Title: Tools for Collecting Social Media Data and Generating Networks
for Analysis
Description: A suite of tools for collecting and constructing networks from
social media data. Provides easy-to-use functions for collecting data across
popular platforms (Instagram, Facebook, Twitter, and YouTube) and generating
different types of networks for analysis.
Author: Timothy Graham & Robert Ackland with contribution from Chung-hong Chan
Maintainer: Timothy Graham <timothy.graham3@uq.net.au>
Diff between SocialMediaLab versions 0.19.0 dated 2015-11-26 and 0.20.0 dated 2016-03-30
DESCRIPTION | 15 - MD5 | 92 +++++---- NAMESPACE | 97 ++++++--- R/Authenticate.R |only R/AuthenticateWithFacebookAPI.R | 56 +++++ R/AuthenticateWithInstagramAPI.R | 48 ++++ R/AuthenticateWithTwitterAPI.R | 40 +++ R/AuthenticateWithYoutubeAPI.R | 29 ++ R/Collect.R |only R/CollectDataFacebook.R | 105 +++++++++- R/CollectDataInstagram.R | 113 ++++++++++- R/CollectDataTwitter.R | 85 ++++++++ R/CollectDataYoutube.R | 362 +++++++++++++++++++++++++++++++++++- R/CollectEgoInstagram.R |only R/Create.R |only R/CreateActorNetwork.R | 80 +++++++ R/CreateActorNetwork.list.R | 1 R/CreateActorNetwork.twitter.R | 1 R/CreateActorNetwork.youtube.R | 1 R/CreateBimodalNetwork.R | 84 ++++++++ R/CreateBimodalNetwork.facebook.R | 1 R/CreateBimodalNetwork.instagram.R | 1 R/CreateBimodalNetwork.list.R | 1 R/CreateBimodalNetwork.twitter.R | 1 R/CreateDynamicNetwork.R | 86 ++++++++ R/CreateEgoNetwork.R | 73 +++++++ R/CreateEgoNetworkFromData.R |only R/CreateSemanticNetwork.R | 99 +++++++++ R/CreateSemanticNetwork.list.R | 1 R/CreateSemanticNetwork.twitter.R | 1 R/GetYoutubeVideoIDs.R | 48 ++++ R/SocialMediaLab-package.R |only man/Authenticate.Rd |only man/AuthenticateWithFacebookAPI.Rd | 90 +++++--- man/AuthenticateWithInstagramAPI.Rd | 75 ++++--- man/AuthenticateWithTwitterAPI.Rd | 76 +++---- man/AuthenticateWithYoutubeAPI.Rd | 53 ++--- man/Collect.Rd |only man/CollectDataFacebook.Rd | 131 ++++++++----- man/CollectDataInstagram.Rd | 148 ++++++++------ man/CollectDataTwitter.Rd | 126 +++++++----- man/CollectDataYoutube.Rd | 115 +++++++---- man/CollectEgoInstagram.Rd |only man/Create.Rd |only man/CreateActorNetwork.Rd | 96 ++++++--- man/CreateBimodalNetwork.Rd | 108 ++++++---- man/CreateDynamicNetwork.Rd | 108 ++++++---- man/CreateEgoNetwork.Rd | 122 +++++++----- man/CreateEgoNetworkFromData.Rd |only man/CreateSemanticNetwork.Rd | 136 ++++++++----- man/GetYoutubeVideoIDs.Rd | 56 +++-- man/SaveCredential.Rd |only man/SocialMediaLab-package.Rd | 37 ++- 53 files changed, 2345 insertions(+), 653 deletions(-)
More information about SocialMediaLab at CRAN
Permanent link
Title: Relative Contribution of Effects in a Regression Model
Description: Functions to facilitate inference on the relative importance of predictors in a linear or generalized linear model, and a couple of useful Tcl/Tk widgets.
Author: David Firth with contributions from Heather Turner and John Fox
Maintainer: David Firth <d.firth@warwick.ac.uk>
Diff between relimp versions 1.0-4 dated 2015-02-03 and 1.0-5 dated 2016-03-30
DESCRIPTION | 13 - MD5 | 8 NAMESPACE | 9 R/showData.R | 598 +++++++++++++++++++++++++------------------------------- man/showData.Rd | 4 5 files changed, 290 insertions(+), 342 deletions(-)
Title: Quasi Variances for Factor Effects in Statistical Models
Description: Functions to compute quasi variances and associated measures of approximation error.
Author: David Firth
Maintainer: David Firth <d.firth@warwick.ac.uk>
Diff between qvcalc versions 0.8-9 dated 2015-02-03 and 0.9-0 dated 2016-03-30
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NAMESPACE | 4 ++++ 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Package Management Tool
Description: Tools to more conveniently perform tasks associated with
add-on packages. pacman conveniently wraps library and package
related functions and names them in an intuitive and consistent
fashion. It seeks to combine functionality from lower level
functions which can speed up workflow.
