Title: Gibbs Samplers for Discrete Bayesian Spatiotemporal Models
Description: Takes Poisson or Binomial discrete spatial data and runs a Gibbs sampler for a variety of Spatiotemporal Conditional Autoregressive (CAR) models. Includes measures to prevent estimate over-smoothing through a restriction of model informativeness for select models. Also provides tools to load output and get median estimates. Implements methods from Besag, York, and Mollié (1991) "Bayesian image restoration, with two applications in spatial statistics" <doi:10.1007/BF00116466>, Gelfand and Vounatsou (2003) "Proper multivariate conditional autoregressive models for spatial data analysis" <doi:10.1093/biostatistics/4.1.11>, Quick et al. (2017) "Multivariate spatiotemporal modeling of age-specific stroke mortality" <doi:10.1214/17-AOAS1068>, and Quick et al. (2021) "Evaluating the informativeness of the Besag-York-Mollié CAR model" <doi:10.1016/j.sste.2021.100420>.
Author: David DeLara [aut, cre] ,
Centers for Disease Control and Prevention [aut, cph]
Maintainer: David DeLara <sfq1@cdc.gov>
Diff between RSTr versions 1.1.4 dated 2026-01-31 and 1.2.0 dated 2026-07-08
DESCRIPTION | 6 MD5 | 49 +++--- R/helper_get_params.R | 6 R/helper_print.R | 15 - R/helper_run_sampler.R | 9 - R/helper_update_sample.R | 8 - R/user_age_standardize.R | 40 ----- R/user_car.R | 11 + R/user_get_estimates.R | 110 ++++++++------ R/user_load_samples.R | 10 - R/user_split_sample_groups.R | 21 -- R/user_suppress_estimates.R | 29 +++ R/user_update_model.R | 17 -- build/partial.rdb |binary inst/doc/RSTr-agestandardize.html | 24 +-- inst/doc/RSTr-informativeness.html | 4 inst/doc/RSTr-reliability.html | 35 ++-- inst/doc/RSTr.Rmd | 69 ++++---- inst/doc/RSTr.html | 284 +++++++++++++++++-------------------- man/age_standardize.Rd | 4 man/car.Rd | 6 man/load_samples.Rd | 2 man/suppress_estimates.Rd | 2 src/update_G.cpp | 1 vignettes/RSTr.Rmd | 69 ++++---- vignettes/images/rstr-workflow.png |only 26 files changed, 423 insertions(+), 408 deletions(-)
Title: R Bindings for 'Automerge' 'CRDT' Library
Description: Provides R bindings to the 'Automerge' Conflict-free
Replicated Data Type ('CRDT') library. 'Automerge' enables automatic
merging of concurrent changes without conflicts, making it ideal for
distributed systems, collaborative applications, and offline-first
architectures. The approach of local-first software was proposed in
Kleppmann, M., Wiggins, A., van Hardenberg, P., McGranaghan, M. (2019)
<doi:10.1145/3359591.3359737>. This package supports all 'Automerge'
data types (maps, lists, text, counters) and provides both low-level
and high-level synchronization protocols for seamless interoperability
with 'JavaScript' and other 'Automerge' implementations.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Authors of the dependency Rust crates [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between automerge versions 0.4.0 dated 2026-02-26 and 0.5.0 dated 2026-07-08
automerge-0.4.0/automerge/src/automerge/rust/automerge-c/CMakeLists.txt |only automerge-0.4.0/automerge/src/automerge/rust/automerge-c/cmake |only automerge-0.5.0/automerge/DESCRIPTION | 13 automerge-0.5.0/automerge/MD5 | 163 - automerge-0.5.0/automerge/NAMESPACE | 3 automerge-0.5.0/automerge/NEWS.md | 6 automerge-0.5.0/automerge/R/constants.R | 4 automerge-0.5.0/automerge/R/import-standalone-defer.R |only automerge-0.5.0/automerge/R/methods.R | 3 automerge-0.5.0/automerge/README.md | 15 automerge-0.5.0/automerge/build/partial.rdb |binary automerge-0.5.0/automerge/build/vignette.rds |binary automerge-0.5.0/automerge/cleanup | 3 automerge-0.5.0/automerge/configure | 68 automerge-0.5.0/automerge/configure.win | 66 automerge-0.5.0/automerge/inst/AUTHORS | 51 automerge-0.5.0/automerge/inst/doc/automerge.R | 7 automerge-0.5.0/automerge/inst/doc/automerge.Rmd | 7 automerge-0.5.0/automerge/inst/doc/automerge.html | 31 automerge-0.5.0/automerge/inst/doc/crdt-concepts.html | 22 automerge-0.5.0/automerge/inst/doc/quick-reference.R | 9 automerge-0.5.0/automerge/inst/doc/quick-reference.Rmd | 20 automerge-0.5.0/automerge/inst/doc/quick-reference.html | 20 automerge-0.5.0/automerge/inst/doc/sync-protocol.html | 22 automerge-0.5.0/automerge/man/automerge-constants.Rd | 19 automerge-0.5.0/automerge/man/automerge-package.Rd | 5 automerge-0.5.0/automerge/src/automerge/rust/Cargo.lock | 168 - automerge-0.5.0/automerge/src/automerge/rust/automerge/Cargo.toml | 16 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/autocommit.rs | 59 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/automerge.rs | 82 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/change_graph.rs | 12 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/change_queue.rs |only automerge-0.5.0/automerge/src/automerge/rust/automerge/src/error.rs | 8 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/lib.rs | 3 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/op_set2/change.rs | 30 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/op_set2/change/batch.rs | 158 - automerge-0.5.0/automerge/src/automerge/rust/automerge/src/op_set2/op_set.rs | 8 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/op_set2/op_set/op_iter.rs | 2 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/op_set2/skip_list.rs | 3 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/patches/patch_log.rs | 236 + automerge-0.5.0/automerge/src/automerge/rust/automerge/src/sequence_tree.rs | 6 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/storage/load.rs | 4 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/sync.rs | 1296 +++++++++- automerge-0.5.0/automerge/src/automerge/rust/automerge/src/sync/message_builder.rs | 19 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/sync/state.rs | 77 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/transaction.rs | 499 +++ automerge-0.5.0/automerge/src/automerge/rust/automerge/src/transaction/inner.rs | 425 ++- automerge-0.5.0/automerge/src/automerge/rust/automerge/src/transaction/manual_transaction.rs | 426 --- automerge-0.5.0/automerge/src/automerge/rust/automerge/src/transaction/owned_transaction.rs |only automerge-0.5.0/automerge/src/automerge/rust/automerge/src/transaction/transactable.rs | 33 automerge-0.5.0/automerge/src/automerge/rust/automerge/src/types.rs | 29 automerge-0.5.0/automerge/src/automerge/rust/hexane/Cargo.toml | 9 automerge-0.5.0/automerge/src/automerge/rust/hexane/README.md | 290 ++ automerge-0.5.0/automerge/src/automerge/rust/hexane/src/aggregate.rs | 20 automerge-0.5.0/automerge/src/automerge/rust/hexane/src/boolean.rs | 5 automerge-0.5.0/automerge/src/automerge/rust/hexane/src/columndata.rs | 502 +++ automerge-0.5.0/automerge/src/automerge/rust/hexane/src/cursor.rs | 92 automerge-0.5.0/automerge/src/automerge/rust/hexane/src/delta.rs | 6 automerge-0.5.0/automerge/src/automerge/rust/hexane/src/encoder.rs | 52 automerge-0.5.0/automerge/src/automerge/rust/hexane/src/lib.rs | 38 automerge-0.5.0/automerge/src/automerge/rust/hexane/src/pack.rs | 25 automerge-0.5.0/automerge/src/automerge/rust/hexane/src/raw.rs | 16 automerge-0.5.0/automerge/src/automerge/rust/hexane/src/rle.rs | 13 automerge-0.5.0/automerge/src/automerge/rust/hexane/src/slab/tree.rs | 37 automerge-0.5.0/automerge/src/automerge/rust/vendor.tar.xz |binary automerge-0.5.0/automerge/tests/testthat/helper-cleanup.R |only automerge-0.5.0/automerge/tests/testthat/test-changes.R | 56 automerge-0.5.0/automerge/tests/testthat/test-convenience.R | 60 automerge-0.5.0/automerge/tests/testthat/test-cursors.R | 78 automerge-0.5.0/automerge/tests/testthat/test-document.R | 272 +- automerge-0.5.0/automerge/tests/testthat/test-edge-cases.R | 166 - automerge-0.5.0/automerge/tests/testthat/test-errors.R | 78 automerge-0.5.0/automerge/tests/testthat/test-marks.R | 146 - automerge-0.5.0/automerge/tests/testthat/test-methods.R | 150 - automerge-0.5.0/automerge/tests/testthat/test-objects.R | 412 +-- automerge-0.5.0/automerge/tests/testthat/test-recursive.R | 30 automerge-0.5.0/automerge/tests/testthat/test-sync.R | 120 automerge-0.5.0/automerge/tools/patch-rust-msrv.sh | 26 automerge-0.5.0/automerge/tools/patch-sources.sh | 352 -- automerge-0.5.0/automerge/tools/vendor-deps.sh | 42 automerge-0.5.0/automerge/vignettes/automerge.Rmd | 7 automerge-0.5.0/automerge/vignettes/quick-reference.Rmd | 20 82 files changed, 4949 insertions(+), 2327 deletions(-)
Title: Download Data from the World Inequality Database
Description: Download data from the online World Inequality Database directly
into R. Data are retrieved from WID.world's online data service. The World
Inequality Database is an extensive source on the historical evolution of
the distribution of income and wealth both within and between countries. It
relies on the combined effort of an international network of over a hundred
researchers covering more than seventy countries from all continents.
Author: Thomas Blanchet [aut],
Ignacio Flores [cre]
Maintainer: Ignacio Flores <stats@wid.world>
Diff between wid versions 0.0.1 dated 2026-02-20 and 0.0.2 dated 2026-07-08
DESCRIPTION | 17 MD5 | 20 R/check-args.R | 126 +++++ R/download-wid.R | 89 ++-- R/get-requests.R | 151 +++++-- README.md | 26 - man/download_wid.Rd | 38 - man/environment.Rd | 7 tests/testthat/test_download.R | 68 +-- tests/testthat/test_download_contract.R | 675 ++++++++++++++++++++++++++++++-- tests/testthat/test_get_requests.R | 7 11 files changed, 1016 insertions(+), 208 deletions(-)
Title: Get Silhouettes of Organisms from PhyloPic
Description: Work with the PhyloPic Web Service (<http://api-docs.phylopic.org/v2/>)
to fetch silhouette images of organisms. Includes functions for adding
silhouettes to both base R plots and ggplot2 plots.
Author: William Gearty [aut, cre] ,
Lewis A. Jones [aut] ,
Scott Chamberlain [ctb] ,
Martin R. Smith [ctb] ,
David L. Miller [ctb]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between rphylopic versions 1.6.0 dated 2025-11-18 and 1.7.0 dated 2026-07-08
DESCRIPTION | 18 +-- MD5 | 162 ++++++++++++++++-------------- NAMESPACE | 5 NEWS.md | 102 ++++++++++-------- R/add_phylopic.r | 7 - R/add_phylopic_base.r | 32 ++--- R/add_phylopic_legend.R | 57 +++++----- R/add_phylopic_tree.R | 40 +++---- R/browse_phylopic.R | 2 R/geom_phylopic.R | 83 ++++++--------- R/get_attribution.R | 26 ++-- R/get_phylopic.R | 58 ++++++++-- R/get_uuid.R | 3 R/igraph.R |only R/phylopic_utils.R | 14 +- R/pick_phylopic.R | 12 +- R/resolve_phylopic.R | 2 R/zzz.r | 83 ++++++++++----- README.md | 4 build/vignette.rds |binary inst/doc/a-getting-started.Rmd | 8 - inst/doc/a-getting-started.html | 14 +- inst/doc/b-advanced-ggplot.Rmd | 64 ++++++++++- inst/doc/b-advanced-ggplot.html | 94 +++++++++++++---- inst/doc/c-advanced-base.Rmd | 63 +++++++++++ inst/doc/c-advanced-base.html | 80 +++++++++++++- man/add_phylopic_legend.Rd | 41 +++---- man/add_phylopic_tree.Rd | 23 ++-- man/clear_phylopic_cache.Rd |only man/flip_phylopic.Rd | 6 - man/geom_phylopic.Rd | 4 man/phylopic_igraph.Rd |only man/recolor_phylopic.Rd | 6 - man/rotate_phylopic.Rd | 6 - man/rphylopic-package.Rd | 8 - man/scales.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/igraph |only tests/testthat/helper-cache.R |only tests/testthat/helper-vdiffr.R | 2 tests/testthat/test-add_phylopic.R | 8 - tests/testthat/test-add_phylopic_base.R | 10 - tests/testthat/test-add_phylopic_legend.R | 24 ++-- tests/testthat/test-add_phylopic_tree.R | 45 ++++---- tests/testthat/test-browse_phylopic.R | 2 tests/testthat/test-caching.R |only tests/testthat/test-geom_phylopic.R | 144 ++++++++++++++------------ tests/testthat/test-get_attribution.R | 4 tests/testthat/test-get_phylopic.R | 2 tests/testthat/test-get_uuid.R | 2 tests/testthat/test-igraph.R |only tests/testthat/test-phylopic_utils.R | 10 - tests/testthat/test-pick_phylo.R | 7 - tests/testthat/test-resolve_phylopic.R | 10 - tests/testthat/test-save_phylopic.R | 2 vignettes/a-getting-started.Rmd | 8 - vignettes/b-advanced-ggplot.Rmd | 64 ++++++++++- vignettes/base-network-plot-1-1.png |only vignettes/base-network-plot-2-1.png |only vignettes/base-penguin-plot-1-1.png |binary vignettes/base-penguin-plot-2-1.png |binary vignettes/base-penguin-plot-3-1.png |binary vignettes/base-penguin-plot-4-1.png |binary vignettes/base-penguin-plot-5-1.png |binary vignettes/base-phylo-plot-3-1.png |binary vignettes/base-phylo-plot-4-1.png |binary vignettes/c-advanced-base.Rmd | 63 +++++++++++ vignettes/ggplot-network-plot-1-1.png |only vignettes/ggplot-penguin-plot-1-1.png |binary vignettes/ggplot-penguin-plot-2-1.png |binary vignettes/ggplot-penguin-plot-3-1.png |binary vignettes/ggplot-penguin-plot-3b-1.png |binary vignettes/ggplot-penguin-plot-4-1.png |binary vignettes/ggplot-penguin-plot-5-1.png |binary vignettes/ggplot-penguin-plot-6-1.png |binary vignettes/ggplot-phylo-plot-1-1.png |binary vignettes/ggplot-phylo-plot-2-1.png |binary vignettes/ggplot-phylo-plot-3-1.png |binary vignettes/ggplot-phylo-plot-4-1.png |binary vignettes/intro-base-plot-1.png |binary vignettes/intro-ggplot-plot-1.png |binary vignettes/intro-transform-plot-1.png |binary vignettes/source/_b-advanced-ggplot.Rmd | 53 ++++++++- vignettes/source/_c-advanced-base.Rmd | 48 ++++++++ 84 files changed, 1075 insertions(+), 564 deletions(-)
Title: Pricing Equity Derivatives with Extensions of Black-Scholes
Description: Algorithms to price American and European equity options,
convertible bonds and a variety of other financial derivatives. It
uses an extension of the usual Black-Scholes model in which jump to
default may occur at a probability specified by a power-law link
between stock price and hazard rate as found in the paper by
Takahashi, Kobayashi, and Nakagawa (2001)
<doi:10.3905/jfi.2001.319302>. We use ideas and techniques from
Andersen and Buffum (2002) <doi:10.2139/ssrn.355308> and Linetsky
(2006) <doi:10.1111/j.1467-9965.2006.00271.x>.
Author: Brian K. Boonstra [aut, cre]
Maintainer: Brian K. Boonstra <ragtop@boonstra.org>
Diff between ragtop versions 1.3.1 dated 2026-06-20 and 2.0.0 dated 2026-07-08
DESCRIPTION | 10 +- MD5 | 50 ++++++---- NAMESPACE | 2 NEWS.md | 10 +- R/calibration.R | 8 + R/greeks.R |only R/implicit.R | 47 ++++++++- R/instruments.R | 23 ++++ R/util.R | 9 + README.md | 36 +++++++ inst/doc/ragtop_convertibles_in_r.R | 23 +++- inst/doc/ragtop_convertibles_in_r.Rmd | 31 ++++-- inst/doc/ragtop_convertibles_in_r.html | 164 +++++++++++++++++---------------- man/ConvertibleBond-class.Rd | 2 man/CouponBond-class.Rd | 2 man/GREEK_NAMES.Rd |only man/GridPricedInstrument-class.Rd | 2 man/construct_descending_bumps.Rd |only man/find_greeks.Rd |only man/find_present_value.Rd | 5 - man/fit_variance_cumulation.Rd | 2 man/greek_by_fd.Rd |only man/grid_delta_gamma.Rd |only man/resolve_bumps.Rd |only man/robust_greek.Rd |only man/safe_reprice.Rd |only tests/testthat/test_bumps.R |only tests/testthat/test_convertibles.R | 1 tests/testthat/test_greeks.R |only tests/testthat/test_options.R | 30 ++++++ tests/testthat/test_reuse_instrument.R |only vignettes/ragtop_convertibles_in_r.Rmd | 31 ++++-- 32 files changed, 345 insertions(+), 143 deletions(-)
Title: Reading Portable Encapsulated Projects
Description: A PEP, or Portable Encapsulated Project, is a dataset that
subscribes to the PEP structure for organizing metadata. It is written using
a simple YAML + CSV format, it is your one-stop solution to metadata
management across data analysis environments. This package reads this
standardized project configuration structure into R.
Described in Sheffield et al. (2021) <doi:10.1093/gigascience/giab077>.
Author: Nathan Sheffield [aut, cph, cre],
Michal Stolarczyk [aut]
Maintainer: Nathan Sheffield <nathan@code.databio.org>
Diff between pepr versions 0.6.0 dated 2026-02-28 and 0.6.1 dated 2026-07-08
DESCRIPTION | 10 ++-- MD5 | 28 +++++++------ NEWS.md | 11 +++++ R/project.R | 14 ++++-- inst/doc/feature1_constantAttributes.html | 8 +-- inst/doc/feature2_impliedAttributes.html | 8 +-- inst/doc/feature3_derivedAttributes.html | 8 +-- inst/doc/feature4_derivedImpliedAttributes.html | 6 +- inst/doc/feature5_sampleSubtable.html | 50 ++++++++++++------------ inst/doc/feature6_amendments.html | 10 ++-- inst/doc/gettingStarted.R | 6 +- inst/doc/gettingStarted.html | 10 ++-- man/pullProject.Rd | 5 +- tests/testthat/helper-integration.R |only tests/testthat/test_integration.R |only tests/testthat/test_project.R | 11 ----- 16 files changed, 99 insertions(+), 86 deletions(-)
Title: Functions to Assess the Business Impact of Churn Prediction
Models
Description: Calculate and visualise the financial impact of using a
classification model, such as a churn model, to target customers. Provides
cost, revenue, profit and return-on-investment curves as a function of the
share of customers targeted, cumulative gains and lift, marginal profit per
bin, and confusion-matrix based payoff across probability thresholds. Also
includes 'ggplot2' 'autoplot()' methods and an interactive 'shiny'
application for exploring the results.
Author: Peer Christensen [aut, cre]
Maintainer: Peer Christensen <hr.pchristensen@gmail.com>
Diff between modelimpact versions 1.0.0 dated 2021-05-06 and 1.1.0 dated 2026-07-08
DESCRIPTION | 24 + MD5 | 68 ++++- NAMESPACE | 40 +++ NEWS.md | 23 + R/bootstrap_profit.R |only R/break_even.R |only R/compare_models.R |only R/confusion_payoff.R |only R/cost_revenue.R | 15 - R/cumulative_gains.R |only R/impact_summary.R |only R/lift_curve.R |only R/marginal_profit.R |only R/modelimpact-package.R |only R/payoff_grid.R |only R/plots.R |only R/profit.R | 15 - R/profit_thresholds.R | 27 +- R/roc_pr.R |only R/roi.R | 17 - R/run_app.R |only R/tornado.R |only README.md | 390 ++++++++++++++++++++----------- inst |only man/bootstrap_profit.Rd |only man/break_even.Rd |only man/compare_models.Rd |only man/confusion_payoff.Rd |only man/cost_revenue.Rd | 10 man/cumulative_gains.Rd |only man/figures/README-compare-plot-1.png |only man/figures/README-cost_rev_plot-1.png |binary man/figures/README-gains-plot-1.png |only man/figures/README-lift-plot-1.png |only man/figures/README-marginal-plot-1.png |only man/figures/README-profit-plot-1.png |binary man/figures/README-roi-plot-1.png |binary man/figures/README-threshold-plot-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/figures/logo.png |only man/impact_summary.Rd |only man/lift_curve.Rd |only man/marginal_profit.Rd |only man/modelimpact-package.Rd |only man/modelimpact-plots.Rd |only man/payoff_grid.Rd |only man/profit.Rd | 10 man/profit_thresholds.Rd | 11 man/roc_pr.Rd |only man/roi.Rd | 17 + man/run_app.Rd |only man/tornado.Rd |only tests |only 53 files changed, 473 insertions(+), 194 deletions(-)
Title: Polished, Editable Tables and Statistical Results
Description: Sends supported 'R' objects to the 'Mellio' web app and creates
polished, editable statistical tables in 'R'. The 'mellio_open' interface
handles common hypothesis tests, model objects, model comparisons,
descriptive summaries, tabular data, plots, and image files. The
'melliotab' interface formats data frames, model summaries, correlation
matrices, and side-by-side comparison tables with APA-style numeric
formatting, confidence intervals, table notes, and optional significance
markers. Manual table helpers can copy or save 'melliotab' output as
'HTML', 'LaTeX', or 'Markdown' when file-based handoff is needed.
