Title: Automatic Generation of Exams in R
Description: Automatic generation of exams based on exercises in Markdown or LaTeX format,
possibly including R code for dynamic generation of exercise elements.
Exercise types include single-choice and multiple-choice questions, arithmetic problems,
string questions, and combinations thereof (cloze). Output formats include standalone
files (PDF, HTML, Docx, ODT, ...), Moodle XML, QTI 1.2, QTI 2.1, Blackboard, Canvas, OpenOLAT,
ARSnova, and TCExam. In addition to fully customizable PDF exams, a standardized PDF format
(NOPS) is provided that can be printed, scanned, and automatically evaluated.
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>),
Bettina Gruen [aut] (<https://orcid.org/0000-0001-7265-4773>),
Friedrich Leisch [aut] (<https://orcid.org/0000-0001-7278-1983>),
Nikolaus Umlauf [aut],
Mirko Birbaumer [ctb],
Dominik Ernst [ctb],
Patrik Keller [ctb],
Niels Smits [ctb],
Reto Stauffer [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between exams versions 2.3-2 dated 2018-12-08 and 2.3-3 dated 2019-07-04
exams-2.3-2/exams/R/exams2ifat.R |only exams-2.3-2/exams/inst/tex/ifat.tex |only exams-2.3-2/exams/inst/tex/ifat8.tex |only exams-2.3-3/exams/DESCRIPTION | 14 - exams-2.3-3/exams/MD5 | 139 +++++------ exams-2.3-3/exams/NAMESPACE | 3 exams-2.3-3/exams/NEWS | 68 +++++ exams-2.3-3/exams/R/exams.R | 16 - exams-2.3-3/exams/R/exams2arsnova.R | 4 exams-2.3-3/exams/R/exams2canvas.R |only exams-2.3-3/exams/R/exams2html.R | 5 exams-2.3-3/exams/R/exams2moodle.R | 4 exams-2.3-3/exams/R/exams2nops.R | 22 + exams-2.3-3/exams/R/exams2openolat.R | 4 exams-2.3-3/exams/R/exams2qti12.R | 296 ++++++++++++++++++++----- exams-2.3-3/exams/R/exams2qti21.R | 93 +++++++ exams-2.3-3/exams/R/exams_eval.R | 8 exams-2.3-3/exams/R/exams_skeleton.R | 81 ++++-- exams-2.3-3/exams/R/formatters.R | 47 +++ exams-2.3-3/exams/R/nops_eval.R | 2 exams-2.3-3/exams/R/nops_scan.R | 3 exams-2.3-3/exams/R/pandoc.R | 7 exams-2.3-3/exams/R/tex2image.R | 4 exams-2.3-3/exams/R/xexams.R | 16 + exams-2.3-3/exams/build/vignette.rds |binary exams-2.3-3/exams/inst/doc/exams.R | 2 exams-2.3-3/exams/inst/doc/exams.Rnw | 2 exams-2.3-3/exams/inst/doc/exams.pdf |binary exams-2.3-3/exams/inst/doc/exams2.R | 2 exams-2.3-3/exams/inst/doc/exams2.Rnw | 6 exams-2.3-3/exams/inst/doc/exams2.pdf |binary exams-2.3-3/exams/inst/nops/da.dcf | 1 exams-2.3-3/exams/inst/nops/de.dcf | 1 exams-2.3-3/exams/inst/nops/es.dcf | 1 exams-2.3-3/exams/inst/nops/fi.dcf | 1 exams-2.3-3/exams/inst/nops/fr.dcf | 1 exams-2.3-3/exams/inst/nops/gsw.dcf | 1 exams-2.3-3/exams/inst/nops/hr.dcf | 1 exams-2.3-3/exams/inst/nops/hu.dcf | 1 exams-2.3-3/exams/inst/nops/it.dcf | 1 exams-2.3-3/exams/inst/nops/nl.dcf | 1 exams-2.3-3/exams/inst/nops/pt-BR.dcf | 1 exams-2.3-3/exams/inst/nops/pt-PT.dcf | 1 exams-2.3-3/exams/inst/nops/pt.dcf | 1 exams-2.3-3/exams/inst/nops/ro.dcf | 1 exams-2.3-3/exams/inst/nops/ru.dcf | 4 exams-2.3-3/exams/inst/nops/sk.dcf | 2 exams-2.3-3/exams/inst/nops/sr.dcf | 1 exams-2.3-3/exams/inst/tex/exam.tex | 1 exams-2.3-3/exams/inst/tex/plain8.tex | 2 exams-2.3-3/exams/inst/tex/solution.tex | 1 exams-2.3-3/exams/inst/xml/canvas_manifest.xml |only exams-2.3-3/exams/inst/xml/canvas_meta.xml |only exams-2.3-3/exams/man/exams.Rd | 3 exams-2.3-3/exams/man/exams2arsnova.Rd | 6 exams-2.3-3/exams/man/exams2blackboard.Rd | 11 exams-2.3-3/exams/man/exams2canvas.Rd |only exams-2.3-3/exams/man/exams2html.Rd | 14 - exams-2.3-3/exams/man/exams2lops.Rd | 11 exams-2.3-3/exams/man/exams2moodle.Rd | 29 +- exams-2.3-3/exams/man/exams2nops.Rd | 8 exams-2.3-3/exams/man/exams2openolat.Rd | 4 exams-2.3-3/exams/man/exams2pandoc.Rd | 11 exams-2.3-3/exams/man/exams2pdf.Rd | 11 exams-2.3-3/exams/man/exams2qti12.Rd | 21 + exams-2.3-3/exams/man/exams_skeleton.Rd | 6 exams-2.3-3/exams/man/fmt.Rd | 20 + exams-2.3-3/exams/man/match_exams_call.Rd | 2 exams-2.3-3/exams/man/nops_eval.Rd | 2 exams-2.3-3/exams/man/nops_scan.Rd | 14 - exams-2.3-3/exams/man/tex2image.Rd | 2 exams-2.3-3/exams/man/xexams.Rd | 28 +- exams-2.3-3/exams/vignettes/exams.Rnw | 2 exams-2.3-3/exams/vignettes/exams2.Rnw | 6 74 files changed, 788 insertions(+), 296 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling based on 'Boost' and 'Eigen'. The 'rvinecopulib'
package implements the core features of the popular 'VineCopula' package, in
particular inference algorithms for both vine copula and bivariate copula
models. Advantages over 'VineCopula' are a sleeker and more modern API,
improved performances, especially in high dimensions, nonparametric and
multi-parameter families. The 'rvinecopulib' package includes 'vinecopulib' as
header-only C++ library (currently version 0.3.1). Thus
users do not need to install 'vinecopulib' itself in order to use
'rvinecopulib'. Since their initial releases, 'vinecopulib' is licensed under
the MIT License, and 'rvinecopulib' is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.3.1.1.0 dated 2019-04-19 and 0.3.2.1.0 dated 2019-07-04
DESCRIPTION | 6 MD5 | 194 +-- NAMESPACE | 7 NEWS.md | 19 R/as_rvine_structure.R | 6 R/bicop.R | 189 +-- R/bicop_methods.R | 295 ++--- R/bicop_plot.R | 354 +++--- R/family_sets.R | 26 R/getters.R | 300 ++--- R/pairs_copula_data.R |only R/rosenblatt.R | 131 +- R/rvine_structure.R | 2 R/rvinecopulib.R | 26 R/tools.R | 392 +++---- R/truncate_model.R | 163 +- R/vine.R | 336 +++--- R/vine_methods.R | 342 +++--- R/vinecop.R | 306 ++--- R/vinecop_methods.R | 286 ++--- R/vinecop_plot.R | 555 +++++----- inst/include/version.hpp | 4 inst/include/vinecopulib.hpp | 1 inst/include/vinecopulib/bicop/abstract.hpp | 17 inst/include/vinecopulib/bicop/bb1.hpp | 1 inst/include/vinecopulib/bicop/class.hpp | 26 inst/include/vinecopulib/bicop/elliptical.hpp | 5 inst/include/vinecopulib/bicop/family.hpp | 21 inst/include/vinecopulib/bicop/fit_controls.hpp | 12 inst/include/vinecopulib/bicop/implementation/abstract.ipp | 41 inst/include/vinecopulib/bicop/implementation/archimedean.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb1.ipp | 4 inst/include/vinecopulib/bicop/implementation/bb6.ipp | 3 inst/include/vinecopulib/bicop/implementation/bb7.ipp | 3 inst/include/vinecopulib/bicop/implementation/bb8.ipp | 3 inst/include/vinecopulib/bicop/implementation/class.ipp | 167 +-- inst/include/vinecopulib/bicop/implementation/clayton.ipp | 4 inst/include/vinecopulib/bicop/implementation/elliptical.ipp | 8 inst/include/vinecopulib/bicop/implementation/family.ipp | 1 inst/include/vinecopulib/bicop/implementation/fit_controls.ipp | 33 inst/include/vinecopulib/bicop/implementation/frank.ipp | 7 inst/include/vinecopulib/bicop/implementation/gaussian.ipp | 3 inst/include/vinecopulib/bicop/implementation/gumbel.ipp | 2 inst/include/vinecopulib/bicop/implementation/indep.ipp | 19 inst/include/vinecopulib/bicop/implementation/joe.ipp | 9 inst/include/vinecopulib/bicop/implementation/kernel.ipp | 38 inst/include/vinecopulib/bicop/implementation/parametric.ipp | 248 ++-- inst/include/vinecopulib/bicop/implementation/student.ipp | 7 inst/include/vinecopulib/bicop/implementation/tll.ipp | 14 inst/include/vinecopulib/bicop/implementation/tools_select.ipp | 12 inst/include/vinecopulib/bicop/kernel.hpp | 13 inst/include/vinecopulib/bicop/parametric.hpp | 29 inst/include/vinecopulib/bicop/tools_select.hpp | 6 inst/include/vinecopulib/misc/implementation/tools_eigen.ipp | 22 inst/include/vinecopulib/misc/implementation/tools_interpolation.ipp | 3 inst/include/vinecopulib/misc/implementation/tools_optimization.ipp | 200 +-- inst/include/vinecopulib/misc/implementation/tools_stats.ipp | 52 inst/include/vinecopulib/misc/tools_batch.hpp | 1 inst/include/vinecopulib/misc/tools_bobyqa.hpp | 38 inst/include/vinecopulib/misc/tools_eigen.hpp | 16 inst/include/vinecopulib/misc/tools_interpolation.hpp | 2 inst/include/vinecopulib/misc/tools_optimization.hpp | 43 inst/include/vinecopulib/misc/tools_stats.hpp | 16 inst/include/vinecopulib/misc/tools_stl.hpp | 92 - inst/include/vinecopulib/misc/tools_thread.hpp | 2 inst/include/vinecopulib/misc/triangular_array.hpp | 40 inst/include/vinecopulib/vinecop/class.hpp | 19 inst/include/vinecopulib/vinecop/implementation/class.ipp | 222 ++-- inst/include/vinecopulib/vinecop/implementation/fit_controls.ipp | 117 +- inst/include/vinecopulib/vinecop/implementation/rvine_structure.ipp | 67 - inst/include/vinecopulib/vinecop/implementation/tools_select.ipp | 3 inst/include/vinecopulib/vinecop/rvine_structure.hpp | 4 inst/include/vinecopulib/vinecop/tools_select.hpp | 17 inst/include/wrappers.hpp | 305 ++++- man/bicop.Rd | 1 man/getters.Rd | 7 man/mBICV.Rd | 2 man/pairs_copula_data.Rd |only man/plot.bicop_dist.Rd | 9 man/plot.vinecop_dist.Rd | 7 man/rosenblatt.Rd | 8 man/rvinecopulib.Rd | 6 man/truncate_model.Rd | 4 man/vine.Rd | 11 man/vine_methods.Rd | 10 man/vinecop.Rd | 11 man/vinecop_methods.Rd | 11 src/wrappers.cpp | 279 ----- tests/testthat/Rplots.pdf |binary tests/testthat/test_bicop.R | 70 - tests/testthat/test_bicop_dist.R | 133 +- tests/testthat/test_rosenblatt.R | 26 tests/testthat/test_rvine_structure.R | 24 tests/testthat/test_tools.R | 31 tests/testthat/test_truncate_model.R | 72 - tests/testthat/test_vine.R | 89 - tests/testthat/test_vine_dist.R | 159 +- tests/testthat/test_vinecop.R | 81 - tests/testthat/test_vinecop_dist.R | 230 ++-- 99 files changed, 3766 insertions(+), 3494 deletions(-)
Title: Australian Government Bureau of Meteorology ('BOM') Data Client
Description: Provides functions to interface with Australian Government Bureau
