Title: Functions for the Analysis of IBD Haplo Output
Description: Functions to analyze, plot, and store the output of running IBD_Haplo software package. More information regarding IBD_Haplo can be found at http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml.
Author: Marshall Brown, Fiona Grimson
Maintainer: Fiona Grimson
Diff between IBDhaploRtools versions 1.7 dated 2014-07-23 and 1.8 dated 2015-02-16
DESCRIPTION | 16 +++++++-------- MD5 | 30 ++++++++++++++--------------- R/ibdhap.make.calls.R | 4 +-- R/ibdhap.make.true.R | 25 ++++++++++++++++++++---- build/vignette.rds |binary data/ids_phased.RData |binary data/ids_unphased.RData |binary data/posvec.RData |binary data/qibd_phased.RData |binary data/qibd_unphased.RData |binary data/trueibd_phased.RData |binary inst/doc/IBDhaploRtools_tutorial.R | 2 - inst/doc/IBDhaploRtools_tutorial.Rnw | 35 +++++++++++++++++++--------------- inst/doc/IBDhaploRtools_tutorial.pdf |binary man/IBDhaploRtools-package.Rd | 4 +-- vignettes/IBDhaploRtools_tutorial.Rnw | 35 +++++++++++++++++++--------------- 16 files changed, 89 insertions(+), 62 deletions(-)
More information about IBDhaploRtools at CRAN
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Title: Random Uniform Forests for Classification, Regression and
Unsupervised Learning
Description: Ensemble model, for classification, regression
and unsupervised learning, based on a forest of unpruned
and randomized binary decision trees. Each tree is grown
by sampling, with replacement, a set of variables at each node.
Each cut-point is generated randomly, according to the continuous
Uniform distribution. For each tree, data are either bootstrapped
or subsampled. The unsupervised mode introduces clustering, dimension reduction
and variable importance, using a three-layer engine. Random Uniform Forests are mainly
aimed to lower correlation between trees (or trees residuals), to provide a deep analysis
of variable importance and to allow native distributed and incremental learning.
Author: Saip Ciss
Maintainer: Saip Ciss
Diff between randomUniformForest versions 1.1.2 dated 2015-01-06 and 1.1.5 dated 2015-02-16
randomUniformForest-1.1.2/randomUniformForest/man/combine.unsupervised.Rd |only randomUniformForest-1.1.5/randomUniformForest/DESCRIPTION | 8 randomUniformForest-1.1.5/randomUniformForest/MD5 | 50 randomUniformForest-1.1.5/randomUniformForest/NAMESPACE | 6 randomUniformForest-1.1.5/randomUniformForest/NEWS | 57 randomUniformForest-1.1.5/randomUniformForest/R/DecisionTreesCPP.R | 23 randomUniformForest-1.1.5/randomUniformForest/R/OnliningRandomUniformForests.R | 44 randomUniformForest-1.1.5/randomUniformForest/R/RandomUniformForestsCPP.R | 1142 +++++++--- randomUniformForest-1.1.5/randomUniformForest/R/genericFunctions.R | 68 randomUniformForest-1.1.5/randomUniformForest/inst/doc/VariableImportanceInRandomUniformForests.pdf |binary randomUniformForest-1.1.5/randomUniformForest/inst/doc/randomUniformForestsOverview.pdf |binary randomUniformForest-1.1.5/randomUniformForest/man/clusterAnalysis.Rd |only randomUniformForest-1.1.5/randomUniformForest/man/clusteringObservations.Rd | 39 randomUniformForest-1.1.5/randomUniformForest/man/combineUnsupervised.Rd |only randomUniformForest-1.1.5/randomUniformForest/man/fillNA2.randomUniformForest.Rd | 97 randomUniformForest-1.1.5/randomUniformForest/man/generic.cv.Rd | 4 randomUniformForest-1.1.5/randomUniformForest/man/importance.randomUniformForest.Rd | 147 - randomUniformForest-1.1.5/randomUniformForest/man/internalFunctions.Rd | 3 randomUniformForest-1.1.5/randomUniformForest/man/modifyClusters.Rd | 2 randomUniformForest-1.1.5/randomUniformForest/man/partialDependenceBetweenPredictors.Rd | 66 randomUniformForest-1.1.5/randomUniformForest/man/predict.randomUniformForest.Rd | 8 randomUniformForest-1.1.5/randomUniformForest/man/rUniformForest.big.Rd | 2 randomUniformForest-1.1.5/randomUniformForest/man/randomUniformForest-package.Rd | 153 + randomUniformForest-1.1.5/randomUniformForest/man/randomUniformForest.Rd | 268 +- randomUniformForest-1.1.5/randomUniformForest/man/reSMOTE.Rd | 147 - randomUniformForest-1.1.5/randomUniformForest/man/splitClusters.Rd |only randomUniformForest-1.1.5/randomUniformForest/man/unsupervised.randomUniformForest.Rd | 335 +- randomUniformForest-1.1.5/randomUniformForest/man/update.unsupervised.Rd | 25 28 files changed, 1932 insertions(+), 762 deletions(-)
More information about randomUniformForest at CRAN
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Title: Wild Binary Segmentation for Multiple Change-Point Detection
Description: Provides efficient implementation of the Wild Binary Segmentation and Binary
Segmentation algorithms for estimation of the number and locations of
multiple change-points in the piecewise constant function plus Gaussian
noise model.
Author: Rafal Baranowski and Piotr Fryzlewicz
Maintainer: Rafal Baranowski
Diff between wbs versions 1.2 dated 2014-08-08 and 1.3 dated 2015-02-16
wbs-1.2/wbs/R/mean.from.cpt.R |only wbs-1.2/wbs/man/mean.from.cpt.Rd |only wbs-1.3/wbs/DESCRIPTION | 12 - wbs-1.3/wbs/MD5 | 45 ++--- wbs-1.3/wbs/NAMESPACE | 4 wbs-1.3/wbs/R/changepoints.R | 2 wbs-1.3/wbs/R/means.between.cpt.R |only wbs-1.3/wbs/R/plot.R | 4 wbs-1.3/wbs/R/sbs.R | 7 wbs-1.3/wbs/R/wbs.R | 25 ++- wbs-1.3/wbs/man/bic.penalty.Rd | 2 wbs-1.3/wbs/man/changepoints.Rd | 8 - wbs-1.3/wbs/man/fixed.intervals.Rd | 2 wbs-1.3/wbs/man/mbic.penalty.Rd | 2 wbs-1.3/wbs/man/means.between.cpt.Rd |only wbs-1.3/wbs/man/plot.sbs.Rd | 2 wbs-1.3/wbs/man/plot.wbs.Rd | 2 wbs-1.3/wbs/man/print.sbs.Rd | 2 wbs-1.3/wbs/man/print.wbs.Rd | 2 wbs-1.3/wbs/man/random.intervals.Rd | 2 wbs-1.3/wbs/man/sbs.Rd | 2 wbs-1.3/wbs/man/ssic.penalty.Rd | 2 wbs-1.3/wbs/man/wbs-package.Rd | 2 wbs-1.3/wbs/man/wbs.Rd | 6 wbs-1.3/wbs/src/wbs.c | 276 +++++++++++++++-------------------- wbs-1.3/wbs/src/wbs.h |only 26 files changed, 196 insertions(+), 215 deletions(-)
Title: An R Convenience Layer for CouchDB
Description: Provides a collection of functions for basic
database and document management operations such as add, get, list or
delete. Every cdbFunction() gets and returns a list() containing the
connection setup.
Such a list (in the documentation mostly called cdb) can be generated by
cdb <- cdbIni(). Then, the list cdb provides some functions respectively
functionality e.g cdb$baseUrl() or cdb$getDocRev().
