Title: Drug Interaction Modeling Based on Loewe Additivity Following
Harbron's Approach
Description: Perform assessment of synergy/antagonism for drug combinations based
on the Loewe additivity model, following Harbron's approach (Statistics in
Medicine, 2010, <doi:10.1002/sim.3916>). The package allows flexible modeling
of the drug interaction index and supports "2-stage" estimation in addition
to "1-stage" estimation, including bootstrap-based confidence intervals.
The method requires data on the monotherapy responses and the package
accommodates both checkerboard and ray designs. Functions are available for
graphical exploration of model goodness-of-fit and diagnostics, as well as
for synergy/antagonism assessment in 2D and 3D.
Author: Maxim Nazarov, Nele Goeyvaerts, Chris Harbron (original article and code)
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>
Diff between drugCombo versions 1.2.0 dated 2021-06-07 and 1.2.1 dated 2021-06-29
DESCRIPTION | 8 MD5 | 10 R/plot.tauSurface.R | 3 build/vignette.rds |binary inst/NEWS | 2 inst/doc/userGuide.html | 4188 +++++++++++++++++++++++++++--------------------- 6 files changed, 2451 insertions(+), 1760 deletions(-)
Title: Biochemically Intuitive Generalized Loewe Model
Description: Response surface methods for drug synergy analysis. Available
methods include generalized and classical Loewe formulations as well as Highest
Single Agent methodology. Response surfaces can be plotted in an interactive
3-D plot and formal statistical tests for presence of synergistic effects are
available. Implemented methods and tests are described in the article
"BIGL: Biochemically Intuitive Generalized Loewe null model for prediction
of the expected combined effect compatible with partial agonism and antagonism"
by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas,
Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017)
<doi:10.1038/s41598-017-18068-5>.
Author: Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas, Stijn Hawinkel
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>
Diff between BIGL versions 1.6.2 dated 2021-03-10 and 1.6.3 dated 2021-06-29
DESCRIPTION | 8 MD5 | 14 R/confInt-functions.R | 5 build/vignette.rds |binary inst/NEWS | 2 inst/doc/analysis.html | 4555 ++++++++++++++++++++++++++-------------------- inst/doc/methodology.html | 30 tests/testthat.R | 3 8 files changed, 2696 insertions(+), 1921 deletions(-)
Title: Tools to Match Corporate Lending Portfolios with Climate Data
Description: These tools implement in R a fundamental part of the software
'PACTA' (Paris Agreement Capital Transition Assessment), which is a
free tool that calculates the alignment between financial portfolios
and climate scenarios (<https://2degrees-investing.org/>). Financial
institutions use 'PACTA' to study how their capital allocation
decisions align with climate change mitigation goals. This package
matches data from corporate lending portfolios to asset level data
from market-intelligence databases (e.g. power plant capacities,
emission factors, etc.). This is the first step to assess if a
financial portfolio aligns with climate goals.
Author: Mauro Lepore [aut, cre, ctr] (<https://orcid.org/0000-0002-1986-7988>),
Jackson Hoffart [aut] (<https://orcid.org/0000-0002-8600-5042>),
Klaus Hagedorn [aut],
Florence Palandri [aut],
Evgeny Petrovsky [aut],
2 Degrees Investing Initiative [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between r2dii.match versions 0.0.9 dated 2021-03-10 and 0.0.10 dated 2021-06-29
DESCRIPTION | 29 ++++++++++++++--------------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ README.md | 8 ++++---- man/r2dii.match-package.Rd | 22 +++++++++++----------- tests/testthat/_snaps/match_name.md | 4 ++-- tests/testthat/test-match_name.R | 1 + 7 files changed, 42 insertions(+), 38 deletions(-)
Title: Collection of Machine Learning Data Sets for 'mlr3'
Description: A small collection of interesting and educational machine
learning data sets which are used as examples in the 'mlr3' book
(<https://mlr3book.mlr-org.com>), the use case gallery
(<https://mlr3gallery.mlr-org.com>), or in other examples. All data
sets are properly preprocessed and ready to be analyzed by most
machine learning algorithms. Data sets are automatically added to the
dictionary of tasks if 'mlr3' is loaded.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Marc Becker [ctb] (<https://orcid.org/0000-0002-8115-0400>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3data versions 0.4.0 dated 2021-06-08 and 0.5.0 dated 2021-06-29
DESCRIPTION | 6 +++--- MD5 | 13 ++++++++----- NEWS.md | 12 +++++++++--- R/bike_sharing.R |only R/zzz.R | 11 ++++++----- README.md | 1 + data/bike_sharing.rda |only man/bike_sharing.Rd |only man/mlr3data-package.Rd | 11 ++++++++--- 9 files changed, 35 insertions(+), 19 deletions(-)
Title: Statistical Tests for Assessing Trinormal ROC Data
Description: Several statistical test functions as well as a function for exploratory data analysis to investigate classifiers allocating individuals to one of three disjoint and ordered classes. In a single classifier assessment the discriminatory power is compared to classification by chance. In a comparison of two classifiers the null hypothesis corresponds to equal discriminatory power of the two classifiers.
Author: Samuel Noll [aut],
Reinhard Furrer [cre, aut],
Benjamin Reiser [ctb],
Christos T. Nakas [ctb]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between trinROC versions 0.5 dated 2021-01-05 and 0.5.1 dated 2021-06-29
DESCRIPTION | 8 MD5 | 14 R/roc.eda.R | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/trinROC_vignette.html | 1151 +++++++++++++++++++----------------- tests/Examples/trinROC-Ex.Rout.save | 6 tests/testthat.Rout.save | 6 8 files changed, 657 insertions(+), 536 deletions(-)
Title: Datasets to Measure the Alignment of Corporate Loan Books with
Climate Goals
Description: These datasets support the implementation in R of the
software 'PACTA' (Paris Agreement Capital Transition Assessment),
which is a free tool that calculates the alignment between corporate
lending portfolios and climate scenarios
(<https://2degrees-investing.org/>). Financial institutions use
'PACTA' to study how their capital allocation decisions align with
climate change mitigation goals. Because both financial institutions
and market data providers keep their data private, this package
provides fake, public data to enable the development and use of
'PACTA' in R.
