Title: Testing Neighbor Effects in Marker-Based Regressions
Description: To incorporate neighbor genotypic identity into genome-wide association studies, the package provides a set of functions for variation partitioning and association mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1038/s41437-020-00401-w>.
Author: Yasuhiro Sato [aut, cre] ,
Eiji Yamamoto [aut],
Kentaro K. Shimizu [aut] ,
Atsushi J. Nagano [aut]
Maintainer: Yasuhiro Sato <sato.yasuhiro.36c@kyoto-u.jp>
Diff between rNeighborGWAS versions 1.2.4 dated 2021-05-10 and 1.2.5 dated 2025-04-22
DESCRIPTION | 8 MD5 | 34 +- R/calc_PVEnei.R | 214 +++++++-------- R/gaston2neiGWAS.R | 64 ++-- R/neiGWAS.R | 246 +++++++++--------- R/nei_lm.R | 8 R/nei_lmm.R | 10 R/qtl_pheno_simu.R | 116 ++++---- build/vignette.rds |binary inst/CITATION | 11 inst/doc/rNeighborGWAS.R | 2 inst/doc/rNeighborGWAS.html | 593 ++++++++++++++++++++++++++++++-------------- man/calc_PVEnei.Rd | 8 man/gaston2neiGWAS.Rd | 10 man/neiGWAS.Rd | 6 man/nei_lm.Rd | 8 man/nei_lmm.Rd | 8 man/qtl_pheno_simu.Rd | 16 - 18 files changed, 794 insertions(+), 568 deletions(-)
Title: Miscellaneous, Analytic R Kernels
Description: Miscellaneous functions and wrappers for development in other
packages created, maintained by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre]
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>
Diff between mark versions 0.8.2 dated 2024-12-07 and 0.8.3 dated 2025-04-22
mark-0.8.2/mark/tests/testthat/test-struct.R |only mark-0.8.3/mark/DESCRIPTION | 6 ++-- mark-0.8.3/mark/MD5 | 30 ++++++++++++------------ mark-0.8.3/mark/NEWS.md | 6 ++++ mark-0.8.3/mark/R/dates.R | 2 - mark-0.8.3/mark/R/depth.R | 12 +++++---- mark-0.8.3/mark/R/detail.R | 2 - mark-0.8.3/mark/R/fact.R | 2 - mark-0.8.3/mark/R/file.R | 33 +++++++++------------------ mark-0.8.3/mark/R/lines-of-code.R | 24 +++++++++---------- mark-0.8.3/mark/R/switch.R | 7 ++--- mark-0.8.3/mark/R/time-report.R | 3 +- mark-0.8.3/mark/R/todos.R | 4 +-- mark-0.8.3/mark/tests/testthat/Rplots.pdf |binary mark-0.8.3/mark/tests/testthat/helper.R |only mark-0.8.3/mark/tests/testthat/test-file.R | 21 +++++++++++------ mark-0.8.3/mark/tests/testthat/test-write.R | 33 +++++++++++++-------------- 17 files changed, 95 insertions(+), 90 deletions(-)
Title: Data Access and Analytical Tools for 'VectorSurv' Users
Description: Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
Author: Christina De Cesaris [aut, cre]
Maintainer: Christina De Cesaris <cmdecesaris@ucdavis.edu>
Diff between vectorsurvR versions 1.3.1 dated 2025-04-14 and 1.3.2 dated 2025-04-22
DESCRIPTION | 6 MD5 | 39 - NAMESPACE | 1 R/data.R | 14 R/getAbundanceMapData.R | 11 R/getInfectionRate.R | 31 - R/getPools.R | 13 R/getPoolsComparisonTable.R | 11 R/getVectorIndex.R | 2 R/globals.R | 8 R/sysdata.rda |binary data/sample_collections.rda |binary data/sample_pools.rda |binary data/sample_spatial.rda |binary inst/doc/vectorsurvR.html | 899 +++++++++++++----------------- man/getInfectionRate.Rd | 2 man/sample_collections.Rd | 1 man/sample_pools.Rd | 9 man/sample_spatial.Rd | 2 tests/testthat/test-getAbundance.R | 10 tests/testthat/test-getAbundanceMapData.R |only 21 files changed, 480 insertions(+), 579 deletions(-)
Title: The Q-Matrix Validation Methods Framework
Description: Provide a variety of Q-matrix validation methods for the generalized cognitive diagnosis models, including the method based on the generalized deterministic input, noisy, and gate model (G-DINA) by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> discrimination index (the GDI method) by de la Torre and Chiu (2016) <DOI:10.1007/s11336-015-9467-8>, the step-wise Wald test method (the Wald method) by Ma and de la Torre (2020) <DOI:10.1111/bmsp.12156>, the Hull method by Najera et al. (2021) <DOI:10.1111/bmsp.12228>, the multiple logistic regression‑based Q‑matrix validation method (the MLR-B method) by Tu et al. (2022) <DOI:10.3758/s13428-022-01880-x>, the beta method based on signal detection theory by Li and Chen (2024) <DOI:10.1111/bmsp.12371> and Q-matrix validation based on relative fit index by Chen et la. (2013) <DOI:10.1111/j.1745-3984.2012.00185.x>. Different research methods and iterative procedures during Q-matrix validating are avai [...truncated...]
Author: Haijiang Qin [aut, cre, cph] ,
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between Qval versions 1.2.0 dated 2025-03-07 and 1.2.1 dated 2025-04-22
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 5 +++++ R/CDM.R | 4 ++-- R/Mmatrix.R | 2 +- R/QvalBeta.R | 2 +- R/QvalGDI.R | 7 ++++--- R/QvalWald.R | 4 ++-- R/Qvalindex.R | 4 ++-- R/Qvalvalidation.R | 7 +++++-- R/convex.R | 20 ++++++++++---------- R/fit.R | 4 ++++ man/get.Mmatrix.Rd | 2 +- man/validation.Rd | 4 ++-- man/zOSR.Rd | 4 ++-- man/zUSR.Rd | 4 ++-- tests/building.R | 3 ++- tests/demo.R | 18 ++++++++++-------- 18 files changed, 76 insertions(+), 60 deletions(-)
Title: Visualizations of Distributions and Uncertainty
Description: Provides primitives for visualizing distributions using 'ggplot2' that are particularly tuned for
visualizing uncertainty in either a frequentist or Bayesian mode. Both analytical distributions (such as
frequentist confidence distributions or Bayesian priors) and distributions represented as samples (such as
bootstrap distributions or Bayesian posterior samples) are easily visualized. Visualization primitives include
but are not limited to: points with multiple uncertainty intervals,
eye plots (Spiegelhalter D., 1999) <https://ideas.repec.org/a/bla/jorssa/v162y1999i1p45-58.html>,
density plots, gradient plots, dot plots (Wilkinson L., 1999) <doi:10.1080/00031305.1999.10474474>,
quantile dot plots (Kay M., Kola T., Hullman J., Munson S., 2016) <doi:10.1145/2858036.2858558>,
complementary cumulative distribution function
barplots (Fernandes M., Walls L., Munson S., Hullman J., Kay M., 2018) <doi:10.1145/3173574.3173718>,
and fit curves with multiple uncertainty ri [...truncated...]
Author: Matthew Kay [aut, cre],
Brenton M. Wiernik [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between ggdist versions 3.3.2 dated 2024-03-05 and 3.3.3 dated 2025-04-22
ggdist-3.3.2/ggdist/man/reexports.Rd |only ggdist-3.3.3/ggdist/DESCRIPTION | 42 ggdist-3.3.3/ggdist/MD5 | 374 +-- ggdist-3.3.3/ggdist/NAMESPACE | 21 ggdist-3.3.3/ggdist/NEWS.md | 1100 +++++----- ggdist-3.3.3/ggdist/R/abstract_geom.R | 16 ggdist-3.3.3/ggdist/R/abstract_stat.R | 6 ggdist-3.3.3/ggdist/R/abstract_stat_slabinterval.R | 18 ggdist-3.3.3/ggdist/R/auto_partial.R | 66 ggdist-3.3.3/ggdist/R/binning_methods.R | 30 ggdist-3.3.3/ggdist/R/bounder.R | 10 ggdist-3.3.3/ggdist/R/curve_interval.R | 36 ggdist-3.3.3/ggdist/R/cut_cdf_qi.R | 10 ggdist-3.3.3/ggdist/R/density.R | 198 + ggdist-3.3.3/ggdist/R/deprecated.R | 9 ggdist-3.3.3/ggdist/R/distributions.R | 4 ggdist-3.3.3/ggdist/R/geom.R | 2 ggdist-3.3.3/ggdist/R/geom_blur_dots.R | 80 ggdist-3.3.3/ggdist/R/geom_dotsinterval.R | 51 ggdist-3.3.3/ggdist/R/geom_interval.R | 2 ggdist-3.3.3/ggdist/R/geom_lineribbon.R | 36 ggdist-3.3.3/ggdist/R/geom_pointinterval.R | 10 ggdist-3.3.3/ggdist/R/geom_slabinterval.R | 176 - ggdist-3.3.3/ggdist/R/geom_spike.R | 19 ggdist-3.3.3/ggdist/R/guide_rampbar.R | 8 ggdist-3.3.3/ggdist/R/interval_widths.R |only ggdist-3.3.3/ggdist/R/lkjcorr_marginal.R | 23 ggdist-3.3.3/ggdist/R/parse_dist.R | 58 ggdist-3.3.3/ggdist/R/partial_colour_ramp.R | 11 ggdist-3.3.3/ggdist/R/point_interval.R | 97 ggdist-3.3.3/ggdist/R/position_dodgejust.R | 2 ggdist-3.3.3/ggdist/R/pr.R | 8 ggdist-3.3.3/ggdist/R/rd.R | 11 ggdist-3.3.3/ggdist/R/rd_density.R |only ggdist-3.3.3/ggdist/R/rd_dotsinterval.R | 8 ggdist-3.3.3/ggdist/R/rd_lineribbon.R | 13 ggdist-3.3.3/ggdist/R/rd_slabinterval.R | 14 ggdist-3.3.3/ggdist/R/scale_.R | 24 ggdist-3.3.3/ggdist/R/scale_colour_ramp.R | 16 ggdist-3.3.3/ggdist/R/scale_side_mirrored.R | 6 ggdist-3.3.3/ggdist/R/scale_thickness.R | 190 - ggdist-3.3.3/ggdist/R/smooth.R | 23 ggdist-3.3.3/ggdist/R/stat_dotsinterval.R | 21 ggdist-3.3.3/ggdist/R/stat_pointinterval.R | 3 ggdist-3.3.3/ggdist/R/stat_slabinterval.R | 154 - ggdist-3.3.3/ggdist/R/stat_spike.R | 29 ggdist-3.3.3/ggdist/R/student_t.R | 4 ggdist-3.3.3/ggdist/R/subguide.R | 76 ggdist-3.3.3/ggdist/R/subscale.R |only ggdist-3.3.3/ggdist/R/testthat.R | 27 ggdist-3.3.3/ggdist/R/thickness.R |only ggdist-3.3.3/ggdist/R/tidy_format_translators.R | 2 ggdist-3.3.3/ggdist/R/util.R | 25 ggdist-3.3.3/ggdist/R/weighted_ecdf.R | 6 ggdist-3.3.3/ggdist/R/weighted_hist.R | 60 ggdist-3.3.3/ggdist/R/weighted_quantile.R | 17 ggdist-3.3.3/ggdist/build/partial.rdb |binary ggdist-3.3.3/ggdist/build/vignette.rds |binary ggdist-3.3.3/ggdist/inst/doc/dotsinterval.R | 2 ggdist-3.3.3/ggdist/inst/doc/dotsinterval.html | 66 ggdist-3.3.3/ggdist/inst/doc/freq-uncertainty-vis.R | 2 ggdist-3.3.3/ggdist/inst/doc/freq-uncertainty-vis.html | 24 ggdist-3.3.3/ggdist/inst/doc/lineribbon.R | 2 ggdist-3.3.3/ggdist/inst/doc/lineribbon.html | 50 ggdist-3.3.3/ggdist/inst/doc/slabinterval.R | 22 ggdist-3.3.3/ggdist/inst/doc/slabinterval.Rmd | 10 ggdist-3.3.3/ggdist/inst/doc/slabinterval.html | 100 ggdist-3.3.3/ggdist/man/Pr_.Rd | 8 ggdist-3.3.3/ggdist/man/align.Rd | 7 ggdist-3.3.3/ggdist/man/auto_partial.Rd | 8 ggdist-3.3.3/ggdist/man/bandwidth.Rd | 13 ggdist-3.3.3/ggdist/man/bin_dots.Rd | 21 ggdist-3.3.3/ggdist/man/blur.Rd | 17 ggdist-3.3.3/ggdist/man/bounder_cdf.Rd | 7 ggdist-3.3.3/ggdist/man/bounder_cooke.Rd | 5 ggdist-3.3.3/ggdist/man/bounder_range.Rd | 5 ggdist-3.3.3/ggdist/man/breaks.Rd | 29 ggdist-3.3.3/ggdist/man/curve_interval.Rd | 26 ggdist-3.3.3/ggdist/man/cut_cdf_qi.Rd | 10 ggdist-3.3.3/ggdist/man/density_bounded.Rd | 36 ggdist-3.3.3/ggdist/man/density_histogram.Rd | 54 ggdist-3.3.3/ggdist/man/density_unbounded.Rd | 31 ggdist-3.3.3/ggdist/man/find_dotplot_binwidth.Rd | 13 ggdist-3.3.3/ggdist/man/geom_blur_dots.Rd | 91 ggdist-3.3.3/ggdist/man/geom_dots.Rd | 81 ggdist-3.3.3/ggdist/man/geom_dotsinterval.Rd | 131 - ggdist-3.3.3/ggdist/man/geom_interval.Rd | 78 