Title: Likelihood-Based Confidence Interval in Structural Equation
Models
Description: Forms likelihood-based confidence intervals
(LBCIs) for parameters in structural equation modeling,
introduced in Cheung and Pesigan (2023)
<doi:10.1080/10705511.2023.2183860>. Currently
implements the algorithm illustrated by Pek and Wu
(2018) <doi:10.1037/met0000163>, and supports the robust
LBCI proposed by Falk (2018)
<doi:10.1080/10705511.2017.1367254>.
Author: Shu Fai Cheung [aut, cre] ,
Ivan Jacob Agaloos Pesigan [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semlbci versions 0.12.0 dated 2026-07-08 and 0.12.1 dated 2026-07-27
DESCRIPTION | 6 MD5 | 44 NEWS.md | 19 R/check_sem_out.R | 12 R/ci_bound_wn_i.R | 7 R/set_start_wn.R | 13 README.md | 2 inst/doc/loglike.Rmd | 340 +++--- inst/doc/loglike.html | 8 inst/doc/semlbci.Rmd | 35 inst/doc/semlbci.html | 672 ++++++------ inst/doc/technical_searching_one_bound.Rmd | 1049 +++++++++---------- inst/doc/technical_searching_one_bound.html | 235 ++-- tests/testthat/test-lav_mod_to_ram.R | 64 - tests/testthat/test-semlbci_wn_mg_ustd_pa_user_eq.R | 6 tests/testthat/test-semlbci_wn_mg_ustd_sem_user_eq.R | 6 vignettes/loglike.Rmd | 340 +++--- vignettes/loglike.Rmd.original | 4 vignettes/loglike_plot_a-1.png |binary vignettes/loglike_plot_ab-1.png |binary vignettes/semlbci.Rmd | 35 vignettes/semlbci.Rmd.original | 6 vignettes/technical_searching_one_bound.Rmd | 1049 +++++++++---------- 23 files changed, 2028 insertions(+), 1924 deletions(-)
Title: Influential Cases in Structural Equation Modeling
Description: Sensitivity analysis in structural equation modeling using
influence measures and diagnostic plots. Support leave-one-out casewise
sensitivity analysis presented by Pek and MacCallum (2011)
<doi:10.1080/00273171.2011.561068> and approximate casewise influence
using scores and casewise likelihood. An introduction to
the package can be found in Cheung and Lai (2026)
<doi:10.1080/00273171.2026.2634293>.
Author: Shu Fai Cheung [aut, cre] ,
Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semfindr versions 0.2.0 dated 2026-03-06 and 0.2.1 dated 2026-07-27
DESCRIPTION | 8 MD5 | 124 ++-- NEWS.md | 24 R/approx_check.R | 12 R/generic_index_plot.R | 27 R/lavaan_rerun.R | 14 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/casewise_scores.Rmd | 4 inst/doc/casewise_scores.html | 14 inst/doc/selecting_cases.html | 10 inst/doc/semfindr.Rmd | 4 inst/doc/semfindr.html | 42 - inst/doc/user_id.Rmd | 253 +++++++- inst/doc/user_id.html | 283 ++++++++-- man/est_change_plot.Rd | 8 man/est_change_raw.Rd | 4 man/index_plot.Rd | 11 man/influence_plot.Rd | 8 man/lavaan_rerun.Rd | 8 man/pars_id.Rd | 2 man/pars_id_to_lorg.Rd | 6 man/semfindr-package.Rd | 1 tests/testthat/test-est_change_loo_multi_select_by_op.R | 4 tests/testthat/test-est_change_raw_approx_multi.R | 3 tests/testthat/test-est_change_raw_approx_multi_labelled.R | 3 tests/testthat/test-est_change_raw_loo_multi.R | 24 tests/testthat/test-est_change_raw_loo_multi_select_by_op.R | 49 + tests/testthat/test-lavaan_rerun_multi_nonconvergence.R | 15 vignettes/articles/user_fun-1.png |binary vignettes/articles/user_fun2-1.png |binary vignettes/articles/user_function.Rmd | 48 + vignettes/articles/user_function.Rmd.original | 23 vignettes/casewise_scores.Rmd | 4 vignettes/compare-approx-gcd-1.png |binary vignettes/compare-est-change-1.png |binary vignettes/plot-change-chisq-1.png |binary vignettes/plot-change-rmsea-1.png |binary vignettes/semfindr.Rmd | 4 vignettes/semfindr_est_chagne_plot_fig-1.png |binary vignettes/semfindr_est_change_gcd_plot_approx_std_fig-1.png |binary vignettes/semfindr_est_change_gcd_plot_approx_std_fig_2-1.png |binary vignettes/semfindr_est_change_gcd_plot_fig-1.png |binary vignettes/semfindr_est_change_gcd_plot_fig_2-1.png |binary vignettes/semfindr_est_change_plot_approx_fig-1.png |binary vignettes/semfindr_est_change_plot_approx_fig_2-1.png |binary vignettes/semfindr_est_change_plot_approx_fig_3-1.png |binary vignettes/semfindr_est_change_plot_fig_2-1.png |binary vignettes/semfindr_est_change_plot_fig_3-1.png |binary vignettes/semfindr_gcd_gof_md_plot_approx_fig-1.png |binary vignettes/semfindr_gcd_gof_md_plot_fig-1.png |binary vignettes/semfindr_gcd_gof_plot_approx_fig-1.png |binary vignettes/semfindr_gcd_gof_plot_fig-1.png |binary vignettes/semfindr_gcd_plot_approx_fig-1.png |binary vignettes/semfindr_gcd_plot_fig-1.png |binary vignettes/semfindr_md_plot_approx_fig-1.png |binary vignettes/semfindr_md_plot_fig-1.png |binary vignettes/user_id.Rmd | 253 +++++++- vignettes/user_id_gcd_gof_md_plot_fig-1.png |binary vignettes/user_id_gcd_gof_plot_fig-1.png |binary vignettes/user_id_gcd_plot_fig-1.png |binary vignettes/user_id_md_plot_fig-1.png |binary 63 files changed, 1004 insertions(+), 295 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: Kevin Ushey [aut, cre] ,
JJ Allaire [aut],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] ,
Hamada S. Badr [ctb] ,
Dirk Eddelbuettel [aut] ,
Intel [aut, cph] ,
UXL Foundation [aut, cph] ,
Microsoft [cph],
Posit, PB [...truncated...]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 6.1.0 dated 2026-07-25 and 6.1.1 dated 2026-07-27
DESCRIPTION | 6 +-- MD5 | 6 +-- NEWS.md | 14 ++++++++ tools/config/configure.R | 81 +---------------------------------------------- 4 files changed, 22 insertions(+), 85 deletions(-)
Title: Utilities for Geo-Spatial Cluster Detection and Significance
Classification
Description: Provides utilities for manipulating time series of location-based counts of events to detect geo-spatial clusters. Significance of these clusters is determined using a set of models that classify based on a learned relationship between observed and the log(observed/expected) ratio of counts. The approach implemented here is similar to prospective space-time estimation of clusters using the scan statistic.
Author: Luke C. Mullany [aut, cre],
Howard S. Burkom [aut]
Maintainer: Luke C. Mullany <luke.mullany@jhuapl.edu>
Diff between gsClusterDetect versions 1.0.0 dated 2026-03-23 and 1.0.1 dated 2026-07-27
DESCRIPTION | 26 +++--- MD5 | 61 +++++++++++---- NAMESPACE | 3 NEWS.md | 15 +++ R/cluster_functions.R | 117 +++++++++++++++++++++++------- R/data.R | 15 +++ R/location_functions.R | 56 ++++++++++++-- R/mapping_functions.R |only R/sysdata.rda |binary README.md | 16 +++- build |only data/states.rda |only inst |only man/create_dist_list.Rd | 12 +-- man/dot-clean_up_alert_table.Rd |only man/find_clusters.Rd | 15 +-- man/gen_nearby_case_info.Rd | 6 - man/generate_case_grids.Rd | 7 + man/generate_observed_expected.Rd | 11 +- man/get_point_data.Rd |only man/gsClusterDetect-package.Rd | 6 + man/map_clusters.Rd |only man/map_clusters_ggplot.Rd |only man/map_clusters_plotly.Rd |only man/prepare_map_data.Rd |only man/sf_to_plotly_polygons.Rd |only man/state_distance_matrix.Rd |only man/states.Rd |only man/validate_clusters.Rd |only man/validate_sf_file.Rd |only tests/testthat/test-cluster-compression.R | 12 ++- tests/testthat/test-cluster-find.R | 4 - tests/testthat/test-location-functions.R | 37 +++++++++ tests/testthat/test-mapping_functions.R |only vignettes |only 35 files changed, 320 insertions(+), 99 deletions(-)
More information about gsClusterDetect at CRAN
Permanent link
Title: Set Alpha Based on Sample Size Using Bayes Factors
Description: Sets the alpha level for coefficients in a regression model
as a decreasing function of the sample size through the use of
Jeffreys' Approximate Bayes factor. You tell alphaN() your sample
size, and it tells you to which value you must lower alpha to avoid
Lindley's Paradox. For details, see Wulff and Taylor (2024)
<doi:10.1177/14761270231214429>. Alpha can also be calibrated to the
effect-size and moment Bayes factors of Klauer, Meyer-Grant, and
Kellen (2025) <doi:10.3758/s13423-024-02612-2>, which center the
alternative hypothesis on an effect size of your choosing.
Author: Jesper Wulff [aut, cre] ,
Luke Taylor [aut]
Maintainer: Jesper Wulff <jwulff@econ.au.dk>
Diff between alphaN versions 0.2.0 dated 2026-07-12 and 0.3.0 dated 2026-07-27
DESCRIPTION | 11 - MD5 | 61 +++++--- NAMESPACE | 14 ++ NEWS.md | 85 ++++++++++++ R/JAB.R | 40 ++++- R/JAB_plot.R | 34 +++- R/alphaN.R | 92 +++++++++---- R/alphaN_plot.R | 123 ++++++++++++----- R/alphaN_power.R |only R/alphaN_report.R |only R/klauer.R | 221 +++++++++++++++++++++++++++----- R/klauerBF.R |only R/n_effective.R |only README.md | 132 ++++++++++++++++++- inst/CITATION | 20 ++ inst/WORDLIST | 33 +++- inst/doc/intro-alphaN.R | 12 + inst/doc/intro-alphaN.Rmd | 31 ++++ inst/doc/intro-alphaN.html | 51 ++++++- man/JAB.Rd | 21 ++- man/alphaN.Rd | 99 ++++++++++---- man/alphaN_plot.Rd | 42 +++++- man/alphaN_power.Rd |only man/alphaN_power_plot.Rd |only man/alphaN_report.Rd |only man/figures/README-JAB-plot-1.png |binary man/figures/README-alphaN-plot-1.png |binary man/figures/README-power-plot-1.png |only man/klauerBF.Rd |only man/n_effective.Rd |only tests/testthat/test-JAB.R | 18 ++ tests/testthat/test-alphaN_report.R |only tests/testthat/test-crossval.R |only tests/testthat/test-klauer-regression.R |only tests/testthat/test-klauerBF.R |only tests/testthat/test-n_effective.R |only tests/testthat/test-numerics.R |only tests/testthat/test-plots.R | 16 ++ tests/testthat/test-power.R |only vignettes/intro-alphaN.Rmd | 31 ++++ 40 files changed, 986 insertions(+), 201 deletions(-)
Title: Poisson Lognormal Models
Description: The Poisson-lognormal model and variants (Chiquet,
Mariadassou and Robin, 2021 <doi:10.3389/fevo.2021.588292>) can be
used for a variety of multivariate problems when count data are at
play, including principal component analysis for count data,
discriminant analysis, model-based clustering and network inference.
Implements variational algorithms to fit such models accompanied with
a set of functions for visualization and diagnostic.
