Title: Alternative Meta-Analysis Methods
Description: Provides alternative statistical methods for meta-analysis, including:
- bivariate generalized linear mixed models for synthesizing odds ratios, relative risks,
and risk differences
(Chu et al., 2012 <doi:10.1177/0962280210393712>)
- tests and measures for between-study heterogeneity
(Lin et al., 2017 <doi:10.1111/biom.12543>;
Wang et al., 2022 <doi:10.1002/sim.9261>);
- measures, tests, and visualization tools for publication bias or small-study effects
(Lin and Chu, 2018 <doi:10.1111/biom.12817>;
Lin, 2019 <doi:10.1002/jrsm.1340>;
Lin, 2020 <doi:10.1177/0962280220910172>;
Shi et al., 2020 <doi:10.1002/jrsm.1415>);
- meta-analysis of combining standardized mean differences and odds ratios
(Jing et al., 2023 <doi:10.1080/10543406.2022.2105345>);
- meta-analysis of diagnostic tests for synthesizing sensitivities, specificities, etc.
(Reitsma et al., 2005 <doi:10.1016/j.jclinepi.2005.02.022>;
Chu and Cole, 2006 <doi:10.1016/j.jclin [...truncated...]
Author: Lifeng Lin [aut, cre] ,
Yaqi Jing [ctb],
Kristine J. Rosenberger [ctb],
Linyu Shi [ctb],
Yipeng Wang [ctb],
Xing Xing [ctb] ,
Zhiyuan Yu [ctb],
Haitao Chu [aut]
Maintainer: Lifeng Lin <lifenglin@arizona.edu>
Diff between altmeta versions 4.2 dated 2024-09-07 and 4.3 dated 2025-10-13
DESCRIPTION | 19 ++++++++++++------- MD5 | 12 ++++++++---- NAMESPACE | 2 +- R/metahet.hybrid.R |only build/partial.rdb |binary data/dat.hughes.rda |only man/dat.dep.Rd | 2 +- man/dat.hughes.Rd |only man/metahet.hybrid.Rd |only 9 files changed, 22 insertions(+), 13 deletions(-)
Title: Pull Spatial Layers from 'WDNR ArcGIS REST API'
Description: Functions for finding and pulling data from the
'Wisconsin Department of Natural Resources ArcGIS REST APIs'
<https://dnrmaps.wi.gov/arcgis/rest/services> and
<https://dnrmaps.wi.gov/arcgis2/rest/services>.
Author: Paul Frater [aut, cre] ,
Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between wdnr.gis versions 0.1.5 dated 2023-10-25 and 0.1.6 dated 2025-10-13
DESCRIPTION | 14 +++---- MD5 | 24 ++++++------ R/get_layer_functions.R | 6 +-- R/utilities.R | 2 - R/wdnr.gis-package.R | 3 - build/vignette.rds |binary data/service_urls.rda |binary inst/doc/wdnr.gis-intro.R | 28 +++++++------- inst/doc/wdnr.gis-intro.html | 14 +++---- man/get_wis_raster_layer.Rd | 4 +- man/wdnr.gis-package.Rd | 9 ++++ tests/testthat/test-get-functions.R | 40 +++++++++++--------- tests/testthat/test-utils.R | 72 ++++++++++++++++++++++++++---------- 13 files changed, 130 insertions(+), 86 deletions(-)
Title: Calculates Bounds for the Selection Bias for Binary Treatment
and Outcome Variables
Description: Computes bounds and sensitivity parameters as part of sensitivity
analysis for selection bias. Different bounds are provided: the SV (Smith
and VanderWeele), sharp bounds, AF (assumption-free) bound, GAF (generalized
AF), and CAF (counterfactual AF) bounds. The calculation of the sensitivity
parameters for the SV, sharp, and GAF bounds assume an additional dependence
structure in form of a generalized M-structure. The bounds can be
calculated for any structure as long as the necessary assumptions hold. See
Smith and VanderWeele (2019) <doi:10.1097/EDE.0000000000001032>,
Zetterstrom, Sjölander, and Waernabum (2025) <doi:10.1177/09622802251374168>,
Zetterstrom and Waernbaum (2022) <doi:10.1515/em-2022-0108>, and
Zetterstrom (2024) <doi:10.1515/em-2023-0033>.
Author: Stina Zetterstrom [aut, cre] ,
Ingeborg Waernbaum [aut]
Maintainer: Stina Zetterstrom <stina.zetterstrom@gmail.com>
Diff between SelectionBias versions 2.0.0 dated 2024-03-27 and 2.1.0 dated 2025-10-13
SelectionBias-2.0.0/SelectionBias/R/SVboundparametersM.R |only SelectionBias-2.0.0/SelectionBias/man/SVboundparametersM.Rd |only SelectionBias-2.0.0/SelectionBias/tests/testthat/test-SVboundparametersM.R |only SelectionBias-2.0.0/SelectionBias/tests/testthat/test-SVboundsharp.R |only SelectionBias-2.1.0/SelectionBias/DESCRIPTION | 33 SelectionBias-2.1.0/SelectionBias/LICENSE | 4 SelectionBias-2.1.0/SelectionBias/MD5 | 78 - SelectionBias-2.1.0/SelectionBias/NAMESPACE | 2 SelectionBias-2.1.0/SelectionBias/NEWS.md | 15 SelectionBias-2.1.0/SelectionBias/R/AFbound.R | 130 - SelectionBias-2.1.0/SelectionBias/R/CAFbound.R | 166 +- SelectionBias-2.1.0/SelectionBias/R/GAFbound.R | 216 +-- SelectionBias-2.1.0/SelectionBias/R/SVbound.R | 399 +++--- SelectionBias-2.1.0/SelectionBias/R/SVboundsharp.R | 99 - SelectionBias-2.1.0/SelectionBias/R/SelectionBias-package.R | 14 SelectionBias-2.1.0/SelectionBias/R/calcSVbound.R | 51 SelectionBias-2.1.0/SelectionBias/R/calcselbias.R | 158 +- SelectionBias-2.1.0/SelectionBias/R/checksharpSVbound.R |only SelectionBias-2.1.0/SelectionBias/R/data.R | 122 - SelectionBias-2.1.0/SelectionBias/R/genprob.R | 184 +- SelectionBias-2.1.0/SelectionBias/R/sensitivityparametersM.R | 476 +++---- SelectionBias-2.1.0/SelectionBias/R/sharpbound.R |only SelectionBias-2.1.0/SelectionBias/build/partial.rdb |binary SelectionBias-2.1.0/SelectionBias/build/vignette.rds |binary SelectionBias-2.1.0/SelectionBias/inst/doc/SelectionBias.R | 74 - SelectionBias-2.1.0/SelectionBias/inst/doc/SelectionBias.Rmd | 343 +++-- SelectionBias-2.1.0/SelectionBias/inst/doc/SelectionBias.html | 663 +++++----- SelectionBias-2.1.0/SelectionBias/man/AFbound.Rd | 120 - SelectionBias-2.1.0/SelectionBias/man/CAFbound.Rd | 150 +- SelectionBias-2.1.0/SelectionBias/man/GAFbound.Rd | 173 +- SelectionBias-2.1.0/SelectionBias/man/SVbound.Rd | 242 ++- SelectionBias-2.1.0/SelectionBias/man/SVboundsharp.Rd | 82 - SelectionBias-2.1.0/SelectionBias/man/SelectionBias-package.Rd | 56 SelectionBias-2.1.0/SelectionBias/man/checksharpSVbound.Rd |only SelectionBias-2.1.0/SelectionBias/man/sensitivityparametersM.Rd | 242 +-- SelectionBias-2.1.0/SelectionBias/man/sharpbound.Rd |only SelectionBias-2.1.0/SelectionBias/man/zika_learner.Rd | 134 +- SelectionBias-2.1.0/SelectionBias/tests/testthat/test-SVbound.R | 136 +- SelectionBias-2.1.0/SelectionBias/tests/testthat/test-calcselbias.R | 52 SelectionBias-2.1.0/SelectionBias/tests/testthat/test-checksharpSVbound.R |only SelectionBias-2.1.0/SelectionBias/tests/testthat/test-genprob.R | 38 SelectionBias-2.1.0/SelectionBias/tests/testthat/test-sensitivityparametersM.R | 61 SelectionBias-2.1.0/SelectionBias/tests/testthat/test-sharpbound.R |only SelectionBias-2.1.0/SelectionBias/vignettes/SelectionBias.Rmd | 343 +++-- SelectionBias-2.1.0/SelectionBias/vignettes/references.bib | 117 - 45 files changed, 2944 insertions(+), 2229 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.17 dated 2025-03-10 and 1.9.18 dated 2025-10-13
DESCRIPTION | 8 MD5 | 36 +- NEWS | 16 + R/TMB.R | 49 +++ R/sdreport.R | 14 - inst/include/TMBad/TMBad.cpp | 439 +++++++++++++++++++-------------- inst/include/TMBad/TMBad.hpp | 153 +++++++---- inst/include/TMBad/ad_blas.hpp | 5 inst/include/TMBad/checkpoint.hpp | 22 + inst/include/TMBad/code_generator.hpp | 1 inst/include/TMBad/compile.hpp | 2 inst/include/TMBad/compression.hpp | 17 - inst/include/TMBad/eigen_numtraits.hpp | 1 inst/include/TMBad/global.hpp | 371 +++++++++++++++++++-------- inst/include/TMBad/graph2dot.hpp | 1 inst/include/TMBad/graph_transform.hpp | 15 - inst/include/TMBad/integrate.hpp | 1 inst/include/TMBad/vectorize.hpp | 120 +++++++-- inst/include/tmbutils/newton.hpp | 4 19 files changed, 868 insertions(+), 407 deletions(-)
Title: A Comprehensive Analysis of High Dimensional Longitudinal Data
Description: To provide a comprehensive analysis of high dimensional longitudinal
data,this package provides analysis for any combination of 1) simultaneous
variable selection and estimation, 2) mean regression or quantile regression
for heterogeneous data, 3) cross-sectional or longitudinal data, 4) balanced
or imbalanced data, 5) moderate, high or even ultra-high dimensional data,
via computationally efficient implementations of penalized generalized
estimating equations.
Author: Tianhai Zu [aut, cre],
Brittany Green [aut, ctb],
Yan Yu [aut, ctb]
Maintainer: Tianhai Zu <zuti@mail.uc.edu>
Diff between geeVerse versions 0.3.0 dated 2025-08-19 and 0.3.1 dated 2025-10-13
DESCRIPTION | 8 +- MD5 | 24 +++--- NAMESPACE | 1 R/PGEE.R | 44 +++++++---- R/RcppExports.R | 4 - R/generate_data.R | 4 - R/qpgee.R | 5 - R/utils.R | 4 - inst/sim/replication_script_for_main.R | 127 ++++++++++++++++----------------- man/PGEE.Rd | 5 + man/generate_data.Rd | 4 - src/RcppExports.cpp | 9 +- src/geninv.cpp | 84 +++++---------------- 13 files changed, 152 insertions(+), 171 deletions(-)
Title: Density, Probability, Quantile ('DPQ') Computations
Description: Computations for approximations and alternatives for the 'DPQ'
(Density (pdf), Probability (cdf) and Quantile) functions for probability
distributions in R.
Primary focus is on (central and non-central) beta, gamma and related
distributions such as the chi-squared, F, and t.
--
For several distribution functions, provide functions implementing formulas from
Johnson, Kotz, and Kemp (1992) <doi:10.1002/bimj.4710360207> and
Johnson, Kotz, and Balakrishnan (1995) for discrete or continuous
distributions respectively.
This is for the use of researchers in these numerical approximation
implementations, notably for my own use in order to improve standard
R pbeta(), qgamma(), ..., etc: {'"dpq"'-functions}.
Author: Martin Maechler [aut, cre] ,
Morten Welinder [ctb] ),
Wolfgang Viechtbauer [ctb] , 2002),
Ross Ihaka [ctb] ,
Marius Hofert [ctb] , lssum),
R-core [ctb] ,
R Foundation [cph]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between DPQ versions 0.6-0 dated 2025-07-08 and 0.6-1 dated 2025-10-13
DESCRIPTION | 12 +-- MD5 | 61 ++++++++------- NAMESPACE | 5 + R/beta-fns.R | 161 +++++++++++++++++++++++++++++++++++++++++- R/dbinom-nbinom.R | 4 - R/expm1x.R | 3 R/pbetaR_v1.R | 38 +++++---- R/pnchisq.R | 44 +++++------ R/qchisqAppr.R | 1 TODO | 17 ++-- build/partial.rdb |binary inst/NEWS.Rd | 35 +++++++++ inst/doc/Noncentral-Chisq.pdf |binary inst/doc/comp-beta.pdf |binary inst/doc/log1pmx-etc.pdf |binary inst/doc/qnorm-asymp.pdf |binary inst/extraR/relErr-plots.R | 4 + man/fr_ld_exp.Rd | 2 man/gam1d.Rd | 56 +++++++------- man/gamln1.Rd | 13 ++- man/pbetaAS_eq20.Rd |only man/pbetaRv1.Rd | 8 +- man/pnbeta.Rd | 1 man/pnchisqAppr.Rd | 74 ++++++++++++------- man/r_pois.Rd | 4 - src/DPQ-misc.c | 40 ++++++---- src/gamma_inc_T1006.c | 5 - src/pnchisq-it.c | 28 +++---- tests/chisq-nonc-ex.R | 59 ++++++++------- tests/dnbinom-tst.R | 7 + tests/qPoisBinom-ex.R | 131 ++++++++++++++++------------------ tests/stirlerr-tst.R | 6 - 32 files changed, 541 insertions(+), 278 deletions(-)
Title: Flexible Mediation Analysis Using Natural Effect Models
Description: Run flexible mediation analyses using natural effect models as described in
Lange, Vansteelandt and Bekaert (2012) <DOI:10.1093/aje/kwr525>,
Vansteelandt, Bekaert and Lange (2012) <DOI:10.1515/2161-962X.1014>
and Loeys, Moerkerke, De Smet, Buysse, Steen and Vansteelandt (2013) <DOI:10.1080/00273171.2013.832132>.