ggdist-3.3.3/ggdist/man/geom_lineribbon.Rd | 85 ggdist-3.3.3/ggdist/man/geom_pointinterval.Rd | 102 ggdist-3.3.3/ggdist/man/geom_slab.Rd | 81 ggdist-3.3.3/ggdist/man/geom_slabinterval.Rd | 127 - ggdist-3.3.3/ggdist/man/geom_spike.Rd | 100 ggdist-3.3.3/ggdist/man/geom_swarm.Rd | 81 ggdist-3.3.3/ggdist/man/geom_weave.Rd | 81 ggdist-3.3.3/ggdist/man/ggdist-deprecated.Rd | 9 ggdist-3.3.3/ggdist/man/ggdist-ggproto.Rd | 2 ggdist-3.3.3/ggdist/man/ggdist-package.Rd | 2 ggdist-3.3.3/ggdist/man/guide_rampbar.Rd | 6 ggdist-3.3.3/ggdist/man/interval_widths.Rd |only ggdist-3.3.3/ggdist/man/lkjcorr_marginal.Rd | 4 ggdist-3.3.3/ggdist/man/marginalize_lkjcorr.Rd | 21 ggdist-3.3.3/ggdist/man/parse_dist.Rd | 62 ggdist-3.3.3/ggdist/man/partial_colour_ramp.Rd | 6 ggdist-3.3.3/ggdist/man/point_interval.Rd | 60 ggdist-3.3.3/ggdist/man/position_dodgejust.Rd | 2 ggdist-3.3.3/ggdist/man/ramp_colours.Rd | 5 ggdist-3.3.3/ggdist/man/scale_colour_ramp.Rd | 16 ggdist-3.3.3/ggdist/man/scale_side_mirrored.Rd | 9 ggdist-3.3.3/ggdist/man/scale_thickness.Rd | 45 ggdist-3.3.3/ggdist/man/smooth_density.Rd | 15 ggdist-3.3.3/ggdist/man/smooth_discrete.Rd | 14 ggdist-3.3.3/ggdist/man/smooth_none.Rd | 5 ggdist-3.3.3/ggdist/man/stat_ccdfinterval.Rd | 229 +- ggdist-3.3.3/ggdist/man/stat_cdfinterval.Rd | 229 +- ggdist-3.3.3/ggdist/man/stat_dots.Rd | 100 ggdist-3.3.3/ggdist/man/stat_dotsinterval.Rd | 142 - ggdist-3.3.3/ggdist/man/stat_eye.Rd | 231 +- ggdist-3.3.3/ggdist/man/stat_gradientinterval.Rd | 231 +- ggdist-3.3.3/ggdist/man/stat_halfeye.Rd | 231 +- ggdist-3.3.3/ggdist/man/stat_histinterval.Rd | 231 +- ggdist-3.3.3/ggdist/man/stat_interval.Rd | 102 ggdist-3.3.3/ggdist/man/stat_lineribbon.Rd | 85 ggdist-3.3.3/ggdist/man/stat_mcse_dots.Rd | 108 ggdist-3.3.3/ggdist/man/stat_pointinterval.Rd | 110 - ggdist-3.3.3/ggdist/man/stat_ribbon.Rd | 85 ggdist-3.3.3/ggdist/man/stat_slab.Rd | 193 - ggdist-3.3.3/ggdist/man/stat_slabinterval.Rd | 231 +- ggdist-3.3.3/ggdist/man/stat_spike.Rd | 227 +- ggdist-3.3.3/ggdist/man/student_t.Rd | 4 ggdist-3.3.3/ggdist/man/sub-geometry-scales.Rd | 24 ggdist-3.3.3/ggdist/man/subguide_axis.Rd | 58 ggdist-3.3.3/ggdist/man/subguide_none.Rd | 14 ggdist-3.3.3/ggdist/man/subscale_identity.Rd |only ggdist-3.3.3/ggdist/man/subscale_thickness.Rd |only ggdist-3.3.3/ggdist/man/thickness.Rd |only ggdist-3.3.3/ggdist/man/tidy-format-translators.Rd | 2 ggdist-3.3.3/ggdist/man/waiver.Rd |only ggdist-3.3.3/ggdist/man/weighted_ecdf.Rd | 6 ggdist-3.3.3/ggdist/man/weighted_quantile.Rd | 17 ggdist-3.3.3/ggdist/tests/testthat/Rplots.pdf |binary ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.density/adapt-n-better-matches-mode.svg | 4 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.density/adaptive-kde-red-better-matches-mode.svg | 4 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.density/plot-ggdist-density-sets-zero-baseline-by-default.svg |only ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.density/plot-ggdist-density-ylim-null-resets-limits.svg |only ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.geom_blur_dots/blur-types-work-correctly.svg | 40 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.geom_blur_dots/square-blur.svg |only ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_dist_slabinterval/ccdfinterval-reverse-scale-transform.svg | 4 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_dist_slabinterval/dist-halfeyeh-reverse-scale-transform.svg | 4 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_dist_slabinterval/dist-sample.svg | 4 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_dist_slabinterval/halfeye-with-rvar-and-cdf.svg | 40 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_dist_slabinterval/transformed-scale-with-dist-sample.svg | 2 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_dist_slabinterval/transformed-scale-with-sample-data-on-x.svg | 2 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/halfeye-dodge-3-groups-just-0-both-scale-4-rev-y.svg | 16 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/one-parameter-horizontal-eye.svg | 2 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/one-parameter-horizontal-half-eye.svg | 2 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/one-parameter-vertical-eye.svg | 2 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/one-parameter-vertical-halfeye.svg | 2 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/two-parameter-factor-horizontal-eye-fill.svg | 4 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/two-parameter-factor-vertical-eye-fill.svg | 4 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/two-parameter-numeric-horizontal-half-eye-fill.svg | 4 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/two-parameter-numeric-vertical-eye.svg | 4 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/vert-dodge-3-groups-just-0-5-top-scale-0-5.svg | 8 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/vert-dodge-3-groups-just-1-top-scale-0-5.svg | 8 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/vert-halfeye-dodge-3-groups-just-0-both-scale-1-5.svg | 8 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/vert-halfeye-dodge-3-groups-just-0-bottom-scale-1-5.svg | 8 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/vert-halfeye-dodge-3-groups-just-0-top-scale-1-5.svg | 8 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/vertical-eye-with-dodging-3-groups-just-0.svg | 8 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/vertical-eye-with-dodging-3-groups-left.svg | 8 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/vertical-halfeye-with-dodging-3-groups-left.svg | 8 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_eye/vertical-halfeye-with-dodging-3-groups-right.svg | 8 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_sample_slabinterval/halfeyeh-log-scale-tri-no-trim.svg | 2 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_sample_slabinterval/halfeyeh-log-scale-tri.svg | 2 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_sample_slabinterval/pdf-and-cdf-on-a-sample-slabinterval.svg | 50 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_sample_slabinterval/slab-with-outline.svg | 8 ggdist-3.3.3/ggdist/tests/testthat/_snaps/test.stat_sample_slabinterval/untrimmed-and-expanded.svg | 12 ggdist-3.3.3/ggdist/tests/testthat/test.curve_interval.R | 15 ggdist-3.3.3/ggdist/tests/testthat/test.density.R | 21 ggdist-3.3.3/ggdist/tests/testthat/test.geom_blur_dots.R | 25 ggdist-3.3.3/ggdist/tests/testthat/test.geom_dotsinterval.R | 3 ggdist-3.3.3/ggdist/tests/testthat/test.geom_lineribbon.R | 21 ggdist-3.3.3/ggdist/tests/testthat/test.interval_widths.R |only ggdist-3.3.3/ggdist/tests/testthat/test.point_interval.R | 13 ggdist-3.3.3/ggdist/tests/testthat/test.rd_dotsinterval.R | 8 ggdist-3.3.3/ggdist/tests/testthat/test.rd_lineribbon.R | 8 ggdist-3.3.3/ggdist/tests/testthat/test.rd_slabinterval.R | 14 ggdist-3.3.3/ggdist/tests/testthat/test.rd_spike.R | 4 ggdist-3.3.3/ggdist/tests/testthat/test.scale_thickness.R | 67 ggdist-3.3.3/ggdist/tests/testthat/test.stat_dist_slabinterval.R | 2 ggdist-3.3.3/ggdist/tests/testthat/test.stat_sample_slabinterval.R | 2 ggdist-3.3.3/ggdist/tests/testthat/test.subguide.R | 11 ggdist-3.3.3/ggdist/tests/testthat/test.subscale.R |only ggdist-3.3.3/ggdist/tests/testthat/test.thickness.R |only ggdist-3.3.3/ggdist/tests/testthat/test.util.R | 17 ggdist-3.3.3/ggdist/tests/testthat/test.weighted_hist.R | 17 ggdist-3.3.3/ggdist/vignettes/children/chunk_options.txt | 2 ggdist-3.3.3/ggdist/vignettes/slabinterval.Rmd | 10 196 files changed, 4766 insertions(+), 3815 deletions(-)
Title: C++ Classes to Embed R in C++ (and C) Applications
Description: C++ classes to embed R in C++ (and C) applications
A C++ class providing the R interpreter is offered by this package
making it easier to have "R inside" your C++ application. As R itself
is embedded into your application, a shared library build of R is
required. This works on Linux, OS X and even on Windows provided you
use the same tools used to build R itself. Numerous examples are
provided in the nine subdirectories of the examples/ directory of
the installed package: standard, 'mpi' (for parallel computing), 'qt'
(showing how to embed 'RInside' inside a Qt GUI application), 'wt'
(showing how to build a "web-application" using the Wt toolkit),
'armadillo' (for 'RInside' use with 'RcppArmadillo'), 'eigen' (for
'RInside' use with 'RcppEigen'), and 'c_interface' for a basic C
interface and 'Ruby' illustration. The examples use 'GNUmakefile(s)'
with GNU extensions, so a GNU make is required (and will use the
'GNUmakefile' automatically). 'Doxygen'-generated documentation of
the C++ cl [...truncated...]
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Lance Bachmeier [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RInside versions 0.2.18 dated 2023-02-01 and 0.2.19 dated 2025-04-22
ChangeLog | 49 +++ DESCRIPTION | 19 - MD5 | 23 - README.md | 2 cleanup | 3 inst/NEWS.Rd | 15 inst/examples/qt/README | 22 - inst/examples/qt/cmake/CMakeLists.txt | 88 ++--- inst/examples/qt/qtdensity.cpp | 7 inst/examples/sandboxed_server/README.md |only inst/examples/sandboxed_server/example_server.cpp | 3 inst/examples/standard/rinside_sample17.cpp | 351 ++++++++++------------ src/tools/RInsideEnvVars.r | 4 13 files changed, 327 insertions(+), 259 deletions(-)
Title: Distance Sampling Survey Design
Description: Creates survey designs for distance sampling surveys. These
designs can be assessed for various effort and coverage statistics.
Once the user is satisfied with the design characteristics they can
generate a set of transects to use in their distance sampling survey.
Many of the designs implemented in this R package were first made
available in our 'Distance' for Windows software and are detailed in
Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008,
ISBN-13: 978-0199225873). Find out more about estimating animal/plant
abundance with distance sampling at <https://distancesampling.org/>.
