Title: Examples of Datasets on Allometry
Description: Examples of datasets on allometry, the study of the relationship of biological traits to body size. This package contains the datasets of morphological measurement taken from 113 maritime earwigs (Anisolabis maritima) by Matsuzawa and Konuma (2025) <doi:10.1093/biolinnean/blaf031>, and taken from 507 Helm’s stag beetles (Geodorcus helmsi) collected by Grey et al. (2025) <doi:10.1093/biolinnean/blae024>.
Author: Takeshi Abe [aut, cre]
Maintainer: Takeshi Abe <tabe@fixedpoint.jp>
Diff between allometry versions 0.1.1 dated 2025-07-17 and 0.2.0 dated 2026-05-23
allometry-0.1.1/allometry/COPYING |only allometry-0.2.0/allometry/DESCRIPTION | 10 +++-- allometry-0.2.0/allometry/MD5 | 12 +++--- allometry-0.2.0/allometry/NEWS.md | 4 ++ allometry-0.2.0/allometry/R/data.R | 30 ++++++++++++++++- allometry-0.2.0/allometry/README.md | 15 ++++++-- allometry-0.2.0/allometry/data/helmsi.rda |only allometry-0.2.0/allometry/man/helmsi.Rd |only allometry-0.2.0/allometry/tests/testthat/test-helmsi.R |only 9 files changed, 58 insertions(+), 13 deletions(-)
Title: Spatial Projection of Network Signals along Geodesic Paths
Description: For a given graph containing vertices, edges, and a signal
associated with the vertices, the 'PathwaySpace' package performs a convolution
operation, which involves a weighted combination of neighboring vertices and
their associated signals. The package uses a decay function to project these
signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' has various
applications, such as visualizing network data in a graphical format that
highlights the relationships and signal strengths between vertices. By
combining graph theory, signal processing, and visualization, 'PathwaySpace'
provides a way of representing graph data on a continuous projection space.
Based on methods introduced in Tercan et al. (2025)
<doi:10.1016/j.xpro.2025.103681> and Ellrott et al. (2025)
<doi:10.1016/j.ccell.2024.12.002>.
Author: Sysbiolab Team [aut],
Victor Apolonio [ctb],
Jonathan Back [ctb],
Lana Querne [ctb],
Vinicius Chagas [ctb],
Bahar Tercan [ctb],
Mauro Castro [cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between PathwaySpace versions 1.2.0 dated 2026-04-25 and 1.3.0 dated 2026-05-23
DESCRIPTION | 8 +-- MD5 | 78 ++++++++++++++++++------------------ R/pspaceDecay.R | 6 +- R/pspaceMisc.R | 30 ++----------- R/pspacePlots.R | 2 R/pspaceWatershed.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 19 ++++++++ inst/doc/PathwaySpace.R | 2 inst/doc/PathwaySpace.Rmd | 6 +- inst/doc/PathwaySpace.html | 47 +++++++++++---------- man/CGC_20211118.Rd | 2 man/Hallmarks_v2023_1_Hs_symbols.Rd | 6 +- man/PCv12_pruned_igraph.Rd | 14 +++--- man/PathwaySpace-package.Rd | 53 +++++++++++++----------- man/buildPathwaySpace.Rd | 12 ++--- man/circularProjection-methods.Rd | 32 +++++++------- man/expDecay.Rd | 42 +++++++++---------- man/getNearestNode.Rd | 4 - man/getPathwaySpace-methods.Rd | 6 +- man/linearDecay.Rd | 46 ++++++++++----------- man/pathDistances.Rd | 4 - man/plotPathDistances.Rd | 2 man/plotPathwaySpace-methods.Rd | 30 ++++++------- man/polarProjection-methods.Rd | 44 ++++++++++---------- man/pspace.pals.Rd | 4 - man/signalAggregation.Rd | 8 +-- man/signalDecay.Rd | 2 man/silhouetteMapping-methods.Rd | 10 ++-- man/summitMapping-methods.Rd | 8 +-- man/summitWatershed.Rd | 2 man/vertexSignal-accessors.Rd | 2 man/weibullDecay.Rd | 48 +++++++++++----------- vignettes/PathwaySpace.Rmd | 6 +- vignettes/bibliography.bib | 28 +++++++++++- vignettes/figures/fig1.png |binary vignettes/figures/fig3.png |binary vignettes/figures/fig4.png |binary vignettes/figures/fig8.png |binary 40 files changed, 321 insertions(+), 294 deletions(-)
Title: Object-Oriented Diagram Plots with 'ggplot2'
Description: Creates diagrams with an object-oriented approach. Geometric
objects have computed properties with information about themselves
(e.g., their area) or about their relationships with other objects
(e.g, the distance between their edges). The objects have methods to
convert them to geoms that can be plotted in 'ggplot2'.
Author: W. Joel Schneider [aut, cre]
Maintainer: W. Joel Schneider <w.joel.schneider@gmail.com>
Diff between ggdiagram versions 0.1.1 dated 2025-09-14 and 0.2.0 dated 2026-05-23
DESCRIPTION | 24 MD5 | 158 +- NAMESPACE | 170 +- NEWS.md | 21 R/a_early.R | 988 +++++++++------ R/angles.R | 283 ++-- R/arcs.R | 741 ++++++----- R/bezier.R | 624 ++++++--- R/circles.R | 407 +++--- R/colors.R | 150 +- R/distances.R | 63 R/ellipses.R | 1485 ++++++++++++---------- R/equations.R | 227 ++- R/inside.R | 92 - R/intersections.R | 1192 ++++++++++-------- R/labels.R | 575 ++++---- R/lines.R | 466 +++---- R/paths.R | 418 +++--- R/points.R | 830 +++++++----- R/polygons.R | 2354 +++++++++++++++++------------------- R/rectangles.R | 469 ++++--- R/rescale.R |only R/rotate.R | 104 - R/segments.R | 388 +++-- R/str.R | 124 - R/style.R | 183 +- R/zzz.R | 2 README.md | 3 build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/ggdiagram.R | 2 inst/doc/ggdiagram.html | 7 inst/doc/ggdiagram.qmd | 2 man/class_color.Rd | 30 man/class_margin.Rd |only man/data2shape.Rd | 3 man/equation.Rd | 13 man/ggdiagram-package.Rd | 5 man/ggdiagram.Rd | 2 man/lead_cycle.Rd |only man/map2_ob.Rd |only man/map_ob.Rd | 2 man/mean_color.Rd | 9 man/ob_angle.Rd | 18 man/ob_arc.Rd | 62 man/ob_array.Rd | 15 man/ob_bezier.Rd | 37 man/ob_circle.Rd | 64 man/ob_covariance.Rd | 35 man/ob_ellipse.Rd | 42 man/ob_intercept.Rd | 29 man/ob_label.Rd | 22 man/ob_latex.Rd | 6 man/ob_line.Rd | 22 man/ob_ngon.Rd | 59 man/ob_path.Rd | 25 man/ob_point.Rd | 36 man/ob_polygon.Rd | 18 man/ob_rectangle.Rd | 33 man/ob_reuleaux.Rd | 47 man/ob_segment.Rd | 32 man/ob_style.Rd | 4 man/ob_variance.Rd | 31 man/reexports.Rd | 2 man/rescale.Rd |only man/subscript.Rd | 5 tests/testthat/test-addition.R | 133 -- tests/testthat/test-angle.R | 81 + tests/testthat/test-arc.R |only tests/testthat/test-bezier.R |only tests/testthat/test-circle.R | 287 +--- tests/testthat/test-color.R |only tests/testthat/test-distance.R |only tests/testthat/test-ellipse.R |only tests/testthat/test-equation.R |only tests/testthat/test-inside.R |only tests/testthat/test-intersections.R |only tests/testthat/test-label.R |only tests/testthat/test-latex.R |only tests/testthat/test-line.R | 138 ++ tests/testthat/test-misc.R | 173 ++ tests/testthat/test-path.R |only tests/testthat/test-point.R | 161 ++ tests/testthat/test-polygon.R |only tests/testthat/test-rectangle.R |only tests/testthat/test-rescale.R |only tests/testthat/test-rotate.R |only tests/testthat/test-segment.R |only tests/testthat/test-str.R |only tests/testthat/test-style.R | 301 ++++ vignettes/ggdiagram.qmd | 2 91 files changed, 8486 insertions(+), 6054 deletions(-)
Title: Risk Tool Library - Trading, Risk, Analytics for Commodities
Description: A toolkit for Commodities 'analytics', risk management and
trading professionals. Includes functions for API calls to
<https://www.zema.global/platforms/zema-marketplace>, <https://developer.genscape.com/>,
and <https://www.bankofcanada.ca/valet/docs>.