Payloads include package-version metadata to support reproducible
reporting and software citation.
Author: Melih Sahin [aut, cre]
Maintainer: Melih Sahin <nicomelpro@pm.me>
Diff between mellio versions 1.0.1 dated 2026-07-06 and 1.0.2 dated 2026-07-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/bridge-extract-lavaan.R | 23 ++++++++++++++++++++++- tests/testthat/test-bridge.R | 27 +++++++++++++++++++++++++++ 5 files changed, 62 insertions(+), 8 deletions(-)
Title: A Next-Generation Grammar of Interactive Graphics
Description: A modern visualization grammar that treats interactivity, animation,
and composable layouts as first-class concepts rather than afterthoughts.
Designed to address key limitations of existing grammars: native hover, click,
and zoom events, 'WebGL'-accelerated rendering for large datasets, built-in
multi-plot composition, and a token-based theming system. Renders to
interactive HTML widgets via 'D3.js' or static SVG from a single
declarative specification.
Author: Joash Joshua Ayo [aut, cre]
Maintainer: Joash Joshua Ayo <joashjoshua789@gmail.com>
Diff between glyph versions 0.1.0 dated 2026-07-06 and 0.1.1 dated 2026-07-08
DESCRIPTION | 9 MD5 | 31 NEWS.md | 12 R/render.R | 43 R/scales.R | 8 build/vignette.rds |binary inst/doc/comparison.R |only inst/doc/comparison.Rmd | 75 + inst/doc/comparison.html | 2378 ++++++++++++++++++++++++++++++++++++++++++ inst/doc/getting-started.R |only inst/doc/getting-started.Rmd |only inst/doc/getting-started.html |only inst/htmlwidgets/glyph.js | 1049 ++++++++++++++++-- inst/htmlwidgets/glyph.yaml | 2 man/animate.Rd | 100 - man/glyph-package.Rd | 1 man/scale.Rd | 5 vignettes/comparison.Rmd | 75 + vignettes/getting-started.Rmd |only 19 files changed, 3605 insertions(+), 183 deletions(-)
Title: Population Genetic Data Analysis Using Genepop
Description: Makes the Genepop software available in R. This software implements a mixture of traditional population genetic methods and some more focused developments: it computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci; it computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc.; and it performs analyses of isolation by distance from pairwise comparisons of individuals or population samples.
Author: Francois Rousset [aut, cre, cph] ,
Jimmy Lopez [ctb],
Alexandre Genin [ctb],
Khalid Belkhir [ctb]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between genepop versions 1.2.14 dated 2026-01-23 and 1.2.17 dated 2026-07-08
DESCRIPTION | 8 MD5 | 42 inst/NEWS.Rd | 7 inst/doc/GenepopS.Rmd | 7 inst/doc/GenepopS.pdf |binary inst/doc/GenepopS.tex | 94 + inst/doc/all-menu-options.html | 37 inst/doc/bibliography.html | 47 inst/doc/code-maintenance-credits-contact-etc..html | 13 inst/doc/copyright.html | 13 inst/doc/evaluating-the-performance-of-inferences-for-isolation-by-distance.html | 13 inst/doc/installing-genepop-and-session-examples.html | 13 inst/doc/introduction.html | 21 inst/doc/libs/anchor-sections-1.1.0/anchor-sections-icon.css | 2 inst/doc/libs/gitbook-2.6.7/css/style.css | 2 inst/doc/methods.html | 27 inst/doc/sec-settings.html | 13 inst/doc/the-input-file.html | 13 src/F_est.cpp | 474 +++++----- src/GenepopS.cpp | 2 src/genepop.cpp | 2 tests/testthat/test_IBD.R | 8 22 files changed, 444 insertions(+), 414 deletions(-)
Title: Retrieve Data on European Union Law
Description: Access to data on European Union laws and court decisions made easy with pre-defined 'SPARQL' queries and 'GET' requests. See Ovadek (2021) <doi:10.1080/2474736X.2020.1870150> .
Author: Michal Ovadek [aut, cre, cph]
Maintainer: Michal Ovadek <michal.ovadek@gmail.com>
This is a re-admission after prior archival of version 0.4.9 dated 2026-02-06
Diff between eurlex versions 0.4.9 dated 2026-02-06 and 0.5.0 dated 2026-07-08
eurlex-0.4.9/eurlex/man/elx_curia_list.Rd |only eurlex-0.5.0/eurlex/DESCRIPTION | 6 ++--- eurlex-0.5.0/eurlex/MD5 | 21 +++++++++---------- eurlex-0.5.0/eurlex/NAMESPACE | 1 eurlex-0.5.0/eurlex/NEWS.md | 16 +++++++++++++- eurlex-0.5.0/eurlex/R/elx_curia_list.R | 5 ++-- eurlex-0.5.0/eurlex/R/elx_make_query.R | 2 - eurlex-0.5.0/eurlex/README.md | 2 - eurlex-0.5.0/eurlex/inst/doc/sparql-queries.R | 10 ++++----- eurlex-0.5.0/eurlex/inst/doc/sparql-queries.Rmd | 2 - eurlex-0.5.0/eurlex/tests/testthat/test-query.R | 25 +++++++++++++++++++++++ eurlex-0.5.0/eurlex/vignettes/sparql-queries.Rmd | 2 - 12 files changed, 65 insertions(+), 27 deletions(-)
Title: Symmetric Linear Regression Models for Small Samples
Description: Ordinary and modified statistics for symmetrical linear
regression models with small samples. The supported ordinary
statistics include Wald, score, likelihood ratio and gradient. The
modified statistics include score, likelihood ratio and gradient.
Diagnostic tools associated with the fitted model are implemented. For
more details see Medeiros and Ferrari (2017) <DOI:10.1111/stan.12107>.
Author: Ivonaldo S. da Silva-Junior [aut, cre],
Francisco Moises C. de Medeiros [aut] ,
Eliardo Costa [aut]
Maintainer: Ivonaldo S. da Silva-Junior <ivosilvestresjr@gmail.com>
Diff between SLRMss versions 1.0.0 dated 2025-07-09 and 1.1.0 dated 2026-07-08
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- R/SLRMss.R | 24 ++++++++++++------------ R/coef.SLRMss.R | 2 +- R/datasets.R | 4 ++-- R/envplot.R | 4 ++-- R/fitted.SLRMss.R | 4 ++-- R/plot.SLRMss.R | 2 +- R/print.SLRMss.R | 2 +- R/residuals.SLRMss.R | 4 ++-- R/summary.SLRMss.R | 4 ++-- build/partial.rdb |binary man/SLRMss.Rd | 4 ++-- man/cheese.Rd | 2 +- man/coef.SLRMss.Rd | 2 +- man/envplot.Rd | 4 ++-- man/fitted.SLRMss.Rd | 4 ++-- man/orange.Rd | 2 +- man/plot.SLRMss.Rd | 2 +- man/print.SLRMss.Rd | 2 +- man/residuals.SLRMss.Rd | 4 ++-- man/summary.SLRMss.Rd | 4 ++-- 22 files changed, 65 insertions(+), 65 deletions(-)
Title: Regression under Interference in Connected Populations
Description: An implementation of generalized linear models (GLMs) for studying relationships among attributes in connected populations, where responses of connected units can be dependent, as introduced by Fritz et al. (2025) <doi:10.1080/01621459.2025.2565851>. 'igml' extends GLMs for independent responses to dependent responses and can be used for studying spillover in connected populations and other network-mediated phenomena.
Author: Cornelius Fritz [aut, cre],
Michael Schweinberger [aut]
Maintainer: Cornelius Fritz <corneliusfritz2010@gmail.com>
Diff between iglm versions 1.2.4 dated 2026-04-23 and 1.2.5 dated 2026-07-08
DESCRIPTION | 12 MD5 | 35 NAMESPACE | 1 R/helper.R | 5 R/iglm.r | 8 R/iglm_data.r | 1 R/init_terms.R | 58 + build/vignette.rds |binary inst/doc/model-terms.R |only inst/doc/model-terms.Rmd |only inst/doc/model-terms.html |only man/iglm.data.Rd | 1 man/iglm.data_generator.Rd | 1218 +++++++++++++++++----------------- man/iglm.object.generator.Rd | 708 ++++++++++--------- man/results.generator.Rd | 433 ++++++------ man/sampler.iglm.generator.Rd | 505 +++++++------- man/sampler.net.attr.generator.Rd | 240 +++--- src/change_statistics.cpp | 29 tests/testthat/test-check_iglm_term.R |only tests/testthat/test-printing.R | 17 vignettes/model-terms.Rmd |only 21 files changed, 1687 insertions(+), 1584 deletions(-)
Title: Generating Cluster Masks for Single-Cell Dimensional Reduction
Plots
Description: Implements a procedure to automatically generate 2D masks
for clusters on dimensional reduction plots from methods like
t-SNE (t-distributed stochastic neighbor embedding) or
UMAP (uniform manifold approximation and projection),
with a focus on single-cell RNA-sequencing data.
Author: Alexey Sergushichev [aut, cre]
Maintainer: Alexey Sergushichev <alsergbox@gmail.com>
Diff between mascarade versions 0.3.4 dated 2026-04-14 and 0.3.5 dated 2026-07-08
DESCRIPTION | 11 +- MD5 | 14 +-- NEWS.md | 3 R/generateMask.R | 8 + build/vignette.rds |binary inst/doc/mascarade-gallery.html | 165 +++++++++++++++++++------------------ inst/doc/mascarade-tutorial.html | 80 ++++++++--------- tests/testthat/test-generateMask.R | 25 +++++ 8 files changed, 174 insertions(+), 132 deletions(-)
Title: Toolkit for Analyzing Curricular Complexity
Description: Enables educational researchers and practitioners to calculate the curricular complexity of a plan of study, visualize its prerequisite structure at scale, and conduct customizable analyses. The original tool can be found at <https://curricularanalytics.org>. Additional functions to explore curriculum complexity from the literature are also included.
Author: David Reeping [aut, cre]
Maintainer: David Reeping <reepindp@ucmail.uc.edu>
Diff between CurricularComplexity versions 1.0.2 dated 2026-06-16 and 1.0.3 dated 2026-07-08
DESCRIPTION | 6 +++--- MD5 | 22 ++++++++++++---------- R/deferment_factor.R | 8 +++----- R/find_inbound_courses.R | 8 +++++++- R/find_number_of_free_terms.R |only R/find_outbound_courses.R | 8 +++++++- inst/doc/CurricularComplexity-demo.Rmd | 2 +- inst/doc/CurricularComplexity-demo.html | 13 +++++++------ man/deferment_factor.Rd | 9 ++++++++- man/find_inbound_courses.Rd | 4 +++- man/find_number_of_free_terms.Rd |only man/find_outbound_courses.Rd | 4 +++- vignettes/CurricularComplexity-demo.Rmd | 2 +- 13 files changed, 55 insertions(+), 31 deletions(-)
More information about CurricularComplexity at CRAN
Permanent link
Title: Access the 'IBGE' Aggregate Data API from 'R'
Description: 'Tidyverse'-friendly interface to the Brazilian Institute of Geography and Statistics ('IBGE') aggregate data 'API'
<https://servicodados.ibge.gov.br/api/docs/agregados?versao=3>. Query aggregates, variables, localities, periods, and metadata
from surveys and censuses conducted by 'IBGE'.
Author: Andre Leite [aut, cre],
Marcos Wasiliew [aut],
Hugo Vasconcelos [aut],
Carlos Amorim [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between ibger versions 0.1.0 dated 2026-02-20 and 0.2.0 dated 2026-07-08
DESCRIPTION | 21 ++++++----- MD5 | 20 ++++++----- NEWS.md | 13 +++++++ R/chunking.R |only R/variaveis.R | 81 +++++++++++++++++++++++++++++++++++++-------- README.md | 51 ++++++++++++++++++---------- build/vignette.rds |binary man/figures/ibger_rpkg.svg |only man/ibge_explorer.Rd | 2 - man/ibge_variables.Rd | 21 +++++++++++ man/ibger-package.Rd | 8 +++- tests |only 12 files changed, 165 insertions(+), 52 deletions(-)
Title: Generalized Boosted Regression Models
Description: An implementation of extensions to Freund and Schapire's AdaBoost
algorithm and Friedman's gradient boosting machine. Includes regression
methods for least squares, absolute loss, t-distribution loss, quantile
regression, logistic, multinomial logistic, Poisson, Cox proportional hazards
partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and
Learning to Rank measures (LambdaMart). Originally developed by Greg Ridgeway.
Newer version available at <https://github.com/gbm-developers/gbm3>.
Author: Greg Ridgeway [aut, cre] ,
Daniel Edwards [ctb],
Brian Kriegler [ctb],
Stefan Schroedl [ctb],
Harry Southworth [ctb],
Brandon Greenwell [ctb] ,
Bradley Boehmke [ctb] ,
Jay Cunningham [ctb],
GBM Developers [aut]
Maintainer: Greg Ridgeway <gridge@upenn.edu>
Diff between gbm versions 2.2.3 dated 2026-01-22 and 2.3.0 dated 2026-07-08
gbm-2.2.3/gbm/inst/doc/gbm.Rnw |only gbm-2.2.3/gbm/inst/doc/gbm.pdf |only gbm-2.2.3/gbm/inst/tinytest |only gbm-2.2.3/gbm/tests/tinytest.R |only gbm-2.2.3/gbm/vignettes/gbm.Rnw |only gbm-2.3.0/gbm/DESCRIPTION | 20 +-- gbm-2.3.0/gbm/MD5 | 101 +++++++++--------- gbm-2.3.0/gbm/NEWS.md | 49 ++++++++ gbm-2.3.0/gbm/R/gbm-internals.R | 16 +- gbm-2.3.0/gbm/R/gbm-package.R | 8 - gbm-2.3.0/gbm/R/gbm.R | 46 ++++---- gbm-2.3.0/gbm/R/gbm.fit.R | 8 - gbm-2.3.0/gbm/R/gbm.more.R | 101 +++++++++++++++--- gbm-2.3.0/gbm/R/gbm.object.R | 9 - gbm-2.3.0/gbm/R/gbmCrossVal.R | 117 ++++++++++----------- gbm-2.3.0/gbm/R/ir.measures.R | 3 gbm-2.3.0/gbm/R/plot.gbm.R | 43 +++++-- gbm-2.3.0/gbm/R/print.gbm.R | 18 +-- gbm-2.3.0/gbm/R/relative.influence.R | 4 gbm-2.3.0/gbm/R/utils.R | 9 - gbm-2.3.0/gbm/README.md | 18 +-- gbm-2.3.0/gbm/build/vignette.rds |binary gbm-2.3.0/gbm/inst/doc/gbm.R |only gbm-2.3.0/gbm/inst/doc/gbm.Rmd |only gbm-2.3.0/gbm/inst/doc/gbm.html |only gbm-2.3.0/gbm/man/gbm-package.Rd | 3 gbm-2.3.0/gbm/man/gbm.Rd | 20 +-- gbm-2.3.0/gbm/man/gbm.fit.Rd | 3 gbm-2.3.0/gbm/man/gbm.object.Rd | 3 gbm-2.3.0/gbm/man/gbmCrossVal.Rd | 13 -- gbm-2.3.0/gbm/man/plot.gbm.Rd | 7 - gbm-2.3.0/gbm/man/print.gbm.Rd | 4 gbm-2.3.0/gbm/src/adaboost.cpp | 4 gbm-2.3.0/gbm/src/coxph.cpp | 1 gbm-2.3.0/gbm/src/gbm-init.c | 4 gbm-2.3.0/gbm/src/gbm.h | 4 gbm-2.3.0/gbm/src/gbmentry.cpp | 37 ++++-- gbm-2.3.0/gbm/src/huberized.cpp | 13 +- gbm-2.3.0/gbm/src/locationm.cpp | 73 +++++++++++++ gbm-2.3.0/gbm/src/locationm.h | 2 gbm-2.3.0/gbm/src/multinomial.cpp | 49 +++++++- gbm-2.3.0/gbm/src/node.h | 5 gbm-2.3.0/gbm/src/node_search.cpp | 5 gbm-2.3.0/gbm/src/pairwise.cpp | 13 -- gbm-2.3.0/gbm/src/poisson.cpp | 16 +- gbm-2.3.0/gbm/src/quantile.cpp | 74 ++++++++----- gbm-2.3.0/gbm/src/quantile.h | 4 gbm-2.3.0/gbm/src/tree.cpp | 3 gbm-2.3.0/gbm/tests/testthat |only gbm-2.3.0/gbm/tests/testthat.R |only gbm-2.3.0/gbm/vignettes/gbm.Rmd |only gbm-2.3.0/gbm/vignettes/oobperf2.png |only gbm-2.3.0/gbm/vignettes/shrinkage-v-iterations.png |only 53 files changed, 603 insertions(+), 327 deletions(-)
Title: Interactive Virtualized Data Explorer Grid Widget
Description: Provides an interactive, virtualized data explorer widget for 'R'.
Built on 'React' (via 'reactR') and 'htmlwidgets', it offers column-type
detection, multi-value checkbox filtering, sorting, column visibility
toggling, virtual scrolling for large datasets, and a full-viewport modal.
Includes 'dtsmartr_launch()' with an interactive, zero-code file upload wizard
using 'datamods'. Widgets can be embedded in 'R Markdown' / 'Quarto' documents,
'Shiny' applications, or exported as standalone HTML files via 'save_dtsmartr()'.
Author: Nikhil Wagh [aut, cre]
Maintainer: Nikhil Wagh <nmw1986@gmail.com>
Diff between dtsmartr versions 0.2.0 dated 2026-06-30 and 0.3.0 dated 2026-07-08
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 2 ++ R/dtsmartr.R | 14 ++++++++++---- inst/htmlwidgets/dtsmartr.js | 2 +- inst/htmlwidgets/dtsmartr.js.map | 2 +- tests/testthat/test-dtsmartr.R | 17 ++++++++++++----- 7 files changed, 37 insertions(+), 22 deletions(-)
Title: Deep Significance Clustering for Clinical Risk Stratification
Description: We provide an R implementation of Deep Significance Clustering (DICE), a self-supervised learning framework designed to identify clinically meaningful and risk-stratified patient subgroups from electronic health record (EHR) data. DICE jointly optimizes deep representation learning, clustering, and outcome prediction while enforcing statistical significance between predicted outcomes and cluster membership. This integrated optimization produces subgroups that are both clinically coherent and predictive, addressing a gap where traditional unsupervised clustering methods and supervised risk prediction models alone may fail to generate actionable clinical groupings. See Huang et al. (2021) <doi:10.1093/jamia/ocab203>.
Author: Sarah Ayton [aut, cre] ,
Yiye Zhang [aut]
Maintainer: Sarah Ayton <sarah.ayton@columbia.edu>
Diff between DICErClust versions 0.1.2 dated 2026-05-28 and 0.1.3 dated 2026-07-08
DESCRIPTION | 10 +++++----- MD5 | 7 ++++--- inst/CITATION |only inst/doc/DICEr-introduction.html | 4 ++-- inst/doc/heart-failure-example.html | 4 ++-- 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Transcription Elongation Profiling
Description: The general principle relies on calculating the cumulative signal of nascent
RNA sequencing over the gene body of any given gene or transcription unit.
'tepr' can identify transcription attenuation sites by comparing profile to
a null model which assumes uniform read density over the entirety of the
transcription unit. It can also identify increased or diminished
transcription attenuation by comparing two conditions. Besides rigorous
statistical testing and high sensitivity, a major feature of 'tepr' is its
ability to provide the elongation pattern of each individual gene, including
the position of the main attenuation point when such a phenomenon occurs.
Using 'tepr', users can visualize and refine genome-wide aggregated analyses
of elongation patterns to robustly identify effects specific to subsets of
genes. These metrics are suitable for internal comparisons (between genes in
each condition) and for studying elongation of the same gene in different
conditions or comparing it to a p [...truncated...]
Author: Nicolas Descostes [cre],
Victor Billon [aut],
Gael Cristofari [aut]
Maintainer: Nicolas Descostes <nicolas.descostes@gmail.com>
Diff between tepr versions 1.1.15 dated 2026-03-06 and 1.1.17 dated 2026-07-08
DESCRIPTION | 8 +++----- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/preprocessing-blacklisthighmap-utils.R | 2 +- R/preprocessing-blacklisthighmap.R | 6 ++++-- build/vignette.rds |binary inst/doc/tepr.html | 4 ++-- 7 files changed, 22 insertions(+), 16 deletions(-)
Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to
visualize the fit of regression models arising from a wide variety
of models in R ('lm', 'glm', 'coxph', 'rlm', 'gam', 'locfit', 'lmer',
'randomForest', etc.)
