Title: Response-Surface Analysis
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 <russell-lenth@uiowa.edu>
Diff between rsm versions 2.07 dated 2014-10-02 and 2.7-2 dated 2015-05-12
DESCRIPTION | 10 +-- MD5 | 32 ++++++------ R/contour-lm.R | 12 ++-- build/vignette.rds |binary inst/NEWS | 6 ++ inst/doc/rs-illus.Rtex | 82 +++++++++++++++++++++++++------ inst/doc/rs-illus.pdf |binary inst/doc/rsm-plots.pdf |binary inst/doc/rsm.pdf |binary vignettes/rs-illus-SA-anal2-fig.pdf |binary vignettes/rs-illus-SA-anal6-fig.pdf |binary vignettes/rs-illus-boot-anal7-fig.pdf |binary vignettes/rs-illus-contour-anal7-fig.pdf |binary vignettes/rs-illus-varfcn-FO-fig.pdf |binary vignettes/rs-illus-varfcn-SO-fig.pdf |binary vignettes/rs-illus-varfcn-SO2-fig.pdf |binary vignettes/rs-illus.Rtex | 82 +++++++++++++++++++++++++------ 17 files changed, 167 insertions(+), 57 deletions(-)
Title: Descriptive Analysis by Groups
Description: 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.
Author: Isaac Subirana, Joan Vila, Héctor Sanz, Gavin Lucas, Judith Peñafiel
and David Giménez
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 3.0 dated 2015-01-23 and 3.0.1 dated 2015-05-12
compareGroups-3.0.1/compareGroups/DESCRIPTION | 12 compareGroups-3.0.1/compareGroups/MD5 | 26 compareGroups-3.0.1/compareGroups/build/vignette.rds |binary compareGroups-3.0.1/compareGroups/inst/app/server.R | 395 +++++----- compareGroups-3.0.1/compareGroups/inst/app/ui.R | 81 +- compareGroups-3.0.1/compareGroups/inst/app/www/tablePDF3046.pdf |only compareGroups-3.0.1/compareGroups/inst/doc/changelog | 3 compareGroups-3.0.1/compareGroups/man/compareGroups-package.Rd | 6 compareGroups-3.0.1/compareGroups/vignettes/figures/bivar/age.pdf |binary compareGroups-3.0.1/compareGroups/vignettes/figures/bivar/sex.pdf |binary compareGroups-3.0.1/compareGroups/vignettes/figures/bivar/tmain.pdf |binary compareGroups-3.0.1/compareGroups/vignettes/figures/univar/age.pdf |binary compareGroups-3.0.1/compareGroups/vignettes/figures/univar/sex.pdf |binary compareGroups-3.0.1/compareGroups/vignettes/figures/univar/tmain.pdf |binary compareGroups-3.0/compareGroups/inst/app/www/tablePDF774.pdf |only 15 files changed, 305 insertions(+), 218 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
Diff between poppr versions 1.1.4 dated 2015-02-06 and 1.1.5 dated 2015-05-12
poppr-1.1.4/poppr/vignettes/figure |only poppr-1.1.5/poppr/DESCRIPTION | 16 - poppr-1.1.5/poppr/MD5 | 160 +++++---------- poppr-1.1.5/poppr/NAMESPACE | 2 poppr-1.1.5/poppr/NEWS | 8 poppr-1.1.5/poppr/R/distances.r | 10 poppr-1.1.5/poppr/R/internal.r | 19 + poppr-1.1.5/poppr/build/vignette.rds |binary poppr-1.1.5/poppr/data/Aeut.rda |binary poppr-1.1.5/poppr/data/Pinf.rda |binary poppr-1.1.5/poppr/data/monpop.rda |binary poppr-1.1.5/poppr/data/partial_clone.rda |binary poppr-1.1.5/poppr/inst/doc/algo.Rnw | 2 poppr-1.1.5/poppr/inst/doc/algo.pdf |binary