Title: R Client for the Microsoft Cognitive Services 'Text-to-Speech'
REST API
Description: R Client for the Microsoft Cognitive Services
'Text-to-Speech' REST API, including voice synthesis. A valid account
must be registered at the Microsoft Cognitive Services website
<https://www.microsoft.com/cognitive-services/> in order to
obtain a (free) API key. Without an API key, this package will not
work properly.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between mscstts versions 0.2.2 dated 2018-07-05 and 0.3.0 dated 2018-08-16
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++++----- NAMESPACE | 3 +++ NEWS.md | 7 +++++++ R/create_ssml.R |only R/language_to_ms_name.R |only R/ms_synthesize.R | 40 +++++++++++++++------------------------- man/create_ssml.Rd |only man/language_to_ms_name.Rd |only man/ms_synthesize.Rd | 10 +++++++--- 10 files changed, 45 insertions(+), 37 deletions(-)
Title: Exploration and Graphics for RivEr Trends (EGRET) Confidence
Intervals
Description: Collection of functions to evaluate uncertainty of results from
water quality analysis using the Weighted Regressions on Time Discharge and
Season (WRTDS) method. This package is an add-on to the EGRET package that
performs the WRTDS analysis.
Author: Robert Hirsch [aut] (<https://orcid.org/0000-0002-4534-075X>),
Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>),
Jennifer Murphy [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between EGRETci versions 1.0.2 dated 2016-04-16 and 2.0.0 dated 2018-08-16
EGRETci-1.0.2/EGRETci/man/estSliceSurfacesSimpleAlt.Rd |only EGRETci-1.0.2/EGRETci/man/makeCombo.Rd |only EGRETci-1.0.2/EGRETci/man/makeTwoYearsResults.Rd |only EGRETci-1.0.2/EGRETci/man/paVector.Rd |only EGRETci-1.0.2/EGRETci/man/wordLike.Rd |only EGRETci-2.0.0/EGRETci/DESCRIPTION | 24 EGRETci-2.0.0/EGRETci/MD5 | 65 +- EGRETci-2.0.0/EGRETci/NAMESPACE | 18 EGRETci-2.0.0/EGRETci/R/plotCIs.R | 278 +++++++-- EGRETci-2.0.0/EGRETci/R/runGroupBoot.R |only EGRETci-2.0.0/EGRETci/R/runPairsBoot.R |only EGRETci-2.0.0/EGRETci/R/wBTCode.R | 465 ++++++++-------- EGRETci-2.0.0/EGRETci/README.md | 122 +++- EGRETci-2.0.0/EGRETci/build/vignette.rds |binary EGRETci-2.0.0/EGRETci/inst/doc/EGRETci.R | 4 EGRETci-2.0.0/EGRETci/inst/doc/EGRETci.Rmd | 8 EGRETci-2.0.0/EGRETci/inst/doc/EGRETci.html | 61 +- EGRETci-2.0.0/EGRETci/inst/doc/Enhancements.R |only EGRETci-2.0.0/EGRETci/inst/doc/Enhancements.Rmd |only EGRETci-2.0.0/EGRETci/inst/doc/Enhancements.html |only EGRETci-2.0.0/EGRETci/man/EGRETci-package.Rd | 17 EGRETci-2.0.0/EGRETci/man/blockSample.Rd | 19 EGRETci-2.0.0/EGRETci/man/bootAnnual.Rd | 12 EGRETci-2.0.0/EGRETci/man/ciBands.Rd | 5 EGRETci-2.0.0/EGRETci/man/ciCalculations.Rd | 16 EGRETci-2.0.0/EGRETci/man/example_data.Rd | 5 EGRETci-2.0.0/EGRETci/man/pVal.Rd | 13 EGRETci-2.0.0/EGRETci/man/plotConcHistBoot.Rd | 9 EGRETci-2.0.0/EGRETci/man/plotFluxHistBoot.Rd | 5 EGRETci-2.0.0/EGRETci/man/plotHistogramTrend.Rd | 18 EGRETci-2.0.0/EGRETci/man/runGroupsBoot.Rd |only EGRETci-2.0.0/EGRETci/man/runPairsBoot.Rd |only EGRETci-2.0.0/EGRETci/man/saveEGRETci.Rd | 3 EGRETci-2.0.0/EGRETci/man/setForBoot.Rd | 3 EGRETci-2.0.0/EGRETci/man/trendSetUp.Rd | 6 EGRETci-2.0.0/EGRETci/man/wBT.Rd | 24 EGRETci-2.0.0/EGRETci/tests/testthat/tests_boot_tests.R |only EGRETci-2.0.0/EGRETci/tests/testthat/tests_general.R | 8 EGRETci-2.0.0/EGRETci/vignettes/EGRETci.Rmd | 8 EGRETci-2.0.0/EGRETci/vignettes/EGRETci.md |only EGRETci-2.0.0/EGRETci/vignettes/Enhancements.Rmd |only 41 files changed, 754 insertions(+), 462 deletions(-)
Title: Complexity of Short and Coarse-Grained Time Series
Description: While there are many well-established measures for identifying critical fluctuations and phase transitions, these measures only work with many points of measurement and thus are unreliable when studying short and coarse-grained time series. This package provides a measure for complexity in a time series that does not rely on long time series (Kaiser (2017), <doi:10.17605/OSF.IO/GWTKX>).
Author: Tim Kaiser
Maintainer: Tim Kaiser <Tim.Kaiser@sbg.ac.at>
Diff between dyncomp versions 0.0.1-5 dated 2017-12-11 and 0.0.2-1 dated 2018-08-16
DESCRIPTION | 7 ++++--- LICENSE | 2 +- MD5 | 6 +++--- R/complexity.R | 13 ++++++++----- 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Implementation of Core Data Structures
Description: Implementation of advanced data structures such as hashmaps,
heaps, or queues. Advanced data structures are essential
in many computer science and statistics problems, for example graph
algorithms or string analysis. The package uses 'Boost' and 'STL' data
types and extends these to R with 'Rcpp' modules.
Author: Simon Dirmeier [aut, cre]
Maintainer: Simon Dirmeier <simon.dirmeier@web.de>
Diff between datastructures versions 0.2.6 dated 2018-05-02 and 0.2.7 dated 2018-08-16
DESCRIPTION | 18 - MD5 | 63 +++-- NAMESPACE | 3 R/ds_deque.R | 16 + R/ds_heap.R | 53 +++- R/ds_map.R | 33 ++ R/ds_map_bimap.R | 36 ++- R/ds_map_multimap.R | 51 ++++ R/ds_map_unordered.R | 36 +-- R/methods_clear.R |only R/methods_remove.R |only inst/doc/datastructures.R | 31 ++ inst/doc/datastructures.Rmd | 59 +++++ inst/doc/datastructures.html | 344 +++++++++++++++++++------------ inst/include/bimap.hpp | 31 ++ inst/include/heap.hpp | 73 ++---- inst/include/map.hpp | 74 +++++- inst/include/queue.hpp | 17 - inst/include/stack.hpp | 17 - man/clear-methods.Rd |only man/insert-methods.Rd | 3 man/remove-methods.Rd |only src/bimap_module.cpp | 36 +++ src/hashmap_module.cpp | 9 src/multimap_module.cpp | 9 src/queue_module.cpp | 1 src/stack_module.cpp | 1 tests/testthat/tests_deque.R | 17 + tests/testthat/tests_heap.R | 18 + tests/testthat/tests_map.R | 24 ++ tests/testthat/tests_map_bimap.R | 18 + tests/testthat/tests_map_hashmap.R |only tests/testthat/tests_map_multimap.R | 16 + tests/testthat/tests_map_unordered_map.R | 14 + vignettes/datastructures.Rmd | 59 +++++ 35 files changed, 899 insertions(+), 281 deletions(-)
More information about datastructures at CRAN
Permanent link
Title: Performs a BLP Demand Estimation
Description: Provides the estimation algorithm to perform the demand estimation described in Berry, Levinsohn and Pakes (1995) <DOI:10.2307/2171802> . The routine uses analytic gradients and offers a large number of implemented integration methods and optimization routines.
Author: Daniel Brunner (aut), Constantin Weiser (ctr), Andre Romahn (ctr)
Maintainer: Daniel Brunner <daniel.brunner@hhu.de>
Diff between BLPestimatoR versions 0.1.5 dated 2017-08-13 and 0.2.3 dated 2018-08-16
BLPestimatoR-0.1.5/BLPestimatoR/R/blpFunctions.R |only BLPestimatoR-0.1.5/BLPestimatoR/R/get.BLP.dataset.R |only BLPestimatoR-0.1.5/BLPestimatoR/man/BLPestimatoR-package.Rd |only BLPestimatoR-0.1.5/BLPestimatoR/man/get.BLP.dataset.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/DESCRIPTION | 15 BLPestimatoR-0.2.3/BLPestimatoR/MD5 | 54 +- BLPestimatoR-0.2.3/BLPestimatoR/NAMESPACE | 19 BLPestimatoR-0.2.3/BLPestimatoR/R/BLP_data.R |only BLPestimatoR-0.2.3/BLPestimatoR/R/RcppExports.R | 12 BLPestimatoR-0.2.3/BLPestimatoR/R/estimateBLP.R |only BLPestimatoR-0.2.3/BLPestimatoR/R/generics.R | 58 +- BLPestimatoR-0.2.3/BLPestimatoR/R/get_BLP_dataset.R |only BLPestimatoR-0.2.3/BLPestimatoR/R/get_elasticities.R |only BLPestimatoR-0.2.3/BLPestimatoR/R/gmm.R |only BLPestimatoR-0.2.3/BLPestimatoR/R/helperFunctions.R | 276 +++++++++++- BLPestimatoR-0.2.3/BLPestimatoR/R/nevo.R |only BLPestimatoR-0.2.3/BLPestimatoR/R/wrappers.R |only BLPestimatoR-0.2.3/BLPestimatoR/build |only BLPestimatoR-0.2.3/BLPestimatoR/data |only BLPestimatoR-0.2.3/BLPestimatoR/inst |only BLPestimatoR-0.2.3/BLPestimatoR/man/BLP_data.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/demographicData.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/dstddelta_wrap.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/dstdtheta_wrap.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/estimateBLP.Rd | 176 ++----- BLPestimatoR-0.2.3/BLPestimatoR/man/getDelta_wrap.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/getJacobian_wrap.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/getShares_wrap.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/get_BLP_dataset.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/get_elasticities.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/gmm_obj_wrap.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/originalDraws.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/productData.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/theta_guesses.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/update_BLP_data.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/man/w_guesses.Rd |only BLPestimatoR-0.2.3/BLPestimatoR/src/Makevars |only BLPestimatoR-0.2.3/BLPestimatoR/src/Makevars.win |only BLPestimatoR-0.2.3/BLPestimatoR/src/RcppExports.cpp | 48 ++ BLPestimatoR-0.2.3/BLPestimatoR/src/cppFunctions.cpp | 241 ++++++++++ BLPestimatoR-0.2.3/BLPestimatoR/vignettes |only 41 files changed, 709 insertions(+), 190 deletions(-)
Title: Phonetic Spelling Algorithms
Description: Provides a collection of phonetic algorithms including
Soundex, Metaphone, NYSIIS, Caverphone, and others.