Author: Julien Chiquet [aut, cre] ,
Mahendra Mariadassou [aut] ,
Stephane Robin [aut],
Francois Gindraud [aut],
Julie Aubert [ctb],
Bastien Batardiere [ctb],
Giovanni Poggiato [ctb],
Cole Trapnell [ctb],
Maddy Duran [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between PLNmodels versions 1.2.2 dated 2025-03-21 and 1.3.0 dated 2026-07-27
PLNmodels-1.2.2/PLNmodels/inst/simus_ZIPLN |only PLNmodels-1.2.2/PLNmodels/man/figures/PLN-1.png |only PLNmodels-1.2.2/PLNmodels/man/figures/PLNLDA-1.png |only PLNmodels-1.2.2/PLNmodels/man/figures/PLNPCA-1.png |only PLNmodels-1.2.2/PLNmodels/man/figures/PLNPCA-2.png |only PLNmodels-1.2.2/PLNmodels/man/figures/PLNnetwork-1.png |only PLNmodels-1.2.2/PLNmodels/man/figures/PLNnetwork-2.png |only PLNmodels-1.2.2/PLNmodels/src/lambertW.cpp |only PLNmodels-1.2.2/PLNmodels/src/lambertW.h |only PLNmodels-1.2.2/PLNmodels/src/optim_diag_cov.cpp |only PLNmodels-1.2.2/PLNmodels/src/optim_fixed_cov.cpp |only PLNmodels-1.2.2/PLNmodels/src/optim_full_cov.cpp |only PLNmodels-1.2.2/PLNmodels/src/optim_rank_cov.cpp |only PLNmodels-1.2.2/PLNmodels/src/optim_spherical.cpp |only PLNmodels-1.2.2/PLNmodels/src/optim_zi-pln.cpp |only PLNmodels-1.2.2/PLNmodels/tests/testthat/_snaps |only PLNmodels-1.2.2/PLNmodels/vignettes/article |only PLNmodels-1.3.0/PLNmodels/DESCRIPTION | 30 PLNmodels-1.3.0/PLNmodels/MD5 | 273 ++- PLNmodels-1.3.0/PLNmodels/NAMESPACE | 19 PLNmodels-1.3.0/PLNmodels/NEWS.md | 49 PLNmodels-1.3.0/PLNmodels/R/PLN.R | 71 PLNmodels-1.3.0/PLNmodels/R/PLNLDA.R | 51 PLNmodels-1.3.0/PLNmodels/R/PLNLDAfit-class.R | 55 PLNmodels-1.3.0/PLNmodels/R/PLNPCA.R | 107 - PLNmodels-1.3.0/PLNmodels/R/PLNPCAfamily-class.R | 91 + PLNmodels-1.3.0/PLNmodels/R/PLNPCAfit-class.R | 282 +++ PLNmodels-1.3.0/PLNmodels/R/PLNfit-S3methods.R | 94 + PLNmodels-1.3.0/PLNmodels/R/PLNfit-class.R | 467 +++--- PLNmodels-1.3.0/PLNmodels/R/PLNmixture.R | 48 PLNmodels-1.3.0/PLNmodels/R/PLNmixturefamily-class.R | 18 PLNmodels-1.3.0/PLNmodels/R/PLNmixturefit-class.R | 26 PLNmodels-1.3.0/PLNmodels/R/PLNmodels-package.R | 2 PLNmodels-1.3.0/PLNmodels/R/PLNnetwork.R | 79 - PLNmodels-1.3.0/PLNmodels/R/PLNnetworkfamily-class.R | 76 - PLNmodels-1.3.0/PLNmodels/R/PLNnetworkfit-class.R | 41 PLNmodels-1.3.0/PLNmodels/R/RcppExports.R | 156 +- PLNmodels-1.3.0/PLNmodels/R/ZIPLN.R | 29 PLNmodels-1.3.0/PLNmodels/R/ZIPLNfit-S3methods.R | 85 + PLNmodels-1.3.0/PLNmodels/R/ZIPLNfit-class.R | 237 +-- PLNmodels-1.3.0/PLNmodels/R/ZIPLNnetwork.R | 16 PLNmodels-1.3.0/PLNmodels/R/microcosm.R |only PLNmodels-1.3.0/PLNmodels/R/plot_utils.R | 53 PLNmodels-1.3.0/PLNmodels/R/utils-zipln.R | 19 PLNmodels-1.3.0/PLNmodels/R/utils.R | 201 ++ PLNmodels-1.3.0/PLNmodels/R/zzz.R | 1 PLNmodels-1.3.0/PLNmodels/build/partial.rdb |binary PLNmodels-1.3.0/PLNmodels/build/vignette.rds |binary PLNmodels-1.3.0/PLNmodels/data/microcosm.rda |only PLNmodels-1.3.0/PLNmodels/inst/WORDLIST | 48 PLNmodels-1.3.0/PLNmodels/inst/doc/Import_data.Rmd | 2 PLNmodels-1.3.0/PLNmodels/inst/doc/Import_data.html | 12 PLNmodels-1.3.0/PLNmodels/inst/doc/PLN.Rmd | 4 PLNmodels-1.3.0/PLNmodels/inst/doc/PLN.html | 106 - PLNmodels-1.3.0/PLNmodels/inst/doc/PLNLDA.Rmd | 2 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNLDA.html | 736 +++++----- PLNmodels-1.3.0/PLNmodels/inst/doc/PLNPCA.R | 9 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNPCA.Rmd | 15 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNPCA.html | 251 +-- PLNmodels-1.3.0/PLNmodels/inst/doc/PLNmixture.R | 9 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNmixture.Rmd | 15 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNmixture.html | 123 - PLNmodels-1.3.0/PLNmodels/inst/doc/PLNnetwork.R | 29 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNnetwork.Rmd | 54 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNnetwork.html | 309 ++-- PLNmodels-1.3.0/PLNmodels/inst/doc/Trichoptera.Rmd | 2 PLNmodels-1.3.0/PLNmodels/inst/doc/Trichoptera.html | 18 PLNmodels-1.3.0/PLNmodels/inst/doc/ZIPLN.R |only PLNmodels-1.3.0/PLNmodels/inst/doc/ZIPLN.Rmd |only PLNmodels-1.3.0/PLNmodels/inst/doc/ZIPLN.html |only PLNmodels-1.3.0/PLNmodels/man/AIC.PLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/AIC.ZIPLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/BIC.PLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/BIC.ZIPLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/ICL.Rd |only PLNmodels-1.3.0/PLNmodels/man/Networkfamily.Rd | 321 ++-- PLNmodels-1.3.0/PLNmodels/man/PLN.Rd | 2 PLNmodels-1.3.0/PLNmodels/man/PLNLDA.Rd | 21 PLNmodels-1.3.0/PLNmodels/man/PLNLDA_param.Rd | 15 PLNmodels-1.3.0/PLNmodels/man/PLNLDAfit.Rd | 431 ++--- PLNmodels-1.3.0/PLNmodels/man/PLNLDAfit_diagonal.Rd | 130 - PLNmodels-1.3.0/PLNmodels/man/PLNPCA.Rd | 9 PLNmodels-1.3.0/PLNmodels/man/PLNPCA_param.Rd | 74 - PLNmodels-1.3.0/PLNmodels/man/PLNPCAfamily.Rd | 263 +-- PLNmodels-1.3.0/PLNmodels/man/PLNPCAfit.Rd | 594 ++++---- PLNmodels-1.3.0/PLNmodels/man/PLN_param.Rd | 35 PLNmodels-1.3.0/PLNmodels/man/PLNfamily.Rd | 253 +-- PLNmodels-1.3.0/PLNmodels/man/PLNfit.Rd | 497 +++--- PLNmodels-1.3.0/PLNmodels/man/PLNfit_diagonal.Rd | 247 +-- PLNmodels-1.3.0/PLNmodels/man/PLNfit_fixedcov.Rd | 161 +- PLNmodels-1.3.0/PLNmodels/man/PLNfit_genpop.Rd |only PLNmodels-1.3.0/PLNmodels/man/PLNfit_spherical.Rd | 119 - PLNmodels-1.3.0/PLNmodels/man/PLNmixture.Rd | 9 PLNmodels-1.3.0/PLNmodels/man/PLNmixture_param.Rd | 66 PLNmodels-1.3.0/PLNmodels/man/PLNmixturefamily.Rd | 287 ++- PLNmodels-1.3.0/PLNmodels/man/PLNmixturefit.Rd | 379 ++--- PLNmodels-1.3.0/PLNmodels/man/PLNmodels-package.Rd | 1 PLNmodels-1.3.0/PLNmodels/man/PLNnetwork.Rd | 2 PLNmodels-1.3.0/PLNmodels/man/PLNnetwork_param.Rd | 100 + PLNmodels-1.3.0/PLNmodels/man/PLNnetworkfamily.Rd | 137 - PLNmodels-1.3.0/PLNmodels/man/PLNnetworkfit.Rd | 240 +-- PLNmodels-1.3.0/PLNmodels/man/ZIPLN.Rd | 2 PLNmodels-1.3.0/PLNmodels/man/ZIPLN_param.Rd | 13 PLNmodels-1.3.0/PLNmodels/man/ZIPLNfit.Rd | 373 ++--- PLNmodels-1.3.0/PLNmodels/man/ZIPLNfit_diagonal.Rd | 101 - PLNmodels-1.3.0/PLNmodels/man/ZIPLNfit_fixed.Rd | 101 - PLNmodels-1.3.0/PLNmodels/man/ZIPLNfit_sparse.Rd | 199 +- PLNmodels-1.3.0/PLNmodels/man/ZIPLNfit_spherical.Rd | 101 - PLNmodels-1.3.0/PLNmodels/man/ZIPLNnetwork.Rd | 2 PLNmodels-1.3.0/PLNmodels/man/ZIPLNnetwork_param.Rd | 14 PLNmodels-1.3.0/PLNmodels/man/ZIPLNnetworkfamily.Rd | 147 + PLNmodels-1.3.0/PLNmodels/man/compute_PLN_starting_point.Rd | 25 PLNmodels-1.3.0/PLNmodels/man/compute_ZIPLN_starting_point.Rd |only PLNmodels-1.3.0/PLNmodels/man/figures/README-pln-corrplot-1.png |only PLNmodels-1.3.0/PLNmodels/man/figures/README-plnlda-1.png |only PLNmodels-1.3.0/PLNmodels/man/figures/README-plnmixture-1.png |only PLNmodels-1.3.0/PLNmodels/man/figures/README-plnnetwork-1.png |only PLNmodels-1.3.0/PLNmodels/man/figures/README-plnpca-1.png |only PLNmodels-1.3.0/PLNmodels/man/logLik.PLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/logLik.ZIPLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/microcosm.Rd |only PLNmodels-1.3.0/PLNmodels/man/predict.ZIPLNfit.Rd | 4 PLNmodels-1.3.0/PLNmodels/src/RcppExports.cpp | 570 +++++-- PLNmodels-1.3.0/PLNmodels/src/builtin_optim_pln.h |only PLNmodels-1.3.0/PLNmodels/src/builtin_optim_zipln.h |only PLNmodels-1.3.0/PLNmodels/src/builtin_plnpca.h |only PLNmodels-1.3.0/PLNmodels/src/covariance_pln.h |only PLNmodels-1.3.0/PLNmodels/src/covariance_plnpca.h |only PLNmodels-1.3.0/PLNmodels/src/covariance_zipln.h |only PLNmodels-1.3.0/PLNmodels/src/nlopt_optim_pln.h |only PLNmodels-1.3.0/PLNmodels/src/nlopt_optim_zipln.h |only PLNmodels-1.3.0/PLNmodels/src/nlopt_wrapper.cpp | 36 PLNmodels-1.3.0/PLNmodels/src/nlopt_wrapper.h | 10 PLNmodels-1.3.0/PLNmodels/src/optim_genet_cov.cpp | 13 PLNmodels-1.3.0/PLNmodels/src/optim_zipln_mstep.cpp |only PLNmodels-1.3.0/PLNmodels/src/packing.cpp | 14 PLNmodels-1.3.0/PLNmodels/src/packing.h | 2 PLNmodels-1.3.0/PLNmodels/src/utils.h | 141 + PLNmodels-1.3.0/PLNmodels/src/wrappers_builtin_optim_pln.cpp |only PLNmodels-1.3.0/PLNmodels/src/wrappers_builtin_optim_plnpca.cpp |only PLNmodels-1.3.0/PLNmodels/src/wrappers_builtin_optim_zipln.cpp |only PLNmodels-1.3.0/PLNmodels/src/wrappers_nlopt_optim_pln.cpp |only PLNmodels-1.3.0/PLNmodels/src/wrappers_nlopt_optim_plnpca.cpp |only PLNmodels-1.3.0/PLNmodels/src/wrappers_nlopt_optim_zipln.cpp |only PLNmodels-1.3.0/PLNmodels/tests/testthat/Rplots.pdf |binary PLNmodels-1.3.0/PLNmodels/tests/testthat/test-backends.R |only PLNmodels-1.3.0/PLNmodels/tests/testthat/test-import-utils.R | 44 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-pln-genpop.R |only PLNmodels-1.3.0/PLNmodels/tests/testthat/test-pln.R | 43 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-plnfit.R | 80 + PLNmodels-1.3.0/PLNmodels/tests/testthat/test-plnlda-fit.R | 22 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-plnnetworkfit.R | 40 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-plnpcafit.R | 58 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-standard-error.R | 2 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-zipln.R | 20 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-ziplnfit.R | 39 PLNmodels-1.3.0/PLNmodels/vignettes/Import_data.Rmd | 2 PLNmodels-1.3.0/PLNmodels/vignettes/PLN.Rmd | 4 PLNmodels-1.3.0/PLNmodels/vignettes/PLNLDA.Rmd | 2 PLNmodels-1.3.0/PLNmodels/vignettes/PLNPCA.Rmd | 15 PLNmodels-1.3.0/PLNmodels/vignettes/PLNmixture.Rmd | 15 PLNmodels-1.3.0/PLNmodels/vignettes/PLNnetwork.Rmd | 54 PLNmodels-1.3.0/PLNmodels/vignettes/Trichoptera.Rmd | 2 PLNmodels-1.3.0/PLNmodels/vignettes/ZIPLN.Rmd |only PLNmodels-1.3.0/PLNmodels/vignettes/articles |only PLNmodels-1.3.0/PLNmodels/vignettes/bib |only 166 files changed, 6375 insertions(+), 4748 deletions(-)
Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanés Bové et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre] ,
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [ [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 2.2.0 dated 2026-07-05 and 2.2.1 dated 2026-07-27
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ build/partial.rdb |binary tests/testthat/test-helpers_design.R | 8 ++++---- tests/testthat/test-helpers_knitr.R | 2 +- tests/testthat/test-mcmc.R | 10 ++++++---- 7 files changed, 26 insertions(+), 18 deletions(-)
Title: Posetic Data Analysis
Description: Build and manipulate partially ordered sets (posets), to perform some data analysis
on them and to implement multi-criteria decision making procedures. Several efficient ways for generating linear extensions are implemented, together with functions for building mutual ranking probabilities, incomparability, dominance and separation scores (Fattore, M., De Capitani, L., Avellone, A., Suardi, A. (2024). A fuzzy posetic toolbox for multi-criteria evaluation on ordinal data systems. ANNALS OF OPERATIONS RESEARCH <doi:10.1007/s10479-024-06352-3>).
Author: Alessandro Avellone [aut, cre],
Lucio De Capitani [aut],
Marco Fattore [aut]
Maintainer: Alessandro Avellone <alessandro.avellone@unimib.it>
Diff between poseticDataAnalysis versions 1.1.0 dated 2026-05-18 and 1.1.1 dated 2026-07-27
DESCRIPTION | 6 MD5 | 40 +++--- R/00package-class.R | 13 +- R/00package-exports.R | 24 +++ R/BubleyDyerMRPGenerator.R | 13 -- R/BuildBubleyDyerEvaluationGenerator.R | 13 -- R/BuildBubleyDyerSeparationGenerator.R | 13 -- R/LEBubleyDyer.R | 17 +- build/partial.rdb |binary man/BubleyDyerEvaluationGenerator-class.Rd | 2 man/BubleyDyerGenerator-class.Rd | 2 man/BubleyDyerMRPGenerator-class.Rd | 2 man/BubleyDyerMRPGenerator.Rd | 2 man/BubleyDyerSeparationGenerator-class.Rd | 2 man/BuildBubleyDyerEvaluationGenerator.Rd | 2 man/BuildBubleyDyerSeparationGenerator.Rd | 2 man/LEBubleyDyer.Rd | 2 src/dimensionalityReduction.cpp | 1 src/dimensionalityReduction.h | 1 src/displayMessage.h | 7 - src/rwrapper.cpp | 181 +++++++++++++++++++---------- 21 files changed, 221 insertions(+), 124 deletions(-)
More information about poseticDataAnalysis at CRAN
Permanent link
Title: Conditional Inference Trees with Stacked Multiple Imputation
Description: Implements the stacked-imputation workflow for conditional
inference trees ('ctree') described in Sherlock et al. (2026)
<doi:10.1080/00273171.2026.2661244>. When data contain missing values,
multiply imputed datasets (e.g., from 'mice') are stacked vertically
and a single 'ctree' is fit on the combined data. To correct for the
artificially inflated sample size introduced by stacking, every
node-level test statistic is divided by the number of imputations M,
the node-level p-values are recomputed from the chi-squared reference
distribution 'ctree' uses (including its multiplicity adjustment across
candidate splitting variables), and the tree is compressed bottom-up
(the Stack/M correction). Degrees of freedom are derived for each node
and each candidate variable, so univariate, bivariate and
higher-dimensional outcomes are all handled, as are unordered factor
predictors, whose degrees of freedom depend on how many levels remain
in a node. The result is a conservative but interpre [...truncated...]
