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Title: Parsing Command-Line Arguments and Variable Interpolation
Description: This is yet another command-line argument parser which wraps the
powerful Perl module Getopt::Long and with some adaptation for easier use
in R. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GetoptLong versions 0.1.4 dated 2016-08-14 and 0.1.5 dated 2016-09-26
DESCRIPTION | 10 ++++----- MD5 | 22 ++++++++++---------- NAMESPACE | 17 +++++----------- NEWS | 7 ++++++ R/GetoptLong.R | 37 +++++++++++++++++++---------------- R/qq.R | 20 +++++++++++++++++- inst/doc/GetoptLong.html | 6 ++--- inst/doc/variable_interpolation.R | 3 ++ inst/doc/variable_interpolation.Rmd | 6 +++++ inst/doc/variable_interpolation.html | 18 ++++++++++++----- man/qqcat.rd | 5 +++- vignettes/variable_interpolation.Rmd | 6 +++++ 12 files changed, 103 insertions(+), 54 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.3.8 dated 2016-08-14 and 0.3.9 dated 2016-09-26
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 6 ++++++ R/chordDiagram.R | 22 ++++++++++++++++------ inst/doc/circlize.pdf |binary inst/doc/circular_phylogenetic_tree.pdf |binary inst/doc/circular_visualization_of_matrix.pdf |binary inst/doc/genomic_plot.pdf |binary inst/doc/interesting_graphics.pdf |binary inst/doc/visualize_relations_by_chord_diagram.pdf |binary 10 files changed, 35 insertions(+), 19 deletions(-)
Title: Biodiversity Assessment Using Functional Tools
Description: The main drawback of the most common biodiversity indices is that different measures may lead to different rankings among communities. This instrument overcomes this limit using some functional tools with the diversity profiles. In particular, the derivatives, the curvature, the radius of curvature, the arc length, and the surface area are proposed. The goal of this method is to interpret in detail the diversity profiles and obtain an ordering between different ecological communities on the basis of diversity. In contrast to the typical indices of diversity, the proposed method is able to capture the multidimensional aspect of biodiversity, because it takes into account both the evenness and the richness of the species present in an ecological community.
Author: Fabrizio Maturo [aut, cre],
Francesca Fortuna [aut],
Tonio Di Battista [aut]
Maintainer: Fabrizio Maturo <f.maturo@unich.it>
Diff between BioFTF versions 1.1-0 dated 2016-09-05 and 1.2-0 dated 2016-09-26
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- man/alltools.Rd | 2 +- man/arc.Rd | 2 +- man/area.Rd | 2 +- man/beta.Rd | 2 +- man/beta_plot.Rd | 2 +- man/betaprime.Rd | 2 +- man/betaprime_plot.Rd | 2 +- man/betasecond.Rd | 2 +- man/betasecond_plot.Rd | 2 +- man/curvature.Rd | 2 +- man/curvature_plot.Rd | 2 +- man/export_plots.Rd | 2 +- man/radius.Rd | 2 +- man/radius_plot.Rd | 2 +- man/ranking.Rd | 2 +- 17 files changed, 36 insertions(+), 36 deletions(-)
Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson
Maintainer: Ian Johnson <ianjjohnson@icloud.com>
Diff between arulesCBA versions 1.0 dated 2016-08-28 and 1.0.1 dated 2016-09-26
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ README.md | 2 ++ inst/doc/arulesCBA.R | 7 ++++--- inst/doc/arulesCBA.pdf |binary inst/doc/arulesCBA.rnw | 5 +++-- vignettes/arulesCBA.rnw | 5 +++-- 7 files changed, 23 insertions(+), 17 deletions(-)
Title: R 'Htmlwidget' to Add Pan and Zoom to Almost any R Graphic
Description: This 'htmlwidget' provides pan and zoom interactivity to R
graphics, including 'base', 'lattice', and 'ggplot2'. The interactivity is
provided through the 'svg-pan-zoom.js' library. Various options to the widget
can tailor the pan and zoom experience to nearly any user desire.
Author: Anders Riutta et. al. [aut, cph] (svg-pan-zoom.js BSD-licensed library
in htmlwidgets/lib, https://github.com/ariutta/svg-pan-zoom),
Jorik Tangelder [aut, cph] (hammer.js MIT-licensed touch library in
htmlwidgets/lib, https://github.com/hammerjs/hammer),
Kent Russell [aut, cre] (R interface to svg-pan-zoom.js)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between svgPanZoom versions 0.3.2 dated 2016-03-09 and 0.3.3 dated 2016-09-26
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- NEWS.md | 5 +++++ inst/htmlwidgets/svgPanZoom.js | 19 ++++++++++++++++--- 4 files changed, 29 insertions(+), 10 deletions(-)
Title: Collecting Twitter Data
Description: An implementation of calls designed to extract
and organize Twitter data via Twitter's REST and stream
APIs. Functions formulate GET and POST requests and
convert response objects to more user friendly structures,
e.g., data frames or lists. Specific consideration is
given to functions designed to return tweets, friends,
and followers.
Author: Michael W. Kearney
Maintainer: Michael W. Kearney <mkearney@ku.edu>
Diff between rtweet versions 0.2.0 dated 2016-08-14 and 0.3.0 dated 2016-09-26
rtweet-0.2.0/rtweet/R/retweeters.R |only rtweet-0.2.0/rtweet/R/text.R |only rtweet-0.2.0/rtweet/man/tweets_df.Rd |only rtweet-0.2.0/rtweet/man/user_df.Rd |only rtweet-0.2.0/rtweet/vignettes/search_tweets.md |only rtweet-0.2.0/rtweet/vignettes/tokens.md |only rtweet-0.3.0/rtweet/DESCRIPTION | 14 - rtweet-0.3.0/rtweet/MD5 | 127 ++++++++++----- rtweet-0.3.0/rtweet/NAMESPACE | 25 ++ rtweet-0.3.0/rtweet/NEWS.md | 89 ++++++++++ rtweet-0.3.0/rtweet/R/TWIT.R | 11 - rtweet-0.3.0/rtweet/R/extractors.R |only rtweet-0.3.0/rtweet/R/favorites.R |only rtweet-0.3.0/rtweet/R/followers.R | 17 +- rtweet-0.3.0/rtweet/R/friends.R | 28 +-- rtweet-0.3.0/rtweet/R/parse.R | 128 ++++++++------- rtweet-0.3.0/rtweet/R/parse.tweets.R | 130 +++++++-------- rtweet-0.3.0/rtweet/R/parse.users.R | 51 ++---- rtweet-0.3.0/rtweet/R/plot.R |only rtweet-0.3.0/rtweet/R/rate.limit.R | 17 +- rtweet-0.3.0/rtweet/R/rtweet-package.R | 17 +- rtweet-0.3.0/rtweet/R/save.csv.R |only rtweet-0.3.0/rtweet/R/scroll.R | 11 - rtweet-0.3.0/rtweet/R/search.R | 138 ++++++++++++++-- rtweet-0.3.0/rtweet/R/statuses.R |only rtweet-0.3.0/rtweet/R/stream.R | 202 ++++++++++++++++++------ rtweet-0.3.0/rtweet/R/sysdata.rda |only rtweet-0.3.0/rtweet/R/timeline.R | 32 +++ rtweet-0.3.0/rtweet/R/tokens.R | 30 ++- rtweet-0.3.0/rtweet/R/trends.R |only rtweet-0.3.0/rtweet/R/tweet.R |only rtweet-0.3.0/rtweet/R/users.R | 22 +- rtweet-0.3.0/rtweet/R/utils.R | 186 ++++++++++++++++++---- rtweet-0.3.0/rtweet/R/woeids.R |only rtweet-0.3.0/rtweet/README.md | 139 ++++++++-------- rtweet-0.3.0/rtweet/build |only rtweet-0.3.0/rtweet/inst/CITATION | 6 rtweet-0.3.0/rtweet/inst/doc |only rtweet-0.3.0/rtweet/man/clean_tweets.Rd | 45 ----- rtweet-0.3.0/rtweet/man/create_token.Rd | 2 rtweet-0.3.0/rtweet/man/find_woeid.Rd |only rtweet-0.3.0/rtweet/man/get_favorites.Rd |only rtweet-0.3.0/rtweet/man/get_followers.Rd | 10 - rtweet-0.3.0/rtweet/man/get_friends.Rd | 15 - rtweet-0.3.0/rtweet/man/get_timeline.Rd | 33 +++ rtweet-0.3.0/rtweet/man/get_tokens.Rd | 3 rtweet-0.3.0/rtweet/man/get_trends.Rd |only rtweet-0.3.0/rtweet/man/lookup_statuses.Rd |only rtweet-0.3.0/rtweet/man/lookup_users.Rd | 18 +- rtweet-0.3.0/rtweet/man/meta_data.Rd |only rtweet-0.3.0/rtweet/man/next_cursor.Rd |only rtweet-0.3.0/rtweet/man/parse_stream.Rd |only rtweet-0.3.0/rtweet/man/parser.Rd |only rtweet-0.3.0/rtweet/man/post_tweet.Rd |only rtweet-0.3.0/rtweet/man/rate_limit.Rd | 7 rtweet-0.3.0/rtweet/man/rtweet.Rd | 17 +- rtweet-0.3.0/rtweet/man/save_as_csv.Rd |only rtweet-0.3.0/rtweet/man/search_tweets.Rd | 35 ++-- rtweet-0.3.0/rtweet/man/search_users.Rd |only rtweet-0.3.0/rtweet/man/stream_tweets.Rd | 101 ++++++++---- rtweet-0.3.0/rtweet/man/trends_available.Rd |only rtweet-0.3.0/rtweet/man/ts_plot.Rd |only rtweet-0.3.0/rtweet/man/tweets_data.Rd |only rtweet-0.3.0/rtweet/man/users_data.Rd |only rtweet-0.3.0/rtweet/man/utf8_tweets.Rd |only rtweet-0.3.0/rtweet/tests |only rtweet-0.3.0/rtweet/vignettes/files/dt.png |only rtweet-0.3.0/rtweet/vignettes/files/hc.png |only rtweet-0.3.0/rtweet/vignettes/files/ts_plot.png |only rtweet-0.3.0/rtweet/vignettes/rtweet.Rmd |only rtweet-0.3.0/rtweet/vignettes/satweets.Rmd |only rtweet-0.3.0/rtweet/vignettes/timeseries.Rmd |only rtweet-0.3.0/rtweet/vignettes/tokens.Rmd |only 73 files changed, 1159 insertions(+), 547 deletions(-)
Title: R Interface to a 'PostGIS' Database
Description: Provides additional functions to the
'RPostgreSQL' package to interface R with a 'PostGIS'-enabled
database, as well as convenient wrappers to common 'PostgreSQL'
queries.