Author: Johan Steen [aut, cre],
Tom Loeys [aut],
Beatrijs Moerkerke [aut],
Stijn Vansteelandt [aut],
Joris Meys [ctb] ,
Theis Lange [ctb] ,
Joscha Legewie [ctb],
Paul Fink [ctb],
Sanford Weisberg [ctb],
Yves Rosseel [ctb]
Maintainer: Johan Steen <johan.steen@gmail.com>
Diff between medflex versions 0.6-10 dated 2023-06-22 and 0.6-11 dated 2025-10-13
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 6 ++++++ NEWS | 4 ++++ R/neImpute.R | 21 ++++++++++++++------- R/neLht.R | 9 +++++---- R/neWeight.R | 22 ++++++++++++---------- R/terms-expand.R | 5 +++++ build/vignette.rds |binary inst/doc/medflex.pdf |binary inst/doc/sandwich.pdf |binary man/neImpute.default.Rd | 17 +++++++++++------ man/neImpute.formula.Rd | 2 ++ man/neLht-methods.Rd | 4 ++-- man/neLht.Rd | 4 ++-- 15 files changed, 82 insertions(+), 50 deletions(-)
Title: Shed Light on Black Box Machine Learning Models
Description: Shed light on black box machine learning models by the help
of model performance, variable importance, global surrogate models,
ICE profiles, partial dependence (Friedman J. H. (2001)
<doi:10.1214/aos/1013203451>), accumulated local effects (Apley D. W.
(2016) <doi:10.48550/arXiv.1612.08468>), further effects plots,
interaction strength, and variable contribution breakdown (Gosiewska
and Biecek (2019) <doi:10.48550/arXiv.1903.11420>). All tools are
implemented to work with case weights and allow for stratified
analysis. Furthermore, multiple flashlights can be combined and
analyzed together.
Author: Michael Mayer [aut, cre, cph]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between flashlight versions 0.9.0 dated 2023-05-09 and 1.0.0 dated 2025-10-13
flashlight-0.9.0/flashlight/R/add_shap.R |only flashlight-0.9.0/flashlight/R/ale_profile.R |only flashlight-0.9.0/flashlight/R/all_identical.R |only flashlight-0.9.0/flashlight/R/auto_cut.R |only flashlight-0.9.0/flashlight/R/common_breaks.R |only flashlight-0.9.0/flashlight/R/cut3.R |only flashlight-0.9.0/flashlight/R/grouped_center.R |only flashlight-0.9.0/flashlight/R/grouped_counts.R |only flashlight-0.9.0/flashlight/R/grouped_stats.R |only flashlight-0.9.0/flashlight/R/grouped_weighted_mean.R |only flashlight-0.9.0/flashlight/R/most_important.R |only flashlight-0.9.0/flashlight/R/plot_counts.R |only flashlight-0.9.0/flashlight/R/plot_light_breakdown.R |only flashlight-0.9.0/flashlight/R/plot_light_effects.R |only flashlight-0.9.0/flashlight/R/plot_light_global_surrogate.R |only flashlight-0.9.0/flashlight/R/plot_light_ice.R |only flashlight-0.9.0/flashlight/R/plot_light_importance.R |only flashlight-0.9.0/flashlight/R/plot_light_performance.R |only flashlight-0.9.0/flashlight/R/plot_light_profile.R |only flashlight-0.9.0/flashlight/R/plot_light_profile2d.R |only flashlight-0.9.0/flashlight/R/plot_light_scatter.R |only flashlight-0.9.0/flashlight/R/predict_flashlight.R |only flashlight-0.9.0/flashlight/R/predict_multiflashlight.R |only flashlight-0.9.0/flashlight/R/print_flashlight.R |only flashlight-0.9.0/flashlight/R/print_light.R |only flashlight-0.9.0/flashlight/R/print_multiflashlight.R |only flashlight-0.9.0/flashlight/R/residuals_flashlight.R |only flashlight-0.9.0/flashlight/R/residuals_multiflashlight.R |only flashlight-0.9.0/flashlight/R/response.R |only flashlight-0.9.0/flashlight/man/all_identical.Rd |only flashlight-0.9.0/flashlight/man/auto_cut.Rd |only flashlight-0.9.0/flashlight/man/cut3.Rd |only flashlight-0.9.0/flashlight/man/grouped_center.Rd |only flashlight-0.9.0/flashlight/man/grouped_counts.Rd |only flashlight-0.9.0/flashlight/man/grouped_stats.Rd |only flashlight-0.9.0/flashlight/man/grouped_weighted_mean.Rd |only flashlight-0.9.0/flashlight/tests/testthat/tests-shap.R |only flashlight-0.9.0/flashlight/tests/testthat/tests-utils.R |only flashlight-1.0.0/flashlight/DESCRIPTION | 25 flashlight-1.0.0/flashlight/MD5 | 177 +--- flashlight-1.0.0/flashlight/NAMESPACE | 14 flashlight-1.0.0/flashlight/NEWS.md | 51 + flashlight-1.0.0/flashlight/R/aa_deprecated.R |only flashlight-1.0.0/flashlight/R/flashlight.R | 2 flashlight-1.0.0/flashlight/R/light_breakdown.R | 137 ++- flashlight-1.0.0/flashlight/R/light_check.R | 2 flashlight-1.0.0/flashlight/R/light_combine.R | 6 flashlight-1.0.0/flashlight/R/light_effects.R | 127 ++- flashlight-1.0.0/flashlight/R/light_global_surrogate.R | 72 + flashlight-1.0.0/flashlight/R/light_ice.R | 123 ++- flashlight-1.0.0/flashlight/R/light_importance.R | 348 +++++--- flashlight-1.0.0/flashlight/R/light_interaction.R | 110 +- flashlight-1.0.0/flashlight/R/light_performance.R | 124 ++- flashlight-1.0.0/flashlight/R/light_profile.R | 396 +++++++--- flashlight-1.0.0/flashlight/R/light_profile2d.R | 152 ++- flashlight-1.0.0/flashlight/R/light_recode.R | 57 - flashlight-1.0.0/flashlight/R/light_scatter.R | 137 ++- flashlight-1.0.0/flashlight/R/methods.R |only flashlight-1.0.0/flashlight/R/utils.R | 78 - flashlight-1.0.0/flashlight/R/utils_cut.R |only flashlight-1.0.0/flashlight/R/utils_grouped.R |only flashlight-1.0.0/flashlight/R/utils_plot.R |only flashlight-1.0.0/flashlight/R/zzz.R | 66 - flashlight-1.0.0/flashlight/README.md | 8 flashlight-1.0.0/flashlight/build/vignette.rds |binary flashlight-1.0.0/flashlight/inst/doc/flashlight.R | 4 flashlight-1.0.0/flashlight/inst/doc/flashlight.Rmd | 2 flashlight-1.0.0/flashlight/inst/doc/flashlight.html | 272 +++--- flashlight-1.0.0/flashlight/man/add_shap.Rd | 90 -- flashlight-1.0.0/flashlight/man/flashlight.Rd | 2 flashlight-1.0.0/flashlight/man/light_breakdown.Rd | 19 flashlight-1.0.0/flashlight/man/light_effects.Rd | 34 flashlight-1.0.0/flashlight/man/light_global_surrogate.Rd | 7 flashlight-1.0.0/flashlight/man/light_ice.Rd | 19 flashlight-1.0.0/flashlight/man/light_importance.Rd | 71 - flashlight-1.0.0/flashlight/man/light_interaction.Rd | 37 flashlight-1.0.0/flashlight/man/light_performance.Rd | 23 flashlight-1.0.0/flashlight/man/light_profile.Rd | 57 - flashlight-1.0.0/flashlight/man/light_profile2d.Rd | 36 flashlight-1.0.0/flashlight/man/light_recode.Rd | 58 - flashlight-1.0.0/flashlight/man/light_scatter.Rd | 34 flashlight-1.0.0/flashlight/man/most_important.Rd | 27 flashlight-1.0.0/flashlight/man/plot.light_breakdown.Rd | 7 flashlight-1.0.0/flashlight/man/plot.light_effects.Rd | 15 flashlight-1.0.0/flashlight/man/plot.light_global_surrogate.Rd | 7 flashlight-1.0.0/flashlight/man/plot.light_ice.Rd | 14 flashlight-1.0.0/flashlight/man/plot.light_importance.Rd | 14 flashlight-1.0.0/flashlight/man/plot.light_performance.Rd | 7 flashlight-1.0.0/flashlight/man/plot.light_profile.Rd | 9 flashlight-1.0.0/flashlight/man/plot.light_profile2d.Rd | 7 flashlight-1.0.0/flashlight/man/plot.light_scatter.Rd | 7 flashlight-1.0.0/flashlight/man/plot_counts.Rd | 54 - flashlight-1.0.0/flashlight/man/predict.flashlight.Rd | 2 flashlight-1.0.0/flashlight/man/predict.multiflashlight.Rd | 2 flashlight-1.0.0/flashlight/man/print.flashlight.Rd | 2 flashlight-1.0.0/flashlight/man/print.light.Rd | 2 flashlight-1.0.0/flashlight/man/print.multiflashlight.Rd | 2 flashlight-1.0.0/flashlight/man/residuals.flashlight.Rd | 2 flashlight-1.0.0/flashlight/man/residuals.multiflashlight.Rd | 2 flashlight-1.0.0/flashlight/man/response.Rd | 2 flashlight-1.0.0/flashlight/tests/testthat/tests-breakdown.R | 66 - flashlight-1.0.0/flashlight/tests/testthat/tests-eff.R | 188 ++-- flashlight-1.0.0/flashlight/tests/testthat/tests-globaltree.R | 26 flashlight-1.0.0/flashlight/tests/testthat/tests-grouped.R | 4 flashlight-1.0.0/flashlight/tests/testthat/tests-ice.R | 91 +- flashlight-1.0.0/flashlight/tests/testthat/tests-importance.R | 131 +-- flashlight-1.0.0/flashlight/tests/testthat/tests-interaction.R | 87 -- flashlight-1.0.0/flashlight/tests/testthat/tests-methods.R | 25 flashlight-1.0.0/flashlight/tests/testthat/tests-perf.R | 20 flashlight-1.0.0/flashlight/tests/testthat/tests-profile2d.R | 179 ++-- flashlight-1.0.0/flashlight/vignettes/flashlight.Rmd | 2 111 files changed, 2217 insertions(+), 1763 deletions(-)
Title: Simple Implementation of Semantic Versioning (SemVer)
Description: Simple implementation of Semantic Versioning 2.0.0 ('SemVer') on the
'vctrs' package. This package provides a simple way to create,
compare, and manipulate semantic versions in R. It is designed to be
lightweight and easy to use.
Author: Tatsuya Shima [aut, cre]
Maintainer: Tatsuya Shima <ts1s1andn@gmail.com>
Diff between smvr versions 0.2.1 dated 2025-08-19 and 0.2.2 dated 2025-10-13
smvr-0.2.1/smvr/tests/testthat/test-utils.R |only smvr-0.2.2/smvr/DESCRIPTION | 6 +++--- smvr-0.2.2/smvr/MD5 | 18 ++++++++++-------- smvr-0.2.2/smvr/NAMESPACE | 1 + smvr-0.2.2/smvr/NEWS.md | 6 ++++++ smvr-0.2.2/smvr/R/parse.R | 2 +- smvr-0.2.2/smvr/R/pattern.R |only smvr-0.2.2/smvr/R/utils.R | 16 ---------------- smvr-0.2.2/smvr/man/SEM_VER_PATTERN.Rd |only smvr-0.2.2/smvr/tests/testthat/_snaps/parse.md | 24 ++++++++++++++++++++++++ smvr-0.2.2/smvr/tests/testthat/test-parse.R | 2 ++ smvr-0.2.2/smvr/tests/testthat/test-pattern.R |only 12 files changed, 47 insertions(+), 28 deletions(-)
Title: High-Dimensional Aggregate Density Forecasts
Description: Provides a forecasting method that efficiently maps vast
numbers of (scalar-valued) signals into an aggregate density forecast
in a time-varying and computationally fast manner. The method proceeds
in two steps: First, it transforms a predictive signal into a density
forecast and, second, it combines the resulting candidate density
forecasts into an ultimate aggregate density forecast. For a detailed
explanation of the method, please refer to Adaemmer et al. (2025)
<doi:10.1080/07350015.2025.2526424>.
