Title: Genome-wide DNA methylation sites screening by use of training
and testing samples.
Diff between ttScreening versions 1.3 dated 2014-02-28 and 1.4 dated 2014-08-28
Description: This package utilizes training and testing samples to filter out uninformative DNA methylation sites. Surrogate variables (SVs) of DNA methylation are included in the filtering process to explain unknown factor effects.
Author: Meredith Ray, Xin Tong, Hongmei Zhang
Maintainer: Meredith Ray
DESCRIPTION | 11 -
MD5 | 17 +
NAMESPACE | 2
R/irwsva.build2.R |only
R/num.sv2.R |only
R/sva2.R |only
R/ttScreening.R | 480 +++++++++------------------------------------
man/irwsva.build2.Rd | 6
man/num.sv2.Rd |only
man/sva2.Rd | 9
man/ttScreening-package.Rd |only
man/ttScreening.Rd | 149 +++++++------
12 files changed, 206 insertions(+), 468 deletions(-)
Title: Recursive Partitioning Based on Psychometric Models
Diff between psychotree versions 0.13-0 dated 2014-02-03 and 0.14-0 dated 2014-08-28
Description: Recursive partitioning based on psychometric models,
employing the general MOB algorithm (from package partykit) to obtain
Bradley-Terry trees, Rasch trees, rating scale and partial credit trees.
Author: Achim Zeileis [aut, cre],
Carolin Strobl [aut],
Florian Wickelmaier [aut],
Basil Abou El-Komboz [aut],
Julia Kopf [aut]
Maintainer: Achim Zeileis
psychotree-0.13-0/psychotree/R/PCModel.R |only
psychotree-0.13-0/psychotree/R/RSModel.R |only
psychotree-0.13-0/psychotree/R/RaschModel.R |only
psychotree-0.13-0/psychotree/R/btReg.R |only
psychotree-0.13-0/psychotree/R/pctree-psychotools.R |only
psychotree-0.13-0/psychotree/man/PCModel.Rd |only
psychotree-0.13-0/psychotree/man/RSModel.Rd |only
psychotree-0.13-0/psychotree/man/RaschModel.Rd |only
psychotree-0.13-0/psychotree/man/btReg.Rd |only
psychotree-0.13-0/psychotree/man/node_effects.Rd |only
psychotree-0.13-0/psychotree/man/node_raschplot.Rd |only
psychotree-0.14-0/psychotree/DESCRIPTION | 28
psychotree-0.14-0/psychotree/MD5 | 76 -
psychotree-0.14-0/psychotree/NAMESPACE | 99 -
psychotree-0.14-0/psychotree/NEWS | 18
psychotree-0.14-0/psychotree/R/bttree.R | 227 +---
psychotree-0.14-0/psychotree/R/graphics.R |only
psychotree-0.14-0/psychotree/R/pctree.R | 478 --------
psychotree-0.14-0/psychotree/R/raschtree.R | 309 +----
psychotree-0.14-0/psychotree/R/rstree.R | 240 +---
psychotree-0.14-0/psychotree/build/vignette.rds |binary
psychotree-0.14-0/psychotree/data/CEMSChoice.rda |binary
psychotree-0.14-0/psychotree/data/DIFSim.rda |binary
psychotree-0.14-0/psychotree/data/EuropeanValuesStudy.rda |binary
psychotree-0.14-0/psychotree/data/SPISA.rda |binary
psychotree-0.14-0/psychotree/data/Topmodel2007.rda |binary
psychotree-0.14-0/psychotree/inst/PCModel.R |only
psychotree-0.14-0/psychotree/inst/RSModel.R |only
psychotree-0.14-0/psychotree/inst/RaschModel.R |only
psychotree-0.14-0/psychotree/inst/btReg.R |only
psychotree-0.14-0/psychotree/inst/doc/raschtree.R | 4
psychotree-0.14-0/psychotree/inst/doc/raschtree.Rnw | 12
psychotree-0.14-0/psychotree/inst/doc/raschtree.pdf |binary
psychotree-0.14-0/psychotree/inst/old-bttree.R |only
psychotree-0.14-0/psychotree/inst/old-pctree.R |only
psychotree-0.14-0/psychotree/inst/old-raschtree.R |only
psychotree-0.14-0/psychotree/inst/old-rstree.R |only
psychotree-0.14-0/psychotree/man/CEMSChoice.Rd | 4
psychotree-0.14-0/psychotree/man/EuropeanValuesStudy.Rd | 4
psychotree-0.14-0/psychotree/man/SPISA.Rd | 9
psychotree-0.14-0/psychotree/man/bttree.Rd | 60 -
psychotree-0.14-0/psychotree/man/node_btplot.Rd | 7
psychotree-0.14-0/psychotree/man/node_profileplot.Rd |only
psychotree-0.14-0/psychotree/man/node_regionplot.Rd |only
psychotree-0.14-0/psychotree/man/pctree.Rd | 108 +-
psychotree-0.14-0/psychotree/man/raschtree.Rd | 91 +
psychotree-0.14-0/psychotree/man/rstree.Rd | 103 +
psychotree-0.14-0/psychotree/tests/Examples/psychotree-Ex.Rout.save | 535 ++++++----
psychotree-0.14-0/psychotree/vignettes/raschtree.Rnw | 12
psychotree-0.14-0/psychotree/vignettes/raschtree.Rout.save | 78 -
50 files changed, 943 insertions(+), 1559 deletions(-)
Title: Infrastructure for Psychometric Modeling
Diff between psychotools versions 0.2-0 dated 2014-02-03 and 0.3-0 dated 2014-08-28
Description: Infrastructure for psychometric modeling such as data classes (for item response data and
paired comparisons), basic model fitting functions (for Bradley-Terry, Rasch, partial credit, and rating
scale models), extractor functions for different types of parameters (item, person, threshold, discrimination),
unified inference and visualizations, and various datasets for illustration. Intended as a common lightweight
and efficient toolbox for psychometric modeling and a common building block for fitting psychometric mixture
models in package "psychomix" and psychometric tree models in package "psychotree".
