Title: Process and Analyze Agilent Cary 620 FTIR Microscope Images
Description: A set of tools to read, process, and summarize Agilent Cary 620 uFTIR Microscope hyperspectral images
primarily intended for microplastic analysis.
Author: Fabio Corradini [aut, cre] (<https://orcid.org/0000-0001-9696-7643>)
Maintainer: Fabio Corradini <fabio.corradini@inia.cl>
Diff between uFTIR versions 0.1.0 dated 2020-03-06 and 0.1.1 dated 2020-03-11
uFTIR-0.1.0/uFTIR/src/cget_particles.cpp |only uFTIR-0.1.1/uFTIR/DESCRIPTION | 10 +- uFTIR-0.1.1/uFTIR/MD5 | 58 +++++++-------- uFTIR-0.1.1/uFTIR/NAMESPACE | 3 uFTIR-0.1.1/uFTIR/R/RcppExports.R | 8 -- uFTIR-0.1.1/uFTIR/R/clipper.R | 41 +++++++++- uFTIR-0.1.1/uFTIR/R/mosaic_compose.R | 24 ++++-- uFTIR-0.1.1/uFTIR/R/preprocess.R | 12 +-- uFTIR-0.1.1/uFTIR/R/profile_methods.R | 20 ++++- uFTIR-0.1.1/uFTIR/R/summary_methods.R | 4 - uFTIR-0.1.1/uFTIR/R/uFTIR.R | 2 uFTIR-0.1.1/uFTIR/README.md | 6 - uFTIR-0.1.1/uFTIR/inst/extdata/mosaic_0000_0000.dmd |binary uFTIR-0.1.1/uFTIR/inst/extdata/mosaic_0001_0000.dmd |binary uFTIR-0.1.1/uFTIR/man/as.clipper.Rd |only uFTIR-0.1.1/uFTIR/man/get_profile.Rd | 6 - uFTIR-0.1.1/uFTIR/man/mosaic_compose.Rd | 11 ++ uFTIR-0.1.1/uFTIR/man/preprocess.Rd | 12 +-- uFTIR-0.1.1/uFTIR/src/RcppExports.cpp | 21 +---- uFTIR-0.1.1/uFTIR/src/cderivate.cpp | 6 - uFTIR-0.1.1/uFTIR/src/cmosaic_clusterfind.cpp | 6 - uFTIR-0.1.1/uFTIR/src/cmosaic_compose.cpp | 9 +- uFTIR-0.1.1/uFTIR/src/csmooth_sam.cpp | 14 ++- uFTIR-0.1.1/uFTIR/src/mosaic_read_chunk.cpp | 5 + uFTIR-0.1.1/uFTIR/src/sam_main.cpp | 4 - uFTIR-0.1.1/uFTIR/tests/testthat.R | 12 ++- uFTIR-0.1.1/uFTIR/tests/testthat/Rplots.pdf |binary uFTIR-0.1.1/uFTIR/tests/testthat/shape_out/clusters.dbf |binary uFTIR-0.1.1/uFTIR/tests/testthat/test-mosaic_functions.R | 27 ++++++ uFTIR-0.1.1/uFTIR/tests/testthat/test-plot_methods.R | 14 +++ uFTIR-0.1.1/uFTIR/tests/testthat/test-tile_functions.R | 26 +++--- 31 files changed, 236 insertions(+), 125 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut],
Romain Francois [aut, cph],
Kevin Ushey [aut, cre],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/),
RStudio [cph],
Intel [aut, cph] (Intel TBB library,
https://www.threadingbuildingblocks.org/),
Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 4.4.4 dated 2019-09-27 and 5.0.0 dated 2020-03-11
RcppParallel-4.4.4/RcppParallel/inst/tests/cpp/malloc.cpp |only RcppParallel-4.4.4/RcppParallel/inst/tests/runit.malloc.R |only RcppParallel-5.0.0/RcppParallel/DESCRIPTION | 6 - RcppParallel-5.0.0/RcppParallel/MD5 | 25 ++--- RcppParallel-5.0.0/RcppParallel/R/hooks.R | 7 - RcppParallel-5.0.0/RcppParallel/R/options.R | 25 ++++- RcppParallel-5.0.0/RcppParallel/inst/NEWS | 7 + RcppParallel-5.0.0/RcppParallel/inst/include/RcppParallel.h | 43 ++++++---- RcppParallel-5.0.0/RcppParallel/inst/include/RcppParallel/Backend.h |only RcppParallel-5.0.0/RcppParallel/inst/include/RcppParallel/TinyThread.h | 2 RcppParallel-5.0.0/RcppParallel/man/setThreadOptions.Rd | 4 RcppParallel-5.0.0/RcppParallel/src/Makevars.in | 8 - RcppParallel-5.0.0/RcppParallel/src/tbb/build/windows.inc | 6 - RcppParallel-5.0.0/RcppParallel/tests/doRUnit.R | 19 +++- RcppParallel-5.0.0/RcppParallel/tools/config/configure.R | 3 15 files changed, 93 insertions(+), 62 deletions(-)
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Author: Karl W Broman <broman@wisc.edu> and Hao Wu, with
ideas from Gary Churchill and Saunak Sen and contributions from
Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr
Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron
Wolen, and Brian Yandell
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl versions 1.45-11 dated 2020-02-02 and 1.46-2 dated 2020-03-11
DESCRIPTION | 9 - MD5 | 70 ++++++------ NEWS.md | 16 ++ R/addqtl.R | 10 - R/effectscan.R | 6 - R/mqmpermutation.R | 9 - R/mqmplots.R | 6 - R/read.cross.csv.R | 8 + R/read.cross.csvs.R | 12 +- R/read.cross.mm.R | 6 - R/readMWril.R | 12 +- R/scanone.R | 6 - R/scantwo.R | 6 - R/summary.scantwo.R | 22 ++- build/vignette.rds |binary data/badorder.RData |binary data/bristle3.RData |binary data/bristleX.RData |binary data/fake.4way.RData |binary data/fake.bc.RData |binary data/fake.f2.RData |binary data/hyper.RData |binary data/listeria.RData |binary data/locations.RData |binary data/map10.RData |binary data/mapthis.RData |binary data/multitrait.RData |binary inst/INSTALL_ME.txt | 16 +- inst/doc/Sources/MQM/MQM-tour.aux | 6 - inst/doc/Sources/MQM/MQM-tour.dvi |binary inst/doc/Sources/MQM/MQM-tour.log | 206 +++++++++++-------------------------- inst/doc/Sources/MQM/SweaveIt.Rout | 2 inst/doc/bcsft.pdf |binary inst/doc/rqtltour.pdf |binary inst/doc/rqtltour2.pdf |binary man/mqmpermutation.Rd | 3 36 files changed, 195 insertions(+), 236 deletions(-)
Title: Construct Process Maps Using Event Data
Description: Visualize event logs using directed graphs, i.e. process maps. Part of the 'bupaR' framework.
Author: Gert Janssenswillen [aut, cre],
Benoît Depaire [ctb],
Felix Mannhardt [ctb],
Thijs Beuving [ctb]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between processmapR versions 0.3.3 dated 2019-02-24 and 0.3.4 dated 2020-03-11
DESCRIPTION | 24 +-- MD5 | 60 +++++---- NAMESPACE | 10 + R/RcppExports.R |only R/custom.R | 10 - R/dotted_chart.R | 116 ++++++++++++----- R/frequency.R | 6 R/get_meta_data.R |only R/layout.R |only R/performance.R | 8 - R/precedence_matrix.R | 154 ++++++++++++++--------- R/precedence_matrix.plot.R | 35 ++--- R/process_map.R | 251 ++++++++++++++++++++++++++++++++++++-- R/processmapR.R | 10 + R/trace_explorer.R | 66 +++++++-- R/utils.R | 4 build/vignette.rds |binary inst/doc/processmapr.html | 197 +++++++++++++++++++++++++++++ man/custom.Rd | 97 +++++++------- man/dotted_chart.Rd | 117 +++++++++-------- man/frequency.Rd | 43 +++--- man/get_activities.Rd |only man/layout_pm.Rd |only man/performance.Rd | 60 ++++----- man/plot.process_matrix.Rd | 36 ++--- man/precedence_matrix.Rd | 59 ++++---- man/precedence_matrix_absolute.Rd |only man/process_map.Rd | 157 +++++++++++++++-------- man/process_matrix.Rd | 52 +++---- man/processmapR.Rd | 17 +- man/resource_map.Rd | 54 ++++---- man/resource_matrix.Rd | 56 ++++---- man/trace_explorer.Rd | 93 ++++++++------ src |only 34 files changed, 1225 insertions(+), 567 deletions(-)
Title: Interface to 'JDemetra+' Seasonal Adjustment Software
Description: Interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially
recommended to the members of the European Statistical System (ESS) and the European System of Central Banks.
It offers full access to all options and outputs of 'JDemetra+', including the two leading seasonal adjustment methods
TRAMO/SEATS+ and X-12ARIMA/X-13ARIMA-SEATS.
Author: Alain Quartier-la-Tente [aut, cre]
(<https://orcid.org/0000-0001-7890-3857>),
Anna Michalek [aut],
Jean Palate [aut],
Raf Baeyens [aut]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between RJDemetra versions 0.1.4 dated 2020-01-09 and 0.1.5 dated 2020-03-11
DESCRIPTION | 12 +++++++----- MD5 | 15 ++++++++------- NAMESPACE | 5 +++++ R/export_workspace.R | 46 +--------------------------------------------- R/get_jspec.R |only R/jsa2r.R | 12 ++++++++++-- R/spec_rjd.R | 6 +++--- man/add_sa_item.Rd | 2 +- man/jSA.Rd | 17 ++++++++++++++--- 9 files changed, 49 insertions(+), 66 deletions(-)
Title: Tools for Generating, Visualizing, and Analysing Link
Communities in Networks
Description: Link communities reveal the nested and overlapping structure in networks, and uncover the key nodes that form connections to multiple communities. linkcomm provides a set of tools for generating, visualizing, and analysing link communities in networks of arbitrary size and type. The linkcomm package also includes tools for generating, visualizing, and analysing Overlapping Cluster Generator (OCG) communities.
Author: Alex T. Kalinka <alex.t.kalinka@gmail.com>, with contributions from Alain Guenoche
Maintainer: Alex T. Kalinka <alex.t.kalinka@gmail.com>
Diff between linkcomm versions 1.0-11 dated 2014-08-13 and 1.0-12 dated 2020-03-11
DESCRIPTION | 8 ++++---- MD5 | 33 ++++++++++++++++++--------------- NAMESPACE | 6 +++++- NEWS | 6 ++++++ R/OCG_main.R | 6 +++--- R/linkcomm_main.R | 2 +- R/linkcomm_misc.R | 6 ++++-- R/linkcomm_plotting.R | 4 ++-- README.md |only inst/doc/linkcomm.Rnw | 36 +++++------------------------------- inst/doc/linkcomm.pdf |binary man/getCommunityCentrality.Rd | 3 --- man/getCommunityConnectedness.Rd | 5 +---- man/human_pp.Rd | 1 - man/linkcomm2clustnsee.Rd | 10 +++------- man/linkcomm2cytoscape.Rd | 2 ++ src/linkcomm_init.c |only vignettes/linkcomm.Rnw | 36 +++++------------------------------- vignettes/linkcomm.pdf |only 19 files changed, 59 insertions(+), 105 deletions(-)
Title: Generate PDFs and CDFs from Binned Data
Description: Provides several methods for generating density functions
based on binned data. Methods include step function, recursive
subdivision, and optimized spline. Data are assumed to be nonnegative,
the top bin is assumed to have no upper bound, but the bin widths need
be equal. All PDF smoothing methods maintain the areas specified by
the binned data. (Equivalently, all CDF smoothing methods interpolate
the points specified by the binned data.) In practice, an estimate for
the mean of the distribution should be supplied as an optional argument.
Doing so greatly improves the reliability of statistics computed from
the smoothed density functions. Includes methods for estimating the Gini
coefficient, the Theil index, percentiles, and random deviates from a
smoothed distribution. Among the three methods, the optimized spline
(splinebins) is recommended for most purposes. The percentile and
random-draw methods should be regarded as experimental, and these methods
only support splinebins.
