Tue, 12 Nov 2024

Package packageRank updated to version 0.9.4 with previous version 0.9.3 dated 2024-10-15

Title: Computation and Visualization of Package Download Counts and Percentile Ranks
Description: Compute and visualize the cross-sectional and longitudinal number and rank percentile of package downloads from Posit/RStudio's CRAN mirror.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>

Diff between packageRank versions 0.9.3 dated 2024-10-15 and 0.9.4 dated 2024-11-12

 DESCRIPTION                                     |    8 -
 MD5                                             |   30 ++--
 NEWS.md                                         |   27 ++++
 R/cranDistribution.R                            |   89 ++++++++-----
 R/filteredDownloads.R                           |    5 
 R/fixDate_2012.R                                |   24 +--
 R/logInfo.R                                     |   17 +-
 R/packageCountry.R                              |    3 
 R/packageDistribution.R                         |   20 +-
 R/packageLog.R                                  |   14 --
 R/packageRank.R                                 |    7 -
 README.md                                       |  162 ++++++++++++++++--------
 man/figures/README-plot_distribution_code-1.png |binary
 man/packageLog.Rd                               |    5 
 man/print.cranDistribution.Rd                   |    4 
 man/queryPackage.Rd                             |    8 -
 16 files changed, 264 insertions(+), 159 deletions(-)

More information about packageRank at CRAN
Permanent link

Package shinylive updated to version 0.3.0 with previous version 0.2.0 dated 2024-07-19

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(-)

More information about shinylive at CRAN
Permanent link

Package philentropy updated to version 0.9.0 with previous version 0.8.0 dated 2023-12-02

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(-)

More information about philentropy at CRAN
Permanent link

Package OmopSketch updated to version 0.1.2 with previous version 0.1.1 dated 2024-10-15

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(-)

More information about OmopSketch at CRAN
Permanent link

Package chngpt updated to version 2024.11-15 with previous version 2023.11-29 dated 2023-12-05

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(-)

More information about chngpt at CRAN
Permanent link

Package MBC updated to version 0.10-7 with previous version 0.10-6 dated 2023-05-02

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(-)

More information about MBC at CRAN
Permanent link

Package miscFuncs updated to version 1.5-10 with previous version 1.5-9 dated 2024-10-18

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(-)

More information about miscFuncs at CRAN
Permanent link

Package fntl updated to version 0.1.2 with previous version 0.1.1 dated 2024-09-07

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(-)

More information about fntl at CRAN
Permanent link

Package DiceView updated to version 3.1-0 with previous version 2.2-0 dated 2024-01-15

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(-)

More information about DiceView at CRAN
Permanent link

Package adea updated to version 1.5.2 with previous version 1.5.1 dated 2023-11-24

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(-)

More information about adea at CRAN
Permanent link

Package GitStats updated to version 2.1.2 with previous version 2.1.1 dated 2024-10-25

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(-)

More information about GitStats at CRAN
Permanent link

Package bgms updated to version 0.1.4.1 with previous version 0.1.4 dated 2024-10-20

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(-)

More information about bgms at CRAN
Permanent link

Package beeca updated to version 0.2.0 with previous version 0.1.3 dated 2024-06-18

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(-)

More information about beeca at CRAN
Permanent link

New package Virusparies with initial version 1.0.0
Package: Virusparies
Title: Visualize and Process Output from 'VirusHunterGatherer'
Version: 1.0.0
Maintainer: Ruff Sergej <serijnh@gmail.com>
Description: A collection of tools for downstream analysis of 'VirusHunterGatherer' output. Processing of hittables and plotting of results, enabling better interpretation, is made easier with the provided functions.
License: GPL (>= 3)
URL: https://github.com/SergejRuff/Virusparies, https://github.com/lauberlab/VirusHunterGatherer
BugReports: https://github.com/SergejRuff/Virusparies/issues
Encoding: UTF-8
Imports: chromote, cowplot, dplyr, ggplot2, gt, parallel, readr, rlang, scales, stats, stringr, tidyr, tools, utils
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-11-10 16:37:26 UTC; sergej
Author: Ruff Sergej [aut, cre] , Lauber Chris [ctb] , Chong Li Chuin [ctb]
Repository: CRAN
Date/Publication: 2024-11-12 14:10:06 UTC