of Meteorology ('BOM') data, fetching data and returning a tidy data frame
of precis forecasts, historical and current weather data from stations,
agriculture bulletin data, 'BOM' 0900 or 1500 weather bulletins and
downloading and importing radar and satellite imagery files. Data (c)
Australian Government Bureau of Meteorology Creative Commons (CC)
Attribution 3.0 licence or Public Access Licence (PAL) as appropriate. See
<http://www.bom.gov.au/other/copyright.shtml> for further details.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Jonathan Carroll [aut] (<https://orcid.org/0000-0002-1404-5264>),
James Goldie [aut] (<https://orcid.org/0000-0002-5024-6207>),
Dean Marchiori [aut],
Mark Padgham [aut, rev] (<https://orcid.org/0000-0003-2172-5265>),
Hugh Parsonage [aut] (<https://orcid.org/0000-0003-4055-0835>),
Keith Pembleton [aut] (<https://orcid.org/0000-0002-1896-4516>),
James Balamuta [ctb] (<https://orcid.org/0000-0003-2826-8458>),
Brooke Anderson [rev] (<https://orcid.org/0000-0002-5012-9035>)
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between bomrang versions 0.5.0 dated 2019-03-21 and 0.6.0 dated 2019-07-04
bomrang-0.5.0/bomrang/man/figures/image_error_message.gif |only bomrang-0.6.0/bomrang/DESCRIPTION | 16 bomrang-0.6.0/bomrang/MD5 | 69 - bomrang-0.6.0/bomrang/NAMESPACE | 3 bomrang-0.6.0/bomrang/NEWS.md | 31 bomrang-0.6.0/bomrang/R/bomrang.r | 2 bomrang-0.6.0/bomrang/R/get_historical.R | 6 bomrang-0.6.0/bomrang/R/get_radar_imagery.R | 16 bomrang-0.6.0/bomrang/R/get_satellite_imagery.R | 7 bomrang-0.6.0/bomrang/R/internal_functions.R | 6 bomrang-0.6.0/bomrang/R/sweep_for_forecast_towns.R |only bomrang-0.6.0/bomrang/R/update_forecast_towns.R | 2 bomrang-0.6.0/bomrang/R/update_station_locations.R | 26 bomrang-0.6.0/bomrang/R/utils-pipe.R | 5 bomrang-0.6.0/bomrang/R/zzz.R | 8 bomrang-0.6.0/bomrang/README.md | 13 bomrang-0.6.0/bomrang/build/vignette.rds |binary bomrang-0.6.0/bomrang/inst/doc/bomrang.R | 4 bomrang-0.6.0/bomrang/inst/doc/bomrang.Rmd | 35 bomrang-0.6.0/bomrang/inst/doc/bomrang.html | 497 +++++----- bomrang-0.6.0/bomrang/inst/doc/use_case.html | 152 +-- bomrang-0.6.0/bomrang/inst/error_images |only bomrang-0.6.0/bomrang/inst/extdata/JSONurl_site_list.rda |binary bomrang-0.6.0/bomrang/inst/extdata/current_stations_site_list.rda |binary bomrang-0.6.0/bomrang/inst/extdata/marine_AAC_codes.rda |binary bomrang-0.6.0/bomrang/inst/extdata/radar_locations.rda |binary bomrang-0.6.0/bomrang/man/bomrang.Rd | 4 bomrang-0.6.0/bomrang/man/get_historical.Rd | 6 bomrang-0.6.0/bomrang/man/get_radar_imagery.Rd | 2 bomrang-0.6.0/bomrang/man/pipe.Rd | 2 bomrang-0.6.0/bomrang/man/reexports.Rd | 5 bomrang-0.6.0/bomrang/man/sweep_for_forecast_towns.Rd |only bomrang-0.6.0/bomrang/tests/testthat/test-get_precis_forecast.R | 3 bomrang-0.6.0/bomrang/tests/testthat/test-get_radar_imagery.R | 4 bomrang-0.6.0/bomrang/tests/testthat/test-sweep_for_forecast_towns.R |only bomrang-0.6.0/bomrang/tests/testthat/test-update_forecast_towns.R | 6 bomrang-0.6.0/bomrang/tests/testthat/test-update_station_locations.R | 8 bomrang-0.6.0/bomrang/vignettes/bomrang.Rmd | 35 38 files changed, 568 insertions(+), 405 deletions(-)
Title: Narrowest-Over-Threshold Change-Point Detection
Description: Provides efficient implementation of the Narrowest-Over-Threshold methodology for detecting an unknown number of change-points occurring at unknown locations in one-dimensional data following deterministic signal + noise model, see R. Baranowski, Y. Chen and P. Fryzlewicz (2019) <doi:10.1111/rssb.12322>. Currently implemented scenarios are: piecewise-constant signal, piecewise-constant signal with a heavy-tailed noise, piecewise-linear signal, piecewise-quadratic signal, piecewise-constant signal and with piecewise-constant variance of the noise.
Author: Rafal Baranowski, Yining Chen, Piotr Fryzlewicz
Maintainer: Rafal Baranowski <package_maintenance@rbaranowski.com>
Diff between not versions 1.0 dated 2016-08-24 and 1.2 dated 2019-07-04
DESCRIPTION | 13 ++++++------- MD5 | 35 ++++++++++++++++++----------------- NAMESPACE | 2 +- R/features.R | 2 +- R/not.R | 8 ++++---- R/penalties.R | 4 ++-- R/random.intervals.R | 22 +++++++++++++++------- man/aic.penalty.Rd | 3 +-- man/features.Rd | 3 +-- man/loglik.not.Rd | 1 - man/not-package.Rd | 3 +-- man/not.Rd | 8 ++++---- man/plot.not.Rd | 1 - man/predict.not.Rd | 1 - man/random.intervals.Rd | 5 +++-- man/residuals.not.Rd | 4 ++-- man/sic.penalty.Rd | 3 +-- src/not.c | 4 +--- src/not_init.c |only 19 files changed, 61 insertions(+), 61 deletions(-)
Title: Medical Devices Surveillance
Description: A set of core functions for handling medical device event data in
the context of post-market surveillance, pharmacovigilance, signal detection
and trending, and regulatory reporting. Primary inputs are data on events by
device and data on exposures by device. Outputs include: standardized
device-event and exposure datasets, defined analyses, and time series.
Author: Gary Chung [aut, cre]
Maintainer: Gary Chung <gchung05@gmail.com>
Diff between mds versions 0.2.1 dated 2018-12-10 and 0.3.0 dated 2019-07-04
DESCRIPTION | 6 MD5 | 78 - NAMESPACE | 23 NEWS.md | 109 - R/data.R | 136 +- R/define_analyses.R | 1134 +++++++++------- R/plot.R | 170 +- R/standardize_device_events.R | 558 ++++---- R/standardize_exposure.R | 430 +++--- R/time_series.R | 881 +++++++----- R/utils.R | 319 ++-- README.md | 178 +- build/vignette.rds |binary data/maude.rda |binary data/sales.rda |binary inst/doc/mds_intro.R | 288 ++-- inst/doc/mds_intro.Rmd | 968 +++++++------- inst/doc/mds_intro.html | 2651 ++++++++++++++++++++------------------- man/char_to_df.Rd | 44 man/convert_date.Rd | 60 man/define_analyses.Rd | 308 ++-- man/define_analyses_dataframe.Rd | 36 man/deviceevent.Rd | 236 +-- man/exposure.Rd | 172 +- man/fNA.Rd | 48 man/input_param_checker.Rd | 66 man/maude.Rd | 98 - man/mds_ts.Rd | 40 man/next_dev.Rd | 40 man/next_ev.Rd | 40 man/plot.mds_ts.Rd | 98 - man/sales.Rd | 54 man/summary.mds_das.Rd | 46 man/time_series.Rd | 217 +-- tests/testthat.R | 8 tests/testthat/test_da.R | 890 ++++++------- tests/testthat/test_de.R | 316 ++-- tests/testthat/test_exp.R | 219 +-- tests/testthat/test_ts.R | 407 ++++- vignettes/mds_intro.Rmd | 968 +++++++------- 40 files changed, 6580 insertions(+), 5760 deletions(-)
Title: Relational Query Generator for Data Manipulation at Scale
Description: A piped query generator based on Edgar F. Codd's relational
algebra, and on production experience using 'SQL' and 'dplyr' at big data
scale. The design represents an attempt to make 'SQL' more teachable by
denoting composition by a sequential pipeline notation instead of nested
queries or functions. The implementation delivers reliable high
performance data processing on large data systems such as 'Spark',
databases, and 'data.table'. Package features include: data processing trees
or pipelines as observable objects (able to report both columns
produced and columns used), optimized 'SQL' generation as an explicit
user visible table modeling step, plus explicit query reasoning and checking.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rquery versions 1.3.5 dated 2019-06-26 and 1.3.6 dated 2019-07-04
DESCRIPTION | 8 ++--- MD5 | 45 +++++++++++++++--------------- NEWS.md | 5 +++ R/drop_columns.R | 16 ++++++++-- R/extend.R | 10 +++++- R/natural_join.R | 26 ++++++++++------- R/order_by.R | 6 ++++ R/rename.R | 6 +++- R/select_columns.R | 4 ++ R/table_source.R | 8 ++++- README.md | 23 ++++++++------- inst/doc/AssigmentPartitioner.html | 4 +- inst/doc/Parameterized_rquery.html | 4 +- inst/doc/PipeableSQL.html | 4 +- inst/doc/QueryGeneration.html | 4 +- inst/doc/R_mapping.html | 4 +- inst/doc/rquery_intro.html | 4 +- inst/doc/rquery_substitution.html | 4 +- inst/doc/sql_quoting.html | 4 +- inst/unit_tests/test_join_check.R | 51 ++++++++++++++++++++++++++++++++++ inst/unit_tests/test_rename_columns.R |only man/drop_columns.Rd | 2 - man/mk_td.Rd | 2 - man/natural_join.Rd | 11 ------- 24 files changed, 172 insertions(+), 83 deletions(-)
Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows
for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rqdatatable versions 1.1.8 dated 2019-06-01 and 1.1.9 dated 2019-07-04
DESCRIPTION | 10 ++-- MD5 | 36 +++++++++------ NEWS.md | 6 ++ R/make_dt_lookup_by_column.R | 3 - R/relop_extend.R | 77 +++++++++++++++++++++------------- R/relop_order_expr.R | 3 - R/relop_project.R | 44 +++++++++++-------- R/relop_select_rows.R | 3 - R/relop_theta_join.R | 3 - README.md | 17 +++++-- build/vignette.rds |binary inst/doc/GroupedSampling.html | 9 ++- inst/doc/R_mapping.R |only inst/doc/R_mapping.Rmd |only inst/doc/R_mapping.html |only inst/doc/logisticexample.html | 69 ++++++++++++++++-------------- inst/unit_tests/test_distinct.R |only inst/unit_tests/test_mk_dt_l_by_col.R |only inst/unit_tests/test_relop_extend.R | 31 ++++++------- inst/unit_tests/test_relop_project.R | 20 +++++++- man/ex_data_table.relop_project.Rd | 5 -- vignettes/R_mapping.Rmd |only 22 files changed, 202 insertions(+), 134 deletions(-)
Title: Utilities for Quantiles
Description: Functions for unconditional and conditional quantiles. These
include methods for transformation-based quantile regression,
quantile-based measures of location, scale and shape, methods for quantiles
of discrete variables, quantile-based multiple imputation, and restricted
quantile regression. A vignette is given in Geraci (2016, The R Journal)
<doi:10.32614/RJ-2016-037> and included in the package.
