Title: Relevance-Integrated Statistical Inference Engine
Description: Provide methods to perform customized inference at individual level by taking
contextual covariates into account. Three main functions are provided
in this package: (i) LASER(): it generates specially-designed artificial relevant
samples for a given case; (ii) g2l.proc(): computes customized fdr(z|x); and (iii)
rEB.proc(): performs empirical Bayes inference based on LASERs. The details can be
found in Mukhopadhyay, S., and Wang, K (2021, <arXiv:2004.09588>).
Author: Subhadeep Mukhopadhyay, Kaijun Wang
Maintainer: Kaijun Wang <kaijunwang.19@gmail.com>
Diff between LPRelevance versions 3.1 dated 2020-05-16 and 3.2 dated 2021-04-22
LPRelevance-3.1/LPRelevance/R/Finite.rEB.R |only LPRelevance-3.2/LPRelevance/DESCRIPTION | 14 LPRelevance-3.2/LPRelevance/MD5 | 28 - LPRelevance-3.2/LPRelevance/R/LASER.R | 8 LPRelevance-3.2/LPRelevance/R/LASER.rEB.R |only LPRelevance-3.2/LPRelevance/R/g2l.infer.R | 94 ++-- LPRelevance-3.2/LPRelevance/R/g2l.infer.boot.R | 27 - LPRelevance-3.2/LPRelevance/R/g2l.proc.R | 341 ++++++++--------- LPRelevance-3.2/LPRelevance/R/rEB.Finite.Bayes.R |only LPRelevance-3.2/LPRelevance/R/rEB.proc.R | 92 ++-- LPRelevance-3.2/LPRelevance/build/partial.rdb |binary LPRelevance-3.2/LPRelevance/man/LASER.Rd | 12 LPRelevance-3.2/LPRelevance/man/LPRelevance-package.Rd | 16 LPRelevance-3.2/LPRelevance/man/funnel.Rd | 6 LPRelevance-3.2/LPRelevance/man/g2l.proc.Rd | 38 - LPRelevance-3.2/LPRelevance/man/rEB.Finite.Bayes.Rd |only LPRelevance-3.2/LPRelevance/man/rEB.proc.Rd | 51 +- 17 files changed, 370 insertions(+), 357 deletions(-)
Title: Mutate Data Frames with Random Variates
Description: Work within the 'dplyr' workflow to add random variates to your data frame.
Variates can be added at any level of an existing column. Also, bounds can be specified
for simulated variates.
Author: Kyle T Baron [aut, cre, cph]
Maintainer: Kyle T Baron <kylebtwin@imap.cc>
Diff between dmutate versions 0.1.2 dated 2017-08-28 and 0.1.3 dated 2021-04-22
DESCRIPTION | 20 ++++++++++---------- MD5 | 23 +++++++++++++++-------- NAMESPACE | 5 +++++ NEWS.md | 8 ++++++++ R/as_idata.R |only R/build.R |only R/dmutate.R | 26 ++++++++++++++++++++++++++ man/as_idata.Rd |only man/build_covform.Rd |only man/covset.Rd | 2 -- man/dmutate.Rd | 20 +++++++++++++++++++- man/mutate_random.Rd | 7 ++----- man/rbinomial.Rd | 3 +++ tests/testthat/test-as_idata.R |only tests/testthat/test-build.R |only tests/testthat/test-dmutate.R |only 16 files changed, 88 insertions(+), 26 deletions(-)
Title: Exploratory Graphics for Pharmacometrics
Description: Supports a structured approach
for exploring PKPD data <https://opensource.nibr.com/xgx/>. It also
contains helper functions for enabling the modeler to follow best R
practices (by appending the program name, figure name location, and
draft status to each plot). In addition, it enables the modeler to
follow best graphical practices (by providing a theme that
reduces chart ink, and by providing time-scale, log-scale, and
reverse-log-transform-scale functions for more readable axes).
Finally, it provides some data checking and summarizing functions for
rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.
Author: Andrew Stein [aut, cre],
Alison Margolskee [aut],
Fariba Khanshan [aut],
Konstantin Krismer [aut] (<https://orcid.org/0000-0001-8994-3416>),
Matthew Fidler [ctb] (<https://orcid.org/0000-0001-8538-6691>),
Novartis Pharma AG [cph, fnd]
Maintainer: Andrew Stein <andy.stein@gmail.com>
Diff between xgxr versions 1.1.0 dated 2021-02-04 and 1.1.1 dated 2021-04-22
DESCRIPTION | 11 MD5 | 30 NAMESPACE | 273 ++--- NEWS | 113 +- R/predict.nls.R |only R/xgx_stat_smooth.R | 1460 +++++++++++++-------------- README.md | 2 build/vignette.rds |binary inst/doc/sad_pkpd.R | 434 ++++---- inst/doc/sad_pkpd.html | 1185 +++++++++++++--------- inst/doc/theoph.R | 488 ++++----- inst/doc/theoph.html | 1652 +++++++++++++++++-------------- inst/doc/xgxr_overview.R | 689 ++++++------- inst/doc/xgxr_overview.Rmd | 1056 ++++++++++---------- inst/doc/xgxr_overview.html | 2322 ++++++++++++++++++++++++-------------------- man/predict.nls.Rd |only vignettes/xgxr_overview.Rmd | 1056 ++++++++++---------- 17 files changed, 5733 insertions(+), 5038 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Description: As a pipeline toolkit for Statistics and data science in R,
the 'targets' package brings together function-oriented programming and
'Make'-like declarative workflows.
It analyzes the dependency relationships among the tasks of a workflow,
skips steps that are already up to date, runs the necessary
computation with optional parallel workers, abstracts files as
R objects, and provides tangible evidence that the results match
the underlying code and data. The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Matthew T. Warkentin [ctb],
Samantha Oliver [rev] (<https://orcid.org/0000-0001-5668-1165>),
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between targets versions 0.3.1 dated 2021-03-28 and 0.4.1 dated 2021-04-22
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|only targets-0.4.1/targets/R/class_database.R | 31 targets-0.4.1/targets/R/class_external.R |only targets-0.4.1/targets/R/class_feather.R | 12 targets-0.4.1/targets/R/class_file.R | 37 targets-0.4.1/targets/R/class_forecast.R | 6 targets-0.4.1/targets/R/class_fst.R | 2 targets-0.4.1/targets/R/class_fst_dt.R | 2 targets-0.4.1/targets/R/class_fst_tbl.R | 2 targets-0.4.1/targets/R/class_future.R | 6 targets-0.4.1/targets/R/class_graph.R | 2 targets-0.4.1/targets/R/class_inspection.R | 7 targets-0.4.1/targets/R/class_meta.R | 6 targets-0.4.1/targets/R/class_metrics.R | 4 targets-0.4.1/targets/R/class_outdated.R | 29 targets-0.4.1/targets/R/class_parquet.R | 12 targets-0.4.1/targets/R/class_pattern.R | 15 targets-0.4.1/targets/R/class_pipeline.R | 6 targets-0.4.1/targets/R/class_progress.R | 65 - targets-0.4.1/targets/R/class_qs.R | 3 targets-0.4.1/targets/R/class_record.R | 14 targets-0.4.1/targets/R/class_reporter.R | 6 targets-0.4.1/targets/R/class_scheduler.R | 2 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targets-0.4.1/targets/tests/testthat/test-class_imports.R | 4 targets-0.4.1/targets/tests/testthat/test-class_junction.R | 4 targets-0.4.1/targets/tests/testthat/test-class_keras.R | 17 targets-0.4.1/targets/tests/testthat/test-class_list.R | 2 targets-0.4.1/targets/tests/testthat/test-class_memory.R | 8 targets-0.4.1/targets/tests/testthat/test-class_meta.R | 45 targets-0.4.1/targets/tests/testthat/test-class_metrics.R | 8 targets-0.4.1/targets/tests/testthat/test-class_parallel.R | 14 targets-0.4.1/targets/tests/testthat/test-class_parquet.R | 50 targets-0.4.1/targets/tests/testthat/test-class_pattern.R | 47 targets-0.4.1/targets/tests/testthat/test-class_patternview.R | 2 targets-0.4.1/targets/tests/testthat/test-class_pedigree.R | 8 targets-0.4.1/targets/tests/testthat/test-class_pipeline.R | 10 targets-0.4.1/targets/tests/testthat/test-class_qs.R | 22 targets-0.4.1/targets/tests/testthat/test-class_rds.R | 22 targets-0.4.1/targets/tests/testthat/test-class_record.R | 42 targets-0.4.1/targets/tests/testthat/test-class_settings.R | 20 targets-0.4.1/targets/tests/testthat/test-class_silent.R | 2 targets-0.4.1/targets/tests/testthat/test-class_stem.R | 42 targets-0.4.1/targets/tests/testthat/test-class_store.R | 59 + targets-0.4.1/targets/tests/testthat/test-class_store_file.R | 31 targets-0.4.1/targets/tests/testthat/test-class_target.R | 6 targets-0.4.1/targets/tests/testthat/test-class_timestamp.R | 4 targets-0.4.1/targets/tests/testthat/test-class_torch.R | 17 targets-0.4.1/targets/tests/testthat/test-class_url.R | 92 + targets-0.4.1/targets/tests/testthat/test-class_verbose.R | 4 targets-0.4.1/targets/tests/testthat/test-class_visnetwork.R | 14 targets-0.4.1/targets/tests/testthat/test-tar_bind.R | 20 targets-0.4.1/targets/tests/testthat/test-tar_config_set.R |only targets-0.4.1/targets/tests/testthat/test-tar_deduplicate.R | 2 targets-0.4.1/targets/tests/testthat/test-tar_envvars.R |only targets-0.4.1/targets/tests/testthat/test-tar_glimpse.R | 1 targets-0.4.1/targets/tests/testthat/test-tar_group.R | 2 targets-0.4.1/targets/tests/testthat/test-tar_make.R | 10 targets-0.4.1/targets/tests/testthat/test-tar_make_future.R | 2 targets-0.4.1/targets/tests/testthat/test-tar_pattern.R | 8 targets-0.4.1/targets/tests/testthat/test-tar_pipeline.R | 9 targets-0.4.1/targets/tests/testthat/test-tar_progress_branches.R | 4 targets-0.4.1/targets/tests/testthat/test-tar_progress_summary.R |only targets-0.4.1/targets/tests/testthat/test-tar_read.R | 4 targets-0.4.1/targets/tests/testthat/test-tar_renv.R | 30 targets-0.4.1/targets/tests/testthat/test-tar_target.R | 13 targets-0.4.1/targets/tests/testthat/test-tar_target_raw.R | 16 targets-0.4.1/targets/tests/testthat/test-tar_timestamp.R |only targets-0.4.1/targets/tests/testthat/test-tar_traceback.R | 16 targets-0.4.1/targets/tests/testthat/test-tar_validate.R | 2 targets-0.4.1/targets/tests/testthat/test-tar_visnetwork.R | 3 targets-0.4.1/targets/tests/testthat/test-tar_workspace.R | 4 targets-0.4.1/targets/tests/testthat/test-utils_assert.R | 73 - targets-0.4.1/targets/tests/testthat/test-utils_logic.R | 6 targets-0.4.1/targets/tests/testthat/test-utils_path.R |only targets-0.4.1/targets/vignettes/overview.Rmd | 2 300 files changed, 3110 insertions(+), 1214 deletions(-)
Title: Create an HTML Vertical Timeline from a Data Frame in
'rmarkdown' and 'shiny'
Description: Creates an HTML vertical timeline from a data frame as an input for
'rmarkdown' documents and 'shiny' applications.
Author: Mohamed El Fodil Ihaddaden
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between cronologia versions 0.1.0 dated 2021-02-07 and 0.2.0 dated 2021-04-22
DESCRIPTION | 7 +- MD5 | 10 ++-- NEWS.md |only R/cronologia.R | 2 README.md | 17 +++++- inst/cronologia/cronologia.css | 92 +++++++++++++++++++++---------------- inst/cronologia/cronologia.min.css |only 7 files changed, 78 insertions(+), 50 deletions(-)
Title: Date-Time Types and Tools
Description: Provides a comprehensive library for date-time manipulations
using a new family of orthogonal date-time classes (durations, time
points, zoned-times, and calendars) that partition responsibilities so
that the complexities of time zones are only considered when they are
really needed. Capabilities include: date-time parsing, formatting,
arithmetic, extraction and updating of components, and rounding.
Author: Davis Vaughan [aut, cre],
RStudio [cph, fnd]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between clock versions 0.2.0 dated 2021-04-12 and 0.3.0 dated 2021-04-22
clock-0.2.0/clock/LICENSE.note |only clock-0.2.0/clock/R/database.R |only clock-0.2.0/clock/inst/include |only clock-0.2.0/clock/man/zone-database.Rd |only clock-0.2.0/clock/src/Makevars |only clock-0.2.0/clock/src/Makevars.win |only clock-0.2.0/clock/src/database.cpp |only clock-0.2.0/clock/src/exported.cpp |only clock-0.2.0/clock/src/install.cpp |only clock-0.2.0/clock/src/tz.cpp |only clock-0.2.0/clock/tests/testthat/test-database.R |only clock-0.3.0/clock/DESCRIPTION | 17 clock-0.3.0/clock/MD5 | 88 +-- clock-0.3.0/clock/NAMESPACE | 9 clock-0.3.0/clock/NEWS.md | 12 clock-0.3.0/clock/R/cpp11.R | 12 clock-0.3.0/clock/R/date.R | 355 ++++++++++++ clock-0.3.0/clock/R/duration.R | 32 - clock-0.3.0/clock/R/posixt.R | 258 ++++++++ clock-0.3.0/clock/R/tzdb.R |only clock-0.3.0/clock/R/utils.R | 3 clock-0.3.0/clock/R/zzz.R | 5 clock-0.3.0/clock/inst/doc/recipes.R | 27 clock-0.3.0/clock/inst/doc/recipes.Rmd | 51 + clock-0.3.0/clock/inst/doc/recipes.html | 578 ++++++++++---------- clock-0.3.0/clock/man/clock-package.Rd | 2 clock-0.3.0/clock/man/date-sequence.Rd |only clock-0.3.0/clock/man/date_seq.Rd |only clock-0.3.0/clock/man/posixt-sequence.Rd |only clock-0.3.0/clock/man/reexports.Rd |only clock-0.3.0/clock/src/clock.h | 15 clock-0.3.0/clock/src/cpp11.cpp | 31 - clock-0.3.0/clock/src/duration.cpp | 2 clock-0.3.0/clock/src/duration.h | 24 clock-0.3.0/clock/src/format.cpp | 2 clock-0.3.0/clock/src/naive-time.cpp | 3 clock-0.3.0/clock/src/ordinal.h |only clock-0.3.0/clock/src/quarterly.h |only clock-0.3.0/clock/src/sys-time.cpp | 2 clock-0.3.0/clock/src/utils.h | 61 ++ clock-0.3.0/clock/src/zone.cpp | 20 clock-0.3.0/clock/src/zoned-time.cpp | 35 - clock-0.3.0/clock/tests/testthat/_snaps/date.md | 74 ++ clock-0.3.0/clock/tests/testthat/_snaps/duration.md | 6 clock-0.3.0/clock/tests/testthat/_snaps/posixt.md | 110 +++ clock-0.3.0/clock/tests/testthat/test-date.R | 126 ++++ clock-0.3.0/clock/tests/testthat/test-posixt.R | 238 ++++++++ clock-0.3.0/clock/vignettes/recipes.Rmd | 51 + 48 files changed, 1796 insertions(+), 453 deletions(-)
Title: Structural Bayesian Vector Autoregression Models
Description: Provides a function for estimating the parameters of Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
Author: Paul Richardson
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>
Diff between BHSBVAR versions 2.1.0 dated 2020-08-26 and 3.0.0 dated 2021-04-22
DESCRIPTION | 10 MD5 | 60 NAMESPACE | 3 NEWS | 2 R/BHSBVAR.R | 3062 ++++++++++++++++------------------------- R/FEVD.R |only R/HD.R |only R/IRF.R |only R/RcppExports.R | 132 + build/vignette.rds |binary data/USLMData.rda |binary inst/doc/BHSBVAR.R | 442 ++--- inst/doc/BHSBVAR.Rnw | 1152 +++++++-------- inst/doc/BHSBVAR.pdf |binary man/BHSBVAR-package.Rd | 50 man/BH_SBVAR.Rd | 393 ++--- man/Dist_Plots.Rd | 269 +-- man/FEVD.Rd |only man/FEVD_Plots.Rd | 291 +-- man/HD.Rd |only man/HD_Plots.Rd | 307 ++-- man/IRF.Rd |only man/IRF_Plots.Rd | 273 +-- man/USLMData.Rd | 54 src/BHSBVAR-init.c | 10 src/BHSBVAR.cpp | 91 - src/RcppExports.cpp | 69 vignettes/BHSBVAR.Rnw | 1152 +++++++-------- vignettes/fig/Dist_plots-1.pdf |binary vignettes/fig/FEVD_plots-1.pdf |binary vignettes/fig/HD_plots-1.pdf |binary vignettes/fig/IRF_plots-1.pdf |binary vignettes/fig/Model-1.pdf |binary vignettes/fig/VD_plots-1.pdf |binary 34 files changed, 3669 insertions(+), 4153 deletions(-)
Title: Magnetic Resonance Binning, Integration and Normalization
Description: Nuclear Magnetic Resonance is widely used in Life Science
research. The package (<doi:10.1021/acs.jproteome.0c00684>) converts 1D
or 2D data into a matrix of values suitable for further data analysis and
performs basic processing steps in a reproducible way. Negative values, a
common issue in such data, are replaced by positive values. All used
parameters are stored in a readable text file and can be restored from that
file to enable exact reproduction of the data at a later time.