Author: Achim Zeileis [aut, cre],
Carolin Strobl [aut],
Florian Wickelmaier [aut],
Basil Abou El-Komboz [aut],
Julia Kopf [aut]
Maintainer: Achim Zeileis
psychotools-0.2-0/psychotools/R/PCModel.R |only
psychotools-0.2-0/psychotools/R/RSModel.R |only
psychotools-0.2-0/psychotools/R/RaschModel.R |only
psychotools-0.2-0/psychotools/R/btReg.R |only
psychotools-0.2-0/psychotools/man/PCModel.fit.Rd |only
psychotools-0.2-0/psychotools/man/RSModel.fit.Rd |only
psychotools-0.2-0/psychotools/man/RaschModel.fit.Rd |only
psychotools-0.2-0/psychotools/man/btReg.fit.Rd |only
psychotools-0.2-0/psychotools/man/plot.PCModel.Rd |only
psychotools-0.2-0/psychotools/man/plot.RSModel.Rd |only
psychotools-0.2-0/psychotools/man/plot.RaschModel.Rd |only
psychotools-0.2-0/psychotools/man/plot.btReg.Rd |only
psychotools-0.3-0/psychotools/DESCRIPTION | 21
psychotools-0.3-0/psychotools/MD5 | 77
psychotools-0.3-0/psychotools/NAMESPACE | 268 -
psychotools-0.3-0/psychotools/NEWS | 65
psychotools-0.3-0/psychotools/R/anchor.R |only
psychotools-0.3-0/psychotools/R/btmodel.R |only
psychotools-0.3-0/psychotools/R/discrpar.R |only
psychotools-0.3-0/psychotools/R/fit_wrappers.R |only
psychotools-0.3-0/psychotools/R/graphics.R |only
psychotools-0.3-0/psychotools/R/itempar.R |only
psychotools-0.3-0/psychotools/R/itemresp.R |only
psychotools-0.3-0/psychotools/R/pcmodel.R |only
psychotools-0.3-0/psychotools/R/personpar.R |only
psychotools-0.3-0/psychotools/R/raschmodel.R |only
psychotools-0.3-0/psychotools/R/rsmodel.R |only
psychotools-0.3-0/psychotools/R/threshpar.R |only
psychotools-0.3-0/psychotools/data/FirstNames.rda |binary
psychotools-0.3-0/psychotools/data/GermanParties2009.rda |binary
psychotools-0.3-0/psychotools/data/MemoryDeficits.rda |binary
psychotools-0.3-0/psychotools/data/SoundQuality.rda |binary
psychotools-0.3-0/psychotools/data/SourceMonitoring.rda |binary
psychotools-0.3-0/psychotools/data/StereotypeThreat.rda |binary
psychotools-0.3-0/psychotools/data/VerbalAggression.rda |binary
psychotools-0.3-0/psychotools/data/YouthGratitude.rda |binary
psychotools-0.3-0/psychotools/man/VerbalAggression.Rd | 4
psychotools-0.3-0/psychotools/man/anchor.Rd |only
psychotools-0.3-0/psychotools/man/anchortest.Rd |only
psychotools-0.3-0/psychotools/man/as.list.itemresp.Rd |only
psychotools-0.3-0/psychotools/man/btmodel.Rd |only
psychotools-0.3-0/psychotools/man/curveplot.Rd |only
psychotools-0.3-0/psychotools/man/discrpar.Rd |only
psychotools-0.3-0/psychotools/man/elementary_symmetric_functions.Rd | 18
psychotools-0.3-0/psychotools/man/infoplot.Rd |only
psychotools-0.3-0/psychotools/man/itempar.Rd |only
psychotools-0.3-0/psychotools/man/itemresp.Rd |only
psychotools-0.3-0/psychotools/man/pcmodel.Rd |only
psychotools-0.3-0/psychotools/man/personpar.Rd |only
psychotools-0.3-0/psychotools/man/piplot.Rd |only
psychotools-0.3-0/psychotools/man/plot.btmodel.Rd |only
psychotools-0.3-0/psychotools/man/plot.raschmodel.Rd |only
psychotools-0.3-0/psychotools/man/predict.pcmodel.Rd |only
psychotools-0.3-0/psychotools/man/print.itemresp.Rd |only
psychotools-0.3-0/psychotools/man/profileplot.Rd |only
psychotools-0.3-0/psychotools/man/raschmodel.Rd |only
psychotools-0.3-0/psychotools/man/regionplot.Rd |only
psychotools-0.3-0/psychotools/man/rsmodel.Rd |only
psychotools-0.3-0/psychotools/man/subset.itemresp.Rd |only
psychotools-0.3-0/psychotools/man/summary.itemresp.Rd |only
psychotools-0.3-0/psychotools/man/threshpar.Rd |only
psychotools-0.3-0/psychotools/man/worth.Rd | 9
psychotools-0.3-0/psychotools/tests/Examples/psychotools-Ex.Rout.save | 2018 ++++++++--
63 files changed, 2084 insertions(+), 396 deletions(-)
Title: Multi-Group Sparse Discriminant Analysis
Diff between MGSDA versions 1.0 dated 2014-07-08 and 1.1 dated 2014-08-28
Description: Implements Multi-Group Sparse Discriminant Analysis proposal of 'I.Gaynanova, J.Booth and M.Wells (2014), Simultaneous sparse estimation of canonical vectors in the p>>N setting'
Author: Irina Gaynanova
Maintainer: Irina Gaynanova
MGSDA-1.0/MGSDA/R/constructCw.R |only
MGSDA-1.1/MGSDA/DESCRIPTION | 8 ++---
MGSDA-1.1/MGSDA/MD5 | 23 +++++++--------
MGSDA-1.1/MGSDA/NAMESPACE | 1
MGSDA-1.1/MGSDA/R/classifyV.R | 51 ++++++++++++++++-------------------
MGSDA-1.1/MGSDA/R/constructD.R | 9 ++----
MGSDA-1.1/MGSDA/R/cv.dLDA.R | 45 +++++++++---------------------
MGSDA-1.1/MGSDA/R/dLDA.R | 17 ++++-------
MGSDA-1.1/MGSDA/R/solveVcoordf2.R | 6 +---
MGSDA-1.1/MGSDA/man/MGSDA-package.Rd | 4 +-
MGSDA-1.1/MGSDA/man/classifyV.Rd | 7 +++-
MGSDA-1.1/MGSDA/man/cv.dLDA.Rd | 12 ++++++--
MGSDA-1.1/MGSDA/man/dLDA.Rd | 7 +++-
13 files changed, 87 insertions(+), 103 deletions(-)
Title: Plot a correlogram
Diff between corrgram versions 1.5 dated 2013-08-29 and 1.6 dated 2014-08-28
Description: Calculates correlation of variables and displays the results graphically.
