Title: Agent-Based Models in R
Description: Supplies tools for running agent-based models (ABM) in R, as discussed in Gochanour et al. (2021) <doi:10.1101/2021.09.15.460374> The package contains two movement functions, each of which is based on the Ornstein-Uhlenbeck (OU) model (Ornstein & Uhlenbeck, 1930) <doi:10.1103/PhysRev.36.823>. It also contains several visualization and data summarization functions to facilitate the presentation of simulation results.
Author: Benjamin Gochanour [aut, cre],
Javier Fernandez-Lopez [aut],
Andrea Contina [aut]
Maintainer: Benjamin Gochanour <ben.gochanour@gmail.com>
Diff between abmR versions 1.0.6 dated 2022-08-16 and 1.0.8 dated 2023-01-15
DESCRIPTION | 13 ++++------ MD5 | 26 ++++++++++---------- NAMESPACE | 2 - R/energySIM.R | 4 +-- R/energySIM_helper.R | 2 - R/energyVIZ.R | 66 +++++++++++++++++++++++++++++++-------------------- R/get_ex_data.R | 2 - R/moveSIM.R | 2 - R/moveSIM_helper.R | 2 - R/moveVIZ.R | 40 +++++++++++++++++------------- README.md | 5 --- man/energySIM.Rd | 2 - man/energyVIZ.Rd | 2 - man/moveVIZ.Rd | 2 - 14 files changed, 91 insertions(+), 79 deletions(-)
Title: moDel Agnostic Language for Exploration and eXplanation
Description: Any unverified black box model is the path to failure. Opaqueness leads to distrust.
Distrust leads to ignoration. Ignoration leads to rejection.
DALEX package xrays any model and helps to explore and explain its behaviour.
Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance. But such black-box models usually lack direct interpretability.
DALEX package contains various methods that help to understand the link between input variables
and model output. Implemented methods help to explore the model on the level of a single instance
as well as a level of the whole dataset.
All model explainers are model agnostic and can be compared across different models.
DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration.
Find more details in (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] ,
Szymon Maksymiuk [aut] ,
Hubert Baniecki [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 2.4.2 dated 2022-06-15 and 2.4.3 dated 2023-01-15
DESCRIPTION | 8 +++--- MD5 | 24 ++++++++++++-------- NAMESPACE | 7 +++++ R/misc_set_theme_dalex.R |only R/model_performance.R | 3 +- R/plot_model_diagnostics.R | 2 - R/plot_model_performance.R | 14 +++++------ R/plot_predict_diagnostics.R | 2 - R/plot_shap_aggregated.R |only R/predict_parts.R | 22 +++++++++++++++--- R/shap_aggregated.R |only man/plot.shap_aggregated.Rd |only man/predict_parts.Rd | 8 +++++- man/shap_aggregated.Rd |only man/theme_dalex.Rd |only tests/testthat/test_predict_parts.R | 43 ++++++++++++++++++++++++++++++++++++ 16 files changed, 105 insertions(+), 28 deletions(-)
Title: Triangle - A 2D Quality Mesh Generator and Delaunay Triangulator
Description: This is a port of Jonathan Shewchuk's Triangle library to
R. From his description: "Triangle generates exact Delaunay
triangulations, constrained Delaunay triangulations, conforming
Delaunay triangulations, Voronoi diagrams, and high-quality
triangular meshes. The latter can be generated with no small or
large angles, and are thus suitable for finite element analysis."
Author: Jonathan Richard Shewchuk [ctb, cph],
David C. Sterratt [cph, aut, cre],
Elias Pipping [ctb],
Michael Sumner [ctb]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between RTriangle versions 1.6-0.11 dated 2022-11-15 and 1.6-0.12 dated 2023-01-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 9 +++++++++ src/interface.c | 26 +++++++++++++------------- 4 files changed, 29 insertions(+), 20 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.11.4.2.1 dated 2022-11-09 and 0.11.4.3.1 dated 2023-01-15
ChangeLog | 25 + DESCRIPTION | 8 MD5 | 34 +- configure | 18 - configure.ac | 4 inst/NEWS.Rd | 18 + inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/RcppArmadillo/config/RcppArmadilloConfig.h | 11 inst/include/RcppArmadillo/interface/RcppArmadilloForward.h | 15 - inst/include/armadillo_bits/arma_config.hpp | 7 inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/compiler_check.hpp | 10 inst/include/armadillo_bits/compiler_setup.hpp | 2 inst/include/armadillo_bits/constants_old.hpp | 159 ++---------- inst/include/armadillo_bits/debug.hpp | 15 - inst/include/armadillo_bits/op_pinv_meat.hpp | 29 -- src/RcppExports.cpp | 2 18 files changed, 155 insertions(+), 204 deletions(-)
Title: Multivariate Normal Distribution
Description: Calculates and differentiates probabilities and density of (conditional) multivariate normal distribution and Gaussian copula (with various marginal distributions) using methods described in A. Genz (2004) <doi:10.1023/B:STCO.0000035304.20635.31>, A. Genz, F. Bretz (2009) <doi:10.1007/978-3-642-01689-9> and E. Kossova, B. Potanin (2018) <https:ideas.repec.org/a/ris/apltrx/0346.html>.
Author: Bogdan Potanin [aut, cre, ctb]
Maintainer: Bogdan Potanin <bogdanpotanin@gmail.com>
Diff between mnorm versions 1.0.1 dated 2022-05-16 and 1.1.0 dated 2023-01-15
DESCRIPTION | 15 MD5 | 23 NAMESPACE | 4 R/RcppExports.R | 42 + inst/include/mnorm_RcppExports.h | 49 - man/cmnorm.Rd | 4 man/dmnorm.Rd | 4 man/pmnorm.Rd | 135 ++++ man/rmnorm.Rd |only src/RcppExports.cpp | 95 +-- src/pmnorm.cpp | 1140 ++++++++++++++++++++++++++++++++++----- src/pmnorm.h | 13 src/rmnorm.cpp |only src/rmnorm.h |only 14 files changed, 1285 insertions(+), 239 deletions(-)
Title: Interfaces to Various State-of-Art SVD and Eigensolvers
Description: R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
Author: Anton Korobeynikov [aut, cre], Rasmus Munk Larsen [ctb, cph], Lawrence Berkeley National Laboratory [ctb, cph]
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between svd versions 0.5.2 dated 2022-07-10 and 0.5.3 dated 2023-01-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/trlan/trlaux.c | 8 ++++---- src/trlan/trlcore.c | 36 ++++++++++++++++++------------------ src/trlan/ztrlcore.c | 28 ++++++++++++++-------------- 5 files changed, 43 insertions(+), 43 deletions(-)
Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in parallel,
so metadata resolution and package downloads are fast. Metadata and package
files are cached on the local disk as well. 'pak' has a dependency solver,
so it finds version conflicts before performing the installation. This
version of 'pak' supports CRAN, 'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pak versions 0.3.1 dated 2022-09-08 and 0.4.0 dated 2023-01-15
pak-0.3.1/pak/man/chunks/config.Rmd |only pak-0.3.1/pak/man/config.Rd |only pak-0.3.1/pak/man/tldr.Rd |only pak-0.4.0/pak/DESCRIPTION | 13 pak-0.4.0/pak/MD5 | 139 +++--- pak-0.4.0/pak/NEWS.md | 59 ++ pak-0.4.0/pak/R/cache.R | 57 +- pak-0.4.0/pak/R/deps-explain.R | 17 pak-0.4.0/pak/R/docs.R | 207 +++++++++ pak-0.4.0/pak/R/errors.R | 147 +++++-- pak-0.4.0/pak/R/global-handler.R | 2 pak-0.4.0/pak/R/library.R | 7 pak-0.4.0/pak/R/local.R | 18 pak-0.4.0/pak/R/name-check.R | 4 pak-0.4.0/pak/R/onload.R | 3 pak-0.4.0/pak/R/package.R | 303 ++++---------- pak-0.4.0/pak/R/pak-install.R | 4 pak-0.4.0/pak/R/pak.R | 4 pak-0.4.0/pak/R/repo.R | 30 + pak-0.4.0/pak/R/search.R | 24 - pak-0.4.0/pak/R/subprocess.R | 41 + pak-0.4.0/pak/R/system-requirements.R | 16 pak-0.4.0/pak/R/utils.R | 23 + pak-0.4.0/pak/cleanup |only pak-0.4.0/pak/configure |only pak-0.4.0/pak/configure.win |only pak-0.4.0/pak/man/cache.Rd | 104 ++++ pak-0.4.0/pak/man/chunks/FAQ.Rmd | 27 + pak-0.4.0/pak/man/chunks/features.Rmd | 8 pak-0.4.0/pak/man/chunks/install.Rmd | 40 + pak-0.4.0/pak/man/chunks/tldr.Rmd | 70 +++ pak-0.4.0/pak/man/faq.Rd | 336 ++++------------ pak-0.4.0/pak/man/features.Rd | 16 pak-0.4.0/pak/man/figures/cran-dark.svg |only pak-0.4.0/pak/man/figures/cran.svg | 2 pak-0.4.0/pak/man/figures/deps-dark.svg |only pak-0.4.0/pak/man/figures/deps.svg | 2 pak-0.4.0/pak/man/figures/explain-dark.svg |only pak-0.4.0/pak/man/figures/explain.svg | 2 pak-0.4.0/pak/man/figures/gh-dark.svg |only pak-0.4.0/pak/man/figures/gh.svg | 2 pak-0.4.0/pak/man/figures/local-dark.svg |only pak-0.4.0/pak/man/figures/local.svg | 2 pak-0.4.0/pak/man/figures/tldr-cran.svg | 2 pak-0.4.0/pak/man/get-started.Rd |only pak-0.4.0/pak/man/handle_package_not_found.Rd | 2 pak-0.4.0/pak/man/install.Rd | 52 +- pak-0.4.0/pak/man/lib_status.Rd | 32 + pak-0.4.0/pak/man/local_deps.Rd | 15 pak-0.4.0/pak/man/local_deps_explain.Rd | 15 pak-0.4.0/pak/man/local_install.Rd | 37 + pak-0.4.0/pak/man/local_install_deps.Rd | 37 + pak-0.4.0/pak/man/local_install_dev_deps.Rd | 39 + pak-0.4.0/pak/man/local_package_trees.Rd | 6 pak-0.4.0/pak/man/lockfile_create.Rd | 54 +- pak-0.4.0/pak/man/macros |only pak-0.4.0/pak/man/metadata.Rd | 125 +++++ pak-0.4.0/pak/man/package-dependency-types.Rd |only pak-0.4.0/pak/man/pak-config.Rd |only pak-0.4.0/pak/man/pak.Rd | 5 pak-0.4.0/pak/man/pak_package_sources.Rd | 184 -------- pak-0.4.0/pak/man/pak_sitrep.Rd | 26 + pak-0.4.0/pak/man/pak_solver.Rd |only pak-0.4.0/pak/man/pkg_deps.Rd | 93 +++- pak-0.4.0/pak/man/pkg_deps_explain.Rd | 77 +++ pak-0.4.0/pak/man/pkg_deps_tree.Rd | 140 ++++++ pak-0.4.0/pak/man/pkg_download.Rd | 85 +++- pak-0.4.0/pak/man/pkg_history.Rd | 38 + pak-0.4.0/pak/man/pkg_install.Rd | 214 ++++++++-- pak-0.4.0/pak/man/pkg_name_check.Rd | 35 + pak-0.4.0/pak/man/pkg_remove.Rd | 6 pak-0.4.0/pak/man/pkg_search.Rd | 78 +++ pak-0.4.0/pak/man/pkg_status.Rd | 31 + pak-0.4.0/pak/man/repo_add.Rd | 82 +++ pak-0.4.0/pak/man/repo_get.Rd | 22 - pak-0.4.0/pak/man/repo_status.Rd | 70 +++ pak-0.4.0/pak/man/roxygen/meta.R | 9 pak-0.4.0/pak/tests/testthat/test-system-requirements.R | 16 pak-0.4.0/pak/tools |only 79 files changed, 2278 insertions(+), 1078 deletions(-)
Title: Client for Dataverse 4+ Repositories
Description: Provides access to Dataverse APIs <https://dataverse.org/> (versions 4-5),
enabling data search, retrieval, and deposit. For Dataverse versions <= 3.0,
use the archived 'dvn' package <https://cran.r-project.org/package=dvn>.