Author: Mauro Lepore [aut, cre, ctr] (<https://orcid.org/0000-0002-1986-7988>),
Jackson Hoffart [aut, dtc] (<https://orcid.org/0000-0002-8600-5042>),
Klaus Hagedorn [aut],
2 Degrees Investing Initiative [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between r2dii.data versions 0.1.9 dated 2021-03-01 and 0.2.0 dated 2021-06-29
DESCRIPTION | 22 ++++---- MD5 | 76 ++++++++++++++-------------- NEWS.md | 17 +++++- README.md | 30 +++++------ data/ald_demo.rda |binary data/cnb_classification.rda |binary data/co2_intensity_scenario_demo.rda |binary data/data_dictionary.rda |binary data/gics_classification.rda |binary data/green_or_brown.rda |binary data/isic_classification.rda |binary data/iso_codes.rda |binary data/loanbook_demo.rda |binary data/nace_classification.rda |binary data/naics_classification.rda |binary data/overwrite_demo.rda |binary data/psic_classification.rda |binary data/region_isos.rda |binary data/region_isos_demo.rda |binary data/scenario_demo_2020.rda |binary data/sector_classifications.rda |binary data/sic_classification.rda |binary inst/WORDLIST | 2 man/ald_demo.Rd | 8 +- man/cnb_classification.Rd | 2 man/gics_classification.Rd | 2 man/nace_classification.Rd | 2 man/naics_classification.Rd | 2 man/psic_classification.Rd | 2 man/r2dii.data-package.Rd | 16 +++-- man/scenario_demo_2020.Rd | 2 man/sic_classification.Rd | 2 tests/testthat/_snaps/ald_demo.md | 54 +++++++++++-------- tests/testthat/_snaps/data_dictionary.md | 6 +- tests/testthat/_snaps/green_or_brown.md | 6 +- tests/testthat/_snaps/scenario_demo_2020.md | 18 +++--- tests/testthat/test-ald_demo.R | 28 ++++++++-- tests/testthat/test-classification_bridge.R | 7 ++ tests/testthat/test-data_dictionary.R | 22 ++++++++ 39 files changed, 200 insertions(+), 126 deletions(-)
Title: Datasets for the 'canvasXpress' Package
Description: Contains the prepared data that is needed for the 'shiny' application examples in the
'canvasXpress' package. This package also includes datasets used for automated 'testthat' tests.
Scotto L, Narayan G, Nandula SV, Arias-Pulido H et al. (2008) <doi:10.1002/gcc.20577>.
Davis S, Meltzer PS (2007) <doi:10.1093/bioinformatics/btm254>.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre],
Ger Inberg [aut]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress.data versions 1.32.7 dated 2021-03-22 and 1.34.2 dated 2021-06-29
canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-CO2-dat.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-CO2-smp.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-CO2T-dat.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-CO2T-var.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-ageheightt-dat.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-ageheightt-smp.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-alcoholtobaccot-dat.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-alcoholtobaccot-smp.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-area-dat.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-area2-dat.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-area3-dat.txt.gz |only canvasXpress.data-1.32.7/canvasXpress.data/inst/extdata/cX-area4-dat.txt.gz 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canvasXpress.data-1.34.2/canvasXpress.data/man/get_data.Rd | 17 169 files changed, 35 insertions(+), 178 deletions(-)
More information about canvasXpress.data at CRAN
Permanent link
Title: Input Validation for Shiny Apps
Description: Improves the user experience of Shiny apps by helping to
provide feedback when required inputs are missing, or input values
are not valid.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>),
Joe Cheng [aut],
RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>
Diff between shinyvalidate versions 0.1.0 dated 2021-05-26 and 0.1.1 dated 2021-06-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/assets/shinyvalidate.js | 6 +++--- man/input_provided.Rd | 2 +- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Access the Twitter Academic Research Product Track V2 API
Endpoint
Description: Package to query the Twitter Academic Research Product Track,
providing access to full-archive search and other v2 API endpoints. Functions
are written with academic research in mind. They provide flexibility in how
the user wishes to store collected data, and encourage regular storage of data
to mitigate loss when collecting large volumes of tweets. They also provide
workarounds to manage and reshape the format in which data is provided on
the client side.
Author: Christopher Barrie [aut, cre] (<https://orcid.org/0000-0002-9156-990X>),
Justin Chun-ting Ho [aut] (<https://orcid.org/0000-0002-7884-1059>),
Chung-hong Chan [ctb] (<https://orcid.org/0000-0002-6232-7530>)
Maintainer: Christopher Barrie <christopher.barrie@ed.ac.uk>
Diff between academictwitteR versions 0.1.0 dated 2021-05-11 and 0.2.0 dated 2021-06-29
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More information about academictwitteR at CRAN
Permanent link
Title: Wrapper Functions for 'ODAM' (Open Data for Access and Mining)
Web Services
Description: 'ODAM' (Open Data for Access and Mining) is a framework that implements a simple way to make research data broadly accessible and fully available for reuse, including by a script language such as R. The main purpose is to make a data set accessible online with a minimal effort from the data provider, and to allow any scientists or bioinformaticians to be able to explore the data set and then extract a subpart or the totality of the data according to their needs. The Rodam package has only one class, 'odamws', that provides methods to allow you to retrieve online data using 'ODAM' Web Services. This obviously requires that data are implemented according the 'ODAM' approach , namely that the data subsets were deposited in the suitable data repository in the form of TSV files associated with their metadata also described in TSV files. See <https://inrae.github.io/ODAM/>.
