Title: Named Capture to Data Tables
Description: User-friendly functions for extracting a data
table (row for each match, column for each group)
from non-tabular text data using regular expressions,
and for melting columns that match a regular expression.
Patterns are defined using a readable syntax
that makes it easy to build complex patterns
in terms of simpler, re-usable sub-patterns.
Named R arguments are translated to column names
in the output; capture groups without names are used
internally in order to provide a standard interface
to three regular expression 'C' libraries
('PCRE', 'RE2', 'ICU').
Output can also include numeric columns via
user-specified type conversion functions.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between nc versions 2024.9.20 dated 2024-09-20 and 2025.1.21 dated 2025-01-21
DESCRIPTION | 6 MD5 | 240 NAMESPACE | 35 NEWS | 464 - R/alternatives.R | 380 - R/apply_type_funs.R | 158 R/capture_all_str.R | 891 +- R/capture_first_df.R | 309 R/capture_first_glob.R | 234 R/capture_first_vec.R | 283 R/capture_longer_spec.R | 80 R/capture_melt_multiple.R | 310 R/capture_melt_single.R | 216 R/check_names.R | 154 R/field.R | 198 R/group.R | 118 R/measure.R | 338 R/only_captures.R | 28 R/quantifier.R | 128 R/stop_for.R | 100 R/try.R | 32 R/var_args_list.R | 265 build/vignette.rds |binary inst/doc/v0-overview.R | 118 inst/doc/v0-overview.Rmd | 280 inst/doc/v0-overview.html | 1008 +- inst/doc/v1-capture-first.R | 428 - inst/doc/v1-capture-first.Rmd | 850 +- inst/doc/v1-capture-first.html | 1936 ++--- inst/doc/v2-capture-all.R | 238 inst/doc/v2-capture-all.Rmd | 514 - inst/doc/v2-capture-all.html | 1518 ++-- inst/doc/v3-capture-melt.R | 300 inst/doc/v3-capture-melt.Rmd | 640 - inst/doc/v3-capture-melt.html | 1612 ++-- inst/doc/v4-comparisons.R | 1030 +- inst/doc/v4-comparisons.Rmd | 1370 +-- inst/doc/v4-comparisons.html | 2646 +++---- inst/doc/v5-helpers.R | 172 inst/doc/v5-helpers.Rmd | 350 inst/doc/v5-helpers.html | 1018 +- inst/doc/v6-engines.R | 40 inst/doc/v6-engines.Rmd | 264 inst/doc/v6-engines.html | 915 +- inst/doc/v7-capture-glob.R | 314 inst/doc/v7-capture-glob.Rmd | 580 - inst/doc/v7-capture-glob.html | 1556 ++-- inst/extdata/MEDLINE_Fields.html | 3586 +++++----- inst/extdata/PMC3045577.nbib | 136 inst/extdata/RD12-0002_PP16HS_5sec_GM_F_1P.csv | 74 inst/extdata/chip-seq-chunk-db.R | 22 inst/extdata/chip-seq-chunk-db/H3K36me3_AM_immune/9/counts/McGill0101.bedGraph.head | 22 inst/extdata/chip-seq-chunk-db/H3K36me3_TDH_other/1/counts/McGill0019.bedGraph.head | 22 inst/extdata/chip-seq-chunk-db/H3K4me3_TDH_immune/9/counts/McGill0024.bedGraph.head | 22 inst/extdata/chip-seq-chunk-db/H3K4me3_XJ_immune/2/counts/McGill0024.bedGraph.head | 22 inst/extdata/compress-sizes.out | 12 inst/extdata/compress-times.out | 50 inst/extdata/namedCapture-refs.bib | 392 - inst/extdata/pepseq.txt | 6 inst/extdata/vignette.Rmd | 460 - inst/extdata/vignette.Rnw | 794 +- inst/extdata/vignettes/v0-overview.Rmd | 204 inst/extdata/vignettes/v1-capture-first.Rmd | 842 +- inst/extdata/vignettes/v2-capture-all.Rmd | 506 - inst/extdata/vignettes/v3-capture-melt.Rmd | 630 - inst/extdata/vignettes/v4-comparisons.Rmd | 1360 +-- inst/extdata/vignettes/v5-helpers.Rmd | 354 inst/extdata/vignettes/v6-engines.Rmd | 256 inst/test_engines.R | 38 man/alternatives.Rd | 94 man/alternatives_with_shared_groups.Rd | 184 man/altlist.Rd | 102 man/apply_type_funs.Rd | 52 man/capture_all_str.Rd | 824 +- man/capture_first_df.Rd | 243 man/capture_first_glob.Rd | 234 man/capture_first_vec.Rd | 235 man/capture_longer_spec.Rd | 70 man/capture_melt_multiple.Rd | 312 man/capture_melt_single.Rd | 216 man/check_df_names.Rd | 36 man/check_names.Rd | 40 man/collapse_some.Rd | 46 man/field.Rd | 204 man/group.Rd | 128 man/measure.Rd | 62 man/measure_multiple.Rd | 48 man/measure_single.Rd | 48 man/melt_list.Rd | 42 man/only_captures.Rd | 40 man/quantifier.Rd | 124 man/stop_for_capture_same_as_id.Rd | 38 man/stop_for_engine.Rd | 34 man/stop_for_subject.Rd | 34 man/subject_var_args.Rd | 37 man/try_or_stop_print_pattern.Rd | 44 man/var_args_list.Rd | 91 tests/testthat.R | 5 tests/testthat/test-CRAN-all.R | 294 tests/testthat/test-CRAN-alternatives.R | 348 tests/testthat/test-CRAN-df.R | 726 +- tests/testthat/test-CRAN-dt.R | 46 tests/testthat/test-CRAN-errors.R | 288 tests/testthat/test-CRAN-field.R | 72 tests/testthat/test-CRAN-glob.R | 67 tests/testthat/test-CRAN-group.R | 56 tests/testthat/test-CRAN-longer.R | 48 tests/testthat/test-CRAN-measure.R | 73 tests/testthat/test-CRAN-melt.R | 260 tests/testthat/test-CRAN-multiple.R | 912 +- tests/testthat/test-CRAN-quantifier.R | 178 tests/testthat/test-CRAN-subject.R | 98 tests/testthat/test-CRAN-vec.R | 724 +- vignettes/v0-overview.Rmd | 280 vignettes/v1-capture-first.Rmd | 850 +- vignettes/v2-capture-all.Rmd | 514 - vignettes/v3-capture-melt.Rmd | 640 - vignettes/v4-comparisons.Rmd | 1370 +-- vignettes/v5-helpers.Rmd | 350 vignettes/v6-engines.Rmd | 264 vignettes/v7-capture-glob.Rmd | 580 - 121 files changed, 23643 insertions(+), 23536 deletions(-)
Title: Geometrically Designed Spline Regression
Description: Spline Regression, Generalized Additive Models, and Component-wise Gradient
Boosting, utilizing Geometrically Designed (GeD) Splines. GeDS regression is a
non-parametric method inspired by geometric principles, for fitting spline regression
models with variable knots in one or two independent variables. It efficiently estimates
the number of knots and their positions, as well as the spline order, assuming the
response variable follows a distribution from the exponential family. GeDS models
integrate the broader category of Generalized (Non-)Linear Models, offering a flexible
approach to modeling complex relationships. A description of the method can be found in
Kaishev et al. (2016) <doi:10.1007/s00180-015-0621-7> and Dimitrova et al. (2023)
<doi:10.1016/j.amc.2022.127493>. Further extending its capabilities, GeDS's implementation
includes Generalized Additive Models (GAM) and Functional Gradient Boosting (FGB),
enabling versatile multivariate predictor modeling, as discuss [...truncated...]
Author: Dimitrina S. Dimitrova [aut],
Vladimir K. Kaishev [aut],
Andrea Lattuada [aut],
Emilio L. Saenz Guillen [aut, cre],
Richard J. Verrall [aut]
Maintainer: Emilio L. Saenz Guillen <Emilio.Saenz-Guillen@bayes.city.ac.uk>
Diff between GeDS versions 0.2.4 dated 2024-09-12 and 0.2.5 dated 2025-01-21
DESCRIPTION | 26 +-- MD5 | 34 ++-- R/BivariateFitter.R | 45 ++++-- R/IntegrateDerive.R | 75 +++++++--- R/Knotnew_R.R |only R/NGeDS.R | 18 +- R/NGeDSboost.R | 4 R/S3methods.R | 42 +++-- R/SplineReg_biv.R | 8 - R/UnivariateFitter.R | 71 ++++++--- R/plot_GeDSMethod.R | 330 ++++++++++++++++++++++++++++++++++++++------- R/tensorProd_R.R |only R/unexported.R | 9 - build/partial.rdb |binary man/Integrate.Rd | 15 +- man/NGeDS.Rd | 12 + man/NGeDSboost.Rd | 2 man/UnivariateFitters.Rd | 9 - man/plot-GeDSgam-method.Rd | 10 + 19 files changed, 535 insertions(+), 175 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2024.11.29 dated 2024-12-02 and 2025.1.21 dated 2025-01-21
DESCRIPTION | 6 MD5 | 94 +-- NAMESPACE | 44 - NEWS | 385 +++++++------ R/atime.R | 577 ++++++++++---------- R/predict.R | 236 ++++---- R/references.R | 370 ++++++------- R/test.R | 618 +++++++++++----------- R/versions.R | 380 ++++++------- build/vignette.rds |binary inst/doc/Custom_Plots.R | 144 ++--- inst/doc/Custom_Plots.Rmd | 200 +++---- inst/doc/Custom_Plots.html | 494 ++++++++--------- inst/doc/Custom_References.R | 134 ++-- inst/doc/Custom_References.Rmd | 284 +++++----- inst/doc/Custom_References.html | 621 +++++++++++----------- inst/doc/Custom_Units.R | 138 ++-- inst/doc/Custom_Units.Rmd | 320 +++++------ inst/doc/Custom_Units.html | 643 +++++++++++------------ inst/doc/cum_median.R | 62 +- inst/doc/cum_median.Rmd | 104 +-- inst/doc/cum_median.html | 408 +++++++------- inst/doc/regex.R | 128 ++-- inst/doc/regex.Rmd | 192 +++--- inst/doc/regex.html | 536 +++++++++---------- inst/doc/sparse.R | 400 +++++++------- inst/doc/sparse.Rmd | 696 ++++++++++++------------ inst/doc/sparse.html | 1115 ++++++++++++++++++++-------------------- inst/example_tests.R | 82 +- inst/global_edit.R | 82 +- man/atime.Rd | 128 ++-- man/atime_grid.Rd | 198 +++---- man/atime_pkg.Rd | 188 +++--- man/atime_test.Rd | 128 ++-- man/atime_test_list.Rd | 164 ++--- man/atime_versions.Rd | 178 +++--- man/atime_versions_exprs.Rd | 174 +++--- man/atime_versions_remove.Rd | 26 man/glob_find_replace.Rd | 38 - man/references_best.Rd | 104 +-- tests/testthat.R | 3 tests/testthat/test-CRAN.R | 1025 ++++++++++++++++++------------------ vignettes/Custom_Plots.Rmd | 200 +++---- vignettes/Custom_References.Rmd | 284 +++++----- vignettes/Custom_Units.Rmd | 320 +++++------ vignettes/cum_median.Rmd | 104 +-- vignettes/regex.Rmd | 192 +++--- vignettes/sparse.Rmd | 696 ++++++++++++------------ 48 files changed, 6852 insertions(+), 6791 deletions(-)
Title: Extend 'tinytest' with 'diffobj' and 'tinysnapshot'
Description: The 'tinytest' package offers a light-weight zero-dependency unit-testing
framework to which this package adds support via the 'diffobj' package for 'diff'-style
textual comparison of R objects, as well as via 'tinysnapshot' package for visual
differences in plots.
Author: Dirk Eddelbuettel [aut, cre] ,
Alton Barbehenn [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between ttdo versions 0.0.9 dated 2023-02-22 and 0.0.10 dated 2025-01-21
ChangeLog | 41 ++++++++++++++++++++++++++++++++++ DESCRIPTION | 29 ++++++++++++++---------- MD5 | 22 +++++++++--------- NAMESPACE | 10 +++++--- R/expectations.R | 28 +++++++++++++++-------- R/expectations_xl.R | 4 +-- R/visual.R |only README.md | 2 - inst/NEWS.Rd | 15 ++++++++++++ man/expect_equal_with_diff.Rd | 5 ++-- man/expect_equal_xl.Rd | 2 - man/expect_visual_equal_with_diff.Rd |only man/ttdo_boolean_and_message_tests.Rd | 2 - 13 files changed, 120 insertions(+), 40 deletions(-)
More information about setariaviridis at CRAN
Permanent link
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play data are also available for the Spanish league. Methods for analysis include a population pyramid,
2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats, team heatmaps,
team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls and offensive rebounds.
Please see Vinue (2020) <doi:10.1089/big.2018.0124> and Vinue (2024) [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.3.2 dated 2024-01-09 and 1.3.3 dated 2025-01-21
DESCRIPTION | 17 - MD5 | 18 - NEWS | 4 R/do_stats_per_period.R | 5 build/vignette.rds |binary inst/doc/BAwiR.R | 214 +++++++++--------- inst/doc/BAwiR.html | 568 +++++++++++++++++++++++++++++++++--------------- inst/doc/BAwiR_pbp.R | 128 +++++----- inst/doc/BAwiR_pbp.html | 482 ++++++++++++++++++++++++++++++---------- man/BAwiR-package.Rd | 10 10 files changed, 955 insertions(+), 491 deletions(-)
Title: Snapshots for Unit Tests using the 'tinytest' Framework
Description: Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Author: Vincent Arel-Bundock [aut, cre, cph]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinysnapshot versions 0.0.7 dated 2025-01-13 and 0.0.8 dated 2025-01-21
DESCRIPTION | 6 +-- MD5 | 14 ++++----- NEWS.md | 4 ++ R/expect_snapshot_plot.R | 62 +++++++++++++++++++++++----------------- build/partial.rdb |binary inst/tinytest/test-png.R | 26 ++++++++++++++++ man/expect_equivalent_images.Rd | 3 + man/expect_snapshot_plot.Rd | 3 + 8 files changed, 81 insertions(+), 37 deletions(-)
Title: Manipulate 'JDemetra+' Workspaces
Description: Set of tools to manipulate the 'JDemetra+' workspaces.
Based on the 'RJDemetra' package (which interfaces with version 2 of the 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially
recommended to the members of the European Statistical System (ESS) and the European System of Central Banks).
This package provides access to additional workspace manipulation functions such as metadata manipulation, raw paths and wrangling of several workspaces simultaneously.
These additional functionalities are useful as part of a CVS data production chain.
Author: Tanguy Barthelemy [aut, cre, art],
Alain Quartier-la-Tente [aut] ,
Institut national de la statistique et des etudes economiques [cph]
,
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjdworkspace versions 1.1.8 dated 2025-01-09 and 1.1.9 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 8 +++++++- R/update_path.R | 23 +++++++++++++++++------ 4 files changed, 30 insertions(+), 13 deletions(-)
Title: High-Dimensional Analysis of Variance
Description: Functions and datasets to support Smilde, Marini, Westerhuis and Liland (2025, ISBN: 978-1-394-21121-0)
"Analysis of Variance for High-Dimensional Data - Applications in Life, Food and Chemical Sciences".
This implements and imports a collection of methods for HD-ANOVA data analysis with common interfaces, result- and plotting
functions, multiple real data sets and four vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between HDANOVA versions 0.8.1 dated 2024-10-16 and 0.8.2 dated 2025-01-21
DESCRIPTION | 13 - MD5 | 52 +++--- NAMESPACE | 3 NEWS | 11 + R/apca.R | 11 + R/asca.R | 9 - R/asca_fit.R | 155 +++++++++++++------- R/asca_plots.R | 140 ++++++++++-------- R/limmpca.R | 6 R/model.frame.asca.R |only R/msca.R | 5 R/pcanova.R | 5 build/vignette.rds |binary inst/doc/vignette_B_ANOVA.R | 3 inst/doc/vignette_B_ANOVA.Rmd | 5 inst/doc/vignette_B_ANOVA.html | 317 ++++++++++++++++++++--------------------- inst/doc/vignette_C_ASCA.R | 5 inst/doc/vignette_C_ASCA.Rmd | 5 inst/doc/vignette_C_ASCA.html | 91 ++++++----- man/apca.Rd | 10 + man/asca.Rd | 8 - man/asca_fit.Rd | 12 + man/limmpca.Rd | 3 man/model.frame.asca.Rd |only man/msca.Rd | 4 man/pcanova.Rd | 4 vignettes/vignette_B_ANOVA.Rmd | 5 vignettes/vignette_C_ASCA.Rmd | 5 28 files changed, 516 insertions(+), 371 deletions(-)
Title: Visualising Multiple Pairwise Variable Correlations and Other
Scores
Description: We provide a tidy data structure and visualisations for multiple or grouped variable correlations,
general association measures scagnostics and other pairwise scores suitable for numerical, ordinal and nominal variables.
Supported measures include distance correlation, maximal information, ace correlation, Kendall's tau, and polychoric correlation.
Author: Amit Chinwan [aut],
Catherine Hurley [aut, cre]
Maintainer: Catherine Hurley <catherine.hurley@mu.ie>
Diff between bullseye versions 0.1.0 dated 2024-08-28 and 0.1.1 dated 2025-01-21
DESCRIPTION | 6 ++--- MD5 | 30 +++++++++++++-------------- NEWS.md | 6 +++++ R/pair_methods.R | 8 +++---- R/pair_scagnostics.R | 2 - R/pairwise.R | 3 +- build/vignette.rds |binary inst/doc/calc_pairwise.html | 2 - inst/doc/integrating.html | 14 ++++++------ inst/doc/vis_pairwise.R | 4 +-- inst/doc/vis_pairwise.html | 40 ++++++++++++++++++------------------- man/bullseye-package.Rd | 2 - man/pair_ace.Rd | 2 - man/pair_nmi.Rd | 4 ++- man/pair_scagnostics.Rd | 2 - tests/testthat/test-pair_methods.R | 12 +++++------ 16 files changed, 73 insertions(+), 64 deletions(-)
Title: Animated Interactive Grammar of Graphics
Description: Functions are provided for defining animated,
interactive data visualizations in R code, and rendering
on a web page. The 2018 Journal of Computational and
Graphical Statistics paper,
<doi:10.1080/10618600.2018.1513367>
describes the concepts implemented.
Author: Toby Hocking [aut, cre] ,
Biplab Sutradhar [ctb] ,
Hadley Wickham [aut] ,
Winston Chang [aut] ,
RStudio [cph] ,
Nicholas Lewin-Koh [aut] ,
Martin Maechler [aut] ,
Randall Prium [aut] ,
Susan VanderPlas [aut] ,
Carson Sievert [aut] ,
Kevin Ferris [aut [...truncated...]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between animint2 versions 2024.11.2 dated 2024-11-05 and 2025.1.21 dated 2025-01-21
DESCRIPTION | 6 MD5 | 1033 - NAMESPACE | 1061 - NEWS.md | 356 R/aaa-.r | 26 R/aes-calculated.r | 100 R/aes-colour-fill-alpha.r | 112 R/aes-group-order.r | 160 R/aes-linetype-size-shape.r | 128 R/aes-position.r | 78 R/aes.r | 472 R/annotation-custom.r | 194 R/annotation-logticks.r | 488 R/annotation-map.r | 144 R/annotation-raster.r | 180 R/annotation.r | 134 R/autoplot.r | 42 R/bench.r | 44 R/bin.R | 342 R/coord-.r | 162 R/coord-cartesian-.r | 206 R/coord-fixed.r | 94 R/coord-flip.r | 126 R/coord-map.r | 498 R/coord-munch.r | 394 R/coord-polar.r | 608 R/coord-quickmap.R | 72 R/coord-transform.r | 344 R/data.R | 378 R/facet-.r | 124 R/facet-grid-.r | 830 R/facet-labels.r | 1150 - R/facet-layout.r | 350 R/facet-locate.r | 168 R/facet-null.r | 152 R/facet-viewports.r | 100 R/facet-wrap.r | 926 R/fortify-lm.r | 172 R/fortify-map.r | 222 R/fortify-spatial.r | 182 R/fortify.r | 54 R/geom-.r | 1328 - R/geom-abline.r | 318 R/geom-bar.r | 268 R/geom-bin2d.r | 146 R/geom-blank.r | 76 R/geom-contour.r | 152 R/geom-count.r | 126 R/geom-crossbar.r | 190 R/geom-curve.r | 122 R/geom-defaults.r | 82 R/geom-density.r | 172 R/geom-density2d.r | 164 R/geom-dotplot.r | 570 R/geom-errorbar.r | 116 R/geom-errorbarh.r | 162 R/geom-freqpoly.r | 74 R/geom-hex.r | 266 R/geom-histogram.r | 190 R/geom-hline.r | 108 R/geom-jitter.r | 120 R/geom-label.R | 294 R/geom-linerange.r | 176 R/geom-map.r | 246 R/geom-path.r | 640 R/geom-point.r | 306 R/geom-pointrange.r | 98 R/geom-polygon.r | 228 R/geom-raster.r | 206 R/geom-rect.r | 162 R/geom-ribbon.r | 310 R/geom-rug.r | 190 R/geom-segment.r | 234 R/geom-smooth.r | 270 R/geom-spoke.r | 130 R/geom-text.r | 486 R/geom-tile.r | 218 R/geom-violin.r | 378 R/geom-vline.r | 108 R/gganimintproto.r | 570 R/ggplot2.r | 8 R/grob-absolute.r | 94 R/grob-dotstack.r | 94 R/grob-null.r | 48 R/grouping.r | 78 R/guide-colorbar.r | 876 R/guide-legend.r | 1038 - R/guides-.r | 586 R/guides-axis.r | 230 R/guides-grid.r | 60 R/hexbin.R | 76 R/labels.r | 188 R/layer.r | 640 R/legend-draw.r | 368 R/limits.r | 264 R/margins.R | 340 R/panel.r | 374 R/plot-build.r | 596 R/plot-construction.r | 238 R/plot-last.r | 38 R/plot.r | 332 R/position-.r | 184 R/position-collide.r | 220 R/position-dodge.r | 116 R/position-fill.r | 48 R/position-identity.r | 34 R/position-jitter.r | 104 R/position-jitterdodge.R | 118 R/position-nudge.R | 92 R/position-stack.r | 148 R/quick-plot.r | 314 R/range.r | 66 R/save.r | 270 R/scale-.r | 1266 - R/scale-alpha.r | 70 R/scale-brewer.r | 190 R/scale-continuous.r | 336 R/scale-date.r | 324 R/scale-discrete-.r | 282 R/scale-gradient.r | 226 R/scale-grey.r | 78 R/scale-hue.r | 116 R/scale-identity.r | 308 R/scale-linetype.r | 58 R/scale-manual.r | 172 R/scale-shape.r | 82 R/scale-size.r | 188 R/scale-type.R | 132 R/scales-.r | 258 R/stat-.r | 276 R/stat-bin.r | 280 R/stat-bin2d.r | 290 R/stat-bindot.r | 344 R/stat-binhex.r | 104 R/stat-contour.r | 226 R/stat-count.r | 142 R/stat-density-2d.r | 148 R/stat-density.r | 204 R/stat-ecdf.r | 154 R/stat-ellipse.R | 236 R/stat-function.r | 206 R/stat-identity.r | 78 R/stat-qq.r | 182 R/stat-smooth-methods.r | 142 R/stat-smooth.r | 264 R/stat-sum.r | 100 R/stat-summary-2d.r | 270 R/stat-summary-bin.R | 178 R/stat-summary-hex.r | 104 R/stat-summary.r | 328 R/stat-unique.r | 72 R/stat-ydensity.r | 218 R/summary.r | 84 R/theme-defaults.r | 616 R/theme-elements.r | 642 R/theme.r | 1200 - R/translate-qplot-ggplot.r | 164 R/translate-qplot-lattice.r | 146 R/utilities-break.r | 232 R/utilities-grid.r | 74 R/utilities-help.r | 66 R/utilities-matrix.r | 76 R/utilities-resolution.r | 60 R/utilities-table.r | 76 R/utilities.r | 616 R/uu_zxx.r | 214 R/uu_zzz.r | 26 R/z_animint.R | 1687 - R/z_animintHelpers.R | 2208 +- R/z_facets.R | 298 R/z_geoms.R | 598 R/z_helperFunctions.R | 82 R/z_knitr.R | 286 R/z_pages.R | 525 R/z_print.R | 206 R/z_scales.R | 20 R/z_theme_animint.R | 52 R/z_transformShape.R | 68 build/partial.rdb |binary inst/htmljs/animint.js | 4986 ++--- inst/htmljs/index.html | 54 inst/htmljs/scripts.html | 18 inst/htmljs/vendor/d3.v3.js |15630 ++++++++-------- inst/htmljs/vendor/jquery-1.11.3.min.js | 10 inst/htmljs/vendor/selectize.css | 634 inst/htmljs/vendor/selectize.min.js | 4 inst/shiny/shinyAnimint.js | 34 man/FluView.Rd | 28 man/UStornadoes.Rd | 104 man/WorldBank.Rd | 68 man/absoluteGrob.Rd | 44 man/addSSandCSasAesthetics.Rd | 48 man/addShowSelectedForLegend.Rd | 42 man/add_theme.Rd | 38 man/aes.Rd | 98 man/aes_.Rd | 114 man/aes_all.Rd | 38 man/aes_auto.Rd | 34 man/aes_colour_fill_alpha.Rd | 122 man/aes_linetype_size_shape.Rd | 138 man/aes_position.Rd | 98 man/animint.Rd | 168 man/animint2-gganimintproto.Rd | 642 man/animint2dir.Rd | 220 man/animint2pages.Rd | 122 man/animintOutput.Rd | 34 man/annotate.Rd | 120 man/annotation_custom.Rd | 106 man/annotation_logticks.Rd | 218 man/annotation_map.Rd | 72 man/annotation_raster.Rd | 98 man/as.list.gganimintproto.Rd | 38 man/as_labeller.Rd | 90 man/autoplot.Rd | 48 man/benchplot.Rd 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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-29 2.1.11
2023-09-20 2.1.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-19 0.0.1
Title: Bayesian partial least squares regression
Description: Fits the Bayesian partial least squares regression model
introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable
for univariate and multivariate regression with high-dimensional data.
Author: Szymon Urbas [aut, cre],
Pierre Lovera [ctb],
Robert Daly [ctb],
Alan O'Riordan [ctb],
Donagh Berry [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Szymon Urbas <szymon.urbas@mu.ie>
Diff between bplsr versions 1.0.2 dated 2025-01-13 and 1.0.3 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/BPLSR.R | 8 ++++++-- README.md | 24 ++++++++++++------------ 4 files changed, 24 insertions(+), 20 deletions(-)
Title: Spatial Network Analysis
Description: Interface package for 'sala', the spatial network analysis library
from the 'depthmapX' software application. The R parts of the code are based
on the 'rdepthmap' package. Allows for the analysis of urban and
building-scale networks and provides metrics and methods usually found
within the Space Syntax domain. Methods in this package are described by K.
Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax
methodology", and also by A. Turner (2004)
<https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's
handbook".
Author: Petros Koutsolampros [cre, aut]
,
Fani Kostourou [ctb] ,
Kimon Krenz [ctb] ,
Alasdair Turner [ctb] ,
Tasos Varoudis [ctb] ,
Christian Sailer [ctb] ,
Eva Friedrich [ctb] ,
University College London [fnd, cph] ,
Spacelab UK [fnd]
Maintainer: Petros Koutsolampros <r-devel@pklampros.net>
Diff between alcyon versions 0.6.0 dated 2024-12-22 and 0.7.0 dated 2025-01-21
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 5 ++++- configure | 18 +++++++++--------- configure.ac | 2 +- src/libs/salalib/CMakeLists.txt | 4 ++++ src/libs/salalib/genlib/p2dpoly.cpp | 32 ++++++++++++++++++++++++-------- src/libs/salalib/genlib/p2dpoly.h | 18 +++++++++++++++--- src/libs/salalib/importutils.cpp | 4 ++-- src/libs/salalib/salashape.cpp | 10 +++++++--- src/libs/salalib/salashape.h | 2 +- src/process_isovist.cpp | 7 ++++++- tests/testthat.R | 6 +++++- 13 files changed, 94 insertions(+), 46 deletions(-)
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools. Additional helpers make it easy
to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.14.3 dated 2025-01-10 and 0.14.4 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/renv_helpers.R | 32 +++++++++++++++++++++++++------- inst/extdata/available_df.csv | 2 ++ tests/testthat/test-renv_helpers.R | 2 +- 6 files changed, 40 insertions(+), 16 deletions(-)
Title: Read Human Mortality Database and Human Fertility Database Data
from the Web
Description: Utilities for reading data from the Human Mortality Database (<https://www.mortality.org>), Human Fertility Database (<https://www.humanfertility.org>), and similar databases from the web or locally into an R session as data.frame objects. These are the two most widely used sources of demographic data to study basic demographic change, trends, and develop new demographic methods. Other supported databases at this time include the Human Fertility Collection (<https://www.fertilitydata.org>), The Japanese Mortality Database (<https://www.ipss.go.jp/p-toukei/JMD/index-en.html>), and the Canadian Human Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and data are standardized.
Author: Tim Riffe [aut, cre],
Carl Boe [aut],
Jason Hilton [aut],
Josh Goldstein [ctb],
Stephen Holzman [ctb],
Sam Hyun Yoo [ctb]
Maintainer: Tim Riffe <tim.riffe@gmail.com>
Diff between HMDHFDplus versions 2.0.3 dated 2023-06-20 and 2.0.6 dated 2025-01-21
DESCRIPTION | 23 ++++++++++++----------- MD5 | 14 +++++++------- NAMESPACE | 2 ++ NEWS.md | 14 ++++++++++++++ R/HFDutils.R | 47 ++++++++++++++++++++++++++++------------------- R/readHFD.R | 7 ++++--- man/HFDparse.Rd | 4 +++- man/readHFD.Rd | 4 +++- 8 files changed, 73 insertions(+), 42 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.2.0 dated 2025-01-14 and 2.2.1 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 4 ++++ R/EngineRestGitHub.R | 5 ++--- R/EngineRestGitLab.R | 8 +++++--- inst/roche/roche_get_package_usage.R |only 6 files changed, 19 insertions(+), 13 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling. The 'rvinecopulib' package implements the core features of the
popular 'VineCopula' package, in particular inference algorithms for both vine
copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker
and more modern API, improved performances, especially in high dimensions,
nonparametric and multi-parameter families, and the ability to model discrete
variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only
C++ library (currently version 0.7.1). Thus users do not need to install
'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial
releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib'
is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.6.3.1.1 dated 2023-02-23 and 0.7.1.1.0 dated 2025-01-21
DESCRIPTION | 16 MD5 | 230 +-- NAMESPACE | 1 NEWS.md | 23 R/RcppExports.R | 28 R/bicop.R | 53 R/bicop_methods.R | 10 R/bicop_plot.R | 6 R/family_sets.R | 14 R/pairs_copula_data.R | 4 R/rosenblatt.R | 56 R/rvinecopulib.R | 2 R/tools.R | 87 - R/vine.R | 29 R/vine_methods.R | 9 R/vinecop.R | 104 + R/vinecop_methods.R | 7 README.md | 10 inst/include/vinecopulib-wrappers.hpp | 22 inst/include/vinecopulib.hpp | 24 inst/include/vinecopulib/bicop/abstract.hpp | 3 inst/include/vinecopulib/bicop/archimedean.hpp | 2 inst/include/vinecopulib/bicop/bb1.hpp | 2 inst/include/vinecopulib/bicop/bb6.hpp | 2 inst/include/vinecopulib/bicop/bb7.hpp | 2 inst/include/vinecopulib/bicop/bb8.hpp | 2 inst/include/vinecopulib/bicop/class.hpp | 29 inst/include/vinecopulib/bicop/clayton.hpp | 2 inst/include/vinecopulib/bicop/elliptical.hpp | 2 inst/include/vinecopulib/bicop/extreme_value.hpp |only inst/include/vinecopulib/bicop/family.hpp | 30 inst/include/vinecopulib/bicop/fit_controls.hpp | 13 inst/include/vinecopulib/bicop/frank.hpp | 2 inst/include/vinecopulib/bicop/gaussian.hpp | 2 inst/include/vinecopulib/bicop/gumbel.hpp | 4 inst/include/vinecopulib/bicop/implementation/abstract.ipp | 100 + inst/include/vinecopulib/bicop/implementation/archimedean.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb1.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb6.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb7.ipp | 17 inst/include/vinecopulib/bicop/implementation/bb8.ipp | 2 inst/include/vinecopulib/bicop/implementation/class.ipp | 216 ++- inst/include/vinecopulib/bicop/implementation/clayton.ipp | 5 inst/include/vinecopulib/bicop/implementation/elliptical.ipp | 2 inst/include/vinecopulib/bicop/implementation/extreme_value.ipp |only inst/include/vinecopulib/bicop/implementation/family.ipp | 37 inst/include/vinecopulib/bicop/implementation/fit_controls.ipp | 95 + inst/include/vinecopulib/bicop/implementation/frank.ipp | 12 inst/include/vinecopulib/bicop/implementation/gaussian.ipp | 2 inst/include/vinecopulib/bicop/implementation/gumbel.ipp | 46 inst/include/vinecopulib/bicop/implementation/indep.ipp | 2 inst/include/vinecopulib/bicop/implementation/joe.ipp | 60 inst/include/vinecopulib/bicop/implementation/kernel.ipp | 2 inst/include/vinecopulib/bicop/implementation/parametric.ipp | 10 inst/include/vinecopulib/bicop/implementation/student.ipp | 2 inst/include/vinecopulib/bicop/implementation/tawn.ipp |only inst/include/vinecopulib/bicop/implementation/tll.ipp | 14 inst/include/vinecopulib/bicop/implementation/tools_select.ipp | 22 inst/include/vinecopulib/bicop/indep.hpp | 2 inst/include/vinecopulib/bicop/joe.hpp | 4 inst/include/vinecopulib/bicop/kernel.hpp | 2 inst/include/vinecopulib/bicop/parametric.hpp | 2 inst/include/vinecopulib/bicop/student.hpp | 2 inst/include/vinecopulib/bicop/tawn.hpp |only inst/include/vinecopulib/bicop/tll.hpp | 2 inst/include/vinecopulib/bicop/tools_select.hpp | 2 inst/include/vinecopulib/misc/fit_controls.hpp |only inst/include/vinecopulib/misc/implementation/tools_eigen.ipp | 7 inst/include/vinecopulib/misc/implementation/tools_interpolation.ipp | 41 inst/include/vinecopulib/misc/implementation/tools_optimization.ipp | 12 inst/include/vinecopulib/misc/implementation/tools_stats.ipp | 236 ++- inst/include/vinecopulib/misc/tools_batch.hpp | 2 inst/include/vinecopulib/misc/tools_bobyqa.hpp | 2 inst/include/vinecopulib/misc/tools_constants.hpp | 2 inst/include/vinecopulib/misc/tools_eigen.hpp | 7 inst/include/vinecopulib/misc/tools_integration.hpp | 2 inst/include/vinecopulib/misc/tools_interface.hpp | 2 inst/include/vinecopulib/misc/tools_interpolation.hpp | 3 inst/include/vinecopulib/misc/tools_optimization.hpp | 12 inst/include/vinecopulib/misc/tools_optional.hpp |only inst/include/vinecopulib/misc/tools_serialization.hpp | 2 inst/include/vinecopulib/misc/tools_stats.hpp | 64 - inst/include/vinecopulib/misc/tools_stats_ghalton.hpp | 2 inst/include/vinecopulib/misc/tools_stats_sobol.hpp | 2 inst/include/vinecopulib/misc/tools_stl.hpp | 33 inst/include/vinecopulib/misc/tools_thread.hpp | 2 inst/include/vinecopulib/misc/triangular_array.hpp | 6 inst/include/vinecopulib/version.hpp | 6 inst/include/vinecopulib/vinecop/class.hpp | 19 inst/include/vinecopulib/vinecop/fit_controls.hpp | 24 inst/include/vinecopulib/vinecop/implementation/class.ipp | 627 +++++++--- inst/include/vinecopulib/vinecop/implementation/fit_controls.ipp | 143 +- inst/include/vinecopulib/vinecop/implementation/rvine_structure.ipp | 54 inst/include/vinecopulib/vinecop/implementation/tools_select.ipp | 40 inst/include/vinecopulib/vinecop/rvine_structure.hpp | 72 - inst/include/vinecopulib/vinecop/tools_select.hpp | 2 man/as.bicop.Rd |only man/bicop.Rd | 10 man/bicop_dist.Rd | 3 man/bicop_methods.Rd | 8 man/emp_cdf.Rd | 2 man/mBICV.Rd | 2 man/pairs_copula_data.Rd | 4 man/plot.bicop_dist.Rd | 6 man/predict_bicop.Rd | 2 man/rosenblatt.Rd | 27 man/rvinecopulib.Rd | 9 man/vine.Rd | 4 man/vinecop.Rd | 15 src/RcppExports.cpp | 100 - src/vinecopulib-interface.cpp | 139 +- tests/testthat/Rplots.pdf | 547 ++++---- tests/testthat/test_bicop.R | 9 tests/testthat/test_bicop_dist.R | 7 tests/testthat/test_rosenblatt.R | 26 tests/testthat/test_rvine_structure.R | 27 tests/testthat/test_vine.R | 12 tests/testthat/test_vine_dist.R | 30 tests/testthat/test_vinecop.R | 25 tests/testthat/testthat-problems.rds |only 120 files changed, 2596 insertions(+), 1344 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.8-0 dated 2025-01-08 and 1.8-1 dated 2025-01-21
DESCRIPTION | 12 +++++++----- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/mixess.R | 8 ++++++-- R/sysdata.rda |binary inst/doc/RBesT.pdf |binary inst/doc/introduction.html | 6 +++--- man/RBesT-package.Rd | 1 + tests/testthat/test-utils.R | 7 +++++++ 9 files changed, 39 insertions(+), 18 deletions(-)
Title: Colors for NEST Graphs
Description: Clinical reporting figures require to use consistent colors
and configurations. As a part of the Roche open-source clinical
reporting project, namely the NEST project, the 'nestcolor' package
specifies the color code and default theme with specifying 'ggplot2'
theme parameters. Users can easily customize color and theme settings
before using the reset of NEST packages to ensure consistent settings
in both static and interactive output at the downstream.
Author: Joe Zhu [aut, cre] ,
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between nestcolor versions 0.1.2 dated 2023-06-09 and 0.1.3 dated 2025-01-21
DESCRIPTION | 40 ++++++++++++++----------- MD5 | 16 +++++----- NEWS.md | 5 ++- R/color_palette.R | 16 +++++----- build/vignette.rds |binary inst/WORDLIST | 4 +- inst/doc/nestcolor.R | 8 ++--- inst/doc/nestcolor.html | 74 ++++++++++++++++++++++-------------------------- man/color_palette.Rd | 16 +++++----- 9 files changed, 90 insertions(+), 89 deletions(-)
Title: Multi-Scale Geomorphometric Terrain Attributes
Description: Calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models using a variable focal windows size (Ilich et al. (2023) <doi:10.1111/tgis.13067>).
Author: Alexander Ilich [aut, cre] ,
Vincent Lecours [aut],
Benjamin Misiuk [aut],
Steven Murawski [aut]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between MultiscaleDTM versions 0.9 dated 2025-01-17 and 0.9.1 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/SlpAsp.R | 19 ++++++++++++------- inst/doc/README.html | 4 ++-- man/SlpAsp.Rd | 9 ++++++--- 5 files changed, 27 insertions(+), 19 deletions(-)
Title: Joint and Individual Regression
Description: An R package that implements the JICO algorithm [Wang, P., Wang, H., Li, Q., Shen, D., & Liu, Y. (2024). <Journal of Computational and Graphical Statistics, 33(3), 763-773>].
It aims at solving the multi-group regression problem. The algorithm decomposes the responses from multiple groups into shared and group-specific
components, which are driven by low-rank approximations of joint and individual structures from the covariates respectively.