Author: James P. Howard, II [aut, cre],
Oliver Keyes [ctb]
Maintainer: "James P. Howard, II" <jh@jameshoward.us>
Diff between phonics versions 1.0.0 dated 2018-02-13 and 1.1.0 dated 2018-08-16
DESCRIPTION | 10 - MD5 | 60 ++++---- R/RcppExports.R | 10 + R/caverphone.R | 9 + R/cologne.R | 6 R/lein.R | 20 +- R/mra.R | 5 R/nysiis.R | 5 R/onca.R | 11 + R/phonex.R | 5 R/rogerroot.R | 5 R/statcan.R | 17 ++ README.md | 1 build/vignette.rds |binary inst/doc/phonics.Rmd | 2 inst/doc/phonics.html | 330 +++++++++++++++++++++++++++++++++++++++--------- man/caverphone.Rd | 8 + man/cologne.Rd | 9 + man/lein.Rd | 8 + man/metaphone.Rd | 8 + man/mra.Rd | 8 + man/nysiis.Rd | 8 + man/onca.Rd | 8 + man/phonex.Rd | 8 + man/rogerroot.Rd | 8 + man/soundex.Rd | 8 + man/statcan.Rd | 7 + src/metaphone.cpp | 7 - src/soundex.cpp | 17 +- tests/testthat/lein.csv | 61 ++------ vignettes/phonics.Rmd | 2 31 files changed, 504 insertions(+), 167 deletions(-)
Title: Exploration and Graphics for RivEr Trends (EGRET)
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut] (<https://orcid.org/0000-0002-4534-075X>),
Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>),
David Watkins [ctb],
Lindsay Carr [ctb],
Jennifer Murphy [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between EGRET versions 2.6.0 dated 2016-07-26 and 3.0.0 dated 2018-08-16
EGRET-2.6.0/EGRET/R/logPretty1.R |only EGRET-2.6.0/EGRET/R/logPretty3.R |only EGRET-2.6.0/EGRET/inst/extdata/eListColumbia.RData |only EGRET-2.6.0/EGRET/inst/extdata/eListMerced.RData |only EGRET-2.6.0/EGRET/inst/extdata/eListMiss.RData |only EGRET-2.6.0/EGRET/man/populateDateColumns.Rd |only EGRET-2.6.0/EGRET/man/print.egret.Rd |only EGRET-2.6.0/EGRET/man/tableChangeSingle.Rd |only EGRET-3.0.0/EGRET/DESCRIPTION | 37 EGRET-3.0.0/EGRET/LICENSE.note | 2 EGRET-3.0.0/EGRET/MD5 | 460 +++--- EGRET-3.0.0/EGRET/NAMESPACE | 25 EGRET-3.0.0/EGRET/NEWS | 10 EGRET-3.0.0/EGRET/R/EGRET.R | 140 +- EGRET-3.0.0/EGRET/R/blankTime.R | 4 EGRET-3.0.0/EGRET/R/boxConcMonth.R | 232 +-- EGRET-3.0.0/EGRET/R/boxConcThree.R | 11 EGRET-3.0.0/EGRET/R/boxQTwice.R | 17 EGRET-3.0.0/EGRET/R/boxResidMonth.R | 3 EGRET-3.0.0/EGRET/R/calculateMonthlyResults.R | 4 EGRET-3.0.0/EGRET/R/censoredSegments.R | 93 - EGRET-3.0.0/EGRET/R/checkStartEndDate.r | 74 - EGRET-3.0.0/EGRET/R/compressData.r | 191 +- EGRET-3.0.0/EGRET/R/dateFormatCheck.r | 60 EGRET-3.0.0/EGRET/R/egret_objects.R |only EGRET-3.0.0/EGRET/R/estCrossVal.R | 162 +- EGRET-3.0.0/EGRET/R/estDailyFromSurfacesJ.R | 159 +- EGRET-3.0.0/EGRET/R/estSurfaces.R | 95 + EGRET-3.0.0/EGRET/R/flexFN.R |only EGRET-3.0.0/EGRET/R/flowDuration.R | 129 + EGRET-3.0.0/EGRET/R/fluxBiasEight.R | 8 EGRET-3.0.0/EGRET/R/fluxBiasStat.R | 50 EGRET-3.0.0/EGRET/R/fluxUnit.R | 5 EGRET-3.0.0/EGRET/R/formatCheckDate.r | 59 EGRET-3.0.0/EGRET/R/formatCheckParameterCd.r | 10 EGRET-3.0.0/EGRET/R/generalAxis.R | 171 +- EGRET-3.0.0/EGRET/R/genericEGRETplot.R | 8 EGRET-3.0.0/EGRET/R/logPretty.R |only EGRET-3.0.0/EGRET/R/makeAnnualSeries.R | 253 +-- EGRET-3.0.0/EGRET/R/makeRandomResiduals.R | 14 EGRET-3.0.0/EGRET/R/mergeReport.r | 343 ----- EGRET-3.0.0/EGRET/R/modelEstimation.R | 74 - EGRET-3.0.0/EGRET/R/multiPlotDataOverview.R | 7 EGRET-3.0.0/EGRET/R/objectDefinitions.R | 93 - EGRET-3.0.0/EGRET/R/plot15.R | 126 - EGRET-3.0.0/EGRET/R/plot1of15.R | 106 - EGRET-3.0.0/EGRET/R/plotConcHist.R | 60 EGRET-3.0.0/EGRET/R/plotConcPred.R | 242 +-- EGRET-3.0.0/EGRET/R/plotConcQ.R | 6 EGRET-3.0.0/EGRET/R/plotConcQSmooth.R | 390 ++--- EGRET-3.0.0/EGRET/R/plotConcTime.R | 348 ++--- EGRET-3.0.0/EGRET/R/plotConcTimeDaily.R | 242 +-- EGRET-3.0.0/EGRET/R/plotConcTimeSmooth.R | 415 +++--- EGRET-3.0.0/EGRET/R/plotContours.R | 76 - EGRET-3.0.0/EGRET/R/plotDiffContours.R | 57 EGRET-3.0.0/EGRET/R/plotFlowSingle.R | 13 EGRET-3.0.0/EGRET/R/plotFluxHist.R | 61 EGRET-3.0.0/EGRET/R/plotFluxPred.R | 15 EGRET-3.0.0/EGRET/R/plotFluxQ.R | 12 EGRET-3.0.0/EGRET/R/plotFluxTimeDaily.R | 7 EGRET-3.0.0/EGRET/R/plotQTimeDaily.R | 7 EGRET-3.0.0/EGRET/R/plotResidPred.R | 10 EGRET-3.0.0/EGRET/R/plotResidQ.R | 6 EGRET-3.0.0/EGRET/R/plotResidTime.R | 240 +-- EGRET-3.0.0/EGRET/R/plotSDLogQ.R | 5 EGRET-3.0.0/EGRET/R/populateConcentrations.r | 8 EGRET-3.0.0/EGRET/R/populateDaily.r | 25 EGRET-3.0.0/EGRET/R/populateDateColumns.r | 26 EGRET-3.0.0/EGRET/R/populateParameterINFO.r | 3 EGRET-3.0.0/EGRET/R/populateSampleColumns.r | 12 EGRET-3.0.0/EGRET/R/populateSiteINFO.r | 3 EGRET-3.0.0/EGRET/R/printFluxUnitCheatSheet.R | 2 EGRET-3.0.0/EGRET/R/printSeries.R | 4 EGRET-3.0.0/EGRET/R/printqUnitCheatSheet.R | 2 EGRET-3.0.0/EGRET/R/processQWData.r | 11 EGRET-3.0.0/EGRET/R/readDataFromFile.r | 98 - EGRET-3.0.0/EGRET/R/readMetaData.r | 1 EGRET-3.0.0/EGRET/R/readNWISDaily.r | 80 - EGRET-3.0.0/EGRET/R/readNWISSample.r | 19 EGRET-3.0.0/EGRET/R/readUserDaily.r | 97 - EGRET-3.0.0/EGRET/R/readUserSample.r | 20 EGRET-3.0.0/EGRET/R/readWQPSample.R | 22 EGRET-3.0.0/EGRET/R/removeDuplicates.r | 2 EGRET-3.0.0/EGRET/R/runGroups.R |only EGRET-3.0.0/EGRET/R/runPairs.R |only EGRET-3.0.0/EGRET/R/runSeries.R |only EGRET-3.0.0/EGRET/R/runSurvReg.R | 272 ++-- EGRET-3.0.0/EGRET/R/selectDays.R | 8 EGRET-3.0.0/EGRET/R/setPA.R | 4 EGRET-3.0.0/EGRET/R/setSeasonLabel.R | 35 EGRET-3.0.0/EGRET/R/setSeasonLabelByUser.R | 2 EGRET-3.0.0/EGRET/R/setupYears.R | 21 EGRET-3.0.0/EGRET/R/startEnd.R |only EGRET-3.0.0/EGRET/R/stitch.R |only EGRET-3.0.0/EGRET/R/surfaceIndex.R | 22 EGRET-3.0.0/EGRET/R/sysdata.rda |binary EGRET-3.0.0/EGRET/R/tableChange.R | 31 EGRET-3.0.0/EGRET/R/tableChangeSingle.R | 31 EGRET-3.0.0/EGRET/R/tableFlowChange.R | 200 +- EGRET-3.0.0/EGRET/R/tableResults.R | 32 EGRET-3.0.0/EGRET/R/triCube.R | 10 EGRET-3.0.0/EGRET/R/yPretty.R | 4 EGRET-3.0.0/EGRET/README.md | 667 +++++++--- EGRET-3.0.0/EGRET/build/vignette.rds |binary EGRET-3.0.0/EGRET/data/Arkansas_eList.RData |binary EGRET-3.0.0/EGRET/data/Choptank_eList.RData |binary EGRET-3.0.0/EGRET/inst/CITATION | 4 EGRET-3.0.0/EGRET/inst/doc/EGRET.R | 66 EGRET-3.0.0/EGRET/inst/doc/EGRET.Rnw | 86 - EGRET-3.0.0/EGRET/inst/doc/EGRET.pdf |binary EGRET-3.0.0/EGRET/inst/doc/Enhancements.R |only EGRET-3.0.0/EGRET/inst/doc/Enhancements.Rmd |only EGRET-3.0.0/EGRET/inst/doc/Enhancements.html |only EGRET-3.0.0/EGRET/inst/doc/parallel.R |only EGRET-3.0.0/EGRET/inst/doc/parallel.Rmd |only EGRET-3.0.0/EGRET/inst/doc/parallel.html |only EGRET-3.0.0/EGRET/inst/doc/rResid.Rmd | 4 EGRET-3.0.0/EGRET/inst/doc/rResid.html | 26 EGRET-3.0.0/EGRET/man/Constants.Rd | 3 EGRET-3.0.0/EGRET/man/EGRET-package.Rd | 11 EGRET-3.0.0/EGRET/man/INFOdataframe.Rd | 3 EGRET-3.0.0/EGRET/man/as.egret.Rd | 3 EGRET-3.0.0/EGRET/man/blankTime.Rd | 5 EGRET-3.0.0/EGRET/man/boxConcMonth.Rd | 1 EGRET-3.0.0/EGRET/man/boxConcThree.Rd | 6 EGRET-3.0.0/EGRET/man/boxQTwice.Rd | 17 EGRET-3.0.0/EGRET/man/boxResidMonth.Rd | 3 EGRET-3.0.0/EGRET/man/calculateMonthlyResults.Rd | 5 EGRET-3.0.0/EGRET/man/censoredSegments.Rd | 4 EGRET-3.0.0/EGRET/man/checkStartEndDate.Rd | 6 EGRET-3.0.0/EGRET/man/checkSurfaceSpan.Rd |only EGRET-3.0.0/EGRET/man/compressData.Rd | 10 EGRET-3.0.0/EGRET/man/dataOverview.Rd | 1 EGRET-3.0.0/EGRET/man/dateFormatCheck.Rd | 3 EGRET-3.0.0/EGRET/man/dateFuncs.Rd |only EGRET-3.0.0/EGRET/man/decimalHighLow.Rd |only EGRET-3.0.0/EGRET/man/estCrossVal.Rd | 10 EGRET-3.0.0/EGRET/man/estDailyFromSurfaces.Rd | 35 EGRET-3.0.0/EGRET/man/estSurfaces.Rd | 32 EGRET-3.0.0/EGRET/man/figures |only EGRET-3.0.0/EGRET/man/fixSampleFrame.Rd | 1 EGRET-3.0.0/EGRET/man/flexFN.Rd |only EGRET-3.0.0/EGRET/man/flexPlotAddOn.Rd |only EGRET-3.0.0/EGRET/man/flowDuration.Rd | 9 EGRET-3.0.0/EGRET/man/fluxBiasMulti.Rd | 13 EGRET-3.0.0/EGRET/man/fluxBiasStat.Rd | 1 EGRET-3.0.0/EGRET/man/fluxUnit-class.Rd | 1 EGRET-3.0.0/EGRET/man/formatCheckDate.Rd | 9 EGRET-3.0.0/EGRET/man/formatCheckParameterCd.Rd | 6 EGRET-3.0.0/EGRET/man/generalAxis.Rd | 1 EGRET-3.0.0/EGRET/man/genericEGRETDotPlot.Rd | 23 EGRET-3.0.0/EGRET/man/getDaily.Rd | 5 EGRET-3.0.0/EGRET/man/getInfo.Rd | 5 EGRET-3.0.0/EGRET/man/getSample.Rd | 3 EGRET-3.0.0/EGRET/man/getSurfaces.Rd | 5 EGRET-3.0.0/EGRET/man/helperEGRET.Rd |only EGRET-3.0.0/EGRET/man/is.egret.Rd | 3 EGRET-3.0.0/EGRET/man/logPretty1.Rd | 19 EGRET-3.0.0/EGRET/man/logPretty3.Rd | 7 EGRET-3.0.0/EGRET/man/makeAnnualSeries.Rd | 3 EGRET-3.0.0/EGRET/man/makeAugmentedSample.Rd | 7 EGRET-3.0.0/EGRET/man/makeDateInfo.Rd |only EGRET-3.0.0/EGRET/man/mergeReport.Rd | 45 EGRET-3.0.0/EGRET/man/modelEstimation.Rd | 30 EGRET-3.0.0/EGRET/man/monthLabel-class.Rd | 1 EGRET-3.0.0/EGRET/man/multiPlotDataOverview.Rd | 7 EGRET-3.0.0/EGRET/man/plot15.Rd | 1 EGRET-3.0.0/EGRET/man/plot1of15.Rd | 1 EGRET-3.0.0/EGRET/man/plotConcHist.Rd | 15 EGRET-3.0.0/EGRET/man/plotConcPred.Rd | 9 EGRET-3.0.0/EGRET/man/plotConcQ.Rd | 12 EGRET-3.0.0/EGRET/man/plotConcQSmooth.Rd | 13 EGRET-3.0.0/EGRET/man/plotConcTime.Rd | 9 EGRET-3.0.0/EGRET/man/plotConcTimeDaily.Rd | 10 EGRET-3.0.0/EGRET/man/plotConcTimeSmooth.Rd | 11 EGRET-3.0.0/EGRET/man/plotContours.Rd | 15 EGRET-3.0.0/EGRET/man/plotDiffContours.Rd | 9 EGRET-3.0.0/EGRET/man/plotFlowSingle.Rd | 9 EGRET-3.0.0/EGRET/man/plotFluxHist.Rd | 17 