Title: Thresholded variable selection and prediction based on
estimating equations
Diff between threeboost versions 1.0 dated 2014-06-27 and 1.1 dated 2014-08-10
Description: This package implements a thresholded version of the EEBoost
algorithm described in [Wolfson (2011, JASA)]. EEBoost is a general-purpose
method for variable selection which can be applied whenever inference would
be based on an estimating equation. The package currently implements
variable selection based on the Generalized Estimating Equations, but can
also accommodate user-provided estimating functions. Thresholded EEBoost is
a generalization which allows multiple variables to enter the model at each
boosting step.
Author: Julian Wolfson and Christopher Miller
Maintainer: Julian Wolfson
threeboost-1.0/threeboost/README.md |only
threeboost-1.1/threeboost/DESCRIPTION | 8 +--
threeboost-1.1/threeboost/MD5 | 17 +++----
threeboost-1.1/threeboost/R/QIC.R | 6 +-
threeboost-1.1/threeboost/R/geeboost.R | 32 ++++++++++---
threeboost-1.1/threeboost/R/geefns.R | 66 ++++++++++++++++++----------
threeboost-1.1/threeboost/R/threeboost.R | 37 +++++++++------
threeboost-1.1/threeboost/man/ee.GEE.Rd | 11 ++--
threeboost-1.1/threeboost/man/geeboost.Rd | 1
threeboost-1.1/threeboost/man/threeboost.Rd | 17 ++++---
10 files changed, 123 insertions(+), 72 deletions(-)
Title: plotting custom sequence logos
Diff between RWebLogo versions 1.0.2 dated 2014-07-02 and 1.0.3 dated 2014-08-10
Description: RWebLogo is a wrapper for the WebLogo python package
that allows generating of customised sequence logos. Sequence logos are
graphical representations of the sequence conservation of nucleotides (in a
strand of DNA/RNA) or amino acids (in protein sequences). Each logo
consists of stacks of symbols, one stack for each position in the sequence.
The overall height of the stack indicates the sequence conservation at that
position, while the height of symbols within the stack indicates the
relative frequency of each amino or nucleic acid at that position. In
general, a sequence logo provides a richer and more precise description of,
for example, a binding site, than would a consensus sequence.
Author: Omar Wagih
Maintainer: Omar Wagih
RWebLogo-1.0.2/RWebLogo/man/plotlogo.Rd |only
RWebLogo-1.0.3/RWebLogo/DESCRIPTION | 8
RWebLogo-1.0.3/RWebLogo/MD5 | 20 -
RWebLogo-1.0.3/RWebLogo/NAMESPACE | 5
RWebLogo-1.0.3/RWebLogo/R/RWebLogo.R | 126 +---------
RWebLogo-1.0.3/RWebLogo/R/plotlogo.R |only
RWebLogo-1.0.3/RWebLogo/build/BUILD.R | 11
RWebLogo-1.0.3/RWebLogo/inst/extdata/weblogo-3.3/weblogolib/__init__.py | 24 +
RWebLogo-1.0.3/RWebLogo/inst/extdata/weblogo-3.3/weblogolib/_cli.py | 24 +
RWebLogo-1.0.3/RWebLogo/inst/extdata/weblogo-3.3/weblogolib/colorscheme.py | 18 +
RWebLogo-1.0.3/RWebLogo/inst/extdata/weblogo-3.3/weblogolib/custom_template.eps |only
RWebLogo-1.0.3/RWebLogo/inst/extdata/weblogo-3.3_bkp.zip |only
RWebLogo-1.0.3/RWebLogo/man/weblogo.Rd | 34 +-
