Title: R Image Processing and Analysis
Diff between ripa versions 2.0-1 dated 2014-05-14 and 2.0-2 dated 2014-05-30
Description: A package including various functions for image processing and analysis. With this package is possible to process and analyse RGB, LAN (multispectral) and AVIRIS (hyperspectral) images. This packages also provides functions for reading JPEG files, extracted from the archived 'rimage' package.
Author: Talita Perciano [aut, cre],
Alejandro C Frery [ctb]
Maintainer: Talita Perciano
DESCRIPTION | 16 +-
MD5 | 6
R/RIPA.R | 404 +++++++++++++++++++++++++++++++++++++++++++----------
man/read.aviris.Rd | 5
4 files changed, 346 insertions(+), 85 deletions(-)
Title: R as a plotting engine
Diff between rplotengine versions 1.0-3 dated 2012-11-03 and 1.0-5 dated 2014-05-30
Description: This package is intended for using R as a plotting engine either by custom
applications, or from a small script launched from the system console, or even within
the R console. Two ASCII text files are necessary:
(1) The graph parameters file, which name is passed to the function 'rplotengine()'.
The user can specify the titles, choose the type of the graph, graph output formats
(e.g. png, eps), proportion of the X-axis and Y-axis, position of the legend,
whether to show or not a grid at the background, etc.
(2) The data to be plotted, which name is specified as a parameter ('data_filename')
in the previous file. This data file has a tabulated format, with a single character
(e.g. tab) between each column, and a headers line located in the first row.
Optionally, the file could include data columns for showing confidence intervals.
Author: Pedro-Pablo Garrido Abenza [aut, cre]
Maintainer: Pedro-Pablo Garrido Abenza
rplotengine-1.0-3/rplotengine/COPYING |only
rplotengine-1.0-3/rplotengine/LICENCE |only
rplotengine-1.0-3/rplotengine/LICENSE |only
rplotengine-1.0-5/rplotengine/DESCRIPTION | 47 +---
rplotengine-1.0-5/rplotengine/MD5 | 13 -
rplotengine-1.0-5/rplotengine/NAMESPACE | 2
rplotengine-1.0-5/rplotengine/R/rplotengine.R | 270 +++++++++++++++--------
rplotengine-1.0-5/rplotengine/inst/mygraph.arg | 17 -
rplotengine-1.0-5/rplotengine/man/rplotengine.Rd | 168 ++++++++++++++
9 files changed, 389 insertions(+), 128 deletions(-)
Title: Dictionaries and word lists for the qdap package.
Diff between qdapDictionaries versions 0.0.4 dated 2014-04-24 and 1.0.1 dated 2014-05-30
More information about qdapDictionaries at CRAN
Description: This package is a collection of dictionaries and word lists for
use with the qdap package.
Author: Tyler Rinker
Maintainer: Tyler Rinker
qdapDictionaries-0.0.4/qdapDictionaries/data/env.pol.rda |only
qdapDictionaries-0.0.4/qdapDictionaries/data/env.power.rda |only
qdapDictionaries-0.0.4/qdapDictionaries/data/env.strength.rda |only
qdapDictionaries-0.0.4/qdapDictionaries/data/env.syl.rda |only
qdapDictionaries-0.0.4/qdapDictionaries/data/env.syn.rda |only
qdapDictionaries-0.0.4/qdapDictionaries/man/env.pol.Rd |only
qdapDictionaries-0.0.4/qdapDictionaries/man/env.power.Rd |only
qdapDictionaries-0.0.4/qdapDictionaries/man/env.strength.Rd |only
qdapDictionaries-0.0.4/qdapDictionaries/man/env.syl.Rd |only
qdapDictionaries-0.0.4/qdapDictionaries/man/env.syn.Rd |only
qdapDictionaries-1.0.1/qdapDictionaries/DESCRIPTION | 6
qdapDictionaries-1.0.1/qdapDictionaries/MD5 | 100 +++++-----
qdapDictionaries-1.0.1/qdapDictionaries/NAMESPACE | 2
qdapDictionaries-1.0.1/qdapDictionaries/NEWS | 24 +-
qdapDictionaries-1.0.1/qdapDictionaries/R/qdapDictionaries-package.R | 54 ++---
qdapDictionaries-1.0.1/qdapDictionaries/R/view_data.R | 2
qdapDictionaries-1.0.1/qdapDictionaries/data/datalist | 10 -
qdapDictionaries-1.0.1/qdapDictionaries/data/key.pol.rda |only