Author: Philippe Cote [aut, cre],
Nima Safaian [aut]
Maintainer: Philippe Cote <pcote@ualberta.ca>
Diff between RTL versions 1.3.7 dated 2025-02-25 and 1.3.9 dated 2026-05-23
RTL-1.3.7/RTL/R/morningstar.R |only RTL-1.3.7/RTL/data/eurodollar.rda |only RTL-1.3.7/RTL/data/fxfwd.rda |only RTL-1.3.7/RTL/data/tradeprocess.rda |only RTL-1.3.7/RTL/man/eurodollar.Rd |only RTL-1.3.7/RTL/man/fxfwd.Rd |only RTL-1.3.7/RTL/man/tradeprocess.Rd |only RTL-1.3.9/RTL/DESCRIPTION | 19 - RTL-1.3.9/RTL/MD5 | 96 ++++----- RTL-1.3.9/RTL/NAMESPACE | 1 RTL-1.3.9/RTL/NEWS.md | 280 ----------------------------- RTL-1.3.9/RTL/R/chart_spreads.R | 6 RTL-1.3.9/RTL/R/data.R | 26 -- RTL-1.3.9/RTL/R/efficientFrontier.R | 1 RTL-1.3.9/RTL/R/promptBeta.R | 31 --- RTL-1.3.9/RTL/R/swapInfo.R | 6 RTL-1.3.9/RTL/R/tradeStats.R | 1 RTL-1.3.9/RTL/R/tradeStrategyDY.R | 1 RTL-1.3.9/RTL/R/tradeStrategySMA.R | 1 RTL-1.3.9/RTL/R/zema.R |only RTL-1.3.9/RTL/README.md | 12 - RTL-1.3.9/RTL/data/cma.rda |binary RTL-1.3.9/RTL/data/cushing.rda |binary RTL-1.3.9/RTL/data/dflong.rda |binary RTL-1.3.9/RTL/data/dfwide.rda |binary RTL-1.3.9/RTL/data/eiaStocks.rda |binary RTL-1.3.9/RTL/data/eiaStorageCap.rda |binary RTL-1.3.9/RTL/data/expiry_table.rda |binary RTL-1.3.9/RTL/data/fizdiffs.rda |binary RTL-1.3.9/RTL/data/futuresRef.rda |binary RTL-1.3.9/RTL/data/holidaysOil.rda |binary RTL-1.3.9/RTL/data/spot2futConvergence.rda |binary RTL-1.3.9/RTL/data/steo.rda |binary RTL-1.3.9/RTL/data/stocks.rda |binary RTL-1.3.9/RTL/data/tickers_eia.rda |binary RTL-1.3.9/RTL/data/tradeCycle.rda |binary RTL-1.3.9/RTL/data/tsQuotes.rda |binary RTL-1.3.9/RTL/data/usSwapCurves.rda |binary RTL-1.3.9/RTL/data/usSwapCurvesPar.rda |binary RTL-1.3.9/RTL/data/wtiSwap.rda |binary RTL-1.3.9/RTL/inst/WORDLIST | 35 --- RTL-1.3.9/RTL/man/RTL-package.Rd | 3 RTL-1.3.9/RTL/man/chart_spreads.Rd | 6 RTL-1.3.9/RTL/man/dflong.Rd | 3 RTL-1.3.9/RTL/man/dfwide.Rd | 3 RTL-1.3.9/RTL/man/getCurve.Rd | 16 - RTL-1.3.9/RTL/man/getPrice.Rd | 21 -- RTL-1.3.9/RTL/man/getPrices.Rd | 12 - RTL-1.3.9/RTL/man/spot2futConvergence.Rd | 2 RTL-1.3.9/RTL/man/spot2futCurve.Rd | 3 RTL-1.3.9/RTL/man/swapInfo.Rd | 6 RTL-1.3.9/RTL/man/usSwapCurves.Rd | 3 RTL-1.3.9/RTL/man/wtiSwap.Rd | 3 53 files changed, 115 insertions(+), 482 deletions(-)
Title: Tools for the Analysis of Clustered Data in QCA
Description: Clustered set-relational data in Qualitative Comparative Analysis
(QCA) can have a hierarchical structure, a panel structure or repeated cross
sections. 'QCAcluster' allows researchers to supplement the analysis
of pooled the data with a differentiated perspective focusing on selected
partitions of the data. The pooled data can be partitioned along the
dimensions of the clustered data (individual cross sections or time series)
to perform partition-specific truth table minimization. Empirical
researchers can further calculate the weight that each partition has on the
parameters of the pooled solution and the diversity of the cases under
analysis within and across partitions
(see <https://ingorohlfing.github.io/QCAcluster/>).
Author: Ingo Rohlfing [aut, cre] ,
Ayjeren Bekmuratovna [aut],
Jan Schwalbach [aut]
Maintainer: Ingo Rohlfing <ingo.rohlfing@uni-passau.de>
This is a re-admission after prior archival of version 0.1.0 dated 2021-10-26
Diff between QCAcluster versions 0.1.0 dated 2021-10-26 and 0.2.0 dated 2026-05-23
DESCRIPTION | 37 - MD5 | 57 +-- NEWS.md |only R/partition_div.R | 4 R/partition_min.R | 12 R/partition_min_inter.R | 4 R/upset_conditions.R | 8 R/upset_configurations.R | 6 R/wop.R | 6 R/wop_inter.R | 4 README.md | 10 build/vignette.rds |binary inst/doc/Aggregation-over-partitions.R | 6 inst/doc/Aggregation-over-partitions.html | 427 +++++++++++++++++----- inst/doc/Diversity-of-partitions.R | 2 inst/doc/Diversity-of-partitions.html | 493 ++++++++++++++++++------- inst/doc/Minimization-of-partitions.R | 6 inst/doc/Minimization-of-partitions.html | 569 ++++++++++++++++++++++-------- inst/doc/Weight-of-partitions.R | 26 - inst/doc/Weight-of-partitions.html | 457 ++++++++++++++++++------ man/Grauvogel2014.Rd | 76 ++-- man/Schwarz2016.Rd | 66 +-- man/Thiem2011.Rd | 78 ++-- man/partition_div.Rd | 4 man/partition_min.Rd | 10 man/partition_min_inter.Rd | 4 man/upset_conditions.Rd | 84 ++-- man/upset_configurations.Rd | 6 man/wop.Rd | 6 man/wop_inter.Rd | 4 30 files changed, 1749 insertions(+), 723 deletions(-)
Title: Machine Learning Feature Selection for High Dimensional Survival
Data
Description: A unified, flexible framework for high dimensional feature
selection in the presence of a survival outcome. Provides multiple
machine learning approaches (Cox elastic net, random survival forest,
accelerated oblique random survival forest, gradient-boosted Cox,
stability selection, classical univariate Cox screening, pseudo-
observation bridging to arbitrary regression learners, and Fine-Gray
competing risks selection) under a single interface. Adds causal
survival forest estimation of heterogeneous treatment effects on
survival (experimental), conformal survival prediction with finite-
sample coverage guarantees, and time-dependent 'SHAP' explanations via
'SurvSHAP(t)'. Methodology is based on regularised Cox regression
(2011) <doi:10.18637/jss.v039.i05>, random survival forests (2008)
<doi:10.1214/08-AOAS169>, oblique random survival forests (2024)
<doi:10.1080/10618600.2023.2231048>, stability selection (2010)
<doi:10.1111/j.1467-9868.2010.00740.x>, causal su [...truncated...]
Author: Atanu Bhattacharjee [aut, cre]
Maintainer: Atanu Bhattacharjee <atanustat@gmail.com>
Diff between highMLR versions 0.1.1 dated 2022-07-18 and 1.0.1 dated 2026-05-23
highMLR-0.1.1/highMLR/R/hnscc.R |only highMLR-0.1.1/highMLR/R/mlclassCox.R |only highMLR-0.1.1/highMLR/R/mlclassKap.R |only highMLR-0.1.1/highMLR/R/mlhighCox.R |only highMLR-0.1.1/highMLR/R/mlhighFrail.R |only highMLR-0.1.1/highMLR/R/mlhighHet.R |only highMLR-0.1.1/highMLR/R/mlhighKap.R |only highMLR-0.1.1/highMLR/R/srdata.R |only highMLR-0.1.1/highMLR/man/mlclassCox.Rd |only highMLR-0.1.1/highMLR/man/mlclassKap.Rd |only highMLR-0.1.1/highMLR/man/mlhighCox.Rd |only highMLR-0.1.1/highMLR/man/mlhighFrail.Rd |only highMLR-0.1.1/highMLR/man/mlhighHet.Rd |only highMLR-0.1.1/highMLR/man/mlhighKap.Rd |only highMLR-1.0.1/highMLR/DESCRIPTION | 67 +++++++++++------- highMLR-1.0.1/highMLR/MD5 | 69 +++++++++++++------ highMLR-1.0.1/highMLR/NAMESPACE | 45 +++++++----- highMLR-1.0.1/highMLR/NEWS.md |only highMLR-1.0.1/highMLR/R/causal.R |only highMLR-1.0.1/highMLR/R/class-highmlr-fit.R |only highMLR-1.0.1/highMLR/R/companions.R |only highMLR-1.0.1/highMLR/R/conformal.R |only highMLR-1.0.1/highMLR/R/fit-aorsf.R |only highMLR-1.0.1/highMLR/R/fit-coxnet.R |only highMLR-1.0.1/highMLR/R/fit-finegray.R |only highMLR-1.0.1/highMLR/R/fit-pseudo.R |only highMLR-1.0.1/highMLR/R/fit-rsf.R |only highMLR-1.0.1/highMLR/R/fit-stability.R |only highMLR-1.0.1/highMLR/R/fit-univariate.R |only highMLR-1.0.1/highMLR/R/fit-xgboost.R |only highMLR-1.0.1/highMLR/R/highMLR-package.R |only highMLR-1.0.1/highMLR/R/highmlr.R |only highMLR-1.0.1/highMLR/README.md |only highMLR-1.0.1/highMLR/build |only highMLR-1.0.1/highMLR/data/hnscc.rda |binary highMLR-1.0.1/highMLR/data/srdata.rda |binary highMLR-1.0.1/highMLR/inst |only highMLR-1.0.1/highMLR/man/coef.highmlr_fit.Rd |only highMLR-1.0.1/highMLR/man/highMLR-package.Rd |only highMLR-1.0.1/highMLR/man/highmlr.Rd |only highMLR-1.0.1/highMLR/man/highmlr_causal.Rd |only highMLR-1.0.1/highMLR/man/highmlr_compare.Rd |only highMLR-1.0.1/highMLR/man/highmlr_conformal.Rd |only highMLR-1.0.1/highMLR/man/highmlr_explain.Rd |only highMLR-1.0.1/highMLR/man/highmlr_report.Rd |only highMLR-1.0.1/highMLR/man/highmlr_screen.Rd |only highMLR-1.0.1/highMLR/man/highmlr_stability.Rd |only highMLR-1.0.1/highMLR/man/hnscc.Rd | 28 ++++--- highMLR-1.0.1/highMLR/man/new_highmlr_fit.Rd |only highMLR-1.0.1/highMLR/man/plot.highmlr_conformal.Rd |only highMLR-1.0.1/highMLR/man/plot.highmlr_fit.Rd |only highMLR-1.0.1/highMLR/man/predict.highmlr_fit.Rd |only highMLR-1.0.1/highMLR/man/print.highmlr_conformal.Rd |only highMLR-1.0.1/highMLR/man/print.highmlr_fit.Rd |only highMLR-1.0.1/highMLR/man/srdata.Rd | 27 +++---- highMLR-1.0.1/highMLR/man/summary.highmlr_fit.Rd |only highMLR-1.0.1/highMLR/tests |only highMLR-1.0.1/highMLR/vignettes |only 58 files changed, 148 insertions(+), 88 deletions(-)
Title: Modeling Species Distributions in Three Dimensions
Description: Facilitates modeling species' ecological niches and
geographic distributions based on occurrences and environments that
have a vertical as well as horizontal component, and projecting models
into three-dimensional geographic space. Working in three dimensions is
useful in an aquatic context when the organisms one wishes to model can
be found across a wide range of depths in the water column. The package
also contains functions to automatically generate marine training
model training regions using machine learning, and interpolate and smooth
patchily sampled environmental rasters using thin plate splines.
Davis Rabosky AR, Cox CL, Rabosky DL, Title PO, Holmes IA, Feldman A, McGuire JA (2016) <doi:10.1038/ncomms11484>.
Nychka D, Furrer R, Paige J, Sain S (2021) <doi:10.5065/D6W957CT>.
Pateiro-Lopez B, Rodriguez-Casal A (2022) <https://CRAN.R-project.org/package=alphahull>.