EGRET-3.0.0/EGRET/man/plotFluxPred.Rd | 7 EGRET-3.0.0/EGRET/man/plotFluxQ.Rd | 9 EGRET-3.0.0/EGRET/man/plotFluxTimeDaily.Rd | 14 EGRET-3.0.0/EGRET/man/plotFour.Rd | 5 EGRET-3.0.0/EGRET/man/plotFourStats.Rd | 1 EGRET-3.0.0/EGRET/man/plotQTimeDaily.Rd | 9 EGRET-3.0.0/EGRET/man/plotResidPred.Rd | 1 EGRET-3.0.0/EGRET/man/plotResidQ.Rd | 5 EGRET-3.0.0/EGRET/man/plotResidTime.Rd | 8 EGRET-3.0.0/EGRET/man/plotSDLogQ.Rd | 9 EGRET-3.0.0/EGRET/man/populateConcentrations.Rd | 4 EGRET-3.0.0/EGRET/man/populateDaily.Rd | 15 EGRET-3.0.0/EGRET/man/populateParameterINFO.Rd | 4 EGRET-3.0.0/EGRET/man/populateSampleColumns.Rd | 6 EGRET-3.0.0/EGRET/man/populateSiteINFO.Rd | 4 EGRET-3.0.0/EGRET/man/printFluxUnitCheatSheet.Rd | 3 EGRET-3.0.0/EGRET/man/printSeries.Rd | 5 EGRET-3.0.0/EGRET/man/printqUnitCheatSheet.Rd | 3 EGRET-3.0.0/EGRET/man/processQWData.Rd | 12 EGRET-3.0.0/EGRET/man/qUnit-class.Rd | 3 EGRET-3.0.0/EGRET/man/readDataFromFile.Rd | 1 EGRET-3.0.0/EGRET/man/readNWISDaily.Rd | 13 EGRET-3.0.0/EGRET/man/readNWISSample.Rd | 13 EGRET-3.0.0/EGRET/man/readUserDaily.Rd | 7 EGRET-3.0.0/EGRET/man/readUserSample.Rd | 14 EGRET-3.0.0/EGRET/man/readWQPSample.Rd | 13 EGRET-3.0.0/EGRET/man/removeDuplicates.Rd | 3 EGRET-3.0.0/EGRET/man/runGroups.Rd |only EGRET-3.0.0/EGRET/man/runPairs.Rd |only EGRET-3.0.0/EGRET/man/runSeries.Rd |only EGRET-3.0.0/EGRET/man/runSurvReg.Rd | 42 EGRET-3.0.0/EGRET/man/sampleData.Rd | 3 EGRET-3.0.0/EGRET/man/saveResults.Rd | 1 EGRET-3.0.0/EGRET/man/selectDays.Rd | 9 EGRET-3.0.0/EGRET/man/setPA.Rd | 5 EGRET-3.0.0/EGRET/man/setSeasonLabel.Rd | 3 EGRET-3.0.0/EGRET/man/setSeasonLabelByUser.Rd | 3 EGRET-3.0.0/EGRET/man/setUpEstimation.Rd | 7 EGRET-3.0.0/EGRET/man/setupYears.Rd | 3 EGRET-3.0.0/EGRET/man/startEnd.Rd |only EGRET-3.0.0/EGRET/man/stitch.Rd |only EGRET-3.0.0/EGRET/man/surfaceIndex.Rd | 1 EGRET-3.0.0/EGRET/man/surfaceStartEnd.Rd |only EGRET-3.0.0/EGRET/man/tableChange.Rd | 33 EGRET-3.0.0/EGRET/man/tableFlowChange.Rd | 4 EGRET-3.0.0/EGRET/man/tableResults.Rd | 11 EGRET-3.0.0/EGRET/man/triCube.Rd | 8 EGRET-3.0.0/EGRET/man/yPretty.Rd | 5 EGRET-3.0.0/EGRET/tests/testthat.R | 4 EGRET-3.0.0/EGRET/tests/testthat/helper-originaldata.R |only EGRET-3.0.0/EGRET/tests/testthat/tests_calculations.R |only EGRET-3.0.0/EGRET/tests/testthat/tests_estCrossVal.R |only EGRET-3.0.0/EGRET/tests/testthat/tests_estDailyFromSurfaces.R |only EGRET-3.0.0/EGRET/tests/testthat/tests_estSurfaces.R |only EGRET-3.0.0/EGRET/tests/testthat/tests_flow_normalization.R |only EGRET-3.0.0/EGRET/tests/testthat/tests_imports.R | 170 +- EGRET-3.0.0/EGRET/tests/testthat/tests_modelEstimation.R |only EGRET-3.0.0/EGRET/tests/testthat/tests_runSurvReg.R |only EGRET-3.0.0/EGRET/tests/testthat/tests_utils.R |only EGRET-3.0.0/EGRET/vignettes/EGRET.Rnw | 86 - EGRET-3.0.0/EGRET/vignettes/Enhancements.Rmd |only EGRET-3.0.0/EGRET/vignettes/parallel.Rmd |only EGRET-3.0.0/EGRET/vignettes/rResid.Rmd | 4 242 files changed, 4631 insertions(+), 3862 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <doi:10.18637/jss.v074.i11>.
Author: Beata Nowok, Gillian M Raab, Joshua Snoke and Chris Dibben
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.4-4 dated 2018-06-27 and 1.5-0 dated 2018-08-16
DESCRIPTION | 10 MD5 | 60 +-- NAMESPACE | 14 NEWS | 49 ++ R/codebook.syn.r |only R/compare.syn.r | 129 ++++--- R/functions.syn.r | 569 +++++++++++++++++++++---------- R/methods.syn.r | 87 ++-- R/numtocat.syn.r |only R/padMis.syn.r | 91 ++--- R/padModel.syn.r | 54 +-- R/sampler.syn.r | 487 ++++++++++++++------------- R/syn.r | 844 +++++++++++++++++++++++++++++------------------ R/syn.strata.r | 13 R/utility.syn.r | 111 ++++-- build/partial.rdb |binary inst/doc/inference.pdf |binary inst/doc/synthpop.pdf |binary man/codebook.syn.Rd |only man/compare.synds.Rd | 14 man/numtocat.syn.Rd |only man/summary.fit.synds.Rd | 3 man/syn.Rd | 74 +++- man/syn.cart.Rd | 15 man/syn.catall.Rd |only man/syn.ipf.Rd |only man/syn.logreg.Rd | 21 - man/syn.nested.Rd | 23 - man/syn.polyreg.Rd | 10 man/syn.satcat.Rd | 8 man/syn.survctree.Rd | 6 man/synthpop-package.Rd | 4 man/utility.gen.Rd | 5 man/utility.tab.Rd | 24 - 34 files changed, 1700 insertions(+), 1025 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 0.2.1 dated 2018-05-30 and 0.2.2 dated 2018-08-16
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ src/capture.c | 33 ++++++++++++++++++++++++--------- src/internal/eval-tidy.c | 5 +++-- src/lib/cnd.c | 4 ++-- src/lib/env.c | 12 +++++++++--- src/lib/squash.c | 4 +++- src/lib/stack.c | 22 ++++++++++++++++------ 9 files changed, 74 insertions(+), 34 deletions(-)
Title: Interactive Editing of Spatial Data in R
Description: Suite of interactive functions and helpers for selecting and editing
geospatial data.
Author: Tim Appelhans [aut, cre],
Kenton Russell [aut]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between mapedit versions 0.4.1 dated 2018-03-02 and 0.4.3 dated 2018-08-16
DESCRIPTION | 16 +++++++++------- MD5 | 29 +++++++++++++++-------------- NEWS | 18 ++++++++++++++++++ NEWS.md | 18 ++++++++++++++++++ R/edit.R | 16 +++++++++++++++- R/edit_map_return_sf.R | 4 ++-- R/helpers.R |only R/modules.R | 5 ++++- R/query.R | 18 +++++++++++++++++- R/select.R | 7 +++++-- man/editFeatures.Rd | 9 +++++---- man/editMap.Rd | 3 --- man/editMod.Rd | 4 ++-- man/selectFeatures.Rd | 8 +++++--- man/selectMap.Rd | 11 +++++++---- man/selectMod.Rd | 6 +++--- 16 files changed, 125 insertions(+), 47 deletions(-)
Title: Graphical Display of Pairwise Linkage Disequilibria Between SNPs
Description: Produces a graphical display, as a heat map, of measures
of pairwise linkage disequilibria between SNPs. Users may
optionally include the physical locations or genetic map
distances of each SNP on the plot.
Author: Ji-Hyung Shin [aut],
Sigal Blay [aut],
Nicholas Lewin-Koh [ctb],
Brad McNeney [aut, cre],
Gloria Yang [ctb],
Matthew Reyers [ctb],
Jinko Graham [aut]
Maintainer: Brad McNeney <mcneney@sfu.ca>
Diff between LDheatmap versions 0.99-4 dated 2018-03-12 and 0.99-5 dated 2018-08-16
LDheatmap-0.99-4/LDheatmap/man/GIMAP5CEU.Rd |only LDheatmap-0.99-5/LDheatmap/DESCRIPTION | 26 LDheatmap-0.99-5/LDheatmap/MD5 | 87 - LDheatmap-0.99-5/LDheatmap/NAMESPACE | 19 LDheatmap-0.99-5/LDheatmap/R/CEUDataRd.R |only LDheatmap-0.99-5/LDheatmap/R/CHBJPTDataRd.R |only LDheatmap-0.99-5/LDheatmap/R/GIMAP5CEUrd.R |only LDheatmap-0.99-5/LDheatmap/R/GIMAP5Rd.R |only LDheatmap-0.99-5/LDheatmap/R/LDheatmap-internal.R |only LDheatmap-0.99-5/LDheatmap/R/LDheatmap.R | 690 ++++++++----- LDheatmap-0.99-5/LDheatmap/R/LDheatmap.addGenes.R | 39 LDheatmap-0.99-5/LDheatmap/R/LDheatmap.addGrob.R | 20 LDheatmap-0.99-5/LDheatmap/R/LDheatmap.addRecombRate.R | 28 LDheatmap-0.99-5/LDheatmap/R/LDheatmap.addScatterplot.R | 52 LDheatmap-0.99-5/LDheatmap/R/LDheatmap.highlight.R | 177 +++ LDheatmap-0.99-5/LDheatmap/R/LDheatmap.marks.R | 53 LDheatmap-0.99-5/LDheatmap/R/LDheatmap.moveGenemap.R |only LDheatmap-0.99-5/LDheatmap/R/LDheatmapHelpers.R |only LDheatmap-0.99-5/LDheatmap/R/import.R |only LDheatmap-0.99-5/LDheatmap/R/plotGenes.R | 33 LDheatmap-0.99-5/LDheatmap/R/recombRate.R | 28 LDheatmap-0.99-5/LDheatmap/build/vignette.rds |binary LDheatmap-0.99-5/LDheatmap/data/CEUData.rda |binary LDheatmap-0.99-5/LDheatmap/data/CHBJPTData.rda |binary LDheatmap-0.99-5/LDheatmap/demo/LDheatmap.R | 1 LDheatmap-0.99-5/LDheatmap/inst/doc/LDheatmap.R | 20 LDheatmap-0.99-5/LDheatmap/inst/doc/LDheatmap.Rnw | 2 LDheatmap-0.99-5/LDheatmap/inst/doc/LDheatmap.pdf |binary LDheatmap-0.99-5/LDheatmap/inst/doc/addTracks.R | 9 LDheatmap-0.99-5/LDheatmap/inst/doc/addTracks.Rnw | 1 LDheatmap-0.99-5/LDheatmap/inst/doc/addTracks.pdf |binary LDheatmap-0.99-5/LDheatmap/man/CEUData.Rd | 54 - LDheatmap-0.99-5/LDheatmap/man/CHBJPTData.Rd | 61 - LDheatmap-0.99-5/LDheatmap/man/GIMAP5.CEU.Rd |only LDheatmap-0.99-5/LDheatmap/man/GIMAP5.Rd | 95 - LDheatmap-0.99-5/LDheatmap/man/LDheatmap-internal.Rd | 13 LDheatmap-0.99-5/LDheatmap/man/LDheatmap.Rd | 399 +++---- LDheatmap-0.99-5/LDheatmap/man/LDheatmap.addGenes.Rd | 75 - LDheatmap-0.99-5/LDheatmap/man/LDheatmap.addGrob.Rd | 42 LDheatmap-0.99-5/LDheatmap/man/LDheatmap.addRecombRate.Rd | 58 - LDheatmap-0.99-5/LDheatmap/man/LDheatmap.addScatterplot.Rd | 83 - LDheatmap-0.99-5/LDheatmap/man/LDheatmap.highlight.Rd | 102 + LDheatmap-0.99-5/LDheatmap/man/LDheatmap.marks.Rd | 89 - LDheatmap-0.99-5/LDheatmap/man/figures |only LDheatmap-0.99-5/LDheatmap/man/plotGenes.Rd | 69 - LDheatmap-0.99-5/LDheatmap/man/recombRate.Rd | 59 - LDheatmap-0.99-5/LDheatmap/vignettes/1KG_sample_info.csv |only LDheatmap-0.99-5/LDheatmap/vignettes/LDheatmap.Rnw | 2 LDheatmap-0.99-5/LDheatmap/vignettes/addTracks.Rnw | 1 LDheatmap-0.99-5/LDheatmap/vignettes/snp_id_dist.csv |only LDheatmap-0.99-5/LDheatmap/vignettes/snp_in_vcf.vcf |only LDheatmap-0.99-5/LDheatmap/vignettes/vcfOnLDheatmap.Rmd |only 52 files changed, 1570 insertions(+), 917 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm versions 3.8.0 dated 2017-08-20 and 3.9.4 dated 2018-08-16
