate() along the boundary,
and quasi-exact methods specific to the integration of the
bivariate Gaussian density over polygonal and circular domains.
For cubature over simple hypercubes, the
packages cubature and R2Cuba are more appropriate.
Author: Sebastian Meyer [aut, cre, trl],
Michael Hoehle [ths]
Maintainer: Sebastian Meyer
polyCub-0.4-1/polyCub/inst/tests |only
polyCub-0.4-2/polyCub/DESCRIPTION | 8 -
polyCub-0.4-2/polyCub/MD5 | 56 +++++------
polyCub-0.4-2/polyCub/R/plotpolyf.R | 18 ++-
polyCub-0.4-2/polyCub/R/polyCub.iso.R | 78 +++++++++------
polyCub-0.4-2/polyCub/R/xylist.R | 8 -
polyCub-0.4-2/polyCub/R/zzz.R | 13 ++
polyCub-0.4-2/polyCub/inst/NEWS.Rd | 19 +++
polyCub-0.4-2/polyCub/inst/examples/polyCub.iso.R | 6 -
polyCub-0.4-2/polyCub/man/circleCub.Gauss.Rd | 34 +++---
polyCub-0.4-2/polyCub/man/coerce-gpc-methods.Rd | 56 +++++------
polyCub-0.4-2/polyCub/man/coerce-sp-methods.Rd | 14 +-
polyCub-0.4-2/polyCub/man/dotprod.Rd | 6 -
polyCub-0.4-2/polyCub/man/gpclibPermit.Rd | 15 +--
polyCub-0.4-2/polyCub/man/isClosed.Rd | 8 -
polyCub-0.4-2/polyCub/man/isScalar.Rd | 8 -
polyCub-0.4-2/polyCub/man/makegrid.Rd | 14 +-
polyCub-0.4-2/polyCub/man/plot_polyregion.Rd | 4
polyCub-0.4-2/polyCub/man/plotpolyf.Rd | 23 +++-
polyCub-0.4-2/polyCub/man/polyCub-package.Rd | 99 ++++++++++---------
polyCub-0.4-2/polyCub/man/polyCub.Rd | 23 ++--
polyCub-0.4-2/polyCub/man/polyCub.SV.Rd | 35 +++----
polyCub-0.4-2/polyCub/man/polyCub.exact.Gauss.Rd | 84 ++++++++--------
polyCub-0.4-2/polyCub/man/polyCub.iso.Rd | 84 +++++++++-------
polyCub-0.4-2/polyCub/man/polyCub.midpoint.Rd | 31 +++---
polyCub-0.4-2/polyCub/man/polygauss.Rd | 12 +-
polyCub-0.4-2/polyCub/man/vecnorm.Rd | 6 -
polyCub-0.4-2/polyCub/man/xylist.Rd | 109 ++++++++++------------
polyCub-0.4-2/polyCub/tests/test-all.R | 8 -
polyCub-0.4-2/polyCub/tests/testthat |only
30 files changed, 469 insertions(+), 410 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Diff between multcomp versions 1.3-1 dated 2013-11-01 and 1.3-2 dated 2014-02-12
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 8
MD5 | 24
NAMESPACE | 1
build/vignette.rds |binary
data/cholesterol.rda |binary
data/litter.rda |binary
inst/MCMT/MCMT.R | 5
inst/MCMT/MCMT.Rout | 1186 +++++++++++++++++------------------
inst/MCMT/MCMT.Rout.save |only
inst/MCMT/Rplots.pdf |only
inst/doc/chfls1.pdf |binary
inst/doc/generalsiminf.pdf |binary
inst/doc/multcomp-examples.pdf |binary
tests/Examples/multcomp-Ex.Rout.save | 12
14 files changed, 631 insertions(+), 605 deletions(-)
Title: Method Comparison Regression
Diff between mcr versions 1.2 dated 2014-02-05 and 1.2.1 dated 2014-02-12
Description: This package provides regression methods to quantify the relation between two measurement methods. In particular it addresses regression problems with errors in both variables and without repeated measurements. The package provides implementations of Deming regression, weighted Deming regression, and Passing-Bablok regression following the CLSI EP09-A3 recommendations for analytical method comparison and bias estimation using patient samples.