Author: Mathieu Basille [aut],
David Bucklin [aut, cre]
Maintainer: David Bucklin <dbucklin@ufl.edu>
Diff between rpostgis versions 1.0.0 dated 2016-08-20 and 1.0.2 dated 2016-09-26
rpostgis-1.0.0/rpostgis/R/dbTableNameFix.R |only rpostgis-1.0.0/rpostgis/TODO |only rpostgis-1.0.2/rpostgis/DESCRIPTION | 9 rpostgis-1.0.2/rpostgis/MD5 | 96 +- rpostgis-1.0.2/rpostgis/NAMESPACE | 79 +- rpostgis-1.0.2/rpostgis/NEWS | 336 ++++----- rpostgis-1.0.2/rpostgis/R/dbAddKey.R | 144 +-- rpostgis-1.0.2/rpostgis/R/dbAsDate.R | 122 +-- rpostgis-1.0.2/rpostgis/R/dbColumn.R | 122 +-- rpostgis-1.0.2/rpostgis/R/dbComment.R | 116 +-- rpostgis-1.0.2/rpostgis/R/dbDrop.R | 126 +-- rpostgis-1.0.2/rpostgis/R/dbIndex.R | 154 ++-- rpostgis-1.0.2/rpostgis/R/dbSchema.R | 114 +-- rpostgis-1.0.2/rpostgis/R/dbTableInfo.R | 66 - rpostgis-1.0.2/rpostgis/R/dbUtils.R |only rpostgis-1.0.2/rpostgis/R/dbVacuum.R | 114 +-- rpostgis-1.0.2/rpostgis/R/pgGetBoundary.R | 168 ++-- rpostgis-1.0.2/rpostgis/R/pgGetGeom.R | 858 +++++++++++------------ rpostgis-1.0.2/rpostgis/R/pgGetRast.R | 188 ++--- rpostgis-1.0.2/rpostgis/R/pgInsert.R | 552 ++++++++------- rpostgis-1.0.2/rpostgis/R/pgInsertize.R | 914 ++++++++++++------------- rpostgis-1.0.2/rpostgis/R/pgListGeom.R | 100 +- rpostgis-1.0.2/rpostgis/R/pgMakePts.R | 390 +++++----- rpostgis-1.0.2/rpostgis/R/pgPostGIS.R | 365 +++++---- rpostgis-1.0.2/rpostgis/R/pgSRID.R | 268 +++---- rpostgis-1.0.2/rpostgis/R/rpostgis-package.R | 86 +- rpostgis-1.0.2/rpostgis/README.md | 105 +- rpostgis-1.0.2/rpostgis/man/dbAddKey.Rd | 106 +- rpostgis-1.0.2/rpostgis/man/dbAsDate.Rd | 94 +- rpostgis-1.0.2/rpostgis/man/dbColumn.Rd | 112 +-- rpostgis-1.0.2/rpostgis/man/dbComment.Rd | 96 +- rpostgis-1.0.2/rpostgis/man/dbDrop.Rd | 106 +- rpostgis-1.0.2/rpostgis/man/dbIndex.Rd | 124 +-- rpostgis-1.0.2/rpostgis/man/dbSchema.Rd | 86 +- rpostgis-1.0.2/rpostgis/man/dbTableInfo.Rd | 68 - rpostgis-1.0.2/rpostgis/man/dbTableNameFix.Rd | 80 +- rpostgis-1.0.2/rpostgis/man/dbVacuum.Rd | 102 +- rpostgis-1.0.2/rpostgis/man/dbVersion.Rd |only rpostgis-1.0.2/rpostgis/man/pgGetBoundary.Rd | 70 - rpostgis-1.0.2/rpostgis/man/pgGetGeom.Rd | 130 +-- rpostgis-1.0.2/rpostgis/man/pgGetLines.Rd | 58 - rpostgis-1.0.2/rpostgis/man/pgGetPolys.Rd | 60 - rpostgis-1.0.2/rpostgis/man/pgGetPts.Rd | 66 - rpostgis-1.0.2/rpostgis/man/pgGetRast.Rd | 90 +- rpostgis-1.0.2/rpostgis/man/pgInsert.Rd | 271 +++---- rpostgis-1.0.2/rpostgis/man/pgInsertizeGeom.Rd | 294 ++++---- rpostgis-1.0.2/rpostgis/man/pgListGeom.Rd | 66 - rpostgis-1.0.2/rpostgis/man/pgMakePts.Rd | 146 +-- rpostgis-1.0.2/rpostgis/man/pgPostGIS.Rd | 100 +- rpostgis-1.0.2/rpostgis/man/pgSRID.Rd | 108 +- rpostgis-1.0.2/rpostgis/man/rpostgis.Rd | 90 +- 51 files changed, 4123 insertions(+), 3992 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 2.0.1 dated 2016-06-22 and 2.1.0 dated 2016-09-26
DESCRIPTION | 6 MD5 | 48 +- NAMESPACE | 3 NEWS | 13 R/as.char.R | 2 R/branches.R | 4 R/describe.col.R | 12 R/layout.R | 2 R/lib.R | 74 +++- R/my.rpartco.R | 14 R/my.snip.rpart.R | 12 R/node.labs.R | 31 + R/palette.R | 496 ++++++++++++++++++--------- R/prp.R | 99 ++--- R/show.prp.palettes.R |only R/split.labs.R | 2 inst/doc/prp.pdf |binary inst/slowtests/make.bat | 2 inst/slowtests/test.na.R | 2 inst/slowtests/test.palette.R | 272 ++++++++++++++- inst/slowtests/test.prp.Rout.save | 675 +++++++++++++++++++++++++++++--------- inst/slowtests/user-manual-figs.R | 16 man/prp.Rd | 96 ++++- man/rpart.plot.Rd | 36 +- man/rpart.plot.version1.Rd | 13 man/show.prp.palettes.Rd |only 26 files changed, 1395 insertions(+), 535 deletions(-)
Title: Implementation of Sampling Formulas for the Unified Neutral
Model of Biodiversity and Biogeography, with or without Guild
Structure
Description: A collection of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned on guild size (Janzen et al. 2015).
Author: Thijs Janzen [aut, cre],
Bart Haegeman [ctb],
Franck Jabot [ctb],
Jerome Chave [ctb]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between GUILDS versions 1.2.1 dated 2015-04-21 and 1.3 dated 2016-09-26
GUILDS-1.2.1/GUILDS/data |only GUILDS-1.2.1/GUILDS/man/exampleData.Rd |only GUILDS-1.3/GUILDS/DESCRIPTION | 27 GUILDS-1.3/GUILDS/MD5 | 66 +- GUILDS-1.3/GUILDS/NAMESPACE | 34 - GUILDS-1.3/GUILDS/R/Condition.R | 416 ++++++++------ GUILDS-1.3/GUILDS/R/ESF_function.R | 153 ++--- GUILDS-1.3/GUILDS/R/LogLikFunctions.R | 349 ++++++----- GUILDS-1.3/GUILDS/R/calcSumKDA2.R | 32 - GUILDS-1.3/GUILDS/R/drawLocal.R | 275 ++++----- GUILDS-1.3/GUILDS/R/evaluateLogLik2.R | 50 - GUILDS-1.3/GUILDS/R/expected.R | 223 ++++--- GUILDS-1.3/GUILDS/R/generateData.R | 347 ++++++----- GUILDS-1.3/GUILDS/R/simplex.R | 291 ++++----- GUILDS-1.3/GUILDS/R/visualisation.R |only GUILDS-1.3/GUILDS/README.md |only GUILDS-1.3/GUILDS/build |only GUILDS-1.3/GUILDS/inst |only GUILDS-1.3/GUILDS/man/GUILDS-internal.Rd | 50 - GUILDS-1.3/GUILDS/man/GUILDS-package.Rd | 79 +- GUILDS-1.3/GUILDS/man/expected.SAD.Guilds.Conditional.Rd | 98 +-- GUILDS-1.3/GUILDS/man/logLikelihood.ESF.Rd | 67 +- GUILDS-1.3/GUILDS/man/logLikelihood.Guilds.Conditional.Rd | 77 +- GUILDS-1.3/GUILDS/man/logLikelihood.Guilds.Rd | 79 +- GUILDS-1.3/GUILDS/man/maxLikelihood.ESF.Rd | 78 +- GUILDS-1.3/GUILDS/man/maxLikelihood.Guilds.Conditional.Rd | 131 ++-- GUILDS-1.3/GUILDS/man/maxLikelihood.Guilds.Rd | 129 ++-- GUILDS-1.3/GUILDS/man/preston_plot.Rd |only GUILDS-1.3/GUILDS/src/KDA_R.cpp | 82 +- GUILDS-1.3/GUILDS/tests |only GUILDS-1.3/GUILDS/vignettes |only 31 files changed, 1733 insertions(+), 1400 deletions(-)
Title: Individual Tree Growth Modeling
Description: Individual tree model is an instrument to support the decision with
regard to forest management. This package provides functions that let you work
with data for this model. Also other support functions and extension related to
this model are available.
Author: Clayton Vieira Fraga Filho, Miqueias Fernandes
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>
Diff between ITGM versions 0.2 dated 2016-09-09 and 0.3 dated 2016-09-26
ITGM-0.2/ITGM/README.md |only ITGM-0.3/ITGM/DESCRIPTION | 6 +++--- ITGM-0.3/ITGM/MD5 | 7 ++++--- ITGM-0.3/ITGM/NAMESPACE | 1 + ITGM-0.3/ITGM/R/project.R |only ITGM-0.3/ITGM/man/project.Rd |only 6 files changed, 8 insertions(+), 6 deletions(-)
Title: Forest Growth Model Utilities
Description: Growth models and forest production require existing data
manipulation and the creation of new data, structured from basic forest
inventory data. The purpose of this package is provide functions to support
these activities.
Author: Clayton Vieira Fraga Filho,
Ana Paula Simiqueli,
Gilson Fernandes da Silva,
Miqueias Fernandes,
Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>
Diff between Fgmutils versions 0.9 dated 2016-09-09 and 0.9.3 dated 2016-09-26
DESCRIPTION | 6 - MD5 | 158 ++++++++++++++++---------------- NAMESPACE | 1 NEWS | 16 +++ R/R21a.R | 16 +++ R/R29a.R | 16 +++ R/add.col.R | 16 +++ R/atualizaCampoBase.R | 16 +++ R/avaliaAjuste.R | 16 +++ R/avaliaEstimativas.R | 6 - R/avaliaVolumeAvancado.R | 35 +++++-- R/bias.R | 16 +++ R/calculaA.R | 16 +++ R/calculaPerc.R | 16 +++ R/calculaVolumeDefault.R | 16 +++ R/ce.R | 16 +++ R/check.integer.R | 16 +++ R/classificaClasseDAP.R | 16 +++ R/classificarDAP.R | 16 +++ R/contemParametros.R | 16 +++ R/converteCampoParaCharacter.R | 16 +++ R/criaDadosPareados.R | 16 +++ R/criaModeloExclusivo.R | 16 +++ R/criaModeloGenerico.R | 16 +++ R/defineClasses.R | 16 +++ R/defineClasses2.R | 16 +++ R/estatisticas.R | 20 +++- R/estatisticasBIAS.R | 21 +++- R/estatisticasBiasPERCENTUAL.R | 21 +++- R/estatisticasCE.R | 21 +++- R/estatisticasCORR.R | 21 +++- R/estatisticasCV.R | 20 +++- R/estatisticasCorrPERCENTUAL.R | 22 +++- R/estatisticasCvPERCENTUAL.R | 21 +++- R/estatisticasMAE.R | 21 +++- R/estatisticasR2.R | 22 +++- R/estatisticasRMSE.R | 21 +++- R/estatisticasRRMSE.R | 21 +++- R/estatisticasResiduoPERCENTUAL.R | 20 +++- R/estatisticasResiduos.R | 20 +++- R/estatisticasRmsePERCENTUAL.R | 21 +++- R/fator_bias.R | 16 +++ R/geraModelo.R | 16 +++ R/getAnoMedicao.R | 16 +++ R/getBaseOfAjust.R | 16 +++ R/getClasses.R | 16 +++ R/getColumnsOfAjust.R | 16 +++ R/getColumnsOfBase.R | 16 +++ R/getFormulaExclusivaOfAjust.R | 16 +++ R/getGraphicHistogram.R | 26 ++++- R/getGraphicObservadoXEstimado.R | 31 +++++- R/getGraphicResiduoAbs.R | 28 ++++- R/getGraphicResiduoPerc.R | 28 ++++- R/getParametrosOfModel.R | 16 +++ R/getggplot2GraphicObservadoXEstimado.R | 23 ++++ R/gravaDocResultado.R | 16 +++ R/gravaResultado.R | 16 +++ R/ifrm.R | 16 +++ R/isfinitedataframe.R | 16 +++ R/listToDataFrame.R | 16 +++ R/mae.R | 16 +++ R/mse.R | 16 +++ R/mspr.R | 16 +++ R/predizer.R | 35 +++++-- R/residuoPerc.R | 16 +++ R/retornaValor.R | 16 +++ R/rmse.R | 16 +++ R/roundAge.R |only R/rrmse.R | 16 +++ R/salvaModelo.R | 16 +++ R/separaDados.R | 16 +++ R/syx.R | 16 +++ R/syxPerc.R | 16 +++ R/verificaTipoColuna.R | 16 +++ R/whichmedian.R | 16 +++ man/estatisticas.Rd | 2 man/getGraphicHistogram.Rd | 4 man/getGraphicObservadoXEstimado.Rd | 5 - man/getGraphicResiduoAbs.Rd | 5 - man/getGraphicResiduoPerc.Rd | 7 + man/roundAge.Rd |only 81 files changed, 1318 insertions(+), 163 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; and the International Tree Ring Data Bank. Additional
data sources are in the works, including global DEM resources (ETOPO1, ETOPO5,
ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National
Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.0.10 dated 2016-09-08 and 2.2.0 dated 2016-09-26
DESCRIPTION | 12 ++--- MD5 | 22 ++++++---- NAMESPACE | 1 R/GHCN_FUNCTIONS.R | 100 ++++++++++++++++++++++++++++++++++--------------- README.md | 4 - inst/CITATION | 4 - man/FedData-package.Rd | 4 - man/get_ghcn_daily.Rd | 6 +- tests/testthat |only tests/testthat.R | 2 10 files changed, 103 insertions(+), 52 deletions(-)
Title: Meta-Analysis of Region-Based Tests of Rare DNA Variants
Description: Computes necessary information to meta analyze region-based
tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and
performs meta analysis.
