Title: Profile Dirichlet Process Mixtures
Diff between profdpm versions 3.2 dated 2012-12-25 and 3.3 dated 2013-05-25
Description: This package facilitates profile inference (inference at
the posterior mode) for a class of product partition models
(PPM). The Dirichlet process mixture is currently the only
available member of this class. These methods search for the
maximum posterior (MAP) estimate for the data partition in a
PPM.
Author: Matt Shotwell
Maintainer: Matt Shotwell
profdpm-3.2/profdpm/TODO |only
profdpm-3.3/profdpm/DESCRIPTION | 9 +++---
profdpm-3.3/profdpm/MD5 | 31 +++++++++++------------
profdpm-3.3/profdpm/inst/CITATION |only
profdpm-3.3/profdpm/inst/doc/profdpm.R |only
profdpm-3.3/profdpm/inst/doc/profdpm.Rnw | 35 ++++++++++++--------------
profdpm-3.3/profdpm/inst/doc/profdpm.pdf |binary
profdpm-3.3/profdpm/man/pci.Rd | 2 +
profdpm-3.3/profdpm/man/profBinary.Rd | 2 +
profdpm-3.3/profdpm/man/profLinear.Rd | 2 +
profdpm-3.3/profdpm/man/profdpm.Rd | 8 +++--
profdpm-3.3/profdpm/man/summary.profBinary.Rd | 3 ++
profdpm-3.3/profdpm/man/summary.profLinear.Rd | 3 ++
profdpm-3.3/profdpm/src/methods.c | 2 -
profdpm-3.3/profdpm/src/pdpmlm.c | 2 -
profdpm-3.3/profdpm/src/profBinary.c | 4 +-
profdpm-3.3/profdpm/vignettes/profdpm.Rnw | 35 ++++++++++++--------------
profdpm-3.3/profdpm/vignettes/profdpm.bib | 9 +++---
18 files changed, 81 insertions(+), 66 deletions(-)
Title: Probabilistic Population Projection
Diff between bayesPop versions 3.2-3 dated 2013-04-11 and 4.0-1 dated 2013-05-24
Description: The package allows to generate population projections for
all countries of the world using several probabilistic
components, such as total fertility rate (TFR) and life
expectancy.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova
bayesPop-3.2-3/bayesPop/data/ASMRFemale2008.R |only
bayesPop-3.2-3/bayesPop/data/ASMRFemale2008.txt |only
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bayesPop-3.2-3/bayesPop/data/MigByAgeFemale2008.R |only
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bayesPop-3.2-3/bayesPop/data/SexRatioAtBirth2008.R |only
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bayesPop-3.2-3/bayesPop/man/MigByAge.Rd |only
bayesPop-3.2-3/bayesPop/man/PercentASFR.Rd |only
bayesPop-3.2-3/bayesPop/man/PopByAge.Rd |only
bayesPop-3.2-3/bayesPop/man/SexRatioAtBirth.Rd |only
bayesPop-4.0-1/bayesPop/ChangeLog | 13
bayesPop-4.0-1/bayesPop/DESCRIPTION | 14
bayesPop-4.0-1/bayesPop/MD5 | 76 ---
bayesPop-4.0-1/bayesPop/R/aggregate.R | 14
bayesPop-4.0-1/bayesPop/R/get_outputs.R | 47 +
bayesPop-4.0-1/bayesPop/R/predict.pop.R | 86 ++-
bayesPop-4.0-1/bayesPop/data/vwBaseYear2008.txt | 236 +++++++++-
bayesPop-4.0-1/bayesPop/data/vwBaseYear2010.txt | 235 +++++++++
bayesPop-4.0-1/bayesPop/data/vwBaseYear2012.R |only
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bayesPop-4.0-1/bayesPop/man/bayesPop-package.Rd | 5
bayesPop-4.0-1/bayesPop/man/expressions.Rd | 5
bayesPop-4.0-1/bayesPop/man/pop.aggregate.Rd | 18
bayesPop-4.0-1/bayesPop/man/pop.map.Rd | 2
bayesPop-4.0-1/bayesPop/man/predict.pop.Rd | 23
bayesPop-4.0-1/bayesPop/man/vwBaseYear.Rd | 1
bayesPop-4.0-1/bayesPop/tests/run_tests.R | 3
60 files changed, 623 insertions(+), 155 deletions(-)
Title: Graphical User Interface for bayesTFR, bayesLife and bayesPop
Diff between bayesDem versions 2.2-1 dated 2013-04-07 and 2.3-0 dated 2013-05-24
Description: Provides Graphical user interface for the packages
bayesTFR, bayesLife and bayesPop
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
DESCRIPTION | 12 +++++----
MD5 | 28 +++++++++++-----------
R/bayesDem.R | 4 +--
R/bayesDem_ini.R | 4 ---
R/e0-mcmc.R | 6 +++-
R/e0-predict.R | 2 -
R/handlers_and_fncs.R | 15 +++--------
R/pop-predict.R | 17 +++++++------
R/pop-results.R | 15 +++++++----
R/tfr-cont-mcmc.R | 3 ++
R/tfr-mcmc.R | 61 ++++++++++++++++++++++++------------------------
R/tfr-predict.R | 51 +++++++++++++++++++++++++---------------
R/tfr-results.R | 5 ---
man/bayesDem-package.Rd | 5 +--
man/bayesDem.go.Rd | 11 +++-----
15 files changed, 130 insertions(+), 109 deletions(-)
Title: A collection of contrast methods
Diff between contrast versions 0.17 dated 2011-12-24 and 0.18 dated 2013-05-24
Description: Contrast methods, in the style of the Design package, for
fit objects produced by the lm, glm, gls, and geese functions.
Author: Max Kuhn, contributions from Steve Weston, Jed Wing and James
Forester
Maintainer: Max Kuhn
contrast-0.17/contrast/inst/CHANGES |only
contrast-0.17/contrast/inst/doc/.Rapp.history |only
contrast-0.18/contrast/DESCRIPTION | 16 +++++++++-------
contrast-0.18/contrast/MD5 | 14 ++++++++------
contrast-0.18/contrast/R/contrast.lm.R | 14 ++++++--------
contrast-0.18/contrast/R/testStatistic.R | 10 ++++++++--
contrast-0.18/contrast/inst/NEWS.Rd |only
contrast-0.18/contrast/inst/doc/contrast.R |only
contrast-0.18/contrast/inst/doc/contrast.Rnw | 2 +-
contrast-0.18/contrast/inst/doc/contrast.pdf |binary
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11 files changed, 32 insertions(+), 24 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Diff between arules versions 1.0-13 dated 2013-04-07 and 1.0-14 dated 2013-05-24
Description: Provides the infrastructure for representing, manipulating
and analyzing transaction data and patterns (frequent itemsets
and association rules). Also provides interfaces to C
implementations of the association mining algorithms Apriori
and Eclat by C. Borgelt.
Author: Michael Hahsler, Christian Buchta, Bettina Gruen and Kurt
Hornik
Maintainer: Michael Hahsler
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
R/discretize.R | 17 ++++++++++-------
R/is.superset.R | 2 +-
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data/AdultUCI.rda |binary
data/Epub.rda |binary
data/Groceries.rda |binary
data/Income.rda |binary
data/IncomeESL.rda |binary
inst/NEWS | 6 +++++-
inst/doc/arules.pdf |binary
12 files changed, 31 insertions(+), 24 deletions(-)
Title: Useful R code for the Estimation of Migration
Diff between migest versions 1.2 dated 2013-04-23 and 1.3 dated 2013-05-24
Description: The migest package contains a collection of R functions
that are useful to estimate migration when there is missing
data. Included is the ffs routine to estimate migration flows
from stock data, as well as various other functions to
indirectly estimate flows where marginal totals are known.
Functions are illustrated with dummy data.
Author: Guy J. Abel
Maintainer: Guy J. Abel
DESCRIPTION | 7 ++++---
MD5 | 10 +++++-----
R/ffs.R | 24 +++++++++++++++++-------
R/ipf2.R | 2 ++
R/ipf3.R | 3 ++-
man/migest-package.Rd | 7 +++----
6 files changed, 33 insertions(+), 20 deletions(-)
Title: Length-biased correction to survival curve estimation.
Diff between lbiassurv versions 1.0 dated 2013-03-11 and 1.1 dated 2013-05-24
Description: The package offers various length-bias corrections to
survival curve estimation.
Author: Pierre-Jerome Bergeron and Vahid Partovi Nia
Maintainer: Vahid Partovi Nia
DESCRIPTION | 12 +--
MD5 | 10 +-
R/lbiassurv.R | 205 +++++++++++++++++++++++++++++++++++-----------------
man/lbfit.nonpar.Rd | 33 ++++++--
man/lbfit.par.Rd | 2
man/lbsample.Rd | 4 -
6 files changed, 178 insertions(+), 88 deletions(-)
Title: Functional Data Analysis
Diff between fda versions 2.3.4 dated 2013-04-21 and 2.3.6 dated 2013-05-24
Description: These functions were developed to support functional data
analysis as described in Ramsay, J. O. and Silverman, B. W.
(2005) Functional Data Analysis. New York: Springer. They were
ported from earlier versions in Matlab and S-PLUS. An
introduction appears in Ramsay, J. O., Hooker, Giles, and
Graves, Spencer (2009) Functional Data Analysis with R and
Matlab (Springer). The package includes data sets and script
files working many examples including all but one of the 76
figures in this latter book. As of this release, the R-Project
is no longer distributing the Matlab versions of the functional
data analysis functions and sample analyses through the CRAN
distribution system. This is due to the pressure placed on
storage required in the many CRAN sites by the rapidly
increasing number of R packages, of which the fda package is
one. The three of us involved in this package have agreed to
help out this situation by switching to distributing the Matlab
functions and analyses through Jim Ramsay's ftp site at McGill
University. To obtain these Matlab files, go to this site
using an ftp utility:
http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/ There
you find a set of .zip files containing the functions and
sample analyses, as well as two .txt files giving instructions
for installation and some additional information.
Author: J. O. Ramsay
Maintainer: J. O. Ramsay
DESCRIPTION | 14
MD5 | 6
man/CSTR.Rd | 936 ++++++++++++++++++++++++++++-----------------------------
man/odesolv.Rd | 138 ++++----
4 files changed, 546 insertions(+), 548 deletions(-)
Title: Order Restricted Clustering for Microarray Experiments
Diff between ORCME versions 1.2 dated 2012-09-18 and 1.2.1 dated 2013-05-24
Description: This package provides clustering of genes with similar
dose response (or time course) profiles. It implements the
method described by Lin et al. (2012).
Author: Adetayo Kasim, Martin Otava, Tobias Verbeke
Maintainer: Martin Otava
DESCRIPTION | 11 ++++++-----
MD5 | 10 +++++-----
NEWS | 2 +-
R/monotoneDirection.R | 6 ++++--
data/doseData.rda |binary
data/geneData.rda |binary
6 files changed, 16 insertions(+), 13 deletions(-)
More information about compositionsGUI at CRAN
Permanent link
Title: Bayesian Simultaneous Quantile Regression
Diff between BSquare versions 1.0 dated 2013-05-22 and 1.1 dated 2013-05-24
Description: This package models the quantile process as a function of
predictors.
Author: Luke Smith & Brian Reich
Maintainer: Luke Smith
BSquare-1.0/BSquare/src/helpers_np.c |only
BSquare-1.0/BSquare/src/helpers_np.h |only
BSquare-1.1/BSquare/DESCRIPTION | 6
BSquare-1.1/BSquare/MD5 | 16
BSquare-1.1/BSquare/R/C_functions.R | 3
BSquare-1.1/BSquare/R/QR_C_functions.R | 1
BSquare-1.1/BSquare/src/MCMC.c | 54 -
BSquare-1.1/BSquare/src/MCMC_IP.c | 47 -
BSquare-1.1/BSquare/src/helpers.c | 1229 ++++++++++++++++++++++++++++++++-
BSquare-1.1/BSquare/src/helpers.h | 195 +++++
10 files changed, 1485 insertions(+), 66 deletions(-)
Title: Bayesian Projection of Life Expectancy
Diff between bayesLife versions 1.1-3 dated 2013-04-06 and 2.0-0 dated 2013-05-24
Description: Making probabilistic projections of life expectancy for
all countries of the world, using a Bayesian hierarchical
model.
Author: Hana Sevcikova, Adrian Raftery; original WinBugs code written
by Jennifer Chunn
Maintainer: Hana Sevcikova
bayesLife-1.1-3/bayesLife/data/UN2008e0F.R |only
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bayesLife-2.0-0/bayesLife/ChangeLog | 18
bayesLife-2.0-0/bayesLife/DESCRIPTION | 12
bayesLife-2.0-0/bayesLife/MD5 | 2320 ++++------
bayesLife-2.0-0/bayesLife/R/plot_functions.R | 33
bayesLife-2.0-0/bayesLife/R/projection_fcns.R | 43
bayesLife-2.0-0/bayesLife/R/run_mcmc.R | 4
bayesLife-2.0-0/bayesLife/R/wpp_data.R | 12
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bayesLife-2.0-0/bayesLife/man/joint.male.predict.Rd | 4
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bayesLife-2.0-0/bayesLife/man/run.e0.mcmc.extra.Rd | 4
bayesLife-2.0-0/bayesLife/man/write.projection.summary.Rd | 5
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1175 files changed, 1266 insertions(+), 1231 deletions(-)
Title: Analysis of evolutionary rates in an OU framework
Diff between OUwie versions 1.33 dated 2013-03-23 and 1.34 dated 2013-05-24
Description: Calculates and compares rate differences of continuous
character evolution under Brownian motion and a new set of
Ornstein-Uhlenbeck-based Hansen models that allow the strength
of selection and stochastic motion to vary across selective
regimes.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
R/OUwie.R | 24 ++++++++++++------------
R/varcov.ou.R | 2 --
R/weight.mat.R | 1 -
man/OUwie.Rd | 2 --
man/OUwie.fixed.Rd | 4 ++--
man/OUwie.sim.Rd | 3 ++-
8 files changed, 28 insertions(+), 32 deletions(-)
Title: Bayesian Fertility Projection
Diff between bayesTFR versions 3.0-8 dated 2013-04-06 and 4.0-0 dated 2013-05-24
Description: Making probabilistic projections of total fertility rate
for all countries of the world, using a Bayesian hierarchical
model.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
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bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country807.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country818.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country826.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country830.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country834.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country84.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country840.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country850.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country854.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country858.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country860.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country862.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country882.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country887.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country894.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country90.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/ex-data/bayesTFR.output/predictions/traj_country96.rda |binary
bayesTFR-4.0-0/bayesTFR/inst/extdata |only
bayesTFR-4.0-0/bayesTFR/man/bayesTFR-internal.Rd | 5
bayesTFR-4.0-0/bayesTFR/man/bayesTFR-package.Rd | 17
bayesTFR-4.0-0/bayesTFR/man/country.names.Rd | 5
bayesTFR-4.0-0/bayesTFR/man/get.country.object.Rd | 5
bayesTFR-4.0-0/bayesTFR/man/include.Rd |only
bayesTFR-4.0-0/bayesTFR/man/plot-trajectories.Rd | 2
bayesTFR-4.0-0/bayesTFR/man/predict-tfr.Rd | 12
bayesTFR-4.0-0/bayesTFR/man/run-mcmc.Rd | 14
bayesTFR-4.0-0/bayesTFR/man/run.tfr.mcmc.extra.Rd | 5
bayesTFR-4.0-0/bayesTFR/man/run.tfr3.mcmc.Rd | 2
bayesTFR-4.0-0/bayesTFR/man/tfr.map.Rd | 4
bayesTFR-4.0-0/bayesTFR/man/write.projection.summary.Rd | 2
bayesTFR-4.0-0/bayesTFR/tests/run_tests.R | 8
bayesTFR-4.0-0/bayesTFR/tests/test_functions.R | 10
245 files changed, 740 insertions(+), 557 deletions(-)
Title: Visualization of regression models
Diff between visreg versions 1.2-1 dated 2013-02-21 and 2.0-0 dated 2013-05-23
Description: Provides convenient interface for constructing plots to
visualize the fit of regression models arising from a wide
variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny
visreg-1.2-1/visreg/WISHLIST |only
visreg-1.2-1/visreg/tests/visreg-effect.R |only
visreg-2.0-0/visreg/DESCRIPTION | 8
visreg-2.0-0/visreg/FAQ.md | 20 -
visreg-2.0-0/visreg/MD5 | 71 ++-
visreg-2.0-0/visreg/NEWS | 25 +
visreg-2.0-0/visreg/R/Response.R | 14
visreg-2.0-0/visreg/R/Terms.R | 17
visreg-2.0-0/visreg/R/factorAxis.R | 30 -
visreg-2.0-0/visreg/R/factorPlot.R | 57 +-
visreg-2.0-0/visreg/R/getXY.R | 15
visreg-2.0-0/visreg/R/pal.R |only
visreg-2.0-0/visreg/R/printCond.R |only
visreg-2.0-0/visreg/R/removeFormulaFormatting.R | 1
visreg-2.0-0/visreg/R/setupCond.R | 76 +--
visreg-2.0-0/visreg/R/setupD.R | 14
visreg-2.0-0/visreg/R/setupF.R | 24 -
visreg-2.0-0/visreg/R/setupV.R |only
visreg-2.0-0/visreg/R/setupV2.R |only
visreg-2.0-0/visreg/R/setupX.R | 38 +
visreg-2.0-0/visreg/R/subsetV.R |only
visreg-2.0-0/visreg/R/toplegend.R |only
visreg-2.0-0/visreg/R/visreg.R | 55 +-
visreg-2.0-0/visreg/R/visreg2d.R | 128 ++----
visreg-2.0-0/visreg/R/visregFactorPanel.R | 26 -
visreg-2.0-0/visreg/R/visregLatticePlot.R | 105 +----
visreg-2.0-0/visreg/R/visregOverlayPlot.R |only
visreg-2.0-0/visreg/R/visregPanel.R | 21 -
visreg-2.0-0/visreg/R/visregPlot.R | 97 ++---
visreg-2.0-0/visreg/man/visreg-package.Rd | 76 +--
visreg-2.0-0/visreg/man/visreg.Rd | 462 ++++++++++++++----------
visreg-2.0-0/visreg/man/visreg2d.Rd | 209 ++++++----
visreg-2.0-0/visreg/tests/missing-data.R | 65 ++-
visreg-2.0-0/visreg/tests/visreg-contrast.R |only
visreg-2.0-0/visreg/tests/visreg-coxph.R | 6
visreg-2.0-0/visreg/tests/visreg-glm.R | 19
visreg-2.0-0/visreg/tests/visreg-interactions.R | 65 ++-
visreg-2.0-0/visreg/tests/visreg-lm.R | 62 +--
visreg-2.0-0/visreg/tests/visreg-mlm.R | 19
visreg-2.0-0/visreg/tests/visreg2d-glm.R | 43 +-
visreg-2.0-0/visreg/tests/visreg2d-lm.R | 108 ++---
visreg-2.0-0/visreg/to-do.txt |only
42 files changed, 1090 insertions(+), 886 deletions(-)
Title: Relational Class Analysis
Diff between RCA versions 1.3.2 dated 2013-04-03 and 1.4 dated 2013-05-23
Description: Relational Class Analysis (RCA) is a method for detecting
heterogeneity in attitudinal data. (as described in Goldberg
A., 2011, Am. J. Soc, 116(5)) . src/ also contains the source
files of igraph-C which was written by Gabor.