Author: Kevin Wright
Maintainer: Kevin Wright
DESCRIPTION | 14 +++++++++-----
MD5 | 31 ++++++++++++++++++-------------
NAMESPACE | 3 +++
NEWS | 16 ++++++++++++----
R/corrgram.r | 51 +++++++++++++++++++++++++++------------------------
build |only
data/auto.rda |binary
data/baseball.rda |binary
data/vote.rda |binary
inst |only
man/auto.Rd | 7 ++++---
man/baseball.Rd | 18 +++++++++---------
man/corrgram.Rd | 34 +++++++++++++++++++++++++---------
man/vote.Rd | 9 +++++----
tests/misc.r | 20 +++++++++++++++-----
tests/spearman.r | 31 +++++++++++++++++++++++++++++++
vignettes |only
17 files changed, 158 insertions(+), 76 deletions(-)
Title: Squared extrapolation methods for accelerating fixed-point
iterations
Diff between SQUAREM versions 2012.7-1 dated 2012-07-26 and 2014.8-1 dated 2014-08-28
Description: Algorithms for accelerating the convergence of slow,
monotone sequences from smooth, contraction mapping such as the
EM algorithm. It can be used to accelerate any smooth, linearly
convergent acceleration scheme. A tutorial style introduction
to this package is available in a vignette on the CRAN download
page or, when the package is loaded in an R session, with
vignette("SQUAREM").
Author: Ravi Varadhan
Maintainer: Ravi Varadhan
SQUAREM-2012.7-1/SQUAREM/LICENSE |only
SQUAREM-2012.7-1/SQUAREM/inst/doc/SQUAREM.Stex |only
SQUAREM-2014.8-1/SQUAREM/DESCRIPTION | 11 ++++++-----
SQUAREM-2014.8-1/SQUAREM/MD5 | 9 +++++----
SQUAREM-2014.8-1/SQUAREM/inst/doc/SQUAREM.R |only
SQUAREM-2014.8-1/SQUAREM/inst/doc/SQUAREM.Rnw |only
SQUAREM-2014.8-1/SQUAREM/inst/doc/SQUAREM.pdf |binary
SQUAREM-2014.8-1/SQUAREM/vignettes |only
8 files changed, 11 insertions(+), 9 deletions(-)
Title: Loglinear Models for Capture-Recapture Experiments
Diff between Rcapture versions 1.3-1 dated 2012-05-31 and 1.4-2 dated 2014-08-28
Description: Estimation of abundance and other of demographic parameters for closed
populations, open populations and the robust design in capture-recapture experiments
using loglinear models.
Author: Louis-Paul Rivest and Sophie Baillargeon
Maintainer: Louis-Paul Rivest
Rcapture-1.3-1/Rcapture/R/histfreq.R |only
Rcapture-1.3-1/Rcapture/R/internal.R |only
Rcapture-1.3-1/Rcapture/R/model.matrices.R |only
Rcapture-1.3-1/Rcapture/data/catb.rda |only
Rcapture-1.3-1/Rcapture/inst |only
Rcapture-1.3-1/Rcapture/man/catb.Rd |only
Rcapture-1.3-1/Rcapture/tests |only
Rcapture-1.3-1/Rcapture/vignettes |only
Rcapture-1.4-2/Rcapture/DESCRIPTION | 20
Rcapture-1.4-2/Rcapture/MD5 | 101 +---
Rcapture-1.4-2/Rcapture/NAMESPACE | 8
Rcapture-1.4-2/Rcapture/NEWS | 168 ++++++-
Rcapture-1.4-2/Rcapture/R/closedp.Mtb.R | 170 ++++---
Rcapture-1.4-2/Rcapture/R/closedp.R | 286 ++++++-----
Rcapture-1.4-2/Rcapture/R/closedp.bc.R | 154 +++---
Rcapture-1.4-2/Rcapture/R/closedpCI.R | 574 +++++++++++-------------
Rcapture-1.4-2/Rcapture/R/closedpMS.R |only
Rcapture-1.4-2/Rcapture/R/internal.DRY.R |only
Rcapture-1.4-2/Rcapture/R/internal.histfreq.R |only
Rcapture-1.4-2/Rcapture/R/internal.matrices.R |only
Rcapture-1.4-2/Rcapture/R/internal.valid.R |only
Rcapture-1.4-2/Rcapture/R/profileCI.R | 9
Rcapture-1.4-2/Rcapture/R/robustd.0.R | 20
Rcapture-1.4-2/Rcapture/R/robustd.t.r | 22
Rcapture-1.4-2/Rcapture/R/uifit.R | 4
Rcapture-1.4-2/Rcapture/data/cbird.rda |only
Rcapture-1.4-2/Rcapture/data/duck.rda |binary
Rcapture-1.4-2/Rcapture/data/hare.rda |binary
Rcapture-1.4-2/Rcapture/data/lesbian.rda |only
Rcapture-1.4-2/Rcapture/man/BBS2001.Rd | 6
Rcapture-1.4-2/Rcapture/man/HIV.Rd | 13
Rcapture-1.4-2/Rcapture/man/Rcapture.package.Rd | 186 ++++++-
Rcapture-1.4-2/Rcapture/man/bunting.Rd | 42 -
Rcapture-1.4-2/Rcapture/man/cbird.Rd |only
Rcapture-1.4-2/Rcapture/man/closedp.Mtb.Rd | 35 +
Rcapture-1.4-2/Rcapture/man/closedp.Rd | 103 ++--
Rcapture-1.4-2/Rcapture/man/closedp.bc.Rd | 85 ++-
Rcapture-1.4-2/Rcapture/man/closedp.custom.Rd | 13
Rcapture-1.4-2/Rcapture/man/closedpCI.Rd | 217 ++++-----
Rcapture-1.4-2/Rcapture/man/closedpMS.Rd |only
Rcapture-1.4-2/Rcapture/man/descriptive.Rd | 18
Rcapture-1.4-2/Rcapture/man/duck.Rd | 46 -
Rcapture-1.4-2/Rcapture/man/hare.Rd | 10