Author: Marco Geraci [aut, cph, cre] (<https://orcid.org/0000-0002-6311-8685>),
Alessio Farcomeni [ctb] (Contributions to midrq code)
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>
Diff between Qtools versions 1.3 dated 2018-04-13 and 1.4 dated 2019-07-04
Qtools-1.3/Qtools/inst/doc/Qtools.pdf |only Qtools-1.3/Qtools/man/coef.rq.bin.Rd |only Qtools-1.3/Qtools/man/fitted.rq.bin.Rd |only Qtools-1.3/Qtools/man/predict.rq.bin.Rd |only Qtools-1.3/Qtools/man/print.rq.bin.Rd |only Qtools-1.3/Qtools/man/rq.bin.Rd |only Qtools-1.3/Qtools/man/rqbinControl.Rd |only Qtools-1.3/Qtools/src/Qtools_init.c |only Qtools-1.3/Qtools/src/simann.f |only Qtools-1.4/Qtools/DESCRIPTION | 23 Qtools-1.4/Qtools/MD5 | 45 - Qtools-1.4/Qtools/NAMESPACE | 27 Qtools-1.4/Qtools/NEWS | 11 Qtools-1.4/Qtools/R/Qtools.R | 906 ++++++++++++++++++------------- Qtools-1.4/Qtools/R/RcppExports.R |only Qtools-1.4/Qtools/build |only Qtools-1.4/Qtools/inst/doc/Qtools.R |only Qtools-1.4/Qtools/inst/doc/Qtools.Rmd |only Qtools-1.4/Qtools/inst/doc/Qtools.html |only Qtools-1.4/Qtools/man/Qtools-internal.Rd | 11 Qtools-1.4/Qtools/man/Qtools-package.Rd | 4 Qtools-1.4/Qtools/man/cmidecdf.Rd |only Qtools-1.4/Qtools/man/coef.midrq.Rd |only Qtools-1.4/Qtools/man/fitted.midrq.Rd |only Qtools-1.4/Qtools/man/mice.impute.rq.Rd | 13 Qtools-1.4/Qtools/man/midrq.Rd |only Qtools-1.4/Qtools/man/midrqControl.Rd |only Qtools-1.4/Qtools/man/predict.midrq.Rd |only Qtools-1.4/Qtools/man/print.cmidecdf.Rd |only Qtools-1.4/Qtools/man/print.midrq.Rd |only Qtools-1.4/Qtools/man/residuals.midrq.Rd |only Qtools-1.4/Qtools/man/rq.counts.Rd | 26 Qtools-1.4/Qtools/man/summary.midrq.Rd |only Qtools-1.4/Qtools/man/vcov.midrq.Rd |only Qtools-1.4/Qtools/src/Qtools.cpp |only Qtools-1.4/Qtools/src/RcppExports.cpp |only Qtools-1.4/Qtools/vignettes |only 37 files changed, 634 insertions(+), 432 deletions(-)
Title: Interfaces to Phylogenetic Software in R
Description: Functions that wrap popular phylogenetic software for sequence
alignment, masking of sequence alignments, and estimation of phylogenies and
ancestral character states.
Author: Christoph Heibl [aut, cre],
Natalie Cusimano [aut],
Franz-Sebastian Krah [aut]
Maintainer: Christoph Heibl <christoph.heibl@gmx.net>
Diff between ips versions 0.0-7 dated 2014-11-09 and 0.0.11 dated 2019-07-04
ips-0.0-7/ips/ChangeLog |only ips-0.0-7/ips/R/mrbayes.mixed.R |only ips-0.0-7/ips/R/write.partitioned.nex.R |only ips-0.0-7/ips/man/noi.Rd |only ips-0.0-7/ips/man/read.fas.Rd |only ips-0.0-7/ips/man/write.partitioned.nex.Rd |only ips-0.0.11/ips/DESCRIPTION | 30 +- ips-0.0.11/ips/MD5 | 176 ++++++++++------ ips-0.0.11/ips/NAMESPACE | 63 +++++ ips-0.0.11/ips/R/DNAbin2index.R |only ips-0.0.11/ips/R/aliscore.R | 106 +++++++-- ips-0.0.11/ips/R/are.tips.consecutive.R |only ips-0.0.11/ips/R/assembleDataNode.R |only ips-0.0.11/ips/R/assembleDistributionNode.R |only ips-0.0.11/ips/R/assembleInitNode.R |only ips-0.0.11/ips/R/assembleLoggers.R |only ips-0.0.11/ips/R/assembleOperators.R |only ips-0.0.11/ips/R/assembleStateNode.R |only ips-0.0.11/ips/R/code.simple.gaps.R | 148 +++++++------ ips-0.0.11/ips/R/collapseUnsupportedEdges.R | 80 ++++++- ips-0.0.11/ips/R/del.miss.R |only ips-0.0.11/ips/R/deleteEmptyCells.R | 95 ++++++-- ips-0.0.11/ips/R/deleteGaps.R | 38 +++ ips-0.0.11/ips/R/descendants.R | 66 ++++-- ips-0.0.11/ips/R/eoi.R |only ips-0.0.11/ips/R/findORF.R |only ips-0.0.11/ips/R/fixNodes.R | 40 +-- ips-0.0.11/ips/R/forceEqualTipHeights.R |only ips-0.0.11/ips/R/formatSet.R |only ips-0.0.11/ips/R/gblocks.R | 151 +++++++++++--- ips-0.0.11/ips/R/index2DNAbin.R |only ips-0.0.11/ips/R/mafft.R | 189 +++++++++++++---- ips-0.0.11/ips/R/mafft.merge.R |only ips-0.0.11/ips/R/matrixBlock.R |only ips-0.0.11/ips/R/mrbayes.R | 150 ++++++++++---- ips-0.0.11/ips/R/mrbayes.lset.R |only ips-0.0.11/ips/R/mrbayes.mcmc.R |only ips-0.0.11/ips/R/mrbayes.prset.R |only ips-0.0.11/ips/R/multistateMCMC.R | 9 ips-0.0.11/ips/R/multistateML.R | 9 ips-0.0.11/ips/R/neighboringPairs.R |only ips-0.0.11/ips/R/noi.R | 34 +-- ips-0.0.11/ips/R/ntip.R |only ips-0.0.11/ips/R/oi.R |only ips-0.0.11/ips/R/partitionfinder.R |only ips-0.0.11/ips/R/pathd8.R |only ips-0.0.11/ips/R/phylo2mafft.R | 40 ++- ips-0.0.11/ips/R/phylo2mst.R |only ips-0.0.11/ips/R/pis.R | 5 ips-0.0.11/ips/R/prank.R | 123 ++++++----- ips-0.0.11/ips/R/raxml.R | 242 +++++++++++++++++----- ips-0.0.11/ips/R/raxml.partitions.R | 8 ips-0.0.11/ips/R/rbeauti.R | 246 ++++------------------- ips-0.0.11/ips/R/rc.R |only ips-0.0.11/ips/R/read.R |only ips-0.0.11/ips/R/read.fas.R | 69 ++++-- ips-0.0.11/ips/R/read.nex.R | 12 - ips-0.0.11/ips/R/read.phy.R | 6 ips-0.0.11/ips/R/setClock.R |only ips-0.0.11/ips/R/setMCMC.R |only ips-0.0.11/ips/R/sister.R | 63 +++++ ips-0.0.11/ips/R/splitIntoClades.R |only ips-0.0.11/ips/R/str2cha.R |only ips-0.0.11/ips/R/terminal.clades.R | 9 ips-0.0.11/ips/R/terminalSisters.R |only ips-0.0.11/ips/R/tipHeights.R | 8 ips-0.0.11/ips/R/trimEnds.R | 132 +++++++++--- ips-0.0.11/ips/R/unlistFirstLevel.R |only ips-0.0.11/ips/R/unresolve.clade.R | 6 ips-0.0.11/ips/R/write.fas.R | 115 ++++++---- ips-0.0.11/ips/R/write.nex.R | 266 ++++++++++++++----------- ips-0.0.11/ips/R/write.phy.R | 50 +++- ips-0.0.11/ips/README.md |only ips-0.0.11/ips/TODO | 1 ips-0.0.11/ips/data/ips.16S.rda |binary ips-0.0.11/ips/data/ips.28S.rda |binary ips-0.0.11/ips/data/ips.cox1.rda |binary ips-0.0.11/ips/data/ips.tree.rda |binary ips-0.0.11/ips/inst/NEWS.Rd |only ips-0.0.11/ips/man/DNAbin2index.Rd |only ips-0.0.11/ips/man/aliscore.Rd | 82 +++---- ips-0.0.11/ips/man/collapseUnsupportedEdges.Rd | 37 +-- ips-0.0.11/ips/man/del.miss.Rd |only ips-0.0.11/ips/man/deleteEmptyCells.Rd | 80 ++++--- ips-0.0.11/ips/man/deleteGaps.Rd | 56 +++-- ips-0.0.11/ips/man/descendants.Rd | 33 +-- ips-0.0.11/ips/man/forceEqualTipHeights.Rd |only ips-0.0.11/ips/man/gblocks.Rd | 133 ++++++++---- ips-0.0.11/ips/man/index2DNAbin.Rd |only ips-0.0.11/ips/man/ips-internal.Rd | 15 + ips-0.0.11/ips/man/ips-package.Rd | 10 ips-0.0.11/ips/man/ips.16S.Rd | 2 ips-0.0.11/ips/man/ips.28S.Rd | 2 ips-0.0.11/ips/man/ips.cox1.Rd | 2 ips-0.0.11/ips/man/mafft.Rd | 170 +++++++++------ ips-0.0.11/ips/man/mafft.merge.Rd |only ips-0.0.11/ips/man/mrbayes.Rd | 103 ++++----- ips-0.0.11/ips/man/mrbayes.lset.Rd |only ips-0.0.11/ips/man/mrbayes.mcmc.Rd |only ips-0.0.11/ips/man/mrbayes.prset.Rd |only ips-0.0.11/ips/man/multistate.Rd | 2 ips-0.0.11/ips/man/neighboringPairs.Rd |only ips-0.0.11/ips/man/ntip.Rd |only ips-0.0.11/ips/man/oi.Rd |only ips-0.0.11/ips/man/partitionfinder.Rd |only ips-0.0.11/ips/man/pathd8.Rd |only ips-0.0.11/ips/man/phylo2mafft.Rd |only ips-0.0.11/ips/man/phylo2mst.Rd |only ips-0.0.11/ips/man/prank.Rd | 90 ++++---- ips-0.0.11/ips/man/raxml.Rd | 224 +++++++++++---------- ips-0.0.11/ips/man/rbeauti.Rd | 7 ips-0.0.11/ips/man/read.Rd |only ips-0.0.11/ips/man/sister.Rd | 74 +++--- ips-0.0.11/ips/man/splitIntoClades.Rd |only ips-0.0.11/ips/man/terminalSisters.Rd |only ips-0.0.11/ips/man/traitRate.Rd | 2 ips-0.0.11/ips/man/trimEnds.Rd | 52 ++-- ips-0.0.11/ips/man/unlistFirstLevel.Rd |only ips-0.0.11/ips/man/write.fas.Rd | 67 +++--- 119 files changed, 2515 insertions(+), 1513 deletions(-)
Title: Additional Layout Algorithms for Network Visualizations
Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'.
Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>.
Some more specific algorithms allow to emphasize hidden group structures in networks or focus on specific nodes.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>
Diff between graphlayouts versions 0.1.0 dated 2019-04-05 and 0.2.0 dated 2019-07-04
DESCRIPTION | 6 - MD5 | 25 ++--- NEWS.md | 6 + R/RcppExports.R | 4 R/backbone_function.R | 161 +++++++++++++++++------------------- R/stress_function.R | 7 + README.md | 22 ++-- build/vignette.rds |binary inst/doc/introduction.html | 20 ++-- man/figures/README-backbone-1.png |binary man/figures/README-flex_cent-1.png |binary man/figures/README-flex_focus-1.png |binary src/RcppExports.cpp | 13 ++ src/reweight.cpp |only 14 files changed, 146 insertions(+), 118 deletions(-)
Title: Data Analysis using Bootstrap-Coupled Estimation
Description: Data Analysis using Bootstrap-Coupled ESTimation.
Estimation statistics is a simple framework that avoids the pitfalls of
significance testing. It uses familiar statistical concepts: means,
mean differences, and error bars. More importantly, it focuses on the
effect size of one's experiment/intervention, as opposed to a false
dichotomy engendered by P values.
An estimation plot has two key features:
1. It presents all datapoints as a swarmplot, which orders each point to
display the underlying distribution.
2. It presents the effect size as a bootstrap 95% confidence interval on a
separate but aligned axes.
Estimation plots are introduced in Ho et al., Nature Methods 2019, 1548-7105.
<doi:10.1038/s41592-019-0470-3>.
The free-to-view PDF is located at <https://rdcu.be/bHhJ4>.
Author: Joses W. Ho [cre, aut],
Tayfun Tumkaya [aut]
Maintainer: Joses W. Ho <joseshowh@gmail.com>
Diff between dabestr versions 0.2.1 dated 2019-06-26 and 0.2.2 dated 2019-07-04
DESCRIPTION | 8 MD5 | 91 NEWS.md | 3 R/main.R | 11 R/plot.R | 11 README.md | 14 inst/doc/bootstrap-confidence-intervals.html | 4 inst/doc/robust-statistical-visualization.R | 2 inst/doc/robust-statistical-visualization.Rmd | 2 inst/doc/robust-statistical-visualization.html | 6 inst/doc/using-dabestr.html | 16 tests/figs/aesthetics/cumming-custom-effect-size-marker.svg |181638 ++++----- tests/figs/aesthetics/cumming-custom-effect-size-ylimits.svg |181638 ++++----- tests/figs/aesthetics/cumming-custom-groupwidth.svg |181634 ++++----- tests/figs/aesthetics/cumming-custom-palette.svg |181634 ++++----- tests/figs/aesthetics/cumming-custom-rawplot-marker-size.svg |181634 ++++----- tests/figs/aesthetics/cumming-custom-swarm-ylimits.svg |181630 ++++----- tests/figs/aesthetics/cumming-custom-theme.svg |181694 +++++----- tests/figs/aesthetics/cumming-custom-ylabels.svg |181634 ++++----- tests/figs/aesthetics/gardner-altman-paired-custom-palette.svg |30178 - tests/figs/aesthetics/gardner-altman-paired-custom-ylabels.svg |30178 - tests/figs/aesthetics/gardner-altman-paired-custom-ylimits.svg |30182 - tests/figs/aesthetics/gardner-altman-unpaired-custom-effect-size-marker.svg |30732 - tests/figs/aesthetics/gardner-altman-unpaired-custom-group-width.svg |30732 - tests/figs/aesthetics/gardner-altman-unpaired-custom-palette.svg |30732 - tests/figs/aesthetics/gardner-altman-unpaired-custom-rawplot-marker-size.svg |30732 - tests/figs/aesthetics/gardner-altman-unpaired-custom-ylabels.svg |30732 - tests/figs/aesthetics/gardner-altman-unpaired-custom-ylimits.svg |30744 - tests/figs/cumming-plots/cumming-multi-group-shared-control.svg |181634 ++++----- tests/figs/cumming-plots/cumming-multi-two-groups-paired-slopegraph.svg |120300 +++--- tests/figs/cumming-plots/cumming-multi-two-groups-paired-swarm.svg |121110 +++--- tests/figs/cumming-plots/cumming-multi-two-groups-unpaired.svg |121106 +++--- tests/figs/cumming-plots/cumming-shared-control.svg |80802 ++-- tests/figs/cumming-plots/cumming-two-group-paired.svg |40186 +- tests/figs/cumming-plots/cumming-two-groups-unpaired.svg |40432 +- tests/figs/deps.txt | 5 tests/figs/gardner-altman-plots/gardner-altman-paired-reverse.svg |30182 - tests/figs/gardner-altman-plots/gardner-altman-paired.svg |30178 - tests/figs/gardner-altman-plots/gardner-altman-unpaired-reverse.svg |30736 - tests/figs/gardner-altman-plots/gardner-altman-unpaired.svg |30732 - tests/figs/test-unquoting |only tests/testthat/Rplots.pdf |only tests/testthat/test-aesthetics.R | 34 tests/testthat/test-bootstrap.R | 6 tests/testthat/test-cumming-plots.R | 14 tests/testthat/test-gardner-altman-plots.R | 8 tests/testthat/test-unquoting.R |only vignettes/robust-statistical-visualization.Rmd | 2 48 files changed, 1277956 insertions(+), 1277757 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.9.3 dated 2019-05-03 and 1.9.4 dated 2019-07-04
DESCRIPTION | 8 MD5 | 24 +- NEWS.md | 4 R/checkList.R | 2 build/vignette.rds |binary inst/doc/checkmate.html | 394 +++++++++++++++++----------------- man/checkmate-package.Rd | 2 src/checks.c | 2 src/init.c | 2 src/integerish.c | 2 tests/testthat/test_checkInteger.R | 6 tests/testthat/test_checkIntegerish.R | 5 tests/testthat/test_checkNumeric.R | 4 13 files changed, 246 insertions(+), 209 deletions(-)
Title: Wrapper to the 'spaCy' 'NLP' Library
Description: An R wrapper to the 'Python' 'spaCy' 'NLP' library,
from <http://spacy.io>.
Author: Kenneth Benoit [cre, aut, cph]
(<https://orcid.org/0000-0002-0797-564X>),
Akitaka Matsuo [aut] (<https://orcid.org/0000-0002-3323-6330>),
European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between spacyr versions 1.0 dated 2018-12-15 and 1.2 dated 2019-07-04
spacyr-1.0/spacyr/inst/doc/using_spacyr.pdf |only spacyr-1.0/spacyr/inst/doc/using_spacyr.pdf.asis |only spacyr-1.0/spacyr/vignettes/using_spacyr.html |only spacyr-1.0/spacyr/vignettes/using_spacyr.pdf.asis |only spacyr-1.0/spacyr/vignettes/using_spacyr_files |only spacyr-1.2/spacyr/DESCRIPTION | 9 spacyr-1.2/spacyr/MD5 | 59 ++--- spacyr-1.2/spacyr/NEWS.md | 27 +- spacyr-1.2/spacyr/R/parse-extractor-functions.R | 5 spacyr-1.2/spacyr/R/spacy_extract_entity.R | 8 spacyr-1.2/spacyr/R/spacy_extract_nounphrases.R | 9 spacyr-1.2/spacyr/R/spacy_initialize.R | 26 +- spacyr-1.2/spacyr/R/spacy_install.R | 103 ++++++---- spacyr-1.2/spacyr/R/spacy_parse.R | 40 ++- spacyr-1.2/spacyr/R/spacy_tokenize.R | 3 spacyr-1.2/spacyr/build/vignette.rds |binary spacyr-1.2/spacyr/inst/WORDLIST | 12 + spacyr-1.2/spacyr/inst/doc/using_spacyr.html |only spacyr-1.2/spacyr/inst/doc/using_spacyr.html.asis |only spacyr-1.2/spacyr/man/spacy_extract_entity.Rd | 4 spacyr-1.2/spacyr/man/spacy_extract_nounphrases.Rd | 4 spacyr-1.2/spacyr/man/spacy_install.Rd | 7 spacyr-1.2/spacyr/man/spacy_parse.Rd | 2 spacyr-1.2/spacyr/man/spacy_tokenize.Rd | 4 spacyr-1.2/spacyr/man/spacy_upgrade.Rd | 9 spacyr-1.2/spacyr/tests/lint.R |only spacyr-1.2/spacyr/tests/spelling.R | 21 -- spacyr-1.2/spacyr/tests/testthat.R | 4 spacyr-1.2/spacyr/tests/testthat/test-2-spacy_parse.R | 18 + spacyr-1.2/spacyr/tests/testthat/test-3-spacy_tokenize.R | 2 spacyr-1.2/spacyr/tests/testthat/test-4-entity-functions.R | 28 ++ spacyr-1.2/spacyr/tests/testthat/test-5-nounphrase-functions.R | 41 +++ spacyr-1.2/spacyr/tests/testthat/test-7-spacy-install.R | 44 +++- spacyr-1.2/spacyr/vignettes/using_spacyr.Rmd | 8 spacyr-1.2/spacyr/vignettes/using_spacyr.html.asis |only 35 files changed, 335 insertions(+), 162 deletions(-)
Title: Credit Risk Scorecard
Description: The `scorecard` package makes the development of credit risk scorecard
easier and efficient by providing functions for some common tasks,
such as data partition, variable selection, woe binning, scorecard scaling,
performance evaluation and report generation. These functions can also used
in the development of machine learning models.