More information about Virusparies at CRAN
Permanent link

New package textAnnotatoR with initial version 0.1.4
Package: textAnnotatoR
Title: Interactive Text Annotation Tool with 'shiny' GUI
Version: 0.1.4
Date: 2024-10-25
Description: A comprehensive text annotation tool built with 'shiny'. Provides an interactive graphical user interface for coding text documents, managing code hierarchies, creating memos, and analyzing coding patterns. Features include code co-occurrence analysis, visualization of coding patterns, comparison of multiple coding sets, and export capabilities. Supports collaborative qualitative research through standardized annotation formats and analysis tools.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: shiny (>= 1.7.0), shinydashboard, shinyjs, shinyFiles, data.tree, jsonlite, DT, readtext, magrittr, tools, utils, stats, grDevices, graphics
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, covr, mockery
URL: https://github.com/chaoliu-cl/textAnnotatoR, http://liu-chao.site/textAnnotatoR/
BugReports: https://github.com/chaoliu-cl/textAnnotatoR/issues
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-11 19:23:25 UTC; chaoliu
Author: Chao Liu [aut, cre, cph]
Maintainer: Chao Liu <chaoliu@cedarville.edu>
Repository: CRAN
Date/Publication: 2024-11-12 14:40:01 UTC

More information about textAnnotatoR at CRAN
Permanent link

New package rOCEAN with initial version 1.0
Package: rOCEAN
Title: Two-Way Feature Set Testing for Multi-Omics
Version: 1.0
Maintainer: Mitra Ebrahimpoor <mitra.ebrahimpoor@gmail.com>
Description: For any two way feature-set from a pair of pre-processed omics data, 3 different true discovery proportions (TDP), namely pairwise-TDP, column-TDP and row-TDP are calculated. Due to embedded closed testing procedure, the choice of feature-sets can be changed infinite times and even after seeing the data without any change in type I error rate. For more details refer to Ebrahimpoor et al., (2024) <doi:10.48550/arXiv.2410.19523>.
License: GPL (>= 2)
Date: 2024-10-31
Encoding: UTF-8
Imports: ff
NeedsCompilation: no
Packaged: 2024-11-10 22:01:22 UTC; mitra
Author: Mitra Ebrahimpoor [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-12 14:10:02 UTC

More information about rOCEAN at CRAN
Permanent link

Package modisfast updated to version 1.0.0 with previous version 0.9.1 dated 2024-07-14

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(-)

More information about modisfast at CRAN
Permanent link

New package fastml with initial version 0.1.0
Package: fastml
Title: Fast Machine Learning Model Training and Evaluation
Version: 0.1.0
Description: Streamlines the training, evaluation, and comparison of multiple machine learning models with minimal code by providing comprehensive data preprocessing and support for a wide range of algorithms with hyperparameter tuning. It offers performance metrics and visualization tools to facilitate efficient and effective machine learning workflows.
License: GPL (>= 2)
Encoding: UTF-8
Imports: caret, pROC, reshape2, ggplot2, foreach, doParallel
Suggests: knitr, rmarkdown, randomForest, kernlab, gbm, nnet, rpart, glmnet, xgboost, pls, C50, mboost, arm, ipred, caTools, e1071, MASS
NeedsCompilation: no
Packaged: 2024-11-11 13:28:27 UTC; selcukkorkmaz
Author: Selcuk Korkmaz [aut, cre] , Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-12 14:30:02 UTC

More information about fastml at CRAN
Permanent link

New package bplsr with initial version 1.0.0
Package: bplsr
Title: Bayesian partial least squares regression
Version: 1.0.0
Maintainer: Szymon Urbas <szymon.urbas@mu.ie>
Description: Fits the Bayesian partial least squares regression model introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable for univariate and multivariate regression with high-dimensional data.
License: GPL (>= 3)
Encoding: UTF-8
Language: eng
Depends: R (>= 2.10)
LazyData: true
Imports: coda, progress, statmod, stats, utils
NeedsCompilation: no
Packaged: 2024-11-11 20:55:25 UTC; surbas
Author: Szymon Urbas [aut, cre], Pierre Lovera [ctb], Robert Daly [ctb], Alan O'Riordan [ctb], Donagh Berry [ctb], Isobel Claire Gormley [ctb]
Repository: CRAN
Date/Publication: 2024-11-12 14:50:02 UTC

More information about bplsr at CRAN
Permanent link

New package BayesGP with initial version 0.1.3
Package: BayesGP
Title: Efficient Implementation of Gaussian Process in Bayesian Hierarchical Models
Version: 0.1.3
Description: Implements Bayesian hierarchical models with flexible Gaussian process priors, focusing on Extended Latent Gaussian Models and incorporating various Gaussian process priors for Bayesian smoothing. Computations leverage finite element approximations and adaptive quadrature for efficient inference. Methods are detailed in Zhang, Stringer, Brown, and Stafford (2023) <doi:10.1177/09622802221134172>; Zhang, Stringer, Brown, and Stafford (2024) <doi:10.1080/10618600.2023.2289532>; Zhang, Brown, and Stafford (2023) <doi:10.48550/arXiv.2305.09914>; and Stringer, Brown, and Stafford (2021) <doi:10.1111/biom.13329>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
LinkingTo: TMB (>= 1.9.7), RcppEigen
Imports: TMB (>= 1.9.7), numDeriv, rstan, sfsmisc, Matrix (>= 1.6.3), aghq (>= 0.4.1), fda, tmbstan, LaplacesDemon, methods
Depends: R (>= 3.6.0)
Suggests: rmarkdown, knitr, survival, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-11-10 22:31:24 UTC; ziangzhang
Author: Ziang Zhang [aut, cre], Yongwei Lin [aut], Alex Stringer [aut], Patrick Brown [aut]
Maintainer: Ziang Zhang <ziangzhang@uchicago.edu>
Repository: CRAN
Date/Publication: 2024-11-12 14:20:03 UTC