Author: Laura Marshall [aut, cre],
Rexstad Eric [ctb]
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between dssd versions 1.0.2 dated 2023-11-17 and 1.0.3 dated 2025-04-22
dssd-1.0.2/dssd/NEWS |only dssd-1.0.3/dssd/DESCRIPTION | 10 ++-- dssd-1.0.3/dssd/MD5 | 28 ++++++------- dssd-1.0.3/dssd/NEWS.md |only dssd-1.0.3/dssd/R/dssd-package.R | 6 +- dssd-1.0.3/dssd/README.md | 12 +++-- dssd-1.0.3/dssd/build/vignette.rds |binary dssd-1.0.3/dssd/inst/doc/GettingStarted.R | 4 - dssd-1.0.3/dssd/inst/doc/GettingStarted.Rmd | 12 +++-- dssd-1.0.3/dssd/inst/doc/GettingStarted.html | 36 ++++++++--------- dssd-1.0.3/dssd/inst/doc/MultiStrataVignette.R | 8 +-- dssd-1.0.3/dssd/inst/doc/MultiStrataVignette.Rmd | 12 +++-- dssd-1.0.3/dssd/inst/doc/MultiStrataVignette.html | 46 +++++++++++----------- dssd-1.0.3/dssd/man/dssd-package.Rd | 6 +- dssd-1.0.3/dssd/vignettes/GettingStarted.Rmd | 12 +++-- dssd-1.0.3/dssd/vignettes/MultiStrataVignette.Rmd | 12 +++-- 16 files changed, 112 insertions(+), 92 deletions(-)
Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among various built-in similarity/distance measures, computation of correlation,
cosine similarity, Dice coefficient and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
,
Robrecht Cannoodt [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.4.1 dated 2024-04-07 and 0.5.0 dated 2025-04-22
proxyC-0.4.1/proxyC/man/images |only proxyC-0.5.0/proxyC/DESCRIPTION | 16 +- proxyC-0.5.0/proxyC/MD5 | 58 +++---- proxyC-0.5.0/proxyC/NAMESPACE | 3 proxyC-0.5.0/proxyC/NEWS.md | 41 ++++- proxyC-0.5.0/proxyC/R/RcppExports.R | 12 + proxyC-0.5.0/proxyC/R/mask.R |only proxyC-0.5.0/proxyC/R/proxy.R | 157 +++++++------------- proxyC-0.5.0/proxyC/R/utils.R |only proxyC-0.5.0/proxyC/README.md | 6 proxyC-0.5.0/proxyC/build/vignette.rds |binary proxyC-0.5.0/proxyC/inst/doc/measures.Rmd | 63 +++++--- proxyC-0.5.0/proxyC/inst/doc/measures.html | 105 ++++++++----- proxyC-0.5.0/proxyC/man/colSds.Rd | 6 proxyC-0.5.0/proxyC/man/colZeros.Rd | 6 proxyC-0.5.0/proxyC/man/crossprod.Rd |only proxyC-0.5.0/proxyC/man/figures |only proxyC-0.5.0/proxyC/man/mask.Rd |only proxyC-0.5.0/proxyC/man/simil.Rd | 29 ++- proxyC-0.5.0/proxyC/src/RcppExports.cpp | 38 +++- proxyC-0.5.0/proxyC/src/linear.cpp | 78 +++++++-- proxyC-0.5.0/proxyC/src/mask.cpp |only proxyC-0.5.0/proxyC/src/pair.cpp | 105 ++++++++----- proxyC-0.5.0/proxyC/src/proxyc.h | 122 +++++++++++---- proxyC-0.5.0/proxyC/tests/testthat/function.R | 10 + proxyC-0.5.0/proxyC/tests/testthat/test-crossprod.R |only proxyC-0.5.0/proxyC/tests/testthat/test-dist.R | 45 +++++ proxyC-0.5.0/proxyC/tests/testthat/test-mask.R |only proxyC-0.5.0/proxyC/tests/testthat/test-proxy.R | 42 ++++- proxyC-0.5.0/proxyC/tests/testthat/test-simil.R | 40 +++++ proxyC-0.5.0/proxyC/vignettes/measures.Rmd | 63 +++++--- 31 files changed, 694 insertions(+), 351 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 0.6.1.0 dated 2025-01-28 and 0.8.1.0 dated 2025-04-22
epiworldR-0.6.1.0/epiworldR/inst/tinytest/test-mixing.R |only epiworldR-0.8.1.0/epiworldR/DESCRIPTION | 9 epiworldR-0.8.1.0/epiworldR/MD5 | 196 epiworldR-0.8.1.0/epiworldR/NAMESPACE | 22 epiworldR-0.8.1.0/epiworldR/NEWS.md | 19 epiworldR-0.8.1.0/epiworldR/R/LFMCMC.R | 10 epiworldR-0.8.1.0/epiworldR/R/ModelDiagram.R |only epiworldR-0.8.1.0/epiworldR/R/ModelDiffNet.R | 17 epiworldR-0.8.1.0/epiworldR/R/ModelMeaslesQuarantine.R |only epiworldR-0.8.1.0/epiworldR/R/ModelSEIR.R | 17 epiworldR-0.8.1.0/epiworldR/R/ModelSEIRCONN.R | 28 epiworldR-0.8.1.0/epiworldR/R/ModelSEIRD.R | 18 epiworldR-0.8.1.0/epiworldR/R/ModelSEIRDCONN.R | 30 epiworldR-0.8.1.0/epiworldR/R/ModelSEIRMixing.R | 30 epiworldR-0.8.1.0/epiworldR/R/ModelSIR.R | 22 epiworldR-0.8.1.0/epiworldR/R/ModelSIRCONN.R | 18 epiworldR-0.8.1.0/epiworldR/R/ModelSIRD.R | 18 epiworldR-0.8.1.0/epiworldR/R/ModelSIRDCONN.R | 26 epiworldR-0.8.1.0/epiworldR/R/ModelSIRLogit.R | 10 epiworldR-0.8.1.0/epiworldR/R/ModelSIRMixing.R | 26 epiworldR-0.8.1.0/epiworldR/R/ModelSIS.R | 23 epiworldR-0.8.1.0/epiworldR/R/ModelSISD.R | 25 epiworldR-0.8.1.0/epiworldR/R/ModelSURV.R | 41 epiworldR-0.8.1.0/epiworldR/R/agents.R | 5 epiworldR-0.8.1.0/epiworldR/R/arg-checks.R |only epiworldR-0.8.1.0/epiworldR/R/cpp11.R | 20 epiworldR-0.8.1.0/epiworldR/R/data.R | 1 epiworldR-0.8.1.0/epiworldR/R/entity.R | 13 epiworldR-0.8.1.0/epiworldR/R/global-actions.R | 7 epiworldR-0.8.1.0/epiworldR/R/model-methods.R | 53 epiworldR-0.8.1.0/epiworldR/R/plot_epi.R | 7 epiworldR-0.8.1.0/epiworldR/R/tool.R | 30 epiworldR-0.8.1.0/epiworldR/R/virus.R | 30 epiworldR-0.8.1.0/epiworldR/README.md | 55 epiworldR-0.8.1.0/epiworldR/build/vignette.rds |binary epiworldR-0.8.1.0/epiworldR/inst/doc/advanced-modeling.R |only epiworldR-0.8.1.0/epiworldR/inst/doc/advanced-modeling.Rmd |only epiworldR-0.8.1.0/epiworldR/inst/doc/advanced-modeling.html |only epiworldR-0.8.1.0/epiworldR/inst/doc/getting-started.R | 10 epiworldR-0.8.1.0/epiworldR/inst/doc/getting-started.Rmd | 15 epiworldR-0.8.1.0/epiworldR/inst/doc/getting-started.html | 2847 +++++++++- epiworldR-0.8.1.0/epiworldR/inst/doc/likelihood-free-mcmc.Rmd | 2 epiworldR-0.8.1.0/epiworldR/inst/doc/likelihood-free-mcmc.html | 10 epiworldR-0.8.1.0/epiworldR/inst/doc/mixing.html | 89 epiworldR-0.8.1.0/epiworldR/inst/doc/run-multiple.html | 9 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/agent-events-meat.hpp | 22 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/database-bones.hpp | 24 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/database-meat.hpp | 69 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/entity-distribute-meat.hpp | 4 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/epiworld.hpp | 8 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/misc.hpp | 67 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/model-bones.hpp | 39 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/model-meat.hpp | 133 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/modeldiagram-bones.hpp |only epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/modeldiagram-meat.hpp |only epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/models/measlesquarantine.hpp |only epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/models/models.hpp | 1 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/models/seir.hpp | 2 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/models/seirdconnected.hpp | 9 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/progress.hpp | 3 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/tool-distribute-meat.hpp | 6 epiworldR-0.8.1.0/epiworldR/inst/include/epiworld/virus-distribute-meat.hpp | 11 epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-diffnet.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-measles-quarantine.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-model-diagram-files |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-model-diagram.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-model-methods.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-seir.R | 58 epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-seirconn.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-seird.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-seirdconn.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-seirmixing.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-sir.R | 48 epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-sirconn.R | 79 epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-sird.R | 58 epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-sirdconn.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-sirlogit.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-sirmixing.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-sis.R | 42 epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-sisd.R |only epiworldR-0.8.1.0/epiworldR/inst/tinytest/test-surv.R |only epiworldR-0.8.1.0/epiworldR/man/ModelDiffNet.Rd | 10 epiworldR-0.8.1.0/epiworldR/man/ModelMeaslesQuarantine.Rd |only epiworldR-0.8.1.0/epiworldR/man/ModelSEIR.Rd | 13 epiworldR-0.8.1.0/epiworldR/man/ModelSEIRCONN.Rd | 13 epiworldR-0.8.1.0/epiworldR/man/ModelSEIRD.Rd | 13 epiworldR-0.8.1.0/epiworldR/man/ModelSEIRDCONN.Rd | 13 epiworldR-0.8.1.0/epiworldR/man/ModelSEIRMixing.Rd | 13 epiworldR-0.8.1.0/epiworldR/man/ModelSIR.Rd | 15 epiworldR-0.8.1.0/epiworldR/man/ModelSIRCONN.Rd | 13 epiworldR-0.8.1.0/epiworldR/man/ModelSIRD.Rd | 15 epiworldR-0.8.1.0/epiworldR/man/ModelSIRDCONN.Rd | 13 epiworldR-0.8.1.0/epiworldR/man/ModelSIRLogit.Rd | 1 epiworldR-0.8.1.0/epiworldR/man/ModelSIRMixing.Rd | 13 epiworldR-0.8.1.0/epiworldR/man/ModelSIS.Rd | 15 epiworldR-0.8.1.0/epiworldR/man/ModelSISD.Rd | 15 epiworldR-0.8.1.0/epiworldR/man/ModelSURV.Rd | 13 epiworldR-0.8.1.0/epiworldR/man/epiworld-data.Rd | 1 epiworldR-0.8.1.0/epiworldR/man/epiworld-methods.Rd | 18 epiworldR-0.8.1.0/epiworldR/man/epiworld-model-diagram.Rd |only epiworldR-0.8.1.0/epiworldR/man/global-events.Rd | 7 epiworldR-0.8.1.0/epiworldR/src/cpp11.cpp | 46 epiworldR-0.8.1.0/epiworldR/src/epimodels.cpp | 86 epiworldR-0.8.1.0/epiworldR/src/model-diagram.cpp |only epiworldR-0.8.1.0/epiworldR/src/model.cpp | 12 epiworldR-0.8.1.0/epiworldR/vignettes/advanced-modeling.Rmd |only epiworldR-0.8.1.0/epiworldR/vignettes/getting-started.Rmd | 15 epiworldR-0.8.1.0/epiworldR/vignettes/likelihood-free-mcmc.Rmd | 2 108 files changed, 3956 insertions(+), 910 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating
and analyzing transaction data and patterns (frequent itemsets and
association rules). Also provides C implementations of the
association mining algorithms Apriori and Eclat. Hahsler, Gruen and
Hornik (2005) <doi:10.18637/jss.v014.i15>.
