Title: Epigenome-Wide Mediation Analysis Study
Description: DNA methylation is essential for human, and environment can change the DNA methylation
and affect body status. Epigenome-Wide Mediation Analysis Study (EMAS) can find
potential mediator CpG sites between exposure (x) and outcome (y) in epigenome-wide.
For more information on the methods we used, please see the following references:
Tingley, D. (2014) <doi:10.18637/jss.v059.i05>,
Turner, S. D. (2018) <doi:10.21105/joss.00731>,
Rosseel, D. (2012) <doi:10.18637/jss.v048.i02>.
Author: Xiuquan Nie [aut, cph, cre],
Mengyi Wang [ctb, rev]
Maintainer: Xiuquan Nie <niexiuquan1995@foxmail.com>
Diff between EMAS versions 0.2.3 dated 2025-09-04 and 0.2.4 dated 2025-12-21
EMAS-0.2.3/EMAS/R/EMAS.manhattan.R |only EMAS-0.2.3/EMAS/man/EMAS.manhattan.Rd |only EMAS-0.2.4/EMAS/DESCRIPTION | 12 +++++------- EMAS-0.2.4/EMAS/MD5 | 8 +++----- EMAS-0.2.4/EMAS/NAMESPACE | 5 ----- EMAS-0.2.4/EMAS/R/open.R | 2 +- 6 files changed, 9 insertions(+), 18 deletions(-)
Title: Japanese Text Processing Tools
Description: A collection of Japanese text processing tools for filling
Japanese iteration marks, Japanese character type conversions,
segmentation by phrase, and text normalization which is based on rules
for the 'Sudachi' morphological analyzer and the 'NEologd' (Neologism
dictionary for 'MeCab'). These features are specific to Japanese and
are not implemented in 'ICU' (International Components for Unicode).
Author: Akiru Kato [cre, aut],
Koki Takahashi [cph] ,
Shuhei Iitsuka [cph] ,
Taku Kudo [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>
Diff between audubon versions 0.5.2 dated 2024-04-26 and 0.6.1 dated 2025-12-21
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Title: Adapted Pair Correlation Function
Description: The adapted pair correlation function transfers the concept of the
pair correlation function from point patterns to patterns of objects of
finite size and irregular shape (e.g. lakes within a country). The pair
correlation function describes the spatial distribution of objects, e.g.
random, aggregated or regularly spaced. This is a reimplementation of the
method suggested by Nuske et al. (2009) <doi:10.1016/j.foreco.2009.09.050>
using the library 'GEOS' <doi:10.5281/zenodo.11396894>.
Author: Robert Nuske [aut, cre]
Maintainer: Robert Nuske <robert.nuske@mailbox.org>
Diff between apcf versions 0.3.2 dated 2025-02-28 and 0.3.3 dated 2025-12-21
DESCRIPTION | 13 +- MD5 | 17 +- NEWS.md | 4 README.md | 2 build/vignette.rds |binary inst/CITATION | 29 ++-- inst/doc/intro.html | 334 ++++++++++++++++++++++++++++++---------------------- src/Makevars.in | 1 src/Makevars.ucrt |only src/Makevars.win | 2 10 files changed, 236 insertions(+), 166 deletions(-)
Title: Statistical Inference for Weighted Data
Description: Analyzes and models data subject to sampling biases.
Provides functions to estimate the density and cumulative distribution
functions from biased samples of continuous distributions. Includes
the estimators proposed by Bhattacharyya et al. (1988)
<doi:10.1080/03610928808829825> and Jones (1991) <doi:10.2307/2337020>
for density, and by Cox (2005, ISBN:052184939X) and Bose and Dutta
(2022) <doi:10.1007/s00184-021-00824-3> for distribution, with
different bandwidth selectors. Also includes a real length-biased
dataset on shrub width from Muttlak (1988)
<https://www.proquest.com/openview/3dd74592e623cdbcfa6176e85bd3d390/1?cbl=18750&diss=y&pq-origsite=gscholar>.
