Title: Run 'shiny' Applications in the Browser
Description: Exporting 'shiny' applications with 'shinylive' allows you to
run them entirely in a web browser, without the need for a separate R
server. The traditional way of deploying 'shiny' applications involves
in a separate server and client: the server runs R and 'shiny', and
clients connect via the web browser. When an application is deployed
with 'shinylive', R and 'shiny' run in the web browser (via 'webR'):
the browser is effectively both the client and server for the
application. This allows for your 'shiny' application exported by
'shinylive' to be hosted by a static web server.
Author: Barret Schloerke [aut, cre] ,
Winston Chang [aut] ,
George Stagg [aut],
Garrick Aden-Buie [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between shinylive versions 0.2.0 dated 2024-07-19 and 0.3.0 dated 2024-11-12
DESCRIPTION | 6 - MD5 | 19 +++--- NEWS.md | 14 ++++ R/export.R | 32 ++++++++-- R/packages.R | 135 ++++++++++++++++++++++++------------------- R/quarto_ext.R | 31 +++++++-- R/version.R | 2 README.md | 2 man/export.Rd | 15 +++- tests/testthat/apps/app-utf8 |only tests/testthat/test-export.R | 58 ++++++++++++++++++ 11 files changed, 225 insertions(+), 89 deletions(-)
Title: Similarity and Distance Quantification Between Probability
Functions
Description: Computes 46 optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.
Author: Hajk-Georg Drost [aut, cre] ,
Jakub Nowosad [ctb]
Maintainer: Hajk-Georg Drost <hajk-georg.drost@tuebingen.mpg.de>
Diff between philentropy versions 0.8.0 dated 2023-12-02 and 0.9.0 dated 2024-11-12
DESCRIPTION | 13 +++++++------ MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/JSD.R | 7 ++++--- R/est.prob.R | 11 +---------- README.md | 30 +++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/Distances.html | 4 ++-- inst/doc/Information_Theory.html | 4 ++-- inst/doc/Many_Distances.html | 32 ++++++++++++++++---------------- man/JSD.Rd | 7 ++++--- man/estimate.probability.Rd | 8 +------- 12 files changed, 77 insertions(+), 65 deletions(-)
Title: Characterise Tables of an OMOP Common Data Model Instance
Description: Summarises key information in data mapped to the Observational
Medical Outcomes Partnership (OMOP) common data model. Assess suitability to
perform specific epidemiological studies and explore the different domains
to obtain feasibility counts and trends.
Author: Marta Alcalde-Herraiz [aut, cre]
,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut] ,
Edward Burn [aut] ,
Marti Catala [aut]
Maintainer: Marta Alcalde-Herraiz <marta.alcaldeherraiz@ndorms.ox.ac.uk>
Diff between OmopSketch versions 0.1.1 dated 2024-10-15 and 0.1.2 dated 2024-11-12
OmopSketch-0.1.1/OmopSketch/inst/doc/C-summarise_pop_characteristics.R |only OmopSketch-0.1.1/OmopSketch/inst/doc/C-summarise_pop_characteristics.Rmd |only OmopSketch-0.1.1/OmopSketch/inst/doc/C-summarise_pop_characteristics.html |only OmopSketch-0.1.1/OmopSketch/vignettes/C-summarise_pop_characteristics.Rmd |only OmopSketch-0.1.2/OmopSketch/DESCRIPTION | 19 OmopSketch-0.1.2/OmopSketch/MD5 | 50 OmopSketch-0.1.2/OmopSketch/R/mockOmopSketch.R | 117 - OmopSketch-0.1.2/OmopSketch/R/plotConceptCounts.R | 128 - OmopSketch-0.1.2/OmopSketch/R/summariseInObservation.R | 666 +++---- OmopSketch-0.1.2/OmopSketch/R/summariseOmopSnapshot.R | 3 OmopSketch-0.1.2/OmopSketch/R/tableOmopSnapshot.R | 3 OmopSketch-0.1.2/OmopSketch/R/tablePopulationCharacteristics.R | 114 - OmopSketch-0.1.2/OmopSketch/build/vignette.rds |binary OmopSketch-0.1.2/OmopSketch/inst/doc/A-summarise_clinical_tables_records.html | 262 +- OmopSketch-0.1.2/OmopSketch/inst/doc/B-summarise_concept_counts.R | 18 OmopSketch-0.1.2/OmopSketch/inst/doc/B-summarise_concept_counts.Rmd | 288 +-- OmopSketch-0.1.2/OmopSketch/inst/doc/B-summarise_concept_counts.html | 48 OmopSketch-0.1.2/OmopSketch/man/mockOmopSketch.Rd | 3 OmopSketch-0.1.2/OmopSketch/man/summariseOmopSnapshot.Rd | 3 OmopSketch-0.1.2/OmopSketch/man/tableOmopSnapshot.Rd | 3 OmopSketch-0.1.2/OmopSketch/tests/testthat/test-plotInObservation.R | 136 - OmopSketch-0.1.2/OmopSketch/tests/testthat/test-summariseConceptCounts.R | 910 +++++----- OmopSketch-0.1.2/OmopSketch/tests/testthat/test-summariseInObservation.R | 488 ++--- OmopSketch-0.1.2/OmopSketch/tests/testthat/test-summariseObservationPeriod.R | 5 OmopSketch-0.1.2/OmopSketch/tests/testthat/test-summariseOmopSnapshot.R | 77 OmopSketch-0.1.2/OmopSketch/tests/testthat/test-summarisePopulationCharacteristics.R | 3 OmopSketch-0.1.2/OmopSketch/tests/testthat/test-summariseRecordCount.R | 539 ++--- OmopSketch-0.1.2/OmopSketch/vignettes/B-summarise_concept_counts.Rmd | 288 +-- 28 files changed, 2070 insertions(+), 2101 deletions(-)
Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models, with and without interaction terms. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) <DOI:10.1186/s12859-017-1863-x> and the package vignette.
Author: Youyi Fong [cre],
Qianqian Chen [aut],
Shuangcheng Hua [aut],
Hyunju Son [aut],
Adam Elder [aut],
Tao Yang [aut],
Zonglin He [aut],
Simone Giannerini [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2023.11-29 dated 2023-12-05 and 2024.11-15 dated 2024-11-12
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ inst/doc/chngpt-vignette.pdf |binary src/doublehinge.c | 20 ++++++++++---------- src/error.h | 4 ++-- src/fastgrid.cc | 12 ++++++------ src/fastgrid2.cc | 26 +++++++++++++------------- src/grid.cc | 12 ++++++------ src/matrix_bidirectional_iterator.h | 2 +- src/matrix_forward_iterator.h | 2 +- src/matrix_random_access_iterator.h | 4 ++-- src/performance.cc | 10 +++++----- src/twoD.cc | 26 +++++++++++++------------- 13 files changed, 74 insertions(+), 74 deletions(-)
Title: Multivariate Bias Correction of Climate Model Outputs
Description: Calibrate and apply multivariate bias correction algorithms
for climate model simulations of multiple climate variables. Three methods
described by Cannon (2016) <doi:10.1175/JCLI-D-15-0679.1> and
Cannon (2018) <doi:10.1007/s00382-017-3580-6> are implemented —
(i) MBC Pearson correlation (MBCp), (ii) MBC rank correlation (MBCr),
and (iii) MBC N-dimensional PDF transform (MBCn) — as is the Rank
Resampling for Distributions and Dependences (R2D2) method.