Author: Amir Goldberg
Maintainer: Yuan Wang
RCA-1.3.2/RCA/src/igraph-R |only
RCA-1.4/RCA/DESCRIPTION | 17
RCA-1.4/RCA/MD5 | 643 +++++++++++++++++---
RCA-1.4/RCA/R/RCA.R | 3
RCA-1.4/RCA/man/RCA-package.Rd | 30
RCA-1.4/RCA/man/RCA.Rd | 62 +
RCA-1.4/RCA/man/Result.Rd | 39 -
RCA-1.4/RCA/man/SampleInputMatrix.Rd | 14
RCA-1.4/RCA/matrix.pmt |only
RCA-1.4/RCA/src/Color.cpp |only
RCA-1.4/RCA/src/Color.h |only
RCA-1.4/RCA/src/DensityGrid.cpp |only
RCA-1.4/RCA/src/DensityGrid.h |only
RCA-1.4/RCA/src/DensityGrid_3d.cpp |only
RCA-1.4/RCA/src/DensityGrid_3d.h |only
RCA-1.4/RCA/src/Light.cpp |only
RCA-1.4/RCA/src/Light.h |only
RCA-1.4/RCA/src/Makevars | 13
RCA-1.4/RCA/src/Makevars.win | 11
RCA-1.4/RCA/src/NetDataTypes.cpp |only
RCA-1.4/RCA/src/NetDataTypes.h |only
RCA-1.4/RCA/src/NetRoutines.cpp |only
RCA-1.4/RCA/src/NetRoutines.h |only
RCA-1.4/RCA/src/Point.cpp |only
RCA-1.4/RCA/src/Point.h |only
RCA-1.4/RCA/src/RCAlib.c | 36 -
RCA-1.4/RCA/src/RIgraphRay.cpp |only
RCA-1.4/RCA/src/Ray.cpp |only
RCA-1.4/RCA/src/Ray.h |only
RCA-1.4/RCA/src/RayTracer.cpp |only
RCA-1.4/RCA/src/RayTracer.h |only
RCA-1.4/RCA/src/RayVector.cpp |only
RCA-1.4/RCA/src/RayVector.h |only
RCA-1.4/RCA/src/Shape.cpp |only
RCA-1.4/RCA/src/Shape.h |only
RCA-1.4/RCA/src/Sphere.cpp |only
RCA-1.4/RCA/src/Sphere.h |only
RCA-1.4/RCA/src/Triangle.cpp |only
RCA-1.4/RCA/src/Triangle.h |only
RCA-1.4/RCA/src/amd_1.c |only
RCA-1.4/RCA/src/amd_2.c |only
RCA-1.4/RCA/src/amd_aat.c |only
RCA-1.4/RCA/src/amd_control.c |only
RCA-1.4/RCA/src/amd_defaults.c |only
RCA-1.4/RCA/src/amd_dump.c |only
RCA-1.4/RCA/src/amd_info.c |only
RCA-1.4/RCA/src/amd_order.c |only
RCA-1.4/RCA/src/amd_post_tree.c |only
RCA-1.4/RCA/src/amd_postorder.c |only
RCA-1.4/RCA/src/amd_preprocess.c |only
RCA-1.4/RCA/src/amd_valid.c |only
RCA-1.4/RCA/src/arpack.c |only
RCA-1.4/RCA/src/atlas-edges.h |only
RCA-1.4/RCA/src/atlas.c |only
RCA-1.4/RCA/src/attributes.c |only
RCA-1.4/RCA/src/autom4te.cache |only
RCA-1.4/RCA/src/basic_query.c |only
RCA-1.4/RCA/src/bfgs.c |only
RCA-1.4/RCA/src/bigint.c |only
RCA-1.4/RCA/src/bigint.h |only
RCA-1.4/RCA/src/bignum.c |only
RCA-1.4/RCA/src/bignum.h |only
RCA-1.4/RCA/src/bipartite.c |only
RCA-1.4/RCA/src/blas.c |only
RCA-1.4/RCA/src/bliss.cc |only
RCA-1.4/RCA/src/bliss_bignum.h |only
RCA-1.4/RCA/src/bliss_defs.h |only
RCA-1.4/RCA/src/bliss_eqrefhash.cc |only
RCA-1.4/RCA/src/bliss_eqrefhash.h |only
RCA-1.4/RCA/src/bliss_graph.cc |only
RCA-1.4/RCA/src/bliss_graph.h |only
RCA-1.4/RCA/src/bliss_heap.cc |only
RCA-1.4/RCA/src/bliss_heap.h |only
RCA-1.4/RCA/src/bliss_kqueue.h |only
RCA-1.4/RCA/src/bliss_kstack.h |only
RCA-1.4/RCA/src/bliss_orbit.cc |only
RCA-1.4/RCA/src/bliss_orbit.h |only
RCA-1.4/RCA/src/bliss_partition.cc |only
RCA-1.4/RCA/src/bliss_partition.h |only
RCA-1.4/RCA/src/bliss_timer.cc |only
RCA-1.4/RCA/src/bliss_timer.h |only
RCA-1.4/RCA/src/bliss_utils.cc |only
RCA-1.4/RCA/src/bliss_utils.h |only
RCA-1.4/RCA/src/cattributes.c |only
RCA-1.4/RCA/src/centrality.c |only
RCA-1.4/RCA/src/cliques.c |only
RCA-1.4/RCA/src/clustertool.cpp |only
RCA-1.4/RCA/src/cocitation.c |only
RCA-1.4/RCA/src/cohesive_blocks.c |only
RCA-1.4/RCA/src/colamd.c |only
RCA-1.4/RCA/src/community.c |only
RCA-1.4/RCA/src/complex.c |only
RCA-1.4/RCA/src/components.c |only
RCA-1.4/RCA/src/config.h |only
RCA-1.4/RCA/src/conversion.c |only
RCA-1.4/RCA/src/cores.c |only
RCA-1.4/RCA/src/cs |only
RCA-1.4/RCA/src/cs_add.c |only
RCA-1.4/RCA/src/cs_amd.c |only
RCA-1.4/RCA/src/cs_chol.c |only
RCA-1.4/RCA/src/cs_cholsol.c |only
RCA-1.4/RCA/src/cs_compress.c |only
RCA-1.4/RCA/src/cs_counts.c |only
RCA-1.4/RCA/src/cs_cumsum.c |only
RCA-1.4/RCA/src/cs_dfs.c |only
RCA-1.4/RCA/src/cs_dmperm.c |only
RCA-1.4/RCA/src/cs_droptol.c |only
RCA-1.4/RCA/src/cs_dropzeros.c |only
RCA-1.4/RCA/src/cs_dupl.c |only
RCA-1.4/RCA/src/cs_entry.c |only
RCA-1.4/RCA/src/cs_ereach.c |only
RCA-1.4/RCA/src/cs_etree.c |only
RCA-1.4/RCA/src/cs_fkeep.c |only
RCA-1.4/RCA/src/cs_gaxpy.c |only
RCA-1.4/RCA/src/cs_happly.c |only
RCA-1.4/RCA/src/cs_house.c |only
RCA-1.4/RCA/src/cs_ipvec.c |only
RCA-1.4/RCA/src/cs_leaf.c |only
RCA-1.4/RCA/src/cs_load.c |only
RCA-1.4/RCA/src/cs_lsolve.c |only
RCA-1.4/RCA/src/cs_ltsolve.c |only
RCA-1.4/RCA/src/cs_lu.c |only
RCA-1.4/RCA/src/cs_lusol.c |only
RCA-1.4/RCA/src/cs_malloc.c |only
RCA-1.4/RCA/src/cs_maxtrans.c |only
RCA-1.4/RCA/src/cs_multiply.c |only
RCA-1.4/RCA/src/cs_norm.c |only
RCA-1.4/RCA/src/cs_permute.c |only
RCA-1.4/RCA/src/cs_pinv.c |only
RCA-1.4/RCA/src/cs_post.c |only
RCA-1.4/RCA/src/cs_print.c |only
RCA-1.4/RCA/src/cs_pvec.c |only
RCA-1.4/RCA/src/cs_qr.c |only
RCA-1.4/RCA/src/cs_qrsol.c |only
RCA-1.4/RCA/src/cs_randperm.c |only
RCA-1.4/RCA/src/cs_reach.c |only
RCA-1.4/RCA/src/cs_scatter.c |only
RCA-1.4/RCA/src/cs_scc.c |only
RCA-1.4/RCA/src/cs_schol.c |only
RCA-1.4/RCA/src/cs_spsolve.c |only
RCA-1.4/RCA/src/cs_sqr.c |only
RCA-1.4/RCA/src/cs_symperm.c |only
RCA-1.4/RCA/src/cs_tdfs.c |only
RCA-1.4/RCA/src/cs_transpose.c |only
RCA-1.4/RCA/src/cs_updown.c |only
RCA-1.4/RCA/src/cs_usolve.c |only
RCA-1.4/RCA/src/cs_util.c |only
RCA-1.4/RCA/src/cs_utsolve.c |only
RCA-1.4/RCA/src/debug.h |only
RCA-1.4/RCA/src/decomposition.c |only
RCA-1.4/RCA/src/dgetv0.f |only
RCA-1.4/RCA/src/distances.c |only
RCA-1.4/RCA/src/dlaqrb.f |only
RCA-1.4/RCA/src/dmout.f |only
RCA-1.4/RCA/src/dnaitr.f |only
RCA-1.4/RCA/src/dnapps.f |only
RCA-1.4/RCA/src/dnaup2.f |only
RCA-1.4/RCA/src/dnaupd.f |only
RCA-1.4/RCA/src/dnconv.f |only
RCA-1.4/RCA/src/dneigh.f |only
RCA-1.4/RCA/src/dneupd.f |only
RCA-1.4/RCA/src/dngets.f |only
RCA-1.4/RCA/src/drl_Node.h |only
RCA-1.4/RCA/src/drl_Node_3d.h |only
RCA-1.4/RCA/src/drl_graph.cpp |only
RCA-1.4/RCA/src/drl_graph.h |only
RCA-1.4/RCA/src/drl_graph_3d.cpp |only
RCA-1.4/RCA/src/drl_graph_3d.h |only
RCA-1.4/RCA/src/drl_layout.cpp |only
RCA-1.4/RCA/src/drl_layout.h |only
RCA-1.4/RCA/src/drl_layout_3d.cpp |only
RCA-1.4/RCA/src/drl_layout_3d.h |only
RCA-1.4/RCA/src/drl_parse.cpp |only
RCA-1.4/RCA/src/drl_parse.h |only
RCA-1.4/RCA/src/dsaitr.f |only
RCA-1.4/RCA/src/dsapps.f |only
RCA-1.4/RCA/src/dsaup2.f |only
RCA-1.4/RCA/src/dsaupd.f |only
RCA-1.4/RCA/src/dsconv.f |only
RCA-1.4/RCA/src/dseigt.f |only
RCA-1.4/RCA/src/dsesrt.f |only
RCA-1.4/RCA/src/dseupd.f |only
RCA-1.4/RCA/src/dsgets.f |only
RCA-1.4/RCA/src/dsortc.f |only
RCA-1.4/RCA/src/dsortr.f |only
RCA-1.4/RCA/src/dstatn.f |only
RCA-1.4/RCA/src/dstats.f |only
RCA-1.4/RCA/src/dstqrb.f |only
RCA-1.4/RCA/src/dvout.f |only
RCA-1.4/RCA/src/eigen.c |only
RCA-1.4/RCA/src/error.c |only
RCA-1.4/RCA/src/evolver_cit.c |only
RCA-1.4/RCA/src/f2c.h |only
RCA-1.4/RCA/src/f2c_dummy.c |only
RCA-1.4/RCA/src/fast_community.c |only
RCA-1.4/RCA/src/feedback_arc_set.c |only
RCA-1.4/RCA/src/flow.c |only
RCA-1.4/RCA/src/foreign-dl-header.h |only
RCA-1.4/RCA/src/foreign-dl-lexer.c |only
RCA-1.4/RCA/src/foreign-dl-parser.c |only
RCA-1.4/RCA/src/foreign-dl-parser.h |only
RCA-1.4/RCA/src/foreign-gml-header.h |only
RCA-1.4/RCA/src/foreign-gml-lexer.c |only
RCA-1.4/RCA/src/foreign-gml-parser.c |only
RCA-1.4/RCA/src/foreign-gml-parser.h |only
RCA-1.4/RCA/src/foreign-graphml.c |only
RCA-1.4/RCA/src/foreign-lgl-header.h |only
RCA-1.4/RCA/src/foreign-lgl-lexer.c |only
RCA-1.4/RCA/src/foreign-lgl-parser.c |only
RCA-1.4/RCA/src/foreign-lgl-parser.h |only
RCA-1.4/RCA/src/foreign-ncol-header.h |only
RCA-1.4/RCA/src/foreign-ncol-lexer.c |only
RCA-1.4/RCA/src/foreign-ncol-parser.c |only
RCA-1.4/RCA/src/foreign-ncol-parser.h |only
RCA-1.4/RCA/src/foreign-pajek-header.h |only
RCA-1.4/RCA/src/foreign-pajek-lexer.c |only
RCA-1.4/RCA/src/foreign-pajek-parser.c |only
RCA-1.4/RCA/src/foreign-pajek-parser.h |only
RCA-1.4/RCA/src/foreign.c |only
RCA-1.4/RCA/src/forestfire.c |only
RCA-1.4/RCA/src/fortran_intrinsics.c |only
RCA-1.4/RCA/src/games.c |only
RCA-1.4/RCA/src/gengraph_box_list.cpp |only
RCA-1.4/RCA/src/gengraph_box_list.h |only
RCA-1.4/RCA/src/gengraph_definitions.h |only
RCA-1.4/RCA/src/gengraph_degree_sequence.cpp |only
RCA-1.4/RCA/src/gengraph_degree_sequence.h |only
RCA-1.4/RCA/src/gengraph_graph_molloy_hash.cpp |only
RCA-1.4/RCA/src/gengraph_graph_molloy_hash.h |only
RCA-1.4/RCA/src/gengraph_graph_molloy_optimized.cpp |only
RCA-1.4/RCA/src/gengraph_graph_molloy_optimized.h |only
RCA-1.4/RCA/src/gengraph_hash.h |only
RCA-1.4/RCA/src/gengraph_header.h |only
RCA-1.4/RCA/src/gengraph_mr-connected.cpp |only
RCA-1.4/RCA/src/gengraph_powerlaw.cpp |only
RCA-1.4/RCA/src/gengraph_powerlaw.h |only
RCA-1.4/RCA/src/gengraph_qsort.h |only
RCA-1.4/RCA/src/gengraph_random.cpp |only
RCA-1.4/RCA/src/gengraph_random.h |only
RCA-1.4/RCA/src/gengraph_vertex_cover.h |only
RCA-1.4/RCA/src/glpapi01.c |only
RCA-1.4/RCA/src/glpapi02.c |only
RCA-1.4/RCA/src/glpapi03.c |only
RCA-1.4/RCA/src/glpapi04.c |only
RCA-1.4/RCA/src/glpapi05.c |only
RCA-1.4/RCA/src/glpapi06.c |only
RCA-1.4/RCA/src/glpapi07.c |only
RCA-1.4/RCA/src/glpapi08.c |only
RCA-1.4/RCA/src/glpapi09.c |only
RCA-1.4/RCA/src/glpapi10.c |only
RCA-1.4/RCA/src/glpapi11.c |only
RCA-1.4/RCA/src/glpapi12.c |only
RCA-1.4/RCA/src/glpapi13.c |only
RCA-1.4/RCA/src/glpapi14.c |only
RCA-1.4/RCA/src/glpapi15.c |only
RCA-1.4/RCA/src/glpapi16.c |only
RCA-1.4/RCA/src/glpapi17.c |only
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RCA-1.4/RCA/src/hrg_splittree_eq.h |only
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RCA-1.4/RCA/src/igraph_cliques.h |only
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RCA-1.4/RCA/src/igraph_dqueue_pmt.h |only
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RCA-1.4/RCA/src/igraph_estack.h |only
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RCA-1.4/RCA/src/igraph_fixed_vectorlist.c |only
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RCA-1.4/RCA/src/igraph_games.h |only
RCA-1.4/RCA/src/igraph_glpk_support.h |only
RCA-1.4/RCA/src/igraph_gml_tree.h |only
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RCA-1.4/RCA/src/igraph_hacks_internal.h |only
RCA-1.4/RCA/src/igraph_hashtable.c |only
RCA-1.4/RCA/src/igraph_heap.h |only
RCA-1.4/RCA/src/igraph_heap_pmt.h |only
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RCA-1.4/RCA/src/igraph_interrupt.h |only
RCA-1.4/RCA/src/igraph_interrupt_internal.h |only
RCA-1.4/RCA/src/igraph_iterators.h |only
RCA-1.4/RCA/src/igraph_lapack.h |only
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RCA-1.4/RCA/src/igraph_marked_queue.c |only
RCA-1.4/RCA/src/igraph_marked_queue.h |only
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RCA-1.4/RCA/src/igraph_matrix_pmt.h |only
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RCA-1.4/RCA/src/igraph_microscopic_update.h |only
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RCA-1.4/RCA/src/igraph_motifs.h |only
RCA-1.4/RCA/src/igraph_neighborhood.h |only
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RCA-1.4/RCA/src/igraph_revolver.h |only
RCA-1.4/RCA/src/igraph_scg.h |only
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RCA-1.4/RCA/src/igraph_set.c |only
RCA-1.4/RCA/src/igraph_sparsemat.h |only
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RCA-1.4/RCA/src/igraph_stack.h |only
RCA-1.4/RCA/src/igraph_stack_pmt.h |only
RCA-1.4/RCA/src/igraph_statusbar.h |only
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RCA-1.4/RCA/src/igraph_vector_ptr.h |only
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RCA-1.4/RCA/src/igraph_visitor.h |only
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RCA-1.4/RCA/src/pottsmodel_2.cpp |only
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RCA-1.4/RCA/src/revolver_cit.c |only
RCA-1.4/RCA/src/revolver_grow.c |only
RCA-1.4/RCA/src/revolver_ml_cit.c |only
RCA-1.4/RCA/src/rinterface.c |only
RCA-1.4/RCA/src/rinterface.h |only
RCA-1.4/RCA/src/scg.c |only
RCA-1.4/RCA/src/scg_approximate_methods.c |only
RCA-1.4/RCA/src/scg_exact_scg.c |only
RCA-1.4/RCA/src/scg_headers.h |only
RCA-1.4/RCA/src/scg_kmeans.c |only
RCA-1.4/RCA/src/scg_optimal_method.c |only
RCA-1.4/RCA/src/scg_utils.c |only
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RCA-1.4/RCA/src/separators.c |only
RCA-1.4/RCA/src/spanning_trees.c |only
RCA-1.4/RCA/src/sparsemat.c |only
RCA-1.4/RCA/src/spectral_properties.c |only
RCA-1.4/RCA/src/spmatrix.c |only
RCA-1.4/RCA/src/st-cuts.c |only
RCA-1.4/RCA/src/stat.h |only
RCA-1.4/RCA/src/statusbar.c |only
RCA-1.4/RCA/src/structural_properties.c |only
RCA-1.4/RCA/src/structure_generators.c |only
RCA-1.4/RCA/src/sugiyama.c |only
RCA-1.4/RCA/src/topology.c |only
RCA-1.4/RCA/src/type_indexededgelist.c |only
RCA-1.4/RCA/src/types.c |only
RCA-1.4/RCA/src/unit_limiter.cpp |only
RCA-1.4/RCA/src/unit_limiter.h |only
RCA-1.4/RCA/src/vector.c |only
RCA-1.4/RCA/src/vector_ptr.c |only
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RCA-1.4/RCA/src/walktrap_communities.h |only
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RCA-1.4/RCA/src/walktrap_heap.h |only
RCA-1.4/RCA/src/zeroin.c |only
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522 files changed, 701 insertions(+), 167 deletions(-)
Title: SNP-set (Sequence) Kernel Association Test
Diff between SKAT versions 0.83 dated 2013-05-09 and 0.90 dated 2013-05-23
Description: Kernel based SNP set test
Author: Seunggeun Lee, Larisa Miropolsky and Micheal Wu
Maintainer: Seunggeun (Shawn) Lee
DESCRIPTION | 9 ++++----
MD5 | 19 +++++++++--------
NAMESPACE | 3 +-
R/Joint_CommonRare.R |only
R/Main.R | 3 +-
R/Null_Model.R | 5 ++--
inst/doc/Example_bped.zip |only
inst/doc/SKAT.Rnw | 40 ++++++++++++++++++++++++++++++++++--
inst/doc/SKAT.pdf |binary
man/SKAT.rd | 2 -
man/SKAT_CommonRare.rd |only
man/SKAT_Null_Model_MomentAdjust.rd | 3 +-
12 files changed, 64 insertions(+), 20 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Diff between MALDIquant versions 1.6 dated 2013-03-01 and 1.7 dated 2013-05-23
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-1.6/MALDIquant/LICENSE |only
MALDIquant-1.6/MALDIquant/R/isValidHalfWindowSize.R |only
MALDIquant-1.6/MALDIquant/R/movingAverage-functions.R |only
MALDIquant-1.6/MALDIquant/inst/tests/test_movingAverage-functions.R |only
MALDIquant-1.6/MALDIquant/src/morphologicalFilters.h |only
MALDIquant-1.7/MALDIquant/DESCRIPTION | 18
MALDIquant-1.7/MALDIquant/MD5 | 122 +--
MALDIquant-1.7/MALDIquant/NAMESPACE | 3
MALDIquant-1.7/MALDIquant/NEWS | 379 +++++++---
MALDIquant-1.7/MALDIquant/R/AllGenerics.R | 4
MALDIquant-1.7/MALDIquant/R/binPeaks-functions.R | 20
MALDIquant-1.7/MALDIquant/R/determineWarpingFunctions-functions.R | 9
MALDIquant-1.7/MALDIquant/R/doByLabels-functions.R | 7
MALDIquant-1.7/MALDIquant/R/estimateBaseline-functions.R | 42 -
MALDIquant-1.7/MALDIquant/R/estimateBaseline-methods.R | 2
MALDIquant-1.7/MALDIquant/R/estimateNoise-methods.R | 2
MALDIquant-1.7/MALDIquant/R/filterPeaks-functions.R | 54 +
MALDIquant-1.7/MALDIquant/R/grouper-functions.R | 6
MALDIquant-1.7/MALDIquant/R/iplot-functions.R | 58 +
MALDIquant-1.7/MALDIquant/R/irregular-functions.R |only
MALDIquant-1.7/MALDIquant/R/isEmpty-methods.R | 11
MALDIquant-1.7/MALDIquant/R/isFunctionList-functions.R | 5
MALDIquant-1.7/MALDIquant/R/isMassObjectList-functions.R | 18
MALDIquant-1.7/MALDIquant/R/isRegular-methods.R |only
MALDIquant-1.7/MALDIquant/R/isValidHalfWindowSize-functions.R |only
MALDIquant-1.7/MALDIquant/R/localMaxima-functions.R | 8
MALDIquant-1.7/MALDIquant/R/memoryUsage-functions.R |only
MALDIquant-1.7/MALDIquant/R/merge-functions.R | 50 +
MALDIquant-1.7/MALDIquant/R/morphologicalFilter-functions.R | 28
MALDIquant-1.7/MALDIquant/R/onAttach.R | 5
MALDIquant-1.7/MALDIquant/R/plot-methods.R | 8
MALDIquant-1.7/MALDIquant/R/show-functions.R | 2
MALDIquant-1.7/MALDIquant/R/show-methods.R | 18
MALDIquant-1.7/MALDIquant/R/smoothingFilters-functions.R |only
MALDIquant-1.7/MALDIquant/R/totalIonCurrent-methods.R | 10
MALDIquant-1.7/MALDIquant/R/valid-methods.R | 12
MALDIquant-1.7/MALDIquant/demo/warping.R | 8
MALDIquant-1.7/MALDIquant/demo/workflow.R | 40 -
MALDIquant-1.7/MALDIquant/inst/tests/test_calibrate-methods.R | 2
MALDIquant-1.7/MALDIquant/inst/tests/test_doByLabel-functions.R | 23
MALDIquant-1.7/MALDIquant/inst/tests/test_estimateBaseline-methods.R | 43 -
MALDIquant-1.7/MALDIquant/inst/tests/test_filterPeaks-functions.R | 18
MALDIquant-1.7/MALDIquant/inst/tests/test_irregular-functions.R |only
MALDIquant-1.7/MALDIquant/inst/tests/test_isEmpty-methods.R | 21
MALDIquant-1.7/MALDIquant/inst/tests/test_isRegular-methods.R |only
MALDIquant-1.7/MALDIquant/inst/tests/test_merge-functions.R | 13
MALDIquant-1.7/MALDIquant/inst/tests/test_morphologicalFilter-functions.R | 19
MALDIquant-1.7/MALDIquant/inst/tests/test_removeBaseline-methods.R | 6
MALDIquant-1.7/MALDIquant/inst/tests/test_show-methods.R | 9
MALDIquant-1.7/MALDIquant/inst/tests/test_smoothingFilters-functions.R |only
MALDIquant-1.7/MALDIquant/inst/tests/test_totalIonCurrent-methods.R | 11
MALDIquant-1.7/MALDIquant/inst/tests/test_transformIntensity-methods.R | 6
MALDIquant-1.7/MALDIquant/man/AbstractMassObject-class.Rd | 3
MALDIquant-1.7/MALDIquant/man/MALDIquant-internal.Rd | 7
MALDIquant-1.7/MALDIquant/man/MALDIquant-package.Rd | 8
MALDIquant-1.7/MALDIquant/man/MassSpectrum-class.Rd | 7
MALDIquant-1.7/MALDIquant/man/calibrate-methods.Rd | 2
MALDIquant-1.7/MALDIquant/man/estimateBaselineSnip-functions.Rd | 20
MALDIquant-1.7/MALDIquant/man/estimateBaselineTopHat-functions.Rd | 2
MALDIquant-1.7/MALDIquant/man/estimateNoiseMad-functions.Rd | 1
MALDIquant-1.7/MALDIquant/man/filterPeaks-functions.Rd | 34
MALDIquant-1.7/MALDIquant/man/iplot-methods.Rd | 11
MALDIquant-1.7/MALDIquant/man/movingAverage-functions.Rd | 20
MALDIquant-1.7/MALDIquant/man/savitzkyGolay-functions.Rd |only
MALDIquant-1.7/MALDIquant/src/MALDIquant.h |only
MALDIquant-1.7/MALDIquant/src/init.c |only
MALDIquant-1.7/MALDIquant/src/localMaxima.c | 75 +
MALDIquant-1.7/MALDIquant/src/lowerConvexHull.c | 78 +-
MALDIquant-1.7/MALDIquant/src/morphologicalFilters.c | 178 ++++
MALDIquant-1.7/MALDIquant/src/snip.c | 98 +-
70 files changed, 1161 insertions(+), 503 deletions(-)
Title: R package for parallelized mRMR ensemble feature selection
Diff between mRMRe versions 2.0.0 dated 2013-04-16 and 2.0.2 dated 2013-05-23
Description: This package contains a set of function to compute mutual
information matrices from continuous, categorical and survival
variables. It also contains function to perform feature
selection with mRMR and a new ensemble mRMR technique.