qdapDictionaries-1.0.1/qdapDictionaries/data/key.power.rda |only
qdapDictionaries-1.0.1/qdapDictionaries/data/key.strength.rda |only
qdapDictionaries-1.0.1/qdapDictionaries/data/key.syl.rda |only
qdapDictionaries-1.0.1/qdapDictionaries/data/key.syn.rda |only
qdapDictionaries-1.0.1/qdapDictionaries/inst/CITATION | 4
qdapDictionaries-1.0.1/qdapDictionaries/man/BuckleySaltonSWL.Rd | 17 -
qdapDictionaries-1.0.1/qdapDictionaries/man/DICTIONARY.Rd | 23 +-
qdapDictionaries-1.0.1/qdapDictionaries/man/Dolch.Rd | 11 -
qdapDictionaries-1.0.1/qdapDictionaries/man/Fry_1000.Rd | 1
qdapDictionaries-1.0.1/qdapDictionaries/man/Leveled_Dolch.Rd | 16 -
qdapDictionaries-1.0.1/qdapDictionaries/man/NAMES.Rd | 20 +-
qdapDictionaries-1.0.1/qdapDictionaries/man/NAMES_LIST.Rd | 18 +
qdapDictionaries-1.0.1/qdapDictionaries/man/NAMES_SEX.Rd | 16 -
qdapDictionaries-1.0.1/qdapDictionaries/man/OnixTxtRetToolkitSWL1.Rd | 11 -
qdapDictionaries-1.0.1/qdapDictionaries/man/SYNONYM.Rd | 19 +
qdapDictionaries-1.0.1/qdapDictionaries/man/Top100Words.Rd | 10 -
qdapDictionaries-1.0.1/qdapDictionaries/man/Top200Words.Rd | 10 -
qdapDictionaries-1.0.1/qdapDictionaries/man/Top25Words.Rd | 10 -
qdapDictionaries-1.0.1/qdapDictionaries/man/abbreviations.Rd | 10 -
qdapDictionaries-1.0.1/qdapDictionaries/man/action.verbs.Rd | 22 +-
qdapDictionaries-1.0.1/qdapDictionaries/man/adverb.Rd | 22 +-
qdapDictionaries-1.0.1/qdapDictionaries/man/amplification.words.Rd | 28 +-
qdapDictionaries-1.0.1/qdapDictionaries/man/contractions.Rd | 10 -
qdapDictionaries-1.0.1/qdapDictionaries/man/deamplification.words.Rd | 28 +-
qdapDictionaries-1.0.1/qdapDictionaries/man/emoticon.Rd | 10 -
qdapDictionaries-1.0.1/qdapDictionaries/man/interjections.Rd | 4
qdapDictionaries-1.0.1/qdapDictionaries/man/key.pol.Rd |only
qdapDictionaries-1.0.1/qdapDictionaries/man/key.power.Rd |only
qdapDictionaries-1.0.1/qdapDictionaries/man/key.strength.Rd |only
qdapDictionaries-1.0.1/qdapDictionaries/man/key.syl.Rd |only
qdapDictionaries-1.0.1/qdapDictionaries/man/key.syn.Rd |only
qdapDictionaries-1.0.1/qdapDictionaries/man/labMT.Rd | 32 +--
qdapDictionaries-1.0.1/qdapDictionaries/man/negation.words.Rd | 28 +-
qdapDictionaries-1.0.1/qdapDictionaries/man/negative.words.Rd | 11 -
qdapDictionaries-1.0.1/qdapDictionaries/man/positive.words.Rd | 11 -
qdapDictionaries-1.0.1/qdapDictionaries/man/power.words.Rd | 6
qdapDictionaries-1.0.1/qdapDictionaries/man/preposition.Rd | 1
qdapDictionaries-1.0.1/qdapDictionaries/man/print.view_data.Rd | 5
qdapDictionaries-1.0.1/qdapDictionaries/man/qdapDictionaries.Rd | 4
qdapDictionaries-1.0.1/qdapDictionaries/man/strong.words.Rd | 6
qdapDictionaries-1.0.1/qdapDictionaries/man/submit.words.Rd | 6
qdapDictionaries-1.0.1/qdapDictionaries/man/view_data.Rd | 4
qdapDictionaries-1.0.1/qdapDictionaries/man/weak.words.Rd | 6
61 files changed, 327 insertions(+), 311 deletions(-)
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-05-04 1.2-3
2012-04-30 1.2-2
2012-03-30 1.2-1
2011-09-16 1.2
2008-02-27 1.1-3
2008-02-24 1.1-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-30 0.2-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-22 0.2-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-22 0.3-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-07-08 0.2-1
2012-06-29 0.2-0
2011-06-15 0.1-1
2011-04-26 0.1-0
Title: Tree Branches Evaluated Statistically for Tightness
Diff between TBEST versions 1.4 dated 2014-02-24 and 3.0 dated 2014-05-30
Description: Our method introduces mathematically well-defined measures for tightness of branches in a hierarchical tree. Statistical significance of the findings is determined, for all branches of the tree, by performing permutation tests, optionally with generalized Pareto p-value estimation.