Author: Peiyao Wang [aut, cre]
Maintainer: Peiyao Wang <peiyaow76@gmail.com>
Diff between JICO versions 0.0 dated 2023-05-08 and 0.1 dated 2025-01-21
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++-- R/continuum.R | 20 ++++++++++---------- R/utils.R | 2 +- README.md | 30 +++++++++++++++++++++++------- man/DIAG.Rd | 2 +- man/continuum.Rd | 4 ++-- man/continuum.multigroup.iter.Rd | 6 +++--- man/cv.continnum.iter.Rd | 4 ++-- tests/testthat/test-continuum.R | 16 ++++++++-------- 11 files changed, 69 insertions(+), 53 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between BiodiversityR versions 2.17-1 dated 2025-01-10 and 2.17-1.1 dated 2025-01-21
DESCRIPTION | 8 +- MD5 | 6 - R/caprescale.R | 173 +++++++++++++++++++++++++++++---------------------------- inst/ChangeLog | 27 +++++--- 4 files changed, 114 insertions(+), 100 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] ,
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb],
Chad Klumb [ctb],
Michal Bojanowski [ctb] ,
[...truncated...]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm versions 4.7.5 dated 2024-11-06 and 4.8.1 dated 2025-01-21
ergm-4.7.5/ergm/tests/testthat/test-Sum.R |only ergm-4.8.1/ergm/DESCRIPTION | 52 ergm-4.8.1/ergm/LICENSE | 2 ergm-4.8.1/ergm/MD5 | 725 +++--- ergm-4.8.1/ergm/NAMESPACE | 2 ergm-4.8.1/ergm/R/InitErgmConstraint.R | 92 ergm-4.8.1/ergm/R/InitErgmConstraint.blockdiag.R | 2 ergm-4.8.1/ergm/R/InitErgmConstraint.hints.R | 2 ergm-4.8.1/ergm/R/InitErgmConstraint.operator.R |only ergm-4.8.1/ergm/R/InitErgmProposal.R | 2 ergm-4.8.1/ergm/R/InitErgmProposal.dyadnoise.R | 2 ergm-4.8.1/ergm/R/InitErgmReference.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.R | 168 - ergm-4.8.1/ergm/R/InitErgmTerm.auxnet.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.bipartite.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.bipartite.degree.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.blockop.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.coincidence.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.dgw_sp.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.diversity.R |only ergm-4.8.1/ergm/R/InitErgmTerm.extra.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.indices.R | 2 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ergm-4.8.1/ergm/R/ergm-defunct.R | 18 ergm-4.8.1/ergm/R/ergm-deprecated.R | 4 ergm-4.8.1/ergm/R/ergm-internal.R | 2 ergm-4.8.1/ergm/R/ergm-options.R | 16 ergm-4.8.1/ergm/R/ergm-package.R | 2 ergm-4.8.1/ergm/R/ergm-terms-index.R | 14 ergm-4.8.1/ergm/R/ergm.CD.fixed.R | 2 ergm-4.8.1/ergm/R/ergm.Cprepare.R | 2 ergm-4.8.1/ergm/R/ergm.MCMCse.R | 2 ergm-4.8.1/ergm/R/ergm.MCMLE.R | 2 ergm-4.8.1/ergm/R/ergm.R | 4 ergm-4.8.1/ergm/R/ergm.allstats.R | 2 ergm-4.8.1/ergm/R/ergm.auxstorage.R | 14 ergm-4.8.1/ergm/R/ergm.bounddeg.R | 2 ergm-4.8.1/ergm/R/ergm.bridge.R | 2 ergm-4.8.1/ergm/R/ergm.design.R | 2 ergm-4.8.1/ergm/R/ergm.errors.R | 2 ergm-4.8.1/ergm/R/ergm.estimate.R | 2 ergm-4.8.1/ergm/R/ergm.eta.R | 2 ergm-4.8.1/ergm/R/ergm.etagrad.R | 2 ergm-4.8.1/ergm/R/ergm.etagradmult.R | 2 ergm-4.8.1/ergm/R/ergm.etamap.R | 2 ergm-4.8.1/ergm/R/ergm.geodistn.R | 2 ergm-4.8.1/ergm/R/ergm.getCDsample.R | 2 ergm-4.8.1/ergm/R/ergm.getMCMCsample.R | 2 ergm-4.8.1/ergm/R/ergm.getnetwork.R | 2 ergm-4.8.1/ergm/R/ergm.initialfit.R | 2 ergm-4.8.1/ergm/R/ergm.llik.R | 2 ergm-4.8.1/ergm/R/ergm.llik.obs.R | 2 ergm-4.8.1/ergm/R/ergm.logitreg.R | 2 ergm-4.8.1/ergm/R/ergm.mple.R | 2 ergm-4.8.1/ergm/R/ergm.pen.glm.R | 2 ergm-4.8.1/ergm/R/ergm.phase12.R | 2 ergm-4.8.1/ergm/R/ergm.pl.R | 12 ergm-4.8.1/ergm/R/ergm.san.R | 2 ergm-4.8.1/ergm/R/ergm.stepping.R | 2 ergm-4.8.1/ergm/R/ergm.stocapprox.R | 4 ergm-4.8.1/ergm/R/ergm.utility.R | 74 ergm-4.8.1/ergm/R/ergmMPLE.R | 2 ergm-4.8.1/ergm/R/ergm_estfun.R | 2 ergm-4.8.1/ergm/R/ergm_keyword.R | 2 ergm-4.8.1/ergm/R/ergm_model.R | 5 ergm-4.8.1/ergm/R/ergm_model.utils.R | 2 ergm-4.8.1/ergm/R/ergm_mplecov.R | 2 ergm-4.8.1/ergm/R/ergm_proposal.R | 13 ergm-4.8.1/ergm/R/ergm_response.R | 2 ergm-4.8.1/ergm/R/ergm_state.R | 2 ergm-4.8.1/ergm/R/ergmlhs.R | 2 ergm-4.8.1/ergm/R/formula.utils.R | 12 ergm-4.8.1/ergm/R/get.node.attr.R | 2 ergm-4.8.1/ergm/R/godfather.R | 2 ergm-4.8.1/ergm/R/gof.ergm.R | 2 ergm-4.8.1/ergm/R/is.curved.R | 2 ergm-4.8.1/ergm/R/is.dyad.independent.R | 2 ergm-4.8.1/ergm/R/is.inCH.R | 2 ergm-4.8.1/ergm/R/is.na.ergm.R | 2 ergm-4.8.1/ergm/R/is.valued.R | 2 ergm-4.8.1/ergm/R/logLik.ergm.R | 7 ergm-4.8.1/ergm/R/mcmc.diagnostics.ergm.R | 2 ergm-4.8.1/ergm/R/network.list.R | 2 ergm-4.8.1/ergm/R/network.update.R | 2 ergm-4.8.1/ergm/R/nonidentifiability.R | 2 ergm-4.8.1/ergm/R/nparam.R | 2 ergm-4.8.1/ergm/R/obs.constraints.R | 2 ergm-4.8.1/ergm/R/parallel.utils.R | 2 ergm-4.8.1/ergm/R/param_names.R | 2 ergm-4.8.1/ergm/R/predict.ergm.R | 2 ergm-4.8.1/ergm/R/print.ergm.R | 2 ergm-4.8.1/ergm/R/print.network.list.R | 2 ergm-4.8.1/ergm/R/print.summary.ergm.R | 2 ergm-4.8.1/ergm/R/rank_test.ergm.R | 2 ergm-4.8.1/ergm/R/rlebdm.R | 17 ergm-4.8.1/ergm/R/simulate.ergm.R | 2 ergm-4.8.1/ergm/R/simulate.formula.R | 2 ergm-4.8.1/ergm/R/summary.ergm.R | 2 ergm-4.8.1/ergm/R/summary.ergm_model.R | 2 ergm-4.8.1/ergm/R/summary.network.list.R | 2 ergm-4.8.1/ergm/R/summary.statistics.network.R | 2 ergm-4.8.1/ergm/R/to_ergm_Cdouble.R | 2 ergm-4.8.1/ergm/R/vcov.ergm.R | 2 ergm-4.8.1/ergm/R/wtd.median.R | 2 ergm-4.8.1/ergm/R/zzz.R | 2 ergm-4.8.1/ergm/build/partial.rdb |binary ergm-4.8.1/ergm/build/stage23.rdb |binary ergm-4.8.1/ergm/inst/CITATION | 4 ergm-4.8.1/ergm/inst/NEWS.Rd | 148 + ergm-4.8.1/ergm/inst/REFERENCES.bib | 14 ergm-4.8.1/ergm/inst/doc/ergm-term-crossRef.html | 1138 +++++++--- ergm-4.8.1/ergm/inst/doc/ergm.R | 42 ergm-4.8.1/ergm/inst/doc/ergm.html | 32 ergm-4.8.1/ergm/inst/doc/nodal_attributes.html | 4 ergm-4.8.1/ergm/inst/include/MHproposal.h | 2 ergm-4.8.1/ergm/inst/include/changestat.h | 2 ergm-4.8.1/ergm/inst/include/edgelist.h | 2 ergm-4.8.1/ergm/inst/include/edgetree.h | 2 ergm-4.8.1/ergm/inst/include/ergm_BDNodeLists.h | 2 ergm-4.8.1/ergm/inst/include/ergm_BDStratBlocks.h | 2 ergm-4.8.1/ergm/inst/include/ergm_BDStrat_proposals.h | 2 ergm-4.8.1/ergm/inst/include/ergm_MHproposal.h | 11 ergm-4.8.1/ergm/inst/include/ergm_MHproposal_bd.h | 2 ergm-4.8.1/ergm/inst/include/ergm_MHproposals_degree.h |only ergm-4.8.1/ergm/inst/include/ergm_MHstorage.h | 2 ergm-4.8.1/ergm/inst/include/ergm_Rutil.h | 2 ergm-4.8.1/ergm/inst/include/ergm_block.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestat.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestat_auxnet.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestat_common.do_not_include_directly.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestat_operator.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestats_auxnet.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestats_operator.h | 2 ergm-4.8.1/ergm/inst/include/ergm_constants.h | 18 ergm-4.8.1/ergm/inst/include/ergm_dyad_hashmap.h | 2 ergm-4.8.1/ergm/inst/include/ergm_dyad_hashmap_utils.h | 2 ergm-4.8.1/ergm/inst/include/ergm_dyadgen.h | 13 ergm-4.8.1/ergm/inst/include/ergm_edgelist.h | 2 ergm-4.8.1/ergm/inst/include/ergm_edgetree.h | 2 ergm-4.8.1/ergm/inst/include/ergm_edgetree_common.do_not_include_directly.h | 2 ergm-4.8.1/ergm/inst/include/ergm_edgetree_inline.do_not_include_directly.h | 2 ergm-4.8.1/ergm/inst/include/ergm_edgetree_types.h | 2 ergm-4.8.1/ergm/inst/include/ergm_etamap.h | 2 ergm-4.8.1/ergm/inst/include/ergm_hash_edgelist.h | 2 ergm-4.8.1/ergm/inst/include/ergm_khash.h | 10 ergm-4.8.1/ergm/inst/include/ergm_kvec.h | 2 ergm-4.8.1/ergm/inst/include/ergm_model.h | 2 ergm-4.8.1/ergm/inst/include/ergm_nodelist.h | 2 ergm-4.8.1/ergm/inst/include/ergm_rlebdm.h | 2 ergm-4.8.1/ergm/inst/include/ergm_state.h | 2 ergm-4.8.1/ergm/inst/include/ergm_storage.h | 2 ergm-4.8.1/ergm/inst/include/ergm_stubs.c | 58 ergm-4.8.1/ergm/inst/include/ergm_unsorted_edgelist.h | 2 ergm-4.8.1/ergm/inst/include/ergm_util.h | 2 ergm-4.8.1/ergm/inst/include/ergm_weighted_population.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtMHproposal.h | 11 ergm-4.8.1/ergm/inst/include/ergm_wtchangestat.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtchangestat_operator.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtchangestats_operator.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtedgetree.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtedgetree_inline.do_not_include_directly.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtmodel.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtstate.h | 2 ergm-4.8.1/ergm/inst/include/model.h | 2 ergm-4.8.1/ergm/inst/include/wtMHproposal.h | 2 ergm-4.8.1/ergm/inst/include/wtchangestat.h | 2 ergm-4.8.1/ergm/inst/include/wtedgetree.h | 2 ergm-4.8.1/ergm/inst/include/wtmodel.h | 2 ergm-4.8.1/ergm/man/Dyads-ergmConstraint-3aee3115.Rd | 2 ergm-4.8.1/ergm/man/Project-ergmTerm-36962a06.Rd |only ergm-4.8.1/ergm/man/b1covrange-ergmTerm-24a903d2.Rd |only ergm-4.8.1/ergm/man/b1factordistinct-ergmTerm-f897b95c.Rd |only ergm-4.8.1/ergm/man/b2covrange-ergmTerm-5e2bcc86.Rd |only ergm-4.8.1/ergm/man/b2factordistinct-ergmTerm-076e6026.Rd |only ergm-4.8.1/ergm/man/ergm-defunct.Rd | 22 ergm-4.8.1/ergm/man/ergm-deprecated.Rd | 32 ergm-4.8.1/ergm/man/ergm-options.Rd | 14 ergm-4.8.1/ergm/man/ergm.mple.Rd | 4 ergm-4.8.1/ergm/man/fixallbut-ergmConstraint-ea96b2e0.Rd | 2 ergm-4.8.1/ergm/man/macros/ergm-spec.Rd | 2 ergm-4.8.1/ergm/man/macros/ergmCSS.Rd | 2 ergm-4.8.1/ergm/man/macros/ergmTerm.Rd | 2 ergm-4.8.1/ergm/man/macros/uid-algo.Rd | 2 ergm-4.8.1/ergm/man/nodecovrange-ergmTerm-7ae91499.Rd |only ergm-4.8.1/ergm/man/nodefactordistinct-ergmTerm-3445048c.Rd |only ergm-4.8.1/ergm/man/nodeicovrange-ergmTerm-29a8edd7.Rd |only ergm-4.8.1/ergm/man/nodeifactordistinct-ergmTerm-25cbd312.Rd |only ergm-4.8.1/ergm/man/nodeocovrange-ergmTerm-382e45c5.Rd |only ergm-4.8.1/ergm/man/nodeofactordistinct-ergmTerm-f159e5dc.Rd |only ergm-4.8.1/ergm/man/rlebdm.Rd | 6 ergm-4.8.1/ergm/man/samplk.Rd | 2 ergm-4.8.1/ergm/man/sampson.Rd | 2 ergm-4.8.1/ergm/src/CD.c | 2 ergm-4.8.1/ergm/src/CD.c.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/CD.h | 2 ergm-4.8.1/ergm/src/CD.h.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/MCMC.c | 2 ergm-4.8.1/ergm/src/MCMC.c.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/MCMC.h | 2 ergm-4.8.1/ergm/src/MCMC.h.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/MHproposal.c | 9 ergm-4.8.1/ergm/src/MHproposal_bd.c | 2 ergm-4.8.1/ergm/src/MHproposals.c | 2 ergm-4.8.1/ergm/src/MHproposals.h | 2 ergm-4.8.1/ergm/src/MHproposals_bipartite.c | 2 ergm-4.8.1/ergm/src/MHproposals_degree.c | 5 ergm-4.8.1/ergm/src/MHproposals_dyadnoise.c | 2 ergm-4.8.1/ergm/src/MHproposals_triadic.c | 14 ergm-4.8.1/ergm/src/MPLE.c | 2 ergm-4.8.1/ergm/src/MPLE.h | 2 ergm-4.8.1/ergm/src/SAN.c | 2 ergm-4.8.1/ergm/src/SAN.c.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/SAN.h | 2 ergm-4.8.1/ergm/src/SAN.h.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/allstatistics.c | 2 ergm-4.8.1/ergm/src/changestat.c | 2 ergm-4.8.1/ergm/src/changestats.c | 65 ergm-4.8.1/ergm/src/changestats.h | 2 ergm-4.8.1/ergm/src/changestats_auxnet.c | 2 ergm-4.8.1/ergm/src/changestats_auxnetalike.c | 2 ergm-4.8.1/ergm/src/changestats_coincidence.c | 2 ergm-4.8.1/ergm/src/changestats_concurrentties.c | 2 ergm-4.8.1/ergm/src/changestats_dgw_sp.c | 80 ergm-4.8.1/ergm/src/changestats_dgw_sp.h | 116 - ergm-4.8.1/ergm/src/changestats_diversity.c |only ergm-4.8.1/ergm/src/changestats_experimental.c | 44 ergm-4.8.1/ergm/src/changestats_experimental.h | 2 ergm-4.8.1/ergm/src/changestats_homoproportion.c | 2 ergm-4.8.1/ergm/src/changestats_indices.c | 2 ergm-4.8.1/ergm/src/changestats_interaction.c | 2 ergm-4.8.1/ergm/src/changestats_internal.c | 2 ergm-4.8.1/ergm/src/changestats_operator.c | 36 ergm-4.8.1/ergm/src/changestats_projection.c |only ergm-4.8.1/ergm/src/changestats_spcache.c | 2 ergm-4.8.1/ergm/src/changestats_test.c | 2 ergm-4.8.1/ergm/src/edgetree.c | 2 ergm-4.8.1/ergm/src/edgetree_inline.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/ergm_Rutil.c |only ergm-4.8.1/ergm/src/ergm_dyad_hashmap_utils.c | 2 ergm-4.8.1/ergm/src/ergm_dyadgen.c | 56 ergm-4.8.1/ergm/src/ergm_omp.c | 2 ergm-4.8.1/ergm/src/ergm_omp.h | 2 ergm-4.8.1/ergm/src/ergm_rlebdm.c | 2 ergm-4.8.1/ergm/src/ergm_state.c | 2 ergm-4.8.1/ergm/src/ergm_type_defs_common.h | 2 ergm-4.8.1/ergm/src/ergm_wtstate.c | 2 ergm-4.8.1/ergm/src/ergm_wttype_defs_common.h | 2 ergm-4.8.1/ergm/src/etamap.c | 31 ergm-4.8.1/ergm/src/geodist.c | 2 ergm-4.8.1/ergm/src/godfather.c | 2 ergm-4.8.1/ergm/src/init.c | 4 ergm-4.8.1/ergm/src/model.c | 25 ergm-4.8.1/ergm/src/netstats.c | 2 ergm-4.8.1/ergm/src/test_weighted_population.c | 2 ergm-4.8.1/ergm/src/wtCD.c | 2 ergm-4.8.1/ergm/src/wtCD.h | 2 ergm-4.8.1/ergm/src/wtMCMC.c | 2 ergm-4.8.1/ergm/src/wtMCMC.h | 2 ergm-4.8.1/ergm/src/wtMHproposal.c | 9 ergm-4.8.1/ergm/src/wtMHproposals.c | 2 ergm-4.8.1/ergm/src/wtSAN.c | 2 ergm-4.8.1/ergm/src/wtSAN.h | 2 ergm-4.8.1/ergm/src/wtchangestats.c | 2 ergm-4.8.1/ergm/src/wtchangestats.h | 2 ergm-4.8.1/ergm/src/wtchangestats_operator.c | 6 ergm-4.8.1/ergm/src/wtchangestats_operator.h | 2 ergm-4.8.1/ergm/src/wtchangestats_test.c | 2 ergm-4.8.1/ergm/src/wtedgetree.c | 2 ergm-4.8.1/ergm/src/wtedgetree_inline.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/wtgodfather.c | 2 ergm-4.8.1/ergm/src/wtmodel.c | 28 ergm-4.8.1/ergm/src/wtnetstats.c | 2 ergm-4.8.1/ergm/tests/requireNamespaceTest.R | 2 ergm-4.8.1/ergm/tests/testthat.R | 2 ergm-4.8.1/ergm/tests/testthat/helper-edges-MLE.R | 2 ergm-4.8.1/ergm/tests/testthat/helper-expect-summary.R | 2 ergm-4.8.1/ergm/tests/testthat/setup.R |only ergm-4.8.1/ergm/tests/testthat/test-C-curved.R | 8 ergm-4.8.1/ergm/tests/testthat/test-as.network.numeric.R | 66 ergm-4.8.1/ergm/tests/testthat/test-basis.R | 2 ergm-4.8.1/ergm/tests/testthat/test-bd.R | 2 ergm-4.8.1/ergm/tests/testthat/test-bipartite-missing-data.R | 2 ergm-4.8.1/ergm/tests/testthat/test-bridge-target.stats.R | 2 ergm-4.8.1/ergm/tests/testthat/test-c-ergm_model.R | 2 ergm-4.8.1/ergm/tests/testthat/test-checkpointing.R | 2 ergm-4.8.1/ergm/tests/testthat/test-constrain-blockdiag.R | 6 ergm-4.8.1/ergm/tests/testthat/test-constrain-degrees-edges.R | 2 ergm-4.8.1/ergm/tests/testthat/test-constrain-dind.R | 2 ergm-4.8.1/ergm/tests/testthat/test-constrain-egocentric.R | 2 ergm-4.8.1/ergm/tests/testthat/test-constraints.R | 29 ergm-4.8.1/ergm/tests/testthat/test-drop.R | 2 ergm-4.8.1/ergm/tests/testthat/test-ergm-godfather.R | 2 ergm-4.8.1/ergm/tests/testthat/test-ergm-proposal-unload.R | 2 ergm-4.8.1/ergm/tests/testthat/test-ergm-san.R | 2 ergm-4.8.1/ergm/tests/testthat/test-ergm-term-doc.R | 6 ergm-4.8.1/ergm/tests/testthat/test-ergm.bridge.llr.R | 2 ergm-4.8.1/ergm/tests/testthat/test-ergmMPLE.R | 2 ergm-4.8.1/ergm/tests/testthat/test-fix.curved.R | 2 ergm-4.8.1/ergm/tests/testthat/test-geodistn.R | 2 ergm-4.8.1/ergm/tests/testthat/test-gflomiss.R | 2 ergm-4.8.1/ergm/tests/testthat/test-gmonkmiss.R | 2 ergm-4.8.1/ergm/tests/testthat/test-gof.R | 2 ergm-4.8.1/ergm/tests/testthat/test-level-select.R | 2 ergm-4.8.1/ergm/tests/testthat/test-metrics.R | 2 ergm-4.8.1/ergm/tests/testthat/test-miss-dep.R | 2 ergm-4.8.1/ergm/tests/testthat/test-miss.CD.R | 4 ergm-4.8.1/ergm/tests/testthat/test-miss.R | 4 ergm-4.8.1/ergm/tests/testthat/test-mple-cov.R | 2 ergm-4.8.1/ergm/tests/testthat/test-mple-largenetwork.R | 2 ergm-4.8.1/ergm/tests/testthat/test-mple-offset.R | 2 ergm-4.8.1/ergm/tests/testthat/test-mple-target.R | 2 ergm-4.8.1/ergm/tests/testthat/test-networkLite.R | 2 ergm-4.8.1/ergm/tests/testthat/test-nodemix.R | 2 ergm-4.8.1/ergm/tests/testthat/test-nodrop.R | 2 ergm-4.8.1/ergm/tests/testthat/test-nonident-test.R | 2 ergm-4.8.1/ergm/tests/testthat/test-nonunique-names.R | 2 ergm-4.8.1/ergm/tests/testthat/test-offsets.R | 2 ergm-4.8.1/ergm/tests/testthat/test-operators.R | 2 ergm-4.8.1/ergm/tests/testthat/test-parallel.R | 2 ergm-4.8.1/ergm/tests/testthat/test-predict.ergm.R | 2 ergm-4.8.1/ergm/tests/testthat/test-proposal-bdstrattnt.R | 2 ergm-4.8.1/ergm/tests/testthat/test-runtime-diags.R | 2 ergm-4.8.1/ergm/tests/testthat/test-scoping.R | 2 ergm-4.8.1/ergm/tests/testthat/test-shrink-into-CH.R | 2 ergm-4.8.1/ergm/tests/testthat/test-simple.R | 2 ergm-4.8.1/ergm/tests/testthat/test-simulate-batch.R | 2 ergm-4.8.1/ergm/tests/testthat/test-snctrl.R | 2 ergm-4.8.1/ergm/tests/testthat/test-stocapprox.R | 6 ergm-4.8.1/ergm/tests/testthat/test-target-offset.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-For.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-Offset.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-Sum.R |only ergm-4.8.1/ergm/tests/testthat/test-term-attrcov.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-b12factor.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-b12nodematch.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-bipartite.R | 42 ergm-4.8.1/ergm/tests/testthat/test-term-directed.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-diversity.R |only ergm-4.8.1/ergm/tests/testthat/test-term-edgecov.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-errors.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-flexible.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-gw-sp.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-hamming.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-mm.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-options.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-project.R |only ergm-4.8.1/ergm/tests/testthat/test-term-undirected.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-valued.R | 2 ergm-4.8.1/ergm/tests/testthat/test-u-function.R | 6 ergm-4.8.1/ergm/tests/testthat/test-update.network.R | 2 ergm-4.8.1/ergm/tests/testthat/test-valued-sim.R | 5 ergm-4.8.1/ergm/tests/testthat/test-valued-terms.R | 6 ergm-4.8.1/ergm/tests/testthat/test-weighted-population.R | 2 375 files changed, 2498 insertions(+), 1632 deletions(-)
Title: Detect Elevations and Gaps in Mapped Sequencing Read Coverage
Description: Automate the detection of gaps and elevations in mapped sequencing
read coverage using a 2D pattern-matching algorithm. 'ProActive' detects, characterizes
and visualizes read coverage patterns in both genomes and metagenomes. Optionally,
users may provide gene annotations associated with their genome or metagenome
in the form of a .gff file. In this case, 'ProActive' will generate an additional
output table containing the gene annotations found within the detected regions of gapped
and elevated read coverage. Additionally, users can search for gene
annotations of interest in the output read coverage plots.
Author: Jessie Maier [aut, cre, cph] ,
Manuel Kleiner [aut, ths]
Maintainer: Jessie Maier <jlmaier@ncsu.edu>
Diff between ProActive versions 0.0.2 dated 2025-01-14 and 0.1.0 dated 2025-01-21
ProActive-0.0.2/ProActive/R/ProActive.R |only ProActive-0.0.2/ProActive/man/ProActive.Rd |only ProActive-0.1.0/ProActive/DESCRIPTION | 13 ProActive-0.1.0/ProActive/MD5 | 50 ProActive-0.1.0/ProActive/NAMESPACE | 5 ProActive-0.1.0/ProActive/NEWS.md | 13 ProActive-0.1.0/ProActive/R/GPsInElevGaps.R | 16 ProActive-0.1.0/ProActive/R/ProActive-package.R | 21 ProActive-0.1.0/ProActive/R/ProActiveDetect.R |only ProActive-0.1.0/ProActive/R/bestMatchListFunctions.R | 19 ProActive-0.1.0/ProActive/R/chunkingFunctions.R | 2 ProActive-0.1.0/ProActive/R/geneAnnotationPlot.R |only ProActive-0.1.0/ProActive/R/geneAnnotationSearch.R |only ProActive-0.1.0/ProActive/R/patternMatcher.R | 7 ProActive-0.1.0/ProActive/R/plotProActiveResults.R | 5 ProActive-0.1.0/ProActive/R/sampleMetagenomeResults.R | 4 ProActive-0.1.0/ProActive/R/sysdata.rda |binary ProActive-0.1.0/ProActive/README.md | 119 + ProActive-0.1.0/ProActive/inst/doc/ProActiveVignette.R | 53 ProActive-0.1.0/ProActive/inst/doc/ProActiveVignette.Rmd | 347 +++-- ProActive-0.1.0/ProActive/inst/doc/ProActiveVignette.html | 678 ++++++---- ProActive-0.1.0/ProActive/man/GPsInElevGaps.Rd | 12 ProActive-0.1.0/ProActive/man/ProActive-package.Rd | 22 ProActive-0.1.0/ProActive/man/ProActiveDetect.Rd |only ProActive-0.1.0/ProActive/man/classifSumm.Rd | 5 ProActive-0.1.0/ProActive/man/geneAnnotationPlot.Rd |only ProActive-0.1.0/ProActive/man/geneAnnotationSearch.Rd |only ProActive-0.1.0/ProActive/man/sampleMetagenomeResults.Rd | 4 ProActive-0.1.0/ProActive/tests/testthat/test-testProActive.R | 4 ProActive-0.1.0/ProActive/vignettes/ProActiveVignette.Rmd | 347 +++-- 30 files changed, 1162 insertions(+), 584 deletions(-)
Title: R Toolkit for 'Databricks'
Description: Collection of utilities that improve using 'Databricks' from R.
Primarily functions that wrap specific 'Databricks' APIs
(<https://docs.databricks.com/api>), 'RStudio' connection pane support, quality
of life functions to make 'Databricks' simpler to use.
Author: Zac Davies [aut, cre],
Rafi Kurlansik [aut],
Databricks [cph, fnd]
Maintainer: Zac Davies <zac@databricks.com>
Diff between brickster versions 0.2.5 dated 2024-11-13 and 0.2.6 dated 2025-01-21
DESCRIPTION | 6 +-- MD5 | 56 +++++++++++++++---------------- NEWS.md | 4 ++ R/package-auth.R | 2 - R/request-helpers.R | 12 +++--- R/volume-fs.R | 2 - inst/doc/cluster-management.html | 4 +- inst/doc/managing-jobs.html | 4 +- inst/doc/remote-repl.html | 4 +- inst/doc/setup-auth.html | 4 +- tests/testthat/test-auth.R | 43 +++++++++++------------ tests/testthat/test-clusters.R | 4 -- tests/testthat/test-dbfs.R | 5 -- tests/testthat/test-execution-contexts.R | 2 - tests/testthat/test-experiments.R | 2 - tests/testthat/test-feature-store.R | 2 - tests/testthat/test-jobs.R | 5 +- tests/testthat/test-libraries.R | 3 - tests/testthat/test-misc-helpers.R | 2 - tests/testthat/test-mlflow-dbrx.R | 4 -- tests/testthat/test-repos.R | 2 - tests/testthat/test-secrets.R | 2 - tests/testthat/test-sql-connector.R | 2 - tests/testthat/test-sql-execution.R | 2 - tests/testthat/test-unity-catalog.R | 5 -- tests/testthat/test-vector-search.R | 4 -- tests/testthat/test-volumes.R | 5 -- tests/testthat/test-warehouses.R | 2 - tests/testthat/test-workspace-folder.R | 2 - 29 files changed, 92 insertions(+), 104 deletions(-)
Title: Robust Bayesian Longitudinal Regularized Semiparametric Mixed
Models
Description: Our recently developed fully robust Bayesian semiparametric mixed-effect model for high-dimensional longitudinal studies with heterogeneous observations can be implemented through this package. This model can distinguish between time-varying interactions and constant-effect-only cases to avoid model misspecifications. Facilitated by spike-and-slab priors, this model leads to superior performance in estimation, identification and statistical inference. In particular, robust Bayesian inferences in terms of valid Bayesian credible intervals on both parametric and nonparametric effects can be validated on finite samples. The Markov chain Monte Carlo algorithms of the proposed and alternative models are efficiently implemented in 'C++'.
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between Blend versions 0.1.0 dated 2024-11-25 and 0.1.1 dated 2025-01-20
DESCRIPTION | 12 +++++----- MD5 | 12 +++++----- R/Blend-package.R | 7 ++---- R/Blend.R | 11 ++++----- README.md | 59 ++++++++++++++++++++++++++++++++++++++++++++++++++- man/Blend-package.Rd | 7 ++---- man/Blend.Rd | 9 ++----- 7 files changed, 84 insertions(+), 33 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-08 2.0.0
Title: NASCAR Race Data
Description: A collection of NASCAR race, driver, owner and manufacturer data across the three major NASCAR divisions: NASCAR Cup Series, NASCAR Xfinity Series, and NASCAR Craftsman Truck Series. The curated data begins with the 1949 season and extends through the end of the 2024 season. Explore race, season, or career performance for drivers, teams, and manufacturers throughout NASCAR's history. Data was sourced with permission from DriverAverages.com.
Author: Kyle Grealis [aut, cre] ,
Gabriel Odom [ctb]
Maintainer: Kyle Grealis <kylegrealis@icloud.com>
Diff between nascaR.data versions 1.0.0 dated 2024-07-09 and 2.1.0 dated 2025-01-20
nascaR.data-1.0.0/nascaR.data/R/cup_driver_career.R |only nascaR.data-1.0.0/nascaR.data/R/cup_driver_season.R |only nascaR.data-1.0.0/nascaR.data/R/cup_mfg_overall.R |only nascaR.data-1.0.0/nascaR.data/R/cup_mfg_season.R |only nascaR.data-1.0.0/nascaR.data/R/cup_owner_career.R |only nascaR.data-1.0.0/nascaR.data/R/cup_owner_season.R |only nascaR.data-1.0.0/nascaR.data/R/cup_race_data.R |only nascaR.data-1.0.0/nascaR.data/R/truck_driver_career.R |only nascaR.data-1.0.0/nascaR.data/R/truck_driver_season.R |only nascaR.data-1.0.0/nascaR.data/R/truck_mfg_overall.R |only nascaR.data-1.0.0/nascaR.data/R/truck_mfg_season.R |only nascaR.data-1.0.0/nascaR.data/R/truck_owner_career.R |only nascaR.data-1.0.0/nascaR.data/R/truck_owner_season.R |only nascaR.data-1.0.0/nascaR.data/R/truck_race_data.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_driver_career.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_driver_season.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_mfg_overall.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_mfg_season.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_owner_career.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_owner_season.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_race_data.R |only nascaR.data-1.0.0/nascaR.data/build |only nascaR.data-1.0.0/nascaR.data/data/cup_driver_career.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_driver_season.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_mfg_overall.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_mfg_season.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_owner_career.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_owner_season.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_race_data.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_driver_career.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_driver_season.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_mfg_overall.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_mfg_season.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_owner_career.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_owner_season.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_race_data.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_driver_career.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_driver_season.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_mfg_overall.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_mfg_season.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_owner_career.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_owner_season.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_race_data.rda |only nascaR.data-1.0.0/nascaR.data/inst/WORDLIST |only nascaR.data-1.0.0/nascaR.data/inst/doc |only nascaR.data-1.0.0/nascaR.data/man/cup_driver_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_driver_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_mfg_overall.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_mfg_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_owner_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_owner_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_race_data.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_driver_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_driver_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_mfg_overall.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_mfg_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_owner_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_owner_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_race_data.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_driver_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_driver_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_mfg_overall.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_mfg_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_owner_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_owner_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_race_data.Rd |only nascaR.data-1.0.0/nascaR.data/vignettes |only nascaR.data-2.1.0/nascaR.data/DESCRIPTION | 22 - nascaR.data-2.1.0/nascaR.data/MD5 | 111 +----- nascaR.data-2.1.0/nascaR.data/NAMESPACE | 33 + nascaR.data-2.1.0/nascaR.data/NEWS.md | 27 + nascaR.data-2.1.0/nascaR.data/R/data.R |only nascaR.data-2.1.0/nascaR.data/R/get_driver.R |only nascaR.data-2.1.0/nascaR.data/R/get_manufacturer.R |only nascaR.data-2.1.0/nascaR.data/R/get_team.R |only nascaR.data-2.1.0/nascaR.data/R/nascaR.data-package.R |only nascaR.data-2.1.0/nascaR.data/R/utils.R |only nascaR.data-2.1.0/nascaR.data/README.md | 195 ++++++----- nascaR.data-2.1.0/nascaR.data/data/cup_series.rda |only nascaR.data-2.1.0/nascaR.data/data/truck_series.rda |only nascaR.data-2.1.0/nascaR.data/data/xfinity_series.rda |only nascaR.data-2.1.0/nascaR.data/inst/extdata |only nascaR.data-2.1.0/nascaR.data/inst/images/hex-logo.png |only nascaR.data-2.1.0/nascaR.data/inst/updates |only nascaR.data-2.1.0/nascaR.data/man/cup_series.Rd |only nascaR.data-2.1.0/nascaR.data/man/figures/logo.svg |only nascaR.data-2.1.0/nascaR.data/man/get_driver_info.Rd |only nascaR.data-2.1.0/nascaR.data/man/get_manufacturer_info.Rd |only nascaR.data-2.1.0/nascaR.data/man/get_team_info.Rd |only nascaR.data-2.1.0/nascaR.data/man/nascaR.data-package.Rd |only nascaR.data-2.1.0/nascaR.data/man/selected_series_data.Rd |only nascaR.data-2.1.0/nascaR.data/man/truck_series.Rd |only nascaR.data-2.1.0/nascaR.data/man/xfinity_series.Rd |only 93 files changed, 215 insertions(+), 173 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre],
Ruth Keogh [aut],
Edouard F. Bonneville [aut],
Claus Thorn Ekstroem [ctb]
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>
Diff between smcfcs versions 1.9.1 dated 2024-12-04 and 1.9.2 dated 2025-01-20
DESCRIPTION | 6 - MD5 | 10 +- R/smcfcs.r | 24 +++--- inst/doc/smcfcs-vignette.html | 4 - inst/doc/smcfcs_coverror-vignette.html | 4 - tests/testthat/test_dtsam.r | 117 +++++++++++++++++++++++++++++++++ 6 files changed, 140 insertions(+), 25 deletions(-)
Title: Empirical Testing of Surrogate Paradox Assumptions
Description: Provides functions to nonparametrically assess assumptions necessary to prevent the surrogate paradox through hypothesis tests of stochastic dominance, monotonicity of regression functions, and non-negative residual treatment effects. More details are available in Hsiao et al 2025 (under review). A tutorial for this package can be found at <https://laylaparast.com/home/SurrogateParadoxTest.html>.
Author: Emily Hsiao [aut, cre]
Maintainer: Emily Hsiao <ehsiao@utexas.edu>
Diff between SurrogateParadoxTest versions 1.0 dated 2024-12-08 and 2.0 dated 2025-01-20
SurrogateParadoxTest-1.0/SurrogateParadoxTest/R/test-script-2024-09-18.R |only SurrogateParadoxTest-2.0/SurrogateParadoxTest/DESCRIPTION | 18 +++++----- SurrogateParadoxTest-2.0/SurrogateParadoxTest/MD5 | 10 ++--- SurrogateParadoxTest-2.0/SurrogateParadoxTest/NAMESPACE | 2 - SurrogateParadoxTest-2.0/SurrogateParadoxTest/R/test-script-2025-01-20.r |only SurrogateParadoxTest-2.0/SurrogateParadoxTest/man/monotonicity_test.Rd | 5 -- SurrogateParadoxTest-2.0/SurrogateParadoxTest/man/test_assumptions.Rd | 16 +++++--- 7 files changed, 25 insertions(+), 26 deletions(-)
More information about SurrogateParadoxTest at CRAN
Permanent link
Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra.
Differences with other sparse matrix packages are:
(1) we only support (essentially) one sparse matrix format,
(2) based on transparent and simple structure(s),
(3) tailored for MCMC calculations within G(M)RF.
(4) and it is fast and scalable (with the extension package spam64).
Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.
Author: Reinhard Furrer [aut, cre] ,
Florian Gerber [aut] ,
Roman Flury [aut] ,
Daniel Gerber [ctb],
Kaspar Moesinger [ctb],
Annina Cincera [ctb],
Youcef Saad [ctb] ,
Esmond G. Ng [ctb] ,
Barry W. Peyton [ctb] ,
Joseph W.H. Liu [ctb] ,
Alan D. George [ctb] , [...truncated...]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam versions 2.11-0 dated 2024-10-03 and 2.11-1 dated 2025-01-20
spam-2.11-0/spam/tests/Examples |only spam-2.11-1/spam/DESCRIPTION | 8 ++-- spam-2.11-1/spam/MD5 | 27 ++++++-------- spam-2.11-1/spam/NEWS.md | 12 +++++- spam-2.11-1/spam/inst/CITATION | 6 +-- spam-2.11-1/spam/inst/doc/spam.pdf |binary spam-2.11-1/spam/tests/demo_cholesky.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_jss10-example1.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_jss10-figures-table.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_jss15-BYM.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_jss15-Leroux.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_spam.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_timing.Rout.save | 4 +- spam-2.11-1/spam/tests/jss_areal_counts.Rout.save | 4 +- spam-2.11-1/spam/tests/testthat.Rout.save | 4 +- 15 files changed, 49 insertions(+), 40 deletions(-)
Title: Multiblock Data Fusion in Statistics and Machine Learning
Description: Functions and datasets to support Smilde, Næs and Liland (2021, ISBN: 978-1-119-60096-1)
"Multiblock Data Fusion in Statistics and Machine Learning - Applications in the Natural and Life Sciences".
This implements and imports a large collection of methods for multiblock data analysis with common interfaces, result- and plotting
functions, several real data sets and six vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
,
Solve Saeboe [ctb],
Stefan Schrunner [rev]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between multiblock versions 0.8.8.2 dated 2024-09-16 and 0.8.9.0 dated 2025-01-20
multiblock-0.8.8.2/multiblock/R/asca.R |only multiblock-0.8.8.2/multiblock/R/asca_plots.R |only multiblock-0.8.8.2/multiblock/R/asca_results.R |only multiblock-0.8.8.2/multiblock/man/asca.Rd |only multiblock-0.8.8.2/multiblock/man/asca_plots.Rd |only multiblock-0.8.8.2/multiblock/man/asca_results.Rd |only multiblock-0.8.9.0/multiblock/DESCRIPTION | 12 multiblock-0.8.9.0/multiblock/MD5 | 36 -- multiblock-0.8.9.0/multiblock/NAMESPACE | 20 - multiblock-0.8.9.0/multiblock/NEWS | 4 multiblock-0.8.9.0/multiblock/R/direct_export.R | 24 + multiblock-0.8.9.0/multiblock/R/lpls_results.R | 1 multiblock-0.8.9.0/multiblock/README.md | 2 multiblock-0.8.9.0/multiblock/build/vignette.rds |binary multiblock-0.8.9.0/multiblock/inst/doc/vignette_A_data.html | 2 multiblock-0.8.9.0/multiblock/inst/doc/vignette_B_basic.html | 6 multiblock-0.8.9.0/multiblock/inst/doc/vignette_C_unsupervised.html | 8 multiblock-0.8.9.0/multiblock/inst/doc/vignette_D_asca.html | 8 multiblock-0.8.9.0/multiblock/inst/doc/vignette_E_supervised.html | 168 +++++----- multiblock-0.8.9.0/multiblock/inst/doc/vignette_F_complex.html | 4 multiblock-0.8.9.0/multiblock/man/reexports.Rd | 10 multiblock-0.8.9.0/multiblock/src/crossprods.cpp | 8 22 files changed, 170 insertions(+), 143 deletions(-)
Title: Simple Handling of Labelled Data
Description: Simple handling of survey data. Smart handling of meta-information like e.g. variable-labels value-labels and scale-levels. Easy access and validation of meta-information. Useage of value labels and values respectively for subsetting and recoding data.
Author: Christof Lewerenz [aut, cre]
Maintainer: Christof Lewerenz <christof.lewerenz@gmx.net>
Diff between ilabelled versions 1.0.0 dated 2024-08-21 and 1.0.1 dated 2025-01-20
ilabelled-1.0.0/ilabelled/R/sample_data.R |only ilabelled-1.0.1/ilabelled/DESCRIPTION | 6 ilabelled-1.0.1/ilabelled/MD5 | 51 ++--- ilabelled-1.0.1/ilabelled/R/coerce.R | 6 ilabelled-1.0.1/ilabelled/R/copy.R | 52 +---- ilabelled-1.0.1/ilabelled/R/helper.R | 24 ++ ilabelled-1.0.1/ilabelled/R/label.R | 12 - ilabelled-1.0.1/ilabelled/R/labelled.R | 29 +- ilabelled-1.0.1/ilabelled/R/labels.R | 130 +++---------- ilabelled-1.0.1/ilabelled/R/missing.R | 5 ilabelled-1.0.1/ilabelled/R/recode.R | 2 ilabelled-1.0.1/ilabelled/R/scale.R | 11 - ilabelled-1.0.1/ilabelled/R/zzz.R | 12 - ilabelled-1.0.1/ilabelled/build/vignette.rds |binary ilabelled-1.0.1/ilabelled/inst/doc/class-coercion.html | 2 ilabelled-1.0.1/ilabelled/inst/doc/class-declaration.html | 2 ilabelled-1.0.1/ilabelled/inst/doc/indexation.html | 2 ilabelled-1.0.1/ilabelled/inst/doc/meta-information.html | 2 ilabelled-1.0.1/ilabelled/man/dot-eval_dots_arg.Rd |only ilabelled-1.0.1/ilabelled/man/dot-valid_labels.Rd | 2 ilabelled-1.0.1/ilabelled/man/i_copy.Rd | 8 ilabelled-1.0.1/ilabelled/man/i_labels.Rd | 2 ilabelled-1.0.1/ilabelled/tests/testthat/test-annotation.R | 7 ilabelled-1.0.1/ilabelled/tests/testthat/test-copy.R | 12 - ilabelled-1.0.1/ilabelled/tests/testthat/test-eval_dots.R |only ilabelled-1.0.1/ilabelled/tests/testthat/test-labels.R | 39 +++ ilabelled-1.0.1/ilabelled/tests/testthat/test-scale.R | 11 - ilabelled-1.0.1/ilabelled/tests/testthat/test-subset.R | 7 28 files changed, 200 insertions(+), 236 deletions(-)
Title: Simple Presentation of Estimated Exponential Semi-Variograms
Description: User friendly interface based on the R package 'gstat' to fit
exponential parametric models to empirical semi-variograms in order to
model the spatial correlation structure of health data. Geo-located
health outcomes of survey participants may be used to model spatial
effects on health in an ego-centred approach. The package contains a
range of functions to help explore the spatial structure of the data
as well as visualize the fit of exponential models for various
metaparameter combinations with respect to the number of lag intervals
and maximal distance. Furthermore, the outcome of interest can be
adjusted for covariates by fitting a linear regression in a
preliminary step before the semi-variogram fitting process.
Author: Julia Dyck [aut, cre],
Odile Sauzet [aut],
Jan-Ole Koslik [aut]
Maintainer: Julia Dyck <j.dyck@uni-bielefeld.de>
Diff between EgoCor versions 1.2.0 dated 2024-03-28 and 1.3.0 dated 2025-01-20
DESCRIPTION | 11 ++++++----- MD5 | 30 ++++++++++++++++++++---------- R/coords.plot.function.R | 21 ++++++++++++++++++--- R/distance.info.function.R | 11 ++++++++--- R/vario.mod.function.gstat.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Intro_to_EgoCor.R | 4 ++-- inst/doc/Intro_to_EgoCor.html | 24 +++++++++++------------- man/coords.plot.Rd | 7 ++++++- man/distance.info.Rd | 6 ++++-- tests |only 12 files changed, 77 insertions(+), 41 deletions(-)
Title: A Class for Working with Time Series Data Based on 'data.table'
and 'R6' with Largely Optional Reference Semantics
Description: Basic time series functionalities such as listing of missing
values, application of arbitrary aggregation as well as rolling (asymmetric)
window functions and automatic detection of periodicity. As it is mainly
based on 'data.table', it is fast and (in combination with the 'R6' package)
offers reference semantics. In addition to its native R6 interface, it
provides an S3 interface for those who prefer the latter. Finally yet
importantly, its functional approach allows for incorporating
functionalities from many other packages.