More information about BayesGP at CRAN
Permanent link

New package SFM with initial version 0.1.0
Package: SFM
Title: A Package for Analyzing Skew Factor Models
Version: 0.1.0
Description: Generates Skew Factor Models data and applies Sparse Online Principal Component (SOPC) method to estimate model parameters. It includes capabilities for calculating mean squared error, relative error, and sparsity of the loading matrix. Additionally, it includes robust regression methods such as adaptive Huber regression.The philosophy of the package is described in Guo G. (2023) <doi:10.1007/s00180-022-01270-z>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: MASS, SOPC, matrixcalc, sn, stats
NeedsCompilation: no
Language: en-US
Author: Guangbao Guo [aut, cre], Yu Jin [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Suggests: testthat (>= 3.0.0), ggplot2, reshape2
Packaged: 2024-11-08 06:55:06 UTC; AIERXUAN
Repository: CRAN
Date/Publication: 2024-11-12 13:10:02 UTC

More information about SFM at CRAN
Permanent link

Package LaMa updated to version 2.0.0 with previous version 1.0.0 dated 2024-06-04

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 -
 LaMa-2.0.0/LaMa/inst/doc/Continuous_time_HMMs.html                                                    |  201 +--
 LaMa-2.0.0/LaMa/inst/doc/HSMMs.R                                                                      |  109 -
 LaMa-2.0.0/LaMa/inst/doc/HSMMs.Rmd                                                                    |  127 --
 LaMa-2.0.0/LaMa/inst/doc/HSMMs.html                                                                   |  213 +--
 LaMa-2.0.0/LaMa/inst/doc/Inhomogeneous_HMMs.R                                                         |  207 ---
 LaMa-2.0.0/LaMa/inst/doc/Inhomogeneous_HMMs.Rmd                                                       |  418 +++---
 LaMa-2.0.0/LaMa/inst/doc/Inhomogeneous_HMMs.html                                                      |  634 ++++------
 LaMa-2.0.0/LaMa/inst/doc/Intro_to_LaMa.R                                                              |   78 -
 LaMa-2.0.0/LaMa/inst/doc/Intro_to_LaMa.Rmd                                                            |  127 +-
 LaMa-2.0.0/LaMa/inst/doc/Intro_to_LaMa.html                                                           |  311 ++--
 LaMa-2.0.0/LaMa/inst/doc/LaMa_and_RTMB.R                                                              |only
 LaMa-2.0.0/LaMa/inst/doc/LaMa_and_RTMB.Rmd                                                            |only
 LaMa-2.0.0/LaMa/inst/doc/LaMa_and_RTMB.html                                                           |only
 LaMa-2.0.0/LaMa/inst/doc/Longitudinal_data.R                                                          |  102 -
 LaMa-2.0.0/LaMa/inst/doc/Longitudinal_data.Rmd                                                        |  115 -
 LaMa-2.0.0/LaMa/inst/doc/Longitudinal_data.html                                                       |  171 +-
 LaMa-2.0.0/LaMa/inst/doc/MMMPPs.R                                                                     |   93 -
 LaMa-2.0.0/LaMa/inst/doc/MMMPPs.Rmd                                                                   |  118 -
 LaMa-2.0.0/LaMa/inst/doc/MMMPPs.html                                                                  |  230 +--
 LaMa-2.0.0/LaMa/inst/doc/Penalised_splines.R                                                          |only
 LaMa-2.0.0/LaMa/inst/doc/Penalised_splines.Rmd                                                        |only
 LaMa-2.0.0/LaMa/inst/doc/Penalised_splines.html                                                       |only
 LaMa-2.0.0/LaMa/inst/doc/Periodic_HMMs.R                                                              |only
 LaMa-2.0.0/LaMa/inst/doc/Periodic_HMMs.Rmd                                                            |only
 LaMa-2.0.0/LaMa/inst/doc/Periodic_HMMs.html                                                           |only
 LaMa-2.0.0/LaMa/inst/doc/State_space_models.R                                                         |   64 -
 LaMa-2.0.0/LaMa/inst/doc/State_space_models.Rmd                                                       |   89 -
 LaMa-2.0.0/LaMa/inst/doc/State_space_models.html                                                      |  161 +-
 LaMa-2.0.0/LaMa/man/LaMa-package.Rd                                                                   |    5 
 LaMa-2.0.0/LaMa/man/buildSmoothDens.Rd                                                                |only
 LaMa-2.0.0/LaMa/man/calc_trackInd.Rd                                                                  |   10 
 LaMa-2.0.0/LaMa/man/dgmrf2.Rd                                                                         |only
 LaMa-2.0.0/LaMa/man/figures/Logo_LaMa.png                                                             |binary
 LaMa-2.0.0/LaMa/man/figures/Logo_LaMa_old.png                                                         |only
 LaMa-2.0.0/LaMa/man/figures/README-data-1.png                                                         |binary
 LaMa-2.0.0/LaMa/man/figures/README-visualization-1.png                                                |binary
 LaMa-2.0.0/LaMa/man/forward.Rd                                                                        |   85 -
 LaMa-2.0.0/LaMa/man/forward_g.Rd                                                                      |   98 -
 LaMa-2.0.0/LaMa/man/forward_hsmm.Rd                                                                   |only
 LaMa-2.0.0/LaMa/man/forward_ihsmm.Rd                                                                  |only
 LaMa-2.0.0/LaMa/man/forward_p.Rd                                                                      |  117 -
 LaMa-2.0.0/LaMa/man/forward_phsmm.Rd                                                                  |only
 LaMa-2.0.0/LaMa/man/forward_s.Rd                                                                      |   18 