Author: Hannah L. Owens [aut, cre, cph] ,
Emmaline Sheahan [aut] ,
Carsten Rahbek [aut]
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
This is a re-admission after prior archival of version 0.2.3 dated 2025-07-18
Diff between voluModel versions 0.2.3 dated 2025-07-18 and 0.2.4 dated 2026-05-23
voluModel-0.2.3/voluModel/man/figures/SoMePreview-01.png |only voluModel-0.2.3/voluModel/man/figures/SoMePreview.eps |only voluModel-0.2.4/voluModel/.aspell |only voluModel-0.2.4/voluModel/DESCRIPTION | 19 +-- voluModel-0.2.4/voluModel/MD5 | 62 ++++++---- voluModel-0.2.4/voluModel/NAMESPACE | 9 + voluModel-0.2.4/voluModel/NEWS.md | 5 voluModel-0.2.4/voluModel/R/cleanDepth.R |only voluModel-0.2.4/voluModel/R/depthMatch.R |only voluModel-0.2.4/voluModel/R/env_stack_transform.R |only voluModel-0.2.4/voluModel/R/maxent_3D.R |only voluModel-0.2.4/voluModel/R/modelDiagnostics.R | 21 +-- voluModel-0.2.4/voluModel/R/partition_3D.R |only voluModel-0.2.4/voluModel/R/threshold_3D.R |only voluModel-0.2.4/voluModel/R/visualizations.R | 2 voluModel-0.2.4/voluModel/build/vignette.rds |binary voluModel-0.2.4/voluModel/inst/doc/a_Introduction.Rmd | 2 voluModel-0.2.4/voluModel/inst/doc/a_Introduction.html | 20 +-- voluModel-0.2.4/voluModel/inst/doc/b_RasterProcessing.html | 12 - voluModel-0.2.4/voluModel/inst/doc/c_DataSampling.Rmd | 2 voluModel-0.2.4/voluModel/inst/doc/c_DataSampling.html | 28 ++-- voluModel-0.2.4/voluModel/inst/doc/d_Visualization.Rmd | 2 voluModel-0.2.4/voluModel/inst/doc/d_Visualization.html | 14 +- voluModel-0.2.4/voluModel/inst/doc/e_GLMWorkflow.R | 7 - voluModel-0.2.4/voluModel/inst/doc/e_GLMWorkflow.Rmd | 9 + voluModel-0.2.4/voluModel/inst/doc/e_GLMWorkflow.html | 39 +++--- voluModel-0.2.4/voluModel/man/MESS3D.Rd | 11 + voluModel-0.2.4/voluModel/man/cleanDepth.Rd |only voluModel-0.2.4/voluModel/man/depthMatch.Rd |only voluModel-0.2.4/voluModel/man/env_stack_transform.Rd |only voluModel-0.2.4/voluModel/man/maxent_3D.Rd |only voluModel-0.2.4/voluModel/man/partition_3D.Rd |only voluModel-0.2.4/voluModel/man/threshold_3D.Rd |only voluModel-0.2.4/voluModel/tests/testthat/test-MaxentModellingFunctions.R |only voluModel-0.2.4/voluModel/tests/testthat/test-cleanDepth.R |only voluModel-0.2.4/voluModel/tests/testthat/test-depthMatch.R |only voluModel-0.2.4/voluModel/tests/testthat/test-env_stack_transform.R |only voluModel-0.2.4/voluModel/tests/testthat/test-modelDiagnostics.R | 15 +- voluModel-0.2.4/voluModel/vignettes/a_Introduction.Rmd | 2 voluModel-0.2.4/voluModel/vignettes/c_DataSampling.Rmd | 2 voluModel-0.2.4/voluModel/vignettes/d_Visualization.Rmd | 2 voluModel-0.2.4/voluModel/vignettes/e_GLMWorkflow.Rmd | 9 + 42 files changed, 177 insertions(+), 117 deletions(-)
Title: Compare and Verify File Contents
Description: Extendable 'R6' file comparison classes, including a 'shiny' app for combining the comparison functionality into a file comparison application. The package idea originates from pharma companies' drug development processes, where statisticians and statistical programmers need to review and compare different versions of the same outputs and datasets. The package implementation itself is not tied to any specific industry and can be used in any context for easy file comparisons between different file version sets.
Author: Juha Javanainen [aut, cre],
Tiina Kirsilae [ctb],
Anna Wiksten [ctb]
Maintainer: Juha Javanainen <ejuhjav@gmail.com>
Diff between verifyr2 versions 1.1.0 dated 2026-01-08 and 1.2.0 dated 2026-05-23
DESCRIPTION | 10 MD5 | 56 - NEWS.md | 21 R/BinaryFileComparator.R | 10 R/Config.R | 138 ++- R/RtfFileComparator.R | 25 R/TxtFileComparator.R | 45 - R/list_folder_files.R | 4 inst/extdata/base_files/file11_spaces.txt |only inst/extdata/compare_files/file11_spaces.txt |only inst/shiny_examples/app/app.R | 437 +++++++--- inst/shiny_examples/app/report_styles.css |only inst/shiny_examples/app/report_template.Rmd |only inst/shiny_examples/app/styles.css | 8 inst/shiny_examples/app/www/verifyr2.ico |binary man/BinaryFileComparator.Rd | 4 man/Config.Rd | 25 man/RtfFileComparator.Rd | 19 man/TxtFileComparator.Rd | 4 tests/testthat.R | 26 tests/testthat/_snaps |only tests/testthat/test-Config.R | 4 tests/testthat/test-app-app.R |only tests/testthat/test-details_comparison_txt.R | 49 + tests/testthat/test-summary_comparison_rtf.R | 19 tests/testthat/test-summary_comparison_txt.R | 33 tests/testthat/test_configs/config1.json | 4 tests/testthat/test_outputs/rtf/base_corrupted.rtf |only tests/testthat/test_outputs/rtf/changes_five_rows_content_corrupted.rtf |only tests/testthat/test_outputs/txt/additional_spaces_and_tabs.txt |only 30 files changed, 743 insertions(+), 198 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Warick Brown [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Martin Hazelton [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oeh [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.7-3 dated 2026-03-23 and 3.8-1 dated 2026-05-23
DESCRIPTION | 18 ++--- MD5 | 82 ++++++++++++------------- NEWS | 80 ++++++++++++++++++++++++ R/as.im.R | 44 ++++++++----- R/distbdry.R | 22 ++---- R/distfun.R | 9 +- R/exactPdt.R | 47 ++++++++++---- R/images.R | 10 ++- R/layered.R | 13 ++- R/nearestsegment.R | 137 +++++++++++++++++++++++++----------------- R/nnfun.R | 11 +-- R/nnmap.R | 4 - R/owin2mask.R | 31 +++++---- R/pixellate.R | 14 ++-- R/plot.im.R | 10 +-- R/plot.ppp.R | 9 +- R/ppp.R | 18 +++-- R/psp2pix.R | 14 ++-- R/randombasic.R | 2 R/util.R | 4 - R/window.R | 31 ++++++--- R/wingeom.R | 92 ++++++++++++++++++---------- inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/Extract.im.Rd | 8 ++ man/as.im.Rd | 23 +++++++ man/as.mask.Rd | 3 man/as.ppp.Rd | 25 +++++++ man/intensity.Rd | 14 ++-- man/intersect.owin.Rd | 14 +++- man/macros/defns.Rd | 1 man/owin2mask.Rd | 78 ++++++++++++----------- man/pixellate.owin.Rd | 19 +++++ man/pixellate.ppp.Rd | 22 +++++- man/pixellate.psp.Rd | 17 ++++- man/plot.im.Rd | 15 +++- man/plot.ppp.Rd | 18 +++++ man/ppp.Rd | 18 +++-- man/project2set.Rd | 55 ++++++++++++---- man/spatstat.geom-internal.Rd | 64 +++++++++---------- tests/testsGtoJ.R | 1 tests/testsUtoZ.R | 24 ++++++- 42 files changed, 753 insertions(+), 370 deletions(-)
Title: Core Utilities for Developing and Running Spatially Explicit
Discrete Event Models
Description: Provides the core framework for a discrete event system to
implement a complete data-to-decisions, reproducible workflow.
The core components facilitate the development of modular pieces,
and enable the user to include additional functionality by running user-built modules.
Includes conditional scheduling, restart after interruption, packaging of
reusable modules, tools for developing arbitrary automated workflows,
automated interweaving of modules of different temporal resolution,
and tools for visualizing and understanding the within-project dependencies.
Author: Alex M Chubaty [aut] ,
Eliot J B McIntire [aut, cre] ,
Yong Luo [ctb],
Steve Cumming [ctb],
Ceres Barros [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between SpaDES.core versions 3.1.0 dated 2026-05-19 and 3.1.2 dated 2026-05-23
DESCRIPTION | 14 +--- MD5 | 27 ++++---- NEWS.md | 35 ++++++++++ R/module-define.R | 2 inst/doc/i-introduction.html | 2 inst/doc/ii-modules.html | 2 inst/doc/iii-cache.R | 31 +-------- inst/doc/iii-cache.Rmd | 41 ++---------- inst/doc/iii-cache.html | 43 +++---------- inst/doc/iv-advanced.html | 2 inst/doc/v-automated-testing.html | 2 inst/sampleModules/randomLandscapes/randomLandscapes.R | 55 +++++++++++------ tests/testthat/setup.R |only tests/testthat/test-module-deps-methods.R | 7 ++ vignettes/iii-cache.Rmd | 41 ++---------- 15 files changed, 139 insertions(+), 165 deletions(-)
Title: Series System Distributions from Dynamic Failure Rate Components
Description: Compose multiple dynamic failure rate distributions into
series system distributions where the system hazard equals the sum
of component hazards. Supports hazard, survival, cumulative
distribution function, density, sampling, and maximum likelihood
estimation fitting via the dfr_dist() class from 'flexhaz'. Series
distributions implement the 'dist.structure' protocol so structural
queries (phi, min_paths, min_cuts, system_signature, structural
importance, reliability, dual) and the importance measures from
'dist.structure' work directly on serieshaz objects. Methods for
series system reliability follow Barlow and Proschan (1975,
ISBN:0898713692).
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between serieshaz versions 0.1.1 dated 2026-04-13 and 0.2.0 dated 2026-05-23
serieshaz-0.1.1/serieshaz/man/component.Rd |only serieshaz-0.1.1/serieshaz/man/ncomponents.Rd |only serieshaz-0.2.0/serieshaz/DESCRIPTION | 17 + serieshaz-0.2.0/serieshaz/MD5 | 27 +-- serieshaz-0.2.0/serieshaz/NAMESPACE | 14 + serieshaz-0.2.0/serieshaz/NEWS.md | 28 +++ serieshaz-0.2.0/serieshaz/R/dfr_dist_series.R | 10 + serieshaz-0.2.0/serieshaz/R/generic_functions.R | 89 ---------- serieshaz-0.2.0/serieshaz/R/methods.R | 47 ++++- serieshaz-0.2.0/serieshaz/R/reexports.R | 20 ++ serieshaz-0.2.0/serieshaz/man/component_hazard.Rd | 2 serieshaz-0.2.0/serieshaz/man/param_layout.Rd | 2 serieshaz-0.2.0/serieshaz/man/reexports.Rd | 8 serieshaz-0.2.0/serieshaz/man/sample_components.Rd | 2 serieshaz-0.2.0/serieshaz/man/serieshaz-package.Rd | 2 serieshaz-0.2.0/serieshaz/tests/testthat/test-dist-structure-interop.R |only 16 files changed, 148 insertions(+), 120 deletions(-)
Title: Interactive Graphics for QTL Experiments
Description: Web-based interactive charts (using D3.js) for the analysis of
experimental crosses to identify genetic loci (quantitative trait
loci, QTL) contributing to variation in quantitative traits.