Author: Ekaterina Manuilova
Maintainer: Fabian Model
DESCRIPTION | 8 +-
MD5 | 20 +++----
R/MCResultMethods.r | 105 ++++++++++++++++++------------------
R/mcBootstrap.r | 27 +++++++--
R/mcPaBa.r | 25 ++++++--
R/mcrInterface.r | 102 +++++++++++++++++++++++------------
inst/unitTests/runit.mcPaBa.R | 49 +++++++++++------
man/mc.bootstrap.Rd | 16 ++++-
man/mc.paba.Rd | 11 +++
man/mcr-package.Rd | 2
man/mcreg.Rd | 120 ++++++++++++++++++++++++++++--------------
11 files changed, 310 insertions(+), 175 deletions(-)
Title: R interface to X-13ARIMA-SEATS
Diff between seasonal versions 0.20.2 dated 2013-12-03 and 0.40.0 dated 2014-02-12
Description: seasonal is an easy-to-use R-interface to X-13ARIMA-SEATS, a
seasonal adjustment software developed by the United States Census Bureau.
X-13ARIMA-SEATS combines and extends the capabilities of the older X-12ARIMA
(developed by the Census Bureau) and the TRAMO-SEATS (developed by the Bank
of Spain) software packages. For installation details, see the vignette.
Author: Christoph Sax
Maintainer: Christoph Sax
seasonal-0.20.2/seasonal/R/default.methods.R |only
seasonal-0.20.2/seasonal/R/parse.R |only
seasonal-0.20.2/seasonal/R/read_data.R |only
seasonal-0.20.2/seasonal/man/monthplot.seas.Rd |only
seasonal-0.20.2/seasonal/man/residplot.Rd |only
seasonal-0.20.2/seasonal/man/spc.Rd |only
seasonal-0.40.0/seasonal/DESCRIPTION | 13
seasonal-0.40.0/seasonal/MD5 | 82 ++-
seasonal-0.40.0/seasonal/NAMESPACE | 17
seasonal-0.40.0/seasonal/NEWS |only
seasonal-0.40.0/seasonal/R/base.methods.R |only
seasonal-0.40.0/seasonal/R/checkX13.R |only
seasonal-0.40.0/seasonal/R/deparse.R |only
seasonal-0.40.0/seasonal/R/detect.R |only
seasonal-0.40.0/seasonal/R/diagnostics.R |only
seasonal-0.40.0/seasonal/R/extractors.R | 132 +++--
seasonal-0.40.0/seasonal/R/genhol.R |only
seasonal-0.40.0/seasonal/R/inspect.R | 132 +++--
seasonal-0.40.0/seasonal/R/outlier.R | 16
seasonal-0.40.0/seasonal/R/plot.R | 164 ++++--
seasonal-0.40.0/seasonal/R/read_est.R | 26 -
seasonal-0.40.0/seasonal/R/read_lks.R | 15
seasonal-0.40.0/seasonal/R/read_mdl.R | 135 +++--
seasonal-0.40.0/seasonal/R/read_series.R |only
seasonal-0.40.0/seasonal/R/reeval.R |only
seasonal-0.40.0/seasonal/R/revisions.R |only
seasonal-0.40.0/seasonal/R/seas.R | 545 ++++++++++-------------
seasonal-0.40.0/seasonal/R/seasonal-package.R | 55 ++
seasonal-0.40.0/seasonal/R/slidingspans.R |only
seasonal-0.40.0/seasonal/R/startup.R | 2
seasonal-0.40.0/seasonal/R/static.R | 77 +--
seasonal-0.40.0/seasonal/R/summary.R | 105 +++-
seasonal-0.40.0/seasonal/README.md | 101 ++--
seasonal-0.40.0/seasonal/data |only
seasonal-0.40.0/seasonal/inst/doc/seas.Rnw | 332 --------------
seasonal-0.40.0/seasonal/inst/doc/seas.pdf |binary
seasonal-0.40.0/seasonal/inst/tests |only
