Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and (multivariate) longitudinal data applying customized linear scan algorithms, proposed by Li and colleagues (2022) <doi:10.1155/2022/1362913>.
The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. The longitudinal
outcome is modelled using a linear mixed effects model. The association is captured by shared random effects. The model
is estimated using an Expectation Maximization algorithm.
Author: Shanpeng Li [aut, cre],
Ning Li [ctb],
Hong Wang [ctb],
Jin Zhou [ctb],
Hua Zhou [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between FastJM versions 1.5.0 dated 2025-06-22 and 1.5.1 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/print.mvjmcs.R | 4 ++++ R/simmvJMdata.R | 2 +- R/summary.mvjmcs.R | 23 +++++++++++++++++++++++ 6 files changed, 43 insertions(+), 10 deletions(-)
Title: Satellite Image Time Series Analysis for Earth Observation Data
Cubes
Description: An end-to-end toolkit for land use and land cover classification
using big Earth observation data. Builds satellite image data cubes from cloud collections.
Supports visualization methods for images and time series and
smoothing filters for dealing with noisy time series.
Enables merging of multi-source imagery (SAR, optical, DEM).
Includes functions for quality assessment of training samples using self-organized maps and
to reduce training samples imbalance. Provides machine learning algorithms including support vector machines,
random forests, extreme gradient boosting, multi-layer perceptrons,
temporal convolution neural networks, and temporal attention encoders.
Performs efficient classification of big Earth observation data cubes and includes
functions for post-classification smoothing based on Bayesian inference.
Enables best practices for estimating area and assessing accuracy of land change.
Includes object-based spatio-temporal segmentation for space-time OBIA.
Minimum recomme [...truncated...]
Author: Rolf Simoes [aut],
Gilberto Camara [aut, cre, ths],
Felipe Souza [aut],
Felipe Carlos [aut],
Lorena Santos [ctb],
Charlotte Pelletier [ctb],
Estefania Pizarro [ctb],
Karine Ferreira [ctb, ths],
Alber Sanchez [ctb],
Alexandre Assuncao [ctb],
Daniel Fa [...truncated...]
Maintainer: Gilberto Camara <gilberto.camara.inpe@gmail.com>
Diff between sits versions 1.5.2 dated 2025-02-12 and 1.5.3 dated 2025-07-23
sits-1.5.2/sits/R/api_preconditions.R |only sits-1.5.2/sits/R/api_raster_sub_image.R |only sits-1.5.2/sits/inst/extdata/accuracy |only sits-1.5.2/sits/inst/extdata/scripts |only sits-1.5.2/sits/inst/extdata/sources/config_source_planet.yaml |only sits-1.5.2/sits/inst/extdata/tmap |only sits-1.5.2/sits/inst/extdata/torch |only sits-1.5.2/sits/man/sits_pred_reference.Rd |only sits-1.5.2/sits/man/sits_som.Rd |only sits-1.5.2/sits/src/normalize_data_0.cpp |only sits-1.5.3/sits/DESCRIPTION | 107 sits-1.5.3/sits/MD5 | 736 ++--- sits-1.5.3/sits/NAMESPACE | 66 sits-1.5.3/sits/NEWS.md | 20 sits-1.5.3/sits/R/RcppExports.R | 60 sits-1.5.3/sits/R/api_accessors.R | 4 sits-1.5.3/sits/R/api_accuracy.R | 76 sits-1.5.3/sits/R/api_apply.R | 116 sits-1.5.3/sits/R/api_band.R | 68 sits-1.5.3/sits/R/api_bayts.R | 26 sits-1.5.3/sits/R/api_bbox.R | 31 sits-1.5.3/sits/R/api_block.R | 12 sits-1.5.3/sits/R/api_check.R | 1423 ++++++---- sits-1.5.3/sits/R/api_chunks.R | 108 sits-1.5.3/sits/R/api_classify.R | 305 +- sits-1.5.3/sits/R/api_clean.R | 26 sits-1.5.3/sits/R/api_cluster.R | 41 sits-1.5.3/sits/R/api_colors.R | 126 sits-1.5.3/sits/R/api_combine_predictions.R | 44 sits-1.5.3/sits/R/api_comp.R | 20 sits-1.5.3/sits/R/api_conf.R | 365 +- sits-1.5.3/sits/R/api_crop.R | 85 sits-1.5.3/sits/R/api_csv.R | 82 sits-1.5.3/sits/R/api_cube.R | 657 ++-- sits-1.5.3/sits/R/api_data.R | 1069 ++----- sits-1.5.3/sits/R/api_debug.R | 10 sits-1.5.3/sits/R/api_detect_change.R | 103 sits-1.5.3/sits/R/api_download.R | 10 sits-1.5.3/sits/R/api_dtw.R | 36 sits-1.5.3/sits/R/api_environment.R | 15 sits-1.5.3/sits/R/api_factory.R | 4 sits-1.5.3/sits/R/api_file.R | 70 sits-1.5.3/sits/R/api_file_info.R | 82 sits-1.5.3/sits/R/api_gdal.R | 118 sits-1.5.3/sits/R/api_gdalcubes.R | 164 - 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sits-1.5.3/sits/R/sits_reduce.R | 39 sits-1.5.3/sits/R/sits_reduce_imbalance.R | 68 sits-1.5.3/sits/R/sits_regularize.R | 326 +- sits-1.5.3/sits/R/sits_resnet.R |only sits-1.5.3/sits/R/sits_sample_functions.R | 383 -- sits-1.5.3/sits/R/sits_segmentation.R | 149 - sits-1.5.3/sits/R/sits_select.R | 77 sits-1.5.3/sits/R/sits_sf.R | 34 sits-1.5.3/sits/R/sits_smooth.R | 88 sits-1.5.3/sits/R/sits_som.R | 202 - sits-1.5.3/sits/R/sits_stars.R |only sits-1.5.3/sits/R/sits_summary.R | 208 - sits-1.5.3/sits/R/sits_tae.R | 64 sits-1.5.3/sits/R/sits_tempcnn.R | 123 sits-1.5.3/sits/R/sits_terra.R |only sits-1.5.3/sits/R/sits_texture.R |only sits-1.5.3/sits/R/sits_timeline.R | 34 sits-1.5.3/sits/R/sits_train.R | 40 sits-1.5.3/sits/R/sits_tuning.R | 64 sits-1.5.3/sits/R/sits_uncertainty.R | 266 + sits-1.5.3/sits/R/sits_utils.R | 8 sits-1.5.3/sits/R/sits_validate.R | 62 sits-1.5.3/sits/R/sits_variance.R | 97 sits-1.5.3/sits/R/sits_view.R | 186 - sits-1.5.3/sits/R/sits_xlsx.R | 26 sits-1.5.3/sits/R/zzz.R | 16 sits-1.5.3/sits/demo/classify_cbers_bdc.R | 2 sits-1.5.3/sits/demo/classify_deeplearning.R | 2 sits-1.5.3/sits/demo/dl_comparison.R | 9 sits-1.5.3/sits/demo/ml_comparison.R | 6 sits-1.5.3/sits/inst/WORDLIST | 75 sits-1.5.3/sits/inst/extdata/config_colors.yml | 180 + sits-1.5.3/sits/inst/extdata/config_internals.yml | 10 sits-1.5.3/sits/inst/extdata/config_messages.yml | 111 sits-1.5.3/sits/inst/extdata/config_test.yml |only sits-1.5.3/sits/inst/extdata/cran/check_package_cran.R | 3 sits-1.5.3/sits/inst/extdata/cran/pkg_size_functions.R | 3 sits-1.5.3/sits/inst/extdata/cran/sits_codecov.R | 17 sits-1.5.3/sits/inst/extdata/sources/config_source_aws.yml | 6 sits-1.5.3/sits/inst/extdata/sources/config_source_bdc.yml | 8 sits-1.5.3/sits/inst/extdata/sources/config_source_cdse.yml | 103 sits-1.5.3/sits/inst/extdata/sources/config_source_cdse_os.yml |only sits-1.5.3/sits/inst/extdata/sources/config_source_chile.yml | 2 sits-1.5.3/sits/inst/extdata/sources/config_source_deafrica.yml | 10 sits-1.5.3/sits/inst/extdata/sources/config_source_deaustralia.yml | 12 sits-1.5.3/sits/inst/extdata/sources/config_source_hls.yml | 4 sits-1.5.3/sits/inst/extdata/sources/config_source_mpc.yml | 153 - sits-1.5.3/sits/inst/extdata/sources/config_source_ogh.yml |only sits-1.5.3/sits/inst/extdata/sources/config_source_planet.yml |only sits-1.5.3/sits/inst/extdata/sources/config_source_sdc.yml | 2 sits-1.5.3/sits/inst/extdata/sources/config_source_terrascope.yml | 22 sits-1.5.3/sits/inst/extdata/sources/config_source_usgs.yml | 4 sits-1.5.3/sits/man/dot-check_date_parameter.Rd | 4 sits-1.5.3/sits/man/hist.probs_cube.Rd | 2 sits-1.5.3/sits/man/hist.raster_cube.Rd | 9 sits-1.5.3/sits/man/hist.sits.Rd | 9 sits-1.5.3/sits/man/hist.uncertainty_cube.Rd | 2 sits-1.5.3/sits/man/plot.Rd | 9 sits-1.5.3/sits/man/plot.class_cube.Rd | 6 sits-1.5.3/sits/man/plot.class_vector_cube.Rd | 2 sits-1.5.3/sits/man/plot.dem_cube.Rd | 12 sits-1.5.3/sits/man/plot.geo_distances.Rd | 2 sits-1.5.3/sits/man/plot.patterns.Rd | 5 sits-1.5.3/sits/man/plot.predicted.Rd | 3 sits-1.5.3/sits/man/plot.probs_cube.Rd | 4 sits-1.5.3/sits/man/plot.probs_vector_cube.Rd | 26 sits-1.5.3/sits/man/plot.raster_cube.Rd | 50 sits-1.5.3/sits/man/plot.sar_cube.Rd | 11 sits-1.5.3/sits/man/plot.sits_accuracy.Rd | 2 sits-1.5.3/sits/man/plot.sits_cluster.Rd | 7 sits-1.5.3/sits/man/plot.som_clean_samples.Rd | 2 sits-1.5.3/sits/man/plot.som_map.Rd | 6 sits-1.5.3/sits/man/plot.torch_model.Rd | 4 sits-1.5.3/sits/man/plot.uncertainty_cube.Rd | 6 sits-1.5.3/sits/man/plot.uncertainty_vector_cube.Rd | 18 sits-1.5.3/sits/man/plot.variance_cube.Rd | 7 sits-1.5.3/sits/man/plot.vector_cube.Rd | 12 sits-1.5.3/sits/man/plot.xgb_model.Rd | 2 sits-1.5.3/sits/man/print.sits_area_accuracy.Rd | 2 sits-1.5.3/sits/man/sits-package.Rd | 39 sits-1.5.3/sits/man/sits_accuracy.Rd | 43 sits-1.5.3/sits/man/sits_add_base_cube.Rd | 74 sits-1.5.3/sits/man/sits_apply.Rd | 71 sits-1.5.3/sits/man/sits_as_sf.Rd | 8 sits-1.5.3/sits/man/sits_as_stars.Rd |only sits-1.5.3/sits/man/sits_as_terra.Rd |only sits-1.5.3/sits/man/sits_bands.Rd | 2 sits-1.5.3/sits/man/sits_bbox.Rd | 23 sits-1.5.3/sits/man/sits_classify.Rd | 297 -- sits-1.5.3/sits/man/sits_classify.raster_cube.Rd |only sits-1.5.3/sits/man/sits_classify.segs_cube.Rd |only sits-1.5.3/sits/man/sits_classify.sits.Rd |only sits-1.5.3/sits/man/sits_clean.Rd | 105 sits-1.5.3/sits/man/sits_cluster_clean.Rd | 2 sits-1.5.3/sits/man/sits_cluster_dendro.Rd | 5 sits-1.5.3/sits/man/sits_cluster_frequency.Rd | 2 sits-1.5.3/sits/man/sits_colors.Rd | 10 sits-1.5.3/sits/man/sits_colors_qgis.Rd | 35 sits-1.5.3/sits/man/sits_combine_predictions.Rd | 30 sits-1.5.3/sits/man/sits_confidence_sampling.Rd | 23 sits-1.5.3/sits/man/sits_config.Rd | 5 sits-1.5.3/sits/man/sits_config_user_file.Rd | 2 sits-1.5.3/sits/man/sits_cube.Rd | 484 --- sits-1.5.3/sits/man/sits_cube.local_cube.Rd |only sits-1.5.3/sits/man/sits_cube.results_cube.Rd |only sits-1.5.3/sits/man/sits_cube.stac_cube.Rd |only sits-1.5.3/sits/man/sits_cube.vector_cube.Rd |only sits-1.5.3/sits/man/sits_cube_copy.Rd | 53 sits-1.5.3/sits/man/sits_factory_function.Rd | 2 sits-1.5.3/sits/man/sits_filter.Rd | 3 sits-1.5.3/sits/man/sits_formula_linear.Rd | 4 sits-1.5.3/sits/man/sits_formula_logref.Rd | 4 sits-1.5.3/sits/man/sits_geo_dist.Rd | 15 sits-1.5.3/sits/man/sits_get_class.Rd | 43 sits-1.5.3/sits/man/sits_get_data.Rd | 202 - sits-1.5.3/sits/man/sits_get_data.csv.Rd |only sits-1.5.3/sits/man/sits_get_data.data.frame.Rd |only sits-1.5.3/sits/man/sits_get_data.sf.Rd |only sits-1.5.3/sits/man/sits_get_data.shp.Rd |only sits-1.5.3/sits/man/sits_get_data.sits.Rd |only sits-1.5.3/sits/man/sits_get_probs.Rd | 52 sits-1.5.3/sits/man/sits_kfold_validate.Rd | 15 sits-1.5.3/sits/man/sits_label_classification.Rd | 29 sits-1.5.3/sits/man/sits_labels.Rd | 2 sits-1.5.3/sits/man/sits_labels_summary.Rd | 2 sits-1.5.3/sits/man/sits_lightgbm.Rd |only sits-1.5.3/sits/man/sits_lighttae.Rd | 14 sits-1.5.3/sits/man/sits_merge.Rd | 4 sits-1.5.3/sits/man/sits_mgrs_to_roi.Rd | 2 sits-1.5.3/sits/man/sits_mixture_model.Rd | 27 sits-1.5.3/sits/man/sits_mlp.Rd | 21 sits-1.5.3/sits/man/sits_model_export.Rd | 2 sits-1.5.3/sits/man/sits_mosaic.Rd | 22 sits-1.5.3/sits/man/sits_patterns.Rd | 4 sits-1.5.3/sits/man/sits_pred_references.Rd |only sits-1.5.3/sits/man/sits_predictors.Rd | 49 sits-1.5.3/sits/man/sits_reclassify.Rd | 149 - sits-1.5.3/sits/man/sits_reduce.Rd | 7 sits-1.5.3/sits/man/sits_reduce_imbalance.Rd | 32 sits-1.5.3/sits/man/sits_regularize.Rd | 120 sits-1.5.3/sits/man/sits_resnet.Rd |only sits-1.5.3/sits/man/sits_rfor.Rd | 4 sits-1.5.3/sits/man/sits_roi_to_mgrs.Rd |only sits-1.5.3/sits/man/sits_roi_to_tiles.Rd |only sits-1.5.3/sits/man/sits_sample.Rd | 4 sits-1.5.3/sits/man/sits_sampling_design.Rd | 8 sits-1.5.3/sits/man/sits_segment.Rd | 56 sits-1.5.3/sits/man/sits_select.Rd | 32 sits-1.5.3/sits/man/sits_sgolay.Rd | 4 sits-1.5.3/sits/man/sits_slic.Rd | 20 sits-1.5.3/sits/man/sits_smooth.Rd | 52 sits-1.5.3/sits/man/sits_som_clean_samples.Rd | 28 sits-1.5.3/sits/man/sits_som_evaluate_cluster.Rd | 7 sits-1.5.3/sits/man/sits_som_map.Rd |only sits-1.5.3/sits/man/sits_som_remove_samples.Rd | 14 sits-1.5.3/sits/man/sits_stratified_sampling.Rd | 20 sits-1.5.3/sits/man/sits_svm.Rd | 10 sits-1.5.3/sits/man/sits_tae.Rd | 20 sits-1.5.3/sits/man/sits_tempcnn.Rd | 33 sits-1.5.3/sits/man/sits_texture.Rd |only sits-1.5.3/sits/man/sits_tiles_to_roi.Rd | 4 sits-1.5.3/sits/man/sits_timeseries_to_csv.Rd | 1 sits-1.5.3/sits/man/sits_train.Rd | 40 sits-1.5.3/sits/man/sits_tuning.Rd | 35 sits-1.5.3/sits/man/sits_tuning_hparams.Rd | 4 sits-1.5.3/sits/man/sits_uncertainty.Rd | 46 sits-1.5.3/sits/man/sits_uncertainty_sampling.Rd | 8 sits-1.5.3/sits/man/sits_validate.Rd | 26 sits-1.5.3/sits/man/sits_variance.Rd | 50 sits-1.5.3/sits/man/sits_view.Rd | 35 sits-1.5.3/sits/man/sits_whittaker.Rd | 5 sits-1.5.3/sits/man/sits_xgboost.Rd | 14 sits-1.5.3/sits/man/summary.sits.Rd | 2 sits-1.5.3/sits/man/summary.sits_accuracy.Rd | 2 sits-1.5.3/sits/man/summary.variance_cube.Rd | 20 sits-1.5.3/sits/man/tick-sits_labels-set-tick.Rd | 2 sits-1.5.3/sits/src/Makevars |only sits-1.5.3/sits/src/RcppExports.cpp | 234 + sits-1.5.3/sits/src/glcm_fns.cpp |only sits-1.5.3/sits/src/kernel.cpp | 2 sits-1.5.3/sits/src/reduce_fns.cpp | 15 sits-1.5.3/sits/src/sampling.cpp |only sits-1.5.3/sits/tests/testthat/test-accuracy.R | 56 sits-1.5.3/sits/tests/testthat/test-active_learning.R | 6 sits-1.5.3/sits/tests/testthat/test-apply.R | 118 sits-1.5.3/sits/tests/testthat/test-bands.R | 12 sits-1.5.3/sits/tests/testthat/test-check.R | 226 - sits-1.5.3/sits/tests/testthat/test-classification.R | 25 sits-1.5.3/sits/tests/testthat/test-clustering.R | 8 sits-1.5.3/sits/tests/testthat/test-color.R | 23 sits-1.5.3/sits/tests/testthat/test-combine_predictions.R | 17 sits-1.5.3/sits/tests/testthat/test-config.R | 77 sits-1.5.3/sits/tests/testthat/test-cube-aws.R | 4 sits-1.5.3/sits/tests/testthat/test-cube-bdc.R | 158 - sits-1.5.3/sits/tests/testthat/test-cube-cdse.R | 54 sits-1.5.3/sits/tests/testthat/test-cube-deafrica.R | 149 - sits-1.5.3/sits/tests/testthat/test-cube-deaustralia.R | 179 - sits-1.5.3/sits/tests/testthat/test-cube-hls.R | 34 sits-1.5.3/sits/tests/testthat/test-cube-mpc.R | 230 + sits-1.5.3/sits/tests/testthat/test-cube-ogh.R |only sits-1.5.3/sits/tests/testthat/test-cube-sdc.R | 44 sits-1.5.3/sits/tests/testthat/test-cube-terrascope.R | 35 sits-1.5.3/sits/tests/testthat/test-cube-usgs.R | 8 sits-1.5.3/sits/tests/testthat/test-cube-vector.R |only sits-1.5.3/sits/tests/testthat/test-cube.R | 240 + sits-1.5.3/sits/tests/testthat/test-cube_copy.R | 80 sits-1.5.3/sits/tests/testthat/test-data.R | 272 - sits-1.5.3/sits/tests/testthat/test-debug.R | 9 sits-1.5.3/sits/tests/testthat/test-export.R |only sits-1.5.3/sits/tests/testthat/test-file_info.R | 5 sits-1.5.3/sits/tests/testthat/test-find_tiles.R |only sits-1.5.3/sits/tests/testthat/test-get_probs_class.R | 28 sits-1.5.3/sits/tests/testthat/test-grid_systems.R |only sits-1.5.3/sits/tests/testthat/test-labels.R | 16 sits-1.5.3/sits/tests/testthat/test-merge.R | 91 sits-1.5.3/sits/tests/testthat/test-mixture_model.R | 46 sits-1.5.3/sits/tests/testthat/test-ml.R | 38 sits-1.5.3/sits/tests/testthat/test-mosaic.R | 7 sits-1.5.3/sits/tests/testthat/test-period.R |only sits-1.5.3/sits/tests/testthat/test-plot.R | 94 sits-1.5.3/sits/tests/testthat/test-raster.R | 257 + sits-1.5.3/sits/tests/testthat/test-reclassify.R | 37 sits-1.5.3/sits/tests/testthat/test-reduce.R | 50 sits-1.5.3/sits/tests/testthat/test-regularize.R | 148 - sits-1.5.3/sits/tests/testthat/test-roi.R | 22 sits-1.5.3/sits/tests/testthat/test-samples.R | 167 - sits-1.5.3/sits/tests/testthat/test-segmentation.R | 169 + sits-1.5.3/sits/tests/testthat/test-select.R |only sits-1.5.3/sits/tests/testthat/test-sf.R | 49 sits-1.5.3/sits/tests/testthat/test-smooth.R | 29 sits-1.5.3/sits/tests/testthat/test-som.R | 37 sits-1.5.3/sits/tests/testthat/test-space-time-operations.R | 6 sits-1.5.3/sits/tests/testthat/test-summary.R | 16 sits-1.5.3/sits/tests/testthat/test-texture.R |only sits-1.5.3/sits/tests/testthat/test-tibble.R | 21 sits-1.5.3/sits/tests/testthat/test-uncertainty.R | 66 sits-1.5.3/sits/tests/testthat/test-utils.R | 27 sits-1.5.3/sits/tests/testthat/test-variance.R | 26 sits-1.5.3/sits/tests/testthat/test-view.R | 91 396 files changed, 16456 insertions(+), 12252 deletions(-)
Title: Access the 'PREDICTS' Biodiversity Database
Description: Fetches the 'PREDICTS' database and relevant metadata from the Data
Portal at the Natural History Museum, London <https://data.nhm.ac.uk>. Data
were collated from over 400 existing spatial comparisons of local-scale
biodiversity exposed to different intensities and types of anthropogenic
pressures, from sites around the world. These data are described in Hudson
et al. (2013) <doi:10.1002/ece3.2579>.
Author: Connor Duffin [aut, cre],
The Trustees of The Natural History Museum, London [cph]
Maintainer: Connor Duffin <connor.p.duffin@gmail.com>
Diff between predictsr versions 0.1.0 dated 2025-07-10 and 0.1.1 dated 2025-07-23
DESCRIPTION | 14 + MD5 | 36 ++-- NEWS.md | 7 R/predictsr.R | 221 +++++++++++++++++++++++------- README.md | 33 +++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/predictsr.R | 136 ++++++++++-------- inst/doc/predictsr.Rmd | 141 +++++++++++-------- inst/doc/predictsr.html | 98 +++++++------ man/GetColumnDescriptions.Rd | 22 ++ man/GetPredictsData.Rd | 21 ++ man/GetSitelevelSummaries.Rd | 25 ++- man/predictsr-package.Rd | 7 tests/testthat/test-column-descriptions.R | 19 ++ tests/testthat/test-predicts.R | 19 ++ tests/testthat/test-site-level.R | 20 ++ tests/testthat/test-utils.R | 77 +++++++++- vignettes/predictsr.Rmd | 141 +++++++++++-------- 19 files changed, 726 insertions(+), 311 deletions(-)
Title: Projection Pursuit Classification Forest
Description: Implements projection pursuit forest algorithm for supervised classification.
Author: Natalia da Silva [aut, cre] ,
Dianne Cook [aut],
Eun-Kyung Lee [aut]
Maintainer: Natalia da Silva <natalia.dasilva@fcea.edu.uy>
Diff between PPforest versions 0.1.3 dated 2022-09-09 and 0.2.0 dated 2025-07-23
PPforest-0.1.3/PPforest/R/PPclassify2.R |only PPforest-0.1.3/PPforest/man/PPclassify2.Rd |only PPforest-0.2.0/PPforest/DESCRIPTION | 35 - PPforest-0.2.0/PPforest/MD5 | 123 ++- PPforest-0.2.0/PPforest/NAMESPACE | 4 PPforest-0.2.0/PPforest/NEWS.md | 12 PPforest-0.2.0/PPforest/R/NCI60.R | 11 PPforest-0.2.0/PPforest/R/PPclassify.R |only PPforest-0.2.0/PPforest/R/PPforest.R | 142 +++- PPforest-0.2.0/PPforest/R/PPtree_split.R | 16 PPforest-0.2.0/PPforest/R/baggtree.R | 26 PPforest-0.2.0/PPforest/R/crab.R | 14 PPforest-0.2.0/PPforest/R/fishcatch.R | 20 PPforest-0.2.0/PPforest/R/glass.R | 24 PPforest-0.2.0/PPforest/R/image.R | 42 - PPforest-0.2.0/PPforest/R/leukemia.R | 10 PPforest-0.2.0/PPforest/R/lymphoma.R | 8 PPforest-0.2.0/PPforest/R/node_data.R | 2 PPforest-0.2.0/PPforest/R/olive.R | 24 PPforest-0.2.0/PPforest/R/parkinson.R | 54 - PPforest-0.2.0/PPforest/R/permute_importance.R | 4 PPforest-0.2.0/PPforest/R/ppf_avg_imp.R | 11 PPforest-0.2.0/PPforest/R/ppf_global_imp.R | 19 PPforest-0.2.0/PPforest/R/predict.PPforest.R |only PPforest-0.2.0/PPforest/R/ternary_str.R | 5 PPforest-0.2.0/PPforest/R/trees_pred.R | 32 - PPforest-0.2.0/PPforest/R/wine.R | 10 PPforest-0.2.0/PPforest/README.md | 132 ++-- PPforest-0.2.0/PPforest/build/vignette.rds |binary PPforest-0.2.0/PPforest/inst/doc/PPforest-vignette.R | 10 PPforest-0.2.0/PPforest/inst/doc/PPforest-vignette.Rmd | 45 - PPforest-0.2.0/PPforest/inst/doc/PPforest-vignette.html | 448 +++++++------- PPforest-0.2.0/PPforest/man/NCI60.Rd | 12 PPforest-0.2.0/PPforest/man/PPclassify.Rd |only PPforest-0.2.0/PPforest/man/PPforest.Rd | 19 PPforest-0.2.0/PPforest/man/PPtree_split.Rd | 6 PPforest-0.2.0/PPforest/man/baggtree.Rd | 13 PPforest-0.2.0/PPforest/man/crab.Rd | 24 PPforest-0.2.0/PPforest/man/figures |only PPforest-0.2.0/PPforest/man/fishcatch.Rd | 26 PPforest-0.2.0/PPforest/man/glass.Rd | 28 PPforest-0.2.0/PPforest/man/image.Rd | 46 - PPforest-0.2.0/PPforest/man/leukemia.Rd | 12 PPforest-0.2.0/PPforest/man/lymphoma.Rd | 12 PPforest-0.2.0/PPforest/man/node_data.Rd | 2 PPforest-0.2.0/PPforest/man/olive.Rd | 28 PPforest-0.2.0/PPforest/man/parkinson.Rd | 56 - PPforest-0.2.0/PPforest/man/permute_importance.Rd | 4 PPforest-0.2.0/PPforest/man/ppf_avg_imp.Rd | 11 PPforest-0.2.0/PPforest/man/ppf_global_imp.Rd | 17 PPforest-0.2.0/PPforest/man/predict.PPforest.Rd |only PPforest-0.2.0/PPforest/man/ternary_str.Rd | 5 PPforest-0.2.0/PPforest/man/trees_pred.Rd | 23 PPforest-0.2.0/PPforest/man/wine.Rd | 14 PPforest-0.2.0/PPforest/src/optim_index.cpp | 8 PPforest-0.2.0/PPforest/vignettes/PPforest-vignette.Rmd | 45 - PPforest-0.2.0/PPforest/vignettes/PPforest-vignette_cache |only PPforest-0.2.0/PPforest/vignettes/biblio.bib | 36 - 58 files changed, 965 insertions(+), 765 deletions(-)
Title: A Comprehensive Microbiome Data Processing Pipeline
Description: Provides tools for cleaning, processing, and preparing microbiome
sequencing data (e.g., 16S rRNA) for downstream analysis. Supports CSV,
TXT, and Excel file formats. The main function, ezclean(), automates
microbiome data transformation, including format validation,
transposition, numeric conversion, and metadata integration. It also
handles taxonomic levels efficiently, resolves duplicated taxa entries,
and outputs a well-structured, analysis-ready dataset. The companion
functions ezstat() run statistical tests and summarize results, while
ezviz() produces publication-ready visualizations.