Author: Guoli Sun, Alex Krasnitz
Maintainer: Guoli Sun
DESCRIPTION | 8 +--
MD5 | 20 ++++----
NAMESPACE | 2
R/PartitionTree.R | 6 +-
R/RandTail.R | 120 +++++++++++++++++++++++----------------------------
R/RandTree.R | 126 ++++++++++++++++++++++++------------------------------
R/SigTree.R | 78 ++++++++++++++++++++++-----------
R/TreeStat.R | 30 +++++++++---
R/plot.best.R | 48 ++++++++++++++------
man/SigTree.Rd | 32 ++++++++-----
man/plot.best.Rd | 18 +++++++
11 files changed, 274 insertions(+), 214 deletions(-)
Title: Sensitivity Analysis for Case-Control Studies
Diff between SensitivityCaseControl versions 1.0 dated 2012-11-08 and 2.1 dated 2014-05-30
More information about SensitivityCaseControl at CRAN
Description: This package performs sensitivity analysis for case-control studies in which some cases may meet a more narrow definition of being a case compared to other cases which only meet a broad definition. The sensitivity analyses are described in Small, Cheng, Halloran and Rosenbaum (2013, "Case Definition and Sensitivity Analysis", Journal of the American Statistical Association, 1457-1468). The functions sens.analysis.mh and sens.analysis.aberrant.rank provide sensitivity analyses based on the Mantel-Haenszel test statistic and aberrant rank test statistic as described in Rosenbaum (1991, "Sensitivity Analysis for Matched Case Control Studies", Biometrics); see also Section 1 of Small et al. The function adaptive.case.test provides adaptive inferences as described in Section 5 of Small et al. The function adaptive.noether.brown provides a sensitivity analysis for a matched cohort study based on an adaptive test. The other functions in the package are internal functions.
Author: Dylan Small
Maintainer: Dylan Small
DESCRIPTION | 26 ++-------
MD5 | 20 +++----
R/adaptive.test.critical.value.func.R | 70 ++++++++++++++-----------
R/jointcrit.R | 85 +++++++++++++++++--------------
man/SensitivityCaseControl-package.Rd | 22 +++++---
man/adaptive.case.test.Rd | 30 ++++++----
man/adaptive.noether.brown.Rd | 5 +
man/adaptive.test.critical.value.func.Rd | 2
man/gconv.Rd | 2
man/sens.analysis.aberrant.rank.Rd | 4 -
man/sens.analysis.mh.Rd | 2
11 files changed, 144 insertions(+), 124 deletions(-)
Permanent link
Title: Multivariate Methods Based on the Oja Median and Related
Concepts
Diff between OjaNP versions 0.9-6 dated 2013-03-20 and 0.9-7 dated 2014-05-30
Description: The package provides functions for the Oja median, Oja
signs and ranks and methods based upon them.
Author: Daniel Fischer, Jyrki Möttönen, Klaus Nordhausen, Daniel Vogel
Maintainer: Klaus Nordhausen
DESCRIPTION | 12 ++++++------
MD5 | 26 +++++++++++++-------------
data/biochem.rda |binary
inst/ChangeLog | 4 ++++
man/OjaNP-package.Rd | 6 +++---
src/SubsetGenerator.cpp | 4 ++--
src/algorithms.cpp | 6 +++---
src/global.cpp | 2 +-
src/global.h | 2 +-
src/matrix.h | 8 +++++---
src/misc.cpp | 8 ++++----
src/ojasr.c | 16 ++++++++--------
src/pipes.h | 13 +++++++------
src/vkm.cpp | 4 ++--
14 files changed, 59 insertions(+), 52 deletions(-)
Title: Data preparation, estimation and prediction in multi-state
models
Diff between mstate versions 0.2.6 dated 2011-01-03 and 0.2.7 dated 2014-05-30
Description: Functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models
Author: Hein Putter, Liesbeth de Wreede, Marta Fiocco
Maintainer: Hein Putter
mstate-0.2.6/mstate/Changelog.txt |only
mstate-0.2.6/mstate/inst/doc/Rplots.pdf |only
mstate-0.2.6/mstate/inst/doc/Tutorial.bib |only
mstate-0.2.6/mstate/inst/doc/agsm.bst |only
mstate-0.2.7/mstate/ChangeLog |only
mstate-0.2.7/mstate/DESCRIPTION | 15
mstate-0.2.7/mstate/MD5 |only
mstate-0.2.7/mstate/NAMESPACE | 6
mstate-0.2.7/mstate/R/ELOS.R |only
mstate-0.2.7/mstate/R/cutLMms.R |only
mstate-0.2.7/mstate/R/misc.R | 62 +--
mstate-0.2.7/mstate/R/msfit.R | 514 +++++++++++++++++-------------
mstate-0.2.7/mstate/R/plot.msfit.R | 71 ++--
mstate-0.2.7/mstate/R/plot.probtrans.R | 224 +++++++------
mstate-0.2.7/mstate/R/probtrans.R | 24 -
mstate-0.2.7/mstate/R/xsect.R |only
mstate-0.2.7/mstate/build |only
mstate-0.2.7/mstate/inst/doc/Tutorial.R |only
mstate-0.2.7/mstate/inst/doc/Tutorial.Rnw | 25 -
mstate-0.2.7/mstate/inst/doc/Tutorial.pdf |binary
mstate-0.2.7/mstate/man/ELOS.Rd |only
mstate-0.2.7/mstate/man/crprep.Rd | 60 ++-
mstate-0.2.7/mstate/man/cutLMms.Rd |only
mstate-0.2.7/mstate/man/ebmt1.Rd | 15
mstate-0.2.7/mstate/man/ebmt2.Rd | 15
mstate-0.2.7/mstate/man/ebmt3.Rd | 15
mstate-0.2.7/mstate/man/ebmt4.Rd | 15
mstate-0.2.7/mstate/man/events.Rd | 2
mstate-0.2.7/mstate/man/msfit.Rd | 9
mstate-0.2.7/mstate/man/mstate-package.Rd | 4
mstate-0.2.7/mstate/man/plot.msfit.Rd | 12
mstate-0.2.7/mstate/man/plot.probtrans.Rd | 13
mstate-0.2.7/mstate/man/probtrans.Rd | 21 -
mstate-0.2.7/mstate/man/redrank.Rd | 53 +--
mstate-0.2.7/mstate/man/xsect.Rd |only
mstate-0.2.7/mstate/vignettes |only
36 files changed, 662 insertions(+), 513 deletions(-)
Title: Simulation of chromosomal regions shared by family members.