Author: Sanchez Martinez Noelia [cre, aut] ,
Borrajo Garcia Maria Isabel [aut] ,
Conde Amboage Mercedes [aut]
Maintainer: Sanchez Martinez Noelia <noelia.sanchez.martinez@rai.usc.es>
Diff between WData versions 0.1.0 dated 2025-08-18 and 0.1.1 dated 2025-12-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 - build/partial.rdb |binary 4 files changed, 7 insertions(+), 8 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre] ,
Terrence D. Jorgensen [aut] ,
Luc De Wilde [aut],
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsika [...truncated...]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.6-20 dated 2025-09-21 and 0.6-21 dated 2025-12-21
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lavaan-0.6-21/lavaan/R/lav_fit_other.R | 2 lavaan-0.6-21/lavaan/R/lav_fit_rmsea.R | 2 lavaan-0.6-21/lavaan/R/lav_fit_srmr.R | 11 lavaan-0.6-21/lavaan/R/lav_fit_utils.R | 1 lavaan-0.6-21/lavaan/R/lav_graph.R |only lavaan-0.6-21/lavaan/R/lav_graphics.R | 2 lavaan-0.6-21/lavaan/R/lav_h1.R | 2 lavaan-0.6-21/lavaan/R/lav_label_code.R |only lavaan-0.6-21/lavaan/R/lav_lavaanList_inspect.R | 22 lavaan-0.6-21/lavaan/R/lav_lavaanList_methods.R | 47 lavaan-0.6-21/lavaan/R/lav_lavaanList_simulate.R | 4 lavaan-0.6-21/lavaan/R/lav_lavaan_step00_init.R | 2 lavaan-0.6-21/lavaan/R/lav_lavaan_step01_ovnames.R | 22 lavaan-0.6-21/lavaan/R/lav_lavaan_step02_options.R | 9 lavaan-0.6-21/lavaan/R/lav_lavaan_step03_data.R | 4 lavaan-0.6-21/lavaan/R/lav_lavaan_step04_partable.R | 9 lavaan-0.6-21/lavaan/R/lav_lavaan_step08_start.R | 24 lavaan-0.6-21/lavaan/R/lav_lavaan_step09_model.R | 27 lavaan-0.6-21/lavaan/R/lav_lavaan_step10_cache.R | 8 lavaan-0.6-21/lavaan/R/lav_lavaan_step11_optim.R | 3 lavaan-0.6-21/lavaan/R/lav_lavaan_step12_implied.R | 9 lavaan-0.6-21/lavaan/R/lav_lavaan_step13_vcov.R | 10 lavaan-0.6-21/lavaan/R/lav_lavaan_step16_rotation.R | 5 lavaan-0.6-21/lavaan/R/lav_lavaan_step17_lavaan.R | 2 lavaan-0.6-21/lavaan/R/lav_matrix.R | 108 - lavaan-0.6-21/lavaan/R/lav_model.R | 8 lavaan-0.6-21/lavaan/R/lav_model_compute.R | 174 +- lavaan-0.6-21/lavaan/R/lav_model_efa.R | 8 lavaan-0.6-21/lavaan/R/lav_model_estimate.R | 6 lavaan-0.6-21/lavaan/R/lav_model_gradient.R | 233 +-- lavaan-0.6-21/lavaan/R/lav_model_gradient_mml.R | 16 lavaan-0.6-21/lavaan/R/lav_model_gradient_pml.R | 100 - lavaan-0.6-21/lavaan/R/lav_model_h1_information.R | 69 - lavaan-0.6-21/lavaan/R/lav_model_h1_omega.R | 10 lavaan-0.6-21/lavaan/R/lav_model_hessian.R | 16 lavaan-0.6-21/lavaan/R/lav_model_implied.R | 8 lavaan-0.6-21/lavaan/R/lav_model_information.R | 28 lavaan-0.6-21/lavaan/R/lav_model_lik.R | 12 lavaan-0.6-21/lavaan/R/lav_model_loglik.R | 22 lavaan-0.6-21/lavaan/R/lav_model_objective.R | 75 - lavaan-0.6-21/lavaan/R/lav_model_plotinfo.R |only lavaan-0.6-21/lavaan/R/lav_model_utils.R | 35 lavaan-0.6-21/lavaan/R/lav_model_vcov.R | 20 lavaan-0.6-21/lavaan/R/lav_model_wls.R | 6 lavaan-0.6-21/lavaan/R/lav_modification.R | 3 lavaan-0.6-21/lavaan/R/lav_mplus_lavaan.R |only lavaan-0.6-21/lavaan/R/lav_msg.R | 20 lavaan-0.6-21/lavaan/R/lav_muthen1984.R | 4 lavaan-0.6-21/lavaan/R/lav_mvnorm_missing_h1.R | 9 lavaan-0.6-21/lavaan/R/lav_object_check_version.R |only lavaan-0.6-21/lavaan/R/lav_object_generate.R | 61 - lavaan-0.6-21/lavaan/R/lav_object_inspect.R | 148 -- lavaan-0.6-21/lavaan/R/lav_object_methods.R | 82 - lavaan-0.6-21/lavaan/R/lav_object_post_check.R | 6 lavaan-0.6-21/lavaan/R/lav_object_summary.R | 31 lavaan-0.6-21/lavaan/R/lav_objective.R | 40 lavaan-0.6-21/lavaan/R/lav_optim_gn.R | 2 lavaan-0.6-21/lavaan/R/lav_optim_noniter.R | 2 lavaan-0.6-21/lavaan/R/lav_options.R | 22 lavaan-0.6-21/lavaan/R/lav_options_default.R | 