Broman (2015) <doi:10.1534/genetics.114.172742>.
Author: Karl W Broman [aut, cre] ,
Michael Bostock [ctb, cph] ,
jQuery Foundation [cph] ,
jQuery contributors [ctb] ,
jQuery UI contributors [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtlcharts versions 0.18 dated 2025-05-10 and 0.20 dated 2026-05-23
DESCRIPTION | 10 ++--- MD5 | 48 +++++++++++++------------- NEWS.md | 7 +++ R/qtlcharts.R | 3 - README.md | 1 data/geneExpr.rda |binary data/grav.rda |binary inst/htmlwidgets/iboxplot.yaml | 4 +- inst/htmlwidgets/idotplot.yaml | 4 +- inst/htmlwidgets/iheatmap.yaml | 4 +- inst/htmlwidgets/ipleiotropy.yaml | 4 +- inst/htmlwidgets/iplot.yaml | 4 +- inst/htmlwidgets/iplotCorr.yaml | 4 +- inst/htmlwidgets/iplotCurves.yaml | 4 +- inst/htmlwidgets/iplotMScanone.yaml | 4 +- inst/htmlwidgets/iplotMap.yaml | 4 +- inst/htmlwidgets/iplotRF.yaml | 4 +- inst/htmlwidgets/iplotScanone.yaml | 4 +- inst/htmlwidgets/iplotScantwo.yaml | 4 +- inst/htmlwidgets/itriplot.yaml | 4 +- inst/htmlwidgets/lib/d3panels/LICENSE.md | 2 - inst/htmlwidgets/lib/d3panels/d3panels.min.js | 2 - inst/htmlwidgets/lib/d3panels/package.json | 2 - inst/htmlwidgets/scat2scat.yaml | 4 +- man/qtlcharts-package.Rd | 28 ++++++++++++++- 25 files changed, 95 insertions(+), 64 deletions(-)
Title: Benchmark for Publication Bias Correction Methods
Description: Implements a unified interface for benchmarking meta-analytic
publication bias correction methods through simulation studies (see
Bartoš et al., 2025, <doi:10.48550/arXiv.2510.19489>). It provides
1) predefined data-generating mechanisms from the literature, 2) functions
for running meta-analytic methods on simulated data, 3) pre-simulated
datasets and pre-computed results for reproducible benchmarks, 4) tools for
visualizing and comparing method performance.
Author: Frantisek Bartos [aut, cre] ,
Samuel Pawel [aut] ,
Bjoern S. Siepe [aut] ,
Petr Čala [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between PublicationBiasBenchmark versions 0.2.0 dated 2026-03-16 and 0.2.1 dated 2026-05-23
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/method-RoBMA.R | 17 +++++++++++------ build/partial.rdb |binary build/vignette.rds |binary man/method.RoBMA.Rd | 6 +++--- 7 files changed, 30 insertions(+), 20 deletions(-)
More information about PublicationBiasBenchmark at CRAN
Permanent link
Title: Access Open Target
Description: Interact seamlessly with Open Target GraphQL endpoint to query and retrieve tidy data tables, facilitating the analysis of gene, disease, drug, and genetic data. For more information about the Open Target API (<https://platform.opentargets.org/api>).
Author: Amir Feizi [aut, cre]
Maintainer: Amir Feizi <afeizi@gmail.com>
Diff between otargen versions 2.0.0 dated 2025-07-15 and 2.0.1 dated 2026-05-23
DESCRIPTION | 9 - MD5 | 43 +++---- NEWS.md | 19 +++ R/chemblQuery.R | 12 -- R/clinvarQuery.R | 5 R/geneBurdenQuery.R | 3 R/geneOntologyQuery.R | 2 R/indicationsQuery.R | 8 - R/interactionsQuery.R | 3 R/knownDrugsChemblQuery.R | 72 +++--------- R/knownDrugsGeneQuery.R | 60 ++++------ R/orphanetQuery.R | 3 README.md | 163 +++++++++++++++++----------- inst |only man/knownDrugsChemblQuery.Rd | 20 +-- man/knownDrugsGeneQuery.Rd | 20 +-- tests/testthat/test_chemblQuery.R | 7 - tests/testthat/test_clinVarQuery.R | 2 tests/testthat/test_geneOntologyQuery.R | 2 tests/testthat/test_interactionsQuery.R | 2 tests/testthat/test_knownDrugsChemblQuery.R | 8 - tests/testthat/test_knownDrugsGeneQuery.R | 5 tests/testthat/test_orphanetQuery.R | 2 23 files changed, 237 insertions(+), 233 deletions(-)
Title: Work with Microsoft Access Files
Description: Work with Microsoft Access '.mdb' and '.accdb' files using the
open source 'MDB Tools' library <https://github.com/mdbtools/mdbtools/>.
The library is compiled and bundled with the package, so no external
installation is required. Provides high-level helpers for reading tables,
exporting to CSV or JSON, inspecting table definitions, and running SQL queries.
Also exposes a full read-only 'DBI' interface for use with standard
database workflows.
Author: Kiernan Nicholls [aut, cre, cph] ,
Bruno Tremblay [ctb]
Maintainer: Kiernan Nicholls <k5cents@gmail.com>
Diff between mdbr versions 0.2.1 dated 2024-03-12 and 0.3.0 dated 2026-05-23
DESCRIPTION | 44 ++++++++++------- MD5 | 108 +++++++++++++++++++++++++++++++++++-------- NAMESPACE | 39 ++++++++++++++- NEWS.md | 31 ++++++++++++ R/advanced.R |only R/dbi.R |only R/example.R | 3 + R/export.R | 64 +++++++++++++++---------- R/native.R |only R/read.R | 58 +++++++++++++---------- R/schema.R | 47 ------------------ R/tables.R | 108 ++++++++++++++++++++++++++++++++++++++++--- R/utils.R | 30 +---------- README.md | 103 +++++++++++++++++++---------------------- cleanup |only cleanup.win |only configure |only configure.win |only man/export_mdb.Rd | 10 +-- man/mdb.Rd |only man/mdb_array.Rd |only man/mdb_count.Rd |only man/mdb_example.Rd | 6 ++ man/mdb_export.Rd |only man/mdb_header.Rd |only man/mdb_hexdump.Rd |only man/mdb_import.Rd |only man/mdb_json.Rd |only man/mdb_prop.Rd |only man/mdb_queries.Rd |only man/mdb_schema.Rd | 77 ++++++++++++++++++++++++++---- man/mdb_sql.Rd |only man/mdb_tables.Rd | 28 +++++++++-- man/mdb_ver.Rd |only man/print.mdblist.Rd |only man/read_mdb.Rd | 20 ++++--- src |only tests/testthat/mdbtestdata |only tests/testthat/test-dbi.R |only tests/testthat/test-export.R | 8 +-- tests/testthat/test-native.R |only tests/testthat/test-read.R | 24 +++------ tests/testthat/test-schema.R | 18 +++---- tests/testthat/test-tables.R | 2 44 files changed, 549 insertions(+), 279 deletions(-)
Title: Local Polynomial Density Estimation and Inference
Description: Implements local polynomial distribution and density methods for point estimation, inference and bandwidth selection, documented in Cattaneo, Jansson and Ma (2020) <doi:10.1080/01621459.2019.1635480>, Cattaneo, Jansson and Ma (2022) <doi:10.18637/jss.v101.i02>, and Cattaneo, Jansson and Ma (2024) <doi:10.1016/j.jeconom.2021.01.006>. lpdensity() constructs local polynomial distribution and density estimators with robust bias-corrected inference, and lpbwdensity() implements data-driven bandwidth selection.
Author: Matias D. Cattaneo [aut, cre],
Michael Jansson [aut],
Xinwei Ma [aut]
Maintainer: Matias D. Cattaneo <matias.d.cattaneo@gmail.com>
Diff between lpdensity versions 3.0 dated 2026-05-21 and 3.0.1 dated 2026-05-23
DESCRIPTION | 8 +++---- MD5 | 4 +-- tests/testthat/test-numerical-baseline.R | 32 +++++++++++++++++++++++++++---- 3 files changed, 34 insertions(+), 10 deletions(-)
Title: Access the Intergovernmental Organizations Database
Description: Tools for searching, extracting and recoding information from
the Intergovernmental Organizations ('IGO') Database (v3), distributed
by the Correlates of War Project <https://correlatesofwar.org/>. See
also Pevehouse, J. C. et al. (2020) <doi:10.1177/0022343319881175>.
Author: Diego Hernangomez [aut, cre, cph] ,
The Correlates of War Project [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between igoR versions 1.0.1 dated 2026-03-13 and 1.0.2 dated 2026-05-23
DESCRIPTION | 19 +- MD5 | 110 ++++++------- NAMESPACE | 24 +- NEWS.md | 57 +++--- R/data.R | 106 ++++++------ R/igoR-package.R | 12 - R/igo_dyadic.R | 108 ++++++------- R/igo_members.R | 69 +++----- R/igo_recode.R | 26 +-- R/igo_search.R | 57 +++--- R/igo_search_states.R | 34 ++-- R/igo_state_membership.R | 72 +++----- R/sysdata.rda |binary README.md | 62 +++---- build/partial.rdb |binary build/vignette.rds |binary data/igo_year_format3.rda |binary data/state_year_format3.rda |binary data/states2016.rda |binary inst/CITATION | 74 ++++---- inst/COPYRIGHTS | 22 +- inst/REFERENCES.bib | 96 +++++------ inst/WORDLIST | 139 ++++++++-------- inst/doc/igoR.R | 37 ++-- inst/doc/igoR.html | 153 ++++++++---------- inst/doc/igoR.qmd | 95 ++++------- inst/doc/mapping.html | 216 ++++++++++++-------------- inst/doc/mapping.qmd | 98 +++++------ inst/schemaorg.json | 10 - man/igoR-package.Rd | 67 ++++---- man/igo_dyadic.Rd | 182 ++++++++++----------- man/igo_members.Rd | 140 ++++++++-------- man/igo_recode.Rd | 120 ++++++-------- man/igo_search.Rd | 154 +++++++++--------- man/igo_search_states.Rd | 88 +++++----- man/igo_state_membership.Rd | 132 +++++++-------- man/igo_year_format3.Rd | 184 +++++++++++----------- man/state_year_format3.Rd | 140 ++++++++-------- man/states2016.Rd | 136 ++++++++-------- tests/testthat/_snaps/igo_dyadic.md | 30 +-- tests/testthat/_snaps/igo_members.md | 14 - tests/testthat/_snaps/igo_search.md | 2 tests/testthat/_snaps/igo_search_states.md | 6 tests/testthat/_snaps/igo_state_membership.md | 20 +- tests/testthat/test-igo_dyadic.R | 100 ++++++------ tests/testthat/test-igo_members.R | 159 ++++++++----------- tests/testthat/test-igo_recode.R | 58 +++--- tests/testthat/test-igo_search.R | 14 - tests/testthat/test-igo_search_states.R | 44 ++--- tests/testthat/test-igo_state_membership.R | 183 +++++++++------------- vignettes/REFERENCES.bib | 96 +++++------ vignettes/fig-AustShared-1.png |binary vignettes/fig-NAShared-1.png |binary vignettes/fig-UNMaps-1.png |binary vignettes/igoR.qmd | 95 ++++------- vignettes/mapping.qmd | 98 +++++------ 56 files changed, 1927 insertions(+), 2031 deletions(-)
Title: Utilities to Weave Hydrologic Fabrics
Description: A collection of utilities that support creation of network attributes for hydrologic networks. Methods and algorithms implemented are documented in Moore et al. (2019) <doi:10.3133/ofr20191096>), Cormen and Leiserson (2022) <ISBN:9780262046305> and Verdin and Verdin (1999) <doi:10.1016/S0022-1694(99)00011-6>.