Author: Tyler Rinker [aut, cre, ctb], Dason Kurkiewicz [aut, ctb],
Keith Hughitt [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between pacman versions 0.3.0 dated 2015-02-20 and 0.4.1 dated 2016-03-30
DESCRIPTION | 37 +++-- MD5 | 163 +++++++++++++------------ NAMESPACE | 11 + NEWS | 33 ++++- R/p_author.R | 6 R/p_boot.R |only R/p_citation.R | 6 R/p_cran.R | 4 R/p_data.R | 6 R/p_delete_single.R | 2 R/p_depends.R | 4 R/p_exists.R | 2 R/p_functions.R | 4 R/p_help.R | 8 - R/p_information.R | 2 R/p_install.R | 26 +++- R/p_install_gh.R | 2 R/p_install_version_gh.R |only R/p_install_version_single.R | 2 R/p_install_version_single_gh.R |only R/p_interactive.R | 12 - R/p_load_current_gh.R |only R/p_load_current_single_gh.R |only R/p_loaded.R | 2 R/p_news.R | 2 R/p_old.R |only R/p_path.R | 18 ++ R/p_search_library.R | 2 R/p_unload.R | 4 R/p_update.R | 4 R/p_version.R | 120 ++++++++++++++++++ R/p_vignette.R | 6 R/p_zip.R | 8 - R/utils.R | 12 - README.md | 10 + build/vignette.rds |binary inst/CITATION | 10 - inst/doc/Introduction_to_pacman.R | 54 ++++---- inst/doc/Introduction_to_pacman.Rmd | 4 inst/doc/Introduction_to_pacman.html | 177 +++++++++++++++------------- inst/doc/pacman_functions_quick_reference.R | 14 +- man/p_author.Rd | 2 man/p_base.Rd | 10 - man/p_boot.Rd |only man/p_citation.Rd | 8 - man/p_cran.Rd | 4 man/p_data.Rd | 6 man/p_delete.Rd | 14 +- man/p_depends.Rd | 20 +-- man/p_detectOS.Rd | 2 man/p_exists.Rd | 6 man/p_extract.Rd | 8 - man/p_functions.Rd | 6 man/p_help.Rd | 10 - man/p_information.Rd | 12 - man/p_install.Rd | 8 - man/p_install_gh.Rd | 6 man/p_install_version.Rd | 8 - man/p_install_version_gh.Rd |only man/p_interactive.Rd | 4 man/p_isinstalled.Rd | 2 man/p_library.Rd | 8 - man/p_load.Rd | 22 +-- man/p_load_current_gh.Rd |only man/p_load_gh.Rd | 20 +-- man/p_loaded.Rd | 14 +- man/p_news.Rd | 4 man/p_old.Rd |only man/p_opendir.Rd | 2 man/p_path.Rd | 9 + man/p_search_any.Rd | 12 - man/p_search_library.Rd | 12 - man/p_set_cranrepo.Rd | 2 man/p_temp.Rd | 2 man/p_unload.Rd | 14 +- man/p_unlock.Rd | 14 +- man/p_update.Rd | 10 - man/p_version.Rd | 31 ++++ man/p_vignette.Rd | 16 +- man/print.p_version_diff.Rd |only man/print.search_any.Rd | 2 man/print.wide_table.Rd | 2 tests/testthat/test-p_author.R | 8 - tests/testthat/test-p_install.R | 8 - tests/testthat/test-p_install_gh.R | 2 tests/testthat/test-p_install_version.R | 16 +- tests/testthat/test-p_version.R | 2 vignettes/Introduction_to_pacman.Rmd | 4 88 files changed, 708 insertions(+), 441 deletions(-)
Title: Tools for Analyzing Mixed Effect Regression Models
Description: Provides methods for extracting results from mixed-effect model
objects fit with the 'lme4' package. Allows construction of prediction intervals
efficiently from large scale linear and generalized linear mixed-effects models.
Author: Jared E. Knowles [aut, cre],
Carl Frederick [aut]
Maintainer: Jared E. Knowles <jknowles@gmail.com>
Diff between merTools versions 0.2.0 dated 2016-02-19 and 0.2.1 dated 2016-03-30
DESCRIPTION | 12 +++---- MD5 | 10 +++--- NEWS.md | 4 ++ README.md | 60 ++++++++++++++++++------------------ inst/doc/Using_predictInterval.html | 43 ++++++++++++------------- inst/doc/merToolsIntro.html | 21 ++++++------ 6 files changed, 76 insertions(+), 74 deletions(-)
Title: Test of Stationarity and Localized Autocovariance
Description: Provides test of second-order stationarity for time
series (for dyadic and arbitrary-n length data). Provides
localized autocovariance, with confidence intervals,
for locally stationary (nonstationary) time series.
