Title: API Client Library for 'Wikidata'
Description: An API client for the Wikidata <http://wikidata.org/> store of
semantic data.
Author: Oliver Keyes [aut, cre], Christian Graul [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between WikidataR versions 1.0.0 dated 2015-06-01 and 1.0.1 dated 2016-01-14
DESCRIPTION | 16 ++++++++++------ MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 2 +- NEWS | 3 +++ R/WikidataR.R | 3 +++ R/prints.R | 6 ++++++ R/utils.R | 6 +++--- README.md | 11 ++++++----- build/vignette.rds |binary inst/doc/Introduction.Rmd | 8 +++----- inst/doc/Introduction.html | 9 ++++----- man/WikidataR.Rd | 5 +++-- man/find_item.Rd | 4 +++- man/get_item.Rd | 4 +++- man/get_random.Rd | 4 +++- man/print.find_item.Rd | 4 ++-- man/print.find_property.Rd | 4 ++-- man/print.wikidata.Rd | 4 ++-- vignettes/Introduction.Rmd | 8 +++----- 19 files changed, 78 insertions(+), 59 deletions(-)
Title: Estimation of the Structural Topic Model
Description: The Structural Topic Model (STM) allows researchers
to estimate topic models with document-level covariates.
The package also includes tools for model selection, visualization,
and estimation of topic-covariate regressions.
Author: Margaret E. Roberts, Brandon M. Stewart and Dustin Tingley
Maintainer: Brandon Stewart <bms4@princeton.edu>
Diff between stm versions 1.1.0 dated 2015-07-27 and 1.1.3 dated 2016-01-14
stm-1.1.0/stm/vignettes/vignetteBib.bib |only stm-1.1.3/stm/DESCRIPTION | 8 stm-1.1.3/stm/LICENSE | 4 stm-1.1.3/stm/MD5 | 228 +- stm-1.1.3/stm/NAMESPACE | 93 stm-1.1.3/stm/R/RcppExports.R | 30 stm-1.1.3/stm/R/STMconvergence.R | 86 stm-1.1.3/stm/R/STMestep.R | 152 - stm-1.1.3/stm/R/STMfunctions.R | 348 +-- stm-1.1.3/stm/R/STMinit.R | 341 +-- stm-1.1.3/stm/R/STMlncpp.R | 32 stm-1.1.3/stm/R/STMmnreg.R | 292 +- stm-1.1.3/stm/R/STMmu.R | 194 - stm-1.1.3/stm/R/STMoptbeta.R | 28 stm-1.1.3/stm/R/STMreport.R | 114 - stm-1.1.3/stm/R/STMsigma.R | 30 stm-1.1.3/stm/R/checkBeta.R | 74 stm-1.1.3/stm/R/checkFactors.R | 174 - stm-1.1.3/stm/R/cloud.R | 104 - stm-1.1.3/stm/R/convertCorpus.R |only stm-1.1.3/stm/R/dmr.R | 404 +-- stm-1.1.3/stm/R/estimateEffect.R | 286 +- stm-1.1.3/stm/R/exclusivity.R | 38 stm-1.1.3/stm/R/findThoughts.R | 106 - stm-1.1.3/stm/R/findTopic.R | 36 stm-1.1.3/stm/R/heldout.R | 148 - stm-1.1.3/stm/R/jeffreyskappa.R | 324 +-- stm-1.1.3/stm/R/labelTopics.R | 220 +- stm-1.1.3/stm/R/manyTopics.R | 134 - stm-1.1.3/stm/R/multiSTM.R | 846 ++++---- stm-1.1.3/stm/R/parseFormulas.R | 88 stm-1.1.3/stm/R/permute.R | 192 - stm-1.1.3/stm/R/plot.STM.R | 496 ++-- stm-1.1.3/stm/R/plot.estimateEffect.R | 186 - stm-1.1.3/stm/R/plot.searchK.R | 54 stm-1.1.3/stm/R/plotModels.R | 38 stm-1.1.3/stm/R/plotQuote.R | 56 stm-1.1.3/stm/R/plotRemoved.R | 122 - stm-1.1.3/stm/R/plotTopicLoess.R | 98 stm-1.1.3/stm/R/plottingutilfns.R | 564 ++--- stm-1.1.3/stm/R/prepDocuments.R | 196 - stm-1.1.3/stm/R/produce_cmatrix.R | 196 - stm-1.1.3/stm/R/readCorpus.R | 125 - stm-1.1.3/stm/R/residuals.R | 70 stm-1.1.3/stm/R/s.R | 46 stm-1.1.3/stm/R/sageLabels.R | 198 - stm-1.1.3/stm/R/searchK.R | 62 stm-1.1.3/stm/R/selectModel.R | 130 - stm-1.1.3/stm/R/semanticCoherence.R | 106 - stm-1.1.3/stm/R/simBetas.R | 24 stm-1.1.3/stm/R/spectral.R | 542 ++--- stm-1.1.3/stm/R/stm.R | 463 ++-- stm-1.1.3/stm/R/stm.control.R | 370 +-- stm-1.1.3/stm/R/summary.STM.R | 32 stm-1.1.3/stm/R/tau.R | 74 stm-1.1.3/stm/R/textProcessor.R | 274 +- stm-1.1.3/stm/R/thetaPosterior.R | 318 +-- stm-1.1.3/stm/R/toLDAvis.R | 32 stm-1.1.3/stm/R/topicCorr.R | 88 stm-1.1.3/stm/R/topicLasso.R | 170 - stm-1.1.3/stm/R/topicQuality.R | 38 stm-1.1.3/stm/R/writeLdac.R | 28 stm-1.1.3/stm/R/zzz.R | 14 stm-1.1.3/stm/build/vignette.rds |binary stm-1.1.3/stm/data/datalist | 6 stm-1.1.3/stm/data/gadarian.RData |binary stm-1.1.3/stm/data/gadarianFit.RData |binary stm-1.1.3/stm/data/poliblog5k.RData |binary stm-1.1.3/stm/inst/CITATION | 46 stm-1.1.3/stm/inst/NEWS.Rd | 280 +- stm-1.1.3/stm/inst/doc/stmVignette.R | 519 ++--- stm-1.1.3/stm/inst/doc/stmVignette.Rnw | 1512 +++++++------- stm-1.1.3/stm/inst/doc/stmVignette.pdf |binary stm-1.1.3/stm/man/checkBeta.rd | 100 stm-1.1.3/stm/man/checkResiduals.Rd | 100 stm-1.1.3/stm/man/cloud.Rd | 98 stm-1.1.3/stm/man/convertCorpus.Rd |only stm-1.1.3/stm/man/estimateEffect.Rd | 152 - stm-1.1.3/stm/man/findThoughts.Rd | 130 - stm-1.1.3/stm/man/findTopic.Rd | 74 stm-1.1.3/stm/man/gadarian.Rd | 85 stm-1.1.3/stm/man/heldout.Rd | 116 - stm-1.1.3/stm/man/labelTopics.Rd | 123 - stm-1.1.3/stm/man/manyTopics.Rd | 277 +- stm-1.1.3/stm/man/multiSTM.Rd | 280 +- stm-1.1.3/stm/man/permutationTest.Rd | 168 - stm-1.1.3/stm/man/plot.MultimodDiagnostic.Rd | 192 - stm-1.1.3/stm/man/plot.STM.Rd | 196 - stm-1.1.3/stm/man/plot.STMpermute.Rd | 124 - stm-1.1.3/stm/man/plot.estimateEffect.Rd | 386 +-- stm-1.1.3/stm/man/plot.searchK.Rd | 74 stm-1.1.3/stm/man/plot.topicCorr.Rd | 112 - stm-1.1.3/stm/man/plotModels.Rd | 126 - stm-1.1.3/stm/man/plotQuote.Rd | 116 - stm-1.1.3/stm/man/plotRemoved.Rd | 78 stm-1.1.3/stm/man/plotTopicLoess.Rd | 96 stm-1.1.3/stm/man/poliblog5k.Rd | 78 stm-1.1.3/stm/man/prepDocuments.Rd | 140 - stm-1.1.3/stm/man/readCorpus.Rd | 118 - stm-1.1.3/stm/man/s.Rd | 68 stm-1.1.3/stm/man/sageLabels.Rd | 112 - stm-1.1.3/stm/man/searchK.Rd | 172 - stm-1.1.3/stm/man/selectModel.Rd | 284 +- stm-1.1.3/stm/man/stm-package.Rd | 132 - stm-1.1.3/stm/man/stm.Rd | 362 +-- stm-1.1.3/stm/man/summary.STM.Rd | 48 stm-1.1.3/stm/man/textProcessor.Rd | 200 - stm-1.1.3/stm/man/thetaPosterior.Rd | 98 stm-1.1.3/stm/man/toLDAvis.Rd | 124 - stm-1.1.3/stm/man/topicCorr.Rd | 110 - stm-1.1.3/stm/man/topicLasso.Rd | 184 - stm-1.1.3/stm/man/topicQuality.Rd | 118 - stm-1.1.3/stm/man/writeLdac.Rd | 80 stm-1.1.3/stm/vignettes/apsr.bst | 2756 +++++++++++++-------------- stm-1.1.3/stm/vignettes/extracted.bib |only stm-1.1.3/stm/vignettes/natbib.bst | 2576 ++++++++++++------------- stm-1.1.3/stm/vignettes/stmVignette.Rnw | 1512 +++++++------- 117 files changed, 12597 insertions(+), 12605 deletions(-)
Title: An API Client for Wikimedia Traffic Data
Description: Pageview data from the 'Wikimedia' sites, such as
'Wikipedia' (https://www.wikipedia.org/), from entire projects to per-article
levels of granularity, through the new RESTful API and data source (https://
wikimedia.org/api/rest_v1/?doc).
