Title: Helper Functions for Structural Equation Modeling
Description: An assortment of helper functions for doing structural equation
modeling, mainly by 'lavaan' for now. Most of them are time-saving functions
for common tasks in doing structural equation modeling and reading the
output. This package is not for functions that implement advanced statistical
procedures. It is a light-weight package for simple functions that do simple
tasks conveniently, with as few dependencies as possible.
Author: Shu Fai Cheung [aut, cre]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semhelpinghands versions 0.1.14 dated 2026-02-10 and 0.1.15 dated 2026-07-08
DESCRIPTION | 8 ++-- MD5 | 28 ++++++++--------- NEWS.md | 10 ++++++ R/ptable_to_syntax.R | 7 ++++ README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/semhelpinghands.html | 2 - man/plot_models_fm.Rd | 2 - man/ptable_to_syntax.Rd | 18 ++++++---- man/semhelpinghands-package.Rd | 5 +++ man/standardizedSolution_boot_ci.Rd | 2 - man/vector_from_lavaan.Rd | 2 - tests/testthat/test-ptable_to_syntax_incomplete.R | 4 ++ tests/testthat/test-standardizedSolution_boot_ci_cfa.R | 6 +-- 15 files changed, 62 insertions(+), 34 deletions(-)
More information about semhelpinghands at CRAN
Permanent link
Title: Fast and Efficient Processing of PAM Data
Description: Processing Chlorophyll Fluorescence & P700 Absorbance data. Four models are provided for the regression of Pi curves, which can be compared with each other in order to select the most suitable model for the data set. Control plots ensure the successful verification of each regression. Bundled output of alpha, ETRmax, Ik etc. enables fast and reliable further processing of the data.
Author: Julien Boehm [cre, aut] ,
Philipp Schrag [aut]
Maintainer: Julien Boehm <julien.boehm@uni-rostock.de>
Diff between pam versions 2.2.1 dated 2026-04-30 and 2.3.0 dated 2026-07-08
DESCRIPTION | 9 - MD5 | 124 ++++++++++++----------- NAMESPACE | 1 R/constants.R | 6 - R/device_diving_pam.R |only R/device_dual_pam.R | 2 R/device_dual_pam_single_channel_fluo.R | 2 R/device_dual_pam_single_channel_p700.R | 2 R/device_junior_pam.R | 2 R/device_pam_2500.R | 2 R/device_universal_data.R | 2 R/model_eilers_peeters.R | 1 R/model_platt.R | 1 R/model_vollenweider.R | 1 R/model_walsby.R | 1 R/plot.R | 59 ++-------- R/util.R | 55 ++++++++++ R/validation.R | 6 + build/partial.rdb |binary inst/extdata/diving_pam_II_data |only man/eilers_peeters_default_start_value_a.Rd | 5 man/eilers_peeters_default_start_value_b.Rd | 5 man/eilers_peeters_default_start_value_c.Rd | 5 man/eilers_peeters_generate_regression_ETR_I.Rd | 112 ++++++++++---------- man/eilers_peeters_generate_regression_ETR_II.Rd | 112 ++++++++++---------- man/eilers_peeters_modified.Rd | 1 man/platt_default_start_value_alpha.Rd | 5 man/platt_default_start_value_beta.Rd | 5 man/platt_default_start_value_ps.Rd | 5 man/platt_generate_regression_ETR_I.Rd | 118 ++++++++++----------- man/platt_generate_regression_ETR_II.Rd | 118 ++++++++++----------- man/platt_modified.Rd | 1 man/read_diving_pam_II_data.Rd |only man/read_dual_pam_data.Rd | 2 man/read_dual_pam_single_channel_fluo_data.Rd | 2 man/read_dual_pam_single_channel_p700_data.Rd | 2 man/read_junior_pam_data.Rd | 2 man/read_pam_2500_data.Rd | 2 man/read_universal_data.Rd | 2 man/vollenweider_default_start_value_a.Rd | 5 man/vollenweider_default_start_value_alpha.Rd | 5 man/vollenweider_default_start_value_n.Rd | 5 man/vollenweider_default_start_value_pmax.Rd | 5 man/vollenweider_generate_regression_ETR_I.Rd | 124 +++++++++++------------ man/vollenweider_generate_regression_ETR_II.Rd | 122 +++++++++++----------- man/vollenweider_modified.Rd | 1 man/walsby_default_start_value_alpha.Rd | 5 man/walsby_default_start_value_beta.Rd | 5 man/walsby_default_start_value_etr_max.Rd | 5 man/walsby_generate_regression_ETR_I.Rd | 116 ++++++++++----------- man/walsby_generate_regression_ETR_II.Rd | 116 ++++++++++----------- man/walsby_modified.Rd | 1 tests/testthat/data/diving_pam_II_data |only tests/testthat/test-combo_plot_control_etr_II.R | 26 ++++ tests/testthat/test-did_etr_saturate.R |only tests/testthat/test-eilers_peeters_etr_I.R | 1 tests/testthat/test-eilers_peeters_etr_II.R | 1 tests/testthat/test-platt_etr_I.R | 1 tests/testthat/test-platt_etr_II.R | 1 tests/testthat/test-read_diving_pam_data.R |only tests/testthat/test-universal_data_etr_I.R | 4 tests/testthat/test-vollenweider_etr_I.R | 1 tests/testthat/test-vollenweider_etr_II.R | 1 tests/testthat/test-walsby_etr_I.R | 1 tests/testthat/test-walsby_etr_II.R | 1 tests/testthat/test-write_model_result_csv.R | 39 ++++++- 66 files changed, 704 insertions(+), 668 deletions(-)
Title: One Sample Mendelian Randomization and Instrumental Variable
Analyses
Description: Useful functions for one-sample (individual level data)
Mendelian randomization and instrumental variable analyses. The
package includes implementations of; the Sanderson and Windmeijer
(2016) <doi:10.1016/j.jeconom.2015.06.004> conditional F-statistic,
the multiplicative structural mean model Hernán and Robins (2006)
<doi:10.1097/01.ede.0000222409.00878.37>, and two-stage predictor
substitution and two-stage residual inclusion estimators explained by
Terza et al. (2008) <doi:10.1016/j.jhealeco.2007.09.009>.
Author: Tom Palmer [aut, cre] ,
Wes Spiller [aut] ,
Eleanor Sanderson [aut] ,
Nicolai Vitt [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between OneSampleMR versions 0.1.7 dated 2026-03-09 and 0.1.8 dated 2026-07-08
DESCRIPTION | 9 MD5 | 44 +- NEWS.md | 18 R/asmm.R | 2 R/fsw.R | 706 ++++++++++++----------------------- R/msmm.R | 61 +-- R/onesamplemr-package.R | 1 R/tsps.R | 348 ++++------------- R/tsri.R | 400 ++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/f-statistic-comparison.html | 55 +- man/OneSampleMR-package.Rd | 2 man/asmm.Rd | 2 man/msmm.Rd | 4 man/summary.msmm.Rd | 2 man/summary.tsps.Rd | 2 man/summary.tsri.Rd | 4 man/tsri.Rd | 2 tests/testthat/test-fsw.R | 68 +++ tests/testthat/test-msmm.R | 91 ++++ tests/testthat/test-tsps.R | 77 +++ tests/testthat/test-tsri.R | 81 ++++ 23 files changed, 848 insertions(+), 1131 deletions(-)
Title: Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Description: Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A) that can be applied either on a lumped or semi-distributed way. A snow accumulation and melt model (CemaNeige) and the associated functions for the calibration and evaluation of models are also included. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] ,
Olivier Delaigue [aut, cre] ,
Guillaume Thirel [aut, ths] ,
David Dorchies [aut] ,
Charles Perrin [aut, ths] ,
Claude Michel [aut, ths],
Vazken Andreassian [ctb, ths] ,
Francois Bourgin [ctb] ,
Pierre Brigode [ctb] ,
Nicola [...truncated...]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGR versions 1.7.8 dated 2025-12-12 and 1.7.9 dated 2026-07-08
DESCRIPTION | 10 - MD5 | 37 ++--- NEWS.md | 215 ++++++++++++++++------------- R/CreateRunOptions.R | 4 R/RunModel_GR2M.R | 6 R/RunModel_Lag.R | 42 ----- R/UtilsRunModel.R | 48 ++++-- R/UtilsSeriesAggreg.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/V01_get_started.html | 79 ++++------ inst/doc/V03_param_sets_GR4J.html | 6 inst/doc/V04_cemaneige_hysteresis.R | 3 inst/doc/V04_cemaneige_hysteresis.Rmd | 3 inst/doc/V04_cemaneige_hysteresis.html | 100 ++++++------- inst/doc/V05_sd_model.html | 239 +++++++++++++++------------------ man/RunModel_CemaNeigeGR4J.Rd | 2 tests/testthat/test-CreateRunOptions.R | 103 ++++++++++---- tests/testthat/test-RunModel_GR2M.R |only vignettes/V04_cemaneige_hysteresis.Rmd | 3 20 files changed, 468 insertions(+), 435 deletions(-)
Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file forma [...truncated...]
Author: Tim Schaefer [aut, cre]
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between freesurferformats versions 1.0.0 dated 2025-09-08 and 1.0.1 dated 2026-07-08
freesurferformats-1.0.0/freesurferformats/R/read_dti_tck.R |only freesurferformats-1.0.1/freesurferformats/DESCRIPTION | 10 freesurferformats-1.0.1/freesurferformats/LICENSE | 4 freesurferformats-1.0.1/freesurferformats/MD5 | 631 +- freesurferformats-1.0.1/freesurferformats/NAMESPACE | 354 - freesurferformats-1.0.1/freesurferformats/R/brainvoyager.R | 880 +- freesurferformats-1.0.1/freesurferformats/R/cifti.R | 226 freesurferformats-1.0.1/freesurferformats/R/gifti_writer.R | 540 - freesurferformats-1.0.1/freesurferformats/R/gifti_xml_tools.R | 452 - freesurferformats-1.0.1/freesurferformats/R/helpers.R | 262 freesurferformats-1.0.1/freesurferformats/R/mghheader.R | 1456 ++-- freesurferformats-1.0.1/freesurferformats/R/nifti_common.R | 384 - freesurferformats-1.0.1/freesurferformats/R/nifti_to_mgh.R | 831 +- freesurferformats-1.0.1/freesurferformats/R/optdata.R | 375 - freesurferformats-1.0.1/freesurferformats/R/read_dti_tcktsf.R |only freesurferformats-1.0.1/freesurferformats/R/read_dti_trk.R | 256 freesurferformats-1.0.1/freesurferformats/R/read_fs_annot.R | 1338 ++-- freesurferformats-1.0.1/freesurferformats/R/read_fs_curv.R | 566 - freesurferformats-1.0.1/freesurferformats/R/read_fs_label.R | 400 - freesurferformats-1.0.1/freesurferformats/R/read_fs_mgh.R | 906 +-- freesurferformats-1.0.1/freesurferformats/R/read_fs_patch.R | 332 - freesurferformats-1.0.1/freesurferformats/R/read_fs_surface.R | 2960 +++++----- freesurferformats-1.0.1/freesurferformats/R/read_fs_transform.R | 552 - freesurferformats-1.0.1/freesurferformats/R/read_fs_volume.R | 98 freesurferformats-1.0.1/freesurferformats/R/read_fs_weight.R | 138 freesurferformats-1.0.1/freesurferformats/R/read_nifti1.R | 438 - freesurferformats-1.0.1/freesurferformats/R/read_nifti2.R | 314 - freesurferformats-1.0.1/freesurferformats/R/read_nisurface.R | 326 - freesurferformats-1.0.1/freesurferformats/R/rotate3d.R | 404 - freesurferformats-1.0.1/freesurferformats/R/surface_dist.R | 210 freesurferformats-1.0.1/freesurferformats/R/write_fs_annot.R | 446 - freesurferformats-1.0.1/freesurferformats/R/write_fs_curv.R | 624 +- freesurferformats-1.0.1/freesurferformats/R/write_fs_label.R | 252 freesurferformats-1.0.1/freesurferformats/R/write_fs_mgh.R | 510 - freesurferformats-1.0.1/freesurferformats/R/write_fs_patch.R | 210 freesurferformats-1.0.1/freesurferformats/R/write_fs_surface.R | 1678 ++--- freesurferformats-1.0.1/freesurferformats/R/write_fs_volume.R |only freesurferformats-1.0.1/freesurferformats/R/write_fs_weight.R | 186 freesurferformats-1.0.1/freesurferformats/R/write_nifti1.R | 488 - freesurferformats-1.0.1/freesurferformats/R/write_nifti2.R | 448 - freesurferformats-1.0.1/freesurferformats/build/vignette.rds |binary freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats.R | 252 freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats.Rmd | 624 +- freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats.html | 1456 ++-- freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_header.R | 44 freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_header.Rmd | 190 freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_header.html | 880 +- freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_write.R | 100 freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_write.Rmd | 314 - freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_write.html | 1042 +-- freesurferformats-1.0.1/freesurferformats/inst/extdata/colorlut.txt | 20 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.geo | 36 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.gii | 34 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.off | 44 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.ply | 58 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.stl | 172 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.tri | 44 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.vtk | 52 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.wobj | 40 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube_quads.byu | 16 freesurferformats-1.0.1/freesurferformats/inst/extdata/lh.entorhinal_exvivo.label | 2174 +++---- freesurferformats-1.0.1/freesurferformats/inst/extdata/lh.testsurface.asc | 20 freesurferformats-1.0.1/freesurferformats/inst/extdata/lh.tinysurface.asc | 20 freesurferformats-1.0.1/freesurferformats/inst/extdata/lh.tinysurface.gii | 126 freesurferformats-1.0.1/freesurferformats/inst/extdata/register.dat | 18 freesurferformats-1.0.1/freesurferformats/inst/extdata/talairach.lta | 60 freesurferformats-1.0.1/freesurferformats/inst/extdata/talairach.xfm | 16 freesurferformats-1.0.1/freesurferformats/inst/extdata/tiny_label.gii | 34 freesurferformats-1.0.1/freesurferformats/inst/extdata/tiny_morph.gii | 26 freesurferformats-1.0.1/freesurferformats/man/adjust.face.indices.to.Rd | 46 freesurferformats-1.0.1/freesurferformats/man/annot.max.region.idx.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/annot.unique.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/assert.surface.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/bvsmp.Rd | 46 freesurferformats-1.0.1/freesurferformats/man/cdata.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/check.dtype.for.data.Rd | 37 freesurferformats-1.0.1/freesurferformats/man/check_data_and_settings_consistency.Rd | 60 freesurferformats-1.0.1/freesurferformats/man/closest.vert.to.point.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/colortable.from.annot.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/coord.to.key.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/delete_all_opt_data.Rd | 28 freesurferformats-1.0.1/freesurferformats/man/doapply.transform.mtx.Rd | 54 freesurferformats-1.0.1/freesurferformats/man/dot-read.dti.tcktsf.Rd |only freesurferformats-1.0.1/freesurferformats/man/download_opt_data.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/euclidian.dist.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/faces.quad.to.tris.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/faces.tris.to.quad.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/fileopen.gz.or.not.Rd | 30 freesurferformats-1.0.1/freesurferformats/man/filepath.ends.with.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/fixed.vec.format.int.Rd | 58 freesurferformats-1.0.1/freesurferformats/man/flip2D.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/flip3D.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/fread3.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/fs.get.morph.file.ext.for.format.Rd | 80 freesurferformats-1.0.1/freesurferformats/man/fs.get.morph.file.format.from.filename.Rd | 80 freesurferformats-1.0.1/freesurferformats/man/fs.patch.Rd | 74 freesurferformats-1.0.1/freesurferformats/man/fs.surface.to.tmesh3d.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/fwrite3.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/get.dti.trk.endianness.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/get.slice.orientation.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/get_opt_data_filepath.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/gifti_writer.Rd | 54 freesurferformats-1.0.1/freesurferformats/man/gifti_xml.Rd | 116 freesurferformats-1.0.1/freesurferformats/man/gifti_xml_add_global_metadata.Rd | 64 freesurferformats-1.0.1/freesurferformats/man/gifti_xml_write.Rd | 70 freesurferformats-1.0.1/freesurferformats/man/giftixml_add_labeltable_from_annot.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/giftixml_add_labeltable_posneg.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/guess.filename.is.gzipped.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/has_pandoc.Rd | 30 freesurferformats-1.0.1/freesurferformats/man/int.to.col.brainvoyager.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/is.bvsmp.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/is.fs.annot.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/is.fs.label.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/is.fs.surface.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/is.fs.volume.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/is.mghheader.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/linesplit.fixed.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/list_opt_data.Rd | 28 freesurferformats-1.0.1/freesurferformats/man/m44_to_quaternion.Rd |only freesurferformats-1.0.1/freesurferformats/man/mgh.is.conformed.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/mghheader.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/mghheader.centervoxelRAS.from.firstvoxelRAS.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/mghheader.crs.orientation.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/mghheader.is.conformed.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/mghheader.is.ras.valid.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/mghheader.primary.slice.direction.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/mghheader.ras2vox.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/mghheader.ras2vox.tkreg.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/mghheader.scanner2tkreg.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/mghheader.tkreg2scanner.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/mghheader.update.from.vox2ras.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/mghheader.vox2ras.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/mghheader.vox2ras.tkreg.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/mghheader.vox2vox.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/mni152reg.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/mri_dtype_numbytes.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/ni1header.for.data.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/ni1header.template.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/ni2header.for.data.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/ni2header.template.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/nifti.datadim.from.dimfield.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/nifti.datadim.to.dimfield.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/nifti.dtype.info.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/nifti.dtypebitpix.info.from.mgh.dtype.Rd |only freesurferformats-1.0.1/freesurferformats/man/nifti.field.check.length.Rd | 44 freesurferformats-1.0.1/freesurferformats/man/nifti.field.check.nchar.max.Rd | 44 freesurferformats-1.0.1/freesurferformats/man/nifti.file.uses.fshack.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/nifti.file.version.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/nifti.header.check.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/nifti.space.info.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/nifti.time.info.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/nifti.transform.type.name.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/nii1header.for.mgh.Rd |only freesurferformats-1.0.1/freesurferformats/man/parse.stl.ascii.face.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/parse.transform.matrix.lines.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/ply.header.lines.Rd | 24 freesurferformats-1.0.1/freesurferformats/man/polygon.soup.to.indexed.mesh.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/print.fs.annot.Rd | 32 freesurferformats-1.0.1/freesurferformats/man/print.fs.label.Rd | 32 freesurferformats-1.0.1/freesurferformats/man/print.fs.patch.Rd | 32 freesurferformats-1.0.1/freesurferformats/man/print.fs.surface.Rd | 32 freesurferformats-1.0.1/freesurferformats/man/print.fs.volume.Rd | 32 freesurferformats-1.0.1/freesurferformats/man/ras.to.surfaceras.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/ras.to.talairachras.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/read.dti.tck.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/read.dti.trk.Rd | 55 freesurferformats-1.0.1/freesurferformats/man/read.dti.tsf.Rd | 54 freesurferformats-1.0.1/freesurferformats/man/read.element.counts.ply.header.Rd | 30 freesurferformats-1.0.1/freesurferformats/man/read.fixed.char.binary.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/read.fs.annot.Rd | 94 freesurferformats-1.0.1/freesurferformats/man/read.fs.annot.gii.Rd | 76 freesurferformats-1.0.1/freesurferformats/man/read.fs.colortable.Rd | 78 freesurferformats-1.0.1/freesurferformats/man/read.fs.curv.Rd | 106 freesurferformats-1.0.1/freesurferformats/man/read.fs.gca.Rd | 54 freesurferformats-1.0.1/freesurferformats/man/read.fs.label.Rd | 66 freesurferformats-1.0.1/freesurferformats/man/read.fs.label.gii.Rd | 74 freesurferformats-1.0.1/freesurferformats/man/read.fs.label.native.Rd | 88 freesurferformats-1.0.1/freesurferformats/man/read.fs.mgh.Rd | 138 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.Rd | 114 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.asc.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.bvsmp.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.cifti.Rd | 104 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.gii.Rd | 102 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.ni1.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.ni2.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.nii.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.txt.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/read.fs.patch.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/read.fs.patch.asc.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.Rd | 100 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.asc.Rd | 94 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.bvsrf.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.byu.Rd | 44 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.geo.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.gii.Rd | 92 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.ico.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.mz3.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.obj.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.off.Rd | 80 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.ply.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.stl.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.stl.ascii.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.stl.bin.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.vtk.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.transform.Rd | 92 freesurferformats-1.0.1/freesurferformats/man/read.fs.transform.dat.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/read.fs.transform.lta.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.transform.xfm.Rd | 88 freesurferformats-1.0.1/freesurferformats/man/read.fs.volume.Rd | 140 freesurferformats-1.0.1/freesurferformats/man/read.fs.volume.nii.Rd | 112 freesurferformats-1.0.1/freesurferformats/man/read.fs.weight.Rd | 84 freesurferformats-1.0.1/freesurferformats/man/read.fs.weight.asc.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/read.mesh.brainvoyager.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.nifti1.data.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/read.nifti1.header.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/read.nifti1.header.internal.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/read.nifti2.data.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/read.nifti2.header.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/read.nifti2.header.internal.Rd | 46 freesurferformats-1.0.1/freesurferformats/man/read.smp.brainvoyager.Rd | 70 freesurferformats-1.0.1/freesurferformats/man/read.smp.brainvoyager.v1or2.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/read.smp.brainvoyager.v3.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/read.smp.brainvoyager.v4or5.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/read_nisurface.Rd | 108 freesurferformats-1.0.1/freesurferformats/man/read_nisurfacefile.Rd | 102 freesurferformats-1.0.1/freesurferformats/man/read_nisurfacefile.fsascii.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/read_nisurfacefile.fsnative.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/read_nisurfacefile.gifti.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/readable.files.Rd | 56 freesurferformats-1.0.1/freesurferformats/man/readcolortable.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/readcolortable_oldformat.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/rotate2D.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/rotate3D.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/rotate90.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/scann.Rd | 44 freesurferformats-1.0.1/freesurferformats/man/sm0to1.Rd | 70 freesurferformats-1.0.1/freesurferformats/man/sm1to0.Rd | 70 freesurferformats-1.0.1/freesurferformats/man/stl.format.file.is.ascii.Rd | 30 freesurferformats-1.0.1/freesurferformats/man/surfaceras.to.ras.Rd | 62 freesurferformats-1.0.1/freesurferformats/man/surfaceras.to.talairach.Rd | 56 freesurferformats-1.0.1/freesurferformats/man/talairachras.to.ras.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/translate.mri.dtype.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/vertex.euclid.dist.Rd | 54 freesurferformats-1.0.1/freesurferformats/man/vertexdists.to.point.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/write.fs.annot.Rd | 114 freesurferformats-1.0.1/freesurferformats/man/write.fs.annot.gii.Rd | 96 freesurferformats-1.0.1/freesurferformats/man/write.fs.colortable.Rd | 66 freesurferformats-1.0.1/freesurferformats/man/write.fs.curv.Rd | 80 freesurferformats-1.0.1/freesurferformats/man/write.fs.label.Rd | 106 freesurferformats-1.0.1/freesurferformats/man/write.fs.label.gii.Rd | 112 freesurferformats-1.0.1/freesurferformats/man/write.fs.mgh.Rd | 102 freesurferformats-1.0.1/freesurferformats/man/write.fs.morph.Rd | 92 freesurferformats-1.0.1/freesurferformats/man/write.fs.morph.asc.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/write.fs.morph.gii.Rd | 96 freesurferformats-1.0.1/freesurferformats/man/write.fs.morph.ni1.Rd | 97 freesurferformats-1.0.1/freesurferformats/man/write.fs.morph.ni2.Rd | 106 freesurferformats-1.0.1/freesurferformats/man/write.fs.morph.smp.Rd | 88 freesurferformats-1.0.1/freesurferformats/man/write.fs.morph.txt.Rd | 78 freesurferformats-1.0.1/freesurferformats/man/write.fs.patch.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.Rd | 134 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.asc.Rd | 114 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.bvsrf.Rd | 62 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.byu.Rd | 118 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.gii.Rd | 124 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.mz3.Rd | 122 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.obj.Rd | 94 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.off.Rd | 90 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.off.ply2.Rd | 96 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.ply.Rd | 104 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.ply2.Rd | 84 freesurferformats-1.0.1/freesurferformats/man/write.fs.surface.vtk.Rd | 112 freesurferformats-1.0.1/freesurferformats/man/write.fs.volume.Rd |only freesurferformats-1.0.1/freesurferformats/man/write.fs.weight.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/write.fs.weight.asc.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/write.nifti1.Rd | 51 freesurferformats-1.0.1/freesurferformats/man/write.nifti2.Rd | 46 freesurferformats-1.0.1/freesurferformats/man/write.smp.brainvoyager.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/write.smp.brainvoyager.v2.Rd | 44 freesurferformats-1.0.1/freesurferformats/man/write.smp.brainvoyager.v3or4or5.Rd | 44 freesurferformats-1.0.1/freesurferformats/man/xml_node_gifti_MD.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/xml_node_gifti_coordtransform.Rd | 56 freesurferformats-1.0.1/freesurferformats/man/xml_node_gifti_label.Rd | 44 freesurferformats-1.0.1/freesurferformats/man/xml_node_gifti_label_table.Rd | 30 freesurferformats-1.0.1/freesurferformats/man/xml_node_gifti_label_table_from_annot.Rd | 36 freesurferformats-1.0.1/freesurferformats/tests/testthat.R | 8 freesurferformats-1.0.1/freesurferformats/tests/testthat/helper-functions-for-tests.R | 48 freesurferformats-1.0.1/freesurferformats/tests/testthat/teardown-cran.R | 20 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-brainvoyager.R | 210 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-cifti.R | 96 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-gifti_writer.R | 36 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-gifti_xml_tools.R | 66 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-helpers.R | 36 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-mgh2nii.R | 152 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-mghheader.R | 474 - freesurferformats-1.0.1/freesurferformats/tests/testthat/test-nifti_to_mgh.R | 90 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_dti_tcktsf.R |only freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_fs_annot.R | 364 - freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_fs_curv.R | 96 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_fs_label.R | 196 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_fs_mgh.R | 354 - freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_fs_patch.R | 96 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_fs_surface.R | 860 +- freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_fs_transform.R | 120 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_fs_weight.R | 16 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_nifti1.R | 202 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_nifti2.R | 146 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-read_nisurface.R | 240 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-rotate3d.R | 186 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-surface_dist.R | 72 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-write_fs_annot.R | 270 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-write_fs_curv.R | 300 - freesurferformats-1.0.1/freesurferformats/tests/testthat/test-write_fs_label.R | 116 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-write_fs_mgh.R | 376 - freesurferformats-1.0.1/freesurferformats/tests/testthat/test-write_fs_patch.R | 56 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-write_fs_surface.R | 366 - freesurferformats-1.0.1/freesurferformats/tests/testthat/test-write_fs_weight.R | 90 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-write_nifti1.R | 158 freesurferformats-1.0.1/freesurferformats/tests/testthat/test-write_nifti2.R | 102 freesurferformats-1.0.1/freesurferformats/vignettes/freesurferformats.Rmd | 624 +- freesurferformats-1.0.1/freesurferformats/vignettes/freesurferformats_header.Rmd | 190 freesurferformats-1.0.1/freesurferformats/vignettes/freesurferformats_write.Rmd | 314 - 321 files changed, 24183 insertions(+), 23970 deletions(-)
More information about freesurferformats at CRAN
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Title: A Lightweight Toolkit for Displaying Customizable Tables
Description: A lightweight toolkit that provides functions for printing tables from
input data in the R console or terminal with customizable formatting. Supported
outputs include American Psychological Association (APA)-style tables
(American Psychological Association, 2020, ISBN:9781433832178),
correlation matrices, contingency tables, and two-column summary tables.
Author: Joshua Marie [aut, cre]
Maintainer: Joshua Marie <joshua.marie.k@gmail.com>
Diff between tabstats versions 0.2.0 dated 2026-05-25 and 0.2.1 dated 2026-07-08
DESCRIPTION | 10 ++-- MD5 | 18 +++---- NEWS.md | 10 ++++ R/helpers-pairwise_matrix-extra.R | 7 +- README.md | 6 +- inst/doc/tabstats.R | 23 +++++++++ inst/doc/tabstats.Rmd | 26 ++++++++++- inst/doc/tabstats.html | 89 ++++++++++++++++++++++++++------------ man/tabstats.Rd | 4 - vignettes/tabstats.Rmd | 26 ++++++++++- 10 files changed, 165 insertions(+), 54 deletions(-)
Title: Obtaining Data Published by the National Statistics Institute
Description: Get open statistical data and metadata disseminated by the
National Statistics Institute of Spain (INE). The functions return
data frames with the requested information thanks to calls to
the 'INE' API <https://www.ine.es/dyngs/DAB/index.htm?cid=1100>.
Author: David Crespo [aut, cre],
National Statistics Institute, INE [cph]
Maintainer: David Crespo <david.crespo.roces@ine.es>
Diff between ineapir versions 0.2.5 dated 2025-09-15 and 0.2.6 dated 2026-07-08
DESCRIPTION | 6 - MD5 | 42 +++---- NEWS.md | 4 R/data_series.R | 12 +- R/data_tables.R | 14 +- R/metadata_series.R | 16 +-- R/metadata_tables.R | 20 +-- R/utils.R | 14 +- README.md | 180 +++++++++++++++++----------------- man/get_data_series.Rd | 10 - man/get_data_table.Rd | 14 +- man/get_metadata_operation_table.Rd | 4 man/get_metadata_series.Rd | 4 man/get_metadata_series_table.Rd | 8 - man/get_metadata_series_values.Rd | 4 man/get_metadata_table_groups.Rd | 4 man/get_metadata_table_values.Rd | 6 - man/get_metadata_table_varval.Rd | 6 - tests/testthat/test-data_series.R | 6 - tests/testthat/test-data_tables.R | 20 +-- tests/testthat/test-metadata_series.R | 8 - tests/testthat/test-metadata_tables.R | 14 +- 22 files changed, 213 insertions(+), 203 deletions(-)
Title: Fast C++ Primitives for the 'NeuroAnatomy Toolbox'
Description: Fast functions implemented in C++ via 'Rcpp' to support the
'NeuroAnatomy Toolbox' ('nat') ecosystem. These functions provide large
speed-ups for basic manipulation of neuronal skeletons over pure R
functions found in the 'nat' package. The expectation is that end
users will not use this package directly, but instead the 'nat'
package will automatically use routines from this package when it is
available to enable large performance gains.
Author: Gregory Jefferis [aut, cre]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between natcpp versions 0.2 dated 2025-10-14 and 0.3.0 dated 2026-07-08
DESCRIPTION | 12 ++++++------ MD5 | 20 +++++++++++++------- NAMESPACE | 3 +++ NEWS.md | 13 +++++++++++++ R/RcppExports.R | 29 +++++++++++++++++++++++++++++ R/weighted_jaccard.R |only inst/WORDLIST | 2 ++ man/c_weighted_jaccard_dense.Rd |only man/c_weighted_jaccard_sparse.Rd |only man/natcpp-package.Rd | 5 +++++ src/Makevars |only src/RcppExports.cpp | 33 +++++++++++++++++++++++++++++++++ src/weighted_jaccard.cpp |only tests/testthat/test-weighted-jaccard.R |only 14 files changed, 104 insertions(+), 13 deletions(-)
Title: Interfaces to Phylogenetic Software in R
Description: Functions that wrap popular phylogenetic software for sequence
alignment, masking of sequence alignments, and estimation of phylogenies and
ancestral character states.
Author: Christoph Heibl [aut] ,
Natalie Cusimano [aut],
Franz-Sebastian Krah [aut],
Martin R. Smith [ctb, cre]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between ips versions 0.0.13 dated 2026-02-23 and 0.1.1 dated 2026-07-08
DESCRIPTION | 28 - MD5 | 164 ++++---- NAMESPACE | 198 ++++++---- NEWS.md | 22 + R/DNAbin2index.R | 48 +- R/EmptyCells.R | 95 ++-- R/aliscore.R | 179 ++++----- R/aperm.DNAbin.R |only R/are.tips.consecutive.R | 22 - R/assembleDataNode.R | 67 +-- R/assembleDistributionNode.R | 25 - R/assembleInitNode.R | 102 ++--- R/assembleLoggers.R | 311 ++++++++-------- R/assembleOperators.R | 336 ++++++++--------- R/assembleStateNode.R | 275 +++++++------- R/blastn.R | 151 +++---- R/code.simple.gaps.R | 157 ++++---- R/collapseUnsupportedEdges.R | 184 ++++----- R/combMyTree.R | 208 +++++++--- R/del.miss.R | 70 +-- R/deleteEmptyCells.R | 108 ++--- R/deleteGaps.R | 72 +-- R/descendants.R | 111 ++--- R/fixNodes.R | 173 +++++---- R/forceEqualTipHeights.R | 2 R/formatSet.R | 32 - R/gblocks.R | 284 +++++++------- R/index2DNAbin.R | 72 +-- R/mafft.R | 385 ++++++++++---------- R/mafft.merge.R | 191 +++++----- R/matrixBlock.R | 50 +- R/mrbayes.R | 365 +++++++++---------- R/mrbayes.lset.R | 145 +++++-- R/mrbayes.mcmc.R | 179 ++++++--- R/mrbayes.prset.R | 141 +++++-- R/multistateMCMC.R | 397 ++++++++++---------- R/multistateML.R | 397 ++++++++++---------- R/neighboringPairs.R | 36 - R/noi.R | 172 ++++----- R/ntip.R | 54 +- R/phylo2mafft.R | 82 ++-- R/phylo2mst.R | 98 ++--- R/pis.R | 122 +++--- R/prank.R | 133 +++--- R/raxml.R | 764 ++++++++++++++++++++-------------------- R/raxml.partitions.R | 38 - R/rbeauti.R | 461 ++++++++++++------------ R/rc.R | 177 ++++----- R/read.beast.R | 184 ++++----- R/read.fas.R | 128 +++--- R/read.mrbayes.R | 161 ++++---- R/read.nex.R | 109 ++--- R/read.phy.R | 89 ++-- R/read.starbeast.R | 171 ++++---- R/read.xml.R | 43 +- R/setClock.R | 109 ++--- R/setMCMC.R | 36 - R/sister.R | 145 +++---- R/splitIntoClades.R | 76 +-- R/str2cha.R | 10 R/terminalSisters.R | 67 +-- R/tipHeights.R | 54 +- R/traitRate.R | 187 ++++----- R/trimEnds.R | 283 +++++++------- R/unresolve.clade.R | 67 +-- R/write.fas.R | 152 +++---- R/write.nex.R | 313 ++++++++-------- inst/CITATION | 18 man/DNAbin2index.Rd | 36 - man/EmptyCells.Rd | 156 ++++---- man/aliscore.Rd | 115 +++--- man/aperm.DNAbin.Rd |only man/collapseUnsupportedEdges.Rd | 82 ++-- man/combMyTree.Rd | 100 +++-- man/fixNodes.Rd | 96 +++-- man/gblocks.Rd | 221 +++++------ man/mafft.merge.Rd | 78 ++-- man/mrbayes.Rd | 179 ++++----- man/mrbayes.lset.Rd | 147 +++---- man/mrbayes.mcmc.Rd | 256 ++++++------- man/mrbayes.prset.Rd | 190 ++++++--- man/raxml.partitions.Rd | 2 man/rbeauti.Rd | 170 ++++---- man/read.beast.Rd | 88 ++-- 84 files changed, 6344 insertions(+), 5857 deletions(-)
Title: Download and Measure Global Trends Through 'Google' Search
Volumes
Description: 'Google' offers public access to global search volumes from its
search engine through the 'Google Trends' portal. The package downloads
these search volumes provided by 'Google Trends' and uses them to
measure and analyze the distribution of search scores across countries
or within countries. The package allows researchers and analysts to
use these search scores to investigate global trends based on patterns
within these scores. This offers insights such as degree of
internationalization of firms and organizations or dissemination of
political, social, or technological trends across the globe or within
single countries. An outline of the package's methodological
foundations and potential applications is available as a working
paper: <doi:10.2139/ssrn.3969013>.
Author: Harald Puhr [aut, cre, cph] ,
Jakob Muellner [ccp]
Maintainer: Harald Puhr <harald.puhr@gmail.com>
Diff between globaltrends versions 0.0.14 dated 2023-03-06 and 0.2.1 dated 2026-07-08
globaltrends-0.0.14/globaltrends/R/get_abnorm_hist.r |only globaltrends-0.0.14/globaltrends/R/plot_bar.r |only globaltrends-0.0.14/globaltrends/R/plot_box.r |only globaltrends-0.0.14/globaltrends/R/plot_ts.r |only globaltrends-0.0.14/globaltrends/R/plot_voi_doi.r |only globaltrends-0.0.14/globaltrends/man/get_abnorm_hist.Rd |only globaltrends-0.0.14/globaltrends/man/plot_bar.Rd |only globaltrends-0.0.14/globaltrends/man/plot_box.Rd |only globaltrends-0.0.14/globaltrends/man/plot_ts.Rd |only globaltrends-0.0.14/globaltrends/man/plot_voi_doi.Rd |only globaltrends-0.0.14/globaltrends/tests/test_functions.r |only globaltrends-0.0.14/globaltrends/tests/testthat.r |only globaltrends-0.0.14/globaltrends/tests/testthat/test-24months.R |only globaltrends-0.0.14/globaltrends/tests/testthat/test-abnorm.R |only globaltrends-0.0.14/globaltrends/tests/testthat/test-plot_bar.R |only globaltrends-0.0.14/globaltrends/tests/testthat/test-plot_box.R |only globaltrends-0.0.14/globaltrends/tests/testthat/test-plot_ts.R |only globaltrends-0.0.14/globaltrends/tests/testthat/test-plot_voi_doi.R |only globaltrends-0.0.14/globaltrends/vignettes/plot009.png |only globaltrends-0.0.14/globaltrends/vignettes/plot010.png |only globaltrends-0.0.14/globaltrends/vignettes/plot_sample01.png |only globaltrends-0.0.14/globaltrends/vignettes/plot_sample02.png |only globaltrends-0.0.14/globaltrends/vignettes/plot_sample03.png |only globaltrends-0.0.14/globaltrends/vignettes/plot_sample04.png |only globaltrends-0.2.1/globaltrends/DESCRIPTION | 45 globaltrends-0.2.1/globaltrends/LICENSE | 4 globaltrends-0.2.1/globaltrends/MD5 | 174 - globaltrends-0.2.1/globaltrends/NAMESPACE | 116 - globaltrends-0.2.1/globaltrends/NEWS.md | 169 + globaltrends-0.2.1/globaltrends/R/add_keywords.r | 320 +-- globaltrends-0.2.1/globaltrends/R/add_locations.r | 251 +- globaltrends-0.2.1/globaltrends/R/aggregate_synonyms.r |only globaltrends-0.2.1/globaltrends/R/check_functions.r | 178 + globaltrends-0.2.1/globaltrends/R/compute_doi.r | 367 ++- globaltrends-0.2.1/globaltrends/R/compute_score.r | 738 ++----- globaltrends-0.2.1/globaltrends/R/data.r | 540 ++--- globaltrends-0.2.1/globaltrends/R/database_functions.r | 545 ++--- globaltrends-0.2.1/globaltrends/R/download_control.r | 294 ++ globaltrends-0.2.1/globaltrends/R/download_object.r | 425 +++- globaltrends-0.2.1/globaltrends/R/download_region.r |only globaltrends-0.2.1/globaltrends/R/download_related.r |only globaltrends-0.2.1/globaltrends/R/export_data.r | 541 ++--- globaltrends-0.2.1/globaltrends/R/globals.r | 30 globaltrends-0.2.1/globaltrends/R/helper_functions.r | 870 +++++++- globaltrends-0.2.1/globaltrends/R/initialize_python.r |only globaltrends-0.2.1/globaltrends/R/remove_data.r | 624 +++--- globaltrends-0.2.1/globaltrends/R/zzz.r | 131 - globaltrends-0.2.1/globaltrends/README.md | 136 - globaltrends-0.2.1/globaltrends/build/partial.rdb |only globaltrends-0.2.1/globaltrends/build/vignette.rds |binary globaltrends-0.2.1/globaltrends/data/example_control.rda |binary globaltrends-0.2.1/globaltrends/data/example_doi.rda |binary globaltrends-0.2.1/globaltrends/data/example_keywords.rda |binary globaltrends-0.2.1/globaltrends/data/example_object.rda |binary globaltrends-0.2.1/globaltrends/data/example_score.rda |binary globaltrends-0.2.1/globaltrends/data/example_time.rda |binary globaltrends-0.2.1/globaltrends/inst/CITATION | 8 globaltrends-0.2.1/globaltrends/inst/doc/globaltrends.R | 506 +--- globaltrends-0.2.1/globaltrends/inst/doc/globaltrends.Rmd | 398 +-- globaltrends-0.2.1/globaltrends/inst/doc/globaltrends.html | 853 +++----- globaltrends-0.2.1/globaltrends/inst/python |only globaltrends-0.2.1/globaltrends/man/add_keyword.Rd | 40 globaltrends-0.2.1/globaltrends/man/add_locations.Rd | 76 globaltrends-0.2.1/globaltrends/man/add_synonym.Rd | 45 globaltrends-0.2.1/globaltrends/man/aggregate_synonyms.Rd |only globaltrends-0.2.1/globaltrends/man/batch_keywords.Rd | 39 globaltrends-0.2.1/globaltrends/man/batch_time.Rd | 38 globaltrends-0.2.1/globaltrends/man/compute_doi.Rd | 91 globaltrends-0.2.1/globaltrends/man/compute_score.Rd | 144 - globaltrends-0.2.1/globaltrends/man/countries.Rd | 98 globaltrends-0.2.1/globaltrends/man/countries_wdi.Rd | 23 globaltrends-0.2.1/globaltrends/man/data_control.Rd | 51 globaltrends-0.2.1/globaltrends/man/data_doi.Rd | 85 globaltrends-0.2.1/globaltrends/man/data_object.Rd | 61 globaltrends-0.2.1/globaltrends/man/data_score.Rd | 76 globaltrends-0.2.1/globaltrends/man/disconnect_db.Rd | 29 globaltrends-0.2.1/globaltrends/man/download_control.Rd | 120 - globaltrends-0.2.1/globaltrends/man/download_object.Rd | 139 - globaltrends-0.2.1/globaltrends/man/download_region.Rd |only globaltrends-0.2.1/globaltrends/man/download_related.Rd |only globaltrends-0.2.1/globaltrends/man/export_data.Rd | 149 - globaltrends-0.2.1/globaltrends/man/get_api_usage.Rd |only globaltrends-0.2.1/globaltrends/man/gt.env.Rd | 57 globaltrends-0.2.1/globaltrends/man/initialize_db.Rd | 57 globaltrends-0.2.1/globaltrends/man/initialize_python.Rd |only globaltrends-0.2.1/globaltrends/man/remove_data.Rd | 96 globaltrends-0.2.1/globaltrends/man/start_db.Rd | 60 globaltrends-0.2.1/globaltrends/man/us_states.Rd | 71 globaltrends-0.2.1/globaltrends/tests/testthat.R |only globaltrends-0.2.1/globaltrends/tests/testthat/_snaps |only globaltrends-0.2.1/globaltrends/tests/testthat/helper-db.R |only globaltrends-0.2.1/globaltrends/tests/testthat/helper-fixtures.R |only globaltrends-0.2.1/globaltrends/tests/testthat/helper-skips.R |only globaltrends-0.2.1/globaltrends/tests/testthat/helper-validation.R |only globaltrends-0.2.1/globaltrends/tests/testthat/setup-language.R |only globaltrends-0.2.1/globaltrends/tests/testthat/test-api-counter.R |only globaltrends-0.2.1/globaltrends/tests/testthat/test-check-functions.R |only globaltrends-0.2.1/globaltrends/tests/testthat/test-computations.R | 731 ++++--- globaltrends-0.2.1/globaltrends/tests/testthat/test-db_functions.R | 350 ++- globaltrends-0.2.1/globaltrends/tests/testthat/test-downloads.R | 1031 +++++++++- globaltrends-0.2.1/globaltrends/tests/testthat/test-export.R | 626 +++--- globaltrends-0.2.1/globaltrends/tests/testthat/test-helper-functions.R |only globaltrends-0.2.1/globaltrends/tests/testthat/test-initialize-python.R |only globaltrends-0.2.1/globaltrends/tests/testthat/test-keywords.R | 478 ++-- globaltrends-0.2.1/globaltrends/tests/testthat/test-locations.R | 280 -- globaltrends-0.2.1/globaltrends/tests/testthat/test-messages.R |only globaltrends-0.2.1/globaltrends/tests/testthat/test-metrics.R |only globaltrends-0.2.1/globaltrends/tests/testthat/test-python.R |only globaltrends-0.2.1/globaltrends/tests/testthat/test-remove-data-selectivity.R |only globaltrends-0.2.1/globaltrends/tests/testthat/test-synonyms.R | 217 +- globaltrends-0.2.1/globaltrends/vignettes/globaltrends.Rmd | 398 +-- globaltrends-0.2.1/globaltrends/vignettes/plot_appendix_a1.png |only globaltrends-0.2.1/globaltrends/vignettes/plot_appendix_a2.png |only globaltrends-0.2.1/globaltrends/vignettes/plot_appendix_a3.png |only globaltrends-0.2.1/globaltrends/vignettes/plot_appendix_a4.png |only 115 files changed, 8162 insertions(+), 5857 deletions(-)
Title: Threshold-Sweep QCA
Description: Provides threshold sweep methods for Qualitative Comparative
Analysis (QCA). Implements Condition Threshold Sweep-Single (CTS-S),
Condition Threshold Sweep-Multiple (CTS-M), Outcome Threshold Sweep (OTS),
and Dual Threshold Sweep (DTS) for systematic exploration of threshold
calibration effects on crisp-set QCA results. These methods extend
traditional robustness approaches by treating threshold variation as an
exploratory tool for discovering causal structures. Also provides Fiss
(2011) <doi:10.5465/amj.2011.60263120> core/peripheral condition
classification via compute_fiss_core() and generate_fiss_chart(), enabling
four-symbol configuration charts that distinguish core conditions (present
in both parsimonious and intermediate solutions) from peripheral conditions
(intermediate only). Built on top of the 'QCA' package by Dusa (2019)
<doi:10.1007/978-3-319-75668-4>, with function arguments following 'QCA'
conventions. Based on set-theoretic methods by Ragin (2008)
<doi: [...truncated...]
Author: Yuki Toyoda [aut, cre],
Japan Society for the Promotion of Science [fnd]
Maintainer: Yuki Toyoda <yuki.toyoda.ds@hosei.ac.jp>
Diff between ThSQCA versions 2.0.0 dated 2026-05-30 and 2.0.1 dated 2026-07-08
DESCRIPTION | 43 - MD5 | 58 +- NEWS.md | 29 + R/ThSQCA-package.R | 2 R/tsqca_config_chart.R | 23 - R/tsqca_core.R | 672 ------------------------------ R/tsqca_cts.R | 2 R/tsqca_fiss_core.R | 11 R/tsqca_helpers.R | 36 + R/tsqca_ots_dts.R | 2 R/tsqca_report.R | 18 build/partial.rdb |binary build/vignette.rds |binary inst/doc/ThSQCA_Reproducible_EN.html | 34 - inst/doc/ThSQCA_Tutorial_EN.html | 20 man/SYMBOL_SETS.Rd | 4 man/SYMBOL_SETS_FISS.Rd | 12 man/ThSQCA-package.Rd | 7 man/build_fiss_matrix.Rd | 8 man/classify_term_conditions.Rd | 13 man/compute_fiss_core.Rd | 72 --- man/extract_cond_status_map.Rd | 9 man/extract_sol_terms.Rd | 8 man/generate_config_chart.Rd | 21 man/generate_cross_threshold_chart.Rd | 2 man/generate_fiss_chart.Rd | 42 - man/generate_report.Rd | 17 man/print_fiss_summary.Rd | 15 man/run_parsimonious.Rd | 8 man/sanitize_truthtable.Rd |only tests/testthat/test-sanitize_truthtable.R |only 31 files changed, 238 insertions(+), 950 deletions(-)
Title: Antigenic Cartography Macros
Description: A toolkit for making antigenic maps from immunological assay data,
in order to quantify and visualize antigenic differences between different
pathogen strains as described in
Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World
Health Organization influenza vaccine strain selection process. Additional
functions allow for the diagnostic evaluation of antigenic maps and an
interactive viewer is provided to explore antigenic relationships amongst
several strains and incorporate the visualization of associated genetic
information.
Author: Sam Wilks [aut, cre]
Maintainer: Sam Wilks <sam.wilks@unimelb.edu.au>
Diff between Racmacs versions 1.2.9 dated 2023-11-30 and 1.2.10 dated 2026-07-08
Racmacs-1.2.10/Racmacs/DESCRIPTION | 17 ++-- Racmacs-1.2.10/Racmacs/MD5 | 27 +++--- Racmacs-1.2.10/Racmacs/NEWS.md | 3 Racmacs-1.2.10/Racmacs/R/map_new.R | 2 Racmacs-1.2.10/Racmacs/R/map_optimize.R | 2 Racmacs-1.2.10/Racmacs/build/vignette.rds |binary Racmacs-1.2.10/Racmacs/inst/doc/adding-sequences.html | 35 +++++++- Racmacs-1.2.10/Racmacs/inst/doc/assessing_map_uncertainty.html | 1 Racmacs-1.2.10/Racmacs/inst/doc/comparing-maps.html | 37 +++++++-- Racmacs-1.2.10/Racmacs/inst/doc/customising-map-appearance.html | 3 Racmacs-1.2.10/Racmacs/inst/doc/making-a-map-from-scratch.html | 39 +++++++--- Racmacs-1.2.10/Racmacs/inst/doc/merging-maps.R | 18 ++-- Racmacs-1.2.10/Racmacs/inst/doc/merging-maps.html | 1 Racmacs-1.2.10/Racmacs/tests/testthat/Rplots.pdf |binary Racmacs-1.2.9/Racmacs/inst/htmlwidgets/RacViewer/tests |only 15 files changed, 127 insertions(+), 58 deletions(-)
Title: Bayesian Summary Data Models for Mendelian Randomization Studies
Description: Bayesian estimation of inverse variance weighted (IVW),
Burgess et al. (2013) <doi:10.1002/gepi.21758>, and MR-Egger, Bowden
et al. (2015) <doi:10.1093/ije/dyv080>, summary data models for
Mendelian randomization analyses.
Author: Okezie Uche-Ikonne [aut] ,
Frank Dondelinger [aut] ,
Tom Palmer [aut, cre]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between mrbayes versions 0.5.2 dated 2024-08-19 and 0.5.3 dated 2026-07-08
mrbayes-0.5.2/mrbayes/src/Makevars |only mrbayes-0.5.3/mrbayes/DESCRIPTION | 19 mrbayes-0.5.3/mrbayes/MD5 | 107 +-- mrbayes-0.5.3/mrbayes/NEWS.md | 17 mrbayes-0.5.3/mrbayes/R/bmi_insulin.R | 6 mrbayes-0.5.3/mrbayes/R/dodata.R | 12 mrbayes-0.5.3/mrbayes/R/mr_egger_rjags.R | 95 +-- mrbayes-0.5.3/mrbayes/R/mr_egger_stan.R | 26 mrbayes-0.5.3/mrbayes/R/mr_format.R | 7 mrbayes-0.5.3/mrbayes/R/mr_ivw_rjags.R | 185 +++--- mrbayes-0.5.3/mrbayes/R/mr_ivw_stan.R | 21 mrbayes-0.5.3/mrbayes/R/mr_radialegger_rjags.R | 88 +- mrbayes-0.5.3/mrbayes/R/mr_radialegger_stan.R | 23 mrbayes-0.5.3/mrbayes/R/mrinput_mrformat.R | 14 mrbayes-0.5.3/mrbayes/R/mvmr_egger_rjags.R | 176 ++--- mrbayes-0.5.3/mrbayes/R/mvmr_egger_stan.R | 35 - mrbayes-0.5.3/mrbayes/R/mvmr_ivw_rjags.R | 261 ++++---- mrbayes-0.5.3/mrbayes/R/mvmr_ivw_stan.R | 22 mrbayes-0.5.3/mrbayes/R/rjags_check.R | 6 mrbayes-0.5.3/mrbayes/R/rstan_check.R | 6 mrbayes-0.5.3/mrbayes/README.md | 9 mrbayes-0.5.3/mrbayes/build/partial.rdb |binary mrbayes-0.5.3/mrbayes/cleanup |only mrbayes-0.5.3/mrbayes/configure | 6 mrbayes-0.5.3/mrbayes/inst/stan/mregger.stan | 2 mrbayes-0.5.3/mrbayes/inst/stan/mvmregger.stan | 2 mrbayes-0.5.3/mrbayes/man/bmi_insulin.Rd | 6 mrbayes-0.5.3/mrbayes/man/dodata.Rd | 12 mrbayes-0.5.3/mrbayes/man/mr_egger_rjags.Rd | 4 mrbayes-0.5.3/mrbayes/man/mr_egger_stan.Rd | 6 mrbayes-0.5.3/mrbayes/man/mr_ivw_rjags.Rd | 2 mrbayes-0.5.3/mrbayes/man/mr_ivw_stan.Rd | 6 mrbayes-0.5.3/mrbayes/man/mr_radialegger_rjags.Rd | 4 mrbayes-0.5.3/mrbayes/man/mr_radialegger_stan.Rd | 6 mrbayes-0.5.3/mrbayes/man/mrbayes-package.Rd | 1 mrbayes-0.5.3/mrbayes/man/mrinput_mr_format.Rd | 2 mrbayes-0.5.3/mrbayes/man/mvmr_egger_rjags.Rd | 5 mrbayes-0.5.3/mrbayes/man/mvmr_egger_stan.Rd | 6 mrbayes-0.5.3/mrbayes/man/mvmr_ivw_rjags.Rd | 2 mrbayes-0.5.3/mrbayes/man/mvmr_ivw_stan.Rd | 6 mrbayes-0.5.3/mrbayes/src/Makevars.in |only mrbayes-0.5.3/mrbayes/src/stanExports_mregger.cc | 34 - mrbayes-0.5.3/mrbayes/src/stanExports_mrivw.cc | 34 - mrbayes-0.5.3/mrbayes/src/stanExports_mrradialegger.cc | 34 - mrbayes-0.5.3/mrbayes/src/stanExports_mvmregger.cc | 34 - mrbayes-0.5.3/mrbayes/src/stanExports_mvmrivw.cc | 34 - mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_egger_rjags.R | 270 ++++----- mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_egger_stan.R | 188 +++--- mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_ivw_rjags.R | 204 +++--- mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_ivw_stan.R | 145 ++-- mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_radialegger_rjags.R | 297 +++++----- mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_radialegger_stan.R | 188 +++--- mrbayes-0.5.3/mrbayes/tests/testthat/test-mvmr_egger_rjags.R | 262 ++++---- mrbayes-0.5.3/mrbayes/tests/testthat/test-mvmr_egger_stan.R | 208 +++---- mrbayes-0.5.3/mrbayes/tests/testthat/test-mvmr_ivw_rjags.R | 285 ++++----- mrbayes-0.5.3/mrbayes/tests/testthat/test-mvmr_ivw_stan.R | 210 +++---- 56 files changed, 1864 insertions(+), 1776 deletions(-)
Title: A Multivariate Meta-Analysis Model for High-Dimensional Data
Description: Performs multivariate meta-analysis for high-dimensional data
to integrate and collectively analyse individual-level data from multiple
studies, as well as to combine summary estimates. This approach accounts
for correlation between outcomes, incorporates within- and between-study
variability, handles missing values, and uses shrinkage estimation to
accommodate high dimensionality. The 'MetaHD' R package provides access
to our multivariate meta-analysis approach, along with a comprehensive
suite of existing meta-analysis methods, including fixed-effects and
random-effects models, Fisher's method, Stouffer's method, the weighted
Z method, Lancaster's method, the weighted Fisher's method, and vote-counting
approach. Visualisation tools are provided for interpreting and comparing
results across methods, including Venn diagrams, UpSet plots, and ROC curves,
heatmaps of pooled effect sizes and correlations among outcomes. A detailed
vignette with example datasets and code for data preparati [...truncated...]
Author: Jayamini Liyanage [aut, cre],
Alysha De Livera [aut],
Luke Prendergast [aut]
Maintainer: Jayamini Liyanage <j.liyanage@latrobe.edu.au>
Diff between MetaHD versions 0.1.4 dated 2026-02-05 and 0.1.5 dated 2026-07-08
DESCRIPTION | 42 ++++- MD5 | 54 +++++-- NAMESPACE | 17 ++ R/MetaHD.R | 298 ++++++++++++++++++++++++++++++++++------ R/MetaHDInput.R | 4 R/MetaHDResult.R |only R/MetaHDpval.R | 12 - R/helper.functions.R | 203 ++++++++++++++++++++++++++- R/plot_MetaHDResult.R |only R/plot_correlation_heatmap.R |only R/plot_dendrogram.R |only R/plot_effect_heatmap.R |only R/simData.R |only build/partial.rdb |binary data/realdata.rda |binary data/simData.complete.rda |only data/simData.missing.rda |only data/simdata.1.rda |binary data/simdata.2.rda |binary man/MetaHD-outputs.Rd |only man/MetaHD.Rd | 56 +++++++ man/MetaHDInput.Rd | 4 man/MetaHDResult.Rd |only man/MetaHDpval.Rd | 12 - man/estimateCorMat.Rd |only man/figures |only man/plot.MetaHDResult.Rd |only man/plot_correlation_heatmap.Rd |only man/plot_dendrogram.Rd |only man/plot_effect_heatmap.Rd |only man/simData.complete.Rd |only man/simData.missing.Rd |only tests |only 33 files changed, 616 insertions(+), 86 deletions(-)
Title: Optimal Group Assignment and Workload Allocation
Description: Integer programming models to assign students to groups by maximising
diversity or topic preferences, and to allocate multi-role teaching workloads
while balancing role demand, preferences, fairness, and cohort protection.
Author: Vik Gopal [aut],
Kevin Lam [aut],
Ju Xue [ctb],
Mingyuan Zhang [aut, cre],
National University of Singapore [cph]
Maintainer: Mingyuan Zhang <e0970135@u.nus.edu>
Diff between grouper versions 0.5.0 dated 2025-10-16 and 0.7.3 dated 2026-07-08
grouper-0.5.0/grouper/vignettes/diversity_skill.R |only grouper-0.5.0/grouper/vignettes/diversity_skill.html |only grouper-0.5.0/grouper/vignettes/related_work.R |only grouper-0.5.0/grouper/vignettes/related_work.html |only grouper-0.5.0/grouper/vignettes/sanity_checks.R |only grouper-0.5.0/grouper/vignettes/sanity_checks.html |only grouper-0.5.0/grouper/vignettes/subgroups_preference.R |only grouper-0.5.0/grouper/vignettes/subgroups_preference.html |only grouper-0.7.3/grouper/DESCRIPTION | 34 grouper-0.7.3/grouper/LICENSE | 4 grouper-0.7.3/grouper/MD5 | 143 grouper-0.7.3/grouper/NAMESPACE | 32 grouper-0.7.3/grouper/NEWS.md | 99 grouper-0.7.3/grouper/R/data.R | 193 - grouper-0.7.3/grouper/R/extract_fns.R | 761 +++- grouper-0.7.3/grouper/R/model_prep.R | 860 ++++ grouper-0.7.3/grouper/R/post_process.R | 309 + grouper-0.7.3/grouper/R/utils-pipe.R | 28 grouper-0.7.3/grouper/R/utils.R |only grouper-0.7.3/grouper/R/zzz.R | 5 grouper-0.7.3/grouper/README.md | 64 grouper-0.7.3/grouper/build/vignette.rds |binary grouper-0.7.3/grouper/data/multirole_demand_ex001.rda |only grouper-0.7.3/grouper/data/multirole_prefmat_ex001.rda |only grouper-0.7.3/grouper/data/multirole_students_ex001.rda |only grouper-0.7.3/grouper/inst/doc/a-related-work.R | 12 grouper-0.7.3/grouper/inst/doc/a-related-work.Rmd | 366 +- grouper-0.7.3/grouper/inst/doc/a-related-work.html | 1062 +++--- grouper-0.7.3/grouper/inst/doc/b-diversity-skill.R | 12 grouper-0.7.3/grouper/inst/doc/b-diversity-skill.Rmd | 272 - grouper-0.7.3/grouper/inst/doc/b-diversity-skill.html | 803 ++-- grouper-0.7.3/grouper/inst/doc/c-subgroups-preference.R | 12 grouper-0.7.3/grouper/inst/doc/c-subgroups-preference.Rmd | 238 - grouper-0.7.3/grouper/inst/doc/c-subgroups-preference.html | 766 ++-- grouper-0.7.3/grouper/inst/doc/d-sanity-checks.R | 533 ++- grouper-0.7.3/grouper/inst/doc/d-sanity-checks.Rmd | 839 +++- grouper-0.7.3/grouper/inst/doc/d-sanity-checks.html | 1749 ++++++---- grouper-0.7.3/grouper/inst/doc/e-phd-workload.R |only grouper-0.7.3/grouper/inst/doc/e-phd-workload.Rmd |only grouper-0.7.3/grouper/inst/doc/e-phd-workload.html |only grouper-0.7.3/grouper/inst/extdata/dba_params_ex001.yml | 11 grouper-0.7.3/grouper/inst/extdata/dba_params_ex003.yml | 11 grouper-0.7.3/grouper/inst/extdata/dba_params_ex004.yml | 11 grouper-0.7.3/grouper/inst/extdata/pba_params_ex002.yml | 13 grouper-0.7.3/grouper/inst/shiny/dbaWebApp/app.R | 544 +-- grouper-0.7.3/grouper/inst/shiny/dbaWebApp/dba_gc_ex001.csv | 10 grouper-0.7.3/grouper/inst/shiny/dbaWebApp/utils.R | 77 grouper-0.7.3/grouper/inst/shiny/grouperWebApp |only grouper-0.7.3/grouper/inst/shiny/pbaWebApp/app.R | 460 +- grouper-0.7.3/grouper/inst/shiny/pbaWebApp/pba_gc_ex002.csv | 18 grouper-0.7.3/grouper/inst/shiny/pbaWebApp/pba_prefmat_ex002.csv | 10 grouper-0.7.3/grouper/inst/shiny/phdWebApp |only grouper-0.7.3/grouper/man/assign_groups.Rd | 78 grouper-0.7.3/grouper/man/assign_job.Rd |only grouper-0.7.3/grouper/man/compute_diversity.Rd |only grouper-0.7.3/grouper/man/convert_pref_mat.Rd |only grouper-0.7.3/grouper/man/dba_gc_ex001.Rd | 55 grouper-0.7.3/grouper/man/dba_gc_ex003.Rd | 13 grouper-0.7.3/grouper/man/dba_gc_ex004.Rd | 13 grouper-0.7.3/grouper/man/extract_info.Rd |only grouper-0.7.3/grouper/man/extract_multirole_info.Rd |only grouper-0.7.3/grouper/man/extract_params_yaml.Rd | 80 grouper-0.7.3/grouper/man/extract_phd_info.Rd |only grouper-0.7.3/grouper/man/extract_student_info.Rd | 183 - grouper-0.7.3/grouper/man/get_group_pref_score.Rd |only grouper-0.7.3/grouper/man/multirole_demand_ex001.Rd |only grouper-0.7.3/grouper/man/multirole_prefmat_ex001.Rd |only grouper-0.7.3/grouper/man/multirole_students_ex001.Rd |only grouper-0.7.3/grouper/man/pba_gc_ex002.Rd | 51 grouper-0.7.3/grouper/man/pba_prefmat_ex002.Rd | 48 grouper-0.7.3/grouper/man/pipe.Rd | 40 grouper-0.7.3/grouper/man/prepare_diversity_model.Rd |only grouper-0.7.3/grouper/man/prepare_model.Rd | 80 grouper-0.7.3/grouper/man/prepare_multirole_model.Rd |only grouper-0.7.3/grouper/man/prepare_phd_model.Rd |only grouper-0.7.3/grouper/man/prepare_preference_model.Rd |only grouper-0.7.3/grouper/man/solve_assignment.Rd |only grouper-0.7.3/grouper/man/summary_dba.Rd |only grouper-0.7.3/grouper/man/summary_pba.Rd |only grouper-0.7.3/grouper/tests |only grouper-0.7.3/grouper/vignettes/a-related-work.Rmd | 366 +- grouper-0.7.3/grouper/vignettes/b-diversity-skill.Rmd | 272 - grouper-0.7.3/grouper/vignettes/c-subgroups-preference.Rmd | 238 - grouper-0.7.3/grouper/vignettes/d-sanity-checks.Rmd | 839 +++- grouper-0.7.3/grouper/vignettes/e-phd-workload.Rmd |only grouper-0.7.3/grouper/vignettes/references.bib | 98 86 files changed, 7832 insertions(+), 4983 deletions(-)
Title: Parsing Glycan Structure Text Representations
Description: Provides functions to parse glycan structure text representations
into 'glyrepr' glycan structures. Currently, it supports StrucGP-style,
pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, IUPAC-compact,
WURCS, LINUCS, Linear Code, GlycoCT, and KCF format. It also provides an automatic parser
to detect the format and parse the structure string.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyparse versions 0.7.0 dated 2026-07-06 and 0.7.1 dated 2026-07-08
DESCRIPTION | 8 +-- MD5 | 13 +++--- NEWS.md | 6 ++ R/struc-parser-wrapper.R | 60 +++++++++++++++-------------- inst/doc/glyparse.html | 9 +--- tests/testthat/test-parse-glycam-iupac.R | 10 +++- tests/testthat/test-performance.R | 22 ++++++++++ tests/testthat/test-struc-parser-wrapper.R |only 8 files changed, 83 insertions(+), 45 deletions(-)
Title: Partitioning Using Deletion, Substitution, and Addition Moves
Description: A novel tool for generating a piecewise
constant estimation list of increasingly complex predictors
based on an intensive and comprehensive search over the entire
covariate space.
