Title: Collection of Correlation and Association Estimators
Description: Compute correlation and other association matrices from
small to high-dimensional datasets with relative simple functions and
sensible defaults. Includes options for shrinkage and robustness to improve
results in noisy or high-dimensional settings (p >= n), plus convenient
print/plot methods for inspection. Implemented with optimised C++ backends
using BLAS/OpenMP and memory-aware symmetric updates. Works with base
matrices and data frames, returning standard R objects via a consistent S3
interface. Useful across genomics, agriculture, and machine-learning
workflows. Supports Pearson, Spearman, Kendall, distance correlation,
partial correlation, and robust biweight mid-correlation; Bland–Altman
analyses and Lin's concordance correlation coefficient (including
repeated-measures extensions). Methods based on Ledoit and Wolf (2004)
<doi:10.1016/S0047-259X(03)00096-4>; Schäfer and Strimmer (2005)
<doi:10.2202/1544-6115.1175>; Lin (1989) <doi:10.2307/2532051>.
Author: Thiago de Paula Oliveira [aut, cre]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@gmail.com>
Diff between matrixCorr versions 0.7.2 dated 2025-12-03 and 0.8.3 dated 2025-12-22
DESCRIPTION | 9 MD5 | 83 +- NAMESPACE | 6 R/biweight_mid_corr.R | 186 +++--- R/bland_altman.R | 128 ++-- R/bland_altman_repeated.R | 76 ++ R/ccc_repeated.R | 865 ++++++++++++++-------------- R/concordance_corr.R | 129 ++-- R/distance_corr.R | 65 +- R/kendall_corr.R | 140 ++-- R/partial_correlation.R | 132 ++-- R/pearson_corr.R | 51 - R/schafer_corr.R | 51 - R/spearman_rho.R | 28 R/validate_corr_input.R | 12 R/view_corr_shiny.R |only man/biweight_mid_corr.Rd | 12 man/ccc.Rd | 5 man/ccc_lmm_reml.Rd | 9 man/ccc_pairwise_u_stat.Rd | 5 man/distance_corr.Rd | 5 man/kendall_tau.Rd | 5 man/partial_correlation.Rd | 9 man/pearson_corr.Rd | 5 man/schafer_corr.Rd | 7 man/spearman_rho.Rd | 4 man/view_corr_shiny.Rd |only src/biweight_mid_corr.cpp | 198 ++++-- src/ccc_repeated.cpp | 4 src/concordance_corr.cpp | 25 src/distance_correlation.cpp | 57 - src/kendall_corr.cpp | 13 src/matrixCorr_detail.h | 9 src/partial_correlation.cpp | 28 tests/testthat/test_biweight_mid_corr.R | 35 - tests/testthat/test_bland_altman.R | 10 tests/testthat/test_bland_altman_repeated.R | 36 + tests/testthat/test_distance_corr.R | 20 tests/testthat/test_kendall.R | 45 - tests/testthat/test_partial_correlation.R |only tests/testthat/test_pearson_corr.R | 22 tests/testthat/test_schafer_corr.R |only tests/testthat/test_spearman_rho.R | 22 tests/testthat/test_view_corr_shiny.R |only tests/testthat/tests_partial_correlation.R | 2 45 files changed, 1539 insertions(+), 1014 deletions(-)
Title: Headers and Static Libraries for 'HDF5'
Description: 'HDF5' (Hierarchical Data Format 5) is a high-performance
library and file format for storing and managing large, complex
data. This package provides the static libraries and headers for
the 'HDF5' 'C' library (release 2.0.0). It is intended for R
package developers to use in the 'LinkingTo' field, which
eliminates the need for users to install system-level 'HDF5'
dependencies. This build is compiled with thread-safety enabled
and supports dynamic loading of external compression filters.
'HDF5' is developed by 'The HDF Group' <https://www.hdfgroup.org/>.
Author: Daniel P. Smith [aut, cre] ,
The HDF Group [cph] ,
Jean-loup Mark [cph] ,
Gailly Adler [cph]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between hdf5lib versions 2.0.0.3 dated 2025-12-14 and 2.0.0.4 dated 2025-12-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ configure | 7 +++++-- src/zlib-1.3.1.tar.gz |binary 5 files changed, 18 insertions(+), 9 deletions(-)
Title: Truncated Functional Generalized Linear Models
Description: An implementation of the methodologies described in Xi Liu, Afshin A. Divani, and Alexander Petersen (2022) <doi:10.1016/j.csda.2022.107421>, including
truncated functional linear and truncated functional logistic regression models.
Author: Xi Liu [aut],
Chau Tran [aut, cre],
Alexander Petersen [aut]
Maintainer: Chau Tran <cbtr@ucdavis.edu>
Diff between FGLMtrunc versions 0.1.0 dated 2022-05-26 and 0.2.0 dated 2025-12-22
DESCRIPTION | 12 - MD5 | 12 - build/vignette.rds |binary inst/doc/FGLMtrunc.R | 34 ++--- inst/doc/FGLMtrunc.html | 294 ++++++++++++++++++++++++------------------------ src/Makevars | 1 src/Makevars.win | 1 7 files changed, 180 insertions(+), 174 deletions(-)
More information about TemporalForest at CRAN
Permanent link
Title: Regularization in Cox Frailty Models
Description: Different regularization approaches for Cox Frailty Models by penalization methods are provided.
see Groll et al. (2017) <doi:10.1111/biom.12637> for effects selection.
See also Groll and Hohberg (2024) <doi:10.1002/bimj.202300020> for classical LASSO approach.
Author: Andreas Groll [aut, cre]
Maintainer: Andreas Groll <groll@statistik.tu-dortmund.de>
Diff between PenCoxFrail versions 2.0.0 dated 2024-07-04 and 2.0.1 dated 2025-12-22
DESCRIPTION | 21 +++++++++++++-------- MD5 | 16 ++++++++-------- demo/pencoxfrail-pbc.r | 4 ++-- man/coxFL.Rd | 4 ++-- man/coxlasso.rd | 4 ++-- man/coxridge.rd | 4 ++-- man/pencoxfrail.rd | 15 ++++++++------- src/IntegrMulti.cpp | 1 - src/Makevars.win | 1 - 9 files changed, 37 insertions(+), 33 deletions(-)
Title: Broken Adaptive Ridge Regression with Cyclops
Description: Approximates best-subset selection (L0) regression with
an iteratively adaptive Ridge (L2) penalty for large-scale models.
This package uses Cyclops for an efficient implementation and the
iterative method is described in Kawaguchi et al (2020)
<doi:10.1002/sim.8438> and Li et al (2021)
<doi:10.1016/j.jspi.2020.12.001>.
Author: Marc A. Suchard [aut, cre],
Eric Kawaguchi [aut],
Ning Li [aut],
Gang Li [aut],
Observational Health Data Sciences and Informatics [cph]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between BrokenAdaptiveRidge versions 1.0.1 dated 2025-07-23 and 1.0.2 dated 2025-12-22
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 8 +++++++- R/Prior.R | 13 ++++++++----- R/fastBarPrior.R | 13 ++++++++----- 5 files changed, 32 insertions(+), 20 deletions(-)
More information about BrokenAdaptiveRidge at CRAN
Permanent link
Title: Tandem Repeat Analysis by Capillary Electrophoresis
Description: A pipeline for short tandem repeat instability analysis from fragment analysis data. Inputs of fsa files or peak tables, and a user supplied metadata data-frame. The package identifies ladders, calls peaks, identifies the modal peaks, calls repeats, then calculates repeat instability metrics (e.g. expansion index from Lee et al. (2010) <doi:10.1186/1752-0509-4-29>).
Author: Zachariah McLean [aut, cre, cph] ,
Kevin Correia [aut],
Andrew Jiang [ctb]
Maintainer: Zachariah McLean <zachariah.louis.mclean@gmail.com>
Diff between trace versions 0.6.0 dated 2025-03-14 and 1.0.0 dated 2025-12-22
trace-0.6.0/trace/R/read_fsa.R |only trace-0.6.0/trace/inst/extdata/_extensions |only trace-0.6.0/trace/man/fragments_repeats.Rd |only trace-0.6.0/trace/man/fragments_trace.Rd |only trace-0.6.0/trace/man/generate_trace_template.Rd |only trace-0.6.0/trace/man/peak_table_to_fragments.Rd |only trace-0.6.0/trace/man/repeat_table_to_repeats.Rd |only trace-0.6.0/trace/tests/testthat/test-classes.R |only trace-0.6.0/trace/tests/testthat/test-tidiers.R |only trace-1.0.0/trace/DESCRIPTION | 19 trace-1.0.0/trace/MD5 | 150 - trace-1.0.0/trace/NAMESPACE | 17 trace-1.0.0/trace/NEWS.md | 64 trace-1.0.0/trace/R/add_metadata.R | 161 - trace-1.0.0/trace/R/assign_index_peaks.R | 162 + trace-1.0.0/trace/R/calculate_instability_metrics.R | 937 +++++----- trace-1.0.0/trace/R/call_repeats.R | 386 ++-- trace-1.0.0/trace/R/classes.R | 234 +- trace-1.0.0/trace/R/config.R |only trace-1.0.0/trace/R/constructors.R | 305 +-- trace-1.0.0/trace/R/extract_functions.R | 115 - trace-1.0.0/trace/R/find_alleles.R | 95 - trace-1.0.0/trace/R/find_fragments.R | 140 - trace-1.0.0/trace/R/find_ladders.R | 716 +++++-- trace-1.0.0/trace/R/fix_ladders_shiny_app.R | 39 trace-1.0.0/trace/R/main.R |only trace-1.0.0/trace/R/misc.R | 115 - trace-1.0.0/trace/R/plotting.R | 134 - trace-1.0.0/trace/README.md | 236 -- trace-1.0.0/trace/build/partial.rdb |binary trace-1.0.0/trace/build/vignette.rds |binary trace-1.0.0/trace/data/cell_line_fsa_list.rda |binary trace-1.0.0/trace/data/example_data_repeat_table.rda |binary trace-1.0.0/trace/inst/doc/plotting_traces.R | 46 trace-1.0.0/trace/inst/doc/plotting_traces.Rmd | 51 trace-1.0.0/trace/inst/doc/plotting_traces.html | 172 - trace-1.0.0/trace/inst/extdata/trace_config.yaml |only trace-1.0.0/trace/man/add_metadata.Rd | 55 trace-1.0.0/trace/man/assign_index_peaks.Rd | 61 trace-1.0.0/trace/man/calculate_instability_metrics.Rd | 71 trace-1.0.0/trace/man/call_repeats.Rd | 86 trace-1.0.0/trace/man/extract_alleles.Rd | 18 trace-1.0.0/trace/man/extract_fragments.Rd | 30 trace-1.0.0/trace/man/extract_ladder_summary.Rd | 12 trace-1.0.0/trace/man/extract_repeat_correction_summary.Rd | 33 trace-1.0.0/trace/man/extract_trace_table.Rd | 12 trace-1.0.0/trace/man/figures/README-ggplot-1.png |binary trace-1.0.0/trace/man/figures/README-plot_fragments-1.png |binary trace-1.0.0/trace/man/figures/README-plot_ladders-1.png |binary trace-1.0.0/trace/man/figures/README-plot_traces-1.png |binary trace-1.0.0/trace/man/figures/README-unnamed-chunk-2-1.png |binary trace-1.0.0/trace/man/find_alleles.Rd | 36 trace-1.0.0/trace/man/find_fragments.Rd | 50 trace-1.0.0/trace/man/find_ladders.Rd | 78 trace-1.0.0/trace/man/fix_ladders_interactive.Rd | 17 trace-1.0.0/trace/man/fix_ladders_manual.Rd | 18 trace-1.0.0/trace/man/fragments.Rd | 155 + trace-1.0.0/trace/man/genemapper_table_to_fragments.Rd |only trace-1.0.0/trace/man/load_config.Rd |only trace-1.0.0/trace/man/plot_batch_correction_samples.Rd | 24 trace-1.0.0/trace/man/plot_data_channels.Rd | 2 trace-1.0.0/trace/man/plot_fragments.Rd | 16 trace-1.0.0/trace/man/plot_ladders.Rd | 12 trace-1.0.0/trace/man/plot_repeat_correction_model.Rd | 26 trace-1.0.0/trace/man/plot_traces.Rd | 21 trace-1.0.0/trace/man/read_fsa.Rd | 8 trace-1.0.0/trace/man/remove_fragments.Rd | 6 trace-1.0.0/trace/man/repeat_table_to_fragments.Rd |only trace-1.0.0/trace/man/size_table_to_fragments.Rd |only trace-1.0.0/trace/man/trace-package.Rd | 1 trace-1.0.0/trace/man/trace.Rd |only trace-1.0.0/trace/tests/testthat/fixtures |only trace-1.0.0/trace/tests/testthat/test-add_metadata.R | 124 - trace-1.0.0/trace/tests/testthat/test-assign_index_peaks.R | 58 trace-1.0.0/trace/tests/testthat/test-calculate_instability_metrics.R | 143 + trace-1.0.0/trace/tests/testthat/test-call_repeats.R | 163 + trace-1.0.0/trace/tests/testthat/test-constructors.R | 23 trace-1.0.0/trace/tests/testthat/test-extract_functions.R | 3 trace-1.0.0/trace/tests/testthat/test-find_alleles.R | 39 trace-1.0.0/trace/tests/testthat/test-find_fragments.R | 15 trace-1.0.0/trace/tests/testthat/test-find_ladders.R | 109 - trace-1.0.0/trace/tests/testthat/test-full-pipeline.R | 24 trace-1.0.0/trace/tests/testthat/test-main.R |only trace-1.0.0/trace/tests/testthat/test-shinytest2.R | 143 - trace-1.0.0/trace/tests/testthat/test-trace_output.R |only trace-1.0.0/trace/vignettes/plotting_traces.Rmd | 51 86 files changed, 3057 insertions(+), 2980 deletions(-)
Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in
many situations it is crucial to understand and explain why a model made a specific
prediction. Shapley values is the only method for such prediction explanation framework
with a solid theoretical foundation. Previously known methods for estimating the Shapley
values do, however, assume feature independence. This package implements methods which accounts for any feature
dependence, and thereby produces more accurate estimates of the true Shapley values.
An accompanying 'Python' wrapper ('shaprpy') is available through PyPI.
