Title: Network Scale-Up Models for Aggregated Relational Data
Description: Provides a variety of Network Scale-up Models for researchers to
analyze Aggregated Relational Data, through the use of Stan and 'glmmTMB'.
Also provides tools for model checking
In this version, the package implements models from
Laga, I., Bao, L., and Niu, X (2023) <doi:10.1080/01621459.2023.2165929>,
Zheng, T., Salganik, M. J., and Gelman, A. (2006) <doi:10.1198/016214505000001168>,
Killworth, P. D., Johnsen, E. C., McCarty, C., Shelley, G. A.,
and Bernard, H. R. (1998) <doi:10.1016/S0378-8733(96)00305-X>, and
Killworth, P. D., McCarty, C., Bernard, H. R., Shelley, G. A., and
Johnsen, E. C. (1998) <doi:10.1177/0193841X9802200205>.
Author: Ian Laga [aut] ,
Owen G. Ward [aut, cre],
Anna L. Smith [aut],
Benjamin Vogel [aut],
Jieyun Wang [aut],
Le Bao [aut],
Xiaoyue Niu [aut]
Maintainer: Owen G. Ward <oward@sfu.ca>
Diff between networkscaleup versions 0.2-1 dated 2025-12-10 and 0.2-2 dated 2026-06-26
DESCRIPTION | 20 ++--- MD5 | 19 ++-- R/aux_functions.R | 22 ----- R/corr_perms.R | 143 ++++++++++++++++++++++++++++-------- R/make_ard.R | 55 ++++++++----- R/plot_fitted.R | 2 R/surrogate.R | 22 ----- inst/doc/FittingNetworkScaleup.html | 59 +++++++------- man/make_ard.Rd | 3 man/networkscaleup.Rd | 4 - man/plot_tw_statistic.Rd |only 11 files changed, 207 insertions(+), 142 deletions(-)
More information about networkscaleup 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 0.3.0 dated 2026-06-22 and 0.3.1 dated 2026-06-26
DESCRIPTION | 6 MD5 | 21 +-- NAMESPACE | 2 NEWS.md | 18 ++ R/cpp11.R | 8 + R/read.r | 78 +++++++++++ man/bigbed_info.Rd |only man/bigwig_info.Rd |only man/read_bigbed.Rd | 11 + src/cpp11.cpp | 16 ++ src/cpp11bigwig.cpp | 194 ++++++++++++++++++++++++++++- tests/testthat/data/test_noschema_bed12.bb |only tests/testthat/test-read.R | 137 ++++++++++++++++++++ 13 files changed, 474 insertions(+), 17 deletions(-)
Title: Convergence and Dynamic Factor Models
Description: Tests convergence in macro-financial panels combining
Dynamic Factor Models (DFM) and mean-reverting, discrete-time
Ornstein-Uhlenbeck/AR(1) factor processes. Provides: (i) static factor
extraction with VAR stability checks, Portmanteau tests and rolling
out-of-sample R^2, in the spirit of Stock and Watson (2002)
<doi:10.1198/073500102317351921> and the Generalized Dynamic Factor Model of
Forni, Hallin, Lippi and Reichlin (2000) <doi:10.1162/003465300559037>;
(ii) cointegration analysis a la Johansen (1988)
<doi:10.1016/0165-1889(88)90041-3>; (iii) Bayesian factor-OU/AR(1) estimation
with convergence and half-life summaries grounded in Uhlenbeck and Ornstein
(1930) <doi:10.1103/PhysRev.36.823> and Vasicek (1977)
<doi:10.1016/0304-405X(77)90016-2>, with full Markov chain Monte Carlo
convergence diagnostics; (iv) heteroskedasticity-consistent (HC) and, when
the suggested 'sandwich' (Zeileis (2004) <doi:10.18637/jss.v011.i10>) and
'lmtest' packages are [...truncated...]