Author: Annette Molinaro [aut, cre],
Adam Olshen [aut],
Karen Lostritto [aut],
Gregory Ryslik [aut],
Steve Weston [aut]
Maintainer: Annette Molinaro <annette.molinaro@ucsf.edu>
Diff between partDSA versions 0.9.14 dated 2017-01-05 and 0.9.15 dated 2026-07-08
DESCRIPTION | 31 +++++++++++++++-------- MD5 | 42 +++++++++++++++++++------------ NEWS.md |only R/addon.R | 14 ++++++---- R/algAlone2.R | 17 ++++++++---- R/code.2.R | 4 ++ R/main.R | 39 +++++++++++++++++----------- R/newfunctions-Survival.R | 28 ++++++++++++++++++++ inst/CITATION | 62 +++++++++++++++++++++++----------------------- inst/doc/partDSAvig.R | 16 +++++------ inst/doc/partDSAvig.Rnw | 11 ++++++++ inst/doc/partDSAvig.pdf |binary inst/doc/survival.R | 17 +++++------- inst/doc/survival.Rnw | 12 ++++++++ inst/doc/survival.pdf |binary tests |only vignettes/partDSAvig.Rnw | 11 ++++++++ vignettes/refs.bib | 2 - vignettes/survival.Rnw | 12 ++++++++ 19 files changed, 213 insertions(+), 105 deletions(-)
Title: Advanced Continuous Glucose Monitoring Analysis with
High-Performance C++ Backend
Description: Tools for advanced analysis of continuous glucose monitoring (CGM)
time-series, implementing GRID (Glucose Rate Increase Detector) and GRID-based
algorithms for postprandial peak detection, and detection of hypoglycemic and
hyperglycemic episodes (Levels 1/2/Extended) aligned with international consensus
CGM metrics. Core algorithms are implemented in optimized C++ using 'Rcpp' to
provide accurate and fast analysis on large datasets.
Author: Sang Ho Park [aut, cre],
Rosa Oh [aut, ctb],
Sang-Man Jin [aut, ctb]
Maintainer: Sang Ho Park <shstat1729@gmail.com>
Diff between cgmguru versions 1.1.0 dated 2026-06-08 and 1.2.0 dated 2026-07-08
cgmguru-1.1.0/cgmguru/inst/doc/cgmguru.pdf |only cgmguru-1.1.0/cgmguru/vignettes/cgmguru.html |only cgmguru-1.2.0/cgmguru/DESCRIPTION | 9 cgmguru-1.2.0/cgmguru/MD5 | 69 + cgmguru-1.2.0/cgmguru/NAMESPACE | 4 cgmguru-1.2.0/cgmguru/NEWS.md | 49 + cgmguru-1.2.0/cgmguru/R/RcppExports.R | 20 cgmguru-1.2.0/cgmguru/R/cgmguru-functions-docs.R | 252 ++++++ cgmguru-1.2.0/cgmguru/R/cgmguru-package.R | 3 cgmguru-1.2.0/cgmguru/R/function_overrides.R | 6 cgmguru-1.2.0/cgmguru/R/input_validation.R | 30 cgmguru-1.2.0/cgmguru/R/rebound_events.R |only cgmguru-1.2.0/cgmguru/R/variability_metrics.R |only cgmguru-1.2.0/cgmguru/build/partial.rdb |only cgmguru-1.2.0/cgmguru/build/vignette.rds |binary cgmguru-1.2.0/cgmguru/inst/doc/cgmguru.R | 203 +++++ cgmguru-1.2.0/cgmguru/inst/doc/cgmguru.Rmd | 386 +++++++++- cgmguru-1.2.0/cgmguru/inst/doc/cgmguru.html |only cgmguru-1.2.0/cgmguru/inst/doc/detect_all_events.html | 104 +- cgmguru-1.2.0/cgmguru/inst/doc/examples.html | 165 +--- cgmguru-1.2.0/cgmguru/inst/doc/excursion.html | 2 cgmguru-1.2.0/cgmguru/inst/doc/grid.html | 4 cgmguru-1.2.0/cgmguru/inst/doc/intro.html | 60 - cgmguru-1.2.0/cgmguru/man/cgmguru-package.Rd | 3 cgmguru-1.2.0/cgmguru/man/conga_rcpp.Rd |only cgmguru-1.2.0/cgmguru/man/detect_all_events.Rd | 44 - cgmguru-1.2.0/cgmguru/man/excursion.Rd | 9 cgmguru-1.2.0/cgmguru/man/mage_rcpp.Rd |only cgmguru-1.2.0/cgmguru/man/modd_rcpp.Rd |only cgmguru-1.2.0/cgmguru/man/rebound_events.Rd |only cgmguru-1.2.0/cgmguru/src/RcppExports.cpp | 79 +- cgmguru-1.2.0/cgmguru/src/detect_all_events.cpp | 186 ++++ cgmguru-1.2.0/cgmguru/src/excursion.cpp | 111 ++ cgmguru-1.2.0/cgmguru/src/rebound_events.cpp |only cgmguru-1.2.0/cgmguru/src/rebound_events_core.h |only cgmguru-1.2.0/cgmguru/src/variability_metrics.cpp |only cgmguru-1.2.0/cgmguru/tests/testthat/test-events.R | 40 + cgmguru-1.2.0/cgmguru/tests/testthat/test-grid_maxima_excursion.R | 37 cgmguru-1.2.0/cgmguru/tests/testthat/test-iglu-episode-parity.R | 3 cgmguru-1.2.0/cgmguru/tests/testthat/test-rebound-events.R |only cgmguru-1.2.0/cgmguru/tests/testthat/test-sensor-wear.R | 79 +- cgmguru-1.2.0/cgmguru/tests/testthat/test-variability-metrics.R |only cgmguru-1.2.0/cgmguru/vignettes/cgmguru.Rmd | 386 +++++++++- 43 files changed, 2020 insertions(+), 323 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-04-23 0.4.6
2025-12-12 0.4.5
2025-12-10 0.4.3
2025-12-02 0.4.2
2023-08-21 0.4.1
2023-07-19 0.4.0
2020-12-17 0.3.2
2020-04-06 0.2.2
2020-01-20 0.2.1
2020-01-19 0.2.0
2019-07-03 0.1.3
2018-09-30 0.1.2
2018-09-27 0.1.1
2018-06-15 0.1.0
Title: Simplex Regression Models with Parametric or Fixed Mean Link
Functions
Description: Fits and analyzes simplex regression models with either
fixed or parametric mean link functions. Implements the simplex
probability density function, cumulative distribution function,
quantile function, random number generation, and variance evaluation.
Offers several fixed and parametric link functions for the mean
submodel, tools for residual analysis and diagnostic plotting,
hypothesis testing procedures, and influence measures such as Cook's
distance and leverage (hat values). Includes the Scout Score (SS)
criterion for model selection, enabling comprehensive inference and
diagnostic analysis within the simplex regression framework.
For more details see Barndorff-Nielsen and Jorgensen (1991)
<doi:10.1016/0047-259X(91)90008-P> and Justino and Cribari-Neto (2026)
<doi:10.1016/j.apm.2025.116713>.
Author: Maria Eduarda da Cruz Justino [aut, cre] ,
Francisco Cribari-Neto [ctb, ths]
Maintainer: Maria Eduarda da Cruz Justino <eueduardacruz@gmail.com>
Diff between SimplexRegression versions 0.1.3 dated 2026-06-30 and 0.1.4 dated 2026-07-08
DESCRIPTION | 10 +- MD5 | 75 ++++++++------- NEWS.md | 12 ++ R/abortionopposition.R |only R/biomass.R | 38 ++++--- R/relativehumidity.R | 40 ++++---- R/simplexreg_fit.R | 2 R/simplexreg_influence.R | 65 ++++++++----- R/simplexreg_links.R | 18 ++- R/simplexreg_methods.R | 47 +++------ R/simplexreg_penalized_ic.R | 25 ++++- R/simplexreg_plots.R | 32 +++++- R/simplexreg_press.R | 8 + R/simplexreg_residuals.R | 4 R/simplexreg_scoretest.R | 2 R/simplexreg_sscriteria.R | 22 +++- data/AbortionOpposition.rda |only data/Biomass.rda |binary data/RelativeHumidity.rda |binary inst/WORDLIST | 5 - inst/doc/relative-humidity.R | 38 +++---- inst/doc/relative-humidity.Rmd | 76 +++++++-------- inst/doc/relative-humidity.html | 178 ++++++++++++++++++------------------- man/AbortionOpposition.Rd |only man/Biomass.Rd | 37 ++++--- man/RelativeHumidity.Rd | 40 ++++---- man/diag.distances.Rd | 15 +-- man/diag.im.Rd | 42 +++++--- man/dispersion_links.Rd | 9 + man/fixed_mean_links.Rd | 3 man/halfnormal.plot.Rd | 2 man/local.influence.Rd | 3 man/parametric_mean_links.Rd | 6 - man/penalized.ic.Rd | 15 ++- man/penalized.ss.Rd | 14 ++ man/plot.simplexregression.Rd | 17 ++- man/press.Rd | 8 + man/residuals.simplexregression.Rd | 4 man/scoretest.Rd | 2 vignettes/relative-humidity.Rmd | 76 +++++++-------- 40 files changed, 558 insertions(+), 432 deletions(-)
More information about SimplexRegression at CRAN
Permanent link
Title: Simulating Oncology Trials using an Illness-Death Model
Description: Based on the illness-death model a large number of clinical
trials with oncology endpoints progression-free survival (PFS) and
overall survival (OS) can be simulated, see Meller, Beyersmann and
Rufibach (2019) <doi:10.1002/sim.8295>. The simulation set-up allows
for random and event-driven censoring, an arbitrary number of
treatment arms, staggered study entry and drop-out. Exponentially,
Weibull and piecewise exponentially distributed survival times can be
generated. The correlation between PFS and OS can be calculated.
Author: Alexandra Erdmann [aut],
Daniel Sabanes Bove [aut, cre],
Kaspar Rufibach [aut],
Holger Loewe [aut],
F. Hoffmann-La Roche AG [cph, fnd],
University of Ulm [cph, fnd]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between simIDM versions 0.1.0 dated 2023-12-11 and 0.1.1 dated 2026-07-08
simIDM-0.1.0/simIDM/man/figures/logo-large.png |only simIDM-0.1.0/simIDM/man/figures/logo.png |only simIDM-0.1.1/simIDM/DESCRIPTION | 20 simIDM-0.1.1/simIDM/MD5 | 27 simIDM-0.1.1/simIDM/NEWS.md | 10 simIDM-0.1.1/simIDM/R/corPFSOS.R | 3 simIDM-0.1.1/simIDM/build/vignette.rds |binary simIDM-0.1.1/simIDM/inst/doc/correlation.html | 380 ++++-- simIDM-0.1.1/simIDM/inst/doc/pwc_survival.html | 138 +- simIDM-0.1.1/simIDM/inst/doc/quickstart.html | 1321 +++++++++--------------- simIDM-0.1.1/simIDM/inst/doc/trialplanning.R | 2 simIDM-0.1.1/simIDM/inst/doc/trialplanning.Rmd | 2 simIDM-0.1.1/simIDM/inst/doc/trialplanning.html | 575 ++++++---- simIDM-0.1.1/simIDM/man/figures/logo.svg |only simIDM-0.1.1/simIDM/man/simIDM-package.Rd | 7 simIDM-0.1.1/simIDM/vignettes/trialplanning.Rmd | 2 16 files changed, 1235 insertions(+), 1252 deletions(-)
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.10.0 dated 2026-06-08 and 1.10.1 dated 2026-07-08
DESCRIPTION | 12 +++--- MD5 | 58 ++++++++++++++++---------------- NEWS.md | 17 ++++++++- R/appDependencies.R | 12 +++--- R/appMetadata.R | 6 +++ R/auth.R | 6 +-- R/bundleFiles.R | 2 - R/bundlePackageRenv.R | 43 +++++++++++++++++------ R/client.R | 2 - R/configureApp.R | 2 - R/deployApp.R | 6 +-- R/deployments.R | 2 - R/envvars.R | 2 - R/http.R | 27 +++++++------- R/usage.R | 10 ++--- man/accountUsage.Rd | 4 +- man/appDependencies.Rd | 12 +++--- man/configureApp.Rd | 2 - man/deployApp.Rd | 4 +- man/deploySite.Rd | 2 - man/deployments.Rd | 2 - man/listAccountEnvVars.Rd | 2 - man/listDeploymentFiles.Rd | 2 - man/showMetrics.Rd | 2 - man/showUsage.Rd | 4 +- tests/testthat/_snaps/deployApp.md | 2 - tests/testthat/test-appMetadata.R | 18 +++++++++ tests/testthat/test-bundlePackage.R | 12 ++++-- tests/testthat/test-bundlePackageRenv.R | 57 +++++++++++++++++++++++++++++++ tests/testthat/test-writeManifest.R | 4 +- 30 files changed, 227 insertions(+), 109 deletions(-)
Title: A Tool for 'Covariate'-Sensitive Longitudinal Analysis on
'omics' Data
Description: This tool takes longitudinal dataset as input and analyzes if there is significant
change of the features over time (a proxy for treatments), while detects and controls
for 'covariates' simultaneously. 'LongDat' is able to take in several data types as input,
including count, proportion, binary, ordinal and continuous data. The output table contains
p values, effect sizes and 'covariates' of each feature, making the downstream analysis easy.
Author: Chia-Yu Chen [aut, cre] ,
Sofia Forslund [ctb]
Maintainer: Chia-Yu Chen <jessica821112@gmail.com>
Diff between LongDat versions 1.1.3 dated 2024-11-18 and 1.1.4 dated 2026-07-08
DESCRIPTION | 15 MD5 | 22 - NEWS.md | 3 build/vignette.rds |binary inst/doc/LongDat_cont_tutorial.R | 2 inst/doc/LongDat_cont_tutorial.Rmd | 2 inst/doc/LongDat_cont_tutorial.html | 560 ++++++++++++--------------------- inst/doc/LongDat_disc_tutorial.R | 2 inst/doc/LongDat_disc_tutorial.Rmd | 2 inst/doc/LongDat_disc_tutorial.html | 605 +++++++++++++----------------------- vignettes/LongDat_cont_tutorial.Rmd | 2 vignettes/LongDat_disc_tutorial.Rmd | 2 12 files changed, 479 insertions(+), 738 deletions(-)
Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr'
and the piping syntax from 'magrittr'. Function 'kable()' is a light weight
table generator coming from 'knitr'. This package simplifies the way to
manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows
users to construct complex tables and customize styles using a readable
syntax.
Author: Hao Zhu [aut, cre] ,
Thomas Travison [ctb],
Timothy Tsai [ctb],
Will Beasley [ctb],
Yihui Xie [ctb],
GuangChuang Yu [ctb],
Stephane Laurent [ctb],
Rob Shepherd [ctb],
Yoni Sidi [ctb],
Brian Salzer [ctb],
George Gui [ctb],
Yeliang Fan [ctb],
Duncan Mu [...truncated...]
Maintainer: Hao Zhu <haozhu233@gmail.com>
Diff between kableExtra versions 1.4.0 dated 2024-01-24 and 1.4.1 dated 2026-07-08
DESCRIPTION | 12 MD5 | 254 +++++- R/add_header_above.R | 65 + R/add_indent.R | 7 R/cell_spec.R | 29 R/collapse_rows.R | 54 + R/column_spec.R | 64 - R/footnote.R | 97 ++ R/group_rows.R | 60 + R/header_separate.R | 7 R/kableExtra-package.R | 5 R/kable_as_image.R | 2 R/kable_styling.R | 22 R/kbl.R | 10 R/landscape.R | 3 R/linebreak.R | 14 R/magic_mirror.R | 46 - R/remove_column.R | 8 R/row_spec.R | 72 + R/save_kable.R | 28 R/scroll_box.R | 6 R/spec_tools.R | 3 R/util.R | 116 ++- README.md | 10 build/vignette.rds |binary inst/NEWS.md | 86 ++ inst/doc/awesome_table_in_html.R | 40 - inst/doc/awesome_table_in_html.Rmd | 8 inst/doc/awesome_table_in_html.html | 641 +++++++++-------- inst/doc/awesome_table_in_pdf.R | 74 + inst/doc/awesome_table_in_pdf.Rmd | 23 inst/doc/awesome_table_in_pdf.pdf |binary inst/doc/best_practice_for_newline_in_latex_table.Rmd | 3 inst/doc/best_practice_for_newline_in_latex_table.pdf |binary inst/doc/legacy_features.html | 4 inst/doc/use_kable_in_shiny.R | 79 +- inst/doc/use_kable_in_shiny.Rmd | 1 inst/doc/use_kable_in_shiny.html | 1 inst/rmarkdown/test_row_spec.Rmd | 3 inst/rmarkdown/test_row_spec.pdf |binary man/add_header_above.Rd | 22 man/cell_spec.Rd | 9 man/collapse_rows.Rd | 4 man/footnote.Rd | 4 man/group_rows.Rd | 25 man/kableExtra-package.Rd | 33 man/kableExtra_latex_packages.Rd | 6 man/kable_styling.Rd | 6 man/kbl.Rd | 12 man/linebreak.Rd | 10 man/scroll_box.Rd | 3 man/use_latex_packages.Rd | 2 vignettes/awesome_table_in_html.Rmd | 8 vignettes/awesome_table_in_pdf.Rmd | 23 vignettes/awesome_table_in_pdf_files |only vignettes/best_practice_for_newline_in_latex_table.Rmd | 3 vignettes/use_kable_in_shiny.Rmd | 1 57 files changed, 1441 insertions(+), 687 deletions(-)
Title: Remedy the Violation of the Proportional Hazards Assumption of
Cox Regression
Description: Remedying proportional hazards
assumption violations of a Cox proportional hazards model using
stepwise changepoint and time-varying coefficient methods based on
Cox (1972) <doi:10.1111/j.2517-6161.1972.tb00899.x> and Grambsch
and Therneau (1994) <doi:10.1093/biomet/81.3.515>.
Author: Hamin Kim [aut, cre]
Maintainer: Hamin Kim <siru9170@naver.com>
Diff between cox.rvph versions 0.1.1 dated 2026-06-09 and 0.1.2 dated 2026-07-08
DESCRIPTION | 6 - MD5 | 6 - R/cox.rvph.R | 275 +++++++++++++++++++++++++++++++++++--------------------- man/cox.rvph.Rd | 49 ++++++--- 4 files changed, 212 insertions(+), 124 deletions(-)
Title: Clean and Harmonise 'Malawi Integrated Household Survey' Data
Description: An offline suite of tools to clean, aggregate, and harmonise data
from the 'Malawi Integrated Household Survey' ('IHS'). Provides crop-specific
unit conversions, stratified winsorization, and automatic cross-round harmonisation
for complex survey designs.
Author: Vitumbiko Kayuni [aut, cre]
Maintainer: Vitumbiko Kayuni <vitumbikokayuni@gmail.com>
Diff between ihsMW versions 0.2.1 dated 2026-06-04 and 1.0.0 dated 2026-07-08
DESCRIPTION | 9 MD5 | 56 NAMESPACE | 5 NEWS.md | 72 R/ihs_crosswalk_check.R | 17 R/ihs_deflate.R |only R/ihs_merge.R |only R/ihs_panel_ids.R |only R/ihs_report.R |only R/ihs_svydesign.R |only R/zzz.R | 3 README.md | 88 build/vignette.rds |binary inst/doc/getting-started.R | 89 inst/doc/getting-started.Rmd | 149 inst/doc/getting-started.html | 234 inst/doc/harmonisation.R | 51 inst/doc/harmonisation.Rmd | 125 inst/doc/harmonisation.html | 214 inst/doc/survey-weights.R | 70 inst/doc/survey-weights.Rmd | 131 inst/doc/survey-weights.html | 257 inst/extdata/ihs_crosswalk.csv |11660 ++++++++++++++++++------------------ inst/extdata/mw_cpi_annual.csv |only man/ihs_deflate.Rd |only man/ihs_merge.Rd |only man/ihs_panel_ids.Rd |only man/ihs_report.Rd |only man/ihs_svydesign.Rd |only tests/testthat/test-ihs_deflate.R |only tests/testthat/test-ihs_merge.R |only tests/testthat/test-ihs_panel_ids.R |only tests/testthat/test-ihs_report.R |only tests/testthat/test-ihs_svydesign.R |only vignettes/getting-started.Rmd | 149 vignettes/harmonisation.Rmd | 125 vignettes/survey-weights.Rmd | 131 37 files changed, 6883 insertions(+), 6752 deletions(-)
Title: Functions and Datasets for Math Used in School
Description: Contains functions and datasets for math taught in school. A main focus is set to prime-calculation.
Author: Joerg grosse Schlarmann [aut, cre]
Maintainer: Joerg grosse Schlarmann <schlarmann@produnis.de>
Diff between schoolmath versions 0.4.2 dated 2023-08-21 and 0.5.0 dated 2026-07-07
schoolmath-0.4.2/schoolmath/man/is.decimal.Rd |only schoolmath-0.4.2/schoolmath/man/is.even.Rd |only schoolmath-0.4.2/schoolmath/man/is.negative.Rd |only schoolmath-0.4.2/schoolmath/man/is.odd.Rd |only schoolmath-0.4.2/schoolmath/man/is.positive.Rd |only schoolmath-0.4.2/schoolmath/man/is.real.positive.Rd |only schoolmath-0.4.2/schoolmath/man/is.whole.Rd |only schoolmath-0.5.0/schoolmath/DESCRIPTION | 22 schoolmath-0.5.0/schoolmath/MD5 | 40 - schoolmath-0.5.0/schoolmath/NAMESPACE | 9 schoolmath-0.5.0/schoolmath/NEWS.md | 6 schoolmath-0.5.0/schoolmath/R/RcppExports.R |only schoolmath-0.5.0/schoolmath/R/datasets.R | 8 schoolmath-0.5.0/schoolmath/R/functions.R | 764 -------------------- schoolmath-0.5.0/schoolmath/R/zzz.R |only schoolmath-0.5.0/schoolmath/data/primlist.rda |binary schoolmath-0.5.0/schoolmath/man/cancel.fraction.Rd | 4 schoolmath-0.5.0/schoolmath/man/decimal2fraction.Rd | 2 schoolmath-0.5.0/schoolmath/man/is.prim.Rd | 14 schoolmath-0.5.0/schoolmath/man/primes.Rd | 7 schoolmath-0.5.0/schoolmath/man/primlist.Rd | 8 schoolmath-0.5.0/schoolmath/src |only 22 files changed, 95 insertions(+), 789 deletions(-)
Title: Bayesian Quantile Regression Models for Complex Survey Data
Analysis
Description: Provides Bayesian quantile regression models for complex survey data
under informative sampling using survey-weighted estimators. Both single- and
multiple-output models are supported. To accelerate computation, all algorithms
are implemented in 'C++' using 'Rcpp', 'RcppArmadillo', and 'RcppEigen', and
are called from 'R'. See Nascimento and Gonçalves (2024) <doi:10.1093/jssam/smae015>
and Nascimento and Gonçalves (2025, in press).
Author: Tomas Rodriguez Taborda [aut, cre],
Johnatan Cardona Jimenez [aut],
Marcus L. Nascimento [aut],
Kelly Cristina Mota Goncalves [aut]
Maintainer: Tomas Rodriguez Taborda <torodriguezt@unal.edu.co>
Diff between bayesQRsurvey versions 0.2.2 dated 2026-04-06 and 0.3.0 dated 2026-07-07
bayesQRsurvey-0.2.2/bayesQRsurvey/NEWS.md |only bayesQRsurvey-0.3.0/bayesQRsurvey/DESCRIPTION | 12 - bayesQRsurvey-0.3.0/bayesQRsurvey/MD5 | 27 +- bayesQRsurvey-0.3.0/bayesQRsurvey/R/RcppExports.R | 4 bayesQRsurvey-0.3.0/bayesQRsurvey/R/bqr.svy.R | 96 +++++--- bayesQRsurvey-0.3.0/bayesQRsurvey/R/mo.bqr.svy.R | 7 bayesQRsurvey-0.3.0/bayesQRsurvey/R/summary_bqr_svy.R | 144 ++++++------ bayesQRsurvey-0.3.0/bayesQRsurvey/man/bqr.svy.Rd | 10 bayesQRsurvey-0.3.0/bayesQRsurvey/man/mo.bqr.svy.Rd | 7 bayesQRsurvey-0.3.0/bayesQRsurvey/src/EM_BWQR_AL_MO.cpp | 25 -- bayesQRsurvey-0.3.0/bayesQRsurvey/src/MCMC_BWQR_AL.cpp | 18 - bayesQRsurvey-0.3.0/bayesQRsurvey/src/MCMC_BWQR_AP.cpp | 182 ++++++++++------ bayesQRsurvey-0.3.0/bayesQRsurvey/src/MCMC_BWQR_SL.cpp | 60 ++--- bayesQRsurvey-0.3.0/bayesQRsurvey/src/RcppExports.cpp | 9 bayesQRsurvey-0.3.0/bayesQRsurvey/src/wrappers_bwqr.cpp | 34 +- 15 files changed, 352 insertions(+), 283 deletions(-)
Title: Publication-Ready Forest Plots with 'ggplot2'
Description: Transform model coefficients into flexible forest
plots using 'ggplot2'. Provides helpers to standardize
coefficient data from a range of modelling workflows and render
publication-ready forest plots with a consistent interface.
Author: Carson Richardson [aut, cre, cph]
Maintainer: Carson Richardson <carson.richardson@outlook.com>
Diff between ggforestplotR versions 0.2.2 dated 2026-06-05 and 0.3.0 dated 2026-07-07
ggforestplotR-0.2.2/ggforestplotR/tests/testthat/test-ggforestplot.R |only ggforestplotR-0.3.0/ggforestplotR/DESCRIPTION | 10 ggforestplotR-0.3.0/ggforestplotR/MD5 | 46 - ggforestplotR-0.3.0/ggforestplotR/NAMESPACE | 2 ggforestplotR-0.3.0/ggforestplotR/NEWS.md | 101 +- ggforestplotR-0.3.0/ggforestplotR/R/add_forest_table.R | 144 --- ggforestplotR-0.3.0/ggforestplotR/R/add_split_table.R | 129 --- ggforestplotR-0.3.0/ggforestplotR/R/bind_forest_models.R |only ggforestplotR-0.3.0/ggforestplotR/R/ggforestplot.R | 369 +++++++-- ggforestplotR-0.3.0/ggforestplotR/R/ggplot_add_scales.R | 99 ++ ggforestplotR-0.3.0/ggforestplotR/R/tidy_forest_model.R | 80 + ggforestplotR-0.3.0/ggforestplotR/R/utils.R | 406 ++++++---- ggforestplotR-0.3.0/ggforestplotR/README.md | 10 ggforestplotR-0.3.0/ggforestplotR/inst/doc/ggforestplotR-plot-customization.R | 17 ggforestplotR-0.3.0/ggforestplotR/inst/doc/ggforestplotR-plot-customization.Rmd | 67 + ggforestplotR-0.3.0/ggforestplotR/inst/doc/ggforestplotR-plot-customization.html | 20 ggforestplotR-0.3.0/ggforestplotR/man/add_forest_table.Rd | 27 ggforestplotR-0.3.0/ggforestplotR/man/add_split_table.Rd | 37 ggforestplotR-0.3.0/ggforestplotR/man/bind_forest_models.Rd |only ggforestplotR-0.3.0/ggforestplotR/man/ggforestplot.Rd | 17 ggforestplotR-0.3.0/ggforestplotR/man/tidy_forest_model.Rd | 7 ggforestplotR-0.3.0/ggforestplotR/tests/testthat/helper-forest-data.R |only ggforestplotR-0.3.0/ggforestplotR/tests/testthat/test-bind_forest_models.R |only ggforestplotR-0.3.0/ggforestplotR/tests/testthat/test-forest-table.R |only ggforestplotR-0.3.0/ggforestplotR/tests/testthat/test-ggforestplot-core.R |only ggforestplotR-0.3.0/ggforestplotR/tests/testthat/test-split-table.R |only ggforestplotR-0.3.0/ggforestplotR/tests/testthat/test-tidy_forest_model.R | 68 + ggforestplotR-0.3.0/ggforestplotR/vignettes/ggforestplotR-plot-customization.Rmd | 67 + 28 files changed, 1126 insertions(+), 597 deletions(-)
Title: Open Trade Statistics API Wrapper and Utility Program
Description: Access 'Open Trade Statistics' API from R to download
international trade data.
Author: Mauricio Vargas [aut, cre, cph] ,
Joshua Kunst [ctb] ,
Alexey Kravchenko [ctb] ,
Emma Mendelsohn [ctb] ,
Daniela de los Santos [ctb] ,
Emily Riederer [rev] ,
Mark Padgham [rev] ,
Amanda Dobbyn [rev] ,
Jorge Cimentada [rev] ,
UN Comtrade [dtc],
The Wo [...truncated...]
Maintainer: Mauricio Vargas <m.vargas.sepulveda@gmail.com>
Diff between tradestatistics versions 6.0.0 dated 2025-09-22 and 7.0.0 dated 2026-07-07
tradestatistics-6.0.0/tradestatistics/R/ots_gdp_deflator_adjustment.R |only tradestatistics-6.0.0/tradestatistics/data/ots_commodities.rda |only tradestatistics-6.0.0/tradestatistics/data/ots_commodities_short.rda |only tradestatistics-6.0.0/tradestatistics/data/ots_gdp_deflator.rda |only tradestatistics-6.0.0/tradestatistics/man/ots_commodities.Rd |only tradestatistics-6.0.0/tradestatistics/man/ots_commodities_short.Rd |only tradestatistics-6.0.0/tradestatistics/man/ots_commodity_code.Rd |only tradestatistics-6.0.0/tradestatistics/man/ots_gdp_deflator.Rd |only tradestatistics-6.0.0/tradestatistics/man/ots_gdp_deflator_adjustment.Rd |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yr.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yr_apple.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrp.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc_cache.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc_fish.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc_fish_3codes.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc_fish_chapter.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc_vegetables_chapter.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2002_yrpc_wheat.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2004_yr.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_arg_2004_yrpc.yml |only tradestatistics-6.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_yug_2002_yrp.yml |only tradestatistics-6.0.0/tradestatistics/tests/testthat/test-ots_inflation_adjustment.R |only tradestatistics-7.0.0/tradestatistics/DESCRIPTION | 10 tradestatistics-7.0.0/tradestatistics/MD5 | 84 - tradestatistics-7.0.0/tradestatistics/NAMESPACE | 6 tradestatistics-7.0.0/tradestatistics/NEWS.md | 5 tradestatistics-7.0.0/tradestatistics/R/ots_cache.R | 2 tradestatistics-7.0.0/tradestatistics/R/ots_create_tidy_data.R | 531 +++------- tradestatistics-7.0.0/tradestatistics/R/ots_read_from_api.R | 76 + tradestatistics-7.0.0/tradestatistics/R/ots_strings_processing.R | 212 +-- tradestatistics-7.0.0/tradestatistics/R/tradestatistics-package.R | 91 - tradestatistics-7.0.0/tradestatistics/build/vignette.rds |binary tradestatistics-7.0.0/tradestatistics/data/ots_countries.rda |binary tradestatistics-7.0.0/tradestatistics/data/ots_industries.rda |only tradestatistics-7.0.0/tradestatistics/data/ots_sectors.rda |only tradestatistics-7.0.0/tradestatistics/data/ots_tables.rda |binary tradestatistics-7.0.0/tradestatistics/inst/doc/basic-usage.R | 88 - tradestatistics-7.0.0/tradestatistics/inst/doc/basic-usage.Rmd | 162 --- tradestatistics-7.0.0/tradestatistics/inst/doc/basic-usage.html | 453 ++++---- tradestatistics-7.0.0/tradestatistics/man/ots_countries.Rd | 14 tradestatistics-7.0.0/tradestatistics/man/ots_create_tidy_data.Rd | 51 tradestatistics-7.0.0/tradestatistics/man/ots_create_tidy_data_memoised.Rd | 11 tradestatistics-7.0.0/tradestatistics/man/ots_create_tidy_data_unmemoised.Rd | 11 tradestatistics-7.0.0/tradestatistics/man/ots_industries.Rd |only tradestatistics-7.0.0/tradestatistics/man/ots_industry_code.Rd |only tradestatistics-7.0.0/tradestatistics/man/ots_read_from_api.Rd | 10 tradestatistics-7.0.0/tradestatistics/man/ots_sector_code.Rd |only tradestatistics-7.0.0/tradestatistics/man/ots_sectors.Rd |only tradestatistics-7.0.0/tradestatistics/man/ots_tables.Rd | 6 tradestatistics-7.0.0/tradestatistics/man/tradestatistics-package.Rd | 5 tradestatistics-7.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_2002_1.yml |only tradestatistics-7.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_2002_2.yml |only tradestatistics-7.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_2002_3.yml |only tradestatistics-7.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_2002_4.yml |only tradestatistics-7.0.0/tradestatistics/tests/fixtures/vcr_cassettes/chl_2002_5.yml |only tradestatistics-7.0.0/tradestatistics/tests/testthat/test-ots_country_code.R | 20 tradestatistics-7.0.0/tradestatistics/tests/testthat/test-ots_create_tidy_data.R | 326 ------ tradestatistics-7.0.0/tradestatistics/tests/testthat/test-ots_strings_processing.R | 72 - tradestatistics-7.0.0/tradestatistics/vignettes/basic-usage.Rmd | 162 --- 60 files changed, 856 insertions(+), 1552 deletions(-)
More information about tradestatistics at CRAN
Permanent link
Title: Inference for Panel Partially Observed Markov Processes
Description: Data analysis based on panel partially-observed Markov process (PanelPOMP) models. To implement such models, simulate them and fit them to panel data, 'panelPomp' extends some of the facilities provided for time series data by the 'pomp' package. Implemented methods include filtering (panel particle filtering) and maximum likelihood estimation (Panel Iterated Filtering) as proposed in Breto, Ionides and King (2020) "Panel Data Analysis via Mechanistic Models" <doi:10.1080/01621459.2019.1604367>.
Author: Carles Breto [aut] ,
Edward L. Ionides [aut] ,
Aaron A. King [aut] ,
Jesse Wheeler [aut, cre] ,
Aaron Abkemeier [ctb]
Maintainer: Jesse Wheeler <jesse.wheeler@usu.edu>
Diff between panelPomp versions 1.7.0.0 dated 2025-05-09 and 1.8.0.0 dated 2026-07-07
DESCRIPTION | 12 +++++----- MD5 | 46 +++++++++++++++++++++--------------------- R/panel_designs.R | 46 ++++++++++++++++++++++++++---------------- R/uk_measles.R | 2 - README.md | 4 ++- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS | 7 ++++++ inst/NEWS.Rd | 6 +++++ inst/doc/getting-started.html | 11 ++++++---- man/as.Rd | 2 - man/contacts.Rd | 8 +++---- man/mif2.Rd | 6 ++--- man/panelGompertz.Rd | 8 +++---- man/panelMeasles.Rd | 8 +++---- man/panelPomp-package.Rd | 3 +- man/panelPomp.Rd | 6 ++--- man/panelPomp_methods.Rd | 4 +-- man/panelRandomWalk.Rd | 8 +++---- man/panel_loglik.Rd | 8 +++---- man/pfilter.Rd | 6 ++--- man/uk_measles.Rd | 2 - tests/panel_designs.R | 14 ++++++++++++ tests/panel_designs.Rout.save | 19 +++++++++++++++-- 24 files changed, 148 insertions(+), 88 deletions(-)
Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from different sources but especially Turboveg 2.0. Taxonomic harmonization (given appropriate taxonomic lists, e.g. GermanSL and EuroSL (Euro+Med extended) see <https://eurosl.infinitenature.org>).
Author: Florian Jansen [aut, cre]
Maintainer: Florian Jansen <florian.jansen@uni-rostock.de>
This is a re-admission after prior archival of version 1.9.15 dated 2025-12-01
Diff between vegdata versions 1.9.15 dated 2025-12-01 and 1.9.18 dated 2026-07-07
vegdata-1.9.15/vegdata/R/db_download.R |only vegdata-1.9.15/vegdata/R/sql.R |only vegdata-1.9.15/vegdata/R/src.R |only vegdata-1.9.15/vegdata/man/db_download.Rd |only vegdata-1.9.15/vegdata/man/sql_collect.Rd |only vegdata-1.9.15/vegdata/man/src_vegdata.Rd |only vegdata-1.9.18/vegdata/DESCRIPTION | 25 vegdata-1.9.18/vegdata/MD5 | 84 +- vegdata-1.9.18/vegdata/NAMESPACE | 9 vegdata-1.9.18/vegdata/R/cwm.R | 3 vegdata-1.9.18/vegdata/R/data.R | 2 vegdata-1.9.18/vegdata/R/reShape.veg.R | 5 vegdata-1.9.18/vegdata/R/syntab.R | 362 ++++++++-- vegdata-1.9.18/vegdata/R/tax.child.R | 15 vegdata-1.9.18/vegdata/R/tax.names.R | 88 +- vegdata-1.9.18/vegdata/R/tax.r | 5 vegdata-1.9.18/vegdata/R/tax.reflist.r | 16 vegdata-1.9.18/vegdata/R/taxref_download.R |only vegdata-1.9.18/vegdata/R/taxval.r | 9 vegdata-1.9.18/vegdata/R/tv.home.R | 16 vegdata-1.9.18/vegdata/R/tv.site.R | 2 vegdata-1.9.18/vegdata/R/vegdata-internal.r | 130 --- vegdata-1.9.18/vegdata/R/vegdata-package.R | 2 vegdata-1.9.18/vegdata/R/zzz.R | 5 vegdata-1.9.18/vegdata/build/vignette.rds |binary vegdata-1.9.18/vegdata/data/taxlevels.rda |binary vegdata-1.9.18/vegdata/inst/ChangeLog | 4 vegdata-1.9.18/vegdata/inst/doc/vegdata.Rnw | 8 vegdata-1.9.18/vegdata/inst/doc/vegdata.pdf |binary vegdata-1.9.18/vegdata/inst/extdata/tvdata/Data/elbaue-esveg.xml | 2 vegdata-1.9.18/vegdata/inst/extdata/tvdata/Species/README | 2 vegdata-1.9.18/vegdata/man/TCS.replace.Rd | 2 vegdata-1.9.18/vegdata/man/child.Rd | 2 vegdata-1.9.18/vegdata/man/db_path.Rd | 2 vegdata-1.9.18/vegdata/man/lc.0.Rd | 2 vegdata-1.9.18/vegdata/man/lc.1.Rd | 2 vegdata-1.9.18/vegdata/man/lc.all.Rd | 2 vegdata-1.9.18/vegdata/man/syntab.Rd | 10 vegdata-1.9.18/vegdata/man/taxlevels.Rd | 4 vegdata-1.9.18/vegdata/man/taxname.simpl.Rd | 3 vegdata-1.9.18/vegdata/man/taxref_download.Rd |only vegdata-1.9.18/vegdata/man/tv.home.Rd | 4 vegdata-1.9.18/vegdata/man/tv.site.Rd | 6 vegdata-1.9.18/vegdata/man/vegdata-package.Rd | 7 vegdata-1.9.18/vegdata/man/vegdata.Rd | 2 vegdata-1.9.18/vegdata/vignettes/lib.bib | 13 vegdata-1.9.18/vegdata/vignettes/vegdata.Rnw | 8 47 files changed, 530 insertions(+), 333 deletions(-)
Title: Automated Soil Profile Classification per WRB 2022, 'SiBCS' 5
and USDA Soil Taxonomy 13
Description: Implements deterministic classification keys for the World
Reference Base for Soil Resources 2022 (4th edition) and the Brazilian
System of Soil Classification ('SiBCS', 5th edition). Provides a unified
profile representation with explicit per-attribute provenance, multimodal
extraction from field reports and photos via vision-language models,
spatial priors from 'SoilGrids' and national soil maps, and gap-filling of
soil attributes from Vis-NIR or MIR spectra via the Open Soil Spectral
Library ('OSSL'). The taxonomic key itself is never delegated to a language
model; LLMs are restricted to schema-validated extraction. Each
classification result reports a key trace, a provenance-aware evidence
grade, and ambiguities that further measurement would resolve.
Author: Hugo Rodrigues [aut, cre]
Maintainer: Hugo Rodrigues <rodrigues.machado.hugo@gmail.com>
Diff between soilKey versions 0.9.157 dated 2026-06-30 and 0.9.184 dated 2026-07-07
soilKey-0.9.157/soilKey/inst/shiny/classify_app_pro/R/mod_spatial.R |only soilKey-0.9.184/soilKey/DESCRIPTION | 12 soilKey-0.9.184/soilKey/MD5 | 88 - soilKey-0.9.184/soilKey/NAMESPACE | 4 soilKey-0.9.184/soilKey/NEWS.md | 593 +++++++ soilKey-0.9.184/soilKey/R/class-ClassificationResult.R | 36 soilKey-0.9.184/soilKey/R/key-trace-format.R |only soilKey-0.9.184/soilKey/R/read-pedon-csv.R |only soilKey-0.9.184/soilKey/R/report-assets.R |only soilKey-0.9.184/soilKey/R/report-html.R | 187 +- soilKey-0.9.184/soilKey/R/report-pdf.R | 170 +- soilKey-0.9.184/soilKey/R/spectra-munsell.R | 155 + soilKey-0.9.184/soilKey/R/spectra-preprocess.R | 145 + soilKey-0.9.184/soilKey/README.md | 5 soilKey-0.9.184/soilKey/inst/doc/v09_perfil_embrapa_pt.html | 94 - soilKey-0.9.184/soilKey/inst/examples |only soilKey-0.9.184/soilKey/inst/extdata/perfil_exemplo.csv |only soilKey-0.9.184/soilKey/inst/i18n/report_translations.yaml | 14 soilKey-0.9.184/soilKey/inst/i18n/translations.yaml | 402 ++++ soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_acknowledgements.R |only soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_chat.R |only soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_classify.R | 269 ++- soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_map.R | 838 +++++++--- soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_map_batch.R | 172 +- soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_map_grid.R | 309 +++ soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_pedon.R | 292 ++- soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_photo.R | 228 ++ soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_report.R | 70 soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_settings.R | 134 + soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_spectra.R | 317 ++- soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/mod_uncertainty.R | 281 +++ soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/R/utils_ui.R | 97 + soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/app.R | 242 ++ soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/www/demo_profile.jpg |only soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/www/demo_spectrum.csv |only soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/www/logo.png |only soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/www/soilgrids_wrb_demo.tif |only soilKey-0.9.184/soilKey/inst/shiny/classify_app_pro/www/soilkey.css | 453 ++++- soilKey-0.9.184/soilKey/man/apply_spectral_preprocessing.Rd |only soilKey-0.9.184/soilKey/man/classify_csv.Rd |only soilKey-0.9.184/soilKey/man/key_trace_table.Rd |only soilKey-0.9.184/soilKey/man/predict_munsell_from_spectra.Rd | 21 soilKey-0.9.184/soilKey/man/read_pedon_csv.Rd |only soilKey-0.9.184/soilKey/tests/testthat/test-app-demos-v09167.R |only soilKey-0.9.184/soilKey/tests/testthat/test-key-trace-format-v09165.R |only soilKey-0.9.184/soilKey/tests/testthat/test-read-pedon-csv.R |only soilKey-0.9.184/soilKey/tests/testthat/test-report-assets-v09168.R |only soilKey-0.9.184/soilKey/tests/testthat/test-shiny-pro-servers.R | 5 soilKey-0.9.184/soilKey/tests/testthat/test-spectra-preprocess.R | 66 soilKey-0.9.184/soilKey/tests/testthat/test-v09101-shiny-map.R | 2 soilKey-0.9.184/soilKey/tests/testthat/test-v09158-munsell-whitepoint.R |only soilKey-0.9.184/soilKey/tests/testthat/test-v09174-shiny-map-unified.R |only soilKey-0.9.184/soilKey/tests/testthat/test-v09175-app-reactivity.R |only soilKey-0.9.184/soilKey/tests/testthat/test-v09176-shiny-chat.R |only soilKey-0.9.184/soilKey/tests/testthat/test-v09177-spectra-preproc-app.R |only soilKey-0.9.184/soilKey/tests/testthat/test-v09178-map-fixes.R |only soilKey-0.9.184/soilKey/tests/testthat/test-v09180-uncertainty-group.R |only soilKey-0.9.184/soilKey/tests/testthat/test-v09183-munsell-value10.R |only soilKey-0.9.184/soilKey/tests/testthat/test-v0997-shiny-pro-app.R | 18 59 files changed, 4793 insertions(+), 926 deletions(-)
Title: 'Serpstat' API Wrapper
Description: The primary goal of 'Serpstat' API <https://api-docs.serpstat.com/docs/serpstat-public-api/jenasqbwtxdlr-introduction-to-serpstat-api>
is to reduce manual SEO (search engine optimization) and PPC (pay-per-click)
tasks. You can automate your keywords research or competitors analysis
with this API wrapper.
Author: Alex Danilin [aut, cre]
Maintainer: Alex Danilin <alexnikdanilin@gmail.com>
Diff between serpstatr versions 0.4.3 dated 2026-07-02 and 0.5.0 dated 2026-07-07
DESCRIPTION | 6 MD5 | 136 ++ NAMESPACE | 111 ++ NEWS.md | 49 R/audit.R | 785 +++++++++++++++ R/backlinks.R | 838 ++++++++++++++++ R/credits.R |only R/domain_classification.R |only R/rank_tracker.R | 900 +++++++++++++++++ R/search_analytics.R | 1303 +++++++++++++++++++++++++- R/serp_crawling.R | 395 +++++-- R/team_management.R |only R/volume_checker.R |only README.md | 139 ++ man/sst_au_export.Rd |only man/sst_au_get_audit.Rd |only man/sst_au_get_categories_statistic.Rd |only man/sst_au_get_default_settings.Rd |only man/sst_au_get_error_elements.Rd |only man/sst_au_get_error_rows.Rd |only man/sst_au_get_history_by_count_error.Rd |only man/sst_au_get_list.Rd |only man/sst_au_get_page_audit.Rd |only man/sst_au_get_pages_list.Rd |only man/sst_au_get_report_without_details.Rd |only man/sst_au_get_reports_list_by_page.Rd |only man/sst_au_get_scan_user_url_list.Rd |only man/sst_au_get_settings.Rd |only man/sst_au_get_sub_elements_by_crc.Rd |only man/sst_au_page_names.Rd |only man/sst_au_remove.Rd |only man/sst_au_rescan.Rd |only man/sst_au_scan.Rd |only man/sst_au_set_settings.Rd |only man/sst_au_stop_page.Rd |only man/sst_au_stop_site.Rd |only man/sst_au_user_log.Rd |only man/sst_bl_anchors.Rd |only man/sst_bl_changes_history.Rd |only man/sst_bl_domains_intersection.Rd |only man/sst_bl_domains_intersection_summary.Rd |only man/sst_bl_lost_backlinks.Rd |only man/sst_bl_lost_outlinks.Rd |only man/sst_bl_new_backlinks.Rd |only man/sst_bl_out_domains.Rd |only man/sst_bl_out_threats.Rd |only man/sst_bl_out_threats_links.Rd |only man/sst_bl_outlinks.Rd |only man/sst_bl_redirected_domains.Rd |only man/sst_bl_sdr_distribution.Rd |only man/sst_bl_threats.Rd |only man/sst_bl_threats_links.Rd |only man/sst_bl_tld_distribution.Rd |only man/sst_bl_top_anchors.Rd |only man/sst_bl_top_pages.Rd |only man/sst_cr_get_audit_stats.Rd |only man/sst_dc_add_task.Rd |only man/sst_dc_get_task.Rd |only man/sst_dc_get_task_list.Rd |only man/sst_rt_add_project_competitor.Rd |only man/sst_rt_add_project_keywords.Rd |only man/sst_rt_add_project_mirror.Rd |only man/sst_rt_add_project_region.Rd |only man/sst_rt_add_rt_project.Rd |only man/sst_rt_create_and_run_project_tracking.Rd |only man/sst_rt_create_project_tags.Rd |only man/sst_rt_delete_project_competitor.Rd |only man/sst_rt_delete_project_keywords.Rd |only man/sst_rt_delete_project_mirror.Rd |only man/sst_rt_delete_project_region.Rd |only man/sst_rt_delete_project_tags.Rd |only man/sst_rt_get_cities.Rd |only man/sst_rt_get_countries.Rd |only man/sst_rt_get_districts.Rd |only man/sst_rt_get_project_competitors.Rd |only man/sst_rt_get_project_keywords.Rd |only man/sst_rt_get_project_mirrors.Rd |only man/sst_rt_get_project_positions.Rd |only man/sst_rt_get_project_regions.Rd |only man/sst_rt_get_project_status.Rd |only man/sst_rt_get_project_tags.Rd |only man/sst_rt_get_projects.Rd |only man/sst_rt_get_rt_project.Rd |only man/sst_rt_get_rt_schedule.Rd |only man/sst_rt_run_project_tracking.Rd |only man/sst_rt_set_rt_schedule.Rd |only man/sst_rt_update_project_keywords.Rd |only man/sst_sa_category_top_domains.Rd |only man/sst_sa_domain_ad_competitors.Rd |only man/sst_sa_domain_ad_keywords.Rd |only man/sst_sa_domain_aio_brand_opportunities.Rd |only man/sst_sa_domain_aio_summary.Rd |only man/sst_sa_domain_all_regions_traffic.Rd |only man/sst_sa_domain_competitors.Rd |only man/sst_sa_domain_export_positions.Rd |only man/sst_sa_domain_keywords_by_language.Rd |only man/sst_sa_domain_urls.Rd |only man/sst_sa_domains_intersection.Rd |only man/sst_sa_domains_rating_data.Rd |only man/sst_sa_domains_unique_keywords.Rd |only man/sst_sa_keyword_export_keywords_phrase.Rd |only man/sst_sa_keyword_export_suggestions.Rd |only man/sst_sa_keyword_get_ad_keywords.Rd |only man/sst_sa_keyword_get_ads_competitors.Rd |only man/sst_sa_keyword_get_competitors.Rd |only man/sst_sa_keyword_get_keyword_top.Rd |only man/sst_sa_keyword_get_suggestions.Rd |only man/sst_sa_keyword_get_top_urls.Rd |only man/sst_sa_market_categories.Rd |only man/sst_sa_url_get_summary_traffic.Rd |only man/sst_sa_url_get_url_competitors.Rd |only man/sst_sa_url_get_url_keywords.Rd |only man/sst_sa_url_get_url_missing_keywords.Rd |only man/sst_sc_add_keyword_list.Rd |only man/sst_sc_get_keyword_serp.Rd |only man/sst_sc_get_list.Rd |only man/sst_sc_get_parsing_balance.Rd |only man/sst_tm_activate_user.Rd |only man/sst_tm_add_user.Rd |only man/sst_tm_deactivate_user.Rd |only man/sst_tm_get_list.Rd |only man/sst_tm_remove_user.Rd |only man/sst_vc_add_keyword_list_freq.Rd |only man/sst_vc_get_task_result.Rd |only man/sst_vc_get_task_status.Rd |only tests/testthat/test_backlinks.R |only tests/testthat/test_new_specs.R |only tests/testthat/test_search_analytics.R |only 128 files changed, 4518 insertions(+), 144 deletions(-)
Title: An R Interface to the California Academy of Sciences Eschmeyer's
Catalog of Fishes
Description: Accesses the California Academy of Sciences Eschmeyer's Catalog of Fishes in R using web requests. The Catalog of fishes is the leading authority in fish taxonomy. Functions in the package allow users to search for fish taxa and valid names, retrieve taxonomic references, retrieve monthly taxonomic changes, obtain natural history collection information, and see the number of species by taxonomic group. For more information on the Catalog: Fricke, R., Eschmeyer, W. N. & R. van der Laan (eds) 2025. ESCHMEYER'S CATALOG OF FISHES <https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp>.
Author: Samuel R. Borstein [aut, cre],
Brandon Dominy [aut],
Brian O'Meara [aut]
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between rcatfish versions 1.0.3 dated 2026-06-12 and 1.0.4 dated 2026-07-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++-- build/vignette.rds |binary inst/doc/rcatfish-vignette.html | 2 +- tests/testthat/test_rcatfish_updates.R | 2 +- 6 files changed, 13 insertions(+), 13 deletions(-)
Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source
package. 'pkgdown' converts your documentation, vignettes, 'README',
and more to 'HTML' making it easy to share information about your
package online.
Author: Hadley Wickham [aut, cre] ,
Jay Hesselberth [aut] ,
Maelle Salmon [aut] ,
Olivier Roy [aut],
Salim Brueggemann [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between pkgdown versions 2.2.0 dated 2025-11-06 and 2.2.1 dated 2026-07-07
DESCRIPTION | 16 +-- MD5 | 101 ++++++++++++------------- NAMESPACE | 1 NEWS.md | 10 ++ R/build-articles.R | 2 R/build-llm.R | 8 + R/build-search-docs.R | 6 - R/build.R | 2 R/pkgdown-package.R | 2 R/preview.R | 49 +++++++++--- R/rd-html.R | 3 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/customise.Rmd | 2 inst/doc/customise.html | 2 inst/doc/quarto.html | 5 - man/build_articles.Rd | 14 +-- man/build_home.Rd | 12 +- man/build_llm_docs.Rd | 12 +- man/build_news.Rd | 12 +- man/build_reference.Rd | 12 +- man/build_search.Rd | 6 - man/build_site.Rd | 2 man/build_tutorials.Rd | 12 +- man/deploy_site_github.Rd | 2 man/deploy_to_branch.Rd | 2 man/index.Rd | 2 man/init_site.Rd | 2 man/pkgdown-package.Rd | 1 man/preview_site.Rd | 10 +- man/stop_preview.Rd |only man/test-crayon.Rd | 2 man/test-dont.Rd | 2 man/test-figures.Rd | 2 man/test-links.Rd | 2 man/test-lists.Rd | 2 man/test-long-lines.Rd | 2 man/test-math-examples.Rd | 2 man/test-output-styles.Rd | 2 man/test-params.Rd | 2 man/test-sexpr-title.Rd | 2 man/test-tables.Rd | 2 man/test-verbatim.Rd | 2 tests/testthat/_snaps/build-quarto-articles.md | 3 tests/testthat/_snaps/build-reference.md | 2 tests/testthat/_snaps/init.md | 6 - tests/testthat/test-build-article.R | 4 tests/testthat/test-build-home-authors.R | 40 --------- tests/testthat/test-preview.R | 88 +++++++++++++++++++++ tests/testthat/test-rd-html.R | 7 + tests/testthat/test-utils.R | 2 vignettes/customise.Rmd | 2 52 files changed, 294 insertions(+), 194 deletions(-)
Title: Heuristic Index-Based Record Linkage
Description: Links records that refer to the same entity across sources that
share no common key, such as people, firms, or addresses with spelling
variation, abbreviations, or reordered words. Linkage is described
declaratively as a strategy that normalises, tokenises, phonetically
encodes, weights, and blocks each field; candidate pairs are then scored
by the rarity-weighted overlap of their tokens and every score is
attributed back to individual tokens for explainability. Strategies
compose into staged pipelines of exact, fuzzy, and optional
embedding-based matching that carry unmatched records forward and resolve
entities as connected components. The same strategy runs on an in-memory
'data.table' backend or an out-of-core 'DuckDB' backend, and diagnostic
and calibration tools help tune a strategy and filter false positives.
The token-retrieval heuristic follows Doherr (2023)
<doi:10.2139/ssrn.4326848>.
Author: Eduard Bruell [aut, cre]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>
Diff between joinery versions 1.0.0 dated 2026-07-07 and 1.0.1 dated 2026-07-07
DESCRIPTION | 6 +- MD5 | 8 +-- NEWS.md | 15 +++++++ R/methods_duckdb_batch.R | 75 ++++++++++++++++++++++++------------- tests/testthat/test_batch_duckdb.R | 54 ++++++++++++++++++++++++++ 5 files changed, 125 insertions(+), 33 deletions(-)
Title: A Framework for Robust Shiny Applications
Description: An opinionated framework for building a production-ready
'Shiny' application. This package contains a series of tools for
building a robust 'Shiny' application from start to finish.
Author: Colin Fay [cre, aut] ,
Vincent Guyader [aut] ,
Sebastien Rochette [aut] ,
Cervan Girard [aut] ,
Novica Nakov [ctb],
David Granjon [ctb],
Arthur Breant [ctb],
Antoine Languillaume [ctb],
Ilya Zarubin [ctb],
ThinkR [cph]
Maintainer: Colin Fay <contact@colinfay.me>
Diff between golem versions 1.0.0 dated 2026-06-26 and 1.0.1 dated 2026-07-07
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 14 +++++++++++++- R/use_favicon.R | 9 ++++----- README.md | 12 ++++++------ build/vignette.rds |binary inst/doc/a-getting-started.html | 4 ++-- inst/doc/b-develop.html | 4 ++-- inst/doc/c-deploy.html | 4 ++-- inst/doc/d-js.html | 4 ++-- inst/doc/e-config.html | 4 ++-- 11 files changed, 46 insertions(+), 35 deletions(-)
Title: Cleaning Geometries from Spatial Objects
Description: Provides a set of utility tools to inspect spatial objects, facilitate
handling and reporting of topology errors and geometry validity issue with sp objects.
Finally, it provides a geometry cleaner that will fix all geometry problems,
and eliminate (at least reduce) the likelihood of having issues when doing
spatial data processing.
Author: Emmanuel Blondel [aut, cre]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between cleangeo versions 0.3-1 dated 2023-09-01 and 0.3-2 dated 2026-07-07
DESCRIPTION | 11 +- MD5 | 17 +-- build/vignette.rds |binary inst/doc/quickstart.R | 4 inst/doc/quickstart.html | 211 +++++++++++++++++++++----------------------- inst/extdata/example.dbf |binary inst/extdata/example.prj |only inst/extdata/example.shp |binary inst/extdata/example.shx |binary tests/testthat/test_Clean.R | 11 +- 10 files changed, 128 insertions(+), 126 deletions(-)
Title: Likelihood Based Inference for ARIMA Modeling
Description: Estimating and analyzing auto regressive integrated moving average
(ARIMA) models. The primary function in this package is arima(), which fits
an ARIMA model to univariate time series data using a random restart
algorithm. This approach frequently leads to models that have model
likelihood greater than or equal to that of the likelihood obtained by
fitting the same model using the arima() function from the 'stats' package.
This package enables proper optimization of model likelihoods, which is a
necessary condition for performing likelihood ratio tests. This package
relies heavily on the source code of the arima() function of the 'stats'
package. For more information, please see Jesse Wheeler and Edward L.
Ionides (2025) <doi:10.1371/journal.pone.0333993>.
Author: Jesse Wheeler [aut, cre, cph],
Noel McAllister [aut],
Dhajanae Sylvertooth [aut],
Edward Ionides [ctb],
Brian Ripley [ctb] ,
R Core Team [cph]
Maintainer: Jesse Wheeler <jesse.wheeler@usu.edu>
Diff between arima2 versions 3.4.3 dated 2025-12-10 and 3.4.4 dated 2026-07-07
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- NEWS.md | 7 ++++++- 3 files changed, 15 insertions(+), 10 deletions(-)
Title: Estimate 3D Orientations from 2D Landmarks
Description: Estimates possible 3D orientations of an object from the 2D image coordinates
of two landmarks and an approximate camera-object elevation angle. Because a projected
2D angle can be compatible with multiple 3D pitch, yaw, and view-elevation angles, the
package returns compatible sets of orientations rather than a single unconstrained
estimate.
