Title: YuGene: A simple approach to scale gene expression data derived
from different platforms for integrated analyses
Diff between YuGene versions 1.1 dated 2014-02-20 and 1.1.1 dated 2014-04-14
Description: YuGene is a simple method for comparison of gene
expression generated across different experiments, and on
different platforms; that does not require global
renormalization, and is not restricted to comparison of
identical probes. YuGene works on a range of microarray dataset
distributions, such as between manufacturers. The resulting
output allows direct comparisons of gene expression between
experiments and experimental platforms.
Author: Kim-Anh Le Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A. Wells
Maintainer: Florian Rohart
DESCRIPTION | 11 ++++++-----
MD5 | 6 +++---
man/YuGene-package.Rd | 6 ++++--
man/YuGene.Rd | 6 ++++--
4 files changed, 17 insertions(+), 12 deletions(-)
Title: Negative Binomial Models for RNA-Sequencing Data
Diff between NBPSeq versions 0.1.8 dated 2012-11-19 and 0.3.0 dated 2014-04-14
Description: Negative Binomial (NB) models for two-group comparisons and
regression inferences from RNA-Sequencing Data.
Author: Yanming Di
Maintainer: Yanming Di
NBPSeq-0.1.8/NBPSeq/R/estimate.disp.mapl.R |only
NBPSeq-0.1.8/NBPSeq/R/nbp-classes.R |only
NBPSeq-0.1.8/NBPSeq/R/nbp-exact-test.R |only
NBPSeq-0.1.8/NBPSeq/R/nbp-main.R |only
NBPSeq-0.1.8/NBPSeq/R/nbp-mcle.R |only
NBPSeq-0.1.8/NBPSeq/R/nbp-plots.R |only
NBPSeq-0.1.8/NBPSeq/R/nbpseq.package.R |only
NBPSeq-0.3.0/NBPSeq/DESCRIPTION | 21 -
NBPSeq-0.3.0/NBPSeq/MD5 | 69 ++-
NBPSeq-0.3.0/NBPSeq/NAMESPACE | 21 -
NBPSeq-0.3.0/NBPSeq/R/NBPSeq.package.R |only
NBPSeq-0.3.0/NBPSeq/R/hoa.1d.R | 8
NBPSeq-0.3.0/NBPSeq/R/hoa.hd.R | 16
NBPSeq-0.3.0/NBPSeq/R/log.likelihood.R | 20 -
NBPSeq-0.3.0/NBPSeq/R/nb.glm.R | 277 ++++----------
NBPSeq-0.3.0/NBPSeq/R/nb.glm.dispersion.models.R |only
NBPSeq-0.3.0/NBPSeq/R/nb.glm.main.R | 434 +++++++++++++----------
NBPSeq-0.3.0/NBPSeq/R/nb.glm.optim.disp.R |only
NBPSeq-0.3.0/NBPSeq/R/nbp.classes.R |only
NBPSeq-0.3.0/NBPSeq/R/nbp.exact.test.R |only
NBPSeq-0.3.0/NBPSeq/R/nbp.main.R |only
NBPSeq-0.3.0/NBPSeq/R/nbp.optim.disp.R |only
NBPSeq-0.3.0/NBPSeq/R/nbp.plots.R |only
NBPSeq-0.3.0/NBPSeq/R/normalization.R |only
NBPSeq-0.3.0/NBPSeq/R/plot.nb.data.R |only
NBPSeq-0.3.0/NBPSeq/R/smart.plot.R | 193 +++++++---
NBPSeq-0.3.0/NBPSeq/inst |only
NBPSeq-0.3.0/NBPSeq/man/NBPSeq-package.Rd |only
NBPSeq-0.3.0/NBPSeq/man/arab.Rd | 64 +--
NBPSeq-0.3.0/NBPSeq/man/estimate.disp.Rd | 165 ++++----
NBPSeq-0.3.0/NBPSeq/man/estimate.dispersion.Rd | 113 +++--
NBPSeq-0.3.0/NBPSeq/man/estimate.norm.factors.Rd | 81 ++--
NBPSeq-0.3.0/NBPSeq/man/exact.nb.test.Rd | 205 +++++-----
NBPSeq-0.3.0/NBPSeq/man/irls.nb.1.Rd |only
NBPSeq-0.3.0/NBPSeq/man/nb.glm.test.Rd | 144 +++----
NBPSeq-0.3.0/NBPSeq/man/nbp.test.Rd | 396 ++++++++++----------
NBPSeq-0.3.0/NBPSeq/man/plot.nb.data.Rd |only
NBPSeq-0.3.0/NBPSeq/man/plot.nb.dispersion.Rd |only
NBPSeq-0.3.0/NBPSeq/man/plot.nbp.Rd | 33 -
NBPSeq-0.3.0/NBPSeq/man/prepare.nb.data.Rd | 33 -
NBPSeq-0.3.0/NBPSeq/man/prepare.nbp.Rd | 181 ++++-----
NBPSeq-0.3.0/NBPSeq/man/print.nb.data.Rd |only
NBPSeq-0.3.0/NBPSeq/man/print.nb.dispersion.Rd |only
NBPSeq-0.3.0/NBPSeq/man/print.nb.test.Rd |only
NBPSeq-0.3.0/NBPSeq/man/print.nbp.Rd | 33 -
NBPSeq-0.3.0/NBPSeq/man/test.coefficient.Rd | 181 ++++++---
46 files changed, 1413 insertions(+), 1275 deletions(-)
Title: Geographic display of survey data statistics
Diff between mapStats versions 1.14 dated 2014-02-28 and 1.17 dated 2014-04-14
Description: A package for calculating and visualizing survey data statistics on a color-coded map.
