Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of
textual data. The package implements a fast Gibbs sampling estimation of
Latent Dirichlet Allocation (Griffiths and Steyvers (2004)
<doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He,
Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of
helpers and visualizations to analyze the result of topic modeling. The
framework also allows enriching topic models with dates and externally
computed sentiment measures. A flexible aggregation scheme enables the
creation of time series of sentiment or topical proportions from the enriched
topic models. Moreover, a novel method jointly aggregates topic proportions
and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre]
,
Samuel Borms [ctb] ,
Chengua Lin [cph] ,
Yulan He [cph] ,
Jose Bernardo [cph] ,
David Robinson [cph] ),
Julia Silge [cph] ,
<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
Diff between sentopics versions 0.6.2 dated 2022-03-15 and 0.7.0 dated 2022-05-09
DESCRIPTION | 18 MD5 | 75 - NAMESPACE | 7 NEWS.md | 11 R/conversions.R | 497 ++++++++ R/functions.R | 87 - R/merging.R | 5 R/methods.R | 412 ++++--- R/models.R | 5 R/others.R | 66 - R/sentopics.R | 2 R/timeSeries.R | 12 R/utils.R | 97 + README.md | 2 build/vignette.rds |binary inst/doc/Basic_usage.R | 15 inst/doc/Basic_usage.Rmd | 15 inst/doc/Basic_usage.html | 1927 --------------------------------- inst/doc/Topical_time_series.R | 29 inst/doc/Topical_time_series.Rmd | 31 inst/doc/Topical_time_series.html | 1929 ---------------------------------- man/LDA.Rd | 2 man/LDAvis.Rd |only man/as.LDA.Rd |only man/as.tokens.dfm.Rd | 2 man/chainsScores.Rd | 19 man/get_ECB_press_conferences.Rd | 8 man/grow.Rd | 42 man/plot.sentopicmodel.Rd | 2 man/sentopics-conversions.Rd | 3 man/sentopics-package.Rd | 2 tests/testthat/test-algorithm.R | 12 tests/testthat/test-conversions.R |only tests/testthat/test-parallel_chains.R | 52 tests/testthat/test-rJST.R | 2 tests/testthat/test-timeSeries.R | 8 tests/testthat/test-utils.R | 19 vignettes/Basic_usage.Rmd | 15 vignettes/Topical_time_series.Rmd | 31 vignettes/plotly1.svg |only vignettes/plotly2.svg |only 41 files changed, 1190 insertions(+), 4271 deletions(-)
Title: Random Iterated Function System
Description: Pointwise generation and display of attractors (prefractals) of the random iterated function system (RIFS) for various combinations of probabilistic and geometric parameters of some fixed point sets (protofractals), described by Bukhovets A.G. (2012) <doi:10.1134/S0005117912020154>.
Author: Pavel V. Moskalev, Alexey G. Bukhovets and Tatyana Ya. Biruchinskay
Maintainer: Pavel V. Moskalev <moskalefff@gmail.com>
Diff between RIFS versions 0.1-5 dated 2012-06-05 and 0.1.6 dated 2022-05-09
DESCRIPTION | 21 ++---- MD5 | 12 +-- NAMESPACE | 9 +- man/RIFS-package.Rd | 45 ++++++-------- man/plotR2pre.Rd | 118 ++++++++++++++++++------------------ man/preRIFS.Rd | 167 ++++++++++++++++++++++++++-------------------------- man/preRSum0.Rd | 132 ++++++++++++++++++++--------------------- 7 files changed, 252 insertions(+), 252 deletions(-)
Title: Collection of Functions for Orthogonal and Orthonormal
Polynomials
Description: A collection of functions to construct sets of orthogonal
polynomials and their recurrence relations. Additional
functions are provided to calculate the derivative, integral,
value and roots of lists of polynomial objects.