Diff between IBDsim versions 0.9-3 dated 2014-05-29 and 0.9-4 dated 2014-05-30
Description: R package for simulation of IBD sharing among family members. Using sex specific recombination rates from the Decode map (2010) of the human genome, phased chromosomes are simulated for all pedigree members, either by unconditional 'gene dropping' or conditional on a specified IBD pattern. Regions compatible with the query IBD pattern (possibly different from the conditional pattern) are subsequently detected and summarized.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/IBDsim.R | 6 +++---
R/genedrop.R | 2 +-
man/IBDsim.Rd | 3 ++-
src/IBDsim.c | 41 ++++++++++++++++++++++-------------------
6 files changed, 37 insertions(+), 33 deletions(-)
Title: Estimation of the Structural Topic Model
Diff between stm versions 0.6.12 dated 2014-05-14 and 0.6.16 dated 2014-05-30
Description: The Structural Topic Model (STM) allows researchers
to estimate topic models with document-level covariates.
The package also includes tools for model selection, visualization,
and estimation of topic-covariate regressions.
Author: Margaret E. Roberts, Brandon M. Stewart and Dustin Tingley
Maintainer: Brandon Stewart
DESCRIPTION | 8 +--
MD5 | 20 ++++----
R/plot.STM.R | 109 ++++++++++++++++++++++++++++++++++++----------
R/prepDocuments.R | 12 ++++-
R/textProcessor.R | 10 +++-
inst/NEWS.Rd | 11 ++++
inst/doc/stmVignette.Rnw | 4 -
inst/doc/stmVignette.pdf |binary
man/plot.STM.Rd | 25 ++++++----
man/prepDocuments.Rd | 5 +-
vignettes/stmVignette.Rnw | 4 -
11 files changed, 154 insertions(+), 54 deletions(-)
Title: Supplementary Item Response Theory Models
Diff between sirt versions 0.44-48 dated 2014-04-27 and 0.45-23 dated 2014-05-30
Description:
Supplementary item response theory models
to complement existing functions in R.
Author: Alexander Robitzsch
Maintainer: Alexander Robitzsch
DESCRIPTION | 13 ++----
MD5 | 42 +++++++++++---------
NAMESPACE | 22 ++++++++--
R/ARb_utils.R |only
R/noharm.sirt.R | 23 ++++++++---
R/noharm.sirt.preprocess.R | 5 +-
R/plot.noharm.sirt.R |only
R/rasch.conquest.R |only
R/rasch.mml2.R | 13 ++++++
R/reliability.nonlinear.sem.R | 9 ++--
R/sia.sirt.R |only
inst/NEWS | 35 +++++++++++-----
man/data.mixed1.Rd | 14 ++++--
man/data.read.Rd | 2
man/data.reck.Rd | 6 ++
man/lc.2raters.Rd | 2
man/mle.pcm.group.Rd | 9 +++-
man/noharm.sirt.Rd | 30 +++++++++++++-
man/rasch.conquest.Rd |only
man/rasch.evm.pcm.Rd | 11 ++++-
man/rasch.mml.Rd | 12 ++---
man/sia.sirt.Rd |only
man/sirt-package.Rd | 81 +++++++++++++++++++++------------------
man/stratified.cronbach.alpha.Rd | 2
man/unidim.test.csn.Rd | 8 ++-
25 files changed, 232 insertions(+), 107 deletions(-)
Title: A Package for Running jags from R
Diff between R2jags versions 0.04-01 dated 2014-02-26 and 0.04-02 dated 2014-05-30
Description: Using this package to call jags from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
CHANGELOG | 128 ++++++++++++++++++++++++++++-------------------------
DESCRIPTION | 10 ++--
MD5 | 12 ++--
R/as.bugs.array2.R | 22 ++++-----
R/jags.R | 110 ++++++++++++++++++++++-----------------------
R/jagsParallel.R | 19 ++++---
man/jags.Rd | 85 +++++++++++++++++------------------
7 files changed, 200 insertions(+), 186 deletions(-)
Title: Geometric morphometric analyses of 2d/3d landmark data
Diff between geomorph versions 2.0.1 dated 2014-04-18 and 2.1 dated 2014-05-30
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation
Author: Dean Adams, Michael Collyer, Erik Otarola-Castillo, Emma Sherratt