Author: Martin Jullum [cre, aut] ,
Lars Henry Berge Olsen [aut] ,
Annabelle Redelmeier [aut],
Jon Lachmann [aut] ,
Nikolai Sellereite [aut] ,
Anders Loeland [ctb],
Jens Christian Wahl [ctb],
Camilla Lingjaerde [ctb],
Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
This is a re-admission after prior archival of version 1.0.6 dated 2025-11-17
Diff between shapr versions 1.0.6 dated 2025-11-17 and 1.0.7 dated 2025-12-22
DESCRIPTION | 20 LICENSE | 4 MD5 | 622 NAMESPACE | 276 NEWS.md | 554 R/RcppExports.R | 590 R/approach.R | 262 R/approach_categorical.R | 506 R/approach_copula.R | 346 R/approach_ctree.R | 610 R/approach_empirical.R | 1222 - R/approach_gaussian.R | 346 R/approach_independence.R | 256 R/approach_regression_separate.R | 1022 R/approach_regression_surrogate.R | 487 R/approach_timeseries.R | 296 R/approach_vaeac.R | 5843 ++-- R/approach_vaeac_torch_modules.R | 4098 +-- R/asymmetric_and_causal_Shapley.R | 1039 R/check_convergence.R | 180 R/cli.R | 840 R/compute_estimates.R | 723 R/compute_vS.R | 611 R/documentation.R | 172 R/explain.R | 1312 - R/explain_forecast.R | 922 R/finalize_explanation.R | 453 R/get_feature_specs.R | 144 R/get_predict_model.R | 176 R/get_results.R | 258 R/model.R | 348 R/model_ar.R | 69 R/model_arima.R | 184 R/model_glm.R | 70 R/model_lm.R | 64 R/model_mgcv_gam.R | 82 R/model_ranger.R | 172 R/model_workflow.R | 64 R/model_xgboost.R | 172 R/plot.R | 4041 +-- R/prepare_next_iteration.R | 194 R/print.R | 52 R/save_results.R | 50 R/setup.R | 3701 +-- R/shapley_setup.R | 1658 - R/shapr-package.R | 66 R/summary.R | 274 R/testthat-helpers.R | 56 R/timing.R | 162 R/utils.R | 22 R/zzz.R | 346 README.md | 736 build/vignette.rds |binary inst/CITATION | 52 inst/REFERENCES.bib | 482 inst/doc/asymmetric_causal.Rmd | 4682 +-- inst/doc/asymmetric_causal.html | 5384 ++-- inst/doc/general_usage.Rmd | 5948 ++--- inst/doc/general_usage.html | 6932 ++--- inst/doc/regression.Rmd |11421 ++++++--- inst/doc/regression.html |11839 ++++++---- inst/doc/vaeac.Rmd | 2726 +- inst/doc/vaeac.html | 3418 +- man/additional_regression_setup.Rd | 38 man/aicc_full_cpp.Rd | 72 man/aicc_full_single_cpp.Rd | 64 man/append_vS_list.Rd | 44 man/categorical_to_one_hot_layer.Rd | 66 man/check_categorical_valid_MCsamp.Rd | 60 man/check_convergence.Rd | 38 man/check_groups.Rd | 24 man/check_verbose.Rd | 66 man/cli_compute_vS.Rd | 38 man/cli_iter.Rd | 72 man/cli_startup.Rd | 66 man/cli_topline.Rd | 96 man/coalition_matrix_cpp.Rd | 50 man/compute_MSEv_eval_crit.Rd | 168 man/compute_estimates.Rd | 44 man/compute_shapley.Rd | 46 man/compute_time.Rd | 38 man/compute_vS.Rd | 38 man/convert_feature_name_to_idx.Rd | 76 man/correction_matrix_cpp.Rd | 50 man/create_coalition_table.Rd | 194 man/create_ctree.Rd | 82 man/create_marginal_data_cat.Rd | 122 man/create_marginal_data_gaussian.Rd | 50 man/create_marginal_data_training.Rd | 74 man/default_doc_export.Rd | 52 man/default_doc_internal.Rd | 142 man/exact_coalition_table.Rd | 56 man/explain.Rd | 1241 - man/explain_forecast.Rd | 768 man/figures/README-basic_example-1.png |binary man/finalize_explanation.Rd | 38 man/format_convergence_info.Rd | 42 man/format_info_basic.Rd | 36 man/format_info_extra.Rd | 36 man/format_round.Rd | 44 man/format_shapley_info.Rd | 50 man/gauss_cat_loss.Rd | 60 man/gauss_cat_parameters.Rd | 64 man/gauss_cat_sampler_most_likely.Rd | 66 man/gauss_cat_sampler_random.Rd | 60 man/gaussian_transform.Rd | 42 man/gaussian_transform_separate.Rd | 48 man/get_S_causal_steps.Rd | 114 man/get_cov_mat.Rd | 42 man/get_data_forecast.Rd | 116 man/get_data_specs.Rd | 66 man/get_extra_comp_args_default.Rd | 168 man/get_extra_parameters.Rd | 24 man/get_feature_specs.Rd | 66 man/get_iterative_args_default.Rd | 106 man/get_max_n_coalitions_causal.Rd | 84 man/get_model_specs.Rd | 169 man/get_mu_vec.Rd | 34 man/get_nice_time.Rd | 36 man/get_output_args_default.Rd | 72 man/get_predict_model.Rd | 42 man/get_results.Rd | 172 man/get_supported_approaches.Rd | 30 man/get_supported_models.Rd | 28 man/get_valid_causal_coalitions.Rd | 82 man/group_forecast_setup.Rd | 48 man/hat_matrix_cpp.Rd | 58 man/inv_gaussian_transform_cpp.Rd | 50 man/lag_data.Rd | 48 man/mahalanobis_distance_cpp.Rd | 82 man/mcar_mask_generator.Rd | 76 man/memory_layer.Rd | 70 man/model_checker.Rd | 113 man/num_str.Rd | 38 man/observation_impute.Rd | 76 man/observation_impute_cpp.Rd | 98 man/paired_sampler.Rd | 54 man/plot.shapr.Rd | 465 man/plot_MSEv_eval_crit.Rd | 427 man/plot_SV_several_approaches.Rd | 473 man/plot_vaeac_eval_crit.Rd | 330 man/plot_vaeac_imputed_ggpairs.Rd | 286 man/predict_model.Rd | 263 man/prepare_data.Rd | 136 man/prepare_data_causal.Rd | 76 man/prepare_data_copula_cpp.Rd | 112 man/prepare_data_copula_cpp_caus.Rd | 112 man/prepare_data_gaussian_cpp.Rd | 76 man/prepare_data_gaussian_cpp_caus.Rd | 76 man/prepare_data_single_coalition.Rd | 44 man/prepare_next_iteration.Rd | 38 man/print.shapr.Rd | 70 man/print.summary.shapr.Rd |only man/print_iter.Rd | 38 man/process_factor_data.Rd | 44 man/quantile_type7_cpp.Rd | 56 man/reg_forecast_setup.Rd | 54 man/regression.check_namespaces.Rd | 32 man/regression.check_parameters.Rd | 50 man/regression.check_recipe_func.Rd | 56 man/regression.check_sur_n_comb.Rd | 54 man/regression.check_vfold_cv_para.Rd | 40 man/regression.cv_message.Rd | 58 man/regression.get_string_to_R.Rd | 36 man/regression.get_tune.Rd | 82 man/regression.get_y_hat.Rd | 66 man/regression.surrogate_aug_data.Rd | 124 man/regression.train_model.Rd | 188 man/release_questions.Rd | 30 man/round_manual.Rd | 44 man/rss_cpp.Rd | 50 man/sample_coalition_table.Rd | 158 man/sample_coalitions_cpp_str_paired.Rd | 48 man/sample_combinations.Rd | 66 man/sample_ctree.Rd | 74 man/save_results.Rd | 38 man/setup.Rd | 494 man/setup_approach.Rd | 586 man/shapley_setup.Rd | 38 man/shapley_weights.Rd | 62 man/shapr-package.Rd | 80 man/skip_connection.Rd | 40 man/specified_masks_mask_generator.Rd | 56 man/specified_prob_mask_generator.Rd | 68 man/summary.shapr.Rd | 95 man/test_predict_model.Rd | 52 man/testing_cleanup.Rd | 36 man/vaeac.Rd | 344 man/vaeac_categorical_parse_params.Rd | 86 man/vaeac_check_activation_func.Rd | 44 man/vaeac_check_cuda.Rd | 76 man/vaeac_check_epoch_values.Rd | 108 man/vaeac_check_extra_named_list.Rd | 36 man/vaeac_check_logicals.Rd | 42 man/vaeac_check_mask_gen.Rd | 62 man/vaeac_check_masking_ratio.Rd | 52 man/vaeac_check_parameters.Rd | 388 man/vaeac_check_positive_integers.Rd | 42 man/vaeac_check_positive_numerics.Rd | 42 man/vaeac_check_probabilities.Rd | 42 man/vaeac_check_save_names.Rd | 56 man/vaeac_check_save_parameters.Rd | 100 man/vaeac_check_which_vaeac_model.Rd | 72 man/vaeac_check_x_colnames.Rd | 46 man/vaeac_compute_normalization.Rd | 52 man/vaeac_dataset.Rd | 62 man/vaeac_extend_batch.Rd | 56 man/vaeac_get_current_save_state.Rd | 48 man/vaeac_get_data_objects.Rd | 172 man/vaeac_get_evaluation_criteria.Rd | 50 man/vaeac_get_extra_para_default.Rd | 368 man/vaeac_get_full_state_list.Rd | 66 man/vaeac_get_mask_generator_name.Rd | 106 man/vaeac_get_model_from_checkp.Rd | 60 man/vaeac_get_n_decimals.Rd | 46 man/vaeac_get_optimizer.Rd | 50 man/vaeac_get_save_file_names.Rd | 112 man/vaeac_get_val_iwae.Rd | 84 man/vaeac_get_x_explain_extended.Rd | 54 man/vaeac_impute_missing_entries.Rd | 140 man/vaeac_kl_normal_normal.Rd | 48 man/vaeac_normal_parse_params.Rd | 72 man/vaeac_normalize_data.Rd | 64 man/vaeac_postprocess_data.Rd | 52 man/vaeac_preprocess_data.Rd | 82 man/vaeac_print_train_summary.Rd | 52 man/vaeac_save_state.Rd | 50 man/vaeac_train_model.Rd | 428 man/vaeac_train_model_auxiliary.Rd | 228 man/vaeac_train_model_continue.Rd | 126 man/vaeac_update_para_locations.Rd | 44 man/vaeac_update_pretrained_model.Rd | 42 man/weight_matrix.Rd | 52 man/weight_matrix_cpp.Rd | 64 tests/testthat.R | 14 tests/testthat/helper-ar-arima.R | 52 tests/testthat/helper-lm.R | 94 tests/testthat/helper-model-classes.R |only tests/testthat/helper-ts.R | 80 tests/testthat/test-asymmetric-causal-output.R | 1115 tests/testthat/test-asymmetric-causal-setup.R | 783 tests/testthat/test-classes.R |only tests/testthat/test-forecast-output.R | 408 tests/testthat/test-forecast-setup.R | 1480 - tests/testthat/test-iterative-output.R | 400 tests/testthat/test-iterative-setup.R | 902 tests/testthat/test-model-classes.R |only tests/testthat/test-plot.R | 624 tests/testthat/test-regression-output.R | 646 tests/testthat/test-regression-setup.R | 746 tests/testthat/test-regular-output.R | 1213 - tests/testthat/test-regular-setup.R | 3798 +-- tests/testthat/test-semi-deterministic-output.R | 142 tests/testthat/test-semi-deterministic-setup.R | 254 tests/testthat/test-summary.R | 92 vignettes/asymmetric_causal.Rmd | 4682 +-- vignettes/figure_asymmetric_causal/compare_plots-1.webp |binary vignettes/figure_asymmetric_causal/explanation_asym_cau_SV-1.webp |binary vignettes/figure_asymmetric_causal/explanation_asym_cau_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_asym_con_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_cau_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_con_SV-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_con_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_mar_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/group_gaussian_plot_SV-1.webp |binary vignettes/figure_asymmetric_causal/group_gaussian_plot_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/n_coalitions_plot_SV-1.webp |binary vignettes/figure_asymmetric_causal/n_coalitions_plot_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/scatter_plots-1.webp |binary vignettes/figure_asymmetric_causal/setup_3-1.webp |binary vignettes/figure_asymmetric_causal/sym_and_asym_Shapley_values-1.webp |binary vignettes/figure_asymmetric_causal/two_dates_1-1.webp |binary vignettes/figure_asymmetric_causal/two_dates_2-1.webp |binary vignettes/figure_asymmetric_causal/two_dates_3-1.webp |binary vignettes/figure_general_usage/MSEv-plot-2-1.webp |binary vignettes/figure_general_usage/MSEv-plot-2-2.webp |binary vignettes/figure_general_usage/MSEv-plot-3-1.webp |binary vignettes/figure_general_usage/MSEv-plot-4-1.webp |binary vignettes/figure_general_usage/combined-1-1.webp |binary vignettes/figure_general_usage/group-1.webp |binary vignettes/figure_general_usage/plot-beeswarm-1.webp |binary vignettes/figure_general_usage/plot-scatter-1.webp |binary vignettes/figure_general_usage/plot-waterfall-1.webp |binary vignettes/figure_general_usage/setup-2-1.webp |binary vignettes/figure_general_usage/vaeac-plot-3-1.webp |binary vignettes/figure_regression/MSEv-sum-1.webp |binary vignettes/figure_regression/MSEv-sum-2-1.webp |binary vignettes/figure_regression/SV-sum-1.webp |binary vignettes/figure_regression/SV-sum-2-1.webp |binary vignettes/figure_regression/SV-sum-2.webp |binary vignettes/figure_regression/SV-sum-3.webp |binary vignettes/figure_regression/decision-tree-plot-1.webp |binary vignettes/figure_regression/dt-cv-plot-1.webp |binary vignettes/figure_regression/lm-emp-msev-1.webp |binary vignettes/figure_regression/mixed-plot-1.webp |binary vignettes/figure_regression/mixed-plot-2-1.webp |binary vignettes/figure_regression/mixed-plot-3-1.webp |binary vignettes/figure_regression/mixed-plot-4-1.webp |binary vignettes/figure_regression/ppr-plot-1.webp |binary vignettes/figure_regression/preproc-plot-1.webp |binary vignettes/figure_regression/surrogate-plot-1.webp |binary vignettes/figure_vaeac/check-n_coalitions-1.webp |binary vignettes/figure_vaeac/continue-training-2-1.webp |binary vignettes/figure_vaeac/continue-training-2-2.webp |binary vignettes/figure_vaeac/continue-training-2.webp |binary vignettes/figure_vaeac/continue-training-5.webp |binary vignettes/figure_vaeac/early-stopping-3-1.webp |binary vignettes/figure_vaeac/early-stopping-3-2.webp |binary vignettes/figure_vaeac/first-vaeac-plots-1.webp |binary vignettes/figure_vaeac/paired-sampling-plotting-2.webp |binary vignettes/figure_vaeac/vaeac-grouping-of-features-1.webp |binary vignettes/general_usage.Rmd | 5948 ++--- vignettes/regression.Rmd |11421 ++++++--- vignettes/vaeac.Rmd | 2726 +- 314 files changed, 79357 insertions(+), 65448 deletions(-)
Title: Simulation and Inference for Stochastic Differential Equations
Description: Description: Provides functions for simulation and inference for stochastic differential equations (SDEs). It accompanies the book "Simulation and Inference for Stochastic Differential Equations: With R Examples" (Iacus, 2008, Springer; ISBN: 978-0-387-75838-1).
Author: Stefano Maria Iacus [aut, cre]
Maintainer: Stefano Maria Iacus <smiacus@gmail.com>
Diff between sde versions 2.0.18 dated 2022-08-09 and 2.0.21 dated 2025-12-22
DESCRIPTION | 18 +++++++------ MD5 | 10 +++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/sde.errata.pdf |binary src/sde.sim.c | 64 +++++++++++++++++++----------------------------- 6 files changed, 41 insertions(+), 51 deletions(-)
Title: An Imputation Approach to Estimating Path-Specific Causal
Effects
Description: In causal mediation analysis with multiple causally ordered mediators, a set of path-specific
effects are identified under standard ignorability assumptions. This package implements an imputation
approach to estimating these effects along with a set of bias formulas for conducting sensitivity analysis
(Zhou and Yamamoto <doi:10.31235/osf.io/2rx6p>). It contains two main functions: paths() for estimating
path-specific effects and sens() for conducting sensitivity analysis. Estimation uncertainty is quantified
using the nonparametric bootstrap.
Author: Minh Trinh [aut],
Teppei Yamamoto [aut],
Xiang Zhou [cre]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>
Diff between paths versions 0.1.1 dated 2021-06-18 and 0.1.2 dated 2025-12-22
paths-0.1.1/paths/ChangeLog |only paths-0.1.2/paths/DESCRIPTION | 28 - paths-0.1.2/paths/MD5 | 35 -- paths-0.1.2/paths/NEWS.md | 24 - paths-0.1.2/paths/R/paths-package.R | 13 paths-0.1.2/paths/R/paths_fit.R | 4 paths-0.1.2/paths/R/plot.sens.R | 2 paths-0.1.2/paths/R/sens.R | 2 paths-0.1.2/paths/README.md | 5 paths-0.1.2/paths/inst/examples/sens.paths-example.R | 2 paths-0.1.2/paths/man/paths-package.Rd | 45 +- paths-0.1.2/paths/man/paths.Rd | 324 +++++++++---------- paths-0.1.2/paths/man/plot.paths.Rd | 174 +++++----- paths-0.1.2/paths/man/plot.sens.Rd | 166 ++++----- paths-0.1.2/paths/man/pred.Rd | 80 ++-- paths-0.1.2/paths/man/sens.Rd | 212 ++++++------ paths-0.1.2/paths/man/summary.paths.Rd | 184 +++++----- paths-0.1.2/paths/man/tatar.Rd | 122 +++---- paths-0.1.2/paths/man/welfare.Rd | 122 +++---- 19 files changed, 775 insertions(+), 769 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
'pathfindR' also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in 'pathfindR' are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 2.6.0 dated 2025-09-20 and 2.7.0 dated 2025-12-22
DESCRIPTION | 16 ++++++++-------- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/utility.R | 12 ++++++++++++ R/visualization.R | 11 +++++++++++ build/vignette.rds |binary inst/doc/comparing_results.html | 9 +++++---- inst/doc/intro_vignette.html | 11 ++++++----- inst/doc/manual_execution.html | 9 +++++---- inst/doc/non_hs_analysis.html | 11 ++++++----- inst/doc/obtain_data.html | 9 +++++---- inst/doc/visualization_vignette.html | 17 +++++++++-------- tests/testthat/test-visualization.R | 4 +++- 13 files changed, 86 insertions(+), 51 deletions(-)
Title: Localization Microscopy Data Analysis
Description: Read, register and compare point sets from single molecule localization microscopy.