Author: Samuel Ackerman
Maintainer: Samuel Ackerman
DESCRIPTION | 18 ++----
MD5 | 23 ++++----
NAMESPACE | 2
R/calcQuantiles.R | 14 ++---
R/calcStats.R | 14 ++---
R/jiggleClass.R | 2
R/mapStats.R | 20 +++----
R/plotStats.R | 8 +-
demo/map_examples.R | 22 +++----
man/jiggleClass.Rd | 14 ++---
man/mapStats-internal.Rd |only
man/mapStats.Rd | 130 +++++++++++++++++++++--------------------------
man/usMap.Rd | 3 -
13 files changed, 126 insertions(+), 144 deletions(-)
Title: Fast access to large ASCII files
Diff between LaF versions 0.5 dated 2013-04-25 and 0.6 dated 2014-04-14
Description: Methods for fast access to large ASCII files. Currently the
following file formats are supported: comma separated format (csv) and fixed
width format. It is assumed that the files are too large to fit into memory,
although the package can also be used to efficiently access files that do
fit into memory. Methods are provided to access and process files blockwise.
Furthermore, an opened file can be accessed as one would an ordinary
data.frame. The LaF vignette gives an overview of the functionality
provided.
Author: Jan van der Laan
Maintainer: Jan van der Laan
LaF-0.5/LaF/inst/doc/LaF-benchmark.Rnw.orig |only
LaF-0.5/LaF/inst/tests |only
LaF-0.5/LaF/man/begin-methods.Rd |only
LaF-0.5/LaF/man/current_line-methods.Rd |only
LaF-0.5/LaF/man/data_model.Rd |only
LaF-0.5/LaF/man/goto-methods.Rd |only
LaF-0.5/LaF/man/laf-package.Rd |only
LaF-0.5/LaF/man/next_block-methods.Rd |only
LaF-0.5/LaF/man/process_blocks-methods.Rd |only
LaF-0.5/LaF/man/read_lines-methods.Rd |only
LaF-0.5/LaF/tests/tests.R |only
LaF-0.6/LaF/DESCRIPTION | 31 ++--
LaF-0.6/LaF/MD5 | 101 +++++++-------
LaF-0.6/LaF/NAMESPACE | 48 ++++++
LaF-0.6/LaF/NEWS | 6
LaF-0.6/LaF/R/generics.R | 104 ++++++++++++--
LaF-0.6/LaF/R/laf.R | 159 +++++++++++++++-------
LaF-0.6/LaF/R/laf_column.R | 82 +++++++----
LaF-0.6/LaF/R/meta.R | 197 ++++++++++++++++++++++++++++
LaF-0.6/LaF/R/open.R | 108 ++++++++++++++-
LaF-0.6/LaF/R/read_dm_blaise.R | 47 ++++++
LaF-0.6/LaF/R/stats.R | 90 ++++++++----
LaF-0.6/LaF/R/textutils.R | 83 +++++++++++
LaF-0.6/LaF/build |only
LaF-0.6/LaF/inst/doc/LaF-benchmark.pdf |binary
LaF-0.6/LaF/inst/doc/LaF-manual.R |only
LaF-0.6/LaF/inst/doc/LaF-manual.pdf |binary
LaF-0.6/LaF/man/begin.Rd |only
LaF-0.6/LaF/man/cindexing.Rd |only
LaF-0.6/LaF/man/close.Rd |only
LaF-0.6/LaF/man/current_line.Rd |only
LaF-0.6/LaF/man/datamodels.Rd |only
LaF-0.6/LaF/man/detect_dm_csv.Rd | 102 ++++++++------
LaF-0.6/LaF/man/determine_nlines.Rd | 50 +++----
LaF-0.6/LaF/man/get_lines.Rd | 42 ++---
LaF-0.6/LaF/man/goto.Rd |only
LaF-0.6/LaF/man/indexing.Rd |only
LaF-0.6/LaF/man/laf-class.Rd | 124 ++---------------
LaF-0.6/LaF/man/laf_column-class.Rd | 62 +-------
LaF-0.6/LaF/man/laf_open.Rd | 48 +++---
LaF-0.6/LaF/man/laf_open_csv.Rd | 90 +++++++-----
LaF-0.6/LaF/man/laf_open_fwf.Rd | 119 +++++-----------
LaF-0.6/LaF/man/levels.Rd |only
LaF-0.6/LaF/man/names.Rd |only
LaF-0.6/LaF/man/ncol.Rd |only
LaF-0.6/LaF/man/next_block.Rd |only
LaF-0.6/LaF/man/nrow.Rd |only
LaF-0.6/LaF/man/process_blocks.Rd |only
LaF-0.6/LaF/man/read_dm_blaise.Rd | 63 ++++----
LaF-0.6/LaF/man/read_lines.Rd |only
LaF-0.6/LaF/man/sample_lines.Rd | 57 ++++----
LaF-0.6/LaF/man/show.Rd |only
LaF-0.6/LaF/man/stats.Rd | 119 ++++++++--------
LaF-0.6/LaF/src/doublecolumn.h | 5
LaF-0.6/LaF/src/factorcolumn.h | 4
LaF-0.6/LaF/src/stats.cpp | 2
LaF-0.6/LaF/tests/test-all.R |only
LaF-0.6/LaF/tests/testthat |only
LaF-0.6/LaF/vignettes |only
59 files changed, 1230 insertions(+), 713 deletions(-)
Title: Estimation of an ETAS model. Mixed FLP (Forward Likelihood
Predictive) and ML estimation of non-parametric and parametric
components of the ETAS model for earthquake description.