Author: Phillip Sherlock [aut, cre]
Maintainer: Phillip Sherlock <phillip.sherlock@ufl.edu>
Diff between ctreeMI versions 0.3.0 dated 2026-07-25 and 1.0.0 dated 2026-07-27
ctreeMI-0.3.0/ctreeMI/R/zzz.R |only ctreeMI-0.3.0/ctreeMI/man/rescale_alpha.Rd |only ctreeMI-1.0.0/ctreeMI/DESCRIPTION | 28 ctreeMI-1.0.0/ctreeMI/MD5 | 44 ctreeMI-1.0.0/ctreeMI/NAMESPACE | 4 ctreeMI-1.0.0/ctreeMI/NEWS.md | 112 + ctreeMI-1.0.0/ctreeMI/R/ctree_stacked.R | 55 ctreeMI-1.0.0/ctreeMI/R/methods.R | 14 ctreeMI-1.0.0/ctreeMI/R/node_table.R | 76 + ctreeMI-1.0.0/ctreeMI/R/stackM.R | 664 ++++++---- ctreeMI-1.0.0/ctreeMI/R/utils.R | 71 - ctreeMI-1.0.0/ctreeMI/build/partial.rdb |binary ctreeMI-1.0.0/ctreeMI/man/check_stackM_extraction.Rd |only ctreeMI-1.0.0/ctreeMI/man/ctreeMI-package.Rd | 119 + ctreeMI-1.0.0/ctreeMI/man/ctree_stacked.Rd | 295 ++-- ctreeMI-1.0.0/ctreeMI/man/node_table.Rd | 113 - ctreeMI-1.0.0/ctreeMI/man/print.ctreeMI.Rd | 32 ctreeMI-1.0.0/ctreeMI/man/print.ctreeMI_nodes.Rd |only ctreeMI-1.0.0/ctreeMI/man/print.ctreeMI_report.Rd |only ctreeMI-1.0.0/ctreeMI/man/prune_stackM.Rd |only ctreeMI-1.0.0/ctreeMI/man/report_ctreeMI.Rd | 77 - ctreeMI-1.0.0/ctreeMI/man/rescale_statistic.Rd |only ctreeMI-1.0.0/ctreeMI/man/stack_imputations.Rd | 65 ctreeMI-1.0.0/ctreeMI/man/summary.ctreeMI.Rd | 38 ctreeMI-1.0.0/ctreeMI/tests/testthat/test-ctreeMI.R | 111 + ctreeMI-1.0.0/ctreeMI/tests/testthat/test-stackM-correction.R | 9 ctreeMI-1.0.0/ctreeMI/tests/testthat/test-stackM-numerics.R |only 27 files changed, 1205 insertions(+), 722 deletions(-)
Title: Collinearity Detection using Redefined Variance Inflation Factor
and Graphical Methods
Description: The detection of troubling approximate collinearity in a multiple linear regression model is a classical problem in Econometrics. This package is focused on determining whether or not the degree of approximate multicollinearity in a multiple linear regression model is of concern, meaning that it affects the statistical analysis (i.e. individual significance tests) of the model. This objective is achieved by using the variance inflation factor redefined and the scatterplot between the variance inflation factor and the coefficient of variation. For more details see Salmerón R., García C.B. and García J. (2018) <doi:10.1080/00949655.2018.1463376>, Salmerón, R., Rodríguez, A. and García C. (2020) <doi:10.1007/s00180-019-00922-x>, Salmerón, R., García, C.B, Rodríguez, A. and García, C. (2022) <doi:10.32614/RJ-2023-010>, Salmerón, R., García, C.B. and García, J. (2025) <doi:10.1007/s10614-024-10575-8> and Salmerón, R., García, C.B, García J. (2023, working paper) < [...truncated...]
Author: R. Salmeron [aut, cre],
C.B. Garcia [aut]
Maintainer: R. Salmeron <romansg@ugr.es>
Diff between rvif versions 3.2 dated 2025-10-09 and 3.2.1 dated 2026-07-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- tests/testthat/test-cv_vif.R | 2 +- tests/testthat/test-rvifs.R | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Generate SVG Information Cards with Embedded Fonts and Badges
Description: Create self-contained SVG information cards with embedded 'Google
Fonts', shields-style badges, and custom logos. Cards are fully
portable SVG files ideal for dashboards, reports, and web applications.
Includes functions to export cards to PNG and PDF formats and display them in
'R Markdown' and 'Quarto' documents.
Author: Andre Leite [aut, cre],
Marcos Wasiliew [aut],
Hugo Vasconcelos [aut],
Carlos Amorim [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between cardargus versions 0.2.3 dated 2026-06-14 and 0.2.5 dated 2026-07-27
cardargus-0.2.3/cardargus/man/start_chrome_session.Rd |only cardargus-0.2.3/cardargus/man/write_svg_html_temp.Rd |only cardargus-0.2.5/cardargus/DESCRIPTION | 20 cardargus-0.2.5/cardargus/MD5 | 66 + cardargus-0.2.5/cardargus/NAMESPACE | 1 cardargus-0.2.5/cardargus/NEWS.md | 71 ++ cardargus-0.2.5/cardargus/R/cards.R | 4 cardargus-0.2.5/cardargus/R/chrome.R | 405 ++++++++---- cardargus-0.2.5/cardargus/R/conversion.R | 97 ++ cardargus-0.2.5/cardargus/R/fonts.R | 28 cardargus-0.2.5/cardargus/R/knitr.R | 28 cardargus-0.2.5/cardargus/R/utils.R | 7 cardargus-0.2.5/cardargus/R/zzz.R | 30 cardargus-0.2.5/cardargus/README.md | 33 cardargus-0.2.5/cardargus/inst/doc/export.R | 19 cardargus-0.2.5/cardargus/inst/doc/export.Rmd | 38 + cardargus-0.2.5/cardargus/inst/doc/export.html | 258 ++++--- cardargus-0.2.5/cardargus/man/batch_svg_to_base64_chrome.Rd | 10 cardargus-0.2.5/cardargus/man/batch_svg_to_png_chrome.Rd | 10 cardargus-0.2.5/cardargus/man/build_svg_html.Rd |only cardargus-0.2.5/cardargus/man/cardargus-package.Rd | 4 cardargus-0.2.5/cardargus/man/chrome_session.Rd |only cardargus-0.2.5/cardargus/man/chrome_session_alive.Rd |only cardargus-0.2.5/cardargus/man/close_chrome_session.Rd |only cardargus-0.2.5/cardargus/man/convert_svg_with_session.Rd | 16 cardargus-0.2.5/cardargus/man/figures/cardargus_card.png |binary cardargus-0.2.5/cardargus/man/font_cache_dir.Rd | 7 cardargus-0.2.5/cardargus/man/load_svg_page.Rd |only cardargus-0.2.5/cardargus/man/running_under_check.Rd |only cardargus-0.2.5/cardargus/man/save_card_for_knitr.Rd | 6 cardargus-0.2.5/cardargus/man/svg_to_pdf.Rd |only cardargus-0.2.5/cardargus/man/svg_to_pdf_chrome.Rd | 14 cardargus-0.2.5/cardargus/man/svg_to_png.Rd | 11 cardargus-0.2.5/cardargus/man/svg_to_png_chrome.Rd | 16 cardargus-0.2.5/cardargus/man/wait_for_page_ready.Rd |only cardargus-0.2.5/cardargus/tests/testthat/test-chrome.R |only cardargus-0.2.5/cardargus/tests/testthat/test-conversion.R | 21 cardargus-0.2.5/cardargus/tests/testthat/test-fonts.R |only cardargus-0.2.5/cardargus/tests/testthat/test-utils.R | 4 cardargus-0.2.5/cardargus/vignettes/export.Rmd | 38 + 40 files changed, 897 insertions(+), 365 deletions(-)
Title: Tools for 'iNZight'
Description: Provides a collection of wrapper functions for common variable and dataset manipulation workflows primarily used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Additionally, many of the functions return the 'tidyverse' code used to obtain the result in an effort to bridge the gap between GUI and coding.
Author: Tom Elliott [aut, cre] ,
Daniel Barnett [aut],
Yiwen He [aut],
Zhaoming Su [aut],
Lushi Cai [ctb],
Akshay Gupta [ctb],
Owen Jin [ctb],
Christoph Knopf [ctb]
Maintainer: Tom Elliott <tom.elliott@auckland.ac.nz>
This is a re-admission after prior archival of version 2.0.3 dated 2025-07-29
Diff between iNZightTools versions 2.0.3 dated 2025-07-29 and 2.0.4 dated 2026-07-27
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/aggregate.R | 20 ++++++++++---------- R/helpers.R | 11 +++++++---- R/import_data.R | 2 +- R/mutate.R | 18 +++++++++++++----- tests/testthat/casdict.csv | 2 +- tests/testthat/test_helpers.R | 15 +++++++++++++++ tests/testthat/test_missing_to_cat.R | 30 ++++++++++++++++++++++++++++++ 9 files changed, 88 insertions(+), 32 deletions(-)
Title: German Election Database (GERDA)
Description: Provides tools to download datasets of German elections
covering local, state, federal, mayoral, European Parliament, and county
(Kreistag) elections, with federal county-level coverage from 1953 and
other families extending through 2025. The package supplies turnout, vote
shares, and derived indicators at the municipal and county level, including
geographically harmonized datasets that account for changes in municipal
boundaries over time and incorporate mail-in voting districts. Bundled data
includes county-level INKAR covariates (1995-2022) and municipality-level
Zensus 2022 indicators. Data is sourced from
<https://github.com/awiedem/german_election_data>.
Author: Hanno Hilbig [aut, cre]
Maintainer: Hanno Hilbig <hhilbig@ucdavis.edu>
Diff between gerda versions 0.8.0 dated 2026-07-24 and 0.8.1 dated 2026-07-27
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 9 +++++++++ R/gerda_cache.R | 3 ++- R/gerda_covariates.R | 5 +++-- R/load_gerda_web.R | 8 ++++++-- man/clear_gerda_cache.Rd | 3 ++- man/gerda_covariates.Rd | 5 +++-- man/load_gerda_web.Rd | 8 ++++++-- 9 files changed, 42 insertions(+), 21 deletions(-)
Title: Formal Concept Analysis
Description: Provides tools to perform fuzzy formal concept analysis, presented in Wille (1982) <doi:10.1007/978-3-642-01815-2_23> and in Ganter and Obiedkov (2016) <doi:10.1007/978-3-662-49291-8>. It provides functions to load and save a formal context, extract its concept lattice and implications. In addition, one can use the implications to compute semantic closures of fuzzy sets and, thus, build recommendation systems. Boolean Matrix Factorization (BMF) is provided by several algorithms (such as GreConD, ASSO, RSF, RSF-ES, GreEss, PaNDa+, and Hyper+).
Author: Domingo Lopez Rodriguez [aut, cre] ,
Angel Mora [aut]
Maintainer: Domingo Lopez Rodriguez <dominlopez78@gmail.com>
Diff between fcaR versions 1.5.0 dated 2026-02-13 and 2.1.0 dated 2026-07-27
DESCRIPTION | 31 - MD5 | 201 +++++++--- NAMESPACE | 10 NEWS.md | 73 +++ R/RcppExports.R | 145 ++++++- R/add_col.R | 2 R/bond_lattice.R |only R/bonds.R |only R/build_sparse_matrix.R | 17 R/compute_closure_fuzzy.R | 5 R/concept_lattice.R | 203 ++++++++++- R/concept_set.R | 34 + R/datasets.R | 22 + R/experimental_blocks.R |only R/experimental_preconcepts.R |only R/fcaR_helpers.R |only R/fcaRviz.R |only R/formal_context.R | 513 +++++++++++++++++++--------- R/implication_set.R | 197 ++++++++-- R/intersection.R | 6 R/lattice_plot.R | 241 +++++++++---- R/logics.R | 25 - R/options.R | 4 R/rule_set.R | 29 + R/subsets.R | 4 R/to_fraction.R | 21 + build/vignette.rds |binary data/guesswho.rda |only inst/doc/bonds.R |only inst/doc/bonds.Rmd |only inst/doc/bonds.html |only inst/doc/concept_lattice.R | 4 inst/doc/concept_lattice.Rmd | 13 inst/doc/concept_lattice.html | 309 ++++++++-------- inst/doc/creating_contexts.R | 28 - inst/doc/creating_contexts.Rmd | 4 inst/doc/creating_contexts.html | 122 ------ inst/doc/fuzzy_fca.html | 69 +-- inst/doc/implications.R | 7 inst/doc/implications.Rmd | 16 inst/doc/implications.html | 41 +- inst/doc/lattice_properties.R | 8 inst/doc/lattice_properties.Rmd | 20 + inst/doc/lattice_properties.html | 32 + inst/doc/lattice_visualization.html | 10 inst/doc/matrix_factorization.R | 62 +-- inst/doc/matrix_factorization.Rmd | 175 ++++++--- inst/doc/matrix_factorization.html | 345 ++++++++++++------ inst/rstudio/addins.dcf | 5 inst/shiny-examples |only man/BondLattice.Rd |only man/ConceptLattice.Rd | 79 ++++ man/ConceptSet.Rd | 22 - man/FormalContext.Rd | 179 ++++++++- man/ImplicationSet.Rd | 20 + man/RuleSet.Rd | 14 man/attribute_set.Rd |only man/bonds.Rd |only man/bonds_mcis.Rd |only man/bonds_standard.Rd |only man/fcaR-package.Rd | 2 man/guesswho.Rd |only man/is_bond.Rd |only man/iterative_recommender.Rd |only man/lattice_plot.Rd | 6 man/object_set.Rd |only man/recommendation_table.Rd |only man/run_fcaRviz.Rd |only src/Logics.cpp | 43 -- src/Logics.h | 6 src/MatrixFactorization.cpp | 392 --------------------- src/RSF_ES_attr.cpp |only src/RSF_attr.cpp |only src/RcppExports.cpp | 456 ++++++++++++++++++++---- src/algorithm1_opt.cpp |only src/arrow_relations.cpp |only src/asso.cpp |only src/aux_functions.h | 5 src/binary_do_optimized.cpp |only src/closure_cpp.cpp |only src/experimental_blocks_cpp.cpp |only src/fastcbo.cpp | 2 src/fcaR_bitset.h |only src/fcaR_utils.h |only src/fuzzy_do.cpp | 68 +-- src/grecond.cpp |only src/greess.cpp |only src/hyper_inclose.cpp |only src/hyper_plus_optimized.cpp |only src/inclose.cpp | 2 src/lattice_algorithms.cpp | 39 +- src/lincbo.cpp |only src/my_tests.cpp | 46 -- src/nextclosure.cpp | 193 +++++++--- src/panda_versions.cpp |only src/poset_metrics.cpp |only src/protoconcepts.cpp |only src/standard_bonds_opt.cpp |only src/vector_operations.cpp | 68 --- tests/testthat/Rplots.pdf |binary tests/testthat/test-arrow_advanced.R |only tests/testthat/test-arrow_relations.R |only tests/testthat/test-bonds.R |only tests/testthat/test-concept_lattice.R | 2 tests/testthat/test-coverage_sniper.R | 365 +++++++++++++++++++ tests/testthat/test-direct_optimal_binary.R |only tests/testthat/test-factorization.R | 67 ++- tests/testthat/test-formal_context.R | 3 tests/testthat/test-helpers.R |only tests/testthat/test-implication_set.R | 2 tests/testthat/test-lincbo.R |only tests/testthat/test-protoconcepts.R |only tests/testthat/test-standard_context.R |only vignettes/bonds.Rmd |only vignettes/concept_lattice.Rmd | 13 vignettes/creating_contexts.Rmd | 4 vignettes/implications.Rmd | 16 vignettes/lattice_properties.Rmd | 20 + vignettes/matrix_factorization.Rmd | 175 ++++++--- 119 files changed, 3558 insertions(+), 1804 deletions(-)
Title: Fast Survival Analysis and Simulation for Clinical Trials
Description: Provides fast alternatives to standard survival analysis functions
in the 'survival' package, together with tools for time-to-event trial
simulation and sequential analysis. The estimation and testing functions
cover a single-time-point Kaplan-Meier estimator (survfit_fast()), log-rank
tests including weighted and stratified variants (survdiff_fast()), a
closed-form hazard ratio estimator based on the Pike-Halley Estimator method
(coxph_fast()), restricted mean survival time (rmst_fast()), window mean
survival time (wmst_fast()), milestone survival comparison
(milestone_fast()), median survival time (medsurv_fast()), the max-combo
test (maxcombo_fast()), the robust modestly-weighted log-rank test
(rmw_fast()), the weighted Kaplan-Meier (Pepe-Fleming) test (wkm_fast()),
the average hazard with survival weight (ahsw_fast()), and the
Kalbfleisch-Prentice average hazard ratio (ahr_fast()). The simulation
layer generates individual patient data (simdata_fast()), performs interim
or sequenti [...truncated...]