Author: Jean-Karim Heriche [cre, aut]
Maintainer: Jean-Karim Heriche <heriche@embl.de>
Diff between LOMAR versions 0.5.0 dated 2024-09-26 and 0.5.1 dated 2025-12-22
DESCRIPTION | 15 ++++----- MD5 | 24 +++++++------- NEWS.md | 9 ++++- R/TDA.R | 10 +++--- R/alpha_shape.R | 4 +- R/registration.R | 71 ++++++++++++++++++++++++++++---------------- R/utils.R | 70 ++++++++++++++++++++++--------------------- man/cpd.Rd | 8 +++- man/icp.Rd | 8 +++- man/shape_features_3d.Rd | 1 man/wgmmreg.Rd | 3 + src/diag.cpp | 6 --- tests/testthat/test-utils.R | 2 - 13 files changed, 136 insertions(+), 95 deletions(-)
Title: Plotting Tool for Brain Atlases
Description: Contains 'ggplot2' geom for plotting brain atlases using
simple features. The largest component of the package is the data
for the two built-in atlases. Mowinckel & Vidal-Piñeiro (2020)
<doi:10.1177/2515245920928009>.
Author: Athanasia Mo Mowinckel [aut, cre] ,
Didac Vidal-Pineiro [aut] ,
Ramiro Magno [aut]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg versions 1.6.7 dated 2025-11-14 and 1.6.8 dated 2025-12-22
DESCRIPTION | 10 - MD5 | 72 ++++---- NEWS.md | 2 R/brain_atlas.R | 108 +++++++------ R/brain_join.R | 48 ++--- R/brain_palettes.R | 79 +++++---- R/coord-funcs.R | 97 ++++++----- R/geom-brain.R | 183 ++++++++++++---------- R/ggseg-adapt_scales.R | 104 ++++++------ R/ggseg.R | 69 ++++---- R/layer-brain.R | 232 ++++++++++++++++------------ R/read_freesurfer.R | 46 ++--- R/scale-brain.R | 66 +++++-- README.md | 22 +- inst/doc/externalData.R | 105 ++++++------ inst/doc/externalData.Rmd | 105 ++++++------ inst/doc/externalData.html | 116 +++++++------- inst/doc/freesurfer_files.R | 16 - inst/doc/freesurfer_files.Rmd | 16 - inst/doc/freesurfer_files.html | 18 +- inst/doc/ggseg.R | 100 +++++++----- inst/doc/ggseg.Rmd | 96 +++++++---- inst/doc/ggseg.html | 180 ++++++++++++--------- man/figures/README-unnamed-chunk-5-1.png |binary tests/testthat/test-brain_atlas.R | 73 +++----- tests/testthat/test-brain_join.R | 18 +- tests/testthat/test-brain_palettes.R | 12 - tests/testthat/test-coord-funcs.R | 1 tests/testthat/test-ggseg-adapt_scales.R | 3 tests/testthat/test-ggseg_atlas.R | 92 +++++------ tests/testthat/test-position-brain.R | 16 + tests/testthat/test-read_freesurfer_stats.R | 120 +++++++++++--- tests/testthat/test-scale_brain.R | 55 +++--- tests/testthat/test-theme_brain.R | 21 -- vignettes/externalData.Rmd | 105 ++++++------ vignettes/freesurfer_files.Rmd | 16 - vignettes/ggseg.Rmd | 96 +++++++---- 37 files changed, 1405 insertions(+), 1113 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre] ,
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Siddharth Agrawal [cph] ),
Brendan Frey [cph] ),
Delbert Dueck [cph] ,
Vitalie Spinu [ctb] ,
Frederiek - Maarten Kerckhof [ctb]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.3.5 dated 2025-10-18 and 1.3.6 dated 2025-12-22
DESCRIPTION | 10 ++--- MD5 | 28 +++++++------- NEWS.md | 6 +++ R/RcppExports.R | 4 +- R/clustering_functions.R | 13 ++++-- README.md | 2 - inst/doc/the_clusterR_package.html | 18 ++++----- inst/include/ClusterRHeader.h | 21 ++++++++-- inst/include/affinity_propagation.h | 23 ++++++------ man/Optimal_Clusters_GMM.Rd | 7 +++ man/tryCatch_optimal_clust_GMM.Rd | 3 + src/RcppExports.cpp | 7 ++- src/export_inst_folder_headers.cpp | 4 +- src/init.c | 44 +++++++++++----------- tests/testthat/test-gmm.R | 69 ++++++++++++++++++++++++++++++++++++ 15 files changed, 180 insertions(+), 79 deletions(-)
Title: Interact with Data on 'SurveyCTO'
Description: 'SurveyCTO' is a platform for mobile data collection in offline settings.
The 'rsurveycto' R package uses the 'SurveyCTO' REST API
<https://docs.surveycto.com/05-exporting-and-publishing-data/05-api-access/01.api-access.html>
to read datasets and forms from a 'SurveyCTO' server into R as 'data.table's
and to download file attachments. The package also has limited support to
write datasets to a server.
Author: Jake Hughey [aut, cre],
Robert On [aut]
Maintainer: Jake Hughey <jake@agency.fund>
Diff between rsurveycto versions 0.2.2 dated 2025-06-18 and 0.2.4 dated 2025-12-22
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS.md |only R/scto_get_form_definitions.R | 2 +- R/scto_get_form_metadata.R | 28 ++++++++++++++++++++++------ R/scto_meta.R | 2 +- R/scto_write.R | 7 ++++--- man/scto_get_form_metadata.Rd | 6 +++++- man/scto_write.Rd | 7 ++++--- tests/testthat/scto_auth.txt | 2 +- tests/testthat/test-scto-write.R | 2 -- 11 files changed, 52 insertions(+), 31 deletions(-)
Title: Regression Data Analysis System
Description: Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as linear regression, penalized regression, k-nearest neighbors, decision trees, ada boosting, extreme gradient boosting, random forest, neural networks, deep learning and support vector machines.
Author: Oldemar Rodriguez [aut, cre],
Andres Navarro D. [ctb, prg],
Diego Jimenez A. [ctb, prg],
Ariel Arroyo S. [ctb, prg],
Joseline Quiros M. [ctb, prg],
Alejandro Vargas V. [ctb, prg],
Jennifer Lobo V. [ctb, prg]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between regressoR versions 4.0.4 dated 2025-05-28 and 4.0.7 dated 2025-12-22
DESCRIPTION | 16 MD5 | 131 +-- NAMESPACE | 154 +-- NEWS.md | 6 R/app_config.R | 70 - R/app_server.R | 374 ++++---- R/app_ui.R | 550 ++++++------- R/cv_utils.R | 780 +++++++++--------- R/general_plots.R | 34 R/generate_code_utils.R | 1162 +++++++++++++-------------- R/golem_utils_server.R | 174 ++-- R/golem_utils_ui.R | 628 +++++++------- R/indices_utils.R | 156 +-- R/mod_Predictive_Power.R | 124 +- R/mod_Predictive_Power_utils.R | 10 R/mod_cross_val.R | 756 ++++++++--------- R/mod_cross_val_utils.R | 186 ++-- R/mod_evaluacion.R | 336 +++---- R/mod_ind_nuevos.R | 1560 +++++++++++++++++++------------------ R/mod_ind_nuevos_utils.R | 114 +- R/mod_information_page.R | 76 - R/mod_model_boost_fct.R | 240 ++--- R/mod_model_boost_utils.R | 2 R/mod_model_nnet_utils.R | 10 R/mod_model_rdim_utils.R | 152 +-- R/mod_model_regp_utils.R | 222 ++--- R/mod_model_rndf_fct.R | 308 +++---- R/mod_model_rndf_utils.R | 114 +- R/mod_model_tree_fct.R | 522 ++++++------ R/mod_model_tree_utils.R | 20 R/mod_models_utils.R | 1128 +++++++++++++------------- R/mod_train_test.R | 1372 ++++++++++++++++---------------- R/mod_varerr.R | 202 ++-- R/regressoR.R | 4 R/run_app.R | 56 - R/string_manipulation.R | 130 +-- R/utils_global.R | 412 ++++----- R/utils_inputs.R | 364 ++++---- R/utils_outputs.R | 292 +++--- inst/app.R |only inst/app/lang/diccionario.csv | 642 +++++++-------- inst/app/www/regressor_inputs.css | 248 ++--- inst/app/www/regressor_inputs.js | 156 +-- inst/app/www/regressor_options.css | 100 +- inst/app/www/regressor_options.js | 26 inst/app/www/script_regressor.js | 74 - inst/app/www/style_regressor.css | 338 ++++---- inst/golem-config.yml | 16 inst/rstudio/addins.dcf | 8 man/as_string_c.Rd | 46 - man/e.rdim.rmse.Rd | 48 - man/e.rdim.vare.Rd | 48 - man/e_JS.Rd | 42 man/e_boost_evol_error.Rd | 56 - man/e_boost_importance.Rd | 52 - man/e_coeff_lambda.Rd | 62 - man/e_posib_lambda.Rd | 64 - man/e_rf_error.Rd | 56 - man/e_rndf_importance.Rd | 54 - man/exe.Rd | 50 - man/extract_code.Rd | 46 - man/general.indices.Rd | 74 - man/mod_ind_nuevos_server.Rd | 24 man/plot_real_prediction.Rd | 48 - man/regressoR.Rd | 68 - man/run_app.Rd | 28 man/summary_indices.Rd | 36 67 files changed, 7793 insertions(+), 7664 deletions(-)
Title: Predictive Data Analysis System
Description: Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as K-Nearest Neighbors, Decision Trees, ADA Boosting, Extreme Gradient Boosting, Random Forest, Neural Networks, Deep Learning, Support Vector Machines and Bayesian Methods.
Author: Oldemar Rodriguez [aut, cre],
Diego Jimenez [ctb, prg],
Andres Navarro [ctb, prg],
Jennifer Lobo [ctb, prg]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between predictoR versions 4.1.5 dated 2025-05-28 and 4.1.6 dated 2025-12-22
DESCRIPTION | 14 MD5 | 19 R/mod_acercade.R | 2 R/mod_evaluacion.R | 17 R/mod_model_xgb_utils.R | 41 - R/mod_models_utils.R | 1124 ++++++++++++++--------------- R/mod_train_test.R | 1824 ++++++++++++++++++++++++------------------------ R/predictoR.R | 4 inst/app.R |only man/e_xgb_importance.Rd | 5 man/predictoR.Rd | 4 11 files changed, 1546 insertions(+), 1508 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-01 0.4.0
2018-08-16 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-13 2.0.0
2025-05-29 1.3.0
2025-04-10 1.2.0
2024-12-12 1.1.0
2024-11-20 1.0.0
Title: Tools for Computational Optimal Transport
Description: Transport theory has seen much success in many fields of statistics and machine learning. We provide a variety of algorithms to compute Wasserstein distance, barycenter, and others. See Peyré and Cuturi (2019) <doi:10.1561/2200000073> for the general exposition to the study of computational optimal transport.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between T4transport versions 0.1.5 dated 2025-11-13 and 0.1.7 dated 2025-12-22
T4transport-0.1.5/T4transport/R/free_median_PF.R |only T4transport-0.1.5/T4transport/man/rmedPF.Rd |only T4transport-0.1.7/T4transport/DESCRIPTION | 8 - T4transport-0.1.7/T4transport/MD5 | 50 +++++--- T4transport-0.1.7/T4transport/NAMESPACE | 15 +- T4transport-0.1.7/T4transport/NEWS.md | 15 ++ T4transport-0.1.7/T4transport/R/RcppExports.R | 16 ++ T4transport-0.1.7/T4transport/R/auxiliary_inputs.R | 59 +++++++++ T4transport-0.1.7/T4transport/R/dist_hdist.R |only T4transport-0.1.7/T4transport/R/free_bary_GradientDescent.R | 4 T4transport-0.1.7/T4transport/R/free_median_Weiszfeld.R |only T4transport-0.1.7/T4transport/R/gromov_barycenter.R |only T4transport-0.1.7/T4transport/R/gromov_distance.R |only T4transport-0.1.7/T4transport/R/hist_bary.R |only T4transport-0.1.7/T4transport/R/hist_bary14C.R | 2 T4transport-0.1.7/T4transport/R/hist_interp.R |only T4transport-0.1.7/T4transport/R/hist_med.R |only T4transport-0.1.7/T4transport/R/other_img2measure.R |only T4transport-0.1.7/T4transport/R/package-T4transport.R | 2 T4transport-0.1.7/T4transport/R/test_time_comparison.R |only T4transport-0.1.7/T4transport/build/partial.rdb |binary T4transport-0.1.7/T4transport/inst/REFERENCES.bib | 13 ++ T4transport-0.1.7/T4transport/man/gwbary.Rd |only T4transport-0.1.7/T4transport/man/gwdist.Rd |only T4transport-0.1.7/T4transport/man/hdist.Rd |only T4transport-0.1.7/T4transport/man/histbary.Rd |only T4transport-0.1.7/T4transport/man/histbary14C.Rd | 2 T4transport-0.1.7/T4transport/man/histinterp.Rd |only T4transport-0.1.7/T4transport/man/histmed.Rd |only T4transport-0.1.7/T4transport/man/img2measure.Rd |only T4transport-0.1.7/T4transport/man/rbaryGD.Rd | 4 T4transport-0.1.7/T4transport/man/rmedWB.Rd |only T4transport-0.1.7/T4transport/src/RcppExports.cpp | 66 +++++++++++ T4transport-0.1.7/T4transport/src/src_gromov.cpp |only T4transport-0.1.7/T4transport/src/utility.cpp | 72 ++++++++++++ T4transport-0.1.7/T4transport/src/utility.h | 1 36 files changed, 289 insertions(+), 40 deletions(-)
Title: Various Functions to Facilitate Visualization of Data and
Analysis
Description: When analyzing data, plots are a helpful tool for visualizing data and interpreting statistical models. This package provides a set of simple tools for building plots incrementally, starting with an empty plot region, and adding bars, data points, regression lines, error bars, gradient legends, density distributions in the margins, and even pictures. The package builds further on R graphics by simply combining functions and settings in order to reduce the amount of code to produce for the user. As a result, the package does not use formula input or special syntax, but can be used in combination with default R plot functions. Note: Most of the functions were part of the package 'itsadug', which is now split in two packages: 1. the package 'itsadug', which contains the core functions for visualizing and evaluating nonlinear regression models, and 2. the package 'plotfunctions', which contains more general plot functions.
