Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.4 dated 2015-11-23 and 0.5 dated 2015-11-27
DESCRIPTION | 10 +- MD5 | 20 ++-- NEWS | 10 ++ R/scatterD3.R | 7 + README.md | 8 + inst/doc/introduction.R | 6 + inst/doc/introduction.Rmd | 12 ++ inst/doc/introduction.html | 49 ++++++---- inst/htmlwidgets/scatterD3.js | 195 +++++++++++++++++++++++++++++++++--------- man/scatterD3.Rd | 11 +- vignettes/introduction.Rmd | 12 ++ 11 files changed, 263 insertions(+), 77 deletions(-)
Title: Practical Numerical Math Functions
Description:
Functions from numerical analysis and linear algebra, numerical
optimization, differential equations, plus some special functions.
Uses Matlab function names where appropriate to simplify porting.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>
Diff between pracma versions 1.8.6 dated 2015-07-14 and 1.8.8 dated 2015-11-27
pracma-1.8.6/pracma/man/invperm.Rd |only pracma-1.8.8/pracma/DESCRIPTION | 13 +++++++----- pracma-1.8.8/pracma/MD5 | 25 +++++++++++------------ pracma-1.8.8/pracma/NEWS | 11 ++++++++++ pracma-1.8.8/pracma/R/findpeaks.R | 32 +++++++++++++++++++++++------- pracma-1.8.8/pracma/R/interp1.R | 2 - pracma-1.8.8/pracma/R/legendre.R | 14 ++++++++----- pracma-1.8.8/pracma/R/perms.R | 9 -------- pracma-1.8.8/pracma/data/brown72.rda |binary pracma-1.8.8/pracma/data/nile.rda |binary pracma-1.8.8/pracma/data/titanium.rda |binary pracma-1.8.8/pracma/man/interp1.Rd | 6 ++--- pracma-1.8.8/pracma/man/pracma-package.Rd | 2 - pracma-1.8.8/pracma/man/rkf54.Rd | 3 -- 14 files changed, 71 insertions(+), 46 deletions(-)
Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files, calculate DVH
metrics as well as generalized equivalent uniform dose (gEUD),
biologically effective dose (BED), equivalent dose in 2 Gy
fractions (EQD2), normal tissue complication probability
(NTCP), and tumor control probability (TCP). Show DVH
diagrams, check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>
Diff between DVHmetrics versions 0.3.3 dated 2015-10-13 and 0.3.4 dated 2015-11-27
DESCRIPTION | 8 - MD5 | 94 ++++++------- NAMESPACE | 12 + R/checkConstraint.R | 11 + R/convertDVH.R | 156 +++++++++++++++++----- R/dvhDistance.R | 2 R/getEUD.R | 6 R/getMeanDVH.R |only R/getMetric.R | 65 ++++++--- R/parseCadplan.R | 3 R/parseEclipse.R | 3 R/parseHiArt.R | 15 -- R/parseMasterplan.R | 3 R/parseMonaco.R | 15 -- R/parsePinnacleDVH.R | 15 -- R/parseRayStation.R | 17 -- R/print.R | 12 + R/readDVH.R | 29 ++++ R/showConstraint.R | 8 - R/showDVH.R | 302 ++++++++++++++++++++++++++++++++------------ R/smoothDVH.R | 169 +++++++++++++++++++----- R/unitConversion.R | 20 +- inst/ChangeLog | 25 +++ inst/DVHshiny/ABOUT.md | 2 inst/DVHshiny/helper.R | 5 inst/DVHshiny/server.R | 72 ++++++++-- inst/DVHshiny/ui.R | 39 +++-- inst/doc/DVHmetrics.R | 18 ++ inst/doc/DVHmetrics.Rnw | 39 ++++- inst/doc/DVHmetrics.pdf |binary inst/doc/DVHshiny.Rnw | 2 inst/doc/DVHshiny.pdf |binary man/DVHmetrics-package.Rd | 4 man/checkConstraint.Rd | 4 man/convertDVH.Rd | 13 + man/getDMEAN.Rd | 4 man/getMeanDVH.Rd |only man/getMetric.Rd | 18 +- man/getNTCP.Rd | 2 man/getTCP.Rd | 2 man/readDVH.Rd | 4 man/saveDVH.Rd | 2 man/saveMetric.Rd | 2 man/showConstraint.Rd | 2 man/showDVH.Rd | 28 ++-- vignettes/DVHmetrics.Rnw | 39 ++++- vignettes/DVHshiny.Rnw | 2 vignettes/appShowConstr.jpg |binary vignettes/lit.bib | 12 - 49 files changed, 917 insertions(+), 388 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and
inference.
This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB,
MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing
and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms
for discrete, Gaussian and conditional Gaussian networks, along with many
score functions and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are
also implemented.