Rcapture-1.4-2/Rcapture/man/histpos.Rd | 6
Rcapture-1.4-2/Rcapture/man/ill.Rd | 10
Rcapture-1.4-2/Rcapture/man/lesbian.Rd |only
Rcapture-1.4-2/Rcapture/man/mvole.Rd | 44 +
Rcapture-1.4-2/Rcapture/man/openp.Rd | 18
Rcapture-1.4-2/Rcapture/man/periodhist.Rd | 8
Rcapture-1.4-2/Rcapture/man/profileCI.Rd | 10
Rcapture-1.4-2/Rcapture/man/rbvole.Rd | 16
Rcapture-1.4-2/Rcapture/man/robustd.Rd | 18
Rcapture-1.4-2/Rcapture/man/uifit.Rd | 6
53 files changed, 1398 insertions(+), 1048 deletions(-)
More information about RcmdrPlugin.FactoMineR at CRAN
Permanent link
Title: R Commander Plugin for (industrial) Design of Experiments
Diff between RcmdrPlugin.DoE versions 0.12-2 dated 2013-08-29 and 0.12-3 dated 2014-08-28
More information about RcmdrPlugin.DoE at CRAN
Description: The package provides a platform-independent GUI for design of experiments.
It is implemented as a plugin to the R-Commander, which is a more general
graphical user interface for statistics in R based on tcl/tk.
DoE functionality can be accessed through the menu Design that is added to the
R-Commander menus.
Author: Ulrike Groemping [aut, cre],
Fox John [ctb]
Maintainer: Ulrike Groemping
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
NAMESPACE | 6 ++++--
R/checkers.R | 7 +++++++
inst/NEWS | 6 ++++++
inst/etc/menus.txt | 2 +-
man/PlotMeansDoE.menu.Rd | 4 ++--
man/RcmdrPlugin.DoEUndocumentedFunctions.Rd | 2 ++
8 files changed, 34 insertions(+), 17 deletions(-)
Permanent link
Title: Hierarchical Climate Regionalization: An Improved Hierarchical
Clustering in R for Climate Regionalization
Diff between HiClimR versions 1.1.2 dated 2014-07-27 and 1.1.3 dated 2014-08-28
Description: HiClimR package modifies and improves hierarchical clustering in R
('hclust' function in 'stats' library), for climate regionalization. It adds a new
clustering method (called, regional linkage) to the set of available methods together
with several features including regridding, coarsening spatial resolution, geographic
masking, data thresholds, detrending and standardization preprocessing, faster correlation
function, hybrid hierarchical clustering, and cluster validation.
Badr et. al (2014) describes the regionalization algorithms and data processing tools
included in the package and presents a demonstration application in which the package
is used to regionalize Africa on the basis of interannual precipitation variability.
It is applicable to any correlation-based clustering.
Author: Hamada S. Badr [aut, cre],
Benjamin F. Zaitchik [aut],
Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr
Changelog | 11 +++++++-
DESCRIPTION | 10 +++----
MD5 | 28 ++++++++++-----------
R/HiClimR.R | 17 ++++++------
R/coarseR.R | 13 +++++----
R/fastCor.R | 3 +-
R/geogMask.R | 35 ++++++++++++++------------
R/grid2D.R | 3 +-
R/minSigCor.R | 3 +-
R/validClimR.R | 3 +-
man/HiClimR.Rd | 71 +++++++++++++++++++++++++++++-------------------------
man/coarseR.Rd | 24 ++++++++++--------
man/grid2D.Rd | 4 +--
man/validClimR.Rd | 14 +++++-----
src/HiClimR.f90 | 3 +-
15 files changed, 136 insertions(+), 106 deletions(-)
Title: Descriptive analysis by groups
Diff between compareGroups versions 2.0.4 dated 2014-05-02 and 2.0.5 dated 2014-08-28
Description: This package is designed to read, interpret, summarise, display and
analyse epidemiological data. Can be used to create data summaries for
quality control, extensive reports for exploring data, including
publication-ready univariate or bivariate tables in plain text HTML and
LaTeX, and a figures to quickly visualise the distribution of your data.
Depending on the nature of the variable, various statistics are
calculated (mean, median, frequencies, incidences) and appropriate
tests are performed (t-test, Analysis of variance, Kruskal-Wallis, Fisher,
log-rank, ...). The latest version includes functionality for summarising
genetic data, and for performing low-level quality control of your database
(see radiograph()) to help identify data-entry errors. This version has
also been implemented in a web-interface to make this package accessible
to non-R-users (see www.comparegroups.eu).
