Title: Additional Predictor with Maximum Effect Size
Description: Methods of selecting one from many numeric predictors
for a regression model, to ensure that the additional
predictor has the maximum effect size.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between maxEff versions 0.2.0 dated 2025-10-14 and 0.2.1 dated 2026-01-24
DESCRIPTION | 17 ++++++++--------- MD5 | 24 ++++++++++++------------ R/0PACKAGE.R | 12 ------------ R/add_dummy.R | 2 +- R/add_dummy_partition.R | 2 +- R/add_numeric.R | 2 +- R/node1.R | 13 +++++++------ build/vignette.rds |binary inst/doc/intro.html | 28 ++++++++++++++-------------- man/add_dummy.Rd | 2 +- man/add_dummy_partition.Rd | 2 +- man/add_numeric.Rd | 2 +- man/maxEff-package.Rd | 6 +++--- 13 files changed, 50 insertions(+), 62 deletions(-)
Title: Generalized Additive Models with Hyper Column
Description: Generalized additive models with a numeric hyper column. Sign-adjustment based on the
correlation of model prediction and a selected slice of the
hyper column. Visualization of the integrand surface over the
hyper column.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [ctb] ,
Erjia Cui [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between hyper.gam versions 0.2.0 dated 2025-10-12 and 0.2.1 dated 2026-01-24
hyper.gam-0.2.0/hyper.gam/inst/doc/applications.R |only hyper.gam-0.2.0/hyper.gam/inst/doc/applications.html |only hyper.gam-0.2.0/hyper.gam/inst/doc/applications.qmd |only hyper.gam-0.2.0/hyper.gam/vignettes/applications.qmd |only hyper.gam-0.2.1/hyper.gam/DESCRIPTION | 22 ++--- hyper.gam-0.2.1/hyper.gam/MD5 | 45 ++++++------ hyper.gam-0.2.1/hyper.gam/NAMESPACE | 10 +- hyper.gam-0.2.1/hyper.gam/R/0PACKAGE.R | 2 hyper.gam-0.2.1/hyper.gam/R/cor_xy.R | 12 +-- hyper.gam-0.2.1/hyper.gam/R/gam_ext.R | 8 +- hyper.gam-0.2.1/hyper.gam/R/hyper_gam.R | 4 - hyper.gam-0.2.1/hyper.gam/R/integrandSurface.R | 24 +++--- hyper.gam-0.2.1/hyper.gam/R/kfoldPredict.R | 4 - hyper.gam-0.2.1/hyper.gam/R/sign_adjust.R | 4 - hyper.gam-0.2.1/hyper.gam/R/update.R | 2 hyper.gam-0.2.1/hyper.gam/build/partial.rdb |binary hyper.gam-0.2.1/hyper.gam/build/vignette.rds |binary hyper.gam-0.2.1/hyper.gam/inst/CITATION | 2 hyper.gam-0.2.1/hyper.gam/inst/doc/intro.R |only hyper.gam-0.2.1/hyper.gam/inst/doc/intro.html |only hyper.gam-0.2.1/hyper.gam/inst/doc/intro.qmd |only hyper.gam-0.2.1/hyper.gam/man/cor_xy.Rd | 6 - hyper.gam-0.2.1/hyper.gam/man/getData.gam.Rd |only hyper.gam-0.2.1/hyper.gam/man/hyper.gam-package.Rd | 10 -- hyper.gam-0.2.1/hyper.gam/man/integrandSurface.Rd | 4 - hyper.gam-0.2.1/hyper.gam/man/sign_adjust.Rd | 2 hyper.gam-0.2.1/hyper.gam/vignettes/hypergam.bib | 71 +------------------ hyper.gam-0.2.1/hyper.gam/vignettes/intro.qmd |only 28 files changed, 85 insertions(+), 147 deletions(-)
Title: Simulated Grouped Hyper Data Frame
Description: An intuitive interface to simulate (1) superimposed (marked) point patterns with vectorized parameterization of random point pattern and distribution of marks; and (2) grouped hyper data frame based on population parameters and subject-specific random effects.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe.random versions 0.2.0 dated 2025-10-14 and 0.2.1 dated 2026-01-24
groupedHyperframe.random-0.2.0/groupedHyperframe.random/inst/doc/groupedHyperframe.random.R |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/inst/doc/groupedHyperframe.random.html |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/inst/doc/groupedHyperframe.random.qmd |only groupedHyperframe.random-0.2.0/groupedHyperframe.random/vignettes/groupedHyperframe.random.qmd |only groupedHyperframe.random-0.2.1/groupedHyperframe.random/DESCRIPTION | 14 +- groupedHyperframe.random-0.2.1/groupedHyperframe.random/MD5 | 26 ++-- groupedHyperframe.random-0.2.1/groupedHyperframe.random/NAMESPACE | 8 - groupedHyperframe.random-0.2.1/groupedHyperframe.random/R/0PACKAGE.R | 10 - groupedHyperframe.random-0.2.1/groupedHyperframe.random/R/mvrnorm2.R | 17 ++ groupedHyperframe.random-0.2.1/groupedHyperframe.random/R/rppp.R | 20 +-- groupedHyperframe.random-0.2.1/groupedHyperframe.random/build/vignette.rds |binary groupedHyperframe.random-0.2.1/groupedHyperframe.random/inst/doc/intro.R |only groupedHyperframe.random-0.2.1/groupedHyperframe.random/inst/doc/intro.html |only groupedHyperframe.random-0.2.1/groupedHyperframe.random/inst/doc/intro.qmd |only groupedHyperframe.random-0.2.1/groupedHyperframe.random/man/groupedHyperframe.random-package.Rd | 13 -- groupedHyperframe.random-0.2.1/groupedHyperframe.random/man/mvrnorm2.Rd | 12 +- groupedHyperframe.random-0.2.1/groupedHyperframe.random/vignettes/groupedHyperframe.random.bib | 57 +--------- groupedHyperframe.random-0.2.1/groupedHyperframe.random/vignettes/intro.qmd |only 18 files changed, 78 insertions(+), 99 deletions(-)
More information about groupedHyperframe.random at CRAN
Permanent link
Title: Utility Functions to Support and Extend the 'rbmi' Package
Description: Provides utility functions that extend the capabilities of the
reference-based multiple imputation package 'rbmi'. It supports clinical
trial analysis workflows with functions for managing imputed datasets,
applying analysis methods across imputations, and tidying results for
reporting.