Some utility functions (model comparison and manipulation, random data
generation, arc orientation testing, simple and advanced plots) are
included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries and
cross-validation. Development snapshots with the latest bugfixes are
available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari <marco.scutari@gmail.com>
Diff between bnlearn versions 3.8.1 dated 2015-05-17 and 3.9 dated 2015-11-27
bnlearn-3.8.1/bnlearn/R/frontend-mvber.R |only bnlearn-3.8.1/bnlearn/R/mvber.R |only bnlearn-3.8.1/bnlearn/man/bn.var.Rd |only bnlearn-3.8.1/bnlearn/src/all.monte.carlo.c |only bnlearn-3.8.1/bnlearn/src/discrete.mutual.information.c |only bnlearn-3.8.1/bnlearn/src/gaussian.mutual.information.c |only bnlearn-3.8.1/bnlearn/src/mvber.c |only bnlearn-3.8.1/bnlearn/src/pearson.x2.c |only bnlearn-3.9/bnlearn/Changelog | 27 bnlearn-3.9/bnlearn/DESCRIPTION | 8 bnlearn-3.9/bnlearn/MD5 | 249 ++++---- bnlearn-3.9/bnlearn/NAMESPACE | 15 bnlearn-3.9/bnlearn/R/custom.fit.R | 15 bnlearn-3.9/bnlearn/R/cv.R | 34 - bnlearn-3.9/bnlearn/R/fast-iamb.R | 45 - bnlearn-3.9/bnlearn/R/fitted.assignment.R | 9 bnlearn-3.9/bnlearn/R/frontend-bn.R | 32 - bnlearn-3.9/bnlearn/R/frontend-bootstrap.R | 46 + bnlearn-3.9/bnlearn/R/frontend-lattice.R | 10 bnlearn-3.9/bnlearn/R/frontend-learning.R | 2 bnlearn-3.9/bnlearn/R/frontend-plot.R | 65 ++ bnlearn-3.9/bnlearn/R/frontend-predict.R | 4 bnlearn-3.9/bnlearn/R/frontend-print.R | 44 - bnlearn-3.9/bnlearn/R/frontend-score.R | 4 bnlearn-3.9/bnlearn/R/frontend-strength.R | 5 bnlearn-3.9/bnlearn/R/globals.R | 25 bnlearn-3.9/bnlearn/R/incremental-association.R | 41 - bnlearn-3.9/bnlearn/R/inter-iamb.R | 43 - bnlearn-3.9/bnlearn/R/lattice.R | 198 ++++-- bnlearn-3.9/bnlearn/R/learning-algorithms.R | 4 bnlearn-3.9/bnlearn/R/loss.R | 41 - bnlearn-3.9/bnlearn/R/nparams.R | 29 - bnlearn-3.9/bnlearn/R/scores.R | 5 bnlearn-3.9/bnlearn/R/test.R | 23 bnlearn-3.9/bnlearn/R/utils-misc.R | 32 + bnlearn-3.9/bnlearn/R/utils-sanitization.R | 62 +- bnlearn-3.9/bnlearn/inst/CITATION | 19 bnlearn-3.9/bnlearn/man/alarm.Rd | 116 +--- bnlearn-3.9/bnlearn/man/arc.strength.Rd | 144 ++--- bnlearn-3.9/bnlearn/man/arcops.Rd | 82 +- bnlearn-3.9/bnlearn/man/asia.Rd | 46 - bnlearn-3.9/bnlearn/man/bn.class.Rd | 123 +--- bnlearn-3.9/bnlearn/man/bn.cv.Rd | 168 ++++- bnlearn-3.9/bnlearn/man/bn.fit.Rd | 57 + bnlearn-3.9/bnlearn/man/bn.fit.class.Rd | 85 +- bnlearn-3.9/bnlearn/man/bn.fit.methods.Rd | 96 +-- bnlearn-3.9/bnlearn/man/bn.fit.plots.Rd | 41 - bnlearn-3.9/bnlearn/man/bn.kcv.class.Rd | 13 bnlearn-3.9/bnlearn/man/bn.strength-class.Rd | 24 bnlearn-3.9/bnlearn/man/bnboot.Rd | 53 - bnlearn-3.9/bnlearn/man/bnlearn-package.Rd | 292 +++++----- bnlearn-3.9/bnlearn/man/choose.direction.Rd | 46 - bnlearn-3.9/bnlearn/man/ci.test.Rd | 57 - bnlearn-3.9/bnlearn/man/clgaussian-test.Rd | 10 bnlearn-3.9/bnlearn/man/compare.Rd | 33 - bnlearn-3.9/bnlearn/man/configs.Rd | 6 bnlearn-3.9/bnlearn/man/constraint.Rd | 94 +-- bnlearn-3.9/bnlearn/man/coronary.Rd | 41 - bnlearn-3.9/bnlearn/man/cpdag.Rd | 82 +- bnlearn-3.9/bnlearn/man/cpquery.Rd | 107 +-- bnlearn-3.9/bnlearn/man/deal.Rd | 10 bnlearn-3.9/bnlearn/man/dsep.Rd | 2 bnlearn-3.9/bnlearn/man/foreign.Rd | 36 - bnlearn-3.9/bnlearn/man/gRain.Rd | 6 bnlearn-3.9/bnlearn/man/gaussian-test.Rd | 8 bnlearn-3.9/bnlearn/man/graph.Rd | 20 bnlearn-3.9/bnlearn/man/graphgen.Rd | 106 +-- bnlearn-3.9/bnlearn/man/graphviz.plot.Rd | 80 +- bnlearn-3.9/bnlearn/man/hailfinder.Rd | 212 +++++-- bnlearn-3.9/bnlearn/man/hc.Rd | 70 +- bnlearn-3.9/bnlearn/man/hybrid.Rd | 110 +-- bnlearn-3.9/bnlearn/man/insurance.Rd | 90 ++- bnlearn-3.9/bnlearn/man/learn.Rd | 64 +- bnlearn-3.9/bnlearn/man/learning-test.Rd | 28 bnlearn-3.9/bnlearn/man/lizards.Rd | 36 - bnlearn-3.9/bnlearn/man/marks.Rd | 15 bnlearn-3.9/bnlearn/man/mb.Rd | 41 - bnlearn-3.9/bnlearn/man/mmpc.Rd | 72 +- bnlearn-3.9/bnlearn/man/modelstring.Rd | 25 bnlearn-3.9/bnlearn/man/naive.bayes.Rd | 77 +- bnlearn-3.9/bnlearn/man/ordering.Rd | 46 - bnlearn-3.9/bnlearn/man/parallel.Rd | 10 bnlearn-3.9/bnlearn/man/plot.bn.Rd | 17 bnlearn-3.9/bnlearn/man/plot.bn.strength.Rd | 6 bnlearn-3.9/bnlearn/man/preprocessing.Rd | 24 bnlearn-3.9/bnlearn/man/rbn.Rd | 28 bnlearn-3.9/bnlearn/man/relevant.Rd | 32 - bnlearn-3.9/bnlearn/man/score.Rd | 104 +-- bnlearn-3.9/bnlearn/man/strength.plot.Rd | 84 +- bnlearn-3.9/bnlearn/man/test.counter.Rd | 6 bnlearn-3.9/bnlearn/src/allocations.c | 74 -- bnlearn-3.9/bnlearn/src/allsubs.test.c | 458 +++------------- bnlearn-3.9/bnlearn/src/bind.c | 4 bnlearn-3.9/bnlearn/src/cache.structure.c | 4 bnlearn-3.9/bnlearn/src/cg.mutual.information.c | 18 bnlearn-3.9/bnlearn/src/configurations.c | 1 bnlearn-3.9/bnlearn/src/contincency.tables.c |only bnlearn-3.9/bnlearn/src/covariance.c | 22 bnlearn-3.9/bnlearn/src/cpdist.c | 18 bnlearn-3.9/bnlearn/src/ctest.c | 427 ++++---------- bnlearn-3.9/bnlearn/src/data.frame.c | 32 + bnlearn-3.9/bnlearn/src/dedup.c | 26 bnlearn-3.9/bnlearn/src/df.adjust.c | 4 bnlearn-3.9/bnlearn/src/discrete.monte.carlo.c | 282 +++------ bnlearn-3.9/bnlearn/src/discrete.tests.c |only bnlearn-3.9/bnlearn/src/enums.c |only bnlearn-3.9/bnlearn/src/fitted.c | 10 bnlearn-3.9/bnlearn/src/gaussian.monte.carlo.c | 189 +++--- bnlearn-3.9/bnlearn/src/gaussian.tests.c |only bnlearn-3.9/bnlearn/src/globals.c | 2 bnlearn-3.9/bnlearn/src/graph.priors.c | 37 + bnlearn-3.9/bnlearn/src/hc.cache.lookup.c | 6 bnlearn-3.9/bnlearn/src/htest.c | 17 bnlearn-3.9/bnlearn/src/include/allocations.h | 10 bnlearn-3.9/bnlearn/src/include/covariance.h | 7 bnlearn-3.9/bnlearn/src/include/dataframe.h | 2 bnlearn-3.9/bnlearn/src/include/rcore.h | 3 bnlearn-3.9/bnlearn/src/include/sampling.h | 4 bnlearn-3.9/bnlearn/src/include/tests.h | 124 ++-- bnlearn-3.9/bnlearn/src/jonckheere.c | 45 - bnlearn-3.9/bnlearn/src/likelihood.weighting.c | 19 bnlearn-3.9/bnlearn/src/linear.algebra.c | 76 -- bnlearn-3.9/bnlearn/src/linear.correlation.c | 43 - bnlearn-3.9/bnlearn/src/map.lw.c | 10 bnlearn-3.9/bnlearn/src/mi.matrix.c | 40 - bnlearn-3.9/bnlearn/src/nparams.c | 157 ++--- bnlearn-3.9/bnlearn/src/rcont2.c | 226 +++---- bnlearn-3.9/bnlearn/src/roundrobin.test.c |only bnlearn-3.9/bnlearn/src/shrinkage.c | 134 +--- bnlearn-3.9/bnlearn/src/strings.c | 22 bnlearn-3.9/bnlearn/src/utest.c | 319 +++-------- bnlearn-3.9/bnlearn/src/which.max.c | 22 132 files changed, 3434 insertions(+), 3877 deletions(-)
Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between archivist versions 1.7 dated 2015-09-25 and 1.8 dated 2015-11-27
DESCRIPTION | 14 - MD5 | 126 +++++---- NAMESPACE | 27 + NEWS.md | 76 +++++ R/Repository.R | 64 +++- R/Tags.R | 69 ++--- R/addTagsRepo.R | 104 ++++--- R/ahistory.R | 60 +++- R/archive.R |only R/archivist-package.R | 49 +++ R/archivistOptions.R | 84 +++++- R/aread.R | 21 - R/asearch.R | 18 - R/cache.R | 5 R/cloneGithubRepo.R |only R/copyToRepo.R | 164 ++++++++--- R/createEmptyRepo.R | 310 +++++++++++++++++++--- R/deleteRepo.R | 76 +++-- R/extractMiniature.R | 27 - R/getTags.R | 121 ++++++-- R/githubFunctions.R |only R/loadFromRepo.R | 110 +++++-- R/magrittr.R | 57 ++-- R/md5hash.R | 29 +- R/rmFromRepo.R | 400 +++++++++++++++++------------ R/saveToRepo.R | 235 ++++++++++++----- R/searchInRepo.R | 95 +++--- R/setRepo.R | 192 ++++++++----- R/shinySearchInLocalRepo.R | 16 - R/showRepo.R | 78 +++-- R/splitTags.R |only R/summaryRepo.R | 53 +-- R/zipRepo.R | 92 +++--- R/zzz.R | 33 ++ man/Repository.Rd | 73 ++++- man/Tags.Rd | 81 +++-- man/addTagsRepo.Rd | 101 +++++-- man/ahistory.Rd | 71 ++--- man/archive.Rd |only man/archivist-github-integration.Rd |only man/archivist-package.Rd | 29 +- man/archivistOptions.Rd | 90 +++++- man/aread.Rd | 36 +- man/asearch.Rd | 31 +- man/cache.Rd | 20 + man/cloneGithubRepo.Rd |only man/copyToRepo.Rd | 132 +++++++-- man/createEmptyRepo.Rd | 155 +++++++++-- man/deleteRepo.Rd | 73 +++-- man/getTags.Rd | 136 +++++++-- man/loadFromRepo.Rd | 90 ++++-- man/magrittr.Rd | 67 +++- man/md5hash.Rd | 43 +-- man/pipe.Rd |only man/rmFromRepo.Rd | 227 +++++++++------- man/saveToRepo.Rd | 125 +++++---- man/searchInRepo.Rd | 101 ++++--- man/setRepo.Rd | 178 +++++++----- man/shinySearchInRepo.Rd | 26 + man/showRepo.Rd | 83 +++--- man/splitTags.Rd |only man/summaryRepo.Rd | 61 ++-- man/zipRepo.Rd | 74 ++--- tests/testthat.R | 2 tests/testthat/test_aoptions.R | 1 tests/testthat/test_base_functionalities.R | 6 tests/testthat/test_jss_artilce.R | 4 tests/testthat/test_showLocal.R |only tests/testthat/test_splitTags.R |only tests/testthat/test_zip.R |only 70 files changed, 3362 insertions(+), 1559 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.8.6-0 dated 2015-10-15 and 0.9.0-1 dated 2015-11-27
DESCRIPTION | 9 MD5 | 127 ++++++----- NAMESPACE | 13 + NEWS | 37 +++ R/RcppExports.R | 12 - R/collocations.R | 424 ++++++++++++++++++++-------------------- R/converters.R | 7 R/corpus.R | 257 ++++++++++++++++-------- R/dataDocs.R | 3 R/dfm-classes.R | 7 R/dfm-main.R | 38 +-- R/dfm-methods.R | 109 +++++++--- R/dictionaries.R | 26 +- R/encoding.R | 4 R/kwic.R | 69 ++++-- R/ngrams.R | 213 +++++--------------- R/plots.R | 70 ++++-- R/readability.R | 14 + R/stopwords.R | 179 ++++++++-------- R/textfile.R | 12 + R/textmodel-wordfish.R | 31 ++ R/toLower.R | 5 R/tokenize.R | 108 +++------- R/wordstem.R | 24 +- README.md | 154 +------------- build/vignette.rds |binary demo/quanteda.R | 150 ++++++++++++-- inst/doc/LitVignette.R |only inst/doc/LitVignette.Rmd |only inst/doc/LitVignette.html |only inst/doc/development-plans.R | 3 inst/doc/development-plans.Rmd | 25 +- inst/doc/development-plans.html | 24 +- inst/doc/quickstart.html | 84 +++---- man/applyDictionary.Rd | 16 - man/cbind.dfm.Rd |only man/changeunits.Rd | 20 + man/collocations.Rd | 20 + man/convert.Rd | 4 man/corpus.Rd | 17 + man/dfm.Rd | 20 - man/docfreq.Rd | 2 man/docnames.Rd | 4 man/docvars.Rd | 8 man/head.dfm.Rd | 2 man/ie2010Corpus.Rd | 9 man/kwic.Rd | 20 + man/metacorpus.Rd | 9 man/metadoc.Rd | 17 + man/ngrams.Rd | 72 +++--- man/ntoken.Rd | 6 man/plot.dfm.Rd | 50 +++- man/plot.kwic.Rd |only man/readability.Rd | 2 man/sample.Rd | 2 man/segment.Rd | 14 - man/selectFeatures.Rd | 1 man/summary.corpus.Rd | 2 man/textmodel_wordfish.Rd | 5 man/texts.Rd | 29 +- man/tokenize.Rd | 25 +- man/trim.Rd | 43 ++-- src/RcppExports.cpp | 35 +++ src/ngrams.cpp |only src/wordfish.cpp | 73 +++++- tests/testthat/testDfm.R | 18 + vignettes/LitVignette.Rmd |only vignettes/development-plans.Rmd | 25 +- 68 files changed, 1604 insertions(+), 1204 deletions(-)
Title: Generating Various Numerical Representation Schemes of Protein
Sequence
Description: Comprehensive toolkit for generating various numerical
representation schemes of protein sequence. The descriptors and similarity
scores included are extensively used in bioinformatics and chemogenomics.
