Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee <leeshawn@umich.edu>
Diff between SKAT versions 1.0.9 dated 2015-06-14 and 1.1.2 dated 2015-09-07
DESCRIPTION | 8 +-- MD5 | 72 +++++++++++++-------------- NAMESPACE | 9 +++ R/Binary_Function.R | 5 + R/Binary_MAIN.R | 2 R/Binary_MAIN_ExactBin.R | 10 +-- R/Function.R | 1 R/Power.R | 72 +++++++++++++++++++-------- R/SKAT_EMMAX.R | 2 inst/doc/SKAT.R | 9 ++- inst/doc/SKAT.Rnw | 48 +++++++++--------- inst/doc/SKAT.pdf |binary man/Generate_SSD_SetID.rd | 13 ++-- man/Get_EffectiveNumberTest.rd | 16 ++++-- man/Get_Genotypes_SSD.rd | 6 +- man/Get_Logistic_Weights.rd | 10 ++- man/Get_RequiredSampleSize.rd | 8 +-- man/Get_Resampling_Pvalue.rd | 4 - man/Open_SSD.rd | 5 - man/Power_Continuous.rd | 36 ++++++++----- man/Power_Logistic.rd | 13 ++-- man/QQPlot_Adj.rd | 12 ++++ man/Read_Plink_FAM.rd | 9 +-- man/Read_SNP_WeightFile.rd | 17 +++--- man/Resampling_FWER.rd | 6 +- man/SKAT.SSD.All.rd | 16 +++--- man/SKAT.haplotypes.rd | 10 ++- man/SKAT.rd | 94 +++++++++++++++++++----------------- man/SKATBinary.rd | 56 +++++++++++++-------- man/SKATBinary_Single.rd | 30 ++++++----- man/SKAT_ChrX.rd | 45 ++++++----------- man/SKAT_CommonRare.rd | 12 ++-- man/SKAT_NULL_emmaX.rd | 10 +-- man/SKAT_Null_Model.rd | 12 +++- man/SKAT_Null_Model_MomentAdjust.rd | 13 +++- man/SSD_FILE_OPEN.rd | 2 vignettes/SKAT.Rnw | 48 +++++++++--------- 37 files changed, 424 insertions(+), 317 deletions(-)
Title: Replicate and Analyse InterVA4
Description: Provides an R version of the InterVA4 software for
coding cause of death from verbal autopsies. It also provides simple
graphical representation of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InterVA4 versions 1.5 dated 2014-10-14 and 1.6 dated 2015-09-07
InterVA4-1.5/InterVA4/R/InterVA4_1.4-package.R |only InterVA4-1.5/InterVA4/man/InterVA.summary.Rd |only InterVA4-1.6/InterVA4/DESCRIPTION | 12 - InterVA4-1.6/InterVA4/MD5 | 27 ++-- InterVA4-1.6/InterVA4/NAMESPACE | 3 InterVA4-1.6/InterVA4/R/InterVA.R | 68 +++++++--- InterVA4-1.6/InterVA4/R/InterVA.plot.R | 120 +++++++++++++----- InterVA4-1.6/InterVA4/R/InterVA4_1.6-package.R |only InterVA4-1.6/InterVA4/man/CSMF.Rd |only InterVA4-1.6/InterVA4/man/CSMF.interVA4.Rd |only InterVA4-1.6/InterVA4/man/InterVA.Rd | 157 ++++++++++++------------ InterVA4-1.6/InterVA4/man/InterVA.plot.Rd | 47 +++---- InterVA4-1.6/InterVA4/man/InterVA4-package.Rd | 25 +-- InterVA4-1.6/InterVA4/man/Population.summary.Rd | 93 ++++---------- InterVA4-1.6/InterVA4/man/SampleInput.Rd | 11 + InterVA4-1.6/InterVA4/man/causetext.Rd | 7 - InterVA4-1.6/InterVA4/man/probbase.Rd | 7 - 17 files changed, 320 insertions(+), 257 deletions(-)
Title: Convert Letters to Numbers and Back as on a Telephone Keypad
Description: Convert English letters to numbers or numbers to English letters as
on a telephone keypad. When converting letters to numbers, a character
vector is returned with "A," "B," or "C" becoming 2, "D," "E", or "F"
becoming 3, etc. When converting numbers to letters, a character vector is
returned with multiple elements (i.e., "2" becomes a vector of "A," "B," and
"C").