seasonal-0.40.0/seasonal/man/checkX13.Rd | 20
seasonal-0.40.0/seasonal/man/cntrade.Rd |only
seasonal-0.40.0/seasonal/man/cpi.Rd |only
seasonal-0.40.0/seasonal/man/easter.Rd |only
seasonal-0.40.0/seasonal/man/exp.Rd |only
seasonal-0.40.0/seasonal/man/final.Rd |only
seasonal-0.40.0/seasonal/man/genhol.Rd |only
seasonal-0.40.0/seasonal/man/inspect.Rd | 50 +-
seasonal-0.40.0/seasonal/man/out.Rd |only
seasonal-0.40.0/seasonal/man/outlier.Rd | 8
seasonal-0.40.0/seasonal/man/plot.seas.Rd | 98 +++-
seasonal-0.40.0/seasonal/man/qs.Rd |only
seasonal-0.40.0/seasonal/man/seas.Rd | 230 +++++----
seasonal-0.40.0/seasonal/man/seasonal-package.Rd | 21
seasonal-0.40.0/seasonal/man/static.Rd | 48 +-
seasonal-0.40.0/seasonal/man/summary.seas.Rd | 26 -
seasonal-0.40.0/seasonal/vignettes/README.tex |only
seasonal-0.40.0/seasonal/vignettes/seas.Rnw | 332 --------------
55 files changed, 1253 insertions(+), 1529 deletions(-)
Title: Model-based clustering for multivariate partial ranking data
Diff between Rankcluster versions 0.91.6 dated 2013-12-19 and 0.92 dated 2014-02-12
Description: This package proposes a model-based clustering algorithm for
ranking data. Multivariate rankings as well as partial rankings are taken
into account. This algorithm is based on an extension of the Insertion
Sorting Rank (ISR) model for ranking data, which is a meaningful and
effective model parametrized by a position parameter (the modal ranking,
quoted by mu) and a dispersion parameter (quoted by pi). The heterogeneity
of the rank population is modelled by a mixture of ISR, whereas conditional
independence assumption is considered for multivariate rankings.
Author: Quentin Grimonprez, Julien Jacques
Maintainer: Quentin Grimonprez
Rankcluster-0.91.6/Rankcluster/LICENSE |only
Rankcluster-0.91.6/Rankcluster/inst/COPYRIGHTS |only
Rankcluster-0.91.6/Rankcluster/src/Eigen |only
Rankcluster-0.92/Rankcluster/DESCRIPTION | 22
Rankcluster-0.92/Rankcluster/MD5 | 426 +--------
Rankcluster-0.92/Rankcluster/NAMESPACE | 8
Rankcluster-0.92/Rankcluster/R/RankFunctions.R | 243 +++++
Rankcluster-0.92/Rankcluster/R/likelihood.R | 234 ++---
Rankcluster-0.92/Rankcluster/R/mixtureSEM.R | 81 +
Rankcluster-0.92/Rankcluster/R/rankclust.R | 23
Rankcluster-0.92/Rankcluster/R/resultClass.R | 137 +--
Rankcluster-0.92/Rankcluster/R/zzz.R |only
Rankcluster-0.92/Rankcluster/data/APA.rda |binary
Rankcluster-0.92/Rankcluster/data/big4.rda |binary
Rankcluster-0.92/Rankcluster/data/eurovision.rda |binary
Rankcluster-0.92/Rankcluster/data/quiz.rda |binary
Rankcluster-0.92/Rankcluster/data/sports.rda |binary
Rankcluster-0.92/Rankcluster/data/words.rda |binary
Rankcluster-0.92/Rankcluster/inst/doc/Rankcluster.pdf |binary
Rankcluster-0.92/Rankcluster/man/APA.Rd | 9