Author: Gerold Hepp [aut, cre]
Maintainer: Gerold Hepp <gisler@hepp.cc>
Diff between DTSg versions 1.1.3 dated 2023-09-27 and 2.0.0 dated 2025-01-20
DTSg-1.1.3/DTSg/R/deprecated.R |only DTSg-1.1.3/DTSg/inst/tinytest/test_deprecated.R |only DTSg-2.0.0/DTSg/DESCRIPTION | 14 DTSg-2.0.0/DTSg/MD5 | 60 DTSg-2.0.0/DTSg/NAMESPACE | 17 DTSg-2.0.0/DTSg/NEWS.md | 122 - DTSg-2.0.0/DTSg/R/ClassDTSg.R | 296 +-- DTSg-2.0.0/DTSg/R/Swrappers.R | 29 DTSg-2.0.0/DTSg/R/TALFs.R | 504 ++---- DTSg-2.0.0/DTSg/R/aaa.R | 17 DTSg-2.0.0/DTSg/R/assertives.R | 68 DTSg-2.0.0/DTSg/R/utils.R | 11 DTSg-2.0.0/DTSg/README.md | 2 DTSg-2.0.0/DTSg/build/vignette.rds |binary DTSg-2.0.0/DTSg/inst/doc/a_basicUsage.R | 32 DTSg-2.0.0/DTSg/inst/doc/a_basicUsage.html | 1275 +++++++++------- DTSg-2.0.0/DTSg/inst/doc/b_advancedUsage.R | 34 DTSg-2.0.0/DTSg/inst/doc/b_advancedUsage.Rmd | 18 DTSg-2.0.0/DTSg/inst/doc/b_advancedUsage.html | 969 +++++++----- DTSg-2.0.0/DTSg/inst/tinytest/data.R | 8 DTSg-2.0.0/DTSg/inst/tinytest/test_DTSg.R | 98 + DTSg-2.0.0/DTSg/inst/tinytest/test_S3WrapperGenerator.R | 11 DTSg-2.0.0/DTSg/inst/tinytest/test_TALFs.R | 10 DTSg-2.0.0/DTSg/inst/tinytest/test_assertives.R | 52 DTSg-2.0.0/DTSg/inst/tinytest/test_utils.R | 4 DTSg-2.0.0/DTSg/man/DTSg.Rd | 25 DTSg-2.0.0/DTSg/man/TALFs.Rd | 61 DTSg-2.0.0/DTSg/man/aggregate.DTSg.Rd | 18 DTSg-2.0.0/DTSg/man/colapply.DTSg.Rd | 15 DTSg-2.0.0/DTSg/man/interpolateLinear.Rd | 6 DTSg-2.0.0/DTSg/man/subset.DTSg.Rd | 15 DTSg-2.0.0/DTSg/vignettes/b_advancedUsage.Rmd | 18 32 files changed, 2029 insertions(+), 1780 deletions(-)
Title: Estimate Quantitative Genetics Parameters from Generalised
Linear Mixed Models
Description: Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observed phenotypic mean, phenotypic variance and additive genetic variance.
Author: Pierre de Villemereuil [aut, cre]
Maintainer: Pierre de Villemereuil <pierre.de-villemereuil@mnhn.fr>
Diff between QGglmm versions 0.7.4 dated 2020-01-07 and 0.8.0 dated 2025-01-20
DESCRIPTION | 16 +- MD5 | 44 +++---- NEWS.md | 11 + R/source.R | 151 +++++++++++++++--------- R/source.icc.R | 193 ++++++++++++++++++++----------- R/source.mv.R | 278 +++++++++++++++++++++++++++++++--------------- R/source.ordinal.R | 16 +- README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/QGglmmHowTo.Rnw | 2 inst/doc/QGglmmHowTo.pdf |binary man/QGicc.Rd | 14 -- man/QGlink.funcs.Rd | 28 +++- man/QGmvicc.Rd | 26 +--- man/QGmvmean.Rd | 7 - man/QGmvparams.Rd | 24 +-- man/QGmvpred.Rd | 12 - man/QGmvpsi.Rd | 7 - man/QGparams.Rd | 17 -- man/QGpred.Rd | 10 - man/QGvcov.Rd | 8 - vignettes/QGglmmHowTo.Rnw | 2 23 files changed, 525 insertions(+), 345 deletions(-)
Title: Fast Creation of Dummy (Binary) Columns and Rows from
Categorical Variables
Description: Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().
Author: Jacob Kaplan [aut, cre] ,
Benjamin Schlegel [ctb]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between fastDummies versions 1.7.4 dated 2024-08-16 and 1.7.5 dated 2025-01-20
DESCRIPTION | 8 - MD5 | 20 +-- NEWS.md | 7 + R/dummy_cols.R | 188 +++++++++++++++++++++-------------- R/dummy_rows.R | 35 ++++-- build/vignette.rds |binary inst/doc/making-dummy-rows.html | 6 - inst/doc/making-dummy-variables.html | 6 - man/dummy_cols.Rd | 20 ++- man/dummy_columns.Rd | 20 ++- tests/testthat/test-columns.R | 17 ++- 11 files changed, 205 insertions(+), 122 deletions(-)
Title: Causal Inference and Prediction in Cohort-Based Analyses
Description: Numerous functions for cohort-based analyses, either for prediction or causal inference. For causal inference, it includes Inverse Probability Weighting and G-computation for marginal estimation of an exposure effect when confounders are expected. We deal with binary outcomes, times-to-events, competing events, and multi-state data. For multistate data, semi-Markov model with interval censoring may be considered, and we propose the possibility to consider the excess of mortality related to the disease compared to reference lifetime tables. For predictive studies, we propose a set of functions to estimate time-dependent receiver operating characteristic (ROC) curves with the possible consideration of right-censoring times-to-events or the presence of confounders. Finally, several functions are available to assess time-dependent ROC curves or survival curves from aggregated data.
Author: Yohann Foucher [aut, cre] ,
Florent Le Borgne [aut],
Arthur Chatton [aut]
Maintainer: Yohann Foucher <Yohann.Foucher@univ-poitiers.fr>
Diff between RISCA versions 1.0.5 dated 2024-03-22 and 1.0.6 dated 2025-01-20
DESCRIPTION | 12 MD5 | 46 NAMESPACE | 2 R/markov.3states.rsadd.R | 1390 ++++++++++++++------------- R/markov.4states.rsadd.R | 1914 ++++++++++++++++++++------------------ R/semi.markov.3states.rsadd.R | 1394 ++++++++++++++------------- R/semi.markov.4states.rsadd.R | 1944 ++++++++++++++++++++------------------- data/dataCSL.rda |binary data/dataDIVAT1.rda |binary data/dataDIVAT2.rda |binary data/dataDIVAT3.rda |binary data/dataDIVAT4.rda |binary data/dataDIVAT5.rda |binary data/dataFTR.rda |binary data/dataHepatology.rda |binary data/dataKTFS.rda |binary data/dataKi67.rda |binary data/dataOFSEP.rda |binary data/dataSTR.rda |binary data/fr.ratetable.rda |binary man/markov.3states.rsadd.Rd | 2 man/markov.4states.rsadd.Rd | 2 man/roc.net.Rd | 2 man/semi.markov.3states.rsadd.Rd | 6 24 files changed, 3536 insertions(+), 3178 deletions(-)
Title: Markdown Parser and Renderer for R Graphics
Description: Provides the mean to parse and render markdown text with grid along
with facilities to define the styling of the text.
Author: Thomas Lin Pedersen [aut, cre]
,
Martin Mitas [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between marquee versions 0.1.0 dated 2024-05-28 and 1.0.0 dated 2025-01-20
DESCRIPTION | 14 - MD5 | 89 ++++----- NAMESPACE | 18 + NEWS.md | 17 + R/backports.R | 7 R/classic_style.R | 14 - R/cpp11.R | 4 R/element_marquee.R | 109 +++++++++-- R/geom_marquee.R | 26 +- R/grob.R | 271 +++++++++++++++++++++------- R/guide_marquee.R |only R/images.R | 2 R/ink.R |only R/style.R | 49 ++++- R/style_helpers.R | 14 + R/style_set.R | 74 ++++--- README.md | 19 + build/vignette.rds |binary inst/doc/marquee.R | 93 ++++----- inst/doc/marquee.Rmd | 97 ++++------ inst/doc/marquee.html | 94 ++++----- inst/doc/marquee_style.html | 4 inst/doc/marquee_syntax.Rmd | 2 inst/doc/marquee_syntax.html | 13 - man/GuideMarquee.Rd |only man/classic_style.Rd | 22 +- man/element_marquee.Rd | 7 man/figures/README-unnamed-chunk-2-1.png |binary man/geom_marquee.Rd | 2 man/guide_marquee.Rd |only man/ink.Rd |only man/marquee_glue.Rd | 5 man/marquee_grob.Rd | 44 +++- man/marquefy_theme.Rd |only man/style.Rd | 27 ++ man/style_set.Rd | 13 - src/cpp11.cpp | 8 src/marquee.cpp | 6 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/grob.md | 16 - tests/testthat/_snaps/grob/marquee_grob.png |binary tests/testthat/_snaps/parse/parsed.csv | 122 ++++++------ tests/testthat/test-element_marquee.R | 4 tests/testthat/test-geom_marquee.R | 2 tests/testthat/test-grob.R | 4 tests/testthat/test-guide_marquee.R |only tests/testthat/test-style_set.R | 9 vignettes/marquee.Rmd | 97 ++++------ vignettes/marquee_syntax.Rmd | 2 49 files changed, 904 insertions(+), 516 deletions(-)
More information about AMISforInfectiousDiseases at CRAN
Permanent link
More information about admiralmetabolic at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-19 0.3.4
2022-01-04 0.3
2021-12-11 0.2.4
2021-02-23 0.2.3
2020-05-25 0.2.2
Title: Relative Survival
Description: Contains functions for analysing relative survival data, including nonparametric estimators of net (marginal relative) survival, relative survival ratio, crude mortality, methods for fitting and checking additive and multiplicative regression models, transformation approach, methods for dealing with population mortality tables. Work has been described in Pohar Perme, Pavlic (2018) <doi:10.18637/jss.v087.i08>.
Author: Maja Pohar Perme [aut],
Damjan Manevski [aut, cre]
Maintainer: Damjan Manevski <damjan.manevski@mf.uni-lj.si>
Diff between relsurv versions 2.2-9 dated 2022-12-22 and 2.3-1 dated 2025-01-20
relsurv-2.2-9/relsurv/src/init.c |only relsurv-2.3-1/relsurv/DESCRIPTION | 20 relsurv-2.3-1/relsurv/MD5 | 88 +- relsurv-2.3-1/relsurv/NAMESPACE | 26 relsurv-2.3-1/relsurv/R/Rcode.r | 839 ++++++++++++++++++------ relsurv-2.3-1/relsurv/R/RcppExports.R |only relsurv-2.3-1/relsurv/R/cmprel.r | 122 +-- relsurv-2.3-1/relsurv/R/dLambdaP.R |only relsurv-2.3-1/relsurv/R/popsurv.R |only relsurv-2.3-1/relsurv/R/predict.aalen.relsurv.R |only relsurv-2.3-1/relsurv/R/predict.rsadd.R |only relsurv-2.3-1/relsurv/R/ratetable_add_vals.R |only relsurv-2.3-1/relsurv/R/rformulate.r | 4 relsurv-2.3-1/relsurv/R/rformulate2.r |only relsurv-2.3-1/relsurv/R/rsaalen.R |only relsurv-2.3-1/relsurv/R/rsdiff.r | 64 - relsurv-2.3-1/relsurv/R/rssurvrsadd.r | 21 relsurv-2.3-1/relsurv/R/survaalen.R |only relsurv-2.3-1/relsurv/R/years.R | 22 relsurv-2.3-1/relsurv/R/zzz.R | 2 relsurv-2.3-1/relsurv/data/colrec.rda |binary relsurv-2.3-1/relsurv/data/ebmt1wide.rda |only relsurv-2.3-1/relsurv/data/rdata.rda |binary relsurv-2.3-1/relsurv/data/slopop.rda |binary relsurv-2.3-1/relsurv/inst/CITATION | 16 relsurv-2.3-1/relsurv/inst/news.Rd | 16 relsurv-2.3-1/relsurv/man/cmp.rel.Rd | 4 relsurv-2.3-1/relsurv/man/ebmt1wide.Rd |only relsurv-2.3-1/relsurv/man/epa.Rd | 132 +-- relsurv-2.3-1/relsurv/man/expprep2.Rd | 94 +- relsurv-2.3-1/relsurv/man/invtime.Rd | 133 ++- relsurv-2.3-1/relsurv/man/joinrate.Rd | 94 +- relsurv-2.3-1/relsurv/man/nessie.Rd | 131 +-- relsurv-2.3-1/relsurv/man/plot.rs.zph.Rd | 2 relsurv-2.3-1/relsurv/man/popsurv.Rd |only relsurv-2.3-1/relsurv/man/predict.rsadd.Rd |only relsurv-2.3-1/relsurv/man/rs.diff.Rd | 4 relsurv-2.3-1/relsurv/man/rs.surv.Rd | 303 ++++---- relsurv-2.3-1/relsurv/man/rs.surv.rsadd.Rd | 2 relsurv-2.3-1/relsurv/man/rs.zph.Rd | 2 relsurv-2.3-1/relsurv/man/rsaalen.Rd |only relsurv-2.3-1/relsurv/man/rsadd.Rd | 294 ++++---- relsurv-2.3-1/relsurv/man/rsmul.Rd | 202 +++-- relsurv-2.3-1/relsurv/man/rstrans.Rd | 204 +++-- relsurv-2.3-1/relsurv/man/summary.cmp.rel.Rd | 91 +- relsurv-2.3-1/relsurv/man/survaalen.Rd |only relsurv-2.3-1/relsurv/man/survsplit.Rd | 89 +- relsurv-2.3-1/relsurv/man/transrate.Rd | 99 +- relsurv-2.3-1/relsurv/man/transrate.hld.Rd | 2 relsurv-2.3-1/relsurv/man/transrate.hmd.Rd | 2 relsurv-2.3-1/relsurv/man/years.Rd | 2 relsurv-2.3-1/relsurv/src/Makevars |only relsurv-2.3-1/relsurv/src/Makevars.win |only relsurv-2.3-1/relsurv/src/RcppExports.cpp |only relsurv-2.3-1/relsurv/src/aalen_beta.cpp |only 55 files changed, 1890 insertions(+), 1236 deletions(-)
Title: Accelerated Stability Kinetic Modelling
Description: Estimate the Šesták–Berggren kinetic model (degradation model) from experimental data. A
A closed-form (analytic) solution to the degradation model is implemented as a non-linear fit,
allowing for the extrapolation of the degradation of a drug product - both in time and
temperature. Parametric bootstrap, with kinetic parameters drawn from the multivariate
t-distribution, and analytical formulae (the delta method) are available options to calculate
the confidence and prediction intervals.
The results (modelling, extrapolations and statistical intervals) can be visualised
with multiple plots. The examples illustrate the accelerated stability modelling in drugs and
vaccines development.
Author: Bernard G Franq [aut, cph],
Ben Wells [cre],
Alex Ball [ctb],
Daniel Williams [ctb]
Maintainer: Ben Wells <wellsbenjy@gmail.com>
Diff between AccelStab versions 2.1.0 dated 2025-01-08 and 2.1.1 dated 2025-01-20
DESCRIPTION | 16 +++++++++------- MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 16 insertions(+), 9 deletions(-)
Title: Tree-Structured Modelling of Varying Coefficients
Description: Fitting tree-structured varying coefficient models (Berger et al. (2019), <doi:10.1007/s11222-018-9804-8>). Simultaneous detection of covariates with varying coefficients and effect modifiers that induce varying coefficients if they are present.
Author: Moritz Berger [aut, cre]
Maintainer: Moritz Berger <moritz.berger@imbie.uni-bonn.de>
Diff between TSVC versions 1.5.3 dated 2023-10-17 and 1.7.2 dated 2025-01-20
DESCRIPTION | 17 +++-- MD5 | 25 ++++---- NAMESPACE | 12 ++++ R/TSVC.R | 13 ++++ R/TSVC.default.R | 8 ++ R/confint.TSVC.R |only R/effmodTree.R | 150 ++++++++++++++++++++++++++++++++++++++++------------ R/functions.R | 144 ++++++++++++++++++++++++++++++++++++++++++++++++- R/plot.TSVC.R | 56 ++++++++++++++++--- R/predict.TSVC.R | 3 - R/ptree.R | 50 +++++++++++++---- man/TSVC.Rd | 17 +++++ man/confint.Rd |only man/confint.TSVC.Rd |only man/plot.TSVC.Rd | 36 ++++++++++++ 15 files changed, 451 insertions(+), 80 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007) (temporarily unavailable)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8. [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre]
,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.5 dated 2024-12-16 and 1.0.6 dated 2025-01-20
modsem-1.0.5/modsem/src/LMS.h |only modsem-1.0.5/modsem/src/QML.h |only modsem-1.0.5/modsem/src/equationsLMS.cpp |only modsem-1.0.5/modsem/src/equationsQML.cpp |only modsem-1.0.6/modsem/DESCRIPTION | 13 modsem-1.0.6/modsem/MD5 | 49 +- modsem-1.0.6/modsem/NAMESPACE | 3 modsem-1.0.6/modsem/R/RcppExports.R | 4 modsem-1.0.6/modsem/R/model_da.R | 11 modsem-1.0.6/modsem/R/plot_interaction.R | 345 +++++++++++----- modsem-1.0.6/modsem/R/simple_slopes.R |only modsem-1.0.6/modsem/build/vignette.rds |binary modsem-1.0.6/modsem/inst/doc/plot_interactions.R | 33 + modsem-1.0.6/modsem/inst/doc/plot_interactions.Rmd | 42 + modsem-1.0.6/modsem/inst/doc/plot_interactions.html | 79 ++- modsem-1.0.6/modsem/inst/doc/simple_slopes.R |only modsem-1.0.6/modsem/inst/doc/simple_slopes.Rmd |only modsem-1.0.6/modsem/inst/doc/simple_slopes.html |only modsem-1.0.6/modsem/man/modsem-package.Rd | 2 modsem-1.0.6/modsem/man/plot_interaction.Rd | 122 ++++- modsem-1.0.6/modsem/man/plot_surface.Rd |only modsem-1.0.6/modsem/man/simple_slopes.Rd |only modsem-1.0.6/modsem/src/RcppExports.cpp | 13 modsem-1.0.6/modsem/src/calc_se_simple_slopes.cpp |only modsem-1.0.6/modsem/src/equations_lms.cpp |only modsem-1.0.6/modsem/src/equations_qml.cpp |only modsem-1.0.6/modsem/src/lms.h |only modsem-1.0.6/modsem/src/qml.h |only modsem-1.0.6/modsem/tests/testthat/test_lms.R | 1 modsem-1.0.6/modsem/tests/testthat/test_qml.R | 2 modsem-1.0.6/modsem/tests/testthat/test_sam.R | 11 modsem-1.0.6/modsem/tests/testthat/test_simple_slopes.R |only modsem-1.0.6/modsem/vignettes/plot_interactions.Rmd | 42 + modsem-1.0.6/modsem/vignettes/simple_slopes.Rmd |only 34 files changed, 557 insertions(+), 215 deletions(-)
Title: Tidy Flowchart Generator
Description: Creates participant flow diagrams directly from a dataframe. Representing the flow of participants through each stage of a study, especially in clinical trials, is essential to assess the generalisability and validity of the results. This package provides a set of functions that can be combined with a pipe operator to create all kinds of flowcharts from a data frame in an easy way.
Author: Pau Satorra [aut, cre] ,
Joao Carmezim [aut] ,
Natalia Pallares [aut] ,
Cristian Tebe [aut] ,
Kenneth Taylor [ctb]
Maintainer: Pau Satorra <psatorra@igtp.cat>
Diff between flowchart versions 0.6.0 dated 2024-11-08 and 0.7.0 dated 2025-01-20
DESCRIPTION | 6 MD5 | 37 +- NEWS.md | 10 R/as_fc.R | 46 ++ R/fc_draw.R | 28 - R/fc_filter.R | 163 ++++++++- R/fc_split.R | 89 ++++- R/fc_stack.R | 2 R/utils.R | 97 +++++ README.md | 2 inst/doc/flowchart.R | 42 ++ inst/doc/flowchart.Rmd | 351 +++----------------- inst/doc/flowchart.html | 742 ++++++++------------------------------------ man/as_fc.Rd | 4 man/fc_filter.Rd | 10 man/fc_split.Rd | 6 man/update_y.Rd | 2 man/update_y_stack.Rd | 2 man/update_y_stack_unite.Rd |only vignettes/flowchart.Rmd | 351 +++----------------- 20 files changed, 714 insertions(+), 1276 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@data-intuitive.com>
Diff between laminr versions 0.3.1 dated 2025-01-08 and 0.4.0 dated 2025-01-20
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------- R/Artifact.R | 3 -- R/Instance.R | 45 +++++++++++++------------------------ R/Registry.R | 4 +-- R/install.R | 2 - tests/testthat/test-instance_api.R | 4 +-- vignettes/laminr.Rmd | 8 ------ vignettes/setup.Rmd | 43 +++++++++++++++++++++++++---------- 9 files changed, 66 insertions(+), 65 deletions(-)
Title: Diagnostic Index Expectation Maximisation in R
Description: Likelihood-based genome polarisation finds which alleles of genomic markers
belong to which side of the barrier.
Co-estimates which individuals belong to either side of the barrier and barrier strength.
Uses expectation maximisation in likelihood framework. The method is described in
Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.4.2 dated 2024-12-02 and 1.4.3 dated 2025-01-20
DESCRIPTION | 6 MD5 | 44 - NEWS.md | 10 R/diem.r | 15 R/importPolarized.r | 2 R/plotPolarized.r | 2 R/smoothPolarizedGenotypes.r | 7 R/vcf2diem.r | 51 + build/vignette.rds |binary inst/doc/Importing-data-for-genome-polarisation.R | 82 +- inst/doc/Importing-data-for-genome-polarisation.html | 4 inst/doc/Understanding-genome-polarisation-output-files.R | 14 inst/doc/Understanding-genome-polarisation-output-files.html | 4 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.R | 288 +++++----- inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 4 inst/extdata/myotis.vcf |binary man/CheckDiemFormat.Rd | 3 man/diem.Rd | 11 man/importPolarized.Rd | 3 man/smoothPolarizedGenotypes.Rd | 7 man/vcf2diem.Rd | 16 tests/testthat/_snaps/vcf2diem.md | 23 tests/testthat/test_vcf2diem.r | 45 + 23 files changed, 380 insertions(+), 261 deletions(-)
Title: Harmonise and Integrate Heterogeneous Areal Data
Description: Many relevant applications in the environmental and socioeconomic
sciences use areal data, such as biodiversity checklists, agricultural statistics,
or socioeconomic surveys. For applications that surpass the spatial, temporal or
thematic scope of any single data source, data must be integrated from several
heterogeneous sources. Inconsistent concepts, definitions, or messy data tables
make this a tedious and error-prone process. 'arealDB' tackles those problems and
helps the user to integrate a harmonised databases of areal data. Read the paper
at Ehrmann, Seppelt & Meyer (2020) <doi:10.1016/j.envsoft.2020.104799>.
Author: Steffen Ehrmann [aut, cre] ,
Arne Ruemmler [aut, ctb] ,
Felipe Melges [ctb] ,
Carsten Meyer [aut]
Maintainer: Steffen Ehrmann <steffen.ehrmann@posteo.de>
Diff between arealDB versions 0.6.3 dated 2023-07-03 and 0.9.4 dated 2025-01-20
arealDB-0.6.3/arealDB/R/makeExampleDB.R |only arealDB-0.6.3/arealDB/R/matchOntology.R |only arealDB-0.6.3/arealDB/R/start_arealDB.R |only arealDB-0.6.3/arealDB/R/updateTable.R |only arealDB-0.6.3/arealDB/inst/test_datasets/match_gadm.csv |only arealDB-0.6.3/arealDB/inst/test_datasets/match_madeUp.csv |only arealDB-0.6.3/arealDB/inst/test_datasets/territories.rds |only arealDB-0.6.3/arealDB/man/getColTypes.Rd |only arealDB-0.6.3/arealDB/man/makeExampleDB.Rd |only arealDB-0.6.3/arealDB/man/matchOntology.Rd |only arealDB-0.6.3/arealDB/man/start_arealDB.Rd |only arealDB-0.6.3/arealDB/man/testCompressed.Rd |only arealDB-0.6.3/arealDB/man/updateTable.Rd |only arealDB-0.6.3/arealDB/tests/testthat/test_01_makeExampleDB.R |only arealDB-0.6.3/arealDB/tests/testthat/test_02_start_arealDB.R |only arealDB-0.6.3/arealDB/tests/testthat/test_03_regDataseries.R |only arealDB-0.6.3/arealDB/tests/testthat/test_04_regGeometry.R |only arealDB-0.6.3/arealDB/tests/testthat/test_05_regTable.R |only arealDB-0.6.3/arealDB/tests/testthat/test_06_normGeometry.R |only arealDB-0.6.3/arealDB/tests/testthat/test_07_normTable.R |only arealDB-0.6.3/arealDB/tests/testthat/test_matchOntology.R |only arealDB-0.6.3/arealDB/tests/testthat/test_testCompressed.R |only arealDB-0.9.4/arealDB/DESCRIPTION | 20 arealDB-0.9.4/arealDB/MD5 | 114 - arealDB-0.9.4/arealDB/NAMESPACE | 42 arealDB-0.9.4/arealDB/NEWS.md | 45 arealDB-0.9.4/arealDB/R/adb_archive.R |only arealDB-0.9.4/arealDB/R/adb_backup.R |only arealDB-0.9.4/arealDB/R/adb_diagnose.R |only arealDB-0.9.4/arealDB/R/adb_example.R |only arealDB-0.9.4/arealDB/R/adb_init.R |only arealDB-0.9.4/arealDB/R/adb_inventory.R |only arealDB-0.9.4/arealDB/R/adb_metadata.R |only arealDB-0.9.4/arealDB/R/adb_ontology.R |only arealDB-0.9.4/arealDB/R/adb_querry.R |only arealDB-0.9.4/arealDB/R/adb_reset.R |only arealDB-0.9.4/arealDB/R/adb_restore.R |only arealDB-0.9.4/arealDB/R/adb_schemas.R |only arealDB-0.9.4/arealDB/R/adb_translations.R |only arealDB-0.9.4/arealDB/R/data.R |only arealDB-0.9.4/arealDB/R/helpers.R | 1005 +++++++++- arealDB-0.9.4/arealDB/R/normGeometry.R | 933 ++++----- arealDB-0.9.4/arealDB/R/normTable.R | 212 -- arealDB-0.9.4/arealDB/R/regDataseries.R | 91 arealDB-0.9.4/arealDB/R/regGeometry.R | 281 +- arealDB-0.9.4/arealDB/R/regTable.R | 356 +-- arealDB-0.9.4/arealDB/R/zzz.R | 84 arealDB-0.9.4/arealDB/README.md | 52 arealDB-0.9.4/arealDB/data |only arealDB-0.9.4/arealDB/inst/doc/arealDB.R | 2 arealDB-0.9.4/arealDB/inst/doc/arealDB.Rmd | 180 - arealDB-0.9.4/arealDB/inst/doc/arealDB.html | 323 +-- arealDB-0.9.4/arealDB/inst/test_datasets/match_gadm.rds |only arealDB-0.9.4/arealDB/inst/test_datasets/match_madeUp.rds |only arealDB-0.9.4/arealDB/man/adb_archive.Rd |only arealDB-0.9.4/arealDB/man/adb_backup.Rd |only arealDB-0.9.4/arealDB/man/adb_diagnose.Rd |only arealDB-0.9.4/arealDB/man/adb_example.Rd |only arealDB-0.9.4/arealDB/man/adb_init.Rd |only arealDB-0.9.4/arealDB/man/adb_inventory.Rd |only arealDB-0.9.4/arealDB/man/adb_metadata.Rd |only arealDB-0.9.4/arealDB/man/adb_ontology.Rd |only arealDB-0.9.4/arealDB/man/adb_querry.Rd |only arealDB-0.9.4/arealDB/man/adb_reset.Rd |only arealDB-0.9.4/arealDB/man/adb_restore.Rd |only arealDB-0.9.4/arealDB/man/adb_schemas.Rd |only arealDB-0.9.4/arealDB/man/adb_translations.Rd |only arealDB-0.9.4/arealDB/man/dot-editMatches.Rd |only arealDB-0.9.4/arealDB/man/dot-getColTypes.Rd |only arealDB-0.9.4/arealDB/man/dot-matchOntology.Rd |only arealDB-0.9.4/arealDB/man/dot-updateOntology.Rd |only arealDB-0.9.4/arealDB/man/normGeometry.Rd | 132 - arealDB-0.9.4/arealDB/man/normTable.Rd | 63 arealDB-0.9.4/arealDB/man/regDataseries.Rd | 38 arealDB-0.9.4/arealDB/man/regGeometry.Rd | 92 arealDB-0.9.4/arealDB/man/regTable.Rd | 121 - arealDB-0.9.4/arealDB/man/territories.Rd |only arealDB-0.9.4/arealDB/tests/testthat/test_01_adb_init.R |only arealDB-0.9.4/arealDB/tests/testthat/test_02_regDataseries.R |only arealDB-0.9.4/arealDB/tests/testthat/test_02_regGeometry.R |only arealDB-0.9.4/arealDB/tests/testthat/test_02_regTable.R |only arealDB-0.9.4/arealDB/tests/testthat/test_03_normGeometry.R |only arealDB-0.9.4/arealDB/tests/testthat/test_03_normTable.R |only arealDB-0.9.4/arealDB/tests/testthat/test_04_adb_backup.R |only arealDB-0.9.4/arealDB/tests/testthat/test_05_adb_data.R |only arealDB-0.9.4/arealDB/tests/testthat/test_05_adb_metadata.R |only arealDB-0.9.4/arealDB/tests/testthat/test_06_adb_inventory.R |only arealDB-0.9.4/arealDB/tests/testthat/test_06_adb_ontology.R |only arealDB-0.9.4/arealDB/tests/testthat/test_06_adb_schemas.R |only arealDB-0.9.4/arealDB/tests/testthat/test_06_adb_translations.R |only arealDB-0.9.4/arealDB/tests/testthat/test_07_matchOntology.R |only arealDB-0.9.4/arealDB/tests/testthat/test_99_adb_exampleDB.R |only arealDB-0.9.4/arealDB/tests/testthat/test_getColTypes.R | 42 arealDB-0.9.4/arealDB/vignettes/arealDB.Rmd | 180 - 94 files changed, 2697 insertions(+), 1711 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
< [...truncated...]
Author: Roger Bivand [cre, aut] ,
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assuncao [ctb],
Anil Bera [ctb],
Olaf Berke [ctb],
F. Guillaume Blanchet [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Steph [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.3-9 dated 2025-01-16 and 1.3-10 dated 2025-01-20
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 12 ++++++++++-- R/skater.R | 2 +- inst/doc/CO69.html | 6 +++--- inst/doc/nb_sf.html | 26 +++++++++++++------------- inst/doc/sids.html | 4 ++-- inst/doc/subgraphs.html | 6 +++--- man/globalG.test.Rd | 1 - man/knearneigh.Rd | 12 +++++++++--- man/moran.test.Rd | 1 - man/read.gwt2nb.Rd | 25 +++++++++++++++++++++++-- man/set.spChkOption.Rd | 4 ---- man/skater.Rd | 25 +++++++++++++------------ src/dfs_ncomp.c | 2 +- src/nbdists.c | 2 +- 16 files changed, 98 insertions(+), 68 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements
into groups (i.e., anticlusters) with the goal of maximizing
between-group similarity or within-group heterogeneity. The
anticlustering approach thereby reverses the logic of cluster analysis
that strives for high within-group homogeneity and clear separation
between groups. Computationally, anticlustering is accomplished by
maximizing instead of minimizing a clustering objective function, such
as the intra-cluster variance (used in k-means clustering) or the sum
of pairwise distances within clusters. The main function
anticlustering() gives access to optimal and heuristic anticlustering
methods described in Papenberg and Klau (2021;
<doi:10.1037/met0000301>), Brusco et al. (2020;
<doi:10.1111/bmsp.12186>), and Papenberg (2024;
<doi:10.1111/bmsp.12315>). The optimal algorithms require that an
integer linear programming solver is installed. This package will install
'lpSolve' (<https://cran.r-project.org/p [...truncated...]
Author: Martin Papenberg [aut, cre] ,
Meik Michalke [ctb] ,
Gunnar W. Klau [ths],
Juliane V. Nagel [ctb] ,
Martin Breuer [ctb] ,
Marie L. Schaper [ctb] ,
Max Diekhoff [ctb] ,
Hannah Hengelbrock [ctb]
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.8.9 dated 2025-01-17 and 0.8.9-1 dated 2025-01-20
DESCRIPTION | 6 - LICENSE | 2 MD5 | 12 +-- inst/doc/Speeding_up_anticlustering.html | 22 ++--- inst/tinytest/test-three-phase-search-dynamic-population-size.R | 38 +++++++--- src/three-phase-dispersion.c | 5 - src/three_phase_search_dynamic_population_size.c | 2 7 files changed, 52 insertions(+), 35 deletions(-)
Title: Spatial Analysis on Network
Description: Perform spatial analysis on network.
Implement several methods for spatial analysis on network: Network Kernel Density estimation,
building of spatial matrices based on network distance ('listw' objects from 'spdep' package), K functions estimation
for point pattern analysis on network, k nearest neighbours on network, reachable area calculation, and graph generation
References: Okabe et al (2019) <doi:10.1080/13658810802475491>;
Okabe et al (2012, ISBN:978-0470770818);Baddeley et al (2015, ISBN:9781482210200).
Author: Jeremy Gelb [aut, cre] ,
Philippe Apparicio [ctb]
Maintainer: Jeremy Gelb <jeremy.gelb@ucs.inrs.ca>
Diff between spNetwork versions 0.4.4.4 dated 2025-01-14 and 0.4.4.5 dated 2025-01-20
DESCRIPTION | 6 - MD5 | 38 +++--- README.md | 11 + build/partial.rdb |binary inst/doc/KNetworkFunctions.html | 4 inst/doc/NKDE.html | 4 inst/doc/NetworkBuilding.html | 4 inst/doc/SpatialWeightMatrices.html | 4 inst/doc/TNKDE.html | 4 man/cross_kfunctions.mc.Rd | 208 +++++++++++++++++------------------ man/ess_kernel.Rd | 64 +++++----- man/figures/unnamed-chunk-8-1.png |binary man/kfunc_cpp2.Rd | 68 +++++------ man/kgfunc_time_counting.Rd | 118 +++++++++---------- man/pair_dists.Rd | 40 +++--- man/rev_matrix.Rd | 38 +++--- man/split_by_grid.mc.Rd | 124 ++++++++++---------- src/k_and_g_func.cpp | 8 + src/k_and_g_func_time.cpp | 130 +++++++++++++-------- tests/testthat/test_k_functions_sf.R | 6 + 20 files changed, 465 insertions(+), 414 deletions(-)
Title: Support for Metrological Applications
Description: Provides classes and calculation and plotting functions
for metrology applications, including measurement uncertainty estimation
and inter-laboratory metrology comparison studies.
Author: Stephen L R Ellison. [aut],
Stephen L R Ellison [cre]
Maintainer: Stephen L R Ellison <s.ellison@lgcgroup.com>
Diff between metRology versions 0.9-28-1 dated 2018-09-10 and 0.9-29-2 dated 2025-01-20
DESCRIPTION | 26 ++++--- MD5 | 150 +++++++++++++++++++++++----------------------- NAMESPACE | 8 ++ R/MSD-class.r | 16 +++- R/M_estimates.r | 6 + R/blockplot.r | 80 +++++++++++++++++++++--- R/boot.pairwise.r |only R/bootMSD.R | 17 ++++- R/contribs.R | 8 +- R/drop1.R | 19 +++-- R/ilab.R | 3 R/msd.R | 4 - R/pdchisq.r |only R/sysdata.rda |binary R/uncert.R | 45 ++++++++++--- R/uncertMC.R | 26 +++---- R/uncertMC_class.R | 24 ++++--- R/uncert_class.R | 14 ++-- build/partial.rdb |binary data/GUM.H.1.rda |binary data/Pb.rda |binary data/RMstudy.rda |binary data/apricot.rda |binary data/chromium.rda |binary data/potassium.rda |binary man/Extract.ilab.Rd | 2 man/GUM.H.1.Rd | 1 man/GUM.Rd | 2 man/LCS.Rd | 2 man/M-estimates.Rd | 2 man/Pb.Rd | 2 man/algA.Rd | 2 man/algS.Rd | 2 man/barplot.mandel.kh.Rd | 2 man/bkp.Rd | 52 +++++++++++---- man/bootMSD.Rd | 33 +++++----- man/bootMSD_class.Rd | 34 +++++----- man/bootMtrPairs_class.Rd |only man/bootMtrPairwise.Rd |only man/boxplot.mandel.kh.Rd | 2 man/buildCor.Rd | 2 man/contribs.Rd | 4 - man/cov.dellipse.Rd | 26 +++---- man/cplot.Rd | 2 man/dmandelh.Rd | 2 man/dmandelk.Rd | 2 man/drop1.uncert.Rd | 2 man/dsl.Rd | 2 man/dt.scaled.Rd | 2 man/dtri.Rd | 2 man/duewer.plot.Rd | 2 man/gplot.Rd | 2 man/ilab.Rd | 2 man/kplot.Rd | 2 man/loc_est.Rd | 2 man/mandel.h.Rd | 2 man/mandel.k.Rd | 2 man/mandel.kh.Rd | 2 man/metRology-package.Rd | 33 +++++++++- man/methods.ilab.Rd | 2 man/mpaule.Rd | 2 man/msd.Rd | 8 ++ man/msd_class.Rd | 13 ++- man/pdchisq.Rd |only man/pdchisq_class.Rd |only man/plot.mandel.kh.Rd | 2 man/plot.uncert.Rd | 4 - man/plot.uncertMC.Rd | 8 +- man/pmsd.Rd | 2 man/pmsd.xnorm.Rd | 2 man/rbind.ilab.Rd | 27 +++----- man/reml_loc.Rd | 2 man/uncertMC.Rd | 4 - man/uncertMC_class.Rd | 2 man/uncert_class.Rd | 2 man/uncertainty.Rd | 23 +++---- man/update.uncert.Rd | 2 man/w.s.Rd | 4 - man/xs.plot.Rd | 6 - 79 files changed, 495 insertions(+), 299 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 0.4-0 dated 2023-01-26 and 0.4-1 dated 2025-01-20
Changelog | 4 ++++ DESCRIPTION | 12 ++++++------ MD5 | 34 +++++++++++++++++----------------- R/write_surmiserelation.R | 1 + build/vignette.rds |binary inst/doc/kstIO.pdf |binary man/kstIO-package.Rd | 4 ++-- man/read_kbase.Rd | 4 ++-- man/read_kdata.Rd | 4 ++-- man/read_kfamset.Rd | 4 ++-- man/read_kspace.Rd | 4 ++-- man/read_kstructure.Rd | 4 ++-- man/read_surmiserelation.Rd | 4 ++-- man/write_kbase.Rd | 4 ++-- man/write_kdata.Rd | 4 ++-- man/write_kspace.Rd | 4 ++-- man/write_kstructure.Rd | 4 ++-- man/write_surmiserelation.Rd | 4 ++-- 18 files changed, 52 insertions(+), 47 deletions(-)
Title: Extended Changes-in-Changes
Description: Extends the Changes-in-Changes model a la Athey and Imbens
(2006) <doi:10.1111/j.1468-0262.2006.00668.x> to multiple cohorts and
time periods, which generalizes difference-in-differences estimation
techniques to the entire distribution. Computes quantile treatment
effects for every possible two-by-two combination in ecic(). Then,
aggregating all bootstrap runs adds the standard errors in
summary_ecic(). Results can be plotted with plot_ecic() aggregated
over all cohort-group combinations or in an event-study style for
either individual periods or individual quantiles.
Author: Frederic Kluser [aut, cre, cph]
Maintainer: Frederic Kluser <frederic.kluser@unibe.ch>
Diff between ecic versions 0.0.3 dated 2023-02-21 and 0.0.4 dated 2025-01-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/ecic.R | 6 ++++-- build/partial.rdb |binary 5 files changed, 17 insertions(+), 10 deletions(-)
Title: Wrapper for the 'AT' Protocol Behind 'Bluesky'
Description: Wraps the 'AT' Protocol (Authenticated Transfer Protocol) behind
'Bluesky' <https://bsky.social>. Functions can be used for, among others,
retrieving posts and followers from the network or posting content.
Author: Johannes B. Gruber [aut, cre] ,
Benjamin Guinaudeau [aut, ctb]
,
Fabio Votta [aut, ctb]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between atrrr versions 0.0.5 dated 2025-01-19 and 0.1.0 dated 2025-01-20
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/auth.r | 1 + R/feed.r | 15 +++++++++++---- README.md | 2 -- 6 files changed, 25 insertions(+), 14 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the
'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi'
library. 'textshaping' is a low-level utility package mainly for
graphic devices that expands upon the font tool-set provided by the
'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between textshaping versions 0.4.1 dated 2024-12-06 and 1.0.0 dated 2025-01-20
DESCRIPTION | 11 MD5 | 49 + NAMESPACE | 3 NEWS.md | 16 R/cpp11.R | 4 R/lorem_text.R |only R/shape_text.R | 166 +++++- README.md | 4 configure | 34 - inst/lorem |only man/lorem_text.Rd |only man/plot_shape.Rd |only man/shape_text.Rd | 34 - src/Makevars.win | 25 src/cpp11.cpp | 8 src/string_bidi.cpp | 11 src/string_bidi.h | 2 src/string_metrics.cpp | 38 - src/string_metrics.h | 3 src/string_shape.cpp | 1271 +++++++++++++++++++++++++++++++------------------ src/string_shape.h | 333 +++++++++++- tests |only 22 files changed, 1395 insertions(+), 617 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS
and Linux for finding font files that can then be used further by e.g.
graphic devices. The main use is intended to be from compiled code but
'systemfonts' also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
,
Jeroen Ooms [aut] ,
Devon Govett [aut] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between systemfonts versions 1.2.0 dated 2025-01-16 and 1.2.1 dated 2025-01-20
DESCRIPTION | 11 +++++------ MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/register_font.R | 2 +- R/web_fonts.R | 28 ++++++++++++++++++++-------- man/web-fonts.Rd | 6 +++++- src/FontDescriptor.h | 17 +++++++++++++++-- 7 files changed, 60 insertions(+), 24 deletions(-)
Title: Interface to the 'HDF5' Binary Data Format
Description: 'HDF5' is a data model, library and file format for storing
and managing large amounts of data. This package provides a nearly
feature complete, object oriented wrapper for the 'HDF5' API
<https://support.hdfgroup.org/documentation/hdf5/latest/_r_m.html> using R6 classes.
Additionally, functionality is added so that 'HDF5' objects behave very
similar to their corresponding R counterparts.
Author: Holger Hoefling [aut, cre],
Mario Annau [aut],
Novartis Institute for BioMedical Research [cph]
Maintainer: Holger Hoefling <hhoeflin@gmail.com>
Diff between hdf5r versions 1.3.11 dated 2024-07-07 and 1.3.12 dated 2025-01-20
DESCRIPTION | 8 +- MD5 | 90 ++++++++++++------------ NEWS.md | 20 +++++ R/Common_functions.R | 126 ++++++++++++++++----------------- R/R6Classes.R | 2 R/R6Classes_H5A.R | 14 +-- R/R6Classes_H5D.R | 28 +++---- R/R6Classes_H5File.R | 10 +- R/R6Classes_H5P.R | 142 +++++++++++++++++++------------------- R/R6Classes_H5R.R | 4 - R/R6Classes_H5S.R | 48 ++++++------ R/R6Classes_H5T.R | 74 +++++++++---------- R/adapt_during_onLoad.R | 6 - R/high_level_UI.R | 4 - inst/doc/hdf5r.Rmd | 2 inst/doc/hdf5r.html | 6 - man/H5A-class.Rd | 18 ++-- man/H5D-class.Rd | 68 +++++++++--------- man/H5File-class.Rd | 126 ++++++++++++++++----------------- man/H5Group-class.Rd | 116 +++++++++++++++---------------- man/H5P-class.Rd | 8 +- man/H5P_ATTRIBUTE_CREATE-class.Rd | 4 - man/H5P_CLASS-class.Rd | 2 man/H5P_DATASET_ACCESS-class.Rd | 4 - man/H5P_DATASET_CREATE-class.Rd | 50 ++++++------- man/H5P_DATASET_XFER-class.Rd | 14 +-- man/H5P_FILE_ACCESS-class.Rd | 4 - man/H5P_FILE_CREATE-class.Rd | 20 ++--- man/H5P_LINK_ACCESS-class.Rd | 12 +-- man/H5P_LINK_CREATE-class.Rd | 8 +- man/H5P_OBJECT_COPY-class.Rd | 4 - man/H5P_OBJECT_CREATE-class.Rd | 12 +-- man/H5R_DATASET_REGION-class.Rd | 2 man/H5R_OBJECT-class.Rd | 2 man/H5RefClass-class.Rd | 12 +-- man/H5S-class.Rd | 50 ++++++------- man/H5S_H5D_subset_assign.Rd | 4 - man/H5T-class.Rd | 72 +++++++++---------- man/H5T_ARRAY-class.Rd | 6 - man/H5T_COMPOUND-class.Rd | 2 man/H5T_FLOAT-class.Rd | 16 ++-- man/H5T_INTEGER-class.Rd | 4 - man/H5T_STRING-class.Rd | 10 +- man/H5T_VLEN-class.Rd | 2 src/H5ls.c | 43 +++++------ vignettes/hdf5r.Rmd | 2 46 files changed, 650 insertions(+), 631 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical
models and returns the result as tidy data frames. These data frames are
ready to use with the 'ggplot2'-package. Effects and predictions can be
calculated for many different models. Interaction terms, splines and
polynomial terms are also supported. The main functions are ggpredict(),
ggemmeans() and ggeffect(). There is a generic plot()-method to plot the
results using 'ggplot2'.