Author: Shiro Kuriwaki [aut, cre] ,
Will Beasley [aut] ,
Thomas J. Leeper [aut] ,
Philip Durbin [aut] ,
Sebastian Karcher [aut] ,
Jan Kanis [ctb],
Edward Jee [ctb]
Maintainer: Shiro Kuriwaki <shirokuriwaki@gmail.com>
Diff between dataverse versions 0.3.11 dated 2022-06-11 and 0.3.12 dated 2023-01-15
DESCRIPTION | 6 MD5 | 16 - NEWS.md | 3 build/vignette.rds |binary inst/constants.yml | 6 inst/doc/A-introduction.html | 393 ++++++++++++++++++++++----- inst/doc/B-search.html | 355 +++++++++++++++++++------ inst/doc/C-download.html | 422 ++++++++++++++++++++++++------ tests/testthat/tests-dataverse_contents.R | 1 9 files changed, 952 insertions(+), 250 deletions(-)
Title: Exploratory and Descriptive Event-Based Data Analysis
Description: Exploratory and descriptive analysis of event based data. Provides methods for describing and selecting process data, and for preparing event log data for process mining. Builds on the S3-class for event logs implemented in the package 'bupaR'.
Author: Gert Janssenswillen [aut, cre],
Gerard van Hulzen [ctb],
Marijke Swennen [ctb],
Ivan Esin [ctb],
Hasselt University [cph]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between edeaR versions 0.9.1 dated 2022-10-03 and 0.9.2 dated 2023-01-15
DESCRIPTION | 17 +- MD5 | 118 ++++++++------- NAMESPACE | 15 ++ NEWS.md | 29 +++ R/create_precedence_df.R |only R/edeaR.R | 2 R/filter_activity_presence.R | 4 R/filter_endpoints_condition.R | 16 +- R/filter_flow_time.R |only R/filter_idle_time.R |only R/filter_idle_time_percentage.R |only R/filter_idle_time_threshold.R |only R/filter_precedence.R | 2 R/filter_processing_time.R | 64 +++++--- R/filter_throughput_time.R | 32 +--- R/filter_time_period.R | 2 R/idle_time.R | 52 +++---- R/idle_time_case.R | 57 ++++++- R/idle_time_resource.R | 58 ++++++- R/processing_time.R | 27 ++- R/resource_involvement_resource_activity.R | 2 R/throughput_time.R | 43 +++-- R/throughput_time_trace.R | 10 - README.md | 2 inst/doc/filters.html | 117 +++++++-------- inst/doc/metrics.html | 115 +++++++-------- inst/doc/queue.html | 115 +++++++-------- inst/doc/work_schedules.html | 115 +++++++-------- man/edeaR.Rd | 2 man/filter_activity.Rd | 2 man/filter_activity_frequency.Rd | 2 man/filter_activity_instance.Rd | 2 man/filter_activity_presence.Rd | 2 man/filter_case.Rd | 2 man/filter_case_condition.Rd | 2 man/filter_endpoints.Rd | 2 man/filter_endpoints_condition.Rd | 2 man/filter_flow_time.Rd |only man/filter_idle_time.Rd |only man/filter_infrequent_flows.Rd | 2 man/filter_lifecycle.Rd | 2 man/filter_lifecycle_presence.Rd | 2 man/filter_precedence.Rd | 4 man/filter_precedence_condition.Rd | 2 man/filter_precedence_resource.Rd | 4 man/filter_processing_time.Rd | 20 +- man/filter_resource.Rd | 2 man/filter_resource_frequency.Rd | 2 man/filter_throughput_time.Rd | 20 +- man/filter_time_period.Rd | 2 man/filter_trace.Rd | 2 man/filter_trace_frequency.Rd | 2 man/filter_trace_length.Rd | 2 man/filter_trim.Rd | 2 man/filter_trim_lifecycle.Rd | 2 man/idle_time.Rd | 16 +- man/processing_time.Rd | 2 man/throughput_time.Rd | 21 +- man/trace_coverage.Rd | 2 man/trace_length.Rd | 2 tests/bench/bench_idle_time.R |only tests/testthat/test_idle_time.R | 160 +++++++++++++++++++++ tests/testthat/test_processing_time.R | 214 ++++++++++++++++++++++++++++- tests/testthat/test_throughput_time.R | 119 +++++++++++++++- 64 files changed, 1147 insertions(+), 493 deletions(-)
Title: Optimal Analysis of Test and Rating Scale Data
Description: Develop, evaluate, and score multiple choice examinations,
psychological scales, questionnaires, and similar types of data involving
sequences of choices among one or more sets of answers.
This version of the package should be considered as brand new. Almost all
of the functions have been changed, including their argument list.
See the file NEWS.Rd in the Inst folder for more information.
Using the package does not require any formal statistical knowledge
beyond what would be provided by a first course in statistics in a
social science department. There the user would encounter the concept
of probability and how it is used to model data and make decisions,
and would become familiar with basic mathematical and statistical notation.
Most of the output is in graphical form.
Author: James Ramsay [aut, cre],
Juan Li [ctb],
Marie Wiberg [ctb],
Joakim Wallmark [ctb],
Spencer Graves [ctb]
Maintainer: James Ramsay <james.ramsay@mcgill.ca>
Diff between TestGardener versions 3.1.1 dated 2022-12-19 and 3.1.4 dated 2023-01-15
DESCRIPTION | 8 +++--- MD5 | 22 +++++++++--------- R/Sensitivity.plot.R | 15 ++++-------- R/Wbinsmth.R | 12 ++++----- R/Wpca.plot.R | 39 ++++++++++++++++++-------------- inst/NEWS.Rd | 44 ++++++++++++++++++++++++++++++++++++ inst/doc/Quantshort.Rmd | 2 - inst/doc/Quantshort.html | 45 +++++++++++++++++++++---------------- inst/doc/SDS.Rmd | 2 - inst/doc/SDS.html | 57 ++++++++++++++++++++++++++++------------------- vignettes/Quantshort.Rmd | 2 - vignettes/SDS.Rmd | 2 - 12 files changed, 155 insertions(+), 95 deletions(-)
Title: Machine Learning and Inference for Topological Data Analysis
Description: Topological data analysis is a powerful tool for finding non-linear global structure
in whole datasets. 'TDApplied' aims to bridge topological data analysis with data, statistical
and machine learning practitioners so that more analyses may benefit from the
power of topological data analysis. The main tool of topological data analysis is
persistent homology, which computes a shape descriptor of a dataset, called
a persistence diagram. There are five goals of this package: (1) deliver a fast implementation
of persistent homology via a python interface, (2) convert persistence diagrams
computed using the two main R packages for topological data analysis into a data frame,
(3) implement fast versions of both distance and kernel calculations
for pairs of persistence diagrams, (4) contribute tools for the interpretation of
persistence diagrams, and (5) provide parallelized methods for machine learning
and inference for persistence diagrams.