Author: Nicolas De Jay, Simon Papillon-Cavanagh, Catharina Olsen,
Gianluca Bontempi, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains
.Rinstignore | 1 +
DESCRIPTION | 10 +++++-----
MD5 | 30 +++++++++++++++---------------
R/generics.R | 11 +++++++----
R/mRMRe.Data.R | 22 ++++++++++++++++++++++
R/mRMRe.Filter.R | 32 +++++++++++++++++++++++++-------
R/mRMRe.Network.R | 24 ++++++++++++++++++++++++
REVISIONS | 37 +++++++++++++++++++++++--------------
data/cgps.rda |binary
inst/doc/mRMRe.pdf |binary
man/mRMRe.Data-class.Rd | 2 +-
man/mRMRe.Filter-class.Rd | 23 ++++++++++++++---------
man/mim.Rd | 5 +++--
man/sampleStrata.Rd | 4 ++--
man/scores.Rd | 9 +++++++--
man/subsetData.Rd | 7 ++++---
src/exports.cpp | 4 ++--
17 files changed, 155 insertions(+), 66 deletions(-)
Title: Fitting finite mixture of scale mixture of skew-normal
distributions .
Diff between mixsmsn versions 1.0-7 dated 2013-05-02 and 1.0-8 dated 2013-05-23
Description: Functions to fit finite mixture of scale mixture of
skew-normal (FM-SMSN) distributions.
Author: Marcos Prates
Maintainer: Marcos Prates
ChangeLog | 10 ++++++++++
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
R/mixsmsn.R | 14 ++++++++------
R/smsn.mmix.R | 29 +++++++++++++++--------------
R/utils.multi.R | 20 ++++++++++----------
6 files changed, 51 insertions(+), 38 deletions(-)
Title: Network analysis and visualization
Diff between igraph versions 0.6.5-1 dated 2013-02-28 and 0.6.5-2 dated 2013-05-23
Description: Routines for simple graphs and network analysis. igraph
can handle large graphs very well and provides functions for
generating random and regular graphs, graph visualization,
centrality indices and much more.
Author: See AUTHORS file.
Maintainer: Gabor Csardi
igraph-0.6.5-1/igraph/LICENSE |only
igraph-0.6.5-2/igraph/DESCRIPTION | 8 +--
igraph-0.6.5-2/igraph/MD5 | 25 +++++----
igraph-0.6.5-2/igraph/NEWS | 13 +++++
igraph-0.6.5-2/igraph/R/auto.R.in |only
igraph-0.6.5-2/igraph/configure | 25 ++++++---
igraph-0.6.5-2/igraph/configure.in | 5 +
igraph-0.6.5-2/igraph/man/graph.graphdb.Rd | 5 +
igraph-0.6.5-2/igraph/man/igraph.vertex.shapes.Rd | 5 +
igraph-0.6.5-2/igraph/src/Makevars |only
igraph-0.6.5-2/igraph/src/arpack.c | 48 +++++++++++++++++++
igraph-0.6.5-2/igraph/src/atlas.c | 2
igraph-0.6.5-2/igraph/src/config.h.in | 3 +
igraph-0.6.5-2/igraph/src/igraph_arpack_internal.h | 53 +++++++++++++++++++++
igraph-0.6.5-2/igraph/src/infomap.cc | 6 +-
15 files changed, 167 insertions(+), 31 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape.
Diff between gamlss versions 4.2-0 dated 2012-09-29 and 4.2-4 dated 2013-05-23
Description: The library for fitting GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss-4.2-0/gamlss/LICENSE |only
gamlss-4.2-0/gamlss/R/HistDist2-12-11.R |only
gamlss-4.2-0/gamlss/R/SUMMARY.R |only
gamlss-4.2-0/gamlss/R/findhyper.R |only
gamlss-4.2-0/gamlss/R/fitDist.R |only
gamlss-4.2-0/gamlss/R/gamlss.R |only
gamlss-4.2-0/gamlss/R/gamlssML-11-9-12.R |only
gamlss-4.2-0/gamlss/R/profterm_new_18_8_12.R |only
gamlss-4.2-0/gamlss/R/qstats-20-09-12.R |only
gamlss-4.2-0/gamlss/R/rqresplot.R |only
gamlss-4.2-0/gamlss/R/stepGAICall-18-03-10.R |only
gamlss-4.2-0/gamlss/R/vcov_gamlss.R |only
gamlss-4.2-0/gamlss/R/wp.R |only
gamlss-4.2-0/gamlss/inst/doc/LICENSE |only
gamlss-4.2-4/gamlss/DESCRIPTION | 21
gamlss-4.2-4/gamlss/MD5 | 88 +-
gamlss-4.2-4/gamlss/NAMESPACE | 4
gamlss-4.2-4/gamlss/R/HistDist-17-05-13.R |only
gamlss-4.2-4/gamlss/R/SUMMARY-26-03-13.R |only
gamlss-4.2-4/gamlss/R/acfResid.R |only
gamlss-4.2-4/gamlss/R/confint-gamlss-02-05-13.R |only
gamlss-4.2-4/gamlss/R/extra.R | 862 ++++++++++----------
gamlss-4.2-4/gamlss/R/findhyper-23-05-13.R |only
gamlss-4.2-4/gamlss/R/fitDist-17-05-13.R |only
gamlss-4.2-4/gamlss/R/gamlss-01-05-13.R |only
gamlss-4.2-4/gamlss/R/gamlssML-17-05-13.R |only
gamlss-4.2-4/gamlss/R/gen-Likelihood-22-03-13.R |only
gamlss-4.2-4/gamlss/R/histSmo-6-03-12.R | 8
gamlss-4.2-4/gamlss/R/lms-23-5-13.r |only
gamlss-4.2-4/gamlss/R/lms.r | 51 -
gamlss-4.2-4/gamlss/R/par_plot-21-5-13.R |only
gamlss-4.2-4/gamlss/R/par_plot.R | 1026 ++++++++++++------------
gamlss-4.2-4/gamlss/R/pb_19-04-2012.R | 1
gamlss-4.2-4/gamlss/R/profterm_18_05_13.R |only
gamlss-4.2-4/gamlss/R/qstats-29-12-12.R |only
gamlss-4.2-4/gamlss/R/rqres.R | 126 +-
gamlss-4.2-4/gamlss/R/rqresplot17-10-12.R |only
gamlss-4.2-4/gamlss/R/stepGAICall-23-05-13.R |only
gamlss-4.2-4/gamlss/R/term-plot.R | 460 +++++-----
gamlss-4.2-4/gamlss/R/vcoc-gamlss-22-03-13.R |only
gamlss-4.2-4/gamlss/R/wp-18-5-13.R |only
gamlss-4.2-4/gamlss/inst/doc/NEWS.txt | 38
gamlss-4.2-4/gamlss/man/IC.Rd | 6
gamlss-4.2-4/gamlss/man/Q.stats.Rd | 26
gamlss-4.2-4/gamlss/man/Rsq.Rd |only
gamlss-4.2-4/gamlss/man/acfResid.Rd |only
gamlss-4.2-4/gamlss/man/calibration.Rd | 3
gamlss-4.2-4/gamlss/man/centiles.pred.Rd | 204 ++--
gamlss-4.2-4/gamlss/man/findhyper.Rd | 187 ++--
gamlss-4.2-4/gamlss/man/gen.likelihood.Rd |only
gamlss-4.2-4/gamlss/man/histDist.Rd | 142 +--
gamlss-4.2-4/gamlss/man/histSmo.Rd | 251 ++---
gamlss-4.2-4/gamlss/man/lms.Rd | 31
gamlss-4.2-4/gamlss/man/par.plot.Rd | 113 +-
gamlss-4.2-4/gamlss/man/prof.dev.Rd | 115 +-
gamlss-4.2-4/gamlss/man/prof.term.Rd | 17
gamlss-4.2-4/gamlss/man/ps.Rd | 373 ++++----
gamlss-4.2-4/gamlss/man/random.Rd | 6
gamlss-4.2-4/gamlss/man/rqres.plot.Rd | 128 +-
gamlss-4.2-4/gamlss/man/stepGAIC.Rd | 498 +++++------
gamlss-4.2-4/gamlss/man/term.plot.Rd | 166 +--
gamlss-4.2-4/gamlss/man/wp.Rd | 190 ++--
62 files changed, 2663 insertions(+), 2478 deletions(-)
Title: Fast hierarchical clustering routines for R and Python
Diff between fastcluster versions 1.1.10 dated 2013-05-23 and 1.1.11 dated 2013-05-23
Description: This is a two-in-one package which provides interfaces to
both R and Python. It implements fast hierarchical,
agglomerative clustering routines. Part of the functionality is
designed as drop-in replacement for existing routines:
“linkage” in the SciPy package “scipy.cluster.hierarchy”,
“hclust” in R's “stats” package, and the “flashClust” package.
It provides the same functionality with the benefit of a much
faster implementation. Moreover, there are memory-saving
routines for clustering of vector data, which go beyond what
the existing packages provide. For information on how to
install the Python files, see the file INSTALL in the source
distribution.
Author: Daniel Müllner, http://math.stanford.edu/~muellner
Maintainer: Daniel Müllner
DESCRIPTION | 8 ++++----
INSTALL | 2 +-
MD5 | 20 ++++++++++----------
NEWS | 7 +++++--
README | 38 +++++++++++++++++++-------------------
inst/doc/fastcluster.Rtex | 4 ++--
inst/doc/fastcluster.pdf |binary
python/fastcluster.py | 2 +-
src/fastcluster.cpp | 15 +++++++++------
src/fastcluster_R.cpp | 12 +++++++++---
src/fastcluster_python.cpp | 4 ++++
11 files changed, 64 insertions(+), 48 deletions(-)
Title: R Interface to C API of IBM ILOG CPLEX
Diff between cplexAPI versions 1.2.6 dated 2013-01-23 and 1.2.9 dated 2013-05-23
Description: R Interface to C API of IBM ILOG CPLEX, depends on IBM
ILOG CPLEX (>= 12.1)
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 9 +-
MD5 | 34 +++++----
NAMESPACE | 5 +
R/cplexAPI.R | 88 +++++++++++++++++++++++
R/cplexConst.R | 144 +++++++++++++++++++-------------------
configure | 18 ++--
configure.ac | 2
inst/NEWS.Rd | 28 +++++++
inst/c2r.map | 5 +
inst/doc/cplexAPI.R |only
inst/doc/cplexAPI.pdf |binary
man/copyOrderCPLEX.Rd |only
man/getMIPrelGapCPLEX.Rd |only
man/getOrderCPLEX.Rd |only
man/ordWriteCPLEX.Rd |only
man/readCopyOrderCPLEX.Rd |only
man/setIntParmCPLEX.Rd | 2
man/setStrParmCPLEX.Rd | 2
src/cplexAPI.c | 170 ++++++++++++++++++++++++++++++++++++++++++++++
src/cplexAPI.h | 15 ++++
src/init.c | 5 +
21 files changed, 424 insertions(+), 103 deletions(-)
Title: RMAWGEN (R Multi-site Auto-regressive Weather GENerator), a
package to generate daily time series of precipitation and
temperature from monthly mean values
Diff between RMAWGEN versions 1.2.5.4 dated 2013-04-24 and 1.2.5.5 dated 2013-05-23
Description: This package contains S3 and S4 functions for spatial
multi-site stochastic generation of daily time series of
temperature and precipitation. The implemented tools make use
of Vector AutoRegressive models (VARs). The VAR is calibrated
by daily instrumental "Gaussianized" time series and then works
with monthly time series as input.
Bugs/comments/questions/collaboration of any kind are warmly
welcome.
Author: Emanuele Cordano, Emanuele Eccel
Maintainer: Emanuele Cordano
DESCRIPTION | 13 -
MD5 | 164 +++++++++---------
R/ComprehensivePrecipitationGenerator.R | 47 +----
R/ComprehensiveTemperatureGenerator.R | 30 ++-
R/PrecipitationEndDay.R | 2
R/PrecipitationStartDay.R | 8
R/RMAWGEN-package.R | 8
R/VAR_mod.R | 2
R/WhereIs.R | 2
R/acvWGEN.R | 2
R/adddate.R | 2
R/addsuffixes.R | 4
R/arch_test.varest2.R | 4
R/continuity_ratio.R | 2
R/countNAs.R | 2
R/covariance.R | 6
R/extractTnFromAnomalies.R | 4
R/extractTxFromAnomalies.R | 2
R/extractdays.R | 2
R/extractmonths.R | 2
R/findDate.R | 12 +
R/generateTemperatureTimeseries.R | 12 -
R/getDailyMean.R | 2
R/getMonthlyMean.R | 6
R/getVARmodel.R | 16 -
R/is.monthly.climate.R | 6
R/normalizeGaussian.R | 4
R/normalizeGaussian_prec.R | 4
R/normalizeGaussian_sevaralstations.R | 6
R/normalizeGaussian_sevaralstations_prec.R | 4
R/plot.sample.R | 34 ++-
R/plotDailyClimate.R | 3
R/qqplot.lagged.R | 6
R/qqplotWGEN.R | 4
R/qqplot_RMAWGENts.R | 12 -
R/qqplotprecWGEN.R | 2
R/qqplotprecWGEN_seasonal.R | 2
R/removeNAs.R | 2
R/setWholeTemperatureGeneratorParameters.R | 12 -
R/splineInterpolateMonthlytoDaily.R | 4
R/splineInterpolateMonthlytoDailyforSeveralYears.R | 2
R/zc0_GPCAiteration.R | 4
man/ComprehensivePrecipitationGenerator.Rd | 21 +-
man/ComprehensiveTemperatureGenerator.Rd | 26 +-
man/GPCAiteration-class.Rd | 4
man/PrecipitationEndDay.Rd | 4
man/PrecipitationStartDay.Rd | 8
man/RMAWGEN-package.Rd | 18 -
man/VAR_mod.Rd | 2
man/WhereIs.Rd | 2
man/acvWGEN.Rd | 6
man/adddate.Rd | 4
man/addsuffixes.Rd | 7
man/arch_test.Rd | 10 -
man/continuity_ratio.Rd | 2
man/countNAs.Rd | 3
man/covariance.Rd | 6
man/extractTnFromAnomalies.Rd | 4
man/extractTxFromAnomalies.Rd | 4
man/extractdays.Rd | 2
man/extractmonths.Rd | 2
man/findDate.Rd | 11 -
man/generateTemperatureTimeseries.Rd | 19 --
man/getDailyMean.Rd | 9
man/getMonthlyMean.Rd | 16 -
man/getVARmodel.Rd | 17 -
man/is.monthly.climate.Rd | 8
man/normalizeGaussian.Rd | 4
man/normalizeGaussian_prec.Rd | 4
man/normalizeGaussian_severalstations.Rd | 12 -
man/normalizeGaussian_severalstations_prec.Rd | 4
man/plotDailyClimate.Rd | 8
man/plot_sample.Rd | 35 ++-
man/qqplot.lagged.Rd | 4
man/qqplotWGEN.Rd | 4
man/qqplot_RMAWGEN_Tx.Rd | 18 -
man/qqplotprecWGEN.Rd | 2
man/qqplotprecWGEN_seasonal.Rd | 2
man/removeNAs.Rd | 4
man/setComprehensiveTemperatureGeneratorParameters.Rd | 16 -
man/splineInterpolateMonthlytoDaily.Rd | 7
man/splineInterpolateMonthlytoDailyforSeveralYears.Rd | 2
man/trentino.Rd | 2
83 files changed, 436 insertions(+), 374 deletions(-)
Title: Handling missing values with/in multivariate data analysis
(principal component methods)
Diff between missMDA versions 1.7 dated 2013-03-30 and 1.7.1 dated 2013-05-23
Description: Imputation of incomplete continuous or categorical
datasets; Missing values are imputed with a principal component
analysis (PCA), a multiple correspondence analysis (MCA) model
or a multiple factor analysis (MFA) model; Perform multiple
imputation with and in PCA
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson
DESCRIPTION | 8 +++----
MD5 | 18 +++++++--------
R/imputePCA.R | 2 -
R/plot.MIPCA.R | 9 +++----
man/MIPCA.Rd | 3 +-
man/imputeFAMD.Rd | 6 +++--
man/imputeMCA.Rd | 6 +++--
man/imputeMFA.Rd | 14 ++++++++----
man/plot.MIPCA.Rd | 2 +
missMDA-Ex.R | 61 +++++++++++++++++++++++++++++++++---------------------
10 files changed, 78 insertions(+), 51 deletions(-)
Title: Calculate generalized eigenvalues of a matrix pair
Diff between geigen versions 1.0 dated 2013-05-15 and 1.1 dated 2013-05-23
Description: Compute generalized eigenvalues and eigenvectors of a pair
of matrices, using routines from Lapack (dggev and zggev).
Compute the generalized Schur decomposition of a pair of
matrices using Lapack routines. In the latter case options for
ordering the generalized eigenvalues are provided.
Author: Berend Hasselman
Maintainer: Berend Hasselman
geigen-1.0/geigen/src/xdgg.f |only
geigen-1.1/geigen/DESCRIPTION | 8 ++--
geigen-1.1/geigen/MD5 | 41 ++++++++++++-----------
geigen-1.1/geigen/NAMESPACE | 2 -
geigen-1.1/geigen/NEWS | 9 +++++
geigen-1.1/geigen/R/geigen.R | 56 ++++++++++++++++++--------------
geigen-1.1/geigen/R/gqz.R | 47 ++++++++++++++++----------
geigen-1.1/geigen/src/xdgges.f | 35 ++++++++++++--------
geigen-1.1/geigen/src/xdggev.f |only
geigen-1.1/geigen/src/xzgges.f | 40 +++++++++++++---------
geigen-1.1/geigen/src/xzggev.f |only
geigen-1.1/geigen/tests/tgqz1.R | 7 ++++
geigen-1.1/geigen/tests/tgqz1.Rout | 18 ++++++++--
geigen-1.1/geigen/tests/tgqz1.Rout.save | 18 ++++++++--
geigen-1.1/geigen/tests/tgqz2.R | 12 +++---
geigen-1.1/geigen/tests/tgqz2.Rout | 14 ++++----
geigen-1.1/geigen/tests/tgqz2.Rout.save | 14 ++++----
geigen-1.1/geigen/tests/tgqz5.R | 8 ++++
geigen-1.1/geigen/tests/tgqz5.Rout | 15 +++++++-
geigen-1.1/geigen/tests/tgqz5.Rout.save | 15 +++++++-
geigen-1.1/geigen/tests/tgqz6.R | 18 +++++-----
geigen-1.1/geigen/tests/tgqz6.Rout | 20 +++++------
geigen-1.1/geigen/tests/tgqz6.Rout.save | 20 +++++------
23 files changed, 259 insertions(+), 158 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Diff between MPTinR versions 1.0.1 dated 2013-02-07 and 1.1.8 dated 2013-05-23
Description: MPTinR provides a user-friendly way for the analysis of
multinomial processing tree (MPT) models (e.g., Riefer, D. M.,
and Batchelder, W. H. [1988]. Multinomial modeling and the
measurement of cognitive processes. Psychological Review, 95,
318-339) for single and multiple datasets. The main functions
perform model fitting and model selection. Model selection can
be done using AIC, BIC, or the Fisher Information Approximation
(FIA) a measure based on the Minimum Description Length (MDL)
framework. The model and restrictions can specified in external
files or within an R script in an intuitive syntax. The
'classical' .EQN file format for model files is also supported.