Author: Daniel Luedecke [aut, cre] ,
Frederik Aust [ctb] ,
Sam Crawley [ctb] ,
Mattan S. Ben-Shachar [ctb] ,
Sean C. Anderson [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between ggeffects versions 2.0.0 dated 2024-11-27 and 2.1.0 dated 2025-01-20
ggeffects-2.0.0/ggeffects/tests/testthat/_snaps |only ggeffects-2.1.0/ggeffects/DESCRIPTION | 20 - ggeffects-2.1.0/ggeffects/LICENSE | 4 ggeffects-2.1.0/ggeffects/MD5 | 164 ++-------- ggeffects-2.1.0/ggeffects/NEWS.md | 15 ggeffects-2.1.0/ggeffects/R/format.R | 7 ggeffects-2.1.0/ggeffects/R/get_predictions_logitr.R | 3 ggeffects-2.1.0/ggeffects/R/ggaverage.R | 3 ggeffects-2.1.0/ggeffects/R/ggeffect.R | 19 - ggeffects-2.1.0/ggeffects/R/ggemmeans.R | 3 ggeffects-2.1.0/ggeffects/R/ggpredict.R | 9 ggeffects-2.1.0/ggeffects/R/moderator_pattern.R | 54 +-- ggeffects-2.1.0/ggeffects/R/plot.R | 67 ++-- ggeffects-2.1.0/ggeffects/R/post_processing_predictions.R | 9 ggeffects-2.1.0/ggeffects/R/predict_response.R | 7 ggeffects-2.1.0/ggeffects/R/sanitize_type_arg.R | 93 +++-- ggeffects-2.1.0/ggeffects/R/standard_error_predictions.R | 14 ggeffects-2.1.0/ggeffects/R/test_predictions.R | 97 ++++- ggeffects-2.1.0/ggeffects/R/tp_label_hypothesis_formula.R |only ggeffects-2.1.0/ggeffects/R/utils.R | 18 - ggeffects-2.1.0/ggeffects/R/utils_get_data_grid.R | 12 ggeffects-2.1.0/ggeffects/R/utils_get_representative_values.R | 6 ggeffects-2.1.0/ggeffects/R/vcov.R | 24 - ggeffects-2.1.0/ggeffects/man/ggpredict.Rd | 11 ggeffects-2.1.0/ggeffects/man/install_latest.Rd | 80 ++-- ggeffects-2.1.0/ggeffects/man/plot.Rd | 4 ggeffects-2.1.0/ggeffects/man/predict_response.Rd | 4 ggeffects-2.1.0/ggeffects/man/test_predictions.Rd | 58 ++- ggeffects-2.1.0/ggeffects/man/values_at.Rd | 43 +- ggeffects-2.1.0/ggeffects/tests/testthat/test-avg_predictions.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-backtransform_response.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-ci_backticks-names.R | 2 ggeffects-2.1.0/ggeffects/tests/testthat/test-condition.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-emmeans-weights.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-focal_only_random.R | 2 ggeffects-2.1.0/ggeffects/tests/testthat/test-gee.R | 2 ggeffects-2.1.0/ggeffects/tests/testthat/test-ggaverage.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-ggeffect.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-glm.R | 2 ggeffects-2.1.0/ggeffects/tests/testthat/test-johnson_neyman.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-logitr.R |only ggeffects-2.1.0/ggeffects/tests/testthat/test-plot-from-vignettes.R | 52 ++- ggeffects-2.1.0/ggeffects/tests/testthat/test-plot-show_data.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-plot-survival.R |only ggeffects-2.1.0/ggeffects/tests/testthat/test-plot.R | 20 + ggeffects-2.1.0/ggeffects/tests/testthat/test-print.R | 20 + ggeffects-2.1.0/ggeffects/tests/testthat/test-test_predictions-formula.R |only ggeffects-2.1.0/ggeffects/tests/testthat/test-test_predictions.R | 2 48 files changed, 544 insertions(+), 414 deletions(-)
Title: Use 'nlmixr2' to Interact with Open Source and Commercial
Software
Description: Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019)
<doi:10.1002/psp4.12445>) interface including 'PKNCA', 'NONMEM' and 'Monolix'. While not required, you can
get/install the 'lixoftConnectors' package in the 'Monolix' installation, as
described at the following url
<https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When
'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up
command line usage.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [aut] ,
Theodoros Papathanasiou [ctb],
Nook Fulloption [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between babelmixr2 versions 0.1.5 dated 2024-11-06 and 0.1.6 dated 2025-01-20
babelmixr2-0.1.5/babelmixr2/tests/testthat/_snaps |only babelmixr2-0.1.6/babelmixr2/DESCRIPTION | 8 +- babelmixr2-0.1.6/babelmixr2/MD5 | 32 +++----- babelmixr2-0.1.6/babelmixr2/NEWS.md | 11 +++ babelmixr2-0.1.6/babelmixr2/R/RcppExports.R | 4 + babelmixr2-0.1.6/babelmixr2/R/monolixNlmixr2est.R | 1 babelmixr2-0.1.6/babelmixr2/R/nonmem.R | 4 - babelmixr2-0.1.6/babelmixr2/R/nonmemNlmixr2est.R | 1 babelmixr2-0.1.6/babelmixr2/R/poped.R | 16 ++++ babelmixr2-0.1.6/babelmixr2/R/zzz.R | 1 babelmixr2-0.1.6/babelmixr2/inst/tools/workaround.R | 24 +++--- babelmixr2-0.1.6/babelmixr2/src/Makevars.in | 6 - babelmixr2-0.1.6/babelmixr2/src/RcppExports.cpp | 10 ++ babelmixr2-0.1.6/babelmixr2/src/init.c | 3 babelmixr2-0.1.6/babelmixr2/src/poped.cpp | 52 ++++++++++++++ babelmixr2-0.1.6/babelmixr2/tests/testthat/test-nonmem.R | 54 +++++++++++++++ 16 files changed, 191 insertions(+), 36 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.5.5 dated 2024-12-20 and 1.5.5.1 dated 2025-01-20
DESCRIPTION | 8 MD5 | 20 - R/GPModel.R | 2 configure.ac | 2 src/include/GPBoost/cov_fcts.h | 358 +++++++++++++++++------- src/include/GPBoost/likelihoods.h | 120 ++++---- src/include/GPBoost/optim_utils.h | 4 src/include/GPBoost/re_model_template.h | 24 - src/include/GPBoost/utils.h | 74 ++++ tests/testthat/test_GPModel_gaussian_process.R | 24 + tests/testthat/test_GPModel_non_Gaussian_data.R | 104 ++++-- 11 files changed, 530 insertions(+), 210 deletions(-)
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.3-3 dated 2024-11-19 and 3.3-4 dated 2025-01-19
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 19 +++++++++++++++++++ R/mpl.R | 14 +++++++++----- inst/doc/packagesizes.txt | 2 ++ inst/info/packagesizes.txt | 2 ++ 6 files changed, 42 insertions(+), 15 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: Deconvolute Mixed Genomes with Unknown Proportions
Description: Traditional phasing programs are limited to diploid organisms.
Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo
(MCMC) approaches, and builds a generic framework that allows haplotype searches
in a multiple infection setting. This package is primarily developed as part of
the Pf3k project, which is a global collaboration using the latest
sequencing technologies to provide a high-resolution view of natural variation
in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from
patient blood sample, which often contains more than one parasite strain, with
unknown proportions. This package is used for deconvoluting mixed haplotypes,
and reporting the mixture proportions from each sample.
Author: Joe Zhu [aut, cre] ,
Jacob Almagro-Garcia [aut],
Gil McVean [aut],
University of Oxford [cph],
Yinghan Liu [ctb],
CodeCogs Zyba Ltd [com, cph],
Deepak Bandyopadhyay [com, cph],
Lutz Kettner [com, cph]
Maintainer: Joe Zhu <sha.joe.zhu@gmail.com>
Diff between DEploid versions 0.5.6 dated 2024-12-23 and 0.5.7 dated 2025-01-19
DEploid-0.5.6/DEploid/src/DEploid/chooseK.cpp |only DEploid-0.5.6/DEploid/src/DEploid/chooseK.hpp |only DEploid-0.5.6/DEploid/src/DEploid/codeCogs |only DEploid-0.5.6/DEploid/src/DEploid/dEploidIO-operation.cpp |only DEploid-0.5.6/DEploid/src/DEploid/dEploidIO-workflow.cpp |only DEploid-0.5.6/DEploid/src/DEploid/dEploidIO.cpp |only DEploid-0.5.6/DEploid/src/DEploid/dEploidIO.hpp |only DEploid-0.5.6/DEploid/src/DEploid/debug |only DEploid-0.5.6/DEploid/src/DEploid/exceptions.hpp |only DEploid-0.5.6/DEploid/src/DEploid/export |only DEploid-0.5.6/DEploid/src/DEploid/global.hpp |only DEploid-0.5.6/DEploid/src/DEploid/ibd.cpp |only DEploid-0.5.6/DEploid/src/DEploid/ibd.hpp |only DEploid-0.5.6/DEploid/src/DEploid/lasso |only DEploid-0.5.6/DEploid/src/DEploid/log-double.hpp |only DEploid-0.5.6/DEploid/src/DEploid/logsum.hpp |only DEploid-0.5.6/DEploid/src/DEploid/mcmc.cpp |only DEploid-0.5.6/DEploid/src/DEploid/mcmc.hpp |only DEploid-0.5.6/DEploid/src/DEploid/panel.cpp |only DEploid-0.5.6/DEploid/src/DEploid/panel.hpp |only DEploid-0.5.6/DEploid/src/DEploid/param.hpp |only DEploid-0.5.6/DEploid/src/DEploid/random |only DEploid-0.5.6/DEploid/src/DEploid/updateHap.cpp |only DEploid-0.5.6/DEploid/src/DEploid/updateHap.hpp |only DEploid-0.5.6/DEploid/src/DEploid/utility.cpp |only DEploid-0.5.6/DEploid/src/DEploid/utility.hpp |only DEploid-0.5.6/DEploid/src/DEploid/vcf |only DEploid-0.5.6/DEploid/tests |only DEploid-0.5.7/DEploid/DESCRIPTION | 11 DEploid-0.5.7/DEploid/MD5 | 251 ++++++++------ DEploid-0.5.7/DEploid/inst/doc/dEploid-Arguments.html | 10 DEploid-0.5.7/DEploid/man/DEploid-package.Rd | 2 DEploid-0.5.7/DEploid/src/DEploid/src |only DEploid-0.5.7/DEploid/src/Makevars | 42 +- DEploid-0.5.7/DEploid/src/Makevars.win | 42 +- DEploid-0.5.7/DEploid/src/dEploidr.cpp | 2 36 files changed, 214 insertions(+), 146 deletions(-)
Title: Quantile Recalibration for Regression Models
Description: Enables the diagnostics and enhancement of regression model calibration.It offers both global and local visualization tools for calibration diagnostics and provides one recalibration method: Torres R, Nott DJ, Sisson SA, Rodrigues T, Reis JG, Rodrigues GS (2024) <doi:10.48550/arXiv.2403.05756>. The method leverages on Probabilistic Integral Transform (PIT) values to both evaluate and perform the calibration of statistical models. For a more detailed description of the package, please refer to the bachelor's thesis available bellow.
Author: Carolina Musso [aut, cre, cph]
,
Ricardo Torres [aut, cph] ,
Joao Reis [aut, cph],
Guilherme Rodrigues [aut, ths, cph]
Maintainer: Carolina Musso <cmusso86@gmail.com>
Diff between recalibratiNN versions 0.3.0 dated 2024-07-05 and 0.3.2 dated 2025-01-19
DESCRIPTION | 6 +-- MD5 | 20 +++++----- NEWS.md | 4 ++ R/gg_CD_local.R | 9 +++- README.md | 36 ++---------------- build/partial.rdb |binary inst/doc/simple_mlp.R | 92 +++++++++++++++++++++++------------------------ inst/doc/simple_mlp.Rmd | 2 - inst/doc/simple_mlp.html | 2 - man/gg_CD_local.Rd | 7 ++- vignettes/simple_mlp.Rmd | 2 - 11 files changed, 82 insertions(+), 98 deletions(-)
Title: R Interface to Google RE2 (C++) Regular Expression Library
Description: Pattern matching, extraction, replacement and other string
processing operations using Google's RE2 <https://github.com/google/re2>
regular-expression engine. Consistent interface (similar to 'stringr').
RE2 uses finite-automata based techniques, and offers a
fast and safe alternative to backtracking regular-expression engines
like those used in 'stringr', 'stringi' and other PCRE implementations.
Author: Girish Palya [aut, cre],
RE2 developers [ctb] ,
Google Inc. [ctb, cph]
Maintainer: Girish Palya <girishji@gmail.com>
Diff between re2 versions 0.1.3 dated 2023-11-28 and 0.1.4 dated 2025-01-19
DESCRIPTION | 28 +++++++++++++++++-------- MD5 | 34 +++++++++++++++--------------- R/RcppExports.R | 15 +++++++++++-- R/re2-package.R | 32 ++++++++++++++-------------- build/vignette.rds |binary inst/doc/re2_intro.R | 2 + inst/doc/re2_intro.Rmd | 2 + inst/doc/re2_intro.html | 7 ++++-- inst/doc/re2_syntax.html | 2 - man/re2-package.Rd | 18 ++++++++-------- man/re2_extract_replace.Rd | 3 ++ man/re2_replace.Rd | 9 ++++++-- src/RcppExports.cpp | 8 +++---- src/re2_re2proxy.cpp | 4 +-- src/re2_re2proxy.h | 2 - src/re2_replace.cpp | 50 +++++++++++++++++++++++++++++++++++++++++---- src/util/README | 2 - vignettes/re2_intro.Rmd | 2 + 18 files changed, 150 insertions(+), 70 deletions(-)
Title: Read/Write, Analyze, and Visualize 'BIOM' Data
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files.
Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and
beta diversity (including 'UniFrac'). Summarize counts by taxonomic level.
Subset based on metadata. Generate visualizations and statistical analyses.
CPU intensive operations are coded in C for speed.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between rbiom versions 2.0.7 dated 2025-01-11 and 2.0.10 dated 2025-01-19
rbiom-2.0.10/rbiom/DESCRIPTION | 15 rbiom-2.0.10/rbiom/MD5 | 93 +- rbiom-2.0.10/rbiom/NAMESPACE | 10 rbiom-2.0.10/rbiom/R/adiv_table.r | 77 +- rbiom-2.0.10/rbiom/R/bdiv_table.r | 97 +-- rbiom-2.0.10/rbiom/R/corrplot.r | 42 - rbiom-2.0.10/rbiom/R/distmat_stats.r | 13 rbiom-2.0.10/rbiom/R/documentation.r | 7 rbiom-2.0.10/rbiom/R/rarefy.r | 530 ++++++++--------- rbiom-2.0.10/rbiom/R/rbiom-deprecated.r | 13 rbiom-2.0.10/rbiom/R/read_tree.r | 11 rbiom-2.0.10/rbiom/R/reexport.r | 3 rbiom-2.0.10/rbiom/R/taxa_table.r | 7 rbiom-2.0.10/rbiom/R/validate.r | 15 rbiom-2.0.10/rbiom/R/write_biom.r | 4 rbiom-2.0.10/rbiom/README.md | 20 rbiom-2.0.10/rbiom/man/adiv_matrix.Rd | 18 rbiom-2.0.10/rbiom/man/adiv_table.Rd | 13 rbiom-2.0.10/rbiom/man/bdiv_corrplot.Rd | 3 rbiom-2.0.10/rbiom/man/bdiv_ord_plot.Rd | 3 rbiom-2.0.10/rbiom/man/bdiv_ord_table.Rd | 3 rbiom-2.0.10/rbiom/man/bdiv_table.Rd | 13 rbiom-2.0.10/rbiom/man/distmat_stats.Rd | 3 rbiom-2.0.10/rbiom/man/documentation_default.Rd | 7 rbiom-2.0.10/rbiom/man/figures/README-bdiv-1.png |binary rbiom-2.0.10/rbiom/man/figures/README-bdiv-2.png |binary rbiom-2.0.10/rbiom/man/figures/README-bdiv-3.png |binary rbiom-2.0.10/rbiom/man/figures/README-taxa-1.png |binary rbiom-2.0.10/rbiom/man/figures/README-taxa-2.png |binary rbiom-2.0.10/rbiom/man/rarefy.Rd | 5 rbiom-2.0.10/rbiom/man/rarefy_cols.Rd | 11 rbiom-2.0.10/rbiom/man/read_tree.Rd | 6 rbiom-2.0.10/rbiom/man/reexports.Rd | 3 rbiom-2.0.10/rbiom/man/taxa_corrplot.Rd | 3 rbiom-2.0.10/rbiom/man/taxa_matrix.Rd | 3 rbiom-2.0.10/rbiom/man/write_biom.Rd | 2 rbiom-2.0.10/rbiom/src/alpha_div.c |only rbiom-2.0.10/rbiom/src/beta_div.c |only rbiom-2.0.10/rbiom/src/init.c |only rbiom-2.0.10/rbiom/src/pthreads.c |only rbiom-2.0.10/rbiom/src/rarefy.c |only rbiom-2.0.10/rbiom/src/read_tree.c |only rbiom-2.0.10/rbiom/src/unifrac.c |only rbiom-2.0.10/rbiom/tests/testthat/helper.r | 1 rbiom-2.0.10/rbiom/tests/testthat/test-adiv_table.r | 4 rbiom-2.0.10/rbiom/tests/testthat/test-bdiv_table.r | 32 - rbiom-2.0.10/rbiom/tests/testthat/test-distmat_stats.r | 2 rbiom-2.0.7/rbiom/R/RcppExports.R |only rbiom-2.0.7/rbiom/src/Makevars |only rbiom-2.0.7/rbiom/src/RcppExports.cpp |only rbiom-2.0.7/rbiom/src/parallel_beta_div.cpp |only rbiom-2.0.7/rbiom/src/parallel_unifrac.cpp |only rbiom-2.0.7/rbiom/src/rcpp_alpha_div.cpp |only rbiom-2.0.7/rbiom/src/rcpp_rarefy.cpp |only rbiom-2.0.7/rbiom/src/rcpp_treeIO.cpp |only 55 files changed, 614 insertions(+), 478 deletions(-)
Title: Comprehensive Analysis of Multi-Omics Data Using an Offset-Based
Method
Description: Priority-ElasticNet extends the Priority-LASSO method (Klau et al. (2018) <doi:10.1186/s12859-018-2344-6>) by incorporating the ElasticNet penalty, allowing for both L1 and L2 regularization.
This approach fits successive ElasticNet models for several blocks of (omics) data with different priorities, using the predicted values from each block as an offset for the subsequent block.
It also offers robust options to handle block-wise missingness in multi-omics data, improving the flexibility and applicability of the model in the presence of incomplete datasets.
Author: Laila Qadir Musib [aut, cre],
Eunice Carrasquinha [aut],
Helena Mourino [aut]
Maintainer: Laila Qadir Musib <statleila98@gmail.com>
Diff between priorityelasticnet versions 0.1.0 dated 2025-01-13 and 0.2.0 dated 2025-01-19
DESCRIPTION | 10 MD5 | 16 NAMESPACE | 1 R/priorityelasticnet.R | 1 build/vignette.rds |binary inst/doc/priorityelasticnet-vignettes.R | 1109 - inst/doc/priorityelasticnet-vignettes.Rmd | 2 inst/doc/priorityelasticnet-vignettes.html |20486 ++++++++++++++--------------- vignettes/priorityelasticnet-vignettes.Rmd | 2 9 files changed, 10803 insertions(+), 10824 deletions(-)
More information about priorityelasticnet at CRAN
Permanent link
Title: Read bigWig and bigBed Files
Description: Read bigWig and bigBed files using "libBigWig"
<https://github.com/dpryan79/libBigWig>. Provides lightweight access
to the binary bigWig and bigBed formats developed by the UCSC Genome
Browser group.
Author: Jay Hesselberth [aut, cre],
RNA Bioscience Initiative [fnd, cph],
Devon Ryan [cph]
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between cpp11bigwig versions 0.1.0 dated 2025-01-07 and 0.1.1 dated 2025-01-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ README.md | 2 ++ src/libBigWig/bigWig.h | 2 +- src/libBigWig/bwValues.c | 4 +--- 6 files changed, 16 insertions(+), 12 deletions(-)
Title: Tidy Plots for Scientific Papers
Description: The goal of 'tidyplots' is to streamline the creation of publication-ready plots for scientific papers. It allows to gradually add, remove and adjust plot components using a consistent and intuitive syntax.
Author: Jan Broder Engler [aut, cre, cph]
Maintainer: Jan Broder Engler <broder.engler@gmail.com>
Diff between tidyplots versions 0.2.0 dated 2024-12-16 and 0.2.1 dated 2025-01-19
tidyplots-0.2.0/tidyplots/tests/testthat/_snaps/add-misc/add-reference-lines.svg |only tidyplots-0.2.0/tidyplots/tests/testthat/_snaps/add-misc/add-title-and-caption.svg |only tidyplots-0.2.1/tidyplots/DESCRIPTION | 10 tidyplots-0.2.1/tidyplots/MD5 | 61 +-- tidyplots-0.2.1/tidyplots/NAMESPACE | 4 tidyplots-0.2.1/tidyplots/NEWS.md | 16 tidyplots-0.2.1/tidyplots/R/add-annotation.R |only tidyplots-0.2.1/tidyplots/R/add-misc.R | 187 ---------- tidyplots-0.2.1/tidyplots/R/add-proportional.R | 30 - tidyplots-0.2.1/tidyplots/R/adjust.R | 9 tidyplots-0.2.1/tidyplots/R/helpers.R | 4 tidyplots-0.2.1/tidyplots/R/plot.R | 13 tidyplots-0.2.1/tidyplots/R/tidycolor.R | 9 tidyplots-0.2.1/tidyplots/README.md | 4 tidyplots-0.2.1/tidyplots/data/energy.rda |binary tidyplots-0.2.1/tidyplots/man/add_annotation_text.Rd |only tidyplots-0.2.1/tidyplots/man/add_areastack_absolute.Rd | 10 tidyplots-0.2.1/tidyplots/man/add_barstack_absolute.Rd | 14 tidyplots-0.2.1/tidyplots/man/add_data_labels.Rd | 2 tidyplots-0.2.1/tidyplots/man/add_histogram.Rd | 4 tidyplots-0.2.1/tidyplots/man/add_pie.Rd | 6 tidyplots-0.2.1/tidyplots/man/add_reference_lines.Rd | 2 tidyplots-0.2.1/tidyplots/man/add_title.Rd | 2 tidyplots-0.2.1/tidyplots/man/colors_discrete_friendly.Rd | 11 tidyplots-0.2.1/tidyplots/man/figures/README-unnamed-chunk-3-1.png |binary tidyplots-0.2.1/tidyplots/man/figures/README-unnamed-chunk-4-1.png |binary tidyplots-0.2.1/tidyplots/man/flip_plot.Rd | 4 tidyplots-0.2.1/tidyplots/man/save_plot.Rd | 3 tidyplots-0.2.1/tidyplots/man/split_plot.Rd | 8 tidyplots-0.2.1/tidyplots/tests/testthat/_snaps/add-annotation |only tidyplots-0.2.1/tidyplots/tests/testthat/test-add-annotation.R |only tidyplots-0.2.1/tidyplots/tests/testthat/test-add-misc.R | 16 32 files changed, 140 insertions(+), 289 deletions(-)
Title: Joint Longitudinal and Survival Model for Big Data
Description: Provides analysis tools for big data where the sample size is very large. It offers
a suite of functions for fitting and predicting joint models, which allow for the simultaneous
analysis of longitudinal and time-to-event data. This statistical methodology is particularly
useful in medical research where there is often interest in understanding the relationship
between a longitudinal biomarker and a clinical outcome, such as survival or disease progression.
This can be particularly useful in a clinical setting where it is important to be able to predict
how a patient's health status may change over time. Overall, this package provides a
comprehensive set of tools for joint modeling of BIG data obtained as survival and
longitudinal outcomes with both Bayesian and non-Bayesian approaches. Its versatility
and flexibility make it a valuable resource for researchers in many different fields,
particularly in the medical and health sciences.
Author: Atanu Bhattacharjee [aut, cre, ctb],
Bhrigu Kumar Rajbongshi [aut, ctb],
Gajendra K Vishwakarma [aut, ctb]
Maintainer: Atanu Bhattacharjee <atanustat@gmail.com>
Diff between jmBIG versions 0.1.2 dated 2024-03-20 and 0.1.3 dated 2025-01-19
jmBIG-0.1.2/jmBIG/man/print.Rd |only jmBIG-0.1.3/jmBIG/DESCRIPTION | 6 +- jmBIG-0.1.3/jmBIG/MD5 | 19 +++---- jmBIG-0.1.3/jmBIG/NAMESPACE | 1 jmBIG-0.1.3/jmBIG/R/prediction.R | 6 +- jmBIG-0.1.3/jmBIG/R/print.R | 80 +++++++----------------------- jmBIG-0.1.3/jmBIG/man/predJRML.Rd | 4 + jmBIG-0.1.3/jmBIG/man/print.jmbayesBig.Rd | 6 -- jmBIG-0.1.3/jmBIG/man/print.jmcsBig.Rd | 6 -- jmBIG-0.1.3/jmBIG/man/print.jmstanBig.Rd | 6 -- jmBIG-0.1.3/jmBIG/man/print.joinRMLBig.Rd | 6 -- 11 files changed, 46 insertions(+), 94 deletions(-)
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 0.9.6 dated 2024-10-11 and 0.9.7 dated 2025-01-19
DESCRIPTION | 6 +-- MD5 | 26 ++++++++-------- NAMESPACE | 2 - NEWS.md | 12 +++++++ R/shapviz.R | 65 ++++++++++++++++++++++------------------ README.md | 2 - inst/doc/basic_use.Rmd | 28 ++++++++++++----- inst/doc/basic_use.html | 58 ++++++++++++++++++++++------------- inst/doc/geographic.html | 10 +++--- inst/doc/multiple_output.html | 16 ++++----- inst/doc/tidymodels.html | 24 +++++++------- man/shapviz.Rd | 52 ++++++++++++++++++++------------ tests/testthat/test-interface.R | 6 +-- vignettes/basic_use.Rmd | 28 ++++++++++++----- 14 files changed, 202 insertions(+), 133 deletions(-)
Title: Wrapper for the 'AT' Protocol Behind 'Bluesky'
Description: Wraps the 'AT' Protocol (Authenticated Transfer Protocol) behind
'Bluesky' <https://bsky.social>. Functions can be used for, among others,
retrieving posts and followers from the network or posting content.
Author: Johannes B. Gruber [aut, cre] ,
Benjamin Guinaudeau [aut, ctb]
,
Fabio Votta [aut, ctb]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between atrrr versions 0.0.4 dated 2024-10-03 and 0.0.5 dated 2025-01-19
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atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/createSession.json | 18 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/deactivateAccount.json |only atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/deleteAccount.json | 2 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/deleteSession.json | 2 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/describeServer.json | 39 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/getAccountInviteCodes.json | 8 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/getServiceAuth.json |only atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/getSession.json | 12 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/listAppPasswords.json | 5 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/refreshSession.json | 11 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/requestEmailConfirmation.json | 2 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/reserveSigningKey.json |only atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/revokeAppPassword.json | 2 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/server/updateEmail.json | 1 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/getBlob.json | 13 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/getBlocks.json | 11 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/getLatestCommit.json | 9 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/getRecord.json | 15 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/getRepo.json | 12 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/getRepoStatus.json |only atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/listBlobs.json | 12 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/listRepos.json | 17 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/notifyOfUpdate.json | 4 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/requestCrawl.json | 4 atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/sync/subscribeRepos.json | 118 ++ atrrr-0.0.5/atrrr/inst/lexicons/com/atproto/temp |only atrrr-0.0.5/atrrr/inst/lexicons/tools |only atrrr-0.0.5/atrrr/man/atrrr-package.Rd | 1 atrrr-0.0.5/atrrr/man/get_actor_likes.Rd |only atrrr-0.0.5/atrrr/man/get_followers.Rd | 4 atrrr-0.0.5/atrrr/man/get_list.Rd |only atrrr-0.0.5/atrrr/man/get_skeets_authored_by.Rd | 3 atrrr-0.0.5/atrrr/man/get_starter_pack.Rd |only atrrr-0.0.5/atrrr/man/post.Rd | 4 atrrr-0.0.5/atrrr/man/search_post.Rd | 77 + atrrr-0.0.5/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_01031.rds |only atrrr-0.0.5/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_0f35e.rds |only atrrr-0.0.5/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_3ed2a.rds |only atrrr-0.0.5/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_a3350.rds |binary atrrr-0.0.5/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_f39c7.rds |binary atrrr-0.0.5/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_f9a85.rds |only 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Title: Parse and Manipulate Research Patient Data Registry ('RPDR')
Text Queries
Description: Functions to load Research Patient Data Registry ('RPDR') text queries from Partners Healthcare institutions into R.
The package also provides helper functions to manipulate data and execute common procedures
such as finding the closest radiological exams considering a given timepoint, or creating a DICOM header database
from the downloaded images. All functionalities are parallelized for fast and efficient analyses.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <mkolossvary@mgh.harvard.edu>
Diff between parseRPDR versions 1.1.1 dated 2024-04-03 and 1.1.2 dated 2025-01-19
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- NEWS.md | 3 +++ R/ZZZ.R | 3 --- R/convert_dia.R | 2 ++ R/convert_enc.R | 3 +++ R/convert_lab.R | 2 +- R/convert_med.R | 2 ++ R/convert_notes.R | 3 +++ R/convert_phy.R | 2 ++ R/convert_prc.R | 2 ++ R/convert_rfv.R | 3 +++ R/find_exam_ram.R | 2 ++ R/load_all_data.R | 3 +++ R/parse_ids.R | 3 +++ R/pretty_mrn.R | 2 ++ 16 files changed, 51 insertions(+), 24 deletions(-)
Title: Infinitesimally Robust Estimators for Preprocessing -Omics Data
Description: Functions for the determination of optimally robust influence curves and
estimators for preprocessing omics data, in particular gene expression data (Kohl
and Deigner (2010), <doi:10.1186/1471-2105-11-583>).
Author: Matthias Kohl [aut, cre, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RobLoxBioC versions 1.2.2 dated 2024-02-11 and 1.2.3 dated 2025-01-19
DESCRIPTION | 20 - MD5 | 12 R/KolmogorovMinDist.R | 686 ++++++++++++++++++++++----------------------- inst/CITATION | 9 inst/NEWS | 12 man/0RobLoxBioC-package.Rd | 88 ++--- man/robloxbioc.Rd | 373 ++++++++++++------------ 7 files changed, 606 insertions(+), 594 deletions(-)
Title: Ternary Residual Effect Designs
Description: There are some experimental scenarios where each experimental unit receives a sequence of treatments across multiple periods, and treatment effects persist beyond the period of application. It focuses on the construction and calculation of the parametric value of the residual effect designs balanced for carryover effects, also referred to as crossover designs, change-over designs, or repeated measurements designs (Aggarwal and Jha, 2010<doi:10.1080/15598608.2010.10412013>). The primary objective of the package is to generate a new class of Balanced Ternary Residual Effect Designs (BTREDs), balanced for carryover effects tailored explicitly for situations where the number of periods is less than or equal to the number of treatments. In addition, the package provides four new classes of Partially Balanced Ternary Residual Effect Designs (PBTREDs), constructed using incomplete block designs, initial sequences, and rectangular association scheme. In addition, one extra function is in [...truncated...]
Author: Akhilesh Jha [aut],
Cini Varghese [aut],
Seema Jaggi [aut],
Mohd Harun [aut],
Ashutosh Dalal [aut, cre]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between TREDesigns versions 1.0.0 dated 2024-12-11 and 1.0.1 dated 2025-01-19
TREDesigns-1.0.0/TREDesigns/man/Study_tRED.Rd |only TREDesigns-1.0.1/TREDesigns/DESCRIPTION | 6 +++--- TREDesigns-1.0.1/TREDesigns/MD5 | 18 +++++++++--------- TREDesigns-1.0.1/TREDesigns/NAMESPACE | 2 +- TREDesigns-1.0.1/TREDesigns/R/BtRED.R | 2 +- TREDesigns-1.0.1/TREDesigns/R/PBtRED1.R | 2 +- TREDesigns-1.0.1/TREDesigns/R/PBtRED2.R | 6 +++--- TREDesigns-1.0.1/TREDesigns/R/PBtRED3.R | 2 +- TREDesigns-1.0.1/TREDesigns/R/PBtRED4.R | 2 +- TREDesigns-1.0.1/TREDesigns/R/Study_RED.R | 16 ++++++++-------- TREDesigns-1.0.1/TREDesigns/man/Study_RED.Rd |only 11 files changed, 28 insertions(+), 28 deletions(-)
Title: Bindings to the 'Geospatial Data Abstraction Library' Raster API
Description: Interface to the Raster API of the 'Geospatial Data Abstraction
Library' ('GDAL', <https://gdal.org>). Bindings are implemented in an
exposed C++ class encapsulating a 'GDALDataset' and its raster band
objects, along with several stand-alone functions. These support manual
creation of uninitialized datasets, creation from existing raster as
template, read/set dataset parameters, low level I/O, color tables, raster
attribute tables, virtual raster (VRT), and 'gdalwarp' wrapper for
reprojection and mosaicing. Includes 'GDAL' algorithms ('dem_proc()',
'polygonize()', 'rasterize()', etc.), and functions for coordinate
transformation and spatial reference systems. Calling signatures resemble
the native C, C++ and Python APIs provided by the 'GDAL' project. Includes
raster 'calc()' to evaluate a given R expression on a layer or stack of
layers, with pixel x/y available as variables in the expression; and raster
'combine()' to identify and count unique pixel combinations across multiple [...truncated...]
Author: Chris Toney [aut, cre] ,
Michael D. Sumner [ctb],
Frank Warmerdam [ctb, cph] ,
Even Rouault [ctb, cph] ,
Marius Appel [ctb, cph] ,
Daniel James [ctb, cph] ,
Peter Dimov [ctb, cph]
Maintainer: Chris Toney <chris.toney@usda.gov>
Diff between gdalraster versions 1.11.1 dated 2024-06-13 and 1.12.0 dated 2025-01-19
DESCRIPTION | 8 MD5 | 139 ++++++----- NEWS.md | 23 + R/RcppExports.R | 131 ++++++++--- R/display.R | 70 +++++ R/gdal_helpers.R | 103 ++++++++ R/gdalraster.R | 30 +- R/gdalraster_proc.R | 73 +++--- R/ogr_define.R | 22 + R/ogr_manage.R | 8 R/vsifile.R | 10 README.md | 16 - build/vignette.rds |binary configure | 18 - configure.ac | 2 inst/doc/gdal-config-quick-ref.Rmd | 36 +-- inst/doc/gdal-config-quick-ref.html | 36 +-- inst/doc/raster-api-tutorial.R | 6 inst/doc/raster-api-tutorial.Rmd | 14 - inst/doc/raster-api-tutorial.html | 388 ++++++++++++++++----------------- inst/doc/raster-attribute-tables.Rmd | 4 inst/doc/raster-attribute-tables.html | 323 ++++++++++++++------------- inst/extdata/poly_multipoly.dbf |only inst/extdata/poly_multipoly.prj |only inst/extdata/poly_multipoly.shp |only inst/extdata/poly_multipoly.shx |only inst/extdata/small_world_and_byte.gpkg |only man/DEFAULT_DEM_PROC.Rd | 21 - man/GDALRaster-class.Rd | 30 +- man/VSIFile-class.Rd | 10 man/addFilesInZip.Rd | 4 man/buildVRT.Rd | 2 man/createColorRamp.Rd | 2 man/dem_proc.Rd | 4 man/footprint.Rd | 2 man/gdal_formats.Rd | 2 man/gdalraster-package.Rd | 18 - man/get_config_option.Rd | 2 man/has_spatialite.Rd | 2 man/identifyDriver.Rd |only man/inspectDataset.Rd |only man/inv_project.Rd | 8 man/ogr2ogr.Rd | 2 man/ogr_define.Rd | 6 man/ogr_manage.Rd | 8 man/ogrinfo.Rd | 2 man/plot_raster.Rd | 17 + man/polygonize.Rd | 2 man/rasterToVRT.Rd | 2 man/rasterize.Rd | 2 man/read_ds.Rd | 1 man/set_config_option.Rd | 2 man/transform_xy.Rd | 14 - man/translate.Rd | 2 man/vsi_copy_file.Rd | 2 man/vsi_get_fs_options.Rd | 2 man/vsi_get_fs_prefixes.Rd | 2 man/vsi_read_dir.Rd | 27 +- man/vsi_stat.Rd | 2 man/warp.Rd | 8 src/RcppExports.cpp | 62 +++-- src/gdal_exp.cpp | 124 +++++++++- src/gdal_vsi.cpp | 54 +++- src/gdalraster.h | 6 src/transform.cpp | 58 ++-- src/transform.h |only src/wkt_conv.cpp | 16 - src/wkt_conv.h |only tests/testthat/test-VSIFile-class.R | 4 tests/testthat/test-gdal_exp.R | 12 + tests/testthat/test-gdal_helpers.R | 52 ++++ tests/testthat/test-gdalraster_proc.R | 9 vignettes/gdal-config-quick-ref.Rmd | 36 +-- vignettes/raster-api-tutorial.Rmd | 14 - vignettes/raster-attribute-tables.Rmd | 4 75 files changed, 1325 insertions(+), 796 deletions(-)
Title: Gene Set Analysis Using the Gene Set Ordinal Association Test
Description: Perform gene set enrichment analyses using the Gene set Ordinal
Association Test (GOAT) algorithm and visualize your
results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.
Author: Frank Koopmans [aut, cre]
Maintainer: Frank Koopmans <ftwkoopmans@gmail.com>
Diff between goat versions 1.0 dated 2024-04-30 and 1.1 dated 2025-01-19
DESCRIPTION | 17 +- LICENSE.note | 4 MD5 | 44 +++-- NAMESPACE | 2 NEWS.md | 8 + R/download_data.R | 46 ++++-- R/load_genesets_go.R | 93 ++++++++++-- R/load_genesets_syngo.R | 2 R/save_genesets.R | 27 ++- R/simplify_ontology.R | 8 - R/test_genesets_goat.R | 10 - R/utils.R | 22 ++ README.md | 259 +++++++++++++++++++--------------- inst/CITATION | 7 man/available_genesets_goatrepo.Rd |only man/download_genesets_goatrepo.Rd | 17 +- man/go_gene2go.Rd | 2 man/go_obo.Rd | 2 man/load_genesets_go_bioconductor.Rd | 19 ++ man/load_genesets_go_fromfile.Rd | 9 - man/load_genesets_syngo.Rd | 2 man/taxonomy_identifiers.Rd |only man/test_genesets_goat_precomputed.Rd | 4 man/treemap_data.Rd | 2 24 files changed, 399 insertions(+), 207 deletions(-)
Title: 'MsgPack' C++ Header Files and Interface Functions for R
Description: 'MsgPack' header files are provided for use by R packages, along
with the ability to access, create and alter 'MsgPack' objects directly from R.
'MsgPack' is an efficient binary serialization format. It lets you exchange
data among multiple languages like 'JSON' but it is faster and smaller.
Small integers are encoded into a single byte, and typical short strings
require only one extra byte in addition to the strings themselves. This
package provides headers from the 'msgpack-c' implementation for C and
C++(11) for use by R, particularly 'Rcpp'. The included 'msgpack-c' headers
are licensed under the Boost Software License (Version 1.0); the code added
by this package as well the R integration are licensed under the GPL (>= 2).
See the files 'COPYRIGHTS' and 'AUTHORS' for a full list of copyright holders
and contributors to 'msgpack-c'.
Author: Dirk Eddelbuettel [aut, cre] ,
Travers Ching [aut],
MsgPack Authors [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppMsgPack versions 0.2.3 dated 2018-11-18 and 0.2.4 dated 2025-01-19
ChangeLog | 71 ++++++++++++ DESCRIPTION | 22 ++- MD5 | 25 ++-- R/functions.r | 70 ++++++------ README.md | 75 ++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/NEWS.Rd | 13 ++ inst/doc/vignette.R | 2 inst/doc/vignette.html | 221 ++++++++++++++++++++++++++-------------- src/Makevars | 6 - src/RcppExports.cpp | 4 src/rcppmsgpack_c_functions.cpp | 6 - 14 files changed, 347 insertions(+), 168 deletions(-)
Title: Version-Control for CRAN, GitHub, and GitLab Packages
Description: Make R scripts reproducible, by ensuring that
every time a given script is run, the same version of the used packages are
loaded (instead of whichever version the user running the script happens to
have installed). This is achieved by using the command
groundhog.library() instead of the base command library(), and including a
date in the call. The date is used to call on the same version of the
package every time (the most recent version available at that date).
Load packages from CRAN, GitHub, or Gitlab.
Author: Uri Simonsohn [aut, cre] ,
Hugo Gruson [ctb, aut]
Maintainer: Uri Simonsohn <urisohn@gmail.com>
Diff between groundhog versions 3.2.1 dated 2024-09-29 and 3.2.2 dated 2025-01-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/toc.R | 15 +++++++++++++++ R/utils.R | 26 ++++++++++++-------------- R/validate.clone_date.R | 2 +- R/validate.groundhog.library.R | 10 ++++------ 6 files changed, 40 insertions(+), 29 deletions(-)
Title: Interface to Bank of Japan Statistics
Description: Provides an interface to Bank of Japan <https://www.boj.or.jp>
statistics.