Author: Mark Baillie [aut, cre, cph] ,
Tobias Muetze [aut] ,
Jack Talboys [aut],
Lukas A. Widmer [ctb]
Maintainer: Mark Baillie <bailliem@gmail.com>
This is a re-admission after prior archival of version 0.1.6 dated 2025-09-13
Diff between rbmiUtils versions 0.1.6 dated 2025-09-13 and 0.1.8 dated 2026-01-24
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 8 ++++++++ R/analysis_utils.R | 35 +++++++++++++++++++++++++++++++++++ R/utils.R | 3 +-- README.md | 8 ++++---- inst/doc/analyse2.html | 17 +++++++++-------- man/gcomp_binary.Rd | 2 +- man/gcomp_responder.Rd | 36 ++++++++++++++++++++++++++++++++++++ 9 files changed, 108 insertions(+), 29 deletions(-)
Title: Assessing Proximal, Distal, and Mediated Causal Excursion
Effects for Micro-Randomized Trials
Description: Provides methods to analyze micro-randomized trials (MRTs) with binary treatment options. Supports four types of analyses: (1) proximal causal excursion effects, including weighted and centered least squares (WCLS) for continuous proximal outcomes by Boruvka et al. (2018) <doi:10.1080/01621459.2017.1305274> and the estimator for marginal excursion effect (EMEE) for binary proximal outcomes by Qian et al. (2021) <doi:10.1093/biomet/asaa070>; (2) distal causal excursion effects (DCEE) for continuous distal outcomes using a two-stage estimator by Qian (2025) <doi:10.1093/biomtc/ujaf134>; (3) mediated causal excursion effects (MCEE) for continuous distal outcomes, estimating natural direct and indirect excursion effects in the presence of time-varying mediators by Qian (2025) <doi:10.48550/arXiv.2506.20027>; and (4) standardized proximal effect size estimation for continuous proximal outcomes, generalizing the approach in Luers et al. (2019) <doi:10.1007/s11121- [...truncated...]
Author: Tianchen Qian [aut, cre] ,
Shaolin Xiang [aut],
Zhaoxi Cheng [aut],
Xinyi Song [aut],
John Dziak [aut],
Audrey Boruvka [ctb]
Maintainer: Tianchen Qian <t.qian@uci.edu>
Diff between MRTAnalysis versions 0.4.0 dated 2026-01-24 and 0.4.1 dated 2026-01-24
DESCRIPTION | 6 ++-- MD5 | 17 ++++++------- NEWS.md | 14 +++++++--- inst/doc/mrt-distal-causal-effect.html | 8 +++--- inst/doc/mrt-mediated-causal-effect-on-distal-outcome.html | 4 +-- inst/doc/mrt-proximal-causal-effect.html | 4 +-- inst/doc/mrt-standardized-effect-size.Rmd | 4 +-- inst/doc/mrt-standardized-effect-size.html | 11 ++++---- tests/manual |only vignettes/mrt-standardized-effect-size.Rmd | 4 +-- 10 files changed, 40 insertions(+), 32 deletions(-)
Title: Biodiversity Data Cleaning
Description: It brings together several aspects of biodiversity
data-cleaning in one place. 'bdc' is organized in thematic modules
related to different biodiversity dimensions, including 1) Merge
datasets: standardization and integration of different datasets; 2)
pre-filter: flagging and removal of invalid or non-interpretable
information, followed by data amendments; 3) taxonomy: cleaning,
parsing, and harmonization of scientific names from several taxonomic
groups against taxonomic databases locally stored through the
application of exact and partial matching algorithms; 4) space:
flagging of erroneous, suspect, and low-precision geographic
coordinates; and 5) time: flagging and, whenever possible, correction
of inconsistent collection date. In addition, it contains
features to visualize, document, and report data quality – which is
essential for making data quality assessment transparent and
reproducible. The reference for the methodology is Ribeiro and colleagues (2022)
<doi:10.1111/2041-210 [...truncated...]
Author: Bruno Ribeiro [aut, cre] ,
Santiago Velazco [aut] ,
Karlo Guidoni-Martins [aut] ,
Geiziane Tessarolo [aut] ,
Lucas Jardim [aut] ,
Steven Bachman [ctb] ,
Rafael Loyola [ctb]
Maintainer: Bruno Ribeiro <ribeiro.brr@gmail.com>
This is a re-admission after prior archival of version 1.1.5 dated 2024-12-17
Diff between bdc versions 1.1.5 dated 2024-12-17 and 1.1.6 dated 2026-01-24
bdc-1.1.5/bdc/inst/extdata/countries_names/reword-countries.csv |only bdc-1.1.6/bdc/DESCRIPTION | 39 +++++----- bdc-1.1.6/bdc/MD5 | 30 +++---- bdc-1.1.6/bdc/NAMESPACE | 4 - bdc-1.1.6/bdc/NEWS.md | 5 + bdc-1.1.6/bdc/R/bdc_clean_names.R | 37 +++++---- bdc-1.1.6/bdc/R/bdc_create_figures.R | 35 +++++--- bdc-1.1.6/bdc/R/bdc_query_names_taxadb.R | 1 bdc-1.1.6/bdc/R/bdc_standardize_country.R | 4 - bdc-1.1.6/bdc/R/bdc_standardize_datasets.R | 30 ++++--- bdc-1.1.6/bdc/R/bdc_stdz_cntr.R | 7 - bdc-1.1.6/bdc/inst/extdata/countries_names/country_names.txt | 30 +++++++ bdc-1.1.6/bdc/inst/extdata/countries_names/reword-countries.txt |only bdc-1.1.6/bdc/man/bdc_clean_names.Rd | 7 + bdc-1.1.6/bdc/man/bdc_query_names_taxadb.Rd | 3 bdc-1.1.6/bdc/man/bdc_standardize_datasets.Rd | 5 - bdc-1.1.6/bdc/tests/testthat/test-bdc_standardize_datasets.R | 30 ++++--- 17 files changed, 165 insertions(+), 102 deletions(-)
Title: Simple Multivariate Statistical Estimation and Tests
Description: A collection of simple parameter estimation and tests for the comparison of multivariate means and variation, to accompany Chapters 4 and 5 of the book Multivariate Statistical Methods. A Primer (5th edition), by Manly BFJ, Navarro Alberto JA & Gerow K (2024) <doi:10.1201/9781003453482>.