Author: Steve Myles [aut, cre]
Maintainer: Steve Myles <steve@mylesandmyles.info>
Diff between phonenumber versions 0.2.1 dated 2015-08-22 and 0.2.2 dated 2015-09-07
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/letterToNumber.R | 2 +- README.md | 2 +- inst/doc/phonenumber.R | 3 +++ inst/doc/phonenumber.Rmd | 9 ++++++++- inst/doc/phonenumber.html | 9 ++++++--- man/letterToNumber.Rd | 2 +- vignettes/phonenumber.Rmd | 9 ++++++++- 9 files changed, 39 insertions(+), 19 deletions(-)
Title: Use the MLS Junk Generator Algorithm to Generate a Stream of
Pseudo-Random Numbers
Description: Generate a stream of pseudo-random numbers generated using the MLS
Junk Generator algorithm. Functions exist to generate single pseudo-random
numbers as well as a vector, data frame, or matrix of pseudo-random numbers.
Author: Steve Myles [aut, cre]
Maintainer: Steve Myles <steve@mylesandmyles.info>
Diff between mlsjunkgen versions 0.1.0 dated 2015-08-16 and 0.1.1 dated 2015-09-07
DESCRIPTION | 8 ++--- MD5 | 24 ++++++++-------- R/mlsjunkgend.R | 2 - R/mlsjunkgenm.R | 2 - R/mlsjunkgenv.R | 2 - README.md | 70 +++++++++++++++++++++++++---------------------- inst/doc/mlsjunkgen.R | 2 - inst/doc/mlsjunkgen.Rmd | 17 ++++++----- inst/doc/mlsjunkgen.html | 38 ++++++++++++------------- man/mlsjunkgend.Rd | 2 - man/mlsjunkgenm.Rd | 2 - man/mlsjunkgenv.Rd | 2 - vignettes/mlsjunkgen.Rmd | 17 ++++++----- 13 files changed, 98 insertions(+), 90 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees.
Author: Luke Harmon <lukeh@uidaho.edu>, Jason Weir, Chad Brock, Rich
Glor, Wendell Challenger, Gene Hunt, Rich FitzJohn, Matt Pennell, Graham Slater, Joseph Brown, Josef Uyeda, and Jon Eastman <jonathan.eastman@gmail.com>
Maintainer: Matt Pennell <mwpennell@gmail.com>
Diff between geiger versions 2.0.5 dated 2015-09-03 and 2.0.6 dated 2015-09-07
DESCRIPTION | 8 +-- MD5 | 14 ++--- R/gbresolve.R | 16 +++--- README.md | 37 ++++++++++++++ man/fitContinuous.Rd | 127 ++++++++++++++++++++++++--------------------------- man/fitDiscrete.Rd | 68 +++++++++++++-------------- man/gbresolve.Rd | 25 +++++----- man/subset.phylo.Rd | 5 -- 8 files changed, 165 insertions(+), 135 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.4.0 dated 2015-09-04 and 0.4.2 dated 2015-09-07
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/vardchangespoor.R | 7 ++----- R/vardcrospoor.R | 7 +++---- inst/CITATION | 2 +- inst/NEWS | 4 ++++ man/vardchangespoor.Rd | 4 ---- man/vardcrospoor.Rd | 5 ----- man/vardpoor-package.Rd | 4 ++-- man/variance_est.Rd | 42 +++++++++++++++++++++++------------------- man/variance_othstr.Rd | 40 +++++++++++++++++++++++----------------- man/varpoord.Rd | 2 ++ 12 files changed, 75 insertions(+), 72 deletions(-)
Title: SEER and Atomic Bomb Survivor Data Analysis Tools
Description: Creates SEER (Surveillance, Epidemiology and End Results) and A-bomb data binaries
from ASCII sources and provides tools for estimating SEER second cancer risks.