Author: Gosuke Homma [aut, cre]
Maintainer: Gosuke Homma <my.name.is.gosuke@gmail.com>
Diff between FastSurvival versions 0.1.0 dated 2026-05-27 and 0.2.0 dated 2026-07-27
FastSurvival-0.1.0/FastSurvival/src/simdata_core.cpp |only FastSurvival-0.2.0/FastSurvival/DESCRIPTION | 50 FastSurvival-0.2.0/FastSurvival/LICENSE | 2 FastSurvival-0.2.0/FastSurvival/MD5 | 197 + FastSurvival-0.2.0/FastSurvival/NAMESPACE | 35 FastSurvival-0.2.0/FastSurvival/NEWS.md | 143 FastSurvival-0.2.0/FastSurvival/R/FastSurvival-package.R | 159 - FastSurvival-0.2.0/FastSurvival/R/RcppExports.R | 374 ++ FastSurvival-0.2.0/FastSurvival/R/ahr_fast.R |only FastSurvival-0.2.0/FastSurvival/R/ahsw_fast.R |only FastSurvival-0.2.0/FastSurvival/R/analysis_fast.R |only FastSurvival-0.2.0/FastSurvival/R/coxph_fast.R | 415 +- FastSurvival-0.2.0/FastSurvival/R/gen_scenario_fast.R |only FastSurvival-0.2.0/FastSurvival/R/kmcurve_fast.R |only FastSurvival-0.2.0/FastSurvival/R/maxcombo_fast.R |only FastSurvival-0.2.0/FastSurvival/R/medsurv_fast.R |only FastSurvival-0.2.0/FastSurvival/R/milestone_fast.R |only FastSurvival-0.2.0/FastSurvival/R/pairwise_fast.R |only FastSurvival-0.2.0/FastSurvival/R/plot.kmcurve_fast.R |only FastSurvival-0.2.0/FastSurvival/R/plot.scenario_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.ahr_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.ahsw_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.coxph_fast.R | 172 - FastSurvival-0.2.0/FastSurvival/R/print.kmcurve_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.maxcombo_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.medsurv_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.milestone_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.rmst_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.rmw_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.scenario_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.simsummary_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.survdiff_fast.R | 97 FastSurvival-0.2.0/FastSurvival/R/print.survfit_fast.R | 132 FastSurvival-0.2.0/FastSurvival/R/print.wkm_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.wmst_fast.R |only FastSurvival-0.2.0/FastSurvival/R/rmst_fast.R |only FastSurvival-0.2.0/FastSurvival/R/rmw_fast.R |only FastSurvival-0.2.0/FastSurvival/R/signif_legend.R |only FastSurvival-0.2.0/FastSurvival/R/signif_star.R |only FastSurvival-0.2.0/FastSurvival/R/simdata_fast.R | 1454 +++++++--- FastSurvival-0.2.0/FastSurvival/R/simsummary_fast.R |only FastSurvival-0.2.0/FastSurvival/R/survdiff_fast.R | 574 ++- FastSurvival-0.2.0/FastSurvival/R/survfit_fast.R | 338 +- FastSurvival-0.2.0/FastSurvival/R/wkm_fast.R |only FastSurvival-0.2.0/FastSurvival/R/wmst_fast.R |only FastSurvival-0.2.0/FastSurvival/README.md | 385 ++ FastSurvival-0.2.0/FastSurvival/build/vignette.rds |binary FastSurvival-0.2.0/FastSurvival/inst/WORDLIST |only FastSurvival-0.2.0/FastSurvival/inst/doc/FastSurvival.R | 150 - FastSurvival-0.2.0/FastSurvival/inst/doc/FastSurvival.Rmd | 370 -- FastSurvival-0.2.0/FastSurvival/inst/doc/FastSurvival.html | 393 -- FastSurvival-0.2.0/FastSurvival/inst/doc/compare-logrank-rmst.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/compare-logrank-rmst.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/compare-logrank-rmst.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/correlated-pfs-os-gsd.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/correlated-pfs-os-gsd.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/correlated-pfs-os-gsd.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/group-sequential-design.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/group-sequential-design.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/group-sequential-design.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/investigate-freidlin-and-korn.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/investigate-freidlin-and-korn.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/investigate-freidlin-and-korn.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/mrct-regional-consistency.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/mrct-regional-consistency.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/mrct-regional-consistency.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/multi-arm-pairwise.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/multi-arm-pairwise.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/multi-arm-pairwise.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/speed-comparison.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/speed-comparison.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/speed-comparison.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/validation.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/validation.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/validation.html |only FastSurvival-0.2.0/FastSurvival/man/FastSurvival-package.Rd | 116 FastSurvival-0.2.0/FastSurvival/man/ahr_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/ahr_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/ahsw_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/ahsw_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/analysis_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/combo_logrank_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/coxph_fast.Rd | 47 FastSurvival-0.2.0/FastSurvival/man/figures |only FastSurvival-0.2.0/FastSurvival/man/gen_scenario_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/km_core.Rd | 15 FastSurvival-0.2.0/FastSurvival/man/kmcurve_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/maxcombo_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/medsurv_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/milestone_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/pairwise_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/plot.kmcurve_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/plot.scenario_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.ahr_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.ahsw_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.kmcurve_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.maxcombo_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.medsurv_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.milestone_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.rmst_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.rmw_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.scenario_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.simsummary_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.survdiff_fast.Rd | 5 FastSurvival-0.2.0/FastSurvival/man/print.wkm_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.wmst_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/rmst_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/rmst_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/rmw_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/rmw_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/simdata_fast.Rd | 393 +- FastSurvival-0.2.0/FastSurvival/man/simsummary_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/stratified_logrank_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/stratified_weighted_logrank_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/survdiff_fast.Rd | 192 + FastSurvival-0.2.0/FastSurvival/man/survfit_fast.Rd | 14 FastSurvival-0.2.0/FastSurvival/man/weighted_logrank_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/wkm_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/wmst_fast.Rd |only FastSurvival-0.2.0/FastSurvival/src/RcppExports.cpp | 333 ++ FastSurvival-0.2.0/FastSurvival/src/ahr_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/ahsw_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/analysis_loop_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/combo_logrank_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/km_core.cpp | 70 FastSurvival-0.2.0/FastSurvival/src/logrank_core.cpp | 21 FastSurvival-0.2.0/FastSurvival/src/medsurv_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/milestone_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/pihe_core.cpp | 65 FastSurvival-0.2.0/FastSurvival/src/rmst_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/rmw_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/simdata_core_full.cpp |only FastSurvival-0.2.0/FastSurvival/src/simdata_core_id.cpp |only FastSurvival-0.2.0/FastSurvival/src/stratified_logrank_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/stratified_weighted_logrank_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/weighted_logrank_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/wkm_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/wmst_core.cpp |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-ahr_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-ahsw_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-analysis_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-coxph_fast.R | 4 FastSurvival-0.2.0/FastSurvival/tests/testthat/test-kmcurve_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-maxcombo_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-medsurv_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-milestone_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-pairwise_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-rmst_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-rmw_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-simdata_fast.R | 473 ++- FastSurvival-0.2.0/FastSurvival/tests/testthat/test-simdata_fast_id.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-simdata_fast_karm.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-simsummary_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-survdiff_fast.R | 517 ++- FastSurvival-0.2.0/FastSurvival/tests/testthat/test-wkm_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-wmst_fast.R |only FastSurvival-0.2.0/FastSurvival/vignettes/FastSurvival.Rmd | 370 -- FastSurvival-0.2.0/FastSurvival/vignettes/compare-logrank-rmst.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/correlated-pfs-os-gsd.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/group-sequential-design.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/investigate-freidlin-and-korn.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/mrct-regional-consistency.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/multi-arm-pairwise.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/speed-comparison.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/validation.Rmd |only 165 files changed, 5263 insertions(+), 2812 deletions(-)
Title: Density Deconvolution Using Bayesian Semiparametric Methods
Description: Estimates the density of a variable in a measurement error setup, potentially with an excess of zero values. For more details see Sarkar (2021). <doi:10.1080/01621459.2020.1782220>.
Author: Blake Moya [aut],
Mainak Manna [cre, aut],
Abhra Sarkar [aut],
The University of Texas at Austin [cph, fnd]
Maintainer: Mainak Manna <mainakmanna29@utexas.edu>
Diff between BayesDecon versions 0.1.6 dated 2026-03-14 and 0.1.7 dated 2026-07-27
DESCRIPTION | 8 +++---- MD5 | 7 +++--- R/bdeconv.R | 61 ++++++++++++++++++++++++++++++++------------------------- inst |only man/bdeconv.Rd | 26 ++++++++++++++---------- 5 files changed, 58 insertions(+), 44 deletions(-)
Title: Simulation of Simple and Complex Survival Data
Description: Simulation of simple and complex survival data including recurrent and multiple events and competing risks. See Moriña D, Navarro A. (2014) <doi:10.18637/jss.v059.i02> and Moriña D, Navarro A. (2017) <doi:10.1080/03610918.2016.1175621>.
Author: David Morina Soler [aut, cre] ,
Albert Navarro [aut]
Maintainer: David Morina Soler <david.morina@uab.cat>
Diff between survsim versions 1.1.8 dated 2021-12-14 and 1.1.9 dated 2026-07-27
DESCRIPTION | 15 ++++++------ MD5 | 4 +-- inst/CITATION | 71 +++++++++++++++++++++++++++++++--------------------------- 3 files changed, 49 insertions(+), 41 deletions(-)
Title: Propagation of Uncertainty
Description: Propagation of uncertainty using higher-order Taylor expansion and Monte Carlo simulation. Calculations of propagated uncertainties are based on matrix calculus including covariance structure according to Arras 1998 <doi:10.3929/ethz-a-010113668> (first order), Wang & Iyer 2005 <doi:10.1088/0026-1394/42/5/011> (second order) and BIPM Supplement 1 (Monte Carlo) <doi:10.59161/JCGM101-2008>.
Author: Andrej-Nikolai Spiess [aut, cre]
Maintainer: Andrej-Nikolai Spiess <draspiess@gmail.com>
Diff between propagate versions 1.1-0 dated 2026-02-25 and 1.2-0 dated 2026-07-27
DESCRIPTION | 8 - MD5 | 13 +- NEWS | 4 R/distr-densities.R | 298 ++++++++++++++++++++++++++++------------------------ R/fitDistr.R | 11 + R/propagate.R | 31 +++-- build |only man/propagate.Rd | 4 8 files changed, 208 insertions(+), 161 deletions(-)
Title: Regression Models for Ordinal Data
Description: Implementation of cumulative link (mixed) models also known
as ordered regression models, proportional odds models, proportional
hazards models for grouped survival times and ordered logit/probit/...
models. Estimation is via maximum likelihood and mixed models are fitted
with the Laplace approximation and adaptive Gauss-Hermite quadrature.
Multiple random effect terms are allowed and they may be nested, crossed or
partially nested/crossed. Restrictions of symmetry and equidistance can be
imposed on the thresholds (cut-points/intercepts). Standard model
methods are available (summary, anova, drop-methods, step,
confint, predict etc.) in addition to profile methods and slice
methods for visualizing the likelihood function and checking
convergence.
Author: Rune Haubo Bojesen Christensen [aut, cre]
Maintainer: Rune Haubo Bojesen Christensen <rune.haubo@gmail.com>
Diff between ordinal versions 2025.12-29 dated 2026-01-10 and 2026.7-26 dated 2026-07-27
DESCRIPTION | 14 ++++++++------ MD5 | 20 ++++++++++---------- NEWS | 4 ++++ build/vignette.rds |binary inst/doc/clm_article.R | 2 -- inst/doc/clm_article.Rnw | 2 +- inst/doc/clm_article.pdf |binary inst/doc/clmm2_tutorial.R | 2 -- inst/doc/clmm2_tutorial.pdf |binary tests/testCLM.R | 4 ++-- vignettes/clm_article.Rnw | 2 +- 11 files changed, 26 insertions(+), 24 deletions(-)
Title: Linear, Quadratic, and Rational Optimization
Description: Solver for linear, quadratic, and rational programs with linear, quadratic, and rational constraints. A unified interface to different R packages is provided. Optimization problems are transformed into equivalent formulations and solved by the respective package. For example, quadratic programming problems with linear, quadratic and rational constraints can be solved by augmented Lagrangian minimization using package 'alabama', or by sequential quadratic programming using solver 'slsqp'. Alternatively, they can be reformulated as optimization problems with second order cone constraints and solved with package 'cccp'.
Author: Robin Wellmann [aut, cre]
Maintainer: Robin Wellmann <ro.wellmann@gmail.com>
Diff between optiSolve versions 1.0 dated 2021-10-13 and 1.0.1 dated 2026-07-27
DESCRIPTION | 26 +++++++++++++++++--------- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 3 +-- R/adjust.R | 8 ++++---- R/asdefinite.R | 4 ++-- R/call_cccp.R | 16 ++++++++-------- R/call_cccp2.R | 10 +++++----- R/f2fun.R | 6 +++--- R/getSover.R | 8 ++++---- R/getX.R | 2 +- R/reduce.R | 6 +++--- R/simplify.R | 4 ++-- R/validate.R | 6 +++--- build/partial.rdb |binary data/myQ.rda |binary data/myQ1.rda |binary data/myQ2.rda |binary data/phenotype.rda |binary 18 files changed, 70 insertions(+), 63 deletions(-)
Title: A Flexible Class for Messy Dates
Description: Contains a set of tools for constructing and coercing
into and from the "mdate" class.
This date class implements ISO 8601-2:2019(E) and
allows regular dates and times to be annotated
to express unspecified date or time components,
approximate or uncertain components,
ranges, and sets of dates.
The package therefore retains, represents, and reasons about data and time imprecision,
resolving to a single data/time only on demand.
This is useful for describing and analysing temporal information,
whether historical or recent, where date or time precision may vary.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Nathan Werth [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between messydates versions 1.0.0 dated 2026-07-16 and 1.1.0 dated 2026-07-27
DESCRIPTION | 7 - MD5 | 68 +++++----- NAMESPACE | 5 NEWS.md | 112 ++++++++++++++++++ R/class_mdate.R | 32 ++--- R/class_methods.R | 50 ++++++-- R/coerce_from_messydate.R | 2 R/coerce_to_messydate.R | 205 ++++++++++++++++++++++++++------- R/convert_contract.R | 25 ++++ R/convert_expand.R | 94 ++++++++++++++- R/convert_sequence.R | 49 +------ R/operate_proportional.R | 7 + R/operate_set.R | 7 + R/operate_statements.R | 6 R/resolve_extrema.R | 4 R/resolve_tendency.R | 10 + R/validate_input.R |only README.md | 18 ++ man/class_methods.Rd | 24 +++ man/coerce_from.Rd | 2 man/coerce_to.Rd | 32 ++++- man/convert_contract.Rd | 10 + man/convert_sequence.Rd | 6 man/md_problems.Rd |only man/operate_proportional.Rd | 8 + man/operate_set.Rd | 8 + man/operate_statements.Rd | 6 man/resolve_tendency.Rd | 10 + tests/testthat/test-class_create.R | 22 +++ tests/testthat/test-coerce_from.R | 12 + tests/testthat/test-coerce_resolve.R | 21 ++- tests/testthat/test-coerce_to.R | 94 ++++++++++++++- tests/testthat/test-convert_contract.R | 16 ++ tests/testthat/test-convert_expand.R | 35 +++++ tests/testthat/test-convert_sequence.R | 17 ++ tests/testthat/test-operate_set.R | 14 ++ 36 files changed, 862 insertions(+), 176 deletions(-)
Title: Get Gene Sets for Gene Enrichment Analysis
Description: Gene sets are fundamental for gene enrichment analysis. The package 'geneset' enables querying
gene sets from public databases including 'GO' (Gene Ontology Consortium. (2004) <doi:10.1093/nar/gkh036>),
'KEGG' (Minoru et al. (2000) <doi:10.1093/nar/28.1.27>),
'WikiPathway' (Marvin et al. (2020) <doi:10.1093/nar/gkaa1024>),
'MsigDb' (Arthur et al. (2015) <doi:10.1016/j.cels.2015.12.004>),
'Reactome' (David et al. (2011) <doi:10.1093/nar/gkq1018>),
'MeSH' (Ish et al. (2014) <doi:10.4103/0019-5413.139827>),
'DisGeNET' (Janet et al. (2017) <doi:10.1093/nar/gkw943>),
'Disease Ontology' (Lynn et al. (2011) <doi:10.1093/nar/gkr972>),
'Network of Cancer Genes' (Dimitra et al. (2019) <doi:10.1186/s13059-018-1612-0>) and
'COVID-19' (Maxim et al. (2020) <doi:10.21203/rs.3.rs-28582/v1>).