Author: Patrick Breheny [aut, cre] ,
Woodrow Burchett [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between visreg versions 2.8.0 dated 2025-08-20 and 2.8.1 dated 2026-07-08
DESCRIPTION | 14 MD5 | 163 +++++----- NAMESPACE | 1 NEWS.md | 513 ++++++++++++++++++---------------- R/Response.R | 57 ++- R/Terms.R | 71 +++- R/abbrNum.R | 2 R/collapseVisregList.R | 24 + R/factorAxis.R | 28 + R/factorPlot.R | 101 ++++-- R/fillFrame.R | 41 ++ R/getXY.R | 12 R/ggContPlot.R | 159 +++++++--- R/ggFactorPlot.R | 216 +++++++++----- R/makeYName.R | 26 + R/pal.R | 11 R/parseFormula.R | 18 - R/plot-visreg.R | 113 ++++++- R/plotVisreg2d.R | 191 ++++++++---- R/plotVisregList.R | 4 R/printCond.R | 29 + R/se.mlm.R | 14 R/setupCond.R | 23 - R/setupD.R | 22 - R/setupF.R | 93 ++++-- R/setupV.R | 114 ++++++- R/setupV2.R | 71 +++- R/setupX.R | 79 +++-- R/subset.R | 4 R/subsetV.R | 16 - R/toplegend.R | 24 + R/visreg-package.R | 3 R/visreg.R | 173 ++++++----- R/visreg2d.R | 65 ++-- R/visregFactorPanel.R | 80 ++++- R/visregLatticePlot.R | 117 +++++-- R/visregList.R | 8 R/visregOverlayPlot.R | 95 ++++-- R/visregPanel.R | 63 +++- R/visregPlot.R | 91 ++++-- R/visregPred.R | 47 ++- R/visregResid.R | 22 - README.md | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/visreg.html | 17 - inst/doc/visreg.rmd | 2 inst/tinytest/_enhances_glmmTMB.R | 39 +- inst/tinytest/_lme4predict.R | 27 - inst/tinytest/_xtrans.r | 8 inst/tinytest/enhances-MASS.R | 14 inst/tinytest/enhances-betareg.R | 8 inst/tinytest/enhances-gamlss.R | 10 inst/tinytest/enhances-gamm4.R | 10 inst/tinytest/enhances-gbm.R | 34 +- inst/tinytest/enhances-loess.R | 2 inst/tinytest/enhances-nlme.R | 22 - inst/tinytest/enhances-nnet.R | 17 - inst/tinytest/enhances-quantreg.R | 44 +- inst/tinytest/enhances-randomForest.R | 2 inst/tinytest/enhances-svm.R | 4 inst/tinytest/ggplot.R | 162 +++++++--- inst/tinytest/missing-data.R | 67 ++-- inst/tinytest/subset.R | 6 inst/tinytest/top.R | 44 +- inst/tinytest/unusual-formulas.R | 46 +-- inst/tinytest/visreg-contrast.R | 56 +-- inst/tinytest/visreg-coxph.R | 34 +- inst/tinytest/visreg-glm.R | 52 +-- inst/tinytest/visreg-interactions.R | 88 ++--- inst/tinytest/visreg-lm.R | 156 ++++++---- inst/tinytest/visreg-mlm.R | 41 +- inst/tinytest/visreg2d-glm.R | 26 - inst/tinytest/visreg2d-lm.R | 87 +++-- inst/tinytest/visregList.R | 38 +- inst/tinytest/weight-char.r |only man/plot.visreg.Rd | 2 man/plot.visreg2d.Rd | 22 - man/visreg-package.Rd | 5 man/visreg.Rd | 81 ++--- man/visreg2d.Rd | 6 tests/test.R | 4 vignettes/visreg.rmd | 2 83 files changed, 2758 insertions(+), 1552 deletions(-)
Title: Run CRAN URL Checks from Older R Versions
Description: Provide the URL checking tools available in R 4.1+ as a
package for earlier versions of R. Also uses concurrent requests so
can be much faster than the serial versions.
Author: R Core team [aut] ,
Jim Hester [aut] ,
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between urlchecker versions 1.0.1 dated 2021-11-30 and 2.0.0 dated 2026-07-08
urlchecker-1.0.1/urlchecker/R/parallel.R |only urlchecker-1.0.1/urlchecker/inst/tools/utils.R |only urlchecker-2.0.0/urlchecker/DESCRIPTION | 28 urlchecker-2.0.0/urlchecker/MD5 | 50 urlchecker-2.0.0/urlchecker/NAMESPACE | 22 urlchecker-2.0.0/urlchecker/NEWS.md | 63 + urlchecker-2.0.0/urlchecker/R/bib.R |only urlchecker-2.0.0/urlchecker/R/files.R |only urlchecker-2.0.0/urlchecker/R/import-standalone-obj-type.R |only urlchecker-2.0.0/urlchecker/R/import-standalone-types-check.R |only urlchecker-2.0.0/urlchecker/R/qmd.R |only urlchecker-2.0.0/urlchecker/R/rmd.R | 81 + urlchecker-2.0.0/urlchecker/R/url_check.R | 245 ++++ urlchecker-2.0.0/urlchecker/R/url_update.R | 9 urlchecker-2.0.0/urlchecker/R/urlchecker-package.R |only urlchecker-2.0.0/urlchecker/R/urlignore.R |only urlchecker-2.0.0/urlchecker/R/utils.R | 116 ++ urlchecker-2.0.0/urlchecker/R/zzz.R | 15 urlchecker-2.0.0/urlchecker/README.md | 80 + urlchecker-2.0.0/urlchecker/inst/tools/README.md | 8 urlchecker-2.0.0/urlchecker/inst/tools/urltools.R | 526 +++++++--- urlchecker-2.0.0/urlchecker/man/url_check.Rd | 58 - urlchecker-2.0.0/urlchecker/man/url_update.Rd | 2 urlchecker-2.0.0/urlchecker/man/urlchecker-package.Rd |only urlchecker-2.0.0/urlchecker/tests |only 25 files changed, 1096 insertions(+), 207 deletions(-)
Title: Select Intervals Suited for Functional Regression
Description: Interval fusion and selection procedures for regression with
functional inputs. Methods include a semiparametric approach based
on Sliced Inverse Regression (SIR), as described in
<doi:10.1007/s11222-018-9806-6> (standard ridge and sparse SIR are
also included in the package) and a random forest based approach,
as described in <doi:10.1002/sam.11705>.
Author: Victor Picheny [aut] ,
Remi Servien [aut] ,
Nathalie Vialaneix [aut, cre]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between SISIR versions 0.2.4 dated 2026-05-14 and 0.2.5 dated 2026-07-08
DESCRIPTION | 16 ++--- MD5 | 24 ++++---- NAMESPACE | 2 NEWS.md | 10 +++ R/SFCB.R | 16 +++-- R/selection_methods.R | 2 R/sfcb_methods.R | 14 ++-- man/SFCB-class.Rd | 14 ++-- man/sfcb.Rd | 6 +- tests/testthat/test_sfcb.R | 74 ++++++++++++------------- tests/testthat/test_sfcbextract.R | 38 ++++++------ tests/testthat/test_sfcbplots.R | 112 +++++++++++++++++++++----------------- tests/testthat/test_sfcbquality.R | 80 ++++++++++++++------------- 13 files changed, 223 insertions(+), 185 deletions(-)
Title: Managing and Visualizing Brain Surface Data
Description: Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Author: Tim Schaefer [aut, cre]
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between fsbrain versions 0.5.6 dated 2025-09-08 and 0.6.0 dated 2026-07-08
DESCRIPTION | 6 LICENSE | 4 MD5 | 814 +++--- NAMESPACE | 566 ++-- R/helpers.R | 7 R/morph_agg.R | 8 R/morph_atlas_agg.R | 6 R/optdata.R | 88 R/vis_multiview.R | 2 R/vis_rglwidget.R |only R/vis_surface_background.R | 5 R/vis_volume.R | 355 ++ R/vis_volume_3d.R | 141 + build/vignette.rds |binary inst/CITATION | 42 inst/doc/fsbrain.R | 664 ++-- inst/doc/fsbrain.Rmd | 1476 +++++------ inst/doc/fsbrain.html | 2400 +++++++++--------- inst/doc/fsbrain_faq.R | 356 +- inst/doc/fsbrain_faq.Rmd | 1010 +++---- inst/doc/fsbrain_faq.html | 1832 ++++++------- inst/doc/fsbrain_vol.R | 84 inst/doc/fsbrain_vol.Rmd | 270 +- inst/doc/fsbrain_vol.html | 998 +++---- inst/extdata/cube.ply | 58 inst/extdata/demographics.tsv | 16 inst/extdata/demographics_nohdr.tsv | 14 inst/extdata/subjects.txt | 8 man/alphablend.Rd | 58 man/annot.outline.Rd | 80 man/annot.outline.border.vertices.Rd | 62 man/apply.label.to.morphdata.Rd | 102 man/apply.labeldata.to.morphdata.Rd | 76 man/apply.transform.Rd | 38 man/arrange.brainview.images.Rd | 80 man/arrange.brainview.images.grid.Rd | 86 man/boxcoords.from.bbox.Rd | 40 man/brain.Rd | 40 man/brainview.sd.Rd | 76 man/brainview.si.Rd | 76 man/brainview.sr.Rd | 106 man/brainview.t4.Rd | 76 man/brainview.t9.Rd | 76 man/brainviews.Rd | 80 man/can.plot.colorbar.Rd | 40 man/can.plot.colorbar.from.coloredmeshes.Rd | 36 man/check.subjects.files.Rd | 54 man/check.subjectslist.Rd | 52 man/clip.data.Rd | 58 man/clip_fun.Rd | 58 man/cm.cbry.Rd | 28 man/cm.div.Rd | 34 man/cm.heat.Rd | 34 man/cm.qual.Rd | 34 man/cm.seq.Rd | 34 man/collayer.bg.Rd | 74 man/collayer.bg.atlas.Rd | 108 man/collayer.bg.meancurv.Rd | 96 man/collayer.bg.sulc.Rd | 96 man/collayer.from.annot.Rd | 74 man/collayer.from.annotdata.Rd | 66 man/collayer.from.mask.data.Rd | 78 man/collayer.from.morphlike.data.Rd | 84 man/collayers.merge.Rd | 62 man/coloredmesh.from.annot.Rd | 88 man/coloredmesh.from.color.Rd | 76 man/coloredmesh.from.label.Rd | 94 man/coloredmesh.from.mask.Rd | 104 man/coloredmesh.from.morph.native.Rd | 100 man/coloredmesh.from.morph.standard.Rd | 118 man/coloredmesh.from.morphdata.Rd | 88 man/coloredmesh.from.preloaded.data.Rd | 62 man/coloredmesh.plot.colorbar.separate.Rd | 126 man/coloredmeshes.combined.data.range.Rd | 36 man/coloredmeshes.from.color.Rd | 88 man/coloredmeshes.get.md.Rd | 40 man/colorlist.brain.clusters.Rd | 34 man/colors.are.grayscale.Rd | 48 man/colors.have.transparency.Rd | 48 man/combine.colorbar.with.brainview.animation.Rd | 86 man/combine.colorbar.with.brainview.image.Rd | 110 man/combine.colorbar.with.brainview.image.vertical.Rd | 88 man/common.makecmap.range.Rd | 58 man/constant.pervertexdata.Rd | 38 man/cube3D.tris.Rd | 102 man/cubes3D.tris.Rd | 50 man/deepcopylist.long.Rd | 46 man/deg2rad.Rd | 24 man/delete_all_optional_data.Rd | 28 man/demo.Rd | 30 man/demographics.to.fsgd.file.Rd | 88 man/demographics.to.qdec.table.dat.Rd | 102 man/desaturate.Rd | 60 man/download_fsaverage.Rd | 36 man/download_fsaverage3.Rd | 42 man/download_fsaverage6.Rd | 42 man/download_fsaverage_minimal.Rd |only man/download_optional_data.Rd | 31 man/download_optional_paper_data.Rd | 37 man/draw.colorbar.Rd | 44 man/draw.segments.on.image.Rd |only man/eeg_coords.Rd | 48 man/ensure.fs.surface.Rd | 36 man/ensure.tmesh3d.Rd | 42 man/export.Rd | 154 - man/export.coloredmesh.ply.Rd | 50 man/extend_neighbors.Rd | 76 man/extract.volume.3D.Rd | 46 man/face.edges.Rd | 56 man/find.freesurferhome.Rd | 40 man/find.subjectsdir.of.Rd | 44 man/flc.Rd | 36 man/force.to.range.Rd | 50 man/fs.coloredmesh.Rd | 68 man/fs.home.Rd | 34 man/fs.surface.as.adjacencylist.Rd | 34 man/fs.surface.to.igraph.Rd | 52 man/fs.surface.to.tmesh3d.Rd | 34 man/fs.surface.vertex.neighbors.Rd | 74 man/fs.value.list.from.agg.res.Rd | 40 man/fsaverage.path.Rd | 40 man/fsbrain.renderable.Rd | 42 man/fsbrain.set.default.figsize.Rd | 46 man/fslong.subjects.detect.Rd | 30 man/fslong.subjects.finished.Rd | 52 man/fup.Rd | 42 man/gen.test.volume.Rd | 44 man/geod.patches.color.overlay.Rd | 82 man/geod.patches.color.overlay.singlehemi.Rd | 58 man/geod.patches.pervertexdata.Rd | 68 man/geod.patches.pervertexdata.singlehemi.Rd | 44 man/geod.vert.neighborhood.Rd | 86 man/geodesic.average.distance.Rd | 36 man/geodesic.ballstats.Rd | 50 man/geodesic.circles.Rd | 64 man/geodesic.dists.to.vertex.Rd | 38 man/geodesic.path.Rd | 70 man/get.atlas.region.names.Rd | 110 man/get.rglstyle.Rd | 40 man/get.rglstyle.default.Rd | 30 man/get.rglstyle.edges.Rd | 30 man/get.rglstyle.glass.Rd | 30 man/get.rglstyle.glass2.Rd | 30 man/get.rglstyle.parameters.Rd | 40 man/get.rglstyle.semitransparent.Rd | 30 man/get.rglstyle.shiny.Rd | 30 man/get.slice.indices.Rd | 44 man/get.subject.class.Rd | 48 man/get.view.angle.names.Rd | 38 man/getIn.Rd | 58 man/get_optional_data_filepath.Rd | 38 man/group.agg.atlas.native.Rd | 150 - man/group.agg.atlas.standard.Rd | 162 - man/group.annot.Rd | 100 man/group.concat.measures.native.Rd | 92 man/group.concat.measures.standard.Rd | 98 man/group.data.to.array.Rd | 48 man/group.label.Rd | 94 man/group.label.from.annot.Rd | 116 man/group.morph.agg.native.Rd | 120 man/group.morph.agg.standard.Rd | 112 man/group.morph.agg.standard.vertex.Rd | 106 man/group.morph.native.Rd | 104 man/group.morph.standard.Rd | 138 - man/group.morph.standard.sf.Rd | 50 man/group.multimorph.agg.native.Rd | 122 man/group.multimorph.agg.standard.Rd | 112 man/group.surface.Rd | 82 man/groupmorph.split.hemilist.Rd | 62 man/handle.rglactions.highlight.points.Rd | 44 man/hasIn.Rd | 48 man/hemi.lobe.labels.Rd | 64 man/hemilist.Rd | 70 man/hemilist.derive.hemi.Rd | 60 man/hemilist.from.prefixed.list.Rd | 70 man/hemilist.get.combined.data.Rd | 54 man/hemilist.unwrap.Rd | 62 man/hemilist.wrap.Rd | 62 man/hemlist.ensure.contains.Rd | 34 man/highlight.points.spheres.Rd | 48 man/highlight.vertices.on.subject.Rd | 170 - man/highlight.vertices.on.subject.spheres.Rd | 182 - man/highlight.vertices.spheres.Rd | 76 man/hull.retain.along.axis.Rd | 64 man/image.remap.color.Rd | 48 man/images.annotate.Rd | 48 man/images.dimmax.Rd | 36 man/images.rescale.to.max.canvas.Rd | 40 man/images.same.height.Rd | 40 man/images.same.width.Rd | 40 man/is.Triangles3D.Rd | 36 man/is.fs.coloredmesh.Rd | 34 man/is.fs.coloredvoxels.Rd | 34 man/is.fsbrain.Rd | 34 man/is.hemilist.Rd | 54 man/label.border.Rd | 80 man/label.border.fast.Rd | 78 man/label.colFn.Rd | 42 man/label.colFn.inv.Rd | 42 man/label.from.annotdata.Rd | 98 man/label.to.annot.Rd | 114 man/labeldata.from.mask.Rd | 52 man/limit_fun.Rd | 52 man/limit_fun_na.Rd | 58 man/limit_fun_na_inside.Rd | 58 man/list_optional_data.Rd | 28 man/magick.grid.Rd | 52 man/mask.from.labeldata.for.hemi.Rd | 142 - man/mergehemi.annots.Rd | 40 man/mesh.ras2crs.Rd |only man/mesh.slice.intersection.Rd |only man/mesh.vertex.included.faces.Rd | 58 man/mesh.vertex.neighbors.Rd | 74 man/mkco.cluster.Rd | 34 man/mkco.div.Rd | 28 man/mkco.heat.Rd | 28 man/mkco.seq.Rd | 28 man/normalize.Rd | 36 man/numverts.lh.Rd | 34 man/numverts.rh.Rd | 34 man/path.colors.from.orientation.Rd | 40 man/path.slopes.Rd | 40 man/per.hemi.vertex.indices.Rd | 40 man/perform.na.mapping.Rd | 40 man/perform.rglactions.Rd | 42 man/pervertexdata.smoothgaussian.Rd | 90 man/pervertexdata.smoothnn.Rd | 80 man/pervertexdata.smoothnn.compute.fwhm.Rd | 66 man/pervertexdata.smoothnn.compute.numiter.Rd | 46 man/plot.fsbrain.colorbar.Rd | 40 man/pp.named.list.Rd | 36 man/principal.curvatures.Rd | 44 man/print.fs.coloredmesh.Rd | 32 man/print.fs.coloredvoxels.Rd | 32 man/print.fsbrain.Rd | 32 man/qc.for.group.Rd | 66 man/qc.from.regionwise.df.Rd | 68 man/qc.from.segstats.table.Rd | 52 man/qc.from.segstats.tables.Rd | 42 man/qc.fslong.checkidenticaldata.Rd | 56 man/qc.report.html.Rd | 80 man/qc.vis.failcount.by.region.Rd | 62 man/qdec.table.filter.Rd | 50 man/qdec.table.skeleton.Rd | 74 man/rad2deg.Rd | 24 man/ras2vox_tkr.Rd | 52 man/read.colorcsv.Rd | 34 man/read.md.demographics.Rd | 110 man/read.md.subjects.Rd | 62 man/read.md.subjects.from.fsgd.Rd | 46 man/recycle.Rd | 46 man/regions.to.ignore.Rd | 80 man/report.on.demographics.Rd | 64 man/rgl.coord.lines.Rd | 42 man/rglactions.Rd | 56 man/rglactions.has.key.Rd | 36 man/rglactions.transform.Rd | 40 man/rglo.Rd | 34 man/rglot.Rd | 28 man/rglvoxels.Rd | 64 man/rotation.matrix.for.axis.rot.Rd | 52 man/scale.to.range.zero.one.Rd | 24 man/scale01.Rd | 38 man/shape.descriptor.names.Rd | 28 man/shape.descriptors.Rd | 44 man/shift.hemis.apart.Rd | 62 man/shift.hemis.rglactions.Rd | 40 man/sjd.demo.Rd | 40 man/sjld.Rd | 40 man/sortcoloredmeshes.by.hemi.Rd | 36 man/sph2fs.Rd | 86 man/spread.values.over.annot.Rd | 120 man/spread.values.over.hemi.Rd | 130 man/spread.values.over.subject.Rd | 134 - man/subject.annot.Rd | 100 man/subject.annot.border.Rd | 74 man/subject.atlas.agg.Rd | 124 man/subject.descriptor.geodesic.average.distance.Rd | 90 man/subject.filepath.any.Rd | 88 man/subject.filepath.morph.native.Rd | 74 man/subject.filepath.morph.standard.Rd | 86 man/subject.label.Rd | 98 man/subject.label.from.annot.Rd | 116 man/subject.lobes.Rd | 114 man/subject.mask.Rd | 118 man/subject.morph.native.Rd | 126 man/subject.morph.standard.Rd | 120 man/subject.num.verts.Rd | 62 man/subject.report.html.Rd | 58 man/subject.surface.Rd | 102 man/subject.volume.Rd | 94 man/submesh.vertex.Rd | 68 man/surf.avg.vertexradius.Rd | 70 man/surf.center.fsaverage.Rd | 42 man/surf.metric.properties.Rd | 58 man/surf.radius.fsaverage.Rd | 48 man/surf.sphere.dist.Rd | 60 man/surf.sphere.gaussianweights.Rd | 72 man/surf.sphere.spatialfilter.Rd | 44 man/surface.curvatures.Rd | 40 man/surfs.props.Rd | 46 man/symmrange.Rd | 30 man/test.numerical.meandiff.Rd | 70 man/test.numerical.meandiff.paired.Rd | 64 man/test.numerical.meandiff.unpaired.Rd | 64 man/tmesh3d.to.fs.surface.Rd | 34 man/track.length.Rd | 36 man/vdata.split.by.hemi.Rd | 68 man/vertex.coords.Rd | 50 man/vertex.hemis.Rd | 52 man/vis.color.on.subject.Rd | 172 - man/vis.coloredmesh.Rd | 40 man/vis.coloredmeshes.Rd | 102 man/vis.coloredmeshes.rotating.Rd | 98 man/vis.colortable.legend.Rd | 60 man/vis.data.on.fsaverage.Rd | 162 - man/vis.data.on.group.native.Rd | 114 man/vis.data.on.group.standard.Rd | 114 man/vis.data.on.subject.Rd | 182 - man/vis.dti.trk.Rd | 72 man/vis.export.from.coloredmeshes.Rd | 154 - man/vis.fs.surface.Rd | 74 man/vis.group.annot.Rd | 110 man/vis.group.coloredmeshes.Rd | 92 man/vis.group.morph.native.Rd | 114 man/vis.group.morph.standard.Rd | 120 man/vis.labeldata.on.subject.Rd | 204 - man/vis.mask.on.subject.Rd | 218 - man/vis.path.along.verts.Rd | 106 man/vis.paths.Rd | 38 man/vis.paths.along.verts.Rd | 44 man/vis.region.values.on.subject.Rd | 212 - man/vis.renderable.Rd | 44 man/vis.rglwidget.Rd |only man/vis.rotated.coloredmeshes.Rd | 70 man/vis.seg.legend.Rd | 54 man/vis.subject.annot.Rd | 154 - man/vis.subject.label.Rd | 194 - man/vis.subject.morph.native.Rd | 178 - man/vis.subject.morph.standard.Rd | 210 - man/vis.subject.pre.Rd | 120 man/vis.symmetric.data.on.subject.Rd | 188 - man/vis.volume.on.surface.Rd |only man/vislayout.from.coloredmeshes.Rd | 168 - man/vol.boundary.box.Rd | 60 man/vol.boundary.box.apply.Rd | 38 man/vol.boundary.mask.Rd | 44 man/vol.hull.Rd | 42 man/vol.imagestack.Rd | 60 man/vol.intensity.to.color.Rd | 56 man/vol.mask.from.segmentation.Rd | 38 man/vol.merge.Rd | 74 man/vol.overlay.colors.from.activation.Rd | 68 man/vol.overlay.colors.from.colortable.Rd | 56 man/vol.plane.axes.Rd | 36 man/vol.planes.Rd | 52 man/vol.slice.Rd | 86 man/vol.vox.from.crs.Rd | 58 man/volvis.contour.Rd | 70 man/volvis.lb.Rd | 124 man/volvis.lb.with.surface.Rd |only man/volvis.lightbox.Rd | 106 man/volvis.voxels.Rd | 64 man/vox2ras_tkr.Rd | 54 man/wrapped.image.append.Rd | 44 man/write.group.morph.standard.Rd | 110 man/write.group.morph.standard.mf.Rd | 56 man/write.group.morph.standard.sf.Rd | 54 man/write.group.morph.standard.singlehemi.Rd | 52 man/write.region.aggregated.Rd | 86 man/write.region.values.Rd | 124 man/write.region.values.fsaverage.Rd | 92 tests/testthat/helper-functions.R | 300 +- tests/testthat/teardown-cran.R | 26 tests/testthat/test-alphablend.R |only tests/testthat/test-atlas.R | 160 - tests/testthat/test-brain_igraph.R | 50 tests/testthat/test-brainview_magic.R | 52 tests/testthat/test-cbar.R | 48 tests/testthat/test-coloredmesh.R | 164 - tests/testthat/test-curvature.R | 102 tests/testthat/test-export.R | 36 tests/testthat/test-fsdir_abstraction_group.R | 278 +- tests/testthat/test-fsdir_abstraction_subject.R | 494 +-- tests/testthat/test-geodesic.R | 180 - tests/testthat/test-helper_magick.R | 36 tests/testthat/test-helpers.R | 132 tests/testthat/test-highlight.R | 470 +-- tests/testthat/test-issue50.R | 78 tests/testthat/test-mesh_helpers.R | 196 - tests/testthat/test-metadata_io.R | 186 - tests/testthat/test-morph_agg.R | 414 +-- tests/testthat/test-morph_atlas_agg.R | 766 ++--- tests/testthat/test-morph_concat.R | 148 - tests/testthat/test-r_vis_volume.R | 506 +-- tests/testthat/test-rglactions.R | 114 tests/testthat/test-seg_stats.R | 58 tests/testthat/test-smooth.R | 151 - tests/testthat/test-spatial.R | 24 tests/testthat/test-spherical.R | 46 tests/testthat/test-u_vis_volume_3d.R | 446 +-- tests/testthat/test-vis-volume-on-surface.R |only tests/testthat/test-vis.R | 714 ++--- tests/testthat/test-volume.R | 258 - tests/testthat/test-w_vis_group.R | 128 tests/testthat/test-x_vis_meshes.R | 60 tests/testthat/test-y_vis_multiview.R | 830 +++--- tests/testthat/test-z_vis_surface_background.R | 242 - tests/testthat_au.R | 12 tests/testthat_vz.R | 12 vignettes/fsbrain.Rmd | 1476 +++++------ vignettes/fsbrain_faq.Rmd | 1010 +++---- vignettes/fsbrain_vol.Rmd | 270 +- 413 files changed, 22881 insertions(+), 22266 deletions(-)
Title: Treatment Effects with Multiple Periods and Groups
Description: The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption [...truncated...]
