Title: Dominance Analysis
Description: Dominance analysis is a method that allows to compare the
relative importance of predictors in multiple regression models:
ordinary least squares, generalized linear models,
hierarchical linear models, beta regression and dynamic linear models.
The main principles and methods of
dominance analysis are described in
Budescu, D. V. (1993) <doi:10.1037/0033-2909.114.3.542> and
Azen, R., & Budescu, D. V. (2003) <doi:10.1037/1082-989X.8.2.129>
for ordinary least squares regression. Subsequently, the extensions
for multivariate regression, logistic regression and
hierarchical linear models were described in
Azen, R., & Budescu, D. V. (2006) <doi:10.3102/10769986031002157>,
Azen, R., & Traxel, N. (2009) <doi:10.3102/1076998609332754> and
Luo, W., & Azen, R. (2013) <doi:10.3102/1076998612458319>,
respectively.
Author: Claudio Bustos Navarrete [aut, cre, cph] ,
Filipa Coutinho Soares [aut]
Maintainer: Claudio Bustos Navarrete <clbustos@gmail.com>
Diff between dominanceanalysis versions 2.1.0 dated 2024-02-05 and 2.1.1 dated 2025-09-30
DESCRIPTION | 17 ++++--- MD5 | 28 ++++++------ NEWS.md | 9 +++- R/bootAverageDominanceAnalysis.r | 4 - R/bootDominanceAnalysis.r | 2 R/dominanceanalysis-package.r | 4 - README.md | 2 build/vignette.rds |binary inst/doc/da-logistic-regression.R | 56 ++++++++++++------------- inst/doc/da-logistic-regression.html | 9 ++-- man/bootAverageDominanceAnalysis.Rd | 4 - man/bootDominanceAnalysis.Rd | 2 tests/testthat/test-daRawResultsLogistic.R | 2 tests/testthat/test-daSubModelsLogistic.R | 3 - tests/testthat/test-dominance-analysis-plots.R | 8 +-- 15 files changed, 78 insertions(+), 72 deletions(-)
More information about dominanceanalysis at CRAN
Permanent link
Title: Unit Root Tests with Structural Breaks and Fully-Modified
Estimators
Description: Procedures include Phillips (1995) FMVAR <doi:10.2307/2171721>, Kitamura and Phillips (1997) FMGMM <doi:10.1016/S0304-4076(97)00004-3>, Park (1992) CCR <doi:10.2307/2951679>, and so on. Tests with 1 or 2 structural breaks include Gregory and Hansen (1996) <doi:10.1016/0304-4076(69)41685-7>, Zivot and Andrews (1992) <doi:10.2307/1391541>, and Kurozumi (2002) <doi:10.1016/S0304-4076(01)00106-3>.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between COINT versions 0.0.1 dated 2025-09-08 and 0.0.2 dated 2025-09-30
DESCRIPTION | 10 - MD5 | 35 ++-- R/fm_coint.R | 390 ++++++++++++++++++++++++++++++++++++++++++++++++------- R/fm_kernel.R | 23 +-- R/fm_utilities.R | 2 man/ZA_2br.Rd | 5 man/bartlett.Rd | 4 man/bohman.Rd | 4 man/cauchy.Rd | 4 man/dchlet.Rd | 4 man/fmgive.Rd |only man/fmgmm.Rd | 13 - man/gw.Rd | 4 man/mdchlet.Rd | 4 man/parzen.Rd | 4 man/qs.Rd | 4 man/reisz.Rd | 4 man/tukham.Rd | 4 man/tukhan.Rd | 4 19 files changed, 420 insertions(+), 102 deletions(-)
Title: Modern Database Engine for Complex Data Based on
Multi-Dimensional Arrays
Description: The modern database 'TileDB' introduces a powerful on-disk
format for storing and accessing any complex data based on multi-dimensional
arrays. It supports dense and sparse arrays, dataframes and key-values stores,
cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded implementation,
supports parallel I/O, data versioning ('time travel'), metadata and groups.
It is implemented as an embeddable cross-platform C++ library with APIs from
several languages, and integrations. This package provides the R support.
Author: TileDB, Inc. [aut, cph],
Isaiah Norton [cre]
Maintainer: Isaiah Norton <isaiah@tiledb.com>
Diff between tiledb versions 0.32.0 dated 2025-05-15 and 0.33.0 dated 2025-09-30
DESCRIPTION | 6 LICENSE | 2 MD5 | 92 - NEWS.md | 25 R/Array.R | 2 R/Attribute.R | 42 R/Config.R | 48 R/Group.R | 82 R/QueryCondition.R | 22 R/TileDBArray.R | 350 +-- README.md | 4 build/vignette.rds |binary inst/doc/data-ingestion-from-sql.html | 297 +-- inst/doc/documentation.html | 1839 +++++++++----------- inst/doc/documentation.md | 2 inst/doc/installation-options.html | 224 +- inst/doc/introduction.html | 464 ++--- inst/doc/tiledb-mariadb-examples.html | 554 ++---- inst/doc/tiledb-mariadb-examples.md | 2 inst/tinytest/test_config.R | 11 man/as.data.frame.tiledb_config.Rd | 6 man/as.vector.tiledb_config.Rd | 10 man/limitTileDBCores.Rd | 2 man/parse_query_condition.Rd | 6 man/schema-character-method.Rd | 2 man/schema-tiledb_array-method.Rd | 2 man/show-tiledb_config-method.Rd | 2 man/sub-tiledb_config-ANY-method.Rd | 4 man/subset-tiledb_array-ANY-ANY-ANY-method.Rd | 2 man/subset-tiledb_config-ANY-ANY-ANY-method.Rd | 4 man/tiledb_array.Rd | 2 man/tiledb_array_get_non_empty_domain_from_index.Rd | 6 man/tiledb_array_get_non_empty_domain_from_name.Rd | 4 man/tiledb_array_has_enumeration.Rd | 2 man/tiledb_attr.Rd | 2 man/tiledb_config.Rd | 4 man/tiledb_config_load.Rd | 6 man/tiledb_config_save.Rd | 6 man/tiledb_config_unset.Rd | 4 man/tiledb_query_condition_combine.Rd | 2 man/tiledb_query_condition_create.Rd | 6 man/tiledb_query_condition_init.Rd | 4 man/tiledb_query_condition_set_use_enumeration.Rd | 2 src/libtiledb.cpp | 34 tools/tiledbVersion.txt | 4 vignettes/documentation.md | 2 vignettes/tiledb-mariadb-examples.md | 2 47 files changed, 2003 insertions(+), 2197 deletions(-)
Title: Spatial Modeling of Infectious Disease with Reinfection
Description: Geographically Dependent Individual Level Models (GDILMs) within the Susceptible-Exposed-Infectious-Recovered-Susceptible (SEIRS) framework are applied to model infectious disease transmission, incorporating reinfection dynamics. This package employs a likelihood based Monte Carlo Expectation Conditional Maximization (MCECM) algorithm for estimating model parameters. It also provides tools for GDILM fitting, parameter estimation, AIC calculation on real pandemic data, and simulation studies customized to user-defined model settings.
Author: Amin Abed [aut, cre, cph] ,
Mahmoud Torabi [ths],
Zeinab Mashreghi [ths]
Maintainer: Amin Abed <abeda@myumanitoba.ca>
Diff between GDILM.SEIRS versions 0.0.3 dated 2025-01-13 and 0.0.4 dated 2025-09-30
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- R/GDILM_SEIRS_Sim_Par_Est.R | 6 +++--- man/GDILM_SEIRS_Sim_Par_Est.Rd | 2 +- tests/testthat/test-GDILM_SEIRS_Sim_Par_Est.R | 2 +- 5 files changed, 14 insertions(+), 13 deletions(-)
Title: Spatial Modeling on Stream Networks
Description: Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance (Ver Hoef, J.M. and Peterson, E.E., (2010) <DOI:10.1198/jasa.2009.ap08248>.) Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.
Author: Michael Dumelle [aut, cre] ,
Jay M. Ver Hoef [aut],
Erin Peterson [aut],
Alan Pearse [ctb],
Dan Isaak [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between SSN2 versions 0.3.0 dated 2025-08-18 and 0.3.1 dated 2025-09-30
DESCRIPTION | 10 - MD5 | 8 - NEWS.md | 7 R/local.R | 333 +++++++++++++++++++++++----------------------- inst/doc/introduction.pdf |binary 5 files changed, 184 insertions(+), 174 deletions(-)
Title: Header-Only C++ Mathematical Optimization Library for
'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library
(by the 'MLPACK' team) that provides a simple set of abstractions for writing an
objective function to optimize. Provided within are various standard and
cutting-edge optimizers that include full-batch gradient descent techniques,
small-batch techniques, gradient-free optimizers, and constrained optimization.
The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library
and pairs the appropriate header files from 'armadillo' through the
'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor
'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under
3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2,
'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under
the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under
similar terms. Note that 'Ensmallen' requires a compiler that supports
'C++14 [...truncated...]
Author: James Joseph Balamuta [aut, cre, cph] ,
Dirk Eddelbuettel [aut, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between RcppEnsmallen versions 0.2.22.1.2 dated 2025-09-10 and 0.3.10.0.1 dated 2025-09-30
RcppEnsmallen-0.2.22.1.2/RcppEnsmallen/inst/include/ensmallen_bits/cmaes/not_empty_transformation.hpp |only RcppEnsmallen-0.2.22.1.2/RcppEnsmallen/inst/include/ensmallen_bits/utility/arma_traits.hpp |only RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/ChangeLog | 7 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/DESCRIPTION | 6 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/MD5 | 398 +++++----- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/NEWS.md | 60 + RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/doc/using-rcppensmallen.html | 20 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen.hpp | 20 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_belief/ada_belief.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_belief/ada_belief_update.hpp | 29 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_bound/ada_bound.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_bound/ada_bound_update.hpp | 57 + RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_bound/ams_bound_update.hpp | 57 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_delta/ada_delta.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_delta/ada_delta_update.hpp | 28 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_grad/ada_grad.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_grad/ada_grad_update.hpp | 14 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_sqrt/ada_sqrt.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ada_sqrt/ada_sqrt_update.hpp | 14 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/adam/adam.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/adam/adam_update.hpp | 31 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/adam/adamax_update.hpp | 34 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/adam/amsgrad_update.hpp | 41 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/adam/nadam_update.hpp | 41 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/adam/nadamax_update.hpp | 36 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/adam/optimisticadam_update.hpp | 40 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/agemoea/agemoea.hpp | 205 ++--- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/agemoea/agemoea_impl.hpp | 393 +++++---- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/aug_lagrangian/aug_lagrangian.hpp | 109 ++ RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/aug_lagrangian/aug_lagrangian_function.hpp | 32 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/aug_lagrangian/aug_lagrangian_function_impl.hpp | 42 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/aug_lagrangian/aug_lagrangian_impl.hpp | 92 +- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/bigbatch_sgd/adaptive_stepsize.hpp | 20 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/bigbatch_sgd/backtracking_line_search.hpp | 8 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/bigbatch_sgd/bigbatch_sgd.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/bigbatch_sgd/bigbatch_sgd_impl.hpp | 29 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/callbacks/timer_stop.hpp | 27 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cd/cd.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cd/cd_impl.hpp | 6 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cd/descent_policies/random_descent.hpp | 5 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cmaes/active_cmaes.hpp | 87 -- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cmaes/active_cmaes_impl.hpp | 70 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cmaes/cmaes.hpp | 44 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cmaes/cmaes_impl.hpp | 114 +- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cmaes/pop_cmaes.hpp | 66 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cmaes/pop_cmaes_impl.hpp | 28 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cne/cne.hpp | 8 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/cne/cne_impl.hpp | 28 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/de/de.hpp | 8 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/de/de_impl.hpp | 21 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/demon_adam/demon_adam.hpp | 10 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/demon_adam/demon_adam_update.hpp | 19 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/demon_sgd/demon_sgd.hpp | 10 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/demon_sgd/demon_sgd_update.hpp | 26 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ens_version.hpp | 14 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/eve/eve.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/eve/eve_impl.hpp | 34 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fasta |only RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fbs |only RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fista |only RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ftml/ftml.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/ftml/ftml_update.hpp | 34 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/function/arma_traits.hpp | 24 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fw/atoms.hpp | 1 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fw/constr_lpball.hpp | 40 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fw/frank_wolfe.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fw/frank_wolfe_impl.hpp | 19 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fw/line_search/line_search_impl.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fw/proximal/proximal_impl.hpp | 29 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fw/update_full_correction.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/fw/update_span.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/gradient_descent/gradient_descent.hpp | 8 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/gradient_descent/gradient_descent_impl.hpp | 6 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/iqn/iqn.hpp | 6 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/iqn/iqn_impl.hpp | 38 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/katyusha/katyusha.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/katyusha/katyusha_impl.hpp | 30 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/lbfgs/lbfgs.hpp | 15 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/lbfgs/lbfgs_impl.hpp | 147 ++- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/lookahead/lookahead.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/lookahead/lookahead_impl.hpp | 36 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/moead/decomposition_policies/pbi_decomposition.hpp | 7 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/moead/decomposition_policies/tchebycheff_decomposition.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/moead/decomposition_policies/weighted_decomposition.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/moead/moead.hpp | 83 +- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/moead/moead_impl.hpp | 237 +++-- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/moead/weight_init_policies/bbs_init.hpp | 10 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/moead/weight_init_policies/dirichlet_init.hpp | 15 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/moead/weight_init_policies/uniform_init.hpp | 14 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/nsga2/nsga2.hpp | 148 +-- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/nsga2/nsga2_impl.hpp | 210 +++-- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/padam/padam_update.hpp | 53 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/parallel_sgd/parallel_sgd_impl.hpp | 6 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/ackley_function_impl.hpp | 17 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/aug_lagrangian_test_functions.hpp | 20 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/aug_lagrangian_test_functions_impl.hpp | 65 + RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/beale_function_impl.hpp | 22 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/booth_function_impl.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/colville_function_impl.hpp | 20 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/cross_in_tray_function_impl.hpp | 10 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/easom_function_impl.hpp | 24 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/fonseca_fleming_function.hpp | 36 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/generalized_rosenbrock_function.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/generalized_rosenbrock_function_impl.hpp | 40 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/goldstein_price_function_impl.hpp | 45 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/gradient_descent_test_function_impl.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/himmelblau_function.hpp | 6 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/himmelblau_function_impl.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/levy_function_n13.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/levy_function_n13_impl.hpp | 33 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/logistic_regression_function.hpp | 70 + RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/logistic_regression_function_impl.hpp | 244 +++--- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/maf/maf1_function.hpp | 243 +++--- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/maf/maf2_function.hpp | 289 +++---- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/maf/maf3_function.hpp | 268 +++--- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/maf/maf4_function.hpp | 295 +++---- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/maf/maf5_function.hpp | 322 +++----- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/maf/maf6_function.hpp | 348 ++++---- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/matyas_function_impl.hpp | 8 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/mc_cormick_function_impl.hpp | 22 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/problems.hpp | 1 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/quadratic_function.hpp |only RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/quadratic_function_impl.hpp |only RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/rastrigin_function.hpp | 10 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/rastrigin_function_impl.hpp | 44 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/rosenbrock_function_impl.hpp | 8 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/rosenbrock_wood_function.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/rosenbrock_wood_function_impl.hpp | 7 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/schaffer_function_n1.hpp | 17 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/schaffer_function_n2_impl.hpp | 17 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/schaffer_function_n4_impl.hpp | 8 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/schwefel_function.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/sgd_test_function_impl.hpp | 15 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/softmax_regression_function.hpp | 47 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/softmax_regression_function_impl.hpp | 118 +- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/sparse_test_function_impl.hpp | 20 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/sphere_function.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/sphere_function_impl.hpp | 8 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/styblinski_tang_function.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/styblinski_tang_function_impl.hpp | 19 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/three_hump_camel_function_impl.hpp | 8 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/wood_function_impl.hpp | 24 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/zdt/zdt1_function.hpp | 176 ++-- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/zdt/zdt2_function.hpp | 5 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/zdt/zdt3_function.hpp | 7 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/zdt/zdt4_function.hpp | 6 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/problems/zdt/zdt6_function.hpp | 6 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/pso/init_policies/default_init.hpp | 22 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/pso/pso.hpp | 19 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/pso/pso_impl.hpp | 46 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/pso/update_policies/lbest_update.hpp | 204 ++--- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/qhadam/qhadam.hpp | 10 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/qhadam/qhadam_update.hpp | 40 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/rmsprop/rmsprop.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/rmsprop/rmsprop_update.hpp | 21 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sa/exponential_schedule.hpp | 7 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sa/sa_impl.hpp | 28 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sarah/sarah.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sarah/sarah_impl.hpp | 13 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sarah/sarah_plus_update.hpp | 8 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sarah/sarah_update.hpp | 6 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sdp/lin_alg.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sdp/lrsdp.hpp | 16 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sdp/lrsdp_function.hpp | 19 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sdp/lrsdp_function_impl.hpp | 47 - RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sdp/lrsdp_impl.hpp | 23 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sdp/primal_dual_impl.hpp | 10 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgd/sgd.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgd/sgd_impl.hpp | 19 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgd/update_policies/momentum_update.hpp | 11 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgd/update_policies/nesterov_momentum_update.hpp | 14 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgd/update_policies/quasi_hyperbolic_update.hpp | 27 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgd/update_policies/vanilla_update.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgdr/cyclical_decay.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgdr/sgdr.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgdr/sgdr_impl.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgdr/snapshot_ensembles.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgdr/snapshot_sgdr.hpp | 36 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/sgdr/snapshot_sgdr_impl.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/smorms3/smorms3.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/smorms3/smorms3_update.hpp | 36 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/spalera_sgd/spalera_sgd.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/spalera_sgd/spalera_sgd_impl.hpp | 13 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/spalera_sgd/spalera_stepsize.hpp | 76 + RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/spsa/spsa_impl.hpp | 18 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/svrg/barzilai_borwein_decay.hpp | 24 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/svrg/svrg.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/svrg/svrg_impl.hpp | 6 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/svrg/svrg_update.hpp | 4 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/swats/swats.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/swats/swats_update.hpp | 78 + RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/utility/detect_callbacks.hpp |only RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/utility/function_traits.hpp |only RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/utility/indicators/epsilon.hpp | 85 +- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/utility/indicators/igd.hpp | 110 +- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/utility/indicators/igd_plus.hpp | 83 +- RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/utility/proxies.hpp |only RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/utility/using.hpp |only RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/wn_grad/wn_grad.hpp | 2 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/wn_grad/wn_grad_update.hpp | 18 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/yogi/yogi.hpp | 14 RcppEnsmallen-0.3.10.0.1/RcppEnsmallen/inst/include/ensmallen_bits/yogi/yogi_update.hpp | 32 202 files changed, 4470 insertions(+), 3603 deletions(-)
Title: Modeling and Map Production using Random Forest and Related
Stochastic Models
Description: Creates sophisticated models of training data and validates the models with an independent test set, cross validation, or Out Of Bag (OOB) predictions on the training data. Create graphs and tables of the model validation results. Applies these models to GIS .img files of predictors to create detailed prediction surfaces. Handles large predictor files for map making, by reading in the .img files in chunks, and output to the .txt file the prediction for each data chunk, before reading the next chunk of data.
