Title: Support for Spatial Objects Within the 'mlr3' Ecosystem
Description: Extends the 'mlr3' ML framework with methods for spatial
objects. Data storage and prediction are supported for packages
'terra', 'raster' and 'stars'.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3spatial versions 0.6.1 dated 2025-09-14 and 0.7.0 dated 2026-07-14
DESCRIPTION | 9 MD5 | 94 +++--- NEWS.md | 6 R/DataBackendRaster.R | 80 +++-- R/DataBackendVector.R | 10 R/LearnerClassifSpatial.R | 11 R/LearnerRegrSpatial.R | 5 R/TaskClassifST.R | 45 ++- R/TaskClassif_leipzig.R | 2 R/TaskRegrST.R | 35 +- R/as_task_classif_st.R | 79 +++++ R/as_task_regr_st.R | 72 ++++- R/data.R | 14 - R/helper.R | 14 - R/predict_spatial.R | 102 +++++-- R/zzz.R | 26 + build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/benchmark.Rmd | 2 inst/doc/benchmark.html | 7 man/DataBackendRaster.Rd | 256 +++++++++--------- man/DataBackendVector.Rd | 69 ++--- man/TaskClassifST.Rd | 218 +++++++--------- man/TaskRegrST.Rd | 215 +++++++-------- man/as_data_backend.Rd | 7 man/block_size.Rd | 2 man/figures/logo.png |binary man/generate_stack.Rd | 2 man/mask_stack.Rd | 4 man/mlr3spatial-package.Rd | 6 man/predict_spatial.Rd | 20 + man/sample_stack.Rd | 2 tests/testthat/helper_expectations.R | 7 tests/testthat/helper_learner.R | 4 tests/testthat/test_DataBackendRaster.R | 381 ++++++++++++++++++++++------ tests/testthat/test_DataBackendVector.R | 4 tests/testthat/test_LearnerClassifSpatial.R | 52 +++ tests/testthat/test_LearnerRegrSpatial.R | 11 tests/testthat/test_TaskClassifST.R | 11 tests/testthat/test_TaskRegrST.R | 11 tests/testthat/test_as_task_classif_st.R | 77 +++-- tests/testthat/test_as_task_regr_st.R | 78 +++-- tests/testthat/test_as_task_unsupervised.R | 47 ++- tests/testthat/test_bock_size.R | 72 +++-- tests/testthat/test_data.R | 9 tests/testthat/test_predict_spatial.R | 193 +++++++++++--- vignettes/benchmark.Rmd | 2 vignettes/benchmark.Rmd.orig | 2 48 files changed, 1570 insertions(+), 806 deletions(-)
Title: Bayesian Hierarchical Analysis of Cognitive Models of Choice
Description: Fit Bayesian (hierarchical) cognitive models
using a linear modeling language interface using particle Metropolis Markov
chain Monte Carlo sampling with Gibbs steps. The diffusion decision model (DDM),
linear ballistic accumulator model (LBA), racing diffusion model (RDM), and the lognormal
race model (LNR) are supported. Additionally, users can specify their own likelihood
function and/or choose for non-hierarchical
estimation, as well as for a diagonal, blocked or full multivariate normal
group-level distribution to test individual differences. Prior specification
is facilitated through methods that visualize the (implied) prior.
A wide range of plotting functions assist in assessing model convergence and
posterior inference. Models can be easily evaluated using functions
that plot posterior predictions or using relative model comparison metrics
such as information criteria or Bayes factors.
References: Stevenson et al. (2024) <doi:10.31234/osf.io/2e4dq>.
Author: Niek Stevenson [aut, cre] ,
Michelle Donzallaz [aut],
Andrew Heathcote [aut],
Steven Miletic [aut],
Luke Strickland [ctb],
Frank Hezemans [ctb],
Raphael Hartmann [ctb],
Karl C. Klauer [ctb],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [...truncated...]
Maintainer: Niek Stevenson <niek.stevenson@gmail.com>
Diff between EMC2 versions 3.4.1 dated 2026-01-12 and 3.5.0 dated 2026-07-14
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EMC2-3.5.0/EMC2/inst/doc/Simulation-based-Calibration.R | 20 EMC2-3.5.0/EMC2/inst/doc/Simulation-based-Calibration.Rmd | 20 EMC2-3.5.0/EMC2/inst/doc/Simulation-based-Calibration.html | 26 EMC2-3.5.0/EMC2/inst/doc/race-models.R |only EMC2-3.5.0/EMC2/inst/doc/race-models.Rmd |only EMC2-3.5.0/EMC2/inst/doc/race-models.html |only EMC2-3.5.0/EMC2/inst/doc/response-models.R |only EMC2-3.5.0/EMC2/inst/doc/response-models.Rmd |only EMC2-3.5.0/EMC2/inst/doc/response-models.html |only EMC2-3.5.0/EMC2/inst/doc/trends.R | 10 EMC2-3.5.0/EMC2/inst/doc/trends.Rmd | 22 EMC2-3.5.0/EMC2/inst/doc/trends.html | 40 EMC2-3.5.0/EMC2/inst/include/build_info.h.in |only EMC2-3.5.0/EMC2/inst/include/build_info.h.win |only EMC2-3.5.0/EMC2/man/add_ICs_MLL.Rd |only EMC2-3.5.0/EMC2/man/align_loadings.Rd | 12 EMC2-3.5.0/EMC2/man/apply_kernel.Rd | 15 EMC2-3.5.0/EMC2/man/compare.Rd | 25 EMC2-3.5.0/EMC2/man/design.Rd | 29 EMC2-3.5.0/EMC2/man/emc2_build_info.Rd |only EMC2-3.5.0/EMC2/man/fix_custom_kernel_pointers.Rd | 7 EMC2-3.5.0/EMC2/man/get_custom_kernel_pointers.Rd | 3 EMC2-3.5.0/EMC2/man/graphical_model.Rd |only EMC2-3.5.0/EMC2/man/group_design.Rd | 12 EMC2-3.5.0/EMC2/man/make_emc.Rd | 3 EMC2-3.5.0/EMC2/man/make_sem_structure.Rd | 9 EMC2-3.5.0/EMC2/man/make_trend.Rd | 18 EMC2-3.5.0/EMC2/man/multinomial_logit.Rd |only EMC2-3.5.0/EMC2/man/multinomial_probit.Rd |only EMC2-3.5.0/EMC2/man/ordered_logit.Rd |only EMC2-3.5.0/EMC2/man/ordered_probit.Rd |only EMC2-3.5.0/EMC2/man/parameters.Rd | 22 EMC2-3.5.0/EMC2/man/plot.emc.prior.Rd | 24 EMC2-3.5.0/EMC2/man/plot_fit_choice.Rd |only EMC2-3.5.0/EMC2/man/plot_trend.Rd | 71 EMC2-3.5.0/EMC2/man/predict.emc.Rd | 3 EMC2-3.5.0/EMC2/man/prior.Rd | 38 EMC2-3.5.0/EMC2/man/prior_help.Rd | 2 EMC2-3.5.0/EMC2/man/register_trend.Rd | 2 EMC2-3.5.0/EMC2/src/Makevars.dev |only EMC2-3.5.0/EMC2/src/Makevars.in |only EMC2-3.5.0/EMC2/src/Makevars.win | 2 EMC2-3.5.0/EMC2/src/ParamTable.cpp |only EMC2-3.5.0/EMC2/src/ParamTable.h |only EMC2-3.5.0/EMC2/src/RaceSetup.h |only EMC2-3.5.0/EMC2/src/RaceSpec.h |only EMC2-3.5.0/EMC2/src/RcppExports.cpp | 81 EMC2-3.5.0/EMC2/src/TrendEngine.cpp |only EMC2-3.5.0/EMC2/src/TrendEngine.h |only EMC2-3.5.0/EMC2/src/build_info.cpp |only EMC2-3.5.0/EMC2/src/custom_trend_interface.cpp |only EMC2-3.5.0/EMC2/src/kernels.cpp |only EMC2-3.5.0/EMC2/src/kernels.h |only EMC2-3.5.0/EMC2/src/math_utils.h |only EMC2-3.5.0/EMC2/src/math_utils_apple.cpp |only EMC2-3.5.0/EMC2/src/math_utils_generic.cpp |only EMC2-3.5.0/EMC2/src/model_DDM.h | 4 EMC2-3.5.0/EMC2/src/model_LBA.h | 399 +- EMC2-3.5.0/EMC2/src/model_MRI.h | 10 EMC2-3.5.0/EMC2/src/model_RDM.h | 803 ++++ EMC2-3.5.0/EMC2/src/model_lnr.h | 136 EMC2-3.5.0/EMC2/src/nan_check.h |only EMC2-3.5.0/EMC2/src/param_table_interface.cpp |only EMC2-3.5.0/EMC2/src/particle_ll.cpp | 952 +++-- EMC2-3.5.0/EMC2/src/pdf_fncs.cpp | 90 EMC2-3.5.0/EMC2/src/pnorm_utils.h |only EMC2-3.5.0/EMC2/src/tools.cpp | 14 EMC2-3.5.0/EMC2/src/transform_utils.cpp |only EMC2-3.5.0/EMC2/src/transform_utils.h |only 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EMC2-3.5.0/EMC2/tests/testthat/_snaps/plot_relations/plot-relations-cred.svg | 16 EMC2-3.5.0/EMC2/tests/testthat/_snaps/plot_relations/plot-relations-mean.svg | 28 EMC2-3.5.0/EMC2/tests/testthat/_snaps/trend.md | 301 - EMC2-3.5.0/EMC2/tests/testthat/test-choice.R |only EMC2-3.5.0/EMC2/tests/testthat/test-kernels.R | 217 - EMC2-3.5.0/EMC2/tests/testthat/test-likelihoods.R |only EMC2-3.5.0/EMC2/tests/testthat/test-memory_saver.R |only EMC2-3.5.0/EMC2/tests/testthat/test-new_models.R | 24 EMC2-3.5.0/EMC2/tests/testthat/test-trend.R | 175 - EMC2-3.5.0/EMC2/vignettes/DDM.Rmd |only EMC2-3.5.0/EMC2/vignettes/Simulation-based-Calibration.Rmd | 20 EMC2-3.5.0/EMC2/vignettes/data |only EMC2-3.5.0/EMC2/vignettes/race-models.Rmd |only EMC2-3.5.0/EMC2/vignettes/response-models.Rmd |only EMC2-3.5.0/EMC2/vignettes/trends.Rmd | 22 153 files changed, 8599 insertions(+), 4953 deletions(-)
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel [aut, cre] ,
QuantLib Authors [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.1.1 dated 2026-04-15 and 0.1.2 dated 2026-07-14
ChangeLog | 44 ++++++ DESCRIPTION | 8 - MD5 | 54 ++++--- R/calendars.R | 11 + build/partial.rdb |binary inst/NEWS.Rd | 12 + src/Makevars.in | 12 + src/Makevars.win.in | 8 + src/calendars.cpp | 32 +++- src/ql/optional.hpp | 3 src/ql/patterns/observable.hpp | 6 src/ql/shared_ptr.hpp | 2 src/ql/time/calendars/all.hpp | 8 + src/ql/time/calendars/croatia.cpp |only src/ql/time/calendars/croatia.hpp |only src/ql/time/calendars/india.cpp | 219 ++++++++++++++++-------------- src/ql/time/calendars/india.hpp | 2 src/ql/time/calendars/islamicholidays.cpp |only src/ql/time/calendars/islamicholidays.hpp |only src/ql/time/calendars/israel.cpp | 79 ++++++++++ src/ql/time/calendars/israel.hpp | 55 ++++++- src/ql/time/calendars/malta.cpp |only src/ql/time/calendars/malta.hpp |only src/ql/time/calendars/montenegro.cpp |only src/ql/time/calendars/montenegro.hpp |only src/ql/time/calendars/northmacedonia.cpp |only src/ql/time/calendars/northmacedonia.hpp |only src/ql/time/calendars/nullcalendar.hpp | 2 src/ql/time/calendars/serbia.cpp |only src/ql/time/calendars/serbia.hpp |only src/ql/time/calendars/slovenia.cpp |only src/ql/time/calendars/slovenia.hpp |only src/ql/time/calendars/southkorea.cpp | 1 src/ql/time/calendars/uzbekistan.cpp |only src/ql/time/calendars/uzbekistan.hpp |only src/ql/time/date.hpp | 2 36 files changed, 416 insertions(+), 144 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-10 0.7.0
2023-06-07 0.6.0
2023-03-06 0.5.0
2022-11-29 0.4.0
2022-09-01 0.3.0
2022-05-30 0.2.0
2022-02-15 0.1.2
Title: S3 Classes and Methods for Tidy Functional Data
Description: Provides S3 vector types for functional data represented on
grids, in spline bases, or via functional principal components.
Supports arithmetic and summary methods, plotting, derivation,
integration, smoothing, registration, and data import/export for these
functional vectors. Includes data-wrangling tools for re-evaluation,
subsetting, sub-assignment, zooming into sub-domains, and extracting
functional features such as minima, maxima, and their locations.
Enables joint analysis of functional and scalar variables by integrating
functional vectors into standard data frames.
Author: Fabian Scheipl [aut, cre, cph] ,
Jeff Goldsmith [aut],
Maximilian Muecke [aut] ,
Julia Wrobel [ctb] ,
Sebastian Fischer [ctb]
Maintainer: Fabian Scheipl <fabian.scheipl@googlemail.com>
Diff between tf versions 0.4.1 dated 2026-04-07 and 0.5.0 dated 2026-07-14
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tf-0.5.0/tf/R/register.R | 212 ++++++++-- tf-0.5.0/tf/R/registration-class.R | 248 +++++++++++- tf-0.5.0/tf/R/rng.R | 107 +++++ tf-0.5.0/tf/R/smooth.R | 72 +++ tf-0.5.0/tf/R/soft-impute-svd.R | 143 ++++--- tf-0.5.0/tf/R/split-combine.R | 16 tf-0.5.0/tf/R/summarize.R | 140 +++++-- tf-0.5.0/tf/R/tf-package.R | 2 tf-0.5.0/tf/R/tf-s4.R | 7 tf-0.5.0/tf/R/tfb-fpc-utils.R | 34 - tf-0.5.0/tf/R/tfb-fpc.R | 19 tf-0.5.0/tf/R/tfb-mfpc.R |only tf-0.5.0/tf/R/tfb-mv.R |only tf-0.5.0/tf/R/tfb-spline.R | 61 +-- tf-0.5.0/tf/R/tfd-class.R | 111 +++++ tf-0.5.0/tf/R/tfd-mv.R |only tf-0.5.0/tf/R/utils.R | 48 +- tf-0.5.0/tf/R/vctrs-cast.R | 34 + tf-0.5.0/tf/R/vctrs-mv.R |only tf-0.5.0/tf/R/vctrs-ptype2.R | 18 tf-0.5.0/tf/R/where.R | 123 ++++++ tf-0.5.0/tf/R/zzz.R | 1 tf-0.5.0/tf/README.md | 23 + tf-0.5.0/tf/build/partial.rdb |binary tf-0.5.0/tf/inst/testdata/make-test-data.R | 8 tf-0.5.0/tf/man/converters-mv.Rd |only tf-0.5.0/tf/man/converters.Rd | 4 tf-0.5.0/tf/man/ensure_list.Rd | 20 - tf-0.5.0/tf/man/fivenum.Rd | 6 tf-0.5.0/tf/man/fpc_wsvd.Rd | 48 +- tf-0.5.0/tf/man/functionwise.Rd | 35 + tf-0.5.0/tf/man/gait.Rd | 11 tf-0.5.0/tf/man/growth.Rd | 9 tf-0.5.0/tf/man/in_range.Rd | 8 tf-0.5.0/tf/man/median.tf_mv.Rd |only tf-0.5.0/tf/man/pinch.Rd | 7 tf-0.5.0/tf/man/plot.tf_mv.Rd |only tf-0.5.0/tf/man/prep_plotting_arg.Rd | 5 tf-0.5.0/tf/man/savgol.Rd |only tf-0.5.0/tf/man/tf-package.Rd | 4 tf-0.5.0/tf/man/tf_align.Rd | 11 tf-0.5.0/tf/man/tf_approx.Rd | 28 - 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Title: Pediatrics Extension Package for ADaM in 'R' Asset Library
Description: A toolbox for programming Clinical Data Standards Interchange
Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R.
ADaM datasets are a mandatory part of any New Drug or Biologics
License Application submitted to the United States Food and Drug
Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam>). The package is
an extension package of the 'admiral' package for pediatric clinical
trials.
Author: Fanny Gautier [aut, cre] ,
Ross Farrugia [aut],
Zelos Zhu [aut],
Sukalpo Saha [aut],
Lina Patil [aut],
Samia Kabi [aut],
Laura Liao [ctb],
Remigiusz Kudlacz [ctb],
Pierre Wallet [ctb],
Amin Sherzad [ctb],
David Freedman [ctb],
Mahmoud Hamza [ctb],
Cy [...truncated...]
Maintainer: Fanny Gautier <fanny.gautier@cytel.com>
Diff between admiralpeds versions 0.3.0 dated 2026-01-23 and 0.4.0 dated 2026-07-14
DESCRIPTION | 15 MD5 | 77 ++-- NAMESPACE | 1 NEWS.md | 29 + R/admiralpeds-package.R | 6 R/derive_params_growth_age.R | 67 +++- README.md | 7 inst/WORDLIST | 2 inst/doc/admiralpeds.Rmd | 2 inst/doc/admiralpeds.html | 2 inst/doc/advs.R | 80 ++++ inst/doc/advs.Rmd | 135 +++++++- inst/doc/advs.html | 412 +++++++++++++++++++------ man/admiralpeds-package.Rd | 9 man/cdc_bmiage.Rd | 4 man/cdc_htage.Rd | 4 man/cdc_wtage.Rd | 4 man/derive_interp_records.Rd | 2 man/derive_params_growth_age.Rd | 48 ++ man/derive_params_growth_height.Rd | 4 man/figures/atorus_logo.png |binary man/figures/pfizer_logo.png |binary man/figures/roche_logo.png |binary man/find_closest_bin.Rd | 6 man/get_bins.Rd | 6 man/set_bins.Rd | 6 man/who_bmi_for_age_boys.Rd | 4 man/who_bmi_for_age_girls.Rd | 4 man/who_hc_for_age_boys.Rd | 4 man/who_hc_for_age_girls.Rd | 4 man/who_lgth_ht_for_age_boys.Rd | 4 man/who_lgth_ht_for_age_girls.Rd | 4 man/who_wt_for_age_boys.Rd | 4 man/who_wt_for_age_girls.Rd | 4 man/who_wt_for_lgth_boys.Rd | 4 man/who_wt_for_lgth_girls.Rd | 4 tests/testthat/test-derive_params_growth_age.R | 145 ++++++++ vignettes/admiralpeds.Rmd | 2 vignettes/advs.Rmd | 135 +++++++- vignettes/articles |only 40 files changed, 1033 insertions(+), 217 deletions(-)
Title: Directly Adjusted Estimates
Description: Compute estimates and confidence intervals of weighted
averages quickly and easily. Weighted averages are computed using
data.table for speed. Confidence intervals are approximated using the
delta method with either using known formulae or via algorithmic or
numerical derivation.
Author: Joonas Miettinen [cre, aut]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>
Diff between directadjusting versions 0.6.1 dated 2026-02-04 and 0.7.0 dated 2026-07-14
DESCRIPTION | 12 - MD5 | 22 +- NEWS.md | 16 + R/delta_method.R | 16 - R/direct_adjusting.R | 351 ++++++++++++++++++++++++------------- R/package_directadjusting.R | 8 R/utils.R | 12 - R/weights.R | 77 ++++---- README.md | 10 - man/confidence_intervals.Rd | 282 ++++++++++++++--------------- man/directadjusting-package.Rd | 320 ++++++++++++++++++--------------- man/directly_adjusted_estimates.Rd | 119 ++++++++++-- 12 files changed, 757 insertions(+), 488 deletions(-)
More information about directadjusting at CRAN
Permanent link
Title: Safe Formula-Based Regularized Generalized Linear Models
Description: A formula-based wrapper around 'glmnet' that brings the
'glm()'-compatible modeling workflow to regularized generalized
linear models. Training-time 'terms', 'xlevels', and 'contrasts'
are stored on the fit object and reused at predict time, so the
design matrix is reconstructed consistently across sessions.
Complete-case bookkeeping is exposed via 'nobs_info', and linearly
dependent columns are detected by a QR pivot and reported as 'NA'
in 'coef()' and 'summary()' (the 'stats::glm()' convention),
distinguishing "not identifiable" from "shrunk to zero by the
penalty". Novel factor levels at predict time raise the same error
'stats::predict.glm()' does by default, with
'on_new_levels = "na"' as a production-style opt-in. Accepts
character family strings ('gaussian', 'binomial', 'poisson',
'cox', 'multinomial', 'mgaussian') and any 'glm' family object the
underlying 'glmnet' itself accepts, including 'Gamma' and
fixed-theta negative binomial via 'MASS::negative.binomial'.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between fbrglm versions 0.0.1 dated 2026-06-22 and 0.1.0 dated 2026-07-14
DESCRIPTION | 8 - MD5 | 25 ++--- NAMESPACE | 6 + NEWS.md | 35 +++++++ R/fbrglm.R | 1 R/methods.R | 200 +++++++++++++++++++++++++++++++++++++++-- R/residuals.R |only README.md | 15 ++- inst/doc/fbrglm.Rmd | 2 inst/doc/fbrglm.html | 2 man/reexports.Rd |only tests/testthat/test-basic.R | 33 +++++- tests/testthat/test-broom.R |only tests/testthat/test-families.R | 55 +++++++++++ vignettes/fbrglm.Rmd | 2 15 files changed, 355 insertions(+), 29 deletions(-)
Title: Multivariate Spatio-Temporal Models using Structural Equations
Description: Fits a wide variety of multivariate spatio-temporal models
with simultaneous and lagged interactions among variables (including
vector autoregressive spatio-temporal ('VAST') dynamics)
for areal, continuous, or network spatial domains.
It includes time-variable, space-variable, and space-time-variable
interactions using dynamic structural equation models ('DSEM')
as expressive interface, and the 'mgcv' package to specify splines
via the formula interface. See Thorson et al. (2025)
<doi:10.1111/geb.70035> for more details.
Author: James T. Thorson [aut, cre] ,
Sean C. Anderson [aut]
Maintainer: James T. Thorson <James.Thorson@noaa.gov>
Diff between tinyVAST versions 1.6.1 dated 2026-06-30 and 1.6.2 dated 2026-07-14
tinyVAST-1.6.1/tinyVAST/tests/testthat/Rplots.pdf |only tinyVAST-1.6.2/tinyVAST/DESCRIPTION | 8 tinyVAST-1.6.2/tinyVAST/MD5 | 32 tinyVAST-1.6.2/tinyVAST/NEWS.md | 7 tinyVAST-1.6.2/tinyVAST/build/partial.rdb |binary tinyVAST-1.6.2/tinyVAST/build/vignette.rds |binary tinyVAST-1.6.2/tinyVAST/inst/doc/dsem.html | 61 tinyVAST-1.6.2/tinyVAST/inst/doc/mgcv.html | 6 tinyVAST-1.6.2/tinyVAST/inst/doc/model-description.html | 97 tinyVAST-1.6.2/tinyVAST/inst/doc/multiple_data.html | 8 tinyVAST-1.6.2/tinyVAST/inst/doc/spatial.html | 8 tinyVAST-1.6.2/tinyVAST/inst/doc/spatial_factor_analysis.html | 15 tinyVAST-1.6.2/tinyVAST/src/tinyVAST.cpp | 1078 ---------- tinyVAST-1.6.2/tinyVAST/src/utils.h |only tinyVAST-1.6.2/tinyVAST/tests/testthat/test-basic-fits.R | 48 tinyVAST-1.6.2/tinyVAST/tests/testthat/test-dsem.R | 1 tinyVAST-1.6.2/tinyVAST/tests/testthat/test-index-standardization.R | 6 tinyVAST-1.6.2/tinyVAST/tests/testthat/test-smooths.R | 4 18 files changed, 175 insertions(+), 1204 deletions(-)
Title: Tools for the IUCN Red List of Ecosystems and Species
Description: A toolbox created by members of the International Union for
Conservation of Nature (IUCN) Red List of Ecosystems Committee for
Scientific Standards. Primarily, it is a set of tools suitable for
calculating the metrics required for making assessments of species and
ecosystems against the IUCN Red List of Threatened Species and the
IUCN Red List of Ecosystems categories and criteria. See the IUCN
website for detailed guidelines, the criteria, publications and other
information.
Author: Calvin Lee [aut] ,
Nicholas Murray [aut] ,
Aniko Toth [cre, aut] ,
Jose R. Ferrer-Paris [aut]
Maintainer: Aniko Toth <anikobtoth@gmail.com>
Diff between redlistr versions 1.0.4 dated 2023-10-02 and 2.1.0 dated 2026-07-14
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Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including 'ADCP'
measurements, measurements made with 'argo' floats, 'CTD' measurements,
sectional data, sea-level time series, coastline and topographic data, etc.
Provides specialized functions for calculating seawater properties such as
potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state.
Produces graphical displays that conform to the conventions of the
Oceanographic literature. This package is discussed extensively by
Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.
Author: Dan Kelley [aut, cre] ,
Clark Richards [aut] ,
Chantelle Layton [ctb] coauthor),
British Geological Survey [ctb, cph]
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between oce versions 1.8-3 dated 2024-08-17 and 1.8-4 dated 2026-07-14
oce-1.8-3/oce/inst/extdata/ctd_aml.csv.gz |only oce-1.8-3/oce/man/ctd_aml.csv.gz.Rd |only oce-1.8-4/oce/DESCRIPTION | 26 oce-1.8-4/oce/MD5 | 628 +++--- oce-1.8-4/oce/NAMESPACE | 78 oce-1.8-4/oce/NEWS.md | 507 +++-- oce-1.8-4/oce/R/AllClass.R | 802 +------- oce-1.8-4/oce/R/AllClassFlags.R |only oce-1.8-4/oce/R/RcppExports.R | 4 oce-1.8-4/oce/R/accessors.R | 47 oce-1.8-4/oce/R/adp.R | 833 +++----- oce-1.8-4/oce/R/adp.nortek.ad2cp.R | 1777 +++++++++++++------ oce-1.8-4/oce/R/adp.nortek.ad2cp.bottom.track.R |only oce-1.8-4/oce/R/adp.rdi.R | 331 ++- oce-1.8-4/oce/R/adp.sontek.R | 34 oce-1.8-4/oce/R/adv.R | 12 oce-1.8-4/oce/R/adv.nortek.R | 2 oce-1.8-4/oce/R/amsr.R | 180 + oce-1.8-4/oce/R/argo.R | 62 oce-1.8-4/oce/R/argo2ctd.R |only oce-1.8-4/oce/R/as_ctd.R |only oce-1.8-4/oce/R/bin.R | 50 oce-1.8-4/oce/R/bodc.R |only oce-1.8-4/oce/R/coastline.R | 96 - oce-1.8-4/oce/R/colors.R | 542 +++++ oce-1.8-4/oce/R/ctd.R | 1093 +---------- oce-1.8-4/oce/R/ctd.aml.R | 211 +- oce-1.8-4/oce/R/ctd.saiv.R | 23 oce-1.8-4/oce/R/ctd.sbe.R | 1295 +++++++------ oce-1.8-4/oce/R/ctd.ssda.R | 2 oce-1.8-4/oce/R/ctd.woce.R | 5 oce-1.8-4/oce/R/echosounder.R | 10 oce-1.8-4/oce/R/extdata.R | 87 oce-1.8-4/oce/R/g1sst.R | 4 oce-1.8-4/oce/R/imagep.R | 27 oce-1.8-4/oce/R/ladp.R | 2 oce-1.8-4/oce/R/landsat.R | 6 oce-1.8-4/oce/R/lobo.R | 2 oce-1.8-4/oce/R/magfield.R |only oce-1.8-4/oce/R/magic.R |only oce-1.8-4/oce/R/map.R | 200 +- oce-1.8-4/oce/R/met.R | 128 - oce-1.8-4/oce/R/misc.R | 451 +--- oce-1.8-4/oce/R/netcdf.R | 477 ++++- oce-1.8-4/oce/R/oce.R | 954 +--------- oce-1.8-4/oce/R/odf.R | 2 oce-1.8-4/oce/R/rename.R |only oce-1.8-4/oce/R/rsk.R | 335 +-- oce-1.8-4/oce/R/rsk2ctd.R |only oce-1.8-4/oce/R/satellite.R | 2 oce-1.8-4/oce/R/sealevel.R | 53 oce-1.8-4/oce/R/sealevel_gc_2026.R |only oce-1.8-4/oce/R/section.R | 201 +- oce-1.8-4/oce/R/spectral.R | 254 +- oce-1.8-4/oce/R/sw.R | 161 + oce-1.8-4/oce/R/tides.R | 324 --- oce-1.8-4/oce/R/units.R | 235 ++ oce-1.8-4/oce/R/webtide.R |only oce-1.8-4/oce/R/windrose.R | 2 oce-1.8-4/oce/R/xbt.R | 396 +++- oce-1.8-4/oce/build/partial.rdb |binary oce-1.8-4/oce/build/vignette.rds |binary oce-1.8-4/oce/data/rsk.rda |binary oce-1.8-4/oce/inst/WORDLIST | 1005 +++++----- oce-1.8-4/oce/inst/doc/A_oce.R | 82 oce-1.8-4/oce/inst/doc/A_oce.Rmd | 60 oce-1.8-4/oce/inst/doc/A_oce.html | 215 -- oce-1.8-4/oce/inst/doc/B_ctd.R | 86 oce-1.8-4/oce/inst/doc/B_ctd.Rmd | 26 oce-1.8-4/oce/inst/doc/B_ctd.html | 82 oce-1.8-4/oce/inst/doc/C_adp.R | 40 oce-1.8-4/oce/inst/doc/C_adp.html | 28 oce-1.8-4/oce/inst/doc/D_map_projections.R | 2 oce-1.8-4/oce/inst/doc/D_map_projections.html | 29 oce-1.8-4/oce/inst/doc/E_flags.R | 42 oce-1.8-4/oce/inst/doc/E_flags.html | 13 oce-1.8-4/oce/inst/doc/F_subclassing.html | 53 oce-1.8-4/oce/inst/doc/G_altering_defaults.R | 2 oce-1.8-4/oce/inst/doc/G_altering_defaults.Rmd | 5 oce-1.8-4/oce/inst/doc/G_altering_defaults.html | 23 oce-1.8-4/oce/inst/doc/H_tides.R |only oce-1.8-4/oce/inst/doc/H_tides.Rmd |only oce-1.8-4/oce/inst/doc/H_tides.html |only oce-1.8-4/oce/inst/extdata/D4902337_219.nc |only oce-1.8-4/oce/inst/extdata/ctd_aml_type1.csv.gz |only oce-1.8-4/oce/inst/extdata/ctd_aml_type3.csv.gz |only oce-1.8-4/oce/inst/extdata/dictionary_codas.csv |only oce-1.8-4/oce/inst/extdata/dictionary_ioos.csv |only oce-1.8-4/oce/inst/extdata/dictionary_sbe.csv |only oce-1.8-4/oce/inst/extdata/xbt2.edf |only oce-1.8-4/oce/inst/extdata/xbt_noaa2 |only oce-1.8-4/oce/man/CTD_BCD2014666_008_1_DN.ODF.gz.Rd | 13 oce-1.8-4/oce/man/D4902337_219.nc.Rd |only oce-1.8-4/oce/man/ODFNames2oceNames.Rd | 7 oce-1.8-4/oce/man/ad2cpCodeToName.Rd | 4 oce-1.8-4/oce/man/ad2cpHeaderValue.Rd | 23 oce-1.8-4/oce/man/adpFlagPastBoundary.Rd | 24 oce-1.8-4/oce/man/adpRdiFileTrim.Rd | 34 oce-1.8-4/oce/man/adp_rdi.000.Rd | 9 oce-1.8-4/oce/man/argo-class.Rd | 2 oce-1.8-4/oce/man/argo.Rd | 4 oce-1.8-4/oce/man/argo2ctd.Rd |only oce-1.8-4/oce/man/argoGrid.Rd | 2 oce-1.8-4/oce/man/argoNames2oceNames.Rd | 9 oce-1.8-4/oce/man/as.argo.Rd | 2 oce-1.8-4/oce/man/as.ctd.Rd | 112 - oce-1.8-4/oce/man/as.sealevel.Rd | 1 oce-1.8-4/oce/man/as.unit.Rd | 35 oce-1.8-4/oce/man/as.xbt.Rd | 4 oce-1.8-4/oce/man/beamToXyzAdpAD2CP.Rd | 2 oce-1.8-4/oce/man/bodcNames2oceNames.Rd |only oce-1.8-4/oce/man/cnvName2oceName.Rd | 174 + oce-1.8-4/oce/man/colormap.Rd | 1 oce-1.8-4/oce/man/colormapGMT.Rd | 1 oce-1.8-4/oce/man/concatenate-adp-method.Rd | 7 oce-1.8-4/oce/man/concatenate-list-method.Rd | 18 oce-1.8-4/oce/man/concatenate-oce-method.Rd | 4 oce-1.8-4/oce/man/concatenate.Rd | 7 oce-1.8-4/oce/man/ctd-class.Rd | 4 oce-1.8-4/oce/man/ctd.Rd | 4 oce-1.8-4/oce/man/ctd.cnv.gz.Rd | 13 oce-1.8-4/oce/man/ctdDecimate.Rd | 6 oce-1.8-4/oce/man/ctdFindProfiles.Rd | 4 oce-1.8-4/oce/man/ctdFindProfilesRBR.Rd | 6 oce-1.8-4/oce/man/ctdRaw.Rd | 4 oce-1.8-4/oce/man/ctdRepair.Rd | 8 oce-1.8-4/oce/man/ctdTrim.Rd | 4 oce-1.8-4/oce/man/ctd_aml_type1.csv.gz.Rd |only oce-1.8-4/oce/man/ctd_aml_type3.csv.gz.Rd |only oce-1.8-4/oce/man/d200321-001.ctd.gz.Rd | 13 oce-1.8-4/oce/man/d201211_0011.cnv.gz.Rd | 13 oce-1.8-4/oce/man/defaultFlags.Rd | 2 oce-1.8-4/oce/man/download.amsr.Rd | 52 oce-1.8-4/oce/man/download.met.Rd | 4 oce-1.8-4/oce/man/handleFlags-argo-method.Rd | 2 oce-1.8-4/oce/man/handleFlags-ctd-method.Rd | 4 oce-1.8-4/oce/man/handleFlags-oce-method.Rd | 2 oce-1.8-4/oce/man/handleFlags-vector-method.Rd | 2 oce-1.8-4/oce/man/handleFlagsInternal.Rd | 2 oce-1.8-4/oce/man/imagep.Rd | 22 oce-1.8-4/oce/man/initialize-ctd-method.Rd | 4 oce-1.8-4/oce/man/initializeFlagScheme-ctd-method.Rd | 4 oce-1.8-4/oce/man/initializeFlagScheme-oce-method.Rd | 2 oce-1.8-4/oce/man/initializeFlagScheme.Rd | 2 oce-1.8-4/oce/man/initializeFlagSchemeInternal.Rd | 2 oce-1.8-4/oce/man/initializeFlags-oce-method.Rd | 2 oce-1.8-4/oce/man/initializeFlags.Rd | 2 oce-1.8-4/oce/man/initializeFlagsInternal.Rd | 2 oce-1.8-4/oce/man/interpBarnes.Rd | 8 oce-1.8-4/oce/man/locationForGsw.Rd | 6 oce-1.8-4/oce/man/lonlat2map.Rd | 9 oce-1.8-4/oce/man/magneticField.Rd | 102 - 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oce-1.8-4/oce/src/echosounder.cpp | 105 - oce-1.8-4/oce/src/fillgap1d.cpp | 2 oce-1.8-4/oce/src/gappy_index.cpp | 63 oce-1.8-4/oce/src/geod.cpp | 199 +- oce-1.8-4/oce/src/get_bit.cpp | 10 oce-1.8-4/oce/src/gradient.cpp | 26 oce-1.8-4/oce/src/igrf14.f |only oce-1.8-4/oce/src/interp_barnes.cpp | 178 - oce-1.8-4/oce/src/ldc_ad2cp_in_file.cpp | 444 ++-- oce-1.8-4/oce/src/ldc_rdi_in_file.cpp | 18 oce-1.8-4/oce/src/ldc_rdi_in_file_new.cpp | 18 oce-1.8-4/oce/src/locate_byte_sequences.cpp | 2 oce-1.8-4/oce/src/magdec.f | 8 oce-1.8-4/oce/src/map.cpp | 28 oce-1.8-4/oce/src/oce_approx.cpp | 213 +- oce-1.8-4/oce/src/oce_convolve.cpp | 93 oce-1.8-4/oce/src/run.cpp | 24 oce-1.8-4/oce/src/sontek_adp.cpp | 95 - oce-1.8-4/oce/src/sontek_adv.cpp | 6 oce-1.8-4/oce/src/trap.cpp | 24 oce-1.8-4/oce/src/trim.cpp | 6 oce-1.8-4/oce/tests/testthat/test_accessors.R | 11 oce-1.8-4/oce/tests/testthat/test_ad2cp_1.R |only oce-1.8-4/oce/tests/testthat/test_ad2cp_2.R | 34 oce-1.8-4/oce/tests/testthat/test_ad2cp_3.R | 16 oce-1.8-4/oce/tests/testthat/test_ad2cp_4.R | 79 oce-1.8-4/oce/tests/testthat/test_adp.R | 13 oce-1.8-4/oce/tests/testthat/test_amsr.R | 10 oce-1.8-4/oce/tests/testthat/test_argo.R | 34 oce-1.8-4/oce/tests/testthat/test_ctd.R | 101 - 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Title: Nested Cross-Validation with 'glmnet' and 'caret'
Description: Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package <doi:10.1093/bioadv/vbad048>. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.
Author: Myles Lewis [aut, cre] ,
Athina Spiliopoulou [aut] ,
Cankut Cubuk [ctb] ,
David Rios Santini [ctb],
Katriona Goldmann [ctb] ,
Ryan C. Thompson [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
This is a re-admission after prior archival of version 0.8.2 dated 2026-04-10
Diff between nestedcv versions 0.8.2 dated 2026-04-10 and 0.9.0 dated 2026-07-14
DESCRIPTION | 17 ++- MD5 | 55 +++++------ NAMESPACE | 2 NEWS.md | 24 ++++ R/cva.glmnet.R | 18 ++- R/nestcv.train.R | 9 - R/nestcv_SuperLearner.R | 6 - R/nestedcv.R | 11 ++ R/outercv.R | 6 - R/plots.R | 3 R/shap.R | 216 ++++++++++++++++++++++++++++++++------------ R/utils.R | 8 + R/varImp.R | 17 +-- build/vignette.rds |binary inst/doc/nestedcv.html | 92 +++++++++--------- inst/doc/nestedcv_shap.R | 46 +++++---- inst/doc/nestedcv_shap.Rmd | 99 ++++++++++++-------- inst/doc/nestedcv_shap.html | 134 +++++++++++++++------------ man/coef.nestcv.glmnet.Rd | 2 man/glmnet_coefs.Rd | 4 man/lm_filter.Rd | 4 man/nestcv.explain.Rd |only man/plot_shap_bar.Rd | 3 man/plot_shap_beeswarm.Rd | 3 man/pls_filter.Rd | 2 man/predSummary.Rd | 2 man/pred_nestcv_glmnet.Rd | 65 ++++++------- man/ttest_filter.Rd | 6 - vignettes/nestedcv_shap.Rmd | 99 ++++++++++++-------- 29 files changed, 593 insertions(+), 360 deletions(-)
Title: Functional Multivariable Mendelian Randomization
Description: Implements Multivariable Functional Mendelian Randomization (MV-FMR) to estimate time-varying causal effects of multiple longitudinal exposures on health outcomes. Extends univariable functional Mendelian Randomisation (MR) (Tian et al., 2024 <doi:10.1002/sim.10222>) to the multivariable setting, enabling joint estimation of multiple time-varying exposures with pleiotropy and mediation scenarios. Key features include: (1) data-driven cross-validation for basis component selection, (2) handling of mediation pathways between exposures, (3) support for both continuous and binary outcomes using Generalized Method of Moments (GMM) and control function approaches, (4) one-sample and two-sample MR designs, (5) bootstrap inference and instrument diagnostics including Q-statistics for overidentification testing. Methods are described in Fontana et al. (2025) <doi:10.48550/arXiv.2512.19064>.
Author: Nicole Fontana [aut, cre],
Francesca Ieva [aut, ths],
Piercesare Secchi [aut, ths]
Maintainer: Nicole Fontana <nicole.fontana@polimi.it>
Diff between mvfmr versions 0.1.0 dated 2026-02-09 and 0.2.0 dated 2026-07-14
DESCRIPTION | 9 MD5 | 77 - R/all_functions.R | 86 - R/estimation_automatic.R | 1798 ++++++++++---------------- R/estimation_beta.R | 25 R/fmvmr_main.R | 595 ++++---- R/simulation.R | 615 ++++---- R/utilities.R | 48 README.md | 483 +++--- demo/tests_manuscript.R | 290 +--- inst/doc/multivariable-fmr.R | 156 +- inst/doc/multivariable-fmr.Rmd | 181 +- inst/doc/multivariable-fmr.html | 493 +++---- inst/doc/univariable-fmr.R | 71 - inst/doc/univariable-fmr.Rmd | 83 - inst/doc/univariable-fmr.html | 267 +-- inst/examples/test_MV-FMR.R | 163 +- inst/examples/test_U-FMR.R | 133 - man/AUTOMATIC_Multi_FMVMR_twosample_simple.Rd | 23 man/AUTOMATIC_Multi_MVFMR.Rd | 37 man/IS.Rd | 9 man/Separate_Multi_FMVMR_twosample_simple.Rd | 44 man/Separate_Multi_MVFMR.Rd | 42 man/block_idx.Rd |only man/cf_logit.Rd | 10 man/compute_offsets.Rd |only man/fmvmr_separate_twosample.Rd | 59 man/fmvmr_twosample.Rd | 37 man/getX_multi_exposure.Rd | 15 man/getX_multi_exposure_mediation.Rd | 26 man/getY_multi_exposure.Rd | 20 man/gmm_lm_onesample.Rd | 9 man/gmm_twosample_simple.Rd | 9 man/mvfmr.Rd | 42 man/mvfmr_separate.Rd | 48 man/recycle_arg.Rd |only tests |only vignettes/multivariable-fmr.Rmd | 181 +- vignettes/univariable-fmr.Rmd | 83 - 39 files changed, 3072 insertions(+), 3195 deletions(-)
Title: Hierarchical Neyman-Pearson Classification for Ordered Classes
Description: The Hierarchical Neyman-Pearson (H-NP) classification framework
extends the Neyman-Pearson classification paradigm to multi-class settings
where classes have a natural priority ordering. This is particularly useful
for classification in unbalanced dataset, for example, disease severity
classification, where under-classification errors (misclassifying patients
into less severe categories) are more consequential than other
misclassifications. The package implements H-NP umbrella algorithms that
controls under-classification errors under user specified control levels
with high probability. It supports the creation of H-NP classifiers using
scoring functions based on built-in classification methods (including
logistic regression, support vector machines, and random forests), as well
as user-trained scoring functions. The package exports `base_function()`
to train these built-in base learners directly for use in the H-NP
pipeline.
Author: Che Shen [aut, cre] ,
Lujia Yang [aut] ,
Lijia Wang [aut] ,
Shunan Yao [aut]
Maintainer: Che Shen <chshen3-c@my.cityu.edu.hk>
Diff between HNPclassifier versions 0.2.0 dated 2026-06-27 and 0.2.1 dated 2026-07-14
DESCRIPTION | 10 ++++++---- MD5 | 9 +++++---- NAMESPACE | 1 + NEWS.md | 48 ++++++------------------------------------------ R/hnp_package.r | 23 +++++++++++++++++++++++ man/base_function.Rd |only 6 files changed, 41 insertions(+), 50 deletions(-)
Title: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for
Complex Organic Matter
Description: Provides tools for assigning molecular formulas from exact masses
obtained by ultrahigh-resolution mass spectrometry. The methodology follows
the workflow described in Leefmann et al. (2019) <doi:10.1002/rcm.8315>.
The package supports the inspection, filtering and visualization of
molecular formula data and includes utilities for calculating common
molecular parameters (e.g., double bond equivalents, DBE). A graphical
user interface is available via the 'shiny'-based 'ume' application.
Author: Boris Koch [aut, cre] ,
Stephan Frickenhaus [ctb] ,
Shuxian Gao [ctb] ,
Oliver Lechtenfeld [ctb] ,
Tim Leefmann [ctb] ,
Fabian Moye [ctb]
Maintainer: Boris Koch <boris.koch@awi.de>
Diff between ume versions 1.6.1 dated 2026-05-09 and 1.7.1 dated 2026-07-14
ume-1.6.1/ume/R/calc_number_assignments.R |only ume-1.6.1/ume/data/nice_labels_dt.rda |only ume-1.6.1/ume/data/tab_ume_labels.rda |only ume-1.6.1/ume/man/nice_labels_dt.Rd |only ume-1.6.1/ume/man/tab_ume_labels.Rd |only ume-1.6.1/ume/tests/testthat/test-calc_number_assignments.R |only ume-1.7.1/ume/DESCRIPTION | 22 ume-1.7.1/ume/LICENSE | 4 ume-1.7.1/ume/MD5 | 311 ++-- ume-1.7.1/ume/NAMESPACE | 8 ume-1.7.1/ume/NEWS.md | 649 +++++----- ume-1.7.1/ume/R/add_known_mf.R | 271 +++- ume-1.7.1/ume/R/as_mfd.R |only ume-1.7.1/ume/R/as_peaklist.R | 97 + ume-1.7.1/ume/R/as_ume_matrix.R |only ume-1.7.1/ume/R/assign_formulas.R | 13 ume-1.7.1/ume/R/calc_data_summary.R | 21 ume-1.7.1/ume/R/calc_isotope_pattern.R | 63 ume-1.7.1/ume/R/calc_logratio.R |only ume-1.7.1/ume/R/calc_neutral_mass.R | 1 ume-1.7.1/ume/R/calc_norm_int.R | 2 ume-1.7.1/ume/R/calc_number_assignment.R |only ume-1.7.1/ume/R/calc_number_occurrence.R | 3 ume-1.7.1/ume/R/calc_recalibrate_ms.R | 11 ume-1.7.1/ume/R/check_objects.R | 2 ume-1.7.1/ume/R/create_custom_formula_library.R | 4 ume-1.7.1/ume/R/create_time_flattened_mfd.R |only ume-1.7.1/ume/R/create_ume_formula_library.R | 2 ume-1.7.1/ume/R/data.R | 128 + ume-1.7.1/ume/R/download_library.R | 270 +++- ume-1.7.1/ume/R/eval_isotopes.R | 4 ume-1.7.1/ume/R/export_ume_results.R | 8 ume-1.7.1/ume/R/filter.R | 2 ume-1.7.1/ume/R/filter_multi_assignments.R |only ume-1.7.1/ume/R/find_kegg_pathways_by_formula.R |only ume-1.7.1/ume/R/get_isotope_info.R | 2 ume-1.7.1/ume/R/global.R | 20 ume-1.7.1/ume/R/main_docu.R | 4 ume-1.7.1/ume/R/tools.R | 195 ++- ume-1.7.1/ume/R/ume_utilities.R | 12 ume-1.7.1/ume/R/uplot_cluster.R | 227 ++- ume-1.7.1/ume/R/uplot_dbe_minus_o_freq.R | 5 ume-1.7.1/ume/R/uplot_diff_ms.R | 6 ume-1.7.1/ume/R/uplot_hc_vs_m.R | 123 - 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ume-1.7.1/ume/vignettes/vignette_ume.pdf |binary 170 files changed, 4455 insertions(+), 2921 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-19 2.4.2
2021-03-08 2.4.1
2020-05-26 2.4.0
2019-11-18 2.3.1
2018-09-19 2.0.2
2018-07-20 2.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-06-30 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-07 0.7
2023-01-29 0.6.2
2022-05-31 0.6.0
2020-07-03 0.5.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-12 0.4.4
2022-11-28 0.4.3
2021-11-04 0.4.2
2021-10-28 0.4.1
2021-10-26 0.4.0
2020-01-18 0.3.2
2019-09-04 0.3.1
2019-06-21 0.3.0
2014-09-29 0.2
2012-03-01 0.1-4
2011-06-25 0.1-3
2011-05-17 0.1-2
2010-09-25 0.1-1
Title: Extract Trends from Time Series
Description: Provides a unified interface to extract trends, cycles, and
seasonal components from monthly and quarterly time series using
established econometric filters and smoothing methods, with
frequency-aware defaults for common economic frequencies.
Author: Vinicius Oike [aut, cre, cph]
Maintainer: Vinicius Oike <viniciusoike@gmail.com>
Diff between trendseries versions 1.2.0 dated 2026-05-02 and 1.4.0 dated 2026-07-13
trendseries-1.2.0/trendseries/data/series_metadata.rda |only trendseries-1.2.0/trendseries/man/figures/README-unnamed-chunk-3-1.png |only trendseries-1.2.0/trendseries/man/figures/README-unnamed-chunk-3-1.svg |only trendseries-1.2.0/trendseries/man/figures/README-unnamed-chunk-5-1.svg |only trendseries-1.2.0/trendseries/man/figures/index_example.png |only trendseries-1.2.0/trendseries/man/list_datasets.Rd |only trendseries-1.2.0/trendseries/man/series_metadata.Rd |only trendseries-1.4.0/trendseries/DESCRIPTION | 32 trendseries-1.4.0/trendseries/MD5 | 123 +- trendseries-1.4.0/trendseries/NAMESPACE | 15 trendseries-1.4.0/trendseries/NEWS.md | 100 + trendseries-1.4.0/trendseries/R/augment_trends.R | 63 - trendseries-1.4.0/trendseries/R/data.R | 36 trendseries-1.4.0/trendseries/R/decompose_series.R |only trendseries-1.4.0/trendseries/R/deseason_series.R |only trendseries-1.4.0/trendseries/R/detrend_series.R |only trendseries-1.4.0/trendseries/R/extract_trends.R | 103 -- trendseries-1.4.0/trendseries/R/filters_econometric.R | 90 + trendseries-1.4.0/trendseries/R/filters_ma.R | 105 +- trendseries-1.4.0/trendseries/R/method_registry.R |only trendseries-1.4.0/trendseries/R/utils.R | 223 +--- trendseries-1.4.0/trendseries/README.md | 168 +-- trendseries-1.4.0/trendseries/build/vignette.rds |binary trendseries-1.4.0/trendseries/data/coffee_arabica.rda |binary trendseries-1.4.0/trendseries/data/coffee_robusta.rda |binary trendseries-1.4.0/trendseries/data/electric.rda |binary trendseries-1.4.0/trendseries/data/electricity.rda |only trendseries-1.4.0/trendseries/data/gdp_construction.rda |binary trendseries-1.4.0/trendseries/data/ibcbr.rda |binary trendseries-1.4.0/trendseries/data/metadata_series.rda |only trendseries-1.4.0/trendseries/data/oil_derivatives.rda |binary trendseries-1.4.0/trendseries/data/retail_autofuel.rda |binary trendseries-1.4.0/trendseries/data/retail_volume.rda |binary trendseries-1.4.0/trendseries/data/transit_london_avgs.rda |binary trendseries-1.4.0/trendseries/data/transit_london_monthly.rda |binary trendseries-1.4.0/trendseries/data/vehicles.rda |binary trendseries-1.4.0/trendseries/inst/doc/augment-trends.R |only trendseries-1.4.0/trendseries/inst/doc/augment-trends.Rmd |only trendseries-1.4.0/trendseries/inst/doc/augment-trends.html |only trendseries-1.4.0/trendseries/inst/doc/decompose-series.R |only trendseries-1.4.0/trendseries/inst/doc/decompose-series.Rmd |only trendseries-1.4.0/trendseries/inst/doc/decompose-series.html |only trendseries-1.4.0/trendseries/inst/doc/detrend-series.R |only trendseries-1.4.0/trendseries/inst/doc/detrend-series.Rmd |only trendseries-1.4.0/trendseries/inst/doc/detrend-series.html |only trendseries-1.4.0/trendseries/inst/doc/econometric-filters.R |only trendseries-1.4.0/trendseries/inst/doc/econometric-filters.Rmd |only trendseries-1.4.0/trendseries/inst/doc/econometric-filters.html |only trendseries-1.4.0/trendseries/inst/doc/methods.R |only trendseries-1.4.0/trendseries/inst/doc/methods.Rmd |only trendseries-1.4.0/trendseries/inst/doc/methods.html |only trendseries-1.4.0/trendseries/inst/doc/moving-averages.R | 57 - trendseries-1.4.0/trendseries/inst/doc/moving-averages.Rmd | 68 - trendseries-1.4.0/trendseries/inst/doc/moving-averages.html | 357 +++--- trendseries-1.4.0/trendseries/inst/doc/trendseries.R | 226 ---- trendseries-1.4.0/trendseries/inst/doc/trendseries.Rmd | 393 +------ trendseries-1.4.0/trendseries/inst/doc/trendseries.html | 486 +++------ trendseries-1.4.0/trendseries/man/augment_trends.Rd | 13 trendseries-1.4.0/trendseries/man/coffee_arabica.Rd | 2 trendseries-1.4.0/trendseries/man/coffee_robusta.Rd | 2 trendseries-1.4.0/trendseries/man/decompose_series.Rd |only trendseries-1.4.0/trendseries/man/deseason_series.Rd |only trendseries-1.4.0/trendseries/man/detrend_series.Rd |only trendseries-1.4.0/trendseries/man/electricity.Rd |only trendseries-1.4.0/trendseries/man/extract_trends.Rd | 17 trendseries-1.4.0/trendseries/man/figures/README-unnamed-chunk-4-1.svg | 515 ++-------- trendseries-1.4.0/trendseries/man/figures/example_trendseries.png |only trendseries-1.4.0/trendseries/man/metadata_series.Rd |only trendseries-1.4.0/trendseries/tests/testthat/test-augment_trends.R | 28 trendseries-1.4.0/trendseries/tests/testthat/test-decompose_series.R |only trendseries-1.4.0/trendseries/tests/testthat/test-deseason_series.R |only trendseries-1.4.0/trendseries/tests/testthat/test-detrend_series.R |only trendseries-1.4.0/trendseries/tests/testthat/test-edge-cases.R | 26 trendseries-1.4.0/trendseries/tests/testthat/test-extract_trends.R | 7 trendseries-1.4.0/trendseries/tests/testthat/test-filters-econometric.R | 21 trendseries-1.4.0/trendseries/tests/testthat/test-method_registry.R |only trendseries-1.4.0/trendseries/tests/testthat/test-params-stl.R | 4 trendseries-1.4.0/trendseries/vignettes/augment-trends.Rmd |only trendseries-1.4.0/trendseries/vignettes/decompose-series.Rmd |only trendseries-1.4.0/trendseries/vignettes/detrend-series.Rmd |only trendseries-1.4.0/trendseries/vignettes/econometric-filters.Rmd |only trendseries-1.4.0/trendseries/vignettes/methods.Rmd |only trendseries-1.4.0/trendseries/vignettes/moving-averages.Rmd | 68 - trendseries-1.4.0/trendseries/vignettes/trendseries.Rmd | 393 +------ 84 files changed, 1516 insertions(+), 2225 deletions(-)
Title: Graph/Network Analysis Based on L1 Centrality
Description: Analyze graph/network data using L1 centrality and prestige. Functions for deriving global, local, and group L1 centrality/prestige are provided. Routines for visual inspection of a graph/network are also provided. Details are in Kang and Oh (2026a) <doi:10.1080/01621459.2025.2520467>, Kang and Oh (2026b) <doi:10.1080/00031305.2025.2563730>, and Kang (2025) <doi:10.23170/snu.000000188358.11032.0001856>.
Author: Seungwoo Kang [aut, cre] ,
Hee-Seok Oh [aut]
Maintainer: Seungwoo Kang <kangsw@skku.edu>
Diff between L1centrality versions 0.5.1 dated 2026-05-04 and 0.5.2 dated 2026-07-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/L1centEDGE.R | 2 +- R/L1centGROUP.R | 2 +- R/L1centLOC.R | 2 +- man/L1centrality-package.Rd | 1 + 7 files changed, 20 insertions(+), 13 deletions(-)
Title: Learning R with Dr. Hu
Description: Provides interactive workshops for learning R easily and happily.
Each workshop is a self-contained 'Quarto' Live document whose code cells run
in the browser via 'WebAssembly', so learners can read the instructions and
run the exercises side by side without a local R setup. The materials
accompany the "Learning R with Dr. Hu" workshop series.
Author: Yue Hu [aut, cre],
Qian Qiu [ctb, trl],
Xinyi Ye [ctb, trl],
Yufei Sun [ctb]
Maintainer: Yue Hu <yuehu@tsinghua.edu.cn>
Diff between drhur versions 2.0.0 dated 2026-05-30 and 2.0.1 dated 2026-07-13
DESCRIPTION | 6 MD5 | 32 +-- NEWS.md | 14 + inst/quarto_live/_quarto.yml | 2 inst/quarto_live/algebra_live.qmd | 116 ++++++++++-- inst/quarto_live/algebra_live_en.qmd | 133 ++++++++++++-- inst/quarto_live/descriptive_live.qmd | 139 +++++++++++++-- inst/quarto_live/descriptive_live_en.qmd | 137 +++++++++++++-- inst/quarto_live/loop_live.qmd | 271 +++++++++++++++++++++++++++--- inst/quarto_live/loop_live_en.qmd | 269 +++++++++++++++++++++++++++-- inst/quarto_live/munging_live.qmd | 140 +++++++++++++-- inst/quarto_live/munging_live_en.qmd | 138 +++++++++++++-- inst/quarto_live/play_live.qmd | 176 ++++++++++++++++--- inst/quarto_live/play_live_en.qmd | 176 ++++++++++++++++--- inst/quarto_live/theme/goldenBlack.scss | 29 ++- inst/quarto_live/visual_basic_live.qmd | 116 +++++++++++- inst/quarto_live/visual_basic_live_en.qmd | 114 +++++++++++- 17 files changed, 1759 insertions(+), 249 deletions(-)
Title: Repel Visually Similar Colors for Colorblind Users in Various
Plots
Description: Iterate and repel visually similar colors away in various 'ggplot2' plots. When many groups are plotted at the same time on multiple axes, for instance stacked bars or scatter plots, effectively ordering colors becomes difficult. This tool iterates through color combinations to find the best solution to maximize visual distinctness of nearby groups, so plots are more friendly toward colorblind users. This is achieved by two distance measurements, distance between groups within the plot, and CIELAB color space distances between colors as described in Carter et al., (2018) <doi:10.25039/TR.015.2018>.
Author: Rui Fu [cre, aut, cph]
Maintainer: Rui Fu <raysinensis@gmail.com>
Diff between colorrepel versions 0.4.3 dated 2025-07-21 and 0.5.0 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 10 ++++++---- NAMESPACE | 5 +++++ NEWS.md | 3 +++ R/for_ggplot.R |only README.md | 1 + man/scale_color_repel.Rd |only 7 files changed, 18 insertions(+), 7 deletions(-)
Title: Discrete Choice Models for Economic Applications
Description: Fast estimation of discrete-choice models for applied economics.
Frequentist likelihoods, analytical gradients, and Hessians are implemented
in C++ with 'OpenMP' parallelism, scaling efficiently to specifications with
many alternative-specific constants. Compiled Gibbs samplers provide Bayesian
multinomial probit and hierarchical models. Post-estimation routines cover
predicted shares, own- and cross-price elasticities, diversion ratios,
willingness to pay, and welfare counterfactuals. Supports multinomial logit
('MNL'), mixed logit ('MXL'), nested logit ('NL'), Bayesian multinomial probit
('MNP'), and hierarchical Bayesian multinomial logit and probit ('HMNL',
'HMNP').