Author: Arie Voorman, Jennifer Brody, Han Chen, Thomas Lumley, Brian Davis
Maintainer: Brian Davis <Brian.Davis281@gmail.com>
Diff between seqMeta versions 1.6.5 dated 2016-01-26 and 1.6.6 dated 2016-09-26
DESCRIPTION | 10 MD5 | 79 - NAMESPACE | 79 - NEWS.md |only R/burdenMeta.R | 392 +++---- R/c.seqMeta.R | 45 R/check_format_skat.R | 40 R/coxlr.fit.R | 172 +-- R/pchisqsum2.R | 142 +- R/prepAdjust.R | 220 ++-- R/prepCox.R | 280 ++--- R/prepScores.R | 1028 +++++++++---------- R/prepScores2.R | 1010 +++++++++---------- R/seqMeta.R | 118 +- R/singlesnpMeta.R | 408 +++---- R/skatMeta.R | 482 ++++----- R/skatOMeta.R | 854 ++++++++-------- R/utils.R | 168 +-- README.md | 173 +-- build/vignette.rds |binary data/datalist | 4 inst/doc/seqMeta.R | 390 +++---- inst/doc/seqMeta.Rnw | 1994 +++++++++++++++++++------------------- man/SNPInfo.Rd | 70 - man/burdenMeta.Rd | 212 ++-- man/prepCondScores.Rd | 222 ++-- man/prepScores.Rd | 330 +++--- man/prepScores2.Rd | 360 +++--- man/seqMeta.Rd | 30 man/seqMetaExample.Rd | 138 +- man/singlesnpMeta.Rd | 210 ++-- man/skatMeta.Rd | 308 ++--- man/skatOMeta.Rd | 382 +++---- tests/testthat.R | 8 tests/testthat/test-bugfixes.R | 142 +- tests/testthat/test-examples.R | 110 +- tests/testthat/test-issue1.R | 670 ++++++------ tests/testthat/test-issue2.R | 692 ++++++------- tests/testthat/test-prepSNPInfo.R | 206 +-- tests/testthat/test-prepScores2.R | 154 +- vignettes/seqMeta.Rnw | 1994 +++++++++++++++++++------------------- 41 files changed, 7169 insertions(+), 7157 deletions(-)
Title: Data Exchange Between R and LabKey Server
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.1.130 dated 2016-05-25 and 2.1.131 dated 2016-09-26
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- NEWS | 4 ++++ R/labkey.defaults.R | 28 +++++++++++++++++++++++----- R/labkey.deleteRows.R | 8 +++++--- R/labkey.executeSql.R | 7 ++++--- R/labkey.getFolders.R | 14 ++++++-------- R/labkey.getQueryInfo.R | 20 +++++++++++++------- R/labkey.getQueryLists.R | 16 +++++++++------- R/labkey.getSchemas.R | 8 +++++--- R/labkey.importRows.R | 8 +++++--- R/labkey.insertRows.R | 8 +++++--- R/labkey.saveBatch.R | 7 ++++--- R/labkey.selectRows.R | 8 +++++--- R/labkey.setCurlOptions.R | 4 ++-- R/labkey.updateRows.R | 8 +++++--- R/schemaObjects.R | 8 +++++--- build/vignette.rds |binary man/Rlabkey-package.Rd | 4 ++-- man/labkey.setDefaults.Rd | 9 ++++++--- 20 files changed, 131 insertions(+), 84 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
Author: Carson Sievert [aut, cre],
Chris Parmer [aut, cph],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut],
Pedro Despouy [aut]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 3.6.0 dated 2016-05-17 and 4.5.2 dated 2016-09-26
plotly-3.6.0/plotly/NEWS |only plotly-3.6.0/plotly/build |only plotly-3.6.0/plotly/inst/arguments.R |only plotly-3.6.0/plotly/inst/doc |only plotly-3.6.0/plotly/man/get_plot.Rd |only plotly-3.6.0/plotly/man/knit_print.figure.Rd |only plotly-3.6.0/plotly/man/knit_print.plotly_built.Rd |only plotly-3.6.0/plotly/man/knit_print.plotly_hash.Rd |only plotly-3.6.0/plotly/man/pipe.Rd |only plotly-3.6.0/plotly/man/print.figure.Rd |only plotly-3.6.0/plotly/man/print.plotly_built.Rd |only plotly-3.6.0/plotly/man/print.plotly_hash.Rd |only plotly-3.6.0/plotly/vignettes |only plotly-4.5.2/plotly/DESCRIPTION | 23 plotly-4.5.2/plotly/LICENSE | 4 plotly-4.5.2/plotly/MD5 | 216 +-- plotly-4.5.2/plotly/NAMESPACE | 128 +- plotly-4.5.2/plotly/NEWS.md |only plotly-4.5.2/plotly/R/add.R |only plotly-4.5.2/plotly/R/coord.R |only plotly-4.5.2/plotly/R/deprecated.R | 19 plotly-4.5.2/plotly/R/dev.R |only plotly-4.5.2/plotly/R/export.R |only plotly-4.5.2/plotly/R/figure.R | 2 plotly-4.5.2/plotly/R/ggplotly.R | 276 ++-- plotly-4.5.2/plotly/R/group2NA.R |only plotly-4.5.2/plotly/R/helpers.R |only plotly-4.5.2/plotly/R/imports.R | 158 ++ plotly-4.5.2/plotly/R/last_plot.R |only plotly-4.5.2/plotly/R/layers2traces.R | 329 +++-- plotly-4.5.2/plotly/R/layout.R |only plotly-4.5.2/plotly/R/pipe.R | 13 plotly-4.5.2/plotly/R/plotly.R | 625 +++------- plotly-4.5.2/plotly/R/plotly_POST.R | 12 plotly-4.5.2/plotly/R/plotly_build.R |only plotly-4.5.2/plotly/R/plotly_data.R |only plotly-4.5.2/plotly/R/print.R | 95 - plotly-4.5.2/plotly/R/process.R | 8 plotly-4.5.2/plotly/R/shiny.R | 18 plotly-4.5.2/plotly/R/style.R |only plotly-4.5.2/plotly/R/subplots.R | 149 +- plotly-4.5.2/plotly/R/sysdata.rda |only plotly-4.5.2/plotly/R/toRGB.R | 15 plotly-4.5.2/plotly/R/utils.R | 535 ++++++-- plotly-4.5.2/plotly/README.md | 20 plotly-4.5.2/plotly/inst/docs.R | 5 plotly-4.5.2/plotly/inst/examples/Movies/server.R | 4 plotly-4.5.2/plotly/inst/examples/UN_Advanced/server.R | 36 plotly-4.5.2/plotly/inst/examples/UN_Simple/server.R | 2 plotly-4.5.2/plotly/inst/examples/crosstalkShinyDT |only plotly-4.5.2/plotly/inst/examples/lmGadget/app.R | 60 plotly-4.5.2/plotly/inst/examples/onRenderHover/index.Rmd | 17 plotly-4.5.2/plotly/inst/examples/plotlyEvents/app.R | 31 plotly-4.5.2/plotly/inst/examples/plotlyLinkedBrush/app.R | 2 plotly-4.5.2/plotly/inst/examples/plotlyLinkedClick/app.R | 7 plotly-4.5.2/plotly/inst/examples/plotlyShinyModules |only plotly-4.5.2/plotly/inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js | 95 - plotly-4.5.2/plotly/inst/htmlwidgets/plotly.js | 16 plotly-4.5.2/plotly/inst/htmlwidgets/plotly.yaml | 2 plotly-4.5.2/plotly/inst/plotlyjs.R | 44 plotly-4.5.2/plotly/man/add_annotations.Rd |only plotly-4.5.2/plotly/man/add_data.Rd |only plotly-4.5.2/plotly/man/add_fun.Rd |only plotly-4.5.2/plotly/man/add_trace.Rd | 177 ++ plotly-4.5.2/plotly/man/as.widget.Rd | 13 plotly-4.5.2/plotly/man/as_widget.Rd |only plotly-4.5.2/plotly/man/colorbar.Rd |only plotly-4.5.2/plotly/man/config.Rd | 4 plotly-4.5.2/plotly/man/embed_notebook.Rd | 4 plotly-4.5.2/plotly/man/event_data.Rd | 10 plotly-4.5.2/plotly/man/export.Rd |only plotly-4.5.2/plotly/man/geom2trace.Rd | 2 plotly-4.5.2/plotly/man/gg2list.Rd | 8 plotly-4.5.2/plotly/man/ggplotly.Rd | 11 plotly-4.5.2/plotly/man/hide_colorbar.Rd |only plotly-4.5.2/plotly/man/hide_guides.Rd |only plotly-4.5.2/plotly/man/hide_legend.Rd |only plotly-4.5.2/plotly/man/knit_print.plotly_figure.Rd |only plotly-4.5.2/plotly/man/last_plot.Rd | 13 plotly-4.5.2/plotly/man/layout.Rd | 10 plotly-4.5.2/plotly/man/plot_geo.Rd |only plotly-4.5.2/plotly/man/plot_ly.Rd | 122 + plotly-4.5.2/plotly/man/plot_mapbox.Rd |only plotly-4.5.2/plotly/man/plotly_POST.Rd | 6 plotly-4.5.2/plotly/man/plotly_build.Rd | 23 plotly-4.5.2/plotly/man/plotly_data.Rd |only plotly-4.5.2/plotly/man/plotly_empty.Rd | 9 plotly-4.5.2/plotly/man/plotly_json.Rd |only plotly-4.5.2/plotly/man/print.plotly_figure.Rd |only plotly-4.5.2/plotly/man/rangeslider.Rd |only plotly-4.5.2/plotly/man/reexports.Rd |only