poppr-1.1.5/poppr/inst/doc/poppr_manual.Rnw | 2 poppr-1.1.5/poppr/inst/doc/poppr_manual.pdf |binary poppr-1.1.5/poppr/man/Aeut.Rd | 2 poppr-1.1.5/poppr/man/Pinf.Rd | 2 poppr-1.1.5/poppr/man/aboot.Rd | 2 poppr-1.1.5/poppr/man/bootgen-class.Rd | 2 poppr-1.1.5/poppr/man/bootgen-methods.Rd | 2 poppr-1.1.5/poppr/man/bruvo.boot.Rd | 2 poppr-1.1.5/poppr/man/bruvo.dist.Rd | 2 poppr-1.1.5/poppr/man/bruvo.msn.Rd | 2 poppr-1.1.5/poppr/man/bruvomat-class.Rd | 2 poppr-1.1.5/poppr/man/bruvomat-methods.Rd | 2 poppr-1.1.5/poppr/man/clonecorrect.Rd | 2 poppr-1.1.5/poppr/man/coercion-methods.Rd | 2 poppr-1.1.5/poppr/man/diss.dist.Rd | 2 poppr-1.1.5/poppr/man/genclone-class.Rd | 2 poppr-1.1.5/poppr/man/genclone-method.Rd | 2 poppr-1.1.5/poppr/man/genetic_distance.Rd | 2 poppr-1.1.5/poppr/man/genind2genalex.Rd | 2 poppr-1.1.5/poppr/man/genotype_curve.Rd | 2 poppr-1.1.5/poppr/man/getfile.Rd | 2 poppr-1.1.5/poppr/man/greycurve.Rd | 2 poppr-1.1.5/poppr/man/hierarchy-methods.Rd | 2 poppr-1.1.5/poppr/man/ia.Rd | 2 poppr-1.1.5/poppr/man/info_table.Rd | 2 poppr-1.1.5/poppr/man/informloci.Rd | 2 poppr-1.1.5/poppr/man/is.genclone.Rd | 2 poppr-1.1.5/poppr/man/locus_table.Rd | 2 poppr-1.1.5/poppr/man/missingno.Rd | 2 poppr-1.1.5/poppr/man/mlg.Rd | 2 poppr-1.1.5/poppr/man/monpop.Rd | 4 poppr-1.1.5/poppr/man/partial_clone.Rd | 2 poppr-1.1.5/poppr/man/plot_poppr_msn.Rd | 2 poppr-1.1.5/poppr/man/poppr-package.Rd | 2 poppr-1.1.5/poppr/man/poppr.Rd | 2 poppr-1.1.5/poppr/man/poppr.all.Rd | 2 poppr-1.1.5/poppr/man/poppr.amova.Rd | 2 poppr-1.1.5/poppr/man/poppr.msn.Rd | 2 poppr-1.1.5/poppr/man/popsub.Rd | 2 poppr-1.1.5/poppr/man/population-methods.Rd | 2 poppr-1.1.5/poppr/man/private_alleles.Rd | 2 poppr-1.1.5/poppr/man/read.genalex.Rd | 2 poppr-1.1.5/poppr/man/recode_polyploids.Rd | 2 poppr-1.1.5/poppr/man/shufflepop.Rd | 2 poppr-1.1.5/poppr/man/splitcombine.Rd | 2 poppr-1.1.5/poppr/tests/testthat/test-values.R | 11 + poppr-1.1.5/poppr/vignettes/algo.Rnw | 2 poppr-1.1.5/poppr/vignettes/poppr_manual-concordance.tex | 2 poppr-1.1.5/poppr/vignettes/poppr_manual.Rnw | 2 63 files changed, 156 insertions(+), 168 deletions(-)
Title: Scores Features for Feature Selection
Description: For each feature, a score is computed that can be useful
for feature selection. Several random subsets are sampled from
the input data and for each random subset, various linear
models are fitted using lars method. A score is assigned to
each feature based on the tendency of LASSO in including that
feature in the models.Finally, the average score and the models
are returned as the output. The features with relatively low
scores are recommended to be ignored because they can lead to
overfitting of the model to the training data. Moreover, for
each random subset, the best set of features in terms of global
error is returned. They are useful for applying Bolasso, the
alternative feature selection method that recommends the
intersection of features subsets.