Author: Matthias Klein [aut, cre] (<https://orcid.org/0000-0001-7455-5381>)
Maintainer: Matthias Klein <klein.663@osu.edu>
Diff between mrbin versions 1.5.0 dated 2021-01-04 and 1.5.1 dated 2021-04-22
DESCRIPTION | 12 ++++++------ MD5 | 15 ++++++++------- NAMESPACE | 2 +- NEWS.md | 6 ++++++ R/mrbin.R | 15 +++++++++++---- inst/CITATION |only inst/doc/mrbin.Rnw | 2 +- inst/doc/mrbin.pdf |binary vignettes/mrbin.Rnw | 2 +- 9 files changed, 34 insertions(+), 20 deletions(-)
Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data
analysis, drake rebuilds intermediate data objects when their
dependencies change, and it skips work when the results are already up
to date. Not every execution starts from scratch, there is native
support for parallel and distributed computing, and completed projects
have tangible evidence that they are reproducible. Extensive
documentation, from beginner-friendly tutorials to practical examples
and more, is available at the reference website
<https://docs.ropensci.org/drake/> and the online manual
<https://books.ropensci.org/drake/>.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Alex Axthelm [ctb],
Jasper Clarkberg [ctb],
Kirill Müller [ctb],
Ben Bond-Lamberty [ctb] (<https://orcid.org/0000-0001-9525-4633>),
Tristan Mahr [ctb] (<https://orcid.org/0000-0002-8890-5116>),
Miles McBain [ctb] (<https://orcid.org/0000-0003-2865-2548>),
Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>),
Ellis Hughes [ctb],
Matthew Mark Strasiotto [ctb],
Ben Marwick [rev],
Peter Slaughter [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between drake versions 7.13.1 dated 2021-02-03 and 7.13.2 dated 2021-04-22
DESCRIPTION | 8 MD5 | 470 +++++++++++++++---------------- NEWS.md | 5 R/zzz.R | 22 - inst/NOTICE | 248 ++++++++++++++++ inst/templates/hpc/slurm_batchtools.tmpl | 47 +-- man/Makefile_recipe.Rd | 2 man/analyses.Rd | 2 man/analysis_wildcard.Rd | 2 man/as_drake_filename.Rd | 2 man/as_file.Rd | 2 man/available_hash_algos.Rd | 2 man/backend.Rd | 2 man/bind_plans.Rd | 2 man/build_drake_graph.Rd | 2 man/build_graph.Rd | 2 man/build_times.Rd | 2 man/built.Rd | 2 man/cache_namespaces.Rd | 2 man/cache_path.Rd | 2 man/cached.Rd | 2 man/cached_planned.Rd | 2 man/cached_unplanned.Rd | 2 man/cancel.Rd | 2 man/cancel_if.Rd | 2 man/check.Rd | 2 man/check_plan.Rd | 2 man/clean.Rd | 2 man/clean_main_example.Rd | 2 man/clean_mtcars_example.Rd | 2 man/cleaned_namespaces.Rd | 2 man/cmq_build.Rd | 2 man/code_to_function.Rd | 2 man/code_to_plan.Rd | 2 man/config.Rd | 2 man/configure_cache.Rd | 2 man/dataframes_graph.Rd | 2 man/dataset_wildcard.Rd | 2 man/debug_and_run.Rd | 2 man/default_Makefile_args.Rd | 2 man/default_Makefile_command.Rd | 2 man/default_graph_title.Rd | 2 man/default_long_hash_algo.Rd | 2 man/default_parallelism.Rd | 2 man/default_recipe_command.Rd | 2 man/default_short_hash_algo.Rd | 2 man/default_system2_args.Rd | 2 man/default_verbose.Rd | 2 man/dependency_profile.Rd | 2 man/deprecate_wildcard.Rd | 2 man/deps.Rd | 2 man/deps_code.Rd | 2 man/deps_knitr.Rd | 2 man/deps_profile.Rd | 2 man/deps_target.Rd | 2 man/deps_targets.Rd | 2 man/diagnose.Rd | 2 man/do_prework.Rd | 2 man/doc_of_function_call.Rd | 2 man/drake_batchtools_tmpl_file.Rd | 2 man/drake_build.Rd | 2 man/drake_cache.Rd | 2 man/drake_cache_log.Rd | 2 man/drake_cache_log_file.Rd | 2 man/drake_cancelled.Rd | 2 man/drake_config.Rd | 2 man/drake_debug.Rd | 2 man/drake_done.Rd | 2 man/drake_envir.Rd | 2 man/drake_example.Rd | 2 man/drake_examples.Rd | 2 man/drake_failed.Rd | 2 man/drake_gc.Rd | 2 man/drake_get_session_info.Rd | 2 man/drake_ggraph.Rd | 2 man/drake_graph_info.Rd | 2 man/drake_history.Rd | 2 man/drake_hpc_template_file.Rd | 2 man/drake_hpc_template_files.Rd | 2 man/drake_meta.Rd | 2 man/drake_palette.Rd | 2 man/drake_plan.Rd | 2 man/drake_plan_source.Rd | 2 man/drake_progress.Rd | 2 man/drake_quotes.Rd | 2 man/drake_running.Rd | 2 man/drake_session.Rd | 2 man/drake_slice.Rd | 2 man/drake_strings.Rd | 2 man/drake_tempfile.Rd | 2 man/drake_tip.Rd | 2 man/drake_unquote.Rd | 2 man/evaluate.Rd | 2 man/evaluate_plan.Rd | 2 man/example_drake.Rd | 2 man/examples_drake.Rd | 2 man/expand.Rd | 2 man/expand_plan.Rd | 2 man/expose_imports.Rd | 2 man/failed.Rd | 2 man/file_in.Rd | 2 man/file_out.Rd | 2 man/file_store.Rd | 2 man/find_cache.Rd | 2 man/find_knitr_doc.Rd | 2 man/find_project.Rd | 2 man/from_plan.Rd | 2 man/future_build.Rd | 2 man/gather.Rd | 2 man/gather_by.Rd | 2 man/gather_plan.Rd | 2 man/get_cache.Rd | 2 man/get_trace.Rd | 2 man/id_chr.Rd | 2 man/ignore.Rd | 2 man/imported.Rd | 2 man/in_progress.Rd | 2 man/is_function_call.Rd | 2 man/isolate_example.Rd | 2 man/knitr_deps.Rd | 2 man/knitr_in.Rd | 2 man/legend_nodes.Rd | 2 man/load_basic_example.Rd | 2 man/load_main_example.Rd | 2 man/load_mtcars_example.Rd | 2 man/long_hash.Rd | 2 man/make.Rd | 2 man/make_imports.Rd | 2 man/make_targets.Rd | 2 man/make_with_config.Rd | 2 man/manage_memory.Rd | 2 man/map_plan.Rd | 2 man/max_useful_jobs.Rd | 2 man/migrate_drake_project.Rd | 2 man/missed.Rd | 2 man/new_cache.Rd | 2 man/no_deps.Rd | 2 man/outdated.Rd | 2 man/parallel_stages.Rd | 2 man/parallelism_choices.Rd | 2 man/plan.Rd | 2 man/plan_analyses.Rd | 2 man/plan_drake.Rd | 2 man/plan_summaries.Rd | 2 man/plan_to_code.Rd | 2 man/plan_to_notebook.Rd | 2 man/plot_graph.Rd | 2 man/predict_load_balancing.Rd | 2 man/predict_runtime.Rd | 2 man/predict_workers.Rd | 2 man/process_import.Rd | 2 man/progress.Rd | 2 man/prune_drake_graph.Rd | 2 man/r_make.Rd | 2 man/r_recipe_wildcard.Rd | 2 man/rate_limiting_times.Rd | 2 man/read_config.Rd | 2 man/read_drake_config.Rd | 2 man/read_drake_graph.Rd | 2 man/read_drake_meta.Rd | 2 man/read_drake_plan.Rd | 2 man/read_drake_seed.Rd | 2 man/read_graph.Rd | 2 man/read_plan.Rd | 2 man/read_trace.Rd | 2 man/readd.Rd | 2 man/recover_cache.Rd | 2 man/recoverable.Rd | 2 man/reduce_by.Rd | 2 man/reduce_plan.Rd | 2 man/render_drake_ggraph.Rd | 2 man/render_drake_graph.Rd | 2 man/render_graph.Rd | 2 man/render_sankey_drake_graph.Rd | 2 man/render_static_drake_graph.Rd | 2 man/render_text_drake_graph.Rd | 2 man/rescue_cache.Rd | 2 man/rs_addin_loadd.Rd | 2 man/rs_addin_r_make.Rd | 2 man/rs_addin_r_outdated.Rd | 2 man/rs_addin_r_vis_drake_graph.Rd | 2 man/running.Rd | 2 man/sankey_drake_graph.Rd | 2 man/session.Rd | 2 man/shell_file.Rd | 2 man/short_hash.Rd | 2 man/show_source.Rd | 2 man/static_drake_graph.Rd | 2 man/subtargets.Rd | 2 man/summaries.Rd | 2 man/target.Rd | 2 man/target_namespaces.Rd | 2 man/text_drake_graph.Rd | 2 man/this_cache.Rd | 2 man/tracked.Rd | 2 man/transform_plan.Rd | 2 man/transformations.Rd | 2 man/trigger.Rd | 2 man/triggers.Rd | 2 man/type_sum.expr_list.Rd | 2 man/use_drake.Rd | 2 man/vis_drake_graph.Rd | 2 man/which_clean.Rd | 2 man/workflow.Rd | 2 man/workplan.Rd | 2 tests/testthat/test-1-hash-tables.R | 1 tests/testthat/test-1-interactive.R | 3 tests/testthat/test-1-missed.R | 4 tests/testthat/test-1-queue.R | 4 tests/testthat/test-2-build.R | 2 tests/testthat/test-2-checks.R | 12 tests/testthat/test-2-lock.R | 1 tests/testthat/test-2-meta.R | 10 tests/testthat/test-2-prework.R | 2 tests/testthat/test-2-testing.R | 13 tests/testthat/test-3-lazy.R | 6 tests/testthat/test-3-utils.R | 2 tests/testthat/test-4-flow.R | 16 - tests/testthat/test-4-imports.R | 4 tests/testthat/test-4-rng.R | 2 tests/testthat/test-5-console.R | 8 tests/testthat/test-5-examples.R | 2 tests/testthat/test-5-graph.R | 12 tests/testthat/test-5-time.R | 10 tests/testthat/test-6-analysis.R | 32 +- tests/testthat/test-6-hpc.R | 10 tests/testthat/test-6-memory.R | 4 tests/testthat/test-6-plans.R | 34 +- tests/testthat/test-6-retry.R | 4 tests/testthat/test-6-triggers.R | 18 - tests/testthat/test-6-visuals.R | 6 tests/testthat/test-7-deprecate.R | 28 - tests/testthat/test-7-files.R | 10 tests/testthat/test-8-cache.R | 38 +- tests/testthat/test-8-decorated-storr.R | 2 tests/testthat/test-9-future.R | 2 236 files changed, 878 insertions(+), 622 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-02 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-19 2.0.6
2015-08-18 2.0.1
2013-12-06 1.302
2013-11-27 1.300
2012-12-19 1.200
2012-05-21 1.003
2012-04-27 1.0
2012-03-10 0.19
2012-01-16 0.10
Title: 'SQLite' Interface for R
Description: Embeds the 'SQLite' database engine in R and
provides an interface compliant with the 'DBI' package. The source for
the 'SQLite' engine is included.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
SQLite Authors [ctb] (for the included SQLite sources),
Liam Healy [ctb] (for the included SQLite sources),
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RSQLite versions 2.2.6 dated 2021-04-11 and 2.2.7 dated 2021-04-22
RSQLite-2.2.6/RSQLite/R/rstudioConnections.R |only RSQLite-2.2.6/RSQLite/inst/icons |only RSQLite-2.2.6/RSQLite/inst/rstudio |only RSQLite-2.2.7/RSQLite/DESCRIPTION | 11 +++---- RSQLite-2.2.7/RSQLite/MD5 | 18 ++++------- RSQLite-2.2.7/RSQLite/NEWS.md | 6 +++ RSQLite-2.2.7/RSQLite/R/connect.R | 7 ---- RSQLite-2.2.7/RSQLite/R/table.R | 12 ------- RSQLite-2.2.7/RSQLite/src/DbConnection.h | 2 - RSQLite-2.2.7/RSQLite/src/vendor/sqlite3/sqlite3.c | 32 ++++++++++++++------- RSQLite-2.2.7/RSQLite/src/vendor/sqlite3/sqlite3.h | 6 +-- 11 files changed, 44 insertions(+), 50 deletions(-)
Title: Generate Random Given and Surnames
Description: Function for generating random gender and ethnicity correct first and/or last names. Names are chosen proportionally based upon their probability of appearing in a large scale data base of real names.
Author: Damian W. Betebenner [aut, cre]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between randomNames versions 1.4-0.0 dated 2019-03-07 and 1.5-0.0 dated 2021-04-22
DESCRIPTION | 12 - MD5 | 17 - R/zzz.R | 2 build/vignette.rds |binary data/randomNamesData.rda |binary inst/CITATION | 8 inst/NEWS | 4 inst/doc/randomNames.html | 292 ++++++----------------------- man/randomNames-package.Rd | 4 vignettes/releases/randomNames-1.5-0.0.Rmd |only 10 files changed, 93 insertions(+), 246 deletions(-)
Title: Working with Sets the Tidy Way
Description: Implements a class and methods to work with sets,
doing intersection, union, complementary sets, power sets, cartesian
product and other set operations in a "tidy" way. These set operations
are available for both classical sets and fuzzy sets. Import sets from
several formats or from other several data structures.
Author: Lluís Revilla Sancho [aut, cre]
(<https://orcid.org/0000-0001-9747-2570>),
Zebulun Arendsee [rev],
Jennifer Chang [rev]
Maintainer: Lluís Revilla Sancho <lluis.revilla@gmail.com>
Diff between BaseSet versions 0.0.15 dated 2021-03-20 and 0.0.16 dated 2021-04-22
DESCRIPTION | 7 +-- MD5 | 12 +++--- NEWS.md | 5 ++ README.md | 10 ++--- inst/doc/advanced.html | 16 ++++---- inst/doc/basic.html | 90 ++++++++++++++++++++++++------------------------- inst/doc/fuzzy.html | 20 +++++----- 7 files changed, 82 insertions(+), 78 deletions(-)
Title: UK Baby Names Data
Description: Full listing of UK baby names occurring more than three times per year between 1974 and 2020, and rankings of baby name popularity by decade from 1904 to 1994.