Author: Sven Lehmann [aut, cre, cph],
Philipp Adaemmer [aut],
Rainer Schuessler [aut]
Maintainer: Sven Lehmann <slehman5@uni-muenster.de>
Diff between hdflex versions 0.3.1 dated 2025-04-30 and 0.3.2 dated 2025-10-13
DESCRIPTION | 12 - MD5 | 18 +- NEWS.md | 4 R/ClassMethods.R | 50 +++----- README.md | 255 ++++++++++++++++++++++++++++++++++++------ build/partial.rdb |binary src/stsc.cpp | 6 src/stsc_parallel.cpp | 6 src/tvc.cpp | 2 tests/testthat/test-summary.R | 16 +- 10 files changed, 277 insertions(+), 92 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
the Hierarchical Mutual Information (Perotti et al. 2015)
<doi:10.1103/PhysRevE.92.062825>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands o [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg] ,
Roy Jonker [prg, cph] ,
Yong Yang [ctb, cph] ,
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.11.0 dated 2025-09-28 and 2.11.1 dated 2025-10-13
DESCRIPTION | 18 MD5 | 280 NAMESPACE | 442 - NEWS.md | 578 - R/HPart.R | 1 R/Information.R | 760 +- R/Islands.R | 156 R/MSTSegments.R | 158 R/Plot3.R | 168 R/Reduce.R | 134 R/TreeDist-package.R | 286 R/VisualizeMatching.R | 450 - R/cluster_stats.R | 548 - R/hierarchical_mutual_information.R | 358 - R/kmeanspp.R | 208 R/lap.R | 130 R/median.R | 172 R/parallel.R | 158 R/plot.R | 150 R/spectral_clustering.R | 162 R/tree_distance.R | 352 - R/tree_distance_info.R | 726 +- R/tree_distance_kendall-colijn.R | 456 - R/tree_distance_mast.R | 220 R/tree_distance_msd.R | 126 R/tree_distance_msi.R | 94 R/tree_distance_nni.R | 332 - R/tree_distance_nye.R | 416 - R/tree_distance_path.R | 216 R/tree_distance_rf.R | 310 R/tree_distance_spr.R | 312 R/tree_distance_utilities.R | 1266 +-- R/tree_information.R | 708 +- R/trustworthiness.R | 154 build/partial.rdb |binary inst/CITATION | 148 inst/REFERENCES.bib | 1458 ++-- inst/WORDLIST | 258 inst/apa-old-doi-prefix.csl | 3172 +++++----- inst/doc/Generalized-RF.Rmd | 586 - inst/doc/Generalized-RF.html | 5 inst/doc/Robinson-Foulds.Rmd | 718 +- inst/doc/Robinson-Foulds.html | 5 inst/doc/Using-TreeDist.Rmd | 304 inst/doc/Using-TreeDist.html | 13 inst/doc/compare-treesets.html | 5 inst/doc/different-leaves.Rmd | 194 inst/doc/different-leaves.html | 5 inst/doc/information.html | 5 inst/doc/landscapes.Rmd | 256 inst/doc/landscapes.html | 5 inst/doc/treespace.Rmd | 942 +- inst/doc/treespace.html | 5 inst/doc/using-distances.Rmd | 850 +- inst/doc/using-distances.html | 160 inst/treespace/app.R | 2964 ++++----- man/CalculateTreeDistance.Rd | 60 man/CompareAll.Rd | 106 man/Entropy.Rd | 66 man/GeneralizedRF.Rd | 128 man/HH.Rd | 24 man/HPart.Rd | 130 man/HierarchicalMutualInfo.Rd | 278 man/HierarchicalMutualInformation.Rd | 24 man/Islands.Rd | 158 man/JaccardRobinsonFoulds.Rd | 290 man/KMeansPP.Rd | 110 man/KendallColijn.Rd | 288 man/LAPJV.Rd | 126 man/MASTSize.Rd | 162 man/MSTSegments.Rd | 170 man/MapTrees.Rd | 250 man/MappingQuality.Rd | 112 man/MatchingSplitDistance.Rd | 206 man/NNIDist.Rd | 240 man/NormalizeInfo.Rd | 192 man/NyeSimilarity.Rd | 282 man/PathDist.Rd | 174 man/ReduceTrees.Rd | 102 man/ReportMatching.Rd | 54 man/Robinson-Foulds.Rd | 326 - man/SPRDist.Rd | 170 man/SpectralEigens.Rd | 102 man/StartParallel.Rd | 126 man/TreeDist-package.Rd | 290 man/TreeDistance.Rd | 644 +- man/VisualizeMatching.Rd | 178 man/clone.Rd | 65 man/cluster-statistics.Rd | 212 man/entropy_int.Rd | 40 man/median.multiPhylo.Rd | 188 src/hpart.cpp | 3 tests/benchmark/benchmark.R | 36 tests/testthat/_snaps/HPart/plot-hpart.svg | 96 tests/testthat/_snaps/MSTSegments/mst-example-plot.svg | 622 - tests/testthat/_snaps/Plot3/plotting-order.svg | 134 tests/testthat/_snaps/Plot3/simple-plot.svg | 134 tests/testthat/_snaps/VisualizeMatching/hidden-edge-labels.svg | 500 - tests/testthat/_snaps/VisualizeMatching/jrf-vm-matchzeros-false.svg | 348 - tests/testthat/_snaps/VisualizeMatching/rf-collapse-a-node.svg | 566 - tests/testthat/_snaps/VisualizeMatching/rf-collapse-and-change.svg | 554 - tests/testthat/_snaps/VisualizeMatching/rf-vm-single-splits-plainedges.svg | 352 - tests/testthat/_snaps/VisualizeMatching/test-vm.svg | 396 - tests/testthat/_snaps/VisualizeMatching/test-vmr.svg | 368 - tests/testthat/_snaps/VisualizeMatching/visualize-mci-matching.svg | 566 - tests/testthat/_snaps/VisualizeMatching/vm-one-rooted.svg | 196 tests/testthat/_snaps/VisualizeMatching/vm-unrooted.svg | 182 tests/testthat/_snaps/plot/test-lc-letters.svg | 162 tests/testthat/_snaps/plot/test-uc-letters.svg | 162 tests/testthat/_snaps/plot/test-with-space.svg | 162 tests/testthat/_snaps/plot/test-without-space.svg | 162 tests/testthat/test-HPart.R | 150 tests/testthat/test-Islands.R | 38 tests/testthat/test-MSTSegments.R | 94 tests/testthat/test-Plot3.R | 56 tests/testthat/test-Reduce.R | 132 tests/testthat/test-VisualizeMatching.R | 310 tests/testthat/test-cluster_stats.R | 170 tests/testthat/test-day_1985.cpp.r | 150 tests/testthat/test-different-tips.R | 166 tests/testthat/test-hierarchical_mutual_information.R | 124 tests/testthat/test-hmi.cpp.R | 316 tests/testthat/test-information.R | 196 tests/testthat/test-kmeanspp.R | 60 tests/testthat/test-lap.R | 720 +- tests/testthat/test-plot.R | 74 tests/testthat/test-spectral_clustering.R | 33 tests/testthat/test-split_info.R | 124 tests/testthat/test-tree_distance.R | 2038 +++--- tests/testthat/test-tree_distance_kc.R | 120 tests/testthat/test-tree_distance_nni.R | 396 - tests/testthat/test-tree_distance_path.R | 66 tests/testthat/test-tree_distance_spr.R | 324 - tests/testthat/test-tree_distance_utilities.R | 714 +- vignettes/Generalized-RF.Rmd | 586 - vignettes/Robinson-Foulds.Rmd | 718 +- vignettes/Using-TreeDist.Rmd | 304 vignettes/different-leaves.Rmd | 194 vignettes/landscapes.Rmd | 256 vignettes/treespace.Rmd | 942 +- vignettes/using-distances.Rmd | 850 +- 141 files changed, 22633 insertions(+), 22625 deletions(-)
Title: Rate Limiting for R
Description: Allows to limit the rate at which one or more functions can be called.
Author: Tarak Shah [aut, cre, cph]
Maintainer: Tarak Shah <tarak.shah@gmail.com>
Diff between ratelimitr versions 0.4.1 dated 2018-10-07 and 0.4.2 dated 2025-10-13
DESCRIPTION | 15 - MD5 | 24 - NEWS.md | 5 README.md | 65 ++-- build/vignette.rds |binary inst/doc/introduction.R | 10 inst/doc/introduction.html | 510 ++++++++++++++++++++++++++-------- tests/testthat/test-function-errors.R | 1 tests/testthat/test-limit-rate.R | 1 tests/testthat/test-network-lag.R | 1 tests/testthat/test-repeated-calls.R | 1 tests/testthat/test-reset.R | 2 tests/testthat/test-update-rate.R | 1 13 files changed, 479 insertions(+), 157 deletions(-)
Title: Extensible Framework for Data Pattern Exploration
Description: A framework for systematic exploration of
association rules (Agrawal et al., 1994, <https://www.vldb.org/conf/1994/P487.PDF>),
contrast patterns (Chen, 2022, <doi:10.48550/arXiv.2209.13556>),
emerging patterns (Dong et al., 1999, <doi:10.1145/312129.312191>),
subgroup discovery (Atzmueller, 2015, <doi:10.1002/widm.1144>),
and conditional correlations (Hájek, 1978, <doi:10.1007/978-3-642-66943-9>).
User-defined functions may also be supplied to guide custom pattern searches.
Supports both crisp (Boolean) and fuzzy data. Generates candidate conditions
expressed as elementary conjunctions, evaluates them on a dataset, and
inspects the induced sub-data for statistical, logical, or structural
properties such as associations, correlations, or contrasts. Includes methods
for visualization of logical structures and supports interactive exploration
through integrated Shiny applications.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between nuggets versions 2.0.0 dated 2025-10-13 and 2.0.1 dated 2025-10-13
nuggets-2.0.0/nuggets/R/dichotomize.R |only nuggets-2.0.0/nuggets/man/dichotomize.Rd |only nuggets-2.0.1/nuggets/DESCRIPTION | 8 ++++---- nuggets-2.0.1/nuggets/MD5 | 18 +++++++++--------- nuggets-2.0.1/nuggets/NAMESPACE | 3 ++- nuggets-2.0.1/nuggets/NEWS.md | 5 +++++ nuggets-2.0.1/nuggets/R/association_matrix.R |only nuggets-2.0.1/nuggets/R/explore-associations.R | 2 +- nuggets-2.0.1/nuggets/R/nuggets-package.R | 1 + nuggets-2.0.1/nuggets/R/testers.R | 20 +++++++++++++++++++- nuggets-2.0.1/nuggets/man/association_matrix.Rd |only nuggets-2.0.1/nuggets/src/Makevars | 7 ------- 12 files changed, 41 insertions(+), 23 deletions(-)
Title: Joint Mean-Covariance Models using 'Armadillo' and S4
Description: Fit joint mean-covariance models for longitudinal data. The models
and their components are represented using S4 classes and methods. The core
computational algorithms are implemented using the 'Armadillo' C++ library
for numerical linear algebra and 'RcppArmadillo' glue.
Author: Jianxin Pan [aut, cre],
Yi Pan [aut]
Maintainer: Jianxin Pan <jianxinpan@uic.edu.cn>
Diff between jmcm versions 0.2.4 dated 2021-01-12 and 0.2.5 dated 2025-10-13
jmcm-0.2.4/jmcm/src/bfgs_impl.h |only jmcm-0.2.4/jmcm/src/linesearch.h |only jmcm-0.2.4/jmcm/src/linesearch_impl.h |only jmcm-0.2.5/jmcm/DESCRIPTION | 11 jmcm-0.2.5/jmcm/MD5 | 78 +- jmcm-0.2.5/jmcm/NAMESPACE | 44 - jmcm-0.2.5/jmcm/R/AllClass.R | 46 - jmcm-0.2.5/jmcm/R/RcppExports.R | 156 ++-- jmcm-0.2.5/jmcm/R/jmcm.R | 961 ++++++++++++------------- jmcm-0.2.5/jmcm/R/jmcmControl.R | 60 - jmcm-0.2.5/jmcm/R/utilities.R | 1084 ++++++++++++++--------------- jmcm-0.2.5/jmcm/build/vignette.rds |binary jmcm-0.2.5/jmcm/inst/NEWS.Rd | 145 ++- jmcm-0.2.5/jmcm/inst/doc/jss2542.pdf.asis | 2 jmcm-0.2.5/jmcm/man/acd_estimation.Rd | 90 +- jmcm-0.2.5/jmcm/man/aids.Rd | 48 - jmcm-0.2.5/jmcm/man/bootcurve.Rd | 56 - jmcm-0.2.5/jmcm/man/cattle.Rd | 56 - jmcm-0.2.5/jmcm/man/getJMCM.Rd | 160 ++-- jmcm-0.2.5/jmcm/man/hpc_estimation.Rd | 90 +- jmcm-0.2.5/jmcm/man/jmcm.Rd | 100 +- jmcm-0.2.5/jmcm/man/jmcmControl.Rd | 58 - jmcm-0.2.5/jmcm/man/jmcmMod-class.Rd | 54 - jmcm-0.2.5/jmcm/man/mcd_estimation.Rd | 90 +- jmcm-0.2.5/jmcm/man/meanplot.Rd | 44 - jmcm-0.2.5/jmcm/man/modular.Rd | 128 +-- jmcm-0.2.5/jmcm/man/regressogram.Rd | 52 - jmcm-0.2.5/jmcm/man/show-jmcmMod-method.Rd | 32 jmcm-0.2.5/jmcm/src/Makevars | 4 jmcm-0.2.5/jmcm/src/Makevars.win | 4 jmcm-0.2.5/jmcm/src/RcppExports.cpp | 17 jmcm-0.2.5/jmcm/src/acd.h | 148 +-- jmcm-0.2.5/jmcm/src/bfgs.h | 211 +++++ jmcm-0.2.5/jmcm/src/external.cpp | 177 +--- jmcm-0.2.5/jmcm/src/hpc.h | 184 ++-- jmcm-0.2.5/jmcm/src/jmcm_base.h | 373 +++------ jmcm-0.2.5/jmcm/src/jmcm_config.h |only jmcm-0.2.5/jmcm/src/jmcm_fit.h | 199 +---- jmcm-0.2.5/jmcm/src/mcd.h | 145 +-- jmcm-0.2.5/jmcm/tests/testthat.R | 8 jmcm-0.2.5/jmcm/tests/testthat/test-jmcm.R | 96 +- jmcm-0.2.5/jmcm/vignettes/jss2542.pdf.asis | 2 42 files changed, 2530 insertions(+), 2683 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and
much more.