Author: Jacolien van Rij [aut, cre]
Maintainer: Jacolien van Rij <j.c.van.rij@rug.nl>
Diff between plotfunctions versions 1.4 dated 2020-04-28 and 1.5 dated 2025-12-22
plotfunctions-1.4/plotfunctions/man/plotfunctions.Rd |only plotfunctions-1.5/plotfunctions/DESCRIPTION | 14 plotfunctions-1.5/plotfunctions/MD5 | 94 plotfunctions-1.5/plotfunctions/NAMESPACE | 2 plotfunctions-1.5/plotfunctions/R/plot.R | 195 + plotfunctions-1.5/plotfunctions/R/plotfunctions.R | 16 plotfunctions-1.5/plotfunctions/R/util.R | 74 plotfunctions-1.5/plotfunctions/build/vignette.rds |binary plotfunctions-1.5/plotfunctions/inst/NEWS | 9 plotfunctions-1.5/plotfunctions/inst/doc/plotfunctions.R | 6 plotfunctions-1.5/plotfunctions/inst/doc/plotfunctions.html | 1211 ++++++----- plotfunctions-1.5/plotfunctions/man/addInterval.Rd | 2 plotfunctions-1.5/plotfunctions/man/add_bars.Rd | 6 plotfunctions-1.5/plotfunctions/man/add_n_points.Rd | 2 plotfunctions-1.5/plotfunctions/man/axesLabels.Rd |only plotfunctions-1.5/plotfunctions/man/check_normaldist.Rd | 2 plotfunctions-1.5/plotfunctions/man/color_contour.Rd | 6 plotfunctions-1.5/plotfunctions/man/dotplot_error.Rd | 2 plotfunctions-1.5/plotfunctions/man/drawDevArrows.Rd | 2 plotfunctions-1.5/plotfunctions/man/emptyPlot.Rd | 6 plotfunctions-1.5/plotfunctions/man/errorBars.Rd | 2 plotfunctions-1.5/plotfunctions/man/fill_area.Rd | 2 plotfunctions-1.5/plotfunctions/man/findAbsMin.Rd | 1 plotfunctions-1.5/plotfunctions/man/find_n_neighbors.Rd | 1 plotfunctions-1.5/plotfunctions/man/firstLetterCap.Rd | 1 plotfunctions-1.5/plotfunctions/man/getArrowPos.Rd | 1 plotfunctions-1.5/plotfunctions/man/getCoords.Rd | 2 plotfunctions-1.5/plotfunctions/man/getDec.Rd | 1 plotfunctions-1.5/plotfunctions/man/getFigCoords.Rd | 2 plotfunctions-1.5/plotfunctions/man/getProps.Rd | 2 plotfunctions-1.5/plotfunctions/man/getRange.Rd | 1 plotfunctions-1.5/plotfunctions/man/getRatioCoords.Rd | 1 plotfunctions-1.5/plotfunctions/man/get_palette.Rd | 1 plotfunctions-1.5/plotfunctions/man/gradientLegend.Rd | 8 plotfunctions-1.5/plotfunctions/man/group_sort.Rd | 1 plotfunctions-1.5/plotfunctions/man/inch2coords.Rd | 1 plotfunctions-1.5/plotfunctions/man/isColor.Rd | 1 plotfunctions-1.5/plotfunctions/man/keepFigRatio.Rd |only plotfunctions-1.5/plotfunctions/man/legend_margin.Rd | 2 plotfunctions-1.5/plotfunctions/man/list2str.Rd | 1 plotfunctions-1.5/plotfunctions/man/marginDensityPlot.Rd | 2 plotfunctions-1.5/plotfunctions/man/move_n_point.Rd | 1 plotfunctions-1.5/plotfunctions/man/orderBoxplot.Rd | 1 plotfunctions-1.5/plotfunctions/man/plot_error.Rd | 2 plotfunctions-1.5/plotfunctions/man/plot_image.Rd | 2 plotfunctions-1.5/plotfunctions/man/plotfunctions-package.Rd |only plotfunctions-1.5/plotfunctions/man/plotsurface.Rd | 2 plotfunctions-1.5/plotfunctions/man/se.Rd | 1 plotfunctions-1.5/plotfunctions/man/sortBoxplot.Rd | 2 plotfunctions-1.5/plotfunctions/man/sortGroups.Rd | 1 50 files changed, 1022 insertions(+), 673 deletions(-)
Title: Utilities for Managing a 'Motherduck' Database
Description: Provides helper functions, metadata utilities, and workflows for
administering and managing databases on the 'Motherduck' cloud platform.
Some features require a 'Motherduck' account (<https://motherduck.com/>).
Author: Alejandro Hagan [aut, cre]
Maintainer: Alejandro Hagan <alejandro.hagan@outlook.com>
Diff between motherduck versions 0.2.0 dated 2025-12-02 and 0.2.1 dated 2025-12-22
DESCRIPTION | 6 MD5 | 13 +- NAMESPACE | 3 NEWS.md | 5 R/connection_fns.R | 4 R/utils-db.R | 213 +++++++++++++++++++++++++++------ man/show_information_schema.Rd |only man/validate_database_exists.Rd |only man/validate_database_schema_exists.Rd |only 9 files changed, 199 insertions(+), 45 deletions(-)
Title: Unit Test Add-on for 'testthat'
Description: Enhance package 'testthat' by allowing tests to be attached to the function/object they test.
This allows to keep functional and unit test code together.
Author: Claudia Beleites [aut, cre],
Erick Oduniyi [aut]
Maintainer: Claudia Beleites <Claudia.Beleites@chemometrix.gmbh>
This is a re-admission after prior archival of version 0.2.1 dated 2020-06-24
Diff between hySpc.testthat versions 0.2.1 dated 2020-06-24 and 0.2.2 dated 2025-12-22
hySpc.testthat-0.2.1/hySpc.testthat/README.md |only hySpc.testthat-0.2.2/hySpc.testthat/DESCRIPTION | 11 ++-- hySpc.testthat-0.2.2/hySpc.testthat/LICENSE | 2 hySpc.testthat-0.2.2/hySpc.testthat/MD5 | 13 ++--- hySpc.testthat-0.2.2/hySpc.testthat/R/test-fun.R | 22 --------- hySpc.testthat-0.2.2/hySpc.testthat/R/unittest.R | 23 ---------- hySpc.testthat-0.2.2/hySpc.testthat/man/test_fun.Rd | 2 hySpc.testthat-0.2.2/hySpc.testthat/tests/testthat/test_attached.R | 2 8 files changed, 16 insertions(+), 59 deletions(-)
More information about hySpc.testthat at CRAN
Permanent link
Title: Extract Centerline from Closed Polygons
Description: Generates skeletons of closed 2D polygons using Voronoi diagrams.
It provides methods for 'sf', 'terra', and 'geos' objects to
compute polygon centerlines based on the generated skeletons.
Voronoi, G. (1908) <doi:10.1515/crll.1908.134.198>.
Author: Anatoly Tsyplenkov [aut, cre, cph]
Maintainer: Anatoly Tsyplenkov <atsyplenkov@fastmail.com>
Diff between centerline versions 0.2.4 dated 2025-09-09 and 0.2.5 dated 2025-12-22
DESCRIPTION | 8 MD5 | 28 NEWS.md | 9 R/cnt_path_guess.R | 646 ++++++++++----------- R/geom_cnt.R | 634 ++++++++++----------- R/transformers.R | 102 +-- R/types-check.R | 230 +++---- R/utils.R | 368 ++++++------ README.md | 666 +++++++++++----------- build/partial.rdb |binary man/geom_cnt.Rd | 4 man/geom_cnt_text.Rd | 422 +++++++------- tests/testthat/test-cnt_path.R | 848 ++++++++++++++-------------- tests/testthat/test-cnt_path_guess.R | 1030 +++++++++++++++++------------------ tests/testthat/test-cnt_skeleton.R | 680 +++++++++++------------ 15 files changed, 2848 insertions(+), 2827 deletions(-)
Title: Mander and Thompson Designs
Description: Implements Mander & Thompson's (2010)
<doi:10.1016/j.cct.2010.07.008> methods for two-stage designs
optimal under the alternative hypothesis for phase II [cancer] trials. Also
provides an implementation of Simon's (1989)
<doi:10.1016/0197-2456(89)90015-9> original methodology and
allows exploration of the operating characteristics of sub-optimal designs.
Author: John Kirkpatrick [aut, cre]
Maintainer: John Kirkpatrick <mtdesign@puzzledface.net>
Diff between mtdesign versions 0.1.3 dated 2025-08-23 and 0.1.4 dated 2025-12-22
DESCRIPTION | 11 +--- MD5 | 20 +++---- NEWS.md | 3 + R/functions.R | 75 ++++++++-------------------- README.md | 81 ++++++++++++++----------------- man/createGrid.Rd | 13 +++- man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary tests/testthat/test-createGrid.R | 12 ---- tests/testthat/test-obtainDesign.R | 2 11 files changed, 87 insertions(+), 130 deletions(-)
Title: Fast Agent-Based Epi Models
Description: A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Author: George Vega Yon [aut, cre] ,
Derek Meyer [aut] ,
Andrew Pulsipher [aut] ,
Susan Holmes [rev] ,
Abinash Satapathy [rev] ,
Carinogurjao [rev],
Centers for Disease Control and Prevention [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between epiworldR versions 0.10.0.0 dated 2025-11-14 and 0.11.0.0 dated 2025-12-22
epiworldR-0.10.0.0/epiworldR/R/ModelMeaslesMixing.R |only epiworldR-0.10.0.0/epiworldR/R/ModelMeaslesMixingRiskQuarantine.R |only epiworldR-0.10.0.0/epiworldR/R/ModelMeaslesSchool.R |only epiworldR-0.10.0.0/epiworldR/R/global-actions.R |only epiworldR-0.10.0.0/epiworldR/build/partial.rdb |only epiworldR-0.10.0.0/epiworldR/inst/include/epiworld/network-bones.hpp |only epiworldR-0.10.0.0/epiworldR/inst/tinytest/test-measles-quarantine-errors.R |only epiworldR-0.10.0.0/epiworldR/inst/tinytest/test-measles-quarantine-math.R |only epiworldR-0.10.0.0/epiworldR/inst/tinytest/test-measlesmixing.R |only epiworldR-0.10.0.0/epiworldR/inst/tinytest/test-measlesmixingriskquarantine-multiple.R |only epiworldR-0.10.0.0/epiworldR/inst/tinytest/test-measlesmixingriskquarantine.R |only epiworldR-0.10.0.0/epiworldR/man/ModelMeaslesMixing.Rd |only epiworldR-0.10.0.0/epiworldR/man/ModelMeaslesMixingRiskQuarantine.Rd |only epiworldR-0.10.0.0/epiworldR/man/ModelMeaslesSchool.Rd |only epiworldR-0.10.0.0/epiworldR/man/epiworld-data.Rd |only epiworldR-0.10.0.0/epiworldR/src/actions.cpp |only epiworldR-0.11.0.0/epiworldR/DESCRIPTION | 8 epiworldR-0.11.0.0/epiworldR/MD5 | 211 +++-- epiworldR-0.11.0.0/epiworldR/NAMESPACE | 11 epiworldR-0.11.0.0/epiworldR/NEWS.md | 21 epiworldR-0.11.0.0/epiworldR/R/arg-checks.R | 23 epiworldR-0.11.0.0/epiworldR/R/cpp11.R | 84 +- epiworldR-0.11.0.0/epiworldR/R/data.R | 352 ++++++++-- epiworldR-0.11.0.0/epiworldR/R/entity_tools.R |only epiworldR-0.11.0.0/epiworldR/R/events.R |only epiworldR-0.11.0.0/epiworldR/R/functions-renamed.R | 10 epiworldR-0.11.0.0/epiworldR/R/make_saver.R | 47 - epiworldR-0.11.0.0/epiworldR/R/tool.R | 25 epiworldR-0.11.0.0/epiworldR/R/virus.R | 24 epiworldR-0.11.0.0/epiworldR/README.md | 36 - epiworldR-0.11.0.0/epiworldR/inst/doc/advanced-modeling.html | 12 epiworldR-0.11.0.0/epiworldR/inst/doc/getting-started.html | 12 epiworldR-0.11.0.0/epiworldR/inst/doc/likelihood-free-mcmc.html | 8 epiworldR-0.11.0.0/epiworldR/inst/doc/mixing.html | 42 - epiworldR-0.11.0.0/epiworldR/inst/doc/run-multiple.html | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/adjlist-bones.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/agent-events-meat.hpp | 22 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/config.hpp | 12 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/database-bones.hpp | 125 ++- epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/database-meat.hpp | 310 ++++++++ epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/entity-bones.hpp | 3 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/epiworld.hpp | 6 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/hospitalizationstracker-bones.hpp |only epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/hospitalizationstracker-meat.hpp |only epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/misc.hpp | 54 - epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/model-bones.hpp | 69 + epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/model-meat.hpp | 284 +++++--- epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/modeldiagram-bones.hpp | 9 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/modeldiagram-meat.hpp | 2 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/diffnet.hpp | 2 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/globalevents.hpp | 3 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/init-functions.hpp | 8 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/measlesmixing.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/measlesmixingriskquarantine.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/measlesschool.hpp | 14 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/models.hpp | 102 ++ epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seir.hpp | 18 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seirconnected.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seird.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seirdconnected.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seirmixing.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seirmixingquarantine.hpp | 5 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sir.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sirconnected.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sird.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sirdconnected.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sirlogit.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sirmixing.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sis.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sisd.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/surveillance.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/randgraph.hpp | 58 - epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/tool-distribute-meat.hpp | 95 ++ epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/userdata-bones.hpp | 16 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/virus-bones.hpp | 8 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/virus-distribute-meat.hpp | 94 ++ epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-agents-and-dist-virus-tool.R | 42 - epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-data.R |only epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-entity_tools.R |only epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-globalevents.R |only epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-outbreak-active-cases.R |only epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-sir.R | 2 epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-sirconn.R | 2 epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-tool.R | 97 ++ epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-virus.R | 108 +++ epiworldR-0.11.0.0/epiworldR/man/ModelDiffNet.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIR.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIRCONN.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIRD.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIRDCONN.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIRMixing.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIRMixingQuarantine.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIR.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIRCONN.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIRD.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIRDCONN.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIRLogit.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIRMixing.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIS.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSISD.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSURV.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/add_entities_from_dataframe.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-gentime.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-history.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-hospitalizations.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-model-diagram.Rd | 4 epiworldR-0.11.0.0/epiworldR/man/epiworld-repnum.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-summaries.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-transition.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-transmissions.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworldR-deprecated.Rd | 33 epiworldR-0.11.0.0/epiworldR/man/global-events.Rd | 5 epiworldR-0.11.0.0/epiworldR/man/run_multiple.Rd | 31 epiworldR-0.11.0.0/epiworldR/man/tool.Rd | 11 epiworldR-0.11.0.0/epiworldR/man/virus.Rd | 11 epiworldR-0.11.0.0/epiworldR/src/cpp11.cpp | 160 ++-- epiworldR-0.11.0.0/epiworldR/src/db.cpp | 89 ++ epiworldR-0.11.0.0/epiworldR/src/epimodels.cpp | 160 ---- epiworldR-0.11.0.0/epiworldR/src/events.cpp |only epiworldR-0.11.0.0/epiworldR/src/model.cpp | 10 epiworldR-0.11.0.0/epiworldR/src/tool.cpp | 18 epiworldR-0.11.0.0/epiworldR/src/virus.cpp | 19 epiworldR-0.11.0.0/epiworldR/tests/tinytest.R | 7 123 files changed, 2328 insertions(+), 908 deletions(-)
Title: Tools and Infrastructure for Developing 'Scalable' 'HDF5'-Based
Methods
Description: A framework for 'scalable' statistical computing on large on-disk
matrices stored in 'HDF5' files. It provides efficient block-wise
implementations of core linear-algebra operations (matrix multiplication,
SVD, PCA, QR decomposition, and canonical correlation analysis) written
in C++ and R. These building blocks are designed not only for direct use,
but also as foundational components for developing new statistical methods
that must operate on datasets too large to fit in memory. The package
supports data provided either as 'HDF5' files or standard R objects, and is
intended for high-dimensional applications such as 'omics' and
precision-medicine research.
Author: Dolors Pelegri-Siso [aut, cre] ,
Juan R. Gonzalez [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
Diff between BigDataStatMeth versions 1.0.2 dated 2025-11-29 and 1.0.3 dated 2025-12-22
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 11 - README.md | 412 +++++++++++++++++++++++++++++++-------- inst/doc/BigDataStatMeth.html | 6 inst/include/BigDataStatMeth.hpp | 10 src/Makevars.in | 5 src/Makevars.win | 5 8 files changed, 359 insertions(+), 110 deletions(-)
More information about BigDataStatMeth at CRAN
Permanent link
Title: Interface to 'Vamp' Audio Analysis Plugins
Description: Provides an interface to the 'Vamp' audio analysis plugin system
<https://www.vamp-plugins.org/> developed by Queen Mary University of London's
Centre for Digital Music. Enables loading and running 'Vamp' plugins for various audio analysis
tasks including tempo detection, onset detection, spectral analysis, and
audio feature extraction. Supports mono and stereo audio with automatic
channel adaptation and domain conversion.