Author: Thomas Bock
Maintainer: Thomas Bock
Diff between R4CouchDB versions 0.6 dated 2014-08-12 and 0.7.1 dated 2015-02-16
DESCRIPTION | 17 ++-- MD5 | 58 ++++++++-------- NAMESPACE | 3 R/cdbAddDocS.R |only R/cdbDeleteDoc.R | 2 R/cdbGetConfig.R | 4 - R/cdbGetDoc.R | 2 R/cdbGetList.R | 3 R/cdbGetUuid.R | 3 R/cdbGetUuidS.R | 4 - R/cdbGetView.R | 4 - R/cdbIni.R | 167 ++++++++++++++++++++++++++---------------------- R/cdbListDB.R | 6 - R/cdbMakeDB.R | 1 R/cdbRemoveDB.R | 1 R/cdbUpdateDoc.R | 8 -- man/cdbAddAttachment.Rd | 3 man/cdbAddDoc.Rd | 3 man/cdbAddDocS.Rd |only man/cdbDeleteDoc.Rd | 6 - man/cdbGetConfig.Rd | 7 -- man/cdbGetDoc.Rd | 6 - man/cdbGetList.Rd | 8 -- man/cdbGetUuid.Rd | 7 -- man/cdbGetUuidS.Rd | 7 -- man/cdbGetView.Rd | 8 -- man/cdbIni.Rd | 5 - man/cdbListDB.Rd | 10 -- man/cdbMakeDB.Rd | 6 - man/cdbRemoveDB.Rd | 6 - man/cdbUpdateDoc.Rd | 7 -- 31 files changed, 167 insertions(+), 205 deletions(-)
Title: Subnetwork Integration for Multi-Modal Signatures
Description: Algorithms to create prognostic biomarkers using biological networks.
Author: Syed Haider, Michal Grzadkowski, Paul C. Boutros
Maintainer: Syed Haider
Diff between SIMMS versions 0.0.1 dated 2013-06-11 and 1.0.0 dated 2015-02-16
mRNA_abundance.txt | 6 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/DESCRIPTION | 15 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/MD5 | 116 ++- tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/NAMESPACE | 26 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/calculate.meta.survival.R | 93 +-- tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/calculate.network.coefficients.R | 301 ++++++--- tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.KM.plot.R | 12 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.classifier.multivariate.R |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.classifier.univariate.R |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.sensitivity.plot.R | 9 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.survivalplots.R | 225 +++---- tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.survobj.R | 7 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/derive.network.features.R | 307 +++++----- tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/dichotomize.meta.dataset.R | 11 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/fit.coxmodel.R | 135 +++- tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/fit.interaction.model.R | 124 ++-- tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/fit.survivalmodel.R | 34 - tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/get.adjacency.matrix.R | 2 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/get.program.defaults.R | 2 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/load.cancer.datasets.R | 7 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/pred.survivalmodel.R | 80 -- tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/prepare.training.validation.datasets.R | 241 +++++-- tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/build |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/doc |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.BRCA |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.COADREAD |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.GBM |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.KIRC |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.OV |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/Mammaprint |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/Oncotypedx |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/PI3K |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/test/pathway_based_networks_flattened.txt | 18 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/test/pathway_based_sub_networks.txt | 19 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/test/pathway_based_sub_networks_all.txt | 19 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/testdata/Breastdata1/mRNA_abundance.txt | 6 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/SIMMS.Rd | 14 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/calculate.meta.survival.Rd | 4 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/calculate.network.coefficients.Rd | 5 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.KM.plot.Rd | 4 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.classifier.multivariate.Rd |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.classifier.univariate.Rd |only tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.survivalplots.Rd | 14 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.survobj.Rd | 6 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/derive.network.features.Rd | 9 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/dichotomize.meta.dataset.Rd | 4 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/fit.coxmodel.Rd | 6 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/fit.interaction.model.Rd | 78 +- tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/fit.survivalmodel.Rd | 5 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/get.program.defaults.Rd | 2 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/load.cancer.datasets.Rd | 7 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/pred.survivalmodel.Rd | 10 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/prepare.training.validation.datasets.Rd | 10 tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/vignettes |only 55 files changed, 1200 insertions(+), 793 deletions(-)
Title: Supervised Component Generalized Linear Regression
Description: The Fisher Scoring Algorithm is extended so as to combine Partial Least Squares
regression with Generalized Linear Model estimation in the multivariate context.
Author: Guillaume Cornu [cre, aut],
Frederic Mortier [aut],
Catherine Trottier [aut],
Xavier Bry [aut]
Maintainer: Guillaume Cornu
Diff between SCGLR versions 2.0.1 dated 2014-10-14 and 2.0.2 dated 2015-02-16
DESCRIPTION | 30 ++++++++------- MD5 | 84 +++++++++++++++++++++--------------------- NAMESPACE | 4 +- NEWS | 3 + R/critConvergence.r | 2 - R/customize.r | 2 - R/data.r | 2 - R/infoCriterion.r | 28 +++++++------- R/ingUtils.r | 26 ++++++------- R/methods.r | 2 - R/metric.r | 2 - R/multivariateFormula.r | 2 - R/multivariateGlm.r | 8 ++-- R/multivariatePredictGlm.r | 4 +- R/oneComponent.r | 10 +++-- R/package.r | 8 ++-- R/plot.r | 4 +- R/print.r | 2 - R/scglrCrossVal.r | 16 +++----- R/summary.r | 6 +-- build/vignette.rds |binary demo/scglrPrediction.r | 4 +- inst/doc/scglrVignettes.R | 6 +-- inst/doc/scglrVignettes.pdf |binary inst/doc/scglrVignettes.rnw | 8 ++-- inst/examples/exPrediction.r | 4 +- man/barplot.SCGLR.Rd | 3 + man/critConvergence.Rd | 3 + man/customize.Rd | 3 + man/genus.Rd | 5 +- man/infoCriterion.Rd | 3 + man/method.Rd | 3 + man/multivariateFormula.Rd | 3 + man/multivariateGlm.Rd | 5 +- man/multivariatePredictGlm.Rd | 5 +- man/pairs.SCGLR.Rd | 3 + man/plot.SCGLR.Rd | 3 + man/print.SCGLR.Rd | 3 + man/scglr-package.Rd | 7 ++- man/scglr.Rd | 3 + man/scglrCrossVal.Rd | 3 + man/summary.SCGLR.Rd | 3 + vignettes/scglrVignettes.rnw | 8 ++-- 43 files changed, 178 insertions(+), 155 deletions(-)
Title: Data Analysis Tool for Pharmacokinetics
Description: A nonlinear regression program which is
designed to perform model/curve fitting and
model simulations for pharmacokinetics.
Author: Chun-ying Lee, Yung-jin Lee
Maintainer: Yung-jin Lee
Diff between PKfit versions 1.2.4 dated 2014-10-21 and 1.2.5 dated 2015-02-16
PKfit-1.2.4/PKfit/inst/CITATION |only PKfit-1.2.4/PKfit/inst/UserDefinedModels/mymodel.R |only PKfit-1.2.5/PKfit/DESCRIPTION | 18 ++++++++--------- PKfit-1.2.5/PKfit/MD5 | 21 +++++++++----------- PKfit-1.2.5/PKfit/NEWS | 16 ++++++++++++++- PKfit-1.2.5/PKfit/R/description_version.r | 7 +++++- PKfit-1.2.5/PKfit/R/finfu2.R | 3 +- PKfit-1.2.5/PKfit/R/fzero.nolag.R | 2 - PKfit-1.2.5/PKfit/R/mmpk.demo.R | 2 - PKfit-1.2.5/PKfit/R/sinfu1.R | 20 ++++--------------- PKfit-1.2.5/PKfit/R/sinfu2.R | 14 +++---------- PKfit-1.2.5/PKfit/R/zzz.R | 2 - PKfit-1.2.5/PKfit/inst/UserDefinedModels/fitmodel.R |only 13 files changed, 54 insertions(+), 51 deletions(-)
Title: Partial Correlation Coefficient with Information Theory
Description: Apply Partial Correlation coefficient with Information
Theory (PCIT) to a correlation matrix.