Author: Elizabeth Freeman [aut, cre],
Tracey Frescino [aut]
Maintainer: Elizabeth Freeman <elizabeth.a.freeman@usda.gov>
Diff between ModelMap versions 3.4.0.4 dated 2023-04-24 and 3.4.0.8 dated 2025-09-30
DESCRIPTION | 20 ++++++++++++++------ MD5 | 18 +++++++++--------- build/vignette.rds |binary inst/CHANGELOG | 12 ++++++++++-- inst/doc/ExploreModelMap.pdf |binary inst/doc/VModelMap.pdf |binary inst/doc/Vquantile.pdf |binary man/ModelMap-package.Rd | 4 ++-- man/model.importance.plot.Rd | 2 +- man/model.mapmake.Rd | 6 +++--- 10 files changed, 39 insertions(+), 23 deletions(-)
Title: Test Theory Analysis and Biclustering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 1.6.1 dated 2025-08-26 and 1.6.3 dated 2025-09-30
exametrika-1.6.1/exametrika/man/Jacobian_grm.Rd |only exametrika-1.6.1/exametrika/man/log_lik_grm.Rd |only exametrika-1.6.1/exametrika/man/params_to_target_jac.Rd |only exametrika-1.6.1/exametrika/man/score_function_with_Jacobian.Rd |only exametrika-1.6.1/exametrika/man/target_to_params_jac.Rd |only exametrika-1.6.3/exametrika/DESCRIPTION | 18 exametrika-1.6.3/exametrika/MD5 | 56 - exametrika-1.6.3/exametrika/NAMESPACE | 3 exametrika-1.6.3/exametrika/NEWS.md | 36 exametrika-1.6.3/exametrika/R/00_EMclus.R | 6 exametrika-1.6.3/exametrika/R/00_GridSearch.R | 96 ++ exametrika-1.6.3/exametrika/R/00_exametrikaPlot.R | 20 exametrika-1.6.3/exametrika/R/01_dataFormat.R | 223 ++++- exametrika-1.6.3/exametrika/R/02_TestItemFunctions.R | 50 - exametrika-1.6.3/exametrika/R/05_LCA.R | 2 exametrika-1.6.3/exametrika/R/06_LRA.R | 9 exametrika-1.6.3/exametrika/R/07_Biclustering.R | 41 - exametrika-1.6.3/exametrika/R/12_OrdinalLatentRank.R | 12 exametrika-1.6.3/exametrika/R/13_RatedLatentRank.R | 12 exametrika-1.6.3/exametrika/R/14_GRM.R | 391 +--------- exametrika-1.6.3/exametrika/R/15_NominalBiclustering.R | 4 exametrika-1.6.3/exametrika/R/16_OrdinalBiclustering.R | 6 exametrika-1.6.3/exametrika/R/RcppExports.R |only exametrika-1.6.3/exametrika/README.md | 34 exametrika-1.6.3/exametrika/man/Biclustering.Rd | 1 exametrika-1.6.3/exametrika/man/GRM.Rd | 2 exametrika-1.6.3/exametrika/man/GridSearch.Rd | 2 exametrika-1.6.3/exametrika/man/LCA.Rd | 1 exametrika-1.6.3/exametrika/man/LRA.Rd | 3 exametrika-1.6.3/exametrika/man/crr.Rd | 4 exametrika-1.6.3/exametrika/man/params_to_target.Rd |only exametrika-1.6.3/exametrika/src |only 32 files changed, 548 insertions(+), 484 deletions(-)
Title: Generate Predicted Writing Quality Scores
Description: Imports variables from 'ReaderBench' (Dascalu et al.,
2018)<doi:10.1007/978-3-319-66610-5_48>, 'Coh-Metrix' (McNamara et
al., 2014)<doi:10.1017/CBO9780511894664>, and/or 'GAMET' (Crossley et
al., 2019) <doi:10.17239/jowr-2019.11.02.01> output files; downloads
predictive scoring models described in Mercer & Cannon
(2022)<doi:10.31244/jero.2022.01.03> and Mercer et
al.(2021)<doi:10.1177/0829573520987753>; and generates predicted
writing quality and curriculum-based measurement (McMaster & Espin,
2007)<doi:10.1177/00224669070410020301> scores.
Author: Sterett H. Mercer [aut, cre]
Maintainer: Sterett H. Mercer <sterett.mercer@ubc.ca>
Diff between writeAlizer versions 1.6.4 dated 2025-09-30 and 1.6.5 dated 2025-09-30
DESCRIPTION | 14 +- MD5 | 19 +- NAMESPACE | 2 NEWS.md | 9 + R/artifact_registry.R | 144 +++++++++++----------- R/download.R | 40 +++--- README.md | 24 ++- man/wa_download.Rd | 26 +++ man/wa_seed_example_models.Rd | 84 ++++++------ tests/testthat/helper-network.R |only tests/testthat/test-integration-predict_quality.R | 16 ++ 11 files changed, 215 insertions(+), 163 deletions(-)
Title: 'R6'-Based Flexible Framework for Permutation Tests
Description: Implements non-parametric tests from Higgins (2004, ISBN:0534387756), including tests for one sample, two samples, k samples, paired comparisons, blocked designs, trends and association. Built with 'Rcpp' for efficiency and 'R6' for flexible, object-oriented design, the package provides a unified framework for performing or creating custom permutation tests.
Author: Yan Du [aut, cre]
Maintainer: Yan Du <isduyan@outlook.com>
Diff between LearnNonparam versions 1.2.9 dated 2025-06-02 and 1.3.0 dated 2025-09-30
LearnNonparam-1.2.9/LearnNonparam/R/ScoreSum.R |only LearnNonparam-1.2.9/LearnNonparam/man/ScoreSum.Rd |only LearnNonparam-1.3.0/LearnNonparam/DESCRIPTION | 12 LearnNonparam-1.3.0/LearnNonparam/MD5 | 140 ++-- LearnNonparam-1.3.0/LearnNonparam/NAMESPACE | 5 LearnNonparam-1.3.0/LearnNonparam/NEWS.md | 18 LearnNonparam-1.3.0/LearnNonparam/R/AndersonDarling.R |only LearnNonparam-1.3.0/LearnNonparam/R/CDF.R | 5 LearnNonparam-1.3.0/LearnNonparam/R/ContingencyTableTest.R | 6 LearnNonparam-1.3.0/LearnNonparam/R/CramerVonMises.R |only LearnNonparam-1.3.0/LearnNonparam/R/Friedman.R | 2 LearnNonparam-1.3.0/LearnNonparam/R/KolmogorovSmirnov.R | 29 - LearnNonparam-1.3.0/LearnNonparam/R/KruskalWallis.R | 2 LearnNonparam-1.3.0/LearnNonparam/R/Kuiper.R |only LearnNonparam-1.3.0/LearnNonparam/R/LearnNonparam-package.R | 13 LearnNonparam-1.3.0/LearnNonparam/R/MultipleComparison.R | 20 LearnNonparam-1.3.0/LearnNonparam/R/Page.R | 2 LearnNonparam-1.3.0/LearnNonparam/R/PermuTest.R | 100 +-- LearnNonparam-1.3.0/LearnNonparam/R/RCBDTest.R | 12 LearnNonparam-1.3.0/LearnNonparam/R/RatioMeanDeviance.R | 26 LearnNonparam-1.3.0/LearnNonparam/R/RcppExports.R | 12 LearnNonparam-1.3.0/LearnNonparam/R/Studentized.R | 44 - LearnNonparam-1.3.0/LearnNonparam/R/TwoSampleDistributionTest.R |only LearnNonparam-1.3.0/LearnNonparam/R/pmt.R | 281 +++++++--- LearnNonparam-1.3.0/LearnNonparam/README.md | 121 ++-- LearnNonparam-1.3.0/LearnNonparam/inst/include/pmt/impl_association_pmt.hpp | 36 - LearnNonparam-1.3.0/LearnNonparam/inst/include/pmt/impl_ksample_pmt.hpp | 40 - LearnNonparam-1.3.0/LearnNonparam/inst/include/pmt/impl_multcomp_pmt.hpp | 56 + LearnNonparam-1.3.0/LearnNonparam/inst/include/pmt/impl_paired_pmt.hpp | 30 - LearnNonparam-1.3.0/LearnNonparam/inst/include/pmt/impl_rcbd_pmt.hpp | 32 - LearnNonparam-1.3.0/LearnNonparam/inst/include/pmt/impl_table_pmt.hpp | 205 ++++++- LearnNonparam-1.3.0/LearnNonparam/inst/include/pmt/impl_twosample_pmt.hpp | 77 +- LearnNonparam-1.3.0/LearnNonparam/inst/include/pmt/permutation.hpp | 55 + LearnNonparam-1.3.0/LearnNonparam/inst/include/pmt/progress.hpp | 123 ++-- LearnNonparam-1.3.0/LearnNonparam/man/AndersonDarling.Rd |only LearnNonparam-1.3.0/LearnNonparam/man/CDF.Rd | 2 LearnNonparam-1.3.0/LearnNonparam/man/CramerVonMises.Rd |only LearnNonparam-1.3.0/LearnNonparam/man/KolmogorovSmirnov.Rd | 13 LearnNonparam-1.3.0/LearnNonparam/man/Kuiper.Rd |only LearnNonparam-1.3.0/LearnNonparam/man/Quantile.Rd | 2 LearnNonparam-1.3.0/LearnNonparam/man/Sign.Rd | 2 LearnNonparam-1.3.0/LearnNonparam/man/TwoSampleDistributionTest.Rd |only LearnNonparam-1.3.0/LearnNonparam/man/Wilcoxon.Rd | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/benchmark-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/benchmark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/benchmark_res-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/benchmark_res.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/define_cpp-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/define_cpp.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/define_quickr-dark.svg |only LearnNonparam-1.3.0/LearnNonparam/man/figures/README/define_quickr.svg |only LearnNonparam-1.3.0/LearnNonparam/man/figures/README/define_r-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/define_r.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/histogram.svg | 214 +++---- LearnNonparam-1.3.0/LearnNonparam/man/figures/README/modify-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/modify.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/p_value-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/p_value.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/plot-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/plot.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/prepare_data-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/prepare_data.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/print-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/print.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/statistic-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/statistic.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/t_cpp_res-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/t_cpp_res.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/t_custom_res-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/t_custom_res.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/t_quickr_res-dark.svg |only LearnNonparam-1.3.0/LearnNonparam/man/figures/README/t_quickr_res.svg |only LearnNonparam-1.3.0/LearnNonparam/man/figures/README/test-dark.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/figures/README/test.svg | 2 LearnNonparam-1.3.0/LearnNonparam/man/pmt.Rd | 70 +- LearnNonparam-1.3.0/LearnNonparam/man/roxygen/templates/active_params.R | 2 LearnNonparam-1.3.0/LearnNonparam/src/RcppExports.cpp | 37 - LearnNonparam-1.3.0/LearnNonparam/src/pmt_interface.cpp | 136 +++- 78 files changed, 1296 insertions(+), 740 deletions(-)
Title: Assesses the Quality of Estimates Made by Complex Sample Designs
Description: Assesses the quality of estimates made by complex sample designs,
following the methodology developed by the National Institute of Statistics Chile (Household Survey Standard 2020, <https://www.ine.cl/docs/default-source/institucionalidad/buenas-pr%C3%A1cticas/clasificaciones-y-estandares/est%C3%A1ndar-evaluaci%C3%B3n-de-calidad-de-estimaciones-publicaci%C3%B3n-27022020.pdf>), (Economics Survey Standard 2024, <https://www.ine.gob.cl/docs/default-source/buenas-practicas/directrices-metodologicas/estandares/documentos/est%C3%A1ndar-evaluaci%C3%B3n-de-calidad-de-estimaciones-econ%C3%B3micas.pdf?sfvrsn=201fbeb9_2>)
and by Economic Commission for Latin America and
Caribbean (2020, <https://repositorio.cepal.org/bitstream/handle/11362/45681/1/S2000293_es.pdf>), (2024, <https://repositorio.cepal.org/server/api/core/bitstreams/f04569e6-4f38-42e7-a32b-e0b298e0ab9c/content>).
Author: Klaus Lehmann [aut, cre],
Ricardo Pizarro [aut],
Ignacio Agloni [ctb],
Andrea Lopez [ctb],
Javiera Preuss [ctb]
Maintainer: Klaus Lehmann <klehmann@fen.uchile.cl>
Diff between calidad versions 0.8.1 dated 2025-06-02 and 0.8.2 dated 2025-09-30
DESCRIPTION | 6 - MD5 | 16 +-- NEWS.md | 7 - R/create_internal.R | 132 +++++-------------------------- inst/doc/tutorial.html | 36 ++++---- man/get_df.Rd | 2 tests/testthat/test-create_prop.R | 61 ++++++++++++++ tests/testthat/test-evaluate_internal.R | 24 ----- tests/testthat/test-internal_functions.R | 63 +++++++++++++- 9 files changed, 173 insertions(+), 174 deletions(-)
Title: Bayesian Dynamic Systems Modeling
Description: Implements methods for building and analyzing models based on panel
data as described in the paper by
Moral-Benito (2013, <doi:10.1080/07350015.2013.818003>).
The package provides functions to estimate dynamic panel data models
and analyze the results of the estimation.
Author: Mateusz Wyszynski [aut],
Marcin Dubel [ctb, cre],
Krzysztof Beck [ctb]
Maintainer: Marcin Dubel <marcindubel@gmail.com>
Diff between bdsm versions 0.2.2 dated 2025-09-02 and 0.3.0 dated 2025-09-30
bdsm-0.2.2/bdsm/tests/testthat/Rplots.pdf |only bdsm-0.3.0/bdsm/DESCRIPTION | 13 - bdsm-0.3.0/bdsm/MD5 | 49 +++--- bdsm-0.3.0/bdsm/NAMESPACE | 3 bdsm-0.3.0/bdsm/NEWS.md | 4 bdsm-0.3.0/bdsm/R/RcppExports.R |only bdsm-0.3.0/bdsm/R/SEM_likelihood.R | 49 +----- bdsm-0.3.0/bdsm/R/SEM_matrices.R | 171 ---------------------- bdsm-0.3.0/bdsm/R/best_models.R | 24 +-- bdsm-0.3.0/bdsm/README.md | 40 ++++- bdsm-0.3.0/bdsm/build/vignette.rds |binary bdsm-0.3.0/bdsm/data/full_bma_results.rda |binary bdsm-0.3.0/bdsm/data/full_model_space.rda |binary bdsm-0.3.0/bdsm/data/small_model_space.rda |binary bdsm-0.3.0/bdsm/inst/doc/bdsm_vignette.pdf |binary bdsm-0.3.0/bdsm/man/residual_maker_matrix.Rd | 2 bdsm-0.3.0/bdsm/man/sem_B_matrix.Rd | 4 bdsm-0.3.0/bdsm/man/sem_C_matrix.Rd | 4 bdsm-0.3.0/bdsm/man/sem_psi_matrix.Rd | 2 bdsm-0.3.0/bdsm/man/sem_sigma_matrix.Rd | 4 bdsm-0.3.0/bdsm/src |only bdsm-0.3.0/bdsm/tests/testthat/test-data.R |only bdsm-0.3.0/bdsm/tests/testthat/test-model_pmp.R | 6 bdsm-0.3.0/bdsm/tests/testthat/test-model_sizes.R | 6 bdsm-0.3.0/bdsm/tests/testthat/test-model_space.R | 97 ++++++++---- 25 files changed, 179 insertions(+), 299 deletions(-)
Title: Exploring Biological Relevance of Environmental Chemistry
Observations
Description: Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell (2017) <doi:10.1021/acs.est.7b01613>.