Author: Daniel Jacob [cre, aut] (<https://orcid.org/0000-0002-6687-7169>)
Maintainer: Daniel Jacob <daniel.jacob@inrae.fr>
Diff between Rodam versions 0.1.6 dated 2019-03-21 and 0.1.8 dated 2021-06-29
DESCRIPTION | 21 +- MD5 | 21 +- R/odamws.R | 46 ++++-- README.md | 2 build/vignette.rds |binary inst/CITATION |only inst/doc/Rodam.R | 6 inst/doc/Rodam.Rmd | 4 inst/doc/Rodam.html | 360 +++++++++++++++++++++++++++------------------------ man/Rodam-package.Rd | 12 - man/odamws.Rd | 4 vignettes/Rodam.Rmd | 4 12 files changed, 265 insertions(+), 215 deletions(-)
Title: Visualize the Climate Scenario Alignment of a Financial
Portfolio
Description: Create plots to visualize the alignment of a corporate
lending portfolio to climate change scenarios based on climate
indicators (production and emission intensities) across key climate
relevant sectors of the 'PACTA' methodology (Paris Agreement Capital
Transition Assessment;
<https://www.transitionmonitor.com/pacta-for-banks-2020/methodology-and-supporting-materials/>).
Financial institutions use 'PACTA' to study how their capital
allocation decisions align with climate change mitigation goals.
Author: Monika Furdyna [aut, ctr, cre]
(<https://orcid.org/0000-0002-3728-0646>),
Mauro Lepore [aut, ctr] (<https://orcid.org/0000-0002-1986-7988>),
Alex Axthelm [aut, ctr] (<https://orcid.org/0000-0001-8579-8565>),
2 Degrees Investing Initiative [cph, fnd]
Maintainer: Monika Furdyna <monika.furdyna@gmail.com>
Diff between r2dii.plot versions 0.0.1 dated 2021-06-21 and 0.1.0 dated 2021-06-29
r2dii.plot-0.0.1/r2dii.plot/tests/testthat/_snaps/plot_trajectory.md |only r2dii.plot-0.1.0/r2dii.plot/DESCRIPTION | 10 r2dii.plot-0.1.0/r2dii.plot/MD5 | 74 + r2dii.plot-0.1.0/r2dii.plot/NAMESPACE | 5 r2dii.plot-0.1.0/r2dii.plot/NEWS.md |only r2dii.plot-0.1.0/r2dii.plot/R/imports.R | 4 r2dii.plot-0.1.0/r2dii.plot/R/plot_emission_intensity.R | 104 +- r2dii.plot-0.1.0/r2dii.plot/R/plot_techmix.R | 207 +++-- r2dii.plot-0.1.0/r2dii.plot/R/plot_trajectory.R | 386 +++++----- r2dii.plot-0.1.0/r2dii.plot/R/qplot_emission_intensity.R |only r2dii.plot-0.1.0/r2dii.plot/R/qplot_techmix.R |only r2dii.plot-0.1.0/r2dii.plot/R/qplot_trajectory.R |only r2dii.plot-0.1.0/r2dii.plot/R/r2dii_colours.R | 1 r2dii.plot-0.1.0/r2dii.plot/R/sysdata.rda |binary r2dii.plot-0.1.0/r2dii.plot/R/theme_2dii.R | 13 r2dii.plot-0.1.0/r2dii.plot/R/utils.R | 225 +++-- r2dii.plot-0.1.0/r2dii.plot/README.md | 221 +---- r2dii.plot-0.1.0/r2dii.plot/inst/WORDLIST | 4 r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-2-1.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-3-1.png |only r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-4-1.png |binary r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-5-1.png |binary r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-6-1.png |binary r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-7-1.png |binary r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-8-1.png |binary r2dii.plot-0.1.0/r2dii.plot/man/figures/README-unnamed-chunk-9-1.png |binary r2dii.plot-0.1.0/r2dii.plot/man/plot_emission_intensity.Rd | 1 r2dii.plot-0.1.0/r2dii.plot/man/plot_techmix.Rd | 3 r2dii.plot-0.1.0/r2dii.plot/man/plot_trajectory.Rd | 1 r2dii.plot-0.1.0/r2dii.plot/man/qplot_emission_intensity.Rd |only r2dii.plot-0.1.0/r2dii.plot/man/qplot_techmix.Rd |only r2dii.plot-0.1.0/r2dii.plot/man/qplot_trajectory.Rd |only r2dii.plot-0.1.0/r2dii.plot/man/r2dii_colours.Rd |only r2dii.plot-0.1.0/r2dii.plot/tests/testthat/_snaps/plot_emission_intensity.md | 20 r2dii.plot-0.1.0/r2dii.plot/tests/testthat/_snaps/plot_techmix.md | 44 - r2dii.plot-0.1.0/r2dii.plot/tests/testthat/_snaps/qplot_emission_intensity.md |only r2dii.plot-0.1.0/r2dii.plot/tests/testthat/_snaps/qplot_techmix.md |only r2dii.plot-0.1.0/r2dii.plot/tests/testthat/_snaps/qplot_trajectory.md |only r2dii.plot-0.1.0/r2dii.plot/tests/testthat/_snaps/r2dii_colours.md | 42 - r2dii.plot-0.1.0/r2dii.plot/tests/testthat/helper.R |only r2dii.plot-0.1.0/r2dii.plot/tests/testthat/test-plot_emission_intensity.R | 35 r2dii.plot-0.1.0/r2dii.plot/tests/testthat/test-plot_techmix.R | 123 +++ r2dii.plot-0.1.0/r2dii.plot/tests/testthat/test-plot_trajectory.R | 227 ----- r2dii.plot-0.1.0/r2dii.plot/tests/testthat/test-qplot_emission_intensity.R |only r2dii.plot-0.1.0/r2dii.plot/tests/testthat/test-qplot_techmix.R |only r2dii.plot-0.1.0/r2dii.plot/tests/testthat/test-qplot_trajectory.R |only r2dii.plot-0.1.0/r2dii.plot/tests/testthat/test-r2dii_colours.R | 4 47 files changed, 858 insertions(+), 896 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions
used in 'mlr3' and its companion packages. Comes with helper functions
for functional programming, for printing, to work with 'data.table',
as well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3misc versions 0.9.1 dated 2021-04-28 and 0.9.2 dated 2021-06-29
DESCRIPTION | 6 ++--- MD5 | 38 +++++++++++++++++----------------- NAMESPACE | 1 NEWS.md | 4 +++ R/Dictionary.R | 2 + R/encapsulate.R | 7 +++--- R/enframe.R | 3 +- R/formulate.R | 5 +--- R/insert_named.R | 4 +-- R/printf.R | 3 +- R/purrr_map.R | 3 +- R/rd_info.R | 7 +++--- R/require_namespaces.R | 6 +++-- R/str_collapse.R | 7 +++--- R/zzz.R | 2 - tests/testthat/test_Dictionary.R | 17 +++++++++++++-- tests/testthat/test_as_short_string.R | 24 ++++++++++----------- tests/testthat/test_encapsulate.R | 6 +++-- tests/testthat/test_has_element.R | 3 +- tests/testthat/test_with_package.R | 4 ++- 20 files changed, 92 insertions(+), 60 deletions(-)
Title: Provides 'mio' C++11 Header Files
Description: Provides header files of 'mio', a cross-platform C++11 header-only
library for memory mapped file IO <https://github.com/mandreyel/mio>.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between rmio versions 0.2.0 dated 2020-07-22 and 0.3.0 dated 2021-06-29
DESCRIPTION | 12 +++++------- MD5 | 6 +++--- NAMESPACE | 2 +- inst/include/rmio/create-file.hpp | 17 +++++++++++------ 4 files changed, 20 insertions(+), 17 deletions(-)
Title: A 'shiny' Application for the (Audio-)Visualization of Adverse
Event Profiles
Description: Contains a 'shiny' application called AdEPro (Animation of Adverse Event Profiles) which (audio-)visualizes adverse events occurring in clinical trials. As this data is usually considered sensitive, this tool is provided as a stand-alone application that can be launched from any local machine on which the data is stored.
Author: Nicole Mentenich, Bastian Becker, Christoph Tasto, Steffen Jeske
Maintainer: Nicole Mentenich <nicole.mentenich@bayer.com>
Diff between adepro versions 3.0.0 dated 2020-03-26 and 3.1.0 dated 2021-06-29
DESCRIPTION | 6 - MD5 | 21 ++-- NAMESPACE | 1 R/bar_chart.R | 10 +- R/launch_adepro.R | 144 +++++++++++++++++++------------- R/prepare_data.R | 22 +--- R/preproc_ae.R | 2 build/vignette.rds |binary inst/doc/adepro.html | 203 ++++++++++++++++++++++++++++++++++++++++++++-- inst/doc/adepro.rmd | 5 + tests/testthat/Rplots.pdf |only vignettes/adepro.rmd | 5 + 12 files changed, 319 insertions(+), 100 deletions(-)
Title: Libraries, Data Dictionaries, and a Data Step for R
Description: Contains a set of functions to create data libraries,
generate data dictionaries, and simulate a data step.
The libname() function will load a directory of data into
a library in one line of code. The dictionary() function
will generate data dictionaries for individual
data frames or an entire library. And the datestep() function
will perform row-by-row data processing.
Author: David J. Bosak
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between libr versions 1.1.3 dated 2021-02-08 and 1.2.0 dated 2021-06-29
DESCRIPTION | 15 - MD5 | 68 +++-- NAMESPACE | 72 ++--- NEWS.md | 22 + R/RcppExports.R |only R/datastep.R | 501 ++++++++++++++++++++++++++++++++----- R/dictionary.R | 24 + R/dsarray.R |only R/dsattr.R |only R/dshelpers.R |only R/libname.R | 256 +++++++++++++----- R/libr-package.R |only R/specs.R | 2 R/utilities.R | 22 + README.md | 1 build/vignette.rds |binary inst/doc/libr-basics.html | 9 inst/doc/libr-datastep.R | 86 ++++++ inst/doc/libr-datastep.Rmd | 117 ++++++++ inst/doc/libr-datastep.html | 105 +++++++ inst/doc/libr-eq.html | 9 inst/doc/libr-management.html | 9 inst/doc/libr.html | 9 man/datastep.Rd | 226 ++++++++++++++-- man/dictionary.Rd | 7 man/dsarray.Rd |only man/dsattr.Rd |only man/length.dsarray.Rd |only man/lib_copy.Rd | 12 man/libname.Rd | 58 ++-- man/sub-.dsarray.Rd |only src |only tests/testthat/test-datastep.R | 220 +++++++++------- tests/testthat/test-dictionary.R | 55 +++- tests/testthat/test-dsarray.R |only tests/testthat/test-dsattr.R |only tests/testthat/test-libname.R | 145 ++++++++++ tests/testthat/test-manipulation.R | 2 tests/testthat/test-performance.R |only tests/testthat/test-utilities.R | 20 + vignettes/libr-datastep.Rmd | 117 ++++++++ 41 files changed, 1840 insertions(+), 349 deletions(-)
Title: Predict Antimicrobial Peptides
Description: A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale.