The PCIT algorithm identifies meaningful correlations to define
edges in a weighted network. The algorithm can be applied to
any correlation-based network including but not limited to gene
co-expression networks.
To reduce compute time by making use of multiple compute cores,
simply run PCIT on a computer with has multiple cores and also
has the Rmpi package installed. PCIT will then auto-detect the
multicore environment and run in parallel mode without the need
to rewrite your scripts. This makes scripts, using PCIT, portable
across single core (or no Rmpi package installed) computers
which will run in serial mode and multicore (with Rmpi package
installed) computers which will run in parallel mode.
Author: Nathan S. Watson-Haigh
Maintainer: Nathan S. Watson-Haigh
Diff between PCIT versions 1.04-5 dated 2014-01-29 and 1.5-3 dated 2015-02-16
ChangeLog | 39 +++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 24 +++++++++++++++--------- MD5 | 12 ++++++------ R/PCIT.R | 36 ++++++++++++++++++------------------ R/internal.R | 28 ++++++++++++++-------------- README.md | 20 ++++++++++++++++++++ inst/CITATION | 3 +-- 7 files changed, 113 insertions(+), 49 deletions(-)
Title: Chi-Square Tests for Non-Parametric Functional Dependencies
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on chi-square statistics. These tests were designed to reveal causality based on evidence from non-parametric functional dependencies. It implements an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song
Diff between FunChisq versions 1.0 dated 2014-03-07 and 2.0.0 dated 2015-02-16
FunChisq-1.0/FunChisq/INDEX |only FunChisq-2.0.0/FunChisq/DESCRIPTION | 22 +- FunChisq-2.0.0/FunChisq/MD5 | 32 +++ FunChisq-2.0.0/FunChisq/NAMESPACE | 6 FunChisq-2.0.0/FunChisq/NEWS |only FunChisq-2.0.0/FunChisq/R/FunChisq.R | 145 ++++++++++++++--- FunChisq-2.0.0/FunChisq/inst |only FunChisq-2.0.0/FunChisq/man/FunChisq-package.Rd | 76 ++++----- FunChisq-2.0.0/FunChisq/man/cp.fun.chisq.test.Rd |only FunChisq-2.0.0/FunChisq/man/fun.chisq.test.Rd | 188 ++++++++++++++++------- FunChisq-2.0.0/FunChisq/src |only FunChisq-2.0.0/FunChisq/tests |only 12 files changed, 333 insertions(+), 136 deletions(-)
Title: Boosting Functional Regression Models
Description: Regression models for functional data, i.e. scalar-on-function,
function-on-scalar and function-on-function regression models are fitted
using a component-wise gradient boosting algorithm.
Author: Sarah Brockhaus
Maintainer: Sarah Brockhaus
Diff between FDboost versions 0.0-5 dated 2014-04-22 and 0.0-8 dated 2015-02-16
FDboost-0.0-5/FDboost/R/bkroneckerTrafo.R |only FDboost-0.0-5/FDboost/data/datalist |only FDboost-0.0-5/FDboost/data/fuel.RData |only FDboost-0.0-5/FDboost/inst/fuelAllModels |only FDboost-0.0-5/FDboost/man/fuel.Rd |only FDboost-0.0-5/FDboost/vignettes/mboostDevel-inference.R |only FDboost-0.0-8/FDboost/DESCRIPTION | 20 FDboost-0.0-8/FDboost/MD5 | 103 - FDboost-0.0-8/FDboost/NAMESPACE | 5 FDboost-0.0-8/FDboost/R/FDboost.R | 189 + FDboost-0.0-8/FDboost/R/baselearners.R | 1645 +++++++++------- FDboost-0.0-8/FDboost/R/crossvalidation.R | 48 FDboost-0.0-8/FDboost/R/internalsMboost.R |only FDboost-0.0-8/FDboost/R/methods.R | 180 + FDboost-0.0-8/FDboost/R/utilityFunctions.R | 155 + FDboost-0.0-8/FDboost/build/vignette.rds |binary FDboost-0.0-8/FDboost/data/fuelSubset.RData |only FDboost-0.0-8/FDboost/inst/CITATION |only FDboost-0.0-8/FDboost/inst/doc/FLAM_canada.R | 2 FDboost-0.0-8/FDboost/inst/doc/FLAM_canada.Rnw | 2 FDboost-0.0-8/FDboost/inst/doc/FLAM_canada.pdf |binary FDboost-0.0-8/FDboost/inst/doc/FLAM_fuel.R | 3 FDboost-0.0-8/FDboost/inst/doc/FLAM_fuel.Rnw | 3 FDboost-0.0-8/FDboost/inst/doc/FLAM_fuel.pdf |binary FDboost-0.0-8/FDboost/inst/doc/FLAM_viscosity.R | 6 FDboost-0.0-8/FDboost/inst/doc/FLAM_viscosity.Rnw | 6 FDboost-0.0-8/FDboost/inst/doc/FLAM_viscosity.pdf |binary FDboost-0.0-8/FDboost/inst/sim/analyze_results.R | 105 - FDboost-0.0-8/FDboost/inst/sim/run_FDboost.R | 182 + FDboost-0.0-8/FDboost/inst/sim/run_PlotModels.R | 150 - FDboost-0.0-8/FDboost/inst/sim/run_pffr.R | 185 + FDboost-0.0-8/FDboost/inst/sim/run_time.R |only FDboost-0.0-8/FDboost/inst/sim/simfuns.R | 102 FDboost-0.0-8/FDboost/man/FDboost.Rd | 234 +- FDboost-0.0-8/FDboost/man/bbsc.Rd | 168 - FDboost-0.0-8/FDboost/man/bsignal.Rd | 242 +- FDboost-0.0-8/FDboost/man/coef.FDboost.Rd | 81 FDboost-0.0-8/FDboost/man/extract.blg.Rd | 46 FDboost-0.0-8/FDboost/man/fitted.FDboost.Rd | 16 FDboost-0.0-8/FDboost/man/fuelSubset.Rd |only FDboost-0.0-8/FDboost/man/funMRD.Rd | 52 FDboost-0.0-8/FDboost/man/funMSE.Rd | 70 FDboost-0.0-8/FDboost/man/funRsquared.Rd | 79 FDboost-0.0-8/FDboost/man/funplot.Rd | 29 FDboost-0.0-8/FDboost/man/integrationWeights.Rd | 72 FDboost-0.0-8/FDboost/man/o_control.Rd | 25 FDboost-0.0-8/FDboost/man/plot.FDboost.Rd | 111 - FDboost-0.0-8/FDboost/man/plot.validateFDboost.Rd | 86 FDboost-0.0-8/FDboost/man/predict.FDboost.Rd | 56 FDboost-0.0-8/FDboost/man/print.FDboost.Rd | 15 FDboost-0.0-8/FDboost/man/residuals.FDboost.Rd | 18 FDboost-0.0-8/FDboost/man/summary.FDboost.Rd | 15 FDboost-0.0-8/FDboost/man/truncateTime.Rd | 25 FDboost-0.0-8/FDboost/man/validateFDboost.Rd | 222 -- FDboost-0.0-8/FDboost/man/viscosity.Rd | 28 FDboost-0.0-8/FDboost/vignettes/FLAM_canada.Rnw | 2 FDboost-0.0-8/FDboost/vignettes/FLAM_fuel.Rnw | 3 FDboost-0.0-8/FDboost/vignettes/FLAM_viscosity.Rnw | 6 58 files changed, 2749 insertions(+), 2043 deletions(-)
Title: Bayesian Network Feature Finder
Description: Provides a full package of posterior inference, model comparison, and graphical illustration of model fitting. A parallel computing algorithm for the Markov chain Monte Carlo (MCMC) based posterior inference and an Expectation-Maximization (EM) based algorithm for posterior approximation are are developed, both of which greatly reduce the computational time for model inference.