Author: Mine Çetinkaya-Rundel [aut, cre, cph]
(<https://orcid.org/0000-0001-6452-2420>),
Thomas J. Leeper [aut],
Nicholas Goguen-Compagnoni [aut]
Maintainer: Mine Çetinkaya-Rundel <cetinkaya.mine@gmail.com>
Diff between ukbabynames versions 0.1.1 dated 2017-06-20 and 0.2.0 dated 2021-04-22
ukbabynames-0.1.1/ukbabynames/R/data.R |only ukbabynames-0.2.0/ukbabynames/DESCRIPTION | 28 ++++-- ukbabynames-0.2.0/ukbabynames/MD5 | 30 +++++-- ukbabynames-0.2.0/ukbabynames/NAMESPACE | 4 ukbabynames-0.2.0/ukbabynames/NEWS.md | 24 +++-- ukbabynames-0.2.0/ukbabynames/R/ewbabynames.R |only ukbabynames-0.2.0/ukbabynames/R/nibabynames.R |only ukbabynames-0.2.0/ukbabynames/R/rankings.R |only ukbabynames-0.2.0/ukbabynames/R/scotbabynames.R |only ukbabynames-0.2.0/ukbabynames/R/ukbabynames.R |only ukbabynames-0.2.0/ukbabynames/README.md | 69 ++++++++-------- ukbabynames-0.2.0/ukbabynames/data/ewbabynames.rda |only ukbabynames-0.2.0/ukbabynames/data/nibabynames.rda |only ukbabynames-0.2.0/ukbabynames/data/rankings.rda |binary ukbabynames-0.2.0/ukbabynames/data/scotbabynames.rda |only ukbabynames-0.2.0/ukbabynames/data/ukbabynames.rda |binary ukbabynames-0.2.0/ukbabynames/man/ewbabynames.Rd |only ukbabynames-0.2.0/ukbabynames/man/nibabynames.Rd |only ukbabynames-0.2.0/ukbabynames/man/rankings.Rd | 61 +++++++------- ukbabynames-0.2.0/ukbabynames/man/scotbabynames.Rd |only ukbabynames-0.2.0/ukbabynames/man/ukbabynames.Rd | 78 +++++++++++-------- ukbabynames-0.2.0/ukbabynames/tests |only 22 files changed, 171 insertions(+), 123 deletions(-)
Title: Manage Data from Stock Exchange Markets
Description: Tools to perform some descriptive data analysis for assets. Manage the portfolio and capital of assets. It also downloads and organizes data from the Tehran Stock Exchange (TSE).
Author: Ali Saeb
Maintainer: Ali Saeb <ali.saeb@gmail.com>
Diff between TSEtools versions 0.2.0 dated 2021-01-24 and 0.2.1 dated 2021-04-22
TSEtools-0.2.0/TSEtools/inst/extdata/sample.csv |only TSEtools-0.2.1/TSEtools/DESCRIPTION | 9 ++++----- TSEtools-0.2.1/TSEtools/MD5 | 22 +++++++++++----------- TSEtools-0.2.1/TSEtools/R/capm.R | 4 ++-- TSEtools-0.2.1/TSEtools/R/getTSE.R | 19 +++++++++++++++++-- TSEtools-0.2.1/TSEtools/R/mcPrt.R | 10 +++++----- TSEtools-0.2.1/TSEtools/R/prtf.R | 16 ++++++++++------ TSEtools-0.2.1/TSEtools/README.md | 4 ++++ TSEtools-0.2.1/TSEtools/inst/extdata/sample.dat |only TSEtools-0.2.1/TSEtools/man/capm.Rd | 10 ++++++---- TSEtools-0.2.1/TSEtools/man/getTSE.Rd | 6 ++++-- TSEtools-0.2.1/TSEtools/man/mcPrt.Rd | 6 ++++-- TSEtools-0.2.1/TSEtools/man/prtf.Rd | 17 ++++++++++------- 13 files changed, 77 insertions(+), 46 deletions(-)
Title: Factor and Autoregressive Models for Tensor Time Series
Description: Factor and autoregressive models for matrix and tensor valued time series.
We provide functions for estimation, simulation and prediction. The models are discussed in Chen et al (2020) <DOI:10.1016/j.jeconom.2020.07.015>,
Chen et al (2020) <arXiv:1905.07530>, and Han et al (2020) <arXiv:2006.02611>.
Author: Zebang Li [aut, cre],
Ruofan Yu [aut],
Rong Chen [aut],
Yuefeng Han [aut],
Han Xiao [aut],
Dan Yang [aut]
Maintainer: Zebang Li <zl326@stat.rutgers.edu>
Diff between tensorTS versions 0.1.0 dated 2021-04-21 and 0.1.1 dated 2021-04-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 1 + NEWS.md | 5 +++-- R/tenAR.r | 1 + 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Staged Event Trees
Description: Creates and fits staged event tree probability models,
which are probabilistic graphical models capable of representing
asymmetric conditional independence statements
for categorical variables.
Includes functions to create, plot and fit staged
event trees from data, as well as many efficient structure
learning algorithms.
References:
Collazo R. A., Görgen C. and Smith J. Q.
(2018, ISBN:9781498729604).
Görgen C., Bigatti A., Riccomagno E. and Smith J. Q. (2018)
<arXiv:1705.09457>.
Thwaites P. A., Smith, J. Q. (2017) <arXiv:1510.00186>.
Barclay L. M., Hutton J. L. and Smith J. Q. (2013)
<doi:10.1016/j.ijar.2013.05.006>.
Smith J. Q. and Anderson P. E. (2008)
<doi:10.1016/j.artint.2007.05.004>.
Author: Gherardo Varando [aut, cre] (<https://orcid.org/0000-0002-6708-1103>),
Federico Carli [aut],
Manuele Leonelli [aut] (<https://orcid.org/0000-0002-2562-5192>),
Eva Riccomagno [aut]
Maintainer: Gherardo Varando <gherardo.varando@gmail.com>
Diff between stagedtrees versions 2.0.1 dated 2020-12-08 and 2.1.0 dated 2021-04-22
DESCRIPTION | 6 MD5 | 53 +++--- NAMESPACE | 13 + NEWS.md | 13 + R/0-util-functions.R | 4 R/1-base-model-function.R | 37 ++-- R/1b-base-model-function.R | 107 ------------ R/3-inference-functions.R | 7 R/4-model-selection.R | 2 R/7-ceg-functions.R | 2 R/8-conversion-functions.R |only README.md | 251 ++++++++++++++++-------------- man/as_adj_matrix.Rd |only man/as_bn.Rd |only man/as_parentslist.Rd |only man/as_sevt.Rd | 36 +++- man/ceg2adjmat.Rd | 2 man/compare_stages.Rd | 2 man/figures/README-unnamed-chunk-17-1.png |binary man/figures/README-unnamed-chunk-18-1.png |binary man/figures/README-unnamed-chunk-19-1.png |binary man/figures/README-unnamed-chunk-20-1.png |binary man/figures/README-unnamed-chunk-21-1.png |binary man/figures/README-unnamed-chunk-22-1.png |only man/figures/README-unnamed-chunk-23-1.png |only man/print.parentslist.Rd |only man/stages_hc.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test_conversions.R | 81 +++++++++ tests/testthat/test_inference.R | 24 ++ tests/testthat/test_util_functions.R | 24 ++ 31 files changed, 391 insertions(+), 275 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Description: Functions for fitting and plotting SITAR (Super
Imposition by Translation And Rotation) growth curve models. SITAR is
a shape-invariant model with a regression B-spline mean curve and
subject-specific random effects on both the measurement and age
scales. The model was first described by Lindstrom (1995)
<doi:10.1002/sim.4780141807> and developed as the SITAR method by Cole
et al (2010) <doi:10.1093/ije/dyq115>.
Author: Tim Cole [aut, cre] (<https://orcid.org/0000-0001-5711-8200>)
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>
Diff between sitar versions 1.1.2 dated 2020-02-17 and 1.2.0 dated 2021-04-22
DESCRIPTION | 11 MD5 | 88 +++--- NAMESPACE | 36 ++ NEWS | 33 ++ R/LMS2z.R | 16 - R/apv_se.R | 6 R/deren.R |only R/dfpower.R | 184 +++++++++---- R/iotf.R | 2 R/ob_convertr.R |only R/optimal_design.R |only R/plot.sitar.R | 1 R/predict.sitar.R | 114 ++++---- R/sitar-package.R | 8 R/sitar.R | 297 +++++++++++++-------- R/uk90.R | 2 R/ukwhopt.R | 2 R/ukwhoterm.R | 2 R/utils-pipe.R |only R/who06.R | 2 R/who0607.R | 2 R/xyadj.R | 23 - build/partial.rdb |only build/vignette.rds |binary data/deren.rda |only data/ukwhopt.rda |binary data/ukwhoterm.rda |binary inst/doc/Fitting_models_with_SITAR.Rmd | 8 inst/doc/Fitting_models_with_SITAR.html | 314 +++++------------------ inst/doc/Optimal_design_for_centile_studies.R |only inst/doc/Optimal_design_for_centile_studies.Rmd |only inst/doc/Optimal_design_for_centile_studies.html |only man/LMS2z.Rd | 4 man/berkeley.Rd | 6 man/cdc2000.Rd | 6 man/deren.Rd |only man/dfpower.Rd | 79 +++-- man/heights.Rd | 6 man/iotf.Rd | 8 man/ob_convertr.Rd |only man/optimal_design.Rd |only man/pipe.Rd |only man/sitar-package.Rd | 8 man/sitar.Rd | 49 ++- man/uk90.Rd | 8 man/ukwhopt.Rd | 8 man/ukwhoterm.Rd | 8 man/who06.Rd | 8 man/who0607.Rd | 8 man/xyadj.Rd | 6 vignettes/Fitting_models_with_SITAR.Rmd | 8 vignettes/Optimal_design_for_centile_studies.Rmd |only 52 files changed, 758 insertions(+), 613 deletions(-)
Title: Submit R Calculations to a 'Slurm' Cluster
Description: Functions that simplify submitting R scripts to a 'Slurm'
workload manager, in part by automating the division of embarrassingly
parallel calculations across cluster nodes.
Author: Philippe Marchand [aut],
Ian Carroll [aut],
Mike Smorul [aut],
Rachael Blake [aut],
Quentin Read [aut, cre],
Dayne Filer [ctb],
Ben Fasoli [ctb],
Pol van Rijn [ctb],
Sebastian Schubert [ctb],
Rob Gilmore [ctb],
Christopher Barrington [ctb],
Se Jong Cho [art]
Maintainer: Quentin Read <qread@sesync.org>
Diff between rslurm versions 0.5.0 dated 2019-11-15 and 0.6.0 dated 2021-04-22
DESCRIPTION | 39 - MD5 | 98 +-- NAMESPACE | 28 NEWS.md | 348 ++++++----- R/cancel_cleanup.R | 86 +- R/get_job_status.R | 124 ++-- R/get_slurm_out.R | 142 ++-- R/local_slurm_array.R |only R/print_job_status.R | 90 +- R/rslurm-deprecated.R | 16 R/rslurm-package.R | 170 ++--- R/slurm_apply.R | 400 ++++++------ R/slurm_call.R | 291 ++++----- R/slurm_job.R | 43 - R/slurm_map.R |only R/slurm_utils.R | 133 +--- README.md | 191 +++--- build/vignette.rds |binary inst/doc/rslurm.Rmd | 451 ++++++++------ inst/doc/rslurm.html | 895 +++++++++++++++-------------- inst/templates/slurm_map_R.txt |only inst/templates/slurm_run_R.txt | 46 - inst/templates/slurm_run_single_R.txt | 28 inst/templates/submit_sh.txt | 26 inst/templates/submit_single_sh.txt | 24 man/cancel_slurm.Rd | 42 - man/cleanup_files.Rd | 62 +- man/get_job_status.Rd | 56 - man/get_slurm_out.Rd | 88 +- man/local_slurm_array.Rd |only man/print_job_status-deprecated.Rd | 56 - man/rslurm-deprecated.Rd | 42 - man/rslurm-package.Rd | 188 +++--- man/slurm_apply.Rd | 280 ++++----- man/slurm_call.Rd | 203 +++--- man/slurm_job.Rd | 58 - man/slurm_map.Rd |only tests/testthat.R | 8 tests/testthat/test-local_slurm_apply.R | 203 +++--- tests/testthat/test-local_slurm_call.R | 62 -- tests/testthat/test-local_slurm_map.R |only tests/testthat/test-slurm_apply.R | 181 +++-- tests/testthat/test-slurm_call.R | 84 +- tests/testthat/test-slurm_map.R |only vignettes/_rslurm_test_apply/f.RDS |binary vignettes/_rslurm_test_apply/more_args.RDS |only vignettes/_rslurm_test_apply/params.RDS |binary vignettes/_rslurm_test_apply/slurm_run.R | 46 - vignettes/_rslurm_test_apply/submit.sh | 14 vignettes/_rslurm_test_call/f.RDS |binary vignettes/_rslurm_test_call/params.RDS |binary vignettes/_rslurm_test_call/slurm_run.R | 28 vignettes/_rslurm_test_call/submit.sh | 12 vignettes/rslurm.Rmd | 451 ++++++++------ 54 files changed, 3098 insertions(+), 2735 deletions(-)
Title: A Time-Travelling Debugger
Description: Uses provenance post-execution to help the user understand
and debug their script by providing functions to look at intermediate steps and
data values, their forwards and backwards lineage, and to understand the
steps leading up to warning and error messages. 'provDebugR' uses
provenance produced by 'rdtLite' (available on CRAN), stored in PROV-JSON format.
Author: Orenna Brand [aut],
Elizabeth Fong [aut],
Barbara Lerner [cre],
Rose Sheehan [aut],
Joseph Wonsil [aut],
Emery Boose [aut]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Diff between provDebugR versions 1.0 dated 2021-02-17 and 1.0.1 dated 2021-04-22
DESCRIPTION | 13 ++++++------- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/Home.html | 10 ++++++++++ inst/doc/debug.errors.html | 10 ++++++++++ inst/doc/debug.lineage.html | 10 ++++++++++ inst/doc/debug.variables.html | 10 ++++++++++ 7 files changed, 52 insertions(+), 13 deletions(-)
Title: Integrative Subtype Generation
Description: Multi-data type subtyping, which is data type agnostic and accepts missing data. Subtyping is performed using intermediary assessments created with autoencoders and similarity calculations.
Author: Natalie Fox
Maintainer: Paul C Boutros <pboutros@mednet.ucla.edu>
Diff between iSubGen versions 1.0.0 dated 2021-04-15 and 1.0.1 dated 2021-04-22
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/cluster.patients.R | 1 - R/write.scaling.factors.R | 6 +++++- build/vignette.rds |binary inst/doc/iSubGenGuide.Rnw | 10 ++++------ inst/doc/iSubGenGuide.pdf | 18 +++++++++--------- man/write.scaling.factors.Rd | 6 ++++-- vignettes/iSubGenGuide.Rnw | 10 ++++------ 9 files changed, 39 insertions(+), 38 deletions(-)
Title: Design Experiments for Batches
Description: Distributes samples in batches while making batches homogeneous
according to their description. Allows for an arbitrary number of variables,
both numeric and categorical. For quality control it provides functions to
subset a representative sample.