Author: Alex J. Cannon [aut, cre]
Maintainer: Alex J. Cannon <alex.cannon@canada.ca>
Diff between MBC versions 0.10-6 dated 2023-05-02 and 0.10-7 dated 2024-11-12
DESCRIPTION | 8 +++--- MD5 | 7 +++--- R/MBC-QDM.R | 15 +++++++------ README.md |only man/MBC-package.Rd | 61 ++++++++++++++++++++++++++++++----------------------- 5 files changed, 52 insertions(+), 39 deletions(-)
Title: Miscellaneous Useful Functions Including LaTeX Tables, Kalman
Filtering, QQplots with Simulation-Based Confidence Intervals,
Linear Regression Diagnostics and Development Tools
Description: Implementing various things including functions for LaTeX tables,
the Kalman filter, QQ-plots with simulation-based confidence intervals, linear regression diagnostics, web scraping, development tools, relative risk and odds
rati, GARCH(1,1) Forecasting.
Author: Benjamin M. Taylor [aut, cre]
Maintainer: Benjamin M. Taylor <benjamin.taylor.software@gmail.com>
Diff between miscFuncs versions 1.5-9 dated 2024-10-18 and 1.5-10 dated 2024-11-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/vignette.rds |binary inst/doc/miscFuncs.pdf |binary 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Numerical Tools for 'Rcpp' and Lambda Functions
Description: Provides a 'C++' API for routinely used numerical tools such as integration,
root-finding, and optimization, where function arguments are given as
lambdas. This facilitates 'Rcpp' programming, enabling the development of
'R'-like code in 'C++' where functions can be defined on the fly and use
variables in the surrounding environment.
Author: Andrew M. Raim [aut, cre]
Maintainer: Andrew M. Raim <andrew.raim@gmail.com>
Diff between fntl versions 0.1.1 dated 2024-09-07 and 0.1.2 dated 2024-11-12
DESCRIPTION | 6 MD5 | 96 +++--- NAMESPACE | 4 NEWS.md |only R/RcppExports.R | 112 +++++++ build/vignette.rds |binary inst/doc/fntl.R | 149 ++++++++- inst/doc/fntl.pdf |binary inst/doc/fntl.qmd | 285 +++++++++++++++++++ inst/include/apply.h | 1 inst/include/args.h | 1 inst/include/bfgs.h | 1 inst/include/cg.h | 1 inst/include/deriv.h | 1 inst/include/deriv2.h | 1 inst/include/fd-deriv.h | 1 inst/include/findroot-bisect.h | 1 inst/include/findroot-brent.h | 1 inst/include/fntl.h | 2 inst/include/goldensection.h | 3 inst/include/gradient.h | 1 inst/include/hessian.h | 1 inst/include/integrate.h | 1 inst/include/jacobian.h | 1 inst/include/lbfgsb.h | 1 inst/include/log-sum-exp.h |only inst/include/neldermead.h | 1 inst/include/nlm.h | 1 inst/include/optimize-brent.h | 5 inst/include/outer.h | 1 inst/include/result.h | 1 inst/include/richardson.h | 1 inst/include/solve-cg.h | 1 inst/include/trunc.h |only inst/include/typedefs-rcpp.h | 1 inst/include/typedefs.h | 5 inst/include/util.h | 7 inst/include/which.h | 1 inst/tinytest/cpp/test-multivariate-optimization.cpp | 65 ++++ inst/tinytest/cpp/test-trunc.cpp |only inst/tinytest/cpp/test-univariate-optimization.cpp | 16 - inst/tinytest/test-multivariate-optimization.R | 37 ++ inst/tinytest/test-trunc.R |only inst/tinytest/test-univariate-optimization.R | 29 + man/trunc.Rd |only src/RcppExports.cpp | 68 ++++ src/rcpp-interface.cpp | 63 ++++ src/rcpp-interface.h | 117 +++++++ vignettes/examples/d_trunc.cpp |only vignettes/examples/p_trunc.cpp |only vignettes/examples/q_trunc.cpp |only vignettes/examples/r_trunc.cpp |only vignettes/fntl.qmd | 285 +++++++++++++++++++ vignettes/references.bib | 8 54 files changed, 1263 insertions(+), 121 deletions(-)
Title: Methods for Visualization of Computer Experiments Design and
Surrogate
Description: View 2D/3D sections, contour plots, mesh of excursion sets for computer experiments designs, surrogates or test functions.
Author: Yann Richet [aut, cre] ,
Yves Deville [aut],
Clement Chevalier [ctb]
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between DiceView versions 2.2-0 dated 2024-01-15 and 3.1-0 dated 2024-11-12
DiceView-2.2-0/DiceView/man/mesh_roots.Rd |only DiceView-3.1-0/DiceView/DESCRIPTION | 10 DiceView-3.1-0/DiceView/MD5 | 43 - DiceView-3.1-0/DiceView/NAMESPACE | 16 DiceView-3.1-0/DiceView/R/Utils.R | 32 DiceView-3.1-0/DiceView/R/contourview.R | 694 ++++++++++++------ DiceView-3.1-0/DiceView/R/filledcontourview.R |only DiceView-3.1-0/DiceView/R/function.R | 94 ++ DiceView-3.1-0/DiceView/R/mesh_set.R | 160 +++- DiceView-3.1-0/DiceView/R/root.R | 167 ++-- DiceView-3.1-0/DiceView/R/sectionview.R | 700 +++++++++++-------- DiceView-3.1-0/DiceView/R/sectionview3d.R | 675 +++++++++++------- DiceView-3.1-0/DiceView/man/EvalInterval.function.Rd |only DiceView-3.1-0/DiceView/man/Vectorize.function.Rd | 15 DiceView-3.1-0/DiceView/man/contourview.Rd | 180 +++- DiceView-3.1-0/DiceView/man/expand.grids.Rd |only DiceView-3.1-0/DiceView/man/filledcontourview.Rd |only DiceView-3.1-0/DiceView/man/is.mesh.Rd |only DiceView-3.1-0/DiceView/man/mesh.Rd |only DiceView-3.1-0/DiceView/man/mesh_exsets.Rd | 8 DiceView-3.1-0/DiceView/man/mesh_level.Rd |only DiceView-3.1-0/DiceView/man/plot2d_mesh.Rd | 16 DiceView-3.1-0/DiceView/man/plot3d_mesh.Rd | 19 DiceView-3.1-0/DiceView/man/plot_mesh.Rd | 15 DiceView-3.1-0/DiceView/man/roots_mesh.Rd |only DiceView-3.1-0/DiceView/man/sectionview.Rd | 145 ++- DiceView-3.1-0/DiceView/man/sectionview3d.Rd | 138 ++- 27 files changed, 2034 insertions(+), 1093 deletions(-)
Title: Alternate DEA Package
Description: The meaning of adea is "alternate DEA". This package is devoted to provide the alternative method of DEA described in the paper entitled "Stepwise Selection of Variables in DEA Using Contribution Load", by F. Fernandez-Palacin, M. A. Lopez-Sanchez and M. Munoz-Marquez. Pesquisa Operacional 38 (1), pg. 1-24, 2018. <doi:10.1590/0101-7438.2018.038.01.0031>.
A full functional on-line and interactive version is available at
<https://knuth.uca.es/shiny/DEA/>.