Gene sets are stored in the list object which provides data frame of 'geneset' and 'geneset_name'.
The 'geneset' has two columns of term ID and gene ID. [...truncated...]
Author: Yunze Liu [aut, cre]
Maintainer: Yunze Liu <jieandze1314@gmail.com>
Diff between geneset versions 0.2.7 dated 2022-11-20 and 0.2.8 dated 2026-07-27
DESCRIPTION | 12 +- MD5 | 14 +- R/getGO.R | 4 R/getKEGG.R | 2 R/getMsigdb.R | 194 ++++++++++++++++++++++++++++++------- R/utilities.R | 285 ++++++++++++++++++++++++++++++++++++++----------------- README.md | 19 +-- man/getMsigdb.Rd | 32 ++++-- 8 files changed, 406 insertions(+), 156 deletions(-)
Title: Greenhouse Gas Flux Calculation from Chamber Measurements
Description: Functions for greenhouse gas flux calculation from chamber
measurements.
Author: Roland Fuss [aut, cre] ,
Roman Hueppi [ctb]
Maintainer: Roland Fuss <roland.fuss@thuenen.de>
Diff between gasfluxes versions 0.7 dated 2024-08-16 and 0.7-2 dated 2026-07-27
DESCRIPTION | 13 ++++++------- MD5 | 18 +++++++++--------- NEWS.md | 3 +++ build/vignette.rds |binary inst/doc/gasfluxes-howto.Rmd | 2 +- inst/doc/gasfluxes-howto.html | 17 +++++++++-------- man/gasfluxes-package.Rd | 5 +++++ tests/testthat/test_aggfluxes.R | 4 ++-- tests/testthat/test_fitting.R | 14 +++++++------- vignettes/gasfluxes-howto.Rmd | 2 +- 10 files changed, 43 insertions(+), 35 deletions(-)
Title: Exploratory Data Analysis for the 'spatstat' Family
Description: Functionality for exploratory data analysis and nonparametric analysis of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Warick Brown [cph],
Achmad Choiruddin [ctb],
Ya-Mei Chang [ctb],
Jean-Francois Coeurjolly [ctb],
Lucia Cobo Sanchez [ctb, cph],
Ottma [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.explore versions 3.8-1 dated 2026-05-24 and 3.8-2 dated 2026-07-27
DESCRIPTION | 10 ++-- MD5 | 52 +++++++++++++------------ NAMESPACE | 4 + NEWS | 39 ++++++++++++++++++ R/Kinhom.R | 2 R/Kmulti.inhom.R | 81 +++++++++++++++++++++++++-------------- R/densityAdaptiveKernel.ppp.R | 54 ++++---------------------- R/densityVoronoi.R | 3 - R/pcfinhom.R | 38 ++++++++++-------- R/pcfmulti.inhom.R | 60 +++++++++++++++++----------- R/rhohat.R | 31 ++++++++++---- R/smoothAdaptiveKernel.ppp.R |only build/partial.rdb |binary inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/Kcross.inhom.Rd | 2 man/Kdot.inhom.Rd | 2 man/Kmulti.inhom.Rd | 9 +++- man/SmoothAdaptiveKernel.Rd |only man/cdf.test.Rd | 6 +- man/densityVoronoi.Rd | 30 ++++++++++---- man/macros/defns.Rd | 30 +++++++++++--- man/pcfmulti.inhom.Rd | 7 +++ man/plot.cdftest.Rd | 3 - man/rhohat.Rd | 11 ++++- man/spatstat.explore-internal.Rd | 6 -- man/spatstat.explore-package.Rd | 18 ++++++-- tests/testsT.R | 10 +++- 28 files changed, 317 insertions(+), 193 deletions(-)
More information about spatstat.explore at CRAN
Permanent link
Title: Inverse-Regression Estimation of Radioactive Doses
Description: Radioactive doses estimation using individual chromosomal
aberrations information. See Higueras M, Puig P, Ainsbury E,
Rothkamm K. (2015) <doi:10.1088/0952-4746/35/3/557>.
Author: David Morina Soler [aut, cre] ,
Manuel Higueras [aut],
Pedro Puig [aut]
Maintainer: David Morina Soler <david.morina@uab.cat>
Diff between radir versions 1.0.4 dated 2019-07-03 and 1.0.5 dated 2026-07-27
DESCRIPTION | 24 +++++++++++---- MD5 | 18 +++++------ R/ci.dose.radir.R | 2 - R/dose.distr.R | 2 - R/lines.dose.radir.R | 2 - R/plot.dose.radir.R | 2 - R/pr.dose.radir.R | 2 - R/summary.dose.radir.R | 2 - inst/CITATION | 75 ++++++++++++++++++++++++++----------------------- man/radir-package.Rd | 6 +-- 10 files changed, 75 insertions(+), 60 deletions(-)
Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. We also provide functions for sample size determination and estimation of diagnostic accuracy measures. We also include graphical tools. The statistical methodology used here can be found in Perez-Jaume et al (2017) <doi:10.18637/jss.v082.i04> and in Skaltsa et al (2010, 2012) <doi:10.1002/bimj.200900294>, <doi:10.1002/sim.4369>.
Author: Sara Perez-Jaume [aut, cre] ,
Natalia Pallares [aut] ,
Konstantina Skaltsa [aut]
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.9.6 dated 2026-05-14 and 2.10.0 dated 2026-07-27
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/ThresholdROC-2states.R | 14 +++++++------- R/diagnostic.R | 10 +++++----- man/chemo.Rd | 2 +- man/diagnostic.Rd | 14 ++++++++++---- man/lines-thres2.Rd | 20 ++++++++++++++++---- man/lines-thres3.Rd | 20 ++++++++++++++++---- man/plot-thres2.Rd | 28 ++++++++++++++++++++++------ man/plot-thres3.Rd | 22 +++++++++++++++++----- man/plotCostROC.Rd | 6 +++++- man/thres2.Rd | 36 ++++++++++++++++++++++++++++-------- man/thres3.Rd | 40 ++++++++++++++++++++++++++++++++-------- man/thresTH2.Rd | 20 +++++++++++++++----- man/thresTH3.Rd | 26 +++++++++++++++++++++----- 15 files changed, 213 insertions(+), 81 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb, cph],
David Bryant [ctb, cph],
Ya-Mei Chang [ctb, cph],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.5-0 dated 2026-05-24 and 3.5-1 dated 2026-07-27
DESCRIPTION | 12 ++++++------ MD5 | 23 ++++++++++++----------- NAMESPACE | 1 + NEWS | 12 ++++++++++++ R/randompp3.R | 2 +- R/randomtess.R | 38 +++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary inst/doc/packagesizes.txt | 1 + inst/info/packagesizes.txt | 1 + man/macros/defns.Rd | 30 +++++++++++++++++++++++------- man/rpoisDirichletTess.Rd |only man/rpoislinetess.Rd | 6 ++++-- man/spatstat.random-package.Rd | 6 ++++-- 13 files changed, 102 insertions(+), 30 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: Unidimensional Item Response Theory Modeling
Description: Fit unidimensional item response theory (IRT) models to test
data, which includes both dichotomous and polytomous items, calibrate
pretest item parameters, estimate examinees' abilities, and examine
the IRT model-data fit on item-level in different ways as well as provide
useful functions related to IRT analyses such as IRT model-data fit
evaluation and differential item functioning analysis.
The bring.flexmirt() and write.flexmirt() functions were written by modifying
the read.flexmirt() function (Pritikin & Falk (2022) <doi:10.1177/0146621620929431>).
The bring.bilog() and bring.parscale() functions were written by modifying the read.bilog()
and read.parscale() functions, respectively (Weeks (2010) <doi:10.18637/jss.v035.i12>).
The bisection() function was written by modifying the bisection() function
(Howard (2017, ISBN:9780367657918)). The code of the inverse test characteristic curve
scoring in the est_score() function was written by modifying the irt.eq.tse() func [...truncated...]
Author: Hwanggyu Lim [aut, cre],
Craig S. Wells [ctb],
James Howard [ctb],
Joshua Pritikin [ctb],
Jonathan P Weeks [ctb],
Jorge Gonzalez [ctb],
David Magis [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Diff between irtQ versions 1.1.0 dated 2026-06-07 and 1.2.0 dated 2026-07-27
DESCRIPTION | 16 - MD5 | 125 +++++----- NAMESPACE | 8 NEWS.md | 95 +++++++ R/EM.R | 2 R/LSAT6.R | 2 R/SimCAT_DC.R | 4 R/catsib.R | 12 - R/collapse_ftable.R | 2 R/crdif.R | 12 - R/est_irt.R | 27 +- R/est_item.R | 8 R/est_mg.R | 37 +-- R/est_score.R | 10 R/estimation.R | 6 R/find_cut.R |only R/gradient.R | 10 R/grdif.R | 2 R/hessian.R | 10 R/inv_tcc.R | 4 R/irtQ-package.R | 34 +- R/irtfit.R | 8 R/likelihood.R | 4 R/llike_score.R | 2 R/loglike_item.R | 10 R/optim_fns.R | 492 ++++++++++++++++++++--------------------- R/panel_info.R |only R/pcd2.R | 84 ++++++- R/plot_traceline.R | 2 R/print.R | 160 +++++++++++++ R/reval_mst.R | 64 ----- R/ripd.R | 248 +++++++++++++++++++- R/run_mst.R |only R/shape_df.R | 4 R/shape_df_fipc.R | 2 R/simIPD.R |only R/simMST.R | 25 +- R/sx2_fit.R | 2 README.md | 113 +++++---- build/partial.rdb |binary data/simIPD.rda |only data/simMST.rda |binary man/LSAT6.Rd | 2 man/catsib.Rd | 14 - man/crdif.Rd | 12 - man/est_irt.Rd | 24 +- man/est_item.Rd | 8 man/est_mg.Rd | 44 +-- man/est_score.Rd | 6 man/find_cut.Rd |only man/grdif.Rd | 2 man/irtQ-package.Rd | 34 +- man/irtfit.Rd | 8 man/llike_score.Rd | 2 man/panel_info.Rd |only man/pcd2.Rd | 88 ++++++- man/plot.find_cut.Rd |only man/plot.info.Rd | 2 man/plot.traceline.Rd | 4 man/reval_mst.Rd | 8 man/ripd.Rd | 247 +++++++++++++++++++- man/run_mst.Rd |only man/shape_df.Rd | 4 man/shape_df_fipc.Rd | 2 man/simCAT_DC.Rd | 4 man/simIPD.Rd |only man/simMST.Rd | 25 +- man/sx2_fit.Rd | 2 tests/testthat/test-find_cut.R |only 69 files changed, 1525 insertions(+), 663 deletions(-)
Title: Generalized Hermite Distribution
Description: Probability functions and other utilities for the generalized Hermite distribution.
Author: David Morina Soler [aut, cre],
Manuel Higueras [aut],
Pedro Puig [aut],
Maria Oliveira [aut]
Maintainer: David Morina Soler <david.morina@uab.cat>
Diff between hermite versions 1.1.2 dated 2018-05-17 and 1.2.1 dated 2026-07-27
DESCRIPTION | 27 ++++++++++++++++++++++----- MD5 | 10 +++++----- R/glm.hermite.R | 6 +++--- man/glm.hermite.Rd | 18 ++++++++---------- man/hermite-package.Rd | 2 +- man/phermite.Rd | 6 +++--- 6 files changed, 42 insertions(+), 27 deletions(-)
Title: Utilities Powering the Globe and Mail's Data Journalism Template
Description: Core functions necessary for using The Globe and Mail's R data journalism template, 'startr', along with utilities for day-to-day data journalism tasks, such as reading and writing files, producing graphics and cleaning up datasets.
