Title: Unidimensional Item Response Theory Modeling
Description: Fits unidimensional item response theory (IRT) models to test
data that include dichotomous and polytomous items, calibrates pretest
items with fixed item and fixed ability parameter calibration, performs
multiple-group calibration, estimates the abilities of examinees, and
evaluates model-data fit at the item level. It also provides tools for
detecting differential item functioning and item parameter drift, for
computing classification accuracy and consistency, and for evaluating and
simulating multistage-adaptive test panels, together with classical test
theory functions for item- and test-level statistics (e.g., item difficulty,
item-total correlation, and coefficient alpha) and for scoring
selected-response item data.
The bring.flexmirt() and write.flexmirt() functions were written by modifying
the read.flexmirt() function (Pritikin & Falk (2020) <doi:10.1177/0146621620929431>).
The bring.bilog() and bring.parscale() functions were written by modifying the read.bilog()
an [...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 1.3.1 dated 2026-10-08 and 1.4.0 dated 2026-11-14
DESCRIPTION | 31 MD5 | 349 ++--- NAMESPACE | 2 NEWS.md | 974 ++++++++++++++ R/EM.R | 72 - R/LSAT6.R | 6 R/SimCAT_DC.R | 18 R/SimCAT_MX.R | 11 R/bisection.R | 30 R/bring_output.R | 361 ++--- R/cac_lee.R | 442 ++---- R/cac_rud.R | 456 +++--- R/catsib.R | 1261 +++++++++++++----- R/chisq_stat.R | 28 R/collapse_ftable.R | 26 R/confirm_df.R | 60 R/covirt.R | 219 ++- R/crdif.R | 1215 ++++++------------ R/ctt.R | 122 + R/ctt_alpha.R | 166 +- R/ctt_distr.R | 207 +-- R/ctt_item.R | 179 +- R/dif_common.R |only R/eap_sum.R | 63 R/equation_scocat.R | 15 R/est_irt.R | 943 +++++++++----- R/est_item.R | 196 ++ R/est_mg.R | 1024 ++++++++++----- R/est_score.R | 841 +++++------- R/estimation.R | 276 +++- R/expFreq.R | 61 R/find_cut.R | 145 +- R/freq_score.R | 49 R/gen_weight.R | 30 R/getirt.R | 166 +- R/gradient.R | 248 --- R/grdif.R | 1944 +++++++++-------------------- R/hessian.R | 166 +- R/info.R | 312 +--- R/info_xpd.R | 43 R/inv_tcc.R | 186 -- R/irtQ-package.R | 144 +- R/irtfit.R | 524 +++---- R/irtmodel.R | 70 - R/likelihood.R | 59 R/ll_score.R | 11 R/llike_score.R | 86 - R/loglike_item.R | 67 R/logprior_deriv.R | 7 R/lubound.R | 10 R/lwrc.R | 136 -- R/optim_fns.R | 36 R/panel_info.R | 72 - R/parloc.R | 5 R/pcd2.R | 397 +++-- R/plot_info.R | 30 R/plot_irtfit.R | 125 + R/plot_traceline.R | 88 - R/print.R | 278 +++- R/rdif.R | 1312 +++++++------------ R/reval_mst.R | 345 ++--- R/ripd.R | 1288 +++++++------------ R/run_flexmirt.R | 86 - R/run_mst.R | 299 +++- R/scale_prior.R | 15 R/score_resp.R | 187 +- R/shape_df.R | 111 + R/shape_df_fipc.R | 74 - R/simIPD.R | 83 - R/simMG.R | 40 R/simMST.R | 31 R/simdat.R | 105 - R/summary.R | 41 R/sx2_fit.R | 686 ++-------- R/traceline.R | 264 --- R/util.R | 94 + R/write_flexmirt.R | 126 + README.md | 103 - inst/doc/irtQ.Rmd | 12 inst/doc/irtQ.html | 26 man/LSAT6.Rd | 6 man/bind.fill.Rd | 89 - man/bisection.Rd | 135 +- man/bring.flexmirt.Rd | 192 +- man/cac_lee.Rd | 121 + man/cac_rud.Rd | 129 + man/catsib.Rd | 576 +++++--- man/covirt.Rd | 175 +- man/crdif.Rd | 353 +++-- man/ctt.Rd | 115 - man/ctt_alpha.Rd | 124 - man/ctt_distr.Rd | 146 +- man/ctt_item.Rd | 113 - man/drm.Rd | 103 - man/est_irt.Rd | 647 ++++++--- man/est_item.Rd | 186 +- man/est_mg.Rd | 647 ++++++--- man/est_score.Rd | 303 ++-- man/find_cut.Rd | 117 + man/freq_score.Rd | 29 man/gen.weight.Rd | 180 +- man/getirt.Rd | 156 +- man/grdif.Rd | 568 +++++--- man/info.Rd | 28 man/irtQ-package.Rd | 142 +- man/irtfit.Rd | 257 ++- man/llike_score.Rd | 216 +-- man/lwrc.Rd | 43 man/panel_info.Rd | 13 man/pcd2.Rd | 310 ++-- man/plot.find_cut.Rd | 7 man/plot.info.Rd | 251 +-- man/plot.irtfit.Rd | 77 - man/plot.traceline.Rd | 326 ++-- man/print.ctt.Rd | 8 man/print.summary.ctt.Rd | 10 man/prm.Rd | 134 + man/rdif.Rd | 411 ++++-- man/reval_mst.Rd | 259 +-- man/ripd.Rd | 411 ++++-- man/run_flexmirt.Rd | 54 man/run_mst.Rd | 171 +- man/score_resp.Rd | 112 - man/shape_df.Rd | 281 ++-- man/shape_df_fipc.Rd | 155 +- man/simCAT_DC.Rd | 18 man/simCAT_MX.Rd | 11 man/simIPD.Rd | 83 - man/simMG.Rd | 40 man/simMST.Rd | 31 man/simdat.Rd | 428 +++--- man/summary.Rd | 180 +- man/sx2_fit.Rd | 469 +++--- man/traceline.Rd | 22 man/write.flexmirt.Rd | 64 tests/testthat/helper-em-independent.R |only tests/testthat/helper-mg-independent.R |only tests/testthat/helper-mst-reference.R |only tests/testthat/test-bring_mirt-mixed.R |only tests/testthat/test-bring_output.R |only tests/testthat/test-cac_lee.R |only tests/testthat/test-cac_rud.R | 71 + tests/testthat/test-catsib.R |only tests/testthat/test-char-resp.R |only tests/testthat/test-confirm_df.R | 116 + tests/testthat/test-covirt.R |only tests/testthat/test-crdif.R |only tests/testthat/test-ctt.R | 217 +++ tests/testthat/test-ctt_distr.R | 137 ++ tests/testthat/test-dif.R | 13 tests/testthat/test-dif_common.R |only tests/testthat/test-drm-prm.R | 103 + tests/testthat/test-em-convergence.R |only tests/testthat/test-em-independent.R |only tests/testthat/test-em-input-checks.R |only tests/testthat/test-em-npar.R |only tests/testthat/test-em-weights-input.R |only tests/testthat/test-est_irt.R | 32 tests/testthat/test-est_item.R | 32 tests/testthat/test-est_mg.R | 95 - tests/testthat/test-est_score.R | 624 ++++++++- tests/testthat/test-fallback-prm.R |only tests/testthat/test-find_cut.R | 68 - tests/testthat/test-freq_score.R | 29 tests/testthat/test-gen_weight.R |only tests/testthat/test-getirt.R |only tests/testthat/test-grdif.R |only tests/testthat/test-grm-order.R |only tests/testthat/test-info.R |only tests/testthat/test-irtfit.R | 310 ++++ tests/testthat/test-item-derivatives.R |only tests/testthat/test-item-id.R |only tests/testthat/test-item-independent.R |only tests/testthat/test-item-inputs.R |only tests/testthat/test-likelihood-underflow.R |only tests/testthat/test-mg-fipc.R |only tests/testthat/test-mg-independent.R |only tests/testthat/test-mg-inputs.R |only tests/testthat/test-mg-messages.R |only tests/testthat/test-mle-warning.R |only tests/testthat/test-panel_info.R |only tests/testthat/test-pcd2.R |only tests/testthat/test-rdif.R |only tests/testthat/test-reval_mst.R | 141 ++ tests/testthat/test-ripd.R |only tests/testthat/test-run_flexmirt.R |only tests/testthat/test-run_mst.R | 157 ++ tests/testthat/test-score_resp.R | 22 tests/testthat/test-se-crossprod.R |only tests/testthat/test-shape_df.R | 84 + tests/testthat/test-shape_df_fipc.R | 50 tests/testthat/test-simdat.R | 82 + tests/testthat/test-sx2_fit.R |only tests/testthat/test-trace-score.R |only tests/testthat/test-traceline.R |only tests/testthat/test-write_flexmirt.R |only vignettes/irtQ.Rmd | 12 197 files changed, 18970 insertions(+), 14073 deletions(-)
Title: Evaluation of Tweedie Exponential Family Models
Description: Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; <doi:10.1007/s11222-005-4070-y>) and the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), and related methods.