Author: Michael Hahsler [aut, cre, cph]
,
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph] ,
Christian Borgelt [ctb, cph],
Ian Johnson [ctb],
Makhlouf Ledmi [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.7-9 dated 2024-12-14 and 1.7-10 dated 2025-04-22
DESCRIPTION | 8 ++++---- MD5 | 27 ++++++++++++++------------- NEWS.md | 12 ++++++++++++ R/apriori.R | 6 ++++-- R/eclat.R | 7 +++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/arules.pdf |binary man/apriori.Rd | 6 ++++-- man/eclat.Rd | 7 +++++-- src/matrix.c | 15 ++++++++------- src/ptree.c | 13 +++++++------ src/r_memcpy.h |only src/similarity.c | 9 +++++---- src/warm.c | 11 ++++++----- 15 files changed, 74 insertions(+), 47 deletions(-)
Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Author: Maxime HERVE [aut, cre]
Maintainer: Maxime HERVE <maxime.herve@univ-rennes.fr>
Diff between RVAideMemoire versions 0.9-83-7 dated 2023-11-06 and 0.9-83-11 dated 2025-04-22
DESCRIPTION | 13 +++++++------ MD5 | 30 +++++++++++++++--------------- NEWS | 3 +++ R/adonis.II.R | 14 +++++++------- R/pairwise.perm.manova.R | 8 ++++---- R/zzz.R | 2 +- man/GPA.test.Rd | 4 ++-- man/MVA.cor.Rd | 2 +- man/MVA.scoreplot.Rd | 2 +- man/MVA.scores.Rd | 2 +- man/MVA.synt.Rd | 2 +- man/RVAideMemoire-package.Rd | 6 +++--- man/adonis.II.Rd | 10 +++++----- man/pairwise.perm.manova.Rd | 8 ++++---- man/rating.emmeans.Rd | 21 ++++++++++----------- man/rating.prob.Rd | 17 +++++++++-------- 16 files changed, 74 insertions(+), 70 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb]
,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between insight versions 1.1.0 dated 2025-03-01 and 1.2.0 dated 2025-04-22
insight-1.1.0/insight/tests/testthat/test-ggeffects.R |only insight-1.2.0/insight/DESCRIPTION | 36 insight-1.2.0/insight/MD5 | 254 ++- insight-1.2.0/insight/NAMESPACE | 30 insight-1.2.0/insight/NEWS.md | 79 + insight-1.2.0/insight/R/clean_parameters.R | 125 + insight-1.2.0/insight/R/compute_variances.R | 7 insight-1.2.0/insight/R/display.R | 41 insight-1.2.0/insight/R/export_table.R | 155 ++ insight-1.2.0/insight/R/find_auxiliary.R |only insight-1.2.0/insight/R/find_formula.R | 213 --- insight-1.2.0/insight/R/find_interactions.R | 22 insight-1.2.0/insight/R/find_offset.R | 27 insight-1.2.0/insight/R/find_parameters_bayesian.R | 200 --- insight-1.2.0/insight/R/find_parameters_brms.R |only insight-1.2.0/insight/R/find_parameters_mixed.R | 2 insight-1.2.0/insight/R/find_predictors.R | 154 ++ insight-1.2.0/insight/R/find_random.R | 87 - insight-1.2.0/insight/R/find_random_slopes.R | 55 insight-1.2.0/insight/R/find_response.R | 30 insight-1.2.0/insight/R/find_terms.R | 39 insight-1.2.0/insight/R/find_variables.R | 8 insight-1.2.0/insight/R/fish.R | 17 insight-1.2.0/insight/R/format_table.R | 7 insight-1.2.0/insight/R/format_table_glue.R | 4 insight-1.2.0/insight/R/get_auxiliary.R | 22 insight-1.2.0/insight/R/get_data.R | 9 insight-1.2.0/insight/R/get_datagrid.R | 549 ++++++-- insight-1.2.0/insight/R/get_df.R | 2 insight-1.2.0/insight/R/get_family.R | 2 insight-1.2.0/insight/R/get_parameters.R | 4 insight-1.2.0/insight/R/get_parameters_bayesian.R | 34 insight-1.2.0/insight/R/get_parameters_others.R | 2 insight-1.2.0/insight/R/get_predicted.R | 21 insight-1.2.0/insight/R/get_predicted_args.R | 15 insight-1.2.0/insight/R/get_predicted_bayesian.R | 40 insight-1.2.0/insight/R/get_predicted_ci.R | 13 insight-1.2.0/insight/R/get_predicted_methods.R | 12 insight-1.2.0/insight/R/get_sigma.R | 2 insight-1.2.0/insight/R/get_statistic.R | 35 insight-1.2.0/insight/R/get_varcov.R | 132 +- insight-1.2.0/insight/R/get_variances.R | 60 insight-1.2.0/insight/R/helper_functions.R | 82 - insight-1.2.0/insight/R/is_converged.R | 27 insight-1.2.0/insight/R/model_info.R | 34 insight-1.2.0/insight/R/n_parameters.R | 44 insight-1.2.0/insight/R/null_model.R | 309 ++++ insight-1.2.0/insight/R/print_parameters.R | 20 insight-1.2.0/insight/R/utilities.R | 13 insight-1.2.0/insight/R/utils_get_data.R | 33 insight-1.2.0/insight/R/utils_model_info.R | 3 insight-1.2.0/insight/R/validate_argument.R | 5 insight-1.2.0/insight/build/partial.rdb |binary insight-1.2.0/insight/build/vignette.rds |binary insight-1.2.0/insight/data/efc_insight.rda |only insight-1.2.0/insight/inst/WORDLIST | 5 insight-1.2.0/insight/inst/doc/display.html | 220 +-- insight-1.2.0/insight/inst/doc/export.R | 2 insight-1.2.0/insight/inst/doc/export.Rmd | 2 insight-1.2.0/insight/inst/doc/export.html | 2 insight-1.2.0/insight/inst/doc/newmodels.R |only insight-1.2.0/insight/inst/doc/newmodels.Rmd |only insight-1.2.0/insight/inst/doc/newmodels.html |only insight-1.2.0/insight/man/clean_parameters.Rd | 19 insight-1.2.0/insight/man/efc_insight.Rd |only insight-1.2.0/insight/man/export_table.Rd | 32 insight-1.2.0/insight/man/find_auxiliary.Rd |only insight-1.2.0/insight/man/find_formula.Rd | 69 - 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Title: Streamlined Simulation of Circadian Gene Networks
Description: A user-friendly workflow for simulating circadian clock gene networks.
Despite decades of advances in modeling circadian clock dynamics,
the lack of accessible tools for reproducible simulation workflows
hinders the integration of computational modeling with experimental studies.
'clockSim' addresses this gap by providing models and helper functions
with step-by-step vignettes. This package opens up system-level exploration
of the circadian clock to wet-lab experimentalists, and future development
will include additional clock architectures and other gene circuit models.
Currently implemented models are based on
Leloup and Goldbeter (1998) <doi:10.1177/074873098128999934>.
Author: Ye Yuan [aut, cre, cph]
Maintainer: Ye Yuan <yeyu@umich.edu>
Diff between clockSim versions 0.1.1 dated 2025-04-07 and 0.1.2 dated 2025-04-22
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 6 +++++- README.md |only inst/doc/clock-models.html | 8 ++++---- inst/doc/grid-scan.html | 10 +++++----- inst/doc/noisy-LG-model.html | 8 ++++---- src/odin.c | 7 ++++--- src/registration.c | 14 +++++++------- 9 files changed, 40 insertions(+), 34 deletions(-)
Title: Data Structures for Single Cell Data
Description: Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. See
Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>,
Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>,
Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and
Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for
more details.
Author: Paul Hoffman [aut] ,
Rahul Satija [aut, cre] ,
David Collins [aut] ,
Yuhan Hao [aut] ,
Austin Hartman [aut] ,
Gesmira Molla [aut] ,
Andrew Butler [aut] ,
Tim Stuart [aut] ,
Madeline Kowalski [ctb] ,
Saket Choudhary [ctb] ,
Skylar Li [ctb],
Longda Jia [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between SeuratObject versions 5.0.2 dated 2024-05-08 and 5.1.0 dated 2025-04-22
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SeuratObject-5.1.0/SeuratObject/man/RegisterSparseMatrix.Rd | 54 SeuratObject-5.1.0/SeuratObject/man/RenameAssays.Rd | 72 SeuratObject-5.1.0/SeuratObject/man/RenameCells-StdAssay.Rd | 56 SeuratObject-5.1.0/SeuratObject/man/RenameCells.Rd | 156 SeuratObject-5.1.0/SeuratObject/man/RowMergeSparseMatrices.Rd | 50 SeuratObject-5.1.0/SeuratObject/man/SaveSeuratRds.Rd | 250 SeuratObject-5.1.0/SeuratObject/man/Segmentation-class.Rd | 40 SeuratObject-5.1.0/SeuratObject/man/Segmentation-methods.Rd | 270 SeuratObject-5.1.0/SeuratObject/man/Seurat-class.Rd | 134 SeuratObject-5.1.0/SeuratObject/man/Seurat-validity.Rd | 50 SeuratObject-5.1.0/SeuratObject/man/SeuratCommand-class.Rd | 70 SeuratObject-5.1.0/SeuratObject/man/SeuratObject-options.Rd | 100 SeuratObject-5.1.0/SeuratObject/man/SeuratObject-package.Rd | 92 SeuratObject-5.1.0/SeuratObject/man/Simplify.Rd | 58 SeuratObject-5.1.0/SeuratObject/man/SparseEmptyMatrix.Rd | 34 SeuratObject-5.1.0/SeuratObject/man/SpatialImage-class.Rd | 58 SeuratObject-5.1.0/SeuratObject/man/SpatialImage-methods.Rd | 438 SeuratObject-5.1.0/SeuratObject/man/SplitLayers.Rd | 64 SeuratObject-5.1.0/SeuratObject/man/StdAssay-class.Rd | 136 SeuratObject-5.1.0/SeuratObject/man/StdAssay-validity.Rd | 90 SeuratObject-5.1.0/SeuratObject/man/Stdev.Rd | 72 SeuratObject-5.1.0/SeuratObject/man/StitchMatrix.Rd | 56 SeuratObject-5.1.0/SeuratObject/man/Theta.Rd | 30 SeuratObject-5.1.0/SeuratObject/man/Tool.Rd | 130 SeuratObject-5.1.0/SeuratObject/man/UpdateSeuratObject.Rd | 52 SeuratObject-5.1.0/SeuratObject/man/UpdateSlots.Rd | 36 SeuratObject-5.1.0/SeuratObject/man/VariableFeatures-StdAssay.Rd | 167 SeuratObject-5.1.0/SeuratObject/man/VariableFeatures.Rd | 374 SeuratObject-5.1.0/SeuratObject/man/Version.Rd | 48 SeuratObject-5.1.0/SeuratObject/man/WhichCells.Rd | 142 SeuratObject-5.1.0/SeuratObject/man/aggregate.Rd | 122 SeuratObject-5.1.0/SeuratObject/man/angles.Rd | 76 SeuratObject-5.1.0/SeuratObject/man/as.Centroids.Rd | 80 SeuratObject-5.1.0/SeuratObject/man/as.Graph.Rd | 102 SeuratObject-5.1.0/SeuratObject/man/as.Neighbor.Rd | 46 SeuratObject-5.1.0/SeuratObject/man/as.Seurat.Rd | 40 SeuratObject-5.1.0/SeuratObject/man/as.list.SeuratCommand.Rd | 76 SeuratObject-5.1.0/SeuratObject/man/as.matrix.LogMap.Rd | 76 SeuratObject-5.1.0/SeuratObject/man/as.sparse.Rd | 70 SeuratObject-5.1.0/SeuratObject/man/cash-.Assay.Rd | 102 SeuratObject-5.1.0/SeuratObject/man/cash-.Assay5.Rd | 78 SeuratObject-5.1.0/SeuratObject/man/cash-.Seurat.Rd | 148 SeuratObject-5.1.0/SeuratObject/man/cash-.SeuratCommand.Rd | 66 SeuratObject-5.1.0/SeuratObject/man/cash-.StdAssay.Rd | 82 SeuratObject-5.1.0/SeuratObject/man/colMeans-Assay-method.Rd | 120 SeuratObject-5.1.0/SeuratObject/man/colMeans-Seurat-method.Rd | 120 SeuratObject-5.1.0/SeuratObject/man/dim.Assay.Rd | 74 SeuratObject-5.1.0/SeuratObject/man/dim.Assay5.Rd | 62 SeuratObject-5.1.0/SeuratObject/man/dim.DimReduc.Rd | 142 SeuratObject-5.1.0/SeuratObject/man/dim.Seurat.Rd | 80 SeuratObject-5.1.0/SeuratObject/man/dim.StdAssay.Rd | 66 SeuratObject-5.1.0/SeuratObject/man/dimnames.Assay.Rd | 126 SeuratObject-5.1.0/SeuratObject/man/dimnames.Assay5.Rd | 96 SeuratObject-5.1.0/SeuratObject/man/dimnames.Seurat.Rd | 122 SeuratObject-5.1.0/SeuratObject/man/dimnames.StdAssay.Rd | 92 SeuratObject-5.1.0/SeuratObject/man/dot-AssayClass.Rd | 48 SeuratObject-5.1.0/SeuratObject/man/dot-BPMatrixMode.Rd | 56 SeuratObject-5.1.0/SeuratObject/man/dot-CalcN.Rd | 50 SeuratObject-5.1.0/SeuratObject/man/dot-CheckFmargin.Rd | 56 SeuratObject-5.1.0/SeuratObject/man/dot-ClassPkg.Rd | 68 SeuratObject-5.1.0/SeuratObject/man/dot-Collections.Rd | 68 SeuratObject-5.1.0/SeuratObject/man/dot-Contains.Rd | 46 SeuratObject-5.1.0/SeuratObject/man/dot-CreateStdAssay.Rd | 218 SeuratObject-5.1.0/SeuratObject/man/dot-DefaultFOV.Rd | 40 SeuratObject-5.1.0/SeuratObject/man/dot-Deprecate.Rd | 152 SeuratObject-5.1.0/SeuratObject/man/dot-DiskLoad.Rd | 98 SeuratObject-5.1.0/SeuratObject/man/dot-DollarNames.Assay.Rd | 54 SeuratObject-5.1.0/SeuratObject/man/dot-DollarNames.Assay5.Rd | 52 SeuratObject-5.1.0/SeuratObject/man/dot-DollarNames.Seurat.Rd | 52 SeuratObject-5.1.0/SeuratObject/man/dot-DollarNames.SeuratCommand.Rd | 62 SeuratObject-5.1.0/SeuratObject/man/dot-DollarNames.StdAssay.Rd | 72 SeuratObject-5.1.0/SeuratObject/man/dot-FileMove.Rd | 72 SeuratObject-5.1.0/SeuratObject/man/dot-FilePath.Rd | 56 SeuratObject-5.1.0/SeuratObject/man/dot-FilterObjects.Rd | 66 SeuratObject-5.1.0/SeuratObject/man/dot-FindObject.Rd | 70 SeuratObject-5.1.0/SeuratObject/man/dot-GetConsensusFeatures.Rd |only SeuratObject-5.1.0/SeuratObject/man/dot-GetMethod.Rd | 54 SeuratObject-5.1.0/SeuratObject/man/dot-GetVariableFeatures.Rd |only SeuratObject-5.1.0/SeuratObject/man/dot-IsFutureSeurat.Rd | 62 SeuratObject-5.1.0/SeuratObject/man/dot-KeyPattern.Rd | 46 SeuratObject-5.1.0/SeuratObject/man/dot-MARGIN.Rd | 36 SeuratObject-5.1.0/SeuratObject/man/dot-PropagateList.Rd | 70 SeuratObject-5.1.0/SeuratObject/man/dot-RandomKey.Rd | 64 SeuratObject-5.1.0/SeuratObject/man/dot-SparseSlots.Rd | 70 SeuratObject-5.1.0/SeuratObject/man/dot-Subobjects.Rd | 76 SeuratObject-5.1.0/SeuratObject/man/droplevels.LogMap.Rd | 80 SeuratObject-5.1.0/SeuratObject/man/intersect.LogMap.Rd | 80 SeuratObject-5.1.0/SeuratObject/man/labels.LogMap.Rd | 120 SeuratObject-5.1.0/SeuratObject/man/merge.Assay.Rd | 104 SeuratObject-5.1.0/SeuratObject/man/merge.Assay5.Rd | 94 SeuratObject-5.1.0/SeuratObject/man/merge.DimReduc.Rd | 74 SeuratObject-5.1.0/SeuratObject/man/merge.Seurat.Rd | 186 SeuratObject-5.1.0/SeuratObject/man/merge.StdAssay.Rd | 78 SeuratObject-5.1.0/SeuratObject/man/names.Seurat.Rd | 82 SeuratObject-5.1.0/SeuratObject/man/old-assign.Rd | 58 SeuratObject-5.1.0/SeuratObject/man/oldseurat-class.Rd | 150 SeuratObject-5.1.0/SeuratObject/man/pbmc_small.Rd | 72 SeuratObject-5.1.0/SeuratObject/man/print.DimReduc.Rd | 94 SeuratObject-5.1.0/SeuratObject/man/reexports.Rd | 46 SeuratObject-5.1.0/SeuratObject/man/roxygen/meta.R | 38 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/desc-validity.R | 4 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/lifecycle-deprecated.R | 10 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/lifecycle-experimental.R | 12 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/lifecycle-superseded.R | 6 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/method-cells.R | 6 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/method-features.R | 8 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/method-lengths.R | 10 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/method-show.R | 6 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/method-stdassay.R | 16 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/name-oldv.R | 16 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/note-reqdpkg.R | 6 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/param-dots-ignored.R | 2 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/param-dots-method.R | 2 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/param-verbose.R | 2 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/return-null.R | 2 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/return-show.R | 4 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/section-future.R | 26 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/section-progressr.R | 16 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/seealso-methods.R | 2 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/slot-key.R | 8 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/slot-misc.R | 2 SeuratObject-5.1.0/SeuratObject/man/roxygen/templates/slot-stdassay.R | 40 SeuratObject-5.1.0/SeuratObject/man/s4list.Rd | 154 SeuratObject-5.1.0/SeuratObject/man/set-if-na.Rd | 90 SeuratObject-5.1.0/SeuratObject/man/set-if-null.Rd | 88 SeuratObject-5.1.0/SeuratObject/man/show-Assay-method.Rd | 50 SeuratObject-5.1.0/SeuratObject/man/show-DimReduc-method.Rd | 54 SeuratObject-5.1.0/SeuratObject/man/show-Graph-method.Rd | 42 SeuratObject-5.1.0/SeuratObject/man/show-LogMap-method.Rd | 38 SeuratObject-5.1.0/SeuratObject/man/show-Seurat-method.Rd | 42 SeuratObject-5.1.0/SeuratObject/man/show-SeuratCommand-method.Rd | 44 SeuratObject-5.1.0/SeuratObject/man/show-StdAssay-method.Rd | 66 SeuratObject-5.1.0/SeuratObject/man/show-oldseurat-method.Rd | 40 SeuratObject-5.1.0/SeuratObject/man/split.Assay.Rd | 98 SeuratObject-5.1.0/SeuratObject/man/split.Assay5.Rd | 166 SeuratObject-5.1.0/SeuratObject/man/split.Seurat.Rd | 116 SeuratObject-5.1.0/SeuratObject/man/split.StdAssay.Rd | 190 SeuratObject-5.1.0/SeuratObject/man/sub-.Assay.Rd | 120 SeuratObject-5.1.0/SeuratObject/man/sub-.Assay5.Rd | 90 SeuratObject-5.1.0/SeuratObject/man/sub-.DimReduc.Rd | 100 SeuratObject-5.1.0/SeuratObject/man/sub-.SeuratCommand.Rd | 70 SeuratObject-5.1.0/SeuratObject/man/sub-.StdAssay.Rd | 90 SeuratObject-5.1.0/SeuratObject/man/sub-LogMap-method.Rd | 132 SeuratObject-5.1.0/SeuratObject/man/sub-sub-.Assay.Rd | 156 SeuratObject-5.1.0/SeuratObject/man/sub-sub-.Assay5.Rd | 116 SeuratObject-5.1.0/SeuratObject/man/sub-sub-.DimReduc.Rd | 90 SeuratObject-5.1.0/SeuratObject/man/sub-sub-.Seurat.Rd | 174 SeuratObject-5.1.0/SeuratObject/man/sub-sub-.StdAssay.Rd | 156 SeuratObject-5.1.0/SeuratObject/man/sub-sub-LogMap-internal-method.Rd | 54 SeuratObject-5.1.0/SeuratObject/man/sub-subset-Seurat-NULL.Rd | 94 SeuratObject-5.1.0/SeuratObject/man/sub-subset-Seurat-character-missing-StdAssay-method.Rd | 96 SeuratObject-5.1.0/SeuratObject/man/sub-subset-Seurat.Rd | 138 SeuratObject-5.1.0/SeuratObject/man/subset.Assay.Rd | 88 SeuratObject-5.1.0/SeuratObject/man/subset.Assay5.Rd | 78 SeuratObject-5.1.0/SeuratObject/man/subset.DimReduc.Rd | 66 SeuratObject-5.1.0/SeuratObject/man/subset.Seurat.Rd | 146 SeuratObject-5.1.0/SeuratObject/man/subset.StdAssay.Rd | 82 SeuratObject-5.1.0/SeuratObject/man/v5-assay-summaries.Rd | 86 SeuratObject-5.1.0/SeuratObject/tests |only 282 files changed, 34853 insertions(+), 34618 deletions(-)
Title: Inference Based on Non-Probability Samples
Description: Statistical inference with non-probability samples when auxiliary information from external sources such as probability samples or population totals or means is available. The package implements various methods such as inverse probability (propensity score) weighting, mass imputation and doubly robust approach. Details can be found in: Chen et al. (2020) <doi:10.1080/01621459.2019.1677241>, Yang et al. (2020) <doi:10.1111/rssb.12354>, Kim et al. (2021) <doi:10.1111/rssa.12696>, Yang et al. (2021) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2021001/article/00004-eng.htm> and Wu (2022) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2022002/article/00002-eng.htm>.
Author: Lukasz Chrostowski [aut, ctb],
Maciej Beresewicz [aut, cre] ,
Piotr Chlebicki [aut, ctb]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>
Diff between nonprobsvy versions 0.2.0 dated 2025-03-27 and 0.2.1 dated 2025-04-22
nonprobsvy-0.2.0/nonprobsvy/R/est_method_dr.R |only nonprobsvy-0.2.1/nonprobsvy/DESCRIPTION | 8 nonprobsvy-0.2.1/nonprobsvy/MD5 | 60 ++-- nonprobsvy-0.2.1/nonprobsvy/NAMESPACE | 8 nonprobsvy-0.2.1/nonprobsvy/NEWS.md | 15 + nonprobsvy-0.2.1/nonprobsvy/R/boot_ipw.R | 4 nonprobsvy-0.2.1/nonprobsvy/R/check_balance.R | 89 ------ nonprobsvy-0.2.1/nonprobsvy/R/data.R | 2 nonprobsvy-0.2.1/nonprobsvy/R/est_method_ipw.R | 28 - nonprobsvy-0.2.1/nonprobsvy/R/method_glm.R | 8 nonprobsvy-0.2.1/nonprobsvy/R/method_ps.R | 91 +++--- nonprobsvy-0.2.1/nonprobsvy/R/methods.R | 145 +++++++++- nonprobsvy-0.2.1/nonprobsvy/R/methods_not_implemented.R | 5 nonprobsvy-0.2.1/nonprobsvy/R/nonprob_documentation.R | 7 nonprobsvy-0.2.1/nonprobsvy/R/nonprob_dr.R | 28 + nonprobsvy-0.2.1/nonprobsvy/R/nonprob_ipw.R | 6 nonprobsvy-0.2.1/nonprobsvy/R/plot.R |only nonprobsvy-0.2.1/nonprobsvy/R/summary.R | 2 nonprobsvy-0.2.1/nonprobsvy/R/variance_ipw.R | 8 nonprobsvy-0.2.1/nonprobsvy/inst/tinytest/test_check_balance.R | 46 ++- nonprobsvy-0.2.1/nonprobsvy/inst/tinytest/test_ipw.R | 3 nonprobsvy-0.2.1/nonprobsvy/inst/tinytest/test_vars_selection.R | 108 +++---- nonprobsvy-0.2.1/nonprobsvy/man/check_balance.Rd | 9 nonprobsvy-0.2.1/nonprobsvy/man/coef.nonprob.Rd |only nonprobsvy-0.2.1/nonprobsvy/man/confint.nonprob.Rd | 18 + nonprobsvy-0.2.1/nonprobsvy/man/extract.Rd |only nonprobsvy-0.2.1/nonprobsvy/man/jvs.Rd | 2 nonprobsvy-0.2.1/nonprobsvy/man/nobs.nonprob.Rd |only nonprobsvy-0.2.1/nonprobsvy/man/nonprob.Rd | 7 nonprobsvy-0.2.1/nonprobsvy/man/plot.nonprob.Rd |only nonprobsvy-0.2.1/nonprobsvy/man/summary.nonprob.Rd | 2 nonprobsvy-0.2.1/nonprobsvy/man/update.nonprob.Rd | 2 nonprobsvy-0.2.1/nonprobsvy/man/weights.nonprob.Rd | 19 + nonprobsvy-0.2.1/nonprobsvy/src/nonprobCV_cpp.cpp | 18 - 34 files changed, 472 insertions(+), 276 deletions(-)
Title: Tools for Managing Imaging FlowCytobot (IFCB) Data
Description: A comprehensive suite of tools for managing, processing, and analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports quality control, geospatial analysis, and preparation of IFCB data for publication in databases like <https://www.gbif.org>, <https://www.obis.org>, <https://emodnet.ec.europa.eu/en>, <https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package integrates with the MATLAB 'ifcb-analysis' tool, which is described in Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides features for working with raw, manually classified, and machine learning–classified image datasets. Key functionalities include image extraction, particle size distribution analysis, taxonomic data handling, and biomass concentration calculations, essential for plankton research.
Author: Anders Torstensson [aut, cre] ,
Kendra Hayashi [ctb] ,
Jamie Enslein [ctb],
Raphael Kudela [ctb] ,
Alle Lie [ctb] ,
Jayme Smith [ctb] ,
DTO-BioFlow [fnd] ,
SBDI [fnd]
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Diff between iRfcb versions 0.5.0 dated 2025-04-15 and 0.5.1 dated 2025-04-22
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ R/ifcb_download_dashboard_data.R | 2 +- R/ifcb_prepare_whoi_plankton.R | 2 +- inst/CITATION | 4 ++-- inst/doc/a-general-tutorial.html | 4 ++-- inst/doc/qc-tutorial.html | 4 ++-- man/ifcb_download_dashboard_data.Rd | 2 +- man/ifcb_prepare_whoi_plankton.Rd | 2 +- tests/testthat/test-ifcb_extract_biovolumes.R | 15 +++++++++++++++ tests/testthat/test-ifcb_summarize_biovolumes.R | 6 ++++++ 12 files changed, 51 insertions(+), 24 deletions(-)
Title: Generalized Bayesian Optimal Phase II Design (G-BOP2)
Description: Provides functions for implementing the Generalized Bayesian Optimal Phase II (G-BOP2) design using various Particle Swarm Optimization (PSO) algorithms, including:
- PSO-Default, based on Kennedy and Eberhart (1995) <doi:10.1109/ICNN.1995.488968>, "Particle Swarm Optimization";
- PSO-Quantum, based on Sun, Xu, and Feng (2004) <doi:10.1109/ICCIS.2004.1460396>, "A Global Search Strategy of Quantum-Behaved Particle Swarm Optimization";
- PSO-Dexp, based on Stehlík et al. (2024) <doi:10.1016/j.asoc.2024.111913>, "A Double Exponential Particle Swarm Optimization with Non-Uniform Variates as Stochastic Tuning and Guaranteed Convergence to a Global Optimum with Sample Applications to Finding Optimal Exact Designs in Biostatistics";
- and PSO-GO.