Author: Joao C T Menezes [aut, cre, cph]
Maintainer: Joao C T Menezes <jocateme@gmail.com>
Diff between araponga versions 1.0.1 dated 2026-07-02 and 1.1.0 dated 2026-07-07
DESCRIPTION | 6 +- MD5 | 37 +++++++------- NEWS.md | 10 +++ R/download.simdata.R | 84 +++++++++++++++++++++++++-------- R/find.3d.R | 29 +++++++---- R/pitch2d.from.3d.R | 12 +++- R/pitch2d.w.error.R | 4 - R/plot.angles.R | 14 +++-- R/simdata-utils.R |only R/summarize.yaws.R | 2 README.md | 18 +++++-- inst/doc/araponga.R | 2 inst/doc/araponga.Rmd | 5 - inst/doc/araponga.html | 6 +- man/download.simdata.Rd | 6 +- man/find.3d.Rd | 8 +-- man/pitch2d.w.error.Rd | 4 - tests/testthat/test-download.simdata.R | 37 +++++++++++++- tests/testthat/test-find.3d.R | 25 +++------ vignettes/araponga.Rmd | 5 - 20 files changed, 209 insertions(+), 105 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385>, Wilson (2025) <DOI:10.1002/mrm.30462> and
spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin.wilson111@gmail.com>
Diff between spant versions 4.2.0 dated 2026-06-20 and 4.3.0 dated 2026-07-07
DESCRIPTION | 8 - MD5 | 26 +++--- NAMESPACE | 2 NEWS.md | 6 + R/fit_svs.R | 32 +++++++ R/fit_svs_edited.R | 2 R/fmrs.R | 31 ++++--- R/mrs_read_dicom.R | 5 - inst/doc/abfit-baseline-opts.html | 12 +- inst/doc/spant-basis-simulation.html | 8 - inst/doc/spant-intro.html | 122 +++++++++++++++--------------- inst/doc/spant-metabolite-simulation.html | 10 +- inst/doc/spant-preprocessing.html | 14 +-- man/auto_pad_seq.Rd |only man/fit_svs_btrg_v1.Rd |only 15 files changed, 164 insertions(+), 114 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 1.21 dated 2026-02-12 and 1.22 dated 2026-07-07
missMDA-1.21/missMDA/R/imputeCA.r |only missMDA-1.22/missMDA/DESCRIPTION | 8 +-- missMDA-1.22/missMDA/MD5 | 30 ++++++------ missMDA-1.22/missMDA/NAMESPACE | 2 missMDA-1.22/missMDA/R/MIFAMD.R | 38 +++++---------- missMDA-1.22/missMDA/R/imputeCA.R |only missMDA-1.22/missMDA/R/imputeMCA.R | 31 +++++++----- missMDA-1.22/missMDA/R/imputeMFA.R | 45 +++++++++--------- missMDA-1.22/missMDA/R/imputeMultilevel.R | 5 -- missMDA-1.22/missMDA/R/imputePCA.R | 22 ++++---- missMDA-1.22/missMDA/R/plot.MIFAMD.R | 2 missMDA-1.22/missMDA/R/plot.MIPCA.R | 2 missMDA-1.22/missMDA/build/partial.rdb |binary missMDA-1.22/missMDA/build/vignette.rds |binary missMDA-1.22/missMDA/inst/doc/MultipleImputation.html | 2 missMDA-1.22/missMDA/inst/doc/missMDA.html | 2 missMDA-1.22/missMDA/man/imputeMCA.Rd | 2 17 files changed, 94 insertions(+), 97 deletions(-)
Title: Binomial Confidence Intervals for Several Parameterizations
Description: Constructs confidence intervals on the probability of
success in a binomial experiment via several parameterizations.
Author: Sundar Dorai-Raj [aut],
Arianna D. Cascone [aut, cre]
Maintainer: Arianna D. Cascone <ariannacascone4@gmail.com>
Diff between binom versions 1.1-1.1 dated 2022-05-02 and 1.1-2 dated 2026-07-07
DESCRIPTION | 21 +++++++++++++++------ MD5 | 9 +++++---- NEWS.md |only R/binom.bayes.R | 12 ++++++------ R/binom.confint.R | 2 +- man/binom.confint.Rd | 2 +- 6 files changed, 28 insertions(+), 18 deletions(-)
Title: G-Wishart Normalising Constants for Gaussian Graphical Models
Description: Computes G-Wishart normalising constants through a Fourier approach. Either exact analytical results, numerical integration or Monte Carlo estimation are employed. Details at C. Wong, G. Moffa and J. Kuipers (2024), <doi:10.48550/arXiv.2404.06803>. Also includes approximations of the ratio of normalising constants, see details at C. Wong, G. Moffa and J. Kuipers (2025), <doi:10.48550/arXiv.2503.13046>.
Author: Ching Wong [aut],
Jack Kuipers [aut, cre]
Maintainer: Jack Kuipers <jack.kuipers@bsse.ethz.ch>
Diff between GWnorm versions 1.0.1 dated 2026-05-27 and 1.0.2 dated 2026-07-07
GWnorm-1.0.1/GWnorm/man/Clique_complete.Rd |only GWnorm-1.0.1/GWnorm/man/annotate_cliques.Rd |only GWnorm-1.0.1/GWnorm/man/chordal_factor.Rd |only GWnorm-1.0.1/GWnorm/man/clique_update_D.Rd |only GWnorm-1.0.1/GWnorm/man/form_triangle.Rd |only GWnorm-1.0.1/GWnorm/man/local_mean_grad.Rd |only GWnorm-1.0.1/GWnorm/man/local_precision.Rd |only GWnorm-1.0.1/GWnorm/man/predict_row.Rd |only GWnorm-1.0.2/GWnorm/DESCRIPTION | 10 +-- GWnorm-1.0.2/GWnorm/MD5 | 37 ++++------- GWnorm-1.0.2/GWnorm/R/Chordal_factor.R | 8 +- GWnorm-1.0.2/GWnorm/R/I_Gapprox.R | 38 ++++++++--- GWnorm-1.0.2/GWnorm/R/I_Gfns.R | 5 + GWnorm-1.0.2/GWnorm/R/I_Gnorm.R | 5 + GWnorm-1.0.2/GWnorm/R/Integrand_fns.R | 26 ++++---- GWnorm-1.0.2/GWnorm/R/PD_complete.R | 70 +++++++++++----------- GWnorm-1.0.2/GWnorm/R/special_tests.R | 16 ++--- GWnorm-1.0.2/GWnorm/R/trace_fns.R |only GWnorm-1.0.2/GWnorm/man/C_GtoI_G.Rd | 5 - GWnorm-1.0.2/GWnorm/man/I_G_BD.Rd | 4 - GWnorm-1.0.2/GWnorm/man/I_G_ratio_approx.Rd | 8 +- GWnorm-1.0.2/GWnorm/man/I_G_ratio_approx_prime.Rd | 21 ++++-- GWnorm-1.0.2/GWnorm/man/I_GtoC_G.Rd | 5 - GWnorm-1.0.2/GWnorm/man/check_prime_connected.Rd | 2 24 files changed, 139 insertions(+), 121 deletions(-)
Title: Package Documentation Websites with 'Quarto', 'Docsify',
'Docute', or 'MkDocs'
Description: This is a simple and powerful package to create, render, preview,
and deploy documentation websites for 'R' packages. It is a lightweight and
flexible alternative to 'pkgdown', with support for many documentation
generators, including 'Quarto', 'Docute', 'Docsify', and 'MkDocs'.
Author: Etienne Bacher [aut, cre, cph],
Vincent Arel-Bundock [aut]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between altdoc versions 0.7.2 dated 2026-03-02 and 0.7.3 dated 2026-07-07
DESCRIPTION | 8 +- MD5 | 14 ++-- NEWS.md | 4 + R/utils.R | 7 -- README.md | 61 +++++++------------ tests/testthat/_snaps/docsify/render_docs/index.html | 2 tests/testthat/examples/testpkg.lifecycle/R/foo.R | 1 tests/testthat/helper.R | 16 ---- 8 files changed, 40 insertions(+), 73 deletions(-)
Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API,
including management of depositions, attribution of DOIs by 'Zenodo' and
upload and download of files.
Author: Emmanuel Blondel [aut, cre] ,
Julien Barde [ctb] ,
Stephen Eglen [ctb] ,
Hans Van Calster [ctb] ,
Floris Vanderhaeghe [ctb] ,
Jemma Stachelek [ctb] ,
Collin Schwantes [ctb] ,
Nicholas Tierney [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between zen4R versions 0.10.5 dated 2026-03-30 and 0.10.6 dated 2026-07-07
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 12 +++++++++--- R/ZenodoRecord.R | 2 +- README.md | 2 +- inst/doc/zen4R.Rmd | 28 ++++++++++++++-------------- inst/doc/zen4R.html | 28 ++++++++++++++-------------- vignettes/zen4R.Rmd | 28 ++++++++++++++-------------- 8 files changed, 64 insertions(+), 58 deletions(-)
Title: Nowcasting with Chain-Ladder Method
Description: Nowcasting using the Chain-Ladder method. Supports both non-cumulative delay-based estimation and model-based completeness fitting (e.g., using logistic or Gompertz curves) to predict final counts from partially reported data.
Author: Mathias Leroy [aut, cre],
Finlay Campbell [aut]
Maintainer: Mathias Leroy <mathias.leroy.rpkg@gmail.com>
Diff between nowcastr versions 0.2.0 dated 2026-04-16 and 0.2.1 dated 2026-07-07
nowcastr-0.2.0/nowcastr/R/explore_nowcast.R |only nowcastr-0.2.0/nowcastr/man/explore_nowcast.Rd |only nowcastr-0.2.0/nowcastr/man/plot_millipede.Rd |only nowcastr-0.2.0/nowcastr/man/plot_triangle.Rd |only nowcastr-0.2.1/nowcastr/DESCRIPTION | 9 nowcastr-0.2.1/nowcastr/MD5 | 63 + nowcastr-0.2.1/nowcastr/NAMESPACE | 6 nowcastr-0.2.1/nowcastr/NEWS.md | 18 nowcastr-0.2.1/nowcastr/R/nowcast_cl.R | 31 nowcastr-0.2.1/nowcastr/R/nowcast_eval.R | 245 +++---- nowcastr-0.2.1/nowcastr/R/nowcast_explore.R |only nowcastr-0.2.1/nowcastr/R/plot.R | 195 ++---- nowcastr-0.2.1/nowcastr/R/tbl_models_stats.R |only nowcastr-0.2.1/nowcastr/R/theme_nowcastr.R |only nowcastr-0.2.1/nowcastr/R/utils.R | 7 nowcastr-0.2.1/nowcastr/README.md | 172 +---- nowcastr-0.2.1/nowcastr/build/vignette.rds |binary nowcastr-0.2.1/nowcastr/inst/doc/eval.R | 163 ++++- nowcastr-0.2.1/nowcastr/inst/doc/eval.html | 322 +++++++--- nowcastr-0.2.1/nowcastr/inst/doc/eval.qmd | 206 +++++- nowcastr-0.2.1/nowcastr/inst/doc/nowcastr.R | 69 +- nowcastr-0.2.1/nowcastr/inst/doc/nowcastr.html | 138 ++-- nowcastr-0.2.1/nowcastr/inst/doc/nowcastr.qmd | 99 +-- nowcastr-0.2.1/nowcastr/man/generate_test_data.Rd | 2 nowcastr-0.2.1/nowcastr/man/nowcast_cl.Rd | 6 nowcastr-0.2.1/nowcastr/man/nowcast_eval.Rd | 17 nowcastr-0.2.1/nowcastr/man/nowcast_eval_results.Rd | 68 +- nowcastr-0.2.1/nowcastr/man/nowcast_explore.Rd |only nowcastr-0.2.1/nowcastr/man/plot_nowcast_eval.Rd | 6 nowcastr-0.2.1/nowcastr/man/plot_nowcast_eval_by_delay.Rd | 7 nowcastr-0.2.1/nowcastr/man/plot_nowcast_eval_detail.Rd | 4 nowcastr-0.2.1/nowcastr/man/rm_repeated_values.Rd | 5 nowcastr-0.2.1/nowcastr/man/tbl_models_stats.Rd |only nowcastr-0.2.1/nowcastr/man/theme_nowcastr.Rd |only nowcastr-0.2.1/nowcastr/tests/testthat/test-eval.R | 8 nowcastr-0.2.1/nowcastr/tests/testthat/test-tbl_model_stats.R |only nowcastr-0.2.1/nowcastr/vignettes/eval.qmd | 206 +++++- nowcastr-0.2.1/nowcastr/vignettes/nowcastr.qmd | 99 +-- 38 files changed, 1346 insertions(+), 825 deletions(-)
Title: Minorization-Maximization via Assembly-Decomposition Technology
Description: A formula-driven framework for maximizing target functions
via the minorization-maximization (MM) algorithm. The package
represents the target as a symbolic expression tree, infers its
curvature via disciplined-convex-programming rules, and constructs
a separable surrogate at each iterate using only Jensen's
inequality and the supporting hyperplane. The driver maximizes the
surrogate via block-coordinate Newton with line search, falling
back to a multivariate step on any non-separable residue. A
formula interface accepts standard R expressions (including
`sum()` reductions and `X %*% theta` design-matrix products) so
statistical models such as Poisson regression can be written in
one line.
Author: Xifen Huang [aut],
Jinfeng Xu [aut],
Jiaqi Gu [aut, cre]
Maintainer: Jiaqi Gu <jiaqigu@usf.edu>
Diff between MMAD versions 2.0.1 dated 2026-03-12 and 3.0.0 dated 2026-07-07
MMAD-2.0.1/MMAD/R/Exponential.R |only MMAD-2.0.1/MMAD/R/Function_construction.R |only MMAD-2.0.1/MMAD/R/Function_evaluation.R |only MMAD-2.0.1/MMAD/R/Function_minorization.R |only MMAD-2.0.1/MMAD/R/Gradient_Exponential.R |only MMAD-2.0.1/MMAD/R/Gradient_Linear_combination.R |only MMAD-2.0.1/MMAD/R/Gradient_Logarithmic.R |only MMAD-2.0.1/MMAD/R/Gradient_Logarithmic_one_minus.R |only MMAD-2.0.1/MMAD/R/Gradient_Power.R |only MMAD-2.0.1/MMAD/R/Hessian_Exponential.R |only MMAD-2.0.1/MMAD/R/Hessian_Linear_combination.R |only MMAD-2.0.1/MMAD/R/Hessian_Logarithmic.R |only MMAD-2.0.1/MMAD/R/Hessian_Logarithmic_one_minus.R |only MMAD-2.0.1/MMAD/R/Hessian_Power.R |only MMAD-2.0.1/MMAD/R/Linear_combination.R |only MMAD-2.0.1/MMAD/R/Logarithmic.R |only MMAD-2.0.1/MMAD/R/Logarithmic_one_minus.R |only MMAD-2.0.1/MMAD/R/MMAD.R |only MMAD-2.0.1/MMAD/R/Power.R |only MMAD-2.0.1/MMAD/R/convexity.R |only MMAD-2.0.1/MMAD/R/is_natural_number.R |only MMAD-2.0.1/MMAD/man/Function_construction.Rd |only MMAD-2.0.1/MMAD/man/Function_evaluation.Rd |only MMAD-2.0.1/MMAD/man/Function_minorization.Rd |only MMAD-2.0.1/MMAD/man/MMAD.Rd |only MMAD-2.0.1/MMAD/tests/testthat/test-Function_evaluation.R |only MMAD-2.0.1/MMAD/tests/testthat/test-Function_minorization.R |only MMAD-2.0.1/MMAD/tests/testthat/test-MMAD.R |only MMAD-3.0.0/MMAD/DESCRIPTION | 29 +++-- MMAD-3.0.0/MMAD/MD5 | 65 ++++++------ MMAD-3.0.0/MMAD/NAMESPACE | 30 ++++- MMAD-3.0.0/MMAD/R/MMAD-package.R |only MMAD-3.0.0/MMAD/R/atoms.R |only MMAD-3.0.0/MMAD/R/dcp.R |only MMAD-3.0.0/MMAD/R/evaluate_expr.R |only MMAD-3.0.0/MMAD/R/expr.R |only MMAD-3.0.0/MMAD/R/function_check.R |only MMAD-3.0.0/MMAD/R/minorize.R |only MMAD-3.0.0/MMAD/R/mmad_driver.R |only MMAD-3.0.0/MMAD/R/parse_formula.R |only MMAD-3.0.0/MMAD/man/Function_check.Rd |only MMAD-3.0.0/MMAD/man/MMAD-package.Rd |only MMAD-3.0.0/MMAD/man/Math.mmad_expr.Rd |only MMAD-3.0.0/MMAD/man/Ops.mmad_expr.Rd |only MMAD-3.0.0/MMAD/man/as_mmad_expr.Rd |only MMAD-3.0.0/MMAD/man/curvature.Rd |only MMAD-3.0.0/MMAD/man/evaluate_expr.Rd |only MMAD-3.0.0/MMAD/man/is_dcp.Rd |only MMAD-3.0.0/MMAD/man/minorize_at.Rd |only MMAD-3.0.0/MMAD/man/mmad.Rd |only MMAD-3.0.0/MMAD/man/mmad_atom_names.Rd |only MMAD-3.0.0/MMAD/man/mmad_call.Rd |only MMAD-3.0.0/MMAD/man/mmad_const.Rd |only MMAD-3.0.0/MMAD/man/mmad_var.Rd |only MMAD-3.0.0/MMAD/man/register_atom.Rd |only MMAD-3.0.0/MMAD/man/sign_of.Rd |only MMAD-3.0.0/MMAD/man/simplify_expr.Rd |only MMAD-3.0.0/MMAD/tests/testthat/test-dcp.R |only MMAD-3.0.0/MMAD/tests/testthat/test-expr.R |only MMAD-3.0.0/MMAD/tests/testthat/test-formula.R |only MMAD-3.0.0/MMAD/tests/testthat/test-function_check.R |only MMAD-3.0.0/MMAD/tests/testthat/test-minorize.R |only MMAD-3.0.0/MMAD/tests/testthat/test-mmad-formula.R |only MMAD-3.0.0/MMAD/tests/testthat/test-mmad_driver.R |only 64 files changed, 80 insertions(+), 44 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@lamin.ai>
Diff between laminr versions 1.3.0 dated 2026-03-13 and 1.3.1 dated 2026-07-07
DESCRIPTION | 11 - MD5 | 75 ++++----- R/Artifact.R | 7 R/BasicQuerySet.R | 3 R/CallableWrappedPythonObject.R | 12 + R/Collection.R | 3 R/Registry.R | 7 R/Transform.R | 3 R/WrappedPythonObject.R | 7 R/arguments.R | 32 +++- R/checks.R | 283 ++++++++++++++++++++++++------------ R/file_loaders.R | 8 - R/file_openers.R | 7 R/help.R | 6 R/import.R | 27 ++- R/install.R | 14 + R/lamin_cli.R | 53 ++++-- R/lamindb.R | 14 + R/packages.R | 112 ++++++++------ R/require.R | 35 +++- R/reticulate-utils.R | 7 R/save_active_file.R | 4 R/status.R | 5 R/temporary-instance.R | 17 +- R/ui.R | 8 - R/utils.R | 61 +++---- R/view.R | 3 R/wrap-python.R | 60 ++++++- R/zzz.R | 8 - build/vignette.rds |binary man/import_module.Rd | 8 - man/laminr-package.Rd | 1 man/require_module.Rd | 4 tests/testthat/setup.R | 5 tests/testthat/test-BasicQuerySet.R | 4 tests/testthat/test-arguments.R |only tests/testthat/test-checks.R | 1 tests/testthat/test-install.R | 4 tests/testthat/test-wrap-python.R | 5 39 files changed, 605 insertions(+), 319 deletions(-)
Title: Indices of Effect Size
Description: Provide utilities to work with indices of effect size for a wide
variety of models and hypothesis tests (see list of supported models using
the function 'insight::supported_models()'), allowing computation of and
conversion between indices such as Cohen's d, r, odds, etc.
References: Ben-Shachar et al. (2020) <doi:10.21105/joss.02815>.
Author: Mattan S. Ben-Shachar [aut, cre] ,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [aut] ,
Ken Kelley [ctb],
David Stanley [ctb],
Aaron Caldwell [ctb] ,
Jessica Burnett [rev] ,
Johan [...truncated...]
Maintainer: Mattan S. Ben-Shachar <mattansb@msbstats.info>
Diff between effectsize versions 1.0.2 dated 2026-03-11 and 1.0.3 dated 2026-07-07
DESCRIPTION | 12 MD5 | 106 +- NEWS.md | 8 R/common_language.R | 2 R/convert_between_common_language.R | 6 R/eta_squared-main.R | 2 R/eta_squared-methods.R | 1122 +++++++++++------------ R/interpret.R | 2 R/rank_diff.R | 591 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/anovaES.html | 3 inst/doc/convert_p_OR_RR.html | 3 inst/doc/convert_r_d_OR.html | 6 inst/doc/effectsize.html | 27 inst/doc/from_test_statistics.R | 24 inst/doc/from_test_statistics.Rmd | 29 inst/doc/from_test_statistics.html | 50 - inst/doc/interpret.html | 39 inst/doc/statistical_power.R | 32 inst/doc/statistical_power.html | 41 man/F_to_eta2.Rd | 6 man/Music_preferences.Rd | 2 man/Music_preferences2.Rd | 2 man/RCT_table.Rd | 2 man/Smoking_FASD.Rd | 2 man/chisq_to_phi.Rd | 6 man/cohens_d.Rd | 12 man/cohens_g.Rd | 6 man/d_to_r.Rd | 10 man/diff_to_cles.Rd | 12 man/effectsize-package.Rd | 1 man/eta2_to_f2.Rd | 10 man/eta_squared.Rd | 4 man/food_class.Rd | 2 man/hardlyworking.Rd | 2 man/mahalanobis_d.Rd | 12 man/means_ratio.Rd | 12 man/odds_to_probs.Rd | 12 man/oddsratio.Rd | 6 man/oddsratio_to_riskratio.Rd | 10 man/p_superiority.Rd | 18 man/phi.Rd | 6 man/preferences2025.Rd | 2 man/rank_biserial.Rd | 19 man/rank_epsilon_squared.Rd | 10 man/reexports.Rd | 8 man/repeated_measures_d.Rd | 12 man/rouder2016.Rd | 2 man/screening_test.Rd | 2 man/t_to_r.Rd | 6 man/w_to_fei.Rd | 10 tests/testthat/test-eta_squared.R | 1741 ++++++++++++++++++------------------ vignettes/from_test_statistics.Rmd | 29 54 files changed, 2089 insertions(+), 2012 deletions(-)
Title: Derivatives of the First-Passage Time Density and Cumulative
Distribution Function, and Random Sampling from the (Truncated)
First-Passage Time Distribution
Description: First, we provide functions to calculate the partial derivative of the first-passage time diffusion probability density function (PDF) and cumulative
distribution function (CDF) with respect to the first-passage time t (only for PDF), the upper barrier a, the drift rate v, the relative starting point w, the
non-decision time t0, the inter-trial variability of the drift rate sv, the inter-trial variability of the rel. starting point sw, and the inter-trial variability
of the non-decision time st0. In addition the PDF and CDF themselves are also provided. Most calculations are done on the logarithmic scale to make it more stable.
Since the PDF, CDF, and their derivatives are represented as infinite series, we give the user the option to control the approximation errors with the argument
'precision'. For the numerical integration we used the C library cubature by Johnson, S. G. (2005-2013) <https://github.com/stevengj/cubature>. Numerical integration is
required whenever sv, sw, and [...truncated...]
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [ctb],
Gerard Jungman [ctb],
Rudolf Schuerer [ctb],
Przemyslaw Sliwa [ctb],
Jason H. Stover [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between WienR versions 0.3-15 dated 2023-11-29 and 0.3-17 dated 2026-07-07
DESCRIPTION | 8 +- MD5 | 75 +++++++++++++------------ NAMESPACE | 3 + R/WienerQuant.R |only R/print_Wiener.R | 10 +++ build/partial.rdb |binary inst |only man/WienerCDF.Rd | 4 - man/WienerPDF.Rd | 4 - man/WienerQuant.Rd |only man/daWienerCDF.Rd | 2 man/daWienerPDF.Rd | 2 man/ddWDM.Rd | 2 man/dpWDM.Rd | 2 man/dst0WienerCDF.Rd | 2 man/dst0WienerPDF.Rd | 2 man/dsvWienerCDF.Rd | 2 man/dsvWienerPDF.Rd | 2 man/dswWienerCDF.Rd | 2 man/dswWienerPDF.Rd | 2 man/dt0WienerCDF.Rd | 2 man/dt0WienerPDF.Rd | 2 man/dtWienerPDF.Rd | 2 man/dvWienerCDF.Rd | 2 man/dvWienerPDF.Rd | 2 man/dwWienerCDF.Rd | 2 man/dwWienerPDF.Rd | 2 man/gradWienerCDF.Rd | 2 man/gradWienerPDF.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 src/R_wrapper.cpp | 139 +++++++++++++++++++++++++++++++++++++++++++++++ src/WienR_init.c | 7 ++ src/cdf_fncs.cpp | 36 ++++++++++++ src/cdf_fncs.h | 3 + src/derivs.cpp | 149 +++++++++++++++++++++++++++++++++++++++++---------- src/derivs.h | 4 + src/fncs_seven.cpp | 35 +++++++++++ src/fncs_seven.h | 2 src/methods.cpp | 39 +++++++------ 40 files changed, 447 insertions(+), 113 deletions(-)
Title: External jars for 'rjdverse' R Packages
Description: It provides external jars required for the 'rjdverse' (as 'rjd3toolkit', 'rjd3x13' and 'rjd3tramoseats').
Author: Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <timeserieswithjdemetraandr@gmail.com>
Diff between rjd3jars versions 0.0.4 dated 2026-07-03 and 0.0.5 dated 2026-07-07
DESCRIPTION | 12 +- MD5 | 26 +++-- NAMESPACE | 20 ++-- NEWS.md | 112 +++++++++++++----------- R/rjd3jars-package.R |only R/utils.R | 11 +- R/zzz.R | 8 + README.md | 82 +++++++++--------- inst/WORDLIST | 202 ++++++++++++++++++++++----------------------- java/README | 12 +- man/java-version.Rd | 76 ++++++++-------- man/reload_dictionaries.Rd | 38 ++++---- man/reload_safactories.Rd | 32 +++---- man/reload_tsproviders.Rd | 38 ++++---- man/rjd3jars-package.Rd |only 15 files changed, 342 insertions(+), 327 deletions(-)
Title: Import, Manipulate and Explore the Results of an 'Antares'
Simulation
Description: Import, manipulate and explore results generated by 'Antares', a
powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems
(more information about 'Antares' here : <https://antares-simulator.org/>).
Author: Tatiana Vargas [aut, cre],
Jalal-Edine ZAWAM [aut],
Frederic Breant [ctb],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Victor Perrier [ctb],
Etienne Sanchez [ctb],
Assil Mansouri [ctb],
Clement Berthet [ctb],
Kamel Kemiha [c [...truncated...]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between antaresRead versions 3.0.1 dated 2026-05-28 and 3.1.0 dated 2026-07-07
DESCRIPTION | 6 LICENSE | 2 MD5 | 320 NAMESPACE | 256 NEWS.md | 1572 +-- R/API-methods.R | 486 - R/aggregateResult.R | 4434 +++++----- R/antaresRead-package.R | 14 R/asAntaresDataList.R | 140 R/asAntaresDataTable.R | 102 R/changeTimeStep.R | 410 R/copyToClipboard.R | 172 R/digest.R | 296 R/extractDataList.R | 206 R/getAreas.R | 186 R/getGeographicTrimming.R | 98 R/getLinks.R | 254 R/getNtcOutput.R | 48 R/giveSize.R | 528 - R/groupByDistrict.R | 170 R/hvdcModification.R | 226 R/importInput.R | 1050 +- R/importOutput.R | 3102 +++--- R/ponderateMcAggregation.R | 84 R/readAntares.R | 1974 ++-- R/readAntaresClusters.R | 182 R/readBindingConstraints.R | 842 - R/readClusterDesc.R | 668 - R/readIniFile.R | 330 R/readInputClusters.R | 498 - R/readInputTS.R | 390 R/readLayout.R | 374 R/read_st_constraints.R | 570 - R/removeVirtualAreas.R | 1284 +- R/reorderCols.R | 100 R/setHvdcAreas.R | 110 R/setSimulationPath.R | 1468 +-- R/setSimulationPathAPI.R | 1069 +- R/showAliases.R | 196 R/simOptions.R | 118 R/subset.R | 264 R/thematic_trimming.R | 344 R/utils.R | 12 R/utils_api.R | 204 R/viewAntares.R | 108 R/zzz.R | 390 build/vignette.rds |binary inst/API/demo_api.R | 414 inst/API/demo_api_enr.R | 388 inst/ENR_cluster/test_clusters_enr.R | 184 inst/doc/antaresRead.Rmd | 316 inst/doc/antaresRead.html | 1029 +- inst/format_output/h5Struct.csv | 522 - inst/format_output/simulation_variables_names_by_support.csv | 22 inst/format_output/tableOutput.csv | 502 - inst/format_output/tableOutput_aggreg.csv | 594 - inst/format_output/tableOutput_aggreg_v8.csv | 674 - inst/referential_properties/cluster_properties.csv | 114 inst/test_files/antares_version_files/antares_version_float.antares | 12 inst/test_files/antares_version_files/antares_version_float_2digit.antares | 12 inst/variables_selection/ref_thematic_by_version/api_ref_conversion.csv | 204 inst/variables_selection/ref_thematic_by_version/ref_880.csv | 234 inst/variables_selection/ref_thematic_by_version/ref_920.csv | 180 inst/variables_selection/ref_thematic_by_version/ref_930.csv | 148 inst/variables_selection/variables_thematic_by_version.csv | 98 man/API-methods.Rd | 154 man/aggregatate_mc_all.Rd | 130 man/antaresRead-package.Rd | 91 man/as.antaresDataList.Rd | 98 man/as.antaresDataTable.Rd | 70 man/changeTimeStep.Rd | 104 man/copyToClipboard.Rd | 88 man/dot-download_api_aggregate_result.Rd | 44 man/dot-filter_bindingConstraints_by_names.Rd | 38 man/dot-transform_antares_version.Rd | 36 man/dot-writeIni.Rd | 58 man/extractDataList.Rd | 56 man/figures/badge_api_no.svg | 38 man/figures/badge_api_ok.svg | 38 man/getAreas.Rd | 128 man/getGeographicTrimming.Rd | 42 man/getLinks.Rd | 178 man/getThematicTrimming.Rd | 66 man/hvdcModification.Rd | 64 man/list_thematic_variables.Rd | 48 man/mergeDigests.Rd | 46 man/ponderateMcAggregation.Rd | 60 man/read-ini.Rd | 122 man/readAntares.Rd | 480 - man/readAntaresAreas.Rd | 118 man/readAntaresClusters.Rd | 74 man/readAntaresSTClusters.Rd | 74 man/readBindingConstraints.Rd | 170 man/readClusterDesc.Rd | 196 man/readDigestFile.Rd | 40 man/readInputRES.Rd | 96 man/readInputTS.Rd | 234 man/readInputThermal.Rd | 128 man/readLayout.Rd | 100 man/readOptimCriteria.Rd | 62 man/read_storages_constraints.Rd | 72 man/removeVirtualAreas.Rd | 338 man/setAlias.Rd | 122 man/setHvdcAreas.Rd | 64 man/setSimulationPath.Rd | 412 man/setTimeoutAPI.Rd | 54 man/simOptions.Rd | 102 man/subset.antaresDataList.Rd | 100 man/summary.bindingConstraints.Rd | 40 man/viewAntares.Rd | 66 man/writeDigest.Rd | 46 tests/testthat.R | 34 tests/testthat/helper_init.R | 262 tests/testthat/test-.timeIdToDate.R | 118 tests/testthat/test-API.R | 46 tests/testthat/test-RemoveInputColumn.R | 88 tests/testthat/test-aggregateResult.R | 72 tests/testthat/test-aliases.R | 86 tests/testthat/test-asAntaresData.R | 140 tests/testthat/test-changeTimeStep.R | 102 tests/testthat/test-digest.R | 70 tests/testthat/test-extractDataList.R | 78 tests/testthat/test-getAreas.R | 106 tests/testthat/test-getGeographicTrimming.R | 30 tests/testthat/test-getLinks.R | 50 tests/testthat/test-getStartDate.R | 506 - tests/testthat/test-giveSize.R | 388 tests/testthat/test-groupByDistrict.R | 50 tests/testthat/test-hvdcModification.R | 62 tests/testthat/test-importOutput.R | 416 tests/testthat/test-importOutputForClusters.R | 126 tests/testthat/test-mcaggreg.R | 110 tests/testthat/test-opts-api.R | 80 tests/testthat/test-ponderate.R | 110 tests/testthat/test-ponderateMcAggregation.R | 26 tests/testthat/test-print.R | 86 tests/testthat/test-readAntares.R | 676 - tests/testthat/test-readAntaresClusters.R | 64 tests/testthat/test-readAntares_STclusters.R | 106 tests/testthat/test-readAntares_bc.R | 32 tests/testthat/test-readAntares_districts.R | 74 tests/testthat/test-readAntares_inputs.R | 128 tests/testthat/test-readAntares_mustRun.R | 154 tests/testthat/test-readAntares_time_columns.R | 64 tests/testthat/test-readBindingConstraints.R | 740 - tests/testthat/test-readClusterDesc.R | 1048 +- tests/testthat/test-readIni.R | 48 tests/testthat/test-readInputAPI.R | 38 tests/testthat/test-readInputClusters.R | 242 tests/testthat/test-readInputTS.R | 566 - tests/testthat/test-readLayout.R | 84 tests/testthat/test-read_optim_criteria.R | 34 tests/testthat/test-read_st_constraints.R | 679 - tests/testthat/test-removeVirtualAreas.R | 976 +- tests/testthat/test-setHvdcAreas.R | 48 tests/testthat/test-setSimulationPath.R | 603 - tests/testthat/test-setSimulationPathAPI.R | 115 tests/testthat/test-subset_antaresDataList.R | 158 tests/testthat/test-thematic_timming.R | 1124 +- tests/testthat/test-viewAntares.R | 90 vignettes/antaresRead.Rmd | 316 161 files changed, 23904 insertions(+), 23834 deletions(-)
Title: Removal of Unwanted Technical Variation from UK Biobank NMR
Metabolomics Biomarker Data
Description: A suite of utilities for working with the UK Biobank
<https://www.ukbiobank.ac.uk/> Nuclear Magnetic Resonance spectroscopy (NMR)
metabolomics data <https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220>.
Includes functions for extracting biomarkers from decoded UK Biobank field
data, removing unwanted technical variation from biomarker concentrations,
computing an extended set of lipid, fatty acid, and cholesterol fractions,
and for re-deriving composite biomarkers and ratios after adjusting data
for unwanted biological variation. For further details on methods see
Ritchie SC et al. Sci Data (2023) <doi:10.1038/s41597-023-01949-y>.
Author: Scott C Ritchie [aut, cre]
Maintainer: Scott C Ritchie <sritchie73@gmail.com>
Diff between ukbnmr versions 3.3.2 dated 2026-04-12 and 3.4 dated 2026-07-07
DESCRIPTION | 8 MD5 | 38 - NAMESPACE | 2 NEWS.md | 13 R/compute_biomarkers_internal.R | 126 +++++ R/compute_biomarkers_user.R | 82 ++- R/compute_qc_flags_internal.R | 127 +++++ R/compute_qc_flags_user.R | 79 ++- R/data.R | 12 R/ukbnmr.R | 47 + data/nmr_info.rda |binary inst/CITATION | 17 inst/extdata/nmr_info.csv | 673 +++++++++++++-------------- man/compute_extended_ratio_qc_flags.Rd | 11 man/compute_extended_ratios.Rd | 10 man/compute_lipoprotein_fatty_acids.Rd |only man/compute_lipoprotein_fatty_acids_flags.Rd |only man/nmr_info.Rd | 12 man/recompute_derived_biomarker_qc_flags.Rd | 11 man/recompute_derived_biomarkers.Rd | 6 man/ukbnmr.Rd | 54 +- 21 files changed, 914 insertions(+), 414 deletions(-)
Title: Trait Specific Gene Selection using SVM and GA
Description: Obtaining relevant set of trait specific genes from gene expression data is important for clinical diagnosis of disease and discovery of disease mechanisms in plants and animals. This process involves identification of relevant genes and removal of redundant genes as much as possible from a whole gene set. This package returns the trait specific gene set from the high dimensional RNA-seq count data by applying combination of two conventional machine learning algorithms, support vector machine (SVM) and genetic algorithm (GA). GA is used to control and optimize the subset of genes sent to the SVM for classification and evaluation. Genetic algorithm uses repeated learning steps and cross validation over number of possible solution and selects the best. The algorithm selects the set of genes based on a fitness function that is obtained via support vector machines. Using SVM as the classifier performance and the genetic algorithm for feature selection, a set of trait specific gene set is o [...truncated...]
Author: Md. Samir Farooqi [aut],
K.K. Chaturvedi [aut],
D.C. Mishra [aut],
Sudhir Srivastava [cre, aut]
Maintainer: Sudhir Srivastava <sudhir0401bm@gmail.com>
Diff between TSGS versions 1.0 dated 2021-09-08 and 1.0.1 dated 2026-07-07
DESCRIPTION | 16 ++++++++-------- MD5 | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-)
Title: Discrete Log-Gaussian Cox Processes for Aggregated Disease
Counts
Description: Fits a spatially discrete approximation to a log-Gaussian Cox process
model for spatially aggregated disease count data, estimated by Monte Carlo
Maximum Likelihood as in Christensen (2004) <doi:10.1198/106186004X2525> and
Johnson, Diggle and Giorgi (2019) <doi:10.1002/sim.8339>. Performance-critical
steps (aggregated correlation assembly, Metropolis-adjusted Langevin
algorithm (MALA) sampling, the Monte Carlo likelihood, and the
Kronecker-structured space-time likelihood) are implemented in
C++ via 'RcppArmadillo'. Provides a one-line, 'glm'-like interface and
statistical extensions including a nugget term, general 'Matern' smoothness,
raster and misaligned covariates, restricted spatial regression,
importance-sampling diagnostics and re-anchored Monte Carlo maximum
likelihood (MCML).
Author: Olatunji Johnson [aut, cre],
Emanuele Giorgi [aut],
Peter Diggle [aut]
Maintainer: Olatunji Johnson <olatunjijohnson21111@gmail.com>
Diff between SDALGCP2 versions 0.1.0 dated 2026-07-02 and 0.1.1 dated 2026-07-07
DESCRIPTION | 20 +++--- MD5 | 18 +++--- NEWS.md | 16 +++++ R/SDALGCP2-package.R | 2 R/zzz.R |only inst/doc/SDALGCP2-intro.R | 7 ++ inst/doc/SDALGCP2-intro.Rmd | 9 +++ inst/doc/SDALGCP2-intro.html | 129 +++++++++++++++++++++---------------------- man/SDALGCP2-package.Rd | 2 man/set_omp_num_threads.Rd |only vignettes/SDALGCP2-intro.Rmd | 9 +++ 11 files changed, 128 insertions(+), 84 deletions(-)
Title: Fast Local Indicators of Spatial Association (LISA)
Description: Computes various Local Indicators of Spatial Association (LISA)
statistics, including univariate and bivariate local Moran's I,
Empirical Bayes local Moran's I, univariate and multivariate local
Geary's C, and Getis-Ord G and G* statistics. The methods follow
Anselin (1995), Getis and Ord (1992), and Anselin (2019). Leverages a
high-performance, plain-C backend with optional 'OpenMP' multi-core
support for fast permutation-based pseudo-p-value calculation. Accepts any
'spdep' listw spatial weight matrix, including custom and
non-contiguity weights. Uses sample standardisation (n-1) and
'rgeoda'-style permutation p-values. Output cluster codes match 'rgeoda'
conventions, including the Isolated category for observations without
neighbours.
Author: Lizhong Chen [aut, cre]
Maintainer: Lizhong Chen <chen.l@wehi.edu.au>
Diff between fastLISA versions 1.0.0 dated 2026-07-06 and 1.0.1 dated 2026-07-07
DESCRIPTION | 10 ++++++---- MD5 | 44 ++++++++++++++++++++++---------------------- NEWS.md | 15 ++++++++++++--- R/local_g.R | 2 ++ R/local_geary.R | 2 ++ R/local_gstar.R | 3 ++- R/local_moran.R | 3 ++- R/local_moran_bv.R | 2 ++ R/local_moran_eb.R | 1 + R/local_multigeary.R | 2 ++ README.md | 9 +++++---- inst/doc/fastLISA.Rnw | 8 +++++--- inst/doc/fastLISA.pdf |binary man/local_g.Rd | 11 +++++++---- man/local_geary.Rd | 11 +++++++---- man/local_gstar.Rd | 11 +++++++---- man/local_moran.Rd | 11 +++++++---- man/local_moran_bv.Rd | 11 +++++++---- man/local_moran_eb.Rd | 11 +++++++---- man/local_multigeary.Rd | 11 +++++++---- src/fastLISA.h | 8 ++++++-- src/init.c | 3 +-- vignettes/fastLISA.Rnw | 8 +++++--- 23 files changed, 124 insertions(+), 73 deletions(-)
Title: Functions for Tabular Reporting
Description: Use a grammar for creating and customizing pretty tables.
The following formats are supported: 'HTML', 'PDF', 'Typst', 'RTF',
'Microsoft Word', 'Microsoft PowerPoint', R 'Grid Graphics' and
'patchwork'. 'R Markdown', 'Quarto' and the package 'officer' can be
used to produce the result files. The syntax is the same for the user
regardless of the type of output to be produced. A set of functions
allows the creation, definition of cell arrangement, addition of
headers or footers, formatting and definition of cell content with
text and or images. The package also offers a set of high-level
functions that allow tabular reporting of statistical models and the
creation of complex cross tabulations.
Author: David Gohel [aut, cre],
ArData [cph],
Clementine Jager [ctb],
Eli Daniels [ctb],
Panagiotis Skintzos [aut],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb],
Titouan Robert [ctb],
Michael Barrowman [ctb],
Atsushi Yasumoto [ctb],
Paul Julian [ctb],
Sean B [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.9.12 dated 2026-06-02 and 0.10.0 dated 2026-07-07
DESCRIPTION | 22 MD5 | 180 ++--- NAMESPACE | 4 NEWS.md | 24 R/01_fpstruct.R | 6 R/05_content.R | 18 R/chunk_images.R | 141 +--- R/flextable.R | 1 R/grid_funs.R | 25 R/grid_grobs.R | 73 +- R/html_str.R | 118 +++ R/latex_chunks.R | 20 R/latex_str.R | 46 + R/printers.R | 201 +++++- R/read_structure.R | 76 ++ R/runs_as_functions.R | 26 R/styles.R | 96 ++ R/typst_str.R |only README.md | 4 build/vignette.rds |binary inst/_extensions/flextable-qmd/flextable-qmd.lua | 25 man/align.Rd | 1 man/as_image.Rd | 4 man/as_qmd.Rd | 2 man/as_word_field.Rd | 2 man/bg.Rd | 1 man/bold.Rd | 1 man/color.Rd | 1 man/df_printer.Rd | 1 man/empty_blanks.Rd | 1 man/flextable.Rd | 1 man/flextable_to_rmd.Rd | 1 man/font.Rd | 1 man/fontsize.Rd | 1 man/gen_grob.Rd | 1 man/gg_chunk.Rd | 4 man/grid_chunk.Rd | 4 man/highlight.Rd | 1 man/htmltools_value.Rd | 1 man/hyperlink_text.Rd | 4 man/indentation.Rd |only man/italic.Rd | 1 man/keep_with_next.Rd | 1 man/knit_print.flextable.Rd | 11 man/line_spacing.Rd | 1 man/linerange.Rd | 4 man/minibar.Rd | 4 man/note_docx_images.Rd |only man/padding.Rd | 1 man/plot.flextable.Rd | 1 man/plot_chunk.Rd | 4 man/print.flextable.Rd | 1 man/repair_docx.Rd |only man/rotate.Rd | 1 man/save_as_docx.Rd | 1 man/save_as_html.Rd | 1 man/save_as_image.Rd | 1 man/save_as_pptx.Rd | 1 man/save_as_rtf.Rd | 1 man/save_as_typst.Rd |only man/style.Rd | 1 man/tab_settings.Rd | 1 man/to_html.flextable.Rd | 1 man/use_flextable_qmd.Rd | 10 man/valign.Rd | 1 man/wrap_flextable.Rd | 1 tests/testthat/setup.R | 9 tests/testthat/test-as_flextable.R | 739 ++++++++++++++++++----- tests/testthat/test-captions-rmd.R | 60 + tests/testthat/test-cell_content.R | 339 ++++++++-- tests/testthat/test-clintables.R | 68 +- tests/testthat/test-df_printer.R | 9 tests/testthat/test-dimensions.R | 39 - tests/testthat/test-docx-images.R |only tests/testthat/test-errors.R | 22 tests/testthat/test-footers.R | 43 + tests/testthat/test-footnote.R | 125 ++- tests/testthat/test-gen_grob.R | 114 ++- tests/testthat/test-headers.R | 91 ++ tests/testthat/test-images.R | 222 ++++-- tests/testthat/test-indentation.R |only tests/testthat/test-keep_next.R | 25 tests/testthat/test-merge.R | 12 tests/testthat/test-misc.R | 74 +- tests/testthat/test-new-rows.R | 202 +++--- tests/testthat/test-padding.R | 16 tests/testthat/test-pptx-tables.R | 7 tests/testthat/test-proc-freq.R | 309 ++++++++- tests/testthat/test-quarto.R | 21 tests/testthat/test-rotations.R | 5 tests/testthat/test-styles.R | 52 + tests/testthat/test-tab_settings.R | 37 - tests/testthat/test-text.R | 179 ++++- tests/testthat/test-themes.R | 14 tests/testthat/test-typst.R |only 95 files changed, 3043 insertions(+), 979 deletions(-)
Title: Tests for Departure from Normality
Description: A toolkit for assessing data normality using a comprehensive collection of statistical methods.
It includes descriptive measures and formal hypothesis tests, such as skewness and kurtosis tests,
the Anderson–Darling test, the Shapiro–Wilk test, and the D'Agostino–Pearson K2 omnibus test.
Author: Joon-Keat Lai [aut, cre, cph]
Maintainer: Joon-Keat Lai <p10911004@gmail.com>
Diff between normality versions 0.0.1 dated 2026-06-09 and 0.0.3 dated 2026-07-07
normality-0.0.1/normality/R/DAgostino-Pearson_test.R |only normality-0.0.1/normality/R/zzz_standard-output.R |only normality-0.0.1/normality/data/cholesterol.rda |only normality-0.0.1/normality/data/leghorn_chick.rda |only normality-0.0.1/normality/man/cholesterol.Rd |only normality-0.0.1/normality/man/dot-Shapiro_Francia.Rd |only normality-0.0.1/normality/man/leghorn_chick.Rd |only normality-0.0.3/normality/DESCRIPTION | 8 normality-0.0.3/normality/MD5 | 63 - normality-0.0.3/normality/NAMESPACE | 6 normality-0.0.3/normality/NEWS.md | 14 normality-0.0.3/normality/R/Anderson_Darling_test.R | 195 ++-- normality-0.0.3/normality/R/D.Agostino_Pearson_test.R |only normality-0.0.3/normality/R/Jarque_Bera_test.R |only normality-0.0.3/normality/R/Lilliefors_test.R |only normality-0.0.3/normality/R/Shapiro_Wilk_test.R | 434 +++++++++- normality-0.0.3/normality/R/check_normality.R |only normality-0.0.3/normality/R/data.R | 39 normality-0.0.3/normality/R/globals.R |only normality-0.0.3/normality/R/is_normal.R |only normality-0.0.3/normality/R/kurtosis.R | 108 +- normality-0.0.3/normality/R/skewness.R | 108 +- normality-0.0.3/normality/R/utils.R |only normality-0.0.3/normality/README.md | 53 - normality-0.0.3/normality/data/Shapiro_Wilk_coef_table.rda |only normality-0.0.3/normality/data/Shapiro_Wilk_pval_table.rda |only normality-0.0.3/normality/man/Anderson_Darling_test.Rd | 52 - normality-0.0.3/normality/man/D.Agostino_Pearson_test.Rd | 57 - normality-0.0.3/normality/man/Jarque_Bera_test.Rd |only normality-0.0.3/normality/man/Lilliefors_test.Rd |only normality-0.0.3/normality/man/Shapiro_Wilk_coef_table.Rd |only normality-0.0.3/normality/man/Shapiro_Wilk_pval_table.Rd |only normality-0.0.3/normality/man/Shapiro_Wilk_test.Rd |only normality-0.0.3/normality/man/check_normality.Rd |only normality-0.0.3/normality/man/is_normal.Rd |only normality-0.0.3/normality/man/is_tied.Rd |only normality-0.0.3/normality/man/kurtosis.Rd | 49 - normality-0.0.3/normality/man/normality_standard_output.Rd | 12 normality-0.0.3/normality/man/skewness.Rd | 49 - normality-0.0.3/normality/tests/testthat/test-Anderson_Darling_test.R | 32 normality-0.0.3/normality/tests/testthat/test-D.Agostino_Pearson_test.R | 42 normality-0.0.3/normality/tests/testthat/test-Jarque_Bera_test.R |only normality-0.0.3/normality/tests/testthat/test-Shapiro_Wilk_test.R |only normality-0.0.3/normality/tests/testthat/test-check_normality.R |only normality-0.0.3/normality/tests/testthat/test-kurtosis.R | 24 normality-0.0.3/normality/tests/testthat/test-skewness.R | 20 46 files changed, 974 insertions(+), 391 deletions(-)
More information about nonprobsampling at CRAN
Permanent link
Title: Fast and Flexible Implementations of Exploratory Factor Analysis
Tools
Description: Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
Author: Markus Steiner [aut, cre] ,
Silvia Steiner [aut] ,
William Revelle [ctb],
Max Auerswald [ctb],
Morten Moshagen [ctb],
John Ruscio [ctb],
Brendan Roche [ctb],
Urbano Lorenzo-Seva [ctb],
David Navarro-Gonzalez [ctb],
Johan Braeken [ctb],
Andreas Soteri [...truncated...]
Maintainer: Markus Steiner <markus.d.steiner@gmail.com>
Diff between EFAtools versions 0.7.1 dated 2026-05-08 and 0.8.0 dated 2026-07-07
EFAtools-0.7.1/EFAtools/R/ROTATE_OBLQ.R |only EFAtools-0.7.1/EFAtools/R/ROTATE_ORTH.R |only EFAtools-0.7.1/EFAtools/R/plot.CD.R |only EFAtools-0.7.1/EFAtools/R/plot.EKC.R |only EFAtools-0.7.1/EFAtools/R/plot.HULL.R |only EFAtools-0.7.1/EFAtools/R/plot.KGC.R |only EFAtools-0.7.1/EFAtools/R/plot.PARALLEL.R |only EFAtools-0.7.1/EFAtools/R/plot.SCREE.R |only EFAtools-0.7.1/EFAtools/R/print.CD.R |only EFAtools-0.7.1/EFAtools/R/print.EKC.R |only EFAtools-0.7.1/EFAtools/R/print.HULL.R |only EFAtools-0.7.1/EFAtools/R/print.KGC.R |only EFAtools-0.7.1/EFAtools/R/print.MAP.R |only EFAtools-0.7.1/EFAtools/R/print.NEST.R |only EFAtools-0.7.1/EFAtools/R/print.N_FACTORS.R |only EFAtools-0.7.1/EFAtools/R/print.PARALLEL.R |only EFAtools-0.7.1/EFAtools/R/print.SCREE.R |only EFAtools-0.7.1/EFAtools/R/print.SMT.R |only EFAtools-0.7.1/EFAtools/R/utils-pipe.R |only EFAtools-0.7.1/EFAtools/man/CONSENSUS_PROCRUSTES.Rd |only EFAtools-0.7.1/EFAtools/man/dot-calc_cis.Rd |only EFAtools-0.7.1/EFAtools/man/dot-nest_sym.Rd |only EFAtools-0.7.1/EFAtools/man/dot-numformat.Rd |only EFAtools-0.7.1/EFAtools/man/dot-stat_over_list.Rd |only EFAtools-0.7.1/EFAtools/man/pipe.Rd |only EFAtools-0.7.1/EFAtools/man/plot.CD.Rd |only EFAtools-0.7.1/EFAtools/man/plot.EKC.Rd |only EFAtools-0.7.1/EFAtools/man/plot.HULL.Rd |only EFAtools-0.7.1/EFAtools/man/plot.KGC.Rd |only EFAtools-0.7.1/EFAtools/man/plot.PARALLEL.Rd |only EFAtools-0.7.1/EFAtools/man/plot.SCREE.Rd |only EFAtools-0.7.1/EFAtools/man/print.CD.Rd |only EFAtools-0.7.1/EFAtools/man/print.EKC.Rd |only EFAtools-0.7.1/EFAtools/man/print.HULL.Rd |only EFAtools-0.7.1/EFAtools/man/print.KGC.Rd |only EFAtools-0.7.1/EFAtools/man/print.MAP.Rd |only EFAtools-0.7.1/EFAtools/man/print.NEST.Rd |only EFAtools-0.7.1/EFAtools/man/print.PARALLEL.Rd |only EFAtools-0.7.1/EFAtools/man/print.SCREE.Rd |only EFAtools-0.7.1/EFAtools/man/print.SMT.Rd |only EFAtools-0.7.1/EFAtools/src/ml_helper.cpp |only EFAtools-0.7.1/EFAtools/src/nest_sym.cpp |only EFAtools-0.7.1/EFAtools/src/uls_helper.cpp |only EFAtools-0.8.0/EFAtools/DESCRIPTION | 36 EFAtools-0.8.0/EFAtools/MD5 | 481 - EFAtools-0.8.0/EFAtools/NAMESPACE | 58 EFAtools-0.8.0/EFAtools/NEWS.md | 145 EFAtools-0.8.0/EFAtools/R/BARTLETT.R | 92 EFAtools-0.8.0/EFAtools/R/CD.R | 285 EFAtools-0.8.0/EFAtools/R/COMPARE.R | 250 EFAtools-0.8.0/EFAtools/R/DOSPERT_doc.R | 4 EFAtools-0.8.0/EFAtools/R/DOSPERT_raw_doc.R | 2 EFAtools-0.8.0/EFAtools/R/DWLS.R |only EFAtools-0.8.0/EFAtools/R/EFA.R | 2380 ++++- EFAtools-0.8.0/EFAtools/R/EFA_AVERAGE.R | 485 - EFAtools-0.8.0/EFAtools/R/EFA_POOLED.R | 1925 +++- EFAtools-0.8.0/EFAtools/R/EKC.R | 200 EFAtools-0.8.0/EFAtools/R/FACTOR_SCORES.R | 234 EFAtools-0.8.0/EFAtools/R/GRiPS_raw_doc.R | 2 EFAtools-0.8.0/EFAtools/R/HULL.R | 473 - EFAtools-0.8.0/EFAtools/R/IDS2_R_doc.R | 2 EFAtools-0.8.0/EFAtools/R/KGC.R | 192 EFAtools-0.8.0/EFAtools/R/KMO.R | 116 EFAtools-0.8.0/EFAtools/R/MAP.R | 185 EFAtools-0.8.0/EFAtools/R/ML.R | 128 EFAtools-0.8.0/EFAtools/R/NEST.R | 204 EFAtools-0.8.0/EFAtools/R/N_FACTORS.R | 688 - EFAtools-0.8.0/EFAtools/R/OMEGA.R | 233 EFAtools-0.8.0/EFAtools/R/OMEGA_helper.R | 1078 +- EFAtools-0.8.0/EFAtools/R/PAF.R | 226 EFAtools-0.8.0/EFAtools/R/PARALLEL.R | 401 EFAtools-0.8.0/EFAtools/R/PROCRUSTES.R | 146 EFAtools-0.8.0/EFAtools/R/PROMAX.R | 364 EFAtools-0.8.0/EFAtools/R/RcppExports.R | 688 + EFAtools-0.8.0/EFAtools/R/SCREE.R | 158 EFAtools-0.8.0/EFAtools/R/SL.R | 153 EFAtools-0.8.0/EFAtools/R/SMT.R | 227 EFAtools-0.8.0/EFAtools/R/SPSS_23_doc.R | 10 EFAtools-0.8.0/EFAtools/R/SPSS_27_doc.R | 10 EFAtools-0.8.0/EFAtools/R/ULS.R | 96 EFAtools-0.8.0/EFAtools/R/UPPS_raw_doc.R | 2 EFAtools-0.8.0/EFAtools/R/VARIMAX.R | 169 EFAtools-0.8.0/EFAtools/R/alignment.R |only EFAtools-0.8.0/EFAtools/R/averaging.R |only EFAtools-0.8.0/EFAtools/R/cor-input.R |only EFAtools-0.8.0/EFAtools/R/efa_group.R |only EFAtools-0.8.0/EFAtools/R/efa_power.R |only EFAtools-0.8.0/EFAtools/R/efa_reliability.R |only EFAtools-0.8.0/EFAtools/R/efa_retention.R |only EFAtools-0.8.0/EFAtools/R/efa_scores.R |only EFAtools-0.8.0/EFAtools/R/efa_screen.R |only EFAtools-0.8.0/EFAtools/R/efa_simulate.R |only EFAtools-0.8.0/EFAtools/R/estimate_model.R |only EFAtools-0.8.0/EFAtools/R/fiml-moments.R |only EFAtools-0.8.0/EFAtools/R/fit-indices.R |only EFAtools-0.8.0/EFAtools/R/format-helpers.R |only EFAtools-0.8.0/EFAtools/R/helper.R | 2143 ----- EFAtools-0.8.0/EFAtools/R/plot.COMPARE.R |only EFAtools-0.8.0/EFAtools/R/plot.EFA_AVERAGE.R | 32 EFAtools-0.8.0/EFAtools/R/plot.efa_group.R |only EFAtools-0.8.0/EFAtools/R/plot.efa_power.R |only EFAtools-0.8.0/EFAtools/R/polychoric.R |only EFAtools-0.8.0/EFAtools/R/population_models_doc.R | 20 EFAtools-0.8.0/EFAtools/R/presets.R |only EFAtools-0.8.0/EFAtools/R/print.BARTLETT.R | 108 EFAtools-0.8.0/EFAtools/R/print.COMPARE.R | 276 EFAtools-0.8.0/EFAtools/R/print.EFA.R | 4222 +++++----- EFAtools-0.8.0/EFAtools/R/print.EFA_AVERAGE.R | 514 - EFAtools-0.8.0/EFAtools/R/print.KMO.R | 161 EFAtools-0.8.0/EFAtools/R/print.LOADINGS.R | 883 -- EFAtools-0.8.0/EFAtools/R/print.OMEGA.R | 276 EFAtools-0.8.0/EFAtools/R/print.SL.R | 124 EFAtools-0.8.0/EFAtools/R/print.SLLOADINGS.R | 139 EFAtools-0.8.0/EFAtools/R/print.efa_group.R |only EFAtools-0.8.0/EFAtools/R/print.efa_reliability.R |only EFAtools-0.8.0/EFAtools/R/print.efa_screen.R |only EFAtools-0.8.0/EFAtools/R/print.efa_simulated.R |only EFAtools-0.8.0/EFAtools/R/procrustes-consensus.R |only EFAtools-0.8.0/EFAtools/R/residuals.EFA.R | 80 EFAtools-0.8.0/EFAtools/R/rotate_model.R |only EFAtools-0.8.0/EFAtools/R/se-fiml.R |only EFAtools-0.8.0/EFAtools/R/test_models_doc.R | 16 EFAtools-0.8.0/EFAtools/README.md | 1145 ++ EFAtools-0.8.0/EFAtools/build/partial.rdb |only EFAtools-0.8.0/EFAtools/inst/doc/EFAtools.Rmd | 4 EFAtools-0.8.0/EFAtools/inst/doc/EFAtools.html | 1861 +--- EFAtools-0.8.0/EFAtools/inst/doc/Replicate_SPSS_psych.html | 1156 +- EFAtools-0.8.0/EFAtools/man/BARTLETT.Rd | 31 EFAtools-0.8.0/EFAtools/man/CD.Rd | 70 EFAtools-0.8.0/EFAtools/man/COMPARE.Rd | 36 EFAtools-0.8.0/EFAtools/man/EFA.Rd | 630 + EFAtools-0.8.0/EFAtools/man/EFA_AVERAGE.Rd | 134 EFAtools-0.8.0/EFAtools/man/EFA_POOLED.Rd | 352 EFAtools-0.8.0/EFAtools/man/EFAtools-package.Rd | 5 EFAtools-0.8.0/EFAtools/man/EKC.Rd | 118 EFAtools-0.8.0/EFAtools/man/FACTOR_SCORES.Rd | 70 EFAtools-0.8.0/EFAtools/man/HULL.Rd | 115 EFAtools-0.8.0/EFAtools/man/IDS2_R.Rd | 30 EFAtools-0.8.0/EFAtools/man/KGC.Rd | 52 EFAtools-0.8.0/EFAtools/man/KMO.Rd | 35 EFAtools-0.8.0/EFAtools/man/MAP.Rd | 99 EFAtools-0.8.0/EFAtools/man/NEST.Rd | 69 EFAtools-0.8.0/EFAtools/man/N_FACTORS.Rd | 131 EFAtools-0.8.0/EFAtools/man/OMEGA.Rd | 93 EFAtools-0.8.0/EFAtools/man/PARALLEL.Rd | 101 EFAtools-0.8.0/EFAtools/man/PROCRUSTES.Rd | 57 EFAtools-0.8.0/EFAtools/man/SCREE.Rd | 39 EFAtools-0.8.0/EFAtools/man/SL.Rd | 39 EFAtools-0.8.0/EFAtools/man/SMT.Rd | 55 EFAtools-0.8.0/EFAtools/man/SPSS_23.Rd | 28 EFAtools-0.8.0/EFAtools/man/SPSS_27.Rd | 28 EFAtools-0.8.0/EFAtools/man/UPPS_raw.Rd | 4 EFAtools-0.8.0/EFAtools/man/WJIV_ages_14_19.Rd | 98 EFAtools-0.8.0/EFAtools/man/WJIV_ages_20_39.Rd | 98 EFAtools-0.8.0/EFAtools/man/WJIV_ages_3_5.Rd | 62 EFAtools-0.8.0/EFAtools/man/WJIV_ages_40_90.Rd | 98 EFAtools-0.8.0/EFAtools/man/WJIV_ages_6_8.Rd | 98 EFAtools-0.8.0/EFAtools/man/WJIV_ages_9_13.Rd | 98 EFAtools-0.8.0/EFAtools/man/dot-average_matrices.Rd | 34 EFAtools-0.8.0/EFAtools/man/dot-change_class.Rd | 2 EFAtools-0.8.0/EFAtools/man/dot-compute_vars.Rd | 8 EFAtools-0.8.0/EFAtools/man/dot-consensus_loss.Rd | 38 EFAtools-0.8.0/EFAtools/man/dot-consensus_target_procrustes_single.Rd | 169 EFAtools-0.8.0/EFAtools/man/dot-extract_list_object.Rd | 6 EFAtools-0.8.0/EFAtools/man/dot-gpa_consensus_target.Rd |only EFAtools-0.8.0/EFAtools/man/dot-hyperplane_count.Rd | 42 EFAtools-0.8.0/EFAtools/man/dot-oblique_procrustes.Rd | 49 EFAtools-0.8.0/EFAtools/man/dot-oblique_procrustes_batch.Rd |only EFAtools-0.8.0/EFAtools/man/dot-orthogonal_procrustes.Rd | 50 EFAtools-0.8.0/EFAtools/man/dot-parallel_sim.Rd | 2 EFAtools-0.8.0/EFAtools/man/dot-rotate_bentler_oblq.Rd |only EFAtools-0.8.0/EFAtools/man/dot-rotate_bentler_orth.Rd |only EFAtools-0.8.0/EFAtools/man/dot-rotate_bifactor_oblq.Rd |only EFAtools-0.8.0/EFAtools/man/dot-rotate_bifactor_orth.Rd |only EFAtools-0.8.0/EFAtools/man/dot-rotate_cf_orth.Rd |only EFAtools-0.8.0/EFAtools/man/dot-rotate_geomin_oblq.Rd |only EFAtools-0.8.0/EFAtools/man/dot-rotate_geomin_orth.Rd |only EFAtools-0.8.0/EFAtools/man/dot-rotate_oblimin.Rd |only EFAtools-0.8.0/EFAtools/man/dot-rotate_simplimax_oblq.Rd |only EFAtools-0.8.0/EFAtools/man/dot-rotation_se_jacobian.Rd |only EFAtools-0.8.0/EFAtools/man/dot-simulate_cfm_eigen.Rd |only EFAtools-0.8.0/EFAtools/man/dot-simulate_cfm_mvn.Rd |only EFAtools-0.8.0/EFAtools/man/dot-tucker_congruence.Rd | 52 EFAtools-0.8.0/EFAtools/man/efa_group.Rd 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EFAtools-0.8.0/EFAtools/man/print.BARTLETT.Rd | 29 EFAtools-0.8.0/EFAtools/man/print.COMPARE.Rd | 32 EFAtools-0.8.0/EFAtools/man/print.EFA.Rd | 223 EFAtools-0.8.0/EFAtools/man/print.EFA_AVERAGE.Rd | 32 EFAtools-0.8.0/EFAtools/man/print.KMO.Rd | 25 EFAtools-0.8.0/EFAtools/man/print.LOADINGS.Rd | 29 EFAtools-0.8.0/EFAtools/man/print.N_FACTORS.Rd | 19 EFAtools-0.8.0/EFAtools/man/print.OMEGA.Rd | 35 EFAtools-0.8.0/EFAtools/man/print.SL.Rd | 27 EFAtools-0.8.0/EFAtools/man/print.SLLOADINGS.Rd | 18 EFAtools-0.8.0/EFAtools/man/print.efa_group.Rd |only EFAtools-0.8.0/EFAtools/man/print.efa_power.Rd |only EFAtools-0.8.0/EFAtools/man/print.efa_reliability.Rd |only EFAtools-0.8.0/EFAtools/man/print.efa_retention.Rd |only EFAtools-0.8.0/EFAtools/man/print.efa_scores.Rd |only EFAtools-0.8.0/EFAtools/man/print.efa_screen.Rd |only EFAtools-0.8.0/EFAtools/man/print.efa_simulated.Rd |only EFAtools-0.8.0/EFAtools/man/residuals.EFA.Rd | 27 EFAtools-0.8.0/EFAtools/man/test_models.Rd | 20 EFAtools-0.8.0/EFAtools/src/Makevars | 3 EFAtools-0.8.0/EFAtools/src/Makevars.win | 3 EFAtools-0.8.0/EFAtools/src/RcppExports.cpp | 433 - EFAtools-0.8.0/EFAtools/src/estimate.cpp |only EFAtools-0.8.0/EFAtools/src/factor_corres.cpp | 15 EFAtools-0.8.0/EFAtools/src/gpf_common.h |only EFAtools-0.8.0/EFAtools/src/gpf_engine.h |only EFAtools-0.8.0/EFAtools/src/oblique_procrustes.cpp | 723 - EFAtools-0.8.0/EFAtools/src/paf_iter.cpp | 400 EFAtools-0.8.0/EFAtools/src/parallel.cpp | 406 EFAtools-0.8.0/EFAtools/src/polychoric.cpp |only EFAtools-0.8.0/EFAtools/src/rotate.cpp |only EFAtools-0.8.0/EFAtools/src/sim.cpp |only EFAtools-0.8.0/EFAtools/tests/testthat/_snaps |only EFAtools-0.8.0/EFAtools/tests/testthat/helper-efa_retention.R |only EFAtools-0.8.0/EFAtools/tests/testthat/helper-slow.R |only EFAtools-0.8.0/EFAtools/tests/testthat/helper-snapshot.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-BARTLETT.R | 84 EFAtools-0.8.0/EFAtools/tests/testthat/test-CD.R | 74 EFAtools-0.8.0/EFAtools/tests/testthat/test-COMPARE.R | 436 - EFAtools-0.8.0/EFAtools/tests/testthat/test-DWLS.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA-boot.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA-fields.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA-fiml.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA-vcov-slot.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA.R | 447 - EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_AVERAGE-fiml.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_AVERAGE-grid.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_AVERAGE.R | 316 EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_POOLED-cfi-scale.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_POOLED-k1-oblique.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_POOLED-mi2s.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_POOLED-routing.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_POOLED-rubin-rotated.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_POOLED-rubin-unrot-procrustes.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_POOLED-rubin-unrot.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EFA_POOLED.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-EKC.R | 71 EFAtools-0.8.0/EFAtools/tests/testthat/test-FACTOR_SCORES.R | 95 EFAtools-0.8.0/EFAtools/tests/testthat/test-HULL.R | 278 EFAtools-0.8.0/EFAtools/tests/testthat/test-KGC.R | 81 EFAtools-0.8.0/EFAtools/tests/testthat/test-KMO.R | 46 EFAtools-0.8.0/EFAtools/tests/testthat/test-MAP.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-ML.R | 72 EFAtools-0.8.0/EFAtools/tests/testthat/test-NEST.R | 268 EFAtools-0.8.0/EFAtools/tests/testthat/test-N_FACTORS.R | 171 EFAtools-0.8.0/EFAtools/tests/testthat/test-OMEGA.R | 182 EFAtools-0.8.0/EFAtools/tests/testthat/test-OMEGA_helper.R | 289 EFAtools-0.8.0/EFAtools/tests/testthat/test-PAF.R | 236 EFAtools-0.8.0/EFAtools/tests/testthat/test-PARALLEL.R | 325 EFAtools-0.8.0/EFAtools/tests/testthat/test-PROCRUSTES.R | 103 EFAtools-0.8.0/EFAtools/tests/testthat/test-PROMAX.R | 81 EFAtools-0.8.0/EFAtools/tests/testthat/test-ROTATE_OBLQ.R | 286 EFAtools-0.8.0/EFAtools/tests/testthat/test-ROTATE_ORTH.R | 158 EFAtools-0.8.0/EFAtools/tests/testthat/test-RcppExports.R | 10 EFAtools-0.8.0/EFAtools/tests/testthat/test-SCREE.R | 60 EFAtools-0.8.0/EFAtools/tests/testthat/test-SL.R | 147 EFAtools-0.8.0/EFAtools/tests/testthat/test-SMT.R | 306 EFAtools-0.8.0/EFAtools/tests/testthat/test-ULS.R | 97 EFAtools-0.8.0/EFAtools/tests/testthat/test-VARIMAX.R | 58 EFAtools-0.8.0/EFAtools/tests/testthat/test-cor-method-poly.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-efa_group.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-efa_power.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-efa_reliability.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-efa_retention.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-efa_scores.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-efa_screen.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-efa_simulate.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-factor_score_diagnostics.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-factor_score_weights.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-fiml-acov.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-fiml-moments.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-format-loadings.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-helper.R | 537 - EFAtools-0.8.0/EFAtools/tests/testthat/test-plot-retention.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-polychoric.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-prepare_cor_input.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-presets.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-procrustes-consensus.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-regression-estimators.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-regression-rotations.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-reliability_adapters.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-reliability_core.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-reliability_result.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-se-information.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-se-sandwich.R |only EFAtools-0.8.0/EFAtools/tests/testthat/test-snapshots.R |only EFAtools-0.8.0/EFAtools/vignettes/EFAtools.Rmd | 4 309 files changed, 20845 insertions(+), 16205 deletions(-)
Title: Analyse Citation Data from Google Scholar
Description: Provides tools to retrieve, analyse, and format publication and
citation data from Google Scholar profiles. It supports profile lookup,
publication records, citation histories, scholar comparison, coauthor
networks, journal ranking queries, CV-ready publication lists, and citation
metric summaries.