Author: Tom Cardoso [aut, cre] ,
Michael Pereira [ctb],
The Globe and Mail Inc. [cph]
Maintainer: Tom Cardoso <tcardoso@globeandmail.com>
Diff between upstartr versions 0.1.2 dated 2024-01-09 and 0.2.0 dated 2026-07-27
DESCRIPTION | 14 +++++++------- MD5 | 15 +++++++++------ NEWS.md | 23 +++++++++++++++++++++++ R/init.R | 13 ++++++++++++- R/run.R | 19 +++++++++++++++++-- R/write.R | 6 +++++- man/initialize_startr.Rd | 10 +++++++++- tests/testthat/test-init.R |only tests/testthat/test-run.R |only tests/testthat/test-write.R |only 10 files changed, 82 insertions(+), 18 deletions(-)
Title: Helper Functions for Creating Tutorials
Description: Helper functions for creating, editing, and testing tutorials
created with the 'learnr' package. Provides a simple method for allowing
students to download their answers to tutorial questions. For examples
of its use, see the 'r4ds.tutorials' package.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between tutorial.helpers versions 0.6.1 dated 2025-12-23 and 0.7.0 dated 2026-07-27
tutorial.helpers-0.6.1/tutorial.helpers/R/set_positron_settings.R |only tutorial.helpers-0.6.1/tutorial.helpers/R/set_r_profile_settings.R |only tutorial.helpers-0.6.1/tutorial.helpers/inst/doc/books.html |only tutorial.helpers-0.6.1/tutorial.helpers/inst/doc/books.qmd |only tutorial.helpers-0.6.1/tutorial.helpers/inst/doc/instructions.R |only tutorial.helpers-0.6.1/tutorial.helpers/inst/doc/instructions.html |only tutorial.helpers-0.6.1/tutorial.helpers/inst/doc/instructions.qmd |only tutorial.helpers-0.6.1/tutorial.helpers/inst/rmarkdown |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/new-window.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/positron-interface.jpeg |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/run-tutorial.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/send-tutorial-to-browser.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/terminal-1.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/terminal-2.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/terminal-3.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/terminal-4.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/tutorial.html |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/introduction-to-python |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/introduction-to-r |only tutorial.helpers-0.6.1/tutorial.helpers/inst/www |only tutorial.helpers-0.6.1/tutorial.helpers/man/set_positron_settings.Rd |only tutorial.helpers-0.6.1/tutorial.helpers/man/set_rprofile_settings.Rd |only tutorial.helpers-0.6.1/tutorial.helpers/tests/testthat/test-set_positron_settings.R |only tutorial.helpers-0.6.1/tutorial.helpers/tests/testthat/test-set_rprofile_settings.R |only tutorial.helpers-0.6.1/tutorial.helpers/vignettes/books.qmd |only tutorial.helpers-0.6.1/tutorial.helpers/vignettes/instructions.qmd |only tutorial.helpers-0.7.0/tutorial.helpers/DESCRIPTION | 15 tutorial.helpers-0.7.0/tutorial.helpers/MD5 | 164 - tutorial.helpers-0.7.0/tutorial.helpers/NAMESPACE | 18 tutorial.helpers-0.7.0/tutorial.helpers/NEWS.md | 16 tutorial.helpers-0.7.0/tutorial.helpers/R/check_current_tutorial.R | 3 tutorial.helpers-0.7.0/tutorial.helpers/R/check_key_vars.R | 11 tutorial.helpers-0.7.0/tutorial.helpers/R/check_membership.R | 29 tutorial.helpers-0.7.0/tutorial.helpers/R/check_tutorial_defaults.R | 4 tutorial.helpers-0.7.0/tutorial.helpers/R/determine_code_chunk_name.R | 5 tutorial.helpers-0.7.0/tutorial.helpers/R/determine_exercise_number.R | 28 tutorial.helpers-0.7.0/tutorial.helpers/R/download_google_drive.R | 13 tutorial.helpers-0.7.0/tutorial.helpers/R/format_tutorial.R | 14 tutorial.helpers-0.7.0/tutorial.helpers/R/gather_submissions.R | 28 tutorial.helpers-0.7.0/tutorial.helpers/R/globals.R | 2 tutorial.helpers-0.7.0/tutorial.helpers/R/make_exercise.R | 2 tutorial.helpers-0.7.0/tutorial.helpers/R/match_questions.R | 15 tutorial.helpers-0.7.0/tutorial.helpers/R/open_github_pages.R | 13 tutorial.helpers-0.7.0/tutorial.helpers/R/show_file.R | 120 - tutorial.helpers-0.7.0/tutorial.helpers/R/submission_functions.R | 3 tutorial.helpers-0.7.0/tutorial.helpers/R/submissions_answers.R | 20 tutorial.helpers-0.7.0/tutorial.helpers/R/submissions_summary.R | 179 - tutorial.helpers-0.7.0/tutorial.helpers/R/utils.R | 6 tutorial.helpers-0.7.0/tutorial.helpers/R/write_answers.R | 14 tutorial.helpers-0.7.0/tutorial.helpers/README.md | 42 tutorial.helpers-0.7.0/tutorial.helpers/build/vignette.rds |binary tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/addins.R | 28 tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/addins.html | 229 +- tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/addins.qmd | 72 tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/ai.R | 350 ++- tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/ai.html | 1041 +++++++--- tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/ai.qmd | 629 ++++-- tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/downloads.html | 144 + tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/testing.html | 152 + tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/testing.qmd | 8 tutorial.helpers-0.7.0/tutorial.helpers/inst/extdata |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/cs-copilot-keep-editor.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/cs-copilot-keep-summary.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/cs-open-copilot-chat.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/cs-run-source.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-1.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-2.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-3.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-4.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-5.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-6.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/neo-cs.gif |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/tutorial.Rmd | 908 +++++--- tutorial.helpers-0.7.0/tutorial.helpers/man/check_current_tutorial.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/man/check_key_vars.Rd | 7 tutorial.helpers-0.7.0/tutorial.helpers/man/check_membership.Rd | 11 tutorial.helpers-0.7.0/tutorial.helpers/man/check_tutorial_defaults.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/man/dot-check_quarto.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/man/gather_submissions.Rd | 5 tutorial.helpers-0.7.0/tutorial.helpers/man/match_questions.Rd | 13 tutorial.helpers-0.7.0/tutorial.helpers/man/open_github_pages.Rd | 2 tutorial.helpers-0.7.0/tutorial.helpers/man/show_file.Rd | 19 tutorial.helpers-0.7.0/tutorial.helpers/man/strip_pagedtable_html.Rd |only tutorial.helpers-0.7.0/tutorial.helpers/man/submissions_answers.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/man/submissions_summary.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/man/write_answers.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/fixtures/show_file_pagedtable_test.qmd |only tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/fixtures/show_file_python_test.qmd |only tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-check_membership.R | 79 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-determine_code_chunk_name.R | 9 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-determine_exercise_number.R | 21 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-format_tutorial.R | 34 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-match_questions.R | 46 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-open_github_pages.R |only tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-render.R | 18 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-show_file.R | 132 + tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-submissions_summary.R | 70 tutorial.helpers-0.7.0/tutorial.helpers/vignettes/addins.qmd | 72 tutorial.helpers-0.7.0/tutorial.helpers/vignettes/ai.qmd | 629 ++++-- tutorial.helpers-0.7.0/tutorial.helpers/vignettes/testing.qmd | 8 100 files changed, 3925 insertions(+), 1599 deletions(-)
More information about tutorial.helpers at CRAN
Permanent link
Title: Tidy Tools for Actuarial Mathematics and Life Contingencies
Description: Provides tidyverse-aligned tools for actuarial mathematics
and life contingencies, including life tables, survival probabilities,
actuarial present values of cash flows, life annuities, life insurance,
premiums, reserves, multiple-life calculations, Monte Carlo simulation,
and deterministic cash-flow diagrams. The package emphasizes clear
actuarial notation, reproducible workflows, and pipe-friendly tools for
actuarial education and applied actuarial analysis.
Author: Julian Fajardo [aut, cre]
Maintainer: Julian Fajardo <julian.fajardo1908@gmail.com>
Diff between tidyactuarial versions 0.1.4 dated 2026-06-01 and 0.1.5 dated 2026-07-27
DESCRIPTION | 8 MD5 | 275 +++-- NAMESPACE | 161 +-- NEWS.md | 2 R/accumulation_factor.R |only R/amort_schedule_general.R |only R/annuity_x.R | 61 - R/annuity_xy.R | 135 ++ R/contract_components.R |only R/contract_components_xy_corrected.R |only R/convexity_cash_flow.R |only R/discount_factor.R |only R/duration_cash_flow.R |only R/globals.R | 200 --- R/imports.R |only R/mc-utils.R | 149 ++ R/mc_annuity.R | 70 + R/mc_insurance.R | 88 + R/mc_loss.R | 620 +++++++---- R/mc_multilife_status.R | 351 +++++- R/mc_premium.R | 705 ++++++++----- R/mc_reserve.R | 1014 ++++++++++++------- R/plot_cash_flow.R | 146 ++ R/premium_gross.R | 577 ++++++++--- R/premium_x.R | 656 +++++++----- R/premium_xy.R | 1193 ++++++++++------------ R/reserve_x.R | 1240 ++++++++++++++--------- R/reserve_xy.R | 1311 +++++++++---------------- R/simulate_life_mc.R | 966 +++++++++++------- R/simulate_lifetime.R | 553 ++++++---- R/simulate_lifetimes.R | 533 +++++++--- R/solve_value_v3.R |only man/a_angle.Rd | 318 +++--- man/accumulation_factor.Rd |only man/add_insurance.Rd |only man/add_premium_schedule.Rd |only man/amort_schedule.Rd | 295 ++--- man/amort_schedule_general.Rd |only man/annuity_arith.Rd | 292 ++--- man/annuity_geom.Rd | 330 +++--- man/annuity_multi.Rd | 298 ++--- man/annuity_x.Rd | 402 +++---- man/annuity_xy.Rd | 385 +++---- man/apv_life_flow.Rd | 248 ++-- man/bond_book_value.Rd | 346 +++--- man/bond_callable_price.Rd | 356 +++--- man/bond_cash_flows.Rd | 102 - man/bond_convexity.Rd | 272 ++--- man/bond_duration.Rd | 298 ++--- man/bond_price.Rd | 274 ++--- man/bond_ytm.Rd | 244 ++-- man/bonds_sample.Rd | 144 +- man/cash_flows_sample.Rd | 140 +- man/commutation_table.Rd | 150 +- man/convexity_cash_flow.Rd |only man/discount_factor.Rd |only man/discount_factor_spot.Rd | 198 +-- man/dot-annuity_factor_count.Rd | 36 man/dot-annuity_payment_count.Rd | 38 man/dot-life_mc_collect_old_args.Rd | 32 man/dot-mc_annuity_payment_times_annual.Rd | 56 - man/dot-mc_annuity_payment_times_fractional.Rd | 76 - man/dot-mc_assert_character_scalar.Rd | 40 man/dot-mc_assert_column.Rd | 44 man/dot-mc_assert_numeric_column.Rd | 44 man/dot-mc_assert_numeric_scalar.Rd | 76 - man/dot-mc_assert_positive_integer.Rd | 40 man/dot-mc_discount_factor.Rd | 72 - man/dot-mc_effective_rate.Rd | 96 - man/dot-mc_normalize_i_type.Rd | 36 man/dot-mc_payment_times.Rd | 46 man/dot-mc_quantile_names.Rd | 36 man/dot-mc_reserve_benefit_info.Rd | 44 man/dot-resolve_life_mc_inputs.Rd | 38 man/dot-simulate_lifetime_inverse_lx.Rd | 55 - man/dot-validate_mc_common.Rd | 40 man/duration_cash_flow.Rd |only man/e_x.Rd | 152 +- man/forward_rate.Rd | 338 +++--- man/future_value.Rd | 215 ++-- man/fv_flow.Rd | 287 ++--- man/immunize_duration.Rd | 274 ++--- man/immunize_duration_convexity.Rd | 274 ++--- man/insurance_variable_k.Rd | 396 +++---- man/insurance_x.Rd | 334 +++--- man/insurance_xj.Rd | 304 ++--- man/insurance_xy.Rd | 350 +++--- man/interest_equivalents.Rd | 174 +-- man/irr_flow.Rd | 241 ++-- man/irr_flow_multi.Rd | 265 ++--- man/life_contract.Rd | 238 ++-- man/lifetable.Rd | 372 +++---- man/loans_sample.Rd | 140 +- man/lt_tau.Rd | 82 - man/mc_annuity.Rd | 550 +++++----- man/mc_insurance.Rd | 535 +++++----- man/mc_loss.Rd | 412 +++---- man/mc_multilife_status.Rd | 164 ++- man/mc_premium.Rd | 441 +++----- man/mc_reserve.Rd | 519 +++------ man/md_table.Rd | 150 +- man/mortality_colombia_tables.Rd | 150 +- man/mortality_law_table.Rd | 404 +++---- man/mortality_world_sample_2015_2023.Rd | 120 +- man/mortality_world_sample_2023.Rd | 116 +- man/multiple_decrement_sample.Rd | 136 +- man/plot_cash_flow.Rd | 321 +++--- man/plot_immunization_gap.Rd | 200 +-- man/plot_km.Rd | 172 +-- man/portfolio_convexity.Rd | 262 ++-- man/portfolio_duration.Rd | 264 ++--- man/premium_gross.Rd | 324 +++--- man/premium_x.Rd | 436 ++++---- man/premium_xy.Rd | 405 ++++--- man/present_value.Rd | 217 ++-- man/pv_flow.Rd | 263 ++--- man/reserve_x.Rd | 361 +++--- man/reserve_xy.Rd | 332 ++---- man/s_angle.Rd | 316 +++--- man/simulate_annuity_x.Rd | 270 ++--- man/simulate_insurance_x.Rd | 236 +--- man/simulate_lifetime.Rd | 297 ++--- man/simulate_lifetimes.Rd | 170 ++- man/sinking_fund_schedule.Rd | 273 ++--- man/soa08lt.Rd | 136 +- man/solve_value.Rd |only man/standardize_interest.Rd | 184 +-- man/summary_mc.Rd | 184 +-- man/t_Ex.Rd | 282 ++--- man/t_px.Rd | 118 +- man/t_pxy.Rd | 218 ++-- man/t_qxj.Rd | 142 +- man/yield_curve.Rd | 282 ++--- tests/testthat.R | 24 tests/testthat/test-accumulation_factor.R |only tests/testthat/test-amort_schedule_general.R |only tests/testthat/test-annuity_x-fractional.R |only tests/testthat/test-annuity_xy-v2.R |only tests/testthat/test-contract_components-xy.R |only tests/testthat/test-convexity_cash_flow.R |only tests/testthat/test-discount_factor.R |only tests/testthat/test-duration_cash_flow.R |only tests/testthat/test-mc-utils-v2.R |only tests/testthat/test-mc_annuity-v2.R |only tests/testthat/test-mc_insurance-v2.R |only tests/testthat/test-mc_loss-v2.R |only tests/testthat/test-mc_multilife_status-v2.R |only tests/testthat/test-mc_premium-v2.R |only tests/testthat/test-mc_reserve_v2.R |only tests/testthat/test-plot_cash_flow.R |only tests/testthat/test-premium_gross-v2.R |only tests/testthat/test-premium_x-v2.R |only tests/testthat/test-premium_xy-v2.R |only tests/testthat/test-reserve_x-v2.R |only tests/testthat/test-reserve_xy-two-tables.R |only tests/testthat/test-reserve_xy-v2.R |only tests/testthat/test-simulate_life_mc-v2.R |only tests/testthat/test-simulate_lifetime-v2.R |only tests/testthat/test-simulate_lifetimes-v2.R |only tests/testthat/test-solve_value_v2.R |only 160 files changed, 16855 insertions(+), 15018 deletions(-)
Title: Personalized Treatment Evaluator
Description: We provide inference for personalized medicine models. Namely, we answer the questions: (1) how much better does a purported personalized recommendation engine for treatments do over a business-as-usual approach and (2) is that difference statistically significant?
Author: Adam Kapelner [aut, cre],
Alina Levine [aut],
Justin Bleich [aut]
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between PTE versions 1.7 dated 2019-01-30 and 2.0 dated 2026-07-27
PTE-1.7/PTE/R/create_PTE_results_object.R |only PTE-1.7/PTE/R/create_cutoffs_for_K_fold_cv.R |only PTE-1.7/PTE/R/create_raw_results_matrix.R |only PTE-1.7/PTE/R/plot.R |only PTE-1.7/PTE/R/print_and_summary.R |only PTE-1.7/PTE/R/run_model_on_left_out_record_results_and_cleanup.R |only PTE-2.0/PTE/CHANGELOG | 14 PTE-2.0/PTE/DESCRIPTION | 31 PTE-2.0/PTE/MD5 | 61 PTE-2.0/PTE/NAMESPACE | 27 PTE-2.0/PTE/R/PTE.R | 80 - PTE-2.0/PTE/R/RcppExports.R |only PTE-2.0/PTE/R/bootstrap_inference.R | 661 ++++++---- PTE-2.0/PTE/R/helpers.R |only PTE-2.0/PTE/R/plot_and_summarize.R |only PTE-2.0/PTE/R/select_optimal_m_prop.R |only PTE-2.0/PTE/R/zzz.R | 6 PTE-2.0/PTE/cleanup |only PTE-2.0/PTE/configure |only PTE-2.0/PTE/configure.win |only PTE-2.0/PTE/man/PTE.Rd | 46 PTE-2.0/PTE/man/PTE_bootstrap_inference.Rd | 395 +++-- PTE-2.0/PTE/man/continuous_example.Rd | 32 PTE-2.0/PTE/man/plot.PTE_bootstrap_results.Rd | 48 PTE-2.0/PTE/man/print.PTE_bootstrap_results.Rd | 48 PTE-2.0/PTE/man/select_optimal_m_prop.Rd |only PTE-2.0/PTE/man/summary.PTE_bootstrap_results.Rd | 48 PTE-2.0/PTE/man/survival_example.Rd | 36 PTE-2.0/PTE/src |only PTE-2.0/PTE/tests |only 30 files changed, 928 insertions(+), 605 deletions(-)
Title: Estimation and Diagnostics for Many-Facet Measurement Models
Description: Native R implementation of many-facet ordered-response
measurement models with arbitrary facet counts, rating-scale and
partial-credit parameterizations, a bounded generalized partial-credit
extension, and both marginal and joint maximum likelihood estimation.