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between pageviews versions 0.1.1 dated 2015-11-25 and 0.2.0 dated 2016-01-14
DESCRIPTION | 15 ++++++++------ MD5 | 30 ++++++++++++++-------------- NAMESPACE | 3 +- NEWS | 11 ++++++++++ R/query.R | 6 +++-- R/timestamps.R |only R/utils.R | 7 ++++++ README.md | 12 +++++++---- build/vignette.rds |binary inst/doc/Accessing_Wikimedia_pageviews.Rmd | 9 ++++---- inst/doc/Accessing_Wikimedia_pageviews.html | 5 ++-- man/article_pageviews.Rd | 6 +++-- man/pageview_timestamps.Rd |only man/pageviews.Rd | 2 - man/project_pageviews.Rd | 6 +++-- man/top_articles.Rd | 3 +- vignettes/Accessing_Wikimedia_pageviews.Rmd | 9 ++++---- 17 files changed, 81 insertions(+), 43 deletions(-)
Title: Dynamic Extensions for Network Objects
Description: Simple interface routines to facilitate the handling of network objects with complex intertemporal data. This is a part of the "statnet" suite of packages for network analysis.
Author: Carter T. Butts [aut],
Ayn Leslie-Cook [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut, cre],
Zack Almquist [ctb],
David R. Hunter [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Steven M. Goodreau [ctb],
Jeffrey Horner [ctb],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between networkDynamic versions 0.8.1 dated 2015-10-07 and 0.9.0 dated 2016-01-14
ChangeLog | 6 DESCRIPTION | 10 - MD5 | 30 ++-- R/extract.R | 7 + R/utilities.R | 22 +-- build/vignette.rds |binary data/McFarland_cls33_10_16_96.rda |binary inst/doc/networkDynamic.R | 222 +++++++++++++++++++++++++----------- inst/doc/networkDynamic.Rnw | 135 +++++++++++++++++++-- inst/doc/networkDynamic.pdf |binary man/as.data.frame.networkDynamic.Rd | 18 +- man/classrooms.Rd | 8 - tests/converter_tests.R | 8 - tests/network_tests.R | 24 +++ tests/tea_tests.R | 7 + vignettes/networkDynamic.Rnw | 135 +++++++++++++++++++-- 16 files changed, 490 insertions(+), 142 deletions(-)
More information about networkDynamic at CRAN
Permanent link
Title: Tests for General Factorial Designs
Description: Implemented are the Wald-type statistic,
a permuted version thereof as well as the ANOVA-type statistic
for general factorial designs, even with non-normal error terms
and/or heteroscedastic variances, for crossed designs with an
arbitrary number of factors and nested designs with up to three factors.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@uni-ulm.de>
Diff between GFD versions 0.1.2 dated 2015-11-18 and 0.1.4 dated 2016-01-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GFD-function.R | 4 +++- man/GFD.Rd | 4 +++- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <daniel.bowman@unc.edu>
Diff between rNOMADS versions 2.1.6 dated 2015-11-13 and 2.1.7 dated 2016-01-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ R/ReadGrib.R | 8 ++++++-- 4 files changed, 17 insertions(+), 9 deletions(-)
Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP' information: http://upwell.pfeg.noaa.gov/erddap/information.html.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rerddap versions 0.3.0 dated 2015-10-09 and 0.3.4 dated 2016-01-14
DESCRIPTION | 13 +- LICENSE | 2 MD5 | 100 ++++++++--------- NAMESPACE | 9 - NEWS | 18 +++ R/cache_delete.R | 6 - R/cache_details.R | 8 - R/cache_list.R | 11 - R/grid.R | 205 ++---------------------------------- R/info.R | 2 R/ncdf_helpers.R | 54 --------- R/rerddap-package.r | 11 + R/search.R | 22 +-- R/search_adv.R | 52 ++++++++- R/version.R | 7 - R/zzz.r | 28 +++- README.md | 107 +++++++++++------- build/vignette.rds |binary inst/doc/rerddap_vignette.Rmd | 133 ++++++++++++++--------- inst/doc/rerddap_vignette.html | 133 ++++++++++++++--------- inst/vign/rerddap_vignette.Rmd | 6 - inst/vign/rerddap_vignette.md | 133 ++++++++++++++--------- man/cache_delete.Rd | 8 - man/cache_details.Rd | 7 - man/cache_list.Rd | 13 +- man/convert_time.Rd | 4 man/convert_units.Rd | 4 man/disk.Rd | 2 man/ed_search.Rd | 2 man/ed_search_adv.Rd | 25 ++-- man/eurl.Rd | 2 man/fipscounty.Rd | 4 man/griddap.Rd | 71 +++++------- man/info.Rd | 4 man/institutions.Rd | 2 man/ioos_categories.Rd | 2 man/key_words.Rd | 4 man/keywords.Rd | 2 man/longnames.Rd | 2 man/rerddap-package.Rd | 13 +- man/servers.Rd | 2 man/standardnames.Rd | 2 man/tabledap.Rd | 2 man/type_sum.Rd | 2 man/variablenames.Rd | 2 man/version.Rd | 9 - tests/testthat/test-ed_search.R | 7 + tests/testthat/test-ed_search_adv.R | 13 +- tests/testthat/test-griddap.r | 2 tests/testthat/test-info.R | 8 - vignettes/rerddap_vignette.Rmd | 133 ++++++++++++++--------- 51 files changed, 718 insertions(+), 695 deletions(-)
Title: Smooth Multivariate Interpolation for Gridded and Scattered Data
Description: Smooth multivariate interpolation for gridded and scattered data
with possibly large datasets. The code for scattered data is taken from the
'SHEPPACK' Fortran package.