13 files changed, 118 insertions(+), 152 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Diff between psych versions 1.4.5 dated 2014-05-14 and 1.4.8 dated 2014-08-10
Description: A number of routines for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle
Maintainer: William Revelle
DESCRIPTION | 12 +--
MD5 | 114 +++++++++++++++-------------
NAMESPACE | 11 ++
R/Promax.R | 26 ++++++
R/VSS.R | 5 -
R/alpha.R | 2
R/cor.ci.R | 87 ++++++++++++++--------
R/densityBy.r | 4 -
R/describe.by.R | 2
R/df2latex.R | 19 +++-
R/diagram.R | 35 +++++---
R/draw.tetra.R | 54 +++++++++++++
R/error.bars.R | 3
R/error.bars.by.R | 61 +++++++++------
R/fa.R | 6 -
R/fa.diagram.R | 54 ++++++++++++-
R/fa.extension.R | 27 +++++-
R/fa.sort.R | 22 -----
R/faBy.R |only
R/lavaan.diagram.R | 5 -
R/misc.R | 26 ++++--
R/mixed.cor.R | 21 ++---
R/multi.hist.R | 30 +++++++
R/omega.diagram.R | 18 +++-
R/outlier.R |only
R/plot.irt.R | 44 ++++++-----
R/polychoric.R | 164 +++++++++++++++++++++++++++++++++--------
R/principal.R | 2
R/print.psych.R | 48 ++++++++++--
R/print.psych.vss.R | 2
R/read.clipboard.R | 11 ++
R/scoreOverlap.r |only
R/statsBy.r | 38 +++++----
R/tetrachor.R | 51 ++++++------
inst/CITATION | 4 -
inst/NEWS.Rd | 70 +++++++++++++++++
inst/doc/overview.R | 177 ++++++++++++++++++++++++---------------------
inst/doc/overview.Rnw | 137 +++++++++++++++++++++++++++-------
inst/doc/overview.pdf |binary
inst/doc/psych_for_sem.pdf |binary
man/Promax.Rd | 36 +++++++--
man/cluster.cor.Rd | 27 +++++-
man/cor.ci.Rd | 26 ++++--
man/df2latex.Rd | 3
man/diagram.Rd | 2
man/draw.tetra.Rd | 19 ++++
man/error.bars.by.Rd | 18 ++--
man/fa.Rd | 2
man/fa.diagram.Rd | 13 ++-
man/fa.extension.Rd | 6 +
man/mixed.cor.Rd | 7 -
man/multi.hist.Rd | 11 ++
man/omega.graph.Rd | 3
man/outlier.Rd |only
man/plot.psych.Rd | 7 +
man/read.clipboard.Rd | 4 -
man/set.cor.Rd | 7 +
man/statsBy.Rd | 27 +++++-
man/tetrachor.Rd | 48 +++++++-----
vignettes/overview.Rnw | 137 +++++++++++++++++++++++++++-------
60 files changed, 1277 insertions(+), 518 deletions(-)
Title: R front-end to PostgreSQL and Pivotal (Greenplum) database,
wrapper for MADlib
Diff between PivotalR versions 0.1.16.12 dated 2014-06-11 and 0.1.16.17 dated 2014-08-10
Description: R interface of Pivotal Data Fabrics running on PostgreSQL
or Pivotal (Greenplum) database with parallel and distributed
computation ability for big data analytics. PivotalR is a
package that enables users of R to interact with the Pivotal
(Greenplum) Database as well as Pivotal HD/HAWQ for Big Data
analytics. It does so by providing an interface to the
operations on tables/views in the database. These operations
are almost the same as those of data.frame. Thus the users of R
do not need to learn SQL when they operate on the objects in
the database. It also provides a wrapper for MADlib, which is
an open-source library for parallel and scalable in-database
analytics.
Author: Predictive Analytics Team at Pivotal Inc.