Author: Fernando Cordeiro [aut, cre, cph]
Maintainer: Fernando Cordeiro <fernandolpcordeiro@gmail.com>
Diff between choicer versions 0.1.0 dated 2026-05-20 and 0.2.0 dated 2026-07-13
.aspell |only DESCRIPTION | 31 MD5 | 274 ++- NAMESPACE | 83 - NEWS.md | 272 +++ R/RcppExports.R | 909 ++++++++++- R/choicer-package.R | 6 R/classes.R | 681 +++++++- R/data.R |only R/gof.R |only R/hb_data.R |only R/hb_diagnostics.R |only R/hb_postest.R |only R/hmnlogit_utils.R |only R/hmnprobit_utils.R |only R/methods.R | 1126 ++++++++++++- R/mnlogit_utils.R | 301 +++ R/mnprobit_utils.R |only R/mxlogit_utils.R | 407 ++++ R/nestlogit_utils.R | 211 ++ R/predict_newdata.R |only R/recovery.R | 113 + R/sampling.R |only R/simulation.R | 391 ++++ R/surplus.R |only R/utils.R | 99 + R/wtp.R |only README.md | 194 ++ build/vignette.rds |only data |only inst/doc |only inst/simulations/hmnl_simulation.R |only inst/simulations/hmnp_simulation.R |only inst/simulations/mnl_simulation.R | 49 inst/simulations/mnp_simulation.R |only inst/simulations/mxl_simulation.R | 71 inst/simulations/nl_simulation.R | 46 man/blp.choicer_nl.Rd |only man/build_var_mat.Rd | 3 man/choicer-package.Rd | 3 man/coef.choicer_hb.Rd |only man/coef.choicer_mnp.Rd |only man/consumer_surplus.Rd |only man/diversion_ratios.Rd | 24 man/diversion_ratios.choicer_nl.Rd |only man/elasticities.Rd | 25 man/elasticities.choicer_nl.Rd |only man/ess.Rd |only man/gof.Rd |only man/hmnl_gibbs.Rd |only man/hmnp_gibbs.Rd |only man/jacobian_vech_Sigma.Rd | 3 man/logsum.Rd |only man/mcse.Rd |only man/mnl_bhhh_parallel.Rd |only man/mnl_diversion_ratios_parallel.Rd | 3 man/mnl_elasticities_parallel.Rd | 3 man/mnl_loglik_gradient_parallel.Rd | 3 man/mnl_loglik_hessian_parallel.Rd | 3 man/mnl_predict.Rd | 3 man/mnl_predict_shares.Rd | 3 man/mnp_gibbs.Rd |only man/mode_choice.Rd |only man/mxl_bhhh_parallel.Rd | 17 man/mxl_blp_contraction.Rd | 14 man/mxl_diversion_ratios_parallel.Rd | 15 man/mxl_elasticities_parallel.Rd | 17 man/mxl_hessian_parallel.Rd | 17 man/mxl_loglik_gradient_parallel.Rd | 17 man/mxl_logsum.Rd |only man/mxl_predict.Rd | 15 man/mxl_predict_shares.Rd | 15 man/new_choicer_sim.Rd | 3 man/nl_bhhh_parallel.Rd |only man/nl_blp_contraction.Rd |only man/nl_diversion_ratios_parallel.Rd |only man/nl_elasticities_parallel.Rd |only man/nl_loglik_gradient_parallel.Rd | 3 man/nl_loglik_hessian_parallel.Rd |only man/nl_loglik_numeric_hessian.Rd | 3 man/nl_predict.Rd |only man/nl_predict_shares.Rd |only man/nobs.choicer_hb.Rd |only man/nobs.choicer_mnp.Rd |only man/ppc_shares.Rd |only man/predict.choicer_hb.Rd |only man/predict.choicer_mnl.Rd | 39 man/predict.choicer_mxl.Rd | 40 man/predict.choicer_nl.Rd |only man/prepare_hmnl_data.Rd |only man/prepare_hmnp_data.Rd |only man/prepare_mnl_data.Rd | 21 man/prepare_mnp_data.Rd |only man/prepare_mxl_data.Rd | 17 man/prepare_nl_data.Rd | 21 man/print.choicer_cs.Rd |only man/print.choicer_gof.Rd |only man/print.choicer_hb.Rd |only man/print.choicer_mnp.Rd |only man/print.choicer_wtp.Rd |only man/print.summary.choicer_hb.Rd |only man/print.summary.choicer_mnp.Rd |only man/recovery_table.Rd | 26 man/rhat.Rd |only man/run_hmnlogit.Rd |only man/run_hmnprobit.Rd |only man/run_mnlogit.Rd | 37 man/run_mnprobit.Rd |only man/run_mxlogit.Rd | 79 man/run_nestlogit.Rd | 29 man/sample_by_choice.Rd |only man/set_num_threads.Rd |only man/simulate_hmnl_data.Rd |only man/simulate_hmnp_data.Rd |only man/simulate_mnp_data.Rd |only man/summary.choicer_hb.Rd |only man/summary.choicer_mnl.Rd | 11 man/summary.choicer_mnp.Rd |only man/summary.choicer_mxl.Rd | 10 man/summary.choicer_nl.Rd | 10 man/thread_info.Rd |only man/traceplot.Rd |only man/traceplot.choicer_hb.Rd |only man/vcov.choicer_fit.Rd | 58 man/vcov.choicer_hb.Rd |only man/vcov.choicer_mnp.Rd |only man/wesml_vcov.Rd |only man/wesml_weights.Rd |only man/wtp.Rd |only src/RcppExports.cpp | 641 +++++++ src/bayes_samplers.h |only src/choicer.h | 87 + src/choicer_internal.h |only src/halton.h |only src/halton_test_exports.cpp |only src/hb_internal.h |only src/hb_test_exports.cpp |only src/hmnlogit.cpp |only src/hmnprobit.cpp |only src/mnlogit.cpp | 803 ++++++--- src/mnprobit.cpp |only src/mxlogit.cpp | 2206 +++++++++++++++------------ src/nestlogit.cpp | 1906 +++++++++++++++++++++-- src/rng.h |only src/utils.cpp | 69 tests/testthat/setup.R | 40 tests/testthat/test-bayes-samplers.R |only tests/testthat/test-blp.R | 158 + tests/testthat/test-cluster-vcov.R |only tests/testthat/test-elasticities.R | 248 +++ tests/testthat/test-gof.R |only tests/testthat/test-halton-generator.R |only tests/testthat/test-hb-data-prep.R |only tests/testthat/test-hb-diagnostics-phase1.R |only tests/testthat/test-hb-internal.R |only tests/testthat/test-hb-postest.R |only tests/testthat/test-hessian.R | 202 ++ tests/testthat/test-hmnl-gibbs.R |only tests/testthat/test-hmnl-recovery.R |only tests/testthat/test-hmnp-gibbs.R |only tests/testthat/test-hmnp-recovery.R |only tests/testthat/test-mnl-scaling.R |only tests/testthat/test-mnp-data-prep.R |only tests/testthat/test-mnp-gibbs.R |only tests/testthat/test-mnp-recovery.R |only tests/testthat/test-mxl-generate-mode.R |only tests/testthat/test-mxl-hessian-o3.R |only tests/testthat/test-nl-hessian-equivalence.R |only tests/testthat/test-nl-hessian.R |only tests/testthat/test-post-estimation.R | 106 + tests/testthat/test-predict-newdata.R |only tests/testthat/test-predictions.R | 63 tests/testthat/test-recovery.R | 32 tests/testthat/test-sampling-wesml.R |only tests/testthat/test-simulation.R | 114 + tests/testthat/test-surplus.R |only tests/testthat/test-utilities.R | 44 tests/testthat/test-wtp.R |only vignettes |only 179 files changed, 10681 insertions(+), 1912 deletions(-)
Title: Useful Tools for Structural Equation Modeling
Description: Provides miscellaneous tools for structural equation modeling,
many of which extend the 'lavaan' package. For example, latent
interactions can be estimated using product indicators (Lin et al.,
2010, <doi:10.1080/10705511.2010.488999>) and simple effects probed;
analytical power analyses can be conducted (Jak et al., 2021,
<doi:10.3758/s13428-020-01479-0>); and scale reliability
can be estimated based on estimated factor-model parameters.
Author: Terrence D. Jorgensen [aut, cre] ,
Sunthud Pornprasertmanit [aut] ,
Alexander M. Schoemann [aut] ,
Yves Rosseel [aut] ,
Patrick Miller [ctb],
Corbin Quick [ctb],
Mauricio Garnier-Villarreal [ctb] ,
James Selig [ctb],
Aaron Boulton [ctb],
Kristopher P [...truncated...]
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>
Diff between semTools versions 0.5-8 dated 2026-02-14 and 0.5-9 dated 2026-07-13
DESCRIPTION | 10 - MD5 | 68 ++++++------ NEWS.md | 16 ++ R/TSML.R | 8 - R/discriminantValidity.R | 5 R/measEq.R | 6 - R/miPowerFit.R | 228 ++++++++++++++++++++++++----------------- R/missingBootstrap.R | 5 R/parcelAllocation.R | 4 R/permuteMeasEq.R | 4 R/reliability.R | 24 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/partialInvariance.pdf |binary man/PAVranking.Rd | 2 man/bsBootMiss.Rd | 4 man/clipboard.Rd | 8 - man/compRelSEM.Rd | 7 - man/compareFit.Rd | 8 - man/dat2way.Rd | 2 man/dat3way.Rd | 2 man/datCat.Rd | 2 man/discriminantValidity.Rd | 11 - man/epcEquivCheck.Rd | 55 +++++---- man/epcEquivFit.Rd | 20 +++ man/exLong.Rd | 2 man/goricaSEM.Rd | 8 - man/mardiaKurtosis.Rd | 2 man/mardiaSkew.Rd | 2 man/measEq.syntax.Rd | 4 man/net.Rd | 2 man/parcelAllocation.Rd | 2 man/permuteMeasEq.Rd | 10 - man/simParcel.Rd | 2 man/twostage.Rd | 8 - 35 files changed, 312 insertions(+), 229 deletions(-)
Title: A Theorical-Practical Approach to Parasitological Data Analysis
Description: Standardizes and streamlines the processing of parasitological data by integrating descriptive analyses of parasite count distributions, automated calculation of parasitological indices and their dispersion measures, and intuitive visualizations for representing these metrics (Bush et al. 1997 <doi:10.2307/3284227>, Reiczigel et al. 2019 <doi:10.1016/j.pt.2019.01.003>).
Author: Exequiel Oscar Furlan [aut] ,
Juan Manuel Cabrera [aut, cre, cph] ,
Elisa Helman [aut]
Maintainer: Juan Manuel Cabrera <juan.cabrera@uner.edu.ar>
Diff between parasiteR versions 1.1 dated 2026-07-12 and 1.1.1 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 27 ++++++++++++++++++++------- R/para_abundance_CI.R | 2 +- R/para_intensity_CI.R | 2 +- R/para_plot_CI.R | 14 +++++++++----- 6 files changed, 39 insertions(+), 22 deletions(-)
Title: Non-Negative Matrix Factorization with Kernel Covariates
Description: Performs Non-negative Matrix Factorization (NMF)
with Kernel Covariates. Given an observation matrix and kernel
covariates, it optimizes both a basis matrix and a parameter matrix.
Notably, if the kernel matrix is an identity matrix, the method
simplifies to standard NMF. Also provides NMF with Random Effects
(NMF-RE) via nmfre(), which estimates a mixed-effects model combining
covariate-driven scores with unit-specific random effects together
with wild bootstrap inference, and NMF-based Structural Equation
Modeling (NMF-SEM) via nmf.sem(), which fits a two-block input-output
model for blind source separation and path analysis.
References: Satoh (2025) <doi:10.48550/arXiv.2403.05359>;
Satoh (2025) <doi:10.48550/arXiv.2510.10375>;
Satoh (2025) <doi:10.48550/arXiv.2512.18250>;
Satoh (2026) <doi:10.48550/arXiv.2603.01468>;
Satoh (2026) <doi:10.1007/s42081-025-00314-0>.
Author: Kenichi Satoh [aut, cre]
Maintainer: Kenichi Satoh <kenichi-satoh@biwako.shiga-u.ac.jp>
Diff between nmfkc versions 0.8.2 dated 2026-06-14 and 0.8.8 dated 2026-07-13
nmfkc-0.8.2/nmfkc/R/nmf.ffb.R |only nmfkc-0.8.2/nmfkc/man/nmf.sem.DOT.Rd |only nmfkc-0.8.2/nmfkc/man/nmf.sem.Rd |only nmfkc-0.8.2/nmfkc/man/nmf.sem.cv.Rd |only nmfkc-0.8.2/nmfkc/man/nmf.sem.inference.Rd |only nmfkc-0.8.2/nmfkc/man/nmf.sem.split.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.DOT.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.cv.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.ecv.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.heatmap.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.inference.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.kernel.beta.cv.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.rank.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.rename.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.signed.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.signed.ecv.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.signed.heatmap.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.signed.inference.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.signed.rank.Rd |only nmfkc-0.8.2/nmfkc/man/nmfae.signed.rename.Rd |only nmfkc-0.8.2/nmfkc/man/nmfre.dfU.scan.Rd |only nmfkc-0.8.8/nmfkc/DESCRIPTION | 11 nmfkc-0.8.8/nmfkc/MD5 | 158 - nmfkc-0.8.8/nmfkc/NAMESPACE | 28 nmfkc-0.8.8/nmfkc/NEWS.md | 287 ++ nmfkc-0.8.8/nmfkc/R/inference-boot.R |only nmfkc-0.8.8/nmfkc/R/nmf.sem-deprecated.R |only nmfkc-0.8.8/nmfkc/R/nmf.sem.R | 112 nmfkc-0.8.8/nmfkc/R/nmfae-deprecated.R |only nmfkc-0.8.8/nmfkc/R/nmfae.R | 358 +-- nmfkc-0.8.8/nmfkc/R/nmfae.signed.R | 214 + nmfkc-0.8.8/nmfkc/R/nmfkc.R | 241 +- nmfkc-0.8.8/nmfkc/R/nmfkc.ard.R | 9 nmfkc-0.8.8/nmfkc/R/nmfkc.bicv.R | 113 nmfkc-0.8.8/nmfkc/R/nmfkc.net.R | 16 nmfkc-0.8.8/nmfkc/R/nmfkc.signed.R | 86 nmfkc-0.8.8/nmfkc/R/nmfre.R | 1177 ++++------ nmfkc-0.8.8/nmfkc/R/s3methods.R | 56 nmfkc-0.8.8/nmfkc/build/vignette.rds |binary nmfkc-0.8.8/nmfkc/inst/doc/nmf-re-with-nmfkc.R | 41 nmfkc-0.8.8/nmfkc/inst/doc/nmf-re-with-nmfkc.Rmd | 181 - nmfkc-0.8.8/nmfkc/inst/doc/nmf-re-with-nmfkc.html | 512 ++-- nmfkc-0.8.8/nmfkc/inst/doc/nmf-rrr-with-nmfkc.R |only nmfkc-0.8.8/nmfkc/inst/doc/nmf-rrr-with-nmfkc.Rmd |only nmfkc-0.8.8/nmfkc/inst/doc/nmf-rrr-with-nmfkc.html |only nmfkc-0.8.8/nmfkc/inst/doc/nmf-sem-with-nmfkc.html | 2 nmfkc-0.8.8/nmfkc/inst/doc/timeseries-with-nmfkc.html | 16 nmfkc-0.8.8/nmfkc/inst/doc/topic-modeling-with-nmfkc.html | 2 nmfkc-0.8.8/nmfkc/man/fitted.nmf.Rd | 90 nmfkc-0.8.8/nmfkc/man/nmf.ffb.DOT.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.ffb.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.ffb.cv.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.ffb.inference.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.ffb.split.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.DOT.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.cv.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.ecv.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.heatmap.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.inference.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.kernel.beta.cv.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.rank.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.rename.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.signed.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.signed.ecv.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.signed.heatmap.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.signed.inference.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.signed.rank.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.rrr.signed.rename.Rd |only nmfkc-0.8.8/nmfkc/man/nmf.sem-deprecated.Rd |only nmfkc-0.8.8/nmfkc/man/nmfae-deprecated.Rd |only nmfkc-0.8.8/nmfkc/man/nmfkc.DOT.Rd | 211 - nmfkc-0.8.8/nmfkc/man/nmfkc.Rd | 14 nmfkc-0.8.8/nmfkc/man/nmfkc.ard.Rd | 4 nmfkc-0.8.8/nmfkc/man/nmfkc.cv.Rd | 2 nmfkc-0.8.8/nmfkc/man/nmfkc.cv.methods.Rd |only nmfkc-0.8.8/nmfkc/man/nmfkc.inference.Rd | 153 - nmfkc-0.8.8/nmfkc/man/nmfkc.signed.Rd | 17 nmfkc-0.8.8/nmfkc/man/nmfre.Rd | 121 - nmfkc-0.8.8/nmfkc/man/nmfre.ecv.Rd |only nmfkc-0.8.8/nmfkc/man/plot.nmfae.Rd | 64 nmfkc-0.8.8/nmfkc/man/plot.nmfae.cv.Rd | 47 nmfkc-0.8.8/nmfkc/man/plot.nmfae.ecv.Rd | 49 nmfkc-0.8.8/nmfkc/man/plot.nmfae.kernel.beta.cv.Rd | 49 nmfkc-0.8.8/nmfkc/man/plot.nmfae.signed.Rd | 1 nmfkc-0.8.8/nmfkc/man/plot.nmfre.Rd | 2 nmfkc-0.8.8/nmfkc/man/plot.nmfre.ecv.Rd |only nmfkc-0.8.8/nmfkc/man/plot.predict.nmfae.Rd | 73 nmfkc-0.8.8/nmfkc/man/predict.nmfae.Rd | 107 nmfkc-0.8.8/nmfkc/man/predict.nmfae.signed.Rd | 1 nmfkc-0.8.8/nmfkc/man/predict.nmfre.Rd |only nmfkc-0.8.8/nmfkc/man/print.nmfre.ecv.Rd |only nmfkc-0.8.8/nmfkc/man/print.summary.nmfae.Rd | 66 nmfkc-0.8.8/nmfkc/man/print.summary.nmfae.inference.Rd | 64 nmfkc-0.8.8/nmfkc/man/print.summary.nmfae.signed.Rd | 1 nmfkc-0.8.8/nmfkc/man/print.summary.nmfae.signed.inference.Rd | 13 nmfkc-0.8.8/nmfkc/man/print.summary.nmfkc.inference.Rd | 63 nmfkc-0.8.8/nmfkc/man/print.summary.nmfkc.net.inference.Rd | 14 nmfkc-0.8.8/nmfkc/man/summary.nmfae.Rd | 83 nmfkc-0.8.8/nmfkc/man/summary.nmfae.inference.Rd | 47 nmfkc-0.8.8/nmfkc/man/summary.nmfae.signed.Rd | 1 nmfkc-0.8.8/nmfkc/man/summary.nmfae.signed.inference.Rd | 1 nmfkc-0.8.8/nmfkc/man/summary.nmfre.Rd | 73 nmfkc-0.8.8/nmfkc/tests/testthat/test-nmfae.R |only nmfkc-0.8.8/nmfkc/tests/testthat/test-nmfkc.R | 36 nmfkc-0.8.8/nmfkc/tests/testthat/test-nmfre.R |only nmfkc-0.8.8/nmfkc/vignettes/nmf-re-with-nmfkc.Rmd | 181 - 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Title: Statistical Methods for the Analysis of Excess Lifetimes
Description: A collection of parametric and nonparametric methods for the analysis of survival data, described in <doi:10.32614/RJ-2025-034>. Parametric families implemented include Gompertz-Makeham, exponential and generalized Pareto models and extended models. The package includes an implementation of the nonparametric maximum likelihood estimator for arbitrary truncation and censoring pattern based on Turnbull (1976) <doi:10.1111/j.2517-6161.1976.tb01597.x>, along with graphical goodness-of-fit diagnostics. Parametric models for positive random variables and peaks over threshold models based on extreme value theory are described in Rootzén and Zholud (2017) <doi:10.1007/s10687-017-0305-5>; Belzile et al. (2021) <doi:10.1098/rsos.202097> and Belzile et al. (2022) <doi:10.1146/annurev-statistics-040120-025426>.
Author: Leo Belzile [aut, cre] ,
Mitchell O'Hara-Wild [ctb]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between longevity versions 1.3 dated 2026-02-03 and 1.3.1 dated 2026-07-13
DESCRIPTION | 10 ++--- MD5 | 19 ++++++--- NEWS.md | 11 +++++ R/datasets.R | 88 +++++++++++++++++++++++++------------------- build/partial.rdb |binary build/vignette.rds |binary data/englandwales.rda |only data/french.rda |only inst/CITATION |only inst/doc/introduction.html | 17 ++++---- inst/doc/nonparametric.html | 9 ++-- man/englandwales.Rd |only man/french.Rd |only 13 files changed, 89 insertions(+), 65 deletions(-)
Title: 'GGML' Tensor Operations for Machine Learning
Description: Provides 'R' bindings to the 'GGML' tensor library for machine
learning, optimized for 'Vulkan' GPU acceleration with a transparent CPU
fallback. The package features a 'Keras'-like sequential API and a
'PyTorch'-style 'autograd' engine for building, training, and deploying
neural networks. Key capabilities include high-performance 5D tensor
operations, 'f16' precision, and efficient quantization. It supports
native 'ONNX' model import (50+ operators) and 'GGUF' weight loading
from the 'llama.cpp' and 'Hugging Face' ecosystems. Designed for
zero-overhead inference via dedicated weight buffering, it integrates
seamlessly as a 'parsnip' engine for 'tidymodels' and provides
first-class learners for the 'mlr3' framework.
See <https://github.com/ggml-org/ggml> for more information about the
underlying library.
Author: Yuri Baramykov [aut, cre] ,
Georgi Gerganov [ctb, cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
Mozilla Foundation [ctb, cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between ggmlR versions 0.7.8 dated 2026-06-04 and 0.8.1 dated 2026-07-13
DESCRIPTION | 13 MD5 | 249 ++++-- NAMESPACE | 57 + NEWS.md | 25 R/LearnerClassifGGML.R | 137 +++ R/LearnerRegrGGML.R | 122 +++ R/ag_device.R | 51 + R/ag_save.R |only R/diagnostics.R |only R/gpu_linalg.R |only R/mlr3_marshal.R | 88 +- R/nn_functional.R | 13 R/nn_model.R | 19 R/parsnip_broom.R |only R/parsnip_mlp.R | 91 +- R/sc_compat.R |only R/sc_contracts.R |only R/sc_dispatch.R |only R/sc_extract.R |only R/sc_inject.R |only R/sc_sce.R |only R/sc_seurat.R |only R/sc_umap.R |only R/seed.R |only R/tensor_parallel.R |only R/vulkan.R | 377 ++++++++++ README.md | 418 +++++++++++ build/vignette.rds |binary configure | 37 + configure.win | 190 +++++ inst/doc/autograd-engine.Rmd | 2 inst/doc/data-parallel-training.Rmd | 2 inst/doc/embedding-ggmlR.Rmd | 91 ++ inst/doc/embedding-ggmlR.html | 243 ++++-- inst/doc/gpu-vulkan.R | 1 inst/doc/gpu-vulkan.Rmd | 19 inst/doc/gpu-vulkan.html | 22 inst/doc/keras-like-api.Rmd | 2 inst/doc/mlr3-integration.R | 4 inst/doc/mlr3-integration.Rmd | 6 inst/doc/multi-gpu.R |only inst/doc/multi-gpu.Rmd |only inst/doc/multi-gpu.html |only inst/doc/onnx-import.Rmd | 2 inst/doc/quantization.Rmd | 2 inst/doc/quickstart.R |only inst/doc/quickstart.Rmd |only inst/doc/quickstart.html |only inst/doc/single-cell-seurat.R |only inst/doc/single-cell-seurat.Rmd |only inst/doc/single-cell-seurat.html |only inst/doc/tidymodels-integration.R | 21 inst/doc/tidymodels-integration.Rmd | 70 + inst/doc/tidymodels-integration.html | 70 + inst/examples/bench_matmul_f64.R |only inst/examples/bench_mulmat_p100.R |only inst/examples/check_fa_p100.R |only inst/examples/debug_gpu_minimal.R |only inst/examples/gpu_linalg.R |only inst/examples/pp_pipeline.R |only inst/examples/seurat_gpu_stress.R |only inst/examples/seurat_neighbors.R |only inst/examples/seurat_op2_gpu.R |only inst/examples/seurat_pca.R |only inst/examples/seurat_pca_large.R |only inst/examples/seurat_preprocess_gpu.R |only inst/examples/seurat_umap.R |only inst/examples/tp_dp_hybrid.R |only inst/examples/tp_p2p_backtrace.sh |only inst/examples/tp_p2p_diagnose.R |only inst/examples/umap_sgd_diag.R |only inst/examples/umap_shaders_bench.R |only inst/examples/vk_buffer_probe.R |only inst/examples/vk_buffer_probe_isolated.R |only inst/examples/vk_probe_split_allocfree.R |only inst/examples/vk_probe_split_errorfree.R |only man/RunGGML.Rd |only man/ag_load_model.Rd |only man/ag_save_model.Rd |only man/as.matrix.ggml_matrix.Rd |only man/as_gpu_matrix.Rd |only man/augment.ggmlr_parsnip_model.Rd |only man/dot-ggmlr_batch_shards.Rd |only man/dot-ggmlr_largest_gene.Rd |only man/dot-ggmlr_neighbors_gpu.Rd |only man/dot-ggmlr_normalize_gpu.Rd |only man/dot-ggmlr_pca_gpu.Rd |only man/dot-ggmlr_scale_gpu.Rd |only man/dot-ggmlr_umap_gpu.Rd |only man/ggml_crossprod.Rd |only man/ggml_evaluate.Rd | 1 man/ggml_extract.Rd |only man/ggml_fit.Rd | 1 man/ggml_inject.Rd |only man/ggml_matmul.Rd |only man/ggml_matmul_f64.Rd |only man/ggml_matrix-class.Rd |only man/ggml_model_backend.Rd |only man/ggml_ops_registry.Rd |only man/ggml_pp_dp_forward.Rd |only man/ggml_pp_forward.Rd |only man/ggml_result.Rd |only man/ggml_run.Rd |only man/ggml_set_seed.Rd |only man/ggml_task.Rd |only man/ggml_tcrossprod.Rd |only man/ggml_tp_dp_forward.Rd |only man/ggml_training_history.Rd |only man/ggml_vulkan_device_groups.Rd |only man/ggml_vulkan_hard_exit_available.Rd |only man/ggml_vulkan_p2p_selftest.Rd |only man/ggml_vulkan_shutdown.Rd |only man/ggml_vulkan_split_buffer_type.Rd |only man/ggml_vulkan_split_mul_mat.Rd |only man/ggml_vulkan_split_row_ranges.Rd |only man/ggml_vulkan_stage_handoff.Rd |only man/ggmlr_parsnip_fit_classif.Rd | 3 man/ggmlr_parsnip_fit_regr.Rd | 3 man/glance.ggmlr_parsnip_model.Rd |only man/tidy.ggmlr_parsnip_model.Rd |only src/Makevars.in | 3 src/Makevars.win.in | 54 + src/ggml-alloc.c | 5 src/ggml-backend-impl.h | 8 src/ggml-backend-meta.cpp | 40 - src/ggml-backend.cpp | 23 src/ggml-context.c | 5 src/ggml-graph.c | 12 src/ggml-vulkan.h | 108 ++ src/ggml-vulkan/ggml-vulkan-device.cpp | 303 ++++++++ src/ggml-vulkan/ggml-vulkan-elemwise.cpp | 8 src/ggml-vulkan/ggml-vulkan-graph.cpp | 356 +++++++++ src/ggml-vulkan/ggml-vulkan-misc.cpp | 24 src/ggml-vulkan/ggml-vulkan-shaders.cpp | 127 ++- src/ggml-vulkan/ggml-vulkan-sparse.cpp |only src/ggml-vulkan/ggml-vulkan-split.cpp |only src/ggml-vulkan/ggml-vulkan-umap.cpp |only src/ggml-vulkan/ggml-vulkan.cpp | 3 src/ggml-vulkan/vulkan-shaders/knn_tiled.comp |only src/ggml-vulkan/vulkan-shaders/matmul_f64.comp |only src/ggml-vulkan/vulkan-shaders/pairwise_dist.comp |only src/ggml-vulkan/vulkan-shaders/sparse_lognorm.comp |only src/ggml-vulkan/vulkan-shaders/umap_sgd.comp |only src/ggml-vulkan/vulkan-shaders/vulkan-shaders-gen.cpp | 19 src/r_dbg_filelog.h |only src/r_interface.c | 35 src/r_interface_graph.c | 56 + src/r_interface_vulkan.c | 664 +++++++++++++++++- src/r_umap_sgd.c |only tests/testthat.R | 15 tests/testthat/helper-device.R |only tests/testthat/test-ag-save.R |only tests/testthat/test-diagnostics.R |only tests/testthat/test-getrows-offload-vulkan.R | 41 - tests/testthat/test-gpu-linalg.R |only tests/testthat/test-mlr3-autograd.R |only tests/testthat/test-mlr3-learner.R | 2 tests/testthat/test-parsnip-broom.R |only tests/testthat/test-parsnip-tidymodels.R |only tests/testthat/test-parsnip.R | 104 ++ tests/testthat/test-sc-chunked.R |only tests/testthat/test-sc-knn-gpu.R |only tests/testthat/test-sc-largest-gene.R |only tests/testthat/test-sc-neighbors.R |only tests/testthat/test-sc-normalize-sparse.R |only tests/testthat/test-sc-sce.R |only tests/testthat/test-sc-seurat.R |only tests/testthat/test-sc-umap.R |only tests/testthat/test-seed.R |only tests/testthat/test-vulkan-caps.R | 5 tests/testthat/test-vulkan-tensor-parallel.R |only vignettes/autograd-engine.Rmd | 2 vignettes/data-parallel-training.Rmd | 2 vignettes/embedding-ggmlR.Rmd | 91 ++ vignettes/gpu-vulkan.Rmd | 19 vignettes/keras-like-api.Rmd | 2 vignettes/mlr3-integration.Rmd | 6 vignettes/multi-gpu.Rmd |only vignettes/onnx-import.Rmd | 2 vignettes/quantization.Rmd | 2 vignettes/quickstart.Rmd |only vignettes/single-cell-seurat.Rmd |only vignettes/tidymodels-integration.Rmd | 70 + 183 files changed, 4310 insertions(+), 358 deletions(-)
Title: Black Marble Data and Statistics
Description: Geographically referenced data and statistics of nighttime lights from NASA Black Marble <https://blackmarble.gsfc.nasa.gov/>.
Author: Robert Marty [aut, cre] ,
Gabriel Stefanini Vicente [aut]
Maintainer: Robert Marty <rmarty@worldbank.org>
Diff between blackmarbler versions 0.2.5 dated 2025-07-29 and 0.2.7 dated 2026-07-13
blackmarbler-0.2.5/blackmarbler/man/wget_h5_files.Rd |only blackmarbler-0.2.7/blackmarbler/DESCRIPTION | 8 blackmarbler-0.2.7/blackmarbler/MD5 | 12 blackmarbler-0.2.7/blackmarbler/NAMESPACE | 2 blackmarbler-0.2.7/blackmarbler/R/blackmarbler.R | 241 ++++++++++----- blackmarbler-0.2.7/blackmarbler/man/bm_extract.Rd | 9 blackmarbler-0.2.7/blackmarbler/man/bm_raster.Rd | 5 blackmarbler-0.2.7/blackmarbler/man/download_h5_files.Rd |only 8 files changed, 193 insertions(+), 84 deletions(-)
Title: Inspect, Read, Edit and Run 'APSIM' "Next Generation" and
'APSIM' Classic
Description: The functions in this package inspect, read, edit and run files for 'APSIM' "Next Generation" ('JSON')
and 'APSIM' "Classic" ('XML'). The files with an 'apsim' extension correspond to
'APSIM' Classic (7.x) - Windows only - and the ones with an 'apsimx' extension correspond to 'APSIM' "Next Generation".
For more information about 'APSIM' see (<https://www.apsim.info/>) and for 'APSIM'
next generation (<https://apsimnextgeneration.netlify.app/>).
Author: Fernando Miguez [aut, cre]
Maintainer: Fernando Miguez <femiguez@iastate.edu>
Diff between apsimx versions 2.8.270 dated 2026-06-27 and 2.8.271 dated 2026-07-13
DESCRIPTION | 6 MD5 | 26 R/wget_apsimx_json.R | 297 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/apsimx-scripts.R | 48 inst/doc/apsimx-scripts.html | 1152 +++++++-------- inst/doc/apsimx.R | 470 +++--- inst/doc/apsimx.html | 2922 ++++++++++++++++++++-------------------- inst/doc/optim-apsim.R | 278 +-- inst/doc/optim-apsim.html | 1516 ++++++++++---------- inst/doc/sensitivity-apsim.R | 172 +- inst/doc/sensitivity-apsim.html | 1200 ++++++++-------- man/get_apsimx_json.Rd | 3 14 files changed, 4046 insertions(+), 4044 deletions(-)
Title: Stepped-Wedge Clinical Trial Analysis and Power Simulation
Description: Provides reusable functions for aggregated cluster-period data,
mixed-effects analysis, and simulation-based power and type I error
evaluation in stepped-wedge cluster randomized trials. The design and
mixed-effects analysis follow Hussey and Hughes (2007)
<doi:10.1016/j.cct.2006.05.007>. Intraclass correlations for binary
outcomes are converted to logistic-normal random-intercept standard
deviations following Eldridge, Ukoumunne and Carlin (2009)
<doi:10.1111/j.1751-5823.2009.00092.x>. Monte Carlo uncertainty in
estimated power is summarized using the exact binomial interval of
Clopper and Pearson (1934) <doi:10.1093/biomet/26.4.404>. The simulation
engine supports sequence-specific baseline risks, cluster random effects,
direct intraclass-correlation specification, Monte Carlo uncertainty
intervals, and model-fitting diagnostics. Applied physician and specialty
helpers are retained for backward compatibility and for an example
health-services workflow.
Author: Lin Li [aut, cre],
Florin Vaida [aut]
Maintainer: Lin (Amanda) Li <amandali14124277@gmail.com>
Diff between stepwedgepower versions 0.1.0 dated 2026-07-10 and 0.1.3 dated 2026-07-13
DESCRIPTION | 31 + MD5 | 22 - NAMESPACE | 3 NEWS.md |only R/power.R | 631 +++++++++++++++++++++++++++++++--------- README.md | 42 +- inst/WORDLIST |only man/cluster_sd_to_icc.Rd |only man/estimate_power.Rd | 99 ++++-- man/estimate_type1_error.Rd | 89 ++++- man/icc_to_cluster_sd.Rd |only man/run_stepwedge_analysis.Rd | 31 + man/simulate_stepwedge_trial.Rd | 87 ++++- tests/testthat/test-core.R | 91 +++++ 14 files changed, 870 insertions(+), 256 deletions(-)
More information about stepwedgepower at CRAN
Permanent link
Title: Consensus Pathway Analysis
Description: Provides a set of functions to perform pathway analysis and meta-analysis from multiple gene expression datasets, as well as visualization of the results. This package wraps functionality from the following packages: Ritchie et al. (2015) <doi:10.1093/nar/gkv007>, Love et al. (2014) <doi:10.1186/s13059-014-0550-8>, Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>, Korotkevich et al. (2016) <arxiv:10.1101/060012>, Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>, and Gu et al. (2012) <https://CRAN.R-project.org/package=CePa>.
Author: Ha Nguyen [aut, cre],
Phi Bya [aut],
Zeynab Maghsoudi [aut],
Tin Nguyen [fnd]
Maintainer: Ha Nguyen <hvn0006@wayne.edu>
Diff between RCPA versions 0.2.8 dated 2025-09-15 and 0.2.9 dated 2026-07-13
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- inst/doc/RCPA.html | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Transparent and Assisted Linear Modeling Engine
Description: Unified estimation, diagnostics, and reporting for ordinary least
squares (OLS) regression, ANOVA/t-tests, logistic regression, panel data
(fixed/random effects with Hausman test), instrumental variables (2SLS with
weak instrument diagnostics), and difference-in-differences. Designed for
applied researchers in social sciences with integrated "Methodological Customs"
that audit assumptions and provide literature references. All methods
implemented in pure base R without external dependencies beyond stats and
graphics packages.
Author: Manuel Soto-Perez [aut, cre]
Maintainer: Manuel Soto-Perez <msoto@up.edu.mx>
Diff between OLSengine versions 1.0.0 dated 2026-05-14 and 1.1.0 dated 2026-07-13
DESCRIPTION | 41 MD5 | 26 NAMESPACE | 2 NEWS.md |only R/OLS_engine.R | 2334 +++++++++++++++++++++++++++------------- R/data_academic_salaries.R |only README.md | 228 ++- build/vignette.rds |binary data |only inst/doc/vignette_tutorial.R | 109 + inst/doc/vignette_tutorial.Rmd | 308 +++-- inst/doc/vignette_tutorial.html | 308 ++++- man/academic_salaries.Rd |only man/paper_engine.Rd | 65 - man/plot_engine.Rd | 10 vignettes/vignette_tutorial.Rmd | 308 +++-- 16 files changed, 2657 insertions(+), 1082 deletions(-)
Title: An Interface to 'nVenn2'
Description: Creates quasi-proportional Venn diagrams with an arbitrary number of sets.
It is related to the old 'nVennR' package, but the algorithm and use have been reworked.
Author: Victor Quesada [aut, cre, cph]
Maintainer: Victor Quesada <quesadavictor@uniovi.es>
Diff between nVennR2 versions 2.0.2 dated 2026-07-10 and 2.0.3 dated 2026-07-13
DESCRIPTION | 8 MD5 | 16 NEWS.md | 6 inst/doc/nVennR2.html | 3372 +++++++++++++++++++++++----------------------- man/nVennR2-package.Rd | 5 src/elements.h | 1 src/nVenn2.cpp | 9 src/topol.h | 51 tests/testthat/Rplots.pdf |binary 9 files changed, 1771 insertions(+), 1697 deletions(-)
Title: Hypothesis Testing for Markov Switching Models
Description: Implementation of hypothesis testing procedures described in Hansen (1992) <doi:10.1002/jae.3950070506>, Carrasco, Hu, & Ploberger (2014) <doi:10.3982/ECTA8609>, Dufour & Luger (2017) <doi:10.1080/07474938.2017.1307548>, and Rodriguez-Rondon & Dufour (2026a) <doi:10.34989/swp-2026-23> that can be used to identify the number of regimes in Markov switching models. For a detailed description of the package, see Rodriguez-Rondon & Dufour (2026b) <doi:10.34989/swp-2026-7>.
Author: Gabriel Rodriguez-Rondon [cre, aut] ,
Jean-Marie Dufour [aut]
Maintainer: Gabriel Rodriguez-Rondon <gabrodriguezrondon@gmail.com>
Diff between MSTest versions 0.1.8 dated 2026-01-09 and 0.1.9 dated 2026-07-13
DESCRIPTION | 27 MD5 | 163 ++--- NAMESPACE | 1 NEWS.md | 89 ++ R/RcppExports.R | 83 +- R/data.R | 40 - R/helperfuncs.R | 542 +++++++++++++++++ R/htest_LRTest.R | 297 +++++++-- R/htest_MomentTest.R | 6 R/methods.R | 189 +++--- R/models.R | 338 +++++++--- README.md | 15 build |only inst/doc |only inst/examples/article.R | 51 - man/DLMMCpval_fun.Rd | 2 man/DLMMCpval_fun_min.Rd | 2 man/HMmdl.Rd | 71 ++ man/LMCLRTest.Rd | 17 man/LR_samp_dist.Rd | 25 man/LR_samp_dist_par.Rd | 21 man/MCpval.Rd | 2 man/MMCLRTest.Rd | 26 man/MMCLRpval_fun.Rd | 16 man/MMCLRpval_fun_min.Rd | 14 man/MMC_bounds.Rd | 4 man/MSARXmdl.Rd | 20 man/MSARmdl.Rd | 12 man/MSTest-package.Rd | 8 man/MSVARXmdl.Rd | 22 man/MSVARmdl.Rd | 14 man/USGNP.Rd | 8 man/USRGDP.Rd | 8 man/chp10GNP.Rd | 6 man/combine_stat.Rd | 2 man/hamilton84GNP.Rd | 6 man/plot.simuARX.Rd | 2 man/plot.simuMSARX.Rd | 2 man/plot.simuMSVARX.Rd | 2 man/plot.simuVARX.Rd | 2 man/predict.HMmdl.Rd | 6 man/predict.MSARmdl.Rd | 6 man/predict.MSVARmdl.Rd | 6 man/print.ARmdl.Rd | 3 man/print.BootLRTest.Rd | 3 man/print.CHPTest.Rd | 3 man/print.DLMCTest.Rd | 3 man/print.DLMMCTest.Rd | 3 man/print.HLRTest.Rd | 9 man/print.HMmdl.Rd | 3 man/print.LMCLRTest.Rd | 3 man/print.MMCLRTest.Rd | 3 man/print.MSARmdl.Rd | 3 man/print.MSVARmdl.Rd | 3 man/print.Nmdl.Rd | 3 man/print.VARmdl.Rd | 3 man/simuNorm.Rd | 2 man/simuVAR.Rd | 20 man/simuVARX.Rd | 24 man/summary.ARmdl.Rd | 8 man/summary.BootLRTest.Rd | 8 man/summary.CHPTest.Rd | 8 man/summary.DLMCTest.Rd | 10 man/summary.DLMMCTest.Rd | 8 man/summary.HLRTest.Rd | 14 man/summary.HMmdl.Rd | 8 man/summary.LMCLRTest.Rd | 8 man/summary.MMCLRTest.Rd | 8 man/summary.MSARmdl.Rd | 8 man/summary.MSVARmdl.Rd | 8 man/summary.Nmdl.Rd | 8 man/summary.VARmdl.Rd | 8 man/thetaSE.Rd | 6 man/thetaSE_louis.Rd |only src/RcppExports.cpp | 34 - src/htest_CHPTest.cpp | 28 src/htest_LRTest.cpp | 239 +++++-- src/htest_MomentTests.cpp | 44 - src/methods.cpp | 1421 ++++++++++++++++++++++++++++++++++++---------- src/methods.h | 4 tests |only vignettes |only 82 files changed, 3093 insertions(+), 1059 deletions(-)
Title: Chat with Large Language Models
Description: Chat with large language models from a range of providers
including 'Claude' <https://claude.ai>, 'OpenAI'
<https://chatgpt.com>, and more. Supports streaming, asynchronous
calls, tool calling, and structured data extraction.
Author: Hadley Wickham [aut, cre] ,
Joe Cheng [aut],
Aaron Jacobs [aut],
Garrick Aden-Buie [aut] ,
Barret Schloerke [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between ellmer versions 0.4.1 dated 2026-05-07 and 0.4.2 dated 2026-07-13
ellmer-0.4.1/ellmer/tests/testthat/_vcr/anthropic-batch.yml |only ellmer-0.4.2/ellmer/DESCRIPTION | 24 ellmer-0.4.2/ellmer/MD5 | 339 +-- ellmer-0.4.2/ellmer/NAMESPACE | 4 ellmer-0.4.2/ellmer/NEWS.md | 29 ellmer-0.4.2/ellmer/R/batch-chat.R | 24 ellmer-0.4.2/ellmer/R/chat-structured.R | 14 ellmer-0.4.2/ellmer/R/chat.R | 30 ellmer-0.4.2/ellmer/R/content-image.R | 6 ellmer-0.4.2/ellmer/R/params.R | 2 ellmer-0.4.2/ellmer/R/provider-aws.R | 85 ellmer-0.4.2/ellmer/R/provider-azure.R | 2 ellmer-0.4.2/ellmer/R/provider-claude.R | 106 - ellmer-0.4.2/ellmer/R/provider-cloudflare.R | 4 ellmer-0.4.2/ellmer/R/provider-databricks.R | 16 ellmer-0.4.2/ellmer/R/provider-deepseek.R | 47 ellmer-0.4.2/ellmer/R/provider-github.R | 39 ellmer-0.4.2/ellmer/R/provider-google-upload.R | 39 ellmer-0.4.2/ellmer/R/provider-google.R | 377 +++- ellmer-0.4.2/ellmer/R/provider-groq.R | 133 + ellmer-0.4.2/ellmer/R/provider-huggingface.R | 2 ellmer-0.4.2/ellmer/R/provider-lmstudio.R | 17 ellmer-0.4.2/ellmer/R/provider-mistral.R | 6 ellmer-0.4.2/ellmer/R/provider-ollama.R | 45 ellmer-0.4.2/ellmer/R/provider-openai-compatible.R | 87 ellmer-0.4.2/ellmer/R/provider-openai-tools.R | 2 ellmer-0.4.2/ellmer/R/provider-openai.R | 56 ellmer-0.4.2/ellmer/R/provider-openrouter.R | 6 ellmer-0.4.2/ellmer/R/provider-perplexity.R | 6 ellmer-0.4.2/ellmer/R/provider-portkey.R | 17 ellmer-0.4.2/ellmer/R/provider-posit.R |only ellmer-0.4.2/ellmer/R/provider-snowflake.R | 6 ellmer-0.4.2/ellmer/R/provider-vllm.R | 19 ellmer-0.4.2/ellmer/R/provider.R | 28 ellmer-0.4.2/ellmer/R/stream-controller.R | 2 ellmer-0.4.2/ellmer/R/sysdata.rda |binary ellmer-0.4.2/ellmer/R/tools-def.R | 4 ellmer-0.4.2/ellmer/R/turns.R | 39 ellmer-0.4.2/ellmer/R/types.R | 23 ellmer-0.4.2/ellmer/R/utils-merge.R | 2 ellmer-0.4.2/ellmer/R/utils.R | 17 ellmer-0.4.2/ellmer/README.md | 62 ellmer-0.4.2/ellmer/build/vignette.rds |binary ellmer-0.4.2/ellmer/inst/_vcr/Chat.yml | 91 - 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ellmer-0.4.2/ellmer/vignettes/_vcr/structured-data-examples-classification.yml | 91 - ellmer-0.4.2/ellmer/vignettes/_vcr/structured-data-examples-image.yml | 91 - ellmer-0.4.2/ellmer/vignettes/_vcr/structured-data-examples-named-entity.yml | 91 - ellmer-0.4.2/ellmer/vignettes/_vcr/structured-data-examples-sentiment.yml | 91 - ellmer-0.4.2/ellmer/vignettes/_vcr/structured-data-examples-summarisation.yml | 93 - ellmer-0.4.2/ellmer/vignettes/_vcr/structured-data-examples-unknown-keys.yml | 61 ellmer-0.4.2/ellmer/vignettes/_vcr/structured-data-parallel-missing-2.yml | 352 ++-- ellmer-0.4.2/ellmer/vignettes/_vcr/structured-data-parallel-missing.yml | 356 ++-- ellmer-0.4.2/ellmer/vignettes/_vcr/structured-data-parallel.yml | 526 +++-- ellmer-0.4.2/ellmer/vignettes/_vcr/tool-calling-inputs-outputs.yml | 179 +- ellmer-0.4.2/ellmer/vignettes/ellmer.Rmd | 2 ellmer-0.4.2/ellmer/vignettes/prompt-design.Rmd | 2 ellmer-0.4.2/ellmer/vignettes/structured-data.Rmd | 21 176 files changed, 8220 insertions(+), 5114 deletions(-)
Title: Modern Data Summaries and Diagnostic Reports for Statistical
Analysis
Description: Provides robust, NA-aware data summaries, variable diagnostics,
normality decisions, missingness and outlier checks, and reproducible
diagnostic report scaffolding for statistical analysis. DataSum is designed
for researchers, professors, scientists, and analysts who need trustworthy
first-pass insight into tabular data before modeling or publication.
Author: Uzair Javid Khan [aut, cre],
Immad Ahmad Shah [aut],
Sukhdev Mishra [aut]
Maintainer: Uzair Javid Khan <uzairkhan11w@gmail.com>
Diff between DataSum versions 0.1.1 dated 2025-11-12 and 1.0.0 dated 2026-07-13
DataSum-0.1.1/DataSum/R/datasum.R |only DataSum-0.1.1/DataSum/man/DataSumm.Rd |only DataSum-0.1.1/DataSum/man/Datum.Rd |only DataSum-0.1.1/DataSum/man/getmode.Rd |only DataSum-0.1.1/DataSum/man/shapiro_normality_test.Rd |only DataSum-0.1.1/DataSum/tests/testthat/test-datasum.R |only DataSum-1.0.0/DataSum/DESCRIPTION | 45 + DataSum-1.0.0/DataSum/MD5 | 35 + DataSum-1.0.0/DataSum/NAMESPACE | 18 DataSum-1.0.0/DataSum/NEWS.md |only DataSum-1.0.0/DataSum/R/app.R |only DataSum-1.0.0/DataSum/R/report.R |only DataSum-1.0.0/DataSum/R/summarize.R |only DataSum-1.0.0/DataSum/README.md | 256 ++++++----- DataSum-1.0.0/DataSum/build |only DataSum-1.0.0/DataSum/inst |only DataSum-1.0.0/DataSum/man/DataSum-package.Rd |only DataSum-1.0.0/DataSum/man/datasum_report.Rd |only DataSum-1.0.0/DataSum/man/figures |only DataSum-1.0.0/DataSum/man/profile_data.Rd |only DataSum-1.0.0/DataSum/man/run_datasum_app.Rd |only DataSum-1.0.0/DataSum/man/summarize_data.Rd |only DataSum-1.0.0/DataSum/man/summarize_vector.Rd |only DataSum-1.0.0/DataSum/tests/testthat.R | 16 DataSum-1.0.0/DataSum/tests/testthat/test-profile-data.R |only DataSum-1.0.0/DataSum/tests/testthat/test-report-app.R |only DataSum-1.0.0/DataSum/tests/testthat/test-summarize-data.R |only DataSum-1.0.0/DataSum/tests/testthat/test-summarize-vector.R |only DataSum-1.0.0/DataSum/vignettes |only 29 files changed, 222 insertions(+), 148 deletions(-)
Title: The Weyl Algebra
Description: A suite of routines for Weyl algebras. Notation follows
Coutinho (1995, ISBN 0-521-55119-6, "A Primer of Algebraic
D-Modules"). Uses 'disordR' discipline
(Hankin 2022 <doi:10.48550/arXiv.2210.03856>). To cite
the package in publications, use Hankin
2022 <doi:10.48550/arXiv.2212.09230>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between weyl versions 0.0-7 dated 2025-04-08 and 0.0-8 dated 2026-07-13
weyl-0.0-7/weyl/inst/weyl_arxiv.Rnw |only weyl-0.0-8/weyl/DESCRIPTION | 14 +++--- weyl-0.0-8/weyl/MD5 | 59 ++++++++++++++-------------- weyl-0.0-8/weyl/NAMESPACE | 4 + weyl-0.0-8/weyl/NEWS.md | 5 ++ weyl-0.0-8/weyl/R/weyl.R | 19 +++------ weyl-0.0-8/weyl/build/partial.rdb |binary weyl-0.0-8/weyl/build/vignette.rds |binary weyl-0.0-8/weyl/data/dot.rda |binary weyl-0.0-8/weyl/data/x_and_d.rda |binary weyl-0.0-8/weyl/inst/doc/borcherds.Rmd | 2 weyl-0.0-8/weyl/inst/doc/borcherds.html | 7 +-- weyl-0.0-8/weyl/inst/doc/weyl.R | 4 - weyl-0.0-8/weyl/inst/doc/weyl.Rmd | 4 - weyl-0.0-8/weyl/inst/doc/weyl.html | 23 +++++------ weyl-0.0-8/weyl/man/coeffs.Rd | 4 - weyl-0.0-8/weyl/man/constant.Rd | 10 ++-- weyl-0.0-8/weyl/man/degree.Rd | 2 weyl-0.0-8/weyl/man/dot.Rd | 16 ++++++- weyl-0.0-8/weyl/man/drop.Rd | 2 weyl-0.0-8/weyl/man/grade.Rd | 20 +++++---- weyl-0.0-8/weyl/man/horner.Rd | 4 - weyl-0.0-8/weyl/man/ooom.Rd | 8 +-- weyl-0.0-8/weyl/man/spray.Rd | 6 +- weyl-0.0-8/weyl/man/weyl-class.Rd | 2 weyl-0.0-8/weyl/man/weyl.Rd | 2 weyl-0.0-8/weyl/man/x_and_d.Rd | 8 ++- weyl-0.0-8/weyl/man/zero.Rd | 14 +++++- weyl-0.0-8/weyl/vignettes/borcherds.Rmd | 2 weyl-0.0-8/weyl/vignettes/weyl.Rmd | 4 - weyl-0.0-8/weyl/vignettes/weyl.bib | 66 +++++++++++++++++++++++++++++++- 31 files changed, 197 insertions(+), 114 deletions(-)
Title: Exact Test and Visualization of Multi-Set Intersections
Description: Identification of sets of objects with shared features is a common operation in all disciplines. Analysis of intersections among multiple sets is fundamental for in-depth understanding of their complex relationships. This package implements a theoretical framework for efficient computation of statistical distributions of multi-set intersections based upon combinatorial theory, and provides multiple scalable techniques for visualizing the intersection statistics. The statistical algorithm behind this package was published in Wang et al. (2015) <doi:10.1038/srep16923>.
Author: Minghui Wang [aut, cre],
Yongzhong Zhao [aut],
Bin Zhang [aut]
Maintainer: Minghui Wang <minghui.wang@mssm.edu>
Diff between SuperExactTest versions 1.1.0 dated 2022-03-25 and 1.2.0 dated 2026-07-13
SuperExactTest-1.1.0/SuperExactTest/src/binom.c |only SuperExactTest-1.1.0/SuperExactTest/src/cmp.c |only SuperExactTest-1.1.0/SuperExactTest/src/dmvhyperLog.c |only SuperExactTest-1.2.0/SuperExactTest/DESCRIPTION | 17 SuperExactTest-1.2.0/SuperExactTest/MD5 | 25 - SuperExactTest-1.2.0/SuperExactTest/R/psets.R | 8 SuperExactTest-1.2.0/SuperExactTest/R/vis.R | 24 - SuperExactTest-1.2.0/SuperExactTest/build/vignette.rds |binary SuperExactTest-1.2.0/SuperExactTest/inst/doc/set_html.R | 8 SuperExactTest-1.2.0/SuperExactTest/inst/doc/set_html.html | 30 - SuperExactTest-1.2.0/SuperExactTest/man/plot.Rd | 2 SuperExactTest-1.2.0/SuperExactTest/src/dmvhyper.c | 125 +++--- SuperExactTest-1.2.0/SuperExactTest/src/mvhyper.h | 142 ++++++- SuperExactTest-1.2.0/SuperExactTest/src/pmvhyper.c | 192 +++++----- SuperExactTest-1.2.0/SuperExactTest/src/registerDynamicSymbol.c | 18 15 files changed, 367 insertions(+), 224 deletions(-)
More information about SuperExactTest at CRAN
Permanent link
Title: Species Identity and Evolution in R
Description: Analysis of species limits and DNA barcoding data. Included are functions for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, testing and optimizing divergence threshold limits, assessment of diagnostic nucleotides, and calculation of the probability of reciprocal monophyly. Additionally, a sliding window function offers opportunities to analyse information across a gene, often used for marker design in degraded DNA studies. Further information on the package has been published in Brown et al (2012) <doi:10.1111/j.1755-0998.2011.03108.x>.
Author: Samuel Brown [aut],
Stephane Boyer [aut],
Marie-Caroline Lefort [aut],
Jagoba Malumbres-Olarte [aut],
Cor Vink [aut],
Rob Cruickshank [aut],
Rupert A. Collins [aut, cre, cph]
Maintainer: Rupert A. Collins <rupertcollins@gmail.com>
Diff between spider versions 1.5.2 dated 2026-04-04 and 1.5.3 dated 2026-07-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 7 +++++++ R/seeBarcode.R | 5 +++-- man/seeBarcode.Rd | 2 +- 5 files changed, 20 insertions(+), 12 deletions(-)
Title: Power Fuzzy Clustering and Cluster-Wise Regression
Description: Implementations of Power Fuzzy Clustering (PFC) and Power Fuzzy
Cluster-wise Regression (PFCR) for multivariate data. The package supports
Minkowski distances, with the L1 case solved via iteratively re-weighted
least squares and the case p > 1 solved via coordinate-wise root finding,
as well as an adaptive, regularised Mahalanobis distance with per-cluster
covariance matrices. Both plain fuzzy clustering and cluster-wise linear
regression are provided. The corresponding paper can be found at Nguyen P.T., Tortora C., and Punzo A. (2026) <doi:10.1109/TFUZZ.2026.3683998>.
Author: Phuc Thinh Nguyen [aut, cre],
Cristina Tortora [aut, ths, dgs],
Antonio Punzo [aut, ths, dgs]
Maintainer: Phuc Thinh Nguyen <phucthinh010603@yahoo.com>
Diff between pfclust versions 0.1.0 dated 2026-04-28 and 0.1.1 dated 2026-07-13
DESCRIPTION | 6 +-- MD5 | 16 ++++---- R/PDVRegressionWithEuclidean.R |only R/PDVWithEuclidean.R |only R/PFC.R | 23 +++++++---- R/PFCR.R | 19 ++++++--- inst/examples/demo.R | 47 ++++++++++++++++++++--- man/PFC.Rd | 63 +++++++++---------------------- man/PFCR.Rd | 82 ++++++++++++----------------------------- man/pfclust-package.Rd | 4 +- 10 files changed, 123 insertions(+), 137 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr2 versions 1.2.3 dated 2026-06-23 and 1.3.0 dated 2026-07-13
DESCRIPTION | 11 - MD5 | 58 ++++----- NAMESPACE | 1 NEWS.md | 8 + R/oauth-flow-auth-code.R | 14 +- R/oauth-flow-client-credentials.R | 11 + R/oauth-flow-device.R | 11 + R/oauth-flow-jwt.R | 11 + R/oauth-flow-password.R | 11 + R/oauth-flow-refresh.R | 11 + R/oauth-flow-token-exchange.R | 11 + R/oauth-token.R | 2 R/oauth.R | 92 ++++++++++++-- R/req-body.R | 2 README.md | 4 inst/doc/httr2.html | 38 +++--- man/oauth_cache_prune.Rd |only man/req_oauth.Rd | 6 man/req_oauth_auth_code.Rd | 7 - man/req_oauth_bearer_jwt.Rd | 7 - man/req_oauth_client_credentials.Rd | 12 + man/req_oauth_device.Rd | 7 - man/req_oauth_password.Rd | 7 - man/req_oauth_refresh.Rd | 7 - man/req_oauth_token_exchange.Rd | 7 - tests/testthat/_snaps/oauth-client.md | 6 tests/testthat/_snaps/oauth.md | 18 ++ tests/testthat/_snaps/req-cache.md | 6 tests/testthat/test-oauth-flow-client-credentials.R |only tests/testthat/test-oauth-token.R | 6 tests/testthat/test-oauth.R | 126 +++++++++++++++++++- 31 files changed, 412 insertions(+), 106 deletions(-)
Title: Probabilistic Regression Trees
Description: Implementation of Probabilistic Regression Trees (PRTree),
providing functions for model fitting and prediction, with specific adaptations
to handle missing values. The main computations are implemented in 'Fortran'
for high efficiency. The package is based on the PRTree methodology described in
Alkhoury et al. (2020), "Smooth and Consistent Probabilistic Regression Trees"
<https://proceedings.neurips.cc/paper_files/paper/2020/file/8289889263db4a40463e3f358bb7c7a1-Paper.pdf>.
Details on the treatment of missing data and implementation aspects are presented
in Prass, T.S.; Neimaier, A.S.; Pumi, G. (2025),
"Handling Missing Data in Probabilistic Regression Trees: Methods and Implementation in R"
<doi:10.48550/arXiv.2510.03634>.
Author: Taiane Schaedler Prass [aut, ths, cre] ,
Alisson Silva Neimaier [aut]
Maintainer: Taiane Schaedler Prass <taianeprass@gmail.com>
Diff between PRTree versions 1.0.3 dated 2026-02-18 and 1.1.0 dated 2026-07-13
PRTree-1.0.3/PRTree/R/misc.R |only PRTree-1.1.0/PRTree/DESCRIPTION | 52 PRTree-1.1.0/PRTree/MD5 | 63 PRTree-1.1.0/PRTree/NAMESPACE | 23 PRTree-1.1.0/PRTree/R/prtree.R | 40 PRTree-1.1.0/PRTree/R/prtree_control.R | 466 ++-- PRTree-1.1.0/PRTree/R/prtree_control_utils.R |only PRTree-1.1.0/PRTree/R/prtree_cv.R |only PRTree-1.1.0/PRTree/R/prtree_cv_methods.R |only PRTree-1.1.0/PRTree/R/prtree_defaults.R |only PRTree-1.1.0/PRTree/R/prtree_grid_expansion.R |only PRTree-1.1.0/PRTree/R/prtree_main.R | 340 ++- PRTree-1.1.0/PRTree/R/prtree_main_methods.R |only PRTree-1.1.0/PRTree/R/prtree_messages.R |only PRTree-1.1.0/PRTree/R/prtree_predict.R | 129 - PRTree-1.1.0/PRTree/R/prtree_rules.R |only PRTree-1.1.0/PRTree/R/prtree_split.R |only PRTree-1.1.0/PRTree/R/prtree_validation.R |only PRTree-1.1.0/PRTree/build |only PRTree-1.1.0/PRTree/inst/news.md | 29 PRTree-1.1.0/PRTree/man/PRTree.Package.Rd | 8 PRTree-1.1.0/PRTree/man/expand_sigma_grid.Rd |only PRTree-1.1.0/PRTree/man/plot.prtree.Rd |only PRTree-1.1.0/PRTree/man/plot.prtree.cv.Rd |only PRTree-1.1.0/PRTree/man/plot_tree.Rd |only PRTree-1.1.0/PRTree/man/pr_tree.Rd | 216 +- PRTree-1.1.0/PRTree/man/pr_tree_control.Rd | 280 +- PRTree-1.1.0/PRTree/man/pr_tree_control_cv.Rd |only PRTree-1.1.0/PRTree/man/pr_tree_cv.Rd |only PRTree-1.1.0/PRTree/man/predict.prtree.Rd | 25 PRTree-1.1.0/PRTree/man/print.idx.split.Rd |only PRTree-1.1.0/PRTree/man/print.prtree.Rd |only PRTree-1.1.0/PRTree/man/print.prtree.control.Rd |only PRTree-1.1.0/PRTree/man/print.prtree.control_cv.Rd |only PRTree-1.1.0/PRTree/man/print.prtree.cv.Rd |only PRTree-1.1.0/PRTree/man/print.sigma_grid.Rd |only PRTree-1.1.0/PRTree/man/print.summary.idx.split.Rd |only PRTree-1.1.0/PRTree/man/print.summary.prtree.Rd |only PRTree-1.1.0/PRTree/man/print.summary.prtree.cv.Rd |only PRTree-1.1.0/PRTree/man/summary.idx.split.Rd |only PRTree-1.1.0/PRTree/man/summary.prtree.Rd |only PRTree-1.1.0/PRTree/man/summary.prtree.cv.Rd |only PRTree-1.1.0/PRTree/man/train_test_split.Rd |only PRTree-1.1.0/PRTree/src/PRTree_init.c | 63 PRTree-1.1.0/PRTree/src/Rcalls.f90 | 300 +- PRTree-1.1.0/PRTree/src/prtree.f90 | 2263 +++++++++++---------- PRTree-1.1.0/PRTree/src/prtree_misc.f90 | 285 +- PRTree-1.1.0/PRTree/src/prtree_types.f90 | 468 +--- 48 files changed, 2770 insertions(+), 2280 deletions(-)
Title: Bayesian Analyses for One- and Two-Sample Inference and
Regression Methods
Description: Perform fundamental analyses using Bayesian parametric and non-parametric inference (regression, anova, 1 and 2 sample inference, non-parametric tests, etc.). (Practically) no Markov chain Monte Carlo (MCMC) is used; all exact finite sample inference is completed via closed form solutions or else through posterior sampling automated to ensure precision in interval estimate bounds. Diagnostic plots for model assessment, and key inferential quantities (point and interval estimates, probability of direction, region of practical equivalence, and Bayes factors) and model visualizations are provided. Bayes factors are computed either by the Savage Dickey ratio given in Dickey (1971) <doi:10.1214/aoms/1177693507> or by Chib's method as given in <doi:10.1080/01621459.1995.10476635>. Interpretations are from Kass and Raftery (1995) <doi:10.1080/01621459.1995.10476572>. ROPE bounds are based on discussions in Kruschke (2018) <doi:10.1177/2515245918771304>. Methods for d [...truncated...]