Author: Peter K. Dunn [cre, aut]
Maintainer: Peter K. Dunn <pdunn2@usc.edu.au>
Diff between tweedie versions 3.1.0 dated 2026-05-19 and 3.2.1 dated 2026-11-14
tweedie-3.1.0/tweedie/src/Doxyfile |only tweedie-3.1.0/tweedie/src/deps.out |only tweedie-3.1.0/tweedie/src/docs |only tweedie-3.2.1/tweedie/DESCRIPTION | 10 tweedie-3.2.1/tweedie/MD5 | 536 ---- tweedie-3.2.1/tweedie/NAMESPACE | 51 tweedie-3.2.1/tweedie/NEWS.md | 83 tweedie-3.2.1/tweedie/R/dtweedie_inversion.R | 157 - tweedie-3.2.1/tweedie/R/dtweedie_saddle.R | 143 + tweedie-3.2.1/tweedie/R/dtweedie_series.R | 546 +++- tweedie-3.2.1/tweedie/R/ptweedie_inversion.R | 201 + tweedie-3.2.1/tweedie/R/ptweedie_saddle.R |only tweedie-3.2.1/tweedie/R/ptweedie_series.R | 294 +- tweedie-3.2.1/tweedie/R/ptweedie_tail_integrate.R |only tweedie-3.2.1/tweedie/R/tweedie-internals.R | 71 tweedie-3.2.1/tweedie/R/tweedie_AIC.R | 31 tweedie-3.2.1/tweedie/R/tweedie_convert.R | 189 + tweedie-3.2.1/tweedie/R/tweedie_dev.R | 131 - tweedie-3.2.1/tweedie/R/tweedie_dpqr.R | 1212 ++++++---- tweedie-3.2.1/tweedie/R/tweedie_integrand.R | 78 tweedie-3.2.1/tweedie/R/tweedie_plot.R | 43 tweedie-3.2.1/tweedie/R/tweedie_profile.R | 1067 ++++---- tweedie-3.2.1/tweedie/R/tweedie_regimes.R |only tweedie-3.2.1/tweedie/R/utils.R | 196 + tweedie-3.2.1/tweedie/README.md | 65 tweedie-3.2.1/tweedie/build/partial.rdb |binary tweedie-3.2.1/tweedie/build/vignette.rds |binary tweedie-3.2.1/tweedie/inst/CITATION | 49 tweedie-3.2.1/tweedie/inst/doc/tweedie.R | 205 + tweedie-3.2.1/tweedie/inst/doc/tweedie.Rmd | 355 ++ tweedie-3.2.1/tweedie/inst/doc/tweedie.html | 465 +++ tweedie-3.2.1/tweedie/inst/extdata/quilpie.csv |only tweedie-3.2.1/tweedie/man/Tweedie.Rd | 92 tweedie-3.2.1/tweedie/man/dtweedie_inversion.Rd | 19 tweedie-3.2.1/tweedie/man/dtweedie_saddle.Rd | 19 tweedie-3.2.1/tweedie/man/dtweedie_series.Rd | 19 tweedie-3.2.1/tweedie/man/ptweedie_inversion.Rd | 56 tweedie-3.2.1/tweedie/man/ptweedie_saddle.Rd |only tweedie-3.2.1/tweedie/man/ptweedie_series.Rd | 44 tweedie-3.2.1/tweedie/man/ptweedie_tail_integrate.Rd |only tweedie-3.2.1/tweedie/man/tweedie-package.Rd | 5 tweedie-3.2.1/tweedie/man/tweedie_convert.Rd | 71 tweedie-3.2.1/tweedie/man/tweedie_dev.Rd | 2 tweedie-3.2.1/tweedie/man/tweedie_profile.Rd | 36 tweedie-3.2.1/tweedie/src/00tweedie_params.f90 | 99 tweedie-3.2.1/tweedie/src/Calcs_Imag.f90 | 54 tweedie-3.2.1/tweedie/src/Calcs_K.f90 | 284 +- tweedie-3.2.1/tweedie/src/Calcs_Real.f90 | 35 tweedie-3.2.1/tweedie/src/Calcs_Solvers.f90 | 1 tweedie-3.2.1/tweedie/src/GaussQuadrature.f90 | 184 + tweedie-3.2.1/tweedie/src/Integrands.f90 | 31 tweedie-3.2.1/tweedie/src/TweedieIntHelpers.f90 | 267 +- tweedie-3.2.1/tweedie/src/TweedieIntegration.f90 | 367 ++- tweedie-3.2.1/tweedie/src/accelerate.f90 | 25 tweedie-3.2.1/tweedie/src/findAccelStart.f90 | 2 tweedie-3.2.1/tweedie/src/init.c | 4 tweedie-3.2.1/tweedie/src/twcomputation.f90 | 6 tweedie-3.2.1/tweedie/src/twcomputation_loop.f90 | 39 tweedie-3.2.1/tweedie/tests/testthat/Rplots.pdf |binary tweedie-3.2.1/tweedie/tests/testthat/test-details.R |only tweedie-3.2.1/tweedie/tests/testthat/test-dtweedie-regimes.R |only tweedie-3.2.1/tweedie/tests/testthat/test-hangs.R |only tweedie-3.2.1/tweedie/tests/testthat/test-inputs.R | 6 tweedie-3.2.1/tweedie/tests/testthat/test-inversion-precap.R |only tweedie-3.2.1/tweedie/tests/testthat/test-inversion-psmall-oscillations.R |only tweedie-3.2.1/tweedie/tests/testthat/test-inversion-small-tail.R |only tweedie-3.2.1/tweedie/tests/testthat/test-log-and-NA.R |only tweedie-3.2.1/tweedie/tests/testthat/test-other-ptweedie.R | 12 tweedie-3.2.1/tweedie/tests/testthat/test-other.R | 17 tweedie-3.2.1/tweedie/tests/testthat/test-output-shape.R |only tweedie-3.2.1/tweedie/tests/testthat/test-poisson-p1.R |only tweedie-3.2.1/tweedie/tests/testthat/test-precision.R |only tweedie-3.2.1/tweedie/tests/testthat/test-ptweedie-large-lambda.R |only tweedie-3.2.1/tweedie/tests/testthat/test-ptweedie-logp-cap.R |only tweedie-3.2.1/tweedie/tests/testthat/test-ptweedie-regimes-small-dispersion.R |only tweedie-3.2.1/tweedie/tests/testthat/test-ptweedie-saddle.R |only tweedie-3.2.1/tweedie/tests/testthat/test-ptweedie-smallp-method.R |only tweedie-3.2.1/tweedie/tests/testthat/test-ptweedie-smallp-tails.R |only tweedie-3.2.1/tweedie/tests/testthat/test-qtweedie-solve.R |only tweedie-3.2.1/tweedie/tests/testthat/test-regimes.R |only tweedie-3.2.1/tweedie/tests/testthat/test-robustness.R |only tweedie-3.2.1/tweedie/tests/testthat/test-series-bigp.R |only tweedie-3.2.1/tweedie/tests/testthat/test-series-limits.R |only tweedie-3.2.1/tweedie/tests/testthat/test-series-maxterms.R |only tweedie-3.2.1/tweedie/tests/testthat/test-tail-integrate.R |only tweedie-3.2.1/tweedie/tests/testthat/test-tails-logp.R |only tweedie-3.2.1/tweedie/tests/testthat/test-tweedie-profile.R |only tweedie-3.2.1/tweedie/vignettes/tweedie.Rmd | 355 ++ 88 files changed, 5778 insertions(+), 2551 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Fits generalized linear and non linear mixed models with flexible covariance structures for multiple random effects. Supports structured random-effect and Gaussian residual covariances, including unstructured, autoregressive, spatial, factor-analytic and reduced-rank models. These structures can be combined using Kronecker products and user-defined covariance functions. Known relationships among random-effect levels, including pedigree and genomic relationship matrices, can be incorporated. Gaussian models are fitted by maximum likelihood or restricted maximum likelihood using complementary coefficient-space Henderson and observation-space direct-inversion engines, with average-information optimization and expectation-maximization recovery. Numerical methods include sparse matrix factorization, preconditioned iterative solvers and stochastic trace and log-determinant approximations for eligible large-scale problems. Generalized models are fitted by penalized quasi-likelihood or native [...truncated...]