Author: Shael Brown [aut, cre],
Dr. Reza Farivar [aut, fnd]
Maintainer: Shael Brown <shaelebrown@gmail.com>
Diff between TDApplied versions 2.0.2 dated 2023-01-12 and 2.0.3 dated 2023-01-15
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 3 +++ build/partial.rdb |binary inst/doc/ML_and_Inference.R | 1 - inst/doc/ML_and_Inference.Rmd | 1 - inst/doc/ML_and_Inference.html | 19 +++++++++---------- vignettes/ML_and_Inference.Rmd | 1 - vignettes/REFERENCES.bib | 22 ++++++++-------------- 9 files changed, 31 insertions(+), 38 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 9.1.2 dated 2022-12-20 and 9.1.3 dated 2023-01-15
rswipl-9.1.2/rswipl/src/swipl-devel/debian/swi-prolog-x.manpages |only rswipl-9.1.3/rswipl/DESCRIPTION | 12 - rswipl-9.1.3/rswipl/MD5 | 13 - rswipl-9.1.3/rswipl/NEWS.md | 7 - rswipl-9.1.3/rswipl/src/swipl-devel/debian/changelog | 66 +--------- rswipl-9.1.3/rswipl/src/swipl-devel/debian/control | 6 rswipl-9.1.3/rswipl/src/swipl-devel/debian/watch | 2 rswipl-9.1.3/rswipl/src/swipl-devel/packages/clib/process.c | 7 - 8 files changed, 34 insertions(+), 79 deletions(-)
Title: Mixed Variable Optimization
Description: Mixed variable optimization for non-linear functions.
Can optimize function whose inputs are a combination of continuous,
ordered, and unordered variables.
Author: Collin Erickson
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between mixopt versions 0.1.1 dated 2022-11-19 and 0.1.2 dated 2023-01-15
DESCRIPTION | 10 - MD5 | 33 +++- NAMESPACE | 14 ++ NEWS.md | 10 + R/full_index_line_search_function.R | 12 + R/globals.R |only R/mixopt_blockcd.R |only R/mixopt_coorddesc.R | 218 ++------------------------------ R/mixopt_list.R |only R/mixopt_multistart.R | 90 ++++++++++++- R/plot_track.R | 13 + man/as.mixopt_list.Rd |only man/c_mixopt_list.Rd |only man/is.mixopt_list.Rd |only man/mixopt.Rd | 66 ++++++++- man/sub-.mixopt_list.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-blockcd.R |only tests/testthat/test-index_line_search.R | 52 +++++++ tests/testthat/test-mixopt_list.R |only tests/testthat/test-multistart.R | 130 ++++++++++++++++++- tests/testthat/test_coorddesc.R | 40 +++++ 22 files changed, 442 insertions(+), 246 deletions(-)
Title: Utilities for Graphical Rendering and Fonts Management
Description: Tools are provided to compute metrics of
formatted strings and to check the availability of a font.
Another set of functions is provided to support the collection
of fonts from 'Google Fonts' in a cache. Their use is simple within
'R Markdown' documents and 'shiny' applications but also with graphic
productions generated with the 'ggiraph', 'ragg' and 'svglite' packages
or with tabular productions from the 'flextable' package.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut] ,
Yixuan Qiu [ctb],
R Core Team [cph] ,
ArData [cph],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.2.4 dated 2022-02-14 and 0.3.0 dated 2023-01-15
DESCRIPTION | 26 +++++++++++++++------- MD5 | 20 ++++++++++++----- NAMESPACE | 19 ++++++++++++++++ NEWS | 9 +++++++ R/font-caching.R |only R/font_family_exists.R | 14 +++++++++++- R/fonts.R |only README.md | 48 +++++++----------------------------------- man/addGFontHtmlDependency.Rd |only man/dummy_setup.Rd |only man/fonts_cache_dir.Rd |only man/gfontHtmlDependency.Rd |only man/install_gfont_script.Rd |only man/register_gfont.Rd |only man/str_metrics.Rd | 4 --- 15 files changed, 82 insertions(+), 58 deletions(-)
Title: Data Set and Helper Functions for Wind Farm Layout Optimization
Problems
Description: Provides a convenient data set, a set of helper functions, and a benchmark function for
economically (profit) driven wind farm layout optimization. This enables researchers in the field
of the NP-hard (non-deterministic polynomial-time hard) problem of wind farm layout optimization
to focus on their optimization methodology contribution and also provides a realistic benchmark
setting for comparability among contributions. See Croonenbroeck, Carsten & Hennecke, David (2020)
<doi:10.1016/j.energy.2020.119244>.
Author: Carsten Croonenbroeck [aut, cre],
David Hennecke [ctb]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>
Diff between wflo versions 1.7 dated 2022-09-25 and 1.8 dated 2023-01-15
DESCRIPTION | 13 ++++++------- MD5 | 18 +++++++++--------- R/Functions.R | 31 ++++++++++++++++--------------- inst/doc/wflo.pdf |binary man/Cost.Rd | 3 ++- man/GK2LonLat.Rd | 2 +- man/LonLat2GK.Rd | 2 +- man/Profit.Rd | 2 +- man/SwitchProfile.Rd | 6 +++--- man/Yield.Rd | 3 ++- 10 files changed, 41 insertions(+), 39 deletions(-)
Title: Quick and Easy Access Tax and Accounting Data of Brazil
Description: Access tax and accounting data of Brazilian states
and municipalities provided by the Brazilian Public Sector
Accounting and Tax Information System.
Author: Pedro Castro [aut, cre]
Maintainer: Pedro Castro <pdesacastro@gmail.com>
Diff between siconfir versions 1.0.5 dated 2021-04-20 and 2.0.3 dated 2023-01-15
siconfir-1.0.5/siconfir/R/req.R |only siconfir-2.0.3/siconfir/DESCRIPTION | 16 ++++---- siconfir-2.0.3/siconfir/MD5 | 50 +++++++++++++------------- siconfir-2.0.3/siconfir/NAMESPACE | 12 +++++- siconfir-2.0.3/siconfir/R/api.R | 4 +- siconfir-2.0.3/siconfir/R/data.R | 2 - siconfir-2.0.3/siconfir/R/find_cod.R | 40 ++++---------------- siconfir-2.0.3/siconfir/R/get.R | 14 +++---- siconfir-2.0.3/siconfir/R/get_annex.R | 6 ++- siconfir-2.0.3/siconfir/R/get_annual_acc.R | 4 +- siconfir-2.0.3/siconfir/R/get_budget.R | 24 ++++++++---- siconfir-2.0.3/siconfir/R/get_fiscal.R | 30 ++++++++++----- siconfir-2.0.3/siconfir/R/get_info.R | 4 +- siconfir-2.0.3/siconfir/R/msc_budget.R | 14 ------- siconfir-2.0.3/siconfir/R/msc_control.R | 14 ------- siconfir-2.0.3/siconfir/R/msc_equity.R | 14 ------- siconfir-2.0.3/siconfir/R/report_status.R | 4 +- siconfir-2.0.3/siconfir/R/request.R |only siconfir-2.0.3/siconfir/R/utils-pipe.R | 2 - siconfir-2.0.3/siconfir/data/br_cods.rda |binary siconfir-2.0.3/siconfir/man/find_cod.Rd | 7 +-- siconfir-2.0.3/siconfir/man/get_annex.Rd | 4 +- siconfir-2.0.3/siconfir/man/get_annual_acc.Rd | 4 +- siconfir-2.0.3/siconfir/man/get_budget.Rd | 16 +++++++- siconfir-2.0.3/siconfir/man/get_fiscal.Rd | 11 ++++- siconfir-2.0.3/siconfir/man/report_status.Rd | 4 +- siconfir-2.0.3/siconfir/tests |only 27 files changed, 151 insertions(+), 149 deletions(-)
Title: Bayesian Change-Point Detection and Time Series Decomposition
Description: Interpretation of time series data is affected by model choices. Different models can give different or even contradicting estimates of patterns, trends, and mechanisms for the same data--a limitation alleviated by the Bayesian estimator of abrupt change,seasonality, and trend (BEAST) of this package. BEAST seeks to improve time series decomposition by forgoing the "single-best-model" concept and embracing all competing models into the inference via a Bayesian model averaging scheme. It is a flexible tool to uncover abrupt changes (i.e., change-points), cyclic variations (e.g., seasonality), and nonlinear trends in time-series observations. BEAST not just tells when changes occur but also quantifies how likely the detected changes are true. It detects not just piecewise linear trends but also arbitrary nonlinear trends. BEAST is applicable to real-valued time series data of all kinds, be it for remote sensing, economics, climate sciences, ecology, and hydrology. Example applications in [...truncated...]