 LaMa-2.0.0/LaMa/man/forward_sp.Rd                                                                     |   28 
 LaMa-2.0.0/LaMa/man/gamma2.Rd                                                                         |only
 LaMa-2.0.0/LaMa/man/generator.Rd                                                                      |only
 LaMa-2.0.0/LaMa/man/make_matrices.Rd                                                                  |only
 LaMa-2.0.0/LaMa/man/make_matrices_dens.Rd                                                             |only
 LaMa-2.0.0/LaMa/man/nessi.Rd                                                                          |only
 LaMa-2.0.0/LaMa/man/penalty.Rd                                                                        |only
 LaMa-2.0.0/LaMa/man/pred_matrix.Rd                                                                    |only
 LaMa-2.0.0/LaMa/man/pseudo_res.Rd                                                                     |only
 LaMa-2.0.0/LaMa/man/pseudo_res_discrete.Rd                                                            |only
 LaMa-2.0.0/LaMa/man/qreml.Rd                                                                          |only
 LaMa-2.0.0/LaMa/man/sdreportMC.Rd                                                                     |only
 LaMa-2.0.0/LaMa/man/stateprobs.Rd                                                                     |   37 
 LaMa-2.0.0/LaMa/man/stateprobs_g.Rd                                                                   |   37 
 LaMa-2.0.0/LaMa/man/stateprobs_p.Rd                                                                   |   39 
 LaMa-2.0.0/LaMa/man/stationary.Rd                                                                     |   22 
 LaMa-2.0.0/LaMa/man/stationary_cont.Rd                                                                |only
 LaMa-2.0.0/LaMa/man/stationary_p.Rd                                                                   |   40 
 LaMa-2.0.0/LaMa/man/stationary_p_sparse.Rd                                                            |only
 LaMa-2.0.0/LaMa/man/stationary_sparse.Rd                                                              |only
 LaMa-2.0.0/LaMa/man/tpm.Rd                                                                            |   35 
 LaMa-2.0.0/LaMa/man/tpm_cont.Rd                                                                       |   42 
 LaMa-2.0.0/LaMa/man/tpm_emb.Rd                                                                        |only
 LaMa-2.0.0/LaMa/man/tpm_emb_g.Rd                                                                      |only
 LaMa-2.0.0/LaMa/man/tpm_g.Rd                                                                          |   45 
 LaMa-2.0.0/LaMa/man/tpm_hsmm.Rd                                                                       |   23 
 LaMa-2.0.0/LaMa/man/tpm_hsmm2.Rd                                                                      |only
 LaMa-2.0.0/LaMa/man/tpm_ihsmm.Rd                                                                      |only
 LaMa-2.0.0/LaMa/man/tpm_p.Rd                                                                          |   81 -
 LaMa-2.0.0/LaMa/man/tpm_phsmm.Rd                                                                      |   41 
 LaMa-2.0.0/LaMa/man/tpm_phsmm2.Rd                                                                     |only
 LaMa-2.0.0/LaMa/man/tpm_thinned.Rd                                                                    |   25 
 LaMa-2.0.0/LaMa/man/trex.Rd                                                                           |only
 LaMa-2.0.0/LaMa/man/trigBasisExp.Rd                                                                   |   22 
 LaMa-2.0.0/LaMa/man/viterbi.Rd                                                                        |   32 
 LaMa-2.0.0/LaMa/man/viterbi_g.Rd                                                                      |   37 
 LaMa-2.0.0/LaMa/man/viterbi_p.Rd                                                                      |   38 
 LaMa-2.0.0/LaMa/man/vm.Rd                                                                             |only
 LaMa-2.0.0/LaMa/src/RcppExports.cpp                                                                   |   17 
 LaMa-2.0.0/LaMa/vignettes/Continuous_time_HMMs.Rmd                                                    |   79 -
 LaMa-2.0.0/LaMa/vignettes/HSMMs.Rmd                                                                   |  127 --
 LaMa-2.0.0/LaMa/vignettes/HSMMs_cache/html/__packages                                                 |    2 
 LaMa-2.0.0/LaMa/vignettes/HSMMs_cache/html/model_muskox_8d66ebbf71b767fb18ffb63472aea360.RData        |only
 LaMa-2.0.0/LaMa/vignettes/HSMMs_cache/html/model_muskox_8d66ebbf71b767fb18ffb63472aea360.rdb          |only
 LaMa-2.0.0/LaMa/vignettes/HSMMs_cache/html/model_muskox_8d66ebbf71b767fb18ffb63472aea360.rdx          |only
 LaMa-2.0.0/LaMa/vignettes/Inhomogeneous_HMMs.Rmd                                                      |  418 +++---
 LaMa-2.0.0/LaMa/vignettes/Inhomogeneous_HMMs_cache/html/__packages                                    |    1 
 LaMa-2.0.0/LaMa/vignettes/Inhomogeneous_HMMs_cache/html/model2_587e60caf9124ca4d36f78515cde9820.RData |only
 LaMa-2.0.0/LaMa/vignettes/Inhomogeneous_HMMs_cache/html/model2_587e60caf9124ca4d36f78515cde9820.rdb   |only
 LaMa-2.0.0/LaMa/vignettes/Inhomogeneous_HMMs_cache/html/model2_587e60caf9124ca4d36f78515cde9820.rdx   |only
 LaMa-2.0.0/LaMa/vignettes/Intro_to_LaMa.Rmd                                                           |  127 +-
 LaMa-2.0.0/LaMa/vignettes/LaMa_and_RTMB.Rmd                                                           |only
 LaMa-2.0.0/LaMa/vignettes/LaMa_and_RTMB_cache                                                         |only
 LaMa-2.0.0/LaMa/vignettes/Longitudinal_data.Rmd                                                       |  115 -
 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(-)