Rankcluster-0.92/Rankcluster/man/Output-class.Rd | 116 +-
Rankcluster-0.92/Rankcluster/man/Rankclust-class.Rd | 26
Rankcluster-0.92/Rankcluster/man/Rankcluster-package.Rd | 7
Rankcluster-0.92/Rankcluster/man/big4.Rd | 14
Rankcluster-0.92/Rankcluster/man/convertRank.Rd | 48 -
Rankcluster-0.92/Rankcluster/man/criteria.Rd | 16
Rankcluster-0.92/Rankcluster/man/distCayley.Rd | 12
Rankcluster-0.92/Rankcluster/man/distHamming.Rd | 16
Rankcluster-0.92/Rankcluster/man/distKendall.Rd | 12
Rankcluster-0.92/Rankcluster/man/distSpearman.Rd | 10
Rankcluster-0.92/Rankcluster/man/eurovision.Rd | 72 -
Rankcluster-0.92/Rankcluster/man/frequence.Rd | 16
Rankcluster-0.92/Rankcluster/man/getter-methods.Rd | 1
Rankcluster-0.92/Rankcluster/man/khi2.Rd | 10
Rankcluster-0.92/Rankcluster/man/kullback.Rd | 13
Rankcluster-0.92/Rankcluster/man/probability.Rd |only
Rankcluster-0.92/Rankcluster/man/quiz.Rd | 92 +-
Rankcluster-0.92/Rankcluster/man/rankclust.Rd | 95 +-
Rankcluster-0.92/Rankcluster/man/show-methods.Rd | 1
Rankcluster-0.92/Rankcluster/man/simulISR.Rd | 35
Rankcluster-0.92/Rankcluster/man/sports.Rd | 10
Rankcluster-0.92/Rankcluster/man/summary-methods.Rd | 10
Rankcluster-0.92/Rankcluster/man/unfrequence.Rd | 14
Rankcluster-0.92/Rankcluster/man/words.Rd | 8
Rankcluster-0.92/Rankcluster/src/Makevars | 1
Rankcluster-0.92/Rankcluster/src/Makevars.win | 3
Rankcluster-0.92/Rankcluster/src/RankCluster.cpp | 698 +++++++++-------
Rankcluster-0.92/Rankcluster/src/RankCluster.h | 130 ++
Rankcluster-0.92/Rankcluster/src/functions.cpp | 84 +
Rankcluster-0.92/Rankcluster/src/functions.h | 10
Rankcluster-0.92/Rankcluster/src/run.cpp | 23
Rankcluster-0.92/Rankcluster/src/run.h | 2
Rankcluster-0.92/Rankcluster/src/runFunctions.cpp | 57 +
Rankcluster-0.92/Rankcluster/src/runFunctions.h | 3
Rankcluster-0.92/Rankcluster/src/runTest.h | 2
55 files changed, 1641 insertions(+), 1209 deletions(-)
Title: Projected Spatial Gaussian Process (psgp) methods
Diff between psgp versions 0.3-4 dated 2013-10-14 and 0.3-5 dated 2014-02-12
Description: Implements projected sparse Gaussian process kriging for the intamap package
Author: Ben Ingram
Maintainer: Remi Barillec
ChangeLog | 5 +++++
DESCRIPTION | 12 ++++++------
MD5 | 14 +++++++-------
NAMESPACE | 1 -
src/Makevars.win | 4 ++--
src/psgp_common.cpp | 4 ++--
tests/meuse_psgp.Rout.save | 12 +++++-------
tests/psgp.Rout.save | 26 ++++++++++++--------------
8 files changed, 39 insertions(+), 39 deletions(-)
Title: Mapping dependencies among R packages
Diff between packdep versions 0.2 dated 2009-07-26 and 0.3.1 dated 2014-02-12
Description: packdep elucidates the dependencies
between user-contributed R packages and
identifies key packages according to social
network analysis metrics.
