Title: ANALYZING RNA SEQUENCE COUNT TABLES USING QUASI-LIKELIHOOD
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with 'QL', 'QLShrink' and 'QLSpline' methods (Lund, Nettleton, McCarthy, and Smyth, 2012).
Author: Steve Lund [aut],
Long Qu [aut, cre, ctb],
Ian Marschner [aut] (The author of glm2::glm.fit2, which was modified
slightly leading to glm.fit3 in this package.),
R Core Team [aut] (The author of stats::glm.fit, which was modified
slightly leading to glm.fit3 in this package.)
Maintainer: Long Qu <long.qu@wright.edu>
Diff between QuasiSeq versions 1.0-6 dated 2015-02-03 and 1.0-7 dated 2015-05-13
QuasiSeq-1.0-6/QuasiSeq/R/fbrglm.R |only QuasiSeq-1.0-6/QuasiSeq/R/glm.fit0.R |only QuasiSeq-1.0-6/QuasiSeq/R/negbin.br.R |only QuasiSeq-1.0-7/QuasiSeq/DESCRIPTION | 33 ++++++++++++++------- QuasiSeq-1.0-7/QuasiSeq/MD5 | 28 +++++++++++------- QuasiSeq-1.0-7/QuasiSeq/NAMESPACE | 17 ++++++++--- QuasiSeq-1.0-7/QuasiSeq/R/NBDev.R | 40 ++++++++++++++++++-------- QuasiSeq-1.0-7/QuasiSeq/R/PoisDev.R | 5 ++- QuasiSeq-1.0-7/QuasiSeq/R/QL.fit.R | 4 +- QuasiSeq-1.0-7/QuasiSeq/R/coefglm.R |only QuasiSeq-1.0-7/QuasiSeq/R/duplicated.matrix.R |only QuasiSeq-1.0-7/QuasiSeq/R/fbrNBglm.R |only QuasiSeq-1.0-7/QuasiSeq/R/glm.fit3.R |only QuasiSeq-1.0-7/QuasiSeq/R/glmsolve.R |only QuasiSeq-1.0-7/QuasiSeq/R/negbin.R |only QuasiSeq-1.0-7/QuasiSeq/R/nlsolve.R |only QuasiSeq-1.0-7/QuasiSeq/man/NBDev.Rd | 17 +++++++++-- QuasiSeq-1.0-7/QuasiSeq/man/QL.fit.Rd | 7 +++- QuasiSeq-1.0-7/QuasiSeq/src |only 19 files changed, 106 insertions(+), 45 deletions(-)
Title: Geological Time Scale Plotting
Description: Function for adding the geological timescale to bivariate plots.
Author: Mark A. Bell <mark.bell521@gmail.com>.
Maintainer: Mark A. Bell <mark.bell521@gmail.com>
Diff between geoscale versions 1.1 dated 2014-03-31 and 2.0 dated 2015-05-13
geoscale-1.1/geoscale/R/geoscale.plot.R |only geoscale-1.1/geoscale/data/timescales.RData |only geoscale-1.1/geoscale/man/geoscale.plot.Rd |only geoscale-2.0/geoscale/DESCRIPTION | 14 ++++++++------ geoscale-2.0/geoscale/MD5 | 14 +++++++++----- geoscale-2.0/geoscale/R/geoscaleBox.R |only geoscale-2.0/geoscale/R/geoscalePlot.R |only geoscale-2.0/geoscale/data/size.rda |only geoscale-2.0/geoscale/data/timescales.rda |only geoscale-2.0/geoscale/man/geoscale-package.Rd | 12 ++++++------ geoscale-2.0/geoscale/man/geoscaleBox.Rd |only geoscale-2.0/geoscale/man/geoscalePlot.Rd |only geoscale-2.0/geoscale/man/size.Rd |only 13 files changed, 23 insertions(+), 17 deletions(-)
Title: R Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI). GloBI provides
access to spatial-temporal species interaction records from
sources all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction dataset.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen <jhpoelen@xs4all.nl>
Diff between rglobi versions 0.2.6 dated 2015-03-17 and 0.2.8 dated 2015-05-13
DESCRIPTION | 10 ++-- MD5 | 33 ++++++------- NAMESPACE | 3 - R/rglobi.R | 98 ++++++++++++++++++++++++++-------------- build/vignette.rds |binary man/get_child_taxa.Rd | 4 - man/get_data_fields.Rd |only man/get_interaction_areas.Rd | 6 +- man/get_interaction_matrix.Rd | 4 - man/get_interaction_table.Rd | 4 - man/get_interaction_types.Rd | 7 ++ man/get_interactions.Rd | 7 +- man/get_interactions_by_taxa.Rd | 20 +++++++- man/get_interactions_in_area.Rd | 6 +- man/get_predators_of.Rd | 6 +- man/get_prey_of.Rd | 6 +- man/query.Rd | 4 - tests/testthat/test-globi.R | 21 +++++++- 18 files changed, 155 insertions(+), 84 deletions(-)