Author: Xinying Fang [aut],
Wanni Lei [aut, cre],
Shouhao Zhou [aut]
Maintainer: Wanni Lei <wanni.lei17@gmail.com>
Diff between GBOP2 versions 0.1.2 dated 2025-04-09 and 0.1.3 dated 2025-04-22
DESCRIPTION | 12 MD5 | 39 R/GBOP2_maxP_TE.gbop2.R | 8 R/GBOP2_maxP_dualE.gbop2.R | 6 R/GBOP2_maxP_singleE.gbop2.R | 8 R/GBOP2_minSS_TE.gbop2.R | 53 R/GBOP2_minSS_dualE.gbop2.R | 6 R/GBOP2_minSS_singleE.gbop2.R | 6 inst/doc/Vignette.html | 3645 +++++++++++++++++++++---- man/GBOP2_maxP_TE.Rd | 2 man/GBOP2_maxP_dualE.Rd | 2 man/GBOP2_maxP_singleE.Rd | 8 man/GBOP2_minSS_TE.Rd | 18 man/GBOP2_minSS_dualE.Rd | 6 man/GBOP2_minSS_singleE.Rd | 6 src/Calculation2_original.cpp | 7 src/Calculation_minimizeN_twolambda_update.cpp | 73 src/Calculation_twoboundaries_jsm.cpp | 109 src/GBOP2_types.h |only src/RcppExports.cpp | 1 vignettes/Vignette.Rmd | 101 21 files changed, 3378 insertions(+), 738 deletions(-)
Title: Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control
Description: Implementation of Sparse-group SLOPE (SGS) (Feser and Evangelou (2023) <doi:10.48550/arXiv.2305.09467>) models. Linear and logistic regression models are supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported. In addition, a general Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) implementation is provided. Group SLOPE (gSLOPE) (Brzyski et al. (2019) <doi:10.1080/01621459.2017.1411269>) and group-based OSCAR models (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) are also implemented. All models are available with strong screening rules (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) for computational speed-up.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between sgs versions 0.3.5 dated 2025-03-04 and 0.3.6 dated 2025-04-22
DESCRIPTION | 8 ++--- MD5 | 50 ++++++++++++++++++------------------- R/as_sgs.R | 10 ++----- R/fit_goscar.R | 9 +++--- R/fit_goscar_cv.R | 7 ++--- R/fit_gslope.R | 8 +++-- R/fit_gslope_cv.R | 7 ++--- R/fit_sgo.R | 7 ++--- R/fit_sgo_cv.R | 7 ++--- R/fit_sgs.R | 5 ++- R/fit_sgs_cv.R | 7 ++--- R/fitting_code.R | 19 +++++++++----- R/gen_toy_data.R | 2 - R/global_wrapper_code.R | 14 +++++----- R/screen.R | 14 ++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/reproducible_example.html | 14 +++++----- man/fit_goscar.Rd | 7 +++-- man/fit_goscar_cv.Rd | 7 +++-- man/fit_gslope.Rd | 7 +++-- man/fit_gslope_cv.Rd | 7 +++-- man/fit_sgo.Rd | 5 ++- man/fit_sgo_cv.Rd | 5 ++- man/fit_sgs.Rd | 5 ++- man/fit_sgs_cv.Rd | 5 ++- 26 files changed, 138 insertions(+), 98 deletions(-)
More information about HiCocietyExample at CRAN
Permanent link
Title: Data Collection from the Central Bank of Brazil
Description: Provides tools to facilitate the access and processing of data
from the Central Bank of Brazil API. The package allows users
to retrieve economic and financial data, transforming them into usable
tabular formats for further analysis. The data is obtained from the
Central Bank of Brazil API: <https://api.bcb.gov.br/dados/serie/bcdata.sgs.{series_code}/dados?formato=json&dataInicial={start_date}&dataFinal={end_date}>.
Author: Paulo Icaro [aut],
Lissandro Sousa [cre, aut],
Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Sousa <lisandrosousa54@gmail.com>
Diff between BacenAPI versions 0.2.0 dated 2025-03-31 and 0.3.1 dated 2025-04-22
BacenAPI-0.2.0/BacenAPI/man/bacen_api.Rd |only BacenAPI-0.3.1/BacenAPI/DESCRIPTION | 10 +- BacenAPI-0.3.1/BacenAPI/MD5 | 21 ++--- BacenAPI-0.3.1/BacenAPI/NAMESPACE | 1 BacenAPI-0.3.1/BacenAPI/R/bacen_api.R | 116 +++++++++------------------- BacenAPI-0.3.1/BacenAPI/R/bacen_search.R | 9 -- BacenAPI-0.3.1/BacenAPI/R/bacen_series.R | 92 +++++++++++----------- BacenAPI-0.3.1/BacenAPI/R/bacen_url.R | 13 --- BacenAPI-0.3.1/BacenAPI/README.md | 52 +----------- BacenAPI-0.3.1/BacenAPI/man/bacen_search.Rd | 3 BacenAPI-0.3.1/BacenAPI/man/bacen_series.Rd | 64 +++++++-------- BacenAPI-0.3.1/BacenAPI/man/bacen_url.Rd | 56 ++++++------- 12 files changed, 170 insertions(+), 267 deletions(-)
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] ,
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifen [...truncated...]
Maintainer: Jiaming Yuan <jm.yuan@outlook.com>
Diff between xgboost versions 1.7.9.1 dated 2025-03-26 and 1.7.10.1 dated 2025-04-22
DESCRIPTION | 8 - MD5 | 18 ++-- configure | 124 +++++++++++++++++++++++++----- configure.ac | 17 ++-- demo/caret_wrapper.R | 1 inst/doc/discoverYourData.html | 4 inst/doc/xgboost.pdf |binary inst/doc/xgboostPresentation.html | 8 - inst/doc/xgboostfromJSON.html | 155 +++++++++++++++++++------------------- src/Makevars.in | 13 ++- 10 files changed, 224 insertions(+), 124 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.3.0 dated 2025-03-29 and 0.4.0 dated 2025-04-22
DESCRIPTION | 12 ++-- MD5 | 27 +++++----- NAMESPACE | 4 + NEWS.md | 13 ++++ R/grouped_tbl_pivot_wider.R |only R/install_dependencies.R | 17 +++++- R/plot_proportions.R | 88 ++++++++++++++++++++++++++++----- R/step_with_na.R | 2 README.md | 3 - inst/WORDLIST | 2 man/grouped_tbl_pivot_wider.Rd |only man/install_dependencies.Rd | 3 - man/plot_proportions.Rd | 55 +++++++++++++++++--- man/step_with_na.Rd | 2 tests/testthat/test-grouped_tbl.R |only tests/testthat/test-plot_proportions.R | 22 ++++++++ 16 files changed, 204 insertions(+), 46 deletions(-)
Title: An Empirical Model for Underdispersed Count Data
Description: Count regression models for underdispersed small counts (lambda < 20) based on the three-parameter exponentially weighted Poisson distribution of Ridout & Besbeas (2004) <DOI:10.1191/1471082X04st064oa>.
Author: Philipp Boersch-Supan [aut, cre]
,
James Clarke [aut]
Maintainer: Philipp Boersch-Supan <pboesu@gmail.com>
Diff between ewp versions 0.1.1 dated 2024-06-26 and 0.1.2 dated 2025-04-22
DESCRIPTION | 10 MD5 | 19 - NAMESPACE | 3 NEWS.md | 5 R/ewp_reg.R | 249 ++++++++++++++++++++++ README.md | 412 +++++++++++++++++++++++++++++++------ man/ewp_reg.Rd | 7 man/figures/README-residuals-1.png |binary man/mmean.Rd |only tests/testthat.R | 25 +- tests/testthat/test-ewp_reg.R | 2 11 files changed, 642 insertions(+), 90 deletions(-)
Title: A Toolkit for Using Whole Building Simulation Program
'EnergyPlus'
Description: A rich toolkit of using the whole building
simulation program 'EnergyPlus'(<https://energyplus.net>), which
enables programmatic navigation, modification of 'EnergyPlus' models
and makes it less painful to do parametric simulations and analysis.
Author: Hongyuan Jia [aut, cre, cph] ,
Adrian Chong [aut]
Maintainer: Hongyuan Jia <hongyuanjia@cqust.edu.cn>
Diff between eplusr versions 0.16.2 dated 2023-08-25 and 0.16.3 dated 2025-04-22
DESCRIPTION | 14 LICENSE | 2 MD5 | 93 NAMESPACE | 717 +- NEWS.md | 36 R/assert.R | 374 - R/constants.R | 74 R/err.R | 864 +-- R/format.R | 2434 ++++----- R/geom.R | 4 R/group.R | 4 R/idd.R | 2766 +++++------ R/iddobj.R | 3960 ++++++++-------- R/idf.R | 21 R/idfobj.R | 4094 ++++++++-------- R/impl-epw.R | 5476 +++++++++++----------- R/impl-geom.R | 3664 +++++++-------- R/impl-idd.R | 2150 ++++---- R/impl-idf.R | 9252 +++++++++++++++++++------------------- R/impl.R | 624 +- R/install.R | 2004 ++++---- R/job.R | 13 R/options.R | 504 +- R/param.R | 8 R/parse.R | 3296 ++++++------- R/run.R | 4988 ++++++++++---------- R/utils.R | 1098 ++-- README.md | 418 - man/EplusGroupJob.Rd | 4 man/EplusJob.Rd | 15 man/Idf.Rd | 19 man/IdfGeometry.Rd | 2 man/IdfObject.Rd | 2 man/ParametricJob.Rd | 8 man/energyplus.Rd | 492 +- man/install_eplus.Rd | 286 - man/print.TransitionErrFile.Rd |only man/read_idfeditor_copy.Rd | 2 man/run_model.Rd | 4 tests/testthat/helper-eplus.R | 16 tests/testthat/test-geom.R | 99 tests/testthat/test-idf.R | 2791 +++++------ tests/testthat/test-impl-idd.R | 770 +-- tests/testthat/test-impl-viewer.R | 199 tests/testthat/test-install.R | 88 tests/testthat/test-parse.R | 1174 ++-- tests/testthat/test-transition.R | 5402 +++++++++++----------- tests/testthat/test-viewer.R | 143 48 files changed, 30460 insertions(+), 30008 deletions(-)
Title: SciViews - Main package
Description: Functions to install SciViews additions to R, and more
tools.
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between SciViews versions 0.9-13.1 dated 2019-11-16 and 0.9-13.2 dated 2025-04-22
DESCRIPTION | 14 +-- MD5 | 40 ++++----- R/SciViews-package.R | 11 +- R/colors.R | 4 R/correlation.R | 12 +- R/panels.R | 22 ++--- R/panels.diag.R | 14 +-- R/pcomp.R | 24 ++--- R/vectorplot.R | 4 inst/CITATION | 27 ++---- man/SciViews-package.Rd | 20 ++++ man/colors.Rd | 23 ++--- man/correlation.Rd | 111 ++++++++++++++++---------- man/enum.Rd | 12 +- man/ln.Rd | 21 +++-- man/nr.Rd | 16 ++- man/panels.Rd | 166 ++++++++++++++++++++++++++++------------ man/panels.diag.Rd | 116 ++++++++++++++++++++-------- man/pcomp.Rd | 198 ++++++++++++++++++++++++++++++------------------ man/timing.Rd | 8 - man/vectorplot.Rd | 59 ++++++++++---- 21 files changed, 583 insertions(+), 339 deletions(-)
Title: Generalized Additive Mixed Models using 'mgcv' and 'lme4'
Description: Estimate generalized additive mixed models via a version of
function gamm() from 'mgcv', using 'lme4' for estimation.
Author: Simon Wood [aut, cre],
Fabian Scheipl [aut]
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between gamm4 versions 0.2-6 dated 2020-04-03 and 0.2-7 dated 2025-04-22
ChangeLog | 7 +++++++ DESCRIPTION | 19 ++++++++++++++----- MD5 | 9 +++++---- R/gamm4.r | 9 ++++----- README.md |only man/gamm4.Rd | 8 ++++---- 6 files changed, 34 insertions(+), 18 deletions(-)
Title: Useful Wrappers Around Commonly Used Functions
Description: The main functionalities of 'wrappedtools' are:
adding backticks to variable names; rounding to desired precision
with special case for p-values;
selecting columns based on pattern and storing their position, name,
and backticked name; computing and formatting of descriptive statistics
(e.g. mean±SD), comparing groups and creating publication-ready tables with
descriptive statistics and p-values; creating specialized plots for
correlation matrices. Functions were mainly written for my own daily work or
teaching, but may be of use to others as well.