The references including:
1. Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard:
Development and Implementation Using SAS.
2. Siddiqi, N. (2006, ISBN: 9780471754510). Credit risk scorecards.
Developing and Implementing Intelligent Credit Scoring.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between scorecard versions 0.2.4 dated 2019-03-26 and 0.2.5 dated 2019-07-04
DESCRIPTION | 6 - MD5 | 30 +++---- NAMESPACE | 4 NEWS.md | 9 ++ R/condition_fun.R | 90 ++++++++++++++++++--- R/perf.R | 39 +++++---- R/scorecard.R | 18 ---- R/var_filter.R | 6 + R/woebin.R | 225 ++++++++++++++++++++++++++++------------------------- build/vignette.rds |binary inst/doc/demo.html | 9 +- man/gains_table.Rd | 6 - man/perf_eva.Rd | 2 man/perf_psi.Rd | 2 man/woebin.Rd | 13 ++- man/woebin_adj.Rd | 5 - 16 files changed, 288 insertions(+), 176 deletions(-)
Title: Patches to Use 'dplyr' on Remote Data Sources
Description: Patches to use 'dplyr' on remote data sources ('SQL' databases,
'Spark' 2.0.0 and above) in a reliable "generic" fashion (generic meaning
user code works similarly on all such sources, without needing per-source
adaption). Due to the fluctuating nature of 'dplyr'/'dbplyr'/'rlang' 'APIs' this package
is going into maintenance mode. Most of the 'replyr' functions are already
done better by one of the non-monolithic replacement packages: 'wrapr', 'seplyr', 'rquery',
or 'cdata'.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between replyr versions 1.0.0 dated 2019-03-31 and 1.0.1 dated 2019-07-04
DESCRIPTION | 10 MD5 | 40 NEWS.md | 4 R/underscoreReplacements.R | 2 build/vignette.rds |binary inst/doc/DependencySorting.R | 5 inst/doc/DependencySorting.Rmd | 2 inst/doc/DependencySorting.html | 2668 ++++++++++++++++++++++++++++++++++++-- inst/doc/ParametricExample.html | 343 +++- inst/doc/coalesce.html | 425 ++++-- inst/doc/joinController.R | 5 inst/doc/joinController.Rmd | 10 inst/doc/joinController.html | 2799 +++++++++++++++++++++++++++++++++++++--- inst/doc/letExample.R | 2 inst/doc/letExample.Rmd | 2 inst/doc/letExample.html | 361 ++++- inst/doc/replyr.html | 558 +++++-- inst/doc/summary.html | 373 ++++- vignettes/DependencySorting.Rmd | 2 vignettes/joinController.Rmd | 10 vignettes/letExample.Rmd | 2 21 files changed, 6815 insertions(+), 808 deletions(-)
Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Unconstrained and constrained maximum likelihood estimation of Gaussian Mixture Vector Autoregressive (GMVAR)
model, quantile residual tests, graphical diagnostics, simulations, and forecasting.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 1.0.3 dated 2018-09-22 and 1.1.0 dated 2019-07-04
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Title: Dynamical Systems Approach to Infectious Disease Epidemiology
Description: A collection of 'shiny' apps that allow for the simulation and
exploration of various infectious disease transmission dynamics scenarios.
The purpose of the package is to help individuals learn
about infectious disease epidemiology from a dynamical systems perspective.
All apps include explanations of the underlying models and instructions on
what to do with the models.
Author: Andreas Handel [aut, cre] (<https://orcid.org/0000-0002-4622-1146>),
Christine Casey [ctb] (Parasite Model App),
Isaac Chun-Hai Fung [ctb],
Ronald Galiwango [ctb] (Surveillance App),
Chase Golden [ctb] (Maternal Immunity App),
Spencer Hall [ctb],
Ben Listyg [ctb],
Brian McKay [ctb],
John Rossow [ctb],
Sina Solaimanpour [ctb],
Kevin Spiegel [ctb] (Global Warming App),
Henok Woldu [ctb]
Maintainer: Andreas Handel <ahandel@uga.edu>
Diff between DSAIDE versions 0.8.0 dated 2019-03-30 and 0.8.2 dated 2019-07-04
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Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Lionel Henry [aut],
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 0.8.2 dated 2019-06-29 and 0.8.3 dated 2019-07-04
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/top-n.R | 22 ++++++++++------------ build/dplyr.pdf |binary inst/doc/dplyr.html | 2 +- inst/doc/programming.html | 10 +++++----- inst/include/dplyr/data/DataMask.h | 3 +++ 8 files changed, 35 insertions(+), 29 deletions(-)
Title: Read Large Text Files
Description: Read large text files by splitting them in smaller files.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigreadr versions 0.1.5 dated 2019-06-17 and 0.1.6 dated 2019-07-04
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/read.R | 13 +++++++++---- README.md | 2 ++ man/fread2.Rd | 9 +++++---- tests/testthat/test-read.R | 9 +++++++++ 6 files changed, 34 insertions(+), 17 deletions(-)
Title: Zig-Zag Sampler
Description: Implements the Zig-Zag algorithm (Bierkens, Fearnhead, Roberts, 2016) <arXiv:1607.03188> applied and Bouncy Particle Sampler <arXiv:1510.02451> for a Gaussian target and Student distribution.
Author: Joris Bierkens
Maintainer: Joris Bierkens <j.bierkens@vu.nl>
Diff between RZigZag versions 0.1.6 dated 2018-04-30 and 0.2.0 dated 2019-07-04
RZigZag-0.1.6/RZigZag/README.md |only RZigZag-0.1.6/RZigZag/src/LogisticData.cpp |only RZigZag-0.1.6/RZigZag/src/LogisticData.h |only RZigZag-0.1.6/RZigZag/src/Makevars |only RZigZag-0.1.6/RZigZag/src/Makevars.win |only RZigZag-0.2.0/RZigZag/DESCRIPTION | 14 RZigZag-0.2.0/RZigZag/MD5 | 49 RZigZag-0.2.0/RZigZag/NAMESPACE | 8 RZigZag-0.2.0/RZigZag/NEWS.md | 8 RZigZag-0.2.0/RZigZag/R/RZigZag.R | 11 RZigZag-0.2.0/RZigZag/R/RcppExports.R | 287 +++- RZigZag-0.2.0/RZigZag/man/BPSGaussian.Rd | 46 RZigZag-0.2.0/RZigZag/man/BPSIIDGaussian.Rd |only RZigZag-0.2.0/RZigZag/man/BPSStudentT.Rd |only RZigZag-0.2.0/RZigZag/man/DiscreteSamples.Rd |only RZigZag-0.2.0/RZigZag/man/EstimateCovarianceMatrix.Rd |only RZigZag-0.2.0/RZigZag/man/EstimateESS.Rd |only RZigZag-0.2.0/RZigZag/man/EstimateMoment.Rd |only RZigZag-0.2.0/RZigZag/man/RZigZag.Rd | 9 RZigZag-0.2.0/RZigZag/man/ZigZagGaussian.Rd | 42 RZigZag-0.2.0/RZigZag/man/ZigZagIIDGaussian.Rd |only RZigZag-0.2.0/RZigZag/man/ZigZagLogistic.Rd | 59 RZigZag-0.2.0/RZigZag/man/ZigZagStudentT.Rd |only RZigZag-0.2.0/RZigZag/src/GaussianSampler.cpp |only RZigZag-0.2.0/RZigZag/src/GaussianSampler.h |only RZigZag-0.2.0/RZigZag/src/LogisticSampler.cpp |only RZigZag-0.2.0/RZigZag/src/LogisticSampler.h |only RZigZag-0.2.0/RZigZag/src/PostProcess.cpp |only RZigZag-0.2.0/RZigZag/src/PostProcess.h |only RZigZag-0.2.0/RZigZag/src/RInterface.cpp |only RZigZag-0.2.0/RZigZag/src/RInterface.h |only RZigZag-0.2.0/RZigZag/src/RZigZag.cpp | 1064 ++++++------------ RZigZag-0.2.0/RZigZag/src/RZigZag.h | 58 RZigZag-0.2.0/RZigZag/src/RcppExports.cpp | 195 ++- RZigZag-0.2.0/RZigZag/src/VariousSamplers.cpp |only RZigZag-0.2.0/RZigZag/src/VariousSamplers.h |only RZigZag-0.2.0/RZigZag/src/ZigZag.cpp |only RZigZag-0.2.0/RZigZag/src/ZigZag.h |only 38 files changed, 883 insertions(+), 967 deletions(-)
Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the
embedded 'ReadStat' C library,
<https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre],
Evan Miller [aut, cph] (Author of included ReadStat code),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between haven versions 2.1.0 dated 2019-02-19 and 2.1.1 dated 2019-07-04
DESCRIPTION | 8 MD5 | 80 +- NEWS.md | 12 R/as_factor.R | 6 R/labelled.R | 2 build/vignette.rds |binary inst/doc/datetimes.html | 3 inst/doc/semantics.html | 291 ++++--- man/as_factor.Rd | 6 man/labelled.Rd | 2 man/read_dta.Rd | 5 man/read_spss.Rd | 5 man/read_xpt.Rd | 5 src/RcppExports.cpp | 6 src/readstat/readstat.h | 11 src/readstat/readstat_error.c | 11 src/readstat/readstat_iconv.h | 11 src/readstat/readstat_value.c | 36 src/readstat/readstat_writer.c | 36 src/readstat/sas/readstat_sas.c | 30 src/readstat/sas/readstat_sas.h | 2 src/readstat/sas/readstat_sas7bcat_write.c | 1 src/readstat/sas/readstat_sas7bdat_read.c | 24 src/readstat/sas/readstat_sas7bdat_write.c | 21 src/readstat/sas/readstat_xport_read.c | 40 - src/readstat/sas/readstat_xport_write.c | 30 src/readstat/spss/readstat_por_parse.c | 6 src/readstat/spss/readstat_por_parse.rl | 6 src/readstat/spss/readstat_por_write.c | 13 src/readstat/spss/readstat_sav.h | 3 src/readstat/spss/readstat_sav_read.c | 153 +++- src/readstat/spss/readstat_sav_write.c | 225 +++++- src/readstat/spss/readstat_spss.h | 2 src/readstat/stata/readstat_dta_write.c | 32 src/readstat/txt/commands_util.c | 10 src/readstat/txt/commands_util.h | 4 src/readstat/txt/readstat_copy.c | 2 src/readstat/txt/readstat_sas_commands_read.c | 874 ++++++++++++------------ src/readstat/txt/readstat_sas_commands_read.rl | 13 src/readstat/txt/readstat_spss_commands_read.c | 105 +- src/readstat/txt/readstat_spss_commands_read.rl | 15 41 files changed, 1292 insertions(+), 855 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation
of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256',
'crc32', 'xxhash', 'murmurhash' and 'spookyhash' algorithms) permitting easy
comparison of R language objects, as well as functions such as'hmac()' to
create hash-based message authentication code. Please note that this package
is not meant to be deployed for cryptographic purposes for which more
comprehensive (and widely tested) libraries such as 'OpenSSL' should be
used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions
by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx,
Michel Lang, Viliam Simko, Kurt Hornik, Radford Neal, and Kendon Bell.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.19 dated 2019-05-20 and 0.6.20 dated 2019-07-04
digest-0.6.19/digest/tests/AESTest.R |only digest-0.6.19/digest/tests/AESTest.Rout.save |only digest-0.6.19/digest/tests/crc32.R |only digest-0.6.19/digest/tests/digest2intTest.R |only digest-0.6.19/digest/tests/digestTest.R |only digest-0.6.19/digest/tests/digestTest.Rout.save |only digest-0.6.19/digest/tests/hmacTest.R |only digest-0.6.19/digest/tests/hmacTest.Rout.save |only digest-0.6.19/digest/tests/load-unload.R |only digest-0.6.19/digest/tests/num2hexTest.R |only digest-0.6.19/digest/tests/raw.R |only digest-0.6.19/digest/tests/sha1Test.R |only digest-0.6.20/digest/ChangeLog | 52 ++++++++++++++++++++++++ digest-0.6.20/digest/DESCRIPTION | 10 ++-- digest-0.6.20/digest/MD5 | 37 +++++++---------- digest-0.6.20/digest/R/AES.R | 5 -- digest-0.6.20/digest/R/digest.R | 8 +-- digest-0.6.20/digest/R/hmac.R | 6 +- digest-0.6.20/digest/R/sha1.R | 4 - digest-0.6.20/digest/README.md | 20 +++++++++ digest-0.6.20/digest/inst/doc/sha1.html | 4 - digest-0.6.20/digest/inst/tinytest |only digest-0.6.20/digest/tests/tinytest.R |only 23 files changed, 107 insertions(+), 39 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-04 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-18 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-04 0.1.0
Title: Test Analysis Modules
Description: Includes marginal maximum likelihood estimation and joint maximum
likelihood estimation for unidimensional and multidimensional
item response models. The package functionality covers the
Rasch model, 2PL model, 3PL model, generalized partial credit model,
multi-faceted Rasch model, nominal item response model,
structured latent class model, mixture distribution IRT models,
and located latent class models. Latent regression models and
plausible value imputation are also supported. For details see
Adams, Wilson and Wang, 1997 <doi:10.1177/0146621697211001>,
Adams, Wilson and Wu, 1997 <doi:10.3102/10769986022001047>,
Formann, 1982 <doi:10.1002/bimj.4710240209>,
Formann, 1992 <doi:10.1080/01621459.1992.10475229>.