Author: David Blodgett [aut, cre] ,
Andrew Psoras [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydroloom versions 1.1.2 dated 2026-02-20 and 1.2.0 dated 2026-05-23
hydroloom-1.1.2/hydroloom/tests/testthat/data/reweight_test.rds |only hydroloom-1.2.0/hydroloom/DESCRIPTION | 18 hydroloom-1.2.0/hydroloom/MD5 | 238 +- hydroloom-1.2.0/hydroloom/NAMESPACE | 61 hydroloom-1.2.0/hydroloom/NEWS.md | 63 hydroloom-1.2.0/hydroloom/R/00_hydroloom.R | 459 ++-- hydroloom-1.2.0/hydroloom/R/accumulate_downstream.R | 580 +++-- hydroloom-1.2.0/hydroloom/R/add_divergence.R | 954 ++++----- hydroloom-1.2.0/hydroloom/R/add_levelpaths.R | 697 +++--- hydroloom-1.2.0/hydroloom/R/add_measures.R | 230 +- hydroloom-1.2.0/hydroloom/R/add_pathlength.R | 143 - hydroloom-1.2.0/hydroloom/R/add_pfafstetter.R | 466 ++-- hydroloom-1.2.0/hydroloom/R/add_streamorder-level.R | 573 +++-- hydroloom-1.2.0/hydroloom/R/add_toids.R | 288 +- hydroloom-1.2.0/hydroloom/R/align_names.R | 278 +- hydroloom-1.2.0/hydroloom/R/check_hy_graph.R | 453 ++-- hydroloom-1.2.0/hydroloom/R/check_valid.R |only hydroloom-1.2.0/hydroloom/R/disambiguate.R | 234 +- hydroloom-1.2.0/hydroloom/R/dissolve_polygons.R |only hydroloom-1.2.0/hydroloom/R/get_bridges.R | 424 ++-- hydroloom-1.2.0/hydroloom/R/get_hydro_location.R | 156 - hydroloom-1.2.0/hydroloom/R/hy.R | 316 +-- hydroloom-1.2.0/hydroloom/R/hy_classes.R |only hydroloom-1.2.0/hydroloom/R/index_points_to_lines.R | 1012 +++++----- hydroloom-1.2.0/hydroloom/R/make_attribute_topology.R | 208 +- hydroloom-1.2.0/hydroloom/R/make_index_ids.R | 942 ++++----- hydroloom-1.2.0/hydroloom/R/make_node_topology.R | 480 ++-- hydroloom-1.2.0/hydroloom/R/navigate_connected_paths.R | 397 +-- hydroloom-1.2.0/hydroloom/R/navigate_network_dfs.R | 530 ++--- hydroloom-1.2.0/hydroloom/R/navigation_network.R | 745 +++---- hydroloom-1.2.0/hydroloom/R/sort_network.R | 586 +++-- hydroloom-1.2.0/hydroloom/R/subset_network.R | 19 hydroloom-1.2.0/hydroloom/R/to_flownetwork.R | 204 +- hydroloom-1.2.0/hydroloom/R/utils.R | 666 +++--- hydroloom-1.2.0/hydroloom/R/zzz.R |only hydroloom-1.2.0/hydroloom/inst/WORDLIST | 275 +- hydroloom-1.2.0/hydroloom/inst/doc/advanced_network.html | 67 hydroloom-1.2.0/hydroloom/inst/doc/flow-table.R | 15 hydroloom-1.2.0/hydroloom/inst/doc/flow-table.Rmd | 15 hydroloom-1.2.0/hydroloom/inst/doc/flow-table.html | 15 hydroloom-1.2.0/hydroloom/inst/doc/hydroloom.R | 27 hydroloom-1.2.0/hydroloom/inst/doc/hydroloom.Rmd | 81 hydroloom-1.2.0/hydroloom/inst/doc/hydroloom.html | 336 ++- hydroloom-1.2.0/hydroloom/inst/doc/network_navigation.R | 55 hydroloom-1.2.0/hydroloom/inst/doc/network_navigation.Rmd | 112 - hydroloom-1.2.0/hydroloom/inst/doc/network_navigation.html | 478 +++- hydroloom-1.2.0/hydroloom/inst/doc/non-dendritic.R | 42 hydroloom-1.2.0/hydroloom/inst/doc/non-dendritic.Rmd | 108 + hydroloom-1.2.0/hydroloom/inst/doc/non-dendritic.html | 258 +- hydroloom-1.2.0/hydroloom/inst/extdata/walker_cats.gpkg |only hydroloom-1.2.0/hydroloom/man/accumulate_downstream.Rd | 227 +- hydroloom-1.2.0/hydroloom/man/add_divergence.Rd | 242 +- hydroloom-1.2.0/hydroloom/man/add_levelpaths.Rd | 206 +- hydroloom-1.2.0/hydroloom/man/add_measures.Rd | 100 hydroloom-1.2.0/hydroloom/man/add_pathlength.Rd | 78 hydroloom-1.2.0/hydroloom/man/add_pfafstetter.Rd | 191 - hydroloom-1.2.0/hydroloom/man/add_return_divergence.Rd | 136 - hydroloom-1.2.0/hydroloom/man/add_streamlevel.Rd | 130 - hydroloom-1.2.0/hydroloom/man/add_streamorder.Rd | 105 - hydroloom-1.2.0/hydroloom/man/add_toids.Rd | 101 hydroloom-1.2.0/hydroloom/man/add_topo_sort.Rd | 69 hydroloom-1.2.0/hydroloom/man/check_hy_graph.Rd | 70 hydroloom-1.2.0/hydroloom/man/check_valid.Rd |only hydroloom-1.2.0/hydroloom/man/disambiguate_indexes.Rd | 130 - hydroloom-1.2.0/hydroloom/man/dissolve_polygons.Rd |only hydroloom-1.2.0/hydroloom/man/format_index_ids.Rd | 46 hydroloom-1.2.0/hydroloom/man/get_bridge_flowlines.Rd | 105 - hydroloom-1.2.0/hydroloom/man/get_hydro_location.Rd | 68 hydroloom-1.2.0/hydroloom/man/get_node.Rd | 72 hydroloom-1.2.0/hydroloom/man/get_partial_length.Rd | 78 hydroloom-1.2.0/hydroloom/man/hy.Rd | 72 hydroloom-1.2.0/hydroloom/man/hy_capabilities.Rd |only hydroloom-1.2.0/hydroloom/man/hy_flownetwork.Rd |only hydroloom-1.2.0/hydroloom/man/hy_leveled.Rd |only hydroloom-1.2.0/hydroloom/man/hy_network_type.Rd |only hydroloom-1.2.0/hydroloom/man/hy_node.Rd |only hydroloom-1.2.0/hydroloom/man/hy_topo.Rd |only hydroloom-1.2.0/hydroloom/man/index_points_to_lines.Rd | 260 +- hydroloom-1.2.0/hydroloom/man/index_points_to_waterbodies.Rd | 112 - hydroloom-1.2.0/hydroloom/man/is_dendritic.Rd |only hydroloom-1.2.0/hydroloom/man/make_attribute_topology.Rd | 100 hydroloom-1.2.0/hydroloom/man/make_fromids.Rd | 52 hydroloom-1.2.0/hydroloom/man/make_index_ids.Rd | 150 - 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Title: Estimate Gaps Under an Intervention
Description: Provides functions to estimate the disparities across categories (e.g. Black and white) that persists if a treatment variable (e.g. college) is equalized. Makes estimates by treatment modeling, outcome modeling, and doubly-robust augmented inverse probability weighting estimation, with standard errors calculated by a nonparametric bootstrap. Cross-fitting is supported. Survey weights are supported for point estimation but not for standard error estimation; those applying this package with complex survey samples should consult the data distributor to select an appropriate approach for standard error construction, which may involve calling the functions repeatedly for many sets of replicate weights provided by the data distributor. The methods in this package are described in the accompanying paper: <doi:10.1177/00491241211055769>.
Author: Ian Lundberg [aut, cre]
Maintainer: Ian Lundberg <ianlundberg@ucla.edu>
This is a re-admission after prior archival of version 1.0.2 dated 2021-10-11
Diff between gapclosing versions 1.0.2 dated 2021-10-11 and 1.0.3 dated 2026-05-23
DESCRIPTION | 16 MD5 | 18 NAMESPACE | 2 R/disparityplot.R | 12 R/gapclosing.R | 6 build/vignette.rds |binary inst/CITATION | 6 inst/WORDLIST | 13 inst/doc/gapclosing.R | 24 - inst/doc/gapclosing.html | 1004 +++++++++++++++++++++++++++++++++++------------ 10 files changed, 805 insertions(+), 296 deletions(-)
Title: Fuzzy C-Means for Fuzzy Data
Description: Implements a fuzzy clustering approach for ordinal Likert-type data
using triangular fuzzy numbers (TFNs). The package extends the classical
fuzzy C-means algorithm to better handle uncertainty in ordinal scales and
includes automatic selection of the number of clusters using the Xie-Beni
validity index. References: Coppi, R., D'Urso, P., and Giordani, P. (2012),
"Fuzzy and possibilistic clustering for fuzzy data", <doi:10.1016/j.csda.2010.09.013>. Xie, X. L. and Beni, G.
(1991), "A validity measure for fuzzy clustering", <doi:10.1109/34.85677>.