Author: Utsav Lamichhane [aut, cre]
Maintainer: Utsav Lamichhane <utsav.lamichhane@gmail.com>
Diff between mbX versions 0.1.3 dated 2025-03-03 and 0.2.0 dated 2025-07-23
DESCRIPTION | 28 + MD5 | 12 NAMESPACE | 12 R/mbX_functions.R | 763 ++++++++++++++++++++++++++++++++++++++++++++++++------ R/zzz.R |only man/ezclean.Rd | 12 man/ezstat.Rd |only man/ezviz.Rd | 21 + 8 files changed, 751 insertions(+), 97 deletions(-)
Title: Dynamic Spectrogram Visualizations
Description: A set of tools to generate dynamic spectrogram visualizations in video format.
Author: Marcelo Araya-Salas [aut, cre]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between dynaSpec versions 1.0.3 dated 2025-04-07 and 1.0.4 dated 2025-07-23
DESCRIPTION | 12 - MD5 | 24 +- NEWS.md | 10 R/dynaSpec-package.R | 1 R/internal_functions.R | 21 + R/paged_spectro.R | 472 +++++++++++++++++++++++++++---------------- R/prep_static_ggspectro.R | 54 ++-- R/processSound.R | 2 R/scrolling_spectro.R | 3 data/canyon_wren.rda |binary man/paged_spectro.Rd | 14 - man/prep_static_ggspectro.Rd | 8 man/scrolling_spectro.Rd | 2 13 files changed, 392 insertions(+), 231 deletions(-)
Title: Practical Tools for Scientific Computations and Visualizations
Description: Collection of routines for efficient scientific computations in physics and astrophysics. These routines include utility functions, numerical computation tools, as well as visualisation tools. They can be used, for example, for generating random numbers from spherical and custom distributions, information and entropy analysis, special Fourier transforms, two-point correlation estimation (e.g. as in Landy & Szalay (1993) <doi:10.1086/172900>), binning & gridding of point sets, 2D interpolation, Monte Carlo integration, vector arithmetic and coordinate transformations. Also included is a non-exhaustive list of important constants and cosmological conversion functions. The graphics routines can be used to produce and export publication-ready scientific plots and movies, e.g. as used in Obreschkow et al. (2020, MNRAS Vol 493, Issue 3, Pages 4551–4569). These routines include special color scales, projection functions, and bitmap handling routines.
Author: Danail Obreschkow [aut, cre]
Maintainer: Danail Obreschkow <danail.obreschkow@gmail.com>
Diff between cooltools versions 2.4 dated 2024-07-18 and 2.18 dated 2025-07-23
DESCRIPTION | 12 +++++----- MD5 | 48 +++++++++++++++++++++++++--------------- NAMESPACE | 17 ++++++++++++-- R/cst.R | 18 +++++++-------- R/error.R |only R/griddata.R | 26 +++++++++++++++------ R/kde2.R | 33 +++++++++++++++------------ R/landyszalay.R | 9 +++++++ R/progress.R |only R/quiet.R | 6 ++--- R/readhdf5.R |only R/sigmoid.R |only R/sortlist.R |only R/sphereplot.R | 2 - R/tick.R | 10 ++++---- R/tock.R | 13 +++++----- R/uniquedouble.R | 60 ++++++++++++++++++++++++++++++++++---------------- R/userattributes.R |only R/writehdf5.R |only man/error.Rd |only man/kde2.Rd | 12 +++++----- man/progress.Rd |only man/quiet.Rd | 4 +-- man/readhdf5.Rd |only man/sigmoid.Rd |only man/sortlist.Rd |only man/sphereplot.Rd | 2 - man/tick.Rd | 4 +-- man/tock.Rd | 6 ++--- man/uniquedouble.Rd | 45 ++++++++++++++++++++++++------------- man/userattributes.Rd |only man/writehdf5.Rd |only 32 files changed, 207 insertions(+), 120 deletions(-)
Title: Stability-enHanced Approaches using Resampling Procedures
Description: In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package (B Bodinier et al (2025) <doi:10.18637/jss.v112.i05>), hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2023a) <doi:10.1093/jrsssc/qlad058> and B Bodinier et al (2023b) <doi:10.1093/bioinformatics/btad635>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <barbara.bodinier@gmail.com>
Diff between sharp versions 1.4.7 dated 2025-04-11 and 1.4.8 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/explanatory_performance.R | 8 ++++---- R/penalised_models.R | 16 +++++++++++----- R/sharp-package.R | 2 +- build/partial.rdb |binary man/Refit.Rd | 8 ++++---- man/sharp-package.Rd | 2 +- 9 files changed, 37 insertions(+), 27 deletions(-)
Title: Funnel Plots for Comparing Institutional Performance
Description: An implementation of methods presented by Spiegelhalter (2005) <doi:10.1002/sim.1970> Funnel plots for comparing institutional performance, for standardised ratios, ratios of counts and proportions with additive overdispersion adjustment.
Author: Chris Mainey [aut, cre] ,
Andrew Johnson [ctb],
Matthew Bass [ctb],
NHS-R Community [cph]
Maintainer: Chris Mainey <c.mainey1@nhs.net>
Diff between FunnelPlotR versions 0.5.0 dated 2024-04-12 and 0.6.0 dated 2025-07-23
DESCRIPTION | 13 MD5 | 84 ++--- NEWS.md | 23 + R/aggregate_func.R | 33 +- R/build_limits_lookup.R | 42 +- R/calculate_limits.R | 209 ++++++++----- R/classes_methods.R | 60 ++- R/draw_plot.R | 291 +++++++++++------- R/funnel_plot.R | 457 ++++++++++++++++++----------- R/funnel_themes.R | 44 +- R/od_adjustment.R | 141 +++++--- R/outliers_func.R | 66 +--- README.md | 16 - build/vignette.rds |binary inst/doc/changing_funnel_plot_options.R | 81 ++--- inst/doc/changing_funnel_plot_options.Rmd | 89 ++--- inst/doc/changing_funnel_plot_options.html | 142 ++++----- inst/doc/funnel_plots.R | 81 ++--- inst/doc/funnel_plots.Rmd | 79 ++--- inst/doc/funnel_plots.html | 156 +++++---- man/aggregate_func.Rd | 9 man/build_limits_lookup.Rd | 12 man/calculate_limits.Rd | 20 - man/draw_plot.Rd | 30 + man/figures/README-funnel1-1.png |binary man/figures/README-funnel2-1.png |binary man/funnel_clean.Rd | 3 man/funnel_grey.Rd | 3 man/funnel_plot.Rd | 187 +++++++---- man/phi_func.Rd | 7 man/tau_func.Rd | 6 man/transformed_zscore.Rd | 10 man/truncation.Rd | 3 man/winsorisation.Rd | 3 tests/testthat/test-aggregate_fun.R | 14 tests/testthat/test-build_limits_lookup.R | 76 ++-- tests/testthat/test-classes_methods.R | 36 +- tests/testthat/test-funnel_plot.R | 71 ++-- tests/testthat/test-funnel_themes.R | 2 tests/testthat/test-outliers_func.R | 49 +-- tests/testthat/test-poisson_limits.R | 25 - vignettes/changing_funnel_plot_options.Rmd | 89 ++--- vignettes/funnel_plots.Rmd | 79 ++--- 43 files changed, 1662 insertions(+), 1179 deletions(-)
Title: Nonparametric Statistical Methods
Description: Accompanies the book "Nonparametric Statistical Methods Using R, 2nd Edition" by Kloke and McKean (2024, ISBN:9780367651350). Includes methods, datasets, and random number generation useful for the study of robust and/or nonparametric statistics. Emphasizes classical nonparametric methods for a variety of designs --- especially one-sample and two-sample problems. Includes methods for general scores, including estimation and testing for the two-sample location problem as well as Hogg's adaptive method.
Author: John Kloke [aut, cre],
Joseph McKean [aut]
Maintainer: John Kloke <johndkloke@gmail.com>
Diff between npsm versions 2.0.0 dated 2024-05-26 and 2.0.1 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- README.md | 2 +- man/aligned.test.Rd | 2 +- man/knn_cv.Rd | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predicti [...truncated...]
Author: John Wambaugh [aut, cre] ,
Sarah Davidson-Fritz [aut] ,
Robert Pearce [aut] ,
Caroline Ring [aut] ,
Greg Honda [aut] ,
Mark Sfeir [aut],
Matt Linakis [aut] ,
Dustin Kapraun [aut] ,
Kimberly Truong [aut] ,
Colin Thomson [aut] ,
Meredith Scherer [aut] [...truncated...]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 2.6.1 dated 2025-05-01 and 2.7.0 dated 2025-07-23
httk-2.6.1/httk/R/do_initial_dose_pbtk.R |only httk-2.6.1/httk/data/armitage_input.RData |only httk-2.6.1/httk/inst/doc/Ve_Linakis2020.R |only httk-2.6.1/httk/inst/doc/Ve_Linakis2020.Rmd |only httk-2.6.1/httk/inst/doc/Ve_Linakis2020.html |only httk-2.6.1/httk/inst/doc/Vf_Kapraun2022.R |only httk-2.6.1/httk/inst/doc/Vf_Kapraun2022.Rmd |only httk-2.6.1/httk/inst/doc/Vf_Kapraun2022.html |only httk-2.6.1/httk/inst/doc/Vg_Truong2025.R |only httk-2.6.1/httk/inst/doc/Vg_Truong2025.Rmd |only httk-2.6.1/httk/inst/doc/Vg_Truong2025.html |only httk-2.6.1/httk/man/armitage_input.Rd |only httk-2.6.1/httk/vignettes/Ve_Linakis2020.Rmd |only httk-2.6.1/httk/vignettes/Vf_Kapraun2022.Rmd |only httk-2.6.1/httk/vignettes/Vg_Truong2025.Rmd |only httk-2.7.0/httk/DESCRIPTION | 27 httk-2.7.0/httk/MD5 | 254 +++-- httk-2.7.0/httk/NAMESPACE | 11 httk-2.7.0/httk/NEWS.md | 69 + httk-2.7.0/httk/R/apply_fup_adjustment.R | 2 httk-2.7.0/httk/R/armitage.R | 812 ++++++++++------- httk-2.7.0/httk/R/benchmark_httk.R | 40 httk-2.7.0/httk/R/calc_analytic_css.R | 4 httk-2.7.0/httk/R/calc_analytic_css_1comp.R | 49 - httk-2.7.0/httk/R/calc_analytic_css_3comp.R | 47 httk-2.7.0/httk/R/calc_analytic_css_3comp2.R | 50 - httk-2.7.0/httk/R/calc_analytic_css_pbtk.R | 44 httk-2.7.0/httk/R/calc_analytic_css_sumclearances.R | 98 +- httk-2.7.0/httk/R/calc_clearance_frac.R |only httk-2.7.0/httk/R/calc_css.R | 4 httk-2.7.0/httk/R/calc_dermal_equiv.R |only httk-2.7.0/httk/R/calc_half_life.R | 2 httk-2.7.0/httk/R/calc_hep_clearance.R | 13 httk-2.7.0/httk/R/calc_ma.R | 43 httk-2.7.0/httk/R/calc_mc_css.R | 177 ++- httk-2.7.0/httk/R/calc_mc_tk.R | 253 +++-- httk-2.7.0/httk/R/calc_oral_bioavailability.R | 2 httk-2.7.0/httk/R/calc_volume_of_distribution.R | 2 httk-2.7.0/httk/R/convert_units.R | 479 +++++++--- httk-2.7.0/httk/R/create_mc_samples.R | 464 +++++---- httk-2.7.0/httk/R/data.R | 169 +++ httk-2.7.0/httk/R/get_2023pfasinfo.R |only httk-2.7.0/httk/R/get_cheminfo.R | 9 httk-2.7.0/httk/R/get_physchem_param.R | 75 + httk-2.7.0/httk/R/ionization_functions.R | 8 httk-2.7.0/httk/R/kramer.R |only httk-2.7.0/httk/R/modelinfo_1comp.R | 8 httk-2.7.0/httk/R/modelinfo_1comp_lifestage.R | 8 httk-2.7.0/httk/R/modelinfo_1comppfas.R |only httk-2.7.0/httk/R/modelinfo_3comp.R | 8 httk-2.7.0/httk/R/modelinfo_3comp2.R | 8 httk-2.7.0/httk/R/modelinfo_3comp_lifestage.R | 8 httk-2.7.0/httk/R/modelinfo_3compss.R | 8 httk-2.7.0/httk/R/modelinfo_armitage.R |only httk-2.7.0/httk/R/modelinfo_dermal.R |only httk-2.7.0/httk/R/modelinfo_dermal_1subcomp.R |only httk-2.7.0/httk/R/modelinfo_gas_pbtk.R | 8 httk-2.7.0/httk/R/modelinfo_pbtk.R | 8 httk-2.7.0/httk/R/modelinfo_pbtk_lifestage.R | 8 httk-2.7.0/httk/R/modelinfo_sumclearances.R | 8 httk-2.7.0/httk/R/modelinfo_sumclearancespfas.R |only httk-2.7.0/httk/R/parameterize_IVD.R |only httk-2.7.0/httk/R/parameterize_armitage.R |only httk-2.7.0/httk/R/parameterize_dermal_pbtk.R |only httk-2.7.0/httk/R/parameterize_gas_pbtk.R | 1 httk-2.7.0/httk/R/parameterize_kramer.R |only httk-2.7.0/httk/R/parameterize_pbtk.R | 8 httk-2.7.0/httk/R/parameterize_pfas1comp.R |only httk-2.7.0/httk/R/parameterize_schmitt.R | 15 httk-2.7.0/httk/R/parameterize_steadystate.R | 2 httk-2.7.0/httk/R/parameterize_sumclearances.R | 3 httk-2.7.0/httk/R/parameterize_sumclearpfas.R |only httk-2.7.0/httk/R/predict_partitioning_schmitt.R | 7 httk-2.7.0/httk/R/propagate_invitrouv_3comp.R | 43 httk-2.7.0/httk/R/propagate_invitrouv_pbtk.R | 39 httk-2.7.0/httk/R/solve_dermal_pbtk.R |only httk-2.7.0/httk/R/solve_model.R | 53 - httk-2.7.0/httk/R/solve_pbtk.R | 2 httk-2.7.0/httk/R/sysdata.rda |binary httk-2.7.0/httk/README.md | 19 httk-2.7.0/httk/build/partial.rdb |binary httk-2.7.0/httk/build/vignette.rds |binary httk-2.7.0/httk/data/Scherer2025Vignette.RData |only httk-2.7.0/httk/data/Tables.RData |binary httk-2.7.0/httk/data/invitro.assay.params.RData |only httk-2.7.0/httk/inst/REFERENCES.bib | 138 ++ httk-2.7.0/httk/inst/doc/V1_IntroToHTTK.html | 48 - httk-2.7.0/httk/inst/doc/V2_IntrotoIVIVE.Rmd | 2 httk-2.7.0/httk/inst/doc/V2_IntrotoIVIVE.html | 2 httk-2.7.0/httk/inst/doc/Va_Pearce2017.html | 268 +++-- httk-2.7.0/httk/inst/doc/Vb_Ring2017.html | 4 httk-2.7.0/httk/inst/doc/Vd_Frank2019.Rmd | 2 httk-2.7.0/httk/inst/doc/Ve_Truong2025.R |only httk-2.7.0/httk/inst/doc/Ve_Truong2025.Rmd |only httk-2.7.0/httk/inst/doc/Ve_Truong2025.html |only httk-2.7.0/httk/inst/doc/Vf_WambaughSubmitted.R |only httk-2.7.0/httk/inst/doc/Vf_WambaughSubmitted.Rmd |only httk-2.7.0/httk/inst/doc/Vf_WambaughSubmitted.html |only httk-2.7.0/httk/inst/doc/Vg_MeadeSubmitted.R |only httk-2.7.0/httk/inst/doc/Vg_MeadeSubmitted.Rmd |only httk-2.7.0/httk/inst/doc/Vg_MeadeSubmitted.html |only httk-2.7.0/httk/inst/doc/Vh_SchererSubmitted.R |only httk-2.7.0/httk/inst/doc/Vh_SchererSubmitted.Rmd |only httk-2.7.0/httk/inst/doc/Vh_SchererSubmitted.html |only httk-2.7.0/httk/man/Dimitrijevic.IVD.Rd |only httk-2.7.0/httk/man/Scherer2025.IVD.Rd |only httk-2.7.0/httk/man/armitage_estimate_sarea.Rd | 12 httk-2.7.0/httk/man/armitage_eval.Rd | 99 +- httk-2.7.0/httk/man/calc_analytic_css.Rd | 3 httk-2.7.0/httk/man/calc_analytic_css_1comp.Rd | 4 httk-2.7.0/httk/man/calc_analytic_css_3comp.Rd | 4 httk-2.7.0/httk/man/calc_analytic_css_3comp2.Rd | 4 httk-2.7.0/httk/man/calc_analytic_css_pbtk.Rd | 4 httk-2.7.0/httk/man/calc_analytic_css_sumclearances.Rd | 8 httk-2.7.0/httk/man/calc_clearance_frac.Rd |only httk-2.7.0/httk/man/calc_dermal_equiv.Rd |only httk-2.7.0/httk/man/calc_ionization.Rd | 8 httk-2.7.0/httk/man/calc_ma.Rd | 12 httk-2.7.0/httk/man/calc_mc_css.Rd | 179 ++- httk-2.7.0/httk/man/calc_mc_tk.Rd | 113 +- httk-2.7.0/httk/man/calc_vdist.Rd | 2 httk-2.7.0/httk/man/create_mc_samples.Rd | 148 +-- httk-2.7.0/httk/man/dawson2023.Rd |only httk-2.7.0/httk/man/get_2023pfasinfo.Rd |only httk-2.7.0/httk/man/httk-package.Rd | 5 httk-2.7.0/httk/man/invitro.assay.params.Rd |only httk-2.7.0/httk/man/kramer_eval.Rd |only httk-2.7.0/httk/man/parameterize_IVD.Rd |only httk-2.7.0/httk/man/parameterize_armitage.Rd |only httk-2.7.0/httk/man/parameterize_dermal_pbtk.Rd |only httk-2.7.0/httk/man/parameterize_kramer.Rd |only httk-2.7.0/httk/man/parameterize_pfas1comp.Rd |only httk-2.7.0/httk/man/parameterize_schmitt.Rd | 6 httk-2.7.0/httk/man/parameterize_sumclearancespfas.Rd |only httk-2.7.0/httk/man/pfas.clearance.Rd |only httk-2.7.0/httk/man/solve_dermal_pbtk.Rd |only httk-2.7.0/httk/man/solve_model.Rd | 11 httk-2.7.0/httk/man/solve_pbtk.Rd | 2 httk-2.7.0/httk/src/dermal.c |only httk-2.7.0/httk/src/dermal_1subcomp.c |only httk-2.7.0/httk/src/init.c | 74 + httk-2.7.0/httk/src/skin_mm.c |only httk-2.7.0/httk/tests/1comp_test.Rout.save | 150 +-- httk-2.7.0/httk/tests/3comp_test.Rout.save | 282 ++--- httk-2.7.0/httk/tests/3compss_test.Rout.save | 6 httk-2.7.0/httk/tests/adddata_test.Rout.save | 8 httk-2.7.0/httk/tests/caco2_test.Rout.save | 188 ++- httk-2.7.0/httk/tests/cheminfo_test.Rout.save | 12 httk-2.7.0/httk/tests/fetal_pbtk_testing.Rout.save | 96 +- httk-2.7.0/httk/tests/ivive_test.Rout.save | 506 +++++----- httk-2.7.0/httk/tests/montecarlo_tests.Rout.save | 182 +-- httk-2.7.0/httk/tests/other_tests.Rout.save | 204 ++-- httk-2.7.0/httk/tests/pbtk_test.Rout.save | 156 +-- httk-2.7.0/httk/tests/solve_dermal_crude_test.R |only httk-2.7.0/httk/tests/solve_dermal_crude_test.Rout |only httk-2.7.0/httk/tests/solve_gas_test.Rout.save | 108 +- httk-2.7.0/httk/tests/unit_test.Rout.save | 18 httk-2.7.0/httk/vignettes/V2_IntrotoIVIVE.Rmd | 2 httk-2.7.0/httk/vignettes/Vd_Frank2019.Rmd | 2 httk-2.7.0/httk/vignettes/Ve_Truong2025.Rmd |only httk-2.7.0/httk/vignettes/Vf_WambaughSubmitted.Rmd |only httk-2.7.0/httk/vignettes/Vg_MeadeSubmitted.Rmd |only httk-2.7.0/httk/vignettes/Vh_SchererSubmitted.Rmd |only 163 files changed, 4035 insertions(+), 2526 deletions(-)
Title: Guidelines for Reporting About Network Data
Description: Interactively applies the Guidelines for Reporting About Network Data (GRAND) to an 'igraph' object, and generates a uniform narrative or tabular description of the object.
Author: Zachary Neal [aut, cre]
Maintainer: Zachary Neal <zpneal@msu.edu>
Diff between grand versions 0.9.0 dated 2023-02-10 and 0.9.1 dated 2025-07-23
grand-0.9.0/grand/R/data.R |only grand-0.9.0/grand/R/grand.table.R |only grand-0.9.0/grand/R/grand.text.R |only grand-0.9.0/grand/build |only grand-0.9.0/grand/data |only grand-0.9.0/grand/inst/doc |only grand-0.9.0/grand/man/airport.Rd |only grand-0.9.0/grand/man/cosponsor.Rd |only grand-0.9.0/grand/man/grand.table.Rd |only grand-0.9.0/grand/man/grand.text.Rd |only grand-0.9.0/grand/man/menu2.Rd |only grand-0.9.0/grand/man/scan2.Rd |only grand-0.9.0/grand/man/senate.Rd |only grand-0.9.0/grand/vignettes |only grand-0.9.1/grand/DESCRIPTION | 15 - grand-0.9.1/grand/MD5 | 42 +---- grand-0.9.1/grand/NAMESPACE | 5 grand-0.9.1/grand/NEWS.md | 14 + grand-0.9.1/grand/R/grand.R | 252 ++++----------------------------- grand-0.9.1/grand/R/grand_interview.R |only grand-0.9.1/grand/R/grand_manual.R |only grand-0.9.1/grand/R/grand_statement.R |only grand-0.9.1/grand/R/utils.R | 127 +++++----------- grand-0.9.1/grand/README.md | 13 + grand-0.9.1/grand/inst/CITATION | 2 grand-0.9.1/grand/man/figures/logo.png |binary grand-0.9.1/grand/man/grand.Rd | 143 ++---------------- grand-0.9.1/grand/man/grand_manual.Rd |only 28 files changed, 148 insertions(+), 465 deletions(-)
Title: Access to Canadian Election Study Data
Description: Provides tools to easily access and analyze Canadian Election Study data.
The package simplifies the process of downloading, cleaning, and using 'CES' datasets
for political science research and analysis. The Canadian Election Study ('CES')
has been conducted during federal elections since 1965, surveying Canadians
on their political preferences, engagement, and demographics. Data is accessed
from multiple sources including the 'Borealis' Data repository
<https://borealisdata.ca/> and the official 'Canadian Election Study' website
<https://ces-eec.arts.ubc.ca/>. This package is not officially affiliated
with the Canadian Election Study, 'Borealis' Data, or the University of British
Columbia, and users should cite the original data sources in their work.