21 lavaan-0.6-21/lavaan/R/lav_options_estimator.R | 43 lavaan-0.6-21/lavaan/R/lav_options_mimic.R | 16 lavaan-0.6-21/lavaan/R/lav_options_se.R | 2 lavaan-0.6-21/lavaan/R/lav_partable.R | 80 - lavaan-0.6-21/lavaan/R/lav_partable_check.R | 12 lavaan-0.6-21/lavaan/R/lav_partable_constraints.R | 19 lavaan-0.6-21/lavaan/R/lav_partable_flat.R | 2 lavaan-0.6-21/lavaan/R/lav_partable_unrestricted.R | 2 lavaan-0.6-21/lavaan/R/lav_partable_vnames.R | 19 lavaan-0.6-21/lavaan/R/lav_plot.R |only lavaan-0.6-21/lavaan/R/lav_plotinfo_positions.R |only lavaan-0.6-21/lavaan/R/lav_plotinfo_rgraph.R |only lavaan-0.6-21/lavaan/R/lav_plotinfo_svgcode.R |only lavaan-0.6-21/lavaan/R/lav_plotinfo_tikzcode.R |only lavaan-0.6-21/lavaan/R/lav_pml_plrt.R |only lavaan-0.6-21/lavaan/R/lav_pml_plrt2.R |only lavaan-0.6-21/lavaan/R/lav_pml_test_plrt.R |only lavaan-0.6-21/lavaan/R/lav_pml_utils.R |only lavaan-0.6-21/lavaan/R/lav_predict.R | 320 ++--- lavaan-0.6-21/lavaan/R/lav_predict_y.R | 19 lavaan-0.6-21/lavaan/R/lav_print.R | 96 - lavaan-0.6-21/lavaan/R/lav_representation_lisrel.R | 736 ++++++------ lavaan-0.6-21/lavaan/R/lav_representation_ram.R | 4 lavaan-0.6-21/lavaan/R/lav_residuals.R | 5 lavaan-0.6-21/lavaan/R/lav_residuals_casewise.R | 4 lavaan-0.6-21/lavaan/R/lav_sam_step0.R | 2 lavaan-0.6-21/lavaan/R/lav_sam_step1_local.R | 15 lavaan-0.6-21/lavaan/R/lav_sam_utils.R | 11 lavaan-0.6-21/lavaan/R/lav_samplestats.R | 60 - lavaan-0.6-21/lavaan/R/lav_samplestats_gamma.R | 32 lavaan-0.6-21/lavaan/R/lav_samplestats_icov.R | 21 lavaan-0.6-21/lavaan/R/lav_scores.R |only lavaan-0.6-21/lavaan/R/lav_simulate.R | 6 lavaan-0.6-21/lavaan/R/lav_simulate_old.R | 92 - lavaan-0.6-21/lavaan/R/lav_standardize.R | 32 lavaan-0.6-21/lavaan/R/lav_start.R | 98 - lavaan-0.6-21/lavaan/R/lav_syntax.R | 17 lavaan-0.6-21/lavaan/R/lav_syntax_parser.R | 243 +--- lavaan-0.6-21/lavaan/R/lav_syntax_parser_cr.R | 15 lavaan-0.6-21/lavaan/R/lav_syntax_parser_r.R | 112 + lavaan-0.6-21/lavaan/R/lav_tables.R | 116 + lavaan-0.6-21/lavaan/R/lav_test.R | 24 lavaan-0.6-21/lavaan/R/lav_test_LRT.R | 14 lavaan-0.6-21/lavaan/R/lav_test_Wald.R | 14 lavaan-0.6-21/lavaan/R/lav_test_browne.R | 10 lavaan-0.6-21/lavaan/R/lav_test_diff.R | 20 lavaan-0.6-21/lavaan/R/lav_test_satorra_bentler.R | 19 lavaan-0.6-21/lavaan/R/lav_test_score.R | 3 lavaan-0.6-21/lavaan/R/lav_test_yuan_bentler.R | 2 lavaan-0.6-21/lavaan/R/lav_trace.R |only lavaan-0.6-21/lavaan/R/lav_utils.R | 779 ------------- lavaan-0.6-21/lavaan/R/lav_uvord.R | 2 lavaan-0.6-21/lavaan/R/xxx_efa.R | 2 lavaan-0.6-21/lavaan/R/xxx_fsr.R | 10 lavaan-0.6-21/lavaan/R/xxx_lavaan.R | 1 lavaan-0.6-21/lavaan/R/xxx_lavaanList.R | 4 lavaan-0.6-21/lavaan/R/zzz.R | 2 lavaan-0.6-21/lavaan/R/zzz_OLDNAMES.R | 151 ++ lavaan-0.6-21/lavaan/build/partial.rdb |binary lavaan-0.6-21/lavaan/inst/understanding_lavaan_internals.R | 44 lavaan-0.6-21/lavaan/man/FacialBurns.Rd | 2 lavaan-0.6-21/lavaan/man/bootstrap.Rd | 39 lavaan-0.6-21/lavaan/man/cfa.Rd | 6 lavaan-0.6-21/lavaan/man/efa.Rd | 6 lavaan-0.6-21/lavaan/man/figures |only lavaan-0.6-21/lavaan/man/getCov.Rd | 17 lavaan-0.6-21/lavaan/man/growth.Rd | 6 lavaan-0.6-21/lavaan/man/inspectSampleCov.Rd | 4 lavaan-0.6-21/lavaan/man/lavCor.Rd | 2 lavaan-0.6-21/lavaan/man/lavInspect.Rd | 6 lavaan-0.6-21/lavaan/man/lavListInspect.Rd | 2 lavaan-0.6-21/lavaan/man/lavMatrixRepresentation.Rd | 2 lavaan-0.6-21/lavaan/man/lavNames.Rd | 4 lavaan-0.6-21/lavaan/man/lavOptions.Rd | 26 lavaan-0.6-21/lavaan/man/lavPredictY.Rd | 8 lavaan-0.6-21/lavaan/man/lavPredictY_cv.Rd | 4 lavaan-0.6-21/lavaan/man/lavTestLRT.Rd | 4 lavaan-0.6-21/lavaan/man/lav_constraints.Rd | 7 lavaan-0.6-21/lavaan/man/lav_export.Rd |only lavaan-0.6-21/lavaan/man/lav_label_code.Rd |only lavaan-0.6-21/lavaan/man/lav_model_plotinfo.Rd |only lavaan-0.6-21/lavaan/man/lav_plotinfo_positions.Rd |only lavaan-0.6-21/lavaan/man/lav_plotinfo_rgraph.Rd |only lavaan-0.6-21/lavaan/man/lav_plotinfo_svgcode.Rd |only lavaan-0.6-21/lavaan/man/lav_plotinfo_tikzcode.Rd |only lavaan-0.6-21/lavaan/man/lav_scores.Rd |only lavaan-0.6-21/lavaan/man/lavaan-class.Rd | 12 lavaan-0.6-21/lavaan/man/lavaan-deprecated.Rd |only lavaan-0.6-21/lavaan/man/lavaan.Rd | 6 lavaan-0.6-21/lavaan/man/lavaanList.Rd | 6 lavaan-0.6-21/lavaan/man/lavplot.Rd |only lavaan-0.6-21/lavaan/man/model.syntax.Rd | 24 lavaan-0.6-21/lavaan/man/mplus2lavaan.Rd | 6 lavaan-0.6-21/lavaan/man/mplus2lavaan.modelSyntax.Rd | 10 lavaan-0.6-21/lavaan/man/parTable.Rd | 4 lavaan-0.6-21/lavaan/man/parameterEstimates.Rd | 19 lavaan-0.6-21/lavaan/man/sam.Rd | 4 lavaan-0.6-21/lavaan/man/sem.Rd | 6 lavaan-0.6-21/lavaan/man/simulateData.Rd | 30 lavaan-0.6-21/lavaan/man/summary.efaList.Rd | 20 201 files changed, 2969 insertions(+), 3349 deletions(-)
Title: Visualization of BART and BARP using SHAP
Description: Complex machine learning models are often difficult to interpret. Shapley values serve as a powerful tool to understand and explain why a model makes a particular prediction. This package computes variable contributions using permutation-based Shapley values for Bayesian Additive Regression Trees (BART) and its extension with Post-Stratification (BARP). The permutation-based SHAP method proposed by Strumbel and Kononenko (2014) <doi:10.1007/s10115-013-0679-x> is grounded in data obtained via MCMC sampling. Similar to the BART model introduced by Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>, this package leverages Bayesian posterior samples generated during model estimation, allowing variable contributions to be computed without requiring additional sampling. The BART model is designed to work with the following R packages: 'BART' <doi:10.18637/jss.v097.i01>, 'bartMachine' <doi:10.18637/jss.v070.i04>, and 'dbarts' <https://CRAN.R-project.org/ [...truncated...]
Author: Dong-eun Lee [aut, cre],
Eun-Kyung Lee [aut]
Maintainer: Dong-eun Lee <ldongeun.leel@gmail.com>
Diff between bartXViz versions 1.0.8 dated 2025-07-28 and 1.0.9 dated 2025-12-21
DESCRIPTION | 11 - MD5 | 44 ++--- NAMESPACE | 233 +++++++++++++-------------- R/Explain_stats.R |only R/plot.explainbarp.R | 53 ++++-- R/plot_default.R | 73 +++++--- R/plot_explainBART.R | 60 ++++--- R/plot_explainbartMachine.R | 16 + R/plot_func.R | 15 - R/waterfall_plot.R | 2 man/Explain.barp.Rd | 104 ++++++------ man/Explain.bart.Rd | 148 ++++++++--------- man/Explain.bartMachine.Rd | 150 ++++++++--------- man/Explain.default.Rd | 350 ++++++++++++++++++++--------------------- man/Explain.wbart.Rd | 148 ++++++++--------- man/Explain_stats.Rd |only man/barps.Rd | 140 ++++++++-------- man/decision_plot.Rd | 130 +++++++-------- man/one_hot.Rd | 114 ++++++------- man/plot.Explain.Rd | 117 +++++++------ man/plot.ExplainBART.Rd | 201 ++++++++++++----------- man/plot.Explainbarp.Rd | 137 ++++++++-------- man/plot.ExplainbartMachine.Rd | 119 +++++++------ man/waterfall_plot.Rd | 126 +++++++------- 24 files changed, 1304 insertions(+), 1187 deletions(-)
Title: Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Description: Provides low-level access to 'GDAL' functionality.
'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats
that presents a single raster abstract data model and single vector abstract data model to the calling application
for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable
developing further tools.