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.5.12 dated 2026-10-25 and 4.5.27 dated 2026-11-14
sommer-4.5.12/sommer/R/vpredict.R |only sommer-4.5.12/sommer/man/print.sommer_mmes_control.Rd |only sommer-4.5.12/sommer/man/vpredict.Rd |only sommer-4.5.27/sommer/CHANGELOG | 474 ++++ sommer-4.5.27/sommer/DESCRIPTION | 17 sommer-4.5.27/sommer/MD5 | 466 ++-- sommer-4.5.27/sommer/NAMESPACE | 54 sommer-4.5.27/sommer/R/DEPRECATED_mmer.R | 116 + sommer-4.5.27/sommer/R/FUN_boot_mmes.R |only sommer-4.5.27/sommer/R/FUN_constraints.R | 32 sommer-4.5.27/sommer/R/FUN_direct_inference.R |only sommer-4.5.27/sommer/R/FUN_fixed_rank.R | 1 sommer-4.5.27/sommer/R/FUN_glmm.R | 975 +++++++++ sommer-4.5.27/sommer/R/FUN_glmm_constraints.R |only sommer-4.5.27/sommer/R/FUN_glmm_families.R |only sommer-4.5.27/sommer/R/FUN_glmm_latent.R |only sommer-4.5.27/sommer/R/FUN_glmm_mixed.R |only sommer-4.5.27/sommer/R/FUN_glmm_nominal.R |only sommer-4.5.27/sommer/R/FUN_glmm_ordinal.R |only sommer-4.5.27/sommer/R/FUN_glmm_paths.R |only sommer-4.5.27/sommer/R/FUN_glmm_residual.R |only sommer-4.5.27/sommer/R/FUN_glmm_system.R |only sommer-4.5.27/sommer/R/FUN_grid_augment.R |only sommer-4.5.27/sommer/R/FUN_markers.R | 36 sommer-4.5.27/sommer/R/FUN_methods_mmes.R | 328 +++ sommer-4.5.27/sommer/R/FUN_mme_benchmark.R | 58 sommer-4.5.27/sommer/R/FUN_mme_capabilities.R | 351 +++ sommer-4.5.27/sommer/R/FUN_mme_control.R | 6 sommer-4.5.27/sommer/R/FUN_mme_modules.R | 230 ++ sommer-4.5.27/sommer/R/FUN_model_interface.R |only sommer-4.5.27/sommer/R/FUN_model_specification.R |only sommer-4.5.27/sommer/R/FUN_multivariate.R | 2 sommer-4.5.27/sommer/R/FUN_nonlinear_comparison.R |only sommer-4.5.27/sommer/R/FUN_nonlinear_family.R |only sommer-4.5.27/sommer/R/FUN_nonlinear_family_methods.R |only sommer-4.5.27/sommer/R/FUN_nonlinear_fit.R |only sommer-4.5.27/sommer/R/FUN_nonlinear_inference.R |only sommer-4.5.27/sommer/R/FUN_nonlinear_methods.R |only sommer-4.5.27/sommer/R/FUN_nonlinear_model.R |only sommer-4.5.27/sommer/R/FUN_nonlinear_paths.R |only sommer-4.5.27/sommer/R/FUN_nonlinear_prediction_inference.R |only sommer-4.5.27/sommer/R/FUN_nonlinear_profile.R |only sommer-4.5.27/sommer/R/FUN_nonlinear_random.R |only sommer-4.5.27/sommer/R/FUN_relationships.R | 81 sommer-4.5.27/sommer/R/FUN_specification_derivatives.R |only sommer-4.5.27/sommer/R/FUN_specification_family.R |only sommer-4.5.27/sommer/R/FUN_specification_inference.R |only sommer-4.5.27/sommer/R/FUN_specification_profile.R |only sommer-4.5.27/sommer/R/FUN_stats.R | 463 ++++ sommer-4.5.27/sommer/R/FUN_vsm.R | 3 sommer-4.5.27/sommer/R/FUN_wald.R | 31 sommer-4.5.27/sommer/R/RcppExports.R | 136 + sommer-4.5.27/sommer/R/mmes.R | 162 + sommer-4.5.27/sommer/R/predict_mmes.R | 633 ++++++ sommer-4.5.27/sommer/R/vcDelta.R |only sommer-4.5.27/sommer/R/zzz.R | 4 sommer-4.5.27/sommer/README.md | 40 sommer-4.5.27/sommer/build/partial.rdb |binary sommer-4.5.27/sommer/build/vignette.rds |binary sommer-4.5.27/sommer/inst/benchmarks |only sommer-4.5.27/sommer/inst/doc/sommer.blas.threads.html | 20 sommer-4.5.27/sommer/inst/doc/sommer.covariance.structures.Rmd | 108 + sommer-4.5.27/sommer/inst/doc/sommer.covariance.structures.html | 158 + sommer-4.5.27/sommer/inst/doc/sommer.fa.and.rr.models.html | 240 +- sommer-4.5.27/sommer/inst/doc/sommer.genetic.evaluation.R | 9 sommer-4.5.27/sommer/inst/doc/sommer.genetic.evaluation.Rmd | 13 sommer-4.5.27/sommer/inst/doc/sommer.genetic.evaluation.html | 39 sommer-4.5.27/sommer/inst/doc/sommer.glmm.R | 170 + sommer-4.5.27/sommer/inst/doc/sommer.glmm.Rmd | 875 ++++++++ sommer-4.5.27/sommer/inst/doc/sommer.glmm.html | 882 ++++++++ sommer-4.5.27/sommer/inst/doc/sommer.glmm.theory.R |only sommer-4.5.27/sommer/inst/doc/sommer.glmm.theory.Rmd |only sommer-4.5.27/sommer/inst/doc/sommer.glmm.theory.html |only sommer-4.5.27/sommer/inst/doc/sommer.gxe.html | 8 sommer-4.5.27/sommer/inst/doc/sommer.machinery.Rmd | 8 sommer-4.5.27/sommer/inst/doc/sommer.machinery.html | 14 sommer-4.5.27/sommer/inst/doc/sommer.mmes.options.R | 29 sommer-4.5.27/sommer/inst/doc/sommer.mmes.options.Rmd | 423 +++- sommer-4.5.27/sommer/inst/doc/sommer.mmes.options.html | 422 +++- sommer-4.5.27/sommer/inst/doc/sommer.models.R |only sommer-4.5.27/sommer/inst/doc/sommer.models.Rmd |only sommer-4.5.27/sommer/inst/doc/sommer.models.html |only sommer-4.5.27/sommer/inst/doc/sommer.qg.R | 707 ++++--- sommer-4.5.27/sommer/inst/doc/sommer.qg.Rmd | 222 +- sommer-4.5.27/sommer/inst/doc/sommer.qg.html | 334 +-- sommer-4.5.27/sommer/inst/doc/sommer.spatial.R | 43 sommer-4.5.27/sommer/inst/doc/sommer.spatial.Rmd | 129 + sommer-4.5.27/sommer/inst/doc/sommer.spatial.html | 253 ++ sommer-4.5.27/sommer/inst/doc/sommer.theory.Rmd | 13 sommer-4.5.27/sommer/inst/doc/sommer.theory.html | 14 sommer-4.5.27/sommer/inst/doc/sommer.vs.lme4.html | 4 sommer-4.5.27/sommer/man/A.mat.Rd | 125 + sommer-4.5.27/sommer/man/D.mat.Rd | 65 sommer-4.5.27/sommer/man/E.mat.Rd | 37 sommer-4.5.27/sommer/man/H.mat.Rd | 30 sommer-4.5.27/sommer/man/MNR.Rd | 2 sommer-4.5.27/sommer/man/binm.Rd | 9 sommer-4.5.27/sommer/man/boot_mmes.Rd |only sommer-4.5.27/sommer/man/covmatrix_mmes.Rd | 2 sommer-4.5.27/sommer/man/curve_term.Rd |only sommer-4.5.27/sommer/man/dot-mmes_control_internal.Rd |only sommer-4.5.27/sommer/man/familym.Rd | 89 sommer-4.5.27/sommer/man/fitted_mmes.Rd | 11 sommer-4.5.27/sommer/man/meffects_mmes.Rd | 26 sommer-4.5.27/sommer/man/mmer.Rd | 17 sommer-4.5.27/sommer/man/mmes.Rd | 1005 +++------- sommer-4.5.27/sommer/man/mmes.specification.Rd |only sommer-4.5.27/sommer/man/mmes_control.Rd | 677 +++--- sommer-4.5.27/sommer/man/mmes_method.Rd |only sommer-4.5.27/sommer/man/multinomial.Rd |only sommer-4.5.27/sommer/man/nbinom2.Rd |only sommer-4.5.27/sommer/man/nonlinear_curve.Rd |only sommer-4.5.27/sommer/man/ordinal.Rd |only sommer-4.5.27/sommer/man/parameter.Rd |only sommer-4.5.27/sommer/man/postPEV.Rd | 84 sommer-4.5.27/sommer/man/postVarU.Rd | 15 sommer-4.5.27/sommer/man/post_nonlinear.Rd |only sommer-4.5.27/sommer/man/predict_mmes.Rd | 151 + sommer-4.5.27/sommer/man/profile_nonlinear.Rd |only sommer-4.5.27/sommer/man/residuals_mmes.Rd | 53 sommer-4.5.27/sommer/man/rrm.Rd | 2 sommer-4.5.27/sommer/man/run_mme_benchmark.Rd | 27 sommer-4.5.27/sommer/man/simulate.mmes.glmm.laplace.Rd |only sommer-4.5.27/sommer/man/sommer-package.Rd | 2 sommer-4.5.27/sommer/man/unsm.Rd | 5 sommer-4.5.27/sommer/man/vcDelta.Rd |only sommer-4.5.27/sommer/man/vcc.Rd | 32 sommer-4.5.27/sommer/man/wald_mmes.Rd | 9 sommer-4.5.27/sommer/man/zipoisson.Rd |only sommer-4.5.27/sommer/src/Makevars.in | 13 sommer-4.5.27/sommer/src/Makevars.win | 13 sommer-4.5.27/sommer/src/RcppExports.cpp | 574 +++++ sommer-4.5.27/sommer/src/ai_mme_sp2.cpp | 964 ++++++++- sommer-4.5.27/sommer/src/mme_ai_augmented.h |only sommer-4.5.27/sommer/src/mme_conditional.cpp | 4 sommer-4.5.27/sommer/src/mme_control.h | 13 sommer-4.5.27/sommer/src/mme_control_r.h | 8 sommer-4.5.27/sommer/src/mme_dense_score.h |only sommer-4.5.27/sommer/src/mme_direct.cpp | 215 -- sommer-4.5.27/sommer/src/mme_direct_inference.cpp |only sommer-4.5.27/sommer/src/mme_direct_residual.h |only sommer-4.5.27/sommer/src/mme_em.h | 51 sommer-4.5.27/sommer/src/mme_fixed_rank.cpp | 17 sommer-4.5.27/sommer/src/mme_glmm_acceleration.h |only sommer-4.5.27/sommer/src/mme_glmm_family.h |only sommer-4.5.27/sommer/src/mme_glmm_laplace.cpp |only sommer-4.5.27/sommer/src/mme_glmm_multinomial.cpp |only sommer-4.5.27/sommer/src/mme_glmm_multinomial.h |only sommer-4.5.27/sommer/src/mme_glmm_multinomial_laplace.cpp |only sommer-4.5.27/sommer/src/mme_glmm_paths.cpp |only sommer-4.5.27/sommer/src/mme_glmm_paths.h |only sommer-4.5.27/sommer/src/mme_glmm_precision.h |only sommer-4.5.27/sommer/src/mme_glmm_residual.h |only sommer-4.5.27/sommer/src/mme_glmm_system.h |only sommer-4.5.27/sommer/src/mme_nonlinear.cpp |only sommer-4.5.27/sommer/src/mme_nonlinear_covariance.h |only sommer-4.5.27/sommer/src/mme_nonlinear_derivatives.h |only sommer-4.5.27/sommer/src/mme_nonlinear_family.cpp |only sommer-4.5.27/sommer/src/mme_nonlinear_family.h |only sommer-4.5.27/sommer/src/mme_nonlinear_gaussian.h |only sommer-4.5.27/sommer/src/mme_nonlinear_laplace.h |only sommer-4.5.27/sommer/src/mme_nonlinear_memory.h |only sommer-4.5.27/sommer/src/mme_nonlinear_mode.h |only sommer-4.5.27/sommer/src/mme_nonlinear_predictor.h |only sommer-4.5.27/sommer/src/mme_rr.h | 69 sommer-4.5.27/sommer/src/mme_scale.h | 26 sommer-4.5.27/sommer/src/mme_sp2_support.h | 2 sommer-4.5.27/sommer/src/native_relationships.cpp | 149 + sommer-4.5.27/sommer/src/native_utils.cpp | 19 sommer-4.5.27/sommer/tests/native/test-mme-ai-augmented.cpp |only sommer-4.5.27/sommer/tests/native/test-mme-dense-score.cpp |only sommer-4.5.27/sommer/tests/testthat/helper-multinomial.R |only sommer-4.5.27/sommer/tests/testthat/test-ai-recovery.R | 16 sommer-4.5.27/sommer/tests/testthat/test-ai-variance-floor.R | 16 sommer-4.5.27/sommer/tests/testthat/test-amat-asv.R |only sommer-4.5.27/sommer/tests/testthat/test-amat-shrink.R |only sommer-4.5.27/sommer/tests/testthat/test-apy.R | 2 sommer-4.5.27/sommer/tests/testthat/test-augmented-ai-benchmark.R |only sommer-4.5.27/sommer/tests/testthat/test-augmented-working-ai.R |only sommer-4.5.27/sommer/tests/testthat/test-boot-mmes.R |only sommer-4.5.27/sommer/tests/testthat/test-common-scale.R | 47 sommer-4.5.27/sommer/tests/testthat/test-conditional-ai.R | 26 sommer-4.5.27/sommer/tests/testthat/test-conditional-fa.R | 40 sommer-4.5.27/sommer/tests/testthat/test-control-contracts.R | 6 sommer-4.5.27/sommer/tests/testthat/test-covariance-information.R | 18 sommer-4.5.27/sommer/tests/testthat/test-dense-gu-schur.R | 14 sommer-4.5.27/sommer/tests/testthat/test-dense-spline-traces.R |only sommer-4.5.27/sommer/tests/testthat/test-direct-em.R | 36 sommer-4.5.27/sommer/tests/testthat/test-direct-engine.R | 10 sommer-4.5.27/sommer/tests/testthat/test-direct-inference.R |only sommer-4.5.27/sommer/tests/testthat/test-em-directions.R | 60 sommer-4.5.27/sommer/tests/testthat/test-emmeans-mmes.R | 4 sommer-4.5.27/sommer/tests/testthat/test-enhancer-models.R | 3 sommer-4.5.27/sommer/tests/testthat/test-fa-covariance-safeguards.R | 11 sommer-4.5.27/sommer/tests/testthat/test-fa-factor-score-augmentation.R | 20 sommer-4.5.27/sommer/tests/testthat/test-fa-latent-schur.R | 21 sommer-4.5.27/sommer/tests/testthat/test-fa-loadings-scores.R | 6 sommer-4.5.27/sommer/tests/testthat/test-fam-dense-gu-memory.R | 6 sommer-4.5.27/sommer/tests/testthat/test-glmm-latent-process.R |only sommer-4.5.27/sommer/tests/testthat/test-grid-augment.R |only sommer-4.5.27/sommer/tests/testthat/test-hybrid-ai.R | 20 sommer-4.5.27/sommer/tests/testthat/test-laplace-acceleration.R |only sommer-4.5.27/sommer/tests/testthat/test-laplace-gaussian-residual.R |only sommer-4.5.27/sommer/tests/testthat/test-laplace-observation.R |only sommer-4.5.27/sommer/tests/testthat/test-laplace-vcc.R |only sommer-4.5.27/sommer/tests/testthat/test-meffects.R | 52 sommer-4.5.27/sommer/tests/testthat/test-metricm.R | 8 sommer-4.5.27/sommer/tests/testthat/test-mme-block-chain.R | 12 sommer-4.5.27/sommer/tests/testthat/test-mme-capabilities.R | 22 sommer-4.5.27/sommer/tests/testthat/test-mme-cfree.R | 14 sommer-4.5.27/sommer/tests/testthat/test-mme-compression.R | 27 sommer-4.5.27/sommer/tests/testthat/test-mme-control-native.R | 1 sommer-4.5.27/sommer/tests/testthat/test-mme-gpu.R | 24 sommer-4.5.27/sommer/tests/testthat/test-mme-modules.R | 56 sommer-4.5.27/sommer/tests/testthat/test-mme-path-reporting.R | 8 sommer-4.5.27/sommer/tests/testthat/test-mme-paths.R | 31 sommer-4.5.27/sommer/tests/testthat/test-mme-profile.R | 50 sommer-4.5.27/sommer/tests/testthat/test-mme-saddle.R | 34 sommer-4.5.27/sommer/tests/testthat/test-mme-solve.R | 31 sommer-4.5.27/sommer/tests/testthat/test-mme-solver.R | 5 sommer-4.5.27/sommer/tests/testthat/test-mmer-migration.