Author: David J. Hunter and McKalie Drown
Maintainer: Dave Hunter <dhunter@westmont.edu>
Diff between binsmooth versions 0.2.1 dated 2019-10-27 and 0.2.2 dated 2020-03-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 7 +++++++ R/splinebins.R | 6 +++++- 4 files changed, 18 insertions(+), 7 deletions(-)
Title: Portfolio Management with R
Description: Functions and examples for 'Portfolio
Management with R': backtesting investment and
trading strategies, computing profit/loss and
returns, analysing trades, handling lists of
transactions, reporting, and more.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between PMwR versions 0.12-0 dated 2019-08-26 and 0.14-0 dated 2020-03-11
PMwR-0.12-0/PMwR/inst/unitTests |only PMwR-0.14-0/PMwR/ChangeLog | 179 ++++++++++++++++- PMwR-0.14-0/PMwR/DESCRIPTION | 10 PMwR-0.14-0/PMwR/MD5 | 113 +++++++--- PMwR-0.14-0/PMwR/NAMESPACE | 1 PMwR-0.14-0/PMwR/NEWS | 65 ++++++ PMwR-0.14-0/PMwR/R/NAVseries.R | 58 +++-- PMwR-0.14-0/PMwR/R/btest.R | 23 +- PMwR-0.14-0/PMwR/R/div_adjust.R | 8 PMwR-0.14-0/PMwR/R/internal.R | 206 ------------------- PMwR-0.14-0/PMwR/R/journal.R | 219 ++++++++++++++++----- PMwR-0.14-0/PMwR/R/pl.R | 26 +- PMwR-0.14-0/PMwR/R/position.R | 77 ++++++- PMwR-0.14-0/PMwR/R/returns.R | 20 + PMwR-0.14-0/PMwR/R/scale1.R | 4 PMwR-0.14-0/PMwR/R/streaks.R | 84 ++++---- PMwR-0.14-0/PMwR/build/vignette.rds |binary PMwR-0.14-0/PMwR/inst/doc/An_overview_of_PMwR.R | 30 ++ PMwR-0.14-0/PMwR/inst/doc/An_overview_of_PMwR.Rnw | 38 ++- PMwR-0.14-0/PMwR/inst/doc/An_overview_of_PMwR.pdf |binary PMwR-0.14-0/PMwR/inst/doc/Computing_returns.pdf |binary PMwR-0.14-0/PMwR/inst/doc/Drawdowns_streaks.pdf |binary PMwR-0.14-0/PMwR/inst/doc/FinTeX.pdf |binary PMwR-0.14-0/PMwR/inst/doc/pl_open_positions.pdf |binary PMwR-0.14-0/PMwR/inst/doc/q32.pdf |binary PMwR-0.14-0/PMwR/inst/tinytest |only PMwR-0.14-0/PMwR/man/NAVseries.Rd | 7 PMwR-0.14-0/PMwR/man/PMwR-package.Rd | 12 - PMwR-0.14-0/PMwR/man/adjust-series.Rd | 19 + PMwR-0.14-0/PMwR/man/btest.Rd | 15 + PMwR-0.14-0/PMwR/man/journal.Rd | 72 ++++-- PMwR-0.14-0/PMwR/man/returns.Rd | 47 ++-- PMwR-0.14-0/PMwR/man/streaks.Rd | 55 +++-- PMwR-0.14-0/PMwR/tests/tinytest.R |only PMwR-0.14-0/PMwR/vignettes/An_overview_of_PMwR.Rnw | 38 ++- 35 files changed, 929 insertions(+), 497 deletions(-)
Title: Geospatial Kriging with Metropolis Sampling
Description: Estimates kriging models for geographical point-referenced data. Method is described in Monogan and Gill (2016) <doi:10.1017/psrm.2015.5>.
Author: Jason S. Byers [aut, cre], Jeff Gill [aut], James E. Monogan III [aut], Jamie Carson [aut], Le Bao [aut]
Maintainer: Jason S. Byers <jaybyers55@gmail.com>
Diff between krige versions 0.3-1 dated 2019-10-29 and 0.4.1 dated 2020-03-11
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NAMESPACE | 3 ++- R/krige.posterior.R | 19 +++++++++++-------- R/metropolis.krige.R | 35 +++++++++++++++++++++++------------ data/congCombined.rda |binary data/lowerCombined.rda |binary data/stateCombined.rda |binary data/upperCombined.rda |binary man/krige.posterior.Rd | 9 +++++++-- man/metropolis.krige.Rd | 16 ++++++---------- 11 files changed, 65 insertions(+), 49 deletions(-)
Title: Visualize Population Pyramids Aggregated by Age
Description: Provides a quick method for visualizing non-aggregated line-list
or aggregated census data stratified by age and one or two categorical
variables (e.g. gender and health status) with any number of values. It
returns a 'ggplot' object, allowing the user to further customize the
output. This package is part of the 'R4Epis' project
<https://r4epis.netlify.com>.
Author: Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>),
Alex Spina [ctb]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between apyramid versions 0.1.0 dated 2020-01-13 and 0.1.1 dated 2020-03-11
DESCRIPTION | 6 - MD5 | 57 +++++----- NEWS.md | 10 + R/age-pyramid.R | 3 README.md | 34 ++++- inst/doc/intro.R | 9 + inst/doc/intro.html | 40 ++++--- man/figures/README-flu-1.png |binary man/figures/README-flu2-1.png |binary man/figures/README-flu3-1.png |binary man/figures/README-srvyr-1.png |binary man/figures/README-us2018-1.png |binary man/figures/README-us2018_factor-1.png |binary man/figures/README-us2018_factor-2.png |binary man/rmdhunks/introduction.Rmd | 31 +++-- tests/figs/age-pyramid-tests/default-age-pyramid.svg | 14 +- tests/figs/age-pyramid-tests/default-no-pyramid.svg | 24 ++-- tests/figs/age-pyramid-tests/gender-age-pyramid.svg | 36 +++--- tests/figs/age-pyramid-tests/ill-age-pyramid.svg | 12 +- tests/figs/age-pyramid-tests/missing-age-pyramid.svg | 16 +- tests/figs/age-pyramid-tests/survey-data.svg | 36 +++--- tests/figs/age-pyramid-tests/us-2018-counts.svg | 36 +++--- tests/figs/age-pyramid-tests/us-2018-proportions.svg | 36 +++--- tests/figs/age-pyramid-tests/us-insured-2018-counts.svg | 36 +++--- tests/figs/age-pyramid-tests/us-insured-2018-proportions.svg | 36 +++--- tests/figs/age-pyramid-tests/with-custom-palette-and-vertical-lines.svg | 36 +++--- vignettes/man |only 27 files changed, 287 insertions(+), 221 deletions(-)
Title: A Framework for Reproducible and Collaborative Data Science
Description: Provides a workflow for your analysis projects by combining
literate programming ('knitr' and 'rmarkdown') and version control
('Git', via 'git2r') to generate a website containing time-stamped,
versioned, and documented results.
Author: John Blischak [aut, cre] (<https://orcid.org/0000-0003-2634-9879>),
Peter Carbonetto [aut] (<https://orcid.org/0000-0003-1144-6780>),
Matthew Stephens [aut] (<https://orcid.org/0000-0001-5397-9257>),
Luke Zappia [ctb] (Instructions for hosting with GitLab),
Pierre Formont [ctb] (Support for hosting with Shiny Server),
Tim Trice [ctb] (Instructions for sharing common code),
Jiaxiang Li [ctb] (Function wflow_toc() to create table of contents),
Michael J. Kane [ctb] (<https://orcid.org/0000-0003-1899-6662>, Option
suppress_report)
Maintainer: John Blischak <jdblischak@uchicago.edu>
Diff between workflowr versions 1.6.0 dated 2019-12-19 and 1.6.1 dated 2020-03-11
DESCRIPTION | 6 MD5 | 145 ++++++------- NEWS.md | 67 +++++- R/assertions.R |only R/git.R | 24 +- R/git2r.R | 2 R/infrastructure.R | 1 R/report.R | 61 +++-- R/utility.R | 15 - R/wflow_build.R | 96 +++----- R/wflow_git_commit.R | 77 ++---- R/wflow_git_config.R | 17 - R/wflow_git_pull.R | 22 - R/wflow_git_push.R | 25 -- R/wflow_git_remote.R | 9 R/wflow_html.R | 7 R/wflow_open.R | 31 -- R/wflow_options.R | 2 R/wflow_paths.R | 4 R/wflow_publish.R | 69 +----- R/wflow_quickstart.R | 77 +++--- R/wflow_remove.R | 26 -- R/wflow_rename.R | 29 -- R/wflow_rename_proj.R | 34 --- R/wflow_run.R | 32 -- R/wflow_start.R | 58 +++-- R/wflow_status.R | 28 -- R/wflow_toc.R | 17 - R/wflow_update.R | 10 R/wflow_use_github.R | 120 +++++++--- R/wflow_use_gitlab.R | 25 +- R/wflow_view.R | 24 -- build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/wflow-01-getting-started.html | 84 +++++-- inst/doc/wflow-02-customization.Rmd | 1 inst/doc/wflow-02-customization.html | 46 +++- inst/doc/wflow-03-migrating.html | 46 +++- inst/doc/wflow-04-how-it-works.html | 22 + inst/doc/wflow-05-faq.Rmd | 142 +++++++++--- inst/doc/wflow-05-faq.html | 102 ++++++--- inst/doc/wflow-06-gitlab.Rmd | 29 ++ inst/doc/wflow-06-gitlab.html | 54 +++- inst/doc/wflow-07-common-code.html | 46 +++- inst/doc/wflow-08-deploy.Rmd | 5 inst/doc/wflow-08-deploy.html | 24 +- inst/doc/wflow-09-workshop.html | 46 +++- inst/doc/wflow-10-data.html | 22 + man/wflow_post_knit.Rd | 13 - man/wflow_pre_processor.Rd | 21 + man/wflow_quickstart.Rd | 14 - man/wflow_use_github.Rd | 14 + man/wflow_use_gitlab.Rd | 10 tests/testthat/files/test-wflow_update/post/_workflowr.yml | 2 tests/testthat/setup.R | 4 tests/testthat/test-assertions.R |only tests/testthat/test-git2r-merge.R | 24 +- tests/testthat/test-git2r.R | 28 +- tests/testthat/test-knitr.R |only tests/testthat/test-report.R | 23 +- tests/testthat/test-utility.R | 22 + tests/testthat/test-wflow_build.R | 4 tests/testthat/test-wflow_git_commit.R | 15 + tests/testthat/test-wflow_git_push_pull.R | 2 tests/testthat/test-wflow_html.R | 48 ++++ tests/testthat/test-wflow_open.R | 4 tests/testthat/test-wflow_quickstart.R | 33 ++ tests/testthat/test-wflow_remove.R | 42 +-- tests/testthat/test-wflow_run.R | 16 - tests/testthat/test-wflow_status.R | 61 +++++ tests/testthat/test-wflow_use_github.R | 23 +- vignettes/wflow-02-customization.Rmd | 1 vignettes/wflow-05-faq.Rmd | 142 +++++++++--- vignettes/wflow-06-gitlab.Rmd | 29 ++ vignettes/wflow-08-deploy.Rmd | 5 75 files changed, 1513 insertions(+), 920 deletions(-)
Title: Computation of Optimal Transport Plans and Wasserstein Distances
Description: Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
Author: Dominic Schuhmacher [aut, cre],
Björn Bähre [aut] (aha and power diagrams),
Nicolas Bonneel [aut] (networkflow),
Carsten Gottschlich [aut] (simplex and shortlist),
Valentin Hartmann [aut] (semidiscrete1),
Florian Heinemann [aut] (transport_track and networkflow integration),
Bernhard Schmitzer [aut] (shielding),
Jörn Schrieber [aut] (subsampling),
Timo Wilm [ctb] (wpp)
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between transport versions 0.12-1 dated 2019-08-19 and 0.12-2 dated 2020-03-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 16 ++++++++++++++++ R/fundament.R | 2 +- R/transporttrack.R | 12 ++++++------ man/transport-internal.Rd | 2 +- man/transport_track.Rd | 6 +++--- 7 files changed, 37 insertions(+), 21 deletions(-)
Title: Extract Genotypes from a PLINK .bed File
Description: A matrix-like data structure that allows for efficient,
convenient, and scalable subsetting of binary genotype/phenotype files
generated by PLINK (<https://www.cog-genomics.org/plink2>), the whole
genome association analysis toolset, without loading the entire file into
memory.
Author: Alexander Grueneberg [aut, cre],
Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between BEDMatrix versions 2.0.1 dated 2019-12-16 and 2.0.2 dated 2020-03-11
DESCRIPTION | 6 +-- MD5 | 16 ++++---- NEWS.md | 6 +++ inst/THANKS | 6 ++- inst/include/BEDMatrix.h | 26 +++++++++---- src/BEDMatrix.c | 2 - src/bed.c | 4 -- src/mapping.c | 91 ++++++++++++++++++++--------------------------- src/mapping.h | 2 - 9 files changed, 82 insertions(+), 77 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. <https://martin3141.github.io/spant/>.