Author: Yves Deville <deville.yves@alpestat.com> Yann Richet
<yann.richet@irsn.fr>. Fortran codes by William Thacker, Manjula Iyer
Jingwei Zhang, Laynet Watson, Jeffrey Birch, Manjula Iyer, Michael Berry
and Robert Renka. Fortran codes by Alain Hebert.
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between smint versions 0.4.0 dated 2015-06-12 and 0.4.2 dated 2016-01-14
ChangeLog | 19 ++++++++++++ DESCRIPTION | 8 ++--- MD5 | 63 ++++++++++++++++++++--------------------- NAMESPACE | 8 +++-- R/GridInt.R | 5 +-- R/gridIntCard.R | 2 - README.md |only inst/doc/smintGuide.pdf |binary man/Grid.Rd | 3 + man/ShepFun1.Rd | 3 + man/apply_Grid.Rd | 3 + man/array_Grid.Rd | 3 + man/as.Grid.Rd | 3 + man/as.Grid.default.Rd | 3 + man/boundary_Grid.Rd | 3 + man/branin.Rd | 3 + man/cardinalBasis_ceschino.Rd | 3 + man/cardinalBasis_lagrange.Rd | 3 + man/cardinalBasis_natSpline.Rd | 3 + man/checkX.Rd | 3 + man/closest.Rd | 3 + man/drop_Grid.Rd | 3 + man/interp_Grid.Rd | 3 + man/interp_ceschino.Rd | 3 + man/qsheppInt.Rd | 3 + man/randGrid.Rd | 3 + man/range_Grid.Rd | 3 + man/round_levels.Rd | 3 + man/sampleIn.Rd | 3 + man/scale_Grid.Rd | 3 + man/smint-package.Rd | 4 +- man/subset_Grid.Rd | 3 + src/gridInt.c | 47 ++++++++++++++++-------------- 33 files changed, 137 insertions(+), 88 deletions(-)
Title: R API for Mixpanel
Description: Provides an interface to many endpoints of Mixpanel's Data Export API. The R functions allow for event and profile data export as well as for segmentation, retention and addiction analysis. Results are always parsed into convenient R objects.
Author: Meinhard Ploner
Maintainer: Meinhard Ploner <meinhard.ploner@prosiebensat1digital.de>
Diff between RMixpanel versions 0.1-2 dated 2015-11-25 and 0.1-3 dated 2016-01-14
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 20 ++++++++++---------- NAMESPACE | 4 +++- R/eventsJson2RMatrix.R | 9 ++++++--- R/mixpanelGetData.R | 2 +- R/mixpanelGetSegmentation.R | 5 +++-- README.md | 2 +- build/partial.rdb |binary man/mixpanelGetProfiles.Rd | 4 ++-- man/mixpanelGetSegmentation.Rd | 3 ++- 11 files changed, 34 insertions(+), 27 deletions(-)
Title: North Symbols and Scale Bars for Maps Created with 'ggplot2' or
'ggmap'
Description: Adds north symbols (18 options) and scale bars in kilometers to
maps in geographic or metric coordinates created with 'ggplot2' or 'ggmap'.
Author: Oswaldo Santos Baquero [aut, cre]
Maintainer: Oswaldo Santos Baquero <oswaldosant@gmail.com>
Diff between ggsn versions 0.2.0 dated 2015-08-22 and 0.3.0 dated 2016-01-14
DESCRIPTION | 12 +++++++----- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 8 ++++++-- NEWS | 8 ++++++++ R/blank.R | 5 +++-- R/ggsn-package.R | 9 +++++---- R/north.R | 5 +++-- R/north2.R | 5 +++-- R/scalebar.R | 34 ++++------------------------------ inst/extdata/sp.dbf |binary man/blank.Rd | 9 +++++---- man/ggsn-package.Rd | 8 ++++---- man/north.Rd | 7 ++++--- man/north2.Rd | 7 ++++--- man/northSymbols.Rd | 2 +- man/scalebar.Rd | 36 +++++------------------------------- 16 files changed, 77 insertions(+), 108 deletions(-)
Title: Calculation of Average Population Attributable Fractions and
Confidence Intervals
Description: Average population attributable fractions are calculated for a set of risk factors (either binary or ordinal valued) for both prospective and case-control designs. Confidence intervals are found by Monte Carlo simulation. The method can be applied to either prospective or case control designs, provided an estimate of disease prevalence is provided. In addition to an exact calculation of AF, an approximate calculation, based on randomly sampling permutations has been implemented to ensure the calculation is computationally tractable when the number of risk factors is large.
Author: John Ferguson [aut, cre]
Maintainer: John Ferguson <john.ferguson@nuigalway.ie>
Diff between averisk versions 1.0 dated 2015-10-29 and 1.0.1 dated 2016-01-14
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/main.R | 16 +++++++++++++++- 3 files changed, 20 insertions(+), 6 deletions(-)
Title: Batch Effect Removal (in Phenotype Prediction using Gene Data)
Description: Various tools dealing with batch effects, in particular enabling the
removal of discrepancies between training and test sets in prediction scenarios.