Author: Lluís Revilla Sancho [aut, cre]
(<https://orcid.org/0000-0001-9747-2570>)
Maintainer: Lluís Revilla Sancho <lluis.revilla@gmail.com>
Diff between experDesign versions 0.0.4 dated 2020-09-28 and 0.1.0 dated 2021-04-22
experDesign-0.0.4/experDesign/tests/testthat/test_batch-names.R |only experDesign-0.0.4/experDesign/tests/testthat/test_create-subset.R |only experDesign-0.0.4/experDesign/tests/testthat/test_design.R |only experDesign-0.0.4/experDesign/tests/testthat/test_entropy.R |only experDesign-0.0.4/experDesign/tests/testthat/test_evaluate-helper.R |only experDesign-0.0.4/experDesign/tests/testthat/test_evaluate-index.R |only experDesign-0.0.4/experDesign/tests/testthat/test_evaluate-mad.R |only experDesign-0.0.4/experDesign/tests/testthat/test_evaluate-mean.R |only experDesign-0.0.4/experDesign/tests/testthat/test_evaluate-na.R |only experDesign-0.0.4/experDesign/tests/testthat/test_evaluate-orig.R |only experDesign-0.0.4/experDesign/tests/testthat/test_evaluate-sd.R |only experDesign-0.0.4/experDesign/tests/testthat/test_insert.R |only experDesign-0.0.4/experDesign/tests/testthat/test_replicates.R |only experDesign-0.0.4/experDesign/tests/testthat/test_simplify2matrix.R |only experDesign-0.1.0/experDesign/DESCRIPTION | 8 experDesign-0.1.0/experDesign/MD5 | 68 experDesign-0.1.0/experDesign/NEWS.md | 14 experDesign-0.1.0/experDesign/R/QC.R | 4 experDesign-0.1.0/experDesign/R/designer.R | 27 experDesign-0.1.0/experDesign/R/evaluate.R | 3 experDesign-0.1.0/experDesign/R/indexing.R | 32 experDesign-0.1.0/experDesign/R/optimum.R | 85 experDesign-0.1.0/experDesign/R/reporting.R | 12 experDesign-0.1.0/experDesign/R/spatial.R | 11 experDesign-0.1.0/experDesign/R/utils.R | 17 experDesign-0.1.0/experDesign/README.md | 175 experDesign-0.1.0/experDesign/inst/doc/experdesign.R | 90 experDesign-0.1.0/experDesign/inst/doc/experdesign.Rmd | 178 experDesign-0.1.0/experDesign/inst/doc/experdesign.html | 1830 +--------- experDesign-0.1.0/experDesign/man/inspect.Rd | 6 experDesign-0.1.0/experDesign/tests/testthat/test-batch_names.R |only experDesign-0.1.0/experDesign/tests/testthat/test-create_subset.R |only experDesign-0.1.0/experDesign/tests/testthat/test-design.R |only experDesign-0.1.0/experDesign/tests/testthat/test-entropy.R |only experDesign-0.1.0/experDesign/tests/testthat/test-evaluate_helper.R |only experDesign-0.1.0/experDesign/tests/testthat/test-evaluate_index.R |only experDesign-0.1.0/experDesign/tests/testthat/test-evaluate_mad.R |only experDesign-0.1.0/experDesign/tests/testthat/test-evaluate_mean.R |only experDesign-0.1.0/experDesign/tests/testthat/test-evaluate_na.R |only experDesign-0.1.0/experDesign/tests/testthat/test-evaluate_orig.R |only experDesign-0.1.0/experDesign/tests/testthat/test-evaluate_sd.R |only experDesign-0.1.0/experDesign/tests/testthat/test-indexing.R | 5 experDesign-0.1.0/experDesign/tests/testthat/test-insert.R |only experDesign-0.1.0/experDesign/tests/testthat/test-inspect.R | 16 experDesign-0.1.0/experDesign/tests/testthat/test-optimum.R | 25 experDesign-0.1.0/experDesign/tests/testthat/test-replicates.R |only experDesign-0.1.0/experDesign/tests/testthat/test-simplify2matrix.R |only experDesign-0.1.0/experDesign/tests/testthat/test-spatial.R | 10 experDesign-0.1.0/experDesign/vignettes/experdesign.Rmd | 178 49 files changed, 733 insertions(+), 2061 deletions(-)
Title: Detect and Check for Separation and Infinite Maximum Likelihood
Estimates
Description: Provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in generalized linear models with categorical responses. The pre-fit methods apply on binomial-response generalized liner models such as logit, probit and cloglog regression, and can be directly supplied as fitting methods to the glm() function. They solve the linear programming problems for the detection of separation developed in Konis (2007, <https://ora.ox.ac.uk/objects/uuid:8f9ee0d0-d78e-4101-9ab4-f9cbceed2a2a>) using 'ROI' <https://cran.r-project.org/package=ROI> or 'lpSolveAPI' <https://cran.r-project.org/package=lpSolveAPI>. The post-fit methods apply to models with categorical responses, including binomial-response generalized linear models and multinomial-response models, such as baseline category logits and adjacent category logits models; for example, the models implemented in the 'brglm2' <https://cran.r-project.org/package=brglm2> package. The post-fit methods successively refit the model with increasing number of iteratively reweighted least squares iterations, and monitor the ratio of the estimated standard error for each parameter to what it has been in the first iteration. According to the results in Lesaffre & Albert (1989, <https://www.jstor.org/stable/2345845>), divergence of those ratios indicates data separation.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>),
Dirk Schumacher [aut],
Kjell Konis [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between detectseparation versions 0.1 dated 2020-03-25 and 0.2 dated 2021-04-22
DESCRIPTION | 8 MD5 | 42 +- NEWS.md | 11 R/check_infinite_estimates.R | 29 + R/detect_separation.R | 44 +- R/detectseparation-package.R | 7 R/separator_ROI.R | 12 R/separator_lpSolveAPI.R | 2 README.md | 21 - build/vignette.rds |binary inst/doc/separation.Rmd | 2 inst/doc/separation.html | 504 ++++++++++--------------------- man/check_infinite_estimates.glm.Rd | 19 - man/detect_separation.Rd | 9 man/detectseparation.Rd | 9 man/endometrial.Rd | 6 man/figures/README-unnamed-chunk-5-1.png |binary man/figures/hex_detectseparation.svg |only man/lizards.Rd | 4 tests/testthat/test-separation.R | 19 + tests/testthat/test-warnings.R |only vignettes/detectseparation.bib | 19 - vignettes/separation.Rmd | 2 23 files changed, 340 insertions(+), 429 deletions(-)
More information about detectseparation at CRAN
Permanent link
Title: Solution Paths for Linear and Logistic Regression Models with
Categorical Predictors, with SCOPE Penalty
Description: Computes solutions for linear and logistic regression models with potentially high-dimensional categorical predictors. This is done by applying a nonconvex penalty (SCOPE) and computing solutions in an efficient path-wise fashion. The scaling of the solution paths is selected automatically. Includes functionality for selecting tuning parameter lambda by k-fold cross-validation and early termination based on information criteria. Solutions are computed by cyclical block-coordinate descent, iterating an innovative dynamic programming algorithm to compute exact solutions for each block.
Author: Benjamin Stokell [aut],
Daniel Grose [ctb, cre],
Rajen Shah [ctb]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between CatReg versions 2.0.1 dated 2020-11-14 and 2.0.2 dated 2021-04-22
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/scope.R | 6 +++--- R/scope.logistic.R | 2 +- man/scope.Rd | 2 +- man/scope.logistic.Rd | 2 +- src/doblock.cpp | 38 ++++---------------------------------- 7 files changed, 22 insertions(+), 52 deletions(-)
Title: Bayesian Estimation of the GARCH(1,1) Model with Student-t
Innovations
Description: Provides the bayesGARCH() function which performs the
Bayesian estimation of the GARCH(1,1) model with Student's t innovations as described in Ardia (2008) <doi:10.1007/978-3-540-78657-3>.
Author: David Ardia [aut, cre, cph] (<https://orcid.org/0000-0003-2823-782X>)
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between bayesGARCH versions 2.1.7 dated 2021-04-20 and 2.1.8 dated 2021-04-22
bayesGARCH-2.1.7/bayesGARCH/README |only bayesGARCH-2.1.7/bayesGARCH/man/bayesGARCH.Rd |only bayesGARCH-2.1.8/bayesGARCH/DESCRIPTION | 13 +++++++------ bayesGARCH-2.1.8/bayesGARCH/MD5 | 13 ++++++------- bayesGARCH-2.1.8/bayesGARCH/NEWS | 10 ++++++++++ bayesGARCH-2.1.8/bayesGARCH/README.md | 24 ++++++++++++------------ bayesGARCH-2.1.8/bayesGARCH/build/partial.rdb |binary bayesGARCH-2.1.8/bayesGARCH/inst/CITATION | 5 ++--- bayesGARCH-2.1.8/bayesGARCH/man/bayesGARCH_.Rd |only 9 files changed, 37 insertions(+), 28 deletions(-)
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] (<https://orcid.org/0000-0002-8226-3132>),
Thomas Kiefer [aut],
Margaret Wu [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between TAM versions 3.5-19 dated 2020-05-06 and 3.6-45 dated 2021-04-22
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Title: Regression Models with Break-Points / Change-Points Estimation
Description: Given a regression model, segmented `updates' it by adding one or more segmented (i.e., piece-wise linear) relationships.
Several variables with multiple breakpoints are allowed. The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>)
and illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented
in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed
in Muggeo (2017, <doi:10.1111/anzs.12200>).
Author: Vito M. R. Muggeo [aut, cre] (<https://orcid.org/0000-0002-3386-4054>)
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 1.3-3 dated 2021-03-08 and 1.3-4 dated 2021-04-22
DESCRIPTION | 12 ++++++------ MD5 | 37 ++++++++++++++++++++----------------- NEWS | 11 +++++++++-- R/plot.segmented.R | 38 +++++++++++++++++++++++++++----------- R/seg.Ar.fit.boot.r | 8 ++++++-- R/seg.def.fit.boot.r | 8 ++++++-- R/seg.glm.fit.boot.r | 14 +++++++++----- R/seg.lm.fit.boot.r | 42 ++++++++++++++++++++++++++---------------- R/selgmented.r | 31 +++++++++++++++++++------------ data/down.R |only data/down.rda |binary data/plant.R |only data/plant.rda |binary data/stagnant.R |only data/stagnant.rda |binary man/davies.test.Rd | 2 +- man/plot.segmented.Rd | 4 ++-- man/pscore.test.rd | 2 +- man/seg.control.Rd | 2 +- man/segmented-package.Rd | 4 ++-- man/selgmented.Rd | 7 +++++-- 21 files changed, 140 insertions(+), 82 deletions(-)
Title: True Random Numbers using the ANU Quantum Random Numbers Server
Description: The ANU Quantum Random Number Generator provided by the Australian National University
generates true random numbers in real-time by measuring the quantum fluctuations of the vacuum. This package offers an interface using their API.
The electromagnetic field of the vacuum exhibits random fluctuations in phase and amplitude at all frequencies.
By carefully measuring these fluctuations, one is able to generate ultra-high bandwidth random numbers.
The quantum Random Number Generator is based on the papers by Symul et al., (2011) <doi:10.1063/1.3597793>
and Haw, et al. (2015) <doi:10.1103/PhysRevApplied.3.054004>.
The package offers functions to retrieve a sequence of random integers or hexadecimals and true random samples from a normal or uniform distribution.
Author: Siegfried Köstlmeier [aut, cre]
(<https://orcid.org/0000-0002-7221-6981>),
Boris Steipe [ctb] (<https://orcid.org/0000-0002-1134-6758>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>
Diff between qrandom versions 1.2.3 dated 2020-09-08 and 1.2.4 dated 2021-04-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/partial.rdb |binary tests/testthat/test-qUUID.R | 2 ++ tests/testthat/test-qrandom.R | 2 ++ tests/testthat/test-qrandommaxint.R | 24 +++++++++++++----------- tests/testthat/test-qrandomnorm.R | 1 + tests/testthat/test-qrandomunif.R | 2 ++ 8 files changed, 31 insertions(+), 22 deletions(-)
Title: Models Bivariate Dependence and Produces Bivariate Return
Periods
Description: Models the dependence between two variables in the extremes, identifies most
relevant models among six models: the conditional extremes model, the Jt-KDE model
and four copulae (Gumbel, Galambos, Normal, FGM). Bivariate return periods for
the six models and bivariate level curves can be created.
Methods used in the package are described in the following reference:
Tilloy, Malamud, Winter and Joly-Laugel (2020) <doi:10.5194/nhess-20-2091-2020>
Supporting references for the conditional extremes model,
Jt-KDE model and for copula modelling are the following:
Heffernan and Tawn (2004) <doi:10.1111/j.1467-9868.2004.02050.x>
Cooley, Thibaud, Castillo and Wehner (2019) <doi:10.1007/s10687-019-00348-0>
Nelsen (2006) <doi:10.1007/0-387-28678-0>.
Author: Alois Tilloy [aut, cre] (<https://orcid.org/0000-0002-5881-0642>)
Maintainer: Alois Tilloy <alois.tilloy@kcl.ac.uk>
Diff between mobirep versions 0.2.2 dated 2021-04-20 and 0.2.3 dated 2021-04-22
mobirep-0.2.2/mobirep/man/curve.funct.a.Rd |only mobirep-0.2.2/mobirep/man/curve.funct.b.Rd |only mobirep-0.2.3/mobirep/DESCRIPTION | 15 + mobirep-0.2.3/mobirep/MD5 | 46 ++--- mobirep-0.2.3/mobirep/NAMESPACE | 3 mobirep-0.2.3/mobirep/R/BvLTDep.R | 9 - mobirep-0.2.3/mobirep/R/digit.curves.R | 11 + mobirep-0.2.3/mobirep/R/jt_kde.R | 66 +++++-- mobirep-0.2.3/mobirep/R/level_curves.R | 218 ++++--------------------- mobirep-0.2.3/mobirep/R/porto_data.R | 22 +- mobirep-0.2.3/mobirep/R/supplement.funct.R | 67 ++++++- mobirep-0.2.3/mobirep/inst/doc/usepackage.Rmd | 4 mobirep-0.2.3/mobirep/inst/doc/usepackage.html | 4 mobirep-0.2.3/mobirep/man/AnalogSel.Rd | 9 - mobirep-0.2.3/mobirep/man/Bv.LT.Dep.Rd | 8 mobirep-0.2.3/mobirep/man/Cond.mod.ap.Rd | 35 +++- mobirep-0.2.3/mobirep/man/JT.KDE.ap.Rd | 26 ++ mobirep-0.2.3/mobirep/man/Margins.mod.Rd | 1 mobirep-0.2.3/mobirep/man/curve.funct.Rd | 49 ++++- mobirep-0.2.3/mobirep/man/densi.curv.cop.Rd | 43 ++++ mobirep-0.2.3/mobirep/man/densi.curv.em.Rd | 13 + mobirep-0.2.3/mobirep/man/digit.curves.p.Rd | 8 mobirep-0.2.3/mobirep/man/evenPts.p.Rd | 7 mobirep-0.2.3/mobirep/man/fire01meantemp.Rd | 18 +- mobirep-0.2.3/mobirep/vignettes/usepackage.Rmd | 4 25 files changed, 385 insertions(+), 301 deletions(-)
Title: Estimation and Prediction Methods for High-Dimensional Mixed
Frequency Time Series Data
Description: The 'midasml' package implements estimation and prediction methods for high-dimensional mixed-frequency (MIDAS) time-series and panel data regression models. The regularized MIDAS models are estimated using orthogonal (e.g. Legendre) polynomials and sparse-group LASSO (sg-LASSO) estimator. For more information on the `midasml' approach see Babii, Ghysels, and Striaukas (2021, JBES forthcoming) <doi:10.1080/07350015.2021.1899933>. The package is equipped with the fast implementation of the sg-LASSO estimator by means of proximal block coordinate descent. High-dimensional mixed frequency time-series data can also be easily manipulated with functions provided in the package.
Author: Jonas Striaukas [cre, aut],
Andrii Babii [aut],
Eric Ghysels [aut],
Alex Kostrov [ctb] (Contributions to analytical gradients for
non-linear low-dimensional MIDAS estimation code)
Maintainer: Jonas Striaukas <jonas.striaukas@gmail.com>
Diff between midasml versions 0.1.2 dated 2021-04-21 and 0.1.3 dated 2021-04-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/maxlambda.f90 | 6 +++--- src/sglfitF.f90 | 8 +++++--- 4 files changed, 14 insertions(+), 12 deletions(-)
Title: ICSS Algorithm by Inclan/Tiao (1994)
Description: The Iterative Cumulative Sum of Squares (ICSS) algorithm by Inclan/Tiao (1994) <https://www.jstor.org/stable/2290916> detects multiple change points, i.e. structural break points, in the variance of a sequence of independent observations. For series of moderate size (i.e. 200 observations and beyond), the ICSS algorithm offers results comparable to those obtained by a Bayesian approach or by likelihood ration tests, without the heavy computational burden required by these approaches.
Author: Siegfried Köstlmeier [aut, cre, cph]
(<https://orcid.org/0000-0002-7221-6981>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>
Diff between ICSS versions 1.0 dated 2020-06-02 and 1.1 dated 2021-04-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ICSS.R | 18 ++++++++++++------ 3 files changed, 18 insertions(+), 12 deletions(-)
Title: Load Environment Variables from '.env'
Description: Load configuration from a '.env' file, that is
in the current working directory, into environment variables.
Author: Gábor Csárdi [aut, cre, cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between dotenv versions 1.0.2 dated 2017-03-01 and 1.0.3 dated 2021-04-22
dotenv-1.0.2/dotenv/inst |only dotenv-1.0.3/dotenv/DESCRIPTION | 7 +++---- dotenv-1.0.3/dotenv/MD5 | 7 ++++--- dotenv-1.0.3/dotenv/NEWS.md |only dotenv-1.0.3/dotenv/R/dotenv-package.r | 4 ++++ dotenv-1.0.3/dotenv/README.md |only 6 files changed, 11 insertions(+), 7 deletions(-)
Title: Balanced Factorial Designs
Description: Generate balanced factorial designs with crossed and nested random and fixed effects <https://github.com/mmrabe/designr>.