Author: Laurence-Olivier M. Foisy [aut, cre]
Maintainer: Laurence-Olivier M. Foisy <mail@mfoisy.com>
Diff between ces versions 0.1.0 dated 2025-05-28 and 1.0.0 dated 2025-07-23
DESCRIPTION | 15 - MD5 | 64 ++--- R/ces-package.R | 10 R/create_codebook.R | 2 R/download_all_ces_datasets.R | 78 ++++-- R/download_ces_dataset.R | 82 +++++- R/download_pdf_codebook.R | 86 ++++++- R/get_ces.R | 130 ++++++++-- R/get_ces_subset.R | 17 + R/list_ces_datasets.R | 61 +++-- R/platform_utils.R | 182 +++++++++++++-- R/sysdata.rda |binary README.md | 14 - build/vignette.rds |binary inst/CITATION | 6 inst/doc/ces-introduction.R | 64 ++++- inst/doc/ces-introduction.Rmd | 92 ++++++- inst/doc/ces-introduction.html | 461 ++++++++++++++++++++++----------------- inst/examples/basic_analysis.R | 18 + inst/examples/download_dataset.R | 28 +- man/ces-package.Rd | 10 man/download_all_ces_datasets.Rd | 14 - man/download_ces_dataset.Rd | 26 +- man/download_pdf_codebook.Rd | 23 + man/export_codebook.Rd | 2 man/extract_data_from_zip.Rd |only man/get_ces.Rd | 18 + man/get_ces_subset.Rd | 15 + man/list_ces_datasets.Rd | 20 - man/safe_download.Rd | 11 man/show_variant_message.Rd |only tests/testthat/test-datasets.R | 44 ++- tests/testthat/test-get_ces.R | 6 vignettes/ces-introduction.Rmd | 92 ++++++- 34 files changed, 1202 insertions(+), 489 deletions(-)
Title: Plot Maps from Switzerland by Swiss Federal Statistical Office
Description: At the Swiss Federal Statistical Office (SFSO), spatial maps of Switzerland are available free of charge as 'Cartographic bases for small-scale thematic mapping'. This package contains convenience functions to import ESRI (Environmental Systems Research Institute) shape files using the package 'sf' and to plot them easily and quickly without having to worry too much about the technical details.
It contains utilities to combine multiple areas to one single polygon and to find neighbours for single regions. For any point on a map, a special locator can be used to determine to which municipality, district or canton it belongs.
Author: Andri Signorell [aut, cre],
Juerg Guggenbuehl [ctb]
Maintainer: Andri Signorell <andri@signorell.net>
Diff between bfsMaps versions 1.99.3 dated 2023-06-30 and 1.99.4 dated 2025-07-23
DESCRIPTION | 12 ++++++------ MD5 | 12 +++++++----- NAMESPACE | 3 ++- NEWS | 8 +++++++- R/geo.R |only build/vignette.rds |binary man/CombinePolygons.Rd | 2 +- man/geocode.Rd |only 8 files changed, 23 insertions(+), 14 deletions(-)
Title: Quotes on Statistics, Data Visualization and Science
Description: Generates a random quotation from a database of quotes on topics
in statistics, data visualization and science. Other functions allow searching
the quotes database by key term tags, or authors or creating a word cloud.
The output is designed to be suitable for use at the console, in Rmarkdown
and LaTeX.
Author: Michael Friendly [aut, cre] ,
Kevin Wright [aut] ,
Phil Chalmers [aut],
Matthew Sigal [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between statquotes versions 0.3.2 dated 2023-10-10 and 0.3.3 dated 2025-07-23
DESCRIPTION | 19 - MD5 | 18 NEWS.md | 31 + R/quote_cloud.R | 14 build/vignette.rds |binary data/quotes.rda |binary inst/doc/statquotes-database.html | 4 inst/doc/statquotes.html | 687 +++++++++++++++++++++++++------------- man/quote_cloud.Rd | 4 man/statquote.Rd | 2 10 files changed, 516 insertions(+), 263 deletions(-)
Title: A Lightweight Interface Between 'ggplot2' and 'igraph' Objects
Description: Interface to integrate 'igraph' and 'ggplot2' graphics within spatial maps. 'RGraphSpace' implements new geometric objects using 'ggplot2' prototypes, customized for representing large 'igraph' objects in a normalized coordinate system. By scaling shapes and graph elements, 'RGraphSpace' can provide a framework for layered visualizations.
Author: Victor Apolonio [ctb],
Vinicius Chagas [ctb],
Mauro Castro [aut, cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between RGraphSpace versions 1.0.8 dated 2025-05-14 and 1.0.9 dated 2025-07-23
DESCRIPTION | 8 MD5 | 40 ++-- NAMESPACE | 28 +++ R/gspaceChecks.R | 8 R/gspaceClasses.R | 38 ++++ R/gspaceGenerics.R | 42 ++++- R/gspaceMethods.R | 346 +++++++++++++++++++++++++++++++++++------ R/gspacePlots.R | 145 ++++++++++------- R/gspaceSupplements.R | 351 ++++++++++++++++++++++++++++-------------- R/gspaceValidation.R | 92 +++++++---- build/vignette.rds |binary data/gtoy1.RData |binary inst/doc/RGraphSpace.R | 31 ++- inst/doc/RGraphSpace.Rmd | 39 ++-- inst/doc/RGraphSpace.html | 75 ++++---- man/GraphSpace-accessors.Rd |only man/GraphSpace-class.Rd | 2 man/GraphSpace.Rd | 14 - man/getGraphSpace-methods.Rd | 4 man/plot.GraphSpace.Rd |only man/plotGraphSpace-methods.Rd | 45 +++-- vignettes/RGraphSpace.Rmd | 39 ++-- 22 files changed, 945 insertions(+), 402 deletions(-)
Title: Simulate a Data Frame Mirroring an Input and Produce Shareable
Simulation Code
Description: The 'dfmirroR' package allows users to input a data frame, simulate some number of observations based on specified columns of that data frame, and then outputs a string that contains the code to re-create the simulation. The goal is to both provide workable test data sets and provide users with the information they need to set up reproducible examples with team members. This package was created out of a need to share examples in cases where data are private and where a full data frame is not needed for testing or coordinating.
Author: Jacob Patterson-Stein [aut, cre]
Maintainer: Jacob Patterson-Stein <jacobpstein@gmail.com>
Diff between dfmirroR versions 2.1.0 dated 2024-01-26 and 2.2.0 dated 2025-07-23
DESCRIPTION | 8 +- MD5 | 14 +-- NAMESPACE | 1 NEWS.md | 2 R/dfmirror_func.R | 137 ++++++++++++++++++++++++++------------ README.md | 23 +++--- man/figures/README-example3-1.png |binary man/simulate_dataframe.Rd | 8 +- 8 files changed, 129 insertions(+), 64 deletions(-)
Title: Censored and Truncated Quantile Regression
Description: Estimation of quantile regression models for survival data.
Author: Paolo Frumento [aut, cre]
Maintainer: Paolo Frumento <paolo.frumento@unipi.it>
Diff between ctqr versions 2.1 dated 2024-02-12 and 2.2 dated 2025-07-23
DESCRIPTION | 14 +++++++++----- MD5 | 8 ++++---- NEWS.md | 9 ++++----- man/ctqr-package.Rd | 6 +++--- man/ctqr.Rd | 8 ++++---- 5 files changed, 24 insertions(+), 21 deletions(-)
Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences
on websites (i.e., clickstream). A click can be represented by a number,
character or string. Clickstreams can be modeled as zero- (only computes
occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz [aut, cre],
Theo van Kraay [aut]
Maintainer: Michael Scholz <michael.scholz@th-deg.de>
Diff between clickstream versions 1.3.3 dated 2023-09-27 and 1.3.4 dated 2025-07-23
DESCRIPTION | 20 MD5 | 16 NEWS | 245 ++++---- R/Clickstream.r | 1305 ++++++++++++++++++++++----------------------- R/Fitting.r | 644 +++++++++++----------- R/clickstream-package.R | 82 +- man/clickstream-package.Rd | 4 man/fitMarkovChain.Rd | 4 man/frequencies.Rd | 3 9 files changed, 1166 insertions(+), 1157 deletions(-)
Title: Perform Inference on Algorithm-Agnostic Variable Importance
Description: Calculate point estimates of and valid confidence intervals for
nonparametric, algorithm-agnostic variable importance measures in high and low dimensions,
using flexible estimators of the underlying regression functions. For more information
about the methods, please see Williamson et al. (Biometrics, 2020), Williamson et al. (JASA, 2021), and Williamson and Feng (ICML, 2020).
Author: Brian D. Williamson [aut, cre] ,
Jean Feng [ctb],
Charlie Wolock [ctb],
Noah Simon [ths] ,
Marco Carone [ths]
Maintainer: Brian D. Williamson <brian.d.williamson@kp.org>
Diff between vimp versions 2.3.3 dated 2023-08-28 and 2.3.5 dated 2025-07-23
DESCRIPTION | 19 - MD5 | 90 ++-- NAMESPACE | 5 NEWS.md | 16 R/average_vim.R | 276 +++++++------- R/estimate_type_predictiveness.R | 10 R/measure_accuracy.R | 15 R/measure_average_value.R | 98 ++--- R/measure_npv.R |only R/measure_ppv.R |only R/measure_sensitivity.R |only R/measure_specificity.R |only R/merge_vim.R | 232 ++++++------ R/predictiveness_measure.R | 359 +++++++++---------- R/utils.R | 627 +++++++++++++++++++++++++++++++++- R/vim.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction-to-vimp.R | 14 inst/doc/introduction-to-vimp.html | 276 +++++++------- inst/doc/ipcw-vim.html | 10 inst/doc/precomputed-regressions.R | 2 inst/doc/precomputed-regressions.html | 90 ++-- inst/doc/types-of-vims.R | 2 inst/doc/types-of-vims.html | 9 man/average_vim.Rd | 2 man/bootstrap_se.Rd | 2 man/check_fitted_values.Rd | 22 + man/check_inputs.Rd | 10 man/create_z.Rd | 6 man/cv_vim.Rd | 2 man/estimate_eif_projection.Rd | 13 man/estimate_nuisances.Rd | 22 + man/get_full_type.Rd | 6 man/get_test_set.Rd | 6 man/make_folds.Rd | 6 man/make_kfold.Rd | 10 man/measure_accuracy.Rd | 3 man/measure_npv.Rd |only man/measure_ppv.Rd |only man/measure_sensitivity.Rd |only man/measure_specificity.Rd |only man/merge_vim.Rd | 2 man/predictiveness_measure.Rd | 2 man/process_arg_lst.Rd | 6 man/run_sl.Rd | 25 + man/scale_est.Rd | 11 man/vim.Rd | 5 man/vimp.Rd | 2 tests/testthat/test-ipcw.R | 247 +++++++++++++ 50 files changed, 1806 insertions(+), 759 deletions(-)
Title: Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: proportional hazards (PH), accelerated failure time (AFT), proportional odds (PO), and accelerated hazards (AH), a super model that includes PH, AFT, PO and AH as special cases, Bayesian nonparametric nonproportional hazards (LDDPM), generalized accelerated failure time (GAFT), and spatially smoothed Polya tree density estimation. The spatial dependence is modeled via frailties under PH, AFT, PO, AH and GAFT, and via copulas under LDDPM and PH. Model choice is carried out via the logarithm of the pseudo marginal likelihood (LPML), the deviance information criterion (DIC), and the Watanabe-Akaike information criterion (WAIC). See Zhou, Hanson and Zhang (2020) <doi:10.18637/jss.v092.i09>.
Author: Haiming Zhou [aut, cre, cph],
Timothy Hanson [aut]
Maintainer: Haiming Zhou <haiming2019@gmail.com>
Diff between spBayesSurv versions 1.1.8 dated 2024-02-23 and 1.1.9 dated 2025-07-23
DESCRIPTION | 8 MD5 | 22 - man/SpatDensReg.Rd | 358 +++++++++++----------- man/SuperSurvRegBayes.Rd | 454 +++++++++++++-------------- man/anovaDDP.Rd | 342 ++++++++++----------- man/cox.snell.survregbayes.Rd | 108 +++--- man/frailtyGAFT.Rd | 544 ++++++++++++++++----------------- man/indeptCoxph.Rd | 358 +++++++++++----------- man/spCopulaCoxph.Rd | 478 ++++++++++++++--------------- man/spCopulaDDP.Rd | 480 ++++++++++++++--------------- man/survregbayes.Rd | 682 +++++++++++++++++++++--------------------- man/survregbayes2.Rd | 390 ++++++++++++------------ 12 files changed, 2112 insertions(+), 2112 deletions(-)
Title: Regression Discontinuity Design Application
Description: Estimation of both single- and multiple-assignment Regression Discontinuity Designs
(RDDs). Provides both parametric (global) and non-parametric (local) estimation choices for
both sharp and fuzzy designs, along with power analysis and assumption checks.
Introductions to the underlying logic and analysis of RDDs are in
Thistlethwaite, D. L., Campbell, D. T. (1960) <doi:10.1037/h0044319> and
Lee, D. S., Lemieux, T. (2010) <doi:10.1257/jel.48.2.281>.
Author: Ze Jin [aut],
Wang Liao [aut],
Irena Papst [aut],
Wenyu Zhang [aut],
Kimberly Hochstedler [aut],
Felix Thoemmes [aut, cre]
Maintainer: Felix Thoemmes <fjt36@cornell.edu>
Diff between rddapp versions 1.3.2 dated 2023-04-05 and 1.3.3 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 4 +++- R/mrd_est.R | 2 +- R/mrd_impute.R | 2 +- R/rd_est.R | 2 +- R/rd_impute.R | 2 +- R/rddapp-package.R | 11 +++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/distance-from-frontier.html | 8 ++++---- inst/doc/rddapp.html | 4 ++-- man/mrd_est.Rd | 2 +- man/mrd_impute.Rd | 2 +- man/rd_est.Rd | 2 +- man/rd_impute.Rd | 2 +- man/rddapp-package.Rd | 3 ++- 17 files changed, 42 insertions(+), 44 deletions(-)
Title: R Commander Miscellaneous Functions
Description: Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut, cre],
Manuel Marquez [aut],
Robert Muenchen [ctb],
Dan Putler [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between RcmdrMisc versions 2.9-1 dated 2023-09-26 and 2.9-2 dated 2025-07-23
DESCRIPTION | 12 +-- MD5 | 44 +++++------ NEWS | 6 + R/numSummary.R | 13 +-- man/Barplot.Rd | 162 ++++++++++++++++++++++---------------------- man/Dotplot.Rd | 118 ++++++++++++++++---------------- man/Hist.Rd | 88 +++++++++++------------ man/binnedCounts.Rd | 88 +++++++++++------------ man/indexplot.Rd | 112 +++++++++++++++--------------- man/normalityTest.Rd | 10 +- man/numSummary.Rd | 4 - man/piechart.Rd | 6 - man/plotDistr.Rd | 108 ++++++++++++++--------------- man/readSAS.Rd | 4 - man/readSPSS.Rd | 8 +- man/readStata.Rd | 4 - man/readXL.Rd | 4 - man/reliability.Rd | 94 ++++++++++++------------- man/repeatedMeasuresPlot.Rd | 2 man/reshapeL2W.Rd | 4 - man/reshapeW2L.Rd | 2 man/stepwise.Rd | 134 ++++++++++++++++++------------------ man/summarySandwich.Rd | 88 +++++++++++------------ 23 files changed, 561 insertions(+), 554 deletions(-)
Title: Construct Nomograms for Competing Risks Regression Models
Description: Nomograms are constructed to predict the cumulative incidence
rate which is calculated after adjusting for competing causes to the event of interest.
K-fold cross-validation is implemented to validate predictive accuracy using a competing-risk version of the concordance index.
Methods are as described in: Kattan MW, Heller G,
Brennan MF (2003).
Author: Michael Kattan [aut],
Changhong Yu [aut],
Xinge Ji [aut],
Zajichek Alex [cre]
Maintainer: Zajichek Alex <zajicha2@ccf.org>
Diff between QHScrnomo versions 3.0.1 dated 2024-03-18 and 3.0.2 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ R/Varcov.R | 6 ------ R/anova.R | 2 +- R/crr.R | 2 +- R/nomogram.R | 2 +- R/summary.R | 2 +- build/vignette.rds |binary inst/doc/QHScrnomo.R | 2 +- inst/doc/QHScrnomo.html | 8 ++++---- man/anova.cmprsk.Rd | 2 +- man/crr.fit.Rd | 2 +- man/nomogram.mk6.Rd | 2 +- man/summary.cmprsk.Rd | 2 +- 15 files changed, 35 insertions(+), 37 deletions(-)
Title: Piecewise Constant Hazard Models for Censored and Truncated Data
Description: Piecewise constant hazard models for survival data.
The package allows for right-censored, left-truncated, and interval-censored data.
Author: Paolo Frumento [aut, cre]
Maintainer: Paolo Frumento <paolo.frumento@unipi.it>
Diff between pch versions 2.1 dated 2024-02-09 and 2.2 dated 2025-07-23
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- NEWS.md | 6 +++--- man/pchreg.Rd | 2 +- 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Influence Measures and Diagnostic Plots for Multivariate Linear
Models
Description: Computes regression deletion diagnostics for multivariate linear models and provides some associated
diagnostic plots. The diagnostic measures include hat-values (leverages), generalized Cook's distance, and
generalized squared 'studentized' residuals. Several types of plots to detect influential observations are
provided.
Author: Michael Friendly [aut, cre]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between mvinfluence versions 0.9.0 dated 2022-09-20 and 0.9.2 dated 2025-07-23
mvinfluence-0.9.0/mvinfluence/NEWS |only mvinfluence-0.9.0/mvinfluence/man/Jtr.Rd |only mvinfluence-0.9.0/mvinfluence/man/mvinfluence.Rd |only mvinfluence-0.9.2/mvinfluence/DESCRIPTION | 18 mvinfluence-0.9.2/mvinfluence/MD5 | 52 mvinfluence-0.9.2/mvinfluence/NEWS.md |only mvinfluence-0.9.2/mvinfluence/R/Jfuns.R | 10 mvinfluence-0.9.2/mvinfluence/R/influencePlot.mlm.R | 18 mvinfluence-0.9.2/mvinfluence/R/lrPlot.R | 2 mvinfluence-0.9.2/mvinfluence/R/mlm.influence.R | 4 mvinfluence-0.9.2/mvinfluence/R/mvinfluence-package.R | 53 mvinfluence-0.9.2/mvinfluence/build/vignette.rds |binary mvinfluence-0.9.2/mvinfluence/inst/doc/uni-vs-multi.R | 37 mvinfluence-0.9.2/mvinfluence/inst/doc/uni-vs-multi.Rmd | 57 mvinfluence-0.9.2/mvinfluence/inst/doc/uni-vs-multi.html | 1450 +++++----- mvinfluence-0.9.2/mvinfluence/man/Fertilizer.Rd | 106 mvinfluence-0.9.2/mvinfluence/man/Jfuns.Rd |only mvinfluence-0.9.2/mvinfluence/man/cooks.distance.mlm.Rd | 94 mvinfluence-0.9.2/mvinfluence/man/figures/README-indexplot-1.png |binary mvinfluence-0.9.2/mvinfluence/man/figures/README-rob-index-plot-1.png |binary mvinfluence-0.9.2/mvinfluence/man/infIndexPlot.mlm.Rd | 210 - mvinfluence-0.9.2/mvinfluence/man/influence.mlm.Rd | 192 - mvinfluence-0.9.2/mvinfluence/man/influencePlot.mlm.Rd | 278 + mvinfluence-0.9.2/mvinfluence/man/lrPlot.Rd | 264 - mvinfluence-0.9.2/mvinfluence/man/mlm.influence.Rd | 172 - mvinfluence-0.9.2/mvinfluence/man/mpower.Rd | 112 mvinfluence-0.9.2/mvinfluence/man/mvinfluence-package.Rd |only mvinfluence-0.9.2/mvinfluence/man/print.inflmlm.Rd | 54 mvinfluence-0.9.2/mvinfluence/man/tr.Rd | 62 mvinfluence-0.9.2/mvinfluence/vignettes/uni-vs-multi.Rmd | 57 30 files changed, 1860 insertions(+), 1442 deletions(-)
Title: Tree Taper Curves and Sorting Based on 'TapeR'
Description: Providing new german-wide 'TapeR' Models and functions for their
evaluation. Included are the most common tree species in Germany (Norway
spruce, Scots pine, European larch, Douglas fir, Silver fir as well as
European beech, Common/Sessile oak and Red oak). Many other species are mapped
to them so that 36 tree species / groups can be processed. Single trees are
defined by species code, one or multiple diameters in arbitrary measuring
height and tree height. The functions then provide information on diameters
along the stem, bark thickness, height of diameters, volume of the total or
parts of the trunk and total and component above-ground biomass. It is also
possible to calculate assortments from the taper curves. Uncertainty
information is provided for diameter, volume and component biomass estimation.
Author: Christian Vonderach [aut, cre],
Edgar Kublin [aut],
Gerald Kaendler [aut]
Maintainer: Christian Vonderach <christian.vonderach@forst.bwl.de>
Diff between TapeS versions 0.13.3 dated 2025-02-14 and 0.13.4 dated 2025-07-23
DESCRIPTION | 6 MD5 | 18 - NEWS.md | 9 R/HDxoR.r | 152 +++++----- R/ParSort.r | 744 ++++++++++++++++++++++++++-------------------------- R/sysdata.rda |binary R/tprAssortment.r | 45 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/tapes.html | 8 10 files changed, 503 insertions(+), 479 deletions(-)
Title: Automated Reproducibility Checks for R Markdown Documents
Description: Provide reproducible R chunks in R Markdown document that automatically check computational results for reproducibility. This is achieved by creating json files storing metadata about computational results. A comprehensive tutorial to the package is available as preprint by Brandmaier & Peikert (2024, <doi:10.31234/osf.io/3zjvf>).
Author: Andreas M. Brandmaier [aut, cre],
Aaron Peikert [ctb]
Maintainer: Andreas M. Brandmaier <andreas.brandmaier@medicalschool-berlin.de>
Diff between reproducibleRchunks versions 1.1.0 dated 2025-07-02 and 1.2.0 dated 2025-07-23
reproducibleRchunks-1.1.0/reproducibleRchunks/inst/examples/plot |only reproducibleRchunks-1.1.0/reproducibleRchunks/inst/img |only reproducibleRchunks-1.1.0/reproducibleRchunks/tests/testthat/testdata/test_empty.html |only reproducibleRchunks-1.1.0/reproducibleRchunks/tests/testthat/testdata/test_plot.html |only reproducibleRchunks-1.1.0/reproducibleRchunks/tests/testthat/testdata/test_simulation.html |only reproducibleRchunks-1.1.0/reproducibleRchunks/tests/testthat/testdata/test_suite.html |only reproducibleRchunks-1.2.0/reproducibleRchunks/DESCRIPTION | 8 reproducibleRchunks-1.2.0/reproducibleRchunks/MD5 | 120 ++++++---- reproducibleRchunks-1.2.0/reproducibleRchunks/NAMESPACE | 19 - reproducibleRchunks-1.2.0/reproducibleRchunks/NEWS.md | 57 ++-- reproducibleRchunks-1.2.0/reproducibleRchunks/R/cleanup.R |only reproducibleRchunks-1.2.0/reproducibleRchunks/R/escaped_quote.R |only reproducibleRchunks-1.2.0/reproducibleRchunks/R/gather.R |only reproducibleRchunks-1.2.0/reproducibleRchunks/R/get_all_metadata_files.R |only reproducibleRchunks-1.2.0/reproducibleRchunks/R/get_reproducibility_summary.R | 66 ++--- reproducibleRchunks-1.2.0/reproducibleRchunks/R/isReproducible.R | 25 +- reproducibleRchunks-1.2.0/reproducibleRchunks/R/load_repro_data.R | 4 reproducibleRchunks-1.2.0/reproducibleRchunks/R/reproducibleR.R | 6 reproducibleRchunks-1.2.0/reproducibleRchunks/R/reset.R |only reproducibleRchunks-1.2.0/reproducibleRchunks/R/save_repro_data.R | 29 -- reproducibleRchunks-1.2.0/reproducibleRchunks/R/use_github_action.R |only reproducibleRchunks-1.2.0/reproducibleRchunks/R/zzz.R | 29 ++ reproducibleRchunks-1.2.0/reproducibleRchunks/README.md | 18 - reproducibleRchunks-1.2.0/reproducibleRchunks/build/vignette.rds |binary reproducibleRchunks-1.2.0/reproducibleRchunks/inst/CITATION | 22 + reproducibleRchunks-1.2.0/reproducibleRchunks/inst/WORDLIST | 12 + reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/custom_reports.R |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/custom_reports.Rmd |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/custom_reports.html |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/minimal_example.html | 14 - reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/plots.R |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/plots.Rmd |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/plots.html |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/regression_example.R |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/regression_example.Rmd |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/regression_example.html |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/renv_example.R |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/renv_example.Rmd |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/renv_example.html |only reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/use_case_simulation.Rmd | 2 reproducibleRchunks-1.2.0/reproducibleRchunks/inst/doc/use_case_simulation.html | 25 +- reproducibleRchunks-1.2.0/reproducibleRchunks/inst/examples/renv |only reproducibleRchunks-1.2.0/reproducibleRchunks/man/escapedQuote.Rd |only reproducibleRchunks-1.2.0/reproducibleRchunks/man/figures |only reproducibleRchunks-1.2.0/reproducibleRchunks/man/gather_package_names.Rd |only reproducibleRchunks-1.2.0/reproducibleRchunks/man/get_all_metadata_files.Rd |only reproducibleRchunks-1.2.0/reproducibleRchunks/man/get_num_reproducibility_errors.Rd | 34 +- reproducibleRchunks-1.2.0/reproducibleRchunks/man/get_reproducibility_summary.Rd | 46 +-- reproducibleRchunks-1.2.0/reproducibleRchunks/man/isReproducible.Rd | 12 - 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More information about reproducibleRchunks at CRAN
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Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel [aut, cre] ,
QuantLib Authors [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.0.15 dated 2025-04-23 and 0.0.16 dated 2025-07-23
ChangeLog | 21 + DESCRIPTION | 11 MD5 | 30 - build/partial.rdb |binary configure | 5 inst/NEWS.Rd | 8 src/Makevars.in | 2 src/Makevars.win.in | 2 src/ql/errors.cpp | 24 - src/ql/optional.hpp | 2 src/ql/time/calendar.cpp | 14 src/ql/time/calendars/israel.cpp | 745 +++++++++++++++++++++++---------------- src/ql/time/calendars/israel.hpp | 11 src/ql/time/date.cpp | 8 src/ql/utilities/null.hpp | 6 tools/configure.R | 4 16 files changed, 530 insertions(+), 363 deletions(-)
Title: Functional Profile Chain Ladder for Claims Reserving
Description: Functional claims reserving methods based on aggregated chain-ladder data, also known as the run-off triangle (functional) development profiles, implemented in three nonparametric algorithms (PARALLAX, REACT, and MACRAME) proposed in Maciak, Mizera, and Pešta (2022) <doi:10.1017/asb.2022.4>.