Author: Fernando Fernandez-Palacin [aut]
,
Manuel Munoz-Marquez [aut, cre]
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between adea versions 1.5.1 dated 2023-11-24 and 1.5.2 dated 2024-11-12
ChangeLog | 3 DESCRIPTION | 11 - MD5 | 32 +- R/adea-package.R | 6 R/adea_load_leverage.R | 25 +- R/print.adealoadleverage.R | 2 build/vignette.rds |binary inst/doc/adea_load_leverage.html | 319 ++++++++++++++++------------- inst/doc/adea_variable_selection.html | 372 +++++++++++++++++++--------------- inst/doc/cadea.html | 367 ++++++++++++++++++--------------- inst/doc/dea_feature_selection.html | 362 ++++++++++++++++++--------------- inst/doc/index.html | 45 +--- inst/po/adea-es |only inst/po/en@quot |only man/adea-package.Rd | 5 po/R-adea.pot | 4 tests/testthat/testdea.R | 1 tests/testthat/testleverage.R | 26 +- 18 files changed, 866 insertions(+), 714 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.1.1 dated 2024-10-25 and 2.1.2 dated 2024-11-12
DESCRIPTION | 14 ++++---- MD5 | 46 +++++++++++++------------- NEWS.md | 9 +++++ R/EngineGraphQLGitHub.R | 26 +++++++++------ R/EngineRestGitHub.R | 11 ++++-- R/EngineRestGitLab.R | 16 ++++++--- R/GQLQueryGitHub.R | 36 +++++++-------------- R/GitHost.R | 9 +++-- R/GitHostGitHub.R | 4 +- R/GitHostGitLab.R | 22 +----------- R/GitStats.R | 2 - README.md | 4 +- inst/get_repos_urls_workflow.R | 27 +++++++++++++++ inst/roche_get_commits_workflow.R | 2 - tests/testthat/_snaps/get_commits-GitHub.md | 4 +- tests/testthat/_snaps/set_host.md | 9 ----- tests/testthat/helper-expect-responses.R | 2 - tests/testthat/helper-expect-tables.R | 4 +- tests/testthat/helper-fixtures.R | 21 +++++++++++- tests/testthat/test-get_commits-GitHub.R | 12 +------ tests/testthat/test-get_urls_repos-GitHub.R | 30 ++++++++++++++--- tests/testthat/test-get_urls_repos-GitLab.R | 48 ++++++++++++++++++++++------ tests/testthat/test-helpers.R | 24 ++++++++++++++ tests/testthat/test-set_host.R | 22 +++++++++++- 24 files changed, 265 insertions(+), 139 deletions(-)
Title: Bayesian Analysis of Networks of Binary and/or Ordinal Variables
Description: Bayesian variable selection methods for analyzing the structure of a Markov Random Field model for a network of binary and/or ordinal variables. Details of the implemented methods can be found in: Marsman, van den Bergh, and Haslbeck (in press) <doi:10.31234/osf.io/ukwrf>.
Author: Maarten Marsman [aut, cre] ,
Karoline Huth [ctb] ,
Nikola Sekulovski [ctb] ,
Don van den Bergh [ctb]
Maintainer: Maarten Marsman <m.marsman@uva.nl>
Diff between bgms versions 0.1.4 dated 2024-10-20 and 0.1.4.1 dated 2024-11-12
DESCRIPTION | 8 - MD5 | 24 ++--- NEWS.md | 16 +++ R/bgmCompare.R | 6 - R/extractor_functions.R | 3 R/utility_functions.R | 2 build/partial.rdb |binary inst/CITATION | 9 -- inst/doc/bgmcompare.R | 50 +++++------ inst/doc/bgmcompare.html | 4 inst/doc/introduction.R | 194 ++++++++++++++++++++++----------------------- inst/doc/introduction.html | 7 - man/bgmCompare.Rd | 6 - 13 files changed, 169 insertions(+), 160 deletions(-)
Title: Binary Endpoint Estimation with Covariate Adjustment
Description: Performs estimation of marginal treatment effects for binary
outcomes when using logistic regression working models with covariate
adjustment (see discussions in Magirr et al (2024) <https://osf.io/9mp58/>).
Implements the variance estimators of Ge et al (2011) <doi:10.1177/009286151104500409>
and Ye et al (2023) <doi:10.1080/24754269.2023.2205802>.
Author: Alex Przybylski [cre, aut],
Mark Baillie [aut] ,
Craig Wang [aut] ,
Dominic Magirr [aut]
Maintainer: Alex Przybylski <alexander.przybylski@novartis.com>
Diff between beeca versions 0.1.3 dated 2024-06-18 and 0.2.0 dated 2024-11-12
DESCRIPTION | 11 MD5 | 90 NAMESPACE | 41 NEWS.md | 20 R/apply_contrast.R | 488 ++- R/average_predictions.R | 154 - R/beeca-package.R | 14 R/estimate_varcov.R | 608 ++-- R/ge_macro_trial01.R | 40 R/get_marginal_effect.R | 245 - R/margins_trial01.R | 48 R/predict_counterfactuals.R | 168 - R/sanitize.R | 304 +- R/trial01.R | 32 R/trial02_cdisc.R | 86 README.md | 153 - build/partial.rdb |binary build/vignette.rds |binary data/trial02_cdisc.rda |binary inst/doc/estimand_and_implementations.R | 256 + inst/doc/estimand_and_implementations.Rmd | 533 ++-- inst/doc/estimand_and_implementations.html | 1435 +++++------ inst/extdata/sim_trial_01.csv | 538 ++-- inst/sasdoc/fusion_63038_24_margins.sas | 3350 +++++++++++++------------- inst/sasdoc/ge_paper_macro.sas | 280 +- man/apply_contrast.Rd | 167 - man/average_predictions.Rd | 132 - man/beeca-package.Rd | 59 man/estimate_varcov.Rd | 224 - man/ge_macro_trial01.Rd | 58 man/get_marginal_effect.Rd | 177 - man/margins_trial01.Rd | 66 man/predict_counterfactuals.Rd | 127 man/sanitize_model.Rd | 54 man/sanitize_model.glm.Rd | 56 man/sanitize_variable.Rd | 40 man/trial01.Rd | 50 man/trial02_cdisc.Rd | 108 tests/testthat.R | 24 tests/testthat/test-apply_contrasts.R | 777 +++--- tests/testthat/test-average_predictions.R | 178 - tests/testthat/test-estimate_varcov.R | 484 ++- tests/testthat/test-get_marginal_effect.R | 103 tests/testthat/test-predict_counterfactuals.R | 34 tests/testthat/test-sanitize.R | 260 +- vignettes/estimand_and_implementations.Rmd | 533 ++-- 46 files changed, 6519 insertions(+), 6086 deletions(-)
Title: Fast and Efficient Access to MODIS Earth Observation Data
Description: Programmatic interface to several NASA Earth Observation 'OPeNDAP' servers (Open-source Project for a Network Data Access Protocol) (<https://www.opendap.org/>). Allows for easy downloads of MODIS subsets, as well as other Earth Observation datacubes, in a time-saving and efficient way : by sampling it at the very downloading phase (spatially, temporally and dimensionally).