Author: Jorge Navarro Alberto [aut, cre, cph]
Maintainer: Jorge Navarro Alberto <ganava4@gmail.com>
Diff between smsets versions 1.2.3 dated 2025-07-08 and 2.0.0 dated 2026-01-24
DESCRIPTION | 12 ++++++------ MD5 | 34 +++++++++++++++++++--------------- NAMESPACE | 9 +++++++++ NEWS.md | 6 ++++++ R/LeveneT2.R | 3 +-- R/Levenetestsms.mv.R |only R/OnewayMANOVA.R | 3 ++- R/print.Levenetestsms.mv.R |only R/smsets-package.R | 6 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/smsets-vignette.R | 8 ++++++++ inst/doc/smsets-vignette.Rmd | 27 ++++++++++++++++++++++++--- inst/doc/smsets-vignette.pdf |binary man/LeveneT2.Rd | 3 +-- man/Levenetestsms.mv.Rd |only man/print.Levenetestsms.mv.Rd |only man/smsets-package.Rd | 6 +++--- vignettes/REFVIGNETTE.bib | 27 ++++++++++++++++++++++++++- vignettes/smsets-vignette.Rmd | 27 ++++++++++++++++++++++++--- 20 files changed, 132 insertions(+), 39 deletions(-)
Title: Dynamic and Interactive EEG Graphics
Description: Allows to visualize high-density electroencephalography (HD-EEG) data through interactive plots and animations, enabling exploratory and communicative analysis of temporal-spatial brain signals. Funder: Masaryk University (Grant No. MUNI/A/1457/2023).
Author: Zdeňka Gerslova [aut, cre] ,
Stanislav Katina [rev] ,
Martin Lamos [ctb]
Maintainer: Zdeňka Gerslova <gerslovaz@math.muni.cz>
Diff between diegr versions 0.1.0 dated 2025-09-23 and 0.2.0 dated 2026-01-24
diegr-0.1.0/diegr/R/interactive_waveforms.R |only diegr-0.1.0/diegr/R/pick_region.R |only diegr-0.1.0/diegr/R/topo_plot.R |only diegr-0.2.0/diegr/DESCRIPTION | 10 diegr-0.2.0/diegr/MD5 | 92 +- diegr-0.2.0/diegr/NAMESPACE | 3 diegr-0.2.0/diegr/NEWS.md |only diegr-0.2.0/diegr/R/animations.R | 187 +--- diegr-0.2.0/diegr/R/baseline_correction.R | 81 + diegr-0.2.0/diegr/R/boxplots.R | 212 ++--- diegr-0.2.0/diegr/R/compute_mean.R | 700 +++++------------ diegr-0.2.0/diegr/R/create_scale.R | 85 +- diegr-0.2.0/diegr/R/helper_functions.R | 276 +++--- diegr-0.2.0/diegr/R/outliers_epoch.R | 111 +- diegr-0.2.0/diegr/R/pick_functions.R |only diegr-0.2.0/diegr/R/point_mesh.R | 11 diegr-0.2.0/diegr/R/scalp_plot.R | 62 - diegr-0.2.0/diegr/R/summary_stats.R |only diegr-0.2.0/diegr/R/timeplots.R |only diegr-0.2.0/diegr/R/topoplots.R |only diegr-0.2.0/diegr/README.md | 59 - diegr-0.2.0/diegr/build/vignette.rds |binary diegr-0.2.0/diegr/inst/doc/diegr.R | 171 ++-- diegr-0.2.0/diegr/inst/doc/diegr.Rmd | 210 +++-- diegr-0.2.0/diegr/inst/doc/diegr.html | 375 +++++---- diegr-0.2.0/diegr/man/animate_scalp.Rd | 6 diegr-0.2.0/diegr/man/animate_topo.Rd | 6 diegr-0.2.0/diegr/man/animate_topo_mean.Rd | 11 diegr-0.2.0/diegr/man/baseline_correction.Rd | 29 diegr-0.2.0/diegr/man/boxplot_epoch.Rd | 34 diegr-0.2.0/diegr/man/boxplot_rt.Rd | 12 diegr-0.2.0/diegr/man/boxplot_subject.Rd | 31 diegr-0.2.0/diegr/man/compute_mean.Rd | 96 +- diegr-0.2.0/diegr/man/create_scale.Rd | 22 diegr-0.2.0/diegr/man/figures/README-timemean-1.png |binary diegr-0.2.0/diegr/man/figures/README-topoplot-1.png |binary diegr-0.2.0/diegr/man/interactive_waveforms.Rd | 44 - diegr-0.2.0/diegr/man/outliers_epoch.Rd | 42 - diegr-0.2.0/diegr/man/pick_data.Rd | 27 diegr-0.2.0/diegr/man/pick_region.Rd | 2 diegr-0.2.0/diegr/man/plot_time_mean.Rd | 57 - diegr-0.2.0/diegr/man/plot_topo_mean.Rd | 16 diegr-0.2.0/diegr/man/scalp_plot.Rd | 14 diegr-0.2.0/diegr/man/summary_stats_rt.Rd |only diegr-0.2.0/diegr/man/topo_plot.Rd | 21 diegr-0.2.0/diegr/tests/testthat/test-animations.R | 2 diegr-0.2.0/diegr/tests/testthat/test-boxplots.R | 14 diegr-0.2.0/diegr/tests/testthat/test-compute_mean.R | 39 diegr-0.2.0/diegr/tests/testthat/test-outliers_epoch.R | 22 diegr-0.2.0/diegr/tests/testthat/test-topo_plot.R | 6 diegr-0.2.0/diegr/vignettes/diegr.Rmd | 210 +++-- diegr-0.2.0/diegr/vignettes/example_animation.gif |only 52 files changed, 1792 insertions(+), 1616 deletions(-)
Title: Apply Functions to All Combinations of List Elements
Description: Provides an extension to the 'purrr' family of mapping
functions to apply a function to each combination of elements in a
list of inputs. Also includes functions for automatically detecting
output type in mapping functions, finding every combination of
elements of lists or rows of data frames, and applying multiple models
to multiple subsets of a dataset.
Author: Alexander Rossell Hayes [aut, cre, cph]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between crossmap versions 0.4.3 dated 2025-12-22 and 0.5.0 dated 2026-01-24
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/future_xmap.R | 7 ++----- R/xmap.R | 4 ++-- man/future_xmap.Rd | 8 -------- man/xmap.Rd | 2 -- tests/testthat/test-future_xmap.R | 6 ------ tests/testthat/test-xmap.R | 10 ---------- 9 files changed, 19 insertions(+), 44 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information see Sparapani, Spanbauer and McCulloch <doi:10.18637/jss.v097.i01>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [ctb],
Matthew Pratola [ctb],
Charles Spanbauer [ctb],
Martyn Plummer [ctb],
Nicky Best [ctb],
Kate Cowles [ctb],
Karen Vines [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 2.9.9 dated 2024-06-21 and 2.9.10 dated 2026-01-24
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- build/vignette.rds |binary data/ACTG175.rda |binary data/alligator.rda |binary data/arq.rda |binary data/bladder.rda |binary data/leukemia.rda |binary data/lung.rda |binary data/transplant.rda |binary data/xdm20.test.rda |binary data/xdm20.train.rda |binary data/ydm20.test.rda |binary data/ydm20.train.rda |binary demo/leuk.R | 9 ++++++--- inst/doc/the-BART-R-package.pdf |binary 16 files changed, 26 insertions(+), 23 deletions(-)
Title: 'REDCap' Data Management
Description: REDCap Data Management - 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application developed at Vanderbilt University, designed for creating and managing online surveys and databases and the REDCap API is an interface that allows external applications to connect to REDCap remotely, and is used to programmatically retrieve or modify project data or settings within REDCap, such as importing or exporting data. REDCapDM is an R package that allows users to manage data exported directly from REDCap or using an API connection. This package includes several functions designed for pre-processing data, generating reports of queries such as outliers or missing values, and following up on previously identified queries.