Author: Matus Maciak [aut, cre],
Rastislav Matus [ctb],
Ivan Mizera [aut],
Michal Pesta [aut]
Maintainer: Matus Maciak <maciak@karlin.mff.cuni.cz>
Diff between ProfileLadder versions 0.1.2 dated 2025-06-11 and 0.1.3 dated 2025-07-23
DESCRIPTION | 6 - MD5 | 86 ++++++++++------- NAMESPACE | 12 ++ R/CameronMutual.R | 2 R/GFCIB.R | 2 R/MidwestMutual.R | 2 R/NevadaGeneral.R | 2 R/as.profileLadder.R | 10 +- R/covid19CZ.R | 2 R/incrExplor.R | 202 +++++------------------------------------ R/mcBreaks.R |only R/mcReserve.R | 48 ++++----- R/mcStates.R |only R/mcTrans.R |only R/observed.R | 6 - R/parallelReserve.R | 6 - R/permuteReserve.R | 39 +++++-- R/plot.mcSetup.R |only R/plot.permutedReserve.R | 2 R/plot.profileLadder.R | 2 R/print.mcSetup.R |only R/print.permutedReserve.R | 2 R/print.profileLadder.R | 2 R/summary.mcSetup.R |only R/summary.permutedReserve.R |only R/summary.profileLadder.R | 52 +++++----- R/xNetSubscribe.R | 2 man/CameronMutual.Rd | 2 man/GFCIB.Rd | 2 man/MidwestMutual.Rd | 2 man/NevadaGeneral.Rd | 2 man/as.profileLadder.Rd | 4 man/covid19CZ.Rd | 2 man/incrExplor.Rd | 23 +--- man/mcBreaks.Rd |only man/mcReserve.Rd | 29 ++--- man/mcStates.Rd |only man/mcTrans.Rd |only man/observed.Rd | 2 man/parallelReserve.Rd | 2 man/permuteReserve.Rd | 10 +- man/plot.mcSetup.Rd |only man/plot.permutedReserve.Rd | 2 man/plot.profileLadder.Rd | 2 man/print.mcSetup.Rd |only man/print.permutedReserve.Rd | 2 man/print.profileLadder.Rd | 2 man/summary.mcSetup.Rd |only man/summary.permutedReserve.Rd |only man/summary.profileLadder.Rd | 2 man/xNetSubscribe.Rd | 2 51 files changed, 232 insertions(+), 347 deletions(-)
Title: Hardy-Weinberg Equilibrium in Polyploids
Description: Inference concerning equilibrium and random mating in
autopolyploids. Methods are available to test for equilibrium
and random mating at any even ploidy level (>2) in the presence
of double reduction at biallelic loci. For autopolyploid populations
in equilibrium, methods are available to estimate the degree of
double reduction. We also provide functions to calculate genotype
frequencies at equilibrium, or after one or several rounds of
random mating, given rates of double reduction. The main function is
hwefit(). This material is based upon work supported by the
National Science Foundation under Grant No. 2132247. The opinions,
findings, and conclusions or recommendations expressed are those of
the author and do not necessarily reflect the views of the National
Science Foundation. For details of these methods, see
Gerard (2023a) <doi:10.1111/biom.13722> and
Gerard (2023b) <doi:10.1111/1755-0998.13856>.
Author: David Gerard [aut, cre] ,
NSF DBI 2132247 [fnd]
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between hwep versions 2.0.2 dated 2023-05-16 and 2.0.3 dated 2025-07-23
DESCRIPTION | 15 MD5 | 148 ++--- NAMESPACE | 82 +-- NEWS.md | 6 R/bayes.R | 8 R/boot.R | 310 +++++------ R/f1dr.R | 176 +++--- R/gmm.R | 798 +++++++++++++++--------------- R/grad.R | 506 +++++++++---------- R/hwe.R | 574 ++++++++++----------- R/hwep-package.R | 83 --- R/like.R | 536 ++++++++++---------- R/multi.R | 343 ++++++------ R/nodr.R | 122 ++-- R/plots.R | 366 ++++++------- R/seg.R | 964 ++++++++++++++++++------------------ R/tetra.R | 468 ++++++++--------- R/theo.R | 756 ++++++++++++++-------------- R/ustat.R | 602 +++++++++++----------- R/utils.R | 500 +++++++++--------- README.md | 45 - build/partial.rdb |binary build/vignette.rds |binary configure.win | 8 inst/CITATION | 22 inst/doc/introduction.R | 31 - inst/doc/introduction.Rmd | 33 - inst/doc/introduction.html | 531 +++++++++++--------- inst/stan/gl_alt.stan | 44 - inst/stan/gl_null.stan | 70 +- inst/stan/include/license.stan | 28 - man/all_multinom.Rd | 62 +- man/dgamete.Rd | 92 +-- man/drbounds.Rd | 78 +- man/f1dr.Rd | 92 +-- man/freqnext.Rd | 100 +-- man/gibbs_gl.Rd | 134 ++--- man/gibbs_gl_alt.Rd | 126 ++-- man/gibbs_known.Rd | 82 +-- man/gsegmat.Rd | 86 +-- man/gsegmat_symb.Rd | 72 +- man/hweboot.Rd | 112 ++-- man/hwefit.Rd | 201 +++---- man/hwefreq.Rd | 148 ++--- man/hwelike.Rd | 108 ++-- man/hwenodr.Rd | 78 +- man/hwep-package.Rd | 110 +--- man/hweustat.Rd | 120 ++-- man/menbayesgl.Rd | 216 ++++---- man/p_from_alpha.Rd | 72 +- man/qqpvalue.Rd | 116 ++-- man/rmbayes.Rd | 166 +++--- man/rmbayesgl.Rd | 228 ++++---- man/rmlike.Rd | 122 ++-- man/simgl.Rd | 122 ++-- man/ts_bands.Rd | 106 ++-- man/zsegarray.Rd | 100 +-- man/zygdist.Rd | 84 +-- src/Makevars | 2 src/stanExports_gl_alt.h | 702 ++++++++++++-------------- src/stanExports_gl_null.h | 834 +++++++++++++++---------------- tests/testthat.R | 8 tests/testthat/test-bayes.R | 1030 +++++++++++++++++++-------------------- tests/testthat/test-choose_agg.R | 20 tests/testthat/test-gmm.R | 116 ++-- tests/testthat/test-grad.R | 460 ++++++++--------- tests/testthat/test-hwe.R | 22 tests/testthat/test-llike.R | 120 ++-- tests/testthat/test-seg.R | 618 +++++++++++------------ tests/testthat/test-tetra.R | 96 +-- tests/testthat/test-theo.R | 128 ++-- tests/testthat/test-ustat.R | 112 ++-- tests/testthat/test-utils.R | 144 ++--- tests/testthat/test-utils_cpp.R | 138 ++--- vignettes/introduction.Rmd | 33 - 75 files changed, 7905 insertions(+), 7986 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 1.0.0 dated 2023-04-07 and 1.0.1 dated 2025-07-23
DESCRIPTION | 10 +++--- MD5 | 15 +++++----- NEWS.md |only R/Prior.R | 2 - R/fastBarPrior.R | 2 - README.md | 66 +++++++++++++++++++++++++--------------------- inst/CITATION | 6 ++-- man/createBarPrior.Rd | 2 - man/createFastBarPrior.Rd | 2 - 9 files changed, 56 insertions(+), 49 deletions(-)
More information about BrokenAdaptiveRidge at CRAN
Permanent link
Title: R Templates from the University of Miami
Description: This holds r markdown and quarto templates for academic papers and
slide decks. It also has templates to create research projects which
contain academic papers as vignettes.
Author: Raymond Balise [aut, cre] ,
Gabriel Odom [aut] ,
Kyle Grealis [aut] ,
Francisco Cardozo [aut] ,
Frank Gutierrez [ctb]
Maintainer: Raymond Balise <balise@miami.edu>
Diff between rUM versions 2.1.0 dated 2025-03-21 and 2.2.0 dated 2025-07-23
rUM-2.1.0/rUM/inst/doc/OO1_using_posit_cloud.R |only rUM-2.1.0/rUM/inst/doc/OO1_using_posit_cloud.Rmd |only rUM-2.1.0/rUM/inst/doc/OO1_using_posit_cloud.html |only rUM-2.1.0/rUM/inst/doc/OO2_make_research_project.R |only rUM-2.1.0/rUM/inst/doc/OO2_make_research_project.Rmd |only rUM-2.1.0/rUM/inst/doc/OO2_make_research_project.html |only rUM-2.1.0/rUM/inst/doc/OO3_make_research_project_markdown.R |only rUM-2.1.0/rUM/inst/doc/OO3_make_research_project_markdown.Rmd |only rUM-2.1.0/rUM/inst/doc/OO3_make_research_project_markdown.html |only rUM-2.1.0/rUM/inst/doc/OO4_R_Markdown_Templates.R |only rUM-2.1.0/rUM/inst/doc/OO4_R_Markdown_Templates.Rmd |only rUM-2.1.0/rUM/inst/doc/OO4_R_Markdown_Templates.html |only rUM-2.1.0/rUM/inst/doc/OO5_make_a_package.R |only rUM-2.1.0/rUM/inst/doc/OO5_make_a_package.Rmd |only rUM-2.1.0/rUM/inst/doc/OO5_make_a_package.html |only rUM-2.1.0/rUM/inst/doc/OO6_show_example.R |only rUM-2.1.0/rUM/inst/doc/OO6_show_example.Rmd |only rUM-2.1.0/rUM/inst/doc/OO6_show_example.html |only rUM-2.1.0/rUM/inst/doc/OO7_write_scss.R |only rUM-2.1.0/rUM/inst/doc/OO7_write_scss.Rmd |only rUM-2.1.0/rUM/inst/doc/OO7_write_scss.html |only rUM-2.1.0/rUM/inst/doc/OO8_write_readme.R |only rUM-2.1.0/rUM/inst/doc/OO8_write_readme.Rmd |only rUM-2.1.0/rUM/inst/doc/OO8_write_readme.html |only rUM-2.1.0/rUM/vignettes/OO1_using_posit_cloud.Rmd |only rUM-2.1.0/rUM/vignettes/OO2_make_research_project.Rmd |only rUM-2.1.0/rUM/vignettes/OO3_make_research_project_markdown.Rmd |only rUM-2.1.0/rUM/vignettes/OO4_R_Markdown_Templates.Rmd |only rUM-2.1.0/rUM/vignettes/OO5_make_a_package.Rmd |only rUM-2.1.0/rUM/vignettes/OO6_show_example.Rmd |only rUM-2.1.0/rUM/vignettes/OO7_write_scss.Rmd |only rUM-2.1.0/rUM/vignettes/OO8_write_readme.Rmd |only rUM-2.2.0/rUM/DESCRIPTION | 35 rUM-2.2.0/rUM/MD5 | 146 ++- rUM-2.2.0/rUM/NAMESPACE | 28 rUM-2.2.0/rUM/NEWS.md | 15 rUM-2.2.0/rUM/R/dependencies_fix.R | 7 rUM-2.2.0/rUM/R/find_slides.R |only rUM-2.2.0/rUM/R/make_package.R |only rUM-2.2.0/rUM/R/make_project.R | 374 +--------- rUM-2.2.0/rUM/R/rUM-package.R | 8 rUM-2.2.0/rUM/R/show_slides.R |only rUM-2.2.0/rUM/R/utils.R |only rUM-2.2.0/rUM/R/write_man.R |only rUM-2.2.0/rUM/R/write_notes.R | 14 rUM-2.2.0/rUM/R/write_quarto.R | 60 + rUM-2.2.0/rUM/R/write_readme.R | 40 - rUM-2.2.0/rUM/R/write_scss.R | 75 +- rUM-2.2.0/rUM/R/write_slides.R |only rUM-2.2.0/rUM/README.md | 17 rUM-2.2.0/rUM/build/vignette.rds |binary rUM-2.2.0/rUM/inst/WORDLIST |only rUM-2.2.0/rUM/inst/doc/aa_using_posit_cloud.R |only rUM-2.2.0/rUM/inst/doc/aa_using_posit_cloud.Rmd |only rUM-2.2.0/rUM/inst/doc/aa_using_posit_cloud.html |only rUM-2.2.0/rUM/inst/doc/ab_make_research_project.R |only rUM-2.2.0/rUM/inst/doc/ab_make_research_project.Rmd |only rUM-2.2.0/rUM/inst/doc/ab_make_research_project.html |only rUM-2.2.0/rUM/inst/doc/ac_make_research_project_markdown.R |only rUM-2.2.0/rUM/inst/doc/ac_make_research_project_markdown.Rmd |only rUM-2.2.0/rUM/inst/doc/ac_make_research_project_markdown.html |only rUM-2.2.0/rUM/inst/doc/ad_R_Markdown_Templates.R |only rUM-2.2.0/rUM/inst/doc/ad_R_Markdown_Templates.Rmd |only rUM-2.2.0/rUM/inst/doc/ad_R_Markdown_Templates.html |only rUM-2.2.0/rUM/inst/doc/ae_make_a_package.R |only rUM-2.2.0/rUM/inst/doc/ae_make_a_package.Rmd |only rUM-2.2.0/rUM/inst/doc/ae_make_a_package.html |only rUM-2.2.0/rUM/inst/doc/af_show_example.R |only rUM-2.2.0/rUM/inst/doc/af_show_example.Rmd |only rUM-2.2.0/rUM/inst/doc/af_show_example.html |only rUM-2.2.0/rUM/inst/doc/ag_write_scss.R |only rUM-2.2.0/rUM/inst/doc/ag_write_scss.Rmd |only rUM-2.2.0/rUM/inst/doc/ag_write_scss.html |only rUM-2.2.0/rUM/inst/doc/ah_write_slides.R |only rUM-2.2.0/rUM/inst/doc/ah_write_slides.Rmd |only rUM-2.2.0/rUM/inst/doc/ah_write_slides.html |only rUM-2.2.0/rUM/inst/doc/ai_find_show_slides.R |only rUM-2.2.0/rUM/inst/doc/ai_find_show_slides.Rmd |only rUM-2.2.0/rUM/inst/doc/ai_find_show_slides.html |only rUM-2.2.0/rUM/inst/doc/aj_write_man.R |only rUM-2.2.0/rUM/inst/doc/aj_write_man.Rmd |only rUM-2.2.0/rUM/inst/doc/aj_write_man.html |only rUM-2.2.0/rUM/inst/gists/analysis_qmd_with_example.qmd | 18 rUM-2.2.0/rUM/inst/gists/analysis_qmd_wo_example.qmd | 18 rUM-2.2.0/rUM/inst/gists/analysis_rmd_with_example.Rmd | 2 rUM-2.2.0/rUM/inst/gists/analysis_rmd_wo_example.Rmd | 2 rUM-2.2.0/rUM/inst/gists/clean_title_page.html |only rUM-2.2.0/rUM/inst/gists/custom_miami.scss |only rUM-2.2.0/rUM/inst/gists/default_quarto.qmd | 10 rUM-2.2.0/rUM/inst/gists/quarto_slides.qmd |only rUM-2.2.0/rUM/inst/gists/quarto_slides_example_miami.qmd |only rUM-2.2.0/rUM/inst/gists/quarto_slides_example_rmed2025.qmd |only rUM-2.2.0/rUM/inst/gists/quarto_slides_miami.qmd |only rUM-2.2.0/rUM/inst/gists/quarto_slides_rmed2025.qmd |only rUM-2.2.0/rUM/inst/gists/rstudio_default-light.theme |only rUM-2.2.0/rUM/inst/gists/slides.scss |only rUM-2.2.0/rUM/inst/gists/slides_example_rmed.scss |only rUM-2.2.0/rUM/inst/slides |only rUM-2.2.0/rUM/man/find_slides.Rd |only rUM-2.2.0/rUM/man/make_package.Rd |only rUM-2.2.0/rUM/man/make_project.Rd | 6 rUM-2.2.0/rUM/man/rUM-package.Rd | 2 rUM-2.2.0/rUM/man/show_slides.Rd |only rUM-2.2.0/rUM/man/write_man.Rd |only rUM-2.2.0/rUM/man/write_notes.Rd | 6 rUM-2.2.0/rUM/man/write_quarto.Rd | 8 rUM-2.2.0/rUM/man/write_readme.Rd | 14 rUM-2.2.0/rUM/man/write_scss.Rd | 8 rUM-2.2.0/rUM/man/write_slides.Rd |only rUM-2.2.0/rUM/tests |only rUM-2.2.0/rUM/vignettes/aa_using_posit_cloud.Rmd |only rUM-2.2.0/rUM/vignettes/ab_make_research_project.Rmd |only rUM-2.2.0/rUM/vignettes/ac_make_research_project_markdown.Rmd |only rUM-2.2.0/rUM/vignettes/ad_R_Markdown_Templates.Rmd |only rUM-2.2.0/rUM/vignettes/ae_make_a_package.Rmd |only rUM-2.2.0/rUM/vignettes/af_show_example.Rmd |only rUM-2.2.0/rUM/vignettes/ag_write_scss.Rmd |only rUM-2.2.0/rUM/vignettes/ah_write_slides.Rmd |only rUM-2.2.0/rUM/vignettes/ai_find_show_slides.Rmd |only rUM-2.2.0/rUM/vignettes/aj_write_man.Rmd |only 120 files changed, 418 insertions(+), 495 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis. Please see Vinue (2017) <doi:10.18637/jss.v077.i06>.
Author: Guillermo Vinue [aut, cre],
Irene Epifanio [aut],
Amelia Simo [aut],
M. Victoria Ibanez [aut],
Juan Domingo [aut],
Guillermo Ayala [aut]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between Anthropometry versions 1.19 dated 2023-02-22 and 1.20 dated 2025-07-23
DESCRIPTION | 38 +++ MD5 | 40 ++-- NEWS | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Anthropometry.R | 272 ++++++++++++++-------------- inst/doc/Anthropometry.pdf |binary man/Anthropometry-internalHipamAnthropom.Rd | 6 man/Anthropometry-package.Rd | 14 - man/HartiganShapes.Rd | 2 man/LloydShapes.Rd | 2 man/archetypesBoundary.Rd | 10 - man/archetypoids.Rd | 10 - man/checkBranchLocalIMO.Rd | 8 man/checkBranchLocalMO.Rd | 8 man/getBestPamsamIMO.Rd | 8 man/getBestPamsamMO.Rd | 8 man/hipamAnthropom.Rd | 10 - man/shapes3dShapes.Rd | 18 - man/stepArchetypesRawData.Rd | 10 - man/stepArchetypoids.Rd | 10 - 21 files changed, 253 insertions(+), 225 deletions(-)
Title: A Concentration-Response Modeling Utility
Description: The tcplfit2 R package performs basic concentration-response curve fitting. The original tcplFit() function in the tcpl R package performed basic concentration-response curvefitting to 3 models. With tcplfit2, the core tcpl concentration-response functionality has been expanded to process diverse high-throughput screen (HTS) data generated at the US Environmental Protection Agency, including targeted ToxCast, high-throughput transcriptomics (HTTr) and high-throughput phenotypic profiling (HTPP). tcplfit2 can be used independently to support analysis for diverse chemical screening efforts.
Author: Thomas Sheffield [aut],
Jason Brown [ctb] ,
Sarah E. Davidson-Fritz [ctb] ,
Madison Feshuk [ctb, cre] ,
Lindsay Knupp [ctb],
Zhihui Zhao [ctb],
Richard S Judson [ctb] ,
Katie Paul Friedman [ctb]
Maintainer: Madison Feshuk <feshuk.madison@epa.gov>
Diff between tcplfit2 versions 0.1.8 dated 2025-04-17 and 0.1.9 dated 2025-07-23
tcplfit2-0.1.8/tcplfit2/vignettes/tcplfit2-vignette_old-2023.html |only tcplfit2-0.1.9/tcplfit2/DESCRIPTION | 27 tcplfit2-0.1.9/tcplfit2/MD5 | 13 tcplfit2-0.1.9/tcplfit2/NEWS.md | 118 tcplfit2-0.1.9/tcplfit2/README.md | 15 tcplfit2-0.1.9/tcplfit2/build/partial.rdb |binary tcplfit2-0.1.9/tcplfit2/build/vignette.rds |binary tcplfit2-0.1.9/tcplfit2/inst/doc/tcplfit2-vignette.html | 3011 +++++----- 8 files changed, 1610 insertions(+), 1574 deletions(-)
Title: 'Neuroconductor' Base Package with Helper Functions for 'nifti'
Objects
Description: Base package for 'Neuroconductor', which includes many helper
functions that interact with objects of class 'nifti', implemented by
package 'oro.nifti', for reading/writing and also other manipulation
functions.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurobase versions 1.32.4 dated 2024-05-09 and 1.33.0 dated 2025-07-23
DESCRIPTION | 8 MD5 | 120 +++--- NEWS.md | 5 R/breaker.R | 2 R/check_nifti.R | 2 R/check_nifti_header.R | 2 R/check_outfile.R | 2 R/checkniigz.R | 2 R/copyNIfTIHeader.R | 8 R/cut.R | 2 R/dicer.R | 2 R/double_ortho.R | 39 +- R/ensure_array.R | 2 R/fast_readnii.R | 6 R/file_imgext.R | 2 R/flip_img.R | 2 R/hist.nifti.R | 2 R/images2matrix.R | 2 R/img_color_df.R | 2 R/img_ts_to_list.R | 20 - R/import_methods.R | 2 R/orient_rpi.R | 2 R/ortho2.R | 4 R/overlay2.R | 2 R/parse_img_ext.R | 2 R/quantile.nifti.R | 2 R/random_nifti.R | 2 R/randomize_mask.R | 2 R/readNIfTI2.R | 12 R/remake_img.R | 8 R/replace_dropped_dimensions.R | 2 R/rescale_img.R | 6 R/robust_window.R | 2 R/same_dims.R | 2 R/tempimg.R | 2 R/write_nifti.R | 2 R/writenii.R | 12 R/zlimmer.R | 2 build/vignette.rds |binary inst/doc/neurobase.html | 49 +- inst/doc/nifti_basics.R | 14 inst/doc/nifti_basics.html | 687 +------------------------------------- inst/doc/simple_io.html | 17 man/copyNIfTIHeader.Rd | 8 man/datatype.Rd | 4 man/double_ortho.Rd | 16 man/ensure_array.Rd | 2 man/fast_readnii.Rd | 4 man/img_list_to_ts.Rd | 4 man/img_ts_to_df.Rd | 4 man/img_ts_to_list.Rd | 6 man/img_ts_to_matrix.Rd | 4 man/ortho2.Rd | 4 man/random_nifti.Rd | 2 man/readNIfTI2.Rd | 10 man/remake_img.Rd | 8 man/replace_dropped_dimensions.Rd | 2 man/rescale_img.Rd | 2 man/tempimg.Rd | 2 man/writeNIfTI2.Rd | 10 man/write_nifti.Rd | 2 61 files changed, 281 insertions(+), 880 deletions(-)
Title: Handling Missing Values with Multivariate Data Analysis
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA or MCA.
Author: Francois Husson [aut, cre] ,
Julie Josse [aut]
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between missMDA versions 1.19 dated 2023-11-17 and 1.20 dated 2025-07-23
DESCRIPTION | 15 +++- MD5 | 24 +++---- R/estim_ncpMCA.R | 6 + R/imputeMFA.R | 15 +++- R/plot.MIMCA.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/MultipleImputation.html | 128 +++++++++++++++++++++++---------------- inst/doc/missMDA.html | 128 +++++++++++++++++++++++---------------- man/MIFAMD.Rd | 2 man/MIMCA.Rd | 2 man/MIPCA.Rd | 2 man/prelim.Rd | 2 13 files changed, 201 insertions(+), 126 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- common effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- three-level meta-analysis model;
- generalised linear mixed model;
- logistic regression with penalised likelihood for rare events;
- Hartung-Knapp method for random effects model;
- Kenward-Roger method for random effects model;
- prediction interval;
- statistical tests for funnel plot asymmetry;
- trim-and-fill method to evaluate bias in meta-analysis;
- meta-regression;
- cumulative meta-analysis and leave-one-out meta-analysis;
- import data from 'RevMan 5';
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between meta versions 8.1-0 dated 2025-05-02 and 8.2-0 dated 2025-07-23
DESCRIPTION | 8 MD5 | 152 ++++----- NEWS.md | 69 ++++ R/catmeth-internal.R | 79 ++--- R/catmeth.R | 170 ++++++---- R/forest-internal.R | 10 R/forest.R | 225 ++++++++------ R/forest.metacum.R | 73 +++- R/forest.metainf.R | 47 -- R/gm.R | 5 R/longarm.R | 135 +++++++- R/meta-aux.R | 103 ++++++ R/meta-internal.R | 8 R/meta-object.R | 27 + R/meta-package.R | 23 + R/meta-set.R | 8 R/metaadd.R | 531 ++++++++++++++++++--------------- R/metabias.rm5.R | 2 R/metabin.R | 87 +++++ R/metabind-internal.R | 11 R/metabind.R | 2 R/metacont.R | 79 ++++- R/metacor.R | 73 ++++ R/metacr.R | 20 + R/metacum.R | 90 +++++ R/metagen.R | 692 +++++++++++++++++++++++++++----------------- R/metainc.R | 94 +++++ R/metainf.R | 90 +++++ R/metamean.R | 74 ++++ R/metaprop.R | 102 +++++- R/metarate.R | 92 +++++ R/nnt.R | 2 R/pairwise.R | 4 R/plot.cidprop.R | 20 - R/print.meta.R | 6 R/print.rm5.R | 2 R/print.summary.meta.R | 22 + R/read.rm5-internal.R | 13 R/settings.meta-internal.R | 2 R/settings.meta.R | 45 ++ R/subgroup.R | 57 ++- R/summary.rm5.R | 2 R/trimfill.R | 18 + R/trimfill.rm5.R | 2 R/update.meta.R | 87 ++++- build/vignette.rds |binary inst/doc/meta-tutorial.R | 3 inst/doc/meta-tutorial.Rmd | 3 inst/doc/meta-tutorial.pdf |binary inst/doc/meta-workflow.pdf |binary man/forest.meta.Rd | 4 man/forest.metacum.Rd | 4 man/forest.metainf.Rd | 49 --- man/longarm.Rd | 22 + man/meta-object.Rd | 27 + man/meta-package.Rd | 23 + man/metaadd.Rd | 54 +-- man/metabias.rm5.Rd | 2 man/metabin.Rd | 14 man/metacont.Rd | 14 man/metacor.Rd | 14 man/metacr.Rd | 5 man/metagen.Rd | 14 man/metainc.Rd | 14 man/metamean.Rd | 14 man/metaprop.Rd | 20 + man/metarate.Rd | 16 + man/nnt.Rd | 2 man/pairwise.Rd | 4 man/plot.cidprop.Rd | 20 - man/print.rm5.Rd | 2 man/settings.meta.Rd | 18 + man/summary.rm5.Rd | 2 man/trimfill.Rd | 5 man/trimfill.rm5.Rd | 2 man/update.meta.Rd | 14 vignettes/meta-tutorial.Rmd | 3 77 files changed, 2784 insertions(+), 1067 deletions(-)
Title: Utility Functions, Datasets and Extended Examples for Survival
Analysis
Description: Utility functions, datasets and extended examples for survival analysis. This extends a range of other packages, some simple wrappers for time-to-event analyses, datasets, and extensive examples in HTML with R scripts. The package also supports the course Biostatistics III entitled "Survival analysis for epidemiologists in R".