More information about LaMa at CRAN
Permanent link

Package GeneNMF updated to version 0.6.2 with previous version 0.6.0 dated 2024-07-22

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(-)

More information about GeneNMF at CRAN
Permanent link

Package cppdoubles updated to version 0.3.0 with previous version 0.2.0 dated 2024-02-21

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(-)

More information about cppdoubles at CRAN
Permanent link

New package CIMPLE with initial version 0.1.0
Package: CIMPLE
Title: Analysis of Longitudinal Electronic Health Record (EHR) Data with Possibly Informative Observational Time
Version: 0.1.0
Description: Analyzes longitudinal Electronic Health Record (EHR) data with possibly informative observational time. These methods are grouped into two classes depending on the inferential task. One group focuses on estimating the effect of an exposure on a longitudinal biomarker while the other group assesses the impact of a longitudinal biomarker on time-to-diagnosis outcomes. The accompanying paper is Du et al (2024) <doi:10.48550/arXiv.2410.13113>.
License: GPL (>= 3)
Depends: R (>= 2.10)
Imports: dplyr, JMbayes2, lme4, mice, nleqslv, nlme, statmod, stats, survival, utils
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-09 05:45:29 UTC; hb636
Author: Jiacong Du [aut] , Howard Baik [cre]
Maintainer: Howard Baik <howard.baik@yale.edu>
Repository: CRAN
Date/Publication: 2024-11-12 13:20:10 UTC

More information about CIMPLE at CRAN
Permanent link

Package explore updated to version 1.3.3 with previous version 1.3.2 dated 2024-09-02

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(-)

More information about explore at CRAN
Permanent link

Package maplegend updated to version 0.2.0 with previous version 0.1.0 dated 2023-10-18

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(-)

More information about maplegend at CRAN
Permanent link

Package FishResp updated to version 1.1.2 with previous version 1.1.1 dated 2022-09-18

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(-)

More information about FishResp at CRAN
Permanent link

Package RGraphSpace updated to version 1.0.7 with previous version 1.0.6 dated 2024-08-18

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(-)

More information about RGraphSpace at CRAN
Permanent link

Package geeVerse updated to version 0.2.2 with previous version 0.2.1 dated 2024-07-29

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(-)