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-acceleration.R | 8 sommer-4.5.27/sommer/tests/testthat/test-mmes-blend.R | 42 sommer-4.5.27/sommer/tests/testthat/test-mmes-categorical-familym.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-direct-pql.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-fixed-design.R | 32 sommer-4.5.27/sommer/tests/testthat/test-mmes-fixed-rank.R | 58 sommer-4.5.27/sommer/tests/testthat/test-mmes-glmm-paths.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-laplace-families.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-laplace.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-multinomial-kernel.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-multinomial-mode.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-multinomial-public.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-multinomial-scores.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-namespace-calls.R | 2 sommer-4.5.27/sommer/tests/testthat/test-mmes-nominal-preparation.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-nominal-residuals.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-ordinal-kernel.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-ordinal-preparation.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-ordinal.R |only sommer-4.5.27/sommer/tests/testthat/test-mmes-pql.R | 20 sommer-4.5.27/sommer/tests/testthat/test-mmes-progress-output.R | 4 sommer-4.5.27/sommer/tests/testthat/test-mmes-reml-vs-ml.R | 29 sommer-4.5.27/sommer/tests/testthat/test-mmes-rotation.R | 24 sommer-4.5.27/sommer/tests/testthat/test-mmes-spatial-residual.R | 24 sommer-4.5.27/sommer/tests/testthat/test-mmes-threads.R | 7 sommer-4.5.27/sommer/tests/testthat/test-mmes-zip-formula.R |only sommer-4.5.27/sommer/tests/testthat/test-model-interface.R |only sommer-4.5.27/sommer/tests/testthat/test-model-specification.R |only sommer-4.5.27/sommer/tests/testthat/test-multivariate.R | 32 sommer-4.5.27/sommer/tests/testthat/test-namespace-loading.R |only sommer-4.5.27/sommer/tests/testthat/test-nonlinear-families.R |only sommer-4.5.27/sommer/tests/testthat/test-nonlinear-inference.R |only sommer-4.5.27/sommer/tests/testthat/test-nonlinear-joint.R |only sommer-4.5.27/sommer/tests/testthat/test-nonlinear-mmes.R |only sommer-4.5.27/sommer/tests/testthat/test-nonlinear-qualification.R |only sommer-4.5.27/sommer/tests/testthat/test-nonlinear-random.R |only sommer-4.5.27/sommer/tests/testthat/test-nonlinear-route-parity.R |only sommer-4.5.27/sommer/tests/testthat/test-nonlinear-structures.R |only sommer-4.5.27/sommer/tests/testthat/test-pcg-compression.R | 16 sommer-4.5.27/sommer/tests/testthat/test-pcg-controls.R | 40 sommer-4.5.27/sommer/tests/testthat/test-pcg-crossfit.R | 22 sommer-4.5.27/sommer/tests/testthat/test-pcg-numerics.R | 10 sommer-4.5.27/sommer/tests/testthat/test-polyploid-relationships.R |only sommer-4.5.27/sommer/tests/testthat/test-postVarU.R | 19 sommer-4.5.27/sommer/tests/testthat/test-predict-fixed-rank.R | 12 sommer-4.5.27/sommer/tests/testthat/test-predict-levels-sed.R | 4 sommer-4.5.27/sommer/tests/testthat/test-predict-mmes-ci.R | 8 sommer-4.5.27/sommer/tests/testthat/test-predict-reported-issues.R | 20 sommer-4.5.27/sommer/tests/testthat/test-pxem-directions.R | 41 sommer-4.5.27/sommer/tests/testthat/test-r-refactor.R | 12 sommer-4.5.27/sommer/tests/testthat/test-reduced-ai.R | 45 sommer-4.5.27/sommer/tests/testthat/test-relationships.R | 93 sommer-4.5.27/sommer/tests/testthat/test-reml-estimability.R | 34 sommer-4.5.27/sommer/tests/testthat/test-reporting-refactor.R | 18 sommer-4.5.27/sommer/tests/testthat/test-rr-average-information.R | 27 sommer-4.5.27/sommer/tests/testthat/test-rr-zero-specific.R | 14 sommer-4.5.27/sommer/tests/testthat/test-specification-families-inference.R |only sommer-4.5.27/sommer/tests/testthat/test-specification-profile.R |only sommer-4.5.27/sommer/tests/testthat/test-strm.R | 2 sommer-4.5.27/sommer/tests/testthat/test-varu-edgecases.R | 8 sommer-4.5.27/sommer/tests/testthat/test-vcc.R | 10 sommer-4.5.27/sommer/tests/testthat/test-vsm-giv-gu.R | 8 sommer-4.5.27/sommer/tests/testthat/test-vsm-variance-modes.R | 25 sommer-4.5.27/sommer/tests/testthat/test-wald-mmes.R | 4 sommer-4.5.27/sommer/tests/testthat/test-weighted-sparse-residual.R | 26 sommer-4.5.27/sommer/vignettes/sommer.covariance.structures.Rmd | 108 + sommer-4.5.27/sommer/vignettes/sommer.genetic.evaluation.Rmd | 13 sommer-4.5.27/sommer/vignettes/sommer.glmm.Rmd | 875 ++++++++ sommer-4.5.27/sommer/vignettes/sommer.glmm.theory.Rmd |only sommer-4.5.27/sommer/vignettes/sommer.machinery.Rmd | 8 sommer-4.5.27/sommer/vignettes/sommer.mmes.options.Rmd | 423 +++- sommer-4.5.27/sommer/vignettes/sommer.models.Rmd |only sommer-4.5.27/sommer/vignettes/sommer.qg.Rmd | 222 +- sommer-4.5.27/sommer/vignettes/sommer.spatial.Rmd | 129 + sommer-4.5.27/sommer/vignettes/sommer.theory.Rmd | 13 296 files changed, 14566 insertions(+), 3230 deletions(-)
More information about qualitranslate at CRAN
Permanent link
Title: Variable Selection for Heterogeneous Populations
Description: Provides variable selection and estimation routines for models
with main effects stratified on multiple binary factors. The 'vennLasso' package
is an implementation of the method introduced in Huling et al. (2018) <doi:10.1111/biom.12769>.