Author: Gabor Csardi [aut] ,
Tamas Nepusz [aut] ,
Vincent Traag [aut] ,
Szabolcs Horvat [aut] ,
Fabio Zanini [aut] ,
Daniel Noom [aut],
Kirill Mueller [aut, cre] ,
Michael Antonov [ctb],
Chan Zuckerberg Initiative [fnd] ,
David Schoch [aut] ,
Maelle Salmon [a [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between igraph versions 2.1.4 dated 2025-01-23 and 2.2.0 dated 2025-10-13
igraph-2.1.4/igraph/R/data_frame.R |only igraph-2.1.4/igraph/R/demo.R |only igraph-2.1.4/igraph/R/layout_drl.R |only igraph-2.1.4/igraph/R/structural.properties.R |only igraph-2.1.4/igraph/R/test.R |only igraph-2.1.4/igraph/demo |only igraph-2.1.4/igraph/man/igraph_demo.Rd |only igraph-2.1.4/igraph/man/igraphdemo.Rd |only igraph-2.1.4/igraph/src/sources.mk |only igraph-2.1.4/igraph/src/vendor/cigraph/vendor/f2c/comptry.bat |only igraph-2.1.4/igraph/src/vendor/cigraph/vendor/f2c/f2c.h0 |only igraph-2.1.4/igraph/src/vendor/cigraph/vendor/f2c/f2ch.add |only igraph-2.1.4/igraph/src/vendor/cigraph/vendor/f2c/libf2c.lbc |only igraph-2.1.4/igraph/src/vendor/cigraph/vendor/f2c/libf2c.sy |only igraph-2.1.4/igraph/src/vendor/cigraph/vendor/f2c/makefile.sy |only igraph-2.1.4/igraph/src/vendor/cigraph/vendor/f2c/makefile.u |only igraph-2.1.4/igraph/src/vendor/cigraph/vendor/f2c/makefile.vc |only igraph-2.1.4/igraph/src/vendor/cigraph/vendor/f2c/makefile.wat |only 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igraph-2.1.4/igraph/tests/testthat/test-graph.subisomorphic.lad.R |only igraph-2.1.4/igraph/tests/testthat/test-graph.subisomorphic.vf2.R |only igraph-2.1.4/igraph/tests/testthat/test-graphNEL.R |only igraph-2.1.4/igraph/tests/testthat/test-graphlets.R |only igraph-2.1.4/igraph/tests/testthat/test-handler.R |only igraph-2.1.4/igraph/tests/testthat/test-hsbm.R |only igraph-2.1.4/igraph/tests/testthat/test-identical_graphs.R |only igraph-2.1.4/igraph/tests/testthat/test-igraph.options.R |only igraph-2.1.4/igraph/tests/testthat/test-index-es.R |only igraph-2.1.4/igraph/tests/testthat/test-indexing2.R |only igraph-2.1.4/igraph/tests/testthat/test-indexing3.R |only igraph-2.1.4/igraph/tests/testthat/test-is.chordal.R |only igraph-2.1.4/igraph/tests/testthat/test-isomorphism.R |only igraph-2.1.4/igraph/tests/testthat/test-label.propagation.community.R |only igraph-2.1.4/igraph/tests/testthat/test-laplacian.spectral.embedding.R |only igraph-2.1.4/igraph/tests/testthat/test-largest.cliques.R |only igraph-2.1.4/igraph/tests/testthat/test-leading.eigenvector.community.R |only igraph-2.1.4/igraph/tests/testthat/test-leiden.R |only igraph-2.1.4/igraph/tests/testthat/test-make_graph.R |only igraph-2.1.4/igraph/tests/testthat/test-make_lattice.R |only igraph-2.1.4/igraph/tests/testthat/test-minimal.st.separators.R |only igraph-2.1.4/igraph/tests/testthat/test-minimum.size.separators.R |only igraph-2.1.4/igraph/tests/testthat/test-modularity_matrix.R |only igraph-2.1.4/igraph/tests/testthat/test-multilevel.community.R |only igraph-2.1.4/igraph/tests/testthat/test-notable.R |only igraph-2.1.4/igraph/tests/testthat/test-old-data-type.R |only igraph-2.1.4/igraph/tests/testthat/test-operators3.R |only igraph-2.1.4/igraph/tests/testthat/test-operators4.R |only igraph-2.1.4/igraph/tests/testthat/test-optimal.community.R |only igraph-2.1.4/igraph/tests/testthat/test-pajek.R |only igraph-2.1.4/igraph/tests/testthat/test-read_graph.R |only 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igraph-2.2.0/igraph/man/graph_from_graphdb.Rd | 6 igraph-2.2.0/igraph/man/graph_from_incidence_matrix.Rd | 2 igraph-2.2.0/igraph/man/graph_from_isomorphism_class.Rd | 2 igraph-2.2.0/igraph/man/graph_from_lcf.Rd | 17 igraph-2.2.0/igraph/man/graphlet_basis.Rd | 32 igraph-2.2.0/igraph/man/graphlets.candidate.basis.Rd | 2 igraph-2.2.0/igraph/man/graphlets.project.Rd | 2 igraph-2.2.0/igraph/man/greedy_vertex_coloring.Rd | 2 igraph-2.2.0/igraph/man/grg.game.Rd | 2 igraph-2.2.0/igraph/man/growing.random.game.Rd | 2 igraph-2.2.0/igraph/man/harmonic_centrality.Rd | 2 igraph-2.2.0/igraph/man/has.multiple.Rd | 4 igraph-2.2.0/igraph/man/has_eulerian_path.Rd | 19 igraph-2.2.0/igraph/man/hits_scores.Rd | 30 igraph-2.2.0/igraph/man/hrg.Rd | 2 igraph-2.2.0/igraph/man/hrg.consensus.Rd | 2 igraph-2.2.0/igraph/man/hrg.create.Rd | 2 igraph-2.2.0/igraph/man/hrg.dendrogram.Rd | 2 igraph-2.2.0/igraph/man/hrg.fit.Rd | 2 igraph-2.2.0/igraph/man/hrg.game.Rd | 2 igraph-2.2.0/igraph/man/hrg.predict.Rd | 2 igraph-2.2.0/igraph/man/hrg_tree.Rd | 2 igraph-2.2.0/igraph/man/hub.score.Rd | 2 igraph-2.2.0/igraph/man/igraph-attribute-combination.Rd | 75 igraph-2.2.0/igraph/man/igraph-dollar.Rd | 1 igraph-2.2.0/igraph/man/igraph-es-indexing.Rd | 42 igraph-2.2.0/igraph/man/igraph-vs-attributes.Rd | 1 igraph-2.2.0/igraph/man/igraph-vs-indexing.Rd | 36 igraph-2.2.0/igraph/man/igraph.console.Rd | 2 igraph-2.2.0/igraph/man/igraph.from.graphNEL.Rd | 2 igraph-2.2.0/igraph/man/igraph.options.Rd | 2 igraph-2.2.0/igraph/man/igraph.sample.Rd | 2 igraph-2.2.0/igraph/man/igraph.shape.noclip.Rd | 2 igraph-2.2.0/igraph/man/igraph.shape.noplot.Rd | 2 igraph-2.2.0/igraph/man/igraph.to.graphNEL.Rd | 2 igraph-2.2.0/igraph/man/igraph.version.Rd | 4 igraph-2.2.0/igraph/man/igraph_options.Rd | 104 igraph-2.2.0/igraph/man/igraph_version.Rd | 14 igraph-2.2.0/igraph/man/independence.number.Rd | 5 igraph-2.2.0/igraph/man/independent.vertex.sets.Rd | 5 igraph-2.2.0/igraph/man/induced.subgraph.Rd | 4 igraph-2.2.0/igraph/man/infomap.community.Rd | 2 igraph-2.2.0/igraph/man/interconnected.islands.game.Rd | 2 igraph-2.2.0/igraph/man/is.bipartite.Rd | 2 igraph-2.2.0/igraph/man/is.chordal.Rd | 2 igraph-2.2.0/igraph/man/is.connected.Rd | 4 igraph-2.2.0/igraph/man/is.dag.Rd | 2 igraph-2.2.0/igraph/man/is.degree.sequence.Rd | 2 igraph-2.2.0/igraph/man/is.directed.Rd | 2 igraph-2.2.0/igraph/man/is.graphical.degree.sequence.Rd | 2 igraph-2.2.0/igraph/man/is.hierarchical.Rd | 2 igraph-2.2.0/igraph/man/is.igraph.Rd | 2 igraph-2.2.0/igraph/man/is.loop.Rd | 4 igraph-2.2.0/igraph/man/is.matching.Rd | 4 igraph-2.2.0/igraph/man/is.maximal.matching.Rd | 4 igraph-2.2.0/igraph/man/is.minimal.separator.Rd | 2 igraph-2.2.0/igraph/man/is.multiple.Rd | 4 igraph-2.2.0/igraph/man/is.mutual.Rd | 4 igraph-2.2.0/igraph/man/is.named.Rd | 2 igraph-2.2.0/igraph/man/is.separator.Rd | 2 igraph-2.2.0/igraph/man/is.simple.Rd | 2 igraph-2.2.0/igraph/man/is.weighted.Rd | 2 igraph-2.2.0/igraph/man/is_acyclic.Rd | 12 igraph-2.2.0/igraph/man/is_biconnected.Rd | 2 igraph-2.2.0/igraph/man/is_chordal.Rd | 17 igraph-2.2.0/igraph/man/is_complete.Rd |only igraph-2.2.0/igraph/man/is_dag.Rd | 8 igraph-2.2.0/igraph/man/is_forest.Rd | 16 igraph-2.2.0/igraph/man/is_graphical.Rd | 2 igraph-2.2.0/igraph/man/is_min_separator.Rd | 2 igraph-2.2.0/igraph/man/is_separator.Rd | 2 igraph-2.2.0/igraph/man/is_tree.Rd | 14 igraph-2.2.0/igraph/man/isomorphic.Rd | 28 igraph-2.2.0/igraph/man/ivs.Rd | 18 igraph-2.2.0/igraph/man/k.regular.game.Rd | 2 igraph-2.2.0/igraph/man/k_shortest_paths.Rd | 15 igraph-2.2.0/igraph/man/knn.Rd | 20 igraph-2.2.0/igraph/man/label.propagation.community.Rd | 2 igraph-2.2.0/igraph/man/laplacian_matrix.Rd | 6 igraph-2.2.0/igraph/man/largest.cliques.Rd | 5 igraph-2.2.0/igraph/man/largest.independent.vertex.sets.Rd | 5 igraph-2.2.0/igraph/man/lastcit.game.Rd | 2 igraph-2.2.0/igraph/man/layout.auto.Rd | 2 igraph-2.2.0/igraph/man/layout.bipartite.Rd | 2 igraph-2.2.0/igraph/man/layout.circle.Rd | 2 igraph-2.2.0/igraph/man/layout.davidson.harel.Rd | 2 igraph-2.2.0/igraph/man/layout.drl.Rd | 4 igraph-2.2.0/igraph/man/layout.fruchterman.reingold.Rd | 2 igraph-2.2.0/igraph/man/layout.gem.Rd | 2 igraph-2.2.0/igraph/man/layout.graphopt.Rd | 2 igraph-2.2.0/igraph/man/layout.grid.Rd | 2 igraph-2.2.0/igraph/man/layout.kamada.kawai.Rd | 2 igraph-2.2.0/igraph/man/layout.lgl.Rd | 2 igraph-2.2.0/igraph/man/layout.mds.Rd | 2 igraph-2.2.0/igraph/man/layout.merge.Rd | 2 igraph-2.2.0/igraph/man/layout.norm.Rd | 2 igraph-2.2.0/igraph/man/layout.random.Rd | 2 igraph-2.2.0/igraph/man/layout.reingold.tilford.Rd | 2 igraph-2.2.0/igraph/man/layout.sphere.Rd | 2 igraph-2.2.0/igraph/man/layout.star.Rd | 2 igraph-2.2.0/igraph/man/layout.sugiyama.Rd | 2 igraph-2.2.0/igraph/man/layout_nicely.Rd | 14 igraph-2.2.0/igraph/man/layout_randomly.Rd | 2 igraph-2.2.0/igraph/man/layout_with_dh.Rd | 14 igraph-2.2.0/igraph/man/layout_with_drl.Rd | 115 igraph-2.2.0/igraph/man/layout_with_fr.Rd | 2 igraph-2.2.0/igraph/man/layout_with_kk.Rd | 8 igraph-2.2.0/igraph/man/layout_with_sugiyama.Rd | 23 igraph-2.2.0/igraph/man/leading.eigenvector.community.Rd | 2 igraph-2.2.0/igraph/man/line.graph.Rd | 2 igraph-2.2.0/igraph/man/list.edge.attributes.Rd | 2 igraph-2.2.0/igraph/man/list.graph.attributes.Rd | 2 igraph-2.2.0/igraph/man/list.vertex.attributes.Rd | 2 igraph-2.2.0/igraph/man/local_scan.Rd | 3 igraph-2.2.0/igraph/man/make_clusters.Rd | 14 igraph-2.2.0/igraph/man/make_empty_graph.Rd | 2 igraph-2.2.0/igraph/man/make_from_prufer.Rd | 2 igraph-2.2.0/igraph/man/make_graph.Rd | 223 igraph-2.2.0/igraph/man/make_lattice.Rd | 2 igraph-2.2.0/igraph/man/matching.Rd | 25 igraph-2.2.0/igraph/man/max_cardinality.Rd | 20 igraph-2.2.0/igraph/man/max_flow.Rd | 58 igraph-2.2.0/igraph/man/maxcohesion.Rd | 2 igraph-2.2.0/igraph/man/maximal.cliques.Rd | 5 igraph-2.2.0/igraph/man/maximal.cliques.count.Rd | 5 igraph-2.2.0/igraph/man/maximal.independent.vertex.sets.Rd | 5 igraph-2.2.0/igraph/man/maximal_ivs.Rd | 5 igraph-2.2.0/igraph/man/maximum.bipartite.matching.Rd | 4 igraph-2.2.0/igraph/man/maximum.cardinality.search.Rd | 2 igraph-2.2.0/igraph/man/min_cut.Rd | 30 igraph-2.2.0/igraph/man/min_separators.Rd | 2 igraph-2.2.0/igraph/man/min_st_separators.Rd | 2 igraph-2.2.0/igraph/man/minimal.st.separators.Rd | 2 igraph-2.2.0/igraph/man/minimum.size.separators.Rd | 2 igraph-2.2.0/igraph/man/minimum.spanning.tree.Rd | 2 igraph-2.2.0/igraph/man/mod.matrix.Rd | 2 igraph-2.2.0/igraph/man/motifs.Rd | 5 igraph-2.2.0/igraph/man/multilevel.community.Rd | 2 igraph-2.2.0/igraph/man/neighborhood.size.Rd | 7 igraph-2.2.0/igraph/man/no.clusters.Rd | 2 igraph-2.2.0/igraph/man/optimal.community.Rd | 2 igraph-2.2.0/igraph/man/page.rank.Rd | 2 igraph-2.2.0/igraph/man/page_rank.Rd | 22 igraph-2.2.0/igraph/man/path.length.hist.Rd | 2 igraph-2.2.0/igraph/man/permute.Rd | 2 igraph-2.2.0/igraph/man/permute.vertices.Rd | 2 igraph-2.2.0/igraph/man/piecewise.layout.Rd | 2 igraph-2.2.0/igraph/man/plot.common.Rd | 514 igraph-2.2.0/igraph/man/plot.igraph.Rd | 10 igraph-2.2.0/igraph/man/plot.sir.Rd | 2 igraph-2.2.0/igraph/man/plotHierarchy.Rd | 2 igraph-2.2.0/igraph/man/power.law.fit.Rd | 2 igraph-2.2.0/igraph/man/power_centrality.Rd | 2 igraph-2.2.0/igraph/man/predict_edges.Rd | 16 igraph-2.2.0/igraph/man/preference.game.Rd | 2 igraph-2.2.0/igraph/man/printer_callback.Rd | 25 igraph-2.2.0/igraph/man/radius.Rd | 2 igraph-2.2.0/igraph/man/random_walk.Rd | 2 igraph-2.2.0/igraph/man/read.graph.Rd | 2 igraph-2.2.0/igraph/man/read_graph.Rd | 121 igraph-2.2.0/igraph/man/realize_bipartite_degseq.Rd | 2 igraph-2.2.0/igraph/man/realize_degseq.Rd | 2 igraph-2.2.0/igraph/man/reciprocity.Rd | 5 igraph-2.2.0/igraph/man/remove.edge.attribute.Rd | 2 igraph-2.2.0/igraph/man/remove.graph.attribute.Rd | 2 igraph-2.2.0/igraph/man/remove.vertex.attribute.Rd | 2 igraph-2.2.0/igraph/man/reverse_edges.Rd | 2 igraph-2.2.0/igraph/man/rglplot.Rd | 6 igraph-2.2.0/igraph/man/roxygen/meta.R | 2 igraph-2.2.0/igraph/man/running.mean.Rd | 2 igraph-2.2.0/igraph/man/sample_.Rd | 1 igraph-2.2.0/igraph/man/sample_bipartite.Rd | 13 igraph-2.2.0/igraph/man/sample_bipartite_gnm.Rd |only igraph-2.2.0/igraph/man/sample_chung_lu.Rd | 19 igraph-2.2.0/igraph/man/sample_correlated_gnp.Rd | 3 igraph-2.2.0/igraph/man/sample_correlated_gnp_pair.Rd | 3 igraph-2.2.0/igraph/man/sample_degseq.Rd | 1 igraph-2.2.0/igraph/man/sample_dot_product.Rd | 3 igraph-2.2.0/igraph/man/sample_fitness.Rd | 3 igraph-2.2.0/igraph/man/sample_fitness_pl.Rd | 3 igraph-2.2.0/igraph/man/sample_forestfire.Rd | 5 igraph-2.2.0/igraph/man/sample_gnm.Rd | 1 igraph-2.2.0/igraph/man/sample_gnp.Rd | 1 igraph-2.2.0/igraph/man/sample_grg.Rd | 3 igraph-2.2.0/igraph/man/sample_growing.Rd | 3 igraph-2.2.0/igraph/man/sample_hierarchical_sbm.Rd | 11 