Author: Zhou Lan, Yize Zhao, Jian Kang, Tianwei Yu
Maintainer: Zhou Lan
Diff between BANFF versions 0.2 dated 2015-01-08 and 0.3 dated 2015-02-16
DESCRIPTION | 10 ++-- MD5 | 16 ++++--- NAMESPACE | 13 ++++++ R/All_functions.R | 10 ---- R/main.R | 89 +++++++++++++++++++++++++++++++++++++++---- man/Networks.Fast.Rd | 5 +- man/Networks.STD.Rd | 7 +-- man/plot.Networks.Fast.Rd |only man/plot.Networks.STD.Rd |only man/summary.Networks.Fast.Rd |only man/summary.Networks.STD.Rd |only 11 files changed, 117 insertions(+), 33 deletions(-)
Title: Simulation Tools for Small Area Estimation
Description: Tools for the simulation of data in the context of small area
estimation. Combine all steps of your simulation - from data generation
over drawing samples to model fitting - in one object. This enables easy
modification and combination of different scenarios. You can store your
results in a folder or start the simulation in parallel.
Author: Sebastian Warnholz [aut, cre],
Timo Schmid [aut]
Maintainer: Sebastian Warnholz
Diff between saeSim versions 0.6.0 dated 2014-10-22 and 0.7.0 dated 2015-02-16
saeSim-0.6.0/saeSim/R/01-s_dplyr.R |only saeSim-0.6.0/saeSim/R/02-mclapply.R |only saeSim-0.6.0/saeSim/inst/doc/addingComputations.R |only saeSim-0.6.0/saeSim/inst/doc/addingComputations.Rmd |only saeSim-0.6.0/saeSim/inst/doc/addingComputations.html |only saeSim-0.6.0/saeSim/inst/doc/drawingSamples.R |only saeSim-0.6.0/saeSim/inst/doc/drawingSamples.Rmd |only saeSim-0.6.0/saeSim/inst/doc/drawingSamples.html |only saeSim-0.6.0/saeSim/inst/doc/generalOverview.R |only saeSim-0.6.0/saeSim/inst/doc/generalOverview.Rmd |only saeSim-0.6.0/saeSim/inst/doc/generalOverview.html |only saeSim-0.6.0/saeSim/inst/doc/generatingData.R |only saeSim-0.6.0/saeSim/inst/doc/generatingData.Rmd |only saeSim-0.6.0/saeSim/inst/doc/generatingData.html |only saeSim-0.6.0/saeSim/man/show-sim_setup-method.Rd |only saeSim-0.6.0/saeSim/man/summary.sim_setup.Rd |only saeSim-0.6.0/saeSim/vignettes/addingComputations.Rmd |only saeSim-0.6.0/saeSim/vignettes/drawingSamples.Rmd |only saeSim-0.6.0/saeSim/vignettes/generalOverview.Rmd |only saeSim-0.6.0/saeSim/vignettes/generatingData.Rmd |only saeSim-0.7.0/saeSim/DESCRIPTION | 19 - saeSim-0.7.0/saeSim/MD5 | 131 ++++------ saeSim-0.7.0/saeSim/NAMESPACE | 13 saeSim-0.7.0/saeSim/NEWS | 27 ++ saeSim-0.7.0/saeSim/R/00-sim-lib.R | 17 - saeSim-0.7.0/saeSim/R/01-as.data.frame.R | 2 saeSim-0.7.0/saeSim/R/01-helper-lib.R | 48 +++ saeSim-0.7.0/saeSim/R/01-plot.R | 1 saeSim-0.7.0/saeSim/R/01-show.R | 7 saeSim-0.7.0/saeSim/R/01-sim.R | 115 +++++--- saeSim-0.7.0/saeSim/R/01-summary.R | 64 ++-- saeSim-0.7.0/saeSim/R/03-agg.R | 12 saeSim-0.7.0/saeSim/R/03-base-lib.R | 2 saeSim-0.7.0/saeSim/R/03-comp_var.R | 24 - saeSim-0.7.0/saeSim/R/03-generator.R | 19 - saeSim-0.7.0/saeSim/R/03-sample.R | 44 +++ saeSim-0.7.0/saeSim/R/03-sim_agg.R | 2 saeSim-0.7.0/saeSim/R/03-sim_base.R | 4 saeSim-0.7.0/saeSim/R/03-sim_comp.R | 6 saeSim-0.7.0/saeSim/R/03-sim_comp_preconf.R | 8 saeSim-0.7.0/saeSim/R/03-sim_gen.R | 13 saeSim-0.7.0/saeSim/R/03-sim_gen_cont.R | 7 saeSim-0.7.0/saeSim/R/03-sim_resp.R | 4 saeSim-0.7.0/saeSim/R/03-sim_sample.R | 2 saeSim-0.7.0/saeSim/R/NAMESPACE.R |only saeSim-0.7.0/saeSim/build/vignette.rds |binary saeSim-0.7.0/saeSim/inst/doc/Introduction.R |only saeSim-0.7.0/saeSim/inst/doc/Introduction.Rmd |only saeSim-0.7.0/saeSim/inst/doc/Introduction.html |only saeSim-0.7.0/saeSim/man/agg_all.Rd | 3 saeSim-0.7.0/saeSim/man/as.data.frame.sim_setup.Rd | 3 saeSim-0.7.0/saeSim/man/autoplot.Rd | 3 saeSim-0.7.0/saeSim/man/base_add_id.Rd | 3 saeSim-0.7.0/saeSim/man/base_id.Rd | 3 saeSim-0.7.0/saeSim/man/comp_var.Rd | 3 saeSim-0.7.0/saeSim/man/generators.Rd | 7 saeSim-0.7.0/saeSim/man/pipe.Rd | 3 saeSim-0.7.0/saeSim/man/plot.sim_setup.Rd | 3 saeSim-0.7.0/saeSim/man/sampling.Rd | 21 + saeSim-0.7.0/saeSim/man/showMethods.Rd |only saeSim-0.7.0/saeSim/man/sim.Rd | 48 ++- saeSim-0.7.0/saeSim/man/sim_agg.Rd | 3 saeSim-0.7.0/saeSim/man/sim_base.Rd | 3 saeSim-0.7.0/saeSim/man/sim_comp.Rd | 3 saeSim-0.7.0/saeSim/man/sim_comp_preconf.Rd | 3 saeSim-0.7.0/saeSim/man/sim_gen.Rd | 13 saeSim-0.7.0/saeSim/man/sim_gen_cont.Rd | 3 saeSim-0.7.0/saeSim/man/sim_gen_preconf.Rd | 3 saeSim-0.7.0/saeSim/man/sim_read_data.Rd | 3 saeSim-0.7.0/saeSim/man/sim_resp.Rd | 3 saeSim-0.7.0/saeSim/man/sim_sample.Rd | 3 saeSim-0.7.0/saeSim/man/sim_setup_preconfigured.Rd | 3 saeSim-0.7.0/saeSim/man/sim_simName.Rd | 3 saeSim-0.7.0/saeSim/man/summary-sim_setup-method.Rd |only saeSim-0.7.0/saeSim/tests/testthat/helper.R |only saeSim-0.7.0/saeSim/tests/testthat/test-preserve_attributes.R |only saeSim-0.7.0/saeSim/tests/testthat/test-sim.R | 2 saeSim-0.7.0/saeSim/tests/testthat/test-sim_comp.R | 7 saeSim-0.7.0/saeSim/tests/testthat/test-sim_generate.R | 12 saeSim-0.7.0/saeSim/tests/testthat/test-sim_sample.R | 26 + saeSim-0.7.0/saeSim/vignettes/Introduction.Rmd |only 81 files changed, 505 insertions(+), 279 deletions(-)
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Description: An R interface for C library libeemd for performing the ensemble
empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the
regular empirical mode decomposition (EMD).