Author: Paul Taconet [aut, cre, cph] ,
Nicolas Moiroux [fnd] ,
French National Research Institute for Sustainable Development, IRD
[fnd]
Maintainer: Paul Taconet <paul.taconet@gmail.com>
Diff between modisfast versions 0.9.1 dated 2024-07-14 and 1.0.0 dated 2024-11-12
modisfast-0.9.1/modisfast/tests/testthat/test_get_url.R |only modisfast-1.0.0/modisfast/DESCRIPTION | 13 modisfast-1.0.0/modisfast/MD5 | 62 modisfast-1.0.0/modisfast/NAMESPACE | 4 modisfast-1.0.0/modisfast/NEWS.md | 28 modisfast-1.0.0/modisfast/R/buildUrls.R | 404 +- modisfast-1.0.0/modisfast/R/functions_import_data.R | 68 modisfast-1.0.0/modisfast/R/internal_ancillary.R | 41 modisfast-1.0.0/modisfast/R/internal_opendap.R | 96 modisfast-1.0.0/modisfast/R/internal_tests.R | 74 modisfast-1.0.0/modisfast/R/mf_download_data.R | 201 - modisfast-1.0.0/modisfast/R/mf_get_opt_param.R | 274 - modisfast-1.0.0/modisfast/R/mf_get_url.R | 131 modisfast-1.0.0/modisfast/R/mf_import_data.R | 67 modisfast-1.0.0/modisfast/R/mf_list_collections.R | 9 modisfast-1.0.0/modisfast/R/mf_list_variables.R | 126 modisfast-1.0.0/modisfast/R/mf_login.R | 51 modisfast-1.0.0/modisfast/R/mf_modisfast.R |only modisfast-1.0.0/modisfast/R/sysdata.rda |binary modisfast-1.0.0/modisfast/README.md | 1538 +++++----- modisfast-1.0.0/modisfast/inst/CITATION | 7 modisfast-1.0.0/modisfast/man/mf_download_data.Rd | 33 modisfast-1.0.0/modisfast/man/mf_get_opt_param.Rd | 47 modisfast-1.0.0/modisfast/man/mf_get_url.Rd | 34 modisfast-1.0.0/modisfast/man/mf_import_data.Rd | 35 modisfast-1.0.0/modisfast/man/mf_list_collections.Rd | 1 modisfast-1.0.0/modisfast/man/mf_list_variables.Rd | 9 modisfast-1.0.0/modisfast/man/mf_login.Rd | 9 modisfast-1.0.0/modisfast/man/mf_modisfast.Rd |only modisfast-1.0.0/modisfast/tests/testthat.R | 7 modisfast-1.0.0/modisfast/tests/testthat/helper-modisfast.R |only modisfast-1.0.0/modisfast/tests/testthat/test-mf_download_data.R |only modisfast-1.0.0/modisfast/tests/testthat/test-mf_get_url.R |only modisfast-1.0.0/modisfast/tests/testthat/test-mf_import_data.R |only modisfast-1.0.0/modisfast/tests/testthat/test-mf_list_collections.R |only modisfast-1.0.0/modisfast/tests/testthat/test-mf_list_variables.R |only modisfast-1.0.0/modisfast/tests/testthat/test-mf_login.R |only 37 files changed, 1922 insertions(+), 1447 deletions(-)
Title: Fast Numerical Maximum Likelihood Estimation for Latent Markov
Models
Description: A variety of latent Markov models, including hidden Markov models, hidden semi-Markov models,
state-space models and continuous-time variants can be formulated and estimated within the same framework via directly maximising the likelihood function using the so-called forward algorithm.
Applied researchers often need custom models that standard software does not easily support.
Writing tailored 'R' code offers flexibility but suffers from slow estimation speeds.
We address these issues by providing easy-to-use functions (written in 'C++' for speed) for common tasks like the forward algorithm.
These functions can be combined into custom models in a Lego-type approach, offering up to 10-20 times faster estimation via standard numerical optimisers.
To aid in building fully custom likelihood functions, several vignettes are included that show how to simulate data from and estimate all the above model classes.
Author: Jan-Ole Koslik [aut, cre]
Maintainer: Jan-Ole Koslik <jan-ole.koslik@uni-bielefeld.de>
Diff between LaMa versions 1.0.0 dated 2024-06-04 and 2.0.0 dated 2024-11-12
LaMa-1.0.0/LaMa/R/calc_trackInd.R |only LaMa-1.0.0/LaMa/R/forward.R |only LaMa-1.0.0/LaMa/R/forward_g.R |only LaMa-1.0.0/LaMa/R/forward_p.R |only LaMa-1.0.0/LaMa/R/forward_s.R |only LaMa-1.0.0/LaMa/R/forward_sp.R |only LaMa-1.0.0/LaMa/R/stateprobs.R |only LaMa-1.0.0/LaMa/R/stateprobs_g.R |only LaMa-1.0.0/LaMa/R/stateprobs_p.R |only LaMa-1.0.0/LaMa/R/stationary.R |only LaMa-1.0.0/LaMa/R/stationary_p.R |only LaMa-1.0.0/LaMa/R/tpm.R |only LaMa-1.0.0/LaMa/R/tpm_cont.R |only LaMa-1.0.0/LaMa/R/tpm_g.R |only LaMa-1.0.0/LaMa/R/tpm_hsmm.R |only LaMa-1.0.0/LaMa/R/tpm_p.R |only LaMa-1.0.0/LaMa/R/tpm_phsmm.R |only LaMa-1.0.0/LaMa/R/tpm_thinned.R |only LaMa-1.0.0/LaMa/R/trigBasisExp.R |only LaMa-1.0.0/LaMa/R/viterbi.R |only LaMa-1.0.0/LaMa/R/viterbi_g.R |only LaMa-1.0.0/LaMa/R/viterbi_p.R |only LaMa-1.0.0/LaMa/build/partial.rdb |only LaMa-1.0.0/LaMa/inst/doc/Periodic_HMM.R |only LaMa-1.0.0/LaMa/inst/doc/Periodic_HMM.Rmd |only LaMa-1.0.0/LaMa/inst/doc/Periodic_HMM.html |only LaMa-1.0.0/LaMa/man/figures/Lcpp_logo_new.png |only LaMa-1.0.0/LaMa/man/figures/README-unnamed-chunk-3-1.png |only LaMa-1.0.0/LaMa/man/figures/README-unnamed-chunk-6-1.png |only LaMa-1.0.0/LaMa/src/forward_flies.cpp |only LaMa-1.0.0/LaMa/vignettes/HSMMs_cache/html/model_muskox_c56c9171b74d91ac986f0d3477faad47.RData |only LaMa-1.0.0/LaMa/vignettes/HSMMs_cache/html/model_muskox_c56c9171b74d91ac986f0d3477faad47.rdb |only LaMa-1.0.0/LaMa/vignettes/HSMMs_cache/html/model_muskox_c56c9171b74d91ac986f0d3477faad47.rdx |only LaMa-1.0.0/LaMa/vignettes/Inhomogeneous_HMMs_cache/html/model2_4c8e459729a675f7b8af02477f237dd0.RData |only LaMa-1.0.0/LaMa/vignettes/Inhomogeneous_HMMs_cache/html/model2_4c8e459729a675f7b8af02477f237dd0.rdb |only LaMa-1.0.0/LaMa/vignettes/Inhomogeneous_HMMs_cache/html/model2_4c8e459729a675f7b8af02477f237dd0.rdx |only LaMa-1.0.0/LaMa/vignettes/Periodic_HMM.Rmd |only LaMa-2.0.0/LaMa/DESCRIPTION | 34 LaMa-2.0.0/LaMa/MD5 | 235 ++- LaMa-2.0.0/LaMa/NAMESPACE | 40 LaMa-2.0.0/LaMa/R/RcppExports.R | 4 LaMa-2.0.0/LaMa/R/data.R |only LaMa-2.0.0/LaMa/R/decoding_functions.R |only LaMa-2.0.0/LaMa/R/distribution_functions.R |only LaMa-2.0.0/LaMa/R/forward_algorithms.R |only LaMa-2.0.0/LaMa/R/helper_functions.R |only LaMa-2.0.0/LaMa/R/hsmm_functions_old.R |only LaMa-2.0.0/LaMa/R/model_matrix_functions.R |only LaMa-2.0.0/LaMa/R/qreml_functions.R |only LaMa-2.0.0/LaMa/R/residual_functions.R |only LaMa-2.0.0/LaMa/R/sdreportMC.R |only LaMa-2.0.0/LaMa/R/stationary_functions.R |only LaMa-2.0.0/LaMa/R/tpm_functions.R |only LaMa-2.0.0/LaMa/README.md | 306 ++-- LaMa-2.0.0/LaMa/build/vignette.rds |binary LaMa-2.0.0/LaMa/data |only LaMa-2.0.0/LaMa/inst/doc/Continuous_time_HMMs.R | 63 LaMa-2.0.0/LaMa/inst/doc/Continuous_time_HMMs.Rmd | 79 - 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LaMa-2.0.0/LaMa/vignettes/Longitudinal_data_cache |only LaMa-2.0.0/LaMa/vignettes/MMMPPs.Rmd | 118 - LaMa-2.0.0/LaMa/vignettes/Penalised_splines.Rmd |only LaMa-2.0.0/LaMa/vignettes/Periodic_HMMs.Rmd |only LaMa-2.0.0/LaMa/vignettes/State_space_models.Rmd | 89 - LaMa-2.0.0/LaMa/vignettes/State_space_models_cache |only LaMa-2.0.0/LaMa/vignettes/man/obj4.RData |only LaMa-2.0.0/LaMa/vignettes/refs.bib | 21 163 files changed, 3299 insertions(+), 3101 deletions(-)
Title: Non-Negative Matrix Factorization for Single-Cell Omics
Description: A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.