Author: Guy Nason [aut, cre]
Maintainer: Guy Nason <g.p.nason@bristol.ac.uk>
Diff between locits versions 1.4 dated 2013-10-18 and 1.7.1 dated 2016-03-30
locits-1.4/locits/R/locits-internal.R |only locits-1.7.1/locits/DESCRIPTION | 17 +++-- locits-1.7.1/locits/MD5 | 45 ++++++++++----- locits-1.7.1/locits/NAMESPACE | 44 ++++++++++++++ locits-1.7.1/locits/R/AutoBestBW.R | 2 locits-1.7.1/locits/R/EstBetaCov.R |only locits-1.7.1/locits/R/StoreStatistics.R | 2 locits-1.7.1/locits/R/hwt.R |only locits-1.7.1/locits/R/hwtos.R |only locits-1.7.1/locits/R/hwtos2.R | 8 ++ locits-1.7.1/locits/R/plot.hwtANYN.R |only locits-1.7.1/locits/R/plot.tosANYN.R |only locits-1.7.1/locits/R/print.hwtANYN.R |only locits-1.7.1/locits/R/print.tosANYN.R |only locits-1.7.1/locits/R/summary.hwtANYN.R |only locits-1.7.1/locits/R/summary.tosANYN.R |only locits-1.7.1/locits/R/zeropad.R |only locits-1.7.1/locits/inst/CHANGES | 40 +++++++++++++ locits-1.7.1/locits/man/AutoBestBW.Rd | 2 locits-1.7.1/locits/man/EstBetaCov.Rd |only locits-1.7.1/locits/man/hwt.Rd |only locits-1.7.1/locits/man/hwtos.Rd |only locits-1.7.1/locits/man/hwtos2.Rd | 5 + locits-1.7.1/locits/man/locits-package.Rd | 9 ++- locits-1.7.1/locits/man/plot.hwtANYN.Rd |only locits-1.7.1/locits/man/plot.tos.Rd | 15 ++--- locits-1.7.1/locits/man/plot.tosANYN.Rd |only locits-1.7.1/locits/man/print.hwtANYN.Rd |only locits-1.7.1/locits/man/print.tosANYN.Rd |only locits-1.7.1/locits/man/summary.hwtANYN.Rd |only locits-1.7.1/locits/man/summary.tos.Rd | 3 - locits-1.7.1/locits/man/summary.tosANYN.Rd |only locits-1.7.1/locits/man/zeropad.Rd |only locits-1.7.1/locits/src/CPkPlj.c | 86 ++++++++++++++++++++++++----- 34 files changed, 228 insertions(+), 50 deletions(-)
Title: Various R Programming Tools for Plotting Data
Description: Various R programming tools for plotting data, including:
- calculating and plotting locally smoothed summary function as
('bandplot', 'wapply'),
- enhanced versions of standard plots ('barplot2', 'boxplot2',
'heatmap.2', 'smartlegend'),
- manipulating colors ('col2hex', 'colorpanel', 'redgreen',
'greenred', 'bluered', 'redblue', 'rich.colors'),
- calculating and plotting two-dimensional data summaries ('ci2d',
'hist2d'),
- enhanced regression diagnostic plots ('lmplot2', 'residplot'),
- formula-enabled interface to 'stats::lowess' function ('lowess'),
- displaying textual data in plots ('textplot', 'sinkplot'),
- plotting a matrix where each cell contains a dot whose size
reflects the relative magnitude of the elements ('balloonplot'),
- plotting "Venn" diagrams ('venn'),
- displaying Open-Office style plots ('ooplot'),
- plotting multiple data on same region, with separate axes
('overplot'),
- plotting means and confidence intervals ('plotCI', 'plotmeans'),
- spacing points in an x-y plot so they don't overlap ('space').
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
Venables
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gplots versions 3.0.0 dated 2016-03-28 and 3.0.1 dated 2016-03-30
ChangeLog | 25 +++++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 13 +++++++++++++ R/plot.lowess.R | 7 ++++--- inst/ChangeLog | 25 +++++++++++++++++++++++++ inst/NEWS | 13 +++++++++++++ inst/doc/venn.pdf |binary man/heatmap.2.Rd | 2 +- man/lowess.Rd | 24 +++++++++++++++++++++++- 10 files changed, 117 insertions(+), 18 deletions(-)
Title: Visualization of Functional Analysis Data
Description: Implementation of multilayered visualizations for enhanced
graphical representation of functional analysis data. It combines and integrates
omics data derived from expression and functional annotation enrichment
analyses. Its plotting functions have been developed with an hierarchical
structure in mind: starting from a general overview to identify the most
enriched categories (modified bar plot, bubble plot) to a more detailed one
displaying different types of relevant information for the molecules in a given
set of categories (circle plot, chord plot, cluster plot, Venn diagram, heatmap).