Author: Frederick Novomestky <fnovomes@poly.edu>
Maintainer: Frederick Novomestky <fnovomes@poly.edu>
Diff between orthopolynom versions 1.0-5 dated 2013-02-04 and 1.0-6 dated 2022-05-09
DESCRIPTION | 16 +++++++++------- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 4 ++++ R/monic.polynomials.R | 1 - R/orthogonal.polynomials.R | 1 - R/orthonormal.polynomials.R | 1 - R/polynomial.coefficients.R | 1 - R/polynomial.derivatives.R | 1 - R/polynomial.integrals.R | 1 - R/polynomial.orders.R | 1 - R/polynomial.powers.R | 1 - R/polynomial.values.R | 1 - R/schebyshev.t.polynomials.R | 1 - R/spherical.polynomials.R | 1 - R/ultraspherical.polynomials.R | 1 - man/orthonormal.polynomials.Rd | 1 + man/pochhammer.Rd | 2 +- 17 files changed, 31 insertions(+), 36 deletions(-)
Title: Semi-Supervised Model for Geographical Document Classification
Description: Semissupervised model for geographical document classification (Watanabe 2018) <doi:10.1080/21670811.2017.1293487>.
This package currently contains seed dictionaries in English, German, French, Spanish, Italian, Russian, Hebrew, Arabic Japanese and Chinese (Simplified and Traditional).
Author: Kohei Watanabe [aut, cre, cph],
Stefan Mueller [aut],
Dani Madrid-Morales [aut],
Katerina Tertytchnaya [aut],
Ke Cheng [aut],
Chung-hong Chan [aut],
Claude Grasland [aut],
Giuseppe Carteny [aut],
Elad Segev [aut],
Dai Yamao [aut],
Barbara Ellynes Zucc [...truncated...]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between newsmap versions 0.8.0 dated 2022-04-10 and 0.8.1 dated 2022-05-09
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ data/data_dictionary_newsmap_ar.RData |binary data/data_dictionary_newsmap_de.RData |binary data/data_dictionary_newsmap_en.RData |binary data/data_dictionary_newsmap_es.RData |binary data/data_dictionary_newsmap_fr.RData |binary data/data_dictionary_newsmap_he.RData |binary data/data_dictionary_newsmap_it.RData |binary data/data_dictionary_newsmap_ja.RData |binary data/data_dictionary_newsmap_pt.RData |binary data/data_dictionary_newsmap_ru.RData |binary data/data_dictionary_newsmap_zh_cn.RData |binary data/data_dictionary_newsmap_zh_tw.RData |binary 15 files changed, 21 insertions(+), 17 deletions(-)
Title: Tools to Process the Munich ChronoType Questionnaire (MCTQ)
Description: A complete toolkit to process the Munich ChronoType
Questionnaire (MCTQ) for its three versions (standard, micro, and shift).
MCTQ is a quantitative and validated tool to assess chronotypes using
peoples' sleep behavior, originally presented by Till Roenneberg, Anna
Wirz-Justice, and Martha Merrow (2003, <doi:10.1177/0748730402239679>).
Author: Daniel Vartanian [aut, cph, cre]
,
Ana Amelia Benedito-Silva [aut, sad]
,
Mario Pedrazzoli [aut, sad] ,
Jonathan Keane [rev] ,
Mario Andre Leocadio-Miguel [rev]
,
Interdisciplinary Sleep Research Group [fnd],
University of Sao Paulo [fnd]
Maintainer: Daniel Vartanian <danvartan@gmail.com>
Diff between mctq versions 0.1.0 dated 2021-11-05 and 0.2.0 dated 2022-05-09