It incorporates two support vector machine models ("precursor" and "mature") trained on publicly available antimicrobial peptide data using calculated
physico-chemical and compositional sequence properties described in Meher et al. (2017) <doi:10.1038/srep42362>.
In order to support genome-wide analyses, these models are designed to accept any type of protein as input
and calculation of compositional properties has been optimised for high-throughput use. For best results it is important to select the model that accurately
represents your sequence type: for full length proteins, it is recommended to use the default "precursor" model. The alternative, "mature", model is best suited
for mature peptide sequences that represent the final antimicrobial peptide sequence after post-translational processing. For details see Fingerhut et al. (2020) <doi:10.1093/bioinformatics/btaa653>.
The 'ampir' package is also available via a Shiny based GUI at <https://ampir.marine-omics.net/>.
Author: Legana Fingerhut [aut, cre] (<https://orcid.org/0000-0002-2482-5336>),
Ira Cooke [aut] (<https://orcid.org/0000-0001-6520-1397>),
Jinlong Zhang [ctb] (R/read_faa.R),
Nan Xiao [ctb] (R/calc_pseudo_comp.R)
Maintainer: Legana Fingerhut <legana.fingerhut@my.jcu.edu.au>
Diff between ampir versions 1.0.0 dated 2020-05-11 and 1.1.0 dated 2021-06-29
DESCRIPTION | 19 - MD5 | 34 +- NEWS.md | 7 R/calculate_features.R | 8 R/predict_amps.R | 11 R/remove_stop_codon.R |only R/sysdata.rda |binary README.md | 82 ++++--- build/vignette.rds |binary inst/doc/ampir.html | 275 +++++------------------ inst/doc/train_model.html | 344 ++++++++---------------------- man/remove_stop_codon.Rd |only tests/testthat/test-calc-pseudo-comp.R | 8 tests/testthat/test-calculate-features.R | 30 +- tests/testthat/test-chunk-rows.R | 14 - tests/testthat/test-df_to_faa.R | 2 tests/testthat/test-predict-amps.R | 73 ++++-- tests/testthat/test-read-faa.R | 5 tests/testthat/test-removenonstandardaa.R | 4 19 files changed, 331 insertions(+), 585 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-28 1.0.0
Title: A Collection of Models that Employ a Prior Distribution on
Partitions
Description: Provides functions that fit hierarchical Gaussian and probit ordinal models.
A (covariate dependent) product partition model is used as a prior.
If a covariate dependent product partition model is selected,
then all the options detailed in Page, G.L.; Quintana, F.A.; (2018)
<doi:10.1007/s11222-017-9777-z> are available. If covariate values
are missing, then the approach detailed in Page, G.L.; Quintana, F.A.;
Mueller, P (2020) <arXiv:1912.13119> is employed. Also included in the
package is a function that fits a Gaussian likelihood spatial product
partition model that is detailed in Page, G.L.; Quintana, F.A.; (2016)
<doi:10.1214/15-BA971>.
Author: Garritt L. Page [aut, cre, cph],
S. McKay Curtis [ctb, cph],
Radford M. Neal [ctb, cph]
Maintainer: Garritt L. Page <page@stat.byu.edu>
Diff between ppmSuite versions 0.1.6 dated 2021-05-29 and 0.1.7 dated 2021-06-29
DESCRIPTION | 6 +- MD5 | 14 +++--- R/ordinal_ppmx.R | 9 ++-- R/ppmx.R | 9 ++-- src/gaussian.ppmx.c | 4 - src/gaussian.ppmx.missing.c | 4 - src/ordinal.ppmx.c | 4 - src/ordinal.ppmx.missing.c | 89 +++----------------------------------------- 8 files changed, 36 insertions(+), 103 deletions(-)
Title: Single Cell Analysis and Differential Expression
Description: Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.
Author: Nikolas Barkas [aut],
Viktor Petukhov [aut],
Peter Kharchenko [aut],
Simon Steiger [ctb],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between pagoda2 versions 1.0.3 dated 2021-05-03 and 1.0.4 dated 2021-06-29
DESCRIPTION | 6 ++-- MD5 | 12 ++++----- R/Pagoda2.R | 1 R/pagoda2WebApp.R | 2 - README.md | 12 ++++----- build/vignette.rds |binary inst/doc/pagoda2.walkthrough.html | 47 +++++++++++++++++++++----------------- 7 files changed, 44 insertions(+), 36 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>, (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- league table with network meta-analysis results;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2019) <DOI:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- 'comparison-adjusted' funnel plot (Chaimani & Salanti, 2012) <DOI:10.1002/jrsm.57>;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>;
- rankograms based on SUCRA;
- contribution matrix as described in Papakonstantinou et al. (2018) <DOI:10.12688/f1000research.14770.3>.