Author: Jared Huling [aut, cre] ,
Muxuan Liang [ctb],
Yixuan Qiu [cph],
Gael Guennebaud [cph],
Ray Gardner [cph],
Jitse Niesen [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
This is a re-admission after prior archival of version 0.1.6 dated 2020-06-03
Diff between vennLasso versions 0.1.6 dated 2020-06-03 and 0.2.0 dated 2026-11-14
vennLasso-0.1.6/vennLasso/inst/doc/using_the_vennLasso_package.pdf |only vennLasso-0.1.6/vennLasso/vignettes/readme_figs |only vennLasso-0.1.6/vennLasso/vignettes/vignette_preamble.tex |only vennLasso-0.2.0/vennLasso/DESCRIPTION | 17 vennLasso-0.2.0/vennLasso/MD5 | 73 - vennLasso-0.2.0/vennLasso/NEWS.md |only vennLasso-0.2.0/vennLasso/R/cv_vennLasso.R | 9 vennLasso-0.2.0/vennLasso/R/oglasso.R | 533 +++++----- vennLasso-0.2.0/vennLasso/R/plot_cv_vennLasso.R | 4 vennLasso-0.2.0/vennLasso/R/predict_vennLasso.R | 29 vennLasso-0.2.0/vennLasso/R/simulate_hierarchically_sparse_data.R | 26 vennLasso-0.2.0/vennLasso/R/utils.R | 28 vennLasso-0.2.0/vennLasso/R/vennLasso.R | 259 ++-- vennLasso-0.2.0/vennLasso/README.md | 50 vennLasso-0.2.0/vennLasso/build/vignette.rds |binary vennLasso-0.2.0/vennLasso/inst/CITATION | 27 vennLasso-0.2.0/vennLasso/inst/doc/using_the_vennLasso_package.R | 26 vennLasso-0.2.0/vennLasso/inst/doc/using_the_vennLasso_package.Rmd | 239 ---- vennLasso-0.2.0/vennLasso/inst/doc/using_the_vennLasso_package.html |only vennLasso-0.2.0/vennLasso/inst/reference |only vennLasso-0.2.0/vennLasso/man/cv.vennLasso.Rd | 2 vennLasso-0.2.0/vennLasso/man/estimate.hier.sparsity.param.Rd | 20 vennLasso-0.2.0/vennLasso/man/figures |only vennLasso-0.2.0/vennLasso/man/genHierSparseData.Rd | 6 vennLasso-0.2.0/vennLasso/man/oglasso.Rd | 88 + vennLasso-0.2.0/vennLasso/man/vennLasso.Rd | 47 vennLasso-0.2.0/vennLasso/src/ADMMogLassoCoxPHTall.h | 104 + vennLasso-0.2.0/vennLasso/src/ADMMogLassoLogisticTall.h | 26 vennLasso-0.2.0/vennLasso/src/ADMMogLassoLogisticWide.h | 28 vennLasso-0.2.0/vennLasso/src/ADMMogLassoTall.h | 26 vennLasso-0.2.0/vennLasso/src/ADMMogLassoWide.h | 32 vennLasso-0.2.0/vennLasso/src/ogLasso.cpp | 137 +- vennLasso-0.2.0/vennLasso/src/utils.h | 2 vennLasso-0.2.0/vennLasso/src/vennLasso_init.c | 13 vennLasso-0.2.0/vennLasso/tests |only vennLasso-0.2.0/vennLasso/vignettes/figures |only vennLasso-0.2.0/vennLasso/vignettes/refs.bib | 8 vennLasso-0.2.0/vennLasso/vignettes/using_the_vennLasso_package.Rmd | 239 ---- 38 files changed, 1034 insertions(+), 1064 deletions(-)
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The functions
are pipe-friendly and provide a consistent syntax to work with tidy
data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'. References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 2.2.1 dated 2026-10-21 and 2.2.2 dated 2026-11-14
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 5 +++++ build/vignette.rds |binary tests/testthat/helper-subject-id.R | 3 ++- 5 files changed, 16 insertions(+), 10 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Simulation and Data Analysis for Plant Breeders
Description: Provides tools for simulation of plant breeding programs
as described, for example, by Melchinger and Frisch
(2023) <doi:10.1007/s00122-023-04446-3>, prediction of
segregation variance (Osthushenrich, Frisch and Herzog
(2017) <doi:10.1371/journal.pone.0188839>), genomic
prediction (Hofheinz and Frisch (2014)
<doi:10.1534/g3.113.010025>), linkage disequilibrium
based haplotype construction, and planning of marker
assisted back crossing programs. Functions to fit
linear mixed models and for phasing and imputation of
DNA marker data are also included.
Author: Matthias Frisch [aut, cre],
Hans Peter Maurer [ctb],
Philipp Heilmann [ctb]
Maintainer: Matthias Frisch <matthias.frisch@uni-giessen.de>
Diff between SelectionTools versions 26.5.2 dated 2026-11-12 and 26.6 dated 2026-11-14
DESCRIPTION | 8 MD5 | 258 NAMESPACE | 4 R/SelectionTools01.R | 591 - R/SelectionTools02.R | 182 R/SelectionTools03.R | 8 R/SelectionTools04.R | 37 R/SelectionTools10.R | 30 R/SelectionTools11.R | 55 R/zzz.R | 12 inst/doc/v-cross.R | 827 ++ inst/doc/v-cross.Rnw | 2850 ++++++++ inst/doc/v-cross.pdf |binary inst/doc/v-enrich.pdf |binary inst/doc/v-hapld.pdf |binary inst/doc/v-lmm.R | 30 inst/doc/v-lmm.Rnw | 31 inst/doc/v-lmm.pdf |binary inst/doc/v-masbc.pdf |binary inst/doc/v-phase.pdf |binary inst/doc/v-simbp.pdf |binary inst/doc/v-simmd.pdf |binary man/copy.population.Rd | 6 man/data.params.Rd | 4 man/define.effects.df.Rd | 6 man/divide.population.Rd | 4 man/evaluate.allele.freq.Rd | 2 man/evaluate.allele.freq2.Rd | 4 man/gd.maize.aflp.Rd | 6 man/gd.salad.aflp.Rd | 6 man/get.population.gvalue.Rd | 2 man/get.population.pvalue.Rd | 2 man/gs.cross.info.gd.Rd | 4 man/gs.esteff.rmlc.Rd | 2 man/gs.esteff.rmlv.Rd | 2 man/gs.get.Z.Rd | 2 man/gs.get.y.Rd | 2 man/gs.mme.restcoeff.Rd | 4 man/gs.mme.restrhs.Rd | 4 man/gs.plot.effects.Rd | 2 man/gs.reset.Rd | 4 man/gs.restrict.marker.data.01.Rd | 4 man/gs.start.timer.Rd | 6 man/gs.stop.timer.Rd | 6 man/influence.st.lmm.Rd | 24 man/init.population.Rd | 19 man/internal-st-legacy-path.Rd | 19 man/internal-st-lmm-influence.Rd | 2 man/linkage.map.get.Rd | 4 man/mab.Input.files.Rd | 2 man/mab.compare.Rd | 7 man/mab.load.data.Rd | 14 man/mab.simulate.Rd | 43 man/mab.tabulate.Rd | 22 man/masbc.input.Rd | 26 man/optimize.population.Rd | 19 man/population.append.Rd | 13 man/population.copy.Rd | 8 man/population.divide.Rd | 6 man/population.individual.remove.Rd | 10 man/population.optimize.Rd | 19 man/population.sample.Rd | 8 man/population.sort.Rd | 2 man/propsd.Rd | 14 man/remove.all.populations.Rd | 2 man/reset.mdp.Rd | 4 man/resources.Rd | 4 man/sample.population.Rd | 6 man/select.genotypes.Rd | 18 man/select.n.best.Rd | 4 man/select.n.best.segments.Rd | 6 man/sm.start.timer.Rd | 6 man/sm.stop.timer.Rd | 6 man/st.LDplot.ld.Rd | 4 man/st.LDplot.map.Rd | 4 man/st.cross.allocate.Rd | 134 man/st.cross.constraints.Rd |only man/st.cross.evaluate.Rd |only man/st.cross.plan.Rd | 358 - man/st.cross.plan.execute.Rd | 43 man/st.data.set.list.Rd | 2 man/st.def.hblocks.Rd | 2 man/st.get.A.Rd | 2 man/st.get.simpop2.Rd | 2 man/st.gwas.Rd | 6 man/st.keep.intersection.markers.Rd | 4 man/st.lmm.Rd | 16 man/st.lmm.allfit.Rd | 4 man/st.lmm.bootstrap.Rd | 6 man/st.lmm.by.Rd | 2 man/st.lmm.compare.Rd | 2 man/st.lmm.diagnostics.Rd | 12 man/st.lmm.profile.Rd | 2 man/st.lmm.refit.Rd | 4 man/st.lmm.simulate.Rd | 2 man/st.load.vcf.data.Rd | 2 man/st.lsm.Rd | 6 man/st.markerdata.to.STvcf.Rd | 2 man/st.ocs.Rd | 23 man/st.oma.Rd | 7 man/st.phase.Rd | 2 man/st.plot.ggt.Rd | 2 man/st.predict.Rd | 2 man/st.read.map.Rd | 2 man/st.reset.Rd | 4 man/st.restrict.marker.Rd | 2 man/st.set.openblas.threads.Rd | 12 man/st.start.timer.Rd | 6 man/st.stop.timer.Rd | 6 man/st.write.marker.data.Rd | 2 man/v-dentmaize-vcf.Rd | 11 man/v-dentmaize2-vcf.Rd | 7 man/v-flintmaize-vcf.Rd | 11 man/v-flintmaize2-vcf.Rd | 7 man/v-hybmaize2-phe.Rd | 9 man/v-lmm-data.Rd | 21 man/v-lmm-fertilizer-replicated.Rd | 9 man/v-lmm-halfdiallel.Rd | 5 man/v-lmm-tropmaize.Rd | 32 src/MathLib11.h | 506 + src/MathLib12.c | 2 src/SelectionTools01.c |12088 ++++++++++++++++++++++++++++++++---- src/SelectionTools01a.h | 135 src/SelectionTools02.c | 7141 ++++++++++++++++----- src/SelectionTools02a.h | 170 src/SelectionTools03.c | 304 src/SelectionTools04.c | 7281 +++++++++++++++++++-- src/SelectionToolsAllele.h | 4 src/init.c | 533 - vignettes/v-cross.Rnw | 2850 ++++++++ vignettes/v-lmm.Rnw | 31 131 files changed, 31873 insertions(+), 5319 deletions(-)
More information about SelectionTools at CRAN
Permanent link
Title: Graph-Based Change-Point Detection (g-Segmentation)
Description: Uses similarity graphs to estimate change-points and their p-values. The main functions accept either observations or dissimilarities, construct a k-MST with k=floor(sqrt(N)) by default, and report the max-type scan. A supplied similarity graph and the generalized, original, and weighted scans remain available explicitly.