For full functionality, the software 'ncbi-blast+' is needed, see
<http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download>
for more information.
Author: Nan Xiao <road2stat@gmail.com>, Qingsong Xu <dasongxu@gmail.com>,
Dongsheng Cao <oriental-cds@163.com>
Maintainer: Nan Xiao <road2stat@gmail.com>
Diff between protr versions 0.5-1 dated 2014-12-23 and 1.0-1 dated 2015-11-27
protr-0.5-1/protr/NEWS |only protr-0.5-1/protr/README |only protr-1.0-1/protr/DESCRIPTION | 18 protr-1.0-1/protr/LICENSE | 2 protr-1.0-1/protr/MD5 | 250 - protr-1.0-1/protr/NAMESPACE | 11 protr-1.0-1/protr/NEWS.md |only protr-1.0-1/protr/R/desc01AAC.R | 40 protr-1.0-1/protr/R/desc02DC.R | 114 protr-1.0-1/protr/R/desc03TC.R | 1822 ++++++------- protr-1.0-1/protr/R/desc04MoreauBroto.R | 116 protr-1.0-1/protr/R/desc05Moran.R | 148 - protr-1.0-1/protr/R/desc06Geary.R | 150 - protr-1.0-1/protr/R/desc07CTDC.R | 88 protr-1.0-1/protr/R/desc07CTDCClass.R | 45 protr-1.0-1/protr/R/desc08CTDT.R | 80 protr-1.0-1/protr/R/desc08CTDTClass.R | 77 protr-1.0-1/protr/R/desc09CTDD.R | 72 protr-1.0-1/protr/R/desc09CTDDClass.R | 53 protr-1.0-1/protr/R/desc10CTriad.R | 3578 +++++++++++++-------------- protr-1.0-1/protr/R/desc10CTriadClass.R | 51 protr-1.0-1/protr/R/desc11SOCN.R | 68 protr-1.0-1/protr/R/desc12QSO.R | 84 protr-1.0-1/protr/R/desc13PAAC.R | 190 - protr-1.0-1/protr/R/desc14APAAC.R | 186 - protr-1.0-1/protr/R/desc15PSSM.R | 295 +- protr-1.0-1/protr/R/desc15PSSMAcc.R | 93 protr-1.0-1/protr/R/desc15PSSMFeature.R | 45 protr-1.0-1/protr/R/misc01readFASTA.R | 156 - protr-1.0-1/protr/R/misc02readPDB.R | 71 protr-1.0-1/protr/R/misc03protcheck.R | 28 protr-1.0-1/protr/R/misc04protseg.R | 47 protr-1.0-1/protr/R/misc05getUniProt.R | 41 protr-1.0-1/protr/R/misc06acc.R | 75 protr-1.0-1/protr/R/par01parSeqSim.R | 86 protr-1.0-1/protr/R/par02parGOSim.R | 106 protr-1.0-1/protr/R/pcm01extractScales.R | 23 protr-1.0-1/protr/R/pcm01extractScalesGap.R | 33 protr-1.0-1/protr/R/pcm02extractDescScales.R | 61 protr-1.0-1/protr/R/pcm03extractProtFP.R | 13 protr-1.0-1/protr/R/pcm04extractFAScales.R | 65 protr-1.0-1/protr/R/pcm05extractMDSScales.R | 59 protr-1.0-1/protr/R/pcm06extractBLOSUM.R | 37 protr-1.0-1/protr/R/protr-datalist.R | 350 +- protr-1.0-1/protr/R/protr-package.R | 18 protr-1.0-1/protr/README.md |only protr-1.0-1/protr/build/vignette.rds |binary protr-1.0-1/protr/inst/CITATION | 29 protr-1.0-1/protr/inst/doc/protr.R | 28 protr-1.0-1/protr/inst/doc/protr.Rnw | 58 protr-1.0-1/protr/inst/doc/protr.pdf |binary protr-1.0-1/protr/man/AA2DACOR.Rd | 3 protr-1.0-1/protr/man/AA3DMoRSE.Rd | 3 protr-1.0-1/protr/man/AAACF.Rd | 3 protr-1.0-1/protr/man/AABLOSUM100.Rd | 3 protr-1.0-1/protr/man/AABLOSUM45.Rd | 3 protr-1.0-1/protr/man/AABLOSUM50.Rd | 3 protr-1.0-1/protr/man/AABLOSUM62.Rd | 3 protr-1.0-1/protr/man/AABLOSUM80.Rd | 3 protr-1.0-1/protr/man/AABurden.Rd | 3 protr-1.0-1/protr/man/AACPSA.Rd | 3 protr-1.0-1/protr/man/AAConn.Rd | 3 protr-1.0-1/protr/man/AAConst.Rd | 3 protr-1.0-1/protr/man/AADescAll.Rd | 3 protr-1.0-1/protr/man/AAEdgeAdj.Rd | 3 protr-1.0-1/protr/man/AAEigIdx.Rd | 3 protr-1.0-1/protr/man/AAFGC.Rd | 3 protr-1.0-1/protr/man/AAGETAWAY.Rd | 3 protr-1.0-1/protr/man/AAGeom.Rd | 3 protr-1.0-1/protr/man/AAInfo.Rd | 3 protr-1.0-1/protr/man/AAMOE2D.Rd | 3 protr-1.0-1/protr/man/AAMOE3D.Rd | 3 protr-1.0-1/protr/man/AAMetaInfo.Rd | 3 protr-1.0-1/protr/man/AAMolProp.Rd | 3 protr-1.0-1/protr/man/AAPAM120.Rd | 3 protr-1.0-1/protr/man/AAPAM250.Rd | 3 protr-1.0-1/protr/man/AAPAM30.Rd | 3 protr-1.0-1/protr/man/AAPAM40.Rd | 3 protr-1.0-1/protr/man/AAPAM70.Rd | 3 protr-1.0-1/protr/man/AARDF.Rd | 3 protr-1.0-1/protr/man/AARandic.Rd | 3 protr-1.0-1/protr/man/AATopo.Rd | 3 protr-1.0-1/protr/man/AATopoChg.Rd | 3 protr-1.0-1/protr/man/AAWHIM.Rd | 3 protr-1.0-1/protr/man/AAWalk.Rd | 3 protr-1.0-1/protr/man/AAindex.Rd | 3 protr-1.0-1/protr/man/OptAA3d.Rd | 2 protr-1.0-1/protr/man/acc.Rd | 4 protr-1.0-1/protr/man/extractAAC.Rd | 4 protr-1.0-1/protr/man/extractAPAAC.Rd | 44 protr-1.0-1/protr/man/extractBLOSUM.Rd | 4 protr-1.0-1/protr/man/extractCTDC.Rd | 4 protr-1.0-1/protr/man/extractCTDCClass.Rd | 4 protr-1.0-1/protr/man/extractCTDD.Rd | 4 protr-1.0-1/protr/man/extractCTDDClass.Rd | 4 protr-1.0-1/protr/man/extractCTDT.Rd | 4 protr-1.0-1/protr/man/extractCTDTClass.Rd | 4 protr-1.0-1/protr/man/extractCTriad.Rd | 4 protr-1.0-1/protr/man/extractCTriadClass.Rd | 4 protr-1.0-1/protr/man/extractDC.Rd | 4 protr-1.0-1/protr/man/extractDescScales.Rd | 10 protr-1.0-1/protr/man/extractFAScales.Rd | 10 protr-1.0-1/protr/man/extractGeary.Rd | 54 protr-1.0-1/protr/man/extractMDSScales.Rd | 8 protr-1.0-1/protr/man/extractMoran.Rd | 54 protr-1.0-1/protr/man/extractMoreauBroto.Rd | 54 protr-1.0-1/protr/man/extractPAAC.Rd | 48 protr-1.0-1/protr/man/extractPSSM.Rd | 4 protr-1.0-1/protr/man/extractPSSMAcc.Rd | 4 protr-1.0-1/protr/man/extractPSSMFeature.Rd | 4 protr-1.0-1/protr/man/extractProtFP.Rd | 10 protr-1.0-1/protr/man/extractProtFPGap.Rd | 9 protr-1.0-1/protr/man/extractQSO.Rd | 4 protr-1.0-1/protr/man/extractSOCN.Rd | 4 protr-1.0-1/protr/man/extractScales.Rd | 10 protr-1.0-1/protr/man/extractScalesGap.Rd | 10 protr-1.0-1/protr/man/extractTC.Rd | 4 protr-1.0-1/protr/man/getUniProt.Rd | 7 protr-1.0-1/protr/man/parGOSim.Rd | 6 protr-1.0-1/protr/man/parSeqSim.Rd | 4 protr-1.0-1/protr/man/protcheck.Rd | 8 protr-1.0-1/protr/man/protr-package.Rd | 17 protr-1.0-1/protr/man/protseg.Rd | 16 protr-1.0-1/protr/man/readFASTA.Rd | 20 protr-1.0-1/protr/man/readPDB.Rd | 14 protr-1.0-1/protr/man/twoGOSim.Rd | 6 protr-1.0-1/protr/man/twoSeqSim.Rd | 4 protr-1.0-1/protr/vignettes/protr.Rnw | 58 128 files changed, 4867 insertions(+), 4853 deletions(-)
Title: Coclustering Package for Binary, Categorical, Contingency and
Continuous Data-Sets
Description: Simultaneous clustering of rows and columns, usually designated by
biclustering, co-clustering or block clustering, is an important technique
in two way data analysis. It consists of estimating a mixture model which
takes into account the block clustering problem on both the individual and
variables sets. The blockcluster package provides a bridge between the C++
core library and the R statistical computing environment. This package
allows to co-cluster binary, contingency, continuous and categorical
data-sets. It also provides utility functions to visualize the results.
This package may be useful for various applications in fields of Data
mining,Information retrieval, Biology, computer vision and many more. More
information about the project and comprehensive tutorial can be found on
the link mentioned in URL.