Author: Isaac Subirana, Joan Vila, Héctor Sanz, Gavin Lucas, Judith Peñafiel
and David Giménez
Maintainer: Isaac Subirana
compareGroups-2.0.4/compareGroups/inst/doc/changelog.txt |only
compareGroups-2.0.5/compareGroups/DESCRIPTION | 10
compareGroups-2.0.5/compareGroups/MD5 | 32
compareGroups-2.0.5/compareGroups/NAMESPACE | 2
compareGroups-2.0.5/compareGroups/R/cGroupsGUI.R | 910 +++++-----
compareGroups-2.0.5/compareGroups/R/missingTable.R | 2
compareGroups-2.0.5/compareGroups/R/z[.cbind.createTable.R | 17
compareGroups-2.0.5/compareGroups/R/z[.createTable.R | 18
compareGroups-2.0.5/compareGroups/R/z[.rbind.createTable.R | 37
compareGroups-2.0.5/compareGroups/build/vignette.rds |binary
compareGroups-2.0.5/compareGroups/inst/doc/changelog |only
compareGroups-2.0.5/compareGroups/man/compareGroups-package.Rd | 6
compareGroups-2.0.5/compareGroups/vignettes/figures/bivar/age.pdf |binary
compareGroups-2.0.5/compareGroups/vignettes/figures/bivar/sex.pdf |binary
compareGroups-2.0.5/compareGroups/vignettes/figures/bivar/tmain.pdf |binary
compareGroups-2.0.5/compareGroups/vignettes/figures/univar/age.pdf |binary
compareGroups-2.0.5/compareGroups/vignettes/figures/univar/sex.pdf |binary
compareGroups-2.0.5/compareGroups/vignettes/figures/univar/tmain.pdf |binary
18 files changed, 506 insertions(+), 528 deletions(-)
Title: Data exchange between R and LabKey Server
Diff between Rlabkey versions 2.1.123 dated 2013-11-04 and 2.1.125 dated 2014-08-28
Description: This package allows an R user to discover, query and modify data in LabKey Server
Author: Peter Hussey
Maintainer: Cory Nathe
DESCRIPTION | 10 ++--
MD5 | 43 +++++++++++---------
NAMESPACE | 6 ++
NEWS | 9 ++++
R/labkey.curlOptions.R |only
R/labkey.deleteRows.R | 20 +++++----
R/labkey.executeSql.R | 18 ++++----
R/labkey.getFolders.R | 12 ++---
R/labkey.getQueryInfo.R | 10 ++--
R/labkey.getQueryLists.R | 10 ++--
R/labkey.getSchemas.R | 10 ++--
R/labkey.importRows.R | 20 +++++----
R/labkey.insertRows.R | 20 +++++----
R/labkey.saveBatch.R | 22 +++++-----
R/labkey.selectRows.R | 8 +--
R/labkey.setCurlOptions.R |only
R/labkey.updateRows.R | 20 +++++----
R/makeDF.R | 63 ++++++++++++++++-------------
R/makeFilter.R | 77 +++++++++++++++++++++++++++---------
build/vignette.rds |binary
man/Rlabkey-package.Rd | 4 -
man/labkey.acceptSelfSignedCerts.Rd |only
man/labkey.curlOptions.Rd |only
man/labkey.setCurlOptions.Rd |only
man/makeFilter.Rd | 30 +++++++-------
25 files changed, 246 insertions(+), 166 deletions(-)
Title: Efficient effect size computation
Diff between effsize versions 0.5.1 dated 2014-05-21 and 0.5.2 dated 2014-08-28
Description: This package contains the functions to compute the standardized
effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha and Delaney A).
The computation algorithms have been optimized to allow efficient computation even
with very large data sets.
Author: Marco Torchiano
Maintainer: Marco Torchiano
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/CliffDelta.R | 2 ++
man/effsize-package.Rd | 9 +++++----
4 files changed, 14 insertions(+), 11 deletions(-)
Title: Initiation à la Statistique avec R
Diff between BioStatR versions 1.0.4 dated 2012-03-30 and 2.0.0 dated 2014-08-28
Description: This packages provides datasets and functions for the book "Initiation à la Statistique avec R", Dunod, 2ed, 2014.
Author: Frederic Bertrand
Maintainer: Frederic Bertrand
BioStatR-1.0.4/BioStatR/BioStatR-Ex.R |only
BioStatR-1.0.4/BioStatR/LICENCE |only
BioStatR-2.0.0/BioStatR/DESCRIPTION | 19 +++++++++----------
BioStatR-2.0.0/BioStatR/INDEX |only
BioStatR-2.0.0/BioStatR/MD5 | 15 ++++++++-------
BioStatR-2.0.0/BioStatR/NAMESPACE | 3 +++
BioStatR-2.0.0/BioStatR/NEWS | 1 +
BioStatR-2.0.0/BioStatR/R/gg_qqplot.R |only
BioStatR-2.0.0/BioStatR/R/plotcdf2.R | 4 ++--
BioStatR-2.0.0/BioStatR/man/gg_qqplot.Rd |only
BioStatR-2.0.0/BioStatR/man/plotcdf2.Rd | 4 ++--
11 files changed, 25 insertions(+), 21 deletions(-)
Title: Automated caret feature selection
Diff between fscaret versions 0.8.5.6 dated 2014-04-14 and 0.8.5.7 dated 2014-08-28
Description: Automated feature selection using variety of models
provided by caret package
Author: Jakub Szlek
Maintainer: Jakub Szlek
DESCRIPTION | 14 +++++++-------
MD5 | 2 +-
2 files changed, 8 insertions(+), 8 deletions(-)
Title: Classes and methods for trajectory data
Diff between trajectories versions 0.1-0 dated 2014-08-27 and 0.1-1 dated 2014-08-28
Description: Classes and methods for trajectory data, with nested classes for individual trips, and collections for different entities. Methods include selection, generalization, aggregation, intersection, and plotting.