Author: Jose Mauricio Gomez Julian [aut, cre]
Maintainer: Jose Mauricio Gomez Julian <isadore.nabi@pm.me>
Diff between convergenceDFM versions 0.1.4 dated 2025-12-01 and 0.3.2 dated 2026-06-26
convergenceDFM-0.1.4/convergenceDFM/R/bayesian_disaggregation.R |only convergenceDFM-0.3.2/convergenceDFM/DESCRIPTION | 56 convergenceDFM-0.3.2/convergenceDFM/MD5 | 111 convergenceDFM-0.3.2/convergenceDFM/NAMESPACE | 9 convergenceDFM-0.3.2/convergenceDFM/NEWS.md | 184 convergenceDFM-0.3.2/convergenceDFM/R/convergenceDFM-package.R | 63 convergenceDFM-0.3.2/convergenceDFM/R/convergence_tests.R | 685 +-- convergenceDFM-0.3.2/convergenceDFM/R/data_io.R |only convergenceDFM-0.3.2/convergenceDFM/R/data_preparation.R | 291 - convergenceDFM-0.3.2/convergenceDFM/R/dfm_estimation.R | 991 ++--- convergenceDFM-0.3.2/convergenceDFM/R/factor_ou.R | 1035 ++--- convergenceDFM-0.3.2/convergenceDFM/R/globals.R | 8 convergenceDFM-0.3.2/convergenceDFM/R/main_wrapper.R | 1655 ++++---- convergenceDFM-0.3.2/convergenceDFM/R/pls_selection.R | 215 - convergenceDFM-0.3.2/convergenceDFM/R/robustness_tests.R | 1427 ++++--- convergenceDFM-0.3.2/convergenceDFM/R/rotation_tests.R | 1894 +++++----- convergenceDFM-0.3.2/convergenceDFM/R/utils.R | 334 + convergenceDFM-0.3.2/convergenceDFM/R/visualization.R | 992 ++--- convergenceDFM-0.3.2/convergenceDFM/R/wedge_diagnostics.R |only convergenceDFM-0.3.2/convergenceDFM/R/zzz.R | 65 convergenceDFM-0.3.2/convergenceDFM/README.md | 247 - convergenceDFM-0.3.2/convergenceDFM/build/vignette.rds |binary convergenceDFM-0.3.2/convergenceDFM/inst/doc/canonical-disaggregation-and-leave-cluster-out.R |only convergenceDFM-0.3.2/convergenceDFM/inst/doc/canonical-disaggregation-and-leave-cluster-out.Rmd |only convergenceDFM-0.3.2/convergenceDFM/inst/doc/canonical-disaggregation-and-leave-cluster-out.html |only convergenceDFM-0.3.2/convergenceDFM/inst/doc/convergence-analysis.R | 70 convergenceDFM-0.3.2/convergenceDFM/inst/doc/convergence-analysis.Rmd | 190 - convergenceDFM-0.3.2/convergenceDFM/inst/doc/convergence-analysis.html | 879 ++-- convergenceDFM-0.3.2/convergenceDFM/man/build_cluster_map.Rd |only convergenceDFM-0.3.2/convergenceDFM/man/compute_wedge.Rd |only convergenceDFM-0.3.2/convergenceDFM/man/convergenceDFM-package.Rd | 5 convergenceDFM-0.3.2/convergenceDFM/man/diagnose_data.Rd | 32 convergenceDFM-0.3.2/convergenceDFM/man/estimate_DFM.Rd | 26 convergenceDFM-0.3.2/convergenceDFM/man/estimate_factor_OU.Rd | 47 convergenceDFM-0.3.2/convergenceDFM/man/make_X_innovations.Rd | 11 convergenceDFM-0.3.2/convergenceDFM/man/placebo_values.Rd |only convergenceDFM-0.3.2/convergenceDFM/man/plot_error_correction_panel.Rd | 10 convergenceDFM-0.3.2/convergenceDFM/man/read_cpi.Rd | 22 convergenceDFM-0.3.2/convergenceDFM/man/rescue_short_run_channel.Rd | 24 convergenceDFM-0.3.2/convergenceDFM/man/rotation_null_test.Rd | 59 convergenceDFM-0.3.2/convergenceDFM/man/row_norm1.Rd | 2 convergenceDFM-0.3.2/convergenceDFM/man/run_complete_factor_analysis_robust.Rd | 251 - convergenceDFM-0.3.2/convergenceDFM/man/run_rotation_null_on_results.Rd | 24 convergenceDFM-0.3.2/convergenceDFM/man/select_optimal_components_safe.Rd | 58 convergenceDFM-0.3.2/convergenceDFM/man/test_jackknife_sectors.Rd | 41 convergenceDFM-0.3.2/convergenceDFM/man/test_leave_cluster_out.Rd |only