The following batch effect removal methods are implemented: FAbatch, ComBat, (f)SVA,
mean-centering, standardization, Ratio-A and Ratio-G. For each of these we provide
an additional function which enables a posteriori ('addon') batch effect removal
in independent batches ('test data'). Here, the (already batch effect adjusted)
training data is not altered. For evaluating the success of batch effect adjustment
several metrics are provided. Moreover, the package implements a plot for the
visualization of batch effects using principal component analysis. The main functions
of the package are ba() and baaddon() which enable batch effect removal and addon
batch effect removal, respectively, with one of the seven methods mentioned above.
Another important function is bametric() which is a wrapper function for all implemented
methods for evaluating the success of batch effect removal.
Author: Roman Hornung, David Causeur
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between bapred versions 0.2 dated 2015-12-02 and 0.3 dated 2016-01-14
DESCRIPTION | 6 +++--- MD5 | 31 ++++++++++++++++--------------- inst |only man/avedist.Rd | 2 +- man/ba.Rd | 2 +- man/baaddon.Rd | 2 +- man/bametric.Rd | 2 +- man/bapred-package.Rd | 2 +- man/diffexprm.Rd | 2 +- man/fabatch.Rd | 2 +- man/fabatchaddon.Rd | 2 +- man/kldist.Rd | 2 +- man/meancenteraddon.Rd | 2 +- man/ratioaaddon.Rd | 2 +- man/ratiogaddon.Rd | 2 +- man/sepscore.Rd | 2 +- man/standardizeaddon.Rd | 2 +- 17 files changed, 33 insertions(+), 32 deletions(-)
Title: Tools for ABC Analyses
Description: Tools for approximate Bayesian computation including summary statistic selection and assessing coverage.
Author: Matt Nunes [aut, cre],
Dennis Prangle [aut]
Maintainer: Matt Nunes <m.nunes@lancaster.ac.uk>
Diff between abctools versions 1.0.3 dated 2015-07-15 and 1.0.4 dated 2016-01-14
DESCRIPTION | 12 ++++++------ MD5 | 30 +++++++++++++++--------------- R/saABC.R | 2 +- R/semiauto.abc.R | 6 ++++-- man/AS.select.Rd | 7 ++++++- man/AS.test.Rd | 7 ++++++- man/abctools-package.Rd | 14 ++++++++++---- man/coal.Rd | 3 +++ man/cov.pi.Rd | 4 ++++ man/mc.ci.Rd | 4 ++++ man/mincrit.Rd | 8 +++++++- man/nn.ent.Rd | 3 +++ man/saABC.Rd | 5 ++++- man/selectsumm.Rd | 7 ++++++- man/semiauto.abc.Rd | 6 +++++- man/stage2.Rd | 7 ++++++- 16 files changed, 90 insertions(+), 35 deletions(-)
Title: Hidden Markov Models for Life Sequences and Other Multivariate,
Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent)
Markov models and mixture hidden Markov models for social
sequence data and other categorical time series. Also some more restricted
versions of these type of models are available: Markov models, mixture
Markov models, and latent class models. The package supports models for one or
multiple subjects with one or multiple parallel sequences (channels). External
covariates can be added to explain cluster membership in mixture models. The
package provides functions for evaluating and comparing models, as well as
functions for easy plotting of multichannel sequence data and hidden Markov
models. Models are estimated using maximum likelihood via the EM algorithm and/or
direct numerical maximization with analytical gradients.
All main algorithms are written in C++ with support for parallel computation.
Author: Jouni Helske, Satu Helske
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between seqHMM versions 1.0.3-1 dated 2015-12-30 and 1.0.4 dated 2016-01-14
DESCRIPTION | 8 MD5 | 140 +-- NEWS | 18 R/HMMplot.R | 839 +++++++++++----------- R/SSPlotter.R | 852 +++++++++++----------- R/build_hmm.R | 83 +- R/build_lcm.R | 74 + R/build_mhmm.R | 51 - R/build_mm.R | 11 R/build_mmm.R | 60 + R/fit_model.R | 58 - R/forwardBackward.R | 17 R/gridplot.R | 36 R/hidden_paths.R | 17 R/import_seqdef.R | 7 R/logLik.hmm.R | 11 R/logLik.mhmm.R | 11 R/mHMMplotgrid.R | 108 +- R/mc_to_sc.R | 51 - R/mc_to_sc_data.R | 67 + R/mssplot.R | 8 R/plot.hmm.R | 23 R/posterior_probs.R | 14 R/separate_mhmm.R | 4 R/seqHMM-package.R | 6 R/simulate_hmm.R | 4 R/simulate_mhmm.R | 53 - R/simulate_pars.R | 3 R/ssp.R | 59 + R/ssplot.R | 49 - R/ssplotM.R | 2 R/trim_hmm.R | 8 build/vignette.rds |binary data/biofam3c.rda |binary data/colorpalette.rda |binary data/hmm_biofam.rda |binary data/hmm_mvad.rda |binary data/mhmm_biofam.rda |binary data/mhmm_mvad.rda |binary inst/doc/seqHMM.R | 698 +++++++++--------- inst/doc/seqHMM.Rnw | 1768 +++++++++++++++++++++++------------------------ inst/doc/seqHMM.pdf |binary man/TraMineR_imports.Rd | 12 man/build_hmm.Rd | 83 +- man/build_lcm.Rd | 72 + man/build_mhmm.Rd | 49 - man/build_mm.Rd | 11 man/build_mmm.Rd | 173 ++-- man/fit_model.Rd | 59 - man/forward_backward.Rd | 17 man/gridplot.Rd | 36 man/hidden_paths.Rd | 17 man/logLik.hmm.Rd | 11 man/logLik.mhmm.Rd | 11 man/mc_to_sc.Rd | 36 man/mc_to_sc_data.Rd | 66 + man/mssplot.Rd | 8 man/plot.hmm.Rd | 2 man/posterior_probs.Rd | 14 man/separate_mhmm.Rd | 3 man/seqHMM-deprecated.Rd | 52 - man/seqHMM.Rd | 6 man/simulate_hmm.Rd | 4 man/simulate_mhmm.Rd | 61 - man/simulate_pars.Rd | 5 man/ssp.Rd | 58 - man/ssplot.Rd | 61 - man/trim_model.Rd | 8 src/log_EM.cpp | 2 vignettes/references.bib | 81 +- vignettes/seqHMM.Rnw | 1768 +++++++++++++++++++++++------------------------ 71 files changed, 4223 insertions(+), 3781 deletions(-)
Title: Extra Map Databases
Description: Supplement to maps package, providing the larger and/or
higher-resolution databases.