Author: Guangchuang Yu [aut, cre] ,
James Keirstead [aut],
Gregory Jefferis [aut] ,
Gordon Getzinger [ctb],
Jorge Cimentada [ctb],
Max Czapanskiy [ctb],
Dominique Makowski [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between scholar versions 0.2.6 dated 2026-02-26 and 1.0.0 dated 2026-07-07
scholar-0.2.6/scholar/R/sysdata.rda |only scholar-0.2.6/scholar/inst/doc/scholar.Rmd |only scholar-0.2.6/scholar/vignettes/scholar.Rmd |only scholar-1.0.0/scholar/DESCRIPTION | 20 scholar-1.0.0/scholar/MD5 | 63 scholar-1.0.0/scholar/NAMESPACE | 5 scholar-1.0.0/scholar/NEWS.md | 18 scholar-1.0.0/scholar/R/coauthors.R | 223 +- scholar-1.0.0/scholar/R/format_publications.R | 9 scholar-1.0.0/scholar/R/getCompleteAuthors.R | 38 scholar-1.0.0/scholar/R/predict.r | 41 scholar-1.0.0/scholar/R/publications.r | 213 ++ scholar-1.0.0/scholar/R/scholar.r | 247 ++- scholar-1.0.0/scholar/R/utils.R | 138 + scholar-1.0.0/scholar/build/partial.rdb |binary scholar-1.0.0/scholar/build/vignette.rds |binary scholar-1.0.0/scholar/inst/WORDLIST | 22 scholar-1.0.0/scholar/inst/doc/scholar.R | 160 +- scholar-1.0.0/scholar/inst/doc/scholar.html | 767 +++++----- scholar-1.0.0/scholar/inst/doc/scholar.qmd |only scholar-1.0.0/scholar/man/format_publications.Rd | 2 scholar-1.0.0/scholar/man/get_coauthors.Rd | 5 scholar-1.0.0/scholar/man/get_journalrank.Rd | 69 scholar-1.0.0/scholar/man/get_profile.Rd | 2 scholar-1.0.0/scholar/man/get_publication_abstract.Rd | 42 scholar-1.0.0/scholar/man/get_publication_metrics.Rd |only scholar-1.0.0/scholar/man/get_publications_all_authors.Rd |only scholar-1.0.0/scholar/man/get_scholar_metrics.Rd |only scholar-1.0.0/scholar/man/scholar-package.Rd | 1 scholar-1.0.0/scholar/man/search_scholar_ids.Rd |only scholar-1.0.0/scholar/tests/testthat/test-author-position.R |only scholar-1.0.0/scholar/tests/testthat/test-citation-history.R |only scholar-1.0.0/scholar/tests/testthat/test-coauthors.R |only scholar-1.0.0/scholar/tests/testthat/test-complete-authors.R |only scholar-1.0.0/scholar/tests/testthat/test-encoding.R |only scholar-1.0.0/scholar/tests/testthat/test-metrics.R |only scholar-1.0.0/scholar/tests/testthat/test-predict.R |only scholar-1.0.0/scholar/tests/testthat/test-publications.R |only scholar-1.0.0/scholar/tests/testthat/test-scholar-id-search.R |only scholar-1.0.0/scholar/tests/testthat/test-scholar-response.R |only scholar-1.0.0/scholar/tests/testthat/test-scholar.R | 111 - scholar-1.0.0/scholar/vignettes/scholar.qmd |only 42 files changed, 1366 insertions(+), 830 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of data analysis approaches for microbiome data based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 2.2.0 dated 2026-05-14 and 2.3.0 dated 2026-07-07
DESCRIPTION | 18 MD5 | 58 NAMESPACE | 2 R/data.R | 412 ++--- R/help.R | 89 - R/import.R | 40 R/microtable.R | 2018 +++++++++++++------------- R/trans_abund.R | 2070 +++++++++++++------------- R/trans_alpha.R | 2472 ++++++++++++++++---------------- R/trans_beta.R | 2135 +++++++++++++-------------- R/trans_classifier.R | 1632 ++++++++++----------- R/trans_diff.R | 3923 +++++++++++++++++++++++++-------------------------- R/trans_env.R | 3307 +++++++++++++++++++++--------------------- R/trans_func.R | 2143 ++++++++++++++------------- R/trans_metab.R | 1639 ++++++++++----------- R/trans_network.R | 3564 +++++++++++++++++++++++----------------------- R/trans_niche.R |only R/trans_norm.R | 15 R/trans_phylo.R |only R/trans_venn.R | 1264 ++++++++-------- R/utility.R | 1706 +++++++++++----------- inst/CITATION | 12 man/microeco.Rd | 11 man/microtable.Rd | 8 man/trans_alpha.Rd | 2 man/trans_beta.Rd | 2 man/trans_diff.Rd | 6 man/trans_env.Rd | 2 man/trans_metab.Rd | 5 man/trans_network.Rd | 17 man/trans_niche.Rd |only man/trans_phylo.Rd |only 32 files changed, 14338 insertions(+), 14234 deletions(-)
Title: Decorate a 'ggplot' with Associated Information
Description: Supports data-driven composition of a main plot with associated subplots that need precise axis alignment. Unlike general layout-focused tools such as 'cowplot' and 'patchwork', it enables related subplots to be integrated on the top, bottom, left, or right sides of a main plot with matched axes, so that the combined panels can be interpreted as a coherent whole. This design was inspired by the 'Method 2' described in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>).
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Thomas Hackl [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplot versions 0.3.0 dated 2026-06-23 and 0.3.1 dated 2026-07-07
DESCRIPTION | 12 - MD5 | 17 +- NAMESPACE | 3 NEWS.md | 6 R/aplot.R | 299 +++++++++++++++++++++---------------- R/guide-area.R |only R/guide-layout.R |only man/aplot-package.Rd | 2 man/set_guide_area.Rd |only man/set_guide_layout.Rd |only tests/testthat/Rplots.pdf |only tests/testthat/test-guide-area.R |only tests/testthat/test-guide-layout.R |only 13 files changed, 203 insertions(+), 136 deletions(-)
Title: High Dimensional Time Series Analysis Tools
Description: An implementation for high-dimensional time series analysis methods, including factor model for vector time series
proposed by Lam and Yao (2012) <doi:10.1214/12-AOS970> and Chang, Guo and Yao (2015)
<doi:10.1016/j.jeconom.2015.03.024>, martingale difference test proposed by
Chang, Jiang and Shao (2023) <doi:10.1016/j.jeconom.2022.09.001>, principal
component analysis for vector time series proposed by Chang, Guo and Yao (2018) <doi:10.1214/17-AOS1613>,
cointegration analysis proposed by Zhang, Robinson and Yao (2019)
<doi:10.1080/01621459.2018.1458620>, unit root test proposed by Chang, Cheng and Yao (2022)
<doi:10.1093/biomet/asab034>, white noise tests proposed by Chang, Yao and Zhou (2017)
<doi:10.1093/biomet/asw066> and Chang et al. (2026+), CP-decomposition for matrix time
series proposed by Chang et al. (2023) <doi:10.1093/jrsssb/qkac011> and
Chang et al. (2026+) <doi:10.48550/arXiv.2410.05634>, CP-decomposition for tensor ti [...truncated...]
Author: Jinyuan Chang [aut],
Jing He [aut],
Chen Lin [aut, cre],
Qiwei Yao [aut]
Maintainer: Chen Lin <linchen@smail.swufe.edu.cn>
Diff between HDTSA versions 1.0.6-1 dated 2026-06-23 and 1.0.6-2 dated 2026-07-07
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/CP_functions_unified.R | 8 ++++++-- R/tools_wntest.R | 1 - 4 files changed, 15 insertions(+), 12 deletions(-)
Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 1.1.5 dated 2026-04-25 and 1.1.6 dated 2026-07-07
aifeducation-1.1.5/aifeducation/inst/python/DataCollatorForMPLM_PT.py |only aifeducation-1.1.5/aifeducation/inst/python/data_collator.py |only aifeducation-1.1.5/aifeducation/tests/testthat/test-02_07_BaseModels_from_hf.R |only aifeducation-1.1.6/aifeducation/DESCRIPTION | 11 aifeducation-1.1.6/aifeducation/MD5 | 436 ++--- aifeducation-1.1.6/aifeducation/NAMESPACE | 8 aifeducation-1.1.6/aifeducation/NEWS.md | 77 - aifeducation-1.1.6/aifeducation/R/Studio_BaseModel_Create.R | 2 aifeducation-1.1.6/aifeducation/R/Studio_BaseModel_Train.R | 2 aifeducation-1.1.6/aifeducation/R/Studio_ErrorModal_ProcessModal.R | 18 aifeducation-1.1.6/aifeducation/R/Studio_ExtendedTasks.R | 7 aifeducation-1.1.6/aifeducation/R/Studio_ProgressModal.R | 2 aifeducation-1.1.6/aifeducation/R/Studio_TextEmbeddingModel_Create.R | 120 + aifeducation-1.1.6/aifeducation/R/def_DocumentationDesc.R | 49 aifeducation-1.1.6/aifeducation/R/def_Object_Management.R | 23 aifeducation-1.1.6/aifeducation/R/def_ParameterDefinitions.R | 165 +- aifeducation-1.1.6/aifeducation/R/install_and_config.R | 174 +- aifeducation-1.1.6/aifeducation/R/obj_AIFEBaseModel.R | 18 aifeducation-1.1.6/aifeducation/R/obj_BaseModelAlbert.R |only aifeducation-1.1.6/aifeducation/R/obj_BaseModelBert.R | 13 aifeducation-1.1.6/aifeducation/R/obj_BaseModelCore.R | 151 + aifeducation-1.1.6/aifeducation/R/obj_BaseModelDebertaV2.R | 9 aifeducation-1.1.6/aifeducation/R/obj_BaseModelDistilBert.R |only aifeducation-1.1.6/aifeducation/R/obj_BaseModelEuroBERT.R |only aifeducation-1.1.6/aifeducation/R/obj_BaseModelFunnel.R | 11 aifeducation-1.1.6/aifeducation/R/obj_BaseModelMPNet.R | 74 aifeducation-1.1.6/aifeducation/R/obj_BaseModelModernBert.R | 20 aifeducation-1.1.6/aifeducation/R/obj_BaseModelRoberta.R | 10 aifeducation-1.1.6/aifeducation/R/obj_BaseModelRobertaXML.R |only aifeducation-1.1.6/aifeducation/R/obj_BaseModelXmod.R |only aifeducation-1.1.6/aifeducation/R/obj_ClassifiersBasedOnTextEmbeddings.R | 194 +- aifeducation-1.1.6/aifeducation/R/obj_DataManager.R | 156 +- aifeducation-1.1.6/aifeducation/R/obj_EmbeddedText.R | 14 aifeducation-1.1.6/aifeducation/R/obj_FeatureExtractor.R | 90 - aifeducation-1.1.6/aifeducation/R/obj_LargeDataSetBase.R | 27 aifeducation-1.1.6/aifeducation/R/obj_LargeDataSetForTextEmbeddings.R | 16 aifeducation-1.1.6/aifeducation/R/obj_ModelsBasedOnTextEmbeddings.R | 267 +++ aifeducation-1.1.6/aifeducation/R/obj_TEClassifierParallel.R | 9 aifeducation-1.1.6/aifeducation/R/obj_TEClassifierParallelPrototype.R | 10 aifeducation-1.1.6/aifeducation/R/obj_TEClassifierProtoNet.R | 9 aifeducation-1.1.6/aifeducation/R/obj_TEClassifierRegular.R | 5 aifeducation-1.1.6/aifeducation/R/obj_TEClassifierSequential.R | 6 aifeducation-1.1.6/aifeducation/R/obj_TEClassifierSequentialPrototype.R | 8 aifeducation-1.1.6/aifeducation/R/obj_TEClassifiersBasedOnProtoNet.R | 117 + aifeducation-1.1.6/aifeducation/R/obj_TEClassifiersBasedOnRegular.R | 14 aifeducation-1.1.6/aifeducation/R/obj_TextEmbeddingModel.R | 80 - aifeducation-1.1.6/aifeducation/R/obj_Tokenizer.R | 162 +- aifeducation-1.1.6/aifeducation/R/onLoad.R | 7 aifeducation-1.1.6/aifeducation/R/saving_and_loading.R | 2 aifeducation-1.1.6/aifeducation/R/utils_DataManager.R | 214 -- aifeducation-1.1.6/aifeducation/R/utils_Studio.R | 6 aifeducation-1.1.6/aifeducation/R/utils_check.R | 2 aifeducation-1.1.6/aifeducation/R/utils_general.R | 131 + aifeducation-1.1.6/aifeducation/R/utils_log.R | 10 aifeducation-1.1.6/aifeducation/R/utils_plot.R | 53 aifeducation-1.1.6/aifeducation/R/utils_python.R | 44 aifeducation-1.1.6/aifeducation/R/utils_python_data_management.R | 23 aifeducation-1.1.6/aifeducation/R/utils_test_that.R | 35 aifeducation-1.1.6/aifeducation/README.md | 9 aifeducation-1.1.6/aifeducation/build/vignette.rds |binary aifeducation-1.1.6/aifeducation/inst/doc/a02_base_model_types.R |only aifeducation-1.1.6/aifeducation/inst/doc/a02_base_model_types.Rmd |only aifeducation-1.1.6/aifeducation/inst/doc/a02_base_model_types.html |only aifeducation-1.1.6/aifeducation/inst/doc/aifeducation.Rmd | 33 aifeducation-1.1.6/aifeducation/inst/doc/aifeducation.html | 59 aifeducation-1.1.6/aifeducation/inst/python/MPNetForMPLM_PT.py | 73 aifeducation-1.1.6/aifeducation/inst/python/__pycache__ |only aifeducation-1.1.6/aifeducation/inst/python/data_collator_factory.py |only aifeducation-1.1.6/aifeducation/inst/python/data_collators.py |only aifeducation-1.1.6/aifeducation/inst/python/py_log.py | 121 + aifeducation-1.1.6/aifeducation/inst/python/pytorch_act_fct.py | 17 aifeducation-1.1.6/aifeducation/inst/python/pytorch_autoencoder.py | 53 aifeducation-1.1.6/aifeducation/inst/python/pytorch_classifier_models.py | 108 - aifeducation-1.1.6/aifeducation/inst/python/pytorch_cls_training_loops.py | 352 +++- aifeducation-1.1.6/aifeducation/inst/python/pytorch_datacollators.py | 6 aifeducation-1.1.6/aifeducation/inst/python/pytorch_distance_fun.py | 48 aifeducation-1.1.6/aifeducation/inst/python/pytorch_layers.py | 96 - aifeducation-1.1.6/aifeducation/inst/python/pytorch_loss_fct.py | 21 aifeducation-1.1.6/aifeducation/inst/python/pytorch_old_scripts.py | 6 aifeducation-1.1.6/aifeducation/inst/python/pytorch_text_embedding_model.py | 13 aifeducation-1.1.6/aifeducation/inst/python/tests |only aifeducation-1.1.6/aifeducation/man/AIFEBaseModel.Rd | 96 - aifeducation-1.1.6/aifeducation/man/AIFEMaster.Rd | 505 +++--- aifeducation-1.1.6/aifeducation/man/BaseModelAlbert.Rd |only aifeducation-1.1.6/aifeducation/man/BaseModelBert.Rd | 195 +- aifeducation-1.1.6/aifeducation/man/BaseModelCore.Rd | 768 +++++----- aifeducation-1.1.6/aifeducation/man/BaseModelDebertaV2.Rd | 193 +- aifeducation-1.1.6/aifeducation/man/BaseModelDistilBERT.Rd |only aifeducation-1.1.6/aifeducation/man/BaseModelEuroBert.Rd |only aifeducation-1.1.6/aifeducation/man/BaseModelFunnel.Rd | 236 +-- aifeducation-1.1.6/aifeducation/man/BaseModelMPNet.Rd | 310 ++-- aifeducation-1.1.6/aifeducation/man/BaseModelModernBert.Rd | 209 +- aifeducation-1.1.6/aifeducation/man/BaseModelRoberta.Rd | 193 +- aifeducation-1.1.6/aifeducation/man/BaseModelRobertaXML.Rd |only aifeducation-1.1.6/aifeducation/man/BaseModelXmod.Rd |only aifeducation-1.1.6/aifeducation/man/BaseModelsIndex.Rd | 23 aifeducation-1.1.6/aifeducation/man/ClassifiersBasedOnTextEmbeddings.Rd | 496 +++--- aifeducation-1.1.6/aifeducation/man/DataManagerClassifier.Rd | 533 +++--- aifeducation-1.1.6/aifeducation/man/DataSetsIndex.Rd | 23 aifeducation-1.1.6/aifeducation/man/EmbeddedText.Rd | 566 +++---- aifeducation-1.1.6/aifeducation/man/HuggingFaceTokenizer.Rd | 147 + aifeducation-1.1.6/aifeducation/man/LargeDataSetBase.Rd | 413 ++--- aifeducation-1.1.6/aifeducation/man/LargeDataSetForText.Rd | 366 ++-- aifeducation-1.1.6/aifeducation/man/LargeDataSetForTextEmbeddings.Rd | 579 +++---- aifeducation-1.1.6/aifeducation/man/ModelsBasedOnTextEmbeddings.Rd | 339 ++-- aifeducation-1.1.6/aifeducation/man/Reliability_Server.Rd | 4 aifeducation-1.1.6/aifeducation/man/Reliability_UI.Rd | 4 aifeducation-1.1.6/aifeducation/man/TEClassifierParallel.Rd | 483 ++++-- aifeducation-1.1.6/aifeducation/man/TEClassifierParallelPrototype.Rd | 501 ++++-- aifeducation-1.1.6/aifeducation/man/TEClassifierProtoNet.Rd | 353 ++-- aifeducation-1.1.6/aifeducation/man/TEClassifierRegular.Rd | 257 +-- aifeducation-1.1.6/aifeducation/man/TEClassifierSequential.Rd | 465 +++--- aifeducation-1.1.6/aifeducation/man/TEClassifierSequentialPrototype.Rd | 483 ++++-- aifeducation-1.1.6/aifeducation/man/TEClassifiersBasedOnProtoNet.Rd | 510 +++--- aifeducation-1.1.6/aifeducation/man/TEClassifiersBasedOnRegular.Rd | 290 ++- aifeducation-1.1.6/aifeducation/man/TEFeatureExtractor.Rd | 444 +++-- aifeducation-1.1.6/aifeducation/man/TextEmbeddingModel.Rd | 648 ++++---- aifeducation-1.1.6/aifeducation/man/TokenizerBase.Rd | 451 +++-- aifeducation-1.1.6/aifeducation/man/TokenizerIndex.Rd | 23 aifeducation-1.1.6/aifeducation/man/WordPieceTokenizer.Rd | 208 +- aifeducation-1.1.6/aifeducation/man/add_missing_args.Rd | 8 aifeducation-1.1.6/aifeducation/man/auto_n_cores.Rd | 20 aifeducation-1.1.6/aifeducation/man/build_documentation_for_model.Rd | 19 aifeducation-1.1.6/aifeducation/man/build_layer_overview_base_models.Rd |only aifeducation-1.1.6/aifeducation/man/build_layer_stack_documentation_for_vignette.Rd | 19 aifeducation-1.1.6/aifeducation/man/calc_standard_classification_measures.Rd | 14 aifeducation-1.1.6/aifeducation/man/calc_tokenizer_statistics.Rd | 4 aifeducation-1.1.6/aifeducation/man/cat_message.Rd | 18 aifeducation-1.1.6/aifeducation/man/check_adjust_n_samples_on_CI.Rd | 18 aifeducation-1.1.6/aifeducation/man/check_aif_py_modules.Rd | 22 aifeducation-1.1.6/aifeducation/man/check_all_args.Rd | 4 aifeducation-1.1.6/aifeducation/man/check_class_and_type.Rd | 4 aifeducation-1.1.6/aifeducation/man/class_vector_to_py_dataset.Rd | 20 aifeducation-1.1.6/aifeducation/man/clean_pytorch_log_transformers.Rd | 18 aifeducation-1.1.6/aifeducation/man/cohens_kappa.Rd | 14 aifeducation-1.1.6/aifeducation/man/create_data_embeddings_description.Rd | 8 aifeducation-1.1.6/aifeducation/man/create_dir.Rd | 4 aifeducation-1.1.6/aifeducation/man/create_object.Rd | 20 aifeducation-1.1.6/aifeducation/man/create_py_dataset_cache_file_path.Rd | 20 aifeducation-1.1.6/aifeducation/man/create_synthetic_units_from_matrix.Rd | 20 aifeducation-1.1.6/aifeducation/man/data.frame_to_py_dataset.Rd | 20 aifeducation-1.1.6/aifeducation/man/doc_formula.Rd | 16 aifeducation-1.1.6/aifeducation/man/extract_column_from_py_dataset.Rd | 20 aifeducation-1.1.6/aifeducation/man/fleiss_kappa.Rd | 14 aifeducation-1.1.6/aifeducation/man/generate_args_for_tests.Rd | 18 aifeducation-1.1.6/aifeducation/man/generate_embeddings.Rd | 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aifeducation-1.1.6/aifeducation/man/install_aifeducation.Rd | 18 aifeducation-1.1.6/aifeducation/man/install_aifeducation_studio.Rd | 18 aifeducation-1.1.6/aifeducation/man/install_protocol_buffer_compiler.Rd |only aifeducation-1.1.6/aifeducation/man/install_py_modules.Rd | 18 aifeducation-1.1.6/aifeducation/man/kendalls_w.Rd | 14 aifeducation-1.1.6/aifeducation/man/kripp_alpha.Rd | 14 aifeducation-1.1.6/aifeducation/man/load_all_py_scripts.Rd | 10 aifeducation-1.1.6/aifeducation/man/load_from_disk.Rd | 4 aifeducation-1.1.6/aifeducation/man/load_py_scripts.Rd | 10 aifeducation-1.1.6/aifeducation/man/long_load_target_data.Rd | 8 aifeducation-1.1.6/aifeducation/man/matrix_to_array_c.Rd | 20 aifeducation-1.1.6/aifeducation/man/monitor_test_time_on_CI.Rd | 18 aifeducation-1.1.6/aifeducation/man/output_message.Rd | 18 aifeducation-1.1.6/aifeducation/man/prepare_r_array_for_dataset.Rd | 20 aifeducation-1.1.6/aifeducation/man/prepare_session.Rd | 24 aifeducation-1.1.6/aifeducation/man/print_message.Rd | 18 aifeducation-1.1.6/aifeducation/man/py_dataset_to_embeddings.Rd | 20 aifeducation-1.1.6/aifeducation/man/random_bool_on_CI.Rd | 18 aifeducation-1.1.6/aifeducation/man/read_log.Rd | 18 aifeducation-1.1.6/aifeducation/man/read_loss_log.Rd | 18 aifeducation-1.1.6/aifeducation/man/reduce_to_unique.Rd | 20 aifeducation-1.1.6/aifeducation/man/reset_log.Rd | 18 aifeducation-1.1.6/aifeducation/man/reset_loss_log.Rd | 18 aifeducation-1.1.6/aifeducation/man/run_py_file.Rd | 10 aifeducation-1.1.6/aifeducation/man/save_to_disk.Rd | 4 aifeducation-1.1.6/aifeducation/man/set_codecarbon_logger.Rd |only aifeducation-1.1.6/aifeducation/man/set_transformers_logger.Rd | 25 aifeducation-1.1.6/aifeducation/man/summarize_args_for_long_task.Rd | 8 aifeducation-1.1.6/aifeducation/man/summarize_tracked_sustainability.Rd | 4 aifeducation-1.1.6/aifeducation/man/tensor_list_to_numpy.Rd | 20 aifeducation-1.1.6/aifeducation/man/tensor_to_matrix_c.Rd | 20 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changed, 10550 insertions(+), 6853 deletions(-)
Title: Visualise and Report 'VALD ForceDecks' Test Results
Description: Provides a 'shiny' dashboard and plotting utilities to explore and
report 'VALD ForceDecks' testing data. Includes interactive modules for
metric exploration, radar charts, longitudinal comparisons, quadrant plots,
and athlete reports.
Author: Kieran Harrison [aut, cre],
VALD Support [ctb],
VALD [cph]
Maintainer: Kieran Harrison <k.harrison@vald.com>
Diff between valdrViz versions 1.0.1 dated 2026-01-20 and 1.0.2 dated 2026-07-07
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 46 +++++++++++++++++++++++----------------------- R/utils.R | 4 ---- man/REQ.Rd | 32 ++++++++++++++++---------------- man/fd_read_folder.Rd | 38 +++++++++++++++++++------------------- man/fd_standardise.Rd | 32 ++++++++++++++++---------------- man/html_to_pdf.Rd | 36 ++++++++++++++++++------------------ man/metric_pal.Rd | 32 ++++++++++++++++---------------- man/pipe.Rd | 34 +++++++++++++++++----------------- man/read_fd.Rd | 36 ++++++++++++++++++------------------ man/rot_theme.Rd | 32 ++++++++++++++++---------------- man/valdrViz-package.Rd | 44 ++++++++++++++++++++++---------------------- man/viz_theme.Rd | 24 ++++++++++++------------ tests/testthat.R | 24 ++++++++++++------------ 15 files changed, 222 insertions(+), 226 deletions(-)
Title: Publication-Quality 'ggplot2' Themes
Description: Complete themes for publication-quality 'ggplot2' visualisation.
Also provides functions to modify these based on the positional axis scales
and orientation of a particular plot.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggrefine versions 0.4.0 dated 2026-05-04 and 0.5.0 dated 2026-07-07
ggrefine-0.4.0/ggrefine/R/classic.R |only ggrefine-0.4.0/ggrefine/R/hybrid.R |only ggrefine-0.4.0/ggrefine/R/minimal.R |only ggrefine-0.4.0/ggrefine/R/modern.R |only ggrefine-0.4.0/ggrefine/R/none.R |only ggrefine-0.4.0/ggrefine/R/theme-dark.R |only ggrefine-0.4.0/ggrefine/R/theme-grey.R |only ggrefine-0.4.0/ggrefine/R/theme-light.R |only ggrefine-0.4.0/ggrefine/R/theme-oat.R |only ggrefine-0.4.0/ggrefine/R/void.R |only ggrefine-0.4.0/ggrefine/man/classic.Rd |only ggrefine-0.4.0/ggrefine/man/hybrid.Rd |only ggrefine-0.4.0/ggrefine/man/minimal.Rd |only ggrefine-0.4.0/ggrefine/man/modern.Rd |only ggrefine-0.4.0/ggrefine/man/none.Rd |only ggrefine-0.4.0/ggrefine/man/theme_oat.Rd |only ggrefine-0.4.0/ggrefine/man/void.Rd |only ggrefine-0.5.0/ggrefine/DESCRIPTION | 13 ggrefine-0.5.0/ggrefine/MD5 | 64 +-- ggrefine-0.5.0/ggrefine/NAMESPACE | 24 - ggrefine-0.5.0/ggrefine/NEWS.md | 7 ggrefine-0.5.0/ggrefine/R/refine.R |only ggrefine-0.5.0/ggrefine/R/theme.R |only ggrefine-0.5.0/ggrefine/README.md | 172 +++++++--- ggrefine-0.5.0/ggrefine/man/classic_drift.Rd |only ggrefine-0.5.0/ggrefine/man/classic_drop.Rd |only ggrefine-0.5.0/ggrefine/man/classic_flow.Rd |only ggrefine-0.5.0/ggrefine/man/classic_keep.Rd |only ggrefine-0.5.0/ggrefine/man/figures/README-example-1.png |binary ggrefine-0.5.0/ggrefine/man/figures/README-unnamed-chunk-2-1.png |binary ggrefine-0.5.0/ggrefine/man/figures/README-unnamed-chunk-3-1.png |binary ggrefine-0.5.0/ggrefine/man/figures/README-unnamed-chunk-4-1.png |binary ggrefine-0.5.0/ggrefine/man/figures/README-unnamed-chunk-5-1.png |binary ggrefine-0.5.0/ggrefine/man/figures/README-unnamed-chunk-6-1.png |binary ggrefine-0.5.0/ggrefine/man/minimal_drift.Rd |only ggrefine-0.5.0/ggrefine/man/minimal_drop.Rd |only ggrefine-0.5.0/ggrefine/man/minimal_flow.Rd |only ggrefine-0.5.0/ggrefine/man/minimal_keep.Rd |only ggrefine-0.5.0/ggrefine/man/modern_drift.Rd |only ggrefine-0.5.0/ggrefine/man/modern_drop.Rd |only ggrefine-0.5.0/ggrefine/man/modern_flow.Rd |only ggrefine-0.5.0/ggrefine/man/modern_keep.Rd |only ggrefine-0.5.0/ggrefine/man/theme_dark.Rd | 96 ++--- ggrefine-0.5.0/ggrefine/man/theme_ggplot2.Rd |only ggrefine-0.5.0/ggrefine/man/theme_grey.Rd | 103 ++--- ggrefine-0.5.0/ggrefine/man/theme_light.Rd | 75 ++-- ggrefine-0.5.0/ggrefine/man/void_drift.Rd |only ggrefine-0.5.0/ggrefine/man/void_drop.Rd |only ggrefine-0.5.0/ggrefine/man/void_flow.Rd |only ggrefine-0.5.0/ggrefine/man/void_keep.Rd |only ggrefine-0.5.0/ggrefine/tests/spelling.R | 10 51 files changed, 342 insertions(+), 222 deletions(-)
Title: Publication-Quality 'ggplot2' Visualisation
Description: Wrapper 'ggplot2' functions for publication-quality visualisation.
Aligned with 'ggplot2' and 'tidyverse'. Covers much of what 'ggplot2' does.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 20.0.0 dated 2026-05-07 and 21.0.0 dated 2026-07-06
DESCRIPTION | 8 MD5 | 159 ++-- NAMESPACE | 2 NEWS.md | 11 R/gg-area.R | 18 R/gg-bar.R | 18 R/gg-bin2d.R | 18 R/gg-blanket-utils.R | 112 +- R/gg-blanket.R | 1184 ++++++++++++++++++------------- R/gg-boxplot.R | 18 R/gg-col.R | 18 R/gg-contour-filled.R | 16 R/gg-contour.R | 16 R/gg-crossbar.R | 18 R/gg-density.R | 18 R/gg-density2d-filled.R | 18 R/gg-density2d.R | 16 R/gg-errorbar.R | 18 R/gg-freqpoly.R | 18 R/gg-hex.R | 18 R/gg-histogram.R | 18 R/gg-jitter.R | 18 R/gg-line.R | 18 R/gg-linerange.R | 18 R/gg-path.R | 18 R/gg-point.R | 18 R/gg-polygon.R | 18 R/gg-qq.R | 18 R/gg-quantile.R | 18 R/gg-raster.R | 18 R/gg-rect.R | 18 R/gg-ribbon.R | 18 R/gg-segment.R | 20 R/gg-sf.R | 16 R/gg-smooth.R | 18 R/gg-spoke.R | 18 R/gg-step.R | 18 R/gg-tile.R | 18 R/gg-violin.R | 18 R/refine.R |only R/set-blanket.R | 194 +++-- README.md | 3 man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/gg_area.Rd | 38 man/gg_bar.Rd | 36 man/gg_bin2d.Rd | 38 man/gg_blanket.Rd | 36 man/gg_boxplot.Rd | 36 man/gg_col.Rd | 38 man/gg_contour.Rd | 34 man/gg_contour_filled.Rd | 36 man/gg_crossbar.Rd | 38 man/gg_density.Rd | 36 man/gg_density2d.Rd | 34 man/gg_density2d_filled.Rd | 38 man/gg_errorbar.Rd | 38 man/gg_freqpoly.Rd | 38 man/gg_hex.Rd | 36 man/gg_histogram.Rd | 36 man/gg_jitter.Rd | 36 man/gg_line.Rd | 38 man/gg_linerange.Rd | 36 man/gg_path.Rd | 36 man/gg_point.Rd | 36 man/gg_polygon.Rd | 36 man/gg_qq.Rd | 36 man/gg_quantile.Rd | 36 man/gg_raster.Rd | 38 man/gg_rect.Rd | 38 man/gg_ribbon.Rd | 36 man/gg_segment.Rd | 38 man/gg_sf.Rd | 36 man/gg_smooth.Rd | 36 man/gg_spoke.Rd | 36 man/gg_step.Rd | 38 man/gg_tile.Rd | 36 man/gg_violin.Rd | 36 man/ggblanket-package.Rd | 7 man/modern_drift.Rd |only man/set_blanket.Rd | 14 man/void_drop.Rd |only 82 files changed, 1910 insertions(+), 1616 deletions(-)
Title: Landscape Connectivity, Habitat, and Protected Area Networks
Description: Given a landscape resistance surface, creates minimum planar graph
(Fall et al. (2007) <doi:10.1007/s10021-007-9038-7>) and grains of connectivity
(Galpern et al. (2012) <doi:10.1111/j.1365-294X.2012.05677.x>) models that can be
used to calculate effective distances for landscape connectivity at multiple scales.
Documentation is provided by several vignettes, and a paper
(Chubaty, Galpern & Doctolero (2020) <doi:10.1111/2041-210X.13350>).
Author: Paul Galpern [aut, cph] ,
Sam Doctolero [aut],
Alex M Chubaty [aut, cre]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Diff between grainscape versions 0.5.0 dated 2025-01-15 and 1.0.0 dated 2026-07-06
grainscape-0.5.0/grainscape/R/grainscape-deprecated.R |only grainscape-0.5.0/grainscape/inst/extdata/issue72_patchID.tif |only grainscape-0.5.0/grainscape/inst/extdata/issue72_resistance.tif |only grainscape-0.5.0/grainscape/inst/extdata/naErrorExample.asc |only grainscape-0.5.0/grainscape/man/grainscape-deprecated.Rd |only grainscape-0.5.0/grainscape/tests/test-all.R |only grainscape-0.5.0/grainscape/tests/testthat/test-examples.R |only grainscape-0.5.0/grainscape/vignettes/figures/HabConnFlowchart.jpg |only grainscape-0.5.0/grainscape/vignettes/figures/cells_diagram.jpg |only grainscape-0.5.0/grainscape/vignettes/figures/data_struct_diagram.jpg |only grainscape-0.5.0/grainscape/vignettes/figures/engine_class_diagram.jpg |only grainscape-0.5.0/grainscape/vignettes/figures/engine_use_snippet.jpg |only grainscape-0.5.0/grainscape/vignettes/figures/typedef_diagram.jpg |only grainscape-0.5.0/grainscape/vignettes/grainscape_vignette_files |only grainscape-1.0.0/grainscape/DESCRIPTION | 32 - grainscape-1.0.0/grainscape/MD5 | 234 ++++---- grainscape-1.0.0/grainscape/NAMESPACE | 62 -- grainscape-1.0.0/grainscape/NEWS.md | 107 +++ grainscape-1.0.0/grainscape/R/GOC.R | 94 ++- grainscape-1.0.0/grainscape/R/MPG.R | 112 ++- grainscape-1.0.0/grainscape/R/classes.R | 172 ++--- grainscape-1.0.0/grainscape/R/corridor.R | 120 +--- grainscape-1.0.0/grainscape/R/distance.R | 50 - grainscape-1.0.0/grainscape/R/export.R | 232 +++++-- grainscape-1.0.0/grainscape/R/extract.R | 2 grainscape-1.0.0/grainscape/R/ggGS.R | 22 grainscape-1.0.0/grainscape/R/grain.R | 32 - grainscape-1.0.0/grainscape/R/grainscape-defunct.R |only grainscape-1.0.0/grainscape/R/grainscape-package.R | 81 ++ grainscape-1.0.0/grainscape/R/graphdf.R | 16 grainscape-1.0.0/grainscape/R/habitatConnectivityEngine.R | 23 grainscape-1.0.0/grainscape/R/patchFilter.R | 26 grainscape-1.0.0/grainscape/R/plot.R | 97 +-- grainscape-1.0.0/grainscape/R/plotResistance.R |only grainscape-1.0.0/grainscape/R/point.R | 46 - grainscape-1.0.0/grainscape/R/theme_grainscape.R | 18 grainscape-1.0.0/grainscape/R/zzz.R | 3 grainscape-1.0.0/grainscape/README.md | 6 grainscape-1.0.0/grainscape/build/partial.rdb |binary grainscape-1.0.0/grainscape/build/vignette.rds |binary grainscape-1.0.0/grainscape/inst/WORDLIST | 24 grainscape-1.0.0/grainscape/inst/doc/MPG_algorithm.R | 128 +++- grainscape-1.0.0/grainscape/inst/doc/MPG_algorithm.Rmd | 220 ++++++- grainscape-1.0.0/grainscape/inst/doc/MPG_algorithm.pdf |binary grainscape-1.0.0/grainscape/inst/doc/grainscape_vignette.R | 125 ++-- grainscape-1.0.0/grainscape/inst/doc/grainscape_vignette.Rmd | 145 ++-- grainscape-1.0.0/grainscape/inst/doc/grainscape_vignette.pdf |binary grainscape-1.0.0/grainscape/inst/examples/example_MPG.R | 6 grainscape-1.0.0/grainscape/inst/examples/example_corridor.R | 14 grainscape-1.0.0/grainscape/inst/examples/example_export.R | 4 grainscape-1.0.0/grainscape/inst/examples/example_filter.R | 12 grainscape-1.0.0/grainscape/inst/examples/example_ggGS.R | 30 - grainscape-1.0.0/grainscape/inst/examples/example_grain.R | 11 grainscape-1.0.0/grainscape/inst/examples/example_graphdf.R | 4 grainscape-1.0.0/grainscape/inst/examples/example_plot.R | 7 grainscape-1.0.0/grainscape/inst/examples/example_preamble.R | 6 grainscape-1.0.0/grainscape/inst/include/DataStruct.h | 16 grainscape-1.0.0/grainscape/inst/include/Engine.h | 8 grainscape-1.0.0/grainscape/man/GOC.Rd | 6 grainscape-1.0.0/grainscape/man/MPG.Rd | 32 - grainscape-1.0.0/grainscape/man/corridor-class.Rd | 10 grainscape-1.0.0/grainscape/man/corridor.Rd | 28 grainscape-1.0.0/grainscape/man/distance.Rd | 12 grainscape-1.0.0/grainscape/man/export.Rd | 18 grainscape-1.0.0/grainscape/man/extract.Rd | 2 grainscape-1.0.0/grainscape/man/ggGS.Rd | 48 - grainscape-1.0.0/grainscape/man/goc-class.Rd | 4 grainscape-1.0.0/grainscape/man/grain-class.Rd | 4 grainscape-1.0.0/grainscape/man/grain.Rd | 21 grainscape-1.0.0/grainscape/man/grainscape-defunct.Rd | 36 + grainscape-1.0.0/grainscape/man/grainscape-maps.Rd | 53 + grainscape-1.0.0/grainscape/man/grainscape-package.Rd | 13 grainscape-1.0.0/grainscape/man/graphdf.Rd | 10 grainscape-1.0.0/grainscape/man/habConnEngine.Rd | 2 grainscape-1.0.0/grainscape/man/hce-class.Rd | 4 grainscape-1.0.0/grainscape/man/mpg-class.Rd | 10 grainscape-1.0.0/grainscape/man/patchFilter.Rd | 24 grainscape-1.0.0/grainscape/man/plot.Rd | 19 grainscape-1.0.0/grainscape/man/plotResistance.Rd |only grainscape-1.0.0/grainscape/man/plotWithResistance.Rd |only grainscape-1.0.0/grainscape/man/point.Rd | 10 grainscape-1.0.0/grainscape/man/theme_grainscape.Rd | 6 grainscape-1.0.0/grainscape/man/threshold.Rd | 6 grainscape-1.0.0/grainscape/src/Engine.cpp | 243 +++++--- grainscape-1.0.0/grainscape/tests/testthat.R |only grainscape-1.0.0/grainscape/tests/testthat/_snaps |only grainscape-1.0.0/grainscape/tests/testthat/fixtures |only grainscape-1.0.0/grainscape/tests/testthat/helper-plotdata.R |only grainscape-1.0.0/grainscape/tests/testthat/helper-testdata.R |only grainscape-1.0.0/grainscape/tests/testthat/test-GOC.R |only grainscape-1.0.0/grainscape/tests/testthat/test-MPG.R | 291 +++++++++- grainscape-1.0.0/grainscape/tests/testthat/test-corridor-distance-point.R | 20 grainscape-1.0.0/grainscape/tests/testthat/test-corridor.R |only grainscape-1.0.0/grainscape/tests/testthat/test-defunct.R |only grainscape-1.0.0/grainscape/tests/testthat/test-distance.R |only grainscape-1.0.0/grainscape/tests/testthat/test-export.R | 6 grainscape-1.0.0/grainscape/tests/testthat/test-extract.R |only grainscape-1.0.0/grainscape/tests/testthat/test-ggGS.R |only grainscape-1.0.0/grainscape/tests/testthat/test-grain.R |only grainscape-1.0.0/grainscape/tests/testthat/test-graphdf.R |only grainscape-1.0.0/grainscape/tests/testthat/test-patchFilter.R |only grainscape-1.0.0/grainscape/tests/testthat/test-plot.R |only grainscape-1.0.0/grainscape/tests/testthat/test-plotResistance.R |only grainscape-1.0.0/grainscape/tests/testthat/test-point.R |only grainscape-1.0.0/grainscape/tests/testthat/test-threshold.R |only grainscape-1.0.0/grainscape/tests/testthat/test-voronoi.R |only grainscape-1.0.0/grainscape/vignettes/MPG_algorithm.Rmd | 220 ++++++- grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/call_graph_engine_initialize-1.pdf |binary grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/call_graph_engine_start-1.pdf |binary grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/cells_diagram-1.pdf |only grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/data_struct_diagram-1.pdf |only grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/engine_class_diagram-1.pdf |only grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/flowchart-1.pdf |only grainscape-1.0.0/grainscape/vignettes/MPG_algorithm_files/figure-latex/typedef_diagram-1.pdf |only grainscape-1.0.0/grainscape/vignettes/figures/partA.png |binary grainscape-1.0.0/grainscape/vignettes/figures/partB.png |binary grainscape-1.0.0/grainscape/vignettes/grainscape_vignette.Rmd | 145 ++-- 117 files changed, 2394 insertions(+), 1256 deletions(-)
Title: Publication-Quality 'ggplot2' Geom Width
Description: Width helper functions for publication-quality 'ggplot2'
visualisation. These functions make it easier to create geoms such
as bars that have a consistent width appearance across plots.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggwidth versions 0.1.1 dated 2026-05-03 and 0.1.2 dated 2026-07-06
ggwidth-0.1.1/ggwidth/R/get-width.R |only ggwidth-0.1.1/ggwidth/R/set-equiwidth.R |only ggwidth-0.1.1/ggwidth/R/utils.R |only ggwidth-0.1.2/ggwidth/DESCRIPTION | 8 - ggwidth-0.1.2/ggwidth/MD5 | 16 +- ggwidth-0.1.2/ggwidth/NEWS.md | 4 ggwidth-0.1.2/ggwidth/R/width.R |only ggwidth-0.1.2/ggwidth/man/get_width.Rd | 133 ++++------------------ ggwidth-0.1.2/ggwidth/man/ggwidth-package.Rd | 7 - ggwidth-0.1.2/ggwidth/man/set_equiwidth.Rd | 21 --- ggwidth-0.1.2/ggwidth/tests/testthat/test-width.R | 111 ------------------ 11 files changed, 54 insertions(+), 246 deletions(-)
Title: Publication-Quality 'ggplot2' Annotation
Description: Annotation helper functions for publication-quality 'ggplot2'
visualisation. These functions make it easier to annotate plots in
a way that stays consistent with the set theme.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggscribe versions 0.1.1 dated 2026-05-04 and 0.2.0 dated 2026-07-06
ggscribe-0.1.1/ggscribe/R/axis-bracket.R |only ggscribe-0.1.1/ggscribe/R/axis-line.R |only ggscribe-0.1.1/ggscribe/R/axis-text.R |only ggscribe-0.1.1/ggscribe/R/axis-ticks.R |only ggscribe-0.1.1/ggscribe/R/guide-sec-axis-text.R |only ggscribe-0.1.1/ggscribe/R/panel-shade.R |only ggscribe-0.1.1/ggscribe/R/reference-line.R |only ggscribe-0.1.1/ggscribe/R/theme-sec-axis-text.R |only ggscribe-0.1.1/ggscribe/R/utils.R |only ggscribe-0.1.1/ggscribe/man/theme_sec_axis_text.Rd |only ggscribe-0.2.0/ggscribe/DESCRIPTION | 14 ggscribe-0.2.0/ggscribe/MD5 | 51 - ggscribe-0.2.0/ggscribe/NAMESPACE | 3 ggscribe-0.2.0/ggscribe/NEWS.md | 14 ggscribe-0.2.0/ggscribe/R/aes-contrast.R | 289 ++++++---- ggscribe-0.2.0/ggscribe/R/axis-panel-reference.R |only ggscribe-0.2.0/ggscribe/R/sec-axis-text.R | 154 ++--- ggscribe-0.2.0/ggscribe/README.md | 52 + ggscribe-0.2.0/ggscribe/man/aes_contrast.Rd | 83 -- ggscribe-0.2.0/ggscribe/man/axis_bracket.Rd | 119 +--- ggscribe-0.2.0/ggscribe/man/axis_line.Rd | 62 +- ggscribe-0.2.0/ggscribe/man/axis_text.Rd | 136 +--- ggscribe-0.2.0/ggscribe/man/axis_ticks.Rd | 80 +- ggscribe-0.2.0/ggscribe/man/figures/README-unnamed-chunk-2-1.png |binary ggscribe-0.2.0/ggscribe/man/figures/README-unnamed-chunk-3-1.png |binary ggscribe-0.2.0/ggscribe/man/ggscribe-package.Rd | 7 ggscribe-0.2.0/ggscribe/man/guide_sec_axis_text.Rd | 72 -- ggscribe-0.2.0/ggscribe/man/panel_background.Rd |only ggscribe-0.2.0/ggscribe/man/panel_grid.Rd |only ggscribe-0.2.0/ggscribe/man/panel_shade.Rd | 101 --- ggscribe-0.2.0/ggscribe/man/reference_line.Rd | 109 +-- ggscribe-0.2.0/ggscribe/man/sec_axis_text.Rd | 86 -- ggscribe-0.2.0/ggscribe/tests/spelling.R | 10 33 files changed, 593 insertions(+), 849 deletions(-)
Title: Functions and Data Sets for "That's Weird: Anomaly Detection
Using R" by Rob J Hyndman
Description: All functions and data sets required for the examples in the book
Hyndman (2026) "That's Weird: Anomaly Detection Using R" <https://OTexts.com/weird/>.
All packages needed to run the examples are also loaded.
Author: Rob Hyndman [aut, cre, cph] ,
Torben Tvedebrink [ctb],
Posit Software, PBC [cph]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between weird versions 2.1.0 dated 2026-05-05 and 3.0.0 dated 2026-07-06
weird-2.1.0/weird/R/gg_density_layer.R |only weird-2.1.0/weird/man/gg_density_layer.Rd |only weird-3.0.0/weird/DESCRIPTION | 31 - weird-3.0.0/weird/MD5 | 140 ++++-- weird-3.0.0/weird/NAMESPACE | 25 + weird-3.0.0/weird/NEWS.md | 18 weird-3.0.0/weird/R/air_quality.R |only weird-3.0.0/weird/R/attach.R | 54 +- weird-3.0.0/weird/R/augment.R |only weird-3.0.0/weird/R/biplot_projection.R |only weird-3.0.0/weird/R/conflicts.R | 39 + weird-3.0.0/weird/R/datasets.R | 19 weird-3.0.0/weird/R/density_df.R |only weird-3.0.0/weird/R/dist_kde.R | 8 weird-3.0.0/weird/R/gg_density.R | 257 ++++++------ weird-3.0.0/weird/R/gmm.R |only weird-3.0.0/weird/R/grubbs.R | 17 weird-3.0.0/weird/R/hampel.R | 2 weird-3.0.0/weird/R/hdr.R | 230 +++++++---- weird-3.0.0/weird/R/interpolation.R | 1 weird-3.0.0/weird/R/kde_bandwidth.R | 10 weird-3.0.0/weird/R/lof_scores.R | 4 weird-3.0.0/weird/R/mvscale.R | 103 +++-- weird-3.0.0/weird/R/outlier_map.R |only weird-3.0.0/weird/R/show_data.R | 14 weird-3.0.0/weird/R/surprisals.R | 2 weird-3.0.0/weird/R/surprisals_models.R | 1 weird-3.0.0/weird/R/utils.R | 27 - weird-3.0.0/weird/R/weird.R | 8 weird-3.0.0/weird/R/wine_reviews.R | 4 weird-3.0.0/weird/R/zzz.R | 18 weird-3.0.0/weird/README.md | 282 -------------- weird-3.0.0/weird/build |only weird-3.0.0/weird/data/gun_deaths.rda |only weird-3.0.0/weird/inst/CITATION | 2 weird-3.0.0/weird/inst/doc |only weird-3.0.0/weird/man/augment.Pca.Rd |only weird-3.0.0/weird/man/biplot_projection.Rd |only weird-3.0.0/weird/man/density_df.Rd |only weird-3.0.0/weird/man/dist_kde.Rd | 2 weird-3.0.0/weird/man/dist_mclust.Rd |only weird-3.0.0/weird/man/fetch_air_quality.Rd |only weird-3.0.0/weird/man/fetch_wine_reviews.Rd | 4 weird-3.0.0/weird/man/figures/README-of-boxplot-1.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot-2.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot-3.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot2-1.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot2-2.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot3-1.png |binary weird-3.0.0/weird/man/figures/README-of-boxplot3-2.png |binary weird-3.0.0/weird/man/figures/README-of-density-1.png |binary weird-3.0.0/weird/man/figures/README-of-density2-1.png |binary weird-3.0.0/weird/man/gg_density.Rd | 6 weird-3.0.0/weird/man/gg_hdrboxplot.Rd | 3 weird-3.0.0/weird/man/gun_deaths.Rd |only weird-3.0.0/weird/man/hampel_anomalies.Rd | 2 weird-3.0.0/weird/man/hdr_table.Rd | 2 weird-3.0.0/weird/man/kde_bandwidth.Rd | 2 weird-3.0.0/weird/man/lof_scores.Rd | 2 weird-3.0.0/weird/man/mvscale.Rd | 40 + weird-3.0.0/weird/man/outlier_map.Rd |only weird-3.0.0/weird/man/reexports.Rd | 3 weird-3.0.0/weird/man/surprisals.Rd | 2 weird-3.0.0/weird/man/surprisals_data.Rd | 2 weird-3.0.0/weird/man/surprisals_model.Rd | 2 weird-3.0.0/weird/man/weird-package.Rd | 1 weird-3.0.0/weird/tests/testthat/_snaps |only weird-3.0.0/weird/tests/testthat/helper_fetch_data.R |only weird-3.0.0/weird/tests/testthat/test_air_quality.R |only weird-3.0.0/weird/tests/testthat/test_augment.R |only weird-3.0.0/weird/tests/testthat/test_bagplot.R | 4 weird-3.0.0/weird/tests/testthat/test_biplot_projection.R |only weird-3.0.0/weird/tests/testthat/test_datasets.R | 44 ++ weird-3.0.0/weird/tests/testthat/test_density_df.R |only weird-3.0.0/weird/tests/testthat/test_dist_kde1.R | 2 weird-3.0.0/weird/tests/testthat/test_dist_mclust.R |only weird-3.0.0/weird/tests/testthat/test_hdr.R | 47 ++ weird-3.0.0/weird/tests/testthat/test_lof_glosh.R | 16 weird-3.0.0/weird/tests/testthat/test_mvscale.R | 105 +++++ weird-3.0.0/weird/tests/testthat/test_outlier_map.R |only weird-3.0.0/weird/tests/testthat/test_stray.R | 14 weird-3.0.0/weird/tests/testthat/test_wine_reviews.R |only weird-3.0.0/weird/vignettes |only 83 files changed, 864 insertions(+), 757 deletions(-)
Title: A Discrete Colour Palette
Description: A discrete colour palette. These colours make it easier to create
relatively accessible and colour-blind safe visualisation.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between jumble versions 0.1.1 dated 2026-05-04 and 0.1.2 dated 2026-07-06
jumble-0.1.1/jumble/R/grey.R |only jumble-0.1.1/jumble/R/navy.R |only jumble-0.1.1/jumble/R/orange.R |only jumble-0.1.1/jumble/R/pink.R |only jumble-0.1.1/jumble/R/red.R |only jumble-0.1.1/jumble/R/slate.R |only jumble-0.1.1/jumble/R/teal.R |only jumble-0.1.2/jumble/DESCRIPTION | 8 - jumble-0.1.2/jumble/MD5 | 33 +++---- jumble-0.1.2/jumble/NEWS.md | 4 jumble-0.1.2/jumble/R/jumble.R | 44 ++++++++++ jumble-0.1.2/jumble/man/grey.Rd | 7 - jumble-0.1.2/jumble/man/jumble.Rd | 2 jumble-0.1.2/jumble/man/navy.Rd | 7 - jumble-0.1.2/jumble/man/orange.Rd | 7 - jumble-0.1.2/jumble/man/pink.Rd | 7 - jumble-0.1.2/jumble/man/red.Rd | 7 - jumble-0.1.2/jumble/man/slate.Rd | 7 - jumble-0.1.2/jumble/man/teal.Rd | 7 - jumble-0.1.2/jumble/tests/spelling.R | 10 +- jumble-0.1.2/jumble/tests/testthat/test-jumble.R | 98 ++++++++++++----------- 21 files changed, 132 insertions(+), 116 deletions(-)
Title: Blend Colours and Palettes
Description: Colour blend functions. These functions make it easier to blend
colours and palettes using digital blend modes such as multiply, screen,
and overlay.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between blends versions 0.1.1 dated 2026-05-04 and 0.1.2 dated 2026-07-06
blends-0.1.1/blends/R/colour-burn.R |only blends-0.1.1/blends/R/colour-dodge.R |only blends-0.1.1/blends/R/darken.R |only blends-0.1.1/blends/R/difference.R |only blends-0.1.1/blends/R/exclusion.R |only blends-0.1.1/blends/R/hard-light.R |only blends-0.1.1/blends/R/lighten.R |only blends-0.1.1/blends/R/multiply.R |only blends-0.1.1/blends/R/overlay.R |only blends-0.1.1/blends/R/screen.R |only blends-0.1.1/blends/R/soft-light.R |only blends-0.1.1/blends/R/utils.R |only blends-0.1.2/blends/DESCRIPTION | 10 +- blends-0.1.2/blends/MD5 | 47 ++++------- blends-0.1.2/blends/NEWS.md | 4 blends-0.1.2/blends/R/blends.R |only blends-0.1.2/blends/man/blends-package.Rd | 7 + blends-0.1.2/blends/man/colour_burn.Rd | 9 +- blends-0.1.2/blends/man/colour_dodge.Rd | 9 +- blends-0.1.2/blends/man/darken.Rd | 9 +- blends-0.1.2/blends/man/difference.Rd | 9 +- blends-0.1.2/blends/man/exclusion.Rd | 9 +- blends-0.1.2/blends/man/figures/README-unnamed-chunk-3-1.png |binary blends-0.1.2/blends/man/figures/README-unnamed-chunk-4-1.png |binary blends-0.1.2/blends/man/hard_light.Rd | 9 +- blends-0.1.2/blends/man/lighten.Rd | 9 +- blends-0.1.2/blends/man/multiply.Rd | 9 +- blends-0.1.2/blends/man/overlay.Rd | 9 +- blends-0.1.2/blends/man/screen.Rd | 17 ++- blends-0.1.2/blends/man/soft_light.Rd | 13 +-- blends-0.1.2/blends/tests/spelling.R | 10 +- 31 files changed, 111 insertions(+), 78 deletions(-)
Title: USGS INL Project Office Publications
Description: Provides bibliographic information and term-frequency text analysis
tools for publications of the U.S. Geological Survey (USGS) Idaho National
Laboratory (INL) Project Office. Includes datasets of publications, authors,
and term frequencies, along with functions to search terms, build word
clouds, and extract text and cover images from publication documents.