Author: Martin Wilson [cre, aut],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 1.1.0 dated 2020-03-01 and 1.2.0 dated 2020-03-11
spant-1.1.0/spant/man/N.Rd |only spant-1.1.0/spant/man/conj.Rd |only spant-1.1.0/spant/man/dyns.Rd |only spant-1.1.0/spant/man/fit_tab2csv.Rd |only spant-1.1.0/spant/tests/testthat/fit_res_abfit_fine.rds |only spant-1.1.0/spant/tests/testthat/fit_res_abfit_no_optim.rds |only spant-1.2.0/spant/DESCRIPTION | 16 spant-1.2.0/spant/MD5 | 65 +- spant-1.2.0/spant/NAMESPACE | 5 spant-1.2.0/spant/NEWS.md | 8 spant-1.2.0/spant/R/amp_scaling.R | 183 +++--- spant-1.2.0/spant/R/fit_display.R | 14 spant-1.2.0/spant/R/fitting.R | 4 spant-1.2.0/spant/R/mrs_data_proc.R | 344 +++++++----- spant-1.2.0/spant/R/spant.R | 2 spant-1.2.0/spant/R/utils.R | 4 spant-1.2.0/spant/build/vignette.rds |binary spant-1.2.0/spant/inst/WORDLIST | 1 spant-1.2.0/spant/inst/doc/spant-intro.R | 2 spant-1.2.0/spant/inst/doc/spant-intro.Rmd | 2 spant-1.2.0/spant/inst/doc/spant-intro.html | 76 +- spant-1.2.0/spant/inst/doc/spant-preprocessing.R |only spant-1.2.0/spant/inst/doc/spant-preprocessing.Rmd |only spant-1.2.0/spant/inst/doc/spant-preprocessing.html |only spant-1.2.0/spant/man/apply_pvc.Rd | 3 spant-1.2.0/spant/man/fit_mrs.Rd | 4 spant-1.2.0/spant/man/fit_res2csv.Rd |only spant-1.2.0/spant/man/hsvd_filt.Rd | 4 spant-1.2.0/spant/man/scale_amp_molal_pvc.Rd | 2 spant-1.2.0/spant/man/scale_amp_molar.Rd | 12 spant-1.2.0/spant/man/scale_amp_ratio.Rd | 2 spant-1.2.0/spant/man/scale_amp_water_ratio.Rd | 2 spant-1.2.0/spant/man/set_lcm_cmd.Rd | 2 spant-1.2.0/spant/tests/testthat/abfit_res_coarse.rds |only spant-1.2.0/spant/tests/testthat/abfit_res_default.rds |only spant-1.2.0/spant/tests/testthat/abfit_res_fine.rds |only spant-1.2.0/spant/tests/testthat/abfit_res_no_optim.rds |only spant-1.2.0/spant/tests/testthat/abfit_sim_mrs_data.rds |only spant-1.2.0/spant/tests/testthat/abfit_sim_res.rds |only spant-1.2.0/spant/tests/testthat/test_fitting.R | 99 +-- spant-1.2.0/spant/vignettes/spant-intro.Rmd | 2 spant-1.2.0/spant/vignettes/spant-preprocessing.Rmd |only 42 files changed, 506 insertions(+), 352 deletions(-)
Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file,
and collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'Roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph]
(<https://orcid.org/0000-0003-4757-117X>),
Peter Danenberg [aut, cph],
Gábor Csárdi [aut],
Manuel Eugster [aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between roxygen2 versions 7.0.2 dated 2019-12-02 and 7.1.0 dated 2020-03-11
DESCRIPTION | 18 +- MD5 | 105 ++++++++------- NAMESPACE | 4 NEWS.md | 59 ++++++++ R/block.R | 8 + R/markdown.R | 180 ++++++++++++++++++++++++-- R/namespace.R | 7 - R/object-from-call.R | 6 R/object-package.R | 14 +- R/object-r6.R | 11 + R/options.R | 39 +++++ R/rd-markdown.R | 11 + R/rd-r6.R | 1 R/rd-section.R | 5 R/rd.R | 3 R/roxygenize.R | 15 +- R/topic.R | 1 R/utils-io.R | 19 +- R/utils.R | 10 + README.md | 7 - inst/doc/namespace.Rmd | 4 inst/doc/namespace.html | 4 inst/doc/rd-formatting.Rmd | 118 +++++++++++++++++ inst/doc/rd-formatting.html | 131 +++++++++++++----- inst/doc/rd.R | 11 + inst/doc/rd.Rmd | 26 ++- inst/doc/rd.html | 175 +++++++++++++------------ inst/doc/roxygen2.Rmd | 4 inst/doc/roxygen2.html | 4 man/RoxyTopic.Rd | 12 + man/figures/test-figure-1.png |only man/load_options.Rd | 29 +++- man/markdown_pass1.Rd |only src/wrapUsage.cpp | 5 tests/testthat/markdown-code-errors.txt |only tests/testthat/roxygen-block-3-A.Rd | 4 tests/testthat/roxygen-block-3-B.Rd | 3 tests/testthat/roxygen-block-3-C.Rd | 3 tests/testthat/test-markdown-code.R |only tests/testthat/test-markdown.R | 31 +--- tests/testthat/test-namespace.R | 7 + tests/testthat/test-object-format-r4.txt |only tests/testthat/test-object-format.R | 7 - tests/testthat/test-object-from-call.R | 7 + tests/testthat/test-object-package-author.txt |only tests/testthat/test-object-package.R | 33 ++-- tests/testthat/test-rd-includermd.R | 42 ++++-- tests/testthat/test-rd-markdown.R | 4 tests/testthat/test-rd.R | 81 +++++++++++ tests/testthat/test-utils-io.R | 10 - tests/testthat/test-utils.R | 39 +++++ tests/testthat/testNamespace |only vignettes/namespace.Rmd | 4 vignettes/rd-formatting.Rmd | 118 +++++++++++++++++ vignettes/rd.Rmd | 26 ++- vignettes/roxygen2.Rmd | 4 56 files changed, 1153 insertions(+), 316 deletions(-)
Title: Analysis of the International Trade Network
Description: Functions to clean and process international trade data into an international trade network (ITN) are provided. It then provides a set a functions to undertake analysis and plots of the ITN (extract the backbone, centrality, blockmodels, clustering). Examining the key players in the ITN and regional trade patterns.
Author: Matthew Smith
Maintainer: Matthew Smith <matt_smith.90@hotmail.co.uk>
Diff between ITNr versions 0.3.0 dated 2018-10-11 and 0.6.0 dated 2020-03-11
ITNr-0.3.0/ITNr/R/RegionalBrokerage_function.R |only ITNr-0.3.0/ITNr/man/RegionalBrokerage.Rd |only ITNr-0.6.0/ITNr/DESCRIPTION | 18 +- ITNr-0.6.0/ITNr/MD5 | 84 +++++---- ITNr-0.6.0/ITNr/NAMESPACE | 9 - ITNr-0.6.0/ITNr/R/Comtradrclean_function.R | 51 ++++-- ITNr-0.6.0/ITNr/R/EI_group_function.R |only ITNr-0.6.0/ITNr/R/EI_network_function.R |only ITNr-0.6.0/ITNr/R/ITNadjust_function.R | 5 ITNr-0.6.0/ITNr/R/ITNcluster_function.R | 24 +- ITNr-0.6.0/ITNr/R/ITNdynamic_function.R | 4 ITNr-0.6.0/ITNr/R/WITSclean_function.R | 152 ++++++++++++++---- ITNr-0.6.0/ITNr/R/adjust_mat_function.R |only ITNr-0.6.0/ITNr/R/core_periphery_weighted_function.R | 2 ITNr-0.6.0/ITNr/R/individual_EI_function.R |only ITNr-0.6.0/ITNr/R/mixing_matrix_igraph_function.R |only ITNr-0.6.0/ITNr/R/plot_degree_distribution_function.R | 14 - ITNr-0.6.0/ITNr/R/reorder_df_function.R |only ITNr-0.6.0/ITNr/man/Comtradrclean.Rd | 108 ++++++------ ITNr-0.6.0/ITNr/man/ELEnet16.Rd | 32 +-- ITNr-0.6.0/ITNr/man/ELEnetList.Rd | 32 +-- ITNr-0.6.0/ITNr/man/ITN_make_plot.Rd | 66 +++---- ITNr-0.6.0/ITNr/man/ITN_map_plot.Rd | 54 +++--- ITNr-0.6.0/ITNr/man/ITNadjust.Rd | 88 +++++----- ITNr-0.6.0/ITNr/man/ITNblock_plot.Rd | 68 ++++---- ITNr-0.6.0/ITNr/man/ITNblock_se.Rd | 64 +++---- ITNr-0.6.0/ITNr/man/ITNcentrality.Rd | 64 +++---- ITNr-0.6.0/ITNr/man/ITNcentrality_binary.Rd | 60 +++---- ITNr-0.6.0/ITNr/man/ITNcluster.Rd | 52 +++--- ITNr-0.6.0/ITNr/man/ITNcorr.Rd | 60 +++---- ITNr-0.6.0/ITNr/man/ITNdegdist.Rd | 54 +++--- ITNr-0.6.0/ITNr/man/ITNdynamic.Rd | 75 ++++---- ITNr-0.6.0/ITNr/man/ITNhistdegdist.Rd | 58 +++--- ITNr-0.6.0/ITNr/man/ITNimvex.Rd | 68 ++++---- ITNr-0.6.0/ITNr/man/ITNplotset.Rd | 58 +++--- ITNr-0.6.0/ITNr/man/ITNproperties.Rd | 60 +++---- ITNr-0.6.0/ITNr/man/WITSclean.Rd | 74 ++++---- ITNr-0.6.0/ITNr/man/adjust_mat.Rd |only ITNr-0.6.0/ITNr/man/cap_lat_lon.Rd | 24 +- ITNr-0.6.0/ITNr/man/core_periphery_weighted.Rd | 78 ++++----- ITNr-0.6.0/ITNr/man/ei_group.Rd |only ITNr-0.6.0/ITNr/man/ei_ind.Rd |only ITNr-0.6.0/ITNr/man/ei_network.Rd |only ITNr-0.6.0/ITNr/man/get.backbone.Rd | 74 ++++---- ITNr-0.6.0/ITNr/man/isEmpty.Rd | 32 +-- ITNr-0.6.0/ITNr/man/mixing_matrix_igraph.Rd |only ITNr-0.6.0/ITNr/man/plot_degree_distribution.Rd | 54 +++--- ITNr-0.6.0/ITNr/man/region_circle_plot.Rd | 52 +++--- ITNr-0.6.0/ITNr/man/reorder_df.Rd |only ITNr-0.6.0/ITNr/man/round_df.Rd | 58 +++--- 50 files changed, 1035 insertions(+), 895 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi [aut],
Yuan Tang [aut, cre] (<https://orcid.org/0000-0001-5243-233X>),
Austin Dickey [ctb],
Matthias Grenié [ctb],
Ryan Thompson [ctb],
Luciano Selzer [ctb],
Dario Strbenac [ctb],
Kirill Voronin [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between ggfortify versions 0.4.8 dated 2019-11-10 and 0.4.9 dated 2020-03-11
DESCRIPTION | 10 +- MD5 | 132 ++++++++++++++++++------------------- NEWS.md | 8 +- R/tslib.R | 6 - build/vignette.rds |binary inst/doc/basics.R | 38 +++++----- inst/doc/basics.html | 38 +++++----- inst/doc/plot_dist.R | 10 +- inst/doc/plot_dist.html | 10 +- inst/doc/plot_lm.R | 16 ++-- inst/doc/plot_map.R | 16 ++-- inst/doc/plot_map.html | 14 +-- inst/doc/plot_pca.R | 40 +++++------ inst/doc/plot_pca.html | 42 +++++------ inst/doc/plot_surv.R | 8 +- inst/doc/plot_surv.html | 12 +-- inst/doc/plot_ts.R | 70 +++++++++---------- inst/doc/plot_ts.html | 64 ++++++++--------- man/apply_facets.Rd | 11 ++- man/autoplot.MSM.lm.Rd | 3 man/autoplot.RasterCommon.Rd | 17 +++- man/autoplot.SpatialCommon.Rd | 23 +++++- man/autoplot.aareg.Rd | 12 ++- man/autoplot.acf.Rd | 27 +++++-- man/autoplot.breakpoints.Rd | 9 +- man/autoplot.cpt.Rd | 9 +- man/autoplot.cv.glmnet.Rd | 33 +++++++-- man/autoplot.density.Rd | 20 ++++- man/autoplot.forecast.Rd | 24 +++++- man/autoplot.glmnet.Rd | 31 ++++++-- man/autoplot.list.Rd | 3 man/autoplot.lm.Rd | 42 ++++++++--- man/autoplot.map.Rd | 25 +++++-- man/autoplot.matrix.Rd | 40 ++++++++--- man/autoplot.pca_common.Rd | 11 ++- man/autoplot.spec.Rd | 14 +++ man/autoplot.stepfun.Rd | 20 ++++- man/autoplot.survfit.Rd | 47 ++++++++++--- man/autoplot.ts.Rd | 46 ++++++++++-- man/autoplot.tsmodel.Rd | 37 +++++++--- man/autoplot.varprd.Rd | 26 +++++-- man/confint.acf.Rd | 4 - man/fitted.ar.Rd | 4 - man/fortify.RasterCommon.Rd | 3 man/fortify.aareg.Rd | 10 ++ man/fortify.acf.Rd | 10 ++ man/fortify.forecast.Rd | 3 man/fortify.survfit.Rd | 3 man/fortify.ts.Rd | 14 +++ man/fortify.tsmodel.Rd | 10 ++ man/fortify.varprd.Rd | 10 ++ man/geom_confint.Rd | 10 ++ man/ggbiplot.Rd | 67 ++++++++++++++---- man/ggcpgram.Rd | 15 +++- man/ggdistribution.Rd | 12 ++- man/ggfortify.Rd | 1 man/ggfreqplot.Rd | 19 +++-- man/ggtsdiag.Rd | 20 ++++- man/plot_confint.Rd | 17 +++- man/plot_label.Rd | 24 +++++- man/plus-ggmultiplot-ANY-method.Rd | 1 man/post_autoplot.Rd | 12 ++- man/print-ggmultiplot-method.Rd | 1 man/rbind_ts.Rd | 9 +- man/residuals.ar.Rd | 4 - man/show-ggmultiplot-method.Rd | 1 tests/testthat/test-ts.R | 12 +-- 67 files changed, 892 insertions(+), 468 deletions(-)
Title: Companion to Applied Regression
Description: Functions to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Third Edition, Sage, 2019.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Brad Price [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Ben Bolker [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Pavel Krivitsky [ctb],
Rafael Laboissiere [ctb],
Martin Maechler [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Steve Walker [ctb],
David Winsemius [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 3.0-6 dated 2019-12-23 and 3.0-7 dated 2020-03-11
DESCRIPTION | 20 MD5 | 32 NAMESPACE | 768 ++++----- NEWS | 6 R/Anova.R | 3955 ++++++++++++++++++++++++------------------------ R/boxCox.R | 3 R/invTranPlot.R | 7 R/powerTransform.R | 7 R/powerTransformlmer.R | 154 - R/utility-functions.R | 7 build/vignette.rds |binary inst/doc/embedding.R | 75 inst/doc/embedding.Rnw | 435 ++--- inst/doc/embedding.pdf |binary man/powerTransform.Rd | 2 vignettes/embedding.Rnw | 435 ++--- vignettes/embedding.bib | 6 17 files changed, 3005 insertions(+), 2907 deletions(-)
Title: R Interface to NLopt
Description: Solve optimization problems using an R interface to NLopt. NLopt is a
free/open-source library for nonlinear optimization, providing a common
interface for a number of different free optimization routines available
online as well as original implementations of various other algorithms.