Author: Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>),
Ulrike Krahn [aut],
Jochem König [aut] (<https://orcid.org/0000-0003-4683-0360>),
Orestis Efthimiou [aut] (<https://orcid.org/0000-0002-0955-7572>),
Theodoros Papakonstantinou [aut]
(<https://orcid.org/0000-0002-6630-6817>),
Guido Schwarzer [aut, cre] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 1.4-0 dated 2021-05-11 and 1.5-0 dated 2021-06-29
DESCRIPTION | 20 ++- MD5 | 52 +++++---- NAMESPACE | 8 + NEWS.md | 55 +++++++++ R/discomb.R | 121 ++++++++++----------- R/forest-internal.R | 8 + R/forest.netmeta.R | 109 ++++++++++++++----- R/forest.netsplit.R | 44 ++++++- R/netcomb.R | 43 +++++++ R/netcontrib.R |only R/netgraph.netimpact.R | 2 R/netgraph.netmeta.R | 30 +++-- R/netleague.R | 8 - R/netposet.R | 122 ++++++++++----------- R/netrank.R | 258 ++++++++++++++++++++++++++++++---------------- R/netsplit.R | 27 ++++ R/plot.netrank.R | 32 ++--- R/plot.rankogram.R |only R/rankogram.R |only man/discomb.Rd | 4 man/forest.netmeta.Rd | 25 ++-- man/forest.netsplit.Rd | 12 +- man/netcomb.Rd | 6 - man/netcontrib.Rd |only man/netgraph.netimpact.Rd | 2 man/netgraph.netmeta.Rd | 17 +-- man/netrank.Rd | 71 ++++++++---- man/netsplit.Rd | 4 man/plot.rankogram.Rd |only man/rankogram.Rd |only 30 files changed, 726 insertions(+), 354 deletions(-)
Title: HTML Metadata Tags for 'R Markdown' and 'Shiny'
Description: Create meta tags for 'R Markdown' HTML documents and 'Shiny'
apps for customized social media cards, for accessibility, and quality
search engine indexing. 'metathis' currently supports HTML documents
created with 'rmarkdown', 'shiny', 'xaringan', 'pagedown', 'bookdown',
and 'flexdashboard'.
Author: Garrick Aden-Buie [aut, cre] (<https://orcid.org/0000-0002-7111-0077>)
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between metathis versions 1.1.0 dated 2021-06-28 and 1.1.1 dated 2021-06-29
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 4 ++++ R/meta.R | 8 +++++++- R/utils.R |only tests/testthat/rmd/test-not-self-contained.Rmd | 4 ++-- tests/testthat/test-rmd.R | 3 ++- 7 files changed, 24 insertions(+), 12 deletions(-)
Title: Group Subset Selection
Description: Provides tools for sparse regression modelling with grouped predictors using the group
subset selection penalty. Uses coordinate descent and local search algorithms to rapidly deliver
near optimal estimates. The group subset penalty can be combined with a group lasso or ridge
penalty for added shrinkage. Linear and logistic regression are supported, as are overlapping
groups.
Author: Ryan Thompson [aut, cre] (<https://orcid.org/0000-0002-9002-0448>)
Maintainer: Ryan Thompson <ryan.thompson@monash.edu>
Diff between grpsel versions 1.0.0 dated 2021-04-21 and 1.1.0 dated 2021-06-29
grpsel-1.0.0/grpsel/R/grpsel-cv.R |only grpsel-1.1.0/grpsel/DESCRIPTION | 15 - grpsel-1.1.0/grpsel/MD5 | 50 ++-- grpsel-1.1.0/grpsel/NEWS.md | 5 grpsel-1.1.0/grpsel/R/cv-grpsel.R |only grpsel-1.1.0/grpsel/R/examples/example-cv-grpsel.R | 5 grpsel-1.1.0/grpsel/R/grpsel.R | 71 +++--- grpsel-1.1.0/grpsel/R/standardise.R | 22 - grpsel-1.1.0/grpsel/README.md | 68 ++++- grpsel-1.1.0/grpsel/build/vignette.rds |binary grpsel-1.1.0/grpsel/inst/CITATION |only grpsel-1.1.0/grpsel/inst/doc/vignette.R | 48 ++-- grpsel-1.1.0/grpsel/inst/doc/vignette.Rmd | 101 ++++---- grpsel-1.1.0/grpsel/inst/doc/vignette.html | 242 +++++++++++---------- grpsel-1.1.0/grpsel/man/coef.cv.grpsel.Rd | 8 grpsel-1.1.0/grpsel/man/coef.grpsel.Rd | 6 grpsel-1.1.0/grpsel/man/cv.grpsel.Rd | 32 +- grpsel-1.1.0/grpsel/man/grpsel.Rd | 17 - grpsel-1.1.0/grpsel/man/plot.cv.grpsel.Rd | 4 grpsel-1.1.0/grpsel/man/plot.grpsel.Rd | 2 grpsel-1.1.0/grpsel/man/predict.cv.grpsel.Rd | 10 grpsel-1.1.0/grpsel/man/predict.grpsel.Rd | 8 grpsel-1.1.0/grpsel/src/include/surface.h | 2 grpsel-1.1.0/grpsel/src/ls.cpp | 6 grpsel-1.1.0/grpsel/src/surface.cpp | 14 - grpsel-1.1.0/grpsel/tests |only grpsel-1.1.0/grpsel/vignettes/vignette.Rmd | 101 ++++---- 27 files changed, 461 insertions(+), 376 deletions(-)
Title: Continuous Time Distance-Based and Network-Based Individual
Level Models for Epidemics
Description: Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks. <doi:10.18637/jss.v098.i10>.
Author: Waleed Almutiry [aut, cre],
Rob Deardon [aut, ths],
Vineetha Warriyar K. V. [ctb]
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>
Diff between EpiILMCT versions 1.1.6 dated 2020-01-21 and 1.1.7 dated 2021-06-29
DESCRIPTION | 10 +++++----- MD5 | 3 ++- inst |only 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Determine and Evaluate Optimal Cutpoints in Binary
Classification Tasks
Description: Estimate cutpoints that optimize a specified metric in binary classification tasks
and validate performance using bootstrapping. Some methods for more robust cutpoint
estimation are supported, e.g. a parametric method assuming normal distributions,
bootstrapped cutpoints, and smoothing of the metric values per cutpoint using
Generalized Additive Models. Various plotting functions are included. For an overview
of the package see Thiele and Hirschfeld (2021) <doi:10.18637/jss.v098.i11>.