Diff between etasFLP versions 1.0.2 dated 2014-04-02 and 1.0.3 dated 2014-04-14
Description: Estimation of the components of an ETAS model for earthquake description.
Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood.
The two estimation steps are alternated until convergence is obtained.
For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class "etasclass").
Author: Marcello Chiodi [aut, cre],
Giada Adelfio [aut]
Maintainer: Marcello Chiodi
ChangeLog | 9 +++++++++
DESCRIPTION | 12 ++++++------
MD5 | 26 +++++++++++++-------------
NAMESPACE | 10 ++++++++--
R/etas.mod2.R | 14 +++++++-------
R/etasclass.R | 17 +++++++++--------
R/flp1.etas.nlm.R | 2 +-
R/plot.etasclass.R | 5 +++--
R/profile.etasclass.R | 12 +++++-------
R/summary.eqcat.R | 8 ++++----
data/californiacatalog.RData |binary
data/italycatalog.RData |binary
man/etasFLP-package.Rd | 4 ++--
man/plot.etasclass.Rd | 3 +--
14 files changed, 68 insertions(+), 54 deletions(-)
Title: Probabilistic Forecasting using Ensembles and Bayesian Model
Averaging
Diff between ensembleBMA versions 5.0.7 dated 2014-01-30 and 5.0.8 dated 2014-04-14
Description: Bayesian Model Averaging to create probabilistic forecasts
from ensemble forecasts and weather observations.
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann
Gneiting, University of Washington.
Maintainer: Chris Fraley
CHANGELOG | 3 +++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/quantileForecast.fitBMAgamma.R | 2 +-
man/fitBMAgamma.Rd | 11 +++--------
5 files changed, 15 insertions(+), 17 deletions(-)
Title: Programmatic interface to the API serving UC Berkeley's Natural
History Data
Diff between ecoengine versions 1.2.6 dated 2014-03-24 and 1.3 dated 2014-04-14
Description: The ecoengine (http://ecoengine.berkeley.edu/) provides access to
more than 2 million georeferenced specimen records from the Berkeley
Natural History Museums. http://bnhm.berkeley.edu/
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram
DESCRIPTION | 6 +++---
MD5 | 18 +++++++++---------
NEWS | 5 +++++
R/ee_observations.R | 3 +--
R/ee_photos.R | 1 -
R/ee_search.R | 1 -
R/ee_sensor_aggregation.R | 1 -
R/ee_sensors.R | 1 -
README.md | 4 ++--
man/ee_observations.Rd | 2 +-
10 files changed, 21 insertions(+), 21 deletions(-)
Title: Calculate and Analyze Blau statuses for measuring social
distance
Diff between Blaunet versions 1.0.0 dated 2014-01-20 and 1.0.1 dated 2014-04-14
Description: An integrated set of tools to calculate and analyze Blau statuses quantifying social distance between individuals belonging to organizations. Relational (network) data may be incorporated for additional analyses.
Author: Michael Genkin [aut], George Berry [aut], Liyuan Chen [aut], Matthew Brashears [aut]
Maintainer: Michael Genkin
DESCRIPTION | 8 +++----
MD5 | 50 ++++++++++++++++++++++++------------------------
R/blau.R | 31 +++++++++++++++++++++--------
R/calc.dyadic.R | 4 +--
R/calc.niches.R | 2 -
R/calc.niches.ecology.R | 4 +--
R/calc.nodal.R | 10 ++++-----
R/calc.nodal.ecology.R | 6 ++---
R/calc.nodal.network.R | 11 +++++-----
R/correctFormat.R | 4 +--
R/ecology.summary.R | 12 +++++------
R/getPresentCases.R | 2 -
R/isBinary.R | 2 -
R/isCorrectLength.R | 2 -
R/niche.summary.R | 8 +++----
R/nodal.global.R | 2 -
man/TwoCities.Rd | 2 -
man/blau.Rd | 16 ++++++++++++---
man/blaunet-package.Rd | 16 +++++++--------
man/dyadic.Rd | 13 +++++-------
man/export.dyadic.Rd | 6 +++--
man/export.nodal.Rd | 2 -
man/niche.summary.Rd | 2 -
man/nodal.global.Rd | 2 -
man/nodal.local.Rd | 2 -
man/nodal.network.Rd | 6 +++--
26 files changed, 126 insertions(+), 99 deletions(-)
Title: Soundscape ecology
Diff between soundecology versions 1.1 dated 2013-11-25 and 1.1.1 dated 2014-04-14
Description: Functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.
Author: Luis J. Villanueva-Rivera and Bryan C. Pijanowski
Maintainer: Luis J. Villanueva-Rivera
soundecology-1.1.1/soundecology/DESCRIPTION | 12
soundecology-1.1.1/soundecology/MD5 | 23 -
soundecology-1.1.1/soundecology/NAMESPACE | 13
soundecology-1.1.1/soundecology/NEWS | 3
soundecology-1.1.1/soundecology/build/vignette.rds |binary
soundecology-1.1.1/soundecology/inst/doc/changeADI.Rmd | 2
soundecology-1.1.1/soundecology/inst/doc/changeADI.html | 2
soundecology-1.1.1/soundecology/inst/doc/intro.Rmd | 20 -
soundecology-1.1.1/soundecology/inst/doc/intro.html | 215 +-----------
soundecology-1.1.1/soundecology/man/soundecology.package.Rd | 4
soundecology-1.1.1/soundecology/vignettes/changeADI.Rmd | 2
soundecology-1.1.1/soundecology/vignettes/intro.Rmd | 20 -
soundecology-1.1/soundecology/inst/doc/intro.R |only
13 files changed, 74 insertions(+), 242 deletions(-)
Title: Methods for statistical disclosure control in tabular data
Diff between sdcTable versions 0.14.0 dated 2014-04-01 and 0.15.0 dated 2014-04-14
Description: Implementation of methods for statistical disclosure control in
tabular data
Author: Bernhard Meindl
Maintainer: Bernhard Meindl
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/export_functions.r | 16 ++++++++++++++--
R/methods_class_dataObj.r | 3 +--
4 files changed, 22 insertions(+), 11 deletions(-)
Title: Response-surface analysis
Diff between rsm versions 2.04 dated 2014-02-05 and 2.05 dated 2014-04-14
Description: Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis.