Author: Daniel K. Sewell [aut, cre, cph] ,
Alan Arakkal [aut]
Maintainer: Daniel K. Sewell <daniel-sewell@uiowa.edu>
Diff between bayesics versions 2.1.1 dated 2026-03-11 and 3.0.0 dated 2026-07-13
bayesics-2.1.1/bayesics/R/predict.aov_b.R |only bayesics-2.1.1/bayesics/R/predict.glm_b.R |only bayesics-2.1.1/bayesics/R/predict.lm_b.R |only bayesics-2.1.1/bayesics/R/predict.lm_b_bma.R |only bayesics-2.1.1/bayesics/R/predict.np_glm_b.R |only bayesics-2.1.1/bayesics/man/predict.aov_b.Rd |only bayesics-2.1.1/bayesics/man/predict.glm_b.Rd |only bayesics-2.1.1/bayesics/man/predict.lm_b.Rd |only bayesics-2.1.1/bayesics/man/predict.lm_b_bma.Rd |only bayesics-2.1.1/bayesics/man/predict.np_glm_b.Rd |only bayesics-2.1.1/bayesics/tests/testthat/test-get_posterior_draws.R |only bayesics-3.0.0/bayesics/DESCRIPTION | 12 bayesics-3.0.0/bayesics/MD5 | 181 bayesics-3.0.0/bayesics/NAMESPACE | 376 - bayesics-3.0.0/bayesics/NEWS.md | 13 bayesics-3.0.0/bayesics/R/IC.R | 740 +-- bayesics-3.0.0/bayesics/R/aov_b.R | 131 bayesics-3.0.0/bayesics/R/b_procedure-class.R |only bayesics-3.0.0/bayesics/R/bayes_factors.R | 73 bayesics-3.0.0/bayesics/R/bayes_pvalue.R |only bayesics-3.0.0/bayesics/R/bayesics-package.R |only bayesics-3.0.0/bayesics/R/bma_inference.R | 262 - bayesics-3.0.0/bayesics/R/case_control_b.R | 376 + bayesics-3.0.0/bayesics/R/chisq_test_b.R | 664 +-- bayesics-3.0.0/bayesics/R/coef.R | 52 bayesics-3.0.0/bayesics/R/cor_test_b.R | 353 - bayesics-3.0.0/bayesics/R/credint.R | 212 - bayesics-3.0.0/bayesics/R/find_beta_parms.R | 2 bayesics-3.0.0/bayesics/R/find_invgamma_parms.R | 2 bayesics-3.0.0/bayesics/R/frac_bayes_factors.R | 4 bayesics-3.0.0/bayesics/R/get_posterior_draws.R | 176 bayesics-3.0.0/bayesics/R/glm_b.R | 47 bayesics-3.0.0/bayesics/R/heteroscedasticity_test.R | 2 bayesics-3.0.0/bayesics/R/imports.R | 7 bayesics-3.0.0/bayesics/R/lm_b-class.R |only bayesics-3.0.0/bayesics/R/lm_b.R | 51 bayesics-3.0.0/bayesics/R/logLik.R |only bayesics-3.0.0/bayesics/R/mediate_b.R | 37 bayesics-3.0.0/bayesics/R/negbinom.R | 2 bayesics-3.0.0/bayesics/R/np_glm_b.R | 31 bayesics-3.0.0/bayesics/R/plot.R | 2018 ---------- bayesics-3.0.0/bayesics/R/plot_bands.R |only bayesics-3.0.0/bayesics/R/plot_dx.R |only bayesics-3.0.0/bayesics/R/poisson_test_b.R | 314 - bayesics-3.0.0/bayesics/R/predict.R |only bayesics-3.0.0/bayesics/R/print.R | 309 + bayesics-3.0.0/bayesics/R/prop_test_b.R | 854 ---- bayesics-3.0.0/bayesics/R/sign_test_b.R | 149 bayesics-3.0.0/bayesics/R/summary.R | 471 +- bayesics-3.0.0/bayesics/R/survfit_b.R | 2 bayesics-3.0.0/bayesics/R/t_test_b.R | 567 ++ bayesics-3.0.0/bayesics/R/vcov.R | 88 bayesics-3.0.0/bayesics/R/wilcoxon_test_b.R | 478 +- bayesics-3.0.0/bayesics/man/IC.Rd | 41 bayesics-3.0.0/bayesics/man/Surv.Rd | 82 bayesics-3.0.0/bayesics/man/aov_b.Rd | 37 bayesics-3.0.0/bayesics/man/b_procedure-class.Rd |only bayesics-3.0.0/bayesics/man/bayes_factors.Rd | 7 bayesics-3.0.0/bayesics/man/bayes_pvalue.Rd |only bayesics-3.0.0/bayesics/man/bayesics-package.Rd |only bayesics-3.0.0/bayesics/man/bma_inference.Rd | 20 bayesics-3.0.0/bayesics/man/case_control_b.Rd | 19 bayesics-3.0.0/bayesics/man/chisq_test_b.Rd | 38 bayesics-3.0.0/bayesics/man/coef.Rd | 13 bayesics-3.0.0/bayesics/man/cor_test_b.Rd | 19 bayesics-3.0.0/bayesics/man/credint.Rd | 11 bayesics-3.0.0/bayesics/man/find_beta_parms.Rd | 4 bayesics-3.0.0/bayesics/man/find_invgamma_parms.Rd | 4 bayesics-3.0.0/bayesics/man/frac_bayes_factors.Rd | 4 bayesics-3.0.0/bayesics/man/get_posterior_draws.Rd | 16 bayesics-3.0.0/bayesics/man/glm_b.Rd | 27 bayesics-3.0.0/bayesics/man/heteroscedasticity_test.Rd | 2 bayesics-3.0.0/bayesics/man/lm_b-class.Rd |only bayesics-3.0.0/bayesics/man/lm_b.Rd | 17 bayesics-3.0.0/bayesics/man/logLik.Rd |only bayesics-3.0.0/bayesics/man/mediate_b.Rd | 9 bayesics-3.0.0/bayesics/man/negbinom.Rd | 2 bayesics-3.0.0/bayesics/man/np_glm_b.Rd | 8 bayesics-3.0.0/bayesics/man/plot.Rd | 104 bayesics-3.0.0/bayesics/man/plot_bands.Rd |only bayesics-3.0.0/bayesics/man/plot_dx.Rd |only bayesics-3.0.0/bayesics/man/poisson_test_b.Rd | 24 bayesics-3.0.0/bayesics/man/predict.Rd |only bayesics-3.0.0/bayesics/man/print.Rd | 18 bayesics-3.0.0/bayesics/man/prop_test_b.Rd | 32 bayesics-3.0.0/bayesics/man/sign_test_b.Rd | 19 bayesics-3.0.0/bayesics/man/summary.Rd | 30 bayesics-3.0.0/bayesics/man/survfit_b.Rd | 2 bayesics-3.0.0/bayesics/man/t_test_b.Rd | 10 bayesics-3.0.0/bayesics/man/vcov.Rd | 11 bayesics-3.0.0/bayesics/man/wilcoxon_test_b.Rd | 36 bayesics-3.0.0/bayesics/tests/testthat/test-aov_b.R | 529 +- bayesics-3.0.0/bayesics/tests/testthat/test-bma_inference.R | 49 bayesics-3.0.0/bayesics/tests/testthat/test-case_control_b.R | 78 bayesics-3.0.0/bayesics/tests/testthat/test-chisq_test_b.R | 85 bayesics-3.0.0/bayesics/tests/testthat/test-cor_test_b.R | 10 bayesics-3.0.0/bayesics/tests/testthat/test-glm_b.R | 1517 ++++--- bayesics-3.0.0/bayesics/tests/testthat/test-lm_b.R | 713 ++- bayesics-3.0.0/bayesics/tests/testthat/test-mediate_b.R | 113 bayesics-3.0.0/bayesics/tests/testthat/test-np_glm_b.R | 931 ++-- bayesics-3.0.0/bayesics/tests/testthat/test-poisson_test_b.R | 52 bayesics-3.0.0/bayesics/tests/testthat/test-prop_test_b.R | 47 bayesics-3.0.0/bayesics/tests/testthat/test-sign_test_b.R | 41 bayesics-3.0.0/bayesics/tests/testthat/test-t_test_b.R | 71 bayesics-3.0.0/bayesics/tests/testthat/test-wilcoxon_test_b.R | 54 105 files changed, 6250 insertions(+), 7762 deletions(-)
Title: ACC Baseball Datasets with Advanced Sabermetric Metrics
Description: Provides curated ACC (Atlantic Coast Conference) baseball
datasets at the player-season level, including traditional statistics
and advanced sabermetric metrics such as weighted on-base average
(wOBA), weighted runs created plus (wRC+), and fielding-independent
pitching (FIP).
Author: Hana Baskin [aut, cre, cph]
Maintainer: Hana Baskin <hana.baskin@gmail.com>
Diff between accbaseballr versions 0.1.3 dated 2026-05-28 and 0.1.4 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 12 ++++++++++++ data/batting.rda |binary data/league_context.rda |binary data/pitching.rda |binary data/players.rda |binary 7 files changed, 21 insertions(+), 9 deletions(-)
Title: Generalized Boosted Regression Models
Description: Extensions to Freund and Schapire's AdaBoost algorithm, Y. Freund
and R. Schapire (1997) <doi:10.1006/jcss.1997.1504> and Friedman's gradient
boosting machine, J.H. Friedman (2001) <doi:10.1214/aos/1013203451>.
Includes regression methods for least squares, absolute loss,
t-distribution loss, quantile regression, logistic, Poisson,
Cox proportional hazards partial likelihood, AdaBoost
exponential loss, Huberized hinge loss,
and Learning to Rank measures (LambdaMART).
Author: James Hickey [aut],
Paul Metcalfe [aut],
Greg Ridgeway [aut, cre],
Stefan Schroedl [aut],
Harry Southworth [aut],
Terry Therneau [aut]
Maintainer: Greg Ridgeway <gridge@upenn.edu>
Diff between gbm3 versions 3.0.1 dated 2026-05-13 and 3.0.2 dated 2026-07-13
DESCRIPTION | 13 - MD5 | 66 +++--- R/create_dist_obj_for_gbmt_fit.R | 19 + R/gbm-distribution.r | 173 ++++++++-------- R/gbm.r | 13 - R/gbmt-fit.r | 6 README.md | 4 build/vignette.rds |binary inst/doc/cox-proportional-hazards-guide.R | 4 inst/doc/cox-proportional-hazards-guide.Rmd | 24 +- inst/doc/cox-proportional-hazards-guide.html | 81 +++---- inst/doc/gbm.R | 2 inst/doc/gbm.Rmd | 149 +++++++++++--- inst/doc/gbm.html | 275 +++++++++++++++++++++------ inst/doc/getting-started-with-gbm.Rmd | 63 +++--- inst/doc/getting-started-with-gbm.html | 240 +++++++++++------------ inst/doc/model-specific-parameters.R | 2 inst/doc/model-specific-parameters.Rmd | 21 -- inst/doc/model-specific-parameters.html | 74 +++---- man/gbm.Rd | 13 - man/gbm3-package.Rd | 1 man/gbm_dist.Rd | 12 - man/gbmt_fit.Rd | 6 src/censored_cox_state.h | 9 src/counting_cox_state.h | 11 - src/gamma.cpp | 15 + src/locationm.cpp | 15 + src/poisson.cpp | 18 + src/tweedie.cpp | 14 - tests/testthat/Rplots.pdf |binary vignettes/cox-proportional-hazards-guide.Rmd | 24 +- vignettes/gbm.Rmd | 149 +++++++++++--- vignettes/getting-started-with-gbm.Rmd | 63 +++--- vignettes/model-specific-parameters.Rmd | 21 -- 34 files changed, 979 insertions(+), 621 deletions(-)
Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function
and random generation for a number of univariate
and multivariate distributions. This package implements the
following distributions: Bernoulli, beta-binomial, beta-negative
binomial, beta prime, Bhattacharjee, Birnbaum-Saunders,
bivariate normal, bivariate Poisson, categorical, Dirichlet,
Dirichlet-multinomial, discrete gamma, discrete Laplace,
discrete normal, discrete uniform, discrete Weibull, Frechet,
gamma-Poisson, generalized extreme value, Gompertz,
generalized Pareto, Gumbel, half-Cauchy, half-normal, half-t,
Huber density, inverse chi-squared, inverse-gamma, Kumaraswamy,
Laplace, location-scale t, logarithmic, Lomax, multivariate
hypergeometric, multinomial, negative hypergeometric,
non-standard beta, normal mixture, Poisson mixture, Pareto,
power, reparametrized beta, Rayleigh, shifted Gompertz, Skellam,
slash, triangular, truncated binomial, truncated normal,
truncated Poisson, Tukey lambda, Wald, zero-inflated binomial,
zer [...truncated...]
Author: Tymoteusz Wolodzko [aut],
Sigbert Klinke [cre],
Thomas Farrar [ctb],
Piero Giovanni Luca Porta-Mana [ctb]
Maintainer: Sigbert Klinke <sigbert@wiwi.hu-berlin.de>
Diff between extraDistr versions 1.10.0.4 dated 2026-05-18 and 1.10.0.5 dated 2026-07-13
DESCRIPTION | 17 +++++++++++------ MD5 | 10 +++++----- NEWS.md | 5 +++++ R/categorical-distribution.R | 5 +++++ man/Categorical.Rd | 4 ++++ man/extraDistr-package.Rd | 1 + 6 files changed, 31 insertions(+), 11 deletions(-)
Title: Runs Allelematch Regression Tests
Description: Automates regression testing of package 'allelematch'. Over
2500 tests cover all functions in 'allelematch', reproduce the
examples from the documentation, and include negative tests. The
implementation is based on 'testthat'.
Author: Department of Wildlife, Fish and Environmental Studies at Swedish
University of Agricultural Sciences [cph],
Goeran Spong [cph] ,
Paul Galpern [ctb] ,
Torvald Staxler [aut, cre]
Maintainer: Torvald Staxler <torvald.staxler@telia.com>
Diff between amregtest versions 1.1.0 dated 2026-07-04 and 1.2.0 dated 2026-07-13
amregtest-1.1.0/amregtest/tests/testthat/_snaps/allelematch_3-amPairwise.md |only amregtest-1.1.0/amregtest/tests/testthat/_snaps/allelematch_4-amCluster.md |only amregtest-1.1.0/amregtest/tests/testthat/_snaps/allelematch_5-amAlleleFreq.md |only amregtest-1.1.0/amregtest/tests/testthat/_snaps/allelematch_6-amUnique.md |only amregtest-1.1.0/amregtest/tests/testthat/_snaps/amExample1.md |only amregtest-1.1.0/amregtest/tests/testthat/_snaps/amExample2.md |only amregtest-1.1.0/amregtest/tests/testthat/_snaps/amExample3.md |only amregtest-1.1.0/amregtest/tests/testthat/_snaps/amExample4.md |only amregtest-1.1.0/amregtest/tests/testthat/_snaps/ggData.md |only amregtest-1.2.0/amregtest/DESCRIPTION | 6 amregtest-1.2.0/amregtest/MD5 | 110 amregtest-1.2.0/amregtest/NEWS.md | 16 amregtest-1.2.0/amregtest/tests/testthat/Rplots.pdf |binary amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_1-amDataset.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_2-amMatrix_negative.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_3-amPairwise.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_3-amPairwise_negative.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_4-amCluster-Ex2.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_4-amCluster-Ex3.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_4-amCluster-Ex4.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_4-amCluster-Ex5.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_5-amAlleleFreq.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_6-amUnique.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/allelematch_6-amUnique_negative.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/amExample1.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/amExample2.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/amExample3.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/amExample4.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.5/ggData.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/allelematch_1-amDataset.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/allelematch_2-amMatrix_negative.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/allelematch_3-amPairwise_negative.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/allelematch_3-amPairwise_print.md | 693 +---- amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/allelematch_4-amCluster_print.md | 958 ++----- amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/allelematch_5-amAlleleFreq.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/allelematch_6-amUnique.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/allelematch_6-amUnique_negative.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/allelematch_6-amUnique_print.md | 1286 +++------- amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/amExample1.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/amExample3.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/2.6/ggData.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/allelematch_1-amDataset.md | 78 amregtest-1.2.0/amregtest/tests/testthat/_snaps/allelematch_2-amMatrix_negative.md | 13 amregtest-1.2.0/amregtest/tests/testthat/_snaps/allelematch_3-amPairwise_negative.md | 26 amregtest-1.2.0/amregtest/tests/testthat/_snaps/allelematch_4-amCluster-Ex1.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/allelematch_4-amCluster-amMini.md |only amregtest-1.2.0/amregtest/tests/testthat/_snaps/allelematch_6-amUnique_negative.md | 13 amregtest-1.2.0/amregtest/tests/testthat/_snaps/allelematch_7-amUniqueProfile.md | 6 amregtest-1.2.0/amregtest/tests/testthat/_snaps/bad-2.6.0 |only amregtest-1.2.0/amregtest/tests/testthat/helper.R | 13 amregtest-1.2.0/amregtest/tests/testthat/setup-snapshot_amCluster.R |only amregtest-1.2.0/amregtest/tests/testthat/setup.R | 13 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_1-amDataset.R | 16 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_2-amMatrix_negative.R | 2 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_3-amPairwise.R | 77 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_3-amPairwise_negative.R | 4 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_3-amPairwise_print.R | 3 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_4-amCluster-Ex1.R |only amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_4-amCluster-Ex2.R |only amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_4-amCluster-Ex3.R |only amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_4-amCluster-Ex4.R |only amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_4-amCluster-Ex5.R |only amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_4-amCluster-amMini.R |only amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_4-amCluster.R | 82 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_4-amCluster_print.R | 4 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_5-amAlleleFreq.R | 40 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_6-amUnique.R | 11 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_6-amUnique_negative.R | 14 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_6-amUnique_print.R | 3 amregtest-1.2.0/amregtest/tests/testthat/test-allelematch_7-amUniqueProfile.R | 11 amregtest-1.2.0/amregtest/tests/testthat/test-amExample1.R | 27 amregtest-1.2.0/amregtest/tests/testthat/test-amExample2.R | 26 amregtest-1.2.0/amregtest/tests/testthat/test-amExample3.R | 20 amregtest-1.2.0/amregtest/tests/testthat/test-amExample4.R | 24 amregtest-1.2.0/amregtest/tests/testthat/test-ggData.R | 12 75 files changed, 1248 insertions(+), 2359 deletions(-)
Title: Adaptive Weights Smoothing
Description: We provide a collection of R-functions implementing
adaptive smoothing procedures in 1D, 2D and 3D. This includes the
Propagation-Separation Approach to adaptive smoothing,
the Intersecting Confidence Intervals (ICI), variational approaches and a non-local means filter.
The package is described in detail in Polzehl J, Papafitsoros K, Tabelow K (2020).
Patch-Wise Adaptive Weights Smoothing in R. Journal of Statistical Software, 95(6), 1-27.
<doi:10.18637/jss.v095.i06>,
Usage of the package in MR imaging is illustrated in Polzehl and Tabelow (2023),
Magnetic Resonance Brain Imaging, 2nd Ed. Appendix A, Springer, Use R! Series.
<doi:10.1007/978-3-031-38949-8>.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between aws versions 2.5-6 dated 2024-09-30 and 2.5-7 dated 2026-07-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/aws-Example.R | 2 -- inst/doc/aws-Example.Rnw | 2 +- inst/doc/aws-Example.pdf |binary man/summary-methods.Rd | 7 ++----- vignettes/aws-Example.Rnw | 2 +- 9 files changed, 16 insertions(+), 21 deletions(-)
Title: Inference for Released Plug-in Sampling Synthetic Dataset
Description: Considering the singly imputed synthetic data generated via plug-in sampling under the multivariate normal model, draws inference procedures including the generalized variance, the sphericity test, the test for independence between two subsets of variables, and the test for the regression of one set of variables on the other. For more details see Klein et al. (2021) <doi:10.1007/s13571-019-00215-9>.
Author: Vitor Augusto [aut] ,
Mina Norouzirad [aut] ,
Miguel Fonseca [ctb] ,
Ricardo Moura [aut, cre, cph] ,
FCT, I.P. [fnd] )
Maintainer: Ricardo Moura <rp.moura@fct.unl.pt>
Diff between PSinference versions 0.2.2 dated 2024-12-10 and 1.0.0 dated 2026-07-13
PSinference-0.2.2/PSinference/R/Canodist.R |only PSinference-0.2.2/PSinference/R/GVdist.R |only PSinference-0.2.2/PSinference/R/Inddist.R |only PSinference-0.2.2/PSinference/R/Sphdist.R |only PSinference-0.2.2/PSinference/R/partition.R |only PSinference-0.2.2/PSinference/R/simSynthData.R |only PSinference-0.2.2/PSinference/R/utils.R |only PSinference-1.0.0/PSinference/DESCRIPTION | 39 +- PSinference-1.0.0/PSinference/MD5 | 69 +++- PSinference-1.0.0/PSinference/NAMESPACE | 41 +- PSinference-1.0.0/PSinference/NEWS.md | 4 PSinference-1.0.0/PSinference/R/data_documentation.R |only PSinference-1.0.0/PSinference/R/data_generation.R |only PSinference-1.0.0/PSinference/R/helper.R |only PSinference-1.0.0/PSinference/R/inference_functions.R |only PSinference-1.0.0/PSinference/R/mvn_test.R |only PSinference-1.0.0/PSinference/R/null_distributions.R |only PSinference-1.0.0/PSinference/R/original_data_test.R |only PSinference-1.0.0/PSinference/R/ps_test_class.R |only PSinference-1.0.0/PSinference/R/ps_test_wrapper.R |only PSinference-1.0.0/PSinference/R/utility_measures.R |only PSinference-1.0.0/PSinference/README.md | 40 ++ PSinference-1.0.0/PSinference/build |only PSinference-1.0.0/PSinference/data |only PSinference-1.0.0/PSinference/inst |only PSinference-1.0.0/PSinference/man/GVdist.Rd | 156 ++++----- PSinference-1.0.0/PSinference/man/Inddist.Rd | 153 +++------ PSinference-1.0.0/PSinference/man/Sphdist.Rd | 140 +++----- PSinference-1.0.0/PSinference/man/brittany_soil_ps.Rd |only PSinference-1.0.0/PSinference/man/canodist.Rd | 164 +++------- PSinference-1.0.0/PSinference/man/gv_ci.Rd |only PSinference-1.0.0/PSinference/man/gv_test.Rd |only PSinference-1.0.0/PSinference/man/independence_test.Rd |only PSinference-1.0.0/PSinference/man/is.ps_test.Rd |only PSinference-1.0.0/PSinference/man/mvn_test.Rd |only PSinference-1.0.0/PSinference/man/original_gv_test.Rd |only PSinference-1.0.0/PSinference/man/original_independence_test.Rd |only PSinference-1.0.0/PSinference/man/original_regression_test.Rd |only PSinference-1.0.0/PSinference/man/original_sphericity_test.Rd |only PSinference-1.0.0/PSinference/man/partition.Rd | 124 +++++-- PSinference-1.0.0/PSinference/man/plot.mvn_test.Rd |only PSinference-1.0.0/PSinference/man/plot.ps_test.Rd |only PSinference-1.0.0/PSinference/man/print.mvn_test.Rd |only PSinference-1.0.0/PSinference/man/print.original_test.Rd |only PSinference-1.0.0/PSinference/man/print.ps_test.Rd |only PSinference-1.0.0/PSinference/man/print.ps_utility.Rd |only PSinference-1.0.0/PSinference/man/ps_test-class.Rd |only PSinference-1.0.0/PSinference/man/ps_test.Rd |only PSinference-1.0.0/PSinference/man/regression_test.Rd |only PSinference-1.0.0/PSinference/man/simSynthData.Rd | 141 +++++--- PSinference-1.0.0/PSinference/man/sphericity_test.Rd |only PSinference-1.0.0/PSinference/man/summary.ps_test.Rd |only PSinference-1.0.0/PSinference/man/utility_measures.Rd |only PSinference-1.0.0/PSinference/vignettes |only 54 files changed, 577 insertions(+), 494 deletions(-)
Title: Efficient Bayesian Inference for Time-Varying Parameter Models
with Shrinkage
Description: Efficient Markov chain Monte Carlo (MCMC) algorithms for fully Bayesian estimation of time-varying parameter models with shrinkage priors, both dynamic and static. Details on the algorithms used are provided in Bitto and Frühwirth-Schnatter (2019) <doi:10.1016/j.jeconom.2018.11.006> and
Cadonna et al. (2020) <doi:10.3390/econometrics8020020> and Knaus and Frühwirth-Schnatter (2023) <doi:10.48550/arXiv.2312.10487>. For details on the package, please see Knaus et al. (2021) <doi:10.18637/jss.v100.i13>. For the multivariate extension, see the 'shrinkTVPVAR' package.
Author: Peter Knaus [aut, cre] ,
Angela Bitto-Nemling [aut],
Annalisa Cadonna [aut] ,
Sylvia Fruehwirth-Schnatter [aut] ,
Daniel Winkler [ctb],
Kemal Dingic [ctb]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>
Diff between shrinkTVP versions 3.1.1 dated 2026-01-08 and 3.1.2 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ inst/doc/shrinkTVP.pdf |binary vignettes/shrinkTVP.bib | 25 +++++++++++++++++++++++++ 5 files changed, 35 insertions(+), 7 deletions(-)
Title: The Symmetric Group: Permutations of a Finite Set
Description: Manipulates invertible functions from a finite set to
itself. Can transform from word form to cycle form and
back. To cite the package in publications please use
Hankin (2020) "Introducing the permutations R package",
SoftwareX, volume 11 <doi:10.1016/j.softx.2020.100453>.
Author: Robin K. S. Hankin [aut, cre] ,
Paul Egeler [ctb]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between permutations versions 1.1-6 dated 2025-02-11 and 1.1-9-1 dated 2026-07-13
permutations-1.1-6/permutations/R/zzz_dodecahedron.R |only permutations-1.1-6/permutations/inst/Matrix_multiplication_associative.svg |only permutations-1.1-6/permutations/inst/allpermutationsofagivenshape.R |only permutations-1.1-6/permutations/inst/dodecahedron_group.py |only permutations-1.1-6/permutations/inst/dot.Rmd |only permutations-1.1-6/permutations/inst/full_dodecahedron_group.py |only permutations-1.1-6/permutations/inst/given_shape.Rmd |only permutations-1.1-6/permutations/inst/guide.R |only permutations-1.1-6/permutations/inst/inversion.svg |only permutations-1.1-6/permutations/inst/megaminx_net_colour.svg |only permutations-1.1-6/permutations/inst/net_coords.txt |only permutations-1.1-6/permutations/inst/outer_automorphisms_of_S6.Rmd |only permutations-1.1-6/permutations/inst/permutations_active_to_passive.svg |only permutations-1.1-6/permutations/inst/permutations_composition_active.svg |only permutations-1.1-6/permutations/inst/read.me |only permutations-1.1-6/permutations/inst/shape_preserved_by_conjugation.svg |only permutations-1.1-6/permutations/inst/starminx.py |only permutations-1.1-6/permutations/inst/starminx_III.py |only permutations-1.1-9-1/permutations/DESCRIPTION | 20 permutations-1.1-9-1/permutations/MD5 | 142 ++-- permutations-1.1-9-1/permutations/NAMESPACE | 201 ++++-- permutations-1.1-9-1/permutations/NEWS.md | 20 permutations-1.1-9-1/permutations/R/all_perms_given_shape.R | 4 permutations-1.1-9-1/permutations/R/allcyc.R | 10 permutations-1.1-9-1/permutations/R/faro.R | 2 permutations-1.1-9-1/permutations/R/flip.R |only permutations-1.1-9-1/permutations/R/megaminx_plotting.R | 317 +++++----- permutations-1.1-9-1/permutations/R/perm_ops.R | 53 + permutations-1.1-9-1/permutations/R/permfuns.R | 242 ++++++- permutations-1.1-9-1/permutations/R/validity_funs.R | 2 permutations-1.1-9-1/permutations/R/zzz_id.R | 5 permutations-1.1-9-1/permutations/build/partial.rdb |binary permutations-1.1-9-1/permutations/build/vignette.rds |binary permutations-1.1-9-1/permutations/data/dodecahedron.rda |only permutations-1.1-9-1/permutations/data/dot.rda |binary permutations-1.1-9-1/permutations/data/megaminx.rda |binary permutations-1.1-9-1/permutations/inst/doc/cyclist.html | 2 permutations-1.1-9-1/permutations/inst/doc/groupaction.R | 20 permutations-1.1-9-1/permutations/inst/doc/groupaction.Rmd | 42 + permutations-1.1-9-1/permutations/inst/doc/groupaction.html | 59 + permutations-1.1-9-1/permutations/inst/doc/order_of_ops.R | 3 permutations-1.1-9-1/permutations/inst/doc/order_of_ops.Rmd | 67 +- permutations-1.1-9-1/permutations/inst/doc/order_of_ops.html | 100 +-- permutations-1.1-9-1/permutations/inst/doc/permutations.R | 16 permutations-1.1-9-1/permutations/inst/doc/permutations.Rnw | 28 permutations-1.1-9-1/permutations/inst/doc/permutations.pdf |binary permutations-1.1-9-1/permutations/inst/doc/print.R | 3 permutations-1.1-9-1/permutations/inst/doc/print.Rmd | 28 permutations-1.1-9-1/permutations/inst/doc/print.html | 301 +++++---- permutations-1.1-9-1/permutations/inst/doc/representation.Rmd | 9 permutations-1.1-9-1/permutations/inst/doc/representation.html | 10 permutations-1.1-9-1/permutations/inst/megaminx.R | 7 permutations-1.1-9-1/permutations/inst/permutations.bib |only permutations-1.1-9-1/permutations/inst/permutations_composition_active.pdf |only permutations-1.1-9-1/permutations/inst/swap.Rmd |only permutations-1.1-9-1/permutations/man/Extract.Rd |only permutations-1.1-9-1/permutations/man/Ops.permutation.Rd | 23 permutations-1.1-9-1/permutations/man/allperms.Rd | 54 - permutations-1.1-9-1/permutations/man/c.Rd | 9 permutations-1.1-9-1/permutations/man/caydist.Rd |only permutations-1.1-9-1/permutations/man/cyclist.Rd | 36 - permutations-1.1-9-1/permutations/man/dodecahedron.Rd | 10 permutations-1.1-9-1/permutations/man/fixed.Rd | 2 permutations-1.1-9-1/permutations/man/keepcyc.Rd | 4 permutations-1.1-9-1/permutations/man/length.Rd | 5 permutations-1.1-9-1/permutations/man/megaminx.Rd | 31 permutations-1.1-9-1/permutations/man/megaminx_superflip.Rd |only permutations-1.1-9-1/permutations/man/permorder.Rd | 8 permutations-1.1-9-1/permutations/man/permutation.Rd | 27 permutations-1.1-9-1/permutations/man/print.Rd | 62 + permutations-1.1-9-1/permutations/man/rperm.Rd | 81 +- permutations-1.1-9-1/permutations/man/sgn.Rd | 6 permutations-1.1-9-1/permutations/man/shape.Rd | 35 - permutations-1.1-9-1/permutations/man/stabilizer.Rd | 80 +- permutations-1.1-9-1/permutations/man/swap.Rd |only permutations-1.1-9-1/permutations/man/tidy.Rd | 10 permutations-1.1-9-1/permutations/tests/testthat/test_aaa.R | 12 permutations-1.1-9-1/permutations/tests/testthat/test_aaj.R | 5 permutations-1.1-9-1/permutations/tests/testthat/test_aam.R |only permutations-1.1-9-1/permutations/tests/testthat/test_aan.R |only permutations-1.1-9-1/permutations/tests/testthat/test_aao.R |only permutations-1.1-9-1/permutations/vignettes/groupaction.Rmd | 42 + permutations-1.1-9-1/permutations/vignettes/order_of_ops.Rmd | 67 +- permutations-1.1-9-1/permutations/vignettes/permutations.Rnw | 28 permutations-1.1-9-1/permutations/vignettes/permutations.bib | 12 permutations-1.1-9-1/permutations/vignettes/print.Rmd | 28 permutations-1.1-9-1/permutations/vignettes/representation.Rmd | 9 87 files changed, 1564 insertions(+), 835 deletions(-)
Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi'
(<https://www.jamovi.org>) aims to make statistical analyses easy and
intuitive. 'jamovi' produces syntax that can directly be used in R (in
connection with the R-package 'jmv'). Having import / export routines for
the data files 'jamovi' produces ('.omv') permits an easy transfer of
data and analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre, cph]
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>
Diff between jmvReadWrite versions 0.4.13 dated 2026-04-27 and 0.4.14 dated 2026-07-13
DESCRIPTION | 14 MD5 | 126 +-- NEWS.md | 9 R/aggregate_omv.R | 170 +--- R/arrange_cols_omv.R | 73 - R/combine_cols_omv.R | 66 - R/convert_to_omv.R | 6 R/describe_omv.R | 278 ++++--- R/distances_omv.R | 164 ++-- R/globals.R | 86 +- R/label_vars_omv.R | 57 - R/long2wide_omv.R | 97 +- R/merge_cols_omv.R | 46 - R/merge_rows_omv.R | 103 +- R/read_omv.R | 49 - R/replace_omv.R | 68 + R/search_omv.R | 36 R/sort_omv.R | 59 - R/transform_vars_omv.R | 82 +- R/transpose_omv.R | 35 R/wide2long_omv.R | 130 +-- R/write_omv.R | 47 - README.md | 8 build/vignette.rds |binary inst/CITATION | 2 inst/WORDLIST | 2 inst/doc/jmvReadWrite.R | 6 inst/doc/jmvReadWrite.Rmd | 6 inst/doc/jmvReadWrite.html | 12 man/aggregate_omv.Rd | 197 ++--- man/arrange_cols_omv.Rd | 67 - man/combine_cols_omv.Rd | 71 - man/convert_to_omv.Rd | 6 man/describe_omv.Rd | 171 ++-- man/distances_omv.Rd | 54 - man/label_vars_omv.Rd | 57 - man/long2wide_omv.Rd | 91 +- man/merge_cols_omv.Rd | 50 - man/merge_rows_omv.Rd | 87 +- man/replace_omv.Rd | 61 + man/search_omv.Rd | 38 man/sort_omv.Rd | 49 - man/transform_vars_omv.Rd | 68 - man/transpose_omv.Rd | 40 - man/wide2long_omv.Rd | 108 +- tests/testthat/test-aggregate_omv.R | 56 - tests/testthat/test-arrange_cols_omv.R | 63 - tests/testthat/test-combine_cols_omv.R | 42 - tests/testthat/test-describe_omv.R | 425 +++++------ tests/testthat/test-distances_omv.R | 1194 ++++++++++++++++--------------- tests/testthat/test-globals.R | 221 +++-- tests/testthat/test-label_vars_omv.R | 66 + tests/testthat/test-long2wide_omv.R | 217 +++-- tests/testthat/test-merge_cols_omv.R | 86 +- tests/testthat/test-merge_rows_omv.R | 41 - tests/testthat/test-read_omv.R | 253 +++--- tests/testthat/test-replace_omv.R | 78 +- tests/testthat/test-search_omv.R | 44 - tests/testthat/test-sort_omv.R | 61 - tests/testthat/test-transform_vars_omv.R | 255 +++--- tests/testthat/test-transpose_omv.R | 30 tests/testthat/test-wide2long_omv.R | 171 ++-- tests/testthat/test-write_omv.R | 260 +++--- vignettes/jmvReadWrite.Rmd | 6 64 files changed, 3558 insertions(+), 3063 deletions(-)
Title: Visual Diagnostic Checks for Vector Autoregressive Models
Description: Provides model-agnostic visual diagnostics for vector
autoregressive (VAR) models. Given empirical data, model predictions,
residuals, and optionally simulated data, the package assembles a
multi-panel diagnostic grid: empirical vs. predicted time series, residual
inspection, residuals vs. predictions scatter, and posterior predictive style
checks via simulated trajectories. Output is a 'patchwork' object composed
of 'ggplot2' plots, allowing further customisation via standard
'ggplot2' theme calls. Follows the approach described in
Haslbeck et al. (2026) <doi:10.31234/osf.io/k6uz4_v3>.
Author: Bjoern S. Siepe [aut, cre, cph] ,
Jonas M. B. Haslbeck [aut]
Maintainer: Bjoern S. Siepe <bjoernsiepe+software@gmail.com>
Diff between VARcheck versions 0.1.0 dated 2026-05-19 and 0.1.1 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 9 +++++++++ R/panels.R | 4 ++-- R/plot_var_check.R | 16 ++++++++++++---- R/plot_var_row.R | 2 +- inst/doc/example-analyses.R | 1 + inst/doc/example-analyses.Rmd | 1 + inst/doc/example-analyses.html | 12 ++++++------ inst/doc/getting-started.html | 17 ++++++++--------- man/plot_var_check.Rd | 7 ++++++- tests/testthat/test-plot_var_check.R | 5 +++++ vignettes/example-analyses.Rmd | 1 + 13 files changed, 67 insertions(+), 38 deletions(-)
Title: Heteroskedasticity-Consistent Inference for Linear Models
Description: Computes heteroskedasticity-consistent covariance matrix
estimators for ordinary least squares regression models. The published HC0
through HC5m estimators implemented in the package follow White (1980)
<doi:10.2307/1912934>, Hinkley (1977)
<doi:10.1080/00401706.1977.10489550>, Horn et al. (1975)
<doi:10.1080/01621459.1975.10479877>, MacKinnon and White (1985)
<doi:10.1016/0304-4076(85)90158-7>, Cribari-Neto (2004)
<doi:10.1016/S0167-9473(02)00366-3>, Cribari-Neto and da Silva
(2011) <doi:10.1007/s10182-010-0141-2>, Cribari-Neto et al. (2007)
<doi:10.1080/03610920601126589>, and Li et al. (2016)
<doi:10.1080/00949655.2016.1198906>. The package also includes HCbeta, a
new estimator proposed by the package authors. It provides normal Wald tests,
confidence intervals, diagnostics, and S3 output for applied inference.
Author: Pedro Rafael D. Marinho [aut, cre] ,
Francisco Cribari-Neto [aut] ,
Marina Oliveira Cunha [aut]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between hcinfer versions 0.1.0 dated 2026-06-10 and 0.1.1 dated 2026-07-13
DESCRIPTION | 6 +- MD5 | 26 ++++++------ NEWS.md | 5 +- R/data.R | 67 +++++++++++++++++++++++++++---- README.md | 25 +++++++---- data/PublicSchools.rda |binary data/PublicSchools2.rda |only inst/doc/hcinfer-hcbeta.html | 28 ++++++------ man/PublicSchools.Rd | 18 ++++---- man/PublicSchools2.Rd |only man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/hcinfer-package.Rd | 1 tests/testthat/helper-data.R | 1 tests/testthat/test-data.R | 53 ++++++++++++++++++++++++ 15 files changed, 176 insertions(+), 54 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.7.0 dated 2026-07-10 and 1.7.0.1 dated 2026-07-13
DESCRIPTION | 8 +-- MD5 | 24 +++++------ R/GPModel.R | 66 ++++++++++++++++++++++++++++++-- configure | 10 ++-- configure.ac | 10 ++-- man/GPModel.Rd | 5 +- man/GPModel_shared_params.Rd | 29 +++++++++++++- man/fitGPModel.Rd | 5 +- src/include/GPBoost/likelihoods.h | 6 +- src/include/GPBoost/re_model.h | 3 - src/include/GPBoost/re_model_template.h | 17 ++++---- src/include/LightGBM/c_api.h | 3 - src/re_model.cpp | 7 ++- 13 files changed, 148 insertions(+), 45 deletions(-)
Title: Securely Wrangle Dataset According to Data Usage Agreement
Description: Create shareable data sets from raw data files that
contain protected elements. Relying on master crosswalk
files that list restricted variables, package functions
warn users about possible violations of data usage
agreement and prevent writing protected elements.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <ben@btskinner.io>
Diff between duawranglr versions 0.6.7 dated 2021-04-15 and 0.6.8 dated 2026-07-13
DESCRIPTION | 31 - MD5 | 22 - NAMESPACE | 1 NEWS.md | 4 R/duawrangler.R | 6 build/vignette.rds |binary inst/doc/duawranglr.Rmd | 2 inst/doc/duawranglr.html | 292 +++++++++++++- inst/doc/securing_data.R | 74 +-- inst/doc/securing_data.html | 865 +++++++++++++++++++++++++++++--------------- man/duawranglr.Rd | 19 vignettes/duawranglr.Rmd | 2 12 files changed, 940 insertions(+), 378 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous (and discrete) time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE) or difference equation, measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or Stan's Hamiltonian Monte Carlo sampling.
See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. See <https://osf.io/preprints/psyarxiv/4q9ex_v2> for a detailed tutorial.
Priors may be used. For the conceptual overview of the hierarchical Bayesian
linear SDE approach,
see <https://www.research [...truncated...]
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver2@uzh.ch>
Diff between ctsem versions 3.11.0 dated 2026-06-30 and 3.11.1 dated 2026-07-13
ctsem-3.11.0/ctsem/R/ctCheckFit.R |only ctsem-3.11.0/ctsem/R/ctStanContinuousPars.R |only ctsem-3.11.0/ctsem/R/ctStanData.R |only ctsem-3.11.0/ctsem/R/ctStanFit.R |only ctsem-3.11.0/ctsem/R/ctStanGenerate.R |only ctsem-3.11.0/ctsem/R/ctStanGenerateFromFit.R |only ctsem-3.11.0/ctsem/R/ctStanKalman.R |only ctsem-3.11.0/ctsem/R/ctStanModelWriter.R |only ctsem-3.11.0/ctsem/R/priorcheck.R |only ctsem-3.11.0/ctsem/man/ctAddSamples.Rd |only ctsem-3.11.0/ctsem/man/ctKalman.Rd |only ctsem-3.11.0/ctsem/man/ctStanUpdModel.Rd |only ctsem-3.11.1/ctsem/DESCRIPTION | 8 ctsem-3.11.1/ctsem/MD5 | 119 - ctsem-3.11.1/ctsem/NAMESPACE | 5 ctsem-3.11.1/ctsem/R/ctCoverageCheck.R | 2 ctsem-3.11.1/ctsem/R/ctData.R |only ctsem-3.11.1/ctsem/R/ctDiscretePars.R | 33 ctsem-3.11.1/ctsem/R/ctFit.R |only ctsem-3.11.1/ctsem/R/ctFitCovCheck.R |only ctsem-3.11.1/ctsem/R/ctGenerate.R | 107 + ctsem-3.11.1/ctsem/R/ctGenerateFromFit.R |only ctsem-3.11.1/ctsem/R/ctKalman.R | 261 ++ ctsem-3.11.1/ctsem/R/ctModelLatex.R | 524 ++++- ctsem-3.11.1/ctsem/R/ctModelWriter.R |only ctsem-3.11.1/ctsem/R/ctOptimUncertainty.R |only ctsem-3.11.1/ctsem/R/ctStanModel.R | 16 ctsem-3.11.1/ctsem/R/ctStanPlotPost.R | 19 ctsem-3.11.1/ctsem/R/ctStanPostPredict.R | 11 ctsem-3.11.1/ctsem/R/ctStanTIpredeffects.R | 13 ctsem-3.11.1/ctsem/R/ctSummarise.R | 4 ctsem-3.11.1/ctsem/R/ctsem-package.R | 2 ctsem-3.11.1/ctsem/R/ctsemUtils.R | 56 ctsem-3.11.1/ctsem/R/plot.ctStanFit.R | 8 ctsem-3.11.1/ctsem/R/sdpcor2cov.R | 2 ctsem-3.11.1/ctsem/R/stanoptimis.R | 1078 +----------- ctsem-3.11.1/ctsem/R/summary.ctStanFit.R | 300 +++ ctsem-3.11.1/ctsem/README.md | 4 ctsem-3.11.1/ctsem/inst/doc/empirical-bayes-fitting.html | 90 - ctsem-3.11.1/ctsem/inst/doc/hierarchicalmanual.pdf |binary ctsem-3.11.1/ctsem/inst/doc/hierarchicalmanual.rnw | 6 ctsem-3.11.1/ctsem/man/ctCheckFit.Rd | 2 ctsem-3.11.1/ctsem/man/ctDiscretePars.Rd | 14 ctsem-3.11.1/ctsem/man/ctDiscreteParsPlot.Rd | 16 ctsem-3.11.1/ctsem/man/ctFit.Rd | 41 ctsem-3.11.1/ctsem/man/ctFitAddSamples.Rd |only ctsem-3.11.1/ctsem/man/ctFitCovCheck.Rd | 12 ctsem-3.11.1/ctsem/man/ctFitCovCheckPlot.Rd | 2 ctsem-3.11.1/ctsem/man/ctFitUpdate.Rd | 4 ctsem-3.11.1/ctsem/man/ctFitUpdateModel.Rd |only ctsem-3.11.1/ctsem/man/ctGenerateFromFit.Rd | 12 ctsem-3.11.1/ctsem/man/ctGenerateFromPriors.Rd | 14 ctsem-3.11.1/ctsem/man/ctKalmanArray.Rd | 21 ctsem-3.11.1/ctsem/man/ctModelConvertOMX.Rd | 2 ctsem-3.11.1/ctsem/man/ctModelLatex.Rd | 8 ctsem-3.11.1/ctsem/man/ctOptimUncertainty.Rd | 77 ctsem-3.11.1/ctsem/man/ctPlotPosterior.Rd | 12 ctsem-3.11.1/ctsem/man/ctPostPredict.Rd | 14 ctsem-3.11.1/ctsem/man/ctPredict.Rd |only ctsem-3.11.1/ctsem/man/ctRawParnames.Rd | 2 ctsem-3.11.1/ctsem/man/ctSubjectPars.Rd | 4 ctsem-3.11.1/ctsem/man/ctSummaryMatrices.Rd | 9 ctsem-3.11.1/ctsem/man/ctTIpredEffects.Rd | 15 ctsem-3.11.1/ctsem/man/plot.ctKalmanDF.Rd | 16 ctsem-3.11.1/ctsem/man/plot.ctStanFit.Rd | 2 ctsem-3.11.1/ctsem/man/print.summary.ctStanFit.Rd |only ctsem-3.11.1/ctsem/man/stanoptimis.Rd | 18 ctsem-3.11.1/ctsem/man/summary.ctStanFit.Rd | 4 ctsem-3.11.1/ctsem/tests/testthat/test-ctModelLatex.R |only ctsem-3.11.1/ctsem/tests/testthat/test-ctOptimUncertainty.R | 182 +- ctsem-3.11.1/ctsem/tests/testthat/test-stantipred.R | 5 ctsem-3.11.1/ctsem/vignettes/hierarchicalmanual.rnw | 6 72 files changed, 1610 insertions(+), 1572 deletions(-)
Title: Core Functions to Read and Fit 13c Time Series from Breath Tests
Description: Reads several formats of 13C data (IRIS/Wagner,
BreathID) and CSV. Creates artificial sample data for testing. Fits
Maes/Ghoos, Bluck-Coward self-correcting formula using 'nls', 'nlme'.
Methods to fit breath test curves with Bayesian Stan methods are
refactored to package 'breathteststan'. For a Shiny GUI, see package
'dmenne/breathtestshiny' on github.
Author: Dieter Menne [aut, cre],
Menne Biomed Consulting Tuebingen [cph],
Benjamin Misselwitz [fnd],
Mark Fox [fnd],
Andreas Steingoetter [dtc],
University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between breathtestcore versions 0.8.10 dated 2025-10-28 and 0.8.11 dated 2026-07-13
DESCRIPTION | 8 MD5 | 164 ++++++++++---------- R/breathtest_data.R | 100 ++++++------ R/breathtest_parameters.R | 77 ++++----- R/breathtest_read_function.R | 33 ++-- R/breathtestcore-package.R | 8 R/breathtestcore.R | 59 +++---- R/breathtestfit_broom.R | 103 +++++++----- R/btcore_file.R | 11 - R/cleanup_data.R | 203 ++++++++++++++---------- R/coef_breathtestfit.R | 34 ++-- R/coef_by_group.R | 108 +++++++------ R/coef_diff_by_group.R | 125 ++++++++------- R/dob_to_pdr.R | 48 +++-- R/exp_beta.R | 47 +++-- R/nlme_fit.R | 89 ++++++---- R/nls_fit.R | 127 +++++++++------ R/null_fit.R | 13 - R/plot_breathtestfit.R | 205 +++++++++++++++---------- R/read_any_breathtest.R | 29 +-- R/read_breathid.R | 56 ++++-- R/read_breathid_xml.R | 103 ++++++------ R/read_breathtest_excel.R | 58 ++++--- R/read_iris.R | 62 ++++--- R/read_iris_csv.R | 94 +++++++---- R/sigma.R | 17 -- R/simulate_breathtest_data.R | 165 +++++++++++++------- R/subsample_data.R | 45 +++-- build/vignette.rds |binary inst/doc/data_formats.html | 10 - inst/doc/methods_and_concepts.R | 4 inst/doc/methods_and_concepts.Rmd | 4 inst/doc/methods_and_concepts.html | 12 - man/augment.breathtestfit.Rd | 12 - man/breathtest_data.Rd | 26 +-- man/breathtest_read_function.Rd | 6 man/btcore_file.Rd | 4 man/cleanup_data.Rd | 34 ++-- man/coef.breathtestfit.Rd | 8 man/coef_by_group.Rd | 14 - man/dob_to_pdr.Rd | 6 man/exp_beta.Rd | 10 - man/extract_id.Rd | 4 man/nlme_fit.Rd | 14 - man/nls_fit.Rd | 24 +- man/null_fit.Rd | 6 man/plot.breathtestfit.Rd | 6 man/read_any_breathtest.Rd | 4 man/read_breathid.Rd | 2 man/read_breathtest_excel.Rd | 14 - man/read_iris.Rd | 2 man/read_iris_csv.Rd | 6 man/sigma.breathtestnlmefit.Rd | 2 man/simulate_breathtest_data.Rd | 8 man/subsample_data.Rd | 8 man/t50_bluck_coward.Rd | 22 +- man/t50_maes_ghoos.Rd | 6 man/t50_maes_ghoos_scintigraphy.Rd | 6 man/tidy.breathtestfit.Rd | 6 man/tlag_maes_ghoos.Rd | 6 man/usz_13c.Rd | 4 man/usz_13c_a.Rd | 4 man/usz_13c_d.Rd | 22 +- tests/testthat/test_breathtest_parameters.R | 31 +-- tests/testthat/test_breathtest_read_function.R | 34 ++-- tests/testthat/test_broom.R | 6 tests/testthat/test_cleanup_data.R | 147 +++++++++++------ tests/testthat/test_coef_by_group.R | 85 +++++++--- tests/testthat/test_coef_diff_by_group.R | 81 ++++++--- tests/testthat/test_exp_beta.R | 9 - tests/testthat/test_nlme_fit.R | 74 ++++++--- tests/testthat/test_nls_fit.R | 24 +- tests/testthat/test_plot_breathtestfit.R | 42 ++--- tests/testthat/test_read_any_breathtest.R | 22 +- tests/testthat/test_read_breathid.R | 16 + tests/testthat/test_read_breathid_xml.R | 8 tests/testthat/test_read_excel.R | 61 ++++--- tests/testthat/test_read_iris.R | 53 +++--- tests/testthat/test_read_iris_csv.R | 14 - tests/testthat/test_simulate_breathtest_data.R | 29 ++- tests/testthat/test_subsample_data.R | 10 - tests/testthat/test_usz_13c.R | 32 +-- vignettes/methods_and_concepts.Rmd | 4 83 files changed, 1904 insertions(+), 1395 deletions(-)
More information about breathtestcore at CRAN
Permanent link
Title: Rapid Asynchronous and Distributed Computing
Description: Package to tackle large-scale problems asynchronously across
a distributed network. Employing a database centric model, rush
enables workers to communicate tasks and their results over a shared
'Redis' database. Key features include low task overhead, efficient
caching, and robust error handling. The package powers the
asynchronous optimization algorithms in the 'bbotk' and 'mlr3tuning'
packages.
Author: Marc Becker [cre, aut, cph]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between rush versions 1.1.0 dated 2026-04-24 and 1.2.0 dated 2026-07-13
rush-1.1.0/rush/man/filter_custom_fields.Rd |only rush-1.2.0/rush/DESCRIPTION | 13 rush-1.2.0/rush/MD5 | 59 rush-1.2.0/rush/NAMESPACE | 2 rush-1.2.0/rush/NEWS.md | 75 rush-1.2.0/rush/R/AppenderRedis.R | 49 rush-1.2.0/rush/R/Rush.R | 804 +++++----- rush-1.2.0/rush/R/RushWorker.R | 235 ++ rush-1.2.0/rush/R/assertions.R | 24 rush-1.2.0/rush/R/heartbeat_loops.R | 2 rush-1.2.0/rush/R/helper.R | 16 rush-1.2.0/rush/R/lua_scripts.R |only rush-1.2.0/rush/R/rush_plan.R | 19 rush-1.2.0/rush/R/start_worker.R | 46 rush-1.2.0/rush/R/store_large_object.R | 15 rush-1.2.0/rush/R/zzz.R | 15 rush-1.2.0/rush/README.md | 22 rush-1.2.0/rush/inst/testthat/helper.R | 11 rush-1.2.0/rush/man/AppenderRedis.Rd | 133 - rush-1.2.0/rush/man/Rush.Rd | 1568 +++++++++----------- rush-1.2.0/rush/man/RushWorker.Rd | 331 ++-- rush-1.2.0/rush/man/heartbeat.Rd | 8 rush-1.2.0/rush/man/rush-package.Rd | 26 rush-1.2.0/rush/man/rush_plan.Rd | 13 rush-1.2.0/rush/man/start_worker.Rd | 22 rush-1.2.0/rush/man/store_large_object.Rd | 7 rush-1.2.0/rush/tests/testthat/helper.R | 35 rush-1.2.0/rush/tests/testthat/test-AppenderRedis.R | 9 rush-1.2.0/rush/tests/testthat/test-Rush.R | 445 +++++ rush-1.2.0/rush/tests/testthat/test-RushWorker.R | 193 +- rush-1.2.0/rush/tests/testthat/test-rush_plan.R | 17 rush-1.2.0/rush/tests/testthat/test-start_worker.R |only 32 files changed, 2596 insertions(+), 1618 deletions(-)
Title: Processing and Transforming Relational Event History Data
Description: Efficiently processes relational event history data and transforms them into formats suitable for other packages. The primary objective of this package is to convert event history data into a format that integrates with the packages in 'remverse' and is compatible with various analytical tools (e.g., computing network statistics, estimating tie-oriented or actor-oriented social network models). Second, it can also transform the data into formats compatible with other packages out of 'remverse'. The package processes the data for two types of temporal social network models: tie-oriented modeling framework (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>) and actor-oriented modeling framework (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>).
Author: Giuseppe Arena [aut, cre] ,
Joris Mulder [aut],
Rumana Lakdawala [ctb],
Marlyne Meijerink-Bosman [ctb],
Diana Karimova [ctb],
Fabio Generoso Vieira [ctb],
Mahdi Shafiee Kamalabad [ctb],
Roger Leenders [ctb]
Maintainer: Giuseppe Arena <g.arena@uva.nl>
Diff between remify versions 4.0.0 dated 2026-05-04 and 4.1.0 dated 2026-07-13
remify-4.0.0/remify/inst/tinytest/test-remify2-thin.R |only remify-4.1.0/remify/DESCRIPTION | 8 remify-4.1.0/remify/MD5 | 59 - remify-4.1.0/remify/NAMESPACE | 3 remify-4.1.0/remify/NEWS.md | 5 remify-4.1.0/remify/R/data.R | 5 remify-4.1.0/remify/R/plot.remify.R |only remify-4.1.0/remify/R/remify2.R | 398 ++++--- remify-4.1.0/remify/R/remify_durem.R |only remify-4.1.0/remify/R/remify_util.R | 562 ---------- remify-4.1.0/remify/R/summary_remify.R | 12 remify-4.1.0/remify/inst/datasets |only remify-4.1.0/remify/inst/doc/remify.R | 2 remify-4.1.0/remify/inst/doc/remify.Rmd | 10 remify-4.1.0/remify/inst/doc/remify.html | 32 remify-4.1.0/remify/inst/doc/riskset.R | 2 remify-4.1.0/remify/inst/doc/riskset.Rmd | 10 remify-4.1.0/remify/inst/doc/riskset.html | 26 remify-4.1.0/remify/inst/tinytest/simple-tests.R | 4 remify-4.1.0/remify/inst/tinytest/test-remify-durem.R |only remify-4.1.0/remify/inst/tinytest/test-remify-methods2.R | 25 remify-4.1.0/remify/inst/tinytest/test-remify2-actor.R | 12 remify-4.1.0/remify/inst/tinytest/test-remify2-aggregate_time.R |only remify-4.1.0/remify/inst/tinytest/test-remify2-typed-events.R | 4 remify-4.1.0/remify/inst/tinytest/test-summary-remify.R | 18 remify-4.1.0/remify/inst/tinytest/tests_remify2.R | 7 remify-4.1.0/remify/man/dot-durem_normalize_edgelist.Rd |only remify-4.1.0/remify/man/dot-remify_durem_init.Rd |only remify-4.1.0/remify/man/history.Rd | 7 remify-4.1.0/remify/man/is.remify_durem.Rd |only remify-4.1.0/remify/man/plot.remify.Rd | 56 remify-4.1.0/remify/man/print.remify_durem.Rd |only remify-4.1.0/remify/man/remify.Rd | 93 + remify-4.1.0/remify/man/summary.remify_durem.Rd |only remify-4.1.0/remify/vignettes/remify.Rmd | 10 remify-4.1.0/remify/vignettes/riskset.Rmd | 10 36 files changed, 487 insertions(+), 893 deletions(-)
Title: Correction of Heaping on Individual Level
Description: Provides methods for correcting heaping (digit preference) in
survey data at the individual record level. Age heaping, where respondents
disproportionately report ages ending in 0 or 5, is a common phenomenon that
can distort demographic analyses. Unlike traditional smoothing methods that
only correct aggregated statistics, this package corrects individual values
by replacing a calculated proportion of heaped observations with draws from
fitted truncated distributions (log-normal, normal, or uniform). Supports
5-year and 10-year heaping patterns, single heap correction, survey
weights, and optional covariate-conditional (model-based) correction via
quantile regression forests or linear models to preserve relationships. A
multiple-imputation wrapper repeats the correction to propagate the added
uncertainty into downstream inference.
Author: Matthias Templ [aut, cre] ,
Bernhard Meindl [ctb]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between heaping versions 0.1.0 dated 2026-02-09 and 0.2.0 dated 2026-07-13
DESCRIPTION | 13 MD5 | 27 - NAMESPACE | 2 NEWS.md |only R/correctHeap.R | 582 +++++++++----------------- R/correctHeapsMI.R |only R/heaping-package.R | 30 - R/impute-model.R |only inst/doc/heaping-intro.html | 755 +++++++++++++++++------------------ man/correctHeaps.Rd | 73 ++- man/correctHeapsMI.Rd |only man/correctSingleHeap.Rd | 16 man/heaping-package.Rd | 30 - tests/testthat/test-conditional.R |only tests/testthat/test-correctHeaps.R | 56 ++ tests/testthat/test-correctHeapsMI.R |only tests/testthat/test-heap-ratios.R |only tests/testthat/test-marginal.R |only tests/testthat/test-select.R |only 19 files changed, 771 insertions(+), 813 deletions(-)
Title: Fuzzy Statistical Tools
Description: The main goal of this package is to present various fuzzy statistical tools. It intends to provide an implementation of the theoretical and empirical approaches presented in the book entitled "The signed distance measure in fuzzy statistical analysis. Some theoretical, empirical and programming advances" <doi: 10.1007/978-3-030-76916-1>. For the theoretical approaches, see Berkachy R. and Donze L. (2019) <doi:10.1007/978-3-030-03368-2_1>. For the empirical approaches, see Berkachy R. and Donze L. (2016) <ISBN: 978-989-758-201-1>). Important (non-exhaustive) implementation highlights of this package are as follows: (1) a numerical procedure to estimate the fuzzy difference and the fuzzy square. (2) two numerical methods of fuzzification. (3) a function performing different possibilities of distances, including the signed distance and the generalized signed distance for instance with all its properties. (4) numerical estimations of fuzzy statistical measures such as the [...truncated...]
Author: Redina Berkachy [aut, cre] ,
Laurent Donze [aut]
Maintainer: Redina Berkachy <redina.berkachy@hefr.ch>
Diff between FuzzySTs versions 0.4 dated 2025-07-31 and 0.5 dated 2026-07-13
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++++++---------- NAMESPACE | 5 +++++ NEWS.md | 9 +++++++-- R/PRM_13072026.R |only README.md | 2 +- build/partial.rdb |only build/vignette.rds |binary inst/doc/Vignette_A.html | 7 ++++--- inst/doc/Vignette_B.html | 7 ++++--- inst/doc/Vignette_C.html | 35 ++++++++++++++++++----------------- inst/doc/Vignette_D.html | 1 + inst/doc/Vignette_E.html | 1 + man/FuzzySTs-package.Rd |only man/prm_polygon.Rd |only man/prm_trapezoid.Rd |only man/prm_triangle.Rd |only man/summary_prm.Rd |only man/summary_prm_scores.Rd |only 19 files changed, 63 insertions(+), 40 deletions(-)
Title: Access the 'CDC PLACES' API
Description: Allows users to seamlessly query several 'CDC PLACES' APIs (<https://data.cdc.gov/browse?q=PLACES%20&sortBy=relevance>)
by geography, state, measure, and release year. This package also contains a
function to explore the available measures for each release year.