Author: Massimo Andreatta [aut, cre] ,
Santiago Carmona [aut]
Maintainer: Massimo Andreatta <massimo.andreatta@unil.ch>
Diff between GeneNMF versions 0.6.0 dated 2024-07-22 and 0.6.2 dated 2024-11-12
DESCRIPTION | 8 ++-- MD5 | 13 +++--- NAMESPACE | 3 + R/main.R | 90 ++++++++++++++++++++++++++++++++++++++++++++++-- R/utils.R | 15 ++++++++ inst/NEWS.Rd | 21 ++++++++--- man/dropMetaPrograms.Rd |only man/plotMetaPrograms.Rd | 7 +++ 8 files changed, 140 insertions(+), 17 deletions(-)
Title: Fast Relative Comparisons of Floating Point Numbers in 'C++'
Description: Compare double-precision floating point vectors using
relative differences. All equality operations are calculated using
'cpp11'.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cppdoubles versions 0.2.0 dated 2024-02-21 and 0.3.0 dated 2024-11-12
cppdoubles-0.2.0/cppdoubles/src/doubles.cpp |only cppdoubles-0.3.0/cppdoubles/DESCRIPTION | 8 cppdoubles-0.3.0/cppdoubles/LICENSE | 4 cppdoubles-0.3.0/cppdoubles/MD5 | 22 - cppdoubles-0.3.0/cppdoubles/NEWS.md | 24 + cppdoubles-0.3.0/cppdoubles/R/all_equal.R | 2 cppdoubles-0.3.0/cppdoubles/R/cpp11.R | 28 - cppdoubles-0.3.0/cppdoubles/R/diff.R | 44 +-- cppdoubles-0.3.0/cppdoubles/R/doubles.R | 40 +- cppdoubles-0.3.0/cppdoubles/README.md | 22 - cppdoubles-0.3.0/cppdoubles/src/cpp11.cpp | 70 ++-- cppdoubles-0.3.0/cppdoubles/src/cppdoubles.cpp |only cppdoubles-0.3.0/cppdoubles/tests/testthat/test-doubles.R | 200 +++++++------- 13 files changed, 250 insertions(+), 214 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code, automated
reporting or use an easy to remember set of tidy functions for low
code exploratory data analysis.
Author: Roland Krasser [aut, cre]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 1.3.2 dated 2024-09-02 and 1.3.3 dated 2024-11-12
DESCRIPTION | 6 +- MD5 | 68 +++++++++++++++-------------- NAMESPACE | 3 + NEWS.md | 14 +++++ R/create-data.R | 4 - R/explore.R | 96 +++++++++++++++++++++++++++++++++++++++++ R/tools.R | 45 +++++++++++++++++++ R/use-data.R | 18 +++++++ README.md | 2 inst/doc/abtest.R | 14 +++++ inst/doc/abtest.Rmd | 20 ++++++++ inst/doc/abtest.html | 21 ++++++++ inst/doc/clean-drop.html | 4 - inst/doc/data.html | 4 - inst/doc/describe.html | 4 - inst/doc/explain.html | 4 - inst/doc/explore-mtcars.html | 4 - inst/doc/explore-penguins.html | 4 - inst/doc/explore-titanic.html | 4 - inst/doc/explore.Rmd | 1 inst/doc/explore.html | 5 +- inst/doc/predict.html | 4 - inst/doc/report-target.html | 4 - inst/doc/report-targetpct.html | 4 - inst/doc/report.html | 4 - inst/doc/tips-tricks.R | 6 ++ inst/doc/tips-tricks.Rmd | 12 +++++ inst/doc/tips-tricks.html | 12 ++++- inst/extdata/wordle.rds |only man/explore_col.Rd |only man/use_data_wordle.Rd |only man/yyyymm_calc.Rd |only tests/testthat/test-tools.R | 37 +++++++++++++++ tests/testthat/test-use-data.R | 2 vignettes/abtest.Rmd | 20 ++++++++ vignettes/explore.Rmd | 1 vignettes/tips-tricks.Rmd | 12 +++++ 37 files changed, 398 insertions(+), 65 deletions(-)
Title: Legends for Maps
Description: Create legends for maps and other graphics. Thematic maps need to
be accompanied by legible legends to be fully comprehensible. This package
offers a wide range of legends useful for cartography, some of which may
also be useful for other types of graphics.
Author: Timothee Giraud [cre, aut]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between maplegend versions 0.1.0 dated 2023-10-18 and 0.2.0 dated 2024-11-12
DESCRIPTION | 8 +-- MD5 | 44 ++++++++++---------- NEWS.md |only R/leg.R | 31 ++++++++------ R/leg_comp.R | 3 + R/leg_draw.R | 2 R/lg_choro.R | 11 +++-- R/lg_choro_horiz.R | 14 +++--- R/lg_cont.R | 5 +- R/lg_cont_horiz.R | 5 +- R/lg_grad_line.R | 5 +- R/lg_prop.R | 4 - R/lg_prop_horiz.R | 4 - R/lg_prop_line.R | 4 - R/lg_symb.R | 68 +++++++++++++++---------------- R/lg_typo.R | 15 ++++-- R/lg_utils.R | 12 +---- R/new_choro.R |only README.md | 20 +++++---- inst/tinytest/test_coords.R | 82 +++++++------------------------------- man/figures/README-example-1.png |binary man/figures/README-example2-1.png |binary man/leg.Rd | 32 ++++++++------ man/leg_comp.Rd | 4 + 24 files changed, 176 insertions(+), 197 deletions(-)
Title: Analytical Tool for Aquatic Respirometry
Description: Calculates metabolic rate of fish and other aquatic organisms measured using
an intermittent-flow respirometry approach. The tool is used to run a set of graphical
QC tests of raw respirometry data, correct it for background respiration and chamber
effect, filter and extract target values of absolute and mass-specific metabolic rate.
Experimental design should include background respiration tests and measuring of one
or more metabolic rate traits. The R package is ideally integrated with the pump
controller 'PumpResp' and the DO meter 'SensResp' (open-source hardware by FishResp).
Raw respirometry data can be also imported from 'AquaResp' (free software), 'AutoResp'
('LoligoSystems'), 'OxyView' ('PreSens'), 'Pyro Oxygen Logger' ('PyroScience') and
'Q-box Aqua' ('QubitSystems'). More information about the R package 'FishResp'is
available in the publication by Morozov et al. (2019) <doi:10.1093/conphys/coz003>.