Author: Tomas Radivoyevitch
Maintainer: Tomas Radivoyevitch <radivot@ccf.org>
Diff between SEERaBomb versions 2015.1 dated 2015-05-05 and 2015.2 dated 2015-09-07
DESCRIPTION | 15 +-- MD5 | 52 +++++++---- NAMESPACE | 13 ++ NEWS | 11 ++ R/getE.R | 29 +++--- R/mapCancs.R | 111 +++++++++++++++++++++---- R/mk2D.R | 10 +- R/mkDF.R |only R/mkExcel.R | 41 +++++---- R/mkSEER.R | 60 +++++++++---- R/pickFields.R | 9 +- R/plot2D.R | 28 ++++-- R/post1PYO.R | 189 ++++++++++++++++++++++++++----------------- R/print.seerSet.summary.R |only R/seerSet.R | 13 +- R/seerStats.R |only R/summary.seerSet.R |only R/tsd.R | 81 ++++++++++++------ data/nvsr.rda |only data/nvsr01.rda |only man/SEERaBomb-package.Rd | 4 man/getE.Rd | 4 man/mkDF.Rd |only man/mkExcel.Rd | 9 +- man/nvsr.Rd |only man/nvsr01.Rd |only man/plot2D.Rd | 3 man/post1PYO.Rd | 5 - man/print.seerSet.summary.Rd |only man/seerSet.Rd | 4 man/seerStats.Rd |only man/summary.seerSet.Rd |only man/tsd.Rd | 8 + 33 files changed, 472 insertions(+), 227 deletions(-)
Title: An Infra-Structure for Performance Estimation of Predictive
Models
Description: An infra-structure for estimating the predictive performance
of predictive models. In this context, it can also be used to compare and/or select among
different alternative ways of solving one or more predictive tasks. The main goal of the
package is to provide a generic infra-structure to estimate the values of different metrics
of predictive performance using different estimation procedures. These estimation tasks can be
applied to any solutions (workflows) to the predictive tasks. The package provides easy to use
standard workflows that allow the usage of any available R modeling algorithm together with
some pre-defined data pre-processing steps and also prediction post-processing methods. It also provides means for addressing issues related with the statistical significance of the observed differences.
Author: Luis Torgo [aut, cre]
Maintainer: Luis Torgo <ltorgo@dcc.fc.up.pt>
Diff between performanceEstimation versions 1.0.1 dated 2015-06-16 and 1.0.2 dated 2015-09-07
performanceEstimation-1.0.1/performanceEstimation/man/WFoutput-class.Rd |only performanceEstimation-1.0.1/performanceEstimation/man/getIterationInfo.Rd |only performanceEstimation-1.0.1/performanceEstimation/man/getIterationPreds.Rd |only performanceEstimation-1.0.1/performanceEstimation/man/workflowInformation.Rd |only performanceEstimation-1.0.1/performanceEstimation/man/workflowPredictions.Rd |only performanceEstimation-1.0.2/performanceEstimation/CHANGES | 14 performanceEstimation-1.0.2/performanceEstimation/DESCRIPTION | 8 performanceEstimation-1.0.2/performanceEstimation/MD5 | 47 +- performanceEstimation-1.0.2/performanceEstimation/NAMESPACE | 13 performanceEstimation-1.0.2/performanceEstimation/R/classDefs.R | 51 --- performanceEstimation-1.0.2/performanceEstimation/R/evaluationMetrics.R | 37 ++ performanceEstimation-1.0.2/performanceEstimation/R/experiments.R | 157 ++++------ performanceEstimation-1.0.2/performanceEstimation/R/methods.R | 19 - performanceEstimation-1.0.2/performanceEstimation/R/resultsManipulation.R | 23 - performanceEstimation-1.0.2/performanceEstimation/R/workflows.R | 44 +- performanceEstimation-1.0.2/performanceEstimation/inst/doc/performanceEstimation.pdf |binary performanceEstimation-1.0.2/performanceEstimation/man/Workflow-class.Rd | 4 performanceEstimation-1.0.2/performanceEstimation/man/classificationMetrics.Rd | 9 performanceEstimation-1.0.2/performanceEstimation/man/cvEstimates.Rd | 5 performanceEstimation-1.0.2/performanceEstimation/man/getIterationsInfo.Rd |only performanceEstimation-1.0.2/performanceEstimation/man/getIterationsPreds.Rd |only performanceEstimation-1.0.2/performanceEstimation/man/hldEstimates.Rd | 5 performanceEstimation-1.0.2/performanceEstimation/man/mcEstimates.Rd | 3 performanceEstimation-1.0.2/performanceEstimation/man/performanceEstimation.Rd | 2 performanceEstimation-1.0.2/performanceEstimation/man/regressionMetrics.Rd | 9 performanceEstimation-1.0.2/performanceEstimation/man/runWorkflow.Rd | 13 performanceEstimation-1.0.2/performanceEstimation/man/standardWF.Rd | 28 - performanceEstimation-1.0.2/performanceEstimation/man/timeseriesWF.Rd | 16 - 28 files changed, 237 insertions(+), 270 deletions(-)
More information about performanceEstimation at CRAN
Permanent link
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 <quentin.grimonprez@inria.fr>
Diff between HDPenReg versions 0.91 dated 2015-02-16 and 0.92 dated 2015-09-07
DESCRIPTION | 16 +-- MD5 | 76 ++++++++--------- NAMESPACE | 9 +- NEWS | 3 R/HDPenReg-package.R | 8 + R/LarsPath.R | 19 ++-- R/cvEM.R | 4 R/lars.R | 108 ++++++++++++------------- R/predict.R | 120 ++++++++++++++-------------- build/vignette.rds |binary inst/doc/HDPenReg.pdf |binary man/EMcvfusedlasso.Rd | 2 man/EMcvlasso.Rd | 2 man/EMfusedlasso.Rd | 2 man/EMlasso.Rd | 2 man/HDPenReg-package.Rd | 6 - man/HDcvlars.Rd | 2 man/HDfusion.Rd | 2 man/HDlars.Rd | 2 man/LarsPath-class.Rd | 2 man/coef.LarsPath.Rd | 2 man/coeff.Rd | 2 man/computeCoefficients.Rd | 2 man/plot-methods.Rd | 2 man/plot.HDcvlars.Rd | 2 man/plotCoefficient.Rd | 2 man/predict.LarsPath.Rd | 2 man/simul.Rd | 2 src/HDPenReg/lars.mk | 2 src/HDPenReg/lars/Cvlars.cpp | 12 +- src/HDPenReg/lars/Lars.cpp | 4 src/HDPenReg/lars/PathState.h | 2 src/HDPenReg/lassoModels.mk | 2 src/HDPenReg/lassoModels/EnetPenalty.h | 2 src/HDPenReg/lassoModels/IMeasure.h | 2 src/HDPenReg/lassoModels/IPenalizedSolver.h | 1 src/HDPenReg/lassoModels/IPenalty.h | 2 src/HDPenReg/lassoModels/PenalizedModels.h | 3 src/Makevars | 10 +- 39 files changed, 227 insertions(+), 216 deletions(-)
Title: Functions and Methods for Correspondence Regression
Description: A collection of tools for correspondence regression, i.e. the
correspondence analysis of the crosstabulation of a categorical variable Y
in function of another one X, where X can in turn be made up of the
combination of various categorical variables. Consequently, correspondence
regression can be used to analyze the effects for a polytomous or
multinomial outcome variable.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between corregp versions 0.1.2 dated 2015-09-02 and 0.1.3 dated 2015-09-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/corregp.r | 4 ++-- man/corregp-package.Rd | 2 +- man/plot3d.corregp.Rd | 2 +- 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Perform figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotids Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana, Joan Vila, Héctor Sanz, Gavin Lucas, judith Peñafiel and David Giménez
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 3.0.1 dated 2015-05-12 and 3.1 dated 2015-09-07
compareGroups-3.0.1/compareGroups/inst/app/help |only compareGroups-3.0.1/compareGroups/inst/app/www/tablePDF3046.pdf |only compareGroups-3.0.1/compareGroups/man/missingTable.rd |only compareGroups-3.1/compareGroups/DESCRIPTION | 31 compareGroups-3.1/compareGroups/MD5 | 72 compareGroups-3.1/compareGroups/NAMESPACE | 10 compareGroups-3.1/compareGroups/R/export2html.R | 18 compareGroups-3.1/compareGroups/R/export2md.R |only compareGroups-3.1/compareGroups/R/export2word.R |only compareGroups-3.1/compareGroups/R/export2xls.R |only compareGroups-3.1/compareGroups/build/vignette.rds |binary