Maintainer: Dean Adams
geomorph-2.0.1/geomorph/man/read.vrml.Rd |only
geomorph-2.1/geomorph/DESCRIPTION | 12
geomorph-2.1/geomorph/MD5 | 107 +++---
geomorph-2.1/geomorph/NAMESPACE | 4
geomorph-2.1/geomorph/NEWS | 30 +
geomorph-2.1/geomorph/R/arrayspecs.r | 2
geomorph-2.1/geomorph/R/bilat.symmetry.r | 20 -
geomorph-2.1/geomorph/R/compare.modular.partitions.r | 37 +-
geomorph-2.1/geomorph/R/define.modules.R | 4
geomorph-2.1/geomorph/R/digitize2d.r | 194 ++++++++----
geomorph-2.1/geomorph/R/estimate.missing.r | 4
geomorph-2.1/geomorph/R/findMeanSpec.R | 2
geomorph-2.1/geomorph/R/geomorph.support.code.r | 146 ++++++++-
geomorph-2.1/geomorph/R/morphol.disparity.R | 1
geomorph-2.1/geomorph/R/morphol.integr.r | 6
geomorph-2.1/geomorph/R/pairwise.slope.test.r |only
geomorph-2.1/geomorph/R/pairwiseD.test.r | 197 ++++++++++--
geomorph-2.1/geomorph/R/phylo.pls.R | 6
geomorph-2.1/geomorph/R/physignal.r | 2
geomorph-2.1/geomorph/R/plotAllometry.r | 51 +--
geomorph-2.1/geomorph/R/plotGMPhyloMorphoSpace.r | 6
geomorph-2.1/geomorph/R/plotTangentSpace.r | 19 -
geomorph-2.1/geomorph/R/procD.lm.r | 186 ++++++++----
geomorph-2.1/geomorph/R/procD.pgls.r |only
geomorph-2.1/geomorph/R/readland.nts.r | 7
geomorph-2.1/geomorph/R/readland.tps.r | 34 +-
geomorph-2.1/geomorph/R/readmulti.nts.r | 7
geomorph-2.1/geomorph/R/trajectory.analysis.r | 4
geomorph-2.1/geomorph/R/two.b.pls.r | 247 +++++++++-------
geomorph-2.1/geomorph/data/hummingbirds.rda |binary
geomorph-2.1/geomorph/data/mosquito.rda |binary
geomorph-2.1/geomorph/data/motionpaths.rda |binary
geomorph-2.1/geomorph/data/plethShapeFood.rda |binary
geomorph-2.1/geomorph/data/plethodon.rda |binary
geomorph-2.1/geomorph/data/plethspecies.rda |binary
geomorph-2.1/geomorph/data/ratland.rda |binary
geomorph-2.1/geomorph/data/scallopPLY.rda |binary
geomorph-2.1/geomorph/data/scallops.rda |binary
geomorph-2.1/geomorph/man/arrayspecs.Rd | 2
geomorph-2.1/geomorph/man/compare.modular.partitions.Rd | 19 -
geomorph-2.1/geomorph/man/define.modules.Rd | 7
geomorph-2.1/geomorph/man/digitize2d.Rd | 102 +++---
geomorph-2.1/geomorph/man/findMeanSpec.Rd | 2
geomorph-2.1/geomorph/man/morphol.integr.Rd | 5
geomorph-2.1/geomorph/man/pairwise.slope.test.Rd |only
geomorph-2.1/geomorph/man/pairwiseD.test.Rd | 78 +++--
geomorph-2.1/geomorph/man/phylo.pls.Rd | 6
geomorph-2.1/geomorph/man/plotAllometry.Rd | 13
geomorph-2.1/geomorph/man/plotGMPhyloMorphoSpace.Rd | 2
geomorph-2.1/geomorph/man/plotTangentSpace.Rd | 18 -
geomorph-2.1/geomorph/man/procD.lm.Rd | 58 ++-
geomorph-2.1/geomorph/man/procD.pgls.Rd |only
geomorph-2.1/geomorph/man/readland.nts.Rd | 6
geomorph-2.1/geomorph/man/readland.tps.Rd | 9
geomorph-2.1/geomorph/man/readmulti.nts.Rd | 6
geomorph-2.1/geomorph/man/two.b.pls.Rd | 17 -
geomorph-2.1/geomorph/src/geomorph.c | 6
57 files changed, 1182 insertions(+), 509 deletions(-)
Title: Structural Time Series Models
Diff between stsm versions 1.2 dated 2014-01-27 and 1.3 dated 2014-05-30
Description: This package provides algorithms to fit
structural time series models by maximum likelihood.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle
stsm-1.2/stsm/data/llm.rda |only
stsm-1.2/stsm/inst/TODO |only
stsm-1.3/stsm/DESCRIPTION | 12 +--
stsm-1.3/stsm/MD5 | 57 +++++++-------
stsm-1.3/stsm/NAMESPACE | 15 +++
stsm-1.3/stsm/R/EM.R | 89 +++++++++++++++++------
stsm-1.3/stsm/R/logLik.R | 6 -
stsm-1.3/stsm/R/maxclik-fd-scoring.R | 1
stsm-1.3/stsm/R/maxlik-fd-optim.R | 116 ++++++++++++++++++++++++++++--