Author: Joao Carmezim [aut, cre],
Pau Satorra [aut],
Judith Penafiel [aut],
Esther Garcia [aut],
Natalia Pallares [aut],
Cristian Tebe [aut]
Maintainer: Joao Carmezim <jcarmezim@igtp.cat>
Diff between REDCapDM versions 1.0.0 dated 2025-11-26 and 1.0.1 dated 2026-01-24
DESCRIPTION | 8 MD5 | 60 ++--- NAMESPACE | 1 NEWS.md | 39 +++ R/rd_checkbox.R | 29 ++ R/rd_query.R | 3 R/redcap_data.R | 5 R/utils-transform.R | 34 +++ README.md | 1 inst/doc/REDCapDM.html | 374 ++++++++++++++++----------------- man/check_proj.Rd | 44 +-- man/checkbox_names.Rd | 40 +-- man/covican.Rd | 96 ++++---- man/figures/lifecycle-deprecated.svg | 42 +-- man/figures/lifecycle-experimental.svg | 42 +-- man/figures/lifecycle-stable.svg | 58 ++--- man/figures/lifecycle-superseded.svg | 42 +-- man/rd_checkbox.Rd | 144 ++++++------ man/rd_dates.Rd | 88 +++---- man/rd_delete_vars.Rd | 130 +++++------ man/rd_dictionary.Rd | 94 ++++---- man/rd_factor.Rd | 100 ++++---- man/rd_recalculate.Rd | 134 +++++------ man/rd_split.Rd | 136 ++++++------ man/recalculate.Rd | 44 +-- man/redcap_data.Rd | 3 man/round.Rd | 50 ++-- man/split_form.Rd | 44 +-- man/to_factor.Rd | 36 +-- man/transform_checkboxes.Rd | 44 +-- tests/testthat.R | 24 +- 31 files changed, 1045 insertions(+), 944 deletions(-)
Title: Generalized Orthogonal GARCH (GO-GARCH) Models
Description: Provision of classes and methods for estimating generalized
orthogonal GARCH models. This is an alternative approach to CC-GARCH models
in the context of multivariate volatility modeling.
Author: Bernhard Pfaff [aut, cre]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between gogarch versions 0.7-5 dated 2022-04-29 and 0.7-6 dated 2026-01-24
DESCRIPTION | 13 +++++-------- MD5 | 14 +++++++------- data/BVDW.rda |binary data/BVDWAIR.rda |binary data/BVDWSTOXX.rda |binary data/VDW.rda |binary man/BVDWAIR.Rd | 2 +- man/BVDWSTOXX.Rd | 16 ++++++++-------- 8 files changed, 21 insertions(+), 24 deletions(-)
Title: Gene Set Analysis Using the Gene Set Ordinal Association Test
Description: Perform gene set enrichment analyses using the Gene set Ordinal
Association Test (GOAT) algorithm and visualize your
results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.
Author: Frank Koopmans [aut, cre]
Maintainer: Frank Koopmans <ftwkoopmans@gmail.com>
Diff between goat versions 1.1.3 dated 2025-08-27 and 1.1.4 dated 2026-01-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 11 ++++++++++- R/simplify_similarity.R | 6 +++++- 4 files changed, 21 insertions(+), 8 deletions(-)
Title: Easy Visualization of Conditional Effects from Regression Models
Description: Offers a flexible and user-friendly interface for visualizing conditional
effects from a broad range of regression models, including mixed-effects and generalized
additive (mixed) models. Compatible model types include lm(), rlm(), glm(), glm.nb(),
betareg(), and gam() (from 'mgcv'); nonlinear models via nls(); generalized least
squares via gls(); and survival models via coxph() (from 'survival').
Mixed-effects models with random intercepts and/or slopes can be fitted using lmer(),
glmer(), glmer.nb(), glmmTMB(), or gam() (from 'mgcv', via smooth terms).
Plots are rendered using base R graphics with extensive customization options.
Approximate confidence intervals for nls() and betareg() models are computed using
the delta method. Robust standard errors for rlm() are computed using the sandwich
estimator (Zeileis 2004) <doi:10.18637/jss.v011.i10>. For beta regression using
'betareg', see Cribari-Neto and Zeileis (2010) <doi:10.18637/jss.v034.i02>. For
mixed-effects models w [...truncated...]
Author: Luca Corlatti [aut, cre]
Maintainer: Luca Corlatti <lucac1980@yahoo.it>
Diff between easyViz versions 2.0.0 dated 2026-01-08 and 2.0.1 dated 2026-01-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/easyViz.R | 18 +++++++++--------- R/ez-utils.R | 23 ++++++++++------------- man/easyViz.Rd | 18 +++++++++--------- 6 files changed, 44 insertions(+), 39 deletions(-)
Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2025) <doi:10.18637/jss.v115.i02>.