Author: Ed Baker [aut, cre] ,
Authors of vamp-sdk [cph] ,
Mark Borgerding [cph]
Maintainer: Ed Baker <ed@ebaker.me.uk>
Diff between ReVAMP versions 1.0.0 dated 2025-12-19 and 1.0.1 dated 2025-12-22
DESCRIPTION | 8 MD5 | 21 +- NAMESPACE | 1 NEWS.md | 6 R/RcppExports.R | 4 R/vamp_functions.R | 15 + man/runPlugins.Rd |only src/PluginLoader.cpp | 2 src/R_host.cpp | 377 +++++++++++++++++++++++++++++++++++++ src/RcppExports.cpp | 19 + src/RealTime.cpp | 4 src/RealTime_impl.cpp |only tests/testthat/test-multi-plugin.R |only 13 files changed, 441 insertions(+), 16 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3."
Klein, A., & Moosb [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.14 dated 2025-11-18 and 1.0.15 dated 2025-12-22
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Title: Generalized Bayesian Optimal Phase II Design (G-BOP2)
Description: Provides functions for implementing the Generalized Bayesian Optimal Phase II (G-BOP2) design using various Particle Swarm Optimization (PSO) algorithms, including:
- PSO-Default, based on Kennedy and Eberhart (1995) <doi:10.1109/ICNN.1995.488968>, "Particle Swarm Optimization";
- PSO-Quantum, based on Sun, Xu, and Feng (2004) <doi:10.1109/ICCIS.2004.1460396>, "A Global Search Strategy of Quantum-Behaved Particle Swarm Optimization";
- PSO-Dexp, based on Stehlík et al. (2024) <doi:10.1016/j.asoc.2024.111913>, "A Double Exponential Particle Swarm Optimization with Non-Uniform Variates as Stochastic Tuning and Guaranteed Convergence to a Global Optimum with Sample Applications to Finding Optimal Exact Designs in Biostatistics";
- and PSO-GO.
Author: Xinying Fang [aut],
Wanni Lei [aut, cre],
Shouhao Zhou [aut],
Ping-Yang Chen [aut],
Ray-Bing Chen [aut],
Weng Kee Wong [aut],
J. Jack Lee [aut]
Maintainer: Wanni Lei <wanni.lei17@gmail.com>
Diff between GBOP2 versions 0.1.3 dated 2025-04-22 and 0.1.4 dated 2025-12-22
GBOP2-0.1.3/GBOP2/inst/doc/Vignette.html |only GBOP2-0.1.3/GBOP2/inst/doc/Vignette.html.asis |only GBOP2-0.1.3/GBOP2/vignettes/Vignette.Rmd |only GBOP2-0.1.3/GBOP2/vignettes/Vignette.html.asis |only GBOP2-0.1.4/GBOP2/DESCRIPTION | 22 ++- GBOP2-0.1.4/GBOP2/MD5 | 57 +++++---- GBOP2-0.1.4/GBOP2/NAMESPACE | 1 GBOP2-0.1.4/GBOP2/R/GBOP2_maxP_TE.gbop2.R | 24 +--- GBOP2-0.1.4/GBOP2/R/GBOP2_maxP_dualE.gbop2.R | 2 GBOP2-0.1.4/GBOP2/R/GBOP2_maxP_singleE.gbop2.R | 2 GBOP2-0.1.4/GBOP2/R/GBOP2_minSS_TE.gbop2.R | 23 +-- GBOP2-0.1.4/GBOP2/R/GBOP2_minSS_dualE.gbop2.R | 2 GBOP2-0.1.4/GBOP2/R/GBOP2_minSS_singleE.gbop2.R | 2 GBOP2-0.1.4/GBOP2/R/PSO_design_TE.gbop2.R | 4 GBOP2-0.1.4/GBOP2/R/PSO_power_TE.gbop2.R | 10 - GBOP2-0.1.4/GBOP2/R/summary.gbop2.R | 8 - GBOP2-0.1.4/GBOP2/build/vignette.rds |binary GBOP2-0.1.4/GBOP2/inst/doc/vignette.html |only GBOP2-0.1.4/GBOP2/inst/doc/vignette.html.asis |only GBOP2-0.1.4/GBOP2/inst/vignette-source |only GBOP2-0.1.4/GBOP2/man/GBOP2_maxP_TE.Rd | 8 - GBOP2-0.1.4/GBOP2/man/GBOP2_maxP_dualE.Rd | 2 GBOP2-0.1.4/GBOP2/man/GBOP2_maxP_singleE.Rd | 2 GBOP2-0.1.4/GBOP2/man/GBOP2_minSS_TE.Rd | 10 - GBOP2-0.1.4/GBOP2/man/GBOP2_minSS_dualE.Rd | 2 GBOP2-0.1.4/GBOP2/man/GBOP2_minSS_singleE.Rd | 2 GBOP2-0.1.4/GBOP2/src/Calculation2_original.cpp | 4 GBOP2-0.1.4/GBOP2/src/Calculation_minimizeN_twolambda_update.cpp | 30 +++-- GBOP2-0.1.4/GBOP2/src/Calculation_twoboundaries_jsm.cpp | 58 ++++++---- GBOP2-0.1.4/GBOP2/src/GBOP2_types.h | 24 +++- GBOP2-0.1.4/GBOP2/src/Makevars | 2 GBOP2-0.1.4/GBOP2/src/Makevars.win |only GBOP2-0.1.4/GBOP2/src/RcppExports.cpp | 1 GBOP2-0.1.4/GBOP2/vignettes/vignette.html.asis |only 34 files changed, 154 insertions(+), 148 deletions(-)
Title: Guarded Resampling Workflows for Safe and Automated Machine
Learning in R
Description: Provides a guarded resampling workflow for training and evaluating machine‑learning models.
When the guarded resampling path is used, preprocessing and model fitting are re‑estimated within
each resampling split to reduce leakage risk. Supports multiple resampling schemes, integrates
with established engines in the 'tidymodels' ecosystem, and aims to improve evaluation reliability by
coordinating preprocessing, fitting, and evaluation within supported workflows. Offers a lightweight
AutoML‑style workflow by automating model training, resampling, and tuning across multiple algorithms,
while keeping evaluation design explicit and user‑controlled.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut] ,
Eda Karaismailoglu [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between fastml versions 0.7.0 dated 2025-10-29 and 0.7.5 dated 2025-12-22
fastml-0.7.0/fastml/man/evaluate_models.Rd |only fastml-0.7.5/fastml/DESCRIPTION | 41 fastml-0.7.5/fastml/MD5 | 96 fastml-0.7.5/fastml/NAMESPACE | 87 fastml-0.7.5/fastml/NEWS.md |only fastml-0.7.5/fastml/R/counterfactual_explain.R | 203 - fastml-0.7.5/fastml/R/engine_helpers.R | 15 fastml-0.7.5/fastml/R/evaluate_models.R | 98 fastml-0.7.5/fastml/R/explain_ale.R | 84 fastml-0.7.5/fastml/R/explain_dalex.R | 463 +- fastml-0.7.5/fastml/R/explain_lime.R | 66 fastml-0.7.5/fastml/R/explainer_helpers.R |only fastml-0.7.5/fastml/R/fastexplain.R | 174 fastml-0.7.5/fastml/R/fastexplore.R | 1840 ++------- fastml-0.7.5/fastml/R/fastml.R | 749 ++- fastml-0.7.5/fastml/R/interaction_strength.R | 64 fastml-0.7.5/fastml/R/model_selection_helpers.R | 4 fastml-0.7.5/fastml/R/model_spec_registry.R |only fastml-0.7.5/fastml/R/plot.fastml.R | 83 fastml-0.7.5/fastml/R/plot_ice.R | 35 fastml-0.7.5/fastml/R/predict.fastml.R | 171 fastml-0.7.5/fastml/R/process_model.R | 275 + fastml-0.7.5/fastml/R/resampling_guard.R |only fastml-0.7.5/fastml/R/resampling_utils.R |only fastml-0.7.5/fastml/R/security_guards.R |only fastml-0.7.5/fastml/R/spec_boosting.R | 1 fastml-0.7.5/fastml/R/spec_other.R | 20 fastml-0.7.5/fastml/R/spec_tree.R | 11 fastml-0.7.5/fastml/R/summary.fastml.R | 466 -- fastml-0.7.5/fastml/R/surrogate_tree.R | 64 fastml-0.7.5/fastml/R/train_models.R | 1994 ++++++++-- fastml-0.7.5/fastml/R/xgboost_survival.R | 71 fastml-0.7.5/fastml/R/zzz_globals.R |only fastml-0.7.5/fastml/README.md | 149 fastml-0.7.5/fastml/man/counterfactual_explain.Rd | 41 fastml-0.7.5/fastml/man/explain_dalex.Rd | 3 fastml-0.7.5/fastml/man/explain_lime.Rd | 6 fastml-0.7.5/fastml/man/fastexplain.Rd | 58 fastml-0.7.5/fastml/man/fastexplore.Rd | 136 fastml-0.7.5/fastml/man/fastml.Rd | 68 fastml-0.7.5/fastml/man/fastml_compute_holdout_results.Rd |only fastml-0.7.5/fastml/man/fastml_guard_detect_full_analysis.Rd |only fastml-0.7.5/fastml/man/fastml_prepare_explainer_inputs.Rd |only fastml-0.7.5/fastml/man/plot.fastml.Rd | 3 fastml-0.7.5/fastml/man/plot_ice.Rd | 5 fastml-0.7.5/fastml/man/predict.fastml.Rd | 17 fastml-0.7.5/fastml/man/predict_model.model_fit.Rd |only fastml-0.7.5/fastml/man/process_model.Rd | 10 fastml-0.7.5/fastml/man/train_models.Rd | 67 fastml-0.7.5/fastml/tests/testthat/Rplots.pdf |only fastml-0.7.5/fastml/tests/testthat/test-fastexplain.R | 23 fastml-0.7.5/fastml/tests/testthat/test-fastml-workflows.R |only fastml-0.7.5/fastml/tests/testthat/test-fastml.R | 272 + fastml-0.7.5/fastml/tests/testthat/test-piecewise-exp-utils.R | 3 fastml-0.7.5/fastml/tests/testthat/test-resampling-methods.R |only fastml-0.7.5/fastml/tests/testthat/test-resampling.R |only fastml-0.7.5/fastml/tests/testthat/test-survival.R | 26 57 files changed, 4887 insertions(+), 3175 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] ,
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb],
Chad Klumb [ctb],
Michal Bojanowski [ctb] ,
[...truncated...]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm versions 4.10.1 dated 2025-08-27 and 4.11.0 dated 2025-12-22
ergm-4.10.1/ergm/man/samplk.Rd |only ergm-4.10.1/ergm/src/MHproposals_triadic.c |only ergm-4.11.0/ergm/DESCRIPTION | 24 ergm-4.11.0/ergm/MD5 | 336 ++++---- ergm-4.11.0/ergm/NAMESPACE | 8 ergm-4.11.0/ergm/R/InitErgmConstraint.R | 2 ergm-4.11.0/ergm/R/InitErgmConstraint.operator.R | 120 ++ ergm-4.11.0/ergm/R/InitErgmProposal.R | 17 ergm-4.11.0/ergm/R/InitErgmTerm.R | 50 - ergm-4.11.0/ergm/R/InitErgmTerm.bipartite.R | 4 ergm-4.11.0/ergm/R/InitErgmTerm.dgw_sp.R | 14 ergm-4.11.0/ergm/R/InitErgmTerm.operator.R | 29 ergm-4.11.0/ergm/R/InitErgmTerm.spcache.R | 2 ergm-4.11.0/ergm/R/InitWtErgmTerm.R | 6 ergm-4.11.0/ergm/R/InitWtErgmTerm.operator.R | 24 ergm-4.11.0/ergm/R/approx.hotelling.diff.test.R | 9 ergm-4.11.0/ergm/R/as.network.numeric.R | 5 ergm-4.11.0/ergm/R/control.ergm.R | 35 ergm-4.11.0/ergm/R/data.R | 412 ++++------ ergm-4.11.0/ergm/R/ergm-defunct.R | 6 ergm-4.11.0/ergm/R/ergm-deprecated.R | 8 ergm-4.11.0/ergm/R/ergm-package.R | 220 ----- ergm-4.11.0/ergm/R/ergm.CD.fixed.R | 9 ergm-4.11.0/ergm/R/ergm.MCMLE.R | 20 ergm-4.11.0/ergm/R/ergm.R | 106 -- ergm-4.11.0/ergm/R/ergm.bridge.R | 15 ergm-4.11.0/ergm/R/ergm.eta.R | 14 ergm-4.11.0/ergm/R/ergm.getMCMCsample.R | 37 ergm-4.11.0/ergm/R/ergm.logitreg.R | 2 ergm-4.11.0/ergm/R/ergm.mple.R | 23 ergm-4.11.0/ergm/R/ergm.san.R | 10 ergm-4.11.0/ergm/R/ergm.utility.R | 24 ergm-4.11.0/ergm/R/ergm_estfun.R | 2 ergm-4.11.0/ergm/R/ergm_model.R | 22 ergm-4.11.0/ergm/R/ergm_model.utils.R | 2 ergm-4.11.0/ergm/R/ergm_mplecov.R | 10 ergm-4.11.0/ergm/R/ergm_proposal.R | 12 ergm-4.11.0/ergm/R/get.node.attr.R | 46 - ergm-4.11.0/ergm/R/godfather.R | 50 - ergm-4.11.0/ergm/R/gof.ergm.R | 248 ++++-- ergm-4.11.0/ergm/R/logLik.ergm.R | 5 ergm-4.11.0/ergm/R/mcmc.diagnostics.ergm.R | 8 ergm-4.11.0/ergm/R/nonidentifiability.R | 90 ++ ergm-4.11.0/ergm/R/simulate.ergm.R | 5 ergm-4.11.0/ergm/R/summary.ergm.R | 69 + ergm-4.11.0/ergm/R/zzz.R | 6 ergm-4.11.0/ergm/build/partial.rdb |binary ergm-4.11.0/ergm/build/stage23.rdb |binary ergm-4.11.0/ergm/build/vignette.rds |binary ergm-4.11.0/ergm/data/datalist | 2 ergm-4.11.0/ergm/data/samplk.RData |binary ergm-4.11.0/ergm/data/sampson.RData |binary ergm-4.11.0/ergm/inst/CITATION | 4 ergm-4.11.0/ergm/inst/NEWS.Rd | 125 +++ ergm-4.11.0/ergm/inst/REFERENCES.bib | 385 +++++++++ ergm-4.11.0/ergm/inst/doc/cpp-api.Rmd |only ergm-4.11.0/ergm/inst/doc/cpp-api.html |only ergm-4.11.0/ergm/inst/doc/ergm-term-crossRef.html | 303 +++++-- ergm-4.11.0/ergm/inst/doc/ergm.html | 63 - ergm-4.11.0/ergm/inst/doc/nodal_attributes.html | 4 ergm-4.11.0/ergm/inst/include/cpp |only ergm-4.11.0/ergm/inst/include/ergm_MHproposal_bd.h | 15 ergm-4.11.0/ergm/inst/include/ergm_MHproposal_changestat.h |only ergm-4.11.0/ergm/inst/include/ergm_MHproposals_degree.h | 8 ergm-4.11.0/ergm/inst/include/ergm_Rutil.h | 39 ergm-4.11.0/ergm/inst/include/ergm_changestat.h | 2 ergm-4.11.0/ergm/inst/include/ergm_constants.h | 2 ergm-4.11.0/ergm/inst/include/ergm_dyad_hashmap.h | 16 ergm-4.11.0/ergm/inst/include/ergm_dyadgen.h | 10 ergm-4.11.0/ergm/inst/include/ergm_edgelist.h | 2 ergm-4.11.0/ergm/inst/include/ergm_wtMHproposal_changestat.h |only ergm-4.11.0/ergm/inst/include/ergm_wtchangestat.h | 2 ergm-4.11.0/ergm/inst/include/inc/ergm_MHproposal.h.template.do_not_include_directly.h | 12 ergm-4.11.0/ergm/inst/include/inc/ergm_MHproposal_changestat.h.template.do_not_include_directly.h |only ergm-4.11.0/ergm/inst/include/inc/ergm_changestat.h.template.do_not_include_directly.h | 14 ergm-4.11.0/ergm/inst/include/inc/ergm_changestat_common.do_not_include_directly.h | 1 ergm-4.11.0/ergm/inst/include/inc/ergm_edgetree.h.template.do_not_include_directly.h | 16 ergm-4.11.0/ergm/inst/include/inc/ergm_edgetree_common.do_not_include_directly.h | 1 ergm-4.11.0/ergm/inst/include/inc/ergm_edgetree_inline_template.do_not_include_directly.h | 18 ergm-4.11.0/ergm/inst/include/inc/ergm_model.h.template.do_not_include_directly.h | 12 ergm-4.11.0/ergm/inst/include/inc/ergm_state.h.template.do_not_include_directly.h | 8 ergm-4.11.0/ergm/man/ChangeStats-ergmConstraint-a69283e7.Rd |only ergm-4.11.0/ergm/man/I-ergmConstraint-ca2567ac.Rd |only