Title: Searching for Footprints of Selection using Haplotype
Homozygosity Based Tests
Description: Functions for the detection of footprints of selection on
dense SNP data using Extended Homozygosity Haplotype (EHH)
based tests. The package includes computation of EHH, iHS
(within population) and Rsb (across pairs of populations)
statistics. Various plotting functions are also included to
facilitate visualization and interpretation of the results.
Author: Mathieu Gautier and Renaud Vitalis
Maintainer: Mathieu Gautier <mathieu.gautier@supagro.inra.fr>
Diff between rehh versions 1.12 dated 2015-04-07 and 1.13 dated 2015-05-13
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/calc_ehh.R | 2 +- R/distribplot.R | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm and the generalized
backdoor criterion is implemented.
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut],
Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb],
Antti Hyttinen [ctb], Jonas Peters [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.0-10 dated 2015-03-19 and 2.2-0 dated 2015-05-13
DESCRIPTION | 26 ++++++++------ MD5 | 47 +++++++++++++++---------- NAMESPACE | 23 ++++++++---- R/AllClasses.R | 90 +++++++++++++++++++++++++------------------------ R/genRandDAG.R |only R/gies.R | 88 +++++++++++++++++++++++------------------------ R/lingamFuns.R |only R/pcalg.R | 58 +++++++++++++++++++++++++++---- R/sysdata.rda |only build/vignette.rds |binary data/gmB.rda |binary data/gmD.rda |binary data/gmG.rda |binary data/gmI.rda |binary data/gmInt.rda |binary data/gmL.rda |binary inst/NEWS.Rd | 28 +++++++++++++++ man/EssGraph-class.Rd | 32 ++++++++--------- man/LINGAM.Rd |only man/ParDAG-class.Rd | 28 +++++++-------- man/ges.Rd | 4 +- man/randDAG.Rd |only man/simy.Rd | 43 +++++++++++++---------- man/unifDAG.Rd |only tests/test_LINGAM.R |only tests/test_pdag2dag.R | 10 ++++- tests/test_randDAG.R |only tests/test_randomDAG.R | 4 ++ tests/test_unifDAG.R |only 29 files changed, 298 insertions(+), 183 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.5.2 dated 2015-03-19 and 1.5.3 dated 2015-05-13
DESCRIPTION | 6 - MD5 | 149 ++++++++++++++++---------------- NAMESPACE | 2 NEWS | 9 + R/anyInfinite.r | 1 R/anyMissing.r | 1 R/asInteger.r | 1 R/assert.r | 7 + R/backports.r |only R/checkArray.r | 25 +++-- R/checkAtomic.r | 5 + R/checkAtomicVector.r | 2 R/checkCount.r | 3 R/checkDirectory.r | 11 +- R/checkFile.r | 14 +-- R/checkFlag.r | 3 R/checkMatrix.r | 5 - R/checkNames.r | 3 R/checkPathForOutput.r | 3 R/checkPercentage.r | 3 R/checkString.r | 3 R/checkVector.r | 1 man/anyInfinite.Rd | 2 man/anyMissing.Rd | 2 man/asInteger.Rd | 2 man/assert.Rd | 8 + man/checkAccess.Rd | 2 man/checkArray.Rd | 29 ++++-- man/checkAtomic.Rd | 41 ++++++++ man/checkAtomicVector.Rd | 7 + man/checkCharacter.Rd | 2 man/checkChoice.Rd | 2 man/checkClass.Rd | 2 man/checkComplex.Rd | 2 man/checkCount.Rd | 4 man/checkDataFrame.Rd | 2 man/checkDirectory.Rd | 2 man/checkEnvironment.Rd | 2 man/checkFactor.Rd | 2 man/checkFile.Rd | 2 man/checkFlag.Rd | 4 man/checkFunction.Rd | 2 man/checkInt.Rd | 2 man/checkInteger.Rd | 2 man/checkIntegerish.Rd | 2 man/checkList.Rd | 2 man/checkLogical.Rd | 2 man/checkMatrix.Rd | 10 +- man/checkNamed.Rd | 2 man/checkNames.Rd | 4 man/checkNull.Rd | 2 man/checkNumber.Rd | 2 man/checkNumeric.Rd | 2 man/checkPathForOutput.Rd | 5 - man/checkPercentage.Rd | 4 man/checkScalar.Rd | 2 man/checkScalarNA.Rd | 2 man/checkSetEqual.Rd | 2 