plotly-4.5.2/plotly/man/schema.Rd |only plotly-4.5.2/plotly/man/style.Rd | 13 plotly-4.5.2/plotly/man/subplot.Rd | 33 plotly-4.5.2/plotly/man/toWebGL.Rd |only plotly-4.5.2/plotly/man/to_basic.Rd | 2 plotly-4.5.2/plotly/tests/testthat.R | 23 plotly-4.5.2/plotly/tests/testthat/test-cookbook-axes.R | 1 plotly-4.5.2/plotly/tests/testthat/test-cookbook-lines.R | 2 plotly-4.5.2/plotly/tests/testthat/test-ggplot-abline.R | 1 plotly-4.5.2/plotly/tests/testthat/test-ggplot-area.R | 6 plotly-4.5.2/plotly/tests/testthat/test-ggplot-bar.R | 3 plotly-4.5.2/plotly/tests/testthat/test-ggplot-boxplot.R | 1 plotly-4.5.2/plotly/tests/testthat/test-ggplot-density.R | 6 plotly-4.5.2/plotly/tests/testthat/test-ggplot-density2d.R | 2 plotly-4.5.2/plotly/tests/testthat/test-ggplot-errorbar.R | 18 plotly-4.5.2/plotly/tests/testthat/test-ggplot-facets.R | 10 plotly-4.5.2/plotly/tests/testthat/test-ggplot-ggplotly.R |only plotly-4.5.2/plotly/tests/testthat/test-ggplot-histogram.R | 1 plotly-4.5.2/plotly/tests/testthat/test-ggplot-jitter.R | 1 plotly-4.5.2/plotly/tests/testthat/test-ggplot-legend.R | 20 plotly-4.5.2/plotly/tests/testthat/test-ggplot-point.R | 10 plotly-4.5.2/plotly/tests/testthat/test-ggplot-polygons.R | 72 - plotly-4.5.2/plotly/tests/testthat/test-ggplot-rect.R | 97 - plotly-4.5.2/plotly/tests/testthat/test-ggplot-ribbon.R | 1 plotly-4.5.2/plotly/tests/testthat/test-ggplot-smooth.R | 1 plotly-4.5.2/plotly/tests/testthat/test-ggplot-text.R | 3 plotly-4.5.2/plotly/tests/testthat/test-ggplot-ticks.R | 1 plotly-4.5.2/plotly/tests/testthat/test-ggplot-tooltip.R | 42 plotly-4.5.2/plotly/tests/testthat/test-ggplot-violin.R | 4 plotly-4.5.2/plotly/tests/testthat/test-ggplot-ylim.R | 1 plotly-4.5.2/plotly/tests/testthat/test-plotly-color.R |only plotly-4.5.2/plotly/tests/testthat/test-plotly-data.R |only plotly-4.5.2/plotly/tests/testthat/test-plotly-filename.R | 3 plotly-4.5.2/plotly/tests/testthat/test-plotly-getfigure.R | 16 plotly-4.5.2/plotly/tests/testthat/test-plotly-group.R |only plotly-4.5.2/plotly/tests/testthat/test-plotly-linetype.R |only plotly-4.5.2/plotly/tests/testthat/test-plotly-subplot.R | 20 plotly-4.5.2/plotly/tests/testthat/test-plotly-symbol.R |only plotly-4.5.2/plotly/tests/testthat/test-plotly.R | 261 ++-- 130 files changed, 2386 insertions(+), 1667 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC) and the Generalized Adjustment Criterion (GAC)
are implemented.
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut],
Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb], Antti Hyttinen [ctb],
Jonas Peters [ctb], Nicoletta Andri [ctb], Emilija Perkovic [ctb], Preetam Nandy [ctb],
Philipp Ruetimann [ctb], Daniel Stekhoven [ctb], Manuel Schuerch [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.2-4 dated 2015-07-23 and 2.4-2 dated 2016-09-26
pcalg-2.2-4/pcalg/tests/gacData.rda |only pcalg-2.4-2/pcalg/DESCRIPTION | 18 pcalg-2.4-2/pcalg/MD5 | 162 +- pcalg-2.4-2/pcalg/NAMESPACE | 18 pcalg-2.4-2/pcalg/R/Aaux.R | 41 pcalg-2.4-2/pcalg/R/AllClasses.R | 1339 +++++++++++++++----- pcalg-2.4-2/pcalg/R/deprecated.R |only pcalg-2.4-2/pcalg/R/genRandDAG.R | 119 - pcalg-2.4-2/pcalg/R/gies.R | 360 ++++- pcalg-2.4-2/pcalg/R/jointIda.R | 6 pcalg-2.4-2/pcalg/R/lingamFuns.R | 49 pcalg-2.4-2/pcalg/R/pcalg.R | 1196 ++++------------- pcalg-2.4-2/pcalg/TODO | 100 - pcalg-2.4-2/pcalg/build |only pcalg-2.4-2/pcalg/cleanup | 1 pcalg-2.4-2/pcalg/data/gmInt.rda |binary pcalg-2.4-2/pcalg/inst/NEWS.Rd | 20 pcalg-2.4-2/pcalg/inst/doc/mkVignettes.R | 5 pcalg-2.4-2/pcalg/inst/doc/pcalgDoc.R |only pcalg-2.4-2/pcalg/inst/doc/pcalgDoc.Rnw |only pcalg-2.4-2/pcalg/inst/doc/pcalgDoc.pdf |binary pcalg-2.4-2/pcalg/inst/external/gac-pags.rds |only pcalg-2.4-2/pcalg/inst/include/pcalg/gies_debug.hpp | 4 pcalg-2.4-2/pcalg/inst/include/pcalg/greedy.hpp | 158 ++ pcalg-2.4-2/pcalg/inst/include/pcalg/score.hpp | 68 - pcalg-2.4-2/pcalg/man/LINGAM.Rd | 67 - pcalg-2.4-2/pcalg/man/Score-class.Rd | 19 pcalg-2.4-2/pcalg/man/amatType.Rd |only pcalg-2.4-2/pcalg/man/backdoor.Rd | 82 - pcalg-2.4-2/pcalg/man/checkTriple.Rd | 9 pcalg-2.4-2/pcalg/man/condIndFisherZ.Rd | 8 pcalg-2.4-2/pcalg/man/corGraph.Rd | 18 pcalg-2.4-2/pcalg/man/dag2cpdag.Rd | 9 pcalg-2.4-2/pcalg/man/dag2essgraph.Rd | 29 pcalg-2.4-2/pcalg/man/dreach.Rd | 10 pcalg-2.4-2/pcalg/man/dsepTest.Rd | 7 pcalg-2.4-2/pcalg/man/fci.Rd | 21 pcalg-2.4-2/pcalg/man/fciAlgo-class.Rd | 41 pcalg-2.4-2/pcalg/man/fciPlus.Rd | 16 pcalg-2.4-2/pcalg/man/find.unsh.triple.Rd | 6 pcalg-2.4-2/pcalg/man/gac.Rd | 115 - pcalg-2.4-2/pcalg/man/gds.Rd | 46 pcalg-2.4-2/pcalg/man/ges.Rd | 67 - pcalg-2.4-2/pcalg/man/gies.Rd | 113 + pcalg-2.4-2/pcalg/man/ida.Rd | 12 pcalg-2.4-2/pcalg/man/idaFast.Rd | 4 pcalg-2.4-2/pcalg/man/jointIda.Rd | 2 pcalg-2.4-2/pcalg/man/legal.path.Rd | 2 pcalg-2.4-2/pcalg/man/mat2targets.Rd | 36 pcalg-2.4-2/pcalg/man/pag2mag.Rd | 18 pcalg-2.4-2/pcalg/man/pc.Rd | 139 +- pcalg-2.4-2/pcalg/man/pc.cons.intern.Rd | 7 pcalg-2.4-2/pcalg/man/pcAlgo-class.Rd | 9 pcalg-2.4-2/pcalg/man/pcorOrder.Rd | 6 pcalg-2.4-2/pcalg/man/pdag2allDags.Rd |only pcalg-2.4-2/pcalg/man/pdsep.Rd | 7 pcalg-2.4-2/pcalg/man/plotSG.Rd | 4 pcalg-2.4-2/pcalg/man/possibleDe.Rd | 18 pcalg-2.4-2/pcalg/man/qreach.Rd | 6 pcalg-2.4-2/pcalg/man/randDAG.Rd | 28 pcalg-2.4-2/pcalg/man/rfci.Rd | 20 pcalg-2.4-2/pcalg/man/showAmat.Rd | 2 pcalg-2.4-2/pcalg/man/simy.Rd | 10 pcalg-2.4-2/pcalg/man/skeleton.Rd | 20 pcalg-2.4-2/pcalg/man/udag2apag.Rd | 24 pcalg-2.4-2/pcalg/man/udag2pag.Rd | 19 pcalg-2.4-2/pcalg/man/udag2pdag.Rd | 14 pcalg-2.4-2/pcalg/man/unifDAG.Rd | 5 pcalg-2.4-2/pcalg/man/visibleEdge.Rd | 17 pcalg-2.4-2/pcalg/src/Makevars.win | 4 pcalg-2.4-2/pcalg/src/constraint.cpp | 127 + pcalg-2.4-2/pcalg/src/gies.cpp | 277 ++-- pcalg-2.4-2/pcalg/src/greedy.cpp | 329 ++++ pcalg-2.4-2/pcalg/src/score.cpp | 155 ++ pcalg-2.4-2/pcalg/tests/test_LINGAM.R | 5 pcalg-2.4-2/pcalg/tests/test_arges.R |only pcalg-2.4-2/pcalg/tests/test_bicscore.R | 185 ++ pcalg-2.4-2/pcalg/tests/test_dag2essgraph.R |only pcalg-2.4-2/pcalg/tests/test_displayAmat.R |only pcalg-2.4-2/pcalg/tests/test_gac.R | 257 ++- pcalg-2.4-2/pcalg/tests/test_getNextSet.R | 10 pcalg-2.4-2/pcalg/tests/test_gies.R | 100 + pcalg-2.4-2/pcalg/tests/test_mat2targets.R | 8 pcalg-2.4-2/pcalg/tests/test_pcSelect.R | 2 pcalg-2.4-2/pcalg/tests/test_pdag2allDags.R |only pcalg-2.4-2/pcalg/tests/test_randDAG.R | 15 pcalg-2.4-2/pcalg/tests/test_randDAG.Rout.save | 26 pcalg-2.4-2/pcalg/vignettes/pcalgDoc.Rnw | 47 88 files changed, 4000 insertions(+), 2323 deletions(-)
Title: Spatial Ecology Miscellaneous Methods
Description: Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre-, core and post- modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) & Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland.