ergm-4.11.0/ergm/man/I-ergmTerm-ca2567ac.Rd |only ergm-4.11.0/ergm/man/altkstar-ergmTerm-201bf7a6.Rd | 6 ergm-4.11.0/ergm/man/approx.hotelling.diff.test.Rd | 5 ergm-4.11.0/ergm/man/as.network.numeric.Rd | 5 ergm-4.11.0/ergm/man/b1nodematch-ergmTerm-110b470e.Rd | 2 ergm-4.11.0/ergm/man/b2nodematch-ergmTerm-126ff8a2.Rd | 2 ergm-4.11.0/ergm/man/balance-ergmTerm-9111bd77.Rd | 2 ergm-4.11.0/ergm/man/cdf-ergmTerm-66ced489.Rd |only ergm-4.11.0/ergm/man/cohab.Rd | 10 ergm-4.11.0/ergm/man/control.ergm.Rd | 34 ergm-4.11.0/ergm/man/cyclicalweights-ergmTerm-994a6687.Rd | 2 ergm-4.11.0/ergm/man/degree15-ergmTerm-ea15bf13.Rd | 2 ergm-4.11.0/ergm/man/dsp-ergmTerm-1a10473d.Rd | 7 ergm-4.11.0/ergm/man/dyadnoise-ergmConstraint-03418976.Rd | 2 ergm-4.11.0/ergm/man/ecoli.Rd | 13 ergm-4.11.0/ergm/man/ergm-defunct.Rd | 5 ergm-4.11.0/ergm/man/ergm-deprecated.Rd | 5 ergm-4.11.0/ergm/man/ergm-package.Rd | 73 - ergm-4.11.0/ergm/man/ergm.Rd | 114 -- ergm-4.11.0/ergm/man/ergm.bridge.llr.Rd | 5 ergm-4.11.0/ergm/man/ergm.estfun.Rd | 2 ergm-4.11.0/ergm/man/ergm.eta.Rd | 12 ergm-4.11.0/ergm/man/ergm.godfather.Rd | 18 ergm-4.11.0/ergm/man/ergmConstraint.Rd | 25 ergm-4.11.0/ergm/man/ergmHint.Rd | 25 ergm-4.11.0/ergm/man/ergmProposal.Rd | 19 ergm-4.11.0/ergm/man/ergmReference.Rd | 12 ergm-4.11.0/ergm/man/ergmTerm.Rd | 43 - ergm-4.11.0/ergm/man/ergm_GWDECAY.Rd | 4 ergm-4.11.0/ergm/man/ergm_model.Rd | 16 ergm-4.11.0/ergm/man/esp-ergmTerm-d2e07fc8.Rd | 7 ergm-4.11.0/ergm/man/faux.desert.high.Rd | 11 ergm-4.11.0/ergm/man/faux.dixon.high.Rd | 11 ergm-4.11.0/ergm/man/faux.magnolia.high.Rd | 9 ergm-4.11.0/ergm/man/faux.mesa.high.Rd | 15 ergm-4.11.0/ergm/man/florentine.Rd | 19 ergm-4.11.0/ergm/man/gof.Rd | 58 - ergm-4.11.0/ergm/man/gwdsp-ergmTerm-4e3dfd97.Rd | 7 ergm-4.11.0/ergm/man/gwesp-ergmTerm-3d6fb5a8.Rd | 7 ergm-4.11.0/ergm/man/gwnsp-ergmTerm-6def2a32.Rd | 7 ergm-4.11.0/ergm/man/idegree15-ergmTerm-b83b1a3a.Rd | 2 ergm-4.11.0/ergm/man/intransitive-ergmTerm-4a599cad.Rd | 2 ergm-4.11.0/ergm/man/kapferer.Rd | 7 ergm-4.11.0/ergm/man/logLik.ergm.Rd | 5 ergm-4.11.0/ergm/man/mcmc.diagnostics.Rd | 7 ergm-4.11.0/ergm/man/mutual-ergmTerm-22863009.Rd | 2 ergm-4.11.0/ergm/man/nearsimmelian-ergmTerm-ba85787e.Rd | 2 ergm-4.11.0/ergm/man/nodal_attributes-API.Rd | 11 ergm-4.11.0/ergm/man/nsp-ergmTerm-4586ea4f.Rd | 7 ergm-4.11.0/ergm/man/odegree15-ergmTerm-8ee8801b.Rd | 2 ergm-4.11.0/ergm/man/sampson.Rd | 219 +++-- ergm-4.11.0/ergm/man/san.Rd | 8 ergm-4.11.0/ergm/man/simmelian-ergmTerm-15e60325.Rd | 2 ergm-4.11.0/ergm/man/simmelianties-ergmTerm-3361aef9.Rd | 4 ergm-4.11.0/ergm/man/simulate.ergm.Rd | 5 ergm-4.11.0/ergm/man/spcachenet-ergmAuxiliary-f1950bb3.Rd | 7 ergm-4.11.0/ergm/man/spectrum0.mvar.Rd | 2 ergm-4.11.0/ergm/man/summary.ergm.Rd | 3 ergm-4.11.0/ergm/man/transitive-ergmTerm-838987d1.Rd | 2 ergm-4.11.0/ergm/man/transitiveweights-ergmTerm-7797c57b.Rd | 2 ergm-4.11.0/ergm/man/triadcensus-ergmTerm-6a6bbd87.Rd | 2 ergm-4.11.0/ergm/man/triadic-ergmHint-b01cc436.Rd | 4 ergm-4.11.0/ergm/src/MHproposals.c | 101 +- ergm-4.11.0/ergm/src/MHproposals.h | 22 ergm-4.11.0/ergm/src/MHproposals_triadic.cpp |only ergm-4.11.0/ergm/src/changestats.c | 355 +------- ergm-4.11.0/ergm/src/changestats_auxnet.c | 10 ergm-4.11.0/ergm/src/changestats_dyad_ind.c.template.do_not_include_directly.h | 16 ergm-4.11.0/ergm/src/changestats_experimental.c | 153 +-- ergm-4.11.0/ergm/src/changestats_operator.c | 26 ergm-4.11.0/ergm/src/changestats_operator.c.template.do_not_include_directly.h | 30 ergm-4.11.0/ergm/src/cpp_changestats.cpp |only ergm-4.11.0/ergm/src/cpp_wtchangestats.cpp |only ergm-4.11.0/ergm/src/model.c.template.do_not_include_directly.h | 2 ergm-4.11.0/ergm/src/wtchangestats.c | 159 --- ergm-4.11.0/ergm/src/wtchangestats_auxnet.c | 8 ergm-4.11.0/ergm/tests/testthat.R | 1 ergm-4.11.0/ergm/tests/testthat/helper-htests.R | 4 ergm-4.11.0/ergm/tests/testthat/test-bridge-target.stats.R | 3 ergm-4.11.0/ergm/tests/testthat/test-constrain-blockdiag.R | 8 ergm-4.11.0/ergm/tests/testthat/test-constrain-dind.R | 8 ergm-4.11.0/ergm/tests/testthat/test-constraints.R | 32 ergm-4.11.0/ergm/tests/testthat/test-ergm-term-doc.R | 6 ergm-4.11.0/ergm/tests/testthat/test-gof.R | 27 ergm-4.11.0/ergm/tests/testthat/test-nonident-test.R | 4 ergm-4.11.0/ergm/tests/testthat/test-parallel.R | 1 ergm-4.11.0/ergm/tests/testthat/test-term-Offset.R | 10 ergm-4.11.0/ergm/vignettes/cpp-api.Rmd |only 171 files changed, 2756 insertions(+), 2388 deletions(-)
Title: Helper Functions for Org Files
Description: Helper functions for Org files (<https://orgmode.org/>):
a generic function 'toOrg' for transforming R objects into Org
markup (most useful for data frames; there are also methods for
Dates/POSIXt) and a function to read Org tables into data frames.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between orgutils versions 0.5-2 dated 2025-12-15 and 0.5-3 dated 2025-12-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 +++++ inst/doc/orgutils_examples.Rnw | 4 ++-- inst/doc/orgutils_examples.pdf |binary vignettes/orgutils_examples.Rnw | 4 ++-- 6 files changed, 18 insertions(+), 13 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks API. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both CPU and GPU devices.
Author: Tomasz Kalinowski [aut, cph, cre],
Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
Francois Chollet [aut, cph],
Posit Software, PBC [cph, fnd],
Google [cph, fnd],
Yuan Tang [ctb, cph] ,
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigri [...truncated...]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between keras3 versions 1.4.0 dated 2025-05-04 and 1.5.0 dated 2025-12-22
DESCRIPTION | 8 MD5 | 1250 +++++----- NAMESPACE | 58 NEWS.md | 102 R/Layer.R | 17 R/activations.R | 26 R/callbacks.R | 12 R/config.R | 79 R/datasets.R | 267 +- R/freeze.R | 7 R/history.R | 2 R/install.R | 181 + R/jax-methods.R | 111 R/layers-backend-wrappers.R | 8 R/layers-convolutional.R | 51 R/layers-core.R | 37 R/layers-merging.R | 16 R/layers-normalization.R | 10 R/layers-pooling.R | 2 R/layers-preprocessing.R | 97 R/layers-regularization.R | 4 R/layers-reshaping.R | 18 R/layers-rnn.R | 3 R/losses.R | 104 R/metrics.R | 12 R/model-persistence.R | 94 R/ops-image.R | 88 R/ops-nn.R | 101 R/ops-numpy.R | 237 + R/ops.R | 119 R/optimizers.R | 176 + R/package.R | 21 R/py-classes.R | 32 R/r-utils.R | 31 R/reexports.R | 21 R/s3-methods.R | 13 R/utils.R | 15 R/variable.R | 11 build/vignette.rds |binary inst/doc/custom_train_step_in_tensorflow.Rmd | 10 inst/doc/custom_train_step_in_tensorflow.html | 10 inst/doc/distributed_training_with_tensorflow.Rmd | 14 inst/doc/distributed_training_with_tensorflow.html | 14 inst/doc/distribution.Rmd | 20 inst/doc/distribution.html | 20 inst/doc/functional_api.Rmd | 6 inst/doc/functional_api.html | 12 inst/doc/getting_started.Rmd | 8 inst/doc/getting_started.html | 12 inst/doc/intro_to_keras_for_engineers.Rmd | 24 inst/doc/intro_to_keras_for_engineers.html | 24 inst/doc/making_new_layers_and_models_via_subclassing.Rmd | 4 inst/doc/making_new_layers_and_models_via_subclassing.html | 4 inst/doc/serialization_and_saving.Rmd | 39 inst/doc/serialization_and_saving.html | 187 - inst/doc/training_with_built_in_methods.Rmd | 32 inst/doc/training_with_built_in_methods.html | 34 inst/doc/transfer_learning.Rmd | 12 inst/doc/transfer_learning.html | 18 inst/doc/writing_a_custom_training_loop_in_tensorflow.Rmd | 36 inst/doc/writing_a_custom_training_loop_in_tensorflow.html | 36 inst/doc/writing_your_own_callbacks.Rmd | 16 inst/doc/writing_your_own_callbacks.html | 16 inst/keras-constraints.txt |only 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man/callback_lambda.Rd | 6 man/callback_model_checkpoint.Rd | 5 man/callback_reduce_lr_on_plateau.Rd | 2 man/config_backend.Rd | 2 man/config_disable_flash_attention.Rd | 2 man/config_disable_interactive_logging.Rd | 2 man/config_disable_traceback_filtering.Rd | 2 man/config_dtype_policy.Rd | 2 man/config_enable_flash_attention.Rd | 2 man/config_enable_interactive_logging.Rd | 2 man/config_enable_traceback_filtering.Rd | 2 man/config_enable_unsafe_deserialization.Rd | 2 man/config_epsilon.Rd | 2 man/config_floatx.Rd | 2 man/config_image_data_format.Rd | 2 man/config_is_interactive_logging_enabled.Rd | 2 man/config_is_nnx_enabled.Rd |only man/config_is_traceback_filtering_enabled.Rd | 2 man/config_max_epochs.Rd |only man/config_set_backend.Rd | 2 man/config_set_dtype_policy.Rd | 2 man/config_set_epsilon.Rd | 2 man/config_set_floatx.Rd | 2 man/config_set_image_data_format.Rd | 2 man/dataset_boston_housing.Rd | 32 man/dataset_california_housing.Rd | 42 man/dataset_cifar10.Rd | 32 man/dataset_cifar100.Rd | 31 man/dataset_fashion_mnist.Rd | 32 man/dataset_imdb.Rd | 54 man/dataset_mnist.Rd | 31 man/dataset_reuters.Rd | 54 man/deserialize_keras_object.Rd | 13 man/figures/op-gelu-plot-1.png |binary man/figures/op-hard-sigmoid-plot-1.png |binary man/figures/op-leaky-relu-plot-1.png |binary man/figures/op-relu-plot-1.png |binary man/figures/op-relu6-plot-1.png |binary man/figures/op-softplus-plot-1.png |binary man/figures/op-softsign-plot-1.png |binary man/freeze_weights.Rd | 7 man/grapes-py_class-grapes.Rd | 2 man/grapes-set-active-grapes.Rd | 2 man/keras_variable.Rd | 10 man/layer_activation.Rd | 1 man/layer_activation_elu.Rd | 1 man/layer_activation_leaky_relu.Rd | 1 man/layer_activation_parametric_relu.Rd | 1 man/layer_activation_relu.Rd | 1 man/layer_activation_softmax.Rd | 1 man/layer_activity_regularization.Rd | 1 man/layer_add.Rd | 1 man/layer_additive_attention.Rd | 1 man/layer_alpha_dropout.Rd | 1 man/layer_attention.Rd | 1 man/layer_aug_mix.Rd | 3 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vignettes/functional_api/unnamed-chunk-10-1.png |binary vignettes/functional_api/unnamed-chunk-11-1.png |binary vignettes/functional_api/unnamed-chunk-20-1.png |binary vignettes/functional_api/unnamed-chunk-25-1.png |binary vignettes/getting_started.Rmd | 8 vignettes/getting_started/unnamed-chunk-12-1.png |binary vignettes/getting_started/unnamed-chunk-9-1.png |binary vignettes/intro_to_keras_for_engineers.Rmd | 24 vignettes/making_new_layers_and_models_via_subclassing.Rmd | 4 vignettes/serialization_and_saving.Rmd | 39 vignettes/training_with_built_in_methods.Rmd | 32 vignettes/training_with_built_in_methods/unnamed-chunk-26-1.png |binary vignettes/transfer_learning.Rmd | 12 vignettes/transfer_learning/unnamed-chunk-13-1.png |binary vignettes/transfer_learning/unnamed-chunk-17-1.png |binary vignettes/writing_a_custom_training_loop_in_tensorflow.Rmd | 36 vignettes/writing_your_own_callbacks.Rmd | 16 639 files changed, 9628 insertions(+), 1392 deletions(-)
Title: Prioritizing Cancer Driver Genes Using Genomics Data
Description: Cancer genomes contain large numbers of somatic alterations but few
genes drive tumor development. Identifying cancer driver genes is critical
for precision oncology. Most of current approaches either identify driver
genes based on mutational recurrence or using estimated scores predicting
the functional consequences of mutations. 'driveR' is a tool for
personalized or batch analysis of genomic data for driver gene prioritization
by combining genomic information and prior biological knowledge. As features,
'driveR' uses coding impact metaprediction scores, non-coding impact scores,
somatic copy number alteration scores, hotspot gene/double-hit gene
condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG
pathways. It uses these features to estimate cancer-type-specific
probability for each gene of being a cancer driver using the related task of
a multi-task learning classification model. The method is described in detail
in Ulgen E, Sezerman OU. 2021. driveR: driveR: [...truncated...]