Author: Laura DeCicco [aut, cre] ,
Steven Corsi [aut] ,
Daniel Villeneuve [aut] ,
Brett Blackwell [aut] ,
Gerald Ankley [aut] ,
Alison Appling [rev] ,
Dalma Martinovic [rev]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between toxEval versions 1.4.0 dated 2024-11-22 and 1.4.1 dated 2025-09-30
DESCRIPTION | 22 +++++++++++--------- MD5 | 33 +++++++++++++++--------------- NEWS | 4 +++ R/plot_chemical_boxplots.R | 35 ++++++++++++++++++++++---------- R/plot_group_boxplots.R | 44 +++++++++++++++++++++++++++-------------- R/plot_tox_endpoints.R | 40 +++++++++++++++++++++++++------------ R/plot_tox_endpoints2.R | 35 +++++++++++++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Chemical_names.html | 7 +++--- inst/doc/Introduction.html | 15 +++++++------ inst/doc/PrepareData.html | 7 +++--- man/figures/logo.png |binary man/figures/tox_Eval_logo.png |only man/plot_tox_boxplots.Rd | 5 +++- man/plot_tox_endpoints.Rd | 6 ++++- man/plot_tox_endpoints2.Rd | 2 + tests/testthat/tests_summary.R | 9 +++++--- 18 files changed, 170 insertions(+), 94 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of blocked and split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible. For details, see Morgan-Wall et al. (2021) <doi:10.18637/jss.v099.i01>.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 1.9.0 dated 2025-09-16 and 1.9.2 dated 2025-09-30
DESCRIPTION | 10 MD5 | 31 - R/calculate_gefficiency.R | 61 +- R/gen_design.R | 9 R/normalize_design.R | 4 R/plot_correlations.R | 126 ++--- R/plot_fds.R | 252 ++++++++--- R/skprGUI.R | 756 +---------------------------------- R/skprGUI_code_pane.R |only man/build_code_pane_html.Rd |only man/create_code_pane_reactives.Rd |only src/blocked_optimality_functions.cpp |only src/design_utils.h |only src/exported_optimality.cpp | 37 - src/exported_optimality_2.cpp |only src/genOptimalDesign.cpp | 508 ++++++++++++----------- src/genSplitPlotOptimalDesign.cpp | 186 ++++---- src/getBlockedOptimalDesign.cpp | 633 +++++++++++++++-------------- src/optimalityfunctions.cpp | 103 ---- src/optimalityfunctions2.cpp |only 20 files changed, 1049 insertions(+), 1667 deletions(-)
Title: Phrase Mining
Description: Functions to extract and handle commonly occurring principal phrases
obtained from collections of texts. Major speed improvements - core functions
rewritten in C++ for faster phrase-document parsing, clustering, and text
distance computations. Based on, Small, E., & Cabrera, J. (2025). Principal
phrase mining, an automated method for extracting meaningful phrases from
text. International Journal of Computers and Applications, 47(1), 84–92.
Author: Ellie Small [aut, cre]
Maintainer: Ellie Small <ellie_small@yahoo.com>
Diff between phm versions 1.1.4 dated 2025-05-16 and 2.1.2 dated 2025-09-30
phm-1.1.4/phm/R/bestDocs.R |only phm-1.1.4/phm/R/freqPhrases.R |only phm-1.1.4/phm/R/getDocs.R |only phm-1.1.4/phm/R/removePhrases.R |only phm-2.1.2/phm/DESCRIPTION | 24 +- phm-2.1.2/phm/MD5 | 70 +++++--- phm-2.1.2/phm/NAMESPACE | 4 phm-2.1.2/phm/NEWS |only phm-2.1.2/phm/R/RcppExports.R |only phm-2.1.2/phm/R/cluster.R | 143 +++++++---------- phm-2.1.2/phm/R/distance.R | 121 +++++++++++--- phm-2.1.2/phm/R/getPubMed.R | 59 ------- phm-2.1.2/phm/R/phm-package.R |only phm-2.1.2/phm/R/phmFunctions.R |only phm-2.1.2/phm/R/phraseDoc.R | 254 ++----------------------------- phm-2.1.2/phm/R/phraseDocFunctions.R |only phm-2.1.2/phm/build/vignette.rds |binary phm-2.1.2/phm/inst/CITATION | 27 +-- phm-2.1.2/phm/inst/doc/phm-intro.Rmd | 1 phm-2.1.2/phm/inst/doc/phm-intro.html | 8 phm-2.1.2/phm/man/as.matrix.phraseDoc.Rd | 2 phm-2.1.2/phm/man/bestDocs.Rd | 2 phm-2.1.2/phm/man/freqPhrases.Rd | 2 phm-2.1.2/phm/man/getDocs.Rd | 2 phm-2.1.2/phm/man/getPhrases.Rd | 2 phm-2.1.2/phm/man/phraseDoc.Rd | 18 -- phm-2.1.2/phm/man/print.phraseDoc.Rd | 2 phm-2.1.2/phm/man/removePhrases.Rd | 2 phm-2.1.2/phm/man/stopEndWords.Rd | 2 phm-2.1.2/phm/man/stopPhrases.Rd | 2 phm-2.1.2/phm/man/stopStartWords.Rd | 2 phm-2.1.2/phm/man/textCluster.Rd | 8 phm-2.1.2/phm/man/textDist.Rd | 2 phm-2.1.2/phm/man/textDist_sparse.Rd |only phm-2.1.2/phm/src |only phm-2.1.2/phm/vignettes/phm-intro.Rmd | 1 36 files changed, 274 insertions(+), 486 deletions(-)
Title: Fast and Robust Multi-Scale Graph Clustering
Description: A graph community detection algorithm that aims to be performant
on large graphs and robust, returning consistent results across runs.
SpeakEasy 2 (SE2), the underlying algorithm, is described in Chris Gaiteri,
David R. Connell & Faraz A. Sultan et al. (2023)
<doi:10.1186/s13059-023-03062-0>. The core algorithm is written in 'C',
providing speed and keeping the memory requirements low. This implementation
can take advantage of multiple computing cores without increasing memory
usage. SE2 can detect community structure across scales, making it a good
choice for biological data, which often has hierarchical structure. Graphs
can be passed to the algorithm as adjacency matrices using base 'R'
matrices, the 'Matrix' library, 'igraph' graphs, or any data that can be
coerced into a matrix.
Author: David Connell [aut, cre, cph] ,
Chris Gaiteri [cph] ,
Gabor Csardi [cph, ctb] ,
Tamas Nepusz [cph, ctb] ,
Szabolcs Horvat [cph, ctb] ,
Vincent Traag [cph, ctb] ,
Fabio Zanini [cph, ctb] ,
Daniel Noom [cph, ctb] ,
The igraph development team [cph] ,
F [...truncated...]
Maintainer: David Connell <david32@dcon.addy.io>
Diff between speakeasyR versions 0.1.7 dated 2025-09-05 and 0.1.8 dated 2025-09-30
speakeasyR-0.1.7/speakeasyR/src/se2/vendor/igraph/include/igraph_array.h |only speakeasyR-0.1.7/speakeasyR/src/se2/vendor/igraph/include/igraph_array_pmt.h |only speakeasyR-0.1.7/speakeasyR/src/se2/vendor/igraph/include/igraph_microscopic_update.h |only speakeasyR-0.1.7/speakeasyR/src/se2/vendor/igraph/include/igraph_topology.h |only speakeasyR-0.1.7/speakeasyR/src/se2/vendor/igraph/src/community/infomap |only speakeasyR-0.1.7/speakeasyR/src/se2/vendor/igraph/src/core/array.c |only speakeasyR-0.1.7/speakeasyR/src/se2/vendor/igraph/src/core/array.pmt |only speakeasyR-0.1.7/speakeasyR/src/se2/vendor/igraph/src/internal/zeroin.c |only speakeasyR-0.1.8/speakeasyR/DESCRIPTION | 6 speakeasyR-0.1.8/speakeasyR/MD5 | 660 + speakeasyR-0.1.8/speakeasyR/NEWS.md | 17 speakeasyR-0.1.8/speakeasyR/R/cluster.R | 28 speakeasyR-0.1.8/speakeasyR/R/cluster_genes.R | 3 speakeasyR-0.1.8/speakeasyR/R/knn_graph.R | 12 speakeasyR-0.1.8/speakeasyR/R/order_nodes.R | 22 speakeasyR-0.1.8/speakeasyR/R/utils.R | 16 speakeasyR-0.1.8/speakeasyR/configure | 19 speakeasyR-0.1.8/speakeasyR/configure.ac | 3 speakeasyR-0.1.8/speakeasyR/configure.win | 1 speakeasyR-0.1.8/speakeasyR/inst/doc/speakeasyR.html | 113 speakeasyR-0.1.8/speakeasyR/man/cluster.Rd | 2 speakeasyR-0.1.8/speakeasyR/src/include/igraph_config.h | 4 speakeasyR-0.1.8/speakeasyR/src/include/igraph_threading.h | 4 speakeasyR-0.1.8/speakeasyR/src/include/igraph_version.h | 25 speakeasyR-0.1.8/speakeasyR/src/se2/CMakeLists.txt | 3 speakeasyR-0.1.8/speakeasyR/src/se2/src/speakeasy2/se2_core.c | 46 speakeasyR-0.1.8/speakeasyR/src/se2/src/speakeasy2/se2_label.c | 144 speakeasyR-0.1.8/speakeasyR/src/se2/src/speakeasy2/se2_neighborlist.c | 97 speakeasyR-0.1.8/speakeasyR/src/se2/src/speakeasy2/se2_neighborlist.h | 8 speakeasyR-0.1.8/speakeasyR/src/se2/src/speakeasy2/se2_partitions.c | 323 speakeasyR-0.1.8/speakeasyR/src/se2/src/speakeasy2/se2_partitions.h | 9 speakeasyR-0.1.8/speakeasyR/src/se2/src/speakeasy2/se2_random.c | 10 speakeasyR-0.1.8/speakeasyR/src/se2/src/speakeasy2/se2_random.h | 3 speakeasyR-0.1.8/speakeasyR/src/se2/src/speakeasy2/se2_reweigh_graph.c | 58 speakeasyR-0.1.8/speakeasyR/src/se2/src/speakeasy2/se2_reweigh_graph.h | 2 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/CMakeLists.txt | 1 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/CHANGELOG.md | 2243 +++--- speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/CONTRIBUTING.md | 26 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/CONTRIBUTORS.md | 16 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/CONTRIBUTORS.txt | 10 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/README.md | 6 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/VERSIONING.md |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/codecov.yml | 1 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph.h | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_adjlist.h | 65 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_arpack.h | 85 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_attributes.h | 396 - speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_bipartite.h | 100 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_bitset.h | 49 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_bitset_list.h | 13 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_blas.h | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_centrality.h | 193 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_cliques.h | 147 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_cocitation.h | 33 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_cohesive_blocks.h | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_coloring.h | 38 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_community.h | 123 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_complex.h | 23 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_components.h | 43 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_config.h.in | 14 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_constants.h | 149 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_constructors.h | 76 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_conversion.h | 23 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_cycles.h | 66 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_datatype.h | 19 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_decls.h | 29 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_dqueue.h | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_dqueue_pmt.h | 18 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_eigen.h | 61 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_embedding.h | 21 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_epidemics.h | 17 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_error.h | 128 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_eulerian.h | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_flow.h | 67 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_foreign.h | 35 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_games.h | 174 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_graph_list.h | 17 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_graphicality.h | 32 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_graphlets.h | 19 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_heap.h | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_heap_pmt.h | 20 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_hrg.h | 32 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_interface.h | 98 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_interrupt.h | 29 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_isomorphism.h |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_iterators.h | 99 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_lapack.h | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_layout.h | 79 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_lsap.h | 23 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_matching.h | 16 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_matrix.h | 18 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_matrix_list.h | 14 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_matrix_pmt.h | 92 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_memory.h | 23 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_mixing.h | 42 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_motifs.h | 41 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_neighborhood.h | 27 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_nongraph.h | 36 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_operators.h | 65 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_paths.h | 293 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_pmt.h | 21 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_pmt_off.h | 11 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_progress.h | 57 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_psumtree.h | 29 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_qsort.h | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_random.h | 54 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_reachability.h | 10 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_sampling.h |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_scan.h | 19 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_separators.h | 20 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_setup.h |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_sparsemat.h | 91 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_spatial.h |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_stack.h | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_stack_pmt.h | 19 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_statusbar.h | 38 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_structural.h | 88 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_strvector.h | 63 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_threading.h.in | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_transitivity.h | 23 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_typed_list_pmt.h | 45 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_types.h | 36 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_vector.h | 43 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_vector_list.h | 14 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_vector_pmt.h | 98 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_vector_ptr.h | 41 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_vector_type.h | 11 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_version.h.in | 17 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/include/igraph_visitor.h | 35 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/community_internal.h |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/community_misc.c | 263 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/edge_betweenness.c | 270 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/fast_modularity.c | 110 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/fluid.c | 67 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/infomap.cpp |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/label_propagation.c | 727 +- speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/leading_eigenvector.c | 195 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/leiden.c | 1191 ++- speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/louvain.c | 98 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/modularity.c | 89 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/optimal_modularity.c | 44 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/spinglass/NetDataTypes.cpp | 9 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/spinglass/NetDataTypes.h | 89 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/spinglass/NetRoutines.cpp | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/spinglass/NetRoutines.h | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/spinglass/clustertool.cpp | 53 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/spinglass/pottsmodel_2.cpp | 177 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/spinglass/pottsmodel_2.h | 41 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/voronoi.c | 63 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/walktrap/walktrap.cpp | 13 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/walktrap/walktrap_communities.cpp | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/walktrap/walktrap_communities.h | 5 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/walktrap/walktrap_graph.cpp | 9 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/walktrap/walktrap_graph.h | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/walktrap/walktrap_heap.cpp | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/community/walktrap/walktrap_heap.h | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/config.h.in | 1 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/adjacency.c | 533 - speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/atlas-edges.h | 17 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/atlas.c | 35 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/basic_constructors.c | 29 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/circulant.c | 14 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/de_bruijn.c | 13 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/famous.c | 77 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/full.c | 75 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/generalized_petersen.c | 8 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/kautz.c | 31 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/lattices.c | 96 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/lcf.c | 74 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/linegraph.c | 39 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/mycielskian.c |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/prufer.c | 15 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/regular.c | 198 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/constructors/trees.c | 14 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/bitset.c | 162 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/bitset_list.c | 2 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/buckets.c | 47 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/buckets.h | 39 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/cutheap.c | 35 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/cutheap.h | 21 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/dqueue.c | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/dqueue.pmt | 25 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/error.c | 121 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/estack.c | 17 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/estack.h | 17 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/fixed_vectorlist.c | 7 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/fixed_vectorlist.h | 11 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/genheap.c | 44 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/genheap.h | 22 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/grid.c | 38 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/grid.h | 31 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/heap.c | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/heap.pmt | 41 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/indheap.c | 273 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/indheap.h | 65 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/interruption.c | 11 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/interruption.h | 18 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/marked_queue.c | 19 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/marked_queue.h | 19 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/math.h | 2 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/matrix.c | 48 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/matrix.pmt | 368 - speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/matrix_list.c | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/memory.c | 2 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/printing.c | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/progress.c | 21 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/psumtree.c | 19 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/set.c | 38 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/set.h | 26 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/setup.c |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/sparsemat.c | 554 - speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/stack.c | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/stack.pmt | 21 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/statusbar.c | 25 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/strvector.c | 233 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/trie.c | 29 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/trie.h | 21 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/typed_list.pmt | 108 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/vector.c | 211 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/vector.pmt | 605 - speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/vector_list.c | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/core/vector_ptr.c | 157 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/cycles/cycle_bases.c |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/cycles/feedback_sets.c |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/cycles/feedback_sets.h |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/cycles/order_cycle.cpp |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/cycles/order_cycle.h |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/cycles/simple_cycles.c | 291 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/adjlist.c | 318 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/attributes.c | 644 + speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/attributes.h | 42 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/basic_query.c | 38 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/caching.c | 2 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/caching.h | 6 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/cattributes.c | 3373 ++-------- speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/graph_list.c | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/internal.h | 16 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/iterators.c | 311 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/type_common.c | 80 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/type_indexededgelist.c | 589 + speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/graph/visitors.c | 75 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/internal/glpk_support.c | 27 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/internal/glpk_support.h | 16 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/internal/gmp_internal.h | 4 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/internal/hacks.c | 3 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/internal/hacks.h | 7 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/internal/lsap.c | 112 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/internal/utils.c | 143 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/internal/utils.h | 9 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/linalg/arpack.c | 296 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/linalg/arpack_internal.h | 7 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/linalg/blas.c | 13 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/linalg/blas_internal.h | 8 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/linalg/eigen.c | 52 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/linalg/lapack.c | 97 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/linalg/lapack_internal.h | 8 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/math/complex.c | 17 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/math/safe_intop.c | 52 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/math/safe_intop.h | 46 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/math/utils.c | 23 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/basic_properties.c | 92 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/complete.c | 39 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/constraint.c | 32 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/convergence_degree.c | 20 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/dag.c | 155 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/degrees.c | 174 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/ecc.c | 58 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/girth.c | 30 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/loops.c | 23 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/multiplicity.c | 114 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/neighborhood.c | 102 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/perfect.c | 25 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/properties/properties_internal.h | 7 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speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/random/rng_pcg64.c | 2 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/random/sampling.c |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/spatial |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/src/version.c | 28 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/vendor/cs/cs.h | 4 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/vendor/cs/cs_randperm.c | 2 speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/vendor/infomap |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/vendor/nanoflann |only speakeasyR-0.1.8/speakeasyR/src/se2/vendor/igraph/vendor/qhull |only speakeasyR-0.1.8/speakeasyR/src/speakeasyR.c | 392 - speakeasyR-0.1.8/speakeasyR/tests/testthat/test-cluster.R | 7 speakeasyR-0.1.8/speakeasyR/tools/config.guess | 11 speakeasyR-0.1.8/speakeasyR/tools/config.sub | 29 298 files changed, 12553 insertions(+), 12816 deletions(-)
Title: Summarise and Visualise Characteristics of Patients in the OMOP
CDM
Description: Summarise and visualise the characteristics of patients in data
mapped to the Observational Medical Outcomes Partnership (OMOP) common data
model (CDM).