man/checkString.Rd | 4 man/checkSubset.Rd | 2 man/checkVector.Rd | 8 + man/checkmate.Rd | 2 man/qassert.Rd | 2 man/qassertr.Rd | 2 src/checks.c | 64 ++++++++----- src/checks.h | 2 src/cmessages.c | 2 src/helper.c | 51 ++++++++-- src/helper.h | 1 src/qassert.c | 4 tests/testthat/test_anyMissing.r | 12 ++ tests/testthat/test_checkArray.r | 25 +++++ tests/testthat/test_checkAtomicVector.r | 5 + tests/testthat/test_checkDataFrame.r | 14 +++ tests/testthat/test_checkInteger.r | 1 tests/testthat/test_checkMatrix.r | 25 +++-- 76 files changed, 429 insertions(+), 222 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-08 0.1
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.18.0 dated 2015-04-10 and 0.18.1 dated 2015-05-13
sdcTable-0.18.0/sdcTable/inst/tests |only sdcTable-0.18.0/sdcTable/tests/test-all.R |only sdcTable-0.18.1/sdcTable/DESCRIPTION | 12 - sdcTable-0.18.1/sdcTable/MD5 | 119 ++++++------ sdcTable-0.18.1/sdcTable/NAMESPACE | 2 sdcTable-0.18.1/sdcTable/R/methods_class_dataObj.r | 21 +- sdcTable-0.18.1/sdcTable/inst/doc/sdcTable.pdf |binary sdcTable-0.18.1/sdcTable/man/attack.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.cutList-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.dimVar-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.linProb-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.multiple-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.problemInstance-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.sdcProblem-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/calc.simpleTriplet-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/cellInfo.Rd | 2 sdcTable-0.18.1/sdcTable/man/changeCellStatus.Rd | 2 sdcTable-0.18.1/sdcTable/man/cutList-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/dataObj-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/dimInfo-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/dimVar-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.cutList-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.dataObj-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.dimInfo-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.dimVar-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.linProb-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.problemInstance-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.safeObj-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.sdcProblem-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/get.simpleTriplet-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/getInfo.Rd | 2 sdcTable-0.18.1/sdcTable/man/init.cutList-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/init.dataObj-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/init.dimVar-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/init.simpleTriplet-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/linProb-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/makeProblem.Rd | 2 sdcTable-0.18.1/sdcTable/man/microData1.Rd | 2 sdcTable-0.18.1/sdcTable/man/microData2.Rd | 2 sdcTable-0.18.1/sdcTable/man/primarySuppression.Rd | 2 sdcTable-0.18.1/sdcTable/man/print-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/problem.Rd | 2 sdcTable-0.18.1/sdcTable/man/problemInstance-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/problemWithSupps.Rd | 2 sdcTable-0.18.1/sdcTable/man/protectLinkedTables.Rd | 2 sdcTable-0.18.1/sdcTable/man/protectTable.Rd | 2 sdcTable-0.18.1/sdcTable/man/protectedData.Rd | 2 