Author: Wencke Walter [aut, cre],
Fatima Sanchez-Cabo [aut]
Maintainer: Wencke Walter <wencke.walter@arcor.de>
Diff between GOplot versions 1.0.1 dated 2015-07-16 and 1.0.2 dated 2016-03-30
GOplot-1.0.1/GOplot/man/bezier.Rd |only GOplot-1.0.1/GOplot/man/circleFun.Rd |only GOplot-1.0.1/GOplot/man/draw_table.Rd |only GOplot-1.0.1/GOplot/man/get_overlap.Rd |only GOplot-1.0.1/GOplot/man/get_overlap2.Rd |only GOplot-1.0.1/GOplot/man/theme_blank.Rd |only GOplot-1.0.2/GOplot/DESCRIPTION | 40 +-- GOplot-1.0.2/GOplot/MD5 | 63 ++--- GOplot-1.0.2/GOplot/NAMESPACE | 4 GOplot-1.0.2/GOplot/NEWS.md |only GOplot-1.0.2/GOplot/R/GOCluster.R | 69 +++-- GOplot-1.0.2/GOplot/R/GOCore.R | 276 ++++++++++------------ GOplot-1.0.2/GOplot/R/GOHeat.R |only GOplot-1.0.2/GOplot/R/GOVenn.R | 183 -------------- GOplot-1.0.2/GOplot/R/Helper.R |only GOplot-1.0.2/GOplot/README.md | 4 GOplot-1.0.2/GOplot/build/vignette.rds |binary GOplot-1.0.2/GOplot/inst/CITATION |only GOplot-1.0.2/GOplot/inst/doc/GOplot_vignette.R | 30 ++ GOplot-1.0.2/GOplot/inst/doc/GOplot_vignette.Rmd | 78 ++++-- GOplot-1.0.2/GOplot/inst/doc/GOplot_vignette.html | 71 +++-- GOplot-1.0.2/GOplot/man/EC.Rd | 2 GOplot-1.0.2/GOplot/man/GOBar.Rd | 22 - GOplot-1.0.2/GOplot/man/GOBubble.Rd | 43 +-- GOplot-1.0.2/GOplot/man/GOChord.Rd | 64 +++-- GOplot-1.0.2/GOplot/man/GOCircle.Rd | 53 ++-- GOplot-1.0.2/GOplot/man/GOCluster.Rd | 28 +- GOplot-1.0.2/GOplot/man/GOHeat.Rd |only GOplot-1.0.2/GOplot/man/GOVenn.Rd | 32 +- GOplot-1.0.2/GOplot/man/chord_dat.Rd | 41 --- GOplot-1.0.2/GOplot/man/circle_dat.Rd | 28 +- GOplot-1.0.2/GOplot/man/reduce_overlap.Rd |only GOplot-1.0.2/GOplot/vignettes/GOBar.png |binary GOplot-1.0.2/GOplot/vignettes/GOBubble1.png |binary GOplot-1.0.2/GOplot/vignettes/GOBubble2.png |binary GOplot-1.0.2/GOplot/vignettes/GOBubble3.png |only GOplot-1.0.2/GOplot/vignettes/GOBubble4.png |only GOplot-1.0.2/GOplot/vignettes/GOHeat_lfc.png |only GOplot-1.0.2/GOplot/vignettes/GOHeat_nolfc.png |only GOplot-1.0.2/GOplot/vignettes/GOplot_vignette.Rmd | 76 ++++-- GOplot-1.0.2/GOplot/vignettes/Titel.png |only 41 files changed, 576 insertions(+), 631 deletions(-)
Title: Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear Mixed Models (AIREML Algorithm),
Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalization trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.4 dated 2016-02-10 and 1.4.5 dated 2016-03-30
gaston-1.4.5/gaston/DESCRIPTION | 8 - gaston-1.4.5/gaston/MD5 | 47 ++++++----- gaston-1.4.5/gaston/NAMESPACE | 8 + gaston-1.4.5/gaston/NEWS | 6 + gaston-1.4.5/gaston/R/bm.r | 4 gaston-1.4.5/gaston/R/bm_genomic_sex.r |only gaston-1.4.5/gaston/R/bm_stats.r | 34 +++----- gaston-1.4.5/gaston/inst/doc/gaston.R | 110 ++++++++++++++------------- gaston-1.4.5/gaston/inst/doc/gaston.Rnw | 37 +++++++-- gaston-1.4.5/gaston/inst/doc/gaston.pdf |binary gaston-1.4.5/gaston/man/set.genomic.sex.Rd |only gaston-1.4.5/gaston/man/set.hwe.Rd | 4 gaston-1.4.5/gaston/man/set.stats.Rd | 2 gaston-1.4.5/gaston/src/ai-reml-1k-covar.h | 66 +++++++++++++--- gaston-1.4.5/gaston/src/ai-reml-1k.h | 67 +++++++++++++--- gaston-1.4.5/gaston/src/ai-reml-nk-covar.h | 70 +++++++++++++---- gaston-1.4.5/gaston/src/ai-reml-nk.h | 78 ++++++++++++++----- gaston-1.4.5/gaston/src/any.h |only gaston-1.4.5/gaston/src/export-aireml-nk.cpp | 1 gaston-1.4.5/gaston/src/m4_kinship.cpp | 65 +++++++++------ gaston-1.4.5/gaston/src/m4_kinship_p.cpp | 77 ++++++++++-------- gaston-1.4.5/gaston/vignettes/gaston-028.pdf |only gaston-1.4.5/gaston/vignettes/gaston-032.pdf |only gaston-1.4.5/gaston/vignettes/gaston-039.pdf |only gaston-1.4.5/gaston/vignettes/gaston-041.pdf |only gaston-1.4.5/gaston/vignettes/gaston-043.pdf |only gaston-1.4.5/gaston/vignettes/gaston-047.pdf |only gaston-1.4.5/gaston/vignettes/gaston-053.pdf |only gaston-1.4.5/gaston/vignettes/gaston.Rnw | 37 +++++++-- gaston-1.4/gaston/vignettes/lapin |only 30 files changed, 486 insertions(+), 235 deletions(-)
Title: Direct, Chain and Average Equating Coefficients with Standard
Errors Using IRT Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items. Test scoring can be performed by true score equating and observed score equating methods.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>
Diff between equateIRT versions 1.2-3 dated 2016-02-04 and 2.0 dated 2016-03-30
DESCRIPTION | 10 MD5 | 27 - NAMESPACE | 3 R/functions.r | 838 ++++++++++++++++++++++++++++++++++++++-------- build/vignette.rds |binary inst/NEWS | 10 inst/doc/equateIRT.pdf |binary man/bisectorec.Rd | 26 - man/convert.Rd | 2 man/eqc.Rd | 8 man/equateIRT-internal.Rd | 9 man/equateIRT-package.Rd | 18 man/itm.Rd | 27 + man/score.Rd |only man/summary.meqc.Rd | 2 15 files changed, 794 insertions(+), 186 deletions(-)
Title: Network Reconstruction and Changepoint Detection
Description: Package EDISON (Estimation of Directed Interactions from
Sequences Of Non-homogeneous gene expression) runs an MCMC
simulation to reconstruct networks from time series data, using
a non-homogeneous, time-varying dynamic Bayesian network.