Author: Brantly Callaway [aut, cre],
Pedro H. C. Sant'Anna [aut]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Diff between did versions 2.5.0 dated 2026-06-13 and 2.5.1 dated 2026-07-08
DESCRIPTION | 6 MD5 | 55 +-- NEWS.md | 16 R/att_gt.R | 34 +- R/compute.aggte.R | 72 ++++ R/compute.att_gt.R | 6 R/compute.att_gt2.R | 6 R/conditional_did_pretest.R | 22 + R/ggdid.R | 11 R/gplot.R | 26 + R/mboot.R | 47 ++ R/pre_process_did.R | 101 ++++-- R/pre_process_did2.R | 95 +++-- R/process_attgt.R | 43 +- R/simulate_data.R | 33 ++ R/utility_functions.R | 191 +++++++++++ README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/TWFE.html | 4 inst/doc/did-basics.html | 4 inst/doc/extensions.html | 4 inst/doc/multi-period-did.html | 4 inst/doc/pre-testing.html | 4 tests/testthat/test-always-treated-invariance.R |only tests/testthat/test-audit-fixes.R |only tests/testthat/test-error-handling.R | 394 +++++++++++++++++++++++- tests/testthat/test-modelmatrix-hoist.R | 20 + tests/testthat/test-mutation-safety.R |only tests/testthat/test-robustness-guards.R | 59 ++- 30 files changed, 1088 insertions(+), 171 deletions(-)
Title: Tools for Descriptive Statistics
Description: A toolbox for descriptive statistics, based on the computation of frequency and contingency tables. Several statistical functions and plot methods are provided to describe univariate or bivariate distributions of factors, integer series and numerical series either provided as individual values or as bins.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between descstat versions 0.1-2 dated 2021-02-17 and 1.0-0 dated 2026-07-08
descstat-0.1-2/descstat/R/bivariate.R |only descstat-0.1-2/descstat/R/pre_plot.R |only descstat-0.1-2/descstat/R/print_methods.R |only descstat-0.1-2/descstat/R/univariate.R |only descstat-0.1-2/descstat/man/pre_plot.Rd |only descstat-0.1-2/descstat/man/print_methods.Rd |only descstat-0.1-2/descstat/man/reexports.Rd |only descstat-1.0-0/descstat/DESCRIPTION | 16 descstat-1.0-0/descstat/MD5 | 65 descstat-1.0-0/descstat/NAMESPACE | 81 - descstat-1.0-0/descstat/NEWS.md | 24 descstat-1.0-0/descstat/R/bin.R | 469 ++++-- descstat-1.0-0/descstat/R/cont_table.R | 217 +-- descstat-1.0-0/descstat/R/datasets.R | 4 descstat-1.0-0/descstat/R/descstat.R | 204 ++ descstat-1.0-0/descstat/R/freq_table.R | 424 +++--- descstat-1.0-0/descstat/R/statistics.R |only descstat-1.0-0/descstat/R/tinyplot.R |only descstat-1.0-0/descstat/README.md | 92 - descstat-1.0-0/descstat/build/partial.rdb |only descstat-1.0-0/descstat/build/vignette.rds |binary descstat-1.0-0/descstat/data/employment.rda |binary descstat-1.0-0/descstat/data/income.rda |binary descstat-1.0-0/descstat/data/padova.rda |binary descstat-1.0-0/descstat/data/rgp.rda |binary descstat-1.0-0/descstat/data/wages.rda |binary descstat-1.0-0/descstat/inst/doc/descstat.R | 440 +++--- descstat-1.0-0/descstat/inst/doc/descstat.Rmd | 1150 ++++++++-------- descstat-1.0-0/descstat/inst/doc/descstat.html | 1695 ++++++++++++------------ descstat-1.0-0/descstat/man/bin.Rd | 163 +- descstat-1.0-0/descstat/man/bivariate.Rd | 18 descstat-1.0-0/descstat/man/cont_table.Rd | 35 descstat-1.0-0/descstat/man/descstat-package.Rd | 51 descstat-1.0-0/descstat/man/freq_table.Rd | 75 - descstat-1.0-0/descstat/man/income.Rd | 2 descstat-1.0-0/descstat/man/padova.Rd | 2 descstat-1.0-0/descstat/man/tinyplot.Rd |only descstat-1.0-0/descstat/man/univariate.Rd | 21 descstat-1.0-0/descstat/vignettes/descstat.Rmd | 1150 ++++++++-------- 39 files changed, 3499 insertions(+), 2899 deletions(-)
Title: Visualization of a Correlation Matrix using 'ggplot2'
Description: The 'ggcorrplot' package can be used to visualize easily a
correlation matrix using 'ggplot2'. It provides a solution for
reordering the correlation matrix and displays the significance level
on the plot. It also includes a function for computing a matrix of
correlation p-values.
Author: Alboukadel Kassambara [aut, cre],
Indrajeet Patil [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggcorrplot versions 0.1.4.1 dated 2023-09-05 and 0.2.0 dated 2026-07-08
DESCRIPTION | 13 MD5 | 35 + NEWS.md | 106 +++++ R/ggcorrplot.R | 225 ++++++++++- README.md | 4 inst/CITATION |only inst/WORDLIST | 3 man/ggcorrplot.Rd | 88 ++++ tests/testthat/Rplots.pdf |only tests/testthat/_snaps/vdiffr/ggcorrplot-works-circle.svg | 23 - tests/testthat/_snaps/vdiffr/ggcorrplot-works-default.svg | 265 +++++++------- tests/testthat/_snaps/vdiffr/ggcorrplot-works-hc.svg | 265 +++++++------- tests/testthat/test-args.R |only tests/testthat/test-circle-scale.R |only tests/testthat/test-colors-vector.R |only tests/testthat/test-cor-pmat-na.R |only tests/testthat/test-cor-pmat-use.R |only tests/testthat/test-display-args.R |only tests/testthat/test-hc-order.R |only tests/testthat/test-leading-zero.R |only tests/testthat/test-nonsquare.R |only tests/testthat/test-pmat.R |only tests/testthat/test-sig-stars.R |only tests/testthat/test-structure.R |only tests/testthat/test-tl-col.R |only tests/testthat/test-vdiffr.R | 3 26 files changed, 696 insertions(+), 334 deletions(-)
Title: Download Administrative Boundary Data from 'geoBoundaries'
Description: Provides tools to download individual country boundaries and
global composite boundaries from 'geoBoundaries'
<https://www.geoboundaries.org/> across multiple administrative
('ADM') levels. Returns boundaries as 'sf' objects for mapping and
spatial analysis. Runfola et al. (2020)
<doi:10.1371/journal.pone.0231866> describe the underlying database.
Author: Diego Hernangomez [aut, cre, cph] ,
William and Mary geoLab [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between geobounds versions 0.1.2 dated 2026-05-29 and 1.0.0 dated 2026-07-08
DESCRIPTION | 35 +-- LICENSE |only MD5 | 99 ++++----- NAMESPACE | 36 +-- NEWS.md | 33 ++- R/gb-cache.R | 220 +++++++++++--------- R/gb-get-adm.R | 63 +++--- R/gb-get-max-lvl.R | 24 +- R/gb-get-metadata.R | 76 ++++--- R/gb-get-world.R | 56 +++-- R/gb-get.R | 170 +++++++++++----- R/geobounds-package.R | 3 R/utils.R | 216 ++++++++++++++++++-- README.md | 115 ++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/COPYRIGHTS | 117 +++++------ inst/REFERENCES.bib | 38 +-- inst/WORDLIST | 68 +++--- inst/doc/geobounds.html | 197 ++++++++++-------- inst/doc/geobounds.qmd | 208 ++++++++++--------- inst/schemaorg.json | 8 man/figures/README-map-coverage-1.png |binary man/figures/README-simple_plot-1.png |binary man/gb_clear_cache.Rd | 37 +-- man/gb_detect_cache_dir.Rd | 14 - man/gb_get.Rd | 253 ++++++++++++------------ man/gb_get_adm.Rd | 325 +++++++++++++++---------------- man/gb_get_max_adm_lvl.Rd | 115 +++++----- man/gb_get_metadata.Rd | 243 +++++++++++------------ man/gb_get_world.Rd | 77 ++++--- man/gb_set_cache_dir.Rd | 66 +++--- man/geobounds-package.Rd | 10 man/roxygen |only tests/testthat/_snaps/gb-get-metadata.md | 6 tests/testthat/_snaps/gb-get-world.md | 8 tests/testthat/_snaps/gb-get.md | 24 +- tests/testthat/_snaps/utils.md | 93 ++++++-- tests/testthat/helper-cache.R |only tests/testthat/test-gb-cache.R | 166 ++++++++++++++- tests/testthat/test-gb-get-adm.R | 211 ++++++++++---------- tests/testthat/test-gb-get-metadata.R | 6 tests/testthat/test-gb-get-world.R | 12 - tests/testthat/test-gb-get.R | 53 +++-- tests/testthat/test-utils.R | 82 ++++++- vignettes/REFERENCES.bib | 38 +-- vignettes/cgaz-1.png |binary vignettes/choro-1.png |binary vignettes/geobounds.qmd | 208 ++++++++++--------- vignettes/intersect-1.png |binary vignettes/norway-1.png |binary 52 files changed, 2273 insertions(+), 1558 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] ,
Atkinson Elizabeth [ctb],
Crowson Cynthia [ctb]
Maintainer: Terry M Therneau <terry.therneau@proton.me>
Diff between survival versions 3.8-6 dated 2026-01-16 and 3.8-9 dated 2026-07-08
survival-3.8-6/survival/R/model.frame.coxphms.R |only survival-3.8-6/survival/R/surv2data.R |only survival-3.8-6/survival/R/timeline.R |only survival-3.8-6/survival/man/Surv2data.Rd |only survival-3.8-6/survival/man/timeline.Rd |only survival-3.8-6/survival/noweb/code.toc |only survival-3.8-6/survival/tests/survexpm.R.notyet |only survival-3.8-9/survival/DESCRIPTION | 14 survival-3.8-9/survival/MD5 | 205 +- survival-3.8-9/survival/NAMESPACE | 6 survival-3.8-9/survival/R/Surv2.R | 23 survival-3.8-9/survival/R/aeqSurv.R | 3 survival-3.8-9/survival/R/agsurv.R | 1 survival-3.8-9/survival/R/clogit.R | 8 survival-3.8-9/survival/R/concordance.R | 2 survival-3.8-9/survival/R/coxph.R | 239 +-- survival-3.8-9/survival/R/coxph.control.R | 5 survival-3.8-9/survival/R/fromtimeline.R |only survival-3.8-9/survival/R/model.matrix.coxph.R | 152 - survival-3.8-9/survival/R/multimiss.R |only survival-3.8-9/survival/R/plot.survfit.R | 2 survival-3.8-9/survival/R/predict.coxph.R | 3 survival-3.8-9/survival/R/residuals.coxph.R | 31 survival-3.8-9/survival/R/residuals.coxphms.R | 14 survival-3.8-9/survival/R/survSplit.R | 234 ++- survival-3.8-9/survival/R/survcheck.R | 113 - survival-3.8-9/survival/R/survfit.R | 127 - survival-3.8-9/survival/R/survfit.coxphms.R | 6 survival-3.8-9/survival/R/survfitAJ.R | 5 survival-3.8-9/survival/R/survfitms.R | 2 survival-3.8-9/survival/R/xtras.R | 12 survival-3.8-9/survival/build/vignette.rds |binary survival-3.8-9/survival/data/nafld.rda |binary survival-3.8-9/survival/inst/NEWS.Rd | 34 survival-3.8-9/survival/inst/doc/adjcurve.R | 2 survival-3.8-9/survival/inst/doc/adjcurve.pdf |binary survival-3.8-9/survival/inst/doc/approximate.R | 2 survival-3.8-9/survival/inst/doc/approximate.pdf |binary survival-3.8-9/survival/inst/doc/compete.R | 6 survival-3.8-9/survival/inst/doc/compete.Rnw | 9 survival-3.8-9/survival/inst/doc/compete.pdf |binary survival-3.8-9/survival/inst/doc/concordance.R | 2 survival-3.8-9/survival/inst/doc/concordance.pdf |binary survival-3.8-9/survival/inst/doc/matrix.R | 2 survival-3.8-9/survival/inst/doc/matrix.pdf |binary survival-3.8-9/survival/inst/doc/methods.R | 21 survival-3.8-9/survival/inst/doc/methods.Rnw | 71 survival-3.8-9/survival/inst/doc/methods.pdf |binary survival-3.8-9/survival/inst/doc/modelframe.Rnw |only survival-3.8-9/survival/inst/doc/modelframe.pdf |only survival-3.8-9/survival/inst/doc/multi.pdf |binary survival-3.8-9/survival/inst/doc/other.Rnw | 3 survival-3.8-9/survival/inst/doc/other.pdf |binary survival-3.8-9/survival/inst/doc/population.R | 2 survival-3.8-9/survival/inst/doc/population.pdf |binary survival-3.8-9/survival/inst/doc/redistribute.R | 2 survival-3.8-9/survival/inst/doc/redistribute.pdf |binary survival-3.8-9/survival/inst/doc/splines.R | 2 survival-3.8-9/survival/inst/doc/splines.pdf |binary survival-3.8-9/survival/inst/doc/survival.R | 2 survival-3.8-9/survival/inst/doc/survival.Rnw | 2 survival-3.8-9/survival/inst/doc/survival.pdf |binary survival-3.8-9/survival/inst/doc/tiedtimes.R | 2 survival-3.8-9/survival/inst/doc/tiedtimes.pdf |binary survival-3.8-9/survival/inst/doc/timedep.R | 181 +- survival-3.8-9/survival/inst/doc/timedep.Rnw | 636 ++++---- survival-3.8-9/survival/inst/doc/timedep.pdf |binary survival-3.8-9/survival/inst/doc/timeline.R |only survival-3.8-9/survival/inst/doc/timeline.Rnw |only survival-3.8-9/survival/inst/doc/timeline.pdf |only survival-3.8-9/survival/inst/doc/validate.R | 2 survival-3.8-9/survival/inst/doc/validate.pdf |binary survival-3.8-9/survival/man/Surv2.Rd | 18 survival-3.8-9/survival/man/coxph.control.Rd | 13 survival-3.8-9/survival/man/fromtimeline.Rd |only survival-3.8-9/survival/man/lvcf.Rd | 9 survival-3.8-9/survival/man/residuals.coxph.Rd | 28 survival-3.8-9/survival/man/survSplit.Rd | 50 survival-3.8-9/survival/man/survival-deprecated.Rd | 2 survival-3.8-9/survival/noweb/Makefile | 4 survival-3.8-9/survival/noweb/code.nw | 1456 ------------------- survival-3.8-9/survival/noweb/coxph.Rnw | 3 survival-3.8-9/survival/noweb/coxsurv.Rnw | 4 survival-3.8-9/survival/noweb/coxsurv3.Rnw | 2 survival-3.8-9/survival/noweb/predict.coxph.Rnw | 3 survival-3.8-9/survival/noweb/survfit.Rnw | 35 survival-3.8-9/survival/tests/badname.R |only survival-3.8-9/survival/tests/badname.Rout.save |only survival-3.8-9/survival/tests/checkSurv2.R | 59 survival-3.8-9/survival/tests/checkSurv2.Rout.save | 70 survival-3.8-9/survival/tests/clogit.R | 6 survival-3.8-9/survival/tests/clogit.Rout.save | 14 survival-3.8-9/survival/tests/concordance2.R | 2 survival-3.8-9/survival/tests/concordance2.Rout.save | 10 survival-3.8-9/survival/tests/model.matrix.R | 4 survival-3.8-9/survival/tests/model.matrix.Rout.save | 33 survival-3.8-9/survival/tests/multistrata.R | 1 survival-3.8-9/survival/tests/residms.R | 18 survival-3.8-9/survival/tests/residms.Rout.save | 37 survival-3.8-9/survival/tests/summarydf.Rout.save |only survival-3.8-9/survival/tests/survSplit.R | 45 survival-3.8-9/survival/tests/survSplit.Rout.save | 68 survival-3.8-9/survival/tests/survexpm.Rout.save |only survival-3.8-9/survival/tests/testci.R | 8 survival-3.8-9/survival/tests/testci.Rout.save | 13 survival-3.8-9/survival/tests/timeline.R |only survival-3.8-9/survival/tests/timeline.Rout.save |only survival-3.8-9/survival/vignettes/compete.Rnw | 9 survival-3.8-9/survival/vignettes/methods.Rnw | 71 survival-3.8-9/survival/vignettes/modelframe.Rnw |only survival-3.8-9/survival/vignettes/other.Rnw | 3 survival-3.8-9/survival/vignettes/refer.bib | 17 survival-3.8-9/survival/vignettes/survival.Rnw | 2 survival-3.8-9/survival/vignettes/timedep.Rnw | 636 ++++---- survival-3.8-9/survival/vignettes/timeline.Rnw |only 115 files changed, 2028 insertions(+), 2915 deletions(-)
Title: Utility Functions Around 'JDemetra+ 3.0'
Description: R Interface to 'JDemetra+ 3.x'
(<https://github.com/jdemetra>) time series analysis software. It
provides functions allowing to model time series (create outlier
regressors, user-defined calendar regressors, Unobserved Components
AutoRegressive Integrated Moving Average (UCARIMA) models...), to test
the presence of trading days or seasonal effects and also to set
specifications in pre-adjustment and benchmarking when using 'rjd3x13'
or 'rjd3tramoseats'.