Author: Yang Li [aut],
Tongxi Hu [aut],
Xuesong Zhang [aut],
Kaiguang Zhao [aut, cre],
Jack Dongarra [ctb],
Cleve Moler [ctb]
Maintainer: Kaiguang Zhao <zhao.1423@osu.edu>
Diff between Rbeast versions 0.9.5 dated 2022-08-09 and 0.9.6 dated 2023-01-15
Rbeast-0.9.5/Rbeast/src/abc_ide_util.c |only Rbeast-0.9.6/Rbeast/DESCRIPTION | 24 Rbeast-0.9.6/Rbeast/MD5 | 135 +- Rbeast-0.9.6/Rbeast/NEWS.md | 7 Rbeast-0.9.6/Rbeast/R/beast.R | 92 - Rbeast-0.9.6/Rbeast/R/beast.irreg.R | 45 Rbeast-0.9.6/Rbeast/data/covid19.RData |binary Rbeast-0.9.6/Rbeast/man/beast.Rd | 145 +- Rbeast-0.9.6/Rbeast/man/beast.irreg.Rd | 132 +- Rbeast-0.9.6/Rbeast/man/beast123.Rd | 81 - Rbeast-0.9.6/Rbeast/man/covid19.Rd | 37 Rbeast-0.9.6/Rbeast/man/print.beast.Rd | 8 Rbeast-0.9.6/Rbeast/src/Makevars | 6 Rbeast-0.9.6/Rbeast/src/Makevars.win | 12 Rbeast-0.9.6/Rbeast/src/_beastv2_gui_plot.c | 32 Rbeast-0.9.6/Rbeast/src/_beastv2_gui_winmain.c | 12 Rbeast-0.9.6/Rbeast/src/abc_000_macro.h | 31 Rbeast-0.9.6/Rbeast/src/abc_001_config.h | 37 Rbeast-0.9.6/Rbeast/src/abc_common.c | 157 +- Rbeast-0.9.6/Rbeast/src/abc_common.h | 7 Rbeast-0.9.6/Rbeast/src/abc_cpu.c | 86 - Rbeast-0.9.6/Rbeast/src/abc_cpu.h | 104 - Rbeast-0.9.6/Rbeast/src/abc_datatype.h | 22 Rbeast-0.9.6/Rbeast/src/abc_date.c | 515 ++++++++ Rbeast-0.9.6/Rbeast/src/abc_date.h | 4 Rbeast-0.9.6/Rbeast/src/abc_dir.h | 1 Rbeast-0.9.6/Rbeast/src/abc_dirent.h | 21 Rbeast-0.9.6/Rbeast/src/abc_ide_util.h | 88 - Rbeast-0.9.6/Rbeast/src/abc_ide_util_R.c |only Rbeast-0.9.6/Rbeast/src/abc_ide_util_common.c |only Rbeast-0.9.6/Rbeast/src/abc_ide_util_matlab.c |only Rbeast-0.9.6/Rbeast/src/abc_ide_util_python.c |only Rbeast-0.9.6/Rbeast/src/abc_ioFlush.c | 8 Rbeast-0.9.6/Rbeast/src/abc_lzw.c | 2 Rbeast-0.9.6/Rbeast/src/abc_mat.c | 2 Rbeast-0.9.6/Rbeast/src/abc_math_avx.h | 1 Rbeast-0.9.6/Rbeast/src/abc_mem.c | 105 + Rbeast-0.9.6/Rbeast/src/abc_mem.h | 31 Rbeast-0.9.6/Rbeast/src/abc_pthread.c | 24 Rbeast-0.9.6/Rbeast/src/abc_pthread.h | 10 Rbeast-0.9.6/Rbeast/src/abc_rand_pcg_global.c | 2 Rbeast-0.9.6/Rbeast/src/abc_rand_pcg_local.h | 6 Rbeast-0.9.6/Rbeast/src/abc_rand_pcg_local_avx2.c | 2 Rbeast-0.9.6/Rbeast/src/abc_rand_pcg_local_avx512.c | 4 Rbeast-0.9.6/Rbeast/src/abc_system.h | 2 Rbeast-0.9.6/Rbeast/src/abc_timer.c | 6 Rbeast-0.9.6/Rbeast/src/abc_timer.h | 20 Rbeast-0.9.6/Rbeast/src/abc_ts_func.c | 148 ++ Rbeast-0.9.6/Rbeast/src/abc_ts_func.h | 15 Rbeast-0.9.6/Rbeast/src/abc_vec.c | 412 +++++- Rbeast-0.9.6/Rbeast/src/abc_vec.h | 29 Rbeast-0.9.6/Rbeast/src/abc_vec_avx2.c | 7 Rbeast-0.9.6/Rbeast/src/abc_vec_avx512.c | 2 Rbeast-0.9.6/Rbeast/src/abc_win32_demo.h | 5 Rbeast-0.9.6/Rbeast/src/beastv2_COREV4.c | 6 Rbeast-0.9.6/Rbeast/src/beastv2_COREV4_gui.c | 6 Rbeast-0.9.6/Rbeast/src/beastv2_COREV4_mthrd.c | 2 Rbeast-0.9.6/Rbeast/src/beastv2_func_q.c | 2 Rbeast-0.9.6/Rbeast/src/beastv2_header.h | 44 Rbeast-0.9.6/Rbeast/src/beastv2_header_solaris.h | 124 - Rbeast-0.9.6/Rbeast/src/beastv2_io.h | 2 Rbeast-0.9.6/Rbeast/src/beastv2_io_in_args.c | 1027 ++++++++-------- Rbeast-0.9.6/Rbeast/src/beastv2_io_in_readts.c | 126 - Rbeast-0.9.6/Rbeast/src/beastv2_io_out_allocmem_q.c | 124 - Rbeast-0.9.6/Rbeast/src/beastv2_io_out_printargs.c | 289 +++- Rbeast-0.9.6/Rbeast/src/beastv2_io_out_tsextractprint.c | 189 +- Rbeast-0.9.6/Rbeast/src/beastv2_io_out_write_q.c | 232 +-- Rbeast-0.9.6/Rbeast/src/beastv2_model_allocinit_q.c | 2 Rbeast-0.9.6/Rbeast/src/globalvars.c | 3 Rbeast-0.9.6/Rbeast/src/globalvars.h | 6 Rbeast-0.9.6/Rbeast/src/glue_code.c | 314 ++-- 71 files changed, 3330 insertions(+), 1852 deletions(-)
Title: Sensitivities of Prices of Financial Options and Implied
Volatilites
Description: Methods to calculate sensitivities of financial option prices for
European, Asian, American and Digital Options options in the Black Scholes
model, and in more general jump diffusion models. A shiny app to interactively
view plot the results is included. Furthermore, methods to
compute implied volatilities are provided for a wide range of option types and
custom payoff functions. Classical formulas are implemented for European
options in the Black Scholes Model, as is presented in Hull, J. C. (2017).
Options, Futures, and Other Derivatives, Global Edition (9th Edition). Pearson.
In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see
Hudde, A. & Rüschendorf, L. (2016). European and Asian Greeks for exponential
Lévy processes. <arXiv:1603.00920>. For American options, the Binomial Tree
Method is implemented, as is presented in Hull, J. C. (2017).
Author: Anselm Hudde [aut, cre]
Maintainer: Anselm Hudde <anselmhudde@gmx.de>
Diff between greeks versions 0.8.0 dated 2023-01-13 and 0.8.1 dated 2023-01-15
greeks-0.8.0/greeks/R/Implied_Volatility_test.R |only greeks-0.8.1/greeks/DESCRIPTION | 9 +-- greeks-0.8.1/greeks/MD5 | 13 +++- greeks-0.8.1/greeks/R/Greeks_UI.R | 2 greeks-0.8.1/greeks/README.md | 66 ++++++++++++++++-------- greeks-0.8.1/greeks/build |only greeks-0.8.1/greeks/inst |only greeks-0.8.1/greeks/vignettes |only 8 files changed, 59 insertions(+), 31 deletions(-)
Title: Call Real Time APIs from Data Gov Singapore
Description: A wrapper for the Data.gov.sg developer resources, which provide
real time and historical information, ranging from carpark availability to
weather forecasts. The functions makes the API calls for a given date and
time, before returning the relevant information in a data frame. All APIs
are supported, less the IPOS one which is not returning any data. Relevant
information can be found here <https://data.gov.sg/developer>.