Author: Jason C. Fisher [aut, cre] ,
Kerri C. Treinen [aut] ,
Allison R. Trcka [aut]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between inlpubs versions 1.3.0 dated 2025-06-25 and 1.4.0 dated 2026-07-06
DESCRIPTION | 44 +-- MD5 | 78 +++--- NAMESPACE | 1 NEWS.md | 140 +++++----- R/add_content.R | 225 ++++++++++++----- R/authors.R | 37 +- R/filter_data_list.R | 56 ++-- R/get_pdf_image.R | 149 ++++++++--- R/get_pdf_text.R | 491 +++++++++++++++++++++++++++++++++----- R/get_person.R | 33 +- R/make_webpages.R | 399 ++++++++++++++++++++---------- R/make_wordcloud.R | 142 +++++----- R/mine_text.R | 358 ++++++++++++++------------- R/plot_pubs.R |only R/pubs.R | 59 ++-- R/search_terms.R | 163 ++++++------ R/terms.R | 33 +- README.md | 75 ++--- build/partial.rdb |binary data/authors.rda |binary data/pubs.rda |binary data/terms.rda |binary inst/REFERENCES.bib | 33 ++ inst/extdata/test.pdf |binary inst/tinytest/test_data.R | 132 ++++++++++ inst/tinytest/test_get_pdf.R |only inst/tinytest/test_mine_text.R | 118 ++++++++- inst/tinytest/test_plot_pubs.R |only inst/tinytest/test_search_terms.R |only inst/tinytest/test_utils.R |only man/add_content.Rd | 88 +++++- man/authors.Rd | 38 +- man/filter_data_list.Rd | 29 +- man/get_pdf_image.Rd | 47 ++- man/get_pdf_text.Rd | 96 ++++++- man/get_person.Rd | 17 - man/make_webpages.Rd | 31 +- man/make_wordcloud.Rd | 51 ++- man/mine_text.Rd | 53 ++-- man/plot_pubs.Rd |only man/pubs.Rd | 60 +++- man/search_terms.Rd | 120 ++++----- man/terms.Rd | 34 +- 43 files changed, 2343 insertions(+), 1087 deletions(-)
Title: Bivariate Hurdle Regression with Bayesian Model Averaging
Description: Provides tools for fitting bivariate hurdle negative binomial
models with horseshoe priors, Bayesian Model Averaging (BMA) via stacking,
and comprehensive causal inference methods including G-computation,
transfer entropy, Threshold Vector Autoregressive (TVAR) and Smooth
Transition Autoregressive (STAR) models, Dynamic Bayesian Networks (DBN),
Hidden Markov Models (HMM), and sensitivity analysis.
Author: Jose Mauricio Gomez Julian [aut, cre]
Maintainer: Jose Mauricio Gomez Julian <isadore.nabi@pm.me>
Diff between bivarhr versions 0.1.5 dated 2025-12-19 and 0.1.6 dated 2026-07-06
bivarhr-0.1.5/bivarhr/R/export-results.R |only bivarhr-0.1.6/bivarhr/DESCRIPTION | 12 bivarhr-0.1.6/bivarhr/MD5 | 64 +- bivarhr-0.1.6/bivarhr/NAMESPACE | 1 bivarhr-0.1.6/bivarhr/NEWS.md | 51 + bivarhr-0.1.6/bivarhr/R/bivarhr-package.R | 29 - bivarhr-0.1.6/bivarhr/R/bma-selection.R | 51 - bivarhr-0.1.6/bivarhr/R/dbn.R | 96 ++- bivarhr-0.1.6/bivarhr/R/eba.R | 112 +--- bivarhr-0.1.6/bivarhr/R/hmm.R | 513 ++++++++++++++++---- bivarhr-0.1.6/bivarhr/R/hurdle-fit.R | 2 bivarhr-0.1.6/bivarhr/R/io.R | 22 bivarhr-0.1.6/bivarhr/R/placebo.R | 41 - bivarhr-0.1.6/bivarhr/R/rolling-oos.R | 17 bivarhr-0.1.6/bivarhr/R/sensemakr.R | 76 +- bivarhr-0.1.6/bivarhr/R/synthetic-control.R | 72 +- bivarhr-0.1.6/bivarhr/R/transfer-entropy.R | 121 ++-- bivarhr-0.1.6/bivarhr/R/tvar-star.R | 95 +-- bivarhr-0.1.6/bivarhr/man/bivarhr-package.Rd | 5 bivarhr-0.1.6/bivarhr/man/export_results.Rd | 9 bivarhr-0.1.6/bivarhr/man/export_results_xlsx.Rd | 13 bivarhr-0.1.6/bivarhr/man/placebo_temporal.Rd | 39 - bivarhr-0.1.6/bivarhr/man/prewhiten_count_glm.Rd | 11 bivarhr-0.1.6/bivarhr/man/print.bivarhr_hmm.Rd |only bivarhr-0.1.6/bivarhr/man/rolling_oos.Rd | 13 bivarhr-0.1.6/bivarhr/man/run_dbn.Rd | 65 +- bivarhr-0.1.6/bivarhr/man/run_eba.Rd | 110 +--- bivarhr-0.1.6/bivarhr/man/run_hmm.Rd | 173 ++++-- bivarhr-0.1.6/bivarhr/man/run_sensemakr.Rd | 54 -- bivarhr-0.1.6/bivarhr/man/run_synth_bsts.Rd | 69 +- bivarhr-0.1.6/bivarhr/man/run_transfer_entropy.Rd | 71 +- bivarhr-0.1.6/bivarhr/man/run_varx.Rd | 63 +- bivarhr-0.1.6/bivarhr/man/select_by_bma.Rd | 51 - bivarhr-0.1.6/bivarhr/tests/testthat/test-bivarhr.R | 69 +- 34 files changed, 1288 insertions(+), 902 deletions(-)
Title: Functions and Data Sets for 'Applied Predictive Modeling'
Description: A few functions and several data set for the Springer book
'Applied Predictive Modeling'.
Author: Max Kuhn [aut, cre],
Kjell Johnson [aut]
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between AppliedPredictiveModeling versions 1.1-7 dated 2018-05-22 and 1.2.0 dated 2026-07-06
AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/R/easyBoundaryFunc.R |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/R/transparentTheme.R |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/man/AppliedPredictiveModeling-package.Rd |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/man/Hepatic.Rd |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/man/internal.Rd |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/man/jobScheduling.Rd |only AppliedPredictiveModeling-1.1-7/AppliedPredictiveModeling/man/segmentationOrignal.Rd |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/DESCRIPTION | 28 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/MD5 | 64 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/NAMESPACE | 15 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/bookTheme.R | 493 ++++++++-- AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/data.R |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/getPackages.R | 25 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/panels.R | 38 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/permuteRelief.R | 78 + AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/quadBoundaryFunc.R | 78 + AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/R/scriptLocation.R | 13 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/README.md | 1 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/inst/NEWS.Rd | 7 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/inst/chapters/12_Discriminant_Analysis.R | 2 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/inst/chapters/14_Class_Trees.R | 4 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/AlzheimerDisease.Rd | 56 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/ChemicalManufacturingProcess.Rd | 59 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/FuelEconomy.Rd | 46 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/abalone.Rd | 32 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/apm-internal.Rd |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/bookTheme.Rd | 54 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/concrete.Rd | 58 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/getPackages.Rd | 34 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/hepatic.Rd |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/logisticCreditPredictions.Rd | 28 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/permeability.Rd | 62 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/permuteRelief.Rd | 103 +- AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/quadBoundaryFunc.Rd | 55 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/schedulingData.Rd |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/scriptLocation.Rd | 20 AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/segmentationOriginal.Rd |only AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/solubility.Rd | 60 - AppliedPredictiveModeling-1.2.0/AppliedPredictiveModeling/man/twoClassData.Rd | 31 39 files changed, 1090 insertions(+), 454 deletions(-)
More information about AppliedPredictiveModeling at CRAN
Permanent link
Title: Provides Batch Functions and Visualisation for Basic Statistical
Procedures
Description: Designed to streamline data analysis and statistical testing, reducing the length of R
scripts while generating well-formatted outputs in 'pdf', 'Microsoft Word', and 'Microsoft Excel'
formats. In essence, the package contains functions which are sophisticated wrappers around
existing R functions that are called by using 'f_' (user f_riendly) prefix followed by the normal
function name. This third version of the 'rfriend' package focuses primarily on data exploration,
including tools for creating summary tables, f_summary(), summary figures, f_scan(),
outlier detection and removal, f_outlier() and f_remove_outliers(), performing data transformations,
f_boxcox() in part based on 'MASS/boxcox' and 'rcompanion', and f_bestNormalize()
which wraps and extends functionality from the 'bestNormalize' package. Furthermore, 'rfriend'
can automatically (or on request) generate visualizations such as boxplots, f_boxplot(),
QQ-plots, f_qqnorm(), and histograms f_hist(). Additionally, the package i [...truncated...]
Author: Sander H. van Delden [aut, cre]
Maintainer: Sander H. van Delden <plantmind@proton.me>
Diff between rfriend versions 3.1.0 dated 2026-05-30 and 3.2.0 dated 2026-07-06
DESCRIPTION | 22 MD5 | 98 + NAMESPACE | 14 NEWS.md | 254 ++++ R/data.R |only R/df_to_table.R | 8 R/faov.R | 1392 +++++++++++++++++++------- R/fbestnormalize.R | 15 R/fboxcox.R | 2 R/fboxplot.R | 10 R/fchisq_test.R | 45 R/fcorplot.R | 2 R/fexample_data.R |only R/ffactors.R | 61 + R/ffriedman.R |only R/fglm.R | 1166 +++++++++++++++++++++- R/fkruskal_test.R | 149 ++ R/flm.R |only R/flmer.R | 1994 ++++++++++++++++++++++++++++++++++++-- R/fqqnorm.R | 338 +++--- R/fscan.R | 2 R/fsetwd.R | 17 R/fttest.R | 768 ++++++++++++-- R/fwilcox_test.R | 294 +++++ R/helper_cld_emmeans.R |only R/helper_coef_ref_caption.R |only R/helper_compact_letters.R |only R/helper_contrast_forest.R |only R/helper_forest_plot.R |only R/helper_get_save_path.R | 274 ++--- R/helper_pub_theme.R |only R/helper_rmd_anova_summary.R | 106 +- R/helper_safe_ad.R |only R/helper_safe_shapiro.R | 3 R/import.R | 8 README.md | 322 +++--- build/partial.rdb |binary data |only inst/extdata/plant_trial.csv |only inst/extdata/plant_trial.rds |only inst/extdata/plant_trial.sav |only inst/extdata/plant_trial_raw.csv |only inst/extdata/plant_trial_raw.xlsx |only inst/extdata/plant_trial_wide.csv |only man/f_aov.Rd | 104 + man/f_example_data.Rd |only man/f_factors.Rd | 21 man/f_friedman.Rd |only man/f_glm.Rd | 43 man/f_lm.Rd |only man/f_lmer.Rd | 138 ++ man/f_qqnorm.Rd | 25 man/f_t_test.Rd | 54 - man/f_wilcox_test.Rd | 22 man/plant_trial.Rd |only man/plot.f_friedman.Rd |only tests/testthat/helper-quiet.R | 24 tests/testthat/test-f_aov.R | 444 ++++++++ tests/testthat/test-f_friedman.R |only tests/testthat/test-f_glm.R | 14 tests/testthat/test-f_lm.R |only tests/testthat/test-f_lmer-3.2.R |only tests/testthat/test-f_scan.R | 17 63 files changed, 7048 insertions(+), 1222 deletions(-)
Title: A Toolkit for Nested Sampling
Description: Bayesian evidence estimation and posterior inference with the
nested sampling algorithm, described in Skilling (2006)
<doi:10.1214/06-BA127> and Buchner (2023) <doi:10.1214/23-SS144>,
along with S3 methods for simulating uncertainty and creating
visualisations.
Author: Kyle Dewsnap [aut, cre, cph] ,
TJ Mahr [rev],
Robert Kubinec [rev],
Michael Hughes [cph]
Maintainer: Kyle Dewsnap <kyle.dewsnap@ubc.ca>
Diff between ernest versions 1.2.4 dated 2026-06-30 and 1.2.5 dated 2026-07-06
DESCRIPTION | 6 MD5 | 72 +++++----- NEWS.md | 12 + R/cpp11.R | 4 R/nested_sampling_impl.R | 11 - R/plot.R | 3 README.md | 29 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/more-ernest-runs.R | 14 - inst/doc/more-ernest-runs.html | 49 +++--- inst/doc/nested-sampling-with-ernest.R | 14 - inst/doc/nested-sampling-with-ernest.html | 36 ++--- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-2-2.png |binary man/plot-ernest.Rd | 3 src/KMeansRexCore.cpp | 2 src/cpp11.cpp | 18 +- src/ellipsoid.cpp | 25 +-- src/ellipsoid.h | 1 src/exported_utils.cpp | 20 -- src/propose-impl.cpp | 4 src/rectangle.h | 4 src/test-bounding.cpp | 2 src/utils.h | 2 tests/testthat/_snaps/plot/estimate-1-draw.svg | 59 ++++---- tests/testthat/_snaps/plot/estimate-500-draws-no-evidence.svg | 1 tests/testthat/_snaps/plot/estimate-500-draws.svg | 69 +++++---- tests/testthat/_snaps/plot/example-run-no-evidence.svg | 40 ++--- tests/testthat/_snaps/plot/example-run.svg | 59 ++++---- tests/testthat/_snaps/visualize/trace-basic.svg | 1 tests/testthat/_snaps/visualize/trace-x.svg | 1 tests/testthat/_snaps/visualize/trace-yz.svg | 1 tests/testthat/_snaps/visualize/visualize-basic.svg | 7 tests/testthat/_snaps/visualize/visualize-x.svg | 38 ++--- tests/testthat/_snaps/visualize/visualize-yz.svg | 69 ++++----- tests/testthat/test-calculate.R | 19 -- 37 files changed, 345 insertions(+), 350 deletions(-)
Title: Sample Size and Simulation for Negative Binomial Outcomes
Description: Provides tools for planning and simulating recurrent event trials
with overdispersed count endpoints analyzed using negative binomial (or
Poisson) rate models. Implements sample size and power calculations for
fixed designs with variable accrual, dropout, maximum follow-up, and event
gaps, including methods of Zhu and Lakkis (2014) <doi:10.1002/sim.5947> and
Friede and Schmidli (2010) <doi:10.3414/ME09-02-0060> as well as
extensions for score-test sizing and gaps between events. Supports group
sequential monitoring by building on the 'gsDesign' package.
Includes recurrent-event simulation utilities (including seasonal rates),
interim data truncation, Wald and score-test inference for rate ratios,
and information estimation and sample size re-estimation with or without
treatment-group labels.
Author: Keaven Anderson [aut, cre],
Hongtao Zhang [aut],
Andrea Maes [aut],
Nan Xiao [ctb],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesignNB versions 0.2.6 dated 2026-02-16 and 0.3.2 dated 2026-07-06
DESCRIPTION | 36 MD5 | 177 NAMESPACE | 13 NEWS.md | 153 R/calculate_blinded_info.R | 105 R/check_gs_bound.R | 46 R/get_cut_date.R | 24 R/globals.R | 8 R/gsNBCalendar.R | 565 ++- R/multiple_imputation_nb.R |only R/mutze_test.R | 346 + R/preview_pkgdown_site.R |only R/run_ssr_shiny.R |only R/sample_size_nbinom.R | 513 ++ R/sim_gs_nbinom.R | 108 R/sim_ssr_nbinom.R |only R/summarize_gs_sim.R | 66 R/unblinded_ssr.R | 99 README.md | 23 build/partial.rdb |binary build/vignette.rds |binary inst/doc/ai-skills.R |only inst/doc/ai-skills.Rmd |only inst/doc/ai-skills.html |only inst/doc/blinded-info-diagnostics.R | 2 inst/doc/blinded-info-diagnostics.Rmd | 42 inst/doc/blinded-info-diagnostics.html | 206 - inst/doc/completers-interim-example.html | 12 inst/doc/group-sequential-simulation.R | 230 - inst/doc/group-sequential-simulation.Rmd | 245 - inst/doc/group-sequential-simulation.html | 2412 ++++--------- inst/doc/multiple-imputation-nb.R |only inst/doc/multiple-imputation-nb.Rmd |only inst/doc/multiple-imputation-nb.html |only inst/doc/sample-size-nbinom.R | 94 inst/doc/sample-size-nbinom.Rmd | 501 ++ inst/doc/sample-size-nbinom.html | 1344 +++++-- inst/doc/sample-size-skills-example.R |only inst/doc/sample-size-skills-example.Rmd |only inst/doc/sample-size-skills-example.html |only inst/doc/score-vs-wald-simulation.R |only inst/doc/score-vs-wald-simulation.Rmd |only inst/doc/score-vs-wald-simulation.html |only inst/doc/simulation-example.R | 12 inst/doc/simulation-example.Rmd | 85 inst/doc/simulation-example.html | 121 inst/doc/ssr-example.R | 30 inst/doc/ssr-example.Rmd | 65 inst/doc/ssr-example.html | 1240 ++++-- inst/doc/ssr-simulation-study.R |only inst/doc/ssr-simulation-study.Rmd |only inst/doc/ssr-simulation-study.html |only inst/doc/verification-simulation.R | 271 + inst/doc/verification-simulation.Rmd | 373 +- inst/doc/verification-simulation.html | 1989 ++++++++-- inst/extdata/gs_simulation_results.rds |binary inst/extdata/jensen_broad_sweep_results.rds |only inst/extdata/jensen_score_broad_sweep_results.rds |only inst/extdata/null_simulation_results.rds |only inst/extdata/score_sweep_summary.rds |only inst/extdata/simulation_results.rds |binary inst/extdata/ssr_sim_vignette_summary_score.rds |only inst/extdata/ssr_sizing_sensitivity.rds |only inst/shiny-examples |only man/calculate_blinded_info.Rd | 65 man/check_gs_bound.Rd | 16 man/compute_info_at_time.Rd | 41 man/dot-bootstrap_by_cluster.Rd |only man/dot-impute_nb_draw.Rd |only man/fit_nb_glmm.Rd |only man/gsNBCalendar.Rd | 45 man/impute_nb.Rd |only man/impute_nb_composite.Rd |only man/impute_nb_mar.Rd |only man/impute_nb_mnar_ref.Rd |only man/mutze_test.Rd | 56 man/preview_pkgdown_site.Rd |only man/reexports.Rd | 2 man/run_ssr_shiny.Rd |only man/sample_size_nbinom.Rd | 209 - man/sim_gs_nbinom.Rd | 85 man/sim_ssr_nbinom.Rd |only man/summarize_gs_sim.Rd | 11 man/summarize_ssr_sim.Rd |only man/toInteger.Rd | 13 man/unblinded_ssr.Rd | 10 man/update_gsNB.Rd |only tests/testthat/test-calculate_blinded_info.R | 88 tests/testthat/test-check_gs_bound.R |only tests/testthat/test-cut_completers.R | 10 tests/testthat/test-cut_data_by_date.R | 121 tests/testthat/test-estimate_mom.R | 10 tests/testthat/test-get_cut_date.R |only tests/testthat/test-gsNBCalendar.R | 234 + tests/testthat/test-independent-test-simulation-accuracy.R |only tests/testthat/test-mutze_test.R | 282 + tests/testthat/test-nb_sim_seasonal.R |only tests/testthat/test-run_ssr_shiny.R |only tests/testthat/test-sample_size_nbinom.R | 410 ++ tests/testthat/test-sim_gs_nbinom.R |only tests/testthat/test-sim_gs_nbinom_parallel.R |only tests/testthat/test-sim_ssr_nbinom.R |only tests/testthat/test-summarize_gs_sim.R |only tests/testthat/test-unblinded_ssr.R |only vignettes/ai-skills.Rmd |only vignettes/blinded-info-diagnostics.Rmd | 42 vignettes/group-sequential-simulation.Rmd | 245 - vignettes/gsDesignNB.bib | 101 vignettes/multiple-imputation-nb.Rmd |only vignettes/sample-size-nbinom.Rmd | 501 ++ vignettes/sample-size-skills-example.Rmd |only vignettes/score-vs-wald-simulation.Rmd |only vignettes/simulation-example.Rmd | 85 vignettes/ssr-example.Rmd | 65 vignettes/ssr-simulation-study.Rmd |only vignettes/verification-simulation.Rmd | 373 +- 116 files changed, 10228 insertions(+), 4448 deletions(-)
Title: Displaying Changes Between Two Points Using Dumbbell Plots
Description: Creates dumbbell plots to visualize changes between two
measurements for the same observations. The package provides
customization options for labels, colors, arrows, delta values,
and paired statistical test annotations.
Author: Foo Cheung [aut, cre]
Maintainer: Foo Cheung <foocheung@yahoo.com>
Diff between dumbbell versions 0.1 dated 2021-02-25 and 0.2 dated 2026-07-06
DESCRIPTION | 26 MD5 | 26 NAMESPACE | 3 R/dumbbell.R | 557 ++++++-------- R/global.R | 6 README.md |only build/vignette.rds |binary inst/doc/dumbbell.R | 230 +++-- inst/doc/dumbbell.Rmd | 312 +++++--- inst/doc/dumbbell.html | 1888 +++++++++++++++++++++++++++++++++++++++++++------ inst/docs |only man/dumbbell.Rd | 132 +-- man/figures |only vignettes/dumbbell.Rmd | 312 +++++--- 14 files changed, 2594 insertions(+), 898 deletions(-)
Title: Retrieve Time Series Data from 'Banco de España'
Description: Tools for retrieving 'Banco de España' ('BdE') time series
data as 'tibble' objects from bulk CSV files and the 'Statistics web
service (API)'. Bulk CSV functions use stable 'BdE' sequential
numbers, while API functions use API series codes. Catalog functions
support discovery and local caching. Plotting helpers provide
'ggplot2' palettes, scales and themes. 'Banco de España' is the
national central bank and, within the framework of the Single
Supervisory Mechanism ('SSM'), the supervisor of the Spanish banking
system alongside the European Central Bank. This package is not
sponsored, endorsed or administered by 'Banco de España'.
Author: Diego H. Herrero [aut, cre, cph] ,
Banco de Espana [cph]
Maintainer: Diego H. Herrero <dev.dieghernan@gmail.com>
Diff between tidyBdE versions 0.6.1 dated 2026-05-21 and 0.7.0 dated 2026-07-06
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Title: 'SAS'-Style 'PROC FORMAT' for R
Description: Provides 'SAS' 'PROC FORMAT'-like functionality for creating and applying
value formats in R. Supports discrete and range-based mapping of values to labels,
reverse formatting (invalue), date/time/datetime formatting with built-in 'SAS' format
names, multi-label formats, expression labels evaluated at apply-time,
case-insensitive matching, import/export of format definitions, and proper handling
of missing values (NA, NULL, NaN).
Author: Vladimir Larchenko [aut, cre],
Igor Aleschenkov [aut]
Maintainer: Vladimir Larchenko <vladimir.larchenko@keystatsolutions.com>
Diff between ksformat versions 0.7.1 dated 2026-05-21 and 0.8.2 dated 2026-07-06
ksformat-0.7.1/ksformat/inst/doc/ksformat-Cheat-Sheet.pdf |only ksformat-0.8.2/ksformat/DESCRIPTION | 8 ksformat-0.8.2/ksformat/MD5 | 56 ksformat-0.8.2/ksformat/NAMESPACE | 1 ksformat-0.8.2/ksformat/NEWS.md | 50 ksformat-0.8.2/ksformat/R/format_apply.R | 22 ksformat-0.8.2/ksformat/R/format_create.R | 38 ksformat-0.8.2/ksformat/R/format_invalue.R | 21 ksformat-0.8.2/ksformat/R/format_library_app.R | 26 ksformat-0.8.2/ksformat/R/format_parse.R | 765 ------------ ksformat-0.8.2/ksformat/R/format_serialize.R |only ksformat-0.8.2/ksformat/R/utilities.R | 158 ++ ksformat-0.8.2/ksformat/README.md | 2 ksformat-0.8.2/ksformat/build/vignette.rds |binary ksformat-0.8.2/ksformat/inst/doc/ksformat-cheatsheet.pdf |only ksformat-0.8.2/ksformat/inst/doc/usage_examples.R | 41 ksformat-0.8.2/ksformat/inst/doc/usage_examples.Rmd | 66 + ksformat-0.8.2/ksformat/inst/doc/usage_examples.html | 807 +++++++------ ksformat-0.8.2/ksformat/man/dot-cntlout_to_ks_format.Rd | 2 ksformat-0.8.2/ksformat/man/dot-cntlout_to_ks_invalue.Rd | 2 ksformat-0.8.2/ksformat/man/dot-datetime_format_to_text.Rd | 2 ksformat-0.8.2/ksformat/man/dot-format_date_bound.Rd | 2 ksformat-0.8.2/ksformat/man/dot-format_range_bound.Rd | 2 ksformat-0.8.2/ksformat/man/dot-format_to_text.Rd | 2 ksformat-0.8.2/ksformat/man/dot-invalue_to_text.Rd | 2 ksformat-0.8.2/ksformat/man/fexport.Rd | 2 ksformat-0.8.2/ksformat/man/fimport.Rd | 2 ksformat-0.8.2/ksformat/man/finput.Rd | 11 ksformat-0.8.2/ksformat/man/flevels.Rd |only ksformat-0.8.2/ksformat/tests/testthat/test-formats.R | 198 +++ ksformat-0.8.2/ksformat/vignettes/usage_examples.Rmd | 66 + 31 files changed, 1098 insertions(+), 1256 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] ,
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
Malcolm Barrett [ctb] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.3.3 dated 2026-05-29 and 0.3.4 dated 2026-07-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/ard_stats_mantelhaen_test.R | 22 ++++++++++++++++------ inst/WORDLIST | 2 ++ 5 files changed, 29 insertions(+), 13 deletions(-)
Title: Add Ipea Editorial Standards to 'ggplot2' Graphics
Description: Convenient functions to create 'ggplot2' graphics following the
editorial guidelines of the Institute for Applied Economic
Research (Ipea).
Author: Pedro Ferreira [aut, cre],
Pedro Jorge [aut],
Daniel Lima [aut],
Gustavo Coelho [aut],
Rafael H. M. Pereira [aut],
Lucas Mation [aut],
Fabio Vaz [ctb],
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro Ferreira <pedro.ferreira2@ipea.gov.br>
Diff between ipeaplot versions 0.5.2 dated 2026-05-20 and 0.5.3 dated 2026-07-06
DESCRIPTION | 13 LICENSE | 4 MD5 | 58 NAMESPACE | 32 NEWS.md | 59 R/ipea_palette.R | 316 +- R/ipeaplot.R | 44 R/save_ipeaplot.R | 356 +-- R/scale_ipea.R | 628 ++--- R/theme_ipea.R | 996 ++++----- README.md | 166 - build/vignette.rds |binary inst/doc/cookbook.R | 710 +++--- inst/doc/cookbook.Rmd | 952 ++++---- inst/doc/cookbook.html | 4048 ++++++++++++++++++------------------- inst/doc/intro_ipeaplot.R | 356 +-- inst/doc/intro_ipeaplot.Rmd | 586 ++--- inst/doc/intro_ipeaplot.html | 1350 ++++++------ man/ipea_pal.Rd | 102 man/ipea_palette.Rd | 108 man/ipeaplot.Rd | 89 man/save_ipeaplot.Rd | 140 - man/scale_color_ipea.Rd | 150 - man/scale_fill_ipea.Rd | 152 - man/theme_ipea.Rd | 166 - tests/tests_pedro_alves/exemplos.R | 540 ++-- tests/tests_pedro_alves/test.R | 400 +-- tests/tests_rafa/test_rafa.R | 264 +- vignettes/cookbook.Rmd | 952 ++++---- vignettes/intro_ipeaplot.Rmd | 586 ++--- 30 files changed, 7164 insertions(+), 7159 deletions(-)
Title: A Comprehensive Toolkit for Clinical HLA Informatics
Description: A comprehensive toolkit for clinical Human Leukocyte Antigen (HLA) informatics, built on 'tidyverse' <https://tidyverse.tidyverse.org/> principles and making use of Genotype List String (GL String, Mack et al. (2023) <doi:10.1111/tan.15126>) for storing and computing HLA genotype data. Specific functionalities include: coercion of HLA data in tabular format to and from GL String; calculation of matching and mismatching in all directions, with multiple output formats; automatic formatting of HLA data for searching within a GL String; truncation of molecular HLA data to a specific number of fields; and reading HLA genotypes in HML files and extracting the GL String. This library is intended for research use. Any application making use of this package in a clinical setting will need to be independently validated according to local regulations.
Author: Nicholas Brown [cre, aut] ,
Busra Coskun [aut]
Maintainer: Nicholas Brown <nicholas.brown@pennmedicine.upenn.edu>
Diff between immunogenetr versions 1.3.0 dated 2026-05-26 and 1.4.0 dated 2026-07-06
DESCRIPTION | 8 MD5 | 139 ++++--- NEWS.md | 24 + R/GLstring_expand_longer.R | 12 R/GLstring_gene_copies_combine.R | 4 R/GLstring_genes.R | 18 - R/GLstring_genes_expanded.R | 8 R/GLstring_genotype_ambiguity.R | 12 R/GLstring_regex.R | 12 R/GLstring_to_ambiguity_table.R | 10 R/HLA_columns_to_GLstring.R | 207 +++++++---- R/HLA_match_number.R | 4 R/HLA_match_summary_HCT.R | 6 R/HLA_mismatch_alleles.R | 8 R/HLA_mismatch_base.R | 46 +- R/HLA_mismatch_logical.R | 4 R/HLA_mismatch_number.R | 10 R/HLA_mismatched_alleles.R | 8 R/HLA_prefix_add.R | 8 R/HLA_prefix_remove.R | 14 R/HLA_truncate.R | 10 R/HLA_typing_synthetic_LIS-data.R |only R/ambiguity_table_to_GLstring.R | 10 R/immunogenetr-package.R | 20 - R/read_HML.R | 12 R/utils-validation.R | 6 README.md | 92 ++--- data/HLA_typing_synthetic_LIS.rda |only inst/doc/immunogenetr.R | 14 inst/doc/immunogenetr.Rmd | 38 +- inst/doc/immunogenetr.html | 233 ++++++------- man/GLstring_expand_longer.Rd | 10 man/GLstring_gene_copies_combine.Rd | 4 man/GLstring_genes.Rd | 6 man/GLstring_genes_expanded.Rd | 6 man/GLstring_genotype_ambiguity.Rd | 6 man/GLstring_regex.Rd | 8 man/GLstring_to_ambiguity_table.Rd | 10 man/HLA_columns_to_GLstring.Rd | 21 - man/HLA_match_number.Rd | 4 man/HLA_match_summary_HCT.Rd | 6 man/HLA_mismatch_alleles.Rd | 8 man/HLA_mismatch_base.Rd | 8 man/HLA_mismatch_logical.Rd | 4 man/HLA_mismatch_number.Rd | 8 man/HLA_mismatched_alleles.Rd | 8 man/HLA_prefix_add.Rd | 4 man/HLA_prefix_remove.Rd | 4 man/HLA_truncate.Rd | 6 man/HLA_typing_synthetic_LIS.Rd |only man/ambiguity_table_to_GLstring.Rd | 8 man/immunogenetr-package.Rd | 2 man/read_HML.Rd | 4 tests/testthat/test-GLstring_expand_longer.R | 2 tests/testthat/test-GLstring_gene_copies_combine.R | 2 tests/testthat/test-GLstring_genes.R | 14 tests/testthat/test-GLstring_genes_expanded.R | 2 tests/testthat/test-GLstring_genotype_ambiguity.R | 6 tests/testthat/test-GLstring_regex.R | 10 tests/testthat/test-HLA_columns_to_GLstring.R | 2 tests/testthat/test-HLA_columns_to_GLstring_nomenclature.R |only tests/testthat/test-HLA_match_number.R | 6 tests/testthat/test-HLA_match_summary_HCT.R | 2 tests/testthat/test-HLA_mismatch_base.R | 26 + tests/testthat/test-HLA_mismatch_logical.R | 6 tests/testthat/test-HLA_mismatch_number.R | 6 tests/testthat/test-HLA_mismatched_alleles.R | 10 tests/testthat/test-HLA_typing_synthetic_LIS-data.R |only tests/testthat/test-ambiguity_table_to_GLstring.R | 2 tests/testthat/test-read_HML.R | 20 - tests/testthat/test-round_trip.R | 2 tests/testthat/test-validation.R | 10 vignettes/immunogenetr.Rmd | 38 +- 73 files changed, 720 insertions(+), 588 deletions(-)
Title: Using Cytogenetics Data in R
Description: Defines classes and methods to process text-based
cytogenetics using the CytoGPS web site, then import the results
into R for further analysis and graphing.
Author: Kevin R. Coombes [aut, cre],
Dwayne Tally [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between RCytoGPS versions 1.2.10 dated 2026-01-29 and 1.2.13 dated 2026-07-06
DESCRIPTION | 8 MD5 | 26 +- R/sysdata.rda |binary build/vignette.rds |binary data/cytoData.rda |binary data/cytobandLocations.rda |binary inst/doc/Gallery.html | 434 ++++++++++++++++++++++-------------------- inst/doc/IntroRCytoGPS.Rmd | 4 inst/doc/IntroRCytoGPS.html | 448 ++++++++++++++++++++++++-------------------- man/01-cytobandLocations.Rd | 3 man/02-readLGF.Rd | 4 man/03-CytobandData.Rd | 3 man/07-preclean.Rd | 4 vignettes/IntroRCytoGPS.Rmd | 4 14 files changed, 513 insertions(+), 425 deletions(-)
Title: Qualitative Palettes with Many Colors
Description: Tools for creating, viewing, and assessing qualitative
palettes with many (20-30 or more) colors. See Coombes and colleagues
(2019) <doi:10.18637/jss.v090.c01>.
Author: Guy Brock [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Polychrome versions 1.5.4 dated 2025-04-06 and 1.6.1 dated 2026-07-06
DESCRIPTION | 8 +++---- MD5 | 42 ++++++++++++++++++++++++----------------- NAMESPACE | 2 - R/palettes.R | 15 ++++++++++++++ build/vignette.rds |binary data/Dark24.rda |binary data/Light24.rda |binary data/alphabet.rda |binary data/colorsafe.rda |binary data/glasbey.rda |binary data/iscc.rda |binary data/palette36.rda |binary data/sky-colors.rda |binary data/xkcd.rda |only inst/doc/color-deficits.html | 24 +++++++++++------------ inst/doc/colornames.R |only inst/doc/colornames.Rmd |only inst/doc/colornames.html |only inst/doc/creatingPalettes.html | 20 +++++++++---------- inst/doc/polychrome.html | 22 ++++++++++----------- inst/doc/testgg.html | 8 +++---- inst/extData/rewrite.R | 8 +++++++ inst/extData/xkcdColors.txt |only man/xkcd.Rd |only man/xkcdNames.Rd |only vignettes/colornames.Rmd |only 26 files changed, 90 insertions(+), 59 deletions(-)
Title: Logit Models w/Preference & WTP Space Utility Parameterizations
Description: Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. [...truncated...]
Author: John Helveston [aut, cre, cph] ,
Connor Forsythe [ctb]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between logitr versions 1.1.3 dated 2025-11-18 and 1.2.0 dated 2026-07-06
DESCRIPTION | 15 MD5 | 113 +++-- NAMESPACE | 3 NEWS.md | 11 R/RcppExports.R |only R/backend_cpp.R |only R/data.R | 91 +++- R/draws.R | 27 - R/inputChecks.R | 41 + R/logit.R | 7 R/logit_batched.R |only R/logitr-package.R |only R/logitr.R | 121 ++++- R/methods.R | 10 R/modelInputs.R | 87 +++ R/optimLoop.R | 53 +- README.md | 34 + build/vignette.rds |binary data/loglik_draws.rda |only data/runtimes.rda |binary data/runtimes_draws.rda |only inst/doc/backends.R |only inst/doc/backends.Rmd |only inst/doc/backends.html |only inst/doc/basic_usage.html | 106 ++-- inst/doc/benchmark.R | 103 ++-- inst/doc/benchmark.Rmd | 141 +++--- inst/doc/benchmark.html | 780 ++++++++++++++++++++++++++--------- inst/doc/data_formatting.html | 22 inst/doc/interactions.html | 120 ++--- inst/doc/mnl_models.html | 87 +-- inst/doc/mnl_models_weighted.html | 165 +++---- inst/doc/mxl_models.html | 267 +++++------ inst/doc/predict.html | 89 +-- inst/doc/summarizing_results.Rmd | 2 inst/doc/summarizing_results.html | 432 +++++++++---------- inst/doc/utility_models.Rmd | 2 inst/doc/utility_models.html | 82 +-- inst/example/examples.R | 38 - inst/extdata/mxl_pref.Rds |binary inst/extdata/mxl_pref_cor.Rds |binary inst/extdata/mxl_wtp.Rds |binary man/logitr-package.Rd |only man/logitr.Rd | 67 ++- man/loglik_draws.Rd |only man/rmdchunks/header.Rmd | 16 man/rmdchunks/installation.Rmd | 8 man/rmdchunks/utilityPreference.Rmd | 4 man/rmdchunks/utilityWtp.Rmd | 4 man/runtimes.Rd | 15 man/runtimes_draws.Rd |only src |only tests/testthat/test_backend.R |only tests/testthat/test_batched.R |only tests/testthat/test_cpp.R |only tests/testthat/test_gradients_pref.R | 3 tests/testthat/test_gradients_wtp.R | 3 tests/testthat/test_panel.R |only tests/testthat/test_parallel.R |only tests/testthat/test_sd_signs.R |only vignettes/backends.Rmd |only vignettes/benchmark.Rmd | 141 +++--- vignettes/benchmark.png |binary vignettes/benchmark_draws.png |only vignettes/benchmark_loglik.png |only vignettes/summarizing_results.Rmd | 2 vignettes/utility_models.Rmd | 2 67 files changed, 2110 insertions(+), 1204 deletions(-)
Title: Simplify Access to Brazilian Social Data
Description: Provides tools for downloading and processing microdata from
the PNAD Contínua (PNADC, Continuous National Household Sample Survey),
a rotating panel survey published quarterly by IBGE (Brazilian Institute
of Geography and Statistics). Includes panel identification algorithms
for linking individuals across survey waves.
Author: Laura Tavares Regadas [aut, cre],
DataZoom [fnd],
Igor Rigolon Veiga [aut],
Arthur Lins de Vasconcellos [aut],
Giulia Toscano Imbuzeiro [aut],
Guilherme Jardim [aut],
Pablo Chaves [aut],
Breno Avidos [aut],
Bernardo Sieira [aut]
Maintainer: Laura Tavares Regadas <lauratregadas@gmail.com>
Diff between datazoom.social versions 0.1.0 dated 2026-05-07 and 0.1.1 dated 2026-07-06
DESCRIPTION | 12 LICENSE | 4 MD5 | 48 - NAMESPACE | 13 NEWS.md | 29 R/build_pnadc_panel.R | 523 +++++++++----- R/calculate_panel_attrition.R | 192 ++--- R/cria_df_de_atrito.R | 160 ++-- R/donate_birth_dates.R |only R/load_pnadc.R | 1443 +++++++++++++++++++--------------------- R/pnad_sample.R | 102 +- R/zzz.R | 26 README.md | 834 ++++++++++++----------- build/vignette.rds |binary inst/doc/BUILD_PNADC_PANEL.R | 53 - inst/doc/BUILD_PNADC_PANEL.Rmd | 191 ++--- inst/doc/BUILD_PNADC_PANEL.html | 975 ++++++++++++++------------- inst/doc/LOAD_PNADC.R | 154 ++-- inst/doc/LOAD_PNADC.Rmd | 406 +++++------ inst/doc/LOAD_PNADC.html | 1233 +++++++++++++++++----------------- man/build_pnadc_panel.Rd | 52 - man/cria_df_de_atrito.Rd |only man/load_pnadc.Rd | 182 ++--- man/pnad_sample.Rd | 126 +-- vignettes/BUILD_PNADC_PANEL.Rmd | 191 ++--- vignettes/LOAD_PNADC.Rmd | 406 +++++------ 26 files changed, 3822 insertions(+), 3533 deletions(-)
More information about datazoom.social at CRAN
Permanent link
Title: Render Tables, Listings, and Figures for Clinical Submissions
Description: Render clinical submission tables, listings, and figures to
'RTF', 'LaTeX', 'HTML', 'PDF', and 'DOCX' from pre-summarised data
frames, with no external 'Java' or 'SAS' dependency. Features include
decimal alignment via font metrics, multi-level column headers with
passthrough leaves, predicate-targeted cell styling, footnotes,
group-aware pagination, and figures that wrap a plot or image in the
same page chrome as a table. Built for Clinical Data Interchange Standards
Consortium (CDISC) Analysis Data Model (ADaM) workflows and
regulatory submissions to agencies such as the Food and Drug
Administration (FDA), European Medicines Agency (EMA), and
Pharmaceuticals and Medical Devices Agency (PMDA).
Author: Vignesh Thanikachalam [aut, cre, cph]
Maintainer: Vignesh Thanikachalam <about.vignesh@gmail.com>
Diff between tabular versions 0.1.0 dated 2026-06-11 and 0.2.0 dated 2026-07-06
tabular-0.1.0/tabular/tests/testthat/testthat-problems.rds |only tabular-0.2.0/tabular/DESCRIPTION | 21 tabular-0.2.0/tabular/MD5 | 319 +-- tabular-0.2.0/tabular/NAMESPACE | 4 tabular-0.2.0/tabular/NEWS.md | 207 ++ tabular-0.2.0/tabular/R/aaa_class.R | 280 ++- tabular-0.2.0/tabular/R/align.R | 19 tabular-0.2.0/tabular/R/as_grid.R | 160 + tabular-0.2.0/tabular/R/backend_docx.R | 778 +++++++- tabular-0.2.0/tabular/R/backend_html.R | 382 +++- tabular-0.2.0/tabular/R/backend_latex.R | 461 ++++- tabular-0.2.0/tabular/R/backend_md.R | 241 ++ tabular-0.2.0/tabular/R/backend_pdf.R | 10 tabular-0.2.0/tabular/R/backend_rtf.R | 546 +++++- tabular-0.2.0/tabular/R/brdr.R | 11 tabular-0.2.0/tabular/R/chrome_style.R | 7 tabular-0.2.0/tabular/R/col_spec.R | 272 +-- tabular-0.2.0/tabular/R/col_width.R | 23 tabular-0.2.0/tabular/R/cols.R | 224 +- tabular-0.2.0/tabular/R/data.R | 98 - tabular-0.2.0/tabular/R/emit.R | 42 tabular-0.2.0/tabular/R/engine_borders.R | 11 tabular-0.2.0/tabular/R/engine_footnotes.R | 82 tabular-0.2.0/tabular/R/engine_format.R | 19 tabular-0.2.0/tabular/R/engine_group_display.R | 221 +- tabular-0.2.0/tabular/R/engine_paginate.R | 185 +- tabular-0.2.0/tabular/R/engine_style.R | 4 tabular-0.2.0/tabular/R/engine_subgroup_split.R | 78 tabular-0.2.0/tabular/R/figure.R |only tabular-0.2.0/tabular/R/figure_raster.R |only tabular-0.2.0/tabular/R/font_metrics.R | 31 tabular-0.2.0/tabular/R/fonts.R | 130 + tabular-0.2.0/tabular/R/footnote.R | 6 tabular-0.2.0/tabular/R/geometry.R | 46 tabular-0.2.0/tabular/R/headers.R | 11 tabular-0.2.0/tabular/R/inline_format.R | 18 tabular-0.2.0/tabular/R/locations.R | 4 tabular-0.2.0/tabular/R/manifest.R | 102 + tabular-0.2.0/tabular/R/page_chrome.R | 12 tabular-0.2.0/tabular/R/paginate.R | 46 tabular-0.2.0/tabular/R/pivot_across.R | 893 +++++++++- tabular-0.2.0/tabular/R/preset.R | 216 +- tabular-0.2.0/tabular/R/preset_minimal.R | 25 tabular-0.2.0/tabular/R/print.R | 105 + tabular-0.2.0/tabular/R/sanity.R | 29 tabular-0.2.0/tabular/R/sort_rows.R | 54 tabular-0.2.0/tabular/R/style.R | 45 tabular-0.2.0/tabular/R/style_template.R | 8 tabular-0.2.0/tabular/R/subgroup.R | 177 + tabular-0.2.0/tabular/R/tabular.R | 102 - tabular-0.2.0/tabular/R/theme.R | 12 tabular-0.2.0/tabular/R/zzz.R | 24 tabular-0.2.0/tabular/README.md | 2 tabular-0.2.0/tabular/data/cdisc_saf_ae.rda |binary tabular-0.2.0/tabular/data/cdisc_saf_demo.rda |binary tabular-0.2.0/tabular/data/cdisc_saf_subgroup.rda |binary tabular-0.2.0/tabular/inst/doc/tabular.R | 2 tabular-0.2.0/tabular/inst/doc/tabular.html | 372 ---- tabular-0.2.0/tabular/inst/doc/tabular.qmd | 2 tabular-0.2.0/tabular/inst/qualification/QUALIFICATION_README.md | 2 tabular-0.2.0/tabular/inst/qualification/qualify_tabular_cdisc.R | 10 tabular-0.2.0/tabular/man/as_grid.Rd | 21 tabular-0.2.0/tabular/man/brdr.Rd | 7 tabular-0.2.0/tabular/man/cdisc_eff_resp.Rd | 5 tabular-0.2.0/tabular/man/cdisc_saf_ae.Rd | 8 tabular-0.2.0/tabular/man/cdisc_saf_aesocpt.Rd | 8 tabular-0.2.0/tabular/man/cdisc_saf_aesocpt_ard.Rd | 8 tabular-0.2.0/tabular/man/cdisc_saf_demo.Rd | 23 tabular-0.2.0/tabular/man/cdisc_saf_subgroup.Rd | 44 tabular-0.2.0/tabular/man/cells.Rd | 4 tabular-0.2.0/tabular/man/check_fonts.Rd | 8 tabular-0.2.0/tabular/man/col_spec.Rd | 181 +- tabular-0.2.0/tabular/man/cols.Rd | 64 tabular-0.2.0/tabular/man/emit.Rd | 23 tabular-0.2.0/tabular/man/figure.Rd |only tabular-0.2.0/tabular/man/figures/README-hero.png |binary tabular-0.2.0/tabular/man/footnote.Rd | 6 tabular-0.2.0/tabular/man/headers.Rd | 11 tabular-0.2.0/tabular/man/html.Rd | 4 tabular-0.2.0/tabular/man/md.Rd | 6 tabular-0.2.0/tabular/man/paginate.Rd | 37 tabular-0.2.0/tabular/man/pivot_across.Rd | 218 ++ tabular-0.2.0/tabular/man/preset.Rd | 156 - tabular-0.2.0/tabular/man/preset_minimal.Rd | 25 tabular-0.2.0/tabular/man/print.tabular_spec.Rd | 2 tabular-0.2.0/tabular/man/set_preset.Rd | 4 tabular-0.2.0/tabular/man/sort_rows.Rd | 54 tabular-0.2.0/tabular/man/style.Rd | 33 tabular-0.2.0/tabular/man/style_template.Rd | 8 tabular-0.2.0/tabular/man/subgroup.Rd | 163 + tabular-0.2.0/tabular/man/tabular-package.Rd | 4 tabular-0.2.0/tabular/man/tabular.Rd | 63 tabular-0.2.0/tabular/man/tabular_classes.Rd | 4 tabular-0.2.0/tabular/man/tabular_predicates.Rd | 8 tabular-0.2.0/tabular/tests/testthat/_problems/test-group_display-1793.R |only tabular-0.2.0/tabular/tests/testthat/_snaps/Total/engine_decimal.md | 46 tabular-0.2.0/tabular/tests/testthat/_snaps/backend_docx/saf_demo_golden.xml | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/backend_html/saf_demo_golden.html | 163 - tabular-0.2.0/tabular/tests/testthat/_snaps/backend_latex/banded_multirange.tex | 10 tabular-0.2.0/tabular/tests/testthat/_snaps/backend_latex/saf_demo_golden.tex | 68 tabular-0.2.0/tabular/tests/testthat/_snaps/backend_md/saf_demo_golden.md | 62 tabular-0.2.0/tabular/tests/testthat/_snaps/backend_rtf/saf_demo_golden.rtf | 705 +------ tabular-0.2.0/tabular/tests/testthat/_snaps/drug_100/engine_decimal.md | 46 tabular-0.2.0/tabular/tests/testthat/_snaps/drug_50/engine_decimal.md | 46 tabular-0.2.0/tabular/tests/testthat/_snaps/engine_decimal.md | 138 - tabular-0.2.0/tabular/tests/testthat/_snaps/engine_headers.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/figure-backends.md |only tabular-0.2.0/tabular/tests/testthat/_snaps/figure.md |only tabular-0.2.0/tabular/tests/testthat/_snaps/headers.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/inline_format.md | 4 tabular-0.2.0/tabular/tests/testthat/_snaps/paginate.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/pivot_across.md |only tabular-0.2.0/tabular/tests/testthat/_snaps/placebo/engine_decimal.md | 46 tabular-0.2.0/tabular/tests/testthat/_snaps/preset.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/set_preset.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/sort_rows.md | 2 tabular-0.2.0/tabular/tests/testthat/_snaps/subgroup.md | 4 tabular-0.2.0/tabular/tests/testthat/_snaps/tabular.md |only tabular-0.2.0/tabular/tests/testthat/fixtures |only tabular-0.2.0/tabular/tests/testthat/tabular.aux | 6 tabular-0.2.0/tabular/tests/testthat/tabular.log |only tabular-0.2.0/tabular/tests/testthat/test-aaa_class.R | 36 tabular-0.2.0/tabular/tests/testthat/test-align.R | 18 tabular-0.2.0/tabular/tests/testthat/test-as_grid.R | 24 tabular-0.2.0/tabular/tests/testthat/test-backend_docx.R | 150 + tabular-0.2.0/tabular/tests/testthat/test-backend_html.R | 200 +- tabular-0.2.0/tabular/tests/testthat/test-backend_latex.R | 326 +++ tabular-0.2.0/tabular/tests/testthat/test-backend_md.R | 86 tabular-0.2.0/tabular/tests/testthat/test-backend_pdf.R | 48 tabular-0.2.0/tabular/tests/testthat/test-backend_rtf.R | 282 ++- tabular-0.2.0/tabular/tests/testthat/test-col_spec.R | 39 tabular-0.2.0/tabular/tests/testthat/test-col_width.R | 14 tabular-0.2.0/tabular/tests/testthat/test-cols.R | 120 + tabular-0.2.0/tabular/tests/testthat/test-data.R |only tabular-0.2.0/tabular/tests/testthat/test-empty-state.R |only tabular-0.2.0/tabular/tests/testthat/test-engine_borders-table-layers.R | 10 tabular-0.2.0/tabular/tests/testthat/test-engine_decimal.R | 155 + tabular-0.2.0/tabular/tests/testthat/test-engine_footnotes.R | 60 tabular-0.2.0/tabular/tests/testthat/test-engine_format.R | 4 tabular-0.2.0/tabular/tests/testthat/test-engine_headers.R | 8 tabular-0.2.0/tabular/tests/testthat/test-engine_paginate.R | 69 tabular-0.2.0/tabular/tests/testthat/test-engine_style.R | 3 tabular-0.2.0/tabular/tests/testthat/test-engine_subgroup_split.R | 16 tabular-0.2.0/tabular/tests/testthat/test-examples-phantom.R | 3 tabular-0.2.0/tabular/tests/testthat/test-figure-backends.R |only tabular-0.2.0/tabular/tests/testthat/test-figure.R |only tabular-0.2.0/tabular/tests/testthat/test-figure_raster.R |only tabular-0.2.0/tabular/tests/testthat/test-font_metrics.R | 10 tabular-0.2.0/tabular/tests/testthat/test-fonts.R | 118 + tabular-0.2.0/tabular/tests/testthat/test-group_display.R | 625 +++++- tabular-0.2.0/tabular/tests/testthat/test-inline_format.R | 110 - tabular-0.2.0/tabular/tests/testthat/test-page_chrome.R | 4 tabular-0.2.0/tabular/tests/testthat/test-paginate.R | 8 tabular-0.2.0/tabular/tests/testthat/test-pivot_across.R | 678 +++++++ tabular-0.2.0/tabular/tests/testthat/test-preset-extended.R | 4 tabular-0.2.0/tabular/tests/testthat/test-preset.R | 44 tabular-0.2.0/tabular/tests/testthat/test-style.R | 47 tabular-0.2.0/tabular/tests/testthat/test-subgroup.R | 249 ++ tabular-0.2.0/tabular/tests/testthat/test-tabular.R | 36 tabular-0.2.0/tabular/tests/testthat/test-theme.R | 16 tabular-0.2.0/tabular/tests/testthat/test-util_ws.R | 2 tabular-0.2.0/tabular/tests/testthat/test-width_mode.R | 18 tabular-0.2.0/tabular/vignettes/articles/data-in.qmd | 166 + tabular-0.2.0/tabular/vignettes/articles/output.qmd | 31 tabular-0.2.0/tabular/vignettes/articles/presentation.qmd | 69 tabular-0.2.0/tabular/vignettes/articles/recipes.qmd | 77 tabular-0.2.0/tabular/vignettes/articles/structure.qmd | 124 + tabular-0.2.0/tabular/vignettes/tabular.qmd | 2 168 files changed, 10174 insertions(+), 3694 deletions(-)
Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative
trait locus (QTL) analysis in experimental crosses. It is a
reimplementation of the 'R/qtl' package to better handle
high-dimensional data and complex cross designs.
Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] ,
R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2 versions 0.42 dated 2026-06-08 and 0.44 dated 2026-07-06
DESCRIPTION | 8 ++-- MD5 | 31 +++++++++------- NAMESPACE | 1 NEWS.md | 22 ++++++++++- R/cluster_util.R | 2 - R/plot_ci.R | 6 ++- R/scan1gen.R |only R/scan1perm.R | 69 +++++++++++++++++++++++++++++++++--- R/scan1perm_gen.R |only README.md | 2 - build/partial.rdb |binary data/CCaltcolors.RData |binary data/CCcolors.RData |binary data/CCorigcolors.RData |binary man/scan1gen.Rd |only man/scan1perm.Rd | 44 ++++++++++++++++++++++ src/linreg_eigen.cpp | 12 ++++-- tests/testthat/test-scan1gen.R |only tests/testthat/test-scan1perm_gen.R |only 19 files changed, 165 insertions(+), 32 deletions(-)
Title: Extending the Newman Studentized Range Statistic to
Transcriptomics
Description: Extends the classical Newman studentized range statistic
in various ways that can be applied to genome-scale transcriptomic
or other expression data.
Author: Zachary B. Abrams [aut],
Greg Gershkowitz [aut],
Anoushka Joglekar [aut],
Chao Liu [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between NewmanOmics versions 1.0.14 dated 2025-04-08 and 1.1.3 dated 2026-07-06
DESCRIPTION | 8 +-- MD5 | 18 ++++--- R/00-pairedStat.R | 37 +++++++++++---- build/vignette.rds |binary data/GSE6631.rda |binary data/LungPair.rda |binary inst/doc/newmanomics.html | 98 +++++++++++++++++++++--------------------- man/02-pairedStat.Rd | 35 ++++++++++++--- tests/00-pairedTest.Rout.save | 44 +++++++++--------- tests/01-testTeho.R |only tests/01-testTeho.Rout |only 11 files changed, 141 insertions(+), 99 deletions(-)
Title: Reference Data and Helpers for Small Island States and
Territories
Description: A curated reference list of countries and territories with
classifications for Small Island Developing States (SIDS),
sub-national island jurisdictions (SNIJ), World Bank region and
income group, and political association. Sub-sovereign cases such
as Aruba, Curacao, Bonaire, Sint Maarten, the French overseas
territories, and Aaland Islands are represented with disambiguating
codes that standard country-code packages often collapse or omit.
Provides predicate helpers and a tidy joiner intended to extend
rather than replace 'countrycode'. Source data is maintained at
<https://github.com/University-of-Aruba/island-research-reference-data>
and licensed CC BY 4.0.
Author: Rendell de Kort [aut, cre] ,
University of Aruba [cph, fnd] Network)
Maintainer: Rendell de Kort <rendell.dekort@ua.aw>
Diff between islandcodes versions 0.1.1 dated 2026-05-15 and 0.2.0 dated 2026-07-06
DESCRIPTION | 6 +-- MD5 | 33 ++++++++++------- NAMESPACE | 2 + NEWS.md | 7 +++ R/coords.R |only R/data.R | 15 +++++++ R/distance.R |only README.md | 15 ++++++- data/islands.rda |binary inst/CITATION | 7 ++- inst/doc/islandcodes.R | 23 +++++++++++- inst/doc/islandcodes.Rmd | 43 ++++++++++++++++++++++ inst/doc/islandcodes.html | 77 ++++++++++++++++++++++++++++++++++++++++- man/figures |only man/island_coords.Rd |only man/island_distance.Rd |only man/islands.Rd | 15 +++++++ tests/testthat/test-coords.R |only tests/testthat/test-distance.R |only tests/testthat/test-lookup.R | 9 +++- vignettes/islandcodes.Rmd | 43 ++++++++++++++++++++++ 21 files changed, 267 insertions(+), 28 deletions(-)
Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data
visualization in R. However the default generated plots require some formatting
before we can send them for publication. Furthermore, to customize a 'ggplot',
the syntax is opaque and this raises the level of difficulty for researchers
with no advanced R programming skills. 'ggpubr' provides some easy-to-use
functions for creating and customizing 'ggplot2'-based publication ready plots.
This version includes modern R ecosystem compatibility updates and customizable
p-value formatting presets (APA, AMA, NEJM, Lancet, GraphPad, and scientific
notation) for publication workflows, plus robust sparse-subset handling in
statistical annotation layers such as 'stat_compare_means()' and 'geom_pwc()',
with informative per-group skip diagnostics for non-comparable subsets.