ergm-3.8.0/ergm/R/InitConstraint.R |only ergm-3.8.0/ergm/R/InitErgmTermcondegmple.R |only ergm-3.8.0/ergm/R/InitMHP.R |only ergm-3.8.0/ergm/R/InitMHP.blockdiag.R |only ergm-3.8.0/ergm/R/InitReferences.R |only ergm-3.8.0/ergm/R/InitWtMHP.R |only ergm-3.8.0/ergm/R/MHproposal.R |only ergm-3.8.0/ergm/R/WtReferences.R |only ergm-3.8.0/ergm/R/coef.ergm.R |only ergm-3.8.0/ergm/R/ergm.getglobalstats.R |only ergm-3.8.0/ergm/R/ergm.getmodel.R |only ergm-3.8.0/ergm/R/ergm.model.utils.R |only ergm-3.8.0/ergm/R/robust.inverse.R |only ergm-3.8.0/ergm/man/MHproposal.Rd |only ergm-3.8.0/ergm/man/coef.ergm.Rd |only ergm-3.8.0/ergm/man/coef.length.model.Rd |only ergm-3.8.0/ergm/man/ergm-MetropolisHastingsProposals.Rd |only ergm-3.8.0/ergm/man/ergm.ConstraintImplication.Rd |only ergm-3.8.0/ergm/man/ergm.Cprepare.Rd |only ergm-3.8.0/ergm/man/ergm.MHP.table.Rd |only ergm-3.8.0/ergm/man/ergm.bridge.dindstart.llk.Rd |only ergm-3.8.0/ergm/man/ergm.getMCMCsample.Rd |only ergm-3.8.0/ergm/man/ergm.getglobalstats.Rd |only ergm-3.8.0/ergm/man/ergm.init.methods.Rd |only ergm-3.8.0/ergm/man/ergm_formula_utils.Rd |only ergm-3.8.0/ergm/man/flobusiness.Rd |only ergm-3.8.0/ergm/man/flomarriage.Rd |only ergm-3.8.0/ergm/man/get.free.dyads.Rd |only ergm-3.8.0/ergm/man/gof.ergm.Rd |only ergm-3.8.0/ergm/man/mcmc.diagnostics.ergm.Rd |only ergm-3.8.0/ergm/man/mcmc.list_utils.Rd |only ergm-3.8.0/ergm/man/plot.ergm.Rd |only ergm-3.8.0/ergm/man/plot.gofobject.Rd |only ergm-3.8.0/ergm/man/plot.network.ergm.Rd |only ergm-3.8.0/ergm/man/print.ergm.Rd |only ergm-3.8.0/ergm/man/summary.gofobject.Rd |only ergm-3.8.0/ergm/man/summary.network.list.Rd |only ergm-3.8.0/ergm/man/summary.statistics.Rd |only ergm-3.8.0/ergm/man/vcov.ergm.Rd |only ergm-3.8.0/ergm/src/MPLEconddeg.c |only ergm-3.8.0/ergm/src/MPLEconddeg.h |only ergm-3.8.0/ergm/src/conddegmple.c |only ergm-3.8.0/ergm/src/conddegmple.h |only ergm-3.8.0/ergm/tests/constrain_blockdiag.R |only ergm-3.8.0/ergm/tests/constrain_degrees.R |only ergm-3.8.0/ergm/tests/constrain_observed.R |only ergm-3.8.0/ergm/tests/ergm.update.formula.R |only ergm-3.8.0/ergm/tests/estflo.R |only ergm-3.8.0/ergm/tests/flomarkov.R |only ergm-3.8.0/ergm/tests/misc_tests.R |only ergm-3.8.0/ergm/vignettes/ergm-term-crossRef.html |only ergm-3.9.4/ergm/DESCRIPTION | 64 ergm-3.9.4/ergm/LICENSE | 2 ergm-3.9.4/ergm/MD5 | 674 +++++---- ergm-3.9.4/ergm/NAMESPACE | 602 +++----- ergm-3.9.4/ergm/R/InitErgm.bipartite.R | 6 ergm-3.9.4/ergm/R/InitErgmConstraint.R |only ergm-3.9.4/ergm/R/InitErgmProposal.R |only ergm-3.9.4/ergm/R/InitErgmProposal.blockdiag.R |only ergm-3.9.4/ergm/R/InitErgmReference.R |only ergm-3.9.4/ergm/R/InitErgmTerm.R | 803 ++++++----- ergm-3.9.4/ergm/R/InitErgmTerm.bipartite.degree.R | 2 ergm-3.9.4/ergm/R/InitErgmTerm.coincidence.R | 2 ergm-3.9.4/ergm/R/InitErgmTerm.dgw_sp.R | 56 ergm-3.9.4/ergm/R/InitErgmTerm.extra.R | 14 ergm-3.9.4/ergm/R/InitErgmTerm.indices.R | 2 ergm-3.9.4/ergm/R/InitErgmTerm.test.R |only ergm-3.9.4/ergm/R/InitErgmTerm.transitiveties.R | 18 ergm-3.9.4/ergm/R/InitWtErgmProposal.R |only ergm-3.9.4/ergm/R/InitWtErgmTerm.R | 518 +------ ergm-3.9.4/ergm/R/anova.ergm.R | 68 ergm-3.9.4/ergm/R/anova.ergmlist.R | 13 ergm-3.9.4/ergm/R/approx.hotelling.diff.test.R | 264 ++- ergm-3.9.4/ergm/R/as.network.numeric.R | 93 - ergm-3.9.4/ergm/R/build_term_index.R | 55 ergm-3.9.4/ergm/R/check.ErgmTerm.R | 91 - ergm-3.9.4/ergm/R/control.ergm.R | 511 +++++-- ergm-3.9.4/ergm/R/control.ergm.bridge.R | 48 ergm-3.9.4/ergm/R/control.gof.R | 102 + ergm-3.9.4/ergm/R/control.logLik.ergm.R | 48 ergm-3.9.4/ergm/R/control.san.R | 89 - ergm-3.9.4/ergm/R/control.simulate.R | 149 +- ergm-3.9.4/ergm/R/data.R |only ergm-3.9.4/ergm/R/ergm-defunct.R | 45 ergm-3.9.4/ergm/R/ergm-deprecated.R |only ergm-3.9.4/ergm/R/ergm.CD.fixed.R | 66 ergm-3.9.4/ergm/R/ergm.Cprepare.R | 270 ++- ergm-3.9.4/ergm/R/ergm.MCMCse.R | 18 ergm-3.9.4/ergm/R/ergm.MCMCse.lognormal.R | 12 ergm-3.9.4/ergm/R/ergm.MCMLE.R | 132 + ergm-3.9.4/ergm/R/ergm.R | 582 ++++++-- ergm-3.9.4/ergm/R/ergm.allstats.R | 138 +- ergm-3.9.4/ergm/R/ergm.bounddeg.R | 90 - ergm-3.9.4/ergm/R/ergm.bridge.R | 156 +- ergm-3.9.4/ergm/R/ergm.check.R | 17 ergm-3.9.4/ergm/R/ergm.coefficient.degeneracy.R | 11 ergm-3.9.4/ergm/R/ergm.curved.statsmatrix.R | 2 ergm-3.9.4/ergm/R/ergm.degeneracy.R | 66 ergm-3.9.4/ergm/R/ergm.design.R | 32 ergm-3.9.4/ergm/R/ergm.errors.R |only ergm-3.9.4/ergm/R/ergm.estimate.R | 25 ergm-3.9.4/ergm/R/ergm.eta.R | 34 ergm-3.9.4/ergm/R/ergm.etagrad.R | 11 ergm-3.9.4/ergm/R/ergm.etagradmult.R | 11 ergm-3.9.4/ergm/R/ergm.etamap.R | 29 ergm-3.9.4/ergm/R/ergm.geodistn.R | 40 ergm-3.9.4/ergm/R/ergm.getCDsample.R | 42 ergm-3.9.4/ergm/R/ergm.getMCMCsample.R | 299 ++-- ergm-3.9.4/ergm/R/ergm.getnetwork.R | 43 ergm-3.9.4/ergm/R/ergm.getterms.R | 5 ergm-3.9.4/ergm/R/ergm.initialfit.R | 37 ergm-3.9.4/ergm/R/ergm.llik.R | 2 ergm-3.9.4/ergm/R/ergm.llik.obs.R | 2 ergm-3.9.4/ergm/R/ergm.logitreg.R | 2 ergm-3.9.4/ergm/R/ergm.mapl.R | 31 ergm-3.9.4/ergm/R/ergm.maple.R | 6 ergm-3.9.4/ergm/R/ergm.mple.R | 130 + ergm-3.9.4/ergm/R/ergm.pen.glm.R | 18 ergm-3.9.4/ergm/R/ergm.phase12.R | 24 ergm-3.9.4/ergm/R/ergm.pl.R | 212 --- ergm-3.9.4/ergm/R/ergm.reviseinit.R | 4 ergm-3.9.4/ergm/R/ergm.robmon.R | 36 ergm-3.9.4/ergm/R/ergm.san.R | 190 +- ergm-3.9.4/ergm/R/ergm.stepping.R | 34 ergm-3.9.4/ergm/R/ergm.stocapprox.R | 22 ergm-3.9.4/ergm/R/ergm.sufftoprob.R | 2 ergm-3.9.4/ergm/R/ergm.utility.R | 328 +++- ergm-3.9.4/ergm/R/ergmMPLE.R | 111 + ergm-3.9.4/ergm/R/ergm_estfun.R |only ergm-3.9.4/ergm/R/ergm_model.R |only ergm-3.9.4/ergm/R/ergm_model.utils.R |only ergm-3.9.4/ergm/R/ergm_proposal.R |only ergm-3.9.4/ergm/R/formula.utils.R | 184 ++ ergm-3.9.4/ergm/R/get.node.attr.R | 384 +++++ ergm-3.9.4/ergm/R/godfather.R |only ergm-3.9.4/ergm/R/gof.ergm.R | 404 +++-- ergm-3.9.4/ergm/R/is.curved.R | 36 ergm-3.9.4/ergm/R/is.durational.R | 40 ergm-3.9.4/ergm/R/is.dyad.independent.R | 52 ergm-3.9.4/ergm/R/is.inCH.R | 54 ergm-3.9.4/ergm/R/locator.R |only ergm-3.9.4/ergm/R/logLik.ergm.R | 108 + ergm-3.9.4/ergm/R/mcmc.diagnostics.ergm.R | 159 +- ergm-3.9.4/ergm/R/network.list.R |only ergm-3.9.4/ergm/R/network.update.R | 68 ergm-3.9.4/ergm/R/nparam.R |only ergm-3.9.4/ergm/R/parallel.utils.R | 115 + ergm-3.9.4/ergm/R/param_names.R |only ergm-3.9.4/ergm/R/plot.ergm.R | 54 ergm-3.9.4/ergm/R/plot.network.ergm.R | 31 ergm-3.9.4/ergm/R/print.ergm.R | 40 ergm-3.9.4/ergm/R/print.network.list.R | 4 ergm-3.9.4/ergm/R/print.summary.ergm.R | 39 ergm-3.9.4/ergm/R/rlebdm.R |only ergm-3.9.4/ergm/R/simulate.ergm.R | 354 +++-- ergm-3.9.4/ergm/R/summary.ergm.R | 115 + ergm-3.9.4/ergm/R/summary.ergm_model.R |only ergm-3.9.4/ergm/R/summary.network.list.R | 29 ergm-3.9.4/ergm/R/summary.statistics.network.R | 174 +- ergm-3.9.4/ergm/R/to_ergm_Cdouble.R |only ergm-3.9.4/ergm/R/vcov.ergm.R |only ergm-3.9.4/ergm/R/wtd.median.R | 28 ergm-3.9.4/ergm/R/zzz.R | 116 - ergm-3.9.4/ergm/README.md | 10 ergm-3.9.4/ergm/build/partial.rdb |binary ergm-3.9.4/ergm/build/vignette.rds |binary ergm-3.9.4/ergm/data/sampson.RData |binary ergm-3.9.4/ergm/inst/CITATION | 79 - ergm-3.9.4/ergm/inst/NEWS.Rd | 189 ++ ergm-3.9.4/ergm/inst/doc/ergm-term-crossRef.R |only ergm-3.9.4/ergm/inst/doc/ergm-term-crossRef.Rmd |only ergm-3.9.4/ergm/inst/doc/ergm-term-crossRef.html |only ergm-3.9.4/ergm/inst/doc/ergm.R | 448 ++---- ergm-3.9.4/ergm/inst/doc/ergm.Rnw | 187 +- ergm-3.9.4/ergm/inst/doc/ergm.pdf |binary ergm-3.9.4/ergm/inst/include/MCMC.h | 4 ergm-3.9.4/ergm/inst/include/MHproposal.h | 4 ergm-3.9.4/ergm/inst/include/changestat.h | 4 ergm-3.9.4/ergm/inst/include/edgelist.h | 4 ergm-3.9.4/ergm/inst/include/edgetree.h | 4 ergm-3.9.4/ergm/inst/include/ergm_rlebdm.h |only ergm-3.9.4/ergm/inst/include/ergm_stubs.c | 18 ergm-3.9.4/ergm/inst/include/model.h | 4 ergm-3.9.4/ergm/inst/include/wtMCMC.h | 4 ergm-3.9.4/ergm/inst/include/wtMHproposal.h | 4 ergm-3.9.4/ergm/inst/include/wtchangestat.h | 4 ergm-3.9.4/ergm/inst/include/wtedgetree.h | 4 ergm-3.9.4/ergm/inst/include/wtmodel.h | 4 ergm-3.9.4/ergm/man/Getting.Started.Rd | 2 ergm-3.9.4/ergm/man/anova.ergm.Rd | 140 -- ergm-3.9.4/ergm/man/approx.hotelling.diff.test.Rd | 74 - ergm-3.9.4/ergm/man/as.edgelist.Rd | 2 ergm-3.9.4/ergm/man/as.network.numeric.Rd | 110 - ergm-3.9.4/ergm/man/as.rlebdm.ergm_conlist.Rd |only ergm-3.9.4/ergm/man/check.ErgmTerm.Rd | 143 -- ergm-3.9.4/ergm/man/control.ergm.Rd | 1104 +++++++--------- ergm-3.9.4/ergm/man/control.ergm.bridge.Rd | 172 +- ergm-3.9.4/ergm/man/control.ergm.godfather.Rd |only ergm-3.9.4/ergm/man/control.gof.Rd | 201 +- ergm-3.9.4/ergm/man/control.logLik.ergm.Rd | 175 +- ergm-3.9.4/ergm/man/control.san.Rd | 187 +- ergm-3.9.4/ergm/man/control.simulate.ergm.Rd | 243 +-- ergm-3.9.4/ergm/man/degreedist.Rd | 72 - ergm-3.9.4/ergm/man/ecoli.Rd | 67 ergm-3.9.4/ergm/man/empty_network.Rd |only ergm-3.9.4/ergm/man/enformulate.curved.Rd | 109 - ergm-3.9.4/ergm/man/ergm-constraints.Rd | 84 - ergm-3.9.4/ergm/man/ergm-defunct.Rd | 101 - ergm-3.9.4/ergm/man/ergm-deprecated.Rd | 230 +++ ergm-3.9.4/ergm/man/ergm-errors.Rd |only ergm-3.9.4/ergm/man/ergm-internal.Rd | 6 ergm-3.9.4/ergm/man/ergm-package.Rd | 2 ergm-3.9.4/ergm/man/ergm-parallel.Rd | 144 +- ergm-3.9.4/ergm/man/ergm-proposals.Rd |only ergm-3.9.4/ergm/man/ergm-references.Rd | 20 ergm-3.9.4/ergm/man/ergm-terms.Rd | 155 +- ergm-3.9.4/ergm/man/ergm.Rd | 669 +++++---- ergm-3.9.4/ergm/man/ergm.allstats.Rd | 103 - ergm-3.9.4/ergm/man/ergm.bounddeg.Rd | 103 - ergm-3.9.4/ergm/man/ergm.bridge.llr.Rd | 192 +- ergm-3.9.4/ergm/man/ergm.degeneracy.Rd | 81 - ergm-3.9.4/ergm/man/ergm.estfun.Rd |only ergm-3.9.4/ergm/man/ergm.eta.Rd | 154 +- ergm-3.9.4/ergm/man/ergm.exact.Rd | 101 - ergm-3.9.4/ergm/man/ergm.geodistdist.Rd | 71 - ergm-3.9.4/ergm/man/ergm.getnetwork.Rd |only ergm-3.9.4/ergm/man/ergm.godfather.Rd |only ergm-3.9.4/ergm/man/ergm.mple.Rd | 242 +-- ergm-3.9.4/ergm/man/ergmMPLE.Rd | 168 +- ergm-3.9.4/ergm/man/ergm_Clist.Rd |only ergm-3.9.4/ergm/man/ergm_MCMC_sample.Rd |only ergm-3.9.4/ergm/man/ergm_model.Rd |only ergm-3.9.4/ergm/man/ergm_plot.mcmc.list.Rd |only ergm-3.9.4/ergm/man/ergm_proposal.Rd |only ergm-3.9.4/ergm/man/ergm_proposal_table.Rd |only ergm-3.9.4/ergm/man/eut-upgrade.Rd | 2 ergm-3.9.4/ergm/man/faux.desert.high.Rd | 150 -- ergm-3.9.4/ergm/man/faux.dixon.high.Rd | 150 -- ergm-3.9.4/ergm/man/faux.magnolia.high.Rd | 146 -- ergm-3.9.4/ergm/man/faux.mesa.high.Rd | 164 +- ergm-3.9.4/ergm/man/fix.curved.Rd | 104 - ergm-3.9.4/ergm/man/florentine.Rd | 96 - ergm-3.9.4/ergm/man/g4.Rd | 42 ergm-3.9.4/ergm/man/get.node.attr.Rd | 67 ergm-3.9.4/ergm/man/geweke.diag.mv.Rd |only ergm-3.9.4/ergm/man/gof.Rd |only ergm-3.9.4/ergm/man/is.curved.Rd | 70 - ergm-3.9.4/ergm/man/is.durational.Rd | 71 - ergm-3.9.4/ergm/man/is.dyad.independent.Rd | 86 - ergm-3.9.4/ergm/man/is.inCH.Rd | 116 - ergm-3.9.4/ergm/man/kapferer.Rd | 88 - ergm-3.9.4/ergm/man/lasttoggle.Rd | 115 - ergm-3.9.4/ergm/man/logLik.ergm.Rd | 129 - ergm-3.9.4/ergm/man/logLikNull.Rd |only ergm-3.9.4/ergm/man/mcmc.diagnostics.Rd |only ergm-3.9.4/ergm/man/molecule.Rd | 30 ergm-3.9.4/ergm/man/network.list.Rd |only ergm-3.9.4/ergm/man/network.update.Rd | 75 - ergm-3.9.4/ergm/man/newnw.extract.Rd | 66 ergm-3.9.4/ergm/man/node-attr-api.Rd |only ergm-3.9.4/ergm/man/node-attr.Rd |only ergm-3.9.4/ergm/man/nparam.Rd |only ergm-3.9.4/ergm/man/nvattr.copy.network.Rd | 53 ergm-3.9.4/ergm/man/param_names.Rd |only ergm-3.9.4/ergm/man/rlebdm.Rd |only ergm-3.9.4/ergm/man/samplk.Rd | 200 +- ergm-3.9.4/ergm/man/sampson.Rd | 209 +-- ergm-3.9.4/ergm/man/san.Rd | 177 +- ergm-3.9.4/ergm/man/search.ergmTerms.Rd | 78 - ergm-3.9.4/ergm/man/simulate.ergm.Rd | 296 ++-- ergm-3.9.4/ergm/man/spectrum0.mvar.Rd |only ergm-3.9.4/ergm/man/standardize.network.Rd | 58 ergm-3.9.4/ergm/man/summary.ergm.Rd | 142 -- ergm-3.9.4/ergm/man/summary.ergm_model.Rd |only ergm-3.9.4/ergm/man/summary.formula.Rd |only ergm-3.9.4/ergm/man/summary_formula.Rd |only ergm-3.9.4/ergm/man/to_ergm_Cdouble.Rd |only ergm-3.9.4/ergm/man/wtd.median.Rd | 38 ergm-3.9.4/ergm/src/CD.c | 2 ergm-3.9.4/ergm/src/CD.h | 2 ergm-3.9.4/ergm/src/MCMC.c | 2 ergm-3.9.4/ergm/src/MCMC.h | 2 ergm-3.9.4/ergm/src/MHproposal.c | 2 ergm-3.9.4/ergm/src/MHproposal.h | 2 ergm-3.9.4/ergm/src/MHproposals.c | 115 + ergm-3.9.4/ergm/src/MHproposals.h | 2 ergm-3.9.4/ergm/src/MHproposals_bipartite.c | 2 ergm-3.9.4/ergm/src/MHproposals_bipartite.h | 2 ergm-3.9.4/ergm/src/MHproposals_block.c | 2 ergm-3.9.4/ergm/src/MHproposals_block.h | 2 ergm-3.9.4/ergm/src/MHproposals_degree.c | 2 ergm-3.9.4/ergm/src/MHproposals_degree.h | 2 ergm-3.9.4/ergm/src/MPLE.c | 189 -- ergm-3.9.4/ergm/src/MPLE.h | 17 ergm-3.9.4/ergm/src/SAN.c | 2 ergm-3.9.4/ergm/src/SAN.h | 2 ergm-3.9.4/ergm/src/allstatistics.c | 2 ergm-3.9.4/ergm/src/changestat.c | 2 ergm-3.9.4/ergm/src/changestat.h | 2 ergm-3.9.4/ergm/src/changestats.c | 144 +- ergm-3.9.4/ergm/src/changestats.dgw_sp.c | 2 ergm-3.9.4/ergm/src/changestats.dgw_sp.h | 2 ergm-3.9.4/ergm/src/changestats.h | 2 ergm-3.9.4/ergm/src/changestats_coincidence.c | 2 ergm-3.9.4/ergm/src/changestats_coincidence.h | 2 ergm-3.9.4/ergm/src/changestats_concurrentties.c | 2 ergm-3.9.4/ergm/src/changestats_concurrentties.h | 2 ergm-3.9.4/ergm/src/changestats_experimental.c | 2 ergm-3.9.4/ergm/src/changestats_experimental.h | 2 ergm-3.9.4/ergm/src/changestats_homoproportion.c | 2 ergm-3.9.4/ergm/src/changestats_homoproportion.h | 2 ergm-3.9.4/ergm/src/changestats_indices.c | 2 ergm-3.9.4/ergm/src/changestats_indices.h | 2 ergm-3.9.4/ergm/src/changestats_internal.c | 2 ergm-3.9.4/ergm/src/changestats_internal.h | 2 ergm-3.9.4/ergm/src/changestats_test.c |only ergm-3.9.4/ergm/src/changestats_transitiveties.c | 2 ergm-3.9.4/ergm/src/changestats_transitiveties.h | 2 ergm-3.9.4/ergm/src/edgelist.c | 2 ergm-3.9.4/ergm/src/edgelist.h | 2 ergm-3.9.4/ergm/src/edgetree.c | 39 ergm-3.9.4/ergm/src/edgetree.h | 2 ergm-3.9.4/ergm/src/ergm_rlebdm.c |only ergm-3.9.4/ergm/src/ergm_rlebdm.h |only ergm-3.9.4/ergm/src/geodist.c | 2 ergm-3.9.4/ergm/src/geodist.h | 2 ergm-3.9.4/ergm/src/godfather.c |only ergm-3.9.4/ergm/src/init.c | 8 ergm-3.9.4/ergm/src/model.c | 2 ergm-3.9.4/ergm/src/model.h | 2 ergm-3.9.4/ergm/src/netstats.c | 2 ergm-3.9.4/ergm/src/netstats.h | 2 ergm-3.9.4/ergm/src/wtCD.c | 2 ergm-3.9.4/ergm/src/wtCD.h | 2 ergm-3.9.4/ergm/src/wtMCMC.c | 2 ergm-3.9.4/ergm/src/wtMCMC.h | 2 ergm-3.9.4/ergm/src/wtMHproposal.c | 2 ergm-3.9.4/ergm/src/wtMHproposal.h | 2 ergm-3.9.4/ergm/src/wtMHproposals.c | 52 ergm-3.9.4/ergm/src/wtMHproposals.h | 2 ergm-3.9.4/ergm/src/wtSAN.c | 2 ergm-3.9.4/ergm/src/wtSAN.h | 2 ergm-3.9.4/ergm/src/wtchangestat.h | 2 ergm-3.9.4/ergm/src/wtchangestats.c | 303 +++- ergm-3.9.4/ergm/src/wtchangestats.h | 2 ergm-3.9.4/ergm/src/wtedgetree.c | 67 ergm-3.9.4/ergm/src/wtedgetree.h | 2 ergm-3.9.4/ergm/src/wtgodfather.c |only ergm-3.9.4/ergm/src/wtmodel.c | 2 ergm-3.9.4/ergm/src/wtmodel.h | 2 ergm-3.9.4/ergm/src/wtnetstats.c | 2 ergm-3.9.4/ergm/src/wtnetstats.h | 2 ergm-3.9.4/ergm/tests/constrain_degrees_edges.R |only ergm-3.9.4/ergm/tests/constrain_dind.R |only ergm-3.9.4/ergm/tests/constraint_conflict.R | 2 ergm-3.9.4/ergm/tests/constraint_generalized.R | 16 ergm-3.9.4/ergm/tests/drop_tests.R | 2 ergm-3.9.4/ergm/tests/ergmMPLEtest.R | 2 ergm-3.9.4/ergm/tests/ergm_term_doc_test.R | 2 ergm-3.9.4/ergm/tests/fix.curved.R | 2 ergm-3.9.4/ergm/tests/gw_sp_tests.R | 2 ergm-3.9.4/ergm/tests/hamming_termtests.R | 2 ergm-3.9.4/ergm/tests/miss_tests.CD.R | 2 ergm-3.9.4/ergm/tests/miss_tests.R | 31 ergm-3.9.4/ergm/tests/mle_offset.R | 5 ergm-3.9.4/ergm/tests/mple_largenetwork.R | 2 ergm-3.9.4/ergm/tests/mple_offset.R | 7 ergm-3.9.4/ergm/tests/mple_target.stats.R | 4 ergm-3.9.4/ergm/tests/nodemix.R | 2 ergm-3.9.4/ergm/tests/nodrop.R | 8 ergm-3.9.4/ergm/tests/parallel.R | 4 ergm-3.9.4/ergm/tests/requireNamespaceTest.R | 10 ergm-3.9.4/ergm/tests/runtime_diags.R | 3 ergm-3.9.4/ergm/tests/scoping.R | 4 ergm-3.9.4/ergm/tests/simpletests.R | 4 ergm-3.9.4/ergm/tests/steppingtest.R | 2 ergm-3.9.4/ergm/tests/stocapprox.R | 3 ergm-3.9.4/ergm/tests/target_offset.R | 3 ergm-3.9.4/ergm/tests/termTests.b12factor.R | 2 ergm-3.9.4/ergm/tests/termTests.b12nodematch.R | 2 ergm-3.9.4/ergm/tests/termTests.bipartite.R | 2 ergm-3.9.4/ergm/tests/termTests.directed.R | 2 ergm-3.9.4/ergm/tests/termTests.flexible.R | 4 ergm-3.9.4/ergm/tests/termTests.undirected.R | 2 ergm-3.9.4/ergm/tests/termTests.valued.R | 83 - ergm-3.9.4/ergm/tests/testgflomiss.R | 2 ergm-3.9.4/ergm/tests/testgmonkmiss.R | 3 ergm-3.9.4/ergm/tests/testthat |only ergm-3.9.4/ergm/tests/testthat.R |only ergm-3.9.4/ergm/tests/utils_tests.R | 2 ergm-3.9.4/ergm/tests/valued_sim.R | 2 ergm-3.9.4/ergm/tests/valued_terms.R | 2 ergm-3.9.4/ergm/vignettes/ergm-term-crossRef.Rmd | 4 ergm-3.9.4/ergm/vignettes/ergm.Rnw | 187 +- 394 files changed, 11869 insertions(+), 9277 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient tree manipulations for large phylogenies, including pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters. Simulating and fitting models of trait evolution, and generating random trees using birth-death models. Dating trees, comparing two trees, and reading/writing trees to a file. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.3.3 dated 2018-04-11 and 1.3.4 dated 2018-08-16
DESCRIPTION | 8 MD5 | 26 - R/RcppExports.R | 4 R/collapse_tree_at_resolution.R | 1 R/count_clades_over_time.R | 3 R/fit_tree_model.R | 82 ++-- R/generate_random_tree.R | 28 + R/simulate_diversification_model.R | 44 +- man/collapse_tree_at_resolution.Rd | 3 man/fit_tree_model.Rd | 8 man/generate_random_tree.Rd | 15 man/simulate_diversification_model.Rd | 63 ++- src/RcppExports.cpp | 11 src/phylogenetics_cpp_routines.cpp | 595 +++++++++++++++++++++------------- 14 files changed, 577 insertions(+), 314 deletions(-)
Title: Stochastic Process Model for Analysis of Longitudinal and
Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions
induced by stochastic covariates. Miscellaneous functions for data preparation
and simulation are also provided. For more information, see:
(i)"Stochastic model for analysis of longitudinal data on aging and mortality"
by Yashin A. et al. (2007),
Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>;
(ii) "Health decline, aging and mortality: how are they related?"