Author: Clinton Wong <cwxy.clinton@gmail.com>
Maintainer: Clinton Wong <cwxy.clinton@gmail.com>
Diff between datagovsgR versions 0.3.3 dated 2022-12-22 and 1.0.0 dated 2023-01-15
datagovsgR-0.3.3/datagovsgR/R/PM2.5.R |only datagovsgR-0.3.3/datagovsgR/R/PM2.5Summary.R |only datagovsgR-0.3.3/datagovsgR/man/pm25.Rd |only datagovsgR-0.3.3/datagovsgR/man/pm25_summary.Rd |only datagovsgR-1.0.0/datagovsgR/DESCRIPTION | 25 - datagovsgR-1.0.0/datagovsgR/MD5 | 28 - datagovsgR-1.0.0/datagovsgR/NAMESPACE | 6 datagovsgR-1.0.0/datagovsgR/R/PSISummary.R | 8 datagovsgR-1.0.0/datagovsgR/R/TrafficImages.R |only datagovsgR-1.0.0/datagovsgR/R/UVI.R |only datagovsgR-1.0.0/datagovsgR/R/WeatherReading.R | 22 - datagovsgR-1.0.0/datagovsgR/README.md | 11 datagovsgR-1.0.0/datagovsgR/inst/doc/datagovsgR-vignette.R | 4 datagovsgR-1.0.0/datagovsgR/inst/doc/datagovsgR-vignette.Rmd | 4 datagovsgR-1.0.0/datagovsgR/inst/doc/datagovsgR-vignette.html | 171 ++-------- datagovsgR-1.0.0/datagovsgR/man/traffic_images.Rd |only datagovsgR-1.0.0/datagovsgR/man/uvi.Rd |only datagovsgR-1.0.0/datagovsgR/man/weather_reading.Rd | 8 datagovsgR-1.0.0/datagovsgR/vignettes/datagovsgR-vignette.Rmd | 4 19 files changed, 101 insertions(+), 190 deletions(-)
Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
Author: Seunggeun Lee and Zhangchen Zhao, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee <lee7801@snu.ac.kr>
Diff between SKAT versions 2.2.4 dated 2022-03-29 and 2.2.5 dated 2023-01-15
DESCRIPTION | 20 ++++++-------------- MD5 | 20 ++++++++++---------- build/vignette.rds |binary data/SKAT.example.ChrX.rda |binary data/SKAT.example.rda |binary data/SKAT.fam.example.rda |binary data/SKAT.haplotypes.rda |binary data/SKATBinary.example.rda |binary inst/doc/SKAT.pdf |binary man/SKAT_ChrX.rd | 10 +++++----- src/mwo_reader.cpp | 17 +++++++++++++---- 11 files changed, 34 insertions(+), 33 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, stats, geoms and scales for plotting
"light" spectra with 'ggplot2', together with specializations of ggplot()
and autoplot() methods for spectral data and waveband definitions
stored in objects of classes defined in package 'photobiology'. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.3.9 dated 2022-10-16 and 0.3.10 dated 2023-01-15
DESCRIPTION | 18 MD5 | 95 +- NAMESPACE | 9 NEWS.md | 17 R/autoplot-calibration-spct.R | 10 R/autoplot-cps-spct.r | 10 R/autoplot-filter-spct.r | 30 R/autoplot-generic-spct.R | 2 R/autoplot-raw-spct.r | 10 R/autoplot-response-spct.r | 12 R/autoplot-source-spct.r | 65 - R/axis-labels-texts.R | 20 R/axis-utils-wlength.R | 438 ++++++++++- R/geom-spct.r | 2 R/ggplot-methods.R | 11 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/userguide-0-r4p-introduction.html | 2 inst/doc/userguide1-grammar.R | 21 inst/doc/userguide1-grammar.Rmd | 83 +- inst/doc/userguide1-grammar.html | 1127 +++++++++++++++-------------- inst/doc/userguide2-autoplot-methods.R | 4 inst/doc/userguide2-autoplot-methods.Rmd | 8 inst/doc/userguide2-autoplot-methods.html | 87 +- inst/doc/userguide3-data-manip.R | 47 - inst/doc/userguide3-data-manip.Rmd | 55 - inst/doc/userguide3-data-manip.html | 156 ++-- man/autoplot.calibration_spct.Rd | 2 man/autoplot.cps_spct.Rd | 2 man/autoplot.filter_spct.Rd | 2 man/autoplot.generic_spct.Rd | 2 man/autoplot.object_spct.Rd | 2 man/autoplot.raw_spct.Rd | 2 man/autoplot.reflector_spct.Rd | 2 man/autoplot.response_spct.Rd | 2 man/autoplot.source_spct.Rd | 5 man/axis_labels.Rd | 18 man/figures/README-example0-1.png |binary man/figures/README-example2-1.png |binary man/scale_x_energy_eV_continuous.Rd |only man/scale_x_frequency_continuous.Rd |only man/scale_x_wavenumber_continuous.Rd |only man/scale_x_wl_continuous.Rd | 22 man/sec_axis_w_number.Rd | 71 + man/w_length_label.Rd | 45 + man/w_number.Rd | 23 vignettes/userguide1-grammar.Rmd | 83 +- vignettes/userguide2-autoplot-methods.Rmd | 8 vignettes/userguide3-data-manip.Rmd | 55 - 50 files changed, 1669 insertions(+), 1022 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic,
and programmer friendly through a flexible, parsimonious, and robust API.
Core functionality includes a rich set of S3 generic grouped and weighted
statistical functions for vectors, matrices and data frames, which provide
efficient low-level vectorizations and OpenMP multithreading (reducing the
need for iteration/vectorization in R), and skip missing values by default.
These are integrated with fast grouping and ordering algorithms (also callable
from C), and efficient data manipulation functions. The package also provides
a flexible and rigorous approach to time series and panel data in R. It further
includes fast functions for common statistical procedures, detailed (grouped,
weighted) summary statistics, powerful tools to work with nested data, fast
data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with v [...truncated...]
Author: Sebastian Krantz [aut, cre],
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [ [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 1.8.9 dated 2022-10-07 and 1.9.0 dated 2023-01-15
collapse-1.8.9/collapse/man/fmedian.Rd |only collapse-1.8.9/collapse/man/fnth.Rd |only collapse-1.8.9/collapse/src/fnth_fmedian.cpp |only collapse-1.9.0/collapse/DESCRIPTION | 49 collapse-1.9.0/collapse/MD5 | 198 +-- collapse-1.9.0/collapse/NAMESPACE | 36 collapse-1.9.0/collapse/NEWS.md | 88 + collapse-1.9.0/collapse/R/BY.R | 81 - collapse-1.9.0/collapse/R/GRP.R | 81 - collapse-1.9.0/collapse/R/RcppExports.R | 12 collapse-1.9.0/collapse/R/TRA.R | 39 collapse-1.9.0/collapse/R/collap.R | 118 - collapse-1.9.0/collapse/R/dapply.R | 56 collapse-1.9.0/collapse/R/descr.R | 422 +++++- collapse-1.9.0/collapse/R/fFtest.R | 2 collapse-1.9.0/collapse/R/fcount.R |only collapse-1.9.0/collapse/R/fhdbetween_fhdwithin.R | 46 collapse-1.9.0/collapse/R/flm.R | 16 collapse-1.9.0/collapse/R/fmean.R | 49 collapse-1.9.0/collapse/R/fndistinct.R | 6 collapse-1.9.0/collapse/R/fnobs.R | 6 collapse-1.9.0/collapse/R/fnth_fmedian.R | 195 --- collapse-1.9.0/collapse/R/fsubset_ftransform_fmutate.R | 229 +-- collapse-1.9.0/collapse/R/fsummarise.R | 113 - 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collapse-1.9.0/collapse/man/efficient-programming.Rd | 29 collapse-1.9.0/collapse/man/extract_list.Rd | 3 collapse-1.9.0/collapse/man/fast-grouping-ordering.Rd | 3 collapse-1.9.0/collapse/man/fcount.Rd |only collapse-1.9.0/collapse/man/fdist.Rd |only collapse-1.9.0/collapse/man/flag.Rd | 18 collapse-1.9.0/collapse/man/fnth_fmedian.Rd |only collapse-1.9.0/collapse/man/fquantile.Rd |only collapse-1.9.0/collapse/man/frename.Rd | 19 collapse-1.9.0/collapse/man/fsummarise.Rd | 32 collapse-1.9.0/collapse/man/ftransform.Rd | 50 collapse-1.9.0/collapse/man/group.Rd | 2 collapse-1.9.0/collapse/man/select_replace_vars.Rd | 10 collapse-1.9.0/collapse/src/ExportSymbols.c | 70 + collapse-1.9.0/collapse/src/RcppExports.cpp | 59 collapse-1.9.0/collapse/src/TRA.c | 2 collapse-1.9.0/collapse/src/base_radixsort.c | 258 +++- collapse-1.9.0/collapse/src/base_radixsort.h | 18 collapse-1.9.0/collapse/src/collapse_c.h | 61 collapse-1.9.0/collapse/src/collapse_cpp.h | 6 collapse-1.9.0/collapse/src/data.table.h | 54 collapse-1.9.0/collapse/src/data.table_init.c | 22 collapse-1.9.0/collapse/src/data.table_rbindlist.c | 629 ++-------- collapse-1.9.0/collapse/src/data.table_subset.c | 47 collapse-1.9.0/collapse/src/data.table_utils.c | 374 ++--- collapse-1.9.0/collapse/src/fmean.c | 364 +++-- collapse-1.9.0/collapse/src/fmin_fmax.c | 7 collapse-1.9.0/collapse/src/fmode.c | 155 +- collapse-1.9.0/collapse/src/fndistinct.c | 73 - collapse-1.9.0/collapse/src/fnth_fmedian_fquantile.c |only collapse-1.9.0/collapse/src/fsum.c | 442 ++++--- collapse-1.9.0/collapse/src/kit_dup.c | 5 collapse-1.9.0/collapse/src/programming.c | 303 ++++ collapse-1.9.0/collapse/src/seqid_groupid.cpp | 4 collapse-1.9.0/collapse/src/small_helper.c | 37 collapse-1.9.0/collapse/tests/testthat.R | 1 collapse-1.9.0/collapse/tests/testthat/test-GRP.R | 26 collapse-1.9.0/collapse/tests/testthat/test-attribute-handling.R | 2 collapse-1.9.0/collapse/tests/testthat/test-fNobs-fNdistinct.R | 13 collapse-1.9.0/collapse/tests/testthat/test-fbetween-fwithin-B-W.R | 150 +- collapse-1.9.0/collapse/tests/testthat/test-flag-L-F.R | 2 collapse-1.9.0/collapse/tests/testthat/test-fmean.R | 54 collapse-1.9.0/collapse/tests/testthat/test-fmedian.R | 241 +-- collapse-1.9.0/collapse/tests/testthat/test-fmode.R | 59 collapse-1.9.0/collapse/tests/testthat/test-fmutate.R | 102 + collapse-1.9.0/collapse/tests/testthat/test-fprod.R | 54 collapse-1.9.0/collapse/tests/testthat/test-fquantile.R |only collapse-1.9.0/collapse/tests/testthat/test-fscale-STD.R | 103 - collapse-1.9.0/collapse/tests/testthat/test-fsum.R | 102 - collapse-1.9.0/collapse/tests/testthat/test-fvar-fsd.R | 102 - collapse-1.9.0/collapse/tests/testthat/test-list-processing.R | 25 collapse-1.9.0/collapse/tests/testthat/test-misc.R | 16 collapse-1.9.0/collapse/tests/testthat/test-miscellaneous-issues.R | 72 + collapse-1.9.0/collapse/tests/testthat/test-roworder-colorder-rename.R | 46 collapse-1.9.0/collapse/tests/testthat/test-seqid-groupid.R | 5 collapse-1.9.0/collapse/tests/testthat/test-sf.R | 8 collapse-1.9.0/collapse/vignettes/collapse_documentation.Rmd | 4 105 files changed, 4007 insertions(+), 3690 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr <fh@fharrell.com>
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between rms versions 6.3-0 dated 2022-04-22 and 6.4-0 dated 2023-01-15
DESCRIPTION | 10 +++--- MD5 | 68 ++++++++++++++++++++++-------------------- NAMESPACE | 7 +++- NEWS | 21 ++++++++++++- R/Glm.r | 30 +++++++++++++++--- R/Rq.s | 7 +--- R/anova.rms.s | 12 ++++--- R/bootcov.s | 4 -- R/ggplot.Predict.s | 14 +++++--- R/impactPO.r | 9 +++-- R/latex.cph.s | 43 ++++++++++++-------------- R/latex.lrm.s | 69 ++++++++++++++++++++----------------------- R/latex.ols.s | 23 ++++++-------- R/latex.pphsm.s | 25 ++++++--------- R/latex.psm.s | 22 +++++-------- R/latex.rms.s | 58 ++++++++++++++++++------------------ R/plotp.Predict.s | 5 +++ R/poma.r | 8 ++++ R/rms.trans.s | 20 ++++++++++++ R/rmsMisc.s | 2 - R/summary.rms.s | 15 +++++---- R/validate.ols.s | 19 +++++++++++ inst/tests/cphexactval.r |only inst/tests/cphtdc2.r | 8 +++- inst/tests/impactPO.r | 4 ++ inst/tests/makepredictcall.r |only inst/tests/rms-lm.r |only inst/tests/rms2.r | 4 +- man/Glm.Rd | 4 -- man/Rq.Rd | 3 - man/anova.rms.Rd | 6 ++- man/bootcov.Rd | 25 ++++++++------- man/orm.Rd | 36 ++++++++++++++++++++++ man/print.Glm.Rd | 4 +- man/residuals.Glm.Rd |only man/rms.trans.Rd | 23 +++++++++++++- man/summary.rms.Rd | 5 ++- 37 files changed, 385 insertions(+), 228 deletions(-)
Title: In-Text Expandable and Resizable Containers, Images and Data
Tables in 'Shiny', 'Markdown' and 'Quarto' Documents
Description: Automatic resizing toolbar for containers, images and tables. Most suitable to include resize functionality in 'Markdown', 'Rmarkdown' and 'Quarto' documents.