Author: Maximilian M. Rabe [aut, cre] (<https://orcid.org/0000-0002-2556-5644>),
Reinhold Kliegl [aut] (<https://orcid.org/0000-0002-0180-8488>),
Daniel J. Schad [aut] (<https://orcid.org/0000-0003-2586-6823>)
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>
Diff between designr versions 0.1.11 dated 2021-03-07 and 0.1.12 dated 2021-04-22
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/simLMM.R | 7 ++++++- build/partial.rdb |binary inst/doc/design-to-dataframe.html | 2 +- man/simLMM.Rd | 2 +- 6 files changed, 18 insertions(+), 13 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Aust Frederik [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Christophe Dervieux [ctb],
Clifton Franklund [ctb],
Daniel Emaasit [ctb],
David Shuman [ctb],
Dean Attali [ctb],
Drew Tyre [ctb],
Ellis Valentiner [ctb],
Frans van Dunne [ctb],
Hadley Wickham [ctb],
Jeff Allen [ctb],
Jennifer Bryan [ctb],
Jonathan McPhers [ctb],
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>),
Joyce Robbins [ctb],
Junwen Huang [ctb],
Kevin Cheung [ctb],
Kevin Ushey [ctb],
Kim Seonghyun [ctb],
Kirill Muller [ctb],
Luciano Selzer [ctb],
Matthew Lincoln [ctb],
Maximilian Held [ctb],
Michael Sachs [ctb],
Michal Bojanowski [ctb],
Nathan Werth [ctb],
Noam Ross [ctb],
Peter Hickey [ctb],
Pedro Rafael D. Marinho [ctb] (<https://orcid.org/0000-0003-1591-8300>),
Romain Lesur [ctb] (<https://orcid.org/0000-0002-0721-5595>),
Sahir Bhatnagar [ctb],
Shir Dekel [ctb] (<https://orcid.org/0000-0003-1773-2446>),
Steve Simpson [ctb],
Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>),
Vincent Fulco [ctb],
Yixuan Qiu [ctb],
Zhuoer Dong [ctb],
RStudio, PBC [cph],
Bartek Szopka [ctb] (The jQuery Highlight plugin),
Zeno Rocha [cph] (clipboard.js library),
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/resources/AUTHORS),
MathQuill contributors [ctb] (The MathQuill library; authors listed in
inst/resources/AUTHORS),
FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.21 dated 2020-10-13 and 0.22 dated 2021-04-22
DESCRIPTION | 24 +++++--- MD5 | 62 ++++++++++++-------- NAMESPACE | 2 R/bs4_book.R |only R/ebook.R | 16 ++--- R/gitbook.R | 8 +- R/html.R | 63 ++++++++++++++------- R/latex.R | 43 +++++++++++--- R/render.R | 40 ++++++++++--- R/site.R | 40 ++++++++++++- R/skeleton.R | 2 R/utils.R | 19 +++--- README.md | 54 ++++++++++++++++-- build |only inst/CITATION | 4 - inst/doc |only inst/resources/bs4_book |only inst/resources/gitbook/css/plugin-fontsettings.css | 11 +++ inst/resources/gitbook/css/style.css | 9 ++- inst/resources/gitbook/js/plugin-sharing.js | 15 ++++- inst/rmarkdown/lua/custom-environment.lua | 3 - inst/templates/bs4_book.html |only inst/templates/default.html | 36 +++++++++++- inst/templates/gitbook.html | 39 +++++++++++-- man/bookdown-package.Rd | 3 + man/bs4_book.Rd |only man/figures |only man/gitbook.Rd | 3 - man/render_book.Rd | 17 ++++- man/resolve_refs_html.Rd | 2 tests/test-rmd.R | 5 + tests/testit/test-html.R |only tests/testit/test-latex.R |only tests/testit/test-site.R |only tests/testit/test-utils.R | 27 ++++----- vignettes |only 36 files changed, 412 insertions(+), 135 deletions(-)
Title: Manipulate and Map Origin-Destination Data
Description: The aim of 'od' is to provide tools and example datasets for working with
origin-destination ('OD') datasets of the type used to describe aggregate
urban mobility patterns (Carey et al. 1981) <doi:10.1287/trsc.15.1.32>.
The package builds on functions for working with 'OD' data in the package 'stplanr',
(Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053> with a focus on computational
efficiency and support for the 'sf' class system (Pebesma 2018) <doi:10.32614/RJ-2018-009>.
With few dependencies and a simple class system based on data frames,
the package is intended to facilitate efficient analysis of 'OD' datasets
and to provide a place for developing new functions.
The package enables the creation and analysis of geographic entities
representing large scale mobility patterns,
from daily travel between zones in cities to migration between countries.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
David Cooley [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between od versions 0.2.0 dated 2021-03-29 and 0.2.1 dated 2021-04-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/aggregate.R | 19 +++++++++++++++++++ inst/doc/od.html | 20 +++++++++++--------- 5 files changed, 41 insertions(+), 16 deletions(-)
Title: Neural Multiplexing Analysis
Description: Statistical methods for whole-trial and time-domain analysis of single cell neural response to multiple stimuli presented simultaneously. The package is based on the paper by C Glynn, ST Tokdar, A Zaman, VC Caruso, JT Mohl, SM Willett, and JM Groh (2021) "Analyzing second order stochasticity of neural spiking under stimuli-bundle exposure", is in press for publication by the Annals of Applied Statistics. A preprint may be found at <arXiv:1911.04387>.
Author: Surya Tokdar <surya.tokdar@duke.edu>
Maintainer: Surya Tokdar <surya.tokdar@duke.edu>
Diff between neuromplex versions 0.0-8 dated 2020-06-04 and 1.0-1 dated 2021-04-22
neuromplex-0.0-8/neuromplex/R/dynamic_neural_model-v5.R |only neuromplex-1.0-1/neuromplex/DESCRIPTION | 10 ++--- neuromplex-1.0-1/neuromplex/MD5 | 16 ++++----- neuromplex-1.0-1/neuromplex/R/dynamic_neural_model-v6.R |only neuromplex-1.0-1/neuromplex/R/poisson_analysis.R | 27 ++++++++++------ neuromplex-1.0-1/neuromplex/man/dapp.Rd | 6 +-- neuromplex-1.0-1/neuromplex/man/mplex.preprocess.Rd | 14 +++++--- neuromplex-1.0-1/neuromplex/man/plot.dapp.Rd | 4 +- neuromplex-1.0-1/neuromplex/man/poisson.tests.Rd | 8 ++-- neuromplex-1.0-1/neuromplex/man/synthesis.dapp.Rd | 4 +- 10 files changed, 52 insertions(+), 37 deletions(-)
Title: Linguistic Matching and Accommodation
Description: Measure similarity between texts. Offers a variety of processing
tools and similarity metrics to facilitate flexible representation of texts and matching.
Implements forms of Language Style Matching (Ireland & Pennebaker, 2010) <doi:10.1037/a0020386>
and Latent Semantic Analysis (Landauer & Dumais, 1997) <doi:10.1037/0033-295X.104.2.211>.
Author: Micah Iserman
Maintainer: Micah Iserman <micah.iserman@gmail.com>
Diff between lingmatch versions 1.0.1 dated 2021-02-25 and 1.0.2 dated 2021-04-22
DESCRIPTION | 7 MD5 | 48 +++--- NEWS.md | 23 +++ R/RcppExports.R | 58 +++----- R/lingmatch.R | 214 +++++++++++++++++++----------- R/sysdata.rda |binary R/utils.R | 268 +++++++++++++++++++++++++------------- README.md | 15 +- man/download.dict.Rd | 2 man/lma_dtm.Rd | 3 man/lma_lspace.Rd | 16 +- man/lma_patcat.Rd | 28 +++ man/lma_simets.Rd | 2 man/lma_termcat.Rd | 28 ++- man/lma_weight.Rd | 18 +- man/read.dic.Rd | 12 + man/select.dict.Rd | 2 src/Makevars.win | 2 src/RcppExports.cpp | 14 - src/utils.cpp | 53 ------- tests/testthat/test-lma_dtm.R | 8 - tests/testthat/test-lma_lspace.R | 2 tests/testthat/test-lma_termcat.R | 11 + tests/testthat/test-lma_weight.R | 2 tests/testthat/test-utils.R | 121 ++++++++++++----- 25 files changed, 593 insertions(+), 364 deletions(-)
Title: Goodness-of-Fit Tests for Copulae
Description: Several Goodness-of-Fit (GoF) tests for Copulae are provided. A new hybrid test, Zhang et al. (2016) <doi:10.1016/j.jeconom.2016.02.017> is implemented which supports all of the individual tests in the package, e.g. Genest et al. (2009) <doi:10.1016/j.insmatheco.2007.10.005>. Estimation methods for the margins are provided and all the tests support parameter estimation and predefined values. The parameters are estimated by pseudo maximum likelihood but if it fails the estimation switches automatically to inversion of Kendall's tau. For reproducibility of results, the functions support the definition of seeds. Also all the tests support automatized parallelization of the bootstrapping tasks. The package provides an interface to perform new GoF tests by submitting the test statistic.
Author: Ostap Okhrin <ostap.okhrin@tu-dresden.de>,
Simon Trimborn <trimborn.econometrics@gmail.com>,
Martin Waltz <martin.waltz@tu-dresden.de>
Maintainer: Simon Trimborn <trimborn.econometrics@gmail.com>
Diff between gofCopula versions 0.3-3 dated 2020-06-14 and 0.4-1 dated 2021-04-22
gofCopula-0.3-3/gofCopula/R/SnK.R |only gofCopula-0.3-3/gofCopula/R/TnK.R |only gofCopula-0.3-3/gofCopula/R/Tstats.R |only gofCopula-0.3-3/gofCopula/R/class_gofCOP.R |only gofCopula-0.3-3/gofCopula/R/estimate_margins.R |only gofCopula-0.3-3/gofCopula/R/functions.R |only gofCopula-0.3-3/gofCopula/R/functions2d.R |only gofCopula-0.3-3/gofCopula/R/functions3d.R |only gofCopula-0.3-3/gofCopula/R/gofGetHybrid.R |only gofCopula-0.3-3/gofCopula/R/goftime.R |only gofCopula-0.3-3/gofCopula/R/margin_param_est.R |only gofCopula-0.3-3/gofCopula/R/tests.R |only gofCopula-0.3-3/gofCopula/R/tests_copula_helper.R |only gofCopula-0.3-3/gofCopula/R/tests_copula_new.R |only gofCopula-0.3-3/gofCopula/R/tests_hybrid.R |only gofCopula-0.3-3/gofCopula/R/tests_stat_PIOS.R |only gofCopula-0.3-3/gofCopula/R/tests_which.R |only gofCopula-0.3-3/gofCopula/man/plot_gofCOP.Rd |only gofCopula-0.3-3/gofCopula/man/print_gofCOP.Rd |only gofCopula-0.3-3/gofCopula/man/test_getHybrid.Rd |only gofCopula-0.3-3/gofCopula/man/test_getOutputHybrid.Rd |only gofCopula-0.3-3/gofCopula/man/test_gofco.Rd |only gofCopula-0.3-3/gofCopula/man/tests11.Rd |only gofCopula-0.3-3/gofCopula/man/tests12.Rd |only gofCopula-0.3-3/gofCopula/man/tests2.Rd |only gofCopula-0.3-3/gofCopula/man/tests_CheckTime.Rd |only gofCopula-0.3-3/gofCopula/man/tests_CustomTest.Rd |only gofCopula-0.3-3/gofCopula/man/tests_KendallCvM.Rd |only gofCopula-0.3-3/gofCopula/man/tests_KendallKS.Rd |only gofCopula-0.3-3/gofCopula/man/tests_White.Rd |only gofCopula-0.3-3/gofCopula/man/tests_copula1.Rd |only gofCopula-0.3-3/gofCopula/man/tests_copula2.Rd |only gofCopula-0.3-3/gofCopula/man/tests_copula4.Rd |only gofCopula-0.3-3/gofCopula/man/tests_copula6.Rd |only gofCopula-0.3-3/gofCopula/man/tests_copula7.Rd |only gofCopula-0.3-3/gofCopula/man/tests_gof.Rd |only gofCopula-0.3-3/gofCopula/man/tests_gofCopula4Test.Rd |only gofCopula-0.3-3/gofCopula/man/tests_gofTest4Copula.Rd |only gofCopula-0.3-3/gofCopula/man/tests_gofWhich.Rd |only gofCopula-0.3-3/gofCopula/man/tests_gofWhichCopula.Rd |only gofCopula-0.4-1/gofCopula/DESCRIPTION | 11 gofCopula-0.4-1/gofCopula/MD5 | 140 ++- gofCopula-0.4-1/gofCopula/NAMESPACE | 6 gofCopula-0.4-1/gofCopula/R/ArchmRtrans.R |only gofCopula-0.4-1/gofCopula/R/Copula4Test.R |only gofCopula-0.4-1/gofCopula/R/CopulaTestTable.R |only gofCopula-0.4-1/gofCopula/R/Test4Copula.R |only gofCopula-0.4-1/gofCopula/R/class_gofCOP_plot.R |only gofCopula-0.4-1/gofCopula/R/class_gofCOP_print.R |only gofCopula-0.4-1/gofCopula/R/datasets.R |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_amh.r |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_clayton.R |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_fgm.R |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_frank.R |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_functions.R |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_galambos.R |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_gumbel.R |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_joe.R |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_normal.R |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_plackett.R |only gofCopula-0.4-1/gofCopula/R/internal_PIOS_t.R |only gofCopula-0.4-1/gofCopula/R/internal_RosenblattTrans.R |only gofCopula-0.4-1/gofCopula/R/internal_Tstats.R |only gofCopula-0.4-1/gofCopula/R/internal_bootstrap.R |only gofCopula-0.4-1/gofCopula/R/internal_est_margin_param.R |only gofCopula-0.4-1/gofCopula/R/internal_est_margins.R |only gofCopula-0.4-1/gofCopula/R/internal_est_time.R |only gofCopula-0.4-1/gofCopula/R/internal_extract_cop_obj.R |only gofCopula-0.4-1/gofCopula/R/internal_hybrid.R |only gofCopula-0.4-1/gofCopula/R/internal_param_est.R |only gofCopula-0.4-1/gofCopula/R/internal_rotateCopula.R |only gofCopula-0.4-1/gofCopula/R/test_GetHybrid.R |only gofCopula-0.4-1/gofCopula/R/test_HybridOutput.R | 71 + gofCopula-0.4-1/gofCopula/R/tests_ArchmChisq.R |only gofCopula-0.4-1/gofCopula/R/tests_ArchmGamma.R |only gofCopula-0.4-1/gofCopula/R/tests_ArchmSnB.R |only gofCopula-0.4-1/gofCopula/R/tests_ArchmSnC.R |only gofCopula-0.4-1/gofCopula/R/tests_CheckTime.R | 305 +++++++ gofCopula-0.4-1/gofCopula/R/tests_CustomTest.R | 215 +++++ gofCopula-0.4-1/gofCopula/R/tests_KS.R |only gofCopula-0.4-1/gofCopula/R/tests_KendallCvM.R | 203 ++++- gofCopula-0.4-1/gofCopula/R/tests_KendallKS.R | 201 ++++- gofCopula-0.4-1/gofCopula/R/tests_Kernel.R |only gofCopula-0.4-1/gofCopula/R/tests_PIOSRn.R |only gofCopula-0.4-1/gofCopula/R/tests_PIOSTn.R |only gofCopula-0.4-1/gofCopula/R/tests_RosenblattChisq.R |only gofCopula-0.4-1/gofCopula/R/tests_RosenblattGamma.R |only gofCopula-0.4-1/gofCopula/R/tests_RosenblattSnB.R |only gofCopula-0.4-1/gofCopula/R/tests_RosenblattSnC.R |only gofCopula-0.4-1/gofCopula/R/tests_White.R | 206 +++++ gofCopula-0.4-1/gofCopula/R/tests_gof.R | 620 ++++++++++++++-- gofCopula-0.4-1/gofCopula/R/tests_gofCvM.R |only gofCopula-0.4-1/gofCopula/R/tests_gofco.R | 270 +++++- gofCopula-0.4-1/gofCopula/build |only gofCopula-0.4-1/gofCopula/man/Banks.Rd | 35 gofCopula-0.4-1/gofCopula/man/CopulaTestTable.Rd |only gofCopula-0.4-1/gofCopula/man/CryptoCurrencies.Rd | 25 gofCopula-0.4-1/gofCopula/man/IndexReturns2D.Rd | 35 gofCopula-0.4-1/gofCopula/man/IndexReturns3D.Rd | 35 gofCopula-0.4-1/gofCopula/man/gof.Rd |only gofCopula-0.4-1/gofCopula/man/gofArchmChisq.Rd |only gofCopula-0.4-1/gofCopula/man/gofArchmGamma.Rd |only gofCopula-0.4-1/gofCopula/man/gofArchmSnB.Rd |only gofCopula-0.4-1/gofCopula/man/gofArchmSnC.Rd |only gofCopula-0.4-1/gofCopula/man/gofCheckTime.Rd |only gofCopula-0.4-1/gofCopula/man/gofCopula4Test.Rd |only gofCopula-0.4-1/gofCopula/man/gofCustomTest.Rd |only gofCopula-0.4-1/gofCopula/man/gofCvM.Rd |only gofCopula-0.4-1/gofCopula/man/gofGetHybrid.Rd |only gofCopula-0.4-1/gofCopula/man/gofKS.Rd |only gofCopula-0.4-1/gofCopula/man/gofKendallCvM.Rd |only gofCopula-0.4-1/gofCopula/man/gofKendallKS.Rd |only gofCopula-0.4-1/gofCopula/man/gofKernel.Rd |only gofCopula-0.4-1/gofCopula/man/gofOutputHybrid.Rd |only gofCopula-0.4-1/gofCopula/man/gofPIOSRn.Rd |only gofCopula-0.4-1/gofCopula/man/gofPIOSTn.Rd |only gofCopula-0.4-1/gofCopula/man/gofRosenblattChisq.Rd |only gofCopula-0.4-1/gofCopula/man/gofRosenblattGamma.Rd |only gofCopula-0.4-1/gofCopula/man/gofRosenblattSnB.Rd |only gofCopula-0.4-1/gofCopula/man/gofRosenblattSnC.Rd |only gofCopula-0.4-1/gofCopula/man/gofTest4Copula.Rd |only gofCopula-0.4-1/gofCopula/man/gofWhich.Rd |only gofCopula-0.4-1/gofCopula/man/gofWhichCopula.Rd |only gofCopula-0.4-1/gofCopula/man/gofWhite.Rd |only gofCopula-0.4-1/gofCopula/man/gofco.Rd |only gofCopula-0.4-1/gofCopula/man/plot.gofCOP.Rd |only gofCopula-0.4-1/gofCopula/man/print.gofCOP.Rd |only 127 files changed, 2033 insertions(+), 345 deletions(-)
Title: Bias Reduction in Binomial-Response Generalized Linear Models
Description: Fit generalized linear models with binomial responses using either an adjusted-score approach to bias reduction or maximum penalized likelihood where penalization is by Jeffreys invariant prior. These procedures return estimates with improved frequentist properties (bias, mean squared error) that are always finite even in cases where the maximum likelihood estimates are infinite (data separation). Fitting takes place by fitting generalized linear models on iteratively updated pseudo-data. The interface is essentially the same as 'glm'. More flexibility is provided by the fact that custom pseudo-data representations can be specified and used for model fitting. Functions are provided for the construction of confidence intervals for the reduced-bias estimates.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>)
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm versions 0.7.1 dated 2020-10-12 and 0.7.2 dated 2021-04-22
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/aaa.R | 2 +- R/separation.detection.R | 9 +++++---- inst/CHANGES | 24 +++++++++++++++--------- inst/CITATION | 7 +++++-- man/brglm.Rd | 13 +++++++------ man/brglm.control.Rd | 6 +++--- man/confint.brglm.Rd | 26 ++++++++++++++------------ man/modifications.Rd | 7 +++---- man/profileObjectives.Rd | 8 ++++---- man/separation.detection.Rd | 13 ++++++------- 12 files changed, 77 insertions(+), 66 deletions(-)
Title: Time Series Forecasting Using GRNN
Description: A general regression neural network (GRNN) is a variant of a
Radial Basis Function Network characterized by a fast single-pass learning.