Author: Stefan Angrick [aut, cre, cph]
Maintainer: Stefan Angrick <contact@stefanangrick.net>
Diff between BOJ versions 0.3 dated 2022-01-04 and 0.3.4 dated 2025-01-19
DESCRIPTION | 11 - LICENSE | 2 MD5 | 23 +- NAMESPACE | 1 R/BOJ.R | 348 ++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/BOJ.R | 70 +++---- inst/doc/BOJ.Rmd | 70 +++---- inst/doc/BOJ.html | 449 +++++++++++++++++++++++++++++++++--------------- man/get_boj.Rd | 20 +- man/get_boj_datasets.Rd | 18 + man/pivot_longer_boj.Rd |only vignettes/BOJ.Rmd | 70 +++---- 13 files changed, 674 insertions(+), 408 deletions(-)
Title: Easy Access to NetCDF Files with CF Metadata Conventions
Description: Network Common Data Form ('netCDF') files are widely used for
scientific data. Library-level access in R is provided through packages
'RNetCDF' and 'ncdf4'. Package 'ncdfCF' is built on top of 'RNetCDF' and
makes the data and its attributes available as a set of R6 classes that are
informed by the Climate and Forecasting Metadata Conventions. Access to the
data uses standard R subsetting operators and common function forms.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between ncdfCF versions 0.2.1 dated 2024-10-14 and 0.3.0 dated 2025-01-19
ncdfCF-0.2.1/ncdfCF/R/CFread.R |only ncdfCF-0.2.1/ncdfCF/man/sub-.CFVariable.Rd |only ncdfCF-0.3.0/ncdfCF/DESCRIPTION | 16 ncdfCF-0.3.0/ncdfCF/MD5 | 151 ++++---- ncdfCF-0.3.0/ncdfCF/NAMESPACE | 24 - ncdfCF-0.3.0/ncdfCF/NEWS.md | 115 +++--- ncdfCF-0.3.0/ncdfCF/R/AOI.R | 16 ncdfCF-0.3.0/ncdfCF/R/AOImethod.R | 6 ncdfCF-0.3.0/ncdfCF/R/CFAuxiliaryLongLat.R | 24 - ncdfCF-0.3.0/ncdfCF/R/CFAxis.R | 160 +++++--- ncdfCF-0.3.0/ncdfCF/R/CFAxisCharacter.R | 108 ++--- ncdfCF-0.3.0/ncdfCF/R/CFAxisDiscrete.R | 45 +- ncdfCF-0.3.0/ncdfCF/R/CFAxisLatitude.R | 19 - ncdfCF-0.3.0/ncdfCF/R/CFAxisLongitude.R | 27 - ncdfCF-0.3.0/ncdfCF/R/CFAxisNumeric.R | 88 ++-- ncdfCF-0.3.0/ncdfCF/R/CFAxisScalar.R | 51 +- ncdfCF-0.3.0/ncdfCF/R/CFAxisTime.R | 111 +++-- ncdfCF-0.3.0/ncdfCF/R/CFAxisVertical.R | 18 ncdfCF-0.3.0/ncdfCF/R/CFBounds.R | 12 ncdfCF-0.3.0/ncdfCF/R/CFData.R | 37 - ncdfCF-0.3.0/ncdfCF/R/CFDataset.R | 142 ++++--- ncdfCF-0.3.0/ncdfCF/R/CFGridMapping.R | 17 ncdfCF-0.3.0/ncdfCF/R/CFLabel.R |only ncdfCF-0.3.0/ncdfCF/R/CFObject.R | 37 + ncdfCF-0.3.0/ncdfCF/R/CFResource.R | 52 +- ncdfCF-0.3.0/ncdfCF/R/CFVariable.R | 414 +--------------------- ncdfCF-0.3.0/ncdfCF/R/CFVariableGeneric.R |only ncdfCF-0.3.0/ncdfCF/R/CFVariableL3b.R |only ncdfCF-0.3.0/ncdfCF/R/NCDimension.R | 24 - ncdfCF-0.3.0/ncdfCF/R/NCGroup.R | 222 +++++++---- ncdfCF-0.3.0/ncdfCF/R/NCObject.R | 42 -- ncdfCF-0.3.0/ncdfCF/R/NCUDT.R | 30 - ncdfCF-0.3.0/ncdfCF/R/NCVariable.R | 38 +- ncdfCF-0.3.0/ncdfCF/R/makeCFObjects.R |only ncdfCF-0.3.0/ncdfCF/R/ncdfCF-package.R | 29 - ncdfCF-0.3.0/ncdfCF/R/readCF.R |only ncdfCF-0.3.0/ncdfCF/R/utils.R | 19 - ncdfCF-0.3.0/ncdfCF/R/wkt2.R | 7 ncdfCF-0.3.0/ncdfCF/README.md | 129 +++--- ncdfCF-0.3.0/ncdfCF/TODO | 16 ncdfCF-0.3.0/ncdfCF/build/vignette.rds |binary ncdfCF-0.3.0/ncdfCF/inst/doc/R-CF.R |only ncdfCF-0.3.0/ncdfCF/inst/doc/R-CF.Rmd |only ncdfCF-0.3.0/ncdfCF/inst/doc/R-CF.html |only ncdfCF-0.3.0/ncdfCF/inst/doc/Using_ncdfCF.R | 12 ncdfCF-0.3.0/ncdfCF/inst/doc/Using_ncdfCF.Rmd | 20 - ncdfCF-0.3.0/ncdfCF/inst/doc/Using_ncdfCF.html | 362 ++++++++----------- ncdfCF-0.3.0/ncdfCF/man/CFAuxiliaryLongLat.Rd | 16 ncdfCF-0.3.0/ncdfCF/man/CFAxis.Rd | 135 ++++--- ncdfCF-0.3.0/ncdfCF/man/CFAxisCharacter.Rd | 20 - ncdfCF-0.3.0/ncdfCF/man/CFAxisDiscrete.Rd | 22 - ncdfCF-0.3.0/ncdfCF/man/CFAxisLatitude.Rd | 20 - ncdfCF-0.3.0/ncdfCF/man/CFAxisLongitude.Rd | 27 - ncdfCF-0.3.0/ncdfCF/man/CFAxisNumeric.Rd | 43 +- ncdfCF-0.3.0/ncdfCF/man/CFAxisScalar.Rd | 31 + ncdfCF-0.3.0/ncdfCF/man/CFAxisTime.Rd | 78 +++- ncdfCF-0.3.0/ncdfCF/man/CFAxisVertical.Rd | 15 ncdfCF-0.3.0/ncdfCF/man/CFBounds.Rd | 11 ncdfCF-0.3.0/ncdfCF/man/CFData.Rd | 16 ncdfCF-0.3.0/ncdfCF/man/CFDataset.Rd | 109 +++-- ncdfCF-0.3.0/ncdfCF/man/CFGridMapping.Rd | 13 ncdfCF-0.3.0/ncdfCF/man/CFLabel.Rd |only ncdfCF-0.3.0/ncdfCF/man/CFObject.Rd | 29 + ncdfCF-0.3.0/ncdfCF/man/CFResource.Rd | 57 +-- ncdfCF-0.3.0/ncdfCF/man/CFVariable.Rd | 152 +------- ncdfCF-0.3.0/ncdfCF/man/CFVariableGeneric.Rd |only ncdfCF-0.3.0/ncdfCF/man/CFVariableL3b.Rd |only ncdfCF-0.3.0/ncdfCF/man/MemoryGroup.Rd | 2 ncdfCF-0.3.0/ncdfCF/man/NCDimension.Rd | 37 + ncdfCF-0.3.0/ncdfCF/man/NCGroup.Rd | 356 +++++++++++++++++- ncdfCF-0.3.0/ncdfCF/man/NCObject.Rd | 49 +- ncdfCF-0.3.0/ncdfCF/man/NCUDT.Rd | 20 - ncdfCF-0.3.0/ncdfCF/man/NCVariable.Rd | 43 +- ncdfCF-0.3.0/ncdfCF/man/aoi.Rd | 10 ncdfCF-0.3.0/ncdfCF/man/makeLatitudeAxis.Rd |only ncdfCF-0.3.0/ncdfCF/man/makeLongitudeAxis.Rd |only ncdfCF-0.3.0/ncdfCF/man/makeMemoryGroup.Rd |only ncdfCF-0.3.0/ncdfCF/man/makeTimeAxis.Rd |only ncdfCF-0.3.0/ncdfCF/man/ncdfCF-package.Rd | 29 - ncdfCF-0.3.0/ncdfCF/man/open_ncdf.Rd | 5 ncdfCF-0.3.0/ncdfCF/man/peek_ncdf.Rd |only ncdfCF-0.3.0/ncdfCF/man/str.CFDataset.Rd |only ncdfCF-0.3.0/ncdfCF/man/sub-.CFVariableGeneric.Rd |only ncdfCF-0.3.0/ncdfCF/man/sub-.CFVariableL3b.Rd |only ncdfCF-0.3.0/ncdfCF/man/sub-sub-.CFDataset.Rd | 8 ncdfCF-0.3.0/ncdfCF/vignettes/CF-elements.png |only ncdfCF-0.3.0/ncdfCF/vignettes/R-CF.Rmd |only ncdfCF-0.3.0/ncdfCF/vignettes/Using_ncdfCF.Rmd | 20 - 88 files changed, 2155 insertions(+), 1858 deletions(-)
Title: Instrumental-Variables Regression by '2SLS', '2SM', or '2SMM',
with Diagnostics
Description: Instrumental variable estimation for linear models by two-stage least-squares (2SLS) regression or by robust-regression via M-estimation (2SM) or MM-estimation (2SMM). The main ivreg() model-fitting function is designed to provide a workflow as similar as possible to standard lm() regression. A wide range of methods is provided for fitted ivreg model objects, including extensive functionality for computing and graphing regression diagnostics in addition to other standard model tools.
Author: John Fox [aut] ,
Christian Kleiber [aut] ,
Achim Zeileis [aut, cre] ,
Nikolas Kuschnig [ctb] ,
R Core Team [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between ivreg versions 0.6-4 dated 2024-09-18 and 0.6-5 dated 2025-01-19
DESCRIPTION | 8 MD5 | 19 - NEWS.md | 11 R/ivreg.R | 4 R/ivregMethods.R | 295 -------------------------- R/summary.ivreg.R |only inst/doc/Diagnostics-for-2SLS-Regression.html | 37 +-- man/ivreg.Rd | 4 man/ivregMethods.Rd | 77 ------ man/summary.ivreg.Rd |only tests/testthat.R | 4 tests/testthat/test-vcov.R |only 12 files changed, 73 insertions(+), 386 deletions(-)
Title: Computation and Decomposition of the Mutual Information Index
Description: The Mutual Information Index (M) introduced to social science literature by
Theil and Finizza (1971) <doi:10.1080/0022250X.1971.9989795> is a multigroup
segregation measure that is highly decomposable and that according to Frankel
and Volij (2011) <doi:10.1016/j.jet.2010.10.008> and Mora and Ruiz-Castillo
(2011) <doi:10.1111/j.1467-9531.2011.01237.x> satisfies the Strong Unit
Decomposability and Strong Group Decomposability properties. This package allows
computing and decomposing the total index value into its "between" and
"within" terms. These last terms can also be decomposed into their
contributions, either by group or unit characteristics. The factors that produce
each "within" term can also be displayed at the user's request. The results can
be computed considering a variable or sets of variables that define separate
clusters.
Author: Cristian Angulo-Gonzalez [aut, cre],
Rafael Fuentealba-Chaura [aut],
Ricardo Mora [aut],
Julio Rojas-Mora [aut],
FONDECYT/ANID Project 11170583 [fnd],
MCIN/AEI/10.13039/501100011033 [fnd],
UCT VIP Project FEQUIP2019-INRN-03 [fnd]
Maintainer: Cristian Angulo-Gonzalez <cristian_world@hotmail.cl>
Diff between mutualinf versions 2.0.2 dated 2025-01-18 and 2.0.3 dated 2025-01-19
DESCRIPTION | 17 +++++++++-------- MD5 | 4 ++-- R/M.R | 6 ++---- 3 files changed, 13 insertions(+), 14 deletions(-)
Title: Interpolate Munsell Renotation Data from Hue Value/Chroma to
CIE/RGB
Description: Methods for interpolating data in the Munsell color system following the ASTM D-1535 standard. Hues and chromas with decimal values can be interpolated and converted to/from the Munsell color system and CIE xyY, CIE XYZ, CIE Lab, CIE Luv, or RGB. Includes ISCC-NBS color block lookup. Based on the work by Paul Centore, "The Munsell and Kubelka-Munk Toolbox".
Author: Jose Gama [aut, trl],
Paul Centore [aut, cph],
Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between munsellinterpol versions 3.0-0 dated 2022-04-07 and 3.1-0 dated 2025-01-19
munsellinterpol-3.0-0/munsellinterpol/R/logging.R |only munsellinterpol-3.0-0/munsellinterpol/man/figures/Thumbs.db |only munsellinterpol-3.0-0/munsellinterpol/vignettes/framed.sty |only munsellinterpol-3.0-0/munsellinterpol/vignettes/iso690-numeric-brackets-cs.csl |only munsellinterpol-3.1-0/munsellinterpol/DESCRIPTION | 13 munsellinterpol-3.1-0/munsellinterpol/MD5 | 73 munsellinterpol-3.1-0/munsellinterpol/NAMESPACE | 2 munsellinterpol-3.1-0/munsellinterpol/NEWS.md | 7 munsellinterpol-3.1-0/munsellinterpol/R/ColorDifference.R | 2 munsellinterpol-3.1-0/munsellinterpol/R/ISCC-NBS.R | 204 - munsellinterpol-3.1-0/munsellinterpol/R/MunsellName.R | 514 +-- munsellinterpol-3.1-0/munsellinterpol/R/MunsellToxyY.R | 566 +-- munsellinterpol-3.1-0/munsellinterpol/R/RGB.R | 260 - munsellinterpol-3.1-0/munsellinterpol/R/VandY.R | 266 - munsellinterpol-3.1-0/munsellinterpol/R/conversions.R | 988 +++--- munsellinterpol-3.1-0/munsellinterpol/R/events.R | 55 munsellinterpol-3.1-0/munsellinterpol/R/inversions.R | 446 +-- munsellinterpol-3.1-0/munsellinterpol/R/logger.R |only munsellinterpol-3.1-0/munsellinterpol/R/lookup.R | 962 +++--- munsellinterpol-3.1-0/munsellinterpol/R/optimals.R | 260 - munsellinterpol-3.1-0/munsellinterpol/R/plots.R | 1416 +++++----- munsellinterpol-3.1-0/munsellinterpol/R/reparam.R | 272 - munsellinterpol-3.1-0/munsellinterpol/R/spline.R | 602 ++-- munsellinterpol-3.1-0/munsellinterpol/R/utils.R | 264 - munsellinterpol-3.1-0/munsellinterpol/R/xyYtoMunsell.R | 922 +++--- munsellinterpol-3.1-0/munsellinterpol/R/zonohedron.R | 10 munsellinterpol-3.1-0/munsellinterpol/build/vignette.rds |binary munsellinterpol-3.1-0/munsellinterpol/inst/doc/dental.R | 2 munsellinterpol-3.1-0/munsellinterpol/inst/doc/dental.html | 377 +- munsellinterpol-3.1-0/munsellinterpol/inst/doc/lightness.pdf |binary munsellinterpol-3.1-0/munsellinterpol/inst/doc/lociHC.pdf |binary munsellinterpol-3.1-0/munsellinterpol/inst/doc/munsellinterpol-guide.R | 10 munsellinterpol-3.1-0/munsellinterpol/inst/doc/munsellinterpol-guide.Rmd | 43 munsellinterpol-3.1-0/munsellinterpol/inst/doc/munsellinterpol-guide.html | 1008 +++++-- munsellinterpol-3.1-0/munsellinterpol/inst/extdata/PantoneCoY.txt | 3 munsellinterpol-3.1-0/munsellinterpol/man/HVCfromMunsellName.Rd | 9 munsellinterpol-3.1-0/munsellinterpol/man/plotLociHC.Rd | 2 munsellinterpol-3.1-0/munsellinterpol/man/xyYtoMunsell.Rd | 15 munsellinterpol-3.1-0/munsellinterpol/vignettes/bibliography.bib | 34 munsellinterpol-3.1-0/munsellinterpol/vignettes/munsellinterpol-guide.Rmd | 43 40 files changed, 5128 insertions(+), 4522 deletions(-)
More information about munsellinterpol at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-23 9.1.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-10 0.9.2
2022-10-30 0.9.1.5
2019-11-24 0.9.1.4
2018-04-10 0.9.1.3
2015-10-17 0.9.1.1
2015-09-22 0.9.1
2015-03-29 0.9
2015-01-01 0.8
2014-12-21 0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-10 1.5.1
Title: Repel Visually Similar Colors for Colorblind Users in Various
Plots
Description: Iterate and repel visually similar colors away in various 'ggplot2' plots. When many groups are plotted at the same time on multiple axes, for instance stacked bars or scatter plots, effectively ordering colors becomes difficult. This tool iterates through color combinations to find the best solution to maximize visual distinctness of nearby groups, so plots are more friendly toward colorblind users. This is achieved by two distance measurements, distance between groups within the plot, and CIELAB color space distances between colors as described in Carter et al., (2018) <doi:10.25039/TR.015.2018>.
Author: Rui Fu [cre, aut, cph]
Maintainer: Rui Fu <raysinensis@gmail.com>
Diff between colorrepel versions 0.3.0 dated 2024-09-29 and 0.4.1 dated 2025-01-18
DESCRIPTION | 10 +- MD5 | 32 ++++----- NAMESPACE | 1 NEWS.md | 12 +++ R/color_repel.R | 39 +++++++++-- R/interactive.R | 66 ++++++++++++++++--- R/utils.R | 135 ++++++++++++++++++++++++++++++++++++---- R/wrappers.R | 23 +++++- README.md | 11 ++- inst/scRNAseqUMAP_extra.png |binary man/average_clusters.Rd | 9 ++ man/average_clusters_rowwise.Rd | 2 man/color_repel.Rd | 8 ++ man/get_labs.Rd | 4 - man/gg_color_repel.Rd | 9 ++ man/ggplotly_background.Rd | 12 +++ man/label_repel.Rd | 3 17 files changed, 314 insertions(+), 62 deletions(-)
Title: Spatially Aware Cell-Cell Interaction Analysis
Description: Provides tools for analyzing spatial cell-cell interactions based on ligand-receptor pairs, including functions for local, regional, and global analysis using spatial transcriptomics data. Integrates with databases like 'CellChat' <http://www.cellchat.org/>, 'CellPhoneDB' <https://www.cellphonedb.org/>, 'Cellinker' <https://www.rna-society.org/cellinker/>, 'ICELLNET' <https://github.com/soumelis-lab/ICELLNET>, and 'ConnectomeDB' <https://humanconnectome.org/software/connectomedb/> to identify ligand-receptor pairs, visualize interactions through heatmaps, chord diagrams, and infer interactions on different spatial scales.
Author: Li-Ting Ku [aut, cre]
Maintainer: Li-Ting Ku <lku@mdanderson.org>
Diff between SpaCCI versions 1.0.2 dated 2024-10-24 and 1.0.3 dated 2025-01-18
DESCRIPTION | 10 MD5 | 49 ++- NAMESPACE | 1 R/RcppExports.R | 4 R/modeling.R | 185 ++++++-------- R/permutation.R | 3 R/result_local.R | 11 R/result_local_spatial_coords_df.R |only R/result_regional.R |only R/run_SpaCCI.R | 4 R/utils.R | 2 R/visiualization.R | 419 +++++++++++++++++++++++++++++++- data/result_global.rda |binary data/result_local.rda |binary data/result_local_spatial_coords_df.rda |only data/result_regional.rda |only man/Global_Permutations.Rd | 3 man/SpaCCI_global.Rd | 3 man/SpaCCI_region.Rd | 3 man/plot_SpaCCI_local.Rd | 9 man/plot_SpaCCI_local_Strength.Rd |only man/plot_Strength_Seurat.Rd |only man/plot_Strength_localized.Rd |only man/plot_localized.Rd | 10 man/result_local.Rd | 12 man/result_local_spatial_coords_df.Rd |only man/result_regional.Rd |only man/run_SpaCCI.Rd | 2 src/RcppExports.cpp | 9 src/permutation_func.cpp | 132 ++++------ 30 files changed, 628 insertions(+), 243 deletions(-)
Title: Data for Package 'Qindex'
Description: Example data used in package 'Qindex'.
Author: Tingting Zhan [aut, cre, cph] ,
Misung Yi [aut, cph] ,
Inna Chervoneva [aut, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between Qindex.data versions 0.1.2 dated 2025-01-17 and 0.1.3 dated 2025-01-18
DESCRIPTION | 27 ++++++++++----------- MD5 | 10 ++++---- R/Ki67.R | 56 ++++++++++++--------------------------------- data/Ki67.rda |binary man/Qindex.data-package.Rd | 6 ---- man/celldata.Rd | 30 ++++++++++++------------ 6 files changed, 49 insertions(+), 80 deletions(-)
Title: Computation and Decomposition of the Mutual Information Index
Description: The Mutual Information Index (M) introduced to social science literature by
Theil and Finizza (1971) <doi:10.1080/0022250X.1971.9989795> is a multigroup
segregation measure that is highly decomposable and that according to Frankel
and Volij (2011) <doi:10.1016/j.jet.2010.10.008> and Mora and Ruiz-Castillo
(2011) <doi:10.1111/j.1467-9531.2011.01237.x> satisfies the Strong Unit
Decomposability and Strong Group Decomposability properties. This package allows
computing and decomposing the total index value into its "between" and
"within" terms. These last terms can also be decomposed into their
contributions, either by group or unit characteristics. The factors that produce
each "within" term can also be displayed at the user's request. The results can
be computed considering a variable or sets of variables that define separate
clusters.
Author: Cristian Angulo-Gonzalez [aut, cre],
Rafael Fuentealba-Chaura [aut],
Ricardo Mora [aut],
Julio Rojas-Mora [aut],
FONDECYT/ANID Project 11170583 [fnd],
MCIN/AEI/10.13039/501100011033 [fnd],
UCT VIP Project FEQUIP2019-INRN-03 [fnd]
Maintainer: Cristian Angulo-Gonzalez <cristian_world@hotmail.cl>
Diff between mutualinf versions 2.0.1 dated 2025-01-16 and 2.0.2 dated 2025-01-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/get_contribution.R | 9 +++------ src/VectorHash.h | 1 + 4 files changed, 11 insertions(+), 13 deletions(-)
Title: Evolutionary Algorithm
Description: Runs a genetic algorithm using the 'AlphaSimR' machinery <doi:10.1093/g3journal/jkaa017> and the coalescent simulator 'MaCS' <doi:10.1101/gr.083634.108>.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between evola versions 1.0.2 dated 2024-09-26 and 1.0.4 dated 2025-01-18
evola-1.0.2/evola/inst/doc/evola.intro.R |only evola-1.0.2/evola/inst/doc/evola.intro.Rmd |only evola-1.0.2/evola/inst/doc/evola.intro.pdf |only evola-1.0.2/evola/vignettes/evola.intro.Rmd |only evola-1.0.2/evola/vignettes/evola.intro.html |only evola-1.0.4/evola/ChangeLog | 10 +- evola-1.0.4/evola/DESCRIPTION | 8 +- evola-1.0.4/evola/MD5 | 26 +++--- evola-1.0.4/evola/NAMESPACE | 5 - evola-1.0.4/evola/R/evolafit.R | 106 ++++++++++++++++++--------- evola-1.0.4/evola/R/utlis.R | 9 ++ evola-1.0.4/evola/build/vignette.rds |binary evola-1.0.4/evola/inst/doc/evola_intro.R |only evola-1.0.4/evola/inst/doc/evola_intro.Rmd |only evola-1.0.4/evola/inst/doc/evola_intro.html |only evola-1.0.4/evola/man/evola-package.Rd | 2 evola-1.0.4/evola/man/evolafit.Rd | 53 +++++++++---- evola-1.0.4/evola/man/fitnessf.Rd |only evola-1.0.4/evola/vignettes/evola_intro.Rmd |only 19 files changed, 147 insertions(+), 72 deletions(-)
Title: Quantity Calculus for R Vectors
Description: Integration of the 'units' and 'errors' packages for a complete
quantity calculus system for R vectors, matrices and arrays, with automatic
propagation, conversion, derivation and simplification of magnitudes and
uncertainties. Documentation about 'units' and 'errors' is provided in the
papers by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>) and
by Ucar, Pebesma & Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in
those packages as vignettes; see 'citation("quantities")' for details.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between quantities versions 0.2.2 dated 2024-07-29 and 0.2.3 dated 2025-01-18
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/errors.R | 17 ++++++++++++++++- README.md | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.R | 10 +++++----- inst/doc/introduction.html | 20 ++++++-------------- inst/doc/parsing.html | 4 ++-- man/correl.Rd | 6 ++++++ 12 files changed, 57 insertions(+), 38 deletions(-)
Title: S3 Resource Resolver
Description: A S3 resource is provided by Amazon Web Services S3 or a S3-compatible object store (such as Minio).
The resource can be a tidy file to be downloaded from the object store, or a data lake (such as Delta Lake)
Parquet file to be read by Apache Spark.
Author: Yannick Marcon [aut, cre] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between s3.resourcer versions 1.1.1 dated 2023-05-07 and 1.1.2 dated 2025-01-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- README.md | 4 ++-- inst/resources/resource.js | 16 ++++++++-------- 4 files changed, 17 insertions(+), 17 deletions(-)
Title: Uncertainty Propagation for R Vectors
Description: Support for measurement errors in R vectors, matrices and arrays:
automatic uncertainty propagation and reporting.
Documentation about 'errors' is provided in the paper by Ucar, Pebesma &
Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in this package as a
vignette; see 'citation("errors")' for details.
Author: Inaki Ucar [aut, cph, cre] ,
Lionel Henry [ctb],
RStudio [cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between errors versions 0.4.2 dated 2024-07-29 and 0.4.3 dated 2025-01-18
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/print.R | 18 +++++++++++++----- R/utils.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rjournal.R | 24 ++++++++++++------------ inst/doc/rjournal.pdf |binary man/format.errors.Rd | 9 ++++++++- tests/testthat/test-print.R | 3 +++ 11 files changed, 56 insertions(+), 32 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 3.0.2 dated 2024-11-23 and 3.0.3 dated 2025-01-18
DESCRIPTION | 6 ++-- MD5 | 46 ++++++++++++++++++----------------- NAMESPACE | 1 NEWS.md | 14 ++++++++++ R/bobyqa.R | 1 R/focei.R | 15 +++++++++-- R/lbfgsb3c.R | 1 R/n1qn1.R | 1 R/newuoa.R | 1 R/nlm.R | 1 R/nlme.R | 1 R/nlminb.R | 1 R/nls.R | 1 R/optim.R | 1 R/preProcessCovariatesPresent.R |only R/rxsolve.R | 6 ++++ R/saem.R | 2 + R/saemControl.R | 2 - R/saemRxUiGet.R | 20 +++++++++++++-- R/saemRxUiGetModel.R | 16 +++++++----- R/uobyqa.R | 2 - man/saemControl.Rd | 2 - tests/testthat.R | 9 ++++++ tests/testthat/test-data-assert.R |only tests/testthat/test-saem-translate.R | 46 +++++++++++++++++++++++++++++++++++ 25 files changed, 157 insertions(+), 39 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr2 versions 1.0.7 dated 2024-11-26 and 1.1.0 dated 2025-01-18
DESCRIPTION | 10 MD5 | 159 ++++++++------- NAMESPACE | 10 NEWS.md | 60 +++++ R/curl.R | 50 ++++ R/headers.R | 14 - R/httr2-package.R | 1 R/is-online.R |only R/iterate-responses.R | 13 + R/oauth-flow-auth-code.R | 31 +-- R/oauth-flow.R | 4 R/progress-bars.R | 3 R/req-auth-aws.R | 4 R/req-auth.R | 4 R/req-body.R | 5 R/req-headers.R | 29 ++ R/req-mock.R | 4 R/req-options.R | 2 R/req-perform-connection.R | 53 ++++- R/req-perform-stream.R | 6 R/req-perform.R | 6 R/req-promise.R | 13 + R/req-retries.R | 118 ++++++++--- R/req-url.R | 62 +++--- R/resp-headers.R | 4 R/resp-request.R |only R/resp-stream-aws.R | 26 +- R/resp-stream.R | 112 ++++++++--- R/sequential.R | 11 - R/test.R | 2 R/url.R | 295 ++++++++++++++++++++++------- R/utils-multi.R | 18 + R/utils.R | 29 ++ README.md | 29 +- inst/doc/httr2.html | 106 +++++----- man/is_online.Rd |only man/multi_req_perform.Rd | 3 man/progress_bars.Rd | 3 man/req_auth_basic.Rd | 4 man/req_body.Rd | 13 - man/req_dry_run.Rd | 7 man/req_headers.Rd | 22 +- man/req_oauth_auth_code.Rd | 27 +- man/req_oauth_password.Rd | 4 man/req_perform_connection.Rd | 24 ++ man/req_perform_iterative.Rd | 8 man/req_perform_parallel.Rd | 11 - man/req_perform_promise.Rd | 14 + man/req_perform_sequential.Rd | 11 - man/req_perform_stream.Rd | 6 man/req_retry.Rd | 70 +++--- man/req_url.Rd | 58 ++++- man/resp_request.Rd |only man/resp_stream_raw.Rd | 25 ++ man/resps_successes.Rd | 14 + man/url_build.Rd |only man/url_modify.Rd |only man/url_parse.Rd | 41 +--- man/url_query_parse.Rd |only tests/testthat/_snaps/curl.md | 79 ++++++- tests/testthat/_snaps/req-mock.md | 6 tests/testthat/_snaps/req-promise.md | 41 ++++ tests/testthat/_snaps/req-retries.md | 15 + tests/testthat/_snaps/req-url.md | 18 + tests/testthat/_snaps/req.md | 18 + tests/testthat/_snaps/resp-stream.md | 48 ++++ tests/testthat/_snaps/url.md | 101 +++++++++ tests/testthat/helper-promise.R |only tests/testthat/helper.R | 2 tests/testthat/test-curl.R | 31 ++- tests/testthat/test-multi-req.R | 8 tests/testthat/test-oauth-flow-auth-code.R | 4 tests/testthat/test-oauth-flow.R | 18 + tests/testthat/test-req-auth-aws.R | 14 - tests/testthat/test-req-headers.R | 2 tests/testthat/test-req-mock.R | 2 tests/testthat/test-req-perform.R | 9 tests/testthat/test-req-promise.R | 50 +--- tests/testthat/test-req-retries.R | 43 +++- tests/testthat/test-req-url.R | 17 + tests/testthat/test-req.R | 6 tests/testthat/test-resp-headers.R | 9 tests/testthat/test-resp-request.R |only tests/testthat/test-resp-stream.R | 87 +++++++- tests/testthat/test-url.R | 187 +++++++++++++++--- 85 files changed, 1857 insertions(+), 616 deletions(-)
Title: Manage Cached Files
Description: Suite of tools for managing cached files, targeting
use in other R packages. Uses 'rappdirs' for cross-platform paths.
Provides utilities to manage cache directories, including targeting
files by path or by key; cached directories can be compressed and
uncompressed easily to save disk space.
Author: Scott Chamberlain [aut] ,
Tamas Stirling [ctb, cre]
Maintainer: Tamas Stirling <stirling.tamas@gmail.com>
Diff between hoardr versions 0.5.4 dated 2024-01-23 and 0.5.5 dated 2025-01-18
DESCRIPTION | 8 +-- MD5 | 18 +++--- NEWS.md | 10 +++ R/hoard-package.R | 2 R/hoard_client.R | 6 +- build/vignette.rds |binary inst/doc/hoardr_vignette.R | 4 - inst/doc/hoardr_vignette.html | 109 +++++++++++++++++++++++++++--------------- man/hoard.Rd | 2 man/hoardr-package.Rd | 9 +++ 10 files changed, 111 insertions(+), 57 deletions(-)
Title: Calibration Performance
Description: Plots calibration curves and computes statistics for assessing calibration performance. See De Cock Campo (2023) <doi:10.48550/arXiv.2309.08559> and Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.
Author: De Cock Bavo [aut, cre],
Nieboer Daan [aut],
Van Calster Ben [aut],
Steyerberg Ewout [aut],
Vergouwe Yvonne [aut]
Maintainer: De Cock Bavo <bavo.decock@kuleuven.be>
Diff between CalibrationCurves versions 2.0.3 dated 2024-07-02 and 2.0.4 dated 2025-01-18
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- R/genCalCurve.R | 2 - inst/doc/CalibrationCurves.R | 12 +++++++- inst/doc/CalibrationCurves.Rmd | 12 +++++++- inst/doc/CalibrationCurves.html | 55 ++++++++++++++++++++++++++-------------- vignettes/CalibrationCurves.Rmd | 12 +++++++- 7 files changed, 77 insertions(+), 34 deletions(-)
More information about CalibrationCurves at CRAN
Permanent link
Title: Cox MultiBlock Survival
Description: This software package provides Cox survival analysis for high-dimensional and multiblock datasets.
It encompasses a suite of functions dedicated from the classical Cox regression to newest analysis,
including Cox proportional hazards model, Stepwise Cox regression, and Elastic-Net Cox regression,
Sparse Partial Least Squares Cox regression (sPLS-COX) incorporating three distinct strategies,
and two Multiblock-PLS Cox regression (MB-sPLS-COX) methods. This tool is designed to adeptly handle
high-dimensional data, and provides tools for cross-validation, plot generation, and additional resources
for interpreting results. While references are available within the corresponding functions,
key literature is mentioned below.
Terry M Therneau (2024) <https://CRAN.R-project.org/package=survival>,
Noah Simon et al. (2011) <doi:10.18637/jss.v039.i05>,
Philippe Bastien et al. (2005) <doi:10.1016/j.csda.2004.02.005>,
Philippe Bastien (2008) <doi:10.1016/j.chemolab.2007.09.009& [...truncated...]
Author: Pedro Salguero Garcia [aut, cre, rev]
,
Sonia Tarazona Campos [ths],
Ana Conesa Cegarra [ths],
Kassu Mehari Beyene [ctb],
Luis Meira Machado [ctb],
Marta Sestelo [ctb],
Artur Araujo [ctb]
Maintainer: Pedro Salguero Garcia <pedrosalguerog@gmail.com>
Diff between Coxmos versions 1.0.2 dated 2024-03-25 and 1.1.0 dated 2025-01-18
Coxmos-1.0.2/Coxmos/man/cv.splsdacox_dynamic.Rd |only Coxmos-1.0.2/Coxmos/man/cv.splsdrcox_dynamic.Rd |only Coxmos-1.0.2/Coxmos/man/save_ggplot.svg.Rd |only Coxmos-1.0.2/Coxmos/man/save_ggplot_lst.svg.Rd |only Coxmos-1.0.2/Coxmos/man/splsdacox_dynamic.Rd |only Coxmos-1.0.2/Coxmos/man/splsdrcox_dynamic.Rd |only Coxmos-1.1.0/Coxmos/DESCRIPTION | 10 Coxmos-1.1.0/Coxmos/MD5 | 153 Coxmos-1.1.0/Coxmos/NAMESPACE | 23 Coxmos-1.1.0/Coxmos/R/Coxmos_common_functions.R |11857 +++++----- Coxmos-1.1.0/Coxmos/R/Coxmos_cox.R | 10 Coxmos-1.1.0/Coxmos/R/Coxmos_coxEN.R | 1928 - Coxmos-1.1.0/Coxmos/R/Coxmos_coxSW.R | 158 Coxmos-1.1.0/Coxmos/R/Coxmos_evaluation_functions.R | 53 Coxmos-1.1.0/Coxmos/R/Coxmos_isb_splsdacox_dynamic.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_isb_splsdrcox.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_isb_splsdrcox_dynamic.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_isb_splsicox.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_mb_splsdacox_dynamic.R | 202 Coxmos-1.1.0/Coxmos/R/Coxmos_mb_splsdrcox_dynamic.R | 248 Coxmos-1.1.0/Coxmos/R/Coxmos_multiblock_functions.R | 107 Coxmos-1.1.0/Coxmos/R/Coxmos_plot_functions.R | 1701 - Coxmos-1.1.0/Coxmos/R/Coxmos_sb_splsdacox_dynamic.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_sb_splsdrcox.R | 2023 - Coxmos-1.1.0/Coxmos/R/Coxmos_sb_splsdrcox_dynamic.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_sb_splsicox.R | 462 Coxmos-1.1.0/Coxmos/R/Coxmos_splsdacox_dynamic.R | 1939 - Coxmos-1.1.0/Coxmos/R/Coxmos_splsdrcox.R | 244 Coxmos-1.1.0/Coxmos/R/Coxmos_splsdrcox_dynamic.R | 146 Coxmos-1.1.0/Coxmos/R/Coxmos_splsdrcox_median.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_splsicox.R | 2208 - Coxmos-1.1.0/Coxmos/R/cenROC.R | 15 Coxmos-1.1.0/Coxmos/README.md | 12 Coxmos-1.1.0/Coxmos/build/partial.rdb |binary Coxmos-1.1.0/Coxmos/inst/REFERENCES.bib | 114 Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-MO-pipeline.R | 101 Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-MO-pipeline.Rmd | 151 Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-MO-pipeline.html | 1225 - Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-pipeline.R | 102 Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-pipeline.Rmd | 143 Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-pipeline.html | 1161 Coxmos-1.1.0/Coxmos/man/coxEN.Rd | 5 Coxmos-1.1.0/Coxmos/man/coxSW.Rd | 4 Coxmos-1.1.0/Coxmos/man/cv.coxEN.Rd | 11 Coxmos-1.1.0/Coxmos/man/cv.isb.splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/cv.isb.splsdrcox.Rd | 464 Coxmos-1.1.0/Coxmos/man/cv.isb.splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/man/cv.isb.splsicox.Rd | 141 Coxmos-1.1.0/Coxmos/man/cv.mb.splsdacox.Rd | 16 Coxmos-1.1.0/Coxmos/man/cv.mb.splsdrcox.Rd | 16 Coxmos-1.1.0/Coxmos/man/cv.sb.splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/cv.sb.splsdrcox.Rd | 475 Coxmos-1.1.0/Coxmos/man/cv.sb.splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/man/cv.sb.splsicox.Rd | 4 Coxmos-1.1.0/Coxmos/man/cv.splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/cv.splsdrcox.Rd | 449 Coxmos-1.1.0/Coxmos/man/cv.splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/man/cv.splsicox.Rd | 2 Coxmos-1.1.0/Coxmos/man/deleteZeroOrNearZeroVariance.mb.Rd | 6 Coxmos-1.1.0/Coxmos/man/eval_Coxmos_model_per_variable.list.Rd |only Coxmos-1.1.0/Coxmos/man/eval_Coxmos_models.Rd | 9 Coxmos-1.1.0/Coxmos/man/getAutoKM.Rd | 4 Coxmos-1.1.0/Coxmos/man/getAutoKM.list.Rd | 14 Coxmos-1.1.0/Coxmos/man/getCutoffAutoKM.list.Rd | 2 Coxmos-1.1.0/Coxmos/man/getDesign.MB.Rd |only Coxmos-1.1.0/Coxmos/man/getEPV.mb.Rd | 2 Coxmos-1.1.0/Coxmos/man/getTestKM.list.Rd | 10 Coxmos-1.1.0/Coxmos/man/isb.splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/isb.splsdrcox.Rd |only Coxmos-1.1.0/Coxmos/man/isb.splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/man/isb.splsicox.Rd |only Coxmos-1.1.0/Coxmos/man/mb.splsdacox.Rd | 19 Coxmos-1.1.0/Coxmos/man/mb.splsdrcox.Rd | 13 Coxmos-1.1.0/Coxmos/man/plot_LP.multipleObservations.list.Rd | 10 Coxmos-1.1.0/Coxmos/man/plot_PLS_Coxmos.Rd | 2 Coxmos-1.1.0/Coxmos/man/plot_cox.event.list.Rd | 3 Coxmos-1.1.0/Coxmos/man/plot_forest.list.Rd | 3 Coxmos-1.1.0/Coxmos/man/plot_proportionalHazard.list.Rd | 3 Coxmos-1.1.0/Coxmos/man/plot_pseudobeta.list.Rd | 3 Coxmos-1.1.0/Coxmos/man/plot_pseudobeta_newObservation.list.Rd | 2 Coxmos-1.1.0/Coxmos/man/plot_time.list.Rd | 37 Coxmos-1.1.0/Coxmos/man/save_ggplot.Rd | 9 Coxmos-1.1.0/Coxmos/man/save_ggplot_lst.Rd | 7 Coxmos-1.1.0/Coxmos/man/sb.splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/sb.splsdrcox.Rd | 378 Coxmos-1.1.0/Coxmos/man/sb.splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/man/sb.splsicox.Rd | 4 Coxmos-1.1.0/Coxmos/man/splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/splsdrcox.Rd | 395 Coxmos-1.1.0/Coxmos/man/splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/vignettes/Coxmos-MO-pipeline.Rmd | 151 Coxmos-1.1.0/Coxmos/vignettes/Coxmos-pipeline.Rmd | 143 92 files changed, 15024 insertions(+), 14288 deletions(-)
Title: Analysis of MHC Data in Non-Model Species
Description: Fifteen tools for bioinformatics processing and analysis of major
histocompatibility complex (MHC) data. The functions are tailored for amplicon data
sets that have been filtered using the dada2 method (for more information on
dada2, visit <https://benjjneb.github.io/dada2/> ), but even other types of data
sets can be analyzed.
The ReplMatch() function matches replicates in data sets in order to evaluate
genotyping success.
The GetReplTable() and GetReplStats() functions perform such an evaluation.
The CreateFas() function creates a fasta file with all the sequences in the data
set.
The CreateSamplesFas() function creates individual fasta files for each sample in
the data set.
The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise
comparisons of all sequences in a data set, and mean distances of all pairwise
comparisons within each sample in a data set. The function additionally outputs five
tables with physico-chemical z-descriptor values (based on S [...truncated...]
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved@biol.lu.se>
Diff between MHCtools versions 1.5.4 dated 2025-01-15 and 1.5.5 dated 2025-01-18
DESCRIPTION | 6 +-- MD5 | 68 +++++++++++++++++------------------ NEWS.md | 10 ++++- R/BootKmeans_func_20250108.R | 2 - R/ClusterMatch_func_20250108.R | 2 - R/CreateFas_func_20230321.R | 2 - R/CreateHpltOccTable_func_20221010.R | 2 - R/CreateSamplesFas_func_20230321.R | 2 - R/DistCalc_func_20230707.R | 2 - R/GetHpltStats_func_20200915.R | 2 - R/GetHpltTable_func_20200915.R | 2 - R/GetReplStats_func_20200914.R | 2 - R/GetReplTable_func_20200914.R | 2 - R/HpltFind_func_20230321.R | 2 - R/HpltMatch_func_20230322.R | 2 - R/NestTablesXL_func_20221012.R | 2 - R/PapaDiv_func_20230630.R | 2 - R/ReplMatch_func_20230321.R | 2 - R/zzz.R | 2 - README.md | 4 +- man/BootKmeans.Rd | 2 - man/ClusterMatch.Rd | 2 - man/CreateFas.Rd | 2 - man/CreateHpltOccTable.Rd | 2 - man/CreateSamplesFas.Rd | 2 - man/DistCalc.Rd | 2 - man/GetHpltStats.Rd | 2 - man/GetHpltTable.Rd | 2 - man/GetReplStats.Rd | 2 - man/GetReplTable.Rd | 2 - man/HpltFind.Rd | 2 - man/HpltMatch.Rd | 2 - man/NestTablesXL.Rd | 2 - man/PapaDiv.Rd | 2 - man/ReplMatch.Rd | 2 - 35 files changed, 78 insertions(+), 72 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-15 2.0.1
2024-02-13 2.0.0
Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob Hyndman [aut] ,
Han Lin Shang [aut, cre, cph]
Maintainer: Han Lin Shang <hanlin.shang@mq.edu.au>
Diff between ftsa versions 6.4 dated 2024-01-23 and 6.5 dated 2025-01-18
ftsa-6.4/ftsa/R/FANOVA.R |only ftsa-6.4/ftsa/R/FCE_means.R |only ftsa-6.4/ftsa/R/FRE_means.R |only ftsa-6.4/ftsa/R/One_way_Residuals.R |only ftsa-6.4/ftsa/R/One_way_median_polish.R |only ftsa-6.4/ftsa/R/Substraction.R |only ftsa-6.4/ftsa/R/Two_way_Residuals.R |only ftsa-6.4/ftsa/R/Two_way_Residuals_means.R |only ftsa-6.4/ftsa/R/Two_way_median_polish.R |only ftsa-6.4/ftsa/R/combinat.R |only ftsa-6.4/ftsa/R/f.R |only ftsa-6.4/ftsa/R/fMBD.R |only ftsa-6.4/ftsa/R/get_median.R |only ftsa-6.4/ftsa/R/list.cbind.R |only ftsa-6.4/ftsa/R/list.do.R |only ftsa-6.4/ftsa/R/list.rbind.R |only ftsa-6.4/ftsa/R/mu_hat.R |only ftsa-6.4/ftsa/R/partition_column_Y_f.R |only ftsa-6.4/ftsa/R/partition_row_Y_f.R |only ftsa-6.4/ftsa/man/FANOVA.Rd |only ftsa-6.4/ftsa/man/One_way_Residuals.Rd |only ftsa-6.4/ftsa/man/One_way_median_polish.Rd |only ftsa-6.4/ftsa/man/Two_way_Residuals.Rd |only ftsa-6.4/ftsa/man/Two_way_Residuals_means.Rd |only ftsa-6.4/ftsa/man/Two_way_median_polish.Rd |only ftsa-6.5/ftsa/ChangeLog | 4 ++ ftsa-6.5/ftsa/DESCRIPTION | 8 ++-- ftsa-6.5/ftsa/MD5 | 35 ++------------------ ftsa-6.5/ftsa/NAMESPACE | 8 ---- ftsa-6.5/ftsa/man/farforecast.Rd | 4 +- ftsa-6.5/ftsa/man/long_run_covariance_estimation.Rd | 2 - 31 files changed, 17 insertions(+), 44 deletions(-)
Title: Read and Write Standard 'C' Types from Files, Connections and
Raw Vectors
Description: Interacting with binary files can be difficult because R's types
are a subset of what is generally supported by 'C'. This package provides a
suite of functions for reading and writing binary data (with files, connections,
and raw vectors) using 'C' type descriptions. These functions convert data
between 'C' types and R types while checking for values outside the
type limits, 'NA' values, etc.