Author: Obinna Obianom
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between r2resize versions 1.3 dated 2022-10-23 and 1.4 dated 2023-01-15
r2resize-1.3/r2resize/inst/examples/sample1.html |only r2resize-1.4/r2resize/DESCRIPTION | 14 +- r2resize-1.4/r2resize/MD5 | 26 +-- r2resize-1.4/r2resize/NAMESPACE | 1 r2resize-1.4/r2resize/NEWS.md | 12 + r2resize-1.4/r2resize/R/containerResizer.R | 22 +++ r2resize-1.4/r2resize/README.md | 25 ++- r2resize-1.4/r2resize/inst/doc/introduction_r2resize.html | 4 r2resize-1.4/r2resize/inst/doc/resizable_containers_split_screen_r2resize.R | 2 r2resize-1.4/r2resize/inst/doc/resizable_containers_split_screen_r2resize.Rmd | 4 r2resize-1.4/r2resize/inst/doc/resizable_containers_split_screen_r2resize.html | 7 - r2resize-1.4/r2resize/inst/examples/sample1.Rmd | 66 ++-------- r2resize-1.4/r2resize/man/emphasisCard.Rd |only r2resize-1.4/r2resize/man/r2resize-package.Rd | 4 r2resize-1.4/r2resize/vignettes/resizable_containers_split_screen_r2resize.Rmd | 4 15 files changed, 95 insertions(+), 96 deletions(-)
Title: Normalize Laboratory Measurements by Age and Sex
Description: Provides functions for normalizing standard laboratory measurements (e.g. hemoglobin, cholesterol levels) according to age and sex, based on the algorithms described in "Personalized lab test models to quantify disease potentials in healthy individuals" (Netta Mendelson Cohen, Omer Schwartzman, Ram Jaschek, Aviezer Lifshitz, Michael Hoichman, Ran Balicer, Liran I. Shlush, Gabi Barbash & Amos Tanay, <doi:10.1038/s41591-021-01468-6>). Allows users to easily obtain normalized values for standard lab results, and to visualize their distributions. See more at <https://tanaylab.weizmann.ac.il/labs/>.
Author: Aviezer Lifshitz [aut, cre],
Netta Mendelson-Cohen [aut],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between labNorm versions 1.0.0 dated 2023-01-12 and 1.0.1 dated 2023-01-15
DESCRIPTION | 9 -- MD5 | 42 +++++----- NEWS.md | 6 + R/download.R | 6 + R/normalize.R | 37 ++++++-- R/plot-distribution.R | 10 +- R/quantile-to-value.R | 10 +- R/utils-quantiles.R | 5 + R/utils.R | 18 +++- R/zzz.R | 1 README.md | 15 ++- inst/WORDLIST | 4 man/ln_normalize.Rd | 14 ++- man/ln_quantile_value.Rd | 2 tests/spelling.R | 9 -- tests/testthat/setup.R |only tests/testthat/test-convert.R | 10 ++ tests/testthat/test-data.R | 6 - tests/testthat/test-download.R | 14 ++- tests/testthat/test-normalize.R | 132 ++++++++++++++++++++++++++++++-- tests/testthat/test-plot-distribution.R | 79 +++++++++++++++++-- tests/testthat/test-quantile-value.R | 54 +++++++++++-- tests/testthat/test-zzz.R |only 23 files changed, 396 insertions(+), 87 deletions(-)
Title: Isolation Forest-Based Presence-Only Species Distribution
Modeling
Description: Collection of R functions to do purely presence-only species
distribution modeling with isolation forest (iForest) and its
variations such as Extended isolation forest and SCiForest. See the
details of these methods in references: Liu, F.T., Ting, K.M. and
Zhou, Z.H. (2008) <doi:10.1109/ICDM.2008.17>, Hariri, S., Kind, M.C.
and Brunner, R.J. (2019) <doi:10.1109/TKDE.2019.2947676>, Liu, F.T.,
Ting, K.M. and Zhou, Z.H. (2010) <doi:10.1007/978-3-642-15883-4_18>,
Guha, S., Mishra, N., Roy, G. and Schrijvers, O. (2016)
<https://proceedings.mlr.press/v48/guha16.html>, Cortes, D. (2021)
<arXiv:2110.13402>. Additionally, Shapley values are used to explain
model inputs and outputs. See details in references: Shapley, L.S.
(1953) <doi:10.1515/9781400881970-018>, Lundberg, S.M. and Lee, S.I.
(2017) <https://dl.acm.org/doi/abs/10.5555/3295222.3295230>, Molnar,
C. (2020) <ISBN:978-0-244-76852-2>, Štrumbelj, E. and Kononenko, I.
(2014) <doi:10.1007 [...truncated...]
