Title: Likelihood-Based Confidence Interval in Structural Equation
Models
Description: Forms likelihood-based confidence intervals
(LBCIs) for parameters in structural equation modeling,
introduced in Cheung and Pesigan (2023)
<doi:10.1080/10705511.2023.2183860>. Currently
implements the algorithm illustrated by Pek and Wu
(2018) <doi:10.1037/met0000163>, and supports the robust
LBCI proposed by Falk (2018)
<doi:10.1080/10705511.2017.1367254>.
Author: Shu Fai Cheung [aut, cre] ,
Ivan Jacob Agaloos Pesigan [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semlbci versions 0.11.6 dated 2026-06-08 and 0.12.0 dated 2026-07-08
DESCRIPTION | 6 - MD5 | 44 ++++++------ NEWS.md | 17 ++++ R/ci_bound_ur_i.R | 4 - R/ci_bound_wn_i.R | 20 ++--- R/scaling_factor3.R | 4 - R/set_start_wn.R | 8 +- R/syntax_to_i.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary tests/testthat/test-ci_bound_wn_i_std_pa_eq.R | 2 tests/testthat/test-ci_bound_wn_i_ustd_pa.R | 9 +- tests/testthat/test-plot_likelihood.R | 2 tests/testthat/test-plot_likelihood_ur.R | 2 tests/testthat/test-ram_to_lav_mod.R | 8 +- tests/testthat/test-scaling_factor3_mg_rb_std_sem_user_eq.R | 2 tests/testthat/test-scaling_factor3_mg_wn_sem_std.R | 2 tests/testthat/test-scaling_factor3_std_sem_user_eq.R | 4 - tests/testthat/test-scaling_factor3_wn_sem_std.R | 4 - tests/testthat/test-std_lav.R | 4 - tests/testthat/test-std_ram.R | 2 tests/testthat/test-ur_gen_est_i.R | 8 +- 23 files changed, 88 insertions(+), 68 deletions(-)
Title: Interface to 'JDemetra+ 3.x' Time Series Analysis Software
Description: R Interface to 'JDemetra+ 3.x'
(<https://github.com/jdemetra>) time series analysis software. It
provides functions allowing to decompose a time series, including
high-frequency data with multiple periodicities.
Author: Jean Palate [aut],
Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjd3xjars versions 0.1.0 dated 2026-04-21 and 0.1.1 dated 2026-07-08
DESCRIPTION | 25 +++++++++++----------- MD5 | 10 ++++---- NAMESPACE | 6 +---- NEWS.md | 6 ++--- R/zzz.R | 53 +++++++++++++++++++++++++---------------------- man/rjd3xjars-package.Rd | 3 +- 6 files changed, 54 insertions(+), 49 deletions(-)
Title: Missingness Alleviation for Network Analysis
Description: Provides functionality for estimating cross-sectional network structures representing partial correlations while accounting for missing data. Networks are estimated via neighborhood selection or regularization, with model selection guided by information criteria. Missing data can be handled primarily via multiple imputation or a maximum likelihood-based approach, as demonstrated by Nehler and Schultze (2025) <doi:10.1080/00273171.2025.2503833> and Nehler and Schultze (2026) <doi:10.1037/met0000828>. Deletion-based approaches are also available but play a secondary role.
Author: Kai Jannik Nehler [aut, cre]
Maintainer: Kai Jannik Nehler <nehler@psych.uni-frankfurt.de>
Diff between mantar versions 0.3.0 dated 2026-05-26 and 0.3.1 dated 2026-07-08
mantar-0.3.0/mantar/README.md |only mantar-0.3.1/mantar/DESCRIPTION | 8 ++-- mantar-0.3.1/mantar/MD5 | 15 +++---- mantar-0.3.1/mantar/NEWS.md | 8 ++++ mantar-0.3.1/mantar/R/data.R | 4 -- mantar-0.3.1/mantar/build/partial.rdb |binary mantar-0.3.1/mantar/build/stage23.rdb |binary mantar-0.3.1/mantar/inst/doc/mantar.html | 12 +++--- mantar-0.3.1/mantar/tests/testthat/test-regularization_net.R | 21 ++++++++--- 9 files changed, 42 insertions(+), 26 deletions(-)
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
Permanent link
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(-)