The package provides a fit / diagnose / report pipeline covering
anchoring, linking, bias and differential-functioning screening, and
publication-oriented reporting summaries, with reproducibility manifests
for replay. See 'Andrich'
(1978) <doi:10.1007/BF02293814>, 'Masters' (1982)
<doi:10.1007/BF02296272>, and 'Muraki' (1992)
<doi:10.1177/014662169201600206> for the underlying ordered-response
models.
Author: Ryuya Komuro [aut, cre, cph]
Maintainer: Ryuya Komuro <ryuya.komuro.c4@tohoku.ac.jp>
Diff between mfrmr versions 0.2.1 dated 2026-06-12 and 0.2.2 dated 2026-07-27
mfrmr-0.2.1/mfrmr/R/api-methods-print-0-1-6.R |only mfrmr-0.2.1/mfrmr/R/api-simulation-future-branch.R |only mfrmr-0.2.1/mfrmr/inst/validation |only mfrmr-0.2.1/mfrmr/man/plot.mfrm_future_branch_active_branch.Rd |only mfrmr-0.2.1/mfrmr/man/summary.mfrm_future_branch_active_branch.Rd |only mfrmr-0.2.1/mfrmr/tests/testthat/test-api-coverage-gaps.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-api-final-coverage.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-bundle-coverage.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-core-coverage-gaps.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-core-coverage.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-coverage-push-95.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-draw-coverage.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-external-recovery-review.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-final-coverage-boost.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-recovery-validation-protocol.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-release-readiness-protocol.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-remaining-coverage.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-reporting-coverage.R |only mfrmr-0.2.1/mfrmr/tests/testthat/test-reporting-gaps.R |only mfrmr-0.2.2/mfrmr/DESCRIPTION | 14 mfrmr-0.2.2/mfrmr/MD5 | 687 +- mfrmr-0.2.2/mfrmr/NAMESPACE | 20 mfrmr-0.2.2/mfrmr/NEWS.md | 2923 +--------- mfrmr-0.2.2/mfrmr/R/api-advanced.R | 447 + mfrmr-0.2.2/mfrmr/R/api-as-ggplot.R |only mfrmr-0.2.2/mfrmr/R/api-bias-collection.R | 30 mfrmr-0.2.2/mfrmr/R/api-dashboards.R | 19 mfrmr-0.2.2/mfrmr/R/api-estimation.R | 1142 +++ mfrmr-0.2.2/mfrmr/R/api-export-bundles.R | 874 ++ mfrmr-0.2.2/mfrmr/R/api-facet-equivalence.R | 11 mfrmr-0.2.2/mfrmr/R/api-generalizability.R | 163 mfrmr-0.2.2/mfrmr/R/api-hierarchical-audit.R | 16 mfrmr-0.2.2/mfrmr/R/api-import.R | 173 mfrmr-0.2.2/mfrmr/R/api-methods-print.R |only mfrmr-0.2.2/mfrmr/R/api-methods.R | 1728 +++++ mfrmr-0.2.2/mfrmr/R/api-person-fit.R | 25 mfrmr-0.2.2/mfrmr/R/api-plotting-extras.R | 85 mfrmr-0.2.2/mfrmr/R/api-plotting-fit-family.R | 1611 +++++ mfrmr-0.2.2/mfrmr/R/api-plotting-screening.R | 6 mfrmr-0.2.2/mfrmr/R/api-plotting-secondary.R | 17 mfrmr-0.2.2/mfrmr/R/api-plotting-wright-facets.R |only mfrmr-0.2.2/mfrmr/R/api-plotting.R | 155 mfrmr-0.2.2/mfrmr/R/api-prediction.R | 89 mfrmr-0.2.2/mfrmr/R/api-q3.R | 153 mfrmr-0.2.2/mfrmr/R/api-reference-benchmark.R | 44 mfrmr-0.2.2/mfrmr/R/api-reporting-checklist.R | 79 mfrmr-0.2.2/mfrmr/R/api-reports.R | 2011 ++++-- mfrmr-0.2.2/mfrmr/R/api-resampling.R | 14 mfrmr-0.2.2/mfrmr/R/api-results.R | 1347 ++++ mfrmr-0.2.2/mfrmr/R/api-shrinkage.R | 8 mfrmr-0.2.2/mfrmr/R/api-simulation-spec.R | 69 mfrmr-0.2.2/mfrmr/R/api-simulation-structural-design.R |only mfrmr-0.2.2/mfrmr/R/api-simulation.R | 207 mfrmr-0.2.2/mfrmr/R/api-tables.R | 75 mfrmr-0.2.2/mfrmr/R/api-viewer.R | 4 mfrmr-0.2.2/mfrmr/R/core-anchor-audit.R | 2 mfrmr-0.2.2/mfrmr/R/core-category-probabilities.R | 71 mfrmr-0.2.2/mfrmr/R/core-data-prep.R | 198 mfrmr-0.2.2/mfrmr/R/core-likelihood.R | 9 mfrmr-0.2.2/mfrmr/R/core-optimizer.R | 716 ++ mfrmr-0.2.2/mfrmr/R/datasets.R | 260 mfrmr-0.2.2/mfrmr/R/facets_mode_api.R | 22 mfrmr-0.2.2/mfrmr/R/facets_mode_methods.R | 12 mfrmr-0.2.2/mfrmr/R/help_compatibility_layer.R | 2 mfrmr-0.2.2/mfrmr/R/help_facets_coverage.R | 312 - mfrmr-0.2.2/mfrmr/R/help_gpcm_scope.R | 571 - mfrmr-0.2.2/mfrmr/R/help_linking_and_dff.R | 8 mfrmr-0.2.2/mfrmr/R/help_reporting_and_apa.R | 94 mfrmr-0.2.2/mfrmr/R/help_reports_and_tables.R | 259 mfrmr-0.2.2/mfrmr/R/help_visual_diagnostics.R | 37 mfrmr-0.2.2/mfrmr/R/help_workflow_methods.R | 69 mfrmr-0.2.2/mfrmr/R/mfrm_core.R | 702 +- mfrmr-0.2.2/mfrmr/R/mfrmr-package.R | 175 mfrmr-0.2.2/mfrmr/R/reporting.R | 30 mfrmr-0.2.2/mfrmr/R/utils-file-integrity.R |only mfrmr-0.2.2/mfrmr/README.md | 2609 +------- mfrmr-0.2.2/mfrmr/build/partial.rdb |binary mfrmr-0.2.2/mfrmr/build/vignette.rds |binary mfrmr-0.2.2/mfrmr/data/mfrmr_example_operational.rda |only mfrmr-0.2.2/mfrmr/data/mfrmr_example_operational_design.rda |only mfrmr-0.2.2/mfrmr/inst/WORDLIST | 2 mfrmr-0.2.2/mfrmr/inst/cheatsheet/mfrmr-cheatsheet.Rmd | 143 mfrmr-0.2.2/mfrmr/inst/cheatsheet/mfrmr-cheatsheet.pdf |binary mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-facets-migration.R | 11 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-facets-migration.Rmd | 125 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-facets-migration.html | 248 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-gpcm-scope.R | 2 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-gpcm-scope.Rmd | 116 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-gpcm-scope.html | 144 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-linking-and-dff.R | 20 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-linking-and-dff.Rmd | 30 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-linking-and-dff.html | 47 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-mml-and-marginal-fit.Rmd | 90 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-mml-and-marginal-fit.html | 116 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-reporting-and-apa.R | 52 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-reporting-and-apa.Rmd | 103 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-reporting-and-apa.html | 156 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-visual-diagnostics.R | 50 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-visual-diagnostics.Rmd | 103 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-visual-diagnostics.html | 342 - mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-workflow.R | 213 mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-workflow.Rmd | 338 - mfrmr-0.2.2/mfrmr/inst/doc/mfrmr-workflow.html | 952 ++- mfrmr-0.2.2/mfrmr/inst/extdata/README_sim_data.txt | 41 mfrmr-0.2.2/mfrmr/inst/extdata/vignette-artifacts |only mfrmr-0.2.2/mfrmr/inst/references/FACETS_manual_mapping.md | 162 mfrmr-0.2.2/mfrmr/man/analyze_dff.Rd | 43 mfrmr-0.2.2/mfrmr/man/analyze_facet_equivalence.Rd | 5 mfrmr-0.2.2/mfrmr/man/analyze_hierarchical_structure.Rd | 4 mfrmr-0.2.2/mfrmr/man/anchor_to_baseline.Rd | 14 mfrmr-0.2.2/mfrmr/man/apa_table.Rd | 7 mfrmr-0.2.2/mfrmr/man/apply_empirical_bayes_shrinkage.Rd | 2 mfrmr-0.2.2/mfrmr/man/as.data.frame.mfrm_fit.Rd | 14 mfrmr-0.2.2/mfrmr/man/as_flextable.Rd | 13 mfrmr-0.2.2/mfrmr/man/as_flextable.apa_table.Rd | 15 mfrmr-0.2.2/mfrmr/man/as_ggplot.Rd |only mfrmr-0.2.2/mfrmr/man/as_kable.Rd | 13 mfrmr-0.2.2/mfrmr/man/as_kable.apa_table.Rd | 18 mfrmr-0.2.2/mfrmr/man/assess_mfrm_recovery.Rd | 6 mfrmr-0.2.2/mfrmr/man/bias_count_table.Rd | 2 mfrmr-0.2.2/mfrmr/man/bias_interaction_report.Rd | 2 mfrmr-0.2.2/mfrmr/man/bias_iteration_report.Rd | 2 mfrmr-0.2.2/mfrmr/man/bias_pairwise_report.Rd | 2 mfrmr-0.2.2/mfrmr/man/build_apa_outputs.Rd | 20 mfrmr-0.2.2/mfrmr/man/build_conquest_overlap_bundle.Rd | 54 mfrmr-0.2.2/mfrmr/man/build_linking_review.Rd | 14 mfrmr-0.2.2/mfrmr/man/build_mfrm_manifest.Rd | 10 mfrmr-0.2.2/mfrmr/man/build_mfrm_network_review.Rd | 3 mfrmr-0.2.2/mfrmr/man/build_mfrm_replay_script.Rd | 9 mfrmr-0.2.2/mfrmr/man/build_mfrm_sim_spec.Rd | 36 mfrmr-0.2.2/mfrmr/man/build_misfit_casebook.Rd | 4 mfrmr-0.2.2/mfrmr/man/build_model_choice_review.Rd | 2 mfrmr-0.2.2/mfrmr/man/build_peer_review_design_review.Rd | 2 mfrmr-0.2.2/mfrmr/man/build_peer_review_sim_spec.Rd | 2 mfrmr-0.2.2/mfrmr/man/build_summary_table_bundle.Rd | 45 mfrmr-0.2.2/mfrmr/man/category_curves_report.Rd | 2 mfrmr-0.2.2/mfrmr/man/category_structure_report.Rd | 2 mfrmr-0.2.2/mfrmr/man/compare_mfrm.Rd | 3 mfrmr-0.2.2/mfrmr/man/compute_information.Rd | 5 mfrmr-0.2.2/mfrmr/man/compute_person_fit_indices.Rd | 2 mfrmr-0.2.2/mfrmr/man/data_quality_report.Rd | 10 mfrmr-0.2.2/mfrmr/man/describe_mfrm_data.Rd | 88 mfrmr-0.2.2/mfrmr/man/detect_anchor_drift.Rd | 12 mfrmr-0.2.2/mfrmr/man/diagnose_mfrm.Rd | 59 mfrmr-0.2.2/mfrmr/man/dif_interaction_table.Rd | 7 mfrmr-0.2.2/mfrmr/man/dif_report.Rd | 26 mfrmr-0.2.2/mfrmr/man/displacement_table.Rd | 2 mfrmr-0.2.2/mfrmr/man/draw_mfrm_resamples.Rd | 15 mfrmr-0.2.2/mfrmr/man/ej2021_data.Rd | 49 mfrmr-0.2.2/mfrmr/man/estimate_all_bias.Rd | 9 mfrmr-0.2.2/mfrmr/man/estimate_bias.Rd | 4 mfrmr-0.2.2/mfrmr/man/estimation_iteration_report.Rd | 18 mfrmr-0.2.2/mfrmr/man/evaluate_mfrm_design.Rd | 20 mfrmr-0.2.2/mfrmr/man/evaluate_mfrm_diagnostic_screening.Rd | 14 mfrmr-0.2.2/mfrmr/man/evaluate_mfrm_recovery.Rd | 12 mfrmr-0.2.2/mfrmr/man/evaluate_mfrm_signal_detection.Rd | 8 mfrmr-0.2.2/mfrmr/man/export_mfrm.Rd | 22 mfrmr-0.2.2/mfrmr/man/export_mfrm_bundle.Rd | 53 mfrmr-0.2.2/mfrmr/man/export_mfrm_results.Rd | 34 mfrmr-0.2.2/mfrmr/man/export_summary_appendix.Rd | 16 mfrmr-0.2.2/mfrmr/man/extract_mfrm_sim_spec.Rd | 9 mfrmr-0.2.2/mfrmr/man/facet_quality_dashboard.Rd | 15 mfrmr-0.2.2/mfrmr/man/facet_small_sample_review.Rd | 5 mfrmr-0.2.2/mfrmr/man/facet_statistics_report.Rd | 2 mfrmr-0.2.2/mfrmr/man/facets_chisq_table.Rd | 2 mfrmr-0.2.2/mfrmr/man/facets_feature_coverage.Rd | 33 mfrmr-0.2.2/mfrmr/man/facets_fit_review.Rd | 11 mfrmr-0.2.2/mfrmr/man/facets_output_contract_review.Rd | 14 mfrmr-0.2.2/mfrmr/man/facets_output_file_bundle.Rd | 7 mfrmr-0.2.2/mfrmr/man/facets_positioning_guide.Rd | 6 mfrmr-0.2.2/mfrmr/man/facets_term_crosswalk.Rd |only mfrmr-0.2.2/mfrmr/man/facets_visual_contract.Rd |only mfrmr-0.2.2/mfrmr/man/figures |only mfrmr-0.2.2/mfrmr/man/fit_measures_table.Rd | 7 mfrmr-0.2.2/mfrmr/man/fit_mfrm.Rd | 333 - mfrmr-0.2.2/mfrmr/man/gpcm_capability_matrix.Rd | 85 mfrmr-0.2.2/mfrmr/man/gpcm_runtime_guard_coverage.Rd | 26 mfrmr-0.2.2/mfrmr/man/gpcm_score_side_contract.Rd | 43 mfrmr-0.2.2/mfrmr/man/import_erm_fit.Rd | 17 mfrmr-0.2.2/mfrmr/man/import_mirt_fit.Rd | 15 mfrmr-0.2.2/mfrmr/man/import_tam_fit.Rd | 11 mfrmr-0.2.2/mfrmr/man/interaction_effect_table.Rd | 12 mfrmr-0.2.2/mfrmr/man/interrater_agreement_table.Rd | 13 mfrmr-0.2.2/mfrmr/man/launch_mfrmr_viewer.Rd | 4 mfrmr-0.2.2/mfrmr/man/list_mfrmr_data.Rd | 29 mfrmr-0.2.2/mfrmr/man/load_mfrmr_data.Rd | 37 mfrmr-0.2.2/mfrmr/man/make_anchor_table.Rd | 7 mfrmr-0.2.2/mfrmr/man/measurable_summary_table.Rd | 2 mfrmr-0.2.2/mfrmr/man/mfrm_d_study.Rd | 9 mfrmr-0.2.2/mfrmr/man/mfrm_generalizability.Rd | 23 mfrmr-0.2.2/mfrmr/man/mfrm_misfit_thresholds.Rd | 11 mfrmr-0.2.2/mfrmr/man/mfrm_network_analysis.Rd | 3 mfrmr-0.2.2/mfrmr/man/mfrm_report.Rd | 9 mfrmr-0.2.2/mfrmr/man/mfrm_results.Rd | 83 mfrmr-0.2.2/mfrmr/man/mfrm_results_interactive.Rd | 2 mfrmr-0.2.2/mfrmr/man/mfrmr-package.Rd | 170 mfrmr-0.2.2/mfrmr/man/mfrmr_compatibility_layer.Rd | 2 mfrmr-0.2.2/mfrmr/man/mfrmr_example_data.Rd | 69 mfrmr-0.2.2/mfrmr/man/mfrmr_example_operational_design.Rd |only mfrmr-0.2.2/mfrmr/man/mfrmr_linking_and_dff.Rd | 8 mfrmr-0.2.2/mfrmr/man/mfrmr_output_guide.Rd | 32 mfrmr-0.2.2/mfrmr/man/mfrmr_reporting_and_apa.Rd | 101 mfrmr-0.2.2/mfrmr/man/mfrmr_reports_and_tables.Rd | 5 mfrmr-0.2.2/mfrmr/man/mfrmr_visual_diagnostics.Rd | 39 mfrmr-0.2.2/mfrmr/man/mfrmr_workflow_methods.Rd | 51 mfrmr-0.2.2/mfrmr/man/normalize_conquest_overlap_exports.Rd |only mfrmr-0.2.2/mfrmr/man/normalize_conquest_overlap_files.Rd | 3 mfrmr-0.2.2/mfrmr/man/plot.mfrm_diagnostic_screening.Rd | 4 mfrmr-0.2.2/mfrmr/man/plot.mfrm_fit.Rd | 183 mfrmr-0.2.2/mfrmr/man/plot.mfrm_recovery_simulation.