See <http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction> for more
information on the available algorithms. During installation of nloptr on
Unix-based systems, the installer checks whether the NLopt library is
installed on the system. If the NLopt library cannot be found, the code
is compiled using the NLopt source included in the nloptr package.
Author: Jelmer Ypma [aut, cre],
Steven G. Johnson [aut] (author of the NLopt C library),
Hans W. Borchers [ctb],
Dirk Eddelbuettel [ctb],
Brian Ripley [ctb] (build process on multiple OS),
Kurt Hornik [ctb] (build process on multiple OS),
Julien Chiquet [ctb],
Avraham Adler [ctb] (removal deprecated calls from tests,
<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Jelmer Ypma <uctpjyy@ucl.ac.uk>
Diff between nloptr versions 1.2.2 dated 2020-02-29 and 1.2.2.1 dated 2020-03-11
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Time Series Management, Analysis and Interpolation for
Hydrological Modelling
Description: S3 functions for management, analysis, interpolation and plotting of time series used in hydrology and related environmental sciences. In particular, this package is highly oriented to hydrological modelling tasks. The focus of this package has been put in providing a collection of tools useful for the daily work of hydrologists (although an effort was made to optimise each function as much as possible, functionality has had priority over speed). Bugs / comments / questions / collaboration of any kind are very welcomed, and in particular, datasets that can be included in this package for academic purposes.
Author: Mauricio Zambrano-Bigiarini [aut, cre, cph]
(<https://orcid.org/0000-0002-9536-643X>)
Maintainer: Mauricio Zambrano-Bigiarini <mzb.devel@gmail.com>
Diff between hydroTSM versions 0.5-1 dated 2017-08-07 and 0.6-0 dated 2020-03-11
hydroTSM-0.5-1/hydroTSM/inst/doc/hydroTSM_Vignette-knitr.Rnw |only hydroTSM-0.5-1/hydroTSM/vignettes/hydroTSM_Vignette-knitr.Rnw |only hydroTSM-0.6-0/hydroTSM/DESCRIPTION | 11 - hydroTSM-0.6-0/hydroTSM/MD5 | 36 ++-- hydroTSM-0.6-0/hydroTSM/NAMESPACE | 10 - hydroTSM-0.6-0/hydroTSM/NEWS | 9 + hydroTSM-0.6-0/hydroTSM/R/climograph.R | 7 hydroTSM-0.6-0/hydroTSM/R/dm2seasonal.R | 9 - hydroTSM-0.6-0/hydroTSM/R/matrixplot.R | 9 - hydroTSM-0.6-0/hydroTSM/R/subdaily2daily.R | 51 ++++-- hydroTSM-0.6-0/hydroTSM/R/time2season.R | 8 hydroTSM-0.6-0/hydroTSM/build/vignette.rds |binary hydroTSM-0.6-0/hydroTSM/inst/CITATION | 4 hydroTSM-0.6-0/hydroTSM/inst/doc/hydroTSM_Vignette-knitr.R | 83 +++++----- hydroTSM-0.6-0/hydroTSM/inst/doc/hydroTSM_Vignette-knitr.Rmd |only hydroTSM-0.6-0/hydroTSM/inst/doc/hydroTSM_Vignette-knitr.pdf |binary hydroTSM-0.6-0/hydroTSM/man/hydroTSM-package.Rd | 8 hydroTSM-0.6-0/hydroTSM/man/mspplot.Rd | 3 hydroTSM-0.6-0/hydroTSM/man/subdaily2daily.Rd | 17 +- hydroTSM-0.6-0/hydroTSM/man/zoo2RHtest.Rd | 11 - hydroTSM-0.6-0/hydroTSM/vignettes/hydroTSM_Vignette-knitr.Rmd |only 21 files changed, 168 insertions(+), 108 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] (<https://orcid.org/0000-0002-3390-5442>),
Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>),
Veronika Braunisch [aut] (<https://orcid.org/0000-0001-7035-4662>),
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>
Diff between SDMtune versions 1.0.1 dated 2019-12-17 and 1.1.0 dated 2020-03-11
DESCRIPTION | 31 +++++------- MD5 | 54 ++++++++++----------- NAMESPACE | 11 ---- NEWS.md | 8 +++ R/SDMtune-class.R | 3 - R/chart-utils.R | 6 +- R/corVar.R | 7 ++ R/doJk.R | 2 R/modelReport.R | 31 +++++++++--- R/plotCor.R | 1 R/plotPA.R | 7 ++ R/plotPred.R | 7 ++ R/plotROC.R | 9 ++- R/plotResponse.R | 9 +-- R/plotVarImp.R | 7 ++ R/thinData.R | 72 ++++++++++++++++++++++------ R/train.R | 2 R/zzz.R | 1 inst/WORDLIST | 2 inst/doc/SDMtune.html | 2 man/plotResponse.Rd | 5 + man/thinData.Rd | 42 ++++++++++++++-- man/train.Rd | 91 ++++++++++++++++++++++++++++++++++++ tests/testthat/test-SDMtune-class.R | 2 tests/testthat/test-doJk.R | 3 + tests/testthat/test-plotJk.R | 3 - tests/testthat/test-plotVarImp.R | 5 - tests/testthat/test-thinData.R | 34 +++++++++---- 28 files changed, 342 insertions(+), 115 deletions(-)
Title: Repeated Measurement Design for Phase I Clinical Trial
Description: Implements our Bayesian phase I repeated measurement design that accounts for multidimensional toxicity endpoints from multiple treatment cycles. The package also provides a novel design to account for both multidimensional toxicity endpoints and early-stage efficacy endpoints in the phase I design. For both designs, functions are provided to recommend the next dosage selection based on the data collected in the available patient cohorts and to simulate trial characteristics given design parameters. Yin, Jun, et al. (2017) <doi:10.1002/sim.7134>.
Author: Jun Yin, Yu Du, Sumithra Mandrekar
Maintainer: Jun Yin <vivien.jyin@gmail.com>
Diff between phase1RMD versions 1.0.8 dated 2017-11-27 and 1.0.9 dated 2020-03-11
phase1RMD-1.0.8/phase1RMD/data/tox_dat2.RData |only phase1RMD-1.0.9/phase1RMD/DESCRIPTION | 11 phase1RMD-1.0.9/phase1RMD/MD5 | 31 phase1RMD-1.0.9/phase1RMD/NAMESPACE | 1 phase1RMD-1.0.9/phase1RMD/R/RunRMDEFF.R | 6 phase1RMD-1.0.9/phase1RMD/R/SimRMD.LMM.Cycle.R | 654 +++++++++--------- phase1RMD-1.0.9/phase1RMD/R/SimRMD.R | 872 ++++++++++++------------ phase1RMD-1.0.9/phase1RMD/R/SimRMDEFF.R | 8 phase1RMD-1.0.9/phase1RMD/R/structure.R | 4 phase1RMD-1.0.9/phase1RMD/R/summaryRMD.R | 110 +-- phase1RMD-1.0.9/phase1RMD/man/GenToxProb.Rd | 2 phase1RMD-1.0.9/phase1RMD/man/RunRMD.Rd | 6 phase1RMD-1.0.9/phase1RMD/man/RunRMDEFF.Rd | 8 phase1RMD-1.0.9/phase1RMD/man/SimRMD.Rd | 18 phase1RMD-1.0.9/phase1RMD/man/Tox2nTTP.Rd | 4 phase1RMD-1.0.9/phase1RMD/man/patdata.Rd | 28 phase1RMD-1.0.9/phase1RMD/man/plot.RunRMDVal.Rd | 8 17 files changed, 886 insertions(+), 885 deletions(-)
More information about factor.switching at CRAN
Permanent link
Title: Interface to 'Container Instances', 'Docker Registry' and
'Kubernetes' in 'Azure'
Description: An interface to container functionality in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/overview/containers/>. Manage 'Azure Container Instance' (ACI), 'Azure Container Registry' (ACR) and 'Azure Kubernetes Service' (AKS) resources, push and pull images, and deploy services. On the client side, lightweight shells to the 'docker', 'docker-compose', 'kubectl' and 'helm' commandline tools are provided. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Bill Liang [ctb] (Assistance debugging MMLS on Kubernetes),
Ramkumar Chandrasekaran [ctb] (Original blog article on Dockerising
MMLS),
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureContainers versions 1.2.0 dated 2019-12-03 and 1.2.1 dated 2020-03-11
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/ext_tools.R | 2 +- build/vignette.rds |binary 5 files changed, 12 insertions(+), 8 deletions(-)
More information about AzureContainers at CRAN
Permanent link
Title: An Integrated Framework for Textual Sentiment Time Series
Aggregation and Prediction
Description: Optimized prediction based on textual sentiment, accounting for the intrinsic challenge that sentiment can be computed and pooled across texts and time in various ways. See Ardia et al. (2020) <doi:10.2139/ssrn.3067734>.
Author: Samuel Borms [aut, cre] (<https://orcid.org/0000-0001-9533-1870>),
David Ardia [aut] (<https://orcid.org/0000-0003-2823-782X>),
Keven Bluteau [aut] (<https://orcid.org/0000-0003-2990-4807>),
Kris Boudt [aut] (<https://orcid.org/0000-0002-1000-5142>),
Jeroen Van Pelt [ctb],
Andres Algaba [ctb]
Maintainer: Samuel Borms <samuel.borms@unine.ch>
Diff between sentometrics versions 0.8.0 dated 2020-01-13 and 0.8.1 dated 2020-03-11
DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++++-------------- NEWS.md | 4 +++ R/sentiment_engines.R | 17 +++++++------- R/sentocorpus.R | 6 +++- R/sentolexicons.R | 2 - R/sentomeasures_methods.R | 32 +++++++++++--------------- R/sentometrics.R | 4 +-- R/sentomodel.R | 4 +-- R/utils.R | 7 +++++ README.md | 16 ++++++------- man/compute_sentiment.Rd | 13 +++++----- man/ctr_model.Rd | 4 +-- man/list_lexicons.Rd | 2 - man/sento_lexicons.Rd | 2 - man/sentometrics-package.Rd | 2 - tests/testthat/test_corpus_building.R | 4 +-- tests/testthat/test_sentiment_computation.R | 2 - 18 files changed, 87 insertions(+), 76 deletions(-)
Title: Access Publisher Copyright & Self-Archiving Policies via the
'SHERPA/RoMEO' API
Description: Fetches information from the 'SHERPA/RoMEO' API
<http://www.sherpa.ac.uk/romeo/apimanual.php> which indexes policies of
journal regarding the archival of scientific manuscripts before and/or after
peer-review as well as formatted manuscripts.