Author: Mike Cheng [aut, cre, cph],
Anne Fu [ctb]
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Diff between ctypesio versions 0.1.1 dated 2024-10-16 and 0.1.2 dated 2025-01-18
DESCRIPTION | 10 +++---- MD5 | 25 +++++++++++-------- NEWS.md | 10 +++++++ R/read-hex.R | 5 +++ R/read-utf.R | 6 ++-- R/write-float.R | 15 +++++++++-- R/write-int.R | 13 +++++++--- R/write-utf8.R | 15 +++++++++-- inst/doc/parse-jpeg.html | 37 +++++++++++++++-------------- inst/doc/wave-format.R | 44 +++++++++++++++++------------------ inst/doc/wave-format.html | 33 +++++++++++++------------- man/ctypesio-package.Rd | 2 - tests/testthat/test-raw-set-endian.R |only tests/testthat/test-str-raw.R |only tests/testthat/test-utf8-read.R |only 15 files changed, 128 insertions(+), 87 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oehlschlaegel [ctb, cph],
Suman Rakshit [ctb], [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.3-4 dated 2024-11-18 and 3.3-5 dated 2025-01-18
DESCRIPTION | 10 +-- MD5 | 85 +++++++++++++------------- NAMESPACE | 2 NEWS | 88 ++++++++++++++++++++++++++- R/colourtables.R | 81 +++++++++++++++---------- R/hyperframe.R | 4 - R/persp.im.R | 4 + R/persp.ppp.R | 26 +++++--- R/plot.anylist.R | 136 ++++++++++++++++++++++++++++++++++--------- R/plot.im.R | 142 +++++++++++++++++++++++++-------------------- R/rotate.R | 3 R/split.ppp.R | 26 +++++--- R/symbolmap.R | 8 +- R/texture.R | 56 +++++++++++++---- R/unstack.R | 4 - inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/as.hyperframe.Rd | 7 -- man/colourmap.Rd | 3 man/distfun.Rd | 12 +++ man/distmap.Rd | 13 +++- man/distmap.owin.Rd | 11 +++ man/distmap.ppp.Rd | 16 ++++- man/distmap.psp.Rd | 11 +++ man/hyperframe.Rd | 8 +- man/nndist.Rd | 11 +++ man/nndist.pp3.Rd | 11 +++ man/nndist.ppx.Rd | 11 +++ man/nndist.psp.Rd | 11 +++ man/pairdist.Rd | 11 +++ man/pairdist.pp3.Rd | 15 ++++ man/pairdist.ppp.Rd | 11 +++ man/pairdist.ppx.Rd | 14 +++- man/pairdist.psp.Rd | 14 +++- man/plot.anylist.Rd | 14 +++- man/plot.colourmap.Rd | 19 ++++-- man/plot.im.Rd | 34 +++++++++- man/plot.imlist.Rd | 30 +++++++-- man/plot.listof.Rd | 8 ++ man/plot.ppp.Rd | 42 +++++++------ man/plot.solist.Rd | 12 +++ man/plot.symbolmap.Rd | 2 man/plot.texturemap.Rd | 12 +++ man/rev.colourmap.Rd |only 44 files changed, 778 insertions(+), 262 deletions(-)
Title: Calculates Microbial Lag Duration (on the Population Level) from
Provided Growth Curve Data
Description: Microbial growth is often measured by growth curves i.e. a table of population sizes and times of measurements.
This package allows to use such growth curve data to determine the duration of "microbial lag phase" i.e. the time needed for microbes to restart divisions.
It implements the most commonly used methods to calculate the lag duration, these methods are discussed and described in Opalek et.al. 2022.
Citation: Smug, B. J., Opalek, M., Necki, M., & Wloch-Salamon, D. (2024). Microbial lag calculator: A shiny-based application and an R package for calculating the duration of microbial lag phase. Methods in Ecology and Evolution, 15, 301–307 <doi:10.1111/2041-210X.14269>.
Author: Bogna Smug [aut, cre]
Maintainer: Bogna Smug <bogna.smug@uj.edu.pl>
Diff between miLAG versions 1.0.4 dated 2024-10-05 and 1.0.5 dated 2025-01-17
DESCRIPTION | 10 MD5 | 80 - NAMESPACE | 40 R/globals.R | 24 R/milags_functions.R | 2340 +++++++++++++++---------------- README.md | 380 ++--- build/vignette.rds |binary inst/doc/calculating_lag.R | 76 - inst/doc/calculating_lag.html | 944 ++++++------ inst/doc/choosing_lag.R | 76 - inst/doc/choosing_lag.html | 948 ++++++------ inst/doc/getting_lag.R | 76 - inst/doc/getting_lag.html | 940 ++++++------ inst/doc/plotting_lag.R | 80 - inst/doc/plotting_lag.html | 866 +++++------ man/calc_baranyi_fit_lag.Rd | 70 man/calc_lag.Rd | 74 man/calc_lag_fit_to_baranyi_with_lag.Rd | 80 - man/calc_lag_fit_to_logistic_with_lag.Rd | 80 - man/calc_lagistic_fit_lag.Rd | 94 - man/choose_lag_fit_algorithm_baranyi.Rd | 74 man/choose_lag_fit_algorithm_logistic.Rd | 74 man/compare_algorithms.Rd | 42 man/cut_the_data.Rd | 44 man/fit_exp_lag.Rd | 52 man/fit_exp_lag_to_curve.Rd | 58 man/fit_max_infl_lag.Rd | 38 man/get_all_methods_lag.Rd | 78 - man/get_def_pars.Rd | 32 man/get_init_pars_baranyi.Rd | 70 man/get_init_pars_logistic.Rd | 76 - man/get_lag.Rd | 76 - man/get_n0.Rd | 46 man/get_theme.Rd | 36 man/lag_biomass_incr.Rd | 44 man/make_grwoth_curve_df.Rd | 42 man/plot_data.Rd | 38 man/plot_lag_fit.Rd | 42 man/smooth_data.Rd | 44 tests/testthat.R | 24 vignettes/example | 2 41 files changed, 4155 insertions(+), 4155 deletions(-)
Title: Relationship-Based Mixed-Effects Models
Description: Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the
'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between lme4breeding versions 1.0.40 dated 2024-10-16 and 1.0.50 dated 2025-01-17
lme4breeding-1.0.40/lme4breeding/R/spatial.R |only lme4breeding-1.0.40/lme4breeding/inst/doc/lmebreed.gxe.pdf |only lme4breeding-1.0.40/lme4breeding/inst/doc/lmebreed.qg.pdf |only lme4breeding-1.0.40/lme4breeding/man/spl2Dmats.Rd |only lme4breeding-1.0.40/lme4breeding/vignettes/lmebreed.gxe.html |only lme4breeding-1.0.40/lme4breeding/vignettes/lmebreed.qg.html |only lme4breeding-1.0.50/lme4breeding/ChangeLog | 2 lme4breeding-1.0.50/lme4breeding/DESCRIPTION | 8 +- lme4breeding-1.0.50/lme4breeding/MD5 | 31 ++++------ lme4breeding-1.0.50/lme4breeding/NAMESPACE | 4 - lme4breeding-1.0.50/lme4breeding/R/funs.R | 15 ++++ lme4breeding-1.0.50/lme4breeding/R/utils.R | 34 ++++++++++- lme4breeding-1.0.50/lme4breeding/build/vignette.rds |binary lme4breeding-1.0.50/lme4breeding/inst/doc/lmebreed.gxe.Rmd | 2 lme4breeding-1.0.50/lme4breeding/inst/doc/lmebreed.gxe.html |only lme4breeding-1.0.50/lme4breeding/inst/doc/lmebreed.qg.Rmd | 2 lme4breeding-1.0.50/lme4breeding/inst/doc/lmebreed.qg.html |only lme4breeding-1.0.50/lme4breeding/man/fillData.Rd |only lme4breeding-1.0.50/lme4breeding/man/lmebreed.Rd | 2 lme4breeding-1.0.50/lme4breeding/vignettes/lmebreed.gxe.Rmd | 2 lme4breeding-1.0.50/lme4breeding/vignettes/lmebreed.qg.Rmd | 2 21 files changed, 73 insertions(+), 31 deletions(-)
Title: Utilities for Data Analysis in Agriculture
Description: Utilities designed to make the analysis of field trials easier and
more accessible for everyone working in plant breeding. It provides a simple
and intuitive interface for conducting single and multi-environmental trial
analysis, with minimal coding required. Whether you're a beginner or an
experienced user, 'agriutilities' will help you quickly and easily carry out
complex analyses with confidence. With built-in functions for fitting Linear
Mixed Models, 'agriutilities' is the ideal choice for anyone who wants to save
time and focus on interpreting their results.
Some of the functions require the R package 'asreml' for the 'ASReml' software,
this can be obtained upon purchase from 'VSN' international <https://vsni.co.uk/software/asreml-r/>.
Author: Johan Aparicio [aut, cre],
Alexia Bornhorst [aut],
The Alliance of Bioversity International and CIAT [cph]
Maintainer: Johan Aparicio <johanstevenapa@gmail.com>
Diff between agriutilities versions 1.2.0 dated 2024-01-20 and 1.2.1 dated 2025-01-17
DESCRIPTION | 12 MD5 | 66 + NAMESPACE | 3 R/SpATS.R | 90 ++ R/checkDesign.R | 10 R/extractRcov.R | 102 ++- R/fitSingle.R | 6 R/icREML.R |only R/lme4.R | 2 README.md | 117 +-- build/vignette.rds |binary inst/doc/how-to-start.R | 6 inst/doc/how-to-start.Rmd | 9 inst/doc/how-to-start.html | 200 +++--- inst/doc/repeated_measurements.R | 312 ++++++++- inst/doc/repeated_measurements.Rmd | 369 +++++++++-- inst/doc/repeated_measurements.html | 995 ++++++++++++++++++++++-------- man/extract_rcov.Rd | 45 - man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-10-2.png |binary man/figures/README-unnamed-chunk-11-1.png |only man/figures/README-unnamed-chunk-11-2.png |only man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-2-2.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-6-2.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-7-2.png |binary man/figures/logo.png |binary man/h_cullis_spt.Rd |only man/ic_reml_asr.Rd |only man/ic_reml_spt.Rd |only man/single_trial_analysis.Rd | 4 vignettes/how-to-start.Rmd | 9 vignettes/repeated_measurements.Rmd | 369 +++++++++-- 37 files changed, 2095 insertions(+), 631 deletions(-)
Title: Joint Modeling of Traditional and Environmental DNA Survey Data
in a Bayesian Framework
Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
Author: Abigail G. Keller [aut, cre],
Ryan P. Kelly [ctb],
Chitra M. Saraswati [rev],
Saras M. Windecker [rev]
Maintainer: Abigail G. Keller <agkeller@berkeley.edu>
Diff between eDNAjoint versions 0.2 dated 2024-10-08 and 0.3 dated 2025-01-17
eDNAjoint-0.2/eDNAjoint/R/detectionCalculate.R |only eDNAjoint-0.2/eDNAjoint/R/detectionPlot.R |only eDNAjoint-0.2/eDNAjoint/R/gobyData.R |only eDNAjoint-0.2/eDNAjoint/R/greencrabData.R |only eDNAjoint-0.2/eDNAjoint/R/jointModel.R |only eDNAjoint-0.2/eDNAjoint/R/jointSelect.R |only eDNAjoint-0.2/eDNAjoint/R/jointSummarize.R |only eDNAjoint-0.2/eDNAjoint/R/muCritical.R |only eDNAjoint-0.2/eDNAjoint/R/traditionalModel.R |only eDNAjoint-0.2/eDNAjoint/data/gobyData.rda |only eDNAjoint-0.2/eDNAjoint/data/greencrabData.rda |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_catchability_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_catchability_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_catchability_pois.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_catchability_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_catchability_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_catchability_pois.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_pois.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_pois.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_catchability_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_catchability_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_catchability_pois.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_pois.stan |only eDNAjoint-0.2/eDNAjoint/man/detectionCalculate.Rd |only eDNAjoint-0.2/eDNAjoint/man/detectionPlot.Rd |only eDNAjoint-0.2/eDNAjoint/man/gobyData.Rd |only eDNAjoint-0.2/eDNAjoint/man/greencrabData.Rd |only eDNAjoint-0.2/eDNAjoint/man/jointModel.Rd |only eDNAjoint-0.2/eDNAjoint/man/jointSelect.Rd |only eDNAjoint-0.2/eDNAjoint/man/jointSummarize.Rd |only eDNAjoint-0.2/eDNAjoint/man/muCritical.Rd |only eDNAjoint-0.2/eDNAjoint/man/traditionalModel.Rd |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_pois.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_pois.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_pois.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_pois.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_pois.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_pois.h |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-detectionCalculate.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-detectionPlot.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-jointModel.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-jointSelect.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-jointSummarize.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-muCritical.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-traditionalModel.R |only eDNAjoint-0.3/eDNAjoint/DESCRIPTION | 18 - eDNAjoint-0.3/eDNAjoint/MD5 | 155 +++------- eDNAjoint-0.3/eDNAjoint/NAMESPACE | 14 eDNAjoint-0.3/eDNAjoint/NEWS.md | 16 + eDNAjoint-0.3/eDNAjoint/R/detection_calculate.R |only eDNAjoint-0.3/eDNAjoint/R/detection_plot.R |only eDNAjoint-0.3/eDNAjoint/R/eDNAjoint-package.R | 23 - eDNAjoint-0.3/eDNAjoint/R/globals.R | 3 eDNAjoint-0.3/eDNAjoint/R/goby_data.R |only eDNAjoint-0.3/eDNAjoint/R/green_crab_data.R |only eDNAjoint-0.3/eDNAjoint/R/joint_model.R |only eDNAjoint-0.3/eDNAjoint/R/joint_select.R |only eDNAjoint-0.3/eDNAjoint/R/joint_summarize.R |only eDNAjoint-0.3/eDNAjoint/R/mu_critical.R |only eDNAjoint-0.3/eDNAjoint/R/srr-stats-standards.R | 10 eDNAjoint-0.3/eDNAjoint/R/stanmodels.R | 39 -- eDNAjoint-0.3/eDNAjoint/R/traditional_model.R |only eDNAjoint-0.3/eDNAjoint/R/utils-joint.R |only eDNAjoint-0.3/eDNAjoint/R/utils-traditional.R |only eDNAjoint-0.3/eDNAjoint/README.md | 45 +- eDNAjoint-0.3/eDNAjoint/build/partial.rdb |binary eDNAjoint-0.3/eDNAjoint/configure | 5 eDNAjoint-0.3/eDNAjoint/configure.win | 4 eDNAjoint-0.3/eDNAjoint/data/goby_data.rda |only eDNAjoint-0.3/eDNAjoint/data/green_crab_data.rda |only eDNAjoint-0.3/eDNAjoint/inst/README.Rmd | 35 +- eDNAjoint-0.3/eDNAjoint/inst/README.md | 152 ++++----- eDNAjoint-0.3/eDNAjoint/inst/stan/functions |only eDNAjoint-0.3/eDNAjoint/inst/stan/joint_continuous.stan |only eDNAjoint-0.3/eDNAjoint/inst/stan/joint_count.stan |only eDNAjoint-0.3/eDNAjoint/inst/stan/traditional_continuous.stan |only eDNAjoint-0.3/eDNAjoint/inst/stan/traditional_count.stan |only eDNAjoint-0.3/eDNAjoint/man/detection_calculate.Rd |only eDNAjoint-0.3/eDNAjoint/man/detection_plot.Rd |only eDNAjoint-0.3/eDNAjoint/man/eDNAjoint-package.Rd | 22 - eDNAjoint-0.3/eDNAjoint/man/goby_data.Rd |only eDNAjoint-0.3/eDNAjoint/man/green_crab_data.Rd |only eDNAjoint-0.3/eDNAjoint/man/joint_model.Rd |only eDNAjoint-0.3/eDNAjoint/man/joint_select.Rd |only eDNAjoint-0.3/eDNAjoint/man/joint_summarize.Rd |only eDNAjoint-0.3/eDNAjoint/man/mu_critical.Rd |only eDNAjoint-0.3/eDNAjoint/man/traditional_model.Rd |only eDNAjoint-0.3/eDNAjoint/src/RcppExports.cpp | 44 -- eDNAjoint-0.3/eDNAjoint/src/stanExports_joint_continuous.cc |only eDNAjoint-0.3/eDNAjoint/src/stanExports_joint_continuous.h |only eDNAjoint-0.3/eDNAjoint/src/stanExports_joint_count.cc |only eDNAjoint-0.3/eDNAjoint/src/stanExports_joint_count.h |only eDNAjoint-0.3/eDNAjoint/src/stanExports_traditional_continuous.cc |only eDNAjoint-0.3/eDNAjoint/src/stanExports_traditional_continuous.h |only eDNAjoint-0.3/eDNAjoint/src/stanExports_traditional_count.cc |only eDNAjoint-0.3/eDNAjoint/src/stanExports_traditional_count.h |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-detection_calculate.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-detection_plot.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-joint_model.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-joint_select.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-joint_summarize.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-mu_critical.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-traditional_model.R |only 139 files changed, 272 insertions(+), 313 deletions(-)
Title: Time Dependent Shared Frailty Cox Model
Description: Fits time-dependent shared frailty Cox model (specifically the adapted Paik et al.'s Model) based on the paper "Centre-Effect on Survival After Bone Marrow Transplantation: Application of Time-Dependent Frailty Models", by C.M. Wintrebert, H. Putter, A.H. Zwinderman and J.C. van Houwelingen (2004) <doi:10.1002/bimj.200310051>.
Author: Alessandra Ragni [aut, cre] ,
Giulia Romani [aut],
Chiara Masci [aut]
Maintainer: Alessandra Ragni <alessandra.ragni@polimi.it>
Diff between TimeDepFrail versions 0.0.0.9 dated 2024-11-21 and 0.0.1 dated 2025-01-17
TimeDepFrail-0.0.0.9/TimeDepFrail/R/bas_hazard.R |only TimeDepFrail-0.0.1/TimeDepFrail/DESCRIPTION | 13 - TimeDepFrail-0.0.1/TimeDepFrail/MD5 | 49 ++-- TimeDepFrail-0.0.1/TimeDepFrail/NAMESPACE | 5 TimeDepFrail-0.0.1/TimeDepFrail/R/AdPaikModel.R | 73 +++--- TimeDepFrail-0.0.1/TimeDepFrail/R/base_hazard.R |only TimeDepFrail-0.0.1/TimeDepFrail/R/extractors.R |only TimeDepFrail-0.0.1/TimeDepFrail/R/frailty_sd.R | 32 -- TimeDepFrail-0.0.1/TimeDepFrail/R/params_se.R | 15 + TimeDepFrail-0.0.1/TimeDepFrail/R/plot.R | 117 ++++++---- TimeDepFrail-0.0.1/TimeDepFrail/R/posterior_frailty.R | 19 + TimeDepFrail-0.0.1/TimeDepFrail/R/summary.R | 6 TimeDepFrail-0.0.1/TimeDepFrail/R/survival.R |only TimeDepFrail-0.0.1/TimeDepFrail/README.md | 31 +- TimeDepFrail-0.0.1/TimeDepFrail/man/AdPaikModel.Rd | 33 +- TimeDepFrail-0.0.1/TimeDepFrail/man/AdPaik_1D.Rd | 35 +- TimeDepFrail-0.0.1/TimeDepFrail/man/bas_hazard.Rd | 2 TimeDepFrail-0.0.1/TimeDepFrail/man/coef.AdPaik.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/coefse.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/confint.AdPaik.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/frailty_sd.AdPaik.Rd | 6 TimeDepFrail-0.0.1/TimeDepFrail/man/frailty_sd.Rd | 4 TimeDepFrail-0.0.1/TimeDepFrail/man/params_CI.Rd | 4 TimeDepFrail-0.0.1/TimeDepFrail/man/plot_bas_hazard.Rd | 14 - TimeDepFrail-0.0.1/TimeDepFrail/man/plot_frailty_sd.Rd | 26 +- TimeDepFrail-0.0.1/TimeDepFrail/man/plot_post_frailty_est.Rd | 24 -- TimeDepFrail-0.0.1/TimeDepFrail/man/plot_survival.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/post_frailty_CI.AdPaik.Rd | 7 TimeDepFrail-0.0.1/TimeDepFrail/man/summary.AdPaik.Rd | 2 TimeDepFrail-0.0.1/TimeDepFrail/man/survival.Rd |only 30 files changed, 298 insertions(+), 219 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 1.3.16 dated 2025-01-06 and 1.3.17 dated 2025-01-17
DESCRIPTION | 6 ++-- MD5 | 22 ++++++++-------- NEWS.md | 8 ++++++ R/zzz.R | 4 +-- configure | 2 - configure.ac | 2 - inst/doc/WebGL.html | 26 +++++++++---------- inst/doc/demos.html | 60 ++++++++++++++++++++++----------------------- inst/doc/deprecation.html | 2 - inst/doc/pkgdown.html | 6 ++-- inst/doc/rgl.html | 36 +++++++++++++-------------- inst/doc/transparency.html | 18 ++++++------- 12 files changed, 100 insertions(+), 92 deletions(-)
Title: High Dimensional Geometry, Set Operations, Projection, and
Inference Using Kernel Density Estimation, Support Vector
Machines, and Convex Hulls
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.
Author: Benjamin Blonder [aut, cre],
Cecina Babich Morrow [aut],
Stuart Brown [aut],
Gregoire Butruille [aut],
Daniel Chen [aut],
Alex Laini [aut],
David J. Harris [aut],
Clement Violet [aut]
Maintainer: Benjamin Blonder <benjamin.blonder@berkeley.edu>
Diff between hypervolume versions 3.1.4 dated 2024-05-01 and 3.1.5 dated 2025-01-17
DESCRIPTION | 44 ++++++++++++++++++++++++++++++----- MD5 | 21 ++++++++++------ NAMESPACE | 2 + R/hypervolume_distance_point.R |only R/hypervolume_set_n_union.R |only R/ignore_unused_imports.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/Hypervolume-Resampling.R | 18 +++++++------- inst/doc/Hypervolume-Resampling.html | 18 +++++++------- inst/doc/occupancy.html | 14 +++++------ man/hypervolume_distance_point.Rd |only man/hypervolume_set.Rd | 2 - man/hypervolume_set_n_union.Rd |only 14 files changed, 79 insertions(+), 40 deletions(-)
Title: Animal Sounds for Bioacustic Analysis
Description: Collection of example animal sounds for bioacoustic analysis.
Author: Marcelo Araya-Salas [aut, cre]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between NatureSounds versions 1.0.4 dated 2021-04-23 and 1.0.5 dated 2025-01-17
NatureSounds-1.0.4/NatureSounds/R/Phae.long.est-data.R |only NatureSounds-1.0.4/NatureSounds/data/Phae.long.est.rda |only NatureSounds-1.0.4/NatureSounds/man/Phae.long.est.Rd |only NatureSounds-1.0.5/NatureSounds/DESCRIPTION | 9 NatureSounds-1.0.5/NatureSounds/MD5 | 48 - NatureSounds-1.0.5/NatureSounds/NAMESPACE | 1 NatureSounds-1.0.5/NatureSounds/NEWS.md | 4 NatureSounds-1.0.5/NatureSounds/R/NatureSounds-package.R | 5 NatureSounds-1.0.5/NatureSounds/R/lbh.est-data.R | 3 NatureSounds-1.0.5/NatureSounds/README.md | 50 - NatureSounds-1.0.5/NatureSounds/build/vignette.rds |binary NatureSounds-1.0.5/NatureSounds/data/Cryp.soui.rda |binary NatureSounds-1.0.5/NatureSounds/data/Phae.long1.rda |binary NatureSounds-1.0.5/NatureSounds/data/Phae.long2.rda |binary NatureSounds-1.0.5/NatureSounds/data/Phae.long3.rda |binary NatureSounds-1.0.5/NatureSounds/data/Phae.long4.rda |binary NatureSounds-1.0.5/NatureSounds/data/lbh.est.rda |binary NatureSounds-1.0.5/NatureSounds/data/monk.parakeet.est.rda |binary NatureSounds-1.0.5/NatureSounds/data/thyroptera.est.rda |binary NatureSounds-1.0.5/NatureSounds/inst/CITATION | 9 NatureSounds-1.0.5/NatureSounds/inst/doc/Acoustic_data_sets_in_NatureSounds.R | 118 +-- NatureSounds-1.0.5/NatureSounds/inst/doc/Acoustic_data_sets_in_NatureSounds.Rmd | 9 NatureSounds-1.0.5/NatureSounds/inst/doc/Acoustic_data_sets_in_NatureSounds.html | 368 +++++----- NatureSounds-1.0.5/NatureSounds/man/NatureSounds.Rd | 11 NatureSounds-1.0.5/NatureSounds/man/lbh.est.Rd | 3 NatureSounds-1.0.5/NatureSounds/vignettes/Acoustic_data_sets_in_NatureSounds.Rmd | 9 NatureSounds-1.0.5/NatureSounds/vignettes/NatureSounds_sticker.png |only 27 files changed, 354 insertions(+), 293 deletions(-)
Title: TH's Data Archive
Description: Contains data sets used in other packages Torsten Hothorn
maintains.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between TH.data versions 1.1-2 dated 2023-04-17 and 1.1-3 dated 2025-01-17
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- build/partial.rdb |binary build/vignette.rds |binary data/geyser.rda |binary data/mammoexp.rda |binary inst/doc/blood_loss_report.R | 22 +++++++++++----------- inst/doc/blood_loss_report.pdf |binary inst/rda/Primary_endpoint_data.rda |binary inst/rda/bloodloss.rda |binary man/wpbc.Rd | 3 +-- 12 files changed, 28 insertions(+), 29 deletions(-)
Title: Estimation of the Structural Topic and Sentiment-Discourse Model
for Text Analysis
Description: The Structural Topic and Sentiment-Discourse (STS) model allows researchers to estimate topic models with document-level metadata that determines both topic prevalence and sentiment-discourse. The sentiment-discourse is modeled as a document-level latent variable for each topic that modulates the word frequency within a topic. These latent topic sentiment-discourse variables are controlled by the document-level metadata. The STS model can be useful for regression analysis with text data in addition to topic modeling’s traditional use of descriptive analysis. The method was developed in Chen and Mankad (2024) <doi:10.1287/mnsc.2022.00261>.
Author: Shawn Mankad [aut, cre],
Li Chen [aut]
Maintainer: Shawn Mankad <smankad@ncsu.edu>
Diff between sts versions 1.2 dated 2024-11-25 and 1.3 dated 2025-01-17
sts-1.2/sts/R/findRepresentativeDocs.R |only sts-1.2/sts/R/printTopWords.R |only sts-1.3/sts/DESCRIPTION | 15 +++---- sts-1.3/sts/MD5 | 55 ++++++++++++++------------ sts-1.3/sts/NAMESPACE | 43 +++++++++++--------- sts-1.3/sts/R/estimateRegns.R | 2 sts-1.3/sts/R/findRepresentativeDocs.STS.R |only sts-1.3/sts/R/heldoutLikelihood.R | 2 sts-1.3/sts/R/plot.STS.R | 1 sts-1.3/sts/R/plotRepresentativeDocs.R | 2 sts-1.3/sts/R/printRegnTables.R | 2 sts-1.3/sts/R/printTopWords.STS.R |only sts-1.3/sts/R/sts-package.R | 21 ++++++++- sts-1.3/sts/R/sts.R | 4 - sts-1.3/sts/R/topicExclusivity.R | 2 sts-1.3/sts/R/topicSemanticCoherence.R | 2 sts-1.3/sts/build |only sts-1.3/sts/inst |only sts-1.3/sts/man/estimateRegns.Rd | 12 ++--- sts-1.3/sts/man/findRepresentativeDocs.Rd | 22 ++-------- sts-1.3/sts/man/findRepresentativeDocs.STS.Rd |only sts-1.3/sts/man/heldoutLikelihood.Rd | 4 - sts-1.3/sts/man/plot.STS.Rd | 4 - sts-1.3/sts/man/plotRepresentativeDocs.Rd | 2 sts-1.3/sts/man/printRegnTables.Rd | 6 +- sts-1.3/sts/man/printTopWords.Rd | 22 +++------- sts-1.3/sts/man/printTopWords.STS.Rd |only sts-1.3/sts/man/sts-package.Rd | 28 ++++++------- sts-1.3/sts/man/sts.Rd | 54 ++++++++++++------------- sts-1.3/sts/man/topicExclusivity.Rd | 28 ++++++------- sts-1.3/sts/man/topicSemanticCoherence.Rd | 4 - sts-1.3/sts/vignettes |only 32 files changed, 174 insertions(+), 163 deletions(-)
Title: Assess Study Cohorts Using a Common Data Model
Description: Phenotype study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model. Diagnostics
are run at the database, code list, cohort, and population level to assess
whether study cohorts are ready for research.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Xihang Chen [aut] ,
Marta Alcalde-Herraiz [aut] ,
Albert Prats-Uribe [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between PhenotypeR versions 0.1.0 dated 2024-12-06 and 0.1.1 dated 2025-01-17
DESCRIPTION | 8 MD5 | 84 +- NAMESPACE | 1 R/addCodelistAttribute.R | 12 R/codelistDiagnostics.R | 22 R/cohortDiagnostics.R | 39 - R/databaseDiagnostics.R | 22 R/matchedDiagnostics.R | 28 R/mockPhenotypeR.R |only R/phenotypeDiagnostics.R | 23 R/phenotypeR-package.R | 16 R/populationDiagnostics.R | 21 R/shinyDiagnostics.R | 26 R/utils-pipe.R | 28 README.md | 30 build/vignette.rds |binary inst/doc/a02_CodelistDiagnostics.R | 12 inst/doc/a02_CodelistDiagnostics.Rmd | 12 inst/doc/a02_CodelistDiagnostics.html | 579 ---------------- inst/doc/a03_CohortDiagnostics.R | 10 inst/doc/a03_CohortDiagnostics.Rmd | 10 inst/doc/a03_CohortDiagnostics.html | 240 +++--- inst/doc/a04_MatchedDiagnostics.html | 2 inst/shiny/global.R | 115 ++- inst/shiny/scripts/preprocess.R | 23 inst/shiny/server.R | 412 ++++++----- inst/shiny/ui.R | 971 ++++++++++++++-------------- man/PhenotypeR-package.Rd | 64 - man/addCodelistAttribute.Rd | 12 man/codelistDiagnostics.Rd | 22 man/cohortDiagnostics.Rd | 23 man/databaseDiagnostics.Rd | 22 man/matchedDiagnostics.Rd | 23 man/mockPhenotypeR.Rd |only man/phenotypeDiagnostics.Rd | 23 man/pipe.Rd | 40 - man/populationDiagnostics.Rd | 21 man/shinyDiagnostics.Rd | 25 tests/testthat/test-addCodelistAttribute.R | 6 tests/testthat/test-cohortDiagnostics.R | 9 tests/testthat/test-dbms.R | 10 tests/testthat/test-populationDiagnostics.R | 4 vignettes/a02_CodelistDiagnostics.Rmd | 12 vignettes/a03_CohortDiagnostics.Rmd | 10 44 files changed, 1289 insertions(+), 1783 deletions(-)
Title: Handwriting Analysis in R
Description: Perform statistical writership analysis of scanned handwritten documents.
Webpage provided at: <https://github.com/CSAFE-ISU/handwriter>.
Author: Iowa State University of Science and Technology on behalf of its Center
for Statistics and Applications in Forensic Evidence [aut, cph,
fnd],
Nick Berry [aut],
Stephanie Reinders [aut, cre],
James Taylor [aut],
Felix Baez-Santiago [ctb],
Jon Gonzalez [...truncated...]
Maintainer: Stephanie Reinders <srein@iastate.edu>
Diff between handwriter versions 3.2.3 dated 2024-11-26 and 3.2.4 dated 2025-01-17
DESCRIPTION | 6 MD5 | 32 +++- NAMESPACE | 3 NEWS.md | 16 ++ R/cluster_assignment.R | 5 R/cluster_format.R | 38 ----- R/cluster_plot.R | 65 ++++++++++ R/cluster_profiles.R |only R/data.R | 40 ++++++ R/globals.R |only README.md | 2 data/templateK40.rda |only man/get_cluster_fill_counts.Rd | 13 +- man/get_cluster_fill_rates.Rd |only man/get_writer_profiles.Rd |only man/plot_writer_profiles.Rd |only man/templateK40.Rd |only tests/testthat/fixtures/processHandwriting/make_fixtures.R | 14 ++ tests/testthat/fixtures/processHandwriting/rates.rds |only tests/testthat/fixtures/processHandwriting/rates_wo_indices.rds |only tests/testthat/test-cluster-format.R | 24 --- tests/testthat/test-cluster_profiles.R |only 22 files changed, 175 insertions(+), 83 deletions(-)
Title: Statistical Methods for Visual Fields
Description: A collection of tools for analyzing the field of vision. It
provides a framework for development and use of innovative methods for
visualization, statistical analysis, and clinical interpretation of
visual-field loss and its change over time. It is intended to be a tool for
collaborative research. The package is described in Marin-Franch and Swanson
(2013) <doi:10.1167/13.4.10> and is part of the Open Perimetry Initiative
(OPI) [Turpin, Artes, and McKendrick (2012) <doi:10.1167/12.11.22>].
Author: Ivan Marin-Franch [cre, aut, rev, cph],
William H Swanson [fnd, dtc],
Michael Wall [fnd, dtc],
Andrew Turpin [ctb],
Paul H Artes [ctb, dtc],
Cord Huchzermeyer [ctb],
Giovanni Montesano [ctb],
Mitchell W Dul [dtc]
Maintainer: Ivan Marin-Franch <imarinfr@optocom.es>
Diff between visualFields versions 1.0.5 dated 2024-09-21 and 1.0.7 dated 2025-01-17
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/vfreports.R | 14 +++++++++++--- data/drasdolut.rda |binary data/gpars.rda |binary data/locmaps.rda |binary data/normvals.rda |binary data/vfctrIowaPC26.rda |binary data/vfctrIowaPeri.rda |binary data/vfctrSunyiu10d2.rda |binary data/vfctrSunyiu24d2.rda |binary data/vfpwgRetest24d2.rda |binary data/vfpwgSunyiu24d2.rda |binary 13 files changed, 27 insertions(+), 19 deletions(-)
Title: An Implementation of Matrix Mathematics that Respects Row and
Column Names
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre]
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsbyname versions 0.6.10 dated 2024-02-12 and 0.6.11 dated 2025-01-17
DESCRIPTION | 12 - LICENSE | 2 MD5 | 54 ++++--- NAMESPACE | 4 NEWS.md | 32 ++++ R/Unary.R | 3 R/Utilities.R | 193 +++++++++++++++++++++++++--- R/aggregates.R | 4 R/named_triplet.R |only R/reallocate.R |only build/vignette.rds |binary inst/CITATION | 8 - inst/WORDLIST | 4 inst/doc/about-vector-arguments.html | 4 inst/doc/aggregation-vignette.R | 4 inst/doc/aggregation-vignette.html | 8 - inst/doc/applybyname-vignette.html | 8 - inst/doc/matsbyname.html | 8 - inst/doc/using-summarise-in-matsbyname.html | 4 man/aggregation_map_helpers.Rd | 4 man/create_triplet.Rd |only man/get_row_col_index_maps.Rd |only man/iszero_byname.Rd | 8 + man/reallocate_byname.Rd |only man/select_cols_byname.Rd | 8 - man/select_rowcol_piece_byname.Rd | 24 ++- man/select_rows_byname.Rd | 7 - man/select_rows_cols_byname.Rd |only man/structure_index_map.Rd |only man/to_named_triplet.Rd |only tests/testthat/test-Utilities.R | 45 ++++++ tests/testthat/test-named_triplet.R |only tests/testthat/test-reallocate.R |only 33 files changed, 360 insertions(+), 88 deletions(-)
Title: Data for Package 'Qindex'
Description: Example data used in package 'Qindex'.
Author: Tingting Zhan [aut, cre, cph] ,
Misung Yi [aut, cph] ,
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between Qindex.data versions 0.1.1 dated 2024-04-24 and 0.1.2 dated 2025-01-17
DESCRIPTION | 24 +++++++++---------- MD5 | 12 ++++----- R/Ki67.R | 56 ++++++++++++++++++++++++++++++++------------- build/partial.rdb |binary data/Ki67.rda |binary man/Qindex.data-package.Rd | 6 ++++ man/celldata.Rd | 30 ++++++++++++------------ 7 files changed, 79 insertions(+), 49 deletions(-)
Title: Code-Logics to Handle Ontologies
Description: Provides tools to build and work with an ontology of linked (open)
data in a tidy workflow. It is inspired by the Food and Agrilculture
Organizations (FAO) caliper platform
<https://www.fao.org/statistics/caliper/web/> and
makes use of the Simple Knowledge Organisation System (SKOS).
Author: Steffen Ehrmann [aut, cre] ,
Arne Ruemmler [aut, ctb] ,
Carsten Meyer [ctb]
Maintainer: Steffen Ehrmann <steffen.ehrmann@posteo.de>
Diff between ontologics versions 0.7.0 dated 2023-05-10 and 0.7.4 dated 2025-01-17
DESCRIPTION | 12 MD5 | 100 - NAMESPACE | 5 NEWS.md | 209 +- R/1onto.R | 503 +++---- R/edit_matches.R | 831 ++++++----- R/export_as_rdf.R | 902 ++++++------ R/get_class.R | 182 +- R/get_concept.R | 215 +-- R/get_source.R | 154 +- R/imports.R | 30 R/load_ontology.R | 70 - R/makeTreeMap.R | 132 - R/make_tree.R | 146 +- R/new_class.R | 184 +- R/new_concept.R | 512 +++---- R/new_mapping.R | 584 ++++---- R/new_source.R | 246 +-- R/start_ontology.R | 180 +- R/zzz.R | 34 README.md | 38 build/vignette.rds |binary inst/doc/conversion_to_rdf.R | 36 inst/doc/conversion_to_rdf.Rmd | 310 ++-- inst/doc/conversion_to_rdf.html | 1270 +++++++++--------- inst/doc/create_an_ontology.R | 192 +- inst/doc/create_an_ontology.Rmd | 278 +-- inst/doc/create_an_ontology.html | 1956 ++++++++++++++-------------- inst/doc/map_new_concepts.R | 180 +- inst/doc/map_new_concepts.Rmd | 252 +-- inst/doc/map_new_concepts.html | 1492 ++++++++++----------- inst/doc/ontology_database_description.Rmd | 220 +-- inst/doc/ontology_database_description.html | 1006 +++++++------- man/edit_matches.Rd | 136 + man/export_as_rdf.Rd | 66 man/figures/logo.svg | 744 +++++----- man/get_class.Rd | 94 - man/get_concept.Rd | 91 - man/get_source.Rd | 80 - man/make_tree.Rd | 42 man/new_class.Rd | 68 man/new_mapping.Rd | 184 +- man/new_source.Rd | 162 +- man/onto-class.Rd | 40 man/pipe.Rd | 40 man/show-onto-method.Rd | 28 vignettes/conversion_to_rdf.Rmd | 310 ++-- vignettes/create_an_ontology.Rmd | 278 +-- vignettes/map_new_concepts.Rmd | 252 +-- vignettes/ontology_database_description.Rmd | 220 +-- vignettes/skos.rdf | 936 ++++++------- 51 files changed, 8192 insertions(+), 8040 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.1-4 dated 2023-05-16 and 1.2-1 dated 2025-01-17
DESCRIPTION | 8 +++---- MD5 | 20 ++++++++++--------- NAMESPACE | 5 ++-- R/cyclic.R | 50 +++++++++++++++++++++++++++++++++++++++++------- R/formula.R | 7 +++--- build |only inst/NEWS.Rd | 14 ++++++++++++- man/Bernstein_basis.Rd | 4 +-- man/Legendre_basis.Rd | 4 +-- man/as.basis.formula.Rd | 3 +- man/cyclic_basis.Rd |only tests/bases-Ex.R | 7 ++++++ 12 files changed, 91 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-16 0.2.0
2020-07-13 0.1.2
2020-04-07 0.1.1
2020-01-29 0.1.0
2019-07-23 0.0.2
2019-07-11 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-29 0.1.2
2020-11-01 0.1.1
2020-05-04 0.1.0
Title: Multi-Scale Geomorphometric Terrain Attributes
Description: Calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models using a variable focal windows size (Ilich et al. (2023) <doi:10.1111/tgis.13067>).
Author: Alexander Ilich [aut, cre] ,
Vincent Lecours [aut],
Benjamin Misiuk [aut],
Steven Murawski [aut]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between MultiscaleDTM versions 0.8.3 dated 2024-01-22 and 0.9 dated 2025-01-17
DESCRIPTION | 14 ++- MD5 | 85 ++++++++++++--------- R/Pfit.R |only R/RcppExports.R | 4 + R/SAPA.R | 35 ++++++-- R/SlpAsp.R | 159 ++++++++++++++++------------------------ README.md | 5 - build/vignette.rds |binary inst/doc/README.R | 2 inst/doc/README.html | 51 ++++++------ inst/testdata |only man/Pfit.Rd |only man/SAPA.Rd | 8 +- man/figures/README-AdjSD-1.png |binary man/figures/README-BPI-1.png |binary man/figures/README-DMV-1.png |binary man/figures/README-RIE-1.png |binary man/figures/README-RP-1.png |binary man/figures/README-SAPA-1.png |binary man/figures/README-SlpAsp-1.png |binary man/figures/README-TPI-1.png |binary man/figures/README-Topo-1.png |binary man/figures/README-VRM-1.png |binary man/figures/SlpAsp.png |binary man/figures/qmetrics.jpg |binary man/figures/sub_qfit01.png |binary man/figures/sub_qfit02.png |binary man/figures/sub_qfit03.png |binary man/figures/sub_qfit04.png |binary man/figures/sub_qfit05.png |binary man/figures/sub_qfit06.png |binary man/figures/sub_qfit07.png |binary man/figures/sub_qfit08.png |binary man/figures/sub_qfit09.png |binary man/figures/sub_qfit10.png |binary man/figures/sub_qfit11.png |binary man/fragments/README_Frag.Rmd | 2 src/RcppExports.cpp | 18 ++++ src/cpp_code.cpp | 29 +++++++ tests |only 40 files changed, 238 insertions(+), 174 deletions(-)
Title: GSL Multi-Start Nonlinear Least-Squares Fitting
Description: An R interface to weighted nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Multi-start optimization based on quasi-random samples is implemented using a modified version of the algorithm in Hickernell and Yuan (1997, OR Transactions). Robust nonlinear regression can be performed using various robust loss functions, in which case the optimization problem is solved by iterative reweighted least squares (IRLS). Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between gslnls versions 1.4.0 dated 2025-01-16 and 1.4.1 dated 2025-01-17
DESCRIPTION | 10 +++---- MD5 | 18 ++++++------- NEWS.md | 4 ++ cleanup | 2 - configure | 26 +++++++++---------- configure.ac | 8 ++--- src/gsl_nls.h | 5 ++- src/nls.c | 2 - src/nls_irls.c | 2 - src/nls_utils.c | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++++--- 10 files changed, 114 insertions(+), 38 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes. This package is part of the RECON
(<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.3.0 dated 2024-11-20 and 1.4.0 dated 2025-01-17
DESCRIPTION | 6 +- MD5 | 23 ++++++----- NEWS.md | 10 ++++ R/scale-epiweek.R | 13 ++++-- R/scale-isoweek.R | 13 ++++-- R/scale-yearweek.R | 9 +++- inst/doc/grates.html | 6 +- man/scale_x_grates_epiweek.Rd | 6 +- man/scale_x_grates_isoweek.Rd | 6 +- man/scale_x_grates_yearweek.Rd | 4 + tests/testthat/_snaps/plots/epiweek_weeks.png |only tests/testthat/_snaps/plots/isoweek_weeks.png |only tests/testthat/_snaps/plots/yearweek_thursday_weeks_only.png |only tests/testthat/test-plots.R | 9 ++++ 14 files changed, 74 insertions(+), 31 deletions(-)
Title: Solve Least Squares with GMRES(k)
Description: Solves a least squares system Ax~=b (dim(A)=(m,n) with m >= n) with a precondition matrix B: BAx=Bb (dim(B)=(n,m)). Implemented method is based on GMRES (Saad, Youcef; Schultz, Martin H. (1986). "GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems" <doi:10.1137/0907058>) with callback functions, i.e. no explicit A, B or b are required.