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg <Ray.Brownrigg@ecs.vuw.ac.nz>.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between mapdata versions 2.2-5 dated 2015-08-03 and 2.2-6 dated 2016-01-14
mapdata-2.2-5/mapdata/src/Makefile |only mapdata-2.2-6/mapdata/DESCRIPTION | 8 ++++---- mapdata-2.2-6/mapdata/MD5 | 9 ++++++--- mapdata-2.2-6/mapdata/cleanup |only mapdata-2.2-6/mapdata/configure |only mapdata-2.2-6/mapdata/configure.ac |only mapdata-2.2-6/mapdata/src/Makefile.in |only mapdata-2.2-6/mapdata/src/Makefile.win | 1 + 8 files changed, 11 insertions(+), 7 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>
Diff between yuima versions 1.0.77 dated 2015-11-20 and 1.0.78 dated 2016-01-14
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS | 3 R/rng.R | 210 +++++++++++++++++++++++++++++++++++------------------ man/adaBayes.Rd | 9 +- man/qmle.Rd | 2 man/rng.Rd | 109 ++++++++++++++++++++++----- man/setModel.Rd | 38 +++++++-- man/spectralcov.Rd | 1 9 files changed, 279 insertions(+), 115 deletions(-)
Title: Change-Point Estimation using Shape-Restricted Splines
Description: In a scatterplot where the response variable is Gaussian, Poisson or binomial, we consider the case in which the mean function is smooth with a change-point, which is a mode, an inflection point or a jump point. The main routine estimates the mean curve and the change-point as well using shape-restricted B-splines. An optional subroutine delivering a bootstrap confidence interval for the change-point is incorporated in the main routine.
Author: Xiyue Liao and Mary C Meyer
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between ShapeChange versions 1.1 dated 2015-11-15 and 1.2 dated 2016-01-14
DESCRIPTION | 12 - MD5 | 12 - NAMESPACE | 2 R/ShapeChange.R | 421 ++++++++++++++++++++++++++++++++------------- man/ShapeChange-package.Rd | 6 man/changept.Rd | 28 +- man/ip.Rd | 2 7 files changed, 332 insertions(+), 151 deletions(-)
Title: Population Viability Analysis with Data Cloning
Description: Likelihood based population viability analysis in the
presence of observation error and missing data.
The package can be used to fit, compare, predict,
and forecast various growth model types using data cloning.
Author: Khurram Nadeem, Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between PVAClone versions 0.1-2 dated 2014-05-19 and 0.1-4 dated 2016-01-14
DESCRIPTION | 15 MD5 | 62 ++-- NAMESPACE | 38 +- R/bevertonholt.R | 696 +++++++++++++++++++++++----------------------- R/fancyPVAmodel.R | 42 +- R/generateMCMC.R | 104 +++--- R/gompertz.R | 692 +++++++++++++++++++++++---------------------- R/internals.R | 38 +- R/modelselection.R | 238 +++++++-------- R/pva-class.R | 52 +-- R/pva-methods.R | 94 ++---- R/pva.R | 124 ++++---- R/ricker.R | 611 ++++++++++++++++++++-------------------- R/thetalogistic.R | 678 ++++++++++++++++++++++---------------------- R/thetalogistic_D.R | 724 ++++++++++++++++++++++++------------------------ data/paurelia.rda |binary data/redstart.rda |binary data/songsparrow.rda |binary inst/ChangeLog | 52 ++- man/PVAClone-package.Rd | 120 +++---- man/fancyPVAmodel.Rd | 60 +-- man/generateLatent.Rd | 98 +++--- man/growthmodels.Rd | 256 ++++++++-------- man/internals.Rd | 116 +++---- man/model.select.Rd | 314 ++++++++++---------- man/paurelia.Rd | 58 +-- man/pva-class.Rd | 125 ++++---- man/pva-methods.Rd | 38 +- man/pva.Rd | 295 +++++++++---------- man/pvamodel-class.Rd | 126 ++++---- man/redstart.Rd | 90 ++--- man/songsparrow.Rd | 78 ++--- 32 files changed, 3029 insertions(+), 3005 deletions(-)
Title: Extension to ggplot2
Description: The R package '\href{http://docs.ggplot2.org/current/}{ggplot2}'
is a plotting system based on the grammar of graphics. '\href{https://
ggobi.github.io/ggally}{GGally}' extends 'ggplot2' by adding several functions to
reduce the complexity of combining geoms with transformed data. Some of these
functions include a pairwise plot matrix, a scatterplot plot matrix, a parallel
coordinates plot, a survival plot, and several functions to plot networks.
