Title: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME
Models
Description: At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling
activities in order to reduce the overall effort required for generating such plots.
For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox,
called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient
for publication and submissions using few lines of code.
Author: Amine Gassem [aut],
Bruno Bieth [aut],
Irina Baltcheva [aut],
Thomas Dumortier [aut],
Christian Bartels [aut],
Souvik Bhattacharya [aut],
Inga Ludwig [aut],
Ines Paule [aut],
Didier Renard [aut],
Matthew Fidler [ctb, cre] (<https://orcid.org/0000-0001-8538-6691>),
Qing Xi Ooi [ctr],
Novartis Pharma AG [cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between ggPMX versions 1.1 dated 2020-04-09 and 1.1.1 dated 2020-05-14
DESCRIPTION | 20 - MD5 | 125 +++++----- build/vignette.rds |binary inst/doc/ggPMX-guide.R | 116 ++++----- inst/doc/ggPMX-guide.pdf |binary inst/doc/ggPMX-nlmixr.R | 14 - inst/doc/ggPMX-nlmixr.html | 515 ++++++++++++------------------------------- man/add_draft.Rd | 10 man/distrib.Rd | 38 ++- man/eta_cov.Rd | 37 ++- man/eta_cov_plot.Rd | 31 ++ man/eta_distribution_plot.Rd | 36 ++- man/eta_pairs.Rd | 41 ++- man/facet_wrap_paginate.Rd | 29 +- man/figures |only man/get_cats.Rd | 20 + man/get_conts.Rd | 20 + man/get_covariates.Rd | 20 + man/get_data.Rd | 27 +- man/get_occ.Rd | 20 + man/get_plot.Rd | 20 + man/get_plot_config.Rd | 20 + man/get_strats.Rd | 20 + man/ggPMX.Rd | 1 man/individual.Rd | 38 ++- man/plot_names.Rd | 20 + man/plot_pmx.Rd | 23 + man/plot_pmx.distrib.Rd | 22 + man/plot_pmx.eta_cov.Rd | 22 + man/plot_pmx.eta_pairs.Rd | 22 + man/plot_pmx.individual.Rd | 22 + man/plot_pmx.pmx_dens.Rd | 22 + man/plot_pmx.pmx_gpar.Rd | 22 + man/plot_pmx.pmx_qq.Rd | 22 + man/plot_pmx.residual.Rd | 22 + man/plots.Rd | 20 + man/pmx.Rd | 44 +++ man/pmx_bloq.Rd | 11 man/pmx_comp_shrink.Rd | 10 man/pmx_dens.Rd | 12 - man/pmx_endpoint.Rd | 3 man/pmx_filter.Rd | 8 man/pmx_gpar.Rd | 23 + man/pmx_nlmixr.Rd | 3 man/pmx_plot_eta_matrix.Rd | 39 ++- man/pmx_plot_individual.Rd | 40 ++- man/pmx_plot_iwres_dens.Rd | 35 ++ man/pmx_plot_vpc.Rd | 51 +++- man/pmx_qq.Rd | 19 + man/pmx_qq_plot.Rd | 37 ++- man/pmx_report.Rd | 15 + man/pmx_settings.Rd | 13 - man/pmx_update.Rd | 34 ++ man/pmx_vpc.Rd | 31 +- man/pmx_vpc_bin.Rd | 11 man/pmx_vpc_ci.Rd | 21 + man/pmx_vpc_obs.Rd | 14 - man/pmx_vpc_pi.Rd | 22 + man/pmx_vpc_rug.Rd | 11 man/read_input.Rd | 14 + man/residual.Rd | 14 + man/residual_scatter.Rd | 34 ++ man/set_data.Rd | 20 + man/set_plot.Rd | 37 ++- 64 files changed, 1218 insertions(+), 865 deletions(-)
Title: Catalogue of Life Toolkit
Description: A programmatic interface to <http://sp2000.org.cn>, re-written based on an accompanying 'Species 2000' API. Access tables describing catalogue of the Chinese known species of animals, plants, fungi, micro-organisms, and more. This package also supports access to catalogue of life global <http://catalogueoflife.org> and catalogue of life Taiwan <http://taibnet.sinica.edu.tw/home_eng.php?>. The development of 'SP2000' package was supported by Yunnan University's Research Innovation Fund for Graduate Students.
Author: Liuyong Ding [aut, cre],
Minrui Huang [ctb],
Ke Yang [ctb],
Jun Wang [ctb],
Juan Tao [ctb],
Chengzhi Ding [ctb],
Daming He [ctb]
Maintainer: Liuyong Ding <ly_ding@126.com>
Diff between SP2000 versions 0.0.5 dated 2020-03-20 and 0.0.6 dated 2020-05-14
SP2000-0.0.5/SP2000/inst |only SP2000-0.0.6/SP2000/DESCRIPTION | 18 ++--- SP2000-0.0.6/SP2000/MD5 | 49 +++++++++------ SP2000-0.0.6/SP2000/NAMESPACE | 6 + SP2000-0.0.6/SP2000/NEWS |only SP2000-0.0.6/SP2000/R/api_key.R |only SP2000-0.0.6/SP2000/R/download_CoLChina.R | 19 +++--- SP2000-0.0.6/SP2000/R/find_Synonyms.R |only SP2000-0.0.6/SP2000/R/get_CoLGlobal.R |only SP2000-0.0.6/SP2000/R/get_CoLTaiwan.R |only SP2000-0.0.6/SP2000/R/get_province.R | 5 - SP2000-0.0.6/SP2000/R/get_top20.R | 4 - SP2000-0.0.6/SP2000/R/list_df.R | 19 ++---- SP2000-0.0.6/SP2000/R/open_URL.R | 16 ++--- SP2000-0.0.6/SP2000/R/search_checklist.R | 36 +++++++---- SP2000-0.0.6/SP2000/R/search_familyID.R | 40 +++++++------ SP2000-0.0.6/SP2000/R/search_taxonID.R | 83 +++++++++++++++------------ SP2000-0.0.6/SP2000/man/api_key.Rd |only SP2000-0.0.6/SP2000/man/download_CoLChina.Rd | 10 +-- SP2000-0.0.6/SP2000/man/find_Synonyms.Rd |only SP2000-0.0.6/SP2000/man/get_CoLGlobal.Rd |only SP2000-0.0.6/SP2000/man/get_CoLTaiwan.Rd |only SP2000-0.0.6/SP2000/man/get_province.Rd | 2 SP2000-0.0.6/SP2000/man/get_top20.Rd | 4 - SP2000-0.0.6/SP2000/man/list_df.Rd | 17 ++--- SP2000-0.0.6/SP2000/man/open_URL.Rd | 14 ++-- SP2000-0.0.6/SP2000/man/search_checklist.Rd | 17 ++--- SP2000-0.0.6/SP2000/man/search_familyID.Rd | 15 +--- SP2000-0.0.6/SP2000/man/search_taxonID.Rd | 36 ++++------- SP2000-0.0.6/SP2000/tests |only 30 files changed, 223 insertions(+), 187 deletions(-)
Title: API Wrapper for 'Ipeadata'
Description: Allows direct access to the macroeconomic,
financial and regional database maintained by
Brazilian Institute for Applied Economic Research ('Ipea').
This R package uses the 'Ipeadata' API. For more information,
see <http://www.ipeadata.gov.br/>.
Author: Luiz Eduardo S. Gomes [aut, cre],
Jessyka A. P. Goltara [ctb]
Maintainer: Luiz Eduardo S. Gomes <gomes.leduardo@gmail.com>
Diff between ipeadatar versions 0.1.0 dated 2019-02-22 and 0.1.1 dated 2020-05-14
ipeadatar-0.1.0/ipeadatar/R/utils-pipe.R |only ipeadatar-0.1.0/ipeadatar/man/pipe.Rd |only ipeadatar-0.1.1/ipeadatar/DESCRIPTION | 13 +++++++------ ipeadatar-0.1.1/ipeadatar/MD5 | 10 ++++------ ipeadatar-0.1.1/ipeadatar/NAMESPACE | 1 - ipeadatar-0.1.1/ipeadatar/R/ipeadata_pkg.R | 16 +++++++++------- ipeadatar-0.1.1/ipeadatar/man/available_countries.Rd | 2 ++ 7 files changed, 22 insertions(+), 20 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS and
Linux for finding font files that can then be used further by e.g. graphic
devices. The main use is intended to be from compiled code but 'systemfonts'
also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
(<https://orcid.org/0000-0002-5147-4711>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
Devon Govett [aut] (Author of font-manager),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between systemfonts versions 0.2.1 dated 2020-04-29 and 0.2.2 dated 2020-05-14
DESCRIPTION | 8 - MD5 | 32 ++-- NEWS.md | 6 R/shape_string.R | 3 build/vignette.rds |binary inst/doc/c_interface.Rmd | 98 +++++++++++-- inst/doc/c_interface.html | 62 +++++++- src/emoji.cpp | 10 - src/font_metrics.cpp | 20 +- src/ft_cache.cpp | 51 +++---- src/ft_cache.h | 2 src/string_metrics.cpp | 38 ++--- src/string_shape.cpp | 303 ++++++++++++++++++++++++++---------------- src/string_shape.h | 24 +-- src/systemfonts.cpp | 14 - src/unix/FontManagerLinux.cpp | 2 vignettes/c_interface.Rmd | 98 +++++++++++-- 17 files changed, 511 insertions(+), 260 deletions(-)
Title: Simple Visualisation with 'ggplot2' and 'leaflet' Wrappers
Description: Provides 'ggplot2' and 'leaflet' wrapper functions designed to simplify the creation of high quality graph and map visualisations. These functions only require inputs of data, variables and titles to provide beautiful interactive or image visualisations. However they allow for more flexibility if required. The intent is that high quality well-designed graphs and maps can be made more consistently with less effort, code and expertise than would otherwise be required.
Author: David Hodge [aut, cre] (<https://orcid.org/0000-0002-3868-7501>),
Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between simplevis versions 1.1.2 dated 2020-05-06 and 1.1.3 dated 2020-05-14
simplevis-1.1.2/simplevis/man/remove_plotly_buttons.Rd |only simplevis-1.1.3/simplevis/DESCRIPTION | 6 simplevis-1.1.3/simplevis/MD5 | 49 +++---- simplevis-1.1.3/simplevis/NAMESPACE | 4 simplevis-1.1.3/simplevis/NEWS.md | 9 + simplevis-1.1.3/simplevis/R/ggplot_hbar_fun.R | 34 +++-- simplevis-1.1.3/simplevis/R/ggplot_vbar_fun.R | 24 ++- simplevis-1.1.3/simplevis/R/other.R | 67 +++------- simplevis-1.1.3/simplevis/R/plotly.R |only simplevis-1.1.3/simplevis/inst/doc/simplevis.R | 30 ++-- simplevis-1.1.3/simplevis/inst/doc/simplevis.Rmd | 6 simplevis-1.1.3/simplevis/inst/doc/simplevis.html | 30 ++-- simplevis-1.1.3/simplevis/inst/shiny/template1/data/template1.zip |binary simplevis-1.1.3/simplevis/inst/shiny/template1/www/style.css | 2 simplevis-1.1.3/simplevis/inst/shiny/template2/data/template2.zip |binary simplevis-1.1.3/simplevis/inst/shiny/template2/www/style.css | 2 simplevis-1.1.3/simplevis/man/ggplot_hbar.Rd | 13 + simplevis-1.1.3/simplevis/man/ggplot_hbar_col.Rd | 4 simplevis-1.1.3/simplevis/man/ggplot_hbar_col_facet.Rd | 16 +- simplevis-1.1.3/simplevis/man/ggplot_hbar_facet.Rd | 4 simplevis-1.1.3/simplevis/man/ggplot_vbar.Rd | 14 +- simplevis-1.1.3/simplevis/man/ggplot_vbar_col.Rd | 4 simplevis-1.1.3/simplevis/man/ggplot_vbar_col_facet.Rd | 15 +- simplevis-1.1.3/simplevis/man/ggplot_vbar_facet.Rd | 4 simplevis-1.1.3/simplevis/man/plotly_order_legend.Rd |only simplevis-1.1.3/simplevis/man/plotly_remove_buttons.Rd |only simplevis-1.1.3/simplevis/man/plotly_reverse_legend.Rd |only simplevis-1.1.3/simplevis/vignettes/simplevis.Rmd | 6 28 files changed, 180 insertions(+), 163 deletions(-)
Title: The Serial Interface Package
Description: Enables reading and writing binary and ASCII data to
RS232/RS422/RS485 or any other virtual serial interface of the
computer.