Author: Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between gmresls versions 0.2.2 dated 2024-10-18 and 0.2.3 dated 2025-01-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/gmresls.R | 15 +++++++++++---- inst/COPYRIGHTS | 2 +- inst/unitTests/runit.gmresls.R | 2 ++ man/gmresls.Rd | 4 +++- 7 files changed, 32 insertions(+), 16 deletions(-)
Title: Multiple Testing Methods for Exploratory Research
Description: Provides an alternative approach to multiple testing
by calculating a simultaneous upper confidence bounds for the
number of true null hypotheses among any subset of the hypotheses of interest,
using the methods of Goeman and Solari (2011) <doi:10.1214/11-STS356>.
Author: Jelle Goeman [aut, cre],
Aldo Solari [aut],
Rosa Meijer [aut]
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between cherry versions 0.6-14 dated 2021-05-07 and 0.6-15 dated 2025-01-17
ChangeLog | 5 +++++ DESCRIPTION | 22 +++++++++++++++++----- MD5 | 20 ++++++++++---------- build/vignette.rds |binary inst/CITATION | 33 +++++++++------------------------ inst/doc/cherry.pdf |binary man/adjusted.Rd | 45 +++++++++++++++++++++++---------------------- man/closed.Rd | 47 ++++++++++++++++++++++++----------------------- man/closure-class.Rd | 45 +++++++++++++++++++++++---------------------- man/hommelFast.Rd | 2 +- man/select.Rd | 39 ++++++++++++++++++++------------------- 11 files changed, 132 insertions(+), 126 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Micah K. Wilson [aut] ,
Brenton M. Wiernik [aut] ,
Paul-Christian Buerkner [rev],
Tristan Mahr [rev] ,
Henrik Singmann [ctb] ,
Quentin F. Gron [...truncated...]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between bayestestR versions 0.15.0 dated 2024-10-17 and 0.15.1 dated 2025-01-17
DESCRIPTION | 12 +-- MD5 | 112 ++++++++++++++--------------- NEWS.md | 10 ++ R/bayesfactor.R | 11 +- R/bayesfactor_parameters.R | 1 R/bci.R | 11 -- R/check_prior.R | 3 R/contr.equalprior.R | 1 R/convert_pd_to_p.R | 1 R/describe_posterior.R | 22 +---- R/describe_prior.R | 1 R/distribution.R | 7 - R/equivalence_test.R | 5 - R/estimate_density.R | 4 - R/eti.R | 7 - R/format.R | 4 - R/hdi.R | 2 R/map_estimate.R | 3 R/mcse.R | 1 R/mediation.R | 5 - R/p_direction.R | 5 - R/p_map.R | 17 ---- R/p_rope.R | 1 R/p_significance.R | 1 R/p_to_bf.R | 1 R/print.R | 2 R/print_html.R | 7 - R/print_md.R | 5 - R/rope.R | 28 +++++-- R/rope_range.R | 1 R/sensitivity_to_prior.R | 5 - R/sexit.R | 3 R/sexit_thresholds.R | 2 R/si.R | 2 R/simulate_data.R | 1 R/simulate_priors.R | 6 - R/spi.R | 2 R/unupdate.R | 2 R/utils.R | 9 +- R/utils_bayesfactor.R | 1 R/utils_hdi_ci.R | 3 build/partial.rdb |binary build/vignette.rds |binary man/bayesfactor.Rd | 11 +- man/describe_posterior.Rd | 10 +- man/diagnostic_posterior.Rd | 32 +++++--- man/equivalence_test.Rd | 10 +- man/p_rope.Rd | 10 +- man/rope.Rd | 26 ++++-- tests/testthat/_snaps/windows/print.md | 106 ++++++++++++++++++--------- tests/testthat/test-data.frame-with-rvar.R | 8 +- tests/testthat/test-describe_posterior.R | 1 tests/testthat/test-emmGrid.R | 32 +++++--- tests/testthat/test-marginaleffects.R | 33 +++++++- tests/testthat/test-p_map.R | 1 tests/testthat/test-rope.R | 1 tests/testthat/test-rope_range.R | 1 57 files changed, 298 insertions(+), 311 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements
into groups (i.e., anticlusters) with the goal of maximizing
between-group similarity or within-group heterogeneity. The
anticlustering approach thereby reverses the logic of cluster analysis
that strives for high within-group homogeneity and clear separation
between groups. Computationally, anticlustering is accomplished by
maximizing instead of minimizing a clustering objective function, such
as the intra-cluster variance (used in k-means clustering) or the sum
of pairwise distances within clusters. The main function
anticlustering() gives access to optimal and heuristic anticlustering
methods described in Papenberg and Klau (2021;
<doi:10.1037/met0000301>), Brusco et al. (2020;
<doi:10.1111/bmsp.12186>), and Papenberg (2024;
<doi:10.1111/bmsp.12315>). The optimal algorithms require that an
integer linear programming solver is installed. This package will install
'lpSolve' (<https://cran.r-project.org/p [...truncated...]
Author: Martin Papenberg [aut, cre] ,
Meik Michalke [ctb] ,
Gunnar W. Klau [ths],
Juliane V. Nagel [ctb] ,
Martin Breuer [ctb] ,
Marie L. Schaper [ctb] ,
Max Diekhoff [ctb] ,
Hannah Hengelbrock [ctb]
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.8.7 dated 2024-10-01 and 0.8.9 dated 2025-01-17
DESCRIPTION | 15 MD5 | 39 - NAMESPACE | 2 R/categories_to_binary.R | 42 + R/input-validation.R | 9 R/must-link-anticlustering.R | 285 +++++++++- R/wrapper-anticlustering.R | 10 R/wrapper-three-phase-search-dynamic-population-size.R |only build/vignette.rds |binary inst/doc/Categorical_vars.Rmd | 2 inst/doc/Categorical_vars.html | 34 - inst/doc/Speeding_up_anticlustering.html | 28 inst/tinytest/test-2pml.R |only inst/tinytest/test-three-phase-search-dynamic-population-size.R |only man/anticlustering.Rd | 10 man/categories_to_binary.Rd | 32 - man/figures/clustering-1.png |binary man/figures/matching-1.png |binary man/three_phase_search_anticlustering.Rd |only src/anticlust_init.c | 4 src/three-phase-dispersion.c |only src/three-phase-header.h |only src/three_phase_search_dynamic_population_size.c |only vignettes/Categorical_vars.Rmd | 2 24 files changed, 421 insertions(+), 93 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.
Author: Marcelo Araya-Salas [aut, cre]
,
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between warbleR versions 1.1.33 dated 2024-12-11 and 1.1.34 dated 2025-01-17
DESCRIPTION | 6 MD5 | 47 build/vignette.rds |binary data/comp_matrix.rda |binary data/lbh_selec_table.rda |binary data/sim_coor_sing.rda |binary data/sth_annotations.rda |binary inst/doc/a_warbleR.Rmd | 10 inst/doc/a_warbleR.html | 1753 ++++++++++++++++++++++---- inst/doc/b_annotation_data_format.R | 71 - inst/doc/b_annotation_data_format.Rmd | 30 inst/doc/b_annotation_data_format.html | 2164 +++++++++++++++++++++++++-------- inst/doc/c_warbleR_workflow_02.Rmd | 10 inst/doc/c_warbleR_workflow_02.html | 1903 +++++++++++++++++++++++------ inst/doc/d_warbleR_workflow_03.Rmd | 10 inst/doc/d_warbleR_workflow_03.html | 2093 +++++++++++++++++++++++++------ man/compare_methods.Rd | 2 man/freq_ts.Rd | 2 man/overlapping_sels.Rd | 2 man/sth_annotations.Rd | 2 vignettes/a_warbleR.Rmd | 10 vignettes/b_annotation_data_format.Rmd | 30 vignettes/by_song.png |only vignettes/c_warbleR_workflow_02.Rmd | 10 vignettes/d_warbleR_workflow_03.Rmd | 10 25 files changed, 6544 insertions(+), 1621 deletions(-)
Title: Shape Constrained Additive Models
Description: Generalized additive models under shape
constraints on the component functions of the linear predictor.
Models can include multiple shape-constrained (univariate
and bivariate) and unconstrained terms. Routines of the
package 'mgcv' are used to set up the model matrix, print,
and plot the results. Multiple smoothing parameter
estimation by the Generalized Cross Validation or similar.
See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7>
for an overview. A broad selection of shape-constrained
smoothers, linear functionals of smooths with shape constraints,
and Gaussian models with AR1 residuals.
Author: Natalya Pya [aut, cre]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-17 dated 2024-06-19 and 1.2-18 dated 2025-01-17
ChangeLog | 16 - DESCRIPTION | 14 MD5 | 90 +++--- NAMESPACE | 22 + R/bfgs.r | 8 R/bivar.smooth.const.R | 90 ++---- R/estimate.scam.R | 2 R/plot.r | 91 ++++-- R/predict.scam.R | 94 ++++-- R/scam.r | 93 +++--- R/uni.smooth.const-lscop.r | 146 ++++++++++ R/uni.smooth.const-with-po.r | 417 +++++++++++++++++++++++++---- build/partial.rdb |binary man/Predict.matrix.mpi.smooth.Rd | 8 man/anova.scam.Rd | 3 man/linear.functional.terms.Rd | 6 man/plot.scam.Rd | 6 man/predict.scam.Rd | 1 man/scam.Rd | 121 ++++---- man/scam.check.Rd | 3 man/shape.constrained.smooth.terms.Rd | 6 man/smooth.construct.cv.smooth.spec.rd | 2 man/smooth.construct.lmpi.smooth.spec.Rd | 22 + man/smooth.construct.mdcv.smooth.spec.Rd | 37 +- man/smooth.construct.mdcx.smooth.spec.Rd | 4 man/smooth.construct.miso.smooth.spec.Rd | 4 man/smooth.construct.mpi.smooth.spec.Rd | 7 man/smooth.construct.po.smooth.spec.Rd | 34 ++ man/smooth.construct.tecvcv.smooth.spec.Rd | 51 +-- man/smooth.construct.tecxcv.smooth.spec.Rd | 52 +-- man/smooth.construct.tecxcx.smooth.spec.Rd | 52 +-- man/smooth.construct.tedecv.smooth.spec.Rd | 51 +-- man/smooth.construct.tedecx.smooth.spec.Rd | 53 +-- man/smooth.construct.tedmd.smooth.spec.Rd | 43 +- man/smooth.construct.tedmi.smooth.spec.Rd | 42 +- man/smooth.construct.temicv.smooth.spec.Rd | 51 +-- man/smooth.construct.temicx.smooth.spec.Rd | 51 +-- man/smooth.construct.tescv.smooth.spec.Rd | 53 +-- man/smooth.construct.tescx.smooth.spec.Rd | 55 +-- man/smooth.construct.tesmd1.smooth.spec.Rd | 85 ++--- man/smooth.construct.tesmd2.smooth.spec.Rd | 87 ++---- man/smooth.construct.tesmi1.smooth.spec.Rd | 88 ++---- man/smooth.construct.tesmi2.smooth.spec.Rd | 83 ++--- man/smooth.construct.tismd.smooth.spec.Rd | 2 man/smooth.construct.tismi.smooth.spec.Rd | 1 man/summary.scam.Rd | 3 46 files changed, 1381 insertions(+), 869 deletions(-)
Title: Self-Adapting Mixture (SAM) Priors
Description: Implementation of the SAM prior and generation of its
operating characteristics for dynamically borrowing information
from historical data. For details, please refer to Yang et al. (2023)
<doi:10.1111/biom.13927>.
Author: Peng Yang [aut, cre] ,
Ying Yuan [aut]
Maintainer: Peng Yang <py11@rice.edu>
Diff between SAMprior versions 1.1.1 dated 2023-09-27 and 2.0.0 dated 2025-01-17
DESCRIPTION | 12 +++++--- MD5 | 33 +++++++++++++---------- NAMESPACE | 5 +++ NEWS.md | 6 +++- R/PS_SAM_data.R |only R/PS_prior.R |only R/SAM_prior.R | 3 -- R/SAM_weight.R | 3 -- R/get_OC.R | 7 ++--- R/support.R | 1 data |only inst/doc/Example_binary.R | 14 +++++----- inst/doc/Example_binary.html | 54 ++++++++++++++++++--------------------- inst/doc/Example_continuous.R | 18 ++++++------- inst/doc/Example_continuous.html | 54 ++++++++++++++++++--------------------- man/PS_SAM_data.Rd |only man/PS_prior.Rd |only man/SAM_prior.Rd | 3 -- man/SAM_weight.Rd | 3 -- man/get_OC.Rd | 7 ++--- 20 files changed, 115 insertions(+), 108 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
mikefc [cph] ,
Yann Collet [cph] ,
Posit, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between rlang versions 1.1.4 dated 2024-06-04 and 1.1.5 dated 2025-01-17
DESCRIPTION | 8 +++--- MD5 | 40 ++++++++++++++++----------------- NEWS.md | 5 ++++ R/cnd-abort.R | 4 --- man/cnd_inherits.Rd | 8 +----- man/glue-operators.Rd | 10 -------- man/missing_arg.Rd | 8 +----- man/qq_show.Rd | 2 - man/rmd/topic-condition-formatting.Rmd | 2 - man/splice-operator.Rd | 4 --- man/topic-condition-formatting.Rd | 2 - man/topic-data-mask-ambiguity.Rd | 2 - man/topic-data-mask-programming.Rd | 8 ------ man/topic-data-mask.Rd | 6 ---- man/topic-defuse.Rd | 4 --- man/topic-error-call.Rd | 4 +-- man/topic-inject-out-of-context.Rd | 12 --------- man/topic-inject.Rd | 2 - man/topic-metaprogramming.Rd | 6 ---- man/topic-multiple-columns.Rd | 2 - src/version.c | 2 - 21 files changed, 39 insertions(+), 102 deletions(-)
Title: Linear Models for Panel Data
Description: A set of estimators for models and (robust) covariance matrices, and tests for panel data
econometrics, including within/fixed effects, random effects, between, first-difference,
nested random effects as well as instrumental-variable (IV) and Hausman-Taylor-style models,
panel generalized method of moments (GMM) and general FGLS models,
mean groups (MG), demeaned MG, and common correlated effects (CCEMG) and pooled (CCEP) estimators
with common factors, variable coefficients and limited dependent variables models.
Test functions include model specification, serial correlation, cross-sectional dependence,
panel unit root and panel Granger (non-)causality. Typical references are general econometrics
text books such as Baltagi (2021), Econometric Analysis of Panel Data (<doi:10.1007/978-3-030-53953-5>),
Hsiao (2014), Analysis of Panel Data (<doi:10.1017/CBO9781139839327>), and Croissant and Millo (2018),
Panel Data Econometrics with R (<doi:10.1002/9781119504641>).
Author: Yves Croissant [aut],
Giovanni Millo [aut],
Kevin Tappe [aut, cre],
Ott Toomet [ctb],
Christian Kleiber [ctb],
Achim Zeileis [ctb],
Arne Henningsen [ctb],
Liviu Andronic [ctb],
Nina Schoenfelder [ctb]
Maintainer: Kevin Tappe <kevin.tappe@bwi.uni-stuttgart.de>
Diff between plm versions 2.6-4 dated 2024-04-01 and 2.6-5 dated 2025-01-17
plm-2.6-4/plm/inst/removed |only plm-2.6-4/plm/inst/tests |only plm-2.6-5/plm/DESCRIPTION | 10 plm-2.6-5/plm/MD5 | 190 ++----------- plm-2.6-5/plm/NAMESPACE | 1 plm-2.6-5/plm/NEWS.md | 23 + plm-2.6-5/plm/R/deprecated.R | 2 plm-2.6-5/plm/R/detect_lin_dep_alias.R | 2 plm-2.6-5/plm/R/est_cce.R | 2 plm-2.6-5/plm/R/est_ggls.R | 13 plm-2.6-5/plm/R/est_gmm.R | 332 ++++++++++++----------- plm-2.6-5/plm/R/est_mg.R | 2 plm-2.6-5/plm/R/est_pi.R | 2 plm-2.6-5/plm/R/est_vcm.R | 47 +-- plm-2.6-5/plm/R/tool_argvalues.R | 6 plm-2.6-5/plm/R/tool_pdata.frame.R | 7 plm-2.6-5/plm/R/tool_ranfixef.R | 2 plm-2.6-5/plm/R/tool_transformations_collapse.R | 2 plm-2.6-5/plm/R/tool_vcovG.R | 111 +++++-- plm-2.6-5/plm/README.md | 5 plm-2.6-5/plm/build/partial.rdb |binary plm-2.6-5/plm/build/vignette.rds |binary plm-2.6-5/plm/inst/DPD98.R |only plm-2.6-5/plm/inst/DPD98.txt |only plm-2.6-5/plm/inst/REFERENCES.bib | 15 - plm-2.6-5/plm/inst/doc/A_plmPackage.R | 2 plm-2.6-5/plm/inst/doc/A_plmPackage.Rmd | 18 - plm-2.6-5/plm/inst/doc/A_plmPackage.html | 154 +++++----- plm-2.6-5/plm/inst/doc/B_plmFunction.html | 11 plm-2.6-5/plm/inst/doc/C_plmModelComponents.R | 32 +- plm-2.6-5/plm/inst/doc/C_plmModelComponents.html | 8 plm-2.6-5/plm/man/detect.lindep.Rd | 2 plm-2.6-5/plm/man/mtest.Rd | 44 ++- plm-2.6-5/plm/man/pgmm.Rd | 58 ++-- plm-2.6-5/plm/man/sargan.Rd | 96 +++--- plm-2.6-5/plm/man/vcovHC.plm.Rd | 5 plm-2.6-5/plm/man/within_intercept.Rd | 2 plm-2.6-5/plm/vignettes/A_plmPackage.Rmd | 18 - 38 files changed, 634 insertions(+), 590 deletions(-)
Title: Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution,
provides a wide variety of shapes with one functional form.
This package provides random numbers, quantiles, probabilities,
densities and density quantiles for four different types of the distribution,
the FKML (Freimer et al 1988), RS (Ramberg and Schmeiser 1974), GPD (van Staden
and Loots 2009) and FM5 - see documentation for details.
It provides the density function, distribution function, and Quantile-Quantile
plots.
It implements a variety of estimation methods for the distribution,
including diagnostic plots.
Estimation methods include the starship (all 4 types),
method of L-Moments for the GPD and FKML types, and a
number of methods for only the FKML type.
These include maximum likelihood, maximum product of spacings,
Titterington's method, Moments, Trimmed L-Moments and
Distributional Least Absolutes.
Author: Robert King [aut, cre] ,
Benjamin Dean [aut],
Sigbert Klinke [aut],
Paul van Staden [aut]
Maintainer: Robert King <Robert.King.Newcastle@gmail.com>
Diff between gld versions 2.6.6 dated 2022-10-23 and 2.6.7 dated 2025-01-17
DESCRIPTION | 8 +++---- MD5 | 18 ++++++++--------- NAMESPACE | 1 R/methods.R | 36 ++++++++++++++++++++++++++++------- TODO | 2 - build/partial.rdb |binary man/GeneralisedLambdaDistribution.Rd | 2 - man/gld.lmoments.Rd | 10 ++++----- man/gld.moments.Rd | 13 ++++++------ man/plot.starship.Rd | 6 +++-- 10 files changed, 61 insertions(+), 35 deletions(-)
Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde-Herraiz [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Xihang Chen [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortConstructor versions 0.3.3 dated 2024-11-26 and 0.3.4 dated 2025-01-17
DESCRIPTION | 12 MD5 | 190 +-- R/collapseCohorts.R | 13 R/conceptCohort.R | 165 ++- R/exitAtColumnDate.R | 11 R/exitAtDate.R | 26 R/intersectCohorts.R | 10 R/matchCohorts.R | 35 R/measurementCohort.R | 23 R/padCohortDate.R | 11 R/requireCohortIntersect.R | 16 R/requireConceptIntersect.R | 15 R/requireDateRange.R | 32 R/requireDeathFlag.R | 9 R/requireDemographics.R | 10 R/requireIsEntry.R | 36 R/requireMinCohortCount.R | 9 R/requireTableIntersect.R | 11 R/sampleCohorts.R | 9 R/stratifyCohorts.R | 8 R/subsetCohorts.R | 8 R/trimDemographics.R | 13 R/unionCohorts.R | 4 R/validateFunctions.R | 98 - R/yearCohorts.R | 10 README.md | 45 inst/doc/a01_building_base_cohorts.R | 6 inst/doc/a01_building_base_cohorts.Rmd | 162 +-- inst/doc/a01_building_base_cohorts.html | 16 inst/doc/a02_cohort_table_requirements.R | 6 inst/doc/a02_cohort_table_requirements.Rmd | 6 inst/doc/a02_cohort_table_requirements.html | 46 inst/doc/a03_require_demographics.R | 6 inst/doc/a03_require_demographics.Rmd | 6 inst/doc/a03_require_demographics.html | 46 inst/doc/a04_require_intersections.R | 6 inst/doc/a04_require_intersections.Rmd | 6 inst/doc/a04_require_intersections.html | 46 inst/doc/a06_concatanate_cohorts.R | 6 inst/doc/a06_concatanate_cohorts.Rmd | 6 inst/doc/a06_concatanate_cohorts.html | 52 inst/doc/a07_filter_cohorts.R | 18 inst/doc/a07_filter_cohorts.Rmd | 216 ++-- inst/doc/a07_filter_cohorts.html | 30 inst/doc/a08_split_cohorts.R | 12 inst/doc/a08_split_cohorts.Rmd | 162 +-- inst/doc/a08_split_cohorts.html | 6 inst/doc/a09_combine_cohorts.R | 24 inst/doc/a09_combine_cohorts.Rmd | 294 ++--- inst/doc/a09_combine_cohorts.html | 6 inst/doc/a10_match_cohorts.R | 66 - inst/doc/a10_match_cohorts.Rmd | 20 inst/doc/a10_match_cohorts.html | 22 inst/doc/a11_benchmark.html | 521 +++++---- man/conceptCohort.Rd | 24 man/matchCohorts.Rd | 9 man/measurementCohort.Rd | 7 man/requireCohortIntersect.Rd | 2 man/requireConceptIntersect.Rd | 4 man/requireIsFirstEntry.Rd | 2 man/requireIsLastEntry.Rd | 5 man/trimToDateRange.Rd | 9 tests/testthat/test-addIndex.R | 138 +- tests/testthat/test-collapseCohorts.R | 621 +++++------ tests/testthat/test-conceptCohort.R | 582 +++++++---- tests/testthat/test-demographicsCohort.R | 13 tests/testthat/test-entryAtColumnDate.R | 18 tests/testthat/test-exitAtColumnDate.R | 12 tests/testthat/test-exitAtDate.R | 22 tests/testthat/test-intersectCohorts.R | 1356 +++++++++++++------------- tests/testthat/test-matchCohorts.R | 696 ++++++------- tests/testthat/test-measurementCohort.R | 753 ++++++++------ tests/testthat/test-padCohortDate.R | 785 +++++++-------- tests/testthat/test-requireCohortIntersect.R | 666 ++++++------ tests/testthat/test-requireConceptIntersect.R | 684 ++++++------- tests/testthat/test-requireDateRange.R | 12 tests/testthat/test-requireDeathFlag.R | 12 tests/testthat/test-requireDemographics.R | 14 tests/testthat/test-requireIsEntry.R | 16 tests/testthat/test-requireMinCohortCount.R | 32 tests/testthat/test-requireTableIntersect.R | 12 tests/testthat/test-sampleCohorts.R | 318 +++--- tests/testthat/test-stratifyCohorts.R | 324 +++--- tests/testthat/test-subsetCohorts.R | 292 ++--- tests/testthat/test-trimDemographics.R | 96 - tests/testthat/test-unionCohorts.R | 758 +++++++------- tests/testthat/test-yearCohorts.R | 12 vignettes/a01_building_base_cohorts.Rmd | 162 +-- vignettes/a02_cohort_table_requirements.Rmd | 6 vignettes/a03_require_demographics.Rmd | 6 vignettes/a04_require_intersections.Rmd | 6 vignettes/a06_concatanate_cohorts.Rmd | 6 vignettes/a07_filter_cohorts.Rmd | 216 ++-- vignettes/a08_split_cohorts.Rmd | 162 +-- vignettes/a09_combine_cohorts.Rmd | 294 ++--- vignettes/a10_match_cohorts.Rmd | 20 96 files changed, 6180 insertions(+), 5652 deletions(-)
More information about CohortConstructor at CRAN
Permanent link
Title: A Template for Creating Reproducible 'shiny' Applications
Description: Create a skeleton 'shiny' application with create_template() that is
reproducible, can be saved and meets academic standards for attribution.
Forked from 'wallace'. Code is split into modules that are loaded and linked
together automatically and each call one function. Guidance pages explain
modules to users and flexible logging informs them of any errors. Options
enable asynchronous operations, viewing of source code, interactive maps and
data tables. Use to create complex analytical applications, following best
practices in open science and software development. Includes functions for
automating repetitive development tasks and an example application at
run_shinyscholar() that requires
install.packages("shinyscholar", dependencies = TRUE). A guide to developing
applications can be found on the package website.
Author: Simon E. H. Smart [aut, cre, cph],
Tim Lucas [aut] ,
Jamie M. Kass [ctb],
Gonzalo E. Pinilla-Buitrago [ctb],
Andrea Paz [ctb],
Bethany A. Johnson [ctb],
Valentina Grisales-Betancur [ctb],
Dean Attali [ctb],
Matthew E. Aiello-Lammens [ctb],
Cory Merow [...truncated...]
Maintainer: Simon E. H. Smart <simon.smart@cantab.net>
Diff between shinyscholar versions 0.2.2 dated 2025-01-15 and 0.2.3 dated 2025-01-17
shinyscholar-0.2.2/shinyscholar/tools |only shinyscholar-0.2.3/shinyscholar/DESCRIPTION | 12 ++++--- shinyscholar-0.2.3/shinyscholar/MD5 | 17 ++++------ shinyscholar-0.2.3/shinyscholar/NEWS.md | 6 +++ shinyscholar-0.2.3/shinyscholar/R/create_template.R | 6 +-- shinyscholar-0.2.3/shinyscholar/README.md | 2 - shinyscholar-0.2.3/shinyscholar/inst/app_skeleton/global.Rmd | 2 - shinyscholar-0.2.3/shinyscholar/inst/shiny/Rmd/text_intro_tab.Rmd | 2 - shinyscholar-0.2.3/shinyscholar/inst/shiny/Rmd/userReport_intro.Rmd | 2 - shinyscholar-0.2.3/shinyscholar/tests/testthat/test-downloads.R | 3 + 10 files changed, 31 insertions(+), 21 deletions(-)
Title: Power and Sample Size Calculation for Non-Proportional Hazards
and Beyond
Description: Performs power and sample size calculation for non-proportional hazards model using the Fleming-Harrington family of weighted log-rank tests. The sequentially calculated log-rank test score statistics are assumed to have independent increments as characterized in Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean and variance of log-rank test score statistics are calculated based on Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities are calculated using the recursive integration algorithm described in Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168). The package can also be used for continuous, binary, and count data. For continuous data, it can handle missing data through mixed-model for repeated measures (MMRM). In crossover designs, it can estimate direct treatment effects while accounting for carryover effects. For binary data, it can design Simon's 2-stage, modified toxicity probability-2 (mTPI-2), a [...truncated...]
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between lrstat versions 0.2.11 dated 2024-12-04 and 0.2.12 dated 2025-01-17
DESCRIPTION | 8 MD5 | 97 +-- NAMESPACE | 3 NEWS.md | 14 R/RcppExports.R | 896 ++++++++++++++++++------------ R/getDesignProportions.R | 209 ------- R/getDesignSurvivals.R | 277 +++++++++ R/prints.R | 312 +++++----- R/wrappers.R | 16 man/binary_tte_sim.Rd | 2 man/float_to_fraction.Rd |only man/getDesignEquiv.Rd | 144 ---- man/getDesignOddsRatioEquiv.Rd | 14 man/getDesignRiskDiffEquiv.Rd | 15 man/getDesignRiskRatioEquiv.Rd | 14 man/getDurationFromNevents.Rd | 6 man/getNeventsFromHazardRatio.Rd | 2 man/kmpower.Rd | 48 + man/kmpowerequiv.Rd | 46 + man/kmstat.Rd | 12 man/kmstat1.Rd | 12 man/logisregr.Rd | 10 man/lrpowerequiv.Rd | 2 man/lrschoenfeld.Rd |only man/natrisk.Rd | 1 man/nbpowerequiv.Rd | 31 - man/nbsamplesizeequiv.Rd | 9 man/nbstat.Rd | 5 man/nevent.Rd | 1 man/nevent2.Rd | 1 man/patrisk.Rd | 1 man/pevent.Rd | 1 man/qrcpp.Rd | 10 man/rmpower.Rd | 48 + man/rmpowerequiv.Rd | 46 + man/rmstat.Rd | 12 man/rmstat1.Rd | 12 man/svdcpp.Rd |only src/RcppExports.cpp | 435 ++------------- src/kmstat.cpp | 1128 +++++++++++++++------------------------ src/logistic_regression.cpp | 204 ++++++- src/logistic_regression.h | 10 src/lrsim.cpp | 2 src/lrstat.cpp | 279 +++------ src/misc.cpp | 5 src/nbstat.cpp | 695 ++++-------------------- src/rmstat.cpp | 546 ++++++++++++++---- src/survival_analysis.cpp | 597 ++++++++++++++++++++ src/survival_analysis.h | 10 src/utilities.cpp | 912 +++++++++++++++++++++++-------- src/utilities.h | 31 - 51 files changed, 3991 insertions(+), 3200 deletions(-)
Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with spatially correlated errors by robust (Kuensch et al. (2011) <doi:10.3929/ethz-a-009900710>) and Gaussian (Harville (1977) <doi:10.1080/01621459.1977.10480998>) (Restricted) Maximum Likelihood and for computing robust and customary point and block external-drift Kriging predictions (Cressie (1993) <doi:10.1002/9781119115151>), along with utility functions for variogram modelling in ad hoc geostatistical analyses, model building, model evaluation by cross-validation, (conditional) simulation of Gaussian processes (Davies and Bryant (2013) <doi:10.18637/jss.v055.i09>), unbiased back-transformation of Kriging predictions of log-transformed data (Cressie (2006) <doi:10.1007/s11004-005-9022-8>).
Author: Andreas Papritz [aut, cre]
Maintainer: Andreas Papritz <papritz@retired.ethz.ch>
Diff between georob versions 0.3-21 dated 2025-01-08 and 0.3-22 dated 2025-01-17
georob-0.3-21/georob/vignettes/fig-ash-Kriging-polygons.pdf |only georob-0.3-21/georob/vignettes/fig-ash-bKriging-plot-robust-gaussian-1.pdf |only georob-0.3-21/georob/vignettes/fig-meuse-zinc-block-Kriging-blocks.pdf |only georob-0.3-21/georob/vignettes/fig-meuse-zinc-block-Kriging-plot.pdf |only georob-0.3-22/georob/ChangeLog | 5 georob-0.3-22/georob/DESCRIPTION | 8 georob-0.3-22/georob/MD5 | 22 georob-0.3-22/georob/inst/NEWS.Rd | 14 georob-0.3-22/georob/inst/doc/georob_vignette.R | 254 +- georob-0.3-22/georob/inst/doc/georob_vignette.Rnw | 1107 +++++----- georob-0.3-22/georob/inst/doc/georob_vignette.pdf |binary georob-0.3-22/georob/vignettes/georob_vignette.Rnw | 1107 +++++----- georob-0.3-22/georob/vignettes/r_coalash_objects.RData |binary georob-0.3-22/georob/vignettes/r_meuse_zinc_objects.RData |binary 14 files changed, 1356 insertions(+), 1161 deletions(-)
More information about rtables.officer at CRAN
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More information about MonotonicityTest at CRAN
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Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr [aut, cre]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between rms versions 6.9-0 dated 2024-12-12 and 7.0-0 dated 2025-01-17
rms-6.9-0/rms/R/LRchunktest.r |only rms-6.9-0/rms/src/ormuv.f90 |only rms-6.9-0/rms/src/ratfor/ormuv.r |only rms-7.0-0/rms/DESCRIPTION | 14 rms-7.0-0/rms/MD5 | 138 +++-- rms-7.0-0/rms/NAMESPACE | 7 rms-7.0-0/rms/NEWS | 41 + rms-7.0-0/rms/R/Glm.r | 2 rms-7.0-0/rms/R/Ocens.r |only rms-7.0-0/rms/R/anova.rms.s | 187 ++++--- rms-7.0-0/rms/R/bootcov.s | 409 +++++++--------- rms-7.0-0/rms/R/calibrate.default.s | 2 rms-7.0-0/rms/R/contrast.s | 137 ++++- rms-7.0-0/rms/R/fastbw.s | 50 +- rms-7.0-0/rms/R/groupkm.s | 2 rms-7.0-0/rms/R/infoMxop.r |only rms-7.0-0/rms/R/lrm.fit.r | 287 +++++++---- rms-7.0-0/rms/R/lrm.s | 43 + rms-7.0-0/rms/R/ols.s | 4 rms-7.0-0/rms/R/orm.fit.s | 720 ++++++++++++++++------------- rms-7.0-0/rms/R/orm.s | 156 +++--- rms-7.0-0/rms/R/pentrace.s | 44 - rms-7.0-0/rms/R/plotIntercepts.r |only rms-7.0-0/rms/R/predab.resample.s | 4 rms-7.0-0/rms/R/predict.lrm.s | 3 rms-7.0-0/rms/R/predictrms.s | 4 rms-7.0-0/rms/R/quickRefit.r |only rms-7.0-0/rms/R/residuals.lrm.s | 2 rms-7.0-0/rms/R/rexVar.r | 14 rms-7.0-0/rms/R/rmsMisc.s | 266 ++++------ rms-7.0-0/rms/R/sensuc.s | 10 rms-7.0-0/rms/R/summary.rms.s | 6 rms-7.0-0/rms/R/val.prob.s | 59 +- rms-7.0-0/rms/R/validate.lrm.s | 66 +- rms-7.0-0/rms/R/validate.psm.s | 6 rms-7.0-0/rms/inst/tests/Glm.s | 3 rms-7.0-0/rms/inst/tests/Rq2.s | 2 rms-7.0-0/rms/inst/tests/bootcov.r | 3 rms-7.0-0/rms/inst/tests/lrm-orm-penalty.r |only rms-7.0-0/rms/inst/tests/lrm.s | 3 rms-7.0-0/rms/inst/tests/lrmMean.s | 4 rms-7.0-0/rms/inst/tests/modelData.r | 4 rms-7.0-0/rms/inst/tests/orm-bootcov.r | 35 - rms-7.0-0/rms/inst/tests/orm-bootcov2.r |only rms-7.0-0/rms/inst/tests/orm-quantile.r |only rms-7.0-0/rms/inst/tests/orm-residuals.r | 4 rms-7.0-0/rms/inst/tests/orm-weight.r |only rms-7.0-0/rms/inst/tests/orm.s | 50 +- rms-7.0-0/rms/inst/tests/orm2.s | 8 rms-7.0-0/rms/inst/tests/orm5.r | 6 rms-7.0-0/rms/inst/tests/orm7.r |only rms-7.0-0/rms/inst/tests/psm.s | 10 rms-7.0-0/rms/inst/tests/rexVar.r | 4 rms-7.0-0/rms/inst/tests/robcov2.r | 2 rms-7.0-0/rms/inst/tests/scale.r | 31 - rms-7.0-0/rms/man/Ocens.Rd |only rms-7.0-0/rms/man/anova.rms.Rd | 6 rms-7.0-0/rms/man/as.data.frame.Ocens.Rd |only rms-7.0-0/rms/man/bootcov.Rd | 32 + rms-7.0-0/rms/man/contrast.Rd | 52 +- rms-7.0-0/rms/man/fastbw.Rd | 5 rms-7.0-0/rms/man/infoMxop.Rd |only rms-7.0-0/rms/man/lrm.Rd | 10 rms-7.0-0/rms/man/lrm.fit.Rd | 28 - rms-7.0-0/rms/man/ols.Rd | 2 rms-7.0-0/rms/man/orm.Rd | 59 +- rms-7.0-0/rms/man/orm.fit.Rd | 65 +- rms-7.0-0/rms/man/pentrace.Rd | 8 rms-7.0-0/rms/man/plotIntercepts.Rd |only rms-7.0-0/rms/man/predab.resample.Rd | 5 rms-7.0-0/rms/man/residuals.lrm.Rd | 4 rms-7.0-0/rms/man/rexVar.Rd | 8 rms-7.0-0/rms/man/rms-internal.Rd | 1 rms-7.0-0/rms/man/sub-.Ocens.Rd |only rms-7.0-0/rms/man/summary.rms.Rd | 4 rms-7.0-0/rms/man/val.prob.Rd | 2 rms-7.0-0/rms/src/init.c | 10 rms-7.0-0/rms/src/lrmll.f90 | 62 +- rms-7.0-0/rms/src/ormll.f90 |only 79 files changed, 1842 insertions(+), 1373 deletions(-)
Title: Disproportionality Functions for Pharmacovigilance
Description: Tools for performing disproportionality analysis using the information component, proportional reporting rate and the reporting odds ratio. The anticipated use is passing data to the da() function, which executes the disproportionality analysis. See Norén et al (2011) <doi:10.1177/0962280211403604> and Montastruc et al (2011) <doi:10.1111/j.1365-2125.2011.04037.x> for further details.
Author: Oskar Gauffin [aut] ,
Michele Fusaroli [cre]
Maintainer: Michele Fusaroli <michele.fusaroli@who-umc.org>
Diff between pvda versions 0.0.3 dated 2024-03-01 and 0.0.4 dated 2025-01-17
DESCRIPTION | 21 +++++++++++-------- MD5 | 24 +++++++++++----------- NEWS.md | 3 ++ R/da_object_oriented_functions.R | 5 +++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Disproportionality_analysis.Rmd | 8 +++---- inst/doc/Disproportionality_analysis.html | 32 +++++++++++++++--------------- man/da.Rd | 3 +- man/print.da.Rd | 2 + vignettes/Disproportionality_analysis.Rmd | 8 +++---- vignettes/print_console_printout.png |binary vignettes/summary_console_printout.png |binary 13 files changed, 59 insertions(+), 47 deletions(-)
Title: Interface for Large Language Model APIs in R
Description: A unified interface to interact with various Large Language Model (LLM) APIs such as 'OpenAI' (see <https://platform.openai.com/docs/quickstart> for details), 'Anthropic' (see <https://docs.anthropic.com/en/api/getting-started> for details), 'Groq' (see <https://console.groq.com/docs/api-reference> for details), 'Together AI' (see <https://docs.together.ai/docs/quickstart> for details), 'DeepSeek' (see <https://api-docs.deepseek.com> for details), and 'Voyage AI' (see <https://docs.voyageai.com/docs/introduction> for details). Allows users to configure API parameters, send messages, and retrieve responses seamlessly within R.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR versions 0.1.1 dated 2024-10-21 and 0.1.2 dated 2025-01-17
DESCRIPTION | 8 - MD5 | 11 + NAMESPACE | 4 R/LLMR.R | 285 +++++++++++++++++++++++++++++------------------- man/call_llm.Rd | 81 +++---------- man/llm_config.Rd | 72 +++++------- man/parse_embeddings.Rd |only 7 files changed, 241 insertions(+), 220 deletions(-)
Title: Slide Automation for Tables, Listings and Figures
Description: The normal process of creating clinical study slides is that
a statistician manually type in the numbers from outputs and a
separate statistician to double check the typed in numbers. This
process is time consuming, resource intensive, and error prone.
Automatic slide generation is a solution to address these issues. It
reduces the amount of work and the required time when creating slides,
and reduces the risk of errors from manually typing or copying numbers
from the output to slides. It also helps users to avoid unnecessary
stress when creating large amounts of slide decks in a short time
window.
Author: Joe Zhu [cre, aut] ,
Heng Wang [aut],
Yinqi Zhao [aut],
Bo Ci [aut],
Liming Li [aut],
Laura Wang [ctb],
Xiaoli Duan [aut],
Stefan Pascal Thoma [aut],
Thomas Neitmann [ctb],
Miles Almond [aut],
Mahdi About [ctb],
Kai Lim [ctb],
Nolan Steed [ctb],
Daol [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between autoslider.core versions 0.2.2 dated 2025-01-07 and 0.2.3 dated 2025-01-17
DESCRIPTION | 12 ++++++------ MD5 | 18 ++++++++++++------ NEWS.md | 6 ++++++ R/t_dor_slide.R | 2 +- inst/WORDLIST | 2 ++ inst/doc/autoslideR.html | 8 ++++---- tests/testthat/_snaps/g_mean_slides |only tests/testthat/t_dm_output.rds |binary 8 files changed, 31 insertions(+), 17 deletions(-)
More information about autoslider.core at CRAN
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Title: CIE XYZ and some of Its Derived Color Spaces
Description: Functions for converting among CIE XYZ, xyY, Lab, and Luv.
Calculate Correlated Color Temperature (CCT) and the Planckian and daylight loci.
The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included.
Three standard color difference metrics are included.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between spacesXYZ versions 1.3-0 dated 2024-01-23 and 1.4-0 dated 2025-01-17
spacesXYZ-1.3-0/spacesXYZ/R/logging.R |only spacesXYZ-1.4-0/spacesXYZ/DESCRIPTION | 14 spacesXYZ-1.4-0/spacesXYZ/MD5 | 36 spacesXYZ-1.4-0/spacesXYZ/NAMESPACE | 1 spacesXYZ-1.4-0/spacesXYZ/NEWS.md | 7 spacesXYZ-1.4-0/spacesXYZ/R/CCT.R | 1618 ++++++++++----------- spacesXYZ-1.4-0/spacesXYZ/R/DeltaE.R | 4 spacesXYZ-1.4-0/spacesXYZ/R/adaptation.R | 564 +++---- spacesXYZ-1.4-0/spacesXYZ/R/basic.R | 748 ++++----- spacesXYZ-1.4-0/spacesXYZ/R/datasets.R | 5 spacesXYZ-1.4-0/spacesXYZ/R/daylight.R | 100 - spacesXYZ-1.4-0/spacesXYZ/R/hooks.R | 60 spacesXYZ-1.4-0/spacesXYZ/R/logger.R |only spacesXYZ-1.4-0/spacesXYZ/R/quintic.R | 234 +-- spacesXYZ-1.4-0/spacesXYZ/R/utils.R | 100 - spacesXYZ-1.4-0/spacesXYZ/build/vignette.rds |binary spacesXYZ-1.4-0/spacesXYZ/inst/doc/adaptation.R | 26 spacesXYZ-1.4-0/spacesXYZ/inst/doc/adaptation.html | 634 +++++--- spacesXYZ-1.4-0/spacesXYZ/inst/doc/isotherms.pdf |binary spacesXYZ-1.4-0/spacesXYZ/man/spacesXYZ-package.Rd | 36 20 files changed, 2255 insertions(+), 1932 deletions(-)
Title: Create Common TLGs Used in Clinical Trials
Description: Table, Listings, and Graphs (TLG) library for common outputs
used in clinical trials.