Author: Olivier Broennimann [aut],
Valeria Di Cola [cre, aut],
Blaise Petitpierre [ctb],
Frank Breiner [ctb],
Manuela D`Amen [ctb],
Christophe Randin [ctb],
Robin Engler [ctb],
Wim Hordijk [ctb],
Julien Pottier [ctb],
Mirko Di Febbraro [ctb],
Loic Pellissier [ctb],
Dorothea Pio [ctb],
Ruben Garcia Mateo [ctb],
Anne Dubuis [ctb],
Daniel Scherrer [ctb],
Luigi Maiorano [ctb],
Achilleas Psomas [ctb],
Charlotte Ndiribe [ctb],
Nicolas Salamin [ctb],
Niklaus Zimmermann [ctb],
Antoine Guisan [aut]
Maintainer: Valeria Di Cola <valeria.dicola@unil.ch>
Diff between ecospat versions 2.0 dated 2016-05-26 and 2.1.0 dated 2016-09-26
ecospat-2.0/ecospat/R/ecospat.constrainedCoOcc.R |only ecospat-2.0/ecospat/R/ecospat.cooccindex.R |only ecospat-2.0/ecospat/R/ecospat.exdet.r |only ecospat-2.1.0/ecospat/DESCRIPTION | 18 ecospat-2.1.0/ecospat/MD5 | 99 ecospat-2.1.0/ecospat/NAMESPACE | 20 ecospat-2.1.0/ecospat/NEWS | 42 ecospat-2.1.0/ecospat/R/ecospat.CommunityEval.R | 102 ecospat-2.1.0/ecospat/R/ecospat.ESM.R | 1383 ++++++------ ecospat-2.1.0/ecospat/R/ecospat.SESAM.prr.R | 58 ecospat-2.1.0/ecospat/R/ecospat.adj.D2.R | 30 ecospat-2.1.0/ecospat/R/ecospat.binary_models.R | 36 ecospat-2.1.0/ecospat/R/ecospat.boyce.R | 112 ecospat-2.1.0/ecospat/R/ecospat.co_occ.R |only ecospat-2.1.0/ecospat/R/ecospat.cor.panel.R | 73 ecospat-2.1.0/ecospat/R/ecospat.cv.R | 1340 +++++------ ecospat-2.1.0/ecospat/R/ecospat.eval.R | 312 +- ecospat-2.1.0/ecospat/R/ecospat.exdet.R |only ecospat-2.1.0/ecospat/R/ecospat.makeDataFrame.R | 466 +--- ecospat-2.1.0/ecospat/R/ecospat.mess.R | 163 - ecospat-2.1.0/ecospat/R/ecospat.migclim.R | 16 ecospat-2.1.0/ecospat/R/ecospat.modelingtools.R | 286 +- ecospat-2.1.0/ecospat/R/ecospat.nichedynamic.R | 590 ++--- ecospat-2.1.0/ecospat/R/ecospat.nicheoverlap.R | 699 +++--- ecospat-2.1.0/ecospat/R/ecospat.occprep.R | 223 + ecospat-2.1.0/ecospat/R/ecospat.pd_measure.R | 280 +- ecospat-2.1.0/ecospat/R/ecospat.sampling.R |only ecospat-2.1.0/ecospat/build |only ecospat-2.1.0/ecospat/inst/doc/vignette_ecospat_package.R |only ecospat-2.1.0/ecospat/inst/doc/vignette_ecospat_package.Rmd |only ecospat-2.1.0/ecospat/inst/doc/vignette_ecospat_package.pdf |only ecospat-2.1.0/ecospat/man/ecospat-package.Rd | 27 ecospat-2.1.0/ecospat/man/ecospat.Cscore.Rd |only ecospat-2.1.0/ecospat/man/ecospat.ESM.EnsembleModeling.Rd | 2 ecospat-2.1.0/ecospat/man/ecospat.ESM.EnsembleProjection.Rd | 2 ecospat-2.1.0/ecospat/man/ecospat.ESM.Modeling.Rd | 6 ecospat-2.1.0/ecospat/man/ecospat.ESM.Projection.Rd | 14 ecospat-2.1.0/ecospat/man/ecospat.boyce.Rd | 8 ecospat-2.1.0/ecospat/man/ecospat.caleval.Rd | 2 ecospat-2.1.0/ecospat/man/ecospat.cons_Cscore.Rd | 8 ecospat-2.1.0/ecospat/man/ecospat.cv.example.Rd | 2 ecospat-2.1.0/ecospat/man/ecospat.cv.gbm.Rd | 70 ecospat-2.1.0/ecospat/man/ecospat.cv.glm.Rd | 66 ecospat-2.1.0/ecospat/man/ecospat.cv.me.Rd | 72 ecospat-2.1.0/ecospat/man/ecospat.cv.rf.Rd | 68 ecospat-2.1.0/ecospat/man/ecospat.grid.clim.dyn.Rd | 23 ecospat-2.1.0/ecospat/man/ecospat.makeDataFrame.Rd | 4 ecospat-2.1.0/ecospat/man/ecospat.niche.dyn.index.Rd | 4 ecospat-2.1.0/ecospat/man/ecospat.niche.equivalency.test.Rd | 17 ecospat-2.1.0/ecospat/man/ecospat.niche.overlap.Rd | 7 ecospat-2.1.0/ecospat/man/ecospat.niche.similarity.test.Rd | 18 ecospat-2.1.0/ecospat/man/ecospat.occ.desaggregation.Rd | 4 ecospat-2.1.0/ecospat/man/ecospat.plot.niche.Rd | 4 ecospat-2.1.0/ecospat/man/ecospat.plot.niche.dyn.Rd | 12 ecospat-2.1.0/ecospat/man/ecospat.rcls.grd.Rd |only ecospat-2.1.0/ecospat/man/ecospat.recstrat_prop.Rd |only ecospat-2.1.0/ecospat/man/ecospat.recstrat_regl.Rd |only ecospat-2.1.0/ecospat/vignettes |only 58 files changed, 3529 insertions(+), 3259 deletions(-)
Title: Stacks, Queues, and 'Deques' for R
Description: Queues, stacks, and 'deques' are list-like, abstract data types.
These are meant to be very cheap to "grow", or insert new objects into.
A typical use case involves storing data in a list in a streaming fashion,
when you do not necessarily know how may elements need to be stored.
Unlike R's lists, the new data structures provided here are not
necessarily stored contiguously, making insertions and deletions at the
front/end of the structure much faster. The underlying implementation
is new and uses a head/tail doubly linked list; thus, we do not rely on R's
environments or hashing. To avoid unnecessary data copying, most operations
on these data structures are performed via side-effects.
Author: Drew Schmidt [aut, cre]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between dequer versions 1.0 dated 2015-07-05 and 2.0-0 dated 2016-09-26
dequer-1.0/dequer/R/converters.r |only dequer-1.0/dequer/R/costructor.r |only dequer-1.0/dequer/R/utils.r |only dequer-1.0/dequer/man/pop.Rd |only dequer-1.0/dequer/man/popback.Rd |only dequer-1.0/dequer/man/print-deque.Rd |only dequer-1.0/dequer/man/push.Rd |only dequer-1.0/dequer/man/pushback.Rd |only dequer-1.0/dequer/man/rev-deque.Rd |only dequer-1.0/dequer/src/Makevars |only dequer-1.0/dequer/tests/basic.r |only dequer-1.0/dequer/tests/big.r |only dequer-1.0/dequer/tests/combine.r |only dequer-1.0/dequer/tests/pops.r |only dequer-1.0/dequer/tests/push.r |only dequer-1.0/dequer/tests/pushback.r |only dequer-1.0/dequer/tests/rev.r |only dequer-1.0/dequer/tests/split.r |only dequer-2.0-0/dequer/ChangeLog | 11 dequer-2.0-0/dequer/DESCRIPTION | 28 +- dequer-2.0-0/dequer/LICENSE | 2 dequer-2.0-0/dequer/MD5 | 87 ++++--- dequer-2.0-0/dequer/NAMESPACE | 60 ++++ dequer-2.0-0/dequer/R/00_global.r |only dequer-2.0-0/dequer/R/01_constructors.r |only dequer-2.0-0/dequer/R/as.deque.r |only dequer-2.0-0/dequer/R/as.list.r |only dequer-2.0-0/dequer/R/as.queue.r |only dequer-2.0-0/dequer/R/as.stack.r |only dequer-2.0-0/dequer/R/combine.r |only dequer-2.0-0/dequer/R/dequer-package.r | 21 + dequer-2.0-0/dequer/R/length.r |only dequer-2.0-0/dequer/R/peeking.r |only dequer-2.0-0/dequer/R/popping.r |only dequer-2.0-0/dequer/R/print.r |only dequer-2.0-0/dequer/R/pushing.r |only dequer-2.0-0/dequer/R/rev.r |only dequer-2.0-0/dequer/R/sep.r |only dequer-2.0-0/dequer/R/str.r |only dequer-2.0-0/dequer/README.md | 327 +++++++++++++++++---------- dequer-2.0-0/dequer/inst/CITATION |only dequer-2.0-0/dequer/inst/benchmarks/insert.r | 57 +--- dequer-2.0-0/dequer/man/as.deque.Rd | 15 - dequer-2.0-0/dequer/man/as.queue.Rd |only dequer-2.0-0/dequer/man/as.stack.Rd |only dequer-2.0-0/dequer/man/combine.Rd | 28 +- dequer-2.0-0/dequer/man/deque.Rd | 15 - dequer-2.0-0/dequer/man/dequer-package.Rd | 16 - dequer-2.0-0/dequer/man/peeking.Rd |only dequer-2.0-0/dequer/man/popping.Rd |only dequer-2.0-0/dequer/man/printer.Rd |only dequer-2.0-0/dequer/man/pushing.Rd |only dequer-2.0-0/dequer/man/queue.Rd |only dequer-2.0-0/dequer/man/revver.Rd |only dequer-2.0-0/dequer/man/sep.Rd | 27 +- dequer-2.0-0/dequer/man/stack.Rd |only dequer-2.0-0/dequer/src/constructor.c | 14 - dequer-2.0-0/dequer/src/converters.c | 37 --- dequer-2.0-0/dequer/src/deque.c | 7 dequer-2.0-0/dequer/src/deque.h | 12 dequer-2.0-0/dequer/src/utils.c | 80 ++++-- dequer-2.0-0/dequer/tests/basic.R |only dequer-2.0-0/dequer/tests/caster.R |only dequer-2.0-0/dequer/tests/combine.R |only dequer-2.0-0/dequer/tests/dontrun |only dequer-2.0-0/dequer/tests/peeks.R |only dequer-2.0-0/dequer/tests/pops.R |only dequer-2.0-0/dequer/tests/push.R |only dequer-2.0-0/dequer/tests/pushback.R |only dequer-2.0-0/dequer/tests/rev.R |only dequer-2.0-0/dequer/tests/split.R |only 71 files changed, 527 insertions(+), 317 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of vine copula models.
The package includes tools for parameter estimation, model selection,
simulation, goodness-of-fit tests, and visualization. Tools for estimation,
selection and exploratory data analysis of bivariate copula models are also
provided.