Author: Christian Thiele [cre, aut] (<https://orcid.org/0000-0002-1156-5117>)
Maintainer: Christian Thiele <c.thiele@gmx-topmail.de>
Diff between cutpointr versions 1.1.0 dated 2021-02-15 and 1.1.1 dated 2021-06-29
DESCRIPTION | 10 MD5 | 29 NEWS.md | 7 R/cutpointr.R | 6 R/data.R | 70 - R/metrics.R | 1694 +++++++++++++++--------------- build/vignette.rds |binary inst/CITATION |only inst/doc/cutpointr.html | 17 man/cutpointr.Rd | 6 man/cutpointr_.Rd | 4 man/figures/README-unnamed-chunk-36-3.png |binary man/figures/README-unnamed-chunk-36-4.png |binary man/figures/README-unnamed-chunk-36-5.png |binary man/figures/README-unnamed-chunk-36-6.png |binary man/metric_constrain.Rd | 42 16 files changed, 986 insertions(+), 899 deletions(-)
Title: Clustering on Network of Samples
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Author: Viktor Petukhov [aut],
Nikolas Barkas [aut],
Peter Kharchenko [aut],
Weiliang Qiu [ctb],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between conos versions 1.4.1 dated 2021-05-15 and 1.4.2 dated 2021-06-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/conclass.R | 2 +- R/conos.R | 8 ++++---- README.md | 4 ++-- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Heart Rate Turbulence Analysis
Description: Methods to scan RR interval data for Premature Ventricular Complexes (PVCs) and parameterise and plot the resulting Heart Rate Turbulence (HRT). The methodology of HRT analysis is based on the original publication by Schmidt et al. <doi:10.1016/S0140-6736(98)08428-1> and extended with suggestions from <doi:10.1088/1361-6579/ab98b3>.
Author: Valeria Blesius [aut, cre] (<https://orcid.org/0000-0002-2391-242X>)
Maintainer: Valeria Blesius <valeria.blesius@mni.thm.de>
Diff between RHRT versions 1.0 dated 2021-06-23 and 1.0.1 dated 2021-06-29
DESCRIPTION | 6 - MD5 | 40 +++++----- R/HRTList.R | 25 ++++-- R/conversion_to_HRT.R | 2 data/testdataLong.rda |binary inst/doc/rhrt-vignette.Rmd | 4 - inst/doc/rhrt-vignette.html | 36 ++++----- man/figures/README-example-1.png |binary man/vectorToHRT.Rd | 11 +- tests/testthat/testdata/testdataRegular.rda |binary tests/testthat/testdata/testdataRegular_HRTObj.rda |binary tests/testthat/testdata/testdataVariant.rda |binary tests/testthat/testdata/testdataVariantNoHRT.rda |binary tests/testthat/testdata/testdataVariant_HRTObj.rda |binary vignettes/rhrt-vignette.Rmd | 4 - vignettes/rhrt-vignette_files/figure-html/unnamed-chunk-10-1.png |binary vignettes/rhrt-vignette_files/figure-html/unnamed-chunk-11-1.png |binary vignettes/rhrt-vignette_files/figure-html/unnamed-chunk-12-1.png |binary vignettes/rhrt-vignette_files/figure-html/unnamed-chunk-13-1.png |binary vignettes/rhrt-vignette_files/figure-html/unnamed-chunk-8-1.png |binary vignettes/rhrt-vignette_files/figure-html/unnamed-chunk-9-1.png |binary 21 files changed, 71 insertions(+), 57 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Creates matrix population models for use in population ecological
analyses. Specializes on the construction of historical matrices,
which are 2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices. Methodology based on Ehrlen
(2000) <doi:10.1890/0012-9658(2000)081[1675:TDOPPD]2.0.CO;2>.
Author: Richard P. Shefferson [aut, cre]
(<https://orcid.org/0000-0002-5234-3131>),
Johan Ehrlen [aut] (<https://orcid.org/0000-0001-8539-8967>)
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 3.4.0 dated 2021-04-02 and 3.5.0 dated 2021-06-29
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lefko3-3.5.0/lefko3/R/matrixcreation.R | 465 +++----- lefko3-3.5.0/lefko3/R/modelselection.R | 294 ++--- lefko3-3.5.0/lefko3/R/popchar.R | 299 +++-- lefko3-3.5.0/lefko3/R/popdyn.R | 500 ++++---- lefko3-3.5.0/lefko3/build/vignette.rds |binary lefko3-3.5.0/lefko3/inst/doc/Chapter1.Rmd | 125 +- lefko3-3.5.0/lefko3/inst/doc/Chapter1.html | 122 +- lefko3-3.5.0/lefko3/inst/doc/Chapter2.Rmd | 256 ++-- lefko3-3.5.0/lefko3/inst/doc/Chapter2.html | 523 ++++----- lefko3-3.5.0/lefko3/inst/doc/Chapter5.Rmd | 205 +-- lefko3-3.5.0/lefko3/inst/doc/Chapter5.html | 413 +++---- lefko3-3.5.0/lefko3/inst/doc/Chapter6.Rmd | 268 +--- lefko3-3.5.0/lefko3/inst/doc/Chapter6.html | 596 ++++------ lefko3-3.5.0/lefko3/inst/doc/Chapter8.Rmd | 165 +- lefko3-3.5.0/lefko3/inst/doc/Chapter8.html | 438 +++---- lefko3-3.5.0/lefko3/man/aflefko2.Rd | 14 lefko3-3.5.0/lefko3/man/cond_hmpm.Rd | 13 lefko3-3.5.0/lefko3/man/cypdata.Rd | 69 + lefko3-3.5.0/lefko3/man/cypvert.Rd | 1 lefko3-3.5.0/lefko3/man/elasticity3.Rd | 13 lefko3-3.5.0/lefko3/man/elasticity3.lefkoMat.Rd | 37 lefko3-3.5.0/lefko3/man/elasticity3.list.Rd | 38 lefko3-3.5.0/lefko3/man/elasticity3.matrix.Rd | 13 lefko3-3.5.0/lefko3/man/flefko2.Rd | 76 - 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Title: Draw Venn Diagram by 'ggplot2'
Description: An easy-to-use way to draw pretty venn diagram by 'ggplot2'.