Besides MPTs, MPTinR can fit a wide variety of other cognitive
models such as SDT models (see fit.model). MPTinR supports
multicore fitting and FIA calculation using the snowfall
package. MPTinR can generate data generating from a model for
e.g., parametric bootstrap and plot predicted versus observed
data.
Author: Henrik Singmann, David Kellen, and Christian Mueller
Maintainer: Henrik Singmann
ChangeLog | 38 ++++++++++++++++++++++++
DESCRIPTION | 25 +++++++++-------
MD5 | 53 ++++++++++++++++++----------------
NAMESPACE | 1
NEWS | 35 ++++++++++++++++++++++
R/bmpt.fia.R | 75 ++++++++++++++++++++++---------------------------
R/fit.model.R | 6 +--
R/fit.mpt.R | 6 +--
R/fit.mptinr.R | 14 +++++++--
R/get.mpt.fia.R | 4 +-
R/make.eqn.R | 2 -
R/select.mpt.R | 3 +
data/d.broeder.rda |binary
data/rb.fig1.data.rda |binary
data/rb.fig2.data.rda |binary
man/MPTinR-package.Rd | 6 +--
man/bmpt.fia.Rd | 17 +++++++++--
man/fit.model.Rd | 15 ++++++---
man/fit.mpt.Rd | 45 +++++++++++++++++------------
man/fit.mpt.old.Rd | 6 +--
man/fit.mptinr.Rd | 9 +++--
man/gen.data.Rd | 15 ++++++---
man/get.mpt.fia.Rd | 13 +++++++-
man/prediction.plot.Rd | 44 +++++++++++++++++++---------
man/prepare.mpt.fia.Rd | 3 +
man/select.mpt.Rd | 10 ++++--
src |only
27 files changed, 297 insertions(+), 148 deletions(-)
Title: Pharmacometric tools for data preparation, modeling, simulation,
and reporting
Diff between metrumrg versions 5.45 dated 2013-05-01 and 5.49 dated 2013-05-23
Description: Pharmacometric tools for common data preparation tasks,
stratified bootstrap resampling of data sets, NONMEM control
stream creation/editing, NONMEM model execution, creation of
standard and user-defined diagnostic plots, execution and
summary of bootstrap and predictive check results,
implementation of simulations from posterior parameter
distributions, reporting of output tables and creation of
detailed analysis logs.
Author: Tim Bergsma, Bill Knebel, Leonid Gibiansky, Natalie Hsiang
Maintainer: Tim Bergsma
ChangeLog | 18 ++++++++++++
DESCRIPTION | 8 ++---
MD5 | 56 ++++++++++++++++++++--------------------
NAMESPACE | 10 +++----
R/cast.R | 1
R/first.R | 23 ++++------------
R/reapply.R | 10 +++++--
R/temporal.R | 12 ++++----
man/NONR.Rd | 3 +-
man/as.pxml.Rd | 22 +++++++--------
man/as.second.Rd | 6 ++++
man/c.temporal.Rd | 26 +++++++++---------
man/electronicAppendix.Rd | 9 +++++-
man/extensions.Rd | 7 ++++-
man/helpList.Rd | 10 +++----
man/index.Rd | 20 ++++++++++++--
man/inner.data.frame.Rd | 2 -
man/iterations.Rd | 64 +++++++++++++++++++++++-----------------------
man/lookup.Rd | 10 +++----
man/metrumrg-package.Rd | 4 +-
man/panel.hist.Rd | 3 +-
man/panel.stratify.Rd | 6 ++--
man/qsub.Rd | 3 +-
man/reapply.Rd | 14 +++++++---
man/runCommand.Rd | 6 ++--
man/runlog.Rd | 27 +++++++++++--------
man/temporal.Rd | 2 -
man/wikiparse.Rd | 15 ++++++++++
man/xyplot.ext.Rd | 22 +++++++--------
29 files changed, 249 insertions(+), 170 deletions(-)
Title: R Interface to C API of GLPK
Diff between glpkAPI versions 1.2.6 dated 2013-02-12 and 1.2.7 dated 2013-05-23
Description: R Interface to C API of GLPK, needs GLPK Version >= 4.42
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 9 +++---
MD5 | 25 ++++++++++--------
NAMESPACE | 2 +
R/glpkAPI.R | 46 +++++++++++++++++++++++++++++++++-
configure | 18 ++++++-------
configure.ac | 2 -
inst/NEWS.Rd | 10 +++++++
inst/doc/glpkAPI.R |only
inst/doc/glpkAPI.pdf |binary
man/setColsNamesGLPK.Rd |only
man/setRowsNamesGLPK.Rd |only
src/Makevars.win | 2 -
src/glpkAPI.c | 64 ++++++++++++++++++++++++++++++++++++++++++++++++
src/glpkAPI.h | 6 ++++
src/init.c | 2 +
15 files changed, 159 insertions(+), 27 deletions(-)
Title: R Interface to C API of COIN-OR Clp
Diff between clpAPI versions 1.2.2 dated 2013-01-16 and 1.2.3 dated 2013-05-23
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 | 9 ++--
MD5 | 33 ++++++++-------
NAMESPACE | 8 +++
R/clpAPI.R | 77 +++++++++++++++++++++++++++++++++++
R/zzz.R | 5 +-
configure | 18 ++++----
configure.ac | 2
inst/NEWS.Rd | 10 ++++
inst/c2r.map | 5 ++
inst/doc/clpAPI.R |only
inst/doc/clpAPI.pdf |binary
man/copyNamesCLP.Rd |only
man/dropNamesCLP.Rd |only
man/lengthNamesCLP.Rd |only
man/loadProblemCLP.Rd | 4 +
man/versionCLP.Rd |only
src/clpAPI.c | 109 ++++++++++++++++++++++++++++++++++++++++++++++++++
src/clpAPI.h | 18 ++++++++
src/clpR.h | 1
src/init.c | 6 ++
20 files changed, 274 insertions(+), 31 deletions(-)
Title: Colocalisation tests of two genetic traits
Diff between coloc versions 1.11 dated 2013-01-25 and 2.0 dated 2013-05-23
Description: Performs the colocalisation tests described in Plagnol et
al (2009), Wallace et al (2013) and Giambartolomei et al
(2013).
Author: Chris Wallace, with contributions from Claudia Giambartolemei
Maintainer: Chris Wallace
coloc-1.11/coloc/R/plots.R |only
coloc-2.0/coloc/ChangeLog | 9
coloc-2.0/coloc/DESCRIPTION | 21 +-
coloc-2.0/coloc/MD5 | 40 ++-
coloc-2.0/coloc/NAMESPACE | 12 +
coloc-2.0/coloc/R/AllClasses.R | 86 ++++----
coloc-2.0/coloc/R/bma.R | 211 ++++++++++----------
coloc-2.0/coloc/R/claudia.R |only
coloc-2.0/coloc/R/coloc.test.R | 304 ++++++++++++++++--------------
coloc-2.0/coloc/R/pcs.R | 2
coloc-2.0/coloc/R/private.R |only
coloc-2.0/coloc/README.md |only
coloc-2.0/coloc/inst |only
coloc-2.0/coloc/man/Var.data.Rd |only
coloc-2.0/coloc/man/Var.data.cc.Rd |only
coloc-2.0/coloc/man/approx.bf.Rd |only
coloc-2.0/coloc/man/bf.Rd |only
coloc-2.0/coloc/man/coloc-class.Rd | 17 -
coloc-2.0/coloc/man/coloc.abf.Rd |only
coloc-2.0/coloc/man/coloc.abf.datasets.Rd |only
coloc-2.0/coloc/man/coloc.abf.snpStats.Rd |only
coloc-2.0/coloc/man/coloc.bma.Rd | 36 ++-
coloc-2.0/coloc/man/coloc.test.Rd | 92 ++-------
coloc-2.0/coloc/man/coloc.test.summary.Rd |only
coloc-2.0/coloc/man/eta.Rd | 39 +--
coloc-2.0/coloc/man/logdiff.Rd |only
coloc-2.0/coloc/man/logsum.Rd |only
27 files changed, 466 insertions(+), 403 deletions(-)
Title: Analyzing case-parent triad and/or case-control data with SNP
haplotypes
Diff between Haplin versions 5.2 dated 2013-05-02 and 5.3 dated 2013-05-23
Description: Haplin performs a genetic association analysis of
case-parent triad (trio) data with multiple markers. It can
also incorporate complete or incomplete control triads, for
instance independent control children. Estimation is based on
haplotypes, for instance SNP haplotypes, even though phase is
not known from the genetic data. Haplin estimates relative risk
(RR + conf.int.) and p-value associated with each haplotype. It
uses maximum likelihood estimation to make optimal use of data
from triads with missing genotypic data, for instance if some
SNPs has not been typed for some individuals. Haplin also
allows estimation of effects of maternal haplotypes and
parent-of-origin effects, particularly appropriate in perinatal
epidemiology. Haplin allows special models, like
X-inactivation, to be fitted on the X-chromosome.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing
DESCRIPTION | 8 ++---
MD5 | 63 ++++++++++++++++++++--------------------
NAMESPACE | 1
R/convertPed.R | 2 -
R/f.Rplot.R | 4 +-
R/f.check.pars.R | 12 ++++---
R/f.data.R | 26 ++++++++--------
R/f.data.ready.R | 9 +----
R/f.get.data.R | 24 +++++++--------
R/f.get.marker.names.R |only
R/f.haptable.list.R | 13 +-------
R/f.plot.effects.R | 3 +
R/f.prep.data.R | 6 +--
R/f.read.data.R | 2 -
R/f.split.matrix.R | 4 +-
R/gwaaToHaplin.R | 4 +-
R/haplin.R | 14 +++-----
R/haplinSlide.R | 31 ++++++++++---------
R/haptable.default.R |only
R/haptable.haplin.R | 7 ++--
R/haptable.haplinSlide.R | 5 ---
R/haptable.haplinStrat.R | 2 -
R/lineByLine.R | 14 ++++----
R/plot.haplin.R | 37 ++++++++++++++---------
R/prepPed.R | 17 ++++++++--
R/print.summary.tri.glm.R | 4 +-
R/textlabel.R |only
R/toDataFrame.R | 19 +++++++-----
inst/doc/Haplin_data_format.pdf |binary
man/convertPed.Rd | 2 -
man/lineByLine.Rd | 16 +++++-----
man/plot.haptable.Rd | 6 ++-
man/prepPed.Rd | 3 +
man/snpPos.Rd | 5 +--
34 files changed, 193 insertions(+), 170 deletions(-)
Title: Flexible regression models for survival data.
Diff between timereg versions 1.7.5 dated 2013-05-02 and 1.7.6 dated 2013-05-23
Description: Programs for Martinussen and Scheike (2006), `Dynamic
Regression Models for Survival Data', Springer Verlag. Plus
more recent developments. Additive survival model,
semiparametric proportional odds model, cumulative residuals,
excess risk models and more. Flexible competing risks
regression including GOF-tests. Two-stage frailty modelling.
PLS for the additive risk model. Lasso in ahaz package.
Author: Thomas Scheike with contributions from Torben Martinussen and
Jeremy Silver
Maintainer: Thomas Scheike
DESCRIPTION | 8
MD5 | 40 -
R/Gprop-odds-subdist.r | 3
R/Gprop-odds.r | 2
R/clusterindex-reshape.r | 5
R/comprisk.r | 1032 +++++++++++++++++++++++------------------------
R/cox-aalen.r | 8
R/mgresid.r | 2
R/new.aalen.r | 3
R/new.cox-aalen.r | 19
R/new.pe-sasieni.r | 2
R/predict-timereg.r | 5
R/prop-odds-subdist.r | 3
R/prop-odds.r | 3
R/read-design.r | 6
R/two-stage-reg.r | 1
man/comp.risk.Rd | 27 -
man/cox.aalen.Rd | 20
src/aalen.c | 104 +++-
src/cox-aalen.c | 444 ++++++++++++++------
src/matrix.c | 11
21 files changed, 993 insertions(+), 755 deletions(-)
Title: Internal validation of forensic STR kits made easy with
strvalidator.
Diff between strvalidator versions 0.1 dated 2013-03-11 and 0.2.0 dated 2013-05-23
Description: strvalidator provide tools that make it easier to perform
an internal validation of a forensic short tandem repeat (STR)
kit for human identification. The tools are developed to
provide all necessary data to conform with the ENFSI guidelines
for internal validation. More information about each function
can be found in the respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson
strvalidator-0.1/strvalidator/R/addZvalue.r |only
strvalidator-0.1/strvalidator/R/addZygosity.r |only
strvalidator-0.1/strvalidator/R/calculateZvalue.r |only
strvalidator-0.1/strvalidator/R/calculateZygosity.r |only
strvalidator-0.1/strvalidator/R/importGM.r |only
strvalidator-0.1/strvalidator/man/addZvalue.Rd |only
strvalidator-0.1/strvalidator/man/addZygosity.Rd |only
strvalidator-0.1/strvalidator/man/calculateZvalue.Rd |only
strvalidator-0.1/strvalidator/man/calculateZygosity.Rd |only
strvalidator-0.1/strvalidator/man/importGM.Rd |only
strvalidator-0.2.0/strvalidator/DESCRIPTION | 19
strvalidator-0.2.0/strvalidator/MD5 | 130 +-
strvalidator-0.2.0/strvalidator/NAMESPACE | 4
strvalidator-0.2.0/strvalidator/NEWS | 16
strvalidator-0.2.0/strvalidator/R/addData.r | 183 ++-
strvalidator-0.2.0/strvalidator/R/addData_gui.r |only
strvalidator-0.2.0/strvalidator/R/addDye_gui.r |only
strvalidator-0.2.0/strvalidator/R/addKitInfo.r | 2
strvalidator-0.2.0/strvalidator/R/calculateBalance.r | 462 ++++++----
strvalidator-0.2.0/strvalidator/R/calculateBalance_gui.r |only
strvalidator-0.2.0/strvalidator/R/calculateDropout.r | 304 ++++--
strvalidator-0.2.0/strvalidator/R/calculateDropout_gui.r |only
strvalidator-0.2.0/strvalidator/R/calculateH.r | 114 +-
strvalidator-0.2.0/strvalidator/R/calculateH_gui.r |only
strvalidator-0.2.0/strvalidator/R/calculateHeterozygous.r |only
strvalidator-0.2.0/strvalidator/R/calculateHeterozygous_gui.r |only
strvalidator-0.2.0/strvalidator/R/calculateMean.r | 3
strvalidator-0.2.0/strvalidator/R/calculateStutter.r | 134 ++
strvalidator-0.2.0/strvalidator/R/calculateStutter_gui.r |only
strvalidator-0.2.0/strvalidator/R/calculateSummary.r | 2
strvalidator-0.2.0/strvalidator/R/checkSubset.r | 24
strvalidator-0.2.0/strvalidator/R/checkSubset_gui.r |only
strvalidator-0.2.0/strvalidator/R/combineRef.r | 2
strvalidator-0.2.0/strvalidator/R/concatenate_gui.r |only
strvalidator-0.2.0/strvalidator/R/countPeaks.r | 2
strvalidator-0.2.0/strvalidator/R/detectKit.r |only
strvalidator-0.2.0/strvalidator/R/editData_gui.r |only
strvalidator-0.2.0/strvalidator/R/filterProfile.r | 319 +++++-
strvalidator-0.2.0/strvalidator/R/filterProfile_gui.r |only
strvalidator-0.2.0/strvalidator/R/getKit.r | 142 ---
strvalidator-0.2.0/strvalidator/R/globals.R |only
strvalidator-0.2.0/strvalidator/R/guessProfile.r |only
strvalidator-0.2.0/strvalidator/R/guessProfile_gui.r |only
strvalidator-0.2.0/strvalidator/R/import.r |only
strvalidator-0.2.0/strvalidator/R/import_gui.r |only
strvalidator-0.2.0/strvalidator/R/listObjects.r |only
strvalidator-0.2.0/strvalidator/R/modelDropout_gui.r |only
strvalidator-0.2.0/strvalidator/R/plotBalance_gui.r |only
strvalidator-0.2.0/strvalidator/R/plotDropout_gui.r |only
strvalidator-0.2.0/strvalidator/R/plotStutter_gui.r |only
strvalidator-0.2.0/strvalidator/R/savePlot_gui.r |only
strvalidator-0.2.0/strvalidator/R/slim.r | 19
strvalidator-0.2.0/strvalidator/R/slim_gui.r |only
strvalidator-0.2.0/strvalidator/R/strvalidator-package.r | 43
strvalidator-0.2.0/strvalidator/R/strvalidator.r |only
strvalidator-0.2.0/strvalidator/R/trim.r | 49 -
strvalidator-0.2.0/strvalidator/R/trim_gui.r |only
strvalidator-0.2.0/strvalidator/data/ref2.RData |only
strvalidator-0.2.0/strvalidator/data/set2.RData |only
strvalidator-0.2.0/strvalidator/inst |only
strvalidator-0.2.0/strvalidator/man/addData.Rd | 14
strvalidator-0.2.0/strvalidator/man/addData_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/addDye_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateBalance.Rd | 54 -
strvalidator-0.2.0/strvalidator/man/calculateBalance_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateDropout.Rd | 5
strvalidator-0.2.0/strvalidator/man/calculateDropout_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateH.Rd | 28
strvalidator-0.2.0/strvalidator/man/calculateH_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateHeterozygous.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateHeterozygous_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateStutter.Rd | 13
strvalidator-0.2.0/strvalidator/man/calculateStutter_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/checkSubset.Rd | 5
strvalidator-0.2.0/strvalidator/man/checkSubset_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/concatenate_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/detectKit.Rd |only
strvalidator-0.2.0/strvalidator/man/editData_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/filterProfile.Rd | 12
strvalidator-0.2.0/strvalidator/man/filterProfile_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/getKit.Rd | 7
strvalidator-0.2.0/strvalidator/man/guessProfile.Rd |only
strvalidator-0.2.0/strvalidator/man/guessProfile_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/import.Rd |only
strvalidator-0.2.0/strvalidator/man/import_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/listObjects.Rd |only
strvalidator-0.2.0/strvalidator/man/modelDropout_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/plotBalance_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/plotDropout_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/plotStutter_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/ref2.Rd |only
strvalidator-0.2.0/strvalidator/man/savePlot_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/set2.Rd |only
strvalidator-0.2.0/strvalidator/man/slim.Rd | 9
strvalidator-0.2.0/strvalidator/man/slim_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/strvalidator-package.Rd | 15
strvalidator-0.2.0/strvalidator/man/strvalidator.Rd |only
strvalidator-0.2.0/strvalidator/man/trim.Rd | 9
strvalidator-0.2.0/strvalidator/man/trim_gui.Rd |only
99 files changed, 1502 insertions(+), 642 deletions(-)
Title: Spatio-Temporal Bayesian Modelling Using R
Diff between spTimer versions 0.6 dated 2013-03-01 and 0.7 dated 2013-05-23
Description: The package is able to fit, spatially predict and
temporally forecast large amounts of space-time data using [1]
Bayesian Gaussian Process (GP) Models, [2] Bayesian
Auto-Regressive (AR) Models, and [3] Bayesian Gaussian
Predictive Processes (GPP) based AR Models.
Author: K. Shuvo Bakar & Sujit K. Sahu
Maintainer: Khandoker Shuvo Bakar
spTimer-0.6/spTimer/man/DataFit.Rd |only
spTimer-0.6/spTimer/man/DataFitFore.Rd |only
spTimer-0.6/spTimer/man/DataValFore.Rd |only
spTimer-0.6/spTimer/man/DataValPred.Rd |only
spTimer-0.7/spTimer/DESCRIPTION | 14 ++--
spTimer-0.7/spTimer/MD5 | 43 +++++-------
spTimer-0.7/spTimer/R/spAR.r | 24 ++-----
spTimer-0.7/spTimer/R/spGP.r | 24 ++-----
spTimer-0.7/spTimer/R/spGPP.r | 68 ++------------------
spTimer-0.7/spTimer/R/spTfnc.R | 44 ++++++-------
spTimer-0.7/spTimer/R/spTimer.R | 10 ++
spTimer-0.7/spTimer/R/useful_commands.R | 76 +++++++++++++++++-----
spTimer-0.7/spTimer/man/NYdata.Rd | 88 ++++++++++++++++++++------
spTimer-0.7/spTimer/man/as.forecast.object.Rd |only
spTimer-0.7/spTimer/man/predict.spT.Rd | 20 +++++
spTimer-0.7/spTimer/man/spT.Gibbs.Rd | 31 +++++----
spTimer-0.7/spTimer/man/spT.initials.Rd | 2
spTimer-0.7/spTimer/man/spT.priors.Rd | 2
spTimer-0.7/spTimer/man/spT.validation.Rd | 6 -
spTimer-0.7/spTimer/man/spTimer-internal.Rd | 1
spTimer-0.7/spTimer/man/spTimer-package.Rd | 13 ++-
spTimer-0.7/spTimer/man/summary.spT.Rd | 12 ++-
spTimer-0.7/spTimer/src/equation_xb_ar.c | 39 ++++++++---
spTimer-0.7/spTimer/src/mathematics.c | 4 -
spTimer-0.7/spTimer/src/randgenerator.c | 3
25 files changed, 305 insertions(+), 219 deletions(-)
Title: Simulation of the forensic DNA process
Diff between pcrsim versions 0.1 dated 2013-04-06 and 0.1.1 dated 2013-05-23
Description: pcrsim is a package for simulating the forensic DNA
process. pcrsim() opens up a graphical user interface which
allow the user to enter parameters required for the simulation.
