Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.6.2 dated 2015-11-10 and 0.6.2-1 dated 2015-11-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/make.table.of.frequencies.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common
to Item Factor Analysis fitting, diagnostics, and analysis. It is
envisioned as core support code suitable for more specialized IRT packages
to build upon. Complete access to optimized C functions are made available
with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 0.48 dated 2015-08-11 and 0.49 dated 2015-11-19
DESCRIPTION | 9 +- MD5 | 170 +++++++++++++++++++++---------------------- NAMESPACE | 2 R/diagnose.R | 22 ++++- R/util.R | 17 ++-- build/vignette.rds |binary configure | 2 inst/doc/diagnostics.html | 44 +++++------ inst/include/libifa-rpf.h | 3 inst/tests/test-sumscore.R | 6 + man/ChenThissen1997.Rd | 6 + man/EAPscores.Rd | 2 man/LSAT6.Rd | 2 man/LSAT7.Rd | 2 man/SitemFit.Rd | 7 + man/SitemFit1.Rd | 2 man/as.IFAgroup.Rd | 2 man/bestToOmit.Rd | 2 man/compressDataFrame.Rd | 2 man/crosstabTest.Rd | 2 man/expandDataFrame.Rd | 2 man/fromFactorLoading.Rd | 2 man/fromFactorThreshold.Rd | 2 man/itemOutcomeBySumScore.Rd | 2 man/kct.Rd | 2 man/logit.Rd | 2 man/multinomialFit.Rd | 2 man/observedSumScore.Rd | 2 man/omitItems.Rd | 2 man/omitMostMissing.Rd | 2 man/orderCompletely.Rd | 2 man/ordinal.gamma.Rd | 2 man/ptw2011.gof.test.Rd | 2 man/read.flexmirt.Rd | 2 man/rpf.1dim-class.Rd | 2 man/rpf.1dim.drm-class.Rd | 2 man/rpf.1dim.fit.Rd | 2 man/rpf.1dim.graded-class.Rd | 2 man/rpf.1dim.grm-class.Rd | 2 man/rpf.1dim.moment.Rd | 2 man/rpf.1dim.residual.Rd | 2 man/rpf.1dim.stdresidual.Rd | 2 man/rpf.base-class.Rd | 2 man/rpf.dLL.Rd | 2 man/rpf.dTheta.Rd | 2 man/rpf.drm.Rd | 2 man/rpf.grm.Rd | 2 man/rpf.id_of.Rd | 2 man/rpf.info.Rd | 2 man/rpf.introduction.Rd | 2 man/rpf.logprob.Rd | 2 man/rpf.mcm.Rd | 2 man/rpf.mdim-class.Rd | 2 man/rpf.mdim.drm-class.Rd | 2 man/rpf.mdim.graded-class.Rd | 2 man/rpf.mdim.grm-class.Rd | 2 man/rpf.mdim.mcm-class.Rd | 2 man/rpf.mdim.nrm-class.Rd | 2 man/rpf.mean.info.Rd | 2 man/rpf.mean.info1.Rd | 2 man/rpf.modify.Rd | 2 man/rpf.nrm.Rd | 2 man/rpf.numParam.Rd | 2 man/rpf.numSpec.Rd | 2 man/rpf.ogive.Rd | 5 - man/rpf.paramInfo.Rd | 2 man/rpf.prob.Rd | 2 man/rpf.rescale.Rd | 2 man/rpf.rparam.Rd | 2 man/rpf.sample.Rd | 2 man/science.Rd | 2 man/stripData.Rd | 2 man/sumScoreEAP.Rd | 6 - man/sumScoreEAPTest.Rd | 8 +- man/tabulateRows.Rd | 2 man/toFactorLoading.Rd | 2 man/toFactorThreshold.Rd | 2 man/write.flexmirt.Rd | 2 src/Makevars | 6 - src/ba81quad.cpp | 35 +++----- src/ba81quad.h | 8 +- src/diagnose.cpp | 32 ++++---- src/eap.cpp | 3 src/glue.cpp | 68 +++++++++-------- src/libifa-rpf.cpp | 3 src/m2.cpp | 3 86 files changed, 313 insertions(+), 278 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirtCAT versions 0.6 dated 2015-10-04 and 0.6.1 dated 2015-11-19
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/TestClass.R | 16 ++++++++-------- R/generate.mirt_object.R | 2 +- R/selection_criteria.R | 14 ++++++-------- 5 files changed, 24 insertions(+), 26 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item functioning and modelling item and person
covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.13 dated 2015-09-09 and 1.14 dated 2015-11-19
DESCRIPTION | 9 MD5 | 241 ++++++++++----------- NAMESPACE | 4 NEWS | 39 +++ R/00-classes.R | 289 +++++-------------------- R/02-item_methods.R | 65 ++--- R/03-estimation.R | 408 ++++++++++++------------------------ R/DIF.R | 24 +- R/DTF.R | 48 +--- R/Discrete-methods.R | 68 +++--- R/EMstep.group.R | 23 -- R/EMstep.utils.R | 18 - R/LoadPars.R | 4 R/M2.R | 48 ++-- R/MHRM.group.R | 6 R/Mixed-methods.R | 95 ++++---- R/MultipleGroup-methods.R | 44 +-- R/PLCI.mirt.R | 74 +++--- R/PrepData.R | 8 R/SE.methods.R | 36 --- R/SingleGroup-methods.R | 320 +++++++++++++++------------- R/boot.mirt.R | 26 -- R/calcLogLik.R | 58 ++--- R/empirical_rxx.R |only R/expected.test.R | 6 R/extract.group.R | 6 R/extract.item.R | 11 R/extract.mirt.R |only R/fixef.R | 4 R/fscores.R | 41 ++- R/fscores.internal.R | 130 +++++------ R/imputeMissing.R | 16 - R/itemGAM.R | 8 R/itemfit.R | 42 +-- R/iteminfo.R | 13 - R/itemplot.R | 16 - R/itemplot.internal.R | 77 +++--- R/key2binary.R | 16 + R/marginal_rxx.R | 9 R/mdirt.R | 13 - R/mirt-package.R | 2 R/mirt.R | 19 + R/mirt.model.R | 12 - R/mod2values.R | 12 - R/model.elements.R | 30 ++ R/multipleGroup.R | 4 R/personfit.R | 22 - R/randef.R | 35 +-- R/shinyItemplot.R | 8 R/simdata.R | 2 R/testinfo.R | 7 R/utils.R | 94 +++----- R/wald.R | 16 - README.md | 4 man/Bock1997.Rd | 5 man/DIF.Rd | 2 man/DTF.Rd | 2 man/DiscreteClass-class.Rd | 55 +--- man/LSAT6.Rd | 3 man/LSAT7.Rd | 3 man/M2.Rd | 2 man/MDIFF.Rd | 2 man/MDISC.Rd | 2 man/MixedClass-class.Rd | 57 +---- man/MultipleGroupClass-class.Rd | 56 +--- man/PLCI.mirt.Rd | 3 man/SAT12.Rd | 3 man/Science.Rd | 3 man/SingleGroupClass-class.Rd | 52 +--- man/anova-method.Rd | 3 man/averageMI.Rd | 3 man/bfactor.Rd | 4 man/boot.mirt.Rd | 3 man/coef-method.Rd | 3 man/createItem.Rd | 3 man/deAyala.Rd | 3 man/empirical_rxx.Rd |only man/expand.table.Rd | 4 man/expected.item.Rd | 3 man/expected.test.Rd | 3 man/extract.group.Rd | 5 man/extract.item.Rd | 5 man/extract.mirt.Rd |only man/fixef.Rd | 2 man/fscores.Rd | 39 ++- man/imputeMissing.Rd | 6 man/itemGAM.Rd | 9 man/itemfit.Rd | 6 man/iteminfo.Rd | 10 man/itemplot.Rd | 5 man/key2binary.Rd | 18 + man/marginal_rxx.Rd | 10 man/mdirt.Rd | 11 man/mirt-package.Rd | 2 man/mirt.Rd | 24 +- man/mirt.model.Rd | 12 - man/mirtCluster.Rd | 3 man/mixedmirt.Rd | 5 man/mod2values.Rd | 2 man/multipleGroup.Rd | 6 man/personfit.Rd | 4 man/plot-method.Rd | 9 man/print-method.Rd | 5 man/probtrace.Rd | 3 man/randef.Rd | 2 man/residuals-method.Rd | 5 man/show-method.Rd | 5 man/simdata.Rd | 8 man/summary-method.Rd | 3 man/testinfo.Rd | 5 man/wald.Rd | 2 src/dpars.cpp | 211 +++++++++++------- tests/extratests/test-02-wideData.R | 4 tests/tests/test-00-basics.R |only tests/tests/test-01-mirtOne.R | 31 +- tests/tests/test-02-mirtTwo.R | 34 +-- tests/tests/test-03-bfactor.R | 22 - tests/tests/test-04-multipleGroup.R | 21 - tests/tests/test-05-confmirtOne.R | 8 tests/tests/test-06-confmirtTwo.R | 20 + tests/tests/test-07-mixedmirt.R | 20 - tests/tests/test-08-createItem.R | 3 tests/tests/test-10-extras.R | 20 - tests/tests/test-11-discrete.R | 19 + 124 files changed, 1681 insertions(+), 1875 deletions(-)
Title: Evaluation of Modeling without Information Leakage
Description: A toolbox for designing and evaluating predictive models with
resampling methods. The aim of this package is to provide a simple and
efficient general framework for working with any type of prediction
problem, be it classification, regression or survival analysis, that is
easy to extend and adapt to your specific setting. Some commonly used
methods for classification, regression and survival analysis are included.
Author: Christofer Backlin [aut, cre],
Mats Gustafsson [aut]
Maintainer: Christofer Backlin <emil@christofer.backlin.se>
Diff between emil versions 2.2.2 dated 2015-09-08 and 2.2.3 dated 2015-11-19
emil-2.2.2/emil/man/has_na.Rd |only emil-2.2.2/emil/src/has_na.cpp |only emil-2.2.3/emil/DESCRIPTION | 17 +++--- emil-2.2.3/emil/MD5 | 33 +++++++------ emil-2.2.3/emil/NAMESPACE | 7 +- emil-2.2.3/emil/NEWS.md | 10 +++- emil-2.2.3/emil/R/RcppExports.R | 16 ------ emil-2.2.3/emil/R/RcppWrappers.r | 28 ----------- emil-2.2.3/emil/R/e1071.r |only emil-2.2.3/emil/R/modeling_procedure.r | 55 +++++++++++++++------- emil-2.2.3/emil/R/preprocessing.r | 2 emil-2.2.3/emil/R/resampling.r | 11 ++-- emil-2.2.3/emil/man/fit_naive_bayes.Rd |only emil-2.2.3/emil/man/fit_svm.Rd |only emil-2.2.3/emil/man/image.resample.Rd | 2 emil-2.2.3/emil/man/learning_curve.Rd | 2 emil-2.2.3/emil/man/predict_naive_bayes.Rd |only emil-2.2.3/emil/man/predict_svm.Rd |only emil-2.2.3/emil/man/subtree.Rd | 2 emil-2.2.3/emil/src/RcppExports.cpp | 44 ----------------- emil-2.2.3/emil/tests/testthat/test-cppfunction.r | 17 ------ 21 files changed, 88 insertions(+), 158 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>
Diff between crunch versions 1.4.2 dated 2015-08-04 and 1.6.1 dated 2015-11-19
DESCRIPTION | 8 MD5 | 287 +++++----- NAMESPACE | 29 - R/AllClasses.R | 85 ++ R/AllGenerics.R | 12 R/R-to-variable.R | 32 - R/add-variable.R | 49 + R/api.R | 63 +- R/append-dataset.R | 42 - R/as-data-frame.R | 2 R/auth.R | 9 R/batches.R | 7 R/categorical-array.R | 26 R/categories.R | 66 +- R/combine.R |only R/context-manager.R |only R/copy.R |only R/crest.R | 10 R/crunch.R | 1 R/cube-query.R | 50 - R/cube-result.R | 54 + R/dataset-extract.R | 96 ++- R/dataset.R | 53 + R/edit-lock.R |only R/expressions.R | 2 R/filters.R |only R/find.R | 10 R/get-datasets.R | 4 R/github.R |only R/hide-variables.R | 37 + R/json.R | 5 R/log.R | 58 +- R/misc.R | 58 +- R/multiple-response.R | 6 R/new-dataset.R | 14 R/share.R | 16 R/show.R | 7 R/subvariables.R | 90 ++- R/teams.R | 7 R/tuple.R | 13 R/univariate.R | 76 +- R/user.R | 4 R/variable-definition.R |only R/variable-summary.R | 43 - R/variable-to-R.R | 38 + R/variable-update.R | 105 ++- R/variable.R | 7 R/versions.R | 2 R/zcl.R | 1 inst/doc/analyze.R | 21 inst/doc/analyze.Rmd | 42 + inst/doc/analyze.html | 69 +- inst/doc/array-variables.R | 23 inst/doc/array-variables.Rmd | 23 inst/doc/array-variables.html | 256 +++----- inst/doc/datasets.R | 9 inst/doc/datasets.Rmd | 9 inst/doc/datasets.html | 11 inst/doc/derive.html | 4 inst/doc/getting-started.html | 12 inst/doc/variable-order.html | 6 inst/doc/variables.R | 13 inst/doc/variables.Rmd | 31 - inst/doc/variables.html | 40 + man/Categories.Rd | 32 - man/ContextManager.Rd |only man/Subvariables.Rd | 5 man/VariableDefinition.Rd |only man/VariableOrder-extract.Rd | 16 man/appendDataset.Rd | 9 man/as.environment-CrunchDataset-method.Rd |only man/c-categories.Rd |only man/catalog-extract.Rd | 40 - man/checkForNewVersion.Rd |only man/consent.Rd |only man/copyVariable.Rd |only man/crunch-uni.Rd | 18 man/crunchAPI.Rd | 14 man/dataset-extract.Rd | 38 - man/dataset-update.Rd | 6 man/delete.Rd | 9 man/deleteSubvariables.Rd |only man/deleteVariables.Rd |only man/describe-catalog.Rd | 5 man/describe.Rd | 8 man/exclusion.Rd |only man/handleAPIresponse.Rd |only man/lock.Rd |only man/logMessage.Rd |only man/makeArray.Rd | 5 man/startLog.Rd |only man/subvars-extract.Rd | 25 man/table.Rd | 2 man/temp.options.Rd |only man/toVariable.Rd | 3 man/tojson-crunch.Rd | 3 man/tuple-methods.Rd | 2 man/variable-extract.Rd | 12 man/variable-to-R.Rd | 12 man/variable-update.Rd | 6 man/with-context-manager.Rd |only tests/testthat/api/datasets/dataset1/variables.json | 8 tests/testthat/api/datasets/dataset1/variables/birthyr.json | 3 tests/testthat/api/datasets/dataset1/variables/catarray.json | 5 tests/testthat/api/datasets/dataset1/variables/gender.json | 3 tests/testthat/api/datasets/dataset1/variables/mymrset.json | 3 tests/testthat/api/datasets/dataset1/variables/starttime.json | 3 tests/testthat/api/datasets/dataset1/variables/subvar1.json | 3 tests/testthat/api/datasets/dataset1/variables/subvar2.json | 3 tests/testthat/api/datasets/dataset1/variables/subvar3.json | 3 tests/testthat/api/datasets/dataset1/variables/textVar.json | 3 tests/testthat/dataset-fixtures |only tests/testthat/github-versions.json |only tests/testthat/helper.R | 126 +++- tests/testthat/test-active-filter.R |only tests/testthat/test-add-array.R | 4 tests/testthat/test-add-variable-definition.R |only tests/testthat/test-add-variable.R | 43 + tests/testthat/test-api.R | 18 tests/testthat/test-append-arrays.R | 105 +++ tests/testthat/test-appending.R | 34 - tests/testthat/test-as-data-frame.R | 35 - tests/testthat/test-auth.R | 12 tests/testthat/test-categories.R | 148 ++++- tests/testthat/test-combine.R |only tests/testthat/test-context-manager.R |only tests/testthat/test-copy-variable.R |only tests/testthat/test-cube-errors.R | 7 tests/testthat/test-cube-with-array.R | 56 + tests/testthat/test-cube-with-expression.R |only tests/testthat/test-cubes.R | 57 + tests/testthat/test-dataset.R | 21 tests/testthat/test-deep-copy-variable.R |only tests/testthat/test-edit-lock.R |only tests/testthat/test-exclusion-filter.R |only tests/testthat/test-expression.R | 23 tests/testthat/test-filters.R |only tests/testthat/test-github.R |only tests/testthat/test-helper.R |only tests/testthat/test-logging.R |only tests/testthat/test-make-array.R | 35 - tests/testthat/test-misc.R | 23 tests/testthat/test-new-dataset.R | 42 + tests/testthat/test-share.R | 43 - tests/testthat/test-teams.R | 6 tests/testthat/test-update-array.R | 10 tests/testthat/test-update-with-missing.R |only tests/testthat/test-update.R | 75 -- tests/testthat/test-variable-catalog.R | 4 tests/testthat/test-variable-delete.R |only tests/testthat/test-variable-summary.R | 54 - tests/testthat/test-variables.R | 31 - tests/testthat/test-versioning.R | 62 +- tests/testthat/test-weighting.R | 54 + vignettes/analyze.RData |binary vignettes/analyze.Rmd | 42 + vignettes/array-variables.RData |binary vignettes/array-variables.Rmd | 23 vignettes/datasets.Rmd | 9 vignettes/derive.RData |binary vignettes/getting-started.RData |binary vignettes/variable-order.RData |binary vignettes/variables.RData |binary vignettes/variables.Rmd | 31 - 164 files changed, 2459 insertions(+), 1234 deletions(-)
Title: Chemical Thermodynamics and Activity Diagrams
Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