Author: Michael Sumner [aut, cre] ,
Simon Wotherspoon [ctb] ,
Mark Padgham [ctb] ),
Edzer Pebesma [ctb] ,
Roger Bivand [ctb] ,
Jim Hester [ctb, cph] ,
Timothy Keitt [ctb] ,
Jeroen Ooms [ctb] ,
Dale Maschette [ctb] ,
Joseph Stachelek [ctb],
Even Rouault [ctb] [...truncated...]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between vapour versions 0.13.0 dated 2025-11-18 and 0.15.0 dated 2025-12-21
vapour-0.13.0/vapour/src/Makevars.win |only vapour-0.15.0/vapour/DESCRIPTION | 8 vapour-0.15.0/vapour/MD5 | 15 vapour-0.15.0/vapour/NEWS.md | 8 vapour-0.15.0/vapour/configure | 2691 +++++++------- vapour-0.15.0/vapour/inst/doc/vapour.html | 6 vapour-0.15.0/vapour/inst/include/gdalapplib/gdalapplib.h | 3 vapour-0.15.0/vapour/src/Makevars.in | 3 vapour-0.15.0/vapour/src/Makevars.ucrt | 1 9 files changed, 1383 insertions(+), 1352 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.15.1 dated 2025-11-02 and 0.15.2 dated 2025-12-21
DESCRIPTION | 6 MD5 | 148 +++++----- NEWS.md | 31 +- R/expand_style.R | 4 R/grid_colspan.R | 2 R/html_finalize.R | 72 +++- R/html_style.R | 37 ++ R/print.R | 2 R/rbind2.R | 8 R/sanity.R | 42 +- R/style_tt.R | 19 - R/tabularray_style.R | 71 ++-- R/tabulator_data.R | 6 R/tabulator_style.R | 2 R/theme_default.R | 3 R/theme_html.R | 12 R/theme_latex.R | 13 README.md | 56 +-- build/partial.rdb |binary inst/tinytable.css | 51 ++- inst/tinytable_dark.css |only inst/tinytest/_tinysnapshot/escape-issue150_caption.html | 4 inst/tinytest/_tinysnapshot/escape-issue150_caption_02.html | 10 inst/tinytest/_tinysnapshot/escape-issue150_caption_03.html | 10 inst/tinytest/_tinysnapshot/escape-latex.html | 4 inst/tinytest/_tinysnapshot/escape-latex_colnames.html | 4 inst/tinytest/_tinysnapshot/escape-simple.html | 4 inst/tinytest/_tinysnapshot/format_tt-conditional_output.html | 4 inst/tinytest/_tinysnapshot/format_tt-vignette_html_markdown.html | 4 inst/tinytest/_tinysnapshot/group-html_tutorial_01.html | 36 +- inst/tinytest/_tinysnapshot/group-issue165_extra_row.html | 14 inst/tinytest/_tinysnapshot/group-issue165_html_centering_style.html | 18 - inst/tinytest/_tinysnapshot/group-issue258_01_html.html | 18 - inst/tinytest/_tinysnapshot/group-issue258_02_html.html | 20 - inst/tinytest/_tinysnapshot/group-multilevel-basic.html | 10 inst/tinytest/_tinysnapshot/group-multilevel-empty.html | 14 inst/tinytest/_tinysnapshot/group-nse.html | 4 inst/tinytest/_tinysnapshot/group_matrix-multiple_positions_multiple_rows.html | 4 inst/tinytest/_tinysnapshot/group_matrix-row_duplication.html | 4 inst/tinytest/_tinysnapshot/group_matrix-single_column_with_styling.html | 4 inst/tinytest/_tinysnapshot/group_matrix-single_position_single_row.html | 4 inst/tinytest/_tinysnapshot/html-alignment.html | 12 inst/tinytest/_tinysnapshot/html-bootstrap_css.html | 4 inst/tinytest/_tinysnapshot/html-caption.html | 4 inst/tinytest/_tinysnapshot/html-conditional_styling.html | 4 inst/tinytest/_tinysnapshot/html-font_size.html | 8 inst/tinytest/_tinysnapshot/html-footnote.html | 4 inst/tinytest/_tinysnapshot/html-formatting.html | 4 inst/tinytest/_tinysnapshot/html-images.html | 4 inst/tinytest/_tinysnapshot/html-individual_cells.html | 4 inst/tinytest/_tinysnapshot/html-issue297.html | 4 inst/tinytest/_tinysnapshot/html-issue355a.html | 72 ++-- inst/tinytest/_tinysnapshot/html-issue355b.html | 42 +- inst/tinytest/_tinysnapshot/html-issue575.html | 54 +-- inst/tinytest/_tinysnapshot/html-issue58.html | 12 inst/tinytest/_tinysnapshot/html-issue88.html | 4 inst/tinytest/_tinysnapshot/html-issue92.html | 8 inst/tinytest/_tinysnapshot/html-line_break.html | 4 inst/tinytest/_tinysnapshot/html-merge_cells.html | 4 inst/tinytest/_tinysnapshot/html-missing_value.html | 4 inst/tinytest/_tinysnapshot/html-omit_headers.html | 4 inst/tinytest/_tinysnapshot/html-spanning_cells.html | 4 inst/tinytest/_tinysnapshot/html-vectorized_color_j.html | 12 inst/tinytest/_tinysnapshot/latex-tabular_caption.tex |only inst/tinytest/_tinysnapshot/style-align_partial.html | 40 +- inst/tinytest/_tinysnapshot/style-issue507_markdown_styles.html | 44 +- inst/tinytest/_tinysnapshot/style-issue514_white_blue.html | 12 inst/tinytest/_tinysnapshot/style-smallcap.html | 20 - inst/tinytest/_tinysnapshot/theme-issue531_style_colors_override_stripes.html | 24 - inst/tinytest/test-latex.R | 7 inst/tinytest/test-misc.R | 1 inst/tinytest/test-tabulator.R | 7 man/rbind2-tinytable-tinytable-method.Rd | 8 man/style_tt.Rd | 6 man/theme_html.Rd | 8 man/tt.Rd | 18 - 76 files changed, 716 insertions(+), 534 deletions(-)
Title: Support Functions for Wrangling and Visualization
Description: Suite of helper functions for data wrangling and visualization.
The only theme for these functions is that they tend towards simple, short, and narrowly-scoped.
These functions are built for tasks that often recur but are not large enough in scope to warrant an ecosystem of interdependent functions.