Author: Sean C. Anderson [aut, cre] ,
Eric J. Ward [aut] ,
Philina A. English [aut] ,
Lewis A. K. Barnett [aut] ,
James T. Thorson [aut, cph] ,
Joe Watson [ctb] ,
Julia Indivero [ctb] ,
Jillian C. Dunic [ctb] ,
Joseph Barss [ctb],
Cole C. Monnahan [ctb, cph] [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between sdmTMB versions 0.8.1 dated 2026-01-08 and 1.0.0 dated 2026-01-24
sdmTMB-0.8.1/sdmTMB/man/sdmTMB_simulate.Rd |only sdmTMB-1.0.0/sdmTMB/DESCRIPTION | 8 sdmTMB-1.0.0/sdmTMB/MD5 | 22 +- sdmTMB-1.0.0/sdmTMB/NAMESPACE | 1 sdmTMB-1.0.0/sdmTMB/NEWS.md | 13 + sdmTMB-1.0.0/sdmTMB/R/fit.R | 25 ++ sdmTMB-1.0.0/sdmTMB/R/tmb-sim.R | 136 +++++++-------- sdmTMB-1.0.0/sdmTMB/inst/CITATION | 23 +- sdmTMB-1.0.0/sdmTMB/man/sdmTMB.Rd | 6 sdmTMB-1.0.0/sdmTMB/man/simulate.sdmTMB.Rd | 4 sdmTMB-1.0.0/sdmTMB/man/simulate_new.Rd |only sdmTMB-1.0.0/sdmTMB/tests/testthat/test-betabinomial.R | 151 +++++++++++++++++ sdmTMB-1.0.0/sdmTMB/tests/testthat/test-time-varying.R | 2 13 files changed, 289 insertions(+), 102 deletions(-)
Title: A Collection of Tools for Network Analysis
Description: Provides a collection of network analytic (convenience) functions which are missing in other standard packages. This includes triad census with attributes <doi:10.1016/j.socnet.2019.04.003>, core-periphery models <doi:10.1016/S0378-8733(99)00019-2>, and several graph generators. Most functions are build upon 'igraph'.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between netUtils versions 0.8.3 dated 2024-10-10 and 0.8.4 dated 2026-01-24
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 4 ++-- src/lfr.cpp | 2 +- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Assessing Proximal, Distal, and Mediated Causal Excursion
Effects for Micro-Randomized Trials
Description: Provides methods to analyze micro-randomized trials (MRTs) with binary treatment options. Supports four types of analyses: (1) proximal causal excursion effects, including weighted and centered least squares (WCLS) for continuous proximal outcomes by Boruvka et al. (2018) <doi:10.1080/01621459.2017.1305274> and the estimator for marginal excursion effect (EMEE) for binary proximal outcomes by Qian et al. (2021) <doi:10.1093/biomet/asaa070>; (2) distal causal excursion effects (DCEE) for continuous distal outcomes using a two-stage estimator by Qian (2025) <doi:10.1093/biomtc/ujaf134>; (3) mediated causal excursion effects (MCEE) for continuous distal outcomes, estimating natural direct and indirect excursion effects in the presence of time-varying mediators by Qian (2025) <doi:10.48550/arXiv.2506.20027>; and (4) standardized proximal effect size estimation for continuous proximal outcomes, generalizing the approach in Luers et al. (2019) <doi:10.1007/s11121- [...truncated...]
Author: Tianchen Qian [aut, cre] ,
Shaolin Xiang [aut],
Zhaoxi Cheng [aut],
Xinyi Song [aut],
John Dziak [aut],
Audrey Boruvka [ctb]
Maintainer: Tianchen Qian <t.qian@uci.edu>
Diff between MRTAnalysis versions 0.3.1 dated 2025-11-05 and 0.4.0 dated 2026-01-24
DESCRIPTION | 16 +++-- MD5 | 36 +++++++++---- NAMESPACE | 14 +++++ NEWS.md | 7 ++ R/calculate_mrt_effect_size.R |only R/calculate_mrt_effect_size_helper.R |only R/data_example_for_standardized_effect.R |only R/dcee.R | 5 + R/summary.mrt_effect_size.R |only README.md | 31 +++++++++-- build/vignette.rds |binary data/data_example_for_standardized_effect.rda |only inst/doc/mrt-distal-causal-effect.html | 12 ++-- inst/doc/mrt-mediated-causal-effect-on-distal-outcome.html | 4 - inst/doc/mrt-proximal-causal-effect.html | 17 +++--- inst/doc/mrt-standardized-effect-size.R |only inst/doc/mrt-standardized-effect-size.Rmd |only inst/doc/mrt-standardized-effect-size.html |only man/calculate_mrt_effect_size.Rd |only man/data_example_for_standardized_effect.Rd |only man/dcee.Rd | 5 + man/plot.mrt_effect_size.Rd |only man/summary.mrt_effect_size.Rd |only tests/testthat/test-calculate_mrt_effect_size.R |only vignettes/mhealth-ref.bib | 23 ++++++-- vignettes/mrt-standardized-effect-size.Rmd |only 26 files changed, 129 insertions(+), 41 deletions(-)
Title: Integrative Subtype Generation
Description: Multi-data type subtyping, which is data type agnostic and accepts missing data. Subtyping is performed using intermediary assessments created with autoencoders and similarity calculations. See Fox et al. (2024) <doi:10.1016/j.crmeth.2024.100884> for details.
Author: Mao Tian [cre],
Paul Boutros [aut],
Natalie Fox [aut],
Dan Knight [ctb]
Maintainer: Mao Tian <mtian@sbpdiscovery.org>
Diff between iSubGen versions 1.0.1 dated 2021-04-22 and 1.0.4 dated 2026-01-24
DESCRIPTION | 24 ++++-- MD5 | 47 ++++++------ NEWS.md |only R/apply.scaling.R | 67 ++++++++--------- R/calculate.cis.matrix.R | 28 ++++--- R/calculate.integrative.similarity.matrix.R | 76 ++++++++++++-------- R/calculate.scaling.R | 16 ++-- R/cluster.patients.R | 24 ++---- R/combine.integrative.features.R | 24 +++--- R/create.autoencoder.R | 26 +++--- R/create.autoencoder.irf.matrix.R | 10 +- R/load.molecular.aberration.data.R | 10 +- R/read.scaling.factors.R | 12 +-- R/write.scaling.factors.R | 12 +-- README.md | 73 +++++++++++-------- build/vignette.rds |binary inst/doc/iSubGenGuide.Rnw | 94 ++++++++++++------------- inst/doc/iSubGenGuide.pdf |binary man/apply.scaling.Rd | 4 - man/calculate.cis.matrix.Rd | 20 ++--- man/calculate.integrative.similarity.matrix.Rd | 10 +- man/calculate.scaling.Rd | 4 - man/create.autoencoder.irf.matrix.Rd | 4 - man/write.scaling.factors.Rd | 10 +- vignettes/iSubGenGuide.Rnw | 94 ++++++++++++------------- 25 files changed, 366 insertions(+), 323 deletions(-)
Title: Representation for Glycan Compositions and Structures
Description: Computational representations of glycan compositions and structures,
including details such as linkages, anomers, and substituents. Supports varying
levels of monosaccharide specificity (e.g., "Hex" or "Gal") and ambiguous linkages.
Provides robust parsing and generation of IUPAC-condensed structure strings.