Author: Serge Iovleff [aut, cre],
Parmeet Singh Bhatia [aut],
Vincent Kubicki [ctb],
Gerard Goavert [ctb],
Vincent Brault [ctb],
Christophe Biernacki [ctb],
Gilles Celeux [ctb]
Maintainer: Serge Iovleff <Serge.Iovleff@stkpp.org>
Diff between blockcluster versions 3.0.2 dated 2015-01-23 and 4.0.2 dated 2015-11-27
blockcluster-3.0.2/blockcluster/R/Rcoclust.R |only blockcluster-3.0.2/blockcluster/R/Strategy.R |only blockcluster-3.0.2/blockcluster/R/plot.R |only blockcluster-3.0.2/blockcluster/R/summary.R |only blockcluster-3.0.2/blockcluster/inst/doc/blockcluster_tutorial_V3.0.Rnw |only blockcluster-3.0.2/blockcluster/inst/doc/blockcluster_tutorial_V3.0.pdf |only blockcluster-3.0.2/blockcluster/man/cocluststrategy.Rd |only blockcluster-3.0.2/blockcluster/man/strategy-class.Rd |only blockcluster-3.0.2/blockcluster/src/Makevars.win |only blockcluster-3.0.2/blockcluster/vignettes/blockcluster_tutorial_V3.0.Rnw |only blockcluster-4.0.2/blockcluster/DESCRIPTION | 48 blockcluster-4.0.2/blockcluster/MD5 | 176 +- blockcluster-4.0.2/blockcluster/NAMESPACE | 20 blockcluster-4.0.2/blockcluster/R/RCocluster.R |only blockcluster-4.0.2/blockcluster/R/cocluster.R | 335 ++-- blockcluster-4.0.2/blockcluster/R/coclusterBinary.R |only blockcluster-4.0.2/blockcluster/R/coclusterCategorical.R |only blockcluster-4.0.2/blockcluster/R/coclusterContingency.R |only blockcluster-4.0.2/blockcluster/R/coclusterContinuous.R |only blockcluster-4.0.2/blockcluster/R/coclusterStrategy.R |only blockcluster-4.0.2/blockcluster/R/optionclasses.R | 745 +++++++++- blockcluster-4.0.2/blockcluster/build/vignette.rds |binary blockcluster-4.0.2/blockcluster/cleanup |only blockcluster-4.0.2/blockcluster/data/binarydata.rda |binary blockcluster-4.0.2/blockcluster/data/categoricaldata.rda |binary blockcluster-4.0.2/blockcluster/data/contingencydatalist.rda |binary blockcluster-4.0.2/blockcluster/data/contingencydataunknown.rda |binary blockcluster-4.0.2/blockcluster/data/gaussiandata.rda |binary blockcluster-4.0.2/blockcluster/inst/doc/blockcluster_tutorial.R |only blockcluster-4.0.2/blockcluster/inst/doc/blockcluster_tutorial.Rnw |only blockcluster-4.0.2/blockcluster/inst/doc/blockcluster_tutorial.pdf |only blockcluster-4.0.2/blockcluster/man/BinaryOptions-class.Rd | 20 blockcluster-4.0.2/blockcluster/man/CategoricalOptions-class.Rd | 18 blockcluster-4.0.2/blockcluster/man/CommonOptions-class.Rd | 44 blockcluster-4.0.2/blockcluster/man/ContingencyOptions-class.Rd | 20 blockcluster-4.0.2/blockcluster/man/ContinuousOptions-class.Rd | 18 blockcluster-4.0.2/blockcluster/man/XEMStrategy.Rd | 35 blockcluster-4.0.2/blockcluster/man/blockcluster.Rd | 53 blockcluster-4.0.2/blockcluster/man/cocluster.Rd | 104 - blockcluster-4.0.2/blockcluster/man/coclusterBinary.Rd |only blockcluster-4.0.2/blockcluster/man/coclusterCategorical.Rd |only blockcluster-4.0.2/blockcluster/man/coclusterContingency.Rd |only blockcluster-4.0.2/blockcluster/man/coclusterContinuous.Rd |only blockcluster-4.0.2/blockcluster/man/coclusterStrategy.Rd |only blockcluster-4.0.2/blockcluster/man/getter-methods.Rd | 33 blockcluster-4.0.2/blockcluster/man/plot-methods.Rd | 36 blockcluster-4.0.2/blockcluster/man/summary-methods.Rd | 31 blockcluster-4.0.2/blockcluster/src/BinaryDataExchange.cpp | 223 +- blockcluster-4.0.2/blockcluster/src/BinaryDataExchange.h | 6 blockcluster-4.0.2/blockcluster/src/CategoricalDataExchange.cpp | 150 -- blockcluster-4.0.2/blockcluster/src/CategoricalDataExchange.h | 4 blockcluster-4.0.2/blockcluster/src/ContingencyDataExchange.cpp | 77 - blockcluster-4.0.2/blockcluster/src/ContingencyDataExchange.h | 12 blockcluster-4.0.2/blockcluster/src/ContinuousDataExchange.cpp | 75 - blockcluster-4.0.2/blockcluster/src/ContinuousDataExchange.h | 4 blockcluster-4.0.2/blockcluster/src/IDataExchange.cpp | 36 blockcluster-4.0.2/blockcluster/src/IDataExchange.h | 17 blockcluster-4.0.2/blockcluster/src/Makevars | 16 blockcluster-4.0.2/blockcluster/src/Rcoclustmain.cpp | 46 blockcluster-4.0.2/blockcluster/src/coclust/makefile | 12 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/CEMAlgo.cpp | 10 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/CEMAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/EMAlgo.cpp | 10 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/EMAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/IAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/SEMAlgo.cpp | 10 blockcluster-4.0.2/blockcluster/src/coclust/src/Algorithms/SEMAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/CoClustFacade/CoCluster.cpp | 2 blockcluster-4.0.2/blockcluster/src/coclust/src/CoClustFacade/CoCluster.h | 2 blockcluster-4.0.2/blockcluster/src/coclust/src/Initialization/CEMInit.h | 4 blockcluster-4.0.2/blockcluster/src/coclust/src/Initialization/FuzzyCEMInit.h | 16 blockcluster-4.0.2/blockcluster/src/coclust/src/Initialization/IInit.h | 2 blockcluster-4.0.2/blockcluster/src/coclust/src/Initialization/RandomInit.h | 4 blockcluster-4.0.2/blockcluster/src/coclust/src/InputParameters/InputParameters.cpp | 16 blockcluster-4.0.2/blockcluster/src/coclust/src/InputParameters/InputParameters.h | 28 blockcluster-4.0.2/blockcluster/src/coclust/src/Models/BinaryLBModel.cpp | 514 +++--- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/BinaryLBModel.h | 108 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/BinaryLBModelequalepsilon.cpp | 469 ++---- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/BinaryLBModelequalepsilon.h | 144 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/CategoricalLBModel.cpp | 577 +++---- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/CategoricalLBModel.h | 54 blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContingencyLBModel.cpp | 412 ++--- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContingencyLBModel.h | 101 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContingencyLBModel_mu_i_nu_j.cpp | 245 +-- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContingencyLBModel_mu_i_nu_j.h | 100 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContinuousLBModel.cpp | 327 ++-- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContinuousLBModel.h | 113 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContinuousLBModelequalsigma.cpp | 289 +-- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ContinuousLBModelequalsigma.h | 104 - blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ICoClustModel.cpp | 637 ++++---- blockcluster-4.0.2/blockcluster/src/coclust/src/Models/ICoClustModel.h | 403 ++--- blockcluster-4.0.2/blockcluster/src/coclust/src/Strategy/IStrategy.h | 2 blockcluster-4.0.2/blockcluster/src/coclust/src/Strategy/XStrategyAlgo.cpp | 133 - blockcluster-4.0.2/blockcluster/src/coclust/src/Strategy/XStrategyAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/Strategy/XStrategyforSEMAlgo.cpp | 30 blockcluster-4.0.2/blockcluster/src/coclust/src/Strategy/XStrategyforSEMAlgo.h | 6 blockcluster-4.0.2/blockcluster/src/coclust/src/enumerations/enumerations.h | 2 blockcluster-4.0.2/blockcluster/src/coclust/src/typedefs/typedef.h | 31 blockcluster-4.0.2/blockcluster/src/conversion.h | 30 blockcluster-4.0.2/blockcluster/src/test/test.cpp | 2 blockcluster-4.0.2/blockcluster/vignettes/biblio.bib | 13 blockcluster-4.0.2/blockcluster/vignettes/blockcluster_tutorial.Rnw |only 102 files changed, 3882 insertions(+), 3512 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner <gregor.kastner@wu.ac.at>
Diff between stochvol versions 1.2.0 dated 2015-07-15 and 1.2.1 dated 2015-11-27
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 10 ++++++++-- R/wrappers.R | 20 +++++++++++++++++--- build/vignette.rds |binary data/exrates.RData |binary inst/doc/article.pdf |binary inst/doc/heavytails.pdf |binary man/svsample.Rd | 18 +++++++++++------- src/progutils.cpp | 4 ++-- src/progutils.h | 16 +++++++++++----- src/sampler.cpp | 24 +++++++++++++++--------- src/sampler.h | 2 +- 13 files changed, 81 insertions(+), 45 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 2.8.1 dated 2015-11-19 and 2.8.2 dated 2015-11-27
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/expose_stan_functions.R | 10 +++++++--- R/rstan.R | 12 +++++++----- R/stanc.R | 4 +--- R/stanmodel-class.R | 25 +++++++++++++++++-------- inst/NEWS | 14 ++++++++++++++ inst/doc/rstan_vignette.R | 2 +- inst/doc/rstan_vignette.Rnw | 2 +- inst/doc/rstan_vignette.pdf |binary man/rstan.Rd | 4 ++-- man/stan.Rd | 3 --- man/stan_model.Rd | 6 ++++-- vignettes/rstan_vignette.Rnw | 2 +- 14 files changed, 72 insertions(+), 46 deletions(-)
Title: A Wrapper for the Pinnacle Sports API
Description: An R interface to the Pinnaclesports.com API.
Author: Marco Blume, Nicholas Jhirad, Amine Gassem
Maintainer: Marco Blume <marco.blume@pinnaclesports.com>
Diff between pinnacle.API versions 1.89 dated 2015-09-18 and 1.90 dated 2015-11-27
DESCRIPTION | 6 +++--- MD5 | 10 ++++++---- NAMESPACE | 1 + NEWS | 7 +++++++ R/pinnRawXMLResponse.R |only R/showOddsDF.R | 10 +++++++--- man/pinnRawXMLResponse.Rd |only 7 files changed, 24 insertions(+), 10 deletions(-)
Title: Calculate Indices and Theoretical Properties of Protein
Sequences
Description: Calculate physicochemical properties and indices from amino-acid sequences of peptides and proteins. Include also the option to read and plot output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres.
Maintainer: Daniel Osorio <daniel.osorio@correo.uis.edu.co>
Diff between Peptides versions 1.1.0 dated 2015-06-03 and 1.1.1 dated 2015-11-27
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 5 ++++- NEWS | 4 ++++ R/aacomp.R | 2 +- R/aindex.R | 2 +- R/boman.R | 2 +- R/charge.R | 2 +- R/hmoment.R | 2 +- R/hydrophobicity.R | 2 +- R/instaindex.R | 2 +- R/kidera.R | 2 +- R/lengthpep.R | 2 +- R/membpos.R | 2 +- R/mw.R | 24 ++++++++++++++++-------- R/pI.R | 2 +- man/Peptides-package.Rd | 4 ++-- man/mw.Rd | 6 +++--- 18 files changed, 61 insertions(+), 46 deletions(-)
Title: Utilities for Producing Maps
Description: A minimal, light-weight set of tools for producing nice looking maps in R, with support for map projections.
Author: Patrick Brown <patrick.brown@utoronto.ca>
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between mapmisc versions 1.4.0 dated 2015-08-26 and 1.4.6 dated 2015-11-27
DESCRIPTION | 16 ++--- MD5 | 43 ++++++++----- NAMESPACE | 12 ++- R/colourScale.R | 6 + R/geonames.R | 28 ++++++++- R/gridlinesWrap.R |only R/legendBreaks.R | 152 +++++++++++++------------------------------------ R/legendTable.R | 2 R/map.new.R | 10 +++ R/moll.R |only R/omerc.R | 17 ----- R/openmap.R | 18 ++--- R/openmapAttribution.R | 4 - R/utils.R | 39 +++++++++--- R/wrapPoly.R |only inst/doc/mapLayers.pdf |binary inst/doc/mapmisc.pdf |binary man/colourScale.Rd | 3 man/geocode.Rd |only man/gridlinesWrap.Rd |only man/legendBreaks.Rd | 4 + man/omerc.Rd | 29 ++++++++- man/scaleBar.Rd | 7 -- man/wrapPoly.Rd |only tests/omerc.R | 1 tests/worldMap.R |only 26 files changed, 203 insertions(+), 188 deletions(-)
Title: Ensemble Partial Least Squares Regression
Description: Ensemble partial least squares regression, a unified
framework for feature selection, outlier detection, and ensemble learning.