Author: Hao Chen [aut, cre] ,
Nancy R. Zhang [aut],
Lynna Chu [aut],
Hoseung Song [aut]
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between gSeg versions 1.1 dated 2026-09-09 and 1.2 dated 2026-11-14
DESCRIPTION | 15 +- MD5 | 52 +++++-- NAMESPACE | 4 NEWS.md | 60 +++++++++ R/NNL.R | 38 ++++- R/canonical-interface.R | 239 ++++++++++++++++++++++++++++------- R/gSeg.r | 172 ++++++++++++------------- R/gSeg_discrete.R | 253 ++++++++++++++++++-------------------- R/native-kernels.R |only R/numerical-stability.R |only R/scan-output.R |only README.md |only inst |only man/gSeg-package.Rd | 166 ++++++------------------ man/gseg1.Rd | 151 +++++++++++----------- man/gseg1_data.Rd | 23 +-- man/gseg1_discrete.Rd | 21 +++ man/gseg1_graph.Rd |only man/gseg2.Rd | 123 ++++++++++-------- man/gseg2_data.Rd | 23 +-- man/gseg2_discrete.Rd | 24 +++ man/gseg2_graph.Rd |only man/gseg_kmst.Rd | 13 + man/nnl.Rd | 8 + src |only tests/canonical-defaults.R | 58 ++++++++ tests/deep-regressions.R |only tests/graph-robustness.R |only tests/native-kernels.R |only tests/numerical-stability.R |only tests/second-review-regressions.R |only 31 files changed, 871 insertions(+), 572 deletions(-)
Title: Discretization and Grouping for Logistic Regression
Description: A Stochastic-Expectation-Maximization (SEM) algorithm (Celeux et al. (1995) <https://inria.hal.science/inria-00074164>) associated with a Gibbs sampler which purpose is to learn a constrained representation for logistic regression that is called quantization (Ehrhardt et al. (2019) <doi:10.48550/arXiv.1903.08920>). Continuous features are discretized and categorical features' values are grouped to produce a better logistic regression model. Pairwise interactions between the discretized and grouped features are dynamically added to the model through a Metropolis-Hastings algorithm (Hastings, W. K. (1970) <doi:10.1093/biomet/57.1.97>).
Author: Adrien Ehrhardt [aut, cre] ,
Vincent Vandewalle [aut] ,
Christophe Biernacki [ctb] ,
Philippe Heinrich [ctb]
Maintainer: Adrien Ehrhardt <adrien.ehrhardt@polytechnique.edu>
This is a re-admission after prior archival of version 0.6 dated 2020-09-30
Diff between glmdisc versions 0.6 dated 2020-09-30 and 0.8.1 dated 2026-11-14
glmdisc-0.6/glmdisc/inst/document.R |only glmdisc-0.6/glmdisc/inst/lint.R |only glmdisc-0.6/glmdisc/inst/rhubcheck.R |only glmdisc-0.6/glmdisc/man/contr.ltfr.Rd |only glmdisc-0.8.1/glmdisc/DESCRIPTION | 59 glmdisc-0.8.1/glmdisc/MD5 | 103 glmdisc-0.8.1/glmdisc/NAMESPACE | 8 glmdisc-0.8.1/glmdisc/NEWS.md |only glmdisc-0.8.1/glmdisc/R/RcppExports.R | 32 glmdisc-0.8.1/glmdisc/R/cut.dataset.R | 54 glmdisc-0.8.1/glmdisc/R/discretize.link.R | 119 glmdisc-0.8.1/glmdisc/R/features.R |only glmdisc-0.8.1/glmdisc/R/generic_cutpoints.R | 2 glmdisc-0.8.1/glmdisc/R/generic_discretize.R | 2 glmdisc-0.8.1/glmdisc/R/glmdisc.R | 7 glmdisc-0.8.1/glmdisc/R/initialization.R | 76 glmdisc-0.8.1/glmdisc/R/link_models.R |only glmdisc-0.8.1/glmdisc/R/logit_codes.R |only glmdisc-0.8.1/glmdisc/R/method_cutpoints.R | 11 glmdisc-0.8.1/glmdisc/R/method_discretize.R | 3 glmdisc-0.8.1/glmdisc/R/method_plot.R | 92 glmdisc-0.8.1/glmdisc/R/method_predict.R | 70 glmdisc-0.8.1/glmdisc/R/methods_disc.R | 54 glmdisc-0.8.1/glmdisc/R/normalizedGini.R | 21 glmdisc-0.8.1/glmdisc/R/semDiscretization.R | 668 --- glmdisc-0.8.1/glmdisc/R/sem_engine.R |only glmdisc-0.8.1/glmdisc/R/utils.R |only glmdisc-0.8.1/glmdisc/build/vignette.rds |binary glmdisc-0.8.1/glmdisc/inst/CITATION | 40 glmdisc-0.8.1/glmdisc/inst/WORDLIST |only glmdisc-0.8.1/glmdisc/inst/doc/glmdisc.R | 248 - glmdisc-0.8.1/glmdisc/inst/doc/glmdisc.Rmd | 198 glmdisc-0.8.1/glmdisc/inst/doc/glmdisc.html | 2005 +++------- glmdisc-0.8.1/glmdisc/man/cutpoints-method.Rd | 5 glmdisc-0.8.1/glmdisc/man/discretize.Rd | 5 glmdisc-0.8.1/glmdisc/man/glmdisc-package.Rd | 10 glmdisc-0.8.1/glmdisc/man/glmdisc.Rd | 41 glmdisc-0.8.1/glmdisc/man/normalizedGini.Rd | 5 glmdisc-0.8.1/glmdisc/man/plot.Rd | 17 glmdisc-0.8.1/glmdisc/man/predict.Rd | 21 glmdisc-0.8.1/glmdisc/man/predictlogisticRegression.Rd | 11 glmdisc-0.8.1/glmdisc/man/print.Rd |only glmdisc-0.8.1/glmdisc/man/summary.Rd |only glmdisc-0.8.1/glmdisc/src/RcppExports.cpp | 42 glmdisc-0.8.1/glmdisc/src/multinomial_link.cpp |only glmdisc-0.8.1/glmdisc/src/rcpp_predictlogisticRegression.cpp | 26 glmdisc-0.8.1/glmdisc/tests/testthat/test-all-classes.R | 1 glmdisc-0.8.1/glmdisc/tests/testthat/test-cut-dataset.R | 27 glmdisc-0.8.1/glmdisc/tests/testthat/test-discretize-link.R | 130 glmdisc-0.8.1/glmdisc/tests/testthat/test-features.R |only glmdisc-0.8.1/glmdisc/tests/testthat/test-glmdisc.R | 312 - glmdisc-0.8.1/glmdisc/tests/testthat/test-link-models.R |only glmdisc-0.8.1/glmdisc/tests/testthat/test-logit-codes.R |only glmdisc-0.8.1/glmdisc/tests/testthat/test-method_cutpoints.R | 5 glmdisc-0.8.1/glmdisc/tests/testthat/test-method_predict.R | 52 glmdisc-0.8.1/glmdisc/tests/testthat/test-methods-disc.R | 7 glmdisc-0.8.1/glmdisc/tests/testthat/test-metropolis-hastings.R |only glmdisc-0.8.1/glmdisc/tests/testthat/test-multinomial-link.R |only glmdisc-0.8.1/glmdisc/tests/testthat/test-normalizedgini.R | 30 glmdisc-0.8.1/glmdisc/tests/testthat/test-plot.R | 23 glmdisc-0.8.1/glmdisc/tests/testthat/test-sem-engine.R |only glmdisc-0.8.1/glmdisc/tests/testthat/test-utils.R |only glmdisc-0.8.1/glmdisc/vignettes/glmdisc.Rmd | 198 63 files changed, 2006 insertions(+), 2834 deletions(-)
Title: Chromatographic File Converter
Description: Reads chromatograms from binary formats into R objects. Currently supports
conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Agilent OpenLab',
'Shimadzu LabSolutions', 'ThermoRaw', 'Varian Workstation', and 'Waters
Empower' files as well as various other formats. In addition to its
internal parsers, chromConverter contains bindings to parsers in
external libraries, such as 'Aston' <https://github.com/bovee/aston>,
'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>,
and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.