by Yashin A. et al. (2007),
Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, Liang He, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.7.5 dated 2018-07-17 and 1.7.7 dated 2018-08-16
DESCRIPTION | 8 MD5 | 24 R/hes_spm_g.r |11440 ++++++++++++++++++++++---------------------- R/lik_con_1d_g.r | 8 R/spm_con_1d_g.r | 108 build/vignette.rds |binary data/ex_spmcon1dg.rda |binary inst/NEWS | 5 inst/doc/stpm-vignette.html | 492 - man/spm_con_1d_g.Rd | 10 src/devlik_g_2.cpp | 90 src/loglik_g_2.cpp | 26 src/stpm_init.c | 8 13 files changed, 6141 insertions(+), 6078 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.8.600.0.0 dated 2018-06-29 and 0.9.100.5.0 dated 2018-08-16
ChangeLog | 27 DESCRIPTION | 8 MD5 | 117 +-- build/vignette.rds |binary inst/NEWS.Rd | 21 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/armadillo | 57 - inst/include/armadillo_bits/Base_bones.hpp | 12 inst/include/armadillo_bits/Base_meat.hpp | 239 +++++++ inst/include/armadillo_bits/MapMat_bones.hpp | 17 inst/include/armadillo_bits/MapMat_meat.hpp | 114 +++ inst/include/armadillo_bits/SpCol_meat.hpp | 4 inst/include/armadillo_bits/SpMat_bones.hpp | 20 inst/include/armadillo_bits/SpMat_meat.hpp | 415 +++++------- inst/include/armadillo_bits/SpRow_meat.hpp | 4 inst/include/armadillo_bits/SpValProxy_bones.hpp | 3 inst/include/armadillo_bits/SpValProxy_meat.hpp | 33 - inst/include/armadillo_bits/access.hpp | 8 inst/include/armadillo_bits/arma_config.hpp | 11 inst/include/armadillo_bits/arma_forward.hpp | 2 inst/include/armadillo_bits/arma_rng_cxx11.hpp | 4 inst/include/armadillo_bits/arma_version.hpp | 8 inst/include/armadillo_bits/arrayops_bones.hpp | 14 inst/include/armadillo_bits/arrayops_meat.hpp | 69 -- inst/include/armadillo_bits/auxlib_bones.hpp | 42 - inst/include/armadillo_bits/auxlib_meat.hpp | 751 ++++++++++++++--------- inst/include/armadillo_bits/compiler_setup.hpp | 14 inst/include/armadillo_bits/config.hpp | 27 inst/include/armadillo_bits/config.hpp.cmake | 27 inst/include/armadillo_bits/def_atlas.hpp | 19 inst/include/armadillo_bits/def_lapack.hpp | 96 +- inst/include/armadillo_bits/fn_spsolve.hpp | 7 inst/include/armadillo_bits/glue_solve_bones.hpp | 5 inst/include/armadillo_bits/glue_solve_meat.hpp | 119 ++- inst/include/armadillo_bits/glue_times_meat.hpp | 58 + inst/include/armadillo_bits/gmm_diag_meat.hpp | 16 inst/include/armadillo_bits/gmm_full_meat.hpp | 14 inst/include/armadillo_bits/memory.hpp | 25 inst/include/armadillo_bits/mul_gemm.hpp | 2 inst/include/armadillo_bits/mul_gemv.hpp | 3 inst/include/armadillo_bits/op_chol_meat.hpp | 2 inst/include/armadillo_bits/op_dot_meat.hpp | 2 inst/include/armadillo_bits/op_inv_bones.hpp | 8 inst/include/armadillo_bits/op_inv_meat.hpp | 67 +- inst/include/armadillo_bits/op_strans_bones.hpp | 4 inst/include/armadillo_bits/op_strans_meat.hpp | 4 inst/include/armadillo_bits/sp_auxlib_bones.hpp | 2 inst/include/armadillo_bits/sp_auxlib_meat.hpp | 18 inst/include/armadillo_bits/strip.hpp | 9 inst/include/armadillo_bits/sympd_helper.hpp |only inst/include/armadillo_bits/unwrap.hpp | 255 ++++++- inst/include/armadillo_bits/wrapper_atlas.hpp | 147 +++- inst/include/armadillo_bits/wrapper_blas.hpp | 24 inst/include/armadillo_bits/wrapper_lapack.hpp | 214 ++---- inst/include/armadillo_bits/xtrans_mat_bones.hpp | 2 inst/include/armadillo_bits/xtrans_mat_meat.hpp | 14 inst/skeleton/Makevars | 2 inst/skeleton/Makevars.win | 2 60 files changed, 2063 insertions(+), 1145 deletions(-)
Title: EBGM Scores for Mining Large Contingency Tables
Description: An implementation of DuMouchel's (1999)
<doi:10.1080/00031305.1999.10474456> Bayesian data mining method for the
market basket problem. Calculates Empirical Bayes Geometric Mean (EBGM) and
quantile scores from the posterior distribution using the Gamma-Poisson
Shrinker (GPS) model to find unusually large cell counts in large, sparse
contingency tables. Can be used to find unusually high reporting rates of
adverse events associated with products. In general, can be used to mine any
database where the co-occurrence of two variables or items is of interest.
Also calculates relative and proportional reporting ratios. Builds on the work
of the 'PhViD' package, from which much of the code is derived. Some of the
added features include stratification to adjust for confounding variables and
data squashing to improve computational efficiency. Now includes an
implementation of the EM algorithm for hyperparameter estimation loosely
derived from the 'mederrRank' package.
Author: John Ihrie [cre, aut],
Travis Canida [aut],
Ismaïl Ahmed [ctb] (author of 'PhViD' package (derived code)),
Antoine Poncet [ctb] (author of 'PhViD'),
Sergio Venturini [ctb] (author of 'mederrRank' package (derived code)),
Jessica Myers [ctb] (author of 'mederrRank')
Maintainer: John Ihrie <John.Ihrie@fda.hhs.gov>
Diff between openEBGM versions 0.6.0 dated 2018-05-21 and 0.7.0 dated 2018-08-16
DESCRIPTION | 8 - MD5 | 61 ++++++------- NAMESPACE | 1 NEWS | 13 ++ R/f_EM_hyperEstimation.R | 13 +- R/f_EM_updateTheta.R | 6 - R/f_checkInputs.R | 23 +++++ R/f_dataSquashing.R | 118 +++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/x1_introAndDataPrepVignette.html | 4 inst/doc/x2_rawDataProcessingVignette.html | 4 inst/doc/x3_hyperParameterVignette.R | 8 + inst/doc/x3_hyperParameterVignette.Rmd | 35 +++++-- inst/doc/x3_hyperParameterVignette.html | 57 ++++++++++-- inst/doc/x4_posteriorCalculationVignette.html | 4 inst/doc/x5_openEBGMObjectVignette.html | 16 +-- man/Qn.Rd | 1 man/autoHyper.Rd | 9 + man/autoSquash.Rd |only man/ebgm.Rd | 1 man/exploreHypers.Rd | 1 man/hyperEM.Rd | 12 +- man/negLL.Rd | 1 man/negLLsquash.Rd | 1 man/negLLzero.Rd | 1 man/negLLzeroSquash.Rd | 1 man/plot.openEBGM.Rd | 3 man/quantBisect.Rd | 5 - man/squashData.Rd | 14 +-- man/summary.openEBGM.Rd | 3 tests/testthat/testB_Squashing.R | 44 ++++++++- vignettes/x3_hyperParameterVignette.Rmd | 35 +++++-- 32 files changed, 388 insertions(+), 115 deletions(-)
Title: Interactive Viewing of Spatial Data in R
Description: Quickly and conveniently create interactive visualisations of spatial data with or without background maps. Attributes of displayed features are fully queryable via pop-up windows. Additional functionality includes methods to visualise true- and false-color raster images, bounding boxes, small multiples and 3D raster data cubes.
Author: Tim Appelhans [cre, aut],
Florian Detsch [aut],
Christoph Reudenbach [aut],
Stefan Woellauer [aut],
Spaska Forteva [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb],
Kenton Russell [ctb],
Michael Sumner [ctb],
Jochen Darley [ctb],
Pierre Roudier [ctb],
Environmental Informatics Marburg [ctb]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between mapview versions 2.4.0 dated 2018-04-28 and 2.5.0 dated 2018-08-16
mapview-2.4.0/mapview/man/addMapPane.Rd |only mapview-2.5.0/mapview/DESCRIPTION | 18 mapview-2.5.0/mapview/MD5 | 93 - mapview-2.5.0/mapview/NAMESPACE | 5 mapview-2.5.0/mapview/NEWS | 33 mapview-2.5.0/mapview/NEWS.md | 33 mapview-2.5.0/mapview/R/extensions.R | 334 +++--- mapview-2.5.0/mapview/R/extent.R | 1 mapview-2.5.0/mapview/R/mapView.R | 304 +++--- mapview-2.5.0/mapview/R/mapshot.R | 12 mapview-2.5.0/mapview/R/mapview-package.R | 4 mapview-2.5.0/mapview/R/mapviewControls.R | 30 mapview-2.5.0/mapview/R/mapviewOptions.R | 4 mapview-2.5.0/mapview/R/plainView.R | 31 mapview-2.5.0/mapview/R/plus.R | 18 mapview-2.5.0/mapview/R/popup.R | 222 +++- mapview-2.5.0/mapview/R/raster.R | 4 mapview-2.5.0/mapview/R/sf.R | 41 mapview-2.5.0/mapview/R/slideView.R | 2 mapview-2.5.0/mapview/R/stars.R | 486 ++++----- mapview-2.5.0/mapview/R/viewRGB.R | 82 + mapview-2.5.0/mapview/README.md | 2 mapview-2.5.0/mapview/data/breweries.rda |binary mapview-2.5.0/mapview/data/franconia.rda |binary mapview-2.5.0/mapview/data/poppendorf.rda |binary mapview-2.5.0/mapview/data/trails.rda |binary mapview-2.5.0/mapview/inst/extdata/basic_small.png |only mapview-2.5.0/mapview/inst/htmlwidgets/lib/HomeButton/home-button.js | 2 mapview-2.5.0/mapview/inst/htmlwidgets/plainView.js | 492 +++++----- mapview-2.5.0/mapview/inst/templates/popup-graph.brew | 20 mapview-2.5.0/mapview/inst/templates/popup.brew | 4 mapview-2.5.0/mapview/man/addHomeButton.Rd | 2 mapview-2.5.0/mapview/man/addImageQuery.Rd | 21 mapview-2.5.0/mapview/man/addMouseCoordinates.Rd | 11 mapview-2.5.0/mapview/man/addStarsImage.Rd |only mapview-2.5.0/mapview/man/addStaticLabels.Rd | 2 mapview-2.5.0/mapview/man/coords2Polygons.Rd | 3 mapview-2.5.0/mapview/man/mapView.Rd | 175 +-- mapview-2.5.0/mapview/man/mapviewColors.Rd | 5 mapview-2.5.0/mapview/man/mapviewOptions.Rd | 7 mapview-2.5.0/mapview/man/npts.Rd | 8 mapview-2.5.0/mapview/man/plainView.Rd | 12 mapview-2.5.0/mapview/man/plus.Rd | 9 mapview-2.5.0/mapview/man/popup.Rd | 7 mapview-2.5.0/mapview/man/slideView.Rd | 18 mapview-2.5.0/mapview/man/viewExtent.Rd | 2 mapview-2.5.0/mapview/man/viewRGB.Rd | 22 mapview-2.5.0/mapview/src/RcppExports.cpp | 2 mapview-2.5.0/mapview/src/brewCppFun.cpp | 4 49 files changed, 1499 insertions(+), 1088 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <http://canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.20.1 dated 2018-07-25 and 1.20.5 dated 2018-08-16
DESCRIPTION | 6 MD5 | 34 NEWS.md | 4 inst/doc/additional_examples.html | 4 inst/doc/getting_started.html | 4 inst/extdata/cX-density-dat.txt |only inst/extdata/cX-density-smp.txt |only inst/extdata/cX-density-var.txt |only inst/extdata/cX-density2-dat.txt |only inst/extdata/cX-density2-smp.txt |only inst/extdata/cX-loess2-dat.txt | 112 inst/extdata/cX-loess3-dat.txt |only inst/extdata/cX-toothgrowth-dat.txt |only inst/extdata/cX-toothgrowth-smp.txt |only inst/htmlwidgets/canvasXpress.yaml | 2 inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 214 + inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 6 tests/cX-function.R | 2028 +++++++++++++++--- tests/testthat/test-boxplot.R | 66 tests/testthat/test-density.R |only tests/testthat/test-dotplot.R | 48 tests/testthat/test-tagcloud.R | 1 tests/testthat/test-violin.R |only 23 files changed, 2129 insertions(+), 400 deletions(-)
Title: Semantic Annotation and Discoverability System for R-Based
Artifacts
Description: Automatically annotates R-based artifacts
with relevant descriptive and provenance-related
and provides a backend-agnostic storage and
discoverability system for organizing, retrieving, and
interrogating such artifacts.