Author: Jean Palate [aut],
Alain Quartier-la-Tente [aut] ,
Tanguy Barthelemy [aut, cre, art],
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjd3toolkit versions 3.7.1 dated 2026-03-10 and 3.8.0 dated 2026-07-08
rjd3toolkit-3.7.1/rjd3toolkit/inst/java/jdplus-sa-base-api-3.7.1.jar |only rjd3toolkit-3.7.1/rjd3toolkit/inst/java/jdplus-sa-base-core-3.7.1.jar |only rjd3toolkit-3.7.1/rjd3toolkit/inst/java/jdplus-sa-base-protobuf-3.7.1.jar |only rjd3toolkit-3.7.1/rjd3toolkit/inst/java/jdplus-sa-base-r-3.7.1.jar |only rjd3toolkit-3.7.1/rjd3toolkit/inst/java/jdplus-toolkit-base-api-3.7.1.jar |only rjd3toolkit-3.7.1/rjd3toolkit/inst/java/jdplus-toolkit-base-core-3.7.1.jar |only rjd3toolkit-3.7.1/rjd3toolkit/inst/java/jdplus-toolkit-base-protobuf-3.7.1.jar |only rjd3toolkit-3.7.1/rjd3toolkit/inst/java/jdplus-toolkit-base-r-3.7.1.jar |only rjd3toolkit-3.7.1/rjd3toolkit/man/reload_dictionaries.Rd |only rjd3toolkit-3.8.0/rjd3toolkit/DESCRIPTION | 24 rjd3toolkit-3.8.0/rjd3toolkit/MD5 | 265 +++++----- rjd3toolkit-3.8.0/rjd3toolkit/NAMESPACE | 13 rjd3toolkit-3.8.0/rjd3toolkit/NEWS.md | 62 +- rjd3toolkit-3.8.0/rjd3toolkit/R/arima.R | 29 - rjd3toolkit-3.8.0/rjd3toolkit/R/calendars.R | 61 +- 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Title: Time Series Analysis Toolkit Based on Symbolic Aggregate
Discretization, i.e. SAX
Description: Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA
algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly),
and characteristic pattern discovery along with interpretable time series classification.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <seninp@gmail.com>
Diff between jmotif versions 1.3.0 dated 2026-07-01 and 1.3.1 dated 2026-07-08
DESCRIPTION | 6 - MD5 | 26 +++--- R/jmotif.R | 6 - README.md | 8 - inst/include/jmotif.h | 12 +- src/hot-sax.cpp | 41 +++------ src/paa.cpp | 192 ++++++++++++++++++-------------------------- src/repair.cpp | 57 ++++++------- src/rra.cpp | 198 ++++++++++++++++++++++++++++++++++++---------- src/sax-vsm.cpp | 21 ---- src/sax.cpp | 98 +++------------------- src/string.cpp | 18 ++-- src/znorm.cpp | 30 ++++++ tests/testthat/test_str.R | 2 14 files changed, 369 insertions(+), 346 deletions(-)
Title: Download and Visualize Essential Climate Change Data
Description: Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, methane, emissions, instrumental and proxy temperature records, sea levels, Arctic/Antarctic sea-ice, Hurricanes, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/home>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.html>, Vostok Paleo carbon dio [...truncated...]
Author: Hernando Cortina [aut, cre]
Maintainer: Hernando Cortina <hch@alum.mit.edu>
Diff between hockeystick versions 0.9.0 dated 2026-07-06 and 0.9.1 dated 2026-07-08
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 28 ++++++++++++++-------------- R/2kyears_temp.R | 2 +- R/carbon.R | 2 +- R/daily_temp.R | 4 ++-- R/emissions.R | 2 +- R/fires.R | 6 +++++- R/hurricanes.R | 3 +++ R/instrumental_temp.R | 2 +- R/methane.R | 2 +- R/paleo.R | 4 ++-- R/seaice.R | 2 +- R/sealevel.R | 4 ++-- inst/doc/usinghockeystick.html | 10 +++++----- 15 files changed, 43 insertions(+), 36 deletions(-)
Title: Multinomial Logit Models with Random Parameters
Description: An implementation of maximum simulated likelihood method for the
estimation of multinomial logit models with random coefficients as presented by Sarrias and Daziano (2017) <doi:10.18637/jss.v079.i02>.
Specifically, it allows estimating models with continuous heterogeneity
such as the mixed multinomial logit and the generalized multinomial logit.
It also allows estimating models with discrete heterogeneity such as the
latent class and the mixed-mixed multinomial logit model.
Author: Mauricio Sarrias [aut, cre] ,
Ricardo Daziano [aut],
Yves Croissant [ctb]
Maintainer: Mauricio Sarrias <msarrias86@gmail.com>
Diff between gmnl versions 1.1-3.2 dated 2020-05-27 and 1.1-4 dated 2026-07-08
DESCRIPTION | 15 +- MD5 | 14 +- NAMESPACE | 5 R/glogitform.R | 49 ++++--- R/gmnl.R | 2 R/gmnl.logliks.R | 371 +++++++++++++++++++++++++++++-------------------------- inst/NEWS.Rd | 32 ++++ man/gmnl.Rd | 2 8 files changed, 279 insertions(+), 211 deletions(-)
Title: Docorate (Decorate + Output) Displays
Description: A framework for creating production outputs. Users can frame a table, listing, or figure with headers and footers and save to an output file. Stores an intermediate 'docorator' object for reproducibility and rendering to multiple output types.
Author: Shannon Haughton [aut, cre],
Becca Krouse [aut],
Seongbin Hong [aut],
Dragoș Moldovan-Gruenfeld [aut],
GlaxoSmithKline Research & Development Limited [cph, fnd]
Maintainer: Shannon Haughton <shannon.l.haughton@gsk.com>
Diff between docorator versions 0.6.0 dated 2026-03-20 and 0.7.0 dated 2026-07-08
DESCRIPTION | 21 - MD5 | 76 +++-- NAMESPACE | 9 NEWS.md | 14 + R/docorate.R | 9 R/geometry.R | 91 +++++- R/prep_obj_docx.R |only R/prep_obj_rtf.R | 16 - R/prep_obj_tex.R | 12 R/render.R | 230 +++++++++------- R/render_docx.R |only R/scale_gt.R | 20 + R/utils.R | 123 ++++++++ R/utils_fancyhdr.R | 349 ++++++++++++++++++------- R/utils_gt.R | 78 +++-- build/vignette.rds |binary inst/doc/display_sizing.R | 9 inst/doc/display_sizing.Rmd | 13 inst/doc/display_sizing.html | 481 +++++++++++++++++------------------ inst/doc/document_sizing.html | 5 inst/doc/headers_footers.html | 5 inst/doc/multi_page.R |only inst/doc/multi_page.Rmd |only inst/doc/multi_page.html |only inst/doc/render.html | 5 inst/template/template.docx |only man/apply_scale.Rd | 3 man/as_docorator.Rd | 3 man/hf_process.Rd | 12 man/prep_obj_docx.Rd |only man/prep_obj_rtf.Rd | 3 man/prep_obj_tex.Rd | 3 man/render_docx.Rd |only tests/testthat/_snaps/geometry.md |only tests/testthat/_snaps/utils.md | 106 ++++++- tests/testthat/test-geometry.R | 175 +++++++++--- tests/testthat/test-prep_obj_docx.R |only tests/testthat/test-prep_obj_rtf.R | 38 ++ tests/testthat/test-render_docx.R |only tests/testthat/test-scale_gt.R | 68 ++++ tests/testthat/test-utils.R | 133 +++++++++ tests/testthat/test-utils_fancyhdr.R | 38 ++ tests/testthat/test-utils_gt.R | 139 ++++++++++ vignettes/display_sizing.Rmd | 13 vignettes/multi_page.Rmd |only 45 files changed, 1661 insertions(+), 639 deletions(-)
Title: Descriptive 2D and 3D Descriptive Multidimensional Item Response
Theory Modeling
Description: For identifying, estimating, and plotting descriptive multidimensional item response theory models, restricted to 2D and 3D and dichotomous or polytomous data that fit the two-parameter logistic model or the graded response model. The method is primarily exploratory and centered on the plot function, which exposes item characteristics and constructs, represented by vector arrows, within a three-dimensional interactive latent space. The results can be useful for item-level analysis as well as test development.
Author: Erik Forsberg [aut, cre, cph]
Maintainer: Erik Forsberg <forsbergpsychometrics@gmail.com>
Diff between D3mirt versions 2.0.5 dated 2026-06-07 and 2.1.0 dated 2026-07-08
D3mirt-2.0.5/D3mirt/R/angles.R |only D3mirt-2.0.5/D3mirt/R/plotD3mirt.R |only D3mirt-2.0.5/D3mirt/data/angles.rda |only D3mirt-2.0.5/D3mirt/inst/extdata/modbi.RData |only D3mirt-2.0.5/D3mirt/man/angles.Rd |only D3mirt-2.0.5/D3mirt/man/plot.D3mirt.Rd |only D3mirt-2.1.0/D3mirt/DESCRIPTION | 15 D3mirt-2.1.0/D3mirt/MD5 | 64 - D3mirt-2.1.0/D3mirt/NAMESPACE | 11 D3mirt-2.1.0/D3mirt/NEWS.md | 13 D3mirt-2.1.0/D3mirt/R/D2mirt.R |only D3mirt-2.1.0/D3mirt/R/D3mirt.R | 74 - D3mirt-2.1.0/D3mirt/R/angles2D.R |only D3mirt-2.1.0/D3mirt/R/angles3D.R |only D3mirt-2.1.0/D3mirt/R/information.R |only D3mirt-2.1.0/D3mirt/R/modid.R | 3 D3mirt-2.1.0/D3mirt/R/plot.R |only D3mirt-2.1.0/D3mirt/R/printD2mirt.R |only D3mirt-2.1.0/D3mirt/R/summaryD2mirt.R |only D3mirt-2.1.0/D3mirt/R/summaryD3mirt.R | 16 D3mirt-2.1.0/D3mirt/R/summarymodid.R | 2 D3mirt-2.1.0/D3mirt/README.md | 135 ++ D3mirt-2.1.0/D3mirt/data/angles2D.rda |only D3mirt-2.1.0/D3mirt/data/angles3D.rda |only D3mirt-2.1.0/D3mirt/inst/CITATION | 2 D3mirt-2.1.0/D3mirt/inst/doc/IntrotoD3mirt.pdf |binary D3mirt-2.1.0/D3mirt/inst/extdata/id.RData |binary D3mirt-2.1.0/D3mirt/inst/extdata/mod1.RData |binary D3mirt-2.1.0/D3mirt/inst/extdata/mod2.RData |binary D3mirt-2.1.0/D3mirt/inst/extdata/mod3.RData |binary D3mirt-2.1.0/D3mirt/inst/extdata/mod4.RData |binary D3mirt-2.1.0/D3mirt/man/D2mirt.Rd |only D3mirt-2.1.0/D3mirt/man/D3mirt.Rd | 10 D3mirt-2.1.0/D3mirt/man/angles2D.Rd |only D3mirt-2.1.0/D3mirt/man/angles3D.Rd |only D3mirt-2.1.0/D3mirt/man/information.Rd |only D3mirt-2.1.0/D3mirt/man/plot-methods.Rd |only D3mirt-2.1.0/D3mirt/man/print.D2mirt.Rd |only D3mirt-2.1.0/D3mirt/man/summary.D2mirt.Rd |only D3mirt-2.1.0/D3mirt/man/summary.D3mirt.Rd | 8 D3mirt-2.1.0/D3mirt/tests/testthat/_snaps/D2mirt.md |only D3mirt-2.1.0/D3mirt/tests/testthat/_snaps/D3mirt.md | 1134 +++++++++++++++++++- D3mirt-2.1.0/D3mirt/tests/testthat/test-D2mirt.R |only D3mirt-2.1.0/D3mirt/tests/testthat/test-D3mirt.R | 39 D3mirt-2.1.0/D3mirt/tests/testthat/test-modid.R | 4 45 files changed, 1407 insertions(+), 123 deletions(-)
Title: Interactive Command-Line Menus
Description: Provides interactive command-line menu functionality with
single and multiple selection menus, keyboard navigation (arrow keys or
vi-style j/k), preselection, and graceful fallback for non-interactive
environments. Inspired by tools such as 'inquirer.js'
<https://github.com/SBoudrias/Inquirer.js>, 'pick'
<https://github.com/aisk/pick>, and 'survey'
<https://github.com/AlecAivazis/survey>. Designed to be lightweight and
easy to integrate into 'R' packages and scripts.
Author: Petr Čala [aut, cre]
Maintainer: Petr Čala <61505008@fsv.cuni.cz>
Diff between climenu versions 0.1.7 dated 2026-04-15 and 0.1.8 dated 2026-07-08
DESCRIPTION | 8 +- MD5 | 25 ++++----- NEWS.md |only R/checkbox.R | 12 ++-- R/menu.R | 16 ++++- R/select.R | 16 +++-- R/utils.R | 112 +++++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/climenu.Rmd | 2 inst/doc/climenu.html | 17 +++--- man/menu.Rd | 11 +++- tests/testthat/test-climenu.R | 89 ++++++++++++++++++++++++++++++++ tests/testthat/test-fallback.R | 37 +++++++++++++ vignettes/climenu.Rmd | 2 14 files changed, 269 insertions(+), 78 deletions(-)
Title: Likelihood-Based Confidence Interval in Structural Equation
Models
Description: Forms likelihood-based confidence intervals
(LBCIs) for parameters in structural equation modeling,
introduced in Cheung and Pesigan (2023)
<doi:10.1080/10705511.2023.2183860>. Currently
implements the algorithm illustrated by Pek and Wu
(2018) <doi:10.1037/met0000163>, and supports the robust
LBCI proposed by Falk (2018)
<doi:10.1080/10705511.2017.1367254>.
Author: Shu Fai Cheung [aut, cre] ,
Ivan Jacob Agaloos Pesigan [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semlbci versions 0.11.6 dated 2026-06-08 and 0.12.0 dated 2026-07-08
DESCRIPTION | 6 - MD5 | 44 ++++++------ NEWS.md | 17 ++++ R/ci_bound_ur_i.R | 4 - R/ci_bound_wn_i.R | 20 ++--- R/scaling_factor3.R | 4 - R/set_start_wn.R | 8 +- R/syntax_to_i.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary tests/testthat/test-ci_bound_wn_i_std_pa_eq.R | 2 tests/testthat/test-ci_bound_wn_i_ustd_pa.R | 9 +- tests/testthat/test-plot_likelihood.R | 2 tests/testthat/test-plot_likelihood_ur.R | 2 tests/testthat/test-ram_to_lav_mod.R | 8 +- tests/testthat/test-scaling_factor3_mg_rb_std_sem_user_eq.R | 2 tests/testthat/test-scaling_factor3_mg_wn_sem_std.R | 2 tests/testthat/test-scaling_factor3_std_sem_user_eq.R | 4 - tests/testthat/test-scaling_factor3_wn_sem_std.R | 4 - tests/testthat/test-std_lav.R | 4 - tests/testthat/test-std_ram.R | 2 tests/testthat/test-ur_gen_est_i.R | 8 +- 23 files changed, 88 insertions(+), 68 deletions(-)
Title: Interface to 'JDemetra+ 3.x' Time Series Analysis Software
Description: R Interface to 'JDemetra+ 3.x'
(<https://github.com/jdemetra>) time series analysis software. It
provides functions allowing to decompose a time series, including
high-frequency data with multiple periodicities.
Author: Jean Palate [aut],
Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjd3xjars versions 0.1.0 dated 2026-04-21 and 0.1.1 dated 2026-07-08
DESCRIPTION | 25 +++++++++++----------- MD5 | 10 ++++---- NAMESPACE | 6 +---- NEWS.md | 6 ++--- R/zzz.R | 53 +++++++++++++++++++++++++---------------------- man/rjd3xjars-package.Rd | 3 +- 6 files changed, 54 insertions(+), 49 deletions(-)
Title: Missingness Alleviation for Network Analysis
Description: Provides functionality for estimating cross-sectional network structures representing partial correlations while accounting for missing data. Networks are estimated via neighborhood selection or regularization, with model selection guided by information criteria. Missing data can be handled primarily via multiple imputation or a maximum likelihood-based approach, as demonstrated by Nehler and Schultze (2025) <doi:10.1080/00273171.2025.2503833> and Nehler and Schultze (2026) <doi:10.1037/met0000828>. Deletion-based approaches are also available but play a secondary role.
Author: Kai Jannik Nehler [aut, cre]
Maintainer: Kai Jannik Nehler <nehler@psych.uni-frankfurt.de>
Diff between mantar versions 0.3.0 dated 2026-05-26 and 0.3.1 dated 2026-07-08
mantar-0.3.0/mantar/README.md |only mantar-0.3.1/mantar/DESCRIPTION | 8 ++-- mantar-0.3.1/mantar/MD5 | 15 +++---- mantar-0.3.1/mantar/NEWS.md | 8 ++++ mantar-0.3.1/mantar/R/data.R | 4 -- mantar-0.3.1/mantar/build/partial.rdb |binary mantar-0.3.1/mantar/build/stage23.rdb |binary mantar-0.3.1/mantar/inst/doc/mantar.html | 12 +++--- mantar-0.3.1/mantar/tests/testthat/test-regularization_net.R | 21 ++++++++--- 9 files changed, 42 insertions(+), 26 deletions(-)
Title: Helper Functions for Structural Equation Modeling
Description: An assortment of helper functions for doing structural equation
modeling, mainly by 'lavaan' for now. Most of them are time-saving functions
for common tasks in doing structural equation modeling and reading the
output. This package is not for functions that implement advanced statistical
procedures. It is a light-weight package for simple functions that do simple
tasks conveniently, with as few dependencies as possible.
Author: Shu Fai Cheung [aut, cre]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semhelpinghands versions 0.1.14 dated 2026-02-10 and 0.1.15 dated 2026-07-08
DESCRIPTION | 8 ++-- MD5 | 28 ++++++++--------- NEWS.md | 10 ++++++ R/ptable_to_syntax.R | 7 ++++ README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/semhelpinghands.html | 2 - man/plot_models_fm.Rd | 2 - man/ptable_to_syntax.Rd | 18 ++++++---- man/semhelpinghands-package.Rd | 5 +++ man/standardizedSolution_boot_ci.Rd | 2 - man/vector_from_lavaan.Rd | 2 - tests/testthat/test-ptable_to_syntax_incomplete.R | 4 ++ tests/testthat/test-standardizedSolution_boot_ci_cfa.R | 6 +-- 15 files changed, 62 insertions(+), 34 deletions(-)
More information about semhelpinghands at CRAN
Permanent link
Title: Fast and Efficient Processing of PAM Data
Description: Processing Chlorophyll Fluorescence & P700 Absorbance data. Four models are provided for the regression of Pi curves, which can be compared with each other in order to select the most suitable model for the data set. Control plots ensure the successful verification of each regression. Bundled output of alpha, ETRmax, Ik etc. enables fast and reliable further processing of the data.
Author: Julien Boehm [cre, aut] ,
Philipp Schrag [aut]
Maintainer: Julien Boehm <julien.boehm@uni-rostock.de>
Diff between pam versions 2.2.1 dated 2026-04-30 and 2.3.0 dated 2026-07-08
DESCRIPTION | 9 - MD5 | 124 ++++++++++++----------- NAMESPACE | 1 R/constants.R | 6 - R/device_diving_pam.R |only R/device_dual_pam.R | 2 R/device_dual_pam_single_channel_fluo.R | 2 R/device_dual_pam_single_channel_p700.R | 2 R/device_junior_pam.R | 2 R/device_pam_2500.R | 2 R/device_universal_data.R | 2 R/model_eilers_peeters.R | 1 R/model_platt.R | 1 R/model_vollenweider.R | 1 R/model_walsby.R | 1 R/plot.R | 59 ++-------- R/util.R | 55 ++++++++++ R/validation.R | 6 + build/partial.rdb |binary inst/extdata/diving_pam_II_data |only man/eilers_peeters_default_start_value_a.Rd | 5 man/eilers_peeters_default_start_value_b.Rd | 5 man/eilers_peeters_default_start_value_c.Rd | 5 man/eilers_peeters_generate_regression_ETR_I.Rd | 112 ++++++++++---------- man/eilers_peeters_generate_regression_ETR_II.Rd | 112 ++++++++++---------- man/eilers_peeters_modified.Rd | 1 man/platt_default_start_value_alpha.Rd | 5 man/platt_default_start_value_beta.Rd | 5 man/platt_default_start_value_ps.Rd | 5 man/platt_generate_regression_ETR_I.Rd | 118 ++++++++++----------- man/platt_generate_regression_ETR_II.Rd | 118 ++++++++++----------- man/platt_modified.Rd | 1 man/read_diving_pam_II_data.Rd |only man/read_dual_pam_data.Rd | 2 man/read_dual_pam_single_channel_fluo_data.Rd | 2 man/read_dual_pam_single_channel_p700_data.Rd | 2 man/read_junior_pam_data.Rd | 2 man/read_pam_2500_data.Rd | 2 man/read_universal_data.Rd | 2 man/vollenweider_default_start_value_a.Rd | 5 man/vollenweider_default_start_value_alpha.Rd | 5 man/vollenweider_default_start_value_n.Rd | 5 man/vollenweider_default_start_value_pmax.Rd | 5 man/vollenweider_generate_regression_ETR_I.Rd | 124 +++++++++++------------ man/vollenweider_generate_regression_ETR_II.Rd | 122 +++++++++++----------- man/vollenweider_modified.Rd | 1 man/walsby_default_start_value_alpha.Rd | 5 man/walsby_default_start_value_beta.Rd | 5 man/walsby_default_start_value_etr_max.Rd | 5 man/walsby_generate_regression_ETR_I.Rd | 116 ++++++++++----------- man/walsby_generate_regression_ETR_II.Rd | 116 ++++++++++----------- man/walsby_modified.Rd | 1 tests/testthat/data/diving_pam_II_data |only tests/testthat/test-combo_plot_control_etr_II.R | 26 ++++ tests/testthat/test-did_etr_saturate.R |only tests/testthat/test-eilers_peeters_etr_I.R | 1 tests/testthat/test-eilers_peeters_etr_II.R | 1 tests/testthat/test-platt_etr_I.R | 1 tests/testthat/test-platt_etr_II.R | 1 tests/testthat/test-read_diving_pam_data.R |only tests/testthat/test-universal_data_etr_I.R | 4 tests/testthat/test-vollenweider_etr_I.R | 1 tests/testthat/test-vollenweider_etr_II.R | 1 tests/testthat/test-walsby_etr_I.R | 1 tests/testthat/test-walsby_etr_II.R | 1 tests/testthat/test-write_model_result_csv.R | 39 ++++++- 66 files changed, 704 insertions(+), 668 deletions(-)
Title: One Sample Mendelian Randomization and Instrumental Variable
Analyses
Description: Useful functions for one-sample (individual level data)
Mendelian randomization and instrumental variable analyses. The
package includes implementations of; the Sanderson and Windmeijer
(2016) <doi:10.1016/j.jeconom.2015.06.004> conditional F-statistic,
the multiplicative structural mean model Hernán and Robins (2006)
<doi:10.1097/01.ede.0000222409.00878.37>, and two-stage predictor
substitution and two-stage residual inclusion estimators explained by
Terza et al. (2008) <doi:10.1016/j.jhealeco.2007.09.009>.