Author: Martin Seilmayer
Maintainer: Martin Seilmayer <m.seilmayer@hzdr.de>
Diff between serial versions 2.1.4 dated 2019-06-04 and 3.0 dated 2020-05-14
serial-2.1.4/serial/R/serial.R |only serial-3.0/serial/DESCRIPTION | 10 - serial-3.0/serial/MD5 | 47 +++- serial-3.0/serial/NAMESPACE | 2 serial-3.0/serial/NEWS |only serial-3.0/serial/R/close.R |only serial-3.0/serial/R/flush.R |only serial-3.0/serial/R/init.R | 180 ++---------------- serial-3.0/serial/R/isOpen.R |only serial-3.0/serial/R/listPorts.R | 189 ++++++++++--------- serial-3.0/serial/R/nBytes.R |only serial-3.0/serial/R/open.R |only serial-3.0/serial/R/pkgname.R | 193 ++++++++++---------- serial-3.0/serial/R/print.R |only serial-3.0/serial/R/read.R |only serial-3.0/serial/R/summary.R |only serial-3.0/serial/R/write.R |only serial-3.0/serial/man/close.serialConnection.Rd | 2 serial-3.0/serial/man/flush.serialConnection.Rd | 50 ++--- serial-3.0/serial/man/isOpen.Rd | 2 serial-3.0/serial/man/isOpen.default.Rd | 2 serial-3.0/serial/man/isOpen.serialConnection.Rd | 2 serial-3.0/serial/man/listPorts.Rd | 103 +++++----- serial-3.0/serial/man/nBytesInQueue.Rd | 46 ++-- serial-3.0/serial/man/open.serialConnection.Rd | 2 serial-3.0/serial/man/print.serialConnection.Rd |only serial-3.0/serial/man/read.serialConnection.Rd | 86 ++++----- serial-3.0/serial/man/serial.Rd | 200 ++++++++++---------- serial-3.0/serial/man/serialConnection.Rd | 210 +++++++++++----------- serial-3.0/serial/man/summary.serialConnection.Rd |only serial-3.0/serial/man/write.serialConnection.Rd | 80 ++++---- 31 files changed, 660 insertions(+), 746 deletions(-)
Title: Interactive Maps Using 'Mapbox GL JS' and 'Deck.gl'
Description: Provides a mechanism to plot an interactive map using 'Mapbox GL'
(<https://www.mapbox.com/mapbox-gl-js/api/>), a javascript library for interactive maps,
and 'Deck.gl' (<http://deck.gl/#/>), a javascript library which uses 'WebGL' for
visualising large data sets.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between mapdeck versions 0.3.2 dated 2020-04-05 and 0.3.3 dated 2020-05-14
DESCRIPTION | 12 ++-- MD5 | 65 +++++++++++++----------- NAMESPACE | 3 + NEWS.md | 7 ++ R/map_layer_animated_line.R |only R/map_layer_column.R | 17 ++++-- R/map_layer_greatcircle.R | 1 R/map_layer_path.R | 25 ++++++++- R/map_layer_pointcloud.R | 4 + R/map_layer_scatterplot.R | 4 + R/map_layer_terrain.R |only R/mapdeck_dependencies.R | 6 +- R/mapdeck_map.R | 12 ++++ R/mapdeck_map_utilities.R | 4 - inst/doc/mapdeck.Rmd | 3 + inst/doc/mapdeck.html | 13 ++-- inst/htmlwidgets/lib/arc/arc_animated.js | 17 ------ inst/htmlwidgets/lib/column/column.js | 4 - inst/htmlwidgets/lib/geojson/geojson.js | 22 +++++--- inst/htmlwidgets/lib/line/line_animated.js |only inst/htmlwidgets/lib/mapbox-gl.js | 6 +- inst/htmlwidgets/lib/path/path.js | 12 ++-- inst/htmlwidgets/lib/pointcloud/pointcloud.js | 4 - inst/htmlwidgets/lib/scatterplot/scatterplot.js | 4 - inst/htmlwidgets/lib/terrain |only inst/htmlwidgets/mapdeck.js | 16 ++++- inst/htmlwidgets/mapdeck_functions.js | 2 inst/include/mapdeck_defaults.hpp | 5 + man/add_animated_line.Rd |only man/add_path.Rd | 23 ++++++++ man/add_terrain.Rd |only man/clear.Rd | 20 ++++--- man/mapdeck.Rd | 12 ++++ src/path.cpp | 3 - tests/testthat/test-layer_path.R | 4 - vignettes/img/hexagons.png |only vignettes/mapdeck.Rmd | 3 + 37 files changed, 226 insertions(+), 107 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 7.12.0 dated 2020-03-25 and 7.12.1 dated 2020-05-14
DESCRIPTION | 10 +- MD5 | 68 ++++++++--------- NAMESPACE | 3 NEWS.md | 18 ++++ R/decorate_storr.R | 4 - R/deps.R | 21 +++-- R/drake_plan.R | 4 - R/dynamic.R | 5 + R/local_build.R | 12 ++- R/manage_memory.R | 2 R/transform_plan.R | 39 ++++++++-- R/walk_code.R | 7 + build/drake.pdf |binary inst/WORDLIST | 5 + inst/testing/cran-checklist.md | 35 ++++----- man/drake_plan.Rd | 8 +- man/figures/unnamed-chunk-13-1.png |binary man/figures/unnamed-chunk-18-1.png |binary man/figures/unnamed-chunk-19-1.png |binary man/figures/unnamed-chunk-9-1.png |binary man/transformations.Rd | 11 +- man/type_sum.expr_list.Rd | 2 tests/testthat/test-4-history.R | 2 tests/testthat/test-5-examples.R | 1 tests/testthat/test-6-analysis.R | 18 ++++ tests/testthat/test-6-memory.R | 7 + tests/testthat/test-6-plans.R | 12 +++ tests/testthat/test-7-config-utils.R | 1 tests/testthat/test-7-deprecate.R | 5 - tests/testthat/test-7-dsl.R | 122 ++++++++++++++++++++++++++++++-- tests/testthat/test-7-files.R | 2 tests/testthat/test-7-recovery.R | 1 tests/testthat/test-8-cache.R | 4 + tests/testthat/test-8-decorated-storr.R | 12 +++ tests/testthat/test-9-dynamic.R | 29 +++++++ 35 files changed, 373 insertions(+), 97 deletions(-)
Title: Conditional Formatting in Data Frames
Description: Apply and visualize conditional formatting to data frames in R.
It renders a data frame with cells formatted according to
criteria defined by rules, using a tidy evaluation syntax. The table is
printed either opening a web browser or within the 'RStudio' viewer if
available. The conditional formatting rules allow to highlight cells
matching a condition or add a gradient background to a given column. This
package supports both 'HTML' and 'LaTeX' outputs in 'knitr' reports, and
exporting to an 'xlsx' file.
Author: Sergio Oller Moreno [aut, cph, cre]
(<https://orcid.org/0000-0002-8994-1549>)
Maintainer: Sergio Oller Moreno <sergioller@gmail.com>
Diff between condformat versions 0.8.0 dated 2018-10-29 and 0.9.0 dated 2020-05-14
condformat-0.8.0/condformat/man/plus-.condformat_tbl.Rd |only condformat-0.8.0/condformat/man/reexports.Rd |only condformat-0.8.0/condformat/man/rule_fill_discrete_.Rd |only condformat-0.8.0/condformat/man/rule_fill_discrete_old.Rd |only condformat-0.8.0/condformat/man/rule_fill_gradient2_.Rd |only condformat-0.8.0/condformat/man/rule_fill_gradient2_old.Rd |only condformat-0.8.0/condformat/man/rule_fill_gradient_.Rd |only condformat-0.8.0/condformat/man/rule_fill_gradient_old.Rd |only condformat-0.8.0/condformat/man/show_columns_.Rd |only condformat-0.8.0/condformat/man/show_columns_old.Rd |only condformat-0.8.0/condformat/man/show_rows_old.Rd |only condformat-0.8.0/condformat/tests/testthat/test_rendering.R |only condformat-0.8.0/condformat/tests/testthat/test_rule_css.R |only condformat-0.8.0/condformat/tests/testthat/test_rule_fill_bar.R |only condformat-0.8.0/condformat/tests/testthat/test_rule_fill_discrete.R |only condformat-0.8.0/condformat/tests/testthat/test_rule_fill_gradient.R |only condformat-0.8.0/condformat/tests/testthat/test_rule_text_bold.R |only condformat-0.8.0/condformat/tests/testthat/test_rule_text_color.R |only condformat-0.8.0/condformat/tests/testthat/test_show.R |only condformat-0.8.0/condformat/tests/testthat/test_theme_htmlTable.R |only condformat-0.9.0/condformat/DESCRIPTION | 23 condformat-0.9.0/condformat/MD5 | 130 +-- condformat-0.9.0/condformat/NAMESPACE | 10 condformat-0.9.0/condformat/NEWS.md | 26 condformat-0.9.0/condformat/R/condformat.R | 64 - condformat-0.9.0/condformat/R/condformat_render.R | 2 condformat-0.9.0/condformat/R/render_html.R | 10 condformat-0.9.0/condformat/R/render_xlsx.R | 136 ++- condformat-0.9.0/condformat/R/rule_css.R | 7 condformat-0.9.0/condformat/R/rule_fill_bar.R | 9 condformat-0.9.0/condformat/R/rule_fill_discrete.R | 206 ----- condformat-0.9.0/condformat/R/rule_fill_gradient.R | 173 ----- condformat-0.9.0/condformat/R/rule_fill_gradient2.R | 183 ----- condformat-0.9.0/condformat/R/rule_helper.R | 62 - condformat-0.9.0/condformat/R/rule_text_bold.R | 7 condformat-0.9.0/condformat/R/rule_text_color.R | 7 condformat-0.9.0/condformat/R/show_columns.R | 137 --- condformat-0.9.0/condformat/R/show_rows.R | 72 -- condformat-0.9.0/condformat/R/theme_caption.R | 5 condformat-0.9.0/condformat/R/theme_grob.R | 5 condformat-0.9.0/condformat/R/theme_htmlTable.R | 31 condformat-0.9.0/condformat/R/theme_htmlWidget.R | 5 condformat-0.9.0/condformat/R/theme_kable.R | 5 condformat-0.9.0/condformat/R/utils-pipe.R |only condformat-0.9.0/condformat/README.md | 59 - condformat-0.9.0/condformat/build/vignette.rds |binary condformat-0.9.0/condformat/inst/doc/introduction.R | 2 condformat-0.9.0/condformat/inst/doc/introduction.html | 344 ++++++++-- condformat-0.9.0/condformat/inst/shinyexample/server.R | 2 condformat-0.9.0/condformat/man/cf_field_to_gtable.Rd | 10 condformat-0.9.0/condformat/man/condformat.Rd | 15 condformat-0.9.0/condformat/man/condformat2excel.Rd | 11 condformat-0.9.0/condformat/man/condformat2html.Rd | 5 condformat-0.9.0/condformat/man/condformat2widget.Rd | 5 condformat-0.9.0/condformat/man/figures/README-fig-example-1.png |binary condformat-0.9.0/condformat/man/pipe.Rd |only condformat-0.9.0/condformat/man/print.condformat_tbl.Rd | 13 condformat-0.9.0/condformat/man/rule_css.Rd | 23 condformat-0.9.0/condformat/man/rule_fill_bar.Rd | 34 condformat-0.9.0/condformat/man/rule_fill_discrete.Rd | 46 - condformat-0.9.0/condformat/man/rule_fill_gradient.Rd | 44 - condformat-0.9.0/condformat/man/rule_fill_gradient2.Rd | 47 - condformat-0.9.0/condformat/man/rule_text_bold.Rd | 23 condformat-0.9.0/condformat/man/rule_text_color.Rd | 23 condformat-0.9.0/condformat/man/show_columns.Rd | 34 condformat-0.9.0/condformat/man/show_rows.Rd | 15 condformat-0.9.0/condformat/man/theme_caption.Rd | 5 condformat-0.9.0/condformat/man/theme_grob.Rd | 5 condformat-0.9.0/condformat/man/theme_htmlTable.Rd | 6 condformat-0.9.0/condformat/man/theme_htmlWidget.Rd | 5 condformat-0.9.0/condformat/man/theme_kable.Rd | 5 condformat-0.9.0/condformat/tests/testthat/test-print-condformat.R |only condformat-0.9.0/condformat/tests/testthat/test-render-excel.R |only condformat-0.9.0/condformat/tests/testthat/test-render-html.R |only condformat-0.9.0/condformat/tests/testthat/test-render-latex.R |only condformat-0.9.0/condformat/tests/testthat/test-rule-css.R |only condformat-0.9.0/condformat/tests/testthat/test-rule-fill-bar.R |only condformat-0.9.0/condformat/tests/testthat/test-rule-fill-discrete.R |only condformat-0.9.0/condformat/tests/testthat/test-rule-fill-gradient.R |only condformat-0.9.0/condformat/tests/testthat/test-rule-text-bold.R |only condformat-0.9.0/condformat/tests/testthat/test-rule-text-color.R |only condformat-0.9.0/condformat/tests/testthat/test-show-columns-and-rows.R |only condformat-0.9.0/condformat/tests/testthat/test-theme-htmlTable.R |only 83 files changed, 945 insertions(+), 1151 deletions(-)
Title: Phylogenetic Comparative Methods for High-Dimensional Traits
Description: Tools for studying the evolution of high-dimensional traits
(morphometric, function-valued, etc.) including ancestral state reconstruction,
estimating phylogenetic signal, and assessing correlated trait evolution. Visit
<http://www.phylocurve.org> for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between phylocurve versions 2.0.10 dated 2019-12-13 and 2.1.1 dated 2020-05-14
DESCRIPTION | 14 - MD5 | 46 +++--- NAMESPACE | 1 R/fast_geomorph_functions.R | 6 R/phylocurve.R | 12 - inst/CITATION | 20 +- man/GP.fit.Rd | 112 +++++++-------- man/K.mult.Rd | 90 ++++++------ man/compare.models.Rd | 122 ++++++++-------- man/fast.geomorph.phylo.integration.Rd | 136 +++++++++--------- man/get.aligned.function.data.Rd | 90 ++++++------ man/get.tip.coefficients.Rd | 106 +++++++------- man/multipic.Rd | 240 ++++++++++++++++----------------- man/nonlinear.fit.Rd | 118 ++++++++-------- man/paint.edges.Rd | 86 +++++------ man/phylocurve-package.Rd | 4 man/phylocurve.Rd | 148 ++++++++++---------- man/phylocurve.generalized.Rd | 108 +++++++------- man/phylocurve.trim.Rd | 120 ++++++++-------- man/polynomial.fit.Rd | 118 ++++++++-------- man/prep_multipic.Rd | 200 +++++++++++++-------------- man/print.evo.model.Rd | 30 ++-- man/sim.curves.Rd | 100 ++++++------- man/sim.traits.Rd | 134 +++++++++--------- 24 files changed, 1080 insertions(+), 1081 deletions(-)
Title: Tools for Handling Spatial Objects
Description: Set of tools for manipulating geographic data. It includes binary access to 'GSHHG' shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat', 'maps', and others.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Nick Bearman [ctb],
Hans-Jörg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stéphane Dray [ctb],
David Forrest [ctb],
Michael Friendly [ctb],
Patrick Giraudoux [ctb],
Duncan Golicher [ctb],
Virgilio Gómez Rubio [ctb],
Patrick Hausmann [ctb],
Karl Ove Hufthammer [ctb],
Thomas Jagger [ctb],
Kent Johnson [ctb],
Sebastian Luque [ctb],
Don MacQueen [ctb],
Andrew Niccolai [ctb],
Edzer Pebesma [ctb],
Oscar Perpiñán Lamigueiro [ctb],
Ethan Plunkett [ctb],
Tom Short [ctb],
Greg Snow [ctb],
Ben Stabler [ctb],
Murray Stokely [ctb],
Rolf Turner [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between maptools versions 0.9-9 dated 2019-12-01 and 1.0-1 dated 2020-05-14
ChangeLog | 24 +++++++++++++ DESCRIPTION | 12 +++--- MD5 | 22 ++++++------ R/SpatialPolys-methods.R | 24 ++++++++++--- R/as.linnet.SL.R | 62 +++++++++++++++++----------------- R/shapelib.R | 75 ++++++++++++++++++++++++++++++++++++++++++ R/sp_bind.R | 6 +-- build/vignette.rds |binary inst/ChangeLog | 12 ++++++ inst/doc/combine_maptools.R | 1 inst/doc/combine_maptools.pdf |binary man/pal2SpatialPolygons.Rd | 28 +++++++-------- 12 files changed, 195 insertions(+), 71 deletions(-)
Title: Penalized Transformation Models
Description: Partially penalized versions of specific transformation models
implemented in package 'mlt'. Available models include a fully parametric version
of the Cox model, other parametric survival models (Weibull, etc.), models for
binary and ordered categorical variables, normal and transformed-normal (Box-Cox type)
linear models, and continuous outcome logistic regression. Hyperparameter tuning
is facilitated through model-based optimization functionalities from package 'mlrMBO'.