Author: Jouni Helske [aut, cre] (R interface),
Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske
Diff between Rlibeemd versions 1.3.1 dated 2015-02-09 and 1.3.2 dated 2015-02-16
DESCRIPTION | 8 MD5 | 18 R/RcppExports.R | 4 R/Rlibeemd-package.R | 2 R/init.R |only configure | 1529 ++++++++++++++++++++++----------------------- configure.ac | 8 inst/CITATION | 5 man/Rlibeemd.Rd | 2 src/RcppExports.cpp | 11 src/gslErrorHandlerOff.cpp |only 11 files changed, 805 insertions(+), 782 deletions(-)
Title: Retinal Reconstruction Program
Description: Reconstructs retinae by morphing a flat surface with
cuts (a dissected flat-mount retina) onto a curvilinear surface (the a
standard retinal shape). It can estimate the position of a point on the
intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis).
The coordinates in reconstructed retinae can be transformed to visuotopic
coordinates.
Author: David C. Sterratt [aut, cre, cph],
Daniel Lyngholm [aut, cph]
Maintainer: David C. Sterratt
Diff between retistruct versions 0.5.9 dated 2014-12-02 and 0.5.10 dated 2015-02-16
DESCRIPTION | 18 +++++++++++------- MD5 | 15 ++++++++------- NAMESPACE | 2 ++ NEWS |only R/ReconstructedDataset.R | 2 +- R/geometry.R | 2 ++ R/revision.R | 2 +- inst/CITATION | 8 ++++++-- man/retistruct.global.revision.Rd | 2 +- 9 files changed, 32 insertions(+), 19 deletions(-)
Title: Least-Squares Bilinear Clustering for Three-Way Data
Description: Functions for performing least-squares bilinear clustering of three-way data. The
method uses the bilinear decomposition (or biadditive model) to model two-way matrix slices
while clustering over the third way. Up to four different types of clusters are included, one
for each term of the bilinear decomposition. In this way, matrices are clustered simultaneously
on (a subset of) their overall means, row margins, column margins and row-column interactions.
The orthogonality of the bilinear model results in separability of the joint clustering problem
into four separate ones. Three of these subproblems are specific k-means problems, while a
special algorithm is implemented for the interactions. Plotting methods are provided, including
biplots for the low-rank approximations of the interactions.
Author: Pieter Schoonees [aut, cre], Patrick Groenen [ctb]
Maintainer: Pieter Schoonees
Diff between lsbclust versions 1.0 dated 2015-02-10 and 1.0.1 dated 2015-02-16
DESCRIPTION | 18 +++- MD5 | 12 +- R/plot.int.lsbclust.R | 5 - R/supermarkets.R | 2 man/supermarkets.Rd | 2 tests/testthat/test_interactions.R | 159 +++++++++++++++++++++++++++++-------- tests/testthat/test_orc.R | 33 ++++++- 7 files changed, 178 insertions(+), 53 deletions(-)
Title: High-Dimensional Penalized Regression
Description: Algorithms for lasso and fused-lasso
problems: implementation of the lars algorithm [1], for the
lasso and fusion penalization and EM-based algorithms for (logistic) lasso
and fused-lasso.
Author: Quentin Grimonprez [aut, cre],
Serge Iovleff [ctb]
Maintainer: Quentin Grimonprez
Diff between HDPenReg versions 0.90 dated 2014-11-03 and 0.91 dated 2015-02-16
HDPenReg-0.90/HDPenReg/inst/doc/vignette.R |only HDPenReg-0.90/HDPenReg/inst/doc/vignette.Rnw |only HDPenReg-0.90/HDPenReg/inst/doc/vignette.pdf |only HDPenReg-0.90/HDPenReg/man/predict.Rd |only HDPenReg-0.90/HDPenReg/src/stkpp |only HDPenReg-0.90/HDPenReg/vignettes/vignette.Rnw |only HDPenReg-0.90/HDPenReg/vignettes/vignette.bib |only HDPenReg-0.91/HDPenReg/DESCRIPTION | 28 HDPenReg-0.91/HDPenReg/MD5 | 434 +--------- HDPenReg-0.91/HDPenReg/NAMESPACE | 6 HDPenReg-0.91/HDPenReg/NEWS | 7 HDPenReg-0.91/HDPenReg/R/HDPenReg-package.R | 6 HDPenReg-0.91/HDPenReg/R/predict.R | 4 HDPenReg-0.91/HDPenReg/build/vignette.rds |binary HDPenReg-0.91/HDPenReg/inst/doc/HDPenReg.R |only HDPenReg-0.91/HDPenReg/inst/doc/HDPenReg.Rnw |only HDPenReg-0.91/HDPenReg/inst/doc/HDPenReg.pdf |only HDPenReg-0.91/HDPenReg/man/EMcvfusedlasso.Rd | 3 HDPenReg-0.91/HDPenReg/man/EMcvlasso.Rd | 3 HDPenReg-0.91/HDPenReg/man/EMfusedlasso.Rd | 3 HDPenReg-0.91/HDPenReg/man/EMlasso.Rd | 3 HDPenReg-0.91/HDPenReg/man/HDPenReg-package.Rd | 7 HDPenReg-0.91/HDPenReg/man/HDcvlars.Rd | 3 HDPenReg-0.91/HDPenReg/man/HDfusion.Rd | 3 HDPenReg-0.91/HDPenReg/man/HDlars.Rd | 3 HDPenReg-0.91/HDPenReg/man/LarsPath-class.Rd | 3 HDPenReg-0.91/HDPenReg/man/coef.LarsPath.Rd | 3 HDPenReg-0.91/HDPenReg/man/coeff.Rd | 3 HDPenReg-0.91/HDPenReg/man/computeCoefficients.Rd | 3 HDPenReg-0.91/HDPenReg/man/plot-methods.Rd | 3 HDPenReg-0.91/HDPenReg/man/plot.HDcvlars.Rd | 3 HDPenReg-0.91/HDPenReg/man/plotCoefficient.Rd | 3 HDPenReg-0.91/HDPenReg/man/predict.LarsPath.Rd |only HDPenReg-0.91/HDPenReg/man/simul.Rd | 3 HDPenReg-0.91/HDPenReg/src/HDPenReg/lars.mk | 6 HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/Cvlars.cpp | 1 HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/Lars.cpp | 7 HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/Lars.h | 2 HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/PathState.h | 2 HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/makefile | 34 HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels.mk | 17 HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/CV.cpp | 1 HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/EM.cpp |only HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/FusedLasso.cpp |only HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/IMeasure.h | 2 HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/IPenalizedSolver.h | 2 HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/IPenalty.h | 2 HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/Lasso.cpp |only HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/LogisticFusedLasso.cpp |only HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/LogisticLasso.cpp |only HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/LogisticLassoPenalty.cpp | 1 HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/PenalizedModels.h | 44 - HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/makefile | 2 HDPenReg-0.91/HDPenReg/src/Makevars | 45 - HDPenReg-0.91/HDPenReg/src/emR.cpp | 3 HDPenReg-0.91/HDPenReg/src/emR.h | 5 HDPenReg-0.91/HDPenReg/src/larsR.cpp | 1 HDPenReg-0.91/HDPenReg/src/larsR.h | 5 HDPenReg-0.91/HDPenReg/vignettes/HDPenReg.Rnw |only HDPenReg-0.91/HDPenReg/vignettes/HDPenReg.bib |only 60 files changed, 182 insertions(+), 537 deletions(-)
More information about fdrDiscreteNull at CRAN
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Title: Bounded Density Estimation
Description: A collection of S4 classes which implements different methods to estimate and deal with densities in bounded domains. That is, densities defined within the interval [lower.limit, upper.limit], where lower.limit and upper.limit are values that can be set by the user.