Author: Russell V. Lenth
Maintainer: Russell V Lenth
DESCRIPTION | 8 +++---
MD5 | 8 +++---
R/rsm.R | 68 ++++++++++++++++++++++++++++++++---------------------
build/vignette.rds |binary
inst/NEWS | 6 ++++
5 files changed, 56 insertions(+), 34 deletions(-)
Title: Analyzing RNA sequence count tables using quasi-likelihood
Diff between QuasiSeq versions 1.0-3 dated 2014-02-12 and 1.0-4 dated 2014-04-14
Description: This package is used to apply the QL, QLShrink and QLSpline methods (Lund, Nettleton, McCarthy, and Smyth, 2012) to quasi-Poisson or quasi-negative binomial models for identifying differentially expressed genes in RNA-seq data.
Author: Steve Lund
Maintainer: Steve Lund
DESCRIPTION | 10 ++++------
MD5 | 16 ++++++++--------
NAMESPACE | 2 +-
R/NBDev.R | 42 +++++++++++++++++++++++++++++++++++++++++-
R/QL.fit.R | 29 +++++++++++++++--------------
R/QL.results.R | 8 +-------
R/negbin.br.R | 2 +-
man/NBDev.Rd | 6 ++++--
man/QL.fit.Rd | 3 ++-
9 files changed, 77 insertions(+), 41 deletions(-)
Title: Pumilio in R
Diff between pumilioR versions 1.2 dated 2014-02-04 and 1.3 dated 2014-04-14
Description: R package to query and get data out of a Pumilio sound archive system (http://ljvillanueva.github.io/pumilio/).
Author: Luis J. Villanueva-Rivera
Maintainer: Luis J. Villanueva-Rivera
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
NEWS | 5 +++++
R/getFile.R | 34 ++++++++++++++++++++++++++--------
build/vignette.rds |binary
inst/doc/pumiliosetup.Rmd | 2 +-
inst/doc/pumiliosetup.html | 2 +-
man/getFile.Rd | 25 ++++++++++++++++++++-----
man/pumilioR.package.Rd | 4 ++--
vignettes/pumiliosetup.Rmd | 2 +-
vignettes/pumiliosetup.md | 2 +-
11 files changed, 71 insertions(+), 33 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Diff between psych versions 1.4.3 dated 2014-03-25 and 1.4.4 dated 2014-04-14
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 | 8 ++--
MD5 | 32 +++++++++----------
R/alpha.R | 7 ++--
R/cor.ci.R | 7 ++--
R/corr.test.R | 75 +++++++++++++++++++++++++++++++++++++++------
R/fa.R | 2 -
R/fa.ci.R | 6 +++
R/print.psych.fa.R | 2 -
R/statsBy.r | 19 +++++++++--
inst/CITATION | 4 +-
inst/NEWS.Rd | 37 +++++++++++++++++++---
inst/doc/overview.pdf |binary
inst/doc/psych_for_sem.pdf |binary
man/corr.test.Rd | 15 ++++++---
man/fa.Rd | 5 ++-
man/factor.congruence.Rd | 4 +-
man/statsBy.Rd | 6 +--
17 files changed, 170 insertions(+), 59 deletions(-)
Title: Rasch Model Parameters by Pairwise Algorithm
Diff between pairwise versions 0.2.2 dated 2014-04-07 and 0.2.4 dated 2014-04-14
Description: The package pairwise offers functions for the explicit calculation
-- not estimation! -- of the Rasch item parameters for dichotomous and
polytomous item responses, using a pairwise comparison approach. Person
parameters (WLE) are calculated according to Warm's weighted likelihood
approach.