Networks segments and changepoints are inferred concurrently,
and information sharing priors provide a reduction of the
inference uncertainty.
Author: Frank Dondelinger, Sophie Lebre
Maintainer: Frank Dondelinger <fdondelinger.work@gmail.com>
Diff between EDISON versions 1.1 dated 2014-09-14 and 1.1.1 dated 2016-03-30
DESCRIPTION | 9 + MD5 | 127 ++++++++++++++-------------- NAMESPACE | 3 NEWS |only R/EDISON-package.R | 2 R/dinvgamma.R | 6 - man/AcceptableMove.Rd | 5 - man/BinoHyperMove.Rd | 3 man/BinoHyperRatio.Rd | 3 man/CalculateChanges.Rd | 3 man/CalculateLikelihoodRatio.Rd | 3 man/CalculatePriorRatio.Rd | 3 man/CollectNetworkInfo.Rd | 3 man/EDISON-package.Rd | 8 + man/EDISON.run.Rd | 15 +-- man/ExpHyperMove.Rd | 3 man/ExpHyperRatioTarget.Rd | 3 man/HyperParms.Rd | 3 man/HyperparameterMove.Rd | 3 man/NetworkProbBino.Rd | 3 man/NetworkProbExp.Rd | 3 man/NetworkRatioBino.Rd | 3 man/NetworkRatioExp.Rd | 3 man/PriorRatioPoisson.Rd | 3 man/ProposeDiscrete.Rd | 5 - man/addProposalNetworkInfo.Rd | 9 + man/bp.computeAlpha.Rd | 3 man/buildXY.Rd | 3 man/calculateCPPGlobal.Rd | 3 man/calculateCPProbabilities.Rd | 5 - man/calculateEdgeProbabilities.Rd | 7 + man/calculateEdgeProbabilitiesSegs.Rd | 3 man/calculateEdgeProbabilitiesTimePoints.Rd | 3 man/computePx.Rd | 3 man/computeRho4.Rd | 3 man/convert_nets.Rd | 3 man/cp.birth.Rd | 3 man/cp.death.Rd | 3 man/cp.shift.Rd | 3 man/defaultOptions.Rd | 7 + man/dinvgamma.Rd | 7 + man/fix_eigenvalues.Rd | 3 man/generateNetwork.Rd | 7 + man/init.Rd | 3 man/main.Rd | 3 man/make_structure_move.Rd | 7 - man/output.Rd | 3 man/phase.update.Rd | 3 man/proposalTuning.Rd | 3 man/proposeContinuous.Rd | 5 - man/psrf.Rd | 8 + man/psrf_check.Rd | 3 man/psrf_check_hyper.Rd | 3 man/readDataTS.Rd | 3 man/rinvgamma.Rd | 7 + man/runDBN.Rd | 7 - man/sampleBinit.Rd | 3 man/sampleBxy.Rd | 3 man/sampleDelta2.Rd | 3 man/sampleK.Rd | 3 man/sampleParms.Rd | 3 man/sampleSig2.Rd | 3 man/simulateNetwork.Rd | 13 +- man/updateSigMulti.Rd | 3 man/updateSigSolo.Rd | 3 65 files changed, 243 insertions(+), 155 deletions(-)
Title: Reading EDF(+) and BDF(+) Files
Description: Reads European Data Format files EDF and EDF+, see http://www.edfplus.info,
BioSemi Data Format files BDF, see http://www.biosemi.com/faq/file_format.htm,
and BDF+ files, see http://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html.
The files are read in two steps: first the header is read
and then the signals (using the header object as a parameter).