Author: Habil Zare
Maintainer: Habil Zare <zare@txstate.edu>
Diff between FeaLect versions 1.8 dated 2015-03-08 and 1.10 dated 2015-05-12
DESCRIPTION | 6 MD5 | 10 - R/FeaLect.R | 359 ++++++++++++++++++++++----------------------- R/compute.logistic.score.R | 41 ++--- R/input.check.FeaLect.R | 90 +++++------ R/train.doctor.R | 348 +++++++++++++++++++++---------------------- 6 files changed, 425 insertions(+), 429 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-19 2.15.1.0
2012-02-18 2.14.1.6
2012-02-12 2.14.1.5
2012-02-08 2.14.1.3
2012-01-29 2.14.1.0
2012-01-16 2.14.0.3
2012-01-10 2.14.0.2
2011-11-16 2.14.0.0
2011-10-26 2.13.2.2
2011-10-04 2.13.2.1
2011-09-29 2.13.1.6
2011-09-07 2.13.1.4
2011-07-25 2.13.1.3
2011-07-23 2.13.1.0
2011-04-11 2.12.2.3
2011-04-10 2.12.2.2
2011-03-06 2.12.2.0
2011-02-22 2.12.1.1
2011-02-20 2.12.1.0
2010-11-07 2.12.0.0
2010-06-26 2.11.1.0
2010-05-22 2.11.0.0
2010-01-29 2.10.1.1
2010-01-18 2.10.1.0
2009-11-03 2.10.0.0
2009-10-16 2.9.2.8
2009-10-11 2.9.2.7
2009-10-01 2.9.2.5
2009-09-28 2.9.2.3
2009-09-23 2.9.2.2
2009-09-21 2.9.2.1
2009-09-03 2.9.2.0
2009-08-25 2.9.1.7
2009-08-21 2.9.1.6
2009-07-31 2.9.1.5
2009-07-30 2.9.1.4
2009-07-26 2.9.1.3
2009-07-18 2.9.1.2
2009-06-25 2.9.0.1
2009-06-25 2.9.0.2
2009-06-24 2.9.0.0
2009-02-15 2.8.1.1
2009-02-04 2.8.1.0
2008-12-14 2.8.0.1
2008-12-01 2.8.0.0
2008-10-07 2.7.2.3
2008-09-07 2.7.2.1
2008-07-11 2.7.1.2
2008-07-08 2.7.1.1
2008-06-20 2.7.1.0
2008-06-15 2.7.0.4
2008-05-06 2.7.0.3
2008-05-02 2.7.0.2
2008-04-27 2.7.0.1
2008-04-25 2.7.0.0
2008-04-20 2.6.2.11
2008-04-06 2.6.2.10
2008-03-29 2.6.2.8
2008-03-24 2.6.2.7
2008-03-12 2.6.2.6
2008-03-09 2.6.2.5
2008-03-02 2.6.2.3
2008-03-02 2.6.2.4
2008-02-26 2.6.2.2
2008-02-12 2.6.2.0
2008-02-05 2.6.1.7
2008-01-13 2.6.1.6
2007-12-30 2.6.1.5
2007-12-24 2.6.1.3
2007-12-10 2.6.1.1
2007-12-05 2.6.1.0
2007-11-24 2.6.0.5
2007-11-18 2.6.0.4
2007-11-17 2.6.0.3
2007-11-03 2.6.0.2
2007-10-07 2.6.0.1
2007-09-28 2.5.1.5
2007-09-21 2.5.1.4
2007-09-07 2.5.1.3
2007-08-27 2.5.1.2
2007-08-12 2.5.1.1
2007-07-31 2.5.1
2007-07-08 2.5.0.4
2007-06-20 2.5.0.3
Title: Modelling the Population Dynamics of a Stage-Structured Species
in Continuous Time
Description: Provides facilities to implement and run population models of
stage-structured species...
Author: Helen Kettle
Maintainer: David Nutter <david.nutter@bioss.ac.uk>
Diff between stagePop versions 1.0-1 dated 2015-02-03 and 1.1-1 dated 2015-05-12
stagePop-1.0-1/stagePop/inst/doc/Appendix1.pdf |only stagePop-1.0-1/stagePop/inst/doc/Appendix1.pdf.asis |only stagePop-1.0-1/stagePop/inst/doc/Appendix2.pdf |only stagePop-1.0-1/stagePop/inst/doc/Appendix2.pdf.asis |only stagePop-1.0-1/stagePop/inst/doc/Appendix3.pdf |only stagePop-1.0-1/stagePop/inst/doc/Appendix3.pdf.asis |only stagePop-1.0-1/stagePop/vignettes/Appendix1.pdf.asis |only stagePop-1.0-1/stagePop/vignettes/Appendix2.pdf.asis |only stagePop-1.0-1/stagePop/vignettes/Appendix3.pdf.asis |only stagePop-1.1-1/stagePop/DESCRIPTION | 9 +++-- stagePop-1.1-1/stagePop/MD5 | 26 +++++------------ stagePop-1.1-1/stagePop/R/genericPlot.R | 8 +++-- stagePop-1.1-1/stagePop/R/popModel.R | 2 - stagePop-1.1-1/stagePop/build/vignette.rds |binary stagePop-1.1-1/stagePop/inst/DemoFiles/BlowFlies.R | 4 +- stagePop-1.1-1/stagePop/inst/DemoFiles/Briggs.R | 2 + stagePop-1.1-1/stagePop/inst/DemoFiles/ClimateChange.R |only stagePop-1.1-1/stagePop/inst/doc/stagePop.pdf |binary stagePop-1.1-1/stagePop/man/popModel.Rd | 2 - 19 files changed, 27 insertions(+), 26 deletions(-)