Author: Brenden Smith [aut, cre]
Maintainer: Brenden Smith <smit2535@msu.edu>
Diff between CDCPLACES versions 1.2.1 dated 2026-05-22 and 1.2.2 dated 2026-07-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/get_places.R | 10 +++++----- R/sysdata.rda |binary 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Nonparametric Bounds for the Average Causal Effect Due to Balke
and Pearl and Extensions
Description: Implementation of the nonparametric bounds for the average
causal effect under an instrumental variable model by Balke and Pearl
(Bounds on Treatment Effects from Studies with Imperfect Compliance,
JASA, 1997, 92, 439, 1171-1176, <doi:10.1080/01621459.1997.10474074>). The package
can calculate bounds for a binary outcome, a binary
treatment/phenotype, and an instrument with either 2 or 3 categories.
The package implements bounds for situations where these 3 variables
are measured in the same dataset (trivariate data) or where the
outcome and instrument are measured in one study and the
treatment/phenotype and instrument are measured in another study
(bivariate data).
Author: Tom Palmer [aut, cre] ,
Roland Ramsahai [aut] ,
Vanessa Didelez [aut] ,
Nuala Sheehan [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between bpbounds versions 0.1.7 dated 2026-05-24 and 0.1.8 dated 2026-07-13
DESCRIPTION | 6 +- MD5 | 30 ++++++------ NEWS.md | 16 ++++++ R/bpbounds.R | 13 +++++ R/bpbounds_calc_biv_z2.R | 26 ++++++---- R/bpbounds_calc_biv_z3.R | 22 +++++--- R/bpbounds_calc_tri_z2.R | 6 ++ R/bpbounds_calc_tri_z3.R | 8 ++- R/bpbounds_tri_x2y2z3.R | 4 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/bpbounds.Rmd | 5 -- inst/doc/bpbounds.html | 25 ++++------ inst/shiny-examples/myapp/app.R | 65 ++++++++++---------------- tests/testthat/test-bpbounds.R | 100 +++++++++++++++++++++++++++++++--------- vignettes/bpbounds.Rmd | 5 -- 16 files changed, 216 insertions(+), 115 deletions(-)
Title: A Docking Layout Manager for 'blockr'
Description: Building on the docking layout manager provided by 'dockViewR',
this provides a flexible front-end to 'blockr.core'. It provides an extension mechanism which allows for providing means to manipulate a board
object via panel-based user interface components.
Author: Nicolas Bennett [aut, cre],
David Granjon [aut]
Maintainer: Nicolas Bennett <nicolas@cynkra.com>
Diff between blockr.dock versions 0.1.1 dated 2026-04-29 and 0.1.2 dated 2026-07-13
blockr.dock-0.1.1/blockr.dock/R/action-modal.R |only blockr.dock-0.1.1/blockr.dock/R/layout-class.R |only blockr.dock-0.1.1/blockr.dock/R/layouts-class.R |only blockr.dock-0.1.1/blockr.dock/R/utils-id.R |only blockr.dock-0.1.1/blockr.dock/R/view-ui.R |only blockr.dock-0.1.1/blockr.dock/man/panel.Rd |only blockr.dock-0.1.1/blockr.dock/tests/testthat/_snaps/utils-serve |only blockr.dock-0.1.1/blockr.dock/vignettes/mermaid |only blockr.dock-0.1.2/blockr.dock/DESCRIPTION | 31 blockr.dock-0.1.2/blockr.dock/MD5 | 177 - blockr.dock-0.1.2/blockr.dock/NAMESPACE | 105 blockr.dock-0.1.2/blockr.dock/NEWS.md | 121 + blockr.dock-0.1.2/blockr.dock/R/action-block.R | 381 --- blockr.dock-0.1.2/blockr.dock/R/action-class.R | 15 blockr.dock-0.1.2/blockr.dock/R/action-link.R | 127 - blockr.dock-0.1.2/blockr.dock/R/action-stack.R | 267 +- blockr.dock-0.1.2/blockr.dock/R/action-utils.R | 16 blockr.dock-0.1.2/blockr.dock/R/block-meta.R | 13 blockr.dock-0.1.2/blockr.dock/R/block-ui.R | 25 blockr.dock-0.1.2/blockr.dock/R/board-plugins.R | 5 blockr.dock-0.1.2/blockr.dock/R/board-server.R | 1059 +++++----- blockr.dock-0.1.2/blockr.dock/R/board-ui.R | 196 + blockr.dock-0.1.2/blockr.dock/R/dock-board.R | 361 ++- blockr.dock-0.1.2/blockr.dock/R/dock-grid.R |only blockr.dock-0.1.2/blockr.dock/R/dock-layout.R |only blockr.dock-0.1.2/blockr.dock/R/dock-stack.R | 19 blockr.dock-0.1.2/blockr.dock/R/dock-view.R |only blockr.dock-0.1.2/blockr.dock/R/ext-class.R | 193 + blockr.dock-0.1.2/blockr.dock/R/ext-delta.R |only blockr.dock-0.1.2/blockr.dock/R/ext-edit.R | 766 ++++++- blockr.dock-0.1.2/blockr.dock/R/ext-ui.R | 20 blockr.dock-0.1.2/blockr.dock/R/panel-id.R |only blockr.dock-0.1.2/blockr.dock/R/panel-ops.R |only blockr.dock-0.1.2/blockr.dock/R/panel-ref.R |only blockr.dock-0.1.2/blockr.dock/R/plugin-block.R | 370 ++- blockr.dock-0.1.2/blockr.dock/R/sidebar-block.R |only blockr.dock-0.1.2/blockr.dock/R/sidebar-link.R |only blockr.dock-0.1.2/blockr.dock/R/sidebar-server.R |only blockr.dock-0.1.2/blockr.dock/R/sidebar-stack.R |only blockr.dock-0.1.2/blockr.dock/R/utils-dock.R | 136 + blockr.dock-0.1.2/blockr.dock/R/utils-misc.R | 21 blockr.dock-0.1.2/blockr.dock/R/utils-serdes.R | 127 - blockr.dock-0.1.2/blockr.dock/R/utils-serve.R | 51 blockr.dock-0.1.2/blockr.dock/R/utils-ui.R | 110 - blockr.dock-0.1.2/blockr.dock/README.md | 27 blockr.dock-0.1.2/blockr.dock/build/vignette.rds |binary blockr.dock-0.1.2/blockr.dock/inst/assets/css/blockr-dock.css | 229 ++ blockr.dock-0.1.2/blockr.dock/inst/assets/css/sidebar-block.css |only blockr.dock-0.1.2/blockr.dock/inst/assets/css/sidebar-link.css |only blockr.dock-0.1.2/blockr.dock/inst/assets/css/sidebar-server.css |only blockr.dock-0.1.2/blockr.dock/inst/assets/css/sidebar-stack.css |only blockr.dock-0.1.2/blockr.dock/inst/assets/js/sidebar-block.js |only blockr.dock-0.1.2/blockr.dock/inst/assets/js/sidebar-link.js |only blockr.dock-0.1.2/blockr.dock/inst/assets/js/sidebar-server.js |only blockr.dock-0.1.2/blockr.dock/inst/assets/js/sidebar-stack.js |only blockr.dock-0.1.2/blockr.dock/inst/assets/js/view-binding.js | 87 blockr.dock-0.1.2/blockr.dock/inst/doc/layouts.R | 125 - blockr.dock-0.1.2/blockr.dock/inst/doc/layouts.Rmd | 522 +++- blockr.dock-0.1.2/blockr.dock/inst/doc/layouts.html | 692 ++++-- blockr.dock-0.1.2/blockr.dock/inst/examples/edit-add |only blockr.dock-0.1.2/blockr.dock/inst/examples/edit-board |only blockr.dock-0.1.2/blockr.dock/inst/examples/locked-dock/app.R | 5 blockr.dock-0.1.2/blockr.dock/inst/examples/multi-view |only blockr.dock-0.1.2/blockr.dock/inst/examples/serdes |only blockr.dock-0.1.2/blockr.dock/inst/examples/single-page/app.R | 5 blockr.dock-0.1.2/blockr.dock/inst/examples/sized-grid |only blockr.dock-0.1.2/blockr.dock/inst/examples/views/app.R | 23 blockr.dock-0.1.2/blockr.dock/man/action.Rd | 8 blockr.dock-0.1.2/blockr.dock/man/dock-grid.Rd |only blockr.dock-0.1.2/blockr.dock/man/dock-layout.Rd |only blockr.dock-0.1.2/blockr.dock/man/dock.Rd | 64 blockr.dock-0.1.2/blockr.dock/man/extension.Rd | 31 blockr.dock-0.1.2/blockr.dock/man/figures/views.png |binary blockr.dock-0.1.2/blockr.dock/man/ids.Rd | 16 blockr.dock-0.1.2/blockr.dock/man/layout.Rd | 118 - 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Title: Optimize PTSD Diagnostic Criteria
Description: Provides tools for analyzing and optimizing PTSD (Post-Traumatic
Stress Disorder) diagnostic criteria using PCL-5 (PTSD Checklist for DSM-5)
and CAPS-5 (Clinician-Administered PTSD Scale for DSM-5) data. Functions identify optimal subsets of PCL-5 items that maintain
diagnostic accuracy while reducing assessment burden. Includes tools for
both hierarchical (cluster-based) and non-hierarchical symptom combinations,
calculation of diagnostic metrics, and comparison with standard DSM-5
criteria. Model validation is conducted using holdout and cross-validation
methods to assess robustness and generalizability of the results. For more
details see Weidmann et al. (2025) <doi:10.31219/osf.io/6rk72_v1>.
Author: Laura Weidmann [aut] ,
Tobias R. Spiller [aut, cre] ,
Flavio A. Schueepp [aut]
Maintainer: Tobias R. Spiller <tobias.spiller@access.uzh.ch>
Diff between PTSDdiag versions 0.1.0 dated 2026-02-13 and 0.4.1 dated 2026-07-13
PTSDdiag-0.1.0/PTSDdiag/inst/doc/introduction.R |only PTSDdiag-0.1.0/PTSDdiag/inst/doc/introduction.Rmd |only PTSDdiag-0.1.0/PTSDdiag/inst/doc/introduction.html |only PTSDdiag-0.1.0/PTSDdiag/vignettes/introduction.Rmd |only PTSDdiag-0.4.1/PTSDdiag/DESCRIPTION | 21 PTSDdiag-0.4.1/PTSDdiag/MD5 | 119 + PTSDdiag-0.4.1/PTSDdiag/NAMESPACE | 22 PTSDdiag-0.4.1/PTSDdiag/NEWS.md | 455 +++++ PTSDdiag-0.4.1/PTSDdiag/R/alternative_criteria.R |only PTSDdiag-0.4.1/PTSDdiag/R/analysis.R | 793 +++++----- PTSDdiag-0.4.1/PTSDdiag/R/apply_combinations.R |only PTSDdiag-0.4.1/PTSDdiag/R/compare_optimizations.R |only PTSDdiag-0.4.1/PTSDdiag/R/data_preparation.R | 312 +++ PTSDdiag-0.4.1/PTSDdiag/R/definitions.R |only PTSDdiag-0.4.1/PTSDdiag/R/helping_functions.R | 162 -- PTSDdiag-0.4.1/PTSDdiag/R/internals.R |only PTSDdiag-0.4.1/PTSDdiag/R/io_combinations.R |only PTSDdiag-0.4.1/PTSDdiag/R/scenario_plots.R |only PTSDdiag-0.4.1/PTSDdiag/R/scenario_tables.R |only PTSDdiag-0.4.1/PTSDdiag/R/score_all_combinations.R |only PTSDdiag-0.4.1/PTSDdiag/R/scoring_and_diagnosis.R | 85 - PTSDdiag-0.4.1/PTSDdiag/R/simulated_ptsd.R | 16 PTSDdiag-0.4.1/PTSDdiag/R/simulated_ptsd_genpop.R |only PTSDdiag-0.4.1/PTSDdiag/R/validation.R | 557 +++---- PTSDdiag-0.4.1/PTSDdiag/README.md | 55 PTSDdiag-0.4.1/PTSDdiag/build/vignette.rds |binary PTSDdiag-0.4.1/PTSDdiag/data/simulated_ptsd.rda |binary PTSDdiag-0.4.1/PTSDdiag/data/simulated_ptsd_genpop.rda |only PTSDdiag-0.4.1/PTSDdiag/inst/CITATION |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/caps5-workflow.R |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/caps5-workflow.Rmd |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/caps5-workflow.html |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/comparing-criteria.R |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/comparing-criteria.Rmd |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/comparing-criteria.html |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/getting-started.R |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/getting-started.Rmd |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/getting-started.html |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/multi-site-validation.R |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/multi-site-validation.Rmd |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/multi-site-validation.html |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/validation.R |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/validation.Rmd |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/validation.html |only PTSDdiag-0.4.1/PTSDdiag/man/analyze_best_six_symptoms_four_required.Rd | 49 PTSDdiag-0.4.1/PTSDdiag/man/analyze_best_six_symptoms_four_required_clusters.Rd | 50 PTSDdiag-0.4.1/PTSDdiag/man/apply_symptom_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/as_definitions.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/check_pcl5_data.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/compare_diagnostic_systems.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/compare_optimizations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/create_caps5_diagnosis.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/create_icd11_diagnosis.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/create_ptsd_diagnosis_nonbinarized.Rd | 6 PTSDdiag-0.4.1/PTSDdiag/man/create_readable_summary.Rd | 13 PTSDdiag-0.4.1/PTSDdiag/man/cross_validation.Rd | 89 - PTSDdiag-0.4.1/PTSDdiag/man/evaluate_definitions.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/extract_definitions.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/holdout_validation.Rd | 75 PTSDdiag-0.4.1/PTSDdiag/man/optimize_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/optimize_combinations_clusters.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/plot_symptom_frequency.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/print.ptsdiag_comparison.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/read_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/rename_caps5_columns.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/rename_ptsd_columns.Rd | 30 PTSDdiag-0.4.1/PTSDdiag/man/score_all_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/simulated_ptsd.Rd | 17 PTSDdiag-0.4.1/PTSDdiag/man/simulated_ptsd_genpop.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/summarize_ptsd.Rd | 4 PTSDdiag-0.4.1/PTSDdiag/man/summarize_ptsd_changes.Rd | 5 PTSDdiag-0.4.1/PTSDdiag/man/summarize_top_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/symptom_frequency.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/write_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-alternative_criteria.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-analysis.R | 293 +++ PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-balanced_accuracy.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-compare_optimizations.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-data.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-data_preparation.R | 194 ++ PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-definitions.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-helping_functions.R | 147 + PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-io_combinations.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-scenario_plots.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-scenario_tables.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-score_all_combinations.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-scoring_and_diagnosis.R | 26 PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-validation.R | 328 +++- PTSDdiag-0.4.1/PTSDdiag/vignettes/caps5-workflow.Rmd |only PTSDdiag-0.4.1/PTSDdiag/vignettes/comparing-criteria.Rmd |only PTSDdiag-0.4.1/PTSDdiag/vignettes/getting-started.Rmd |only PTSDdiag-0.4.1/PTSDdiag/vignettes/multi-site-validation.Rmd |only PTSDdiag-0.4.1/PTSDdiag/vignettes/validation.Rmd |only 93 files changed, 2878 insertions(+), 1045 deletions(-)
Title: Fitting the Multinomial Probit Model
Description: Fits the Bayesian multinomial probit model via Markov chain
Monte Carlo. The multinomial probit model is often used to analyze
the discrete choices made by individuals recorded in survey data.
Examples where the multinomial probit model may be useful include the
analysis of product choice by consumers in market research and the
analysis of candidate or party choice by voters in electoral studies.
The MNP package can also fit the model with different choice sets for
each individual, and complete or partial individual choice orderings
of the available alternatives from the choice set. The estimation is
based on the efficient marginal data augmentation algorithm that is
developed by Imai and van Dyk (2005). "A Bayesian Analysis of the
Multinomial Probit Model Using the Data Augmentation." Journal of
Econometrics, Vol. 124, No. 2 (February), pp. 311-334.
<doi:10.1016/j.jeconom.2004.02.002> Detailed examples are given in
Imai and van Dyk (2005). "MNP: R Package for Fitting the Multi [...truncated...]
Author: Kosuke Imai [aut, cre],
David van Dyk [aut],
Hubert Jin [ctb]
Maintainer: Kosuke Imai <imai@harvard.edu>
Diff between MNP versions 3.1-5 dated 2024-06-20 and 3.1-6 dated 2026-07-13
ChangeLog | 3 ++- DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/MNP.Rnw | 4 ++-- inst/doc/MNP.pdf |binary vignettes/MNP.Rnw | 4 ++-- 7 files changed, 15 insertions(+), 14 deletions(-)
Title: Continuous Norming
Description: Generates continuous test norms in
psychometrics and biometrics, and analyzing model fit. The package offers
both distribution-free modeling using Taylor polynomials and parametric
modeling using the beta-binomial and the 'Sinh-Arcsinh' distribution.
Originally developed for achievement tests, it is applicable to a wide
range of mental, physical, or other test scores dependent on continuous or
discrete explanatory variables. The package provides several advantages:
It minimizes deviations from representativeness in subsamples, interpolates
between discrete levels of explanatory variables, and significantly reduces
the required sample size compared to conventional norming per age group.
cNORM enables graphical and analytical evaluation of model fit,
accommodates a wide range of scales including those with negative and
descending values, and as well supports conventional norming. It generates
norm tables including confidence intervals. Methods for addressing
representativeness issues are [...truncated...]
Author: Alexandra Lenhard [aut] ,
Wolfgang Lenhard [cre, aut] ,
Sebastian Gary [aut],
WPS Publisher [fnd]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 3.6.0 dated 2026-06-17 and 3.6.1 dated 2026-07-13
DESCRIPTION | 6 MD5 | 107 - NAMESPACE | 4 NEWS.md | 99 + R/betaBinomial.R | 2347 ++++++++++++++++++-------------------- R/cNORM.R | 11 R/modelling.R | 1633 +++++++++++++------------- R/plot.R | 711 +++++------ inst/doc/BetaBinomial.html | 48 inst/doc/WeightedRegression.html | 41 inst/doc/cNORM-Demo.html | 236 +-- inst/doc/sinh.html | 56 man/autoselect.betabinomial.Rd | 17 man/bb_design_matrix.Rd |only man/bb_distribution.Rd |only man/bb_prepare_data.Rd |only man/bb_resolve_scale.Rd |only man/bestModel.Rd | 70 - man/betaCoefficients.Rd | 33 man/buildFunction.Rd | 1 man/cNORM.Rd | 5 man/checkConsistency.Rd | 38 man/checkWeights.Rd | 29 man/cnorm.betabinomial.Rd | 64 - man/cnorm.betabinomial1.Rd | 44 man/cnorm.betabinomial2.Rd | 42 man/cnorm.cv.Rd | 78 - man/compare.Rd | 17 man/computeWeights.Rd | 170 +- man/derive.Rd | 16 man/diagnostics.betabinomial.Rd | 47 man/getNormScoreSE.Rd | 21 man/log_likelihood.Rd | 20 man/log_likelihood2.Rd | 30 man/modelSummary.Rd | 3 man/normTable.betabinomial.Rd | 30 man/plot.cnormBetaBinomial.Rd | 32 man/plot.cnormBetaBinomial2.Rd | 19 man/plotPercentileSeries.Rd | 46 man/plotSubset.Rd | 49 man/predict.cnormBetaBinomial.Rd | 25 man/predict.cnormBetaBinomial2.Rd | 28 man/predictCoefficients.Rd | 18 man/predictCoefficients2.Rd | 14 man/print.cnorm.Rd | 3 man/printSubset.Rd | 10 man/rangeCheck.Rd | 10 man/regressionFunction.Rd | 3 man/standardizeRakingWeights.Rd | 43 man/subsample_lm.Rd | 26 man/summary.cnorm.Rd | 3 man/summary.cnormBetaBinomial.Rd | 25 man/summary.cnormBetaBinomial2.Rd | 39 man/taylorSwift.Rd | 7 man/weighted.rank.Rd | 46 man/weightedAverageModel.Rd |only tests/testthat/test.modelling.R | 145 ++ 57 files changed, 3553 insertions(+), 3112 deletions(-)
Title: Clinical Publication
Description: Accelerate the process from clinical data to medical publication,
including clinical data cleaning, significant result screening, and the
generation of publish-ready tables and figures.
Author: Yue Niu [aut, cre, cph] ,
Keyun Wang [aut]
Maintainer: Yue Niu <niuyuesam@163.com>
Diff between clinpubr versions 1.4.0 dated 2026-05-24 and 1.4.1 dated 2026-07-13
DESCRIPTION | 32 +- MD5 | 44 +-- NAMESPACE | 6 NEWS.md | 10 R/RcppExports.R |only R/extract_history.R |only R/group_by_range.R |only R/interactions.R | 11 R/misc.R | 8 R/regressions.R | 4 R/to_date.R | 2 R/unit_standardize.R | 16 - R/utils.R | 2 inst/doc/baseline-table.html | 4 inst/doc/data-cleaning.html | 476 ++++++++++++++++----------------- inst/doc/model-evaluation.html | 14 inst/doc/regression-analysis.html | 16 - man/emp_colors.Rd | 5 man/extract_history.Rd |only man/extract_history_single.Rd |only man/group_by_range.Rd |only man/group_by_range_cpp.Rd |only man/regression_basic_results.Rd | 4 src |only tests/testthat/test-extract_history.R |only tests/testthat/test-group_by_range.R |only tests/testthat/test-unit_standardize.R | 92 ++++++ tools |only 28 files changed, 445 insertions(+), 301 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and inference.
This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, MMPC,
Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing,
Tabu Search, DirectLiNGAM) and hybrid (MMHC, RSMAX2, H2PC) structure learning
algorithms for discrete, Gaussian, conditional Gaussian and zero-inflated
networks, along with many score functions and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also
implemented. Some utility functions (model comparison and manipulation,
random data generation, arc orientation testing, simple and advanced plots)
are included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries, interventions,
counterfactuals, cross-validation, bootstrap and model averaging. Development
snapshots with the latest bugfixes are available from
<https://www.bnlearn.com/>.
Author: Marco Scutari [aut, cre],
Tomi Silander [ctb]
Maintainer: Marco Scutari <scutari@bnlearn.com>
Diff between bnlearn versions 5.1 dated 2025-08-20 and 5.2 dated 2026-07-13
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bnlearn-5.2/bnlearn/src/core/sets.h | 1 bnlearn-5.2/bnlearn/src/core/uppertriangular.c | 2 bnlearn-5.2/bnlearn/src/fitted/enums.c | 6 bnlearn-5.2/bnlearn/src/fitted/fitted.c | 38 bnlearn-5.2/bnlearn/src/fitted/fitted.h | 31 bnlearn-5.2/bnlearn/src/fitted/nparams.c | 12 bnlearn-5.2/bnlearn/src/fitted/rinterface/nodes.and.arcs.c |only bnlearn-5.2/bnlearn/src/fitted/topological.sort.c |only bnlearn-5.2/bnlearn/src/globals.c | 23 bnlearn-5.2/bnlearn/src/graphs/graphs.h | 14 bnlearn-5.2/bnlearn/src/graphs/nparams.c |only bnlearn-5.2/bnlearn/src/graphs/path.c | 2 bnlearn-5.2/bnlearn/src/graphs/pdag2dag.c | 5 bnlearn-5.2/bnlearn/src/graphs/random/graph.generation.c | 15 bnlearn-5.2/bnlearn/src/graphs/rinterface/all.equal.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/cache.structure.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/cextend.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/colliders.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/connected.components.c | 4 bnlearn-5.2/bnlearn/src/graphs/rinterface/cpdag.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/nodes.and.arcs.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/nparams.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/shd.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/sid.c | 425 ++++++- bnlearn-5.2/bnlearn/src/graphs/topological.ordering.c | 18 bnlearn-5.2/bnlearn/src/include/globals.h | 4 bnlearn-5.2/bnlearn/src/include/graph.h | 1 bnlearn-5.2/bnlearn/src/include/register.h | 23 bnlearn-5.2/bnlearn/src/include/sampling.h | 30 bnlearn-5.2/bnlearn/src/inference/likelihood.weighting.c | 61 - bnlearn-5.2/bnlearn/src/inference/loglikelihood/common.c | 2 bnlearn-5.2/bnlearn/src/inference/loglikelihood/conditional.gaussian.c | 50 bnlearn-5.2/bnlearn/src/inference/loglikelihood/discrete.c | 34 bnlearn-5.2/bnlearn/src/inference/loglikelihood/gaussian.c | 18 bnlearn-5.2/bnlearn/src/inference/loglikelihood/loglikelihood.h | 16 bnlearn-5.2/bnlearn/src/inference/loglikelihood/zero.inflated.c |only bnlearn-5.2/bnlearn/src/inference/rbn.c | 503 ++++---- bnlearn-5.2/bnlearn/src/inference/rinterface/cpdist.c | 24 bnlearn-5.2/bnlearn/src/inference/rinterface/likelihood.weighting.c | 28 bnlearn-5.2/bnlearn/src/inference/rinterface/loglikelihood.c | 44 bnlearn-5.2/bnlearn/src/inference/rinterface/rbn.c | 120 ++ bnlearn-5.2/bnlearn/src/learning/averaging/averaging.c | 6 bnlearn-5.2/bnlearn/src/learning/averaging/bootstrap.c | 8 bnlearn-5.2/bnlearn/src/learning/local/mi.matrix.c | 58 - bnlearn-5.2/bnlearn/src/learning/rinterface |only bnlearn-5.2/bnlearn/src/learning/score/hc.cache.lookup.c | 12 bnlearn-5.2/bnlearn/src/learning/score/score.delta.c | 7 bnlearn-5.2/bnlearn/src/learning/score/tabu.c | 2 bnlearn-5.2/bnlearn/src/math/conditional.least.squares.c | 2 bnlearn-5.2/bnlearn/src/math/hypergeometric.c |only bnlearn-5.2/bnlearn/src/math/hypergeometric.h |only bnlearn-5.2/bnlearn/src/math/hyperpoisson.c |only bnlearn-5.2/bnlearn/src/math/hyperpoisson.h |only bnlearn-5.2/bnlearn/src/math/linear.algebra.c | 29 bnlearn-5.2/bnlearn/src/math/reweighted.least.squares.c |only bnlearn-5.2/bnlearn/src/math/reweighted.least.squares.h |only bnlearn-5.2/bnlearn/src/math/sparse.amat.c |only bnlearn-5.2/bnlearn/src/math/sparse.amat.h |only bnlearn-5.2/bnlearn/src/math/xnegbin.c |only bnlearn-5.2/bnlearn/src/math/xnegbin.h |only bnlearn-5.2/bnlearn/src/minimal/common.c | 2 bnlearn-5.2/bnlearn/src/minimal/data.frame.c | 34 bnlearn-5.2/bnlearn/src/minimal/data.frame.h | 2 bnlearn-5.2/bnlearn/src/minimal/tiers.c | 3 bnlearn-5.2/bnlearn/src/parameters/discrete/classic.discrete.c | 1 bnlearn-5.2/bnlearn/src/parameters/discrete/hierarchical.dirichlet.c | 2 bnlearn-5.2/bnlearn/src/parameters/enums.c |only bnlearn-5.2/bnlearn/src/parameters/parameters.h | 26 bnlearn-5.2/bnlearn/src/parameters/rinterface/classic.discrete.c | 1 bnlearn-5.2/bnlearn/src/parameters/rinterface/hierarchical.dirichlet.c | 5 bnlearn-5.2/bnlearn/src/parameters/rinterface/mixture.ordinary.least.squares.c | 6 bnlearn-5.2/bnlearn/src/parameters/rinterface/ordinary.least.squares.c | 2 bnlearn-5.2/bnlearn/src/parameters/rinterface/zero.inflated.c |only bnlearn-5.2/bnlearn/src/predict/map.lw.c | 229 +--- bnlearn-5.2/bnlearn/src/predict/naivebayes.c |only bnlearn-5.2/bnlearn/src/predict/parents.c |only bnlearn-5.2/bnlearn/src/predict/predict.h |only bnlearn-5.2/bnlearn/src/predict/rinterface |only bnlearn-5.2/bnlearn/src/preprocessing/dedup.c | 26 bnlearn-5.2/bnlearn/src/preprocessing/discretize.c | 12 bnlearn-5.2/bnlearn/src/preprocessing/enums.c | 5 bnlearn-5.2/bnlearn/src/preprocessing/preprocessing.h | 2 bnlearn-5.2/bnlearn/src/preprocessing/rinterface/discretize.c | 65 - bnlearn-5.2/bnlearn/src/sanitization/cg.assumptions.c | 4 bnlearn-5.2/bnlearn/src/sanitization/covariance.c | 2 bnlearn-5.2/bnlearn/src/sanitization/data.c | 43 bnlearn-5.2/bnlearn/src/sanitization/data.h | 1 bnlearn-5.2/bnlearn/src/scores/alpha.star.c | 8 bnlearn-5.2/bnlearn/src/scores/cg.loglikelihood.c | 8 bnlearn-5.2/bnlearn/src/scores/cg.nal.c | 6 bnlearn-5.2/bnlearn/src/scores/cg.predictive.loglikelihood.c | 6 bnlearn-5.2/bnlearn/src/scores/custom.score.c | 1 bnlearn-5.2/bnlearn/src/scores/dirichlet.posterior.c | 2 bnlearn-5.2/bnlearn/src/scores/discrete.loglikelihood.c | 4 bnlearn-5.2/bnlearn/src/scores/discrete.nal.c | 4 bnlearn-5.2/bnlearn/src/scores/discrete.predictive.loglikelihood.c | 5 bnlearn-5.2/bnlearn/src/scores/enum.c | 16 bnlearn-5.2/bnlearn/src/scores/gaussian.loglikelihood.c | 5 bnlearn-5.2/bnlearn/src/scores/gaussian.nal.c | 5 bnlearn-5.2/bnlearn/src/scores/gaussian.predictive.loglikelihood.c | 5 bnlearn-5.2/bnlearn/src/scores/graph.priors.c | 14 bnlearn-5.2/bnlearn/src/scores/nml.regret.c | 1 bnlearn-5.2/bnlearn/src/scores/normalized.maximum.likelihood.c | 4 bnlearn-5.2/bnlearn/src/scores/per.node.score.c | 128 +- bnlearn-5.2/bnlearn/src/scores/scores.h | 34 bnlearn-5.2/bnlearn/src/scores/wishart.posterior.c | 22 bnlearn-5.2/bnlearn/src/scores/zero.inflated.coefs.c |only bnlearn-5.2/bnlearn/src/scores/zero.inflated.em.c |only bnlearn-5.2/bnlearn/src/tests/conditional.gaussian/cg.mutual.information.c | 3 bnlearn-5.2/bnlearn/src/tests/discrete/jonckheere.c | 2 bnlearn-5.2/bnlearn/src/tests/discrete/shrinkage.c | 8 bnlearn-5.2/bnlearn/src/tests/enums.c | 5 bnlearn-5.2/bnlearn/src/tests/gaussian/shrinkage.c | 9 bnlearn-5.2/bnlearn/src/tests/patterns.h | 47 bnlearn-5.2/bnlearn/src/tests/patterns/allsubs.test.c | 252 ++-- bnlearn-5.2/bnlearn/src/tests/patterns/ctest.c | 141 +- bnlearn-5.2/bnlearn/src/tests/patterns/roundrobin.test.c | 178 +-- bnlearn-5.2/bnlearn/src/tests/patterns/utest.c | 10 bnlearn-5.2/bnlearn/src/tests/permutation/discrete.monte.carlo.c | 5 bnlearn-5.2/bnlearn/src/tests/permutation/gaussian.monte.carlo.c | 7 bnlearn-5.2/bnlearn/src/tests/rinterface/allsubs.test.c | 62 - bnlearn-5.2/bnlearn/src/tests/rinterface/ctest.c | 56 bnlearn-5.2/bnlearn/src/tests/rinterface/htest.c | 2 bnlearn-5.2/bnlearn/src/tests/rinterface/roundrobin.test.c | 40 bnlearn-5.2/bnlearn/src/tests/rinterface/utest.c | 4 307 files changed, 6569 insertions(+), 4215 deletions(-)
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of
covariate-dependent binomial probabilities, and the Dirichlet Kernel Process (DKP) for
categorical or multinomial response data. Scalable global-local approximations
are provided through TwinBKP and TwinDKP, using twinning-selected global subsets
and local nearest-neighbour updates.
Functions are included for model fitting, predictive inference with
uncertainty quantification, posterior simulation,
and visualization in one- and two-dimensional input spaces.
Gaussian, Matern 5/2, Matern 3/2, and Wendland kernels are supported,
with hyperparameters selected by multi-start derivative-free optimization.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.3.0 dated 2026-07-02 and 0.3.1 dated 2026-07-13
DESCRIPTION | 9 MD5 | 27 NEWS.md | 6 R/fit_BKP.R | 849 ++++++++++------------ R/fit_DKP.R | 859 +++++++++++----------- R/plot_BKP.R | 860 +++++++++++----------- R/plot_DKP.R | 820 ++++++++++----------- R/plot_TwinBKP.R | 748 +++++++++---------- R/plot_TwinDKP.R | 1118 ++++++++++++++--------------- README.md | 278 +++++-- inst/CITATION | 2 man/figures/README-bkp-demonstration-1.png |only man/fit_BKP.Rd | 36 man/fit_DKP.Rd | 36 man/plot.Rd | 6 15 files changed, 2909 insertions(+), 2745 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: Choice models are a widely used technique across numerous scientific disciplines. The Apollo package is a very flexible tool for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
<https://www.ApolloChoiceModelling.com>. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and [...truncated...]
Author: Stephane Hess [aut, cre],
David Palma [aut],
Thomas Hancock [ctb]
Maintainer: Stephane Hess <S.Hess@leeds.ac.uk>
Diff between apollo versions 0.3.8 dated 2026-05-17 and 0.3.9 dated 2026-07-13
apollo-0.3.8/apollo/R/apollo_cnl2.R |only apollo-0.3.8/apollo/man/apollo_cnl2.Rd |only apollo-0.3.9/apollo/DESCRIPTION | 6 apollo-0.3.9/apollo/MD5 | 309 ++++---- apollo-0.3.9/apollo/NAMESPACE | 1 apollo-0.3.9/apollo/R/apollo_avgInterDraws.R | 9 apollo-0.3.9/apollo/R/apollo_avgIntraDraws.R | 3 apollo-0.3.9/apollo/R/apollo_basTest.R | 3 apollo-0.3.9/apollo/R/apollo_bootstrap.R | 53 + apollo-0.3.9/apollo/R/apollo_checkArguments.R | 26 apollo-0.3.9/apollo/R/apollo_choiceAnalysis.R | 32 apollo-0.3.9/apollo/R/apollo_classAlloc.R | 41 + apollo-0.3.9/apollo/R/apollo_cnl.R | 49 + apollo-0.3.9/apollo/R/apollo_combineModels.R | 7 apollo-0.3.9/apollo/R/apollo_combineResults.R | 57 + apollo-0.3.9/apollo/R/apollo_compareInputs.R | 6 apollo-0.3.9/apollo/R/apollo_conditionals.R | 4 apollo-0.3.9/apollo/R/apollo_dVdB.R | 8 apollo-0.3.9/apollo/R/apollo_deltaMethod.R | 40 - apollo-0.3.9/apollo/R/apollo_detach.R | 4 apollo-0.3.9/apollo/R/apollo_dft.R | 52 + apollo-0.3.9/apollo/R/apollo_diagnostics.R | 13 apollo-0.3.9/apollo/R/apollo_drugChoiceData.R | 2 apollo-0.3.9/apollo/R/apollo_el.R | 74 +- apollo-0.3.9/apollo/R/apollo_emdc.R | 40 - apollo-0.3.9/apollo/R/apollo_estimate.R | 79 +- apollo-0.3.9/apollo/R/apollo_expandLoop.R | 145 +--- apollo-0.3.9/apollo/R/apollo_firstRow.R | 7 apollo-0.3.9/apollo/R/apollo_fitsTest.R | 15 apollo-0.3.9/apollo/R/apollo_fmnl.R | 34 apollo-0.3.9/apollo/R/apollo_fnl.R | 87 ++ apollo-0.3.9/apollo/R/apollo_initialise.R | 2 apollo-0.3.9/apollo/R/apollo_insertComponentName.R | 18 apollo-0.3.9/apollo/R/apollo_insertFunc.R | 20 apollo-0.3.9/apollo/R/apollo_insertOLList.R | 262 +++---- apollo-0.3.9/apollo/R/apollo_insertQuotes.R | 184 ++--- apollo-0.3.9/apollo/R/apollo_lc.R | 40 - apollo-0.3.9/apollo/R/apollo_lcConditionals.R | 16 apollo-0.3.9/apollo/R/apollo_lcEM.R | 133 +++ apollo-0.3.9/apollo/R/apollo_lcUnconditionals.R | 18 apollo-0.3.9/apollo/R/apollo_llCalc.R | 13 apollo-0.3.9/apollo/R/apollo_loadModel.R | 20 apollo-0.3.9/apollo/R/apollo_longToWide.R | 58 + apollo-0.3.9/apollo/R/apollo_lrTest.R | 25 apollo-0.3.9/apollo/R/apollo_makeDraws.R | 20 apollo-0.3.9/apollo/R/apollo_mdcev.R | 37 - apollo-0.3.9/apollo/R/apollo_mdcnev.R | 100 ++ apollo-0.3.9/apollo/R/apollo_mixConditionals.R | 19 apollo-0.3.9/apollo/R/apollo_mixEM.R | 125 ++- apollo-0.3.9/apollo/R/apollo_mixUnconditionals.R | 28 apollo-0.3.9/apollo/R/apollo_mnl.R | 57 + apollo-0.3.9/apollo/R/apollo_mnl_hessian_fix.R |only apollo-0.3.9/apollo/R/apollo_modeChoiceData.R | 6 apollo-0.3.9/apollo/R/apollo_modelOutput.R | 46 + apollo-0.3.9/apollo/R/apollo_modifyUserDefFunc.R | 5 apollo-0.3.9/apollo/R/apollo_nl.R | 93 ++ apollo-0.3.9/apollo/R/apollo_normalDensity.R | 99 ++ apollo-0.3.9/apollo/R/apollo_ol.R | 93 ++ apollo-0.3.9/apollo/R/apollo_op.R | 100 ++ apollo-0.3.9/apollo/R/apollo_outOfSample.R | 101 ++ apollo-0.3.9/apollo/R/apollo_ownModel.R | 45 + apollo-0.3.9/apollo/R/apollo_panelProd.R | 15 apollo-0.3.9/apollo/R/apollo_prediction.R | 153 +++- apollo-0.3.9/apollo/R/apollo_prepareProb.R | 19 apollo-0.3.9/apollo/R/apollo_print.R | 34 apollo-0.3.9/apollo/R/apollo_readBeta.R | 12 apollo-0.3.9/apollo/R/apollo_rrm.R | 81 +- apollo-0.3.9/apollo/R/apollo_saveOutput.R | 114 ++- apollo-0.3.9/apollo/R/apollo_searchStart.R | 590 +++++++++-------- apollo-0.3.9/apollo/R/apollo_setRows.R | 9 apollo-0.3.9/apollo/R/apollo_setWorkDir.R | 43 - apollo-0.3.9/apollo/R/apollo_sharesTest.R | 57 + apollo-0.3.9/apollo/R/apollo_sink.R | 68 + apollo-0.3.9/apollo/R/apollo_speedTest.R | 95 ++ apollo-0.3.9/apollo/R/apollo_swissRouteChoiceData.R | 16 apollo-0.3.9/apollo/R/apollo_timeUseData.R | 21 apollo-0.3.9/apollo/R/apollo_tobit.R | 97 ++ apollo-0.3.9/apollo/R/apollo_unconditionals.R | 38 - apollo-0.3.9/apollo/R/apollo_validate.R | 12 apollo-0.3.9/apollo/R/apollo_validateControl.R | 73 +- apollo-0.3.9/apollo/R/apollo_validateData.R | 23 apollo-0.3.9/apollo/R/apollo_validateInputs.R | 9 apollo-0.3.9/apollo/R/apollo_varList.R | 7 apollo-0.3.9/apollo/R/apollo_varcov.R | 49 + apollo-0.3.9/apollo/R/apollo_weighting.R | 28 apollo-0.3.9/apollo/R/apollo_writeF12.R | 202 ++--- apollo-0.3.9/apollo/R/summary.apollo.R | 2 apollo-0.3.9/apollo/inst/doc/apollofirstexample.html | 28 apollo-0.3.9/apollo/man/apollo_avgInterDraws.Rd | 7 apollo-0.3.9/apollo/man/apollo_avgIntraDraws.Rd | 3 apollo-0.3.9/apollo/man/apollo_bootstrap.Rd | 11 apollo-0.3.9/apollo/man/apollo_choiceAnalysis.Rd | 19 apollo-0.3.9/apollo/man/apollo_classAlloc.Rd | 4 apollo-0.3.9/apollo/man/apollo_cnl.Rd | 6 apollo-0.3.9/apollo/man/apollo_combineModels.Rd | 7 apollo-0.3.9/apollo/man/apollo_combineResults.Rd | 2 apollo-0.3.9/apollo/man/apollo_compareInputs.Rd | 6 apollo-0.3.9/apollo/man/apollo_conditionals.Rd | 4 apollo-0.3.9/apollo/man/apollo_dVdB.Rd | 2 apollo-0.3.9/apollo/man/apollo_deltaMethod.Rd | 8 apollo-0.3.9/apollo/man/apollo_detach.Rd | 4 apollo-0.3.9/apollo/man/apollo_dft.Rd | 10 apollo-0.3.9/apollo/man/apollo_diagnostics.Rd | 12 apollo-0.3.9/apollo/man/apollo_drugChoiceData.Rd | 2 apollo-0.3.9/apollo/man/apollo_el.Rd | 12 apollo-0.3.9/apollo/man/apollo_estimate.Rd | 24 apollo-0.3.9/apollo/man/apollo_expandLoop.Rd | 10 apollo-0.3.9/apollo/man/apollo_firstRow.Rd | 3 apollo-0.3.9/apollo/man/apollo_fitsTest.Rd | 6 apollo-0.3.9/apollo/man/apollo_fmnl.Rd | 10 apollo-0.3.9/apollo/man/apollo_fnl.Rd | 21 apollo-0.3.9/apollo/man/apollo_insertComponentName.Rd | 6 apollo-0.3.9/apollo/man/apollo_insertFunc.Rd | 14 apollo-0.3.9/apollo/man/apollo_insertOLList.Rd | 2 apollo-0.3.9/apollo/man/apollo_insertRRMQuotes.Rd | 2 apollo-0.3.9/apollo/man/apollo_lc.Rd | 10 apollo-0.3.9/apollo/man/apollo_lcConditionals.Rd | 4 apollo-0.3.9/apollo/man/apollo_lcEM.Rd | 10 apollo-0.3.9/apollo/man/apollo_lcUnconditionals.Rd | 6 apollo-0.3.9/apollo/man/apollo_loadModel.Rd | 2 apollo-0.3.9/apollo/man/apollo_longToWide.Rd | 7 apollo-0.3.9/apollo/man/apollo_mdcev.Rd | 12 apollo-0.3.9/apollo/man/apollo_mdcnev.Rd | 10 apollo-0.3.9/apollo/man/apollo_mixConditionals.Rd | 11 apollo-0.3.9/apollo/man/apollo_mixEM.Rd | 12 apollo-0.3.9/apollo/man/apollo_mixUnconditionals.Rd | 2 apollo-0.3.9/apollo/man/apollo_mnl.Rd | 33 apollo-0.3.9/apollo/man/apollo_modeChoiceData.Rd | 6 apollo-0.3.9/apollo/man/apollo_modelOutput.Rd | 9 apollo-0.3.9/apollo/man/apollo_nl.Rd | 8 apollo-0.3.9/apollo/man/apollo_normalDensity.Rd | 10 apollo-0.3.9/apollo/man/apollo_ol.Rd | 11 apollo-0.3.9/apollo/man/apollo_op.Rd | 8 apollo-0.3.9/apollo/man/apollo_outOfSample.Rd | 18 apollo-0.3.9/apollo/man/apollo_ownModel.Rd | 11 apollo-0.3.9/apollo/man/apollo_panelProd.Rd | 8 apollo-0.3.9/apollo/man/apollo_prediction.Rd | 8 apollo-0.3.9/apollo/man/apollo_prepareProb.Rd | 8 apollo-0.3.9/apollo/man/apollo_readBeta.Rd | 4 apollo-0.3.9/apollo/man/apollo_rrm.Rd | 16 apollo-0.3.9/apollo/man/apollo_saveOutput.Rd | 21 apollo-0.3.9/apollo/man/apollo_searchStart.Rd | 10 apollo-0.3.9/apollo/man/apollo_setWorkDir.Rd | 7 apollo-0.3.9/apollo/man/apollo_sharesTest.Rd | 4 apollo-0.3.9/apollo/man/apollo_sink.Rd | 5 apollo-0.3.9/apollo/man/apollo_speedTest.Rd | 8 apollo-0.3.9/apollo/man/apollo_swissRouteChoiceData.Rd | 16 apollo-0.3.9/apollo/man/apollo_timeUseData.Rd | 54 - apollo-0.3.9/apollo/man/apollo_tobit.Rd | 13 apollo-0.3.9/apollo/man/apollo_unconditionals.Rd | 18 apollo-0.3.9/apollo/man/apollo_validateControl.Rd | 24 apollo-0.3.9/apollo/man/apollo_validateData.Rd | 6 apollo-0.3.9/apollo/man/apollo_validateInputs.Rd | 5 apollo-0.3.9/apollo/man/apollo_varList.Rd | 9 apollo-0.3.9/apollo/man/apollo_varcov.Rd | 18 apollo-0.3.9/apollo/man/apollo_weighting.Rd | 4 apollo-0.3.9/apollo/man/apollo_writeF12.Rd | 2 157 files changed, 3679 insertions(+), 1890 deletions(-)
Title: Cross-Platform 'zip' Compression
Description: Cross-Platform 'zip' Compression Library. A replacement for
the 'zip' function, that does not require any additional external
tools on any platform.
Author: Gabor Csardi [aut, cre],
Kuba Podgorski [ctb],
Rich Geldreich [ctb],
Arm Limited [ctb, cph] ),
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between zip versions 3.0.0 dated 2026-06-10 and 3.0.1 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 27 ++++++++++++++------------- NEWS.md | 17 +++++++++++++++++ R/threaded.R | 10 ++++++++++ R/utils.R | 5 +++-- R/zip.R | 3 ++- man/unzip.Rd | 3 ++- src/miniz.c | 21 +++++++++++++++++++++ src/zip.c | 7 +++++-- tests/testthat/_snaps/threaded-unzip.md | 8 ++++++++ tests/testthat/test-threaded-unzip.R | 26 +++++++++++++++++++++++++- tests/testthat/test-unzip.R | 6 +++--- tests/testthat/test-utils.R |only tests/testthat/test-zip.R | 19 +++++++++++++++++-- tools/extra/miniz.patch | 27 +++++++++++++++++++++++++++ 15 files changed, 157 insertions(+), 28 deletions(-)
Title: Time Series Analysis and Computational Finance
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre] ,
Blake LeBaron [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tseries versions 0.10-61 dated 2026-03-26 and 0.10-62 dated 2026-07-13
ChangeLog | 4 ++++ DESCRIPTION | 9 ++++----- MD5 | 24 ++++++++++++------------ build/partial.rdb |binary data/NelPlo.rda |binary data/USeconomic.rda |binary data/bev.rda |binary data/camp.rda |binary data/ice.river.rda |binary data/nino.rda |binary data/tcm.rda |binary data/tcmd.rda |binary man/white.test.Rd | 3 +++ 13 files changed, 23 insertions(+), 17 deletions(-)
Title: Text Analysis Utilities
Description: Utilities for text analysis.
Author: Christian Buchta [aut],
Kurt Hornik [aut, cre] ,
Ingo Feinerer [aut] ,
David Meyer [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tau versions 0.0-28 dated 2026-03-26 and 0.0-29 dated 2026-07-13
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------ R/sysdata.rda |binary build/partial.rdb |binary src/textcnt.c | 6 +++- tests/counting.R | 20 ++++++++-------- tests/counting.Rout.save | 47 ++++++++++++++------------------------ tests/counting_useBytes.R | 20 ++++++++-------- tests/counting_useBytes.Rout.save | 45 +++++++++++++----------------------- 9 files changed, 72 insertions(+), 88 deletions(-)
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre] ,
David Meyer [aut] ,
Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between slam versions 0.1-55 dated 2024-11-13 and 0.1-56 dated 2026-07-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/array.Rd | 5 +++++ tests/stm_rollup.R | 2 +- tests/stm_rollup.Rout.save | 12 +++++------- 5 files changed, 20 insertions(+), 17 deletions(-)
Title: R/Weka Interface
Description: An R interface to Weka (Version 3.9.3).
Weka is a collection of machine learning algorithms for data mining
tasks written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package 'RWeka' contains the interface code, the
Weka jar is in a separate package 'RWekajars'. For more information
on Weka see <https://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre] ,
Christian Buchta [ctb],
Torsten Hothorn [ctb],
Alexandros Karatzoglou [ctb],
David Meyer [ctb],
Achim Zeileis [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between RWeka versions 0.4-48 dated 2026-03-26 and 0.4-49 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/RWeka.R | 2 -- inst/doc/RWeka.pdf |binary man/Weka_classifier_trees.Rd | 11 +++++++++++ tests/data_exchange.R | 14 ++++++++++++-- tests/data_exchange.Rout.save | 22 ++++++++++++++++------ 9 files changed, 50 insertions(+), 21 deletions(-)
Title: Apache OpenNLP Tools Interface
Description: An interface to the Apache OpenNLP tools (version 1.5.3).
The Apache OpenNLP library is a machine learning based toolkit for the
processing of natural language text written in Java.
It supports the most common NLP tasks, such as tokenization, sentence
segmentation, part-of-speech tagging, named entity extraction, chunking,
parsing, and coreference resolution.
See <https://opennlp.apache.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between openNLP versions 0.2-7 dated 2019-10-26 and 0.2-8 dated 2026-07-13
DESCRIPTION | 8 +++--- MD5 | 14 +++++----- man/Maxent_Chunk_Annotator.Rd | 41 +++++++++++++++--------------- man/Maxent_Entity_Annotator.Rd | 49 ++++++++++++++++++------------------- man/Maxent_POS_Tag_Annotator.Rd | 4 +-- man/Maxent_Sent_Token_Annotator.Rd | 4 +-- man/Maxent_Word_Token_Annotator.Rd | 4 +-- man/Parse_Annotator.Rd | 45 ++++++++++++++++----------------- 8 files changed, 83 insertions(+), 86 deletions(-)
Title: Natural Language Processing Infrastructure
Description: Basic classes and methods for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between NLP versions 0.3-2 dated 2024-11-20 and 0.3-3 dated 2026-07-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/sysdata.rda |binary build/partial.rdb |binary man/CoNLLTextDocument.Rd | 9 ++++++--- man/Tokenizer.Rd | 2 ++ man/datetime.Rd | 3 +++ man/ngrams.Rd | 3 +++ man/viewers.Rd | 1 + 9 files changed, 27 insertions(+), 15 deletions(-)
Title: Machine Learning Benchmark Problems
Description: A collection of artificial and real-world machine learning
benchmark problems, including, e.g., several
data sets from the UCI repository.
Author: Friedrich Leisch [aut] ,
Evgenia Dimitriadou [aut],
Kurt Hornik [cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between mlbench versions 2.1-8 dated 2026-03-26 and 2.1-9 dated 2026-07-13
DESCRIPTION | 7 ++---- MD5 | 48 +++++++++++++++++++++--------------------- NAMESPACE | 22 +++++++++++++++++-- NEWS | 5 ++++ build/partial.rdb |binary data/BostonHousing.rda |binary data/BostonHousing2.rda |binary data/BreastCancer.rda |binary data/DNA.rda |binary data/Glass.rda |binary data/HouseVotes84.rda |binary data/Ionosphere.rda |binary data/LetterRecognition.rda |binary data/Ozone.rda |binary data/PimaIndiansDiabetes.rda |binary data/PimaIndiansDiabetes2.rda |binary data/Satellite.rda |binary data/Servo.rda |binary data/Shuttle.rda |binary data/Sonar.rda |binary data/Soybean.rda |binary data/Vehicle.rda |binary data/Vowel.rda |binary data/Zoo.rda |binary man/mlbench.hypercube.Rd | 1 25 files changed, 52 insertions(+), 31 deletions(-)
Title: Continuous Time Structural Equation Modelling - Old
'OpenMx'-Based Version
Description: Original 'ctsem' (continuous time structural equation modelling)
functionality, based on the 'OpenMx' software, as described in
Driver, Oud, Voelkle (2017) <doi:10.18637/jss.v077.i05>, with updated details in vignette.
Combines stochastic differential equations representing latent processes with
structural equation measurement models. This package is maintained for consistency with the
original 'ctsem' paper, but for the much newer and more capable 'ctsem' package, see
<https://cran.r-project.org/package=ctsem>.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph]
Maintainer: Charles Driver <charles.driver2@uzh.ch>
Diff between ctsemOMX versions 2.0.0 dated 2026-03-19 and 2.0.1 dated 2026-07-13
DESCRIPTION | 10 MD5 | 22 R/ctDataHelp.R | 214 ++++---- R/ctDiscretiseData.R | 114 ++-- R/ctLongtowide.r | 308 ++++++------ R/ctModel.R | 1212 ++++++++++++++++++++++++------------------------- R/ctsemOMX-package.R | 140 ++--- build/vignette.rds |binary inst/doc/ctsemOMX.pdf |binary inst/doc/ctsemOMX.rnw | 2 man/ctsemOMX.Rd | 1 vignettes/ctsemOMX.rnw | 2 12 files changed, 1013 insertions(+), 1012 deletions(-)
Title: Creating Composite Plots using 'aplot'
Description: Many complex plots are actually composite plots, such as 'oncoplot', 'funkyheatmap', 'upsetplot', etc. We can produce subplots using 'ggplot2' and combine them to create composite plots using 'aplot'. In this way, it is easy to customize these complex plots, by adding, deleting or modifying subplots in the final plot. This package provides a set of utilities to help users to create subplots and complex plots.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Chun-Hui Gao [ctb] ,
Shensuo Li [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplotExtra versions 0.0.4 dated 2025-06-12 and 0.0.5 dated 2026-07-13
DESCRIPTION | 12 +++++++----- MD5 | 17 ++++++++++------- NEWS.md | 9 +++++++++ R/funkyheatmap.R | 6 ++---- R/oncoplot.r | 2 +- R/upset.R | 4 ++-- man/aplotExtra-package.Rd | 5 +++++ man/upset_plot.Rd | 2 +- tests |only 9 files changed, 37 insertions(+), 20 deletions(-)
Title: 'rcpp' Wrapper for 'mecab' Library
Description: R package based on 'Rcpp' for 'MeCab': Yet Another Part-of-Speech and Morphological Analyzer.
It provides install-time engine profiles and dictionaries for Japanese,
Korean, and Mandarin Chinese text. Runtime dictionary selection does not
change the installed engine.
This package utilizes parallel programming for providing highly efficient text preprocessing 'posParallel()' function.
For installation, please refer to README.md file.
Author: Junhewk Kim [aut, cre],
Taku Kudo [aut],
Akiru Kato [ctb],
Patrick Schratz [ctb]
Maintainer: Junhewk Kim <junhewk.kim@gmail.com>
Diff between RcppMeCab versions 0.0.1.6 dated 2026-07-12 and 0.0.1.7 dated 2026-07-13
DESCRIPTION | 20 ++++--- MD5 | 37 +++++++------ NEWS.md | 6 +- R/RcppMeCab-package.r | 7 +- R/dic.R | 21 +++++-- R/pos.r | 16 ++++- R/posParallel.R | 16 ++++- README.md | 108 ++++++++++++++++++++++++++++------------ cleanup | 1 configure | 103 ++++++++++++++++++++++++++++++++------ inst/COPYRIGHTS |only man/RcppMeCab.Rd | 7 +- man/download_dic.Rd | 6 +- man/pos.Rd | 16 ++++- man/posParallel.Rd | 16 ++++- man/set_dic.Rd | 13 ++-- src/Makevars.win | 22 ++++++++ tests/testthat/test_pos_ko.R | 2 tests/testthat/test_pos_zh.R |only tools/mecab-dict-index-main.cpp |only tools/winlibs.R | 26 ++++++++- 21 files changed, 331 insertions(+), 112 deletions(-)
Title: Bayesian Inference Using 'RTMB'
Description: Provides tools for Markov chain Monte Carlo (MCMC) and Maximum A Posteriori (MAP) estimation utilizing the 'RTMB' package. It supports various statistical models including generalized linear mixed models, factor analysis, item response theory, and multidimensional unfolding. The package allows users to easily transition between frequentist and Bayesian paradigms using a unified interface. Automatic differentiation and Laplace approximation follow Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>, and MCMC sampling uses the No-U-Turn Sampler described by Hoffman and Gelman (2014) <https://jmlr.org/papers/v15/hoffman14a.html>.
Author: Hiroshi Shimizu [aut, cre]
Maintainer: Hiroshi Shimizu <simizu706@gmail.com>
Diff between BayesRTMB versions 0.2.1 dated 2026-06-23 and 0.2.3 dated 2026-07-13
DESCRIPTION | 6 MD5 | 74 NAMESPACE | 2 NEWS.md | 22 R/Base_Fit.R | 114 R/RTMB_Model_impl_ast.R | 16 R/distributions.R | 152 R/model.R | 200 + R/parameters.R | 29 R/wrapper_corr.R | 2 R/wrapper_fa.R | 62 R/wrapper_lrt.R | 38 R/wrapper_mixture.R | 33 inst/doc/analysis_reference.R | 3 inst/doc/analysis_reference.Rmd | 8 inst/doc/analysis_reference.html | 135 inst/doc/ja-analysis_reference.Rmd | 3396 +++++++++++----------- inst/doc/ja-wrapper_functions.R | 4 inst/doc/ja-wrapper_functions.Rmd | 4 inst/doc/ja-writing_models.R | 89 inst/doc/ja-writing_models.Rmd | 122 inst/doc/ja-writing_models.html | 546 ++- inst/doc/writing_models.R | 88 inst/doc/writing_models.Rmd | 117 inst/doc/writing_models.html | 163 - inst/examples/ex_fa.R | 30 man/RTMB_Fit_Base.Rd | 20 man/diffusion_lpdf.Rd |only man/distributions.Rd | 6 man/exp_mod_normal_lpdf.Rd |only man/rtmb_fa.Rd | 30 tests/testthat/test-obs-syntax.R |only tests/testthat/test-response-time-distributions.R |only tests/testthat/test-rtmb-containers.R | 13 tests/testthat/test-wrappers.R | 119 vignettes/analysis_reference.Rmd | 8 vignettes/ja-analysis_reference.Rmd | 3396 +++++++++++----------- vignettes/ja-wrapper_functions.Rmd | 4 vignettes/ja-writing_models.Rmd | 122 vignettes/writing_models.Rmd | 117 40 files changed, 5427 insertions(+), 3863 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-17 2.0.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-05-18 3.1.1
2026-05-16 3.1.0
2026-01-08 3.0.0
2024-12-12 2.1.2
2024-05-29 2.1.0
2024-04-15 2.0.12
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-11 2.1.1
2025-10-14 2.0.9
2025-10-11 2.0.8
2024-05-15 2.0.7
2024-04-15 2.0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-05-23 3.1.2
2026-05-19 3.1.0
2026-01-11 3.0.4
2025-09-18 2.1.8
2025-09-02 2.1.6
2024-06-02 2.1.0
2024-04-25 2.0.5
2024-04-16 2.0.4
Title: Bayesian Network Meta-Analysis with Missing Participants
Description: A comprehensive suite of functions to perform and visualise
pairwise and network meta-analysis with aggregate binary or continuous
missing participant outcome data. The package covers core Bayesian one-stage
models implemented in a systematic review with multiple interventions,
including fixed-effect and random-effects network meta-analysis,
meta-regression, and evaluation of the consistency assumption via the
node-splitting approach and the unrelated mean effects model (original and
revised model proposed by Spineli, (2021) <doi:10.1177/0272989X211068005>).
Missing participant outcome data are addressed in all models of the package
(see Spineli, (2019) <doi:10.1186/s12874-019-0731-y>, Spineli et al., (2019)
<doi:10.1002/sim.8207>, Spineli, (2019) <doi:10.1016/j.jclinepi.2018.09.002>,
and Spineli et al., (2021) <doi:10.1177/0962280220983544>).
The robustness to primary analysis results can also be investigated using a
novel intuitive index (see Spineli et [...truncated...]
Author: Loukia Spineli [aut, cre],
Chrysostomos Kalyvas [ctb],
Katerina Papadimitropoulou [ctb]
Maintainer: Loukia Spineli <Spineli.Loukia@mh-hannover.de>
Diff between rnmamod versions 0.5.0 dated 2025-06-13 and 0.5.1 dated 2026-07-13
DESCRIPTION | 25 ++++++------ MD5 | 44 ++++++++++----------- NEWS.md | 4 + R/comp.clustering_function.R | 27 +++++++------ R/dendro.heatmap_function.R | 10 +++- R/distr.characteristics_function.R | 8 +++ R/gower.distance_function.R | 26 +++++++++++- R/kld.inconsistency.user_function.R | 6 ++ R/kld.inconsistency_function.R | 6 ++ R/miss.characteristics_function.R | 9 +++- R/plot.study.dissimilarities_function.R | 2 R/rnmamod.R.R | 59 ++++++++++++++++++++++++----- inst/doc/network_description.html | 13 +++--- inst/doc/perform_network_metaanalysis.html | 9 ++-- man/comp_clustering.Rd | 22 ++++++---- man/dendro_heatmap.Rd | 10 +++- man/distr_characteristics.Rd | 8 +++ man/gower_distance.Rd | 20 +++++++++ man/kld_inconsistency.Rd | 6 ++ man/kld_inconsistency_user.Rd | 6 ++ man/miss_characteristics.Rd | 9 +++- man/plot_study_dissimilarities.Rd | 2 man/rnmamod-package.Rd | 59 ++++++++++++++++++++++++----- 23 files changed, 290 insertions(+), 100 deletions(-)
Title: Interface to 'JDemetra+' 3.x Time Series Analysis Software
Description: Interface to 'JDemetra+' 3.x (<https://github.com/jdemetra>)
time series analysis software. It offers full access to txt, csv, xml
and spreadsheets files which are meant to be read by 'JDemetra+'
Graphical User Interface.