Author: Jose Ortigas [aut, cre]
Maintainer: Jose Ortigas <jose.ortigas@unmsm.edu.pe>
Diff between fcmfd versions 0.1.0 dated 2026-05-05 and 0.1.1 dated 2026-05-23
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/fcmTFN.R | 24 +++++++++--------------- man/fcmTFN.Rd | 24 +++++++++--------------- 4 files changed, 26 insertions(+), 38 deletions(-)
Title: Data Science Infrastructure for Global Health
Description: Supports global health data analysis, including a
publication-ready 'ggplot2' theme, a 'flextable' defaults helper,
a thin pie chart wrapper, built-in regional country-code datasets
with a WHO region lookup helper, a geometric mean function for
indicator aggregation, and convenience clients for the World
Health Organization Global Health Observatory (GHO) OData API
<https://ghoapi.azureedge.net/api/> and the United Nations
Sustainable Development Goals (SDG) API
<https://unstats.un.org/SDGAPI/swagger/>.
Author: Shanlong Ding [aut, cre]
Maintainer: Shanlong Ding <dings@who.int>
Diff between DSIR versions 0.7.0 dated 2026-05-21 and 0.7.1 dated 2026-05-23
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/DSIR.html | 46 +++++++++++++++++++++++----------------------- man/DSIR-package.Rd | 4 ++-- 5 files changed, 38 insertions(+), 34 deletions(-)
Title: Optimal Pairing and Matching via Linear Assignment
Description: Solves optimal pairing and matching problems using linear assignment
algorithms. Provides implementations of the Hungarian method (Kuhn 1955)
<doi:10.1002/nav.3800020109>, Jonker-Volgenant shortest path algorithm
(Jonker and Volgenant 1987) <doi:10.1007/BF02278710>, Auction algorithm
(Bertsekas 1988) <doi:10.1007/BF02186476>, cost-scaling
(Goldberg and Kennedy 1995) <doi:10.1007/BF01585996>, scaling algorithms
(Gabow and Tarjan 1989) <doi:10.1137/0218069>, push-relabel (Goldberg and
Tarjan 1988) <doi:10.1145/48014.61051>, and Sinkhorn entropy-regularized
transport (Cuturi 2013) <doi:10.48550/arxiv.1306.0895>. Designed for
matching plots, sites, samples, or any pairwise optimization problem.
Supports rectangular matrices, forbidden assignments, data frame inputs,
batch solving, k-best solutions, and pixel-level image morphing for
visualization. Includes automatic preprocessing with variable health
checks, multiple scaling methods (standardized, [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between couplr versions 1.4.0 dated 2026-05-18 and 1.4.1 dated 2026-05-23
DESCRIPTION | 6 MD5 | 34 ++--- NEWS.md | 40 ++++++ R/lap_solve.R | 6 R/matching_constraints.R | 11 + R/matching_core.R | 142 +++++++++++++--------- README.md | 2 inst/doc/algorithms.Rmd | 2 inst/doc/algorithms.html | 14 +- inst/doc/comparison.html | 4 inst/doc/getting-started.html | 22 ++- inst/doc/matching-workflows.html | 80 ++++++------ inst/doc/pixel-morphing.html | 4 inst/doc/troubleshooting.html | 110 +++++++++++------ src/solvers/jv_core.cpp | 15 +- tests/testthat/test-lap-solve-extended-coverage.R | 4 tests/testthat/test-matching-core-coverage-4.R | 4 vignettes/algorithms.Rmd | 2 18 files changed, 320 insertions(+), 182 deletions(-)
Title: Integrating Multi-Source Block-Wise Missing Data in Model
Selection
Description: Model selection method with multiple block-wise imputation for block-wise missing data; see Xue, F., and Qu, A. (2021) <doi:10.1080/01621459.2020.1751176>.
Author: Fei Xue [aut, cre],
Annie Qu [aut]
Maintainer: Fei Xue <feixue@purdue.edu>
This is a re-admission after prior archival of version 0.1.0 dated 2023-09-12
Diff between BlockMissingData versions 0.1.0 dated 2023-09-12 and 0.1.1 dated 2026-05-23
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- NAMESPACE | 1 - R/MBI.R | 2 -- R/imputeglm.predict.R | 1 - 5 files changed, 8 insertions(+), 13 deletions(-)
More information about BlockMissingData at CRAN
Permanent link
Title: Ensemble Platform for Species Distribution Modeling
Description: Functions for species distribution modeling, calibration and evaluation,
ensemble of models, ensemble forecasting and visualization. The package permits to run
consistently up to 10 single models on a presence/absences (resp presences/pseudo-absences)
dataset and to combine them in ensemble models and ensemble projections. Some bench of other
evaluation and visualisation tools are also available within the package.
Author: Maya Gueguen [aut, cre],
Helene Blancheteau [aut],
Remi Lemaire-Patin [aut],
Wilfried Thuiller [aut]
Maintainer: Maya Gueguen <maya.gueguen@univ-grenoble-alpes.fr>
Diff between biomod2 versions 4.3-4-5 dated 2026-01-30 and 4.3-4-6 dated 2026-05-23
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Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray,
Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Author: Klaus K. Holst [aut, cre],
Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.3.9 dated 2026-01-11 and 1.3.10 dated 2026-05-23
mets-1.3.10/mets/DESCRIPTION | 17 mets-1.3.10/mets/MD5 | 525 +- mets-1.3.10/mets/NAMESPACE | 243 mets-1.3.10/mets/NEWS.md | 23 mets-1.3.10/mets/R/Event.Split.R | 125 mets-1.3.10/mets/R/RcppExports.R | 8 mets-1.3.10/mets/R/WA-estimands.R | 230 mets-1.3.10/mets/R/bicomprisk.R | 113 mets-1.3.10/mets/R/binomial.regression.R | 1217 ----- mets-1.3.10/mets/R/binomial.twostage.R | 424 - mets-1.3.10/mets/R/binregTSR.R | 125 mets-1.3.10/mets/R/biprobit.R | 13 mets-1.3.10/mets/R/blocksample.R | 2 mets-1.3.10/mets/R/bptwin.R | 2 mets-1.3.10/mets/R/casewise.R | 153 mets-1.3.10/mets/R/cifreg.R | 492 -- mets-1.3.10/mets/R/claytonakes.R | 7 mets-1.3.10/mets/R/clusterindex-reshape.R | 75 mets-1.3.10/mets/R/cor.R | 100 mets-1.3.10/mets/R/discrete-survival-haplo.R | 153 mets-1.3.10/mets/R/divide.conquer.R | 63 mets-1.3.10/mets/R/drop.strata.R | 17 mets-1.3.10/mets/R/dutils.R | 18 mets-1.3.10/mets/R/event.r | 5 mets-1.3.10/mets/R/fastcluster.R | 7 mets-1.3.10/mets/R/fastreshape.R | 6 mets-1.3.10/mets/R/force.same.cens.R | 69 mets-1.3.10/mets/R/glm-utils.R | 21 mets-1.3.10/mets/R/gof-phreg.R | 299 - mets-1.3.10/mets/R/interval-cumoddsreg.r | 128 mets-1.3.10/mets/R/ipw.R | 6 mets-1.3.10/mets/R/jumptimes.R | 15 mets-1.3.10/mets/R/lifecourse.R | 8 mets-1.3.10/mets/R/mediator-survival.R | 4 mets-1.3.10/mets/R/mets-package.R | 48 mets-1.3.10/mets/R/multinomialreg.R |only mets-1.3.10/mets/R/npc.R | 76 mets-1.3.10/mets/R/phreg.R | 2431 ++++------ mets-1.3.10/mets/R/phreg_rct.R | 137 mets-1.3.10/mets/R/phreg_weibull.R | 4 mets-1.3.10/mets/R/plotcr.R | 7 mets-1.3.10/mets/R/pmvn.R | 2 mets-1.3.10/mets/R/procformula.R | 5 mets-1.3.10/mets/R/prop-odds.R | 2 mets-1.3.10/mets/R/ratio.regression.R | 189 mets-1.3.10/mets/R/recreg.R | 557 +- mets-1.3.10/mets/R/recurrent.marginal.R | 1670 ++++-- mets-1.3.10/mets/R/restricted.mean.R | 219 mets-1.3.10/mets/R/score-mean-tests.R |only mets-1.3.10/mets/R/sim-docs.R |only mets-1.3.10/mets/R/sim-nordic-twin.R | 30 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Title: Provider-Agnostic OAuth Authentication for 'shiny' Applications
Description: Provides a simple, configurable, provider-agnostic 'OAuth 2.0' and
'OpenID Connect' (OIDC) authentication framework for 'shiny' applications
using 'S7' classes. Defines providers, clients, and tokens, as well
as various supporting functions and a 'shiny' module. Features include
cross-site request forgery (CSRF) protection, state encryption,
'Proof Key for Code Exchange' (PKCE) handling, validation of OIDC identity
tokens (nonces, signatures, claims), automatic user info retrieval, asynchronous
flows, and hooks for audit logging.
Author: Luka Koning [aut, cre, cph]
Maintainer: Luka Koning <koningluka@gmail.com>
Diff between shinyOAuth versions 0.4.0 dated 2026-02-14 and 0.5.0 dated 2026-05-23
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shinyOAuth-0.5.0/shinyOAuth/R/utils__shiny_dispatch.R |only shinyOAuth-0.5.0/shinyOAuth/R/utils__shiny_otel.R |only shinyOAuth-0.5.0/shinyOAuth/R/utils__shiny_request_uri.R |only shinyOAuth-0.5.0/shinyOAuth/R/utils__state.R | 821 +- shinyOAuth-0.5.0/shinyOAuth/R/utils__url_helpers.R |only shinyOAuth-0.5.0/shinyOAuth/R/utils__validators.R |only shinyOAuth-0.5.0/shinyOAuth/R/zzz.R | 17 shinyOAuth-0.5.0/shinyOAuth/README.md | 43 shinyOAuth-0.5.0/shinyOAuth/build/vignette.rds |binary shinyOAuth-0.5.0/shinyOAuth/inst/doc/audit-logging.Rmd | 262 shinyOAuth-0.5.0/shinyOAuth/inst/doc/audit-logging.html | 440 - shinyOAuth-0.5.0/shinyOAuth/inst/doc/authentication-flow.Rmd | 523 - shinyOAuth-0.5.0/shinyOAuth/inst/doc/authentication-flow.html | 670 + shinyOAuth-0.5.0/shinyOAuth/inst/doc/example-spotify.R | 45 shinyOAuth-0.5.0/shinyOAuth/inst/doc/example-spotify.Rmd | 53 shinyOAuth-0.5.0/shinyOAuth/inst/doc/example-spotify.html | 2043 ++--- shinyOAuth-0.5.0/shinyOAuth/inst/doc/opentelemetry.Rmd 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Title: Univariate GARCH Models
Description: Multiple flavors of the Generalized Autoregressive Conditional Heteroskedasticity (GARCH) model with a large choice of conditional distributions. Methods for specification, estimation, prediction, filtering, simulation, statistical testing and more. Represents a partial re-write and re-think of 'rugarch', making use of automatic differentiation for estimation.