Author: Guzman Santafe, Borja Calvo, Aritz Perez and Jose A. Lozano
Maintainer: Guzman Santafe
Diff between bde versions 1.0 dated 2014-11-13 and 1.0.1 dated 2015-02-16
DESCRIPTION | 12 ++++++------ MD5 | 5 +++-- NEWS |only inst/App/server.R | 10 +++++----- 4 files changed, 14 insertions(+), 13 deletions(-)
Title: Using Gene Expression Data to Improve Flux Balance Analysis
Predictions
Description: Three different approaches to use gene expression data (or protein measurements) for improving FBA predictions.
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki
Diff between sybilEFBA versions 1.0.1 dated 2013-10-24 and 1.0.2 dated 2015-02-16
DESCRIPTION | 16 +- MD5 | 28 ++-- NEWS | 10 + R/FECorr.R | 27 +++- R/eFBA_gene.R | 329 +++++++++++++++++++++++++++++++++++------------------ R/eFBA_rxn.R | 105 +++++++--------- R/findMDCFlux.R | 7 - R/gene2Rule.R | 8 - data/iAF1260.RData |binary data/iMM904.RData |binary data/iND750.RData |binary man/eFBA_gene.Rd | 6 man/eFBA_rxn.Rd | 6 man/findMDCFlux.Rd | 7 - man/gen2Rule.Rd | 2 15 files changed, 344 insertions(+), 207 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. rms is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. rms works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr
Diff between rms versions 4.2-1 dated 2014-09-18 and 4.3-0 dated 2015-02-16
DESCRIPTION | 11 INDEX | 2 MD5 | 113 ++++---- NAMESPACE | 12 NEWS | 30 ++ R/Function.rms.s | 10 R/Glm.s | 5 R/Predict.s | 433 ++++++++++++++++----------------- R/Rq.s | 3 R/anova.rms.s | 14 - R/bj.s | 7 R/bootcov.s | 11 R/calibrate.s | 190 +++++++------- R/contrast.s | 110 +++++--- R/cph.s | 7 R/datadist.s | 295 ++++++++++------------ R/ggplot.Predict.s |only R/latex.rms.s | 33 +- R/lrm.s | 3 R/ols.s | 7 R/orm.s | 3 R/plot.Predict.s | 146 +++++++---- R/pphsm.s | 2 R/predictrms.s | 67 ++--- R/print.psm.s | 17 - R/residuals.lrm.s | 30 +- R/rmsMisc.s | 52 +++ R/robcov.s | 35 +- R/summary.rms.s | 8 R/survplot.npsurv.s | 6 R/survplot.rms.s | 3 R/validate.cph.s | 25 - man/Gls.Rd | 7 man/Predict.Rd | 10 man/anova.rms.Rd | 3 man/bootcov.Rd | 7 man/calibrate.Rd | 6 man/contrast.Rd | 52 ++- man/cph.Rd | 8 man/datadist.Rd | 7 man/ggplot.Predict.Rd |only man/lrm.Rd | 4 man/nomogram.Rd | 4 man/npsurv.Rd | 8 man/plot.Predict.Rd | 5 man/predictrms.Rd | 15 - man/psm.Rd | 4 man/residuals.lrm.Rd | 20 + man/rms-internal.Rd | 2 man/rms.Rd | 8 man/robcov.Rd | 6 man/sensuc.Rd | 3 man/survplot.Rd | 2 man/zzzrmsOverview.Rd | 9 tests/cph3.r |only tests/ggplot2-without-ggplot.Predict.r |only tests/ggplot2.r |only tests/orm-bootcov.r |only tests/orm-residuals.r |only tests/robcov.r |only tests/summary.r |only tests/validate.cph.s | 2 62 files changed, 1068 insertions(+), 814 deletions(-)
Title: Bayesian Geostatistical Modeling with RAMPS
Description: Bayesian geostatistical modeling of Gaussian processes using a reparameterized and marginalized posterior sampling (RAMPS) algorithm designed to lower autocorrelation in MCMC samples. Package performance is tuned for large spatial datasets.
Author: Brian J Smith [aut, cre],
Jun Yan [aut],
Mary Kathryn Cowles [aut]
Maintainer: Brian J Smith
Diff between ramps versions 0.6-12 dated 2013-11-12 and 0.6-13 dated 2015-02-16
ramps-0.6-12/ramps/man/corClasses.Rd |only ramps-0.6-13/ramps/DESCRIPTION | 8 +- ramps-0.6-13/ramps/MD5 | 34 ++++---- ramps-0.6-13/ramps/NAMESPACE | 30 +++---- ramps-0.6-13/ramps/R/corStruct.R | 88 +++++++++++------------ ramps-0.6-13/ramps/man/corRCauchy.Rd | 126 ++++++++++++++++----------------- ramps-0.6-13/ramps/man/corRClasses.Rd |only ramps-0.6-13/ramps/man/corRExp.Rd | 126 ++++++++++++++++----------------- ramps-0.6-13/ramps/man/corRExp2.Rd | 6 - ramps-0.6-13/ramps/man/corRExpwr.Rd | 6 - ramps-0.6-13/ramps/man/corRExpwr2.Rd | 6 - ramps-0.6-13/ramps/man/corRExpwr2Dt.Rd | 6 - ramps-0.6-13/ramps/man/corRGaus.Rd | 126 ++++++++++++++++----------------- ramps-0.6-13/ramps/man/corRGneit.Rd | 126 ++++++++++++++++----------------- ramps-0.6-13/ramps/man/corRLin.Rd | 126 ++++++++++++++++----------------- ramps-0.6-13/ramps/man/corRMatern.Rd | 6 - ramps-0.6-13/ramps/man/corRSpher.Rd | 126 ++++++++++++++++----------------- ramps-0.6-13/ramps/man/corRWave.Rd | 126 ++++++++++++++++----------------- ramps-0.6-13/ramps/man/georamps.Rd | 6 - 19 files changed, 527 insertions(+), 551 deletions(-)
Title: Post-Hoc Interaction Analysis
Description: Analysis of terms in linear, generalized and mixed linear models,
on the basis of multiple comparisons of factor contrasts. Specially suited
for the analysis of interaction terms.