DESCRIPTION | 20 LICENSE | 2 MD5 | 222 +++---- NAMESPACE | 4 NEWS.md | 34 - R/assign_date.R | 27 R/cycle_time.R | 51 - R/fd.R | 18 R/gu.R | 42 - R/le_week.R | 61 +- R/micro_mctq.R | 109 ++- R/msl.R | 155 ++--- R/pretty_mctq.R | 31 - R/qplot_walk.R | 103 +-- R/random_mctq.R | 21 R/raw_data.R | 16 R/round_time.R | 45 - R/sdu.R | 275 ++++----- R/shift_mctq.R | 232 +++++-- R/shorter_interval.R | 142 +++- R/sjl.R | 373 ++++++++++-- R/sloss_week.R | 41 - R/so.R | 42 - R/std_mctq.R | 182 ++++-- R/sum_time.R | 72 +- R/tbt.R | 44 - R/utils-checks.R | 16 R/utils-dialogs.R | 18 R/utils-mocks.R | 3 R/utils.R | 72 -- README.md | 94 +-- build/partial.rdb |binary build/vignette.rds |binary data/micro_mctq.rda |binary data/shift_mctq.rda |binary data/std_mctq.rda |binary inst/CITATION | 10 inst/WORDLIST | 10 inst/doc/mctq.R | 7 inst/doc/mctq.Rmd | 30 - inst/doc/mctq.html | 974 ++++++++++++++++++++++----------- inst/doc/missing-sections.Rmd | 12 inst/doc/missing-sections.html | 287 +++++++++ inst/doc/sjl-computation.Rmd | 15 inst/doc/sjl-computation.html | 353 ++++++++++- inst/doc/time-span-objects.Rmd | 2 inst/doc/time-span-objects.html | 265 ++++++++ man/assign_date.Rd | 23 man/cycle_time.Rd | 55 + man/fd.Rd | 17 man/figures/logo.png |binary man/gu.Rd | 43 - man/le_week.Rd | 84 +- man/mctq-package.Rd | 2 man/micro_mctq.Rd | 117 ++- man/msf_sc.Rd | 126 +--- man/msl.Rd | 57 + man/napd.Rd | 36 - man/pretty_mctq.Rd | 31 - man/qplot_walk.Rd | 103 +-- man/random_mctq.Rd | 13 man/raw_data.Rd | 14 man/round_time.Rd | 41 - man/sd24.Rd | 52 - man/sd_overall.Rd | 91 +-- man/sd_week.Rd | 78 +- man/sdu.Rd | 56 - man/shift_mctq.Rd | 236 +++++-- man/shorter_interval.Rd | 105 ++- man/sjl.Rd | 106 +-- man/sjl_sc.Rd |only man/sjl_weighted.Rd | 68 +- man/sloss_week.Rd | 77 -- man/so.Rd | 46 - man/std_mctq.Rd | 186 ++++-- man/sum_time.Rd | 73 +- man/tbt.Rd | 44 - tests/spelling.R | 8 tests/testthat.R | 18 tests/testthat/Rplots.pdf |binary tests/testthat/test-assign_date.R | 138 +++- tests/testthat/test-cycle_time.R | 328 +++++++---- tests/testthat/test-fd.R | 7 tests/testthat/test-gu.R | 67 +- tests/testthat/test-le_week.R | 148 +++-- tests/testthat/test-msf_sc.R | 275 +++++---- tests/testthat/test-na_as.R | 20 tests/testthat/test-napd.R | 52 + tests/testthat/test-pretty_mctq.R | 32 - tests/testthat/test-qplot_walk.R | 99 ++- tests/testthat/test-random_mctq.R | 609 +++++++++++++------- tests/testthat/test-raw_data.R | 13 tests/testthat/test-round_time.R | 45 + tests/testthat/test-sd24.R | 100 ++- tests/testthat/test-sd_overall.R | 172 +++-- tests/testthat/test-sd_week.R | 140 +++- tests/testthat/test-sdu.R | 51 + tests/testthat/test-shorter_interval.R | 238 +++++--- tests/testthat/test-sjl.R | 291 ++++++--- tests/testthat/test-sjl_sc.R |only tests/testthat/test-sjl_weighted.R | 130 ++-- tests/testthat/test-sloss_week.R | 127 +++- tests/testthat/test-so.R | 68 +- tests/testthat/test-sum_time.R | 505 +++++++++-------- tests/testthat/test-tbt.R | 66 +- tests/testthat/test-utils-checks.R | 479 ++++++++++------ tests/testthat/test-utils-dialogs.R | 50 + tests/testthat/test-utils-mocks.R | 7 tests/testthat/test-utils.R | 415 +++++++++----- vignettes/mctq.Rmd | 30 - vignettes/missing-sections.Rmd | 12 vignettes/sjl-computation.Rmd | 15 vignettes/time-span-objects.Rmd | 2 113 files changed, 7275 insertions(+), 3994 deletions(-)
Title: Monotonic Association on Zero-Inflated Data
Description: Methods for calculating and testing the significance of
pairwise monotonic association from and based on the work of
Pimentel (2009) <doi:10.4135/9781412985291.n2>. Computation of association of vectors from one
or multiple sets can be performed in parallel thanks to the
packages 'foreach' and 'doMC'.