Author: Barret Schloerke [aut, cre] (author for ggpairs and ggally_*.
contributor for all functions.),
Jason Crowley [aut] (ggparcoord),
Di Cook [aut, ths] (ggscatmat, gglyph),
Heike Hofmann [ths],
Hadley Wickham [ths],
Francois Briatte [aut] (ggcorr, ggnet, ggnet2),
Moritz Marbach [aut] (ggnet, ggnet2),
Edwin Thoen [aut] (ggsurv),
Amos Elberg [aut] (ggnetworkmap)
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between GGally versions 1.0.0 dated 2015-12-30 and 1.0.1 dated 2016-01-14
GGally-1.0.0/GGally/man/set_to_blank_list_if_blank.Rd |only GGally-1.0.1/GGally/DESCRIPTION | 24 GGally-1.0.1/GGally/MD5 | 105 +- GGally-1.0.1/GGally/NEWS | 16 GGally-1.0.1/GGally/R/find-combo.R | 6 GGally-1.0.1/GGally/R/gg-plots.R | 130 +-- GGally-1.0.1/GGally/R/gglyph.R | 8 GGally-1.0.1/GGally/R/ggmatrix.R | 4 GGally-1.0.1/GGally/R/ggmatrix_print.R | 30 GGally-1.0.1/GGally/R/ggpairs.R | 86 +- GGally-1.0.1/GGally/R/ggpairs_add.R | 2 GGally-1.0.1/GGally/R/ggpairs_getput.R | 34 GGally-1.0.1/GGally/R/ggpairs_internal_plots.R | 2 GGally-1.0.1/GGally/R/ggparcoord.R | 167 ++-- GGally-1.0.1/GGally/R/ggscatmat.R | 83 +- GGally-1.0.1/GGally/build/vignette.rds |binary GGally-1.0.1/GGally/inst/doc/gglyph.Rmd | 8 GGally-1.0.1/GGally/inst/doc/gglyph.html | 292 ++------ GGally-1.0.1/GGally/inst/doc/ggmatrix.Rmd | 8 GGally-1.0.1/GGally/inst/doc/ggmatrix.html | 452 ++++-------- GGally-1.0.1/GGally/inst/doc/ggnetworkmap.R | 1 GGally-1.0.1/GGally/inst/doc/ggnetworkmap.Rmd | 10 GGally-1.0.1/GGally/inst/doc/ggnetworkmap.html | 342 ++------- GGally-1.0.1/GGally/inst/doc/ggpairs.Rmd | 9 GGally-1.0.1/GGally/inst/doc/ggpairs.html | 498 ++++---------- GGally-1.0.1/GGally/inst/doc/ggscatmat.Rmd | 9 GGally-1.0.1/GGally/inst/doc/ggscatmat.html | 276 ++----- GGally-1.0.1/GGally/man/add_and_overwrite_aes.Rd | 2 GGally-1.0.1/GGally/man/getPlot.Rd | 2 GGally-1.0.1/GGally/man/gg-add.Rd | 2 GGally-1.0.1/GGally/man/ggally_density.Rd | 2 GGally-1.0.1/GGally/man/ggally_ratio.Rd | 6 GGally-1.0.1/GGally/man/ggfluctuation2.Rd | 2 GGally-1.0.1/GGally/man/ggpairs.Rd | 20 GGally-1.0.1/GGally/man/ggparcoord.Rd | 14 GGally-1.0.1/GGally/man/ggscatmat.Rd | 2 GGally-1.0.1/GGally/man/glyphs.Rd | 7 GGally-1.0.1/GGally/man/print.ggmatrix.Rd | 5 GGally-1.0.1/GGally/man/putPlot.Rd | 6 GGally-1.0.1/GGally/tests/testthat/test-gg-plots.R | 6 GGally-1.0.1/GGally/tests/testthat/test-gglyph.R | 4 GGally-1.0.1/GGally/tests/testthat/test-ggmatrix.R | 18 GGally-1.0.1/GGally/tests/testthat/test-ggmatrix_getput.R | 2 GGally-1.0.1/GGally/tests/testthat/test-ggnet.R | 15 GGally-1.0.1/GGally/tests/testthat/test-ggnet2.R | 17 GGally-1.0.1/GGally/tests/testthat/test-ggnetworkmap.R | 13 GGally-1.0.1/GGally/tests/testthat/test-ggpairs.R | 82 +- GGally-1.0.1/GGally/tests/testthat/test-ggparcoord.R | 30 GGally-1.0.1/GGally/tests/testthat/test-ggscatmat.R | 8 GGally-1.0.1/GGally/vignettes/gglyph.Rmd | 8 GGally-1.0.1/GGally/vignettes/ggmatrix.Rmd | 8 GGally-1.0.1/GGally/vignettes/ggnetworkmap.Rmd | 10 GGally-1.0.1/GGally/vignettes/ggpairs.Rmd | 9 GGally-1.0.1/GGally/vignettes/ggscatmat.Rmd | 9 54 files changed, 1116 insertions(+), 1795 deletions(-)
Title: Tools Developed for Structured Sufficient Dimension Reduction
(sSDR)
Description: Performs structured OLS (sOLS) and structured SIR (sSIR).