and low-temperature geochemistry. The features include calculation of the standard molal
thermodynamic properties and chemical affinities of reactions involving minerals and/or
biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous
species; amino acid group additivity for the standard molal thermodynamic properties of
neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state
for aqueous species; construction of equilibrium activity diagrams as a function of
temperature, pressure, and chemical activities or fugacities of basis species.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.0.6 dated 2015-10-19 and 1.0.7 dated 2015-11-19
CHNOSZ-1.0.6/CHNOSZ/demo/CO2Ac.R |only CHNOSZ-1.0.6/CHNOSZ/demo/diagram.R |only CHNOSZ-1.0.6/CHNOSZ/demo/nonideal.R |only CHNOSZ-1.0.6/CHNOSZ/demo/phosphate.R |only CHNOSZ-1.0.6/CHNOSZ/tests/testthat/test-mosaic.R.old |only CHNOSZ-1.0.7/CHNOSZ/DESCRIPTION | 8 CHNOSZ-1.0.7/CHNOSZ/MD5 | 114 CHNOSZ-1.0.7/CHNOSZ/NAMESPACE | 3 CHNOSZ-1.0.7/CHNOSZ/R/EOSregress.R | 8 CHNOSZ-1.0.7/CHNOSZ/R/diagram.R | 12 CHNOSZ-1.0.7/CHNOSZ/R/equilibrate.R | 82 CHNOSZ-1.0.7/CHNOSZ/R/examples.R | 6 CHNOSZ-1.0.7/CHNOSZ/R/mosaic.R | 11 CHNOSZ-1.0.7/CHNOSZ/R/nonideal.R |only CHNOSZ-1.0.7/CHNOSZ/R/protein.info.R | 34 CHNOSZ-1.0.7/CHNOSZ/R/species.R | 6 CHNOSZ-1.0.7/CHNOSZ/R/swap.basis.R | 24 CHNOSZ-1.0.7/CHNOSZ/R/util.affinity.R | 5 CHNOSZ-1.0.7/CHNOSZ/R/util.expression.R | 8 CHNOSZ-1.0.7/CHNOSZ/R/util.misc.R | 63 CHNOSZ-1.0.7/CHNOSZ/R/util.plot.R | 42 CHNOSZ-1.0.7/CHNOSZ/R/util.program.R | 11 CHNOSZ-1.0.7/CHNOSZ/R/water.R | 2 CHNOSZ-1.0.7/CHNOSZ/build/vignette.rds |binary CHNOSZ-1.0.7/CHNOSZ/data/opt.csv | 4 CHNOSZ-1.0.7/CHNOSZ/demo/00Index | 5 CHNOSZ-1.0.7/CHNOSZ/demo/buffer.R | 4 CHNOSZ-1.0.7/CHNOSZ/demo/copper.R |only CHNOSZ-1.0.7/CHNOSZ/demo/nucleobase.R | 27 CHNOSZ-1.0.7/CHNOSZ/demo/solubility.R | 4 CHNOSZ-1.0.7/CHNOSZ/demo/wjd.R | 6 CHNOSZ-1.0.7/CHNOSZ/demo/yeastgfp.R | 2 CHNOSZ-1.0.7/CHNOSZ/inst/NEWS | 45 CHNOSZ-1.0.7/CHNOSZ/inst/doc/anintro.pdf |binary CHNOSZ-1.0.7/CHNOSZ/inst/doc/equilibrium.R | 411 - CHNOSZ-1.0.7/CHNOSZ/inst/doc/equilibrium.Rnw | 1010 ++- CHNOSZ-1.0.7/CHNOSZ/inst/doc/equilibrium.pdf |binary CHNOSZ-1.0.7/CHNOSZ/inst/doc/hotspring.R | 86 CHNOSZ-1.0.7/CHNOSZ/inst/doc/hotspring.pdf |binary CHNOSZ-1.0.7/CHNOSZ/inst/doc/wjd.pdf |binary CHNOSZ-1.0.7/CHNOSZ/man/CHNOSZ-package.Rd | 2 CHNOSZ-1.0.7/CHNOSZ/man/buffer.Rd | 30 CHNOSZ-1.0.7/CHNOSZ/man/data.Rd | 39 CHNOSZ-1.0.7/CHNOSZ/man/diagram.Rd | 5 CHNOSZ-1.0.7/CHNOSZ/man/equilibrate.Rd | 11 CHNOSZ-1.0.7/CHNOSZ/man/examples.Rd | 13 CHNOSZ-1.0.7/CHNOSZ/man/nonideal.Rd |only CHNOSZ-1.0.7/CHNOSZ/man/protein.info.Rd | 3 CHNOSZ-1.0.7/CHNOSZ/man/species.Rd | 2 CHNOSZ-1.0.7/CHNOSZ/man/swap.basis.Rd | 17 CHNOSZ-1.0.7/CHNOSZ/man/util.misc.Rd | 7 CHNOSZ-1.0.7/CHNOSZ/man/util.plot.Rd | 25 CHNOSZ-1.0.7/CHNOSZ/man/util.water.Rd | 12 CHNOSZ-1.0.7/CHNOSZ/man/water.Rd | 2 CHNOSZ-1.0.7/CHNOSZ/tests/testthat/test-affinity.R | 5 CHNOSZ-1.0.7/CHNOSZ/tests/testthat/test-diagram.R | 6 CHNOSZ-1.0.7/CHNOSZ/tests/testthat/test-equilibrate.R | 65 CHNOSZ-1.0.7/CHNOSZ/tests/testthat/test-makeup.R | 2 CHNOSZ-1.0.7/CHNOSZ/tests/testthat/test-util.affinity.R | 2 CHNOSZ-1.0.7/CHNOSZ/vignettes/equilibrium.Rnw | 1010 ++- CHNOSZ-1.0.7/CHNOSZ/vignettes/equilibrium.lyx | 4912 +++++++++++----- CHNOSZ-1.0.7/CHNOSZ/vignettes/vig.bib | 215 62 files changed, 6017 insertions(+), 2411 deletions(-)
Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>
Diff between BDgraph versions 2.24 dated 2015-11-18 and 2.25 dated 2015-11-19
DESCRIPTION | 8 +- MD5 | 26 +++---- src/Ig.cpp | 10 +- src/copula.cpp | 26 +++---- src/gcgm_bd.cpp | 142 +++++++++++++++++++++-------------------- src/gcgm_bd_multi_update.cpp | 146 +++++++++++++++++++++---------------------- src/gcgm_rj.cpp | 139 +++++++++++++++++++++------------------- src/ggm_bd.cpp | 140 ++++++++++++++++++++--------------------- src/ggm_bd_multi_update.cpp | 138 ++++++++++++++++++++-------------------- src/ggm_rj.cpp | 128 +++++++++++++++++++------------------ src/matrix.cpp | 35 ++++------ src/matrix.h | 2 src/rgwish.cpp | 32 ++++----- src/scaleFree.cpp | 2 14 files changed, 489 insertions(+), 485 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan versions 2.3-1 dated 2015-09-25 and 2.3-2 dated 2015-11-19