Author: Ulf Schepsmeier [aut],
Jakob Stoeber [aut],
Eike Christian Brechmann [aut],
Benedikt Graeler [aut],
Thomas Nagler [aut, cre],
Tobias Erhardt [aut],
Carlos Almeida [ctb],
Aleksey Min [ctb, ths],
Claudia Czado [ctb, ths],
Mathias Hofmann [ctb],
Matthias Killiches [ctb],
Harry Joe [ctb]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between VineCopula versions 2.0.4 dated 2016-08-08 and 2.0.5 dated 2016-09-26
DESCRIPTION | 10 +- MD5 | 46 ++++----- NEWS.md | 23 ++++ R/BiCop.R | 1 R/BiCopEst.R | 83 +++-------------- R/BiCopGofTest.R | 201 +++++++++++++++++++++++++++++------------- R/BiCopHfunc.R | 2 R/BiCopSelect.R | 5 - R/RVineCopSelect.R | 15 ++- R/RVineMLE.R | 17 +-- R/RVineStructureSelect.R | 31 ++++-- R/VineCopula-package.R | 6 - R/preprocessors.R | 4 man/BiCopEst.Rd | 4 man/BiCopGofTest.Rd | 29 +++--- man/BiCopHfunc.Rd | 2 man/BiCopSelect.Rd | 4 man/RVineCopSelect.Rd | 7 + man/RVineStructureSelect.Rd | 5 - man/VineCopula-package.Rd | 6 - src/deriv.c | 56 +++++++---- src/logderiv.c | 61 ++++++++++++ src/tcopuladeriv.c | 69 ++++++++++---- src/tcopuladeriv_new.c | 208 +++++++++++++++++++++++--------------------- 24 files changed, 541 insertions(+), 354 deletions(-)
Title: 3D Animated Interactive Visualizations Using SVG
Description: Creates 3D animated, interactive visualizations in Scalable Vector Graphics (SVG) format that can be viewed in a web browser.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aarolsen@gmail.com>
Diff between svgViewR versions 1.0.1 dated 2015-06-17 and 1.2 dated 2016-09-26
svgViewR-1.0.1/svgViewR/inst/extdata/control_panel.js |only svgViewR-1.0.1/svgViewR/inst/extdata/math.js |only svgViewR-1.0.1/svgViewR/inst/extdata/shape_operations.js |only svgViewR-1.0.1/svgViewR/inst/extdata/shapes.js |only svgViewR-1.0.1/svgViewR/inst/extdata/ui_functions.js |only svgViewR-1.0.1/svgViewR/man/svgviewr.lines.Rd |only svgViewR-1.0.1/svgViewR/man/svgviewr.new.Rd |only svgViewR-1.0.1/svgViewR/man/svgviewr.pathsC.Rd |only svgViewR-1.0.1/svgViewR/man/svgviewr.points.Rd |only svgViewR-1.2/svgViewR/DESCRIPTION | 14 - svgViewR-1.2/svgViewR/MD5 | 65 ++++-- svgViewR-1.2/svgViewR/NAMESPACE | 4 svgViewR-1.2/svgViewR/R/sd_linkr.R |only svgViewR-1.2/svgViewR/R/svg.arrows.R |only svgViewR-1.2/svgViewR/R/svg.box.R |only svgViewR-1.2/svgViewR/R/svg.circles.R |only svgViewR-1.2/svgViewR/R/svg.close.R |only svgViewR-1.2/svgViewR/R/svg.frame.R |only svgViewR-1.2/svgViewR/R/svg.lines.R |only svgViewR-1.2/svgViewR/R/svg.new.R |only svgViewR-1.2/svgViewR/R/svg.open.R |only svgViewR-1.2/svgViewR/R/svg.paths.R |only svgViewR-1.2/svgViewR/R/svg.pathsC.R |only svgViewR-1.2/svgViewR/R/svg.points.R |only svgViewR-1.2/svgViewR/R/svg.pointsC.R |only svgViewR-1.2/svgViewR/R/svg.text.R |only svgViewR-1.2/svgViewR/R/svg_axis_grids.R |only svgViewR-1.2/svgViewR/R/svg_axis_polygons.R |only svgViewR-1.2/svgViewR/R/svg_axis_ticks.R |only svgViewR-1.2/svgViewR/R/svgviewr.circles.R | 2 svgViewR-1.2/svgViewR/R/svgviewr.lines.R | 26 +- svgViewR-1.2/svgViewR/R/svgviewr.new.R | 161 +++++++++++---- svgViewR-1.2/svgViewR/R/svgviewr.paths.R | 10 svgViewR-1.2/svgViewR/R/svgviewr.pathsC.R | 9 svgViewR-1.2/svgViewR/R/svgviewr.points.R | 20 + svgViewR-1.2/svgViewR/R/svgviewr.pointsC.R | 46 +++- svgViewR-1.2/svgViewR/R/svgviewr.text.R | 7 svgViewR-1.2/svgViewR/R/svgviewr.write.R | 56 +++-- svgViewR-1.2/svgViewR/R/svgviewr_ranges.R |only svgViewR-1.2/svgViewR/R/uvector_svg.R |only svgViewR-1.2/svgViewR/R/webColor.R |only svgViewR-1.2/svgViewR/inst/extdata/css |only svgViewR-1.2/svgViewR/inst/extdata/html |only svgViewR-1.2/svgViewR/inst/extdata/js |only svgViewR-1.2/svgViewR/man/svg.lines.Rd |only svgViewR-1.2/svgViewR/man/svg.new.Rd |only svgViewR-1.2/svgViewR/man/svg.pathsC.Rd |only svgViewR-1.2/svgViewR/man/svg.points.Rd |only svgViewR-1.2/svgViewR/man/svgViewR-package.Rd | 28 ++ 49 files changed, 324 insertions(+), 124 deletions(-)
Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other
'dplyr' inspired syntactic style when calculating summary statistics on survey
data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>
Diff between srvyr versions 0.1.2 dated 2016-06-28 and 0.2.0 dated 2016-09-26
srvyr-0.1.2/srvyr/inst/doc/Intro_to_srvyr.R |only srvyr-0.1.2/srvyr/inst/doc/Intro_to_srvyr.Rmd |only srvyr-0.1.2/srvyr/inst/doc/Intro_to_srvyr.html |only srvyr-0.2.0/srvyr/DESCRIPTION | 13 srvyr-0.2.0/srvyr/MD5 | 66 ++- srvyr-0.2.0/srvyr/NAMESPACE | 8 srvyr-0.2.0/srvyr/NEWS.md | 5 srvyr-0.2.0/srvyr/R/as_survey.r | 10 srvyr-0.2.0/srvyr/R/as_survey_design.r | 46 +- srvyr-0.2.0/srvyr/R/as_survey_rep.r | 45 +- srvyr-0.2.0/srvyr/R/as_survey_twophase.r | 17 - srvyr-0.2.0/srvyr/R/manip.r | 58 --- srvyr-0.2.0/srvyr/R/subset_svy_vars.R |only srvyr-0.2.0/srvyr/R/summarise.r | 24 + srvyr-0.2.0/srvyr/R/survey_statistics.r | 202 +++++++++--- srvyr-0.2.0/srvyr/R/survey_vars.r | 16 srvyr-0.2.0/srvyr/R/tbl-svy.r | 77 +++- srvyr-0.2.0/srvyr/R/utils-db.R |only srvyr-0.2.0/srvyr/R/utils.r | 44 ++ srvyr-0.2.0/srvyr/README.md | 2 srvyr-0.2.0/srvyr/build/vignette.rds |binary srvyr-0.2.0/srvyr/inst/doc/srvyr-database.R |only srvyr-0.2.0/srvyr/inst/doc/srvyr-database.Rmd |only srvyr-0.2.0/srvyr/inst/doc/srvyr-database.html |only srvyr-0.2.0/srvyr/inst/doc/srvyr-vs-survey.R | 21 + srvyr-0.2.0/srvyr/inst/doc/srvyr-vs-survey.Rmd | 84 +++- srvyr-0.2.0/srvyr/inst/doc/srvyr-vs-survey.html | 191 ++++++----- srvyr-0.2.0/srvyr/man/as_survey.Rd | 11 srvyr-0.2.0/srvyr/man/as_survey_design.Rd | 18 - srvyr-0.2.0/srvyr/man/as_survey_rep.Rd | 19 + srvyr-0.2.0/srvyr/man/as_survey_twophase.Rd | 6 srvyr-0.2.0/srvyr/man/as_tibble.Rd |only srvyr-0.2.0/srvyr/man/survey_quantile.Rd | 7 srvyr-0.2.0/srvyr/tests/testthat/test_database.R |only srvyr-0.2.0/srvyr/tests/testthat/test_survey_proportion.R | 1 srvyr-0.2.0/srvyr/tests/testthat/test_survey_statistics.r | 30 + srvyr-0.2.0/srvyr/vignettes/acs_m.RData |only srvyr-0.2.0/srvyr/vignettes/ignore/database.R |only srvyr-0.2.0/srvyr/vignettes/ignore/my_db.sqlite3 |only srvyr-0.2.0/srvyr/vignettes/ignore/srvyr-database-speed.Rmd |only srvyr-0.2.0/srvyr/vignettes/save_acs_data.R |only srvyr-0.2.0/srvyr/vignettes/srvyr-database.Rmd |only 42 files changed, 722 insertions(+), 299 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models and mixed effects models. However, some of the functions
also deal with other statistical measures, like Cronbach's Alpha,
Cramer's V, Phi etc.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.4.0 dated 2016-08-26 and 0.5.0 dated 2016-09-26
DESCRIPTION | 16 - MD5 | 82 ++++---- NAMESPACE | 229 ++++++++++++----------- NEWS | 89 +++++---- NEWS.md | 52 ++--- R/S3-methods.R | 96 ++++++++-- R/boot_ci.R | 63 ++++-- R/bootstrap.R | 20 +- R/cv.R | 6 R/gof.R | 2 R/helpfunctions.R | 61 +++--- R/icc.R | 45 +++- R/merMod_p.R | 192 ++++++++++++-------- R/mic.R | 145 +++++++-------- R/mwu.R | 268 ++++++++++++---------------- R/overdisp.R | 190 +++++++++---------- R/pseudo_r2.R | 468 ++++++++++++++++++++++++++----------------------- R/reliab_test.R | 2 R/rmse.R | 6 R/samplesize_lme.R | 231 ++++++++++++++---------- R/se.R | 259 ++++++++++++++++++--------- R/std.R |only R/std_b.R | 102 ++++------ R/weight.R | 8 README.md | 84 ++++---- build/partial.rdb |binary man/boot_ci.Rd | 49 ++++- man/bootstrap.Rd | 11 - man/chisq_gof.Rd | 2 man/cv.Rd | 6 man/deff.Rd | 11 - man/get_model_pval.Rd |only man/icc.Rd | 28 ++ man/merMod_p.Rd | 8 man/mic.Rd | 3 man/overdisp.Rd | 2 man/r2.Rd | 66 ++++-- man/rmse.Rd | 6 man/se.Rd | 39 +++- man/se_ybar.Rd |only man/sjstats-package.Rd | 4 man/smpsize_lmm.Rd | 4 man/std.Rd |only man/std_beta.Rd | 34 +-- 44 files changed, 1726 insertions(+), 1263 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help safely and efficiently organize Monte Carlo simulations in R.