The suggested packages 'entab' and 'chromConverterExtraTests' are not on
CRAN: both are available from the repository given in
'Additional_repositories', and the latest test fixtures can also be
installed from <https://github.com/ethanbass/chromConverterExtraTests>.
Author: Ethan Bass [aut, cre] ,
James Dillon [ctb, cph] ,
Evan Shi [ctb, cph] ,
Roderick Bovee [ctb, cph]
Maintainer: Ethan Bass <ethanbass@gmail.com>
Diff between chromConverter versions 0.11.2 dated 2026-10-25 and 0.12.0 dated 2026-11-14
DESCRIPTION | 14 - MD5 | 132 +++++----- NAMESPACE | 2 NEWS.md | 46 +++ R/attach_metadata.R | 20 + R/call_aston.R | 2 R/call_entab.R | 2 R/call_openchrom.R | 6 R/call_rainbow.R | 2 R/metadata_maps.R | 25 + R/metadata_registry.R | 2 R/olefile_utilities.R | 38 +- R/parser_registry.R | 40 +++ R/read_acaml.R | 9 R/read_agilent_d.R | 46 ++- R/read_agilent_dx.R | 269 ++++++++++++++------ R/read_cdf.R | 46 +++ R/read_chemstation_ms.R | 3 R/read_chemstation_uv.R | 165 ++++++++---- R/read_chromeleon.R | 43 +++ R/read_chroms.R | 130 +++++++++- R/read_mzml.R | 9 R/read_peaklist.R | 5 R/read_shimadzu_ascii.R | 37 ++ R/read_shimadzu_ittof.R |only R/read_shimadzu_lcd.R | 68 ++++- R/read_shimadzu_method.R | 6 R/read_shimadzu_qgd.R | 186 ++++++++++---- R/read_shimadzu_sq.R |only R/read_shimadzu_tlm.R | 4 R/read_thermoraw.R | 95 +++++-- R/read_varian_sms.R | 36 ++ R/read_waters_arw.R | 17 + R/utils.R | 29 +- R/write_agilent_amx.R |only R/write_andi_ms.R | 6 R/write_mzml.R | 301 ++++++++++++++++++----- R/zzz-roxygen.R | 3 README.md | 2 man/read_agilent_d.Rd | 27 +- man/read_chroms.Rd | 5 man/read_metadata.Rd |only man/read_peaklist.Rd | 5 man/read_shimadzu_lcd.Rd | 25 + man/read_shimadzu_qgd.Rd | 49 ++- man/read_sz_ittof.Rd |only man/read_sz_ittof_tic.Rd |only man/read_sz_sq.Rd |only man/read_sz_sq_tic.Rd |only man/read_sz_tlm.Rd | 3 man/read_thermoraw.Rd | 8 man/shared_params.Rd | 3 man/write_agilent_amx.Rd |only man/write_andi_chrom.Rd | 1 man/write_andi_ms.Rd | 1 man/write_chroms.Rd | 1 man/write_mzml.Rd | 20 + tests/testthat/fixtures.csv |only tests/testthat/helpers.R | 43 +++ tests/testthat/test-extra-agilent.R | 414 +++++++++++++++++++++++++++++--- tests/testthat/test-extra-chromeleon.R | 2 tests/testthat/test-extra-export.R | 14 - tests/testthat/test-extra-misc.R | 95 +++++++ tests/testthat/test-extra-shimadzu.R | 250 +++++++++++++++++++ tests/testthat/test-extra-waters.R | 2 tests/testthat/test-metadata_registry.R | 16 + tests/testthat/test-parser_registry.R | 11 tests/testthat/test-read_agilent_ms.R | 91 ++++++- tests/testthat/test-read_cdf.R | 20 + tests/testthat/test-read_chroms.R | 27 ++ tests/testthat/test-utils.R | 49 +++ tests/testthat/test-write_mzml.R | 102 +++++++ 72 files changed, 2589 insertions(+), 541 deletions(-)
More information about chromConverter at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-04 0.9.2
2021-01-18 0.9.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-15 1.0.3
2021-04-21 1.0.2
2017-11-24 1.0.0
2017-09-25 0.5.4
2015-06-08 0.4.62
2015-03-09 0.4.61
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-21 1.0.1
2024-05-09 0.2.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-05 2.0.1
2021-12-08 2.0.0
2015-06-02 1.1.0
2014-06-10 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-02-20 0.0.1
Title: Draw Beautiful Symbol Nomenclature for Glycans
Description: A 'ggplot2'-native plotting engine for drawing reproducible beautiful
Symbol Nomenclature for Glycans (SNFG) glycan cartoons from glycan structure
objects or text notations, with support for batch export, structural
highlighting, and deep appearance customization. It follows the SNFG
specification described at <https://www.ncbi.nlm.nih.gov/glycans/snfg.html>.
Author: Bin Fu [aut, cre, cph] ,
Xisong Feng [aut]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glydraw versions 0.9.0 dated 2026-08-26 and 0.10.0 dated 2026-11-14
DESCRIPTION | 11 MD5 | 115 +++++----- NAMESPACE | 4 NEWS.md | 17 + R/anno-glycan.R | 35 ++- R/auto-glycan-size.R |only R/draw-cartoon-sketch.R | 2 R/draw-cartoon.R | 7 R/draw-cartoons.R |only R/export-cartoons.R | 11 R/geom-glycan.R | 37 ++- R/geom-node-glycan.R | 5 R/ggplot2-compat.R | 3 R/glycan-grob.R | 5 R/guide-glycan.R | 73 +++++- R/internal-cartoon.R | 5 R/internal-coordinates.R | 5 R/internal-fit.R |only R/internal-floating-parts.R | 24 +- R/internal-linear-layout.R |only R/save-cartoon.R | 3 R/scale-glycan.R | 30 ++ R/style-glydraw.R | 32 ++ README.md | 9 inst/doc/complex-heatmap.R | 2 inst/doc/complex-heatmap.Rmd | 14 + inst/doc/complex-heatmap.html | 37 ++- inst/doc/ggplot2-extension.R | 3 inst/doc/ggplot2-extension.Rmd | 26 +- inst/doc/ggplot2-extension.html | 48 ++-- inst/doc/glydraw.html | 51 ++-- man/anno_glycan.Rd | 7 man/auto_glycan_size.Rd |only man/draw_cartoon.Rd | 2 man/draw_cartoon_sketch.Rd | 2 man/draw_cartoons.Rd |only man/export_cartoons.Rd | 2 man/figures/README-complexheatmap-extension-1.png |binary man/figures/draw-cartoons-example.png |only man/figures/issue-8-arabinoxylan-linear.png |only man/figures/issue-8-galactoglucomannan-linear.png |only man/figures/issue-8-xyloglucan-linear.png |only man/figures/lifecycle-experimental.svg |only man/geom_glycan.Rd | 12 - man/geom_node_glycan.Rd | 7 man/glycanGrob.Rd | 2 man/guide_glycan.Rd | 7 man/print.glydraw_cartoon.Rd | 2 man/save_cartoon.Rd | 2 man/scale_x_glycan.Rd | 9 man/style_glydraw.Rd | 24 +- tests/testthat/_snaps/auto-glycan-size.md |only tests/testthat/_snaps/cases/automatically-sized-glycan-bars.svg |only tests/testthat/_snaps/cases/automatically-sized-glycan-heatmap.svg |only tests/testthat/_snaps/draw-cartoons.md |only tests/testthat/_snaps/internal-linear-layout.md |only tests/testthat/test-anno-glycan.R | 50 ++++ tests/testthat/test-auto-glycan-size.R |only tests/testthat/test-cases.R | 57 ++++ tests/testthat/test-draw-cartoons.R |only tests/testthat/test-empty-dots.R |only tests/testthat/test-export-cartoons.R | 23 ++ tests/testthat/test-geom-glycan.R | 73 ++++++ tests/testthat/test-guide-glycan.R | 46 ++++ tests/testthat/test-internal-fit.R |only tests/testthat/test-internal-linear-layout.R |only tests/testthat/test-scale-glycan.R | 37 +++ vignettes/complex-heatmap.Rmd | 14 + vignettes/ggplot2-extension.Rmd | 26 +- 69 files changed, 816 insertions(+), 202 deletions(-)