Author: Nan Xiao <road2stat@gmail.com>, Dong-Sheng Cao <oriental-cds@163.com>,
Qing-Song Xu <dasongxu@gmail.com>
Maintainer: Nan Xiao <road2stat@gmail.com>
Diff between enpls versions 1.0 dated 2014-10-03 and 1.1 dated 2015-11-27
enpls-1.0/enpls/vignettes/fig/plot-cv-enpls.pdf |only enpls-1.1/enpls/DESCRIPTION | 13 ++-- enpls-1.1/enpls/MD5 | 67 ++++++++++++------------ enpls-1.1/enpls/NAMESPACE | 11 +++ enpls-1.1/enpls/NEWS |only enpls-1.1/enpls/R/cv.enpls.R | 4 - enpls-1.1/enpls/R/enpls-package.R | 19 +++--- enpls-1.1/enpls/R/enpls.en.R | 8 +- enpls-1.1/enpls/R/enpls.fs.R | 8 +- enpls-1.1/enpls/R/enpls.od.R | 8 +- enpls-1.1/enpls/R/plot.R | 15 ++--- enpls-1.1/enpls/R/predict.R | 5 - enpls-1.1/enpls/R/print.R | 20 ++----- enpls-1.1/enpls/README.md |only enpls-1.1/enpls/build/vignette.rds |binary enpls-1.1/enpls/inst/doc/enpls.R | 23 +++----- enpls-1.1/enpls/inst/doc/enpls.Rnw | 29 +++------- enpls-1.1/enpls/inst/doc/enpls.pdf |binary enpls-1.1/enpls/man/alkanes.Rd | 11 ++- enpls-1.1/enpls/man/cv.enpls.Rd | 17 ++---- enpls-1.1/enpls/man/enpls-package.Rd | 21 +++---- enpls-1.1/enpls/man/enpls.en.Rd | 21 +++---- enpls-1.1/enpls/man/enpls.en.core.Rd | 3 - enpls-1.1/enpls/man/enpls.fs.Rd | 21 +++---- enpls-1.1/enpls/man/enpls.fs.core.Rd | 3 - enpls-1.1/enpls/man/enpls.od.Rd | 23 ++++---- enpls-1.1/enpls/man/enpls.od.core.Rd | 5 + enpls-1.1/enpls/man/plot.cv.enpls.Rd | 8 +- enpls-1.1/enpls/man/plot.enpls.fs.Rd | 8 +- enpls-1.1/enpls/man/plot.enpls.od.Rd | 10 +-- enpls-1.1/enpls/man/predict.enpls.en.Rd | 14 ++--- enpls-1.1/enpls/man/print.cv.enpls.Rd | 8 +- enpls-1.1/enpls/man/print.enpls.en.Rd | 8 +- enpls-1.1/enpls/man/print.enpls.fs.Rd | 8 +- enpls-1.1/enpls/man/print.enpls.od.Rd | 8 +- enpls-1.1/enpls/vignettes/enpls.Rnw | 29 +++------- 36 files changed, 216 insertions(+), 240 deletions(-)
Title: Embedded Conic Solver in R
Description: R interface to the Embedded COnic Solver (ECOS), an efficient
and robust C library for convex problems. Conic and equality
constraints can be specified in addition to integer and
boolean variable constraints for mixed-integer problems. This
R interface is inspired by the python interface and has
similar calling conventions.
Author: Anqi Fu [aut],
Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between ECOSolveR versions 0.1-1 dated 2015-11-25 and 0.2 dated 2015-11-27
ECOSolveR-0.1-1/ECOSolveR/inst/misc/ECOS.Rmd |only ECOSolveR-0.1-1/ECOSolveR/inst/misc/ECOSolver.Rmd |only ECOSolveR-0.1-1/ECOSolveR/src/configure |only ECOSolveR-0.1-1/ECOSolveR/src/ecos/Makefile.orig |only ECOSolveR-0.1-1/ECOSolveR/src/ecos/Makefile.unix |only ECOSolveR-0.1-1/ECOSolveR/src/ecos/Makefile.win |only ECOSolveR-0.1-1/ECOSolveR/src/ecos/ecos.mk.orig |only ECOSolveR-0.2/ECOSolveR/DESCRIPTION | 20 ++++--- ECOSolveR-0.2/ECOSolveR/MD5 | 35 +++++-------- ECOSolveR-0.2/ECOSolveR/README.md | 14 ++++- ECOSolveR-0.2/ECOSolveR/inst/doc/examples.html | 4 - ECOSolveR-0.2/ECOSolveR/src/Makevars.in | 4 + ECOSolveR-0.2/ECOSolveR/src/Makevars.win | 6 +- ECOSolveR-0.2/ECOSolveR/src/ecos/Makefile | 22 +++----- ECOSolveR-0.2/ECOSolveR/src/ecos/README.md | 2 ECOSolveR-0.2/ECOSolveR/src/ecos/__.SYMDEF |binary ECOSolveR-0.2/ECOSolveR/src/ecos/ecos-unix.mk | 30 ++++------- ECOSolveR-0.2/ECOSolveR/src/ecos/ecos-win.mk | 18 +++--- ECOSolveR-0.2/ECOSolveR/src/ecos/ecos.mk | 30 ++++------- ECOSolveR-0.2/ECOSolveR/src/ecos/ecos_bb/ecos_bb_preproc.c | 2 ECOSolveR-0.2/ECOSolveR/src/ecos/external/amd/Makefile | 2 ECOSolveR-0.2/ECOSolveR/src/ecos/external/ldl/Makefile | 2 22 files changed, 94 insertions(+), 97 deletions(-)
Title: Feature Selection and Classification with the Embedded
Validation Procedures for Biomedical Data Analysis
Description: Contains functions for the data analysis with the emphasis on biological data, including several algorithms for feature ranking, feature selection, classification
algorithms with the embedded validation procedures.
The functions can deal with numerical as well as with nominal features. Includes also the functions for calculation
of feature AUC (Area Under the ROC Curve) and HUM (hypervolume under manifold) values and construction 2D- and 3D- ROC curves.
Biocomb provides the calculation of Area Above the RCC (AAC) values and construction of Relative Cost Curves
(RCC) to estimate the classifier performance under unequal misclassification costs problem.
Biocomb has the special function to deal with missing values, including different imputing schemes.
Author: Natalia Novoselova,Junxi Wang,Frank Pessler,Frank Klawonn
Maintainer: Natalia Novoselova <novos65@mail.ru>
Diff between Biocomb versions 0.1 dated 2015-10-28 and 0.2 dated 2015-11-27
DESCRIPTION | 16 - MD5 | 52 +++-- NAMESPACE | 2 R/CalculateHUM_ROC.R | 4 R/CalculateHUM_seq.R | 2 R/ROC_Plot.R | 7 R/RcppExports.R | 24 ++ R/class_cross.R | 38 +++- R/input_miss.R | 4 R/select.feature.info.R | 375 +++++------------------------------------- man/Biocomb-package.Rd | 2 man/CalculateHUM_Ex.Rd | 4 man/chi2.algorithm.Rd | 6 man/classifier.loop.Rd | 2 man/compute.aucs.Rd | 2 man/data_test.Rd | 2 man/input_miss.Rd | 2 man/leukemia72.Rd | 3 man/leukemia72_2.Rd | 3 man/select.cfs.Rd |only man/select.fast.filter.Rd | 2 man/select.forward.wrapper.Rd | 2 man/select.inf.gain.Rd | 2 man/select.inf.symm.Rd | 2 man/select.process.Rd | 6 man/select.relief.Rd |only src/CHI2.cpp |only src/CorrF.cpp |only src/RcppExports.cpp | 87 +++++++++ 29 files changed, 252 insertions(+), 399 deletions(-)