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [ctb] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between CohortCharacteristics versions 1.0.0 dated 2025-05-20 and 1.0.1 dated 2025-09-30
DESCRIPTION | 12 MD5 | 206 - NAMESPACE | 2 NEWS.md | 24 R/benchmarkCohortCharacteristics.R | 12 R/plotCharacteristics.R | 1 R/plotCohortAttrition.R | 1 R/plotCohortCount.R | 1 R/plotCohortOverlap.R | 1 R/plotCohortTiming.R | 8 R/plotComparedLargeScaleCharacteristics.R | 5 R/plotLargeScaleCharacteristics.R | 6 R/reexports.R | 6 R/summariseCharacteristics.R | 12 R/summariseCohortAttrition.R | 1 R/summariseCohortCodelist.R | 18 R/summariseCohortCount.R | 1 R/summariseCohortOverlap.R | 1 R/summariseCohortTiming.R | 9 R/summariseLargeScaleCharacteristics.R | 47 R/table.R | 2 R/tableCharacteristics.R | 1 R/tableCohortAttrition.R | 1 R/tableCohortCount.R | 1 R/tableCohortOverlap.R | 1 R/tableCohortTiming.R | 6 R/tableLargeScaleCharacteristics.R | 14 README.md | 7 inst/doc/summarise_characteristics.R | 9 inst/doc/summarise_characteristics.Rmd | 9 inst/doc/summarise_characteristics.html | 2120 +++++++-------- inst/doc/summarise_cohort_overlap.R | 9 inst/doc/summarise_cohort_overlap.Rmd | 9 inst/doc/summarise_cohort_overlap.html | 609 ++-- inst/doc/summarise_cohort_timing.R | 9 inst/doc/summarise_cohort_timing.Rmd | 9 inst/doc/summarise_cohort_timing.html | 687 ++-- inst/doc/summarise_large_scale_characteristics.R | 9 inst/doc/summarise_large_scale_characteristics.Rmd | 9 inst/doc/summarise_large_scale_characteristics.html | 285 -- man/availablePlotColumns.Rd | 1 man/availableTableColumns.Rd | 1 man/benchmarkCohortCharacteristics.Rd | 12 man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-16-1.png |binary man/figures/README-unnamed-chunk-19-1.png |binary man/figures/README-unnamed-chunk-20-1.png |binary man/figures/README-unnamed-chunk-21-1.png |binary man/figures/README-unnamed-chunk-23-1.png |binary man/figures/README-unnamed-chunk-24-1.png |binary man/figures/README-unnamed-chunk-26-1.png |binary man/figures/README-unnamed-chunk-27-1.png |binary man/figures/README-unnamed-chunk-28-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/mockCohortCharacteristics.Rd | 2 man/plotCharacteristics.Rd | 1 man/plotCohortAttrition.Rd | 1 man/plotCohortCount.Rd | 1 man/plotCohortOverlap.Rd | 1 man/plotCohortTiming.Rd | 8 man/plotComparedLargeScaleCharacteristics.Rd | 5 man/plotLargeScaleCharacteristics.Rd | 6 man/reexports.Rd | 3 man/summariseCharacteristics.Rd | 1 man/summariseCohortAttrition.Rd | 1 man/summariseCohortCodelist.Rd | 9 man/summariseCohortCount.Rd | 1 man/summariseCohortOverlap.Rd | 1 man/summariseCohortTiming.Rd | 1 man/summariseLargeScaleCharacteristics.Rd | 6 man/tableCharacteristics.Rd | 1 man/tableCohortAttrition.Rd | 1 man/tableCohortCodelist.Rd | 9 man/tableCohortCount.Rd | 1 man/tableCohortOverlap.Rd | 1 man/tableCohortTiming.Rd | 6 man/tableLargeScaleCharacteristics.Rd | 6 man/tableTopLargeScaleCharacteristics.Rd | 8 tests/testthat/setup.R | 83 tests/testthat/test-benchmarkCohortCharacteristics.R | 15 tests/testthat/test-plotCharacteristics.R | 22 tests/testthat/test-plotCohortAttrition.R | 5 tests/testthat/test-plotCohortCount.R | 5 tests/testthat/test-plotCohortOverlap.R | 7 tests/testthat/test-plotCohortTiming.R | 20 tests/testthat/test-plotLargeScaleCharacteristics.R | 26 tests/testthat/test-summariseCharacteristics.R | 109 tests/testthat/test-summariseCohortAttrition.R | 5 tests/testthat/test-summariseCohortCodelist.R | 15 tests/testthat/test-summariseCohortCount.R | 12 tests/testthat/test-summariseCohortOverlap.R | 36 tests/testthat/test-summariseCohortTiming.R | 43 tests/testthat/test-summariseLargeScaleCharacteristics.R | 37 tests/testthat/test-table.R | 5 tests/testthat/test-tableCharacteristics.R | 12 tests/testthat/test-tableCohortAttrition.R | 5 tests/testthat/test-tableCohortCount.R | 5 tests/testthat/test-tableCohortOverlap.R | 7 tests/testthat/test-tableCohortTiming.R | 9 tests/testthat/test-tableLargeScaleCharacteristics.R | 26 vignettes/summarise_characteristics.Rmd | 9 vignettes/summarise_cohort_overlap.Rmd | 9 vignettes/summarise_cohort_timing.Rmd | 9 vignettes/summarise_large_scale_characteristics.Rmd | 9 104 files changed, 2366 insertions(+), 2454 deletions(-)
More information about CohortCharacteristics at CRAN
Permanent link
Title: Streamlining Complex Survey Estimation and Reliability
Assessment in R
Description: Short and understandable commands that generate tabulated,
formatted, and rounded survey estimates. Mostly a wrapper for the
'survey' package (Lumley (2004) <doi:10.18637/jss.v009.i08>
<https://CRAN.R-project.org/package=survey>) that identifies
low-precision estimates using the National Center for Health
Statistics (NCHS) presentation standards (Parker et al. (2017)
<https://www.cdc.gov/nchs/data/series/sr_02/sr02_175.pdf>,
Parker et al. (2023) <doi:10.15620/cdc:124368>).
Author: Alex Strashny [aut, cre]
Maintainer: Alex Strashny <alex.strashny@gmail.com>
Diff between surveytable versions 0.9.9 dated 2025-08-25 and 0.9.10 dated 2025-09-30
DESCRIPTION | 6 MD5 | 44 NEWS.md | 4 R/set_opts.R | 446 ++-- R/z_print_csv.R | 96 - R/z_print_excel.R | 302 +-- R/z_print_gt.R | 107 - R/z_print_huxtable.R | 129 - R/z_print_kableExtra.R | 187 + R/z_print_raw.R | 67 README.md | 4 inst/doc/Example-National-Ambulatory-Medical-Care-Survey-NAMCS-tables.html | 92 inst/doc/Example-Residential-Care-Community-Services-User-NSLTCP-RCC-SU-report.html | 72 inst/doc/Printing-HTML.html | 254 +- inst/doc/Printing-PDF.pdf |binary inst/doc/Tips-tricks.R | 3 inst/doc/Tips-tricks.Rmd | 15 inst/doc/Tips-tricks.html | 38 inst/doc/surveytable.R | 3 inst/doc/surveytable.Rmd | 948 +++++----- inst/doc/surveytable.html | 134 - vignettes/Tips-tricks.Rmd | 15 vignettes/surveytable.Rmd | 948 +++++----- 23 files changed, 1971 insertions(+), 1943 deletions(-)
Title: Bayesian Modeling: Estimate a Computer Model and Make Uncertain
Predictions
Description: An interface to the 'BaM' (Bayesian Modeling) engine,
a 'Fortran'-based executable aimed at estimating a model
with a Bayesian approach and using it for prediction,
with a particular focus on uncertainty quantification.
Classes are defined for the various building blocks of
'BaM' inference (model, data, error models, Markov Chain Monte Carlo (MCMC) samplers, predictions).
The typical usage is as follows:
(1) specify the model to be estimated;
(2) specify the inference setting (dataset, parameters, error models...);
(3) perform Bayesian-MCMC inference;
(4) read, analyse and use MCMC samples;
(5) perform prediction experiments.
Technical details are available (in French) in
Renard (2017) <https://hal.science/hal-02606929v1>.
Examples of applications include
Mansanarez et al. (2019) <doi:10.1029/2018WR023389>,
Le Coz et al. (2021) <doi:10.1002/hyp.14169>,
Perret et al. (2021) <doi:10.1029/2020WR027745>,
Darienzo et al. (2021) <doi:10.1029/2020WR028607> and
Pe [...truncated...]
Author: Benjamin Renard [aut, cre, cph] ,
INRAE [fnd],
Ministere de la Transition Ecologique - SCHAPI [fnd]
Maintainer: Benjamin Renard <benjamin.renard@inrae.fr>
Diff between RBaM versions 1.0.1 dated 2025-07-10 and 1.1.1 dated 2025-09-30
RBaM-1.0.1/RBaM/man/readme/README-unnamed-chunk-10-1.png |only RBaM-1.0.1/RBaM/man/readme/README-unnamed-chunk-12-1.png |only RBaM-1.0.1/RBaM/man/readme/README-unnamed-chunk-13-1.png |only RBaM-1.0.1/RBaM/man/readme/README-unnamed-chunk-8-1.png |only RBaM-1.0.1/RBaM/man/readme/README-unnamed-chunk-9-1.png |only RBaM-1.1.1/RBaM/DESCRIPTION | 10 - RBaM-1.1.1/RBaM/MD5 | 55 ++++-- RBaM-1.1.1/RBaM/NAMESPACE | 22 ++ RBaM-1.1.1/RBaM/NEWS.md | 14 + RBaM-1.1.1/RBaM/R/MCMC.R |only RBaM-1.1.1/RBaM/R/RUI.R | 118 ++++++++++++++- RBaM-1.1.1/RBaM/R/RUI_modelSpecific.R | 31 +++ RBaM-1.1.1/RBaM/R/class_parameter.R | 39 ++++ RBaM-1.1.1/RBaM/R/inferenceFunk.R |only RBaM-1.1.1/RBaM/R/utilities_SPD.R |only RBaM-1.1.1/RBaM/R/utilities_private.R | 21 +- RBaM-1.1.1/RBaM/R/utilities_public.R | 21 ++ RBaM-1.1.1/RBaM/R/zzz.R | 15 + RBaM-1.1.1/RBaM/README.md | 56 +++++-- RBaM-1.1.1/RBaM/inst/bin/README.md | 2 RBaM-1.1.1/RBaM/man/BaM.Rd | 7 RBaM-1.1.1/RBaM/man/MCMC_AM.Rd |only RBaM-1.1.1/RBaM/man/MCMC_OAAT.Rd |only RBaM-1.1.1/RBaM/man/SPD_estimate.Rd |only RBaM-1.1.1/RBaM/man/SPD_getVARproperties.Rd |only RBaM-1.1.1/RBaM/man/applyMetropolisRule.Rd |only RBaM-1.1.1/RBaM/man/blocDiag.Rd |only RBaM-1.1.1/RBaM/man/getComponents.Rd |only RBaM-1.1.1/RBaM/man/getInitPar.Rd |only RBaM-1.1.1/RBaM/man/llfunk_iLinear_Gaussian.Rd |only RBaM-1.1.1/RBaM/man/llfunk_iid_Gaussian.Rd |only RBaM-1.1.1/RBaM/man/logLikelihood_BaM.Rd |only RBaM-1.1.1/RBaM/man/logPosterior_BaM.Rd |only RBaM-1.1.1/RBaM/man/logPosterior_BaM_wrapped.Rd |only RBaM-1.1.1/RBaM/man/logPrior_Flat.Rd |only RBaM-1.1.1/RBaM/man/readme/README-RC_env-1.png |only RBaM-1.1.1/RBaM/man/readme/README-RC_spag-1.png |only RBaM-1.1.1/RBaM/man/readme/README-densityPlot-1.png |only RBaM-1.1.1/RBaM/man/readme/README-tracePlot-1.png |only RBaM-1.1.1/RBaM/man/readme/README-violinPlot-1.png |only RBaM-1.1.1/RBaM/man/runExe.Rd | 15 + RBaM-1.1.1/RBaM/man/runModel.Rd |only RBaM-1.1.1/RBaM/man/setInitPar.Rd |only 43 files changed, 373 insertions(+), 53 deletions(-)
Title: Data Analysis for Censored Environmental Data
Description: Contains methods described by Dennis Helsel in
his book "Statistics for Censored Environmental Data
using Minitab and R" (2011) and courses and videos at
<https://practicalstats.com>. This package incorporates functions
of NADA and adds new functionality.
Author: Paul Julian [aut, cre],
Dennis Helsel [aut, cph],
Lopaka Lee [aut, cph]
Maintainer: Paul Julian <pauljulianphd@gmail.com>
Diff between NADA2 versions 2.0.0 dated 2025-09-23 and 2.0.1 dated 2025-09-30
DESCRIPTION | 8 +-- MD5 | 12 ++--- R/NADA_ros.R | 118 +++++++++++++++++++++++++++++++----------------------- R/cboxplot.R | 65 +++++++++++++++++++++-------- R/equivalent_n.R | 12 +++++ build/partial.rdb |binary man/cboxplot.Rd | 5 +- 7 files changed, 141 insertions(+), 79 deletions(-)
Title: Stepwise Regression Analysis
Description: Stepwise regression is a statistical technique used for model selection. This package streamlines stepwise regression analysis by supporting multiple regression types(linear, Cox, logistic, Poisson, Gamma, and negative binomial), incorporating popular selection strategies(forward, backward, bidirectional, and subset), and offering essential metrics. It enables users to apply multiple selection strategies and metrics in a single function call, visualize variable selection processes, and export results in various formats. StepReg offers a data-splitting option to address potential issues with invalid statistical inference and a randomized forward selection option to avoid overfitting. We validated StepReg's accuracy using public datasets within the SAS software environment. Additionally, StepReg features an interactive Shiny application to enhance usability and accessibility.
Author: Junhui Li [cre] ,
Junhui Li [aut],
Kai Hu [aut],
Xiaohuan Lu [aut],
Sushmita N Nayak [ctb],
Cesar Bautista Sotelo [ctb],
Michael A Lodato [ctb],
Wenxin Liu [aut],
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <junhui.li11@umassmed.edu>
Diff between StepReg versions 1.5.8 dated 2025-02-07 and 1.6.0 dated 2025-09-30
StepReg-1.5.8/StepReg/R/CreditCard.R |only StepReg-1.5.8/StepReg/R/vote.R |only StepReg-1.5.8/StepReg/man/vote.Rd |only StepReg-1.5.8/StepReg/vignettes/src/StepReg_shiny_UI_description_Analyze.png |only StepReg-1.5.8/StepReg/vignettes/src/StepReg_shiny_UI_description_File.png |only StepReg-1.6.0/StepReg/DESCRIPTION | 16 StepReg-1.6.0/StepReg/MD5 | 76 StepReg-1.6.0/StepReg/NAMESPACE | 11 StepReg-1.6.0/StepReg/NEWS.md |only StepReg-1.6.0/StepReg/R/StepRegShinyApp.R | 66 StepReg-1.6.0/StepReg/R/affairs.R |only StepReg-1.6.0/StepReg/R/creditCard.R |only StepReg-1.6.0/StepReg/R/lung.R |only StepReg-1.6.0/StepReg/R/performance.R |only StepReg-1.6.0/StepReg/R/plot.StepReg.R | 109 StepReg-1.6.0/StepReg/R/print.StepReg.R | 40 StepReg-1.6.0/StepReg/R/remission.R | 74 StepReg-1.6.0/StepReg/R/report.R | 78 StepReg-1.6.0/StepReg/R/stepwise.R | 356 +- StepReg-1.6.0/StepReg/R/stepwiseUtils.R | 1508 +++++----- StepReg-1.6.0/StepReg/R/tobacco.R | 58 StepReg-1.6.0/StepReg/R/validateUtils.R | 32 StepReg-1.6.0/StepReg/README.md | 114 StepReg-1.6.0/StepReg/data/affairs.RData |only StepReg-1.6.0/StepReg/data/lung.RData |only StepReg-1.6.0/StepReg/inst/doc/StepReg.R | 136 StepReg-1.6.0/StepReg/inst/doc/StepReg.Rmd | 289 + StepReg-1.6.0/StepReg/inst/doc/StepReg.html | 924 ++++-- StepReg-1.6.0/StepReg/inst/shiny/rsconnect/shinyapps.io/junhuili1017/StepReg.dcf |only StepReg-1.6.0/StepReg/inst/shiny/rsconnect/shinyapps.io/junhuili1017/shiny.dcf | 2 StepReg-1.6.0/StepReg/inst/shiny/server.R | 344 +- StepReg-1.6.0/StepReg/inst/shiny/ui.R | 381 ++ StepReg-1.6.0/StepReg/man/StepReg-package.Rd | 3 StepReg-1.6.0/StepReg/man/StepRegShinyApp.Rd | 68 StepReg-1.6.0/StepReg/man/affairs.Rd |only StepReg-1.6.0/StepReg/man/creditCard.Rd | 49 StepReg-1.6.0/StepReg/man/figures/logo.png |binary StepReg-1.6.0/StepReg/man/lung.Rd |only StepReg-1.6.0/StepReg/man/performance.Rd |only StepReg-1.6.0/StepReg/man/plot.StepReg.Rd | 83 StepReg-1.6.0/StepReg/man/print.StepReg.Rd | 45 StepReg-1.6.0/StepReg/man/remission.Rd | 62 StepReg-1.6.0/StepReg/man/report.Rd | 67 StepReg-1.6.0/StepReg/man/stepwise.Rd | 277 + StepReg-1.6.0/StepReg/man/tobacco.Rd | 52 StepReg-1.6.0/StepReg/vignettes/StepReg.Rmd | 289 + StepReg-1.6.0/StepReg/vignettes/src/StepReg_shiny_UI_description_Data.png |only StepReg-1.6.0/StepReg/vignettes/src/StepReg_shiny_UI_description_Stepwise.png |only 48 files changed, 4005 insertions(+), 1604 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS
and Linux for finding font files that can then be used further by e.g.
graphic devices. The main use is intended to be from compiled code but
'systemfonts' also provides access from R.