Once calibrated the program can be used to: reduce the
laboratory work needed for validation of new STR kits, help
develop methods for interpretation of DNA evidence, etc. This
is a first version which is still experimental and under
development.
Author: Oskar Hansson
Maintainer: Oskar Hansson
DESCRIPTION | 8 ++++----
MD5 | 20 +++++++++++---------
NEWS | 5 +++++
R/findScaling.r |only
R/generateEPG.r | 5 -----
R/generateEPGgui.r | 6 +++---
R/pcrsim.r | 15 ++++++++++-----
R/simPCR.r | 18 ++++++++++--------
R/simulateprofile.r | 31 +++++++++++++++++--------------
man/findScaling.Rd |only
man/simPCR.Rd | 2 +-
man/simulateProfile.Rd | 7 +++++--
12 files changed, 66 insertions(+), 51 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Diff between MKmisc versions 0.93 dated 2013-02-17 and 0.94 dated 2013-05-23
Description: Miscellaneous Functions from M. Kohl
Author: Matthias Kohl
Maintainer: Matthias Kohl
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++++------
NAMESPACE | 2 ++
NEWS | 11 +++++++++++
R/stringDist.R | 17 ++++++++++++-----
R/stringSim.R |only
R/traceBack.R |only
man/heatmapCol.Rd | 6 ++++--
man/stringDist.Rd | 16 ++++++++++------
man/stringSim.Rd |only
man/traceBack.Rd |only
11 files changed, 53 insertions(+), 23 deletions(-)
Title: Citations for knitr markdown files
Diff between knitcitations versions 0.4-4 dated 2013-03-18 and 0.4-7 dated 2013-05-23
Description: knitcitations provides the ability to create dynamic
citations in which the bibliographic information is pulled from
the web rather than having to be entered into a local database
such as bibtex ahead of time. Knitcitations is primarily aimed
at authoring in the R markdown format, and can provide outputs
for web-based authoring such as linked text and tooltips over
inline citations. Cite using a DOI, URL, or bibtex file key.
See the package URL for details.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger
DESCRIPTION | 9 ++++---
MD5 | 58 +++++++++++++++++++++++++-------------------------
NEWS | 45 +++++++++++++++++++++++++++++++-------
R/bibliography.R | 36 +++++++++++++++++++++++--------
R/cite.R | 9 +++++--
R/cite_options.R | 7 ++++--
R/citep.R | 23 ++++++++++++++-----
R/citet.R | 48 +++++++++++++++++++++++++++++++----------
R/create_bibkey.R | 11 ++++++---
R/formatref.R | 4 ++-
R/functiontable.R | 9 ++++---
R/init_knitbib.R | 6 +++--
R/inline_formats.R | 34 +++++++++++++++++++----------
R/print_html.R |only
R/print_markdown.R | 16 ++++++++-----
R/print_rdfa.R | 14 +++++++++---
R/read.bibtex.R | 2 -
R/write.bibtex.R | 28 ++++++++++++++----------
R/write_cache.R | 9 +++++--
man/bib_format.Rd | 3 +-
man/bibliography.Rd | 12 ++++++----
man/cite_options.Rd | 4 +--
man/citep.Rd | 10 +++++++-
man/citet.Rd | 4 ++-
man/functiontable.Rd | 8 +++---
man/print_html.Rd |only
man/print_markdown.Rd | 10 ++++++--
man/print_rdfa.Rd | 3 +-
man/unique_inline.Rd | 2 -
man/write.bibtex.Rd | 6 +++--
man/write_cache.Rd | 2 -
31 files changed, 293 insertions(+), 139 deletions(-)
Title: Fast hierarchical clustering routines for R and Python
Diff between fastcluster versions 1.1.9 dated 2013-03-17 and 1.1.10 dated 2013-05-23
Description: This is a two-in-one package which provides interfaces to
both R and Python. It implements fast hierarchical,
agglomerative clustering routines. Part of the functionality is
designed as drop-in replacement for existing routines:
“linkage” in the SciPy package “scipy.cluster.hierarchy”,
“hclust” in R's “stats” package, and the “flashClust” package.
It provides the same functionality with the benefit of a much
faster implementation. Moreover, there are memory-saving
routines for clustering of vector data, which go beyond what
the existing packages provide. For information on how to
install the Python files, see the file INSTALL in the source
distribution.
Author: Daniel Müllner, http://math.stanford.edu/~muellner
Maintainer: Daniel Müllner
DESCRIPTION | 16 +--
MD5 | 24 ++---
NEWS | 13 ++
inst/CITATION | 25 +++--
inst/doc/fastcluster.Rtex | 8 +
inst/doc/fastcluster.pdf |binary
man/fastcluster.Rd | 2
python/fastcluster.py | 4
python/setup.py | 13 ++
src/Makevars | 2
src/fastcluster.cpp | 200 ++++++++++++++++++++++++++++++++++-------
src/fastcluster_R.cpp | 132 ++++++++++++++++++++++-----
src/fastcluster_python.cpp | 215 +++++++++++++++++++++++++++++++++++++++++----
13 files changed, 540 insertions(+), 114 deletions(-)
Title: Differential Co-expression Analysis and Differential Regulation
Analysis of Gene Expression Microarray Data
Diff between DCGL versions 2.0 dated 2013-03-28 and 2.0.1 dated 2013-05-23
Description: Functions for 1) gene filtration; 2) link filtration; 3)
differential co-expression analysis: DCG (Differential
Coexpressed Gene) identification and DCL (Differentially
Coexpressed Link) identification; and 4) differential
regulation analysis: DRG (Differential Regulated Gene)
identification, DRL (Differential Regulated Link)
identification, DRL visualization and regulator ranking.
Author: Jing Yang, Hui Yu, Bao-Hong Liu
Maintainer: Bao-Hong Liu
DESCRIPTION | 10 +++++-----
MD5 | 26 +++++++++++++-------------
R/DCGL.r | 4 ++--
doc/DCGL_2.0.pdf |binary
man/ASC.Rd | 5 +++--
man/DCGL-package.Rd | 47 +++++++++++++++++++++++++++++++----------------
man/DCe.Rd | 18 ++++++++++++++----
man/DCp.Rd | 20 +++++++++++++++-----
man/DCsum.Rd | 6 ++++--
man/DRplot.Rd | 23 ++++++++++++++++-------
man/DRrank.Rd | 23 +++++++++++++++--------
man/DRsort.Rd | 17 ++++++++++++-----
man/LRC.Rd | 2 +-
man/qLinkfilter.Rd | 10 ++++++++--
14 files changed, 139 insertions(+), 72 deletions(-)
Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.2-50 dated 2013-04-20 and 0.2-70 dated 2013-05-22
Description: phytools provides various functions for phylogenetic
analysis, mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
phytools-0.2-50/phytools/man/applyEdgeLengths.Rd |only
phytools-0.2-70/phytools/DESCRIPTION | 8
phytools-0.2-70/phytools/MD5 | 234 +++---
phytools-0.2-70/phytools/NAMESPACE | 13
phytools-0.2-70/phytools/R/contMap.R | 77 +-
phytools-0.2-70/phytools/R/densityMap.R | 40 -
phytools-0.2-70/phytools/R/estDiversity.R | 6
phytools-0.2-70/phytools/R/evol.vcv.R | 28
phytools-0.2-70/phytools/R/fastAnc.R | 6
phytools-0.2-70/phytools/R/make.simmap.R | 290 ++++++--
phytools-0.2-70/phytools/R/phylomorphospace.R | 17
phytools-0.2-70/phytools/R/read.simmap.R | 707 ++++++++------------
phytools-0.2-70/phytools/R/rerootingMethod.R | 6
phytools-0.2-70/phytools/R/utilities.R | 157 +++-
phytools-0.2-70/phytools/man/add.color.bar.Rd | 2
phytools-0.2-70/phytools/man/add.everywhere.Rd | 13
phytools-0.2-70/phytools/man/add.random.Rd | 4
phytools-0.2-70/phytools/man/allFurcTrees.Rd | 18
phytools-0.2-70/phytools/man/anc.Bayes.Rd | 12
phytools-0.2-70/phytools/man/anc.ML.Rd | 10
phytools-0.2-70/phytools/man/anc.trend.Rd | 25
phytools-0.2-70/phytools/man/applyBranchLengths.Rd |only
phytools-0.2-70/phytools/man/ave.rates.Rd | 6
phytools-0.2-70/phytools/man/bind.tip.Rd | 4
phytools-0.2-70/phytools/man/bmPlot.Rd | 34
phytools-0.2-70/phytools/man/branching.diffusion.Rd | 25
phytools-0.2-70/phytools/man/brownie.lite.Rd | 9
phytools-0.2-70/phytools/man/brownieREML.Rd | 29
phytools-0.2-70/phytools/man/contMap.Rd | 15
phytools-0.2-70/phytools/man/countSimmap.Rd | 14
phytools-0.2-70/phytools/man/densityMap.Rd | 12
phytools-0.2-70/phytools/man/describe.simmap.Rd | 4
phytools-0.2-70/phytools/man/drop.clade.Rd | 12
phytools-0.2-70/phytools/man/drop.tip.simmap.Rd | 17
phytools-0.2-70/phytools/man/estDiversity.Rd | 6
phytools-0.2-70/phytools/man/evol.rate.mcmc.Rd | 6
phytools-0.2-70/phytools/man/evol.vcv.Rd | 40 -
phytools-0.2-70/phytools/man/evolvcv.lite.Rd | 16
phytools-0.2-70/phytools/man/exhaustiveMP.Rd | 18
phytools-0.2-70/phytools/man/expm.Rd | 6
phytools-0.2-70/phytools/man/export.as.xml.Rd | 6
phytools-0.2-70/phytools/man/fancyTree.Rd | 62 -
phytools-0.2-70/phytools/man/fastAnc.Rd | 4
phytools-0.2-70/phytools/man/fastBM.Rd | 20
phytools-0.2-70/phytools/man/fastMRCA.Rd | 12
phytools-0.2-70/phytools/man/findMRCA.Rd | 4
phytools-0.2-70/phytools/man/fitBayes.Rd | 4
phytools-0.2-70/phytools/man/fitDiversityModel.Rd | 26
phytools-0.2-70/phytools/man/gammatest.Rd | 12
phytools-0.2-70/phytools/man/getCladesofSize.Rd |only
phytools-0.2-70/phytools/man/getDescendants.Rd | 10
phytools-0.2-70/phytools/man/getExtant.Rd | 10
phytools-0.2-70/phytools/man/getSisters.Rd | 6
phytools-0.2-70/phytools/man/getStates.Rd | 6
phytools-0.2-70/phytools/man/lambda.transform.Rd | 14
phytools-0.2-70/phytools/man/likMlambda.Rd | 12
phytools-0.2-70/phytools/man/ls.tree.Rd | 10
phytools-0.2-70/phytools/man/ltt.Rd | 18
phytools-0.2-70/phytools/man/ltt95.Rd | 8
phytools-0.2-70/phytools/man/make.era.map.Rd | 10
phytools-0.2-70/phytools/man/make.simmap.Rd | 28
phytools-0.2-70/phytools/man/map.overlap.Rd | 12
phytools-0.2-70/phytools/man/matchNodes.Rd | 4
phytools-0.2-70/phytools/man/mergeMappedStates.Rd |only
phytools-0.2-70/phytools/man/minSplit.Rd | 21
phytools-0.2-70/phytools/man/mrp.supertree.Rd | 14
phytools-0.2-70/phytools/man/multi.mantel.Rd | 9
phytools-0.2-70/phytools/man/multiC.Rd | 8
phytools-0.2-70/phytools/man/nodeHeights.Rd | 14
phytools-0.2-70/phytools/man/optim.phylo.ls.Rd | 30
phytools-0.2-70/phytools/man/orderMappedEdge.Rd | 4
phytools-0.2-70/phytools/man/paintSubTree.Rd | 20
phytools-0.2-70/phytools/man/paste.tree.Rd | 20
phytools-0.2-70/phytools/man/pbtree.Rd | 16
phytools-0.2-70/phytools/man/pgls.Ives.Rd | 11
phytools-0.2-70/phytools/man/phenogram.Rd | 30
phytools-0.2-70/phytools/man/phyl.RMA.Rd | 6
phytools-0.2-70/phytools/man/phyl.cca.Rd | 6
phytools-0.2-70/phytools/man/phyl.pairedttest.Rd | 42 -
phytools-0.2-70/phytools/man/phyl.pca.Rd | 8
phytools-0.2-70/phytools/man/phyl.resid.Rd | 10
phytools-0.2-70/phytools/man/phyl.vcv.Rd | 4
phytools-0.2-70/phytools/man/phylANOVA.Rd | 32
phytools-0.2-70/phytools/man/phyloDesign.Rd | 6
phytools-0.2-70/phytools/man/phylomorphospace.Rd | 16
phytools-0.2-70/phytools/man/phylomorphospace3d.Rd | 16
phytools-0.2-70/phytools/man/phylosig.Rd | 20
phytools-0.2-70/phytools/man/plotBranchbyTrait.Rd | 4
phytools-0.2-70/phytools/man/plotSimmap.Rd | 22
phytools-0.2-70/phytools/man/plotThresh.Rd | 4
phytools-0.2-70/phytools/man/plotTree.Rd | 10
phytools-0.2-70/phytools/man/posterior.evolrate.Rd | 6
phytools-0.2-70/phytools/man/read.newick.Rd | 12
phytools-0.2-70/phytools/man/read.simmap.Rd | 8
phytools-0.2-70/phytools/man/reorderSimmap.Rd | 10
phytools-0.2-70/phytools/man/repPhylo.Rd | 6
phytools-0.2-70/phytools/man/reroot.Rd | 6
phytools-0.2-70/phytools/man/rerootingMethod.Rd | 4
phytools-0.2-70/phytools/man/rescaleSimmap.Rd | 8
phytools-0.2-70/phytools/man/roundBranches.Rd | 4
phytools-0.2-70/phytools/man/rstate.Rd | 4
phytools-0.2-70/phytools/man/sampleFrom.Rd | 14
phytools-0.2-70/phytools/man/sim.corrs.Rd | 14
phytools-0.2-70/phytools/man/sim.history.Rd | 20
phytools-0.2-70/phytools/man/sim.ratebystate.Rd | 2
phytools-0.2-70/phytools/man/sim.rates.Rd | 18
phytools-0.2-70/phytools/man/splitTree.Rd | 10
phytools-0.2-70/phytools/man/splitplotTree.Rd | 4
phytools-0.2-70/phytools/man/starTree.Rd | 12
phytools-0.2-70/phytools/man/strahlerNumber.Rd | 4
phytools-0.2-70/phytools/man/threshBayes.Rd | 16
phytools-0.2-70/phytools/man/threshDIC.Rd | 4
phytools-0.2-70/phytools/man/threshState.Rd | 4
phytools-0.2-70/phytools/man/to.matrix.Rd | 2
phytools-0.2-70/phytools/man/treeSlice.Rd | 12
phytools-0.2-70/phytools/man/untangle.Rd | 4
phytools-0.2-70/phytools/man/vcvPhylo.Rd | 8
phytools-0.2-70/phytools/man/write.simmap.Rd | 24
phytools-0.2-70/phytools/man/writeAncestors.Rd | 2
phytools-0.2-70/phytools/man/writeNexus.Rd | 2
120 files changed, 1548 insertions(+), 1343 deletions(-)
Title: Exploring water quality monitoring data
Diff between wq versions 0.3-8 dated 2012-09-09 and 0.3-9 dated 2013-05-22
Description: Functions to assist in the processing and exploration of
data from monitoring programs for aquatic ecosystems. The name
"wq" stands for "water quality" and reflects a focus on time
series data for physical and chemical properties of water, as
well as the plankton. The package is intended for programs that
sample approximately monthly at discrete stations, a feature of
many legacy data sets. Although our emphasis is on aquatic
ecosystems, most of the functions should be useful for analysis
of similar-frequency time series regardless of the subject
matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby
ChangeLog | 6 +++++-
DESCRIPTION | 9 +++++----
MD5 | 19 +++++++++++++------
R/plotSeason.R | 4 ++--
R/plotTsAnom.R | 16 ++++++++--------
inst/CITATION | 2 +-
inst/doc |only
man/wq-package.Rd | 4 ++--
vignettes |only
9 files changed, 36 insertions(+), 24 deletions(-)
Title: Automate parallelization of function calls by means of dynamic
code analysis
Diff between parallelize.dynamic versions 0.9 dated 2013-05-08 and 0.9-1 dated 2013-05-22
More information about parallelize.dynamic at CRAN
Description: Passing a given function name or a call to the
parallelize/parallelize_call functions analyses and executes
the code, if possible in parallel. Parallel code execution can
be performed locally or on remote batch queuing systems.
Author: Stefan Boehringer
Maintainer: Stefan Boehringer
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
R/Rdata.R | 14 ++++++++++++--
R/Rparallel.R | 4 +++-
R/Rparallel.back.R | 3 ++-
R/Rsystem.R | 16 ++++++++--------
6 files changed, 33 insertions(+), 20 deletions(-)
Permanent link
Title: Sample size calculations for longitudinal data
Diff between longpower versions 1.0-4 dated 2013-01-23 and 1.0-7 dated 2013-05-22
Description: The longpower package contains functions for computing
power and sample size for linear models of longitudinal data
based on the formula due to Liu and Liang (1997) and Diggle et
al (2002). Either formula is expressed in terms of marginal
model or Generalized Estimating Equations (GEE) parameters.
This package contains functions which translate pilot mixed
effect model parameters (e.g. random intercept and/or slope)
into marginal model parameters so that the formulas of Diggle
et al or Liu and Liang formula can be applied to produce sample
size calculations for two sample longitudinal designs assuming
known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue
DESCRIPTION | 14 +++---
MD5 | 31 +++++++-------
NAMESPACE | 2
R/lmmpower.R | 4 -
README.markdown |only
inst/CITATION | 2
inst/doc/longpower.R |only
inst/doc/longpower.Rnw | 90 ++++++++++++++++++++++--------------------
inst/doc/longpower.bib |only
inst/doc/longpower.pdf |binary
man/diggle.linear.power.Rd | 74 +++++++++-------------------------
man/edland.linear.power.Rd | 12 -----
man/liu.liang.linear.power.Rd | 31 +-------------
man/lmmpower-methods.Rd | 50 ++---------------------
man/longpower-package.Rd | 16 ++-----
man/power.mmrm.Rd | 10 ----
man/power.mmrm.ar1.Rd | 44 ++++++++++++--------
man/print.power.longtest.Rd | 5 --
18 files changed, 143 insertions(+), 242 deletions(-)
Title: Genetic diversity partition statistics and Informative locus
selection using Fst, Gst, Dest(Jost Chao) G'st and In.
Diff between diveRsity versions 1.4.6 dated 2013-04-01 and 1.5.0 dated 2013-05-22
Description: diveRsity is a package which allows the calculation of
both genetic diversity partition statistics, genetic
differentiation statistics and locus informativeness for
ancestry assignment. It also provides users with various option
to calculate bootstrapped 95% confidence intervals both across
loci, for pairwise population comparisons and to plot these
results interactively. V1.2 and up provides parallel computing
capabilities and pairwise results without bootstrapping. Weir
and Cockerham's 1984 F-statistics are now also calculated.
Various plotting features are also provided. Chi-square tests
of genetic heterogeneity are also provided. Functionality for
the calculation of various diversity parameters is also
possible for RAD-seq derived SNP data sets containing thousands
of marker loci.
Author: Kevin Keenan,
Maintainer: Kevin Keenan
diveRsity-1.4.6/diveRsity/R/diveRsity_v1.4.6.R |only
diveRsity-1.5.0/diveRsity/DESCRIPTION | 10 +++++-----
diveRsity-1.5.0/diveRsity/MD5 | 10 ++++++----
diveRsity-1.5.0/diveRsity/R/diveRsity_v1.5.0.R |only
diveRsity-1.5.0/diveRsity/data/pop_stats.rda |binary
diveRsity-1.5.0/diveRsity/inst/CITATION |only
diveRsity-1.5.0/diveRsity/inst/doc/diveRsity.R |only
diveRsity-1.5.0/diveRsity/inst/doc/diveRsity.pdf |binary
8 files changed, 11 insertions(+), 9 deletions(-)
Title: Logistic Regression
Diff between BayesLogit versions 0.2-2 dated 2013-05-07 and 0.2-4 dated 2013-05-22
Description: The BayesLogit package does posterior simulation for
binomial and multinomial logistic regression using the
Polya-Gamma latent variable technique. This method is fully
automatic, exact, and fast. A routine to efficiently sample
from the Polya-Gamma class of distributions is included.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle
DESCRIPTION | 8 ++--
MD5 | 20 +++++------
inst/Dynamic/DESCRIPTION | 6 +--
inst/Static/DESCRIPTION | 4 +-
man/rpg.Rd | 10 ++---
src/Makevars | 4 +-
src/Matrix.h | 33 +++++++++----------
src/MatrixFrame.cpp | 4 ++
src/MatrixFrame.h | 79 ++++++++++++++++++++++++++++++++++++++++++++---
src/PolyaGamma.cpp | 28 ++++++++++++----
src/PolyaGamma.h | 2 -
11 files changed, 142 insertions(+), 56 deletions(-)
Title: Analysis of Multivariate Event Times
Diff between mets versions 0.2.2 dated 2013-05-21 and 0.2.3 dated 2013-05-22
Description: Implementation of various statistical models for
multivariate event history data. Including multivariate
cumulative incidence models, and bivariate random effects
probit models (Liability models)
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst
DESCRIPTION | 8 ++++----
MD5 | 34 ++++++++++++++++++----------------
NAMESPACE | 16 ++++++++--------
R/bicomprisk.R | 2 +-
R/biprobit.R | 2 +-
R/biprobit.strata.R | 3 ++-
R/bptwin.R | 2 +-
R/fastreshape.R | 5 +++--
R/logLik.biprobit.R | 2 +-
R/mets-packages.R | 8 ++++++++
R/surv.boxarea.R | 2 +-
R/twinlm.R | 11 ++++++-----
R/twinsim.R | 15 ++++++++++++---
data/datalist | 1 +
data/migr.txt.gz |only
inst/tests/test_reshape.R | 29 ++++++++++++++++++-----------
man/fast.reshape.Rd | 2 +-
man/migr.Rd |only
man/twinlm.Rd | 9 +++++----
19 files changed, 91 insertions(+), 60 deletions(-)
Title: adephylo: exploratory analyses for the phylogenetic comparative
method.