Author: Joe Zhu [aut, cre],
Daniel Sabanes Bove [aut],
Jana Stoilova [aut],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [aut],
Heng Wang [aut],
Francois Collin [aut],
Adrian Waddell [aut],
Pawel Rucki [aut],
Chendi Liao [aut],
Jennifer [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between tern versions 0.9.6 dated 2024-09-24 and 0.9.7 dated 2025-01-17
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tern-0.9.7/tern/R/count_cumulative.R | 21 tern-0.9.7/tern/R/count_missed_doses.R | 13 tern-0.9.7/tern/R/count_occurrences.R | 67 tern-0.9.7/tern/R/count_occurrences_by_grade.R | 156 + tern-0.9.7/tern/R/count_patients_events_in_cols.R | 7 tern-0.9.7/tern/R/count_patients_with_event.R | 107 - tern-0.9.7/tern/R/count_patients_with_flags.R | 143 + tern-0.9.7/tern/R/count_values.R | 96 - tern-0.9.7/tern/R/estimate_multinomial_rsp.R | 5 tern-0.9.7/tern/R/estimate_proportion.R | 5 tern-0.9.7/tern/R/formatting_functions.R | 2 tern-0.9.7/tern/R/g_forest.R | 1 tern-0.9.7/tern/R/g_ipp.R | 2 tern-0.9.7/tern/R/g_km.R | 1 tern-0.9.7/tern/R/g_lineplot.R | 39 tern-0.9.7/tern/R/g_step.R | 1 tern-0.9.7/tern/R/g_waterfall.R | 1 tern-0.9.7/tern/R/incidence_rate.R | 5 tern-0.9.7/tern/R/odds_ratio.R | 34 tern-0.9.7/tern/R/package.R | 3 tern-0.9.7/tern/R/prop_diff.R | 5 tern-0.9.7/tern/R/prop_diff_test.R | 5 tern-0.9.7/tern/R/riskdiff.R | 3 tern-0.9.7/tern/R/summarize_ancova.R | 5 tern-0.9.7/tern/R/summarize_change.R | 150 + tern-0.9.7/tern/R/summarize_coxreg.R | 5 tern-0.9.7/tern/R/summarize_glm_count.R | 85 - 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Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO, Artificial Neural Network (ANN), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Oblique Random Forest ('aorsf'), Recursive Partitioning ('RPART') or step wise regression models are fit. Cross validation leave out samples (leading to nested cross validation) or bootstrap out-of-bag samples are used to evaluate and compare performances between these models with results presented in tabular or graphical means. Calibration plots can also be generated, again based upon (outer nested) cross validation or bootstrap leave out (out of bag) samples.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience when fitting Cox models on data with many predictors and many patients, making it difficult to get solutions from either glmnet() or cv.glmnet(). This may be remedied by using the 'path=TRUE' option when calling [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.5-4 dated 2024-10-24 and 0.5-5 dated 2025-01-17
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glmnetr-0.5-5/glmnetr/man/boot.factor.foldid.Rd | 2 glmnetr-0.5-5/glmnetr/man/calplot.Rd | 19 + glmnetr-0.5-5/glmnetr/man/cox.sat.dev.Rd | 2 glmnetr-0.5-5/glmnetr/man/devrat_.Rd | 2 glmnetr-0.5-5/glmnetr/man/diff_time.Rd | 2 glmnetr-0.5-5/glmnetr/man/diff_time1.Rd | 2 glmnetr-0.5-5/glmnetr/man/factor.foldid.Rd | 2 glmnetr-0.5-5/glmnetr/man/get.foldid.Rd | 2 glmnetr-0.5-5/glmnetr/man/get.id.foldid.Rd | 2 glmnetr-0.5-5/glmnetr/man/glmnetr.compcv.Rd | 24 + glmnetr-0.5-5/glmnetr/man/glmnetr.simdata.Rd | 2 glmnetr-0.5-5/glmnetr/man/glmnetr_seed.Rd | 6 glmnetr-0.5-5/glmnetr/man/nested.cis.Rd | 11 glmnetr-0.5-5/glmnetr/man/nested.compare.Rd | 8 glmnetr-0.5-5/glmnetr/man/nested.compare_0_5_1.Rd |only glmnetr-0.5-5/glmnetr/man/nested.glmnetr.Rd | 43 ++- glmnetr-0.5-5/glmnetr/man/orf_tune.Rd | 6 glmnetr-0.5-5/glmnetr/man/plot.cv.glmnetr.Rd | 2 glmnetr-0.5-5/glmnetr/man/plot.glmnetr.Rd | 2 glmnetr-0.5-5/glmnetr/man/plot.nested.glmnetr.Rd | 4 glmnetr-0.5-5/glmnetr/man/plot_perf_glmnetr.Rd | 2 glmnetr-0.5-5/glmnetr/man/print.nested.glmnetr.Rd | 2 glmnetr-0.5-5/glmnetr/man/print.orf_tune.Rd | 2 glmnetr-0.5-5/glmnetr/man/roundperf.Rd | 2 glmnetr-0.5-5/glmnetr/man/summary.nested.glmnetr.Rd | 2 glmnetr-0.5-5/glmnetr/man/summary.orf_tune.Rd | 2 glmnetr-0.5-5/glmnetr/vignettes/An_Overview_of_glmnetr_241228.Rmd |only glmnetr-0.5-5/glmnetr/vignettes/An_Overview_of_glmnetr_241228.pdf.asis |only glmnetr-0.5-5/glmnetr/vignettes/Calibration_241228.Rmd |only glmnetr-0.5-5/glmnetr/vignettes/Calibration_241228.pdf.asis |only glmnetr-0.5-5/glmnetr/vignettes/Ridge_and_Lasso_241228.Rmd |only glmnetr-0.5-5/glmnetr/vignettes/Ridge_and_Lasso_241228.pdf.asis |only glmnetr-0.5-5/glmnetr/vignettes/Using_ann_tab_cv_241228.Rmd |only glmnetr-0.5-5/glmnetr/vignettes/Using_ann_tab_cv_241228.pdf.asis |only glmnetr-0.5-5/glmnetr/vignettes/Using_stepreg_241228.Rmd |only glmnetr-0.5-5/glmnetr/vignettes/Using_stepreg_241228.pdf.asis |only 99 files changed, 202 insertions(+), 117 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-28 0.2.1
2022-08-31 0.2.0
2021-01-19 0.1.0
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS
and Linux for finding font files that can then be used further by e.g.
graphic devices. The main use is intended to be from compiled code but
'systemfonts' also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
,
Jeroen Ooms [aut] ,
Devon Govett [aut] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between systemfonts versions 1.1.0 dated 2024-05-15 and 1.2.0 dated 2025-01-16
DESCRIPTION | 14 ++- MD5 | 71 +++++++++++-------- NAMESPACE | 10 ++ NEWS.md | 39 +++++++--- R/cpp11.R | 16 ++++ R/font_outline.R |only R/match_fonts.R | 71 ++++++++++++------- R/register_font.R | 146 +++++++++++++++++++++++++++++------------ R/web_fonts.R |only R/zzz.R | 3 build/vignette.rds |binary inst/doc/c_interface.html | 2 inst/include/systemfonts-ft.h | 6 + inst/include/systemfonts.h | 20 +++-- man/add_fonts.Rd |only man/as_font_weight.Rd | 4 - man/glyph_outline.Rd |only man/glyph_raster.Rd |only man/glyph_raster_grob.Rd |only man/match_fonts.Rd | 18 +++++ man/register_font.Rd | 24 +++++- man/register_variant.Rd | 23 +++++- man/require_font.Rd |only man/search_web_fonts.Rd |only man/web-fonts.Rd |only src/FontDescriptor.h | 81 ++++++++++++++++++++-- src/Makevars.in | 6 - src/Makevars.win | 34 +++++---- src/caches.cpp | 10 ++ src/caches.h | 2 src/cpp11.cpp | 33 +++++++++ src/font_local.cpp |only src/font_local.h |only src/font_matching.cpp | 70 ++++++++++--------- src/font_outlines.cpp |only src/font_outlines.h |only src/ft_cache.cpp | 88 ++++++++++++------------ src/ft_cache.h | 48 +++++++------ src/mac/FontManagerMac.mm | 9 ++ src/unix/FontManagerLinux.cpp | 15 ++++ src/utils.h | 10 -- src/win/FontManagerWindows.cpp | 130 ++++++++++++++++-------------------- tools/winlibs.R | 2 43 files changed, 667 insertions(+), 338 deletions(-)
Title: Wrangle and Analyze Growth Curve Data
Description: Easy wrangling and model-free analysis of
microbial growth curve data, as commonly output by plate readers.
Tools for reshaping common plate reader outputs into 'tidy' formats and
merging them with design information, making data easy to work with using
'gcplyr' and other packages. Also streamlines common growth curve
processing steps, like smoothing and calculating derivatives, and
facilitates model-free characterization and analysis of growth data.
See methods at <https://mikeblazanin.github.io/gcplyr/>.
Author: Mike Blazanin [aut, cre]
Maintainer: Mike Blazanin <mikeblazanin@gmail.com>
Diff between gcplyr versions 1.10.0 dated 2024-07-09 and 1.11.0 dated 2025-01-16
DESCRIPTION | 14 +- MD5 | 78 ++++++++-------- NEWS.md | 6 + R/example_functions.R | 74 ++++++++++++--- R/functions.R | 63 ++++++++++--- README.md | 2 build/vignette.rds |binary inst/doc/gc01_gcplyr.R | 3 inst/doc/gc01_gcplyr.Rmd | 3 inst/doc/gc01_gcplyr.pdf |binary inst/doc/gc02_import_reshape.pdf |binary inst/doc/gc03_incorporate_designs.pdf |binary inst/doc/gc04_preprocess_plot.R | 30 +++++- inst/doc/gc04_preprocess_plot.Rmd | 47 +++++++++ inst/doc/gc04_preprocess_plot.pdf |binary inst/doc/gc05_process.Rmd | 2 inst/doc/gc05_process.pdf |binary inst/doc/gc06_analyze.R | 5 - inst/doc/gc06_analyze.Rmd | 7 - inst/doc/gc06_analyze.pdf |binary inst/doc/gc07_noise.pdf |binary inst/doc/gc08_conclusion.pdf |binary inst/doc/gc09_multiple_plates.pdf |binary inst/doc/gc10_using_make_design.pdf |binary man/lag_time.Rd | 29 ++++- tests/testthat/test_analysisfunctions.R | 74 ++++++++++++--- vignettes/gc01_gcplyr.Rmd | 3 vignettes/gc01_gcplyr.html | 81 ++++++++-------- vignettes/gc02_import_reshape.html | 18 +-- vignettes/gc03_incorporate_designs.html | 4 vignettes/gc04_preprocess_plot.Rmd | 47 +++++++++ vignettes/gc04_preprocess_plot.html | 113 +++++++++++++++++------ vignettes/gc05_process.Rmd | 2 vignettes/gc05_process.html | 21 ++-- vignettes/gc06_analyze.Rmd | 7 - vignettes/gc06_analyze.html | 123 +++++++++++++------------ vignettes/gc07_noise.html | 155 +++++++++++++++++--------------- vignettes/gc08_conclusion.html | 29 ++--- vignettes/gc09_multiple_plates.html | 40 ++++---- vignettes/gc10_using_make_design.html | 4 40 files changed, 721 insertions(+), 363 deletions(-)
Title: Characterise Tables of an OMOP Common Data Model Instance
Description: Summarises key information in data mapped to the Observational
Medical Outcomes Partnership (OMOP) common data model. Assess suitability to
perform specific epidemiological studies and explore the different domains
to obtain feasibility counts and trends.
Author: Marta Alcalde-Herraiz [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut] ,
Cecilia Campanile [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut]
Maintainer: Cecilia Campanile <cecilia.campanile@ndorms.ox.ac.uk>
Diff between OmopSketch versions 0.2.0 dated 2025-01-08 and 0.2.1 dated 2025-01-16
DESCRIPTION | 6 MD5 | 64 ++++---- R/mockOmopSketch.R | 6 R/summariseClinicalRecords.R | 5 R/summariseConceptIdCounts.R | 2 R/summariseConceptSetCounts.R | 4 R/summariseInObservation.R | 4 R/summariseInternal.R | 14 - R/summariseOmopSnapshot.R | 2 R/summariseRecordCount.R | 4 R/tableObservationPeriod.R | 4 README.md | 5 build/vignette.rds |binary inst/doc/A-summarise_clinical_tables_records.html | 176 +++++++++++----------- inst/doc/B-summarise_concept_set_counts.R | 2 inst/doc/B-summarise_concept_set_counts.Rmd | 2 inst/doc/B-summarise_concept_set_counts.html | 16 +- inst/doc/C-summarise_observation_period.R |only inst/doc/C-summarise_observation_period.Rmd |only inst/doc/C-summarise_observation_period.html |only man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/mockOmopSketch.Rd | 2 man/summariseClinicalRecords.Rd | 4 man/summariseConceptSetCounts.Rd | 4 tests/testthat/setup.R | 2 tests/testthat/test-summariseClinicalRecords.R | 17 -- tests/testthat/test-summariseConceptIdCounts.R | 6 tests/testthat/test-summariseConceptSetCounts.R | 15 - tests/testthat/test-summariseRecordCount.R | 6 vignettes/B-summarise_concept_set_counts.Rmd | 2 vignettes/C-summarise_observation_period.Rmd |only 35 files changed, 174 insertions(+), 200 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Designed for simplicity, a 'mirai' evaluates an R expression
asynchronously in a parallel process, locally or distributed over the
network, with the result automatically available upon completion. Modern
networking and concurrency built on 'nanonext' and 'NNG' (Nanomsg Next Gen)
ensure reliable and efficient scheduling, over fast inter-process
communications or TCP/IP secured by TLS. Advantages include being inherently
queued thus handling many more tasks than available processes, no storage on
the file system, support for otherwise non-exportable reference objects, an
event-driven promises implementation, and built-in asynchronous parallel
map.
Author: Charlie Gao [aut, cre] ,
Joe Cheng [ctb],
Hibiki AI Limited [cph],
Posit Software, PBC [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 2.0.0 dated 2025-01-08 and 2.0.1 dated 2025-01-16
DESCRIPTION | 6 - MD5 | 54 ++++++++--------- NAMESPACE | 2 NEWS.md | 13 ++++ R/daemon.R | 51 +++++++++++----- R/dispatcher.R | 60 +++++++++---------- R/launchers.R | 4 - R/map.R | 139 +++++++++++++++++++++++++++------------------- R/mirai.R | 60 ++++++++++++------- R/next.R | 28 +++++++++ inst/doc/mirai.Rmd | 142 +++++++++++++++++++++++++---------------------- inst/doc/mirai.html | 139 ++++++++++++++++++++++++---------------------- inst/doc/shiny.Rmd | 115 ++++++++++++++++++++++++++++++-------- inst/doc/shiny.html | 108 ++++++++++++++++++++++++++++------- man/call_mirai.Rd | 7 +- man/collect_mirai.Rd | 17 +++-- man/daemon.Rd | 12 ++- man/dot-flat.Rd | 15 +--- man/everywhere.Rd | 4 - man/is_mirai_error.Rd | 5 - man/mirai.Rd | 19 +++--- man/mirai_map.Rd | 66 +++++++++++---------- man/nextstream.Rd | 13 ++++ tests/tests.R | 38 ++++++++---- vignettes/mirai.Rmd | 142 +++++++++++++++++++++++++---------------------- vignettes/mirai.Rmd.orig | 33 ++++++---- vignettes/shiny.Rmd | 115 ++++++++++++++++++++++++++++++-------- vignettes/shiny.Rmd.orig | 114 ++++++++++++++++++++++++++++++------- 28 files changed, 982 insertions(+), 539 deletions(-)
Title: GSL Multi-Start Nonlinear Least-Squares Fitting
Description: An R interface to weighted nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Multi-start optimization based on quasi-random samples is implemented using a modified version of the algorithm in Hickernell and Yuan (1997, OR Transactions). Robust nonlinear regression can be performed using various robust loss functions, in which case the optimization problem is solved by iterative reweighted least squares (IRLS). Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between gslnls versions 1.3.2 dated 2024-05-01 and 1.4.0 dated 2025-01-16
DESCRIPTION | 12 MD5 | 46 +- NAMESPACE | 7 NEWS.md | 13 R/nls.R | 217 ++++++++-- R/nls_large.R | 20 R/nls_methods.R | 257 ++++++++---- R/nls_rho.R |only configure | 22 - configure.ac | 2 inst/unit_tests/unit_tests_gslnls.R | 362 +++++++++++------ man/cooks.distance.gsl_nls.Rd |only man/gsl_nls.Rd | 61 ++ man/gsl_nls_control.Rd | 13 man/gsl_nls_large.Rd | 9 man/gsl_nls_loss.Rd |only man/summary.gsl_nls.Rd | 2 src/fdf.c |only src/fdfvv.c |only src/fdjac.c |only src/gsl_nls.h | 255 +++++++++--- src/init.c | 4 src/nls.c | 733 ++++++++++++------------------------ src/nls_fit.c |only src/nls_irls.c |only src/nls_large.c | 127 ------ src/nls_mstart.c |only src/nls_utils.c |only src/trust.c | 333 ++++++++++++---- 29 files changed, 1441 insertions(+), 1054 deletions(-)
Title: Fast Agent-Based Epi Models
Description: A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Author: George Vega Yon [aut] ,
Derek Meyer [aut] ,
Andrew Pulsipher [aut, cre] ,
Susan Holmes [rev] ,
Abinash Satapathy [rev] ,
Carinogurjao [rev],
Centers for Disease Control and Prevention [fnd]
Maintainer: Andrew Pulsipher <pulsipher.a@gmail.com>
Diff between epiworldR versions 0.3-2 dated 2024-10-08 and 0.6.0.0 dated 2025-01-16
epiworldR-0.3-2/epiworldR/man/global-actions.Rd |only epiworldR-0.6.0.0/epiworldR/DESCRIPTION | 15 epiworldR-0.6.0.0/epiworldR/MD5 | 138 ++-- epiworldR-0.6.0.0/epiworldR/NAMESPACE | 40 + epiworldR-0.6.0.0/epiworldR/NEWS.md | 24 epiworldR-0.6.0.0/epiworldR/R/LFMCMC.R |only epiworldR-0.6.0.0/epiworldR/R/cpp11.R | 140 ++++ epiworldR-0.6.0.0/epiworldR/R/global-actions.R | 52 + epiworldR-0.6.0.0/epiworldR/R/model-methods.R | 49 + epiworldR-0.6.0.0/epiworldR/R/plot_epi.R | 3 epiworldR-0.6.0.0/epiworldR/README.md | 57 - epiworldR-0.6.0.0/epiworldR/build/vignette.rds |binary epiworldR-0.6.0.0/epiworldR/inst/CITATION | 3 epiworldR-0.6.0.0/epiworldR/inst/doc/getting-started.html | 87 +- epiworldR-0.6.0.0/epiworldR/inst/doc/likelihood-free-mcmc.R |only epiworldR-0.6.0.0/epiworldR/inst/doc/likelihood-free-mcmc.Rmd |only epiworldR-0.6.0.0/epiworldR/inst/doc/likelihood-free-mcmc.html |only epiworldR-0.6.0.0/epiworldR/inst/doc/mixing.html | 14 epiworldR-0.6.0.0/epiworldR/inst/doc/run-multiple.html | 22 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/agent-meat-virus-sampling.hpp | 6 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/database-bones.hpp | 21 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/database-meat.hpp | 18 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/epiworld.hpp | 6 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/math/distributions.hpp |only epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/math/lfmcmc/lfmcmc-bones.hpp | 187 +++--- epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp | 90 +- epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/math/lfmcmc/lfmcmc-meat.hpp | 306 +++++----- epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/misc.hpp | 2 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/model-bones.hpp | 20 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/model-meat.hpp | 68 -- epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/models/seirconnected.hpp | 67 ++ epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/models/sirconnected.hpp | 58 + epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/models/surveillance.hpp | 2 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/progress.hpp | 12 epiworldR-0.6.0.0/epiworldR/inst/include/epiworld/random_graph.hpp | 13 epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-lfmcmc.R |only epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-multiple.R | 2 epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-seir.R |only epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-sir.R | 93 +-- epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-sirconn.R |only epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-sird.R |only epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-sis.R |only epiworldR-0.6.0.0/epiworldR/inst/tinytest/test-tool.R |only epiworldR-0.6.0.0/epiworldR/man/LFMCMC.Rd |only epiworldR-0.6.0.0/epiworldR/man/ModelDiffNet.Rd | 4 epiworldR-0.6.0.0/epiworldR/man/ModelSEIR.Rd | 8 epiworldR-0.6.0.0/epiworldR/man/ModelSEIRCONN.Rd | 10 epiworldR-0.6.0.0/epiworldR/man/ModelSEIRD.Rd | 10 epiworldR-0.6.0.0/epiworldR/man/ModelSEIRDCONN.Rd | 10 epiworldR-0.6.0.0/epiworldR/man/ModelSIR.Rd | 8 epiworldR-0.6.0.0/epiworldR/man/ModelSIRCONN.Rd | 2 epiworldR-0.6.0.0/epiworldR/man/ModelSIRD.Rd | 14 epiworldR-0.6.0.0/epiworldR/man/ModelSIRDCONN.Rd | 2 epiworldR-0.6.0.0/epiworldR/man/ModelSIRLogit.Rd | 16 epiworldR-0.6.0.0/epiworldR/man/ModelSIS.Rd | 8 epiworldR-0.6.0.0/epiworldR/man/ModelSISD.Rd | 16 epiworldR-0.6.0.0/epiworldR/man/ModelSURV.Rd | 6 epiworldR-0.6.0.0/epiworldR/man/agents.Rd | 36 - epiworldR-0.6.0.0/epiworldR/man/agents_smallworld.Rd | 22 epiworldR-0.6.0.0/epiworldR/man/entities.Rd | 14 epiworldR-0.6.0.0/epiworldR/man/epiworld-data.Rd | 10 epiworldR-0.6.0.0/epiworldR/man/epiworld-methods.Rd | 141 ++-- epiworldR-0.6.0.0/epiworldR/man/epiworldR-package.Rd | 3 epiworldR-0.6.0.0/epiworldR/man/figures/README-logit-model-1.png |binary epiworldR-0.6.0.0/epiworldR/man/figures/README-multiple-example-1.png |binary epiworldR-0.6.0.0/epiworldR/man/figures/README-sir-figures-1.png |binary epiworldR-0.6.0.0/epiworldR/man/figures/README-sir-figures-2.png |binary epiworldR-0.6.0.0/epiworldR/man/figures/README-transmission-net-1.png |binary epiworldR-0.6.0.0/epiworldR/man/global-events.Rd |only epiworldR-0.6.0.0/epiworldR/man/run_multiple.Rd | 4 epiworldR-0.6.0.0/epiworldR/man/tool.Rd | 25 epiworldR-0.6.0.0/epiworldR/man/virus.Rd | 19 epiworldR-0.6.0.0/epiworldR/src/Makevars.in | 2 epiworldR-0.6.0.0/epiworldR/src/Makevars.win | 2 epiworldR-0.6.0.0/epiworldR/src/cpp11.cpp | 280 +++++++++ epiworldR-0.6.0.0/epiworldR/src/lfmcmc.cpp |only epiworldR-0.6.0.0/epiworldR/src/model.cpp | 17 epiworldR-0.6.0.0/epiworldR/vignettes/likelihood-free-mcmc.Rmd |only 78 files changed, 1566 insertions(+), 738 deletions(-)
Title: High Precision Timing of R Expressions
Description: Tools to accurately benchmark and analyze execution times for
R expressions.
Author: Jim Hester [aut],
Davis Vaughan [aut, cre],
Drew Schmidt [ctb] ,
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between bench versions 1.1.3 dated 2023-05-04 and 1.1.4 dated 2025-01-16
DESCRIPTION | 22 ++- LICENSE | 2 MD5 | 55 ++++----- NAMESPACE | 1 NEWS.md | 16 ++ R/autoplot.R | 73 ++++++------ R/bench-package.R | 1 R/bench_time.R | 8 + R/bytes.R | 84 +++++++++++--- R/expression.R | 11 + R/import-standalone-s3-register.R | 54 +++++---- R/load.R | 1 R/mark.R | 135 ++++++++++++++++------- R/press.R | 59 +++++----- R/time.R | 81 +++++++++----- R/utils.R | 31 +++-- R/workout.R | 6 - README.md | 24 ++-- man/autoplot.bench_mark.Rd | 2 man/press.Rd | 10 + tests/testthat/test-autoplot.R |only tests/testthat/test-bench_process_memory.R | 8 - tests/testthat/test-bench_time.R | 4 tests/testthat/test-bytes.R | 5 tests/testthat/test-expression.R | 5 tests/testthat/test-mark.R | 167 ++++++++++++++++++++--------- tests/testthat/test-press.R | 36 +++--- tests/testthat/test-time.R | 5 tests/testthat/test-workout.R | 5 29 files changed, 596 insertions(+), 315 deletions(-)
Title: Create Interactive Web Maps Using 'The National Map' Services
Description: Creates interactive web maps using the 'JavaScript' 'Leaflet'
library with base layers of 'The National Map' ('TNM'). 'TNM' services
provide access to base geospatial information that describes the landscape
of the United States and its territories. This package is dependent on, and
intended to be used with, the 'leaflet' package.
Author: Jason C. Fisher [aut, cre] ,
Stefano Cudini [ctb, cph] ,
John Firebaugh [ctb, cph]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between webmap versions 1.1.0 dated 2024-03-25 and 1.1.1 dated 2025-01-16
DESCRIPTION | 8 - MD5 | 28 ++-- NEWS.md | 4 R/add_home_button.R | 7 - R/add_legend.R | 4 R/make_map.R | 2 README.md | 58 +++++----- data/us_cities.rda |binary inst/htmlwidgets/plugins/leaflet-search/leaflet-search.min.css | 2 man/add_cluster_button.Rd | 2 man/add_fullscreen_button.Rd | 2 man/add_home_button.Rd | 7 - man/add_legend.Rd | 6 - man/add_search_button.Rd | 2 man/make_map.Rd | 2 15 files changed, 71 insertions(+), 63 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://euroqol.org/>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-3l/>) or a five-level
(EQ-5D-5L, <https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-5l/>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.15.5 dated 2024-11-20 and 0.15.6 dated 2025-01-16
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/data.R | 1 + R/sysdata.rda |binary build/partial.rdb |binary build/vignette.rds |binary inst/doc/eq5d.html | 12 ++++++------ man/VT.Rd | 3 ++- man/eq5d-package.Rd | 2 +- tests/testthat/test-eq5d5l.R | 9 +++++++++ 11 files changed, 37 insertions(+), 22 deletions(-)
Title: Accessing and Analyzing Large-Scale Environmental Data
Description: Functions are designed to facilitate access to and utility with large scale, publicly available environmental data in R. The package contains functions for downloading raw data files from web URLs (download_data()), processing the raw data files into clean spatial objects (process_covariates()), and extracting values from the spatial data objects at point and polygon locations (calculate_covariates()). These functions call a series of source-specific functions which are tailored to each data sources/datasets particular URL structure, data format, and spatial/temporal resolution. The functions are tested, versioned, and open source and open access. For sum_edc() method details, see Messier, Akita, and Serre (2012) <doi:10.1021/es203152a>.
Author: Mitchell Manware [aut, ctb] ,
Insang Song [aut, ctb] ,
Eva Marques [aut, ctb] ,
Mariana Alifa Kassien [aut, ctb]
,
Elizabeth Scholl [ctb] ,
Kyle Messier [aut, cre] ,
Spatiotemporal Exposures and Toxicology Group [cph]
Maintainer: Kyle Messier <kyle.messier@nih.gov>
Diff between amadeus versions 1.2.2 dated 2025-01-08 and 1.2.3 dated 2025-01-16
DESCRIPTION | 9 - MD5 | 26 ++--- NAMESPACE | 2 R/calculate_covariates.R | 173 ++++++++++++++++++++---------------- R/download_auxiliary.R | 15 --- build/partial.rdb |binary inst/doc/gridmet_workflow.html | 4 inst/doc/narr_workflow.html | 4 inst/doc/terraclimate_workflow.html | 4 man/calculate_nlcd.Rd | 4 man/calculate_terraclimate.Rd | 3 man/calculate_tri.Rd | 6 - man/download_hash.Rd | 7 - man/sum_edc.Rd | 4 14 files changed, 135 insertions(+), 126 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
< [...truncated...]
Author: Roger Bivand [cre, aut] ,
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assuncao [ctb],
Anil Bera [ctb],
Olaf Berke [ctb],
F. Guillaume Blanchet [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Steph [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.3-8 dated 2024-12-02 and 1.3-9 dated 2025-01-16
DESCRIPTION | 11 MD5 | 73 +++--- NEWS.md | 11 R/components.R | 4 R/diffnb.R | 40 ++- R/listw2sn.R | 4 R/nb2listw.R | 2 R/nb2mat.R | 6 R/nblag.R | 4 R/nboperations.R | 44 +-- inst/doc/CO69.R | 4 inst/doc/CO69.Rmd | 4 inst/doc/CO69.html | 8 inst/doc/nb_sf.html | 28 +- inst/doc/sids.html | 4 inst/doc/subgraphs.Rmd | 2 inst/doc/subgraphs.html | 8 inst/tinytest/test_nb_setops.R |only man/diffnb.Rd | 17 + man/localC.Rd | 467 ++++++++++++++++++++++++++++++++++++++++- man/nboperations.Rd | 10 src/card.c | 6 src/dfs_ncomp.c | 12 - src/dnn.c | 12 - src/gabriel.c | 2 src/gearyw.c | 2 src/gsymtest.c | 2 src/jc.c | 2 src/knn.c | 2 src/lagw.c | 6 src/nbdists.c | 8 src/perm_no_replace.c | 4 src/polypoly.c | 111 --------- src/relative.c | 2 src/spdep.h | 9 src/symtest.c | 2 vignettes/CO69.Rmd | 4 vignettes/subgraphs.Rmd | 2 38 files changed, 667 insertions(+), 272 deletions(-)
Title: Radiation and Photovoltaic Systems
Description: Provides tools for calculating solar geometry, solar radiation on horizontal and inclined planes, and simulating the performance of various photovoltaic (PV) systems. Supports daily and intradaily irradiation data, enabling detailed analysis of grid-connected and water-pumping PV systems, including shading effects and solar angle calculations.
Author: Oscar Perpinan-Lamigueiro [aut]
,
Francisco Delgado-Lopez [aut, cre]
Maintainer: Francisco Delgado-Lopez <f.delgadol@alumnos.upm.es>
Diff between solaR2 versions 0.10 dated 2024-09-16 and 0.11 dated 2025-01-16
DESCRIPTION | 15 ++++--- MD5 | 82 +++++++++++++++++++++--------------------- NAMESPACE | 7 +++ R/calcG0.R | 11 ++++- R/fSolD.R | 2 - README.md | 42 +++++++++++++++++++++ man/HQCurve.Rd | 4 +- man/Meteo2Meteo.Rd | 19 +++++---- man/NmgSFB.Rd | 3 + man/as.data.tableD-methods.Rd | 3 + man/as.data.tableI-methods.Rd | 3 + man/as.data.tableM-methods.Rd | 9 +++- man/as.data.tableY-methods.Rd | 5 ++ man/calcG0.Rd | 7 ++- man/calcGef.Rd | 3 + man/calcSol.Rd | 15 ++++--- man/compare-methods.Rd | 13 ++++-- man/compareLosses-methods.Rd | 11 +++-- man/corrFdKt.Rd | 29 ++++++++------ man/fBTd.Rd | 3 + man/fBTi.Rd | 3 + man/fCompD.Rd | 25 +++++++----- man/fCompI.Rd | 2 + man/fProd.Rd | 11 +++-- man/fPump.Rd | 14 +++++-- man/fSolD.Rd | 16 ++++---- man/fSolI.Rd | 18 +++++---- man/fSombra.Rd | 5 ++ man/local2UTC.Rd | 3 + man/mergesolaR-methods.Rd | 11 +++-- man/optimShd.Rd | 34 +++++++++-------- man/prodGCPV.Rd | 4 +- man/readBD.Rd | 3 + man/readG0dm.Rd | 7 ++- man/readSIAR.Rd | 6 ++- man/sample2Diff.Rd | 3 + man/solar2-package.Rd | 1 man/solarAngles.Rd | 2 + man/window-methods.Rd | 7 ++- man/writeSolar.Rd | 2 + tests/testthat.R | 2 + tests/testthat/test-calcG0.R | 2 - 42 files changed, 307 insertions(+), 160 deletions(-)
Title: Create Custom Research Compendiums
Description: Provides functions to create and manage research compendiums for data analysis. Research compendiums are a standard and intuitive folder structure for organizing the digital materials of a research project, which can significantly improve reproducibility. The package offers several compendium structure options that fit different research project as well as the ability of duplicating the folder structure of existing projects or implementing custom structures. It also simplifies the use of version control.
Author: Marcelo Araya-Salas [aut, cre]
,
Andrea Yure Arriaga Madrigal [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between sketchy versions 1.0.4 dated 2024-09-02 and 1.0.5 dated 2025-01-16
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/add_to_gitignore.R | 5 ++++- R/sysdata.rda |binary data/compendiums.rda |binary 6 files changed, 19 insertions(+), 9 deletions(-)
Title: Cryptographic Hash, Extendable-Output and Base64 Functions
Description: Fast and memory-efficient streaming hash functions and base64
encoding / decoding. Hashes strings and raw vectors directly. Stream hashes
files which can be larger than memory, as well as in-memory objects through
R's serialization mechanism. Implementations include the SHA-256, SHA-3 and
'Keccak' cryptographic hash functions, SHAKE256 extendable-output function
(XOF), and 'SipHash' pseudo-random function.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between secretbase versions 1.0.3 dated 2024-10-02 and 1.0.4 dated 2025-01-16
DESCRIPTION | 8 +- MD5 | 42 +++++------ NEWS.md | 4 + R/base.R | 56 +++++++------- R/secret.R | 173 ++++++++++++++++++++++------------------------ README.md | 22 ++--- build/partial.rdb |binary inst/CITATION | 2 man/base64dec.Rd | 23 ++---- man/base64enc.Rd | 21 ++--- man/keccak.Rd | 53 +++++++------- man/secretbase-package.Rd | 12 +-- man/sha256.Rd | 56 +++++++------- man/sha3.Rd | 48 ++++++------ man/shake256.Rd | 47 ++++++------ man/siphash13.Rd | 68 +++++++++--------- src/base.c | 21 +---- src/secret.c | 24 ++---- src/secret.h | 23 +----- src/secret2.c | 15 ++- src/secret3.c | 15 ++- tests/tests.R | 6 - 22 files changed, 359 insertions(+), 380 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.8.5 dated 2024-11-04 and 2.8.7 dated 2025-01-16
DESCRIPTION | 6 MD5 | 106 +- NAMESPACE | 1 NEWS.md | 31 R/AAAA.R | 30 R/createSSURGO.R | 354 ++++++--- R/createStaticNASIS.R | 93 +- R/fetchNASIS.R | 4 R/fetchNASISLabData.R | 2 R/fetchNASIS_components.R | 6 R/fetchNASIS_pedons.R | 19 R/fetchSOLUS.R | 9 R/fetchSoilGrids.R | 2 R/fetchVegdata.R | 100 +- R/getHzErrorsNASIS.R | 12 R/get_NASIS_table_name_by_purpose.R | 60 - R/get_colors_from_NASIS_db.R | 20 R/get_component_data_from_NASIS_db.R | 6 R/get_ecosite_history_from_NASIS_db.R | 4 R/get_hz_data_from_NASIS_db.R | 20 R/get_hz_data_from_pedon_db.R | 4 R/get_lablayer_data_from_NASIS_db.R | 7 R/get_labpedon_data_from_NASIS_db.R | 4 R/get_site_data_from_NASIS_db.R | 141 ++- R/get_text_notes_from_NASIS_db.R | 8 R/get_veg_data_from_NASIS_db.R | 6 R/get_vegplot_data_from_NASIS_db.R | 206 +++-- R/soilDB-package.R | 4 R/utils.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/gopheridge.rda |binary data/loafercreek.rda |binary data/mineralKing.rda |binary inst/CITATION | 6 inst/doc/fetchNASIS.R | 2 inst/doc/fetchNASIS.Rmd | 2 inst/doc/fetchNASIS.html | 28 inst/doc/wcs-ssurgo.R | 54 - inst/doc/wcs-ssurgo.html | 1270 +++++++++++++++++----------------- man/createSSURGO.Rd | 52 + man/downloadSSURGO.Rd | 58 + man/fetchNASIS.Rd | 4 man/fetchSOLUS.Rd | 7 man/fetchVegdata.Rd | 25 man/getHzErrorsNASIS.Rd | 2 man/get_colors_from_NASIS_db.Rd | 11 man/get_site_data_from_NASIS_db.Rd | 26 man/loafercreek.Rd | 4 tests/testthat.R | 10 tests/testthat/test-fetchLDM.R | 54 - tests/testthat/test-fetchNASIS.R | 3 tests/testthat/test-soilDBdata.R | 60 + vignettes/fetchNASIS.Rmd | 2 54 files changed, 1709 insertions(+), 1238 deletions(-)
Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in
parallel, so metadata resolution and package downloads are fast.
Metadata and package files are cached on the local disk as well. 'pak'
has a dependency solver, so it finds version conflicts before
performing the installation. This version of 'pak' supports CRAN,
'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
Posit Software, PBC [cph, fnd],
Winston Chang [ctb] ,
Ascent Digital Services [cph, fnd] ,
Hadley Wickham [ctb, cph] ,
Jeroen Ooms [ctb] ,
Maelle Salmon [ctb] ,
Duncan Temple Lang [ctb] ,
Lloyd Hilaiel [cph] [...truncated...]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pak versions 0.8.0 dated 2024-08-26 and 0.8.0.1 dated 2025-01-16
DESCRIPTION | 10 ++-- MD5 | 40 ++++++++--------- NEWS.md | 4 + R/push-packages.R | 49 +++++++++++++++++++++ R/repo.R | 2 man/chunks/install.Rmd | 18 ++++--- man/install.Rd | 4 + man/repo_add.Rd | 2 src/library/curl/configure | 3 - src/library/lpSolve/DESCRIPTION | 15 +++--- src/library/lpSolve/src/commonlib.c | 6 -- src/library/lpSolve/src/lp_lib.c | 2 src/library/lpSolve/src/lp_utils.c | 1 src/library/lpSolve/src/lusol.c | 2 src/library/lpSolve/src/myblas.c | 68 +++--------------------------- src/library/pkgsearch/DESCRIPTION | 9 +-- src/library/pkgsearch/NEWS.md | 5 ++ src/library/pkgsearch/R/advanced_search.R | 6 -- src/library/pkgsearch/R/api.R | 32 ++++++-------- src/library/pkgsearch/R/http.R | 26 ++++++++++- src/library/pkgsearch/R/utils.R | 18 ++++--- 21 files changed, 178 insertions(+), 144 deletions(-)
Title: 'grid' Pattern Grobs
Description: Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.
Author: Trevor L. Davis [aut, cre] ,
Mike FC [aut] ,
ggplot2 authors [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between gridpattern versions 1.2.2 dated 2024-06-03 and 1.3.1 dated 2025-01-16
DESCRIPTION | 12 ++-- LICENSE | 2 MD5 | 43 ++++++++-------- NAMESPACE | 2 NEWS.md | 8 ++- R/alphaMaskGrob.R | 2 R/grid-pattern.R | 9 ++- R/pattern-pattern-aRtsy.R |only R/utils-ggplot2.R | 12 ++++ R/utils-params.R | 1 README.md | 100 +++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/developing-patterns.R | 10 +-- inst/doc/developing-patterns.Rmd | 6 +- inst/doc/developing-patterns.html | 8 +-- inst/doc/tiling.R | 38 +++++++------- inst/doc/tiling.Rmd | 38 +++++++------- inst/doc/tiling.html | 38 +++++++------- man/alphaMaskGrob.Rd | 2 man/grid.pattern.Rd | 6 +- man/grid.pattern_aRtsy.Rd |only tests/testthat/test_aRtsy.R |only vignettes/developing-patterns.Rmd | 6 +- vignettes/tiling.Rmd | 38 +++++++------- 24 files changed, 206 insertions(+), 175 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.
Author: Robert J. Hijmans [cre, aut] ,
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Dan Baston [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
Ben Fasoli [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ct [...truncated...]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 3.6-30 dated 2024-10-02 and 3.6-31 dated 2025-01-16
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 + NEWS | 3 +++ build/partial.rdb |binary 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates
compilers needed to build R packages on various platforms and ensures
the PATH is configured appropriately so R can use them.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgbuild versions 1.4.5 dated 2024-10-28 and 1.4.6 dated 2025-01-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/compile-dll.R | 4 +++- man/compile_dll.Rd | 4 +++- tests/testthat/test-withr.R | 6 ++++++ 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Effective Reproduction Number Estimation
Description: Estimate the effective reproduction number from wastewater
and clinical data sources.
Author: David Champredon [aut, cre] ,
Warsame Yusuf [aut] ,
Irena Papst [aut]
Maintainer: David Champredon <david.champredon@canada.ca>
Diff between ern versions 2.0.0 dated 2024-04-22 and 2.1.2 dated 2025-01-16
ern-2.0.0/ern/R/format_ww.smooth.R |only ern-2.0.0/ern/README.md |only ern-2.0.0/ern/man/summarise_by_date_ens.Rd |only ern-2.1.2/ern/DESCRIPTION | 6 ern-2.1.2/ern/MD5 | 26 +- ern-2.1.2/ern/R/estimate_R_cl_rep.R | 21 -- ern-2.1.2/ern/R/estimate_R_cl_single.R | 151 +++++++-------- ern-2.1.2/ern/R/estimate_R_ww.R | 28 +- ern-2.1.2/ern/R/get_use_dates.R | 21 -- ern-2.1.2/ern/R/globals.R | 1 ern-2.1.2/ern/R/incidence_to_R.R | 68 ++++-- ern-2.1.2/ern/R/summary_postsamples.R |only ern-2.1.2/ern/inst/doc/est-rt.html | 16 - ern-2.1.2/ern/man/sample_post_ee.Rd |only ern-2.1.2/ern/man/summary_postsamples.Rd |only ern-2.1.2/ern/tests/testthat/test-estimate_R_cl_single.R | 25 -- ern-2.1.2/ern/tests/testthat/test-get_use_dates.R | 3 17 files changed, 179 insertions(+), 187 deletions(-)
Title: Tests for Segregation Distortion in Polyploids
Description: Provides a suite of tests for
segregation distortion in F1 polyploid populations (for
now, just tetraploids). This is under different assumptions of
meiosis. Details of these methods are described in
Gerard et al. (2025) <doi:10.1007/s00122-025-04816-z>.
This material is based upon work supported by the
National Science Foundation under Grant No. 2132247. The
opinions, findings, and conclusions or recommendations expressed
are those of the author and do not necessarily reflect the views
of the National Science Foundation.
Author: David Gerard [aut, cre] ,
Mira Thakkar [aut],
NSF DBI 2132247 [fnd]
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between segtest versions 1.0.1 dated 2024-10-21 and 1.0.2 dated 2025-01-16
DESCRIPTION | 8 - MD5 | 53 ++++---- NAMESPACE | 74 +++++------ R/lrt_gl.R | 200 +++++++++++++++---------------- R/overall.R | 262 ++++++++++++++++++++-------------------- R/segtest-package.R | 18 +- README.md | 18 ++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/intro.Rmd | 6 inst/doc/intro.html | 11 - man/gcount_to_gvec.Rd | 58 ++++----- man/gvec_to_gcount.Rd | 64 ++++----- man/is_valid_2.Rd | 66 +++++----- man/iter.array.Rd | 76 +++++------ man/lrt_men_gl4.Rd | 188 ++++++++++++++--------------- man/multi_lrt.Rd | 270 +++++++++++++++++++++--------------------- man/multidog_to_g.Rd | 140 ++++++++++----------- man/nextElem.arrayiter.Rd | 68 +++++----- man/otest_g.Rd | 186 ++++++++++++++-------------- man/po_gl.Rd | 100 +++++++-------- man/segtest-package.Rd | 2 man/simgl.Rd | 74 +++++------ man/ufit.Rd | 80 ++++++------ tests/testthat/test-corner.R | 66 +++++----- tests/testthat/test-overall.R | 14 +- vignettes/intro.Rmd | 6 28 files changed, 1060 insertions(+), 1048 deletions(-)