Author: Yang Liu <zjubioly@gmail.com>, Francesca Chiaromonte, Bing Li
Maintainer: Yang Liu <zjubioly@gmail.com>
Diff between sSDR versions 1.0.0 dated 2015-10-01 and 1.1.0 dated 2016-01-14
DESCRIPTION | 10 +++++----- MD5 | 7 ++++--- NAMESPACE | 1 + R/sSDR.R | 41 +++++++++++++++++++++++++++++++++++++++++ man/sOLS.comp.d.Rd |only 5 files changed, 51 insertions(+), 8 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate.
Author: Chung-hong Chan [aut],
Geoffrey CH Chan [aut],
Thomas J. Leeper [aut, cre],
Christopher Gandrud [aut],
Ista Zahn [aut]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between rio versions 0.2 dated 2015-05-07 and 0.3.0 dated 2016-01-14
rio-0.2/rio/tests/testthat/errors.R |only rio-0.2/rio/tests/testthat/identical.R |only rio-0.2/rio/tests/testthat/noheader.csv |only rio-0.2/rio/tests/testthat/test_header.R |only rio-0.3.0/rio/DESCRIPTION | 21 +-- rio-0.3.0/rio/MD5 | 46 ++++--- rio-0.3.0/rio/NAMESPACE | 12 + rio-0.3.0/rio/NEWS | 48 +++++++ rio-0.3.0/rio/R/export.R | 25 ++-- rio-0.3.0/rio/R/import.R | 160 ++++++++++++++++++-------- rio-0.3.0/rio/R/set_class.R | 5 rio-0.3.0/rio/R/utils.R | 102 +++++++++++++++- rio-0.3.0/rio/README.md | 9 + rio-0.3.0/rio/inst/doc/rio.R | 4 rio-0.3.0/rio/inst/doc/rio.Rmd | 5 rio-0.3.0/rio/inst/doc/rio.html | 13 +- rio-0.3.0/rio/inst/examples |only rio-0.3.0/rio/man/convert.Rd | 3 rio-0.3.0/rio/man/import.Rd | 8 - rio-0.3.0/rio/po |only rio-0.3.0/rio/tests/test-all.R | 3 rio-0.3.0/rio/tests/testthat/test_convert.R |only rio-0.3.0/rio/tests/testthat/test_errors.R |only rio-0.3.0/rio/tests/testthat/test_export.R |only rio-0.3.0/rio/tests/testthat/test_guess.R | 1 rio-0.3.0/rio/tests/testthat/test_identical.R |only rio-0.3.0/rio/tests/testthat/test_import.R |only rio-0.3.0/rio/tests/testthat/test_remote.R |only rio-0.3.0/rio/tests/testthat/test_set_class.R |only rio-0.3.0/rio/vignettes/rio.Rmd | 5 30 files changed, 357 insertions(+), 113 deletions(-)
Title: Hierarchical Models Made Easy with Data Cloning
Description: S4 classes around infrastructure provided by the
coda and dclone packages to make package development easy as a breeze
with data cloning for hierarchical models.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between dcmle versions 0.2-4 dated 2013-10-01 and 0.3-0 dated 2016-01-14
dcmle-0.2-4/dcmle/R/dcexample.R |only dcmle-0.2-4/dcmle/man/dcexample.Rd |only dcmle-0.3-0/dcmle/DESCRIPTION | 25 dcmle-0.3-0/dcmle/MD5 | 23 dcmle-0.3-0/dcmle/NAMESPACE | 124 ++- dcmle-0.3-0/dcmle/R/dcmle-classes.R | 427 ++++++------ dcmle-0.3-0/dcmle/R/dcmle-graphics.R | 265 ++++---- dcmle-0.3-0/dcmle/R/dcmle-methods.R | 993 ++++++++++++++---------------- dcmle-0.3-0/dcmle/R/dcmle.R | 43 - dcmle-0.3-0/dcmle/R/zzz.R | 4 dcmle-0.3-0/dcmle/inst/ChangeLog | 52 + dcmle-0.3-0/dcmle/man/dcCodaMCMC-class.Rd | 167 ++--- dcmle-0.3-0/dcmle/man/dcmle-package.Rd | 15 dcmle-0.3-0/dcmle/tests |only 14 files changed, 1120 insertions(+), 1018 deletions(-)