Author: Alice Albasi [aut, cre]
Maintainer: Alice Albasi <albasialice@gmail.com>
Diff between mazeinda versions 0.0.1 dated 2018-01-16 and 0.0.2 dated 2022-05-09
DESCRIPTION | 7 +++---- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/my-vignette.R | 16 ++++++++-------- inst/doc/my-vignette.Rmd | 2 +- inst/doc/my-vignette.pdf |binary vignettes/my-vignette.Rmd | 2 +- 7 files changed, 19 insertions(+), 20 deletions(-)
Title: Latent Semantic Analysis
Description: The basic idea of latent semantic analysis (LSA) is,
that text do have a higher order (=latent semantic) structure which,
however, is obscured by word usage (e.g. through the use of synonyms
or polysemy). By using conceptual indices that are derived statistically
via a truncated singular value decomposition (a two-mode factor analysis)
over a given document-term matrix, this variability problem can be overcome.
Author: Fridolin Wild
Maintainer: Fridolin Wild <wild@brookes.ac.uk>
Diff between lsa versions 0.73.2 dated 2020-05-04 and 0.73.3 dated 2022-05-09
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/sample.textmatrix.R | 2 +- R/textmatrix.R | 2 +- man/weightings.Rd | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: Low Rank Quadratic Programming
Description: Solves quadratic programming problems where the Hessian is represented as the product of two matrices.
Author: John T. Ormerod [aut, cre],
Matt P. Wand [aut]
Maintainer: John T. Ormerod <john.ormerod@sydney.edu.au>
Diff between LowRankQP versions 1.0.4 dated 2020-04-12 and 1.0.5 dated 2022-05-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/LowRankQP.c | 34 ++++++++++++++++++++-------------- 3 files changed, 26 insertions(+), 20 deletions(-)
Title: Inference About the Standardized Mortality Ratio when Evaluating
the Effect of a Screening Program on Survival
Description: Functions to make inference about the
standardized mortality ratio (SMR) when evaluating the
effect of a screening program. The package is
based on methods described in Sasieni (2003)
<doi: 10.1097/00001648-200301000-00026> and
Talbot et al. (2011) <doi: 10.1002/sim.4334>.
Author: Denis Talbot, Thierry Duchesne, Jacques Brisson, Nathalie
Vandal
Maintainer: Denis Talbot <denis.talbot@fmed.ulaval.ca>
Diff between InferenceSMR versions 1.0 dated 2013-05-23 and 1.0.1 dated 2022-05-09
InferenceSMR-1.0.1/InferenceSMR/ChangeLog |only InferenceSMR-1.0.1/InferenceSMR/DESCRIPTION | 28 - InferenceSMR-1.0.1/InferenceSMR/MD5 | 42 +- InferenceSMR-1.0.1/InferenceSMR/NAMESPACE | 4 InferenceSMR-1.0.1/InferenceSMR/R/contrib.R | 92 ++-- InferenceSMR-1.0.1/InferenceSMR/R/covariance.R | 23 - InferenceSMR-1.0.1/InferenceSMR/R/est.expDeath.R | 59 +-- InferenceSMR-1.0.1/InferenceSMR/R/function1.R | 63 +-- InferenceSMR-1.0.1/InferenceSMR/R/h.R | 14 InferenceSMR-1.0.1/InferenceSMR/R/incidences.R | 82 ++-- InferenceSMR-1.0.1/InferenceSMR/R/inference.SMR.R | 100 +---- InferenceSMR-1.0.1/InferenceSMR/R/var.expDeath.R | 217 +++++------ InferenceSMR-1.0.1/InferenceSMR/man/contrib.Rd | 148 +++---- InferenceSMR-1.0.1/InferenceSMR/man/covariance.Rd | 121 ++---- InferenceSMR-1.0.1/InferenceSMR/man/est.expDeath.Rd | 112 ++--- InferenceSMR-1.0.1/InferenceSMR/man/function1.Rd | 40 -- InferenceSMR-1.0.1/InferenceSMR/man/h.Rd | 88 +--- InferenceSMR-1.0.1/InferenceSMR/man/incidences.Rd | 92 ++-- InferenceSMR-1.0.1/InferenceSMR/man/inference.SMR.Rd | 272 ++++++-------- InferenceSMR-1.0.1/InferenceSMR/man/req.objects.Rd | 174 ++++---- InferenceSMR-1.0.1/InferenceSMR/man/screening.rd |only InferenceSMR-1.0.1/InferenceSMR/man/var.expDeath.Rd | 114 ++--- InferenceSMR-1.0/InferenceSMR/man/InferenceSMR-package.Rd |only InferenceSMR-1.0/InferenceSMR/man/screening.Rd |only 24 files changed, 884 insertions(+), 1001 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions
by code inspection using various strategies (ordered, liberal, or
conservative). The objective of this package is to make it as simple as
possible to identify global objects for the purpose of exporting them in
parallel, distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph],
Davis Vaughan [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.14.0 dated 2020-11-22 and 0.15.0 dated 2022-05-09
DESCRIPTION | 11 ++++++----- MD5 | 31 +++++++++++++++++-------------- NEWS | 22 ++++++++++++++++++++++ R/Globals-class.R | 31 ++++++++++++------------------- R/environment_of.R |only R/globalsOf.R | 31 +++++++++++++++++++++++++++++-- R/options.R |only R/packagesOf.R | 2 +- R/utils.R | 21 +++++++++++++++++++++ R/zzz.R | 6 ++++++ man/Globals.Rd | 5 ++++- man/globalsOf.Rd | 4 ++++ tests/Globals.R | 32 ++++++++++++++++++++++++++++++++ tests/dotdotdot.R | 9 ++++++--- tests/findGlobals.R | 4 ++++ tests/globalsOf,locals.R |only tests/globalsOf.R | 2 +- tests/utils.R | 2 +- 18 files changed, 166 insertions(+), 47 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees
Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Author: Luke Harmon, Matthew Pennell, Chad Brock, Joseph Brown, Wendell Challenger,
Jon Eastman, Rich FitzJohn, Rich Glor, Gene Hunt, Liam Revell, Graham Slater,
Josef Uyeda, Jason Weir and CRAN team
Maintainer: ORPHANED
Diff between geiger versions 2.0.7 dated 2020-06-02 and 2.0.7.1 dated 2022-05-09
DESCRIPTION | 13 - MD5 | 28 ++-- R/congruify.R | 2 R/diversification.R | 58 ++++---- R/glomogram.R | 60 ++++---- R/mecca.R | 2 R/medusa.R | 10 - R/traits-fossil.R | 352 ++++++++++++++++++++++++++-------------------------- R/utilities-misc.R | 2 R/utilities-phylo.R | 2 README.md | 22 --- man/gbresolve.Rd | 2 man/geiger-data.Rd | 2 man/rjmcmc.bm.Rd | 6 src/util.c | 3 15 files changed, 277 insertions(+), 287 deletions(-)
Title: Robust Analysis using Forward Search
Description: Robust analysis using forward search in linear and
generalized linear regression models, as described in Atkinson, A.C. and Riani, M. (2000), Robust Diagnostic Regression Analysis, First Edition. New York: Springer.
Author: Originally written for S-Plus by: Kjell Konis
<kkonis@insightful.com> and Marco Riani <mriani@unipr.it>
Ported to R by Luca Scrucca <luca@stat.unipg.it>
Ken Beath <ken@kjbeath.com.au>
Maintainer: Ken Beath <ken@kjbeath.com.au>
Diff between forward versions 1.0.5 dated 2019-12-10 and 1.0.6 dated 2022-05-09
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- inst/NEWS | 6 ++++++ 3 files changed, 14 insertions(+), 8 deletions(-)
Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Description: Creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Provides diverse quality criteria. Provides utility functions for the class design, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping <ulrike.groemping@bht-berlin.de>
Diff between DoE.base versions 1.2 dated 2021-09-02 and 1.2-1 dated 2022-05-09
DESCRIPTION | 16 ++--- MD5 | 8 +- build/partial.rdb |binary inst/NEWS | 150 ++++++++++++++++++++++++++-------------------------- man/add.response.Rd | 9 +-- 5 files changed, 94 insertions(+), 89 deletions(-)
Title: Functions for Cosmological Distances, Times, Luminosities, Etc
Description: Package encapsulates standard expressions for distances, times, luminosities, and other quantities useful in observational cosmology, including molecular line observations. Currently coded for a flat universe only.