Author: Sergey Morozov [aut, cre],
Scott McCairns [aut],
Juha Merila [ctb]
Maintainer: Sergey Morozov <sergey.morozov@helsinki.fi>
Diff between FishResp versions 1.1.1 dated 2022-09-18 and 1.1.2 dated 2024-11-12
DESCRIPTION | 35 +--- MD5 | 32 ++-- NAMESPACE | 1 NEWS.md | 21 ++ R/FishResp.R | 3 R/convert.rMR.R | 10 - R/convert.respirometry.R | 8 - R/import.meas.R | 341 +++++++++++++++++--------------------------- R/presens.aquaresp.R | 4 R/pyroscience.aquaresp.R | 4 README.md | 12 - inst/CITATION | 34 ++-- man/FishResp.Rd | 5 man/convert.rMR.Rd | 10 - man/convert.respirometry.Rd | 8 - man/presens.aquaresp.Rd | 4 man/pyroscience.aquaresp.Rd | 4 17 files changed, 244 insertions(+), 292 deletions(-)
Title: A Lightweight Interface Between 'ggplot2' and 'igraph' Objects
Description: Interface to integrate 'igraph' and 'ggplot2' graphics within spatial maps. 'RGraphSpace' implements new geometric objects using 'ggplot2' prototypes, customized for representing large 'igraph' objects in a normalized coordinate system. By scaling shapes and graph elements, 'RGraphSpace' can provide a framework for layered visualizations.
Author: Victor Apolonio [ctb],
Vinicius Chagas [ctb],
Mauro Castro [aut, cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between RGraphSpace versions 1.0.6 dated 2024-08-18 and 1.0.7 dated 2024-11-12
DESCRIPTION | 6 ++--- MD5 | 10 ++++---- R/gspacePlots.R | 2 - build/vignette.rds |binary inst/CITATION | 5 +--- inst/doc/RGraphSpace.html | 55 +++++++++++++++++++++++----------------------- 6 files changed, 39 insertions(+), 39 deletions(-)
Title: A Comprehensive Analysis of High Dimensional Longitudinal Data
Description: To provide a comprehensive analysis of high dimensional longitudinal
data,this package provides analysis for any combination of 1) simultaneous
variable selection and estimation, 2) mean regression or quantile regression
for heterogeneous data, 3) cross-sectional or longitudinal data, 4) balanced
or imbalanced data, 5) moderate, high or even ultra-high dimensional data,
via computationally efficient implementations of penalized generalized
estimating equations.
Author: Tianhai Zu [aut, cre],
Brittany Green [aut, ctb],
Yan Yu [aut, ctb]
Maintainer: Tianhai Zu <zuti@mail.uc.edu>
Diff between geeVerse versions 0.2.1 dated 2024-07-29 and 0.2.2 dated 2024-11-12
DESCRIPTION | 6 MD5 | 28 NAMESPACE | 2 R/CVfit.R | 242 +++--- R/PGEE.R | 1038 ++++++++++++++---------------- R/geeVerse.R |only R/generateData.R | 28 R/qpgee.R | 753 +++++++++++---------- R/qpgee_sim.R |only R/utils.R | 201 ++++- inst/sim/generate_vis_table.R |only inst/sim/replication_script_for_all.R | 756 ++++++++++----------- inst/sim/replication_script_for_all_new.R |only inst/sim/replication_script_for_main.R |only inst/sim/replication_script_for_supp.R |only man/compile_result.Rd | 4 man/qpgee.Rd | 2 man/qpgee.est.Rd | 2 18 files changed, 1611 insertions(+), 1451 deletions(-)
Title: Interact with 'Condor' from R via SSH
Description: Interact with 'Condor' from R via SSH connection. Files are first
uploaded from user machine to submitter machine, and the job is then submitted
from the submitter machine to 'Condor'. Functions are provided to submit,
list, and download 'Condor' jobs from R. 'Condor' is an open source
high-throughput computing software framework for distributed parallelization
of computationally intensive tasks.
Author: Arni Magnusson [aut, cre],
Nan Yao [aut],
Jemery Day [ctb],
Thomas Teears [ctb]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between condor versions 2.1.0 dated 2023-08-27 and 3.0.0 dated 2024-11-12
DESCRIPTION | 10 +++++----- MD5 | 37 ++++++++++++++++++++----------------- NAMESPACE | 6 ++++++ NEWS.md | 21 +++++++++++++++++++++ R/condor-package.R | 8 ++++---- R/condor_dir.R | 5 ++--- R/condor_q.R | 29 +++++++++++++++++++++++++---- R/condor_rm.R | 8 ++++---- R/condor_rmdir.R | 8 ++++---- R/condor_submit.R | 22 ++++++++++++++++++---- R/dos2unix.R |only R/summary.condor_log.R | 2 ++ R/unix2dos.R |only man/condor-internal.Rd | 8 +++++++- man/condor-package.Rd | 4 +++- man/condor_dir.Rd | 5 ++--- man/condor_q.Rd | 5 ++--- man/condor_rm.Rd | 8 ++++---- man/condor_rmdir.Rd | 8 ++++---- man/condor_submit.Rd | 15 +++++++++++---- man/dos2unix.Rd |only 21 files changed, 144 insertions(+), 65 deletions(-)
Title: Serialize Model Objects with a Consistent Interface
Description: Typically, models in 'R' exist in memory and can be saved via
regular 'R' serialization. However, some models store information in
locations that cannot be saved using 'R' serialization alone. The goal
of 'bundle' is to provide a common interface to capture this
information, situate it within a portable object, and restore it for
use in new settings.
Author: Julia Silge [aut, cre] ,
Simon Couch [aut],
Qiushi Yan [aut],
Max Kuhn [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Julia Silge <julia.silge@posit.co>
Diff between bundle versions 0.1.1 dated 2023-09-09 and 0.1.2 dated 2024-11-12
DESCRIPTION | 17 - LICENSE | 2 MD5 | 56 ++-- NAMESPACE | 2 NEWS.md | 8 R/bundle_bart.R |only R/bundle_embed.R | 2 R/bundle_xgboost.R | 3 README.md | 55 ++-- build/vignette.rds |binary inst/doc/bundle.R | 4 inst/doc/bundle.html | 401 ++++++++++++++++----------------- man/bundle.Rd | 1 man/bundle_bart.Rd |only man/bundle_caret.Rd | 5 man/bundle_description.Rd | 7 man/bundle_embed.Rd | 7 man/bundle_h2o.Rd | 5 man/bundle_keras.Rd | 5 man/bundle_parsnip.Rd | 5 man/bundle_recipe.Rd | 5 man/bundle_stacks.Rd | 5 man/bundle_torch.Rd | 5 man/bundle_workflows.Rd | 5 man/bundle_xgboost.Rd | 5 tests/testthat/_snaps |only tests/testthat/test_bundle_bart.R |only tests/testthat/test_bundle_embed.R | 1 tests/testthat/test_bundle_h2o.R | 1 tests/testthat/test_bundle_workflows.R | 1 tests/testthat/test_bundle_xgboost.R | 4 31 files changed, 326 insertions(+), 291 deletions(-)
Title: Functions for Elementary Bayesian Inference
Description: A set of R functions and data sets for the book Introduction to Bayesian Statistics, Bolstad, W.M. (2017), John Wiley & Sons ISBN 978-1-118-09156-2.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between Bolstad versions 0.2-41 dated 2020-10-05 and 0.2.42 dated 2024-11-12
DESCRIPTION | 20 - MD5 | 36 +- NAMESPACE | 2 R/Bolstad-package.R | 88 ----- R/bayes.lin.reg.r | 763 ++++++++++++++++++++++++------------------------- R/cdf.R | 3 R/data.R |only R/decomp.R | 122 +++---- R/median.Bolstad.R | 22 - R/print.sintegral.R | 12 R/sintegral.r | 177 +++++------ README.md |only inst/CITATION | 5 man/bayes.lin.reg.Rd | 9 man/bayes.t.test.Rd | 6 man/cdf.Rd | 4 man/median.Bolstad.Rd |only man/moisture.df.Rd | 5 man/print.sintegral.Rd |only man/slug.Rd | 5 man/sscsample.data.Rd | 5 21 files changed, 612 insertions(+), 672 deletions(-)
Title: Pandemic Prediction Model in an SIRS Framework
Description: A suite of methods to fit and predict case count data using
a compartmental SIRS (Susceptible – Infectious – Recovered – Susceptible)
model, based on an assumed specification of the effective reproduction
number. The significance of this approach is that it relates epidemic
progression to the average number of contacts of infected individuals,
which decays as a function of the total susceptible fraction remaining
in the population. The main functions are pred.curve(), which computes
the epidemic curve for a set of parameters, and estimate.mle(), which
finds the best fitting curve to observed data. The easiest way to pass
arguments to the functions is via a config file, which contains input
settings required for prediction, and the package offers two methods,
navigate_to_config() which points the user to the configuration file,
and re_predict() for starting the fit-predict process. The main model was published in
Razvan G. Romanescu et al. <doi:10.1016/j.epidem.2023.100708>.