Author: Linlin Yan [aut, cre] (<https://orcid.org/0000-0002-4990-6239>)
Maintainer: Linlin Yan <yanlinlin82@gmail.com>
Diff between ggvenn versions 0.1.8 dated 2021-01-13 and 0.1.9 dated 2021-06-29
DESCRIPTION | 7 +++---- MD5 | 6 +++--- R/ggvenn.R | 5 +++-- README.md | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-06 4.1-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-01 0.2.3
2021-04-23 0.2.2
Title: Simple Features for R
Description: Support for simple features, a standardized way to
encode spatial vector data. Binds to 'GDAL' for reading and writing
data, to 'GEOS' for geometrical operations, and to 'PROJ' for
projection conversions and datum transformations. Uses by default the 's2'
package for spherical geometry operations on ellipsoidal (long/lat) coordinates.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Kirill Müller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [ctb],
Dewey Dunnington [ctb] (<https://orcid.org/0000-0002-9415-4582>)
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 1.0-0 dated 2021-06-09 and 1.0-1 dated 2021-06-29
DESCRIPTION | 15 ++++++++------- MD5 | 46 +++++++++++++++++++++++----------------------- NAMESPACE | 2 ++ NEWS.md | 10 ++++++++++ R/aggregate.R | 2 +- R/crs.R | 9 +++++++-- R/geom-transformers.R | 34 +++++++++++++--------------------- R/init.R | 2 +- R/plot.R | 2 ++ R/sp.R | 12 +++++++++--- configure | 6 +++++- configure.ac | 6 +++++- inst/doc/sf1.html | 6 +++--- inst/doc/sf2.html | 6 +++--- inst/doc/sf4.html | 2 +- inst/doc/sf5.html | 6 +++--- inst/doc/sf6.html | 2 +- inst/doc/sf7.html | 8 ++++---- man/geos_unary.Rd | 6 +++--- man/interpolate_aw.Rd | 2 +- src/gdal.cpp | 16 ++++++++++++++-- tests/crs.Rout.save | 19 +++++++++++-------- tests/geos.Rout.save | 6 +++--- tests/roundtrip.Rout.save | 10 ++++------ 24 files changed, 137 insertions(+), 98 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from <http://tamivox.org/dave/multinomial/index.html> and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here <https://jeromekelleher.net/category/combinatorics.html>. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between multicool versions 0.1-11 dated 2019-12-05 and 0.1-12 dated 2021-06-29
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- R/Stirling2.R | 4 ++-- R/genComp.R | 7 +++---- man/Bell.Rd | 2 +- man/Stirling2.Rd | 2 +- man/genComp.Rd | 7 +++---- man/nextPerm.Rd | 2 +- src/compositions.cpp | 2 +- src/multicool.cpp | 8 ++++---- 10 files changed, 31 insertions(+), 33 deletions(-)
Title: Multivariate Analysis for Neuroimaging Data
Description: Several functions can be used to analyze neuroimaging data using multivariate methods based on the 'msma' package. The functions used in the book entitled "Multivariate Analysis for Neuroimaging Data" (2021, ISBN-13: 978-0367255329) are contained. Please also see Kawaguchi et al. (2017) <doi:10.1093/biostatistics/kxx011> and Kawaguchi (2019) <DOI:10.5772/intechopen.80531>.
Author: Atsushi Kawaguchi [aut, cre]
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>
Diff between mand versions 0.1 dated 2020-05-06 and 1.0 dated 2021-06-29
DESCRIPTION | 15 ++++++++------- MD5 | 37 ++++++++++++++++++++++++++++++++++--- R/src.r | 28 +++++++++++++++++++++------- build |only data/sdevimg.rda |only inst/CITATION | 25 ++++++++----------------- inst/doc |only man/sdevimg.Rd |only vignettes |only 9 files changed, 71 insertions(+), 34 deletions(-)
Title: Task Oriented Interface for Exploratory Data Analysis
Description: Enables users to create visualizations using functions
based on the data analysis task rather than on plotting mechanics. It hides
the details of the individual 'ggplot2' function calls and
allows the user to focus on the end goal. Useful for quick preliminary explorations.
Provides functions for common exploration patterns. Some of the ideas in this
package are motivated by Fox (2015, ISBN:1938377052).
Author: Viswa Viswanathan [aut, cre] (<https://orcid.org/0000-0003-4395-5061>)
Maintainer: Viswa Viswanathan <kv.viswana@gmail.com>
Diff between ezEDA versions 0.1.0 dated 2020-06-25 and 0.1.1 dated 2021-06-29
DESCRIPTION | 13 MD5 | 31 R/contributions.R | 2 build/vignette.rds |binary inst/doc/ezEDA.html | 491 ++++++++--- man/figures |only tests/testthat/test_category_contribution.R | 7 tests/testthat/test_category_tally.R | 4 tests/testthat/test_measure_change_over_time_long.R | 4 tests/testthat/test_measure_change_over_time_wide.R | 4 tests/testthat/test_measure_distribution.R | 12 tests/testthat/test_measure_distribution_by_category.R | 18 tests/testthat/test_measure_distribution_by_two_caregories.R | 6 tests/testthat/test_measure_distribution_over_time.R | 6 tests/testthat/test_two_category_contribution.R | 2 tests/testthat/test_two_category_tally.R | 4 tests/testthat/test_two_measures_relationship.R | 4 17 files changed, 420 insertions(+), 188 deletions(-)