Optimized for vectorized operations on glycan structures, with efficient handling
of duplications. As the cornerstone of the glycoverse ecosystem, this package
delivers the foundational data structures that power glycomics and glycoproteomics
analysis workflows.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyrepr versions 0.9.0 dated 2025-11-23 and 0.10.0 dated 2026-01-24
DESCRIPTION | 6 MD5 | 92 +- NAMESPACE | 31 NEWS.md | 23 R/composition.R | 721 ++++++++++++++-------- R/count-mono.R | 11 R/glyrepr-package.R | 1 R/mono-type.R | 159 ++-- R/reorder-graph.R | 29 R/smap.R | 690 ++++++++++++++------- R/structure-level.R | 33 - R/structure-to-iupac.R | 7 R/structure.R | 625 ++++++++++++------- R/substituent.R | 2 README.md | 17 inst/doc/glycan-graph.html | 17 inst/doc/glyrepr.R | 21 inst/doc/glyrepr.Rmd | 21 inst/doc/glyrepr.html | 82 +- inst/doc/smap.html | 43 - man/as_glycan_composition.Rd | 40 - man/convert_to_generic.Rd | 5 man/count_mono.Rd | 2 man/get_mono_type.Rd | 14 man/get_structure_graphs.Rd | 2 man/get_structure_level.Rd | 10 man/glycan_composition.Rd | 5 man/glycan_structure.Rd | 20 man/remove_substituents.Rd | 2 man/simap.Rd | 4 man/smap.Rd | 2 man/smap2.Rd | 8 man/smap_predicates.Rd | 2 man/smap_unique.Rd | 2 man/spmap.Rd | 10 man/structure_to_iupac.Rd | 2 tests/testthat/_snaps/composition.md | 4 tests/testthat/_snaps/structure-level.md | 2 tests/testthat/_snaps/structure.md | 16 tests/testthat/test-composition.R | 348 +++++++++- tests/testthat/test-count-mono.R | 34 + tests/testthat/test-iupac-to-structure.R | 4 tests/testthat/test-mono-type.R | 88 ++ tests/testthat/test-smap.R | 486 ++++++++++++--- tests/testthat/test-structure-level.R | 90 +- tests/testthat/test-structure.R | 992 ++++++++++++++++++++++++++----- vignettes/glyrepr.Rmd | 21 47 files changed, 3469 insertions(+), 1377 deletions(-)
Title: Conduct Simulation Studies with a Minimal Amount of Source Code
Description: Tool for statistical simulations that have two components.
One component generates the data and the other one
analyzes the data. The main aims of the package are the reduction
of the administrative source code (mainly loops and management code for the
results) and a simple applicability of the package that allows the user to
quickly learn how to work with it. Parallel computing is
also supported. Finally, convenient functions are provided to summarize the
simulation results.
Author: Marsel Scheer [aut, cre]
Maintainer: Marsel Scheer <scheer@freescience.de>
Diff between simTool versions 1.1.8 dated 2025-04-09 and 1.1.9 dated 2026-01-24
DESCRIPTION | 8 - MD5 | 14 +- NEWS.md | 5 R/define_simulation.R | 3 README.md | 7 - build/vignette.rds |binary inst/doc/simTool.R | 298 +++++++++++++++++++++++++------------------------- inst/doc/simTool.html | 196 ++++++++------------------------ 8 files changed, 223 insertions(+), 308 deletions(-)
Title: MareFrame DB Querying Library
Description: Creates and manages a PostgreSQL database suitable for storing fisheries data
and aggregating ready for use within a Gadget <https://gadget-framework.github.io/gadget2/> model.
See <https://mareframe.github.io/mfdb/> for more information.
Author: Jamie Lentin [aut, cre, cph],
Bjarki Thor Elvarsson [aut]
Maintainer: Jamie Lentin <lentinj@shuttlethread.com>
Diff between mfdb versions 7.3-1 dated 2022-06-21 and 7.4-0 dated 2026-01-24
mfdb-7.3-1/mfdb/demo/inttest-tibble.R |only mfdb-7.4-0/mfdb/DESCRIPTION | 15 - mfdb-7.4-0/mfdb/MD5 | 52 +-- mfdb-7.4-0/mfdb/NEWS.md |only mfdb-7.4-0/mfdb/R/mfdb.R | 12 mfdb-7.4-0/mfdb/README.md | 49 ++- mfdb-7.4-0/mfdb/build/vignette.rds |binary mfdb-7.4-0/mfdb/demo/00Index | 1 mfdb-7.4-0/mfdb/inst/doc/import_hydrography_cmems.R | 173 +++++------ mfdb-7.4-0/mfdb/inst/doc/import_hydrography_cmems.Rmd | 7 mfdb-7.4-0/mfdb/inst/doc/import_hydrography_cmems.html | 183 ++++++------ mfdb-7.4-0/mfdb/inst/doc/population.R | 7 mfdb-7.4-0/mfdb/inst/doc/population.Rmd | 3 mfdb-7.4-0/mfdb/inst/doc/population.html | 171 ++++++----- mfdb-7.4-0/mfdb/inst/doc/tow_data.R | 17 - mfdb-7.4-0/mfdb/inst/doc/tow_data.Rmd | 3 mfdb-7.4-0/mfdb/inst/doc/tow_data.html | 251 +++++++++-------- mfdb-7.4-0/mfdb/inst/doc/trip.R | 11 mfdb-7.4-0/mfdb/inst/doc/trip.Rmd | 3 mfdb-7.4-0/mfdb/inst/doc/trip.html | 198 +++++++------ mfdb-7.4-0/mfdb/inst/doc/weightmeasurements.R | 13 mfdb-7.4-0/mfdb/inst/doc/weightmeasurements.Rmd | 3 mfdb-7.4-0/mfdb/inst/doc/weightmeasurements.html | 174 ++++++----- mfdb-7.4-0/mfdb/vignettes/import_hydrography_cmems.Rmd | 7 mfdb-7.4-0/mfdb/vignettes/population.Rmd | 3 mfdb-7.4-0/mfdb/vignettes/tow_data.Rmd | 3 mfdb-7.4-0/mfdb/vignettes/trip.Rmd | 3 mfdb-7.4-0/mfdb/vignettes/weightmeasurements.Rmd | 3 28 files changed, 738 insertions(+), 627 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Author: Carson Sievert [aut, cre] ,