Author: Andreas Busjahn [cre, aut] ,
Franziska Eidloth [aut],
Bilal Asser [aut]
Maintainer: Andreas Busjahn <andreas@busjahn.net>
Diff between wrappedtools versions 0.9.6 dated 2024-10-10 and 0.9.7 dated 2025-04-22
DESCRIPTION | 14 + MD5 | 30 ++-- NAMESPACE | 3 NEWS.md | 7 R/basefunctions.R | 111 +++++++++++++++ R/descriptives.R | 63 +++++++- R/pkgstart.R | 2 R/tests.R | 234 ++++++++++++++++++++++++-------- build/vignette.rds |binary inst/doc/wrappedtools.html | 6 man/compare2numvars.Rd | 22 ++- man/identical_cols.Rd |only man/mean_cl_boot.Rd |only man/median_cl_boot.Rd | 13 + man/wrappedtools-package.Rd | 1 tests/testthat/compare2numvars_out.rda |binary tests/testthat/test-compare_2_numvars.R | 13 + 17 files changed, 431 insertions(+), 88 deletions(-)
Title: Exporting Tools for 'rtables'
Description: Designed to create and display complex tables with R, the
'rtables' R package allows cells in an 'rtables' object to contain any
high-dimensional data structure, which can then be displayed with
cell-specific formatting instructions. Additionally, the
'rtables.officer' package supports export formats related to the
Microsoft Office software suite, including Microsoft Word ('docx') and
Microsoft PowerPoint ('pptx').
Author: Gabriel Becker [ctb],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [aut] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rtables.officer versions 0.0.2 dated 2025-01-17 and 0.1.0 dated 2025-04-22
rtables.officer-0.0.2/rtables.officer/tests/testthat/Rplots.pdf |only rtables.officer-0.0.2/rtables.officer/vignettes/images |only rtables.officer-0.1.0/rtables.officer/DESCRIPTION | 46 - rtables.officer-0.1.0/rtables.officer/MD5 | 48 - rtables.officer-0.1.0/rtables.officer/NAMESPACE | 2 rtables.officer-0.1.0/rtables.officer/NEWS.md | 10 rtables.officer-0.1.0/rtables.officer/R/add_flextable_separators.R |only rtables.officer-0.1.0/rtables.officer/R/as_flextable.R | 412 +-------- rtables.officer-0.1.0/rtables.officer/R/export_as_docx.R | 173 ++-- rtables.officer-0.1.0/rtables.officer/R/package.R | 1 rtables.officer-0.1.0/rtables.officer/R/theme_defaults.R |only rtables.officer-0.1.0/rtables.officer/README.md | 82 + rtables.officer-0.1.0/rtables.officer/build/vignette.rds |binary rtables.officer-0.1.0/rtables.officer/inst/WORDLIST | 3 rtables.officer-0.1.0/rtables.officer/inst/doc/export_rlistings.R |only rtables.officer-0.1.0/rtables.officer/inst/doc/export_rlistings.Rmd |only rtables.officer-0.1.0/rtables.officer/inst/doc/export_rlistings.html |only rtables.officer-0.1.0/rtables.officer/inst/doc/rtables.officer.R | 164 ++- rtables.officer-0.1.0/rtables.officer/inst/doc/rtables.officer.Rmd | 235 +++-- rtables.officer-0.1.0/rtables.officer/inst/doc/rtables.officer.html | 425 ++++++---- rtables.officer-0.1.0/rtables.officer/man/add_flextable_separators.Rd |only rtables.officer-0.1.0/rtables.officer/man/export_as_docx.Rd | 53 - rtables.officer-0.1.0/rtables.officer/man/figures/README-unnamed-chunk-2-1.png |only rtables.officer-0.1.0/rtables.officer/man/rtables.officer-package.Rd | 6 rtables.officer-0.1.0/rtables.officer/man/tt_to_flextable.Rd | 48 - rtables.officer-0.1.0/rtables.officer/tests/testthat/test-add_flextable_separators.R |only rtables.officer-0.1.0/rtables.officer/tests/testthat/test-as_flextable.R | 106 ++ rtables.officer-0.1.0/rtables.officer/tests/testthat/test-export_as_docx.R | 18 rtables.officer-0.1.0/rtables.officer/tests/testthat/test-pagination.R |only rtables.officer-0.1.0/rtables.officer/vignettes/export_rlistings.Rmd |only rtables.officer-0.1.0/rtables.officer/vignettes/rtables.officer.Rmd | 235 +++-- 31 files changed, 1191 insertions(+), 876 deletions(-)
More information about rtables.officer at CRAN
Permanent link
Title: Tools for Statistical Content Analysis
Description: A framework for statistical analysis in content analysis. In addition to a pipeline for preprocessing text corpora and linking to the latent Dirichlet allocation from the 'lda' package, plots are offered for the descriptive analysis of text corpora and topic models. In addition, an implementation of Chang's intruder words and intruder topics is provided. Sample data for the vignette is included in the toscaData package, which is available on gitHub: <https://github.com/Docma-TU/toscaData>.
Author: Lars Koppers [aut, cre] ,
Jonas Rieger [aut] ,
Karin Boczek [ctb] ,
Gerret von Nordheim [ctb]
Maintainer: Lars Koppers <koppers@statistik.tu-dortmund.de>
Diff between tosca versions 0.3-2 dated 2021-10-28 and 0.3-4 dated 2025-04-22
DESCRIPTION | 9 MD5 | 274 NAMESPACE | 156 R/LDAgen.R | 214 R/LDAprep.R | 134 R/as.corpus.textmeta.R | 116 R/as.meta.R | 110 R/as.textmeta.corpus.R | 248 R/cleanTexts.R | 254 R/clusterTopics.R | 112 R/deleteAndRenameDuplicates.R | 294 R/duplist.R | 384 R/filterCount.R | 130 R/filterDate.R | 146 R/filterID.R | 104 R/filterWord.R | 256 R/intruderTopics.R | 332 R/intruderWords.R | 266 R/makeWordlist.R | 102 R/mergeLDA.R | 96 R/mergeTextmeta.R | 160 R/plotArea.R | 272 R/plotFreq.R | 472 R/plotHeat.R | 222 R/plotScot.R | 316 R/plotTopic.R | 406 R/plotTopicWord.R | 594 - R/plotWordSub.R | 438 R/plotWordpt.R | 608 - R/precisionrecall.R | 157 R/readTextmeta.R | 392 R/readWhatsApp.R | 316 R/readWiki.R | 154 R/readWikinews.R | 150 R/removeXML.R | 4902 +++++----- R/sampling.R | 290 R/showMeta.R | 100 R/showTexts.R | 114 R/textmeta.R | 356 R/tidy.textmeta.R | 220 R/topTexts.R | 124 R/topWords.R | 155 R/topicCoherence.R | 114 R/topicsInText.R | 210 build/vignette.rds |binary inst/CITATION | 36 inst/doc/Vignette.R | 16 inst/doc/Vignette.Rmd | 1192 +- inst/doc/Vignette.pdf |binary man/LDAgen.Rd | 170 man/LDAprep.Rd | 90 man/as.corpus.textmeta.Rd | 98 man/as.meta.Rd | 82 man/as.textmeta.corpus.Rd | 148 man/cleanTexts.Rd | 160 man/clusterTopics.Rd | 128 man/deleteAndRenameDuplicates.Rd | 140 man/duplist.Rd | 126 man/filterCount.Rd | 112 man/filterDate.Rd | 138 man/filterID.Rd | 104 man/filterWord.Rd | 162 man/intruderTopics.Rd | 168 man/intruderWords.Rd | 132 man/makeWordlist.Rd | 78 man/mergeLDA.Rd | 88 man/mergeTextmeta.Rd | 94 man/plotArea.Rd | 150 man/plotFreq.Rd | 246 man/plotHeat.Rd | 144 man/plotScot.Rd | 210 man/plotTopic.Rd | 252 man/plotTopicWord.Rd | 330 man/plotWordSub.Rd | 276 man/plotWordpt.Rd | 318 man/precisionRecall.Rd | 92 man/readTextmeta.Rd | 142 man/readWhatsApp.Rd | 50 man/readWiki.Rd | 78 man/readWikinews.Rd | 46 man/removeXML.Rd | 120 man/sampling.Rd | 78 man/showMeta.Rd | 84 man/showTexts.Rd | 78 man/textmeta.Rd | 130 man/tidy.textmeta.Rd | 92 man/topTexts.Rd | 118 man/topWords.Rd | 126 man/topicCoherence.Rd | 114 man/topicsInText.Rd | 132 tests/run-all.R | 20 tests/testthat/data/WhatsApp/WhatsApp1.html | 334 tests/testthat/data/WhatsApp/WhatsApp2.html | 352 tests/testthat/data/Wikinews/Wikinews1.xml | 632 - tests/testthat/data/Wikinews/Wikinews2.xml | 382 tests/testthat/data/readTextmeta.csv | 16 tests/testthat/data/test-k3i20b70s24602alpha0.33eta0.33_orig.csv | 24 tests/testthat/data/topicsInText.csv | 292 tests/testthat/test_LDAgen.R | 86 tests/testthat/test_LDAprep.R | 32 tests/testthat/test_as.corpus.textmeta.R | 34 tests/testthat/test_as.meta.R | 30 tests/testthat/test_as.textmeta.corpus.R | 42 tests/testthat/test_cleanTexts.R | 124 tests/testthat/test_clusterTopics.R | 30 tests/testthat/test_duplist.R | 246 tests/testthat/test_filterCount.R | 70 tests/testthat/test_filterDate.R | 38 tests/testthat/test_filterID.R | 74 tests/testthat/test_filterWord.R | 220 tests/testthat/test_intruderTopics.R | 110 tests/testthat/test_intruderWords.R | 110 tests/testthat/test_makeWordlist.R | 72 tests/testthat/test_mergeLDA.R | 66 tests/testthat/test_mergeTextmeta.R | 42 tests/testthat/test_plotArea.R | 58 tests/testthat/test_plotFreq.R | 70 tests/testthat/test_plotHeat.R | 80 tests/testthat/test_plotScot.R | 64 tests/testthat/test_plotTopic.R | 84 tests/testthat/test_plotTopicWord.R | 98 tests/testthat/test_plotWordSub.R | 148 tests/testthat/test_plotWordpt.R | 98 tests/testthat/test_precisionrecall.R | 70 tests/testthat/test_readTextmeta.R | 96 tests/testthat/test_readWhatsApp.R | 50 tests/testthat/test_readWikinews.R | 58 tests/testthat/test_removeXML.R | 148 tests/testthat/test_sampling.R | 50 tests/testthat/test_showMeta.R | 26 tests/testthat/test_showTexts.R | 34 tests/testthat/test_textmeta.R | 68 tests/testthat/test_tidy.textmeta.R | 86 tests/testthat/test_topTexts.R | 60 tests/testthat/test_topWords.R | 44 tests/testthat/test_topicCoherence.R | 42 tests/testthat/test_topicsInText.R | 86 vignettes/Vignette.Rmd | 1192 +- 138 files changed, 14070 insertions(+), 14065 deletions(-)
Title: Create Pivot Tables
Description: Create regular pivot tables with just a few lines of R.
More complex pivot tables can also be created, e.g. pivot tables
with irregular layouts, multiple calculations and/or derived
calculations based on multiple data frames. Pivot tables are
constructed using R only and can be written to a range of
output formats (plain text, 'HTML', 'Latex' and 'Excel'),
including with styling/formatting.
Author: Christopher Bailiss [aut, cre]
Maintainer: Christopher Bailiss <cbailiss@gmail.com>
Diff between pivottabler versions 1.5.5 dated 2023-10-01 and 1.5.6 dated 2025-04-22
DESCRIPTION | 8 - MD5 | 98 ++++++------- NEWS.md | 9 + R/PivotBatch.R | 2 R/PivotBatchCalculator.R | 2 R/PivotBatchStatistics.R | 2 R/PivotCalculation.R | 2 R/PivotCalculationGroup.R | 2 R/PivotCalculationGroups.R | 2 R/PivotCalculator.R | 2 R/PivotCell.R | 2 R/PivotCells.R | 2 R/PivotData.R | 2 R/PivotDataGroup.R | 10 - R/PivotFilter.R | 2 R/PivotFilterOverrides.R | 2 R/PivotFilters.R | 2 R/PivotHtmlRenderer.R | 2 R/PivotLatexRenderer.R | 2 R/PivotOpenXlsxRenderer.R | 2 R/PivotOpenXlsxStyle.R | 2 R/PivotOpenXlsxStyles.R | 2 R/PivotStyle.R | 14 - R/PivotStyles.R | 14 - R/PivotTable.R | 22 +-- build/vignette.rds |binary inst/doc/v00-vignettes.R | 304 +++++++++++++++++++++--------------------- inst/doc/v00-vignettes.html | 72 ++++----- man/PivotBatch.Rd | 2 man/PivotBatchCalculator.Rd | 2 man/PivotBatchStatistics.Rd | 2 man/PivotCalculation.Rd | 2 man/PivotCalculationGroup.Rd | 2 man/PivotCalculationGroups.Rd | 2 man/PivotCalculator.Rd | 2 man/PivotCell.Rd | 2 man/PivotCells.Rd | 2 man/PivotData.Rd | 2 man/PivotDataGroup.Rd | 10 - man/PivotFilter.Rd | 2 man/PivotFilterOverrides.Rd | 2 man/PivotFilters.Rd | 2 man/PivotHtmlRenderer.Rd | 2 man/PivotLatexRenderer.Rd | 2 man/PivotOpenXlsxRenderer.Rd | 2 man/PivotOpenXlsxStyle.Rd | 2 man/PivotOpenXlsxStyles.Rd | 2 man/PivotStyle.Rd | 14 - man/PivotStyles.Rd | 14 - man/PivotTable.Rd | 26 --- 50 files changed, 339 insertions(+), 348 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@citystgeorges.ac.uk>
Diff between GeDS versions 0.3.0 dated 2025-04-16 and 0.3.1 dated 2025-04-22
DESCRIPTION | 8 - MD5 | 12 - R/NGeDSboost.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/jss_article.pdf |binary tests/testthat/test-predictions.R | 284 +++++++++++++++++++------------------- 7 files changed, 153 insertions(+), 153 deletions(-)
Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Processes the raw data from closed loop flux chamber (or tent)
setups into ecosystem gas fluxes usable for analysis. It goes from a
data frame of gas concentration over time (which can contain several
measurements) and a meta data file indicating which measurement was done
when, to a data frame of ecosystem gas fluxes including quality diagnostics.