Author: Alboukadel Kassambara [aut, cre],
Laszlo Erdey [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggpubr versions 0.6.3 dated 2026-02-24 and 1.0.0 dated 2026-07-06
DESCRIPTION | 49 MD5 | 454 ++- NAMESPACE | 7 NEWS.md | 811 +++++-- R/add_summary.R | 236 +- R/annotate_figure.R | 155 + R/as_ggplot.R | 37 R/as_npc.R | 50 R/axis_scale.R | 136 - R/background_image.R | 40 R/bgcolor.R | 26 R/border.R | 36 R/compare_means.R | 582 +++-- R/create_aes.R | 64 R/desc_statby.R | 54 R/diff_express.R | 40 R/facet.R | 154 - R/font.R | 137 - R/gene_citation.R | 33 R/gene_expression.R | 26 R/geom_bracket.R | 518 +++- R/geom_exec.R | 83 R/geom_pwc.R | 979 +++++--- R/get_breaks.R | 38 R/get_coord.R | 22 R/get_legend.R | 40 R/get_palette.R | 101 R/ggadd.R | 180 - R/ggadjust_pvalue.R | 113 R/ggarrange.R | 267 +- R/ggballoonplot.R | 223 + R/ggbarplot.R | 584 +++-- R/ggboxplot.R | 245 +- R/ggdensity.R | 133 - R/ggdonutchart.R | 139 - R/ggdotchart.R | 265 +- R/ggdotplot.R | 148 - R/ggecdf.R | 78 R/ggerrorplot.R | 168 - R/ggexport.R | 78 R/gghistogram.R | 205 + R/ggline.R | 329 +- R/ggmaplot.R | 312 +- R/ggpaired.R | 174 - R/ggpar.R | 141 - R/ggparagraph.R | 81 R/ggpie.R | 182 - R/ggpubr-package.R | 21 R/ggpubr_args.R | 36 R/ggpubr_options.R | 4 R/ggqqplot.R | 211 + R/ggscatter.R | 412 ++- R/ggscatterhist.R | 333 +- R/ggstripchart.R | 182 - R/ggsummarystats.R | 85 R/ggtext.R | 219 - R/ggtexttable.R | 1137 +++++----- R/ggviolin.R | 306 +- R/gradient_color.R | 26 R/grids.R | 51 R/npc_to_data_coord.R | 4 R/p_format_utils.R |only R/rotate.R | 32 R/rotate_axis_text.R | 75 R/rremove.R | 85 R/set_palette.R | 105 R/shared_docs.R | 10 R/show_line_types.R | 27 R/show_point_shapes.R | 25 R/stat_anova_test.R | 523 ++-- R/stat_central_tendency.R | 70 R/stat_chull.R | 17 R/stat_compare_means.R | 720 ++++-- R/stat_conf_ellipse.R | 73 R/stat_cor.R | 536 +++- R/stat_friedman_test.R | 79 R/stat_kruskal_test.R | 66 R/stat_mean.R | 28 R/stat_overlay_normal_density.R | 36 R/stat_pvalue_manual.R | 389 ++- R/stat_regline_equation.R | 251 +- R/stat_stars.R | 34 R/stat_welch_anova_test.R | 67 R/text_grob.R | 36 R/theme_pubr.R | 149 - R/theme_transparent.R | 33 R/utilities.R | 1030 +++++---- R/utilities_base.R | 82 R/utilities_color.R | 193 + R/utilities_label.R | 146 - R/utils-aes.R | 6 R/utils-tidyr.R | 2 R/utils_stat_test_label.R | 264 +- R/zzz.R |only README.md | 71 inst/CITATION |only man/add_summary.Rd | 5 man/annotate_figure.Rd | 49 man/as_ggplot.Rd | 10 man/as_npc.Rd | 2 man/axis_scale.Rd | 2 man/background_image.Rd | 15 man/bgcolor.Rd | 2 man/build_symnum_args.Rd |only man/clean_lock_files.Rd |only man/compare_means.Rd | 140 + man/create_aes.Rd | 8 man/create_p_label.Rd |only man/desc_statby.Rd | 6 man/diff_express.Rd | 40 man/facet.Rd | 18 man/font.Rd | 28 man/format_p_value.Rd |only man/format_single_p.Rd |only man/gene_citation.Rd | 17 man/gene_expression.Rd | 14 man/geom_bracket.Rd | 73 man/geom_exec.Rd | 13 man/geom_pwc.Rd | 131 - man/get_breaks.Rd | 12 man/get_legend.Rd | 8 man/get_p_format_style.Rd |only man/get_palette.Rd | 48 man/ggadjust_pvalue.Rd | 70 man/ggarrange.Rd | 61 man/ggballoonplot.Rd | 88 man/ggbarplot.Rd | 133 - man/ggboxplot.Rd | 66 man/ggdensity.Rd | 38 man/ggdonutchart.Rd | 41 man/ggdotchart.Rd | 50 man/ggdotplot.Rd | 46 man/ggecdf.Rd | 17 man/ggerrorplot.Rd | 71 man/ggexport.Rd | 16 man/gghistogram.Rd | 46 man/ggline.Rd | 93 man/ggmaplot.Rd | 76 man/ggpaired.Rd | 36 man/ggpar.Rd | 58 man/ggparagraph.Rd | 23 man/ggpie.Rd | 37 man/ggpubr-common-params.Rd | 8 man/ggpubr-package.Rd | 22 man/ggpubr_args.Rd | 2 man/ggpubr_options.Rd | 2 man/ggqqplot.Rd | 15 man/ggscatter.Rd | 62 man/ggscatterhist.Rd | 34 man/ggstripchart.Rd | 80 man/ggsummarystats.Rd | 31 man/ggtext.Rd | 21 man/ggtexttable.Rd | 131 - man/ggviolin.Rd | 118 - man/gradient_color.Rd | 8 man/list_p_format_styles.Rd |only man/npc_to_data_coord.Rd | 2 man/p_format_styles.Rd |only man/resolve_p_format_params.Rd |only man/rotate.Rd | 6 man/rremove.Rd | 6 man/set_palette.Rd | 6 man/show_line_types.Rd | 4 man/show_point_shapes.Rd | 4 man/stat_anova_test.Rd | 102 man/stat_central_tendency.Rd | 23 man/stat_chull.Rd | 16 man/stat_compare_means.Rd | 189 + man/stat_conf_ellipse.Rd | 16 man/stat_cor.Rd | 136 + man/stat_friedman_test.Rd | 91 man/stat_kruskal_test.Rd | 85 man/stat_mean.Rd | 16 man/stat_overlay_normal_density.Rd | 12 man/stat_pvalue_manual.Rd | 116 - man/stat_regline_equation.Rd | 64 man/stat_stars.Rd | 18 man/stat_welch_anova_test.Rd | 85 man/text_grob.Rd | 10 man/theme_pubr.Rd | 13 man/theme_transparent.Rd | 8 tests/testthat/Rplots.pdf |only tests/testthat/test-add_stat_label.R | 155 + tests/testthat/test-annotate-figure-label.R |only tests/testthat/test-annotate-figure-titles.R |only tests/testthat/test-as_npc.R | 2 tests/testthat/test-check_data.R | 94 tests/testthat/test-clean_lock_files.R |only tests/testthat/test-colour-alias.R |only tests/testthat/test-compare-means-comparisons-note.R |only tests/testthat/test-compare-means-family.R |only tests/testthat/test-compare-means-padjust-group.R |only tests/testthat/test-compare-means-paired-id.R |only tests/testthat/test-compare-means-spaced-names.R |only tests/testthat/test-compare_means.R | 124 - tests/testthat/test-convert_label_dotdot_notation_to_after_stat.R | 81 tests/testthat/test-create_aes.R | 1 tests/testthat/test-facet-panel-labs.R |only tests/testthat/test-facet.R | 6 tests/testthat/test-geom-bracket-horizontal.R |only tests/testthat/test-geom-bracket-tip-collapse.R |only tests/testthat/test-geom-bracket-vertical.R |only tests/testthat/test-geom-exec-linewidth.R |only tests/testthat/test-geom-pwc-p-adjust-n.R |only tests/testthat/test-geom_pwc.R | 277 ++ tests/testthat/test-get-breaks-anchor.R |only tests/testthat/test-get_coord.R | 3 tests/testthat/test-ggadjust_pvalue.R | 27 tests/testthat/test-ggarrange-byrow.R |only tests/testthat/test-ggarrange-common-legend.R |only tests/testthat/test-ggarrange-spacing.R |only tests/testthat/test-ggballoonplot.R |only tests/testthat/test-ggbarplot-alpha-errorbar.R |only tests/testthat/test-ggbarplot-dodge2-errorbar.R |only tests/testthat/test-ggbarplot-facet-summary.R |only tests/testthat/test-ggbarplot-numeric-x.R |only tests/testthat/test-ggbarplot-stacked-posneg.R |only tests/testthat/test-ggboxplot-coef.R |only tests/testthat/test-ggboxplot.R | 100 tests/testthat/test-ggexport.R |only tests/testthat/test-ggline-jitter-dodge.R |only tests/testthat/test-ggline-multi-group.R |only tests/testthat/test-ggmaplot-facet.R |only tests/testthat/test-ggmaplot-ns-order.R |only tests/testthat/test-ggmaplot.R |only tests/testthat/test-ggpaired-jitter.R |only tests/testthat/test-ggpar-element-markdown.R |only tests/testthat/test-ggpar-legend-title.R |only tests/testthat/test-ggpie-donut-repel.R |only tests/testthat/test-ggscatter.R | 4 tests/testthat/test-ggscatterhist.R |only tests/testthat/test-ggstripchart.R | 37 tests/testthat/test-ggsummarystats.R |only tests/testthat/test-ggtext.R | 12 tests/testthat/test-ggtheme-null.R |only tests/testthat/test-ggviolin-align.R |only tests/testthat/test-ggviolin-scales.R |only tests/testthat/test-ggviolin.R |only tests/testthat/test-group-coord-zero-id.R |only tests/testthat/test-legend-direction.R |only tests/testthat/test-named-palette.R |only tests/testthat/test-null-default-import.R |only tests/testthat/test-orientation-axis-limits.R |only tests/testthat/test-p_format_utils.R |only tests/testthat/test-parse_font.R |only tests/testthat/test-regline-digits.R |only tests/testthat/test-set-ticksby.R |only tests/testthat/test-show-n.R |only tests/testthat/test-stat-compare-means-id.R |only tests/testthat/test-stat-cor-conf-int.R |only tests/testthat/test-stat-cor-label-anchor.R |only tests/testthat/test-stat-cor-rmse.R |only tests/testthat/test-stat-pvalue-manual-pdigits.R |only tests/testthat/test-stat-pvalue-manual-pformat.R |only tests/testthat/test-stat_anova_test.R | 214 + tests/testthat/test-stat_compare_means.R | 317 ++ tests/testthat/test-stat_cor.R |only tests/testthat/test-stat_friedman_test.R | 10 tests/testthat/test-stat_kruskal_test.R | 6 tests/testthat/test-stat_pvalue_manual.R | 153 + tests/testthat/test-stat_welch_anova_test.R | 6 tests/testthat/test-tab-add-title-just.R |only tests/testthat/test-table-cell-header-font.R |only tests/testthat/test-theme-pubr-ticks.R |only tests/testthat/test-utilities_color.R |only tests/testthat/test-utils-tidyr.R | 22 266 files changed, 14123 insertions(+), 8037 deletions(-)
More information about deckglgeoarrow at CRAN
Permanent link
Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards
Consortium) compliant Analysis Results Data objects. These objects are
used and re-used to construct summary tables, visualizations, and
written reports. The package also exports utilities for working with
these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] ,
Becca Krouse [aut],
Emily de la Rua [aut] ,
Davide Garolini [aut] ,
Malan Bosman [aut] ,
F. Hoffmann-La Roche AG [cph, fnd],
Alanah Jonas [aut],
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cards versions 0.8.0 dated 2026-05-28 and 0.8.1 dated 2026-07-06
DESCRIPTION | 11 ++- MD5 | 40 ++++++------ NEWS.md | 8 ++ R/ard_summary.R | 100 +++++++++++++++---------------- R/ard_tabulate.R | 57 ++++++++++++----- R/ard_tabulate_value.R | 23 ++++--- R/ard_total_n.R | 23 ++++--- R/bind_ard.R | 7 +- R/get_ard_statistics.R | 10 ++- R/rename_ard_columns.R | 14 +++- R/tidy_ard_order.R | 90 ++++++++++++++++----------- R/unlist_ard_columns.R | 6 + inst/WORDLIST | 1 man/cards-package.Rd | 2 man/rename_ard_columns.Rd | 4 - man/unlist_ard_columns.Rd | 2 tests/testthat/_snaps/tidy_as_ard.md | 98 ------------------------------ tests/testthat/test-bind_ard.R | 6 + tests/testthat/test-rename_ard_columns.R | 19 +++++ tests/testthat/test-tidy_as_ard.R | 48 +++++++++----- tests/testthat/test-unlist_ard_columns.R | 9 ++ 21 files changed, 309 insertions(+), 269 deletions(-)
Title: Work with 'BIDS' (Brain Imaging Data Structure) Projects
Description: Tools for working with 'BIDS' (Brain Imaging Data Structure)
formatted neuroimaging datasets. The package provides functionality for
reading and querying 'BIDS'-compliant projects, creating mock 'BIDS'
datasets for testing, and extracting preprocessed data from 'fMRIPrep'
derivatives. It supports searching and filtering 'BIDS' files by various
entities such as subject, session, task, and run to streamline
neuroimaging data workflows. See Gorgolewski et al. (2016)
<doi:10.1038/sdata.2016.44> for the 'BIDS' specification.
Author: Bradley Buchsbaum [aut, cre]
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Diff between bidser versions 0.2.0 dated 2026-02-19 and 0.5.0 dated 2026-07-06
DESCRIPTION | 19 MD5 | 254 ++- NAMESPACE | 77 - NEWS.md | 132 + R/all_generic.R | 470 +++++- R/bids.R | 949 +++++++++--- R/bids_uri.R |only R/bidsio.R | 184 +- R/check.R | 42 R/confounds.R | 413 +++++ R/dataset_description.R |only R/datatype_registry.R |only R/entity_filters.R |only R/events.R | 151 + R/index_dt.R |only R/matchers.R | 43 R/mock_bids.R | 281 ++- R/pack_bids.R | 164 +- R/plot_bids.R | 237 ++- R/plot_bids_project.R | 2 R/project_extensions.R |only R/query.R |only R/regex_parsers.R | 159 +- R/schema.R |only R/sidecar.R | 240 ++- R/specs.R | 120 + R/tabulars.R |only R/zzz.R |only README.md | 35 build/vignette.rds |binary inst/CITATION | 9 inst/bids-schema |only inst/doc/confounds-and-variables.R |only inst/doc/confounds-and-variables.Rmd |only inst/doc/confounds-and-variables.html |only inst/doc/derivatives.R |only inst/doc/derivatives.Rmd |only inst/doc/derivatives.html |only inst/doc/mock-bids.R |only inst/doc/mock-bids.Rmd |only inst/doc/mock-bids.html |only inst/doc/quickstart.R | 179 ++ inst/doc/quickstart.Rmd | 275 ++- inst/doc/quickstart.html | 1665 +++++++++++++++++----- man/as_bids_uri.Rd |only man/bids_check_compliance.Rd | 15 man/bids_datatype_spec.Rd |only man/bids_entities.Rd |only man/bids_heatmap.Rd | 2 man/bids_index.Rd |only man/bids_parser.Rd | 3 man/bids_project.Rd | 43 man/bids_report.Rd |only man/bids_report_data.Rd |only man/bids_schema.Rd |only man/bids_schema_versions.Rd |only man/bids_subject.Rd | 2 man/bids_summary.Rd | 2 man/bids_transform.Rd | 8 man/bids_uri.Rd |only man/bids_version.Rd |only man/bidser_pkg_env.Rd | 2 man/brain_mask.Rd | 2 man/build_subject_graph.Rd | 2 man/check_confounds.Rd |only man/check_func_scans.Rd | 2 man/confound_files-method.Rd | 2 man/confound_set.Rd | 14 man/create_preproc_mask.Rd | 2 man/create_preproc_mask.bids_project.Rd | 2 man/dataset_description.Rd |only man/dataset_name.Rd |only man/derivative_files.Rd |only man/derivative_pipelines.Rd |only man/dot-bids_schema_entities.Rd |only man/dot-bids_schema_suffixes.Rd |only man/dot-bids_schema_validate_filename.Rd |only man/dot-bidser_schema_check_tree.Rd |only man/event_files-method.Rd | 4 man/file_pairs.Rd | 2 man/flat_list-method.Rd | 2 man/func_scans.Rd | 2 man/func_scans.bids_project.Rd | 2 man/gen_parser.Rd |only man/get_metadata.Rd |only man/get_repetition_time.Rd | 2 man/is_bids_uri.Rd |only man/list_datatypes.Rd |only man/list_pack_bids.Rd | 2 man/load_all_events-method.Rd | 2 man/mask_files.Rd | 2 man/n_volumes.Rd |only man/pack_bids.Rd | 2 man/participants-method.Rd | 31 man/participants.mock_bids_project.Rd | 6 man/plot.bids_project.Rd | 2 man/plot_bids.Rd | 2 man/preproc_scans-method.Rd | 2 man/preproc_scans.bids_project.Rd | 2 man/query_files.Rd |only man/read_confounds-method.Rd | 10 man/read_confounds.Rd | 38 man/read_confounds.bids_project.Rd | 52 man/read_dataset_description.Rd |only man/read_events.Rd | 15 man/read_events.bids_project.Rd | 2 man/read_func_scans.Rd | 2 man/read_participants.Rd |only man/read_preproc_scans.bids_project.Rd | 9 man/read_scans_tsv.Rd |only man/read_sessions_tsv.Rd |only man/read_sidecar.Rd | 27 man/register_datatype.Rd |only man/resolve_bids_uri.Rd |only man/search_files.Rd | 14 man/sidecar.Rd |only man/surface_files.Rd | 2 man/tasks-method.Rd | 2 man/transform_files.Rd | 2 man/unregister_datatype.Rd |only man/variables_table.Rd |only tests/testthat/helper-bids-examples.R | 9 tests/testthat/test_bids_core.R |only tests/testthat/test_bids_remaining.R |only tests/testthat/test_bids_subject.R | 6 tests/testthat/test_bids_subject_local.R |only tests/testthat/test_bids_uri.R |only tests/testthat/test_bidsio_coverage.R |only tests/testthat/test_build_subject_graph.R | 2 tests/testthat/test_check_func.R |only tests/testthat/test_confounds.R | 140 + tests/testthat/test_coverage_boost.R |only tests/testthat/test_coverage_final.R |only tests/testthat/test_coverage_sessions.R |only tests/testthat/test_dataset_description.R |only tests/testthat/test_datatype_registry.R |only tests/testthat/test_dwi_datatype.R |only tests/testthat/test_formula_filters.R |only tests/testthat/test_index_dt.R |only tests/testthat/test_infer_tr.R |only tests/testthat/test_metadata_inheritance.R |only tests/testthat/test_mock_bids.R | 66 tests/testthat/test_mock_bids_methods.R |only tests/testthat/test_n_volumes.R |only tests/testthat/test_pack_bids.R | 49 tests/testthat/test_pack_bids_coverage.R |only tests/testthat/test_plot_bids.R | 8 tests/testthat/test_plot_bids_coverage.R |only tests/testthat/test_plot_internals.R |only tests/testthat/test_preproc_mask.R | 39 tests/testthat/test_preproc_scans_sessions_runs.R | 2 tests/testthat/test_project_ext_helpers.R |only tests/testthat/test_project_extensions.R |only tests/testthat/test_query_files.R |only tests/testthat/test_query_helpers.R |only tests/testthat/test_read_confounds.R | 250 +++ tests/testthat/test_read_preproc_scans.R |only tests/testthat/test_regression_fixes.R |only tests/testthat/test_schema.R |only tests/testthat/test_sidecar.R | 4 tests/testthat/test_summary_compliance.R | 3 tests/testthat/test_tabulars.R |only tools |only vignettes/albers.css | 1039 +++++++++++-- vignettes/albers.js | 321 +++- vignettes/confounds-and-variables.Rmd |only vignettes/derivatives.Rmd |only vignettes/mock-bids.Rmd |only vignettes/quickstart.Rmd | 275 ++- 169 files changed, 7118 insertions(+), 1540 deletions(-)
Title: Five Novel Stochastic Regression Models with Arvind-Distributed
Errors and Effects
Description: Implements the 'Arvind' distribution and five novel stochastic
regression models that replace the traditional Gaussian error assumption
with 'Arvind'-distributed errors. The 'Arvind' distribution is a flexible
single-parameter continuous distribution on the positive real line
characterised by a polynomial numerator with Gaussian-type decay. The
package provides complete distribution functions (darvind(), parvind(),
qarvind(), rarvind()), maximum likelihood estimation via
fit_arvind_mle(), and five model-fitting routines: Random Walk on
Coefficients via fit_rw1(), Time-Varying Coefficient Linear Model via
fit_tvlm(), Simulation-Extrapolation via fit_simex(), Mixed-Effects
Regression via fit_mixed(), and Regime-Switching Hidden Markov Model via
fit_hmm(). Additionally provides Monte Carlo forecasting with prediction
intervals via forecast_arvind(), comprehensive goodness-of-fit
diagnostics (21 metrics and 25 plots) via diagnostics_arvind() and
plot_arvind(), k-fold and rolling-window cro [...truncated...]
Author: Shikhar Tyagi [aut, cre] ,
Arvind Pandey [aut]
Maintainer: Shikhar Tyagi <shikhar1093tyagi@gmail.com>
This is a re-admission after prior archival of version 1.0.0 dated 2026-05-11
Diff between ArvindSt versions 1.0.0 dated 2026-05-11 and 1.1.0 dated 2026-07-06
ArvindSt-1.0.0/ArvindSt/build |only ArvindSt-1.0.0/ArvindSt/vignettes |only ArvindSt-1.1.0/ArvindSt/DESCRIPTION | 15 - ArvindSt-1.1.0/ArvindSt/MD5 | 12 ArvindSt-1.1.0/ArvindSt/R/model_hmm.R | 155 +++++++++--- ArvindSt-1.1.0/ArvindSt/inst/WORDLIST | 1 ArvindSt-1.1.0/ArvindSt/inst/doc/ArvindSt-introduction.html | 4 ArvindSt-1.1.0/ArvindSt/man/fit_hmm.Rd | 8 8 files changed, 147 insertions(+), 48 deletions(-)
Title: Sequential Threshold-Spatial-Quantile Panel Estimation
Description: Implements a sequential panel estimation protocol for regional
economic panels that combines three estimation layers in a fixed order.
The first layer applies a two-way fixed effects baseline. The second
layer applies the panel threshold regression method of Hansen (1999)
<doi:10.1016/S0304-4076(99)00025-1> to identify structural breaks at an
unknown threshold of a moderating variable, with bootstrap inference
following Hansen (2000) <doi:10.1111/1468-0262.00124>. The third layer
applies a spatial Durbin model with an impact decomposition following
LeSage and Pace (2009, ISBN:978-1-4200-6424-7) to quantify direct and
indirect spillover effects. The fourth layer applies the two-step panel
quantile estimator of Canay (2011) <doi:10.1111/j.1368-423X.2011.00349.x>
to document distributional heterogeneity in the outcome. The threshold
identified in the second layer defines a subsample used as structured
input to the fourth layer, and a consistency check evaluates whether t [...truncated...]
Author: Prakash Vhankade [aut, cre]
Maintainer: Prakash Vhankade <prakash.vhankade@gipe.ac.in>
Diff between tsqr versions 0.1.2 dated 2026-06-22 and 0.2.0 dated 2026-07-06
DESCRIPTION | 6 MD5 | 39 ++--- NAMESPACE | 9 + R/canay_quantile.R | 243 +++++++++++++++----------------- R/data.R | 40 ++--- R/ptr_hansen.R | 264 +++++++++++++++++------------------ R/sdm_impact.R | 187 +++++++++++------------- R/tsq_consistency.R | 87 ++++------- R/tsq_panel.R | 95 ++++++------ R/tsq_plot.R | 103 +++++-------- build |only man/canay_quantile.Rd | 51 ++---- man/maharashtra_panel.Rd | 38 ++--- man/ptr_hansen.Rd | 49 ++---- man/sdm_impact.Rd | 43 +---- man/tsq_consistency_check.Rd | 24 +-- man/tsq_panel.Rd | 27 +-- man/tsq_plot.Rd | 8 - tests/testthat/test-canay_quantile.R | 25 +-- tests/testthat/test-consistency.R | 18 -- tests/testthat/test-ptr_hansen.R | 55 ++----- 21 files changed, 640 insertions(+), 771 deletions(-)
Title: Parallel GLM
Description: Provides a parallel estimation method for generalized linear
models without compiling with a multithreaded LAPACK or BLAS.
Author: Benjamin Christoffersen [aut] ,
Anthony Williams [cph],
Boost developers [cph],
Tom Palmer [aut, cre]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between parglm versions 0.1.10 dated 2026-05-22 and 0.2.0 dated 2026-07-06
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++--------- NEWS.md | 8 +++++++ R/parglm.R | 14 +++++++++++++ build/vignette.rds |binary src/family.cpp | 2 - src/parallel_glm.cpp | 16 ++++++++++++++- src/parallel_qr.cpp | 7 ------ src/parallel_qr.h | 2 - tests/testthat/test_misc.R | 46 +++++++++++++++++++++++++++++++++++++++++++++ 10 files changed, 96 insertions(+), 23 deletions(-)
Title: Smooth L0 Penalty Approximations for Gaussian Graphical Models
Description: Provides smooth approximations to the L0 norm penalty for
estimating sparse Gaussian graphical models (GGMs). Network estimation
is performed using the Local Linear Approximation (LLA) framework
(Fan & Li, 2001 <doi:10.1198/016214501753382273>;
Zou & Li, 2008 <doi:10.1214/009053607000000802>) with five penalty
functions: arctangent (Wang & Zhu, 2016 <doi:10.1155/2016/6495417>),
EXP (Wang, Fan, & Zhu, 2018 <doi:10.1007/s10463-016-0588-3>), Gumbel,
Log (Candes, Wakin, & Boyd, 2008 <doi:10.1007/s00041-008-9045-x>),
and Weibull. Adaptive penalty parameters for EXP, Gumbel, and Weibull
are estimated via maximum likelihood, and model selection uses
information criteria including AIC, BIC, and EBIC (Extended BIC).
Simulation functions generate multivariate normal data from GGMs with
stochastic block model or small-world (Watts-Strogatz) network structures.
Author: Alexander Christensen [aut, cre] ,
Jeongwon Choi [ctb] ,
John Fox [cph, ctb] ,
Yves Rosseel [cph, ctb] ,
Alexander Robitzsch [cph, ctb] ,
David Blackman [ctb] ,
Sebastiano Vigna [ctb] ,
John Burkardt [cph, ctb]
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Diff between L0ggm versions 0.1.0 dated 2026-05-15 and 0.1.1 dated 2026-07-06
DESCRIPTION | 8 +++---- MD5 | 28 ++++++++++++------------ NEWS | 12 ++++++++++ R/edge_confusion.R | 2 - R/network_estimation.R | 51 +++++++++++++++++++++++++++++++-------------- R/polychoric_matrix.R | 2 + R/proxswap_lattice.R | 4 +-- R/simulate_smallworld.R | 5 +--- R/smallworldness.R | 2 - R/weibull_parameters.R | 9 ++++--- man/network_estimation.Rd | 24 +++++++++++++-------- man/polychoric_matrix.Rd | 2 + man/proxswap_lattice.Rd | 4 +-- man/simulate_smallworld.Rd | 5 +--- man/weibull_parameters.Rd | 9 ++++--- 15 files changed, 105 insertions(+), 62 deletions(-)
Title: Download and Visualize Essential Climate Change Data
Description: Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, methane, emissions, instrumental and proxy temperature records, sea levels, Arctic/Antarctic sea-ice, Hurricanes, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/home>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.html>, Vostok Paleo carbon dio [...truncated...]
Author: Hernando Cortina [aut, cre]
Maintainer: Hernando Cortina <hch@alum.mit.edu>
Diff between hockeystick versions 0.8.7 dated 2026-05-11 and 0.9.0 dated 2026-07-06
DESCRIPTION | 6 MD5 | 73 +++++----- NAMESPACE | 6 NEWS.md | 3 R/2kyears_temp.R | 6 R/carbon.R | 254 ++++++++++++++++++------------------ R/daily_temp.R | 12 + R/emissions.R | 5 R/fires.R |only R/globalvars.R | 7 R/hurricanes.R | 2 R/icecurves.R | 6 R/instrumental_temp.R | 6 R/methane.R | 6 R/paleo.R | 12 + R/seaice.R | 6 R/sealevel.R | 13 + README.md | 34 +++- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/usinghockeystick.R | 32 ++-- inst/doc/usinghockeystick.html | 44 ++++-- inst/doc/usinghockeystick.qmd | 9 + man/figures/README-carbon-1.png |binary man/figures/README-dailytemp-1.png |binary man/figures/README-fires-1.png |only man/figures/README-fires-2.png |only man/figures/README-grid-1.png |binary man/figures/README-icecurves-1.png |binary man/figures/README-methane-1.png |binary man/figures/README-stripes-1.png |binary man/figures/README-stripes2-1.png |binary man/figures/README-temp-1.png |binary man/figures/README-tempcarbon-1.png |binary man/get_fires_area.Rd |only man/get_fires_emissions.Rd |only man/plot_fires_area.Rd |only man/plot_fires_emissions.Rd |only tests/testthat/test-functions.R | 107 +++++++++++++++ vignettes/usinghockeystick.qmd | 9 + 41 files changed, 441 insertions(+), 221 deletions(-)
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://cordis.europa.eu/project/id/731013>).
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Emilie J Millet [aut] ,
Maria Xose Rodriguez Alvarez [aut] ,
Diana Marcela Perez Valencia [aut] ,
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre] ,
Fred van Eeuwijk [aut] ,
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.9.3 dated 2026-07-01 and 1.0.9.4 dated 2026-07-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/Overview_HTP.html | 4 ++-- inst/tinytest/test_detectSerieOut.R | 3 ++- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Spatial Component Analysis for Spatial Sequencing Data
Description: Spatial components offer tools for dimension reduction and
spatially variable gene detection for high dimensional spatial transcriptomics
data. Construction of a projection onto low-dimensional feature space of
spatially dependent metagenes offers pre-processing to clustering, testing for
spatial variability and denoising of spatial expression patterns. For more
details, see Koehler et al. (2026) <doi:10.1093/bioinformatics/btag052>.
Author: David Koehler [aut, cre]
Maintainer: David Koehler <koehler@imbie.uni-bonn.de>
Diff between SPACO versions 1.0.0 dated 2026-03-31 and 1.0.2 dated 2026-07-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/EvalFunctions.R | 33 +++++++++++++++++++++++---------- src/Rcpp_Functions.cpp | 3 +++ tests/testthat/test-SCA.R | 13 +++++++++---- 5 files changed, 43 insertions(+), 22 deletions(-)
Title: Assessing Package Risk Metrics
Description: A reliable and validated tool that captures detailed risk metrics
such as R 'CMD' check, test coverage, traceability matrix, documentation, dependencies,
reverse dependencies, suggested dependency analysis, repository data,
and enhanced reporting for R packages that are local or stored
on remote repositories such as GitHub, CRAN, and Bioconductor.
Author: Edward Gillian [cre, aut] ,
Hugo Bottois [aut] ,
Paulin Charliquart [aut],
Andre Couturier [aut],
Sanofi [cph, fnd]
Maintainer: Edward Gillian <edward.gillian-ext@sanofi.com>
Diff between risk.assessr versions 4.1.0 dated 2026-06-11 and 4.1.1 dated 2026-07-06
DESCRIPTION | 6 MD5 | 82 ++++--- NAMESPACE | 5 NEWS.md | 11 + R/assess_pkg.R | 3 R/create_empty_results.R | 3 R/generate_html_report.R | 65 +++++ R/get_frugal_metrics.R |only R/get_risk_analysis.R | 83 +++++-- R/get_security_vulnerabilities.R |only R/setup_rcmdcheck_args.R | 93 +++++--- R/write_summary_report.R | 29 ++ build/vignette.rds |binary inst/config/risk-definition.json | 31 ++ inst/doc/Popularity_metric.html | 22 -- inst/doc/Pubmed_data.Rmd | 2 inst/doc/Pubmed_data.html | 2 inst/doc/dependency_tree.html | 186 ++++++++++------- inst/doc/security_vulnerabilities.R |only inst/doc/security_vulnerabilities.Rmd |only inst/doc/security_vulnerabilities.html |only inst/report_templates/risk_report_template.Rmd | 50 ++++ inst/report_templates/summary.Rmd | 5 man/convert_number_to_abbreviation.Rd | 2 man/convert_number_to_percent.Rd | 2 man/fetch_osv_data.Rd |only man/generate_vulnerabilities_section.Rd |only man/get_frugal_metrics.Rd |only man/get_risk_analysis.Rd | 6 man/get_security_vulnerabilities.Rd |only man/init_frugal_covr_list.Rd |only man/init_frugal_results.Rd |only man/risk.assessr-package.Rd | 1 man/safe_value.Rd | 2 man/setup_rcmdcheck_args.Rd | 6 tests/testthat/test-assess_pkg.R | 53 ++++ tests/testthat/test-check_suggested_exp_funcs.R | 64 +++-- tests/testthat/test-create_empty_results.R | 2 tests/testthat/test-generate_html_report.R | 68 +++++- tests/testthat/test-get_frugal_metrics.R |only tests/testthat/test-get_github_data.R | 130 +++++++++++ tests/testthat/test-get_risk_analysis.R | 228 +++++++++++++++++++++ tests/testthat/test-get_security_vulnerabilities.R |only tests/testthat/test-parse_dcf_dependencies.R | 22 +- tests/testthat/test-risk_assess_pkg.R | 32 ++ tests/testthat/test-setup_rcmdcheck_args.R | 146 ++++++++----- tests/testthat/test-write_summary_report.R | 113 +++++++++- vignettes/Pubmed_data.Rmd | 2 vignettes/security_vulnerabilities.Rmd |only 49 files changed, 1237 insertions(+), 320 deletions(-)
Title: Bayes Factor Design for Two-Arm Binomial Trials
Description: Design and analysis of one- and two-stage binomial
clinical phase II trials using Bayes factors. Implements Bayes factors
for point-null and directional hypotheses, predictive densities under
different hypotheses, and power and sample size calibration. Both one-arm
trials with only a single treatment arm and two-arm trials with treatment
and control arm are implemented for the one- and two-stage designs.
Author: Riko Kelter [aut, cre]
Maintainer: Riko Kelter <rkelter@uni-koeln.de>
Diff between bfbin2arm versions 0.1.4 dated 2026-06-23 and 0.1.5 dated 2026-07-06
bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-calibration.R |only bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-calibration.Rmd |only bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-calibration.html |only bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-design.R |only bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-design.Rmd |only bfbin2arm-0.1.4/bfbin2arm/inst/doc/bfbin2arm-rope-singlearm-onestage-design.html |only bfbin2arm-0.1.4/bfbin2arm/vignettes/bfbin2arm-rope-singlearm-onestage-calibration.Rmd |only bfbin2arm-0.1.4/bfbin2arm/vignettes/bfbin2arm-rope-singlearm-onestage-design.Rmd |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig10.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig11.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig12.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig5.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig6.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig7.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig8.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-fig9.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-scenario1.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-scenario2.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-scenario3.png |only bfbin2arm-0.1.4/bfbin2arm/vignettes/figures/singlearm-onestage-rope-scenario4.png |only bfbin2arm-0.1.5/bfbin2arm/DESCRIPTION | 8 bfbin2arm-0.1.5/bfbin2arm/MD5 | 126 +-- bfbin2arm-0.1.5/bfbin2arm/NAMESPACE | 11 bfbin2arm-0.1.5/bfbin2arm/R/design_singlearm_onestage_bf.R | 2 bfbin2arm-0.1.5/bfbin2arm/R/design_singlearm_twostage_rope.R |only bfbin2arm-0.1.5/bfbin2arm/R/helpers_singlearm_bf.R | 55 + bfbin2arm-0.1.5/bfbin2arm/R/s3-singlearm_bf_onestage_design.R | 393 ++++++---- bfbin2arm-0.1.5/bfbin2arm/R/s3-singlearm_rope_onestage.R | 2 bfbin2arm-0.1.5/bfbin2arm/R/s3-singlearm_rope_twostage.R |only bfbin2arm-0.1.5/bfbin2arm/R/utils_rope_twostage.R |only bfbin2arm-0.1.5/bfbin2arm/build/vignette.rds |binary bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-overview.html | 22 bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm-onestage.R | 74 - bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm-onestage.Rmd | 79 -- bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm-onestage.html | 334 ++++---- bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm-twostage_bayesian.html | 63 - bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm_twostage_frequentist.html | 18 bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm_twostage_full.html | 73 - bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-singlearm_twostage_hybrid.html | 250 ++++-- bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-twoarm-twostage_Bayesian.html | 243 +++--- bfbin2arm-0.1.5/bfbin2arm/inst/doc/bfbin2arm-twoarm_onestage_Bayesian.html | 34 bfbin2arm-0.1.5/bfbin2arm/man/as.data.frame.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/coef.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/design_singlearm_twostage_rope.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/plot.singlearm_onestage_bf_design.Rd | 32 bfbin2arm-0.1.5/bfbin2arm/man/plot.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/print.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/print.summary.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/man/summary.singlearm_rope_twostage_design.Rd |only bfbin2arm-0.1.5/bfbin2arm/vignettes/bfbin2arm-singlearm-onestage.Rmd | 79 -- bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/algorithm_bayes.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-single_arm_two_stage_bayes_fig3fig.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-two-stage-design-more-inf-des-priors-no-ce.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-two-stage-design-riociguat-more-informative-design-priors.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-two-stage-design-riociguat.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-twoarm-twostage-vignette-fixed-design-ss-reduc.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal-twoarm-twostage-vignette-twostage-opt-des-ss-reduc.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_bayes_fig2.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_bayes_fig3.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_bayes_fig4.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_bayes_flowchart_rootfinding.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_full_fig1.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_hybrid_fig1.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/optimal_single_arm_two_stage_hybrid_fig2.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig1.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig2.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig3.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig4.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig5.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-fig6.png |only bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-rope-calibration-bayes.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-rope-calibration-frequentist.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-rope-calibration-full.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm-onestage-rope-calibration-hybrid.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/singlearm_twostage_freq_fig1.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm-onestage-design.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm_onestage_fig1.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm_onestage_fig2.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm_onestage_fig3.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm_onestage_fig4.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/figures/twoarm_onestage_fig5.png |binary bfbin2arm-0.1.5/bfbin2arm/vignettes/references.bib | 50 + 82 files changed, 1143 insertions(+), 805 deletions(-)
Title: Coefficient of Variation (CV) with Confidence Intervals (CI)
Description: Provides some easy-to-use functions and classes to calculate
variability measures such as coefficient of variation with confidence
intervals provided with all available methods. References are
'Panichkitkosolkul' (2013) <doi:10.1155/2013/324940>,
'Altunkaynak' & 'Gamgam' (2018) <doi:10.1080/03610918.2018.1435800>,
'Albatineh', 'Kibria', Wilcox & 'Zogheib' (2014) <doi:10.1080/02664763.2013.847405>.
Author: Maani Beigy [aut, cre]
Maintainer: Maani Beigy <manibeygi@gmail.com>
Diff between cvcqv versions 1.0.3 dated 2026-05-21 and 1.0.4 dated 2026-07-06
DESCRIPTION | 10 MD5 | 83 NEWS.md | 24 R/BootCoefQuartVar.R | 314 +- R/BootCoefVar.R | 323 +- R/CoefQuartVar.R | 282 +- R/CoefQuartVarCI.R | 637 ++-- R/CoefVar.R | 136 - R/CoefVarCI.R | 3479 ++++++++++++++------------- R/SampleQuantiles.R | 197 - R/aak_helpers.R |only R/cqv_versatile.R | 644 ++-- R/cv_versatile.R | 2571 +++++++++++-------- R/zzz.R |only README.md | 9 inst/doc/cqv_versatile.R | 655 ++--- inst/doc/cqv_versatile.Rmd | 655 ++--- inst/doc/cqv_versatile.html | 38 inst/doc/cv_versatile.R | 2422 +++++++++--------- inst/doc/cv_versatile.Rmd | 2422 +++++++++--------- inst/doc/cv_versatile.html | 132 - man/CoefVarCI.Rd | 21 man/cv_versatile.Rd | 18 tests/testthat/test_state_BootCoefQuartVar.R | 265 +- tests/testthat/test_state_BootCoefVar.R | 243 - tests/testthat/test_state_CoefQuartVar.R | 337 +- tests/testthat/test_state_CoefQuartVarCI.R | 344 +- tests/testthat/test_state_CoefVar.R | 52 tests/testthat/test_state_CoefVarCI.R | 2131 ++++++++-------- tests/testthat/test_state_R.R | 94 tests/testthat/test_state_SampleQuantiles.R | 79 tests/testthat/test_state_aak_adj.R |only tests/testthat/test_state_aak_als.R |only tests/testthat/test_state_aak_ls.R |only tests/testthat/test_state_alpha.R | 117 tests/testthat/test_state_cqv_versatile.R | 620 ++-- tests/testthat/test_state_cv_versatile.R | 1846 +++++++------- tests/testthat/test_state_digits.R | 425 +-- tests/testthat/test_state_na_rm.R | 168 - tests/testthat/test_state_names.R | 53 tests/testthat/test_state_probs.R | 119 tests/testthat/test_state_type.R | 26 tests/testthat/test_state_x.R | 393 +-- vignettes/cqv_versatile.Rmd | 655 ++--- vignettes/cv_versatile.Rmd | 2422 +++++++++--------- 45 files changed, 13250 insertions(+), 12211 deletions(-)
Title: 'Galaxy' API Implementation
Description: On 'Galaxy' platforms like 'Galaxy Europe' <https://usegalaxy.eu>, many tools and workflows can run directly on a high-performance computer. 'GalaxyR' connects R with 'Galaxy' platforms API <https://usegalaxy.eu/api/docs> and allows credential management, uploading data, invoking workflows or tools, checking their status, and downloading results.
Author: Julian Frey [aut, cre] ,
Zoe Schindler [ctb]
Maintainer: Julian Frey <julian.frey@wwd.uni-freiburg.de>
Diff between GalaxyR versions 0.1.1 dated 2026-02-17 and 0.1.2 dated 2026-07-06
DESCRIPTION | 9 MD5 | 32 +-- NAMESPACE | 5 NEWS.md | 7 R/2025-10-27_JF_R_Galaxy_functions.R | 124 ++++++------ R/2026-01-21_s4_class_methods.R | 349 ++++++++++++++++++++++++++++++++++- README.md | 340 +++++++++++++++++----------------- inst/examples |only man/galaxy_delete_dataset.Rd | 2 man/galaxy_delete_history.Rd |only man/galaxy_get_file_info.Rd | 82 ++++---- man/galaxy_get_tool.Rd | 76 +++---- man/galaxy_get_tool_id.Rd | 108 +++++----- man/galaxy_get_workflow_inputs.Rd | 70 +++---- man/galaxy_history_size.Rd | 86 ++++---- man/galaxy_list_files.Rd |only man/galaxy_list_histories.Rd | 48 ++-- man/galaxy_list_invocations.Rd | 42 ++-- man/galaxy_print_tool_inputs.Rd |only 19 files changed, 879 insertions(+), 501 deletions(-)
Title: Spatial Machine Learning
Description: Implements a spatial extension of the random forest algorithm
(Georganos et al. (2019) <doi:10.1080/10106049.2019.1595177>). Provides
a Geographically Weighted Random Forest regression and a routine to
find the optimal bandwidth (Georganos and Kalogirou (2022)
<doi:10.3390/ijgi11090471>). A lightweight cross-validation helper for
tuning the 'mtry' parameter of a random forest and a generator of
synthetic spatial test data are also included. The package depends on
'ranger' as its single random-forest back-end.
Author: Stamatis Kalogirou [aut, cre, cph] ,
Stefanos Georganos [aut]
Maintainer: Stamatis Kalogirou <stamatis.science@gmail.com>
This is a re-admission after prior archival of version 0.1.7 dated 2024-04-01
Diff between SpatialML versions 0.1.7 dated 2024-04-01 and 1.8.2 dated 2026-07-06
DESCRIPTION | 43 ++- MD5 | 42 ++- NAMESPACE | 18 + NEWS.md |only R/grf.R | 531 +++++++++++++++++++++++++++-------------------- R/grf.bw.R | 172 +++++++++------ R/predict.grf.R | 91 +++++--- R/random.test.data.R | 78 ++++-- R/rf.mtry.optim.R | 184 +++++++++++++--- R/utils-internal.R |only build |only inst |only man/Income.Rd | 95 ++++---- man/SpatialML-package.Rd |only man/grf.Rd | 269 +++++++++++++++-------- man/grf.bw.Rd | 224 +++++++++++-------- man/predict.grf.Rd | 159 ++++++++------ man/random.test.data.Rd | 75 ++++-- man/rf.mtry.optim.Rd | 156 +++++++++---- tests |only vignettes |only 21 files changed, 1370 insertions(+), 767 deletions(-)
Title: Access Data from Marineregions.org: Gazetteer & Data Products
Description: Explore and retrieve marine geospatial data from the Marine Regions Gazetteer <https://marineregions.org/gazetteer.php?p=webservices> and the Marine Regions Data Products <https://marineregions.org/webservices.php>.
Author: Michelle Guevara [aut, cre] ,
Salvador Jesus Fernandez Bejarano [aut] ,
Lotte Pohl [aut] ,
Julia Gustavsen [rev],
Muralidhar M.A. [rev],
Sheila M. Saia [rev],
LifeWatch Belgium [fnd]
Maintainer: Michelle Guevara <michelle.guevara@vliz.be>
Diff between mregions2 versions 1.1.2 dated 2025-03-21 and 1.3.0 dated 2026-07-06
DESCRIPTION | 38 LICENSE | 4 MD5 | 252 NAMESPACE | 126 NEWS.md | 4 R/00_gaz_geom.R | 722 +- R/01_gaz_search.R | 1096 +-- R/02_gaz_relations.R | 236 R/03_gaz_sources.R | 454 - R/04_gaz_types.R | 368 - R/05_gaz_wmses.R | 68 R/07_mrp_view.R | 528 - R/08_mrp_get.R | 700 +- R/data.R | 88 R/mregions2-package.R | 172 R/utils-pipe.R | 28 R/utils.R | 410 - README.md | 802 +- build/vignette.rds |binary inst/CITATION | 14 inst/doc/mregions2.R | 332 - inst/doc/mregions2.Rmd | 808 +- inst/doc/mregions2.html | 2521 +++---- inst/mrp_list.csv | 44 inst/mrp_ontology.csv | 750 +- inst/pkgdown.yml | 26 man/MRGID.Rd | 108 man/gaz_geometry.Rd | 128 man/gaz_relations.Rd | 118 man/gaz_rest.Rd | 62 man/gaz_rest_geometries.Rd | 90 man/gaz_rest_names_by_mrgid.Rd | 48 man/gaz_rest_record_by_mrgid.Rd | 62 man/gaz_rest_records_by_lat_long.Rd | 78 man/gaz_rest_records_by_name.Rd | 88 man/gaz_rest_records_by_names.Rd | 76 man/gaz_rest_records_by_source.Rd | 54 man/gaz_rest_records_by_type.Rd | 56 man/gaz_rest_relations_by_mrgid.Rd | 82 man/gaz_rest_source_by_sourceid.Rd | 52 man/gaz_rest_sources.Rd | 68 man/gaz_rest_types.Rd | 62 man/gaz_rest_wmses.Rd | 66 man/gaz_search.Rd | 142 man/gaz_search_by_source.Rd | 88 man/gaz_search_by_type.Rd | 92 man/gaz_sources.Rd | 68 man/gaz_types.Rd | 62 man/mregions2-package.Rd | 74 man/mrp_col_unique.Rd | 86 man/mrp_colnames.Rd | 72 man/mrp_get.Rd | 212 man/mrp_list.Rd | 78 man/mrp_ontology.Rd | 62 man/mrp_view.Rd | 294 man/pipe.Rd | 40 tests/testthat.R | 16 tests/testthat/gaz/api/mrgid/14.R | 866 +- tests/testthat/gaz/api/mrgid/17.json | 32 tests/testthat/gaz/api/mrgid/30666.json | 32 tests/testthat/gaz/api/mrgid/49243.json | 32 tests/testthat/gaz/api/mrgid/8399.json | 32 tests/testthat/gaz/api/mrgid/999999999.R | 16 tests/testthat/gaz/api/rest/1geom/58-c83a0d.R | 34 tests/testthat/gaz/api/rest/bylatlong/51.21551/2.927-0a955a.R | 18 tests/testthat/gaz/api/rest/bylatlong/51.21551/2.927-2c70ba.R | 18 tests/testthat/gaz/api/rest/bylatlong/51.21551/2.927-ae5945.json | 68 tests/testthat/gaz/api/rest/bylatlong/51.21551/2.927-aff46e.json | 1732 ++--- tests/testthat/gaz/api/rest/byname/Belgie-09a3d0.R | 16 tests/testthat/gaz/api/rest/byname/Belgium-773121.json | 100 tests/testthat/gaz/api/rest/byname/Belgium-965816.R | 16 tests/testthat/gaz/api/rest/byname/Belgium-ef9d65.R | 16 tests/testthat/gaz/api/rest/byname/Belgium-f42f5c.R | 18 tests/testthat/gaz/api/rest/byname/Belgiun-505272.R | 16 tests/testthat/gaz/api/rest/byname/Belgiun-773121.json | 132 tests/testthat/gaz/api/rest/byname/Belgiun-965816.R | 16 tests/testthat/gaz/api/rest/byname/test_like_is_false-bd74f7.R | 18 tests/testthat/gaz/api/rest/byname/test_not_found-773121.R | 18 tests/testthat/gaz/api/rest/bynames/true/true/Belgique/Framce.json | 172 tests/testthat/gaz/api/rest/bysource/Belgian+Sea+Fisheries.json | 964 +- tests/testthat/gaz/api/rest/bysource/This+is+not+a+source.R | 16 tests/testthat/gaz/api/rest/bysource/Victor+Scarabino.json | 10 tests/testthat/gaz/api/rest/bytype/diving+spot-0cae27.R | 16 tests/testthat/gaz/api/rest/bytype/diving+spot-95f866.json | 580 - tests/testthat/gaz/api/rest/bytype/this+is+not+a+type-95f866.R | 16 tests/testthat/gaz/api/rest/bytype/wreck-0cae27.R | 16 tests/testthat/gaz/api/rest/bytype/wreck-95f866.json | 164 tests/testthat/gaz/api/rest/geom/30666.R | 18 tests/testthat/gaz/api/rest/geom/4280.R | 64 tests/testthat/gaz/api/rest/geom/49243.R | 46 tests/testthat/gaz/api/rest/geom/58.R | 50 tests/testthat/gaz/api/rest/relations/49243-8ef451.R | 18 tests/testthat/gaz/api/rest/relations/49243-e78ab2.json | 36 tests/testthat/gaz/api/rest/sourceid/53.json | 12 tests/testthat/gaz/api/rest/sourceid/77.json | 12 tests/testthat/gaz/api/rest/sources/-0cae27.json | 1004 +-- tests/testthat/gaz/api/rest/sources/-2642ef.json | 1004 +-- tests/testthat/gaz/api/rest/sources/-5fcbb3.R | 16 tests/testthat/gaz/api/rest/sources/-95f866.json | 1004 +-- tests/testthat/gaz/api/rest/sources/-b71d9d.json | 234 tests/testthat/gaz/api/rest/sources/-e6f0e7.json | 1004 +-- tests/testthat/gaz/api/rest/toname/3293.json | 8 tests/testthat/gaz/api/rest/toname/49243.json | 6 tests/testthat/gaz/api/rest/toname/999999999.R | 18 tests/testthat/gaz/api/rest/types.json | 3254 +++++----- tests/testthat/gaz/api/rest/wms/3293.json | 20 tests/testthat/prod/fail/geo/eez-13c29b58.zip | 10 tests/testthat/prod/fail/geo/eez-419caace.zip | 12 tests/testthat/prod/fail/geo/eez-58a78801.zip | 10 tests/testthat/prod/fail/geo/eez-713ad0ad.zip | 12 tests/testthat/prod/fail/geo/ows-38243e.R | 12 tests/testthat/prod/fail/geo/ows-4cb98d.R | 12 tests/testthat/prod/fail/geo/ows-85ca5a.R | 12 tests/testthat/prod/fail/geo/ows-8d68a6.R | 12 tests/testthat/prod/fail/geo/ows-9545b5.R | 12 tests/testthat/prod/ok/geo/ows-10d21b.R | 12 tests/testthat/prod/ok/geo/ows-1af2a2.R | 12 tests/testthat/prod/ok/geo/ows-62a7cf.R | 12 tests/testthat/prod/ok/geo/ows-b0edf4.R | 12 tests/testthat/prod/ok/geo/ows-bca3eb.R | 12 tests/testthat/prod/ok/geo/ows-db8988.R | 940 +- tests/testthat/setup.R | 52 tests/testthat/test-gaz.R | 559 - tests/testthat/test-mrp_view_helpers.R | 46 tests/testthat/test-prod.R | 709 +- tests/testthat/test-utils.R | 274 vignettes/mregions2.Rmd | 808 +- 127 files changed, 14940 insertions(+), 14915 deletions(-)
Title: Read Spectrometric Data and Metadata
Description: Parse various reflectance/transmittance/absorbance spectra file
formats to extract spectral data and metadata, as described in Gruson, White
& Maia (2019) <doi:10.21105/joss.01857>. Among other formats, it can import
files from 'Avantes' <https://www.avantes.com/>, 'CRAIC'
<https://www.microspectra.com/>, and 'OceanOptics'/'OceanInsight'
<https://www.oceanoptics.com/> brands.
Author: Hugo Gruson [cre, aut, cph] ,
Rafael Maia [aut, cph] ,
Thomas White [aut, cph] ,
Kotya Karapetyan [ctb, cph] )
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>
Diff between lightr versions 2.0.0 dated 2026-04-11 and 2.1.0 dated 2026-07-06
DESCRIPTION | 8 ++-- MD5 | 48 ++++++++++++------------ NEWS.md | 15 +++++++ R/compute_processed.R | 2 - R/convert_tocsv.R | 6 ++- R/deprecated.R | 6 ++- R/get_metadata.R | 6 ++- R/get_spec.R | 25 +++++++++++- R/parse_avantes_binary.R | 17 +++----- R/parse_csv.R | 2 - R/parse_generic.R | 3 - R/parse_jdx.R | 75 +++++++++++--------------------------- R/parse_oceanoptics_converted.R | 44 +++++++++++++++------- R/utils.R | 2 - inst/doc/batch_import.html | 4 +- inst/doc/renormalise.html | 7 +-- inst/doc/true_example.html | 4 +- man/lightr-package.Rd | 3 + man/lr_convert_tocsv.Rd | 23 +++++++++++ man/lr_get_metadata.Rd | 23 +++++++++++ man/lr_get_spec.Rd | 23 +++++++++++ man/lr_parse_csv.Rd | 2 - tests/testthat/_snaps/metadata.md | 14 +++++++ tests/testthat/test_dispatch.R | 5 ++ tests/testthat/test_metadata.R | 15 +++++++ 25 files changed, 255 insertions(+), 127 deletions(-)
Title: Scale Space Multiresolution Analysis of Random Signals
Description: A method for the multiresolution analysis of spatial fields and images to capture scale-dependent features.
mrbsizeR is based on scale space smoothing and uses differences of smooths at neighbouring scales for finding features on different scales.
To infer which of the captured features are credible, Bayesian analysis is used.
The scale space multiresolution analysis has three steps: (1) Bayesian signal reconstruction.
(2) Using differences of smooths, scale-dependent features of the reconstructed signal can be found.
(3) Posterior credibility analysis of the differences of smooths created.
The method has first been proposed by Holmstrom, Pasanen, Furrer, Sain (2011) <DOI:10.1016/j.csda.2011.04.011> and extended in Flury, Gerber, Schmid and Furrer (2021) <DOI:10.1016/j.spasta.2020.100483>.
Author: Thimo Schuster [aut],
Roman Flury [cre, aut],
Leena Pasanen [ctb],
Reinhard Furrer [ctb]
Maintainer: Roman Flury <fluryro@gmail.com>
Diff between mrbsizeR versions 1.3 dated 2024-02-13 and 1.3.1 dated 2026-07-06
mrbsizeR-1.3.1/mrbsizeR/DESCRIPTION | 16 mrbsizeR-1.3.1/mrbsizeR/MD5 | 74 mrbsizeR-1.3.1/mrbsizeR/NEWS.md | 87 - mrbsizeR-1.3.1/mrbsizeR/R/RcppExports.R | 94 - mrbsizeR-1.3.1/mrbsizeR/R/mrbsizeR.R | 211 +- mrbsizeR-1.3.1/mrbsizeR/build/vignette.rds |binary mrbsizeR-1.3.1/mrbsizeR/inst/doc/mrbsizeR.R | 320 +-- mrbsizeR-1.3.1/mrbsizeR/inst/doc/mrbsizeR.Rmd | 982 ++++++------ mrbsizeR-1.3.1/mrbsizeR/inst/doc/mrbsizeR.pdf |binary mrbsizeR-1.3.1/mrbsizeR/man/CImap.Rd | 82 - mrbsizeR-1.3.1/mrbsizeR/man/HPWmap.Rd | 90 - mrbsizeR-1.3.1/mrbsizeR/man/MinLambda.Rd | 148 - mrbsizeR-1.3.1/mrbsizeR/man/TaperingPlot.Rd | 136 - mrbsizeR-1.3.1/mrbsizeR/man/dctMatrix.Rd | 74 mrbsizeR-1.3.1/mrbsizeR/man/dftMatrix.Rd | 70 mrbsizeR-1.3.1/mrbsizeR/man/eigenLaplace.Rd | 50 mrbsizeR-1.3.1/mrbsizeR/man/eigenQsphere.Rd | 70 mrbsizeR-1.3.1/mrbsizeR/man/fftshift.Rd | 94 - mrbsizeR-1.3.1/mrbsizeR/man/ifftshift.Rd | 88 - mrbsizeR-1.3.1/mrbsizeR/man/mrbsizeR-package.Rd |only mrbsizeR-1.3.1/mrbsizeR/man/mrbsizeRgrid.Rd | 166 +- mrbsizeR-1.3.1/mrbsizeR/man/mrbsizeRsphere.Rd | 136 - mrbsizeR-1.3.1/mrbsizeR/man/plot.CImapGrid.Rd | 150 - mrbsizeR-1.3.1/mrbsizeR/man/plot.CImapSphere.Rd | 152 - mrbsizeR-1.3.1/mrbsizeR/man/plot.HPWmapGrid.Rd | 164 +- mrbsizeR-1.3.1/mrbsizeR/man/plot.HPWmapSphere.Rd | 168 +- mrbsizeR-1.3.1/mrbsizeR/man/plot.minLambda.Rd | 76 mrbsizeR-1.3.1/mrbsizeR/man/plot.smMeanGrid.Rd | 124 - mrbsizeR-1.3.1/mrbsizeR/man/plot.smMeanSphere.Rd | 128 - mrbsizeR-1.3.1/mrbsizeR/man/rmvtDCT.Rd | 100 - mrbsizeR-1.3.1/mrbsizeR/man/tridiag.Rd | 62 mrbsizeR-1.3.1/mrbsizeR/man/turnmat.Rd | 52 mrbsizeR-1.3.1/mrbsizeR/src/rcpp_helper.cpp | 4 mrbsizeR-1.3.1/mrbsizeR/tests/testthat.R | 8 mrbsizeR-1.3.1/mrbsizeR/tests/testthat/test-rcpp.R | 410 ++--- mrbsizeR-1.3.1/mrbsizeR/tests/testthat/test-trigonometric.R | 22 mrbsizeR-1.3.1/mrbsizeR/vignettes/bibliography.bib | 147 - mrbsizeR-1.3.1/mrbsizeR/vignettes/mrbsizeR.Rmd | 982 ++++++------ mrbsizeR-1.3/mrbsizeR/man/mrbsizeR.Rd |only 39 files changed, 2871 insertions(+), 2866 deletions(-)
Title: Kernel-Based Regularized Least Squares
Description: Implements Kernel-based Regularized Least Squares (KRLS), a
machine learning method to fit multidimensional functions y = f(x) for
regression and classification problems without relying on linearity or
additivity assumptions. KRLS finds the best fitting function by
minimizing the squared loss of a Tikhonov regularization problem,
using Gaussian kernels as radial basis functions. For further details
see Hainmueller and Hazlett (2014, <doi:10.1093/pan/mpt019>).
Author: Jens Hainmueller [aut, cre],
Chad Hazlett [aut]
Maintainer: Jens Hainmueller <jhain@stanford.edu>
Diff between KRLS versions 1.7-0 dated 2026-06-05 and 1.7-1 dated 2026-07-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 18 ++++++++++++++++++ inst/doc/krls-nystrom-scaling.html | 8 ++++---- inst/doc/krls-quickstart.html | 2 +- tests/testthat/test-krls.R | 12 +++++++++++- 6 files changed, 43 insertions(+), 15 deletions(-)
Title: VCG Sampling using Energy-Based Covariate Balancing
Description: Provides a principled framework for sampling Virtual Control Group (VCG) using energy distance-based covariate balancing. The package offers visualization tools to assess covariate balance and includes a permutation test to evaluate the statistical significance of observed deviations.
Author: Andreas Schulz [aut, cre] ,
Sanofi [cph, fnd]
Maintainer: Andreas Schulz <andreas.schulz2@sanofi.com>
Diff between eVCGsampler versions 1.0.0 dated 2026-03-10 and 1.1.0 dated 2026-07-06
DESCRIPTION | 8 +- MD5 | 21 +++++- man/combine_data.Rd | 78 ++++++++++++------------- man/combine_variables.Rd | 98 +++++++++++++++---------------- man/find_outliers.Rd | 144 +++++++++++++++++++++++------------------------ man/multiSampler.Rd | 104 ++++++++++++++++----------------- tests |only 7 files changed, 232 insertions(+), 221 deletions(-)
Title: Functions to Streamline Statistical Analysis and Reporting
Description: Built upon popular R packages such as 'ggstatsplot' and 'ARTool', this collection offers a wide array of tools for simplifying reproducible analyses, generating high-quality visualizations, and producing 'APA'-compliant outputs. The primary goal of this package is to significantly reduce repetitive coding efforts, allowing you to focus on interpreting results. Whether you're dealing with ANOVA assumptions, reporting effect sizes, or creating publication-ready visualizations, this package makes these tasks easier.
Author: Mark Colley [aut, cre, cph]
Maintainer: Mark Colley <mark.colley@yahoo.de>
Diff between colleyRstats versions 0.1.1 dated 2026-06-22 and 0.1.2 dated 2026-07-06
DESCRIPTION | 26 ++++---- MD5 | 47 +++++++++++---- NAMESPACE | 14 ++++ R/latex-output.R |only R/mixed-models.R |only R/paper.R | 48 +++++++++++++-- R/reporting.R | 108 ++++++++++++++++++++--------------- R/utils.R | 112 ++++++++++++++++++++++++++++++++++++- R/zzz-aliases.R | 12 +++ build/vignette.rds |binary inst/WORDLIST | 22 +++++++ inst/colleyRstats.sty |only inst/doc/choosing-a-test.R |only inst/doc/choosing-a-test.Rmd |only inst/doc/choosing-a-test.html |only inst/doc/getting-started.html | 6 - inst/doc/overleaf.R |only inst/doc/overleaf.Rmd |only inst/doc/overleaf.html |only man/classify_outcome.Rd |only man/define_result_macro.Rd |only man/emit_name_macros.Rd |only man/emit_overleaf.Rd |only man/expand_latex_macros.Rd |only man/latex_escape.Rd |only man/latex_preamble.Rd | 5 + man/recommend_test.Rd |only man/reportArtConTable.Rd | 6 + man/reportCLMM.Rd |only man/reportDunnTestTable.Rd | 7 ++ man/reportGLMM.Rd |only man/use_colleyrstats_sty.Rd |only tests/testthat/test-latex-output.R |only tests/testthat/test-mixed-models.R |only vignettes/choosing-a-test.Rmd |only vignettes/overleaf.Rmd |only 36 files changed, 326 insertions(+), 87 deletions(-)
Title: Scalable Statistical Computing with HDF5-Backed Matrices
Description: A framework for 'scalable' statistical computing on large on-disk
matrices stored in 'HDF5' files. It provides efficient block-wise
implementations of core linear-algebra operations (matrix multiplication,
SVD, PCA, and QR decomposition) written in C++ and R, along with building
blocks from which higher-level multivariate methods such as canonical
correlation analysis can be constructed. These building blocks are designed
not only for direct use, but also as foundational components for developing
new statistical methods that must operate on datasets too large to fit in
memory. The package supports data provided either as 'HDF5' files or
standard R objects, and is intended for high-dimensional applications such
as 'omics' and precision-medicine research.
Author: Dolors Pelegri-Siso [aut, cre] ,
Juan R. Gonzalez [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
Diff between BigDataStatMeth versions 2.0.2 dated 2026-06-08 and 2.0.3 dated 2026-07-06
BigDataStatMeth-2.0.2/BigDataStatMeth/R/S3_eigen_pseudoinv.R |only BigDataStatMeth-2.0.3/BigDataStatMeth/DESCRIPTION | 23 ++--- BigDataStatMeth-2.0.3/BigDataStatMeth/MD5 | 45 ++++------ BigDataStatMeth-2.0.3/BigDataStatMeth/NAMESPACE | 1 BigDataStatMeth-2.0.3/BigDataStatMeth/NEWS.md | 31 ++++++ BigDataStatMeth-2.0.3/BigDataStatMeth/R/HDF5Matrix_op_factorizations.R | 8 + BigDataStatMeth-2.0.3/BigDataStatMeth/R/RcppExports.R | 28 +++--- BigDataStatMeth-2.0.3/BigDataStatMeth/R/S3_decompositions.R | 19 ++++ BigDataStatMeth-2.0.3/BigDataStatMeth/R/S3_factorizations.R | 8 + BigDataStatMeth-2.0.3/BigDataStatMeth/R/S3_pseudoinverse.R | 44 +++++++-- BigDataStatMeth-2.0.3/BigDataStatMeth/README.md | 4 BigDataStatMeth-2.0.3/BigDataStatMeth/inst/doc/BigDataStatMeth.html | 28 +++--- BigDataStatMeth-2.0.3/BigDataStatMeth/inst/include/hdf5Algebra/matrixCorrelation.hpp | 6 - BigDataStatMeth-2.0.3/BigDataStatMeth/inst/include/hdf5Algebra/matrixPseudoinverse.hpp | 16 ++- BigDataStatMeth-2.0.3/BigDataStatMeth/inst/include/hdf5Algebra/matrixQR.hpp | 21 ++++ BigDataStatMeth-2.0.3/BigDataStatMeth/man/bdpseudoinv_hdf5.Rd | 25 ++--- BigDataStatMeth-2.0.3/BigDataStatMeth/man/chol.HDF5Matrix.Rd | 8 + BigDataStatMeth-2.0.3/BigDataStatMeth/man/prcomp.HDF5Matrix.Rd | 19 ++++ BigDataStatMeth-2.0.3/BigDataStatMeth/man/pseudoinverse.Rd | 40 +++++++- BigDataStatMeth-2.0.3/BigDataStatMeth/src/hdf5_pseudoinverse.cpp | 44 +++++---- BigDataStatMeth-2.0.3/BigDataStatMeth/src/hdf5_r6_cholesky.cpp | 12 +- BigDataStatMeth-2.0.3/BigDataStatMeth/src/mem_crossprod.cpp | 14 ++- BigDataStatMeth-2.0.3/BigDataStatMeth/src/mem_tcrossprod.cpp | 4 BigDataStatMeth-2.0.3/BigDataStatMeth/src/mem_weightprod.cpp | 45 ++++++---- 24 files changed, 331 insertions(+), 162 deletions(-)
More information about BigDataStatMeth at CRAN
Permanent link
Title: Factor and Autoregressive Models for Tensor Time Series
Description: Factor and autoregressive models for matrix and tensor valued time series. We provide functions for estimation, simulation and prediction. The models are discussed in
Li et al (2021) <doi:10.48550/arXiv.2110.00928>, Chen et al (2020) <DOI:10.1080/01621459.2021.1912757>,
Chen et al (2020) <DOI:10.1016/j.jeconom.2020.07.015>, and Xiao et al (2020) <doi:10.48550/arXiv.2006.02611>.