The package controls the structure and back-end of Monte Carlo simulations
by utilizing a general generate-analyse-summarise strategy. The functions provided control
common simulation issues such as re-simulating non-convergent results, support parallel
back-end and MPI distributed computations, save and restore temporary files,
aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 1.2 dated 2016-09-09 and 1.3 dated 2016-09-26
DESCRIPTION | 8 +++---- MD5 | 28 ++++++++++++------------ NAMESPACE | 1 R/Attach.R | 10 +++++++- R/SimDesign.R | 3 +- R/SimFunctions.R | 28 ++++++++++++++---------- R/analysis.R | 57 +++++++++++++++++++++++++++++++++++--------------- R/runSimulation.R | 37 +++++++++++++++++++++----------- R/summary_functions.R | 43 +++++++++++++++++++++++++++++++++++-- R/util.R | 33 ++++++++++++++++++++++++++++ build/vignette.rds |binary man/Attach.Rd | 6 ++++- man/ECR.Rd | 22 +++++++++++++++++-- man/SimFunctions.Rd | 18 +++++++-------- man/runSimulation.Rd | 13 +++++++++-- 15 files changed, 229 insertions(+), 78 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between RODBC versions 1.3-13 dated 2016-04-14 and 1.3-14 dated 2016-09-26
ChangeLog | 8 DESCRIPTION | 10 MD5 | 18 build/vignette.rds |binary configure | 6396 ++++++++++++++++++++++++++-------------------------- configure.ac | 10 inst/doc/RODBC.Rnw | 81 inst/doc/RODBC.pdf |binary src/RODBC.c | 4 vignettes/RODBC.Rnw | 81 10 files changed, 3369 insertions(+), 3239 deletions(-)
Title: Access WHO Global Health Observatory Data from R
Description: Access WHO Global Health Observatory
data from R via the Athena web service,
an application program interface providing
a simple query interface to the World
Health Organization's data and statistics content.
Author: Antoine Filipovic-Pierucci [aut,cre]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>
Diff between rgho versions 0.2.1 dated 2016-09-08 and 0.2.2 dated 2016-09-26
DESCRIPTION | 10 ++-- MD5 | 20 ++++----- NAMESPACE | 1 NEWS.md | 8 +++ R/rgho.R | 1 inst/doc/a-intro.html | 90 +++++++++++++++++++++--------------------- inst/doc/b-dimensions.html | 4 - inst/doc/c-codes-gho.html | 62 ++++++++++++++++++++-------- inst/doc/d-codes-country.html | 4 - inst/doc/e-details.html | 4 - tests/testthat/test-filter.R | 18 -------- 11 files changed, 118 insertions(+), 104 deletions(-)
Title: Read-Write Support for 'NumPy' Files via 'Rcpp'
Description: The 'cnpy' library written by Carl Rogers provides read and write
facilities for files created with (or for) the 'NumPy' extension for 'Python'.
Vectors and matrices of numeric types can be read or written to and from
files as well as compressed files. Support for integer files is available if
the package has been built with -std=c++11 which is the default starting
with release 0.2.3 following the release of R 3.1.0, and available on all
platforms following the release of R 3.3.0 with the updated 'Rtools'.
Author: Dirk Eddelbuettel and Wush Wu
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCNPy versions 0.2.5 dated 2016-08-26 and 0.2.6 dated 2016-09-26
ChangeLog | 24 +++++++++++++ DESCRIPTION | 8 ++-- MD5 | 13 ++++--- README.md | 76 ++++++++++++++++++++++++++++++++++++++++++-- inst/CITATION |only inst/NEWS.Rd | 10 +++++ inst/doc/RcppCNPy-intro.pdf |binary man/RcppCNPy-package.Rd | 23 ++++++++++++- 8 files changed, 139 insertions(+), 15 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions where showing the progress is
useful (e.g. bootstrap). The type and style of the
progress bar (with percentages or remaining time)
can be set through options.
Functions can exploit parallel processing resources.
Author: Peter Solymos [aut, cre], Zygmunt Zawadzki [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between pbapply versions 1.2-2 dated 2016-08-26 and 1.3-0 dated 2016-09-26
DESCRIPTION | 11 +++--- MD5 | 28 ++++++++-------- NAMESPACE | 4 +- R/pblapply.R | 70 ++++++++++++++++++++++++++++++++++------ R/pbreplicate.R | 6 +-- R/pbsapply.R | 8 ++-- R/splitpb.R |only R/timerProgressBar.R | 14 +++++--- R/unix/dopb.R | 2 - R/windows/dopb.R | 2 - R/zzz.R | 31 ++++++++++------- man/pbapply.Rd | 83 +++++++++++++++++++++++++++++++++++++++++------- man/pboptions.Rd | 6 ++- man/splitpb.Rd |only man/timerProgressBar.Rd | 6 +-- tests/tests.R | 49 +++++++++++++++------------- 16 files changed, 225 insertions(+), 95 deletions(-)
Title: Fast and Simple MongoDB Client for R
Description: High-performance MongoDB client based on 'libmongoc' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, SSL
encryption and SASL authentication. The vignette gives a brief overview
of the available methods in the package.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.8.1 dated 2016-03-21 and 0.9 dated 2016-09-26
mongolite-0.8.1/mongolite/R/hacks.R |only mongolite-0.8.1/mongolite/src/mongoc/mongoc-rand.c |only mongolite-0.8.1/mongolite/src/onload.c |only mongolite-0.9/mongolite/DESCRIPTION | 16 mongolite-0.9/mongolite/MD5 | 342 +-- mongolite-0.9/mongolite/NAMESPACE | 3 mongolite-0.9/mongolite/NEWS | 11 mongolite-0.9/mongolite/R/bson.R | 5 mongolite-0.9/mongolite/R/loglevel.R |only mongolite-0.9/mongolite/R/mongo.R | 20 mongolite-0.9/mongolite/R/object.R | 93 mongolite-0.9/mongolite/R/stream.R | 20 mongolite-0.9/mongolite/build/vignette.rds |binary mongolite-0.9/mongolite/configure | 14 mongolite-0.9/mongolite/inst/CITATION | 2 mongolite-0.9/mongolite/inst/doc/intro.html | 55 mongolite-0.9/mongolite/man/mongo.Rd | 2 mongolite-0.9/mongolite/man/mongo_log_level.Rd |only mongolite-0.9/mongolite/src/Makevars.in | 24 mongolite-0.9/mongolite/src/Makevars.win | 89 mongolite-0.9/mongolite/src/bson.c | 6 mongolite-0.9/mongolite/src/bson/bcon.c | 29 mongolite-0.9/mongolite/src/bson/bcon.h | 16 mongolite-0.9/mongolite/src/bson/bson-atomic.c | 1 mongolite-0.9/mongolite/src/bson/bson-clock.c | 4 mongolite-0.9/mongolite/src/bson/bson-compat.h | 8 mongolite-0.9/mongolite/src/bson/bson-config.h | 68 mongolite-0.9/mongolite/src/bson/bson-context.c | 12 mongolite-0.9/mongolite/src/bson/bson-decimal128.c |only mongolite-0.9/mongolite/src/bson/bson-decimal128.h |only mongolite-0.9/mongolite/src/bson/bson-error.h | 2 mongolite-0.9/mongolite/src/bson/bson-iter.c | 194 + mongolite-0.9/mongolite/src/bson/bson-iter.h | 42 mongolite-0.9/mongolite/src/bson/bson-json.c | 69 mongolite-0.9/mongolite/src/bson/bson-macros.h | 2 mongolite-0.9/mongolite/src/bson/bson-memory.c | 4 mongolite-0.9/mongolite/src/bson/bson-oid.c | 6 mongolite-0.9/mongolite/src/bson/bson-private.h | 4 mongolite-0.9/mongolite/src/bson/bson-reader.c | 27 mongolite-0.9/mongolite/src/bson/bson-reader.h | 2 mongolite-0.9/mongolite/src/bson/bson-stdint.h | 2 mongolite-0.9/mongolite/src/bson/bson-string.c | 91 mongolite-0.9/mongolite/src/bson/bson-timegm.c | 15 mongolite-0.9/mongolite/src/bson/bson-types.h | 252 +- mongolite-0.9/mongolite/src/bson/bson-value.c | 8 mongolite-0.9/mongolite/src/bson/bson-version.h | 8 mongolite-0.9/mongolite/src/bson/bson.c | 152 + mongolite-0.9/mongolite/src/bson/bson.h | 37 mongolite-0.9/mongolite/src/collection.c | 31 mongolite-0.9/mongolite/src/mongo_log.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-apm-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-apm.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-apm.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-array-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-async-cmd-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-async-cmd.c | 32 mongolite-0.9/mongolite/src/mongoc/mongoc-async-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-b64-private.h | 4 mongolite-0.9/mongolite/src/mongoc/mongoc-b64.c | 3 mongolite-0.9/mongolite/src/mongoc/mongoc-buffer-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-bulk-operation-private.h | 5 mongolite-0.9/mongolite/src/mongoc/mongoc-bulk-operation.c | 84 mongolite-0.9/mongolite/src/mongoc/mongoc-bulk-operation.h | 6 mongolite-0.9/mongolite/src/mongoc/mongoc-client-pool-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-client-pool.c | 133 + mongolite-0.9/mongolite/src/mongoc/mongoc-client-pool.h | 36 mongolite-0.9/mongolite/src/mongoc/mongoc-client-private.h | 31 mongolite-0.9/mongolite/src/mongoc/mongoc-client.c | 614 ++++-- mongolite-0.9/mongolite/src/mongoc/mongoc-client.h | 140 - mongolite-0.9/mongolite/src/mongoc/mongoc-cluster-private.h | 22 mongolite-0.9/mongolite/src/mongoc/mongoc-cluster.c | 485 ++-- mongolite-0.9/mongolite/src/mongoc/mongoc-collection-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-collection.c | 194 + mongolite-0.9/mongolite/src/mongoc/mongoc-config.h | 117 + mongolite-0.9/mongolite/src/mongoc/mongoc-counters-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-counters.c | 14 mongolite-0.9/mongolite/src/mongoc/mongoc-crypto-cng-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-crypto-cng.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-crypto-common-crypto-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-crypto-common-crypto.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-crypto-openssl-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-crypto-openssl.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-crypto-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-crypto.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-cursor-array-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-cursor-array.c | 44 mongolite-0.9/mongolite/src/mongoc/mongoc-cursor-cursorid-private.h | 20 mongolite-0.9/mongolite/src/mongoc/mongoc-cursor-cursorid.c | 118 - mongolite-0.9/mongolite/src/mongoc/mongoc-cursor-private.h | 18 mongolite-0.9/mongolite/src/mongoc/mongoc-cursor-transform-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-cursor.c | 550 ++++- mongolite-0.9/mongolite/src/mongoc/mongoc-cursor.h | 53 mongolite-0.9/mongolite/src/mongoc/mongoc-database-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-database.c | 20 mongolite-0.9/mongolite/src/mongoc/mongoc-errno-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-error.h | 4 mongolite-0.9/mongolite/src/mongoc/mongoc-find-and-modify-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-find-and-modify.c | 22 mongolite-0.9/mongolite/src/mongoc/mongoc-find-and-modify.h | 8 mongolite-0.9/mongolite/src/mongoc/mongoc-gridfs-file-list-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-gridfs-file-page-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-gridfs-file-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-gridfs-file.c | 24 mongolite-0.9/mongolite/src/mongoc/mongoc-gridfs-file.h | 5 mongolite-0.9/mongolite/src/mongoc/mongoc-gridfs-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-gridfs.c | 13 mongolite-0.9/mongolite/src/mongoc/mongoc-host-list-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-init.c | 35 mongolite-0.9/mongolite/src/mongoc/mongoc-linux-distro-scanner-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-linux-distro-scanner.