Functions provided include different models (exponential as described in
Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, quadratic and
linear) to estimate the fluxes from the raw data, quality assessment,
plotting for visual check and calculation of fluxes based on the setup
specific parameters (chamber size, plot area, ...).
Author: Joseph Gaudard [aut, cre] ,
Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>
Diff between fluxible versions 1.0.0 dated 2025-02-13 and 1.1.0 dated 2025-04-22
fluxible-1.0.0/fluxible/R/data-conc_poster.R |only fluxible-1.0.0/fluxible/R/data-slopes0.R |only fluxible-1.0.0/fluxible/R/data-slopes0_flag.R |only fluxible-1.0.0/fluxible/R/data-slopes0_vol.R |only fluxible-1.0.0/fluxible/R/data-slopes0lin.R |only fluxible-1.0.0/fluxible/R/data-slopes0lin_flag.R |only fluxible-1.0.0/fluxible/R/data-slopes30.R |only fluxible-1.0.0/fluxible/R/data-slopes30_flag.R |only fluxible-1.0.0/fluxible/R/data-slopes30lin.R |only fluxible-1.0.0/fluxible/R/data-slopes30lin_flag.R |only fluxible-1.0.0/fluxible/R/data-slopes30qua.R |only fluxible-1.0.0/fluxible/R/data-slopes30qua_flag.R |only fluxible-1.0.0/fluxible/R/data-slopes60.R |only fluxible-1.0.0/fluxible/R/data-slopes60lin.R |only fluxible-1.0.0/fluxible/R/flux_fitting_exp.R |only fluxible-1.0.0/fluxible/R/flux_fitting_lin.R |only fluxible-1.0.0/fluxible/data/conc_poster.rda |only fluxible-1.0.0/fluxible/data/slopes0.rda |only fluxible-1.0.0/fluxible/data/slopes0_flag.rda |only fluxible-1.0.0/fluxible/data/slopes0_vol.rda |only fluxible-1.0.0/fluxible/data/slopes0lin.rda |only fluxible-1.0.0/fluxible/data/slopes0lin_flag.rda |only fluxible-1.0.0/fluxible/data/slopes30.rda |only fluxible-1.0.0/fluxible/data/slopes30_flag.rda |only fluxible-1.0.0/fluxible/data/slopes30lin.rda |only fluxible-1.0.0/fluxible/data/slopes30lin_flag.rda |only fluxible-1.0.0/fluxible/data/slopes30qua.rda |only fluxible-1.0.0/fluxible/data/slopes30qua_flag.rda |only fluxible-1.0.0/fluxible/data/slopes60.rda |only fluxible-1.0.0/fluxible/data/slopes60lin.rda |only fluxible-1.0.0/fluxible/man/conc_poster.Rd |only fluxible-1.0.0/fluxible/man/flux_fitting_exp.Rd |only fluxible-1.0.0/fluxible/man/flux_fitting_lin.Rd |only fluxible-1.0.0/fluxible/man/slopes0.Rd |only fluxible-1.0.0/fluxible/man/slopes0_flag.Rd |only fluxible-1.0.0/fluxible/man/slopes0_vol.Rd |only fluxible-1.0.0/fluxible/man/slopes0lin.Rd |only fluxible-1.0.0/fluxible/man/slopes0lin_flag.Rd |only fluxible-1.0.0/fluxible/man/slopes30.Rd |only fluxible-1.0.0/fluxible/man/slopes30_flag.Rd |only fluxible-1.0.0/fluxible/man/slopes30lin.Rd |only fluxible-1.0.0/fluxible/man/slopes30lin_flag.Rd |only fluxible-1.0.0/fluxible/man/slopes30qua.Rd |only fluxible-1.0.0/fluxible/man/slopes30qua_flag.Rd |only fluxible-1.0.0/fluxible/man/slopes60.Rd |only fluxible-1.0.0/fluxible/man/slopes60lin.Rd |only fluxible-1.0.0/fluxible/tests/testthat/_snaps/flux_fitting_exp.md |only fluxible-1.0.0/fluxible/tests/testthat/_snaps/flux_fitting_lin.md |only fluxible-1.0.0/fluxible/tests/testthat/_snaps/flux_fitting_quadratic.md |only fluxible-1.0.0/fluxible/tests/testthat/test-flux_fitting_exp.R |only fluxible-1.0.0/fluxible/tests/testthat/test-flux_fitting_lin.R |only fluxible-1.0.0/fluxible/tests/testthat/test-flux_fitting_quadratic.R |only fluxible-1.1.0/fluxible/DESCRIPTION | 10 fluxible-1.1.0/fluxible/MD5 | 232 fluxible-1.1.0/fluxible/NAMESPACE | 10 fluxible-1.1.0/fluxible/NEWS.md | 34 fluxible-1.1.0/fluxible/R/data-co2_conc_mid_missing.R |only fluxible-1.1.0/fluxible/R/data-slopes0_temp.R | 8 fluxible-1.1.0/fluxible/R/flux_calc.R | 108 fluxible-1.1.0/fluxible/R/flux_fit_type.R | 12 fluxible-1.1.0/fluxible/R/flux_fitting.R | 194 fluxible-1.1.0/fluxible/R/flux_fitting_exptz.R |only fluxible-1.1.0/fluxible/R/flux_fitting_hm.R |only fluxible-1.1.0/fluxible/R/flux_fitting_lm.R |only fluxible-1.1.0/fluxible/R/flux_fitting_quadratic.R | 89 fluxible-1.1.0/fluxible/R/flux_fitting_zhao18.R |only fluxible-1.1.0/fluxible/R/flux_flag_count.R | 14 fluxible-1.1.0/fluxible/R/flux_gep.R | 25 fluxible-1.1.0/fluxible/R/flux_match.R | 53 fluxible-1.1.0/fluxible/R/flux_match_col.R |only fluxible-1.1.0/fluxible/R/flux_match_fixed.R |only fluxible-1.1.0/fluxible/R/flux_param_exp.R | 9 fluxible-1.1.0/fluxible/R/flux_param_kappamax.R |only fluxible-1.1.0/fluxible/R/flux_param_lm.R | 4 fluxible-1.1.0/fluxible/R/flux_param_qua.R |only fluxible-1.1.0/fluxible/R/flux_plot.R | 26 fluxible-1.1.0/fluxible/R/flux_plot_exp.R | 17 fluxible-1.1.0/fluxible/R/flux_plot_lin.R | 2 fluxible-1.1.0/fluxible/R/flux_plot_quadratic.R | 4 fluxible-1.1.0/fluxible/R/flux_quality.R | 211 fluxible-1.1.0/fluxible/R/flux_quality_exp.R | 65 fluxible-1.1.0/fluxible/R/flux_quality_kappamax.R |only fluxible-1.1.0/fluxible/R/flux_quality_lm.R | 11 fluxible-1.1.0/fluxible/R/flux_quality_qua.R |only fluxible-1.1.0/fluxible/R/stupeflux.R |only fluxible-1.1.0/fluxible/R/sysdata.rda |only fluxible-1.1.0/fluxible/README.md | 120 fluxible-1.1.0/fluxible/build/partial.rdb |binary fluxible-1.1.0/fluxible/build/vignette.rds |binary fluxible-1.1.0/fluxible/data/co2_conc.rda |binary fluxible-1.1.0/fluxible/data/co2_conc_mid_missing.rda |only fluxible-1.1.0/fluxible/data/co2_conc_missing.rda |binary fluxible-1.1.0/fluxible/data/co2_df_missing.rda |binary fluxible-1.1.0/fluxible/data/co2_df_short.rda |binary fluxible-1.1.0/fluxible/data/co2_fluxes.rda |binary 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fluxible-1.1.0/fluxible/vignettes/fluxible.Rmd | 2 159 files changed, 7468 insertions(+), 4329 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-31 0.1.7
2023-03-02 0.1.6
2022-04-14 0.1.5
2021-05-25 0.1.4
2021-05-12 0.1.3
2018-05-23 0.1.2
2014-06-08 0.1.1
2014-03-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-28 2.0.2
2020-06-02 2.0.1
2020-05-17 2.0.0
2019-02-12 1.1.0
2019-02-12 1.1.1
2018-12-18 1.0.1
2018-12-16 1.0.0
Title: Kornbrot's Rank Difference Test
Description: Implements Kornbrot's rank difference test as described in
<doi:10.1111/j.2044-8317.1990.tb00939.x>. This method is a modified
Wilcoxon signed-rank test which produces consistent and meaningful
results for ordinal or monotonically-transformed data.
Author: Brett Klamer [aut, cre]
Maintainer: Brett Klamer <code@brettklamer.com>
Diff between rankdifferencetest versions 2021-11-25 dated 2021-11-29 and 2025.4.21 dated 2025-04-22
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/rdt.r | 3 +-- build/partial.rdb |binary man/rankdifferencetest-package.Rd | 4 ++-- man/rdt.Rd | 3 +-- 7 files changed, 19 insertions(+), 17 deletions(-)
More information about rankdifferencetest at CRAN
Permanent link
Title: Semi-Supervised Algorithm for Document Scaling
Description: A word embeddings-based semi-supervised model for document scaling Watanabe (2020) <doi:10.1080/19312458.2020.1832976>.
LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove).
It can generate word vectors on a users-provided corpus or incorporate a pre-trained word vectors.
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between LSX versions 1.4.2 dated 2025-01-08 and 1.4.3 dated 2025-04-22
LSX-1.4.2/LSX/tests/data/lss_test.RDS |only LSX-1.4.2/LSX/tests/data/matrix_embedding.RDS |only LSX-1.4.2/LSX/tests/data/tokens_test.RDS |only LSX-1.4.2/LSX/tests/data/word2vec_test.RDS |only LSX-1.4.3/LSX/DESCRIPTION | 6 - LSX-1.4.3/LSX/MD5 | 40 +++++----- LSX-1.4.3/LSX/NEWS.md | 10 ++ LSX-1.4.3/LSX/R/as.textmodel.R | 86 ++++++++++++++++------- LSX-1.4.3/LSX/R/textmodel.R | 8 +- LSX-1.4.3/LSX/R/textplot.R | 1 LSX-1.4.3/LSX/inst/WORDLIST | 7 + LSX-1.4.3/LSX/man/as.textmodel_lss.Rd | 31 ++++---- LSX-1.4.3/LSX/man/textmodel_lss.Rd | 2 LSX-1.4.3/LSX/tests/data/lss_k300.RDS |only LSX-1.4.3/LSX/tests/data/matrix_k100.RDS |only LSX-1.4.3/LSX/tests/data/save.R | 22 +++-- LSX-1.4.3/LSX/tests/data/tokens.RDS |only LSX-1.4.3/LSX/tests/data/word2vec-prob.RDS |only LSX-1.4.3/LSX/tests/data/word2vec.RDS |only LSX-1.4.3/LSX/tests/misc |only LSX-1.4.3/LSX/tests/testthat/test-as.textmodel.R | 32 ++++++-- LSX-1.4.3/LSX/tests/testthat/test-bootstrap.R | 14 --- LSX-1.4.3/LSX/tests/testthat/test-textmodel.R | 27 +++++-- LSX-1.4.3/LSX/tests/testthat/test-textplot.R | 16 ++-- LSX-1.4.3/LSX/tests/testthat/test-textstat.R | 2 LSX-1.4.3/LSX/tests/testthat/test-utils.R | 2 26 files changed, 199 insertions(+), 107 deletions(-)
Title: Item Response Theory Demo Collection
Description: Includes a collection of shiny applications to demonstrate
or to explore fundamental item response theory (IRT) concepts
such as estimation, scoring, and multidimensional IRT models.
Author: Metin Bulus [aut, cre],
Wes Bonifay [aut, ctb]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between irtDemo versions 0.1.4 dated 2018-04-05 and 0.1.5 dated 2025-04-22
DESCRIPTION | 15 +++++++++------ MD5 | 9 +++++---- NEWS.md | 4 ++++ README.md | 13 +++++++++++-- build |only man/irtDemo.Rd | 4 ++++ 6 files changed, 33 insertions(+), 12 deletions(-)