igraph-2.2.0/igraph/man/sample_hrg.Rd | 2 igraph-2.2.0/igraph/man/sample_islands.Rd | 3 igraph-2.2.0/igraph/man/sample_k_regular.Rd | 3 igraph-2.2.0/igraph/man/sample_last_cit.Rd | 1 igraph-2.2.0/igraph/man/sample_motifs.Rd | 3 igraph-2.2.0/igraph/man/sample_pa.Rd | 1 igraph-2.2.0/igraph/man/sample_pa_age.Rd | 1 igraph-2.2.0/igraph/man/sample_pref.Rd | 1 igraph-2.2.0/igraph/man/sample_sbm.Rd | 3 igraph-2.2.0/igraph/man/sample_smallworld.Rd | 1 igraph-2.2.0/igraph/man/sample_spanning_tree.Rd | 2 igraph-2.2.0/igraph/man/sample_traits_callaway.Rd | 1 igraph-2.2.0/igraph/man/sample_tree.Rd | 3 igraph-2.2.0/igraph/man/sbm.game.Rd | 2 igraph-2.2.0/igraph/man/scan_stat.Rd | 15 igraph-2.2.0/igraph/man/set.edge.attribute.Rd | 2 igraph-2.2.0/igraph/man/set.graph.attribute.Rd | 2 igraph-2.2.0/igraph/man/set.vertex.attribute.Rd | 2 igraph-2.2.0/igraph/man/set_edge_attr.Rd | 1 igraph-2.2.0/igraph/man/set_graph_attr.Rd | 1 igraph-2.2.0/igraph/man/set_vertex_attr.Rd | 1 igraph-2.2.0/igraph/man/set_vertex_attrs.Rd |only igraph-2.2.0/igraph/man/shapes.Rd | 61 igraph-2.2.0/igraph/man/shortest.paths.Rd | 4 igraph-2.2.0/igraph/man/showtrace.Rd | 2 igraph-2.2.0/igraph/man/similarity.Rd | 2 igraph-2.2.0/igraph/man/simple_cycles.Rd |only igraph-2.2.0/igraph/man/simplify.Rd | 2 igraph-2.2.0/igraph/man/sir.Rd | 25 igraph-2.2.0/igraph/man/spectrum.Rd | 16 igraph-2.2.0/igraph/man/spinglass.community.Rd | 2 igraph-2.2.0/igraph/man/stCuts.Rd | 2 igraph-2.2.0/igraph/man/stMincuts.Rd | 2 igraph-2.2.0/igraph/man/st_cuts.Rd | 22 igraph-2.2.0/igraph/man/st_min_cuts.Rd | 26 igraph-2.2.0/igraph/man/static.fitness.game.Rd | 2 igraph-2.2.0/igraph/man/static.power.law.game.Rd | 2 igraph-2.2.0/igraph/man/strength.Rd | 2 igraph-2.2.0/igraph/man/subcomponent.Rd | 3 igraph-2.2.0/igraph/man/subgraph.Rd | 3 igraph-2.2.0/igraph/man/subgraph.centrality.Rd | 2 igraph-2.2.0/igraph/man/subgraph.edges.Rd | 4 igraph-2.2.0/igraph/man/subgraph_isomorphic.Rd | 47 igraph-2.2.0/igraph/man/subgraph_isomorphisms.Rd | 47 igraph-2.2.0/igraph/man/tkplot.canvas.Rd | 2 igraph-2.2.0/igraph/man/tkplot.center.Rd | 2 igraph-2.2.0/igraph/man/tkplot.close.Rd | 2 igraph-2.2.0/igraph/man/tkplot.export.postscript.Rd | 2 igraph-2.2.0/igraph/man/tkplot.fit.to.screen.Rd | 2 igraph-2.2.0/igraph/man/tkplot.getcoords.Rd | 2 igraph-2.2.0/igraph/man/tkplot.off.Rd | 2 igraph-2.2.0/igraph/man/tkplot.reshape.Rd | 2 igraph-2.2.0/igraph/man/tkplot.rotate.Rd | 2 igraph-2.2.0/igraph/man/tkplot.setcoords.Rd | 2 igraph-2.2.0/igraph/man/to_prufer.Rd | 2 igraph-2.2.0/igraph/man/topo_sort.Rd | 3 igraph-2.2.0/igraph/man/topological.sort.Rd | 4 igraph-2.2.0/igraph/man/transitivity.Rd | 46 igraph-2.2.0/igraph/man/triad.census.Rd | 2 igraph-2.2.0/igraph/man/triad_census.Rd | 62 igraph-2.2.0/igraph/man/unfold.tree.Rd | 4 igraph-2.2.0/igraph/man/unfold_tree.Rd | 16 igraph-2.2.0/igraph/man/vertex.connectivity.Rd | 2 igraph-2.2.0/igraph/man/vertex.disjoint.paths.Rd | 2 igraph-2.2.0/igraph/man/vertex.shape.pie.Rd | 50 igraph-2.2.0/igraph/man/vertex.shapes.Rd | 2 igraph-2.2.0/igraph/man/vertex_attr-set.Rd | 1 igraph-2.2.0/igraph/man/vertex_attr.Rd | 1 igraph-2.2.0/igraph/man/vertex_attr_names.Rd | 1 igraph-2.2.0/igraph/man/vertex_connectivity.Rd | 3 igraph-2.2.0/igraph/man/voronoi_cells.Rd | 18 igraph-2.2.0/igraph/man/walktrap.community.Rd | 2 igraph-2.2.0/igraph/man/watts.strogatz.game.Rd | 2 igraph-2.2.0/igraph/man/weighted_cliques.Rd | 5 igraph-2.2.0/igraph/man/which_multiple.Rd | 5 igraph-2.2.0/igraph/man/which_mutual.Rd | 5 igraph-2.2.0/igraph/man/write.graph.Rd | 2 igraph-2.2.0/igraph/man/write_graph.Rd | 92 igraph-2.2.0/igraph/src/Makevars.in | 18 igraph-2.2.0/igraph/src/Makevars.ucrt | 18 igraph-2.2.0/igraph/src/Makevars.win | 18 igraph-2.2.0/igraph/src/README.md | 2 igraph-2.2.0/igraph/src/cpp11.cpp | 56 igraph-2.2.0/igraph/src/cpp11.dd |only igraph-2.2.0/igraph/src/cpprinterface.dd |only igraph-2.2.0/igraph/src/init.dd |only igraph-2.2.0/igraph/src/rinterface.c | 2290 ++-- igraph-2.2.0/igraph/src/rinterface.dd |only igraph-2.2.0/igraph/src/rinterface_extra.c | 190 igraph-2.2.0/igraph/src/rinterface_extra.dd |only igraph-2.2.0/igraph/src/rrandom.dd |only igraph-2.2.0/igraph/src/simpleraytracer.dd |only igraph-2.2.0/igraph/src/sources-glpk.mk | 2 igraph-2.2.0/igraph/src/sources-glue-c.mk |only igraph-2.2.0/igraph/src/sources-glue-cpp.mk |only igraph-2.2.0/igraph/src/sources-igraph.mk |only igraph-2.2.0/igraph/src/sources-mini-gmp.mk | 2 igraph-2.2.0/igraph/src/uuid.c |only igraph-2.2.0/igraph/src/uuid.dd |only igraph-2.2.0/igraph/src/vendor/cigraph/ACKNOWLEDGEMENTS.md | 57 igraph-2.2.0/igraph/src/vendor/cigraph/CHANGELOG.md | 1986 +-- igraph-2.2.0/igraph/src/vendor/cigraph/CMakeLists.txt | 22 igraph-2.2.0/igraph/src/vendor/cigraph/CONTRIBUTING.md | 14 igraph-2.2.0/igraph/src/vendor/cigraph/CONTRIBUTORS.md | 183 igraph-2.2.0/igraph/src/vendor/cigraph/CONTRIBUTORS.txt | 11 igraph-2.2.0/igraph/src/vendor/cigraph/azure-pipelines.yml | 17 igraph-2.2.0/igraph/src/vendor/cigraph/etc/cmake/CodeCoverage.cmake | 142 igraph-2.2.0/igraph/src/vendor/cigraph/etc/cmake/compilers.cmake | 7 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph.h | 5 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_arpack.h | 3 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_bitset.h | 2 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_bitset_list.h | 2 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_coloring.h | 4 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_components.h | 15 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_constants.h | 7 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_constructors.h | 7 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_cycles.h | 52 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_decls.h | 20 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_error.h | 34 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_layout.h | 1 igraph-2.2.0/igraph/src/vendor/cigraph/include/igraph_memory.h | 2 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igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlaqr3.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlaqr4.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlaqr5.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlaqtr.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlar1v.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarf.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarfb.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarfg.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarft.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarfx.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarnv.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarra.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarrb.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarrc.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarrd.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarre.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarrf.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarrj.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarrk.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarrr.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlarrv.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlartg.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlaruv.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlascl.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlaset.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlasq2.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlasq3.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlasq4.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlasq5.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlasq6.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlasr.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlasrt.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlassq.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlaswp.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlasy2.c | 12 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dlatrd.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dmout.c | 58 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dnaitr.c | 906 - igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dnapps.c | 660 - igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dnaup2.c | 805 - igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dnaupd.c | 1008 - igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dnconv.c | 168 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dneigh.c | 350 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dneupd.c | 1278 +- 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igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dsteqr.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dsterf.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dstqrb.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dswap.c | 12 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dsyevr.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dsymv.c | 11 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dsyr2.c | 11 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dsyr2k.c | 11 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dsyrk.c | 11 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dsytd2.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dsytrd.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dtrevc.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dtrexc.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dtrmm.c | 11 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/dtrmv.c | 11 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igraph-2.2.0/igraph/src/vendor/cigraph/vendor/lapack/xerbla.c | 2 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/CMakeLists.txt | 1 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/arithmetic_ansi.h | 4 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/arithmetic_sse_double.h | 20 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/arithmetic_sse_float.h | 21 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/gss.c | 1 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/gss.h | 10 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/hzeta.c | 13 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/hzeta.h | 10 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/kolmogorov.h | 11 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/lbfgs.c | 191 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/lbfgs.h | 55 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/plfit.c | 3 igraph-2.2.0/igraph/src/vendor/cigraph/vendor/plfit/plfit.h | 49 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Title: Efficient Estimation of Bid-Ask Spreads from Open, High, Low,
and Close Prices
Description: Implements the efficient estimator of bid-ask spreads from open, high, low, and close prices
described in Ardia, Guidotti, & Kroencke (JFE, 2024) <doi:10.1016/j.jfineco.2024.103916>.
It also provides an implementation of the estimators described in
Roll (JF, 1984) <doi:10.1111/j.1540-6261.1984.tb03897.x>,
Corwin & Schultz (JF, 2012) <doi:10.1111/j.1540-6261.2012.01729.x>,
and Abdi & Ranaldo (RFS, 2017) <doi:10.1093/rfs/hhx084>.
Author: Emanuele Guidotti [aut, cre] ,
David Ardia [ctb] ,
Tim Kroencke [ctb]
Maintainer: Emanuele Guidotti <emanuele.guidotti@usi.ch>
Diff between bidask versions 2.1.4 dated 2025-02-26 and 2.1.5 dated 2025-10-13
DESCRIPTION | 13 +++--- MD5 | 10 ++-- inst/doc/bidask.R | 12 ++++- inst/doc/bidask.Rmd | 13 +++++- inst/doc/bidask.html | 108 ++++++++++++++++++++++++++------------------------- vignettes/bidask.Rmd | 13 +++++- 6 files changed, 100 insertions(+), 69 deletions(-)
Title: Fusing Machine Learning in R
Description: Recent technological advances have enable the simultaneous collection
of multi-omics data i.e., different types or modalities of molecular data,
presenting challenges for integrative prediction modeling due to the heterogeneous,
high-dimensional nature and possible missing modalities of some individuals.