Author: Matthias Grenié [aut, cre] (<https://orcid.org/0000-0002-4659-7522>),
Hugo Gruson [aut] (<https://orcid.org/0000-0002-4094-1476>)
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>
Diff between rromeo versions 0.1.0 dated 2019-05-16 and 0.1.1 dated 2020-03-11
rromeo-0.1.0/rromeo/inst/doc/rromeo.R |only rromeo-0.1.0/rromeo/inst/doc/setting_up_api_key.R |only rromeo-0.1.0/rromeo/inst/vignette_cassette.yml |only rromeo-0.1.0/rromeo/man/figures/README-dependency_network_full-1.png |only rromeo-0.1.0/rromeo/man/figures/README-dependency_network_imports-1.png |only rromeo-0.1.0/rromeo/tests/fixtures/vcr_cassettes/rr_journal_name_multiple_fetch.yml |only rromeo-0.1.0/rromeo/tests/fixtures/vcr_cassettes/rr_romeo_colour.yml |only rromeo-0.1.0/rromeo/vignettes/overview.html |only rromeo-0.1.1/rromeo/DESCRIPTION | 14 rromeo-0.1.1/rromeo/MD5 | 183 rromeo-0.1.1/rromeo/NAMESPACE | 44 rromeo-0.1.1/rromeo/NEWS.md |only rromeo-0.1.1/rromeo/R/parse_generic.R | 110 rromeo-0.1.1/rromeo/R/parse_journal.R | 307 rromeo-0.1.1/rromeo/R/parse_publisher.R | 122 rromeo-0.1.1/rromeo/R/rr_api_version.R | 30 rromeo-0.1.1/rromeo/R/rr_auth.R | 38 rromeo-0.1.1/rromeo/R/rr_base_functions.R | 48 rromeo-0.1.1/rromeo/R/rr_journal_find.R | 83 rromeo-0.1.1/rromeo/R/rr_journal_issn.R | 83 rromeo-0.1.1/rromeo/R/rr_journal_name.R | 126 rromeo-0.1.1/rromeo/R/rr_publisher_all.R | 40 rromeo-0.1.1/rromeo/R/rr_publisher_continent.R | 122 rromeo-0.1.1/rromeo/R/rr_publisher_country.R | 88 rromeo-0.1.1/rromeo/R/rr_publisher_id.R | 76 rromeo-0.1.1/rromeo/R/rr_publisher_name.R | 98 rromeo-0.1.1/rromeo/R/rr_romeo_colour.R | 93 rromeo-0.1.1/rromeo/R/rromeo-package.R | 16 rromeo-0.1.1/rromeo/R/utils.R | 262 rromeo-0.1.1/rromeo/README.md | 305 rromeo-0.1.1/rromeo/build/vignette.rds |binary rromeo-0.1.1/rromeo/inst/CITATION | 40 rromeo-0.1.1/rromeo/inst/WORDLIST | 6 rromeo-0.1.1/rromeo/inst/doc/rromeo.Rmd | 736 rromeo-0.1.1/rromeo/inst/doc/rromeo.html | 1569 - rromeo-0.1.1/rromeo/inst/doc/setting_up_api_key.Rmd | 281 rromeo-0.1.1/rromeo/inst/doc/setting_up_api_key.html | 787 rromeo-0.1.1/rromeo/man/figures/README-dependency_network_full-1.svg |only rromeo-0.1.1/rromeo/man/figures/README-dependency_network_imports-1.svg |only rromeo-0.1.1/rromeo/man/parse_journal.Rd | 24 rromeo-0.1.1/rromeo/man/rr_GET.Rd | 2 rromeo-0.1.1/rromeo/man/rr_api_version.Rd | 2 rromeo-0.1.1/rromeo/man/rr_journal_find.Rd | 12 rromeo-0.1.1/rromeo/man/rr_journal_issn.Rd | 40 rromeo-0.1.1/rromeo/man/rr_journal_name.Rd | 30 rromeo-0.1.1/rromeo/man/rr_publisher_continent.Rd | 12 rromeo-0.1.1/rromeo/man/rr_publisher_country.Rd | 4 rromeo-0.1.1/rromeo/man/rr_publisher_id.Rd | 2 rromeo-0.1.1/rromeo/man/rr_publisher_name.Rd | 2 rromeo-0.1.1/rromeo/man/rr_romeo_colour.Rd | 11 rromeo-0.1.1/rromeo/man/rr_ua.Rd | 2 rromeo-0.1.1/rromeo/man/rromeo-package.Rd | 7 rromeo-0.1.1/rromeo/man/validate_country_code.Rd | 4 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/api_unreachable.yml | 54 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/api_unreachable_publisher.yml | 54 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/invalid_api_key_journal.yml | 132 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/invalid_api_key_publisher.yml | 124 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/missing_issn.yml | 1485 - rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_api_version.yml | 120 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_find.yml | 232 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_find_excess.yml | 740 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_find_multiple.yml | 200 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_find_multiple_exact.yml | 504 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_find_notfound.yml | 138 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_issn.yml | 240 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_issn_multiple.yml | 466 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_issn_provided_issn.yml |only rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_name.yml | 155 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_name_excess.yml |11352 +++++----- rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_name_multiple.yml | 1276 - rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_name_multiple_exact.yml | 503 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_journal_name_notfound.yml | 136 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_publisher_continent.yml | 33 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_publisher_continent_notfound.yml | 129 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_publisher_country.yml | 1507 - rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_publisher_country_notfound.yml | 129 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_publisher_id.yml | 264 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_publisher_id_multiple.yml | 453 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_publisher_id_notfound.yml | 129 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_publisher_name.yml | 223 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_publisher_name_multiple.yml | 442 rromeo-0.1.1/rromeo/tests/fixtures/vcr_cassettes/rr_publisher_name_notfound.yml | 137 rromeo-0.1.1/rromeo/tests/testthat.R | 8 rromeo-0.1.1/rromeo/tests/testthat/helper-rromeo.R | 7 rromeo-0.1.1/rromeo/tests/testthat/test-rr_journal_find.R | 140 rromeo-0.1.1/rromeo/tests/testthat/test-rr_journal_issn.R | 142 rromeo-0.1.1/rromeo/tests/testthat/test-rr_journal_name.R | 222 rromeo-0.1.1/rromeo/tests/testthat/test-rr_publisher_continent.R | 96 rromeo-0.1.1/rromeo/tests/testthat/test-rr_publisher_country.R | 75 rromeo-0.1.1/rromeo/tests/testthat/test-rr_publisher_id.R | 129 rromeo-0.1.1/rromeo/tests/testthat/test-rr_publisher_name.R | 113 rromeo-0.1.1/rromeo/tests/testthat/test-rr_romeo_colour.R | 36 rromeo-0.1.1/rromeo/tests/testthat/test-rromeo_base.R | 38 rromeo-0.1.1/rromeo/tests/testthat/test-utils.R | 152 rromeo-0.1.1/rromeo/vignettes/bar_graph-1.png |only rromeo-0.1.1/rromeo/vignettes/pie_chart-1.png |only rromeo-0.1.1/rromeo/vignettes/precompile.R |only rromeo-0.1.1/rromeo/vignettes/rromeo.Rmd | 736 rromeo-0.1.1/rromeo/vignettes/rromeo.Rmd.orig |only rromeo-0.1.1/rromeo/vignettes/setting_up_api_key.Rmd | 281 rromeo-0.1.1/rromeo/vignettes/setting_up_api_key.Rmd.orig |only 101 files changed, 15077 insertions(+), 14316 deletions(-)
Title: Download, Compile and Link 'OpenBLAS' Library with R
Description: The 'ropenblas' package (<https://prdm0.github.io/ropenblas/>) is useful for users of any 'GNU/Linux' distribution. It will be possible to download, compile and link the 'OpenBLAS' library (<https://www.openblas.net/>) with the R language, always by the same procedure, regardless of the 'GNU/Linux' distribution used. With the 'ropenblas' package it is possible to download, compile and link the latest version of the 'OpenBLAS' library even the repositories of the 'GNU/Linux' distribution used do not include the latest versions of 'OpenBLAS'. If of interest, older versions of the 'OpenBLAS' library may be considered. Linking R with an optimized version of 'BLAS' (<http://www.netlib.org/blas/>) may improve the computational performance of R code. The 'OpenBLAS' library is an optimized implementation of 'BLAS' that can be easily linked to R with the 'ropenblas' package.
Author: Pedro Rafael D. Marinho [aut, cre]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between ropenblas versions 0.2.1 dated 2020-02-06 and 0.2.2 dated 2020-03-11
ropenblas-0.2.1/ropenblas/NEWS.md |only ropenblas-0.2.1/ropenblas/README.md |only ropenblas-0.2.2/ropenblas/DESCRIPTION | 6 - ropenblas-0.2.2/ropenblas/MD5 | 15 ++-- ropenblas-0.2.2/ropenblas/NAMESPACE | 3 ropenblas-0.2.2/ropenblas/R/ropenblas.R | 52 +++++++++++++++-- ropenblas-0.2.2/ropenblas/man/last_version_openblas.Rd |only ropenblas-0.2.2/ropenblas/man/last_version_r.Rd | 6 - ropenblas-0.2.2/ropenblas/man/rcompiler.Rd | 2 ropenblas-0.2.2/ropenblas/man/ropenblas.Rd | 2 10 files changed, 64 insertions(+), 22 deletions(-)
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] (<https://orcid.org/0000-0003-3716-0668>)
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.0.6 dated 2020-02-11 and 0.0.7 dated 2020-03-11
DESCRIPTION | 16 ++-- MD5 | 15 ++-- R/map_nigeria.R | 53 +++++++------- R/numbers.R | 9 +- README.md | 91 +++++++++++++++++++++++-- man/map_ng.Rd | 10 +- tests/testthat/data/map_xcoord.rds |only tests/testthat/data/map_ycoord.rds |only tests/testthat/test-map_nigeria.R |only tests/testthat/test-numbers.R | 134 ++++++++++++++++++++++++++++++++----- 10 files changed, 259 insertions(+), 69 deletions(-)
Title: Design and Analysis of Experiments with R
Description: Contains Data frames and functions used in the book "Design and Analysis of Experiments with R".
Author: John Lawson [aut, cre],
Gerhard Krennrich [aut]
Maintainer: John Lawson <lawsonjsl7net@gmail.com>
Diff between daewr versions 1.1-8 dated 2020-01-16 and 1.2-2 dated 2020-03-11
daewr-1.1-8/daewr/R/stepforward.R |only daewr-1.1-8/daewr/man/bstep.Rd |only daewr-1.1-8/daewr/man/stepforward.Rd |only daewr-1.2-2/daewr/DESCRIPTION | 18 ++-- daewr-1.2-2/daewr/MD5 | 151 +++++++++++++++++----------------- daewr-1.2-2/daewr/NAMESPACE | 13 +- daewr-1.2-2/daewr/R/HierAFS.R |only daewr-1.2-2/daewr/R/LenthPlot.R |only daewr-1.2-2/daewr/R/Tukey1df.R | 2 daewr-1.2-2/daewr/R/fhstep.R | 88 +++++++------------ daewr-1.2-2/daewr/R/firstm.R |only daewr-1.2-2/daewr/R/fnextrm.R |only daewr-1.2-2/daewr/R/ihstep.R | 132 ++++++++++++++++------------- daewr-1.2-2/daewr/data/Apo.rda |binary daewr-1.2-2/daewr/data/BPmonitor.rda |binary daewr-1.2-2/daewr/data/Bdish.rda |binary daewr-1.2-2/daewr/data/Bff.rda |binary daewr-1.2-2/daewr/data/BoxM.rda |binary daewr-1.2-2/daewr/data/COdata.rda |binary daewr-1.2-2/daewr/data/MPV.rda |binary daewr-1.2-2/daewr/data/Naph.rda |binary daewr-1.2-2/daewr/data/SPMPV.rda |binary daewr-1.2-2/daewr/data/Smotor.rda |binary daewr-1.2-2/daewr/data/Tet.rda |binary daewr-1.2-2/daewr/data/Treb.rda |binary daewr-1.2-2/daewr/data/antifungal.rda |binary daewr-1.2-2/daewr/data/apple.rda |binary daewr-1.2-2/daewr/data/arso.rda |binary daewr-1.2-2/daewr/data/augm.rda |binary daewr-1.2-2/daewr/data/bha.rda |binary daewr-1.2-2/daewr/data/bioequiv.rda |binary daewr-1.2-2/daewr/data/bioeqv.rda |binary daewr-1.2-2/daewr/data/blood.rda |binary daewr-1.2-2/daewr/data/bread.rda |binary daewr-1.2-2/daewr/data/cake.rda |binary daewr-1.2-2/daewr/data/cement.rda |binary daewr-1.2-2/daewr/data/chem.rda |binary daewr-1.2-2/daewr/data/chipman.rda |binary daewr-1.2-2/daewr/data/cont.rda |binary daewr-1.2-2/daewr/data/cpipe.rda |binary daewr-1.2-2/daewr/data/culture.rda |binary daewr-1.2-2/daewr/data/dairy.rda |binary daewr-1.2-2/daewr/data/drug.rda |binary daewr-1.2-2/daewr/data/eptaxr.rda |binary daewr-1.2-2/daewr/data/eptaxs2.rda |binary daewr-1.2-2/daewr/data/eptaxyb.rda |binary daewr-1.2-2/daewr/data/gagerr.rda |binary daewr-1.2-2/daewr/data/gear.rda |binary daewr-1.2-2/daewr/data/hardwood.rda |binary daewr-1.2-2/daewr/data/inject.rda |binary daewr-1.2-2/daewr/data/pastry.rda |binary daewr-1.2-2/daewr/data/pest.rda |binary daewr-1.2-2/daewr/data/pesticide.rda |binary daewr-1.2-2/daewr/data/plasma.rda |binary daewr-1.2-2/daewr/data/polvdat.rda |binary daewr-1.2-2/daewr/data/polymer.rda |binary daewr-1.2-2/daewr/data/prodstd.rda |binary daewr-1.2-2/daewr/data/qsar.rda |binary daewr-1.2-2/daewr/data/rcb.rda |binary daewr-1.2-2/daewr/data/residue.rda |binary daewr-1.2-2/daewr/data/rubber.rda |binary daewr-1.2-2/daewr/data/sausage.rda |binary daewr-1.2-2/daewr/data/soup.rda |binary daewr-1.2-2/daewr/data/soupmx.rda |binary daewr-1.2-2/daewr/data/splitPdes.rda |binary daewr-1.2-2/daewr/data/strung.rda |binary daewr-1.2-2/daewr/data/strungtile.rda |binary daewr-1.2-2/daewr/data/sugarbeet.rda |binary daewr-1.2-2/daewr/data/taste.rda |binary daewr-1.2-2/daewr/data/teach.rda |binary daewr-1.2-2/daewr/data/tile.rda |binary daewr-1.2-2/daewr/data/virus.rda |binary daewr-1.2-2/daewr/data/volt.rda |binary daewr-1.2-2/daewr/data/web.rda |binary daewr-1.2-2/daewr/man/HierAFS.Rd |only daewr-1.2-2/daewr/man/LenthPlot.Rd |only daewr-1.2-2/daewr/man/fhstep.Rd | 22 +++- daewr-1.2-2/daewr/man/firstm.Rd |only daewr-1.2-2/daewr/man/fnextrm.Rd |only daewr-1.2-2/daewr/man/fullnormal.Rd | 1 daewr-1.2-2/daewr/man/halfnorm.Rd | 1 daewr-1.2-2/daewr/man/ihstep.Rd | 17 ++- 82 files changed, 229 insertions(+), 216 deletions(-)
More information about aws.transcribe at CRAN
Permanent link
Title: 'Asio' C++ Header Files
Description: 'Asio' is a cross-platform C++ library for network and low-level
I/O programming that provides developers with a consistent asynchronous model
using a modern C++ approach. It is also included in Boost but requires linking
when used with Boost. Standalone it can be used header-only (provided a recent
compiler). 'Asio' is written and maintained by Christopher M. Kohlhoff, and
released under the 'Boost Software License', Version 1.0.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between AsioHeaders versions 1.12.1 dated 2018-09-10 and 1.12.2-1 dated 2020-03-11
ChangeLog | 9 ++ DESCRIPTION | 8 +- MD5 | 61 +++++++++--------- README.md | 6 - inst/NEWS.Rd | 6 + inst/include/asio/buffer.hpp | 81 +++++++++++++----------- inst/include/asio/connect.hpp | 31 ++++----- inst/include/asio/detail/config.hpp | 71 +++++++++++++-------- inst/include/asio/detail/future.hpp |only inst/include/asio/detail/impl/socket_ops.ipp | 2 inst/include/asio/detail/is_buffer_sequence.hpp | 52 +++++++++++---- inst/include/asio/detail/timer_queue.hpp | 2 inst/include/asio/detail/win_global.hpp | 3 inst/include/asio/impl/io_context.hpp | 2 inst/include/asio/impl/read_until.hpp | 4 - inst/include/asio/impl/use_future.hpp | 1 inst/include/asio/ip/bad_address_cast.hpp | 7 +- inst/include/asio/ip/basic_resolver.hpp | 10 +- inst/include/asio/ip/basic_resolver_results.hpp | 8 +- inst/include/asio/packaged_task.hpp | 6 - inst/include/asio/read.hpp | 8 +- inst/include/asio/read_at.hpp | 8 +- inst/include/asio/read_until.hpp | 14 ++-- inst/include/asio/ssl/context_base.hpp | 17 +++++ inst/include/asio/ssl/impl/context.ipp | 55 ++++++++++++++-- inst/include/asio/ssl/stream.hpp | 3 inst/include/asio/thread_pool.hpp | 2 inst/include/asio/use_future.hpp | 5 - inst/include/asio/version.hpp | 2 inst/include/asio/write.hpp | 7 +- inst/include/asio/write_at.hpp | 8 +- man/AsioHeaders-package.Rd | 2 32 files changed, 324 insertions(+), 177 deletions(-)
Title: Tools and Tests for Experiments with Partially Synthetic Data
Sets
Description: A set of functions to support experimentation in the utility of partially synthetic data sets. All functions compare an observed data set to one or a set of partially synthetic data sets derived from the observed data to (1) check that data sets have identical attributes, (2) calculate overall and specific variable perturbation rates, (3) check for potential logical inconsistencies, and (4) calculate confidence intervals and standard errors of desired variables in multiple imputed data sets. Confidence interval and standard error formulas have options for either synthetic data sets or multiple imputed data sets. For more information on the formulas and methods used, see Reiter & Raghunathan (2007) <doi:10.1198/016214507000000932>.