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut] ,
Pedro Despouy [aut],
Salim Brueggemann [ctb] ,
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.11.0 dated 2025-06-19 and 4.12.0 dated 2026-01-24
plotly-4.11.0/plotly/tests/testthat/Rplots.pdf |only plotly-4.12.0/plotly/DESCRIPTION | 10 plotly-4.12.0/plotly/MD5 | 704 +++++----- plotly-4.12.0/plotly/NAMESPACE | 1 plotly-4.12.0/plotly/NEWS.md | 40 plotly-4.12.0/plotly/R/api_exports.R | 22 plotly-4.12.0/plotly/R/ggplotly.R | 56 plotly-4.12.0/plotly/R/kaleido.R | 65 plotly-4.12.0/plotly/R/layers2traces.R | 21 plotly-4.12.0/plotly/R/layout.R | 2 plotly-4.12.0/plotly/R/plotly.R | 2 plotly-4.12.0/plotly/R/plotly_build.R | 5 plotly-4.12.0/plotly/R/sysdata.rda |binary plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/001.json | 32 plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/001_.png |binary plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/002.json | 34 plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/002_.png |binary plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/003.json | 34 plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/003_.png |binary plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/004.json | 34 plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/_snaps/shinytest2/004_.png |binary plotly-4.12.0/plotly/inst/examples/shiny/event_data/tests/testthat/test-shinytest2.R | 19 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/es-pe.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/fr.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/hr.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/nl.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/no.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/si.js |only plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/sk.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/locales/zh-tw.js | 2 plotly-4.12.0/plotly/inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js | 69 plotly-4.12.0/plotly/man/TeX.Rd | 2 plotly-4.12.0/plotly/man/add_data.Rd | 2 plotly-4.12.0/plotly/man/add_trace.Rd | 2 plotly-4.12.0/plotly/man/animation.Rd | 2 plotly-4.12.0/plotly/man/api.Rd | 20 plotly-4.12.0/plotly/man/as_widget.Rd | 2 plotly-4.12.0/plotly/man/colorbar.Rd | 2 plotly-4.12.0/plotly/man/config.Rd | 2 plotly-4.12.0/plotly/man/group2NA.Rd | 2 plotly-4.12.0/plotly/man/hide_colorbar.Rd | 2 plotly-4.12.0/plotly/man/hide_legend.Rd | 2 plotly-4.12.0/plotly/man/highlight.Rd | 2 plotly-4.12.0/plotly/man/last_plot.Rd | 2 plotly-4.12.0/plotly/man/layout.Rd | 2 plotly-4.12.0/plotly/man/orca.Rd | 2 plotly-4.12.0/plotly/man/partial_bundle.Rd | 2 plotly-4.12.0/plotly/man/plot_dendro.Rd | 2 plotly-4.12.0/plotly/man/plot_geo.Rd | 2 plotly-4.12.0/plotly/man/plot_ly.Rd | 2 plotly-4.12.0/plotly/man/plotlyProxy.Rd | 2 plotly-4.12.0/plotly/man/plotly_build.Rd | 2 plotly-4.12.0/plotly/man/plotly_data.Rd | 2 plotly-4.12.0/plotly/man/plotly_json.Rd | 2 plotly-4.12.0/plotly/man/rangeslider.Rd | 2 plotly-4.12.0/plotly/man/raster2uri.Rd | 2 plotly-4.12.0/plotly/man/remove_typedarray_polyfill.Rd | 2 plotly-4.12.0/plotly/man/save_image.Rd | 2 plotly-4.12.0/plotly/man/schema.Rd | 2 plotly-4.12.0/plotly/man/showRGB.Rd | 2 plotly-4.12.0/plotly/man/style.Rd | 2 plotly-4.12.0/plotly/man/subplot.Rd | 2 plotly-4.12.0/plotly/man/toRGB.Rd | 2 plotly-4.12.0/plotly/man/toWebGL.Rd | 2 plotly-4.12.0/plotly/tests/testthat/_snaps/cookbook-axes/cookbook-axes-blank-minor-major.svg | 2 plotly-4.12.0/plotly/tests/testthat/_snaps/cookbook-axes/cookbook-axes-blank-minor.svg | 2 plotly-4.12.0/plotly/tests/testthat/_snaps/cookbook-axes/cookbook-axes-blank-x.svg | 2 plotly-4.12.0/plotly/tests/testthat/_snaps/cookbook-axes/cookbook-axes-blank-y.svg | 2 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plotly-4.12.0/plotly/tests/testthat/test-ggplot-blank.R | 26 plotly-4.12.0/plotly/tests/testthat/test-ggplot-boxplot.R | 26 plotly-4.12.0/plotly/tests/testthat/test-ggplot-color.R | 33 plotly-4.12.0/plotly/tests/testthat/test-ggplot-theme.R | 62 plotly-4.12.0/plotly/tests/testthat/test-ggplot-tooltip.R | 16 plotly-4.12.0/plotly/tools/update_plotlyjs.R | 19 354 files changed, 1095 insertions(+), 905 deletions(-)
Title: Applies Display Metadata to Analysis Results Datasets
Description: Creates a framework to store and apply display metadata to
Analysis Results Datasets (ARDs). The use of 'tfrmt' allows users to
define table format and styling without the data, and later apply the
format to the data.