Author: Ege Ulgen [aut, cre, cph]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between driveR versions 0.4.1 dated 2023-08-19 and 0.5.0 dated 2025-12-22
DESCRIPTION | 21 +- MD5 | 46 +++--- NEWS.md | 7 R/core_functions.R | 176 ++++++++++------------- R/data.R | 26 ++- R/utility.R | 228 ++++++++++++++++++++----------- README.md | 2 build/vignette.rds |binary data/example_gene_scna_table.rda |only inst/doc/how_to_use.R | 62 ++++---- inst/doc/how_to_use.html | 1 man/KEGG_cancer_pathways_descriptions.Rd | 4 man/create_SCNA_score_df.Rd | 6 man/create_features_df.Rd | 25 +-- man/create_gene_level_scna_df.Rd | 6 man/create_noncoding_impact_score_df.Rd | 2 man/determine_double_hit_genes.Rd | 4 man/driveR.Rd | 2 man/example_cohort_features_table.Rd | 2 man/example_features_table.Rd | 2 man/example_gene_scna_table.Rd |only man/predict_coding_impact.Rd | 6 man/prioritize_driver_genes.Rd | 4 tests/testthat/test-core_functions.R | 218 ++++++++++++----------------- tests/testthat/test-utility.R | 199 +++++++++++---------------- 25 files changed, 530 insertions(+), 519 deletions(-)
Title: Analysis of Stable Matchings
Description: Implements structural estimators to estimate preferences and correct for
the sample selection bias of observed outcomes in matching
markets. This includes one-sided matching of agents into groups
(Klein, 2015) <doi:10.17863/CAM.5812>
as well as two-sided matching of students to schools
(Klein et al., 2024) <doi:10.1016/j.geb.2024.07.003>.
The package also contains algorithms to find stable matchings
in the three most common matching problems: the stable roommates
problem (Irving, 1985) <doi:10.1016/0196-6774(85)90033-1>,
the college admissions problem (Gale and Shapley, 1962) <doi:10.2307/2312726>,
and the house allocation problem (Shapley and Scarf, 1974) <doi:10.1016/0304-4068(74)90033-0>.
Author: Thilo Klein [aut, cre, cph],
Robert Aue [ctb],
Fahiem Bacchus [cph],
Sven Giegerich [ctb],
Matthias Hericks [ctb],
Alexander Sauer [ctb],
Niklas Sorensson [cph]
Maintainer: Thilo Klein <thilo@klein.uk>
Diff between matchingMarkets versions 1.0-4 dated 2023-08-08 and 1.0-5 dated 2025-12-22
DESCRIPTION | 18 +++++++------- MD5 | 40 ++++++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 2 - R/RcppExports.R | 4 +++ R/hri3.R |only R/stabit.R | 37 +++++++++++++++++------------- README.md | 6 ++-- build/partial.rdb |only inst/CITATION | 4 +-- inst/doc/matching.Rnw | 6 ++++ inst/doc/matching.pdf |binary inst/include/System.h | 2 - man/baac00.Rd | 2 - man/hri3.Rd |only man/klein15b.Rd | 2 - man/matchingMarkets-package.Rd | 7 ++--- man/stabit.Rd | 6 +++- src/RcppExports.cpp | 17 ++++++++++++++ src/eadam.cpp |only src/stabitSel2.cpp | 41 +++++++++++++++++++++++++++------- vignettes/Sections/1_Introduction.tex | 6 ++-- vignettes/matching.Rnw | 6 ++++ 23 files changed, 138 insertions(+), 69 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Time Series Analysis Toolkit Based on Symbolic Aggregate
Discretization, i.e. SAX
Description: Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA
algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly),
and characteristic pattern discovery along with interpretable time series classification.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <seninp@gmail.com>
Diff between jmotif versions 1.2.0 dated 2025-10-23 and 1.2.1 dated 2025-12-22
DESCRIPTION | 7 +++---- MD5 | 4 ++-- README.md | 2 +- 3 files changed, 6 insertions(+), 7 deletions(-)
Title: R Integration for 'Goose' AI
Description: Seamless integration between R and 'Goose' AI capabilities
including memory management, visualization enhancements, and workflow
automation. Save R objects to 'Goose' memory, apply Block branding to
visualizations, and manage data science project workflows.
For more information about 'Goose' AI, see <https://github.com/block/goose>.
Author: Brandon Theriault [aut, cre]
Maintainer: Brandon Theriault <btheriault@block.xyz>
Diff between gooseR versions 0.1.0 dated 2025-12-17 and 0.1.1 dated 2025-12-22
DESCRIPTION | 6 ++--- MD5 | 33 ++++++++++++++++++-------------- NAMESPACE | 1 NEWS.md | 20 +++++++++++++++++-- R/addins.R | 9 +++----- R/async.R | 6 ----- R/cache.R | 1 R/memory_bulk.R | 45 +++++++++++++++++++++++++++++++------------- R/quarto_integration.R | 1 R/streaming.R | 1 R/ui_components.R | 16 ++++++--------- README.md | 7 ++++-- inst/doc/use-case-demo.html | 4 +-- man/goose_addins.Rd |only man/goose_async.Rd | 4 ++- man/goose_cache.Rd |only man/goose_exists.Rd | 4 +-- man/goose_quarto.Rd |only man/goose_streaming.Rd |only man/goose_ui_components.Rd |only 20 files changed, 99 insertions(+), 59 deletions(-)
Title: Extract Drugs from Differential Expression Data from LINCS
Database
Description: Get Drug information from given differential expression profile. The package search for the bioactive compounds from reference databases such as LINCS containing the genome-wide gene expression signature (GES) from tens of thousands of drug and genetic perturbations (Subramanian et al. (2017) <DOI:10.1016/j.cell.2017.10.049>).
Author: Mohamed Soudy [aut, cre]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between DFD versions 0.3.0 dated 2025-02-11 and 0.4.0 dated 2025-12-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 2 -- R/get_drugs.R | 12 ++++++++++-- 4 files changed, 17 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-10 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-20 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-19 0.1.3
2021-02-19 0.1.4
2020-05-25 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-28 2.2.0
2024-03-19 2.1.0
2023-11-28 2.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-03 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-20 1.0.1
2020-09-10 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-14 0.6.1
2019-06-11 0.6
2017-09-27 0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-12 1.0.1
2022-04-06 1.0.0
2021-05-12 0.2.1
2020-11-16 0.2.0
2020-05-11 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-07 0.9.2.1
2015-10-09 0.7.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-20 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-26 0.6.0
2019-05-24 0.5.0
2018-12-16 0.4.0
2018-07-11 0.3.0
2016-10-12 0.2.0
2016-05-22 0.1.1
2016-04-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-08 1.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-12 1.4.3
2023-08-21 1.4.2
2023-05-04 1.4.1
2020-05-26 1.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-11 0.8.2
2018-11-03 0.8.1
2017-01-14 0.7.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-21 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-12 0.3.0
2023-01-05 0.2.0
2021-02-01 0.1.0
Title: Modified Poisson Regression for Binary Outcome and Related
Methods Involving Target Trial Emulations
Description: Modified Poisson, logistic and least-squares regression analyses for binary outcomes of Zou (2004) <doi:10.1093/aje/kwh090>, Noma (2025)<Forthcoming>, and Cheung (2007) <doi:10.1093/aje/kwm223> have been standard multivariate analysis methods to estimate risk ratio and risk difference in clinical and epidemiological studies. This R package involves an easy-to-handle function to implement these analyses by simple commands. Missing data analysis tools (multiple imputation) are also involved. In addition, recent studies have shown the ordinary robust variance estimator possibly has serious bias under small or moderate sample size situations for these methods. This package also provides computational tools to calculate alternative accurate confidence intervals. Also, standard computational tools for target trial emulation are included.
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between rqlm versions 4.2-1 dated 2025-12-15 and 4.2-2 dated 2025-12-22
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS.md | 4 ++++ R/ttemsm.r | 4 ++-- man/rqlm-package.Rd | 4 +++- man/ttemsm.Rd | 18 +++++++++++++++--- 6 files changed, 35 insertions(+), 17 deletions(-)
Title: Czekanowski's Diagrams
Description: Allows for production of Czekanowski's Diagrams with clusters. See K. Bartoszek, A. Vasterlund (2020) <doi:10.2478/bile-2020-0008> and K. Bartoszek, Y. Luo (2023) <doi:10.14708/ma.v51i2.7259>. The suggested 'FuzzyDBScan' package (which allows for fuzzy clustering) can be obtained from
<https://github.com/henrifnk/FuzzyDBScan/> (or from CRAN's Archive <https://cran.r-project.org/src/contrib/Archive/FuzzyDBScan/>).
Author: Albin Vasterlund [aut],
Krzysztof Bartoszek [cre, aut, ths],
Ying Luo [aut],
Piotr Jaskulski [ctb]
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
This is a re-admission after prior archival of version 1.6.0 dated 2024-06-23
Diff between RMaCzek versions 1.6.0 dated 2024-06-23 and 1.6.1 dated 2025-12-22
DESCRIPTION | 16 +++--- MD5 | 10 +-- R/czek_matrix.R | 128 +++++++++++++++++++++++++----------------------- R/plot.czek_matrix.R | 11 ++-- man/czek_matrix.Rd | 14 +++-- man/plot.czek_matrix.Rd | 11 ++-- 6 files changed, 103 insertions(+), 87 deletions(-)
Title: Empirical Likelihood Analysis for the Cox Model and
Yang-Prentice (2005) Model
Description: Empirical likelihood ratio tests for the Yang and Prentice (short/long term hazards ratio) model.
Empirical likelihood tests within a Cox model, for parameters defined via
both baseline hazard function and regression parameters.
Author: Mai Zhou [aut, cre]
Maintainer: Mai Zhou <maizhou@gmail.com>
Diff between ELYP versions 0.7-5 dated 2018-08-19 and 0.7-6 dated 2025-12-22
DESCRIPTION | 16 ++++++++++------ MD5 | 4 ++-- man/CoxEL.Rd | 15 +++++++++++---- 3 files changed, 23 insertions(+), 12 deletions(-)
Title: Ensemble Platform for Species Distribution Modeling
Description: Functions for species distribution modeling, calibration and evaluation,
ensemble of models, ensemble forecasting and visualization. The package permits to run
consistently up to 10 single models on a presence/absences (resp presences/pseudo-absences)
dataset and to combine them in ensemble models and ensemble projections. Some bench of other
evaluation and visualisation tools are also available within the package.
Author: Maya Gueguen [aut, cre],
Helene Blancheteau [aut],
Remi Lemaire-Patin [aut],
Wilfried Thuiller [aut]
Maintainer: Maya Gueguen <maya.gueguen@univ-grenoble-alpes.fr>
Diff between biomod2 versions 4.2-6-2 dated 2025-01-24 and 4.3-4-3 dated 2025-12-22
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biomod2-4.3-4-3/biomod2/man/BIOMOD_LoadModels.Rd | 31 biomod2-4.3-4-3/biomod2/man/BIOMOD_Modeling.Rd | 168 - biomod2-4.3-4-3/biomod2/man/BIOMOD_Projection.Rd | 75 biomod2-4.3-4-3/biomod2/man/BIOMOD_RangeSize.Rd | 150 - biomod2-4.3-4-3/biomod2/man/BIOMOD_Report.Rd |only biomod2-4.3-4-3/biomod2/man/DataSTOC.Rd |only biomod2-4.3-4-3/biomod2/man/ModelsTable.Rd | 2 biomod2-4.3-4-3/biomod2/man/ODMAP.Rd |only biomod2-4.3-4-3/biomod2/man/OptionsBigboss.Rd | 48 biomod2-4.3-4-3/biomod2/man/bioclim_current.Rd | 2 biomod2-4.3-4-3/biomod2/man/biomod2-deprecated.Rd | 2 biomod2-4.3-4-3/biomod2/man/biomod2_ensemble_model.Rd | 7 biomod2-4.3-4-3/biomod2/man/biomod2_model.Rd | 8 biomod2-4.3-4-3/biomod2/man/bm_BinaryTransformation.Rd | 4 biomod2-4.3-4-3/biomod2/man/bm_CrossValidation.Rd | 15 biomod2-4.3-4-3/biomod2/man/bm_FindOptimStat.Rd | 58 biomod2-4.3-4-3/biomod2/man/bm_MakeFormula.Rd | 10 biomod2-4.3-4-3/biomod2/man/bm_ModelAnalysis.Rd |only biomod2-4.3-4-3/biomod2/man/bm_ModelingOptions.Rd | 162 - biomod2-4.3-4-3/biomod2/man/bm_PlotEvalBoxplot.Rd | 13 biomod2-4.3-4-3/biomod2/man/bm_PlotEvalMean.Rd | 20 biomod2-4.3-4-3/biomod2/man/bm_PlotRangeSize.Rd | 45 biomod2-4.3-4-3/biomod2/man/bm_PlotResponseCurves.Rd | 15 biomod2-4.3-4-3/biomod2/man/bm_PlotVarImpBoxplot.Rd | 11 biomod2-4.3-4-3/biomod2/man/bm_PseudoAbsences.Rd | 22 biomod2-4.3-4-3/biomod2/man/bm_RangeSize.Rd |only biomod2-4.3-4-3/biomod2/man/bm_RunModelsLoop.Rd | 52 biomod2-4.3-4-3/biomod2/man/bm_SRE.Rd | 2 biomod2-4.3-4-3/biomod2/man/bm_SampleBinaryVector.Rd | 2 biomod2-4.3-4-3/biomod2/man/bm_SampleFactorLevels.Rd | 2 biomod2-4.3-4-3/biomod2/man/bm_Tuning.Rd | 47 biomod2-4.3-4-3/biomod2/man/bm_VariablesImportance.Rd | 2 biomod2-4.3-4-3/biomod2/man/calculate.stat-deprecated.Rd | 2 biomod2-4.3-4-3/biomod2/man/dot-check_duplicated_cells.Rd |only biomod2-4.3-4-3/biomod2/man/dot-load_gam_namespace.Rd | 4 biomod2-4.3-4-3/biomod2/man/dot-transform_model.as.col.Rd | 2 biomod2-4.3-4-3/biomod2/man/getters.bm.Rd | 3 biomod2-4.3-4-3/biomod2/man/getters.out.Rd | 15 biomod2-4.3-4-3/biomod2/man/load_stored_object.Rd | 3 biomod2-4.3-4-3/biomod2/man/plot.Rd | 64 biomod2-4.3-4-3/biomod2/man/predict.bm.Rd | 3 biomod2-4.3-4-3/biomod2/man/predict.em.Rd | 3 biomod2-4.3-4-3/biomod2/man/predict2.bm.Rd | 13 biomod2-4.3-4-3/biomod2/man/predict2.em.Rd | 21 biomod2-4.3-4-3/biomod2/man/setters.Rd |only biomod2-4.3-4-3/biomod2/man/summary.Rd | 8 biomod2-4.3-4-3/biomod2/vignettes/examples_1_mainFunctions_AB.Rmd |only biomod2-4.3-4-3/biomod2/vignettes/examples_1_mainFunctions_BIN.Rmd |only biomod2-4.3-4-3/biomod2/vignettes/examples_2_auxiliaryFunctions.Rmd |only biomod2-4.3-4-3/biomod2/vignettes/news.Rmd | 134 + biomod2-4.3-4-3/biomod2/vignettes/pictures/SCHEMA_BIOMOD2_WORKFLOW_functions.pdf |binary biomod2-4.3-4-3/biomod2/vignettes/pictures/SCHEMA_BIOMOD2_WORKFLOW_functions.png |binary biomod2-4.3-4-3/biomod2/vignettes/pictures/biomod2_presentation.workflow_05_2024.pdf |binary biomod2-4.3-4-3/biomod2/vignettes/vignette_crossValidation.Rmd | 4 biomod2-4.3-4-3/biomod2/vignettes/vignette_modelingOptions.Rmd | 4 biomod2-4.3-4-3/biomod2/vignettes/vignette_pseudoAbsences.Rmd | 20 147 files changed, 8316 insertions(+), 5610 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-06 0.1.2
2020-11-23 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-09 1.0.1
2022-06-09 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-24 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-12 1.8.0
2025-03-17 1.7.0
2024-12-11 1.6.0
2024-07-19 1.5.0
2024-02-22 1.4.1
2024-02-15 1.4.0
2023-09-05 1.3.2
2023-02-20 1.3.1
2023-02-13 1.3.0
2022-06-15 1.2.0
2021-10-01 1.1.0
2021-03-15 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-27 0.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-04 1.0.0
2016-03-26 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-18 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-03 1.0.2
2021-09-02 1.0.1
2021-06-21 0.0.2
2021-06-11 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-16 3.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-06 0.5.6
2024-10-30 0.5.5
2022-10-01 0.5.4
2022-06-25 0.5.3
2022-04-14 0.5.0
2022-04-14 0.5.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-18 1.1.2
2018-02-19 1.1.1
2017-03-02 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-25 0.2.0
2019-08-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-27 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-24 0.1.2
2021-01-21 0.1.1
2021-01-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-22 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-25 0.2.1
2016-03-22 0.2.0
2016-02-27 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-14 1.5-10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-11 0.2.0
2017-09-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-12 1.0.0
Title: A Common Representation of Time Indices of Different Types
Description: Provides an easy-to-use tind class representing time indices
of different types (years, quarters, months, ISO 8601 weeks, dates,
time of day, date-time, and arbitrary integer/numeric indices).