Author: Annika Tillander [ctb],
Andreas Karlsson [aut],
Johan Zetterqvist [ctb],
Peter Strom [ctb],
Benedicte Delcoigne [ctb],
Mark Clements [aut, cre]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between biostat3 versions 0.2.2 dated 2024-10-29 and 0.2.3 dated 2025-07-23
biostat3-0.2.2/biostat3/inst/doc/labs/q2.rmarkdown |only biostat3-0.2.3/biostat3/DESCRIPTION | 7 biostat3-0.2.3/biostat3/MD5 | 126 ++-- biostat3-0.2.3/biostat3/NAMESPACE | 1 biostat3-0.2.3/biostat3/R/lifetab2.R | 11 biostat3-0.2.3/biostat3/R/poisson.ci.R | 3 biostat3-0.2.3/biostat3/build/partial.rdb |binary biostat3-0.2.3/biostat3/inst/doc/labs/q10.html | 2 biostat3-0.2.3/biostat3/inst/doc/labs/q10.qmd | 2 biostat3-0.2.3/biostat3/inst/doc/labs/q2.html | 42 - biostat3-0.2.3/biostat3/inst/doc/labs/q2.qmd | 5 biostat3-0.2.3/biostat3/inst/doc/labs/q3.html | 2 biostat3-0.2.3/biostat3/inst/doc/labs/q3.qmd | 2 biostat3-0.2.3/biostat3/inst/doc/labs/q4.html | 2 biostat3-0.2.3/biostat3/inst/doc/labs/q4.qmd | 2 biostat3-0.2.3/biostat3/inst/doc/labs/q7.html | 2 biostat3-0.2.3/biostat3/inst/doc/labs/q7.qmd | 15 biostat3-0.2.3/biostat3/inst/doc/labs/q9.html | 2 biostat3-0.2.3/biostat3/inst/doc/labs/q9.qmd | 1 biostat3-0.2.3/biostat3/inst/doc/q12.R | 22 biostat3-0.2.3/biostat3/inst/doc/q2.R | 1 biostat3-0.2.3/biostat3/inst/doc/q25.R | 4 biostat3-0.2.3/biostat3/inst/doc/q7.R | 6 biostat3-0.2.3/biostat3/inst/doc/q9.R | 5 biostat3-0.2.3/biostat3/inst/doc/solutions/q1.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q1.html | 11 biostat3-0.2.3/biostat3/inst/doc/solutions/q10.Rmd | 8 biostat3-0.2.3/biostat3/inst/doc/solutions/q10.html | 225 ++++---- biostat3-0.2.3/biostat3/inst/doc/solutions/q11.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q11.html | 11 biostat3-0.2.3/biostat3/inst/doc/solutions/q12.Rmd | 3 biostat3-0.2.3/biostat3/inst/doc/solutions/q12.html | 113 ++-- biostat3-0.2.3/biostat3/inst/doc/solutions/q13.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q13.html | 11 biostat3-0.2.3/biostat3/inst/doc/solutions/q14.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q14.html | 50 - biostat3-0.2.3/biostat3/inst/doc/solutions/q2.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q2.html | 18 biostat3-0.2.3/biostat3/inst/doc/solutions/q22.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q22.html | 59 -- biostat3-0.2.3/biostat3/inst/doc/solutions/q23.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q23.html | 169 +++--- biostat3-0.2.3/biostat3/inst/doc/solutions/q25.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q25.html | 55 - biostat3-0.2.3/biostat3/inst/doc/solutions/q28.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q28.html | 386 +++++++------- biostat3-0.2.3/biostat3/inst/doc/solutions/q3.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q3.html | 20 biostat3-0.2.3/biostat3/inst/doc/solutions/q4.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q4.html | 11 biostat3-0.2.3/biostat3/inst/doc/solutions/q6.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q6.html | 342 ------------ biostat3-0.2.3/biostat3/inst/doc/solutions/q7.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q7.html | 65 +- biostat3-0.2.3/biostat3/inst/doc/solutions/q8.Rmd | 1 biostat3-0.2.3/biostat3/inst/doc/solutions/q8.html | 11 biostat3-0.2.3/biostat3/inst/doc/solutions/q9.Rmd | 5 biostat3-0.2.3/biostat3/inst/doc/solutions/q9.html | 249 ++++----- biostat3-0.2.3/biostat3/inst/doc/solutions/schoenfeld.pdf |only biostat3-0.2.3/biostat3/inst/doc/solutions/temp.Rmd |only biostat3-0.2.3/biostat3/inst/doc/solutions/temp.html |only biostat3-0.2.3/biostat3/man/colon.Rd | 20 biostat3-0.2.3/biostat3/man/colon_sample.Rd | 13 biostat3-0.2.3/biostat3/man/diet.Rd | 24 biostat3-0.2.3/biostat3/man/lifetab2.Rd | 7 biostat3-0.2.3/biostat3/man/melanoma.Rd | 18 66 files changed, 972 insertions(+), 1211 deletions(-)
Title: White Matter Normalization for Magnetic Resonance Images
Description: Shinohara (2014) <doi:10.1016/j.nicl.2014.08.008>
introduced 'WhiteStripe', an intensity-based normalization of T1
and T2 images, where normal
appearing white matter performs well, but requires segmentation.
This method performs white matter mean and standard deviation
estimates on data that has been rigidly-registered to the 'MNI'
template and uses histogram-based methods.
Author: R. Taki Shinohara [aut],
John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between WhiteStripe versions 2.4.3 dated 2024-05-09 and 2.5.0 dated 2025-07-23
DESCRIPTION | 11 ++++++----- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/download_img_data.R | 2 +- R/smooth_hist.R | 6 +++--- R/whitestripe_ind.R | 2 +- build/vignette.rds |binary inst/doc/Running_WhiteStripe.R | 6 +++--- inst/doc/Running_WhiteStripe.html | 17 +++++++++-------- man/download_img_data.Rd | 2 +- man/smooth_hist.Rd | 6 +++--- man/whitestripe_ind_to_mask.Rd | 2 +- 12 files changed, 43 insertions(+), 37 deletions(-)
Title: Functions for Tidy Analysis and Generation of Random Data
Description: To make it easy to generate random numbers based upon the underlying stats
distribution functions. All data is returned in a tidy and structured
format making working with the data simple and straight forward. Given that the
data is returned in a tidy 'tibble' it lends itself to working with the rest of the
'tidyverse'.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between TidyDensity versions 1.5.0 dated 2024-05-28 and 1.5.1 dated 2025-07-23
DESCRIPTION | 13 MD5 | 570 +++--- NEWS.md | 12 R/00_global_variables.R | 24 R/augment-bootstrap-density.R | 178 +- R/augment-bootstrap-p.R | 142 - R/augment-bootstrap-q.R | 144 - R/autoplot-combined-dist.R | 564 +++--- R/autoplot-four-graphs.R | 194 +- R/autoplot-multi-dist.R | 756 ++++----- R/autoplot-randomwalk.R | 404 ++-- R/autoplot-triangular.R | 288 +-- R/autoplot.R | 734 ++++----- R/bootstrap-unnest-tbl.R | 108 - R/combine-multi-single-dist-tbl.R | 250 +-- R/combine-tidy-distributions-tbl.R | 140 - R/empirical-tidy-bootstrap.R | 186 +- R/empirical-tidy.R | 278 +-- R/est-param-bernoulli.R | 228 +- R/est-param-beta.R | 314 +-- R/est-param-binomial.R | 330 ++-- R/est-param-burr.R | 272 +-- R/est-param-cauchy.R | 192 +- R/est-param-chisq.R | 358 ++-- R/est-param-exponential.R | 206 +- R/est-param-f.R | 274 +-- R/est-param-gamma.R | 252 +-- R/est-param-gen-beta.R | 250 +-- R/est-param-gen-pareto.R | 264 +-- R/est-param-geometric.R | 236 +- R/est-param-hypergeometric.R | 446 ++--- R/est-param-inv-burr.R | 264 +-- R/est-param-inv-pareto.R | 256 +-- R/est-param-inv-weibull.R | 238 +- R/est-param-logistic.R | 280 +-- R/est-param-lognormal.R | 226 +- R/est-param-negative-binomial.R | 342 ++-- R/est-param-normal.R | 226 +- R/est-param-paralogistic.R | 272 +-- R/est-param-pareto.R | 238 +- R/est-param-pareto1.R | 246 +-- R/est-param-poisson.R | 212 +- R/est-param-t.R | 224 +- R/est-param-triangular.R | 226 +- R/est-param-uniform.R | 216 +- R/est-param-zt-binom.R | 264 +-- R/est-param-zt-geometric.R | 242 +- R/est-param-ztn-binmoial.R | 252 +-- R/est-param-ztpois.R | 254 +-- R/helper-dist-type-extract.R | 84 - R/palette-color-blind.R | 80 R/plot-bootstrap-stat.R | 510 +++--- R/random-tidy-bernoulli.R | 256 +-- R/random-tidy-beta.R | 286 +-- R/random-tidy-binomial.R | 286 +-- R/random-tidy-burr-inverse.R | 306 +-- R/random-tidy-burr.R | 304 +-- R/random-tidy-cauchy.R | 280 +-- R/random-tidy-chisquare.R | 284 +-- R/random-tidy-exponential-inverse.R | 292 +-- R/random-tidy-exponential.R | 272 +-- R/random-tidy-f.R | 290 +-- R/random-tidy-gamma-inverse.R | 298 +-- R/random-tidy-gamma.R | 296 +-- R/random-tidy-general-beta.R | 326 ++-- R/random-tidy-general-pareto.R | 326 ++-- R/random-tidy-geom.R | 2 R/random-tidy-hypergeometric.R | 290 +-- R/random-tidy-logistic.R | 278 +-- R/random-tidy-lognormal.R | 286 +-- R/random-tidy-mixture.R | 298 +-- R/random-tidy-negative-binomial.R | 300 +-- R/random-tidy-normal-inverse.R | 296 +-- R/random-tidy-normal.R | 292 +-- R/random-tidy-paralogistic.R | 296 +-- R/random-tidy-pareto-inverse.R | 296 +-- R/random-tidy-pareto-single-param.R | 294 +-- R/random-tidy-pareto.R | 292 +-- R/random-tidy-poisson.R | 274 +-- R/random-tidy-t.R | 286 +-- R/random-tidy-triangular.R | 260 +-- R/random-tidy-uniform.R | 278 +-- R/random-tidy-weibull-inverse.R | 298 +-- R/random-tidy-weibull.R | 286 +-- R/random-tidy-zero-truc-poisson.R | 274 +-- R/random-tidy-zero-trunc-geometric.R | 276 +-- R/random-tidy-zero-truncated-binomial.R | 296 +-- R/random-zero-trunc-negative-binomial.R | 298 +-- R/stats-bernoulli-tbl.R | 188 +- R/stats-beta-tbl.R | 164 +- R/stats-binomial-tbl.R | 168 +- R/stats-burr-tbl.R | 174 +- R/stats-cauchy-tbl.R | 164 +- R/stats-chisquare-tbl.R | 174 +- R/stats-exponential-tbl.R | 166 +- R/stats-f-tbl.R | 202 +- R/stats-gamma-tbl.R | 162 - R/stats-gen-beta-tbl.R | 174 +- R/stats-gen-pareto-tbl.R | 170 +- R/stats-geometric-tbl.R | 170 +- R/stats-hypergeometric-tbl.R | 190 +- R/stats-inv-burr-tbl.R | 176 +- R/stats-inv-pareto-tbl.R | 172 +- R/stats-inv-weibull-tbl.R | 216 +- R/stats-logistic-tbl.R | 166 +- R/stats-lognormal-tbl.R | 168 +- R/stats-negative-binomial-tbl.R | 168 +- R/stats-normal-tbl.R | 164 +- R/stats-paarlogistic-tbl.R | 170 +- R/stats-pareto-tbl.R | 166 +- R/stats-pareto1-tbl.R | 198 +- R/stats-poisson-tbl.R | 164 +- R/stats-t-tbl.R | 164 +- R/stats-tidy-stat-func-tbl.R | 510 +++--- R/stats-triangular-tbl.R | 190 +- R/stats-uniform-tbl.R | 170 +- R/stats-weibull-tbl.R | 196 +- R/stats-zt-binomial-tbl.R | 162 - R/stats-zt-geometric-tbl.R | 172 +- R/stats-ztn-binomial-tbl.R | 174 +- R/stats-ztpoisson-tbl.R | 172 +- R/tidy_distribution_summary_tbl.R | 170 +- R/utils-aic-beta.R | 168 +- R/utils-aic-binomial.R | 124 - R/utils-aic-cauchy.R | 166 +- R/utils-aic-chisq.R | 116 - R/utils-aic-exponential.R | 146 - R/utils-aic-f.R | 152 - R/utils-aic-gamma.R | 160 - R/utils-aic-gen-beta.R | 178 +- R/utils-aic-gen-pareto.R | 168 +- R/utils-aic-geometric.R | 118 - R/utils-aic-hypergeometric.R | 126 - R/utils-aic-inv-burr.R | 162 - R/utils-aic-inv-pareto.R | 166 +- R/utils-aic-inv-weibull.R | 162 - R/utils-aic-logistic.R | 158 - R/utils-aic-lognormal.R | 160 - R/utils-aic-negative-binomial.R | 132 - R/utils-aic-normal.R | 116 - R/utils-aic-paralogistic.R | 162 - R/utils-aic-pareto.R | 156 - R/utils-aic-poisson.R | 116 - R/utils-aic-t.R | 152 - R/utils-aic-triangular.R | 198 +- R/utils-aic-uniform.R | 122 - R/utils-aic-weibull.R | 156 - R/utils-aic-zt-binom.R | 192 +- R/utils-aic-zt-geometric.R | 150 - R/utils-aic-ztn-binomial.R | 186 +- R/utils-aic-ztpoisson.R | 134 - R/utils-check-dupe-rows.R | 66 R/utils-convert-to-ts.R | 224 +- R/utils-distribution-comparison.R | 978 ++++++------ R/utils-mcmc-sampling.R | 220 +- R/utils-quantile-normalize.R | 302 +-- R/utis-aic-pareto1.R | 158 - R/vec-cumulative-functions.R | 534 +++--- README.md | 24 build/vignette.rds |binary inst/doc/getting-started.html | 42 man/bootstrap_density_augment.Rd | 116 - man/bootstrap_p_augment.Rd | 106 - man/bootstrap_p_vec.Rd | 110 - man/bootstrap_q_augment.Rd | 108 - man/bootstrap_q_vec.Rd | 112 - man/bootstrap_stat_plot.Rd | 190 +- man/cgmean.Rd | 92 - man/check_duplicate_rows.Rd | 148 - man/chmean.Rd | 92 - man/ckurtosis.Rd | 90 - man/cmean.Rd | 92 - man/cmedian.Rd | 90 - man/convert_to_ts.Rd | 200 +- man/csd.Rd | 92 - man/cskewness.Rd | 90 - man/cvar.Rd | 94 - man/dist_type_extractor.Rd | 72 man/figures/README-more_than_nine_simulations-1.png |binary man/figures/README-more_than_nine_simulations-2.png |binary man/figures/README-more_than_nine_simulations-3.png |binary man/figures/README-more_than_nine_simulations-4.png |binary man/figures/README-plot_density-1.png |binary man/figures/README-plot_density-2.png |binary man/figures/README-plot_density-3.png |binary man/figures/README-plot_density-4.png |binary man/quantile_normalize.Rd | 200 +- man/tidy_bernoulli.Rd | 143 - man/tidy_beta.Rd | 1 man/tidy_binomial.Rd | 1 man/tidy_burr.Rd | 1 man/tidy_cauchy.Rd | 1 man/tidy_chisquare.Rd | 1 man/tidy_exponential.Rd | 1 man/tidy_f.Rd | 1 man/tidy_gamma.Rd | 1 man/tidy_generalized_beta.Rd | 1 man/tidy_generalized_pareto.Rd | 1 man/tidy_geometric.Rd | 38 man/tidy_hypergeometric.Rd | 1 man/tidy_inverse_burr.Rd | 1 man/tidy_inverse_exponential.Rd | 1 man/tidy_inverse_gamma.Rd | 1 man/tidy_inverse_normal.Rd | 3 man/tidy_inverse_pareto.Rd | 1 man/tidy_inverse_weibull.Rd | 1 man/tidy_logistic.Rd | 1 man/tidy_lognormal.Rd | 1 man/tidy_mcmc_sampling.Rd | 162 - man/tidy_negative_binomial.Rd | 1 man/tidy_normal.Rd | 1 man/tidy_paralogistic.Rd | 1 man/tidy_pareto.Rd | 1 man/tidy_pareto1.Rd | 1 man/tidy_poisson.Rd | 1 man/tidy_stat_tbl.Rd | 182 +- man/tidy_t.Rd | 1 man/tidy_triangular.Rd | 169 +- man/tidy_uniform.Rd | 1 man/tidy_weibull.Rd | 1 man/tidy_zero_truncated_binomial.Rd | 1 man/tidy_zero_truncated_geometric.Rd | 1 man/tidy_zero_truncated_negative_binomial.Rd | 1 man/tidy_zero_truncated_poisson.Rd | 1 man/triangle_plot.Rd | 70 man/util_bernoulli_param_estimate.Rd | 174 +- man/util_bernoulli_stats_tbl.Rd | 146 - man/util_beta_aic.Rd | 170 +- man/util_binomial_aic.Rd | 168 +- man/util_burr_param_estimate.Rd | 176 +- man/util_burr_stats_tbl.Rd | 148 - man/util_cauchy_aic.Rd | 180 +- man/util_chisq_aic.Rd | 136 - man/util_chisquare_param_estimate.Rd | 232 +- man/util_exponential_aic.Rd | 158 - man/util_f_aic.Rd | 162 - man/util_f_param_estimate.Rd | 170 +- man/util_gamma_aic.Rd | 174 +- man/util_generalized_beta_aic.Rd | 176 +- man/util_generalized_beta_param_estimate.Rd | 172 +- man/util_generalized_beta_stats_tbl.Rd | 146 - man/util_generalized_pareto_aic.Rd | 170 +- man/util_generalized_pareto_param_estimate.Rd | 170 +- man/util_generalized_pareto_stats_tbl.Rd | 144 - man/util_geometric_aic.Rd | 168 +- man/util_hypergeometric_aic.Rd | 170 +- man/util_inverse_burr_aic.Rd | 172 +- man/util_inverse_burr_param_estimate.Rd | 170 +- man/util_inverse_burr_stats_tbl.Rd | 146 - man/util_inverse_pareto_aic.Rd | 172 +- man/util_inverse_pareto_param_estimate.Rd | 170 +- man/util_inverse_pareto_stats_tbl.Rd | 144 - man/util_inverse_weibull_aic.Rd | 174 +- man/util_inverse_weibull_param_estimate.Rd | 170 +- man/util_inverse_weibull_stats_tbl.Rd | 146 - man/util_logistic_aic.Rd | 172 +- man/util_lognormal_aic.Rd | 172 +- man/util_negative_binomial_aic.Rd | 172 +- man/util_normal_aic.Rd | 136 - man/util_paralogistic_aic.Rd | 182 +- man/util_paralogistic_param_estimate.Rd | 180 +- man/util_paralogistic_stats_tbl.Rd | 142 - man/util_pareto1_aic.Rd | 192 +- man/util_pareto1_param_estimate.Rd | 202 +- man/util_pareto1_stats_tbl.Rd | 152 - man/util_pareto_aic.Rd | 170 +- man/util_poisson_aic.Rd | 166 +- man/util_t_aic.Rd | 162 - man/util_t_param_estimate.Rd | 162 - man/util_triangular_aic.Rd | 182 +- man/util_triangular_param_estimate.Rd | 186 +- man/util_triangular_stats_tbl.Rd | 146 - man/util_uniform_aic.Rd | 170 +- man/util_weibull_aic.Rd | 174 +- man/util_zero_truncated_binomial_aic.Rd | 194 +- man/util_zero_truncated_binomial_param_estimate.Rd | 216 +- man/util_zero_truncated_binomial_stats_tbl.Rd | 158 - man/util_zero_truncated_geometric_aic.Rd | 170 +- man/util_zero_truncated_geometric_param_estimate.Rd | 176 +- man/util_zero_truncated_geometric_stats_tbl.Rd | 144 - man/util_zero_truncated_negative_binomial_aic.Rd | 192 +- man/util_zero_truncated_negative_binomial_param_estimate.Rd | 220 +- man/util_zero_truncated_negative_binomial_stats_tbl.Rd | 172 +- man/util_zero_truncated_poisson_aic.Rd | 140 - man/util_zero_truncated_poisson_param_estimate.Rd | 230 +- man/util_zero_truncated_poisson_stats_tbl.Rd | 154 - 286 files changed, 25180 insertions(+), 25203 deletions(-)
Title: Tools Inspired by 'Stata' to Manipulate Tabular Data
Description: A set of tools inspired by 'Stata' to explore data.frames ('summarize',
'tabulate', 'xtile', 'pctile', 'binscatter', elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mg3901@columbia.edu>
Diff between statar versions 0.7.6 dated 2023-08-19 and 0.7.7 dated 2025-07-23
DESCRIPTION | 8 ++--- MD5 | 22 +++++++-------- NEWS.md | 3 ++ R/elapsed_dates.R | 2 - build/vignette.rds |binary inst/doc/data-frames.html | 4 +- inst/doc/graph.html | 4 +- inst/doc/panel-data.html | 4 +- inst/doc/vector.html | 4 +- man/elapsed.Rd | 2 - man/stat_binmean.Rd | 64 +++++++++++++++++++++++++++++++++++++--------- man/statar.Rd | 12 ++++++++ 12 files changed, 92 insertions(+), 37 deletions(-)
Title: Sensory Data Analysis
Description: Statistical Methods to Analyse Sensory Data. SensoMineR: A package for sensory data analysis. S. Le and F. Husson (2008).
Author: Francois Husson [aut, cre] ,
Sebastien Le [aut],
Marine Cadoret [aut]
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between SensoMineR versions 1.27 dated 2023-11-28 and 1.28 dated 2025-07-23
DESCRIPTION | 17 +++++++++++++---- MD5 | 10 +++++----- data/hedochoc.rda |binary data/sensopanels.rda |binary man/WordCountAna.Rd | 2 +- man/analyse_holos.Rd | 2 +- 6 files changed, 20 insertions(+), 11 deletions(-)
Title: 'React Router' for 'shiny' Apps and 'Quarto'
Description: You can easily share url pages using 'React Router' in 'shiny' applications
and 'Quarto' documents. The package wraps the 'react-router-dom' 'React' library and
provides access to hash routing to navigate on multiple url pages.
Author: Felix Luginbuhl [aut, cre] ,
Andryas Waurzenczak [ctb],
Shopify Inc. [ctb, cph]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between reactRouter versions 0.1.0 dated 2025-04-29 and 0.1.1 dated 2025-07-23
DESCRIPTION | 13 LICENSE | 4 MD5 | 90 + NAMESPACE | 2 NEWS.md | 5 R/components.R | 74 + R/inputs.R | 34 R/reactRouterExample.R |only README.md | 20 build/vignette.rds |binary inst/doc/introduction.R | 1 inst/doc/introduction.Rmd | 609 +++++------- inst/doc/introduction.html | 794 +++++++--------- inst/doc/shiny.fluent.R |only inst/doc/shiny.fluent.Rmd |only inst/doc/shiny.fluent.html |only inst/examples/basic/app.R | 4 inst/examples/bslib |only inst/examples/dynamic-segment |only inst/examples/shiny.fluent |only inst/reactRouter-6.30.0/react-router-dom.js.LICENSE.txt | 64 - man/BrowserRouter.Rd |only man/HashRouter.Rd | 34 man/Link.Rd | 71 - man/MemoryRouter.Rd | 34 man/NavLink.Rd | 71 - man/Navigate.Rd | 34 man/Outlet.Rd | 34 man/Route.Rd | 43 man/Routes.Rd | 34 man/component.Rd | 32 man/figures |only man/reactRouterDependency.Rd | 28 man/reactRouterExample.Rd |only man/reexports.Rd | 32 tests/testthat/setup-shinytest2.R | 4 tests/testthat/test-apps/HashRouter/App.R | 8 vignettes/introduction.Rmd | 609 +++++------- vignettes/shiny.fluent.Rmd |only 39 files changed, 1321 insertions(+), 1461 deletions(-)
Title: Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS'
Description: Invoke a 'BUGS' model in 'OpenBUGS' or 'WinBUGS', a class "bugs" for 'BUGS'
results and functions to work with that class.
Function write.model() allows a 'BUGS' model file to be written.
The class and auxiliary functions could be used with other MCMC programs, including 'JAGS'.
The suggested package 'BRugs' (only needed for function openbugs()) is only available from the CRAN archives,
see <https://cran.r-project.org/package=BRugs>.
Author: Andrew Gelman [aut],
Sibylle Sturtz [aut],
Uwe Ligges [cre, aut],
Gregor Gorjanc [ctb],
Jouni Kerman [ctb],
Insightful Corp. [ctb]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between R2WinBUGS versions 2.1-22.1 dated 2024-02-05 and 2.1-23 dated 2025-07-23
DESCRIPTION | 50 +++++++++++++++++++++++++++++++++++++------------ MD5 | 10 ++++----- build/vignette.rds |binary data/schools.txt.gz |binary inst/doc/R2WinBUGS.pdf |binary man/openbugs.Rd | 4 +-- 6 files changed, 45 insertions(+), 19 deletions(-)
Title: Non-Linear Transformation Models
Description: Fits a non-linear transformation model ('nltm') for
analyzing survival data, see Tsodikov (2003) <doi:10.1111/1467-9868.00414>. The
class of 'nltm' includes the following currently supported
models: Cox proportional hazard, proportional hazard cure,
proportional odds, proportional hazard - proportional hazard
cure, proportional hazard - proportional odds cure, Gamma
frailty, and proportional hazard - proportional odds.