Author: Jan Vis [aut, cre]
Maintainer: Jan Vis <jan@visconsultancy.eu>
Diff between edfReader versions 1.0.0 dated 2016-02-07 and 1.1.0 dated 2016-03-30
edfReader-1.0.0/edfReader/inst/extdata/bdfPlusD.bdf |only edfReader-1.0.0/edfReader/inst/extdata/bdfPlusD_annotations.txt |only edfReader-1.0.0/edfReader/inst/extdata/bdfPlusD_data.txt |only edfReader-1.0.0/edfReader/inst/extdata/bdfPlusD_header.txt |only edfReader-1.0.0/edfReader/inst/extdata/bdfPlusD_signals.txt |only edfReader-1.0.0/edfReader/tests/testthat/testSampleFiles.R |only edfReader-1.1.0/edfReader/DESCRIPTION | 9 edfReader-1.1.0/edfReader/MD5 | 49 edfReader-1.1.0/edfReader/NAMESPACE | 1 edfReader-1.1.0/edfReader/NEWS.md |only edfReader-1.1.0/edfReader/R/edfReader.R | 9 edfReader-1.1.0/edfReader/R/readHeaderFunctions.R | 61 edfReader-1.1.0/edfReader/R/readSignalFunctions.R | 492 ++++-- edfReader-1.1.0/edfReader/R/s3functions.R | 418 +++-- edfReader-1.1.0/edfReader/build/vignette.rds |binary edfReader-1.1.0/edfReader/inst/doc/edfReaderVignette.R | 57 edfReader-1.1.0/edfReader/inst/doc/edfReaderVignette.Rmd | 275 ++- edfReader-1.1.0/edfReader/inst/doc/edfReaderVignette.html | 720 +++++----- edfReader-1.1.0/edfReader/inst/extdata/bdfPlusC.bdf |only edfReader-1.1.0/edfReader/inst/extdata/bdfPlusC_annotations.txt |only edfReader-1.1.0/edfReader/inst/extdata/bdfPlusC_data.txt |only edfReader-1.1.0/edfReader/inst/extdata/bdfPlusC_header.txt |only edfReader-1.1.0/edfReader/inst/extdata/bdfPlusC_signals.txt |only edfReader-1.1.0/edfReader/inst/extdata/edfAnnonC.edf |only edfReader-1.1.0/edfReader/inst/extdata/edfAnnonC_annotations.txt |only edfReader-1.1.0/edfReader/inst/extdata/edfAnnonC_header.txt |only edfReader-1.1.0/edfReader/inst/extdata/edfAnnonC_signals.txt |only edfReader-1.1.0/edfReader/inst/extdata/edfPlusD.edf |only edfReader-1.1.0/edfReader/man/edfReader.Rd | 6 edfReader-1.1.0/edfReader/man/readEdfSignals.Rd | 14 edfReader-1.1.0/edfReader/tests/testthat/testCSampleFiles.R |only edfReader-1.1.0/edfReader/tests/testthat/testDSampleFiles.R |only edfReader-1.1.0/edfReader/tests/testthat/testFromTill.R | 302 ++-- edfReader-1.1.0/edfReader/tests/testthat/testReadEdfSignalsParams.R | 132 + edfReader-1.1.0/edfReader/vignettes/edfReaderVignette.Rmd | 275 ++- 35 files changed, 1722 insertions(+), 1098 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.5.1 dated 2016-03-25 and 3.5.2 dated 2016-03-30
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS | 5 +++++ R/startup_messages.R | 2 +- inst/doc/a-introduction.html | 16 +++++++++++++++- inst/doc/h-creating-your-own-maps.html | 2 +- 6 files changed, 33 insertions(+), 14 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre],
Yves Rosseel [aut]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.1-2 dated 2016-01-27 and 0.1-3 dated 2016-03-30
DESCRIPTION | 8 ++-- MD5 | 14 +++---- NEWS | 9 ++++ R/blav_object_methods.R | 2 + R/blav_utils.R | 34 +++++++++++++++++ R/blavaan.R | 68 ++++++++++++++++++++++++---------- R/lav_export_jags.R | 95 ++++++++++++++++++++++++++++++++++-------------- R/set_priors.R | 2 + 8 files changed, 174 insertions(+), 58 deletions(-)
Title: Estimation and Testing of Average Hazard Ratios
Description: Methods for estimation of multivariate average hazard ratios as
defined by Kalbfleisch and Prentice. The underlying survival functions of the
event of interest in each group can be estimated using either the (weighted)
Kaplan-Meier estimator or the Aalen-Johansen estimator for the transition
probabilities in Markov multi-state models. Right-censored and left-truncated
data is supported. Moreover, the difference in restricted mean survival can be
estimated.
Author: Matthias Brueckner <mwb@math.uni-bremen.de>
Maintainer: Matthias Brueckner <mwb@math.uni-bremen.de>
Diff between AHR versions 1.3 dated 2015-10-30 and 1.4 dated 2016-03-30
AHR-1.3/AHR/inst |only AHR-1.4/AHR/DESCRIPTION | 17 ++++++-- AHR-1.4/AHR/MD5 | 53 ++++++++++++++------------- AHR-1.4/AHR/NAMESPACE | 2 - AHR-1.4/AHR/NEWS.md |only AHR-1.4/AHR/R/ahr.R | 56 +++++++++++++++------------- AHR-1.4/AHR/R/quantiles.R | 40 ++++++++++++-------- AHR-1.4/AHR/R/rmean.R | 34 ++++++++++------- AHR-1.4/AHR/R/wkm.R | 64 ++++++++++++++++++++------------- AHR-1.4/AHR/README.md |only AHR-1.4/AHR/man/AHR.Rd | 5 +- AHR-1.4/AHR/man/ahrAJ.Rd | 2 - AHR-1.4/AHR/man/ahrKM.Rd | 2 - AHR-1.4/AHR/man/ahrWKM.Rd | 11 +++-- AHR-1.4/AHR/man/aj.Rd | 4 +- AHR-1.4/AHR/man/avgHR.Rd | 2 - AHR-1.4/AHR/man/fastkm.Rd | 2 - AHR-1.4/AHR/man/print.ahr.Rd | 2 - AHR-1.4/AHR/man/print.rmd.Rd | 2 - AHR-1.4/AHR/man/print.survQuantile.Rd | 2 - AHR-1.4/AHR/man/rmeanDiff.Rd | 6 ++- AHR-1.4/AHR/man/rmeanDiff.ahr.Rd | 2 - AHR-1.4/AHR/man/wkm.Rd | 17 ++++---- AHR-1.4/AHR/man/wkmCompareQuantiles.Rd | 2 - AHR-1.4/AHR/man/wkmQuantile.Rd | 6 +-- AHR-1.4/AHR/tests |only 26 files changed, 191 insertions(+), 142 deletions(-)
Title: Improved False Positive Control of Gene-Permuting GSEA with
Absolute Filtering
Description: Gene-set enrichment analysis (GSEA) is popularly used to assess the enrichment of differential signal in a pre-defined gene-set without using a cutoff threshold for differential expression. The significance of enrichment is evaluated through sample- or gene-permutation method. Although the sample-permutation approach is highly recommended due to its good false positive control, we must use gene-permuting method if the number of samples is small. However, such gene-permuting GSEA (or preranked GSEA) generates a lot of false positive gene-sets as the inter-gene correlation in each gene set increases. These false positives can be successfully reduced by filtering with the one-tailed absolute GSEA results. This package provides a function that performs gene-permuting GSEA calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.