Author: Thomas Lin Pedersen [aut, cre] ,
Jeroen Ooms [aut] ,
Devon Govett [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between systemfonts versions 1.2.3 dated 2025-04-30 and 1.3.0 dated 2025-09-30
DESCRIPTION | 9 - MD5 | 135 ++++++++++-------- NAMESPACE | 12 + NEWS.md | 31 ++++ R/cpp11.R | 36 +++-- R/font_fallback.R | 26 ++- R/font_feature.R | 4 R/font_info.R | 105 ++++++++++++-- R/font_outline.R | 193 ++++++++++++++++++++++++++- R/font_variation.R |only R/match_fonts.R | 34 ---- R/register_font.R | 58 +++++--- R/shape_string.R | 54 +++++-- R/web_fonts.R | 237 ++++++++++++++++++++++++++++----- R/zzz.R | 14 + README.md | 35 ++-- build/vignette.rds |binary inst/doc/c_interface.Rmd | 226 ++++++++++++------------------- inst/doc/c_interface.html | 263 +++++++++++++++---------------------- inst/doc/fonts_basics.R |only inst/doc/fonts_basics.Rmd |only inst/doc/fonts_basics.html |only inst/doc/systemfonts.R |only inst/doc/systemfonts.Rmd |only inst/doc/systemfonts.html |only inst/include/systemfonts-ft.h | 26 +++ inst/include/systemfonts.h | 123 +++++++++++++++++ man/add_fonts.Rd | 2 man/figures/logo.png |only man/font_fallback.Rd | 26 +++ man/font_feature.Rd | 4 man/font_info.Rd | 29 +++- man/font_variation.Rd |only man/fonts_as_import.Rd | 15 +- man/glyph_info.Rd | 26 +++ man/glyph_outline.Rd | 4 man/glyph_raster.Rd | 4 man/plot_glyph_stats.Rd |only man/require_font.Rd | 9 - man/search_web_fonts.Rd | 7 man/shape_string.Rd | 26 ++- man/string_width.Rd | 24 ++- man/systemfonts-package.Rd | 2 src/FontDescriptor.h | 68 ++++++++- src/Makevars.in | 2 src/Makevars.win | 2 src/cache_store.cpp | 32 +++- src/cache_store.h | 2 src/caches.cpp | 8 - src/cpp11.cpp | 78 +++++++--- src/font_fallback.cpp | 32 +++- src/font_fallback.h | 4 src/font_local.cpp | 35 +--- src/font_matching.cpp | 195 +++++++++++++++++++-------- src/font_matching.h | 11 - src/font_metrics.cpp | 147 +++++++++++++++----- src/font_metrics.h | 11 + src/font_outlines.cpp | 88 +++++++++--- src/font_outlines.h | 5 src/font_registry.cpp | 20 +- src/font_variation.cpp |only src/font_variation.h |only src/ft_cache.cpp | 240 +++++++++++++++++++++++++++++++++ src/ft_cache.h | 34 ++++ src/init.cpp | 1 src/mac/FontManagerMac.mm | 53 +++++-- src/types.h | 31 +++- src/unix/FontManagerLinux.cpp | 51 +++++-- src/utils.h | 21 ++ src/win/FontManagerWindows.cpp | 13 + tests/testthat/test-match_font.R | 10 - tests/testthat/test-system_fonts.R | 3 vignettes/c_interface.Rmd | 226 ++++++++++++------------------- vignettes/fonts_basics.Rmd |only vignettes/systemfonts.Rmd |only vignettes/text_call_flow.svg |only 76 files changed, 2301 insertions(+), 921 deletions(-)
Title: Miscellaneous Functions for Metabarcoding Analysis
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Author: Adrien Taudiere [aut, cre, cph]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
Diff between MiscMetabar versions 0.14.3 dated 2025-06-21 and 0.14.4 dated 2025-09-30
DESCRIPTION | 20 +- MD5 | 271 ++++++++++++++++---------------- NAMESPACE | 1 NEWS.md | 27 +++ R/Deseq2_edgeR.R | 4 R/MiscMetabar-package.R | 3 R/alpha_div_test.R | 4 R/beta_div_test.R | 52 +++--- R/blast.R | 26 +-- R/dada_phyloseq.R | 33 +-- R/krona.R | 6 R/miscellanous.R | 4 R/plot_functions.R | 271 ++++++++++++++++++++++++-------- R/speedyseq_functions.R | 3 R/table_functions.R | 2 R/vsearch.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 27 +-- inst/doc/MiscMetabar.R | 4 inst/doc/MiscMetabar.Rmd | 4 inst/doc/MiscMetabar.html | 125 +++++++------- man/LCBD_pq.Rd | 2 man/SRS_curve_pq.Rd | 2 man/accu_plot.Rd | 2 man/accu_plot_balanced_modality.Rd | 2 man/add_blast_info.Rd | 2 man/add_dna_to_phyloseq.Rd | 2 man/add_funguild_info.Rd | 2 man/add_info_to_sam_data.Rd | 2 man/add_new_taxonomy_pq.Rd | 2 man/adonis_pq.Rd | 2 man/adonis_rarperm_pq.Rd | 2 man/ancombc_pq.Rd | 2 man/are_modality_even_depth.Rd | 4 man/as_binary_otu_table.Rd | 2 man/assign_blastn.Rd | 2 man/assign_dada2.Rd | 2 man/assign_idtaxa.Rd | 2 man/assign_sintax.Rd | 4 man/assign_vsearch_lca.Rd | 4 man/biplot_pq.Rd | 2 man/blast_pq.Rd | 2 man/blast_to_phyloseq.Rd | 2 man/build_phytree_pq.Rd | 4 man/chimera_detection_vs.Rd | 2 man/chimera_removal_vs.Rd | 2 man/circle_pq.Rd | 4 man/clean_pq.Rd | 2 man/compare_pairs_pq.Rd | 2 man/count_seq.Rd | 2 man/cutadapt_remove_primers.Rd | 2 man/dist_pos_control.Rd | 2 man/distri_1_taxa.Rd | 4 man/filt_taxa_pq.Rd | 2 man/filt_taxa_wo_NA.Rd | 2 man/filter_asv_blast.Rd | 2 man/formattable_pq.Rd | 2 man/get_file_extension.Rd | 2 man/ggaluv_pq.Rd | 2 man/ggbetween_pq.Rd | 4 man/ggscatt_pq.Rd | 2 man/ggvenn_pq.Rd | 4 man/glmutli_pq.Rd | 2 man/graph_test_pq.Rd | 2 man/hill_curves_pq.Rd | 2 man/hill_pq.Rd | 4 man/hill_test_rarperm_pq.Rd | 2 man/hill_tuckey_pq.Rd | 2 man/iNEXT_pq.Rd | 2 man/krona.Rd | 8 man/lulu_pq.Rd | 4 man/merge_krona.Rd | 2 man/merge_taxa_vec.Rd | 3 man/multi_biplot_pq.Rd | 2 man/multipatt_pq.Rd | 4 man/multitax_bar_pq.Rd | 2 man/mumu_pq.Rd | 4 man/normalize_prop_pq.Rd | 2 man/perc.Rd | 2 man/phyloseq_to_edgeR.Rd | 2 man/physeq_or_string_to_dna.Rd | 2 man/plot_LCBD_pq.Rd | 2 man/plot_SCBD_pq.Rd | 2 man/plot_ancombc_pq.Rd | 2 man/plot_complexity_pq.Rd | 2 man/plot_edgeR_pq.Rd | 8 man/plot_guild_pq.Rd | 2 man/plot_mt.Rd | 4 man/plot_refseq_extremity_pq.Rd | 2 man/plot_refseq_pq.Rd | 2 man/plot_seq_ratio_pq.Rd |only man/plot_tax_pq.Rd | 4 man/plot_tsne_pq.Rd | 4 man/postcluster_pq.Rd | 2 man/psmelt_samples_pq.Rd | 2 man/rarefy_sample_count_by_modality.Rd | 4 man/rename_samples_otu_table.Rd | 2 man/reorder_taxa_pq.Rd | 4 man/ridges_pq.Rd | 2 man/rotl_pq.Rd | 39 +++- man/sankey_pq.Rd | 2 man/save_pq.Rd | 4 man/search_exact_seq_pq.Rd | 2 man/select_one_sample.Rd | 2 man/simplify_taxo.Rd | 2 man/subset_samples_pq.Rd | 2 man/subset_taxa_pq.Rd | 2 man/subset_taxa_tax_control.Rd | 2 man/summary_plot_pq.Rd | 2 man/swarm_clustering.Rd | 8 man/tax_bar_pq.Rd | 2 man/tax_datatable.Rd | 6 man/taxa_as_columns.Rd | 2 man/taxa_as_rows.Rd | 2 man/taxa_only_in_one_level.Rd | 2 man/tbl_sum_samdata.Rd | 2 man/tbl_sum_taxtable.Rd | 2 man/track_wkflow.Rd | 2 man/track_wkflow_samples.Rd | 4 man/treemap_pq.Rd | 2 man/tsne_pq.Rd | 4 man/umap_pq.Rd | 2 man/upset_pq.Rd | 8 man/upset_test_pq.Rd | 7 man/var_par_pq.Rd | 2 man/var_par_rarperm_pq.Rd | 2 man/venn_pq.Rd | 8 man/verify_pq.Rd | 2 man/vs_search_global.Rd | 4 man/vsearch_clustering.Rd | 4 man/write_pq.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test_figures_alpha_div.R | 6 tests/testthat/test_figures_beta_div.R | 32 +-- tests/testthat/test_figures_misc.R | 2 vignettes/MiscMetabar.Rmd | 4 137 files changed, 739 insertions(+), 533 deletions(-)
Title: Extracts the Backbone from Networks
Description: An implementation of methods for extracting a sparse unweighted network (i.e. a backbone)
from an unweighted network (e.g., Hamann et al., 2016 <doi:10.1007/s13278-016-0332-2>), a weighted network
(e.g., Serrano et al., 2009 <doi:10.1073/pnas.0808904106>), or a weighted projection (e.g., Neal et al., 2021
<doi:10.1038/s41598-021-03238-3>).
Author: Zachary Neal [aut, cre] ,
Rachel Domagalski [ctb],
Bruce Sagan [ctb],
Karl Godard [ctb]
Maintainer: Zachary Neal <zpneal@msu.edu>
Diff between backbone versions 3.0.0 dated 2025-09-15 and 3.0.1 dated 2025-09-30
DESCRIPTION | 6 MD5 | 72 +- NAMESPACE | 2 NEWS.md | 9 R/backbone.R | 68 +- R/backbone_from_projection.R | 77 -- R/backbone_from_unweighted.R | 80 -- R/backbone_from_weighted.R | 67 -- R/depricated.R | 8 R/functions_projection.R | 29 R/functions_weighted.R | 4 R/senate108.R | 2 R/utils.R | 190 +++++ inst/doc/backbone.R | 17 inst/doc/backbone.Rmd | 48 - inst/doc/backbone.html | 344 +++++----- inst/doc/senate.html | 20 inst/doc/unit_tests.R | 180 +++-- inst/doc/unit_tests.Rmd | 192 ++++- inst/doc/unit_tests.html | 1340 ++++++++++++++++++++++------------------ inst/tinytest/test_backbone.R | 179 +++-- man/backbone.Rd | 62 + man/backbone_from_projection.Rd | 18 man/backbone_from_unweighted.Rd | 12 man/backbone_from_weighted.Rd | 14 man/bicm.Rd | 2 man/disparity.Rd | 1 man/fdsm.Rd | 1 man/fixedcol.Rd | 1 man/fixedfill.Rd | 1 man/fixedrow.Rd | 1 man/lans.Rd | 1 man/mlf.Rd | 1 man/sdsm.Rd | 1 man/senate108.Rd | 2 vignettes/backbone.Rmd | 48 - vignettes/unit_tests.Rmd | 192 ++++- 37 files changed, 1972 insertions(+), 1320 deletions(-)
Title: A Code Generator for ODE-Based Models
Description: Provides an R6 class and several utility methods to
facilitate the implementation of models based on ordinary
differential equations. The heart of the package is a code generator
that creates compiled 'Fortran' (or 'R') code which can be passed to
a numerical solver. There is direct support for solvers contained
in packages 'deSolve' and 'rootSolve'.
Author: David Kneis [cre, aut]
Maintainer: David Kneis <david.kneis@tu-dresden.de>
Diff between rodeo versions 0.8.2 dated 2024-07-08 and 0.9.2 dated 2025-09-30
rodeo-0.8.2/rodeo/inst/fortran/forcingsGenericMethods.f95 |only rodeo-0.8.2/rodeo/inst/fortran/forcingsInclude.f95 |only rodeo-0.9.2/rodeo/DESCRIPTION | 15 rodeo-0.9.2/rodeo/MD5 | 85 rodeo-0.9.2/rodeo/NAMESPACE | 2 rodeo-0.9.2/rodeo/R/0_package.r | 2 rodeo-0.9.2/rodeo/R/classMethod_compile.r | 9 rodeo-0.9.2/rodeo/R/classMethod_dynamics.r | 4 rodeo-0.9.2/rodeo/R/classMethod_initStepper.r | 2 rodeo-0.9.2/rodeo/R/classMethod_scenarios.r |only rodeo-0.9.2/rodeo/R/classMethods_forcings.r |only rodeo-0.9.2/rodeo/R/plainMethod_buildFromText.r |only rodeo-0.9.2/rodeo/R/plainMethod_buildFromWorkbook.r | 134 - rodeo-0.9.2/rodeo/R/plainMethod_forcingFunctions.r | 407 +++ rodeo-0.9.2/rodeo/build/vignette.rds |binary rodeo-0.9.2/rodeo/data/funs.rda |binary rodeo-0.9.2/rodeo/data/pars.rda |binary rodeo-0.9.2/rodeo/data/pros.rda |binary rodeo-0.9.2/rodeo/data/stoi.rda |binary rodeo-0.9.2/rodeo/data/vars.rda |binary rodeo-0.9.2/rodeo/inst/doc/examples/0D/twoZonesStirredTank/xecute.r | 2 rodeo-0.9.2/rodeo/inst/doc/examples/1D/advectionDispersion/xecute.r | 4 rodeo-0.9.2/rodeo/inst/doc/examples/1D/diffusion/xecute.r | 5 rodeo-0.9.2/rodeo/inst/doc/examples/1D/groundwater/xecute.r | 5 rodeo-0.9.2/rodeo/inst/doc/examples/1D/tetracycline/xecute.r | 2 rodeo-0.9.2/rodeo/inst/doc/examples/linked/waterSediment/xecute_multiObject.r | 4 rodeo-0.9.2/rodeo/inst/doc/examples/linked/waterSediment/xecute_singleObject.r | 4 rodeo-0.9.2/rodeo/inst/doc/rodeoVignette.R | 1049 +++++----- rodeo-0.9.2/rodeo/inst/doc/rodeoVignette.Rmd | 103 rodeo-0.9.2/rodeo/inst/doc/rodeoVignette.pdf |binary rodeo-0.9.2/rodeo/inst/models/SEIR.xlsx |binary rodeo-0.9.2/rodeo/inst/models/SEIR_declarations.txt |only rodeo-0.9.2/rodeo/inst/models/SEIR_equations.txt |only rodeo-0.9.2/rodeo/man/buildFromText.Rd |only rodeo-0.9.2/rodeo/man/buildFromWorkbook.Rd | 63 rodeo-0.9.2/rodeo/man/compile.Rd | 7 rodeo-0.9.2/rodeo/man/dynamics.Rd | 2 rodeo-0.9.2/rodeo/man/forcings_clear.Rd |only rodeo-0.9.2/rodeo/man/forcings_init.Rd |only rodeo-0.9.2/rodeo/man/initStepper.Rd | 2 rodeo-0.9.2/rodeo/man/scenarios.Rd |only rodeo-0.9.2/rodeo/vignettes/examples/0D/twoZonesStirredTank/xecute.r | 2 rodeo-0.9.2/rodeo/vignettes/examples/1D/advectionDispersion/xecute.r | 4 rodeo-0.9.2/rodeo/vignettes/examples/1D/diffusion/xecute.r | 5 rodeo-0.9.2/rodeo/vignettes/examples/1D/groundwater/xecute.r | 5 rodeo-0.9.2/rodeo/vignettes/examples/1D/tetracycline/xecute.r | 2 rodeo-0.9.2/rodeo/vignettes/examples/linked/waterSediment/xecute_multiObject.r | 4 rodeo-0.9.2/rodeo/vignettes/examples/linked/waterSediment/xecute_singleObject.r | 4 rodeo-0.9.2/rodeo/vignettes/rodeoVignette.Rmd | 103 49 files changed, 1343 insertions(+), 698 deletions(-)
Title: Functions for Forest Biometrics
Description: Functions for different purposes related to forest biometrics, including illustrative graphics, numerical computation, modeling height-diameter relationships, prediction of tree volumes, modelling of diameter distributions and estimation off stand density using ITD. Several empirical datasets are also included.
Author: Lauri Mehtatalo [aut, cre],
Kasper Kansanen [aut]
Maintainer: Lauri Mehtatalo <lauri.mehtatalo@luke.fi>
Diff between lmfor versions 1.6 dated 2022-04-29 and 1.7 dated 2025-09-30
DESCRIPTION | 19 +++++++++++++------ MD5 | 44 ++++++++++++++++++++++---------------------- R/lmfor.R | 12 ++++++++---- R/predvff.R | 23 ++++++++++++++++------- build/partial.rdb |binary data/BrkRes.RData |binary data/afterthin.RData |binary data/alsTree.RData |binary data/foto.RData |binary data/ips.RData |binary data/patti.RData |binary data/plants.RData |binary data/plants2.RData |binary data/spati.RData |binary data/spati2.RData |binary data/stumplift.RData |binary data/thefdata.RData |binary data/thinning.RData |binary data/treevol.RData |binary man/fithd.Rd | 6 +++--- man/mywhiskers.Rd | 6 +++++- man/predvff.Rd | 10 +++++++--- man/treevol.Rd | 1 + 23 files changed, 75 insertions(+), 46 deletions(-)
Title: Component-Wise Gradient Boosting after Multiple Imputation
Description: Component-wise gradient boosting for analysis of multiply
imputed datasets. Implements the algorithm Boosting after Multiple
Imputation (MIBoost), which enforces uniform variable selection across
imputations and provides utilities for pooling. Includes a cross-validation
workflow that first splits the data into training and validation sets and
then performs imputation on the training data, applying the learned
imputation models to the validation data to avoid information leakage.
Supports Gaussian and logistic loss. Methods relate to gradient boosting
and multiple imputation as in Buehlmann and Hothorn (2007) <doi:10.1214/07-STS242>,
Friedman (2001) <doi:10.1214/aos/1013203451>, and van Buuren (2018, ISBN:9781138588318)
and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>; see also Kuchen (2025)
<doi:10.48550/arXiv.2507.21807>.