Author: Tom Palmer [aut, cre] ,
Wes Spiller [aut] ,
Eleanor Sanderson [aut] ,
Nicolai Vitt [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between OneSampleMR versions 0.1.7 dated 2026-03-09 and 0.1.8 dated 2026-07-08
DESCRIPTION | 9 MD5 | 44 +- NEWS.md | 18 R/asmm.R | 2 R/fsw.R | 706 ++++++++++++----------------------- R/msmm.R | 61 +-- R/onesamplemr-package.R | 1 R/tsps.R | 348 ++++------------- R/tsri.R | 400 ++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/f-statistic-comparison.html | 55 +- man/OneSampleMR-package.Rd | 2 man/asmm.Rd | 2 man/msmm.Rd | 4 man/summary.msmm.Rd | 2 man/summary.tsps.Rd | 2 man/summary.tsri.Rd | 4 man/tsri.Rd | 2 tests/testthat/test-fsw.R | 68 +++ tests/testthat/test-msmm.R | 91 ++++ tests/testthat/test-tsps.R | 77 +++ tests/testthat/test-tsri.R | 81 ++++ 23 files changed, 848 insertions(+), 1131 deletions(-)
Title: Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Description: Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A) that can be applied either on a lumped or semi-distributed way. A snow accumulation and melt model (CemaNeige) and the associated functions for the calibration and evaluation of models are also included. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] ,
Olivier Delaigue [aut, cre] ,
Guillaume Thirel [aut, ths] ,
David Dorchies [aut] ,
Charles Perrin [aut, ths] ,
Claude Michel [aut, ths],
Vazken Andreassian [ctb, ths] ,
Francois Bourgin [ctb] ,
Pierre Brigode [ctb] ,
Nicola [...truncated...]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGR versions 1.7.8 dated 2025-12-12 and 1.7.9 dated 2026-07-08
DESCRIPTION | 10 - MD5 | 37 ++--- NEWS.md | 215 ++++++++++++++++------------- R/CreateRunOptions.R | 4 R/RunModel_GR2M.R | 6 R/RunModel_Lag.R | 42 ----- R/UtilsRunModel.R | 48 ++++-- R/UtilsSeriesAggreg.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/V01_get_started.html | 79 ++++------ inst/doc/V03_param_sets_GR4J.html | 6 inst/doc/V04_cemaneige_hysteresis.R | 3 inst/doc/V04_cemaneige_hysteresis.Rmd | 3 inst/doc/V04_cemaneige_hysteresis.html | 100 ++++++------- inst/doc/V05_sd_model.html | 239 +++++++++++++++------------------ man/RunModel_CemaNeigeGR4J.Rd | 2 tests/testthat/test-CreateRunOptions.R | 103 ++++++++++---- tests/testthat/test-RunModel_GR2M.R |only vignettes/V04_cemaneige_hysteresis.Rmd | 3 20 files changed, 468 insertions(+), 435 deletions(-)
Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file forma [...truncated...]
Author: Tim Schaefer [aut, cre]
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between freesurferformats versions 1.0.0 dated 2025-09-08 and 1.0.1 dated 2026-07-08
freesurferformats-1.0.0/freesurferformats/R/read_dti_tck.R |only freesurferformats-1.0.1/freesurferformats/DESCRIPTION | 10 freesurferformats-1.0.1/freesurferformats/LICENSE | 4 freesurferformats-1.0.1/freesurferformats/MD5 | 631 +- freesurferformats-1.0.1/freesurferformats/NAMESPACE | 354 - freesurferformats-1.0.1/freesurferformats/R/brainvoyager.R | 880 +- freesurferformats-1.0.1/freesurferformats/R/cifti.R | 226 freesurferformats-1.0.1/freesurferformats/R/gifti_writer.R | 540 - freesurferformats-1.0.1/freesurferformats/R/gifti_xml_tools.R | 452 - freesurferformats-1.0.1/freesurferformats/R/helpers.R | 262 freesurferformats-1.0.1/freesurferformats/R/mghheader.R | 1456 ++-- freesurferformats-1.0.1/freesurferformats/R/nifti_common.R | 384 - freesurferformats-1.0.1/freesurferformats/R/nifti_to_mgh.R | 831 +- freesurferformats-1.0.1/freesurferformats/R/optdata.R | 375 - freesurferformats-1.0.1/freesurferformats/R/read_dti_tcktsf.R |only freesurferformats-1.0.1/freesurferformats/R/read_dti_trk.R | 256 freesurferformats-1.0.1/freesurferformats/R/read_fs_annot.R | 1338 ++-- freesurferformats-1.0.1/freesurferformats/R/read_fs_curv.R | 566 - freesurferformats-1.0.1/freesurferformats/R/read_fs_label.R | 400 - freesurferformats-1.0.1/freesurferformats/R/read_fs_mgh.R | 906 +-- freesurferformats-1.0.1/freesurferformats/R/read_fs_patch.R | 332 - freesurferformats-1.0.1/freesurferformats/R/read_fs_surface.R | 2960 +++++----- freesurferformats-1.0.1/freesurferformats/R/read_fs_transform.R | 552 - freesurferformats-1.0.1/freesurferformats/R/read_fs_volume.R | 98 freesurferformats-1.0.1/freesurferformats/R/read_fs_weight.R | 138 freesurferformats-1.0.1/freesurferformats/R/read_nifti1.R | 438 - freesurferformats-1.0.1/freesurferformats/R/read_nifti2.R | 314 - freesurferformats-1.0.1/freesurferformats/R/read_nisurface.R | 326 - freesurferformats-1.0.1/freesurferformats/R/rotate3d.R | 404 - freesurferformats-1.0.1/freesurferformats/R/surface_dist.R | 210 freesurferformats-1.0.1/freesurferformats/R/write_fs_annot.R | 446 - freesurferformats-1.0.1/freesurferformats/R/write_fs_curv.R | 624 +- freesurferformats-1.0.1/freesurferformats/R/write_fs_label.R | 252 freesurferformats-1.0.1/freesurferformats/R/write_fs_mgh.R | 510 - freesurferformats-1.0.1/freesurferformats/R/write_fs_patch.R | 210 freesurferformats-1.0.1/freesurferformats/R/write_fs_surface.R | 1678 ++--- freesurferformats-1.0.1/freesurferformats/R/write_fs_volume.R |only freesurferformats-1.0.1/freesurferformats/R/write_fs_weight.R | 186 freesurferformats-1.0.1/freesurferformats/R/write_nifti1.R | 488 - freesurferformats-1.0.1/freesurferformats/R/write_nifti2.R | 448 - freesurferformats-1.0.1/freesurferformats/build/vignette.rds |binary freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats.R | 252 freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats.Rmd | 624 +- freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats.html | 1456 ++-- freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_header.R | 44 freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_header.Rmd | 190 freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_header.html | 880 +- freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_write.R | 100 freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_write.Rmd | 314 - freesurferformats-1.0.1/freesurferformats/inst/doc/freesurferformats_write.html | 1042 +-- freesurferformats-1.0.1/freesurferformats/inst/extdata/colorlut.txt | 20 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.geo | 36 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.gii | 34 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.off | 44 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.ply | 58 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.stl | 172 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.tri | 44 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.vtk | 52 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube.wobj | 40 freesurferformats-1.0.1/freesurferformats/inst/extdata/cube_quads.byu | 16 freesurferformats-1.0.1/freesurferformats/inst/extdata/lh.entorhinal_exvivo.label | 2174 +++---- freesurferformats-1.0.1/freesurferformats/inst/extdata/lh.testsurface.asc | 20 freesurferformats-1.0.1/freesurferformats/inst/extdata/lh.tinysurface.asc | 20 freesurferformats-1.0.1/freesurferformats/inst/extdata/lh.tinysurface.gii | 126 freesurferformats-1.0.1/freesurferformats/inst/extdata/register.dat | 18 freesurferformats-1.0.1/freesurferformats/inst/extdata/talairach.lta | 60 freesurferformats-1.0.1/freesurferformats/inst/extdata/talairach.xfm | 16 freesurferformats-1.0.1/freesurferformats/inst/extdata/tiny_label.gii | 34 freesurferformats-1.0.1/freesurferformats/inst/extdata/tiny_morph.gii | 26 freesurferformats-1.0.1/freesurferformats/man/adjust.face.indices.to.Rd | 46 freesurferformats-1.0.1/freesurferformats/man/annot.max.region.idx.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/annot.unique.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/assert.surface.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/bvsmp.Rd | 46 freesurferformats-1.0.1/freesurferformats/man/cdata.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/check.dtype.for.data.Rd | 37 freesurferformats-1.0.1/freesurferformats/man/check_data_and_settings_consistency.Rd | 60 freesurferformats-1.0.1/freesurferformats/man/closest.vert.to.point.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/colortable.from.annot.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/coord.to.key.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/delete_all_opt_data.Rd | 28 freesurferformats-1.0.1/freesurferformats/man/doapply.transform.mtx.Rd | 54 freesurferformats-1.0.1/freesurferformats/man/dot-read.dti.tcktsf.Rd |only freesurferformats-1.0.1/freesurferformats/man/download_opt_data.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/euclidian.dist.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/faces.quad.to.tris.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/faces.tris.to.quad.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/fileopen.gz.or.not.Rd | 30 freesurferformats-1.0.1/freesurferformats/man/filepath.ends.with.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/fixed.vec.format.int.Rd | 58 freesurferformats-1.0.1/freesurferformats/man/flip2D.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/flip3D.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/fread3.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/fs.get.morph.file.ext.for.format.Rd | 80 freesurferformats-1.0.1/freesurferformats/man/fs.get.morph.file.format.from.filename.Rd | 80 freesurferformats-1.0.1/freesurferformats/man/fs.patch.Rd | 74 freesurferformats-1.0.1/freesurferformats/man/fs.surface.to.tmesh3d.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/fwrite3.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/get.dti.trk.endianness.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/get.slice.orientation.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/get_opt_data_filepath.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/gifti_writer.Rd | 54 freesurferformats-1.0.1/freesurferformats/man/gifti_xml.Rd | 116 freesurferformats-1.0.1/freesurferformats/man/gifti_xml_add_global_metadata.Rd | 64 freesurferformats-1.0.1/freesurferformats/man/gifti_xml_write.Rd | 70 freesurferformats-1.0.1/freesurferformats/man/giftixml_add_labeltable_from_annot.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/giftixml_add_labeltable_posneg.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/guess.filename.is.gzipped.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/has_pandoc.Rd | 30 freesurferformats-1.0.1/freesurferformats/man/int.to.col.brainvoyager.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/is.bvsmp.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/is.fs.annot.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/is.fs.label.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/is.fs.surface.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/is.fs.volume.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/is.mghheader.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/linesplit.fixed.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/list_opt_data.Rd | 28 freesurferformats-1.0.1/freesurferformats/man/m44_to_quaternion.Rd |only freesurferformats-1.0.1/freesurferformats/man/mgh.is.conformed.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/mghheader.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/mghheader.centervoxelRAS.from.firstvoxelRAS.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/mghheader.crs.orientation.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/mghheader.is.conformed.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/mghheader.is.ras.valid.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/mghheader.primary.slice.direction.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/mghheader.ras2vox.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/mghheader.ras2vox.tkreg.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/mghheader.scanner2tkreg.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/mghheader.tkreg2scanner.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/mghheader.update.from.vox2ras.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/mghheader.vox2ras.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/mghheader.vox2ras.tkreg.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/mghheader.vox2vox.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/mni152reg.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/mri_dtype_numbytes.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/ni1header.for.data.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/ni1header.template.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/ni2header.for.data.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/ni2header.template.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/nifti.datadim.from.dimfield.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/nifti.datadim.to.dimfield.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/nifti.dtype.info.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/nifti.dtypebitpix.info.from.mgh.dtype.Rd |only freesurferformats-1.0.1/freesurferformats/man/nifti.field.check.length.Rd | 44 freesurferformats-1.0.1/freesurferformats/man/nifti.field.check.nchar.max.Rd | 44 freesurferformats-1.0.1/freesurferformats/man/nifti.file.uses.fshack.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/nifti.file.version.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/nifti.header.check.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/nifti.space.info.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/nifti.time.info.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/nifti.transform.type.name.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/nii1header.for.mgh.Rd |only freesurferformats-1.0.1/freesurferformats/man/parse.stl.ascii.face.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/parse.transform.matrix.lines.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/ply.header.lines.Rd | 24 freesurferformats-1.0.1/freesurferformats/man/polygon.soup.to.indexed.mesh.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/print.fs.annot.Rd | 32 freesurferformats-1.0.1/freesurferformats/man/print.fs.label.Rd | 32 freesurferformats-1.0.1/freesurferformats/man/print.fs.patch.Rd | 32 freesurferformats-1.0.1/freesurferformats/man/print.fs.surface.Rd | 32 freesurferformats-1.0.1/freesurferformats/man/print.fs.volume.Rd | 32 freesurferformats-1.0.1/freesurferformats/man/ras.to.surfaceras.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/ras.to.talairachras.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/read.dti.tck.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/read.dti.trk.Rd | 55 freesurferformats-1.0.1/freesurferformats/man/read.dti.tsf.Rd | 54 freesurferformats-1.0.1/freesurferformats/man/read.element.counts.ply.header.Rd | 30 freesurferformats-1.0.1/freesurferformats/man/read.fixed.char.binary.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/read.fs.annot.Rd | 94 freesurferformats-1.0.1/freesurferformats/man/read.fs.annot.gii.Rd | 76 freesurferformats-1.0.1/freesurferformats/man/read.fs.colortable.Rd | 78 freesurferformats-1.0.1/freesurferformats/man/read.fs.curv.Rd | 106 freesurferformats-1.0.1/freesurferformats/man/read.fs.gca.Rd | 54 freesurferformats-1.0.1/freesurferformats/man/read.fs.label.Rd | 66 freesurferformats-1.0.1/freesurferformats/man/read.fs.label.gii.Rd | 74 freesurferformats-1.0.1/freesurferformats/man/read.fs.label.native.Rd | 88 freesurferformats-1.0.1/freesurferformats/man/read.fs.mgh.Rd | 138 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.Rd | 114 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.asc.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.bvsmp.Rd | 38 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.cifti.Rd | 104 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.gii.Rd | 102 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.ni1.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.ni2.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.nii.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/read.fs.morph.txt.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/read.fs.patch.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/read.fs.patch.asc.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.Rd | 100 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.asc.Rd | 94 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.bvsrf.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.byu.Rd | 44 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.geo.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.gii.Rd | 92 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.ico.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.mz3.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.obj.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.off.Rd | 80 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.ply.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.stl.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.stl.ascii.Rd | 52 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.stl.bin.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/read.fs.surface.vtk.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.transform.Rd | 92 freesurferformats-1.0.1/freesurferformats/man/read.fs.transform.dat.Rd | 82 freesurferformats-1.0.1/freesurferformats/man/read.fs.transform.lta.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.fs.transform.xfm.Rd | 88 freesurferformats-1.0.1/freesurferformats/man/read.fs.volume.Rd | 140 freesurferformats-1.0.1/freesurferformats/man/read.fs.volume.nii.Rd | 112 freesurferformats-1.0.1/freesurferformats/man/read.fs.weight.Rd | 84 freesurferformats-1.0.1/freesurferformats/man/read.fs.weight.asc.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/read.mesh.brainvoyager.Rd | 86 freesurferformats-1.0.1/freesurferformats/man/read.nifti1.data.Rd | 48 freesurferformats-1.0.1/freesurferformats/man/read.nifti1.header.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/read.nifti1.header.internal.Rd | 40 freesurferformats-1.0.1/freesurferformats/man/read.nifti2.data.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/read.nifti2.header.Rd | 34 freesurferformats-1.0.1/freesurferformats/man/read.nifti2.header.internal.Rd | 46 freesurferformats-1.0.1/freesurferformats/man/read.smp.brainvoyager.Rd | 70 freesurferformats-1.0.1/freesurferformats/man/read.smp.brainvoyager.v1or2.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/read.smp.brainvoyager.v3.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/read.smp.brainvoyager.v4or5.Rd | 42 freesurferformats-1.0.1/freesurferformats/man/read_nisurface.Rd | 108 freesurferformats-1.0.1/freesurferformats/man/read_nisurfacefile.Rd | 102 freesurferformats-1.0.1/freesurferformats/man/read_nisurfacefile.fsascii.Rd | 38 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freesurferformats-1.0.1/freesurferformats/man/talairachras.to.ras.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/translate.mri.dtype.Rd | 36 freesurferformats-1.0.1/freesurferformats/man/vertex.euclid.dist.Rd | 54 freesurferformats-1.0.1/freesurferformats/man/vertexdists.to.point.Rd | 50 freesurferformats-1.0.1/freesurferformats/man/write.fs.annot.Rd | 114 freesurferformats-1.0.1/freesurferformats/man/write.fs.annot.gii.Rd | 96 freesurferformats-1.0.1/freesurferformats/man/write.fs.colortable.Rd | 66 freesurferformats-1.0.1/freesurferformats/man/write.fs.curv.Rd | 80 freesurferformats-1.0.1/freesurferformats/man/write.fs.label.Rd | 106 freesurferformats-1.0.1/freesurferformats/man/write.fs.label.gii.Rd | 112 freesurferformats-1.0.1/freesurferformats/man/write.fs.mgh.Rd | 102 freesurferformats-1.0.1/freesurferformats/man/write.fs.morph.Rd | 92 freesurferformats-1.0.1/freesurferformats/man/write.fs.morph.asc.Rd | 82 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More information about freesurferformats at CRAN
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Title: A Lightweight Toolkit for Displaying Customizable Tables
Description: A lightweight toolkit that provides functions for printing tables from
input data in the R console or terminal with customizable formatting. Supported
outputs include American Psychological Association (APA)-style tables
(American Psychological Association, 2020, ISBN:9781433832178),
correlation matrices, contingency tables, and two-column summary tables.
Author: Joshua Marie [aut, cre]
Maintainer: Joshua Marie <joshua.marie.k@gmail.com>
Diff between tabstats versions 0.2.0 dated 2026-05-25 and 0.2.1 dated 2026-07-08
DESCRIPTION | 10 ++-- MD5 | 18 +++---- NEWS.md | 10 ++++ R/helpers-pairwise_matrix-extra.R | 7 +- README.md | 6 +- inst/doc/tabstats.R | 23 +++++++++ inst/doc/tabstats.Rmd | 26 ++++++++++- inst/doc/tabstats.html | 89 ++++++++++++++++++++++++++------------ man/tabstats.Rd | 4 - vignettes/tabstats.Rmd | 26 ++++++++++- 10 files changed, 165 insertions(+), 54 deletions(-)
Title: Obtaining Data Published by the National Statistics Institute
Description: Get open statistical data and metadata disseminated by the
National Statistics Institute of Spain (INE). The functions return
data frames with the requested information thanks to calls to
the 'INE' API <https://www.ine.es/dyngs/DAB/index.htm?cid=1100>.