compareGroups-3.1/compareGroups/inst/app/global.R |only compareGroups-3.1/compareGroups/inst/app/help.html |only compareGroups-3.1/compareGroups/inst/app/server.R | 3169 ++++------ compareGroups-3.1/compareGroups/inst/app/spss_varlist.R |only compareGroups-3.1/compareGroups/inst/app/ui.R | 457 - compareGroups-3.1/compareGroups/inst/app/www/examples |only compareGroups-3.1/compareGroups/inst/app/www/images |only compareGroups-3.1/compareGroups/inst/app/www/tablePDF6755.pdf |only compareGroups-3.1/compareGroups/inst/doc/changelog | 6 compareGroups-3.1/compareGroups/inst/exdata/predimed.csv |only compareGroups-3.1/compareGroups/inst/exdata/predimed.dat |only compareGroups-3.1/compareGroups/inst/exdata/predimed.sav |only compareGroups-3.1/compareGroups/inst/exdata/predimed.xls |only compareGroups-3.1/compareGroups/inst/exdata/predimed.xlsx |only compareGroups-3.1/compareGroups/inst/exdata/regicor.csv |only compareGroups-3.1/compareGroups/inst/exdata/regicor.dat |only compareGroups-3.1/compareGroups/inst/exdata/regicor.sav |only compareGroups-3.1/compareGroups/man/compareGroups-package.Rd | 115 compareGroups-3.1/compareGroups/man/compareGroups.Rd | 4 compareGroups-3.1/compareGroups/man/createTable.Rd | 9 compareGroups-3.1/compareGroups/man/export2csv.Rd | 113 compareGroups-3.1/compareGroups/man/export2html.Rd | 4 compareGroups-3.1/compareGroups/man/export2latex.Rd | 2 compareGroups-3.1/compareGroups/man/export2md.Rd |only compareGroups-3.1/compareGroups/man/export2pdf.Rd | 2 compareGroups-3.1/compareGroups/man/export2word.Rd |only compareGroups-3.1/compareGroups/man/export2xls.Rd |only compareGroups-3.1/compareGroups/man/missingTable.Rd |only compareGroups-3.1/compareGroups/man/varinfo.Rd | 2 compareGroups-3.1/compareGroups/vignettes/figures/bivar/age.pdf |binary compareGroups-3.1/compareGroups/vignettes/figures/bivar/sex.pdf |binary compareGroups-3.1/compareGroups/vignettes/figures/bivar/tmain.pdf |binary compareGroups-3.1/compareGroups/vignettes/figures/univar/age.pdf |binary compareGroups-3.1/compareGroups/vignettes/figures/univar/sex.pdf |binary compareGroups-3.1/compareGroups/vignettes/figures/univar/tmain.pdf |binary 46 files changed, 2065 insertions(+), 1949 deletions(-)
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso', a method to model heterogeneity in paired comparison data. Subject-specific covariates are allowed to have an influence on the attractivity/strength of the objects. An L1 penalty on the pairwise differences between the object-specific parameters allows for both clustering of objects with regard to covariates and elimination of irrelevant covariates.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>
Diff between BTLLasso versions 0.1 dated 2015-09-03 and 0.1-1 dated 2015-09-07
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Find Biomarkers in Two-Class Discrimination Problems
Description: Variable selection methods are provided for several classification methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests. Two approaches for selecting cutoffs can be used, one based on the stability of model coefficients under perturbation, and the other on higher criticism.
Author: Ron Wehrens, Pietro Franceschi
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between BioMark versions 0.4.2 dated 2014-08-06 and 0.4.5 dated 2015-09-07
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 7 ++++++- man/gen.data.Rd | 6 ++---- man/get.biom.Rd | 2 -- 5 files changed, 17 insertions(+), 16 deletions(-)
Title: Phylogenetic Methods for Multiple Gene Data
Description: Toolkit for the analysis of multiple gene data. Apex implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.