Author: Sora Yoon <yoonsora@unist.ac.kr>
Maintainer: Sora Yoon <yoonsora@unist.ac.kr>
Diff between AbsFilterGSEA versions 1.0 dated 2016-03-16 and 1.2 dated 2016-03-30
DESCRIPTION | 10 ++--- MD5 | 18 +++++----- NAMESPACE | 18 ++++++---- R/GenePermGSEA.R | 85 ++++++++++++++++++++++++++++++++++++++++---------- R/RcppExports.R | 22 ++++++------ data/example.rda |binary man/GenePermGSEA.Rd | 31 ++++++++++-------- man/example.Rd | 10 +---- src/AbsFilterGSEA.cpp | 7 ++++ vignettes |only 10 files changed, 133 insertions(+), 68 deletions(-)
Title: A Boosted Tweedie Compound Poisson Model
Description: A boosted Tweedie compound Poisson model using the gradient boosting. It is capable of fitting a flexible nonlinear Tweedie compound Poisson model (or a gamma model) and capturing interactions among predictors.
Author: Yi Yang <yi.yang6@mcgill.ca>, Wei Qian <wxqsma@rit.edu>, Hui Zou <hzou@stat.umn.edu>
Maintainer: Yi Yang <yi.yang6@mcgill.ca>
Diff between TDboost versions 1.1 dated 2015-03-15 and 1.2 dated 2016-03-30
ChangeLog | 12 ++++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 10 ++++++++++ R/TDboost.R | 5 +++-- man/TDboost.Rd | 6 ++---- man/TDboost.object.Rd | 2 +- man/TDboost.perf.Rd | 9 ++------- man/plot.TDboost.Rd | 4 +--- man/predict.TDboost.Rd | 9 +++++++-- man/relative.influence.Rd | 4 ++-- man/summary.TDboost.Rd | 3 +-- 12 files changed, 58 insertions(+), 40 deletions(-)
Title: Phonetic Spelling Algorithms
Description: Provides a collection of phonetic algorithms including
Soundex, Metaphone, NYSIIS, Caverphone, and others.
Author: James P. Howard, II [aut, cre]
Maintainer: "James P. Howard, II" <jh@jameshoward.us>
Diff between phonics versions 0.6.3 dated 2016-02-15 and 0.7.3 dated 2016-03-30
DESCRIPTION | 13 +++++++------ MD5 | 26 +++++++++++++++----------- NAMESPACE | 1 + R/cologne.R |only README.md | 3 ++- man/caverphone.Rd | 8 ++++---- man/cologne.Rd |only man/lein.Rd | 7 ++++--- man/metaphone.Rd | 7 ++++--- man/mra.Rd | 7 ++++--- man/nysiis.Rd | 7 ++++--- man/rogerroot.Rd | 7 ++++--- man/soundex.Rd | 7 ++++--- man/statcan.Rd | 7 ++++--- tests/testthat/cologne.csv |only tests/testthat/test-cologne.R |only 16 files changed, 57 insertions(+), 43 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.5 dated 2016-03-19 and 1.6 dated 2016-03-30
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/hisse.R | 9 +++++++++ R/marginRecon.R | 9 +++++++++ man/hisse.Rd | 4 +++- man/hisseNull4.Rd | 5 ++++- man/marginRecon.Rd | 7 ++++++- man/supportRegion.Rd | 2 +- 8 files changed, 43 insertions(+), 15 deletions(-)
Title: Forecastable Component Analysis
Description: Implementation of Forecastable Component Analysis ('ForeCA'),
including main algorithms and auxiliary function (summary, plotting, etc.) to
apply 'ForeCA' to multivariate time series data. 'ForeCA' is a novel dimension
reduction (DR) technique for temporally dependent signals. Contrary to other
popular DR methods, such as 'PCA' or 'ICA', 'ForeCA' takes time dependency
explicitly into account and searches for the most ''forecastable'' signal.