Title: Estimation, Simulation and Visualization of Hierarchical
Archimedean Copulae (HAC)
Description: Package provides the estimation of the structure and the parameters, sampling methods and structural plots of Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin <ostap.okhrin@wiwi.hu-berlin.de> and Alexander Ristig <ristigal@hu-berlin.de>
Maintainer: Alexander Ristig <ristigal@hu-berlin.de>
Diff between HAC versions 1.0-2 dated 2015-02-05 and 1.0-3 dated 2015-05-12
DESCRIPTION | 12 +- MD5 | 32 +++--- NAMESPACE | 2 R/cdf.r | 3 R/constructor.r | 19 ++-- R/estimate.r | 232 +++++++++++++++++++++++++++++++++++++++---------- R/functions.r | 8 - R/pdf.r | 170 ++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/ChangeLog | 10 ++ inst/doc/HAC.R | 26 ++--- inst/doc/HAC.Rnw | 18 ++- inst/doc/HAC.pdf |binary man/dHAC.Rd | 195 ++++++++++++++++++++--------------------- man/estimate.copula.Rd | 161 +++++++++++++++++----------------- vignettes/HAC.Rnw | 18 ++- vignettes/ref.bib | 23 +++- 17 files changed, 613 insertions(+), 316 deletions(-)
Title: Functions for Processing Minute-to-Minute Accelerometer Data
Description: A collection of functions that perform operations on time-series accelerometer data, such as identify non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented. Most of the functions are written in C++ for efficiency.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen <vandomed@gmail.com>
Diff between accelerometry versions 2.2.4 dated 2014-12-09 and 2.2.5 dated 2015-05-12
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/RcppExports.R | 13 +++++++------ man/accelerometry-package.Rd | 4 ++-- src/RcppExports.cpp | 4 ++-- src/intensities.cpp | 2 +- 6 files changed, 23 insertions(+), 22 deletions(-)
Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
'mvabund-package.Rd' for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: David Warton <David.Warton@unsw.edu.au>
Diff between mvabund versions 3.9.3 dated 2014-11-02 and 3.10.4 dated 2015-05-12
DESCRIPTION | 17 - MD5 | 74 +++-- NAMESPACE | 41 ++- R/AllClass.R | 2 R/anova.manyany.R | 116 +++++--- R/anova.manyglm.R | 43 ++- R/anova.manylm.R | 546 ++++++++++++++++++++-------------------- R/anova.traitglm.R |only R/cv.glm1path.R |only R/default.plot.manyglm.R | 108 +++---- R/default.plot.manylm.R | 20 - R/default.plot.mvformula.R | 24 - R/default.print.anova.manyglm.R | 24 + R/glm1.R |only R/glm1path.R |only R/manyany.R | 275 ++++++++++++++------ R/manyglm.R | 5 R/plot.manylm.R | 8 R/plot.mvformula.R | 6 R/plotFormulafeature.R | 4 R/predict.manyglm.R | 44 ++- R/predict.manylm.R | 1 R/predict.traitglm.R |only R/qordinal.R |only R/residuals.glm1path.R |only R/residuals.manyglm.R | 3 R/traitglm.R |only data/antTraits.RData |only man/anova.manyany.Rd | 21 - man/anova.manyglm.Rd | 13 man/anova.manylm.Rd | 2 man/anova.traitglm.Rd |only man/antTraits.Rd |only man/cv.glm1path.Rd |only man/glm1.Rd |only man/glm1path.Rd |only man/manyany.Rd | 49 +++ man/manyglm.Rd | 79 ++--- man/mvabund-package.Rd | 59 ++-- man/plot.manyany.Rd | 11 man/predict.traitglm.Rd |only man/residuals.manyglm.Rd | 13 man/traitglm.Rd |only src/Makevars.in | 11 src/Makevars.win | 4 src/RtoAnovaCpp.cpp | 4 46 files changed, 966 insertions(+), 661 deletions(-)
Title: Dual-Agent Dose Escalation for Phase I Trials using the PIPE
Design
Description: Implements the Product of Independent beta Probabilities dose Escalation (PIPE) design for dual-agent Phase I trials as described in Mander AP, Sweeting MJ. Statistics in Medicine 2015. doi: 10.1002/sim.6434.