Author: Jean Palate [aut],
Alessandro Piovani [aut, cre],
Tanguy Barthelemy [ctb, art]
Maintainer: Alessandro Piovani <alessandro.piovani@istat.it>
Diff between rjd3providers versions 3.7.1 dated 2026-03-11 and 3.8.0 dated 2026-07-13
rjd3providers-3.7.1/rjd3providers/R/deprecated.R |only rjd3providers-3.7.1/rjd3providers/inst/java/caffeine-3.2.3.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/java-io-base-0.0.35.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/java-io-picocsv-0.0.35.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/java-io-xml-0.0.35.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/java-io-xml-bind-0.0.35.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-spreadsheet-base-api-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-spreadsheet-base-r-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-text-base-api-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-text-base-r-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-toolkit-base-tsp-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-toolkit-base-xml-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/spreadsheet-api-2.5.10.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/spreadsheet-standalone-2.5.10.jar |only rjd3providers-3.7.1/rjd3providers/man/deprecated-rjd3providers.Rd |only rjd3providers-3.8.0/rjd3providers/DESCRIPTION | 14 rjd3providers-3.8.0/rjd3providers/MD5 | 116 rjd3providers-3.8.0/rjd3providers/NAMESPACE | 84 rjd3providers-3.8.0/rjd3providers/NEWS.md | 224 - rjd3providers-3.8.0/rjd3providers/R/jd3spreadsheet.R | 768 +++-- rjd3providers-3.8.0/rjd3providers/R/jd3txt.R | 927 ++++--- rjd3providers-3.8.0/rjd3providers/R/jd3xml.R | 576 ++-- rjd3providers-3.8.0/rjd3providers/R/providers.R | 143 - rjd3providers-3.8.0/rjd3providers/R/rjd3providers-package.R |only rjd3providers-3.8.0/rjd3providers/R/zzz.R | 106 rjd3providers-3.8.0/rjd3providers/README.md | 481 +-- rjd3providers-3.8.0/rjd3providers/inst/extdata/ABS.csv | 852 +++--- rjd3providers-3.8.0/rjd3providers/inst/extdata/Prod.xml | 1286 +++++----- rjd3providers-3.8.0/rjd3providers/inst/java/caffeine-3.2.4.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/java-io-base-0.0.38.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/java-io-picocsv-0.0.38.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/java-io-xml-0.0.38.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/java-io-xml-bind-0.0.38.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-spreadsheet-base-api-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-spreadsheet-base-r-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-text-base-api-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-text-base-r-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-toolkit-base-tsp-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-toolkit-base-xml-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/spreadsheet-api-2.6.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/spreadsheet-standalone-2.6.0.jar |only rjd3providers-3.8.0/rjd3providers/java/README | 12 rjd3providers-3.8.0/rjd3providers/man/dot-obs_format.Rd | 68 rjd3providers-3.8.0/rjd3providers/man/dot-obs_gathering.Rd | 68 rjd3providers-3.8.0/rjd3providers/man/dot-spreadsheet_moniker.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/dot-txt_moniker.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/dot-xml_moniker.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/figures/logo.svg | 188 - rjd3providers-3.8.0/rjd3providers/man/get_providers_option.Rd |only rjd3providers-3.8.0/rjd3providers/man/providers_option.Rd |only rjd3providers-3.8.0/rjd3providers/man/rjd3providers-package.Rd |only rjd3providers-3.8.0/rjd3providers/man/set_spreadsheet_paths.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/set_txt_paths.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/set_xml_paths.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_change_file.Rd | 62 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_content.Rd | 50 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_data.Rd | 92 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_id_to_properties.Rd | 66 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_name.Rd | 40 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_properties_to_id.Rd | 68 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_series.Rd | 98 rjd3providers-3.8.0/rjd3providers/man/txt_change_file.Rd | 62 rjd3providers-3.8.0/rjd3providers/man/txt_content.Rd | 132 - rjd3providers-3.8.0/rjd3providers/man/txt_data.Rd | 132 - rjd3providers-3.8.0/rjd3providers/man/txt_id_to_properties.Rd | 54 rjd3providers-3.8.0/rjd3providers/man/txt_name.Rd | 40 rjd3providers-3.8.0/rjd3providers/man/txt_properties_to_id.Rd | 68 rjd3providers-3.8.0/rjd3providers/man/txt_series.Rd | 140 - rjd3providers-3.8.0/rjd3providers/man/xml_change_file.Rd | 62 rjd3providers-3.8.0/rjd3providers/man/xml_content.Rd | 56 rjd3providers-3.8.0/rjd3providers/man/xml_data.Rd | 64 rjd3providers-3.8.0/rjd3providers/man/xml_id_to_properties.Rd | 56 rjd3providers-3.8.0/rjd3providers/man/xml_name.Rd | 40 rjd3providers-3.8.0/rjd3providers/man/xml_properties_to_id.Rd | 56 rjd3providers-3.8.0/rjd3providers/man/xml_series.Rd | 70 75 files changed, 4048 insertions(+), 3649 deletions(-)
Title: A Comprehensive Toolkit for Environmental Mixtures Analysis
Description: Quantitative characterization of the health impacts associated with exposure to chemical mixtures has received considerable attention in current environmental and epidemiological studies. 'CompMix' package allows practitioners to estimate the health impacts from exposure to chemical mixtures data through various statistical approaches, including Lasso, Elastic net, Bayesian kernel machine regression (BKMR), hierNet, Quantile g-computation, Weighted quantile sum (WQS) and Random forest. Methods and recommendations are described in Hao et al. (2025) <doi:10.1289/EHP15305>.
Author: Wei Hao [aut, cre]
Maintainer: Wei Hao <weihao@umich.edu>
This is a re-admission after prior archival of version 0.1.0 dated 2024-05-22
Diff between CompMix versions 0.1.0 dated 2024-05-22 and 1.1.0 dated 2026-07-13
DESCRIPTION | 15 - MD5 | 9 - NAMESPACE | 2 R/environment_mix_lib_package.R | 324 +++++++++++++--------------------------- inst |only man/Comp.Mix.Rd | 30 ++- 6 files changed, 139 insertions(+), 241 deletions(-)
Title: Clustering-Based K-Nearest Neighbor Regression for Longitudinal
Data
Description: Implements the 'CKNNRLD' algorithm (Clustering-Based K-Nearest
Neighbor Regression for Longitudinal Data) for improving K-Nearest
Neighbor ('KNN') regression on longitudinal data through cluster-based
partitioning and localized prediction. Offers enhanced computational
efficiency and accuracy for high-volume longitudinal datasets. The
acronym 'KNN' stands for K-Nearest Neighbor. References: Loeloe MS,
Tabatabaei SM, Sefidkar R, Mehrparvar AH, Jambarsang S (2025).
"Boosting K-nearest neighbor regression performance for longitudinal
data through a novel learning approach." BMC Bioinformatics, 26, 232.
<doi:10.1186/s12859-025-06205-1>.
Author: Mohammad Sadegh Loeloe [aut, cre],
Seyyed Mohammad Tabatabaei [aut],
Reyhane Sefidkar [aut],
Amir Houshang Mehrparvar [aut],
Sara Jambarsang [aut, ths]
Maintainer: Mohammad Sadegh Loeloe <mslbiostat@gmail.com>
Diff between CKNNRLD versions 0.2.0 dated 2026-07-10 and 0.2.2 dated 2026-07-13
CKNNRLD-0.2.0/CKNNRLD/R/return_model.R |only CKNNRLD-0.2.2/CKNNRLD/DESCRIPTION | 6 +++--- CKNNRLD-0.2.2/CKNNRLD/MD5 | 6 +++--- CKNNRLD-0.2.2/CKNNRLD/R/CKNNRLD.R |only CKNNRLD-0.2.2/CKNNRLD/man/CKNNRLD.Rd | 20 ++++++++++---------- 5 files changed, 16 insertions(+), 16 deletions(-)
Title: Bayesian Simultaneous Credible Bands for Polynomial Regression
Description: Provides functions to construct two-sided Bayesian simultaneous
credible bands (BSCBs) for the regression curve in univariate polynomial
regression over a finite covariate interval. Six methods are implemented,
including Normal-Gamma conjugate priors (with empirical Bayes,
unit-information, and g-prior hyperparameter specifications),
non-conjugate priors fitted via Hamiltonian Monte Carlo (HMC) using
'cmdstanr', and a non-informative independent Jeffreys prior approach.
Also includes functions for computing the empirical simultaneous coverage
rate (ESCR) and posterior simultaneous coverage probability (PSCP),
enabling performance comparison across methods. The methodology is
described in:
Yang, F., Han, Y., Liu, W., & Hall, I. (2026). "Bayesian simultaneous
credible bands for polynomial regression" <doi:10.48550/arXiv.2606.28015>.
Author: Fei Yang [aut, cre]
Maintainer: Fei Yang <fei.yang@manchester.ac.uk>
Diff between BSCB versions 1.0.0 dated 2026-07-10 and 1.0.1 dated 2026-07-13
BSCB-1.0.0/BSCB/inst/BSCB_1.0.0.pdf |only BSCB-1.0.1/BSCB/DESCRIPTION | 8 ++++---- BSCB-1.0.1/BSCB/MD5 | 14 +++++++------- BSCB-1.0.1/BSCB/NEWS.md | 13 +++++++++++-- BSCB-1.0.1/BSCB/R/generate_data.R | 12 ++++++++---- BSCB-1.0.1/BSCB/README.md | 15 +++++++++++++++ BSCB-1.0.1/BSCB/inst/BSCB_1.0.1.pdf |only BSCB-1.0.1/BSCB/inst/doc/BSCB-vignette.html | 19 +++++++++---------- BSCB-1.0.1/BSCB/man/generate_simulation_data.Rd | 9 ++++++--- 9 files changed, 60 insertions(+), 30 deletions(-)
Title: Branding, Theme Application and Navigation Utilities for
'bs4Dash' Dashboards
Description: Provides branding, theme application, and navigation utilities for
applications built with 'bs4Dash' and 'shiny'. Supports configurable
sidebar brand display modes, hover-expand behavior, and theme
customization using CSS variables. Includes complete navbar item helpers,
navbar structure validation, reusable brand configuration, prototype
top-navigation support, and helpers for common navigation bar and footer
layouts.
Author: George Arthur [aut, cre]
Maintainer: George Arthur <prigasgenthian48@gmail.com>
Diff between bs4Dashkit versions 0.2.0 dated 2026-04-21 and 0.3.0 dated 2026-07-13
DESCRIPTION | 18 MD5 | 108 ++- NAMESPACE | 49 - NEWS.md | 303 ++++++--- R/assets.R | 62 + R/nav_buttons.R | 207 ++++++ R/navbar_title.R | 4 R/sidebar.R | 22 R/sidebar_mode.R | 995 +++++++++++++++---------------- R/theme.R | 154 ++-- R/titles.R | 391 +++++++----- R/topnav.R |only R/use_core.R | 216 ++++-- R/utils.R | 242 +++++-- README.md | 224 ++++-- build/vignette.rds |binary inst/app-assets/dash-demo-brand.js |only inst/app-assets/dash-topnav.css |only inst/app-assets/dash-topnav.js |only inst/doc/branding-and-sidebar-modes.R | 26 inst/doc/branding-and-sidebar-modes.Rmd | 132 ++-- inst/doc/branding-and-sidebar-modes.html | 259 ++++---- inst/doc/complete-example-app.R | 23 inst/doc/complete-example-app.Rmd | 57 - inst/doc/complete-example-app.html | 203 +++--- inst/doc/getting-started.R | 25 inst/doc/getting-started.Rmd | 195 +++--- inst/doc/getting-started.html | 132 ++-- inst/doc/global-options.Rmd | 26 inst/doc/global-options.html | 6 inst/doc/navigation-utilities.R | 123 ++- inst/doc/navigation-utilities.Rmd | 250 ++++--- inst/doc/navigation-utilities.html | 382 ++++++----- inst/doc/packaged-examples.R |only inst/doc/packaged-examples.Rmd |only inst/doc/packaged-examples.html |only inst/doc/top-navigation.R |only inst/doc/top-navigation.Rmd |only inst/doc/top-navigation.html |only inst/examples/hardening-regression |only inst/examples/real-shiny-app/app.R | 834 ++++++++++++------------- inst/examples/test-all/app.R | 461 +++++++------- inst/examples/topnav-prototype |only man/dash_brand_options.Rd |only man/dash_nav_help_item.Rd |only man/dash_nav_refresh_item.Rd |only man/dash_nav_status_badge.Rd |only man/dash_nav_status_item.Rd |only man/dash_titles_from.Rd |only man/dash_topnav_options.Rd |only man/use_bs4Dashkit.Rd | 41 - man/use_bs4Dashkit_core.Rd | 135 ++-- man/use_dash_sidebar_behavior.Rd | 46 - man/use_dash_topnav.Rd |only man/validate_bs4dash_navbar.Rd |only tests/testthat/test-dash-titles.R | 477 ++++++++------ tests/testthat/test-nav-buttons.R | 65 +- tests/testthat/test-packaged-examples.R |only tests/testthat/test-theme-presets.R | 110 ++- tests/testthat/test-topnav.R |only tests/testthat/test-use-core.R |only vignettes/branding-and-sidebar-modes.Rmd | 132 ++-- vignettes/complete-example-app.Rmd | 57 - vignettes/getting-started.Rmd | 195 +++--- vignettes/global-options.Rmd | 26 vignettes/navigation-utilities.Rmd | 250 ++++--- vignettes/packaged-examples.Rmd |only vignettes/top-navigation.Rmd |only 68 files changed, 4403 insertions(+), 3260 deletions(-)
Title: Spatial Interpolation using Bayesian Maximum Entropy (BME)
Description: Provides an accessible and robust implementation of core BME
methodologies for spatial prediction. It enables the systematic integration
of heterogeneous data sources including both hard data (precise
measurements) and soft interval data (bounded or uncertain observations)
while incorporating prior knowledge and supporting variogram-based spatial
modeling. The BME methodology is described in Christakos (1990)
<doi:10.1007/BF00890661>, Serre and Christakos (1999)
<doi:10.1007/s004770050029> and Duah (2025, 2026)
<doi:10.1016/j.spasta.2026.100974>.
Author: Kinspride Duah [aut, cre, cph] ,
Yan Sun [aut]
Maintainer: Kinspride Duah <kinspride2020@gmail.com>
Diff between BMEmapping versions 1.2.2 dated 2025-08-19 and 2.0.0 dated 2026-07-13
DESCRIPTION | 18 MD5 | 92 +- NAMESPACE | 15 NEWS.md | 65 - R/bme_cv.R | 138 ++- R/bme_estimate.R | 55 + R/bme_kfcv.R |only R/bme_loocv.R |only R/bme_map.R | 9 R/bme_predict.R | 93 +- R/bme_predict_ci.R |only R/ch_nhmax.R | 3 R/check_x.R | 4 R/combine_data.R |only R/covmat.R | 10 R/covmat_avg.R |only R/cs_nsmax.R | 4 R/data.R | 3 R/exponential.R | 2 R/extended_range.R | 4 R/gaussian.R | 2 R/plot.BMEmapping.R | 452 +++++++++---- R/prob_zk.R | 38 - R/q_bme_cv.R |only R/q_bme_estimate.R |only R/q_bme_kfcv.R |only R/q_bme_loocv.R |only R/q_bme_predict.R |only R/q_bme_predict_ci.R |only R/q_prob_zk.R |only R/spherical.R | 4 R/summary.BMEmapping.R | 15 R/vg_results.R |only R/zzz.R | 3 README.md | 86 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_BMEmapping.R | 294 +++++--- inst/doc/Introduction_to_BMEmapping.Rmd | 578 +++++++++++----- inst/doc/Introduction_to_BMEmapping.html | 1072 ++++++++++++++++++++++--------- man/bme_cv.Rd | 59 + man/bme_map.Rd | 4 man/bme_predict.Rd | 39 - man/bme_predict_ci.Rd |only man/casnowload.Rd | 2 man/plot.BMEmapping.Rd | 19 man/prob_zk.Rd | 22 man/q_bme_cv.Rd |only man/q_bme_predict.Rd |only man/q_bme_predict_ci.Rd |only man/q_prob_zk.Rd |only tests/testthat/test-bme_cv.R | 24 tests/testthat/test-bme_predict.R | 57 + tests/testthat/test-covmat.R | 3 tests/testthat/test-prob_zk.R | 13 vignettes/Introduction_to_BMEmapping.Rmd | 578 +++++++++++----- 56 files changed, 2630 insertions(+), 1249 deletions(-)
Title: Modified Poisson Regression for Binary Outcome and Related
Methods
Description: Modified Poisson, logistic and least-squares regression analyses for binary outcomes of Zou (2004) <doi:10.1093/aje/kwh090>, Noma (2026)<doi:10.1016/j.spl.2026.110698>, and Cheung (2007) <doi:10.1093/aje/kwm223> have been standard multivariate analysis methods to estimate risk ratio and risk difference in clinical and epidemiological studies. This R package involves an easy-to-handle function to implement these analyses by simple commands. Missing data analysis tools (multiple imputation) are also involved. In addition, recent studies have shown the ordinary robust variance estimator possibly has serious bias under small or moderate sample size situations for these methods. This package also provides computational tools to calculate alternative accurate confidence intervals.
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between rqlm versions 4.3-2 dated 2026-02-28 and 4.4-1 dated 2026-07-13
DESCRIPTION | 8 MD5 | 12 - NAMESPACE | 1 NEWS.md | 4 R/rqlm.r | 622 +++++++++++++++++++++++++++++++++++----------------- man/rqlm-package.Rd | 2 man/rqlm.Rd | 297 ++++++++++++++++++++---- 7 files changed, 680 insertions(+), 266 deletions(-)
Title: A Fast and Flexible Pipeline for Text Classification
Description: A high-level pipeline that simplifies text classification into three streamlined steps:
preprocessing, model training, and standardized prediction.
It unifies the interface for multiple algorithms (including 'glmnet', 'ranger',
'xgboost', and 'naivebayes') and memory-efficient sparse matrix vectorization
methods (Bag-of-Words, Term Frequency, TF-IDF, and Binary). Users can go from
raw text to a fully evaluated sentiment model, complete with ROC-optimized
thresholds, in just a few function calls. The resulting model artifact
automatically aligns the vocabulary of new datasets during the prediction phase,
safely appending predicted classes and probability matrices directly to the
user's original dataframe to preserve metadata.
Author: Alabhya Dahal [aut, cre]
Maintainer: Alabhya Dahal <alabhya.dahal@gmail.com>
Diff between quickSentiment versions 0.3.4 dated 2026-04-16 and 0.3.5 dated 2026-07-13
DESCRIPTION | 6 +-- MD5 | 36 +++++++++--------- NEWS.md | 5 +- R/logit.R | 15 ++++++- R/nb.R | 3 + R/pipeline.R | 25 +++++++++++- R/rf.R | 14 +++++-- R/xgb.R | 13 ++++-- README.md | 2 + inst/WORDLIST | 15 ++++--- inst/doc/introduction-to-quickSentiment.R | 2 + inst/doc/introduction-to-quickSentiment.Rmd | 2 + inst/doc/introduction-to-quickSentiment.html | 52 ++++++++++++++------------- man/logit_model.Rd | 5 ++ man/nb_model.Rd | 11 +++++ man/pipeline.Rd | 3 + man/rf_model.Rd | 11 +++++ man/xgb_model.Rd | 11 +++++ vignettes/introduction-to-quickSentiment.Rmd | 2 + 19 files changed, 162 insertions(+), 71 deletions(-)
More information about quickSentiment at CRAN
Permanent link
Title: Build 'pkgdown' Websites Offline
Description: Provides support for building 'pkgdown' websites without an
internet connection. Works by bundling cached dependencies and
implementing drop-in replacements for key 'pkgdown' functions.
Enables package documentation websites to be built in environments
where internet access is unavailable or restricted.
For more details on generating 'pkgdown' websites, see
Wickham et al. (2025) <doi:10.32614/CRAN.package.pkgdown>.
Author: Nan Xiao [aut, cre, cph] ,
John Blischak [aut] ,
Algolia, Inc. and other contributors [ctb, cph] ,
Aidan Feldman [ctb, cph] ,
Zeno Rocha [ctb, cph] ,
Nick Williams [ctb, cph] ,
Julian Kuehnel [ctb, cph] ,
Kiro Risk [ctb, cph] ,
Khan Academy and other [...truncated...]
Maintainer: Nan Xiao <me@nanx.me>
Diff between pkgdown.offline versions 0.1.2 dated 2025-11-08 and 0.1.3 dated 2026-07-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 11 +++++++++++ R/build.R | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/cache/MD5 | 7 +++++++ man/pkgdown.offline-package.Rd | 1 + 8 files changed, 35 insertions(+), 11 deletions(-)
More information about pkgdown.offline at CRAN
Permanent link
Title: Performing Comprehensive Overlap Assessments
Description: The implementation of a statistical framework for performing overlap assessments on
lists comprising sets of strings (such as lists of gene sets) described in Stoica (2023)
<https://ora.ox.ac.uk/objects/uuid:b0847284-a02f-47ee-88e3-a3c4e0cdb8b1>.
It can assess overlaps of pairs of sets of strings selected either from the same universe or
from different universes, and overlaps of triplets of sets of strings selected from the same
universe. Designed for single-cell RNA-sequencing data analysis applications, but suitable
for other purposes as well.
Author: Andrei-Florian Stoica [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica@foxmail.com>
Diff between LISTO versions 0.7.3 dated 2026-04-25 and 0.8.1 dated 2026-07-13
DESCRIPTION | 6 ++-- MD5 | 42 ++++++++++++++++---------------- R/checks.R | 5 +-- R/cutoffs.R | 52 ++++++++++++++++------------------------ R/multiple_testing.R | 5 --- R/prob_counts.R | 1 R/pval_objects.R | 12 +++------ R/run_listo.R | 21 +++++++--------- R/seurat_demo.R | 2 - R/vectors.R | 4 +++ README.md | 10 +++---- man/filterItems.Rd | 2 - man/generateCutoffs.Rd | 16 +++++++----- man/getObjectValues.Rd | 10 +++---- man/mtCorrectDF.Rd | 2 - man/mtCorrectHelper.Rd | 2 - man/mtCorrectV.Rd | 2 - man/pvalObjects.Rd | 20 +++++++++------ man/pvalObjectsCore.Rd | 9 ++++-- man/runLISTO.Rd | 22 +++++++++------- tests/testthat/helper-globals.R | 1 tests/testthat/test-LISTO.R | 30 ++++++++++++----------- 22 files changed, 140 insertions(+), 136 deletions(-)
Title: Delayed Read for 'GDAL' Vector Data Sources
Description: Lazy read for drawings. A 'dplyr' back end for data sources supported by
'GDAL' vector drivers, that allows working with local or remote sources as if they
are in-memory data frames. Basic features work with any drawing format ('GDAL vector
data source') supported by the 'gdalraster' package.
Author: Michael Sumner [aut, cre]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between lazysf versions 0.3.0 dated 2026-02-17 and 0.4.0 dated 2026-07-13
lazysf-0.3.0/lazysf/R/SFSQLConnection.R |only lazysf-0.3.0/lazysf/R/SFSQLDriver.R |only lazysf-0.3.0/lazysf/R/SFSQLResult.R |only lazysf-0.3.0/lazysf/R/utils-pipe.R |only lazysf-0.3.0/lazysf/man/SFSQL.Rd |only lazysf-0.3.0/lazysf/man/SFSQLConnection-class.Rd |only lazysf-0.3.0/lazysf/man/SFSQLDriver-class.Rd |only lazysf-0.3.0/lazysf/man/SFSQLResult-class.Rd |only lazysf-0.3.0/lazysf/man/dbConnect-SFSQLDriver-method.Rd |only lazysf-0.3.0/lazysf/man/pipe.Rd |only lazysf-0.3.0/lazysf/man/st_as_sf.Rd |only lazysf-0.4.0/lazysf/DESCRIPTION | 27 lazysf-0.4.0/lazysf/MD5 | 71 + lazysf-0.4.0/lazysf/NAMESPACE | 61 - lazysf-0.4.0/lazysf/NEWS.md | 150 +++ lazysf-0.4.0/lazysf/R/GDALVectorConnection.R |only lazysf-0.4.0/lazysf/R/GDALVectorDriver.R |only lazysf-0.4.0/lazysf/R/GDALVectorResult.R |only lazysf-0.4.0/lazysf/R/connect.R | 73 + lazysf-0.4.0/lazysf/R/dbplyr.R | 38 lazysf-0.4.0/lazysf/R/helper.R |only lazysf-0.4.0/lazysf/R/lazysf-package.R | 33 lazysf-0.4.0/lazysf/R/lazysf.R | 125 +- lazysf-0.4.0/lazysf/R/sql-query-fields.R |only lazysf-0.4.0/lazysf/R/sql-translation.R |only lazysf-0.4.0/lazysf/R/zzz.R | 41 lazysf-0.4.0/lazysf/README.md | 484 +++++------ lazysf-0.4.0/lazysf/build/vignette.rds |binary lazysf-0.4.0/lazysf/inst/doc/GDALSQL.R | 102 ++ lazysf-0.4.0/lazysf/inst/doc/GDALSQL.Rmd | 247 ++++- lazysf-0.4.0/lazysf/inst/doc/GDALSQL.html | 337 +++++-- lazysf-0.4.0/lazysf/inst/extdata/nc.dbf |only lazysf-0.4.0/lazysf/inst/extdata/nc.gpkg |only lazysf-0.4.0/lazysf/inst/extdata/nc.prj |only lazysf-0.4.0/lazysf/inst/extdata/nc.shp |only lazysf-0.4.0/lazysf/inst/extdata/nc.shx |only lazysf-0.4.0/lazysf/man/GDALSQL.Rd |only lazysf-0.4.0/lazysf/man/GDALVectorConnection-class.Rd |only lazysf-0.4.0/lazysf/man/GDALVectorDriver-class.Rd |only lazysf-0.4.0/lazysf/man/GDALVectorResult-class.Rd |only lazysf-0.4.0/lazysf/man/collect.tbl_GDALVectorConnection.Rd |only lazysf-0.4.0/lazysf/man/dbConnect-GDALVectorDriver-method.Rd |only lazysf-0.4.0/lazysf/man/lazysf-package.Rd | 15 lazysf-0.4.0/lazysf/man/lazysf.Rd | 91 +- lazysf-0.4.0/lazysf/man/reexports.Rd |only lazysf-0.4.0/lazysf/tests |only lazysf-0.4.0/lazysf/vignettes/GDALSQL.Rmd | 247 ++++- 47 files changed, 1396 insertions(+), 746 deletions(-)
Title: A Versatile Visualization Suite
Description: A visualization suite primarily designed for single-cell
RNA-sequencing data analysis applications but well-suited for
other purposes as well. It introduces novel plots to represent two-variable
and frequency data and optimizes some commonly used plotting options
(e.g., correlation, network, density, alluvial and volcano plots)
for ease of usage and flexibility.
Author: Andrei-Florian Stoica [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica@foxmail.com>
Diff between henna versions 0.7.5 dated 2026-02-17 and 0.8.5 dated 2026-07-13
DESCRIPTION | 6 ++--- MD5 | 36 +++++++++++++++---------------- R/documentation.R | 4 ++- R/label_points.R | 5 +--- R/rank_plot.R | 5 ++-- R/tile_plot.R | 43 ++++++++++++++++++++++---------------- README.md | 32 +++++++++++++--------------- inst/figures/correlation_plot.png |binary inst/figures/density_plot.png |binary inst/figures/hull_plot.png |binary inst/figures/network_plot.png |binary inst/figures/radial_plot.png |binary inst/figures/rank_plot.png |binary inst/figures/tile_plot.png |binary inst/figures/volcano_plot.png |binary man/documentFun.Rd | 5 +++- man/rankPlot.Rd | 5 +++- man/tilePlot.Rd | 18 ++++++++++++--- tests/testthat/test-henna.R | 12 ++++------ 19 files changed, 97 insertions(+), 74 deletions(-)
Title: Access and Work with HCUP Resources and Datasets
Description: A comprehensive R package for accessing and working with publicly
available and free resources from the Agency for Healthcare Research and Quality
(AHRQ) Healthcare Cost and Utilization Project (HCUP). The package provides
streamlined access to HCUP's Clinical Classifications Software Refined (CCSR)
mapping files and Summary Trend Tables, enabling researchers and analysts to
efficiently map ICD-10-CM diagnosis codes and ICD-10-PCS procedure codes to
CCSR categories and access HCUP statistical reports. Key features include:
direct download from HCUP website, multiple output formats (long/wide/default),
cross-classification support, version management, citation generation, and
intelligent caching. The package does not redistribute HCUP data files but
facilitates direct download from the official HCUP website, ensuring users
always have access to the latest versions and maintain compliance with HCUP
data use policies. This package only accesses free public tools and reports;
it does NOT a [...truncated...]
Author: Vikrant Dev Rathore [aut, cre]
Maintainer: Vikrant Dev Rathore <rathore.vikrant@gmail.com>
Diff between HCUPtools versions 1.0.1 dated 2026-05-11 and 1.0.2 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 10 ++++++++++ inst/CITATION | 30 +++++++++++++++++++++++------- inst/doc/HCUPtools.html | 4 ++-- 5 files changed, 42 insertions(+), 16 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor
Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to
a three-way or four-way data array. See Harshman and Lundy (1994):
<doi:10.1016/0167-9473(94)90132-5>. Classification using principal component
analysis (PCA) fit to a two-way data matrix is also supported. Uses component
weights from one mode of a Parafac, Parafac2, or PCA model as features to tune
parameters for one or more classification methods via a k-fold cross-validation
procedure. Allows for constraints on different tensor modes. Allows for
inclusion of additional features alongside features generated by the component
model. Supports penalized logistic regression, support vector machine, random
forest, feed-forward neural network, regularized discriminant analysis, and
gradient boosting machine. Supports binary and multiclass classification.
Predicts class labels or class probabilities and calculates multiple
classification performanc [...truncated...]
Author: Matthew A. Asisgress [aut, cre]
Maintainer: Matthew A. Asisgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.3.0 dated 2026-06-02 and 1.3.1 dated 2026-07-13
ChangeLog | 14 +++++++++++++- DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/pficpfa.R | 40 ++++++++++++++++++++++++++++++++-------- inst/doc/cpfa.pdf |binary man/cpfa.Rd | 3 ++- 6 files changed, 56 insertions(+), 19 deletions(-)
Title: High-Level Modeling Functions with 'torch'
Description: Provides high-level modeling functions to define and train
models using the 'torch' R package. Models include linear, logistic,
and multinomial regression as well as multilayer perceptrons.
Author: Max Kuhn [aut, cre] ,
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between brulee versions 1.1.0 dated 2026-07-02 and 1.1.1 dated 2026-07-13
DESCRIPTION | 6 +- MD5 | 41 +++++++++--------- NEWS.md | 8 +++ R/0_utils.R | 46 +++++++++++++++++++++ R/aaa.R | 46 --------------------- R/chronos2-fit.R | 20 +++++---- R/chronos2-misc.R | 25 ++++++++++- R/tabicl-download.R | 46 +++++++++++---------- R/tabicl-fit.R | 12 +++-- R/training_loop.R | 9 +++- README.md | 70 ++++++++++++++++++-------------- man/brulee_chronos.Rd | 17 ++++--- man/brulee_tab_icl.Rd | 12 +++-- man/tab_icl_download_weights.Rd | 9 ++-- tests/testthat/helper-chronos2.R | 7 ++- tests/testthat/setup.R | 5 -- tests/testthat/test-0_utils.R |only tests/testthat/test-autoint.R | 2 tests/testthat/test-chronos2-misc.R | 65 +++++++++++++++++++++++++++++ tests/testthat/test-resnet-regression.R | 35 ++++++++++++++++ tests/testthat/test-tabicl-download.R | 68 ++++++++++++++++++++++++++++--- tests/testthat/test-tabicl-fit.R | 4 - 22 files changed, 388 insertions(+), 165 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-11 1.1.0
2018-06-15 1.0.0
Title: Data Frames with Persistent Columns and Attributes
Description: Provides data frames that hold certain columns and attributes
persistently for data processing in 'dplyr'.
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>
Diff between stickyr versions 0.1.2 dated 2023-03-26 and 0.1.3 dated 2026-07-12
DESCRIPTION | 12 MD5 | 52 - NAMESPACE | 3 NEWS.md | 29 - R/distinct.R | 14 R/dplyr.R | 850 +++++++++++++++++--------------- R/mutate.R | 80 +-- R/select.R | 8 R/sticky_grouped_df.R | 26 R/sticky_rowwise_df.R | 26 R/sticky_tbl_df.R | 78 +- R/summarise.R | 13 R/utils.R | 74 ++ README.md | 54 +- man/as_sticky_tibble.Rd | 38 - man/is_sticky_tibble.Rd | 36 - man/new_sticky_tibble.Rd | 94 +-- man/reexports.Rd | 42 - tests/testthat/test-distinct.R | 33 - tests/testthat/test-group_by.R | 13 tests/testthat/test-mutate.R | 23 tests/testthat/test-select.R | 3 tests/testthat/test-slice.R | 3 tests/testthat/test-sticky_grouped_df.R | 10 tests/testthat/test-sticky_rowwise_df.R | 40 - tests/testthat/test-sticky_tbl_df.R | 35 - tests/testthat/test-summarise.R | 42 - 27 files changed, 923 insertions(+), 808 deletions(-)
Title: Predict Gender from Brazilian First Names
Description: A generalized method to predict and report gender from Brazilian first names
using the Brazilian Institute of Geography and Statistics' Census data and
neural networks.
Author: Fernando Meireles [aut, cre]
Maintainer: Fernando Meireles <fernando.meireles@iesp.uerj.br>
Diff between genderBR versions 1.3.0 dated 2026-03-30 and 1.4.0 dated 2026-07-12
genderBR-1.3.0/genderBR/inst |only genderBR-1.4.0/genderBR/DESCRIPTION | 10 genderBR-1.4.0/genderBR/MD5 | 30 +- genderBR-1.4.0/genderBR/NAMESPACE | 1 genderBR-1.4.0/genderBR/NEWS.md | 15 + genderBR-1.4.0/genderBR/R/get_gender.R | 33 ++ genderBR-1.4.0/genderBR/R/get_gender_nn.R | 115 +++++++--- genderBR-1.4.0/genderBR/R/model.R | 91 ++++--- genderBR-1.4.0/genderBR/R/utils.R | 31 ++ genderBR-1.4.0/genderBR/README.md | 6 genderBR-1.4.0/genderBR/man/get_gender.Rd | 32 ++ genderBR-1.4.0/genderBR/man/get_gender_nn.Rd | 19 + genderBR-1.4.0/genderBR/tests/testthat/test-encode-name.R |only genderBR-1.4.0/genderBR/tests/testthat/test-get_gender_nn-inputs.R | 18 + genderBR-1.4.0/genderBR/tests/testthat/test-predict-nn.R | 17 + genderBR-1.4.0/genderBR/tests/testthat/test-threshold.R |only genderBR-1.4.0/genderBR/tests/testthat/test_inputs.R | 2 17 files changed, 315 insertions(+), 105 deletions(-)
Title: Managing and Compiling Manuscript Templates
Description: Managing and generating standardised text for methods and results sections of scientific reports. It handles template variable substitution and supports hierarchical organisation of text through dot-separated paths. Databases are stored as JSON by default for version control and cross-language compatibility; trusted legacy RDS databases remain readable through import and migration utilities.
Author: Joseph Bulbulia [aut, cre]
Maintainer: Joseph Bulbulia <joseph.bulbulia@gmail.com>
Diff between boilerplate versions 1.3.0 dated 2025-06-24 and 1.4.0 dated 2026-07-12
DESCRIPTION | 10 MD5 | 131 +++++----- NEWS.md | 52 ++++ R/boilerplate_batch_edit_functions.R | 26 +- R/import-export-functions.R | 70 +---- R/import-functions.R | 128 +++++---- R/init-functions.R | 14 - R/json-support.R | 55 ++-- R/migration-utilities.R | 8 R/utilities.R | 32 ++ README.md | 119 +++++---- build/vignette.rds |binary inst/doc/boilerplate-architecture.Rmd | 21 + inst/doc/boilerplate-architecture.html | 22 + inst/doc/boilerplate-bibliography-workflow.R | 26 +- inst/doc/boilerplate-bibliography-workflow.Rmd | 44 +-- inst/doc/boilerplate-bibliography-workflow.html | 61 +--- inst/doc/boilerplate-getting-started.Rmd | 22 - inst/doc/boilerplate-getting-started.html | 42 +-- inst/doc/boilerplate-internals.Rmd | 8 inst/doc/boilerplate-internals.html | 12 inst/doc/boilerplate-intro-enhanced.R | 4 inst/doc/boilerplate-intro-enhanced.Rmd | 14 - inst/doc/boilerplate-intro-enhanced.html | 18 - inst/doc/boilerplate-intro.R | 6 inst/doc/boilerplate-intro.Rmd | 6 inst/doc/boilerplate-intro.html | 8 inst/doc/boilerplate-json-schema.Rmd | 27 +- inst/doc/boilerplate-json-schema.html | 39 +-- inst/doc/boilerplate-json-workflow.Rmd | 17 + inst/doc/boilerplate-json-workflow.html | 96 ++++--- inst/doc/boilerplate-measures-workflow.Rmd | 6 inst/doc/boilerplate-measures-workflow.html | 17 - inst/doc/boilerplate-projects.Rmd | 8 inst/doc/boilerplate-projects.html | 17 - inst/doc/boilerplate-quarto-workflow.Rmd | 8 inst/doc/boilerplate-quarto-workflow.html | 21 - inst/doc/version-management-section.R | 8 inst/doc/version-management-section.Rmd | 18 - inst/doc/version-management-section.html | 24 - man/boilerplate_batch_edit.Rd | 7 man/boilerplate_export.Rd | 10 man/boilerplate_import.Rd | 11 man/boilerplate_init.Rd | 10 man/boilerplate_save.Rd | 8 tests/testthat/test-batch-edit.R | 48 +++ tests/testthat/test-generate-text.R | 6 tests/testthat/test-import-export.R | 208 ++++++++++++---- tests/testthat/test-json-support.R | 285 +++++++++++----------- tests/testthat/test-migration-utilities.R | 84 ++++-- tests/testthat/test-rds-deprecation.R |only tests/testthat/test-version-management.R | 28 +- tests/testthat/test-vignette-internals.R | 2 tests/testthat/test-vignette-json-workflow.R | 22 + tests/testthat/test-vignette-version-management.R | 59 ++-- vignettes/boilerplate-architecture.Rmd | 21 + vignettes/boilerplate-bibliography-workflow.Rmd | 44 +-- vignettes/boilerplate-getting-started.Rmd | 22 - vignettes/boilerplate-internals.Rmd | 8 vignettes/boilerplate-intro-enhanced.Rmd | 14 - vignettes/boilerplate-intro.Rmd | 6 vignettes/boilerplate-json-schema.Rmd | 27 +- vignettes/boilerplate-json-workflow.Rmd | 17 + vignettes/boilerplate-measures-workflow.Rmd | 6 vignettes/boilerplate-projects.Rmd | 8 vignettes/boilerplate-quarto-workflow.Rmd | 8 vignettes/version-management-section.Rmd | 18 - 67 files changed, 1322 insertions(+), 930 deletions(-)
Title: A Theorical-Practical Approach to Parasitological Data Analysis
Description: Standardizes and streamlines the processing of parasitological data by integrating descriptive analyses of parasite count distributions, automated calculation of parasitological indices and their dispersion measures, and intuitive visualizations for representing these metrics (Bush et al. 1997 <doi:10.2307/3284227>, Reiczigel et al. 2019 <doi:10.1016/j.pt.2019.01.003>).
Author: Exequiel Oscar Furlan [aut] ,
Juan Manuel Cabrera [aut, cre, cph] ,
Elisa Helman [aut]
Maintainer: Juan Manuel Cabrera <juan.cabrera@uner.edu.ar>
Diff between parasiteR versions 1.0 dated 2026-05-13 and 1.1 dated 2026-07-12
DESCRIPTION | 13 +- MD5 | 40 +++--- NAMESPACE | 1 NEWS.md | 12 + R/para_abundance_CI.R | 87 ++++++++++---- R/para_aggregation_CI.R |only R/para_data.R | 2 R/para_descriptors.R | 28 +++- R/para_explo_abund.R | 30 ++++ R/para_explo_prev.R | 30 ++++ R/para_intensity_CI.R | 93 +++++++++++---- R/para_plot_CI.R | 276 ++++++++++++++++++++++++++++++--------------- R/para_prevalence_CI.R | 139 ++++++++++++++-------- man/para_abundance_CI.Rd | 29 +++- man/para_aggregation_CI.Rd |only man/para_data.Rd | 2 man/para_descriptors.Rd | 17 +- man/para_explo_abund.Rd | 10 + man/para_explo_prev.Rd | 10 + man/para_intensity_CI.Rd | 220 ++++++++++++++++++----------------- man/para_plot_CI.Rd | 33 +++-- man/para_prevalence_CI.Rd | 34 +++-- 22 files changed, 721 insertions(+), 385 deletions(-)
Title: Regularized Linear Models
Description: Algorithms compute robust estimators for loss functions in the concave convex (CC) family by the iteratively reweighted convex optimization (IRCO), an extension of the iteratively reweighted least squares (IRLS). The IRCO reduces the weight of the observation that leads to a large loss; it also provides weights to help identify outliers. Applications include robust (penalized) generalized linear models and robust support vector machines. The package also contains penalized Poisson, negative binomial, zero-inflated Poisson, zero-inflated negative binomial regression models and robust models with non-convex loss functions. Wang et al. (2014) <doi:10.1002/sim.6314>,
Wang et al. (2015) <doi:10.1002/bimj.201400143>,
Wang et al. (2016) <doi:10.1177/0962280214530608>,
Wang (2021) <doi:10.1007/s11749-021-00770-2>,
Wang (2024) <doi:10.1111/anzs.12409>.
Author: Zhu Wang [aut, cre],
Achim Zeileis [aut],
Simon Jackman [aut],
Brian Ripley [aut],
Patrick Breheny [aut]
Maintainer: Zhu Wang <zwang145@uthsc.edu>
Diff between mpath versions 0.4-2.26 dated 2024-06-27 and 0.4-2.27 dated 2026-07-12
mpath-0.4-2.26/mpath/inst/doc/brcancer.R |only mpath-0.4-2.26/mpath/inst/doc/brcancer.Rnw |only mpath-0.4-2.26/mpath/inst/doc/kkt.Rnw |only mpath-0.4-2.26/mpath/vignettes/brcancer.Rnw |only mpath-0.4-2.26/mpath/vignettes/german.pdf |only mpath-0.4-2.26/mpath/vignettes/irglmExample.pdf |only mpath-0.4-2.26/mpath/vignettes/irsvmExample.pdf |only mpath-0.4-2.26/mpath/vignettes/kkt.Rnw |only mpath-0.4-2.27/mpath/DESCRIPTION | 27 ++-- mpath-0.4-2.27/mpath/MD5 | 40 ++--- mpath-0.4-2.27/mpath/NAMESPACE | 2 mpath-0.4-2.27/mpath/R/glmreg.R | 121 ++++++++++++------ mpath-0.4-2.27/mpath/build/partial.rdb |binary mpath-0.4-2.27/mpath/build/vignette.rds |binary mpath-0.4-2.27/mpath/inst/doc/brcancer.pdf |binary mpath-0.4-2.27/mpath/inst/doc/index.html |only mpath-0.4-2.27/mpath/inst/doc/kkt.pdf |binary mpath-0.4-2.27/mpath/inst/doc/static_brcancer.pdf |binary mpath-0.4-2.27/mpath/inst/doc/static_german.pdf |binary mpath-0.4-2.27/mpath/inst/doc/static_irglmExample.pdf |binary mpath-0.4-2.27/mpath/inst/doc/static_irsvmExample.pdf |binary mpath-0.4-2.27/mpath/man/cv.irsvm_fit.Rd | 5 mpath-0.4-2.27/mpath/man/irglm.Rd | 4 mpath-0.4-2.27/mpath/man/irsvm_fit.Rd | 4 mpath-0.4-2.27/mpath/vignettes/README |only mpath-0.4-2.27/mpath/vignettes/mpath.bib | 40 +++-- 26 files changed, 154 insertions(+), 89 deletions(-)
Title: Distributional Synthetic Controls Estimation
Description: The method of synthetic controls is a widely-adopted tool for evaluating causal effects of policy changes in settings with observational data. In many settings where it is applicable, researchers want to identify causal effects of policy changes on a treated unit at an aggregate level while having access to data at a finer granularity. This package implements a simple extension of the synthetic controls estimator, developed in Gunsilius (2023) <doi:10.3982/ECTA18260>, that takes advantage of this additional structure and provides nonparametric estimates of the heterogeneity within the aggregate unit. The idea is to replicate the quantile function associated with the treated unit by a weighted average of quantile functions of the control units. The package contains tools for aggregating and plotting the resulting distributional estimates, as well as for carrying out inference on them.
Author: David Van Dijcke [aut, cre] ,
Florian Gunsilius [aut] ,
Siyun He [aut]
Maintainer: David Van Dijcke <dvdijcke@umich.edu>
Diff between DiSCos versions 0.1.3 dated 2026-03-07 and 0.1.4 dated 2026-07-12
DESCRIPTION | 6 +-- MD5 | 26 ++++++++--------- NEWS.md | 8 +++++ R/DiSCo.R | 7 +++- R/DiSCo_CI.R | 70 ++++++++++++++++++++++++++++++++++++++-------- R/DiSCo_iter.R | 30 +++++++++++++++++-- R/DiSCo_per.R | 8 +++-- R/DiSCo_per_iter.R | 12 +++++-- R/DiSCo_weights_reg.R | 19 ++++++++++-- R/utils.R | 39 +++++++++++++++++++++++++ build/partial.rdb |binary inst/doc/Dube2019.html | 4 +- man/DiSCo_weights_reg.Rd | 8 ++++- tests/testthat/Rplots.pdf | 4 +- 14 files changed, 195 insertions(+), 46 deletions(-)
Title: Graphical Web-Framework for Data Manipulation and Visualization
Description: A framework for data manipulation and visualization using a
web-based point and click user interface where analysis pipelines are decomposed into re-usable and parameterizable blocks.
Author: Nicolas Bennett [aut, cre],
David Granjon [aut],
Christoph Sax [aut],
Bristol Myers Squibb [fnd]
Maintainer: Nicolas Bennett <nicolas@cynkra.com>
Diff between blockr.core versions 0.1.2 dated 2026-04-28 and 0.1.3 dated 2026-07-12
blockr.core-0.1.2/blockr.core/tests/testthat/_snaps/utils-serve/rbind-001.json |only blockr.core-0.1.3/blockr.core/DESCRIPTION | 44 blockr.core-0.1.3/blockr.core/MD5 | 263 +- blockr.core-0.1.3/blockr.core/NAMESPACE | 117 blockr.core-0.1.3/blockr.core/NEWS.md | 79 blockr.core-0.1.3/blockr.core/R/block-args.R |only blockr.core-0.1.3/blockr.core/R/block-class.R | 260 +- blockr.core-0.1.3/blockr.core/R/block-meta.R |only blockr.core-0.1.3/blockr.core/R/block-registry.R | 257 +- blockr.core-0.1.3/blockr.core/R/block-roclet.R |only blockr.core-0.1.3/blockr.core/R/block-server.R | 453 ++- blockr.core-0.1.3/blockr.core/R/blocks-class.R | 10 blockr.core-0.1.3/blockr.core/R/board-class.R | 53 blockr.core-0.1.3/blockr.core/R/board-loader.R |only blockr.core-0.1.3/blockr.core/R/board-lock.R |only blockr.core-0.1.3/blockr.core/R/board-option.R | 17 blockr.core-0.1.3/blockr.core/R/board-options.R | 28 blockr.core-0.1.3/blockr.core/R/board-plugins.R | 20 blockr.core-0.1.3/blockr.core/R/board-server.R | 1174 ++++++--- blockr.core-0.1.3/blockr.core/R/board-ui.R | 2 blockr.core-0.1.3/blockr.core/R/data-block.R | 4 blockr.core-0.1.3/blockr.core/R/data-dataset.R | 15 blockr.core-0.1.3/blockr.core/R/file-block.R | 3 blockr.core-0.1.3/blockr.core/R/file-browser.R | 11 blockr.core-0.1.3/blockr.core/R/file-upload.R | 9 blockr.core-0.1.3/blockr.core/R/link-class.R | 48 blockr.core-0.1.3/blockr.core/R/links-class.R | 10 blockr.core-0.1.3/blockr.core/R/parser-block.R | 4 blockr.core-0.1.3/blockr.core/R/parser-csv.R | 14 blockr.core-0.1.3/blockr.core/R/plot-block.R | 4 blockr.core-0.1.3/blockr.core/R/plot-scatter.R | 15 blockr.core-0.1.3/blockr.core/R/plugin-block.R | 19 blockr.core-0.1.3/blockr.core/R/plugin-code.R | 48 blockr.core-0.1.3/blockr.core/R/plugin-control.R | 9 blockr.core-0.1.3/blockr.core/R/plugin-links.R | 45 blockr.core-0.1.3/blockr.core/R/plugin-notification.R | 163 - blockr.core-0.1.3/blockr.core/R/plugin-serdes.R | 39 blockr.core-0.1.3/blockr.core/R/plugin-stack.R | 14 blockr.core-0.1.3/blockr.core/R/plugin-stacks.R | 45 blockr.core-0.1.3/blockr.core/R/reactives.R |only blockr.core-0.1.3/blockr.core/R/stack-class.R | 61 blockr.core-0.1.3/blockr.core/R/stacks-class.R | 10 blockr.core-0.1.3/blockr.core/R/str-value.R |only blockr.core-0.1.3/blockr.core/R/text-glue.R | 15 blockr.core-0.1.3/blockr.core/R/transform-block.R | 4 blockr.core-0.1.3/blockr.core/R/transform-head.R | 15 blockr.core-0.1.3/blockr.core/R/transform-merge.R | 20 blockr.core-0.1.3/blockr.core/R/transform-rbind.R | 15 blockr.core-0.1.3/blockr.core/R/transform-subset.R | 16 blockr.core-0.1.3/blockr.core/R/utils-cnd.R | 104 blockr.core-0.1.3/blockr.core/R/utils-code.R | 5 blockr.core-0.1.3/blockr.core/R/utils-graph.R | 15 blockr.core-0.1.3/blockr.core/R/utils-logging.R | 12 blockr.core-0.1.3/blockr.core/R/utils-misc.R | 27 blockr.core-0.1.3/blockr.core/R/utils-serdes.R | 13 blockr.core-0.1.3/blockr.core/R/utils-serve.R | 108 blockr.core-0.1.3/blockr.core/R/utils-shiny.R | 75 blockr.core-0.1.3/blockr.core/R/utils-tests.R | 46 blockr.core-0.1.3/blockr.core/build/vignette.rds |binary blockr.core-0.1.3/blockr.core/inst/doc/blocks-registry.html | 80 blockr.core-0.1.3/blockr.core/inst/doc/blocks-registry.qmd | 28 blockr.core-0.1.3/blockr.core/inst/examples/block/rbind/app.R | 6 blockr.core-0.1.3/blockr.core/inst/registry |only blockr.core-0.1.3/blockr.core/man/block_metadata.Rd |only blockr.core-0.1.3/blockr.core/man/block_name.Rd | 30 blockr.core-0.1.3/blockr.core/man/block_roclet.Rd |only blockr.core-0.1.3/blockr.core/man/block_server.Rd | 72 blockr.core-0.1.3/blockr.core/man/block_ui.Rd | 4 blockr.core-0.1.3/blockr.core/man/blockr_abort.Rd | 4 blockr.core-0.1.3/blockr.core/man/blockr_option.Rd | 2 blockr.core-0.1.3/blockr.core/man/blockr_ser.Rd | 7 blockr.core-0.1.3/blockr.core/man/board_loader.Rd |only blockr.core-0.1.3/blockr.core/man/board_server.Rd | 12 blockr.core-0.1.3/blockr.core/man/board_ui.Rd | 6 blockr.core-0.1.3/blockr.core/man/board_update.Rd |only blockr.core-0.1.3/blockr.core/man/chr_ply.Rd | 6 blockr.core-0.1.3/blockr.core/man/ctrl_block.Rd | 5 blockr.core-0.1.3/blockr.core/man/edit_block.Rd | 2 blockr.core-0.1.3/blockr.core/man/edit_stack.Rd | 2 blockr.core-0.1.3/blockr.core/man/generate_code.Rd | 2 blockr.core-0.1.3/blockr.core/man/get_session.Rd | 9 blockr.core-0.1.3/blockr.core/man/locked-board.Rd |only blockr.core-0.1.3/blockr.core/man/manage_blocks.Rd | 2 blockr.core-0.1.3/blockr.core/man/manage_links.Rd | 2 blockr.core-0.1.3/blockr.core/man/manage_stacks.Rd | 2 blockr.core-0.1.3/blockr.core/man/new_block.Rd | 33 blockr.core-0.1.3/blockr.core/man/new_block_arg.Rd |only blockr.core-0.1.3/blockr.core/man/new_board_options.Rd | 5 blockr.core-0.1.3/blockr.core/man/new_data_block.Rd | 8 blockr.core-0.1.3/blockr.core/man/new_file_block.Rd | 7 blockr.core-0.1.3/blockr.core/man/new_link.Rd | 20 blockr.core-0.1.3/blockr.core/man/new_parser_block.Rd | 5 blockr.core-0.1.3/blockr.core/man/new_plot_block.Rd | 9 blockr.core-0.1.3/blockr.core/man/new_stack.Rd | 20 blockr.core-0.1.3/blockr.core/man/new_transform_block.Rd | 9 blockr.core-0.1.3/blockr.core/man/notify_user.Rd | 24 blockr.core-0.1.3/blockr.core/man/preserve_board.Rd | 17 blockr.core-0.1.3/blockr.core/man/rand_names.Rd | 2 blockr.core-0.1.3/blockr.core/man/register_block.Rd | 47 blockr.core-0.1.3/blockr.core/man/serve.Rd | 7 blockr.core-0.1.3/blockr.core/man/stack_ui.Rd | 6 blockr.core-0.1.3/blockr.core/man/str_value.Rd |only blockr.core-0.1.3/blockr.core/man/testing.Rd | 6 blockr.core-0.1.3/blockr.core/man/topo_sort.Rd | 3 blockr.core-0.1.3/blockr.core/man/trim_rv.Rd |only blockr.core-0.1.3/blockr.core/man/write_log.Rd | 15 blockr.core-0.1.3/blockr.core/tests/testthat/setup-chrome-ci.R |only blockr.core-0.1.3/blockr.core/tests/testthat/test-block-args.R |only blockr.core-0.1.3/blockr.core/tests/testthat/test-block-class.R | 179 - blockr.core-0.1.3/blockr.core/tests/testthat/test-block-meta.R |only blockr.core-0.1.3/blockr.core/tests/testthat/test-block-registry.R | 10 blockr.core-0.1.3/blockr.core/tests/testthat/test-block-roclet.R |only blockr.core-0.1.3/blockr.core/tests/testthat/test-block-server.R | 239 + blockr.core-0.1.3/blockr.core/tests/testthat/test-blocks-class.R | 47 blockr.core-0.1.3/blockr.core/tests/testthat/test-board-class.R | 96 blockr.core-0.1.3/blockr.core/tests/testthat/test-board-lock.R |only blockr.core-0.1.3/blockr.core/tests/testthat/test-board-option.R | 20 blockr.core-0.1.3/blockr.core/tests/testthat/test-board-options.R | 17 blockr.core-0.1.3/blockr.core/tests/testthat/test-board-plugins.R | 22 blockr.core-0.1.3/blockr.core/tests/testthat/test-board-server.R | 1262 ++++++++-- blockr.core-0.1.3/blockr.core/tests/testthat/test-link-class.R | 15 blockr.core-0.1.3/blockr.core/tests/testthat/test-links-class.R | 19 blockr.core-0.1.3/blockr.core/tests/testthat/test-plugin-block.R | 2 blockr.core-0.1.3/blockr.core/tests/testthat/test-plugin-blocks.R | 83 blockr.core-0.1.3/blockr.core/tests/testthat/test-plugin-code.R | 69 blockr.core-0.1.3/blockr.core/tests/testthat/test-plugin-control.R | 23 blockr.core-0.1.3/blockr.core/tests/testthat/test-plugin-links.R | 328 ++ blockr.core-0.1.3/blockr.core/tests/testthat/test-plugin-notification.R | 252 + blockr.core-0.1.3/blockr.core/tests/testthat/test-plugin-serdes.R | 353 ++ blockr.core-0.1.3/blockr.core/tests/testthat/test-plugin-stack.R | 2 blockr.core-0.1.3/blockr.core/tests/testthat/test-plugin-stacks.R | 260 +- blockr.core-0.1.3/blockr.core/tests/testthat/test-reactives.R |only blockr.core-0.1.3/blockr.core/tests/testthat/test-stack-class.R | 33 blockr.core-0.1.3/blockr.core/tests/testthat/test-stacks-class.R | 14 blockr.core-0.1.3/blockr.core/tests/testthat/test-text-glue.R | 4 blockr.core-0.1.3/blockr.core/tests/testthat/test-transform-rbind.R | 192 + blockr.core-0.1.3/blockr.core/tests/testthat/test-utils-cnd.R | 65 blockr.core-0.1.3/blockr.core/tests/testthat/test-utils-graph.R | 20 blockr.core-0.1.3/blockr.core/tests/testthat/test-utils-logging.R | 23 blockr.core-0.1.3/blockr.core/tests/testthat/test-utils-serdes.R | 63 blockr.core-0.1.3/blockr.core/tests/testthat/test-utils-serve.R | 8 blockr.core-0.1.3/blockr.core/tests/testthat/test-utils-shiny.R | 143 + blockr.core-0.1.3/blockr.core/tests/testthat/test-utils-tests.R |only blockr.core-0.1.3/blockr.core/tests/testthat/test-visibility-gating.R |only blockr.core-0.1.3/blockr.core/vignettes/blocks-registry.qmd | 28 145 files changed, 6448 insertions(+), 1826 deletions(-)
Title: Convert Tibbles or Data Frames to Xts Easily
Description: Facilitate the movement between data frames to 'xts'. Particularly
useful when moving from 'tidyverse' to the widely used 'xts' package, which is
the input format of choice to various other packages. It also allows the user
to use a 'spread_by' argument for a character column 'xts' conversion.
Author: Nico Katzke [aut, cre]
Maintainer: Nico Katzke <nfkatzke@gmail.com>
Diff between tbl2xts versions 1.0.4 dated 2021-01-12 and 1.0.6 dated 2026-07-12
DESCRIPTION | 11 +-- MD5 | 16 ++-- R/tbl_xts.R | 9 +- R/xts_tbl.R | 4 - README.md | 63 +++++++---------- build/vignette.rds |binary inst/doc/tbl2xts_vignette.html | 147 ++++++++++++++++++++--------------------- man/tbl_xts.Rd | 4 - man/xts_tbl.Rd | 4 - 9 files changed, 124 insertions(+), 134 deletions(-)
Title: An R Interface to the 'ROPTLIB' Library for Riemannian Manifold
Optimization
Description: An R interface to version 0.3 of the 'ROPTLIB' optimization library
(see <https://www.math.fsu.edu/~whuang2/> for more information). Optimize
real-valued functions over manifolds such as Stiefel, Grassmann, and
symmetric positive definite matrices. For details see Martin et al. (2020)
<doi:10.18637/jss.v093.i01>. Note that the optional 'ldr' package used in
some of this package's examples can be obtained from either the article
<doi:10.18637/jss.v061.i03> or from the 'ldr' package
<https://cran.r-project.org/package=ldr>.
Author: Kofi P. Adragni [aut, cph],
Sean R. Martin [aut, cre, cph],
Andrew M. Raim [aut, cph],
Wen Huang [aut, cph]
Maintainer: Sean R. Martin <sean.martin@jhuapl.edu>
Diff between ManifoldOptim versions 1.0.1 dated 2021-12-14 and 1.0.2 dated 2026-07-12
ManifoldOptim-1.0.1/ManifoldOptim/R/ManifoldOptim-package.R |only ManifoldOptim-1.0.2/ManifoldOptim/DESCRIPTION | 38 +-- ManifoldOptim-1.0.2/ManifoldOptim/MD5 | 78 +++--- ManifoldOptim-1.0.2/ManifoldOptim/NAMESPACE | 26 +- ManifoldOptim-1.0.2/ManifoldOptim/R/manifold_optim.R | 112 ++++------ ManifoldOptim-1.0.2/ManifoldOptim/R/manifolds.R | 38 +-- ManifoldOptim-1.0.2/ManifoldOptim/R/package.R |only ManifoldOptim-1.0.2/ManifoldOptim/R/params.R | 27 +- ManifoldOptim-1.0.2/ManifoldOptim/R/util.R | 7 ManifoldOptim-1.0.2/ManifoldOptim/man/Design-of-C-plus-plus-code.Rd | 29 ++ ManifoldOptim-1.0.2/ManifoldOptim/man/Manifold-definitions.Rd | 14 - ManifoldOptim-1.0.2/ManifoldOptim/man/Problem-definition.Rd | 10 ManifoldOptim-1.0.2/ManifoldOptim/man/get.deriv.params.Rd | 6 ManifoldOptim-1.0.2/ManifoldOptim/man/get.manifold.params.Rd | 2 ManifoldOptim-1.0.2/ManifoldOptim/man/get.solver.params.Rd | 11 ManifoldOptim-1.0.2/ManifoldOptim/man/manifold.optim.Rd | 66 +++-- ManifoldOptim-1.0.2/ManifoldOptim/src/Makevars | 4 ManifoldOptim-1.0.2/ManifoldOptim/src/Makevars.win | 25 -- ManifoldOptim-1.0.2/ManifoldOptim/src/ManifoldOptim/Util.cpp | 6 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/Grassmann/Grassmann.cpp | 25 +- ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/L2Sphere/L2Sphere.cpp | 10 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/LowRank/LowRank.cpp | 11 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/Manifold.cpp | 6 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/ProductElement.cpp | 2 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/ProductManifold.cpp | 4 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/SPDManifold.cpp | 4 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/SharedSpace.cpp | 2 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/SharedSpace.h | 5 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/SmartSpace.cpp | 5 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/SmartSpace.h | 5 ManifoldOptim-1.0.2/ManifoldOptim/src/Manifolds/Stiefel/Stiefel.cpp | 29 +- ManifoldOptim-1.0.2/ManifoldOptim/src/Problems/ElasticCurvesRO/DriverElasticCurvesRO.cpp | 4 ManifoldOptim-1.0.2/ManifoldOptim/src/Problems/ElasticCurvesRO/ElasticCurvesRO.cpp | 2 ManifoldOptim-1.0.2/ManifoldOptim/src/Problems/GrassRQ/GrassRQ.cpp | 4 ManifoldOptim-1.0.2/ManifoldOptim/src/Problems/ObliqueTestSparsePCA/ObliqueTestSparsePCA.cpp | 2 ManifoldOptim-1.0.2/ManifoldOptim/src/Problems/Problem.cpp | 5 ManifoldOptim-1.0.2/ManifoldOptim/src/Problems/StieBrockett/StieBrockett.cpp | 4 ManifoldOptim-1.0.2/ManifoldOptim/src/Problems/StieSoftICA/StieSoftICA.cpp | 5 ManifoldOptim-1.0.2/ManifoldOptim/src/Problems/StieSumBrockett/StieSumBrockett.cpp | 6 ManifoldOptim-1.0.2/ManifoldOptim/src/Solvers/RTRSR1.cpp | 2 ManifoldOptim-1.0.2/ManifoldOptim/src/Solvers/SolversLS.cpp | 10 41 files changed, 340 insertions(+), 311 deletions(-)
Title: Retrieve and Analyze Clinical Trials Data from Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<https://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Protocols, statistical analysis plans, informed consent sheets and other
documents in registers associated with trials can also be downloaded.