Author: Zebang Li [aut, cre],
Ruofan Yu [aut],
Rong Chen [aut],
Yuefeng Han [aut],
Han Xiao [aut],
Dan Yang [aut]
Maintainer: Zebang Li <zebangmail@gmail.com>
Diff between tensorTS versions 1.0.2 dated 2024-04-27 and 1.0.3 dated 2026-07-06
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Monte Carlo and Bayesian Stop-Signal Reaction Time Estimation
Description: Estimates stop-signal reaction time (SSRT) in the stop-signal
task using the integration and mean methods described by Verbruggen and
colleagues (2019) <doi:10.7554/eLife.46323>. In addition to point
estimates, the package provides Monte Carlo tools (nonparametric bootstrap
confidence intervals, parametric ex-Gaussian simulation, minimum-trial-count
and power analysis, and sensitivity analysis under violations of the
horse-race assumptions) and Bayesian estimation via 'Stan', including
single-subject and hierarchical ex-Gaussian horse-race models with an
optional trigger-failure parameter following Matzke and colleagues (2013)
<doi:10.1037/a0030543>, posterior inhibition functions, and posterior
predictive checks. The Bayesian layer works with either the 'cmdstanr' or
'rstan' backend.
Author: Anton Leontyev [aut, cre]
Maintainer: Anton Leontyev <antonleontyev@missouristate.edu>
Diff between SSRTcalc versions 0.3.3 dated 2021-04-19 and 2.1.1 dated 2026-07-06
SSRTcalc-0.3.3/SSRTcalc/R/adaptive-data.R |only SSRTcalc-0.3.3/SSRTcalc/R/fixed-data.R |only SSRTcalc-0.3.3/SSRTcalc/R/integration_adaptiveSSD.R |only SSRTcalc-0.3.3/SSRTcalc/R/integration_fixedSSD.R |only SSRTcalc-0.3.3/SSRTcalc/R/mean_adaptiveSSD.R |only SSRTcalc-0.3.3/SSRTcalc/R/mean_fixedSSD.R |only SSRTcalc-0.3.3/SSRTcalc/R/plotInhFunc.R |only SSRTcalc-0.3.3/SSRTcalc/data/adaptive.RData |only SSRTcalc-0.3.3/SSRTcalc/data/fixed.RData |only SSRTcalc-0.3.3/SSRTcalc/man/plotInhFunc.Rd |only SSRTcalc-2.1.1/SSRTcalc/DESCRIPTION | 46 +++- SSRTcalc-2.1.1/SSRTcalc/MD5 | 60 ++++-- SSRTcalc-2.1.1/SSRTcalc/NAMESPACE | 48 ++++- SSRTcalc-2.1.1/SSRTcalc/NEWS.md | 126 ++++++++----- SSRTcalc-2.1.1/SSRTcalc/R/SSRTcalc-package.R |only SSRTcalc-2.1.1/SSRTcalc/R/core_ssrt.R |only SSRTcalc-2.1.1/SSRTcalc/R/data.R |only SSRTcalc-2.1.1/SSRTcalc/R/helpers.R |only SSRTcalc-2.1.1/SSRTcalc/R/mc_extensions.R |only SSRTcalc-2.1.1/SSRTcalc/R/stan_extensions.R |only SSRTcalc-2.1.1/SSRTcalc/README.md | 161 +++++++++++++---- SSRTcalc-2.1.1/SSRTcalc/build/partial.rdb |binary SSRTcalc-2.1.1/SSRTcalc/data/adaptive.rda |only SSRTcalc-2.1.1/SSRTcalc/data/fixed.rda |only SSRTcalc-2.1.1/SSRTcalc/inst |only SSRTcalc-2.1.1/SSRTcalc/man/SSRTcalc-package.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/adaptive.Rd | 42 ++-- SSRTcalc-2.1.1/SSRTcalc/man/fixed.Rd | 98 ++++++---- SSRTcalc-2.1.1/SSRTcalc/man/integration_adaptiveSSD.Rd | 47 +++- SSRTcalc-2.1.1/SSRTcalc/man/integration_fixedSSD.Rd | 44 +++- SSRTcalc-2.1.1/SSRTcalc/man/mean_adaptiveSSD.Rd | 39 ++-- SSRTcalc-2.1.1/SSRTcalc/man/mean_fixedSSD.Rd | 39 ++-- SSRTcalc-2.1.1/SSRTcalc/man/ranef.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ranef.ssrt_stan.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/run_all_mc.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_boot.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_power.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_robustness.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_simulate.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_stan.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_stan_compare.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_stan_inhibition_fn.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_stan_loo.Rd |only SSRTcalc-2.1.1/SSRTcalc/man/ssrt_stan_pp_check.Rd |only SSRTcalc-2.1.1/SSRTcalc/tests |only 45 files changed, 533 insertions(+), 217 deletions(-)
Title: An Interface to IMF (International Monetary Fund) Data
Description: Provides low-level access to the International Monetary Fund
Statistical Data and Metadata eXchange ('SDMX') 3.0 API, available at
<https://data.imf.org/>, and a concise workflow for discovering datasets,
inspecting dimensions, and downloading observations as tidy data frames.
Author: Pedro Baltazar [aut, cre, cph]
Maintainer: Pedro Baltazar <pedrobtz@gmail.com>
Diff between imf.data versions 0.1.7 dated 2024-09-14 and 0.2.0 dated 2026-07-06
imf.data-0.1.7/imf.data/R/database.R |only imf.data-0.1.7/imf.data/R/methods.R |only imf.data-0.1.7/imf.data/R/package.R |only imf.data-0.1.7/imf.data/R/request.R |only imf.data-0.1.7/imf.data/R/settings.R |only imf.data-0.1.7/imf.data/R/zzz.R |only imf.data-0.1.7/imf.data/man/imf.data-package.Rd |only imf.data-0.1.7/imf.data/man/load_datasets.Rd |only imf.data-0.1.7/imf.data/man/mt_compact_data.Rd |only imf.data-0.1.7/imf.data/man/mt_data_structure.Rd |only imf.data-0.1.7/imf.data/man/mt_dataflow.Rd |only imf.data-0.2.0/imf.data/DESCRIPTION | 34 ++++----- imf.data-0.2.0/imf.data/LICENSE | 2 imf.data-0.2.0/imf.data/MD5 | 70 ++++++++++++++----- imf.data-0.2.0/imf.data/NAMESPACE | 16 ++-- imf.data-0.2.0/imf.data/NEWS.md | 5 + imf.data-0.2.0/imf.data/R/imf_api.R |only imf.data-0.2.0/imf.data/R/sdmx_api.R |only imf.data-0.2.0/imf.data/README.md |only imf.data-0.2.0/imf.data/build |only imf.data-0.2.0/imf.data/inst |only imf.data-0.2.0/imf.data/man/get_data.Rd |only imf.data-0.2.0/imf.data/man/list_datasets.Rd | 20 +++-- imf.data-0.2.0/imf.data/man/list_dimension_values.Rd |only imf.data-0.2.0/imf.data/man/list_dimensions.Rd |only imf.data-0.2.0/imf.data/man/sdmx_api.Rd |only imf.data-0.2.0/imf.data/man/sdmx_availability.Rd |only imf.data-0.2.0/imf.data/man/sdmx_data.Rd |only imf.data-0.2.0/imf.data/man/sdmx_metadata.Rd |only imf.data-0.2.0/imf.data/man/sdmx_structure.Rd |only imf.data-0.2.0/imf.data/man/set_imf_proxy.Rd |only imf.data-0.2.0/imf.data/tests |only imf.data-0.2.0/imf.data/vignettes |only 33 files changed, 96 insertions(+), 51 deletions(-)
Title: Parsing Glycan Structure Text Representations
Description: Provides functions to parse glycan structure text representations
into 'glyrepr' glycan structures. Currently, it supports StrucGP-style,
pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, IUPAC-compact,
WURCS, LINUCS, Linear Code, GlycoCT, and KCF format. It also provides an automatic parser
to detect the format and parse the structure string.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyparse versions 0.6.1 dated 2026-06-20 and 0.7.0 dated 2026-07-06
DESCRIPTION | 16 MD5 | 65 +-- NAMESPACE | 4 NEWS.md | 24 + R/auto-parse.R | 34 + R/parse-glycam-iupac.R |only R/parse-glycoct.R | 629 ++++++++++++++++++++++++++++-- R/parse-iupac-compact.R |only R/parse-iupac-condensed.R | 10 R/parse-iupac-extended.R | 10 R/parse-iupac-short.R | 10 R/parse-kcf.R |only R/parse-linear-code.R | 10 R/parse-linucs.R |only R/parse-pglyco.R | 10 R/parse-strucgp.R | 10 R/parse-wurcs.R | 263 +++++++++++- R/struc-parser-wrapper.R | 35 + man/auto_parse.Rd | 8 man/parse_glycam_iupac.Rd |only man/parse_glycoct.Rd | 7 man/parse_iupac_compact.Rd |only man/parse_iupac_condensed.Rd | 4 man/parse_iupac_extended.Rd | 4 man/parse_iupac_short.Rd | 4 man/parse_kcf.Rd |only man/parse_linear_code.Rd | 4 man/parse_linucs.Rd |only man/parse_pglyco_struc.Rd | 4 man/parse_strucgp_struc.Rd | 4 man/parse_wurcs.Rd | 6 tests/testthat/test-auto-parse.R | 51 ++ tests/testthat/test-na-support.R | 13 tests/testthat/test-parse-glycam-iupac.R |only tests/testthat/test-parse-glycoct.R | 297 ++++++++++++++ tests/testthat/test-parse-iupac-compact.R |only tests/testthat/test-parse-kcf.R |only tests/testthat/test-parse-linucs.R |only tests/testthat/test-parse-wurcs.R | 153 +++++++ tests/testthat/test-progress.R |only 40 files changed, 1576 insertions(+), 113 deletions(-)
Title: A Collection of Database, Data Structure, Visualization, and
Utility Functions for R
Description: The caroline R library contains dozens of functions useful
for: database migration (dbWriteTable2), database style joins &
aggregation (nerge, groupBy, & bestBy), data structure
conversion (nv, tab2df), legend table making (sstable & leghead),
automatic legend positioning for scatter and box plots (legend.position),
plot annotation (labsegs & mvlabs), data visualization
(pies & raPlot), character string manipulation (m & pad),
file I/O (write.delim), batch scripting, data exploration, and more.
The package's greatest contributions stem from its database style merge,
aggregation and interface functions as well as in it's extensive
use and propagation of row, column and vector names in most functions.
The latest additions are plotting functions (confound.grid & sparge)
that intake a dataframe & formulas to visually resolve variable confounding.
Author: David Schruth [aut, cre]
Maintainer: David Schruth <code@anthropoidea.org>
Diff between caroline versions 1.0.0 dated 2026-06-16 and 1.1.1 dated 2026-07-06
DESCRIPTION | 18 +- MD5 | 55 ++++-- NAMESPACE | 5 NEWS.md |only R/aggregate.R | 62 ------- R/convert.R | 48 ++++- R/database.R | 84 ++++++++++ R/models.R | 11 + R/plot.sparge.R | 437 ++++++++++++++++++++++++++++++++++++++--------------- R/plots.R | 19 +- R/string.R | 4 R/zzz.R |only README.md |only build |only inst |only man/bestBy.Rd | 12 + man/heatmatrix.Rd | 7 man/nerge.Rd | 47 ++++- man/nv.Rd | 12 + man/nv2df.Rd |only man/pct.Rd | 10 - man/plot.sparge.Rd | 135 ++++++++++++---- man/tab2df.Rd | 3 vignettes |only 24 files changed, 692 insertions(+), 277 deletions(-)
Title: Modular Cohort-Building Framework for Analytical Dashboards
Description: You can easily add advanced cohort-building component
to your analytical dashboard or simple 'Shiny' app.
Then you can instantly start building cohorts using multiple
filters of different types, filtering datasets, and filtering steps.
Filters can be complex and data-specific, and together
with multiple filtering steps you can use complex filtering rules.
The cohort-building sidebar panel allows you to easily
work with filters, add and remove filtering steps.
It helps you with handling missing values during filtering,
and provides instant filtering feedback with filter feedback plots.
The GUI panel is not only compatible with native shiny
bookmarking, but also provides reproducible R code.
Author: Krystian Igras [cre, aut],
Kamil Wais [aut],
Adam Forys [ctb]
Maintainer: Krystian Igras <krystian8207@gmail.com>
Diff between shinyCohortBuilder versions 0.4.0 dated 2026-02-25 and 1.0.0 dated 2026-07-05
shinyCohortBuilder-0.4.0/shinyCohortBuilder/man/autofilter.Rd |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/DESCRIPTION | 33 shinyCohortBuilder-1.0.0/shinyCohortBuilder/MD5 | 149 + shinyCohortBuilder-1.0.0/shinyCohortBuilder/NAMESPACE | 14 shinyCohortBuilder-1.0.0/shinyCohortBuilder/NEWS.md | 24 shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/actions.R | 765 ++++++---- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/app.R | 14 shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/cb_layer.R | 351 ++++ shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/chat.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/control_utils.R | 196 ++ shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/feedback_html.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_date_range.R | 59 shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_datetime_range.R | 83 - shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_discrete.R | 392 +++-- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_discrete_text.R | 157 -- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_multi_discrete.R | 210 +- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_query.R | 114 + shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_range.R | 266 ++- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/renders.R | 468 ++++-- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/shinyCohortBuilder-package.R | 18 shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/source.R | 47 shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/source_tblist.R | 248 +-- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/ui_utils.R | 93 + shinyCohortBuilder-1.0.0/shinyCohortBuilder/README.md | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/build/vignette.rds |binary shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/custom-gui-layer.R | 42 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/custom-gui-layer.Rmd | 46 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/custom-gui-layer.html | 53 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/gui-filter-layer.R | 21 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/gui-filter-layer.Rmd | 25 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/gui-filter-layer.html | 70 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/package-options.Rmd | 30 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/package-options.html | 133 + shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/shinyCohortBuilder.R | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/shinyCohortBuilder.Rmd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/shinyCohortBuilder.html | 118 - shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/updating-source.html | 3 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/www/scb.css | 277 +++ shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/www/scb.js | 10 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/www/scb.min.css | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/www/scb.min.js | 199 ++ shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/available-filters-choices.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/cb_chat.Rd |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/cb_ui.Rd | 67 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/demo_app.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/dot-render_filter.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/gui-filter-layer.Rd | 45 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/gui.Rd | 4 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/keep_na_input.Rd | 3 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/rendering-custom-attrition.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/rendering-filters.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/rendering-step-attrition.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/scb_icons.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/scb_labels.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/trigger-action.Rd | 23 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/updating-data-statistics.Rd | 6 shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/apps |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/helper-shinytest2.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/setup.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-cb_input.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-cb_layer.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-cb_server.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-cb_ui.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-defaults.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-domains.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-filter_discrete.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-filter_helpers.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-filter_range.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-pre_post_stats.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-render_filter.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-shinytest2.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-should-run-step-on-render.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-source_tblist.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-trigger_action.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-basic.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-configure-step.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-feedback.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-matrix-add-step.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-matrix-update-filter.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-run-button.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-stats.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui_utils.R | 8 shinyCohortBuilder-1.0.0/shinyCohortBuilder/vignettes/custom-gui-layer.Rmd | 46 shinyCohortBuilder-1.0.0/shinyCohortBuilder/vignettes/gui-filter-layer.Rmd | 25 shinyCohortBuilder-1.0.0/shinyCohortBuilder/vignettes/package-options.Rmd | 30 shinyCohortBuilder-1.0.0/shinyCohortBuilder/vignettes/shinyCohortBuilder.Rmd | 2 86 files changed, 3453 insertions(+), 1558 deletions(-)
More information about shinyCohortBuilder at CRAN
Permanent link
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Statistics to locate and tag peaks and valleys and to label plots
with the equation of a fitted polynomial model by ordinary least squares,
major axis, quantile and robust and resistant regression approaches. Line
and model equation for Normal mixture models. Labels for P-value,
R^2 or adjusted R^2 or information criteria for fitted models; parametric
and non-parametric correlation; ANOVA table or summary table for fitted
models as plot insets; annotations for multiple pairwise
comparisons with adjusted P-values. Model fit classes for which suitable
methods are provided by package 'broom' and 'broom.mixed' are supported as
well as user-defined wrappers on model fit functions, allowing model
selection and conditional labelling. Scales and stats to
build volcano and quadrant plots based on
outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Samer Mouksassi [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.7.0 dated 2026-03-23 and 1.0.0 dated 2026-07-05
ggpmisc-0.7.0/ggpmisc/R/stat-fit-broom-tb.R |only ggpmisc-0.7.0/ggpmisc/man/stat_distrmix_line.Rd |only ggpmisc-0.7.0/ggpmisc/man/stat_fit_deviations.Rd |only ggpmisc-0.7.0/ggpmisc/man/stat_ma_line.Rd |only ggpmisc-0.7.0/ggpmisc/man/stat_poly_line.Rd |only ggpmisc-0.7.0/ggpmisc/man/stat_quant_band.Rd |only ggpmisc-0.7.0/ggpmisc/man/stat_quant_line.Rd |only ggpmisc-1.0.0/ggpmisc/DESCRIPTION | 29 ggpmisc-1.0.0/ggpmisc/MD5 | 758 ++ ggpmisc-1.0.0/ggpmisc/NAMESPACE | 5 ggpmisc-1.0.0/ggpmisc/NEWS.md | 67 ggpmisc-1.0.0/ggpmisc/R/check-poly-formula.R | 188 ggpmisc-1.0.0/ggpmisc/R/distrmix-helper-fun.R | 2 ggpmisc-1.0.0/ggpmisc/R/find-quantiles.R |only ggpmisc-1.0.0/ggpmisc/R/find-spikes.R |only ggpmisc-1.0.0/ggpmisc/R/ggpmisc.R | 15 ggpmisc-1.0.0/ggpmisc/R/lmodel2-util.R | 148 ggpmisc-1.0.0/ggpmisc/R/outcome2factor.r | 8 ggpmisc-1.0.0/ggpmisc/R/quant-helper-fun.R | 4 ggpmisc-1.0.0/ggpmisc/R/scale-colour-outcome.r | 4 ggpmisc-1.0.0/ggpmisc/R/scale-continuous-Pvalue.r | 25 ggpmisc-1.0.0/ggpmisc/R/scale-continuous-logFC.r | 2 ggpmisc-1.0.0/ggpmisc/R/scale-shape-outcome.r | 2 ggpmisc-1.0.0/ggpmisc/R/stat-correlation.R | 106 ggpmisc-1.0.0/ggpmisc/R/stat-distrmix-eq.R | 253 ggpmisc-1.0.0/ggpmisc/R/stat-distrmix-line.R | 352 - ggpmisc-1.0.0/ggpmisc/R/stat-fit-broom.R | 641 +- ggpmisc-1.0.0/ggpmisc/R/stat-fit-deviations.R | 248 ggpmisc-1.0.0/ggpmisc/R/stat-fit-residuals.R | 333 - ggpmisc-1.0.0/ggpmisc/R/stat-fit-tb.R |only ggpmisc-1.0.0/ggpmisc/R/stat-ma-eq.R | 388 - ggpmisc-1.0.0/ggpmisc/R/stat-ma-line.R | 292 - ggpmisc-1.0.0/ggpmisc/R/stat-multcomp.R | 525 - ggpmisc-1.0.0/ggpmisc/R/stat-peaks.R | 128 ggpmisc-1.0.0/ggpmisc/R/stat-poly-eq.R | 578 +- ggpmisc-1.0.0/ggpmisc/R/stat-poly-line.R | 328 - ggpmisc-1.0.0/ggpmisc/R/stat-quant-band.r | 206 ggpmisc-1.0.0/ggpmisc/R/stat-quant-eq.R | 402 - ggpmisc-1.0.0/ggpmisc/R/stat-quant-line.r | 235 ggpmisc-1.0.0/ggpmisc/R/stat-spikes.R | 343 - ggpmisc-1.0.0/ggpmisc/R/use-label.R | 287 - 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ggpmisc-1.0.0/ggpmisc/tests/testthat/test-stat-ma-line.R | 121 ggpmisc-1.0.0/ggpmisc/tests/testthat/test-stat-multcomp.R | 82 ggpmisc-1.0.0/ggpmisc/tests/testthat/test-stat-poly-eq.R | 165 ggpmisc-1.0.0/ggpmisc/tests/testthat/test-stat-poly-line.R | 121 ggpmisc-1.0.0/ggpmisc/tests/testthat/test-stat-quant-band.R | 83 ggpmisc-1.0.0/ggpmisc/tests/testthat/test-stat-quant-eq.R | 2 ggpmisc-1.0.0/ggpmisc/tests/testthat/test-stat-quant-line.R | 84 ggpmisc-1.0.0/ggpmisc/tests/testthat/test-stat-spikes.R |only ggpmisc-1.0.0/ggpmisc/tests/testthat/test-use-label.R |only ggpmisc-1.0.0/ggpmisc/vignettes/cheat-sheet.Rmd | 71 ggpmisc-1.0.0/ggpmisc/vignettes/user-guide.Rmd | 1049 ++- 227 files changed, 15642 insertions(+), 9299 deletions(-)
Title: Species Distribution Modeling with H3 Grids
Description: Provides tools for species distribution modeling using H3
hexagonal grids (Uber Technologies Inc., 2022, <https://h3geo.org>).
Facilitates retrieval of species occurrence records, generation of H3 grids,
computation of landscape metrics, and preparation of spatial data for modern
species distribution models workflows. Designed for biodiversity and landscape ecology research.
Author: Manuel Spinola [aut, cre]
Maintainer: Manuel Spinola <mspinola10@gmail.com>
Diff between h3sdm versions 0.1.6 dated 2026-06-15 and 0.1.7 dated 2026-07-05
DESCRIPTION | 9 ++-- MD5 | 21 +++++---- NAMESPACE | 1 NEWS.md | 17 +++++++ R/h3sdm_aoa.R | 101 ++++++++++++++++++++++++++++++++++++++-------- R/h3sdm_workflow.R | 18 +++++++- R/h3sdm_workflow_checks.R |only R/h3sdm_workflows.R | 40 ++++++++++++++---- inst/doc/h3sdm.html | 36 ++++++++-------- man/h3sdm_aoa.Rd | 17 ++++++- man/h3sdm_workflow.Rd | 14 +++++- man/h3sdm_workflows.Rd | 37 +++++++++++++--- 12 files changed, 241 insertions(+), 70 deletions(-)
Title: Complex-Valued Lasso and Complex-Valued Graphical Lasso
Description: Implements 'glmnet'-style complex-valued lasso (CLASSO) and
complex-valued graphical lasso (CGLASSO) via a pathwise coordinate
descent algorithm for complex-valued parameters, using an isomorphism
between complex numbers and 2x2 orthogonal matrices. Also provides a
full inference pipeline for high-dimensional sparse spectral precision
matrices, including data-driven bandwidth selection, one-step
debiasing, asymptotic variance estimation, entry-wise confidence
regions, and FDR-controlled hypothesis testing. Supporting tools for
cross-validation, simulation, coefficient extraction, and plotting are
included. See Deb, Kuceyeski, and Basu (2024)
<doi:10.48550/arXiv.2401.11128> and Deb, Kim, and Basu (2026)
<doi:10.48550/arXiv.2606.07986>.
Author: Younghoon Kim [aut, cre],
Navonil Deb [aut],
Sumanta Basu [aut]
Maintainer: Younghoon Kim <ykim124@ua.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2025-09-17
Diff between cxreg versions 1.0.0 dated 2025-09-17 and 1.1.2 dated 2026-07-05
cxreg-1.0.0/cxreg/man/buildPredmat.default.Rd |only cxreg-1.0.0/cxreg/man/dft.X.Rd |only cxreg-1.0.0/cxreg/man/fixm.Rd |only cxreg-1.1.2/cxreg/DESCRIPTION | 36 ++-- cxreg-1.1.2/cxreg/MD5 | 139 ++++++++++------- cxreg-1.1.2/cxreg/NAMESPACE | 17 +- cxreg-1.1.2/cxreg/NEWS.md |only cxreg-1.1.2/cxreg/R/buildPremat.default.R | 90 +++++------ cxreg-1.1.2/cxreg/R/cglasso.R | 129 ++++++++-------- cxreg-1.1.2/cxreg/R/cglassoFlex.R | 139 ++++------------- cxreg-1.1.2/cxreg/R/classo.R | 103 +++++++----- cxreg-1.1.2/cxreg/R/classo.control.R | 133 +++++++--------- cxreg-1.1.2/cxreg/R/classoFlex.R | 123 +++------------ cxreg-1.1.2/cxreg/R/coef.classo.R | 18 +- cxreg-1.1.2/cxreg/R/coef.cv.classo.R | 47 +++-- cxreg-1.1.2/cxreg/R/cv.classo.R | 53 +++--- cxreg-1.1.2/cxreg/R/cv.classo.raw.R | 206 ++++++++++++------------- cxreg-1.1.2/cxreg/R/cv.classofit.R | 20 +- cxreg-1.1.2/cxreg/R/cvstats.R | 27 ++- cxreg-1.1.2/cxreg/R/cvtype.R | 46 +++-- cxreg-1.1.2/cxreg/R/cxreg-package.R | 133 +++++++++++----- cxreg-1.1.2/cxreg/R/data-documentation.R | 61 ++++++- cxreg-1.1.2/cxreg/R/decglasso.R |only cxreg-1.1.2/cxreg/R/error.bars.R | 32 ++-- cxreg-1.1.2/cxreg/R/family.classo.R | 27 ++- cxreg-1.1.2/cxreg/R/gcvFlex.R |only cxreg-1.1.2/cxreg/R/getOptcv.classo.R | 29 +-- cxreg-1.1.2/cxreg/R/inference.R |only cxreg-1.1.2/cxreg/R/lambda.interp.R | 97 ++++++++---- cxreg-1.1.2/cxreg/R/nonzeroCoef.R | 106 ++++++++----- cxreg-1.1.2/cxreg/R/plot.cglasso.R | 189 +++++++++++------------ cxreg-1.1.2/cxreg/R/plot.classo.R | 12 - cxreg-1.1.2/cxreg/R/plot.cv.classo.R | 71 ++++---- cxreg-1.1.2/cxreg/R/plotCoef.R | 207 +++++++++++--------------- cxreg-1.1.2/cxreg/R/predict.classo.R | 142 ++++++++--------- cxreg-1.1.2/cxreg/R/predict.cv.classo.R | 80 ++++------ cxreg-1.1.2/cxreg/R/print.classo.R | 15 + cxreg-1.1.2/cxreg/R/print.cv.classo.R | 19 +- cxreg-1.1.2/cxreg/R/spectral.functions.R |only cxreg-1.1.2/cxreg/R/var.cov.R |only cxreg-1.1.2/cxreg/README.md |only cxreg-1.1.2/cxreg/build |only cxreg-1.1.2/cxreg/inst |only cxreg-1.1.2/cxreg/man/buildPredmat.Rd | 27 ++- cxreg-1.1.2/cxreg/man/cglasso.Rd | 38 ++-- cxreg-1.1.2/cxreg/man/cglasso.path.Rd | 62 ++----- cxreg-1.1.2/cxreg/man/cglasso_example.Rd | 36 +++- cxreg-1.1.2/cxreg/man/classo-internal.Rd | 7 cxreg-1.1.2/cxreg/man/classo.Rd | 30 +-- cxreg-1.1.2/cxreg/man/classo.control.Rd | 40 ++--- cxreg-1.1.2/cxreg/man/classo.path.Rd | 14 - cxreg-1.1.2/cxreg/man/classo_example.Rd | 35 +++- cxreg-1.1.2/cxreg/man/coef.cv.classo.Rd |only cxreg-1.1.2/cxreg/man/cv.classo.Rd | 32 ++-- cxreg-1.1.2/cxreg/man/cxreg-package.Rd | 108 ++++++++++--- cxreg-1.1.2/cxreg/man/cxreg.Rd | 8 - cxreg-1.1.2/cxreg/man/decglasso.Rd |only cxreg-1.1.2/cxreg/man/dft.all.Rd |only cxreg-1.1.2/cxreg/man/dft.j.Rd |only cxreg-1.1.2/cxreg/man/error.bars.Rd |only cxreg-1.1.2/cxreg/man/family.classo.Rd |only cxreg-1.1.2/cxreg/man/fhat_at.Rd |only cxreg-1.1.2/cxreg/man/lambda.interp.Rd |only cxreg-1.1.2/cxreg/man/nonzeroCoef.Rd |only cxreg-1.1.2/cxreg/man/plot.cglasso.Rd | 31 ++- cxreg-1.1.2/cxreg/man/plot.classo.Rd | 2 cxreg-1.1.2/cxreg/man/plot.cv.classo.Rd | 20 +- cxreg-1.1.2/cxreg/man/plotCoef.Rd |only cxreg-1.1.2/cxreg/man/predict.classo.Rd | 60 +++---- cxreg-1.1.2/cxreg/man/predict.cv.classo.Rd | 33 +--- cxreg-1.1.2/cxreg/man/print.cv.classo.Rd | 9 - cxreg-1.1.2/cxreg/man/select_m.Rd |only cxreg-1.1.2/cxreg/man/spec.fdr.Rd |only cxreg-1.1.2/cxreg/man/spec.test.Rd |only cxreg-1.1.2/cxreg/man/var.cov.Rd |only cxreg-1.1.2/cxreg/src/Makevars.win.txt |only cxreg-1.1.2/cxreg/src/cglassocd_scaled.f | 2 cxreg-1.1.2/cxreg/src/classo_init.cpp | 26 --- cxreg-1.1.2/cxreg/src/classocd_warm.f | 4 cxreg-1.1.2/cxreg/tests |only cxreg-1.1.2/cxreg/vignettes |only 81 files changed, 1632 insertions(+), 1538 deletions(-)
Title: Microstructure Information from Diffusion Imaging
Description: An implementation of a taxonomy of models of restricted diffusion
in biological tissues parametrized by the tissue geometry (axis, diameter,
density, etc.). This is primarily used in the context of diffusion magnetic
resonance (MR) imaging to model the MR signal attenuation in the presence of
diffusion gradients. The goal is to provide tools to simulate the MR signal
attenuation predicted by these models under different experimental
conditions. The package feeds a companion 'shiny' app available at
<https://midi-pastrami.apps.math.cnrs.fr> that serves as a graphical
interface to the models and tools provided by the package. Models currently
available are the ones in Neuman (1974) <doi:10.1063/1.1680931>, Van
Gelderen et al. (1994) <doi:10.1006/jmrb.1994.1038>, Stanisz et al. (1997)
<doi:10.1002/mrm.1910370115>, Soderman & Jonsson (1995)
<doi:10.1006/jmra.1995.0014> and Callaghan (1995)
<doi:10.1006/jmra.1995.1055>.
Author: Aymeric Stamm [aut, cre]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Diff between midi versions 0.1.0 dated 2024-04-03 and 0.2.0 dated 2026-07-05
midi-0.1.0/midi/R/cylinder-radial-compartment.R |only midi-0.1.0/midi/R/samplers.R |only midi-0.1.0/midi/man/CylinderRadialCompartment.Rd |only midi-0.1.0/midi/tests/testthat/test-samplers.R |only midi-0.2.0/midi/DESCRIPTION | 18 midi-0.2.0/midi/MD5 | 79 +- midi-0.2.0/midi/NAMESPACE | 6 midi-0.2.0/midi/NEWS.md | 41 + midi-0.2.0/midi/R/base-compartment.R |only midi-0.2.0/midi/R/circularly-shaped-compartments.R |only midi-0.2.0/midi/R/constants.R | 23 midi-0.2.0/midi/R/cylinder-bundle-compartment.R | 271 ++++------ midi-0.2.0/midi/R/cylinder-bundle-geometry.R | 37 - midi-0.2.0/midi/R/cylinder-compartment.R | 107 +-- midi-0.2.0/midi/R/distributions.R |only midi-0.2.0/midi/R/free-compartment.R |only midi-0.2.0/midi/R/rcylinders.R |only midi-0.2.0/midi/R/sphere-compartment.R |only midi-0.2.0/midi/R/sysdata.rda |binary midi-0.2.0/midi/R/utils.R | 47 + midi-0.2.0/midi/README.md | 72 +- midi-0.2.0/midi/build/partial.rdb |binary midi-0.2.0/midi/man/BaseCompartment.Rd |only midi-0.2.0/midi/man/BaseDistribution.Rd |only midi-0.2.0/midi/man/CallaghanCompartment.Rd | 50 - midi-0.2.0/midi/man/CircularlyShapedCompartment.Rd |only midi-0.2.0/midi/man/CylinderBundleCompartment.Rd | 237 ++------ midi-0.2.0/midi/man/CylinderCompartment.Rd | 190 ++----- midi-0.2.0/midi/man/FreeCompartment.Rd |only midi-0.2.0/midi/man/GammaDistribution.Rd |only midi-0.2.0/midi/man/NeumanCompartment.Rd | 50 - midi-0.2.0/midi/man/SodermanCompartment.Rd | 50 - midi-0.2.0/midi/man/SphereCompartment.Rd |only midi-0.2.0/midi/man/StaniszCompartment.Rd | 50 - midi-0.2.0/midi/man/VanGelderenCompartment.Rd | 50 - midi-0.2.0/midi/man/WatsonDistribution.Rd |only midi-0.2.0/midi/man/bvalue.Rd |only midi-0.2.0/midi/man/figures/README-unnamed-chunk-4-1.png |binary midi-0.2.0/midi/man/figures/README-unnamed-chunk-5-1.png |only midi-0.2.0/midi/man/midi-package.Rd | 11 midi-0.2.0/midi/man/rcylinders.Rd |only midi-0.2.0/midi/tests/testthat/test-callaghan-compartment.R | 15 midi-0.2.0/midi/tests/testthat/test-cylinder-bundle-compartment.R | 41 + midi-0.2.0/midi/tests/testthat/test-cylinder-bundle-geometry.R |only midi-0.2.0/midi/tests/testthat/test-cylinder-compartment.R | 26 midi-0.2.0/midi/tests/testthat/test-distributions.R |only midi-0.2.0/midi/tests/testthat/test-neuman-compartment.R | 17 midi-0.2.0/midi/tests/testthat/test-rcylinders.R |only midi-0.2.0/midi/tests/testthat/test-soderman-compartment.R | 15 midi-0.2.0/midi/tests/testthat/test-sphere-compartment.R |only midi-0.2.0/midi/tests/testthat/test-stanisz-compartment.R | 15 midi-0.2.0/midi/tests/testthat/test-utils.R |only midi-0.2.0/midi/tests/testthat/test-vangelderen-compartment.R | 15 53 files changed, 787 insertions(+), 746 deletions(-)
Title: Creates Define XML Documents
Description: Creates 'define.xml' documents used for regulatory
submissions based on spreadsheet metadata. Can also help
create metadata and generate HTML data explorer.
Author: David Bosak [aut, cre],
Aheer Alvi [aut],
Jonathan Stallings [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between defineR versions 0.0.5 dated 2025-12-15 and 0.0.6 dated 2026-07-05
defineR-0.0.5/defineR/tests/testthat/output/check.sdtm.pdf |only defineR-0.0.6/defineR/DESCRIPTION | 6 defineR-0.0.6/defineR/MD5 | 28 defineR-0.0.6/defineR/NEWS.md | 4 defineR-0.0.6/defineR/R/create_adam_xml.R | 2 defineR-0.0.6/defineR/R/create_sdtm_xml.R | 2 defineR-0.0.6/defineR/R/write.R | 2 defineR-0.0.6/defineR/inst/extdata/adam/define.xml | 26 defineR-0.0.6/defineR/inst/extdata/sdtm/define.xml | 12 defineR-0.0.6/defineR/tests/testthat/adam/define.xml | 26 defineR-0.0.6/defineR/tests/testthat/metadata/demo/SDTM_METADATA3_CN.xlsx |only defineR-0.0.6/defineR/tests/testthat/output/define.adam.xml | 300 +++++----- defineR-0.0.6/defineR/tests/testthat/output/define.sdtm.html | 20 defineR-0.0.6/defineR/tests/testthat/output/define.sdtm.xml | 38 - defineR-0.0.6/defineR/tests/testthat/test-write.R | 31 + defineR-0.0.6/defineR/tests/testthat/xlsx/SDTM_METADATA.xlsx |binary 16 files changed, 249 insertions(+), 248 deletions(-)
Title: Dynamic Copula VAR Models for Time-Varying Dependence
Description: Fits Bayesian copula vector autoregressive models for bivariate
time series with dynamic, regime-switching, and constant dependence
structures. The package includes simulation, data preparation,
estimation with 'Stan' through 'rstan' or 'cmdstanr', posterior
summaries, diagnostics, trajectory extraction, fitted and predictive
summaries, and approximate leave-one-out cross-validation model
comparison for supported fits. For Bayesian computation and model
comparison, see Carpenter et al. (2017)
<doi:10.18637/jss.v076.i01> and Vehtari, Gelman and Gabry (2017)
<doi:10.1007/s11222-016-9696-4>.
Author: Benedikt Lugauer [aut, cre]
Maintainer: Benedikt Lugauer <benedikt.lugauer@uni-leipzig.de>
Diff between dcvar versions 0.2.0 dated 2026-04-27 and 0.9.3 dated 2026-07-05
DESCRIPTION | 8 MD5 | 287 +++-- NAMESPACE | 46 NEWS.md | 395 +++++++ R/applicability.R |only R/as-data-frame.R | 5 R/backend.R | 74 + R/constant_fit-class.R | 7 R/covariate_fit-class.R | 33 R/data-preparation.R | 559 +++++++++- R/dcvar-package.R | 16 R/dcvar_fit-class.R | 49 R/diagnostics.R | 231 +++- R/extract.R | 1032 +++++++++++++++++-- R/fit-constant.R | 68 - R/fit-covariate.R | 93 + R/fit-dcvar.R | 210 +++ R/fit-hmm.R | 143 ++ R/fit-multilevel.R | 132 +- R/fit-sem.R | 149 ++ R/hmm_fit-class.R | 69 + R/interpret.R | 35 R/loo.R | 71 - R/margins.R | 364 +++++- R/metrics.R | 52 R/multilevel_fit-class.R | 194 +++ R/pit.R | 201 +++ R/plot-trajectories.R | 24 R/plot.R | 286 ++++- R/predict.R | 350 ++++++ R/sem_fit-class.R | 177 +++ R/simulate-breakpoint.R | 23 R/simulate-multilevel.R | 135 ++ R/simulate-sem.R | 156 ++ R/simulate.R | 347 ++++-- R/stan-utils.R | 84 + R/trajectories.R | 44 R/tv_fit-class.R |only R/utils.R | 415 +++++++ README.md | 138 +- inst/CITATION | 2 inst/doc/model-comparison.R | 64 + inst/doc/model-comparison.Rmd | 123 ++ inst/doc/model-comparison.html | 203 ++- inst/doc/simulation-tools.html | 2 inst/stan/constant_EG.stan | 11 inst/stan/constant_GG.stan | 2 inst/stan/constant_NCl.stan | 13 inst/stan/constant_SNG.stan | 2 inst/stan/constant_copula_var.stan | 4 inst/stan/constant_mixed.stan |only inst/stan/constant_mixed_clayton.stan |only inst/stan/dcvar_EG_ncp.stan | 11 inst/stan/dcvar_GG_ncp.stan | 2 inst/stan/dcvar_SNG_ncp.stan | 2 inst/stan/dcvar_covariate_ncp.stan | 2 inst/stan/dcvar_covariate_nodrift.stan | 2 inst/stan/dcvar_dynamic.stan |only inst/stan/dcvar_mixed_ncp.stan |only inst/stan/dcvar_model_ncp.stan | 6 inst/stan/dcvar_tv_mixed.stan |only inst/stan/functions/clayton_copula.stan | 15 inst/stan/functions/ncp_random_walk.stan | 23 inst/stan/functions/softplus.stan |only inst/stan/functions/var_residuals.stan | 18 inst/stan/hmm_EG.stan | 28 inst/stan/hmm_GG.stan | 9 inst/stan/hmm_SNG.stan | 9 inst/stan/hmm_copula_model.stan | 14 inst/stan/hmm_mixed.stan |only inst/stan/hmm_switching.stan |only inst/stan/multilevel_copula_var.stan | 14 inst/stan/multilevel_mixed.stan |only inst/stan/multilevel_tv_mixed.stan |only inst/stan/sem_mixed.stan |only inst/stan/sem_naive_mixed.stan |only inst/stan/sem_tv_mixed.stan |only man/applicability_check.Rd |only man/as.data.frame.dcvar_model_fit.Rd | 5 man/compute_param_metrics.Rd | 4 man/compute_rho_metrics.Rd | 12 man/dcvar-package.Rd | 16 man/dcvar.Rd | 83 + man/dcvar_compare.Rd | 10 man/dcvar_constant.Rd | 24 man/dcvar_constant_fit-methods.Rd | 4 man/dcvar_covariate.Rd | 7 man/dcvar_fit-methods.Rd | 3 man/dcvar_hmm.Rd | 45 man/dcvar_hmm_fit-methods.Rd | 3 man/dcvar_multilevel.Rd | 51 man/dcvar_multilevel_fit-methods.Rd | 23 man/dcvar_sem.Rd | 62 - man/dcvar_sem_fit-methods.Rd | 16 man/dcvar_stan_path.Rd | 10 man/dcvar_tv_fit-methods.Rd |only man/dependence_summary.Rd | 6 man/fitted.dcvar_hmm_fit.Rd |only man/fitted.dcvar_model_fit.Rd | 19 man/hmm_state_params.Rd |only man/hmm_states.Rd | 5 man/interpret_rho_trajectory.Rd | 11 man/loo.dcvar.Rd | 16 man/phi_trajectory.Rd |only man/pit_values.Rd | 6 man/plot_phi_trajectory.Rd |only man/plot_rho.Rd | 3 man/plot_sigma_trajectory.Rd |only man/plot_trajectories.Rd | 4 man/predict.dcvar_hmm_fit.Rd |only man/predict.dcvar_model_fit.Rd | 11 man/prepare_constant_data.Rd | 16 man/prepare_dcvar_covariate_data.Rd | 4 man/prepare_dcvar_data.Rd | 45 man/prepare_hmm_data.Rd | 13 man/prepare_multilevel_data.Rd | 27 man/prepare_sem_data.Rd | 32 man/print.dcvar_applicability.Rd |only man/print.dcvar_multilevel_tv_summary.Rd |only man/print.dcvar_sem_tv_summary.Rd |only man/print.dcvar_tv_summary.Rd |only man/rho_decreasing.Rd | 4 man/rho_increasing.Rd | 4 man/rho_trajectory.Rd | 9 man/sigma_trajectory.Rd |only man/simulate_breakpoint_data.Rd | 8 man/simulate_dcvar.Rd | 56 - man/simulate_dcvar_multilevel.Rd | 42 man/simulate_dcvar_sem.Rd | 45 man/var_params.Rd | 19 tests/testthat/helper-fits.R | 457 ++++++++ tests/testthat/test-applicability.R |only tests/testthat/test-constant-clayton.R | 19 tests/testthat/test-convergence.R | 3 tests/testthat/test-covariate.R | 20 tests/testthat/test-data-preparation-extensions.R | 29 tests/testthat/test-data-preparation.R | 64 + tests/testthat/test-dcvar-dynamic-equivalence.R |only tests/testthat/test-diagnostics.R | 50 tests/testthat/test-extract.R | 34 tests/testthat/test-fit-cmdstanr.R | 44 tests/testthat/test-fit-constant-mixed.R |only tests/testthat/test-fit-mixed-dynamic.R |only tests/testthat/test-fit-mixed-hier.R |only tests/testthat/test-fit-multilevel-tv.R |only tests/testthat/test-fit-multilevel.R | 129 ++ tests/testthat/test-fit-sem-tv.R |only tests/testthat/test-fit-sem.R | 125 ++ tests/testthat/test-fit-tv-sem-multilevel-recovery.R |only tests/testthat/test-fit-tv.R |only tests/testthat/test-hmm-switching.R |only tests/testthat/test-loo-compare.R | 34 tests/testthat/test-margins.R | 139 ++ tests/testthat/test-metrics.R | 27 tests/testthat/test-multilevel-exponential.R | 28 tests/testthat/test-reproducibility.R |only tests/testthat/test-sem-naive.R | 71 + tests/testthat/test-simulate-margins.R | 65 + tests/testthat/test-simulate-multilevel.R | 60 - tests/testthat/test-simulate-orientation.R |only tests/testthat/test-simulate-sem.R | 35 tests/testthat/test-simulate-tv.R |only tests/testthat/test-stan-utils.R | 15 tests/testthat/test-validation-edges.R | 32 vignettes/model-comparison.Rmd | 123 ++ 165 files changed, 8503 insertions(+), 1166 deletions(-)
Title: Statistical Tools for Modelling Climate-Health Impacts
Description: Tools for producing climate-health indicators and supporting
official statistics from health and climate data. Implements analytical
workflows for temperature-related mortality, wildfire smoke exposure,
air pollution, suicides related to extreme heat, malaria, and
diarrhoeal disease outcomes, with utilities for descriptive statistics, model
validation, attributable fraction and attributable number estimation,
relative risk estimation, minimum mortality temperature estimation,
and plotting for reporting. These six indicators are endorsed by
the United Nations Statistical Commission for inclusion in the
Global Set of Environment and Climate Change Statistics.
Implemented methods include distributed lag non-linear models (DLNM),
quasi-Poisson time-series regression, case-crossover analysis,
Bayesian spatio-temporal models using the Integrated Nested Laplace
Approximation ('INLA'), and multivariate meta-analysis for
sub-national estimates. The package is based on methods developed
in the S [...truncated...]
Author: Charlie Browning [aut],
Kenechi Omeke [aut, cre],
Etse Yawo Dzakpa [aut],
Gladin Jose [aut],
Matt Pearce [aut],
Ellie Watkins [aut],
Claire Hunt [aut],
Beatrice Byukusenge [aut],
Cassien Habyarimana [aut],
Venuste Nyagahakwa [aut],
Felix Scarbrough [ [...truncated...]
Maintainer: Kenechi Omeke <climate.health@ons.gov.uk>
Diff between climatehealth versions 1.0.2 dated 2026-06-09 and 1.0.3 dated 2026-07-05
DESCRIPTION | 8 MD5 | 64 ++--- NEWS.md | 17 + R/mental_health.R | 14 + R/temp_mortality.R | 199 ++++++++-------- R/wildfire.R | 15 - README.md | 416 +++++++++++++++++------------------ man/extract_means_for_geography.Rd | 4 man/hc_add_national_data.Rd | 7 man/hc_adf.Rd | 2 man/hc_attr.Rd | 12 - man/hc_attr_tables.Rd | 6 man/hc_create_crossbasis.Rd | 7 man/hc_model_combo_res.Rd | 4 man/hc_model_validation.Rd | 12 - man/hc_plot_af_cold_monthly.Rd | 2 man/hc_plot_af_heat_monthly.Rd | 2 man/hc_plot_ar_cold_monthly.Rd | 2 man/hc_plot_ar_heat_monthly.Rd | 2 man/hc_plot_attr_cold_totals.Rd | 2 man/hc_plot_attr_heat_totals.Rd | 2 man/hc_plot_rr.Rd | 2 man/hc_predict_subnat.Rd | 2 man/hc_quasipoisson_dlnm.Rd | 2 man/hc_read_data.Rd | 12 - man/hc_rr_results.Rd | 4 man/hc_save_results.Rd | 2 man/join_health_and_climate_data.Rd | 3 man/suicides_heat_do_analysis.Rd | 3 man/temp_mortality_do_analysis.Rd | 38 +-- man/wildfire_do_analysis.Rd | 2 tests/testthat/test_temp_mortality.R | 101 ++++++-- tests/testthat/test_wildfire.R | 37 ++- 33 files changed, 565 insertions(+), 442 deletions(-)
Title: Automated Functional Annotation of Genetic Variants and Linked
Proxies
Description: To automated functional annotation of genetic variants and linked proxies. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.
Author: Alireza Ani [aut, cre],
Zoha Kamali [aut],
Ahmad Vaez [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between SNPannotator versions 1.4.7 dated 2026-06-08 and 1.4.8 dated 2026-07-05
DESCRIPTION | 8 - MD5 | 23 ++--- NAMESPACE | 1 R/aaa.R | 2 R/configFile_funcs.R | 24 ++--- R/ensembl_funcs.R | 174 +++++++++++++++++++++++++++++++++++++++++++ R/eqtl_funcs.R | 2 R/eqtl_graph_funcs.R | 3 R/gwascat_graph_funcs.R | 2 R/merge_funcs.R | 35 +++++--- R/misc_files.R | 10 ++ inst/extdata/demo_config.ini | 20 ++-- man/findSynonyms.Rd |only 13 files changed, 251 insertions(+), 53 deletions(-)
Title: Tour Methods for Multivariate Data Visualisation
Description: Implements geodesic interpolation and basis
generation functions that allow you to create new tour
methods from R.
Author: Hadley Wickham [aut, ctb] ,
Dianne Cook [aut, cre] ,
Nick Spyrison [ctb] ,
Ursula Laa [ctb] ,
H. Sherry Zhang [ctb] ,
Stuart Lee [ctb]
Maintainer: Dianne Cook <dicook@monash.edu>
Diff between tourr versions 1.2.7 dated 2026-05-15 and 1.2.8 dated 2026-07-05
DESCRIPTION | 6 +++--- MD5 | 17 ++++++++++------- NAMESPACE | 5 +++++ NEWS.md | 6 ++++++ R/display-dependence.r |only R/history.r | 18 +++++++----------- R/tour-dependence.r | 27 ++++++++++++++++++++++++--- build/vignette.rds |binary man/basis_dep_init.Rd |only man/dependence_tour.Rd | 4 ++-- man/display_dependence.Rd |only 11 files changed, 57 insertions(+), 26 deletions(-)
Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with the
'stringr' or 'stringi' packages. The foremost of these is the
extraction of numbers from strings. 'stringr' and 'stringi' make you
figure out the regular expression for yourself; 'strex' takes care of
this for you. There are many other handy functionalities in 'strex'.
Contributions to this package are encouraged; it is intended as a
miscellany of string manipulation functions that cannot be found in
'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between strex versions 2.0.1 dated 2024-10-03 and 2.1.0 dated 2026-07-05
DESCRIPTION | 10 ++++---- MD5 | 34 ++++++++++++++--------------- NEWS.md | 6 +++++ R/extract-nums.R | 9 +++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/alphordering-numbers.html | 9 ++++--- inst/doc/argument-matching.R | 14 +++++++++++ inst/doc/argument-matching.html | 9 ++++--- inst/doc/before-and-after.html | 9 ++++--- inst/doc/detection.html | 9 ++++--- inst/doc/important-miscellany.R | 2 + inst/doc/important-miscellany.html | 9 ++++--- inst/doc/numbers-in-strings.html | 9 ++++--- tests/testthat/test-extract-non-numerics.R | 11 +++++++++ tests/testthat/test-extract-nums.R | 15 ++++++++++++ tests/testthat/test-num-before.R | 17 ++++++++++++++ tests/testthat/test-split-by-nums.R | 7 +++++ 18 files changed, 131 insertions(+), 48 deletions(-)
Title: Fast Molecular Clock Dating of Phylogenetic Trees with Rate
Variation
Description: Functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. For more details see Volz and Frost (2017) <doi:10.1093/ve/vex025>.
Author: Erik Volz [aut, cre]
Maintainer: Erik Volz <erik.volz@gmail.com>
Diff between treedater versions 1.0.2 dated 2025-09-03 and 2.0.0 dated 2026-07-05
DESCRIPTION | 16 ++- MD5 | 17 ++- NAMESPACE | 2 NEWS.md |only R/treedater.R | 2 R/treedater0.R | 228 ++++++++++++++++++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/h3n2.html | 150 +++++++++++++++++----------------- man/dater.Rd | 4 tests |only 10 files changed, 307 insertions(+), 112 deletions(-)
Title: Generalized L-Moments Estimation for Extreme Value Distributions
Description: Provides generalized L-moments estimation methods for the
generalized extreme value ('GEV') distribution. Implements both stationary
'GEV' and non-stationary 'GEV11' models where location and scale parameters
vary with time. Includes various penalty functions (Martins-Stedinger,
Park, Cannon, Coles-Dixon) for shape parameter regularization.
Also provides model averaging estimation ('ma.gev') that combines MLE and
L-moment methods with multiple weighting schemes for robust high quantile
estimation. The 'GLME' methodology is described in Shin et al. (2025a)
<doi:10.48550/arXiv.2512.20385>. The non-stationary L-moment method
is based on Shin et al. (2025b) <doi:10.1007/s42952-025-00325-3>.
The model averaging method is described in Shin et al. (2026)
<doi:10.1007/s00477-025-03167-x>.
See also Hosking (1990) <doi:10.1111/j.2517-6161.1990.tb01775.x> for
L-moments theory and Martins and Stedinger (2000)
<doi:10.1029/1999WR900330> for penalized likelihood methods [...truncated...]
Author: Yonggwan Shin [aut, cre] ,
Seokkap Ko [aut, ctb] ,
Jihong Park [ctb] ,
Yire Shin [aut, dtc] ,
Jeong-Soo Park [aut, ths]
Maintainer: Yonggwan Shin <syg.stat@etri.re.kr>
Diff between GLmom versions 1.3.1 dated 2026-02-27 and 2.0.0 dated 2026-07-05
GLmom-1.3.1/GLmom/data/Trehafod.rda |only GLmom-1.3.1/GLmom/data/streamflow.rda |only GLmom-1.3.1/GLmom/man/Trehafod.Rd |only GLmom-1.3.1/GLmom/man/gev11.GLD.Rd |only GLmom-1.3.1/GLmom/man/init.glme.gev11.Rd |only GLmom-1.3.1/GLmom/man/obj.lme.gev11.Rd |only GLmom-1.3.1/GLmom/man/optim.glme.gev11.Rd |only GLmom-1.3.1/GLmom/man/pk.beta.ns.Rd |only GLmom-1.3.1/GLmom/man/pk.beta.stnary.Rd |only GLmom-1.3.1/GLmom/man/streamflow.Rd |only GLmom-1.3.1/GLmom/man/strup.glme.gev11.Rd |only GLmom-2.0.0/GLmom/DESCRIPTION | 14 GLmom-2.0.0/GLmom/MD5 | 106 +- GLmom-2.0.0/GLmom/NAMESPACE | 25 GLmom-2.0.0/GLmom/NEWS.md | 110 ++ GLmom-2.0.0/GLmom/R/GN16.gev11.R |only GLmom-2.0.0/GLmom/R/data.R | 67 - GLmom-2.0.0/GLmom/R/glme.gev.R | 633 ++++-------- GLmom-2.0.0/GLmom/R/glme.gev11.R | 1480 +++++++----------------------- GLmom-2.0.0/GLmom/R/lme.gev11.R |only GLmom-2.0.0/GLmom/R/magev.R | 6 GLmom-2.0.0/GLmom/R/magev_helpers.R | 61 + GLmom-2.0.0/GLmom/R/magev_plots.R | 16 GLmom-2.0.0/GLmom/R/methods.R |only GLmom-2.0.0/GLmom/R/nsgev.R | 70 - GLmom-2.0.0/GLmom/R/penalty.R |only GLmom-2.0.0/GLmom/R/ran.gev.R |only GLmom-2.0.0/GLmom/R/strup.gev11.R |only GLmom-2.0.0/GLmom/build/partial.rdb |binary GLmom-2.0.0/GLmom/man/Befun.Rd | 2 GLmom-2.0.0/GLmom/man/GLmom-methods.Rd |only GLmom-2.0.0/GLmom/man/GN16.gev11.Rd |only GLmom-2.0.0/GLmom/man/MS_pk.Rd | 4 GLmom-2.0.0/GLmom/man/PhliuAgromet.Rd | 14 GLmom-2.0.0/GLmom/man/boot.cov.Rd |only GLmom-2.0.0/GLmom/man/check.penalty.Rd |only GLmom-2.0.0/GLmom/man/find_max_beta.pk.Rd |only GLmom-2.0.0/GLmom/man/fun.lme.gev11.Rd |only GLmom-2.0.0/GLmom/man/gado.prop_11.Rd | 26 GLmom-2.0.0/GLmom/man/glme.gev.Rd | 72 + GLmom-2.0.0/GLmom/man/glme.gev11.Rd | 97 + GLmom-2.0.0/GLmom/man/glme.like.Rd | 16 GLmom-2.0.0/GLmom/man/gof.ene_all.Rd | 16 GLmom-2.0.0/GLmom/man/init.glme.Rd | 41 GLmom-2.0.0/GLmom/man/lme.gev11.Rd |only GLmom-2.0.0/GLmom/man/lmoms.md.park.Rd | 23 GLmom-2.0.0/GLmom/man/ma.gev.Rd | 4 GLmom-2.0.0/GLmom/man/magev.ksensplot.Rd | 4 GLmom-2.0.0/GLmom/man/magev.qqplot.Rd | 6 GLmom-2.0.0/GLmom/man/magev.rlplot.Rd | 6 GLmom-2.0.0/GLmom/man/make.qmax.gev11.Rd | 23 GLmom-2.0.0/GLmom/man/nllh.glme.gev11.Rd | 14 GLmom-2.0.0/GLmom/man/nsgev.Rd | 13 GLmom-2.0.0/GLmom/man/opt.glme.gev11.Rd |only GLmom-2.0.0/GLmom/man/pargev.kfix.Rd | 4 GLmom-2.0.0/GLmom/man/penalty.fun.Rd |only GLmom-2.0.0/GLmom/man/pk.beta.Rd |only GLmom-2.0.0/GLmom/man/pk.norm.stnary.Rd | 6 GLmom-2.0.0/GLmom/man/qns.gev11.Rd | 2 GLmom-2.0.0/GLmom/man/qns.gev_all.Rd | 2 GLmom-2.0.0/GLmom/man/quagev.NS.Rd | 5 GLmom-2.0.0/GLmom/man/ran.gev_all.Rd |only GLmom-2.0.0/GLmom/man/sel.para_all.Rd | 22 GLmom-2.0.0/GLmom/man/set.para.model.Rd | 2 GLmom-2.0.0/GLmom/man/strup.gev11.Rd |only GLmom-2.0.0/GLmom/man/time.m.gev11.Rd | 27 GLmom-2.0.0/GLmom/man/trans.gum01.Rd |only GLmom-2.0.0/GLmom/man/wls.gev11.Rd | 24 GLmom-2.0.0/GLmom/tests/test.R | 126 ++ 69 files changed, 1306 insertions(+), 1883 deletions(-)
Title: Automated Gene Identification for Post-GWAS and QTL Analysis
Description: Facilitates the post-Genome Wide Association Studies (GWAS) and Quantitative Trait Loci (QTL) analysis of identifying candidate genes within user-defined search window, based on the identified Single Nucleotide Polymorphisms (SNPs) as given by Mazumder AK (2024) <doi:10.1038/s41598-024-66903-3>. It supports candidate gene analysis for wheat and rice. Just import your GWAS result as explained in the sample_data file and the function does all the manual search and retrieve candidate genes for you, while exporting the results into ready-to-use output.
Author: Rajamani Nirmalaruban [aut, cre, cph],
R. Suvitha [aut],
Rajbir Yadav [aut],
Meda Alekya [aut],
Amit Kumar Mazumder [aut],
Thirumurugan Sathya [aut],
Subramani Sugumar [aut],
Prashanth babu [aut],
Manjeet Kumar [aut],
Kiran B Gaikwad [aut],
Naresh Ku [...truncated...]
Maintainer: Rajamani Nirmalaruban <nirmalaruban97@gmail.com>
Diff between geneNR versions 2.0.1 dated 2025-03-29 and 3.0.0 dated 2026-07-05
DESCRIPTION | 12 MD5 | 25 + NEWS.md | 9 R/geneQTL.R | 108 ++++++-- R/geneSNP.R | 172 +++++++------ R/geneSNPcustom.R | 174 +++++++------ inst/doc/geneNR_1.R | 122 +++++---- inst/doc/geneNR_1.Rmd | 332 ++++++++++---------------- inst/doc/geneNR_1.html | 531 ++++++++++++++++++++++++------------------ inst/extdata/sample_crop.gff3 |only man/geneQTL.Rd | 17 - man/geneSNP.Rd | 24 + man/geneSNPcustom.Rd | 19 + vignettes/geneNR_1.Rmd | 332 ++++++++++---------------- 14 files changed, 1012 insertions(+), 865 deletions(-)
Title: Psychometric Analysis with Rasch Measurement Theory
Description: Streamlines reproducible Rasch measurement theory analyses
for ordinal item-response data, combining estimation routines from
'eRm', 'psychotools', 'mirt', 'iarm', and 'lavaan' with consistent
diagnostic, plotting, and reporting layers. Covers the four basic
psychometric criteria summarised by Christensen et al. (2021)
<doi:10.1111/sms.13908> -- unidimensionality, local independence,
ordered response category thresholds, and invariance across
subgroups -- together with item fit, targeting, reliability,
category functioning, and descriptive item-response plots. A
distinguishing feature is the use of simulation-based critical
values to replace rule-of-thumb cutoffs for conditional infit mean-square,
Yen's Q3 local-dependence statistic, the largest residual-PCA eigenvalue,
ordinal CFA fit indices, and partial-gamma DIF and local-dependence
coefficients, optionally augmented with multiplicity-corrected bootstrap
p-values. Outputs are knitr::kable() tables and
'ggplot2' figures suitab [...truncated...]
Author: Magnus Johansson [aut, cre] ,
Nicklas Korsell [ctb] ,
Mirka Henninger [ctb] ,
Jan Radek [ctb]
Maintainer: Magnus Johansson <pgmj@pm.me>
Diff between easyRasch2 versions 0.8.0 dated 2026-06-08 and 1.0.0 dated 2026-07-05
easyRasch2-0.8.0/easyRasch2/man/RMitemInfitCutoffPlot.Rd |only easyRasch2-1.0.0/easyRasch2/DESCRIPTION | 21 easyRasch2-1.0.0/easyRasch2/MD5 | 227 - easyRasch2-1.0.0/easyRasch2/NAMESPACE | 5 easyRasch2-1.0.0/easyRasch2/NEWS.md | 241 + easyRasch2-1.0.0/easyRasch2/R/bootstrap_restscore.R | 294 + easyRasch2-1.0.0/easyRasch2/R/cfa_cutoff.R | 1568 +++++++--- easyRasch2-1.0.0/easyRasch2/R/cicc_plot.R | 524 ++- easyRasch2-1.0.0/easyRasch2/R/conditional_infit.R | 449 ++ easyRasch2-1.0.0/easyRasch2/R/conditional_infit_mi.R | 304 + easyRasch2-1.0.0/easyRasch2/R/data_plots.R | 316 +- easyRasch2-1.0.0/easyRasch2/R/dif_lr.R | 463 +- easyRasch2-1.0.0/easyRasch2/R/dif_partgam.R | 834 +++-- easyRasch2-1.0.0/easyRasch2/R/dif_tree.R | 1166 ++++--- easyRasch2-1.0.0/easyRasch2/R/infit_cutoff.R | 369 +- easyRasch2-1.0.0/easyRasch2/R/infit_cutoff_mi.R | 207 - easyRasch2-1.0.0/easyRasch2/R/infitcutoff_plot.R | 219 - easyRasch2-1.0.0/easyRasch2/R/item_cat_prob.R | 324 +- easyRasch2-1.0.0/easyRasch2/R/item_hierarchy.R | 217 - 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Title: Arbitrary Dimensional Clifford Algebras
Description: A suite of routines for Clifford algebras, using the
'Map' class of the Standard Template Library. Canonical
reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra
to geometric calculus"). Special cases including Lorentz transforms,
quaternion multiplication, and Grassmann algebra, are discussed.