Author: Robert Kuchen [aut, cre]
Maintainer: Robert Kuchen <rokuchen@uni-mainz.de>
Diff between booami versions 0.1.0 dated 2025-09-04 and 0.1.1 dated 2025-09-30
DESCRIPTION | 6 MD5 | 10 R/cv_boost_core.R | 2 R/impu_boos.R | 575 +++++++++++++++++++---------------------------- R/simulate_booami_data.R | 9 man/impu_boost.Rd | 72 ++++- 6 files changed, 307 insertions(+), 367 deletions(-)
Title: Fast Text Tokenization
Description: Interfaces with the 'Hugging Face' tokenizers library to provide implementations
of today's most used tokenizers such as the 'Byte-Pair Encoding' algorithm
<https://huggingface.co/docs/tokenizers/index>. It's extremely fast for both
training new vocabularies and tokenizing texts.
Author: Daniel Falbel [aut, cre],
Regouby Christophe [ctb],
Posit [cph]
Maintainer: Daniel Falbel <daniel@posit.co>
Diff between tok versions 0.2.0 dated 2025-08-27 and 0.2.1 dated 2025-09-30
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/normalizers.R | 4 ++-- R/pre_tokenizers.R | 2 +- README.md | 1 + man/normalizer_nfkc.Rd | 14 +++++++------- man/pre_tokenizer_byte_level.Rd | 14 +++++++------- 8 files changed, 33 insertions(+), 28 deletions(-)
Title: Ising Model for Spatial Data
Description: Performs simulations of binary spatial raster data using
the Ising model (Ising (1925) <doi:10.1007/BF02980577>;
Onsager (1944) <doi:10.1103/PhysRev.65.117>). It allows to set a few
parameters that represent internal and external pressures, and the number
of simulations (Stepinski and Nowosad (2023) <doi:10.1098/rsos.231005>).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between spatialising versions 0.6.0 dated 2023-11-27 and 0.6.2 dated 2025-09-30
spatialising-0.6.0/spatialising/man/figures/README-unnamed-chunk-2-1.png |only spatialising-0.6.0/spatialising/man/figures/README-unnamed-chunk-2-2.png |only spatialising-0.6.0/spatialising/man/figures/README-unnamed-chunk-2-3.png |only spatialising-0.6.0/spatialising/man/figures/README-unnamed-chunk-2-4.png |only spatialising-0.6.0/spatialising/man/figures/README-unnamed-chunk-2-5.png |only spatialising-0.6.2/spatialising/DESCRIPTION | 15 ++-- spatialising-0.6.2/spatialising/MD5 | 33 ++++------ spatialising-0.6.2/spatialising/R/kinetic_ising.R | 2 spatialising-0.6.2/spatialising/R/spatial_metrics.R | 2 spatialising-0.6.2/spatialising/README.md | 14 +++- spatialising-0.6.2/spatialising/build/partial.rdb |binary spatialising-0.6.2/spatialising/build/vignette.rds |binary spatialising-0.6.2/spatialising/inst/doc/Optimizing_spatialising_parameters.html | 9 +- spatialising-0.6.2/spatialising/man/figures/README-unnamed-chunk-3-1.png |binary spatialising-0.6.2/spatialising/man/figures/README-unnamed-chunk-4-1.png |binary spatialising-0.6.2/spatialising/man/figures/README-unnamed-chunk-5-1.png |binary spatialising-0.6.2/spatialising/man/figures/README-unnamed-chunk-6-1.png |binary spatialising-0.6.2/spatialising/man/figures/README-unnamed-chunk-7-1.png |binary spatialising-0.6.2/spatialising/man/spatialising-package.Rd | 2 spatialising-0.6.2/spatialising/tests/testthat/test-metrics.R | 1 20 files changed, 41 insertions(+), 37 deletions(-)
Title: Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control
Description: Implementation of Sparse-group SLOPE (SGS) (Feser and Evangelou (2023) <doi:10.48550/arXiv.2305.09467>) models. Linear and logistic regression models are supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported. In addition, a general Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) implementation is provided. Group SLOPE (gSLOPE) (Brzyski et al. (2019) <doi:10.1080/01621459.2017.1411269>) and group-based OSCAR models (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) are also implemented. All models are available with strong screening rules (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) for computational speed-up.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between sgs versions 0.3.8 dated 2025-06-12 and 0.3.9 dated 2025-09-30
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/global_wrapper_code.R | 4 ++++ inst/doc/reproducible_example.html | 12 ++++++------ 4 files changed, 17 insertions(+), 13 deletions(-)
Title: Penalized Semiparametric Bayesian Cox Models
Description: Algorithms to speed up the Bayesian Lasso Cox model (Lee et al., Int J Biostat, 2011 <doi:10.2202/1557-4679.1301>) and the Bayesian Lasso Cox with mandatory variables (Zucknick et al. Biometrical J, 2015 <doi:10.1002/bimj.201400160>).
Author: Zhi Zhao [aut, cre],
Manuela Zucknick [aut],
Maral Saadati [aut],
Axel Benner [aut]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between psbcSpeedUp versions 2.0.7 dated 2024-07-01 and 2.1.0 dated 2025-09-30
psbcSpeedUp-2.0.7/psbcSpeedUp/man/figures/README_plot_beta.png |only psbcSpeedUp-2.0.7/psbcSpeedUp/man/figures/README_plot_brier.png |only psbcSpeedUp-2.0.7/psbcSpeedUp/src/pugiconfig.h |only psbcSpeedUp-2.0.7/psbcSpeedUp/src/pugixml.cpp |only psbcSpeedUp-2.0.7/psbcSpeedUp/src/pugixml.h |only psbcSpeedUp-2.0.7/psbcSpeedUp/src/utils.cpp |only psbcSpeedUp-2.0.7/psbcSpeedUp/src/utils.h |only psbcSpeedUp-2.1.0/psbcSpeedUp/DESCRIPTION | 23 psbcSpeedUp-2.1.0/psbcSpeedUp/MD5 | 66 - psbcSpeedUp-2.1.0/psbcSpeedUp/NAMESPACE | 4 psbcSpeedUp-2.1.0/psbcSpeedUp/NEWS.md | 31 psbcSpeedUp-2.1.0/psbcSpeedUp/R/RcppExports.R | 4 psbcSpeedUp-2.1.0/psbcSpeedUp/R/plotBrier.R | 24 psbcSpeedUp-2.1.0/psbcSpeedUp/R/predict.psbcSpeedUp.R | 2 psbcSpeedUp-2.1.0/psbcSpeedUp/R/psbcSpeedUp-package.R |only psbcSpeedUp-2.1.0/psbcSpeedUp/R/psbcSpeedUp.R | 35 psbcSpeedUp-2.1.0/psbcSpeedUp/README.md | 30 psbcSpeedUp-2.1.0/psbcSpeedUp/build/partial.rdb |only psbcSpeedUp-2.1.0/psbcSpeedUp/build/vignette.rds |binary psbcSpeedUp-2.1.0/psbcSpeedUp/cleanup | 6 psbcSpeedUp-2.1.0/psbcSpeedUp/configure | 35 psbcSpeedUp-2.1.0/psbcSpeedUp/configure.ac | 28 psbcSpeedUp-2.1.0/psbcSpeedUp/inst/CITATION | 6 psbcSpeedUp-2.1.0/psbcSpeedUp/inst/doc/BayesCox.R | 56 - psbcSpeedUp-2.1.0/psbcSpeedUp/inst/doc/BayesCox.Rmd | 56 + psbcSpeedUp-2.1.0/psbcSpeedUp/inst/doc/BayesCox.html | 55 - psbcSpeedUp-2.1.0/psbcSpeedUp/man/figures/estimate_beta.png |only psbcSpeedUp-2.1.0/psbcSpeedUp/man/figures/estimate_brier.png |only psbcSpeedUp-2.1.0/psbcSpeedUp/man/psbcSpeedUp-package.Rd |only psbcSpeedUp-2.1.0/psbcSpeedUp/man/psbcSpeedUp.Rd | 1 psbcSpeedUp-2.1.0/psbcSpeedUp/src/Makevars.in | 5 psbcSpeedUp-2.1.0/psbcSpeedUp/src/Makevars.win | 6 psbcSpeedUp-2.1.0/psbcSpeedUp/src/RcppExports.cpp | 21 psbcSpeedUp-2.1.0/psbcSpeedUp/src/drive.cpp | 174 ++-- psbcSpeedUp-2.1.0/psbcSpeedUp/src/drive.h | 36 - psbcSpeedUp-2.1.0/psbcSpeedUp/src/global.h | 10 psbcSpeedUp-2.1.0/psbcSpeedUp/src/init.c | 10 psbcSpeedUp-2.1.0/psbcSpeedUp/src/psbc.cpp | 360 ++++++---- psbcSpeedUp-2.1.0/psbcSpeedUp/src/psbc.h | 140 ++- psbcSpeedUp-2.1.0/psbcSpeedUp/vignettes/BayesCox.Rmd | 56 + 40 files changed, 724 insertions(+), 556 deletions(-)
Title: Microclimatic Data Processing
Description: Handling the microclimatic data in R. The 'myClim' workflow begins
at the reading data primary from microclimatic dataloggers,
but can be also reading of meteorological station data from files.
Cleaning time step, time zone settings and metadata collecting is the next step of the work flow.
With 'myClim' tools one can crop, join, downscale, and convert microclimatic data formats, sort them into localities,
request descriptive characteristics and compute microclimatic variables.
Handy plotting functions are provided with smart defaults.
Author: Matej Man [aut],
Vojtech Kalcik [aut, cre],
Martin Macek [aut],
Josef Bruna [aut],
Lucia Hederova [aut],
Jan Wild [aut],
Martin Kopecky [aut],
Institute of Botany of the Czech Academy of Sciences [cph]
Maintainer: Vojtech Kalcik <Vojtech.Kalcik@ibot.cas.cz>
Diff between myClim versions 1.4.0 dated 2025-02-21 and 1.5.0 dated 2025-09-30
DESCRIPTION | 8 MD5 | 96 ++++---- NAMESPACE | 3 NEWS.md | 29 ++ R/calc.R | 2 R/filter.R | 162 +++++++++----- R/info.R | 65 +++++ R/join.R | 10 R/model.R | 35 ++- R/myClim-package.R | 1 R/plot.R | 7 R/prep.R | 206 ++++++++++++++++++- R/read.R | 32 ++ R/reshape.R | 44 ++-- R/serialize.R | 7 R/states.R | 43 +++ build/vignette.rds |binary data/mc_data_example_agg.rda |binary data/mc_data_example_clean.rda |binary data/mc_data_example_raw.rda |binary data/mc_data_formats.rda |binary data/mc_data_heights.rda |binary data/mc_data_physical.rda |binary data/mc_data_sensors.rda |binary data/mc_data_vwc_parameters.rda |binary inst/doc/myclim-custom-loggers.html | 2 inst/doc/myclim-demo.html | 60 +++++ man/mc_DataFormat-class.Rd | 2 man/mc_LoggerMetadata-class.Rd | 2 man/mc_filter.Rd | 34 +-- man/mc_info.Rd | 2 man/mc_info_calib.Rd |only man/mc_prep_delete.Rd |only man/mc_prep_expandtime.Rd |only man/mc_reshape_wide.Rd | 17 - man/mc_states_join.Rd | 15 + man/myClim-package.Rd | 1 tests/data/HOBO/20847126_empty.txt |only tests/data/expandtime |only tests/data/join_tolerance/data_94184101_1.csv | 25 -- tests/data/join_tolerance/data_94184101_2.csv |only tests/data/joined_TOMST/problems/202310_94218703.csv |only tests/data/serialize/raw_data_1.4.1.rds |only tests/testthat/libtest.R | 7 tests/testthat/test-filter.R | 59 ++++- tests/testthat/test-info.R | 3 tests/testthat/test-join.R | 3 tests/testthat/test-plot.R | 4 tests/testthat/test-prep.R | 52 ++++ tests/testthat/test-read.R | 22 ++ tests/testthat/test-reshape.R | 16 - tests/testthat/test-serialize.R | 2 tests/testthat/test-states.R | 23 ++ 53 files changed, 878 insertions(+), 223 deletions(-)
Title: Dual Feature Reduction for SGL
Description: Implementation of the Dual Feature Reduction (DFR) approach for the Sparse Group Lasso (SGL) and the Adaptive Sparse Group Lasso (aSGL) (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.17094>). The DFR approach is a feature reduction approach that applies strong screening to reduce the feature space before optimisation, leading to speed-up improvements for fitting SGL (Simon et al. (2013) <doi:10.1080/10618600.2012.681250>) and aSGL (Mendez-Civieta et al. (2020) <doi:10.1007/s11634-020-00413-8> and Poignard (2020) <doi:10.1007/s10463-018-0692-7>) models. DFR is implemented using the Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) algorithm, with linear and logistic SGL models supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between dfr versions 0.1.5 dated 2025-03-06 and 0.1.6 dated 2025-09-30
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/global_wrapper_code.R | 5 +++++ 3 files changed, 12 insertions(+), 7 deletions(-)
Title: Spatial Bayesian Factor Analysis
Description: Implements a spatial Bayesian non-parametric factor analysis model
with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC).
Spatial correlation is introduced in the columns of the factor loadings
matrix using a Bayesian non-parametric prior, the probit stick-breaking
process. Areal spatial data is modeled using a conditional autoregressive
(CAR) prior and point-referenced spatial data is treated using a Gaussian
process. The response variable can be modeled as Gaussian, probit, Tobit, or
Binomial (using Polya-Gamma augmentation). Temporal correlation is
introduced for the latent factors through a hierarchical structure and can
be specified as exponential or first-order autoregressive. Full details of
the package can be found in the accompanying vignette. Furthermore, the
details of the package can be found in "Bayesian Non-Parametric Factor
Analysis for Longitudinal Spatial Surfaces", by Berchuck et al (2019),
<doi:10.1214/20-BA1253> in Bayesian Analysis.
Author: Samuel I. Berchuck [aut, cre]
Maintainer: Samuel I. Berchuck <sib2@duke.edu>
Diff between spBFA versions 1.3 dated 2023-03-21 and 1.4.0 dated 2025-09-30
DESCRIPTION | 12 +- MD5 | 17 ++- NEWS.md |only R/spBFA-package.R | 3 build/vignette.rds |binary inst/doc/spBFA-example.R | 22 ++--- inst/doc/spBFA-example.html | 168 ++++++++++++++++++++------------------ man/spBFA.Rd | 1 src/DistributionFunctions.cpp | 48 +++++------ src/MCMC_Samplers.cpp | 183 +++++++++++++++++++++--------------------- 10 files changed, 235 insertions(+), 219 deletions(-)
Title: Many Global Governance Datacubes
Description: This is the core package offering a portal to the many packages universe.