More information about geeVerse at CRAN
Permanent link

New package forestGYM with initial version 1.0.0
Package: forestGYM
Title: Forest Growth and Yield Model Based on Clutter Model
Version: 1.0.0
Depends: R (>= 3.5.0)
Imports: gtools(>= 3.8.5),stats(>= 4.3.1)
Description: The Clutter model is a significant forest growth simulation tool. Grounded on individual trees and comprehensively considering factors such as competition among trees and the impact of environmental elements on growth, it can accurately reflect the growth process of forest stands. It can be applied in areas like forest resource management, harvesting planning, and ecological research. With the help of the Clutter model, people can better understand the dynamic changes of forests and provide a scientific basis for rational forest management and protecting the ecological environment. This R package can effectively realize the construction of forest growth and harvest models based on the Clutter model and achieve optimized forest management.References: Farias A, Soares C, Leite H et al(2021)<doi:10.1007/s10342-021-01380-1>. Guera O, Silva J, Ferreira R, et al(2019)<doi:10.1590/2179-8087.038117>.
License: GPL-2
LazyData: TRUE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-12 01:39:36 UTC; 78438
Author: Zongzheng Chai [aut, cre]
Maintainer: Zongzheng Chai <chaizz@126.com>
Repository: CRAN
Date/Publication: 2024-11-12 10:20:05 UTC

More information about forestGYM at CRAN
Permanent link

Package condor updated to version 3.0.0 with previous version 2.1.0 dated 2023-08-27

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(-)

More information about condor at CRAN
Permanent link

Package bundle updated to version 0.1.2 with previous version 0.1.1 dated 2023-09-09

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(-)

More information about bundle at CRAN
Permanent link

Package Bolstad updated to version 0.2.42 with previous version 0.2-41 dated 2020-10-05

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(-)

More information about Bolstad at CRAN
Permanent link

Package REffectivePred updated to version 1.0.1 with previous version 1.0.0 dated 2024-02-02

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

Package PEPBVS updated to version 2.1 with previous version 2.0 dated 2024-10-30

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(-)

More information about PEPBVS at CRAN
Permanent link

Package LearnNonparam updated to version 1.2.4 with previous version 1.2.3 dated 2024-10-15

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(-)

More information about LearnNonparam at CRAN
Permanent link

Package Ecfun updated to version 0.3-6 with previous version 0.3-2 dated 2022-10-09

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(-)

More information about Ecfun at CRAN
Permanent link

Package bootcluster updated to version 0.4.1 with previous version 0.3.2 dated 2022-01-29

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(-)

More information about bootcluster at CRAN
Permanent link

Package netseer updated to version 0.1.1 with previous version 0.1.0 dated 2024-02-21

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(-)

More information about netseer at CRAN
Permanent link

Package greta updated to version 0.5.0 with previous version 0.4.5 dated 2024-03-11