Vignettes presenting conformal geometric algebra, quaternions and
split quaternions, dual numbers, and Lorentz transforms are
included. The package follows 'disordR' discipline.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between clifford versions 1.2-0 dated 2026-06-30 and 1.2-0-1 dated 2026-07-05
DESCRIPTION | 6 ++-- MD5 | 42 +++++++++++++++---------------- NEWS.md | 3 ++ build/partial.rdb |binary inst/doc/clifford.pdf |binary inst/doc/complex_clifford.html | 3 +- inst/doc/conformal_algebra_clifford.html | 3 +- inst/doc/cramer_clifford.html | 3 +- inst/doc/determinants_clifford.html | 3 +- inst/doc/dual_quaternion_clifford.R | 1 inst/doc/dual_quaternion_clifford.Rmd | 1 inst/doc/dual_quaternion_clifford.html | 5 ++- inst/doc/getcoeffs.html | 3 +- inst/doc/lorentz_clifford.html | 3 +- inst/doc/pauli_clifford.html | 3 +- inst/doc/pseudoscalar.html | 3 +- inst/doc/quaternion_clifford.R | 1 inst/doc/quaternion_clifford.Rmd | 1 inst/doc/quaternion_clifford.html | 5 ++- inst/doc/signature.html | 3 +- vignettes/dual_quaternion_clifford.Rmd | 1 vignettes/quaternion_clifford.Rmd | 1 22 files changed, 51 insertions(+), 43 deletions(-)
Title: Representation for Glycan Compositions and Structures
Description: Computational representations of glycan compositions and structures,
including details such as linkages, anomers, and substituents. Supports varying
levels of monosaccharide specificity (e.g., "Hex" or "Gal") and ambiguous linkages.
Provides robust parsing and generation of IUPAC-condensed structure strings.
Optimized for vectorized operations on glycan structures, with efficient handling
of duplications. As the cornerstone of the glycoverse ecosystem, this package
delivers the foundational data structures that power glycomics and glycoproteomics
analysis workflows.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyrepr versions 0.12.1 dated 2026-06-19 and 0.13.0 dated 2026-07-05
glyrepr-0.12.1/glyrepr/man/get_anomer_pos.Rd |only glyrepr-0.13.0/glyrepr/DESCRIPTION | 17 glyrepr-0.13.0/glyrepr/MD5 | 79 - glyrepr-0.13.0/glyrepr/NAMESPACE | 8 glyrepr-0.13.0/glyrepr/NEWS.md | 22 glyrepr-0.13.0/glyrepr/R/color-utils.R | 6 glyrepr-0.13.0/glyrepr/R/composition.R | 12 glyrepr-0.13.0/glyrepr/R/fill-anomer-pos.R | 2 glyrepr-0.13.0/glyrepr/R/iupac-to-structure.R | 61 - glyrepr-0.13.0/glyrepr/R/linkage.R | 5 glyrepr-0.13.0/glyrepr/R/monosaccharide.R | 31 glyrepr-0.13.0/glyrepr/R/smap.R | 505 ++-------- glyrepr-0.13.0/glyrepr/R/structure-level.R | 4 glyrepr-0.13.0/glyrepr/R/structure-tables.R |only glyrepr-0.13.0/glyrepr/R/structure.R | 189 ++- glyrepr-0.13.0/glyrepr/R/substituent.R | 94 + glyrepr-0.13.0/glyrepr/R/validate-helper.R | 50 glyrepr-0.13.0/glyrepr/inst/doc/glycan-graph.html | 6 glyrepr-0.13.0/glyrepr/inst/doc/glyrepr.html | 8 glyrepr-0.13.0/glyrepr/inst/doc/smap.R | 2 glyrepr-0.13.0/glyrepr/inst/doc/smap.Rmd | 2 glyrepr-0.13.0/glyrepr/inst/doc/smap.html | 18 glyrepr-0.13.0/glyrepr/man/get_structure_level.Rd | 4 glyrepr-0.13.0/glyrepr/man/glycan_structure.Rd | 16 glyrepr-0.13.0/glyrepr/man/glyrepr-package.Rd | 5 glyrepr-0.13.0/glyrepr/man/has_linkages.Rd | 2 glyrepr-0.13.0/glyrepr/man/infer_anomer_pos.Rd |only glyrepr-0.13.0/glyrepr/man/smap.Rd | 17 glyrepr-0.13.0/glyrepr/man/smap2.Rd | 18 glyrepr-0.13.0/glyrepr/man/smap_unique.Rd | 6 glyrepr-0.13.0/glyrepr/man/spmap.Rd | 18 glyrepr-0.13.0/glyrepr/man/structure_tables.Rd |only glyrepr-0.13.0/glyrepr/tests/testthat/test-color-substituents.R | 2 glyrepr-0.13.0/glyrepr/tests/testthat/test-composition.R | 28 glyrepr-0.13.0/glyrepr/tests/testthat/test-iupac-to-structure.R | 57 + glyrepr-0.13.0/glyrepr/tests/testthat/test-monosaccharide.R | 35 glyrepr-0.13.0/glyrepr/tests/testthat/test-smap.R | 119 -- glyrepr-0.13.0/glyrepr/tests/testthat/test-structure-level.R | 5 glyrepr-0.13.0/glyrepr/tests/testthat/test-structure-tables.R |only glyrepr-0.13.0/glyrepr/tests/testthat/test-structure.R | 54 + glyrepr-0.13.0/glyrepr/tests/testthat/test-substituent.R | 11 glyrepr-0.13.0/glyrepr/tests/testthat/test-validate-helper.R | 14 glyrepr-0.13.0/glyrepr/vignettes/smap.Rmd | 2 43 files changed, 811 insertions(+), 723 deletions(-)
Title: Geometric Morphometric Analyses of 2D and 3D Landmark Data
Description: Read and manipulate landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams [aut, cre],
Michael Collyer [aut],
Antigoni Kaliontzopoulou [aut],
Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 4.1.0 dated 2026-03-14 and 4.1.1 dated 2026-07-05
DESCRIPTION | 6 - MD5 | 35 +++++----- NEWS.md | 11 +++ R/compare.CR.R | 2 R/compare.physign.z.r | 2 R/compare.pls.r | 13 +++ R/geomorph.support.code.r | 2 R/geomorph.utils.r | 2 R/integration.test.r | 34 +++++++-- R/phylo.integration.r | 37 ++++++++-- R/physignal.z.r | 7 +- R/plotAllSpecimens.r | 1 R/plotOutliers.r | 2 R/shared.support.code.R | 160 ++++------------------------------------------ R/two.b.pls.r | 2 README.md | 2 man/integration.test.Rd | 13 +++ man/phylo.integration.Rd | 12 ++- tests/testthat/Rplots.pdf |only 19 files changed, 147 insertions(+), 196 deletions(-)
Title: Convenience Functions for Arrays
Description: Some convenient functions to work with arrays.
Author: Claudia Beleites [aut, cre]
Maintainer: Claudia Beleites <Claudia.Beleites@chemometrix.eu>
Diff between arrayhelpers versions 1.1-0 dated 2020-02-04 and 1.1-1 dated 2026-07-05
arrayhelpers-1.1-0/arrayhelpers/tests/tests.R |only arrayhelpers-1.1-1/arrayhelpers/DESCRIPTION | 29 +++++++----- arrayhelpers-1.1-1/arrayhelpers/MD5 | 16 +++--- arrayhelpers-1.1-1/arrayhelpers/R/apply.R | 2 arrayhelpers-1.1-1/arrayhelpers/R/arrayhelpers-package.R |only arrayhelpers-1.1-1/arrayhelpers/R/arrayhelpers.R | 9 --- arrayhelpers-1.1-1/arrayhelpers/man/arrayhelpers-package.Rd | 24 +++++++-- arrayhelpers-1.1-1/arrayhelpers/man/ensuredim.Rd | 2 arrayhelpers-1.1-1/arrayhelpers/man/makeNd.Rd | 2 arrayhelpers-1.1-1/arrayhelpers/tests/testthat |only arrayhelpers-1.1-1/arrayhelpers/tests/testthat.R |only 11 files changed, 46 insertions(+), 38 deletions(-)
Title: Statistical Tools for Immune Correlates Analysis of Vaccine
Clinical Trial Data
Description: Various semiparametric and nonparametric statistical tools for
immune correlates analysis of vaccine clinical trial data. This includes
calculation of summary statistics and estimation of risk, vaccine efficacy,
controlled effects (controlled risk and controlled vaccine efficacy), and
mediation effects (natural direct effect, natural indirect effect,
proportion mediated). See Gilbert P, Fong Y, Kenny A, and Carone, M (2022)
<doi:10.1093/biostatistics/kxac024> and Fay MP and Follmann DA (2023)
<doi:10.48550/arXiv.2208.06465>.
Author: Avi Kenny [aut, cre]
Maintainer: Avi Kenny <avi.kenny@gmail.com>
Diff between vaccine versions 1.3.1 dated 2025-09-07 and 1.4.0 dated 2026-07-05
DESCRIPTION | 8 +- MD5 | 23 +++-- NAMESPACE | 1 NEWS.md | 13 +++ R/est_cox.R | 153 ++++++++++++++++++++++++++++++++------ R/est_med.R | 198 +++++++++++++++++++++++++++++++++----------------- R/est_np.R | 16 ++-- R/est_overall.R | 40 ++++++++-- R/params.R | 31 +++++++ R/zzz.R | 5 + inst/doc/vaccine.html | 15 ++- man/est_med.Rd | 5 + man/params_med_cox.Rd |only 13 files changed, 384 insertions(+), 124 deletions(-)
Title: Extreme Value Modeling for r-Largest Order Statistics
Description: Tools for extreme value modeling based on the r-largest
order statistics framework. The package provides functions for
parameter estimation via maximum likelihood, return level
estimation with standard errors, profile likelihood-based
confidence intervals, random sample generation, and entropy
difference tests for selecting the number of order statistics r.
Several r-largest order statistics models are implemented,
including the four-parameter kappa (rK4D), generalized logistic
(rGLO), generalized Gumbel (rGGD), logistic (rLD), and Gumbel
(rGD) distributions. The rK4D methodology is described in
Shin et al. (2022) <doi:10.1016/j.wace.2022.100533>, the rGLO
model in Shin and Park (2024) <doi:10.1007/s00477-023-02642-7>,
and the rGGD model in Shin and Park (2025)
<doi:10.1038/s41598-024-83273-y>. The underlying distributions
are related to the kappa distribution of Hosking (1994)
<doi:10.1017/CBO9780511529443>, the generalized logistic
distribution discussed by Ah [...truncated...]
Author: Yire Shin [aut, cre] ,
Jeong-Soo Park [aut, ths]
Maintainer: Yire Shin <shinyire87@gmail.com>
Diff between evmr versions 0.1.0 dated 2026-03-29 and 0.2.0 dated 2026-07-05
evmr-0.1.0/evmr/R/bevern.R |only evmr-0.1.0/evmr/R/oykel.R |only evmr-0.1.0/evmr/data/bevern.rda |only evmr-0.1.0/evmr/data/oykel.rda |only evmr-0.1.0/evmr/man/bevern.Rd |only evmr-0.1.0/evmr/man/oykel.Rd |only evmr-0.2.0/evmr/DESCRIPTION | 8 evmr-0.2.0/evmr/MD5 | 181 ++--- evmr-0.2.0/evmr/NAMESPACE | 84 +- evmr-0.2.0/evmr/NEWS.md |only evmr-0.2.0/evmr/R/bangkok.R | 66 +- evmr-0.2.0/evmr/R/evmr.R | 205 +++--- evmr-0.2.0/evmr/R/qgd.R | 110 +-- evmr-0.2.0/evmr/R/qggd.R | 178 ++--- evmr-0.2.0/evmr/R/qglo.R | 180 ++--- evmr-0.2.0/evmr/R/qk4d.R | 250 +++---- evmr-0.2.0/evmr/R/qld.R | 120 +-- evmr-0.2.0/evmr/R/rgd.fit.R | 470 +++++++------- evmr-0.2.0/evmr/R/rgd.prof.R | 329 +++++----- evmr-0.2.0/evmr/R/rgd.rl.R | 155 ++-- evmr-0.2.0/evmr/R/rgd.summary.R | 224 +++--- evmr-0.2.0/evmr/R/rgdr.R | 144 ++-- evmr-0.2.0/evmr/R/rggd.fit.R | 648 ++++++++++---------- evmr-0.2.0/evmr/R/rggd.prof.R | 483 +++++++-------- evmr-0.2.0/evmr/R/rggd.rl.R | 183 ++--- evmr-0.2.0/evmr/R/rggd.summary.R | 232 +++---- evmr-0.2.0/evmr/R/rggdEd.R | 278 ++++---- evmr-0.2.0/evmr/R/rggdEdtest.R | 204 +++--- evmr-0.2.0/evmr/R/rggdLh.R | 195 ++---- evmr-0.2.0/evmr/R/rggdr.R | 220 +++--- evmr-0.2.0/evmr/R/rglo.fit.R | 757 +++++++++++------------ evmr-0.2.0/evmr/R/rglo.prof.R | 513 +++++++-------- evmr-0.2.0/evmr/R/rglo.rl.R | 200 ++---- evmr-0.2.0/evmr/R/rglo.summary.R | 294 ++++----- evmr-0.2.0/evmr/R/rgloEd.R | 216 +++--- evmr-0.2.0/evmr/R/rgloEdtest.R | 223 +++--- evmr-0.2.0/evmr/R/rgloLh.R | 195 ++---- evmr-0.2.0/evmr/R/rglor.R | 224 +++--- evmr-0.2.0/evmr/R/rk4d.fit.R | 932 ++++++++++++++--------------- evmr-0.2.0/evmr/R/rk4d.prof.R | 517 +++++++--------- evmr-0.2.0/evmr/R/rk4d.rl.R | 222 +++--- evmr-0.2.0/evmr/R/rk4d.summary.R | 327 ++++------ evmr-0.2.0/evmr/R/rk4dEd.R | 260 ++++---- evmr-0.2.0/evmr/R/rk4dEdtest.R | 210 +++--- evmr-0.2.0/evmr/R/rk4dLh.R | 202 ++---- evmr-0.2.0/evmr/R/rk4dr.R | 250 +++---- evmr-0.2.0/evmr/R/rld.fit.R | 653 ++++++++++---------- evmr-0.2.0/evmr/R/rld.prof.R | 460 +++++++------- evmr-0.2.0/evmr/R/rld.rl.R | 185 ++--- evmr-0.2.0/evmr/R/rld.summary.R | 282 ++++---- evmr-0.2.0/evmr/R/rldr.R | 201 ++---- evmr-0.2.0/evmr/build/partial.rdb |binary evmr-0.2.0/evmr/man/bangkok.Rd | 86 +- evmr-0.2.0/evmr/man/evmr.Rd | 63 - evmr-0.2.0/evmr/man/qgd.Rd | 64 - evmr-0.2.0/evmr/man/qggd.Rd | 88 +- evmr-0.2.0/evmr/man/qglo.Rd | 86 +- evmr-0.2.0/evmr/man/qk4d.Rd | 102 +-- evmr-0.2.0/evmr/man/qld.Rd | 64 - evmr-0.2.0/evmr/man/rgd.fit.Rd | 202 +++--- evmr-0.2.0/evmr/man/rgd.prof.Rd | 94 +- evmr-0.2.0/evmr/man/rgd.rl.Rd | 86 +- evmr-0.2.0/evmr/man/rgd.summary.Rd | 150 ++-- evmr-0.2.0/evmr/man/rgdr.Rd | 78 +- evmr-0.2.0/evmr/man/rggd.fit.Rd | 198 +++--- evmr-0.2.0/evmr/man/rggd.prof.Rd | 110 +-- evmr-0.2.0/evmr/man/rggd.rl.Rd | 86 +- evmr-0.2.0/evmr/man/rggd.summary.Rd | 158 ++-- evmr-0.2.0/evmr/man/rggdEd.Rd | 108 +-- evmr-0.2.0/evmr/man/rggdEdtest.Rd | 134 ++-- evmr-0.2.0/evmr/man/rggdLh.Rd | 81 +- evmr-0.2.0/evmr/man/rggdr.Rd | 92 +- evmr-0.2.0/evmr/man/rglo.fit.Rd | 215 +++--- evmr-0.2.0/evmr/man/rglo.prof.Rd | 114 +-- evmr-0.2.0/evmr/man/rglo.rl.Rd | 108 +-- evmr-0.2.0/evmr/man/rglo.summary.Rd | 175 ++--- evmr-0.2.0/evmr/man/rgloEd.Rd | 122 +-- evmr-0.2.0/evmr/man/rgloEdtest.Rd | 142 ++-- evmr-0.2.0/evmr/man/rgloLh.Rd | 83 -- evmr-0.2.0/evmr/man/rglor.Rd | 107 +-- evmr-0.2.0/evmr/man/rk4d.fit.Rd | 258 ++++---- evmr-0.2.0/evmr/man/rk4d.prof.Rd | 113 +-- evmr-0.2.0/evmr/man/rk4d.rl.Rd | 112 +-- evmr-0.2.0/evmr/man/rk4d.summary.Rd | 204 ++---- evmr-0.2.0/evmr/man/rk4dEd.Rd | 116 +-- evmr-0.2.0/evmr/man/rk4dEdtest.Rd | 139 +--- evmr-0.2.0/evmr/man/rk4dLh.Rd | 73 -- evmr-0.2.0/evmr/man/rk4dr.Rd | 122 +-- evmr-0.2.0/evmr/man/rld.fit.Rd | 202 +++--- evmr-0.2.0/evmr/man/rld.prof.Rd | 108 +-- evmr-0.2.0/evmr/man/rld.rl.Rd | 101 +-- evmr-0.2.0/evmr/man/rld.summary.Rd | 163 ++--- evmr-0.2.0/evmr/man/rldr.Rd | 95 +- evmr-0.2.0/evmr/tests/testthat.R | 24 evmr-0.2.0/evmr/tests/testthat/test-evmr.R | 320 ++++----- 95 files changed, 8676 insertions(+), 9140 deletions(-)
Title: Subset and Flag Data Frames with Times by the Use of Periods
Description: Data frames with time information are subset and flagged with period information. Data frames with times are dealt as timeDF objects and periods are represented as periodDF objects.
Author: Toshihiro Umehara [aut, cre]
Maintainer: Toshihiro Umehara <toshi@niceume.com>
Diff between timeDF versions 0.9.1 dated 2024-04-28 and 0.9.2 dated 2026-07-05
DESCRIPTION | 10 ++++----- MD5 | 28 +++++++++++++-------------- R/condense_periodDF.R | 5 ++++ R/examine_with_date_periods.R | 13 ++++++------ R/examine_with_time_periods.R | 13 ++++++------ R/examine_with_time_periods_within_a_day.R | 11 +++++----- R/extract_with_periodDF.R | 28 ++++++++++++++++++--------- R/flag_with_periodDF.R | 16 ++++++++++++--- R/listTimeDF.R | 2 - README.md | 8 +++---- build/partial.rdb |binary inst/unit_tests/test_extract_with_periodDF.R | 6 ++--- inst/unit_tests/test_flag_with_periodDF.R | 4 +-- man/extract_with_periodDF.Rd | 5 ++-- man/flag_with_periodDF.Rd | 5 ++-- 15 files changed, 92 insertions(+), 62 deletions(-)
Title: Minimalist Theme and Vignette Kit for 'pkgdown' and R Markdown
Description: Provides a minimalist 'ggplot2' theme, colour scales, and
'pkgdown' template built around a curated colour palette system
inspired by Josef Albers' colour theory
(Albers (1963, ISBN:978-0-300-17935-4) "Interaction of Color").
Includes helpers to apply consistent theming to 'ggplot2' plots, 'gt'
tables, and 'bslib' Bootstrap 5 sites, along with one-command setup
functions for adopting the style across an R package.
Author: Bradley R. Buchsbaum [aut, cre]
Maintainer: Bradley R. Buchsbaum <brad.buchsbaum@gmail.com>
Diff between albersdown versions 1.0.0 dated 2026-04-01 and 2.0.0 dated 2026-07-05
DESCRIPTION | 8 MD5 | 133 NAMESPACE | 1 R/bs_theme.R | 27 R/gt_albers.R | 4 R/migrate_albersdown.R | 2 R/register_fonts.R |only R/theme_albers.R | 53 R/use_albers.R | 10 R/use_albersdown.R | 470 ++ build/vignette.rds |binary inst/doc/design-notes.R | 32 inst/doc/design-notes.Rmd | 49 inst/doc/design-notes.html | 1755 ++++++++- inst/doc/getting-started.R | 31 inst/doc/getting-started.Rmd | 48 inst/doc/getting-started.html | 1751 ++++++++- inst/doc/interaction.R |only inst/doc/interaction.Rmd |only inst/doc/interaction.html |only inst/doc/proof-ochre-structural.R |only inst/doc/proof-ochre-structural.Rmd |only inst/doc/proof-ochre-structural.html |only inst/doc/proof-teal-study.R |only inst/doc/proof-teal-study.Rmd |only inst/doc/proof-teal-study.html |only inst/doc/theme-lab.R | 42 inst/doc/theme-lab.Rmd | 167 inst/doc/theme-lab.html | 1891 ++++++++- inst/doc/theme-showcase.R | 97 inst/doc/theme-showcase.Rmd | 160 inst/doc/theme-showcase.html | 1934 ++++++++-- inst/fonts |only inst/pkgdown/assets/albers.css | 429 +- inst/pkgdown/assets/albers.js | 2 inst/pkgdown/assets/fonts |only inst/rmarkdown/templates/albers_vignette/skeleton/albers-header.html |only inst/rmarkdown/templates/albers_vignette/skeleton/albers.css | 429 +- inst/rmarkdown/templates/albers_vignette/skeleton/fonts |only inst/rmarkdown/templates/albers_vignette/skeleton/skeleton.Rmd | 33 man/albers_bs_theme.Rd | 2 man/albers_presets.Rd | 12 man/albers_register_fonts.Rd |only man/dot-albers_direction_font.Rd |only man/dot-albers_font_available.Rd |only man/dot-preset_colors.Rd | 6 man/gt_albers.Rd | 2 man/migrate_albersdown.Rd | 2 man/theme_albers.Rd | 15 man/theme_albers_void.Rd | 15 man/use_albers_vignettes.Rd | 8 man/use_albersdown.Rd | 12 tests/testthat/test-migrate-albersdown.R | 408 ++ vignettes/albers-header.html |only vignettes/albers.css | 429 +- vignettes/albers.js | 33 vignettes/design-notes.Rmd | 49 vignettes/fonts |only vignettes/getting-started.Rmd | 48 vignettes/interaction.Rmd |only vignettes/proof-ochre-structural.Rmd |only vignettes/proof-teal-study.Rmd |only vignettes/theme-lab.Rmd | 167 vignettes/theme-showcase.Rmd | 160 64 files changed, 9386 insertions(+), 1540 deletions(-)
Title: Detect Population Structure Within Phylogenetic Trees
Description: Algorithms for detecting population structure from the history of
coalescent events recorded in phylogenetic trees. This method classifies each
tip and internal node of a tree into disjoint sets characterized by similar
coalescent patterns.
Author: Erik Volz [aut, cre] ,
Fabricia F. Nascimento [ctb] ,
Vinicius B. Franceschi [ctb]
Maintainer: Erik Volz <erik.volz@gmail.com>
Diff between treestructure versions 0.7.0 dated 2025-09-27 and 1.0.1 dated 2026-07-05
DESCRIPTION | 15 - MD5 | 56 +++--- NEWS.md |only R/RcppExports.R | 4 R/m13.R | 262 ++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/false_discovery_rate.R |only inst/doc/false_discovery_rate.Rmd |only inst/doc/false_discovery_rate.html |only inst/doc/supportValues.R | 86 +++++---- inst/doc/supportValues.Rmd | 169 ++++++++++--------- inst/doc/supportValues.html | 302 +++++++++++++++++++--------------- inst/doc/treestructure.R | 24 +- inst/doc/treestructure.Rmd | 129 +++++++++----- inst/doc/treestructure.html | 306 ++++++++++++++++++++++------------- inst/doc/updating_treestructure.Rmd | 5 inst/doc/updating_treestructure.html | 78 +++++--- inst/trestruct_chindex.rds |binary inst/trestruct_res.rds |binary inst/trestruct_res_nobt.rds |binary inst/trestruct_res_nobt_mcs20.rds |only inst/vignette_fwer.rds |only inst/vignette_hetero.rds |only man/treestructure.test.Rd | 10 - man/trestruct.Rd | 75 +++++++- src/RcppExports.cpp | 13 + src/uv_ranksum_moments.cpp |only src/uv_ranksum_nulldist0.cpp | 60 +++--- tests |only vignettes/false_discovery_rate.Rmd |only vignettes/supportValues.Rmd | 169 ++++++++++--------- vignettes/treestructure.Rmd | 129 +++++++++----- vignettes/updating_treestructure.Rmd | 5 33 files changed, 1217 insertions(+), 680 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features like
the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
mikefc [cph] ,
Yann Collet [cph] ,
Posit, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between rlang versions 1.2.0 dated 2026-04-06 and 1.3.0 dated 2026-07-05
DESCRIPTION | 43 MD5 | 345 ++-- NEWS.md | 10 R/hash.R | 31 R/nse-inject.R | 3 R/utils.R | 3 man/abort.Rd | 2 man/are_na.Rd | 2 man/as_name.Rd | 4 man/as_string.Rd | 2 man/box.Rd | 2 man/call2.Rd | 2 man/check_data_frame.Rd | 4 man/check_dots_empty.Rd | 6 man/check_dots_unnamed.Rd | 6 man/check_dots_used.Rd | 6 man/check_type_number.Rd | 6 man/check_type_scalar.Rd | 6 man/cnd_muffle.Rd | 8 man/defusing-advanced.Rd | 2 man/dot-data.Rd | 2 man/englue.Rd | 3 man/env_bind.Rd | 2 man/env_get.Rd | 2 man/hash.Rd | 29 man/inherits_any.Rd | 2 man/is_function.Rd | 2 man/is_integerish.Rd | 2 man/missing.Rd | 13 man/names_inform_repair.Rd | 2 man/new_function.Rd | 2 man/new_node.Rd | 2 man/ns_env.Rd | 2 man/return_from.Rd | 2 man/rlang-package.Rd | 1 man/splice-operator.Rd | 4 man/stop_input_type.Rd | 4 man/switch_type.Rd | 2 man/topic-condition-formatting.Rd | 2 man/try_fetch.Rd | 2 man/vector-coercion.Rd | 2 man/with_env.Rd | 2 src/capture.c | 27 src/internal/arg.c | 505 +++--- src/internal/ast-rotate.c | 478 ++--- src/internal/ast-rotate.h | 50 src/internal/attr.c | 404 ++-- src/internal/call.c | 425 ++--- src/internal/call.h | 1 src/internal/cnd-handlers.c | 145 - src/internal/cnd.c | 381 ++-- src/internal/decl/arg-decl.h | 20 src/internal/decl/ast-rotate-decl.h | 26 src/internal/decl/attr-decl.h | 36 src/internal/decl/call-decl.h | 27 src/internal/decl/cnd-decl.h | 22 src/internal/decl/cnd-handlers-decl.h | 3 src/internal/decl/dots-decl.h | 29 src/internal/decl/encoding-decl.h | 18 src/internal/decl/env-binding-decl.h | 13 src/internal/decl/hash-decl.h | 10 src/internal/decl/names-decl.h | 21 src/internal/decl/standalone-types-check-decl.h | 30 src/internal/decl/vec-decl.h | 14 src/internal/dots-ellipsis.c | 60 src/internal/dots.c | 2003 ++++++++++++------------ src/internal/dots.h | 51 src/internal/encoding.c | 219 +- src/internal/env-binding.c | 599 +++---- src/internal/env.c | 89 - src/internal/eval-tidy.c | 906 +++++----- src/internal/eval.c | 35 src/internal/exported.c | 1239 +++++++------- src/internal/file.c | 46 src/internal/fn.c | 40 src/internal/globals.c | 2 src/internal/globals.h | 4 src/internal/hash.c | 584 ++++-- src/internal/internal.c | 769 +++++---- src/internal/internal.h | 45 src/internal/names.c | 320 +-- src/internal/nse-defuse.c | 11 src/internal/nse-inject.c | 630 +++---- src/internal/nse-inject.h | 80 src/internal/parse.c | 969 ++++++----- src/internal/parse.h | 130 - src/internal/quo.c | 109 - src/internal/quo.h | 7 src/internal/replace-na.c | 400 ++-- src/internal/squash.c | 551 +++--- src/internal/squash.h | 9 src/internal/standalone-types-check.c | 327 +-- src/internal/sym-unescape.c | 274 +-- src/internal/tests.c | 151 - src/internal/utils.c | 338 ++-- src/internal/utils.h | 29 src/internal/vec-raw.c | 83 src/internal/vec.c | 343 ++-- src/internal/vec.h | 36 src/internal/weakref.c | 33 src/rlang/arg.c | 14 src/rlang/arg.h | 11 src/rlang/attrib.c | 56 src/rlang/attrib.h | 54 src/rlang/c-utils.c | 42 src/rlang/c-utils.h | 220 +- src/rlang/call.c | 87 - src/rlang/call.h | 2 src/rlang/cnd.c | 225 +- src/rlang/cnd.h | 90 - src/rlang/debug.c | 29 src/rlang/debug.h | 1 src/rlang/decl/df-decl.h | 6 src/rlang/decl/dict-decl.h | 27 src/rlang/decl/dyn-list-of-decl.h | 10 src/rlang/decl/env-decl.h | 27 src/rlang/decl/obj-decl.h | 12 src/rlang/decl/walk-decl.h | 65 src/rlang/df.c | 86 - src/rlang/df.h | 12 src/rlang/dict.c | 462 ++--- src/rlang/dict.h | 37 src/rlang/dots-info.c | 36 src/rlang/dyn-array.c | 193 +- src/rlang/dyn-array.h | 344 ++-- src/rlang/dyn-list-of.c | 398 ++-- src/rlang/dyn-list-of.h | 86 - src/rlang/env-binding.c | 377 ++-- src/rlang/env-binding.h | 29 src/rlang/env.c | 398 ++-- src/rlang/env.h | 98 - src/rlang/eval.c | 265 +-- src/rlang/eval.h | 370 ++-- src/rlang/export.c | 12 src/rlang/export.h | 19 src/rlang/fn.c | 48 src/rlang/fn.h | 75 src/rlang/formula.c | 137 - src/rlang/formula.h | 1 src/rlang/globals.c | 158 - src/rlang/globals.h | 141 - src/rlang/node.c | 104 - src/rlang/node.h | 118 - src/rlang/obj.c | 198 +- src/rlang/obj.h | 138 - src/rlang/parse.c | 39 src/rlang/parse.h | 1 src/rlang/quo.c | 12 src/rlang/quo.h | 1 src/rlang/rlang-types.h | 210 +- src/rlang/rlang.c | 146 - src/rlang/rlang.h | 22 src/rlang/session.c | 84 - src/rlang/session.h | 1 src/rlang/stack.c | 113 - src/rlang/stack.h | 6 src/rlang/state.h | 19 src/rlang/sym.c | 69 src/rlang/sym.h | 16 src/rlang/vec-chr.c | 102 - src/rlang/vec-chr.h | 47 src/rlang/vec-lgl.c | 163 - src/rlang/vec-lgl.h | 2 src/rlang/vec.c | 457 ++--- src/rlang/vec.h | 844 ++++------ src/rlang/vendor.c | 3 src/rlang/vendor.h | 2 src/rlang/walk.c | 835 +++++----- src/rlang/walk.h | 186 +- src/version.c | 4 tests/testthat/_snaps/c-api.md | 4 tests/testthat/_snaps/hash.md |only tests/testthat/test-env-binding.R | 15 tests/testthat/test-hash.R | 314 +++ 174 files changed, 12303 insertions(+), 11517 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
JJ Allaire [aut] ,
Kevin Ushey [aut] ,
Qiang Kou [aut] ,
Nathan Russell [aut],
Inaki Ucar [aut] ,
Doug Bates [aut] ,
John Chambers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.1.1-1.1 dated 2026-04-24 and 1.1.2 dated 2026-07-05
ChangeLog | 243 +++++++++- DESCRIPTION | 9 MD5 | 122 ++--- R/Attributes.R | 20 R/RcppLdpath.R | 6 README.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 64 ++ inst/bib/Rcpp.bib | 69 +- inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-jss-2011.pdf |binary inst/doc/Rcpp-libraries.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/include/Rcpp/DataFrame.h | 9 inst/include/Rcpp/Environment.h | 5 inst/include/Rcpp/Function.h | 13 inst/include/Rcpp/Nullable.h | 19 inst/include/Rcpp/Promise.h | 3 inst/include/Rcpp/api/meat/Rcpp_eval.h | 2 inst/include/Rcpp/config.h | 11 inst/include/Rcpp/date_datetime/Datetime.h | 7 inst/include/Rcpp/exceptions.h | 13 inst/include/Rcpp/exceptions_impl.h | 34 + inst/include/Rcpp/internal/r_vector.h | 18 inst/include/Rcpp/proxy/AttributeProxy.h | 18 inst/include/Rcpp/proxy/NamesProxy.h | 23 inst/include/Rcpp/sugar/functions/cumprod.h | 13 inst/include/Rcpp/sugar/functions/cumsum.h | 5 inst/include/Rcpp/sugar/functions/diff.h | 11 inst/include/Rcpp/sugar/functions/max.h | 15 inst/include/Rcpp/sugar/functions/min.h | 15 inst/include/Rcpp/sugar/functions/rowSums.h | 184 ++----- inst/include/Rcpp/sugar/functions/sum.h | 7 inst/include/Rcpp/sugar/operators/Comparator_With_One_Value.h | 5 inst/include/Rcpp/sugar/operators/minus.h | 21 inst/include/Rcpp/sugar/operators/plus.h | 20 inst/include/Rcpp/sugar/operators/times.h | 19 inst/include/Rcpp/sugar/sugar.h | 4 inst/include/Rcpp/sugar/tools/safe_math.h |only inst/include/Rcpp/vector/ListOf.h | 9 inst/include/Rcpp/vector/Vector.h | 15 inst/tinytest/cpp/ListOf.cpp | 10 inst/tinytest/cpp/Vector.cpp | 16 inst/tinytest/cpp/attributes_extended.cpp |only inst/tinytest/cpp/sugar.cpp | 92 +++ inst/tinytest/cpp/sugar_safe_math.cpp |only inst/tinytest/cpp/sugar_safe_math_fallback.cpp |only inst/tinytest/test_attributes_extended.R |only inst/tinytest/test_compile_attributes_errors.R |only inst/tinytest/test_cppfunction_errors.R |only inst/tinytest/test_dataframe.R | 10 inst/tinytest/test_global_rostream.R | 2 inst/tinytest/test_listof.R | 12 inst/tinytest/test_misc.R | 2 inst/tinytest/test_sourcecpp_errors.R |only inst/tinytest/test_sugar.R | 88 +++ inst/tinytest/test_vector.R | 13 src/attributes.cpp | 16 tests/tinytest.R | 3 66 files changed, 899 insertions(+), 424 deletions(-)
Title: Calculates Bond Values and Interest Rate Curves for Finance
Description: Values different types of assets and calibrates discount curves
for quantitative financial analysis. It covers fixed coupon assets,
floating note assets, interest and cross currency swaps with different
payment frequencies. Enables the calibration of spot, instantaneous forward
and basis curves, making it a powerful tool for accurate and flexible bond
valuation and curve generation. The valuation and calibration techniques
presented here are consistent with industry standards and incorporates
author's own calculations. Tuckman, B., Serrat, A. (2022, ISBN: 978-1-119-83555-4).
Author: Camilo Diaz [aut, cre, com],
Andres Galeano [aut],
Julian Rojas [aut],
Quantil S.A.S [aut, cph]
Maintainer: Camilo Diaz <kamodiaz@gmail.com>
This is a re-admission after prior archival of version 0.3.2 dated 2025-07-06
Diff between QuantBondCurves versions 0.3.2 dated 2025-07-06 and 0.3.3 dated 2026-07-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/bondValuation.R | 6 +++--- man/valuation.bonds.Rd | 4 ++-- man/valuation.swaps.Rd | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
More information about QuantBondCurves at CRAN
Permanent link
Title: Draws Overview of Outliers (O3) Plots
Description: Potential outliers are identified for all combinations of a dataset's variables. O3 plots are described in Unwin(2019) <doi:10.1080/10618600.2019.1575226>. The available methods are FastPCS() from the package 'FastPCS', mvBACON() from 'robustX', adjOutlyingness() from 'robustbase', DectectDeviatingCells() from 'cellWise', covMcd() from 'robustbase'.
Author: Antony Unwin [aut, cre, cph]
Maintainer: Antony Unwin <unwin@math.uni-augsburg.de>
Diff between OutliersO3 versions 0.6.3 dated 2020-04-24 and 0.7 dated 2026-07-05
DESCRIPTION | 19 - MD5 | 67 +++-- NAMESPACE | 2 NEWS | 4 NEWS.md |only R/O3a.R | 23 -- R/O3plotM.R | 9 R/O3plotT.R | 8 R/O3prep.R | 11 README.md | 13 - build/vignette.rds |binary inst/doc/DrawingO3plots.R | 8 inst/doc/DrawingO3plots.Rmd | 34 +-- inst/doc/DrawingO3plots.html | 350 ++++++++++++++++++++----------- inst/doc/MultTolLevels.R | 15 - inst/doc/MultTolLevels.Rmd | 27 -- inst/doc/MultTolLevels.html | 311 ++++++++++++++++----------- inst/doc/PCPsO3.R | 9 inst/doc/PCPsO3.Rmd | 13 - inst/doc/PCPsO3.html | 276 ++++++++++++++---------- inst/doc/xtraO3methods.R | 2 inst/doc/xtraO3methods.Rmd | 6 inst/doc/xtraO3methods.html | 238 +++++++++++++-------- man/Election2005.Rd | 2 man/O3plotColours.Rd | 2 man/O3plotM.Rd | 6 man/O3plotT.Rd | 2 man/O3prep.Rd | 17 - man/OutliersO3.Rd | 6 man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary vignettes/DrawingO3plots.Rmd | 34 +-- vignettes/MultTolLevels.Rmd | 27 -- vignettes/PCPsO3.Rmd | 13 - vignettes/xtraO3methods.Rmd | 6 35 files changed, 905 insertions(+), 655 deletions(-)
Title: Lag Penalized Weighted Correlation for Time Series Clustering
Description: Computes a time series distance measure for clustering based on weighted correlation and introduction of lags. The lags capture delayed responses in a time series dataset. The timepoints must be specified. T. Chandereng, A. Gitter (2020) <doi:10.1186/s12859-019-3324-1>.
Author: Thevaa Chandereng [aut, cre, cph] ,
Anthony Gitter [aut, cph]
Maintainer: Thevaa Chandereng <thevaasiinen@gmail.com>
This is a re-admission after prior archival of version 1.0.0 dated 2020-01-23
Diff between LPWC versions 1.0.0 dated 2020-01-23 and 1.0.1 dated 2026-07-05
DESCRIPTION | 17 +++--- MD5 | 14 ++--- NEWS.md | 8 +++ README.md | 4 - build/vignette.rds |binary inst/CITATION | 2 inst/doc/LPWC.R | 140 ++++++++++++++++++++++++++--------------------------- inst/doc/LPWC.html | 130 +++++++++++++++++++++++++++++-------------------- 8 files changed, 176 insertions(+), 139 deletions(-)
Title: Bridging Log-Odds Ratios and Correspondence Analysis via
Closeness-of-Concordance Measures
Description: Provides a unified analytical workflow that bridges conventional
binary and multinomial logistic regression with singly-ordered (SONSCA)
and doubly-ordered (DONSCA) nonsymmetric correspondence analysis.
Log-odds ratios (LORs) from logistic regression are re-expressed as
cosine theta estimates and closeness-of-concordance measures (CCMs) --
including Yule's Q, Yule's Y, and r_meta -- on the familiar [-1, +1]
scale introduced by Kim and Grochowalski (2019)
<doi:10.1007/s00357-018-9277-7>. Bootstrap confidence intervals for
cosine theta are provided throughout. The package is intended to help
clinical and medical researchers interpret association strength from
logistic regression in an intuitive, correlation-like metric, and to
connect conventional regression results with geometric correspondence
analysis visualisations.
Author: Se-Kang Kim [aut, cre]
Maintainer: Se-Kang Kim <se-kang.kim@bcm.edu>
Diff between lorbridge versions 0.1.0 dated 2026-04-21 and 0.1.1 dated 2026-07-05
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.html | 4 ++-- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Draw Gene Arrow Maps in 'ggplot2'
Description: A 'ggplot2' extension for drawing gene arrow maps.
Author: David Wilkins [aut, cre],
Zachary Kurtz [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between gggenes versions 0.6.0 dated 2025-12-14 and 0.7.0 dated 2026-07-05
DESCRIPTION | 28 MD5 | 109 +- NAMESPACE | 7 NEWS.md | 52 + R/compose_grob.R |only R/data.R | 2 R/geom_feature.R | 184 ++-- R/geom_feature_label.R | 209 +--- R/geom_gene_arrow.R | 191 ++-- R/geom_gene_label.R | 153 +-- R/geom_subgene_arrow.R | 450 +++------- R/geom_subgene_label.R | 134 +- R/geom_terminator.R | 125 +- R/geom_terminator_label.R | 209 +--- R/gggenes-package.R | 1 R/make_alignment_dummies.R | 81 + R/theme_genes.R | 56 - R/utilities.R | 350 ++----- README.md | 15 build/vignette.rds |binary inst/WORDLIST | 16 inst/doc/introduction-to-gggenes.html | 6 man/figures/README-geom_gene_arrow-1.png |binary man/figures/README-labelled_genes-1.png |binary man/figures/README-make_alignment_dummies-1.png |binary man/figures/README-reversing_direction-1.png |binary man/figures/README-subgene_labels-1.png |binary man/figures/README-subgenes-1.png |binary man/figures/README-theme_genes-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/geom_feature.Rd | 8 man/geom_feature_label.Rd | 16 man/geom_gene_label.Rd | 4 man/geom_subgene_label.Rd | 4 man/geom_terminator.Rd | 6 man/geom_terminator_label.Rd | 12 man/gggenes-package.Rd | 5 tests/testthat/Rplots.pdf |only tests/testthat/_snaps/feature/geom-feature-and-geom-feature-label-in-polar-coordinates.svg | 48 - tests/testthat/_snaps/feature/oriented-feature-labels-in-polar-coordinates.svg |only tests/testthat/_snaps/gene_arrow/gene-arrow-and-label-in-cartesian-coordinates.svg | 168 +-- tests/testthat/_snaps/gene_arrow/gene-arrow-and-label-in-flipped-coordinates.svg | 168 +-- tests/testthat/_snaps/gene_arrow/gene-arrow-and-label-in-polar-coordinates.svg | 60 - tests/testthat/_snaps/subgene_arrow/subgene-arrow-and-label-in-cartesian-coordinates.svg | 310 +++--- tests/testthat/_snaps/subgene_arrow/subgene-arrow-and-label-in-flipped-coordinates.svg | 310 +++--- tests/testthat/_snaps/subgene_arrow/subgene-arrow-in-polar-coordinates.svg |only tests/testthat/_snaps/subgene_arrow/subgene-label-in-polar-coordinates.svg |only tests/testthat/_snaps/terminator/terminator-and-label-in-polar-coordinates.svg | 40 tests/testthat/helpers.R | 106 ++ tests/testthat/test-compose_grob.R |only tests/testthat/test-feature.R | 245 ++++- tests/testthat/test-gene_arrow.R | 126 ++ tests/testthat/test-make_alignment_dummies.R | 115 ++ tests/testthat/test-reverse_strand.R |only tests/testthat/test-subgene_arrow.R | 269 +++++ tests/testthat/test-terminator.R | 144 ++- tests/testthat/test-utilities.R |only vignettes/articles |only 60 files changed, 2536 insertions(+), 2006 deletions(-)
Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanés Bové et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre] ,
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [ [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 2.1.0 dated 2026-01-30 and 2.2.0 dated 2026-07-05
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crmPack-2.2.0/crmPack/vignettes/vignettes.bib | 16 366 files changed, 18365 insertions(+), 4860 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.4.6 dated 2026-04-07 and 0.4.7 dated 2026-07-05
DESCRIPTION | 14 - MD5 | 85 +++--- NAMESPACE | 1 NEWS.md | 9 R/cms_catalogue_entry.R | 41 +-- R/cms_cite_product.r | 47 +-- R/cms_download_native.R | 501 ++++++++++++++++++++++------------------ R/cms_download_subset.r | 6 R/cms_glossary.R | 1 R/cms_login.r | 265 ++++++++++----------- R/cms_product_details.r | 73 ++--- R/cms_product_metadata.r | 65 ++--- R/cms_product_services.r | 79 +++--- R/cms_products_list.r | 204 ++++++++-------- R/cms_wmts.r | 3 R/translate.R | 251 ++++++++++---------- README.md | 2 build/vignette.rds |binary inst/doc/glossary.R | 30 +- inst/doc/glossary.Rmd | 32 +- inst/doc/glossary.html | 6 inst/doc/product-info.html | 2 inst/doc/proxy.html | 2 inst/doc/translate.html | 4 inst/glossary.rdata |binary man/CopernicusMarine-package.Rd | 7 man/account.Rd | 5 man/cms_cite_product.Rd | 12 man/cms_download_native.Rd | 16 + man/cms_download_subset.Rd | 10 man/cms_get_client_info.Rd | 6 man/cms_glossary.Rd | 6 man/cms_login.Rd | 5 man/cms_native_proxy.Rd | 10 man/cms_native_s3.Rd |only man/cms_product_details.Rd | 12 man/cms_product_metadata.Rd | 9 man/cms_product_services.Rd | 12 man/cms_products_list.Rd | 12 man/cms_translate.Rd | 8 man/cms_wmts.Rd | 5 man/cms_zarr_proxy.Rd | 10 tests/testthat/test_native.r | 144 +++++------ vignettes/glossary.Rmd | 32 +- 44 files changed, 1121 insertions(+), 923 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Identifying Unique Multilocus Genotypes where Genotyping Error
and Missing Data may be Present
Description: Tools for the identification of unique multilocus genotypes when
both genotyping error and missing data may be present. Includes a data
pre-screening utility to analyze pairwise locus overlap and protect against
underlying mathematical sorting constraints. Targeted for use with large
datasets and databases containing multiple samples of each individual (a common
situation in conservation genetics, particularly in non-invasive wildlife
sampling applications). Functions explicitly incorporate missing data and can
tolerate allele mismatches created by genotyping error. If you use this package,
please cite the original publication in Molecular Ecology Resources (Galpern
et al., 2012), the details for which can be generated using
citation('allelematch'). The complete user manual and analytical tutorials
are included locally as an R vignette and can be accessed within an active R
session using vignette('allelematch').
Author: Paul Galpern [aut],
Micheline Manseau [aut],
Pete Hettinga [aut],
Karen Smith [aut],
Paul Wilson [aut],
Todd Cross [cre]
Maintainer: Todd Cross <todd.cross@gmail.com>
Diff between allelematch versions 2.5.5 dated 2025-07-26 and 2.6.0 dated 2026-07-05
allelematch-2.5.5/allelematch/build/partial.rdb |only allelematch-2.6.0/allelematch/DESCRIPTION | 28 allelematch-2.6.0/allelematch/MD5 | 22 allelematch-2.6.0/allelematch/NAMESPACE | 29 allelematch-2.6.0/allelematch/R/allelematch.r | 4606 +++++---------- allelematch-2.6.0/allelematch/build/vignette.rds |only allelematch-2.6.0/allelematch/data/amExample5.RData |binary allelematch-2.6.0/allelematch/inst/doc |only allelematch-2.6.0/allelematch/man/allelematch-package.Rd | 120 allelematch-2.6.0/allelematch/man/amPreCheck.Rd |only allelematch-2.6.0/allelematch/vignettes |only 11 files changed, 1711 insertions(+), 3094 deletions(-)
Title: Linear Innovations State Space Unobserved Components Model
Description: Unobserved components time series model using the linear innovations state space representation (single source of error) with choice of error distributions and option for dynamic variance. Methods for estimation using automatic differentiation, automatic model selection and ensembling, prediction, filtering, simulation and backtesting. Based on the model described in Hyndman et al (2012) <doi:10.1198/jasa.2011.tm09771>.
Author: Alexios Galanos [aut, cre]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsissm versions 1.0.2 dated 2025-07-12 and 1.0.3 dated 2026-07-05
DESCRIPTION | 6 - MD5 | 36 ++++---- NAMESPACE | 1 NEWS.md | 22 +++++ R/capabilities.R |only R/constraint.R | 103 ++++++++++++++++++++++++ R/estimation.R | 9 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/demo_ensembling.R | 2 inst/doc/demo_ensembling.Rmd | 2 inst/doc/demo_ensembling.html | 149 ++++++++++------------------------- inst/doc/demo_filtering.html | 7 - inst/doc/demo_missing_data.html | 13 +-- inst/doc/demo_variance_dynamics.html | 58 ++++++------- inst/doc/issm_introduction.pdf |binary man/estimate.Rd | 9 +- man/tsissm_capabilities.Rd |only tests/longtests/test-backtest.R | 14 --- vignettes/demo_ensembling.Rmd | 2 20 files changed, 252 insertions(+), 181 deletions(-)
Title: Draw Treemaps in 'ggplot2'
Description: Provides 'ggplot2' geoms for drawing treemaps.
Author: David Wilkins [aut, cre] ,
Bob Rudis [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between treemapify versions 2.6.0 dated 2025-12-14 and 2.6.1 dated 2026-07-05
treemapify-2.6.0/treemapify/R/a-rect.R |only treemapify-2.6.1/treemapify/DESCRIPTION | 15 - treemapify-2.6.1/treemapify/MD5 | 47 ++--- treemapify-2.6.1/treemapify/NAMESPACE | 3 treemapify-2.6.1/treemapify/NEWS.md | 26 ++ treemapify-2.6.1/treemapify/R/geom_treemap_subgroup_border.R | 9 treemapify-2.6.1/treemapify/R/geom_treemap_subgroup_text.R | 9 treemapify-2.6.1/treemapify/R/treemap_fixed.R | 4 treemapify-2.6.1/treemapify/R/treemap_squarified.R | 4 treemapify-2.6.1/treemapify/R/treemapify-package.R | 2 treemapify-2.6.1/treemapify/R/treemapify.R | 48 ++++- treemapify-2.6.1/treemapify/README.md | 2 treemapify-2.6.1/treemapify/build/vignette.rds |binary treemapify-2.6.1/treemapify/inst/WORDLIST | 2 treemapify-2.6.1/treemapify/inst/doc/introduction-to-treemapify.html | 4 treemapify-2.6.1/treemapify/man/figures/animated_treemap.gif |binary treemapify-2.6.1/treemapify/man/geom_treemap_subgroup_border.Rd | 2 treemapify-2.6.1/treemapify/man/treemapify-ggproto.Rd | 2 treemapify-2.6.1/treemapify/man/treemapify-package.Rd | 6 treemapify-2.6.1/treemapify/man/treemapify.Rd | 18 + treemapify-2.6.1/treemapify/tests/testthat/test_G20.R | 2 treemapify-2.6.1/treemapify/tests/testthat/test_geoms.R | 71 +++++++ treemapify-2.6.1/treemapify/tests/testthat/test_layout_functions.R | 4 treemapify-2.6.1/treemapify/tests/testthat/test_plots.R | 2 treemapify-2.6.1/treemapify/tests/testthat/test_treemapify.R | 93 +++++++++- 25 files changed, 300 insertions(+), 75 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled. For regression versions of the methods, Monte Carlo and asymptotic methods are used.
Author: Ivair Ramos Silva [aut, cre],
Martin Kulldorff [aut]
Maintainer: Ivair Ramos Silva <ivair@ufop.edu.br>
Diff between Sequential versions 4.6.0 dated 2026-04-21 and 4.6.1 dated 2026-07-05
DESCRIPTION | 10 +- MD5 | 14 +- NAMESPACE | 3 R/Analyze.Multinomial.R | 187 ++++++++++++++++++++++++++-------------- R/AnalyzeSetUp.Multinomial.R | 7 - man/Analyze.Multinomial.Rd | 6 - man/AnalyzeSetUp.Multinomial.Rd | 5 - man/Sequential-package.Rd | 13 +- 8 files changed, 155 insertions(+), 90 deletions(-)
Title: A 'Shiny' Gadget for Interactive 'QRA' Visualizations
Description: Upload raster data and easily create interactive quantitative risk analysis 'QRA' visualizations. Select
from numerous color palettes, base-maps, and different configurations.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between QRAGadget versions 0.3.0 dated 2023-06-23 and 0.4 dated 2026-07-05
QRAGadget-0.3.0/QRAGadget/R/tableinput.R |only QRAGadget-0.3.0/QRAGadget/inst/images/InputOutput.png |only QRAGadget-0.3.0/QRAGadget/inst/images/map.png |only QRAGadget-0.3.0/QRAGadget/inst/images/map2.png |only QRAGadget-0.3.0/QRAGadget/inst/images/preferences.png |only QRAGadget-0.3.0/QRAGadget/inst/images/raster.png |only QRAGadget-0.3.0/QRAGadget/inst/tableinput |only QRAGadget-0.3.0/QRAGadget/man/matrixInput.Rd |only QRAGadget-0.4/QRAGadget/DESCRIPTION | 30 +- QRAGadget-0.4/QRAGadget/MD5 | 35 +- QRAGadget-0.4/QRAGadget/NAMESPACE | 20 - QRAGadget-0.4/QRAGadget/NEWS.md | 26 + QRAGadget-0.4/QRAGadget/R/QRAGadget.R | 248 ++++++++++-------- QRAGadget-0.4/QRAGadget/README.md | 116 +++----- QRAGadget-0.4/QRAGadget/build |only QRAGadget-0.4/QRAGadget/inst/CITATION |only QRAGadget-0.4/QRAGadget/inst/doc |only QRAGadget-0.4/QRAGadget/inst/images/InputOutput.PNG |only QRAGadget-0.4/QRAGadget/inst/images/Map2.PNG |only QRAGadget-0.4/QRAGadget/inst/images/map.PNG |only QRAGadget-0.4/QRAGadget/inst/images/preferences.PNG |only QRAGadget-0.4/QRAGadget/inst/images/raster.PNG |only QRAGadget-0.4/QRAGadget/man/QRAGadget.Rd | 4 QRAGadget-0.4/QRAGadget/tests |only QRAGadget-0.4/QRAGadget/vignettes |only 25 files changed, 259 insertions(+), 220 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for
model-based clustering, classification, and density estimation,
including Bayesian regularization, dimension reduction for
visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut] ,
Luca Scrucca [aut, cre] ,
Thomas Brendan Murphy [ctb] ,
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between mclust versions 6.1.2 dated 2025-10-31 and 6.1.3 dated 2026-07-05
DESCRIPTION | 8 ++-- MD5 | 25 ++++++------- NAMESPACE | 6 +++ NEWS.md | 7 +++ R/bootstrap.R | 2 - R/mclust.R | 20 +++++++--- R/mclustda.R | 2 - R/util.R | 37 +++++++++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/mclust.html | 96 +++++++++++++++++++++++++-------------------------- man/hypvol.Rd | 2 - man/simulate.Rd |only src/mclust.f | 3 + 14 files changed, 135 insertions(+), 73 deletions(-)
Title: Fit Text Inside a Box in 'ggplot2'
Description: A 'ggplot2' extension to fit text into a box by growing, shrinking or wrapping the text.
Author: David Wilkins [aut, cre],
Brady Johnston [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between ggfittext versions 0.10.3 dated 2025-12-13 and 0.10.4 dated 2026-07-05
DESCRIPTION | 8 - MD5 | 63 ++++---- NEWS.md | 23 +++ R/data.R | 44 +++--- R/geom_bar_text.R | 47 +++--- R/geom_fit_text.R | 212 ++++++++++++++++++------------ README.md | 18 +- build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/introduction-to-ggfittext.R | 5 inst/doc/introduction-to-ggfittext.Rmd | 30 +++- inst/doc/introduction-to-ggfittext.html | 96 +++++++------ man/animals_rich.Rd | 2 man/figures/README-hero-1.png |binary man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.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-16-1.png |binary man/figures/README-unnamed-chunk-17-1.png |binary man/figures/README-unnamed-chunk-4-1.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-9-1.png |binary man/geom_fit_text.Rd | 39 +++-- man/ggfittext-package.Rd | 5 man/gold.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/test-geom_bar_text.R | 103 ++++++++++++++ tests/testthat/test-geom_fit_text.R | 180 +++++++++++++++++++++++++ vignettes/introduction-to-ggfittext.Rmd | 30 +++- 33 files changed, 670 insertions(+), 239 deletions(-)
Title: Fuzzy C-Means for Fuzzy Data
Description: Implements a fuzzy clustering approach for ordinal Likert-type data
using triangular fuzzy numbers (TFNs). The package extends the classical
fuzzy C-means algorithm to better handle uncertainty in ordinal scales and
includes automatic selection of the number of clusters using the Xie-Beni
validity index. References: Coppi, R., D'Urso, P., and Giordani, P. (2012),
"Fuzzy and possibilistic clustering for fuzzy data", <doi:10.1016/j.csda.2010.09.013>. Xie, X. L. and Beni, G.
(1991), "A validity measure for fuzzy clustering", <doi:10.1109/34.85677>.
Author: Jose Ortigas [aut, cre]
Maintainer: Jose Ortigas <jose.ortigas@unmsm.edu.pe>
Diff between fcmfd versions 0.1.1 dated 2026-05-23 and 0.1.2 dated 2026-07-05
fcmfd-0.1.1/fcmfd/R/data_sim_likert_0_10.R |only fcmfd-0.1.1/fcmfd/R/prototype_matrix.R |only fcmfd-0.1.1/fcmfd/data/sim_likert_0_10.rda |only fcmfd-0.1.1/fcmfd/man/prototype_matrix.Rd |only fcmfd-0.1.1/fcmfd/man/sim_likert_0_10.Rd |only fcmfd-0.1.2/fcmfd/DESCRIPTION | 6 fcmfd-0.1.2/fcmfd/MD5 | 48 +- fcmfd-0.1.2/fcmfd/NAMESPACE | 6 fcmfd-0.1.2/fcmfd/NEWS.md | 13 fcmfd-0.1.2/fcmfd/R/cluster_size.R |only fcmfd-0.1.2/fcmfd/R/data_sim_likert7.R | 50 +- fcmfd-0.1.2/fcmfd/R/membership_quality.R |only fcmfd-0.1.2/fcmfd/R/plot_dictionary.R | 206 +++++++++- fcmfd-0.1.2/fcmfd/R/plot_prototypes.R | 388 ++++++++++++++++++-- fcmfd-0.1.2/fcmfd/R/plot_xb.R | 58 ++ fcmfd-0.1.2/fcmfd/R/prototype_results.R |only fcmfd-0.1.2/fcmfd/R/students_wellbeing.R |only fcmfd-0.1.2/fcmfd/README.md | 87 ++-- fcmfd-0.1.2/fcmfd/build/vignette.rds |binary fcmfd-0.1.2/fcmfd/data/students_wellbeing.rda |only fcmfd-0.1.2/fcmfd/inst/doc/fcmTFN-introduction.R | 8 fcmfd-0.1.2/fcmfd/inst/doc/fcmTFN-introduction.Rmd | 24 - fcmfd-0.1.2/fcmfd/inst/doc/fcmTFN-introduction.html | 104 +++-- fcmfd-0.1.2/fcmfd/man/cluster_size.Rd |only fcmfd-0.1.2/fcmfd/man/membership_quality.Rd |only fcmfd-0.1.2/fcmfd/man/plot_dictionary.Rd | 9 fcmfd-0.1.2/fcmfd/man/plot_prototypes.Rd | 13 fcmfd-0.1.2/fcmfd/man/plot_xb.Rd | 8 fcmfd-0.1.2/fcmfd/man/prototype_results.Rd |only fcmfd-0.1.2/fcmfd/man/sim_likert7.Rd | 51 +- fcmfd-0.1.2/fcmfd/man/students_wellbeing.Rd |only fcmfd-0.1.2/fcmfd/vignettes/fcmTFN-introduction.Rmd | 24 - 32 files changed, 841 insertions(+), 262 deletions(-)
Title: Download Spatial Datasets of Peru
Description: Provides access to official spatial datasets of Peru as 'sf'
objects in 'R'. Includes administrative boundaries from the National
Institute of Statistics and Informatics (INEI) <https://ide.inei.gob.pe/>
and protected natural areas from the National Service of Natural Areas
Protected by the State (SERNANP)
<https://www.gob.pe/institucion/sernanp/pages/21261-acceder-a-informacion-espacial-de-las-area-naturales-protegidas-visor-de-informacion-geografica>.
Harmonizes attributes, coordinate reference systems, and topology to
support consistent spatial analysis and visualization.
Author: Paul E. Santos Andrade [aut, cre, cph]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
Diff between geoperu versions 0.0.0.2 dated 2024-04-01 and 0.0.1 dated 2026-07-05
geoperu-0.0.0.2/geoperu/man/check_connection.Rd |only geoperu-0.0.0.2/geoperu/man/check_connection_anp.Rd |only geoperu-0.0.0.2/geoperu/man/download_gpkg.Rd |only geoperu-0.0.0.2/geoperu/man/download_gpkg_anp.Rd |only geoperu-0.0.0.2/geoperu/man/download_metadata.Rd |only geoperu-0.0.0.2/geoperu/man/download_metadata_anp.Rd |only geoperu-0.0.0.2/geoperu/man/load_gpkg.Rd |only geoperu-0.0.0.2/geoperu/man/select_data_level.Rd |only geoperu-0.0.0.2/geoperu/man/select_data_type.Rd |only geoperu-0.0.0.2/geoperu/man/select_metadata.Rd |only geoperu-0.0.0.2/geoperu/man/select_metadata_anp.Rd |only geoperu-0.0.1/geoperu/DESCRIPTION | 25 geoperu-0.0.1/geoperu/LICENSE | 4 geoperu-0.0.1/geoperu/MD5 | 49 geoperu-0.0.1/geoperu/NAMESPACE | 8 geoperu-0.0.1/geoperu/NEWS.md |only geoperu-0.0.1/geoperu/R/distritos.R | 13 geoperu-0.0.1/geoperu/R/get_anp_peru.R | 150 + geoperu-0.0.1/geoperu/R/get_geo_peru.R | 138 + geoperu-0.0.1/geoperu/R/global.R | 68 geoperu-0.0.1/geoperu/R/utils.R | 780 ++-------- geoperu-0.0.1/geoperu/README.md | 128 + geoperu-0.0.1/geoperu/inst/CITATION | 20 geoperu-0.0.1/geoperu/inst/figures |only geoperu-0.0.1/geoperu/man/figures/README-unnamed-chunk-2-1.png |binary geoperu-0.0.1/geoperu/man/figures/README-unnamed-chunk-3-1.png |binary geoperu-0.0.1/geoperu/man/figures/logo.png |only geoperu-0.0.1/geoperu/man/get_anp_peru.Rd | 61 geoperu-0.0.1/geoperu/man/get_geo_peru.Rd | 90 - geoperu-0.0.1/geoperu/man/peru.Rd | 45 geoperu-0.0.1/geoperu/tests |only 31 files changed, 663 insertions(+), 916 deletions(-)