DESCRIPTION | 8 +-- MD5 | 56 +++++++++++++-------------- R/adonis.R | 7 ++- R/capscale.R | 4 + R/howHead.R | 4 - R/lines.procrustes.R | 13 ++++-- R/mso.R | 9 +++- R/ordiArgAbsorber.R | 2 R/ordicluster.R | 11 ++--- R/ordiellipse.R | 2 R/points.procrustes.R | 22 +++++++--- R/rrarefy.R | 16 ++++++- R/vegdist.R | 4 - inst/NEWS.Rd | 49 +++++++++++++++++++++++ inst/doc/FAQ-vegan.pdf |binary inst/doc/NEWS.html | 61 +++++++++++++++++++++++++++++ inst/doc/decision-vegan.pdf |binary inst/doc/diversity-vegan.pdf |binary inst/doc/intro-vegan.pdf |binary man/clamtest.Rd | 2 man/mso.Rd | 13 +++--- man/procrustes.Rd | 12 +++-- man/rarefy.Rd | 23 ++++++----- man/vegan-internal.Rd | 2 vignettes/FAQ-vegan.pdf |binary vignettes/NEWS.html | 61 +++++++++++++++++++++++++++++ vignettes/decision-vegan.tex | 20 ++++----- vignettes/diversity-vegan.tex | 86 +++++++++++++++++++++--------------------- vignettes/intro-vegan.tex | 45 ++++++++++----------- 29 files changed, 375 insertions(+), 157 deletions(-)
Title: Seasonal/Sequential (Instants/Durations, Even or not) Time
Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>
Diff between timetools versions 1.7.2 dated 2015-09-09 and 1.7.3 dated 2015-11-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/TimeIntervalDataFrame.R | 2 +- man/timetools-package.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Biclustering via Sparse Singular Value Decomposition
Incorporating Stability Selection
Description: The main function s4vd() performs a biclustering via sparse
singular value decomposition with a nested stability selection.
The results is an biclust object and thus all methods of the
biclust package can be applied.
Author: Martin Sill, Sebastian Kaiser
Maintainer: Martin Sill <m.sill@dkfz.de>
Diff between s4vd versions 1.0 dated 2011-07-23 and 1.1-1 dated 2015-11-19
s4vd-1.0/s4vd/.project |only s4vd-1.0/s4vd/data/datalist |only s4vd-1.0/s4vd/data/lung.RData |only s4vd-1.0/s4vd/man/lung.Rd |only s4vd-1.1-1/s4vd/DESCRIPTION | 21 +- s4vd-1.1-1/s4vd/MD5 |only s4vd-1.1-1/s4vd/NAMESPACE | 10 + s4vd-1.1-1/s4vd/R/heatmap.r | 312 +++++++++++++++++++------------------ s4vd-1.1-1/s4vd/R/s4vd.R | 2 s4vd-1.1-1/s4vd/R/spca.R |only s4vd-1.1-1/s4vd/R/ssvd.R | 241 ++++++++++++++-------------- s4vd-1.1-1/s4vd/R/ssvdBC.R | 48 +++-- s4vd-1.1-1/s4vd/data/lung200.RData |binary s4vd-1.1-1/s4vd/man/BCheatmap.Rd | 10 - s4vd-1.1-1/s4vd/man/BCs4vd.Rd | 26 --- s4vd-1.1-1/s4vd/man/BCssvd.Rd | 10 - s4vd-1.1-1/s4vd/man/jaccard.Rd | 2 s4vd-1.1-1/s4vd/man/stabpath.Rd | 11 - 18 files changed, 361 insertions(+), 332 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. These functions are
mainly for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm.
Author: Michael Friendly [aut, cre], John Fox [ctb], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 0.5.1 dated 2015-11-10 and 0.5.2 dated 2015-11-19
DESCRIPTION | 10 +++++----- MD5 | 32 +++++++++++++++++++------------- R/QR.R | 6 +++++- R/eig.R | 13 +++++++++++++ R/gaussian-elimination.R | 8 +++++--- R/len.R | 2 +- R/swp.R |only R/vectors.R | 22 ++++++++++++++-------- README.md | 7 ++++++- build/vignette.rds |binary inst/doc/gramreg.R |only inst/doc/gramreg.Rmd |only inst/doc/gramreg.html |only man/Ginv.Rd | 8 +++++--- man/QR.Rd | 6 +++++- man/SVD.Rd | 11 +++++++++++ man/len.Rd | 2 +- man/swp.Rd |only man/vectors.Rd | 19 +++++++++++++------ vignettes/gramreg.Rmd |only 20 files changed, 103 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-20 1.0.3
2014-08-20 1.0.2
2014-05-25 1.0.1
2014-05-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-22 1.1.2
2013-09-26 1.1.1
2012-09-28 1.0.3
2012-03-29 1.0.2
2011-11-21 1.0.1
2011-10-27 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-05 1.2.2
2015-04-20 1.2.1
2015-04-13 1.2
2014-10-06 1.1.1
2014-10-01 1.1
2014-05-29 1.0.1
2014-01-31 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-04 2.0.0.3
2014-12-22 2.0.0.2
2014-11-01 2.0.0.1
2014-03-06 2.0.0.0
2013-12-03 1.0.4.5
2012-10-24 1.0.4.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-17 0.4
2014-06-04 0.3
2014-02-07 0.2
2013-05-27 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-04 1.0.3
2015-03-05 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-27 0.3.3
2012-02-06 0.3.1.1
2011-11-25 0.3
2011-09-23 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-06 0.7-4
2014-08-15 0.7-3
2014-01-25 0.7-2
2012-07-03 0.7-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-20 1.1
2014-11-25 1.0
Title: Variable Selection for Model-Based Clustering
Description: A function which implements variable selection methodology for model-based clustering which allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting MCLUST models. By default the algorithm uses a sequential search, but parallelisation is also available.