stsm-1.3/stsm/R/maxlik-fd-scoring.R | 83 +++++++++++++++++++--
stsm-1.3/stsm/R/maxlik-td-optim.R | 87 ++++++++++++++++++++--
stsm-1.3/stsm/R/maxlik-td-scoring.R | 83 ++++++++++++++++++---
stsm-1.3/stsm/R/methods-stsmFit.R | 51 ++++++++++---
stsm-1.3/stsm/R/methods-vcov-confint.R | 5 -
stsm-1.3/stsm/R/mloglik-fd.R | 37 ++++++++-
stsm-1.3/stsm/R/mloglik-td.R | 33 +++++++-
stsm-1.3/stsm/R/stsmFit.R |only
stsm-1.3/stsm/data/datalist | 1
stsm-1.3/stsm/data/llmseas.rda |binary
stsm-1.3/stsm/inst/CHANGES |only
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stsm-1.3/stsm/man/datagen-stsm.Rd | 6 -
stsm-1.3/stsm/man/maxlik-em.Rd | 9 +-
stsm-1.3/stsm/man/maxlik-fd.Rd | 17 ++--
stsm-1.3/stsm/man/maxlik-td.Rd | 32 ++++----
stsm-1.3/stsm/man/method-logLik.Rd | 7 +
stsm-1.3/stsm/man/methods-stsmFit.Rd | 2
stsm-1.3/stsm/man/methods-vcov-confint.Rd | 2
stsm-1.3/stsm/man/mloglik-fd.Rd | 11 +-
stsm-1.3/stsm/man/mloglik-td.Rd | 9 +-
stsm-1.3/stsm/man/sim-data.Rd | 21 ++---
stsm-1.3/stsm/man/stsmFit.Rd |only
32 files changed, 628 insertions(+), 168 deletions(-)
Title: The sparr package: SPAtial Relative Risk
Diff between sparr versions 0.3-4 dated 2013-12-10 and 0.3-5 dated 2014-05-30
Description: Provides functions to estimate kernel-smoothed relative risk functions and perform subsequent inference.
Author: T.M. Davies, M.L. Hazelton and J.C. Marshall
Maintainer: Tilman M. Davies
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/bivariate.density.R | 30 ++++++++++--------------------
R/zzz.R | 2 +-
man/bivariate.density.Rd | 2 +-
man/sparr-package.Rd | 4 ++--
6 files changed, 23 insertions(+), 33 deletions(-)
Title: A Laboratory for Recursive Partytioning
Diff between party versions 1.0-13 dated 2014-02-01 and 1.0-14 dated 2014-05-30
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 11 ++--
MD5 | 26 +++++------
R/Classes.R | 2
R/ConditionalTree.R | 2
R/Memory.R | 2
R/RandomForest.R | 2
R/varimp.R | 86 +++++++++++++++++++++++++++++++++++++-
R/zInitMethods.R | 5 +-
build/vignette.rds |binary
inst/NEWS | 10 ++++
inst/doc/MOB.pdf |binary
inst/doc/party.pdf |binary
man/varimp.Rd | 17 +++++++
tests/Examples/party-Ex.Rout.save | 21 +++++++--
14 files changed, 156 insertions(+), 28 deletions(-)
Title: NbClust package for determining the best number of clusters
Diff between NbClust versions 1.4 dated 2013-08-17 and 2.0 dated 2014-05-30
Description: NbClust package provides 30 indices for determining the optimal number of clusters in a dataset.
Author: Malika Charrad
Maintainer: Malika Charrad
DESCRIPTION | 19 -
MD5 | 8
NAMESPACE | 2
R/NbClust.R | 931 +++++++++++++++++++++++++++++----------------------------
man/NbClust.Rd | 780 +++++++++--------------------------------------
5 files changed, 643 insertions(+), 1097 deletions(-)
Title: MultiVariate Stochastic Linear Ornstein-Uhlenbeck models for
phylogenetic Comparative hypotHeses
Diff between mvSLOUCH versions 1.1 dated 2013-12-27 and 1.1.1 dated 2014-05-30
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek
Maintainer: Krzysztof Bartoszek
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/estimGLSGC.R | 2 +-
R/phylgls.R | 4 ++--
4 files changed, 9 insertions(+), 9 deletions(-)
Title: Interventional Inference for Dynamic Bayesian Networks
Diff between interventionalDBN versions 1.2.1 dated 2014-05-29 and 1.2.2 dated 2014-05-30
More information about interventionalDBN at CRAN
Description: This package allows a dynamic Bayesian network to be inferred from microarray timecourse data with interventions (inhibitors).