Author: Helios De Rosario-Martinez [aut, cre],
John Fox [ctb],
R Core Team [ctb]
Maintainer: Helios De Rosario-Martinez
Diff between phia versions 0.1-5 dated 2013-10-12 and 0.2-0 dated 2015-02-16
ChangeLog | 19 ++++ DESCRIPTION | 10 +- MD5 | 34 ++++---- NAMESPACE | 4 - R/contrastCoefficients.R | 2 R/getElements.R | 5 - R/interactionMeans.R | 91 ++++++++++++++++++++-- R/testFactors.R | 187 +++++++++++++++++++---------------------------- build/vignette.rds |binary data/Boik.rda |binary data/Keselman.rda |binary data/Rosnow.rda |binary inst/doc/phia.Rnw | 97 ++++++++++++++---------- inst/doc/phia.pdf |binary man/interactionMeans.Rd | 11 ++ man/phia-package.Rd | 6 - man/testFactors.Rd | 5 - vignettes/phia.Rnw | 97 ++++++++++++++---------- 18 files changed, 334 insertions(+), 234 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data. Including multivariate cumulative incidence models, and
bivariate random effects probit models (Liability models). Also contains
two-stage binomial modelling that can do pairwise odds-ratio dependence
modelling based marginal logistic regression models. This is an alternative
to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst
Diff between mets versions 1.0 dated 2014-11-18 and 1.1.0 dated 2015-02-16
mets-1.0/mets/R/newbptwin.R |only mets-1.1.0/mets/DESCRIPTION | 10 - mets-1.1.0/mets/MD5 | 159 +++++++++++++------------- mets-1.1.0/mets/NAMESPACE | 14 -- mets-1.1.0/mets/NEWS | 8 + mets-1.1.0/mets/R/aalenfrailty.R | 8 - mets-1.1.0/mets/R/bicomprisk.R | 2 mets-1.1.0/mets/R/biprobit.R | 20 +-- mets-1.1.0/mets/R/bptwin.R | 4 mets-1.1.0/mets/R/bptwin2.R | 2 mets-1.1.0/mets/R/cor.R | 14 -- mets-1.1.0/mets/R/divide.conquer.R | 6 mets-1.1.0/mets/R/event.R | 10 - mets-1.1.0/mets/R/fastapprox.R | 33 +++-- mets-1.1.0/mets/R/fastreshape.R | 29 +++- mets-1.1.0/mets/R/ipw.R | 1 mets-1.1.0/mets/R/lifetable.R | 120 ++++++++++++++++++- mets-1.1.0/mets/R/mets-package.R | 2 mets-1.1.0/mets/R/normal0.R | 20 ++- mets-1.1.0/mets/R/onload.R | 4 mets-1.1.0/mets/R/phreg.par.R | 6 mets-1.1.0/mets/R/tetrachor.R | 16 ++ mets-1.1.0/mets/R/twinlm.R | 6 mets-1.1.0/mets/R/twostage.R | 2 mets-1.1.0/mets/inst/mets1.png |only mets-1.1.0/mets/man/ClaytonOakes.Rd | 3 mets-1.1.0/mets/man/Dbvn.Rd | 3 mets-1.1.0/mets/man/Event.Rd | 3 mets-1.1.0/mets/man/Grandom.cif.Rd | 19 +-- mets-1.1.0/mets/man/aalenfrailty.Rd | 11 + mets-1.1.0/mets/man/back2timereg.Rd | 3 mets-1.1.0/mets/man/bicomprisk.Rd | 3 mets-1.1.0/mets/man/binomial.twostage.Rd | 3 mets-1.1.0/mets/man/biprobit.Rd | 23 +-- mets-1.1.0/mets/man/blocksample.Rd | 7 - mets-1.1.0/mets/man/bptwin.Rd | 13 -- mets-1.1.0/mets/man/casewise.Rd | 3 mets-1.1.0/mets/man/casewise.test.Rd | 3 mets-1.1.0/mets/man/concordance.Rd | 3 mets-1.1.0/mets/man/cor.cif.Rd | 5 mets-1.1.0/mets/man/dermalridges.Rd | 3 mets-1.1.0/mets/man/dermalridgesMZ.Rd | 3 mets-1.1.0/mets/man/divide.conquer.Rd | 5 mets-1.1.0/mets/man/divide.conquer.timereg.Rd | 7 - mets-1.1.0/mets/man/easy.binomial.twostage.Rd | 7 - mets-1.1.0/mets/man/easy.twostage.Rd | 3 mets-1.1.0/mets/man/fast.approx.Rd | 13 +- mets-1.1.0/mets/man/fast.pattern.Rd | 3 mets-1.1.0/mets/man/fast.reshape.Rd | 12 + mets-1.1.0/mets/man/internal.Rd | 4 mets-1.1.0/mets/man/ipw.Rd | 3 mets-1.1.0/mets/man/lifetable.matrix.Rd | 11 - mets-1.1.0/mets/man/mena.Rd | 3 mets-1.1.0/mets/man/mets-package.Rd | 3 mets-1.1.0/mets/man/migr.Rd | 3 mets-1.1.0/mets/man/multcif.Rd | 3 mets-1.1.0/mets/man/np.Rd | 3 mets-1.1.0/mets/man/phreg.Rd | 3 mets-1.1.0/mets/man/plack.cif.Rd | 3 mets-1.1.0/mets/man/printcasewisetest.Rd | 3 mets-1.1.0/mets/man/prt.Rd | 3 mets-1.1.0/mets/man/random.cif.Rd | 3 mets-1.1.0/mets/man/simAalenFrailty.Rd | 3 mets-1.1.0/mets/man/simClaytonOakes.Rd | 3 mets-1.1.0/mets/man/simClaytonOakesWei.Rd | 3 mets-1.1.0/mets/man/summary.cor.Rd | 3 mets-1.1.0/mets/man/survpois.Rd |only mets-1.1.0/mets/man/test.conc.Rd | 3 mets-1.1.0/mets/man/tetrachoric.Rd |only mets-1.1.0/mets/man/twin.clustertrunc.Rd | 3 mets-1.1.0/mets/man/twinbmi.Rd | 3 mets-1.1.0/mets/man/twinlm.Rd | 7 - mets-1.1.0/mets/man/twinsim.Rd | 3 mets-1.1.0/mets/man/twinstut.Rd | 3 mets-1.1.0/mets/man/twostage.Rd | 3 mets-1.1.0/mets/src/fastcox.cpp | 2 mets-1.1.0/mets/src/mvn.cpp | 48 ++++++- mets-1.1.0/mets/src/mvn.h | 5 mets-1.1.0/mets/src/mvt.f | 14 +- mets-1.1.0/mets/src/tools.cpp | 35 +++-- mets-1.1.0/mets/src/tools.h | 2 mets-1.1.0/mets/src/tvpack.f | 8 - mets-1.1.0/mets/tests/testthat/test_approx.R |only 83 files changed, 551 insertions(+), 305 deletions(-)
Title: Linear Predictor Score, for Binary Inference from Multiple
Continuous Variables
Description: An implementation of the Linear Predictor Score approach, as initiated by Radmacher et al. (J Comput Biol 2001) and enhanced by Wright et al. (PNAS 2003) for gene expression signatures. Several tools for unsupervised clustering of gene expression data are also provided.