Author: Gilda Garibotti [aut],
Alexander Tsodikov [aut],
Mark Clements [aut, cre]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between nltm versions 1.4.5 dated 2023-12-03 and 1.4.6 dated 2025-07-23
DESCRIPTION | 23 +++++++++++++++++------ MD5 | 4 ++-- man/nltm.control.Rd | 2 +- 3 files changed, 20 insertions(+), 9 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson [aut, cre] ,
Julie Josse [aut],
Sebastien Le [aut],
Jeremy Mazet [aut]
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between FactoMineR versions 2.11 dated 2024-04-20 and 2.12 dated 2025-07-23
DESCRIPTION | 20 +++- MD5 | 30 +++--- R/CA.R | 16 ++- R/GPA.R | 3 R/HCPC.R | 20 ++-- R/MFA.R | 52 +++++------ R/plot.MFA.R | 2 build/vignette.rds |binary data/children.rda |binary data/poison.rda |binary data/poison.text.rda |binary inst/doc/clustering.html | 124 ++++++++++++++++---------- man/HCPC.Rd | 212 +++++++++++++++++++++++----------------------- man/meansComp.Rd | 2 man/plotellipses.Rd | 2 vignettes/FactoMineR.html | 128 +++++++++++++++++---------- 16 files changed, 349 insertions(+), 262 deletions(-)
Title: Support Functions and Data for "Ecological Models and Data"
Description: Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).
Author: Ben Bolker [aut, cre],
Sang Woo Park [ctb],
James Vonesh [dtc],
Jacqueline Wilson [dtc],
Russ Schmitt [dtc],
Sally Holbrook [dtc],
James D. Thomson [dtc],
R. Scot Duncan [dtc]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between emdbook versions 1.3.13 dated 2023-07-03 and 1.3.14 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 5 +++-- R/utils3d.R | 4 ++-- build/partial.rdb |binary inst/NEWS.Rd | 13 ++++++++++--- man/Damsel.Rd | 2 -- man/apply2d.Rd | 2 +- man/curve3d.Rd | 8 +++++--- 9 files changed, 33 insertions(+), 25 deletions(-)
Title: Boundary Overlap Statistics
Description: Analysis workflow for finding geographic boundaries of ecological or landscape traits and comparing the placement of geographic boundaries of two traits. If data are trait values, trait data are transformed to boundary intensities based on approximate first derivatives across latitude and longitude. The package includes functions to create custom null models based on the input data. The boundary statistics are described in: Fortin, Drapeau, and Jacquez (1996) <doi:10.2307/3545584>.
Author: Amy Luo [aut, cre, cph] ,
Elizabeth Derryberry [ths]
Maintainer: Amy Luo <amy.luo.15@gmail.com>
Diff between BoundaryStats versions 2.2.0 dated 2024-10-25 and 2.3.0 dated 2025-07-23
BoundaryStats-2.2.0/BoundaryStats/R/lisa_clusters.R |only BoundaryStats-2.2.0/BoundaryStats/man/Odirect.Rd |only BoundaryStats-2.2.0/BoundaryStats/man/Ox.Rd |only BoundaryStats-2.2.0/BoundaryStats/man/Oxy.Rd |only BoundaryStats-2.2.0/BoundaryStats/man/lisa_clusters.Rd |only BoundaryStats-2.2.0/BoundaryStats/man/max_subgraph.Rd |only BoundaryStats-2.2.0/BoundaryStats/man/n_subgraph.Rd |only BoundaryStats-2.3.0/BoundaryStats/DESCRIPTION | 20 - BoundaryStats-2.3.0/BoundaryStats/MD5 | 64 +--- BoundaryStats-2.3.0/BoundaryStats/NAMESPACE | 12 BoundaryStats-2.3.0/BoundaryStats/NEWS.md | 14 BoundaryStats-2.3.0/BoundaryStats/R/boundary_null_distrib.R | 115 ++++--- BoundaryStats-2.3.0/BoundaryStats/R/boundary_statistics.R | 105 ++++-- BoundaryStats-2.3.0/BoundaryStats/R/categorical_boundary.R | 6 BoundaryStats-2.3.0/BoundaryStats/R/define_boundary.R | 158 ++++------ BoundaryStats-2.3.0/BoundaryStats/R/gauss_random_field_sim.R | 31 - BoundaryStats-2.3.0/BoundaryStats/R/globals.R | 4 BoundaryStats-2.3.0/BoundaryStats/R/mod_random_clust_sim.R | 27 - BoundaryStats-2.3.0/BoundaryStats/R/overlap_null_distrib.R | 72 ++-- BoundaryStats-2.3.0/BoundaryStats/R/overlap_statistics.R | 60 +-- BoundaryStats-2.3.0/BoundaryStats/R/plot_boundary.R | 60 ++- BoundaryStats-2.3.0/BoundaryStats/R/random_raster_sim.R | 8 BoundaryStats-2.3.0/BoundaryStats/R/sobel_operator.R | 45 -- BoundaryStats-2.3.0/BoundaryStats/README.md | 106 +++++- BoundaryStats-2.3.0/BoundaryStats/inst/doc/BoundaryStats.R | 27 - BoundaryStats-2.3.0/BoundaryStats/inst/doc/BoundaryStats.Rmd | 43 +- BoundaryStats-2.3.0/BoundaryStats/inst/doc/BoundaryStats.html | 144 ++++----- BoundaryStats-2.3.0/BoundaryStats/man/average_min_distance.Rd |only BoundaryStats-2.3.0/BoundaryStats/man/average_min_x_to_y.Rd |only BoundaryStats-2.3.0/BoundaryStats/man/boundary_null_distrib.Rd | 10 BoundaryStats-2.3.0/BoundaryStats/man/categorical_boundary.Rd | 2 BoundaryStats-2.3.0/BoundaryStats/man/define_boundary.Rd | 23 + BoundaryStats-2.3.0/BoundaryStats/man/gauss_random_field_sim.Rd | 9 BoundaryStats-2.3.0/BoundaryStats/man/longest_boundary.Rd |only BoundaryStats-2.3.0/BoundaryStats/man/n_boundaries.Rd |only BoundaryStats-2.3.0/BoundaryStats/man/n_overlap_boundaries.Rd |only BoundaryStats-2.3.0/BoundaryStats/man/overlap_null_distrib.Rd | 8 BoundaryStats-2.3.0/BoundaryStats/man/plot_boundary.Rd | 9 BoundaryStats-2.3.0/BoundaryStats/vignettes/BoundaryStats.Rmd | 43 +- 39 files changed, 680 insertions(+), 545 deletions(-)
Title: Tissue-Adjusted Pathway Analysis of Cancer (TPAC)
Description: Contains logic for single sample gene set testing of cancer transcriptomic data with adjustment for normal tissue-specificity.
Frost, H. Robert (2023) "Tissue-adjusted pathway analysis of cancer (TPAC)" <doi:10.1101/2022.03.17.484779>.
Author: H. Robert Frost [aut, cre]
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>
Diff between TPAC versions 0.2.0 dated 2023-10-26 and 0.3.0 dated 2025-07-23
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 5 +++++ build/vignette.rds |binary inst/doc/TPAC_liver_hallmark.pdf |binary man/TPACForCancer.Rd | 4 ++-- 6 files changed, 15 insertions(+), 10 deletions(-)
Title: Collecting and Analyzing 'Tumblr' Data
Description: An implementation of calls designed to collect 'Tumblr' data via its Application Program Interfaces (API), which can be found at the following URL: <https://www.tumblr.com/docs/en/api/v2>.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between Rtumblr versions 0.1.0 dated 2023-04-05 and 0.1.1 dated 2025-07-23
DESCRIPTION | 12 MD5 | 20 NEWS.md | 4 tests/fixtures/blog_info_default.yml | 50 tests/fixtures/blog_posts_default.yml | 52 tests/fixtures/tagged_link_default.yml | 1015 +++++------ tests/fixtures/tagged_photo_default.yml | 1294 +++++++++----- tests/fixtures/tagged_text_default.yml | 2909 +++++++++++++++++++++----------- tests/fixtures/tagged_video_default.yml | 1837 ++++++++++++++------ tests/testthat/setup-Rtumblr.R | 3 tests/testthat/test-blogs.R | 9 11 files changed, 4707 insertions(+), 2498 deletions(-)
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
'lbfgsb_cpp' is a 'C++' port around by Pascal Have of 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Yann Richet [aut, cre] ,
Pascal Have [aut],
Yves Deville [aut],
Conrad Sanderson [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Mike Smith [ctb]
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between rlibkriging versions 0.9-2 dated 2025-07-22 and 0.9-2.1 dated 2025-07-23
DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++----------- cleanup | 5 +++- cleanup.win | 5 +++- src/Makevars | 4 +-- src/libK/bindings/R/rlibkriging/src/Makevars | 4 +-- src/libK/cmake/update_version.sh | 2 - src/libK/lbfgsb_cpp/include/lbfgsb_cpp/lbfgsb.hpp | 2 - src/libK/travis-ci/common/before_script.sh | 2 - src/libK/travis-ci/linux-macos/install.sh | 2 - src/libK/travis-ci/linux-macos/loadenv.sh | 2 - src/libK/travis-ci/linux-macos/test.sh | 2 - tools/setup.sh | 3 ++ 13 files changed, 37 insertions(+), 28 deletions(-)
Title: An Ensemble Modeling using Random Machines
Description: A novel ensemble method employing Support Vector Machines (SVMs) as base learners. This powerful ensemble model is designed for both classification (Ara A., et. al, 2021) <doi:10.6339/21-JDS1014>, and regression (Ara A., et. al, 2021) <doi:10.1016/j.eswa.2022.117107> problems, offering versatility and robust performance across different datasets and compared with other consolidated methods as Random Forests (Maia M, et. al, 2021) <doi:10.6339/21-JDS1025>.
Author: Mateus Maia [aut, cre] ,
Anderson Ara [cte] ,
Gabriel Ribeiro [cte]
Maintainer: Mateus Maia <mateus.maiamarques@glasgow.ac.uk>
Diff between randomMachines versions 0.1.0 dated 2023-12-14 and 0.1.1 dated 2025-07-23
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- R/main_functions.R | 4 ++-- 3 files changed, 11 insertions(+), 11 deletions(-)
More information about randomMachines at CRAN
Permanent link
Title: Two-Locus Family-Based Association Test with Polytomous Outcome
Description: Performs family-based association tests with a polytomous outcome under 2-locus and 1-locus models
defined by some design matrix.
Author: Alexandre Bureau [aut, cre],
Jordie Croteau [aut]
Maintainer: Alexandre Bureau <alexandre.bureau@msp.ulaval.ca>
Diff between fat2Lpoly versions 1.2.5 dated 2022-01-04 and 1.2.6 dated 2025-07-23
DESCRIPTION | 22 +++++++++++++++------- MD5 | 10 +++++----- data/fat2Lpoly.allSNPs.rda |binary data/ped.x.all.rda |binary man/fat2Lpoly.Rd | 6 +++--- man/fat2Lpoly.withinR.Rd | 4 ++-- 6 files changed, 25 insertions(+), 17 deletions(-)
Title: Presenting Pairwise Comparisons
Description: The tools herein calculate, print, summarize and plot pairwise differences that result from generalized linear models, general linear hypothesis tests and multinomial logistic regression models. For more information, see Armstrong (2013) <doi:10.32614/RJ-2013-021>.
Author: Dave Armstrong [aut, cre]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Diff between factorplot versions 1.2.3 dated 2024-05-23 and 1.2.4 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/factorplot.R | 32 ++++++++++++++++---------------- man/factorplot.Rd | 12 ++++++------ man/plot.factorplot.Rd | 4 ++-- man/print.factorplot.Rd | 6 +++--- man/squares.Rd | 4 ++-- man/summary.factorplot.Rd | 6 +++--- 8 files changed, 43 insertions(+), 43 deletions(-)
Title: Locate Errors with Validation Rules
Description: Errors in data can be located and removed using validation rules from package
'validate'. See also Van der Loo and De Jonge (2018) <doi:10.1002/9781118897126>,
chapter 7.
Author: Edwin de Jonge [aut, cre] ,
Mark van der Loo [aut]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between errorlocate versions 1.1.1 dated 2023-09-30 and 1.1.2 dated 2025-07-23
DESCRIPTION | 11 ++++++----- MD5 | 42 +++++++++++++++++++++--------------------- NAMESPACE | 1 + R/MipRules.R | 2 +- R/errorlocate-package.r | 2 +- R/errorlocation.R | 4 ++-- R/linear.R | 2 +- R/mip_lpsolve.R | 2 +- R/mip_rule.R | 2 ++ R/replace-errors.R | 2 +- R/soft-rule.R | 4 ++++ build/vignette.rds |binary inst/doc/errorlocate.R | 4 ++-- inst/doc/errorlocate.html | 4 ++-- inst/doc/inspect_mip.R | 26 +++++++++++++------------- inst/doc/inspect_mip.html | 2 +- man/MipRules-class.Rd | 2 +- man/errorlocate-package.Rd | 2 +- man/errorlocation.Rd | 4 ++-- man/is_linear.Rd | 2 +- man/replace_errors.Rd | 2 +- man/translate_mip_lp.Rd | 2 +- 22 files changed, 66 insertions(+), 58 deletions(-)
Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during
future runs. A port of the Ruby gem of the same name
(<https://github.com/vcr/vcr/>). Works by recording real 'HTTP'
requests/responses on disk in 'cassettes', and then replaying
matching responses on subsequent requests.
Author: Scott Chamberlain [aut, cre] ,
Aaron Wolen [aut] ,
Maelle Salmon [aut] ,
Daniel Possenriede [aut] ,
Hadley Wickham [aut],
rOpenSci [fnd]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between vcr versions 1.7.0 dated 2025-03-10 and 2.0.0 dated 2025-07-23
vcr-1.7.0/vcr/R/as-casette.R |only vcr-1.7.0/vcr/R/eject_cassette.R |only vcr-1.7.0/vcr/R/error_suggestions.R |only vcr-1.7.0/vcr/R/errors.R |only vcr-1.7.0/vcr/R/filter_headers.R |only vcr-1.7.0/vcr/R/filter_query_parameters.R |only vcr-1.7.0/vcr/R/filter_sensitive_data.R |only vcr-1.7.0/vcr/R/hooks.R |only vcr-1.7.0/vcr/R/http_interaction.R |only vcr-1.7.0/vcr/R/http_interaction_list.R |only vcr-1.7.0/vcr/R/http_interactions.R |only vcr-1.7.0/vcr/R/insert_cassette.R |only vcr-1.7.0/vcr/R/match_helpers.R |only vcr-1.7.0/vcr/R/onLoad.R |only vcr-1.7.0/vcr/R/persisters-file.R |only vcr-1.7.0/vcr/R/persisters.R |only vcr-1.7.0/vcr/R/print_cassette.R |only vcr-1.7.0/vcr/R/real_connections.R |only vcr-1.7.0/vcr/R/recording.R |only vcr-1.7.0/vcr/R/request_class.R |only vcr-1.7.0/vcr/R/request_matcher_registry.R |only vcr-1.7.0/vcr/R/request_matching.R |only vcr-1.7.0/vcr/R/response_class.R |only vcr-1.7.0/vcr/R/serialize_to_crul.R |only vcr-1.7.0/vcr/R/serialize_to_httr.R |only vcr-1.7.0/vcr/R/serialize_to_httr2.R |only vcr-1.7.0/vcr/R/serializers-json.R |only vcr-1.7.0/vcr/R/serializers-yaml.R |only vcr-1.7.0/vcr/R/serializers.R |only vcr-1.7.0/vcr/R/skip-vcr-off.R |only vcr-1.7.0/vcr/R/split_string.R |only vcr-1.7.0/vcr/R/write.R |only vcr-1.7.0/vcr/data |only vcr-1.7.0/vcr/inst/doc/cassette-manual-editing.R |only vcr-1.7.0/vcr/inst/doc/cassette-manual-editing.Rmd |only vcr-1.7.0/vcr/inst/doc/cassette-manual-editing.html |only vcr-1.7.0/vcr/inst/doc/configuration.R |only vcr-1.7.0/vcr/inst/doc/configuration.Rmd |only vcr-1.7.0/vcr/inst/doc/configuration.html |only vcr-1.7.0/vcr/inst/doc/internals.R |only vcr-1.7.0/vcr/inst/doc/internals.Rmd |only vcr-1.7.0/vcr/inst/doc/internals.html |only vcr-1.7.0/vcr/inst/doc/lightswitch.R |only vcr-1.7.0/vcr/inst/doc/lightswitch.Rmd |only vcr-1.7.0/vcr/inst/doc/lightswitch.html |only vcr-1.7.0/vcr/inst/doc/record-modes.R |only vcr-1.7.0/vcr/inst/doc/record-modes.Rmd |only vcr-1.7.0/vcr/inst/doc/record-modes.html |only vcr-1.7.0/vcr/inst/doc/request_matching.R |only vcr-1.7.0/vcr/inst/doc/request_matching.Rmd |only vcr-1.7.0/vcr/inst/doc/request_matching.html |only vcr-1.7.0/vcr/inst/doc/write-to-disk.R |only vcr-1.7.0/vcr/inst/doc/write-to-disk.Rmd |only vcr-1.7.0/vcr/inst/doc/write-to-disk.html |only vcr-1.7.0/vcr/man/FileSystem.Rd |only vcr-1.7.0/vcr/man/HTTPInteraction.Rd |only vcr-1.7.0/vcr/man/HTTPInteractionList.Rd |only vcr-1.7.0/vcr/man/Hooks.Rd |only vcr-1.7.0/vcr/man/JSON.Rd |only vcr-1.7.0/vcr/man/Persisters.Rd |only vcr-1.7.0/vcr/man/Request.Rd |only vcr-1.7.0/vcr/man/RequestHandlerCrul.Rd |only vcr-1.7.0/vcr/man/RequestHandlerHttr.Rd |only vcr-1.7.0/vcr/man/RequestHandlerHttr2.Rd |only vcr-1.7.0/vcr/man/RequestIgnorer.Rd |only vcr-1.7.0/vcr/man/RequestMatcherRegistry.Rd |only vcr-1.7.0/vcr/man/Serializer.Rd |only vcr-1.7.0/vcr/man/Serializers.Rd |only vcr-1.7.0/vcr/man/UnhandledHTTPRequestError.Rd |only vcr-1.7.0/vcr/man/VcrResponse.Rd |only vcr-1.7.0/vcr/man/YAML.Rd |only vcr-1.7.0/vcr/man/as.cassette.Rd |only vcr-1.7.0/vcr/man/crul_request.Rd |only vcr-1.7.0/vcr/man/eject_cassette.Rd |only vcr-1.7.0/vcr/man/http_interactions.Rd |only vcr-1.7.0/vcr/man/real_http_connections_allowed.Rd |only vcr-1.7.0/vcr/man/recording.Rd |only vcr-1.7.0/vcr/man/request-matching.Rd |only vcr-1.7.0/vcr/man/request_response.Rd |only vcr-1.7.0/vcr/man/rmdhunks |only vcr-1.7.0/vcr/man/skip_if_vcr_off.Rd |only vcr-1.7.0/vcr/man/str_splitter.Rd |only vcr-1.7.0/vcr/man/vcr_logging.Rd |only vcr-1.7.0/vcr/tests/test-all.R |only vcr-1.7.0/vcr/tests/testthat/cassettes/ropenaq-encoding.yaml |only vcr-1.7.0/vcr/tests/testthat/crul_resp1.rda |only vcr-1.7.0/vcr/tests/testthat/crul_resp2.rda |only vcr-1.7.0/vcr/tests/testthat/google_response.rda |only vcr-1.7.0/vcr/tests/testthat/httr2_obj.rda |only vcr-1.7.0/vcr/tests/testthat/httr_resp1.rda |only vcr-1.7.0/vcr/tests/testthat/httr_resp2.rda |only vcr-1.7.0/vcr/tests/testthat/png_eg.rda |only vcr-1.7.0/vcr/tests/testthat/test-Cassette.R |only vcr-1.7.0/vcr/tests/testthat/test-Filesystem.R |only vcr-1.7.0/vcr/tests/testthat/test-HttpInteraction.R |only vcr-1.7.0/vcr/tests/testthat/test-HttpInteractionList.R |only vcr-1.7.0/vcr/tests/testthat/test-Persisters.R |only vcr-1.7.0/vcr/tests/testthat/test-Request.R |only vcr-1.7.0/vcr/tests/testthat/test-RequestHandler.R |only vcr-1.7.0/vcr/tests/testthat/test-RequestIgnorer.R |only vcr-1.7.0/vcr/tests/testthat/test-RequestMatcherRegistry.R |only vcr-1.7.0/vcr/tests/testthat/test-ause_cassette.R |only vcr-1.7.0/vcr/tests/testthat/test-ause_cassette_match_body_empty_body.R |only vcr-1.7.0/vcr/tests/testthat/test-ause_cassette_match_query.R |only vcr-1.7.0/vcr/tests/testthat/test-ause_cassette_match_requests_on.R |only vcr-1.7.0/vcr/tests/testthat/test-ause_cassette_match_requests_on_json.R |only vcr-1.7.0/vcr/tests/testthat/test-ause_cassette_write_to_disk.R |only vcr-1.7.0/vcr/tests/testthat/test-ause_cassette_write_to_disk_binary_files.R |only vcr-1.7.0/vcr/tests/testthat/test-binary_images.R |only vcr-1.7.0/vcr/tests/testthat/test-cassette_options.R |only vcr-1.7.0/vcr/tests/testthat/test-configuration-inheritance.R |only vcr-1.7.0/vcr/tests/testthat/test-crul.R |only vcr-1.7.0/vcr/tests/testthat/test-eject_cassette.R |only vcr-1.7.0/vcr/tests/testthat/test-errors.R |only vcr-1.7.0/vcr/tests/testthat/test-filter-sensitive-strings.R |only vcr-1.7.0/vcr/tests/testthat/test-filter_headers.R |only vcr-1.7.0/vcr/tests/testthat/test-filter_query_parameters.R |only vcr-1.7.0/vcr/tests/testthat/test-httr.R |only vcr-1.7.0/vcr/tests/testthat/test-httr2.R |only vcr-1.7.0/vcr/tests/testthat/test-insert_cassette.R |only vcr-1.7.0/vcr/tests/testthat/test-issues.R |only vcr-1.7.0/vcr/tests/testthat/test-localhost_port.R |only vcr-1.7.0/vcr/tests/testthat/test-no-cassette-in-use.R |only vcr-1.7.0/vcr/tests/testthat/test-quiet.R |only vcr-1.7.0/vcr/tests/testthat/test-request_summary.R |only vcr-1.7.0/vcr/tests/testthat/test-response_summary.R |only vcr-1.7.0/vcr/tests/testthat/test-serializers.R |only vcr-1.7.0/vcr/tests/testthat/test-serializers_json.R |only vcr-1.7.0/vcr/tests/testthat/test-serializers_yaml.R |only vcr-1.7.0/vcr/tests/testthat/test-skip-vcr-off.R |only vcr-1.7.0/vcr/tests/testthat/test-use_vcr.R |only vcr-1.7.0/vcr/tests/testthat/test-vcr_last_error.R |only vcr-1.7.0/vcr/tests/testthat/test-write_disk_path_package_context.R |only vcr-1.7.0/vcr/tests/testthat/test-write_interactions.R |only vcr-1.7.0/vcr/tests/testthat/test-write_utils.R |only vcr-1.7.0/vcr/vignettes/cassette-manual-editing.Rmd |only vcr-1.7.0/vcr/vignettes/configuration.Rmd |only vcr-1.7.0/vcr/vignettes/internals.Rmd |only vcr-1.7.0/vcr/vignettes/lightswitch.Rmd |only vcr-1.7.0/vcr/vignettes/record-modes.Rmd |only vcr-1.7.0/vcr/vignettes/request_matching.Rmd |only vcr-1.7.0/vcr/vignettes/write-to-disk.Rmd |only vcr-2.0.0/vcr/DESCRIPTION | 71 vcr-2.0.0/vcr/LICENSE | 4 vcr-2.0.0/vcr/MD5 | 345 - vcr-2.0.0/vcr/NAMESPACE | 60 vcr-2.0.0/vcr/NEWS.md | 115 vcr-2.0.0/vcr/R/binary-content.R |only vcr-2.0.0/vcr/R/cassette_class.R | 824 --- vcr-2.0.0/vcr/R/cassettes.R | 219 vcr-2.0.0/vcr/R/check_cassette_names.R | 45 vcr-2.0.0/vcr/R/configuration.R | 664 -- vcr-2.0.0/vcr/R/examples.R |only vcr-2.0.0/vcr/R/import-standalone-obj-type.R |only vcr-2.0.0/vcr/R/import-standalone-types-check.R |only vcr-2.0.0/vcr/R/interaction.R |only vcr-2.0.0/vcr/R/interactions.R |only vcr-2.0.0/vcr/R/knitr.R |only vcr-2.0.0/vcr/R/lightswitch.R | 185 vcr-2.0.0/vcr/R/logger.R | 167 vcr-2.0.0/vcr/R/mocks.R |only vcr-2.0.0/vcr/R/request_handler-crul.R | 234 vcr-2.0.0/vcr/R/request_handler-httr.R | 285 - vcr-2.0.0/vcr/R/request_handler-httr2.R | 216 vcr-2.0.0/vcr/R/request_handler.R | 239 vcr-2.0.0/vcr/R/request_ignorer.R | 116 vcr-2.0.0/vcr/R/request_matcher.R |only vcr-2.0.0/vcr/R/request_response.R | 96 vcr-2.0.0/vcr/R/serialize-body.R |only vcr-2.0.0/vcr/R/serialize-headers.R |only vcr-2.0.0/vcr/R/serialize-interaction.R |only vcr-2.0.0/vcr/R/serialize-sensitive.R |only vcr-2.0.0/vcr/R/serialize-uri.R |only vcr-2.0.0/vcr/R/serializer.R | 201 vcr-2.0.0/vcr/R/use_cassette.R | 375 - vcr-2.0.0/vcr/R/utils.R |only vcr-2.0.0/vcr/R/vcr-package.R | 49 vcr-2.0.0/vcr/R/vcr_setup.R | 152 vcr-2.0.0/vcr/R/vcr_test_path.R | 16 vcr-2.0.0/vcr/R/zzz.R | 138 vcr-2.0.0/vcr/build/vignette.rds |binary vcr-2.0.0/vcr/inst/_vcr |only vcr-2.0.0/vcr/inst/doc/debugging.R | 113 vcr-2.0.0/vcr/inst/doc/debugging.Rmd | 203 vcr-2.0.0/vcr/inst/doc/debugging.html | 2098 ++------ vcr-2.0.0/vcr/inst/doc/design.Rmd | 118 vcr-2.0.0/vcr/inst/doc/design.html | 149 vcr-2.0.0/vcr/inst/doc/knitr-test.R |only vcr-2.0.0/vcr/inst/doc/knitr-test.Rmd |only vcr-2.0.0/vcr/inst/doc/knitr-test.html |only vcr-2.0.0/vcr/inst/doc/secrets.R |only vcr-2.0.0/vcr/inst/doc/secrets.Rmd |only vcr-2.0.0/vcr/inst/doc/secrets.html |only vcr-2.0.0/vcr/inst/doc/vcr.R | 131 vcr-2.0.0/vcr/inst/doc/vcr.Rmd | 237 vcr-2.0.0/vcr/inst/doc/vcr.html | 2443 ++-------- vcr-2.0.0/vcr/man/Cassette.Rd | 537 -- vcr-2.0.0/vcr/man/RequestHandler.Rd | 153 vcr-2.0.0/vcr/man/cassettes.Rd | 36 vcr-2.0.0/vcr/man/check_cassette_names.Rd | 45 vcr-2.0.0/vcr/man/figures |only vcr-2.0.0/vcr/man/insert_cassette.Rd | 186 vcr-2.0.0/vcr/man/insert_example_cassette.Rd |only vcr-2.0.0/vcr/man/is_recording.Rd |only vcr-2.0.0/vcr/man/lightswitch.Rd | 207 vcr-2.0.0/vcr/man/setup_knitr.Rd |only vcr-2.0.0/vcr/man/use_cassette.Rd | 244 vcr-2.0.0/vcr/man/use_vcr.Rd | 8 vcr-2.0.0/vcr/man/vcr-package.Rd | 27 vcr-2.0.0/vcr/man/vcr_configure.Rd | 278 - vcr-2.0.0/vcr/man/vcr_configure_log.Rd |only vcr-2.0.0/vcr/man/vcr_last_request.Rd |only vcr-2.0.0/vcr/man/vcr_test_path.Rd | 4 vcr-2.0.0/vcr/tests/testthat.R |only vcr-2.0.0/vcr/tests/testthat/_snaps |only vcr-2.0.0/vcr/tests/testthat/_vcr |only vcr-2.0.0/vcr/tests/testthat/cassettes/ropenaq-encoding.yml |only vcr-2.0.0/vcr/tests/testthat/helper-vcr.R | 142 vcr-2.0.0/vcr/tests/testthat/httr_obj.rda |binary vcr-2.0.0/vcr/tests/testthat/test-ause_cassette_re_record.R | 75 vcr-2.0.0/vcr/tests/testthat/test-ause_cassette_record_modes.R | 201 vcr-2.0.0/vcr/tests/testthat/test-binary-content.R |only vcr-2.0.0/vcr/tests/testthat/test-cassette_class.R |only vcr-2.0.0/vcr/tests/testthat/test-cassettes.R | 83 vcr-2.0.0/vcr/tests/testthat/test-check_cassette_names.R | 55 vcr-2.0.0/vcr/tests/testthat/test-configuration.R | 67 vcr-2.0.0/vcr/tests/testthat/test-interactions.R |only vcr-2.0.0/vcr/tests/testthat/test-knitr.R |only vcr-2.0.0/vcr/tests/testthat/test-lightswitch.R | 202 vcr-2.0.0/vcr/tests/testthat/test-logger.R | 82 vcr-2.0.0/vcr/tests/testthat/test-request_handler-crul.R |only vcr-2.0.0/vcr/tests/testthat/test-request_handler-httr.R |only vcr-2.0.0/vcr/tests/testthat/test-request_handler-httr2.R |only vcr-2.0.0/vcr/tests/testthat/test-request_handler.R |only vcr-2.0.0/vcr/tests/testthat/test-request_ignorer.R |only vcr-2.0.0/vcr/tests/testthat/test-request_matcher.R |only vcr-2.0.0/vcr/tests/testthat/test-request_response.R |only vcr-2.0.0/vcr/tests/testthat/test-serialize-body.R |only vcr-2.0.0/vcr/tests/testthat/test-serialize-headers.R |only vcr-2.0.0/vcr/tests/testthat/test-serialize-interaction.R |only vcr-2.0.0/vcr/tests/testthat/test-serialize-sensitive.R |only vcr-2.0.0/vcr/tests/testthat/test-serialize-uri.R |only vcr-2.0.0/vcr/tests/testthat/test-serializer.R | 291 + vcr-2.0.0/vcr/tests/testthat/test-use_cassette.R |only vcr-2.0.0/vcr/tests/testthat/test-utils.R | 100 vcr-2.0.0/vcr/tests/testthat/test-vcr_setup.R |only vcr-2.0.0/vcr/tests/testthat/test-vcr_test_path.R | 21 vcr-2.0.0/vcr/vignettes/_vcr |only vcr-2.0.0/vcr/vignettes/debugging.Rmd | 203 vcr-2.0.0/vcr/vignettes/design.Rmd | 118 vcr-2.0.0/vcr/vignettes/knitr-test.Rmd |only vcr-2.0.0/vcr/vignettes/secrets.Rmd |only vcr-2.0.0/vcr/vignettes/vcr.Rmd | 237 253 files changed, 5401 insertions(+), 8509 deletions(-)
Title: Combine and Export Data Frames
Description: Functions to combine data.frames in ways that require
additional effort in base R, and to add metadata (id, title, ...) that
can be used for printing and xlsx export. The 'Tatoo_report' class is
provided as a convenient helper to write several such tables to a
workbook, one table per worksheet. Tatoo is built on top of
'openxlsx', but intimate knowledge of that package is not required to
use tatoo.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between tatoo versions 1.1.2 dated 2023-03-26 and 1.1.3 dated 2025-07-23
DESCRIPTION | 39 ++--- MD5 | 42 +++--- NEWS.md | 5 R/Mashed_table.R | 6 R/Tagged_table.R | 2 R/as_workbook.R | 6 build/vignette.rds |binary inst/doc/named_regions.R | 18 +- inst/doc/named_regions.html | 136 +++++++++---------- inst/doc/tatoo.R | 12 - inst/doc/tatoo.html | 266 +++++++++++++++++++------------------- man/Tagged_table.Rd | 2 man/as.data.table.Mashed_table.Rd | 4 man/as_latex.Composite_table.Rd | 4 man/as_latex.Mashed_table.Rd | 4 man/as_latex.Tagged_table.Rd | 4 man/as_latex.Tatoo_report.Rd | 4 man/as_latex.data.frame.Rd | 4 man/as_workbook.Rd | 2 man/cmash.Rd | 2 man/tatoo.Rd | 2 man/write_worksheet.Rd | 4 22 files changed, 289 insertions(+), 279 deletions(-)
Title: Utility Sparse Matrix Functions for Quantitative Language
Comparison
Description: Extension of the functionality of the 'Matrix' package for using sparse matrices. Some of the functions are very general, while other are highly specific for special data format as used for quantitative language comparison.