Author: Radhakrishnan Nagarajan
Maintainer: Marco Scutari
Changelog | 12 ++++++++
DESCRIPTION | 24 +++++++++--------
MD5 |only
NAMESPACE | 6 +++-
R/analyze.R | 53 ++++++++++++++++++++++++++++++---------
R/funcmap.R |only
R/init.R |only
R/plot.R | 11 ++++----
R/related.packages.R | 40 +++++++++++++++++++++++------
R/retrieve.R | 53 +++++++++++++++++++++++++++++----------
man/centrality.Rd | 5 ++-
man/dependencies.Rd | 4 ++
man/funcmap.Rd |only
man/map.depends.Rd | 8 ++++-
man/packdep-package.Rd | 34 +++++++++++++------------
man/plot.packdep.centrality.Rd | 12 +++++---
man/plot.packdep.dependencies.Rd | 10 +++----
man/related.packages.Rd | 7 +++--
18 files changed, 196 insertions(+), 83 deletions(-)
Title: Calls CNV from exome sequence data
Diff between ExomeDepth versions 0.9.8 dated 2013-12-11 and 1.0.0 dated 2014-02-12
Description: Calls copy number variants (CNVs) from targeted sequence data
Author: Vincent Plagnol
Maintainer: Vincent Plagnol
DESCRIPTION | 8 +--
MD5 | 37 ++++++++------
NAMESPACE | 6 ++
R/class_definition.R | 3 +
R/countBamInGranges.R | 96 +++++++++++++++++++++++++++++++++++---
build |only
data/Conrad.hg19.RData |binary
data/ExomeCount.RData |binary
data/datalist | 1
data/exons.hg19.RData |binary
data/exons.hg19.X.RData |binary
data/genes.hg19.RData |only
inst/doc/ExomeDepth-vignette.R | 15 +++++
inst/doc/ExomeDepth-vignette.Rnw | 36 ++++++++++++++
inst/doc/ExomeDepth-vignette.pdf |binary
man/count.everted.reads.Rd |only
man/countBam.everted.Rd |only
man/exons.hg19.Rd | 8 +--
man/exons.hg19.X.Rd | 4 -
man/genes.hg19.Rd |only
src/CNV_estimate.cpp | 5 +
vignettes/ExomeDepth-vignette.Rnw | 36 ++++++++++++++
22 files changed, 220 insertions(+), 35 deletions(-)
Title: An R-package for estimating absolute protein quantities from
label-free LC-MS/MS proteomics data
Diff between aLFQ versions 1.2 dated 2013-10-18 and 1.3 dated 2014-02-12
Description: Determination of absolute protein quantities is necessary for multiple applications, such as mechanistic modeling of biological systems. Quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics can measure relative protein abundance on a system-wide scale. To estimate absolute quantitative information using these relative abundance measurements requires additional information such as heavy-labeled references of known concentration. Multiple methods have been using different references and strategies; some are easily available whereas others require more effort on the users end. Hence, we believe the field might benefit from making some of these methods available under an automated framework, which also facilitates validation of the chosen strategy. We have implemented the most commonly used absolute label-free protein abundance estimation methods for LC-MS/MS modes quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, we used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. Our open-source software is written in the statistical programming language R and validated and demonstrated on a synthetic sample.
Author: aLFQ: George Rosenberger, Hannes Roest, Christina Ludwig. AAindex: Barry Grant.
Maintainer: George Rosenberger
DESCRIPTION | 15
MD5 | 41 -
NAMESPACE | 21
R/ALF.R | 75 ++
R/AbsoluteQuantification.R | 18
R/ProteinInference.R | 94 ++-
R/import.R | 123 ++--
R/proteotypic.R | 11
inst/extdata/example_openswath.txt | 2
inst/tests/test_AbsoluteQuantification.R | 22
inst/tests/test_ProteinInference.R | 140 ++---
man/ALF.Rd | 62 +-
man/APEXMS.Rd | 3
man/AbsoluteQuantification.Rd | 51 -
man/LUDWIGMS.Rd | 1
man/PeptideInference.Rd |only
man/ProteinInference.Rd | 62 +-
man/UPS2MS.Rd | 1
man/aLFQ.package.Rd | 13
man/import.Rd | 66 +-
man/proteotypic.Rd | 6
tests/Examples/aLFQ-Ex.Rout.save | 835 ++++++++++++++++++++++++++-----
22 files changed, 1158 insertions(+), 504 deletions(-)
Title: Sparse Additive Modelling
Diff between SAM versions 1.0.4 dated 2013-09-18 and 1.0.5 dated 2014-02-12
Description: The package SAM targets at high dimensional predictive
modeling (regression and classification) for complex data
analysis. SAM is short for sparse additive modeling, and adopts
the computationally efficient basis spline technique. We solve
the optimization problems by various computational algorithms
including the block coordinate descent algorithm, fast
iterative soft-thresholding algorithm, and newton method. The
computation is further accelerated by warm-start and active-set
tricks.