It includes functions to help researchers access, work across, and maintain
ensembles of datasets on global governance called datacubes.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [aut, ctb] ,
Bernhard Bieri [ctb] ,
Esther Peev [ctb] ,
Jael Tan [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manydata versions 1.0.3 dated 2025-06-18 and 1.1.3 dated 2025-09-30
manydata-1.0.3/manydata/R/compare.R |only manydata-1.0.3/manydata/R/consolidate.R |only manydata-1.0.3/manydata/R/describe_data.R |only manydata-1.0.3/manydata/R/resolve.R |only manydata-1.0.3/manydata/R/wrangling_data.R |only manydata-1.1.3/manydata/DESCRIPTION | 31 +++++------- manydata-1.1.3/manydata/MD5 | 56 ++++++++++++---------- manydata-1.1.3/manydata/NAMESPACE | 28 +++++++++++ manydata-1.1.3/manydata/NEWS.md | 34 +++++++++++++ manydata-1.1.3/manydata/R/call_sources.R | 31 ++++++++++-- manydata-1.1.3/manydata/R/code_extend.R |only manydata-1.1.3/manydata/R/compare_diff.R |only manydata-1.1.3/manydata/R/compare_dimensions.R |only manydata-1.1.3/manydata/R/compare_scores.R |only manydata-1.1.3/manydata/R/data_description.R |only manydata-1.1.3/manydata/R/data_find.R |only manydata-1.1.3/manydata/R/data_wrangling.R |only manydata-1.1.3/manydata/R/merge_consolidate.R |only manydata-1.1.3/manydata/R/merge_resolve.R |only manydata-1.1.3/manydata/R/zzz.R | 4 + manydata-1.1.3/manydata/inst/CITATION | 13 +++-- manydata-1.1.3/manydata/man/code_extend.Rd |only manydata-1.1.3/manydata/man/compare_categories.Rd | 2 manydata-1.1.3/manydata/man/compare_diff.Rd |only manydata-1.1.3/manydata/man/compare_dimensions.Rd | 2 manydata-1.1.3/manydata/man/compare_missing.Rd | 2 manydata-1.1.3/manydata/man/compare_overlap.Rd | 2 manydata-1.1.3/manydata/man/consolidate.Rd | 2 manydata-1.1.3/manydata/man/describe.Rd | 2 manydata-1.1.3/manydata/man/filter_datacube.Rd |only manydata-1.1.3/manydata/man/find.Rd |only manydata-1.1.3/manydata/man/find_year.Rd |only manydata-1.1.3/manydata/man/pluck.Rd | 2 manydata-1.1.3/manydata/man/recollect.Rd | 2 manydata-1.1.3/manydata/man/repaint.Rd | 2 manydata-1.1.3/manydata/man/resolving.Rd | 2 manydata-1.1.3/manydata/man/reunite.Rd | 2 manydata-1.1.3/manydata/man/scores.Rd |only manydata-1.1.3/manydata/man/transmutate.Rd | 2 39 files changed, 160 insertions(+), 61 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Wai Wong [ctb]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 1.2-0 dated 2025-04-02 and 1.3-0 dated 2025-09-30
Changelog | 4 + DESCRIPTION | 12 +-- MD5 | 127 +++++++++++++++++++++++------------------- NAMESPACE | 9 ++ R/cad.R | 63 ++++++++++---------- R/fractions.R | 55 ++++++++---------- R/kmSRdiagram.R | 1 R/kmassess.R |only R/kmassessbayesian.R |only R/kmassesshalfsplit.R |only R/kmassessinformative.R |only R/kmassessmultiplicative.R |only R/kmassesssimulation.R |only R/kmbasis.R | 93 +++++++++++++++--------------- R/kmbasisdiagram.R | 1 R/kmcolors.R | 2 R/kmdist.R | 1 R/kmdoubleequal.R |only R/kmeqreduction.R | 1 R/kmfringe.R | 1 R/kmgenerate.R | 2 R/kmhasse.R | 1 R/kmiswellgraded.R | 93 +++++++++++++++--------------- R/kmneighbourhood.R | 1 R/kmnotions.R | 1 R/kmsassess.R |only R/kmsf2basis.R | 2 R/kmsimulate.R | 125 ++++++++++++++++++++--------------------- R/kmsrvalidate.R | 3 R/kmsurmisefunction.R | 1 R/kmsurmiserelation.R | 1 R/kmsymmsetdiff.R | 3 R/kmtrivial.R | 1 R/kmunionclosure.R | 97 +++++++++++++++----------------- R/kmvalidate.R | 1 R/readwrite.R | 67 ++++++++++------------ R/xpl.R | 1 build/partial.rdb |only build/vignette.rds |binary inst/doc/kstMatrix.html | 62 ++++++++++---------- man/cad.Rd | 10 +-- man/fractions.Rd | 6 - man/kmSRdiagram.Rd | 2 man/kmSRvalidate.Rd | 5 - man/kmassess.Rd |only man/kmassessbayesian.Rd |only man/kmassesshalfsplit.Rd |only man/kmassessinformative.Rd |only man/kmassessmentsimulation.Rd |only man/kmassessmultiplicative.Rd |only man/kmbasis.Rd | 2 man/kmbasisdiagram.Rd | 2 man/kmcolors.Rd | 8 ++ man/kmdist.Rd | 1 man/kmdoubleequal.Rd |only man/kmeqreduction.Rd | 1 man/kmfringe.Rd | 1 man/kmgenerate.Rd | 2 man/kmhasse.Rd | 4 - man/kmiswellgraded.Rd | 5 - man/kmneighbourhood.Rd | 1 man/kmnotions.Rd | 1 man/kmsassess.Rd |only man/kmsf2basis.Rd | 8 ++ man/kmsimulate.Rd | 7 -- man/kmsurmisefunction.Rd | 2 man/kmsurmiserelation.Rd | 2 man/kmsymmsetdiff.Rd | 8 ++ man/kmtrivial.Rd | 1 man/kmunionclosure.Rd | 8 +- man/kmvalidate.Rd | 9 +- man/readwrite.Rd | 10 +-- man/xpl.Rd | 4 - 73 files changed, 482 insertions(+), 460 deletions(-)
Title: Markdown-Based Programmable Surveys Using 'Quarto' and 'shiny'
Description: Generate programmable surveys using markdown and R code chunks. Surveys
are composed of two files: a survey.qmd 'Quarto' file defining the
survey content (pages, questions, etc), and an app.R file defining a
'shiny' app with global settings (libraries, database configuration,
etc.) and server configuration options (e.g., conditional skipping /
display, etc.). Survey data collected from respondents is stored in a
'PostgreSQL' database. Features include controls for conditional skip
logic (skip to a page based on an answer to a question), conditional
display logic (display a question based on an answer to a question), a
customizable progress bar, and a wide variety of question types,
including multiple choice (single choice and multiple choices),
select, text, numeric, multiple choice buttons, text area, and dates.
Because the surveys render into a 'shiny' app, designers can also
leverage the reactive capabilities of 'shiny' to create dynamic and
interactive surveys.
Author: John Paul Helveston [aut, cre, cph] ,
Pingfan Hu [aut, cph] ,
Bogdan Bunea [aut, cph] ,
Stefan Munnes [ctb]
Maintainer: John Paul Helveston <john.helveston@gmail.com>
Diff between surveydown versions 0.13.0 dated 2025-08-20 and 0.13.3 dated 2025-09-30
DESCRIPTION | 8 MD5 | 36 +- NAMESPACE | 1 NEWS.md | 19 + R/config.R | 19 - R/server.R | 638 ++++++++++++++++++++++++++++++++-------- R/ui.R | 85 +++-- R/util.R | 389 ++++++++++++++++++++++-- README.md | 42 ++ inst/CITATION | 14 inst/css/surveydown.css | 97 ++++++ inst/js/highlight_unanswered.js | 72 ++++ inst/template/README.md |only inst/template/app.R | 8 inst/template/survey.qmd | 17 + man/sd_create_survey.Rd | 5 man/sd_show_if.Rd | 2 man/sd_skip_forward.Rd | 42 -- man/sd_skip_if.Rd | 47 ++ man/sd_stop_if.Rd |only 20 files changed, 1264 insertions(+), 277 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.4.1 dated 2025-06-07 and 3.4.2 dated 2025-09-30
randomForestSRC-3.4.1/randomForestSRC/R/find.interaction.rfsrc.R |only randomForestSRC-3.4.1/randomForestSRC/R/stat.split.rfsrc.R |only randomForestSRC-3.4.1/randomForestSRC/R/synthetic.rfsrc.R |only randomForestSRC-3.4.1/randomForestSRC/R/utilities_sgreedy.R |only randomForestSRC-3.4.1/randomForestSRC/R/utilities_tdc.R |only randomForestSRC-3.4.1/randomForestSRC/man/find.interaction.rfsrc.Rd |only randomForestSRC-3.4.1/randomForestSRC/man/stat.split.rfsrc.Rd |only randomForestSRC-3.4.1/randomForestSRC/man/synthetic.rfsrc.Rd |only randomForestSRC-3.4.1/randomForestSRC/src/Makevars.win |only randomForestSRC-3.4.1/randomForestSRC/src/randomForestSRC.c |only randomForestSRC-3.4.1/randomForestSRC/src/randomForestSRC.h |only randomForestSRC-3.4.2/randomForestSRC/DESCRIPTION | 8 randomForestSRC-3.4.2/randomForestSRC/MD5 | 215 +++- randomForestSRC-3.4.2/randomForestSRC/NAMESPACE | 10 randomForestSRC-3.4.2/randomForestSRC/R/generic.predict.rfsrc.R | 58 - randomForestSRC-3.4.2/randomForestSRC/R/partial.rfsrc.R | 58 - randomForestSRC-3.4.2/randomForestSRC/R/predict.rfsrc.R | 2 randomForestSRC-3.4.2/randomForestSRC/R/print.rfsrc.R | 515 ++++------ randomForestSRC-3.4.2/randomForestSRC/R/quantreg.rfsrc.R | 1 randomForestSRC-3.4.2/randomForestSRC/R/rfsrc.R | 110 -- randomForestSRC-3.4.2/randomForestSRC/R/rfsrc.anonymous.R | 1 randomForestSRC-3.4.2/randomForestSRC/R/rfsrc.fast.R | 1 randomForestSRC-3.4.2/randomForestSRC/R/subsample.rfsrc.R | 1 randomForestSRC-3.4.2/randomForestSRC/R/tune.nodesize.rfsrc.R | 243 +++- randomForestSRC-3.4.2/randomForestSRC/R/tune.rfsrc.R | 463 ++++++-- randomForestSRC-3.4.2/randomForestSRC/R/utilities.R | 140 -- randomForestSRC-3.4.2/randomForestSRC/R/utilities_data.R | 8 randomForestSRC-3.4.2/randomForestSRC/R/utilities_imbalanced.R | 331 ++++-- randomForestSRC-3.4.2/randomForestSRC/configure | 220 +++- randomForestSRC-3.4.2/randomForestSRC/configure.ac | 88 + randomForestSRC-3.4.2/randomForestSRC/data/breast.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/follic.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/hd.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/housing.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/nutrigenomic.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/pbc.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/peakVO2.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/vdv.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/veteran.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/wihs.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/wine.rda |binary randomForestSRC-3.4.2/randomForestSRC/inst/NEWS | 11 randomForestSRC-3.4.2/randomForestSRC/man/breast.Rd | 1 randomForestSRC-3.4.2/randomForestSRC/man/max.subtree.rfsrc.Rd | 3 randomForestSRC-3.4.2/randomForestSRC/man/plot.rfsrc.Rd | 2 randomForestSRC-3.4.2/randomForestSRC/man/plot.variable.rfsrc.Rd | 1 randomForestSRC-3.4.2/randomForestSRC/man/predict.rfsrc.Rd | 7 randomForestSRC-3.4.2/randomForestSRC/man/print.rfsrc.Rd | 2 randomForestSRC-3.4.2/randomForestSRC/man/randomForestSRC_package.Rd | 3 randomForestSRC-3.4.2/randomForestSRC/man/rfsrc.Rd | 7 randomForestSRC-3.4.2/randomForestSRC/man/tune.rfsrc.Rd | 212 ++-- randomForestSRC-3.4.2/randomForestSRC/man/utilities_internal.Rd | 5 randomForestSRC-3.4.2/randomForestSRC/src/R_init_randomForestSRC.c | 28 randomForestSRC-3.4.2/randomForestSRC/src/bootstrap.c |only randomForestSRC-3.4.2/randomForestSRC/src/bootstrap.h |only randomForestSRC-3.4.2/randomForestSRC/src/cindex.c |only randomForestSRC-3.4.2/randomForestSRC/src/cindex.h |only randomForestSRC-3.4.2/randomForestSRC/src/classification.c |only randomForestSRC-3.4.2/randomForestSRC/src/classification.h |only randomForestSRC-3.4.2/randomForestSRC/src/diagnostic.c |only randomForestSRC-3.4.2/randomForestSRC/src/diagnostic.h |only randomForestSRC-3.4.2/randomForestSRC/src/distance.c |only randomForestSRC-3.4.2/randomForestSRC/src/distance.h |only randomForestSRC-3.4.2/randomForestSRC/src/entry.c |only randomForestSRC-3.4.2/randomForestSRC/src/entry.h |only randomForestSRC-3.4.2/randomForestSRC/src/entryGeneric.c |only randomForestSRC-3.4.2/randomForestSRC/src/entryGeneric.h |only randomForestSRC-3.4.2/randomForestSRC/src/error.c |only randomForestSRC-3.4.2/randomForestSRC/src/error.h |only randomForestSRC-3.4.2/randomForestSRC/src/external.h |only randomForestSRC-3.4.2/randomForestSRC/src/factor.h |only randomForestSRC-3.4.2/randomForestSRC/src/factorOps.c |only randomForestSRC-3.4.2/randomForestSRC/src/factorOps.h |only randomForestSRC-3.4.2/randomForestSRC/src/global.h |only randomForestSRC-3.4.2/randomForestSRC/src/importance.c |only randomForestSRC-3.4.2/randomForestSRC/src/importance.h |only randomForestSRC-3.4.2/randomForestSRC/src/importanceAnti.c |only randomForestSRC-3.4.2/randomForestSRC/src/importanceAnti.h |only randomForestSRC-3.4.2/randomForestSRC/src/importancePerm.c |only randomForestSRC-3.4.2/randomForestSRC/src/importancePerm.h |only randomForestSRC-3.4.2/randomForestSRC/src/importanceRand.c |only randomForestSRC-3.4.2/randomForestSRC/src/importanceRand.h |only randomForestSRC-3.4.2/randomForestSRC/src/impute.c |only randomForestSRC-3.4.2/randomForestSRC/src/impute.h |only randomForestSRC-3.4.2/randomForestSRC/src/internal.c |only randomForestSRC-3.4.2/randomForestSRC/src/leafLink.c |only randomForestSRC-3.4.2/randomForestSRC/src/leafLink.h |only randomForestSRC-3.4.2/randomForestSRC/src/marginal.c |only randomForestSRC-3.4.2/randomForestSRC/src/marginal.h |only randomForestSRC-3.4.2/randomForestSRC/src/nativeInfo.h |only randomForestSRC-3.4.2/randomForestSRC/src/nativeUtil.c |only randomForestSRC-3.4.2/randomForestSRC/src/nativeUtil.h |only randomForestSRC-3.4.2/randomForestSRC/src/node.h |only randomForestSRC-3.4.2/randomForestSRC/src/nodeOps.c |only randomForestSRC-3.4.2/randomForestSRC/src/nodeOps.h |only randomForestSRC-3.4.2/randomForestSRC/src/nrutil.c |only randomForestSRC-3.4.2/randomForestSRC/src/nrutil.h |only randomForestSRC-3.4.2/randomForestSRC/src/partial.c |only randomForestSRC-3.4.2/randomForestSRC/src/partial.h |only randomForestSRC-3.4.2/randomForestSRC/src/polarity.c |only randomForestSRC-3.4.2/randomForestSRC/src/polarity.h |only randomForestSRC-3.4.2/randomForestSRC/src/processEnsemble.c |only randomForestSRC-3.4.2/randomForestSRC/src/processEnsemble.h |only randomForestSRC-3.4.2/randomForestSRC/src/quantile.c |only randomForestSRC-3.4.2/randomForestSRC/src/quantile.h |only randomForestSRC-3.4.2/randomForestSRC/src/random.c |only randomForestSRC-3.4.2/randomForestSRC/src/random.h |only randomForestSRC-3.4.2/randomForestSRC/src/regression.c |only randomForestSRC-3.4.2/randomForestSRC/src/regression.h |only randomForestSRC-3.4.2/randomForestSRC/src/rfsrc.c |only randomForestSRC-3.4.2/randomForestSRC/src/rfsrc.h |only randomForestSRC-3.4.2/randomForestSRC/src/rfsrcUtil.c |only randomForestSRC-3.4.2/randomForestSRC/src/rfsrcUtil.h |only randomForestSRC-3.4.2/randomForestSRC/src/sampling.c |only randomForestSRC-3.4.2/randomForestSRC/src/sampling.h |only randomForestSRC-3.4.2/randomForestSRC/src/sexpOutgoing.c |only randomForestSRC-3.4.2/randomForestSRC/src/sexpOutgoing.h |only randomForestSRC-3.4.2/randomForestSRC/src/snpAuxiliaryInfo.h |only randomForestSRC-3.4.2/randomForestSRC/src/sortedLink.c |only randomForestSRC-3.4.2/randomForestSRC/src/sortedLink.h |only randomForestSRC-3.4.2/randomForestSRC/src/sources.list |only randomForestSRC-3.4.2/randomForestSRC/src/split.c |only randomForestSRC-3.4.2/randomForestSRC/src/split.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitClas.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitClas.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitCustom.c | 353 ------ randomForestSRC-3.4.2/randomForestSRC/src/splitCustom.h | 59 - randomForestSRC-3.4.2/randomForestSRC/src/splitCustomDriver.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitCustomDriver.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitGreedy.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitGreedy.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitInfo.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitMahalanobis.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitMahalanobis.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitMult.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitMult.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitQuantile.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitQuantile.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitRegr.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitRegr.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitSurv.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitSurv.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitUtil.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitUtil.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitUtilSurv.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitUtilSurv.h |only randomForestSRC-3.4.2/randomForestSRC/src/stack.c |only randomForestSRC-3.4.2/randomForestSRC/src/stack.h |only randomForestSRC-3.4.2/randomForestSRC/src/stackOutput.c |only randomForestSRC-3.4.2/randomForestSRC/src/stackOutput.h |only randomForestSRC-3.4.2/randomForestSRC/src/stackOutputQQ.c |only randomForestSRC-3.4.2/randomForestSRC/src/stackOutputQQ.h |only randomForestSRC-3.4.2/randomForestSRC/src/stackParallel.c |only randomForestSRC-3.4.2/randomForestSRC/src/stackParallel.h |only randomForestSRC-3.4.2/randomForestSRC/src/stackPreDefined.c |only randomForestSRC-3.4.2/randomForestSRC/src/stackPreDefined.h |only randomForestSRC-3.4.2/randomForestSRC/src/survival.c |only randomForestSRC-3.4.2/randomForestSRC/src/survival.h |only randomForestSRC-3.4.2/randomForestSRC/src/survivalE.c |only randomForestSRC-3.4.2/randomForestSRC/src/survivalE.h |only randomForestSRC-3.4.2/randomForestSRC/src/svdUtil.c |only randomForestSRC-3.4.2/randomForestSRC/src/svdUtil.h |only randomForestSRC-3.4.2/randomForestSRC/src/termOps.c |only randomForestSRC-3.4.2/randomForestSRC/src/termOps.h |only randomForestSRC-3.4.2/randomForestSRC/src/terminal.h |only randomForestSRC-3.4.2/randomForestSRC/src/trace.c |only randomForestSRC-3.4.2/randomForestSRC/src/trace.h |only randomForestSRC-3.4.2/randomForestSRC/src/tree.c |only randomForestSRC-3.4.2/randomForestSRC/src/tree.h |only randomForestSRC-3.4.2/randomForestSRC/src/treeJIT.c |only randomForestSRC-3.4.2/randomForestSRC/src/treeJIT.h |only randomForestSRC-3.4.2/randomForestSRC/src/treeUtil.c |only randomForestSRC-3.4.2/randomForestSRC/src/treeUtil.h |only 173 files changed, 1568 insertions(+), 1599 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Nicely Formatted Contingency Tables and Frequency Tables
Description: Nicely formatted frequency tables and contingency tables (1-way, 2-way, 3-way and 4-way tables), that can easily be exported to HTML or 'Office' documents. Designed to work with pipes.