Other functions implement trial concepts canonically across registers,
identify deduplicated records, easily find and extract variables
(fields) of interest even from complex nested data as used by the
r [...truncated...]
Author: Ralf Herold [aut, cre] ,
Marek Kubica [cph] ,
Ivan Bozhanov [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.26.1 dated 2026-03-08 and 1.26.2 dated 2026-07-12
DESCRIPTION | 13 MD5 | 108 +- NEWS.md | 10 R/ctrGenerateQueries.R | 6 R/ctrGetQueryUrl.R | 20 R/ctrLoadQueryIntoDb.R | 21 R/ctrLoadQueryIntoDbCtgov2.R | 24 R/ctrLoadQueryIntoDbCtis.R | 16 R/ctrLoadQueryIntoDbEuctr.R | 6 R/ctrLoadQueryIntoDbIsrctn.R | 12 R/ctrRerunQuery.R | 26 R/ctrdata-package.R | 14 R/ctrdata-registers.R | 23 R/ctrdata-trial-concepts.R | 4 R/dbFindIdsUniqueTrials.R | 29 R/dbGetFieldsIntoDf.R | 7 R/dbQueryHistory.R | 6 R/dfName2Value.R | 5 R/f_likelyPlatformTrial.R | 12 R/f_primaryEndpointDescription.R | 2 R/f_primaryEndpointResults.R | 10 R/f_sampleSize.R | 20 R/f_sponsorType.R | 6 R/util_fields.R | 9 R/util_functions.R | 141 ++- README.md | 59 + build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 14 inst/doc/ctrdata_install.R | 9 inst/doc/ctrdata_install.Rmd | 19 inst/doc/ctrdata_install.html | 30 inst/doc/ctrdata_retrieve.html | 729 +++++++++---------- inst/doc/ctrdata_summarise.R | 2 inst/doc/ctrdata_summarise.Rmd | 2 inst/doc/ctrdata_summarise.html | 11 inst/tinytest/more_test_ctrdata_duckdb_ctis.R | 3 inst/tinytest/more_test_ctrdata_duckdb_euctr.R | 3 inst/tinytest/more_test_ctrdata_duckdb_isrctn.R | 3 inst/tinytest/setup_ctrdata.R | 4 inst/tinytest/test_ctrdata_duckdb_ctgov2.R | 3 inst/tinytest/test_ctrdata_function_trial-concepts.R | 8 inst/tinytest/test_ctrdata_function_various.R | 12 inst/tinytest/test_error_trials_euctr.txt | 340 ++++---- inst/tinytest/test_euctr_error_sample.R | 39 - man/ctrLoadQueryIntoDb.Rd | 4 man/ctrdata-package.Rd | 7 man/ctrdata-registers.Rd | 21 man/ctrdata-trial-concepts.Rd | 4 man/ctrdata.Rd | 17 man/dbFindIdsUniqueTrials.Rd | 15 man/f.likelyPlatformTrial.Rd | 10 man/f.sampleSize.Rd | 3 vignettes/ctrdata_install.Rmd | 19 vignettes/ctrdata_summarise.Rmd | 2 55 files changed, 1101 insertions(+), 841 deletions(-)
Title: Gaussian and Student-t Copula Models for Count Time Series
Description: Provides likelihood-based inference for Gaussian and Student-t
copula models for univariate count time series. Supports Poisson,
negative binomial, binomial, beta-binomial, and zero-inflated
marginals with ARMA dependence structures. Includes simulation,
maximum-likelihood estimation, residual diagnostics, and predictive
inference. Implements Time Series Minimax Exponential Tilting (TMET)
<doi:10.1016/j.csda.2026.108344>, an adaptation of minimax exponential
tilting of Botev (2017) <doi:10.1111/rssb.12162>. Also provides a
linear-cost implementation of the Geweke–Hajivassiliou–Keane (GHK)
simulator following Masarotto and Varin (2012) <doi:10.1214/12-EJS721>,
and the Continuous Extension (CE) approximation of Nguyen and
De Oliveira (2025) <doi:10.1080/02664763.2025.2498502>. The package
follows the S3 design philosophy of 'gcmr' but is developed independently.
Author: Quynh Nguyen [aut, cre]
Maintainer: Quynh Nguyen <nqnhu2209@gmail.com>
Diff between gctsc versions 0.2.4 dated 2026-05-20 and 0.2.5 dated 2026-07-12
gctsc-0.2.4/gctsc/LICENSE |only gctsc-0.2.5/gctsc/DESCRIPTION | 14 gctsc-0.2.5/gctsc/MD5 | 89 ++--- gctsc-0.2.5/gctsc/R/cormat.R | 24 + gctsc-0.2.5/gctsc/R/data.R | 61 +++ gctsc-0.2.5/gctsc/R/loglik_ghk.R | 15 gctsc-0.2.5/gctsc/R/loglik_tmet.R | 66 +--- gctsc-0.2.5/gctsc/R/main.R | 101 +++--- gctsc-0.2.5/gctsc/R/marginals.R | 62 ++-- gctsc-0.2.5/gctsc/R/methods-print.R | 2 gctsc-0.2.5/gctsc/R/pmvt.R | 2 gctsc-0.2.5/gctsc/R/prediction.R | 209 ++++++------- gctsc-0.2.5/gctsc/R/residuals.R | 2 gctsc-0.2.5/gctsc/R/simulate-gctsc.R | 2 gctsc-0.2.5/gctsc/data/KCMR.rda |only gctsc-0.2.5/gctsc/data/KCWC.rda |binary gctsc-0.2.5/gctsc/data/campyl.rda |binary gctsc-0.2.5/gctsc/data/rota.rda |binary gctsc-0.2.5/gctsc/inst/doc/gctsc_vignette.R | 23 - gctsc-0.2.5/gctsc/inst/doc/gctsc_vignette.Rmd | 23 - gctsc-0.2.5/gctsc/inst/doc/gctsc_vignette.html | 215 +++++++------- gctsc-0.2.5/gctsc/inst/examples/gaussian/Beta-Binomial.R | 73 ++-- gctsc-0.2.5/gctsc/inst/examples/gaussian/Binomial.R | 33 +- gctsc-0.2.5/gctsc/inst/examples/gaussian/NB.R | 39 -- gctsc-0.2.5/gctsc/inst/examples/gaussian/Poisson.R | 30 - gctsc-0.2.5/gctsc/inst/examples/gaussian/ZIB.R | 49 +-- gctsc-0.2.5/gctsc/inst/examples/gaussian/ZIBB.R | 90 ++--- gctsc-0.2.5/gctsc/inst/examples/gaussian/ZIP.R | 17 - gctsc-0.2.5/gctsc/inst/examples/student_t/Beta-Binomial.R | 32 -- gctsc-0.2.5/gctsc/inst/examples/student_t/Binomial.R | 16 - gctsc-0.2.5/gctsc/inst/examples/student_t/ZIB.R | 54 --- gctsc-0.2.5/gctsc/inst/examples/student_t/ZIBB.R | 58 --- gctsc-0.2.5/gctsc/inst/examples/student_t/ZIP.R | 17 - gctsc-0.2.5/gctsc/man/KCMR.Rd |only gctsc-0.2.5/gctsc/man/KCWC.Rd | 19 + gctsc-0.2.5/gctsc/man/arma.cormat.Rd | 6 gctsc-0.2.5/gctsc/man/campyl.Rd | 9 gctsc-0.2.5/gctsc/man/gctsc.Rd | 8 gctsc-0.2.5/gctsc/man/gctsc.opts.Rd | 7 gctsc-0.2.5/gctsc/man/marginal.gctsc.Rd | 45 +- gctsc-0.2.5/gctsc/man/pmvt.Rd | 2 gctsc-0.2.5/gctsc/man/predict.gctsc.Rd | 62 ++-- gctsc-0.2.5/gctsc/man/residuals.gctsc.Rd | 2 gctsc-0.2.5/gctsc/man/rota.Rd | 9 gctsc-0.2.5/gctsc/man/summary.gctsc.Rd | 2 gctsc-0.2.5/gctsc/tests/testthat/test-MLE.R |only gctsc-0.2.5/gctsc/tests/testthat/test-loglik.R |only gctsc-0.2.5/gctsc/vignettes/gctsc_vignette.Rmd | 23 - 48 files changed, 729 insertions(+), 883 deletions(-)
Title: Calculate Concentration and Dispersion in Ordered Rating Scales
Description: Calculates concentration and dispersion in ordered rating scales. It implements various measures of concentration and dispersion to describe what researchers variably call agreement, concentration, consensus, dispersion, or polarization among respondents in ordered data. It also implements other related measures to classify distributions. In addition to a generic city-block based concentration measure and a generic dispersion measure, the package implements various measures, including van der Eijk's (2001) <DOI: 10.1023/A:1010374114305> measure of agreement A, measures of concentration by Leik, Tatsle and Wierman, Blair and Lacy, Kvalseth, Berry and Mielke, Reardon, and Garcia-Montalvo and Reynal-Querol. Furthermore, the package provides an implementation of Galtungs AJUS-system to classify distributions, as well as a function to identify the position of multiple modes.
Author: Didier Ruedin [aut, cre] ,
Clem Aeppli [ctb]
Maintainer: Didier Ruedin <didier.ruedin@unine.ch>
Diff between agrmt versions 1.42.19 dated 2026-04-08 and 1.42.21 dated 2026-07-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 8 ++++++++ build/vignette.rds |binary inst/doc/agrmt.R | 2 -- inst/doc/agrmt.Rnw | 2 +- inst/doc/agrmt.pdf |binary vignettes/agrmt.Rnw | 2 +- 8 files changed, 21 insertions(+), 15 deletions(-)
Title: Tissot Indicatrix for Map Projection Distortion
Description: Compute and visualize the 'Tissot Indicatrix' for map projections.
The indicatrix characterizes projection distortion by computing scale
factors, angular deformation, areal distortion, and convergence at
arbitrary points. Based on the calculations shared by Bill Huber on
<https://gis.stackexchange.com/a/5075/482>. Uses 'PROJ' for coordinate
transformation and distortion factor computation.
Developed using the method published in Snyder, JP (1987) <doi:10.3133/pp1395>.
Author: Michael Sumner [aut, cre, cph] ,
Bill Huber [aut]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between tissot versions 0.2.0 dated 2026-02-12 and 0.3.0 dated 2026-07-12
DESCRIPTION | 22 +- MD5 | 77 ++++----- NAMESPACE | 9 - NEWS.md | 34 ++++ R/tissot-package.R | 2 R/tissot.R | 236 +++++++++++++++++------------ R/tissot_map.R | 29 ++- R/tissot_raster.R |only R/utils.R | 24 ++ README.md | 235 ++++++++++++++++++---------- build/partial.rdb |binary man/figures/README-aeqd-1.png |binary man/figures/README-angle_deformation-1.png |binary man/figures/README-coloured-1.png |binary man/figures/README-laea-1.png |binary man/figures/README-lcc-1.png |binary man/figures/README-mercator-1.png |binary man/figures/README-mollweide-1.png |binary man/figures/README-polar-1.png |binary man/figures/README-polar-proj-1.png |binary man/figures/README-robinson-1.png |binary man/figures/README-single2-1.png |binary man/figures/README-single3-1.png |binary man/figures/README-topleft-1.png |binary man/figures/README-utm-1.png |binary man/figures/README-utm55-1.png |binary man/figures/README-very-bad-trouble-1.png |binary man/figures/README-very-bad-trouble-2.png |binary man/figures/README-very-bad-trouble-3.png |binary man/indicatrix.Rd | 6 man/plot.indicatrix.Rd | 4 man/plot.indicatrix_list.Rd | 2 man/ti_ellipse.Rd | 9 + man/tissot-package.Rd | 5 man/tissot.Rd | 43 +++-- man/tissot_get_proj.Rd | 11 - man/tissot_map.Rd | 6 man/tissot_raster.Rd |only man/tissot_unproject.Rd | 4 tests/testthat/test-tissot-raster.R |only tests/testthat/test-tissot.R | 13 + 41 files changed, 500 insertions(+), 271 deletions(-)
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
'lbfgsb_cpp' is a 'C++' port around by Pascal Have of 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Yann Richet [aut, cre] ,
Pascal Have [aut],
Yves Deville [aut],
Conrad Sanderson [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Mike Smith [ctb]
Maintainer: Yann Richet <yann.richet@asnr.fr>
Diff between rlibkriging versions 1.1-0 dated 2026-07-11 and 1.1-1 dated 2026-07-12
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 8 ++++++++ src/libK/cmake/update_version.sh | 2 +- src/libK/tools/common/before_script.sh | 2 +- src/libK/tools/linux-macos/install.sh | 2 +- src/libK/tools/linux-macos/loadenv.sh | 2 +- src/libK/tools/linux-macos/test.sh | 2 +- tests/test-NestedKriging.R | 4 ++-- tools/setup.sh | 8 ++++++++ 10 files changed, 37 insertions(+), 21 deletions(-)
Title: Actuarial Functions for Non-Life Insurance Modelling
Description: Assists actuaries and other insurance modellers in pricing,
reserving and capital modelling for non-life insurance and
reinsurance modelling. Provides functions that help model
excess levels, capping and pure Incurred but not reported
claims (pure IBNR).
Includes capped mean, exposure curves and increased limit
factor curves (ILFs) for LogNormal, Gamma, Pareto, Sliced
LogNormal-Pareto and Sliced Gamma-Pareto distributions.
Includes mean, probability density function (pdf), cumulative
probability function (cdf) and inverse cumulative probability
function for Sliced LogNormal-Pareto and Sliced Gamma-Pareto
distributions.
Includes calculating pure IBNR exposure with LogNormal and
Gamma distribution for reporting delay.
Includes three shiny tools, one to simulate insurance claims applying
reinsurance structures, fit generalised linear models and fit claims
frequency or severity distributions.
Methods used in the package refer to
Free for All by Yiannis Parizas (2023) <https://www.theact [...truncated...]
Author: Yiannis Parizas [aut, cre]
Maintainer: Yiannis Parizas <yiannis.parizas@gmail.com>
Diff between NetSimR versions 0.1.5 dated 2023-12-02 and 0.1.6 dated 2026-07-12
NetSimR-0.1.5/NetSimR/man/NetSimR.Rd |only NetSimR-0.1.6/NetSimR/DESCRIPTION | 11 NetSimR-0.1.6/NetSimR/MD5 | 76 NetSimR-0.1.6/NetSimR/NAMESPACE | 14 NetSimR-0.1.6/NetSimR/R/GLMFittingToolServer.R | 8 NetSimR-0.1.6/NetSimR/R/GLMFittingToolUI.R | 778 ++++++++-- NetSimR-0.1.6/NetSimR/R/NetSimR.R | 5 NetSimR-0.1.6/NetSimR/R/ShinySimulatorGlobal.R | 176 +- NetSimR-0.1.6/NetSimR/R/ShinySimulatorServer.R | 106 + NetSimR-0.1.6/NetSimR/R/ShinySimulatorUI.R | 169 +- NetSimR-0.1.6/NetSimR/R/distribution_fitting_tool_Server.R | 6 NetSimR-0.1.6/NetSimR/R/distribution_fitting_tool_UI.R | 2 NetSimR-0.1.6/NetSimR/build/vignette.rds |binary NetSimR-0.1.6/NetSimR/inst/doc/CappedMean.R | 6 NetSimR-0.1.6/NetSimR/inst/doc/CappedMean.Rmd | 6 NetSimR-0.1.6/NetSimR/inst/doc/CappedMean.html | 95 - NetSimR-0.1.6/NetSimR/inst/doc/PureIBNR.R | 5 NetSimR-0.1.6/NetSimR/inst/doc/PureIBNR.Rmd | 7 NetSimR-0.1.6/NetSimR/inst/doc/PureIBNR.html | 14 NetSimR-0.1.6/NetSimR/inst/doc/SlicedDistributions.Rmd | 2 NetSimR-0.1.6/NetSimR/inst/doc/SlicedDistributions.html | 9 NetSimR-0.1.6/NetSimR/inst/rmd/ShinySimulatorReport.Rmd | 269 ++- NetSimR-0.1.6/NetSimR/man/GLMFittingToolServer.Rd | 42 NetSimR-0.1.6/NetSimR/man/GLMFittingToolUI.Rd | 33 NetSimR-0.1.6/NetSimR/man/NetSimR-package.Rd |only NetSimR-0.1.6/NetSimR/man/distribution_fitting_tool_Server.Rd | 42 NetSimR-0.1.6/NetSimR/man/distribution_fitting_tool_UI.Rd | 33 NetSimR-0.1.6/NetSimR/man/freq_dist_options.Rd | 5 NetSimR-0.1.6/NetSimR/man/freq_dist_parameter_placeholders.Rd | 5 NetSimR-0.1.6/NetSimR/man/max_number_of_pareto_slices.Rd | 5 NetSimR-0.1.6/NetSimR/man/reinsurance_structures_options.Rd | 5 NetSimR-0.1.6/NetSimR/man/run_shiny_distribution_fitting_tool.Rd | 28 NetSimR-0.1.6/NetSimR/man/run_shiny_glm_fitting_tool.Rd | 28 NetSimR-0.1.6/NetSimR/man/sev_dist_options.Rd | 5 NetSimR-0.1.6/NetSimR/man/sev_dist_parameter_placeholders.Rd | 5 NetSimR-0.1.6/NetSimR/man/shiny_simulator_ui.Rd | 9 NetSimR-0.1.6/NetSimR/man/simulate_function.Rd | 15 NetSimR-0.1.6/NetSimR/vignettes/CappedMean.Rmd | 6 NetSimR-0.1.6/NetSimR/vignettes/PureIBNR.Rmd | 7 NetSimR-0.1.6/NetSimR/vignettes/SlicedDistributions.Rmd | 2 40 files changed, 1440 insertions(+), 599 deletions(-)
Title: Fast and Unified Synthetic Control Methods
Description: A unified 'Formula' interface to the Synthetic Control Method
(SCM) and related panel-data causal inference estimators: Synthetic
Difference-in-Differences (SDID), Generalized Synthetic Control (GSC),
Matrix Completion (MC), Time-Aware Synthetic Control (TASC), and Synthetic
Interventions (SI), together with an experimental-design variant.
Computational bottlenecks (quadratic programming, singular value
decomposition, and Kalman filtering) are implemented in 'C++' via
'RcppArmadillo'. Methods are described in Abadie, Diamond and Hainmueller
(2010) <doi:10.1198/jasa.2009.ap08746>, Arkhangelsky, Athey, Hirshberg,
Imbens and Wager (2021) <doi:10.1257/aer.20190159>, Xu (2017)
<doi:10.1017/pan.2016.2>, Athey, Bayati, Doudchenko, Imbens and Khosravi
(2021) <doi:10.1080/01621459.2021.1891924>, and Agarwal, Shah and Shen
(2025) <doi:10.1287/opre.2025.1590>.
Author: Yosuke Abe [aut, cre]
Maintainer: Yosuke Abe <yosuke.abe0507@gmail.com>
Diff between coresynth versions 0.2.4 dated 2026-07-04 and 0.3.0 dated 2026-07-12
DESCRIPTION | 6 MD5 | 66 ++-- NAMESPACE | 19 + NEWS.md | 435 ++++++++++++++++---------- R/RcppExports.R | 1 R/accessors.R |only R/broom.R | 108 +++--- R/conformal.R | 520 +++++++++++++++----------------- R/coresynth-package.R | 24 - R/export.R | 355 +++++++++++---------- R/gsc.R | 8 R/plot.R | 430 +++++++++++++++++++++----- R/scm.R | 62 ++- R/scm_design.R | 100 ++++-- R/scm_fit.R | 65 +++- R/sdid.R | 4 R/si.R | 8 README.md | 123 +++++-- inst/doc/coresynth.R | 5 inst/doc/coresynth.Rmd | 9 inst/doc/coresynth.html | 13 man/figures/README-placebo-gaps-1.png |only man/figures/README-placebo-ratios-1.png |only man/figures/README-plot-gap-1.png |binary man/figures/README-plot-trend-1.png |binary man/figures/README-plot-weights-1.png |binary man/mspe_ratio_pval.Rd | 11 man/plot.coresynth.Rd | 100 ++++-- man/plot.scm_placebo.Rd |only man/scm_design.Rd | 13 man/scm_fit.Rd | 4 man/scm_placebo_cpp.Rd | 1 man/treated_outcomes.Rd |only src/inference.cpp | 6 tests/testthat/test-integration.R | 331 ++++++++++++++++++++ tests/testthat/test-object-model.R |only vignettes/coresynth.Rmd | 9 37 files changed, 1908 insertions(+), 928 deletions(-)
Title: Controlled Interrupted Time Series Analysis and Visualization
Description: Implements controlled interrupted time series (CITS) analysis for evaluating interventions in comparative time-series data.
The package provides tools for preparing panel time-series datasets, fitting models using generalized least squares (GLS) with optional autoregressive–moving-average (ARMA) error structures,
and computing fitted values and robust standard errors using cluster-robust variance estimators (CR2).
Visualization functions enable clear presentation of estimated effects and counterfactual trajectories following interventions.
Background on methods for causal inference in interrupted time series can be found in Linden and Adams (2011) <doi:10.1111/j.1365-2753.2010.01504.x>
and Lopez Bernal, Cummins, and Gasparrini (2018) <doi:10.1093/ije/dyy135>.
Author: Hanmin Gu [aut, cre]
Maintainer: Hanmin Gu <ghm21@yonsei.ac.kr>
Diff between citsr versions 0.1.3 dated 2025-12-22 and 0.1.4 dated 2026-07-12
DESCRIPTION | 12 +++---- MD5 | 10 +++--- build/vignette.rds |binary inst/doc/citsr_cits_methodology.html | 4 +- inst/doc/citsr_examples.R | 54 +++++++++++++++++------------------ inst/doc/citsr_examples.html | 8 +---- 6 files changed, 42 insertions(+), 46 deletions(-)
Title: Easily Extract Data from 'StatsWales'
Description: Download data from the 'StatsWales' public API
(<https://api.stats.gov.wales/v2>) into R. Provides functions to list,
search, and browse datasets by topic, retrieve data with optional
filtering, sorting, and pivoting, and download datasets as CSV or Excel
files.
Author: Jamie Ralph [aut, cre]
Maintainer: Jamie Ralph <jamesryanralph@outlook.com>
Diff between statswalesr versions 0.2.0 dated 2022-04-03 and 1.0.0 dated 2026-07-12
DESCRIPTION | 25 +- LICENSE | 4 MD5 | 52 +++-- NAMESPACE | 19 + NEWS.md | 98 +++++++--- R/statswales_create_query.R |only R/statswales_download_dataset.R |only R/statswales_get_dataset.R | 283 +++++++++++------------------ R/statswales_get_filters.R |only R/statswales_get_metadata.R | 127 ++----------- R/statswales_get_pivot.R |only R/statswales_get_query.R |only R/statswales_get_topic.R |only R/statswales_list_datasets.R |only R/statswales_list_topics.R |only R/statswales_search.R | 181 +++++++----------- R/statswalesr-package.R |only R/utils.R |only README.md | 238 +++++++++++++++++------- man/figures |only man/statswales_create_query.Rd |only man/statswales_download_dataset.Rd |only man/statswales_get_dataset.Rd | 127 +++++++++---- man/statswales_get_filters.Rd |only man/statswales_get_metadata.Rd | 58 +++-- man/statswales_get_pivot.Rd |only man/statswales_get_query.Rd |only man/statswales_get_topic.Rd |only man/statswales_list_datasets.Rd |only man/statswales_list_topics.Rd |only man/statswales_search.Rd | 75 ++++--- man/statswalesr-package.Rd |only tests/testthat.R | 8 tests/testthat/helper-api.R |only tests/testthat/test-get-data.R | 360 +++++++++++++++++++++++++++++++++++-- tests/testthat/test-search.R | 61 +++++- tests/testthat/test-utils.R |only tests/testthat/test-welsh-lang.R | 66 +++--- 38 files changed, 1127 insertions(+), 655 deletions(-)
Title: Rich Text Format ('RTF') Output
Description: A set of R functions to output Rich Text Format ('RTF') files with high resolution tables and graphics that may be edited with a standard word processor such as Microsoft Word.
Author: Michael E. Schaffer [aut, cph],
Kyun-Seop Bae [ctb, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
This is a re-admission after prior archival of version 0.4-14.1 dated 2020-03-22
Diff between rtf versions 0.4-14.1 dated 2020-03-22 and 0.4-15 dated 2026-07-12
rtf-0.4-14.1/rtf/NEWS |only rtf-0.4-14.1/rtf/build |only rtf-0.4-14.1/rtf/inst/doc/rtf.Rnw |only rtf-0.4-14.1/rtf/tests |only rtf-0.4-14.1/rtf/vignettes |only rtf-0.4-15/rtf/DESCRIPTION | 25 rtf-0.4-15/rtf/MD5 | 71 rtf-0.4-15/rtf/NAMESPACE | 50 rtf-0.4-15/rtf/NEWS.md |only rtf-0.4-15/rtf/R/000.R | 24 rtf-0.4-15/rtf/R/999.NonDocumentedObjects.R | 92 rtf-0.4-15/rtf/R/999.package.R | 94 rtf-0.4-15/rtf/R/forest.plot.R | 208 - rtf-0.4-15/rtf/R/rtf.R | 3114 +++++++++++++-------------- rtf-0.4-15/rtf/README.md | 48 rtf-0.4-15/rtf/inst/doc/rtf-manual.pdf |only rtf-0.4-15/rtf/inst/doc/rtf.R | 64 rtf-0.4-15/rtf/inst/doc/rtf.pdf |binary rtf-0.4-15/rtf/man/Non-documented_objects.Rd | 102 rtf-0.4-15/rtf/man/RTF.Rd | 232 +- rtf-0.4-15/rtf/man/addHeader.RTF.Rd | 80 rtf-0.4-15/rtf/man/addNewLine.RTF.Rd | 74 rtf-0.4-15/rtf/man/addPageBreak.RTF.Rd | 90 rtf-0.4-15/rtf/man/addParagraph.RTF.Rd | 72 rtf-0.4-15/rtf/man/addPlot.RTF.Rd | 114 rtf-0.4-15/rtf/man/addPng.RTF.Rd | 86 rtf-0.4-15/rtf/man/addSessionInfo.RTF.Rd | 94 rtf-0.4-15/rtf/man/addTOC.RTF.Rd | 72 rtf-0.4-15/rtf/man/addTable.RTF.Rd | 118 - rtf-0.4-15/rtf/man/addText.RTF.Rd | 76 rtf-0.4-15/rtf/man/addTrellisObject.RTF.Rd | 126 - rtf-0.4-15/rtf/man/decreaseIndent.RTF.Rd | 72 rtf-0.4-15/rtf/man/done.RTF.Rd | 72 rtf-0.4-15/rtf/man/endParagraph.RTF.Rd | 72 rtf-0.4-15/rtf/man/increaseIndent.RTF.Rd | 72 rtf-0.4-15/rtf/man/rtf-package.Rd | 118 - rtf-0.4-15/rtf/man/rtf.forest.plot.Rd | 146 - rtf-0.4-15/rtf/man/setFontSize.RTF.Rd | 74 rtf-0.4-15/rtf/man/startParagraph.RTF.Rd | 72 rtf-0.4-15/rtf/man/view.RTF.Rd | 80 40 files changed, 2950 insertions(+), 2954 deletions(-)
Title: Core Mathematical Functions for Multi-Objective Optimization
Description: Fast implementations of mathematical operations and performance metrics for multi-objective optimization, including filtering and ranking of dominated vectors according to Pareto optimality, hypervolume metric, C.M. Fonseca, L. Paquete, M. López-Ibáñez (2006) <doi:10.1109/CEC.2006.1688440>, epsilon indicator, inverted generational distance, computation of the empirical attainment function, V.G. da Fonseca, C.M. Fonseca, A.O. Hall (2001) <doi:10.1007/3-540-44719-9_15>, and Vorob'ev threshold, expectation and deviation, M. Binois, D. Ginsbourger, O. Roustant (2015) <doi:10.1016/j.ejor.2014.07.032>, among others.
Author: Manuel Lopez-Ibanez [aut, cre] ,
Carlos Fonseca [ctb],
Luis Paquete [ctb],
Andreia P. Guerreiro [ctb],
Mickael Binois [ctb],
Michael H. Buselli [cph] ,
Wessel Dankers [cph] ,
NumPy Developers [cph] ,
Jean-Sebastien Roy [cph] ,
Makoto Matsumoto [cph] [...truncated...]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between moocore versions 0.3.1 dated 2026-05-04 and 0.3.2 dated 2026-07-12
DESCRIPTION | 6 - MD5 | 73 +++++++++---------- NEWS.md | 9 ++ R/epsilon.R | 3 R/hv.R | 18 ++-- R/hv_approx.R | 4 + R/igd.R | 14 ++- R/nondominated.R | 18 ++-- R/normalise.R | 2 R/utils.R | 6 + R/whv.R | 24 +++--- R/zzz.R | 5 + README.md | 15 ++-- build/partial.rdb |binary man/hypervolume.Rd | 13 +-- man/igd.Rd | 10 +- man/macros/macros.Rd | 2 man/whv_rect.Rd | 28 +++---- src/Rmoocore.c | 35 +++++++++ src/init.c | 6 + src/init.h | 1 src/libmoocore/Makefile | 42 ++++++++--- src/libmoocore/NEWS.md | 8 ++ src/libmoocore/config.h | 7 + src/libmoocore/epsilon.h | 5 - src/libmoocore/gcc.mk | 8 +- src/libmoocore/hv.c | 21 ++--- src/libmoocore/hv.h | 2 src/libmoocore/hv3d_priv.h | 2 src/libmoocore/hvapprox.c | 123 ++++++++++++++++----------------- src/libmoocore/igd.h | 2 src/libmoocore/nondominated.h | 46 ++++-------- src/libmoocore/nondominated_kung.h | 95 +++++++++++++------------ src/libmoocore/pareto.c | 2 src/libmoocore/sort.h | 19 ++--- src/libmoocore/whv.c | 4 - tests/testthat/test-doctest-whv_rect.R |only tests/testthat/test-whv.R | 16 ---- 38 files changed, 403 insertions(+), 291 deletions(-)
Title: A 'C++20' API for R
Description: A header-only 'C++20' API for manipulating R data structures
from 'C++'. Provides 'C++20' concepts specific to R, custom scalar and
vector classes with built-in NA handling, automatic object protection,
'SIMD' (single-instruction-multiple-data), parallelisation, and a
streamlined system for registering 'C++' functions, including
templates, to R. Full API reference and documentation are available at
<https://nicchr.github.io/cppally/>.
Author: Nick Christofides [aut, cre, cph] ,
Martin Leitner-Ankerl [cph] ,
Malte Skarupke [cph] ,
Posit Software, PBC [cph]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cppally versions 1.0.0 dated 2026-07-02 and 1.1.0 dated 2026-07-12
cppally-1.0.0/cppally/inst/include/cppally/r_df_methods.h |only cppally-1.0.0/cppally/inst/include/cppally/r_list_helpers.h |only cppally-1.1.0/cppally/DESCRIPTION | 6 cppally-1.1.0/cppally/MD5 | 114 cppally-1.1.0/cppally/NEWS.md | 335 - cppally-1.1.0/cppally/R/cpp_source.R | 6 cppally-1.1.0/cppally/R/register.R | 7 cppally-1.1.0/cppally/inst/doc/cppally.R | 2 cppally-1.1.0/cppally/inst/doc/cppally.Rmd | 2998 +++++----- cppally-1.1.0/cppally/inst/doc/cppally.html | 25 cppally-1.1.0/cppally/inst/doc/functionals.Rmd | 870 +- cppally-1.1.0/cppally/inst/doc/protection.html | 24 cppally-1.1.0/cppally/inst/doc/vector_name_hashing.html | 28 cppally-1.1.0/cppally/inst/include/cppally.hpp | 4 cppally-1.1.0/cppally/inst/include/cppally/r_attrs.h | 28 cppally-1.1.0/cppally/inst/include/cppally/r_coerce.h | 6 cppally-1.1.0/cppally/inst/include/cppally/r_coerce_scalars.h | 102 cppally-1.1.0/cppally/inst/include/cppally/r_concepts.h | 133 cppally-1.1.0/cppally/inst/include/cppally/r_cplx.h | 12 cppally-1.1.0/cppally/inst/include/cppally/r_date.h | 51 cppally-1.1.0/cppally/inst/include/cppally/r_dbl.h | 21 cppally-1.1.0/cppally/inst/include/cppally/r_df.h | 3 cppally-1.1.0/cppally/inst/include/cppally/r_dispatch.h | 180 cppally-1.1.0/cppally/inst/include/cppally/r_factor.h | 2 cppally-1.1.0/cppally/inst/include/cppally/r_hash_names.h | 10 cppally-1.1.0/cppally/inst/include/cppally/r_identical.h | 16 cppally-1.1.0/cppally/inst/include/cppally/r_int.h | 20 cppally-1.1.0/cppally/inst/include/cppally/r_int64.h | 20 cppally-1.1.0/cppally/inst/include/cppally/r_length.h | 2 cppally-1.1.0/cppally/inst/include/cppally/r_lgl.h | 61 cppally-1.1.0/cppally/inst/include/cppally/r_limits.h | 4 cppally-1.1.0/cppally/inst/include/cppally/r_nas.h | 56 cppally-1.1.0/cppally/inst/include/cppally/r_pmap.h | 11 cppally-1.1.0/cppally/inst/include/cppally/r_protect.h | 123 cppally-1.1.0/cppally/inst/include/cppally/r_psxct.h | 40 cppally-1.1.0/cppally/inst/include/cppally/r_raw.h | 12 cppally-1.1.0/cppally/inst/include/cppally/r_scalar_ops.h | 314 - cppally-1.1.0/cppally/inst/include/cppally/r_setup.h | 9 cppally-1.1.0/cppally/inst/include/cppally/r_sexp_types.h | 12 cppally-1.1.0/cppally/inst/include/cppally/r_str.h | 23 cppally-1.1.0/cppally/inst/include/cppally/r_utils.h | 42 cppally-1.1.0/cppally/inst/include/cppally/r_vec.h | 15 cppally-1.1.0/cppally/inst/include/cppally/r_vec_ops.h | 106 cppally-1.1.0/cppally/inst/include/cppally/r_vec_utils.h | 31 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_combine.h | 2 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_df_methods.h |only cppally-1.1.0/cppally/inst/include/cppally/sugar/r_equal.h | 2 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_hash.h | 4 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_list_helpers.h |only cppally-1.1.0/cppally/inst/include/cppally/sugar/r_math.h | 174 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_paste.h | 2 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_recycle.h | 2 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_rep.h | 12 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_seq.h | 19 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_sort.h | 4 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_stats.h | 44 cppally-1.1.0/cppally/inst/include/cppally/sugar/r_subset.h | 13 cppally-1.1.0/cppally/inst/include/cppally_light.hpp | 2 cppally-1.1.0/cppally/vignettes/cppally.Rmd | 2998 +++++----- cppally-1.1.0/cppally/vignettes/functionals.Rmd | 870 +- 60 files changed, 5272 insertions(+), 4760 deletions(-)
Title: Beta Regression
Description: Beta regression for modeling beta-distributed dependent variables on the open unit interval (0, 1),
e.g., rates and proportions, see Cribari-Neto and Zeileis (2010) <doi:10.18637/jss.v034.i02>.
Moreover, extended-support beta regression models can accommodate dependent variables with
boundary observations at 0 and/or 1, see Kosmidis and Zeileis (2025) <doi:10.1093/jrsssc/qlaf039>.
For the classical beta regression model, alternative specifications are provided:
Bias-corrected and bias-reduced estimation, finite mixture models, and recursive partitioning for
beta regression, see Grün, Kosmidis, and Zeileis (2012) <doi:10.18637/jss.v048.i11>.
Author: Achim Zeileis [aut, cre] ,
Francisco Cribari-Neto [aut] ,
Bettina Gruen [aut] ,
Ioannis Kosmidis [aut] ,
Alexandre B. Simas [ctb] ,
Andrea V. Rocha [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between betareg versions 3.2-4 dated 2025-08-19 and 3.2-5 dated 2026-07-12
DESCRIPTION | 8 - MD5 | 36 +++--- NEWS.md | 9 + R/betareg.R | 4 R/leverage.R | 4 README.md | 6 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 - inst/doc/betareg-ext.html | 173 +++++++++++++++++++++++++++--- inst/doc/betareg.html | 205 ++++++++++++++++++++++++++++++------ man/LossAversion.Rd | 6 - man/ReadingSkills.Rd | 8 - man/betar_family.Rd | 6 - man/betareg.Rd | 6 - man/residuals.betareg.Rd | 4 tests/Examples/betareg-Ex.Rout.save | 2 tests/betatree.R | 3 tests/betatree.Rout.save | 3 19 files changed, 390 insertions(+), 99 deletions(-)
Title: Helper Tools for Australian Hydrologists
Description: Functions to speed up work flow for hydrological analysis.
Focused on Australian climate data (SILO climate data), hydrological models (eWater Source) and in particular South Australia (<https://water.data.sa.gov.au> hydrological data).
Author: Matt Gibbs [aut, cre]
Maintainer: Matt Gibbs <gibbs.ms@gmail.com>
Diff between SWTools versions 1.1.0 dated 2024-10-14 and 1.1.1 dated 2026-07-12
DESCRIPTION | 6 MD5 | 28 NEWS.md | 6 R/HydstraSiteDetails.R | 4 R/SILO.R | 4 R/SILOCheckConsistency.R | 42 R/SILOCorrectSite.R | 8 inst/extdata/24001.txt | 2564 +++++++++++++++++++++++++++++++------------- inst/extdata/24002.txt | 2564 +++++++++++++++++++++++++++++++------------- inst/extdata/24003.txt | 2564 +++++++++++++++++++++++++++++++------------- man/AQWPDownload.Rd | 2 man/HydstraSiteDetails.Rd | 2 man/SILOCheckConsistency.Rd | 2 man/SILOReport.Rd | 5 man/SILOSitesfromPolygon.Rd | 68 - 15 files changed, 5594 insertions(+), 2275 deletions(-)
Title: Reproduce Statistical Analyses and Meta-Analyses
Description: Includes data analysis and meta-analysis functions (e.g., to
calculate effect sizes and 95% Confidence Intervals (CI) on Standardised
Effect Sizes (d) for AB/BA cross-over repeated-measures experimental
designs), data presentation functions (e.g., density curve overlaid on
histogram),and the data sets analyzed in different research papers in
software engineering (e.g., related to software defect prediction or multi-
site experiment concerning the extent to which structured abstracts were
clearer and more complete than conventional abstracts) to streamline
reproducible research in software engineering.
Author: Lech Madeyski [cre, aut, ctb] ,
Barbara Kitchenham [aut, ctb] ,
Tomasz Lewowski [aut, ctb] ,
Marian Jureczko [ctb] ,
David Budgen [ctb] ,
Pearl Brereton [ctb] ,
Jacky Keung [ctb] ,
Stuart Charters [ctb] ,
Shirley Gibbs [ctb] ,
Amnart Pohthong [ctb] , [...truncated...]
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>
Diff between reproducer versions 0.6.0 dated 2026-06-09 and 0.7.0 dated 2026-07-12
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++++------ NAMESPACE | 4 ++++ NEWS.md | 8 ++++++++ R/LLM4ScreenLitMetrics.R |only R/reproducer.R | 5 +++-- README.md | 6 +++--- inst/CITATION | 19 +++++++++++++++++++ man/compute_mcc.Rd |only man/compute_wmcc.Rd |only man/llm4screenlit_metrics.Rd |only man/wmcc_sensitivity.Rd |only tests/testthat/test-LLM4ScreenLitMetrics.R |only 13 files changed, 53 insertions(+), 15 deletions(-)
Title: 'rcpp' Wrapper for 'mecab' Library
Description: R package based on 'Rcpp' for 'MeCab': Yet Another Part-of-Speech and Morphological Analyzer.
The purpose of this package is providing a seamless developing and analyzing environment for CJK texts.
This package utilizes parallel programming for providing highly efficient text preprocessing 'posParallel()' function.
For installation, please refer to README.md file.
Author: Junhewk Kim [aut, cre],
Taku Kudo [aut],
Akiru Kato [ctb],
Patrick Schratz [ctb]
Maintainer: Junhewk Kim <junhewk.kim@gmail.com>
Diff between RcppMeCab versions 0.0.1.5 dated 2026-03-24 and 0.0.1.6 dated 2026-07-12
DESCRIPTION | 7 ++++--- MD5 | 16 ++++++++++------ NAMESPACE | 1 + NEWS.md | 5 +++++ R/RcppExports.R | 4 ++++ R/dictionary.R |only README.md | 6 ++++++ man/dictionary_info.Rd |only src/RcppExports.cpp | 13 +++++++++++++ src/dictionaryInfoRcpp.cpp |only tests/testthat/test_dictionary_info.R |only 11 files changed, 43 insertions(+), 9 deletions(-)
Title: Data Validation Based on 'YAML' Rules
Description: A comprehensive data validation package that allows comparing
datasets using configurable validation rules defined in 'YAML' files.
Built on top of the 'pointblank' package for robust data validation, it
supports exact matching, tolerance-based numeric comparisons, text
normalization, and row count validation.
Author: Vincent Guyader [cre, aut] ,
ThinkR [cph],
Agence technique de l'information sur l'hospitalisation [spn]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between datadiff versions 0.5.0 dated 2026-06-18 and 0.6.0 dated 2026-07-12
datadiff-0.5.0/datadiff/R/globals.R |only datadiff-0.5.0/datadiff/inst/templates |only datadiff-0.5.0/datadiff/man/or_operator.Rd |only datadiff-0.5.0/datadiff/tests/testthat/rules.yaml |only datadiff-0.5.0/datadiff/tests/testthat/test-huge-parquet.R |only datadiff-0.5.0/datadiff/tests/testthat/test.yaml |only datadiff-0.6.0/datadiff/DESCRIPTION | 8 datadiff-0.6.0/datadiff/MD5 | 128 datadiff-0.6.0/datadiff/NAMESPACE | 66 datadiff-0.6.0/datadiff/NEWS.md | 990 +++-- datadiff-0.6.0/datadiff/R/compare_datasets_from_yaml.R | 1575 +++++--- datadiff-0.6.0/datadiff/R/constants.R |only datadiff-0.6.0/datadiff/R/coverage.R | 309 - datadiff-0.6.0/datadiff/R/data_types.R | 6 datadiff-0.6.0/datadiff/R/datadiff-result.R |only datadiff-0.6.0/datadiff/R/duplicate_keys.R | 130 datadiff-0.6.0/datadiff/R/fast_path.R | 212 - datadiff-0.6.0/datadiff/R/pointblank_setup.R | 317 - datadiff-0.6.0/datadiff/R/preprocessing.R | 66 datadiff-0.6.0/datadiff/R/report.R | 592 +-- datadiff-0.6.0/datadiff/R/tolerance.R | 675 ++- datadiff-0.6.0/datadiff/R/utils.R | 109 datadiff-0.6.0/datadiff/R/validation.R | 21 datadiff-0.6.0/datadiff/README.md | 891 ++-- datadiff-0.6.0/datadiff/build/vignette.rds |binary datadiff-0.6.0/datadiff/inst/WORDLIST | 88 datadiff-0.6.0/datadiff/inst/doc/datadiff.R | 16 datadiff-0.6.0/datadiff/inst/doc/datadiff.Rmd | 1901 +++++----- datadiff-0.6.0/datadiff/inst/doc/datadiff.html | 968 ++--- datadiff-0.6.0/datadiff/man/compare_datasets_from_yaml.Rd | 280 - datadiff-0.6.0/datadiff/man/datadiff_report_html.Rd | 56 datadiff-0.6.0/datadiff/man/detect_column_types.Rd | 7 datadiff-0.6.0/datadiff/man/preprocess_dataframe.Rd | 9 datadiff-0.6.0/datadiff/man/print.datadiff_coverage.Rd | 40 datadiff-0.6.0/datadiff/man/print.datadiff_report.Rd | 42 datadiff-0.6.0/datadiff/man/setup_pointblank_agent.Rd | 175 datadiff-0.6.0/datadiff/man/validate_row_counts.Rd | 14 datadiff-0.6.0/datadiff/man/write_rules_template.Rd | 167 datadiff-0.6.0/datadiff/tests/testthat/helper-equivalence.R | 200 - datadiff-0.6.0/datadiff/tests/testthat/test-arrow-dataset-to-duckdb.R |only datadiff-0.6.0/datadiff/tests/testthat/test-avoidable-scans.R |only datadiff-0.6.0/datadiff/tests/testthat/test-boolean-column-guards.R |only datadiff-0.6.0/datadiff/tests/testthat/test-coverage.R | 506 +- datadiff-0.6.0/datadiff/tests/testthat/test-default-rules.R | 6 datadiff-0.6.0/datadiff/tests/testthat/test-duplicate-keys.R | 206 - datadiff-0.6.0/datadiff/tests/testthat/test-edge-cases.R | 1705 ++++---- datadiff-0.6.0/datadiff/tests/testthat/test-equivalence-guard.R | 348 - datadiff-0.6.0/datadiff/tests/testthat/test-extract-diagnostics.R |only datadiff-0.6.0/datadiff/tests/testthat/test-extraction-params.R | 111 datadiff-0.6.0/datadiff/tests/testthat/test-factor-columns.R |only datadiff-0.6.0/datadiff/tests/testthat/test-fast_path.R | 68 datadiff-0.6.0/datadiff/tests/testthat/test-input-validation.R | 423 +- datadiff-0.6.0/datadiff/tests/testthat/test-internal-coverage.R | 110 datadiff-0.6.0/datadiff/tests/testthat/test-internal-helpers.R |only datadiff-0.6.0/datadiff/tests/testthat/test-key-parameter.R | 689 +-- datadiff-0.6.0/datadiff/tests/testthat/test-lazy-aggregates.R |only datadiff-0.6.0/datadiff/tests/testthat/test-lazy-sql-bool.R | 194 - datadiff-0.6.0/datadiff/tests/testthat/test-lazy-tables.R | 1834 ++++----- datadiff-0.6.0/datadiff/tests/testthat/test-main-integration.R | 664 +-- datadiff-0.6.0/datadiff/tests/testthat/test-main.R | 189 datadiff-0.6.0/datadiff/tests/testthat/test-na-equality-semantics.R |only datadiff-0.6.0/datadiff/tests/testthat/test-nan-inf-sql-equivalence.R |only datadiff-0.6.0/datadiff/tests/testthat/test-pointblank-setup.R | 353 + datadiff-0.6.0/datadiff/tests/testthat/test-report-extracts-dir.R |only datadiff-0.6.0/datadiff/tests/testthat/test-report-robustness.R |only datadiff-0.6.0/datadiff/tests/testthat/test-report.R | 808 ++-- datadiff-0.6.0/datadiff/tests/testthat/test-response-field.R |only datadiff-0.6.0/datadiff/tests/testthat/test-row-validation.R | 274 - datadiff-0.6.0/datadiff/tests/testthat/test-temp-tables.R |only datadiff-0.6.0/datadiff/tests/testthat/test-template-parameters.R | 392 +- datadiff-0.6.0/datadiff/tests/testthat/test-tolerance-kernel.R | 142 datadiff-0.6.0/datadiff/tests/testthat/test-tolerance-ok.R | 172 datadiff-0.6.0/datadiff/tests/testthat/test-tolerance.R | 1312 +++--- datadiff-0.6.0/datadiff/tests/testthat/test-utils.R | 285 - datadiff-0.6.0/datadiff/tests/testthat/test-yaml-arg-precedence.R |only datadiff-0.6.0/datadiff/vignettes/datadiff.Rmd | 1901 +++++----- 76 files changed, 12277 insertions(+), 10473 deletions(-)
Title: Ecological Indices Calculator for Nematode Communities
Description: Provides a computational toolkit for analyzing nematode communities in ecological studies.
Includes methods to quantify nematode-based ecological indicators such as metabolic footprints,
energy flow metrics, and community structure. These tools support assessments of soil health,
ecosystem functioning, and trophic interactions, standardizing the use of nematodes as
bioindicators.
Author: Yuxuan He [aut, cre] ,
Dong Wang [ths],
Yuan Miao [ths]
Maintainer: Yuxuan He <heyuxuan0525@outlook.com>
Diff between Nematode versions 0.3.0 dated 2026-04-07 and 0.3.1 dated 2026-07-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/nematode_metabolic_footprints.R | 8 ++++---- README.md | 5 ++++- 5 files changed, 23 insertions(+), 13 deletions(-)
Title: Make Your 'targets' Pipelines into a Package
Description: Runs 'targets' pipelines bundled inside a package and caches
the results in the R user cache directory, so that users of the package
do not need to rerun the pipeline themselves. Package authors can update
the cached results at any time by releasing a new package version.
Author: Mizuki Uchida [aut, cre, cph]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>
This is a re-admission after prior archival of version 0.1.1 dated 2025-06-22
Diff between tarchives versions 0.1.1 dated 2025-06-22 and 0.2.0 dated 2026-07-12
DESCRIPTION | 26 +- LICENSE | 4 MD5 | 84 ++++-- NAMESPACE | 30 +- NEWS.md | 14 + R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/tar_archive.R | 106 +++++++- R/tar_archive_pipelines.R |only R/tar_destroy_archive.R |only R/tar_load_archive.R |only R/tar_make_archive.R | 12 R/tar_manifest_archive.R |only R/tar_meta_archive.R |only R/tar_read_archive.R | 19 + R/tar_source_archive.R | 13 - R/tar_target_archive.R | 87 ++++-- R/tarchives-package.R | 1 R/use_tarchives.R | 29 ++ README.md | 13 - inst/tarchives/R/utils.R | 10 inst/tarchives/example-model/_targets.R | 4 inst/tarchives/example-plot/R/plot.R | 13 - inst/tarchives/example-plot/_targets.R | 2 man/tar_archive.Rd | 143 ++++++----- man/tar_archive_pipelines.Rd |only man/tar_archive_script.Rd | 94 +++---- man/tar_archive_store.Rd | 62 ++-- man/tar_destroy_archive.Rd |only man/tar_load_archive.Rd |only man/tar_make_archive.Rd | 349 ++++++++++++++-------------- man/tar_manifest_archive.Rd |only man/tar_meta_archive.Rd |only man/tar_read_archive.Rd | 16 + man/tar_source_archive.Rd | 72 +++-- man/tar_target_archive.Rd | 37 ++ man/tarchives-package.Rd | 44 ++- man/use_tarchives.Rd | 54 ++-- tests/testthat/_snaps |only tests/testthat/setup.R |only tests/testthat/test-tar_archive.R | 5 tests/testthat/test-tar_archive_pipelines.R |only tests/testthat/test-tar_destroy_archive.R |only tests/testthat/test-tar_load_archive.R |only tests/testthat/test-tar_make_archive.R | 58 +++- tests/testthat/test-tar_manifest_archive.R |only tests/testthat/test-tar_meta_archive.R |only tests/testthat/test-tar_read_archive.R | 11 tests/testthat/test-tar_source_archive.R | 28 +- tests/testthat/test-tar_target_archive.R |only tests/testthat/test-use_tarchives.R |only 51 files changed, 896 insertions(+), 544 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates,
and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae
parameterised by Cholesky factors of covariance or precision matrices are implemented
for interval-censored and exact data, or a mix thereof. Score functions for these
log-likelihoods are available. A class representing multiple lower triangular matrices
and corresponding methods are part of this package.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] ,
Martin Maechler [ctb] ,
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.4-1 dated 2026-06-06 and 1.4-2 dated 2026-07-12
DESCRIPTION | 7 +++---- MD5 | 18 +++++++++--------- build/partial.rdb |binary build/vignette.rds |binary cleanup | 4 ++++ inst/NEWS.Rd | 8 ++++++++ inst/doc/MVT_Rnews.pdf |binary inst/doc/lmvnorm_src.pdf |binary tests/bugfix-tests.R | 2 +- tests/bugfix-tests.Rout.save | 6 +++--- 10 files changed, 28 insertions(+), 17 deletions(-)
Title: Isotope Origin Clustering and Assignment Tools
Description: This resource provides tools to create, compare, and post-process
spatial isotope assignment models of animal origin. It generates
probability-of-origin maps for individuals based on user-provided tissue and
environment isotope values (e.g., as generated by IsoMAP, Bowen et al. [2013]
<doi:10.1111/2041-210X.12147>) using the framework established in Bowen et al.
(2010) <doi:10.1146/annurev-earth-040809-152429>). The package 'isocat' can then
quantitatively compare and cluster these maps to group individuals by
similar origin. It also includes techniques for applying four approaches
(cumulative sum, odds ratio, quantile only, and quantile simulation) with
which users can summarize geographic origins and probable distance traveled
by individuals. Campbell et al. [2020] establishes several of the functions
included in this package <doi:10.1515/ami-2020-0004>.
Author: Caitlin Campbell [aut, cre]
Maintainer: Caitlin Campbell <caitjcampbell@gmail.com>
Diff between isocat versions 1.0.0 dated 2026-07-09 and 1.0.1 dated 2026-07-12
DESCRIPTION | 6 +- MD5 | 20 ++++----- NEWS.md | 56 ++++++++++++++++++++++----- R/isotopeAssignmentModel.R | 2 R/schoenersD.R | 13 +++--- R/simmatrixMaker.R | 4 - README.md | 5 ++ inst/doc/isocat.html | 7 +-- tests/testthat/helper-isocat.R | 22 ++++++++++ tests/testthat/test-isotopeAssignmentModel.R | 12 +++++ tests/testthat/test-simmatrix.R | 43 ++++++++++++++++++++ 11 files changed, 156 insertions(+), 34 deletions(-)
Title: Set Alpha Based on Sample Size Using Bayes Factors
Description: Sets the alpha level for coefficients in a regression model
as a decreasing function of the sample size through the use of
Jeffreys' Approximate Bayes factor. You tell alphaN() your sample
size, and it tells you to which value you must lower alpha to avoid
Lindley's Paradox. For details, see Wulff and Taylor (2024)
<doi:10.1177/14761270231214429>. Alpha can also be calibrated to the
effect-size and moment Bayes factors of Klauer, Meyer-Grant, and
Kellen (2024) <doi:10.3758/s13423-024-02612-2>, which center the
alternative hypothesis on an effect size of your choosing.
Author: Jesper Wulff [aut, cre] ,
Luke Taylor [aut]
Maintainer: Jesper Wulff <jwulff@econ.au.dk>
Diff between alphaN versions 0.1.2 dated 2025-07-13 and 0.2.0 dated 2026-07-12
DESCRIPTION | 17 +++-- MD5 | 61 +++++++++++--------- NAMESPACE | 4 + NEWS.md | 53 +++++++++++++++++ R/JAB.R | 32 ++++++---- R/JAB_plot.R | 31 ++-------- R/JABp.R | 33 +++++++--- R/JABt.R | 19 ++---- R/alphaN.R | 86 +++++++++++++++++++++++----- R/alphaN_plot.R | 29 ++++++--- R/helper_functions.R | 35 ++++++++++- R/klauer.R |only README.md | 106 ++++++++++++++++++++++++++++++++++- build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 53 +++++++++-------- inst/doc/intro-alphaN.R | 12 +++ inst/doc/intro-alphaN.Rmd | 38 ++++++++++-- inst/doc/intro-alphaN.html | 79 +++++++++++++++++++------- man/JAB.Rd | 8 +- man/JAB_plot.Rd | 14 ++-- man/JABp.Rd | 13 ++-- man/JABt.Rd | 9 +- man/alphaN.Rd | 69 +++++++++++++++++++--- man/alphaN_plot.Rd | 5 + man/figures/README-JAB-plot-1.png |only man/figures/README-alphaN-plot-1.png |only tests/testthat/test-JAB.R | 33 ++++++++++ tests/testthat/test-JABp.R | 11 +++ tests/testthat/test-JABt.R | 21 ++++++ tests/testthat/test-alphaN.R | 25 ++++++++ tests/testthat/test-klauer.R |only tests/testthat/test-plots.R |only vignettes/intro-alphaN.Rmd | 38 ++++++++++-- 35 files changed, 735 insertions(+), 199 deletions(-)
Title: Robust Covariance Matrix Estimators
Description: Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic
robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC)
covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC)
covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators);
clustered covariances (one-way and multi-way); panel and panel-corrected covariances;
outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are
applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted
to other classes through S3 methods. Details can be found in Zeileis et al. (2020) <doi:10.18637/jss.v095.i01>,
Zeileis (2004) <doi:10.18637/jss.v011.i10> and Zeileis (2006) <doi:10.18637/jss.v016.i09>.
Author: Achim Zeileis [aut, cre] ,
Thomas Lumley [aut] ,
Nathaniel Graham [ctb] ,
Susanne Koell [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between sandwich versions 3.1-1 dated 2024-09-15 and 3.1-2 dated 2026-07-12
DESCRIPTION | 15 +- MD5 | 50 ++++---- NAMESPACE | 1 NEWS.md | 14 ++ R/bread.R | 4 R/estfun.R | 20 +++ R/vcovHC.R | 1 R/vcovPC.R | 1 README.md | 6 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/sandwich-CL.R | 52 +++++--- inst/doc/sandwich-CL.Rnw | 7 + inst/doc/sandwich-CL.pdf |binary inst/doc/sandwich-OOP.R | 2 inst/doc/sandwich-OOP.Rnw | 2 inst/doc/sandwich-OOP.pdf |binary inst/doc/sandwich.R | 2 inst/doc/sandwich.Rnw | 4 inst/doc/sandwich.pdf |binary man/figures/README-sandwich.svg | 232 ++++++++++++++++++---------------------- vignettes/hac.bib | 20 +-- vignettes/sandwich-CL.Rnw | 7 + vignettes/sandwich-CL.Rout.save | 3 vignettes/sandwich-OOP.Rnw | 2 vignettes/sandwich.Rnw | 4 26 files changed, 243 insertions(+), 206 deletions(-)
Title: Simultaneous Selection by Trait and WAASB Index
Description: This tool proposes a new ranking algorithm that utilizes a "Y*WAASB" biplot generated by the 'metan'. The aim of the current package is to effectively distinguish the top-ranked genotypes in MET (Multi-Environmental Trials). For a detailed explanation of the process of obtaining "WAASB", "WAASBY" indices, and a "Y*WAASB" biplot, refer to the manual included in this package as well as the study by Olivoto & Lúcio (2020) <doi:10.1111/2041-210X.13384>. In this context, "WAASB" refers to the "Weighted Average of Absolute Scores" provided by Olivoto et al. (2019) <doi:10.2134/agronj2019.03.0220>, which quantifies the stability of genotypes across different environments using linear mixed-effect models. To run the package, you need to extract the "WAASB" and "WAASBY" coefficients using the 'metan' and apply them. This tool utilizes PCA (Principal Component Analysis) and differentiates the entries which may be genotypes, hybrids, varieties, etc using "WAASB", "WAASBY", and a c [...truncated...]