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot.mfrm_summary_table_bundle.Rd | 3 mfrmr-0.2.2/mfrmr/man/plot_apa_figure_one.Rd | 19 mfrmr-0.2.2/mfrmr/man/plot_bias_interaction.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_bubble.Rd | 14 mfrmr-0.2.2/mfrmr/man/plot_data.Rd | 8 mfrmr-0.2.2/mfrmr/man/plot_dif_heatmap.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_dif_summary.Rd | 16 mfrmr-0.2.2/mfrmr/man/plot_displacement.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_facet_equivalence.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_facet_quality_dashboard.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_facets_chisq.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_fair_average.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_guttman_scalogram.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_information.Rd | 5 mfrmr-0.2.2/mfrmr/man/plot_local_dependence_heatmap.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_person_fit.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_qc_dashboard.Rd | 4 mfrmr-0.2.2/mfrmr/man/plot_rater_agreement_heatmap.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_rater_severity_profile.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_reliability_snapshot.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_residual_matrix.Rd | 11 mfrmr-0.2.2/mfrmr/man/plot_residual_pca.Rd | 4 mfrmr-0.2.2/mfrmr/man/plot_residual_qq.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_shrinkage_funnel.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_threshold_ladder.Rd | 4 mfrmr-0.2.2/mfrmr/man/plot_unexpected.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_wright_unified.Rd | 93 mfrmr-0.2.2/mfrmr/man/precision_review_report.Rd | 8 mfrmr-0.2.2/mfrmr/man/predict_mfrm_population.Rd | 14 mfrmr-0.2.2/mfrmr/man/predict_mfrm_units.Rd | 14 mfrmr-0.2.2/mfrmr/man/print.mfrm_apa_text.Rd | 2 mfrmr-0.2.2/mfrmr/man/q3_statistic.Rd | 87 mfrmr-0.2.2/mfrmr/man/rater_halo_network_analysis.Rd | 3 mfrmr-0.2.2/mfrmr/man/rater_network_analysis.Rd | 3 mfrmr-0.2.2/mfrmr/man/rating_scale_table.Rd | 4 mfrmr-0.2.2/mfrmr/man/recode_missing_codes.Rd | 5 mfrmr-0.2.2/mfrmr/man/recommend_mfrm_design.Rd | 2 mfrmr-0.2.2/mfrmr/man/reference_case_benchmark.Rd | 4 mfrmr-0.2.2/mfrmr/man/reporting_checklist.Rd | 16 mfrmr-0.2.2/mfrmr/man/review_conquest_overlap.Rd | 55 mfrmr-0.2.2/mfrmr/man/review_mfrm_anchors.Rd | 5 mfrmr-0.2.2/mfrmr/man/run_mfrm_facets.Rd | 16 mfrmr-0.2.2/mfrmr/man/run_qc_pipeline.Rd | 3 mfrmr-0.2.2/mfrmr/man/sample_mfrm_plausible_values.Rd | 14 mfrmr-0.2.2/mfrmr/man/shrinkage_report.Rd | 2 mfrmr-0.2.2/mfrmr/man/simulate_mfrm_data.Rd | 21 mfrmr-0.2.2/mfrmr/man/specifications_report.Rd | 7 mfrmr-0.2.2/mfrmr/man/subset_connectivity_report.Rd | 2 mfrmr-0.2.2/mfrmr/man/summary.apa_table.Rd | 2 mfrmr-0.2.2/mfrmr/man/summary.mfrm_apa_outputs.Rd | 2 mfrmr-0.2.2/mfrmr/man/summary.mfrm_bias.Rd | 6 mfrmr-0.2.2/mfrmr/man/summary.mfrm_bundle.Rd | 13 mfrmr-0.2.2/mfrmr/man/summary.mfrm_data_description.Rd | 15 mfrmr-0.2.2/mfrmr/man/summary.mfrm_design_evaluation.Rd | 8 mfrmr-0.2.2/mfrmr/man/summary.mfrm_diagnostic_screening.Rd | 4 mfrmr-0.2.2/mfrmr/man/summary.mfrm_diagnostics.Rd | 28 mfrmr-0.2.2/mfrmr/man/summary.mfrm_facet_dashboard.Rd | 2 mfrmr-0.2.2/mfrmr/man/summary.mfrm_facets_run.Rd | 2 mfrmr-0.2.2/mfrmr/man/summary.mfrm_fit.Rd | 125 mfrmr-0.2.2/mfrmr/man/summary.mfrm_person_fit_indices.Rd | 6 mfrmr-0.2.2/mfrmr/man/summary.mfrm_plausible_values.Rd | 14 mfrmr-0.2.2/mfrmr/man/summary.mfrm_population_prediction.Rd | 8 mfrmr-0.2.2/mfrmr/man/summary.mfrm_signal_detection.Rd | 8 mfrmr-0.2.2/mfrmr/man/summary.mfrm_summary_table_bundle.Rd | 3 mfrmr-0.2.2/mfrmr/man/summary.mfrm_unit_prediction.Rd | 14 mfrmr-0.2.2/mfrmr/man/unexpected_after_bias_table.Rd | 11 mfrmr-0.2.2/mfrmr/man/unexpected_response_table.Rd | 2 mfrmr-0.2.2/mfrmr/tests/testthat.R | 17 mfrmr-0.2.2/mfrmr/tests/testthat/helper-fixtures.R | 21 mfrmr-0.2.2/mfrmr/tests/testthat/test-anchor-equating.R | 2 mfrmr-0.2.2/mfrmr/tests/testthat/test-api-error-and-edge-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-api-guard-paths.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-api-public-method-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-as-ggplot.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-as-kable.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-attach-diagnostics.R | 23 mfrmr-0.2.2/mfrmr/tests/testthat/test-bias-collection.R | 24 mfrmr-0.2.2/mfrmr/tests/testthat/test-bubble-chart.R | 27 mfrmr-0.2.2/mfrmr/tests/testthat/test-bundle-dispatch-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-bundle-summary-privacy.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-calc-subsets-parity.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-ci-api-consistency.R | 7 mfrmr-0.2.2/mfrmr/tests/testthat/test-compatibility-aliases.R | 29 mfrmr-0.2.2/mfrmr/tests/testthat/test-console-output-contract.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-core-behavior-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-core-edge-paths.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-core-workflow.R | 64 mfrmr-0.2.2/mfrmr/tests/testthat/test-cran-smoke.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-data-and-citation.R | 6 mfrmr-0.2.2/mfrmr/tests/testthat/test-data-design-audit.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-data-processing.R | 12 mfrmr-0.2.2/mfrmr/tests/testthat/test-diagnostic-screening-validation.R | 2 mfrmr-0.2.2/mfrmr/tests/testthat/test-dif-module.R | 128 mfrmr-0.2.2/mfrmr/tests/testthat/test-documentation-terminology.R | 688 -- mfrmr-0.2.2/mfrmr/tests/testthat/test-draw-and-plot-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-edge-cases.R | 37 mfrmr-0.2.2/mfrmr/tests/testthat/test-estimation-core.R | 167 mfrmr-0.2.2/mfrmr/tests/testthat/test-example-datasets.R | 107 mfrmr-0.2.2/mfrmr/tests/testthat/test-example-policy.R | 156 mfrmr-0.2.2/mfrmr/tests/testthat/test-exception-regression.R | 9 mfrmr-0.2.2/mfrmr/tests/testthat/test-export-bundles.R | 365 + mfrmr-0.2.2/mfrmr/tests/testthat/test-export-mfrm.R | 34 mfrmr-0.2.2/mfrmr/tests/testthat/test-facet-equivalence.R | 34 mfrmr-0.2.2/mfrmr/tests/testthat/test-facet-interactions.R | 2 mfrmr-0.2.2/mfrmr/tests/testthat/test-facets-column-contract.R | 19 mfrmr-0.2.2/mfrmr/tests/testthat/test-facets-metric-contract.R | 38 mfrmr-0.2.2/mfrmr/tests/testthat/test-facets-mode-api.R | 13 mfrmr-0.2.2/mfrmr/tests/testthat/test-facets-summary-profile.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-first-use-readiness-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-fit-pathway.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-gpcm-capability-matrix.R | 279 mfrmr-0.2.2/mfrmr/tests/testthat/test-gpcm-fair-average.R | 21 mfrmr-0.2.2/mfrmr/tests/testthat/test-gpcm-verification.R | 28 mfrmr-0.2.2/mfrmr/tests/testthat/test-import-full.R | 39 mfrmr-0.2.2/mfrmr/tests/testthat/test-information-module.R | 10 mfrmr-0.2.2/mfrmr/tests/testthat/test-marginal-fit-diagnostics.R | 9 mfrmr-0.2.2/mfrmr/tests/testthat/test-mathematical-consistency.R | 18 mfrmr-0.2.2/mfrmr/tests/testthat/test-mfrm-results.R | 150 mfrmr-0.2.2/mfrmr/tests/testthat/test-missing-codes-integration.R | 110 mfrmr-0.2.2/mfrmr/tests/testthat/test-mml-cpp11-backend.R | 4 mfrmr-0.2.2/mfrmr/tests/testthat/test-model-choice-review.R | 60 mfrmr-0.2.2/mfrmr/tests/testthat/test-namespace-contract.R | 35 mfrmr-0.2.2/mfrmr/tests/testthat/test-numerical-validation.R | 10 mfrmr-0.2.2/mfrmr/tests/testthat/test-output-guide.R | 203 mfrmr-0.2.2/mfrmr/tests/testthat/test-output-stability.R | 51 mfrmr-0.2.2/mfrmr/tests/testthat/test-parameter-recovery.R | 18 mfrmr-0.2.2/mfrmr/tests/testthat/test-plot-customization.R | 22 mfrmr-0.2.2/mfrmr/tests/testthat/test-plotting-extras.R | 49 mfrmr-0.2.2/mfrmr/tests/testthat/test-q3-and-person-fit.R | 112 mfrmr-0.2.2/mfrmr/tests/testthat/test-qc-pipeline.R | 53 mfrmr-0.2.2/mfrmr/tests/testthat/test-recovery-simulation.R | 14 mfrmr-0.2.2/mfrmr/tests/testthat/test-reference-benchmark.R | 96 mfrmr-0.2.2/mfrmr/tests/testthat/test-regression-edge-paths.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-replay-roundtrip.R | 5 mfrmr-0.2.2/mfrmr/tests/testthat/test-report-functions.R | 43 mfrmr-0.2.2/mfrmr/tests/testthat/test-reporting-and-facets-edge-paths.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-reporting-checklist.R | 2 mfrmr-0.2.2/mfrmr/tests/testthat/test-reporting-edge-paths.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-reporting-method-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-results-readiness-propagation.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-shrinkage.R | 17 mfrmr-0.2.2/mfrmr/tests/testthat/test-simulation-design.R | 981 +-- mfrmr-0.2.2/mfrmr/tests/testthat/test-summary-reporting-blocks.R | 18 mfrmr-0.2.2/mfrmr/tests/testthat/test-summary-table-bundle.R | 324 - mfrmr-0.2.2/mfrmr/tests/testthat/test-vignette-artifacts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-wright-facets-style.R |only mfrmr-0.2.2/mfrmr/vignettes/mfrmr-facets-migration.Rmd | 125 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-gpcm-scope.Rmd | 116 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-linking-and-dff.Rmd | 30 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-mml-and-marginal-fit.Rmd | 90 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-reporting-and-apa.Rmd | 103 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-visual-diagnostics.Rmd | 103 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-workflow.Rmd | 338 - 363 files changed, 21097 insertions(+), 11812 deletions(-)
Title: Modified Generalized Estimating Equations for Small-Sample Data
Description: Analyze small-sample clustered or longitudinal data using modified
generalized estimating equations with bias-adjusted covariance estimator.
The package provides any combination of three modified generalized
estimating equations and 11 bias-adjusted covariance estimators.
Author: Ryota Ishii [aut, cre],
Kazushi Maruo [ctb],
Masahiko Gosho [ctb]
Maintainer: Ryota Ishii <r.ishii0808@gmail.com>
Diff between geess versions 1.0.1 dated 2026-04-27 and 1.0.2 dated 2026-07-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/geess.R | 8 ++++---- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: GCC Estimation of the Multilevel Factor Model
Description: Provides methods for model selection, estimation, inference, and simulation for the
multilevel factor model, based on the principal component estimation and generalised
canonical correlation approach. Details can be found in "Generalised Canonical Correlation
Estimation of the Multilevel Factor Model." Lin and Shin (2025) <doi:10.2139/ssrn.4295429>.
Author: Rui Lin [aut, cre],
Yongcheol Shin [aut]
Maintainer: Rui Lin <ruilin1081@gmail.com>
Diff between GCCfactor versions 1.1.6 dated 2026-04-18 and 1.2.0 dated 2026-07-27
DESCRIPTION | 8 MD5 | 15 R/2D_functions.R | 381 ++++++++++++------------ R/internal_functions.R | 184 ++++++----- R/main_functions.R | 57 ++- R/vcov_functions.R | 754 +++++++++++++++++++++++++------------------------ README.md |only man/GCC.Rd | 21 - man/multilevel.Rd | 20 - 9 files changed, 766 insertions(+), 674 deletions(-)