Author: Simon Spencer
Maintainer: Simon Spencer
DESCRIPTION | 6 +++---
MD5 | 6 +++---
man/interventionalDBN-package.Rd | 2 +-
man/interventionalData.Rd | 16 +++++++++++++++-
4 files changed, 22 insertions(+), 8 deletions(-)
Permanent link
Title: Functions for Hierarchical Bayesian Estimation: A Flexible
Approach
Diff between RSGHB versions 1.0.1 dated 2013-04-10 and 1.0.2 dated 2014-05-30
Description: This package can be used to estimate models using a hierarchical Bayesian framework. The flexibility comes in allowing the user to specify the likelihood function directly instead of assuming predetermined model structures. Types of models that can be estimated with this code include the family of discrete choice models (Multinomial Logit, Mixed Logit, Nested Logit, Error Components Logit and Latent Class) as well ordered response models like ordered probit and ordered logit. In addition, the package allows for flexibility in specifying parameters as either fixed (non-varying across individuals) or random with continuous distributions. Parameter distributions supported include normal, positive/negative log-normal, positive/negative censored normal, and the Johnson SB distribution. Kenneth Train's Matlab and Gauss code for doing hierarchical Bayesian estimation has served as the basis for a few of the functions included in this package. These Matlab/Gauss functions have been rewritten to be optimized within R. Considerable code has been added to increase the flexibility and usability of the code base. Train's original Gauss and Matlab code can be found here: http://elsa.berkeley.edu/Software/abstracts/train1006mxlhb.html See Train's chapter on HB in Discrete Choice with Simulation here: http://elsa.berkeley.edu/books/choice2.html; and his paper on using HB with non-normal distributions here: http://elsa.berkeley.edu/~train/trainsonnier.pdf
Author: Jeff Dumont
Maintainer: Jeff Dumont
RSGHB-1.0.1/RSGHB/Readme.md |only
RSGHB-1.0.1/RSGHB/vignettes/MNL.log |only
RSGHB-1.0.1/RSGHB/vignettes/Rplots.pdf |only
RSGHB-1.0.2/RSGHB/DESCRIPTION | 44 +-----
RSGHB-1.0.2/RSGHB/MD5 | 45 +++---
RSGHB-1.0.2/RSGHB/NAMESPACE | 1
RSGHB-1.0.2/RSGHB/R/checkModel.R | 72 ++++++---
RSGHB-1.0.2/RSGHB/R/doHB.R | 117 +++++++++++++---
RSGHB-1.0.2/RSGHB/R/hb.R | 83 ++++++++++-
RSGHB-1.0.2/RSGHB/R/nextB.R | 24 +--
RSGHB-1.0.2/RSGHB/R/nextD.R | 2
RSGHB-1.0.2/RSGHB/R/nextF.R | 7
RSGHB-1.0.2/RSGHB/R/plotC.R |only
RSGHB-1.0.2/RSGHB/R/trans.R | 19 +-
RSGHB-1.0.2/RSGHB/R/writeLog.R | 86 ++++++++---
RSGHB-1.0.2/RSGHB/R/xpnd.R | 2
RSGHB-1.0.2/RSGHB/build |only
RSGHB-1.0.2/RSGHB/inst/doc/RSGHB_HowTo.R |only
RSGHB-1.0.2/RSGHB/inst/doc/RSGHB_HowTo.pdf |binary
RSGHB-1.0.2/RSGHB/inst/doc/RSGHB_HowTo.rnw | 108 +++++++++++---
RSGHB-1.0.2/RSGHB/man/doHB.Rd | 44 +++---
RSGHB-1.0.2/RSGHB/man/plotC.Rd |only
RSGHB-1.0.2/RSGHB/src/RSGHB.c | 1
RSGHB-1.0.2/RSGHB/tools |only
RSGHB-1.0.2/RSGHB/vignettes/RSGHB_HowTo-concordance.tex | 4
RSGHB-1.0.2/RSGHB/vignettes/RSGHB_HowTo.rnw | 108 +++++++++++---
RSGHB-1.0.2/RSGHB/vignettes/RSGHB_HowTo.synctex.gz |only
RSGHB-1.0.2/RSGHB/vignettes/RSGHB_HowTo.tex | 108 +++++++++++---
28 files changed, 634 insertions(+), 241 deletions(-)
Title: Multiple Contrast Profiles
Diff between mcprofile versions 0.1-7 dated 2013-09-10 and 0.2-0 dated 2014-05-30
Description: Calculation of signed root deviance profiles for linear combinations of parameters in a generalized linear model. Multiple tests and simultaneous confidence intervals are provided.
Author: Daniel Gerhard
Maintainer: Daniel Gerhard
mcprofile-0.1-7/mcprofile/inst/doc/mcprofile.Rnw |only
mcprofile-0.1-7/mcprofile/inst/doc/mcprofile.pdf |only
mcprofile-0.1-7/mcprofile/man/orglm.Rd |only
mcprofile-0.1-7/mcprofile/vignettes/mcprofile.Rnw |only
mcprofile-0.2-0/mcprofile/DESCRIPTION | 11 ++--
mcprofile-0.2-0/mcprofile/MD5 | 24 +++++-----
mcprofile-0.2-0/mcprofile/NAMESPACE | 7 ++-
mcprofile-0.2-0/mcprofile/R/glm_profiling.R | 16 +++++--
mcprofile-0.2-0/mcprofile/R/hoa.R | 7 ++-
mcprofile-0.2-0/mcprofile/build |only
mcprofile-0.2-0/mcprofile/inst/doc/mcprofile.R | 49 +++++++---------------
mcprofile-0.2-0/mcprofile/inst/doc/mcprofile.Rmd |only
mcprofile-0.2-0/mcprofile/inst/doc/mcprofile.html |only
mcprofile-0.2-0/mcprofile/man/hoa.Rd | 3 -
mcprofile-0.2-0/mcprofile/man/mcprofile.Rd | 2
mcprofile-0.2-0/mcprofile/man/toxinLD.Rd | 4 -
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17 files changed, 64 insertions(+), 59 deletions(-)
Title: Weighted Subspace Random Forest
Diff between wsrf versions 1.3.0 dated 2014-02-09 and 1.4.0 dated 2014-05-30
Description: The wsrf package is a parallel implementation of the
Weighted Subspace Random Forest algorithm proposed (wsrf). A
novel variable weighting method is used for variable subspace
selection in place of the traditional approach of random
variable sampling. This new approach is particularly useful
in building models for high dimensional data---often
consisting of thousands of variables. Parallel computation is
used to take advantage of multi-core machines and clusters of
machines to build random forest models from high dimensional
data with reduced elapsed times.