convergenceDFM-0.3.2/convergenceDFM/man/test_permutation_robustness.Rd | 47 convergenceDFM-0.3.2/convergenceDFM/man/test_reweighting_robustness.Rd | 33 convergenceDFM-0.3.2/convergenceDFM/man/to_num_commas.Rd | 39 convergenceDFM-0.3.2/convergenceDFM/man/visualize_factor_dynamics.Rd | 19 convergenceDFM-0.3.2/convergenceDFM/man/wedge_stationarity.Rd |only convergenceDFM-0.3.2/convergenceDFM/tests/testthat.R | 8 convergenceDFM-0.3.2/convergenceDFM/tests/testthat/fixtures |only convergenceDFM-0.3.2/convergenceDFM/tests/testthat/test-convergence.R | 94 convergenceDFM-0.3.2/convergenceDFM/tests/testthat/test-dfm.R | 46 convergenceDFM-0.3.2/convergenceDFM/tests/testthat/test-disaggregation-import.R |only convergenceDFM-0.3.2/convergenceDFM/tests/testthat/test-golden-convergence.R |only convergenceDFM-0.3.2/convergenceDFM/tests/testthat/test-leave-cluster-out.R |only convergenceDFM-0.3.2/convergenceDFM/tests/testthat/test-ou.R | 51 convergenceDFM-0.3.2/convergenceDFM/tests/testthat/test-utils.R | 52 convergenceDFM-0.3.2/convergenceDFM/tests/testthat/test-wedge.R |only convergenceDFM-0.3.2/convergenceDFM/vignettes/canonical-disaggregation-and-leave-cluster-out.Rmd |only convergenceDFM-0.3.2/convergenceDFM/vignettes/convergence-analysis.Rmd | 190 - 63 files changed, 7125 insertions(+), 5467 deletions(-)
More information about convergenceDFM at CRAN
Permanent link
Title: Parallel Nonparametric Kernel Smoothing Methods for Mixed Data
Types Using 'MPI'
Description: Nonparametric (and semiparametric) kernel methods that seamlessly
handle a mix of continuous, unordered, and ordered factor data types. This
package is a parallel implementation of the 'np' package based on the 'MPI'
specification that incorporates the 'Rmpi' package (Hao Yu
<hyu@stats.uwo.ca>) with minor modifications and we are extremely grateful
to Hao Yu for his contributions to the 'R' community. We would like to
gratefully acknowledge support from the Natural Sciences and Engineering
Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the
Social Sciences and Humanities Research Council of Canada (SSHRC,
<https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic
Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would
also like to acknowledge the contributions of the 'GNU GSL' authors. In
particular, we adapt the 'GNU GSL' B-spline routine 'gsl_bspline.c' adding
automated support for quantile knots (in addition t [...truncated...]
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut],
Hao Yu [ctb, cph],
The GSL Team [cph],
Numerical Recipes Software [cph]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between npRmpi versions 0.70-3 dated 2026-06-03 and 0.70-4 dated 2026-06-26
CHANGELOG | 73 DESCRIPTION | 8 MD5 | 141 NEWS.md | 218 R/Rcoll.R | 2 R/Rparutilities.R | 5 R/a.bw.dispatch.R | 10 R/condensity.R | 9 R/condistribution.R | 9 R/np.condensity.R | 56 R/np.condensity.bw.R | 49 R/np.condistribution.R | 56 R/np.condistribution.bw.R | 93 R/np.conmode.R | 2 R/np.copula.R | 8 R/np.lp.degree.search.R | 218 R/np.plot.engine.bandwidth.R | 148 R/np.plot.engine.conbandwidth.R | 179 R/np.plot.engine.condbandwidth.R | 192 R/np.plot.engine.dbandwidth.R | 34 R/np.plot.engine.plbandwidth.R | 107 R/np.plot.engine.rbandwidth.R | 164 R/np.plot.engine.scbandwidth.R | 161 R/np.plot.engine.sibandwidth.R | 175 R/np.plot.helpers.R | 3082 +++++++++- R/np.plot.methods.R | 4 R/np.plregression.R | 6 R/np.plregression.bw.R | 88 R/np.qregression.R | 15 R/np.reghat.R | 218 R/np.regression.R | 78 R/np.regression.bw.R | 130 R/np.semihat.R | 87 R/np.singleindex.R | 106 R/np.singleindex.bw.R | 57 R/np.smoothcoef.R | 4 R/np.smoothcoef.bw.R | 52 R/progress.R | 8 R/regression.R | 17 R/util.R | 310 - R/zzz.R | 49 configure | 15 configure.ac | 14 inst/sentinels |only man/np.condensity.bw.Rd | 11 man/np.condistribution.bw.Rd | 11 man/np.copula.Rd | 6 man/np.options.Rd | 255 man/np.plot.Rd | 175 man/np.plregression.bw.Rd | 11 man/np.regression.bw.Rd | 15 man/np.singleindex.bw.Rd | 11 man/np.smoothcoef.bw.Rd | 11 src/Makevars.in | 2 src/jksum.c | 1270 ++++ src/linalg.c | 30 src/np.c | 218 tests/testthat/test-nomad-degree-search-family-progress-contract.R | 2 tests/testthat/test-npcdensbw-degree-search-nomad-progress-contract.R | 2 tests/testthat/test-npindexbw-degree-search-contract.R | 2 tests/testthat/test-npqreg.R | 38 tests/testthat/test-npreg-arg-contract.R | 47 tests/testthat/test-npregbw-degree-search-helper-contract.R | 18 tests/testthat/test-npregbw-degree-search-nomad-progress-contract.R | 3 tests/testthat/test-plot-bootstrap-arg-contract.R | 20 tests/testthat/test-plot-plbandwidth-bias-center-contract.R |only tests/testthat/test-plot-scbandwidth-bias-center-contract.R |only tests/testthat/test-progress-bandwidth-common-contract.R | 4 tests/testthat/test-progress-condensdist-fit-contract.R | 12 tests/testthat/test-progress-npindex-fit-contract.R | 2 tests/testthat/test-progress-npplreg-fit-contract.R | 2 tests/testthat/test-progress-npreg-fit-contract.R | 6 tests/testthat/test-progress-npscoef-fit-contract.R | 2 73 files changed, 7478 insertions(+), 1165 deletions(-)
Title: Nonparametric Kernel Smoothing Methods for Mixed Data Types
Description: Nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would also like to acknowledge the contributions of the GNU GSL authors. In particular, we adapt the GNU GSL B-spline routine gsl_bspline.c adding automated support for quantile knots (in addition to uniform knots), providing missing functionality for derivatives, and for extending the splines beyond their endpoints.
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between np versions 0.70-3 dated 2026-06-04 and 0.70-4 dated 2026-06-26
np-0.70-3/np/src/Makevars |only np-0.70-4/np/CHANGELOG | 65 np-0.70-4/np/DESCRIPTION | 8 np-0.70-4/np/MD5 | 138 np-0.70-4/np/NEWS.md | 188 np-0.70-4/np/R/a.bw.dispatch.R | 10 np-0.70-4/np/R/condensity.R | 9 np-0.70-4/np/R/condistribution.R | 9 np-0.70-4/np/R/np.condensity.R | 20 np-0.70-4/np/R/np.condensity.bw.R | 68 np-0.70-4/np/R/np.condistribution.R | 20 np-0.70-4/np/R/np.condistribution.bw.R | 81 np-0.70-4/np/R/np.conmode.R | 2 np-0.70-4/np/R/np.copula.R | 8 np-0.70-4/np/R/np.lp.degree.search.R | 221 np-0.70-4/np/R/np.plot.engine.bandwidth.R | 146 np-0.70-4/np/R/np.plot.engine.conbandwidth.R | 179 np-0.70-4/np/R/np.plot.engine.condbandwidth.R | 194 np-0.70-4/np/R/np.plot.engine.dbandwidth.R | 32 np-0.70-4/np/R/np.plot.engine.plbandwidth.R | 72 np-0.70-4/np/R/np.plot.engine.rbandwidth.R | 167 np-0.70-4/np/R/np.plot.engine.scbandwidth.R | 154 np-0.70-4/np/R/np.plot.engine.sibandwidth.R | 175 np-0.70-4/np/R/np.plot.helpers.R | 2878 +++++++++- np-0.70-4/np/R/np.plot.methods.R | 9 np-0.70-4/np/R/np.plregression.R | 2 np-0.70-4/np/R/np.plregression.bw.R | 52 np-0.70-4/np/R/np.qregression.R | 16 np-0.70-4/np/R/np.reghat.R | 263 np-0.70-4/np/R/np.regression.R | 32 np-0.70-4/np/R/np.regression.bw.R | 102 np-0.70-4/np/R/np.semihat.R | 87 np-0.70-4/np/R/np.singleindex.R | 51 np-0.70-4/np/R/np.singleindex.bw.R | 51 np-0.70-4/np/R/np.smoothcoef.R | 2 np-0.70-4/np/R/np.smoothcoef.bw.R | 47 np-0.70-4/np/R/progress.R | 8 np-0.70-4/np/R/regression.R | 17 np-0.70-4/np/R/util.R | 302 - np-0.70-4/np/R/zzz.R | 13 np-0.70-4/np/cleanup | 1 np-0.70-4/np/configure |only np-0.70-4/np/inst/doc/np_entropy_tests.html | 2 np-0.70-4/np/inst/doc/np_getting_started.html | 49 np-0.70-4/np/inst/sentinels |only np-0.70-4/np/man/np.condensity.bw.Rd | 11 np-0.70-4/np/man/np.condistribution.bw.Rd | 11 np-0.70-4/np/man/np.copula.Rd | 6 np-0.70-4/np/man/np.options.Rd | 228 np-0.70-4/np/man/np.plot.Rd | 175 np-0.70-4/np/man/np.plregression.bw.Rd | 11 np-0.70-4/np/man/np.regression.bw.Rd | 15 np-0.70-4/np/man/np.singleindex.bw.Rd | 11 np-0.70-4/np/man/np.smoothcoef.bw.Rd | 11 np-0.70-4/np/src/Makevars.in |only np-0.70-4/np/src/jksum.c | 1166 +++- np-0.70-4/np/src/np.c | 218 np-0.70-4/np/tests/testthat/test-nomad-degree-search-family-progress-contract.R | 2 np-0.70-4/np/tests/testthat/test-npcdensbw-degree-search-nomad-progress-contract.R | 2 np-0.70-4/np/tests/testthat/test-npindexbw-degree-search-contract.R | 2 np-0.70-4/np/tests/testthat/test-npqreg.R | 35 np-0.70-4/np/tests/testthat/test-npreg-arg-contract.R | 41 np-0.70-4/np/tests/testthat/test-npregbw-degree-search-helper-contract.R | 18 np-0.70-4/np/tests/testthat/test-npregbw-degree-search-nomad-progress-contract.R | 3 np-0.70-4/np/tests/testthat/test-plot-contract.R | 20 np-0.70-4/np/tests/testthat/test-plot-plbandwidth-bias-center-contract.R |only np-0.70-4/np/tests/testthat/test-plot-scbandwidth-bias-center-contract.R |only np-0.70-4/np/tests/testthat/test-progress-bandwidth-common-contract.R | 2 np-0.70-4/np/tests/testthat/test-progress-condensdist-fit-contract.R | 4 np-0.70-4/np/tests/testthat/test-progress-npindex-fit-contract.R | 2 np-0.70-4/np/tests/testthat/test-progress-npplreg-fit-contract.R | 2 np-0.70-4/np/tests/testthat/test-progress-npreg-fit-contract.R | 2 np-0.70-4/np/tests/testthat/test-progress-npscoef-fit-contract.R | 2 73 files changed, 6882 insertions(+), 1068 deletions(-)
Title: Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'
Description: A collection of 'ggplot2' color palettes inspired by
plots in scientific journals, data visualization libraries,
science fiction movies, and TV shows.
Author: Nan Xiao [aut, cre, cph] ,
Joshua Cook [ctb],
Clara Jegousse [ctb],
Hui Chen [ctb],
Miaozhu Li [ctb],
iTerm2-Color-Schemes contributors [ctb, cph] ,
Winston Chang [ctb, cph]
Maintainer: Nan Xiao <me@nanx.me>
Diff between ggsci versions 5.0.0 dated 2026-04-17 and 5.1.0 dated 2026-06-26
DESCRIPTION | 8 MD5 | 16 NEWS.md | 29 + R/continuous-gsea.R | 2 R/palettes-iterm.R | 1330 +++++++++++++++++++++++++++++++++++++++++++++++++-- build/vignette.rds |binary man/ggsci-package.Rd | 5 man/pal_gephi.Rd | 2 man/rgb_gsea.Rd | 2 9 files changed, 1341 insertions(+), 53 deletions(-)
Title: Parse and Render Molecular Structures in 3D
Description: Downloads and parses 'SDF' (Structural Description Format) and 'PDB' (Protein Database) files for 3D rendering.