Author: Ali Arminian [aut, cre, cph]
Maintainer: Ali Arminian <abeyran@gmail.com>
Diff between rYWAASB versions 0.4 dated 2026-06-10 and 0.4.1 dated 2026-07-12
DESCRIPTION | 14 ++-- MD5 | 22 +++---- NEWS.md | 3 R/PCA_biplot.R | 3 R/bar_plot1.R | 2 R/bar_plot2.R | 2 R/nbclust.R | 2 R/ranki.R | 2 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/rYWAASB_manual.html | 134 +++++++++++++++++++++++-------------------- man/PCA_biplot.Rd | 1 12 files changed, 103 insertions(+), 82 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] ,
Heidi Seibold [ctb] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.2-27 dated 2026-03-13 and 1.2-28 dated 2026-07-12
partykit-1.2-27/partykit/tests/Rplots.pdf |only partykit-1.2-28/partykit/DESCRIPTION | 9 - partykit-1.2-28/partykit/MD5 | 73 +++++++------- partykit-1.2-28/partykit/R/modelparty.R | 4 partykit-1.2-28/partykit/R/party.R | 8 - partykit-1.2-28/partykit/R/simpleparty.R | 10 - partykit-1.2-28/partykit/build/partial.rdb |binary partykit-1.2-28/partykit/build/vignette.rds |binary partykit-1.2-28/partykit/inst/NEWS.Rd | 8 + partykit-1.2-28/partykit/inst/doc/constparty.R | 11 ++ partykit-1.2-28/partykit/inst/doc/constparty.Rnw | 13 ++ partykit-1.2-28/partykit/inst/doc/constparty.pdf |binary partykit-1.2-28/partykit/inst/doc/ctree.R | 11 ++ partykit-1.2-28/partykit/inst/doc/ctree.Rnw | 13 ++ partykit-1.2-28/partykit/inst/doc/ctree.pdf |binary partykit-1.2-28/partykit/inst/doc/mob.R | 11 ++ partykit-1.2-28/partykit/inst/doc/mob.Rnw | 13 ++ partykit-1.2-28/partykit/inst/doc/mob.pdf |binary partykit-1.2-28/partykit/inst/doc/partykit.R | 11 ++ partykit-1.2-28/partykit/inst/doc/partykit.Rnw | 13 ++ partykit-1.2-28/partykit/inst/doc/partykit.pdf |binary partykit-1.2-28/partykit/tests/bugfixes.R | 17 +-- partykit-1.2-28/partykit/tests/bugfixes.Rout.save | 21 ++-- partykit-1.2-28/partykit/tests/constparty.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-MIA.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-cforest.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-ctree.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-glmtree.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-nmax.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-node.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-party.Rout.save | 76 +++++++-------- partykit-1.2-28/partykit/tests/regtest-split.Rout.save | 4 partykit-1.2-28/partykit/tests/regtest-weights.Rout.save | 4 partykit-1.2-28/partykit/vignettes/constparty.Rnw | 13 ++ partykit-1.2-28/partykit/vignettes/ctree.Rnw | 13 ++ partykit-1.2-28/partykit/vignettes/mob.Rnw | 13 ++ partykit-1.2-28/partykit/vignettes/partykit.Rnw | 13 ++ partykit-1.2-28/partykit/vignettes/partykit.Rout.save | 11 +- 38 files changed, 285 insertions(+), 136 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available. The methods are described in
Hothorn et al. (2006) <doi:10.1198/106186006X133933>,
Zeileis et al. (2008) <d [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Kurt Hornik [aut] ,
Carolin Strobl [aut] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.3-20 dated 2026-03-26 and 1.3-21 dated 2026-07-12
DESCRIPTION | 9 +-- MD5 | 96 ++++++++++++++++---------------- R/AAA.R | 2 R/Classes.R | 2 R/ConditionalTree.R | 2 R/Plot.R | 2 R/Predict.R | 2 R/Print.R | 2 R/RandomForest.R | 2 R/Utils.R | 2 R/Variables.R | 2 R/zInitMethods.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 6 ++ inst/doc/MOB.R | 12 ++++ inst/doc/MOB.Rnw | 13 ++++ inst/doc/MOB.pdf |binary inst/doc/party.R | 20 +++++- inst/doc/party.Rnw | 13 ++++ inst/doc/party.pdf |binary src/Classes.c | 4 - src/Convenience.c | 4 - src/Distributions.c | 4 - src/IndependenceTest.c | 4 - src/LinearStatistic.c | 4 - src/Node.c | 4 - src/Predict.c | 4 - src/RandomForest.c | 4 - src/S3Classes.c | 4 - src/Splits.c | 4 - src/SurrogateSplits.c | 4 - src/TestStatistic.c | 4 - src/TreeGrow.c | 4 - src/Utils.c | 4 - tests/Distributions.Rout.save | 8 +- tests/LinearStatistic-regtest.Rout.save | 8 +- tests/Predict-regtest.Rout.save | 8 +- tests/RandomForest-regtest.Rout.save | 8 +- tests/TestStatistic-regtest.Rout.save | 8 +- tests/TreeGrow-regtest.Rout.save | 8 +- tests/Utils-regtest.Rout.save | 8 +- tests/bugfixes.R | 13 ++-- tests/bugfixes.Rout.save | 21 +++---- tests/mob.Rout.save | 8 +- vignettes/MOB.Rnw | 13 ++++ vignettes/MOB.Rout.save | 19 ++++-- vignettes/party.Rnw | 13 ++++ vignettes/party.Rout.save | 11 +++ 49 files changed, 246 insertions(+), 153 deletions(-)
Title: Access the U.S. National Provider Identifier Registry API
Description: Access the United States National Provider Identifier
Registry API <https://npiregistry.cms.hhs.gov/api/>. Obtain and transform
administrative data linked to a specific individual or organizational
healthcare provider, or perform advanced searches based on provider name,
location, type of service, credentials, and other attributes exposed by
the API.
Author: Frank Farach [cre, aut, cph] ,
Sam Parmar [ctb],
Matthias Grenie [rev] ,
Emily C. Zabor [rev]
Maintainer: Frank Farach <frank.farach@gmail.com>
Diff between npi versions 0.2.0 dated 2022-11-14 and 0.3.0 dated 2026-07-12
DESCRIPTION | 17 +- MD5 | 37 ++--- NEWS.md | 33 +++- R/extractors.R | 2 R/npi_results_s3.R | 147 ++++++++++++++++---- R/npi_search.R | 73 ++++++---- R/utils.R | 14 - README.md | 250 ++++++++++++++++------------------ build/vignette.rds |binary inst/CITATION | 13 - inst/doc/advanced-use.R | 2 inst/doc/advanced-use.html | 159 ++++++++++------------ inst/doc/npi.R | 2 inst/doc/npi.html | 281 +++++++++++++++++++-------------------- man/npi_search.Rd | 15 -- man/npi_summarize.Rd | 4 man/npi_summarize.npi_results.Rd | 4 tests/spelling.Rout.save |only tests/testthat/test-api.R | 40 +++++ tests/testthat/test-validators.R | 8 + 20 files changed, 626 insertions(+), 475 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre] ,
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb],
Christian Ritz [ctb],
Christian B. Pipper [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between multcomp versions 1.4-30 dated 2026-03-09 and 1.4-31 dated 2026-07-12
multcomp-1.4-30/multcomp/inst/NEWS |only multcomp-1.4-31/multcomp/DESCRIPTION | 9 - multcomp-1.4-31/multcomp/MD5 | 82 +++++----- multcomp-1.4-31/multcomp/R/contrMat.R | 2 multcomp-1.4-31/multcomp/R/expressions.R | 2 multcomp-1.4-31/multcomp/R/glht.R | 2 multcomp-1.4-31/multcomp/R/helpers.R | 2 multcomp-1.4-31/multcomp/R/maxsets.R | 2 multcomp-1.4-31/multcomp/R/mcp.R | 2 multcomp-1.4-31/multcomp/R/methods.R | 2 multcomp-1.4-31/multcomp/R/parm.R | 2 multcomp-1.4-31/multcomp/R/plot.R | 2 multcomp-1.4-31/multcomp/R/pqfunctions.R | 2 multcomp-1.4-31/multcomp/R/print.R | 2 multcomp-1.4-31/multcomp/build/partial.rdb |binary multcomp-1.4-31/multcomp/build/vignette.rds |binary multcomp-1.4-31/multcomp/data/cholesterol.rda |binary multcomp-1.4-31/multcomp/data/litter.rda |binary multcomp-1.4-31/multcomp/inst/NEWS.Rd | 8 multcomp-1.4-31/multcomp/inst/NEWS.old |only multcomp-1.4-31/multcomp/inst/doc/chfls1.R | 12 + multcomp-1.4-31/multcomp/inst/doc/chfls1.Rnw | 21 ++ multcomp-1.4-31/multcomp/inst/doc/chfls1.pdf |binary multcomp-1.4-31/multcomp/inst/doc/generalsiminf.R | 12 + multcomp-1.4-31/multcomp/inst/doc/generalsiminf.Rnw | 19 ++ multcomp-1.4-31/multcomp/inst/doc/generalsiminf.pdf |binary multcomp-1.4-31/multcomp/inst/doc/multcomp-examples.R | 12 + multcomp-1.4-31/multcomp/inst/doc/multcomp-examples.Rnw | 17 +- multcomp-1.4-31/multcomp/inst/doc/multcomp-examples.pdf |binary multcomp-1.4-31/multcomp/man/mmm.Rd | 4 multcomp-1.4-31/multcomp/tests/Examples/multcomp-Ex.Rout.save | 8 multcomp-1.4-31/multcomp/tests/bugfix.R | 4 multcomp-1.4-31/multcomp/tests/bugfix.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-Tukey.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-anova.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-interface-extended.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-interface.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-lme.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-mmm.Rout.save | 8 multcomp-1.4-31/multcomp/tests/regtest-survival.Rout.save | 4 multcomp-1.4-31/multcomp/vignettes/chfls1.Rnw | 21 ++ multcomp-1.4-31/multcomp/vignettes/generalsiminf.Rnw | 19 ++ multcomp-1.4-31/multcomp/vignettes/multcomp-examples.Rnw | 17 +- 43 files changed, 246 insertions(+), 101 deletions(-)
Title: A Toolbox for Manipulating and Assessing Colors and Palettes
Description: Carries out mapping between assorted color spaces including RGB, HSV, HLS,
CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB.
Qualitative, sequential, and diverging color palettes based on HCL colors
are provided along with corresponding ggplot2 color scales.
Color palette choice is aided by an interactive app (with either a Tcl/Tk
or a shiny graphical user interface) and shiny apps with an HCL color picker and a
color vision deficiency emulator. Plotting functions for displaying
and assessing palettes include color swatches, visualizations of the
HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation
functions include: desaturation, lightening/darkening, mixing, and
simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly).
Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/>
and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical
Software, <doi:10.18637/ [...truncated...]
Author: Ross Ihaka [aut],
Paul Murrell [aut] ,
Kurt Hornik [aut] ,
Jason C. Fisher [aut] ,
Reto Stauffer [aut] ,
Claus O. Wilke [aut] ,
Claire D. McWhite [aut] ,
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between colorspace versions 2.1-2 dated 2025-09-22 and 2.1-3 dated 2026-07-12
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 7 +++++++ R/hcl_palettes.R | 6 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/colorspace.html | 16 ++++++++-------- inst/doc/hcl-colors.R | 8 ++++---- inst/doc/hcl-colors.Rnw | 10 ++++++---- inst/doc/hcl-colors.pdf |binary vignettes/hcl-colors.Rnw | 10 ++++++---- vignettes/hcl-colors.Rout.save | 4 ++-- 12 files changed, 51 insertions(+), 40 deletions(-)
Title: 115 Data Sets from "Introductory Econometrics: A Modern
Approach, 8e" by Jeffrey M. Wooldridge
Description: Students learning both econometrics and R may find the introduction
to both challenging. The wooldridge data package aims to lighten the task by efficiently
loading any data set found in the text with a single command. Data sets have been
compressed to a fraction of their original size. Documentation files contain page numbers,
the original source, time of publication, and notes from the author suggesting avenues for
further analysis and research. If one needs an introduction to R model syntax, a
vignette contains solutions to examples from chapters of the text.
Data sets are from the 7th edition (Wooldridge 2020, ISBN-13 978-1-337-55886-0),
and are backwards compatible with all previous versions of the text.
Author: Justin M. Shea [aut, cre],
Kennth H. Brown [ctb]
Maintainer: Justin M. Shea <jshea01@uic.edu>
Diff between wooldridge versions 1.4-4 dated 2024-12-04 and 1.4-7 dated 2026-07-12
DESCRIPTION | 14 MD5 | 58 +-- NEWS.md | 15 + R/approval.R | 2 R/beveridge.R | 8 R/catholic.R | 2 R/census2000.R | 2 R/countymurders.R | 2 R/econmath.R | 2 R/happiness.R | 10 R/jtrain98.R | 2 R/labsup.R | 2 R/meapsingle.R | 2 R/ncaa_rpi.R | 2 R/school93_98.R | 2 README.md | 23 - build/vignette.rds |binary inst/doc/Introductory-Econometrics-Examples.html | 343 +++++++++++------------ man/approval.Rd | 2 man/beveridge.Rd | 8 man/catholic.Rd | 2 man/census2000.Rd | 2 man/countymurders.Rd | 2 man/econmath.Rd | 2 man/happiness.Rd | 10 man/jtrain98.Rd | 2 man/labsup.Rd | 2 man/meapsingle.Rd | 2 man/ncaa_rpi.Rd | 2 man/school93_98.Rd | 2 30 files changed, 268 insertions(+), 261 deletions(-)
Title: R Interface to the 'OKX' REST API
Description: Provides lightweight R wrappers for the 'OKX' REST API, covering
endpoints for market data, trading, account management, asset balances,
and copy trading. The upstream API reference is available at
<https://www.okx.com/docs-v5/en/>.
Author: Oliver Zhou [aut, cre],
Lily Li [aut]
Maintainer: Oliver Zhou <oliver.yxzhou@gmail.com>
Diff between okxr versions 0.4.5 dated 2026-05-08 and 0.4.7 dated 2026-07-12
DESCRIPTION | 8 MD5 | 125 ++++++------- NAMESPACE | 7 NEWS.md | 19 ++ R/def_constants.R | 209 ++++++++++++++++------ R/wrappers_get_account.R | 22 ++ R/wrappers_get_asset.R | 8 R/wrappers_get_market.R | 128 +++++++++++++ R/wrappers_post_trade.R | 167 +++++++++++++++-- README.md | 11 + man/dot-execute_get_action.Rd | 7 man/dot-gets.Rd | 4 man/dot-okx_default_tz.Rd | 4 man/dot-posts.Rd | 4 man/get_account_bill_types.Rd |only man/get_account_instruments.Rd | 6 man/get_account_interest_rate.Rd | 6 man/get_account_leverage_info.Rd | 7 man/get_account_max_withdrawal.Rd | 6 man/get_account_mmp_config.Rd | 6 man/get_account_position_risk.Rd | 6 man/get_account_precheck_set_delta_neutral.Rd | 6 man/get_account_set_account_switch_precheck.Rd | 6 man/get_account_subaccount_balances.Rd | 6 man/get_account_trade_fee.Rd | 2 man/get_asset_asset_valuation.Rd | 6 man/get_asset_bills.Rd | 3 man/get_asset_bills_history.Rd | 3 man/get_asset_non_tradable_assets.Rd | 6 man/get_copy_trade_instruments.Rd | 6 man/get_copy_trade_public_config.Rd | 5 man/get_market_block_ticker.Rd | 6 man/get_market_books.Rd | 7 man/get_market_books_rpi.Rd |only man/get_market_index_components.Rd | 6 man/get_market_platform_24_volume.Rd | 5 man/get_market_trades.Rd | 7 man/get_public_block_trades.Rd | 6 man/get_public_event_contract_events.Rd |only man/get_public_event_contract_markets.Rd |only man/get_public_event_contract_series.Rd |only man/get_public_funding_rate.Rd | 6 man/get_public_instrument_tick_bands.Rd | 2 man/get_public_instruments.Rd | 6 man/get_public_mm_instrument_types.Rd |only man/get_public_price_limit.Rd | 6 man/get_public_underlying.Rd | 6 man/get_trade_one_click_repay_currency_list_v2.Rd | 5 man/get_trade_orders_history_7d.Rd | 6 man/okxr-package.Rd | 1 man/post_account_set_account_level.Rd | 6 man/post_account_set_auto_loan.Rd | 6 man/post_account_set_auto_repay.Rd | 6 man/post_account_set_greeks.Rd | 6 man/post_account_set_position_mode.Rd | 6 man/post_trade_amend_algos.Rd | 3 man/post_trade_amend_batch_orders.Rd | 10 - man/post_trade_amend_order.Rd | 4 man/post_trade_batch_orders.Rd | 4 man/post_trade_cancel_all_after.Rd | 7 man/post_trade_cancel_batch_orders.Rd | 6 man/post_trade_order.Rd | 15 + man/post_trade_order_algo.Rd |only man/post_trade_order_precheck.Rd | 8 man/set_okxr_options.Rd | 4 tests/testthat/test-request-helpers.R | 6 tests/testthat/test-wrapper-queries.R | 102 ++++++++++ 67 files changed, 750 insertions(+), 333 deletions(-)
Title: Negative Binomial Mixed Models Using Large-Sample Approximation
for Differential Expression Analysis of ScRNA-Seq Data
Description: A fast negative binomial mixed model for conducting association analysis of multi-subject single-cell data. It can be used for identifying marker genes, differential expression and co-expression analyses. The model includes subject-level random effects to account for the hierarchical structure in multi-subject single-cell data. See He et al. (2021) <doi:10.1038/s42003-021-02146-6>.
Author: Liang He [aut, cre],
Raghav Sharma [ctb]
Maintainer: Liang He <hyx520101@gmail.com>
Diff between nebula versions 1.5.6 dated 2025-12-07 and 1.5.8 dated 2026-07-12
nebula-1.5.6/nebula/data/sample_seurat.rda |only nebula-1.5.6/nebula/man/sample_seurat.Rd |only nebula-1.5.8/nebula/DESCRIPTION | 20 +- nebula-1.5.8/nebula/LICENSE |only nebula-1.5.8/nebula/MD5 | 49 +++--- nebula-1.5.8/nebula/NAMESPACE | 7 nebula-1.5.8/nebula/R/data.R | 28 +-- nebula-1.5.8/nebula/R/group_cell.R | 4 nebula-1.5.8/nebula/R/nbresidual.R | 4 nebula-1.5.8/nebula/R/nebula.R | 16 -- nebula-1.5.8/nebula/R/scToNeb.R | 24 ++- nebula-1.5.8/nebula/R/utils.R | 46 +++++ nebula-1.5.8/nebula/README.md | 164 +++++++++----------- nebula-1.5.8/nebula/build/partial.rdb |binary nebula-1.5.8/nebula/build/vignette.rds |binary nebula-1.5.8/nebula/inst/doc/nebula_example.R | 45 +++-- nebula-1.5.8/nebula/inst/doc/nebula_example.Rmd | 17 +- nebula-1.5.8/nebula/inst/doc/nebula_example.html | 90 ++++++----- nebula-1.5.8/nebula/inst/extdata |only nebula-1.5.8/nebula/man/group_cell.Rd | 75 ++++----- nebula-1.5.8/nebula/man/load_sample_seurat.Rd |only nebula-1.5.8/nebula/man/nbresidual.Rd | 77 +++++---- nebula-1.5.8/nebula/man/nebula.Rd | 183 +++++++++++------------ nebula-1.5.8/nebula/man/sample_data.Rd | 6 nebula-1.5.8/nebula/man/scToNeb.Rd | 89 +++++------ nebula-1.5.8/nebula/src/optimization.cpp | 6 nebula-1.5.8/nebula/tests |only nebula-1.5.8/nebula/vignettes/nebula_example.Rmd | 17 +- 28 files changed, 541 insertions(+), 426 deletions(-)
Title: Breeding-Related Mixed-Effects Models
Description: Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the
'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between lme4breeding versions 1.1.2 dated 2026-05-20 and 1.1.3 dated 2026-07-12
DESCRIPTION | 8 MD5 | 18 - R/lmeb.R | 52 +++- inst/doc/lmebreed.gxe.html | 8 inst/doc/lmebreed.qg.R | 32 ++ inst/doc/lmebreed.qg.Rmd | 42 +++ inst/doc/lmebreed.qg.html | 427 +++++++++++++++++++++------------------ inst/doc/lmebreed.summaries.html | 4 man/lmeb.Rd | 44 +--- vignettes/lmebreed.qg.Rmd | 42 +++ 10 files changed, 423 insertions(+), 254 deletions(-)
Title: Kabaila and Giri (2009) Confidence Interval
Description: Computes a confidence interval for a specified linear combination of
the regression parameters in a linear regression model with iid normal
errors with unknown variance when there is uncertain prior information
that a distinct specified linear combination of the regression
parameters takes a specified number. This confidence interval, found by
numerical nonlinear constrained optimization, has the required minimum coverage
and utilizes this uncertain prior information through desirable
expected length properties. This confidence interval is proposed by
Kabaila, P. and Giri, K. (2009) <doi:10.1016/j.jspi.2009.03.018>.
Author: Nishika Ranathunga [aut],
Paul Kabaila [aut, cre]
Maintainer: Paul Kabaila <P.Kabaila@latrobe.edu.au>
Diff between ciuupi2 versions 1.0.1 dated 2021-03-11 and 1.0.2 dated 2026-07-12
DESCRIPTION | 9 +- MD5 | 8 +- R/optimize_knots.R | 21 ++--- build/vignette.rds |binary inst/doc/description-ciuupi2.html | 151 +++++++++++++++++++++++++++++--------- 5 files changed, 136 insertions(+), 53 deletions(-)
Title: A Unified and Longitudinally Aware Framework for ICD-Based
Comorbidity Assessment
Description: Provides comorbidity classification algorithms such as the
Pediatric Complex Chronic Conditions (PCCC), Charlson, and Elixhauser indices,
supports longitudinal comorbidity flagging across encounters, and includes
utilities for working with medical coding schemas such as the International
Classification of Diseases (ICD).
Author: Peter DeWitt [aut, cre, cov] ,
Tell Bennett [ctb] ,
Seth Russell [ctb] ,
Meg Rebull [ctb] ,
Vincent Rubinetti [cov]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between medicalcoder versions 0.8.1 dated 2026-05-05 and 0.9.0 dated 2026-07-11
DESCRIPTION | 13 MD5 | 168 +- NEWS.md | 68 R/charlson.R | 4 R/comorbidities.R | 439 +++++- R/datasets.R | 8 R/elixhauser.R | 6 R/get_charlson_codes.R | 18 R/get_charlson_index_scores.R | 10 R/get_elixhauser_codes.R | 12 R/get_elixhauser_index_scores.R | 9 R/get_elixhauser_poa.R | 5 R/get_icd_codes.R | 53 R/get_pccc_codes.R | 8 R/get_pccc_conditions.R | 14 R/icd_compact_to_full.R | 4 R/is_icd.R | 4 R/lookup_icd_codes.R | 12 R/medicalcoder-pkg.R | 27 R/pccc.R | 8 R/summary.R | 127 + R/sysdata.rda |binary R/utilities.R | 30 R/zzz.R | 11 README.md | 173 +- build/vignette.rds |binary data/mdcr.rda |binary data/mdcr_longitudinal.rda |binary inst/WORDLIST | 26 inst/doc/charlson.R | 17 inst/doc/charlson.Rmd | 28 inst/doc/charlson.html | 123 + inst/doc/comorbidities.R | 12 inst/doc/comorbidities.Rmd | 81 - inst/doc/comorbidities.html | 207 +-- inst/doc/elixhauser.R | 28 inst/doc/elixhauser.Rmd | 36 inst/doc/elixhauser.html | 73 - inst/doc/icd.R | 54 inst/doc/icd.Rmd | 110 - inst/doc/icd.html | 495 ++++--- inst/doc/pccc.R | 351 ++--- inst/doc/pccc.Rmd | 435 +++--- inst/doc/pccc.html | 758 +++++------ inst/mappings/icd-codes-and-mappings.R | 102 - inst/sql |only man/comorbidities.Rd | 118 + man/get_charlson_codes.Rd | 18 man/get_charlson_index_scores.Rd | 10 man/get_elixhauser_codes.Rd | 12 man/get_elixhauser_index_scores.Rd | 9 man/get_elixhauser_poa.Rd | 5 man/get_icd_codes.Rd | 49 man/get_pccc_codes.Rd | 8 man/get_pccc_conditions.Rd | 14 man/icd_compact_to_full.Rd | 6 man/is_icd.Rd | 63 man/lookup_icd_codes.Rd | 17 man/mdcr.Rd | 6 man/mdcr_longitudinal.Rd | 2 man/medicalcoder-package.Rd | 25 man/summary.medicalcoder_comorbidities.Rd | 15 man/summary.medicalcoder_comorbidities_with_subconditions.Rd | 2 tests/results_pccc_1.0.7.rds |binary tests/test-asserts.R | 89 + tests/test-charlson.R | 8 tests/test-comorbidities.R | 286 ++++ tests/test-data-frame-tools.R | 25 tests/test-elixhauser-sas-poa.R |only tests/test-internal-data.R | 93 + tests/test-is_icd.R | 26 tests/test-locked-bindings.R | 20 tests/test-longitudinal-comorbidities.R | 8 tests/test-lookup_icd_codes.R | 12 tests/test-modified-comorbidities-methods.R |only tests/test-pccc-deltas.R | 101 + tests/test-poa-in-cumulative.R | 124 + tests/test-precomputed-vs-regex.R |only tests/test-summary-pccc-subconditions.R | 25 tests/test-tibble-datatable.R | 10 tests/test-vs-pccc_1.0.7.R | 22 vignettes/charlson.Rmd | 28 vignettes/comorbidities.Rmd | 81 - vignettes/elixhauser.Rmd | 36 vignettes/icd.Rmd | 110 - vignettes/pccc.Rmd | 435 +++--- vignettes/references.bib | 63 87 files changed, 3934 insertions(+), 2214 deletions(-)
Title: Statistical Methods for Psychologists
Description: Implements confidence interval and sample size methods that are especially
useful in psychological research but are also useful in educational, social science,
business, and biological research. This package includes more than 100 confidence
interval functions and more than 80 sample size functions for 1-group, 2-group,
paired-samples, and multiple-group designs and for a variety of parameters including
means, medians, proportions, slopes, standardized mean differences, standardized
linear contrasts of means, and several measures of correlation and association. The
sample size functions can be used to approximate the sample size needed to estimate
a parameter or function of parameters with desired confidence interval precision or
to perform a variety of hypothesis tests (directional two-sided, equivalence,
superiority, noninferiority) with desired power. For details about these methods see:
Statistical Methods for Psychologists, Volumes 1 – 4, <https://dgbonett.sites.ucsc.edu/>.
Author: Douglas G. Bonett [aut, cre],
Robert J. Calin-Jageman [ctb]
Maintainer: Douglas G. Bonett <dgbonett@ucsc.edu>
Diff between statpsych versions 1.9.0 dated 2026-01-12 and 2.0.0 dated 2026-07-11
statpsych-1.9.0/statpsych/man/iqv.Rd |only statpsych-2.0.0/statpsych/DESCRIPTION | 36 statpsych-2.0.0/statpsych/MD5 | 185 statpsych-2.0.0/statpsych/NAMESPACE | 11 statpsych-2.0.0/statpsych/NEWS.md | 625 statpsych-2.0.0/statpsych/R/statpsych1.R | 325 statpsych-2.0.0/statpsych/R/statpsych2.R |10125 +++++----- statpsych-2.0.0/statpsych/R/statpsych3.R | 8909 ++++---- statpsych-2.0.0/statpsych/build/partial.rdb |binary statpsych-2.0.0/statpsych/inst/REFERENCES.bib | 18 statpsych-2.0.0/statpsych/man/ci.agree.3rater.Rd | 2 statpsych-2.0.0/statpsych/man/ci.bayes.cor.Rd | 122 statpsych-2.0.0/statpsych/man/ci.bayes.spcor.Rd | 4 statpsych-2.0.0/statpsych/man/ci.biphi.Rd | 2 statpsych-2.0.0/statpsych/man/ci.cod.Rd | 3 statpsych-2.0.0/statpsych/man/ci.cor2.gen.Rd | 2 statpsych-2.0.0/statpsych/man/ci.cqv.Rd | 3 statpsych-2.0.0/statpsych/man/ci.cramer.Rd | 2 statpsych-2.0.0/statpsych/man/ci.cv.Rd | 2 statpsych-2.0.0/statpsych/man/ci.diversity.Rd | 92 statpsych-2.0.0/statpsych/man/ci.icc.Rd | 114 statpsych-2.0.0/statpsych/man/ci.kappa.Rd | 2 statpsych-2.0.0/statpsych/man/ci.kendalltau.Rd |only statpsych-2.0.0/statpsych/man/ci.lc.gen.bs.Rd | 2 statpsych-2.0.0/statpsych/man/ci.lc.glm.Rd | 2 statpsych-2.0.0/statpsych/man/ci.lc.mean.scheffe.Rd | 118 statpsych-2.0.0/statpsych/man/ci.lc.prop.scheffe.Rd | 120 statpsych-2.0.0/statpsych/man/ci.lc.stdmean.bs.Rd | 3 statpsych-2.0.0/statpsych/man/ci.mean.gen.Rd | 82 statpsych-2.0.0/statpsych/man/ci.oddsratio.Rd | 2 statpsych-2.0.0/statpsych/man/ci.pbcor.Rd | 4 statpsych-2.0.0/statpsych/man/ci.phi.Rd | 2 statpsych-2.0.0/statpsych/man/ci.poisson.Rd | 4 statpsych-2.0.0/statpsych/man/ci.popsize.Rd | 2 statpsych-2.0.0/statpsych/man/ci.prop.inv.Rd | 2 statpsych-2.0.0/statpsych/man/ci.prop2.inv.Rd | 2 statpsych-2.0.0/statpsych/man/ci.random.anova.Rd | 2 statpsych-2.0.0/statpsych/man/ci.ratio.poisson2.Rd | 2 statpsych-2.0.0/statpsych/man/ci.ratio.prop.ps.Rd | 2 statpsych-2.0.0/statpsych/man/ci.rsqr.Rd | 2 statpsych-2.0.0/statpsych/man/ci.sd.Rd | 80 statpsych-2.0.0/statpsych/man/ci.sign.Rd | 5 statpsych-2.0.0/statpsych/man/ci.slope.Rd | 102 statpsych-2.0.0/statpsych/man/ci.tetra.Rd | 2 statpsych-2.0.0/statpsych/man/ci.yule.Rd | 2 statpsych-2.0.0/statpsych/man/etasqr.gen.2way.Rd | 2 statpsych-2.0.0/statpsych/man/expon.slope.Rd | 90 statpsych-2.0.0/statpsych/man/logitfit.Rd |only statpsych-2.0.0/statpsych/man/pi.cronbach.Rd | 120 statpsych-2.0.0/statpsych/man/pi.prop.Rd | 2 statpsych-2.0.0/statpsych/man/power.cor.Rd | 4 statpsych-2.0.0/statpsych/man/power.cor2.Rd | 4 statpsych-2.0.0/statpsych/man/power.lc.mean.bs.Rd | 4 statpsych-2.0.0/statpsych/man/power.mann.Rd |only statpsych-2.0.0/statpsych/man/power.mean.Rd | 4 statpsych-2.0.0/statpsych/man/power.mean.ps.Rd | 4 statpsych-2.0.0/statpsych/man/power.mean2.Rd | 4 statpsych-2.0.0/statpsych/man/power.prop.Rd | 4 statpsych-2.0.0/statpsych/man/power.prop.ps.Rd | 4 statpsych-2.0.0/statpsych/man/power.prop2.Rd | 4 statpsych-2.0.0/statpsych/man/random.yx.Rd | 2 statpsych-2.0.0/statpsych/man/random.yx.nonnormal.Rd |only statpsych-2.0.0/statpsych/man/sim.ci.cor.Rd | 2 statpsych-2.0.0/statpsych/man/sim.ci.mean.ps.Rd | 2 statpsych-2.0.0/statpsych/man/sim.ci.median.ps.Rd | 2 statpsych-2.0.0/statpsych/man/sim.ci.stdmean.ps.Rd | 3 statpsych-2.0.0/statpsych/man/size.ci.ancova2.Rd | 126 statpsych-2.0.0/statpsych/man/size.ci.biphi.Rd | 78 statpsych-2.0.0/statpsych/man/size.ci.cor.prior.Rd | 5 statpsych-2.0.0/statpsych/man/size.ci.cronbach.prior.Rd | 113 statpsych-2.0.0/statpsych/man/size.ci.cv.Rd | 66 statpsych-2.0.0/statpsych/man/size.ci.gen.Rd | 76 statpsych-2.0.0/statpsych/man/size.ci.gen2.Rd | 84 statpsych-2.0.0/statpsych/man/size.ci.icc.Rd | 100 statpsych-2.0.0/statpsych/man/size.ci.icc.prior.Rd | 116 statpsych-2.0.0/statpsych/man/size.ci.kendalltau.Rd |only statpsych-2.0.0/statpsych/man/size.ci.mean.prior.Rd | 6 statpsych-2.0.0/statpsych/man/size.ci.mean.ps.prior.Rd |only statpsych-2.0.0/statpsych/man/size.ci.oddsratio.Rd | 70 statpsych-2.0.0/statpsych/man/size.ci.phi.Rd | 74 statpsych-2.0.0/statpsych/man/size.ci.prop.prior.Rd | 7 statpsych-2.0.0/statpsych/man/size.ci.sd.Rd | 68 statpsych-2.0.0/statpsych/man/size.ci.yule.Rd | 74 statpsych-2.0.0/statpsych/man/size.test.ancova2.Rd | 128 statpsych-2.0.0/statpsych/man/size.test.icc.Rd |only statpsych-2.0.0/statpsych/man/size.test.mean2.Rd | 2 statpsych-2.0.0/statpsych/man/spearmanbrown.Rd | 2 statpsych-2.0.0/statpsych/man/test.cor2.Rd | 2 statpsych-2.0.0/statpsych/man/test.kurtosis.Rd | 6 statpsych-2.0.0/statpsych/man/test.kurtosis.geary.Rd |only statpsych-2.0.0/statpsych/man/test.spear.Rd | 4 statpsych-2.0.0/statpsych/man/test.spear2.Rd | 2 statpsych-2.0.0/statpsych/tests/testthat/_snaps/statpsych1.md | 50 statpsych-2.0.0/statpsych/tests/testthat/_snaps/statpsych2.md | 18 statpsych-2.0.0/statpsych/tests/testthat/_snaps/statpsych3.md | 45 statpsych-2.0.0/statpsych/tests/testthat/test_statpsych1.R | 2774 +- statpsych-2.0.0/statpsych/tests/testthat/test_statpsych2.R | 1889 - statpsych-2.0.0/statpsych/tests/testthat/test_statpsych3.R | 1717 - 98 files changed, 14904 insertions(+), 14187 deletions(-)
Title: Native and Extensible R Driver for 'Zarr'
Description: The 'Zarr' specification is widely used to build libraries for the storage and retrieval of n-dimensional array data from data stores ranging from local file systems to the cloud. This package is a native 'Zarr' implementation in R with support for all required features of 'Zarr' version 3. It is designed to be extensible such that new stores, codecs and extensions can be added easily.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between zarr versions 0.4.1 dated 2026-06-14 and 0.4.2 dated 2026-07-11
zarr-0.4.1/zarr/man/zarr_conv_ref.Rd |only zarr-0.4.1/zarr/man/zarr_conv_uom.Rd |only zarr-0.4.1/zarr/tests/testthat/helper-string-arrays.R |only zarr-0.4.2/zarr/DESCRIPTION | 6 zarr-0.4.2/zarr/MD5 | 71 ++++---- zarr-0.4.2/zarr/NAMESPACE | 7 zarr-0.4.2/zarr/NEWS.md | 14 + zarr-0.4.2/zarr/R/api.R | 23 +- zarr-0.4.2/zarr/R/array.R | 5 zarr-0.4.2/zarr/R/array_builder.R | 26 +-- zarr-0.4.2/zarr/R/chunking.R | 2 zarr-0.4.2/zarr/R/chunking_regular.R | 5 zarr-0.4.2/zarr/R/convention.R | 46 +++-- zarr-0.4.2/zarr/R/convention_ref.R | 148 ++++++++---------- zarr-0.4.2/zarr/R/convention_uom.R | 99 +++++------- zarr-0.4.2/zarr/R/group.R | 35 +++- zarr-0.4.2/zarr/R/node.R | 102 +++++++++++- zarr-0.4.2/zarr/R/store.R | 6 zarr-0.4.2/zarr/R/store_local.R | 1 zarr-0.4.2/zarr/R/store_memory.R | 27 ++- zarr-0.4.2/zarr/R/utils.R | 67 ++++++-- zarr-0.4.2/zarr/R/zarr.R | 14 + zarr-0.4.2/zarr/R/zzz.R | 3 zarr-0.4.2/zarr/README.md | 2 zarr-0.4.2/zarr/man/array_builder.Rd | 6 zarr-0.4.2/zarr/man/chunk_grid_regular.Rd | 3 zarr-0.4.2/zarr/man/create_zarr.Rd | 11 - zarr-0.4.2/zarr/man/is_valid_node_name.Rd |only zarr-0.4.2/zarr/man/sub-sub-.zarr_group.Rd | 3 zarr-0.4.2/zarr/man/zarr.Rd | 7 zarr-0.4.2/zarr/man/zarr_array.Rd | 9 - zarr-0.4.2/zarr/man/zarr_convention.Rd | 70 +++++--- zarr-0.4.2/zarr/man/zarr_convention_ref.Rd |only zarr-0.4.2/zarr/man/zarr_convention_uom.Rd |only zarr-0.4.2/zarr/man/zarr_group.Rd | 52 ++++++ zarr-0.4.2/zarr/man/zarr_memorystore.Rd | 28 +++ zarr-0.4.2/zarr/man/zarr_node.Rd | 116 +++++++++++++- zarr-0.4.2/zarr/man/zarr_options.Rd |only zarr-0.4.2/zarr/tests/testthat/test-strings.R | 51 +++++- zarr-0.4.2/zarr/tests/testthat/test-zarr.R | 11 - 40 files changed, 780 insertions(+), 296 deletions(-)
Title: Robust Median-Based Bayesian Growth Curve Modeling
Description: Implements robust median-based Bayesian linear growth curve models
for complete data and for data with Missing Completely at Random (MCAR),
Missing At Random (MAR), or Missing Not At Random (MNAR) mechanisms.
Models are fitted using 'rjags' through 'JAGS' and posterior summaries are
computed with 'coda'. The main function allows users to specify outcome
variables, auxiliary variables for MNAR missingness models, prior
hyperparameters, and initial values directly through function arguments.
Author: Dandan Tang [aut, cre] ,
Xin Tong [aut]
Maintainer: Dandan Tang <tangdd20@gmail.com>
Diff between Romeb versions 0.1.2 dated 2025-11-17 and 0.2.0 dated 2026-07-11
Romeb-0.1.2/Romeb/inst/CITATION |only Romeb-0.1.2/Romeb/inst/doc/romeb-intro.R |only Romeb-0.1.2/Romeb/inst/doc/romeb-intro.Rmd |only Romeb-0.1.2/Romeb/inst/doc/romeb-intro.html |only Romeb-0.1.2/Romeb/tests/testthat/test-sanity.R |only Romeb-0.1.2/Romeb/vignettes/romeb-intro.Rmd |only Romeb-0.2.0/Romeb/DESCRIPTION | 40 - Romeb-0.2.0/Romeb/MD5 | 40 - Romeb-0.2.0/Romeb/NAMESPACE | 1 Romeb-0.2.0/Romeb/NEWS.md | 26 Romeb-0.2.0/Romeb/R/Romeb-package.R | 13 Romeb-0.2.0/Romeb/R/Romeb.R | 599 +++++++++++++--- Romeb-0.2.0/Romeb/R/model.R | 44 - Romeb-0.2.0/Romeb/R/model_MNAR.R | 51 - Romeb-0.2.0/Romeb/R/model_MNAR_k.R | 70 - Romeb-0.2.0/Romeb/README.md |only Romeb-0.2.0/Romeb/build/vignette.rds |binary Romeb-0.2.0/Romeb/inst/doc/Romeb-introduction.R |only Romeb-0.2.0/Romeb/inst/doc/Romeb-introduction.Rmd |only Romeb-0.2.0/Romeb/inst/doc/Romeb-introduction.html |only Romeb-0.2.0/Romeb/man/Romeb.Rd | 140 ++- Romeb-0.2.0/Romeb/man/model.Rd | 8 Romeb-0.2.0/Romeb/man/model_MNAR.Rd | 6 Romeb-0.2.0/Romeb/man/model_MNAR_k.Rd | 6 Romeb-0.2.0/Romeb/tests/testthat.R |only Romeb-0.2.0/Romeb/tests/testthat/test-romeb-fit-smoke.R |only Romeb-0.2.0/Romeb/tests/testthat/test-romeb-interface.R |only Romeb-0.2.0/Romeb/vignettes/Romeb-introduction.Rmd |only 28 files changed, 760 insertions(+), 284 deletions(-)
Title: Survey Instrument Workflows
Description: Supports survey research workflows built around a typed
instrument object (the sframe). Features include visual instrument
design via a browser-based builder or 'Shiny' studio, export to a
self-contained static HTML survey, an embeddable 'Shiny' module, SHA-256
integrity-checked serialisation to the '.sframe' format, multi-page survey
rendering, branching logic, response quality checking, scale scoring,
psychometric diagnostics, analysis-plan execution, model syntax planning,
an interactive response dashboard, codebook generation, and reproducible
HTML reporting.
Author: Mohammed Ali Sharafuddin [aut, cre]
Maintainer: Mohammed Ali Sharafuddin <mohammedali.page@gmail.com>
Diff between surveyframe versions 0.3.2 dated 2026-06-17 and 0.3.3 dated 2026-07-11
DESCRIPTION | 12 MD5 | 75 +- NAMESPACE | 2 NEWS.md | 177 ++++-- R/analysis_plan.R | 123 +++- R/google_sheets.R | 30 - R/model_layer.R | 39 + R/plots.R |only R/read_responses.R | 47 + R/reporting.R | 59 +- demo/screenshots |only inst/builder/survey_builder.html | 565 ++++++++++++++------ inst/doc/analysing-survey-responses.R | 4 inst/doc/analysing-survey-responses.Rmd | 10 inst/doc/analysing-survey-responses.html | 56 + inst/doc/deploying-and-collecting.Rmd | 7 inst/doc/deploying-and-collecting.html | 9 inst/doc/efa-cfa-sem-pls-syntax.html | 69 +- inst/doc/surveyframe.R | 8 inst/doc/surveyframe.Rmd | 61 ++ inst/doc/surveyframe.html | 646 ++++++++++++----------- inst/extdata/surveyframe_input_types_demo.sframe | 6 inst/shiny/app.R | 9 inst/static_survey/template.html | 461 +++++++++++----- inst/templates/report.qmd | 47 + man/read_sheet_responses.Rd | 8 man/run_analysis_plan.Rd | 14 man/theme_surveyframe.Rd |only tests/testthat/test-0.3.1-fixes.R | 81 ++ tests/testthat/test-builder-analysis.R | 23 tests/testthat/test-v03-analysis-models.R | 62 ++ tests/testthat/test-v034-plots.R |only vignettes/analysing-survey-responses.Rmd | 10 vignettes/deploying-and-collecting.Rmd | 7 vignettes/surveyframe.Rmd | 61 ++ 35 files changed, 1980 insertions(+), 808 deletions(-)
Title: Companion to "Learning Statistics with R"
Description: A collection of tools intended to make introductory
statistics easier to teach, including wrappers for common
hypothesis tests and basic data manipulation. Accompanies the
textbook "Learning Statistics with R: A Tutorial for Psychology
Students and Other Beginners" by Navarro.
Author: Danielle Navarro [aut, cre]
Maintainer: Danielle Navarro <djnavarro@protonmail.com>
Diff between lsr versions 0.5.2 dated 2021-12-01 and 1.0.0 dated 2026-07-11
lsr-0.5.2/lsr/NEWS |only lsr-0.5.2/lsr/inst/CITATION |only lsr-0.5.2/lsr/tests/testthat/Rplots.pdf |only lsr-1.0.0/lsr/DESCRIPTION | 28 lsr-1.0.0/lsr/MD5 | 182 ++--- lsr-1.0.0/lsr/NEWS.md |only lsr-1.0.0/lsr/R/aad.R | 53 - lsr-1.0.0/lsr/R/associationTest.R | 239 +++--- lsr-1.0.0/lsr/R/bars.R | 436 ++++++------ lsr-1.0.0/lsr/R/ciMean.R | 155 ++-- lsr-1.0.0/lsr/R/cohensD.R | 321 ++++---- lsr-1.0.0/lsr/R/colCopy.R | 64 - lsr-1.0.0/lsr/R/correlate.R | 395 +++++----- lsr-1.0.0/lsr/R/cramersV.R | 80 +- lsr-1.0.0/lsr/R/etaSquared.R | 215 ++--- lsr-1.0.0/lsr/R/expandFactors.R | 61 - lsr-1.0.0/lsr/R/goodnessOfFitTest.R | 207 +++-- lsr-1.0.0/lsr/R/importList.R | 111 +-- lsr-1.0.0/lsr/R/independentSamplesTTest.R | 230 +++--- lsr-1.0.0/lsr/R/longToWide.R | 96 +- lsr-1.0.0/lsr/R/modeOf.R | 147 +--- lsr-1.0.0/lsr/R/oneSampleTTest.R | 123 +-- lsr-1.0.0/lsr/R/pairedSamplesTTest.R | 434 +++++------ lsr-1.0.0/lsr/R/permuteLevels.R | 104 +- lsr-1.0.0/lsr/R/posthocPairwiseT.R | 71 - lsr-1.0.0/lsr/R/printTTest.R | 173 ++-- lsr-1.0.0/lsr/R/quantileCut.R | 80 -- lsr-1.0.0/lsr/R/rmAll.R | 59 - lsr-1.0.0/lsr/R/rowCopy.R | 15 lsr-1.0.0/lsr/R/sortFrame.R | 117 +-- lsr-1.0.0/lsr/R/standardCoefs.R | 91 +- lsr-1.0.0/lsr/R/tFrame.R | 50 - lsr-1.0.0/lsr/R/unlibrary.R | 43 - lsr-1.0.0/lsr/R/who.R | 166 ++-- lsr-1.0.0/lsr/R/wideToLong.R | 226 +++--- lsr-1.0.0/lsr/README.md | 80 +- lsr-1.0.0/lsr/inst/WORDLIST |only lsr-1.0.0/lsr/man/aad.Rd | 34 lsr-1.0.0/lsr/man/associationTest.Rd | 51 - lsr-1.0.0/lsr/man/bars.Rd | 104 +- lsr-1.0.0/lsr/man/ciMean.Rd | 46 - lsr-1.0.0/lsr/man/cohensD.Rd | 123 +-- lsr-1.0.0/lsr/man/copy.Rd | 49 - lsr-1.0.0/lsr/man/correlate.Rd | 143 +-- lsr-1.0.0/lsr/man/cramersV.Rd | 49 - lsr-1.0.0/lsr/man/etaSquared.Rd | 77 +- lsr-1.0.0/lsr/man/expandFactors.Rd | 40 - lsr-1.0.0/lsr/man/goodnessOfFitTest.Rd | 60 - lsr-1.0.0/lsr/man/importList.Rd | 71 - lsr-1.0.0/lsr/man/independentSamplesTTest.Rd | 85 +- lsr-1.0.0/lsr/man/longToWide.Rd | 66 - lsr-1.0.0/lsr/man/mode.Rd | 76 -- lsr-1.0.0/lsr/man/oneSampleTTest.Rd | 60 - lsr-1.0.0/lsr/man/pairedSamplesTTest.Rd | 140 +-- lsr-1.0.0/lsr/man/permuteLevels.Rd | 63 - lsr-1.0.0/lsr/man/posthocPairwiseT.Rd | 52 - lsr-1.0.0/lsr/man/print.TTest.Rd | 14 lsr-1.0.0/lsr/man/print.assocTest.Rd | 13 lsr-1.0.0/lsr/man/print.correlate.Rd | 12 lsr-1.0.0/lsr/man/print.gofTest.Rd | 13 lsr-1.0.0/lsr/man/print.whoList.Rd | 12 lsr-1.0.0/lsr/man/quantileCut.Rd | 58 - lsr-1.0.0/lsr/man/rmAll.Rd | 33 lsr-1.0.0/lsr/man/sortFrame.Rd | 79 -- lsr-1.0.0/lsr/man/standardCoefs.Rd | 62 - lsr-1.0.0/lsr/man/tFrame.Rd | 44 - lsr-1.0.0/lsr/man/unlibrary.Rd | 32 lsr-1.0.0/lsr/man/who.Rd | 43 - lsr-1.0.0/lsr/man/wideToLong.Rd | 141 +-- lsr-1.0.0/lsr/tests/testthat/test-aad.R | 18 lsr-1.0.0/lsr/tests/testthat/test-associationTest.R | 30 lsr-1.0.0/lsr/tests/testthat/test-bars.R | 4 lsr-1.0.0/lsr/tests/testthat/test-ciMean.R | 27 lsr-1.0.0/lsr/tests/testthat/test-cohensD.R | 59 + lsr-1.0.0/lsr/tests/testthat/test-copy.R |only lsr-1.0.0/lsr/tests/testthat/test-correlate.R | 151 +++- lsr-1.0.0/lsr/tests/testthat/test-cramersV.R | 68 + lsr-1.0.0/lsr/tests/testthat/test-etaSquared.R | 74 +- lsr-1.0.0/lsr/tests/testthat/test-expandFactors.R | 56 + lsr-1.0.0/lsr/tests/testthat/test-goodnessOfFitTest.R | 100 ++ lsr-1.0.0/lsr/tests/testthat/test-importList.R | 55 + lsr-1.0.0/lsr/tests/testthat/test-independentSamplesTTest.R | 134 +++ lsr-1.0.0/lsr/tests/testthat/test-longToWide.R | 65 + lsr-1.0.0/lsr/tests/testthat/test-modeOf.R | 64 + lsr-1.0.0/lsr/tests/testthat/test-oneSampleTTest.R | 106 ++ lsr-1.0.0/lsr/tests/testthat/test-pairedSamplesTTest.R | 151 +++- lsr-1.0.0/lsr/tests/testthat/test-permuteLevels.R | 56 + lsr-1.0.0/lsr/tests/testthat/test-posthocPairwiseT.R | 50 + lsr-1.0.0/lsr/tests/testthat/test-printTTest.R |only lsr-1.0.0/lsr/tests/testthat/test-quantileCut.R | 44 + lsr-1.0.0/lsr/tests/testthat/test-rmAll.R |only lsr-1.0.0/lsr/tests/testthat/test-sortFrame.R | 97 ++ lsr-1.0.0/lsr/tests/testthat/test-standardCoefs.R | 63 + lsr-1.0.0/lsr/tests/testthat/test-tFrame.R | 35 lsr-1.0.0/lsr/tests/testthat/test-unlibrary.R |only lsr-1.0.0/lsr/tests/testthat/test-who.R |only lsr-1.0.0/lsr/tests/testthat/test-wideToLong.R | 99 +- 97 files changed, 4758 insertions(+), 3645 deletions(-)
Title: Complex-Valued Lasso and Complex-Valued Graphical Lasso
Description: Implements 'glmnet'-style complex-valued lasso (CLASSO) and
complex-valued graphical lasso (CGLASSO) via a pathwise coordinate
descent algorithm for complex-valued parameters, using an isomorphism
between complex numbers and 2x2 orthogonal matrices. Also provides a
full inference pipeline for high-dimensional sparse spectral precision
matrices, including data-driven bandwidth selection, one-step
debiasing, asymptotic variance estimation, entry-wise confidence
regions, and FDR-controlled hypothesis testing. Supporting tools for
cross-validation, simulation, coefficient extraction, and plotting are
included. See Deb, Kuceyeski, and Basu (2024)
<doi:10.48550/arXiv.2401.11128> and Deb, Kim, and Basu (2026)
<doi:10.48550/arXiv.2606.07986>.
Author: Younghoon Kim [aut, cre],
Navonil Deb [aut],
Sumanta Basu [aut]
Maintainer: Younghoon Kim <ykim124@ua.edu>
Diff between cxreg versions 1.1.2 dated 2026-07-05 and 1.1.4 dated 2026-07-11
DESCRIPTION | 6 ++-- MD5 | 14 +++++++---- NEWS.md | 52 +++++++++++++++++++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/cxreg-inference.R |only inst/doc/cxreg-inference.Rmd |only inst/doc/cxreg-inference.pdf |only inst/doc/cxreg.pdf |binary vignettes/cxreg-inference.Rmd |only vignettes/cxreg_refs.bib | 32 +++++++++++++++++++++++++ 10 files changed, 94 insertions(+), 10 deletions(-)
Title: Bindings for 'Open Source Routing Machine'
Description: Install and control 'Open Source Routing Machine' ('OSRM')
backend executables to prepare routing data and run/stop a local
'OSRM' server. For computations with the running server use the 'osrm'
package for 'R' (<https://cran.r-project.org/package=osrm>).
Author: Egor Kotov [aut, cre, cph]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between osrm.backend versions 0.3.1 dated 2026-04-26 and 0.4.0 dated 2026-07-11
osrm.backend-0.3.1/osrm.backend/man/dot-get_pbf_extent.Rd |only osrm.backend-0.3.1/osrm.backend/man/read_pbf_header_bbox.Rd |only osrm.backend-0.4.0/osrm.backend/DESCRIPTION | 18 osrm.backend-0.4.0/osrm.backend/LICENSE | 2 osrm.backend-0.4.0/osrm.backend/MD5 | 63 osrm.backend-0.4.0/osrm.backend/NAMESPACE | 1 osrm.backend-0.4.0/osrm.backend/NEWS.md | 14 osrm.backend-0.4.0/osrm.backend/R/osrm_contract.R | 3 osrm.backend-0.4.0/osrm.backend/R/osrm_customize.R | 9 osrm.backend-0.4.0/osrm.backend/R/osrm_extract.R | 19 osrm.backend-0.4.0/osrm.backend/R/osrm_gui.R | 4 osrm.backend-0.4.0/osrm.backend/R/osrm_install.R | 644 +++++++--- osrm.backend-0.4.0/osrm.backend/R/osrm_partition.R | 8 osrm.backend-0.4.0/osrm.backend/R/osrm_server_registry.R | 4 osrm.backend-0.4.0/osrm.backend/R/osrm_validated_versions.R |only osrm.backend-0.4.0/osrm.backend/R/pbf_header_reader.R | 6 osrm.backend-0.4.0/osrm.backend/README.md | 68 - osrm.backend-0.4.0/osrm.backend/build/vignette.rds |binary osrm.backend-0.4.0/osrm.backend/inst/doc/osrm-backend.Rmd | 2 osrm.backend-0.4.0/osrm.backend/inst/doc/osrm-backend.html | 4 osrm.backend-0.4.0/osrm.backend/man/figures/logo.png |only osrm.backend-0.4.0/osrm.backend/man/osrm.backend-package.Rd | 4 osrm.backend-0.4.0/osrm.backend/man/osrm_clear_path.Rd | 3 osrm.backend-0.4.0/osrm.backend/man/osrm_contract.Rd | 4 osrm.backend-0.4.0/osrm.backend/man/osrm_customize.Rd | 10 osrm.backend-0.4.0/osrm.backend/man/osrm_get_server_profile.Rd | 5 osrm.backend-0.4.0/osrm.backend/man/osrm_install.Rd | 96 - osrm.backend-0.4.0/osrm.backend/man/osrm_partition.Rd | 14 osrm.backend-0.4.0/osrm.backend/man/osrm_validated_versions.Rd |only osrm.backend-0.4.0/osrm.backend/tests/testthat/setup-osrm.R | 30 osrm.backend-0.4.0/osrm.backend/tests/testthat/test-compatibility.R |only osrm.backend-0.4.0/osrm.backend/tests/testthat/test-live-integration.R | 67 + osrm.backend-0.4.0/osrm.backend/tests/testthat/test-osrm_install.R | 221 +++ osrm.backend-0.4.0/osrm.backend/tests/testthat/test_results.rds |only osrm.backend-0.4.0/osrm.backend/vignettes/binary-providers.qmd |only osrm.backend-0.4.0/osrm.backend/vignettes/generated-tested-versions.md |only osrm.backend-0.4.0/osrm.backend/vignettes/osrm-backend.Rmd | 2 37 files changed, 1037 insertions(+), 288 deletions(-)
Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008),
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2. <doi:10.1007/978-0-387-77318-6>
(See the vignette "AER" for a package overview.)
Author: Christian Kleiber [aut] ,
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between AER versions 1.2-16 dated 2026-02-09 and 1.2-17 dated 2026-07-11
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 5 +++++ R/ivreg.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary demo/Ch-LinearRegression.R | 2 +- inst/doc/AER.R | 2 -- inst/doc/AER.pdf |binary inst/doc/Sweave-journals.R | 2 -- inst/doc/Sweave-journals.pdf |binary tests/Ch-Intro.R | 2 +- tests/Ch-Intro.Rout.save | 7 +------ tests/Ch-LinearRegression.R | 2 +- tests/Ch-LinearRegression.Rout.save | 2 +- tests/Ch-Validation.R | 2 +- tests/Ch-Validation.Rout.save | 2 +- 17 files changed, 34 insertions(+), 38 deletions(-)
Title: Client for US Treasury XML Feed and Published Data
Description: Download daily interest rates from the US Treasury XML feed.
Leveraging
<https://home.treasury.gov/treasury-daily-interest-rate-xml-feed>,
this package serves as a wrapper, facilitating the retrieval of daily
treasury rates across various categories, including par yield curves,
treasury bills, long-term rates, and real yield curves.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between treasury versions 0.5.0 dated 2026-03-21 and 0.6.0 dated 2026-07-11
treasury-0.5.0/treasury/R/assertions.R |only treasury-0.6.0/treasury/DESCRIPTION | 12 treasury-0.6.0/treasury/MD5 | 37 +- treasury-0.6.0/treasury/NEWS.md | 9 treasury-0.6.0/treasury/R/cache.R | 16 treasury-0.6.0/treasury/R/httr2.R |only treasury-0.6.0/treasury/R/interest-rate.R | 217 ++++-------- treasury-0.6.0/treasury/R/treasury-package.R | 6 treasury-0.6.0/treasury/R/utils.R |only treasury-0.6.0/treasury/R/yield-curve.R | 99 ++--- treasury-0.6.0/treasury/README.md | 18 treasury-0.6.0/treasury/man/figures/README-plot-1.png |binary treasury-0.6.0/treasury/man/tr_bill_rate.Rd | 16 treasury-0.6.0/treasury/man/tr_cache_dir.Rd | 8 treasury-0.6.0/treasury/man/tr_long_term_rate.Rd | 18 treasury-0.6.0/treasury/man/tr_real_long_term.Rd | 13 treasury-0.6.0/treasury/man/tr_real_yield_curve.Rd | 13 treasury-0.6.0/treasury/man/tr_yield_curve.Rd | 13 treasury-0.6.0/treasury/man/treasury-package.Rd | 5 treasury-0.6.0/treasury/tests/testthat/_snaps |only treasury-0.6.0/treasury/tests/testthat/test-interest-rate.R | 134 +++++-- treasury-0.6.0/treasury/tests/testthat/test-utils.R |only 22 files changed, 336 insertions(+), 298 deletions(-)
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
'lbfgsb_cpp' is a 'C++' port around by Pascal Have of 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Yann Richet [aut, cre] ,
Pascal Have [aut],
Yves Deville [aut],
Conrad Sanderson [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Mike Smith [ctb]
Maintainer: Yann Richet <yann.richet@asnr.fr>
Diff between rlibkriging versions 1.0-0 dated 2026-05-13 and 1.1-0 dated 2026-07-11
rlibkriging-1.0-0/rlibkriging/src/libK/refactor_table.md |only rlibkriging-1.1-0/rlibkriging/DESCRIPTION | 8 rlibkriging-1.1-0/rlibkriging/MD5 | 79 - rlibkriging-1.1-0/rlibkriging/NAMESPACE | 3 rlibkriging-1.1-0/rlibkriging/NEWS.md |only rlibkriging-1.1-0/rlibkriging/R/KrigingClass.R | 34 rlibkriging-1.1-0/rlibkriging/R/NestedKrigingClass.R |only rlibkriging-1.1-0/rlibkriging/R/RcppExports.R | 52 + rlibkriging-1.1-0/rlibkriging/R/WarpKrigingClass.R | 14 rlibkriging-1.1-0/rlibkriging/man/Kriging.Rd | 20 rlibkriging-1.1-0/rlibkriging/man/NestedKriging.Rd |only rlibkriging-1.1-0/rlibkriging/man/classNestedKriging.Rd |only rlibkriging-1.1-0/rlibkriging/man/fit.Kriging.Rd | 12 rlibkriging-1.1-0/rlibkriging/man/predict.NestedKriging.Rd |only rlibkriging-1.1-0/rlibkriging/man/predict.WarpKriging.Rd | 15 rlibkriging-1.1-0/rlibkriging/man/print.NestedKriging.Rd |only rlibkriging-1.1-0/rlibkriging/src/RcppExports.cpp | 169 +++ rlibkriging-1.1-0/rlibkriging/src/WarpKriging_binding.cpp | 5 rlibkriging-1.1-0/rlibkriging/src/libK/CHANGELOG.md |only rlibkriging-1.1-0/rlibkriging/src/libK/CMakeLists.txt | 2 rlibkriging-1.1-0/rlibkriging/src/libK/CONTRIBUTING.md | 12 rlibkriging-1.1-0/rlibkriging/src/libK/NOTICE |only rlibkriging-1.1-0/rlibkriging/src/libK/README.md | 39 rlibkriging-1.1-0/rlibkriging/src/libK/cmake/update_version.sh | 2 rlibkriging-1.1-0/rlibkriging/src/libK/cmake/version.cmake | 2 rlibkriging-1.1-0/rlibkriging/src/libK/src/lib/CMakeLists.txt | 1 rlibkriging-1.1-0/rlibkriging/src/libK/src/lib/Kriging.cpp | 483 +++++++++- rlibkriging-1.1-0/rlibkriging/src/libK/src/lib/NestedKriging.cpp |only rlibkriging-1.1-0/rlibkriging/src/libK/src/lib/WarpKriging.cpp | 32 rlibkriging-1.1-0/rlibkriging/src/libK/src/lib/include/libKriging/Kriging.hpp | 60 + rlibkriging-1.1-0/rlibkriging/src/libK/src/lib/include/libKriging/NestedKriging.hpp |only rlibkriging-1.1-0/rlibkriging/src/libK/src/lib/include/libKriging/WarpKriging.hpp | 14 rlibkriging-1.1-0/rlibkriging/src/libK/tools/common/before_script.sh | 2 rlibkriging-1.1-0/rlibkriging/src/libK/tools/common/choco.sh |only rlibkriging-1.1-0/rlibkriging/src/libK/tools/linux-macos/install.sh | 2 rlibkriging-1.1-0/rlibkriging/src/libK/tools/linux-macos/loadenv.sh | 2 rlibkriging-1.1-0/rlibkriging/src/libK/tools/linux-macos/test.sh | 20 rlibkriging-1.1-0/rlibkriging/src/libK/tools/octave-windows/install.sh | 9 rlibkriging-1.1-0/rlibkriging/src/libK/tools/r-windows/install.sh | 3 rlibkriging-1.1-0/rlibkriging/src/libK/tools/windows/install.sh | 5 rlibkriging-1.1-0/rlibkriging/src/nestedkriging_binding.cpp |only rlibkriging-1.1-0/rlibkriging/tests/test-KrigingConstructorConsistency.R |only rlibkriging-1.1-0/rlibkriging/tests/test-NestedKriging.R |only rlibkriging-1.1-0/rlibkriging/tests/test-WarpKriging.R | 12 rlibkriging-1.1-0/rlibkriging/tools/build.sh | 37 rlibkriging-1.1-0/rlibkriging/tools/gitmodules-shas | 2 rlibkriging-1.1-0/rlibkriging/tools/install_packages.R | 25 rlibkriging-1.1-0/rlibkriging/tools/setup.sh | 3 48 files changed, 1058 insertions(+), 122 deletions(-)
Title: Estimation of Ploidy and Detection of Aneuploidy Using
Genotyping Data
Description: Provides functions for estimating ploidy levels and detecting aneuploidy
in individuals using allele intensities or allele count data from high-throughput genotyping platforms, including
single nucleotide polymorphism (SNP) arrays and sequencing-based technologies. Implements method described
in Taniguti et al. (2025) <doi:10.1002/tpg2.70044> an extended version of the 'PennCNV'
signal standardization method by Wang et al. (2007) <doi:10.1101/gr.6861907> for higher ploidy
levels. Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation patterns.