'tsfgrnn' allows you to forecast time series using a GRNN model Francisco
Martinez et al. (2019) <doi:10.1007/978-3-030-20521-8_17> and Weizhong Yan
(2012) <doi:10.1109/TNNLS.2012.2198074>. When the forecasting horizon
is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is autoregressive, that is, it is only based on the
observations of the time series. You can consult and plot how the
prediction was done. It is also possible to assess the forecasting accuracy
of the model using rolling origin evaluation.
Author: Maria Pilar Frias-Bustamante [aut],
Ana Maria Martinez-Rodriguez [aut],
Antonio Conde-Sanchez [aut],
Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfgrnn versions 1.0.0 dated 2021-03-08 and 1.0.1 dated 2021-04-22
DESCRIPTION | 7 ++---- MD5 | 12 +++++------ NEWS.md | 4 +++ R/forecasting.R | 4 +-- build/vignette.rds |binary inst/doc/tsfgrnn.html | 50 ++++++++++++++++++++++++------------------------ man/grnn_forecasting.Rd | 4 +-- 7 files changed, 42 insertions(+), 39 deletions(-)
Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs including homoscedastic and heteroscedastic tests. These are one-way analysis of variance (ANOVA), Welch's heteroscedastic F test, Welch's heteroscedastic F test with trimmed means and Winsorized variances, Brown-Forsythe test, Alexander-Govern test, James second order test, Kruskal-Wallis test, Scott-Smith test, Box F test and Johansen F test, Generalized tests equivalent to Parametric Bootstrap and Fiducial tests. The package performs pairwise comparisons and graphical approaches. Also, the package includes Student's t test, Welch's t test and Mann-Whitney U test for two samples. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots (Dag et al., 2018, <https://journal.r-project.org/archive/2018/RJ-2018-022/RJ-2018-022.pdf>).
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut], Sam Weerahandi [ctb], Malwane Ananda [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between onewaytests versions 2.5 dated 2021-01-07 and 2.6 dated 2021-04-22
DESCRIPTION | 10 +++++----- MD5 | 42 +++++++++++++++++++++--------------------- NAMESPACE | 2 +- R/ag.test.R | 4 ++-- R/aov.test.R | 5 +++-- R/bf.test.R | 4 ++-- R/box.test.R | 3 ++- R/describe.R | 3 ++- R/gp.test.R | 3 ++- R/gplot.R | 6 ++++-- R/homog.test.R | 6 +++--- R/james.test.R | 3 ++- R/johansen.test.R | 3 ++- R/kw.test.R | 3 ++- R/mw.test.R | 3 ++- R/nor.test.R | 3 ++- R/ss.test.R | 4 ++-- R/st.test.R | 3 ++- R/welch.test.R | 3 ++- R/wt.test.R | 3 ++- man/gp.test.Rd | 7 +++---- man/welch.test.Rd | 1 - 22 files changed, 68 insertions(+), 56 deletions(-)
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut, cre],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>),
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifeng Geng [aut],
Yutian Li [aut],
XGBoost contributors [cph] (base XGBoost implementation)
Maintainer: Tong He <hetong007@gmail.com>
Diff between xgboost versions 1.3.2.1 dated 2021-01-18 and 1.4.1.1 dated 2021-04-22
DESCRIPTION | 12 MD5 | 216 ++++++------ NAMESPACE | 4 R/xgb.Booster.R | 1 R/xgb.DMatrix.R | 17 R/xgb.DMatrix.save.R | 4 R/xgb.config.R |only R/xgb.create.features.R | 4 R/xgb.cv.R | 2 R/xgb.dump.R | 1 R/xgb.save.R | 1 R/xgb.train.R | 10 R/xgboost.R | 2 inst/doc/discoverYourData.html | 8 inst/doc/xgboost.pdf |binary inst/doc/xgboostPresentation.html | 26 - inst/doc/xgboostfromJSON.html | 4 man/xgbConfig.Rd |only src/amalgamation/xgboost-all0.cc | 2 src/dmlc-core/include/dmlc/base.h | 52 ++ src/dmlc-core/include/dmlc/build_config_default.h | 12 src/dmlc-core/include/dmlc/data.h | 2 src/dmlc-core/include/dmlc/logging.h | 140 ++++--- src/dmlc-core/include/dmlc/omp.h | 1 src/dmlc-core/include/dmlc/parameter.h | 38 -- src/dmlc-core/include/dmlc/registry.h | 2 src/dmlc-core/src/io/hdfs_filesys.cc | 23 - src/include/xgboost/c_api.h | 255 ++++++++++++++ src/include/xgboost/data.h | 27 - src/include/xgboost/gbm.h | 47 +- src/include/xgboost/generic_parameters.h | 5 src/include/xgboost/global_config.h |only src/include/xgboost/json.h | 19 - src/include/xgboost/learner.h | 62 ++- src/include/xgboost/logging.h | 17 src/include/xgboost/parameter.h | 7 src/include/xgboost/predictor.h | 54 +-- src/include/xgboost/span.h | 61 +-- src/include/xgboost/tree_updater.h | 13 src/include/xgboost/version_config.h | 4 src/init.c | 4 src/src/c_api/c_api.cc | 348 +++++++++++++++---- src/src/c_api/c_api.cu | 94 ++--- src/src/c_api/c_api_utils.h |only src/src/cli_main.cc | 17 src/src/common/column_matrix.h | 5 src/src/common/common.h | 12 src/src/common/device_helpers.cuh | 265 ++++++++++++++ src/src/common/group_data.h | 85 +++- src/src/common/hist_util.cc | 111 +++--- src/src/common/hist_util.cu | 28 + src/src/common/hist_util.cuh | 5 src/src/common/hist_util.h | 5 src/src/common/host_device_vector.cu | 5 src/src/common/json.cc | 9 src/src/common/math.h | 3 src/src/common/quantile.cc | 12 src/src/common/random.h | 2 src/src/common/ranking_utils.cuh |only src/src/common/threading_utils.h | 28 - src/src/common/transform.h | 10 src/src/data/adapter.h | 149 ++++++++ src/src/data/array_interface.cu |only src/src/data/array_interface.h | 250 ++++++++------ src/src/data/data.cc | 68 +++ src/src/data/data.cu | 78 +++- src/src/data/device_adapter.cuh | 13 src/src/data/ellpack_page.cu | 16 src/src/data/simple_dmatrix.cc | 11 src/src/data/simple_dmatrix.cu | 13 src/src/gbm/gblinear.cc | 47 +- src/src/gbm/gblinear_model.cc | 2 src/src/gbm/gblinear_model.h | 3 src/src/gbm/gbtree.cc | 392 ++++++++++++++-------- src/src/gbm/gbtree.cu |only src/src/gbm/gbtree.h | 92 +++-- src/src/global_config.cc |only src/src/learner.cc | 194 ++++++---- src/src/linear/coordinate_common.h | 78 ++-- src/src/linear/updater_gpu_coordinate.cu | 5 src/src/linear/updater_shotgun.cc | 61 +-- src/src/logging.cc | 55 +-- src/src/metric/auc.cc |only src/src/metric/auc.cu |only src/src/metric/auc.h |only src/src/metric/elementwise_metric.cu | 49 +- src/src/metric/multiclass_metric.cu | 23 - src/src/metric/rank_metric.cc | 265 ++++---------- src/src/metric/rank_metric.cu | 235 ------------- src/src/metric/survival_metric.cu | 16 src/src/objective/aft_obj.cu | 2 src/src/objective/hinge.cu | 2 src/src/objective/multiclass_obj.cu | 2 src/src/objective/rank_obj.cu | 128 +++---- src/src/objective/regression_loss.h | 2 src/src/objective/regression_obj.cu | 18 - src/src/predictor/cpu_predictor.cc | 207 +++++------ src/src/predictor/gpu_predictor.cu | 264 ++++++-------- src/src/tree/gpu_hist/row_partitioner.cu | 34 + src/src/tree/gpu_hist/row_partitioner.cuh | 20 - src/src/tree/param.h | 10 src/src/tree/split_evaluator.h | 2 src/src/tree/tree_model.cc | 2 src/src/tree/updater_basemaker-inl.h | 44 +- src/src/tree/updater_colmaker.cc | 39 +- src/src/tree/updater_gpu_hist.cu | 9 src/src/tree/updater_histmaker.cc | 88 ++-- src/src/tree/updater_quantile_hist.cc | 217 ++++++++---- src/src/tree/updater_quantile_hist.h | 23 - src/src/tree/updater_refresh.cc | 34 + src/xgboost_R.cc | 53 ++ src/xgboost_R.h | 13 src/xgboost_custom.cc | 2 tests/testthat/test_basic.R | 2 tests/testthat/test_config.R |only 115 files changed, 3400 insertions(+), 2135 deletions(-)
Title: Utilities Dealing with Solar Time Such as Sun Position and Time
of Sunrise
Description: Provide utilities to work with solar time,
i.e. where noon is exactly when sun culminates.
Provides functions for computing sun position and times of sunrise and sunset.
Author: Thomas Wutzler
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between solartime versions 0.0.1 dated 2018-12-03 and 0.0.2 dated 2021-04-22
DESCRIPTION | 10 +-- MD5 | 43 +++++++-------- NEWS.md | 4 + R/utilSolarTime.R | 10 +-- build/vignette.rds |binary inst/WORDLIST |only inst/doc/overview.Rmd | 6 +- inst/doc/overview.html | 83 ++++++++++++++++++++++------- man/computeDayLength.Rd | 38 ++++++------- man/computeDayLengthDoy.Rd | 52 +++++++++--------- man/computeIsDayByHour.Rd | 48 ++++++++-------- man/computeIsDayByLocation.Rd | 82 ++++++++++++++-------------- man/computeSolarToLocalTimeDifference.Rd | 74 +++++++++++++------------- man/computeSunPosition.Rd | 38 ++++++------- man/computeSunPositionDoyHour.Rd | 88 +++++++++++++++---------------- man/computeSunriseHour.Rd | 50 ++++++++--------- man/computeSunriseHourDoy.Rd | 84 ++++++++++++++--------------- man/computeSunsetHour.Rd | 50 ++++++++--------- man/computeSunsetHourDoy.Rd | 80 ++++++++++++++-------------- man/getFractionalHours.Rd | 34 +++++------ man/getHoursAheadOfUTC.Rd | 36 ++++++------ man/getSolarTimeHour.Rd | 36 ++++++------ vignettes/overview.Rmd | 6 +- 23 files changed, 500 insertions(+), 452 deletions(-)
Title: Project Future Case Incidence
Description: Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>. The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.
Author: Thibaut Jombart [aut, cre],
Pierre Nouvellet [aut],
Sangeeta Bhatia [ctb],
Zhian N. Kamvar [ctb],
Tim Taylor [ctb],
Stephane Ghozzi [ctb]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between projections versions 0.5.2 dated 2020-12-17 and 0.5.4 dated 2021-04-22
DESCRIPTION | 9 MD5 | 40 NEWS.md | 14 R/compute_force_infection.R | 27 R/project.R | 42 man/project.Rd | 18 tests/testthat/_snaps/plots/basic-example-plot.svg | 144 tests/testthat/_snaps/plots/evd-proj-box-no-outliers.svg | 812 ++--- tests/testthat/_snaps/plots/evd-proj-box-only.svg | 746 ++-- tests/testthat/_snaps/plots/evd-proj-full-red-ribbon-narrow-range.svg | 110 tests/testthat/_snaps/plots/evd-proj-no-box-custom-lines.svg | 166 - tests/testthat/_snaps/plots/evd-proj-no-ribbon.svg | 160 - tests/testthat/_snaps/plots/evd-proj-red-box.svg | 812 ++--- tests/testthat/_snaps/plots/evd-proj-red-ribbon.svg | 106 tests/testthat/_snaps/plots/evd-proj-ribbon-only.svg | 106 tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-and-custom.svg | 608 +-- tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-box-only.svg | 1526 ++++----- tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-no-box.svg | 1592 +++++----- tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence.svg | 946 ++--- tests/testthat/_snaps/plots/evd-proj.svg | 166 - tests/testthat/test-project.R | 91 21 files changed, 4228 insertions(+), 4013 deletions(-)
Title: Monte Carlo Data Simulation Package
Description: Monte Carlo simulation allows to test different conditions given to the correct structural equation models. This package runs Monte Carlo simulations under different conditions (such as sample size or normality of data). Within the package data sets can be simulated and run based on the given model.
First, continuous and normal data sets are generated based on the given model. Later Fleishman's power method (1978) <DOI:10.1007/BF02293811> is used to add non-normality if exists.
When data generation is completed (or when generated data sets are given) model test can also be run.