Author: Lei Song [aut, cre] ,
Lyndon Estes [ths]
Maintainer: Lei Song <lsong@clarku.edu>
Diff between itsdm versions 0.1.3 dated 2022-09-11 and 0.2.0 dated 2023-01-15
DESCRIPTION | 12 MD5 | 186 ++++---- NAMESPACE | 22 + NEWS.md | 8 R/convert_to_pa.R | 39 + R/data.R | 13 R/detect_envi_change.R |only R/dim_reduce.R | 15 R/evaluate_po.R | 46 +- R/format_observation.R |only R/independent_response.R | 36 + R/isotree_po.R | 536 ++++++++++++++++--------- R/marginal_response.R | 33 - R/plot.R | 491 +++++++++++++++++----- R/print.R | 292 ++++++++++--- R/probability.R | 43 +- R/shap_dependence.R | 131 +++++- R/shap_spatial_response.R |only R/spatial_response.R | 94 +--- R/suspicious_env_outliers.R | 12 R/utils.R | 168 +++++++ R/variable_analysis.R | 38 + R/variable_contrib.R | 50 +- README.md | 76 ++- build/partial.rdb |binary build/vignette.rds |binary data/occ_virtual_species.rda |binary inst/doc/introduction_of_itsdm.Rmd | 49 +- inst/doc/introduction_of_itsdm.html | 95 ++-- inst/doc/itsdm_example.Rmd | 275 ++++++------ inst/doc/itsdm_example.html | 312 +++++++------- inst/doc/shap_application.Rmd |only inst/doc/shap_application.html |only inst/extdata/future_bioclim_tanzania_10min.tif |only man/convert_to_pa.Rd | 37 + man/detect_envi_change.Rd |only man/dim_reduce.Rd | 9 man/evaluate_po.Rd | 46 +- man/format_observation.Rd |only man/independent_response.Rd | 28 - man/isotree_po.Rd | 153 +++++-- man/marginal_response.Rd | 31 - man/occ_virtual_species.Rd | 13 man/plot.EnviChange.Rd |only man/plot.EnvironmentalOutlier.Rd | 5 man/plot.IndependentResponse.Rd | 34 - man/plot.MarginalResponse.Rd | 34 - man/plot.PAConversion.Rd | 31 - man/plot.POEvaluation.Rd | 34 - man/plot.SHAPSpatial.Rd |only man/plot.ShapDependence.Rd | 45 +- man/plot.SpatialResponse.Rd | 39 + man/plot.VariableAnalysis.Rd | 35 - man/plot.VariableContribution.Rd | 49 +- man/print.EnviChange.Rd |only man/print.EnvironmentalOutlier.Rd | 6 man/print.FormatOccurrence.Rd |only man/print.PAConversion.Rd | 32 - man/print.POEvaluation.Rd | 29 - man/print.POIsotree.Rd | 37 + man/print.ReducedImageStack.Rd | 5 man/print.VariableAnalysis.Rd | 42 + man/probability.Rd | 41 + man/shap_dependence.Rd | 113 ++++- man/shap_spatial_response.Rd |only man/spatial_response.Rd | 34 - man/suspicious_env_outliers.Rd | 6 man/variable_analysis.Rd | 28 - man/variable_contrib.Rd | 49 +- vignettes/intro-evaluation-1.png |binary vignettes/intro-independent_responses-1.png |binary vignettes/intro-marginal_responses-1.png |binary vignettes/intro-pa-1.png |binary vignettes/intro-prediction-1.png |binary vignettes/intro-raw_suit-1.png |binary vignettes/intro-remove_outliers-1.png |binary vignettes/intro-spatial_response-1.png |binary vignettes/intro-var_contrib-1.png |binary vignettes/intro-var_contrib_plot-1.png |binary vignettes/intro-var_inter_dependence-1.png |binary vignettes/intro-variable_analysis-1.png |binary vignettes/intro-variable_dependence-1.png |binary vignettes/intro-virtualspecies-1.png |binary vignettes/introduction_of_itsdm.Rmd | 49 +- vignettes/itsdm-eval-1.png |binary vignettes/itsdm-independent_responses-1.png |binary vignettes/itsdm-marginal_responses-1.png |binary vignettes/itsdm-outliers-1.png |binary vignettes/itsdm-pa-1.png |binary vignettes/itsdm-prediction-1.png |binary vignettes/itsdm-var_contrib-1.png |binary vignettes/itsdm-var_contrib_general-1.png |binary vignettes/itsdm-var_inter_dependence-1.png |binary vignettes/itsdm-variable_dependence-1.png |binary vignettes/itsdm_example.Rmd | 275 ++++++------ vignettes/itsdm_example.Rmd.orig | 28 - vignettes/shap-chanEnv-1.png |only vignettes/shap-envCtr-1.png |only vignettes/shap-envCtr-2.png |only vignettes/shap-predSuit-1.png |only vignettes/shap-rspCurve-1.png |only vignettes/shap-rspCurve-2.png |only vignettes/shap-rspMap-1.png |only vignettes/shap_application.Rmd |only vignettes/shap_application.Rmd.orig |only 105 files changed, 2910 insertions(+), 1559 deletions(-)
Title: Non-Invasive Pretty Printing of R Code
Description: Pretty-prints R code without changing the user's formatting
intent.
Author: Kirill Mueller [aut] ,
Lorenz Walthert [cre, aut],
Indrajeet Patil [ctb]
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between styler versions 1.8.1 dated 2022-11-07 and 1.9.0 dated 2023-01-15
styler-1.8.1/styler/R/styler.R |only styler-1.8.1/styler/man/drop_cached_children.Rd |only styler-1.9.0/styler/DESCRIPTION | 10 styler-1.9.0/styler/MD5 | 221 +++++----- styler-1.9.0/styler/NAMESPACE | 10 styler-1.9.0/styler/NEWS.md | 65 ++ styler-1.9.0/styler/R/addins.R | 11 styler-1.9.0/styler/R/communicate.R | 7 styler-1.9.0/styler/R/compat-dplyr.R | 5 styler-1.9.0/styler/R/detect-alignment-utils.R | 42 - styler-1.9.0/styler/R/detect-alignment.R | 6 styler-1.9.0/styler/R/environments.R | 6 styler-1.9.0/styler/R/expr-is.R | 2 styler-1.9.0/styler/R/indent.R | 15 styler-1.9.0/styler/R/initialize.R | 7 styler-1.9.0/styler/R/io.R | 9 styler-1.9.0/styler/R/nest.R | 87 +-- styler-1.9.0/styler/R/nested-to-tree.R | 2 styler-1.9.0/styler/R/parse.R | 28 - styler-1.9.0/styler/R/reindent.R | 1 styler-1.9.0/styler/R/relevel.R | 20 styler-1.9.0/styler/R/roxygen-examples-add-remove.R | 5 styler-1.9.0/styler/R/roxygen-examples-find.R | 14 styler-1.9.0/styler/R/roxygen-examples.R | 18 styler-1.9.0/styler/R/rules-indention.R | 35 + styler-1.9.0/styler/R/rules-line-breaks.R | 30 - styler-1.9.0/styler/R/rules-spaces.R | 1 styler-1.9.0/styler/R/rules-tokens.R | 33 - styler-1.9.0/styler/R/set-assert-args.R | 10 styler-1.9.0/styler/R/style-guides.R | 10 styler-1.9.0/styler/R/styler-package.R |only styler-1.9.0/styler/R/stylerignore.R | 7 styler-1.9.0/styler/R/testing-public-api.R | 5 styler-1.9.0/styler/R/testing.R | 24 - styler-1.9.0/styler/R/token-create.R | 6 styler-1.9.0/styler/R/token-define.R | 1 styler-1.9.0/styler/R/transform-block.R | 68 ++- styler-1.9.0/styler/R/transform-code.R | 13 styler-1.9.0/styler/R/transform-files.R | 56 +- styler-1.9.0/styler/R/ui-caching.R | 28 + styler-1.9.0/styler/R/ui-styling.R | 20 styler-1.9.0/styler/R/unindent.R | 6 styler-1.9.0/styler/R/utils-cache.R | 2 styler-1.9.0/styler/R/utils-navigate-nest.R | 22 styler-1.9.0/styler/R/utils.R | 10 styler-1.9.0/styler/R/vertical.R | 1 styler-1.9.0/styler/R/visit.R | 2 styler-1.9.0/styler/R/zzz.R | 26 - styler-1.9.0/styler/inst/doc/customizing_styler.html | 78 +-- styler-1.9.0/styler/inst/doc/remove_rules.html | 2 styler-1.9.0/styler/inst/doc/styler.html | 3 styler-1.9.0/styler/man/add_cache_block.Rd | 2 styler-1.9.0/styler/man/add_token_terminal.Rd | 2 styler-1.9.0/styler/man/alignment_drop_last_expr.Rd | 18 styler-1.9.0/styler/man/cache_find_block.Rd | 36 - 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Title: Effects and Importances of Model Ingredients
Description: Collection of tools for assessment of feature importance and feature effects.
Key functions are:
feature_importance() for assessment of global level feature importance,
ceteris_paribus() for calculation of the what-if plots,
partial_dependence() for partial dependence plots,
conditional_dependence() for conditional dependence plots,
accumulated_dependence() for accumulated local effects plots,
aggregate_profiles() and cluster_profiles() for aggregation of ceteris paribus profiles,
generic print() and plot() for better usability of selected explainers,
generic plotD3() for interactive, D3 based explanations, and
generic describe() for explanations in natural language.
The package 'ingredients' is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] ,
Hubert Baniecki [aut] ,
Adam Izdebski [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between ingredients versions 2.2.0 dated 2021-04-10 and 2.3.0 dated 2023-01-15
DESCRIPTION | 8 MD5 | 36 +- NAMESPACE | 1 NEWS.md | 12 R/aggregate_profiles.R | 4 R/calculate_variable_profile.R | 13 R/describe_aggregated_profiles.R | 6 R/describe_ceteris_paribus.R | 12 R/describe_feature_importance.R | 3 R/plot_aggregated_profiles.R | 4 R/plot_ceteris_paribus.R | 23 + R/show_observations.R | 6 build/vignette.rds |binary inst/doc/vignette_describe.html | 425 +++++++++++++----------------- inst/doc/vignette_simulated.html | 237 +++++++--------- inst/doc/vignette_titanic.html | 262 ++++++++---------- man/plot.aggregated_profiles_explainer.Rd | 3 man/plot.ceteris_paribus_explainer.Rd | 4 tests/testthat/test_ceteris_paribus.R | 19 + 19 files changed, 529 insertions(+), 549 deletions(-)
Title: Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD
Description: Contains Probability Mass Functions, Cumulative Mass
Functions, Negative Log Likelihood value, parameter estimation and
modeling data using Binomial Mixture Distributions (BMD) (Manoj et al
(2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial
Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>),
also Journal article to use the package(<doi:10.21105/joss.01505>).