Author: Cristiane Taniguti [cre, aut],
Jeekin Lau [ctb],
Oscar Riera-Lizarazu [ctb]
Maintainer: Cristiane Taniguti <ctaniguti@ufl.edu>
Diff between Qploidy versions 1.0.1 dated 2025-05-01 and 1.5.4 dated 2026-07-11
Qploidy-1.0.1/Qploidy/R/plots.R |only Qploidy-1.5.4/Qploidy/DESCRIPTION | 27 Qploidy-1.5.4/Qploidy/MD5 | 91 + Qploidy-1.5.4/Qploidy/NAMESPACE | 7 Qploidy-1.5.4/Qploidy/NEWS.md | 47 Qploidy-1.5.4/Qploidy/R/ploidy_est.R | 96 - Qploidy-1.5.4/Qploidy/R/plots_standardization.R |only Qploidy-1.5.4/Qploidy/R/prepare.R | 105 +- Qploidy-1.5.4/Qploidy/R/simulate_inputs.R | 3 Qploidy-1.5.4/Qploidy/R/standardization.R | 260 +++-- Qploidy-1.5.4/Qploidy/R/utils.R | 333 ------ Qploidy-1.5.4/Qploidy/R/vcf_sanity_check.R |only Qploidy-1.5.4/Qploidy/R/zzz.R |only Qploidy-1.5.4/Qploidy/build/partial.rdb |binary Qploidy-1.5.4/Qploidy/build/vignette.rds |binary Qploidy-1.5.4/Qploidy/inst/AxiomGT1_summary.txt |only Qploidy-1.5.4/Qploidy/inst/CITATION | 39 Qploidy-1.5.4/Qploidy/inst/WORDLIST | 1 Qploidy-1.5.4/Qploidy/inst/app |only Qploidy-1.5.4/Qploidy/inst/doc/Qploidy.R | 6 Qploidy-1.5.4/Qploidy/inst/doc/Qploidy.Rmd | 41 Qploidy-1.5.4/Qploidy/inst/doc/Qploidy.html | 608 +++++------- Qploidy-1.5.4/Qploidy/inst/help_files |only Qploidy-1.5.4/Qploidy/inst/logo.svg |only Qploidy-1.5.4/Qploidy/inst/vcf_example_simulated.vcf.gz |only Qploidy-1.5.4/Qploidy/man/all_resolutions_plots.Rd | 2 Qploidy-1.5.4/Qploidy/man/area_estimate_ploidy.Rd | 22 Qploidy-1.5.4/Qploidy/man/clean_summary.Rd | 2 Qploidy-1.5.4/Qploidy/man/find_header_line.Rd | 6 Qploidy-1.5.4/Qploidy/man/get_R_theta.Rd | 2 Qploidy-1.5.4/Qploidy/man/get_aneuploids.Rd | 4 Qploidy-1.5.4/Qploidy/man/is_compressed_file.Rd |only Qploidy-1.5.4/Qploidy/man/merge_arms_format.Rd | 4 Qploidy-1.5.4/Qploidy/man/plot_baf.Rd | 2 Qploidy-1.5.4/Qploidy/man/plot_baf_hist.Rd | 2 Qploidy-1.5.4/Qploidy/man/plot_baf_with_ploidy_guides.Rd |only Qploidy-1.5.4/Qploidy/man/plot_qploidy_standardization.Rd | 2 Qploidy-1.5.4/Qploidy/man/plot_xy_with_ploidy_guides.Rd |only Qploidy-1.5.4/Qploidy/man/qploidy_read_vcf.Rd | 10 Qploidy-1.5.4/Qploidy/man/read_axiom.Rd | 4 Qploidy-1.5.4/Qploidy/man/read_illumina_array.Rd | 4 Qploidy-1.5.4/Qploidy/man/read_qploidy_standardization.Rd | 29 Qploidy-1.5.4/Qploidy/man/standardize.Rd | 74 - Qploidy-1.5.4/Qploidy/man/vcf_sanity_check.Rd | 7 Qploidy-1.5.4/Qploidy/man/write_qploidy_standardization.Rd |only Qploidy-1.5.4/Qploidy/tests/testthat/test-prepare.R | 2 Qploidy-1.5.4/Qploidy/tests/testthat/test-standardization.R | 2 Qploidy-1.5.4/Qploidy/vignettes/Qploidy.Rmd | 41 48 files changed, 901 insertions(+), 984 deletions(-)
Title: 'OpenCL' Tools for R Package Developers
Description: Runtime 'OpenCL' support for R package developers: probe hardware
and drivers, load and concatenate kernel sources, and manage
dependency-annotated '.cl' libraries, so packages like 'nmathopencl' and
other ported libraries can offer GPU acceleration without each re-implementing
the same plumbing. Vignettes illustrate integration with suggested packages
'nmathopencl' and 'glmbayes'; production kernels for those applications
ship in those packages rather than here.
Author: Kjell Nygren [aut, cre],
The R Core Team [ctb, cph] ,
The R Foundation [cph] ,
Ross Ihaka [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Simon Davies [ctb] ,
Morten Welinder [ctb, cph] ,
Martin Maechler [ctb]
Maintainer: Kjell Nygren <kjell.a.nygren@gmail.com>
Diff between opencltools versions 0.8.1 dated 2026-06-03 and 0.8.2 dated 2026-07-11
DESCRIPTION | 18 MD5 | 74 +- NAMESPACE | 5 NEWS.md | 313 +++++----- R/RcppExports.R | 12 R/attach_kernel_call_tags.R | 6 R/load_library_for_kernel_cross_package.R |only R/load_program_preload.R |only R/opencltools-package.R | 109 +-- R/program_preload_internals.R |only R/rcpp_wrappers.R | 30 README.md | 27 inst/CITATION | 31 inst/COPYRIGHTS | 67 -- inst/REFERENCES.bib | 468 --------------- inst/cl/program_preload_manifest.tsv |only inst/examples/Ex_attach_kernel_dependency_tags.R | 2 inst/examples/Ex_kernel_tagging_workflow.R | 16 inst/examples/Ex_load_library_for_kernel_cross_package.R |only inst/examples/Ex_load_program_preload.R |only inst/examples/Ex_stage_kernel_dependency_sort.R | 2 inst/examples/Ex_write_kernel_dependency_index.R | 2 inst/examples/Ex_write_program_preload_manifest.R |only inst/include/opencltools/openclPort.h | 41 + inst/include/opencltools/opencltools_capi.h | 46 + man/attach_cross_library_tags.Rd | 16 man/attach_kernel_call_tags.Rd | 22 man/attach_kernel_dependency_tags.Rd | 2 man/extract_library_subset.Rd | 1 man/load_library_for_kernel.Rd | 1 man/load_library_for_kernel_cross_package.Rd |only man/load_program_preload.Rd |only man/opencltools-package.Rd | 14 man/print.opencl_dependency_tags.Rd | 2 man/read_program_preload_manifest.Rd |only man/stage_kernel_dependency_sort.Rd | 2 man/write_kernel_dependency_index.Rd | 5 man/write_program_preload_manifest.Rd |only src/RcppExports.cpp | 43 + src/export_wrappers.cpp | 48 + src/kernel_loader.cpp | 444 ++++++++++++++ src/openclPort.h | 41 + src/opencltools_ccallables.cpp | 42 + tests/testthat/test-program-preload.R |only 44 files changed, 1132 insertions(+), 820 deletions(-)
Title: Converts Conductance Units
Description: For plant physiologists, converts conductance (e.g. stomatal conductance) to different units: m/s, mol/m^2/s, and umol/m^2/s/Pa.
Author: Chris Muir [aut, cre]
Maintainer: Chris Muir <cdmuir@wisc.edu>
Diff between gunit versions 1.0.2 dated 2022-10-18 and 1.0.3 dated 2026-07-11
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS.md | 4 +++- inst/CITATION | 6 ++---- 4 files changed, 14 insertions(+), 14 deletions(-)
Title: Scraper for Chess-Results.com
Description: Scrape data from <https://chess-results.com> and get a clean
'tibble'. Currently supports tournament information, starting rank,
playing schedule, pairings/results for rounds, and closing rank.
All requests to the <https://chess-results.com> server are made using
'polite'.
Author: Sirf Haru [aut, cre, cph]
Maintainer: Sirf Haru <sirfharu@proton.me>
Diff between chessResults versions 2026.07.05 dated 2026-07-11 and 2026.07.12 dated 2026-07-11
chessResults-2026.07.05/chessResults/tests/testthat.R |only chessResults-2026.07.12/chessResults/DESCRIPTION | 37 chessResults-2026.07.12/chessResults/MD5 | 12 chessResults-2026.07.12/chessResults/NEWS.md |only chessResults-2026.07.12/chessResults/R/chess_results.R | 555 ++++++++++---- chessResults-2026.07.12/chessResults/README.md | 86 +- chessResults-2026.07.12/chessResults/inst |only chessResults-2026.07.12/chessResults/man/chess_results.Rd | 27 chessResults-2026.07.12/chessResults/tests/spelling.R |only 9 files changed, 517 insertions(+), 200 deletions(-)
Title: Biological Geometries
Description: Is used to simulate and fit biological geometries. 'biogeom' incorporates several novel universal parametric equations that can generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings (Gielis (2003) <doi:10.3732/ajb.90.3.333>; Shi et al. (2020) <doi:10.3390/sym12040645>), three growth-rate curves representing the ontogenetic growth trajectories of animals and plants against time, and the axially symmetrical and integral forms of all these functions (Shi et al. (2017) <doi:10.1016/j.ecolmodel.2017.01.012>; Shi et al. (2021) <doi:10.3390/sym13081524>). The optimization method proposed by Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> was used to estimate model parameters. 'biogeom' includes several real data sets of the boundary coordinates of natural shapes, including avian eggs, fruit, lanceolate and ovate leaves, tree rings, seeds, and sea stars,and can be potentially applied to other natural shapes. [...truncated...]
Author: Peijian Shi [aut, cre],
Johan Gielis [aut],
Brady K. Quinn [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>
Diff between biogeom versions 1.5.1 dated 2026-04-16 and 1.5.2 dated 2026-07-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/lmPE.R | 11 +++++++++++ R/lmTE.R | 11 +++++++++++ build/partial.rdb |binary 5 files changed, 30 insertions(+), 8 deletions(-)
Title: Approximate Bayesian Latent Variable Analysis
Description: Implements approximate Bayesian inference for Structural
Equation Models (SEM) using a custom adaptation of the Integrated
Nested Laplace Approximation (Rue et al., 2009)
<doi:10.1111/j.1467-9868.2008.00700.x> as described in Jamil and Rue
(2026a) <doi:10.48550/arXiv.2603.25690>. Provides a computationally
efficient alternative to Markov Chain Monte Carlo (MCMC) for Bayesian
estimation, allowing users to fit latent variable models using the
'lavaan' syntax. See also the companion paper on implementation and
workflows, Jamil and Rue (2026b) <doi:10.48550/arXiv.2604.00671>.
Author: Haziq Jamil [aut, cre, cph] ,
Havard Rue [ctb] ,
Alvin Bong [ctb]
Maintainer: Haziq Jamil <haziq.jamil@gmail.com>
Diff between INLAvaan versions 0.2.5 dated 2026-06-11 and 0.3.0 dated 2026-07-11
DESCRIPTION | 9 MD5 | 141 ++++++----- NAMESPACE | 30 ++ NEWS.md | 259 ++++++++++++++++++-- R/INLAvaan-package.R | 1 R/compare.R | 291 ++++++++++++++++++++--- R/create_lav_from_inlavaan_internal.R | 3 R/inlavaan.R | 349 +++++++++++++++++++++++++--- R/lavaan-argnames.R |only R/lavaan-unexported.R | 36 ++ R/log-likelihood-and-grad.R | 58 ++++ R/loo.R |only R/method-anova.R |only R/method-deviance.R |only R/method-diagnostics.R | 304 +++++++++++++++++++----- R/method-fitmeasures.R | 114 ++++++++- R/method-fitted.R |only R/method-loglik.R |only R/method-loo.R |only R/method-others.R | 20 + R/method-predict.R | 70 ++++- R/method-residuals.R |only R/method-sampling.R | 76 ++++-- R/method-show.R | 3 R/method-simulate.R | 43 +++ R/method-summary.R | 275 ++++++++++++---------- R/method-update.R |only R/method-waic.R |only R/posterior-sampling.R | 5 R/standardisedsolution.R | 22 + R/utils-compare_mcmc.R | 18 + R/utils-optim.R | 53 ++++ R/utils.R | 15 - R/zzz.R | 11 README.md | 91 +++---- inst/doc/INLAvaan.R | 21 + inst/doc/INLAvaan.html | 315 +++++++++++++++---------- inst/doc/INLAvaan.qmd | 53 ++++ inst/doc/mediation.html | 28 +- inst/examples/ex-loo.R |only man/INLAvaan-class.Rd | 15 - man/INLAvaan-package.Rd | 7 man/acfa.Rd | 17 - man/agrowth.Rd | 17 - man/asem.Rd | 17 - man/compare.Rd | 46 +++ man/deviance.Rd |only man/diagnostics.Rd | 17 + man/figures/README-fig-compare-poldem-1.png |binary man/fitmeasures.Rd | 32 -- man/fitted.Rd |only man/get_inlavaan_internal.Rd | 2 man/inlavaan.Rd | 37 ++ man/logLik.Rd |only man/loo.Rd |only man/predict.Rd | 18 + man/residuals.Rd |only man/standardisedsolution.Rd | 43 ++- man/update.Rd |only man/waic.Rd |only tests/testthat/test-anova.R |only tests/testthat/test-binary.R | 1 tests/testthat/test-cfa.R | 29 ++ tests/testthat/test-compare.R | 186 +++++++++++++- tests/testthat/test-diagnostics.R | 99 +++++++ tests/testthat/test-fitted.R |only tests/testthat/test-loglik.R | 20 + tests/testthat/test-loo-fixedx.R |only tests/testthat/test-loo-loco.R |only tests/testthat/test-loo-loso.R |only tests/testthat/test-loo-missing-2l.R |only tests/testthat/test-loo-missing.R |only tests/testthat/test-loo-multigroup.R |only tests/testthat/test-method-deviance.R |only tests/testthat/test-method-loglik.R |only tests/testthat/test-method-summary.R |only tests/testthat/test-method-update.R |only tests/testthat/test-multigroup.R | 4 tests/testthat/test-multilevel.R | 41 +++ tests/testthat/test-mvn_loglik.R | 6 tests/testthat/test-predict.R | 31 ++ tests/testthat/test-residuals.R |only tests/testthat/test-sampling.R | 65 ++++- tests/testthat/test-sem.R | 2 tests/testthat/test-simulate.R | 77 +++++- vignettes/INLAvaan.qmd | 53 ++++ vignettes/refs.bib | 45 +++ 87 files changed, 2943 insertions(+), 698 deletions(-)
More information about saeproj.multilevel at CRAN
Permanent link
Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut] ,
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.9.1 dated 2026-04-03 and 2.9.2 dated 2026-07-11
DESCRIPTION | 8 MD5 | 564 +- NAMESPACE | 439 +- NEWS.md | 1918 ++++----- R/AAAA.R | 206 - R/ISSR800.R | 543 +- R/KSSL_VG_model.R | 242 - R/OSDquery.R | 324 - R/ROSETTA.R | 544 +- R/SDA-spatial.R | 1096 ++--- R/SDA_query.R | 720 +-- R/SDA_utils.R | 66 R/SSURGO_spatial_query.R | 166 R/STR.R | 694 +-- R/SoilDataViewer.R | 267 - R/WCS-utils.R | 2363 ++++++++---- R/aqp_data.R | 96 R/createSSURGO.R | 1756 +++++--- R/createStaticNASIS.R | 372 - R/database-sources.R | 34 R/dbQueryNASIS.R | 168 R/estimateColorMixture.R | 174 R/fetchEDIT_tools.R | 316 - R/fetchHWSD.R | 244 - R/fetchHenry.R | 902 ++-- R/fetchKSSL.R | 898 ++-- R/fetchLDM.R | 765 +-- R/fetchNASIS.R | 269 - R/fetchNASISLabData.R | 148 R/fetchNASISWebReport.R | 712 +-- R/fetchNASIS_components.R | 382 - R/fetchNOAA.R | 262 - R/fetchOSD.R | 922 ++-- R/fetchPedonPC.R | 242 - R/fetchRaCA.R | 402 +- R/fetchSCAN.R | 1190 +++--- R/fetchSDA_spatial.R | 776 +-- R/fetchSOLUS.R | 734 +-- R/fetchSRI.R | 362 - R/fetchSoilGrids.R | 942 ++-- R/fetchVegdata.R | 192 R/filter_KSSL.R | 88 R/getHzErrorsNASIS.R | 92 R/getHzErrorsPedonPC.R | 48 R/get_NASIS_table_key_by_name.R | 126 R/get_NASIS_table_name_by_purpose.R | 478 +- R/get_OSD.R | 471 +- R/get_RMF_from_NASIS_db.R | 136 R/get_SDA_NASIS_keys.R | 156 R/get_SDA_coecoclass.R | 646 +-- R/get_SDA_cosurfmorph.R | 372 - R/get_SDA_hydric.R | 264 - R/get_SDA_interpretation.R | 2042 +++++----- R/get_SDA_metrics.R | 124 R/get_SDA_muaggatt.R | 100 R/get_SDA_pmgroupname.R | 434 +- R/get_SDA_property.R | 1452 +++---- R/get_SSURGO_utils.R | 739 +-- R/get_colors_from_NASIS_db.R | 286 - R/get_component_data_from_NASIS_db.R | 1380 +++---- R/get_component_from_GDB.R | 1589 ++++---- R/get_component_from_SDA.R | 2066 +++++----- R/get_concentrations_from_NASIS_db.R | 102 R/get_cosoilmoist_from_NASIS.R | 134 R/get_cosoilmoist_from_NASISWebReport.R | 86 R/get_cosoilmoist_from_SDA.R | 90 R/get_ecosite_history_from_NASIS_db.R | 92 R/get_extended_data_from_NASIS_db.R | 690 +-- R/get_extended_data_from_pedon_db.R | 286 - R/get_hz_data_from_NASIS_db.R | 138 R/get_hz_data_from_pedon_db.R | 168 R/get_lablayer_data_from_NASIS_db.R | 120 R/get_labpedon_data_from_NASIS_db.R | 76 R/get_mapunit_from_NASIS.R | 376 - R/get_phfmp_from_NASIS_db.R | 60 R/get_phlabresults_data_from_NASIS_db.R | 276 - R/get_phroots_from_NASIS_db.R | 102 R/get_project_from_NASIS.R | 192 R/get_site_data_from_NASIS_db.R | 512 +- R/get_site_data_from_pedon_db.R | 190 R/get_soilseries_from_NASIS.R | 240 - R/get_text_notes_from_NASIS_db.R | 366 - R/get_veg_data_from_NASIS_db.R | 134 R/get_veg_from_AK_Site.R | 88 R/get_veg_from_MT_veg_db.R | 84 R/get_veg_from_NPS_PLOTS_db.R | 78 R/get_veg_other_from_MT_veg_db.R | 84 R/get_veg_species_from_MT_veg_db.R | 80 R/get_vegplot_data_from_NASIS_db.R | 1178 ++--- R/mukey-WCS.R | 554 +- R/openNASISchannel.R | 188 R/parseWebReport.R | 246 - R/seriesExtent.R | 323 - R/siblings.R | 272 - R/simplifyArtifactData.R | 298 - R/simplifyColorData.R | 366 - R/simplifyFragmentData.R | 526 +- R/soilColorWCS.R | 492 +- R/soilDB-package.R | 324 - R/soilDB_user_dir.R | 122 R/taxaExtent.R | 748 +-- R/uncode.R | 796 ++-- R/utils.R | 2693 ++++++------- R/waterDayYear.R | 102 build/partial.rdb |binary build/vignette.rds |binary data/SCAN_SNOTEL_metadata.rda |binary data/gopheridge.R | 28 data/loafercreek.R | 28 data/mineralKing.R | 28 inst/CITATION | 36 inst/WORDLIST | 1570 +++---- inst/doc/dominant-es.R | 288 - inst/doc/dominant-es.Rmd | 578 +- inst/doc/dominant-es.html | 1326 +++--- inst/doc/fetchNASIS.R | 510 +- inst/doc/fetchNASIS.Rmd | 544 +- inst/doc/fetchNASIS.html | 2538 +----------- inst/doc/local-ssurgo.R | 290 - inst/doc/local-ssurgo.Rmd | 628 +-- inst/doc/local-ssurgo.html | 1372 +++--- inst/doc/sda.R | 1962 ++++----- inst/doc/sda.Rmd | 4380 +++++++++++----------- inst/doc/sda.html | 5316 +++++++++++++-------------- inst/doc/soilweb-data-functions.R | 252 - inst/doc/soilweb-data-functions.Rmd | 1118 ++--- inst/doc/soilweb-data-functions.html | 1994 +++++----- inst/doc/wcs-ssurgo.R | 1195 +++--- inst/doc/wcs-ssurgo.Rmd | 1706 ++++---- inst/doc/wcs-ssurgo.html | 2434 ++++++------ man/ISSR800.wcs.Rd | 156 man/KSSL_VG_model.Rd | 122 man/NASISChoiceList.Rd | 120 man/NASISDomainsAsFactor.Rd | 44 man/NASISLocalDatabase.Rd | 36 man/OSDquery.Rd | 258 - man/ROSETTA.Rd | 222 - man/SCAN_SNOTEL_metadata.Rd | 28 man/SDA_query.Rd | 162 man/SDA_spatialQuery.Rd | 472 +- man/STRplot.Rd | 88 man/SoilWeb_spatial_query.Rd | 110 man/WCS_details.Rd | 42 man/createSSURGO.Rd | 189 man/createStaticNASIS.Rd | 84 man/dbConnectNASIS.Rd | 44 man/dbQueryNASIS.Rd | 46 man/downloadSSURGO.Rd | 183 man/estimateColorMixture.Rd | 54 man/fetchGDB.Rd | 186 man/fetchHWSD.Rd | 138 man/fetchHenry.Rd | 198 - man/fetchKSSL.Rd | 262 - man/fetchLDM.Rd | 175 man/fetchNASIS.Rd | 242 - man/fetchNASISLabData.Rd | 58 man/fetchNASISWebReport.Rd | 188 man/fetchOSD.Rd | 254 - man/fetchPedonPC.Rd | 78 man/fetchRaCA.Rd | 116 man/fetchSCAN.Rd | 250 - man/fetchSDA.Rd | 230 - man/fetchSDA_spatial.Rd | 182 man/fetchSOLUS.Rd | 282 - man/fetchSRI.Rd | 70 man/fetchSoilGrids.Rd | 370 - man/fetchVegdata.Rd | 230 - man/filter_geochem.Rd | 68 man/format_SQL_in_statement.Rd | 46 man/getHzErrorsNASIS.Rd | 50 man/get_EDIT_ecoclass_by_geoUnit.Rd | 52 man/get_NASIS_metadata.Rd | 90 man/get_NASIS_table_key_by_name.Rd | 60 man/get_NASIS_table_metadata.Rd | 92 man/get_NASIS_table_name_by_purpose.Rd | 82 man/get_NOAA_GHCND.Rd | 76 man/get_NOAA_stations_nearXY.Rd | 72 man/get_OSD.Rd | 94 man/get_RMF_from_NASIS_db.Rd | 46 man/get_SDA_NASIS_key.Rd | 118 man/get_SDA_coecoclass.Rd | 176 man/get_SDA_cosurfmorph.Rd | 170 man/get_SDA_hydric.Rd | 114 man/get_SDA_interpretation.Rd | 1428 +++---- man/get_SDA_metrics.Rd | 62 man/get_SDA_muaggatt.Rd | 68 man/get_SDA_pmgroupname.Rd | 98 man/get_SDA_property.Rd | 310 - man/get_SDV_legend_elements.Rd | 56 man/get_SRI.Rd | 158 man/get_SRI_layers.Rd | 58 man/get_colors_from_NASIS_db.Rd | 78 man/get_colors_from_pedon_db.Rd | 50 man/get_comonth_from_NASIS_db.Rd | 90 man/get_component_data_from_NASIS_db.Rd | 182 man/get_cosoilmoist_from_NASIS.Rd | 108 man/get_ecosite_history_from_NASIS_db.Rd | 62 man/get_extended_data_from_NASIS_db.Rd | 94 man/get_extended_data_from_pedon_db.Rd | 50 man/get_hz_data_from_NASIS_db.Rd | 64 man/get_hz_data_from_pedon_db.Rd | 58 man/get_lablayer_data_from_NASIS_db.Rd | 64 man/get_labpedon_data_from_NASIS_db.Rd | 64 man/get_mapunit_from_NASIS.Rd | 90 man/get_phroots_from_NASIS_db.Rd | 38 man/get_project_from_NASIS.Rd | 48 man/get_site_data_from_NASIS_db.Rd | 114 man/get_site_data_from_pedon_db.Rd | 50 man/get_soilDB_env.Rd | 47 man/get_soilseries_from_NASIS.Rd | 92 man/get_text_notes_from_NASIS_db.Rd | 110 man/get_veg_data_from_NASIS_db.Rd | 56 man/get_veg_from_AK_Site.Rd | 50 man/get_veg_from_MT_veg_db.Rd | 52 man/get_veg_from_NPS_PLOTS_db.Rd | 54 man/get_veg_other_from_MT_veg_db.Rd | 52 man/get_veg_species_from_MT_veg_db.Rd | 52 man/loafercreek.Rd | 162 man/local_NASIS_defined.Rd | 64 man/make_EDIT_service_URL.Rd | 184 man/metadata.Rd | 52 man/mukey.wcs.Rd | 165 man/parseWebReport.Rd | 66 man/processSDA_WKT.Rd | 76 man/seriesExtent.Rd | 130 man/siblings.Rd | 124 man/simplifyColorData.Rd | 102 man/simplifyFragmentData.Rd | 138 man/soilColor.wcs.Rd | 181 man/soilDB-package.Rd | 42 man/soilDB_user_dir.Rd | 124 man/taxaExtent.Rd | 520 +- man/uncode.Rd | 138 man/waterDayYear.Rd | 72 tests/testthat/test-ISSR800.R | 208 - tests/testthat/test-OSDquery.R | 74 tests/testthat/test-ROSETTA.R | 392 - tests/testthat/test-SDA_query.R | 618 +-- tests/testthat/test-SoilDataViewer.R | 60 tests/testthat/test-aqp_data.R | 38 tests/testthat/test-createSSURGO.R |only tests/testthat/test-dbQueryNASIS.R | 64 tests/testthat/test-estimateColorMixture.R | 94 tests/testthat/test-estimateSTR.R | 86 tests/testthat/test-fetchEDIT_tools.R | 92 tests/testthat/test-fetchGDB.R |only tests/testthat/test-fetchHenry.R | 412 +- tests/testthat/test-fetchKSSL.R | 400 +- tests/testthat/test-fetchLDM.R | 130 tests/testthat/test-fetchNASIS.R | 310 - tests/testthat/test-fetchNASISLabData.R | 94 tests/testthat/test-fetchNASISWebReport.R | 198 - tests/testthat/test-fetchOSD.R | 286 - tests/testthat/test-fetchSCAN.R | 156 tests/testthat/test-fetchSDA.R | 146 tests/testthat/test-fetchSDA_spatial.R | 184 tests/testthat/test-fetchSOLUS.R | 210 - tests/testthat/test-fetchSRI.R | 92 tests/testthat/test-fetchSoilGrids.R | 80 tests/testthat/test-get_OSD.R | 126 tests/testthat/test-get_SDA_coecoclass.R | 120 tests/testthat/test-get_SDA_cosurfmorph.R | 62 tests/testthat/test-get_SDA_hydric.R | 62 tests/testthat/test-get_SDA_interpretation.R | 208 - tests/testthat/test-get_SDA_muaggatt.R | 28 tests/testthat/test-get_SDA_pmgroupname.R | 52 tests/testthat/test-get_SDA_property.R | 678 +-- tests/testthat/test-get_SSURGO_utils.R | 30 tests/testthat/test-mukey-WCS.R | 94 tests/testthat/test-seriesExtent.R | 52 tests/testthat/test-siblings.R | 124 tests/testthat/test-simplifyArtifactData.R | 388 - tests/testthat/test-simplifyColorData.R | 326 - tests/testthat/test-simplifyFragmentData.R | 980 ++-- tests/testthat/test-soilDBdata.R | 190 tests/testthat/test-taxaExtent.R | 74 tests/testthat/test-uncode.R | 110 tests/testthat/test-waterDayYear.R | 216 - vignettes/dominant-es.Rmd | 578 +- vignettes/fetchNASIS.Rmd | 544 +- vignettes/local-ssurgo.Rmd | 628 +-- vignettes/sda.Rmd | 4380 +++++++++++----------- vignettes/soilweb-data-functions.Rmd | 1118 ++--- vignettes/wcs-ssurgo.Rmd | 1706 ++++---- 284 files changed, 55806 insertions(+), 56016 deletions(-)
Title: Betas-Select in Structural Equation Models and Linear Models
Description: It computes betas-select, coefficients after standardization in
structural equation models and regression models, standardizing only selected
variables. Supports models with moderation, with product terms formed after
standardization. It also offers confidence intervals that account for
standardization, including bootstrap confidence intervals as proposed by
Cheung et al. (2022) <doi:10.1037/hea0001188>. An introduction to the package
can be found in Sun et al. (2026) <doi:10.1080/00273171.2026.2672692>.
Author: Shu Fai Cheung [aut, cre] ,
Rong Wei Sun [aut] ,
Florbela Chang [aut] ,
Wendie Yang [aut] ,
Sing-Hang Cheung [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between betaselectr versions 0.2.1 dated 2026-06-09 and 0.2.2 dated 2026-07-11
DESCRIPTION | 6 MD5 | 122 NEWS.md | 12 R/lav_betaselect.R | 1378 ++--- R/lm_betaselect.R | 1576 +++--- R/lm_betaselect_methods.R | 5144 ++++++++++----------- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 30 man/anova.lm_betaselect.Rd | 194 man/coef.lav_betaselect.Rd | 120 man/coef.lm_betaselect.Rd | 190 man/confint.lav_betaselect.Rd | 134 man/confint.lm_betaselect.Rd | 356 - man/data_test_medmod.Rd | 86 man/data_test_mod_cat.Rd | 70 man/data_test_mod_cat2.Rd | 76 man/data_test_mod_cat_binary.Rd | 68 man/getCall.lm_betaselect.Rd | 156 man/lav_betaselect.Rd | 818 +-- man/lm_betaselect.Rd | 978 +-- man/predict.glm_betaselect.Rd | 182 man/predict.lm_betaselect.Rd | 174 man/print.lav_betaselect.Rd | 298 - man/std_data.Rd | 90 man/summary.glm_betaselect.Rd | 524 +- man/summary.lm_betaselect.Rd | 444 - man/vcov.lm_betaselect.Rd | 282 - tests/testthat/test-lav_betaselect.R | 274 - tests/testthat/test-lav_betaselect_check.R | 96 tests/testthat/test-lav_betaselect_coef.R | 140 tests/testthat/test-lav_betaselect_confint.R | 84 tests/testthat/test-lav_betaselect_mg.R | 306 - tests/testthat/test-lav_betaselect_mg_eq.R | 298 - tests/testthat/test-lav_betaselect_mod.R | 200 tests/testthat/test-lav_betaselect_mod_Intercept.R | 180 tests/testthat/test-lav_betaselect_mod_boot_1.R | 140 tests/testthat/test-lav_betaselect_mod_boot_2.R | 114 tests/testthat/test-lav_betaselect_mod_boot_3.R | 104 tests/testthat/test-lav_betaselect_mod_boot_4.R | 110 tests/testthat/test-lav_betaselect_mod_colon.R | 200 tests/testthat/test-lav_betaselect_mod_mg.R | 240 tests/testthat/test-lav_betaselect_mod_no_center.R | 168 tests/testthat/test-lav_betaselect_one_iv.R | 215 tests/testthat/test-lav_betaselect_ord.R | 136 tests/testthat/test-lav_betaselect_parallel.R | 122 tests/testthat/test-lav_betaselect_print_ustd.R | 82 tests/testthat/test-lav_betaselect_tmp.R | 136 tests/testthat/test-lav_betaselect_user_1.R | 135 tests/testthat/test-lav_betaselect_user_2.R | 86 tests/testthat/test-lav_betaselect_user_boot_1.R | 168 tests/testthat/test_find_all_products_cats.R | 102 tests/testthat/test_glm_betaselect_skip_def.R | 28 vignettes/apa.csl | 3832 +++++++-------- vignettes/articles/apa.csl | 3832 +++++++-------- vignettes/articles/lav_betaselect_technical.Rmd | 496 +- vignettes/articles/lm_betaselect_technical.Rmd | 208 vignettes/betaselectr_glm.Rmd.original | 822 +-- vignettes/betaselectr_lav.Rmd.original | 812 +-- vignettes/betaselectr_lm.Rmd.original | 846 +-- vignettes/references.bib | 378 - 62 files changed, 14324 insertions(+), 14276 deletions(-)
More information about BayesSurveillance at CRAN
Permanent link
Title: Construction of Genetic Maps in Experimental Crosses
Description: Analysis of molecular marker data from model and non-model systems.
For the later, it allows statistical analysis by simultaneously estimating
linkage and linkage phases (genetic map construction) according to Wu and
colleagues (2002)
<doi:10.1006/tpbi.2002.1577>. All analysis are based on multi-point
approaches using hidden Markov models.
Author: Cristiane Taniguti [aut, cre],
Marcelo Mollinari [aut],
Rodrigo Amadeu [ctb],
Getulio Ferreira [ctb],
Gabriel Margarido [aut],
Jeekin Lau [ctb],
Karl Broman [ctb],
Katharine Preedy [ctb, cph] ,
Bastian Schiffthaler [ctb, cph] ,
Augusto Garcia [aut, c [...truncated...]
Maintainer: Cristiane Taniguti <ctaniguti@ufl.edu>
Diff between onemap versions 3.2.4 dated 2026-01-12 and 3.2.6 dated 2026-07-11
DESCRIPTION | 10 ++--- MD5 | 24 ++++++------- NEWS.md | 10 +++++ R/create_probs.R | 56 +++++++++++++------------------- R/onemap_read_vcfR.R | 57 +++++++++++++++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Inbred_Based_Populations.html | 9 ++--- inst/doc/Introduction_R.Rmd | 2 - inst/doc/Introduction_R.html | 57 +++++++++++++++++---------------- inst/doc/Outcrossing_Populations.html | 9 ++--- inst/doc/Overview.html | 4 +- vignettes/Introduction_R.Rmd | 2 - 13 files changed, 136 insertions(+), 104 deletions(-)
Title: Healthcare Analysis Methods
Description: Conducts analyses for healthcare program evaluations or intervention
studies. Calculates regression analyses for standard ordinary least squares
(OLS or linear) or logistic models. Performs regression models used for
causal modeling such as differences-in-differences (DID) and interrupted
time series (ITS) models. Provides limited interpretations of model
results and a ranking of variable importance in models. Performs
propensity score models, top-coding of model outcome variables, and
can return new data with the newly formed variables. Conducts Bayesian
analysis summaries and graphs, decision curve analysis, and produces some
Shewhart control charts. Also performs Cronbach's alpha for various scale
items (e.g., survey questions). See Github URL for examples in the README
file. For more details on the statistical methods, see
Allen & Yen (1979, ISBN:0-8185-0283-5),
Angrist & Pischke (2009, ISBN:9780691120355),
Cohen (1988, ISBN:0-8058-0283-5),
Gebski (2012) <doi:10.1017/S0 [...truncated...]
Author: Stephen Zuniga [aut, cre, cph]
Maintainer: Stephen Zuniga <rms.shiny@gmail.com>
Diff between ham versions 1.2.0 dated 2026-03-19 and 1.3.0 dated 2026-07-11
DESCRIPTION | 12 MD5 | 120 +-- NAMESPACE | 179 ++-- NEWS.md | 2 R/Bayes.R | 391 ++++++++-- R/alpha.R | 2 R/assess.R | 230 +++++- R/control.R | 10 R/data.R | 25 R/decide.R | 3 R/group.R | 9 R/importance.R | 6 R/interpret.R | 511 ++++++++++++- R/itsEffect.R | 16 R/plot.Bayes.R | 51 - R/plot.assess.R | 2 R/plot.control.R | 32 R/plot.decide.R | 3 R/plot.group.R | 64 + R/plot.importance.R | 7 R/plot.review.R |only R/print.alpha.R | 3 R/print.interpret.R | 72 + R/print.review.R |only R/review.R |only README.md | 325 +++++++- data/NHSN.rda |only data/co2multi.rda |binary inst/doc/Bayes.R | 18 inst/doc/Bayes.Rmd | 70 + inst/doc/Bayes.html | 429 ++++++++--- inst/doc/control.R | 4 inst/doc/control.Rmd | 4 inst/doc/control.html | 8 inst/doc/ham-package.R | 81 ++ inst/doc/ham-package.Rmd | 151 +++- inst/doc/ham-package.html | 1251 ++++++++++++++++++++++------------ man/Bayes.Rd | 61 + man/NHSN.Rd |only man/alpha.Rd | 3 man/assess.Rd | 57 + man/control.Rd | 6 man/decide.Rd | 3 man/figures/README-chartU1-1.png |binary man/figures/README-plotreview2b-1.png |only man/group.Rd | 3 man/importance.Rd | 7 man/interpret.Rd | 30 man/itsEffect.Rd | 17 man/plot.Bayes.Rd | 3 man/plot.assess.Rd | 3 man/plot.control.Rd | 9 man/plot.decide.Rd | 3 man/plot.group.Rd | 16 man/plot.importance.Rd | 7 man/plot.review.Rd |only man/print.alpha.Rd | 3 man/print.interpret.Rd | 7 man/print.review.Rd |only man/review.Rd |only tests/testthat/test-Bayes.R | 2 tests/testthat/test-interpret.R | 2 tests/testthat/test-review.R |only vignettes/Bayes.Rmd | 70 + vignettes/control.Rmd | 4 vignettes/ham-package.Rmd | 151 +++- 66 files changed, 3481 insertions(+), 1077 deletions(-)
Title: Tree-Spatial Scan Statistic for Cluster Detection
Description: Implements the tree-spatial scan statistic for detecting clusters
that combine both spatial and hierarchical structures, as proposed by
Cancado et al. (2025) <doi:10.1007/s10651-025-00670-w>. The method extends
Kulldorff (1997) <doi:10.1080/03610929708831995> circular spatial scan
statistic and the tree-based scan statistic of Kulldorff et al. (2003)
<doi:10.1111/1541-0420.00039> by searching for anomalies in both
geographic regions and branches of hierarchical trees simultaneously. The
package also provides standalone implementations of Kulldorff's circular
spatial scan statistic and the tree-based scan statistic. Statistical
significance is assessed via Monte Carlo simulation under a Poisson or
binomial model, with optional 'OpenMP' parallelization.
Author: Allan Quadros [aut, cre] ,
Andre L. F. Cancado [aut] ,
Geiziane S. Oliveira [aut],
Luiz H. Duczmal [aut]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between treeSS versions 0.2.4 dated 2026-07-02 and 0.2.5 dated 2026-07-11
DESCRIPTION | 6 MD5 | 12 NEWS.md | 33 ++ R/build_zones.R | 58 +++- R/csr_helpers.R | 53 ++- inst/doc/florida.html | 636 +++++++++++++++++++-------------------------- inst/doc/introduction.html | 504 ++++++++++++++--------------------- 7 files changed, 597 insertions(+), 705 deletions(-)
Title: An IMAP Client for R
Description: A session-based IMAP client that implements the full functionality of
the IMAP4rev1 protocol (RFC 3501), allowing virtually all e-mail operations to be
performed from within R, paving the way for e-mail data analysis.
Author: Allan Quadros [aut, cre] ,
Paul Smith [ctb],
Kurt Hornik [ctb]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between mRpostman versions 1.1.4 dated 2024-09-17 and 1.2.2 dated 2026-07-11
mRpostman-1.1.4/mRpostman/inst/doc/code_migration.R |only mRpostman-1.1.4/mRpostman/inst/doc/code_migration.Rmd |only mRpostman-1.1.4/mRpostman/inst/doc/code_migration.html |only mRpostman-1.1.4/mRpostman/vignettes/code_migration.Rmd |only mRpostman-1.1.4/mRpostman/vignettes/figures/xoauth |only mRpostman-1.2.2/mRpostman/DESCRIPTION | 20 mRpostman-1.2.2/mRpostman/MD5 | 194 - mRpostman-1.2.2/mRpostman/R/AND.R | 4 mRpostman-1.2.2/mRpostman/R/OR.R | 4 mRpostman-1.2.2/mRpostman/R/R6.R | 400 ++- mRpostman-1.2.2/mRpostman/R/add-flags-int.R | 6 mRpostman-1.2.2/mRpostman/R/adjust-folder-name.R | 2 mRpostman-1.2.2/mRpostman/R/adjust_repeated_filenames.R | 2 mRpostman-1.2.2/mRpostman/R/append-int.R |only mRpostman-1.2.2/mRpostman/R/apply-charset.R |only mRpostman-1.2.2/mRpostman/R/assert-capability.R |only mRpostman-1.2.2/mRpostman/R/check-args.R | 6 mRpostman-1.2.2/mRpostman/R/clean-msg-text.R | 15 mRpostman-1.2.2/mRpostman/R/close-folder-int.R |only mRpostman-1.2.2/mRpostman/R/config-con-handle-and-params.R | 4 mRpostman-1.2.2/mRpostman/R/create-folder-int.R | 2 mRpostman-1.2.2/mRpostman/R/decode-mime-header.R | 11 mRpostman-1.2.2/mRpostman/R/decode-mime-text.R | 11 mRpostman-1.2.2/mRpostman/R/decode-quoted-printable-header.R | 59 mRpostman-1.2.2/mRpostman/R/decode-quoted-printable-text.R | 51 mRpostman-1.2.2/mRpostman/R/define-searchrequest-custom.R | 12 mRpostman-1.2.2/mRpostman/R/define-searchrequest-size.R | 4 mRpostman-1.2.2/mRpostman/R/define-searchrequest-string.R | 14 mRpostman-1.2.2/mRpostman/R/delete-folder-int.R |only mRpostman-1.2.2/mRpostman/R/esearch-count-int.R | 8 mRpostman-1.2.2/mRpostman/R/esearch-max-id-int.R | 10 mRpostman-1.2.2/mRpostman/R/esearch-min-id-int.R | 10 mRpostman-1.2.2/mRpostman/R/examine-folder-int.R | 17 mRpostman-1.2.2/mRpostman/R/execute-attachment-fetch.R | 6 mRpostman-1.2.2/mRpostman/R/execute-ordered-search.R |only mRpostman-1.2.2/mRpostman/R/execute-search.R | 22 mRpostman-1.2.2/mRpostman/R/expunge-int.R | 2 mRpostman-1.2.2/mRpostman/R/extract-MIME-level-and-filenames.R | 2 mRpostman-1.2.2/mRpostman/R/fetch-attachments-int.R | 4 mRpostman-1.2.2/mRpostman/R/fetch-body-int.R | 2 mRpostman-1.2.2/mRpostman/R/fetch-header-int.R | 2 mRpostman-1.2.2/mRpostman/R/fetch-metadata-int.R | 2 mRpostman-1.2.2/mRpostman/R/fetch-text-int.R | 2 mRpostman-1.2.2/mRpostman/R/get-attachments-int.R | 4 mRpostman-1.2.2/mRpostman/R/get-quota-int.R |only mRpostman-1.2.2/mRpostman/R/get-quota-root-int.R |only mRpostman-1.2.2/mRpostman/R/id-int.R |only mRpostman-1.2.2/mRpostman/R/list-attachments.R | 2 mRpostman-1.2.2/mRpostman/R/list-mail-folders-int.R | 122 mRpostman-1.2.2/mRpostman/R/list-special-use-folders-int.R |only mRpostman-1.2.2/mRpostman/R/list-subscribed-folders-int.R |only mRpostman-1.2.2/mRpostman/R/modify-con-handle.R | 2 mRpostman-1.2.2/mRpostman/R/move-msg-int.R | 6 mRpostman-1.2.2/mRpostman/R/namespace-int.R |only mRpostman-1.2.2/mRpostman/R/noop-int.R |only mRpostman-1.2.2/mRpostman/R/parse-esearch-all.R |only mRpostman-1.2.2/mRpostman/R/parse-examine-counts.R |only mRpostman-1.2.2/mRpostman/R/parse-folder-list.R |only mRpostman-1.2.2/mRpostman/R/parse-id.R |only mRpostman-1.2.2/mRpostman/R/parse-namespace.R |only mRpostman-1.2.2/mRpostman/R/parse-quota.R |only mRpostman-1.2.2/mRpostman/R/parse-sort.R |only mRpostman-1.2.2/mRpostman/R/parse-special-use.R |only mRpostman-1.2.2/mRpostman/R/parse-status-counts.R |only mRpostman-1.2.2/mRpostman/R/parse-thread.R |only mRpostman-1.2.2/mRpostman/R/remove-flags-int.R | 6 mRpostman-1.2.2/mRpostman/R/rename-folder-int.R | 2 mRpostman-1.2.2/mRpostman/R/replace-flags-int.R | 6 mRpostman-1.2.2/mRpostman/R/search-int.R | 2 mRpostman-1.2.2/mRpostman/R/sent-before.R | 4 mRpostman-1.2.2/mRpostman/R/sent-on.R | 2 mRpostman-1.2.2/mRpostman/R/serialize-filename.R | 2 mRpostman-1.2.2/mRpostman/R/smaller-than.R | 2 mRpostman-1.2.2/mRpostman/R/sort-int.R |only mRpostman-1.2.2/mRpostman/R/status-int.R |only mRpostman-1.2.2/mRpostman/R/subscribe-folder-int.R |only mRpostman-1.2.2/mRpostman/R/thread-int.R |only mRpostman-1.2.2/mRpostman/R/unselect-folder-int.R |only mRpostman-1.2.2/mRpostman/R/unsubscribe-folder-int.R |only mRpostman-1.2.2/mRpostman/R/zzz.R | 2 mRpostman-1.2.2/mRpostman/README.md | 247 + mRpostman-1.2.2/mRpostman/build/vignette.rds |binary mRpostman-1.2.2/mRpostman/inst/doc/basics.R | 73 mRpostman-1.2.2/mRpostman/inst/doc/basics.Rmd | 191 + mRpostman-1.2.2/mRpostman/inst/doc/basics.html | 1271 ++++------ mRpostman-1.2.2/mRpostman/inst/doc/xoauth2.0.R | 110 mRpostman-1.2.2/mRpostman/inst/doc/xoauth2.0.Rmd | 367 +- mRpostman-1.2.2/mRpostman/inst/doc/xoauth2.0.html | 528 +--- mRpostman-1.2.2/mRpostman/man/AND.Rd | 4 mRpostman-1.2.2/mRpostman/man/ImapCon.Rd | 918 ++++++- mRpostman-1.2.2/mRpostman/man/OR.Rd | 4 mRpostman-1.2.2/mRpostman/man/decode_mime_header.Rd | 4 mRpostman-1.2.2/mRpostman/man/larger_than.Rd | 2 mRpostman-1.2.2/mRpostman/man/list_attachments.Rd | 2 mRpostman-1.2.2/mRpostman/man/mRpostman-package.Rd | 6 mRpostman-1.2.2/mRpostman/man/sent_before.Rd | 4 mRpostman-1.2.2/mRpostman/man/sent_on.Rd | 2 mRpostman-1.2.2/mRpostman/man/smaller_than.Rd | 2 mRpostman-1.2.2/mRpostman/tests |only mRpostman-1.2.2/mRpostman/vignettes/basics.Rmd | 191 + mRpostman-1.2.2/mRpostman/vignettes/xoauth2.0.Rmd | 367 +- 101 files changed, 3442 insertions(+), 1925 deletions(-)
Title: A Lightweight Version of R Markdown
Description: Render R Markdown to Markdown (without using 'knitr'), and Markdown
to lightweight HTML or 'LaTeX' documents with the 'commonmark' package (instead
of 'Pandoc'). Some missing Markdown features in 'commonmark' are also
supported, such as raw HTML or 'LaTeX' blocks, 'LaTeX' math, superscripts,
subscripts, footnotes, element attributes, and appendices,
but not all 'Pandoc' Markdown features are (or will be) supported. With
additional JavaScript and CSS, you can also create HTML slides and articles.
This package can be viewed as a trimmed-down version of R Markdown and
'knitr'. It does not aim at rich Markdown features or a large variety of
output formats (the primary formats are HTML and 'LaTeX'). Book and website
projects of multiple input documents are also supported.
Author: Yihui Xie [aut, cre] ,
Tim Taylor [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between litedown versions 0.9 dated 2025-12-18 and 0.10 dated 2026-07-11
litedown-0.10/litedown/DESCRIPTION | 10 +- litedown-0.10/litedown/LICENSE | 2 litedown-0.10/litedown/MD5 | 64 +++++++++++------- litedown-0.10/litedown/NAMESPACE | 1 litedown-0.10/litedown/NEWS.md | 38 ++++++++-- litedown-0.10/litedown/R/format.R | 4 - litedown-0.10/litedown/R/fuse.R | 70 +++++++++++++++++++- litedown-0.10/litedown/R/mark.R | 46 ++++++++----- litedown-0.10/litedown/R/package.R | 2 litedown-0.10/litedown/R/site.R | 61 ++++++++++++++--- litedown-0.10/litedown/R/utils.R | 24 +++++- litedown-0.10/litedown/build/vignette.rds |binary litedown-0.10/litedown/inst/doc/slides.Rmd | 2 litedown-0.10/litedown/inst/doc/slides.html | 36 +++++----- litedown-0.10/litedown/inst/resources/default.css | 14 ++-- litedown-0.10/litedown/inst/resources/litedown.html | 2 litedown-0.10/litedown/inst/rstudio |only litedown-0.10/litedown/man/fuse_book.Rd | 9 ++ litedown-0.10/litedown/man/fuse_exit.Rd |only litedown-0.10/litedown/man/fuse_site.Rd | 9 ++ litedown-0.10/litedown/man/html_format.Rd | 2 litedown-0.10/litedown/man/litedown-package.Rd | 7 +- litedown-0.10/litedown/man/mark.Rd | 9 ++ litedown-0.10/litedown/man/markdown_options.Rd | 2 litedown-0.10/litedown/tests/test-cran |only litedown-0.10/litedown/tests/test-cran.R |only litedown-0.10/litedown/vignettes/slides.Rmd | 2 litedown-0.9/litedown/tests/empty.R |only litedown-0.9/litedown/tests/fig_path.R |only litedown-0.9/litedown/tests/smartypants.R |only 30 files changed, 309 insertions(+), 107 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel [aut, cre] ,
Khanh Nguyen [aut] ,
Terry Leitch [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.27 dated 2026-06-07 and 0.4.28 dated 2026-07-10
ChangeLog | 21 +++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- configure | 18 +++++++++--------- configure.ac | 2 +- data/tsQuotes.RData |binary data/vcube.RData |binary inst/NEWS.Rd | 7 +++++++ man/Enum.Rd | 4 +++- src/calendars.cpp | 15 +++++++++++---- 10 files changed, 65 insertions(+), 28 deletions(-)
Title: Quadrangle Mesh
Description: Create surface forms from matrix or 'raster' data for flexible plotting and
conversion to other mesh types. The functions 'quadmesh' or 'triangmesh'
produce a continuous surface as a 'mesh3d' object as used by the 'rgl'
package. This is used for plotting raster data in 3D (optionally with
texture), and allows the application of a map projection without data loss and
many processing applications that are restricted by inflexible regular grid rasters.
There are discrete forms of these continuous surfaces available with
'dquadmesh' and 'dtriangmesh' functions.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between quadmesh versions 0.5.5 dated 2022-08-31 and 0.6.0 dated 2026-07-10
DESCRIPTION | 10 MD5 | 46 ++-- NAMESPACE | 4 NEWS.md | 17 + R/mesh-plot.R | 318 +++++++++++++++---------------- R/qsc.R | 4 R/quadmesh.R | 39 ++- R/triangmesh.R | 5 README.md | 19 + build/vignette.rds |binary inst/doc/quadmesh.html | 267 +++++++++++++------------- inst/doc/topography.R | 8 inst/doc/topography.html | 203 ++++++++++--------- man/cmip6.Rd | 2 man/etopo.Rd | 2 man/figures/README-unnamed-chunk-9-2.png |binary man/mesh_plot.Rd | 51 +++- man/quadmesh-package.Rd | 6 man/quadmesh.Rd | 43 +++- man/triangmesh.Rd | 2 man/worldll.Rd | 2 man/xymap.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-triangle-mesh.R | 2 24 files changed, 594 insertions(+), 458 deletions(-)
Title: Psychometric Modeling Infrastructure
Description: Infrastructure for psychometric modeling such as data classes (for
item response data and paired comparisons), basic model fitting functions (for
Bradley-Terry, Rasch, parametric logistic IRT, generalized partial credit,
rating scale, multinomial processing tree models), extractor functions for
different types of parameters (item, person, threshold, discrimination,
guessing, upper asymptotes), unified inference and visualizations, and various
datasets for illustration. Intended as a common lightweight and efficient
toolbox for psychometric modeling and a common building block for fitting
psychometric mixture models in package "psychomix" and trees based on
psychometric models in package "psychotree".
Author: Achim Zeileis [aut, cre] ,
Carolin Strobl [aut] ,
Florian Wickelmaier [aut],
Basil Komboz [aut],
Julia Kopf [aut],
Lennart Schneider [aut] ,
Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychotools versions 0.7-6 dated 2026-02-11 and 0.7-7 dated 2026-07-10
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 6 +++++- R/btmodel.R | 2 +- R/gpcmodel.R | 4 ++-- R/itemresp.R | 2 +- R/mptmodel.R | 2 +- R/nplmodel.R | 4 ++-- R/paircomp.R | 2 +- R/pcmodel.R | 6 +++--- R/raschmodel.R | 6 +++--- R/rsmodel.R | 6 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/toolbox-simulation.Rnw | 1 - inst/doc/toolbox-simulation.pdf |binary vignettes/toolbox-simulation.Rnw | 1 - 17 files changed, 42 insertions(+), 40 deletions(-)
Title: Psychometric Mixture Models
Description: Psychometric mixture models based on 'flexmix' infrastructure. At the moment Rasch mixture models
with different parameterizations of the score distribution (saturated vs. mean/variance specification),
Bradley-Terry mixture models, and MPT mixture models are implemented. These mixture models can be estimated
with or without concomitant variables. See Frick et al. (2012) <doi:10.18637/jss.v048.i07> and
Frick et al. (2015) <doi:10.1177/0013164414536183> for details on the Rasch mixture models.
Author: Hannah Frick [aut] ,
Friedrich Leisch [aut] ,
Carolin Strobl [aut] ,
Florian Wickelmaier [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychomix versions 1.1-9 dated 2024-09-10 and 1.1-10 dated 2026-07-10
DESCRIPTION | 17 +++++++++-------- MD5 | 28 ++++++++++++++-------------- NEWS.md | 8 ++++++++ R/raschmix.R | 5 ++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/raschmix.R | 2 -- inst/doc/raschmix.Rnw | 8 +++----- inst/doc/raschmix.pdf |binary inst/doc/scores.R | 2 -- inst/doc/scores.Rnw | 7 +++---- inst/doc/scores.pdf |binary vignettes/psychomix.bib | 19 +++++++++---------- vignettes/raschmix.Rnw | 8 +++----- vignettes/scores.Rnw | 7 +++---- 15 files changed, 56 insertions(+), 55 deletions(-)
Title: A Shiny App to Visualize Genetic Maps and QTL Analysis in
Polyploid Species
Description: Provides a graphical user interface to integrate, visualize and explore results
from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid
species. The app is meant for interactive use and allows users to optionally upload different sources
of information, including gene annotation and alignment files, enabling the exploitation and search for
candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly',
'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.
Author: Cristiane Taniguti [aut, cre],
Gabriel de Siqueira Gesteira [aut],
Jeekin Lau [aut],
Olivia Angelin-Bonnet [aut],
Susan Thomson [ctb],
Guilherme da Silva Pereira [ctb],
David Byrne [ctb],
Zhao-Bang Zeng [ctb],
Oscar Riera-Lizarazu [ctb],
Marcelo Moll [...truncated...]
Maintainer: Cristiane Taniguti <ctaniguti@ufl.edu>
Diff between viewpoly versions 0.4.1 dated 2024-03-28 and 1.0.2 dated 2026-07-10
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Title: Search, Inspect, and Replace Text Across Files
Description: An inspectable and composable workflow for search-and-replace in text
files. Files can be listed, filtered, and searched separately, with
inspectable exclusions showing what was excluded and why. Matches are
represented as structured vectors that can be printed with context,
summarized, and filtered. Replacements can be defined at search time or set
and updated after the search. Only matches present in the vector are modified
when files are written. Backup and restore helpers are provided for file
workflows. Text that has already been read can also be searched and updated
directly, giving users control over input, output, and encoding when needed.
Author: Sacha Martingay [aut, cre, cph]
Maintainer: Sacha Martingay <martingay.sacha@hotmail.com>
Diff between seekr versions 0.1.4 dated 2026-02-08 and 0.2.0 dated 2026-07-10
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Title: Evaluate Partitioned Survival and State Transition Models
Description: Fits and evaluates three-state partitioned survival analyses
(PartSAs) and Markov models (clock forward or clock reset) to
progression and overall survival data typically collected in oncology clinical trials. These model structures are typically considered in
cost-effectiveness modeling in advanced/metastatic cancer indications.
Muston (2024). "Informing structural assumptions for three state oncology cost-effectiveness models through model efficiency and fit". Applied Health Economics and Health Policy.
Author: Dominic Muston [aut, cre] ,
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph, fnd]
Maintainer: Dominic Muston <dom.muston@gmail.com>
Diff between psm3mkv versions 0.3.2 dated 2024-06-07 and 0.3.3 dated 2026-07-10
DESCRIPTION | 17 ++++---- MD5 | 28 ++++++------- NEWS.md | 6 ++ R/datasets.R | 74 +++++++++++------------------------- R/discrmd.R | 6 +- R/lhoods.R | 12 ++--- R/ltablesurv.R | 6 +- R/resmeans.R | 34 ++++++++-------- build/vignette.rds |binary inst/doc/example.html | 34 ++++++++-------- inst/doc/mortality-adjustments.R | 40 +++++++++---------- inst/doc/mortality-adjustments.html | 27 ++++++------- man/create_dummydata.Rd | 4 - man/psm3mkv-package.Rd | 7 ++- man/vlookup.Rd | 2 15 files changed, 140 insertions(+), 157 deletions(-)
Title: Network Estimation, Bootstrap, and Higher-Order Analysis
Description: Estimate, compare, and analyze dynamic and psychological networks
using a unified interface. Provides transition network analysis
estimation (transition, frequency, co-occurrence, attention-weighted)
Saqr et al. (2025) <doi:10.1145/3706468.3706513>, psychological
network methods (correlation, partial correlation, 'graphical lasso',
'Ising') Saqr, Beck, and Lopez-Pernas (2024)
<doi:10.1007/978-3-031-54464-4_19>,
and higher-order network methods including higher-order networks,
higher-order network embedding, hyper-path anomaly, and multi-order
generative model. Supports bootstrap inference, permutation testing,
split-half reliability, centrality stability analysis, mixed Markov
models, multi-cluster multi-layer networks and clustering.
Author: Mohammed Saqr [aut, cre, cph],
Sonsoles Lopez-Pernas [aut],
Kamila Misiejuk [aut]
Maintainer: Mohammed Saqr <saqr@saqr.me>
Diff between Nestimate versions 0.6.0 dated 2026-05-31 and 0.8.0 dated 2026-07-10
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Title: Instrumental-Variables Regression by '2SLS', '2SM', or '2SMM',
with Diagnostics
Description: Instrumental variable estimation for linear models by two-stage least-squares (2SLS) regression or by robust-regression via M-estimation (2SM) or MM-estimation (2SMM). The main ivreg() model-fitting function is designed to provide a workflow as similar as possible to standard lm() regression. A wide range of methods is provided for fitted ivreg model objects, including extensive functionality for computing and graphing regression diagnostics in addition to other standard model tools.
Author: John Fox [aut] ,
Christian Kleiber [aut] ,
Achim Zeileis [aut, cre] ,
Nikolas Kuschnig [ctb] ,
R Core Team [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between ivreg versions 0.6-7 dated 2026-03-02 and 0.6-8 dated 2026-07-10
DESCRIPTION | 8 MD5 | 16 NEWS.md | 5 R/ivreg.fit.R | 2 R/ivregMethods.R | 6 R/summary.ivreg.R | 4 build/vignette.rds |binary inst/doc/Diagnostics-for-2SLS-Regression.html | 259 +++++----- inst/doc/ivreg.html | 653 ++++++++++++++++++++------ 9 files changed, 672 insertions(+), 281 deletions(-)