Includes an extensive collection of functions for calendrical computations
(including business applications), index conversions, index parsing,
and other operations. Auxiliary classes representing time differences and
time intervals (with set operations and index matching functionality) are
also provided. All routines have been optimised for speed in order
to facilitate computations on large datasets. More details regarding
calendars in general and calendrical algorithms can be found in
"Calendar FAQ" by Claus Tøndering <https://www.tondering.dk/claus/calendar.html>.
Author: Grzegorz Klima [aut, cre, cph]
Maintainer: Grzegorz Klima <dever@post.pl>
This is a re-admission after prior archival of version 0.2.2 dated 2025-11-07
Diff between tind versions 0.2.2 dated 2025-11-07 and 0.2.3 dated 2025-12-22
DESCRIPTION | 8 - MD5 | 80 +++++++------- R/base-parse.R | 2 R/base-th.R | 4 R/base-tz.R | 181 +++++++++++++++++++++++++++++++- R/plot-scales.R | 38 ++++-- build/vignette.rds |binary inst/doc/calendar.html | 176 +++++++++++++++---------------- inst/doc/indices.html | 3 inst/po/en@quot/LC_MESSAGES/R-tind.mo |binary inst/po/pl/LC_MESSAGES/R-tind.mo |binary man/scale_tind.Rd | 38 ++++-- po/R-pl.po | 11 + po/R-tind.pot | 7 - src/parse.c | 80 +++++--------- tests/testthat/test-03-base-tz.R | 27 +++- tests/testthat/test-04-base-th.R | 20 +-- tests/testthat/test-05-base-res.R | 2 tests/testthat/test-06-base-pretty.R | 2 tests/testthat/test-08-base-types.R | 2 tests/testthat/test-09-base-parse.R | 2 tests/testthat/test-10-tind.R | 4 tests/testthat/test-11-format_parse.R | 4 tests/testthat/test-12-coercion.R | 2 tests/testthat/test-13-methods.R | 2 tests/testthat/test-15-tinterval.R | 2 tests/testthat/test-17-ops.R | 2 tests/testthat/test-18-setops_match.R | 2 tests/testthat/test-19-tzone.R | 4 tests/testthat/test-20-tspan.R | 2 tests/testthat/test-21-resolution.R | 2 tests/testthat/test-22-print_summ_str.R | 2 tests/testthat/test-23-round.R | 2 tests/testthat/test-24-cut.R | 2 tests/testthat/test-25-seq.R | 2 tests/testthat/test-26-ord_reg.R | 4 tests/testthat/test-27-calendar.R | 6 - tests/testthat/test-30-other.R | 2 tests/testthat/test-31-merge.R | 2 tests/testthat/test-32-pretty.R | 2 tests/testthat/test-33-plot-scales.R | 2 41 files changed, 467 insertions(+), 268 deletions(-)
Title: Personalized Network-Based Anti-Cancer Therapy Evaluation
Description: Identification of the most appropriate pharmacotherapy for each
patient based on genomic alterations is a major challenge in personalized
oncology. 'PANACEA' is a collection of personalized anti-cancer drug
prioritization approaches utilizing network methods. The methods utilize
personalized "driverness" scores from 'driveR' to rank drugs, mapping these
onto a protein-protein interaction network. The "distance-based" method
scores each drug based on these scores and distances between drugs and genes
to rank given drugs. The "RWR" method propagates these scores via a
random-walk with restart framework to rank the drugs. The methods are
described in detail in Ulgen E, Ozisik O, Sezerman OU. 2023. PANACEA:
network-based methods for pharmacotherapy prioritization in personalized
oncology. Bioinformatics <doi:10.1093/bioinformatics/btad022>.
Author: Ege Ulgen [aut, cre, cph]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between PANACEA versions 1.0.1 dated 2023-08-19 and 1.1.0 dated 2025-12-22
DESCRIPTION | 15 ++++++++------- MD5 | 16 ++++++++-------- NEWS.md | 6 +++++- R/utility.R | 9 +++++++++ README.md | 2 +- build/vignette.rds |binary inst/doc/how_to_use.R | 10 +++++----- inst/doc/how_to_use.html | 1 + tests/testthat/test-utility.R | 12 +++++++++--- 9 files changed, 46 insertions(+), 25 deletions(-)
Title: Boundary Line Analysis
Description: Fits boundary line models to datasets as proposed by Webb
(1972) <doi:10.1080/00221589.1972.11514472> and makes statistical
inferences about their parameters. Provides additional tools for
testing datasets for evidence of boundary presence and selecting
initial starting values for model optimization prior to fitting the
boundary line models. It also includes tools for conducting post-hoc
analyses such as predicting boundary values and identifying the most
limiting factor (Miti, Milne, Giller, Lark (2024)
<doi:10.1016/j.fcr.2024.109365>). This ensures a comprehensive
analysis for datasets that exhibit upper boundary structures.
Author: Chawezi Miti [cre, aut, cph] ,
Richard M Lark [aut] ,
Alice E Milne [aut] ,
Ken E Giller [aut] ,
Victor O Sadras [ctb],
University of Nottingham/Rothamsted Research [fnd]
Maintainer: Chawezi Miti <mitichawezi14@gmail.com>
Diff between BLA versions 1.0.1 dated 2024-05-28 and 1.0.2 dated 2025-12-22
DESCRIPTION | 21 +-- MD5 | 38 ++--- NAMESPACE | 2 NEWS.md | 6 R/Perimeter_Area_calc.R |only R/ble_profiling.R | 17 +- R/cbvn.R | 6 R/exp_boundary.R | 175 ++++++++++++++++++++------ README.md | 19 ++ build/partial.rdb |binary build/vignette.rds |binary data/soil.rda |binary inst/doc/BLA.R | 48 +++---- inst/doc/BLA.html | 62 ++++----- inst/doc/Censored_bivariate_normal_model.R | 102 +++++++-------- inst/doc/Censored_bivariate_normal_model.html | 25 +-- inst/doc/Introduction_to_BLA.R | 48 +++---- inst/doc/Introduction_to_BLA.html | 62 ++++----- man/AP.Rd |only man/expl_boundary.Rd | 134 ++++++++++--------- man/figures/README-unnamed-chunk-8-1.png |binary 21 files changed, 453 insertions(+), 312 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-05 3.4.0
2016-06-28 3.3.0
2015-07-21 3.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-16 3.2.2
2025-04-25 3.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-05 1.0.4
2013-09-19 0.9.0
2013-05-07 0.8.6
2012-12-03 0.8.3
2012-11-06 0.7.2
2012-10-25 0.7.0
2012-10-23 0.6.7
2012-10-02 0.6.6
2012-09-27 0.6.4
2012-09-18 0.6.1
2012-05-31 0.5.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-31 2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-15 1.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-30 1.0.7
2025-08-23 1.0.6
2025-05-12 1.0.5
2025-04-05 1.0.4
2024-10-03 1.0.3
2024-06-19 1.0.2
2024-01-18 1.0.1
2024-01-10 1.0.0
Title: Conversion of R Regression Output to LaTeX or HTML Tables
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented. Details can be found in Leifeld (2013), JStatSoft <doi:10.18637/jss.v055.i08>.)
Author: Philip Leifeld [aut, cre],
Claudia Zucca [ctb]
Maintainer: Philip Leifeld <philip.leifeld@manchester.ac.uk>
Diff between texreg versions 1.39.4 dated 2024-07-24 and 1.39.5 dated 2025-12-22
DESCRIPTION | 31 ++++++++------- MD5 | 29 +++++++------- R/extract.R | 75 ++++++++++++++++++++++++++++++++++++-- R/texreg.R | 7 ++- inst/doc/texreg.Rnw | 12 +++--- inst/doc/texreg.pdf |binary man/createTexreg.Rd | 3 - man/extract-oglmx-method.Rd | 4 +- man/extract-prais-method.Rd |only tests/testthat/test-extract.R | 48 ++++++++++++++++++------ tests/testthat/test-huxtablereg.R | 2 - tests/testthat/test-jss.R | 2 + tests/testthat/test-plotreg.R | 15 ++++--- tests/testthat/test-texreg.R | 71 +++++++++++++++++++++-------------- vignettes/texreg.Rnw | 12 +++--- vignettes/texreg.bib | 63 +++++++++++++------------------ 16 files changed, 241 insertions(+), 133 deletions(-)
Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in
parallel, so metadata resolution and package downloads are fast.
Metadata and package files are cached on the local disk as well. 'pak'
has a dependency solver, so it finds version conflicts before
performing the installation. This version of 'pak' supports CRAN,
'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
Posit Software, PBC [cph, fnd] ,
Winston Chang [ctb] ,
Ascent Digital Services [cph, fnd] ,
Hadley Wickham [ctb, cph] ,
Jeroen Ooms [ctb] ,
Maelle Salmon [ctb] ,
Duncan Temple Lang [ctb] ,
Lloyd Hilaiel [cph [...truncated...]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pak versions 0.9.1 dated 2025-12-01 and 0.9.2 dated 2025-12-22
DESCRIPTION | 6 - MD5 | 41 ++++--- NEWS.md | 4 src/library/pkgdepends/DESCRIPTION | 2 src/library/pkgdepends/R/install-binary.R | 4 src/library/yaml/COPYING | 3 src/library/yaml/DESCRIPTION | 64 +++++++++--- src/library/yaml/LICENSE | 6 - src/library/yaml/NAMESPACE | 9 + src/library/yaml/R/as.yaml.R | 146 ++++++++++++++++++++++++++-- src/library/yaml/R/read_yaml.R | 85 ++++++++++++++-- src/library/yaml/R/verbatim_logical.R | 21 ++++ src/library/yaml/R/write_yaml.R | 42 +++++++- src/library/yaml/R/yaml-package.R |only src/library/yaml/R/yaml.load.R | 154 ++++++++++++++++++++++++++++-- src/library/yaml/R/yaml.load_file.R | 22 ++-- src/library/yaml/src/emitter.c | 18 +-- src/library/yaml/src/r_emit.c | 11 -- src/library/yaml/src/r_ext.c | 8 - src/library/yaml/src/r_ext.h | 4 src/library/yaml/src/r_parse.c | 12 +- tests/testthat/test-repo.R | 2 22 files changed, 549 insertions(+), 115 deletions(-)
Title: Extension to 'ggplot2' for Plotting Stats
Description: Provides new statistics, new geometries and new positions for
'ggplot2' and a suite of functions to facilitate the creation of
statistical plots.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between ggstats versions 0.11.0 dated 2025-09-15 and 0.12.0 dated 2025-12-22
DESCRIPTION | 8 +- MD5 | 65 ++++++++++--------- NEWS.md | 8 ++ R/deprecated.R | 4 - R/geom_connector.R | 18 +++++ R/ggcoef_model.R | 3 R/gglikert.R | 17 ++++- R/stat_prop.R | 6 + R/vdiffr-helper.R |only R/weighted_quantile.R | 2 build/vignette.rds |binary inst/doc/ggcoef_model.R | 2 inst/doc/ggcoef_model.Rmd | 2 inst/doc/ggcoef_model.html | 10 --- man/geom_connector.Rd | 8 +- man/geom_stripped_rows.Rd | 10 +-- man/ggcoef_model.Rd | 6 - man/gglikert.Rd | 3 man/ggsurvey.Rd | 2 man/hex_bw.Rd | 2 man/stat_cross.Rd | 6 + man/stat_prop.Rd | 10 +-- man/stat_weighted_mean.Rd | 10 +-- tests/testthat/test-geom_connector.R | 18 ++--- tests/testthat/test-geom_stripped.R | 2 tests/testthat/test-ggcascade.R | 8 +- tests/testthat/test-ggcoef_model.R | 96 ++++++++++++++--------------- tests/testthat/test-gglikert.R | 101 +++++++++++++++++++------------ tests/testthat/test-position_likert.R | 22 +++--- tests/testthat/test-stat_cross.R | 20 +++--- tests/testthat/test-stat_prop.R | 32 ++++----- tests/testthat/test-stat_weighted_mean.R | 14 ++-- tests/testthat/test_ggsurvey.R | 4 - vignettes/ggcoef_model.Rmd | 2 34 files changed, 294 insertions(+), 227 deletions(-)
Title: A 'ggplot2' Extension for Drawing Publication-Ready Sequence
Logos
Description: The extensive range of functions provided by this package makes it possible to draw highly versatile sequence logos. Features include, but not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other plots 'ggplot2' plots.
Author: Omar Wagih [aut, cre]
Maintainer: Omar Wagih <omarwagih@gmail.com>
Diff between ggseqlogo versions 0.2 dated 2024-02-08 and 0.2.2 dated 2025-12-22
DESCRIPTION | 16 +++++++++------- MD5 | 12 ++++++------ R/ggseqlogo.r | 4 ++-- inst/doc/ggseqlogo_introduction.html | 4 ++-- man/geom_logo.Rd | 19 +++++++++++++++---- man/ggseqlogo.Rd | 14 ++++++++++---- man/make_col_scheme.Rd | 9 +++++++-- 7 files changed, 51 insertions(+), 27 deletions(-)
Title: Required 'libphonenumber' jars for the 'dialr' Package
Description: Collects 'libphonenumber' jars required for the
'dialr' package.
Author: Danny Smith [aut, cre],
Google Inc. [ctb, cph] ,
Vonage Holdings Corp. [ctb, cph] ,
Ian Galpin [ctb, cph] ,
Ben Gertzfield [ctb, cph]
Maintainer: Danny Smith <danny@gorcha.org>
Diff between dialrjars versions 9.0.14 dated 2025-09-16 and 9.0.21 dated 2025-12-22
dialrjars-9.0.14/dialrjars/inst/java/carrier-2.14.jar |only dialrjars-9.0.14/dialrjars/inst/java/geocoder-3.14.jar |only dialrjars-9.0.14/dialrjars/inst/java/libphonenumber-9.0.14.jar |only dialrjars-9.0.14/dialrjars/inst/java/prefixmapper-3.14.jar |only dialrjars-9.0.21/dialrjars/DESCRIPTION | 6 dialrjars-9.0.21/dialrjars/MD5 | 26 +-- dialrjars-9.0.21/dialrjars/NAMESPACE | 6 dialrjars-9.0.21/dialrjars/NEWS.md | 70 +++++++++ dialrjars-9.0.21/dialrjars/R/dialrjars.R | 6 dialrjars-9.0.21/dialrjars/inst/COPYRIGHTS | 18 +- dialrjars-9.0.21/dialrjars/inst/java/carrier-2.21.jar |only dialrjars-9.0.21/dialrjars/inst/java/geocoder-3.21.jar |only dialrjars-9.0.21/dialrjars/inst/java/libphonenumber-9.0.21.jar |only dialrjars-9.0.21/dialrjars/inst/java/prefixmapper-3.21.jar |only dialrjars-9.0.21/dialrjars/java/README | 14 - dialrjars-9.0.21/dialrjars/man/dialrjars-package.Rd | 64 ++++---- dialrjars-9.0.21/dialrjars/tests/testthat.R | 8 - dialrjars-9.0.21/dialrjars/tests/testthat/test-dialrjars.R | 76 +++++----- 18 files changed, 182 insertions(+), 112 deletions(-)