Author: Tyler Morgan-Wall [aut, cph, cre]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between raymolecule versions 0.5.3 dated 2024-02-21 and 0.9.0 dated 2026-06-26
raymolecule-0.5.3/raymolecule/R/run_documentation.R |only raymolecule-0.5.3/raymolecule/R/utils-pipe.R |only raymolecule-0.5.3/raymolecule/man/pipe.Rd |only raymolecule-0.5.3/raymolecule/man/run_documentation.Rd |only raymolecule-0.9.0/raymolecule/DESCRIPTION | 20 raymolecule-0.9.0/raymolecule/MD5 | 56 raymolecule-0.9.0/raymolecule/NAMESPACE | 7 raymolecule-0.9.0/raymolecule/R/convert_color.R | 27 raymolecule-0.9.0/raymolecule/R/download_pdb.R |only raymolecule-0.9.0/raymolecule/R/generate_atom_scene.R | 175 raymolecule-0.9.0/raymolecule/R/generate_bond_scene.R | 457 -- raymolecule-0.9.0/raymolecule/R/generate_full_scene.R | 344 - raymolecule-0.9.0/raymolecule/R/generate_ribbon_scene.R |only raymolecule-0.9.0/raymolecule/R/get_example_molecule.R | 25 raymolecule-0.9.0/raymolecule/R/get_molecule.R | 101 raymolecule-0.9.0/raymolecule/R/read_pdb.R | 2034 +++++++++- raymolecule-0.9.0/raymolecule/R/read_sdf.R | 93 raymolecule-0.9.0/raymolecule/R/render_model.R | 720 ++- raymolecule-0.9.0/raymolecule/R/ribbon_helpers.R |only raymolecule-0.9.0/raymolecule/R/util.R | 28 raymolecule-0.9.0/raymolecule/inst/extdata/4fsp_assembly-1.jpeg |only raymolecule-0.9.0/raymolecule/man/download_pdb.Rd |only raymolecule-0.9.0/raymolecule/man/generate_atom_scene.Rd | 89 raymolecule-0.9.0/raymolecule/man/generate_bond_scene.Rd | 94 raymolecule-0.9.0/raymolecule/man/generate_full_scene.Rd | 104 raymolecule-0.9.0/raymolecule/man/generate_ribbon_scene.Rd |only raymolecule-0.9.0/raymolecule/man/get_molecule.Rd | 53 raymolecule-0.9.0/raymolecule/man/read_pdb.Rd | 88 raymolecule-0.9.0/raymolecule/man/read_sdf.Rd | 4 raymolecule-0.9.0/raymolecule/man/render_model.Rd | 198 raymolecule-0.9.0/raymolecule/tests |only 31 files changed, 3620 insertions(+), 1097 deletions(-)
Title: Visualizes Preferential Data in One and More Contests
Description: A visualization toolkit for preferential data, such as ranked-choice election results, tournament outcomes,
and survey responses. The package provides methods to visualise the preference distribution of one contest with
bar charts and pairwise comparisons of two contestants, as well as methods to visualise multiple contests through
2D and high-dimensional simplex plots both statically and interactively. HD simplex displays are implemented via projection
methods using the 'tourr' and 'detourr' packages, enabling dynamic exploration of high-dimensional preference structure.
For more details on HD simplex projection, see Wickham et al. (2011) <doi:10.21105/joss.03419>.
Author: Linh Ngo [aut, cre],
Dianne Cook [aut] ,
Damjan Vukcevic [aut]
Maintainer: Linh Ngo <linhngo66.work@gmail.com>
Diff between prefviz versions 0.1.2 dated 2026-05-01 and 0.1.3 dated 2026-06-26
DESCRIPTION | 6 MD5 | 18 +- NEWS.md | 4 R/quick_plots.R | 6 README.md | 235 ++++++++++++++++-------------- inst/doc/add_ordered_path.html | 2 inst/doc/draw_ternary_plot.html | 4 man/figures/README-dop-bar-1.png |only man/figures/README-pairwise-heatmap-1.png |only man/figures/README-ternary-2d-1.png |only man/figures/README-ternary-hd-1.png |only man/figures/README-ternary-hd-2.png |only man/figures/prefviz-sticker.png |only 13 files changed, 155 insertions(+), 120 deletions(-)
Title: Spatial Projection of Network Signals along Geodesic Paths
Description: For a given graph containing vertices, edges, and a signal
associated with the vertices, the 'PathwaySpace' package performs a convolution
operation, which involves a weighted combination of neighboring vertices and
their associated signals. The package uses a decay function to project these
signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' has various
applications, such as visualizing network data in a graphical format that
highlights the relationships and signal strengths between vertices. By
combining graph theory, signal processing, and visualization, 'PathwaySpace'
provides a way of representing graph data on a continuous projection space.
Based on methods introduced in Tercan et al. (2025)
<doi:10.1016/j.xpro.2025.103681> and Ellrott et al. (2025)
<doi:10.1016/j.ccell.2024.12.002>.