Author: Alexios Galanos [aut, cre, cph]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsgarch versions 1.0.3 dated 2024-10-11 and 1.0.4 dated 2026-05-23
DESCRIPTION | 18 ++--- MD5 | 50 +++++++------- NAMESPACE | 1 NEWS.md | 24 ++++++ R/estimate.R | 27 +++++++ R/initialization.R | 140 ++++++++++++++++++++++++++++++++++++++++ R/methods.R | 37 ++++++++++ R/multispec.R | 3 R/specification.R | 13 ++- R/tsgarch-package.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/benchmark.html | 46 ++++++++----- inst/doc/demonstration.R | 4 - inst/doc/demonstration.Rmd | 21 +++--- inst/doc/demonstration.html | 80 ++++++++++++---------- inst/doc/garch_models.pdf |binary man/figures |only man/garch_modelspec.Rd | 8 +- man/reexports.Rd | 4 - man/tsgarch-package.Rd | 8 ++ src/TMB/distfun.h | 8 -- src/TMB/realgarch.hpp.cpp |only src/TMB/tsgarch_TMBExports.cpp | 11 ++- tests/longtests/test-backtest.R | 8 +- tests/testthat/helper-global.R | 38 +++++----- vignettes/demonstration.Rmd | 21 +++--- 27 files changed, 420 insertions(+), 152 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine and for various extensions is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 3.52.0 dated 2026-05-10 and 3.53.1 dated 2026-05-23
DESCRIPTION | 8 MD5 | 14 NEWS.md | 7 src/vendor/extensions/csv.c | 17 src/vendor/extensions/regexp.c | 19 src/vendor/extensions/series.c | 8 src/vendor/sqlite3/sqlite3.c | 3311 +++++++++++++++++++++++++++++------------ src/vendor/sqlite3/sqlite3.h | 364 +++- 8 files changed, 2692 insertions(+), 1056 deletions(-)
Title: Easy to Configure an Isolated 'Python' Environment
Description: Aims to create a single isolated 'Miniconda'
and 'Python' environment for reproducible pipeline scripts.
The package provides utilities to run system command within the 'conda'
environment, making it easy to install, launch, manage, and stop
'Jupyter-lab'.
Author: Zhengjia Wang [cph, aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between rpymat versions 0.1.8 dated 2025-07-22 and 0.1.9 dated 2026-05-23
DESCRIPTION | 8 - MD5 | 44 +++--- NAMESPACE | 2 NEWS.md | 8 + R/aaa.R | 46 +++---- R/background.R | 12 - R/cmd.R | 90 +++++++------- R/download.R | 8 - R/exec_py.R | 48 +++---- R/file_choose.R | 14 +- R/fixes.R |only R/install.R | 255 ++++++++++++++++++++-------------------- R/jupyter.R | 81 ++++++------ R/ported.R | 6 R/reexports.R | 50 +++---- R/rstudioapi.R | 35 ++--- R/utils-readxlsx.R | 30 ++-- R/utils.R | 6 R/zzz.R | 10 - inst/matlab-python-versions.txt | 2 man/conda-env.Rd | 3 man/fix_omp_conflict.Rd |only man/reexports.Rd | 2 tests/spelling.R | 2 24 files changed, 387 insertions(+), 375 deletions(-)
Title: Read 'Blackrock-Microsystems' Files ('NEV', 'NSx')
Description: Loads 'Blackrock' <https://blackrockneurotech.com> neural signal
data files into the memory, provides utility tools to extract the data into
common formats such as plain-text 'tsv' and 'HDF5'.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between readNSx versions 0.0.6 dated 2025-10-24 and 0.0.7 dated 2026-05-23
DESCRIPTION | 10 MD5 | 48 +-- NEWS.md | 6 R/bci2000.R | 22 - R/blackrock.R | 281 ++++++++++++++++++--- R/cpp11.R | 12 R/formats.R | 16 - R/hdf5-alternative.R | 187 +++++++++++--- R/hdf5.R | 470 +++++++++++++++++++++++++++--------- R/nev.R | 56 ++-- R/nsx.R | 369 +++++++++++++++++++++++++--- R/parsers.R | 22 - R/specifications.R | 6 R/utils.R | 104 ++++--- R/validators.R | 6 build/vignette.rds |binary man/compare_nsx_methods.Rd |only src/common.h | 73 +++++ src/cpp11.cpp | 24 + src/readBCI.h | 88 +++--- src/readNSxDataPacket.cpp | 230 +++++++++++++++++ tests/spelling.R | 2 tests/testthat/test-bci2000.R |only tests/testthat/test-fileimport.R | 18 - tests/testthat/test-h5-allocation.R |only tests/testthat/test-nsx-local.R |only tests/testthat/test-rawToSEXP.R | 12 27 files changed, 1632 insertions(+), 430 deletions(-)
Title: Estimation and Inference for Boundary Discontinuity Designs
Description: Provides pointwise and uniform estimation and inference methods for boundary discontinuity (BD) designs,
a causal inference design that generalizes univariate regression discontinuity (RD) designs to settings with bivariate scores.
Implements local polynomial methods for location-based and distance-based analyses, including sharp and fuzzy designs,
data-driven bandwidth selection, pointwise confidence intervals, and uniform confidence bands. Methodology is developed in
Cattaneo, Titiunik, and Yu (2026) <doi:10.48550/arXiv.2505.05670> for location-based methods and
Cattaneo, Titiunik, and Yu (2026) <doi:10.48550/arXiv.2510.26051> for distance-based methods.
For an overview and empirical guidance, see Cattaneo, Titiunik, and Yu (2026) <doi:10.48550/arXiv.2511.06474>.
The companion software article is Cattaneo, Titiunik, and Yu (2025) <doi:10.48550/arXiv.2505.07989>.
Author: Matias D. Cattaneo [aut, cre],
Rocio Titiunik [aut],
Ruiqi Rae Yu [aut]
Maintainer: Matias D. Cattaneo <matias.d.cattaneo@gmail.com>
Diff between rd2d versions 0.1.0 dated 2026-05-14 and 0.2.0 dated 2026-05-23
DESCRIPTION | 8 - MD5 | 50 ++++----- NEWS.md | 5 R/rd2d-package.R | 2 R/rd2d.R | 108 ++++++++++++-------- R/rd2d_distance.R | 128 +++++++++++++++-------- R/rd2d_distance_fn.R | 155 +++++++++++++++++++---------- R/rd2d_fn.R | 82 ++++++++++----- R/rdbw2d.R | 61 ++++++----- R/rdbw2d_distance.R | 15 +- man/print.rd2d.Rd | 2 man/print.rd2d.distance.Rd | 2 man/print.rdbw2d.Rd | 2 man/print.rdbw2d.distance.Rd | 2 man/rd2d-package.Rd | 2 man/rd2d.Rd | 14 -- man/rd2d.distance.Rd | 7 - man/rdbw2d.Rd | 2 man/rdbw2d.distance.Rd | 2 man/summary.rd2d.Rd | 15 +- man/summary.rd2d.distance.Rd | 12 +- man/summary.rdbw2d.Rd | 2 man/summary.rdbw2d.distance.Rd | 2 tests/testthat/test-distance-methods.R | 47 +++++--- tests/testthat/test-numerical-regression.R | 14 -- tests/testthat/test-package.R | 74 ++++++++----- 26 files changed, 497 insertions(+), 318 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://rave.wiki>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlage [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.2.4 dated 2025-09-10 and 0.2.5 dated 2026-05-23
DESCRIPTION | 11 MD5 | 196 ++++++----- NAMESPACE | 16 NEWS.md | 17 + R/RcppExports.R | 16 R/aaa.R | 38 +- R/band-pass.R | 40 +- R/baseline.R | 69 ++-- R/carla.R |only R/class-Matrix4.R | 64 +-- R/class-Quaternion.R | 18 - R/class-Vector3.R | 26 - R/collapse.R | 26 - R/convolve.R | 26 - R/crp.R |only R/curve-catmull.R |only R/detrend.R | 14 R/dijkstras-path.R | 44 +- R/fast_cov.R | 16 R/fast_quantile.R | 4 R/fftw.R |only R/filter-butter.R | 10 R/filter-cutoff.R | 4 R/filter-decimate.R | 14 R/filter-diagnosis.R | 102 +++--- R/filter-fftfilt.R | 14 R/filter-filtfilt.R | 69 ++-- R/filter-fir-design.R | 98 ++++- R/filter-fir.R | 110 ++++-- R/filter-notch.R | 24 - R/filter-utils.R | 34 +- R/filter.R | 111 ++++-- R/find_peaks.R | 8 R/gammatone.R | 30 - R/geometry-plane.R | 69 ++-- R/guess_number.R | 16 R/image-mesh-from-volume.R | 17 - R/image-resample3d.R | 13 R/imaging-fill-surface.R | 39 +- R/imaging-registration.R | 4 R/interpolate.R | 56 +-- R/misc.R | 11 R/multitaper.R | 148 ++++----- R/nmf.R | 16 R/parse_svec.R | 56 +-- R/plot-signals.R | 19 - R/pwelch-diagnosis.R | 80 ++-- R/pwelch.R | 110 +++--- R/rgl.R | 16 R/shift_array.R | 10 R/spike_sorting.R |only R/stimulation_pauses.R | 50 +-- R/vcg.R | 58 +-- R/wavelet-double.R |only R/wavelet-float.R |only R/wavelet.R | 559 ++++++++-------------------------- build |only inst/CITATION | 61 +++ inst/WORDLIST | 4 inst/include/ravetools_RcppExports.h | 43 +- man/baseline_array.Rd | 45 +- man/carla.Rd |only man/catmull_rom_3d.Rd |only man/collapse.Rd | 4 man/crp.Rd |only man/design_filter.Rd | 10 man/design_filter_iir.Rd | 19 - man/dijkstras-path.Rd | 4 man/fftw-internal.Rd |only man/filtfilt.Rd | 15 man/firls.Rd | 9 man/plot.ravetools_crp.Rd |only man/plot.ravetools_curve.Rd |only man/print.ravetools_curve.Rd |only man/project_plane.Rd | 5 man/pwelch.Rd | 2 man/reexports.Rd | 2 man/shift_array.Rd | 2 man/vcg_uniform_remesh.Rd | 2 man/wavelet.Rd | 14 src/RcppExports.cpp | 236 ++++++++------ src/baseline.cpp | 54 ++- src/ffts.cpp | 43 +- src/fftw-wrapper.cpp | 148 ++++++--- src/fftw-wrapper.h | 12 src/glQuaternion.cpp | 23 + src/glQuaternion.h | 2 src/vcgCommon.cpp | 2 tests/spelling.R | 6 tests/testthat.R | 2 tests/testthat/test-baseline.R | 372 ++++++++++++++++------ tests/testthat/test-collapse.R | 148 ++++----- tests/testthat/test-convolve.R | 24 - tests/testthat/test-extra.R | 2 tests/testthat/test-fftw.R | 312 ++++++++++++++---- tests/testthat/test-fftw2D.R | 73 ++++ tests/testthat/test-fftw3D.R | 75 ++++ tests/testthat/test-filter.R | 48 +- tests/testthat/test-fir-design.R |only tests/testthat/test-firls-fast-path.R |only tests/testthat/test-matrix4.R | 86 ++--- tests/testthat/test-pwelch.R | 48 ++ tests/testthat/test-quaternion.R | 41 +- tests/testthat/test-rawToSEXP.R | 28 - tests/testthat/test-resample3D.R | 18 - tests/testthat/test-shiftarray.R | 55 +-- tests/testthat/test-vector3.R | 331 +++++++++++--------- tests/testthat/test-wavelet.R |only 108 files changed, 2922 insertions(+), 2124 deletions(-)
Title: Likelihood Models for Systems with Masked Component Cause of
Failure
Description: Maximum likelihood estimation for series systems where the
component cause of failure is masked. Implements analytical log-likelihood,
score, and Hessian functions for exponential, homogeneous Weibull, and
heterogeneous Weibull component lifetimes under masked cause conditions
(C1, C2, C3). Supports exact, right-censored, left-censored, and
interval-censored observations via composable observation functors.