sdcTable-0.18.1/sdcTable/man/safeObj-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/sdcProblem-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.cutList-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.dataObj-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.dimInfo-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.linProb-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.problemInstance-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/set.sdcProblem-method.Rd | 2 sdcTable-0.18.1/sdcTable/man/setInfo.Rd | 2 sdcTable-0.18.1/sdcTable/man/simpleTriplet-class.Rd | 2 sdcTable-0.18.1/sdcTable/man/summary-method.Rd | 2 sdcTable-0.18.1/sdcTable/tests/testthat |only sdcTable-0.18.1/sdcTable/tests/testthat.R |only 60 files changed, 129 insertions(+), 127 deletions(-)
Title: Patient-Centered Network Meta-Analysis
Description: Provides functions to perform arm-based network meta-analysis for datasets with binary, continuous, and count outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin <linl@umn.edu>
Diff between pcnetmeta versions 2.1 dated 2015-04-27 and 2.2 dated 2015-05-13
pcnetmeta-2.1/pcnetmeta/R/ci.plot.R |only pcnetmeta-2.1/pcnetmeta/R/forest.plot.R |only pcnetmeta-2.1/pcnetmeta/man/ci.plot.Rd |only pcnetmeta-2.1/pcnetmeta/man/forest.plot.Rd |only pcnetmeta-2.2/pcnetmeta/DESCRIPTION | 10 +- pcnetmeta-2.2/pcnetmeta/MD5 | 70 +++++++++---------- pcnetmeta-2.2/pcnetmeta/NAMESPACE | 2 pcnetmeta-2.2/pcnetmeta/R/absolute.plot.R |only pcnetmeta-2.2/pcnetmeta/R/contrast.plot.R |only pcnetmeta-2.2/pcnetmeta/R/model.binary.het.cor.R | 18 ++-- pcnetmeta-2.2/pcnetmeta/R/model.binary.het.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.binary.het.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.binary.hom.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.binary.hom.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.cont.het.cor.R | 18 ++-- pcnetmeta-2.2/pcnetmeta/R/model.cont.het.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.cont.het.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.cont.hom.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.cont.hom.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.followup.het.cor.R | 18 ++-- pcnetmeta-2.2/pcnetmeta/R/model.followup.het.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.followup.het.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.followup.hom.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.followup.hom.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.py.het.cor.R | 18 ++-- pcnetmeta-2.2/pcnetmeta/R/model.py.het.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.py.het.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.py.hom.eqcor.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/model.py.hom.ind.R | 32 +++++--- pcnetmeta-2.2/pcnetmeta/R/nma.ab.R | 21 +++-- pcnetmeta-2.2/pcnetmeta/R/nma.ab.cont.R | 21 +++-- pcnetmeta-2.2/pcnetmeta/R/nma.ab.followup.R | 43 ++++++----- pcnetmeta-2.2/pcnetmeta/R/nma.ab.py.R | 43 ++++++----- pcnetmeta-2.2/pcnetmeta/man/absolute.plot.Rd |only pcnetmeta-2.2/pcnetmeta/man/contrast.plot.Rd |only pcnetmeta-2.2/pcnetmeta/man/nma.ab.Rd | 6 + pcnetmeta-2.2/pcnetmeta/man/nma.ab.cont.Rd | 6 + pcnetmeta-2.2/pcnetmeta/man/nma.ab.followup.Rd | 5 + pcnetmeta-2.2/pcnetmeta/man/nma.ab.py.Rd | 6 + pcnetmeta-2.2/pcnetmeta/man/pcnetmeta-package.Rd | 2 40 files changed, 479 insertions(+), 340 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-level 'MongoDB' client based on 'jsonlite' and mongo-c-driver.