Author: Razvan Romanescu [aut, cre],
Songdi Hu [aut],
Md Ashiqul Haque [aut],
Olivier Tremblay-Savard [aut]
Maintainer: Razvan Romanescu <razvan_romanescu@hotmail.com>
Diff between REffectivePred versions 1.0.0 dated 2024-02-02 and 1.0.1 dated 2024-11-12
DESCRIPTION | 16 MD5 | 11 R/executions.v16.R | 426 +++--- R/prediction_model.v16.R | 3262 +++++++++++++++++++++++------------------------ build |only inst/config.yml | 6 man/pred.curve.Rd | 8 7 files changed, 1854 insertions(+), 1875 deletions(-)
More information about REffectivePred at CRAN
Permanent link
Title: Bayesian Variable Selection using Power-Expected-Posterior Prior
Description: Performs Bayesian variable selection under normal linear
models for the data with the model parameters following as prior distributions either
the power-expected-posterior (PEP) or the intrinsic (a special case of the former)
(Fouskakis and Ntzoufras (2022) <doi: 10.1214/21-BA1288>,
Fouskakis and Ntzoufras (2020) <doi: 10.3390/econometrics8020017>).
The prior distribution on model space is the uniform over all models
or the uniform on model dimension (a special case of the beta-binomial prior).
The selection is performed by either implementing a full enumeration
and evaluation of all possible models or using the Markov Chain
Monte Carlo Model Composition (MC3) algorithm (Madigan and York (1995) <doi: 10.2307/1403615>).
Complementary functions for hypothesis testing, estimation and
predictions under Bayesian model averaging, as well as, plotting and
printing the results are also provided. The results can be compared to the
ones obtained under other well-known priors on [...truncated...]
Author: Konstantina Charmpi [aut, cre],
Dimitris Fouskakis [aut],
Ioannis Ntzoufras [aut]
Maintainer: Konstantina Charmpi <xarmpi.kon@gmail.com>
Diff between PEPBVS versions 2.0 dated 2024-10-30 and 2.1 dated 2024-11-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/comparepriors.lm.R | 2 +- man/comparepriors.lm.Rd | 2 +- man/pep.lm.Rd | 4 ++-- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: 'R6'-Based Flexible Framework for Permutation Tests
Description: Implements non-parametric tests from Higgins (2004, ISBN:0534387756), including tests for one sample, two samples, k samples, paired comparisons, blocked designs, trends and association. Built with 'Rcpp' for efficiency and 'R6' for flexible, object-oriented design, the package provides a unified framework for performing or creating custom permutation tests.
Author: Yan Du [aut, cre]
Maintainer: Yan Du <isduyan@outlook.com>
Diff between LearnNonparam versions 1.2.3 dated 2024-10-15 and 1.2.4 dated 2024-11-12
LearnNonparam-1.2.3/LearnNonparam/R/utils.R |only LearnNonparam-1.2.4/LearnNonparam/DESCRIPTION | 12 - LearnNonparam-1.2.4/LearnNonparam/MD5 | 108 ++++----- LearnNonparam-1.2.4/LearnNonparam/NAMESPACE | 1 LearnNonparam-1.2.4/LearnNonparam/NEWS.md | 120 +++++----- LearnNonparam-1.2.4/LearnNonparam/R/CDF.R | 5 LearnNonparam-1.2.4/LearnNonparam/R/JonckheereTerpstra.R | 3 LearnNonparam-1.2.4/LearnNonparam/R/KruskalWallis.R | 8 LearnNonparam-1.2.4/LearnNonparam/R/OneWay.R | 5 LearnNonparam-1.2.4/LearnNonparam/R/PermuTest.R | 41 +++ LearnNonparam-1.2.4/LearnNonparam/R/Studentized.R | 14 - LearnNonparam-1.2.4/LearnNonparam/R/Wilcoxon.R | 4 LearnNonparam-1.2.4/LearnNonparam/R/do_call.R |only LearnNonparam-1.2.4/LearnNonparam/R/get_p.R |only LearnNonparam-1.2.4/LearnNonparam/R/get_score.R |only LearnNonparam-1.2.4/LearnNonparam/R/pmt.R | 117 ++++++--- LearnNonparam-1.2.4/LearnNonparam/README.md | 53 ++-- LearnNonparam-1.2.4/LearnNonparam/inst/include/pmt/impl_twosample_pmt.hpp | 18 - LearnNonparam-1.2.4/LearnNonparam/inst/include/pmt/progress.hpp | 8 LearnNonparam-1.2.4/LearnNonparam/inst/include/pmt/reorder.hpp | 5 LearnNonparam-1.2.4/LearnNonparam/man/AnsariBradley.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/ChiSquare.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/Correlation.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/Difference.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/Friedman.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/JonckheereTerpstra.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/KolmogorovSmirnov.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/KruskalWallis.Rd | 4 LearnNonparam-1.2.4/LearnNonparam/man/OneWay.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/Page.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/PairedDifference.Rd | 4 LearnNonparam-1.2.4/LearnNonparam/man/RCBDOneWay.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/RatioMeanDeviance.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/ScoreSum.Rd | 4 LearnNonparam-1.2.4/LearnNonparam/man/SiegelTukey.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/Sign.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/Studentized.Rd | 4 LearnNonparam-1.2.4/LearnNonparam/man/Wilcoxon.Rd | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/define-dark.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/define.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/modify-dark.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/modify.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/p_value-dark.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/p_value.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/plot-dark.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/plot.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/print-dark.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/print.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/statistic-dark.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/statistic.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/test-dark.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/figures/README/test.svg | 2 LearnNonparam-1.2.4/LearnNonparam/man/pmt.Rd | 59 ++-- LearnNonparam-1.2.4/LearnNonparam/man/references/ref.bib | 3 LearnNonparam-1.2.4/LearnNonparam/man/roxygen/templates/pmt_init_params.R | 4 LearnNonparam-1.2.4/LearnNonparam/src/RcppExports.cpp | 58 ++-- LearnNonparam-1.2.4/LearnNonparam/src/pmt_interface.cpp | 90 +++---- 57 files changed, 444 insertions(+), 364 deletions(-)
Title: Functions for 'Ecdat'
Description: Functions and vignettes to update
data sets in 'Ecdat' and to create, manipulate,
plot, and analyze those and similar data sets.