Author: Sylvain Mareschal
Maintainer: Sylvain Mareschal
Diff between LPS versions 1.0.4 dated 2013-12-20 and 1.0.10 dated 2015-02-16
DESCRIPTION | 17 +++++----- MD5 | 31 +++++++++--------- R/LPS.coeff.r | 13 ++----- R/LPS.r | 2 + R/clusterize.r | 44 +++++++++++++++++++------- R/heat.map.r | 89 ++++++++++++++++++++++++++++++++--------------------- R/heat.r | 2 - R/heat.scale.r | 22 ++++++++++--- R/plot.LPS.r | 75 ++++++++++++++++++++++++++++++++++++++------ R/predict.LPS.r | 68 +++++++++++++++++++++++++--------------- README.md |only inst/NEWS.Rd | 45 ++++++++++++++++++++++++++ man/clusterize.Rd | 22 ++++++++----- man/heat.map.Rd | 24 ++++++++------ man/heat.scale.Rd | 9 ++++- man/plot.LPS.Rd | 20 ++++++++++- man/predict.LPS.Rd | 22 ++++++++----- 17 files changed, 359 insertions(+), 146 deletions(-)
Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX code,
and recoding variables.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr
Diff between Hmisc versions 3.14-6 dated 2014-11-21 and 3.15-0 dated 2015-02-16
DESCRIPTION | 17 ++-- INDEX | 2 MD5 | 59 ++++++++------- NAMESPACE | 190 ++++++++++++++++++++++++++++++++++++++++++++++++++ NEWS | 18 ++++ R/Misc.s | 16 +--- R/aregImpute.s | 47 ++++++------ R/histSpikeg.s |only R/labcurve.s | 13 +-- R/latex.s | 58 +++++++++++---- R/rcspline.plot.s | 9 -- R/rcspline.restate.s | 12 +-- R/sas.get.s | 3 R/scat1d.s | 53 ++++++------- R/stat-plsmo.r |only R/summary.formula.s | 1 R/summaryM.s | 23 +++--- R/summaryP.s | 81 +++++++++++++++++++++ R/transace.s | 2 R/transcan.s | 54 +++++++++++++- man/Hmisc-internal.Rd | 3 man/describe.Rd | 3 man/format.df.Rd | 9 +- man/getHdata.Rd | 13 --- man/labcurve.Rd | 12 +-- man/plsmo.Rd | 10 ++ man/scat1d.Rd | 86 +++++++++++++++++++--- man/stat_plsmo.Rd |only man/summaryM.Rd | 10 +- man/summaryP.Rd | 25 +++++- man/transcan.Rd | 30 +++++-- tests/histSpike.r |only tests/histSpikeg.r |only 33 files changed, 659 insertions(+), 200 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (First Edition, Springer, ISBN 0-387-40270-5, 2004) and (Second Edition, Springer, ISBN 978-1-4939-2121-8, anticipated 2015) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger
Diff between HH versions 3.1-14 dated 2015-01-09 and 3.1-15 dated 2015-02-16
HH-3.1-14/HH/R/t.trellis.R |only HH-3.1-14/HH/man/t.trellis.Rd |only HH-3.1-15/HH/DESCRIPTION | 8 HH-3.1-15/HH/MD5 | 76 ++-- HH-3.1-15/HH/NAMESPACE | 7 HH-3.1-15/HH/NEWS | 47 ++- HH-3.1-15/HH/R/ARIMA-trellis.R | 65 ---- HH-3.1-15/HH/R/extra.r | 5 HH-3.1-15/HH/R/interaction2wt.R | 2 HH-3.1-15/HH/R/intxplot.s | 24 - HH-3.1-15/HH/R/matrix.trellis.r | 8 HH-3.1-15/HH/R/mmcplot.R | 22 + HH-3.1-15/HH/R/normal.and.t.R | 27 - HH-3.1-15/HH/R/normal.and.t.power.R | 30 + HH-3.1-15/HH/R/normal.and.t.shiny.R | 80 ++--- HH-3.1-15/HH/R/normal.and.t.support.R | 2 HH-3.1-15/HH/R/panel.interaction2wt.R | 23 + HH-3.1-15/HH/R/rbind.trellis.R | 111 +++++-- HH-3.1-15/HH/R/transpose.trellis.R | 20 - HH-3.1-15/HH/inst/CITATION | 2 HH-3.1-15/HH/inst/scripts/hh2/conc.R | 196 ++++++++---- HH-3.1-15/HH/inst/scripts/hh2/grap.R | 48 +-- HH-3.1-15/HH/inst/scripts/hh2/iinf.R | 451 +++++++++++++++++++++++++++++ HH-3.1-15/HH/inst/scripts/hh2/logi.R | 30 - HH-3.1-15/HH/inst/shiny/PopulationPyramid |only HH-3.1-15/HH/man/NormalAndT.Rd | 8 HH-3.1-15/HH/man/NormalAndTplot.Rd | 10 HH-3.1-15/HH/man/ae.dotplot.Rd | 60 +-- HH-3.1-15/HH/man/as.vector.trellis.Rd | 37 +- HH-3.1-15/HH/man/datasets.Rd | 3 HH-3.1-15/HH/man/extra.Rd | 3 HH-3.1-15/HH/man/intxplot.Rd | 5 HH-3.1-15/HH/man/mmc.Rd | 248 ++++++--------- HH-3.1-15/HH/man/normal.and.t.and.power.Rd | 4 HH-3.1-15/HH/man/normalApproxBinomial.Rd | 7 HH-3.1-15/HH/man/panel.confintMMC.Rd | 4 HH-3.1-15/HH/man/panel.interaction2wt.Rd | 2 HH-3.1-15/HH/man/rbind.trellis.Rd | 24 - HH-3.1-15/HH/man/seqplot.Rd | 2 39 files changed, 1138 insertions(+), 563 deletions(-)
Title: High Dimensional Supervised Classification and Clustering
Description: Discriminant analysis and data clustering methods for high dimensional data, based on the assumption that high-dimensional data live in different subspaces with low dimensionality proposing a new parametrization of the Gaussian mixture model which combines the ideas of dimension reduction and constraints on the model.
Author: Laurent Berge, Charles Bouveyron and Stephane Girard
Maintainer: Laurent Berge
Diff between HDclassif versions 1.2.2 dated 2013-01-08 and 1.2.3 dated 2015-02-16
HDclassif-1.2.2/HDclassif/HDclassif-Ex.R |only HDclassif-1.2.2/HDclassif/R/demo_hddc.R |only HDclassif-1.2.2/HDclassif/R/demo_hddc_acp.R |only HDclassif-1.2.2/HDclassif/R/demo_hddc_crabs.R |only HDclassif-1.2.2/HDclassif/R/hdda.R |only HDclassif-1.2.2/HDclassif/R/hddc.R |only HDclassif-1.2.2/HDclassif/R/pck_hdclassif_dim_choice.R |only HDclassif-1.2.2/HDclassif/R/pck_hdda_bic.R |only HDclassif-1.2.2/HDclassif/R/pck_hdda_prms.R |only HDclassif-1.2.2/HDclassif/R/pck_hdda_prms_bis.R |only HDclassif-1.2.2/HDclassif/R/pck_hdda_tclass.R |only HDclassif-1.2.2/HDclassif/R/pck_hddc.R |only HDclassif-1.2.2/HDclassif/R/pck_hddc_e_step.R |only HDclassif-1.2.2/HDclassif/R/pck_hddc_m_step.R |only HDclassif-1.2.2/HDclassif/R/plot.hdc.R |only HDclassif-1.2.2/HDclassif/R/predict.hdc.R |only HDclassif-1.2.2/HDclassif/R/print.hd.R |only HDclassif-1.2.2/HDclassif/R/print.hdc.R |only HDclassif-1.2.2/HDclassif/R/simuldata.R |only HDclassif-1.2.3/HDclassif/ChangeLog | 4 HDclassif-1.2.3/HDclassif/DESCRIPTION | 20 +- HDclassif-1.2.3/HDclassif/MD5 | 40 +---- HDclassif-1.2.3/HDclassif/R/hdclassif.R |only HDclassif-1.2.3/HDclassif/man/Crabs.Rd | 2 HDclassif-1.2.3/HDclassif/man/HDclassif-package.Rd | 12 - HDclassif-1.2.3/HDclassif/man/demo_hddc.Rd | 4 HDclassif-1.2.3/HDclassif/man/hdda.Rd | 130 ++++++++--------- HDclassif-1.2.3/HDclassif/man/hddc.Rd | 118 +++++++++++---- HDclassif-1.2.3/HDclassif/man/plot.hdc.Rd | 8 - HDclassif-1.2.3/HDclassif/man/predict.hdc.Rd | 14 - HDclassif-1.2.3/HDclassif/man/simuldata.Rd | 2 31 files changed, 196 insertions(+), 158 deletions(-)