Author: Amalan Mahendran [aut, cre] ,
Pushpakanthie Wijekoon [aut, ctb]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between fitODBOD versions 1.4.1-1 dated 2020-01-16 and 1.5.0 dated 2023-01-15
fitODBOD-1.4.1-1/fitODBOD/man/figures/table1.JPG |only fitODBOD-1.4.1-1/fitODBOD/man/figures/table2.JPG |only fitODBOD-1.5.0/fitODBOD/DESCRIPTION | 43 ++-- fitODBOD-1.5.0/fitODBOD/LICENSE |only fitODBOD-1.5.0/fitODBOD/MD5 | 205 +++++++++++----------- fitODBOD-1.5.0/fitODBOD/NAMESPACE | 2 fitODBOD-1.5.0/fitODBOD/R/AddBin.R | 81 +++----- fitODBOD-1.5.0/fitODBOD/R/BMD_ABD.R | 3 fitODBOD-1.5.0/fitODBOD/R/Beta.R | 114 +++++------- fitODBOD-1.5.0/fitODBOD/R/BetaCorrBin.R | 140 +++++---------- fitODBOD-1.5.0/fitODBOD/R/COMPBin.R | 49 +---- fitODBOD-1.5.0/fitODBOD/R/CorrBin.R | 63 +----- fitODBOD-1.5.0/fitODBOD/R/Data.R | 24 +- fitODBOD-1.5.0/fitODBOD/R/GHGbeta.R | 78 +++----- fitODBOD-1.5.0/fitODBOD/R/Gamma.R | 110 ++++------- fitODBOD-1.5.0/fitODBOD/R/Gbeta1.R | 116 +++++------- fitODBOD-1.5.0/fitODBOD/R/Kumaraswamy.R | 106 ++++------- fitODBOD-1.5.0/fitODBOD/R/LMultiBin.R | 51 +---- fitODBOD-1.5.0/fitODBOD/R/MultiBin.R | 69 +++---- fitODBOD-1.5.0/fitODBOD/R/Triangle.R | 137 ++++---------- fitODBOD-1.5.0/fitODBOD/R/Uniform.R | 14 - fitODBOD-1.5.0/fitODBOD/R/ml.R | 4 fitODBOD-1.5.0/fitODBOD/build |only fitODBOD-1.5.0/fitODBOD/inst |only fitODBOD-1.5.0/fitODBOD/man/Alcohol_data.Rd | 8 fitODBOD-1.5.0/fitODBOD/man/Chromosome_data.Rd | 8 fitODBOD-1.5.0/fitODBOD/man/Course_data.Rd | 8 fitODBOD-1.5.0/fitODBOD/man/Epidemic_Cold.Rd | 6 fitODBOD-1.5.0/fitODBOD/man/EstMGFBetaBin.Rd | 6 fitODBOD-1.5.0/fitODBOD/man/EstMLEAddBin.Rd | 4 fitODBOD-1.5.0/fitODBOD/man/EstMLEBetaBin.Rd | 6 fitODBOD-1.5.0/fitODBOD/man/EstMLEBetaCorrBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/EstMLECOMPBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/EstMLECorrBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/EstMLEGHGBB.Rd | 1 fitODBOD-1.5.0/fitODBOD/man/EstMLEKumBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/EstMLEMcGBB.Rd | 6 fitODBOD-1.5.0/fitODBOD/man/EstMLEMultiBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/EstMLETriBin.Rd | 6 fitODBOD-1.5.0/fitODBOD/man/Exam_data.Rd | 8 fitODBOD-1.5.0/fitODBOD/man/Male_Children.Rd | 8 fitODBOD-1.5.0/fitODBOD/man/NegLLAddBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/NegLLBetaBin.Rd | 6 fitODBOD-1.5.0/fitODBOD/man/NegLLBetaCorrBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/NegLLCOMPBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/NegLLCorrBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/NegLLGHGBB.Rd | 1 fitODBOD-1.5.0/fitODBOD/man/NegLLKumBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/NegLLMcGBB.Rd | 4 fitODBOD-1.5.0/fitODBOD/man/NegLLMultiBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/NegLLTriBin.Rd | 4 fitODBOD-1.5.0/fitODBOD/man/Plant_DiseaseData.Rd | 8 fitODBOD-1.5.0/fitODBOD/man/Terror_data_ARG.Rd | 6 fitODBOD-1.5.0/fitODBOD/man/Terror_data_USA.Rd | 6 fitODBOD-1.5.0/fitODBOD/man/dAddBin.Rd | 196 ++++++++++----------- fitODBOD-1.5.0/fitODBOD/man/dBETA.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/dBetaBin.Rd | 4 fitODBOD-1.5.0/fitODBOD/man/dBetaCorrBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/dCOMPBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/dCorrBin.Rd | 5 fitODBOD-1.5.0/fitODBOD/man/dGBeta1.Rd | 4 fitODBOD-1.5.0/fitODBOD/man/dGHGBB.Rd | 1 fitODBOD-1.5.0/fitODBOD/man/dGHGBeta.Rd | 1 fitODBOD-1.5.0/fitODBOD/man/dGrassiaIIBin.Rd | 1 fitODBOD-1.5.0/fitODBOD/man/dKUM.Rd | 4 fitODBOD-1.5.0/fitODBOD/man/dKumBin.Rd | 10 - 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fitODBOD-1.5.0/fitODBOD/man/pMcGBB.Rd | 4 fitODBOD-1.5.0/fitODBOD/man/pMultiBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/man/pTRI.Rd | 11 - fitODBOD-1.5.0/fitODBOD/man/pTriBin.Rd | 4 fitODBOD-1.5.0/fitODBOD/man/pUniBin.Rd | 2 fitODBOD-1.5.0/fitODBOD/tests/spelling.R |only fitODBOD-1.5.0/fitODBOD/tests/testthat/test-AIC.R | 2 107 files changed, 798 insertions(+), 1118 deletions(-)
Title: See a Forest for the Trees
Description: Get insight into a forest of classification trees, by calculating similarities between the trees, and subsequently clustering them. Each cluster is represented by it's most central cluster member. The package implements the methodology described in Sies & Van Mechelen (2020) <doi:10.1007/s00357-019-09350-4>.
Author: Aniek Sies [aut, cre],
Kristof Meers [ctb],
Iven Van Mechelen [ths]
Maintainer: Aniek Sies <aniek.sies@kuleuven.be>
Diff between C443 versions 3.3 dated 2022-11-20 and 3.3.1 dated 2023-01-15
DESCRIPTION | 12 +-- MD5 | 40 +++++----- NAMESPACE | 122 +++++++++++++++--------------- R/clusterforest.R | 16 +--- man/clusterforest.Rd | 6 - man/clusters.Rd | 32 ++++---- man/clusters.clusterforest.Rd | 32 ++++---- man/clusters.default.Rd | 32 ++++---- man/drugs.Rd | 124 +++++++++++++++---------------- man/medoidtrees.Rd | 32 ++++---- man/medoidtrees.clusterforest.Rd | 32 ++++---- man/medoidtrees.default.Rd | 32 ++++---- man/plot.clusterforest.Rd | 132 ++++++++++++++++----------------- man/print.clusterforest.Rd | 36 ++++----- man/summary.clusterforest.Rd | 32 ++++---- man/treesimilarities.Rd | 28 +++---- man/treesimilarities.clusterforest.Rd | 28 +++---- man/treesimilarities.default.Rd | 28 +++---- man/treesource.Rd | 136 +++++++++++++++++----------------- man/treesource.clusterforest.Rd | 36 ++++----- man/treesource.default.Rd | 36 ++++----- 21 files changed, 500 insertions(+), 504 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.54 dated 2022-12-12 and 2.0.56 dated 2023-01-15
DESCRIPTION | 8 MD5 | 68 - NEWS | 13 R/epi.sscc.R | 58 - R/epi.ssclus1estb.R | 41 R/epi.ssclus1estc.R | 35 R/epi.ssclus2estb.R | 36 R/epi.ssclus2estc.R | 40 R/epi.sscohortc.R | 10 R/epi.sscohortt.R | 2 R/epi.sscompb.R | 32 R/epi.sscompc.R | 29 R/epi.sssimpleestb.R | 17 R/epi.sssimpleestc.R | 14 R/epi.ssxsectn.R | 30 inst/doc/epiR_descriptive.html | 880 ++++++++++++-------- inst/doc/epiR_measures_of_association.html | 1248 ++++++++++++++++------------- inst/doc/epiR_sample_size.html | 345 +++++--- inst/doc/epiR_surveillance.Rmd | 2 inst/doc/epiR_surveillance.html | 1063 ++++++++++++++++-------- man/epi.2by2.Rd | 88 +- man/epi.sscc.Rd | 29 man/epi.ssclus1estb.Rd | 22 man/epi.ssclus1estc.Rd | 7 man/epi.ssclus2estb.Rd | 9 man/epi.ssclus2estc.Rd | 9 man/epi.sscohortc.Rd | 24 man/epi.sscohortt.Rd | 9 man/epi.sscompb.Rd | 9 man/epi.sscompc.Rd | 16 man/epi.sssimpleestb.Rd | 28 man/epi.sssimpleestc.Rd | 10 man/epi.ssxsectn.Rd | 22 vignettes/epiR_surveillance.Rmd | 2 vignettes/epiR_surveillance.bib | 6 35 files changed, 2562 insertions(+), 1699 deletions(-)
Title: Linear Ridge Regression with Ridge Penalty and Ridge Statistics
Description: Linear ridge regression coefficient's estimation and testing with different ridge related measures such as MSE, R-squared etc.
REFERENCES
i. Hoerl and Kennard (1970) <doi:10.1080/00401706.1970.10488634>,
ii. Halawa and El-Bassiouni (2000) <doi:10.1080/00949650008812006>,
iii. Imdadullah, Aslam, and Saima (2017),
iv. Marquardt (1970) <doi:10.2307/1267205>.
Author: Imdad Ullah Muhammad [aut, cre]
,
Aslam Muhammad [aut, ctb]
Maintainer: Imdad Ullah Muhammad <mimdadasad@gmail.com>
Diff between lmridge versions 1.2.1 dated 2021-11-11 and 1.2.2 dated 2023-01-15
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- R/kest.R | 16 +++++++++------- R/lmridge.R | 4 ++-- R/lmridgeEst.R | 12 ++++++------ R/print.klmridge.R | 50 +++++++++++++++++++++++++------------------------- R/rstats1.R | 10 +++++----- build/partial.rdb |binary inst/NEWS.Rd | 10 ++++++++++ man/hatr.Rd | 2 +- man/kest.Rd | 9 ++++++++- man/lmridge.Rd | 10 ++++++---- man/rstats1.Rd | 6 ++++++ man/rstats2.Rd | 3 +++ 14 files changed, 97 insertions(+), 67 deletions(-)