Author: Joerg-Henrik Heine
Maintainer: Joerg-Henrik Heine
pairwise-0.2.2/pairwise/man/pairwise.Rd |only
pairwise-0.2.4/pairwise/DESCRIPTION | 32 ++++----
pairwise-0.2.4/pairwise/MD5 | 78 ++++++++++-----------
pairwise-0.2.4/pairwise/NAMESPACE | 1
pairwise-0.2.4/pairwise/NEWS | 10 ++
pairwise-0.2.4/pairwise/R/catprob.R | 6 -
pairwise-0.2.4/pairwise/R/esc.R | 4 -
pairwise-0.2.4/pairwise/R/ftab.R | 10 +-
pairwise-0.2.4/pairwise/R/gif.R | 4 -
pairwise-0.2.4/pairwise/R/grm.R | 12 +--
pairwise-0.2.4/pairwise/R/i.expscore.R | 6 +
pairwise-0.2.4/pairwise/R/i.ptb.R | 18 ++--
pairwise-0.2.4/pairwise/R/i.pvx.R | 2
pairwise-0.2.4/pairwise/R/make.incidenz.R | 16 ++--
pairwise-0.2.4/pairwise/R/pair.R | 8 +-
pairwise-0.2.4/pairwise/R/pairSE.R | 12 +--
pairwise-0.2.4/pairwise/R/pairwise-package.r | 22 ++++-
pairwise-0.2.4/pairwise/R/pairwise.item.fit.R | 18 +++-
pairwise-0.2.4/pairwise/R/pairwise.person.fit.R | 16 ++--
pairwise-0.2.4/pairwise/R/pers.R | 78 +++++++++++----------
pairwise-0.2.4/pairwise/R/plot.pairSE.R | 2
pairwise-0.2.4/pairwise/R/plot.pers.R |only
pairwise-0.2.4/pairwise/R/ptbis.R | 19 +++--
pairwise-0.2.4/pairwise/R/summary.pers.R | 47 +++++-------
pairwise-0.2.4/pairwise/man/bfiN_miss.Rd | 2
pairwise-0.2.4/pairwise/man/catprob.Rd | 14 ++-
pairwise-0.2.4/pairwise/man/cogBOOKLET.Rd | 2
pairwise-0.2.4/pairwise/man/esc.Rd | 4 -
pairwise-0.2.4/pairwise/man/gif.Rd | 2
pairwise-0.2.4/pairwise/man/grm.Rd | 23 ++----
pairwise-0.2.4/pairwise/man/make.incidenz.Rd | 20 ++---
pairwise-0.2.4/pairwise/man/pair.Rd | 13 ++-
pairwise-0.2.4/pairwise/man/pairSE.Rd | 33 ++++----
pairwise-0.2.4/pairwise/man/pairwise-package.Rd |only
pairwise-0.2.4/pairwise/man/pairwise.item.fit.Rd | 16 +++-
pairwise-0.2.4/pairwise/man/pairwise.person.fit.Rd | 18 ++--
pairwise-0.2.4/pairwise/man/pers.Rd | 24 +++---
pairwise-0.2.4/pairwise/man/plot.pairSE.Rd | 2
pairwise-0.2.4/pairwise/man/plot.pers.Rd |only
pairwise-0.2.4/pairwise/man/ptbis.Rd | 8 +-
pairwise-0.2.4/pairwise/man/sim200x3.Rd | 2
pairwise-0.2.4/pairwise/man/summary.pers.Rd | 15 ++--
42 files changed, 350 insertions(+), 269 deletions(-)
Title: Analysis of Multiple Time Course Data
Diff between longitudinal versions 1.1.8 dated 2013-09-15 and 1.1.9 dated 2014-04-14
Description: This package contains general data structures and
functions for longitudinal data with multiple variables,
repeated measurements, and irregularly spaced time points.
It also implements a shrinkage estimator of dynamical correlation
and dynamical covariance.
Author: Rainer Opgen-Rhein and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NAMESPACE | 3 +++
NEWS | 4 ++++
4 files changed, 14 insertions(+), 7 deletions(-)
Title: Automated caret feature selection
Diff between fscaret versions 0.8.5.5 dated 2014-04-01 and 0.8.5.6 dated 2014-04-14
Description: Automated feature selection using variety of models
provided by caret package
Author: Jakub Szlek
Maintainer: Jakub Szlek
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/fscaret.R | 2 +-
build/vignette.rds |binary
inst/NEWS.Rd | 8 ++++++++
inst/doc/fscaret.pdf |binary
man/fscaret-package.Rd | 4 ++--
man/fscaret.Rd | 2 +-
8 files changed, 23 insertions(+), 15 deletions(-)
Title: Boost C++ header files
Diff between BH versions 1.54.0-1 dated 2014-04-08 and 1.54.0-2 dated 2014-04-14
Description: Boost provides free peer-reviewed portable C++ source
libraries. A large part of Boost is provided as C++ template code
which is resolved entirely at compile-time without linking. This
package aims to provide the most useful subset of Boost libraries
for template use among CRAN package. By placing these libraries in
this package, we offer a more efficient distribution system for CRAN
as replication of this code in the sources of other packages is
avoided.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel
ChangeLog |only
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
inst/NEWS.Rd | 7 +++++++
inst/include/boost/lexical_cast.hpp | 2 ++
5 files changed, 17 insertions(+), 7 deletions(-)
Title: Efficiently Read Sequence Data (VCF format, BCF format and METAL
format) into R
Diff between seqminer versions 2.2 dated 2014-01-27 and 2.7 dated 2014-04-14
Description: Integrate sequencing data (VCF) or meta-analysis results in R
Author: Xiaowei Zhan
Maintainer: Xiaowei Zhan
ChangeLog | 23
DESCRIPTION | 10
MD5 | 85 +-
NAMESPACE | 6
R/seqminer.R | 580 +++++++++-----
inst/tabanno |only
inst/tests/testthat.R | 11
man/annotateGene.Rd |only
man/annotatePlain.Rd |only
man/annotateVcf.Rd |only
man/getRefBase.Rd |only
man/makeAnnotationParameter.Rd |only
man/rvmeta.writeScoreData.Rd | 5
man/tabix.read.header.Rd | 4