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 -
 greta-0.5.0/greta/R/operators.R                                      |   32 
 greta-0.5.0/greta/R/optimiser_class.R                                |only
 greta-0.5.0/greta/R/optimisers.R                                     |  485 ++
 greta-0.5.0/greta/R/package.R                                        |   16 
 greta-0.5.0/greta/R/probability_distributions.R                      |  258 -
 greta-0.5.0/greta/R/progress_bar.R                                   |   19 
 greta-0.5.0/greta/R/reinstallers.R                                   |   64 
 greta-0.5.0/greta/R/samplers.R                                       |    4 
 greta-0.5.0/greta/R/simulate.R                                       |   12 
 greta-0.5.0/greta/R/structures.R                                     |   14 
 greta-0.5.0/greta/R/sysdata.rda                                      |only
 greta-0.5.0/greta/R/test_if_forked_cluster.R                         |    6 
 greta-0.5.0/greta/R/testthat-helpers.R                               |    9 
 greta-0.5.0/greta/R/tf_functions.R                                   |   81 
 greta-0.5.0/greta/R/transforms.R                                     |   14 
 greta-0.5.0/greta/R/unknowns_class.R                                 |   37 
 greta-0.5.0/greta/R/utils.R                                          |  497 ++-
 greta-0.5.0/greta/R/variable.R                                       |   77 
 greta-0.5.0/greta/R/write-logfiles.R                                 |only
 greta-0.5.0/greta/R/zzz.R                                            |    1 
 greta-0.5.0/greta/build/partial.rdb                                  |only
 greta-0.5.0/greta/build/vignette.rds                                 |binary
 greta-0.5.0/greta/data                                               |only
 greta-0.5.0/greta/inst/CITATION                                      |   28 
 greta-0.5.0/greta/inst/WORDLIST                                      |  107 
 greta-0.5.0/greta/inst/doc/example_models.R                          |  577 +++
 greta-0.5.0/greta/inst/doc/example_models.Rmd                        |    2 
 greta-0.5.0/greta/inst/doc/example_models.html                       | 1149 +++++++
 greta-0.5.0/greta/inst/doc/faq.R                                     |   21 
 greta-0.5.0/greta/inst/doc/faq.Rmd                                   |   21 
 greta-0.5.0/greta/inst/doc/faq.html                                  |   39 
 greta-0.5.0/greta/inst/doc/get_started.R                             |  238 -
 greta-0.5.0/greta/inst/doc/get_started.Rmd                           |   70 
 greta-0.5.0/greta/inst/doc/get_started.html                          |  363 +-
 greta-0.5.0/greta/inst/doc/installation.R                            |only
 greta-0.5.0/greta/inst/doc/installation.Rmd                          |only
 greta-0.5.0/greta/inst/doc/installation.html                         |only
 greta-0.5.0/greta/man/are_null.Rd                                    |only
 greta-0.5.0/greta/man/as.greta_model.Rd                              |only
 greta-0.5.0/greta/man/as.unknowns.Rd                                 |only
 greta-0.5.0/greta/man/calculate.Rd                                   |   12 
 greta-0.5.0/greta/man/chol.greta_array.Rd                            |only
 greta-0.5.0/greta/man/chol2symm.Rd                                   |    3 
 greta-0.5.0/greta/man/destroy_greta_deps.Rd                          |only
 greta-0.5.0/greta/man/dim-set-.unknowns.Rd                           |only
 greta-0.5.0/greta/man/dim.node.Rd                                    |only
 greta-0.5.0/greta/man/gpu_cpu.Rd                                     |only
 greta-0.5.0/greta/man/greta.Rd                                       |    1 
 greta-0.5.0/greta/man/greta_create_conda_env.Rd                      |only
 greta-0.5.0/greta/man/greta_deps_receipt.Rd                          |only
 greta-0.5.0/greta/man/greta_deps_spec.Rd                             |only
 greta-0.5.0/greta/man/greta_deps_tf_tfp.Rd                           |only
 greta-0.5.0/greta/man/greta_install_miniconda.Rd                     |only
 greta-0.5.0/greta/man/greta_set_install_logfile.Rd                   |only
 greta-0.5.0/greta/man/inference.Rd                                   |   17 
 greta-0.5.0/greta/man/install_greta_deps.Rd                          |   64 
 greta-0.5.0/greta/man/is.greta_array.Rd                              |only
 greta-0.5.0/greta/man/is.greta_mcmc_list.Rd                          |only
 greta-0.5.0/greta/man/open_greta_install_log.Rd                      |only
 greta-0.5.0/greta/man/optimisers.Rd                                  |  238 +
 greta-0.5.0/greta/man/print.greta_deps_spec.Rd                       |only
 greta-0.5.0/greta/man/print.greta_mcmc_list.Rd                       |only
 greta-0.5.0/greta/man/reinstallers.Rd                                |   13 
 greta-0.5.0/greta/man/run_optimiser.Rd                               |only
 greta-0.5.0/greta/man/samplers.Rd                                    |    4 
 greta-0.5.0/greta/man/stash-notes.Rd                                 |   32 
 greta-0.5.0/greta/man/write_greta_install_log.Rd                     |only
 greta-0.5.0/greta/tests/testthat/Rplots.pdf                          |binary
 greta-0.5.0/greta/tests/testthat/_snaps/as_data.md                   |  100 
 greta-0.5.0/greta/tests/testthat/_snaps/calculate.md                 |  118 
 greta-0.5.0/greta/tests/testthat/_snaps/diagrammer-installed.md      |   10 
 greta-0.5.0/greta/tests/testthat/_snaps/distributions.md             |  426 +-
 greta-0.5.0/greta/tests/testthat/_snaps/distributions_cholesky.md    |only
 greta-0.5.0/greta/tests/testthat/_snaps/extract_replace_combine.md   |   90 