Author: Nicholas J Lyon [aut, cre, cph]
Maintainer: Nicholas J Lyon <njlyon@alumni.iastate.edu>
Diff between supportR versions 1.5.0 dated 2025-06-03 and 1.6.0 dated 2025-12-21
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 10 +++++++++- R/count_diff.R | 6 +++++- R/diff_check.R | 11 +++++++---- R/num_check.R | 10 +++++----- README.md | 6 +++--- inst/doc/supportr_01_wrangle.html | 5 +++-- inst/doc/supportr_02_quality-control.html | 5 +++-- inst/doc/supportr_03_visualizations.html | 7 ++++--- inst/doc/supportr_04_outside-of-r.html | 5 +++-- man/count_diff.Rd | 2 +- man/num_check.Rd | 8 ++++---- 13 files changed, 63 insertions(+), 44 deletions(-)
Title: Select and Download Climate Data from 'DWD' (German Weather
Service)
Description: Handle climate data from the 'DWD' ('Deutscher Wetterdienst', see
<https://www.dwd.de/EN/climate_environment/cdc/cdc_node_en.html> for more information).
Choose observational time series from meteorological stations with 'selectDWD()'.
Find raster data from radar and interpolation according to <https://brry.github.io/rdwd/raster-data.html>.
Download (multiple) data sets with progress bars and no re-downloads through 'dataDWD()'.
Read both tabular observational data and binary gridded datasets with 'readDWD()'.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rdwd versions 1.9.3 dated 2025-08-18 and 1.9.8 dated 2025-12-21
DESCRIPTION | 14 MD5 | 112 +++---- NAMESPACE | 143 ++++----- NEWS.md | 5 R/addBorders.R | 2 R/checkUpdates.R | 2 R/createIndex.R | 2 R/dataDWD.R | 21 + R/dirDWD.R | 11 R/fileType.R | 4 R/index.R | 4 R/indexFTP.R | 2 R/locdir.R | 21 - R/metaInfo.R | 2 R/nearbyStations.R | 6 R/plotRadar.R | 4 R/projectRasterDWD.R | 2 R/rdwd-package.R | 4 R/readDWD.R | 10 R/readVars.R | 2 R/runLocalTests.R | 2 R/selectDWD.R | 8 R/updateIndexes.R | 4 R/zzz.R | 6 README.md | 16 - build/vignette.rds |binary data/datalist | 10 data/fileIndex.rda |binary data/formatIndex.rda |binary data/geoIndex.rda |binary data/gridIndex.rda |binary data/metaIndex.rda |binary inst/doc/rdwd.Rmd | 60 +-- inst/doc/rdwd.html | 562 ++++++++++++++++++------------------- inst/shinyapps/compare_years/app.R | 2 man/addBorders.Rd | 2 man/checkIndex.Rd | 112 +++---- man/checkUpdates.Rd | 2 man/createIndex.Rd | 2 man/dataDWD.Rd | 15 man/dirDWD.Rd | 4 man/dwdbase.Rd | 6 man/fileType.Rd | 4 man/index.Rd | 4 man/indexFTP.Rd | 2 man/locdir.Rd | 15 man/nearbyStations.Rd | 6 man/plotRadar.Rd | 4 man/projectRasterDWD.Rd | 2 man/rdwd.Rd | 4 man/readDWD.Rd | 2 man/readDWD.data.Rd | 2 man/readDWD.deriv.Rd | 2 man/readVars.Rd | 2 man/selectDWD.Rd | 8 man/updateIndexes.Rd | 4 vignettes/rdwd.Rmd | 60 +-- 57 files changed, 662 insertions(+), 645 deletions(-)
Title: Spatial and Spatio-Temporal Models using 'INLA'
Description: Prepare objects to implement models over spatial and
spacetime domains with the 'INLA' package (<https://www.r-inla.org>).
These objects contain data to for the 'cgeneric' interface in
'INLA', enabling fast parallel computations.
We implemented the spatial barrier model, see Bakka et. al. (2019)
<doi:10.1016/j.spasta.2019.01.002>, and some of the spatio-temporal
models proposed in Lindgren et. al. (2024)
<https://raco.cat/index.php/SORT/article/view/428665>.
Details are provided in the available vignettes and from the URL bellow.