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between TAM versions 3.1-45 dated 2019-03-18 and 3.2-24 dated 2019-07-04
DESCRIPTION | 17 - MD5 | 106 +++++---- NAMESPACE | 28 +- R/IRT.WrightMap.R | 114 ++++------ R/IRT.cv.R |only R/IRT.cv.tam.np.R |only R/IRT.expectedCounts.tam.R | 5 R/IRTLikelihood.cfa.R | 4 R/RcppExports.R | 2 R/designMatrices.mfr.R | 17 - R/designMatrices.mfr_aux.R | 15 - R/designMatrices_aux.R | 32 -- R/plot.tam.R | 9 R/sirt_import_sfsmisc_QUnif.R |only R/summary.msq.itemfit.R | 4 R/summary.tam.jml.R | 101 +------- R/summary.tam.linking.R | 15 + R/tam.jml.R | 16 - R/tam.linking.R | 78 +++--- R/tam.mml.mfr.R | 2 R/tam.np.R | 8 R/tam_Rhat_3splits.R | 3 R/tam_cat_flush_console.R |only R/tam_dmvnorm.R | 7 R/tam_fa_reliability_nonlinearSEM.R | 7 R/tam_ginv.R | 5 R/tam_ginv_scaled.R | 4 R/tam_import_MASS_ginv.R |only R/tam_import_mvtnorm_dmvnorm.R |only R/tam_import_mvtnorm_pmvnorm.R |only R/tam_include_arguments_in_list.R |only R/tam_jml_version2.R | 315 +++++++++++----------------- R/tam_jml_version2_calc_xsi.R | 15 - R/tam_jml_wle.R | 6 R/tam_linking_2studies.R | 31 -- R/tam_linking_chain.R |only R/tam_linking_extract_parameters.R | 11 R/tam_linking_function_haebara_loss.R |only R/tam_linking_irf_discrepancy.R |only R/tam_linking_joint.R |only R/tam_linking_joint_calc_probs.R |only R/tam_mml_3pl_ic.R | 8 R/tam_mml_calc_prob.R | 8 R/tam_mml_create_nodes.R | 4 R/tam_mml_inits_beta.R | 5 R/tam_mml_mfr_dataprep.R | 18 - R/tam_mml_mfr_proc_create_design_matrices.R | 10 R/tam_mml_update_stochastic_nodes.R | 5 R/tam_pv_mcmc_parameter_samples.R | 3 R/tam_pv_mcmc_parameter_summary.R | 3 README.md | 4 build/partial.rdb |binary inst/CITATION | 2 inst/NEWS | 28 ++ man/IRT.cv.Rd |only man/tam.linking.Rd | 61 ++++- man/tam.mml.Rd | 5 man/tam.np.Rd | 8 src/RcppExports.cpp | 2 src/init.c | 2 src/tam_rcpp_tam_np.cpp | 13 - 61 files changed, 547 insertions(+), 619 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for
quantitative text analysis in R. Provides functionality for corpus management,
creating and manipulating tokens and ngrams, exploring keywords in context,
forming and manipulating sparse matrices
of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and
distances, applying content dictionaries, applying supervised and unsupervised machine learning,
visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph]
(<https://orcid.org/0000-0002-0797-564X>),
Kohei Watanabe [aut] (<https://orcid.org/0000-0001-6519-5265>),
Haiyan Wang [aut] (<https://orcid.org/0000-0003-4992-4311>),
Paul Nulty [aut] (<https://orcid.org/0000-0002-7214-4666>),
Adam Obeng [aut] (<https://orcid.org/0000-0002-2906-4775>),
Stefan Müller [aut] (<https://orcid.org/0000-0002-6315-4125>),
Akitaka Matsuo [aut] (<https://orcid.org/0000-0002-3323-6330>),
Jiong Wei Lua [aut],
Patrick O. Perry [aut] (<https://orcid.org/0000-0001-7460-127X>),
Jouni Kuha [aut] (<https://orcid.org/0000-0002-1156-8465>),
Benjamin Lauderdale [aut] (<https://orcid.org/0000-0003-3090-0969>),
William Lowe [aut] (<https://orcid.org/0000-0002-1549-6163>),
Christian Müller [ctb],
Lori Young [dtc] (Lexicoder Sentiment Dictionary 2015),
Stuart Soroka [dtc] (Lexicoder Sentiment Dictionary 2015),
Ian Fellows [cph] (authored wordcloud C source code (modified)),
European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 1.4.3 dated 2019-04-01 and 1.5.0 dated 2019-07-04
quanteda-1.4.3/quanteda/man/read_dict_lexicoder.Rd |only quanteda-1.4.3/quanteda/man/read_dict_liwc.Rd |only quanteda-1.4.3/quanteda/man/read_dict_wordstat.Rd |only quanteda-1.4.3/quanteda/man/read_dict_yoshikoder.Rd |only quanteda-1.4.3/quanteda/src/armadillo.h |only quanteda-1.4.3/quanteda/src/dev.h |only quanteda-1.4.3/quanteda/src/quanteda.h |only quanteda-1.4.3/quanteda/src/recompile.h |only quanteda-1.4.3/quanteda/src/simil_mt.cpp |only quanteda-1.5.0/quanteda/DESCRIPTION | 8 quanteda-1.5.0/quanteda/MD5 | 218 +-- quanteda-1.5.0/quanteda/NAMESPACE | 7 quanteda-1.5.0/quanteda/NEWS.md | 23 quanteda-1.5.0/quanteda/R/RcppExports.R | 20 quanteda-1.5.0/quanteda/R/corpus-methods-base.R | 14 quanteda-1.5.0/quanteda/R/corpus.R | 2 quanteda-1.5.0/quanteda/R/corpus_sample.R | 20 quanteda-1.5.0/quanteda/R/dfm_group.R | 5 quanteda-1.5.0/quanteda/R/dfm_select.R | 96 - quanteda-1.5.0/quanteda/R/dfm_weight.R | 3 quanteda-1.5.0/quanteda/R/dictionaries.R | 84 - quanteda-1.5.0/quanteda/R/docnames.R | 11 quanteda-1.5.0/quanteda/R/docvars.R | 14 quanteda-1.5.0/quanteda/R/fcm-methods.R | 2 quanteda-1.5.0/quanteda/R/fcm.R | 87 - quanteda-1.5.0/quanteda/R/kwic.R | 32 quanteda-1.5.0/quanteda/R/pattern2fixed.R | 36 quanteda-1.5.0/quanteda/R/textplot_network.R | 27 quanteda-1.5.0/quanteda/R/textstat_frequency.R | 4 quanteda-1.5.0/quanteda/R/textstat_keyness.R | 4 quanteda-1.5.0/quanteda/R/textstat_readability.R | 12 quanteda-1.5.0/quanteda/R/textstat_simil.R | 646 ++++++--- quanteda-1.5.0/quanteda/R/textstat_simil_old.R | 30 quanteda-1.5.0/quanteda/R/tokens.R | 152 +- quanteda-1.5.0/quanteda/R/tokens_lookup.R | 92 - quanteda-1.5.0/quanteda/R/tokens_select.R | 79 - quanteda-1.5.0/quanteda/R/utils.R | 21 quanteda-1.5.0/quanteda/build/vignette.rds |binary quanteda-1.5.0/quanteda/inst/WORDLIST | 6 quanteda-1.5.0/quanteda/inst/doc/quickstart.R | 205 +- quanteda-1.5.0/quanteda/inst/doc/quickstart.Rmd | 212 +-- quanteda-1.5.0/quanteda/inst/doc/quickstart.html | 406 +++-- quanteda-1.5.0/quanteda/inst/extdata |only quanteda-1.5.0/quanteda/inst/include |only quanteda-1.5.0/quanteda/man/as.matrix.simil.Rd | 2 quanteda-1.5.0/quanteda/man/as.matrix.textstat_simil_sparse.Rd |only quanteda-1.5.0/quanteda/man/corpus-class.Rd | 10 quanteda-1.5.0/quanteda/man/corpus.Rd | 2 quanteda-1.5.0/quanteda/man/corpus_sample.Rd | 10 quanteda-1.5.0/quanteda/man/dfm_select.Rd | 12 quanteda-1.5.0/quanteda/man/diag2na.Rd |only quanteda-1.5.0/quanteda/man/dictionary-class.Rd | 7 quanteda-1.5.0/quanteda/man/dictionary.Rd | 8 quanteda-1.5.0/quanteda/man/docvars.Rd | 16 quanteda-1.5.0/quanteda/man/fcm.Rd | 9 quanteda-1.5.0/quanteda/man/head.textstat_proxy.Rd |only quanteda-1.5.0/quanteda/man/kwic.Rd | 1 quanteda-1.5.0/quanteda/man/read_dict_functions.Rd |only quanteda-1.5.0/quanteda/man/sample_bygroup.Rd | 9 quanteda-1.5.0/quanteda/man/summary.corpus.Rd | 2 quanteda-1.5.0/quanteda/man/textplot_network.Rd | 11 quanteda-1.5.0/quanteda/man/textstat_frequency.Rd | 4 quanteda-1.5.0/quanteda/man/textstat_proxy-class.Rd |only quanteda-1.5.0/quanteda/man/textstat_proxy.Rd | 9 quanteda-1.5.0/quanteda/man/textstat_readability.Rd | 4 quanteda-1.5.0/quanteda/man/textstat_simil.Rd | 154 +- quanteda-1.5.0/quanteda/man/tokens.Rd | 2 quanteda-1.5.0/quanteda/man/tokens_lookup.Rd | 80 - quanteda-1.5.0/quanteda/man/tokens_select.Rd | 12 quanteda-1.5.0/quanteda/man/unlist_character.Rd |only quanteda-1.5.0/quanteda/man/unlist_integer.Rd |only quanteda-1.5.0/quanteda/src/Makevars | 2 quanteda-1.5.0/quanteda/src/Makevars.win | 2 quanteda-1.5.0/quanteda/src/RcppExports.cpp | 76 - quanteda-1.5.0/quanteda/src/ca_mt.cpp | 3 quanteda-1.5.0/quanteda/src/collocations_mt_.cpp | 2 quanteda-1.5.0/quanteda/src/dist_mt.cpp | 3 quanteda-1.5.0/quanteda/src/fcm_mt.cpp | 162 -- quanteda-1.5.0/quanteda/src/kwic_mt.cpp | 2 quanteda-1.5.0/quanteda/src/tokens_chunk_mt.cpp | 2 quanteda-1.5.0/quanteda/src/tokens_compound_mt.cpp | 2 quanteda-1.5.0/quanteda/src/tokens_lookup_mt.cpp | 70 - quanteda-1.5.0/quanteda/src/tokens_ngrams_mt.cpp | 2 quanteda-1.5.0/quanteda/src/tokens_recompile_mt.cpp | 2 quanteda-1.5.0/quanteda/src/tokens_replace_mt.cpp | 5 quanteda-1.5.0/quanteda/src/tokens_segment_mt.cpp | 2 quanteda-1.5.0/quanteda/src/tokens_select_mt.cpp | 2 quanteda-1.5.0/quanteda/src/utility.cpp | 3 quanteda-1.5.0/quanteda/src/wordfish_dense.cpp | 4 quanteda-1.5.0/quanteda/src/wordfish_mt.cpp | 3 quanteda-1.5.0/quanteda/tests/data/old_dfmSparse.RData |binary quanteda-1.5.0/quanteda/tests/testthat/test-as.dictionary.R | 9 quanteda-1.5.0/quanteda/tests/testthat/test-bootstrap.R | 2 quanteda-1.5.0/quanteda/tests/testthat/test-corpus-compress.R | 13 quanteda-1.5.0/quanteda/tests/testthat/test-corpus.R | 7 quanteda-1.5.0/quanteda/tests/testthat/test-corpus_sample.R | 21 quanteda-1.5.0/quanteda/tests/testthat/test-dfm_group.R | 11 quanteda-1.5.0/quanteda/tests/testthat/test-dfm_sample.R | 3 quanteda-1.5.0/quanteda/tests/testthat/test-dfm_select.R | 7 quanteda-1.5.0/quanteda/tests/testthat/test-dictionaries.R | 33 quanteda-1.5.0/quanteda/tests/testthat/test-fcm.R | 215 +-- quanteda-1.5.0/quanteda/tests/testthat/test-features.R | 2 quanteda-1.5.0/quanteda/tests/testthat/test-kwic.R | 41 quanteda-1.5.0/quanteda/tests/testthat/test-nfunctions.R | 2 quanteda-1.5.0/quanteda/tests/testthat/test-pattern2fixed.R | 25 quanteda-1.5.0/quanteda/tests/testthat/test-textstat_dist.R |only quanteda-1.5.0/quanteda/tests/testthat/test-textstat_keyness.R | 2 quanteda-1.5.0/quanteda/tests/testthat/test-textstat_lexdiv.R | 2 quanteda-1.5.0/quanteda/tests/testthat/test-textstat_proxy.R | 22 quanteda-1.5.0/quanteda/tests/testthat/test-textstat_readability.R | 13 quanteda-1.5.0/quanteda/tests/testthat/test-textstat_simil.R | 688 ++++++---- quanteda-1.5.0/quanteda/tests/testthat/test-textstat_simil_old.R | 9 quanteda-1.5.0/quanteda/tests/testthat/test-tokens.R | 231 +++ quanteda-1.5.0/quanteda/tests/testthat/test-tokens_lookup.R | 57 quanteda-1.5.0/quanteda/tests/testthat/test-tokens_select.R | 6 quanteda-1.5.0/quanteda/tests/testthat/test-utils.R | 46 quanteda-1.5.0/quanteda/vignettes/quickstart.Rmd | 212 +-- 117 files changed, 3026 insertions(+), 1944 deletions(-)
Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are otherwise
performed manually. This includes setting up unit testing, test
coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio'
projects, and more.
Author: Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between usethis versions 1.5.0 dated 2019-04-07 and 1.5.1 dated 2019-07-04
usethis-1.5.0/usethis/man/use_course.Rd |only usethis-1.5.1/usethis/DESCRIPTION | 12 usethis-1.5.1/usethis/MD5 | 200 ++++----- usethis-1.5.1/usethis/NAMESPACE | 4 usethis-1.5.1/usethis/NEWS.md | 73 +++ usethis-1.5.1/usethis/R/badge.R | 23 - usethis-1.5.1/usethis/R/ci.R | 69 +++ usethis-1.5.1/usethis/R/code-of-conduct.R | 4 usethis-1.5.1/usethis/R/course.R | 218 +++++----- usethis-1.5.1/usethis/R/create.R | 40 + usethis-1.5.1/usethis/R/data.R | 4 usethis-1.5.1/usethis/R/description.R | 10 usethis-1.5.1/usethis/R/directory.R | 2 usethis-1.5.1/usethis/R/documentation.R | 8 usethis-1.5.1/usethis/R/edit.R | 6 usethis-1.5.1/usethis/R/git-utils.R | 9 usethis-1.5.1/usethis/R/git.R | 69 +-- usethis-1.5.1/usethis/R/github-labels.R | 121 +++-- usethis-1.5.1/usethis/R/github.R | 8 usethis-1.5.1/usethis/R/jenkins.R |only usethis-1.5.1/usethis/R/make.R |only usethis-1.5.1/usethis/R/namespace.R | 4 usethis-1.5.1/usethis/R/news.R | 12 usethis-1.5.1/usethis/R/package.R | 4 usethis-1.5.1/usethis/R/pipe.R | 50 +- usethis-1.5.1/usethis/R/pr.R | 18 usethis-1.5.1/usethis/R/proj.R | 6 usethis-1.5.1/usethis/R/r.R | 8 usethis-1.5.1/usethis/R/readme.R | 4 usethis-1.5.1/usethis/R/release.R | 17 usethis-1.5.1/usethis/R/roxygen.R | 18 usethis-1.5.1/usethis/R/rprofile.R | 5 usethis-1.5.1/usethis/R/rstudio.R | 2 usethis-1.5.1/usethis/R/template.R | 2 usethis-1.5.1/usethis/R/tidyverse.R | 13 usethis-1.5.1/usethis/R/ui.R | 10 usethis-1.5.1/usethis/R/usethis-package.R | 3 usethis-1.5.1/usethis/R/utils.R | 6 usethis-1.5.1/usethis/R/version.R | 4 usethis-1.5.1/usethis/R/vignette.R | 4 usethis-1.5.1/usethis/README.md | 28 - 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Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006,
2014). Includes a function for conveniently defining differential equation
models, model solution based on eigenvalues if possible or using numerical
solvers and a choice of the optimisation methods made available by the 'FME'
package. If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions. Please note that no
warranty is implied for correctness of results or fitness for a particular
purpose.
Author: Johannes Ranke [aut, cre, cph]
(<https://orcid.org/0000-0003-4371-6538>),
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9.48.1 dated 2019-03-04 and 0.9.49.5 dated 2019-07-04
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Title: Build and Tune Several Models
Description: Frequently one needs a convenient way to build and tune
several models in one go.The goal is to provide a number of convenience functions useful in machine learning
applications. It provides the ability to build, tune and obtain predictions of
several models in one function. The models are built using 'caret' functions with
easier to read syntax.
Kuhn(2014)<arXiv:1405.6974v14>.
Kuhn(2008)<doi10.18637/jss.v028.i05>.
Chambers,J.M.(1992)<doi:10.1371/journal.pone.0053143>.
Wilkinson,G.N. and Rogers, C. E. (1973)<doi:10.2307/2346786>.
Author: Nelson Gonzabato [aut, cre]
Maintainer: Nelson Gonzabato <gonzabato@hotmail.com>
Diff between manymodelr versions 0.1.0 dated 2019-03-02 and 0.2.1 dated 2019-07-04
DESCRIPTION | 18 +++--- MD5 | 51 ++++++++++++------ NAMESPACE | 10 +++ NEWS.md |only R/agg_by_group.R |only R/expo.R | 2 R/get_mode.R | 42 +++++++++++---- R/get_stats.R | 39 +++++++------- R/get_this.R |only R/get_var_corr.R |only R/get_var_corr_.R |only R/modeleR.R | 130 ++++++++++++++++++++++++++++------------------- R/multi_model_1.R | 87 +++++++++++++++++++++++-------- R/row_mean_na.R | 45 +++++++++++++--- R/rowdiff.R |only R/select_col.R | 2 R/select_percentile.R | 55 +++++++++++++++---- build |only inst |only man/agg_by_group.Rd |only man/expo1.Rd | 2 man/get_data_Stats.Rd | 22 +++---- man/get_mode.Rd | 7 ++ man/get_this.Rd |only man/get_var_corr.Rd |only man/get_var_corr_.Rd |only man/modeleR.Rd | 8 +- man/multi_model_1.Rd | 15 +++-- man/na_replace.Rd |only man/row_mean_na.Rd | 9 --- man/rowdiff.Rd |only man/select_percentile.Rd | 22 +++++-- vignettes |only 33 files changed, 382 insertions(+), 184 deletions(-)
Title: Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution, provides a wide variety of shapes with one functional form.