Diff between adephylo versions 1.1-3 dated 2012-10-31 and 1.1-4 dated 2013-05-22
Description: Multivariate tools to analyze comparative data, i.e. a
phylogeny and some traits measured for each taxa.
Author: Thibaut Jombart
Maintainer: Thibaut Jombart
ChangeLog | 12 +++
DESCRIPTION | 13 ++-
MD5 | 95 ++++++++++++++--------------
R/bullseye.R |only
R/dibas.R | 110 +++++++++++++++++++++++++++++++--
data/carni19.RData |binary
data/carni70.RData |binary
data/lizards.RData |binary
data/maples.RData |binary
data/mjrochet.RData |binary
data/palm.RData |binary
data/procella.RData |binary
data/tithonia.RData |binary
data/ungulates.RData |binary
inst/doc/adephylo.R |only
inst/doc/adephylo.pdf |binary
man/abouheif.Rd | 22 +++---
man/adephylo.package.Rd | 29 +++++---
man/bullseye.Rd |only
man/carni19.Rd | 9 +-
man/carni70.Rd | 10 ++-
man/dibas.Rd | 28 ++++++--
man/distRoot.Rd | 5 -
man/distTips.Rd | 9 +-
man/lizards.Rd | 10 +--
man/maples.Rd | 14 ++--
man/mjrochet.Rd | 19 +++--
man/orthobasis.Rd | 8 +-
man/orthogram.Rd | 56 ++++++++++++----
man/palm.Rd | 7 +-
man/ppca.Rd | 12 ++-
man/procella.Rd | 9 +-
man/proxTips.Rd | 7 +-
man/sp.tips.Rd | 6 -
man/table.phylo4d.Rd | 43 +++++++-----
man/tithonia.Rd | 4 -
man/treePart.Rd | 7 +-
man/ungulates.Rd | 4 -
vignettes/figs/adephylo-012.pdf |binary
vignettes/figs/adephylo-016.pdf |binary
vignettes/figs/adephylo-018.pdf |binary
vignettes/figs/adephylo-aboutest.pdf |binary
vignettes/figs/adephylo-figFourBas.pdf |binary
vignettes/figs/adephylo-lm1.pdf |binary
vignettes/figs/adephylo-loadings.pdf |binary
vignettes/figs/adephylo-orthobas1.pdf |binary
vignettes/figs/adephylo-pca1.pdf |binary
vignettes/figs/adephylo-pca2.pdf |binary
vignettes/figs/adephylo-phylo4d.pdf |binary
vignettes/figs/adephylo-resid.pdf |binary
50 files changed, 384 insertions(+), 164 deletions(-)
Title: Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
Diff between SNPRelate versions 0.9.13 dated 2013-02-26 and 0.9.14 dated 2013-05-22
Description: A High-performance computing toolset for relatedness and
principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
SNPRelate-0.9.13/SNPRelate/R/main.r |only
SNPRelate-0.9.13/SNPRelate/src/main.cpp |only
SNPRelate-0.9.14/SNPRelate/DESCRIPTION | 8
SNPRelate-0.9.14/SNPRelate/MD5 | 82 +--
SNPRelate-0.9.14/SNPRelate/NEWS | 56 +-
SNPRelate-0.9.14/SNPRelate/R/IBD.r |only
SNPRelate-0.9.14/SNPRelate/R/IBS.r |only
SNPRelate-0.9.14/SNPRelate/R/LD.r |only
SNPRelate-0.9.14/SNPRelate/R/PCA.r |only
SNPRelate-0.9.14/SNPRelate/R/SNPRelate_Main.r |only
SNPRelate-0.9.14/SNPRelate/inst/CITATION | 10
SNPRelate-0.9.14/SNPRelate/inst/doc/SNPRelateTutorial.R |only
SNPRelate-0.9.14/SNPRelate/inst/doc/SNPRelateTutorial.Rnw | 9
SNPRelate-0.9.14/SNPRelate/inst/doc/SNPRelateTutorial.pdf |binary
SNPRelate-0.9.14/SNPRelate/man/SNPRelate-package.Rd | 10
SNPRelate-0.9.14/SNPRelate/man/snpgdsCutTree.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsDiss.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsDrawTree.Rd | 8
SNPRelate-0.9.14/SNPRelate/man/snpgdsGDS2BED.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsGDS2Eigen.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsGDS2PED.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsGetGeno.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsHCluster.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBDKING.Rd |only
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBDMLE.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBDMLELogLik.Rd | 5
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBDMoM.Rd | 10
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBS.Rd | 7
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBSNum.Rd | 7
SNPRelate-0.9.14/SNPRelate/man/snpgdsIndInb.Rd | 6
SNPRelate-0.9.14/SNPRelate/man/snpgdsLDMat.Rd | 9
SNPRelate-0.9.14/SNPRelate/man/snpgdsLDpair.Rd | 7
SNPRelate-0.9.14/SNPRelate/man/snpgdsLDpruning.Rd | 11
SNPRelate-0.9.14/SNPRelate/man/snpgdsOption.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsPCA.Rd | 6
SNPRelate-0.9.14/SNPRelate/man/snpgdsPCACorr.Rd | 6
SNPRelate-0.9.14/SNPRelate/man/snpgdsPCASNPLoading.Rd | 4
SNPRelate-0.9.14/SNPRelate/man/snpgdsPCASampLoading.Rd | 6
SNPRelate-0.9.14/SNPRelate/man/snpgdsPairIBDMLELogLik.Rd | 4
SNPRelate-0.9.14/SNPRelate/man/snpgdsSNPList.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsSNPRateFreq.Rd | 4
SNPRelate-0.9.14/SNPRelate/man/snpgdsSampMissrate.Rd | 4
SNPRelate-0.9.14/SNPRelate/man/snpgdsSelectSNP.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsSummary.Rd | 2
SNPRelate-0.9.14/SNPRelate/src/SNPRelate.cpp |only
SNPRelate-0.9.14/SNPRelate/src/genIBS.cpp | 322 +++++++++++--
SNPRelate-0.9.14/SNPRelate/vignettes/SNPRelateTutorial.Rnw | 9
47 files changed, 446 insertions(+), 188 deletions(-)
Title: Solving biasing produced by tied values in cluster analysis.
Diff between recluster versions 1.9 dated 2013-03-29 and 2.1 dated 2013-05-22
Description: A high frequency of ties and zero values produces
hierarchical cluster dendrograms whose topology and bootstrap
supports are affected by the order of rows in the original
matrix. The recluster package evaluates the magnitude of this
bias and computes consensus trees after re-sampling the
original row order also applying this algorithm to a multiscale
bootstrap procedure.
Author: Leonardo Dapporto, Matteo Ramazzotti, Simone Fattorini, Roger
Vila, Gerard Talavera, Roger H.L. Dennis
Maintainer: Leonardo Dapporto
DESCRIPTION | 10 ++++-----
MD5 | 42 +++++++++++++++++++++++++---------------
NAMESPACE | 4 +--
R/recluster.boot.R | 2 -
R/recluster.col.R |only
R/recluster.cons.R | 31 ++++++++++++++++++++++-------
R/recluster.dist.R | 4 +--
R/recluster.expl.diss.R |only
R/recluster.group.colours.R |only
R/recluster.node.strength.R | 13 ++++++------
R/recluster.plot.col.R |only
R/recluster.plot.matrix.R |only
R/recluster.plot.sites.col.R |only
man/recluster.Rd | 42 +++++++++++++++++++++++++++++++---------
man/recluster.boot.Rd | 13 ++++++------
man/recluster.check.Rd | 2 -
man/recluster.col.Rd |only
man/recluster.cons.Rd | 38 ++++++++++++++++++++++++------------
man/recluster.dist.Rd | 13 ++++++++++--
man/recluster.expl.diss.Rd |only
man/recluster.group.col.Rd |only
man/recluster.hist.Rd | 4 +--
man/recluster.multi.Rd | 9 ++++----
man/recluster.node.strength.Rd | 15 ++++++++++++--
man/recluster.plot.Rd | 9 ++++----
man/recluster.plot.col.Rd |only
man/recluster.plot.matrix.Rd |only
man/recluster.plot.sites.col.Rd |only
28 files changed, 171 insertions(+), 80 deletions(-)
Title: Composite-likelihood based Analysis of Random Fields
Diff between CompRandFld versions 1.0.2 dated 2012-04-13 and 1.0.3 dated 2013-05-22
Description: The aim of this package is to collect a set of procedures
for the analysis of Random Fields by Composite Likelihood
methods. Spatial analysis often involves dealing with large
dataset. Therefore even simple studies may be too
computationally demanding. Composite likelihood based methods
are emerging as useful tools for mitigating such computational
problems and show satisfactory results when compared with other
techniques such as, for example the tapering method. Moreover,
composite likelihood (and related quantities) have some good
properties similar to those of the standard likelihood.
Author: Simone Padoan
Maintainer: Simone Padoan
CompRandFld-1.0.2/CompRandFld/R/zzz.r |only
CompRandFld-1.0.3/CompRandFld/DESCRIPTION | 22
CompRandFld-1.0.3/CompRandFld/MD5 | 91
CompRandFld-1.0.3/CompRandFld/R/CompositeLikelihood.r | 83
CompRandFld-1.0.3/CompRandFld/R/Covariogram.r | 22
CompRandFld-1.0.3/CompRandFld/R/Covmatrix.r |only
CompRandFld-1.0.3/CompRandFld/R/Distributions.r | 10
CompRandFld-1.0.3/CompRandFld/R/EmpiricalEstimators.r | 33
CompRandFld-1.0.3/CompRandFld/R/Fitting.r | 61
CompRandFld-1.0.3/CompRandFld/R/Kriging.r |only
CompRandFld-1.0.3/CompRandFld/R/Likelihood.r | 95
CompRandFld-1.0.3/CompRandFld/R/Simulation.r | 55
CompRandFld-1.0.3/CompRandFld/R/Statistics.r | 28
CompRandFld-1.0.3/CompRandFld/R/Utility.r | 284 +
CompRandFld-1.0.3/CompRandFld/R/WeightedLeastSquare.r | 68
CompRandFld-1.0.3/CompRandFld/data |only
CompRandFld-1.0.3/CompRandFld/inst/doc/CompRandFld-manual.pdf |binary
CompRandFld-1.0.3/CompRandFld/man/CheckCorrModel.Rd | 10
CompRandFld-1.0.3/CompRandFld/man/CheckInput.Rd | 23
CompRandFld-1.0.3/CompRandFld/man/CheckLikelihood.Rd | 8
CompRandFld-1.0.3/CompRandFld/man/CheckModel.Rd | 8
CompRandFld-1.0.3/CompRandFld/man/CheckType.Rd | 8
CompRandFld-1.0.3/CompRandFld/man/CheckVarType.Rd | 6
CompRandFld-1.0.3/CompRandFld/man/CompLikelihood.Rd | 17
CompRandFld-1.0.3/CompRandFld/man/CorrelationParam.Rd | 10
CompRandFld-1.0.3/CompRandFld/man/Covariogram.Rd | 31
CompRandFld-1.0.3/CompRandFld/man/Covmatrix.Rd |only
CompRandFld-1.0.3/CompRandFld/man/Dist2Dist.Rd | 10
CompRandFld-1.0.3/CompRandFld/man/EVariogram.Rd | 119
CompRandFld-1.0.3/CompRandFld/man/FitComposite.Rd | 348 +-
CompRandFld-1.0.3/CompRandFld/man/FitGev.Rd | 8
CompRandFld-1.0.3/CompRandFld/man/GevLogLik.Rd | 8
CompRandFld-1.0.3/CompRandFld/man/HypoTest.Rd | 7
CompRandFld-1.0.3/CompRandFld/man/InitParam.Rd | 28
CompRandFld-1.0.3/CompRandFld/man/Irishcoords.Rd |only
CompRandFld-1.0.3/CompRandFld/man/Irishwinds.Rd |only
CompRandFld-1.0.3/CompRandFld/man/Kri.Rd |only
CompRandFld-1.0.3/CompRandFld/man/Likelihood.Rd | 9
CompRandFld-1.0.3/CompRandFld/man/MomEst.Rd | 7
CompRandFld-1.0.3/CompRandFld/man/NuisanceParam.Rd | 7
CompRandFld-1.0.3/CompRandFld/man/RFsim.Rd | 88
CompRandFld-1.0.3/CompRandFld/man/USarain.Rd |only
CompRandFld-1.0.3/CompRandFld/man/UScoord.Rd |only
CompRandFld-1.0.3/CompRandFld/man/WLeastSquare.Rd | 46
CompRandFld-1.0.3/CompRandFld/man/WlsInit.Rd | 29
CompRandFld-1.0.3/CompRandFld/src/CompositeLikelihood.c | 193 -
CompRandFld-1.0.3/CompRandFld/src/CorrelationFunction.c | 1218 +++++---
CompRandFld-1.0.3/CompRandFld/src/Godambe.c | 1520 +++++-----
CompRandFld-1.0.3/CompRandFld/src/Utility.c | 745 +++-
CompRandFld-1.0.3/CompRandFld/src/header.h | 154 -
CompRandFld-1.0.3/CompRandFld/src/weightedleastsquare.c | 415 +-
51 files changed, 3488 insertions(+), 2444 deletions(-)
Title: Graph Probability Distributions with User Supplied Parameters
and Stats.
Diff between visualize versions 3.0 dated 2013-02-15 and 4.1 dated 2013-05-22
Description: Graphs the pdf or pmf and highlights what area or
probability is present in user defined locations. Visualize is
able to provide lower tail, bounded, upper tail, and two tail
calculations. Supports strict and equal to inequalities. Also
provided on the graph is the mean and variance of the
distribution.
Author: James Balamuta
Maintainer: James Balamuta
DESCRIPTION | 10 ++---
MD5 | 50 ++++++++++++++---------------
R/visualize.continuous.R | 74 +++++++++++++++++++++++++++++++++-----------
R/visualize.discrete.R | 53 ++++++++++++++++++++++++++++++-
R/visualize.it.R | 6 +--
man/visualize-package.Rd | 17 +++++++---
man/visualize.beta.Rd | 2 -
man/visualize.binom.Rd | 5 --
man/visualize.cauchy.Rd | 2 -
man/visualize.chisq.Rd | 2 -
man/visualize.continuous.Rd | 2 -
man/visualize.discrete.Rd | 7 ++--
man/visualize.exp.Rd | 2 -
man/visualize.f.Rd | 2 -
man/visualize.gamma.Rd | 2 -
man/visualize.geom.Rd | 8 +---
man/visualize.hyper.Rd | 7 +---
man/visualize.it.Rd | 10 +++--
man/visualize.lnorm.Rd | 2 -
man/visualize.logis.Rd | 2 -
man/visualize.nbinom.Rd | 11 ++----
man/visualize.norm.Rd | 2 -
man/visualize.pois.Rd | 7 +---
man/visualize.t.Rd | 2 -
man/visualize.unif.Rd | 2 -
man/visualize.wilcox.Rd | 2 -
26 files changed, 188 insertions(+), 103 deletions(-)
Title: PopGen: A simple way to analyse and visualize population genetic
data
Diff between PopGenReport versions 0.96 dated 2012-11-28 and 1.01 dated 2013-05-22
Description: This package provides an easy way to analyse population
genetic data
Author: Aaron Adamack & Bernd Gruber
Maintainer: Bernd Gruber,
DESCRIPTION | 12
MD5 | 42 +-
R/gd_kosman.r | 66 +--
R/popgenreport.r | 534 ++++++++++++++++---------------
R/read.genetable.r | 6
inst/swchunks/allele.dist.snw | 47 +-
inst/swchunks/counts.snw | 208 ++++++------
inst/swchunks/differ.stats.snw | 128 ++-----
inst/swchunks/fst.snw | 136 ++++----
inst/swchunks/gd.kosman.snw | 17 -
inst/swchunks/gd.smouse.snw | 20 -
inst/swchunks/header.snw | 10
inst/swchunks/hwe.snw | 87 ++---
inst/swchunks/load.data.snw | 4
inst/swchunks/locihz.snw | 34 --
inst/swchunks/map.snw | 109 +++---
inst/swchunks/required.snw | 7
inst/swchunks/subgroups.header.snw | 391 ++++++++---------------
inst/swchunks/subgroups.sectionout.snw | 557 ++++++++++++++++-----------------
man/PopGen-package.Rd | 6
man/popgenreport.Rd | 27 -
man/read.genetable.Rd | 7
22 files changed, 1167 insertions(+), 1288 deletions(-)
Title: Bayesian semi and nonparametric growth curve models that
additionally include multiple membership random effects.
Diff between growcurves versions 0.2.3.4 dated 2013-03-16 and 0.2.3.5 dated 2013-05-22
Description: Employs a non-parametric formulation for by-subject random
effect parameters to borrow strength over a constrained number
of repeated measurement waves in a fashion that permits
multiple effects per subject. One class of models employs a
Dirichlet process (DP) prior for the subject random effects and
includes an additional set of random effects that utilize a
different grouping factor and are mapped back to clients
through a multiple membership weight matrix; e.g. treatment(s)
exposure or dosage. A second class of models employs a
dependent DP (DDP) prior for the subject random effects that
directly incorporates the multiple membership pattern.
Author: Terrance Savitsky
Maintainer: "terrance savitsky"
DESCRIPTION | 8 ++--
MD5 | 32 +++++++++---------
NEWS | 12 +++++--
R/ddp_quantiles.R | 2 -
R/ddpeffectsplot.R | 2 -
R/ddpgrow.R | 21 +++++++-----
R/dpgrow.R | 17 +++++-----
R/dpgrowmm.R | 30 +++++++++++------
R/dpgrowmult.R | 20 +++++++----
R/help.R | 71 ++++++++++++++++++++++++++----------------
inst/tests/test-dpgrowmm-mv.R | 55 ++++++++++++++++++++++++++------
man/ddpgrow.Rd | 21 +++++++-----
man/dpgrow.Rd | 17 +++++-----
man/dpgrowmm.Rd | 24 ++++++++------
man/dpgrowmult.Rd | 20 +++++++----
man/growcurves-package.Rd | 71 ++++++++++++++++++++++++++----------------
src/mmCmiar.cpp | 11 ++++--
17 files changed, 274 insertions(+), 160 deletions(-)
Title: An interface package (beta) for the BIOM file format.
Diff between biom versions 0.3.8 dated 2013-04-29 and 0.3.9 dated 2013-05-22
Description: This is an R package for interfacing with the BIOM format.
Currently in beta form, this package includes basic tools for
reading biom-format files, accessing and subsetting data tables
from a biom object (which is more complex than a single table),
as well as limited support for writing a biom-object back to a
biom-format file. The design of this API is intended to match
the python API and other tools included with the biom-format
project, but with a decidedly "R flavor" that should be
familiar to R users. This includes S4 classes and methods, as
well as extensions of common core functions/methods.