Maintainer: Hai Qian
DESCRIPTION | 8 -
MD5 | 186 ++++++++++++++++++++--------------------
R/method-ops.R | 12 +-
R/method-sort_.R | 17 +--
R/utility-generic.R | 9 +
README.md | 13 +-
build/vignette.rds |binary
data/abalone.RData |binary
data/null.data.RData |binary
inst/doc/pivotalr.pdf |binary
man/aggregate-methods.Rd | 2
man/aic.Rd | 2
man/arith-methods.Rd | 2
man/array.len.Rd | 2
man/arraydb.to.arrayr.Rd | 2
man/as.db.data.frame-methods.Rd | 2
man/as.environment.Rd | 4
man/as.factor-methods.Rd | 2
man/by-methods.Rd | 2
man/cbind2.Rd | 2
man/clean.madlib.temp.Rd | 2
man/coef.Rd | 4
man/compare-methods.Rd | 2
man/conn.eql.Rd | 2
man/conn.id.Rd | 2
man/connection-info.Rd | 2
man/content.Rd | 2
man/crossprod.Rd | 2
man/db.Rcrossprod-class.Rd | 2
man/db.Rquery-class.Rd | 2
man/db.connect.Rd | 2
man/db.data.frame-class.Rd | 2
man/db.data.frame.Rd | 2
man/db.disconnect.Rd | 2
man/db.existsObject.Rd | 2
man/db.list.Rd | 2
man/db.obj-class.Rd | 2
man/db.objects.Rd | 2
man/db.q.Rd | 2
man/db.search.path.Rd | 2
man/db.table-class.Rd | 2
man/db.view-class.Rd | 2
man/delete-methods.Rd | 2
man/dim-methods.Rd | 2
man/eql-methods.Rd | 2
man/extract-replace-methods.Rd | 2
man/func-methods.Rd | 2
man/generic.bagging.Rd | 2
man/generic.cv.Rd | 2
man/groups.Rd | 2
man/ifelse.Rd | 2
man/is.db.data.frame.Rd | 2
man/is.factor-methods.Rd | 2
man/is.na-methods.Rd | 2
man/key.Rd | 2
man/logical-methods.Rd | 2
man/madlib.arima.Rd | 2
man/madlib.elnet.Rd | 2
man/madlib.glm.Rd | 2
man/madlib.lm.Rd | 2
man/madlib.summary.Rd | 2
man/margins.Rd | 2
man/merge-methods.Rd | 2
man/na.action.Rd | 2
man/names-methods.Rd | 2
man/pivotalr.Rd | 2
man/pkg-package.Rd | 2
man/predict.Rd | 2
man/predict.arima.madlib.Rd | 2
man/predict.bagging.model.Rd | 2
man/predict.elnet.madlib.Rd | 2
man/preview.Rd | 4
man/print-methods.Rd | 2
man/print.arima.madlib.Rd | 2
man/print.elnet.madlib.Rd | 2
man/print.lm.madlib.Rd | 2
man/print.logregr.madlib.Rd | 2
man/print.none.obj.Rd | 2
man/print.summary.madlib.Rd | 2
man/residuals.Rd | 2
man/row_actions.Rd | 2
man/sample-methods.Rd | 2
man/scale-methods.Rd | 2
man/sort-methods.Rd | 2
man/subset-methods.Rd | 2
man/summary.arima.madlib.Rd | 2
man/summary.elnet.madlib.Rd | 2
man/summary.lm.madlib.Rd | 2
man/summary.logregr.madlib.Rd | 2
man/type-cast.Rd | 2
man/unique-methods.Rd | 2
man/vcov.Rd | 2
vignettes/qian.bib | 4
vignettes/qian.tex | 4
94 files changed, 212 insertions(+), 211 deletions(-)
Title: Omics Data Integration Project
Diff between mixOmics versions 5.0-1 dated 2013-11-10 and 5.0-2 dated 2014-08-10
Description: The package provide statistical integrative techniques and
variants to analyse highly dimensional data sets: regularized
CCA and sparse PLS to unravel relationships between two
heterogeneous data sets of size (nxp) and (nxq) where the p and
q variables are measured on the same samples or individuals n.
These data may come from high throughput technologies, such as
omics data (e.g. transcriptomics, metabolomics or proteomics
data) that require an integrative or joint analysis. However,
mixOmics can also be applied to any other large data sets where
p + q >> n. rCCA is a regularized version of CCA to deal with
the large number of variables. sPLS allows variable selection
in a one step procedure and two frameworks are proposed:
regression and canonical analysis. Numerous graphical outputs
are provided to help interpreting the results. Recent
methodological developments include: sparse PLS-Discriminant
Analysis, Independent Principal Component Analysis and
multilevel analysis using variance decomposition of the data.