Author: Charlotte Looby [aut, cre]
Maintainer: Charlotte Looby <clooby@rti.org>
Diff between SynthTools versions 1.0.0 dated 2019-09-04 and 1.0.1 dated 2020-03-11
DESCRIPTION | 8 +- MD5 | 51 +++++++++--------- NAMESPACE | 2 NEWS.md |only R/dataComp.R | 34 ++++++------ R/logicCheck.R | 14 ++-- R/oneCatCI.R | 29 ++++++---- R/pertRates.R | 27 +++++---- R/twoCatCI.R | 22 ++++--- README.md | 2 build/partial.rdb |binary inst/WORDLIST | 4 + man/ContCI.Rd | 86 +++++++++++++++--------------- man/PPA.Rd | 52 +++++++++--------- man/PPAm5.Rd | 52 +++++++++--------- man/PPAps1.Rd | 52 +++++++++--------- man/PPAps2.Rd | 52 +++++++++--------- man/PPAps3.Rd | 52 +++++++++--------- man/PPAps4.Rd | 52 +++++++++--------- man/PPAps5.Rd | 52 +++++++++--------- man/dataComp.Rd | 88 +++++++++++++++---------------- man/logicCheck.Rd | 102 ++++++++++++++++++------------------ man/oneCatCI.Rd | 95 +++++++++++++++++---------------- man/pertRates.Rd | 90 +++++++++++++++---------------- man/twoCatCI.Rd | 116 ++++++++++++++++++++--------------------- tests/testthat/test-oneCatCI.R | 8 +- tests/testthat/test-twoCatCI.R | 4 - 27 files changed, 584 insertions(+), 562 deletions(-)
Title: Open Document Databases (.odb) Management
Description: Functions to create, connect, update and query 'HSQL' databases embedded in Open Document Databases files, as 'OpenOffice' and 'LibreOffice' do.
Author: Sylvain Mareschal
Maintainer: Sylvain Mareschal <maressyl@gmail.com>
Diff between ODB versions 1.1.1 dated 2012-07-23 and 1.2.1 dated 2020-03-11
ODB-1.1.1/ODB/inst/tools |only ODB-1.2.1/ODB/DESCRIPTION | 19 +++++++------- ODB-1.2.1/ODB/MD5 | 47 +++++++++++++++++++----------------- ODB-1.2.1/ODB/NAMESPACE | 6 ++++ ODB-1.2.1/ODB/R/isClosed.r | 22 ++++++++++------ ODB-1.2.1/ODB/R/odb.create.r | 2 - ODB-1.2.1/ODB/R/odb.open.r | 8 +++--- ODB-1.2.1/ODB/R/progress-class.r | 6 ++-- ODB-1.2.1/ODB/README.md |only ODB-1.2.1/ODB/build |only ODB-1.2.1/ODB/inst/NEWS.Rd | 35 +++++++++++++++++++------- ODB-1.2.1/ODB/inst/java |only ODB-1.2.1/ODB/inst/template.odb |only ODB-1.2.1/ODB/java |only ODB-1.2.1/ODB/man/ODB-package.Rd | 39 +++++++++++++++-------------- ODB-1.2.1/ODB/man/isClosed.Rd | 5 ++- ODB-1.2.1/ODB/man/odb.close.Rd | 5 ++- ODB-1.2.1/ODB/man/odb.comments.Rd | 5 ++- ODB-1.2.1/ODB/man/odb.create.Rd | 10 ++++--- ODB-1.2.1/ODB/man/odb.export.Rd | 8 +++--- ODB-1.2.1/ODB/man/odb.insert.Rd | 5 ++- ODB-1.2.1/ODB/man/odb.open.Rd | 5 ++- ODB-1.2.1/ODB/man/odb.queries.Rd | 5 ++- ODB-1.2.1/ODB/man/odb.read.Rd | 5 ++- ODB-1.2.1/ODB/man/odb.tables.Rd | 5 ++- ODB-1.2.1/ODB/man/odb.write.Rd | 5 ++- ODB-1.2.1/ODB/man/progress-class.Rd | 8 +++--- 27 files changed, 151 insertions(+), 104 deletions(-)
Title: Install the 'Natverse' Packages from Scratch
Description: Provides streamlined installation for packages from the 'natverse',
a suite of R packages for computational neuroanatomy built on top of the
'nat' 'NeuroAnatomy Toolbox' package. Installation of the complete
'natverse' suite requires a 'GitHub' user account and personal access token
'GITHUB_PAT'. 'natmanager' will help the end user set this up if necessary.
Author: Sridhar Jagannathan [aut, cre]
(<https://orcid.org/0000-0002-2078-1145>),
Gregory Jefferis [aut] (<https://orcid.org/0000-0002-0587-9355>)
Maintainer: Sridhar Jagannathan <j.sridharrajan@gmail.com>
Diff between natmanager versions 0.1.0 dated 2020-02-11 and 0.4.0 dated 2020-03-11
DESCRIPTION | 42 +++++++------- MD5 | 25 +++++--- NAMESPACE | 12 ++++ NEWS.md |only R/install.R | 77 +++++++++++++++++++++---- R/natmanager-package.R |only R/update.R |only R/utils.R | 16 ++--- R/zzz.R | 88 ++++++++++++++++++++--------- README.md | 125 +++--------------------------------------- inst/WORDLIST | 6 +- man/install.Rd | 69 ++++++++++++++++++++--- man/list_repo.Rd | 14 ++-- man/natmanager-package.Rd |only man/selfupdate.Rd |only tests/testthat/test-install.R | 21 +++++-- 16 files changed, 279 insertions(+), 216 deletions(-)
Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
'vtreat' prepares variables so that data has fewer exceptional cases, making
it easier to safely use models in production. Common problems 'vtreat' defends
against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new
categorical levels (levels seen during application, but not during training). Reference:
"'vtreat': a data.frame Processor for Predictive Modeling", Zumel, Mount, 2016, <DOI:10.5281/zenodo.1173313>.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 1.5.2 dated 2020-02-08 and 1.6.0 dated 2020-03-11
DESCRIPTION | 10 - MD5 | 54 +++--- NAMESPACE | 15 + NEWS.md | 5 R/ft.R | 270 +++++++++++++++++++++++++++--- R/mult_class.R | 128 ++++++++------ R/vtreat.R | 25 ++ README.md | 22 +- inst/doc/MultiClassVtreat.html | 4 inst/doc/SavingTreamentPlans.html | 4 inst/doc/VariableImportance.html | 10 - inst/doc/vtreat.html | 6 inst/doc/vtreatCrossFrames.html | 38 ++-- inst/doc/vtreatGrouping.html | 4 inst/doc/vtreatOverfit.html | 50 ++--- inst/doc/vtreatRareLevels.html | 4 inst/doc/vtreatScaleMode.html | 16 - inst/doc/vtreatSignificance.html | 18 +- inst/doc/vtreatSplitting.html | 4 inst/doc/vtreatVariableTypes.html | 42 ++-- inst/unit_tests/test_imputation_control.R |only man/BinomialOutcomeTreatment.Rd | 2 man/MultinomialOutcomeTreatment.Rd | 2 man/NumericOutcomeTreatment.Rd | 2 man/UnsupervisedTreatment.Rd | 2 man/apply_transform.Rd |only man/fit.Rd |only man/fit_prepare.Rd |only man/fit_transform.Rd |only man/get_feature_names.Rd |only man/get_score_frame.Rd |only man/get_transform.Rd |only 32 files changed, 511 insertions(+), 226 deletions(-)
Title: HTML Output Formats and Templates for 'rmarkdown' Documents
Description: HTML formats and templates for 'rmarkdown' documents, with some extra
features such as automatic table of contents, lightboxed figures, dynamic
crosstab helper.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between rmdformats versions 0.3.6 dated 2019-12-16 and 0.3.7 dated 2020-03-11
rmdformats-0.3.6/rmdformats/inst/templates/bootstrap-3.3.6 |only rmdformats-0.3.7/rmdformats/DESCRIPTION | 14 rmdformats-0.3.7/rmdformats/MD5 | 84 -- rmdformats-0.3.7/rmdformats/NEWS | 7 rmdformats-0.3.7/rmdformats/R/html_dependencies.R | 8 rmdformats-0.3.7/rmdformats/README.md | 2 rmdformats-0.3.7/rmdformats/build/vignette.rds |binary rmdformats-0.3.7/rmdformats/inst/doc/introduction.R | 2 rmdformats-0.3.7/rmdformats/inst/doc/introduction.html | 395 +++------- rmdformats-0.3.7/rmdformats/inst/templates/bootstrap-3.3.7 |only rmdformats-0.3.7/rmdformats/inst/templates/readthedown/readthedown.css | 43 - rmdformats-0.3.7/rmdformats/inst/templates/readthedown/readthedown.html | 42 - rmdformats-0.3.7/rmdformats/inst/templates/readthedown/readthedown.js | 4 rmdformats-0.3.7/rmdformats/man/create.doc.Rd | 8 rmdformats-0.3.7/rmdformats/man/html_clean.Rd | 21 rmdformats-0.3.7/rmdformats/man/html_docco.Rd | 18 rmdformats-0.3.7/rmdformats/man/material.Rd | 20 rmdformats-0.3.7/rmdformats/man/pilltabs.Rd | 11 rmdformats-0.3.7/rmdformats/man/readthedown.Rd | 19 19 files changed, 312 insertions(+), 386 deletions(-)
Title: Representative and Adequate Prioritization Toolkit in R
Description: Biodiversity is in crisis. The overarching aim of conservation
is to preserve biodiversity patterns and processes. To this end, protected
areas are established to buffer species and preserve biodiversity processes.
But resources are limited and so protected areas must be cost-effective.
This package contains tools to generate plans for protected areas
(prioritizations), using spatially explicit targets for biodiversity
patterns and processes. To obtain solutions in a feasible amount of time,
this package uses the commercial 'Gurobi' software package (obtained from
<http://www.gurobi.com/>). For more information on using
this package, see Hanson et al. (2018) <doi:10.1111/2041-210X.12862>.
Author: Jeffrey O Hanson [aut, cre],
Jonathan R Rhodes [aut],
Hugh P Possingham [aut],
Richard A Fuller [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between raptr versions 0.1.5 dated 2020-02-12 and 0.1.6 dated 2020-03-11
DESCRIPTION | 10 MD5 | 22 - NEWS.md | 6 R/RapResults.R | 2 R/data.R | 2 R/raptr.R | 2 inst/doc/raptr.Rmd | 4 inst/doc/raptr.html | 430 ++++++++++++++++++++--------------- man/casestudy_data.Rd | 2 man/raptr.Rd | 2 tests/testthat/test-11-RapUnsolved.R | 6 vignettes/raptr.Rmd | 4 12 files changed, 287 insertions(+), 205 deletions(-)
Title: Optimal Project Prioritization
Description: A decision support tool for prioritizing conservation projects.
Prioritizations can be developed by maximizing expected feature richness,
expected phylogenetic diversity, the number of features that meet
persistence targets, or identifying a set of projects that meet persistence
targets for minimal cost. Constraints (e.g. lock in specific actions) and
feature weights can also be specified to further customize prioritizations.