Author: Michael Sweeting
Maintainer: Michael Sweeting <mjs212@medschl.cam.ac.uk>
Diff between pipe.design versions 0.1 dated 2015-03-19 and 0.2 dated 2015-05-12
pipe.design-0.1/pipe.design/R/pipe.design_0.1.R |only pipe.design-0.2/pipe.design/DESCRIPTION | 8 - pipe.design-0.2/pipe.design/MD5 | 12 - pipe.design-0.2/pipe.design/NAMESPACE | 4 pipe.design-0.2/pipe.design/NEWS | 7 + pipe.design-0.2/pipe.design/R/pipe.design_0.2.R |only pipe.design-0.2/pipe.design/man/pipe.design.Rd | 148 ++++++++++++------------ pipe.design-0.2/pipe.design/man/print.pipe.Rd | 26 ++-- 8 files changed, 106 insertions(+), 99 deletions(-)
Title: Data from the US National Health and Nutrition Examination Study
Description: Body Shape and related measurements from the US National Health
and Nutrition Examination Survey (NHANES, 1999-2004). See
http://www.cdc.gov/nchs/nhanes.htm for details.
Author: Randall Pruim <rpruim@calvin.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between NHANES versions 1.0 dated 2014-08-22 and 2.0 dated 2015-05-12
DESCRIPTION | 15 +- MD5 | 15 +- NAMESPACE | 1 R/datasets.R | 340 +++++++++++++++++++++++++++++++++++++++++++-------- README.md | 14 +- data/NHANES.rda |binary data/NHANESraw.rda |only data/datalist | 1 man/NHANES.Rd | 349 +++++++++++++++++++++++++++++++++++++++++++++-------- 9 files changed, 611 insertions(+), 124 deletions(-)
Title: Management, Display, and Processing of Medical Imaging Data
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
Author: Brice Ozenne
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>
Diff between MRIaggr versions 1.1 dated 2015-04-22 and 1.1.2 dated 2015-05-12
MRIaggr-1.1.2/MRIaggr/DESCRIPTION | 13 MRIaggr-1.1.2/MRIaggr/MD5 | 157 +- MRIaggr-1.1.2/MRIaggr/NAMESPACE | 18 MRIaggr-1.1.2/MRIaggr/R/Associated_functions.R | 92 + MRIaggr-1.1.2/MRIaggr/R/Class_Carto3D.R | 56 MRIaggr-1.1.2/MRIaggr/R/Class_MRIaggr.R | 893 +++++++-------- MRIaggr-1.1.2/MRIaggr/R/Generic_functions.R | 114 - MRIaggr-1.1.2/MRIaggr/R/RcppExports.R | 4 MRIaggr-1.1.2/MRIaggr/data/MRIaggr.Pat1_red.RData |binary MRIaggr-1.1.2/MRIaggr/demo/00Index | 2 MRIaggr-1.1.2/MRIaggr/demo/Analysis.R | 8 MRIaggr-1.1.2/MRIaggr/demo/ExtractNifti.R |only MRIaggr-1.1.2/MRIaggr/demo/preProcessing.R | 24 MRIaggr-1.1.2/MRIaggr/inst/List_of_arguments.R | 614 +++++----- MRIaggr-1.1.2/MRIaggr/inst/NEWS | 18 MRIaggr-1.1.2/MRIaggr/inst/Tests/Test2-1_Carto3D.R | 12 MRIaggr-1.1.2/MRIaggr/inst/Tests/Test2-1_IRMaggr.R | 114 - MRIaggr-1.1.2/MRIaggr/inst/Tests/Test2-3_fctsAssociees.R | 30 MRIaggr-1.1.2/MRIaggr/inst/Tests/Test2-4_fctsGR.R | 4 MRIaggr-1.1.2/MRIaggr/inst/Tests/Test2-5_Sweave.R | 4 MRIaggr-1.1.2/MRIaggr/inst/calcSigmaGR.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/Carto3D-class.Rd | 8 MRIaggr-1.1.2/MRIaggr/man/Carto3D2MRIaggr.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/MRIaggr-class.Rd | 34 MRIaggr-1.1.2/MRIaggr/man/MRIaggr.Pat1_red.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/allocClinic.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocContrast.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocDescStats.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocHemisphere.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocNormalization.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocTable.Rd |only MRIaggr-1.1.2/MRIaggr/man/array2df.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/calcBrainMask.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/calcContro_cpp.Rd | 16 MRIaggr-1.1.2/MRIaggr/man/calcControlateral.Rd | 32 MRIaggr-1.1.2/MRIaggr/man/calcDistTissues.Rd | 5 MRIaggr-1.1.2/MRIaggr/man/calcFilter.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/calcGR.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcGroupsMask.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcGroupsW.Rd | 3 MRIaggr-1.1.2/MRIaggr/man/calcHemi_cpp.Rd | 11 MRIaggr-1.1.2/MRIaggr/man/calcHemisphere.Rd | 30 MRIaggr-1.1.2/MRIaggr/man/calcNormalization.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcRegionaContrast.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcSmoothMask.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/calcTableHypoReperf.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcThresholdMRIaggr.Rd | 5 MRIaggr-1.1.2/MRIaggr/man/calcTissueType.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/calcW.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/constCarto3D.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/constCompressMRIaggr.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/constMRIaggr.Rd | 8 MRIaggr-1.1.2/MRIaggr/man/constReduceMRIaggr.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/df2array.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/initIndex.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/multiplot.Rd | 10 MRIaggr-1.1.2/MRIaggr/man/outline.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/outlineMRIaggr.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/plotDistClass.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/pointsHemisphere.Rd | 8 MRIaggr-1.1.2/MRIaggr/man/readMRI.Rd | 10 MRIaggr-1.1.2/MRIaggr/man/selectClinic.Rd | 5 MRIaggr-1.1.2/MRIaggr/man/selectContrast.Rd | 28 MRIaggr-1.1.2/MRIaggr/man/selectCoords.Rd | 2 MRIaggr-1.1.2/MRIaggr/man/selectDescStats.Rd | 8 MRIaggr-1.1.2/MRIaggr/man/selectHemispheres.Rd | 7 MRIaggr-1.1.2/MRIaggr/man/selectMidplane.Rd | 4 MRIaggr-1.1.2/MRIaggr/man/selectNormalization.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/selectParameter.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/selectTable.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/selectVoxelDim.Rd | 20 MRIaggr-1.1.2/MRIaggr/man/selectVoxelSize.Rd | 12 MRIaggr-1.1.2/MRIaggr/man/summary.MRIaggr.Rd | 18 MRIaggr-1.1.2/MRIaggr/man/supprContrast.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/supprDescStats.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/writeMRI.Rd | 6 MRIaggr-1.1.2/MRIaggr/man/writeMRIaggr.Rd | 4 MRIaggr-1.1.2/MRIaggr/src/Associated_functions.cpp | 213 ++- MRIaggr-1.1.2/MRIaggr/src/RcppExports.cpp | 7 MRIaggr-1.1.2/MRIaggr/tests/additionalTest |only MRIaggr-1.1/MRIaggr/demo/ExtractNifty.R |only MRIaggr-1.1/MRIaggr/man/affectClinic.Rd |only MRIaggr-1.1/MRIaggr/man/affectContrast.Rd |only MRIaggr-1.1/MRIaggr/man/affectDescStats.Rd |only MRIaggr-1.1/MRIaggr/man/affectHemisphere.Rd |only MRIaggr-1.1/MRIaggr/man/affectNormalization.Rd |only MRIaggr-1.1/MRIaggr/man/affectTable.Rd |only 87 files changed, 1508 insertions(+), 1291 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.2 dated 2015-04-29 and 0.2.1 dated 2015-05-12
ChangeLog | 6 +++++ DESCRIPTION | 6 ++--- MD5 | 20 +++++++++---------- NEWS | 5 ++++ R/0_classesAndMethods.R | 3 +- build/vignette.rds |binary inst/CITATION | 4 +-- inst/doc/an_introduction_to_markovchain_package.Rnw | 2 - inst/doc/an_introduction_to_markovchain_package.pdf |binary tests/testthat/testBasic1.R | 10 +++++++++ vignettes/an_introduction_to_markovchain_package.Rnw | 2 - 11 files changed, 40 insertions(+), 18 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman <Rob.Hyndman@monash.edu> with contributions from
George Athanasopoulos, Slava Razbash, Drew Schmidt, Zhenyu Zhou, Yousaf Khan,
Christoph Bergmeir, Earo Wang
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 6.0 dated 2015-05-09 and 6.1 dated 2015-05-12
ChangeLog | 3 ++ DESCRIPTION | 8 ++--- MD5 | 8 ++--- R/bootstrap.R | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-- R/newarima2.R | 42 +++++++++++++++++++++++++++-- 5 files changed, 132 insertions(+), 12 deletions(-)
Title: Hierarchical Independent Component Analysis: a Multi-Scale
Sparse Non-Orthogonal Data-Driven Basis
Description: It implements HICA (Hierarchical Independent Component Analysis) algorithm. This approach, obtained through the integration between treelets and Independent Component Analysis, is able to provide a multi-scale non-orthogonal data-driven basis, whose elements have a phenomenological interpretation according to the problem under study.