Author: Paul J. McMurdie
Maintainer: Paul J. McMurdie
DESCRIPTION | 12 ++++++------
MD5 | 7 ++++---
R/BIOM-class.R | 32 ++++++++++++++++++--------------
R/allPackage.R | 2 +-
inst/NEWS |only
5 files changed, 29 insertions(+), 24 deletions(-)
More information about SphericalCubature at CRAN
Permanent link
Title: Analysis of Multivariate Event Times
Diff between mets versions 0.2.1 dated 2013-04-24 and 0.2.2 dated 2013-05-21
Description: Implementation of various statistical models for
multivariate event history data. Including multivariate
cumulative incidence models, and bivariate random effects
probit models (Liability models)
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst
mets-0.2.1/mets/inst/misc/workshop-ts.R |only
mets-0.2.1/mets/inst/misc/workshop.R |only
mets-0.2.1/mets/inst/misc/workshop.org |only
mets-0.2.2/mets/DESCRIPTION | 14
mets-0.2.2/mets/MD5 | 113 +
mets-0.2.2/mets/NAMESPACE | 26
mets-0.2.2/mets/NEWS | 8
mets-0.2.2/mets/R/Dbvn.R | 10
mets-0.2.2/mets/R/aalenfrailty.R | 11
mets-0.2.2/mets/R/bicomprisk.R | 4
mets-0.2.2/mets/R/binomial.twostage.R | 79 +
mets-0.2.2/mets/R/biprobit.R | 26
mets-0.2.2/mets/R/bptwin.R | 486 ++++----
mets-0.2.2/mets/R/casewise.R | 32
mets-0.2.2/mets/R/claytonakes.R | 27
mets-0.2.2/mets/R/clusterindex-reshape.R | 4
mets-0.2.2/mets/R/cor.R | 32
mets-0.2.2/mets/R/cumh.R | 152 ++
mets-0.2.2/mets/R/fastreshape.R | 86 -
mets-0.2.2/mets/R/methodstwinlm.R | 160 +-
mets-0.2.2/mets/R/mets-packages.R | 14
mets-0.2.2/mets/R/phreg.R |only
mets-0.2.2/mets/R/prop-odds.R |only
mets-0.2.2/mets/R/summary.bptwin.R | 66 -
mets-0.2.2/mets/R/twinlm.R | 266 +---
mets-0.2.2/mets/R/twinlm2.R |only
mets-0.2.2/mets/R/twostage.R | 297 ++++
mets-0.2.2/mets/data/datalist | 1
mets-0.2.2/mets/data/mena.rda |only
mets-0.2.2/mets/inst/misc/casewisea.png |only
mets-0.2.2/mets/inst/misc/cif2.png |only
mets-0.2.2/mets/inst/misc/cifMZ.png |only
mets-0.2.2/mets/inst/misc/conc2.png |only
mets-0.2.2/mets/inst/misc/concordance.png |only
mets-0.2.2/mets/inst/misc/cumh.png |only
mets-0.2.2/mets/inst/misc/ipw.png |only
mets-0.2.2/mets/inst/misc/mena.html |only
mets-0.2.2/mets/inst/misc/obs |only
mets-0.2.2/mets/inst/misc/orgmode1.css |only
mets-0.2.2/mets/inst/misc/orgmode2.css |only
mets-0.2.2/mets/inst/misc/pcif.png |only
mets-0.2.2/mets/inst/misc/pcif2.png |only
mets-0.2.2/mets/inst/misc/pcifl.png |only
mets-0.2.2/mets/inst/misc/workshop-run.html |only
mets-0.2.2/mets/inst/misc/workshop.html | 1558 +++++++-------------------
mets-0.2.2/mets/man/ClaytonOakes.Rd | 18
mets-0.2.2/mets/man/Dbvn.Rd | 8
mets-0.2.2/mets/man/aalenfrailty.Rd | 9
mets-0.2.2/mets/man/binomial.twostage.Rd | 9
mets-0.2.2/mets/man/bptwin.Rd | 23
mets-0.2.2/mets/man/casewise.test.Rd | 17
mets-0.2.2/mets/man/cor.cif.Rd | 26
mets-0.2.2/mets/man/easy.binomial.twostage.Rd | 14
mets-0.2.2/mets/man/easy.twostage.Rd |only
mets-0.2.2/mets/man/fast.reshape.Rd | 20
mets-0.2.2/mets/man/internal.Rd | 5
mets-0.2.2/mets/man/mena.Rd |only
mets-0.2.2/mets/man/multcif.Rd | 5
mets-0.2.2/mets/man/phreg.Rd |only
mets-0.2.2/mets/man/prt.Rd | 4
mets-0.2.2/mets/man/random.cif.Rd | 6
mets-0.2.2/mets/man/twinstut.Rd | 4
mets-0.2.2/mets/man/twostage.Rd | 37
mets-0.2.2/mets/src/Makevars | 2
mets-0.2.2/mets/src/claytonoakes.cpp | 7
mets-0.2.2/mets/src/clusterindex.cpp | 30
mets-0.2.2/mets/src/fastcox.cpp |only
mets-0.2.2/mets/src/fastcox.h |only
mets-0.2.2/mets/src/prop-odd.cpp |only
mets-0.2.2/mets/src/tools.cpp | 4
70 files changed, 1807 insertions(+), 1913 deletions(-)
Title: R interface to the iPlant Discovery Environment
Diff between rPlant versions 2.3 dated 2013-03-12 and 2.7 dated 2013-05-21
Description: rPlant is an R interface to the the many computational
resources iPlant offers through their RESTful application
programming interface. Currently, rPlant functions interact
with the iPlant foundational API, the Taxonomic Name Resolution
Service API, and the Phylotastic Taxosaurus API. Before using
rPlant, users will have to register with the iPlant
Collaborative.
http://www.iplantcollaborative.org/discover/discovery-environment
Author: Barb Banbury
Maintainer: Barb Banbury
DESCRIPTION | 15 --
MD5 | 52 +++----
R/RunClustal.R | 17 +-
R/RunMafft.R | 17 +-
R/RunMuscle.R | 17 +-
R/RunParsdna.R | 20 +-
R/RunParsprotein.R | 21 +-
R/RunQuicktree.R | 17 +-
R/RunRAxMLdna.R | 22 +--
R/RunRAxMLprotein.R | 13 +
R/TNRS.R | 1
R/rPlant.R | 357 ++++++++++++++++++++++++++++++++-----------------
data/ex.lp.fasta.rda |binary
man/GetAppList.Rd | 5
man/GetToken.Rd | 6
man/ListDir.Rd | 7
man/RunClustal.Rd | 11 -
man/RunMafft.Rd | 9 -
man/RunMuscle.Rd | 10 -
man/RunParsdna.Rd | 7
man/RunParsprotein.Rd | 8 -
man/RunQuicktree.Rd | 8 -
man/RunRAxMLdna.Rd | 19 +-
man/RunRAxMLprotein.Rd | 10 -
man/SubmitJob.Rd | 25 ++-
man/TNRS.Rd | 3
man/UploadFile.Rd | 46 ++++--
27 files changed, 480 insertions(+), 263 deletions(-)
Title: Linear Latent Variable Models
Diff between lava versions 1.2.0 dated 2013-04-24 and 1.2.1 dated 2013-05-21
Description: Estimation and simulation of latent variable models
Author: Klaus K. Holst
Maintainer: Klaus K. Holst
lava-1.2.0/lava/simulate.R |only
lava-1.2.1/lava/DESCRIPTION | 10
lava-1.2.1/lava/MD5 | 81 +--
lava-1.2.1/lava/NAMESPACE | 2
lava-1.2.1/lava/NEWS | 3
lava-1.2.1/lava/R/Objective.R | 33 -
lava-1.2.1/lava/R/addhook.R | 37 -
lava-1.2.1/lava/R/bootstrap.R | 28 -
lava-1.2.1/lava/R/constrain.R | 25 -
lava-1.2.1/lava/R/covariance.R | 4
lava-1.2.1/lava/R/deriv.R | 55 +-
lava-1.2.1/lava/R/estimate.R | 91 ++-
lava-1.2.1/lava/R/estimate.multigroup.R | 50 +-
lava-1.2.1/lava/R/fix.R | 6
lava-1.2.1/lava/R/gof.R | 8
lava-1.2.1/lava/R/index.sem.R | 7
lava-1.2.1/lava/R/information.R | 33 -
lava-1.2.1/lava/R/labels.R | 4
lava-1.2.1/lava/R/lava-package.R | 2
lava-1.2.1/lava/R/logLik.R | 10
lava-1.2.1/lava/R/matrices.R | 638 +++++++++++++++++++--------
lava-1.2.1/lava/R/missingMLE.R | 34 -
lava-1.2.1/lava/R/modelPar.R | 100 ++--
lava-1.2.1/lava/R/moments.R | 1
lava-1.2.1/lava/R/multigroup.R | 36 +
lava-1.2.1/lava/R/plot.R | 17
lava-1.2.1/lava/R/predict.R | 2
lava-1.2.1/lava/R/residuals.R | 17
lava-1.2.1/lava/R/score.R | 118 ----
lava-1.2.1/lava/R/utils.R | 30 -
lava-1.2.1/lava/R/zblockdiag.R | 7
lava-1.2.1/lava/R/ztr.R | 2
lava-1.2.1/lava/demo/model.R | 2
lava-1.2.1/lava/inst/doc/reference.pdf |binary
lava-1.2.1/lava/inst/tests/test-constrain.R | 41 +
lava-1.2.1/lava/inst/tests/test-multigroup.R | 1
lava-1.2.1/lava/man/bootstrap.lvm.Rd | 8
lava-1.2.1/lava/man/constrain-set.Rd | 2
lava-1.2.1/lava/man/estimate.lvm.Rd | 4
lava-1.2.1/lava/man/gof.Rd | 9
lava-1.2.1/lava/man/internal.Rd | 1
lava-1.2.1/lava/man/labels-set.Rd | 3
42 files changed, 946 insertions(+), 616 deletions(-)
Title: Learn from training data then quickly fill in missing data.
Diff between FastImputation versions 1.0 dated 2012-04-10 and 1.1 dated 2013-05-21
More information about FastImputation at CRAN
Description: TrainFastImputation uses training data to describe a
multivariate normal distribution that the data approximates or
can be transformed into approximating and stores this
information as an object of class FastImputationPatterns. The
FastImputation function uses this FastImputationPatterns object
to impute (make a good guess at) missing data in a single line
or a whole dataframe of data. This approximates the process
used by Amelia [http://gking.harvard.edu/amelia/] but is much
faster when filling in values for a single line of data.
Author: Stephen R. Haptonstahl
Maintainer: Stephen R. Haptonstahl
DESCRIPTION | 14 ++++++++------
MD5 | 25 ++++++++++++++-----------
R/BoundNormalizedVariable.R | 22 ++++++++++++++++++----
R/FastImputation.R | 31 ++++++++++++++++++-------------
R/NormalizeBoundedVariable.R | 21 +++++++++++++++++----
data/FItest.RData |binary
data/FItrain.RData |binary
data/FItrue.RData |binary
inst/tests |only
man/FItest.Rd | 18 +++++++++++++++++-
man/FItrain.Rd | 18 +++++++++++++++++-
man/FItrue.Rd | 20 ++++++++++++++++++--
man/NormalizeBoundedVariable.Rd | 21 +++++++++++++++++++--
tests |only
14 files changed, 146 insertions(+), 44 deletions(-)
Permanent link
Title: Nonparametric Multiple Change Point Analysis of Multivariate
Data
Diff between ecp versions 1.5.2 dated 2013-02-08 and 1.5.3 dated 2013-05-21
Description: This package performs hierarchical change point analysis
through the use of U-statistics. Both agglomerative and
divisive procedures return the set of change points estimates,
and other summary information.
Author: Nicholas A. James and David S. Matteson
Maintainer: Nicholas A. James
ecp-1.5.2/ecp/data/acgh.RData |only
ecp-1.5.2/ecp/data/stpp.RData |only
ecp-1.5.2/ecp/man/acgh.RData.Rd |only
ecp-1.5.2/ecp/man/stpp.RData.Rd |only
ecp-1.5.3/ecp/DESCRIPTION | 19 ++++---
ecp-1.5.3/ecp/MD5 | 38 +++++++--------
ecp-1.5.3/ecp/NEWS | 24 +++++++++
ecp-1.5.3/ecp/R/e_agglomerative.R | 9 ++-
ecp-1.5.3/ecp/R/e_divisive.R | 81 ++++++++++++++++++--------------
ecp-1.5.3/ecp/R/energyChangePoint.R | 3 +
ecp-1.5.3/ecp/data/ACGH.RData |only
ecp-1.5.3/ecp/data/DJIA.RData |binary
ecp-1.5.3/ecp/data/STPP.RData |only
ecp-1.5.3/ecp/data/datalist | 4 -
ecp-1.5.3/ecp/inst/CITATION | 6 +-
ecp-1.5.3/ecp/man/ACGH.RData.Rd |only
ecp-1.5.3/ecp/man/DJIA.RData.Rd | 4 -
ecp-1.5.3/ecp/man/STPP.RData.Rd |only
ecp-1.5.3/ecp/man/e.agglo.Rd | 66 +++++++++++++++++---------
ecp-1.5.3/ecp/man/e.divisive.Rd | 70 ++++++++++++++++-----------
ecp-1.5.3/ecp/man/e.split.Rd | 14 ++---
ecp-1.5.3/ecp/man/sig.test.Rd | 17 +++---
ecp-1.5.3/ecp/man/splitPoint.Rd | 12 ++--
ecp-1.5.3/ecp/src/energyChangePoint.cpp | 36 ++++++++++++++
24 files changed, 265 insertions(+), 138 deletions(-)
Title: Helper package to facilitate the generation of distance matrices
used in the package spacom.
Diff between geospacom versions 0.5-4 dated 2013-03-17 and 0.5-6 dated 2013-05-21
Description: Generates distance matrices from shape files and
represents spatially weighted multilevel analysis results (see
spacom)
Author: Davide Morselli [aut], Mathieu Cossuta [aut, cre], Till Junge
[aut], Sandra Penic [aut], Guy Elcheroth [ctb], Stephanie
Glaeser [ctb]
Maintainer: Davide Morselli
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
R/ReadPoly.R | 2 +-
R/fixholes.R | 9 +++------
data/CH1903.rda |binary
data/GPS.rda |binary
data/yu.reg.rda |binary
man/DistanceMatrix.Rd | 15 ++-------------
man/ImagePoly.Rd | 20 ++++++--------------
man/ReadPoly.Rd | 4 ++--
man/geospacom-package.Rd | 10 +++++-----
11 files changed, 34 insertions(+), 56 deletions(-)
Title: Exact Distributions for Rank and Permutation Tests
Diff between exactRankTests versions 0.8-24 dated 2013-01-12 and 0.8-25 dated 2013-05-21
More information about exactRankTests at CRAN
Description: Computes exact conditional p-values and quantiles using an
implementation of the Shift-Algorithm by Streitberg & Roehmel.
Author: Torsten Hothorn and Kurt Hornik
Maintainer: Torsten Hothorn
DESCRIPTION | 9 +++++----
MD5 | 30 +++++++++++++++---------------
R/perm.test.R | 10 +++++-----
data/ASAT.rda |binary
data/bloodp.rda |binary
data/ears.rda |binary
data/glioma.rda |binary
data/globulin.rda |binary
data/lungcancer.rda |binary
data/neuropathy.rda |binary
data/ocarcinoma.rda |binary
data/rotarod.rda |binary
data/sal.rda |binary
inst/NEWS | 6 ++++++
tests/dtest.R | 16 ++++++++++++----
tests/dtest.Rout.save | 25 ++++++++++++++++++-------
16 files changed, 61 insertions(+), 35 deletions(-)
Permanent link
Title: Fire Weather Index System and Fire Behaviour Prediction System
Calculations
Diff between fwi.fbp versions 1.01 dated 2012-10-30 and 1.2 dated 2013-05-21
Description: This package provides three new functions to calculate the
outputs of the two main components of the Canadian Forest Fire
Danger Rating System (CFFDRS): the Fire Weather Index (FWI)
System and the Fire Behaviour Prediction (FBP) System.
Author: Xianli Wang, Alan Cantin, Marc-Andre Parisien, Mike Wotton,
Kerry Anderson, and Mike Flannigan
Maintainer: Alan Cantin
DESCRIPTION | 12 +-
MD5 | 16 +--
R/fwi.r | 235 ++++++++++++++++++++++++-------------------------
data/test_fbp.csv.gz |binary
data/test_fwi.csv.gz |binary
man/fbp.Rd | 9 +
man/fwi.Rd | 9 +
man/fwi.fbp-package.Rd | 4
man/fwiBAT.Rd | 9 +
9 files changed, 156 insertions(+), 138 deletions(-)
Title: Multivariate Dependence with Copulas
Diff between copula versions 0.999-6 dated 2013-05-14 and 0.999-7 dated 2013-05-21
Description: Classes (S4) of commonly used elliptical, Archimedean,
extreme value and some more copula families. Methods for
density, distribution, random number generation, bivariate
dependence measures, perspective and contour plots. Fitting
copula models including variance estimates. Independence and
serial (univariate and multivariate) independence tests, and
other copula related tests. Goodness-of-fit tests for copulas
based on multipliers, the parametric bootstrap with several
transformation options. Merged former package 'nacopula' for
nested Archimedean copulas: Efficient sampling algorithms,
various estimators, goodness-of-fit tests and related tools and
special functions.
Author: Marius Hofert
Maintainer: Martin Maechler
DESCRIPTION | 10 +++----
MD5 | 16 +++++------
NAMESPACE | 2 -
R/empcop.R | 2 -
R/gofTests.R | 54 +++++++++++++-------------------------
inst/doc/Frank-Rmpfr.pdf |binary
inst/doc/nacopula-pkg.pdf |binary
man/empcop.Rd | 46 ++++++++++++++------------------
man/gofCopula.Rd | 65 ++++++++++++++++++++++++++++++++++------------
9 files changed, 104 insertions(+), 91 deletions(-)
Title: Miscellaneous Useful Functions
Diff between miscFuncs versions 1.2 dated 2012-06-14 and 1.2-2 dated 2013-05-21
Description: LaTeX tables, Kalman filter, web scraping, development
tools
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor
miscFuncs-1.2-2/miscFuncs/DESCRIPTION | 11 -
miscFuncs-1.2-2/miscFuncs/MD5 | 47 +++----
miscFuncs-1.2-2/miscFuncs/NAMESPACE | 10 -
miscFuncs-1.2-2/miscFuncs/R/KFtemplates.R | 3
miscFuncs-1.2-2/miscFuncs/R/latextable.R | 61 +++------
miscFuncs-1.2-2/miscFuncs/R/roxbc.R | 4
miscFuncs-1.2-2/miscFuncs/R/roxtext.R | 4
miscFuncs-1.2-2/miscFuncs/inst/doc/miscFuncs.R |only
miscFuncs-1.2-2/miscFuncs/inst/doc/miscFuncs.Rtex | 8 -
miscFuncs-1.2-2/miscFuncs/inst/doc/miscFuncs.pdf |binary
miscFuncs-1.2-2/miscFuncs/man/EKFadvance.Rd | 61 ++++++---
miscFuncs-1.2-2/miscFuncs/man/KFadvance.Rd | 94 +++++++++-----
miscFuncs-1.2-2/miscFuncs/man/KFadvanceAR2.Rd | 107 +++++++++++------
miscFuncs-1.2-2/miscFuncs/man/KFtemplates.Rd | 18 ++
miscFuncs-1.2-2/miscFuncs/man/bin.Rd | 20 ++-
miscFuncs-1.2-2/miscFuncs/man/generic.Rd | 32 +++--
miscFuncs-1.2-2/miscFuncs/man/getstrbetween.Rd | 37 ++++-
miscFuncs-1.2-2/miscFuncs/man/getwikicoords.Rd | 30 +++-
miscFuncs-1.2-2/miscFuncs/man/latextable.Rd | 61 ++++++---
miscFuncs-1.2-2/miscFuncs/man/method.Rd | 29 +++-
miscFuncs-1.2-2/miscFuncs/man/roxbc.Rd | 25 ++-
miscFuncs-1.2-2/miscFuncs/man/roxtext.Rd | 29 +++-
miscFuncs-1.2-2/miscFuncs/man/timeop.Rd | 20 ++-
miscFuncs-1.2-2/miscFuncs/man/vdc.Rd | 21 ++-
miscFuncs-1.2/miscFuncs/inst/doc/miscFuncs.Rtex.backup |only
miscFuncs-1.2/miscFuncs/man/dot-onAttach.Rd |only
26 files changed, 474 insertions(+), 258 deletions(-)
Title: R tools for making it easier to combine and clean data sets.
Diff between DataCombine versions 0.1.3 dated 2013-05-16 and 0.1.5 dated 2013-05-21
Description: R tools for combining and cleaning data sets, including
filling in missing observations with data from another data
frame.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 17 +++++++++--------
MD5 | 15 +++++++++------
NAMESPACE | 3 +++
NEWS | 11 +++++++++++
R/MoveFront.R | 44 +++++++++++++++++++++++++++++---------------
R/slide.R |only
README.md | 20 ++++++++++++++------
man/MoveFront.Rd | 22 +++++++++++++++-------
man/shift.Rd |only
man/slide.Rd |only
10 files changed, 90 insertions(+), 42 deletions(-)
Title: FastICA Algorithms to perform ICA and Projection Pursuit
Diff between fastICA versions 1.1-16 dated 2012-05-21 and 1.2-0 dated 2013-05-21
Description: Implementation of FastICA algorithm to perform Independent
Component Analysis (ICA) and Projection Pursuit.
Author: J L Marchini
Maintainer: Brian Ripley
fastICA-1.1-16/fastICA/cleanup |only
fastICA-1.1-16/fastICA/configure |only
fastICA-1.1-16/fastICA/configure.ac |only
fastICA-1.1-16/fastICA/configure.win |only
fastICA-1.1-16/fastICA/src/Makevars.in |only
fastICA-1.1-16/fastICA/src/Makevars.win |only
fastICA-1.1-16/fastICA/src/lsame.unused |only
fastICA-1.1-16/fastICA/src/sblas.unused |only
fastICA-1.1-16/fastICA/src/slamc.unused |only
fastICA-1.1-16/fastICA/src/slapack.unused |only
fastICA-1.2-0/fastICA/DESCRIPTION | 9 -
fastICA-1.2-0/fastICA/MD5 | 21 --
fastICA-1.2-0/fastICA/NAMESPACE | 2
fastICA-1.2-0/fastICA/R/fastICA.R | 35 ++--
fastICA-1.2-0/fastICA/man/fastICA.Rd | 8 -
fastICA-1.2-0/fastICA/src/Makevars |only
fastICA-1.2-0/fastICA/src/ica.c | 231 ++++++++++++++----------------
17 files changed, 145 insertions(+), 161 deletions(-)
Title: Statistical significance of Sharpe ratio
Diff between SharpeR versions 0.1305 dated 2013-05-11 and 0.1306 dated 2013-05-21
Description: a collection of tools for analyzing significance of
trading strategies, based on the Sharpe ratio and overfit of
the same.