Author: Sebastien Dejean, Ignacio Gonzalez, Kim-Anh Le Cao with
contributions from Pierre Monget, Jeff Coquery, FangZou Yao,
Benoit Liquet, Florian Rohart
Maintainer: Kim-Anh Le Cao
mixOmics-5.0-1/mixOmics/R/plot.valid.R |only
mixOmics-5.0-1/mixOmics/R/spls.model.R |only
mixOmics-5.0-1/mixOmics/R/splsda.model.R |only
mixOmics-5.0-1/mixOmics/R/valid.R |only
mixOmics-5.0-1/mixOmics/man/plot.valid.Rd |only
mixOmics-5.0-1/mixOmics/man/valid.Rd |only
mixOmics-5.0-2/mixOmics/DESCRIPTION | 6
mixOmics-5.0-2/mixOmics/MD5 | 66 -
mixOmics-5.0-2/mixOmics/NAMESPACE | 19
mixOmics-5.0-2/mixOmics/NEWS | 392 ++++----
mixOmics-5.0-2/mixOmics/R/cim.R | 1053 +++++++++++-----------
mixOmics-5.0-2/mixOmics/R/multilevel.R | 612 +++++++-----
mixOmics-5.0-2/mixOmics/R/perf.R |only
mixOmics-5.0-2/mixOmics/R/plot.perf.R |only
mixOmics-5.0-2/mixOmics/R/plotIndiv.R | 982 ++++++++++----------
mixOmics-5.0-2/mixOmics/R/plotVar.R | 24
mixOmics-5.0-2/mixOmics/R/pls.R | 21
mixOmics-5.0-2/mixOmics/R/plsda.R | 140 +-
mixOmics-5.0-2/mixOmics/R/spls.R | 47
mixOmics-5.0-2/mixOmics/R/splsda.R | 144 +--
mixOmics-5.0-2/mixOmics/R/tune.multilevel.R | 45
mixOmics-5.0-2/mixOmics/data/breast.tumors.rda |binary
mixOmics-5.0-2/mixOmics/data/data.simu.rda |binary
mixOmics-5.0-2/mixOmics/data/linnerud.rda |binary
mixOmics-5.0-2/mixOmics/data/liver.toxicity.rda |binary
mixOmics-5.0-2/mixOmics/data/multidrug.rda |binary
mixOmics-5.0-2/mixOmics/data/nutrimouse.rda |binary
mixOmics-5.0-2/mixOmics/data/prostate.rda |binary
mixOmics-5.0-2/mixOmics/data/srbct.rda |binary
mixOmics-5.0-2/mixOmics/data/vac18.rda |binary
mixOmics-5.0-2/mixOmics/data/yeast.rda |binary
mixOmics-5.0-2/mixOmics/man/internal-functions.Rd | 49 -
mixOmics-5.0-2/mixOmics/man/perf.Rd |only
mixOmics-5.0-2/mixOmics/man/plot.perf.Rd |only
mixOmics-5.0-2/mixOmics/man/plotIndiv.Rd | 16
mixOmics-5.0-2/mixOmics/man/pls.Rd | 7
mixOmics-5.0-2/mixOmics/man/plsda.Rd | 187 +--
mixOmics-5.0-2/mixOmics/man/spls.Rd | 7
mixOmics-5.0-2/mixOmics/man/splsda.Rd | 6
39 files changed, 1994 insertions(+), 1829 deletions(-)
Title: A set of methods for longitudinal data objects.
Description: A very simple implementation of a class for
longitudinal data.