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-list-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-log-private.h | 10 mongolite-0.9/mongolite/src/mongoc/mongoc-log.c | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-log.h | 18 mongolite-0.9/mongolite/src/mongoc/mongoc-matcher-op-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-matcher-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-memcmp-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-metadata-os-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-metadata-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-metadata.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-metadata.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-openssl-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-openssl.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-queue-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-rand-cng.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-rand-common-crypto.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-rand-openssl.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-rand-private.h | 3 mongolite-0.9/mongolite/src/mongoc/mongoc-read-concern-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-read-prefs-private.h | 7 mongolite-0.9/mongolite/src/mongoc/mongoc-read-prefs.c | 56 mongolite-0.9/mongolite/src/mongoc/mongoc-read-prefs.h | 28 mongolite-0.9/mongolite/src/mongoc/mongoc-rpc-private.h | 57 mongolite-0.9/mongolite/src/mongoc/mongoc-rpc.c | 129 - mongolite-0.9/mongolite/src/mongoc/mongoc-sasl-private.h | 6 mongolite-0.9/mongolite/src/mongoc/mongoc-sasl.c | 61 mongolite-0.9/mongolite/src/mongoc/mongoc-scram-private.h | 27 mongolite-0.9/mongolite/src/mongoc/mongoc-scram.c | 126 - mongolite-0.9/mongolite/src/mongoc/mongoc-secure-channel-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-secure-channel.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-secure-transport-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-secure-transport.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-server-description-private.h | 29 mongolite-0.9/mongolite/src/mongoc/mongoc-server-description.c | 307 ++- mongolite-0.9/mongolite/src/mongoc/mongoc-server-description.h | 10 mongolite-0.9/mongolite/src/mongoc/mongoc-server-stream-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-set-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-socket.c | 3 mongolite-0.9/mongolite/src/mongoc/mongoc-ssl-private.h | 23 mongolite-0.9/mongolite/src/mongoc/mongoc-ssl.c | 535 ----- mongolite-0.9/mongolite/src/mongoc/mongoc-ssl.h | 3 mongolite-0.9/mongolite/src/mongoc/mongoc-stream-private.h | 2 mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-openssl-bio-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-openssl-bio.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-openssl-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-openssl.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-openssl.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-secure-channel-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-secure-channel.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-secure-channel.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-secure-transport-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-secure-transport.c |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls-secure-transport.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls.c | 1023 +--------- mongolite-0.9/mongolite/src/mongoc/mongoc-stream-tls.h | 24 mongolite-0.9/mongolite/src/mongoc/mongoc-stream.c | 11 mongolite-0.9/mongolite/src/mongoc/mongoc-stream.h | 1 mongolite-0.9/mongolite/src/mongoc/mongoc-thread-private.h | 4 mongolite-0.9/mongolite/src/mongoc/mongoc-topology-description-private.h | 20 mongolite-0.9/mongolite/src/mongoc/mongoc-topology-description.c | 252 ++ mongolite-0.9/mongolite/src/mongoc/mongoc-topology-private.h | 82 mongolite-0.9/mongolite/src/mongoc/mongoc-topology-scanner-private.h | 20 mongolite-0.9/mongolite/src/mongoc/mongoc-topology-scanner.c | 213 +- mongolite-0.9/mongolite/src/mongoc/mongoc-topology.c | 382 ++- mongolite-0.9/mongolite/src/mongoc/mongoc-trace-private.h |only mongolite-0.9/mongolite/src/mongoc/mongoc-trace.h | 20 mongolite-0.9/mongolite/src/mongoc/mongoc-uri-private.h | 44 mongolite-0.9/mongolite/src/mongoc/mongoc-uri.c | 123 + mongolite-0.9/mongolite/src/mongoc/mongoc-uri.h | 87 mongolite-0.9/mongolite/src/mongoc/mongoc-util-private.h | 5 mongolite-0.9/mongolite/src/mongoc/mongoc-util.c | 32 mongolite-0.9/mongolite/src/mongoc/mongoc-version.h | 8 mongolite-0.9/mongolite/src/mongoc/mongoc-write-command-private.h | 15 mongolite-0.9/mongolite/src/mongoc/mongoc-write-command.c | 515 ++++- mongolite-0.9/mongolite/src/mongoc/mongoc-write-concern-private.h | 12 mongolite-0.9/mongolite/src/mongoc/mongoc-write-concern.c | 134 + mongolite-0.9/mongolite/src/mongoc/mongoc-write-concern.h | 50 mongolite-0.9/mongolite/src/mongoc/mongoc.h | 5 mongolite-0.9/mongolite/src/mongoc/op-reply-header.def |only mongolite-0.9/mongolite/src/reader.c | 2 mongolite-0.9/mongolite/src/utils.c | 4 mongolite-0.9/mongolite/src/yajl/yajl_gen.c | 4 mongolite-0.9/mongolite/src/yajl/yajl_lex.c | 5 mongolite-0.9/mongolite/src/yajl/yajl_tree.c | 4 mongolite-0.9/mongolite/tools/winlibs.R | 4 196 files changed, 5800 insertions(+), 3439 deletions(-)
Title: Moment-Matching Methods for Weighted Sums of Chi-Squared Random
Variables
Description: A collection of moment-matching methods for computing the cumulative distribution function of a positively-weighted sum of chi-squared random variables. Methods include the Satterthwaite-Welch method, Hall-Buckley-Eagleson method, Wood's F method, and the Lindsay-Pilla-Basak method.
Author: Dean Bodenham
Maintainer: Dean Bodenham <deanbodenhambsse@gmail.com>
Diff between momentchi2 versions 0.1.0 dated 2015-02-25 and 0.1.5 dated 2016-09-26
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NAMESPACE | 5 ++++- R/imports.R |only man/hbe.Rd | 2 +- man/lpb4.Rd | 2 +- man/momentchi2.Rd | 2 +- man/sw.Rd | 2 +- man/wf.Rd | 2 +- 9 files changed, 21 insertions(+), 17 deletions(-)
Title: Extract-Transform-Load Framework for Medium Data
Description: A framework for loading medium-sized data from
the Internet to a local or remote relational database management system.
This package itself doesn't do much more than provide a toy example and set up
the method structure. Packages that depend on this package will facilitate the
construction and maintenance of their respective databases.
Author: Ben Baumer [aut, cre],
Carson Sievert [ctb]
Maintainer: Ben Baumer <ben.baumer@gmail.com>
Diff between etl versions 0.3.3 dated 2016-07-27 and 0.3.3.1 dated 2016-09-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/etl.R | 2 +- tests/testthat/test-etl.R | 9 ++++++--- 4 files changed, 13 insertions(+), 10 deletions(-)
Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre],
Mei-Ling Ting Lee [ctb],
Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>
Diff between clusrank versions 0.4-3 dated 2016-09-05 and 0.4-4 dated 2016-09-26
DESCRIPTION | 8 +++--- MD5 | 8 +++--- R/clusWilcox.R | 16 +++++++++++- R/clusranksum.R | 71 ++++++++++++++++++++++++++++---------------------------- R/special.R | 5 +++ 5 files changed, 62 insertions(+), 46 deletions(-)
Title: Lasso Estimation of Conditional Logistic Regression Models for
Matched Case-Control Studies
Description: Fit a sequence of conditional logistic regression models with lasso, for small to large sized samples.
Author: Marius Kwemou <marius.kwemou@gmail.com> and Marta Avalos
Maintainer: Marius Kwemou <marius.kwemou@gmail.com>
Diff between clogitLasso versions 1.0 dated 2016-08-01 and 1.0.1 dated 2016-09-26
DESCRIPTION | 11 - MD5 | 16 +- NAMESPACE | 8 + R/clogitLasso.R | 302 +++++++++++------------------------------------- R/crosval.R |only R/crosval1M.R |only R/cv.clogitLasso.R |only R/plot.clogitLasso.R |only R/regdiff.R |only R/regdiff1M.R |only man/clogitLasso.Rd | 21 +-- man/cv.clogitLasso.Rd |only man/plot.clogitLasso.Rd |only 13 files changed, 107 insertions(+), 251 deletions(-)
Title: Finite Mixture Models and Meta-Analysis Tools - Based on C.A.MAN
Description: Tools for the analysis of finite semiparametric mixtures.
These are useful when data is heterogeneous, e.g. in
pharmacokinetics or meta-analysis. The NPMLE and VEM algorithms
(flexible support size) and EM algorithms (fixed support size)
are provided for univariate and bivariate data.
Author: Peter Schlattmann <peter.schlattmann@mti.uni-jena.de>, Johannes
Hoehne, Maryna Verba
Maintainer: Philipp Doebler <philipp.doebler@googlemail.com>
Diff between CAMAN versions 0.73 dated 2015-09-01 and 0.74 dated 2016-09-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/golubMerge.Rd | 6 ++---- src/methods.cpp | 6 +++--- 4 files changed, 12 insertions(+), 14 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between boral versions 1.0.1 dated 2016-07-25 and 1.1 dated 2016-09-26
DESCRIPTION | 8 MD5 | 34 - R/auxilaryfunctions.R | 1184 +++++++++++------------------------------ R/boral.jags.R | 405 ++++++-------- R/makejagsscriptfunctions.R |only R/unseenfunctions.R |only inst/NEWS.Rd | 45 - man/boral.Rd | 106 ++- man/calc.condlogLik.Rd | 43 - man/calc.logLik.lv0.Rd | 48 - man/calc.marglogLik.Rd | 40 - man/coefsplot.Rd | 7 man/create.life.Rd | 21 man/get.hpdintervals.Rd | 11 man/get.measures.Rd | 26 man/get.more.measures.Rd | 55 + man/lvsplot.Rd | 17 man/make.jagsboralmodel.Rd | 20 man/make.jagsboralnullmodel.Rd | 16 19 files changed, 796 insertions(+), 1290 deletions(-)
Title: Animal Activity Statistics
Description: Provides functions to fit kernel density functions
to animal activity time data; plot activity distributions;
quantify overall levels of activity; statistically compare
activity metrics through bootstrapping; and evaluate variation
in linear variables with time (or other circular variables).
Author: Marcus Rowcliffe <marcus.rowcliffe@ioz.ac.uk>
Maintainer: Marcus Rowcliffe <marcus.rowcliffe@ioz.ac.uk>
Diff between activity versions 1.0 dated 2014-09-29 and 1.1 dated 2016-09-26
activity-1.0/activity/R/activity_code_1_0.r |only activity-1.1/activity/DESCRIPTION | 12 +++-- activity-1.1/activity/MD5 | 42 +++++++++---------- activity-1.1/activity/NAMESPACE | 2 activity-1.1/activity/R/activity_code_1_1.r |only activity-1.1/activity/man/BCIspeed.Rd | 3 - activity-1.1/activity/man/BCItime.Rd | 3 - activity-1.1/activity/man/activity.Rd | 3 - activity-1.1/activity/man/actmod-class.Rd | 3 - activity-1.1/activity/man/bwcalc.Rd | 3 - activity-1.1/activity/man/compareAct.Rd | 3 - activity-1.1/activity/man/compareCkern.Rd | 13 +++-- activity-1.1/activity/man/compareTimes.Rd | 3 - activity-1.1/activity/man/dvmkern.Rd | 11 ++-- activity-1.1/activity/man/fitact.Rd | 3 - activity-1.1/activity/man/fitlincirc.Rd | 3 - activity-1.1/activity/man/lincircKern.Rd | 3 - activity-1.1/activity/man/lincircmod-class.Rd | 3 - activity-1.1/activity/man/plot-actmod-methods.Rd | 16 ++++--- activity-1.1/activity/man/plot-lincircmod-methods.Rd | 5 +- activity-1.1/activity/man/rvmkern.Rd | 21 ++++----- activity-1.1/activity/man/show-actmod-method.Rd | 3 - activity-1.1/activity/man/yfromx.Rd | 3 - 23 files changed, 93 insertions(+), 68 deletions(-)