man/validateAnnotationParameter.Rd |only
src/AnnotationController.h |only
src/AnnotationInputFile.h |only
src/AnnotationOutput.h |only
src/AnnotationOutputFile.h |only
src/AnnotationResult.h |only
src/AnnotationResultCollection.h |only
src/AnnotationString.h |only
src/BCFReader.cpp | 2
src/BedReader.h |only
src/Codon.h |only
src/Common.h |only
src/FileFormat.h | 2
src/FreqTable.h |only
src/Gene.h |only
src/GeneAnnotation.h |only
src/GeneFormat.h |only
src/GenomeScore.h |only
src/GenomeSequence.h |only
src/IO.cpp | 4
src/IO.h | 4
src/LogFile.h |only
src/Maximum.h | 4
src/ModelParser.h |only
src/OrderedMap.h | 178 ++--
src/Priority.h |only
src/Range.h |only
src/RangeList.cpp | 4
src/RangeList.h | 9
src/Rannotation.cpp |only
src/Rannotation.h |only
src/SequenceUtil.h |only
src/StringTemplate.h |only
src/StringUtil.h |only
src/TabixData.h |only
src/Type.h |only
src/TypeConversion.h | 26
src/Utils.h | 452 ++++-------
src/VCFInputFile.cpp | 7
src/rvMetaLoader.cpp | 8
src/seqForStat.c |only
src/tabix_index.c | 1495 ++++++++++++++++++-------------------
src/vcf2genoLoader.cpp | 2
57 files changed, 1587 insertions(+), 1334 deletions(-)
Title: Multivariate Permutation Tests
Diff between flip versions 2.4 dated 2013-10-09 and 2.4.1 dated 2014-04-14
Description: It implements many univariate and multivariate permutation (and rotation) tests. Allowed tests: the t one and two samples, ANOVA, linear models, Chi Squared test, rank tests (i.e. Wilcoxon, Mann-Whitney, Kruskal-Wallis), Sign test and McNemar. Test on Linear Models are performed also in presence of covariates (i.e. nuisance parameters). The permutation and the rotation methods to get the null distribution of the test statistics are available. It also implements methods for multiplicity control such as Westfall-Young minP procedure and Closed Testing (Marcus, 1976) and k-FWER. Moreover, it allows to test for fixed effects in mixed effects models.
Author: Livio Finos, with contributions by Dario Basso, Aldo Solari, Jelle Goeman and Marco Rinaldo. Special thanks are due to Ivan Marin-Franch and Fredrik Nilsson for the debugging and the good questions.
Maintainer: Livio Finos
ChangeLog | 12 ++-
DESCRIPTION | 16 ++--
MD5 | 48 +++++++-------
NAMESPACE | 7 +-
R/Padjust.R | 30 ++++++--
R/between.R | 160 ++++++++++++++++++++++++++++-------------------
R/dependence.R | 36 ++++++----
R/estimateSu.R | 8 +-
R/flip-object.R | 87 ++++++++++++++++++-------
R/flip.R | 18 ++---
R/flipMix.R | 34 ++++++---
R/flipMixWithin.R | 10 +-
R/kfwer.R |only
R/npc.R | 17 ++--
R/obs2coeffWithin.R | 94 ++++++++++++++++-----------
R/permSpace.R | 33 ++++++---
R/symmetry.R | 19 ++---
R/utilities.R | 87 ++++++++++++++-----------
README |only
man/flip.Rd | 21 +++---
man/flip.object-class.Rd | 13 ++-
man/flipMix.Rd | 30 ++++----
man/multiplicity.Rd | 21 ++++--
man/permutationSpace.Rd | 23 +++++-
src |only
25 files changed, 512 insertions(+), 312 deletions(-)
Title: Network meta-analysis with R
Diff between netmeta versions 0.4-2 dated 2014-03-31 and 0.4-3 dated 2014-04-14
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013)
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 17 ++++++++-----
MD5 | 12 ++++-----
NEWS | 20 +++++++++++++++
R/forest.netmeta.R | 6 ++++
R/netmeta.R | 13 ++++++++--
R/nma.ruecker.R | 58 +++++++++++++++++++++++++---------------------
R/print.summary.netmeta.R | 3 --
7 files changed, 87 insertions(+), 42 deletions(-)
More information about rHealthDataGov at CRAN
Permanent link
Title: Variable Importance Analysis with Population Intervention Models
Diff between multiPIM versions 1.3-1 dated 2013-01-18 and 1.4-1 dated 2014-04-14
Description: Performs variable importance analysis using a causal inference approach. This is done by fitting Population Intervention Models. The default is to use a Targeted Maximum Likelihood Estimator (TMLE). The other available estimators are Inverse Probability of Censoring Weighted (IPCW), Double-Robust IPCW (DR-IPCW), and Graphical Computation (G-COMP) estimators. Inference can be obtained from the influence curve (plug-in) or by bootstrapping.
Author: Stephan Ritter
Maintainer: Stephan Ritter
ChangeLog | 7 +++++++
DESCRIPTION | 27 ++++++++++-----------------
MD5 | 13 +++++++------
NAMESPACE | 5 +++++
inst |only
man/Candidates.Rd | 4 ++--
man/multiPIM.Rd | 4 ++--
man/multiPIMboot.Rd | 4 ++--
8 files changed, 35 insertions(+), 29 deletions(-)
Title: Package for Luminescence Dating data analysis
Diff between Luminescence versions 0.3.2 dated 2014-01-07 and 0.3.3 dated 2014-04-14
Description: Package provides a collection of various R functions for Luminescence Dating data analysis.