The measure of forecastability is based on the Shannon entropy of the spectral
density of the transformed signal.
Author: Georg M. Goerg <im@gmge.org>
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between ForeCA versions 0.2.2 dated 2015-04-29 and 0.2.4 dated 2016-03-30
DESCRIPTION | 27 +++---- MD5 | 76 ++++++++++----------- NAMESPACE | 7 + NEWS | 12 +++ R/ForeCA-package.R | 1 R/Omega.R | 11 +-- R/complete_controls.R | 2 R/foreca-utils.R | 2 R/foreca.R | 62 ++++++++--------- R/initialize_weightvector.R | 2 R/mvspectrum.R | 4 - R/quadratic_form.R | 8 -- R/spectral_entropy.R | 13 +-- R/whiten.R | 117 +++++++++++++++++++++----------- man/ForeCA-package.Rd | 17 ++-- man/Omega.Rd | 32 ++++---- man/common-arguments.Rd | 26 +++---- man/complete-controls.Rd | 32 ++++---- man/continuous_entropy.Rd | 11 +-- man/discrete_entropy.Rd | 30 ++++---- man/foreca-utils.Rd | 13 +-- man/foreca.EM-aux.Rd | 59 ++++++++-------- man/foreca.EM.one_weightvector.Rd | 27 +++---- man/foreca.Rd | 121 ++++++++++++++++------------------ man/foreca.one_weightvector-utils.Rd | 21 +++-- man/initialize_weightvector.Rd | 26 +++---- man/mvspectrum-utils.Rd | 10 +- man/mvspectrum.Rd | 82 ++++++++++++----------- man/mvspectrum2wcov.Rd | 24 +++--- man/quadratic_form.Rd | 18 +++-- man/sfa.Rd | 25 +++---- man/spectral_entropy.Rd | 36 +++++----- man/whiten.Rd | 57 +++++++++------- tests/testthat/test_foreca.EM-aux.R | 39 +++++----- tests/testthat/test_foreca.R | 34 +++++---- tests/testthat/test_mvspectrum2wcov.R | 5 - tests/testthat/test_quadratic_form.R | 23 +++++- tests/testthat/test_sfa.R | 6 + tests/testthat/test_whiten.R | 18 +++-- 39 files changed, 620 insertions(+), 516 deletions(-)
Title: Bindings to the CommonMark Reference Implementation
Description: The CommonMark specification defines a rationalized version of markdown
syntax. This package uses the libcmark reference implementation for converting
markdown text into various formats including html, latex and groff man. In
addition it exposes the markdown parse tree in xml format.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between commonmark versions 0.7 dated 2016-01-20 and 0.8 dated 2016-03-30
DESCRIPTION | 8 MD5 | 36 NEWS | 3 src/cmark/blocks.c | 664 +++--- src/cmark/buffer.c | 5 src/cmark/chunk.h | 8 src/cmark/cmark.h | 6 src/cmark/cmark_version.h | 4 src/cmark/commonmark.c | 35 src/cmark/html.c | 16 src/cmark/inlines.c | 22 src/cmark/latex.c | 8 src/cmark/main.c | 2 src/cmark/man.c | 5 src/cmark/node.c | 4 src/cmark/parser.h | 2 src/cmark/render.c | 26 src/cmark/scanners.c | 5051 ++++++++++++++++++++++------------------------ src/cmark/xml.c | 20 19 files changed, 2958 insertions(+), 2967 deletions(-)
Title: Species Richness Estimation and Modeling
Description: Species richness estimation is an important problem in biodiversity analysis. This package provides methods for total species richness estimation (observed plus unobserved) and a method for modelling total diversity with covariates. breakaway() estimates total (observed plus unobserved) species richness. Microbial diversity datasets are characterized by a large number of rare species and a small number of highly abundant species. The class of models implemented by breakaway() is flexible enough to model both these features. breakaway_nof1() implements a similar procedure however does not require a singleton count. betta() provides a method for modelling total diversity with covariates in a way that accounts for its estimated nature and thus accounts for unobserved taxa, and betta_random() permits random effects modelling.
Author: Amy Willis and John Bunge
Maintainer: Amy Willis <adw96@cornell.edu>
Diff between breakaway versions 2.0 dated 2015-10-01 and 3.0 dated 2016-03-30
DESCRIPTION | 11 +-- MD5 | 29 +++++++-- NAMESPACE | 8 ++ R/betta.R | 87 ++++++++++++++--------------- R/betta_pic.R |only R/betta_random.R |only R/breakaway.R | 105 +++++++++++++++++------------------ R/breakaway_nof1.R | 136 +++++++++++++++++++++++----------------------- R/chao1.R |only R/chao1_bc.R |only R/chao_bunge.R |only R/wlrm_transformed.R |only R/wlrm_untransformed.R |only man/betta.Rd | 25 +++++--- man/betta_pic.Rd | 22 +++---- man/betta_random.Rd |only man/breakaway-package.Rd | 17 +++-- man/chao1.Rd |only man/chao1_bc.Rd |only man/chao_bunge.Rd |only man/wlrm_transformed.Rd |only man/wlrm_untransformed.Rd |only 22 files changed, 231 insertions(+), 209 deletions(-)