We introduce this package for late integrative prediction modeling, enabling
modality-specific variable selection and prediction modeling, followed by the
aggregation of the modality-specific predictions to train a final meta-model.
This package facilitates conducting late integration predictive modeling in a
systematic, structured, and reproducible way.
Author: Cesaire J. K. Fouodo [aut, cre]
Maintainer: Cesaire J. K. Fouodo <cesaire.kuetefouodo@uni-luebeck.de>
Diff between fuseMLR versions 0.0.1 dated 2024-12-17 and 0.0.2 dated 2025-10-13
DESCRIPTION | 6 - MD5 | 26 +++---- R/Data.R | 10 ++ R/Training.R | 2 R/bestLayerLearner.R | 11 ++- R/trainingFunctions.R | 6 - README.md | 21 ++++- build/vignette.rds |binary inst/doc/fuseMLR.R | 164 +++++++++++++++++++++++----------------------- inst/doc/fuseMLR.Rmd | 2 inst/doc/fuseMLR.html | 109 +++++++++++++++--------------- man/createTrainLayer.Rd | 2 tests/testthat/Rplots.pdf |binary vignettes/fuseMLR.Rmd | 2 14 files changed, 195 insertions(+), 166 deletions(-)
Title: Collection of Functions for Working with Age Intervals
Description: Provides a collection of efficient functions for working with
individual ages and corresponding intervals. These include functions for
conversion from an age to an interval, aggregation of ages with associated
counts in to intervals and the splitting of interval counts based on
specified age distributions.
Author: Tim Taylor [aut, cre, cph] ,
Edwin van Leeuwen [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ageutils versions 0.1.0 dated 2025-07-08 and 0.1.1 dated 2025-10-13
ageutils-0.1.0/ageutils/man/figures |only ageutils-0.1.1/ageutils/DESCRIPTION | 13 ageutils-0.1.1/ageutils/MD5 | 40 ageutils-0.1.1/ageutils/NEWS.md | 6 ageutils-0.1.1/ageutils/R/cut_ages.R | 12 ageutils-0.1.1/ageutils/R/defunct.R | 2 ageutils-0.1.1/ageutils/R/reaggregate_counts.R | 52 - ageutils-0.1.1/ageutils/R/reaggregate_rates.R | 27 ageutils-0.1.1/ageutils/R/utils.R | 18 ageutils-0.1.1/ageutils/README.md | 14 ageutils-0.1.1/ageutils/build |only ageutils-0.1.1/ageutils/inst |only ageutils-0.1.1/ageutils/man/cut_ages.Rd | 8 ageutils-0.1.1/ageutils/man/reaggregate_counts.Rd | 4 ageutils-0.1.1/ageutils/tests/testthat/_snaps/cut_ages.md | 16 ageutils-0.1.1/ageutils/tests/testthat/_snaps/reaggregate_counts.md | 204 ++++ ageutils-0.1.1/ageutils/tests/testthat/helpers.R | 54 - ageutils-0.1.1/ageutils/tests/testthat/test-breaks_to_interval.R | 12 ageutils-0.1.1/ageutils/tests/testthat/test-cut_ages.R | 12 ageutils-0.1.1/ageutils/tests/testthat/test-reaggregate_counts.R | 458 +++++++++- ageutils-0.1.1/ageutils/tests/testthat/test-reaggregate_rates.R | 14 ageutils-0.1.1/ageutils/vignettes |only 22 files changed, 813 insertions(+), 153 deletions(-)
Title: Spatial Deformation and Dimension Expansion Gaussian Processes
Description: Methods for fitting nonstationary Gaussian process models by spatial deformation, as introduced by Sampson and Guttorp (1992) <doi:10.1080/01621459.1992.10475181>, and by dimension expansion, as introduced by Bornn et al. (2012) <doi:10.1080/01621459.2011.646919>. Low-rank thin-plate regression splines, as developed in Wood, S.N. (2003) <doi:10.1111/1467-9868.00374>, are used to either transform co-ordinates or create new latent dimensions.
Author: Ben Youngman [aut, cre]
Maintainer: Ben Youngman <b.youngman@exeter.ac.uk>
Diff between deform versions 1.0.0 dated 2023-10-19 and 1.0.1 dated 2025-10-13
DESCRIPTION | 22 +++++++++++----------- MD5 | 15 ++++++++------- NAMESPACE | 7 +------ NEWS.md |only build/partial.rdb |binary src/Makevars | 19 +------------------ src/Makevars.win | 19 +------------------ src/cnorm.cpp | 12 ++++++------ src/tnorm.cpp | 6 +++--- 9 files changed, 31 insertions(+), 69 deletions(-)
Title: Penalized Synthetic Control Estimation
Description: Estimate penalized synthetic control models
and perform hold-out validation to determine their
penalty parameter. This method is based on the work by
Abadie & L'Hour (2021) <doi:10.1080/01621459.2021.1971535>.
Penalized synthetic controls smoothly interpolate between
one-to-one matching and the synthetic control method.
Author: Erik-Jan van Kesteren [cre, aut] ,
Isaac Slaughter [ctb]
Maintainer: Erik-Jan van Kesteren <e.vankesteren1@uu.nl>
Diff between pensynth versions 0.5.1 dated 2024-03-28 and 0.8.1 dated 2025-10-13
pensynth-0.5.1/pensynth/man/simulate_data.Rd |only pensynth-0.8.1/pensynth/DESCRIPTION | 17 pensynth-0.8.1/pensynth/MD5 | 49 + pensynth-0.8.1/pensynth/NAMESPACE | 3 pensynth-0.8.1/pensynth/R/convex_hull.R | 11 pensynth-0.8.1/pensynth/R/cv_pensynth.R | 191 ++++++- pensynth-0.8.1/pensynth/R/examples/example_cv_pensynth.R | 2 pensynth-0.8.1/pensynth/R/examples/example_placebo_test.R | 2 pensynth-0.8.1/pensynth/R/examples/example_showcase.R |only pensynth-0.8.1/pensynth/R/examples/example_simulate.R | 14 pensynth-0.8.1/pensynth/R/examples/example_simulate_factor.R |only pensynth-0.8.1/pensynth/R/pensynth.R | 44 + pensynth-0.8.1/pensynth/R/placebo_test.R | 84 +-- pensynth-0.8.1/pensynth/R/simulate_data.R | 299 +++++++++-- pensynth-0.8.1/pensynth/man/cv_pensynth.Rd | 28 - pensynth-0.8.1/pensynth/man/get_mse_cvpensynth.Rd |only pensynth-0.8.1/pensynth/man/in_convex_hull.Rd | 6 pensynth-0.8.1/pensynth/man/mvrarnorm.Rd |only pensynth-0.8.1/pensynth/man/pensynth.Rd | 13 pensynth-0.8.1/pensynth/man/placebo_test.Rd | 16 pensynth-0.8.1/pensynth/man/plot.cvpensynth.Rd | 4 pensynth-0.8.1/pensynth/man/plot.pensynthtest.Rd | 4 pensynth-0.8.1/pensynth/man/rarnorm.Rd |only pensynth-0.8.1/pensynth/man/simulate_data_factor.Rd |only pensynth-0.8.1/pensynth/man/simulate_data_synth.Rd |only pensynth-0.8.1/pensynth/tests/testthat/Rplots.pdf |only pensynth-0.8.1/pensynth/tests/testthat/test-cvpensynth.R | 12 pensynth-0.8.1/pensynth/tests/testthat/test-pensynth.R | 13 pensynth-0.8.1/pensynth/tests/testthat/test-placebo_test.R | 33 - pensynth-0.8.1/pensynth/tests/testthat/test-simulate_data.R | 38 + 30 files changed, 704 insertions(+), 179 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Hosszejni and Kastner (2021) <doi:10.18637/jss.v100.i12> and Kastner (2016) <doi:10.18637/jss.v069.i05> and the package examples.
Author: Darjus Hosszejni [aut, cre] ,
Gregor Kastner [aut]
Maintainer: Darjus Hosszejni <darjus.hosszejni@icloud.com>
Diff between stochvol versions 3.2.7 dated 2025-08-20 and 3.2.8 dated 2025-10-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/doc/article.pdf |binary inst/doc/article2.pdf |binary src/utils_main.h | 2 +- 6 files changed, 13 insertions(+), 9 deletions(-)
Title: An Extended Mixed-Effects Framework for Meta-Analysis
Description: A collection of functions to perform various meta-analytical models
through a unified mixed-effects framework, including standard univariate
fixed and random-effects meta-analysis and meta-regression, and non-standard
extensions such as multivariate, multilevel, longitudinal, and dose-response
models.
Author: Antonio Gasparrini [cre, aut, cph] ,
Francesco Sera [aut]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between mixmeta versions 1.2.0 dated 2021-10-16 and 1.2.2 dated 2025-10-13
mixmeta-1.2.0/mixmeta/R/getFullFormula.R |only mixmeta-1.2.2/mixmeta/DESCRIPTION | 30 + mixmeta-1.2.2/mixmeta/MD5 | 40 +- mixmeta-1.2.2/mixmeta/NAMESPACE | 202 +++++------ mixmeta-1.2.2/mixmeta/NEWS.md | 468 +++++++++++++-------------- mixmeta-1.2.2/mixmeta/R/formula.mixmeta.R | 34 - mixmeta-1.2.2/mixmeta/R/getFixTerms.R | 52 +-- mixmeta-1.2.2/mixmeta/R/getFullformula.R |only mixmeta-1.2.2/mixmeta/R/mixmeta.R | 258 +++++++------- mixmeta-1.2.2/mixmeta/R/terms.mixmeta.R | 34 - mixmeta-1.2.2/mixmeta/inst/CITATION | 39 +- mixmeta-1.2.2/mixmeta/inst/NEWS | 468 +++++++++++++-------------- mixmeta-1.2.2/mixmeta/man/alcohol.Rd | 206 +++++------ mixmeta-1.2.2/mixmeta/man/coef.mixmeta.Rd | 106 +++--- mixmeta-1.2.2/mixmeta/man/gliomas.Rd | 184 +++++----- mixmeta-1.2.2/mixmeta/man/mixmeta-package.Rd | 260 +++++++-------- mixmeta-1.2.2/mixmeta/man/mixmeta.control.Rd | 2 mixmeta-1.2.2/mixmeta/man/mixmeta.ml.Rd | 2 mixmeta-1.2.2/mixmeta/man/mixmetaObject.Rd | 168 ++++----- mixmeta-1.2.2/mixmeta/man/ml.igls.Rd | 2 mixmeta-1.2.2/mixmeta/man/predict.mixmeta.Rd | 148 ++++---- mixmeta-1.2.2/mixmeta/man/terms.mixmeta.Rd | 100 ++--- 22 files changed, 1417 insertions(+), 1386 deletions(-)
Title: Workflows for Health Technology Assessments in R using Discrete
EveNts
Description: Toolkit to support and perform discrete event simulations with and without
resource constraints in the context of health technology assessments (HTA).
The package focuses on cost-effectiveness modelling and aims to be submission-ready
to relevant HTA bodies in alignment with 'NICE TSD 15'
<https://sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>.
More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.
Author: Javier Sanchez Alvarez [aut, cre],
Gabriel Lemyre [ctb],
Valerie Aponte Ribero [ctb]
Maintainer: Javier Sanchez Alvarez <javiersanchezeco@gmail.com>
Diff between WARDEN versions 1.2.5 dated 2025-07-10 and 2.0.0 dated 2025-10-13
DESCRIPTION | 14 MD5 | 118 +- NAMESPACE | 19 NEWS.md | 221 ++- R/RcppExports.R |only R/WARDEN-package.R |only R/calculator_f.R | 581 ++-------- R/engine_helper_f.R | 303 +++-- R/input_f.R | 1827 ++++++++++++++++++++------------ R/old_R_nowincpp.R |only R/run_engine.R | 324 ++--- R/run_engine_constrained.R |only R/run_sim.R | 324 +---- R/run_sim_parallel.R | 289 +---- README.md | 12 build/vignette.rds |binary inst/doc/example_ssd.R | 23 inst/doc/example_ssd.Rmd | 89 - inst/doc/example_ssd.html | 586 ++++------ man/add_item.Rd | 47 man/add_item2.Rd | 30 man/ast_as_list.Rd | 126 +- man/disc_cycle_v.Rd | 8 man/disc_instant_v.Rd | 4 man/disc_ongoing_v.Rd | 4 man/discrete_resource_clone.Rd |only man/dot-resource_discrete_from_xptr.Rd |only man/extract_elements_from_list.Rd | 122 +- man/get_event.Rd |only man/has_event.Rd |only man/luck_adj.Rd | 2 man/modify_event.Rd | 25 man/modify_item.Rd | 2 man/new_event.Rd | 22 man/next_event.Rd |only man/next_event_pt.Rd |only man/pick_val_v.Rd | 10 man/pop_and_return_event.Rd |only man/pop_event.Rd |only man/print.resource_discrete.Rd |only man/qcond_exp.Rd | 4 man/qcond_gamma.Rd | 4 man/qcond_gompertz.Rd | 4 man/qcond_llogis.Rd | 4 man/qcond_lnorm.Rd | 4 man/qcond_norm.Rd | 4 man/qcond_weibull.Rd | 4 man/qcond_weibullPH.Rd | 4 man/qgamma_mse.Rd | 54 man/qtimecov.Rd | 24 man/queue_create.Rd |only man/queue_empty.Rd |only man/queue_size.Rd |only man/rcond_gompertz_lu.Rd | 4 man/remove_event.Rd |only man/resource_discrete.Rd |only man/rpoisgamma_rcpp.Rd |only man/run_sim.Rd | 23 man/run_sim_parallel.Rd | 23 man/shared_input.Rd |only man/with_write_flags_lang.Rd |only src |only tests/testthat/test-input_f.R | 397 ++++-- tests/testthat/test-resource_discrete.R |only tests/testthat/test_model_runs.R | 604 ++++++++++ tests/testthat/test_queues.R |only vignettes/example_ssd.Rmd | 89 - 67 files changed, 3609 insertions(+), 2773 deletions(-)
Title: Simple Methods for Calculating and Backtesting Value at Risk and
Expected Shortfall
Description: Enables the user to calculate Value at Risk (VaR)
and Expected Shortfall (ES) by means of various types of historical
simulation. Currently plain-, age-, volatility-weighted- and filtered
historical simulation are implemented in this package. Volatility weighting
can be carried out via an exponentially weighted moving average model
(EWMA) or other GARCH-type models. The performance can be assessed via
Traffic Light Test, Coverage Tests and Loss Functions. The methods of the
package are described in Gurrola-Perez, P. and Murphy, D. (2015)
<https://EconPapers.repec.org/RePEc:boe:boeewp:0525> as well as McNeil, J.,
Frey, R., and Embrechts, P. (2015) <https://ideas.repec.org/b/pup/pbooks/10496.html>.