The accompanying vignette describes the methodology used in 'tramnet' in detail.
Transformation models and model-based optimization are described in
Hothorn et al. (2019) <doi:10.1111/sjos.12291> and
Bischl et al. (2016) <arxiv:1703.03373>, respectively.
Author: Lucas Kook [cre, aut],
Balint Tamasi [ctb],
Sandra Siegfried [ctb],
Samuel Pawel [ctb],
Torsten Hothorn [ctb] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Lucas Kook <lucasheinrich.kook@uzh.ch>
Diff between tramnet versions 0.0-2 dated 2020-03-20 and 0.0-3 dated 2020-05-14
DESCRIPTION | 22 +++++++++++----------- MD5 | 7 ++++--- build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/tramnet.pdf |binary 5 files changed, 15 insertions(+), 14 deletions(-)
Title: Spatial Early Warning Signals of Ecosystem Degradation
Description: Tools to compute and assess significance of early-warnings signals (EWS) of ecosystem degradation on raster data sets. EWS are metrics derived from the observed spatial structure of an ecosystem -- e.g. spatial autocorrelation -- that increase before an ecosystem undergoes a non-linear transition (Genin et al. (2018) <doi:10.1111/2041-210X.13058>).
Author: Alain Danet, Alexandre Genin, Vishwesha Guttal, Sonia Kefi,
Sabiha Majumder, Sumithra Sankaran, Florian Schneider
Maintainer: Alexandre Genin <alexandre.genin@umontpellier.fr>
Diff between spatialwarnings versions 1.3.1 dated 2018-12-20 and 2.0.0 dated 2020-05-14
spatialwarnings-1.3.1/spatialwarnings/R/combined_sews.R |only spatialwarnings-1.3.1/spatialwarnings/R/imports.R |only spatialwarnings-1.3.1/spatialwarnings/R/indicator_moran.R |only spatialwarnings-1.3.1/spatialwarnings/R/indicator_sdr.R |only spatialwarnings-1.3.1/spatialwarnings/R/indicator_skewness.R |only spatialwarnings-1.3.1/spatialwarnings/R/indicator_variance.R |only spatialwarnings-1.3.1/spatialwarnings/R/task_custom.R |only spatialwarnings-1.3.1/spatialwarnings/R/task_generic_indic_indictest.R |only spatialwarnings-1.3.1/spatialwarnings/R/task_generic_indic_indictest_methods.R |only spatialwarnings-1.3.1/spatialwarnings/R/task_generic_indic_methods.R |only spatialwarnings-1.3.1/spatialwarnings/R/task_spectral_indic_indictest.R |only spatialwarnings-1.3.1/spatialwarnings/R/task_spectral_indic_indictest_methods.R |only spatialwarnings-1.3.1/spatialwarnings/R/task_spectral_indic_plot.R |only spatialwarnings-1.3.1/spatialwarnings/R/zzz.R |only spatialwarnings-1.3.1/spatialwarnings/tests/testthat/test-indicators.R |only spatialwarnings-2.0.0/spatialwarnings/DESCRIPTION | 18 spatialwarnings-2.0.0/spatialwarnings/MD5 | 181 ++-- spatialwarnings-2.0.0/spatialwarnings/NAMESPACE | 59 - spatialwarnings-2.0.0/spatialwarnings/NEWS | 91 +- spatialwarnings-2.0.0/spatialwarnings/R/000_package_options.R | 18 spatialwarnings-2.0.0/spatialwarnings/R/RcppExports.R | 10 spatialwarnings-2.0.0/spatialwarnings/R/checks.R | 61 - spatialwarnings-2.0.0/spatialwarnings/R/convert_matrix.R |only spatialwarnings-2.0.0/spatialwarnings/R/deprecation.R | 441 +++++++++- spatialwarnings-2.0.0/spatialwarnings/R/display_matrix.R |only spatialwarnings-2.0.0/spatialwarnings/R/fitpsd.R | 275 +++--- spatialwarnings-2.0.0/spatialwarnings/R/forestgap.R | 2 spatialwarnings-2.0.0/spatialwarnings/R/helpers.R | 25 spatialwarnings-2.0.0/spatialwarnings/R/indicator_plrange.R | 38 spatialwarnings-2.0.0/spatialwarnings/R/indicator_psdtype.R | 10 spatialwarnings-2.0.0/spatialwarnings/R/indictest.R | 74 + spatialwarnings-2.0.0/spatialwarnings/R/label.R | 25 spatialwarnings-2.0.0/spatialwarnings/R/null_model_helpers.R | 291 +++++- spatialwarnings-2.0.0/spatialwarnings/R/roxygen-tags.R | 13 spatialwarnings-2.0.0/spatialwarnings/R/simple_indic.R |only spatialwarnings-2.0.0/spatialwarnings/R/simple_indic_indictest.R | 224 +++-- spatialwarnings-2.0.0/spatialwarnings/R/simple_indic_methods.R | 52 - spatialwarnings-2.0.0/spatialwarnings/R/spatialwarnings.R | 83 - spatialwarnings-2.0.0/spatialwarnings/R/task_flowlength.R | 54 - spatialwarnings-2.0.0/spatialwarnings/R/task_generic_indic.R | 323 +++++-- spatialwarnings-2.0.0/spatialwarnings/R/task_kbdm.R | 41 spatialwarnings-2.0.0/spatialwarnings/R/task_patch_indic.R | 74 + spatialwarnings-2.0.0/spatialwarnings/R/task_patch_indic_indictest.R |only spatialwarnings-2.0.0/spatialwarnings/R/task_patch_indic_methods.R | 113 +- spatialwarnings-2.0.0/spatialwarnings/R/task_spectral_indic.R | 185 +++- spatialwarnings-2.0.0/spatialwarnings/R/task_spectral_indic_methods.R | 278 ++++-- spatialwarnings-2.0.0/spatialwarnings/build |only spatialwarnings-2.0.0/spatialwarnings/inst/CITATION | 3 spatialwarnings-2.0.0/spatialwarnings/man/arizona.Rd | 6 spatialwarnings-2.0.0/spatialwarnings/man/convert_to_matrix.Rd |only spatialwarnings-2.0.0/spatialwarnings/man/create_indicator.Rd | 53 - spatialwarnings-2.0.0/spatialwarnings/man/display_matrix.Rd |only spatialwarnings-2.0.0/spatialwarnings/man/extract_spectrum.Rd |only spatialwarnings-2.0.0/spatialwarnings/man/flowlength_sews.Rd | 12 spatialwarnings-2.0.0/spatialwarnings/man/forestgap.Rd | 10 spatialwarnings-2.0.0/spatialwarnings/man/generic_sews.Rd | 55 - spatialwarnings-2.0.0/spatialwarnings/man/generic_spews-deprecated.Rd | 10 spatialwarnings-2.0.0/spatialwarnings/man/indicator_moran.Rd | 12 spatialwarnings-2.0.0/spatialwarnings/man/indicator_psdtype.Rd | 13 spatialwarnings-2.0.0/spatialwarnings/man/indicator_sdr.Rd | 13 spatialwarnings-2.0.0/spatialwarnings/man/indicator_skewness.Rd | 15 spatialwarnings-2.0.0/spatialwarnings/man/indicator_variance.Rd | 14 spatialwarnings-2.0.0/spatialwarnings/man/indictest.Rd | 59 - spatialwarnings-2.0.0/spatialwarnings/man/kbdm_sews.Rd | 7 spatialwarnings-2.0.0/spatialwarnings/man/label.Rd | 26 spatialwarnings-2.0.0/spatialwarnings/man/patchdistr_sews.Rd | 42 spatialwarnings-2.0.0/spatialwarnings/man/patchdistr_sews_plot.Rd | 18 spatialwarnings-2.0.0/spatialwarnings/man/patchdistr_sews_predict.Rd | 7 spatialwarnings-2.0.0/spatialwarnings/man/patchdistr_spews-deprecated.Rd | 13 spatialwarnings-2.0.0/spatialwarnings/man/patchsizes.Rd | 14 spatialwarnings-2.0.0/spatialwarnings/man/plot_spectrum.Rd |only spatialwarnings-2.0.0/spatialwarnings/man/raw_cg_moran.Rd |only spatialwarnings-2.0.0/spatialwarnings/man/raw_cg_skewness.Rd | 77 + spatialwarnings-2.0.0/spatialwarnings/man/raw_cg_variance.Rd |only spatialwarnings-2.0.0/spatialwarnings/man/raw_flowlength_uniform.Rd | 2 spatialwarnings-2.0.0/spatialwarnings/man/raw_kbdm.Rd | 2 spatialwarnings-2.0.0/spatialwarnings/man/raw_plrange.Rd | 27 spatialwarnings-2.0.0/spatialwarnings/man/raw_sdr.Rd |only spatialwarnings-2.0.0/spatialwarnings/man/reexports.Rd |only spatialwarnings-2.0.0/spatialwarnings/man/rspectrum.Rd | 2 spatialwarnings-2.0.0/spatialwarnings/man/serengeti.Rd | 7 spatialwarnings-2.0.0/spatialwarnings/man/simple_sews_methods.Rd |only spatialwarnings-2.0.0/spatialwarnings/man/spatialwarnings.Rd | 77 - spatialwarnings-2.0.0/spatialwarnings/man/spectral_sews.Rd | 44 spatialwarnings-2.0.0/spatialwarnings/man/spectral_spews-deprecated.Rd | 5 spatialwarnings-2.0.0/spatialwarnings/man/xmin_estim.Rd | 3 spatialwarnings-2.0.0/spatialwarnings/src/RcppExports.cpp | 36 spatialwarnings-2.0.0/spatialwarnings/src/coarse_graining.cpp | 22 spatialwarnings-2.0.0/spatialwarnings/src/headers.h | 13 spatialwarnings-2.0.0/spatialwarnings/src/label.cpp | 88 - spatialwarnings-2.0.0/spatialwarnings/src/norm_constants.cpp | 71 + spatialwarnings-2.0.0/spatialwarnings/src/rspectrum.cpp | 2 spatialwarnings-2.0.0/spatialwarnings/src/skewness.cpp | 9 spatialwarnings-2.0.0/spatialwarnings/tests/testthat.R | 7 spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-custom_indicator.R | 20 spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-deprecated.R | 19 spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-display_matrix.R |only spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-flowlength.R | 2 spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-indicator_values-plosone.R | 85 + spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-indicator_values.R | 255 ++--- spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-kbdm.R | 17 spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-nullfun.R |only spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-parallelism.R |only spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-psdfit.R | 162 ++- spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-size-reporting.R |only spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-skewness.R | 8 spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-workflows.R | 68 - spatialwarnings-2.0.0/spatialwarnings/tests/testthat/test-xminest.R | 26 108 files changed, 3104 insertions(+), 1513 deletions(-)
More information about spatialwarnings at CRAN
Permanent link
Title: Statistical Inference for Systems of Ordinary Differential
Equations using Separable Integral-Matching
Description: Implements statistical inference for systems of ordinary differential equations,
that uses the integral-matching criterion and takes advantage of the separability of parameters,
in order to obtain initial parameter estimates for nonlinear least squares optimization.
Dattner & Yaari (2018) <arXiv:1807.04202>.
Dattner et al. (2017) <doi:10.1098/rsif.2016.0525>.
Dattner & Klaassen (2015) <doi:10.1214/15-EJS1053>.
Author: Itai Dattner [aut],
Rami Yaari [aut, cre]
Maintainer: Rami Yaari <ramiyaari@gmail.com>
Diff between simode versions 1.1.9 dated 2020-05-13 and 1.2.0 dated 2020-05-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/utils.R | 1 + README.md | 4 ++-- inst/simode-manual.pdf |binary 5 files changed, 11 insertions(+), 10 deletions(-)
Title: Extract, Analyze and Visualize Signatures for Genomic Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff,
et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Tao Wu [aut, ctb],
Ziyu Tao [aut, ctb],
Geoffrey Macintyre [ctb],
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 1.0.3 dated 2020-04-30 and 1.0.5 dated 2020-05-14
DESCRIPTION | 12 +- MD5 | 72 +++++++++------- NAMESPACE | 7 + NEWS.md | 13 +++ R/generate_matrices.R | 5 + R/get_bayesian_result.R | 1 R/get_sig_similarity.R | 56 +++++++------ R/helper_fit_cn_components.R | 5 - R/helper_sort_signature.R | 6 + R/read_copynumber.R | 4 R/show_catalogue.R | 2 R/show_cosmic_signatures.R | 53 ++++++++---- R/show_sig_bootstrap.R |only R/show_sig_fit.R |only R/show_sig_profile.R | 133 ++++++++++++++++++++++++++++--- R/sig_auto_extract.R | 4 R/sig_extract.R | 9 -- R/sig_fit.R | 76 +++++++++++------ R/sig_fit_bootstrap.R | 20 +++- R/sig_fit_bootstrap_batch.R |only R/sig_tally.R | 88 +++++++++++++------- R/utils-tidy-eval.R | 6 - R/utils.R | 71 ++++++++++++---- README.md | 17 +++ inst/extdata/DBS_signatures.rds |only inst/extdata/ID_signatures.rds |only man/figures/README-unnamed-chunk-3-1.png |only man/figures/README-unnamed-chunk-4-1.png |only man/get_sig_similarity.Rd | 6 - man/read_copynumber.Rd | 3 man/show_catalogue.Rd | 4 man/show_cosmic_sig_profile.Rd | 2 man/show_sig_bootstrap.Rd |only man/show_sig_fit.Rd |only man/show_sig_profile.Rd | 8 - man/sig_auto_extract.Rd | 4 man/sig_fit.Rd | 18 +++- man/sig_fit_bootstrap.Rd | 11 ++ man/sig_fit_bootstrap_batch.Rd |only man/sig_tally.Rd | 2 man/tidyeval.Rd | 1 man/use_color_style.Rd | 5 - 42 files changed, 519 insertions(+), 205 deletions(-)
Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications.
Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
David Granjon [aut],
Ian Fellows [ctb] (Methods for mutating vertical tabs &
updateMultiInput),
Wil Davis [ctb] (numericRangeInput function),
SnapAppointments [cph] (bootstrap-select),
Mattia Larentis [ctb, cph] (Bootstrap Switch),
Emanuele Marchi [ctb, cph] (Bootstrap Switch),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Flatlogic [cph] (Awesome Bootstrap Checkbox),
mouse0270 [ctb, cph] (Material Design Switch),
Tristan Edwards [ctb, cph] (SweetAlert),
Fabian Lindfors [ctb, cph] (multi.js),
Anthony Terrien [ctb, cph] (jQuery Knob),
Daniel Eden [ctb, cph] (animate.css),
Ganapati V S [ctb, cph] (bttn.css),
Brian Grinstead [ctb, cph] (Spectrum),
Lokesh Rajendran [ctb, cph] (pretty-checkbox),
Leon Gersen [ctb, cph] (wnumb & noUiSlider),
Timofey Marochkin [ctb, cph] (air-datepicker),
Tobias Ahlin [ctb, cph] (CSS spin),
atomiks [ctb, cph] (tippy.js)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinyWidgets versions 0.5.1 dated 2020-03-04 and 0.5.2 dated 2020-05-14
shinyWidgets-0.5.1/shinyWidgets/LICENSE |only shinyWidgets-0.5.1/shinyWidgets/R/attachShinyWidgetsDep.R |only shinyWidgets-0.5.1/shinyWidgets/R/panel.R |only shinyWidgets-0.5.1/shinyWidgets/inst/assets/awesomeRadioCheckbox |only shinyWidgets-0.5.1/shinyWidgets/inst/assets/sweetalert2/css/sweetalert2.min.css |only shinyWidgets-0.5.1/shinyWidgets/man/confirmSweetAlert.Rd |only shinyWidgets-0.5.1/shinyWidgets/man/panel.Rd |only shinyWidgets-0.5.1/shinyWidgets/man/sendSweetAlert.Rd |only shinyWidgets-0.5.2/shinyWidgets/DESCRIPTION | 18 shinyWidgets-0.5.2/shinyWidgets/MD5 | 151 ++- shinyWidgets-0.5.2/shinyWidgets/NAMESPACE | 16 shinyWidgets-0.5.2/shinyWidgets/NEWS.md | 22 shinyWidgets-0.5.2/shinyWidgets/R/actionBttn.R | 17 shinyWidgets-0.5.2/shinyWidgets/R/bootstrap-utils.R |only shinyWidgets-0.5.2/shinyWidgets/R/dependencies.R |only shinyWidgets-0.5.2/shinyWidgets/R/drop-menu.R | 24 shinyWidgets-0.5.2/shinyWidgets/R/execute_safely.R |only shinyWidgets-0.5.2/shinyWidgets/R/input-airDatepicker.R | 24 shinyWidgets-0.5.2/shinyWidgets/R/input-awesomecheckbox.R | 123 +- shinyWidgets-0.5.2/shinyWidgets/R/input-awesomeradio.R | 106 +- shinyWidgets-0.5.2/shinyWidgets/R/input-icon.R | 82 + shinyWidgets-0.5.2/shinyWidgets/R/input-knob.R | 50 - shinyWidgets-0.5.2/shinyWidgets/R/input-numericRange.R | 2 shinyWidgets-0.5.2/shinyWidgets/R/module-selectizeGroup.R | 4 shinyWidgets-0.5.2/shinyWidgets/R/setSliderColor.R | 2 shinyWidgets-0.5.2/shinyWidgets/R/sw-dropdown.R | 2 shinyWidgets-0.5.2/shinyWidgets/R/sweetalert.R | 432 +++------- shinyWidgets-0.5.2/shinyWidgets/README.md | 6 shinyWidgets-0.5.2/shinyWidgets/inst/assets/air-datepicker/datepicker-bindings.js | 8 shinyWidgets-0.5.2/shinyWidgets/inst/assets/air-datepicker2 |only shinyWidgets-0.5.2/shinyWidgets/inst/assets/awesome-bootstrap-checkbox |only shinyWidgets-0.5.2/shinyWidgets/inst/assets/checkboxGroupButtons/checkboxGroupButtons-bindings.js | 129 +- shinyWidgets-0.5.2/shinyWidgets/inst/assets/jquery-knob/knob-bindings.js | 331 ++++--- shinyWidgets-0.5.2/shinyWidgets/inst/assets/multi/multi-bindings.js | 150 +-- shinyWidgets-0.5.2/shinyWidgets/inst/assets/nouislider/nouislider-bindings.js | 195 ++-- shinyWidgets-0.5.2/shinyWidgets/inst/assets/progress-bars/progress-bars-bindings.js | 38 shinyWidgets-0.5.2/shinyWidgets/inst/assets/radioGroupButtons/radioGroupButtons-bindings.js | 105 +- shinyWidgets-0.5.2/shinyWidgets/inst/assets/search-input/search-bindings.js | 87 -- shinyWidgets-0.5.2/shinyWidgets/inst/assets/selectPicker/picker-bindings.js | 139 +-- shinyWidgets-0.5.2/shinyWidgets/inst/assets/shinyWidgets-bindings.min.js | 2 shinyWidgets-0.5.2/shinyWidgets/inst/assets/sliderText/sliderTextInput-bindings.js | 219 ++--- shinyWidgets-0.5.2/shinyWidgets/inst/assets/sweetalert2/css/bootstrap-4.min.css | 2 shinyWidgets-0.5.2/shinyWidgets/inst/assets/sweetalert2/css/borderless.min.css | 2 shinyWidgets-0.5.2/shinyWidgets/inst/assets/sweetalert2/css/dark.min.css | 2 shinyWidgets-0.5.2/shinyWidgets/inst/assets/sweetalert2/css/default.min.css |only shinyWidgets-0.5.2/shinyWidgets/inst/assets/sweetalert2/css/material-ui.min.css |only shinyWidgets-0.5.2/shinyWidgets/inst/assets/sweetalert2/css/minimal.min.css | 2 shinyWidgets-0.5.2/shinyWidgets/inst/assets/sweetalert2/js/sweetalert2.min.js | 2 shinyWidgets-0.5.2/shinyWidgets/inst/assets/tippy/drop-menu-bindings.js | 37 shinyWidgets-0.5.2/shinyWidgets/inst/assets/tools.R | 1 shinyWidgets-0.5.2/shinyWidgets/inst/examples/airDatepicker/timepicker/app.R | 11 shinyWidgets-0.5.2/shinyWidgets/man/airDatepicker.Rd | 14 shinyWidgets-0.5.2/shinyWidgets/man/animations.Rd | 8 shinyWidgets-0.5.2/shinyWidgets/man/bootstrap-utils.Rd |only shinyWidgets-0.5.2/shinyWidgets/man/closeSweetAlert.Rd | 4 shinyWidgets-0.5.2/shinyWidgets/man/demoNoUiSlider.Rd | 2 shinyWidgets-0.5.2/shinyWidgets/man/demoNumericRange.Rd | 2 shinyWidgets-0.5.2/shinyWidgets/man/dropMenu.Rd | 4 shinyWidgets-0.5.2/shinyWidgets/man/execute_safely.Rd |only shinyWidgets-0.5.2/shinyWidgets/man/html-dependencies.Rd |only shinyWidgets-0.5.2/shinyWidgets/man/inputSweetAlert.Rd | 5 shinyWidgets-0.5.2/shinyWidgets/man/knobInput.Rd | 9 shinyWidgets-0.5.2/shinyWidgets/man/shinyWidgets.Rd | 2 shinyWidgets-0.5.2/shinyWidgets/man/shinyWidgetsGallery.Rd | 2 shinyWidgets-0.5.2/shinyWidgets/man/show_toast.Rd |only shinyWidgets-0.5.2/shinyWidgets/man/sweetalert-confirmation.Rd |only shinyWidgets-0.5.2/shinyWidgets/man/sweetalert.Rd |only shinyWidgets-0.5.2/shinyWidgets/man/tooltipOptions.Rd | 2 shinyWidgets-0.5.2/shinyWidgets/man/updateNumericInputIcon.Rd |only shinyWidgets-0.5.2/shinyWidgets/man/updateNumericRangeInput.Rd | 2 shinyWidgets-0.5.2/shinyWidgets/man/updateTextInputIcon.Rd |only shinyWidgets-0.5.2/shinyWidgets/man/useSweetAlert.Rd | 12 shinyWidgets-0.5.2/shinyWidgets/tests/testthat/test-SweetAlert.R | 4 shinyWidgets-0.5.2/shinyWidgets/tests/testthat/test-knob.R | 4 shinyWidgets-0.5.2/shinyWidgets/tests/testthat/test-panel.R | 7 75 files changed, 1434 insertions(+), 1192 deletions(-)
Title: Named Capture to Data Tables
Description: User-friendly functions for extracting a data
table (row for each match, column for each group)
from non-tabular text data using regular expressions,
and for melting columns that match a regular expression.
Patterns are defined using a readable syntax
that makes it easy to build complex patterns
in terms of simpler, re-usable sub-patterns.
Named R arguments are translated to column names
in the output; capture groups without names are used
internally in order to provide a standard interface
to three regular expression C libraries (PCRE, RE2, ICU).
Output can also include numeric columns via
user-specified type conversion functions.
RE2 engine (re2r package) was removed from CRAN in Mar 2020
so must be installed from github.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between nc versions 2020.3.23 dated 2020-03-25 and 2020.5.13 dated 2020-05-14
DESCRIPTION | 8 MD5 | 144 NAMESPACE | 22 NEWS | 308 R/alternatives.R | 86 R/apply_type_funs.R | 94 R/capture_all_str.R | 882 - R/capture_df_names.R | 50 R/capture_first_df.R | 302 R/capture_first_vec.R | 254 R/capture_melt_multiple.R | 416 R/capture_melt_single.R | 282 R/field.R | 186 R/group.R | 103 R/only_captures.R | 18 R/quantifier.R | 130 R/stop_for.R | 119 R/try.R | 24 R/var_args_list.R | 236 build/vignette.rds |binary inst/doc/v1-capture-first.R | 414 inst/doc/v1-capture-first.Rmd | 806 - inst/doc/v1-capture-first.html | 1656 +- inst/doc/v2-capture-all.R | 238 inst/doc/v2-capture-all.Rmd | 498 inst/doc/v2-capture-all.html | 1326 +- inst/doc/v3-capture-melt.R | 275 inst/doc/v3-capture-melt.Rmd | 632 - inst/doc/v3-capture-melt.html | 1469 +- inst/doc/v4-comparisons.R | 968 - inst/doc/v4-comparisons.Rmd | 1301 +- inst/doc/v4-comparisons.html |19058 +++++++++++++++++++++++++++++--- inst/extdata/MEDLINE_Fields.html | 3586 +++--- inst/extdata/PMC3045577.nbib | 136 inst/extdata/compress-sizes.out | 12 inst/extdata/compress-times.out | 50 inst/extdata/namedCapture-refs.bib | 392 inst/extdata/vignette.Rmd | 460 inst/extdata/vignette.Rnw | 794 - inst/test_engines.R | 38 man/alternatives.Rd | 88 man/apply_type_funs.Rd | 42 man/capture_all_str.Rd | 824 - man/capture_df_names.Rd | 44 man/capture_first_df.Rd | 218 man/capture_first_vec.Rd | 178 man/capture_melt_multiple.Rd | 222 man/capture_melt_single.Rd | 226 man/field.Rd | 192 man/group.Rd | 113 man/only_captures.Rd | 44 man/quantifier.Rd | 122 man/stop_for_capture_same_as_id.Rd | 42 man/stop_for_engine.Rd | 34 man/stop_for_subject.Rd | 42 man/try_or_stop_print_pattern.Rd | 50 man/var_args_list.Rd | 84 tests/testthat.R | 3 tests/testthat/test-CRAN-all.R | 236 tests/testthat/test-CRAN-alternatives.R | 96 tests/testthat/test-CRAN-df.R | 632 - tests/testthat/test-CRAN-dt.R | 142 tests/testthat/test-CRAN-errors.R | 272 tests/testthat/test-CRAN-field.R | 72 tests/testthat/test-CRAN-group.R | 56 tests/testthat/test-CRAN-melt.R | 226 tests/testthat/test-CRAN-multiple.R | 568 tests/testthat/test-CRAN-quantifier.R | 178 tests/testthat/test-CRAN-vec.R | 604 - vignettes/v1-capture-first.Rmd | 806 - vignettes/v2-capture-all.Rmd | 498 vignettes/v3-capture-melt.Rmd | 632 - vignettes/v4-comparisons.Rmd | 1301 +- 73 files changed, 31454 insertions(+), 15206 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression, Cox model, multiple-response Gaussian, and the grouped multinomial regression. There are two new and important additions. The family argument can be a GLM family object, which opens the door to any programmed family. This comes with a modest computational cost, so when the built-in families suffice, they should be used instead. The other novelty is the relax option, which refits each of the active sets in the path unpenalized. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers listed in the URL below.
Author: Jerome Friedman [aut],
Trevor Hastie [aut, cre],
Rob Tibshirani [aut],
Balasubramanian Narasimhan [aut],
Kenneth Tay [aut],
Noah Simon [aut],
Junyang Qian [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 3.0-2 dated 2019-12-11 and 4.0 dated 2020-05-14
DESCRIPTION | 14 +- MD5 | 92 ++++++++++++------- NAMESPACE | 8 + NEWS.md | 17 +++ R/assess.glmnet.R | 22 +++- R/buildPredmat.array.R | 9 + R/buildPredmat.default.R | 1 R/cv.glmnet.raw.R | 13 +- R/cv.glmnetfit.R |only R/cv.lognet.R | 2 R/cv.multnet.R | 2 R/cv.relaxed.raw.R | 21 ++-- R/cvtype.R | 9 + R/elnet.R | 2 R/family.glmnet.R | 5 + R/glmnet-package.R | 8 - R/glmnet.R | 72 ++++++++++----- R/glmnet.control.R | 31 ++++-- R/glmnet.measures.R | 4 R/glmnetFlex.R |only R/makeX.R | 2 R/onAttach.R | 2 README.md | 5 - build/vignette.rds |binary inst/doc/Coxnet.pdf |binary inst/doc/glmnet.Rmd | 15 ++- inst/doc/glmnet.pdf |binary inst/doc/glmnetFamily.R |only inst/doc/glmnetFamily.Rmd |only inst/doc/glmnetFamily.pdf |only inst/doc/relax.pdf |binary inst/mortran/README.Rmd | 2 inst/mortran/glmnet5dpclean.m | 12 +- inst/mortran/wls.m |only inst/testscripts |only man/assess.glmnet.Rd | 2 man/dev_function.Rd |only man/elnet.fit.Rd |only man/figures |only man/get_start.Rd |only man/glmnet-package.Rd | 6 - man/glmnet.Rd | 47 ++++++---- man/glmnet.control.Rd | 11 +- man/glmnet.fit.Rd |only man/glmnet.measures.Rd | 2 man/glmnet.path.Rd |only man/obj_function.Rd |only man/pen_function.Rd |only man/predict.glmnetfit.Rd |only man/spelnet.fit.Rd |only man/spglmnet.fit.Rd |only src/glmnet5dpclean.f | 8 - src/glmnet_init.c | 155 +++++++++++++++++++++++++++++++++ src/wls.f |only vignettes/assets/vignette_binomial.png |only vignettes/assets/vignette_gaussian.png |only vignettes/glmnet.Rmd | 15 ++- vignettes/glmnetFamily.Rmd |only 58 files changed, 467 insertions(+), 149 deletions(-)
Title: Tools for Reading and Writing ISO/OGC Geographic Metadata
Description: Provides facilities to handle reading and writing of geographic metadata
defined with OGC/ISO 19115, 11119 and 19110 geographic information metadata standards,
and encoded using the ISO 19139 (XML) standard. It includes also a facility to check
the validity of ISO 19139 XML encoded metadata.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geometa versions 0.6-1 dated 2019-10-31 and 0.6-2 dated 2020-05-14
DESCRIPTION | 8 ++-- MD5 | 38 +++++++++++----------- R/GMLAbstractGML.R | 10 +++++ R/GMLUnitDefinition.R | 51 +++++++++++++++++++++++++++++- R/ISOAbstractCatalogue.R | 2 - R/ISOAbstractObject.R | 49 +++++++++++++++++++++++----- R/ISOBaseDecimal.R | 4 +- R/ISODistribution.R | 2 - R/ISOUnlimitedInteger.R | 10 +++++ R/geometa.R | 4 +- R/geometa_mapping.R | 24 +++++++++++--- R/readISO19139.R | 7 +--- README.md | 2 - inst/extdata/examples/metadata_i18n.R |only inst/extdata/examples/metadata_i18n.xml |only inst/extdata/mappings/geometa_mapping.csv | 2 - man/GMLAbstractGML.Rd | 3 + man/geometa.Rd | 4 +- tests/testthat/test_ISOBaseDateTime.R | 36 +++++++++++++++++++++ tests/testthat/test_ISOUnlimitedInteger.R | 20 +++++++++++ tests/testthat/test_geometa_mapping.R | 6 ++- 21 files changed, 228 insertions(+), 54 deletions(-)
Title: A Basic Set of Functions for Compositional Data Analysis
Description: A minimum set of functions to perform compositional data analysis
using the log-ratio approach introduced by John Aitchison (1982) <http://www.jstor.org/stable/2345821>. Main functions
have been implemented in c++ for better performance.