Includes support for aggregation, indexing, map-reduce, streaming, TLS and
LDAP (SASL) authentication.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.2 dated 2015-04-12 and 0.3 dated 2015-05-13
mongolite-0.2/mongolite/R/onLoad.R |only mongolite-0.2/mongolite/src/utils.h |only mongolite-0.3/mongolite/DESCRIPTION | 17 mongolite-0.3/mongolite/MD5 | 85 +- mongolite-0.3/mongolite/NAMESPACE | 6 mongolite-0.3/mongolite/NEWS |only mongolite-0.3/mongolite/R/jeroen.R | 3 mongolite-0.3/mongolite/R/mongo.R | 44 + mongolite-0.3/mongolite/R/object.R | 46 + mongolite-0.3/mongolite/build/vignette.rds |binary mongolite-0.3/mongolite/configure | 1 mongolite-0.3/mongolite/inst/doc/intro.Rmd | 37 - mongolite-0.3/mongolite/inst/doc/intro.html | 327 +++------- mongolite-0.3/mongolite/man/mongo.Rd | 25 mongolite-0.3/mongolite/src/Makevars | 72 +- mongolite-0.3/mongolite/src/apple.h | 1 mongolite-0.3/mongolite/src/bson.c | 11 mongolite-0.3/mongolite/src/bson/bson-atomic.c | 1 mongolite-0.3/mongolite/src/bson/bson-atomic.h | 58 - mongolite-0.3/mongolite/src/bson/bson-config.h | 10 mongolite-0.3/mongolite/src/bson/bson-iter.c | 2 mongolite-0.3/mongolite/src/bson/bson-macros.h | 12 mongolite-0.3/mongolite/src/bson/bson-stdint.h | 2 mongolite-0.3/mongolite/src/bson/bson-string.c | 6 mongolite-0.3/mongolite/src/bson/bson-version.h | 6 mongolite-0.3/mongolite/src/bson/bson.c | 8 mongolite-0.3/mongolite/src/client.c | 25 mongolite-0.3/mongolite/src/collection.c | 68 -- mongolite-0.3/mongolite/src/cursor.c | 21 mongolite-0.3/mongolite/src/mongoc/mongoc-bulk-operation.c | 9 mongolite-0.3/mongolite/src/mongoc/mongoc-client-pool.c | 2 mongolite-0.3/mongolite/src/mongoc/mongoc-client.c | 20 mongolite-0.3/mongolite/src/mongoc/mongoc-counters.c | 6 mongolite-0.3/mongolite/src/mongoc/mongoc-database.c | 13 mongolite-0.3/mongolite/src/mongoc/mongoc-gridfs-file-page.c | 2 mongolite-0.3/mongolite/src/mongoc/mongoc-scram.c | 29 mongolite-0.3/mongolite/src/mongoc/mongoc-stream-tls.c | 14 mongolite-0.3/mongolite/src/mongoc/mongoc-uri.c | 24 mongolite-0.3/mongolite/src/mongoc/mongoc-version.h | 6 mongolite-0.3/mongolite/src/mongoc/mongoc-write-command.c | 9 mongolite-0.3/mongolite/src/mongoc/mongoc-write-concern-private.h | 11 mongolite-0.3/mongolite/src/mongoc/mongoc-write-concern.c | 55 + mongolite-0.3/mongolite/src/mongolite.h |only mongolite-0.3/mongolite/src/onload.c |only mongolite-0.3/mongolite/src/utils.c | 35 - mongolite-0.3/mongolite/vignettes/intro.Rmd | 37 - 46 files changed, 615 insertions(+), 551 deletions(-)
Title: Multinomial Logit Model
Description: Time and memory efficient estimation of multinomial logit models using maximum likelihood method. Numerical optimization performed by Newton-Raphson method using an optimized, parallel C++ library to achieve fast computation of Hessian matrices. Motivated by large scale multiclass classification problems in econometrics and machine learning.