Author: Sebastian Letmathe [aut, cre]
Maintainer: Sebastian Letmathe <sebastian.let@yahoo.com>
Diff between quarks versions 1.1.4 dated 2024-06-08 and 1.1.5 dated 2025-10-13
DESCRIPTION | 12 ++++----- MD5 | 8 +++--- NEWS.md | 5 ++++ R/Welcome.R | 2 - R/runFTSdata.R | 69 ++++++++++++++++++++++++++++++++++++++++++--------------- 5 files changed, 68 insertions(+), 28 deletions(-)
Title: Extensible Framework for Data Pattern Exploration
Description: A framework for systematic exploration of
association rules (Agrawal et al., 1994, <https://www.vldb.org/conf/1994/P487.PDF>),
contrast patterns (Chen, 2022, <doi:10.48550/arXiv.2209.13556>),
emerging patterns (Dong et al., 1999, <doi:10.1145/312129.312191>),
subgroup discovery (Atzmueller, 2015, <doi:10.1002/widm.1144>),
and conditional correlations (Hájek, 1978, <doi:10.1007/978-3-642-66943-9>).
User-defined functions may also be supplied to guide custom pattern searches.
Supports both crisp (Boolean) and fuzzy data. Generates candidate conditions
expressed as elementary conjunctions, evaluates them on a dataset, and
inspects the induced sub-data for statistical, logical, or structural
properties such as associations, correlations, or contrasts. Includes methods
for visualization of logical structures and supports interactive exploration
through integrated Shiny applications.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between nuggets versions 1.4.0 dated 2025-01-08 and 2.0.0 dated 2025-10-13
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nuggets-2.0.0/nuggets/man/var_names.Rd | 41 nuggets-2.0.0/nuggets/src/AlignedVector.h | 9 nuggets-2.0.0/nuggets/src/Makevars | 26 nuggets-2.0.0/nuggets/src/RcppExports.cpp | 227 ++ nuggets-2.0.0/nuggets/src/algebra.cpp |only nuggets-2.0.0/nuggets/src/common.h | 39 nuggets-2.0.0/nuggets/src/dig.cpp | 99 - nuggets-2.0.0/nuggets/src/dig/BaseChain.h |only nuggets-2.0.0/nuggets/src/dig/BinomialCoefficients.h |only nuggets-2.0.0/nuggets/src/dig/BitChain.h | 100 - nuggets-2.0.0/nuggets/src/dig/CallbackCaller.h |only nuggets-2.0.0/nuggets/src/dig/ChainCollection.h |only nuggets-2.0.0/nuggets/src/dig/Clause.h |only nuggets-2.0.0/nuggets/src/dig/CombinatorialProgress.h |only nuggets-2.0.0/nuggets/src/dig/Config.h | 288 +-- nuggets-2.0.0/nuggets/src/dig/Digger.h | 441 +--- nuggets-2.0.0/nuggets/src/dig/FloatChain.h |only nuggets-2.0.0/nuggets/src/dig/FubitChain.h |only nuggets-2.0.0/nuggets/src/dig/Selector.h |only nuggets-2.0.0/nuggets/src/dig/SimdChain.h |only nuggets-2.0.0/nuggets/src/dig/TautologyTree.h |only nuggets-2.0.0/nuggets/src/raisedcos.cpp | 17 nuggets-2.0.0/nuggets/src/test-dig-BinomialCoefficients.cpp |only nuggets-2.0.0/nuggets/src/test-dig-BitChain.cpp | 126 + nuggets-2.0.0/nuggets/src/test-dig-ChainCollection.cpp |only nuggets-2.0.0/nuggets/src/test-dig-Config.cpp |only nuggets-2.0.0/nuggets/src/test-dig-FloatChain.cpp |only nuggets-2.0.0/nuggets/src/test-dig-FubitChain.cpp |only nuggets-2.0.0/nuggets/src/test-dig-Selector.cpp |only nuggets-2.0.0/nuggets/src/test-dig-TautologyTree.cpp |only nuggets-2.0.0/nuggets/src/triangle.cpp | 17 nuggets-2.0.0/nuggets/tests/testthat/test-algebra.R |only nuggets-2.0.0/nuggets/tests/testthat/test-bound_range.R |only nuggets-2.0.0/nuggets/tests/testthat/test-dig.R | 876 ++++++++- nuggets-2.0.0/nuggets/tests/testthat/test-dig_associations.R | 320 +++ nuggets-2.0.0/nuggets/tests/testthat/test-dig_baseline_contrasts.R | 89 - nuggets-2.0.0/nuggets/tests/testthat/test-dig_complement_contrasts.R | 88 nuggets-2.0.0/nuggets/tests/testthat/test-dig_correlations.R | 64 nuggets-2.0.0/nuggets/tests/testthat/test-dig_grid.R | 155 + nuggets-2.0.0/nuggets/tests/testthat/test-dig_paired_baseline_contrasts.R | 86 nuggets-2.0.0/nuggets/tests/testthat/test-dig_tautologies.R |only nuggets-2.0.0/nuggets/tests/testthat/test-extract_cols.R | 6 nuggets-2.0.0/nuggets/tests/testthat/test-fire.R |only nuggets-2.0.0/nuggets/tests/testthat/test-geom_diamond.R |only nuggets-2.0.0/nuggets/tests/testthat/test-is_almost_constant.R |only nuggets-2.0.0/nuggets/tests/testthat/test-is_condition.R |only nuggets-2.0.0/nuggets/tests/testthat/test-parse_condition.R |only nuggets-2.0.0/nuggets/tests/testthat/test-partition.R | 161 + nuggets-2.0.0/nuggets/tests/testthat/test-remove_almost_constant.R |only nuggets-2.0.0/nuggets/tests/testthat/test-remove_ill_conditions.R |only nuggets-2.0.0/nuggets/tests/testthat/test-shorten_condition.R |only nuggets-2.0.0/nuggets/tests/testthat/test-ui-aboutTable.R |only nuggets-2.0.0/nuggets/tests/testthat/test-ui-conditionFilterModule.R |only nuggets-2.0.0/nuggets/tests/testthat/test-ui-creationParamsTable.R |only nuggets-2.0.0/nuggets/tests/testthat/test-ui-formatRulesForTable.R |only nuggets-2.0.0/nuggets/tests/testthat/test-ui-highlightCondition.R |only nuggets-2.0.0/nuggets/tests/testthat/test-ui-infoBox.R |only nuggets-2.0.0/nuggets/tests/testthat/test-ui-infoTable.R |only nuggets-2.0.0/nuggets/tests/testthat/test-ui-numericFilterModule.R |only nuggets-2.0.0/nuggets/tests/testthat/test-ui-rulebaseTable.R |only nuggets-2.0.0/nuggets/tests/testthat/test-values.R |only nuggets-2.0.0/nuggets/tests/testthat/test-var_grid.R | 50 nuggets-2.0.0/nuggets/vignettes/nuggets.Rmd | 684 +++++-- 203 files changed, 6831 insertions(+), 2636 deletions(-)
Title: Continuous-Time Mediation
Description: Computes effect sizes, standard errors, and confidence intervals
for total, direct, and indirect effects in continuous-time mediation models
as described in Pesigan, Russell, and Chow (2025) <doi:10.1037/met0000779>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph] ,
Michael A. Russell [ctb] ,
Sy-Miin Chow [ctb]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between cTMed versions 1.0.7 dated 2025-10-02 and 1.0.8 dated 2025-10-13
DESCRIPTION | 39 +++++--- MD5 | 160 +++++++++++++++++------------------ NEWS.md | 6 + R/cTMed-boot-beta-std.R | 2 R/cTMed-boot-beta.R | 2 R/cTMed-boot-indirect-central.R | 2 R/cTMed-boot-med-std.R | 2 R/cTMed-boot-med.R | 2 R/cTMed-boot-total-central.R | 2 R/cTMed-delta-beta-std.R | 2 R/cTMed-delta-beta.R | 2 R/cTMed-delta-indirect-central.R | 2 R/cTMed-delta-med-std.R | 2 R/cTMed-delta-med.R | 2 R/cTMed-delta-total-central.R | 2 R/cTMed-direct-std.R | 2 R/cTMed-direct.R | 2 R/cTMed-indirect-central.R | 2 R/cTMed-indirect-std.R | 2 R/cTMed-indirect.R | 2 R/cTMed-mc-beta-std.R | 2 R/cTMed-mc-beta.R | 2 R/cTMed-mc-indirect-central.R | 2 R/cTMed-mc-med-std.R | 2 R/cTMed-mc-med.R | 2 R/cTMed-mc-phi-sigma.R | 2 R/cTMed-mc-phi.R | 2 R/cTMed-mc-total-central.R | 2 R/cTMed-med-std.R | 2 R/cTMed-med.R | 2 R/cTMed-plot-beta-ci-dot.R | 2 R/cTMed-plot-central-ci-dot.R | 2 R/cTMed-plot-central-dot.R | 2 R/cTMed-plot-med-ci-dot.R | 2 R/cTMed-plot-med-dot.R | 2 R/cTMed-plot-trajectory-dot.R | 2 R/cTMed-posterior-beta.R | 8 + R/cTMed-posterior-indirect-central.R | 2 R/cTMed-posterior-med.R | 2 R/cTMed-posterior-total-central.R | 2 R/cTMed-total-central.R | 2 R/cTMed-total-std.R | 2 R/cTMed-total.R | 2 R/cTMed-trajectory.R | 2 inst/CITATION | 36 +++++-- man/BootBeta.Rd | 4 man/BootBetaStd.Rd | 4 man/BootIndirectCentral.Rd | 4 man/BootMed.Rd | 4 man/BootMedStd.Rd | 4 man/BootTotalCentral.Rd | 4 man/DeltaBeta.Rd | 4 man/DeltaBetaStd.Rd | 4 man/DeltaIndirectCentral.Rd | 4 man/DeltaMed.Rd | 4 man/DeltaMedStd.Rd | 4 man/DeltaTotalCentral.Rd | 4 man/Direct.Rd | 4 man/DirectStd.Rd | 4 man/Indirect.Rd | 4 man/IndirectCentral.Rd | 4 man/IndirectStd.Rd | 4 man/MCBeta.Rd | 4 man/MCBetaStd.Rd | 4 man/MCIndirectCentral.Rd | 4 man/MCMed.Rd | 4 man/MCMedStd.Rd | 4 man/MCPhi.Rd | 4 man/MCPhiSigma.Rd | 4 man/MCTotalCentral.Rd | 4 man/Med.Rd | 4 man/MedStd.Rd | 4 man/PosteriorBeta.Rd | 12 +- man/PosteriorIndirectCentral.Rd | 4 man/PosteriorMed.Rd | 4 man/PosteriorTotalCentral.Rd | 4 man/Total.Rd | 4 man/TotalCentral.Rd | 4 man/TotalStd.Rd | 4 man/Trajectory.Rd | 4 man/cTMed-package.Rd | 10 +- 81 files changed, 265 insertions(+), 222 deletions(-)
Title: Soil Organic Carbon and CN Ratio Driven Nitrogen Modelling
Framework
Description: Can be used to model the fate of soil organic carbon and soil organic nitrogen and to calculate N mineralisation rates. Provides a framework that numerically solves differential equations of soil organic carbon models based on first-order kinetics and extends these models to include the nitrogen component. The name 'sorcering' is an acronym for 'Soil ORganic Carbon & CN Ratio drIven Nitrogen modellinG framework'.
Author: Marc Scherstjanoi [aut, cre],
Rene Dechow [aut]
Maintainer: Marc Scherstjanoi <marc.scherstjanoi@thuenen.de>
Diff between sorcering versions 1.2.0 dated 2025-06-02 and 1.2.1 dated 2025-10-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ build/partial.rdb |binary build/sorcering.pdf |binary build/stage23.rdb |binary inst/doc/sorcering.pdf |binary src/sorcering.cpp | 30 +++++++++++------------------- 8 files changed, 27 insertions(+), 30 deletions(-)
Title: Streamlined Data Processing Tools for Genomic Selection
Description: A toolkit for genomic selection in animal breeding with
emphasis on multi-breed and multi-trait nested grouping operations.
Streamlines iterative analysis workflows when working with 'ASReml-R'
package. Includes utility functions for phenotypic data processing
commonly used by animal breeders.