Author: Tuo Zhao, Xingguo Li, Han Liu, and Kathryn Roeder
Maintainer: Tuo Zhao
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
R/samEL.R | 11 +++++++----
R/samHL.R | 11 +++++++----
R/samLL.R | 13 ++++++++-----
R/samQL.R | 10 +++++++---
man/SAM-package.Rd | 4 ++--
man/samEL.Rd | 6 ++++++
man/samHL.Rd | 6 ++++++
man/samLL.Rd | 6 ++++++
man/samQL.Rd | 6 ++++++
11 files changed, 69 insertions(+), 32 deletions(-)
Title: Maximum Likelihood Conjoint Measurement
Diff between MLCM versions 0.4 dated 2014-01-20 and 0.4.1 dated 2014-02-12
Description: Conjoint measurement is a psychophysical procedure in which stimulus pairs are presented that vary along 2 or more dimensions and the observer is required to compare the stimuli along one of them. This package contains functions to estimate the contribution of the n scales to the judgment by a maximum likelihood method under several hypotheses of how the perceptual dimensions interact.
Author: Ken Knoblauch [aut, cre],
Laurence T. Maloney [aut]
Maintainer: Ken Knoblauch
DESCRIPTION | 8 +++---
MD5 | 10 ++++----
NAMESPACE | 3 +-
R/as.mlcm.df.R |only
R/plot.mlcm.df.R | 67 +++++++++++++++++++++++++++++++-----------------------
inst/NEWS | 7 +++++
man/as.mlcm.df.Rd |only
7 files changed, 58 insertions(+), 37 deletions(-)
Title: Modelling with Sparse And Dense Matrices
Diff between MatrixModels versions 0.3-1 dated 2012-01-12 and 0.3-1.1 dated 2014-02-12
Description: Modelling with sparse and dense 'Matrix' matrices, using
modular prediction and response module classes.
Author: Douglas Bates
Maintainer: Doug and Martin
DESCRIPTION | 7 ++++---
MD5 | 4 ++--
man/glm4.Rd | 2 +-
3 files changed, 7 insertions(+), 6 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Diff between JMbayes versions 0.5-1 dated 2014-02-05 and 0.5-2 dated 2014-02-12
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC.
Author: Dimitris Rizopoulos
Maintainer: Dimitris Rizopoulos
DESCRIPTION | 8 +-
MD5 | 26 ++++----
R/MCMCfit.R | 148 ++++++++++++++++++++-----------------------------
R/cd.vec.R | 2
R/fd.vec.R | 2
R/fitted.JMbayes.R | 3
R/gaussKronrod.R | 8 +-
R/gaussLegendre.R | 5 +
R/jointModelBayes.R | 94 +++++++++++++++++++------------
R/plot.JMbayes.R | 10 +--
R/slice.shape.R | 11 +--
inst/NEWS | 6 +
man/JMbayes.Rd | 4 -
man/jointModelBayes.Rd | 3
14 files changed, 174 insertions(+), 156 deletions(-)
Title: Matrix exponential
Diff between expm versions 0.99-1 dated 2013-12-10 and 0.99-1.1 dated 2014-02-12
Description: Computation of the matrix exponential and related quantities.
Author: Vincent Goulet, Christophe Dutang, Martin Maechler,
David Firth, Marina Shapira, Michael Stadelmann,
expm-developers@lists.R-forge.R-project.org
Maintainer: Martin Maechler
DESCRIPTION | 6 +++---
MD5 | 6 +++---
tests/ex.R | 40 ++++++++++++++++++++--------------------
tests/ex2.R | 8 ++++----
4 files changed, 30 insertions(+), 30 deletions(-)
Title: Chemical Thermodynamics and Activity Diagrams
Diff between CHNOSZ versions 1.0.3 dated 2014-01-12 and 1.0.3.1 dated 2014-02-12
Description: This package includes functions and data sets to support chemical thermodynamic
modeling in biochemistry and low-temperature geochemistry. The features include calculation
of the standard molal thermodynamic properties and chemical affinities of reactions involving
minerals and/or biomolecules; a database of thermodynamic properties of aqueous, crystalline
and gaseous species; amino acid group additivity for the standard molal thermodynamic
properties of neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers
equations of state for aqueous species; construction of equilibrium activity diagrams as a
function of temperature, pressure, and chemical activities or fugacities of basis species.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick
DESCRIPTION | 6 +++---
MD5 | 4 ++--
inst/tests/test-EOSregress.R | 16 ++++++++--------
3 files changed, 13 insertions(+), 13 deletions(-)
Title: Algorithmic Experimental Design
Diff between AlgDesign versions 1.1-7.1 dated 2014-02-11 and 1.1-7.2 dated 2014-02-12
Description: Algorithmic experimental designs. Calculates exact and
approximate theory experimental designs for D,A, and I
criteria. Very large designs may be created. Experimental
designs may be blocked or blocked designs created from a
candidate list, using several criteria. The blocking can be
done when whole and within plot factors interact.