Provides random data generation, model fitting, and Fisher information
for asymptotic inference. See Lin, Loh, and Bai (1993)
<doi:10.1109/24.257799> and Craiu and Reiser (2006)
<doi:10.1111/j.1541-0420.2005.00498.x>.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between maskedcauses versions 0.9.3 dated 2026-03-17 and 0.10.0 dated 2026-05-23
maskedcauses-0.10.0/maskedcauses/DESCRIPTION | 11 maskedcauses-0.10.0/maskedcauses/MD5 | 36 +- maskedcauses-0.10.0/maskedcauses/NAMESPACE | 2 maskedcauses-0.10.0/maskedcauses/NEWS.md | 34 ++ maskedcauses-0.10.0/maskedcauses/R/exp_series.R | 129 +++++++--- maskedcauses-0.10.0/maskedcauses/R/utils.R | 18 + maskedcauses-0.10.0/maskedcauses/R/zzz.R |only maskedcauses-0.10.0/maskedcauses/inst/doc/censoring_comparison.html | 6 maskedcauses-0.10.0/maskedcauses/inst/doc/weibull_series.html | 6 maskedcauses-0.10.0/maskedcauses/man/Exponential-series-system.Rd | 15 - maskedcauses-0.10.0/maskedcauses/man/dexp_series.Rd | 9 maskedcauses-0.10.0/maskedcauses/man/hazard_exp_series.Rd | 8 maskedcauses-0.10.0/maskedcauses/man/integrate_hazard.Rd |only maskedcauses-0.10.0/maskedcauses/man/mean.exp_series.Rd | 27 +- maskedcauses-0.10.0/maskedcauses/man/pexp_series.Rd | 7 maskedcauses-0.10.0/maskedcauses/man/qexp_series.Rd | 7 maskedcauses-0.10.0/maskedcauses/man/rexp_series.Rd | 8 maskedcauses-0.10.0/maskedcauses/man/surv.exp_series.Rd | 7 maskedcauses-0.10.0/maskedcauses/tests/testthat/test-dist-structure-interop.R |only maskedcauses-0.10.0/maskedcauses/tests/testthat/test-utils.R | 26 +- maskedcauses-0.9.3/maskedcauses/man/cum_haz.Rd |only 21 files changed, 252 insertions(+), 104 deletions(-)
Title: Dynamic Failure Rate Distributions for Survival Analysis
Description: Flexible framework for specifying survival distributions through
their hazard (failure rate) functions. Define arbitrary time-varying
hazard functions to model complex failure patterns including bathtub
curves, proportional hazards with covariates, and other non-standard
hazard behaviors. Provides automatic computation of survival, CDF, PDF,
quantiles, and sampling. Implements the likelihood model interface for
maximum likelihood estimation with right-censored and left-censored
survival data.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <queelius@gmail.com>
Diff between flexhaz versions 0.5.1 dated 2026-03-19 and 0.5.2 dated 2026-05-23
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 9 +++++++++ R/distributions.R | 32 ++++++++++++++++++++------------ inst/doc/custom_distributions.html | 6 +++--- inst/doc/failure_rate.html | 4 ++-- inst/doc/flexhaz-package.html | 4 ++-- man/dfr_exponential.Rd | 3 +-- man/dfr_gompertz.Rd | 3 +-- man/dfr_loglogistic.Rd | 3 +-- man/dfr_weibull.Rd | 3 +-- tests/testthat/Rplots.pdf |binary 12 files changed, 54 insertions(+), 41 deletions(-)
Title: File-Backed Array for Out-of-Memory Computation
Description: Stores large arrays in files to avoid occupying large
memories. Implemented with super fast gigabyte-level multi-threaded
reading/writing via 'OpenMP'. Supports multiple non-character data
types (double, float, complex, integer, logical, and raw).
Author: Zhengjia Wang [aut, cre, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between filearray versions 0.2.1 dated 2026-03-23 and 0.2.2 dated 2026-05-23
DESCRIPTION | 8 MD5 | 88 ++--- NEWS.md | 5 R/aaa.R | 40 +- R/bind.R | 52 +-- R/class-filearray.R | 289 ++++++++--------- R/class-proxy.R | 88 ++--- R/filearray-package.R | 48 +- R/header.R | 46 +- R/helpers.R | 88 ++--- R/internal_misc.R | 40 +- R/load.R | 56 +-- R/mapreduce.R | 42 +- R/method-map.R | 86 ++--- R/methods-add.R | 34 +- R/methods-apply.R | 14 R/methods-subset.R | 50 +-- R/methods-subsetAssign.R | 76 ++-- R/methods-typeof.R | 10 R/methods.R | 96 ++--- R/misc-docs.R | 6 R/write.R | 32 - build/vignette.rds |binary inst/doc/performance.R | 232 ++++++++----- inst/doc/performance.Rmd | 232 ++++++++----- inst/doc/performance.html | 368 ++++++++++++---------- man/S4-filearray.Rd | 3 man/filearray.Rd | 2 man/fmap.Rd | 12 man/mapreduce.Rd | 8 src/core.cpp | 38 ++ src/load.cpp | 9 tests/testthat/test-bind.R | 134 ++++---- tests/testthat/test-collapse.R | 499 +++++++++++++++++++----------- tests/testthat/test-cpp.R | 207 ++++++------ tests/testthat/test-dimnames.R | 54 +-- tests/testthat/test-helpers.R | 64 ++- tests/testthat/test-map.R | 90 +++-- tests/testthat/test-method_add.R | 18 - tests/testthat/test-method_sub.R | 18 - tests/testthat/test-method_subset.R | 49 ++ tests/testthat/test-method_subsetAssign.R | 20 - tests/testthat/test-methods.R | 12 tests/testthat/test-methods_simple.R | 14 vignettes/performance.Rmd | 232 ++++++++----- 45 files changed, 2077 insertions(+), 1532 deletions(-)
Title: Ecological Limit Function Model Generation and Analysis Toolkit
Description: A toolset for generating Ecological Limit Function (ELF) models and evaluating potential species loss resulting from flow change, based on the 'elfgen' framework. ELFs describe the relation between aquatic species richness (fish or benthic macroinvertebrates) and stream size characteristics (streamflow or drainage area). Journal publications are available outlining framework methodology (Kleiner et al. (2020) <doi:10.1111/1752-1688.12876>) and application (Rapp et al. (2020) <doi:10.1111/1752-1688.12877>).
Author: Joseph Kleiner [aut] ,
Robert Burgholzer [ctb] ,
Connor Brogan [cre]
Maintainer: Connor Brogan <connor.brogan@deq.virginia.gov>
Diff between elfgen versions 2.3.4 dated 2025-11-28 and 2.3.5 dated 2026-05-23
DESCRIPTION | 9 ++++++--- MD5 | 41 ++++++++++++++++++++++------------------- NEWS.md | 3 +++ R/bkpt-pwit.R | 7 +------ R/bkpt-ymax.R | 7 +------ R/clean-vahydro.R | 4 ---- R/data.R |only R/elfchange.R | 8 +------- R/elfdata-vahydro.R | 4 ---- R/elfdata.R | 22 +++++++++++----------- R/elfgen.R | 7 +------ R/richness-change.R | 7 +------ data |only man/bkpt_pwit.Rd | 7 +------ man/bkpt_ymax.Rd | 7 +------ man/clean_vahydro.Rd | 4 ---- man/elfchange.Rd | 8 +------- man/elfdata.Rd | 6 +++--- man/elfdata_vahydro.Rd | 4 ---- man/elfgen.Rd | 7 +------ man/richness_change.Rd | 7 +------ man/watershed.df.Rd |only tests/testthat/test-elfdata.R | 37 +++++++++++++++++++++++++++++-------- 23 files changed, 84 insertions(+), 122 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using the 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre],
John Magnotti [ctb] ,
Xiang Zhang [ctb]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between dipsaus versions 0.3.4 dated 2026-03-20 and 0.3.5 dated 2026-05-23
dipsaus-0.3.4/dipsaus/man/attached_packages.Rd |only dipsaus-0.3.4/dipsaus/man/update_fastmap2.Rd |only dipsaus-0.3.5/dipsaus/DESCRIPTION | 12 dipsaus-0.3.5/dipsaus/MD5 | 264 +++++------ dipsaus-0.3.5/dipsaus/NAMESPACE | 1 dipsaus-0.3.5/dipsaus/NEWS.md | 14 dipsaus-0.3.5/dipsaus/R/aaa.R | 23 dipsaus-0.3.5/dipsaus/R/apply.R | 38 - dipsaus-0.3.5/dipsaus/R/cpp-baseline_array.R | 38 - dipsaus-0.3.5/dipsaus/R/cpp-collapse.R | 24 - dipsaus-0.3.5/dipsaus/R/cpp-fastcov2.R | 16 dipsaus-0.3.5/dipsaus/R/cpp-fastquantile.R | 4 dipsaus-0.3.5/dipsaus/R/credentials.R | 62 +- dipsaus-0.3.5/dipsaus/R/fastmap2.R | 94 ++- dipsaus-0.3.5/dipsaus/R/fastqueue2.R | 48 +- dipsaus-0.3.5/dipsaus/R/graphics.R | 70 +- dipsaus-0.3.5/dipsaus/R/language.R | 261 +++++----- dipsaus-0.3.5/dipsaus/R/lock.R | 100 ++-- dipsaus-0.3.5/dipsaus/R/map-abstract.R | 122 ++--- dipsaus-0.3.5/dipsaus/R/map-memory.R | 40 - dipsaus-0.3.5/dipsaus/R/map-rds.R | 86 +-- dipsaus-0.3.5/dipsaus/R/map-s3.R | 8 dipsaus-0.3.5/dipsaus/R/map-txt.R | 28 - 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Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data--based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>.
b) Tsagris M. (2014). "The k--NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv. [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 8.1 dated 2026-02-17 and 8.2 dated 2026-05-23
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