Author: David Crespo [aut, cre],
National Statistics Institute, INE [cph]
Maintainer: David Crespo <david.crespo.roces@ine.es>
Diff between ineapir versions 0.2.5 dated 2025-09-15 and 0.2.6 dated 2026-07-08
DESCRIPTION | 6 - MD5 | 42 +++---- NEWS.md | 4 R/data_series.R | 12 +- R/data_tables.R | 14 +- R/metadata_series.R | 16 +-- R/metadata_tables.R | 20 +-- R/utils.R | 14 +- README.md | 180 +++++++++++++++++----------------- man/get_data_series.Rd | 10 - man/get_data_table.Rd | 14 +- man/get_metadata_operation_table.Rd | 4 man/get_metadata_series.Rd | 4 man/get_metadata_series_table.Rd | 8 - man/get_metadata_series_values.Rd | 4 man/get_metadata_table_groups.Rd | 4 man/get_metadata_table_values.Rd | 6 - man/get_metadata_table_varval.Rd | 6 - tests/testthat/test-data_series.R | 6 - tests/testthat/test-data_tables.R | 20 +-- tests/testthat/test-metadata_series.R | 8 - tests/testthat/test-metadata_tables.R | 14 +- 22 files changed, 213 insertions(+), 203 deletions(-)
Title: Fast C++ Primitives for the 'NeuroAnatomy Toolbox'
Description: Fast functions implemented in C++ via 'Rcpp' to support the
'NeuroAnatomy Toolbox' ('nat') ecosystem. These functions provide large
speed-ups for basic manipulation of neuronal skeletons over pure R
functions found in the 'nat' package. The expectation is that end
users will not use this package directly, but instead the 'nat'
package will automatically use routines from this package when it is
available to enable large performance gains.
Author: Gregory Jefferis [aut, cre]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between natcpp versions 0.2 dated 2025-10-14 and 0.3.0 dated 2026-07-08
DESCRIPTION | 12 ++++++------ MD5 | 20 +++++++++++++------- NAMESPACE | 3 +++ NEWS.md | 13 +++++++++++++ R/RcppExports.R | 29 +++++++++++++++++++++++++++++ R/weighted_jaccard.R |only inst/WORDLIST | 2 ++ man/c_weighted_jaccard_dense.Rd |only man/c_weighted_jaccard_sparse.Rd |only man/natcpp-package.Rd | 5 +++++ src/Makevars |only src/RcppExports.cpp | 33 +++++++++++++++++++++++++++++++++ src/weighted_jaccard.cpp |only tests/testthat/test-weighted-jaccard.R |only 14 files changed, 104 insertions(+), 13 deletions(-)
Title: Interfaces to Phylogenetic Software in R
Description: Functions that wrap popular phylogenetic software for sequence
alignment, masking of sequence alignments, and estimation of phylogenies and
ancestral character states.
Author: Christoph Heibl [aut] ,
Natalie Cusimano [aut],
Franz-Sebastian Krah [aut],
Martin R. Smith [ctb, cre]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between ips versions 0.0.13 dated 2026-02-23 and 0.1.1 dated 2026-07-08
DESCRIPTION | 28 - MD5 | 164 ++++---- NAMESPACE | 198 ++++++---- NEWS.md | 22 + R/DNAbin2index.R | 48 +- R/EmptyCells.R | 95 ++-- R/aliscore.R | 179 ++++----- R/aperm.DNAbin.R |only R/are.tips.consecutive.R | 22 - R/assembleDataNode.R | 67 +-- R/assembleDistributionNode.R | 25 - R/assembleInitNode.R | 102 ++--- R/assembleLoggers.R | 311 ++++++++-------- R/assembleOperators.R | 336 ++++++++--------- R/assembleStateNode.R | 275 +++++++------- R/blastn.R | 151 +++---- R/code.simple.gaps.R | 157 ++++---- R/collapseUnsupportedEdges.R | 184 ++++----- R/combMyTree.R | 208 +++++++--- R/del.miss.R | 70 +-- R/deleteEmptyCells.R | 108 ++--- R/deleteGaps.R | 72 +-- R/descendants.R | 111 ++--- R/fixNodes.R | 173 +++++---- R/forceEqualTipHeights.R | 2 R/formatSet.R | 32 - R/gblocks.R | 284 +++++++------- R/index2DNAbin.R | 72 +-- R/mafft.R | 385 ++++++++++---------- R/mafft.merge.R | 191 +++++----- R/matrixBlock.R | 50 +- R/mrbayes.R | 365 +++++++++---------- R/mrbayes.lset.R | 145 +++++-- R/mrbayes.mcmc.R | 179 ++++++--- R/mrbayes.prset.R | 141 +++++-- R/multistateMCMC.R | 397 ++++++++++---------- R/multistateML.R | 397 ++++++++++---------- R/neighboringPairs.R | 36 - R/noi.R | 172 ++++----- R/ntip.R | 54 +- R/phylo2mafft.R | 82 ++-- R/phylo2mst.R | 98 ++--- R/pis.R | 122 +++--- R/prank.R | 133 +++--- R/raxml.R | 764 ++++++++++++++++++++-------------------- R/raxml.partitions.R | 38 - R/rbeauti.R | 461 ++++++++++++------------ R/rc.R | 177 ++++----- R/read.beast.R | 184 ++++----- R/read.fas.R | 128 +++--- R/read.mrbayes.R | 161 ++++---- R/read.nex.R | 109 ++--- R/read.phy.R | 89 ++-- R/read.starbeast.R | 171 ++++---- R/read.xml.R | 43 +- R/setClock.R | 109 ++--- R/setMCMC.R | 36 - R/sister.R | 145 +++---- R/splitIntoClades.R | 76 +-- R/str2cha.R | 10 R/terminalSisters.R | 67 +-- R/tipHeights.R | 54 +- R/traitRate.R | 187 ++++----- R/trimEnds.R | 283 +++++++------- R/unresolve.clade.R | 67 +-- R/write.fas.R | 152 +++---- R/write.nex.R | 313 ++++++++-------- inst/CITATION | 18 man/DNAbin2index.Rd | 36 - man/EmptyCells.Rd | 156 ++++---- man/aliscore.Rd | 115 +++--- man/aperm.DNAbin.Rd |only man/collapseUnsupportedEdges.Rd | 82 ++-- man/combMyTree.Rd | 100 +++-- man/fixNodes.Rd | 96 +++-- man/gblocks.Rd | 221 +++++------ man/mafft.merge.Rd | 78 ++-- man/mrbayes.Rd | 179 ++++----- man/mrbayes.lset.Rd | 147 +++---- man/mrbayes.mcmc.Rd | 256 ++++++------- man/mrbayes.prset.Rd | 190 ++++++--- man/raxml.partitions.Rd | 2 man/rbeauti.Rd | 170 ++++---- man/read.beast.Rd | 88 ++-- 84 files changed, 6344 insertions(+), 5857 deletions(-)
Title: Download and Measure Global Trends Through 'Google' Search
Volumes
Description: 'Google' offers public access to global search volumes from its
search engine through the 'Google Trends' portal. The package downloads
these search volumes provided by 'Google Trends' and uses them to
measure and analyze the distribution of search scores across countries
or within countries. The package allows researchers and analysts to
use these search scores to investigate global trends based on patterns
within these scores. This offers insights such as degree of
internationalization of firms and organizations or dissemination of
political, social, or technological trends across the globe or within
single countries. An outline of the package's methodological
foundations and potential applications is available as a working
paper: <doi:10.2139/ssrn.3969013>.
Author: Harald Puhr [aut, cre, cph] ,
Jakob Muellner [ccp]
Maintainer: Harald Puhr <harald.puhr@gmail.com>
Diff between globaltrends versions 0.0.14 dated 2023-03-06 and 0.2.1 dated 2026-07-08
globaltrends-0.0.14/globaltrends/R/get_abnorm_hist.r |only globaltrends-0.0.14/globaltrends/R/plot_bar.r |only globaltrends-0.0.14/globaltrends/R/plot_box.r |only globaltrends-0.0.14/globaltrends/R/plot_ts.r |only globaltrends-0.0.14/globaltrends/R/plot_voi_doi.r |only globaltrends-0.0.14/globaltrends/man/get_abnorm_hist.Rd |only globaltrends-0.0.14/globaltrends/man/plot_bar.Rd |only globaltrends-0.0.14/globaltrends/man/plot_box.Rd |only globaltrends-0.0.14/globaltrends/man/plot_ts.Rd |only globaltrends-0.0.14/globaltrends/man/plot_voi_doi.Rd |only globaltrends-0.0.14/globaltrends/tests/test_functions.r |only globaltrends-0.0.14/globaltrends/tests/testthat.r |only globaltrends-0.0.14/globaltrends/tests/testthat/test-24months.R |only globaltrends-0.0.14/globaltrends/tests/testthat/test-abnorm.R |only globaltrends-0.0.14/globaltrends/tests/testthat/test-plot_bar.R |only globaltrends-0.0.14/globaltrends/tests/testthat/test-plot_box.R |only globaltrends-0.0.14/globaltrends/tests/testthat/test-plot_ts.R |only globaltrends-0.0.14/globaltrends/tests/testthat/test-plot_voi_doi.R |only globaltrends-0.0.14/globaltrends/vignettes/plot009.png |only globaltrends-0.0.14/globaltrends/vignettes/plot010.png |only globaltrends-0.0.14/globaltrends/vignettes/plot_sample01.png |only globaltrends-0.0.14/globaltrends/vignettes/plot_sample02.png |only globaltrends-0.0.14/globaltrends/vignettes/plot_sample03.png |only globaltrends-0.0.14/globaltrends/vignettes/plot_sample04.png |only globaltrends-0.2.1/globaltrends/DESCRIPTION | 45 globaltrends-0.2.1/globaltrends/LICENSE | 4 globaltrends-0.2.1/globaltrends/MD5 | 174 - globaltrends-0.2.1/globaltrends/NAMESPACE | 116 - globaltrends-0.2.1/globaltrends/NEWS.md | 169 + globaltrends-0.2.1/globaltrends/R/add_keywords.r | 320 +-- globaltrends-0.2.1/globaltrends/R/add_locations.r | 251 +- globaltrends-0.2.1/globaltrends/R/aggregate_synonyms.r |only globaltrends-0.2.1/globaltrends/R/check_functions.r | 178 + globaltrends-0.2.1/globaltrends/R/compute_doi.r | 367 ++- globaltrends-0.2.1/globaltrends/R/compute_score.r | 738 ++----- globaltrends-0.2.1/globaltrends/R/data.r | 540 ++--- globaltrends-0.2.1/globaltrends/R/database_functions.r | 545 ++--- globaltrends-0.2.1/globaltrends/R/download_control.r | 294 ++ globaltrends-0.2.1/globaltrends/R/download_object.r | 425 +++- globaltrends-0.2.1/globaltrends/R/download_region.r |only globaltrends-0.2.1/globaltrends/R/download_related.r |only globaltrends-0.2.1/globaltrends/R/export_data.r | 541 ++--- globaltrends-0.2.1/globaltrends/R/globals.r | 30 globaltrends-0.2.1/globaltrends/R/helper_functions.r | 870 +++++++- globaltrends-0.2.1/globaltrends/R/initialize_python.r |only globaltrends-0.2.1/globaltrends/R/remove_data.r | 624 +++--- globaltrends-0.2.1/globaltrends/R/zzz.r | 131 - globaltrends-0.2.1/globaltrends/README.md | 136 - globaltrends-0.2.1/globaltrends/build/partial.rdb |only globaltrends-0.2.1/globaltrends/build/vignette.rds |binary globaltrends-0.2.1/globaltrends/data/example_control.rda |binary globaltrends-0.2.1/globaltrends/data/example_doi.rda |binary globaltrends-0.2.1/globaltrends/data/example_keywords.rda |binary globaltrends-0.2.1/globaltrends/data/example_object.rda |binary globaltrends-0.2.1/globaltrends/data/example_score.rda |binary globaltrends-0.2.1/globaltrends/data/example_time.rda |binary globaltrends-0.2.1/globaltrends/inst/CITATION | 8 globaltrends-0.2.1/globaltrends/inst/doc/globaltrends.R | 506 +--- globaltrends-0.2.1/globaltrends/inst/doc/globaltrends.Rmd | 398 +-- globaltrends-0.2.1/globaltrends/inst/doc/globaltrends.html | 853 +++----- globaltrends-0.2.1/globaltrends/inst/python |only globaltrends-0.2.1/globaltrends/man/add_keyword.Rd | 40 globaltrends-0.2.1/globaltrends/man/add_locations.Rd | 76 globaltrends-0.2.1/globaltrends/man/add_synonym.Rd | 45 globaltrends-0.2.1/globaltrends/man/aggregate_synonyms.Rd |only globaltrends-0.2.1/globaltrends/man/batch_keywords.Rd | 39 globaltrends-0.2.1/globaltrends/man/batch_time.Rd | 38 globaltrends-0.2.1/globaltrends/man/compute_doi.Rd | 91 globaltrends-0.2.1/globaltrends/man/compute_score.Rd | 144 - 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Title: Threshold-Sweep QCA
Description: Provides threshold sweep methods for Qualitative Comparative
Analysis (QCA). Implements Condition Threshold Sweep-Single (CTS-S),
Condition Threshold Sweep-Multiple (CTS-M), Outcome Threshold Sweep (OTS),
and Dual Threshold Sweep (DTS) for systematic exploration of threshold
calibration effects on crisp-set QCA results. These methods extend
traditional robustness approaches by treating threshold variation as an
exploratory tool for discovering causal structures. Also provides Fiss
(2011) <doi:10.5465/amj.2011.60263120> core/peripheral condition
classification via compute_fiss_core() and generate_fiss_chart(), enabling
four-symbol configuration charts that distinguish core conditions (present
in both parsimonious and intermediate solutions) from peripheral conditions
(intermediate only). Built on top of the 'QCA' package by Dusa (2019)
<doi:10.1007/978-3-319-75668-4>, with function arguments following 'QCA'
conventions. Based on set-theoretic methods by Ragin (2008)
<doi: [...truncated...]
Author: Yuki Toyoda [aut, cre],
Japan Society for the Promotion of Science [fnd]
Maintainer: Yuki Toyoda <yuki.toyoda.ds@hosei.ac.jp>
Diff between ThSQCA versions 2.0.0 dated 2026-05-30 and 2.0.1 dated 2026-07-08
DESCRIPTION | 43 - MD5 | 58 +- NEWS.md | 29 + R/ThSQCA-package.R | 2 R/tsqca_config_chart.R | 23 - R/tsqca_core.R | 672 ------------------------------ R/tsqca_cts.R | 2 R/tsqca_fiss_core.R | 11 R/tsqca_helpers.R | 36 + R/tsqca_ots_dts.R | 2 R/tsqca_report.R | 18 build/partial.rdb |binary build/vignette.rds |binary inst/doc/ThSQCA_Reproducible_EN.html | 34 - inst/doc/ThSQCA_Tutorial_EN.html | 20 man/SYMBOL_SETS.Rd | 4 man/SYMBOL_SETS_FISS.Rd | 12 man/ThSQCA-package.Rd | 7 man/build_fiss_matrix.Rd | 8 man/classify_term_conditions.Rd | 13 man/compute_fiss_core.Rd | 72 --- man/extract_cond_status_map.Rd | 9 man/extract_sol_terms.Rd | 8 man/generate_config_chart.Rd | 21 man/generate_cross_threshold_chart.Rd | 2 man/generate_fiss_chart.Rd | 42 - man/generate_report.Rd | 17 man/print_fiss_summary.Rd | 15 man/run_parsimonious.Rd | 8 man/sanitize_truthtable.Rd |only tests/testthat/test-sanitize_truthtable.R |only 31 files changed, 238 insertions(+), 950 deletions(-)
Title: Antigenic Cartography Macros
Description: A toolkit for making antigenic maps from immunological assay data,
in order to quantify and visualize antigenic differences between different
pathogen strains as described in
Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World
Health Organization influenza vaccine strain selection process. Additional
functions allow for the diagnostic evaluation of antigenic maps and an
interactive viewer is provided to explore antigenic relationships amongst
several strains and incorporate the visualization of associated genetic
information.
Author: Sam Wilks [aut, cre]
Maintainer: Sam Wilks <sam.wilks@unimelb.edu.au>
Diff between Racmacs versions 1.2.9 dated 2023-11-30 and 1.2.10 dated 2026-07-08
Racmacs-1.2.10/Racmacs/DESCRIPTION | 17 ++-- Racmacs-1.2.10/Racmacs/MD5 | 27 +++--- Racmacs-1.2.10/Racmacs/NEWS.md | 3 Racmacs-1.2.10/Racmacs/R/map_new.R | 2 Racmacs-1.2.10/Racmacs/R/map_optimize.R | 2 Racmacs-1.2.10/Racmacs/build/vignette.rds |binary Racmacs-1.2.10/Racmacs/inst/doc/adding-sequences.html | 35 +++++++- Racmacs-1.2.10/Racmacs/inst/doc/assessing_map_uncertainty.html | 1 Racmacs-1.2.10/Racmacs/inst/doc/comparing-maps.html | 37 +++++++-- Racmacs-1.2.10/Racmacs/inst/doc/customising-map-appearance.html | 3 Racmacs-1.2.10/Racmacs/inst/doc/making-a-map-from-scratch.html | 39 +++++++--- Racmacs-1.2.10/Racmacs/inst/doc/merging-maps.R | 18 ++-- Racmacs-1.2.10/Racmacs/inst/doc/merging-maps.html | 1 Racmacs-1.2.10/Racmacs/tests/testthat/Rplots.pdf |binary Racmacs-1.2.9/Racmacs/inst/htmlwidgets/RacViewer/tests |only 15 files changed, 127 insertions(+), 58 deletions(-)
Title: Bayesian Summary Data Models for Mendelian Randomization Studies
Description: Bayesian estimation of inverse variance weighted (IVW),
Burgess et al. (2013) <doi:10.1002/gepi.21758>, and MR-Egger, Bowden
et al. (2015) <doi:10.1093/ije/dyv080>, summary data models for
Mendelian randomization analyses.
Author: Okezie Uche-Ikonne [aut] ,
Frank Dondelinger [aut] ,
Tom Palmer [aut, cre]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between mrbayes versions 0.5.2 dated 2024-08-19 and 0.5.3 dated 2026-07-08
mrbayes-0.5.2/mrbayes/src/Makevars |only mrbayes-0.5.3/mrbayes/DESCRIPTION | 19 mrbayes-0.5.3/mrbayes/MD5 | 107 +-- mrbayes-0.5.3/mrbayes/NEWS.md | 17 mrbayes-0.5.3/mrbayes/R/bmi_insulin.R | 6 mrbayes-0.5.3/mrbayes/R/dodata.R | 12 mrbayes-0.5.3/mrbayes/R/mr_egger_rjags.R | 95 +-- mrbayes-0.5.3/mrbayes/R/mr_egger_stan.R | 26 mrbayes-0.5.3/mrbayes/R/mr_format.R | 7 mrbayes-0.5.3/mrbayes/R/mr_ivw_rjags.R | 185 +++--- mrbayes-0.5.3/mrbayes/R/mr_ivw_stan.R | 21 mrbayes-0.5.3/mrbayes/R/mr_radialegger_rjags.R | 88 +- mrbayes-0.5.3/mrbayes/R/mr_radialegger_stan.R | 23 mrbayes-0.5.3/mrbayes/R/mrinput_mrformat.R | 14 mrbayes-0.5.3/mrbayes/R/mvmr_egger_rjags.R | 176 ++--- mrbayes-0.5.3/mrbayes/R/mvmr_egger_stan.R | 35 - mrbayes-0.5.3/mrbayes/R/mvmr_ivw_rjags.R | 261 ++++---- mrbayes-0.5.3/mrbayes/R/mvmr_ivw_stan.R | 22 mrbayes-0.5.3/mrbayes/R/rjags_check.R | 6 mrbayes-0.5.3/mrbayes/R/rstan_check.R | 6 mrbayes-0.5.3/mrbayes/README.md | 9 mrbayes-0.5.3/mrbayes/build/partial.rdb |binary mrbayes-0.5.3/mrbayes/cleanup |only mrbayes-0.5.3/mrbayes/configure | 6 mrbayes-0.5.3/mrbayes/inst/stan/mregger.stan | 2 mrbayes-0.5.3/mrbayes/inst/stan/mvmregger.stan | 2 mrbayes-0.5.3/mrbayes/man/bmi_insulin.Rd | 6 mrbayes-0.5.3/mrbayes/man/dodata.Rd | 12 mrbayes-0.5.3/mrbayes/man/mr_egger_rjags.Rd | 4 mrbayes-0.5.3/mrbayes/man/mr_egger_stan.Rd | 6 mrbayes-0.5.3/mrbayes/man/mr_ivw_rjags.Rd | 2 mrbayes-0.5.3/mrbayes/man/mr_ivw_stan.Rd | 6 mrbayes-0.5.3/mrbayes/man/mr_radialegger_rjags.Rd | 4 mrbayes-0.5.3/mrbayes/man/mr_radialegger_stan.Rd | 6 mrbayes-0.5.3/mrbayes/man/mrbayes-package.Rd | 1 mrbayes-0.5.3/mrbayes/man/mrinput_mr_format.Rd | 2 mrbayes-0.5.3/mrbayes/man/mvmr_egger_rjags.Rd | 5 mrbayes-0.5.3/mrbayes/man/mvmr_egger_stan.Rd | 6 mrbayes-0.5.3/mrbayes/man/mvmr_ivw_rjags.Rd | 2 mrbayes-0.5.3/mrbayes/man/mvmr_ivw_stan.Rd | 6 mrbayes-0.5.3/mrbayes/src/Makevars.in |only mrbayes-0.5.3/mrbayes/src/stanExports_mregger.cc | 34 - mrbayes-0.5.3/mrbayes/src/stanExports_mrivw.cc | 34 - mrbayes-0.5.3/mrbayes/src/stanExports_mrradialegger.cc | 34 - mrbayes-0.5.3/mrbayes/src/stanExports_mvmregger.cc | 34 - mrbayes-0.5.3/mrbayes/src/stanExports_mvmrivw.cc | 34 - mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_egger_rjags.R | 270 ++++----- mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_egger_stan.R | 188 +++--- mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_ivw_rjags.R | 204 +++--- mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_ivw_stan.R | 145 ++-- mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_radialegger_rjags.R | 297 +++++----- mrbayes-0.5.3/mrbayes/tests/testthat/test-mr_radialegger_stan.R | 188 +++--- mrbayes-0.5.3/mrbayes/tests/testthat/test-mvmr_egger_rjags.R | 262 ++++---- mrbayes-0.5.3/mrbayes/tests/testthat/test-mvmr_egger_stan.R | 208 +++---- mrbayes-0.5.3/mrbayes/tests/testthat/test-mvmr_ivw_rjags.R | 285 ++++----- mrbayes-0.5.3/mrbayes/tests/testthat/test-mvmr_ivw_stan.R | 210 +++---- 56 files changed, 1864 insertions(+), 1776 deletions(-)
Title: A Multivariate Meta-Analysis Model for High-Dimensional Data
Description: Performs multivariate meta-analysis for high-dimensional data
to integrate and collectively analyse individual-level data from multiple
studies, as well as to combine summary estimates. This approach accounts
for correlation between outcomes, incorporates within- and between-study
variability, handles missing values, and uses shrinkage estimation to
accommodate high dimensionality. The 'MetaHD' R package provides access
to our multivariate meta-analysis approach, along with a comprehensive
suite of existing meta-analysis methods, including fixed-effects and
random-effects models, Fisher's method, Stouffer's method, the weighted
Z method, Lancaster's method, the weighted Fisher's method, and vote-counting
approach. Visualisation tools are provided for interpreting and comparing
results across methods, including Venn diagrams, UpSet plots, and ROC curves,
heatmaps of pooled effect sizes and correlations among outcomes. A detailed
vignette with example datasets and code for data preparati [...truncated...]