Author: Asad Hasan, Wang Zhiyu, Alireza S. Mahani
Maintainer: Asad Hasan <asad.hasan@sentrana.com>
Diff between mnlogit versions 1.2.0 dated 2014-09-09 and 1.2.1 dated 2015-05-13
mnlogit-1.2.0/mnlogit/inst/doc/mnlogit_tests.R |only mnlogit-1.2.0/mnlogit/vignettes/tests_sample_output |only mnlogit-1.2.1/mnlogit/ChangeLog | 18 mnlogit-1.2.1/mnlogit/DESCRIPTION | 8 mnlogit-1.2.1/mnlogit/MD5 | 31 mnlogit-1.2.1/mnlogit/NAMESPACE | 1 mnlogit-1.2.1/mnlogit/R/mnlogit.R | 7 mnlogit-1.2.1/mnlogit/R/mnlogit.methods.R | 36 mnlogit-1.2.1/mnlogit/R/predict.R | 20 mnlogit-1.2.1/mnlogit/inst/doc/mnlogit.R | 84 +- mnlogit-1.2.1/mnlogit/inst/doc/mnlogit.Rnw | 601 ++++++++-------- mnlogit-1.2.1/mnlogit/inst/doc/mnlogit.pdf |binary mnlogit-1.2.1/mnlogit/man/hyptests.Rd | 1 mnlogit-1.2.1/mnlogit/man/mnlogit.Rd | 9 mnlogit-1.2.1/mnlogit/src/hessian.h | 2 mnlogit-1.2.1/mnlogit/vignettes/mnlogit.Rnw | 347 +++++---- mnlogit-1.2.1/mnlogit/vignettes/mnlogit.bib | 721 ++++++++++---------- mnlogit-1.2.1/mnlogit/vignettes/table2_Code.R |only 18 files changed, 1014 insertions(+), 872 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized
additive models, as described in chapter 7 of "Statistical Models in
S" (Chambers and Hastie (eds), 1991), and "Generalized Additive
Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between gam versions 1.09.1 dated 2013-09-12 and 1.12 dated 2015-05-13
gam-1.09.1/gam/R/all.wam.R |only gam-1.09.1/gam/R/deviance.default.R |only gam-1.09.1/gam/R/deviance.glm.R |only gam-1.09.1/gam/R/deviance.lm.R |only gam-1.12/gam/DESCRIPTION | 12 +++++------ gam-1.12/gam/MD5 | 39 ++++++++++++++++-------------------- gam-1.12/gam/NAMESPACE | 12 +++++++++-- gam-1.12/gam/R/anova.gam.R | 7 ++---- gam-1.12/gam/R/anova.gamlist.R | 4 +-- gam-1.12/gam/R/gam.R | 2 - gam-1.12/gam/R/gam.fit.R | 4 +-- gam-1.12/gam/R/general.wam.R |only gam-1.12/gam/R/gplot.matrix.R | 14 ++++++++++-- gam-1.12/gam/R/s.wam.R | 3 ++ gam-1.12/gam/R/step.gam.R | 13 ++++++++---- gam-1.12/gam/R/summary.gam.R | 5 ++-- gam-1.12/gam/man/gam-internal.Rd | 5 ---- gam-1.12/gam/man/gam.Rd | 6 +++-- gam-1.12/gam/man/gam.exact.Rd | 7 +++--- gam-1.12/gam/man/lo.Rd | 4 +-- gam-1.12/gam/man/s.Rd | 4 +-- gam-1.12/gam/man/step.gam.Rd | 2 - gam-1.12/gam/src/Makevars.win | 2 - 23 files changed, 83 insertions(+), 62 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Description: R functions for processing 'lm', 'glm', 'svy.glm', 'merMod' and 'polr' outputs.
Author: Andrew Gelman [aut],
Yu-Sung Su [aut, cre],
Masanao Yajima [ctb],
Jennifer Hill [ctb],
Maria Grazia Pittau [ctb],
Jouni Kerman [ctb],
Tian Zheng [ctb],
Vicent Dorie [ctb]
Maintainer: Yu-Sung Su <suyusung@tsinghua.edu.cn>
Diff between arm versions 1.8-4 dated 2015-04-07 and 1.8-5 dated 2015-05-13
CHANGELOG | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/bayesglm.R | 1 + 4 files changed, 12 insertions(+), 7 deletions(-)