Author: Fatih Orcan [aut, cre] (<https://orcid.org/0000-0003-1727-0456>)
Maintainer: Fatih Orcan <fatihorcan84@gmail.com>
Diff between MonteCarloSEM versions 0.0.1 dated 2020-09-22 and 0.0.2 dated 2021-04-22
DESCRIPTION | 9 ++++----- MD5 | 14 +++++++------- R/Input_fcors.R | 2 +- R/Input_floads.R | 2 +- R/run.sem.sim.R | 39 +++++++++++++++++++++++---------------- R/sim_CFA_Skewed.R | 2 +- man/fit.simulation.Rd | 4 ++-- man/sim.skewed.Rd | 2 +- 8 files changed, 40 insertions(+), 34 deletions(-)
Title: Convert Plot to 'grob' or 'ggplot' Object
Description: Convert plot function call (using expression or formula) to 'grob' or 'ggplot' object that compatible to the 'grid' and 'ggplot2' ecosystem. With this package, we are able to e.g. using 'cowplot' to align plots produced by 'base' graphics, 'ComplexHeatmap', 'eulerr', 'grid', 'lattice', 'magick', 'pheatmap', 'vcd' etc. by converting them to 'ggplot' objects.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggplotify versions 0.0.5 dated 2020-03-12 and 0.0.6 dated 2021-04-22
DESCRIPTION | 12 +-- MD5 | 19 +++-- NAMESPACE | 2 NEWS.md | 8 ++ R/as-ggplot.R | 24 +++++++ R/as-grob.R | 8 ++ R/rotate.R |only build/vignette.rds |binary inst/doc/ggplotify.html | 153 +++++++++++++++++++++--------------------------- man/as-grob.Rd | 3 man/as.ggplot.Rd | 4 - 11 files changed, 130 insertions(+), 103 deletions(-)
Title: Automatic Generation of Exams in R for 'Sakai'
Description: Automatic Generation of Exams in R for 'Sakai'.
Question templates in the form of the 'exams' package (see <http://www.r-exams.org/>)
are transformed into XML format required by 'Sakai'.
Author: Fuensanta Arnaldos García [aut],
María Victoria Caballero Pintado [aut],
Úrsula Faura Martínez [aut],
María Teresa Díaz Delfa [aut],
Jesús María Méndez Pérez [aut, cre],
Lourdes Molera Peris [aut],
José Antonio Palazón Ferrando [aut],
Juan José Pérez Castejón [aut],
Isabel Parra Frutos [aut],
Raúl Sánchez Sánchez [aut],
Nicolás Andrés Ubero Pascal [aut],
Nikolaus Umlauf [ctb],
Achim Zeileis [ctb] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Jesús María Méndez Pérez <jesus.mendez@ticarum.es>
Diff between exams2sakai versions 0.2 dated 2021-04-09 and 0.3 dated 2021-04-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/exams2sakai.R | 10 ++++++++-- man/exams2sakai.Rd | 11 +++++++++++ 5 files changed, 34 insertions(+), 9 deletions(-)
Title: Core Functions to Read and Fit 13c Time Series from Breath Tests
Description: Reads several formats of 13C data (IRIS/Wagner,
BreathID) and CSV. Creates artificial sample data for testing. Fits
Maes/Ghoos, Bluck-Coward self-correcting formula using 'nls', 'nlme'.
Methods to fit breath test curves with Bayesian Stan methods are
refactored to package 'breathteststan'. For a Shiny GUI, see package
'dmenne/breathtestshiny' on github.
Author: Dieter Menne [aut, cre],
Menne Biomed Consulting Tuebingen [cph],
Benjamin Misselwitz [fnd],
Mark Fox [fnd],
Andreas Steingoetter [dtc],
University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between breathtestcore versions 0.8.0 dated 2020-07-14 and 0.8.1 dated 2021-04-22
DESCRIPTION | 15 - MD5 | 87 ++++---- R/breathtestcore.R | 2 R/breathtestfit_broom.R | 8 R/nls_fit.R | 10 build/vignette.rds |binary inst/doc/data_formats.html | 386 +++++++++---------------------------- inst/doc/methods_and_concepts.Rmd | 2 inst/doc/methods_and_concepts.html | 325 +++++++------------------------ inst/extdata/invalid_records.xml |only man/augment.breathtestfit.Rd | 92 ++++---- man/breathtest_read_function.Rd | 70 +++--- man/btcore_file.Rd | 52 ++-- man/cleanup_data.Rd | 200 +++++++++---------- man/coef.breathtestfit.Rd | 86 ++++---- man/coef_by_group.Rd | 106 +++++----- man/coef_diff_by_group.Rd | 118 +++++------ man/cum_exp_beta.Rd | 54 ++--- man/dob_to_pdr.Rd | 116 +++++------ man/exp_beta.Rd | 300 ++++++++++++++-------------- man/extract_id.Rd | 40 +-- man/nlme_fit.Rd | 162 +++++++-------- man/nls_fit.Rd | 118 +++++------ man/null_fit.Rd | 46 ++-- man/plot.breathtestfit.Rd | 86 ++++---- man/read_any_breathtest.Rd | 78 +++---- man/read_breathid.Rd | 56 ++--- man/read_breathid_xml.Rd | 88 ++++---- man/read_breathtest_excel.Rd | 92 ++++---- man/read_iris.Rd | 70 +++--- man/read_iris_csv.Rd | 70 +++--- man/sigma.breathtestnlmefit.Rd | 40 +-- man/simulate_breathtest_data.Rd | 176 ++++++++-------- man/subsample_data.Rd | 48 ++-- man/t50_maes_ghoos.Rd | 74 +++---- man/t50_maes_ghoos_scintigraphy.Rd | 54 ++--- man/tidy.breathtestfit.Rd | 88 ++++---- man/tlag_bluck_coward.Rd | 46 ++-- man/tlag_maes_ghoos.Rd | 52 ++-- man/usz_13c.Rd | 100 ++++----- man/usz_13c_a.Rd | 60 ++--- man/usz_13c_d.Rd | 136 ++++++------- tests/test-all.R | 4 tests/testthat/test_broom.R | 1 vignettes/methods_and_concepts.Rmd | 2 45 files changed, 1732 insertions(+), 2084 deletions(-)
More information about breathtestcore at CRAN
Permanent link
Title: Write Reusable, Composable and Modular R Code
Description: A modern module system for R. Organise code into hierarchical,
composable, reusable modules, and use it effortlessly across projects via a
flexible, declarative dependency loading syntax.
Author: Konrad Rudolph [aut, cre] (<https://orcid.org/0000-0002-9866-7051>),
Michael Schubert [ctb] (<https://orcid.org/0000-0002-6862-5221>)
Maintainer: Konrad Rudolph <konrad.rudolph@gmail.com>
Diff between box versions 1.0.1 dated 2021-03-20 and 1.0.2 dated 2021-04-22
box-1.0.1/box/man/figures/box.png |only box-1.0.1/box/man/figures/box.svg |only box-1.0.2/box/DESCRIPTION | 7 - box-1.0.2/box/MD5 | 63 +++++----- box-1.0.2/box/NEWS.md | 59 +++++---- box-1.0.2/box/R/box-package.r | 41 +++--- box-1.0.2/box/R/env.r | 13 +- box-1.0.2/box/R/help.r | 128 ++++++++++++--------- box-1.0.2/box/R/spec.r | 13 -- box-1.0.2/box/R/use.r | 6 box-1.0.2/box/inst/doc/box.html | 31 +++-- box-1.0.2/box/inst/doc/box.rmd | 37 ++++-- box-1.0.2/box/inst/doc/compiled-code.html | 37 ++++-- box-1.0.2/box/inst/doc/compiled-code.rmd | 13 ++ box-1.0.2/box/inst/doc/migration.html | 43 ++++--- box-1.0.2/box/inst/doc/migration.rmd | 39 ++++-- box-1.0.2/box/inst/doc/mod-env-hierarchy.html | 23 +++ box-1.0.2/box/inst/doc/mod-env-hierarchy.rmd | 13 ++ box-1.0.2/box/inst/doc/testing.html | 34 +++-- box-1.0.2/box/inst/doc/testing.rmd | 31 +++-- box-1.0.2/box/man/figures/logo.png |only box-1.0.2/box/man/figures/logo.svg |only box-1.0.2/box/man/help-internal.Rd | 13 +- box-1.0.2/box/man/help.Rd | 5 box-1.0.2/box/man/importing.Rd | 2 box-1.0.2/box/tests/testthat/mod/b/b.r |only box-1.0.2/box/tests/testthat/test-basic.r | 7 + box-1.0.2/box/tests/testthat/test-help.r | 2 box-1.0.2/box/tests/testthat/test-parse-mod-spec.r | 3 box-1.0.2/box/tests/testthat/test-pkg.r | 4 box-1.0.2/box/vignettes/box.rmd | 37 ++++-- box-1.0.2/box/vignettes/compiled-code.rmd | 13 ++ box-1.0.2/box/vignettes/migration.rmd | 39 ++++-- box-1.0.2/box/vignettes/mod-env-hierarchy.rmd | 13 ++ box-1.0.2/box/vignettes/testing.rmd | 31 +++-- 35 files changed, 528 insertions(+), 272 deletions(-)
Title: The Genie++ Hierarchical Clustering Algorithm with Noise Points
Detection
Description: A retake on the Genie algorithm - a robust
hierarchical clustering method
(Gagolewski, Bartoszuk, Cena, 2016 <DOI:10.1016/j.ins.2016.05.003>).
Now faster and more memory efficient; determining the whole hierarchy
for datasets of 10M points in low dimensional Euclidean spaces or
100K points in high-dimensional ones takes only 1-2 minutes.
Allows clustering with respect to mutual reachability distances
so that it can act as a noise point detector or a robustified version of
'HDBSCAN*' (that is able to detect a predefined number of
clusters and hence it does not dependent on the somewhat
fragile 'eps' parameter).
The package also features an implementation of economic inequity indices
(the Gini, Bonferroni index) and external cluster validity measures
(partition similarity scores; e.g., the adjusted Rand, Fowlkes-Mallows,
adjusted mutual information, pair sets index).
See also the 'Python' version of 'genieclust' available on 'PyPI', which
supports sparse data, more metrics, and even larger datasets.
Author: Marek Gagolewski [aut, cre, cph]
(<https://orcid.org/0000-0003-0637-6028>),
Maciej Bartoszuk [ctb],
Anna Cena [ctb],
Peter M. Larsen [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between genieclust versions 0.9.8 dated 2021-01-08 and 1.0.0 dated 2021-04-22
DESCRIPTION | 12 +++---- MD5 | 51 ++++++++++++++++--------------- NEWS | 41 +++++++++---------------- R/RcppExports.R | 18 ++++------- R/gclust.R | 2 - R/genieclust-package.R | 2 - R/mst.R | 25 +++++++++++---- inst |only man/comparing_partitions.Rd | 14 ++++---- man/emst_mlpack.Rd | 12 +++++-- man/gclust.Rd | 2 - src/RcppExports.cpp | 14 -------- src/c_argfuns.h | 2 - src/c_compare_partitions.h | 2 - src/c_disjoint_sets.h | 2 - src/c_distance.h | 2 - src/c_genie.h | 2 - src/c_gini_disjoint_sets.h | 2 - src/c_inequity.h | 2 - src/c_int_dict.h | 2 - src/c_matrix.h | 2 - src/c_mst.h | 2 - src/c_postprocess.h | 2 - src/c_preprocess.h | 2 - src/r_compare_partitions.cpp | 14 ++++---- src/r_emst.cpp | 69 ++++++++++++++++++++++--------------------- src/r_inequity.cpp | 4 -- 27 files changed, 147 insertions(+), 157 deletions(-)
More information about epanet2toolkit at CRAN
Permanent link
Title: Sparse Tables
Description: Fast Multiplication and Marginalization of Sparse Tables.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between sparta versions 0.7.2 dated 2021-04-03 and 0.7.3 dated 2021-04-22
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/api_sparta.R | 2 +- README.md | 2 +- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Running Operations for Vectors
Description: Lightweight library for rolling windows operations. Package enables
full control over the window length, window lag and a time indices. With a runner
one can apply any R function on a rolling windows. The package eases work with
equally and unequally spaced time series.
Author: Dawid Kałędkowski [aut, cre] (<https://orcid.org/0000-0001-9533-457X>)
Maintainer: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>
Diff between runner versions 0.3.8 dated 2021-02-22 and 0.4.0 dated 2021-04-22
DESCRIPTION | 6 MD5 | 28 +-- NEWS.md | 8 - R/run.R | 78 +++------- build/vignette.rds |binary inst/doc/apply_any_r_function.html | 4 inst/tinytest/test_max_run.R | 26 +-- inst/tinytest/test_mean_run.R | 10 - inst/tinytest/test_min_run.R | 23 +-- inst/tinytest/test_runner.R | 264 +++++++++++++------------------------ inst/tinytest/test_runner_vec.R | 109 +++++++++------ inst/tinytest/test_streak_run.R | 13 - inst/tinytest/test_sum_run.R | 24 +-- man/runner.Rd | 35 ++-- src/vector_funs.h | 8 - 15 files changed, 271 insertions(+), 365 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-25 2.0.3
2020-07-19 2.0.2
2020-03-02 2.0.1
2020-02-17 2.0.0
2019-09-10 1.10.1
2019-07-11 1.10.0
2019-04-25 1.9.2
2019-04-17 1.9.1
2019-02-04 1.9
2018-01-23 1.8
2017-07-15 1.7
2017-06-08 1.6
2017-03-03 1.5
2016-02-02 1.4
2015-10-14 1.3
2015-05-11 1.2
2015-03-06 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-04 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-18 1.1.0
2019-06-24 1.0.0
Title: Correlation-Based Feature Selection for Single-Cell RNA
Sequencing Data
Description: Determining the optimal set of feature genes to characterise cell types in single-cell RNA sequencing data using stepwise regression on gene-gene correlations. <doi:10.1101/2020.10.07.330563>.
Author: Bobby Ranjan [aut, cre],
Kunal Mishra [ctb],
Shyam Lab [cph],
Bryan Hanson [ctb],
Damian Coventry [ctb],
Brandon Crosby [ctb],
Gregoire Thomas [ctb]
Maintainer: Bobby Ranjan <ranjan_bobby@gis.a-star.edu.sg>
Diff between DUBStepR versions 1.1 dated 2021-03-15 and 1.1.1 dated 2021-04-22
DESCRIPTION | 16 +++++++++------- LICENSE | 4 ++-- MD5 | 20 +++++++++++++------- R/DUBStepR.R | 9 +++++---- R/getCorrelationRange.R | 2 +- R/getFilteredData.R | 11 ++++++++--- R/getOptimalFeatureSet.R | 3 ++- build |only inst |only man/getCorrelationRange.Rd | 4 ++-- vignettes |only 11 files changed, 42 insertions(+), 27 deletions(-)
Title: Best Subset Selection in Linear, Logistic and CoxPH Models
Description: An implementation of best subset selection in generalized linear model and Cox proportional hazard model via the primal dual active set algorithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2020) <doi:10.18637/jss.v094.i04>. The algorithm formulates coefficient parameters and residuals as primal and dual variables and utilizes efficient active set selection strategies based on the complementarity of the primal and dual variables.