After defining a project prioritization problem, solutions can be obtained
using exact algorithms, heuristic algorithms, or random processes. In
particular, it is recommended to install the 'Gurobi' optimizer (available
from <https://www.gurobi.com>) because it can identify optimal solutions
very quickly. Finally, methods are provided for comparing different
prioritizations and evaluating their benefits. For more information, see
Hanson et al. (2019) <doi:10.1111/2041-210X.13264>.
Author: Jeffrey O Hanson [aut, cre],
Richard Schuster [aut],
Matthew Strimas-Mackey [aut],
Joseph Bennett [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between oppr versions 1.0.0 dated 2020-02-07 and 1.0.1 dated 2020-03-11
DESCRIPTION | 6 - MD5 | 10 +-- NEWS.md | 8 ++ R/project_cost_effectiveness.R | 9 +- README.md | 2 inst/doc/oppr.html | 126 ++++++++++++++++++++--------------------- 6 files changed, 87 insertions(+), 74 deletions(-)
Title: 'BaseX' Client
Description: 'BaseX' <http://basex.org> is a XML database engine and a compliant 'XQuery 3.1' processor with full support of 'W3C Update Facility'. This package is a full client-implementation of the client/server protocol for 'BaseX' and provides functionalities to create, manipulate and query on XML-data.
Author: Ben Engbers [aut, cre]
Maintainer: Ben Engbers <Ben.Engbers@Be-Logical.nl>
Diff between RBaseX versions 0.1.4 dated 2019-12-22 and 0.2.4 dated 2020-03-11
RBaseX-0.1.4/RBaseX/R/RbaseX_Utility.R |only RBaseX-0.1.4/RBaseX/man/BasexClient.Rd |only RBaseX-0.2.4/RBaseX/DESCRIPTION | 12 - RBaseX-0.2.4/RBaseX/MD5 | 72 +++++-- RBaseX-0.2.4/RBaseX/NAMESPACE | 10 + RBaseX-0.2.4/RBaseX/R/Add.R | 7 RBaseX-0.2.4/RBaseX/R/Full.R | 9 RBaseX-0.2.4/RBaseX/R/GetIntercept.R |only RBaseX-0.2.4/RBaseX/R/GetSuccess.R |only RBaseX-0.2.4/RBaseX/R/More.R | 10 - RBaseX-0.2.4/RBaseX/R/Next.R | 10 - RBaseX-0.2.4/RBaseX/R/Options.R | 2 RBaseX-0.2.4/RBaseX/R/Query.R | 25 ++ RBaseX-0.2.4/RBaseX/R/QueryClass.R | 206 +++++++++++---------- RBaseX-0.2.4/RBaseX/R/RBaseX.R | 3 RBaseX-0.2.4/RBaseX/R/RbaseXClient.R | 204 ++++++++++----------- RBaseX-0.2.4/RBaseX/R/RestoreIntercept.R |only RBaseX-0.2.4/RBaseX/R/SetIntercept.R |only RBaseX-0.2.4/RBaseX/R/SetSuccess.R |only RBaseX-0.2.4/RBaseX/R/SocketClass.R |only RBaseX-0.2.4/RBaseX/R/Store.R | 3 RBaseX-0.2.4/RBaseX/R/input_to_raw.R |only RBaseX-0.2.4/RBaseX/R/result2frame.R |only RBaseX-0.2.4/RBaseX/R/result2matrix.R |only RBaseX-0.2.4/RBaseX/R/result2tibble.R |only RBaseX-0.2.4/RBaseX/inst |only RBaseX-0.2.4/RBaseX/man/Add.Rd | 7 RBaseX-0.2.4/RBaseX/man/Full.Rd | 7 RBaseX-0.2.4/RBaseX/man/GetIntercept.Rd |only RBaseX-0.2.4/RBaseX/man/GetSuccess.Rd |only RBaseX-0.2.4/RBaseX/man/More.Rd | 10 - RBaseX-0.2.4/RBaseX/man/Next.Rd | 10 - RBaseX-0.2.4/RBaseX/man/Options.Rd | 2 RBaseX-0.2.4/RBaseX/man/QueryClass.Rd | 123 ++++++------ RBaseX-0.2.4/RBaseX/man/RBaseX.Rd | 267 +++++++++++++++++++++++++++- RBaseX-0.2.4/RBaseX/man/RestoreIntercept.Rd |only RBaseX-0.2.4/RBaseX/man/SetIntercept.Rd |only RBaseX-0.2.4/RBaseX/man/SetSuccess.Rd |only RBaseX-0.2.4/RBaseX/man/SocketClass.Rd |only RBaseX-0.2.4/RBaseX/man/Store.Rd | 3 RBaseX-0.2.4/RBaseX/man/input_to_raw.Rd | 4 RBaseX-0.2.4/RBaseX/man/result2frame.Rd |only RBaseX-0.2.4/RBaseX/man/result2matrix.Rd |only RBaseX-0.2.4/RBaseX/man/result2tibble.Rd |only RBaseX-0.2.4/RBaseX/tests |only 45 files changed, 677 insertions(+), 329 deletions(-)
Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA')
and fuzzy sets ('fsQCA'), using a GUI - graphical user interface.
'QCA' is a methodology that bridges the qualitative and quantitative divide
in social science research. It uses a Boolean algorithm that results in a
minimal causal combination that explains a given phenomenon.
Author: Adrian Dusa [aut, cre, cph],
Ciprian Paduraru [ctb],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/gui/www/shared/jquery-AUTHORS.txt),
Vasil Dinkov [ctb, cph] (jquery.smartmenus.js library),
Dmitry Baranovskiy [ctb, cph] (raphael.js library),
Emmanuel Quentin [ctb, cph] (raphael.inline_text_editing.js library),
Jimmy Breck-McKye [ctb, cph] (raphael-paragraph.js library),
Alrik Thiem [aut] (from version 1.0-0 up to version 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 3.6 dated 2019-11-17 and 3.7 dated 2020-03-11
QCA-3.6/QCA/R/uninstall.R |only QCA-3.6/QCA/R/writePrimeimp.R |only QCA-3.6/QCA/data/LF.tab.gz |only QCA-3.6/QCA/data/d.BWB.tab.gz |only QCA-3.6/QCA/data/d.Bas.tab.gz |only QCA-3.6/QCA/data/d.Emm.tab.gz |only QCA-3.6/QCA/data/d.autonomy.tab.gz |only QCA-3.6/QCA/data/d.biodiversity.tab.gz |only QCA-3.6/QCA/data/d.health.tab.gz |only QCA-3.6/QCA/data/d.jobsecurity.tab.gz |only QCA-3.6/QCA/inst/gui/www/lib/shiny_0.12.2 |only QCA-3.6/QCA/inst/staticdocs/SOPexpression.html |only QCA-3.7/QCA/DESCRIPTION | 15 QCA-3.7/QCA/MD5 | 246 QCA-3.7/QCA/NAMESPACE | 30 QCA-3.7/QCA/R/XYplot.R | 54 QCA-3.7/QCA/R/Xplot.R | 2 QCA-3.7/QCA/R/allExpressions.R | 4 QCA-3.7/QCA/R/calibrate.R | 14 QCA-3.7/QCA/R/causalChain.R | 6 QCA-3.7/QCA/R/combint.R | 8 QCA-3.7/QCA/R/complexity.R |only QCA-3.7/QCA/R/createMatrix.R | 2 QCA-3.7/QCA/R/dimnames.R | 2 QCA-3.7/QCA/R/export.R | 2 QCA-3.7/QCA/R/findRows.R | 14 QCA-3.7/QCA/R/findSubsets.R | 2 QCA-3.7/QCA/R/findSupersets.R | 2 QCA-3.7/QCA/R/findTh.R | 2 QCA-3.7/QCA/R/findmin.R | 21 QCA-3.7/QCA/R/fuzzyand.R | 27 QCA-3.7/QCA/R/fuzzyor.R | 27 QCA-3.7/QCA/R/generate.R |only QCA-3.7/QCA/R/getRow.R | 2 QCA-3.7/QCA/R/getSolution.R | 13 QCA-3.7/QCA/R/makeChart.R | 11 QCA-3.7/QCA/R/minimize.R | 226 QCA-3.7/QCA/R/modelFit.R | 15 QCA-3.7/QCA/R/onAttach.R | 8 QCA-3.7/QCA/R/onUnload.R |only QCA-3.7/QCA/R/panel.R | 6 QCA-3.7/QCA/R/pof.R | 207 QCA-3.7/QCA/R/pofind.R | 25 QCA-3.7/QCA/R/print.R | 130 QCA-3.7/QCA/R/removeRedundants.R | 2 QCA-3.7/QCA/R/retention.R | 5 QCA-3.7/QCA/R/rowDominance.R | 2 QCA-3.7/QCA/R/runGUI.R | 2 QCA-3.7/QCA/R/solveChart.R | 16 QCA-3.7/QCA/R/sortMatrix.R | 2 QCA-3.7/QCA/R/sortVector.R | 2 QCA-3.7/QCA/R/string.R | 2 QCA-3.7/QCA/R/superSubset.R | 31 QCA-3.7/QCA/R/truthTable.R | 86 QCA-3.7/QCA/R/verifyQCA.R | 34 QCA-3.7/QCA/R/writeSolution.R | 2 QCA-3.7/QCA/data/CVF.tab.gz |binary QCA-3.7/QCA/data/Emme.tab.gz |binary QCA-3.7/QCA/data/HC.tab.gz |binary QCA-3.7/QCA/data/HarKem.RData |binary QCA-3.7/QCA/data/Krook.tab.gz |binary QCA-3.7/QCA/data/LF.tab.bz2 |only QCA-3.7/QCA/data/NF.tab.gz |binary QCA-3.7/QCA/data/d.BWB.tab.bz2 |only QCA-3.7/QCA/data/d.Bas.tab.bz2 |only QCA-3.7/QCA/data/d.Emm.tab.bz2 |only QCA-3.7/QCA/data/d.HK.RData |binary QCA-3.7/QCA/data/d.HMN.tab.gz |binary QCA-3.7/QCA/data/d.Kro.tab.gz |binary QCA-3.7/QCA/data/d.SA.tab.gz |binary QCA-3.7/QCA/data/d.autonomy.tab.bz2 |only QCA-3.7/QCA/data/d.biodiversity.tab.bz2 |only QCA-3.7/QCA/data/d.health.tab.bz2 |only QCA-3.7/QCA/data/d.jobsecurity.tab.bz2 |only QCA-3.7/QCA/data/d.partybans.RData |binary QCA-3.7/QCA/data/d.represent.tab.gz |binary QCA-3.7/QCA/data/d.socialsecurity.tab.gz |binary QCA-3.7/QCA/data/d.transport.tab.gz |binary QCA-3.7/QCA/data/d.women.tab.gz |binary QCA-3.7/QCA/inst/ChangeLog | 47 QCA-3.7/QCA/inst/gui/server.R | 75 QCA-3.7/QCA/inst/gui/www/index.html | 4 QCA-3.7/QCA/inst/gui/www/js/maincode.js | 795 +- QCA-3.7/QCA/inst/gui/www/js/utils.js | 2 QCA-3.7/QCA/inst/gui/www/lib/shiny_1.4.0 |only QCA-3.7/QCA/inst/staticdocs/CV.html | 4 QCA-3.7/QCA/inst/staticdocs/LegacyDatasets.html | 4 QCA-3.7/QCA/inst/staticdocs/Lipset.html | 4 QCA-3.7/QCA/inst/staticdocs/QCA.package.html | 13 QCA-3.7/QCA/inst/staticdocs/RS.html | 4 QCA-3.7/QCA/inst/staticdocs/SOPexpressions.html |only QCA-3.7/QCA/inst/staticdocs/XYplot.html | 34 QCA-3.7/QCA/inst/staticdocs/Xplot.html | 14 QCA-3.7/QCA/inst/staticdocs/calibrate.html | 47 QCA-3.7/QCA/inst/staticdocs/causalChain.html | 41 QCA-3.7/QCA/inst/staticdocs/chartFunctions.html | 94 QCA-3.7/QCA/inst/staticdocs/export.html | 4 QCA-3.7/QCA/inst/staticdocs/factorize.html | 149 QCA-3.7/QCA/inst/staticdocs/findRows.html | 13 QCA-3.7/QCA/inst/staticdocs/findTh.html | 13 QCA-3.7/QCA/inst/staticdocs/fuzzyops.html | 29 QCA-3.7/QCA/inst/staticdocs/generate.html |only QCA-3.7/QCA/inst/staticdocs/img/XYplot-15.svg |only QCA-3.7/QCA/inst/staticdocs/img/XYplot-8.svg | 4052 +++++++------- QCA-3.7/QCA/inst/staticdocs/implicantMatrixFunctions.html | 81 QCA-3.7/QCA/inst/staticdocs/index.html | 13 QCA-3.7/QCA/inst/staticdocs/intersection.html | 47 QCA-3.7/QCA/inst/staticdocs/minimize.html | 225 QCA-3.7/QCA/inst/staticdocs/modelFit.html | 105 QCA-3.7/QCA/inst/staticdocs/negate.html | 35 QCA-3.7/QCA/inst/staticdocs/pof.html | 113 QCA-3.7/QCA/inst/staticdocs/recode.html | 4 QCA-3.7/QCA/inst/staticdocs/retention.html | 4 QCA-3.7/QCA/inst/staticdocs/runGUI.html | 4 QCA-3.7/QCA/inst/staticdocs/subsetsAndSupersets.html | 111 QCA-3.7/QCA/inst/staticdocs/truthTable.html | 23 QCA-3.7/QCA/man/HC.Rd | 2 QCA-3.7/QCA/man/QCA-internal.Rd | 2 QCA-3.7/QCA/man/QCA.package.Rd | 4 QCA-3.7/QCA/man/XYplot.Rd | 2 QCA-3.7/QCA/man/Xplot.Rd | 2 QCA-3.7/QCA/man/causalChain.Rd | 10 QCA-3.7/QCA/man/chartFunctions.Rd | 73 QCA-3.7/QCA/man/complexity.Rd |only QCA-3.7/QCA/man/findRows.Rd | 12 QCA-3.7/QCA/man/findTh.Rd | 7 QCA-3.7/QCA/man/fuzzyops.Rd | 17 QCA-3.7/QCA/man/generate.Rd |only QCA-3.7/QCA/man/implicantMatrixFunctions.Rd | 22 QCA-3.7/QCA/man/minimize.Rd | 82 QCA-3.7/QCA/man/modelFit.Rd | 10 QCA-3.7/QCA/man/pof.Rd | 28 QCA-3.7/QCA/man/subsetsAndSupersets.Rd | 51 QCA-3.7/QCA/man/truthTable.Rd | 8 QCA-3.7/QCA/src/QCA.c | 731 +- QCA-3.7/QCA/src/registerDynamicSymbol.c | 2 QCA-3.7/QCA/src/truthTable.c | 2 137 files changed, 4053 insertions(+), 4530 deletions(-)
Title: Parse XML
Description: Work with XML files using a simple, consistent
interface. Built on top of the 'libxml2' C library.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Jeroen Ooms [aut],
RStudio [cph],
R Foundation [ctb] (Copy of R-project homepage cached as example)
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between xml2 versions 1.2.4 dated 2020-03-10 and 1.2.5 dated 2020-03-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++-- build/xml2.pdf |binary configure | 2 +- inst/doc/modification.html | 8 ++++---- 6 files changed, 17 insertions(+), 15 deletions(-)
Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the
'CDK', a Java framework for chemoinformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors and so on.