Author: Gabriel Becker [aut, cre],
Sara Moore [aut]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between trackr versions 0.9.5 dated 2018-08-15 and 0.9.6 dated 2018-08-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/Extending-trackr.pdf |binary inst/doc/index.html | 10 +++++----- tests/trackr-tests.R | 9 ++++++--- 5 files changed, 19 insertions(+), 16 deletions(-)
More information about NetworkInference at CRAN
Permanent link
Title: Low-Level Support for Provenance Capture Between in-Memory R
Objects
Description: A suite of classes and methods which provide low-level support for modeling provenance between in-memory R objects. This is an infrastructure package and is not intended to be used directly by end-users.
Author: Gabriel Becker
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between roprov versions 0.1.0 dated 2018-06-24 and 0.1.1 dated 2018-08-16
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/prov.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Selection of Training Populations by Genetic Algorithm
Description: To be utilized to select a test data calibrated training population in high dimensional prediction problems and assumes that the explanatory variables are observed for all of the individuals. Once a "good" training set is identified, the response variable can be obtained only for this set to build a model for predicting the response in the test set. The algorithms in the package can be tweaked to solve some other subset selection problems.
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between STPGA versions 5.0 dated 2018-07-22 and 5.1 dated 2018-08-16
STPGA-5.0/STPGA/inst |only STPGA-5.1/STPGA/DESCRIPTION | 11 +++--- STPGA-5.1/STPGA/MD5 | 22 +++++++----- STPGA-5.1/STPGA/NAMESPACE | 6 ++- STPGA-5.1/STPGA/R/DistanceBasedCriteria.R |only STPGA-5.1/STPGA/R/GenAlgForSubsetSelection.R | 29 ++++++++++++---- STPGA-5.1/STPGA/R/GenAlgForSubsetSelectionMO.R |only STPGA-5.1/STPGA/R/GenAlgForSubsetSelectionMONoTest.R |only STPGA-5.1/STPGA/R/GenAlgForSubsetSelectionNoTest.R | 23 +++++++++--- STPGA-5.1/STPGA/R/disttoideal.R |only STPGA-5.1/STPGA/R/makeonecross.R | 2 - STPGA-5.1/STPGA/man/CRITERIA.Rd | 17 +++++++-- STPGA-5.1/STPGA/man/GenAlgForSubsetSelectionMO.Rd |only STPGA-5.1/STPGA/man/GenAlgForSubsetSelectionMONoTest.Rd |only STPGA-5.1/STPGA/man/GenAlgForSubsetSelectionNoTest.Rd | 12 ++---- STPGA-5.1/STPGA/man/disttoideal.Rd |only 16 files changed, 83 insertions(+), 39 deletions(-)
Title: Trends and Indices for Monitoring Data
Description: The TRIM model is widely used for estimating growth and decline of
animal populations based on (possibly sparsely available) count data. The
current package is a reimplementation of the original TRIM software developed
at Statistics Netherlands by Jeroen Pannekoek. See
<https://www.cbs.nl/en-gb/society/nature-and-environment/indices-and-trends%2d%2dtrim%2d%2d>
for more information about TRIM.
Author: Patrick Bogaart [aut, cre],
Mark van der Loo [aut],
Jeroen Pannekoek [aut]
Maintainer: Patrick Bogaart <rtrim@cbs.nl>
Diff between rtrim versions 2.0.4 dated 2018-03-15 and 2.0.5 dated 2018-08-16
DESCRIPTION | 11 MD5 | 104 +++---- NEWS | 7 R/rtrim-pkg.R | 2 R/trim_index.R | 31 +- build/vignette.rds |binary inst/doc/Skylark_example.Rmd | 6 inst/doc/Skylark_example.html | 410 +++++++++++++++++++++++++++---- inst/doc/TRIM_methods_v2.pdf |binary inst/doc/rtrim_2_extensions.html | 341 ++++++++++++++++++++++++- inst/doc/rtrim_confidence_intervals.html | 27 +- inst/doc/rtrim_for_TRIM_users.html | 4 inst/doc/taming_overdispersion.html | 60 ++++ man/check_observations.Rd | 1 man/coef.trim.Rd | 1 man/confint.trim.Rd | 5 man/get_coef.Rd | 1 man/get_estimation_method.Rd | 1 man/get_gof.Rd | 1 man/get_model.Rd | 1 man/get_n_site.Rd | 1 man/get_n_time.Rd | 1 man/get_overal_imputed_slope.Rd | 1 man/get_time_indices.Rd | 1 man/get_time_totals.Rd | 1 man/get_version.Rd | 1 man/get_wald.Rd | 1 man/gof.Rd | 1 man/heatmap.Rd | 1 man/index.Rd | 5 man/now_what.Rd | 1 man/overall.Rd | 1 man/overdispersion.Rd | 1 man/plot.trim.index.Rd | 2 man/plot.trim.overall.Rd | 1 man/plot.trim.totals.Rd | 1 man/read_tcf.Rd | 1 man/read_tdf.Rd | 5 man/read_tof.Rd | 1 man/read_vcv.Rd | 1 man/results.Rd | 1 man/serial_correlation.Rd | 1 man/set_trim_verbose.Rd | 1 man/summary.trim.Rd | 1 man/totals.Rd | 1 man/trim.Rd | 13 man/trim_estimate.Rd | 5 man/trim_refine.Rd | 4 man/trim_workhorse.Rd | 8 man/trimcommand.Rd | 1 man/vcov.trim.Rd | 1 man/wald.Rd | 1 vignettes/Skylark_example.Rmd | 6 53 files changed, 913 insertions(+), 174 deletions(-)
Title: Tools to Support the Sheffield Elicitation Framework
Description: Implements various methods for eliciting a probability distribution
for a single parameter from an expert or a group of experts. The expert
provides a small number of probability judgements, corresponding
to points on his or her cumulative distribution function. A range of parametric
distributions can then be fitted and displayed, with feedback provided in the
form of fitted probabilities and percentiles. A graphical interface for the roulette elicitation
method is also provided. For multiple experts, a weighted linear pool can be
calculated. Also includes functions for eliciting beliefs about population distributions.
Author: Jeremy Oakley
Maintainer: Jeremy Oakley <j.oakley@sheffield.ac.uk>
Diff between SHELF versions 1.3.0 dated 2017-10-31 and 1.4.0 dated 2018-08-16
DESCRIPTION | 17 +++--- MD5 | 62 +++++++++++++++--------- NAMESPACE | 6 ++ R/SHELF-package.R | 2 R/condDirichlet.R |only R/elicit.R | 74 ++++++++++++++++++----------- R/elicitDirichlet.R | 13 +++-- R/elicitQuartiles.R |only R/elicitTertiles.R |only R/expertdensity.R | 4 - R/extractDistributions.R |only R/generateReport.R |only R/makeLinearPoolPlot.R | 30 ++++++++---- R/makeSingleExpertPlot.R | 3 - R/plotQuartiles.R |only R/plotTertiles.R |only R/plotfit.R | 4 + R/roulette.R | 80 ++++++++++++++------------------ R/shinyplotgroup.R | 29 ++++++++--- build/vignette.rds |binary inst/NEWS.md | 64 ++++++++++++++++--------- inst/doc/Dirichlet-elicitation.pdf |binary inst/doc/Multivariate-normal-copula.pdf |binary inst/doc/SHELF-overview.pdf |binary inst/elicitationReportFile |only man/SHELF-package.Rd | 2 man/cdffeedback.Rd | 6 +- man/condDirichlet.Rd |only man/elicit.Rd | 6 ++ man/elicitQuartiles.Rd |only man/elicitTertiles.Rd |only man/fitDirichlet.Rd | 7 ++ man/fitdist.Rd | 3 - man/generateReport.Rd |only man/pdfplots.Rd | 4 - man/plotQuartiles.Rd |only man/plotTertiles.Rd |only man/plotfit.Rd | 8 +-- man/roulette.Rd | 17 ++---- 39 files changed, 262 insertions(+), 179 deletions(-)
Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
this package provides a parallel implementation of the Map function for high
performance computing systems managed by schedulers 'IBM Spectrum LSF'
(<https://www.ibm.com/us-en/marketplace/hpc-workload-management>),
'OpenLava' (<http://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
Engine' (<http://www.univa.com/>), 'Slurm' (<http://slurm.schedmd.com/>),
'TORQUE/PBS'
(<http://www.adaptivecomputing.com/products/open-source/torque/>), or
'Docker Swarm' (<https://docs.docker.com/swarm/>).
A multicore and socket mode allow the parallelization on a local machines,
and multiple machines can be hooked up via SSH to create a makeshift
cluster. Moreover, the package provides an abstraction mechanism to define
large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut],
Dirk Surmann [ctb] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between batchtools versions 0.9.10 dated 2018-05-19 and 0.9.11 dated 2018-08-16
batchtools-0.9.10/batchtools/man/batchtools-deprecated.Rd |only batchtools-0.9.10/batchtools/man/chunkIds.Rd |only batchtools-0.9.10/batchtools/tests/testthat/test_chunkIds.R |only batchtools-0.9.11/batchtools/DESCRIPTION | 15 batchtools-0.9.11/batchtools/MD5 | 157 ++++------ batchtools-0.9.11/batchtools/NAMESPACE | 1 batchtools-0.9.11/batchtools/NEWS.md | 7 batchtools-0.9.11/batchtools/R/Logs.R | 4 batchtools-0.9.11/batchtools/R/Registry.R | 2 batchtools-0.9.11/batchtools/R/chunkIds.R | 39 -- batchtools-0.9.11/batchtools/R/clusterFunctions.R | 24 - batchtools-0.9.11/batchtools/R/clusterFunctionsInteractive.R | 2 batchtools-0.9.11/batchtools/R/clusterFunctionsLSF.R | 2 batchtools-0.9.11/batchtools/R/clusterFunctionsMulticore.R | 2 batchtools-0.9.11/batchtools/R/clusterFunctionsSGE.R | 2 batchtools-0.9.11/batchtools/R/clusterFunctionsSlurm.R | 2 batchtools-0.9.11/batchtools/R/doJobCollection.R | 15 batchtools-0.9.11/batchtools/R/execJob.R | 8 batchtools-0.9.11/batchtools/R/files.R | 7 batchtools-0.9.11/batchtools/R/findJobs.R | 2 batchtools-0.9.11/batchtools/R/getStatus.R | 2 batchtools-0.9.11/batchtools/R/helpers.R | 10 batchtools-0.9.11/batchtools/R/submitJobs.R | 42 ++ batchtools-0.9.11/batchtools/R/waitForFiles.R | 25 - batchtools-0.9.11/batchtools/R/waitForJobs.R | 13 batchtools-0.9.11/batchtools/R/zzz.R | 11 batchtools-0.9.11/batchtools/README.md | 3 batchtools-0.9.11/batchtools/build/vignette.rds |binary batchtools-0.9.11/batchtools/inst/doc/batchtools.pdf |binary batchtools-0.9.11/batchtools/man/JobCollection.Rd | 1 batchtools-0.9.11/batchtools/man/addExperiments.Rd | 1 batchtools-0.9.11/batchtools/man/addProblem.Rd | 4 batchtools-0.9.11/batchtools/man/batchMapResults.Rd | 1 batchtools-0.9.11/batchtools/man/btlapply.Rd | 6 batchtools-0.9.11/batchtools/man/cfBrewTemplate.Rd | 8 batchtools-0.9.11/batchtools/man/cfHandleUnknownSubmitError.Rd | 1 batchtools-0.9.11/batchtools/man/cfKillJob.Rd | 1 batchtools-0.9.11/batchtools/man/cfReadBrewTemplate.Rd | 1 batchtools-0.9.11/batchtools/man/chunk.Rd | 2 batchtools-0.9.11/batchtools/man/clearRegistry.Rd | 1 batchtools-0.9.11/batchtools/man/doJobCollection.Rd | 1 batchtools-0.9.11/batchtools/man/findJobs.Rd | 3 batchtools-0.9.11/batchtools/man/getDefaultRegistry.Rd | 1 batchtools-0.9.11/batchtools/man/getErrorMessages.Rd | 1 batchtools-0.9.11/batchtools/man/getStatus.Rd | 3 batchtools-0.9.11/batchtools/man/grepLogs.Rd | 1 batchtools-0.9.11/batchtools/man/killJobs.Rd | 1 batchtools-0.9.11/batchtools/man/loadRegistry.Rd | 1 batchtools-0.9.11/batchtools/man/loadResult.Rd | 1 batchtools-0.9.11/batchtools/man/makeClusterFunctions.Rd | 13 batchtools-0.9.11/batchtools/man/makeClusterFunctionsDocker.Rd | 3 batchtools-0.9.11/batchtools/man/makeClusterFunctionsInteractive.Rd | 5 batchtools-0.9.11/batchtools/man/makeClusterFunctionsLSF.Rd | 5 batchtools-0.9.11/batchtools/man/makeClusterFunctionsMulticore.Rd | 5 batchtools-0.9.11/batchtools/man/makeClusterFunctionsOpenLava.Rd | 7 batchtools-0.9.11/batchtools/man/makeClusterFunctionsSGE.Rd | 3 batchtools-0.9.11/batchtools/man/makeClusterFunctionsSSH.Rd | 3 batchtools-0.9.11/batchtools/man/makeClusterFunctionsSlurm.Rd | 3 batchtools-0.9.11/batchtools/man/makeClusterFunctionsSocket.Rd | 3 batchtools-0.9.11/batchtools/man/makeClusterFunctionsTORQUE.Rd | 3 batchtools-0.9.11/batchtools/man/makeExperimentRegistry.Rd | 1 batchtools-0.9.11/batchtools/man/makeRegistry.Rd | 1 batchtools-0.9.11/batchtools/man/makeSubmitJobResult.Rd | 1 batchtools-0.9.11/batchtools/man/reduceResults.Rd | 1 batchtools-0.9.11/batchtools/man/reduceResultsList.Rd | 1 batchtools-0.9.11/batchtools/man/removeExperiments.Rd | 1 batchtools-0.9.11/batchtools/man/removeRegistry.Rd | 1 batchtools-0.9.11/batchtools/man/resetJobs.Rd | 1 batchtools-0.9.11/batchtools/man/runOSCommand.Rd | 1 batchtools-0.9.11/batchtools/man/saveRegistry.Rd | 1 batchtools-0.9.11/batchtools/man/showLog.Rd | 1 batchtools-0.9.11/batchtools/man/submitJobs.Rd | 37 ++ batchtools-0.9.11/batchtools/man/summarizeExperiments.Rd | 1 batchtools-0.9.11/batchtools/man/sweepRegistry.Rd | 1 batchtools-0.9.11/batchtools/man/syncRegistry.Rd | 1 batchtools-0.9.11/batchtools/man/testJob.Rd | 1 batchtools-0.9.11/batchtools/tests/testthat/helper.R | 2 batchtools-0.9.11/batchtools/tests/testthat/test_JobCollection.R | 8 batchtools-0.9.11/batchtools/tests/testthat/test_doJobCollection.R | 3 batchtools-0.9.11/batchtools/tests/testthat/test_findConfFile.R | 2 batchtools-0.9.11/batchtools/tests/testthat/test_submitJobs.R | 2 81 files changed, 319 insertions(+), 240 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.0-1 dated 2018-06-22 and 1.0-2 dated 2018-08-16
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/mlt.R | 4 ++-- inst/doc/mlt.Rnw | 4 ++-- inst/doc/mlt.pdf |binary vignettes/mlt.Rnw | 4 ++-- 8 files changed, 24 insertions(+), 17 deletions(-)
Title: Analysis and Presentation of Social Scientific Data
Description: This is a collection of tools that the author (Jacob) has written
for the purpose of more efficiently understanding and sharing the results of
(primarily) regression analyses. There are a number of functions focused
specifically on the interpretation and presentation of interactions.