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Finn Lindgren [aut] ,
Haavard Rue [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAspacetime versions 0.1.12 dated 2025-03-14 and 0.1.13 dated 2025-12-21
INLAspacetime-0.1.12/INLAspacetime/R/upperPadding.R |only INLAspacetime-0.1.12/INLAspacetime/R/utils.R |only INLAspacetime-0.1.12/INLAspacetime/README.md |only INLAspacetime-0.1.12/INLAspacetime/inst/examples |only INLAspacetime-0.1.12/INLAspacetime/man/check_package_version_and_load.Rd |only INLAspacetime-0.1.12/INLAspacetime/man/upperPadding.Rd |only INLAspacetime-0.1.12/INLAspacetime/vignettes/web/result_barrier.R |only INLAspacetime-0.1.13/INLAspacetime/DESCRIPTION | 26 +- INLAspacetime-0.1.13/INLAspacetime/MD5 | 92 ++++---- INLAspacetime-0.1.13/INLAspacetime/NAMESPACE | 4 INLAspacetime-0.1.13/INLAspacetime/R/INLAspacetime.R | 2 INLAspacetime-0.1.13/INLAspacetime/R/ar2cov.R | 5 INLAspacetime-0.1.13/INLAspacetime/R/ar2precision.R | 51 ++-- INLAspacetime-0.1.13/INLAspacetime/R/barrierModel.define.R | 46 ++-- INLAspacetime-0.1.13/INLAspacetime/R/cgeneric_sspde.R | 99 ++++---- INLAspacetime-0.1.13/INLAspacetime/R/inlabru.R | 6 INLAspacetime-0.1.13/INLAspacetime/R/mesh2d.R | 7 INLAspacetime-0.1.13/INLAspacetime/R/mesh2fem.R | 2 INLAspacetime-0.1.13/INLAspacetime/R/mesh2projector.R | 6 INLAspacetime-0.1.13/INLAspacetime/R/paramsUtils.R | 36 ++- INLAspacetime-0.1.13/INLAspacetime/R/stModel.define.R | 65 ++++- INLAspacetime-0.1.13/INLAspacetime/R/stModel.matrices.R | 112 ++++------ INLAspacetime-0.1.13/INLAspacetime/build/partial.rdb |binary INLAspacetime-0.1.13/INLAspacetime/build/vignette.rds |binary INLAspacetime-0.1.13/INLAspacetime/demo |only INLAspacetime-0.1.13/INLAspacetime/inst/doc/transparent_barriers.Rmd | 16 - INLAspacetime-0.1.13/INLAspacetime/inst/doc/transparent_barriers.html | 15 - INLAspacetime-0.1.13/INLAspacetime/inst/doc/website_examples.html | 2 INLAspacetime-0.1.13/INLAspacetime/man/Jmatrices.Rd | 2 INLAspacetime-0.1.13/INLAspacetime/man/ar2cov.Rd | 3 INLAspacetime-0.1.13/INLAspacetime/man/ar2precision.Rd | 21 - INLAspacetime-0.1.13/INLAspacetime/man/barrierModel.define.Rd | 20 - INLAspacetime-0.1.13/INLAspacetime/man/bru_get_mapper.stModel_cgeneric.Rd | 2 INLAspacetime-0.1.13/INLAspacetime/man/cgeneric_sspde.Rd | 32 -- INLAspacetime-0.1.13/INLAspacetime/man/mesh2d.Rd | 5 INLAspacetime-0.1.13/INLAspacetime/man/mesh2projector.Rd | 4 INLAspacetime-0.1.13/INLAspacetime/man/paramsUtils.Rd | 11 INLAspacetime-0.1.13/INLAspacetime/man/pcrange.Rd |only INLAspacetime-0.1.13/INLAspacetime/man/stModel.define.Rd | 28 +- INLAspacetime-0.1.13/INLAspacetime/man/stModel.matrices.Rd | 2 INLAspacetime-0.1.13/INLAspacetime/man/stModel.precision.Rd | 2 INLAspacetime-0.1.13/INLAspacetime/src/INLAspacetime.c | 27 +- INLAspacetime-0.1.13/INLAspacetime/src/INLAspacetime.h | 24 -- INLAspacetime-0.1.13/INLAspacetime/src/INLAspacetime_init.c |only INLAspacetime-0.1.13/INLAspacetime/src/cgeneric_ast.c |only INLAspacetime-0.1.13/INLAspacetime/src/cgeneric_vrst.c |only INLAspacetime-0.1.13/INLAspacetime/vignettes/transparent_barriers.Rmd | 16 - INLAspacetime-0.1.13/INLAspacetime/vignettes/web/INLAspacetime.bib | 13 - INLAspacetime-0.1.13/INLAspacetime/vignettes/web/barrierExample.Rmd | 23 +- INLAspacetime-0.1.13/INLAspacetime/vignettes/web/barrier_global.Rmd |only INLAspacetime-0.1.13/INLAspacetime/vignettes/web/piemonte.Rmd | 18 - 51 files changed, 463 insertions(+), 382 deletions(-)
Title: Network Reconstruction and Changepoint Detection
Description: Package EDISON (Estimation of Directed Interactions from
Sequences Of Non-homogeneous gene expression) runs an MCMC
simulation to reconstruct networks from time series data, using
a non-homogeneous, time-varying dynamic Bayesian network.
Networks segments and changepoints are inferred concurrently,
and information sharing priors provide a reduction of the
inference uncertainty.