Author: Nema Dean, Adrian E. Raftery, and Luca Scrucca
Maintainer: Luca Scrucca <luca@stat.unipg.it>
Diff between clustvarsel versions 2.1 dated 2014-10-15 and 2.2 dated 2015-11-19
DESCRIPTION | 13 ++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 9 +++++++-- R/clustvarsel.R | 29 +++++++++++++++++++++-------- R/clvarselhlbkw.R | 4 ++++ R/clvarselhlfwd.R | 23 +++++++++-------------- inst/CITATION | 4 ++-- inst/NEWS | 4 ++++ man/clustvarsel.Rd | 46 ++++++++++++++++++++++++++-------------------- 9 files changed, 87 insertions(+), 61 deletions(-)
Title: Generalized Linear Models Extended
Description: Extended techniques for generalized linear models (GLMs), especially for binary responses,
including parametric links and heteroskedastic latent variables.
Author: Achim Zeileis [aut, cre],
Roger Koenker [aut],
Philipp Doebler [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between glmx versions 0.1-0 dated 2013-12-10 and 0.1-1 dated 2015-11-19
DESCRIPTION | 10 ++++----- MD5 | 22 ++++++++++---------- NAMESPACE | 3 +- NEWS | 7 ++++++ R/glmx.R | 46 +++++++++++++++++++++++++++++++++++++++++-- R/pregibon.R | 12 +++-------- data/AbortionAmbivalence.rda |binary data/BeetleMortality.rda |binary data/MexicanLabor.rda |binary data/WECO.rda |binary man/AbortionAmbivalence.Rd | 2 - man/glmx.Rd | 1 12 files changed, 75 insertions(+), 28 deletions(-)
Title: Spatial Exposure-Hazard Model for Exposure and Impact Assessment
on Exposed Individuals
Description: A model coupling polygon and point processes for assessing
risk due to contaminant sources and their impact on exposed individuals.
Author: Marc Bourotte [ctb],
Melen Leclerc [aut],
Jean-Francois Rey [aut, cre],
Samuel Soubeyrand [ctb],
Emily Walker [aut]
Maintainer: Jean-Francois Rey <jean-francois.rey@paca.inra.fr>
Diff between SEHmodel versions 0.0.9 dated 2015-10-02 and 0.0.10 dated 2015-11-19
SEHmodel-0.0.10/SEHmodel/DESCRIPTION | 9 +++-- SEHmodel-0.0.10/SEHmodel/MD5 | 16 +++++----- SEHmodel-0.0.10/SEHmodel/NAMESPACE | 3 + SEHmodel-0.0.10/SEHmodel/R/Class-Individuals.R | 4 +- SEHmodel-0.0.10/SEHmodel/R/Individuals-Methods.R | 15 +++++---- SEHmodel-0.0.10/SEHmodel/R/ecoToxic.R | 15 ++++++--- SEHmodel-0.0.10/SEHmodel/R/toxicIntensity.R | 3 + SEHmodel-0.0.10/SEHmodel/man/Individuals-class.Rd | 2 - SEHmodel-0.0.10/SEHmodel/man/Individuals-get-methods.Rd |only SEHmodel-0.0.9/SEHmodel/man/sub-Individuals-numeric-numeric-logical-method.Rd |only 10 files changed, 39 insertions(+), 28 deletions(-)
Title: Log-Gaussian Cox Process
Description: Spatial and spatio-temporal modelling of point patterns using the
log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle. Additional
code contributions from Edzer Pebesma.
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between lgcp versions 1.3-11 dated 2015-09-10 and 1.3-13 dated 2015-11-19
DESCRIPTION | 13 +++++++------ MD5 | 13 +++++++------ R/lgcpMethods.R | 3 ++- README.md |only data/wpopdata.rda |binary data/wtowncoords.rda |binary data/wtowns.rda |binary inst/doc/lgcp.pdf |binary 8 files changed, 16 insertions(+), 13 deletions(-)
Title: A Simple Approach to Scale Gene Expression Data Derived from
Different Platforms for Integrated Analyses
Description: Simple method for comparison of gene
expression generated across different experiments, and on
different platforms; that does not require global
renormalization, and is not restricted to comparison of
identical probes. YuGene works on a range of microarray dataset
distributions, such as between manufacturers. The resulting
output allows direct comparisons of gene expression between
experiments and experimental platforms.
Author: Kim-Anh Le Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A. Wells
Maintainer: Florian Rohart <f.rohart@uq.edu.au>
Diff between YuGene versions 1.1.4 dated 2015-07-30 and 1.1.5 dated 2015-11-19
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 5 +++++ R/pca.YuGene.R | 11 +++++------ man/pca.YuGene.Rd | 5 ++--- man/pca.default.Rd | 5 ++--- 6 files changed, 24 insertions(+), 22 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided by this package to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo and (optionally penalized) maximum likelihood estimation via optimization. In both cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Author: Jiqiang Guo [aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Joel de Guzman [cph] (Boost),
Eric Niebler [cph] (Boost),
Thomas Heller [cph] (Boost),
John Fletcher [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.8.0 dated 2015-09-19 and 2.8.1 dated 2015-11-19
DESCRIPTION | 13 ++- MD5 | 60 ++++++++--------- NAMESPACE | 11 ++- R/AllClass.R | 1 R/cxxdso-class.R | 2 R/expose_stan_functions.R | 57 ++++++++++++---- R/extract_sparse_parts.R | 12 +-- R/misc.R | 13 ++- R/pairs.R | 4 - R/plugin.R | 2 R/rstan.R | 8 +- R/rstan_package_skeleton.R |only R/stan_plot.R | 71 ++++++++++---------- R/stan_plot_helpers.R | 83 +++++++++++++---------- R/stanc.R | 48 ++++++++----- R/stanfit-class.R | 26 ++++--- R/stanmodel-class.R | 129 ++++++++++++++++++++++++------------- inst/doc/rstan_vignette.R | 2 inst/doc/rstan_vignette.Rnw | 2 inst/doc/rstan_vignette.pdf |binary man/rstan-internal.Rd | 2 man/rstan.package.skeleton.Rd |only man/sflist2stanfit.Rd | 17 ++-- man/stan_plot.Rd | 9 +- man/stan_plot_diagnostics.Rd | 62 +++++++++++++++-- man/stanc.Rd | 55 ++++++++++----- man/stanfit-method-plot.Rd | 59 +++++----------- man/stanmodel-class.Rd | 3 man/stanmodel-method-optimizing.Rd | 18 ++++- src/sparse_extractors.cpp | 2 src/stanc.cpp | 24 ++++++ vignettes/rstan_vignette.Rnw | 2 32 files changed, 499 insertions(+), 298 deletions(-)
Title: Data and Functions from the Book R Graphics, Second Edition
Description: Data and Functions from the book R Graphics, Second Edition. There is a function to produce each figure in the book, plus several functions, classes, and methods defined in Chapter 8.