Author: Mans Thulin [aut, cre],
Kajsa Grind [aut],
Stefan Furne [aut]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Diff between ivo.table versions 0.6 dated 2025-01-15 and 0.7.0 dated 2025-09-30
DESCRIPTION | 12 ++-- MD5 | 29 +++++++--- NAMESPACE | 57 +++++++++++++++++++++ NEWS.md | 3 + R/ivo_table_gt.R |only R/ivo_tables.R | 16 ++--- README.md | 4 + build/vignette.rds |binary inst/doc/ivo_table.R | 8 +- inst/doc/ivo_table.Rmd | 6 +- inst/doc/ivo_table.html | 122 ++++++++++++++++++++++++++------------------- inst/doc/ivo_table_gt.R |only inst/doc/ivo_table_gt.Rmd |only inst/doc/ivo_table_gt.html |only man/figures |only man/ivo_gt_theme.Rd |only man/ivo_table_gt.Rd |only vignettes/ivo_table.Rmd | 6 +- vignettes/ivo_table_gt.Rmd |only vignettes/patchwork.png |only 20 files changed, 181 insertions(+), 82 deletions(-)
Title: Clinical Stroke Research
Description: A collection of tools for clinical trial data management and
analysis in research and teaching.
The package is mainly collected for personal use, but any use beyond that is encouraged.
This package has migrated functions from 'agdamsbo/daDoctoR', and new functions has been added.
Version follows months and year. See NEWS/Changelog for release notes.
This package includes sampled data from the TALOS trial (Kraglund et al (2018) <doi:10.1161/STROKEAHA.117.020067>).
The win_prob() function is based on work by Zou et al (2022) <doi:10.1161/STROKEAHA.121.037744>.
The age_calc() function is based on work by Becker (2020) <doi:10.18637/jss.v093.i02>.
Author: Andreas Gammelgaard Damsbo [aut, cre]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>
Diff between stRoke versions 25.9.1 dated 2025-09-02 and 25.9.2 dated 2025-09-30
DESCRIPTION | 6 +- MD5 | 11 +++- NEWS.md | 4 + R/trial.R |only data/trial.rda |only inst/WORDLIST | 2 inst/doc/toolbox.html | 114 +++++++++++++++++++++++++------------------------- man/trial.Rd |only 8 files changed, 73 insertions(+), 64 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre2' (BSD license, see <https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stephanie Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.6.9 dated 2025-09-27 and 0.6.10 dated 2025-09-30
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 7 ++++++- inst/doc/vignette.html | 4 ++-- src/cwb/cl/registry.tab.c | 14 +++++++++++++- src/cwb/cqp/context_descriptor.c | 8 ++++++++ 6 files changed, 38 insertions(+), 13 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between openssl versions 2.3.3 dated 2025-05-26 and 2.3.4 dated 2025-09-30
DESCRIPTION | 6 ++--- MD5 | 22 +++++++++--------- NEWS | 3 ++ build/vignette.rds |binary inst/doc/bignum.html | 32 +++++++++++++------------- inst/doc/crypto_hashing.html | 8 +++--- inst/doc/keys.html | 48 ++++++++++++++++++++-------------------- inst/doc/secure_rng.html | 18 +++++++-------- src/cert.c | 9 ++++--- src/info.c | 5 ++++ tests/testthat/helper-version.R | 2 - tests/testthat/test_ssl_ctx.R | 3 +- 12 files changed, 83 insertions(+), 73 deletions(-)
Title: Visualisation and Analysis of Ocean Data Derived from Satellites
Description: With 'satin' functions, visualisation, data extraction and further analysis like producing climatologies from several images, and anomalies of satellite derived ocean data can be easily done. Reading functions can import a user defined geographical extent of data stored in netCDF files. Currently supported ocean data sources include NASA's Oceancolor web page <https://oceancolor.gsfc.nasa.gov/>, sensors VIIRS-SNPP; MODIS-Terra; MODIS-Aqua; and SeaWiFS. Available variables from this source includes chlorophyll concentration, sea surface temperature (SST), and several others. Data sources specific for SST that can be imported too includes Pathfinder AVHRR <https://www.ncei.noaa.gov/products/avhrr-pathfinder-sst> and GHRSST <https://www.ghrsst.org/>. In addition, ocean productivity data produced by Oregon State University can also be handled previous conversion from HDF4 to HDF5 format. Many other ocean variables can be processed by importing netCDF data files from [...truncated...]
Author: Hector Villalobos [aut, cre] ,
Eduardo Gonzalez-Rodriguez [aut]
Maintainer: Hector Villalobos <hvillalo@ipn.mx>
Diff between satin versions 1.1.0 dated 2022-09-22 and 1.2.0 dated 2025-09-30
DESCRIPTION | 26 +++++++++++++++++++------- MD5 | 52 +++++++++++++++++++++++++++------------------------- NEWS | 4 ++++ NEWS.md | 8 +++++++- R/climatology.R | 7 +++++-- R/imageScale.R | 2 +- R/name_ncvars.R |only R/plot.satin.R | 25 +++++++++++++++---------- R/read.cmems.R | 6 ++++-- R/satinDataframe.R | 4 ++-- R/satinMean.R | 4 ++-- README.md | 3 ++- data/dchl.rda |binary data/dcmems.rda |binary data/dmap.rda |binary data/dnpp.rda |binary data/dsst.rda |binary man/crop.Rd | 2 +- man/dchl.Rd | 4 ++-- man/dnpp.Rd | 4 ++-- man/dsst.Rd | 4 ++-- man/isolines.Rd | 4 ++-- man/name_ncvars.Rd |only man/plot.satin.Rd | 9 +++++---- man/read.cmems.Rd | 5 +++-- man/read.ghrsst.Rd | 2 +- man/read.osunpp.Rd | 2 +- man/satinMean.Rd | 4 +++- 28 files changed, 110 insertions(+), 71 deletions(-)
Title: Download Paleoclimate Data from 'PaleoClim'
Description: 'PaleoClim' <http://www.paleoclim.org> (Brown et al. 2019,
<doi:10.1038/sdata.2018.254>) is a set of free, high resolution paleoclimate
surfaces covering the whole globe. It includes data on surface temperature,
precipitation and the standard bioclimatic variables commonly used in
ecological modelling, derived from the 'HadCM3' general circulation model and
downscaled to a spatial resolution of up to 2.5 minutes. Simulations are
available for key time periods from the Late Holocene to mid-Pliocene. Data on
current and Last Glacial Maximum climate is derived from 'CHELSA' (Karger et
al. 2017, <doi:10.1038/sdata.2017.122>) and reprocessed by 'PaleoClim' to
match their format; it is available at up to 30 seconds resolution. This
package provides a simple interface for downloading 'PaleoClim' data in R,
with support for caching and filtering retrieved data by period, resolution,
and geographic extent.
Author: Joe Roe [aut, cre, cph]
Maintainer: Joe Roe <joe@joeroe.io>
Diff between rpaleoclim versions 1.0.1 dated 2023-08-09 and 1.1.0 dated 2025-09-30
rpaleoclim-1.0.1/rpaleoclim/inst/doc/rpaleoclim.R |only rpaleoclim-1.0.1/rpaleoclim/tests/testthat/helper-download.R |only rpaleoclim-1.1.0/rpaleoclim/DESCRIPTION | 12 rpaleoclim-1.1.0/rpaleoclim/MD5 | 30 - rpaleoclim-1.1.0/rpaleoclim/NEWS.md | 7 rpaleoclim-1.1.0/rpaleoclim/R/paleoclim.R | 38 +- rpaleoclim-1.1.0/rpaleoclim/R/rpaleoclim-package.R | 4 rpaleoclim-1.1.0/rpaleoclim/README.md | 4 rpaleoclim-1.1.0/rpaleoclim/build/partial.rdb |binary rpaleoclim-1.1.0/rpaleoclim/build/vignette.rds |binary rpaleoclim-1.1.0/rpaleoclim/inst/CITATION | 6 rpaleoclim-1.1.0/rpaleoclim/inst/doc/rpaleoclim.Rmd | 157 ++++++---- rpaleoclim-1.1.0/rpaleoclim/inst/doc/rpaleoclim.html | 52 +-- rpaleoclim-1.1.0/rpaleoclim/man/figures/README-rpaleoclim-demo-1.png |binary rpaleoclim-1.1.0/rpaleoclim/tests/testthat/test-paleoclim.R | 40 +- rpaleoclim-1.1.0/rpaleoclim/vignettes/eg-paleoclim-crop-1.png |only rpaleoclim-1.1.0/rpaleoclim/vignettes/rpaleoclim.Rmd | 157 ++++++---- rpaleoclim-1.1.0/rpaleoclim/vignettes/rpaleoclim.Rmd.source |only 18 files changed, 309 insertions(+), 198 deletions(-)
Title: Calculate 3D Contour Meshes Using the Marching Cubes Algorithm
Description: A port of the C++ routine for applying the marching cubes algorithm written by
Thomas Lewiner et al. (2012) <doi:10.1080/10867651.2003.10487582> into an R package.
The package supplies the contour3d() function, which takes a 3-dimensional array of voxel
data and calculates the vertices, vertex normals, and faces for a 3d mesh representing
the contour(s) at a given level.
Author: S. H. Wilks [aut, cre],
Thomas Lewiner [aut]
Maintainer: S. H. Wilks <sam.wilks@unimelb.edu.au>
Diff between rmarchingcubes versions 0.1.2 dated 2021-06-16 and 0.1.4 dated 2025-09-30
DESCRIPTION | 25 + MD5 | 31 +- NEWS.md | 11 README.md | 9 build/vignette.rds |binary inst/doc/calculating_3d_contours.R | 48 +-- inst/doc/calculating_3d_contours.Rmd | 2 inst/doc/calculating_3d_contours.html | 442 +++++++++++++++++++++++++--------- src/LookUpTable.h | 96 +++---- src/Makevars | 12 src/Makevars.win | 12 src/MarchingCubes.cpp | 6 src/MarchingCubes.h | 2 src/RcppExports.cpp | 5 tests/testthat/_snaps |only tests/testthat/test-marchingcubes.R | 42 ++- vignettes/calculating_3d_contours.Rmd | 2 17 files changed, 488 insertions(+), 257 deletions(-)
More information about rmarchingcubes at CRAN
Permanent link
Title: Analysis of Aerobiological Data
Description: Supports analysis of aerobiological data.
Available features include determination of pollen season limits,
replacement of outliers (Kasprzyk and Walanus (2014) <doi:10.1007/s10453-014-9332-8>),
calculation of growing degree days (Baskerville and Emin (1969) <doi:10.2307/1933912>),
and determination of the base temperature for growing degree days
(Yang et al. (1995) <doi:10.1016/0168-1923(94)02185-M).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between pollen versions 0.82.0 dated 2021-12-03 and 0.83.0 dated 2025-09-30
DESCRIPTION | 14 - MD5 | 21 - README.md | 33 +- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 20 - inst/doc/gdd.R | 2 inst/doc/gdd.html | 479 ++++++++++++++++++++++++++--------- inst/doc/intro.R | 12 inst/doc/intro.html | 596 ++++++++++++++++++++++++++++++-------------- man/pollen-package.Rd | 4 tests/testthat/test-zeros.R | 14 - 12 files changed, 831 insertions(+), 364 deletions(-)
Title: Add a Scale Bar to 'OpenStreetMap' Plots
Description: Functionality to handle and project lat-long coordinates, easily download background maps
and add a correct scale bar to 'OpenStreetMap' plots in any map projection.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between OSMscale versions 0.5.22 dated 2025-07-27 and 0.5.23 dated 2025-09-30
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/mapComp.R | 13 ++++++++----- R/pointsMap.R | 7 +++++-- R/projectPoints.R | 2 ++ R/scaleBar.R | 11 +++++++++-- man/mapComp.Rd | 5 +++-- man/pointsMap.Rd | 2 ++ man/projectPoints.Rd | 2 ++ man/scaleBar.Rd | 11 +++++++++-- 10 files changed, 54 insertions(+), 27 deletions(-)
Title: Facilitation of Data Preparation and Plotting Procedures for RDA
and PCA Analyses
Description: Help to the occasional R user for synthesis and enhanced graphical visualization of redundancy analysis (RDA) and principal component analysis (PCA) methods and objects.
Inputs are : data frame, RDA (package 'vegan') and PCA (package 'FactoMineR') objects.
Outputs are : synthesized results of RDA, displayed in console and saved in tables ; displayed and saved objects of PCA graphic visualization of individuals and variables projections with multiple graphic parameters.
Author: Gregoire Bianchetti [aut, cre]
Maintainer: Gregoire Bianchetti <auguste.blam@gmail.com>
Diff between GABB versions 0.3.9 dated 2025-05-14 and 0.3.10 dated 2025-09-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/PCA_RDA_graphics.R | 13 ++++++++++--- 3 files changed, 16 insertions(+), 9 deletions(-)
Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan'
package, which provides the R interface to the Stan C++ library for Bayesian
estimation. Users specify models via the customary R syntax with a formula and
data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut],
Imad Ali [ctb],
Sam Brilleman [ctb],
Jacqueline Buros Novik [ctb] ,
AstraZeneca [ctb] ,
Trustees of Columbia University [cph],
Simon Wood [cph] ,
R Core Deveopment Team [cph] ,
Douglas Bates [cph] ,
Martin Maechler [cph] ,
Ben Bolk [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstanarm versions 2.32.1 dated 2024-01-18 and 2.32.2 dated 2025-09-30
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More information about OmopConstructor at CRAN
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More information about nonParQuantileCausality at CRAN
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Title: An Analysis Toolbox for Hermitian Positive Definite Matrices
Description: An implementation of data analysis tools for samples of symmetric or
Hermitian positive definite matrices, such as collections of covariance matrices
or spectral density matrices. The tools in this package can be used to perform: (i)
intrinsic wavelet transforms for curves (1D) or surfaces (2D) of Hermitian positive
definite matrices with applications to dimension reduction, denoising and clustering in the
space of Hermitian positive definite matrices; and (ii) exploratory data analysis and inference
for samples of positive definite matrices by means of intrinsic data depth functions and
rank-based hypothesis tests in the space of Hermitian positive definite matrices.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between pdSpecEst versions 1.2.4 dated 2020-01-08 and 1.2.6 dated 2025-09-30
pdSpecEst-1.2.4/pdSpecEst/R/pdSpecEst.R |only pdSpecEst-1.2.4/pdSpecEst/README.md |only pdSpecEst-1.2.4/pdSpecEst/man/pdSpecEst.Rd |only pdSpecEst-1.2.6/pdSpecEst/DESCRIPTION | 10 pdSpecEst-1.2.6/pdSpecEst/MD5 | 63 pdSpecEst-1.2.6/pdSpecEst/NEWS.md | 8 pdSpecEst-1.2.6/pdSpecEst/R/cluster.R | 2 pdSpecEst-1.2.6/pdSpecEst/R/pdSpecEst-package.R |only pdSpecEst-1.2.6/pdSpecEst/build/partial.rdb |binary pdSpecEst-1.2.6/pdSpecEst/build/vignette.rds |binary pdSpecEst-1.2.6/pdSpecEst/inst/doc/depth_ranktests.R | 20 pdSpecEst-1.2.6/pdSpecEst/inst/doc/depth_ranktests.html | 788 +++++++----- pdSpecEst-1.2.6/pdSpecEst/inst/doc/wavelet_est_clust.R | 34 pdSpecEst-1.2.6/pdSpecEst/inst/doc/wavelet_est_clust.Rmd | 26 pdSpecEst-1.2.6/pdSpecEst/inst/doc/wavelet_est_clust.html | 919 ++++++++++---- pdSpecEst-1.2.6/pdSpecEst/man/InvWavTransf1D.Rd | 11 pdSpecEst-1.2.6/pdSpecEst/man/InvWavTransf2D.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/WavTransf1D.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/pdMean.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/pdPgram.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/pdPgram2D.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/pdRankTests.Rd | 10 pdSpecEst-1.2.6/pdSpecEst/man/pdSpecClust1D.Rd | 16 pdSpecEst-1.2.6/pdSpecEst/man/pdSpecClust2D.Rd | 16 pdSpecEst-1.2.6/pdSpecEst/man/pdSpecEst-package.Rd |only pdSpecEst-1.2.6/pdSpecEst/man/pdSpecEst1D.Rd | 10 pdSpecEst-1.2.6/pdSpecEst/man/pdSpecEst2D.Rd | 10 pdSpecEst-1.2.6/pdSpecEst/man/pdSplineReg.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/pdkMeans.Rd | 13 pdSpecEst-1.2.6/pdSpecEst/man/rExamples1D.Rd | 17 pdSpecEst-1.2.6/pdSpecEst/man/rExamples2D.Rd | 12 pdSpecEst-1.2.6/pdSpecEst/src/Makevars | 11 pdSpecEst-1.2.6/pdSpecEst/src/Makevars.win | 11 pdSpecEst-1.2.6/pdSpecEst/src/RcppExports.cpp | 5 pdSpecEst-1.2.6/pdSpecEst/vignettes/wavelet_est_clust.Rmd | 26 35 files changed, 1395 insertions(+), 661 deletions(-)
Title: Spatial Analysis and Modelling Utilities
Description: Utilities to support spatial data manipulation, query, sampling
and modelling in ecological applications. Functions include models for species
population density, spatial smoothing, multivariate separability, point process
model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and
analysis, auto-logistic modeling, sampling models, cluster optimization, statistical
exploratory tools and raster-based metrics.
Author: Jeffrey S. Evans [aut, cre] ,
Melanie A. Murphy [ctb],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 2.0-2 dated 2023-11-17 and 2.0-3 dated 2025-09-30
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Title: Procrustes Matching for Latent Space Item Response Model
Description: Procrustes matching of the posterior samples of person and item latent positions from latent space item response models. The methods implemented in this package are based on work by Borg, I., Groenen, P. (1997, ISBN:978-0-387-94845-4), Jeon, M., Jin, I. H., Schweinberger, M., Baugh, S. (2021) <doi:10.1007/s11336-021-09762-5>, and Andrew, D. M., Kevin M. Q., Jong Hee Park. (2011) <doi:10.18637/jss.v042.i09>.
Author: Jinwen Luo [aut, cre] ,
Minjeong Jeon [aut]
Maintainer: Jinwen Luo <jevanluo@ucla.edu>
Diff between prolsirm versions 0.1.0 dated 2023-09-20 and 0.1.1 dated 2025-09-30
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/procrustes.R | 6 ++++-- man/procrustes.Rd | 13 ++++++++----- 4 files changed, 20 insertions(+), 15 deletions(-)