Author: Thibaut Jombart [aut, cre],
Zhian Namir Kamvar [aut],
Klaus Schliep [aut],
Eric Archer [aut],
Rebecca Harris [aut]
Maintainer: Thibaut Jombart <t.jombart@imperial.ac.uk>
Diff between apex versions 1.0.0 dated 2015-04-15 and 1.0.1 dated 2015-09-07
apex-1.0.0/apex/R/handling.R |only apex-1.0.0/apex/man/sub-multidna-ANY-ANY-ANY-method.Rd |only apex-1.0.1/apex/DESCRIPTION | 20 - apex-1.0.1/apex/MD5 | 71 ++-- apex-1.0.1/apex/NAMESPACE | 25 + apex-1.0.1/apex/R/accessors.R | 266 +++++++++-------- apex-1.0.1/apex/R/add.gaps.R |only apex-1.0.1/apex/R/concatenate.R |only apex-1.0.1/apex/R/doc.R | 5 apex-1.0.1/apex/R/exports.R | 132 +++++++- apex-1.0.1/apex/R/internal.R | 55 +++ apex-1.0.1/apex/R/multidna.class.R | 12 apex-1.0.1/apex/R/multidna.constructor.R | 39 -- apex-1.0.1/apex/R/multiphyDat.class.R | 25 - apex-1.0.1/apex/R/multiphyDat.constructor.R | 68 +--- apex-1.0.1/apex/R/readfiles.R | 15 apex-1.0.1/apex/R/rm.gaps.R |only apex-1.0.1/apex/R/show.R | 63 +++- apex-1.0.1/apex/R/subset.R |only apex-1.0.1/apex/README.md | 248 +++------------ apex-1.0.1/apex/man/accessors.Rd |only apex-1.0.1/apex/man/add.gaps.Rd |only apex-1.0.1/apex/man/apex.Rd | 2 apex-1.0.1/apex/man/concatenate.Rd | 24 + apex-1.0.1/apex/man/dist.multidna.Rd | 2 apex-1.0.1/apex/man/getTree.Rd | 2 apex-1.0.1/apex/man/initialize-multidna-method.Rd | 8 apex-1.0.1/apex/man/initialize-multiphyDat-method.Rd | 13 apex-1.0.1/apex/man/multidna.Rd | 2 apex-1.0.1/apex/man/multidna2alignment.Rd |only apex-1.0.1/apex/man/multidna2genind.Rd | 19 - apex-1.0.1/apex/man/multidna2multiphyDat.Rd |only apex-1.0.1/apex/man/multiphyDat.Rd | 14 apex-1.0.1/apex/man/plot-multidna-ANY-method.Rd | 2 apex-1.0.1/apex/man/readfiles.Rd | 12 apex-1.0.1/apex/man/rm.gaps.Rd |only apex-1.0.1/apex/man/show-multidna-method.Rd | 2 apex-1.0.1/apex/man/show-multiphyDat-method.Rd |only apex-1.0.1/apex/man/subset.multidna.Rd |only apex-1.0.1/apex/tests/testthat/test_export.R | 6 apex-1.0.1/apex/vignettes/apex.Rmd | 18 - apex-1.0.1/apex/vignettes/figs/concat-2.png |binary apex-1.0.1/apex/vignettes/figs/plotPmlPart-1.png |binary 43 files changed, 661 insertions(+), 509 deletions(-)
Title: Analyze Shot Group Data
Description: Analyzes shooting data with respect to group shape,
precision, and accuracy. This includes graphical methods,
descriptive statistics, and inference tests using standard,
but also non-parametric and robust statistical methods.
Implements distributions for radial error in bivariate normal
variables. Works with files exported by OnTarget PC/TDS or
Taran, as well as with custom data files in text format.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger <dwoll@kuci.org>
Diff between shotGroups versions 0.6 dated 2014-08-25 and 0.6.1 dated 2015-09-07
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Title: Three-Way Component Analysis
Description: Component analysis for three-way data arrays by means of Candecomp/Parafac, Tucker3, Tucker2 and Tucker1 models.
Author: Maria Antonietta Del Ferraro, Henk A.L. Kiers, Paolo Giordani
Maintainer: Paolo Giordani <paolo.giordani@uniroma1.it>
Diff between ThreeWay versions 1.1.2 dated 2014-04-09 and 1.1.3 dated 2015-09-07
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- NAMESPACE | 5 ++++- 3 files changed, 13 insertions(+), 10 deletions(-)
Title: Interface to Colombos Compendia using the Exposed REST API
Description: Provides programmatic access to Colombos, a web based
interface for exploring and analyzing comprehensive organism-specific
cross-platform expression compendia of bacterial organisms.