Author: Sysbiolab Team [aut],
Victor Apolonio [ctb],
Jonathan Back [ctb],
Lana Querne [ctb],
Vinicius Chagas [ctb],
Bahar Tercan [ctb],
Mauro Castro [cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between PathwaySpace versions 1.3.0 dated 2026-05-23 and 1.4.1 dated 2026-06-26
PathwaySpace-1.3.0/PathwaySpace/R/pspaceChecks.R |only PathwaySpace-1.3.0/PathwaySpace/R/pspaceClasses.R |only PathwaySpace-1.3.0/PathwaySpace/R/pspaceDecay.R |only PathwaySpace-1.3.0/PathwaySpace/R/pspaceGenerics.R |only PathwaySpace-1.3.0/PathwaySpace/R/pspaceMethods.R |only PathwaySpace-1.3.0/PathwaySpace/R/pspaceMisc.R |only PathwaySpace-1.3.0/PathwaySpace/R/pspacePlots.R |only PathwaySpace-1.3.0/PathwaySpace/R/pspaceSupplements.R |only PathwaySpace-1.3.0/PathwaySpace/R/pspaceWatershed.R |only PathwaySpace-1.3.0/PathwaySpace/man/signalDecay.Rd |only PathwaySpace-1.4.1/PathwaySpace/DESCRIPTION | 19 - PathwaySpace-1.4.1/PathwaySpace/MD5 | 108 +++++----- PathwaySpace-1.4.1/PathwaySpace/NAMESPACE | 15 + PathwaySpace-1.4.1/PathwaySpace/R/annotation-pspace.R |only PathwaySpace-1.4.1/PathwaySpace/R/pspace-checks.R |only PathwaySpace-1.4.1/PathwaySpace/R/pspace-classes.R |only PathwaySpace-1.4.1/PathwaySpace/R/pspace-decay.R |only PathwaySpace-1.4.1/PathwaySpace/R/pspace-generics.R |only PathwaySpace-1.4.1/PathwaySpace/R/pspace-methods.R |only PathwaySpace-1.4.1/PathwaySpace/R/pspace-misc.R |only PathwaySpace-1.4.1/PathwaySpace/R/pspace-plots.R |only PathwaySpace-1.4.1/PathwaySpace/R/pspace-supplements.R |only PathwaySpace-1.4.1/PathwaySpace/R/pspace-watershed.R |only PathwaySpace-1.4.1/PathwaySpace/inst/CITATION | 2 PathwaySpace-1.4.1/PathwaySpace/inst/NEWS.Rd | 8 PathwaySpace-1.4.1/PathwaySpace/inst/doc/PathwaySpace.R | 46 +--- PathwaySpace-1.4.1/PathwaySpace/inst/doc/PathwaySpace.Rmd | 69 +++--- PathwaySpace-1.4.1/PathwaySpace/inst/doc/PathwaySpace.html | 86 +++---- PathwaySpace-1.4.1/PathwaySpace/man/CGC_20211118.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/Hallmarks_v2023_1_Hs_symbols.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/PCv12_pruned_igraph.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/PathwaySpace-accessors.Rd | 12 - PathwaySpace-1.4.1/PathwaySpace/man/PathwaySpace-class.Rd | 40 ++- PathwaySpace-1.4.1/PathwaySpace/man/PathwaySpace-package.Rd | 37 --- PathwaySpace-1.4.1/PathwaySpace/man/SpaceProjection-class.Rd |only PathwaySpace-1.4.1/PathwaySpace/man/annotation_pspace_signal.Rd |only PathwaySpace-1.4.1/PathwaySpace/man/buildPathwaySpace.Rd | 10 PathwaySpace-1.4.1/PathwaySpace/man/circularProjection-methods.Rd | 29 +- PathwaySpace-1.4.1/PathwaySpace/man/expDecay.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/getNearestNode.Rd | 7 PathwaySpace-1.4.1/PathwaySpace/man/getPathwaySpace-methods.Rd | 6 PathwaySpace-1.4.1/PathwaySpace/man/gimage.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/linearDecay.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/pathDistances.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/plotPathDistances.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/plotPathwaySpace-methods.Rd | 16 - PathwaySpace-1.4.1/PathwaySpace/man/polarDecay.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/polarProjection-methods.Rd | 64 ++++- PathwaySpace-1.4.1/PathwaySpace/man/pspace.cols.Rd | 6 PathwaySpace-1.4.1/PathwaySpace/man/pspace.pals.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/signalAggregation.Rd | 30 ++ PathwaySpace-1.4.1/PathwaySpace/man/silhouetteMapping-methods.Rd | 6 PathwaySpace-1.4.1/PathwaySpace/man/summitMapping-methods.Rd | 12 - PathwaySpace-1.4.1/PathwaySpace/man/summitWatershed.