Author: Marc Comas-Cufí [aut, cre] (<https://orcid.org/0000-0001-9759-0622>)
Maintainer: Marc Comas-Cufí <mcomas@imae.udg.edu>
Diff between coda.base versions 0.2.2 dated 2020-04-16 and 0.3.1 dated 2020-05-14
coda.base-0.2.2/coda.base/src/balance_optim.cpp |only coda.base-0.2.2/coda.base/src/principal_balances.h |only coda.base-0.2.2/coda.base/src/principal_balances_1.cpp |only coda.base-0.2.2/coda.base/src/principal_balances_2.cpp |only coda.base-0.2.2/coda.base/src/principal_balances_3.cpp |only coda.base-0.2.2/coda.base/src/sbp.cpp |only coda.base-0.2.2/coda.base/src/sbp.h |only coda.base-0.3.1/coda.base/DESCRIPTION | 10 coda.base-0.3.1/coda.base/MD5 | 42 coda.base-0.3.1/coda.base/NEWS | 6 coda.base-0.3.1/coda.base/R/RcppExports.R | 52 coda.base-0.3.1/coda.base/R/basis.R | 94 + coda.base-0.3.1/coda.base/R/constrained_pb.R |only coda.base-0.3.1/coda.base/inst/doc/coordinates.R | 50 coda.base-0.3.1/coda.base/inst/doc/coordinates.Rmd | 10 coda.base-0.3.1/coda.base/inst/doc/coordinates.html | 45 coda.base-0.3.1/coda.base/man/alr_basis.Rd | 3 coda.base-0.3.1/coda.base/man/coda.base.Rd | 1 coda.base-0.3.1/coda.base/man/coordinates.Rd | 8 coda.base-0.3.1/coda.base/man/pb_basis.Rd | 35 coda.base-0.3.1/coda.base/src/RcppExports.cpp | 170 --- coda.base-0.3.1/coda.base/src/balance.h | 515 +++------ coda.base-0.3.1/coda.base/src/balance_evaluate.h |only coda.base-0.3.1/coda.base/src/balance_optimal.h |only coda.base-0.3.1/coda.base/src/coda.h | 2 coda.base-0.3.1/coda.base/src/principal_balances.cpp | 893 ++++++----------- coda.base-0.3.1/coda.base/vignettes/coordinates.Rmd | 10 27 files changed, 699 insertions(+), 1247 deletions(-)
Title: Management of Deterministic and Stochastic Projects
Description: Management problems of deterministic and stochastic projects. It obtains the duration of a project and the appropriate slack for each activity in a deterministic context. In addition it obtains a schedule of activities' time (Castro, Gómez & Tejada (2007) <doi:10.1016/j.orl.2007.01.003>). It also allows the management of resources. When the project is done, and the actual duration for each activity is known, then it can know how long the project is delayed and make a fair delivery of the delay between each activity (Bergantiños, Valencia-Toledo & Vidal-Puga (2018) <doi:10.1016/j.dam.2017.08.012>). In a stochastic context it can estimate the average duration of the project and plot the density of this duration, as well as, the density of the early and last times of the chosen activities. As in the deterministic case, it can make a distribution of the delay generated by observing the project already carried out.
Author: Juan Carlos Gonçalves Dosantos [aut, cre],
Ignacio García Jurado [aut],
Julián Costa Bouzas [aut]
Maintainer: Juan Carlos Gonçalves Dosantos <juan.carlos.goncalves@udc.es>
Diff between ProjectManagement versions 1.3.1 dated 2020-05-07 and 1.3.3 dated 2020-05-14
DESCRIPTION | 14 ++-- MD5 | 32 ++++----- R/function_dag.R | 10 +-- R/function_pert_calendario.R | 25 +++---- man/ProjectManagement-package.Rd | 34 +++++----- man/dag.plot.Rd | 60 +++++++++--------- man/delay.pert.Rd | 118 ++++++++++++++++++----------------- man/delay.stochastic.pert.Rd | 130 ++++++++++++++++++++------------------- man/early.time.Rd | 62 +++++++++--------- man/last.time.Rd | 69 ++++++++++---------- man/levelling.resources.Rd | 89 ++++++++++++++------------ man/mce.Rd | 98 +++++++++++++++-------------- man/organize.Rd | 54 ++++++++-------- man/rebuild.Rd | 82 ++++++++++++------------ man/resource.allocation.Rd | 96 +++++++++++++++------------- man/schedule.pert.Rd | 72 +++++++++++---------- man/stochastic.pert.Rd | 88 ++++++++++++++------------ 17 files changed, 588 insertions(+), 545 deletions(-)
More information about ProjectManagement at CRAN
Permanent link
Title: Penalty Learning
Description: Implementations of algorithms from
Learning Sparse Penalties for Change-point Detection
using Max Margin Interval Regression, by
Hocking, Rigaill, Vert, Bach
<http://proceedings.mlr.press/v28/hocking13.html>
published in proceedings of ICML2013.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between penaltyLearning versions 2019.5.29 dated 2019-06-09 and 2020.5.13 dated 2020-05-14
DESCRIPTION | 12 MD5 | 107 - NAMESPACE | 27 NEWS | 382 ++--- R/IntervalRegression.R | 1814 ++++++++++++------------- R/ROChange.R | 626 +++++--- R/featureVector.R | 223 +-- R/geoms.R | 142 - R/labelError.R | 514 +++---- R/modelSelection.R | 507 +++--- R/targetIntervals.R | 626 ++++---- data/datalist | 7 data/notConverging.RData |only man/GeomTallRect.Rd | 22 man/IntervalRegressionCV.Rd | 214 +- man/IntervalRegressionCVmargin.Rd | 114 - man/IntervalRegressionInternal.Rd | 94 - man/IntervalRegressionRegularized.Rd | 96 - man/IntervalRegressionUnregularized.Rd | 40 man/ROChange.Rd | 258 ++- man/change.colors.Rd | 24 man/change.labels.Rd | 22 man/changeLabel.Rd | 50 man/check_features_targets.Rd | 39 man/check_target_pred.Rd | 43 man/coef.IntervalRegression.Rd | 45 man/demo8.Rd | 30 man/featureMatrix.Rd | 65 man/featureVector.Rd | 57 man/geom_tallrect.Rd | 73 - man/labelError.Rd | 245 +-- man/largestContinuousMinimumC.Rd | 65 man/largestContinuousMinimumR.Rd | 65 man/modelSelection.Rd | 65 man/modelSelectionC.Rd | 131 - man/modelSelectionR.Rd | 101 - man/neuroblastomaProcessed.Rd | 48 man/notConverging.Rd |only man/oneSkip.Rd | 36 man/plot.IntervalRegression.Rd | 41 man/predict.IntervalRegression.Rd | 45 man/print.IntervalRegression.Rd | 41 man/squared.hinge.Rd | 40 man/targetIntervalROC.Rd | 111 - man/targetIntervalResidual.Rd | 133 - man/targetIntervals.Rd | 71 man/theme_no_space.Rd | 36 tests/testthat.R | 5 tests/testthat/test-ROChange-aum.R |only tests/testthat/test-ROChange-no-thresh.R | 220 +-- tests/testthat/test-ROChange.R |only tests/testthat/test-demo8.R | 104 - tests/testthat/test-errors.R | 270 +-- tests/testthat/test-features.R | 71 tests/testthat/test-labelError.R |only tests/testthat/test-largestContinuousMinimum.R | 170 +- tests/testthat/test-long.R |only tests/testthat/test-modelSelection.R |only 58 files changed, 4311 insertions(+), 4076 deletions(-)
More information about penaltyLearning at CRAN
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Title: Efficient Computation of Ordinary and Generalized Poisson
Binomial Distributions
Description: Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between PoissonBinomial versions 1.1.0 dated 2020-03-28 and 1.1.1 dated 2020-05-14
PoissonBinomial-1.1.0/PoissonBinomial/src/Makevars.win |only PoissonBinomial-1.1.1/PoissonBinomial/DESCRIPTION | 8 PoissonBinomial-1.1.1/PoissonBinomial/MD5 | 31 PoissonBinomial-1.1.1/PoissonBinomial/NEWS.md | 75 PoissonBinomial-1.1.1/PoissonBinomial/R/RcppExports.R | 212 PoissonBinomial-1.1.1/PoissonBinomial/R/gpbinom.R | 729 +-- PoissonBinomial-1.1.1/PoissonBinomial/R/pbinom.R | 858 +-- PoissonBinomial-1.1.1/PoissonBinomial/build/vignette.rds |binary PoissonBinomial-1.1.1/PoissonBinomial/inst/doc/intro.R | 182 PoissonBinomial-1.1.1/PoissonBinomial/inst/doc/intro.html | 1204 ++--- PoissonBinomial-1.1.1/PoissonBinomial/inst/doc/proc_approx.R | 584 +- PoissonBinomial-1.1.1/PoissonBinomial/inst/doc/proc_approx.html | 2278 +++++----- PoissonBinomial-1.1.1/PoissonBinomial/inst/doc/proc_exact.R | 284 - PoissonBinomial-1.1.1/PoissonBinomial/inst/doc/proc_exact.html | 1764 +++---- PoissonBinomial-1.1.1/PoissonBinomial/inst/doc/use_with_rcpp.R | 12 PoissonBinomial-1.1.1/PoissonBinomial/inst/doc/use_with_rcpp.html | 644 +- PoissonBinomial-1.1.1/PoissonBinomial/src/PoissonBinomial.cpp | 75 17 files changed, 4514 insertions(+), 4426 deletions(-)
More information about PoissonBinomial at CRAN
Permanent link
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 1.6.0 dated 2020-03-17 and 1.7.0 dated 2020-05-14
DESCRIPTION | 8 - MD5 | 89 ++++++++++--------- NAMESPACE | 2 NEWS.md | 87 +++++++++++++------ R/Connection.R | 137 +++++++++++++++++++++++++++--- R/Driver.R | 6 - R/Options.R | 25 ++++- R/Result.R | 96 +++++++++++++++------ R/Table.R | 96 ++++++++++++++++++--- R/athena_low_api.R | 18 +++ R/dplyr_integration.R | 35 +------ R/sql_translate_env.R | 2 R/utils.R | 67 ++++++++++++++ build/vignette.rds |binary inst/doc/aws_athena_query_caching.Rmd | 2 inst/doc/aws_athena_query_caching.html | 2 inst/doc/aws_s3_backend.R | 2 inst/doc/aws_s3_backend.Rmd | 2 inst/doc/aws_s3_backend.html | 2 inst/doc/convert_and_save_cost.Rmd |only inst/doc/convert_and_save_cost.html |only inst/doc/how_to_retry.Rmd |only inst/doc/how_to_retry.html |only man/AthenaWriteTables.Rd | 10 +- man/Query.Rd | 2 man/backend_dbplyr.Rd | 7 + man/dbClearResult.Rd | 2 man/dbColumnInfo.Rd | 2 man/dbConnect-AthenaDriver-method.Rd | 6 - man/dbConvertTable.Rd |only man/dbDataType.Rd | 2 man/dbDisconnect.Rd | 2 man/dbFetch.Rd | 2 man/dbGetInfo.Rd | 2 man/dbGetQuery.Rd | 2 man/dbHasCompleted.Rd | 2 man/dbIsValid.Rd | 2 man/dbStatistics.Rd | 2 man/noctua_options.Rd | 17 ++- man/sqlCreateTable.Rd | 6 - man/work_group.Rd | 2 tests/testthat/helper.R | 4 tests/testthat/test-dbConvertTable.R |only tests/testthat/test-dplyr-sql-trans-env.R | 10 +- tests/testthat/test-metadata.R | 2 tests/testthat/test-retry.R |only vignettes/aws_athena_query_caching.Rmd | 2 vignettes/aws_s3_backend.Rmd | 2 vignettes/convert_and_save_cost.Rmd |only vignettes/how_to_retry.Rmd |only 50 files changed, 567 insertions(+), 201 deletions(-)
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS)
implemented by the MICE algorithm as described in Van Buuren and
Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has
its own imputation model. Built-in imputation models are provided for
continuous data (predictive mean matching, normal), binary data (logistic
regression), unordered categorical data (polytomous logistic regression)
and ordered categorical data (proportional odds). MICE can also impute
continuous two-level data (normal model, pan, second-level variables).
Passive imputation can be used to maintain consistency between variables.
Various diagnostic plots are available to inspect the quality of the
imputations.