Author: Andrew Harris
Maintainer: Andrew Harris <harris@astro.umd.edu>
Diff between cosmoFns versions 1.0-1 dated 2012-12-15 and 1.1-1 dated 2022-05-09
DESCRIPTION | 16 +++++++--------- MD5 | 10 ++++++---- NAMESPACE | 4 +++- R/sedFitThin.R |only man/cosmoFns-package.Rd | 8 ++++++-- man/mass.CO.Rd | 3 ++- man/sedFitThin.Rd |only 7 files changed, 24 insertions(+), 17 deletions(-)
Title: Contingency Measure-Based Networks for Binary Time Series
Description: The ConNEcT approach investigates the pairwise association strength of binary time series by calculating contingency measures and depicts the results in a network. The package includes features to explore and visualize the data. To calculate the pairwise concurrent or temporal sequenced relationship between the variables, the package provides seven contingency measures (proportion of agreement, classical & corrected Jaccard, Cohen's kappa, phi correlation coefficient, odds ratio, and log odds ratio), however, others can easily be implemented. The package also includes non-parametric significance tests, that can be applied to test whether the contingency value quantifying the relationship between the variables is significantly higher than chance level. Most importantly this test accounts for auto-dependence and relative frequency.See Bodner et al.(2021) <doi: 10.1111/bmsp.12222>.Finally, a network can be drawn. Variables depicted the nodes of the network, with the node size adapted to the prevalence. The association strength between the variables defines the undirected (concurrent) or directed (temporal sequenced) links between the nodes. The results of the non-parametric significance test can be included by depicting either all links or only the significant ones. Tutorial see Bodner et al.(2021) <doi:10.3758/s13428-021-01760-w>.
Author: Nadja Bodner [aut, cre],
Eva Ceulemans [ctb, rev]
Maintainer: Nadja Bodner <nadja.bodner@kuleuven.be>
Diff between ConNEcT versions 0.7.26 dated 2021-11-02 and 0.7.27 dated 2022-05-09
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/conTest.R | 16 +++++++++------- R/modelAD.R | 20 +++++++++----------- R/modelNO.R | 16 ++++++++-------- man/conTest.Rd | 2 +- 7 files changed, 39 insertions(+), 39 deletions(-)
Title: Bayesian Inference for Directed Acyclic Graphs
Description: Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data or categorical data. The algorithms may provide the maximum a posteriori
(MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks.
References:
J. Kuipers, P. Suter, G. Moffa (2022) <doi:10.1080/10618600.2021.2020127>,
N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>,
J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>,
M. Kalisch et al. (2012) <doi:10.18637/jss.v047.i11>,
D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.suter@bsse.ethz.ch>
Diff between BiDAG versions 2.0.5 dated 2022-04-13 and 2.0.6 dated 2022-05-09
DESCRIPTION | 14 ++++++------- MD5 | 52 +++++++++++++++++++++++++++---------------------- NAMESPACE | 6 +++++ R/bidag2coda.R |only R/graphhelpfns.R | 4 +-- R/initpar.R | 21 +++++++------------ R/iterativeMCMC.R | 2 - R/main.R | 19 ++++++++++------- R/orderMCMCbase.R | 2 - R/orderMCMCbasemax.R | 4 +-- R/orderMCMCmain.R | 8 ++++--- R/orderMCMCplus1.R | 4 +-- R/orderMCMCplus1max.R | 2 - R/other.R | 9 ++++++-- R/partitionMCMC.R | 2 - R/partitionMCMCmain.R | 19 +++++++++++------ R/performanceassess.R | 4 +-- R/plotfns.R | 3 +- R/plotusingrgraphviz.R | 25 ++++++++++++++++++----- R/printmethods.R | 24 +++++++++++++++------- R/samplefns.R | 2 - R/spacefns.R | 2 - R/summary.R | 2 - R/wrappers.R |only man/bidag2coda.Rd |only man/bidag2codalist.Rd |only man/learnBN.Rd |only man/partitionMCMC.Rd | 3 ++ man/sampleBN.Rd |only man/scoreparameters.Rd | 2 - 30 files changed, 142 insertions(+), 93 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models' literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Mohammadi et al. (2021) <doi:10.1080/01621459.2021.1996377>, and Mohammadi and Wit (2019) <doi:10.18637/jss.v089.i03>.