Author: R. Gentleman
Maintainer: ORPHANED
Diff between lgtdl versions 1.1.1 dated 2010-04-13 and 1.1.3 dated 2014-08-10
DESCRIPTION | 20 +++++++++++++------- MD5 |only man/getcov.Rd | 2 +- man/interplinear.Rd | 4 ++-- man/interpprev.Rd | 4 ++-- man/isString.lgtdl.Rd | 2 +- man/lgtdl.Rd | 7 ++++++- man/plot.lgtdl.Rd | 2 +- 8 files changed, 26 insertions(+), 15 deletions(-)
Title: TIme series of Grouped ERrors
Diff between tiger versions 0.2.3 dated 2013-08-12 and 0.2.3.1 dated 2014-08-10
Description: Temporally resolved groups of typical differences (errors) between two time series are determined and visualized
Author: Dominik Reusser
Maintainer: Dominik Reusser
DESCRIPTION | 7 ++++---
MD5 | 14 +++++++-------
NAMESPACE | 2 ++
R/diagnostic_dawson.R | 2 +-
R/scatterplot.R | 2 +-
R/som.measure.level.R | 2 +-
R/tiger.cluster.R | 4 ++--
R/tiger.som.peaks.R | 2 +-
8 files changed, 19 insertions(+), 16 deletions(-)
Title: Variance Ratio tests and other tests for Martingale Difference
Hypothesis
Diff between vrtest versions 0.96 dated 2014-04-22 and 0.97 dated 2014-08-10
Description: A collection of statistical tests for martingale difference hypothesis
Author: Jae H. Kim
Maintainer: Jae H. Kim
DESCRIPTION | 8 ++++----
MD5 | 12 +++++++-----
NAMESPACE | 2 +-
R/Panel.VR.R |only
R/stat.R | 2 +-
man/Panel.VR.Rd |only
man/VR.minus.1.Rd | 4 ++--
man/vrtest-package.Rd | 4 ++--
8 files changed, 17 insertions(+), 15 deletions(-)
Title: Fetch economic and financial time series data from public
sources
Diff between pdfetch versions 0.1.4 dated 2014-07-23 and 0.1.5 dated 2014-08-10
Description: A package for downloading economic and financial time series from
public sources.
Author: Abiel Reinhart
Maintainer: Abiel Reinhart
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 5 +++++
R/pdfetch.R | 2 +-
4 files changed, 13 insertions(+), 8 deletions(-)
Title: Explorer of World Population Prospects
Diff between wppExplorer versions 1.2-0 dated 2013-12-20 and 1.3-0 dated 2014-08-10
Description: A shiny interface for exploring data in wpp2008-wpp2012 packages.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 24 +++++++++++++-----------
R/global.R | 9 +++++++++
R/wpp.R | 25 ++++++++++++++++---------
data/iso3166.R | 4 ++++
data/iso3166ud.R |only
data/iso3166ud.txt |only
inst/explore/server.R | 40 +++++++++++++++++++++++++---------------
inst/explore/ui.R | 6 ++++--
man/iso3166.Rd | 19 ++++++++++++-------
man/wpp.explore.Rd | 2 +-
man/wppExplorer-package.Rd | 4 ++--
tests/test_functions.R | 4 ++--
14 files changed, 98 insertions(+), 53 deletions(-)
Title: ExtraTrees method
Diff between extraTrees versions 0.4-5 dated 2013-10-05 and 1.0.1 dated 2014-08-10
Description: A package implementing ExtraTrees method for classification and
regression. Uses Java implementation of the method.
Author: Jaak Simm, Ildefons Magrans de Abril
Maintainer: Jaak Simm
extraTrees-0.4-5/extraTrees/R/selectTrees.extraTrees.R |only
extraTrees-0.4-5/extraTrees/inst/javasrc |only
extraTrees-1.0.1/extraTrees/DESCRIPTION | 12 -
extraTrees-1.0.1/extraTrees/MD5 | 61 ++++---
extraTrees-1.0.1/extraTrees/NAMESPACE | 2
extraTrees-1.0.1/extraTrees/R/extraTrees.default.R | 126 +++++++++++++-
extraTrees-1.0.1/extraTrees/R/predict.extraTrees.R | 56 ++++--
extraTrees-1.0.1/extraTrees/R/print.extraTrees.R | 1
extraTrees-1.0.1/extraTrees/build/vignette.rds |binary
extraTrees-1.0.1/extraTrees/inst/CHANGELOG |only
extraTrees-1.0.1/extraTrees/inst/doc/extraTrees.pdf |binary
extraTrees-1.0.1/extraTrees/inst/java/ExtraTrees.jar |binary
extraTrees-1.0.1/extraTrees/inst/tests |only
extraTrees-1.0.1/extraTrees/java |only
extraTrees-1.0.1/extraTrees/man/extraTrees.Rd | 148 +++++++++--------
extraTrees-1.0.1/extraTrees/man/predict.extraTrees.Rd | 67 +++----
extraTrees-1.0.1/extraTrees/man/toJavaCSMatrix.Rd |only
extraTrees-1.0.1/extraTrees/man/toJavaMatrix.Rd | 4
extraTrees-1.0.1/extraTrees/man/toJavaMatrix2D.Rd |only
19 files changed, 317 insertions(+), 160 deletions(-)