Author: Guo Meng [aut, cre],
Guo Meng [cph]
Maintainer: Guo Meng <tony2015116@163.com>
Diff between mintyr versions 0.1.0 dated 2024-12-13 and 0.1.1 dated 2025-10-13
mintyr-0.1.0/mintyr/R/data.R |only mintyr-0.1.0/mintyr/R/fires.R |only mintyr-0.1.0/mintyr/R/nedaps.R |only mintyr-0.1.0/mintyr/data |only mintyr-0.1.0/mintyr/man/fire.Rd |only mintyr-0.1.0/mintyr/man/fires.Rd |only mintyr-0.1.0/mintyr/man/nedap.Rd |only mintyr-0.1.0/mintyr/man/nedaps.Rd |only mintyr-0.1.1/mintyr/DESCRIPTION | 15 mintyr-0.1.1/mintyr/MD5 | 38 mintyr-0.1.1/mintyr/NAMESPACE | 5 mintyr-0.1.1/mintyr/NEWS.md | 6 mintyr-0.1.1/mintyr/R/export_nest.R | 374 +++- mintyr-0.1.1/mintyr/R/import_csv.R | 75 mintyr-0.1.1/mintyr/README.md | 35 mintyr-0.1.1/mintyr/inst/doc/get-started.R | 12 mintyr-0.1.1/mintyr/inst/doc/get-started.Rmd | 25 mintyr-0.1.1/mintyr/inst/doc/get-started.html | 1436 ++++++++---------- mintyr-0.1.1/mintyr/man/export_nest.Rd | 143 + mintyr-0.1.1/mintyr/man/figures/cheatsheet.svg |only mintyr-0.1.1/mintyr/man/import_csv.Rd | 46 mintyr-0.1.1/mintyr/tests/testthat/test-export_nest.R | 135 + mintyr-0.1.1/mintyr/tests/testthat/test-import_csv.R | 70 mintyr-0.1.1/mintyr/vignettes/get-started.Rmd | 25 24 files changed, 1357 insertions(+), 1083 deletions(-)
Title: Generation of Virtual Species Distributions
Description: Provides a framework for generating virtual species distributions,
a procedure increasingly used in ecology to improve species distribution
models. This package integrates the existing methodological approaches
with the objective of generating virtual species distributions with
increased ecological realism.
Author: Boris Leroy [cre, aut],
Christine N. Meynard [ctb],
Celine Bellard [ctb],
Franck Courchamp [ctb],
Robin Delsol [ctb],
Willson Gaul [ctb]
Maintainer: Boris Leroy <leroy.boris@gmail.com>
Diff between virtualspecies versions 1.6 dated 2023-09-26 and 1.6.1 dated 2025-10-13
DESCRIPTION | 39 +++++++++++++++++++++++++++++++-------- MD5 | 30 +++++++++++++++--------------- R/convertToPA.R | 2 +- R/generateRandomSp.R | 2 +- R/generateSpFromFun.R | 2 +- R/generateSpFromPCA.R | 2 +- R/limitDistribution.R | 2 +- R/sampleOccurrences.R | 2 +- R/virtualspecies-package.R | 9 +++++---- man/convertToPA.Rd | 2 +- man/generateRandomSp.Rd | 2 +- man/generateSpFromFun.Rd | 2 +- man/generateSpFromPCA.Rd | 2 +- man/limitDistribution.Rd | 2 +- man/sampleOccurrences.Rd | 2 +- man/virtualspecies-package.Rd | 16 +++++++++++++--- 16 files changed, 76 insertions(+), 42 deletions(-)
More information about virtualspecies at CRAN
Permanent link
Title: Non-Invasive Pretty Printing of R Code
Description: Pretty-prints R code without changing the user's formatting
intent.
Author: Kirill Mueller [aut] ,
Lorenz Walthert [cre, aut],
Indrajeet Patil [aut]
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between styler versions 1.10.3 dated 2024-04-07 and 1.11.0 dated 2025-10-13
styler-1.10.3/styler/man/calls_sys.Rd |only styler-1.10.3/styler/man/extend_if_comment.Rd |only styler-1.10.3/styler/man/generate_test_samples.Rd |only styler-1.10.3/styler/man/is_double_indent_function_declaration.Rd |only styler-1.10.3/styler/man/set_arg_write_tree.Rd |only styler-1.10.3/styler/man/set_space_around_op.Rd |only styler-1.10.3/styler/man/unindent_fun_dec.Rd |only styler-1.10.3/styler/man/wrap_if_else_while_for_fun_multi_line_in_curly.Rd |only styler-1.10.3/styler/tests/testthat/indention_multiple/curly_and_round_in_tree |only styler-1.11.0/styler/DESCRIPTION | 26 styler-1.11.0/styler/MD5 | 377 +++++----- styler-1.11.0/styler/NEWS.md | 117 ++- styler-1.11.0/styler/R/addins.R | 4 styler-1.11.0/styler/R/communicate.R | 9 styler-1.11.0/styler/R/compat-dplyr.R | 12 styler-1.11.0/styler/R/detect-alignment-utils.R | 2 styler-1.11.0/styler/R/environments.R | 10 styler-1.11.0/styler/R/io.R | 6 styler-1.11.0/styler/R/options.R |only styler-1.11.0/styler/R/parse.R | 37 styler-1.11.0/styler/R/roxygen-examples-find.R | 11 styler-1.11.0/styler/R/roxygen-examples-parse.R | 4 styler-1.11.0/styler/R/rules-indention.R | 22 styler-1.11.0/styler/R/rules-line-breaks.R | 128 ++- styler-1.11.0/styler/R/rules-spaces.R | 25 styler-1.11.0/styler/R/rules-tokens.R | 4 styler-1.11.0/styler/R/set-assert-args.R | 16 styler-1.11.0/styler/R/style-guides.R | 46 - 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Title: SHAP Visualizations
Description: Visualizations for SHAP (SHapley Additive exPlanations), such
as waterfall plots, force plots, various types of importance plots,
dependence plots, and interaction plots. These plots act on a
'shapviz' object created from a matrix of SHAP values and a
corresponding feature dataset. Wrappers for the R packages 'xgboost',
'lightgbm', 'fastshap', 'shapr', 'h2o', 'treeshap', 'DALEX', and
'kernelshap' are added for convenience. By separating visualization
and computation, it is possible to display factor variables in graphs,
even if the SHAP values are calculated by a model that requires
numerical features. The plots are inspired by those provided by the
'shap' package in Python, but there is no dependency on it.
Author: Michael Mayer [aut, cre],
Adrian Stando [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between shapviz versions 0.10.2 dated 2025-07-17 and 0.10.3 dated 2025-10-13
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ R/sv_force.R | 2 +- R/sv_importance.R | 10 ++++------ R/sv_interaction.R | 6 ++---- R/sv_waterfall.R | 2 +- build/vignette.rds |binary inst/doc/basic_use.html | 23 ++++++++++++----------- inst/doc/geographic.html | 13 +++++++------ inst/doc/multiple_output.html | 13 +++++++------ inst/doc/tidymodels.html | 5 +++-- 12 files changed, 57 insertions(+), 51 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.3.1 dated 2025-09-18 and 1.3.2 dated 2025-10-13
DESCRIPTION | 10 MD5 | 38 - NAMESPACE | 1 NEWS.md | 10 R/classConceptSetExpression.R | 35 R/cohortCodelist.R | 94 +- R/columns.R | 3 R/compute.R | 38 - R/exportSummarisedResult.R | 25 R/logger.R | 95 ++ R/validate.R | 23 README.md | 67 - inst/doc/cohorts.html | 9 inst/doc/logging.html | 52 - inst/doc/summarised_result.html | 894 +++++++++++------------- man/cohortCodelist.Rd | 13 man/exportSummarisedResult.Rd | 9 tests/testthat/test-classConceptSetExpression.R | 10 tests/testthat/test-cohortCodelist.R | 73 + tests/testthat/test-logger.R | 29 20 files changed, 923 insertions(+), 605 deletions(-)
Title: Work with Hyperspectral Data, i.e. Spectra + Meta Information
(Spatial, Time, Concentration, ...)
Description: Comfortable ways to work with hyperspectral data sets.
I.e. spatially or time-resolved spectra, or spectra with any other kind
of information associated with each of the spectra. The spectra can be data
as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS,
etc. More generally, any data that is recorded over a discretized variable,
e.g. absorbance = f(wavelength), stored as a vector of absorbance values
for discrete wavelengths is suitable.
Author: Claudia Beleites [aut, cre, dtc] ,
Valter Sergo [aut],
Alois Bonifacio [ctb, dtc],
Marcel Dahms [ctb],
Bjoern Egert [ctb],
Simon Fuller [ctb],
Vilmantas Gegzna [aut],
Rustam Guliev [ctb],
Bryan A. Hanson [ctb],
Michael Hermes [ctb],
Martin Kammer [dtc [...truncated...]
Maintainer: Claudia Beleites <Claudia.Beleites@chemometrix.gmbh>
Diff between hyperSpec versions 0.100.2 dated 2024-05-01 and 0.100.3 dated 2025-10-13
hyperSpec-0.100.2/hyperSpec/tests/testthat/_snaps |only hyperSpec-0.100.3/hyperSpec/DESCRIPTION | 14 ++-- hyperSpec-0.100.3/hyperSpec/MD5 | 60 +++++++------------ hyperSpec-0.100.3/hyperSpec/R/all.equal.R | 8 +- hyperSpec-0.100.3/hyperSpec/R/decomposition.R | 2 hyperSpec-0.100.3/hyperSpec/R/extract.R | 2 hyperSpec-0.100.3/hyperSpec/R/hyperspec-package.R | 3 hyperSpec-0.100.3/hyperSpec/R/map.sel.poly.R | 4 - hyperSpec-0.100.3/hyperSpec/R/read.ENVI.R | 4 - hyperSpec-0.100.3/hyperSpec/R/read.jdx.R | 2 hyperSpec-0.100.3/hyperSpec/R/read.txt.Witec.R | 5 - hyperSpec-0.100.3/hyperSpec/R/split.string.R | 2 hyperSpec-0.100.3/hyperSpec/build/vignette.rds |binary hyperSpec-0.100.3/hyperSpec/inst/doc/hyperSpec.html | 33 ++-------- hyperSpec-0.100.3/hyperSpec/man/Comparison.Rd | 2 hyperSpec-0.100.3/hyperSpec/man/extractreplace.Rd | 2 hyperSpec-0.100.3/hyperSpec/man/hyperSpec-package.Rd | 2 hyperSpec-0.100.3/hyperSpec/man/map-sel-poly.Rd | 4 - hyperSpec-0.100.3/hyperSpec/man/plotspc.Rd | 2 hyperSpec-0.100.3/hyperSpec/man/qplotmix.Rd | 4 - hyperSpec-0.100.3/hyperSpec/man/read.ENVI.Rd | 6 - hyperSpec-0.100.3/hyperSpec/man/read.spe.Rd | 6 - hyperSpec-0.100.3/hyperSpec/man/read.txt.Witec.Rd | 4 - hyperSpec-0.100.3/hyperSpec/man/textio.Rd | 4 - hyperSpec-0.100.3/hyperSpec/man/wlconv.Rd | 42 ++++++------- 25 files changed, 90 insertions(+), 127 deletions(-)
Title: Interaction Statistics
Description: Fast, model-agnostic implementation of different H-statistics
introduced by Jerome H. Friedman and Bogdan E. Popescu (2008)
<doi:10.1214/07-AOAS148>. These statistics quantify interaction
strength per feature, feature pair, and feature triple. The package
supports multi-output predictions and can account for case weights.
In addition, several variants of the original statistics are provided.
The shape of the interactions can be explored through partial
dependence plots or individual conditional expectation plots. 'DALEX'
explainers, meta learners ('mlr3', 'tidymodels', 'caret') and most
other models work out-of-the-box.
Author: Michael Mayer [aut, cre] ,
Przemyslaw Biecek [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between hstats versions 1.2.1 dated 2024-08-17 and 1.2.2 dated 2025-10-13
hstats-1.2.1/hstats/R/h2.R |only hstats-1.2.1/hstats/R/h2_overall.R |only hstats-1.2.1/hstats/R/h2_pairwise.R |only hstats-1.2.1/hstats/R/h2_threeway.R |only hstats-1.2.2/hstats/DESCRIPTION | 12 hstats-1.2.2/hstats/MD5 | 33 +- hstats-1.2.2/hstats/NEWS.md | 14 + hstats-1.2.2/hstats/R/H2.R |only hstats-1.2.2/hstats/R/H2_overall.R |only hstats-1.2.2/hstats/R/H2_pairwise.R |only hstats-1.2.2/hstats/R/H2_threeway.R |only hstats-1.2.2/hstats/R/hstats.R | 2 hstats-1.2.2/hstats/R/pd_raw.R | 96 ++++--- hstats-1.2.2/hstats/R/utils_statistics.R | 2 hstats-1.2.2/hstats/README.md | 62 +++- hstats-1.2.2/hstats/man/figures/tidymodels_h_abs.svg |only hstats-1.2.2/hstats/man/figures/tidymodels_pdp.svg |only hstats-1.2.2/hstats/man/figures/tidymodels_perm_imp.svg |only hstats-1.2.2/hstats/man/h2.Rd | 2 hstats-1.2.2/hstats/man/h2_overall.Rd | 2 hstats-1.2.2/hstats/man/h2_pairwise.Rd | 2 hstats-1.2.2/hstats/man/h2_threeway.Rd | 2 hstats-1.2.2/hstats/tests/testthat/test_partial_dep.R | 199 ++++++++++------ 23 files changed, 272 insertions(+), 156 deletions(-)
Title: Detection and Reconstruction of Muscle Fibers from diceCT Image
Data
Description: Reconstruction of muscle fibers from image stacks using textural analysis. Includes functions for tracking, smoothing, cleaning, plotting and exporting muscle fibers. Also calculates basic fiber properties (e.g., length and curvature).
Author: Jessica Arbour [aut, cre]
Maintainer: Jessica Arbour <jessica.arbour@mtsu.edu>
Diff between GoodFibes versions 0.1.10 dated 2023-08-18 and 0.1.12 dated 2025-10-13
DESCRIPTION | 24 ++++++----- MD5 | 12 ++--- NAMESPACE | 2 R/crop.stack.R | 2 R/fiber.angle.R | 109 ++++++++++++++++++++++++++++++++--------------------- build/partial.rdb |binary man/fiber.angle.Rd | 17 +++++--- 7 files changed, 98 insertions(+), 68 deletions(-)
Title: Knowledge Space Theory Input/Output
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstIO' package
provides basic functionalities to read and write KST data from/to
files to be used together with the 'kst', 'kstMatrix', 'CDSS', 'pks', or
'DAKS' packages.
Author: Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstIO versions 0.4-2 dated 2025-04-04 and 0.4-3 dated 2025-10-13
Changelog | 5 ++++- DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/read_kbase.R | 1 + R/read_kdata.R | 1 + R/read_kfamset.R | 1 + R/read_kspace.R | 1 + R/read_kstructure.R | 1 + R/read_surmisefunction.R | 3 ++- R/read_surmiserelation.R | 1 + build/vignette.rds |binary inst/doc/kstIO.pdf |binary 12 files changed, 27 insertions(+), 17 deletions(-)