Author: Stef van Buuren [aut, cre],
Karin Groothuis-Oudshoorn [aut],
Gerko Vink [ctb],
Rianne Schouten [ctb],
Alexander Robitzsch [ctb],
Lisa Doove [ctb],
Shahab Jolani [ctb],
Margarita Moreno-Betancur [ctb],
Ian White [ctb],
Philipp Gaffert [ctb],
Florian Meinfelder [ctb],
Bernie Gray [ctb]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between mice versions 3.8.0 dated 2020-02-21 and 3.9.0 dated 2020-05-14
mice-3.8.0/mice/inst/NEWS |only mice-3.9.0/mice/DESCRIPTION | 12 mice-3.9.0/mice/MD5 | 73 ++--- mice-3.9.0/mice/NEWS.md | 13 + mice-3.9.0/mice/R/D3.R | 46 ++- mice-3.9.0/mice/R/fix.coef.R | 180 +++++++------- mice-3.9.0/mice/R/internal.R | 258 ++++++++++---------- mice-3.9.0/mice/R/mice.impute.2lonly.pmm.R | 323 +++++++++++++------------- mice-3.9.0/mice/R/mice.impute.mnar.norm.R | 6 mice-3.9.0/mice/R/plot.R | 213 ++++++++--------- mice-3.9.0/mice/R/pool.R | 34 +- mice-3.9.0/mice/man/D3.Rd | 28 ++ mice-3.9.0/mice/man/boys.Rd | 6 mice-3.9.0/mice/man/brandsma.Rd | 6 mice-3.9.0/mice/man/employee.Rd | 6 mice-3.9.0/mice/man/fdd.Rd | 6 mice-3.9.0/mice/man/fdgs.Rd | 6 mice-3.9.0/mice/man/fix.coef.Rd | 2 mice-3.9.0/mice/man/leiden85.Rd | 4 mice-3.9.0/mice/man/mammalsleep.Rd | 6 mice-3.9.0/mice/man/mice.impute.2lonly.pmm.Rd | 5 mice-3.9.0/mice/man/mice.impute.mnar.Rd | 6 mice-3.9.0/mice/man/mnar_demo_data.Rd | 4 mice-3.9.0/mice/man/nhanes.Rd | 6 mice-3.9.0/mice/man/nhanes2.Rd | 6 mice-3.9.0/mice/man/pattern.Rd | 6 mice-3.9.0/mice/man/plot.mids.Rd | 4 mice-3.9.0/mice/man/pool.Rd | 27 +- mice-3.9.0/mice/man/popmis.Rd | 6 mice-3.9.0/mice/man/pops.Rd | 6 mice-3.9.0/mice/man/potthoffroy.Rd | 6 mice-3.9.0/mice/man/selfreport.Rd | 6 mice-3.9.0/mice/man/tbc.Rd | 6 mice-3.9.0/mice/man/toenail.Rd | 6 mice-3.9.0/mice/man/toenail2.Rd | 6 mice-3.9.0/mice/man/walking.Rd | 6 mice-3.9.0/mice/man/windspeed.Rd | 6 mice-3.9.0/mice/tests/testthat/test-D3.R | 37 ++ 38 files changed, 775 insertions(+), 608 deletions(-)
Title: Open GenBank Files
Description: Opens complete record(s) with .gb extension from the NCBI/GenBank Nucleotide database and returns a list containing shaped record(s). These kind of files contains detailed records of DNA samples (locus, organism, type of sequence, source of the sequence...). An example of record can be found at <https://www.ncbi.nlm.nih.gov/nuccore/HE799070>.
Author: Robin Mercier
Maintainer: Robin Mercier <robin.largon.mercier@hotmail.fr>
Diff between read.gb versions 1.6 dated 2018-11-26 and 2.0.1 dated 2020-05-14
read.gb-1.6/read.gb/R/read.gb-internal.R |only read.gb-2.0.1/read.gb/DESCRIPTION | 11 +- read.gb-2.0.1/read.gb/MD5 | 122 ++++++++++++++-------------- read.gb-2.0.1/read.gb/NAMESPACE | 1 read.gb-2.0.1/read.gb/R/CDS.F.R | 6 - read.gb-2.0.1/read.gb/R/C_region.F.R | 6 - read.gb-2.0.1/read.gb/R/D_loop.F.R | 6 - read.gb-2.0.1/read.gb/R/D_segment.F.R | 6 - read.gb-2.0.1/read.gb/R/F_UTR.F.R | 6 - read.gb-2.0.1/read.gb/R/Feature.sep.R | 1 read.gb-2.0.1/read.gb/R/J_segment.F.R | 6 - read.gb-2.0.1/read.gb/R/N_region.F.R | 6 - read.gb-2.0.1/read.gb/R/Reference.sep.R | 14 ++- read.gb-2.0.1/read.gb/R/Reorganize.report.R | 37 ++++---- read.gb-2.0.1/read.gb/R/STS.F.R | 6 - read.gb-2.0.1/read.gb/R/S_region.F.R | 6 - read.gb-2.0.1/read.gb/R/T_UTR.F.R | 6 - read.gb-2.0.1/read.gb/R/V_region.F.R | 6 - read.gb-2.0.1/read.gb/R/V_segment.F.R | 6 - read.gb-2.0.1/read.gb/R/assembly_gap.F.R | 6 - read.gb-2.0.1/read.gb/R/centromere.F.R | 6 - read.gb-2.0.1/read.gb/R/exon.F.R | 6 - read.gb-2.0.1/read.gb/R/extract.gb.R |only read.gb-2.0.1/read.gb/R/gap.F.R | 6 - read.gb-2.0.1/read.gb/R/gene.F.R | 6 - read.gb-2.0.1/read.gb/R/iDNA.F.R | 6 - read.gb-2.0.1/read.gb/R/intron.F.R | 6 - read.gb-2.0.1/read.gb/R/mRNA.F.R | 6 - read.gb-2.0.1/read.gb/R/mat_peptide.F.R | 6 - read.gb-2.0.1/read.gb/R/misc_RNA.F.R | 6 - read.gb-2.0.1/read.gb/R/misc_binding.F.R | 6 - read.gb-2.0.1/read.gb/R/misc_difference.F.R | 6 - read.gb-2.0.1/read.gb/R/misc_feature.F.R | 6 - read.gb-2.0.1/read.gb/R/misc_recomb.F.R | 6 - read.gb-2.0.1/read.gb/R/misc_structure.F.R | 6 - read.gb-2.0.1/read.gb/R/mobile_element.F.R | 6 - read.gb-2.0.1/read.gb/R/modified_base.F.R | 6 - read.gb-2.0.1/read.gb/R/ncRNA.F.R | 6 - read.gb-2.0.1/read.gb/R/old_sequence.F.R | 6 - read.gb-2.0.1/read.gb/R/operon.F.R | 6 - read.gb-2.0.1/read.gb/R/oriT.F.R | 6 - read.gb-2.0.1/read.gb/R/polyA_site.F.R | 6 - read.gb-2.0.1/read.gb/R/precursor_RNA.F.R | 6 - read.gb-2.0.1/read.gb/R/prim_transcript.F.R | 6 - read.gb-2.0.1/read.gb/R/primer_bind.F.R | 6 - read.gb-2.0.1/read.gb/R/propeptide.F.R | 6 - read.gb-2.0.1/read.gb/R/protein_bind.F.R | 6 - read.gb-2.0.1/read.gb/R/rRNA.F.R | 6 - read.gb-2.0.1/read.gb/R/read.gb.R | 36 +++++--- read.gb-2.0.1/read.gb/R/regulatory.F.R | 6 - read.gb-2.0.1/read.gb/R/rep_origin.F.R | 6 - read.gb-2.0.1/read.gb/R/repeat_region.F.R | 6 - read.gb-2.0.1/read.gb/R/sig_peptide.F.R | 6 - read.gb-2.0.1/read.gb/R/source.F.R | 2 read.gb-2.0.1/read.gb/R/stem_loop.F.R | 6 - read.gb-2.0.1/read.gb/R/sysdata.rda |only read.gb-2.0.1/read.gb/R/tRNA.F.R | 6 - read.gb-2.0.1/read.gb/R/telomere.F.R | 6 - read.gb-2.0.1/read.gb/R/tmRNA.F.R | 6 - read.gb-2.0.1/read.gb/R/transit_peptide.F.R | 6 - read.gb-2.0.1/read.gb/R/unsure.F.R | 6 - read.gb-2.0.1/read.gb/R/variation.F.R | 6 - read.gb-2.0.1/read.gb/man/extract.gb.Rd |only read.gb-2.0.1/read.gb/man/read.gb.Rd | 59 ++++++------- 64 files changed, 311 insertions(+), 278 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 1.8.0 dated 2020-03-17 and 1.9.0 dated 2020-05-14
DESCRIPTION | 8 - MD5 | 99 ++++++++++--------- NAMESPACE | 2 NEWS.md | 77 +++++++++++---- R/Connection.R | 146 +++++++++++++++++++++++++---- R/Driver.R | 8 - R/Options.R | 25 +++- R/Result.R | 110 ++++++++++++++------- R/athena_low_api.R | 24 ++++ R/dplyr_integration.R | 36 +------ R/sql_translate_env.R | 2 R/table.R | 97 ++++++++++++++++--- R/util.R | 74 ++++++++++++++ build/vignette.rds |binary inst/doc/aws_athena_query_caching.Rmd | 2 inst/doc/aws_athena_query_caching.html | 2 inst/doc/aws_s3_backend.R | 2 inst/doc/aws_s3_backend.Rmd | 2 inst/doc/aws_s3_backend.html | 2 inst/doc/changing_backend_file_parser.Rmd | 2 inst/doc/changing_backend_file_parser.html | 2 inst/doc/convert_and_save_cost.Rmd |only inst/doc/convert_and_save_cost.html |only inst/doc/how_to_retry.Rmd |only inst/doc/how_to_retry.html |only man/AthenaWriteTables.Rd | 10 + man/Query.Rd | 2 man/RAthena_options.Rd | 17 ++- man/backend_dbplyr.Rd | 7 - man/dbClearResult.Rd | 2 man/dbColumnInfo.Rd | 2 man/dbConnect-AthenaDriver-method.Rd | 4 man/dbConvertTable.Rd |only man/dbDataType.Rd | 2 man/dbDisconnect.Rd | 2 man/dbFetch.Rd | 2 man/dbGetInfo.Rd | 2 man/dbGetQuery.Rd | 2 man/dbHasCompleted.Rd | 2 man/dbIsValid.Rd | 2 man/dbStatistics.Rd | 2 man/install_boto.Rd | 4 man/session_token.Rd | 4 man/sqlCreateTable.Rd | 6 - man/work_group.Rd | 2 tests/testthat/helper.R | 4 tests/testthat/test-dbConvertTable.R |only tests/testthat/test-dplyr-sql-trans-env.R | 10 - tests/testthat/test-metadata.R | 2 tests/testthat/test-retry.R |only vignettes/aws_athena_query_caching.Rmd | 2 vignettes/aws_s3_backend.Rmd | 2 vignettes/changing_backend_file_parser.Rmd | 2 vignettes/convert_and_save_cost.Rmd |only vignettes/how_to_retry.Rmd |only 55 files changed, 597 insertions(+), 223 deletions(-)
Title: Sequential Quadratic Programming for Fast Maximum-Likelihood
Estimation of Mixture Proportions
Description: Provides an optimization method based on sequential
quadratic programming (SQP) for maximum likelihood estimation of
the mixture proportions in a finite mixture model where the
component densities are known. The algorithm is expected to obtain
solutions that are at least as accurate as the state-of-the-art
MOSEK interior-point solver (called by function "KWDual" in the
'REBayes' package), and they are expected to arrive at solutions
more quickly when the number of samples is large and the number of
mixture components is not too large. This implements the "mix-SQP"
algorithm, with some improvements, described in Y. Kim,
P. Carbonetto, M. Stephens & M. Anitescu (2020)
<DOI:10.1080/10618600.2019.1689985>.
Author: Youngseok Kim [aut],
Peter Carbonetto [aut, cre],
Mihai Anitescu [aut],
Matthew Stephens [aut],
Jason Willwerscheid [ctb],
Jean Morrison [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between mixsqp versions 0.3-17 dated 2020-01-29 and 0.3-43 dated 2020-05-14
DESCRIPTION | 33 - MD5 | 36 - NAMESPACE | 1 R/RcppExports.R | 8 R/mixsqp-package.R | 2 R/mixsqp.R | 187 +++---- R/zzz.R |only README.md | 33 - inst/CITATION | 27 - inst/doc/mixsqp-intro.html | 801 ++++++++++++++++---------------- man/mixsqp-package.Rd | 3 man/mixsqp.Rd | 29 - man/tacks.Rd | 6 src/RcppExports.cpp | 28 - src/misc.cpp |only src/misc.h |only src/mixem.cpp |only src/mixem.h |only src/mixsqp.cpp | 135 ++--- src/objective.cpp |only src/objective.h |only tests/testthat/ashr.binom.example.RData |only tests/testthat/test_mixsqp.R | 100 ++- 23 files changed, 779 insertions(+), 650 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-02 0.1.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-04 0.1.0
Title: Sliding Window Functions
Description: Provides type-stable rolling window functions over
any R data type. Cumulative and expanding windows are also supported.
For more advanced usage, an index can be used as a secondary vector
that defines how sliding windows are to be created.
Author: Davis Vaughan [aut, cre],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between slider versions 0.1.2 dated 2020-03-10 and 0.1.3 dated 2020-05-14
DESCRIPTION | 12 +- MD5 | 119 +++++++++++------------ NEWS.md | 23 ++++ R/hop-common.R | 5 R/hop-index-common.R | 14 -- R/hop-index.R | 49 +-------- R/hop-index2.R | 52 +--------- R/hop.R | 47 ++------- R/hop2.R | 49 +-------- R/phop-index.R | 50 ++------- R/phop.R | 47 ++------- R/pslide-index.R | 69 +++++-------- R/pslide-period.R | 78 ++++++--------- R/pslide.R | 67 +++++-------- R/slide-index-common.R | 12 -- R/slide-index.R | 110 +++++++++++++-------- R/slide-index2.R | 72 ++++++-------- R/slide-period-common.R | 23 +++- R/slide-period.R | 78 ++++++--------- R/slide-period2.R | 81 ++++++--------- R/slide.R | 67 +++++-------- R/slide2.R | 70 +++++-------- R/utils.R | 38 +------ README.md | 27 ++--- inst/doc/rowwise.html | 20 +-- man/slide.Rd | 16 ++- man/slide2.Rd | 18 ++- man/slide_index.Rd | 57 +++++++++-- man/slide_index2.Rd | 18 ++- man/slide_period.Rd | 16 ++- man/slide_period2.Rd | 18 ++- src/hop.c | 22 ++-- src/index.c | 164 ++++++++++++++------------------ src/init.c | 8 - src/params.c | 13 +- src/params.h | 1 src/slide.c | 40 ++++--- src/utils.c | 7 + src/utils.h | 2 tests/testthat/helper-s3.R |only tests/testthat/test-hop-index-vec.R | 65 +++++------- tests/testthat/test-hop-index.R | 19 +++ tests/testthat/test-hop-index2-vec.R | 35 ++++++ tests/testthat/test-hop-index2.R | 2 tests/testthat/test-hop-vec.R | 55 ++++------ tests/testthat/test-hop.R | 15 ++ tests/testthat/test-hop2-vec.R | 24 ++++ tests/testthat/test-phop-index-vec.R | 52 +++++++++- tests/testthat/test-phop-index.R | 9 + tests/testthat/test-phop-vec.R | 24 ++++ tests/testthat/test-pslide-index-vec.R | 36 +++++-- tests/testthat/test-pslide-period-vec.R | 52 ++++++++-- tests/testthat/test-pslide-vec.R | 38 ++++++- tests/testthat/test-slide-index-vec.R | 41 ++++++-- tests/testthat/test-slide-index.R | 12 +- tests/testthat/test-slide-index2-vec.R | 41 ++++++-- tests/testthat/test-slide-period-vec.R | 69 ++++++++++++- tests/testthat/test-slide-period2-vec.R | 52 ++++++++-- tests/testthat/test-slide-vec.R | 61 +++++++++-- tests/testthat/test-slide.R | 18 +-- tests/testthat/test-slide2-vec.R | 39 ++++++- 61 files changed, 1379 insertions(+), 1059 deletions(-)
Title: Tools for Post-Processing Class Probability Estimates
Description: Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations.