Author: Jayamini Liyanage [aut, cre],
Alysha De Livera [aut],
Luke Prendergast [aut]
Maintainer: Jayamini Liyanage <j.liyanage@latrobe.edu.au>
Diff between MetaHD versions 0.1.4 dated 2026-02-05 and 0.1.5 dated 2026-07-08
DESCRIPTION | 42 ++++- MD5 | 54 +++++-- NAMESPACE | 17 ++ R/MetaHD.R | 298 ++++++++++++++++++++++++++++++++++------ R/MetaHDInput.R | 4 R/MetaHDResult.R |only R/MetaHDpval.R | 12 - R/helper.functions.R | 203 ++++++++++++++++++++++++++- R/plot_MetaHDResult.R |only R/plot_correlation_heatmap.R |only R/plot_dendrogram.R |only R/plot_effect_heatmap.R |only R/simData.R |only build/partial.rdb |binary data/realdata.rda |binary data/simData.complete.rda |only data/simData.missing.rda |only data/simdata.1.rda |binary data/simdata.2.rda |binary man/MetaHD-outputs.Rd |only man/MetaHD.Rd | 56 +++++++ man/MetaHDInput.Rd | 4 man/MetaHDResult.Rd |only man/MetaHDpval.Rd | 12 - man/estimateCorMat.Rd |only man/figures |only man/plot.MetaHDResult.Rd |only man/plot_correlation_heatmap.Rd |only man/plot_dendrogram.Rd |only man/plot_effect_heatmap.Rd |only man/simData.complete.Rd |only man/simData.missing.Rd |only tests |only 33 files changed, 616 insertions(+), 86 deletions(-)
Title: Optimal Group Assignment and Workload Allocation
Description: Integer programming models to assign students to groups by maximising
diversity or topic preferences, and to allocate multi-role teaching workloads
while balancing role demand, preferences, fairness, and cohort protection.
Author: Vik Gopal [aut],
Kevin Lam [aut],
Ju Xue [ctb],
Mingyuan Zhang [aut, cre],
National University of Singapore [cph]
Maintainer: Mingyuan Zhang <e0970135@u.nus.edu>
Diff between grouper versions 0.5.0 dated 2025-10-16 and 0.7.3 dated 2026-07-08
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Title: Parsing Glycan Structure Text Representations
Description: Provides functions to parse glycan structure text representations
into 'glyrepr' glycan structures. Currently, it supports StrucGP-style,
pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, IUPAC-compact,
WURCS, LINUCS, Linear Code, GlycoCT, and KCF format. It also provides an automatic parser
to detect the format and parse the structure string.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyparse versions 0.7.0 dated 2026-07-06 and 0.7.1 dated 2026-07-08
DESCRIPTION | 8 +-- MD5 | 13 +++--- NEWS.md | 6 ++ R/struc-parser-wrapper.R | 60 +++++++++++++++-------------- inst/doc/glyparse.html | 9 +--- tests/testthat/test-parse-glycam-iupac.R | 10 +++- tests/testthat/test-performance.R | 22 ++++++++++ tests/testthat/test-struc-parser-wrapper.R |only 8 files changed, 83 insertions(+), 45 deletions(-)
Title: Partitioning Using Deletion, Substitution, and Addition Moves
Description: A novel tool for generating a piecewise
constant estimation list of increasingly complex predictors
based on an intensive and comprehensive search over the entire
covariate space.
Author: Annette Molinaro [aut, cre],
Adam Olshen [aut],
Karen Lostritto [aut],
Gregory Ryslik [aut],
Steve Weston [aut]
Maintainer: Annette Molinaro <annette.molinaro@ucsf.edu>
Diff between partDSA versions 0.9.14 dated 2017-01-05 and 0.9.15 dated 2026-07-08
DESCRIPTION | 31 +++++++++++++++-------- MD5 | 42 +++++++++++++++++++------------ NEWS.md |only R/addon.R | 14 ++++++---- R/algAlone2.R | 17 ++++++++---- R/code.2.R | 4 ++ R/main.R | 39 +++++++++++++++++----------- R/newfunctions-Survival.R | 28 ++++++++++++++++++++ inst/CITATION | 62 +++++++++++++++++++++++----------------------- inst/doc/partDSAvig.R | 16 +++++------ inst/doc/partDSAvig.Rnw | 11 ++++++++ inst/doc/partDSAvig.pdf |binary inst/doc/survival.R | 17 +++++------- inst/doc/survival.Rnw | 12 ++++++++ inst/doc/survival.pdf |binary tests |only vignettes/partDSAvig.Rnw | 11 ++++++++ vignettes/refs.bib | 2 - vignettes/survival.Rnw | 12 ++++++++ 19 files changed, 213 insertions(+), 105 deletions(-)
Title: Advanced Continuous Glucose Monitoring Analysis with
High-Performance C++ Backend
Description: Tools for advanced analysis of continuous glucose monitoring (CGM)
time-series, implementing GRID (Glucose Rate Increase Detector) and GRID-based
algorithms for postprandial peak detection, and detection of hypoglycemic and
hyperglycemic episodes (Levels 1/2/Extended) aligned with international consensus
CGM metrics. Core algorithms are implemented in optimized C++ using 'Rcpp' to
provide accurate and fast analysis on large datasets.
Author: Sang Ho Park [aut, cre],
Rosa Oh [aut, ctb],
Sang-Man Jin [aut, ctb]
Maintainer: Sang Ho Park <shstat1729@gmail.com>
Diff between cgmguru versions 1.1.0 dated 2026-06-08 and 1.2.0 dated 2026-07-08
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-04-23 0.4.6
2025-12-12 0.4.5
2025-12-10 0.4.3
2025-12-02 0.4.2
2023-08-21 0.4.1
2023-07-19 0.4.0
2020-12-17 0.3.2
2020-04-06 0.2.2
2020-01-20 0.2.1
2020-01-19 0.2.0
2019-07-03 0.1.3
2018-09-30 0.1.2
2018-09-27 0.1.1
2018-06-15 0.1.0
Title: Simplex Regression Models with Parametric or Fixed Mean Link
Functions
Description: Fits and analyzes simplex regression models with either
fixed or parametric mean link functions. Implements the simplex
probability density function, cumulative distribution function,
quantile function, random number generation, and variance evaluation.
Offers several fixed and parametric link functions for the mean
submodel, tools for residual analysis and diagnostic plotting,
hypothesis testing procedures, and influence measures such as Cook's
distance and leverage (hat values). Includes the Scout Score (SS)
criterion for model selection, enabling comprehensive inference and
diagnostic analysis within the simplex regression framework.
For more details see Barndorff-Nielsen and Jorgensen (1991)
<doi:10.1016/0047-259X(91)90008-P> and Justino and Cribari-Neto (2026)
<doi:10.1016/j.apm.2025.116713>.
Author: Maria Eduarda da Cruz Justino [aut, cre] ,
Francisco Cribari-Neto [ctb, ths]
Maintainer: Maria Eduarda da Cruz Justino <eueduardacruz@gmail.com>
Diff between SimplexRegression versions 0.1.3 dated 2026-06-30 and 0.1.4 dated 2026-07-08
DESCRIPTION | 10 +- MD5 | 75 ++++++++------- NEWS.md | 12 ++ R/abortionopposition.R |only R/biomass.R | 38 ++++--- R/relativehumidity.R | 40 ++++---- R/simplexreg_fit.R | 2 R/simplexreg_influence.R | 65 ++++++++----- R/simplexreg_links.R | 18 ++- R/simplexreg_methods.R | 47 +++------ R/simplexreg_penalized_ic.R | 25 ++++- R/simplexreg_plots.R | 32 +++++- R/simplexreg_press.R | 8 + R/simplexreg_residuals.R | 4 R/simplexreg_scoretest.R | 2 R/simplexreg_sscriteria.R | 22 +++- data/AbortionOpposition.rda |only data/Biomass.rda |binary data/RelativeHumidity.rda |binary inst/WORDLIST | 5 - inst/doc/relative-humidity.R | 38 +++---- inst/doc/relative-humidity.Rmd | 76 +++++++-------- inst/doc/relative-humidity.html | 178 ++++++++++++++++++------------------- man/AbortionOpposition.Rd |only man/Biomass.Rd | 37 ++++--- man/RelativeHumidity.Rd | 40 ++++---- man/diag.distances.Rd | 15 +-- man/diag.im.Rd | 42 +++++--- man/dispersion_links.Rd | 9 + man/fixed_mean_links.Rd | 3 man/halfnormal.plot.Rd | 2 man/local.influence.Rd | 3 man/parametric_mean_links.Rd | 6 - man/penalized.ic.Rd | 15 ++- man/penalized.ss.Rd | 14 ++ man/plot.simplexregression.Rd | 17 ++- man/press.Rd | 8 + man/residuals.simplexregression.Rd | 4 man/scoretest.Rd | 2 vignettes/relative-humidity.Rmd | 76 +++++++-------- 40 files changed, 558 insertions(+), 432 deletions(-)
More information about SimplexRegression at CRAN
Permanent link
Title: Simulating Oncology Trials using an Illness-Death Model
Description: Based on the illness-death model a large number of clinical
trials with oncology endpoints progression-free survival (PFS) and
overall survival (OS) can be simulated, see Meller, Beyersmann and
Rufibach (2019) <doi:10.1002/sim.8295>. The simulation set-up allows
for random and event-driven censoring, an arbitrary number of
treatment arms, staggered study entry and drop-out. Exponentially,
Weibull and piecewise exponentially distributed survival times can be
generated. The correlation between PFS and OS can be calculated.
Author: Alexandra Erdmann [aut],
Daniel Sabanes Bove [aut, cre],
Kaspar Rufibach [aut],
Holger Loewe [aut],
F. Hoffmann-La Roche AG [cph, fnd],
University of Ulm [cph, fnd]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between simIDM versions 0.1.0 dated 2023-12-11 and 0.1.1 dated 2026-07-08
simIDM-0.1.0/simIDM/man/figures/logo-large.png |only simIDM-0.1.0/simIDM/man/figures/logo.png |only simIDM-0.1.1/simIDM/DESCRIPTION | 20 simIDM-0.1.1/simIDM/MD5 | 27 simIDM-0.1.1/simIDM/NEWS.md | 10 simIDM-0.1.1/simIDM/R/corPFSOS.R | 3 simIDM-0.1.1/simIDM/build/vignette.rds |binary simIDM-0.1.1/simIDM/inst/doc/correlation.html | 380 ++++-- simIDM-0.1.1/simIDM/inst/doc/pwc_survival.html | 138 +- simIDM-0.1.1/simIDM/inst/doc/quickstart.html | 1321 +++++++++--------------- simIDM-0.1.1/simIDM/inst/doc/trialplanning.R | 2 simIDM-0.1.1/simIDM/inst/doc/trialplanning.Rmd | 2 simIDM-0.1.1/simIDM/inst/doc/trialplanning.html | 575 ++++++---- simIDM-0.1.1/simIDM/man/figures/logo.svg |only simIDM-0.1.1/simIDM/man/simIDM-package.Rd | 7 simIDM-0.1.1/simIDM/vignettes/trialplanning.Rmd | 2 16 files changed, 1235 insertions(+), 1252 deletions(-)
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.10.0 dated 2026-06-08 and 1.10.1 dated 2026-07-08
DESCRIPTION | 12 +++--- MD5 | 58 ++++++++++++++++---------------- NEWS.md | 17 ++++++++- R/appDependencies.R | 12 +++--- R/appMetadata.R | 6 +++ R/auth.R | 6 +-- R/bundleFiles.R | 2 - R/bundlePackageRenv.R | 43 +++++++++++++++++------ R/client.R | 2 - R/configureApp.R | 2 - R/deployApp.R | 6 +-- R/deployments.R | 2 - R/envvars.R | 2 - R/http.R | 27 +++++++------- R/usage.R | 10 ++--- man/accountUsage.Rd | 4 +- man/appDependencies.Rd | 12 +++--- man/configureApp.Rd | 2 - man/deployApp.Rd | 4 +- man/deploySite.Rd | 2 - man/deployments.Rd | 2 - man/listAccountEnvVars.Rd | 2 - man/listDeploymentFiles.Rd | 2 - man/showMetrics.Rd | 2 - man/showUsage.Rd | 4 +- tests/testthat/_snaps/deployApp.md | 2 - tests/testthat/test-appMetadata.R | 18 +++++++++ tests/testthat/test-bundlePackage.R | 12 ++++-- tests/testthat/test-bundlePackageRenv.R | 57 +++++++++++++++++++++++++++++++ tests/testthat/test-writeManifest.R | 4 +- 30 files changed, 227 insertions(+), 109 deletions(-)
Title: A Tool for 'Covariate'-Sensitive Longitudinal Analysis on
'omics' Data
Description: This tool takes longitudinal dataset as input and analyzes if there is significant
change of the features over time (a proxy for treatments), while detects and controls
for 'covariates' simultaneously. 'LongDat' is able to take in several data types as input,
including count, proportion, binary, ordinal and continuous data. The output table contains
p values, effect sizes and 'covariates' of each feature, making the downstream analysis easy.
Author: Chia-Yu Chen [aut, cre] ,
Sofia Forslund [ctb]
Maintainer: Chia-Yu Chen <jessica821112@gmail.com>
Diff between LongDat versions 1.1.3 dated 2024-11-18 and 1.1.4 dated 2026-07-08
DESCRIPTION | 15 MD5 | 22 - NEWS.md | 3 build/vignette.rds |binary inst/doc/LongDat_cont_tutorial.R | 2 inst/doc/LongDat_cont_tutorial.Rmd | 2 inst/doc/LongDat_cont_tutorial.html | 560 ++++++++++++--------------------- inst/doc/LongDat_disc_tutorial.R | 2 inst/doc/LongDat_disc_tutorial.Rmd | 2 inst/doc/LongDat_disc_tutorial.html | 605 +++++++++++++----------------------- vignettes/LongDat_cont_tutorial.Rmd | 2 vignettes/LongDat_disc_tutorial.Rmd | 2 12 files changed, 479 insertions(+), 738 deletions(-)
Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr'
and the piping syntax from 'magrittr'. Function 'kable()' is a light weight
table generator coming from 'knitr'. This package simplifies the way to
manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows
users to construct complex tables and customize styles using a readable
syntax.
Author: Hao Zhu [aut, cre] ,
Thomas Travison [ctb],
Timothy Tsai [ctb],
Will Beasley [ctb],
Yihui Xie [ctb],
GuangChuang Yu [ctb],
Stephane Laurent [ctb],
Rob Shepherd [ctb],
Yoni Sidi [ctb],
Brian Salzer [ctb],
George Gui [ctb],
Yeliang Fan [ctb],
Duncan Mu [...truncated...]
Maintainer: Hao Zhu <haozhu233@gmail.com>
Diff between kableExtra versions 1.4.0 dated 2024-01-24 and 1.4.1 dated 2026-07-08
DESCRIPTION | 12 MD5 | 254 +++++- R/add_header_above.R | 65 + R/add_indent.R | 7 R/cell_spec.R | 29 R/collapse_rows.R | 54 + R/column_spec.R | 64 - R/footnote.R | 97 ++ R/group_rows.R | 60 + R/header_separate.R | 7 R/kableExtra-package.R | 5 R/kable_as_image.R | 2 R/kable_styling.R | 22 R/kbl.R | 10 R/landscape.R | 3 R/linebreak.R | 14 R/magic_mirror.R | 46 - R/remove_column.R | 8 R/row_spec.R | 72 + R/save_kable.R | 28 R/scroll_box.R | 6 R/spec_tools.R | 3 R/util.R | 116 ++- README.md | 10 build/vignette.rds |binary inst/NEWS.md | 86 ++ inst/doc/awesome_table_in_html.R | 40 - inst/doc/awesome_table_in_html.Rmd | 8 inst/doc/awesome_table_in_html.html | 641 +++++++++-------- inst/doc/awesome_table_in_pdf.R | 74 + inst/doc/awesome_table_in_pdf.Rmd | 23 inst/doc/awesome_table_in_pdf.pdf |binary inst/doc/best_practice_for_newline_in_latex_table.Rmd | 3 inst/doc/best_practice_for_newline_in_latex_table.pdf |binary inst/doc/legacy_features.html | 4 inst/doc/use_kable_in_shiny.R | 79 +- inst/doc/use_kable_in_shiny.Rmd | 1 inst/doc/use_kable_in_shiny.html | 1 inst/rmarkdown/test_row_spec.Rmd | 3 inst/rmarkdown/test_row_spec.pdf |binary man/add_header_above.Rd | 22 man/cell_spec.Rd | 9 man/collapse_rows.Rd | 4 man/footnote.Rd | 4 man/group_rows.Rd | 25 man/kableExtra-package.Rd | 33 man/kableExtra_latex_packages.Rd | 6 man/kable_styling.Rd | 6 man/kbl.Rd | 12 man/linebreak.Rd | 10 man/scroll_box.Rd | 3 man/use_latex_packages.Rd | 2 vignettes/awesome_table_in_html.Rmd | 8 vignettes/awesome_table_in_pdf.Rmd | 23 vignettes/awesome_table_in_pdf_files |only vignettes/best_practice_for_newline_in_latex_table.Rmd | 3 vignettes/use_kable_in_shiny.Rmd | 1 57 files changed, 1441 insertions(+), 687 deletions(-)
Title: Remedy the Violation of the Proportional Hazards Assumption of
Cox Regression
Description: Remedying proportional hazards
assumption violations of a Cox proportional hazards model using
stepwise changepoint and time-varying coefficient methods based on
Cox (1972) <doi:10.1111/j.2517-6161.1972.tb00899.x> and Grambsch
and Therneau (1994) <doi:10.1093/biomet/81.3.515>.
Author: Hamin Kim [aut, cre]
Maintainer: Hamin Kim <siru9170@naver.com>
Diff between cox.rvph versions 0.1.1 dated 2026-06-09 and 0.1.2 dated 2026-07-08
DESCRIPTION | 6 - MD5 | 6 - R/cox.rvph.R | 275 +++++++++++++++++++++++++++++++++++--------------------- man/cox.rvph.Rd | 49 ++++++--- 4 files changed, 212 insertions(+), 124 deletions(-)
Title: Clean and Harmonise 'Malawi Integrated Household Survey' Data
Description: An offline suite of tools to clean, aggregate, and harmonise data
from the 'Malawi Integrated Household Survey' ('IHS'). Provides crop-specific
unit conversions, stratified winsorization, and automatic cross-round harmonisation
for complex survey designs.
Author: Vitumbiko Kayuni [aut, cre]
Maintainer: Vitumbiko Kayuni <vitumbikokayuni@gmail.com>
Diff between ihsMW versions 0.2.1 dated 2026-06-04 and 1.0.0 dated 2026-07-08
DESCRIPTION | 9 MD5 | 56 NAMESPACE | 5 NEWS.md | 72 R/ihs_crosswalk_check.R | 17 R/ihs_deflate.R |only R/ihs_merge.R |only R/ihs_panel_ids.R |only R/ihs_report.R |only R/ihs_svydesign.R |only R/zzz.R | 3 README.md | 88 build/vignette.rds |binary inst/doc/getting-started.R | 89 inst/doc/getting-started.Rmd | 149 inst/doc/getting-started.html | 234 inst/doc/harmonisation.R | 51 inst/doc/harmonisation.Rmd | 125 inst/doc/harmonisation.html | 214 inst/doc/survey-weights.R | 70 inst/doc/survey-weights.Rmd | 131 inst/doc/survey-weights.html | 257 inst/extdata/ihs_crosswalk.csv |11660 ++++++++++++++++++------------------ inst/extdata/mw_cpi_annual.csv |only man/ihs_deflate.Rd |only man/ihs_merge.Rd |only man/ihs_panel_ids.Rd |only man/ihs_report.Rd |only man/ihs_svydesign.Rd |only tests/testthat/test-ihs_deflate.R |only tests/testthat/test-ihs_merge.R |only tests/testthat/test-ihs_panel_ids.R |only tests/testthat/test-ihs_report.R |only tests/testthat/test-ihs_svydesign.R |only vignettes/getting-started.Rmd | 149 vignettes/harmonisation.Rmd | 125 vignettes/survey-weights.Rmd | 131 37 files changed, 6883 insertions(+), 6752 deletions(-)