Author: Canhong Wen [aut, cre],
Aijun Zhang [aut],
Shijie Quan [aut],
Xueqin Wang [aut]
Maintainer: Canhong Wen <wencanhong@gmail.com>
Diff between BeSS versions 2.0.2 dated 2021-01-23 and 2.0.3 dated 2021-04-22
BeSS-2.0.2/BeSS/NEWS.md |only BeSS-2.0.2/BeSS/R/data.R |only BeSS-2.0.2/BeSS/R/deviance_all.R |only BeSS-2.0.2/BeSS/R/package.R |only BeSS-2.0.2/BeSS/R/recover.R |only BeSS-2.0.2/BeSS/R/utilize.R |only BeSS-2.0.2/BeSS/README.md |only BeSS-2.0.2/BeSS/build |only BeSS-2.0.2/BeSS/data/duke.rda |only BeSS-2.0.2/BeSS/data/trim32.rda |only BeSS-2.0.2/BeSS/inst/doc |only BeSS-2.0.2/BeSS/man/BeSS-package.Rd |only BeSS-2.0.2/BeSS/man/duke.Rd |only BeSS-2.0.2/BeSS/man/trim32.Rd |only BeSS-2.0.2/BeSS/src/Algorithm.cpp |only BeSS-2.0.2/BeSS/src/Algorithm.h |only BeSS-2.0.2/BeSS/src/Data.cpp |only BeSS-2.0.2/BeSS/src/Data.h |only BeSS-2.0.2/BeSS/src/Makevars |only BeSS-2.0.2/BeSS/src/Makevars.win |only BeSS-2.0.2/BeSS/src/Metric.cpp |only BeSS-2.0.2/BeSS/src/Metric.h |only BeSS-2.0.2/BeSS/src/bess.h |only BeSS-2.0.2/BeSS/src/coxph.cpp |only BeSS-2.0.2/BeSS/src/coxph.h |only BeSS-2.0.2/BeSS/src/logistic.cpp |only BeSS-2.0.2/BeSS/src/logistic.h |only BeSS-2.0.2/BeSS/src/normalize.cpp |only BeSS-2.0.2/BeSS/src/normalize.h |only BeSS-2.0.2/BeSS/src/path.cpp |only BeSS-2.0.2/BeSS/src/path.h |only BeSS-2.0.2/BeSS/src/poisson.cpp |only BeSS-2.0.2/BeSS/src/poisson.h |only BeSS-2.0.2/BeSS/src/screening.cpp |only BeSS-2.0.2/BeSS/src/screening.h |only BeSS-2.0.2/BeSS/src/utilities.cpp |only BeSS-2.0.2/BeSS/src/utilities.h |only BeSS-2.0.2/BeSS/vignettes |only BeSS-2.0.3/BeSS/DESCRIPTION | 30 BeSS-2.0.3/BeSS/MD5 | 123 +- BeSS-2.0.3/BeSS/NAMESPACE | 75 - BeSS-2.0.3/BeSS/R/RcppExports.R | 32 BeSS-2.0.3/BeSS/R/aic.R | 88 -- BeSS-2.0.3/BeSS/R/bess.R | 1301 +++++++++++++------------------ BeSS-2.0.3/BeSS/R/bess.cox.R |only BeSS-2.0.3/BeSS/R/bess.glm.R |only BeSS-2.0.3/BeSS/R/bess.lm.R |only BeSS-2.0.3/BeSS/R/bess.one.R | 340 +------- BeSS-2.0.3/BeSS/R/coef.bess.R | 67 - BeSS-2.0.3/BeSS/R/deviance.bess.R | 125 -- BeSS-2.0.3/BeSS/R/gbess.cox.R |only BeSS-2.0.3/BeSS/R/gbess.glm.R |only BeSS-2.0.3/BeSS/R/gbess.lm.R |only BeSS-2.0.3/BeSS/R/gen.data.R | 304 +------ BeSS-2.0.3/BeSS/R/logLik.bess.R | 102 -- BeSS-2.0.3/BeSS/R/plot.bess.R | 527 ------------ BeSS-2.0.3/BeSS/R/predict.bess.R | 258 ++---- BeSS-2.0.3/BeSS/R/print.bess.R | 101 -- BeSS-2.0.3/BeSS/R/print.bess.one.R |only BeSS-2.0.3/BeSS/R/summary.bess.R | 172 +--- BeSS-2.0.3/BeSS/R/summary.bess.one.R |only BeSS-2.0.3/BeSS/README |only BeSS-2.0.3/BeSS/data/SAheart.RData |only BeSS-2.0.3/BeSS/data/gravier.RData |only BeSS-2.0.3/BeSS/data/prostate.RData |only BeSS-2.0.3/BeSS/inst/CITATION |only BeSS-2.0.3/BeSS/inst/include |only BeSS-2.0.3/BeSS/man/SAheart.Rd |only BeSS-2.0.3/BeSS/man/aic.Rd |only BeSS-2.0.3/BeSS/man/bess-internal.Rd |only BeSS-2.0.3/BeSS/man/bess.Rd | 502 +++-------- BeSS-2.0.3/BeSS/man/bess.one.Rd | 373 +++----- BeSS-2.0.3/BeSS/man/coef.bess.Rd | 83 - BeSS-2.0.3/BeSS/man/coef.bess.one.Rd |only BeSS-2.0.3/BeSS/man/deviance.bess.Rd | 68 - BeSS-2.0.3/BeSS/man/deviance.bess.one.Rd |only BeSS-2.0.3/BeSS/man/gen.data.Rd | 169 +--- BeSS-2.0.3/BeSS/man/gravier.Rd |only BeSS-2.0.3/BeSS/man/logLik.bess.Rd | 106 -- BeSS-2.0.3/BeSS/man/logLik.bess.one.Rd |only BeSS-2.0.3/BeSS/man/plot.bess.Rd | 80 - BeSS-2.0.3/BeSS/man/predict.bess.Rd | 117 -- BeSS-2.0.3/BeSS/man/predict.bess.one.Rd |only BeSS-2.0.3/BeSS/man/print.bess.Rd | 57 - BeSS-2.0.3/BeSS/man/print.bess.one.Rd |only BeSS-2.0.3/BeSS/man/prostate.Rd |only BeSS-2.0.3/BeSS/man/summary.bess.Rd | 74 - BeSS-2.0.3/BeSS/man/summary.bess.one.Rd |only BeSS-2.0.3/BeSS/src/RcppExports.cpp | 355 +++++++- BeSS-2.0.3/BeSS/src/bess.cpp | 469 ++++------- BeSS-2.0.3/BeSS/src/group.cpp |only 91 files changed, 2102 insertions(+), 3996 deletions(-)
Title: Who are You? Bayesian Prediction of Racial Category Using
Surname and Geolocation
Description: Predicts individual race/ethnicity using surname, geolocation,
and other attributes, such as gender and age. The method utilizes the Bayes'
Rule to compute the posterior probability of each racial category for any given
individual. The package implements methods described in Imai and Khanna (2015)
"Improving Ecological Inference by Predicting Individual Ethnicity from Voter
Registration Records" <DOI:10.1093/pan/mpw001>.
Author: Kabir Khanna [aut, cre],
Kosuke Imai [aut]
Maintainer: Kabir Khanna <kabirkhanna@gmail.com>
Diff between wru versions 0.1-10 dated 2020-10-22 and 0.1-11 dated 2021-04-22
DESCRIPTION | 9 +++++---- MD5 | 3 ++- data/datalist |only 3 files changed, 7 insertions(+), 5 deletions(-)
Title: Time Zone Database Information
Description: Provides an up-to-date copy of the Internet Assigned Numbers
Authority (IANA) Time Zone Database. It is updated periodically to
reflect changes made by political bodies to time zone boundaries, UTC
offsets, and daylight saving time rules. Additionally, this package
provides a C++ interface for working with the 'date' library. 'date'
provides comprehensive support for working with dates and date-times,
which this package exposes to make it easier for other R packages to
utilize. Headers are provided for calendar specific calculations,
along with a limited interface for time zone manipulations.
Author: Davis Vaughan [aut, cre],
Howard Hinnant [cph] (Author of the included date library),
RStudio [cph, fnd]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between tzdb versions 0.1.0 dated 2021-03-04 and 0.1.1 dated 2021-04-22
DESCRIPTION | 31 ++++++++++++++++------- LICENSE.note |only MD5 | 51 +++++++++++++++++++++++++++++++++------ NAMESPACE | 3 ++ NEWS.md |only R/cpp11.R |only R/initialize.R |only R/names.R |only R/tzdb-package.R | 1 R/version.R | 11 ++++++-- R/zzz.R |only README.md | 24 ++++++++++++++++-- inst/include |only man/tzdb-package.Rd | 15 ++++++++--- man/tzdb_initialize.Rd |only man/tzdb_names.Rd |only man/tzdb_version.Rd | 7 +++-- src |only tests/testthat/test-initialize.R |only tests/testthat/test-names.R |only 20 files changed, 114 insertions(+), 29 deletions(-)
Title: R to Solr Interface
Description: A comprehensive R API for querying Apache Solr databases.
A Solr core is represented as a data frame or list that
supports Solr-side filtering, sorting,
transformation and aggregation, all through the familiar
base R API. Queries are processed
lazily, i.e., a query is only sent to the database when
the data are required.
Author: Michael Lawrence, Gabe Becker, Jan Vogel
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between rsolr versions 0.0.10 dated 2020-10-12 and 0.0.11 dated 2021-04-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/test.R | 5 ++--- R/zzz.R | 10 ---------- build/vignette.rds |binary inst/doc/intro.pdf |binary 6 files changed, 10 insertions(+), 21 deletions(-)
Title: Downloading, Reading and Analysing POF Microdata
Description: Provides tools for downloading, reading and analysing the POF,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre],
Luna Hidalgo [aut],
Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between POFIBGE versions 0.1.0 dated 2020-12-16 and 0.1.1 dated 2021-04-22
DESCRIPTION | 17 MD5 | 36 NAMESPACE | 2 R/example.R | 4 R/get_pof.R | 61 - R/pof_deflator.R | 13 R/pof_design.R | 13 R/pof_labeller.R | 47 R/read_pof.R | 14 inst/extdata/deflatorexample.xls |binary inst/extdata/dictionaryexample.xls |binary inst/extdata/exampledata.txt | 2218 +++++++++++++------------------------ inst/extdata/input_example.txt | 921 +++++++++++---- man/get_pof.Rd | 8 man/pof_deflator.Rd | 4 man/pof_design.Rd | 4 man/pof_example.Rd | 2 man/pof_labeller.Rd | 2 man/read_pof.Rd | 6 19 files changed, 1672 insertions(+), 1700 deletions(-)
Title: Downloading, Reading and Analysing PNADC Microdata
Description: Provides tools for downloading, reading and analysing the PNADC,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Douglas Braga [aut],
Gabriel Assuncao [aut, cre],
Luna Hidalgo [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between PNADcIBGE versions 0.6.2 dated 2021-01-26 and 0.6.3 dated 2021-04-22
DESCRIPTION | 11 ++--- MD5 | 22 +++++------ NAMESPACE | 2 + R/example.R | 4 +- R/get_pnadc.R | 100 ++++++++++++++++++++++++++++++++++----------------- R/pnadc_deflator.R | 6 +-- R/pnadc_design.R | 10 ++--- R/pnadc_labeller.R | 4 +- R/read_pnadc.R | 4 +- man/get_pnadc.Rd | 6 +-- man/pnadc_design.Rd | 4 +- man/pnadc_example.Rd | 2 - 12 files changed, 105 insertions(+), 70 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC)
and some related functions are implemented. Functions for incorporating
background knowledge are provided.
Author: Markus Kalisch [aut, cre],
Alain Hauser [aut],
Martin Maechler [aut],
Diego Colombo [ctb],
Doris Entner [ctb],
Patrik Hoyer [ctb],
Antti Hyttinen [ctb],
Jonas Peters [ctb],
Nicoletta Andri [ctb],
Emilija Perkovic [ctb],
Preetam Nandy [ctb],
Philipp Ruetimann [ctb],
Daniel Stekhoven [ctb],
Manuel Schuerch [ctb],
Marco Eigenmann [ctb],
Leonard Henckel [ctb],
Joris Mooij [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.7-1 dated 2021-01-09 and 2.7-2 dated 2021-04-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/AllClasses.R | 2 +- build/vignette.rds |binary inst/doc/pcalgDoc.pdf |binary inst/doc/vignette2018.pdf |binary man/fciPlus.Rd | 44 ++++++++++++++++++++++---------------------- 7 files changed, 33 insertions(+), 33 deletions(-)
Title: Multiple Locus Association Mapping on a Genome-Wide Scale
Description: An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Author: Andrew George [aut, cre],
Joshua Bowden [ctb],
Ryan Stephenson [ctb],
Hyun Kang [ctb],
Noah Zaitlen [ctb],
Claire Wade [ctb],
Andrew Kirby [ctb],
David Heckerman [ctb],
Mark Daly [ctb],
Eleazar Eskin [ctb]
Maintainer: Andrew George <andrew.george@csiro.au>
Diff between Eagle versions 2.4.3 dated 2021-01-12 and 2.4.4 dated 2021-04-22
Eagle-2.4.3/Eagle/build |only Eagle-2.4.3/Eagle/inst/doc |only Eagle-2.4.3/Eagle/vignettes |only Eagle-2.4.4/Eagle/DESCRIPTION | 9 +++------ Eagle-2.4.4/Eagle/MD5 | 19 ++++--------------- Eagle-2.4.4/Eagle/NEWS | 5 +++++ Eagle-2.4.4/Eagle/R/onAttach.R | 2 +- Eagle-2.4.4/Eagle/R/print_title.R | 2 +- 8 files changed, 14 insertions(+), 23 deletions(-)
Title: 'Drat' R Archive Template
Description: Creation and use of R Repositories via helper functions
to insert packages into a repository, and to add repository information
to the current R session. Two primary types of repositories are support:
gh-pages at GitHub, as well as local repositories on either the same machine
or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel with contributions by Carl Boettiger, Neal Fultz,
Sebastian Gibb, Colin Gillespie, Jan Górecki, Matt Jones, Thomas Leeper,
Steven Pav, Jan Schulz, Christoph Stepper, Felix G.M. Ernst and Patrick
Schratz.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between drat versions 0.1.8 dated 2020-07-18 and 0.2.0 dated 2021-04-22
ChangeLog | 116 +++++++++ DESCRIPTION | 17 - MD5 | 62 ++--- R/archivePackages.R | 7 R/initRepo.R | 30 +- R/insertPackage.R | 39 ++- R/pruneRepo.R | 19 + README.md | 71 +++-- build/vignette.rds |binary inst/NEWS.Rd | 27 ++ inst/doc/CombiningDratAndTravis.Rmd | 13 - inst/doc/CombiningDratAndTravis.html | 337 +++++----------------------- inst/doc/DratFAQ.Rmd | 22 + inst/doc/DratFAQ.html | 412 +++++++--------------------------- inst/doc/DratForPackageAuthors.Rmd | 48 ++-- inst/doc/DratForPackageAuthors.html | 417 ++++++++--------------------------- inst/doc/DratForPackageUsers.Rmd | 16 - inst/doc/DratForPackageUsers.html | 373 +++++-------------------------- inst/doc/DratStepByStep.Rmd |only inst/doc/DratStepByStep.html |only inst/doc/WhyDrat.Rmd | 12 - inst/doc/WhyDrat.html | 368 +++++------------------------- man/drat-package.Rd | 2 man/initRepo.Rd | 22 + man/insertPackage.Rd | 6 man/pruneRepo.Rd | 11 tests/skeleton_git2r.R | 157 +++++++++---- tests/version.R |only vignettes/CombiningDratAndTravis.Rmd | 13 - vignettes/DratFAQ.Rmd | 22 + vignettes/DratForPackageAuthors.Rmd | 48 ++-- vignettes/DratForPackageUsers.Rmd | 16 - vignettes/DratStepByStep.Rmd |only vignettes/WhyDrat.Rmd | 12 - 34 files changed, 961 insertions(+), 1754 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of
the DBSCAN family for spatial data. Includes the clustering algorithms
DBSCAN (density-based spatial clustering of applications with noise)
and HDBSCAN (hierarchical DBSCAN), the ordering algorithm
OPTICS (ordering points to identify the clustering structure),
and the outlier detection algorithm LOF (local outlier factor).
The implementations use the kd-tree data structure (from library ANN) for faster k-nearest neighbor search.
An R interface to fast kNN and fixed-radius NN search is also provided.
Hahsler, Piekenbrock and Doran (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph],
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.1-6 dated 2021-02-26 and 1.1-7 dated 2021-04-22
DESCRIPTION | 10 +- MD5 | 63 ++++++++-------- NEWS.md | 9 ++ R/LOF.R | 88 +++++++++++++++++++---- R/RcppExports.R | 4 + R/dbscan.R | 9 -- R/frNN.R | 8 -- R/kNN.R | 19 +++-- R/kNNdist.R | 2 R/optics.R | 10 +- R/pointdensity.R | 7 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/dbscan.R | 18 ++-- inst/doc/dbscan.Rnw | 19 ++--- inst/doc/dbscan.pdf |binary inst/doc/hdbscan.html | 64 ++++++---------- man/dbscan.Rd | 79 ++++++++++++-------- man/frNN.Rd | 9 +- man/kNN.Rd | 22 +++-- man/kNNdist.Rd | 44 +++++------ man/lof.Rd | 39 +++++----- man/optics.Rd | 4 - src/R_dbscan.cpp | 2 src/R_frNN.cpp | 2 src/R_kNN.cpp | 2 src/R_lof.cpp |only src/R_optics.cpp | 2 src/R_regionQuery.cpp | 2 src/R_regionQuery.h | 2 src/RcppExports.cpp | 17 ++++ tests/testthat/test-lof.R | 174 ++++++++++++++++++++++++++++++++++++++++++++-- vignettes/dbscan.Rnw | 19 ++--- 33 files changed, 501 insertions(+), 248 deletions(-)
Title: Downloading, Reading and Analysing PNAD COVID19 Microdata
Description: Provides tools for downloading, reading and analysing the PNAD COVID19,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre],
Luna Hidalgo [aut],
Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between COVIDIBGE versions 0.1.2 dated 2021-01-31 and 0.1.3 dated 2021-04-22
DESCRIPTION | 11 +++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ R/covid_deflator.R | 6 +++--- R/covid_design.R | 10 +++++----- R/covid_labeller.R | 4 ++-- R/example.R | 4 ++-- R/get_covid.R | 45 +++++++++++++++++++++++++-------------------- R/read_covid.R | 4 ++-- man/covid_design.Rd | 4 ++-- man/covid_example.Rd | 2 +- man/get_covid.Rd | 6 +++--- 12 files changed, 63 insertions(+), 57 deletions(-)