Author: Paolo Sonego <paolo.sonego@fmach.it>
Maintainer: Paolo Sonego <paolo.sonego@fmach.it>
Diff between Rcolombos versions 1.5.2 dated 2015-03-04 and 1.5.3 dated 2015-09-07
DESCRIPTION | 7 +++---- MD5 | 8 ++++---- NAMESPACE | 2 ++ R/Rcolombos.R | 24 ++++++++++++------------ R/utilities.R | 12 ++++++------ 5 files changed, 27 insertions(+), 26 deletions(-)
Title: Interface for MOA Stream Clustering Algorithms
Description: Interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between streamMOA versions 1.1-1 dated 2015-07-02 and 1.1-2 dated 2015-09-07
streamMOA-1.1-1/streamMOA/R/AAA.R |only streamMOA-1.1-1/streamMOA/man/saveMOA.Rd |only streamMOA-1.1-2/streamMOA/DESCRIPTION | 8 ++++---- streamMOA-1.1-2/streamMOA/MD5 | 16 +++++++--------- streamMOA-1.1-2/streamMOA/NAMESPACE | 4 +--- streamMOA-1.1-2/streamMOA/inst/NEWS | 3 +++ streamMOA-1.1-2/streamMOA/inst/doc/streamMOA.R | 6 +++--- streamMOA-1.1-2/streamMOA/inst/doc/streamMOA.Rnw | 6 +++--- streamMOA-1.1-2/streamMOA/inst/doc/streamMOA.pdf |binary streamMOA-1.1-2/streamMOA/vignettes/streamMOA.Rnw | 6 +++--- 10 files changed, 24 insertions(+), 25 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.1-5 dated 2015-07-02 and 1.2-0 dated 2015-09-07
stream-1.1-5/stream/R/dbscan.R |only stream-1.2-0/stream/DESCRIPTION | 17 stream-1.2-0/stream/MD5 | 69 +- stream-1.2-0/stream/NAMESPACE | 25 stream-1.2-0/stream/R/DSC.R | 1 stream-1.2-0/stream/R/DSC_DBSCAN.R | 5 stream-1.2-0/stream/R/DSC_DBSTREAM.R | 162 ++-- stream-1.2-0/stream/R/DSC_DStream.R | 49 + stream-1.2-0/stream/R/DSD_Gaussians.R | 2 stream-1.2-0/stream/R/DSD_ReadCSV.R | 184 ++++- stream-1.2-0/stream/R/animation.R | 117 +-- stream-1.2-0/stream/R/description.R |only stream-1.2-0/stream/R/evaluate.R | 173 ++--- stream-1.2-0/stream/R/recluster.R | 10 stream-1.2-0/stream/R/save.R |only stream-1.2-0/stream/R/write_stream.R | 28 stream-1.2-0/stream/build/vignette.rds |binary stream-1.2-0/stream/inst/NEWS | 20 stream-1.2-0/stream/inst/doc/stream.R | 188 ++--- stream-1.2-0/stream/inst/doc/stream.Rnw | 690 +++++++++++---------- stream-1.2-0/stream/inst/doc/stream.pdf |binary stream-1.2-0/stream/inst/doc/stream_extension.R |only stream-1.2-0/stream/inst/doc/stream_extension.Rnw |only stream-1.2-0/stream/inst/doc/stream_extension.pdf |only stream-1.2-0/stream/inst/tests/test-DSC.R |only stream-1.2-0/stream/man/DSC.Rd | 8 stream-1.2-0/stream/man/DSC_DBSTREAM.Rd | 40 - stream-1.2-0/stream/man/DSD.Rd | 4 stream-1.2-0/stream/man/DSD_ReadCSV.Rd | 27 stream-1.2-0/stream/man/DSD_ReadDB.Rd | 4 stream-1.2-0/stream/man/animation.Rd | 41 - stream-1.2-0/stream/man/evaluate.Rd | 29 stream-1.2-0/stream/man/recluster.Rd | 4 stream-1.2-0/stream/man/save.Rd |only stream-1.2-0/stream/man/write_stream.Rd | 11 stream-1.2-0/stream/src/DBSTREAM.cpp | 149 +++- stream-1.2-0/stream/src/DStream.cpp | 27 stream-1.2-0/stream/vignettes/stream.Rnw | 690 +++++++++++---------- stream-1.2-0/stream/vignettes/stream.bib | 83 ++ stream-1.2-0/stream/vignettes/stream_extension.Rnw |only 40 files changed, 1673 insertions(+), 1184 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.7.0 dated 2015-07-14 and 0.8.0 dated 2015-09-07