In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph],
Zachary Charlop-Powers [cre],
Emma Schymanski [ctb]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdk versions 3.4.7.2 dated 2019-12-21 and 3.5.0 dated 2020-03-11
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Title: Effects and Importances of Model Ingredients
Description: Collection of tools for assessment of feature importance and feature effects.
Key functions are:
feature_importance() for assessment of global level feature importance,
ceteris_paribus() for calculation of the what-if plots,
partial_dependence() for partial dependence plots,
conditional_dependence() for conditional dependence plots,
accumulated_dependence() for accumulated local effects plots,
aggregate_profiles() and cluster_profiles() for aggregation of ceteris paribus profiles,
generic print() and plot() for better usability of selected explainers,
generic plotD3() for interactive, D3 based explanations, and
generic describe() for explanations in natural language.
The package 'ingredients' is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>),
Adam Izdebski [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between ingredients versions 1.0 dated 2020-02-18 and 1.1 dated 2020-03-11
DESCRIPTION | 8 MD5 | 34 ++-- NEWS.md | 5 R/feature_importance.R | 5 R/plotD3_aggregated_profiles.R | 3 R/plotD3_ceteris_paribus.R | 3 R/plot_aggregated_profiles.R | 32 +++ R/plot_ceteris_paribus.R | 49 +++--- R/plot_feature_importance.R | 26 ++- inst/doc/vignette_describe.html | 194 ++++++++++++------------ inst/doc/vignette_simulated.html | 22 +- inst/doc/vignette_titanic.html | 24 +- man/feature_importance.Rd | 5 man/plot.aggregated_profiles_explainer.Rd | 8 man/plot.ceteris_paribus_explainer.Rd | 9 - man/plot.feature_importance_explainer.Rd | 11 + tests/testthat/test_cluster_profiles_describe.R | 3 tests/testthat/test_plot.R | 54 ++++++ 18 files changed, 311 insertions(+), 184 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from
National Water Information System (NWIS) <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>.
Both EPA and USGS water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>),
Robert Hirsch [aut] (<https://orcid.org/0000-0002-4534-075X>),
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Carr [ctb],
David Watkins [aut] (<https://orcid.org/0000-0002-7544-0700>)
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.5 dated 2019-06-05 and 2.7.6 dated 2020-03-11
DESCRIPTION | 8 MD5 | 126 ++++++------ NAMESPACE | 2 NEWS | 7 R/importNGWMN_wml2.R | 2 R/importRDB1.r | 6 R/importWQP.R | 22 +- R/readNGWMNdata.R | 6 R/readWQPdata.R | 67 +++--- R/readWQPqw.r | 40 +-- R/setAccess.R | 8 R/tabbedDataRetrievals.R | 2 build/vignette.rds |binary inst/CITATION | 2 inst/doc/dataRetrieval.html | 19 - man/addWaterYear.Rd | 66 +++--- man/calcWaterYear.Rd | 60 ++--- man/checkWQPdates.Rd | 48 ++-- man/constructNWISURL.Rd | 165 ++++++++-------- man/constructUseURL.Rd | 54 ++--- man/constructWQPURL.Rd | 102 +++++----- man/convertLists.Rd | 22 +- man/countyCd.Rd | 54 ++--- man/countyCdLookup.Rd | 52 ++--- man/dataRetrieval.Rd | 55 ++--- man/getQuerySummary.Rd | 26 +- man/getWebServiceData.Rd | 62 +++--- man/importNGWMN.Rd | 78 +++---- man/importRDB1.Rd | 185 +++++++++--------- man/importWQP.Rd | 92 ++++----- man/importWaterML1.Rd | 220 ++++++++++----------- man/importWaterML2.Rd | 66 +++--- man/pCodeToName.Rd | 66 +++--- man/parameterCdFile.Rd | 50 ++-- man/readNGWMNdata.Rd | 112 +++++----- man/readNGWMNlevels.Rd | 90 ++++---- man/readNGWMNsites.Rd | 72 +++---- man/readNWISdata.Rd | 300 ++++++++++++++--------------- man/readNWISdots.Rd | 22 +- man/readNWISdv.Rd | 167 ++++++++-------- man/readNWISgwl.Rd | 153 +++++++-------- man/readNWISmeas.Rd | 152 +++++++------- man/readNWISpCode.Rd | 82 ++++---- man/readNWISpeak.Rd | 145 +++++++------- man/readNWISqw.Rd | 253 ++++++++++++------------ man/readNWISrating.Rd | 112 +++++----- man/readNWISsite.Rd | 162 +++++++-------- man/readNWISstat.Rd | 159 ++++++++------- man/readNWISuse.Rd | 130 ++++++------ man/readNWISuv.Rd | 185 +++++++++--------- man/readWQPdata.Rd | 316 +++++++++++++++---------------- man/readWQPdots.Rd | 22 +- man/readWQPqw.Rd | 282 ++++++++++++++------------- man/renameNWISColumns.Rd | 174 +++++++++-------- man/setAccess.Rd | 68 +++--- man/stateCd.Rd | 52 ++--- man/stateCdLookup.Rd | 52 ++--- man/whatNWISdata.Rd | 148 +++++++------- man/whatNWISsites.Rd | 84 ++++---- man/whatWQPdata.Rd | 130 ++++++------ man/wqpSpecials.Rd | 222 ++++++++++----------- man/zeroPad.Rd | 64 +++--- tests/testthat/tests_general.R | 20 - tests/testthat/tests_userFriendly_fxns.R | 12 - 64 files changed, 2929 insertions(+), 2853 deletions(-)
Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging and variable selection for linear models,
generalized linear models and survival models (cox
regression).
Author: Adrian Raftery <raftery@uw.edu>, Jennifer Hoeting,
Chris Volinsky, Ian Painter, Ka Yee Yeung
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between BMA versions 3.18.11 dated 2019-11-22 and 3.18.12 dated 2020-03-11
ChangeLog | 5 DESCRIPTION | 11 MD5 | 8 R/bic.glm.R | 2141 ++++++++++++++++++++++++++++----------------------------- man/bic.glm.Rd | 480 ++++++------ 5 files changed, 1326 insertions(+), 1319 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-25 1.0.0
Title: Connect to the 'jamovi' Statistical Spreadsheet
Description: Methods to access data sets from the 'jamovi' statistical
spreadsheet (see <https://www.jamovi.org> for more information) from R.
Author: Jonathon Love [aut, cre]
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvconnect versions 1.0.9 dated 2019-09-01 and 1.2.8 dated 2020-03-11
DESCRIPTION | 12 - MD5 | 18 +- src/column.cpp | 325 +++++++++++++++++++++++++++++++++++++++++++++++++++++- src/column.h | 32 +++++ src/dataset.cpp | 21 +-- src/dataset.h | 4 src/level.h | 13 +- src/memorymap.cpp | 2 src/memorymap.h | 2 src/readdf.cpp | 40 +++++- 10 files changed, 427 insertions(+), 42 deletions(-)
Title: Basket Trial Analysis
Description: Implementation of multisource exchangeability models for Bayesian analyses of prespecified subgroups arising in the context of basket trial design and monitoring. The R 'basket' package facilitates implementation of the binary, symmetric multi-source exchangeability model (MEM) with posterior inference arising from both exact computation and Markov chain Monte Carlo sampling. Analysis output includes full posterior samples as well as posterior probabilities, highest posterior density (HPD) interval boundaries, effective sample sizes (ESS), mean and median estimations, posterior exchangeability probability matrices, and maximum a posteriori MEMs. In addition to providing "basketwise" analyses, the package includes similar calculations for "clusterwise" analyses for which subgroups are combined into meta-baskets, or clusters, using graphical clustering algorithms that treat the posterior exchangeability probabilities as edge weights. In addition plotting tools are provided to visualize basket and cluster densities as well as their exchangeability. References include Hyman, D.M., Puzanov, I., Subbiah, V., Faris, J.E., Chau, I., Blay, J.Y., Wolf, J., Raje, N.S., Diamond, E.L., Hollebecque, A. and Gervais, R (2015) <doi:10.1056/NEJMoa1502309>; Hobbs, B.P. and Landin, R. (2018) <doi:10.1002/sim.7893>; Hobbs, B.P., Kane, M.J., Hong, D.S. and Landin, R. (2018) <doi:10.1093/annonc/mdy457>; and Kaizer, A.M., Koopmeiners, J.S. and Hobbs, B.P. (2017) <doi:10.1093/biostatistics/kxx031>.
Author: Nan Chen [aut],
Brian Hobbs [aut],
Alex Kaizer [aut],
Michael J. Kane [aut, cre] (<https://orcid.org/0000-0003-1899-6662>)
Maintainer: Michael J. Kane <michael.kane@yale.edu>
Diff between basket versions 0.9.10 dated 2019-10-23 and 0.10.1 dated 2020-03-11
basket-0.10.1/basket/DESCRIPTION | 11 basket-0.10.1/basket/MD5 | 80 basket-0.10.1/basket/NAMESPACE | 227 +- basket-0.10.1/basket/NEWS.md | 9 basket-0.10.1/basket/R/accessors.r | 92 basket-0.10.1/basket/R/basket.r | 395 ++-- basket-0.10.1/basket/R/mem-exact.r | 881 ++++----- basket-0.10.1/basket/R/mem-mcmc.r | 832 ++++---- basket-0.10.1/basket/R/package-doc.r | 48 basket-0.10.1/basket/R/plot.r | 273 +- basket-0.10.1/basket/R/summary.r | 49 basket-0.10.1/basket/R/update.r | 78 basket-0.10.1/basket/R/util.r | 1130 +++++------- basket-0.10.1/basket/build/vignette.rds |binary basket-0.10.1/basket/inst/doc/using-the-basket-package.R | 23 basket-0.10.1/basket/inst/doc/using-the-basket-package.Rmd | 11 basket-0.10.1/basket/inst/doc/using-the-basket-package.html | 617 ++---- basket-0.10.1/basket/man/basket-package.Rd | 48 basket-0.10.1/basket/man/basket.Rd | 56 basket-0.10.1/basket/man/basket_map.Rd | 12 basket-0.10.1/basket/man/basket_pep.Rd | 10 basket-0.10.1/basket/man/cluster_baskets.Rd | 12 basket-0.10.1/basket/man/cluster_map.Rd | 12 basket-0.10.1/basket/man/cluster_membership.Rd | 12 basket-0.10.1/basket/man/cluster_pep.Rd | 10 basket-0.10.1/basket/man/get_seed.Rd |only basket-0.10.1/basket/man/mem_exact.Rd | 23 basket-0.10.1/basket/man/mem_mcmc.Rd | 27 basket-0.10.1/basket/man/plot_density.Rd | 12 basket-0.10.1/basket/man/plot_map.Rd | 36 basket-0.10.1/basket/man/plot_mem.Rd | 2 basket-0.10.1/basket/man/plot_pep.Rd | 41 basket-0.10.1/basket/man/plot_pep_graph.Rd |only basket-0.10.1/basket/man/update_p0.Rd | 8 basket-0.10.1/basket/tests/testthat/test-errors.r | 1 basket-0.10.1/basket/tests/testthat/test-exact.r | 152 - basket-0.10.1/basket/tests/testthat/test-mcmc.r | 192 +- basket-0.10.1/basket/tests/testthat/test-plot.r | 18 basket-0.10.1/basket/tests/testthat/test-update.r | 14 basket-0.10.1/basket/vignettes/using-the-basket-package.Rmd | 11 basket-0.10.1/basket/vignettes/vemu-basket.rds |only basket-0.9.10/basket/inst/code-from-brian |only basket-0.9.10/basket/inst/working-example |only basket-0.9.10/basket/vignettes/vemu_basket.rds |only 44 files changed, 2816 insertions(+), 2649 deletions(-)