Author: Sebastian Kreutzer [aut, trl, cre],
Christoph Schmidt [aut],
Margret C. Fuchs [aut],
Michael Dietze [aut],
Manfred Fischer [aut, trl],
Christoph Burow [aut],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer
Luminescence-0.3.2/Luminescence/man/calc_FadingCorr.rd |only
Luminescence-0.3.3/Luminescence/DESCRIPTION | 12
Luminescence-0.3.3/Luminescence/MD5 | 210 -
Luminescence-0.3.3/Luminescence/NEWS | 187 +
Luminescence-0.3.3/Luminescence/R/Analyse_SAR.OSLdata.R | 52
Luminescence-0.3.3/Luminescence/R/CW2pHMi.R | 6
Luminescence-0.3.3/Luminescence/R/CW2pLM.R | 6
Luminescence-0.3.3/Luminescence/R/CW2pLMi.R | 6
Luminescence-0.3.3/Luminescence/R/CW2pPMi.R | 4
Luminescence-0.3.3/Luminescence/R/RLum.Analysis-class.R | 43
Luminescence-0.3.3/Luminescence/R/RLum.Data.Curve-class.R | 4
Luminescence-0.3.3/Luminescence/R/RLum.Data.Spectrum-class.R | 8
Luminescence-0.3.3/Luminescence/R/RLum.Results-class.R | 42
Luminescence-0.3.3/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 69
Luminescence-0.3.3/Luminescence/R/Risoe.BINfileData2RLum.Data.Curve.R | 8
Luminescence-0.3.3/Luminescence/R/RisoeBINfileData-class.R | 14
Luminescence-0.3.3/Luminescence/R/Second2Gray.R | 10
Luminescence-0.3.3/Luminescence/R/analyse_IRSAR.RF.R | 101
Luminescence-0.3.3/Luminescence/R/analyse_SAR.CWOSL.R | 91
Luminescence-0.3.3/Luminescence/R/analyse_SAR.TL.R | 50
Luminescence-0.3.3/Luminescence/R/apply_CosmicRayRemoval.R |only
Luminescence-0.3.3/Luminescence/R/apply_EfficiencyCorrection.R |only
Luminescence-0.3.3/Luminescence/R/calc_AliquotSize.R | 329 ++
Luminescence-0.3.3/Luminescence/R/calc_CentralDose.R | 21
Luminescence-0.3.3/Luminescence/R/calc_CommonDose.R | 4
Luminescence-0.3.3/Luminescence/R/calc_CosmicDoseRate.R | 1131 +++++-----
Luminescence-0.3.3/Luminescence/R/calc_FadingCorr.R | 60
Luminescence-0.3.3/Luminescence/R/calc_FiniteMixture.R | 931 ++++++--
Luminescence-0.3.3/Luminescence/R/calc_FuchsLang2001.R | 135 -
Luminescence-0.3.3/Luminescence/R/calc_HomogeneityTest.R | 31
Luminescence-0.3.3/Luminescence/R/calc_MaxDose3.R | 96
Luminescence-0.3.3/Luminescence/R/calc_MinDose3.R | 90
Luminescence-0.3.3/Luminescence/R/calc_MinDose4.R | 108
Luminescence-0.3.3/Luminescence/R/calc_OSLLxTxRatio.R | 250 +-
Luminescence-0.3.3/Luminescence/R/calc_Statistics.R |only
Luminescence-0.3.3/Luminescence/R/calc_TLLxTxRatio.R | 6
Luminescence-0.3.3/Luminescence/R/fit_CWCurve.R | 37
Luminescence-0.3.3/Luminescence/R/fit_LMCurve.R | 89
Luminescence-0.3.3/Luminescence/R/merge_Risoe.BINfileData.R | 63
Luminescence-0.3.3/Luminescence/R/plot_AbanicoPlot.R |only
Luminescence-0.3.3/Luminescence/R/plot_DRTResults.R |only
Luminescence-0.3.3/Luminescence/R/plot_GrowthCurve.R | 114 -
Luminescence-0.3.3/Luminescence/R/plot_Histogram.R | 150 -
Luminescence-0.3.3/Luminescence/R/plot_KDE.R | 984 +++++---
Luminescence-0.3.3/Luminescence/R/plot_RLum.Analysis.R | 20
Luminescence-0.3.3/Luminescence/R/plot_RLum.Data.Curve.R | 18
Luminescence-0.3.3/Luminescence/R/plot_RLum.Data.Spectrum.R | 427 +++
Luminescence-0.3.3/Luminescence/R/plot_RLum.R | 8
Luminescence-0.3.3/Luminescence/R/plot_RadialPlot.R | 479 +++-
Luminescence-0.3.3/Luminescence/R/plot_Risoe.BINfileData.R | 12
Luminescence-0.3.3/Luminescence/R/readBIN2R.R | 14
Luminescence-0.3.3/Luminescence/R/readXSYG2R.R | 174 -
Luminescence-0.3.3/Luminescence/R/writeR2BIN.R | 4
Luminescence-0.3.3/Luminescence/data/ExampleData.XSYG.RData |only
Luminescence-0.3.3/Luminescence/data/datalist | 1
Luminescence-0.3.3/Luminescence/inst/NEWS.Rd | 177 +
Luminescence-0.3.3/Luminescence/inst/doc/S4-class_objects.pdf |binary
Luminescence-0.3.3/Luminescence/man/Analyse_SAR.OSLdata.Rd | 15
Luminescence-0.3.3/Luminescence/man/BaseDataSet.CosmicDoseRate.Rd | 244 +-
Luminescence-0.3.3/Luminescence/man/CW2pHMi.Rd | 3
Luminescence-0.3.3/Luminescence/man/CW2pLM.Rd | 3
Luminescence-0.3.3/Luminescence/man/CW2pLMi.Rd | 3
Luminescence-0.3.3/Luminescence/man/CW2pPMi.Rd | 1
Luminescence-0.3.3/Luminescence/man/ExampleData.BINfileData.Rd | 4