Author: Steven E. Pav
Maintainer: Steven E. Pav
SharpeR-0.1305/SharpeR/inst/doc/SharpeR.R |only
SharpeR-0.1305/SharpeR/inst/doc/SharpeR.Rnw |only
SharpeR-0.1305/SharpeR/inst/doc/SharpeR.bib |only
SharpeR-0.1305/SharpeR/inst/tests/test-estimation.r |only
SharpeR-0.1306/SharpeR/DESCRIPTION | 8
SharpeR-0.1306/SharpeR/MD5 | 49 ++---
SharpeR-0.1306/SharpeR/Makefile | 165 +++++++++++++----
SharpeR-0.1306/SharpeR/R/distributions.r | 18 +
SharpeR-0.1306/SharpeR/R/estimation.r | 20 +-
SharpeR-0.1306/SharpeR/R/sr.r | 10 -
SharpeR-0.1306/SharpeR/R/tests.r | 10 -
SharpeR-0.1306/SharpeR/README.md | 2
SharpeR-0.1306/SharpeR/inst/doc/SharpeR.pdf |binary
SharpeR-0.1306/SharpeR/inst/doc/figure |only
SharpeR-0.1306/SharpeR/inst/doc/index.html |only
SharpeR-0.1306/SharpeR/inst/tests/test-distributions.r | 15 -
SharpeR-0.1306/SharpeR/man/as.sr.Rd | 6
SharpeR-0.1306/SharpeR/man/as.sropt.Rd | 2
SharpeR-0.1306/SharpeR/man/confint.Rd | 8
SharpeR-0.1306/SharpeR/man/dsr.Rd | 12 -
SharpeR-0.1306/SharpeR/man/dsropt.Rd | 2
SharpeR-0.1306/SharpeR/man/inference.Rd | 10 -
SharpeR-0.1306/SharpeR/man/power.sr_test.Rd | 2
SharpeR-0.1306/SharpeR/man/se.Rd | 2
SharpeR-0.1306/SharpeR/man/sr.Rd | 2
SharpeR-0.1306/SharpeR/man/sr_equality_test.Rd | 4
SharpeR-0.1306/SharpeR/man/sr_test.Rd | 2
SharpeR-0.1306/SharpeR/man/sropt_test.Rd | 2
28 files changed, 236 insertions(+), 115 deletions(-)
Title: ML and MCMC Methods for Pedigree Reconstruction and Analysis
Diff between MasterBayes versions 2.50 dated 2012-07-15 and 2.50.1 dated 2013-05-21
Description: The primary aim of MasterBayes is to use MCMC techniques
to integrate over uncertainty in pedigree configurations
estimated from molecular markers and phenotypic data. Emphasis
is put on the marginal distribution of parameters that relate
the phenotypic data to the pedigree. All simulation is done in
compiled C++ for efficiency.
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield
MasterBayes-2.50.1/MasterBayes/DESCRIPTION | 9
MasterBayes-2.50.1/MasterBayes/MD5 | 10
MasterBayes-2.50.1/MasterBayes/src/Makevars | 2
MasterBayes-2.50.1/MasterBayes/src/matrix.h | 350 ++++++++++++------------
MasterBayes-2.50.1/MasterBayes/src/smath.h | 34 +-
MasterBayes-2.50.1/MasterBayes/src/stat.h | 2
MasterBayes-2.50/MasterBayes/inst/doc/.Rhistory |only
7 files changed, 204 insertions(+), 203 deletions(-)
Title: Package required POI jars for the xlsx package
Diff between xlsxjars versions 0.4.0 dated 2012-04-16 and 0.5.0 dated 2013-05-20
Description: The xlsxjars package collects all the external jars
required for the xlxs package. These external jars are quite
large in size (15MB) and have a slow release cycle. By
separating the Java and R development, the storage footprint on
CRAN is reduced. This release corresponds to POI 3.9.
Author: Adrian A. Dragulescu
Maintainer: Adrian A. Dragulescu
xlsxjars-0.4.0/xlsxjars/inst/java/poi-3.8-20120326.jar |only
xlsxjars-0.4.0/xlsxjars/inst/java/poi-ooxml-3.8-20120326.jar |only
xlsxjars-0.4.0/xlsxjars/inst/java/poi-ooxml-schemas-3.8-20120326.jar |only
xlsxjars-0.5.0/xlsxjars/DESCRIPTION | 13 +++++----
xlsxjars-0.5.0/xlsxjars/MD5 | 14 +++++-----
xlsxjars-0.5.0/xlsxjars/NEWS | 5 +++
xlsxjars-0.5.0/xlsxjars/inst/java/poi-3.9-20121203.jar |only
xlsxjars-0.5.0/xlsxjars/inst/java/poi-ooxml-3.9-20121203.jar |only
xlsxjars-0.5.0/xlsxjars/inst/java/poi-ooxml-schemas-3.9-20121203.jar |only
xlsxjars-0.5.0/xlsxjars/man/xlsxjars-package.Rd | 4 +-
xlsxjars-0.5.0/xlsxjars/other/make.package.R | 10 ++-----
11 files changed, 24 insertions(+), 22 deletions(-)
Title: Read, write, format Excel 2007 and Excel 97/2000/XP/2003 files
Diff between xlsx versions 0.5.0 dated 2012-09-26 and 0.5.1 dated 2013-05-20
Description: Provide R functions to read/write/format Excel 2007 and
Excel 97/2000/XP/2003 file formats.
Author: Adrian A. Dragulescu
Maintainer: Adrian A. Dragulescu
xlsx-0.5.0/xlsx/inst/java/rexcel-0.5.0.jar |only
xlsx-0.5.0/xlsx/other/target |only
xlsx-0.5.1/xlsx/DESCRIPTION | 9
xlsx-0.5.1/xlsx/MD5 | 60 --
xlsx-0.5.1/xlsx/NEWS | 22
xlsx-0.5.1/xlsx/R/Cell.R | 14
xlsx-0.5.1/xlsx/R/addDataFrame.R | 17
xlsx-0.5.1/xlsx/R/read.xlsx.R | 34 -
xlsx-0.5.1/xlsx/R/read.xlsx2.R | 4
xlsx-0.5.1/xlsx/R/readColumns.R | 6
xlsx-0.5.1/xlsx/R/write.xlsx.R | 12
xlsx-0.5.1/xlsx/inst/doc/xlsx.R |only
xlsx-0.5.1/xlsx/inst/doc/xlsx.pdf |binary
xlsx-0.5.1/xlsx/inst/java/rexcel-0.5.1.jar |only
xlsx-0.5.1/xlsx/inst/tests/lib_test_issues.R |only
xlsx-0.5.1/xlsx/inst/tests/lib_tests_xlsx.R | 15
xlsx-0.5.1/xlsx/inst/tests/test_import.xlsx |binary
xlsx-0.5.1/xlsx/man/Cell.Rd | 6
xlsx-0.5.1/xlsx/man/read.xlsx.Rd | 13
xlsx-0.5.1/xlsx/man/write.xlsx.Rd | 5
xlsx-0.5.1/xlsx/man/xlsx-package.Rd | 15
xlsx-0.5.1/xlsx/other/make.package.R | 64 --
xlsx-0.5.1/xlsx/other/pom.xml | 297 +++++++---
xlsx-0.5.1/xlsx/other/src/main/java/org/cran/rexcel/RInterface.java | 12
xlsx-0.5.1/xlsx/other/src/test/java/org/cran/rexcel/DebugRexcel.java |only
xlsx-0.5.1/xlsx/other/src/test/java/org/cran/rexcel/TestRCellBlock.java | 1
xlsx-0.5.1/xlsx/other/src/test/java/org/cran/rexcel/TestRInterface.java | 24
27 files changed, 431 insertions(+), 199 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness
estimation
Diff between mgcv versions 1.7-22 dated 2012-10-15 and 1.7-23 dated 2013-05-20
Description: Routines for GAMs and other generalized ridge regression
with multiple smoothing parameter selection by GCV, REML or
UBRE/AIC. Also GAMMs. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood
DESCRIPTION | 7 -
MD5 | 64 +++++-----
NAMESPACE | 2
R/bam.r | 4
R/gam.fit3.r | 17 +-
R/gamm.r | 6
R/mgcv.r | 163 +++++++++++++++-----------
R/plots.r | 28 +++-
R/smooth.r | 124 +++++++++++++-------
R/soap.r | 21 +--
changeLog | 61 ++++++++-
man/anova.gam.Rd | 2
man/extract.lme.cov.Rd | 1
man/formXtViX.Rd | 15 ++
man/formula.gam.Rd | 10 +
man/gam.Rd | 14 +-
man/gam.models.Rd | 34 ++---
man/gam.side.Rd | 24 +++
man/ldTweedie.Rd | 4
man/mgcv-package.Rd | 3
man/mroot.Rd | 4
man/smooth.construct.fs.smooth.spec.Rd | 4
man/smooth.construct.tp.smooth.spec.Rd | 6
man/smooth.terms.Rd | 7 -
man/summary.gam.Rd | 10 -
man/te.Rd | 35 +++--
src/init.c | 2
src/mat.c | 203 +++++++++++++++++++++++++--------
src/mgcv.c | 2
src/mgcv.h | 3
src/misc.c | 2
src/soap.c | 6
src/tprs.c | 4
33 files changed, 591 insertions(+), 301 deletions(-)
Title: Package for statistical age models analysis in optically
stimulated luminescence dating
Diff between RadialPlotter versions 1.5 dated 2013-04-20 and 1.6 dated 2013-05-20
Description: Package for estimating parameters of statistical age
models in optically stimulated luminescence dating dynamically.
Author: Peng Jun
Maintainer: Peng Jun
DESCRIPTION | 8
MD5 | 25
NEWS | 3
man/EDdata.Rd | 1
man/RadialPlotter-package.Rd | 6
man/RadialPlotter.Rd | 5
src/MamED.f90 | 2
src/blas.f |only
src/fdhessian.f90 | 137 ++-
src/gradient.f90 | 20
src/kmeans.f90 | 2
src/lbfgsb.f | 1560 ++++++++++++++-----------------------------
src/linpack.f |only
src/pnorm.f90 | 8
src/timer.f |only
15 files changed, 675 insertions(+), 1102 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-06 2.4.8
2009-11-17 2.4.6
2009-10-29 2.4.4
2009-09-18 2.4.2
Title: SSD for R to analyze single system data
Diff between SSDforR versions 1.1 dated 2013-04-24 and 1.2 dated 2013-05-20
Description: Package to visually and statistically analyze single
system data
Author: Charles Auerbach,PHD Wendy Zeitlin Schudrich,PHD Wurzweiler
School of Social Work
Maintainer: Charles Auerbach
SSDforR-1.1/SSDforR/R/ABautoacf.R |only
SSDforR-1.1/SSDforR/R/ABautopacf.R |only
SSDforR-1.1/SSDforR/R/Arimadiff.R |only
SSDforR-1.1/SSDforR/R/Arimama.R |only
SSDforR-1.1/SSDforR/R/CDC.R |only
SSDforR-1.1/SSDforR/R/robustCDC.R |only
SSDforR-1.1/SSDforR/man/abarrow.rd |only
SSDforR-1.1/SSDforR/man/cdc.rd |only
SSDforR-1.1/SSDforR/man/robustCDC.Rd |only
SSDforR-1.2/SSDforR/DESCRIPTION | 6 -
SSDforR-1.2/SSDforR/MD5 | 180 +++++++++++++++---------------
SSDforR-1.2/SSDforR/R/ABlineD.R | 6 -
SSDforR-1.2/SSDforR/R/ABlines.R | 4
SSDforR-1.2/SSDforR/R/ABplot.R | 12 +-
SSDforR-1.2/SSDforR/R/ABstat.R | 6 -
SSDforR-1.2/SSDforR/R/ABtext.R | 7 -
SSDforR-1.2/SSDforR/R/ABtsplot.R | 8 +
SSDforR-1.2/SSDforR/R/CDCabove.R |only
SSDforR-1.2/SSDforR/R/CDCbelow.R |only
SSDforR-1.2/SSDforR/R/Gindex.R | 5
SSDforR-1.2/SSDforR/R/RobustCDCabove.R |only
SSDforR-1.2/SSDforR/R/RobustCDCbelow.R |only
SSDforR-1.2/SSDforR/R/Trimline.R | 5
SSDforR-1.2/SSDforR/R/abarrow.r | 21 ++-
SSDforR-1.2/SSDforR/R/abautoacf.r |only
SSDforR-1.2/SSDforR/R/abautopacf.r |only
SSDforR-1.2/SSDforR/R/arimadiff.r |only
SSDforR-1.2/SSDforR/R/arimama.r |only
SSDforR-1.2/SSDforR/man/ABWilcox.Rd | 3
SSDforR-1.2/SSDforR/man/ABanova.Rd | 7 -
SSDforR-1.2/SSDforR/man/ABarrow.Rd |only
SSDforR-1.2/SSDforR/man/ABautoacf.Rd | 3
SSDforR-1.2/SSDforR/man/ABautopacf.Rd | 3
SSDforR-1.2/SSDforR/man/ABbinomial.Rd | 3
SSDforR-1.2/SSDforR/man/ABdescrip.Rd | 3
SSDforR-1.2/SSDforR/man/ABiqr.Rd | 3
SSDforR-1.2/SSDforR/man/ABlineD.Rd | 3
SSDforR-1.2/SSDforR/man/ABlines.Rd | 3
SSDforR-1.2/SSDforR/man/ABma.Rd | 3
SSDforR-1.2/SSDforR/man/ABplot.Rd | 3
SSDforR-1.2/SSDforR/man/ABplotm.Rd | 3
SSDforR-1.2/SSDforR/man/ABregres.Rd | 3
SSDforR-1.2/SSDforR/man/ABrf2.Rd | 3
SSDforR-1.2/SSDforR/man/ABrobust.Rd | 3
SSDforR-1.2/SSDforR/man/ABstat.Rd | 3
SSDforR-1.2/SSDforR/man/ABtext.Rd | 3
SSDforR-1.2/SSDforR/man/ABtsplot.Rd | 3
SSDforR-1.2/SSDforR/man/ABttest.Rd | 3
SSDforR-1.2/SSDforR/man/Aregres.Rd | 3
SSDforR-1.2/SSDforR/man/Arimadiff.Rd | 3
SSDforR-1.2/SSDforR/man/Arimama.Rd | 3
SSDforR-1.2/SSDforR/man/Arobust.Rd | 3
SSDforR-1.2/SSDforR/man/Cchart.Rd | 3
SSDforR-1.2/SSDforR/man/Effectsize.Rd | 3
SSDforR-1.2/SSDforR/man/GABrf2.Rd | 6 -
SSDforR-1.2/SSDforR/man/GABttest.Rd | 15 +-
SSDforR-1.2/SSDforR/man/Gindex.Rd | 3
SSDforR-1.2/SSDforR/man/Gmedian.Rd | 24 ++--
SSDforR-1.2/SSDforR/man/IQRbandgraph.Rd | 5
SSDforR-1.2/SSDforR/man/IQRlegend.Rd | 3
SSDforR-1.2/SSDforR/man/IQRline.Rd | 3
SSDforR-1.2/SSDforR/man/PANDlegend.Rd | 3
SSDforR-1.2/SSDforR/man/PEMabove.Rd | 3
SSDforR-1.2/SSDforR/man/PEMbelow.Rd | 3
SSDforR-1.2/SSDforR/man/PNDbelow.Rd | 3
SSDforR-1.2/SSDforR/man/PNDlegend.Rd | 3
SSDforR-1.2/SSDforR/man/Pchart.Rd | 6 -
SSDforR-1.2/SSDforR/man/Rchart.Rd | 24 ++--
SSDforR-1.2/SSDforR/man/Rchartsd.Rd | 18 ++-
SSDforR-1.2/SSDforR/man/SD1.Rd | 3
SSDforR-1.2/SSDforR/man/SD1legend.Rd | 7 -
SSDforR-1.2/SSDforR/man/SD2.Rd | 7 -
SSDforR-1.2/SSDforR/man/SD2legend.Rd | 3
SSDforR-1.2/SSDforR/man/SDAband.Rd | 3
SSDforR-1.2/SSDforR/man/SPClegend.Rd | 27 +++-
SSDforR-1.2/SSDforR/man/SPCline.Rd | 21 ++-
SSDforR-1.2/SSDforR/man/Trimline.Rd | 3
SSDforR-1.2/SSDforR/man/XRchart.Rd | 24 ++--
SSDforR-1.2/SSDforR/man/Xmrchart.Rd | 3
SSDforR-1.2/SSDforR/man/cdcabove.rd |only
SSDforR-1.2/SSDforR/man/cdcbelow.rd |only
SSDforR-1.2/SSDforR/man/diffchart.Rd | 3
SSDforR-1.2/SSDforR/man/ird.rd | 3
SSDforR-1.2/SSDforR/man/meanabove.rd | 7 -
SSDforR-1.2/SSDforR/man/meanbelow.rd | 7 -
SSDforR-1.2/SSDforR/man/medabove.rd | 7 -
SSDforR-1.2/SSDforR/man/medbelow.rd | 3
SSDforR-1.2/SSDforR/man/pandabove.rd | 3
SSDforR-1.2/SSDforR/man/pandbelow.rd | 3
SSDforR-1.2/SSDforR/man/pemlegend.rd | 3
SSDforR-1.2/SSDforR/man/plotnum.Rd | 3
SSDforR-1.2/SSDforR/man/pndabove.rd | 3
SSDforR-1.2/SSDforR/man/regabove.Rd | 3
SSDforR-1.2/SSDforR/man/regbelow.Rd | 3
SSDforR-1.2/SSDforR/man/robregabove.Rd | 3
SSDforR-1.2/SSDforR/man/robregbelow.Rd | 3
SSDforR-1.2/SSDforR/man/robustCDCabove.Rd |only
SSDforR-1.2/SSDforR/man/robustCDCbelow.Rd |only
SSDforR-1.2/SSDforR/man/sd1bandgraph.rd | 3
SSDforR-1.2/SSDforR/man/sd2bandgraph.rd | 8 +
SSDforR-1.2/SSDforR/man/trimabove.Rd | 3
SSDforR-1.2/SSDforR/man/trimbelow.Rd | 3
102 files changed, 399 insertions(+), 237 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-06-14 1.03
2009-03-21 1.02
2009-03-14 1.01
2009-03-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-03-19 0.9-9
2008-09-16 0.5-20
2008-02-04 0.5-19
2007-10-09 0.5-18
2007-07-18 0.5-7.1
2007-07-18 0.5-17
2006-08-05 0.5-16
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-05 2.3
2011-11-02 2.2
2011-08-23 2.1.2
2011-07-23 2.1
2011-05-10 1.4
2011-03-30 1.3
2011-03-21 1.2
2011-01-25 1.1
2010-06-18 1.0
Title: Data exchange between R and LabKey Server
Diff between Rlabkey versions 2.1.121 dated 2013-02-14 and 2.1.122 dated 2013-05-20
Description: This package allows an R user to discover, query and
modify data in LabKey Server
Author: Peter Hussey
Maintainer: Cory Nathe
Rlabkey-2.1.121/Rlabkey/license |only
Rlabkey-2.1.122/Rlabkey/DESCRIPTION | 10 +
Rlabkey-2.1.122/Rlabkey/MD5 | 72 ++++++------
Rlabkey-2.1.122/Rlabkey/NEWS | 3
Rlabkey-2.1.122/Rlabkey/R/ifcookie.R | 27 +++-
Rlabkey-2.1.122/Rlabkey/R/labkey.deleteRows.R | 2
Rlabkey-2.1.122/Rlabkey/R/labkey.getFolders.R | 2
Rlabkey-2.1.122/Rlabkey/R/labkey.getQueryInfo.R | 2
Rlabkey-2.1.122/Rlabkey/R/labkey.getQueryLists.R | 2
Rlabkey-2.1.122/Rlabkey/R/labkey.getSchemas.R | 2
Rlabkey-2.1.122/Rlabkey/R/labkey.insertRows.R | 2
Rlabkey-2.1.122/Rlabkey/R/labkey.saveBatch.R | 2
Rlabkey-2.1.122/Rlabkey/R/labkey.selectRows.R | 9 -
Rlabkey-2.1.122/Rlabkey/R/labkey.updateRows.R | 2
Rlabkey-2.1.122/Rlabkey/inst/doc/RlabkeyExample.R |only
Rlabkey-2.1.122/Rlabkey/inst/doc/RlabkeyExample.pdf |binary
Rlabkey-2.1.122/Rlabkey/man/Rlabkey-package.Rd | 4
Rlabkey-2.1.122/Rlabkey/man/getFolderPath.Rd | 3
Rlabkey-2.1.122/Rlabkey/man/getLookups.Rd | 9 +
Rlabkey-2.1.122/Rlabkey/man/getRows.Rd | 3
Rlabkey-2.1.122/Rlabkey/man/getSchema.Rd | 9 +
Rlabkey-2.1.122/Rlabkey/man/getSession.Rd | 30 +++--
Rlabkey-2.1.122/Rlabkey/man/labkey.deleteRows.Rd | 25 ++--
Rlabkey-2.1.122/Rlabkey/man/labkey.executeSql.Rd | 26 ++--
Rlabkey-2.1.122/Rlabkey/man/labkey.getDefaultViewDetails.Rd | 3
Rlabkey-2.1.122/Rlabkey/man/labkey.getFolders.Rd | 6 -
Rlabkey-2.1.122/Rlabkey/man/labkey.getLookupDetails.Rd | 19 ++-
Rlabkey-2.1.122/Rlabkey/man/labkey.getSchemas.Rd | 3
Rlabkey-2.1.122/Rlabkey/man/labkey.insertRows.Rd | 25 ++--
Rlabkey-2.1.122/Rlabkey/man/labkey.saveBatch.Rd | 11 +
Rlabkey-2.1.122/Rlabkey/man/labkey.selectRows.Rd | 14 +-
Rlabkey-2.1.122/Rlabkey/man/labkey.updateRows.Rd | 25 ++--
Rlabkey-2.1.122/Rlabkey/man/lsFolders.Rd | 10 +
Rlabkey-2.1.122/Rlabkey/man/lsProjects.Rd | 3
Rlabkey-2.1.122/Rlabkey/man/lsSchemas.Rd | 6 -
Rlabkey-2.1.122/Rlabkey/man/makeFilter.Rd | 3
Rlabkey-2.1.122/Rlabkey/man/saveResults.Rd | 15 +-
Rlabkey-2.1.122/Rlabkey/src/JSON_parser.h | 2
38 files changed, 239 insertions(+), 152 deletions(-)