Author: Spencer Graves [aut, cre]
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>
Diff between Ecfun versions 0.3-2 dated 2022-10-09 and 0.3-6 dated 2024-11-12
DESCRIPTION | 18 - MD5 | 60 +-- NAMESPACE | 4 NEWS.md | 4 R/findCountry.R |only R/qqnorm2s.R | 5 R/readDW_NOMINATE.R |only README.md | 4 build/vignette.rds |binary inst/WORDLIST | 12 inst/doc/UpdatingUSGDPpresidents.R | 42 +- inst/doc/UpdatingUSGDPpresidents.Rmd | 4 inst/doc/UpdatingUSGDPpresidents.html | 115 ++---- inst/doc/nuclearArmageddon.Rmd | 4 inst/doc/nuclearArmageddon.html | 223 +++++------- inst/doc/updateOCC1950.Rmd | 2 inst/doc/updateOCC1950.html | 549 +++++++++++-------------------- inst/doc/update_nuclearWeaponStates.Rmd | 4 inst/doc/update_nuclearWeaponStates.html | 117 ++---- man/BoxCox.Rd | 2 man/Newdata.Rd | 4 man/asNumericDF.Rd | 13 man/findCountry.Rd |only man/interpPairs.Rd | 2 man/logVarCor.Rd | 2 man/matchQuote.Rd | 2 man/readDW_NOMINATE.Rd |only man/simulate.bic.glm.Rd | 15 man/simulate.glm.Rd | 15 vignettes/UpdatingUSGDPpresidents.Rmd | 4 vignettes/nuclearArmageddon.Rmd | 4 vignettes/updateOCC1950.Rmd | 2 vignettes/update_nuclearWeaponStates.Rmd | 4 33 files changed, 544 insertions(+), 692 deletions(-)
Title: Bootstrapping Estimates of Clustering Stability
Description: Implementation of the bootstrapping approach for the estimation of clustering stability and its application in estimating the number of clusters, as introduced by Yu et al (2016)<doi:10.1142/9789814749411_0007>. Implementation of the non-parametric bootstrap approach to assessing the stability of module detection in a graph, the extension for the selection of a parameter set that defines a graph from data in a way that optimizes stability and the corresponding visualization functions, as introduced by Tian et al (2021) <doi:10.1002/sam.11495>. Implemented out-of-bag stability estimation function and k-select Smin-based k-selection function as introduced by Liu et al (2022) <doi:10.1002/sam.11593>. Implemented ensemble clustering method based-on k-means clustering method, spectral clustering method and hierarchical clustering method.
Author: Han Yu [aut],
Mingmei Tian [aut],
Tianmou Liu [aut, cre]
Maintainer: Tianmou Liu <tianmouliu@outlook.com>
Diff between bootcluster versions 0.3.2 dated 2022-01-29 and 0.4.1 dated 2024-11-12
DESCRIPTION | 18 +++--- MD5 | 29 +++++++--- NAMESPACE | 92 ++++++++++++++++++--------------- R/ensemble_cluster_multi.R |only R/esmbl_stability.R |only R/helpers.R | 117 ++++++++++++++++-------------------------- R/kselect.R | 14 ----- R/networkstability.R | 4 - R/plotcode.R | 7 +- R/ref_dist.R |only R/scheme_sub.R |only R/thresholdselect.R | 10 +-- man/agreement.Rd |only man/agreement_nk.Rd |only man/ensemble.cluster.multi.Rd |only man/esmbl.stability.Rd |only man/min_agreement.Rd |only man/ref_dist.Rd |only man/ref_dist_bin.Rd |only man/ref_dist_pca.Rd |only man/scheme_sub_hc.Rd |only man/scheme_sub_km.Rd |only man/scheme_sub_spectral.Rd |only 23 files changed, 142 insertions(+), 149 deletions(-)
Title: Graph Prediction from a Graph Time Series
Description: Predicting the structure of a graph including new nodes and edges using
a time series of graphs. Flux balance analysis, a linear and integer programming
technique used in biochemistry is used with time series prediction methods to
predict the graph structure at a future time point
Kandanaarachchi (2024) <doi:10.48550/arXiv.2401.04280>.
Author: Sevvandi Kandanaarachchi [aut, cre]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between netseer versions 0.1.0 dated 2024-02-21 and 0.1.1 dated 2024-11-12
netseer-0.1.0/netseer/man/generate_graph.Rd |only netseer-0.1.1/netseer/DESCRIPTION | 14 netseer-0.1.1/netseer/MD5 | 30 netseer-0.1.1/netseer/NAMESPACE | 3 netseer-0.1.1/netseer/R/functions.R | 681 +++++----------- netseer-0.1.1/netseer/R/graph_generation.R | 76 + netseer-0.1.1/netseer/R/network_prediction.R | 22 netseer-0.1.1/netseer/R/utils.R |only netseer-0.1.1/netseer/README.md | 91 -- netseer-0.1.1/netseer/man/figures/README-grpred1-1.png |binary netseer-0.1.1/netseer/man/figures/README-grpred2-1.png |binary netseer-0.1.1/netseer/man/figures/README-grpred3-1.png |binary netseer-0.1.1/netseer/man/figures/README-plotdata-1.png |binary netseer-0.1.1/netseer/man/figures/README-plotdata-2.png |binary netseer-0.1.1/netseer/man/figures/README-plotdata-3.png |binary netseer-0.1.1/netseer/man/generate_graph_exp.Rd |only netseer-0.1.1/netseer/man/generate_graph_linear.Rd |only netseer-0.1.1/netseer/man/predict_graph.Rd | 19 18 files changed, 407 insertions(+), 529 deletions(-)
Title: Simple and Scalable Statistical Modelling in R
Description: Write statistical models in R and fit them by MCMC and
optimisation on CPUs and GPUs, using Google 'TensorFlow'. greta lets
you write your own model like in BUGS, JAGS and Stan, except that you
write models right in R, it scales well to massive datasets, and it’s
easy to extend and build on. See the website for more information,
including tutorials, examples, package documentation, and the greta
forum.
Author: Nick Golding [aut] ,
Nicholas Tierney [aut, cre] ,
Simon Dirmeier [ctb],
Adam Fleischhacker [ctb],
Shirin Glander [ctb],
Martin Ingram [ctb],
Lee Hazel [ctb],
Lionel Hertzog [ctb],
Tiphaine Martin [ctb],
Matt Mulvahill [ctb],
Michael Quinn [ctb],
Dav [...truncated...]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between greta versions 0.4.5 dated 2024-03-11 and 0.5.0 dated 2024-11-12
greta-0.4.5/greta/tests/testthat/_snaps/check-m1.md |only greta-0.4.5/greta/tests/testthat/test-check-m1.R |only greta-0.4.5/greta/tests/testthat/test_posteriors.R |only greta-0.5.0/greta/DESCRIPTION | 52 greta-0.5.0/greta/MD5 | 297 + greta-0.5.0/greta/NAMESPACE | 30 greta-0.5.0/greta/NEWS.md | 90 greta-0.5.0/greta/R/as_data.R | 11 greta-0.5.0/greta/R/calculate.R | 464 +- greta-0.5.0/greta/R/checkers.R | 1636 ++++++++-- greta-0.5.0/greta/R/chol2symm.R | 38 greta-0.5.0/greta/R/conda_greta_env.R | 6 greta-0.5.0/greta/R/dag_class.R | 466 +- greta-0.5.0/greta/R/data-deps-tf-tfp.R |only greta-0.5.0/greta/R/distribution.R | 64 greta-0.5.0/greta/R/extract_replace_combine.R | 247 - greta-0.5.0/greta/R/functions.R | 378 -- greta-0.5.0/greta/R/greta_array_class.R | 154 greta-0.5.0/greta/R/greta_create_conda_env.R | 43 greta-0.5.0/greta/R/greta_install_miniconda.R | 17 greta-0.5.0/greta/R/greta_install_python_deps.R | 47 greta-0.5.0/greta/R/greta_mcmc_list.R | 78 greta-0.5.0/greta/R/greta_model_class.R | 135 greta-0.5.0/greta/R/greta_stash.R | 57 greta-0.5.0/greta/R/inference.R | 489 +- greta-0.5.0/greta/R/inference_class.R | 827 +---- greta-0.5.0/greta/R/install_greta_deps.R | 521 +++ greta-0.5.0/greta/R/joint.R | 42 greta-0.5.0/greta/R/mixture.R | 104 greta-0.5.0/greta/R/new_install_process.R | 15 greta-0.5.0/greta/R/node_class.R | 133 greta-0.5.0/greta/R/node_types.R | 178 - 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