Author: Reza Mohammadi [aut, cre] ,
Ernst Wit [aut] ,
Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.66 dated 2022-04-14 and 2.67 dated 2022-05-09
BDgraph-2.66/BDgraph/vignettes/BDgraph-Examples.Rmd |only BDgraph-2.67/BDgraph/DESCRIPTION | 11 BDgraph-2.67/BDgraph/MD5 | 29 - BDgraph-2.67/BDgraph/README.md | 2 BDgraph-2.67/BDgraph/build/partial.rdb |binary BDgraph-2.67/BDgraph/data/churn.RData |binary BDgraph-2.67/BDgraph/data/geneExpression.RData |binary BDgraph-2.67/BDgraph/data/reinis.RData |binary BDgraph-2.67/BDgraph/data/surveyData.RData |binary BDgraph-2.67/BDgraph/inst/doc/BDgraph-Examples.Rmd | 32 - BDgraph-2.67/BDgraph/inst/doc/BDgraph-Examples.html | 392 +++++-------------- BDgraph-2.67/BDgraph/inst/doc/BDgraph.pdf |only BDgraph-2.67/BDgraph/inst/doc/BDgraph_examples.R | 158 ++----- BDgraph-2.67/BDgraph/inst/doc/BDgraph_examples_JSS.R |only BDgraph-2.67/BDgraph/inst/doc/vignette.pdf |binary BDgraph-2.67/BDgraph/man/figures/logo.png |binary BDgraph-2.67/BDgraph/vignettes/BDgraph-Examples.html | 392 +++++-------------- 17 files changed, 327 insertions(+), 689 deletions(-)
Title: Create Visual Citations for Presentation Slides
Description: Provides 'visual citations' containing the metadata of a scientific paper and a 'QR' code.
A 'visual citation' is a banner containing title, authors, journal and year of a publication.
This package can create such banners based on 'BibTeX' and 'BibLaTeX' references
and includes a QR code pointing to the 'DOI'.
The resulting HTML object or PNG image can be included in a presentation to point the audience to good resources for further reading.
Styling is possible via predefined designs or via custom 'CSS'.
This package is not intended as replacement for proper reference manager packages,
but a tool to enrich scientific presentation slides.
Author: Christian A. Gebhard [aut, cre]
Maintainer: Christian A. Gebhard <christian.gebhard@posteo.de>
Diff between namedropR versions 2.2.3 dated 2022-02-13 and 2.3.2 dated 2022-05-09
DESCRIPTION | 8 - MD5 | 34 ++-- NAMESPACE | 2 NEWS.md | 17 ++ R/drop_html.R | 29 ++- R/drop_name.R | 21 ++ R/get_css_styles.R | 112 +++++++++++++- README.md | 6 build/vignette.rds |binary inst/doc/custom_styling.R |only inst/doc/custom_styling.Rmd |only inst/doc/custom_styling.html |only inst/doc/namedropR.html | 321 ++++++++++++++++++++++++++++++++++++----- inst/doc/use_rmarkdown.html | 278 ++++++++++++++++++++++++++++++++--- inst/styles/styles.csv | 8 - man/drop_html.Rd | 8 - man/drop_name.Rd | 10 + man/get_css_styles.Rd | 4 tests/testthat/test-write_vc.R | 44 ----- vignettes/custom_styling.Rmd |only 20 files changed, 759 insertions(+), 143 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-14 1.3.3
2020-11-06 1.3.2
2020-05-19 1.3.1
2019-02-19 1.3
2017-04-03 1.2.3
2016-12-14 1.2.2
2016-09-18 1.2
2016-07-15 1.1
2015-12-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-02 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-16 1.94
2011-05-18 1.92
2011-02-18 1.91
2010-12-02 1.89
2010-09-21 1.88
2010-09-13 1.87
2010-09-09 1.86
2010-08-28 1.85
2010-08-16 1.80
2009-10-13 1.79
2008-11-07 1.74
2008-10-01 1.73
2008-08-24 1.72
2008-07-16 1.71
2008-06-25 1.7
2008-06-19 1.6
2008-06-18 1.5
2008-04-14 1.4
2008-03-02 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-18 2.4
2015-11-23 2.3
2015-03-09 2.2
2014-08-01 2.1
2014-07-29 2.0
2013-04-17 1.2
2012-03-16 1.1
2012-03-08 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-29 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-03 0.9-3
2017-01-23 0.9-2
2016-08-31 0.9-1
2016-05-31 0.9
2013-12-17 0.8-1
2013-05-24 0.8-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-14 0.9.9.2
2018-07-29 0.9.9.1
2014-04-04 0.9.9
2014-03-19 0.9.2
2012-01-12 0.7.7
2009-10-15 0.7.6
2008-07-16 0.7.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-23 1.1.0
2021-06-04 1.0.4
2021-04-17 1.0.3
2021-03-18 1.0.2
2021-01-30 1.0.1
2020-07-07 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-10 1.35
2012-12-15 1.33
2012-09-22 1.3.2
2012-04-10 1.03
2011-12-22 1.0