Author: Bob Wheeler
Maintainer: ORPHANED
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
NAMESPACE | 4 ++++
src/FederovOpt.c | 6 +++---
src/OptBlock.c | 10 ++--------
5 files changed, 16 insertions(+), 18 deletions(-)
Title: C++ classes to embed R in C++ applications
Diff between RInside versions 0.2.10 dated 2012-12-05 and 0.2.11 dated 2014-02-12
Description: C++ classes to embed R in C++ applications
The RInside packages makes it easier to have 'R inside' your C++ application
by providing a C++ wrapper class providing the R interpreter.
As R itself is embedded into your application, a shared library build of R
is required. This works on Linux, OS X and even on Windows provided you use
the same tools used to build R itself.
Numerous examples are provided in the six subdirectories of the examples/
directory of the installed package: standard, mpi (for parallel computing)
qt (showing how to embed RInside inside a Qt GUI application), wt (showing
how to build a 'web-application' using the Wt toolkit), armadillo (for
RInside use with RcppArmadillo) and eigen (for RInside use with RcppEigen).
Doxygen-generated documentation of the C++ classes is available at the
RInside website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel
RInside-0.2.10/doxyfile |only
RInside-0.2.11/ChangeLog | 67 +++++++++++++-
RInside-0.2.11/DESCRIPTION | 44 ++++-----
RInside-0.2.11/MD5 | 43 ++++----
RInside-0.2.11/NAMESPACE | 3
RInside-0.2.11/README.md |only
RInside-0.2.11/inst/NEWS.Rd | 27 +++++
RInside-0.2.11/inst/THANKS | 4
RInside-0.2.11/inst/examples/armadillo/Makefile | 1
RInside-0.2.11/inst/examples/armadillo/rinside_arma0.cpp | 4
RInside-0.2.11/inst/examples/armadillo/rinside_arma1.cpp | 4
RInside-0.2.11/inst/examples/eigen/Makefile | 1
RInside-0.2.11/inst/examples/mpi/rinside_mpi_sample4.cpp |only
RInside-0.2.11/inst/examples/qt/qtdensity.cpp | 4
RInside-0.2.11/inst/examples/qt/qtdensity.h | 9 +
RInside-0.2.11/inst/examples/qt/qtdensity.pro | 1
RInside-0.2.11/inst/examples/standard/Makefile | 3
RInside-0.2.11/inst/examples/standard/rinside_sample9.cpp | 4
RInside-0.2.11/inst/examples/standard/rinside_test0.cpp | 6 -
RInside-0.2.11/inst/examples/wt/Makefile | 1
RInside-0.2.11/inst/include/RInside.h | 9 +
RInside-0.2.11/src/Makevars | 4
RInside-0.2.11/src/RInside.cpp | 31 +++---
24 files changed, 188 insertions(+), 83 deletions(-)
Title: Predict environmental conditions from biological observations
Diff between bio.infer versions 1.3-1 dated 2012-03-19 and 1.3-3 dated 2014-02-12
Description: Imports benthic count data, reformats this data, and
computes environmental inferences from this data.
Author: Lester L. Yuan
Maintainer: Lester L. Yuan
DESCRIPTION | 9 +++++----
MD5 | 14 +++++++-------
R/get.otu.R | 7 +------
R/infergui.R | 22 +++++++++++-----------
R/makess.R | 9 +++++----
R/parse.taxon.name.R | 50 +++++++++++++++++++++++++++++---------------------
R/view.te.R | 6 +++---
data/itis.ttable.rda |binary
8 files changed, 61 insertions(+), 56 deletions(-)