Author: Edzer Pebesma [cre, aut],
Benedikt Klus [aut]
Maintainer: Edzer Pebesma
DESCRIPTION | 8 +-
MD5 | 12 ++--
R/Tracks-methods.R | 146 +++++++++++++++++++++++++------------------------
demo/geolife.R | 1
inst/doc/tracks.pdf |binary
tests/tracks.R | 1
tests/tracks.Rout.save | 3 -
7 files changed, 90 insertions(+), 81 deletions(-)
Title: Estimation of conditional quantiles using optimal quantization
Diff between QuantifQuantile versions 0.2 dated 2014-06-13 and 1.0 dated 2014-08-28
More information about QuantifQuantile at CRAN
Description: Estimation of conditional quantiles using optimal quantization.
Construction of an optimal grid of N quantizers, estimation of conditional
quantiles and data driven selection of the size N of the grid. Graphical
illustrations for the selection of N and of resulting estimated curves or
surfaces when the dimension of the covariate is one or two.
Author: Isabelle Charlier and Davy Paindaveine and Jerome Saracco
Maintainer: Isabelle Charlier
DESCRIPTION | 8 +-
MD5 | 36 ++++++------
NAMESPACE | 2
R/QuantifQuantile.R | 67 +++++++++++------------
R/QuantifQuantile.d.R | 65 +++++++++++------------
R/QuantifQuantile.d2.R | 69 ++++++++++++------------
R/choice.grid.R | 98 ++++++++++++++++-------------------
R/plot.QuantifQuantile.R | 17 +++---
R/plot.select.N.QuantifQuantile.R | 58 ++++++++++----------
R/print.QuantifQuantile.R | 18 +++---
R/summary.QuantifQuantile.R | 16 ++---
man/QuantifQuantile.Rd | 36 ++++++------
man/QuantifQuantile.d.Rd | 34 ++++++------
man/QuantifQuantile.d2.Rd | 38 ++++++-------
man/choice.grid.Rd | 25 +++-----
man/plot.QuantifQuantile.Rd | 15 ++---
man/plot.select.N.QuantifQuantile.Rd | 20 +++----
man/print.QuantifQuantile.Rd | 12 ++--
man/summary.QuantifQuantile.Rd | 14 ++---
19 files changed, 319 insertions(+), 329 deletions(-)
Permanent link
Title: Robust Geostatistical Analysis of Spatial Data
Diff between georob versions 0.1-4 dated 2014-06-02 and 0.1-5 dated 2014-08-28
Description: The georob package provides functions for fitting linear models
with spatially correlated errors by robust and Gaussian Restricted
Maximum Likelihood and for computing robust and customary point
and block kriging predictions, along with utility functions for
cross-validation and for unbiased back-transformation of kriging
predictions of log-transformed data.
Author: Andreas Papritz [cre, aut],
Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz
ChangeLog | 31
DESCRIPTION | 11
MD5 | 41
NAMESPACE | 14
NEWS | 3
R/georob.S3methods.R | 130 +-
R/georob.cv.R | 7
R/georob.exported.functions.R | 207 ++-
R/georob.predict.R | 211 ++-
R/georob.private.functions.R | 2460 ++++++++++++++++++++----------------------
demo/georob_example.R | 12
man/S3methods.georob.Rd | 2
man/georob.Rd | 7
man/georob.control.Rd | 35
man/georobModelBuilding.Rd | 8
man/georobObject.Rd | 62 -
man/internal.functions.Rd | 30
man/lgnpp.Rd | 18
man/plot.georob.Rd | 4
man/pmm.Rd |only
man/predict.georob.Rd | 56
man/sample.variogram.Rd | 2
22 files changed, 1811 insertions(+), 1540 deletions(-)
Title: Analysis and visualisation of ecological communities
Diff between cheddar versions 0.1-625 dated 2014-02-26 and 0.1-626 dated 2014-08-28
Description: Cheddar provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. It also allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson
cheddar-0.1-625/cheddar/README.md |only
cheddar-0.1-625/cheddar/tests/CommunitiesLike.Rd |only
cheddar-0.1-626/cheddar/DESCRIPTION | 8 ++---
cheddar-0.1-626/cheddar/MD5 | 24 +++++++---------
cheddar-0.1-626/cheddar/R/chains.R | 25 ++++++++---------
cheddar-0.1-626/cheddar/R/community_trophic_links.R | 6 ++--
cheddar-0.1-626/cheddar/build/vignette.rds |binary
cheddar-0.1-626/cheddar/inst/doc/CheddarQuickstart.pdf |binary
cheddar-0.1-626/cheddar/inst/doc/Collections.pdf |binary
cheddar-0.1-626/cheddar/inst/doc/Community.pdf |binary
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cheddar-0.1-626/cheddar/man/cheddar.Rd | 4 +-
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Title: Bayesian analysis for exponential random graph models
Diff between Bergm versions 2.9 dated 2014-07-22 and 2.9.1 dated 2014-08-28
Description: Set of tools to analyse Bayesian exponential random graph models
Author: Alberto Caimo and Nial Friel
Maintainer: Alberto Caimo
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/bbeta.output.R | 2 +-
R/bergm.output.R | 6 +++---
R/bergmS.R | 10 +++-------
R/bergmS.output.R | 20 ++++++--------------
R/bgof.R | 4 ++--
7 files changed, 25 insertions(+), 37 deletions(-)
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Diff between spatstat versions 1.38-0 dated 2014-08-15 and 1.38-1 dated 2014-08-28
Description: A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley
Maintainer: Adrian Baddeley
DESCRIPTION | 12 +
MD5 | 106 ++++++++---------
NAMESPACE | 4
NEWS | 70 +++++++++++
R/cdftest.R | 10 -
R/clarkevans.R | 13 +-
R/dclftest.R | 5
R/envelope.R | 31 +++--
R/fv.R | 47 ++++++-
R/hyperframe.R | 7 -