Author: Michael Cysouw [aut, cre]
Maintainer: Michael Cysouw <cysouw@mac.com>
Diff between qlcMatrix versions 0.9.8 dated 2024-05-08 and 0.9.9 dated 2025-07-23
DESCRIPTION | 11 +- MD5 | 40 +++---- NEWS.md | 20 +++ R/assoc.R | 6 - R/base.R | 25 +++- R/sim.R | 137 ++++++++++++++++----------- R/split.R | 176 +++++++++++++++-------------------- build/vignette.rds |binary inst/doc/transformingDataSparse.R | 7 - inst/doc/transformingDataSparse.Rmd | 19 +-- inst/doc/transformingDataSparse.html | 80 +++++++++------ man/array.Rd | 10 - man/jMatrix.Rd | 5 man/pwMatrix.Rd | 7 - man/rKhatriRao.Rd | 4 man/sim.strings.Rd | 21 ++-- man/sim.wordlist.Rd | 16 +-- man/splitStrings.Rd | 47 +++------ man/splitWordlist.Rd | 48 ++++----- man/ttMatrix.Rd | 9 - vignettes/transformingDataSparse.Rmd | 19 +-- 21 files changed, 375 insertions(+), 332 deletions(-)
Title: G-Functions
Description: Modified versions of the lag() and summary() functions: glag() and gsummary(). The prefix 'g' is a reminder of who to blame if things do not work as they should.
Author: Genaro Sucarrat [aut, cre]
Maintainer: Genaro Sucarrat <gsucarrat@gmail.com>
Diff between gfunctions versions 1.0 dated 2024-04-17 and 1.1 dated 2025-07-23
DESCRIPTION | 14 ++++++++------ MD5 | 10 +++++----- NEWS | 6 ++++++ man/gfunctions-package.Rd | 10 +++++----- man/glag.Rd | 16 +++++++++------- man/gsummary.Rd | 14 +++++++------- 6 files changed, 40 insertions(+), 30 deletions(-)
Title: HTTP Client
Description: A simple HTTP client, with tools for making HTTP requests,
and mocking HTTP requests. The package is built on R6, and takes
inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>).
The package name is a play on curl, the widely used command line tool
for HTTP, and this package is built on top of the R package 'curl', an
interface to 'libcurl' (<https://curl.se/libcurl/>).
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between crul versions 1.5.0 dated 2024-07-19 and 1.6.0 dated 2025-07-23
DESCRIPTION | 17 - LICENSE | 4 MD5 | 172 +++++----- NAMESPACE | 2 NEWS.md | 44 +- R/async-queue.R | 29 + R/async.R | 478 ++++++++++++++++++++++-------- R/asyncvaried.R | 248 ++++++++++----- R/auth.R | 28 + R/body.R | 16 - R/client.R | 331 ++++++++++++++------ R/content-types.R | 2 R/crul-package.r | 36 +- R/curl-options.R | 14 R/curl_options.R | 32 +- R/headers.R | 3 R/hooks.R | 28 - R/httprequest.R | 197 +++++++++--- R/make_url.R | 15 R/mocking.R | 66 +--- R/ok.R | 88 +++-- R/onLoad.R | 5 R/paginator.R | 271 ++++++++++++----- R/progress.R | 8 R/proxies.R | 36 +- R/query.R | 7 R/response.R | 152 ++++++--- R/set.R | 36 +- R/upload.R | 4 R/verbs.R | 102 +++--- R/zzz.R | 39 +- build/vignette.rds |binary inst/doc/async.html | 5 inst/doc/best-practices-api-packages.html | 5 inst/doc/choosing-a-client.html | 14 inst/doc/crul.Rmd | 108 ++---- inst/doc/crul.html | 87 +---- inst/doc/curl-options.Rmd | 4 inst/doc/curl-options.html | 11 inst/doc/how-to-use-crul.html | 5 man/Async.Rd | 59 +++ man/AsyncVaried.Rd | 33 +- man/HttpClient.Rd | 60 +++ man/HttpRequest.Rd | 47 ++ man/crul-options.Rd | 2 man/curl-options.Rd | 2 man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/mock.Rd | 53 --- man/ok.Rd | 8 tests/testthat/helper-crul.R | 25 - tests/testthat/test-async.R | 299 +++++++++--------- tests/testthat/test-asyncqueue.R | 59 ++- tests/testthat/test-asyncvaried.R | 98 ++---- tests/testthat/test-auth.R | 22 - tests/testthat/test-client-delete.R | 25 - tests/testthat/test-client-get.R | 47 +- tests/testthat/test-client-head.R | 25 - tests/testthat/test-client-hooks.R | 81 ++--- tests/testthat/test-client-patch.R | 26 - tests/testthat/test-client-post.R | 77 ++-- tests/testthat/test-client-put.R | 25 - tests/testthat/test-client-query.R | 11 tests/testthat/test-client-status.R | 17 - tests/testthat/test-client-verb.R | 33 +- tests/testthat/test-client.R | 30 - tests/testthat/test-content-type.R | 75 ++-- tests/testthat/test-curl_verbose.R | 9 tests/testthat/test-handle.R | 7 tests/testthat/test-head_parse.R | 13 tests/testthat/test-headers.R | 64 ++-- tests/testthat/test-mocking.R | 169 ++++++---- tests/testthat/test-ok.R | 21 - tests/testthat/test-paginator.R | 201 +++++++++--- tests/testthat/test-paths.R | 9 tests/testthat/test-proxies.R | 35 +- tests/testthat/test-request.R | 30 - tests/testthat/test-response.R | 64 ++-- tests/testthat/test-retry.R | 234 ++++++++------ tests/testthat/test-set.R | 87 ++--- tests/testthat/test-url_build_parse.R | 64 ++-- tests/testthat/test-url_fetch.R | 49 +-- tests/testthat/test-user-agent.R | 33 +- tests/testthat/test-utils.R | 22 - vignettes/crul.Rmd | 108 ++---- vignettes/curl-options.Rmd | 4 vignettes/curl-options.Rmd.og | 2 89 files changed, 3158 insertions(+), 2055 deletions(-)
Title: Statistical Models of Repeated Categorical Rating Data
Description: Fit statistical models based on the Dawid-Skene model - Dawid
and Skene (1979) <doi:10.2307/2346806> - to repeated categorical
rating data. Full Bayesian inference for these models is supported
through the Stan modelling language. 'rater' also allows the user to
extract and plot key parameters of these models.
Author: Jeffrey Pullin [aut, cre, cph] ,
Damjan Vukcevic [aut] ,
Lars Moelgaard Saxhaug [ctb]
Maintainer: Jeffrey Pullin <jeffrey.pullin@gmail.com>
Diff between rater versions 1.3.1 dated 2023-09-11 and 1.3.2 dated 2025-07-23
DESCRIPTION | 15 MD5 | 20 NEWS.md | 4 R/rater_fit_class.R | 4 inst/doc/workflow.html | 8 man/as_mcmc.list.Rd | 6 src/stanExports_class_conditional_dawid_skene.h | 1267 ++++++++---------- src/stanExports_dawid_skene.h | 1235 ++++++++---------- src/stanExports_grouped_data.h | 1139 +++++++--------- src/stanExports_hierarchical_dawid_skene.h | 1645 +++++++++++------------- tests/testthat/test_plotting.R | 4 11 files changed, 2482 insertions(+), 2865 deletions(-)
Title: Multi-Layer Group-Lasso
Description: It implements a new procedure of variable selection in the context of redundancy between explanatory variables, which holds true with high dimensional data (Grimonprez et al. (2023) <doi:10.18637/jss.v106.i03>).
Author: Quentin Grimonprez [aut, cre],
Samuel Blanck [ctb],
Alain Celisse [ths],
Guillemette Marot [ths],
Yi Yang [ctb],
Hui Zou [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between MLGL versions 1.0.0 dated 2023-03-15 and 1.0.1 dated 2025-07-23
DESCRIPTION | 10 ++-- MD5 | 88 +++++++++++++++++++++--------------------- NEWS | 18 +++++--- R/HMT.R | 18 +++----- R/MLGL-package.R | 12 ++--- R/MLGL.R | 57 +++++++++++---------------- R/cv.MLGL.R | 27 ++++++------ R/fullProcess.R | 25 +++++------ R/hierarchicalFDR.R | 32 ++++++++------- R/hierarchicalFWER.R | 34 +++++++--------- R/hierarchicalTestClassical.R | 4 - R/overlap.R | 13 +++--- R/plot.R | 9 ++-- R/predict.R | 31 ++++++++------ R/print.R | 6 ++ R/simuBlockGaussian.R | 17 +++----- R/stability.R | 29 ++++++------- R/testFunction.R | 3 - R/treeFunction.R | 18 ++------ R/uniqueGroupHclust.R | 3 - R/utilities.R | 10 +--- man/HMT.Rd | 4 - man/MLGL-package.Rd | 10 ++-- man/MLGL.Rd | 19 ++++----- man/cv.MLGL.Rd | 12 ++--- man/fullProcess.Rd | 8 +-- man/hierarchicalFDR.Rd | 12 +++-- man/hierarchicalFWER.Rd | 6 +- man/listToMatrix.Rd | 4 - man/overlapgglasso.Rd | 13 +++--- man/plot.HMT.Rd | 1 man/plot.MLGL.Rd | 1 man/plot.cv.MLGL.Rd | 1 man/plot.fullProcess.Rd | 1 man/predict.MLGL.Rd | 6 +- man/predict.cv.MLGL.Rd | 2 man/print.HMT.Rd | 1 man/print.MLGL.Rd | 1 man/print.fullProcess.Rd | 1 man/selFDR.Rd | 5 +- man/simuBlockGaussian.Rd | 2 man/stability.MLGL.Rd | 15 +++---- man/summary.HMT.Rd | 1 man/summary.MLGL.Rd | 1 man/summary.fullProcess.Rd | 1 45 files changed, 298 insertions(+), 294 deletions(-)
Title: Extra Appenders for 'lgr'
Description: Additional appenders for the logging package 'lgr' that
support logging to 'Elasticsearch', 'Dynatrace', 'AWSCloudWatchLog', databases,
'syslog', email- and push notifications, and more.
Author: Stefan Fleck [aut, cre] ,
Jimmy Briggs [ctb, rev]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between lgrExtra versions 0.1.1 dated 2025-07-09 and 0.2.0 dated 2025-07-23
lgrExtra-0.1.1/lgrExtra/R/AppenderDt.R |only lgrExtra-0.1.1/lgrExtra/R/LayoutDynatrace.R |only lgrExtra-0.1.1/lgrExtra/man/AppenderDt.Rd |only lgrExtra-0.1.1/lgrExtra/man/LayoutDynatrace.Rd |only lgrExtra-0.1.1/lgrExtra/man/transform_event_dynatrace.Rd |only lgrExtra-0.1.1/lgrExtra/tests/testthat/test_AppenderDt.R |only lgrExtra-0.2.0/lgrExtra/DESCRIPTION | 12 lgrExtra-0.2.0/lgrExtra/MD5 | 58 +- lgrExtra-0.2.0/lgrExtra/NAMESPACE | 5 lgrExtra-0.2.0/lgrExtra/NEWS.md | 42 + lgrExtra-0.2.0/lgrExtra/R/AppenderDynatrace.R | 13 lgrExtra-0.2.0/lgrExtra/R/DynatraceLayout.R |only lgrExtra-0.2.0/lgrExtra/R/ElasticSearchLayout.R |only lgrExtra-0.2.0/lgrExtra/R/LayoutDbi.R | 3 lgrExtra-0.2.0/lgrExtra/R/LayoutElasticSearch.R | 1 lgrExtra-0.2.0/lgrExtra/R/utils.R | 7 lgrExtra-0.2.0/lgrExtra/README.md | 5 lgrExtra-0.2.0/lgrExtra/inst/WORDLIST | 1 lgrExtra-0.2.0/lgrExtra/man/AppenderAWSCloudWatchLog.Rd | 1 lgrExtra-0.2.0/lgrExtra/man/AppenderDbi.Rd | 1 lgrExtra-0.2.0/lgrExtra/man/AppenderDynatrace.Rd | 7 lgrExtra-0.2.0/lgrExtra/man/AppenderElasticSearch.Rd | 1 lgrExtra-0.2.0/lgrExtra/man/AppenderGmail.Rd | 1 lgrExtra-0.2.0/lgrExtra/man/AppenderPool.Rd | 1 lgrExtra-0.2.0/lgrExtra/man/AppenderPushbullet.Rd | 1 lgrExtra-0.2.0/lgrExtra/man/AppenderSendmail.Rd | 1 lgrExtra-0.2.0/lgrExtra/man/AppenderSyslog.Rd | 1 lgrExtra-0.2.0/lgrExtra/man/DynatraceLayout.Rd |only lgrExtra-0.2.0/lgrExtra/man/ElasticSearchLayout.Rd |only lgrExtra-0.2.0/lgrExtra/man/LayoutDbi.Rd | 4 lgrExtra-0.2.0/lgrExtra/man/LayoutElasticSearch.Rd | 212 +++++----- lgrExtra-0.2.0/lgrExtra/man/lgrExtra-package.Rd | 9 lgrExtra-0.2.0/lgrExtra/tests/testthat/test_AppenderDbi.R | 9 lgrExtra-0.2.0/lgrExtra/tests/testthat/test_AppenderDynatrace.R | 12 lgrExtra-0.2.0/lgrExtra/tests/testthat/test_DynatraceLayout.R |only lgrExtra-0.2.0/lgrExtra/tests/testthat/test_ElasticsearchLayout.R |only 36 files changed, 220 insertions(+), 188 deletions(-)
Title: Model Fine-Scale Age-Structured Population Data using
Open-Source Data
Description: Automate the modelling of age-structured population data
using survey data, grid population estimates and urban-rural extents.
Author: Mohamed A. Yusuf [aut, cre] ,
Victor A. Alegana [aut] ,
Chibuzor Christopher Nnanatu [aut] ,
Andrew Tatem [aut]
Maintainer: Mohamed A. Yusuf <moyusuf@who.int>
Diff between AgePopDenom versions 1.2.2 dated 2025-07-22 and 1.2.3 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/setup.R | 13 ++++++++++++- inst/doc/using_agepopdenom.html | 5 ++--- 4 files changed, 21 insertions(+), 11 deletions(-)
Title: Marker-Based Cell Type Purification for Single-Cell Sequencing
Data
Description: A common bioinformatics task in single-cell data analysis is to purify a cell type or cell population of interest from heterogeneous datasets. 'scGate' automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. Briefly, 'scGate' takes as input: i) a gene expression matrix stored in a 'Seurat' object and ii) a “gating model” (GM), consisting of a set of marker genes that define the cell population of interest. The GM can be as simple as a single marker gene, or a combination of positive and negative markers. More complex GMs can be constructed in a hierarchical fashion, akin to gating strategies employed in flow cytometry. 'scGate' evaluates the strength of signature marker expression in each cell using the rank-based method 'UCell', and then performs k-nearest neighbor (kNN) smoothing by calculating the mean 'UCell' score across neighboring cells. kNN-smoothing aims at compensating for the large degree of s [...truncated...]
Author: Massimo Andreatta [aut, cre] ,
Ariel Berenstein [aut] ,
Josep Garnica [aut],
Santiago Carmona [aut]
Maintainer: Massimo Andreatta <massimo.andreatta@unige.ch>
Diff between scGate versions 1.7.0 dated 2025-04-24 and 1.7.2 dated 2025-07-23
DESCRIPTION | 16 +++++++++------- MD5 | 14 +++++++------- NAMESPACE | 1 + R/main.R | 9 ++++++--- build/vignette.rds |binary man/get_testing_data.Rd | 2 +- man/scGate.Rd | 2 ++ man/test_my_model.Rd | 2 +- 8 files changed, 27 insertions(+), 19 deletions(-)
Title: Regression Trees with Random Effects for Longitudinal (Panel)
Data
Description: A data mining approach for longitudinal and clustered data,
which combines the structure of mixed effects model with tree-based
estimation methods. See Sela, R.J. and Simonoff, J.S. (2012) RE-EM
trees: a data mining approach for longitudinal and clustered data
<doi:10.1007/s10994-011-5258-3>.
Author: Rebecca Sela [aut],
Jeffrey Simonoff [aut],
Wenbo Jing [ctb, cre]
Maintainer: Wenbo Jing <wj2093@stern.nyu.edu>
Diff between REEMtree versions 0.90.5 dated 2023-10-24 and 0.90.6 dated 2025-07-23
DESCRIPTION | 25 - MD5 | 20 - NAMESPACE | 1 R/EMtree-functions.r | 848 +++++++++++++++++++++---------------------- man/AutoCorrelationLRtest.Rd | 90 ++-- man/REEMtree.Rd | 126 +++--- man/REEMtree.object.Rd | 74 +-- man/plot.Rd | 2 man/predict.Rd | 2 man/print.Rd | 2 man/tree.Rd | 2 11 files changed, 602 insertions(+), 590 deletions(-)
Title: Differential Item Functioning in Generalized Partial Credit
Models
Description: Provides a framework to detect Differential Item Functioning (DIF) in Generalized Partial Credit Models (GPCM) and special cases of the GPCM as proposed by Schauberger and Mair (2019) <doi:10.3758/s13428-019-01224-2>. A joint model is set up where DIF is explicitly parametrized and penalized likelihood estimation is used for parameter selection. The big advantage of the method called GPCMlasso is that several variables can be treated simultaneously and that both continuous and categorical variables can be used to detect DIF.
Author: Gunther Schauberger [aut, cre]
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between GPCMlasso versions 0.1-7 dated 2024-01-23 and 0.1-8 dated 2025-07-23
DESCRIPTION | 16 +- MD5 | 36 ++--- R/GPCMlasso-package.R | 3 R/GPCMlasso.R | 8 - R/ctrl_GPCMlasso.R | 16 +- R/design_GPCMlasso.R | 11 + R/fit_GPCMlasso.R | 27 +++- R/fit_cv_GPCMlasso.R | 12 + R/get_designX.R | 96 +++++++++++++++ R/help_fit.R | 23 ++- R/person.posterior.R | 2 R/plot.GPCMlasso.R | 288 ++++++++++++++++++++++++++++++++++++----------- R/predict.GPCMlasso.R | 10 + R/print.GPCMlasso.R | 2 man/GPCMlasso-package.Rd | 3 man/ctrl_GPCMlasso.Rd | 14 +- man/plot.GPCMlasso.Rd | 11 + man/trait.posterior.Rd | 2 src/cppGPCMlasso.cpp | 6 19 files changed, 452 insertions(+), 134 deletions(-)
Title: Geographic Networks
Description: Provides classes and methods for handling networks or
graphs whose nodes are geographical (i.e. locations in the globe).
The functionality includes the creation of objects of class geonetwork
as a graph with node coordinates, the computation of network measures,
the support of spatial operations (projection to different Coordinate
Reference Systems, handling of bounding boxes, etc.) and the plotting of
the geonetwork object combined with supplementary cartography for spatial
representation.
Author: Facundo Munoz [aut, cre]
Maintainer: Facundo Munoz <facundo.munoz@cirad.fr>
Diff between geonetwork versions 0.5.0 dated 2023-04-14 and 0.6.0 dated 2025-07-23
DESCRIPTION | 20 +++++++++++--------- MD5 | 16 +++++++++------- NEWS.md | 4 ++++ R/plot.R | 9 ++++++--- README.md | 12 ++++++------ data/eurodist.rda |binary man/figures/README-plotting-1.png |binary man/plot.geonetwork.Rd | 2 +- tests |only 9 files changed, 37 insertions(+), 26 deletions(-)
Title: A Repository of Bayesian Networks from the Academic Literature
Description: A collection of Bayesian networks (discrete, Gaussian, and conditional linear Gaussian) collated from recent academic literature. The 'bnRep_summary' object provides an overview of the Bayesian networks in the repository and the package documentation includes details about the variables in each network. A Shiny app to explore the repository can be launched with 'bnRep_app()' and is available online at <https://manueleleonelli.shinyapps.io/bnRep>. Reference: 'M. Leonelli' (2025) <doi:10.1016/j.neucom.2025.129502>.