 greta-0.5.0/greta/tests/testthat/_snaps/functions.md                 |  303 +
 greta-0.5.0/greta/tests/testthat/_snaps/future.md                    |   28 
 greta-0.5.0/greta/tests/testthat/_snaps/greta_array_class.md         |  398 ++
 greta-0.5.0/greta/tests/testthat/_snaps/greta_deps_spec.md           |only
 greta-0.5.0/greta/tests/testthat/_snaps/greta_mcmc_list_class.md     |only
 greta-0.5.0/greta/tests/testthat/_snaps/iid_samples.md               |   13 
 greta-0.5.0/greta/tests/testthat/_snaps/inference.md                 |  282 -
 greta-0.5.0/greta/tests/testthat/_snaps/install_greta_deps.md        |   21 
 greta-0.5.0/greta/tests/testthat/_snaps/joint.md                     |   28 
 greta-0.5.0/greta/tests/testthat/_snaps/message_if_using_gpu.md      |only
 greta-0.5.0/greta/tests/testthat/_snaps/misc.md                      |  104 
 greta-0.5.0/greta/tests/testthat/_snaps/mixture.md                   |   57 
 greta-0.5.0/greta/tests/testthat/_snaps/operators.md                 |  106 
 greta-0.5.0/greta/tests/testthat/_snaps/opt.md                       |only
 greta-0.5.0/greta/tests/testthat/_snaps/print_calculate.md           |only
 greta-0.5.0/greta/tests/testthat/_snaps/simulate.md                  |   36 
 greta-0.5.0/greta/tests/testthat/_snaps/syntax.md                    |   64 
 greta-0.5.0/greta/tests/testthat/_snaps/tensorflow-rpkg-stability.md |  257 +
 greta-0.5.0/greta/tests/testthat/_snaps/transforms.md                |    8 
 greta-0.5.0/greta/tests/testthat/_snaps/truncated.md                 |   18 
 greta-0.5.0/greta/tests/testthat/_snaps/variables.md                 |  117 
 greta-0.5.0/greta/tests/testthat/helper-expectations.R               |only
 greta-0.5.0/greta/tests/testthat/helpers.R                           |  431 ++
 greta-0.5.0/greta/tests/testthat/test-diagrammer-installed.R         |   11 
 greta-0.5.0/greta/tests/testthat/test-lkj-log-prob-works.R           |only
 greta-0.5.0/greta/tests/testthat/test-message_if_using_gpu.R         |only
 greta-0.5.0/greta/tests/testthat/test-print_calculate.R              |only
 greta-0.5.0/greta/tests/testthat/test-tensorflow-rpkg-stability.R    |  146 
 greta-0.5.0/greta/tests/testthat/test-wishart-log-prob-works.R       |only
 greta-0.5.0/greta/tests/testthat/test-zzzzzz.R                       |    2 
 greta-0.5.0/greta/tests/testthat/test_as_data.R                      |   40 
 greta-0.5.0/greta/tests/testthat/test_calculate.R                    |  107 
 greta-0.5.0/greta/tests/testthat/test_check_tf_installed.R           |   12 
 greta-0.5.0/greta/tests/testthat/test_distributions.R                |  322 -
 greta-0.5.0/greta/tests/testthat/test_distributions_cholesky.R       |only
 greta-0.5.0/greta/tests/testthat/test_extract_replace_combine.R      |   48 
 greta-0.5.0/greta/tests/testthat/test_functions.R                    |  103 
 greta-0.5.0/greta/tests/testthat/test_future.R                       |   83 
 greta-0.5.0/greta/tests/testthat/test_greta_array_class.R            |   48 
 greta-0.5.0/greta/tests/testthat/test_greta_deps_spec.R              |only
 greta-0.5.0/greta/tests/testthat/test_greta_mcmc_list_class.R        |   61 
 greta-0.5.0/greta/tests/testthat/test_head_tail_work.R               |    4 
 greta-0.5.0/greta/tests/testthat/test_iid_samples.R                  |   19 
 greta-0.5.0/greta/tests/testthat/test_inference.R                    |  380 --
 greta-0.5.0/greta/tests/testthat/test_inference_numerical_issues.R   |only
 greta-0.5.0/greta/tests/testthat/test_install_greta_deps.R           |    4 
 greta-0.5.0/greta/tests/testthat/test_joint.R                        |   23 
 greta-0.5.0/greta/tests/testthat/test_misc.R                         |   22 
 greta-0.5.0/greta/tests/testthat/test_mixture.R                      |   28 
 greta-0.5.0/greta/tests/testthat/test_operators.R                    |   39 
 greta-0.5.0/greta/tests/testthat/test_opt.R                          |only
 greta-0.5.0/greta/tests/testthat/test_posteriors_binomial.R          |only
 greta-0.5.0/greta/tests/testthat/test_posteriors_bivariate_normal.R  |only
 greta-0.5.0/greta/tests/testthat/test_posteriors_chi_squared.R       |only
 greta-0.5.0/greta/tests/testthat/test_posteriors_geweke.R            |only
 greta-0.5.0/greta/tests/testthat/test_posteriors_lkj.R               |only
 greta-0.5.0/greta/tests/testthat/test_posteriors_standard_uniform.R  |only
 greta-0.5.0/greta/tests/testthat/test_posteriors_wishart.R           |only
 greta-0.5.0/greta/tests/testthat/test_representations.R              |    1 
 greta-0.5.0/greta/tests/testthat/test_seed.R                         |only
 greta-0.5.0/greta/tests/testthat/test_simulate.R                     |   48 
 greta-0.5.0/greta/tests/testthat/test_syntax.R                       |   25 
 greta-0.5.0/greta/tests/testthat/test_transforms.R                   |    5 
 greta-0.5.0/greta/tests/testthat/test_truncated.R                    |   21 
 greta-0.5.0/greta/tests/testthat/test_variables.R                    |   38 
 greta-0.5.0/greta/vignettes/example_models.Rmd                       |    2 
 greta-0.5.0/greta/vignettes/faq.Rmd                                  |   21 
 greta-0.5.0/greta/vignettes/figures/coef_graph.png                   |binary
 greta-0.5.0/greta/vignettes/figures/full_graph.png                   |binary
 greta-0.5.0/greta/vignettes/figures/likelihood_graph.png             |binary
 greta-0.5.0/greta/vignettes/get_started.Rmd                          |   70 
 greta-0.5.0/greta/vignettes/installation.Rmd                         |only
 178 files changed, 10202 insertions(+), 5790 deletions(-)

More information about greta at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.