R/iplot.R | 214 ++++++++++++++++++-----------------
R/iplotlayered.R | 205 +++++++++++++++++----------------
R/istat.R | 63 +++++-----
R/kppm.R | 13 +-
R/markcorr.R | 26 ++--
R/plot.fv.R | 6
R/plot.owin.R | 5
R/rLGCP.R | 8 -
R/resolve.defaults.R | 3
R/tess.R | 6
R/update.ppm.R | 273 ++++++++++++++++++++++++++-------------------
R/vcov.kppm.R | 5
inst/doc/getstart.pdf |binary
inst/doc/replicated.pdf |binary
inst/doc/shapefiles.pdf |binary
inst/doc/updates.R | 4
inst/doc/updates.Rnw | 14 ++
inst/doc/updates.pdf |binary
man/Extract.fv.Rd | 67 +++++++++--
man/Extract.im.Rd | 4
man/Kest.Rd | 2
man/Kmeasure.Rd | 2
man/Replace.im.Rd | 4
man/add.texture.Rd | 2
man/cdf.test.Rd | 4
man/centroid.owin.Rd | 2
man/clarkevans.Rd | 4
man/clarkevans.test.Rd | 5
man/crossing.psp.Rd | 2
man/default.expand.Rd | 6
man/envelope.Rd | 7 -
man/hextess.Rd | 2
man/plot.owin.Rd | 4
man/plot.ppp.Rd | 2
man/predict.ppm.Rd | 2
man/rLGCP.Rd | 2
man/rSSI.Rd | 2
man/rgbim.Rd | 2
man/rmh.default.Rd | 2
man/spatstat-package.Rd | 22 ++-
man/suffstat.Rd | 2
tests/alltests.R | 89 ++++++++++++++
vignettes/packagesizes.txt | 1
vignettes/updates.Rnw | 14 ++
54 files changed, 885 insertions(+), 522 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining with R
Diff between FactoMineR versions 1.26 dated 2014-04-09 and 1.27 dated 2014-08-28
Description: an R package for exploratory data analysis
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson
DESCRIPTION | 11
MD5 | 84 ++--
NAMESPACE | 3
R/CA.R | 2
R/CaGalt.R |only
R/FAMD.R | 2
R/HCPC.R | 312 ++++++++++-------
R/catdes.r | 66 ++-
R/condes.r | 89 ++--
R/dimdesc.r | 54 ++
R/ellipseCA.R |only
R/plot.CA.R | 43 +-
R/plot.CaGalt.R |only
R/plot.FAMD.R | 11
R/plot.HCPC.R | 6
R/plot.MCA.R | 3
R/plot.MFA.R | 151 +++-----
R/print.CaGalt.R |only
R/reconst.R | 35 +
R/summary.CaGalt.R |only
R/summary.MCA.r | 2
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man/FAMD.Rd | 4
man/HCPC.Rd | 31 +
man/MCA.Rd | 4
man/MFA.Rd | 6
man/PCA.Rd | 3
man/catdes.Rd | 2
man/children.Rd | 2
man/condes.Rd | 3
man/dimdesc.Rd | 4
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man/plot.CA.Rd | 5
man/plot.CaGalt.Rd |only
man/plot.MFA.Rd | 9
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man/reconst.Rd | 12
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Title: Interface to the bird-watching datasets at proyectoavis.com
Diff between rAvis versions 0.1.1 dated 2014-03-07 and 0.1.2 dated 2014-08-28
Description: Interface to the proyectoavis.com bird observations records
database. It provides means to download datasets filtered by species, order,
family, and several other criteria. Provides also basic functionality to
plot exploratory maps of the datasets.
Author: Javier González Hernández
Maintainer: Sara Varela
DESCRIPTION | 20 ++---
MD5 | 24 +++---
R/loginFunctions.R | 8 +-
R/plotFunctions.R | 18 ++--
R/rAvis_package.R | 9 +-
R/remoteSpeciesDataFunctions.R | 2
R/remoteUsersDataFunctions.R | 4 -
R/searchInterfaceFunctions.R | 5 +
README.md | 161 ++++++++++++++++++++++++++++++++++-------
inst |only
man/avisMapSpecies.Rd | 2
man/rAvis.Rd | 11 +-
12 files changed, 196 insertions(+), 68 deletions(-)
Title: Multiresolution Kriging based on Markov random fields
Diff between LatticeKrig versions 3.3 dated 2014-07-11 and 3.4 dated 2014-08-28
Description: Functions for the interpolation of large spatial
datasets. This package follows a "fixed rank Kriging" approach using
a large number of basis functions and provides spatial estimates
that are comparable to standard families of covariance functions.
Using a large number of basis functions allows for estimates that
can come close to interpolating the observations (a spatial model
with a small nugget variance.) The covariance model for this method
can approximate the Matern covariance family but also allows for a
multi-resolution model and supports efficient computation of the
profile likelihood for estimating covariance parameters. This is
accomplished through compactly supported basis functions and a
Markov random field model for the basis coefficients. These features
lead to sparse matrices for the computations. One benefit of this
approach is the facilty to do unconditional and conditional
simulation of the field for large numbers of arbitrary points. There
is also the flexibility for estimating nonstationary covariances. Included are
generic methods for prediction, standard errors for prediction,
plotting of the estimated surface and conditional and unconditional
simulation.
Author: Douglas Nychka [aut, cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen [aut]
Maintainer: Douglas Nychka
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
R/LKrig.precision.R | 4 ++--
man/LatticeKrig.Rd | 7 +++++++
tests/LKrig.test.NonStationary.R |only
5 files changed, 17 insertions(+), 9 deletions(-)
Title: Insightful Research Tools
Diff between ifultools versions 2.0-0 dated 2013-12-30 and 2.0-1 dated 2014-08-28
Description: Insightful Research Tools.