Author: Frank Dondelinger [aut, cre],
Sophie Lebre [aut]
Maintainer: Frank Dondelinger <fdondelinger.work@gmail.com>
Diff between EDISON versions 1.1.1 dated 2016-03-30 and 1.1.2 dated 2025-12-21
DESCRIPTION | 24 MD5 | 251 +++++----- NAMESPACE | 130 ++--- NEWS | 30 - R/BinoHyperMove.R | 174 +++---- R/BinoHyperRatio.R | 166 +++--- R/CalculateChanges.R | 160 +++--- R/CalculateLikelihoodRatio.R | 110 ++-- R/CalculatePriorRatio.R | 126 ++--- R/CollectNetworkInfo.R | 184 +++---- R/EDISON-package.R | 86 +-- R/EDISON.run.R | 196 ++++---- R/ExpHyperMove.R | 352 +++++++------- R/ExpHyperRatioTarget.R | 130 ++--- R/HyperParms.R | 158 +++--- R/HyperparameterMove.R | 150 +++--- R/NetworkProbBino.R | 148 +++--- R/NetworkProbExp.R | 100 ++-- R/NetworkRatioBino.R | 102 ++-- R/NetworkRatioExp.R | 92 +-- R/PriorRatioPoisson.R | 142 ++--- R/ProposeDiscrete.R | 104 ++-- R/addProposalNetworkInfo.R | 62 +- R/bp.computeAlpha.R | 126 ++--- R/buildXY.R | 80 +-- R/calculateCPPGlobal.R | 48 - R/calculateCPProbabilities.R | 104 ++-- R/calculateEdgeProbabilities.R | 102 ++-- R/calculateEdgeProbabilitiesSegs.R | 80 +-- R/calculateEdgeProbabilitiesTimePoints.R | 136 ++--- R/computePx.R | 74 +-- R/computeRho4.R | 82 +-- R/convert_nets.R | 120 ++-- R/cp.birth.R | 558 +++++++++++------------ R/cp.death.R | 404 ++++++++-------- R/cp.shift.R | 426 ++++++++--------- R/defaultOptions.R | 196 ++++---- R/dinvgamma.R | 68 +- R/fix_eigenvalues.R | 94 +-- R/generateNetwork.R | 402 ++++++++-------- R/imports.R |only R/init.R | 224 ++++----- R/main.R | 402 ++++++++-------- R/make_structure_move.R | 402 ++++++++-------- R/output.R | 172 +++---- R/phase.update.R | 272 +++++------ R/proposalTuning.R | 56 +- R/proposeContinuous.R | 74 +-- R/psrf.R | 176 +++---- R/psrf_check.R | 94 +-- R/psrf_check_hyper.R | 80 +-- R/readDataTS.R | 80 +-- R/rinvgamma.R | 52 +- R/runDBN.R | 382 +++++++-------- R/sampleBinit.R | 68 +- R/sampleBxy.R | 54 +- R/sampleDelta2.R | 86 +-- R/sampleK.R | 58 +- R/sampleParms.R | 374 +++++++-------- R/sampleSig2.R | 50 +- R/simulateNetwork.R | 298 ++++++------ R/updateNetworkInfo.R | 38 - R/updateSigMulti.R | 92 +-- R/updateSigSolo.R | 112 ++-- inst/CITATION | 24 man/AcceptableMove.Rd | 77 +-- man/BinoHyperMove.Rd | 93 +-- man/BinoHyperRatio.Rd | 93 +-- man/CalculateChanges.Rd | 63 +- man/CalculateLikelihoodRatio.Rd | 93 +-- man/CalculatePriorRatio.Rd | 97 +--- man/CollectNetworkInfo.Rd | 104 ++-- man/EDISON-package.Rd | 103 ++-- man/EDISON.run.Rd | 175 +++---- man/ExpHyperMove.Rd | 101 ++-- man/ExpHyperRatioTarget.Rd | 89 +-- man/HyperParms.Rd | 65 +- man/HyperparameterMove.Rd | 99 ++-- man/NetworkProbBino.Rd | 83 +-- man/NetworkProbExp.Rd | 73 +-- man/NetworkRatioBino.Rd | 73 +-- man/NetworkRatioExp.Rd | 75 +-- man/PriorRatioPoisson.Rd | 73 +-- man/ProposeDiscrete.Rd | 81 +-- man/addProposalNetworkInfo.Rd | 55 +- man/bp.computeAlpha.Rd | 156 +++--- man/buildXY.Rd | 53 +- man/calculateCPPGlobal.Rd | 53 +- man/calculateCPProbabilities.Rd | 75 +-- man/calculateEdgeProbabilities.Rd | 103 ++-- man/calculateEdgeProbabilitiesSegs.Rd | 73 +-- man/calculateEdgeProbabilitiesTimePoints.Rd | 69 +- man/computePx.Rd | 73 +-- man/computeRho4.Rd | 79 +-- man/convert_nets.Rd | 59 +- man/cp.birth.Rd | 123 ++--- man/cp.death.Rd | 127 ++--- man/cp.shift.Rd | 119 ++-- man/defaultOptions.Rd | 107 ++-- man/dinvgamma.Rd | 73 +-- man/fix_eigenvalues.Rd | 65 +- man/generateNetwork.Rd | 168 +++--- man/init.Rd | 81 +-- man/main.Rd | 91 +-- man/make_structure_move.Rd | 140 +++-- man/output.Rd | 77 +-- man/phase.update.Rd | 125 ++--- man/proposalTuning.Rd | 49 -- man/proposeContinuous.Rd | 77 +-- man/psrf.Rd | 123 ++--- man/psrf_check.Rd | 69 +- man/psrf_check_hyper.Rd | 61 +- man/readDataTS.Rd | 67 +- man/rinvgamma.Rd | 75 +-- man/runDBN.Rd | 176 +++---- man/sampleBinit.Rd | 71 +- man/sampleBxy.Rd | 69 +- man/sampleDelta2.Rd | 83 +-- man/sampleK.Rd | 69 +- man/sampleParms.Rd | 95 +-- man/sampleSig2.Rd | 69 +- man/simulateNetwork.Rd | 216 ++++---- man/updateSigMulti.Rd | 121 ++--- man/updateSigSolo.Rd | 103 ++-- tests/test-all.R | 2 tests/testthat/test-fixed-edges.r | 100 ++-- tests/testthat/test-structure-moves.r | 674 ++++++++++++++-------------- 127 files changed, 8132 insertions(+), 8088 deletions(-)