Author: Manuele Leonelli [aut, cre, cph]
Maintainer: Manuele Leonelli <manuele.leonelli@ie.edu>
Diff between bnRep versions 0.0.4 dated 2025-05-24 and 0.0.5 dated 2025-07-23
DESCRIPTION | 8 +- MD5 | 41 +++++++----- R/realestate1.R |only R/realestate2.R |only R/realestate3.R |only R/zzz.R | 2 README.md | 4 - data/bnRep_summary.rda |binary data/realestate1.rda |only data/realestate2.rda |only data/realestate3.rda |only inst/doc/overview.R | 10 +- inst/doc/overview.html | 24 +++---- inst/shiny/rsconnect/shinyapps.io/manueleleonelli/bnRep.dcf | 2 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/realestate1.Rd |only man/realestate2.Rd |only man/realestate3.Rd |only 26 files changed, 51 insertions(+), 40 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-26 0.1.3
2020-05-26 0.1.2
2020-05-21 0.1.1
2019-10-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-12 0.99.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-07 0.99.4
Title: Uncertainty in Partial Credit Models
Description: Provides an extension to the Partial Credit Model and Generalized Partial Credit Models which allows for an additional person parameter that characterizes the uncertainty of the person. The method was originally proposed by Tutz and Schauberger (2020) <doi:10.1177/0146621620920932>.
Author: Gunther Schauberger [aut, cre]
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between UPCM versions 0.0-3 dated 2021-04-27 and 0.0-4 dated 2025-07-23
DESCRIPTION | 18 +++++++++++------- MD5 | 10 +++++----- R/UPCM-package.R | 3 +-- R/UPCM.R | 6 +++--- man/UPCM-package.Rd | 3 +++ src/RcppExports.cpp | 5 +++++ 6 files changed, 28 insertions(+), 17 deletions(-)
Title: Spatial Position Models
Description: Computes spatial position models: the potential model as defined
by Stewart (1941) <doi:10.1126/science.93.2404.89> and catchment areas as
defined by Reilly (1931) or Huff (1964) <doi:10.2307/1249154>.
Author: Timothee Giraud [cre, aut] ,
Hadrien Commenges [aut],
Joel Boulier [ctb]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between SpatialPosition versions 2.1.2 dated 2023-09-14 and 2.1.3 dated 2025-07-23
DESCRIPTION | 11 MD5 | 22 - NEWS | 7 R/reilly.R | 2 README.md | 18 - build/vignette.rds |binary inst/doc/SpatialPosition.Rmd | 2 inst/doc/SpatialPosition.html | 269 +++++++++++------------- inst/doc/StewartExample.html | 467 +++++++++++++++++++++--------------------- man/SpatialPosition.Rd | 2 man/rasterReilly.Rd | 2 vignettes/SpatialPosition.Rmd | 2 12 files changed, 395 insertions(+), 409 deletions(-)
More information about SpatialPosition at CRAN
Permanent link
Title: 'CARTOColors' Palettes
Description: Provides color schemes for maps and other graphics
designed by 'CARTO' as described at <https://carto.com/carto-colors/>.
It includes four types of palettes: aggregation, diverging, qualitative,
and quantitative.
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between rcartocolor versions 2.1.1 dated 2023-05-13 and 2.1.2 dated 2025-07-23
DESCRIPTION | 14 ++++++++------ MD5 | 19 ++++++++++--------- R/carto_scale.R | 4 ++-- README.md | 13 +++++-------- man/carto_scale.Rd | 4 ++-- man/figures/README-example-1.png |binary man/figures/README-example3-1.png |binary man/figures/README-example4-1.png |binary man/figures/README-examplegg1-1.png |binary man/figures/README-examplegg2-1.png |binary man/figures/logo.png |only 11 files changed, 27 insertions(+), 27 deletions(-)
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 1.3.1 dated 2025-06-03 and 1.3.2 dated 2025-07-23
DESCRIPTION | 6 MD5 | 22 +-- NEWS.md | 11 + R/overview.R | 2 R/sset.R | 2 src/cheapr.h | 14 ++ src/combine.cpp | 77 +++-------- src/lag.cpp | 16 +- src/nas.cpp | 16 +- src/set_math.cpp | 2 src/sset.cpp | 357 ++++++++++++++++++++++++------------------------------- src/utils.cpp | 14 -- 12 files changed, 240 insertions(+), 299 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-04 0.9.2
2023-06-01 0.8.0
2023-05-25 0.7.4
2023-02-15 0.7.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-10 0.1.6
2023-10-19 0.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-10 0.8.2
2023-02-03 0.8.1
2022-09-20 0.8.0
2022-08-16 0.7.2
2017-11-30 0.4.3
2017-07-10 0.3.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-20 1.1.0
2023-04-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-06 1.0.2
2023-09-20 1.0.1
2023-07-18 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-10 0.1.9
2023-10-20 0.1.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-26 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-31 3.1.2
2023-02-28 3.1.1
2023-02-22 3.1.0
2020-06-22 3.0.0
2020-02-24 2.1.2
2019-09-07 2.1.0
2019-06-19 2.0.0
2019-02-12 1.6.1
2018-08-15 1.5.1
2018-06-21 1.5.0
2018-05-06 1.4.0
2018-03-30 1.3.0
2018-01-23 1.2.0
2017-11-21 1.1.1
2017-11-09 1.1.0
2017-09-21 1.0.2
2017-09-19 1.0.1
2017-09-16 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-24 0.1.1
2023-09-12 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-27 3.1.1
2022-05-13 3.1
2022-03-22 3.0
2021-05-03 2.0
Title: Multi-Trait and Multi-Trial Genome Wide Association Studies
Description: Fast multi-trait and multi-trail Genome Wide Association Studies
(GWAS) following the method described in Zhou and Stephens. (2014),
<doi:10.1038/nmeth.2848>. One of a series of statistical genetic packages
for streamlining the analysis of typical plant breeding experiments
developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre] ,
Willem Kruijer [aut] ,
Fred van Eeuwijk [ctb] ,
Martin P Boer [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie J Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Ron Wehrens [ctb] ,
Choazhi Zheng [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenQTLxT versions 1.0.2 dated 2024-01-23 and 1.0.3 dated 2025-07-23
DESCRIPTION | 37 ++++++++-------- MD5 | 28 ++++++------ NEWS.md | 6 ++ R/GWASHelp.R | 2 R/RcppExports.R | 8 +-- R/covUnstr.R | 2 R/runMultiTraitGwas.R | 22 ++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/statgenQTLxT.R | 76 ++++++++++++++++----------------- inst/doc/statgenQTLxT.html | 102 ++++++++++++++++++++++++++------------------- man/exclMarkers.Rd | 54 +++++++++++------------ man/runMultiTraitGwas.Rd | 22 ++++----- src/EMFA.cpp | 4 - src/estEffsCPP.cpp | 4 - 15 files changed, 194 insertions(+), 173 deletions(-)
Title: Root Mean Square Curvature Calculation
Description: Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.
Author: Peijian Shi [aut, cre],
Peter M. Ridland [aut],
David A. Ratkowsky [aut],
Yang Li [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>
Diff between IPEC versions 1.1.0 dated 2024-01-13 and 1.1.1 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- build/partial.rdb |binary man/aic.Rd | 2 +- man/bic.Rd | 2 +- man/bootIPEC.Rd | 4 ++-- man/confcurves.Rd | 4 ++-- man/curvIPEC.Rd | 10 +++++----- man/fitIPEC.Rd | 10 +++++----- man/skewIPEC.Rd | 2 +- 10 files changed, 30 insertions(+), 30 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.6.0 dated 2025-07-22 and 1.6.1 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- configure.ac | 2 +- src/include/GPBoost/cov_fcts.h | 5 +++++ src/include/GPBoost/likelihoods.h | 27 ++++++++++++++++++++++++--- 5 files changed, 38 insertions(+), 12 deletions(-)
Title: Fit GLD Regression/Quantile/AFT Model to Data
Description: Owing to the rich shapes of Generalised Lambda Distributions (GLDs), GLD standard/quantile/Accelerated Failure Time (AFT) regression is a competitive flexible model compared to standard/quantile/AFT regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. For AFT model, it also eliminates the needs to try several different AFT models, owing to the flexible shapes of GLD. The goodness of fit of the proposed model can be assessed via QQ plots and Kolmogorov-Smirnov tests and data driven smooth test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly fro [...truncated...]
Author: Steve Su [aut, cre, cph] ,
R Core Team [aut]
Maintainer: Steve Su <allegro.su@gmail.com>
Diff between GLDreg versions 1.1.1 dated 2024-01-22 and 1.1.2 dated 2025-07-23
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ man/GLD.lm.Rd | 12 ++++++------ man/GLD.lm.full.Rd | 12 ++++++------ man/GLD.lm.full.surv.Rd | 8 ++++---- man/GLD.lm.surv.Rd | 8 ++++---- man/qqgld.default.Rd | 2 +- 7 files changed, 33 insertions(+), 32 deletions(-)
Title: Fitting Single and Mixture of Generalised Lambda Distributions
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution. References include the following: Karvanen and Nuutinen (2008) "Characterizing the generalized lambda distribution by L-moments" <doi:10.1016/j.csda.2007.06.021>, King and MacGillivray (1999) "A starship method for fitting the generalised lambda distributions" <doi:10.1111/1467-842X.00089>, Su (2005) "A Discretized Approach to Flexibly Fit Generalized Lambda Distribut [...truncated...]
Author: Steve Su [aut, cre, cph] ,
Martin Maechler [aut],
Juha Karvanen [aut],
Robert King [aut],
Benjamin Dean [ctb],
R Core Team [aut]
Maintainer: Steve Su <allegro.su@gmail.com>
Diff between GLDEX versions 2.0.0.9.3 dated 2023-08-21 and 2.0.0.9.4 dated 2025-07-23
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- man/fun.class.regime.bi.Rd | 6 +++--- 3 files changed, 11 insertions(+), 10 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package helps
to design cartographic representations such as proportional symbols,
choropleth, typology, flows or discontinuities maps. It also offers several
features that improve the graphic presentation of maps, for instance, map
palettes, layout elements (scale, north arrow, title...), labels or legends.
See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.
Author: Timothee Giraud [cre, aut] ,
Nicolas Lambert [aut],
Diego Hernangomez [ctb] ,
Ian Fellows [cph]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between cartography versions 3.1.4 dated 2023-09-14 and 3.1.5 dated 2025-07-23
DESCRIPTION | 14 MD5 | 42 +- NEWS.md | 7 R/Package.R | 2 R/data.R | 18 R/dotDensityLayer.R | 2 R/getBreaks.R | 4 README.md | 76 ---- build/vignette.rds |binary inst/doc/cartography.html | 832 ++++++++++++++++++++++------------------------ inst/doc/cheatsheet.html | 18 man/cartography.Rd | 4 man/coasts.spdf.Rd | 2 man/countries.spdf.Rd | 2 man/dotDensityLayer.Rd | 2 man/frame.spdf.Rd | 2 man/graticule.spdf.Rd | 2 man/nuts0.spdf.Rd | 2 man/nuts1.spdf.Rd | 2 man/nuts2.spdf.Rd | 2 man/nuts3.spdf.Rd | 2 man/world.spdf.Rd | 2 22 files changed, 489 insertions(+), 550 deletions(-)
Title: Toolkit for Investigation and Visualization of Young Anchovies
Description: Specialized toolkit for processing biological and fisheries data from Peru's anchovy (Engraulis ringens) fishery. Provides functions to analyze fishing logbooks, calculate biological indicators (length-weight relationships, juvenile percentages), generate spatial fishing indicators, and visualize regulatory measures from Peru's Ministry of Production. Features automated data processing from multiple file formats, coordinate validation, spatial analysis of fishing zones, and tools for analyzing fishing closure announcements and regulatory compliance. Includes built-in datasets of Peruvian coastal coordinates and parallel lines for analyzing fishing activities within regulatory zones.
Author: Hans Ttito [aut, cre]
Maintainer: Hans Ttito <kvttitos@gmail.com>
Diff between Tivy versions 0.1.0 dated 2025-07-22 and 0.1.1 dated 2025-07-23
DESCRIPTION | 8 - MD5 | 24 ++--- NEWS.md | 13 ++- R/02-merge-data.R | 16 +-- R/05-spatial.R | 7 - R/09-helpers-announcement.R | 152 ++++++++++++++++++------------------ README.md | 10 +- inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 6 - man/Tivy-package.Rd | 2 man/validate_polygon_data.Rd | 4 tests/testthat/test-announcements.R | 99 +++++++++++------------ vignettes/introduction.Rmd | 2 13 files changed, 179 insertions(+), 166 deletions(-)
Title: 'systemPipeShiny' UI and Server Components
Description: The systemPipeShiny (SPS) framework comes with many UI and server components. However, installing the whole framework is heavy and takes some time. If you would like to use UI and server components from SPS in your own Shiny apps, do not hesitate to try this package.
Author: Le Zhang [aut, cre]
Maintainer: Le Zhang <lezhang100@gmail.com>
Diff between spsComps versions 0.3.3.0 dated 2023-07-12 and 0.3.4.0 dated 2025-07-23
DESCRIPTION | 9 ++++----- MD5 | 12 ++++++------ NEWS.md | 10 ++++++++++ R/spsServerCollections.R | 2 +- R/spsUIcollections.R | 12 +++++++++--- man/gallery.Rd | 8 +++++++- man/onNextInput.Rd | 2 +- 7 files changed, 38 insertions(+), 17 deletions(-)
Title: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS
Tool
Description: A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can
(1) effectively process large data,
(2) rapidly evaluate population structure,
(3) efficiently estimate variance components several algorithms,
(4) implement parallel-accelerated association tests of markers three methods,
(5) globally efficient design on GWAS process computing,
(6) enhance visualization of related information.
'rMVP' contains three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jianming Yu (2006) <DOI:10.1038/ng1702>)
and FarmCPU (Xiaolei Liu (2016) <doi:10.1371/journal.pgen.1005767>); variance components estimation methods EMMAX
(Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>,
R implementation from 'GAPIT2': You Tang and Xiaolei Liu (2016) <DOI:10.1371/journal.pone.0107684> and
'SUPER': Qishan Wang and Feng Tian (2014) <DOI:10.1371/ [...truncated...]
Author: Lilin Yin [aut],
Haohao Zhang [aut],
Zhenshuang Tang [aut],
Jingya Xu [aut],
Dong Yin [aut],
Zhiwu Zhang [aut],
Xiaohui Yuan [aut],
Mengjin Zhu [aut],
Shuhong Zhao [aut],
Xinyun Li [aut],
Qishan Wang [ctb],
Feng Tian [ctb],
Hyunmin Kang [ctb],
Xiang [...truncated...]
Maintainer: Xiaolei Liu <xll198708@gmail.com>
Diff between rMVP versions 1.4.0 dated 2025-01-22 and 1.4.5 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/MVP.Data.r | 2 +- R/MVP.GLM.r | 6 +++++- R/MVP.r | 8 ++++---- src/assoc.cpp | 31 ++++++++++++++++++------------- src/data_converter.cpp | 22 +++++++++++----------- src/kinship.cpp | 1 - 8 files changed, 50 insertions(+), 42 deletions(-)
Title: Balanced Sample Size and Power Calculation Tools
Description: Implements sample size and power calculation methods with a focus on balance and fairness in study design, inspired by the Zoroastrian deity Rashnu, the judge who weighs truth. Supports survival analysis and various hypothesis testing frameworks.
Author: Sungho Choi [aut],
Gyeom Hwangbo [ctb, cre],
Zarathu [cph, fnd]
Maintainer: Gyeom Hwangbo <hbgyeom@gmail.com>
Diff between rashnu versions 0.1.1 dated 2025-06-18 and 0.1.2 dated 2025-07-23
DESCRIPTION | 14 +++++---- MD5 | 70 +++++++++++++++++++++++++++++++++++++++++++++--- NAMESPACE | 12 ++++++++ NEWS.md | 18 ++++++++++++ R/addin2.R |only R/coxph_size.R |only R/k_mean_size.R |only R/k_prop_size.R |only R/one_bino_size.R |only R/one_mean_size.R |only R/one_norm_size.R |only R/one_prop_size.R |only R/or_size.R |only R/pair_prop_size.R |only R/sccs_size.R |only R/two_mean_size.R |only R/two_prop_size.R |only inst/rstudio/addins.dcf | 5 +++ inst/shiny |only man/coxph_size.Rd |only man/k_mean_size.Rd |only man/k_prop_size.Rd |only man/one_bino_size.Rd |only man/one_mean_size.Rd |only man/one_norm_size.Rd |only man/one_prop_size.Rd |only man/or_size.Rd |only man/pair_prop_size.Rd |only man/sccs_size.Rd |only man/two_mean_size.Rd |only man/two_prop_size.Rd |only 31 files changed, 109 insertions(+), 10 deletions(-)
Title: Translate Text
Description: Provide easy methods to translate pieces of text.
Functions send requests to translation services online.
Author: Tomer Iwan [aut, cre, cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between polyglotr versions 1.6.1 dated 2025-07-09 and 1.7.0 dated 2025-07-23
DESCRIPTION | 9 MD5 | 35 ++ NAMESPACE | 3 NEWS.md | 3 R/apertium_get_language_pairs.R |only R/launch_polyglotr_app.R |only R/translate_apertium.R |only README.md | 177 ++++++++++----- build/vignette.rds |binary inst/doc/apertium-intro.R |only inst/doc/apertium-intro.Rmd |only inst/doc/apertium-intro.html |only inst/doc/language-detection-conditional-translation.R |only inst/doc/language-detection-conditional-translation.Rmd |only inst/doc/language-detection-conditional-translation.html |only inst/doc/translation-table-workflow.R |only inst/doc/translation-table-workflow.Rmd |only inst/doc/translation-table-workflow.html |only inst/examples |only inst/shiny-app |only man/apertium_get_language_pairs.Rd |only man/apertium_translate.Rd |only man/launch_polyglotr_app.Rd |only tests/testthat/test-translate_apertium.R |only vignettes/apertium-intro.Rmd |only vignettes/language-detection-conditional-translation.Rmd |only vignettes/translation-table-workflow.Rmd |only 27 files changed, 164 insertions(+), 63 deletions(-)
Title: Solve Generalized Estimating Equations for Clustered Data
Description: Estimation of generalized linear models with
correlated/clustered observations by use of generalized estimating
equations (GEE). See e.g. Halekoh and Højsgaard, (2005,
<doi:10.18637/jss.v015.i02>), for details. Several types of
clustering are supported, including exchangeable variance
structures, AR1 structures, M-dependent, user-specified variance
structures and more. The model fitting computations are performed
using modified code from the 'geeM' package, while the interface
and output objects have been written to resemble the 'geepack'
package. The package also contains additional tools for working
with and inspecting results from the 'geepack' package, e.g. a
'confint' method for 'geeglm' objects from 'geepack'.
Author: Anne Helby Petersen [aut],
Lee McDaniel [aut] ,
Claus Ekstroem [ctb] ,
Soeren Hoejsgaard [aut, cre]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between geeasy versions 0.1.2 dated 2024-04-29 and 0.1.3 dated 2025-07-23
DESCRIPTION | 9 ++++----- MD5 | 6 +++--- R/geelm.R | 45 +++++++++++++++++++++++++-------------------- man/geelm.Rd | 45 +++++++++++++++++++++++++-------------------- 4 files changed, 57 insertions(+), 48 deletions(-)
Title: A Fully Featured Logging Framework
Description: A flexible, feature-rich yet light-weight logging
framework based on 'R6' classes. It supports hierarchical loggers,
custom log levels, arbitrary data fields in log events, logging to
plaintext, 'JSON', (rotating) files, memory buffers. For extra
appenders that support logging to databases, email and push
notifications see the the package lgr.app.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between lgr versions 0.4.4 dated 2022-09-05 and 0.5.0 dated 2025-07-23
DESCRIPTION | 25 MD5 | 98 +-- NAMESPACE | 1 NEWS.md | 210 +++--- R/Appender.R | 38 + R/Filterable.R | 4 R/Layout.R | 170 +---- R/LayoutJson.R |only R/LogEvent.R | 34 - R/Logger.R | 190 ++++-- R/basic_config.R | 24 R/log_levels.R | 2 R/string_repr.R | 2 R/utils-sfmisc.R | 32 - R/utils.R | 2 README.md | 176 ++--- build/vignette.rds |binary inst/WORDLIST | 8 inst/doc/lgr.R | 108 +-- inst/doc/lgr.Rmd | 2 inst/doc/lgr.html | 871 ++++++++++++++--------------- man/Appender.Rd | 4 man/AppenderBuffer.Rd | 8 man/AppenderConsole.Rd | 39 + man/AppenderFile.Rd | 12 man/AppenderFileRotating.Rd | 6 man/AppenderFileRotatingDate.Rd | 8 man/AppenderFileRotatingTime.Rd | 8 man/AppenderMemory.Rd | 2 man/AppenderTable.Rd | 10 man/Filterable.Rd | 4 man/Layout.Rd | 17 man/LayoutFormat.Rd | 15 man/LayoutGlue.Rd | 11 man/LayoutJson.Rd | 155 ++++- man/LogEvent.Rd | 4 man/Logger.Rd | 27 man/LoggerGlue.Rd | 47 + man/basic_config.Rd | 3 man/print.LogEvent.Rd | 6 man/string_repr.Rd | 3 tests/testthat/test_Appender.R | 61 +- tests/testthat/test_AppenderFileRotating.R | 49 - tests/testthat/test_Layout.R | 66 -- tests/testthat/test_LayoutJson.R |only tests/testthat/test_Logger.R | 114 +++ tests/testthat/test_logger_config.R | 3 tests/testthat/test_parallel.R | 2 tests/testthat/test_print_Appender.R | 4 tests/testthat/test_print_LogEvent.R | 25 vignettes/lgr.Rmd | 2 51 files changed, 1558 insertions(+), 1154 deletions(-)
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.3-6 dated 2025-05-22 and 3.4-0 dated 2025-07-23
spatstat.model-3.3-6/spatstat.model/R/auc.R |only spatstat.model-3.3-6/spatstat.model/man/auc.Rd |only spatstat.model-3.3-6/spatstat.model/man/roc.Rd |only spatstat.model-3.4-0/spatstat.model/DESCRIPTION | 20 - spatstat.model-3.4-0/spatstat.model/MD5 | 41 ++- spatstat.model-3.4-0/spatstat.model/NAMESPACE | 6 spatstat.model-3.4-0/spatstat.model/NEWS | 40 +++ spatstat.model-3.4-0/spatstat.model/R/aucmodel.R |only spatstat.model-3.4-0/spatstat.model/R/evidence.R | 16 + spatstat.model-3.4-0/spatstat.model/R/mpl.R | 39 ++- spatstat.model-3.4-0/spatstat.model/R/mppm.R | 12 - spatstat.model-3.4-0/spatstat.model/R/rocdropadd.R |only spatstat.model-3.4-0/spatstat.model/R/rocmodel.R |only spatstat.model-3.4-0/spatstat.model/R/sysdata.rda |binary spatstat.model-3.4-0/spatstat.model/R/zgibbsmodel.R | 38 ++- spatstat.model-3.4-0/spatstat.model/build |only spatstat.model-3.4-0/spatstat.model/inst/doc/packagesizes.txt | 1 spatstat.model-3.4-0/spatstat.model/inst/info/packagesizes.txt | 1 spatstat.model-3.4-0/spatstat.model/man/addROC.Rd |only spatstat.model-3.4-0/spatstat.model/man/addapply.Rd |only spatstat.model-3.4-0/spatstat.model/man/auc.ppm.Rd |only spatstat.model-3.4-0/spatstat.model/man/dropROC.Rd |only spatstat.model-3.4-0/spatstat.model/man/dropply.Rd |only spatstat.model-3.4-0/spatstat.model/man/macros/defns.Rd | 25 +- spatstat.model-3.4-0/spatstat.model/man/predict.ppm.Rd | 107 ++++++++-- spatstat.model-3.4-0/spatstat.model/man/roc.ppm.Rd |only spatstat.model-3.4-0/spatstat.model/man/spatstat.model-internal.Rd | 8 spatstat.model-3.4-0/spatstat.model/tests/testsUtoZ.R | 20 + 28 files changed, 282 insertions(+), 92 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.10.5 dated 2024-10-02 and 0.10.6 dated 2025-07-23
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/Drift.R | 2 +- R/ExitP.R | 2 +- R/ORmn.R | 31 +++++++++++++++---------------- R/RDmn.R | 6 +++--- R/RDmn1.R | 4 ++-- R/RRmn.R | 23 +++++++++++++---------- R/seqBound.R | 2 +- inst/NEWS.Rd | 5 +++++ man/ORmn.Rd | 2 ++ man/RDmn.Rd | 2 ++ man/RRmn.Rd | 2 ++ man/vtest.Rd | 2 +- tests/Test.R | 2 ++ 15 files changed, 67 insertions(+), 52 deletions(-)
Title: Case Influence in Structural Equation Models
Description: A set of tools for evaluating several measures of case influence for structural equation models.
Author: Massimiliano Pastore [aut, cre],
Gianmarco Altoe' [ctb]
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between influence.SEM versions 2.3 dated 2022-05-11 and 2.4 dated 2025-07-23
DESCRIPTION | 18 +++++++++++++----- MD5 | 14 +++++++------- NEWS | 6 ++++++ man/Deltachi.Rd | 6 ++++-- man/Likedist.Rd | 6 ++++-- man/fitinfluence.Rd | 6 ++++-- man/genCookDist.Rd | 6 ++++-- man/parinfluence.Rd | 6 ++++-- 8 files changed, 46 insertions(+), 22 deletions(-)
Title: Creation and Evaluation of Acceptance Sampling Plans
Description: Provides functionality for creating and
evaluating acceptance sampling plans. Sampling plans can be single,
double or multiple.
Author: Andreas Kiermeier [aut, cre],
Peter Bloomfield [ctb]
Maintainer: Andreas Kiermeier <Andreas.Kiermeier@gmail.com>
Diff between AcceptanceSampling versions 1.0-10 dated 2023-12-06 and 1.0.11 dated 2025-07-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 9 ++++++++- R/code_twoclass.R | 20 +++++++------------- build/vignette.rds |binary inst/doc/acceptance_sampling_manual.pdf |binary 6 files changed, 24 insertions(+), 23 deletions(-)
More information about AcceptanceSampling at CRAN
Permanent link