Luminescence-0.3.3/Luminescence/man/ExampleData.FittingLM.Rd | 2
Luminescence-0.3.3/Luminescence/man/ExampleData.XSYG.Rd |only
Luminescence-0.3.3/Luminescence/man/Luminescence-package.Rd | 22
Luminescence-0.3.3/Luminescence/man/RLum-class.Rd | 2
Luminescence-0.3.3/Luminescence/man/RLum.Analysis-class.Rd | 15
Luminescence-0.3.3/Luminescence/man/RLum.Data-class.Rd | 7
Luminescence-0.3.3/Luminescence/man/RLum.Data.Curve-class.Rd | 2
Luminescence-0.3.3/Luminescence/man/RLum.Data.Spectrum-class.Rd | 8
Luminescence-0.3.3/Luminescence/man/RLum.Results-class.Rd | 2
Luminescence-0.3.3/Luminescence/man/Risoe.BINfileData-class.Rd | 4
Luminescence-0.3.3/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 13
Luminescence-0.3.3/Luminescence/man/Risoe.BINfileData2RLum.Data.Curve.Rd | 5
Luminescence-0.3.3/Luminescence/man/Second2Gray.Rd | 9
Luminescence-0.3.3/Luminescence/man/analyse_IRSAR.RF.Rd | 8
Luminescence-0.3.3/Luminescence/man/analyse_SAR.CWOSL.Rd | 10
Luminescence-0.3.3/Luminescence/man/analyse_SAR.TL.Rd | 7
Luminescence-0.3.3/Luminescence/man/apply_CosmicRayRemoval.Rd |only
Luminescence-0.3.3/Luminescence/man/apply_EfficiencyCorrection.Rd |only
Luminescence-0.3.3/Luminescence/man/calc_AliquotSize.Rd | 64
Luminescence-0.3.3/Luminescence/man/calc_CentralDose.Rd | 2
Luminescence-0.3.3/Luminescence/man/calc_CommonDose.Rd | 3
Luminescence-0.3.3/Luminescence/man/calc_CosmicDoseRate.Rd | 18
Luminescence-0.3.3/Luminescence/man/calc_FadingCorr.Rd |only
Luminescence-0.3.3/Luminescence/man/calc_FiniteMixture.Rd | 85
Luminescence-0.3.3/Luminescence/man/calc_FuchsLang2001.rd | 23
Luminescence-0.3.3/Luminescence/man/calc_HomogeneityTest.Rd | 9
Luminescence-0.3.3/Luminescence/man/calc_MaxDose3.Rd | 25
Luminescence-0.3.3/Luminescence/man/calc_MinDose3.Rd | 19
Luminescence-0.3.3/Luminescence/man/calc_MinDose4.Rd | 12
Luminescence-0.3.3/Luminescence/man/calc_OSLLxTxRatio.Rd | 43
Luminescence-0.3.3/Luminescence/man/calc_Statistics.Rd |only
Luminescence-0.3.3/Luminescence/man/calc_TLLxTxRatio.Rd | 3
Luminescence-0.3.3/Luminescence/man/fit_CWCurve.Rd | 9
Luminescence-0.3.3/Luminescence/man/fit_LMCurve.Rd | 7
Luminescence-0.3.3/Luminescence/man/merge_Risoe.BINfileData.Rd | 36
Luminescence-0.3.3/Luminescence/man/plot_AbanicoPlot.Rd |only
Luminescence-0.3.3/Luminescence/man/plot_DRTResults.Rd |only
Luminescence-0.3.3/Luminescence/man/plot_GrowthCurve.Rd | 235 +-
Luminescence-0.3.3/Luminescence/man/plot_Histogram.Rd | 35
Luminescence-0.3.3/Luminescence/man/plot_KDE.Rd | 169 -
Luminescence-0.3.3/Luminescence/man/plot_RLum.Analysis.Rd | 5
Luminescence-0.3.3/Luminescence/man/plot_RLum.Data.Curve.Rd | 5
Luminescence-0.3.3/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 76
Luminescence-0.3.3/Luminescence/man/plot_RLum.Rd | 5
Luminescence-0.3.3/Luminescence/man/plot_RadialPlot.Rd | 85
Luminescence-0.3.3/Luminescence/man/plot_Risoe.BINfileData.Rd | 9
Luminescence-0.3.3/Luminescence/man/readBIN2R.Rd | 13
Luminescence-0.3.3/Luminescence/man/readXSYG2R.Rd | 64
Luminescence-0.3.3/Luminescence/man/writeR2BIN.Rd | 5
113 files changed, 5548 insertions(+), 2791 deletions(-)
Title: A MORE flexible neural network package
Diff between AMORE versions 0.2-14 dated 2013-12-17 and 0.2-15 dated 2014-04-14
Description: This package was born to release the TAO robust neural
network algorithm to the R users. It has grown and I think it
can be of interest for the users wanting to implement their own
training algorithms as well as for those others whose needs lye
only in the "user space".
Author: Manuel Castejon Limas, Joaquin B. Ordieres Mere, Ana Gonzalez
Marcos, Francisco Javier Martinez de Pison Ascacibar, Alpha V.
Pernia Espinoza, Fernando Alba Elias, Jose Maria Perez Ramos
Maintainer: Manuel Castejón Limas
ChangeLog | 10 ++++++++++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/sim.R | 20 ++++++++++++++++++++
src/BATCHgd.c | 17 +++++++++++++----
src/BATCHgdwm.c | 20 ++++++++++++++++----
6 files changed, 68 insertions(+), 17 deletions(-)