Just about everything supports models from the survey package.
Author: Jacob A. Long [aut, cre] (<https://orcid.org/0000-0002-1582-6214>)
Maintainer: Jacob A. Long <long.1377@osu.edu>
Diff between jtools versions 1.0.0 dated 2018-05-07 and 1.1.0 dated 2018-08-16
DESCRIPTION | 15 MD5 | 143 + NAMESPACE | 9 NEWS.md | 65 R/colors.R | 4 R/export_summ.R | 98 + R/int_utils.R | 134 + R/interact_plot.R | 94 - R/internal.R | 123 + R/johnson_neyman.R | 76 - R/make_predictions.R | 73 - R/mer_utils.r | 37 R/plot_predictions.R | 92 - R/scale_lm.R | 12 R/simple_slopes.R | 329 +++- R/summ.R | 698 ++++++++- R/summ_rq.R | 111 + R/zzz.R | 20 README.md | 106 - build/vignette.rds |binary inst/CITATION | 2 inst/doc/categorical.html | 415 +++++ inst/doc/interactions.R | 22 inst/doc/interactions.Rmd | 49 inst/doc/interactions.html | 1574 ++++++++++++++++++---- inst/doc/summ.R | 13 inst/doc/summ.Rmd | 22 inst/doc/summ.html | 746 +++++++--- inst/doc/svycor.html | 18 man/as_huxtable.sim_slopes.Rd |only man/cat_plot.Rd | 38 man/center.Rd | 1 man/center_mod.Rd | 4 man/effect_plot.Rd | 15 man/export_summs.Rd | 10 man/figures/interact_plot_continuous-1.png |binary man/figures/interact_plot_continuous_points-1.png |binary man/figures/interact_plot_factor-1.png |binary man/figures/j-n-plot-1.png |binary man/figures/unnamed-chunk-7-1.png |binary man/figures/unnamed-chunk-8-1.png |binary man/glance.summ.Rd | 5 man/gscale.Rd | 5 man/interact_plot.Rd | 54 man/johnson_neyman.Rd | 38 man/knit_print.summ.Rd |only man/make_predictions.Rd | 39 man/make_predictions.brmsfit.Rd | 35 man/make_predictions.merMod.Rd | 38 man/make_predictions.rq.Rd | 37 man/make_predictions.stanreg.Rd | 35 man/pf_sv_test.Rd | 1 man/plot.sim_slopes.Rd |only man/plot_predictions.Rd | 46 man/plot_summs.Rd | 26 man/probe_interaction.Rd | 7 man/scale_mod.Rd | 5 man/sim_slopes.Rd | 38 man/standardize.Rd | 1 man/summ.glm.Rd | 15 man/summ.lm.Rd | 10 man/summ.merMod.Rd | 45 man/summ.rq.Rd | 13 man/summ.svyglm.Rd | 5 man/svycor.Rd | 7 man/svysd.Rd | 6 man/weights_tests.Rd | 1 man/wgttest.Rd | 5 tests/testthat/Rplots.pdf |binary tests/testthat/test-export-summs.R | 7 tests/testthat/test-jsumm.R | 13 tests/testthat/test-misc.R | 35 vignettes/interactions.Rmd | 49 vignettes/summ.Rmd | 22 74 files changed, 4572 insertions(+), 1239 deletions(-)
Title: Text Mining E-Mail Plug-in
Description: A plug-in for the tm text mining framework providing mail handling
functionality.
Author: Ingo Feinerer [aut] (<https://orcid.org/0000-0001-7656-8338>),
Wolfgang Mauerer [aut],
Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tm.plugin.mail versions 0.2-0 dated 2018-08-09 and 0.2-1 dated 2018-08-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/source.R | 26 +++++++++++++++++++++++++- 3 files changed, 31 insertions(+), 7 deletions(-)
More information about tm.plugin.mail at CRAN
Permanent link
Title: Execute and Control System Processes
Description: Tools to run system processes in the background.
It can check if a background process is running; wait on a background
process to finish; get the exit status of finished processes; kill
background processes. It can read the standard output and error of
the processes, using non-blocking connections. 'processx' can poll
a process for standard output or error, with a timeout. It can also
poll several processes at once.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between processx versions 3.1.0 dated 2018-05-15 and 3.2.0 dated 2018-08-16
processx-3.1.0/processx/src/test-connections.cpp |only processx-3.1.0/processx/src/test-runner.cpp |only processx-3.1.0/processx/tests/testthat/test-cpp.R |only processx-3.2.0/processx/DESCRIPTION | 19 processx-3.2.0/processx/MD5 | 100 +- processx-3.2.0/processx/NAMESPACE | 15 processx-3.2.0/processx/R/assertions.R | 43 + processx-3.2.0/processx/R/connections.R |only processx-3.2.0/processx/R/initialize.R | 91 ++ processx-3.2.0/processx/R/io.R | 37 + processx-3.2.0/processx/R/on-load.R | 5 processx-3.2.0/processx/R/poll.R | 63 - processx-3.2.0/processx/R/print.R | 8 processx-3.2.0/processx/R/process.R | 351 +++++++--- processx-3.2.0/processx/R/run.R | 24 processx-3.2.0/processx/R/utils.R | 47 + processx-3.2.0/processx/inst/NEWS.md | 46 + processx-3.2.0/processx/inst/README.markdown | 94 +- processx-3.2.0/processx/man/poll.Rd | 45 - processx-3.2.0/processx/man/process.Rd | 142 +++- processx-3.2.0/processx/man/process_initialize.Rd | 20 processx-3.2.0/processx/man/processx_connections.Rd |only processx-3.2.0/processx/man/run.Rd | 16 processx-3.2.0/processx/src/Makevars | 5 processx-3.2.0/processx/src/Makevars.win | 14 processx-3.2.0/processx/src/create-time.c |only processx-3.2.0/processx/src/init.c | 23 processx-3.2.0/processx/src/install.libs.R | 2 processx-3.2.0/processx/src/poll.c | 62 + processx-3.2.0/processx/src/processx-connection.c | 330 ++++++++- processx-3.2.0/processx/src/processx-connection.h | 32 processx-3.2.0/processx/src/processx.h | 14 processx-3.2.0/processx/src/tools/interrupt.c |only processx-3.2.0/processx/src/tools/px.c | 92 ++ processx-3.2.0/processx/src/unix/childlist.c | 19 processx-3.2.0/processx/src/unix/connection.c | 8 processx-3.2.0/processx/src/unix/processx-unix.h | 17 processx-3.2.0/processx/src/unix/processx.c | 210 +++-- processx-3.2.0/processx/src/unix/sigchld.c | 9 processx-3.2.0/processx/src/unix/utils.c | 12 processx-3.2.0/processx/src/win/processx-win.h | 12 processx-3.2.0/processx/src/win/processx.c | 340 ++++++++- processx-3.2.0/processx/src/win/stdio.c | 259 ++++++- processx-3.2.0/processx/src/win/utils.c |only processx-3.2.0/processx/tests/testthat/helper.R | 25 processx-3.2.0/processx/tests/testthat/test-env.R |only processx-3.2.0/processx/tests/testthat/test-extra-connections.R |only processx-3.2.0/processx/tests/testthat/test-kill-tree.R |only processx-3.2.0/processx/tests/testthat/test-poll-connections.R |only processx-3.2.0/processx/tests/testthat/test-poll.R | 36 - processx-3.2.0/processx/tests/testthat/test-poll2.R | 33 processx-3.2.0/processx/tests/testthat/test-poll3.R |only processx-3.2.0/processx/tests/testthat/test-process.R | 16 processx-3.2.0/processx/tests/testthat/test-ps-methods.R |only processx-3.2.0/processx/tests/testthat/test-set-std.R |only processx-3.2.0/processx/tests/testthat/test-sigchld.R | 6 processx-3.2.0/processx/tests/testthat/test-stdin.R |only processx-3.2.0/processx/tests/testthat/test-stress.R | 21 processx-3.2.0/processx/tests/testthat/test-wait.R | 4 59 files changed, 2152 insertions(+), 615 deletions(-)
Title: Private Configuration for 'R' Packages
Description: Set configuration options on a per-package basis.
Options set by a given package only apply to that package,
other packages are unaffected.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between pkgconfig versions 2.0.1 dated 2017-03-21 and 2.0.2 dated 2018-08-16
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- inst/NEWS.markdown | 4 ++++ inst/README.Rmd | 10 +++++----- inst/README.markdown | 10 +++++----- tests/testthat/test-api.R | 14 +++++++------- tests/testthat/test-globalenv.R | 4 ++-- tests/testthat/tests.R | 18 +++++++----------- 8 files changed, 42 insertions(+), 42 deletions(-)
More information about GenomicTools.fileHandler at CRAN
Permanent link
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling
for dichotomous and polytomous item responses. This package enables the estimation of
the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>),
the multiple group (polytomous) GDINA model (de la Torre, 2011,
<doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009,
<doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008,
<doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992,
<doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis
(Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>).
See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02>
for further details on estimation and the package structure.
For tutorials on how to use the CDM package see
George and Robitzsch (2015, <doi:10.20982/tqmp.11.3.p189>) as well as
Ravand and Robitzsch (2015).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 6.4-23 dated 2018-07-06 and 6.5-12 dated 2018-08-16
DESCRIPTION | 9 ++- MD5 | 40 ++++++++-------- NAMESPACE | 4 + R/IRT.RMSD.R | 6 +- R/IRT_RMSD_calc_rmsd.R | 15 ++++-- R/RcppExports.R | 2 R/cdm_replace_inf.R |only R/gdina.R | 6 +- R/gdina_mstep_item_ml.R | 14 +++-- R/gdina_mstep_item_ml_algorithm.R | 7 +- R/gdina_mstep_item_ml_update_parameter.R | 18 ++++--- R/gdina_mstep_item_ml_update_parameter_regularization.R | 10 +++- R/gdina_mstep_item_parameters.R | 7 +- R/reglca.R | 2 R/reglca_threshold_parameter.R |only R/reglca_update_parameter.R | 7 +- R/summary.slca.R | 4 - inst/NEWS | 18 +++++++ man/CDM-utilities.Rd | 18 ++++++- src/RcppExports.cpp | 2 src/cdm_rcpp_mcdina_probs_multcat_items_counts.cpp | 5 -- src/init.c | 2 22 files changed, 126 insertions(+), 70 deletions(-)
Title: The Complex Multivariate Gaussian Distribution
Description: Various utilities for the complex multivariate Gaussian distribution.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between cmvnorm versions 1.0-3 dated 2015-11-24 and 1.0-5 dated 2018-08-16
DESCRIPTION | 10 +++++--- MD5 | 15 ++++++------ R/cmvnorm.R | 4 ++- build/partial.rdb |only build/vignette.rds |binary inst/doc/complicator.pdf |binary man/Mvcnorm.Rd | 32 +++++++++++--------------- man/cmvnorm-package.Rd | 56 ++++++++++++++++++++++++++--------------------- man/corr_complex.Rd | 8 ++---- 9 files changed, 66 insertions(+), 59 deletions(-)