Author: Qinghan Meng [aut],
He Zhao [aut, cre],
Graham Williams [aut],
Junchao Lv [ctb]
Maintainer: He Zhao
DESCRIPTION | 12 +-
MD5 | 53 ++++++----
R/oobErrorRate.wsrf.R | 4
R/predict.wsrf.R | 7 +
R/wsrf.R | 3
R/wsrf.R.in |only
R/wsrfParallelInfo.R |only
R/wsrfParallelInfo.R.in |only
build |only
cleanup |only
cleanup.win |only
configure | 199 ++++++++++++++++++++++-------------------
configure.win |only
inst/NEWS.Rd | 43 ++++++++
inst/doc/wsrfGuide.R | 32 +++---
inst/doc/wsrfGuide.Rnw |only
inst/doc/wsrfGuide.pdf |binary
man/correlation.wsrf.Rd | 3
man/oobErrorRate.wsrf.Rd | 3
man/predict.wsrf.Rd | 3
man/print.wsrf.Rd | 3
man/strength.wsrf.Rd | 3
man/summary.wsrf.Rd | 3
man/wsrfParallelInfo.Rd |only
src/Makevars.in | 3
src/Makevars.win | 2
src/training_set.cpp | 4
src/training_set.h | 3
src/weighted_random_forest.cpp | 2
tests/wsrftest.R | 8 -
tests/wsrftest.Rout.save | 169 +++++++++++-----------------------
vignettes |only
32 files changed, 295 insertions(+), 267 deletions(-)
Title: Statistics with Interactive R Learning
Diff between swirl versions 2.2.6 dated 2014-05-10 and 2.2.9 dated 2014-05-30
Description: swirl turns the R console into an interactive learning
environment. Users receive immediate feedback as they are guided through
self-paced lessons in data science and R programming.
Author: Nick Carchedi [aut, cre],
Bill Bauer [aut],
Gina Grdina [aut],
Sean Kross [aut]
Maintainer: Nick Carchedi
DESCRIPTION | 7 -
MD5 | 74 +++++------
NAMESPACE | 2
R/answerTests.R | 41 ++++--
R/answerTests2.R | 236 ++++++++++++++++++++++++++++--------
R/courseraCheck.R | 17 +-
R/install_course.R | 37 +++--
R/instructionSet.R | 11 +
R/menu.R | 45 +++---
R/swirl.R | 26 ++-
R/utilities.R | 18 +-
inst/Courses/suggested_courses.yaml | 3
man/AnswerTests.Rd |only
man/any_of_exprs.Rd |only
man/bye.Rd | 2
man/expr_creates_var.Rd | 22 ++-
man/expr_identical_to.Rd | 16 +-
man/expr_is_a.Rd | 20 ++-
man/expr_uses_func.Rd | 18 +-
man/func_of_newvar_equals.Rd | 22 ++-
man/info.Rd | 2
man/install_course_directory.Rd | 2
man/install_course_dropbox.Rd | 2
man/install_course_github.Rd | 2
man/install_course_google_drive.Rd | 2
man/install_course_url.Rd | 2
man/install_course_zip.Rd | 2
man/install_from_swirl.Rd | 2
man/main.Rd | 2
man/nxt.Rd | 2
man/omnitest.Rd | 17 +-
man/play.Rd | 2
man/skip.Rd | 2
man/swirl.Rd | 2
man/uninstall_course.Rd | 2
man/val_has_length.Rd | 19 ++
man/val_matches.Rd | 19 ++
man/var_is_a.Rd | 19 ++
man/zip_course.Rd | 2
39 files changed, 495 insertions(+), 226 deletions(-)
Title: Variable selection for generalized linear mixed models by
L1-penalized estimation
Diff between glmmLasso versions 1.2.2 dated 2013-11-18 and 1.3.0 dated 2014-05-30
Description: Variable selection for generalized linear mixed models by L1-penalized estimation
Author: Andreas Groll
Maintainer: Andreas Groll
DESCRIPTION | 8
MD5 | 21
R/glmmLasso.r | 4066 +++++++++++++++++++++++++++++++------
R/glmmLassoControl.r | 12
R/glmm_final.r | 155 +
R/glmm_final.smooth.r | 176 +
R/glmm_final_multi_random.r | 58
R/glmm_final_multi_random_smooth.r | 57
R/logLik.glmmLasso.r |only
demo/glmmLasso-soccer.r | 79
man/glmmLasso.rd | 31
man/glmmLassoControl.rd | 22
12 files changed, 3953 insertions(+), 732 deletions(-)