Author: Becca Krouse [aut, cre],
Christina Fillmore [aut] ,
Ellis Hughes [aut] ,
Karima Ahmad [aut] ,
Shannon Haughton [aut],
Dragoș Moldovan-Gruenfeld [aut],
Alanah Jonas [aut],
GlaxoSmithKline Research & Development Limited [cph, fnd],
Atorus Research LLC [ [...truncated...]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Diff between tfrmt versions 0.2.1 dated 2025-10-04 and 0.3.0 dated 2026-01-24
DESCRIPTION | 14 MD5 | 98 +++--- NAMESPACE | 9 NEWS.md | 43 +- R/JSON.R | 61 ++- R/apply_col_plan.R | 79 +++-- R/apply_col_style_plan.R | 13 R/apply_footnote_meta.R | 24 + R/apply_footnote_plan.R | 16 - R/apply_frmt_methods.R | 8 R/apply_page_plan.R | 89 ++++- R/apply_row_grp_plan.R | 89 +++-- R/apply_table_frmt_plan.R | 7 R/apply_tfrmt.R | 55 ++- R/body_plan.R | 5 R/col_plan.R | 148 +++++---- R/display_insights.R | 49 ++- R/eval_tidyselect.R | 17 - R/mock_tbl.R | 32 +- R/page_plan.R | 67 +++- R/prep_card.R | 2 R/print_to_ggplot.R | 9 R/print_to_gt.R | 116 +++++-- R/shuffle_card.R | 23 + R/struct_utils.R | 9 R/tfrmt_checks.R | 13 R/tfrmt_sigdig.R | 21 + README.md | 27 - inst/create_json_example_tfrmts.R | 6 man/col_plan.Rd | 12 man/display_row_frmts.Rd | 6 man/page_plan.Rd | 40 ++ man/print_mock_gt.Rd | 2 man/print_to_ggplot.Rd | 2 man/print_to_gt.Rd | 6 man/tfrmt_sigdig.Rd | 4 man/tfrmt_to_json.Rd | 2 tests/testthat/_snaps/JSON.md | 64 +++- tests/testthat/_snaps/prep_card.md | 320 ++++++++++---------- tests/testthat/test-JSON.R | 94 +++++- tests/testthat/test-apply_col_plan.R |only tests/testthat/test-apply_page_plan.R | 485 ++++++++++++++++++++++++++++++- tests/testthat/test-apply_row_grp_plan.R | 139 ++++++-- tests/testthat/test-big_n.R | 8 tests/testthat/test-col_plan.R | 73 ++++ tests/testthat/test-make_mock_data.R | 3 tests/testthat/test-mrkdown_labels.R | 14 tests/testthat/test-print_to_gt.R |only tests/testthat/test-shuffle_card.R | 11 tests/testthat/test-tfrmt_checks.R | 6 tests/testthat/test-utils_tfrmt.R | 34 +- 51 files changed, 1842 insertions(+), 632 deletions(-)
Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matt Higham [aut] ,
Ryan A. Hill [ctb] ,
Michael Mahon [ctb] ,
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spmodel versions 0.11.1 dated 2025-11-14 and 0.12.0 dated 2026-01-24
DESCRIPTION | 6 MD5 | 64 - NAMESPACE | 2 NEWS.md | 17 R/covmatrix.R | 460 +++---- R/data.R | 466 +++---- R/dispersion_optim2orig.R | 40 R/dispersion_orig2optim.R | 34 R/eacf.R |only R/esv.R | 2 R/get_data_object.R | 1179 +++++++++---------- R/get_data_object_glm.R | 1289 ++++++++++----------- R/get_eacf.R |only R/get_eacf_dotlist.R |only R/get_esv.R | 146 +- R/get_local_list.R | 407 +++--- R/glances.R | 308 ++--- R/glances_glm.R | 82 - R/laploglik_products.R | 1026 ++++++++--------- R/predict.R | 2550 +++++++++++++++++++++---------------------- R/predict_block.R | 496 ++++---- R/sf_to_df.R | 54 R/spcov_matrix.R | 426 +++---- R/spcov_vector.R | 306 ++--- R/use_gloglik_iid.R | 116 - inst/doc/introduction.Rmd | 810 ++++++------- inst/doc/introduction.html | 8 inst/references.bib | 1612 +++++++++++++-------------- man/eacf.Rd |only man/fc_borders.Rd | 56 man/predict.spmodel.Rd | 2 tests/testthat/test-extras.R | 92 + tests/testthat/test-spglm.R | 9 tests/testthat/test-splm.R | 959 ++++++++-------- vignettes/introduction.Rmd | 810 ++++++------- 35 files changed, 7008 insertions(+), 6826 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier [aut, cre],
William Muir [aut],
Katy Rainey [aut],
Shizhong Xu [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.7.3 dated 2019-09-23 and 1.8.0 dated 2026-01-24
NAM-1.7.3/NAM/inst/doc/background_stat_gen.pdf |only NAM-1.7.3/NAM/inst/doc/gwa_description.pdf |only NAM-1.7.3/NAM/inst/doc/gwa_ge_interactions.pdf |only NAM-1.8.0/NAM/DESCRIPTION | 15 NAM-1.8.0/NAM/MD5 | 40 NAM-1.8.0/NAM/NAMESPACE | 3 NAM-1.8.0/NAM/R/RcppExports.R | 318 ++-- NAM-1.8.0/NAM/R/gibbs.R | 24 NAM-1.8.0/NAM/R/pegs.R |only NAM-1.8.0/NAM/R/reml.R | 14 NAM-1.8.0/NAM/build/vignette.rds |binary NAM-1.8.0/NAM/data/test.RData |only NAM-1.8.0/NAM/demo/fieldvar.R | 51 NAM-1.8.0/NAM/inst/CITATION | 20 NAM-1.8.0/NAM/inst/doc/vignette1.html | 1774 +++++++++++++------------ NAM-1.8.0/NAM/inst/doc/vignette2.R | 38 NAM-1.8.0/NAM/inst/doc/vignette2.html | 756 ++++++---- NAM-1.8.0/NAM/man/Internals.Rd | 52 NAM-1.8.0/NAM/man/NAM-package.Rd | 6 NAM-1.8.0/NAM/man/pegs.Rd |only NAM-1.8.0/NAM/src/Functions.cpp | 13 NAM-1.8.0/NAM/src/Makevars |only NAM-1.8.0/NAM/src/Makevars.win |only NAM-1.8.0/NAM/src/RcppExports.cpp | 8 NAM-1.8.0/NAM/src/init.cpp |only NAM-1.8.0/NAM/src/pegs.cpp |only 26 files changed, 1744 insertions(+), 1388 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions
to help the fit of a parametric distribution to non-censored or censored data.
Censored data may contain left censored, right censored and interval censored values,
with several lower and upper bounds. In addition to maximum likelihood estimation (MLE),
the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit
estimation (MGE) and maximum spacing estimation (MSE) methods (available only for
non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g.
Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction
to parametric estimation.
Author: Marie-Laure Delignette-Muller [aut] ,
Christophe Dutang [aut] ,
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between fitdistrplus versions 1.2-5 dated 2026-01-22 and 1.2-6 dated 2026-01-24
DESCRIPTION | 6 +- MD5 | 16 +++--- NEWS.md | 14 +++++ inst/doc/FAQ.html | 8 +-- inst/doc/Optimalgo.html | 96 ++++++++++++++++++------------------ inst/doc/fitdistrplus_vignette.html | 4 - inst/doc/starting-values.html | 4 - tests/t-ppcomp.R | 68 +++++++++++++------------ tests/t-qqcomp.R | 68 +++++++++++++------------ 9 files changed, 151 insertions(+), 133 deletions(-)
Title: Genomic Region Processing using Tools Such as 'BEDTools',
'BEDOPS' and 'Tabix'
Description: Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'.
These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging.
bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.
Author: Syed Haider [aut],
Daryl Waggott [aut],
Emilie Lalonde [ctb],
Clement Fung [ctb],
Helena Winata [ctb],
Dan Knight [ctb],
Michael Chirico [ctb],
Melinda Luo [ctb],
Paul C. Boutros [aut, cre, cph]
Maintainer: Paul C. Boutros <pboutros@sbpdiscovery.org>
Diff between bedr versions 1.1.3 dated 2025-04-06 and 1.1.5 dated 2026-01-24
DESCRIPTION | 15 MD5 | 8 NEWS.md | 15 build/vignette.rds |binary inst/doc/Using-bedr.html | 821 +---------------------------------------------- 5 files changed, 45 insertions(+), 814 deletions(-)