Author: Piercesare Secchi, Simone Vantini, and Paolo Zanini
Maintainer: Paolo Zanini <paolo.zanini@polimi.it>
Diff between fastHICA versions 1.0 dated 2014-01-16 and 1.0.2 dated 2015-05-12
DESCRIPTION | 14 ++--- MD5 | 6 +- R/energy_hica.R | 138 ++++++++++++++++++++++++++--------------------------- man/energy_hica.Rd | 2 4 files changed, 80 insertions(+), 80 deletions(-)
Title: Fuzzy Clustering
Description: Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.
Author: Paolo Giordani, Maria Brigida Ferraro
Maintainer: Paolo Giordani <paolo.giordani@uniroma1.it>
Diff between fclust versions 1.1 dated 2015-01-31 and 1.1.1 dated 2015-05-12
fclust-1.1.1/fclust/DESCRIPTION | 10 +++++----- fclust-1.1.1/fclust/MD5 | 5 +++-- fclust-1.1.1/fclust/R/fclust.R |only fclust-1.1.1/fclust/inst |only fclust-1.1/fclust/R/Fclust.R |only 5 files changed, 8 insertions(+), 7 deletions(-)
Title: BiCluster Algorithms
Description: The main function biclust provides several algorithms to
find biclusters in two-dimensional data: Cheng and Church,
Spectral, Plaid Model, Xmotifs and Bimax. In addition, the
package provides methods for data preprocessing (normalization
and discretisation), visualisation, and validation of bicluster
solutions.
Author: Sebastian Kaiser, Rodrigo Santamaria, Tatsiana Khamiakova,
Martin Sill, Roberto Theron, Luis Quintales, Friedrich
Leisch and Ewoud De Troyer.
Maintainer: Sebastian Kaiser <Sebastian.Kaiser@stat.uni-muenchen.de>
Diff between biclust versions 1.1.0 dated 2015-03-19 and 1.2.0 dated 2015-05-12
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/plaid.r | 2 +- data/BicatYeast.rda |binary data/EisenYeast.rda |binary data/SyntrenEcoli.rda |binary src/rbimax.c | 12 ++++++++---- 7 files changed, 21 insertions(+), 17 deletions(-)
Title: Relative Risk Regression Using the Log-Binomial Model
Description: Methods for fitting log-link GLMs and GAMs to binomial data,
using EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe <mark.donoghoe@mq.edu.au>
Maintainer: Mark W. Donoghoe <mark.donoghoe@mq.edu.au>
Diff between logbin versions 1.0 dated 2014-10-16 and 1.2 dated 2015-05-12
ChangeLog | 10 ++++- DESCRIPTION | 18 ++++----- MD5 | 44 +++++++++++------------ man/B.Iso.Rd | 6 +-- man/anova.logbin.Rd | 10 ++--- man/confint.logbin.Rd | 4 +- man/contr.isotonic.rev.Rd | 19 +++++----- man/conv.test.Rd | 8 ++-- man/interpret.logbin.smooth.Rd | 4 +- man/logbin-package.Rd | 32 ++++++++--------- man/logbin.Rd | 77 ++++++++++++++++++++--------------------- man/logbin.allref.Rd | 38 ++++++++++---------- man/logbin.control.Rd | 10 ++--- man/logbin.design.Rd | 12 +++--- man/logbin.smooth.Rd | 45 +++++++++++------------ man/logbin.smooth.allref.Rd | 30 +++++++-------- man/logbin.smooth.design.Rd | 30 +++++++-------- man/nplbin.Rd | 32 ++++++++--------- man/plot.logbin.smooth.Rd | 8 ++-- man/predict.logbin.Rd | 10 ++--- man/predict.logbin.smooth.Rd | 8 ++-- man/summary.logbin.Rd | 14 +++---- man/vcov.logbin.Rd | 2 - 23 files changed, 240 insertions(+), 231 deletions(-)
Title: Additive Regression for Discrete Data
Description: Methods for fitting identity-link GLMs and GAMs to discrete data,
using EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe <mark.donoghoe@mq.edu.au>
Maintainer: Mark W. Donoghoe <mark.donoghoe@mq.edu.au>
Diff between addreg versions 1.2 dated 2014-10-29 and 2.0 dated 2015-05-12
addreg-1.2/addreg/R/bin.identity.r |only addreg-2.0/addreg/ChangeLog | 8 + addreg-2.0/addreg/DESCRIPTION | 15 +- addreg-2.0/addreg/MD5 | 72 +++++++------ addreg-2.0/addreg/NAMESPACE | 5 addreg-2.0/addreg/R/addbin.r | 2 addreg-2.0/addreg/R/addreg.allref.r | 15 ++ addreg-2.0/addreg/R/addreg.r | 33 ++++-- addreg-2.0/addreg/R/addreg.smooth.allref.r | 2 addreg-2.0/addreg/R/addreg.smooth.r | 20 ++- addreg-2.0/addreg/R/negbin1.r |only addreg-2.0/addreg/R/nnnegbin.r |only addreg-2.0/addreg/R/nnpois.r | 2 addreg-2.0/addreg/R/predict.addreg.r | 1 addreg-2.0/addreg/R/print.addreg.r |only addreg-2.0/addreg/R/print.summary.addreg.r | 11 +- addreg-2.0/addreg/R/summary.addreg.r | 45 +++++++- addreg-2.0/addreg/man/B.Iso.Rd | 6 - addreg-2.0/addreg/man/addbin.Rd | 22 ++-- addreg-2.0/addreg/man/addreg-package.Rd | 58 +++++------ addreg-2.0/addreg/man/addreg.Rd | 120 +++++++++++++---------- addreg-2.0/addreg/man/addreg.allref.Rd | 46 ++++---- addreg-2.0/addreg/man/addreg.control.Rd | 20 +-- addreg-2.0/addreg/man/addreg.design.Rd | 12 +- addreg-2.0/addreg/man/addreg.smooth.Rd | 59 +++++------ addreg-2.0/addreg/man/addreg.smooth.allref.Rd | 32 +++--- addreg-2.0/addreg/man/addreg.smooth.design.Rd | 30 ++--- addreg-2.0/addreg/man/anova.addreg.Rd | 12 +- addreg-2.0/addreg/man/confint.addreg.Rd | 4 addreg-2.0/addreg/man/contr.isotonic.Rd | 12 +- addreg-2.0/addreg/man/conv.test.Rd | 6 - addreg-2.0/addreg/man/interpret.addreg.smooth.Rd | 4 addreg-2.0/addreg/man/negbin1.Rd |only addreg-2.0/addreg/man/nnnegbin.Rd |only addreg-2.0/addreg/man/nnpois.Rd | 52 ++++----- addreg-2.0/addreg/man/plot.addreg.smooth.Rd | 10 - addreg-2.0/addreg/man/predict.addreg.Rd | 10 - addreg-2.0/addreg/man/predict.addreg.smooth.Rd | 8 - addreg-2.0/addreg/man/summary.addreg.Rd | 23 ++-- addreg-2.0/addreg/man/vcov.addreg.Rd | 2 40 files changed, 444 insertions(+), 335 deletions(-)
Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while controlling false discovery rate for RNA-seq experimental design. Our procedure depends on the Voom method proposed for RNA-seq data analysis by Law et al. (2014) and the sample size calculation method proposed for microarray experiments by Liu and Hwang (2007). We develop a set of functions that calculates appropriate sample sizes for two-sample t-test for RNA-seq experiments with fixed or varied set of parameters. The outputs also contain a plot of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes. To install this package, please use "source('http://bioconductor.org/biocLite.R'); biocLite('ssizeRNA', type = 'source')".
Author: Ran Bi <biran@iastate.edu>, Peng Liu <pliu@iastate.edu>
Maintainer: Ran Bi <biran@iastate.edu>
Diff between ssizeRNA versions 1.1.1 dated 2015-04-29 and 1.1.2 dated 2015-05-12
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 2 +- man/check.power.Rd | 2 +- man/sim.counts.Rd | 2 +- man/ssize.twoSampVaryDelta.Rd | 2 +- man/ssizeRNA_single.Rd | 2 +- man/ssizeRNA_vary.Rd | 2 +- 8 files changed, 19 insertions(+), 19 deletions(-)