Author: William Constantine and Donald Percival (Applied Physics
Laboratory, University of Washington)
Maintainer: Don Percival
DESCRIPTION | 6 +-
MD5 | 24 ++++----
NAMESPACE | 132 ++++++++++++++++++++++++-----------------------
src/RS_fra_surr.c | 6 +-
src/RS_wav_var.c | 3 -
src/fra_dim.c | 28 +++++-----
src/fra_surr.c | 6 +-
src/fra_tdmi.c | 1
src/ut_debug.c | 2
src/ut_mem.c | 4 -
src/wav_filt.c | 150 +++++++++++++++++++++++++++++-------------------------
src/wav_shrk.c | 4 -
src/wav_var.c | 2
13 files changed, 194 insertions(+), 174 deletions(-)
Title: Data sets and utilities for Foundations and Applications of
Statistics by R Pruim
Diff between fastR versions 0.4-2 dated 2013-04-11 and 0.8-1 dated 2014-08-28
Description: Data sets and utilities for Foundations and Applications of
Statistics:an Introduction using R by R Pruim
Author: Randall Pruim
Maintainer: Randall Pruim
fastR-0.4-2/fastR/bin |only
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fastR-0.8-1/fastR/MD5 | 306 ++++++------
fastR-0.8-1/fastR/NAMESPACE | 23
fastR-0.8-1/fastR/R/datasets.R | 688 ++++++++++++++---------------
fastR-0.8-1/fastR/R/fastR-package.R | 7
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fastR-0.8-1/fastR/R/ntigram.R | 1
fastR-0.8-1/fastR/R/pmfplot.R | 1
fastR-0.8-1/fastR/R/tdf.R | 2
fastR-0.8-1/fastR/R/vaov.R | 4
fastR-0.8-1/fastR/R/wilson.ci.R | 2
fastR-0.8-1/fastR/R/xplot.R | 53 +-
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fastR-0.8-1/fastR/man/miaa05.Rd | 41 -
fastR-0.8-1/fastR/man/mlb2004.Rd | 33 -
fastR-0.8-1/fastR/man/ncaa2010.Rd | 15
fastR-0.8-1/fastR/man/nfl2007.Rd | 14
fastR-0.8-1/fastR/man/nlmax.Rd | 34 -
fastR-0.8-1/fastR/man/noise.Rd | 20
fastR-0.8-1/fastR/man/palettes.Rd | 23
fastR-0.8-1/fastR/man/paperplanes.Rd | 96 +---
fastR-0.8-1/fastR/man/pendulum.Rd | 20
fastR-0.8-1/fastR/man/petstress.Rd | 31 -
fastR-0.8-1/fastR/man/pigs.Rd | 69 +-
fastR-0.8-1/fastR/man/pitching2005.Rd | 38 -
fastR-0.8-1/fastR/man/poison.Rd | 44 -
fastR-0.8-1/fastR/man/punting.Rd | 42 -
fastR-0.8-1/fastR/man/ratpoison.Rd | 11
fastR-0.8-1/fastR/man/rgolfballs.Rd | 5
fastR-0.8-1/fastR/man/rubberband.Rd | 11
fastR-0.8-1/fastR/man/scent.Rd | 37 -
fastR-0.8-1/fastR/man/snippet.Rd | 78 +--
fastR-0.8-1/fastR/man/soap.Rd | 42 -
fastR-0.8-1/fastR/man/spheres.Rd | 15
fastR-0.8-1/fastR/man/step.Rd | 63 +-
fastR-0.8-1/fastR/man/stereogram.Rd | 30 -
fastR-0.8-1/fastR/man/students.Rd | 15
fastR-0.8-1/fastR/man/tastetest.Rd | 40 -
fastR-0.8-1/fastR/man/tdf.Rd | 20
fastR-0.8-1/fastR/man/tirewear.Rd | 19
fastR-0.8-1/fastR/man/traffic.Rd | 49 --
fastR-0.8-1/fastR/man/trebuchet.Rd | 26 -
fastR-0.8-1/fastR/man/undocumented.Rd | 23
fastR-0.8-1/fastR/man/utilities.Rd | 43 -
fastR-0.8-1/fastR/man/vaov.Rd | 34 -
fastR-0.8-1/fastR/man/wilson.ci.Rd | 33 -
fastR-0.8-1/fastR/man/workingWomen.Rd | 26 -
fastR-0.8-1/fastR/man/xplot.Rd | 91 +--
fastR-0.8-1/fastR/vignettes |only
152 files changed, 1554 insertions(+), 1652 deletions(-)
Title: Calculate AUC-type measure when gold standard is continuous and
the corresponding optimal linear combination of variables with
respect to it.
Diff between cgAUC versions 1.1.2 dated 2013-01-16 and 1.2.1 dated 2014-08-28
Description: The cgAUC can calculate the AUC-type measure of Obuchowski(2006) when gold standard is continuous, and find the optimal linear combination of variables with respect to this measure.
Author: Yuan-chin I. Chang, Yu-chia Chang, and Ling-wan Chen
Maintainer: Yu-chia Chang
cgAUC-1.1.2/cgAUC/R/cgAUC.r |only
cgAUC-1.1.2/cgAUC/man/cntin.Rd |only
cgAUC-1.1.2/cgAUC/man/d.theta.sh.h.p.Rd |only
cgAUC-1.1.2/cgAUC/man/dscrt.Rd |only
cgAUC-1.1.2/cgAUC/man/s.h.Rd |only
cgAUC-1.2.1/cgAUC/DESCRIPTION | 18 +++++++++---------
cgAUC-1.2.1/cgAUC/MD5 | 21 ++++++++++++---------
cgAUC-1.2.1/cgAUC/NAMESPACE | 2 ++
cgAUC-1.2.1/cgAUC/R/MainFunction.R |only
cgAUC-1.2.1/cgAUC/R/RcppExports.R |only
cgAUC-1.2.1/cgAUC/man/c_cntin.Rd |only
cgAUC-1.2.1/cgAUC/man/c_d_theta_sh_h_p.Rd |only
cgAUC-1.2.1/cgAUC/man/c_dscrt.Rd |only
cgAUC-1.2.1/cgAUC/man/c_s_h.Rd |only
cgAUC-1.2.1/cgAUC/man/cgAUC-package.Rd | 17 +++++++++++------
cgAUC-1.2.1/cgAUC/man/cgAUC.Rd | 1 +
cgAUC-1.2.1/cgAUC/src |only
17 files changed, 35 insertions(+), 24 deletions(-)