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/man/updatePathwaySpace.Rd |only PathwaySpace-1.4.1/PathwaySpace/man/vertexSignal-accessors.Rd | 64 +++++ PathwaySpace-1.4.1/PathwaySpace/man/weibullDecay.Rd | 2 PathwaySpace-1.4.1/PathwaySpace/tests/testthat/test-PathwaySpace.R | 4 PathwaySpace-1.4.1/PathwaySpace/tests/testthat/test-projections.R |only PathwaySpace-1.4.1/PathwaySpace/vignettes/PathwaySpace.Rmd | 69 +++--- PathwaySpace-1.4.1/PathwaySpace/vignettes/figures/fig2.png |binary PathwaySpace-1.4.1/PathwaySpace/vignettes/figures/fig3.png |binary PathwaySpace-1.4.1/PathwaySpace/vignettes/figures/fig4.png |binary PathwaySpace-1.4.1/PathwaySpace/vignettes/figures/fig5.png |binary PathwaySpace-1.4.1/PathwaySpace/vignettes/figures/fig6.png |binary PathwaySpace-1.4.1/PathwaySpace/vignettes/figures/fig7.png |binary PathwaySpace-1.4.1/PathwaySpace/vignettes/figures/fig8.png |binary 67 files changed, 460 insertions(+), 329 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.93 dated 2026-05-18 and 2.0.94 dated 2026-06-26
DESCRIPTION | 8 +++--- MD5 | 18 +++++++-------- NEWS | 8 ++++++ R/zORscore.R | 5 ++-- R/zlimit.R | 42 +++++++++++++++++++++++------------ inst/doc/epiR_descriptive_epi.html | 16 ++++++------- inst/doc/epiR_diagnostic_tests.html | 21 +++++++++-------- inst/doc/epiR_measures_of_assoc.html | 12 +++++----- inst/doc/epiR_sample_size.html | 4 +-- inst/doc/epiR_surveillance.html | 14 +++++------ 10 files changed, 86 insertions(+), 62 deletions(-)
Title: A Computational Tool for Astrochronology
Description: Routines for astrochronologic testing, astronomical time scale construction, and time series analysis <doi:10.1016/j.earscirev.2018.11.015>. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Author: Stephen Meyers [aut, cre],
Alberto Malinverno [ctb],
Linda Hinnov [ctb],
Christian Zeeden [ctb],
Huaran Liu [ctb],
Vincent Moron [ctb],
Michel Crucifix [ctb]
Maintainer: Stephen Meyers <smeyers@geology.wisc.edu>
Diff between astrochron versions 1.6 dated 2026-02-25 and 1.7 dated 2026-06-26
astrochron-1.6/astrochron/R/FUNCTION-accum_v4.R |only astrochron-1.6/astrochron/R/FUNCTION-getData_v10.R |only astrochron-1.6/astrochron/R/FUNCTION-getLaskar_v4.R |only astrochron-1.6/astrochron/R/FUNCTION-timeOptBMCMCplot_v5.R |only astrochron-1.6/astrochron/R/FUNCTION-timeOptB_v5.R |only astrochron-1.7/astrochron/DESCRIPTION | 8 +-- astrochron-1.7/astrochron/MD5 | 34 ++++++------- astrochron-1.7/astrochron/NAMESPACE | 1 astrochron-1.7/astrochron/NEWS | 20 +++++++ astrochron-1.7/astrochron/R/FUNCTION-accum_v5.R |only astrochron-1.7/astrochron/R/FUNCTION-getData_v11.R |only astrochron-1.7/astrochron/R/FUNCTION-getLaskar_v5.R |only astrochron-1.7/astrochron/R/FUNCTION-hoangPriors.R |only astrochron-1.7/astrochron/R/FUNCTION-timeOptBMCMCplot_v7.R |only astrochron-1.7/astrochron/R/FUNCTION-timeOptB_v6.R |only astrochron-1.7/astrochron/R/startupMessage.R | 4 - astrochron-1.7/astrochron/man/accum.Rd | 3 - astrochron-1.7/astrochron/man/astrochron-package.Rd | 4 - astrochron-1.7/astrochron/man/getData.Rd | 2 astrochron-1.7/astrochron/man/hoangPriors.Rd |only astrochron-1.7/astrochron/man/timeOptB.Rd | 18 ++++++ astrochron-1.7/astrochron/man/timeOptBMCMC.Rd | 21 ++++++++ astrochron-1.7/astrochron/man/timeOptBMCMCplot.Rd | 21 ++++++++ astrochron-1.7/astrochron/man/timeOptBSim.Rd | 18 ++++++ 24 files changed, 127 insertions(+), 27 deletions(-)