DESCRIPTION | 6 - MD5 | 26 +++--- NEWS | 10 ++ R/availableCores.R | 2 R/plan.R | 40 ++++++++-- R/zzz.R |only build/vignette.rds |binary demo/mandelbrot.R | 51 ++++++++----- inst/doc/future.html | 5 - inst/doc/future.md.rsp | 4 - man/lazy.Rd | 179 +++++++++++++++++++++++++++-------------------- man/plan.Rd | 6 + tests/globalsOf,tweaks.R |only tests/plan.R | 43 ++++++++++- vignettes/future.md.rsp | 4 - 15 files changed, 253 insertions(+), 123 deletions(-)
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and use the utility
methods to traverse the tree in various orders. Aggregate, cumulate, print, convert to and from data.frame,
and apply functions to your tree data. Useful for decision trees, machine learning, finance, conversion
from and to JSON, and many other applications.
Author: Christoph Glur
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between data.tree versions 0.1.6 dated 2015-04-10 and 0.2.0-3 dated 2015-09-07
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data.tree-0.2.0-3/data.tree/tests/testthat/test-treeMethods.R | 533 +++ data.tree-0.2.0-3/data.tree/tests/testthat/test-treeMethodsSideEffect.R |only data.tree-0.2.0-3/data.tree/tests/testthat/test-util.R |only data.tree-0.2.0-3/data.tree/vignettes/applications.Rmd |only data.tree-0.2.0-3/data.tree/vignettes/applications.banner.html |only data.tree-0.2.0-3/data.tree/vignettes/assets/bubbles.jpg |only data.tree-0.2.0-3/data.tree/vignettes/assets/listviewer.jpg |only data.tree-0.2.0-3/data.tree/vignettes/banner_applications.jpg |only data.tree-0.2.0-3/data.tree/vignettes/data.tree.Rmd | 871 ++++- 99 files changed, 3964 insertions(+), 1851 deletions(-)
Title: Bayesian Survival Model with Lasso Shrinkage Using Generalized
Weibull Regression
Description: Bayesian survival model using Weibull regression on both scale and shape parameters. Dependence of shape parameter on covariates permits deviation from proportional-hazard assumption, leading to dynamic - i.e. non-constant with time - hazard ratios between subjects. Bayesian Lasso shrinkage in the form of two Laplace priors - one for scale and one for shape coefficients - allows for many covariates to be included. Cross-validation helper functions can be used to tune the shrinkage parameters. Monte Carlo Markov Chain (MCMC) sampling using a Gibbs wrapper around Radford Neal's univariate slice sampler (R package MfUSampler) is used for coefficient estimation.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.mahani@sentrana.com>
Diff between BSGW versions 0.9 dated 2014-10-11 and 0.9.1 dated 2015-09-07
BSGW-0.9.1/BSGW/ChangeLog |only BSGW-0.9.1/BSGW/DESCRIPTION | 16 +-- BSGW-0.9.1/BSGW/MD5 | 22 ++-- BSGW-0.9.1/BSGW/NAMESPACE | 12 ++ BSGW-0.9.1/BSGW/R/BSGW.R | 184 +++++++++++++++++++++++++---------- BSGW-0.9.1/BSGW/R/Sample.R | 41 +++---- BSGW-0.9.1/BSGW/R/utils.R | 2 BSGW-0.9.1/BSGW/man/bsgw.Rd | 6 - BSGW-0.9.1/BSGW/man/crossval_bsgw.Rd | 10 + BSGW-0.9.1/BSGW/man/plot_bsgw.Rd | 3 BSGW-0.9.1/BSGW/man/predict_bsgw.Rd | 6 - BSGW-0.9.1/BSGW/man/summary_bsgw.Rd | 3 BSGW-0.9/BSGW/R/SliceSampler.R |only 13 files changed, 197 insertions(+), 108 deletions(-)