Author: Paul Murrell
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between RGraphics versions 2.0-12 dated 2014-09-12 and 2.0-13 dated 2015-11-19
DESCRIPTION | 11 - MD5 | 18 +- NAMESPACE | 23 +++ R/figures.R | 382 ++++++++++++++++++++++++++++---------------------------- R/globals.R | 11 + data/ocean.rda |binary data/ozTemp.rda |binary data/wind.rda |binary data/xmm.rda |binary man/ozTemp.Rd | 3 10 files changed, 239 insertions(+), 209 deletions(-)
Title: Use Python from Within R
Description: Interact with Python from within R.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between PythonInR versions 0.1-2 dated 2015-11-14 and 0.1-3 dated 2015-11-19
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- README.md | 22 ++++++++++++---------- inst/testing/NA_NaN_Inf.R | 1 + inst/testing/PyExec.R | 3 ++- inst/testing/PyOptions.R | 3 +++ inst/testing/all.R | 9 +++++---- src/PythonFunctions.c | 2 +- src/PythonFunctions.h | 4 ++++ src/Python_Explicit_Linking.c | 2 +- src/Python_Explicit_Linking.h | 15 ++++++++------- 11 files changed, 50 insertions(+), 37 deletions(-)
Title: Modelling and Analysis of Leaf Gas Exchange Data
Description: Coupled leaf gas exchange model, A-Ci curve simulation and
fitting, leaf energy balance using Penman-Monteith, Cowan-Farquhar
optimization, unit conversions.
Author: Remko Duursma [aut, cre]
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between plantecophys versions 0.6-3 dated 2015-07-10 and 1.0 dated 2015-11-19
DESCRIPTION | 14 +++-- MD5 | 45 ++++++++++++++---- R/LeafEnergyBalance.R | 11 +++- R/Tresponsefunctions.R | 12 ++-- R/fitBB.R | 55 +++++++++++++--------- R/fitaci.R | 118 ++++++++++++++++++++++++++++++++++++------------- R/fitacis.R | 42 +++++++++++++++-- R/photosyn.R | 22 ++++++--- inst |only man/Photosyn.Rd | 17 +++++-- man/fitBB.Rd | 8 ++- man/fitaci.Rd | 32 ++++++++++--- 12 files changed, 278 insertions(+), 98 deletions(-)
Title: Omics Data Integration Project
Description: We provide statistical integrative techniques and
variants to analyse highly dimensional data sets: regularized
Canonical Correlation Analysis ('rCCA') and sparse Partial Least Squares variants ('sPLS')
to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and
q variables are measured on the same samples or individuals n. These data may come from high throughput
technologies, such as 'omics' data (e.g. transcriptomics, metabolomics or proteomics
data) that require an integrative or joint analysis. However, 'mixOmics' can also be applied to any other
large data sets where p + q >> n. 'rCCA' is a regularized version of Canonical Correlation Analysis to deal with
the large number of variables. 'sPLS' allows variable selection in a one step procedure and two frameworks
are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting
the results. Recent methodological developments include: sparse PLS-Discriminant Analysis ('sPLS-DA'), Independent
Principal Component Analysis ('IPCA'), multilevel analysis using variance decomposition of the data and integration
of multiple data sets with regularized Generalised Canonical Correlation Analysis ('rGCCA') and variants (sparse 'GCCA'). More details can be found
on our website.
Author: Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean with key contributors Florian Rohart, Benoit Gautier
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>
Diff between mixOmics versions 5.1.2 dated 2015-08-29 and 5.2.0 dated 2015-11-19
mixOmics-5.1.2/mixOmics/R/network.rcc.R |only mixOmics-5.1.2/mixOmics/R/network.spls.R |only mixOmics-5.1.2/mixOmics/R/pheatmap.multilevel.R |only mixOmics-5.1.2/mixOmics/R/pheatmap.multilevel.splsda1fact.R |only mixOmics-5.1.2/mixOmics/R/pheatmap.multilevel.splsda2fact.R |only mixOmics-5.1.2/mixOmics/R/plot3dIndiv.R |only mixOmics-5.1.2/mixOmics/R/plot3dVar.R |only mixOmics-5.1.2/mixOmics/man/pheatmap.multilevel.Rd |only mixOmics-5.1.2/mixOmics/man/plot3dIndiv.Rd |only mixOmics-5.1.2/mixOmics/man/plot3dVar.Rd |only mixOmics-5.1.2/mixOmics/man/tau.estimate.Rd |only mixOmics-5.2.0/mixOmics/DESCRIPTION | 10 mixOmics-5.2.0/mixOmics/MD5 | 131 - mixOmics-5.2.0/mixOmics/NAMESPACE | 42 mixOmics-5.2.0/mixOmics/NEWS | 30 mixOmics-5.2.0/mixOmics/R/Mfold.R | 2 mixOmics-5.2.0/mixOmics/R/bin.color.R | 5 mixOmics-5.2.0/mixOmics/R/cim.R | 865 ++---- mixOmics-5.2.0/mixOmics/R/helpers.R | 6 mixOmics-5.2.0/mixOmics/R/image.tune.rcc.R | 77 mixOmics-5.2.0/mixOmics/R/imageMap.R |only mixOmics-5.2.0/mixOmics/R/imgCor.R | 290 +- mixOmics-5.2.0/mixOmics/R/ipca.R | 310 +- mixOmics-5.2.0/mixOmics/R/loo.R | 2 mixOmics-5.2.0/mixOmics/R/nearZeroVar.R | 2 mixOmics-5.2.0/mixOmics/R/network.R | 1543 +++++++----- mixOmics-5.2.0/mixOmics/R/nipals.R | 76 mixOmics-5.2.0/mixOmics/R/pca.R | 271 +- mixOmics-5.2.0/mixOmics/R/plot.pca.R | 53 mixOmics-5.2.0/mixOmics/R/plotArrow.R |only mixOmics-5.2.0/mixOmics/R/plotContrib.R | 451 +-- mixOmics-5.2.0/mixOmics/R/plotIndiv.R | 1082 ++++++-- mixOmics-5.2.0/mixOmics/R/plotVar.R | 585 +++- mixOmics-5.2.0/mixOmics/R/rcc.R | 219 + mixOmics-5.2.0/mixOmics/R/scatterutil.R | 602 ++-- mixOmics-5.2.0/mixOmics/R/selectVar.R | 181 - mixOmics-5.2.0/mixOmics/R/sipca.R | 14 mixOmics-5.2.0/mixOmics/R/spca.R | 6 mixOmics-5.2.0/mixOmics/R/spls.R | 4 mixOmics-5.2.0/mixOmics/R/srgcca.R | 8 mixOmics-5.2.0/mixOmics/R/wrappers.R | 12 mixOmics-5.2.0/mixOmics/R/zzz.R |only mixOmics-5.2.0/mixOmics/data/breast.tumors.rda |binary mixOmics-5.2.0/mixOmics/data/linnerud.rda |binary mixOmics-5.2.0/mixOmics/data/liver.toxicity.rda |binary mixOmics-5.2.0/mixOmics/data/multidrug.rda |binary mixOmics-5.2.0/mixOmics/data/nutrimouse.rda |binary mixOmics-5.2.0/mixOmics/data/prostate.rda |binary mixOmics-5.2.0/mixOmics/data/srbct.rda |binary mixOmics-5.2.0/mixOmics/data/vac18.rda |binary mixOmics-5.2.0/mixOmics/data/vac18.simulated.rda |binary mixOmics-5.2.0/mixOmics/data/yeast.rda |binary mixOmics-5.2.0/mixOmics/man/cim.Rd | 250 - mixOmics-5.2.0/mixOmics/man/imgCor.Rd | 65 mixOmics-5.2.0/mixOmics/man/internal-functions.Rd | 2 mixOmics-5.2.0/mixOmics/man/ipca.Rd | 22 mixOmics-5.2.0/mixOmics/man/multilevel.Rd | 1 mixOmics-5.2.0/mixOmics/man/network.Rd | 243 - mixOmics-5.2.0/mixOmics/man/pca.Rd | 29 mixOmics-5.2.0/mixOmics/man/plotArrow.Rd |only mixOmics-5.2.0/mixOmics/man/plotContrib.Rd | 88 mixOmics-5.2.0/mixOmics/man/plotIndiv.Rd | 275 +- mixOmics-5.2.0/mixOmics/man/plotVar.Rd | 265 -- mixOmics-5.2.0/mixOmics/man/plsda.Rd | 2 mixOmics-5.2.0/mixOmics/man/rcc.Rd | 36 mixOmics-5.2.0/mixOmics/man/s.match.Rd | 1 mixOmics-5.2.0/mixOmics/man/selectVar.Rd | 36 mixOmics-5.2.0/mixOmics/man/sipca.Rd | 12 mixOmics-5.2.0/mixOmics/man/spca.Rd | 11 mixOmics-5.2.0/mixOmics/man/spls.Rd | 1 mixOmics-5.2.0/mixOmics/man/splsda.Rd | 3 mixOmics-5.2.0/mixOmics/man/tune.pca.Rd | 4 mixOmics-5.2.0/mixOmics/man/withinVariation.Rd | 1 mixOmics-5.2.0/mixOmics/man/wrappers.Rd | 45 74 files changed, 4889 insertions(+), 3382 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for binary classification models using weight-of-evidence (WOE) and information value (IV). In order to make the package as efficient as possible, aggregations are done in data.table and creation of WOE vectors can be distributed across multiple cores. The package also supports exploration for uplift models (NWOE and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.6 dated 2015-11-13 and 0.0.7 dated 2015-11-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/Information-vignette.Rmd | 22 +++++++++++----------- inst/doc/Information-vignette.html | 28 ++++++++++++++-------------- vignettes/Information-vignette.Rmd | 22 +++++++++++----------- 5 files changed, 44 insertions(+), 44 deletions(-)
Title: Package for Environmental Statistics, Including US EPA Guidance
Description: Graphical and statistical analyses of environmental data, with
focus on analyzing chemical concentrations and physical parameters, usually in
the context of mandated environmental monitoring. Major environmental
statistical methods found in the literature and regulatory guidance documents,
with extensive help that explains what these methods do, how to use them,
and where to find them in the literature. Numerous built-in data sets from
regulatory guidance documents and environmental statistics literature. Includes
scripts reproducing analyses presented in the book "EnvStats: An R Package for
Environmental Statistics" (Millard, 2013, Springer).
Author: Steven P. Millard <EnvStats@ProbStatInfo.com>
Maintainer: Steven P. Millard <EnvStats@ProbStatInfo.com>
Diff between EnvStats versions 2.0.1 dated 2015-05-25 and 2.0.2 dated 2015-11-19
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Title: Bagging Whole-Genome Regression
Description: Designed for whole-genome regressions using Bayesian models fitted via Gibbs sampling with optional resampling techniques and polygenic term with reduced dimensionality.
Author: Alencar Xavier, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between bWGR versions 1.2 dated 2015-10-28 and 1.3 dated 2015-11-19
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Title: Learning Discrete Bayesian Network Classifiers from Data
Description: Implements state-of-the art algorithms for learning discrete Bayesian network classifiers from data, as well as functions for using these classifiers for prediction, assessing their predictive performance, and inspecting their properties.
Author: Mihaljevic Bojan [aut, cre],
Bielza Concha [aut],
Larranaga Pedro [aut],
Wickham Hadley [ctb] (some code extracted from memoise package)
Maintainer: Mihaljevic Bojan <bmihaljevic@fi.upm.es>
Diff between bnclassify versions 0.3.1 dated 2015-10-29 and 0.3.2 dated 2015-11-19
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