This package provides random numbers, quantiles, probabilities, densities and density quantiles for four different types of the distribution;
see documentation for details.
It provides the density function, distribution function, and Quantile-Quantile plots.
It implements a variety of estimation methods for the distribution, including diagnostic plots.
Estimation methods include the starship (all 4 types),
method of L-Moments for the GPD and FKML types, and a number of methods for only the FKML parameterisation.
These include maximum likelihood, maximum product of spacings, Titterington's method, Moments, Trimmed L-Moments and Distributional Least Absolutes.
Author: Robert King <Robert.King@newcastle.edu.au>,
Benjamin Dean <Benjamin.Dean@uon.edu.au>, Sigbert Klinke, Paul van Staden
Maintainer: Robert King <Robert.King@newcastle.edu.au>
Diff between gld versions 2.4.2 dated 2019-04-30 and 2.5 dated 2019-07-04
gld-2.4.2/gld/src/init.c |only gld-2.5/gld/Changelog | 4 +- gld-2.5/gld/DESCRIPTION | 8 ++-- gld-2.5/gld/MD5 | 20 +++++------ gld-2.5/gld/NEWS | 4 +- gld-2.5/gld/R/CheckParameters.R | 4 +- gld-2.5/gld/R/fit.gpd.R | 71 ++++++++++++++++++++++++++++++---------- gld-2.5/gld/R/gld.gpd.se.R | 10 ++--- gld-2.5/gld/R/gldgpdNus.R | 14 +++---- gld-2.5/gld/R/methods.R | 6 +-- gld-2.5/gld/man/fit.gpd.Rd | 32 +++++++++--------- gld-2.5/gld/src/gld_init.c |only 12 files changed, 108 insertions(+), 65 deletions(-)
Title: Assess the Stability of Candidate Housekeeping Genes
Description: A simple way to assess the stability of candidate housekeeping genes is implemented in this package.
Author: Shanliang Zhong [aut, cre]
Maintainer: Shanliang Zhong <slzhong@foxmail.com>
Diff between ctrlGene versions 1.0.0 dated 2018-09-30 and 1.0.1 dated 2019-07-04
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- R/bestKeeper.R | 7 +------ 3 files changed, 10 insertions(+), 15 deletions(-)
Title: Call R from R
Description: It is sometimes useful to perform a computation in a
separate R process, without affecting the current R process at all.
This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between callr versions 3.2.0 dated 2019-03-15 and 3.3.0 dated 2019-07-04
callr-3.2.0/callr/man/make_error.Rd |only callr-3.3.0/callr/DESCRIPTION | 13 callr-3.3.0/callr/MD5 | 92 +- callr-3.3.0/callr/NAMESPACE | 2 callr-3.3.0/callr/NEWS.md | 31 callr-3.3.0/callr/R/error.R | 46 - callr-3.3.0/callr/R/errors.R |only callr-3.3.0/callr/R/eval-bg.R | 1 callr-3.3.0/callr/R/eval.R | 9 callr-3.3.0/callr/R/hook.R |only callr-3.3.0/callr/R/options.R | 6 callr-3.3.0/callr/R/package.R | 48 + callr-3.3.0/callr/R/r-process.R | 2 callr-3.3.0/callr/R/r-session.R | 90 +- callr-3.3.0/callr/R/rcmd-bg.R | 2 callr-3.3.0/callr/R/rcmd-process.R | 2 callr-3.3.0/callr/R/rcmd.R | 14 callr-3.3.0/callr/R/result.R | 23 callr-3.3.0/callr/R/rscript.R | 6 callr-3.3.0/callr/R/script.R | 35 callr-3.3.0/callr/README.md | 489 ++++++++----- callr-3.3.0/callr/build |only callr-3.3.0/callr/inst/WORDLIST |only callr-3.3.0/callr/inst/_pkgdown.yml | 18 callr-3.3.0/callr/inst/client.R |only callr-3.3.0/callr/inst/doc |only callr-3.3.0/callr/man/get_result.Rd | 4 callr-3.3.0/callr/man/new_callr_error.Rd |only callr-3.3.0/callr/man/r.Rd | 8 callr-3.3.0/callr/man/r_bg.Rd | 6 callr-3.3.0/callr/man/r_copycat.Rd | 4 callr-3.3.0/callr/man/r_session.Rd | 20 callr-3.3.0/callr/man/r_vanilla.Rd | 4 callr-3.3.0/callr/man/rcmd.Rd | 14 callr-3.3.0/callr/man/rcmd_bg.Rd | 12 callr-3.3.0/callr/man/rcmd_copycat.Rd | 12 callr-3.3.0/callr/man/rcmd_process.Rd | 2 callr-3.3.0/callr/man/rcmd_safe.Rd | 2 callr-3.3.0/callr/man/rscript.Rd | 8 callr-3.3.0/callr/man/rscript_process.Rd | 2 callr-3.3.0/callr/tests/testthat.R | 13 callr-3.3.0/callr/tests/testthat/helper.R | 30 callr-3.3.0/callr/tests/testthat/test-clean-subprocess.R |only callr-3.3.0/callr/tests/testthat/test-error.R | 174 ++++ callr-3.3.0/callr/tests/testthat/test-messages.R | 4 callr-3.3.0/callr/tests/testthat/test-quit.R | 7 callr-3.3.0/callr/tests/testthat/test-r-session-messages.R | 2 callr-3.3.0/callr/tests/testthat/test-r-session.R | 26 callr-3.3.0/callr/tests/testthat/test-rcmd.R | 3 callr-3.3.0/callr/tests/testthat/test-spelling.R |only callr-3.3.0/callr/vignettes |only 51 files changed, 925 insertions(+), 361 deletions(-)
Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from <http://www.r-inla.org>. A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the 'abn' website <http://r-bayesian-networks.org>.
Author: Gilles Kratzer [aut, cre] (<https://orcid.org/0000-0002-5929-8935>),
Fraser Ian Lewis [aut],
Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>),
Marta Pittavino [ctb] (<https://orcid.org/0000-0002-1232-1034>)
Maintainer: Gilles Kratzer <gilles.kratzer@math.uzh.ch>
Diff between abn versions 2.0 dated 2019-07-01 and 2.1 dated 2019-07-04
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars.in | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>
Diff between gprofiler2 versions 0.1.4 dated 2019-05-24 and 0.1.5 dated 2019-07-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/gprofiler2.R | 21 +++++++++++++-------- man/gost.Rd | 2 +- 4 files changed, 20 insertions(+), 15 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data
processing, see <http://spark.apache.org>. This package supports connecting to
local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end,
and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut, cre],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
RStudio [cph],
The Apache Software Foundation [aut, cph]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between sparklyr versions 1.0.1 dated 2019-05-17 and 1.0.2 dated 2019-07-04
DESCRIPTION | 8 +- MD5 | 81 ++++++++++++++-------------- NAMESPACE | 2 NEWS.md | 35 +++++++++++- R/arrow_data.R | 2 R/config_settings.R | 1 R/connection_spark.R | 27 +++++++-- R/core_arrow.R | 16 ++++- R/data_copy.R | 5 + R/data_interface.R | 12 +++- R/dplyr_spark_data.R | 5 + R/install_spark.R | 36 +++++++----- R/install_spark_windows.R | 2 R/livy_connection.R | 7 +- R/ml_model_generalized_linear_regression.R | 4 - R/ml_stat.R | 2 R/mutation.R | 2 R/qubole_connection.R |only R/sdf_interface.R | 7 ++ R/sdf_wrapper.R | 4 - R/shell_connection.R | 2 R/spark_apply.R | 3 - R/spark_connection.R | 2 R/stream_operations.R | 2 R/tidiers_ml_lda.R | 2 README.md | 48 ++++++++-------- inst/java/sparklyr-1.5-2.10.jar |binary inst/java/sparklyr-1.6-2.10.jar |binary inst/java/sparklyr-2.0-2.11.jar |binary inst/java/sparklyr-2.3-2.11.jar |binary inst/livy/spark-1.5.2/invoke.scala | 15 ++++- inst/livy/spark-1.6.0/sources.scala | 16 ++++- java/spark-1.5.2/invoke.scala | 15 ++++- java/spark-1.6.0/sources.scala | 21 +++++-- man/spark-connections.Rd | 8 +- man/spark_read_csv.Rd | 4 - tests/testthat/output/print/glm-summary.txt | 4 - tests/testthat/test-copy-to.R | 8 +- tests/testthat/test-dplyr-lead-lag.R | 2 tests/testthat/test-dplyr-top-n.R | 1 tests/testthat/test-read-write.R | 14 ++++ tests/testthat/test-serialization.R | 8 ++ 42 files changed, 289 insertions(+), 144 deletions(-)
Title: Mixed Effects Cox Models
Description: This package fits Cox proportional hazards models containing both
fixed and random effects. The random effects can have a general form, of which
familial interactions (a "kinship" matrix) is a particular special case.
Note that the simplest case of a mixed effects Cox model, i.e. a single random
per-group intercept, is also called a "frailty" model. The approach is based
on Rippatti and Palgren, Biometrics 2002.
Author: Terry M. Therneau [aut, cre]
Maintainer: Terry M. Therneau <therneau@mayo.edu>
Diff between coxme versions 2.2-10 dated 2018-05-13 and 2.2-14 dated 2019-07-04
DESCRIPTION | 16 ++++++++++------ MD5 | 38 +++++++++++++++++++------------------- R/formula.R | 1 + build/vignette.rds |binary data/eortc.rda |binary inst/NEWS.Rd | 14 ++++++++++++++ inst/doc/coxme.R | 13 +++++++------ inst/doc/coxme.Rnw | 1 + inst/doc/coxme.pdf |binary inst/doc/laplace.R | 4 ++-- inst/doc/laplace.Rnw | 11 +++++------ inst/doc/laplace.pdf |binary inst/doc/lmekin.pdf |binary inst/doc/variance.R | 2 +- inst/doc/variance.Rnw | 2 +- inst/doc/variance.pdf |binary noweb/ranef.Rnw | 5 ++++- vignettes/coxme.Rnw | 1 + vignettes/laplace.Rnw | 11 +++++------ vignettes/variance.Rnw | 2 +- 20 files changed, 72 insertions(+), 49 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al. (2019)<DOI:10.1016/j.cmpb.2018.10.020>.
Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.17 dated 2019-06-01 and 3.18 dated 2019-07-04
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/CG.Clayton.R | 3 +++ man/CG.Clayton.Rd | 15 ++++++++++----- man/CG.Gumbel.Rd | 11 ++++++++--- man/Lung.Rd | 8 +++++++- man/compound.Cox-package.Rd | 4 ++-- man/uni.Wald.Rd | 6 +++--- man/uni.score.Rd | 2 +- man/uni.selection.Rd | 10 +++++----- 10 files changed, 52 insertions(+), 33 deletions(-)