Author: Max Kuhn [aut],
Davis Vaughan [aut, cre],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between probably versions 0.0.4 dated 2020-01-13 and 0.0.5 dated 2020-05-14
probably-0.0.4/probably/man/vec_cast.class_pred.Rd |only probably-0.0.4/probably/man/vec_proxy_equal.class_pred.Rd |only probably-0.0.4/probably/man/vec_ptype2.class_pred.Rd |only probably-0.0.5/probably/DESCRIPTION | 13 probably-0.0.5/probably/MD5 | 25 probably-0.0.5/probably/NAMESPACE | 39 probably-0.0.5/probably/NEWS.md | 4 probably-0.0.5/probably/R/class-pred.R | 5 probably-0.0.5/probably/R/vctrs-compat.R | 125 -- probably-0.0.5/probably/README.md | 7 probably-0.0.5/probably/inst/doc/equivocal-zones.html | 305 ++--- probably-0.0.5/probably/inst/doc/where-to-use.html | 565 +++++----- probably-0.0.5/probably/man/probably-package.Rd | 1 probably-0.0.5/probably/tests/testthat/output/test-error-subset.txt | 5 probably-0.0.5/probably/tests/testthat/test-class-pred.R | 40 15 files changed, 524 insertions(+), 610 deletions(-)
Title: Tools for Binning Data
Description: Manually bin data using weight of evidence and information value. Includes other binning
methods such as equal length, quantile and winsorized. Options for combining levels of categorical
data are also available. Dummy variables can be generated based on the bins created using any of
the available binning methods. References: Siddiqi, N. (2006) <doi:10.1002/9781119201731.biblio>.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between rbin versions 0.1.2 dated 2020-02-04 and 0.2.0 dated 2020-05-14
DESCRIPTION | 16 MD5 | 69 NAMESPACE | 19 NEWS.md | 4 R/rbin-addins.R | 52 R/rbin-create-bins.R | 39 R/rbin-equal-freq.R | 130 R/rbin-equal-length.R | 59 R/rbin-factor.R | 157 R/rbin-manual.R | 58 R/rbin-quantile.R | 50 R/rbin-shiny.R |only R/rbin-winsorize.R | 93 R/rbin.R | 2 R/utils.R | 158 R/zzz.R | 11 README.md | 120 build/vignette.rds |binary inst/doc/introduction.R | 30 inst/doc/introduction.html |28559 +++++++++++++++++++++++++++++++++++++- man/mbank.Rd | 6 man/rbin.Rd | 1 man/rbinAddin.Rd | 2 man/rbin_equal_freq.Rd | 18 man/rbin_equal_length.Rd | 10 man/rbin_factor.Rd | 3 man/rbin_manual.Rd | 9 man/rbin_quantiles.Rd | 9 man/rbin_winsorize.Rd | 21 tests/figs/test-plots/ef-plot.svg |only tests/figs/test-plots/fl-plot.svg | 10 tests/testthat/test-bins.R | 84 tests/testthat/test-plots.R | 7 tools/README-equal_length-2.png |only tools/README-factor-1.png |binary tools/README-factor-2.png |only tools/README-manual-2.png |only tools/README-quantile-2.png |only tools/README-winsorize-2.png |only 39 files changed, 29066 insertions(+), 740 deletions(-)
Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word' and 'Microsoft PowerPoint' documents from R.
The package focuses on tabular and graphical reporting from R; it also provides two functions
that let users get document content into data objects. A set of functions
lets add and remove images, tables and paragraphs of text in new or existing documents.
When working with 'PowerPoint' presentations, slides can be added or removed; shapes inside
slides can also be added or removed. When working with 'Word' documents, a cursor can be
used to help insert or delete content at a specific location in the document. The package
does not require any installation of Microsoft products to be able to write Microsoft files.
Author: David Gohel [aut, cre],
Frank Hangler [ctb] (function body_replace_all_text),
Liz Sander [ctb] (several documentation fixes),
Anton Victorson [ctb] (fixes xml structures),
Jon Calder [ctb] (update vignettes),
John Harrold [ctb] (fuction annotate_base),
John Muschelli [ctb] (google doc compatibility)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officer versions 0.3.9 dated 2020-05-04 and 0.3.10 dated 2020-05-14
officer-0.3.10/officer/DESCRIPTION | 6 officer-0.3.10/officer/MD5 | 65 ++--- officer-0.3.10/officer/NAMESPACE | 1 officer-0.3.10/officer/NEWS | 15 + officer-0.3.10/officer/R/docx_add.R | 13 - officer-0.3.10/officer/R/docx_img.R | 2 officer-0.3.10/officer/R/knitr_utils.R |only officer-0.3.10/officer/R/ooxml_block_objects.R | 165 +++++++++----- officer-0.3.10/officer/R/ooxml_run_objects.R | 52 +++- officer-0.3.10/officer/R/ph_location.R | 1 officer-0.3.10/officer/R/ppt_ph_with_methods.R | 32 ++ officer-0.3.10/officer/R/read_docx.R | 18 - officer-0.3.10/officer/R/utils.R | 1 officer-0.3.10/officer/inst/template/template.docx |binary officer-0.3.10/officer/man/block_caption.Rd | 11 officer-0.3.10/officer/man/block_pour_docx.Rd | 2 officer-0.3.10/officer/man/block_table.Rd | 5 officer-0.3.10/officer/man/block_toc.Rd | 11 officer-0.3.10/officer/man/body_add.Rd | 10 officer-0.3.10/officer/man/body_add_table.Rd | 4 officer-0.3.10/officer/man/change_styles.Rd | 3 officer-0.3.10/officer/man/docx_reference_img.Rd | 10 officer-0.3.10/officer/man/figures |only officer-0.3.10/officer/man/fortify_location.Rd | 9 officer-0.3.10/officer/man/get_reference_value.Rd | 13 - officer-0.3.10/officer/man/opts_current_table.Rd |only officer-0.3.10/officer/man/ph_with.Rd | 18 + officer-0.3.10/officer/man/prop_table.Rd | 7 officer-0.3.10/officer/man/run_autonum.Rd | 23 + officer-0.3.10/officer/man/to_pml.Rd | 10 officer-0.3.10/officer/man/to_wml.Rd | 10 officer-0.3.10/officer/man/wml_link_images.Rd | 10 officer-0.3.10/officer/tests/testthat/test-docx-misc.R | 4 officer-0.3.10/officer/tests/testthat/test-docx-replace.R | 6 officer-0.3.9/officer/R/get_reference_templates.R |only 35 files changed, 401 insertions(+), 136 deletions(-)
Title: Preprocess Data and Get Better Insights from Machine Learning
Models
Description: The main focus is on preprocessing and data visualization of machine learning models performances.
Some functions allow to fill in gaps in time series using linear interpolation on panel data, some functions
permit to draw lift effect and lift curve in order to benchmark machine learning models or you can even find
the optimal number of clusters in agglomerative clustering algorithm.
Author: Simon Corde [aut, cre]
Maintainer: Simon Corde <simon.corde@hotmail.fr>
Diff between helda versions 1.1.0 dated 2020-05-01 and 1.1.1 dated 2020-05-14
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 4 ++++ data/titanic_testing.RData |binary data/titanic_training.RData |binary data/titanic_validation.RData |binary data/world_countries_pop.RData |binary man/titanic_testing.Rd | 6 ++++-- man/titanic_training.Rd | 6 ++++-- man/titanic_validation.Rd | 6 ++++-- man/world_countries_pop.Rd | 6 ++++-- tests/testthat/lift_curve_test_v3.Rda |binary tests/testthat/lift_curve_test_v4.Rda |binary tests/testthat/lift_effect_test_v3.Rda |binary tests/testthat/lift_effect_test_v4.Rda |binary tests/testthat/test-lift_curve.R | 2 +- tests/testthat/test-lift_effect.R | 2 +- 17 files changed, 41 insertions(+), 29 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-29 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-30 1.0.1
2015-12-19 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-10 1.4
2020-01-22 1.3
2019-08-08 1.2.4
2019-06-24 1.2.3
2019-05-09 1.2.2
2019-01-24 1.2
2018-07-27 1.1.0
2017-09-06 1.0.1
2017-05-04 1.0.0
2017-01-17 0.4
2016-09-04 0.3
2016-01-19 0.2
2015-03-02 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-29 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-20 0.2-6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-13 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-20 1.0
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearization of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow,Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@gmail.com>
Diff between vardpoor versions 0.16.0 dated 2019-08-28 and 0.17.0 dated 2020-05-14
vardpoor-0.16.0/vardpoor/R/vardcro2s.R |only vardpoor-0.17.0/vardpoor/DESCRIPTION | 13 vardpoor-0.17.0/vardpoor/MD5 | 16 vardpoor-0.17.0/vardpoor/R/linarpr.R | 470 +++++------ vardpoor-0.17.0/vardpoor/R/vardcros.R |only vardpoor-0.17.0/vardpoor/R/vardom.R | 18 vardpoor-0.17.0/vardpoor/R/vardom_othstr.R | 80 - vardpoor-0.17.0/vardpoor/R/vardomh.R | 26 vardpoor-0.17.0/vardpoor/R/varpoord.R | 1178 ++++++++++++++--------------- vardpoor-0.17.0/vardpoor/man/vardomh.Rd | 2 10 files changed, 901 insertions(+), 902 deletions(-)
Title: Stochastic Profiling using Maximum Likelihood Estimation
Description: New Version of the R package originally accompanying the paper
"Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles"
by Sameer S Bajikar, Christiane Fuchs, Andreas Roller, Fabian J Theis and Kevin A Janes
(PNAS 2014, 111(5), E626-635 <doi:10.1073/pnas.1311647111>). In this paper, we measure expression profiles
from small heterogeneous populations of cells, where each cell is assumed to be from a mixture of
lognormal distributions. We perform maximum likelihood estimation in order to infer the mixture ratio and
the parameters of these lognormal distributions from the cumulated expression measurements.
The main difference of this new package version to the previous one is that it is now possible to use
different n's, i.e. a dataset where each tissue sample originates from a different number of cells.
We used this on pheno-seq data, see: Tirier, S.M., Park, J., Preusser, F. et al. Pheno-seq - linking visual
features and gene expression in 3D cell culture systems. Sci Rep 9, 12367 (2019)
<doi:10.1038/s41598-019-48771-4>).
Author: Lisa Amrhein [aut, cre],
Christiane Fuchs [aut],
Christoph Kurz [ctb] (Author to function comb.summands.R')
Maintainer: Lisa Amrhein <amrheinlisa@gmail.com>
Diff between stochprofML versions 2.0.1 dated 2020-03-13 and 2.0.2 dated 2020-05-14
DESCRIPTION | 8 ++-- MD5 | 70 ++++++++++++++++++------------------- NEWS.md | 7 +++ R/calculate.ci.EXPLN.R | 2 - R/calculate.ci.LNLN.R | 2 - R/calculate.ci.rLNLN.R | 2 - R/d.sum.of.lognormal.types.R | 34 +++++++++-------- R/d.sum.of.lognormals.R | 33 ++++++++++------- R/d.sum.of.types.LNLN.R | 34 +++++++++-------- R/d.sum.of.types.rLNLN.R | 30 ++++++++------- man/analyze.sod2.Rd | 4 +- man/analyze.toycluster.Rd | 4 +- man/calculate.ci.EXPLN.Rd | 6 +-- man/calculate.ci.LNLN.Rd | 6 +-- man/calculate.ci.rLNLN.Rd | 6 +-- man/comb.summands.Rd | 4 +- man/d.sum.of.mixtures.EXPLN.Rd | 4 +- man/d.sum.of.mixtures.LNLN.Rd | 4 +- man/d.sum.of.mixtures.rLNLN.Rd | 4 +- man/generate.toydata.Rd | 4 +- man/mix.d.sum.of.mixtures.EXPLN.Rd | 6 +-- man/mix.d.sum.of.mixtures.LNLN.Rd | 6 +-- man/mix.d.sum.of.mixtures.rLNLN.Rd | 7 +++ man/penalty.constraint.EXPLN.Rd | 4 +- man/penalty.constraint.LNLN.Rd | 4 +- man/penalty.constraint.rLNLN.Rd | 4 +- man/stochasticProfilingData.Rd | 4 +- man/stochasticProfilingML.Rd | 4 +- man/stochprof.loop.Rd | 4 +- man/stochprof.results.EXPLN.Rd | 4 +- man/stochprof.results.LNLN.Rd | 4 +- man/stochprof.results.rLNLN.Rd | 4 +- man/stochprof.search.EXPLN.Rd | 4 +- man/stochprof.search.LNLN.Rd | 4 +- man/stochprof.search.rLNLN.Rd | 4 +- man/stochprofML-package.Rd | 4 +- 36 files changed, 181 insertions(+), 158 deletions(-)
Title: Bayesian Graphical Estimation using Spike-and-Slab Priors
Description: Bayesian estimation for undirected graphical models using spike-and-slab priors. The package handles continuous, discrete, and mixed data.
Author: Reza Mohammadi [aut, cre] (<https://orcid.org/0000-0001-9538-0648>)
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between ssgraph versions 1.10 dated 2019-09-14 and 1.11 dated 2020-05-14
ssgraph-1.10/ssgraph/NEWS |only ssgraph-1.11/ssgraph/DESCRIPTION | 20 +++++++++++++------- ssgraph-1.11/ssgraph/MD5 | 10 +++++----- ssgraph-1.11/ssgraph/NEWS.md |only ssgraph-1.11/ssgraph/R/ssgraph.R | 3 +-- ssgraph-1.11/ssgraph/man/ssgraph-package.Rd | 4 ++-- ssgraph-1.11/ssgraph/src/copula.cpp | 2 +- 7 files changed, 22 insertions(+), 17 deletions(-)
Title: Representing and Inferring Single-Cell Trajectories
Description: Provides functionality to infer trajectories from single-cell data,
represent them into a common format, and adapt them. Other biological information
can also be added, such as cellular grouping, RNA velocity and annotation.
Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dynwrap versions 1.2.0 dated 2020-03-09 and 1.2.1 dated 2020-05-14
DESCRIPTION | 10 MD5 | 69 +++--- NEWS.md | 16 + R/convert_milestone_percentages_to_progressions.R | 16 - R/convert_progressions_to_milestone_percentages.R | 26 +- R/project_waypoints.R | 38 ++- R/wrap_add_dimred.R | 33 +-- R/wrap_add_trajectory.R | 29 +- R/wrap_add_waypoints.R | 127 ++++++----- R/wrap_data.R | 4 R/wrap_gather_cells_at_milestones.R | 3 README.md | 29 +- data/example_dataset.rda |binary data/example_trajectory.rda |binary inst/doc/create_ti_method_container.html | 142 ++++++------- inst/doc/create_ti_method_definition.html | 172 +++++++--------- inst/doc/create_ti_method_r.html | 124 +++++------ inst/doc/create_ti_method_wrappers.html | 66 ++---- inst/examples/docker/Dockerfile | 5 man/add_waypoints.Rd | 28 +- man/allowed_inputs.Rd | 4 man/allowed_outputs.Rd | 4 man/convert_milestone_percentages_to_progressions.Rd | 28 -- man/convert_progressions_to_milestone_percentages.Rd |only man/dynwrap.Rd | 2 man/example_dataset.Rd | 4 man/example_trajectory.Rd | 4 man/prior_usages.Rd | 4 man/priors.Rd | 4 man/project_trajectory.Rd | 11 - man/project_waypoints.Rd | 2 man/trajectory_type_dag.Rd | 4 man/trajectory_types.Rd | 4 man/wrapper_types.Rd | 4 tests/testthat/test-method_create_ti_method_container.R | 2 tests/testthat/test-wrap_add_root_and_add_pseudotime.R | 2 36 files changed, 544 insertions(+), 476 deletions(-)
Title: Graphic Devices Based on AGG
Description: Anti-Grain Geometry (AGG) is a high-quality and high-performance
2D drawing library. The 'ragg' package provides a set of graphic devices
based on AGG to use as alternative to the raster devices provided through
the 'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
Maxim Shemanarev [aut, cph] (Author of AGG),
Tony Juricic [ctb, cph] (Contributor to AGG),
Milan Marusinec [ctb, cph] (Contributor to AGG),
Spencer Garrett [ctb] (Contributor to AGG),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between ragg versions 0.1.5 dated 2020-03-04 and 0.2.0 dated 2020-05-14
ragg-0.1.5/ragg/src/fonts.h |only ragg-0.1.5/ragg/tools/autobrew |only ragg-0.2.0/ragg/DESCRIPTION | 17 +- ragg-0.2.0/ragg/MD5 | 81 +++++---- ragg-0.2.0/ragg/NAMESPACE | 1 ragg-0.2.0/ragg/NEWS.md | 12 + ragg-0.2.0/ragg/R/agg_dev.R | 74 ++++++++ ragg-0.2.0/ragg/README.md | 29 +-- ragg-0.2.0/ragg/cleanup |only ragg-0.2.0/ragg/configure | 30 ++- ragg-0.2.0/ragg/man/agg_capture.Rd | 5 ragg-0.2.0/ragg/man/agg_jpeg.Rd |only ragg-0.2.0/ragg/man/agg_png.Rd | 7 ragg-0.2.0/ragg/man/agg_ppm.Rd | 5 ragg-0.2.0/ragg/man/agg_supertransparent.Rd | 5 ragg-0.2.0/ragg/man/agg_tiff.Rd | 5 ragg-0.2.0/ragg/man/figures/README-unnamed-chunk-3-1.png |binary ragg-0.2.0/ragg/man/figures/README-unnamed-chunk-4-1.png |binary ragg-0.2.0/ragg/man/ragg-package.Rd | 1 ragg-0.2.0/ragg/src/AggDevice.h | 32 ++- ragg-0.2.0/ragg/src/AggDevice16.h | 5 ragg-0.2.0/ragg/src/AggDeviceCapture.h | 9 - ragg-0.2.0/ragg/src/AggDeviceJpeg.h |only ragg-0.2.0/ragg/src/AggDevicePng.h | 5 ragg-0.2.0/ragg/src/AggDevicePpm.h | 5 ragg-0.2.0/ragg/src/AggDeviceTiff.h | 4 ragg-0.2.0/ragg/src/Makevars.win | 2 ragg-0.2.0/ragg/src/agg/include/agg_color_rgba.h | 2 ragg-0.2.0/ragg/src/agg/include/agg_rasterizer_scanline_aa.h | 4 ragg-0.2.0/ragg/src/capture_dev.cpp | 4 ragg-0.2.0/ragg/src/init.cpp | 17 -- ragg-0.2.0/ragg/src/init_device.h | 61 +++++++ ragg-0.2.0/ragg/src/jpeg_dev.cpp |only ragg-0.2.0/ragg/src/png_dev.cpp | 6 ragg-0.2.0/ragg/src/ppm_dev.cpp | 3 ragg-0.2.0/ragg/src/ragg.h | 40 +--- ragg-0.2.0/ragg/src/text_renderer.h | 91 ++++++----- ragg-0.2.0/ragg/src/tiff_dev.cpp | 3 ragg-0.2.0/ragg/tests |only 39 files changed, 394 insertions(+), 171 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-20 1.6-1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-23 0.4.9
2017-04-21 0.4.8
2015-05-25 0.4.7
2015-02-20 0.4.2
2013-12-08 0.4.1
2013-01-29 0.3.7
2013-01-04 0.3.5
2012-11-13 0.3.1
2012-01-23 0.2-2
2012-01-03 0.2-1
2011-12-19 0.2-0
2010-08-10 0.1-11
2010-07-27 0.1-10
2010-07-26 0.1-8
2010-07-24 0.1-7
2010-06-29 0.1-6
2010-05-20 0.1-5
2009-07-21 0.1-4
2009-05-19 0.1-3
2009-05-10 0.1-2
2009-05-04 0.1-1
2009-04-15 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-19 0.1-11.1
2012-12-21 0.1-11
2011-06-30 0.1-10
2008-03-27 0.1-8
2005-11-29 0.1-6
Title: Interface to 'Keras Tuner'
Description: 'Keras Tuner' <https://keras-team.github.io/keras-tuner/> is a hypertuning framework made for humans.
It aims at making the life of AI practitioners, hypertuner
algorithm creators and model designers as simple as possible by
providing them with a clean and easy to use API for hypertuning.
'Keras Tuner' makes moving from a base model to a hypertuned one quick and
easy by only requiring you to change a few lines of code.
Author: Turgut Abdullayev [aut, cre],
Google Inc. [cph]
Maintainer: Turgut Abdullayev <turqut.a.314@gmail.com>
Diff between kerastuneR versions 0.1.0.1 dated 2020-03-20 and 0.1.0.2 dated 2020-05-14
DESCRIPTION | 12 +++--- MD5 | 65 ++++++++++++++++++++++--------------- NAMESPACE | 14 +++++++ R/HyperResNet_HyperXception.R | 64 +++++++++++++++++++++++++++--------- R/Hyperclass.R | 2 - R/bayesian_optimisation.R | 49 +++++++++++++++++++++------ R/install.R | 33 +++++++++++++++--- R/oracle.R |only R/plot_keras_model.R |only R/plot_tuner.R | 61 +++++++++++++++++++--------------- R/random_search.R | 28 +++++++++++++-- R/save_load.R |only R/search.R | 49 +++++++++++++++++++-------- R/tensorboard.R |only R/version.R |only README.md | 38 +++++++++++++++++---- build/vignette.rds |binary inst/doc/BayesianOptimisation.R | 10 +++-- inst/doc/BayesianOptimisation.Rmd | 10 +++-- inst/doc/BayesianOptimisation.html | 40 +++++++++++----------- man/BayesianOptimization.Rd | 33 ++++++++++++------ man/HyperResNet.Rd | 13 +++---- man/HyperXception.Rd | 13 +++---- man/Hyperband.Rd | 14 +++++-- man/Oracle.Rd |only man/RandomSearch.Rd | 6 +-- man/TensorBoard.Rd |only man/fit_tuner.Rd | 6 ++- man/install_kerastuner.Rd | 11 +++++- man/keras_tuner_version.Rd |only man/load_model.Rd |only man/plot_keras_model.Rd |only man/plot_tuner.Rd | 7 +++ man/save_model.Rd |only tests/testthat/test-BayesOptim.R | 8 ++-- tests/testthat/test-build.R | 29 ++++++++++------ vignettes/BayesianOptimisation.Rmd | 10 +++-- vignettes/BayesianOptimisation.md |only vignettes/HyperModel_subclass.md |only vignettes/Introduction.md |only vignettes/MNIST.md |only 41 files changed, 427 insertions(+), 198 deletions(-)
Title: Star Layer for 'ggplot2'
Description: To create the regular polygon layer for easily discernible shapes,
we developed the package, it can be easily used if you know the 'ggplot2'.
Author: Shuangbin Xu [aut, cre] (<https://orcid.org/0000-0003-3513-5362>)
Maintainer: Shuangbin Xu <xshuangbin@163.com>
Diff between ggstar versions 0.0.4 dated 2020-03-19 and 0.0.5 dated 2020-05-14
ggstar-0.0.4/ggstar/inst/extdata |only ggstar-0.0.5/ggstar/DESCRIPTION | 13 ++++--- ggstar-0.0.5/ggstar/MD5 | 23 +++++-------- ggstar-0.0.5/ggstar/NEWS.md |only ggstar-0.0.5/ggstar/R/draw-key.R | 9 ++--- ggstar-0.0.5/ggstar/R/geom-star.R | 24 ++------------ ggstar-0.0.5/ggstar/R/primitive.R | 53 ++++++++++++------------------- ggstar-0.0.5/ggstar/R/utilities.R | 6 ++- ggstar-0.0.5/ggstar/inst/doc/ggstar.R | 4 +- ggstar-0.0.5/ggstar/inst/doc/ggstar.Rmd | 4 +- ggstar-0.0.5/ggstar/inst/doc/ggstar.html | 35 ++++++++++---------- ggstar-0.0.5/ggstar/vignettes/ggstar.Rmd | 4 +- 12 files changed, 78 insertions(+), 97 deletions(-)
Title: Material Management
Description: A set of functions, classes and methods for performing ABC and ABC/XYZ analyses, identifying overperforming, underperforming and constantly performing items, and plotting, analyzing as well as predicting the temporal development of items.
Author: Leon Binder [cre, aut],
Bernhard Bauer [aut],
Michael Scholz [aut]
Maintainer: Leon Binder <leon.binder@th-deg.de>
Diff between matman versions 1.0.0 dated 2020-04-28 and 1.1.0 dated 2020-05-14
DESCRIPTION | 14 +-- MD5 | 29 ++++--- NAMESPACE | 22 ++++++ NEWS.md |only R/ABCXYZanalysis.R | 49 ++++++++++--- R/DataPreparation.R | 9 +- R/Performer.R | 121 +++++++++++++++++++++++++++------ R/launchApp.R |only R/matman-package.R | 13 ++- R/shinyAppServer.R |only R/shinyAppUI.R |only man/ABCXYZComparison-class.Rd | 2 man/computeOverperformer.Rd | 8 +- man/computeUnderperformer.Rd | 8 +- man/expandData.Rd | 2 man/matman-package.Rd | 2 man/matmanDemo.Rd |only man/summary-ABCXYZComparison-method.Rd | 6 + 18 files changed, 220 insertions(+), 65 deletions(-)
Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene sets
typically used with the 'Gene Set Enrichment Analysis' (GSEA) software
(Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015
<doi:10.1016/j.cels.2015.12.004>) in a standard R data frame with key-value
pairs. The package includes the original human gene symbols and NCBI/Entrez
IDs as well as the equivalents for frequently studied model organisms such
as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 7.0.1 dated 2019-09-04 and 7.1.1 dated 2020-05-14
DESCRIPTION | 8 - MD5 | 24 ++--- NEWS.md | 5 + R/functions.R | 54 +++++++---- R/sysdata.rda |binary build/vignette.rds |binary inst/doc/msigdbr-intro.R | 3 inst/doc/msigdbr-intro.Rmd | 14 ++- inst/doc/msigdbr-intro.html | 181 ++++++++++++++++++++++------------------ man/msigdbr.Rd | 25 +++-- man/msigdbr_show_species.Rd | 5 - tests/testthat/test-functions.R | 6 + vignettes/msigdbr-intro.Rmd | 14 ++- 13 files changed, 202 insertions(+), 137 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi
platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 1.2.5 dated 2020-02-05 and 1.2.19 dated 2020-05-14
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- R/analysis.R | 28 ++++++++++++++++++++++++---- R/array.R | 8 ++++---- R/group.R | 2 +- R/image.R | 2 ++ R/options.R | 1 - R/results.R | 1 - R/table.R | 7 +++---- R/utils.R | 19 ++++++++++++++----- 11 files changed, 65 insertions(+), 36 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-11 1.2
2015-02-21 1.1
Title: SHAP Plots for 'XGBoost'
Description: The aim of 'SHAPforxgboost' is to aid in visual data investigations
using SHAP (SHapley Additive exPlanation) visualization plots for 'XGBoost'.
It provides summary plot, dependence plot, interaction plot, and force plot.
It relies on the 'dmlc/xgboost' package to produce SHAP values.
Please refer to 'slundberg/shap' for the original implementation of SHAP in 'Python'.
Author: Yang Liu [aut, cre] (<https://orcid.org/0000-0001-6557-6439>),
Allan Just [aut, ctb] (<https://orcid.org/0000-0003-4312-5957>)
Maintainer: Yang Liu <lyhello@gmail.com>
Diff between SHAPforxgboost versions 0.0.3 dated 2020-02-09 and 0.0.4 dated 2020-05-14
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/SHAP_funcs.R | 11 ++++++++++- R/example/example_categorical.R | 1 + R/example/example_dependence_plot.R | 3 ++- R/simple_plots.R | 23 ++++++++++++++++------- man/scatter.plot.diagonal.Rd | 5 ++++- man/scatter.plot.simple.Rd | 7 +++++-- man/shap.plot.dependence.Rd | 8 ++++++-- man/shap.prep.Rd | 1 + 10 files changed, 57 insertions(+), 26 deletions(-)
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Title: Phylogenetic Comparative Tools for Missing Data and
Within-Species Variation
Description: Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data. Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.
Author: Eric W. Goolsby, Jorn Bruggeman, Cecile Ane
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between Rphylopars versions 0.2.12 dated 2019-12-12 and 0.3.0 dated 2020-05-14
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 1 - man/Rphylopars-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 12 deletions(-)