Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-27 1.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-05 1.2.2
2013-11-20 1.2.1
2013-05-13 1.2
2011-09-07 1.1
2011-06-04 1.0
Title: Variance Component Analysis
Description: ANOVA and REML estimation of linear mixed models is implemented, once following
Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package.
The primary objective of this package is to perform a variance component analysis (VCA)
according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement
Procedures" (2014). There are plotting methods for visualization of an experimental design,
plotting random effects and residuals. For ANOVA type estimation two methods for computing
ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of
variance components can be derived, which is used in estimating confidence intervals. Linear
hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific
values of covariables and with custom weighting schemes for factor variables. See ?VCA for a
more comprehensive description of the features.
Author: Andre Schuetzenmeister [aut, cre] ,
Florian Dufey [aut]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VCA versions 1.5.1 dated 2024-03-07 and 1.5.2 dated 2025-09-06
DESCRIPTION | 20 MD5 | 24 R/model_check.R | 2 R/reml.R | 24 R/utils.R | 5887 +++++++++++++++++++++++------------------------ data/LSMeans_Data2.RData |only inst/ChangeLog.txt | 7 man/SattDF.Rd | 7 man/VCA-Package.Rd | 4 man/combineVC.Rd |only man/lmerMatrices.Rd | 2 man/lmerSummary.Rd | 8 man/remlMM.Rd | 6 man/remlVCA.Rd | 4 14 files changed, 3058 insertions(+), 2937 deletions(-)
Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are otherwise
performed manually. This includes setting up unit testing, test
coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp',
'RStudio' projects, and more.
Author: Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Malcolm Barrett [aut] ,
Andy Teucher [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between usethis versions 3.2.0 dated 2025-08-27 and 3.2.1 dated 2025-09-06
DESCRIPTION | 17 +++++++++-------- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/create.R | 7 +++++++ R/proj.R | 3 +-- R/release.R | 2 +- tests/testthat/_snaps/release.md | 1 - tests/testthat/test-create.R | 1 + 8 files changed, 31 insertions(+), 19 deletions(-)
Title: Tools for Trade Practitioners
Description: A collection of tools for trade practitioners, including the ability to calibrate different consumer demand systems and simulate the effects of tariffs and quotas under different competitive regimes. These tools are derived from Anderson et al. (2001) <doi:10.1016/S0047-2727(00)00085-2> and Froeb et al. (2003) <doi:10.1016/S0304-4076(02)00166-5>.
Author: Charles Taragin [aut, cre]
Maintainer: Charles Taragin <ctaragin+trader@gmail.com>
Diff between trade versions 0.8.1 dated 2022-08-24 and 0.8.3 dated 2025-09-06
DESCRIPTION | 18 +-- MD5 | 14 +- R/SimFunctions.R | 22 ++-- R/cournot_tariff.R | 2 build/vignette.rds |binary inst/doc/Reference.html | 241 +++++++++++++++++++++--------------------------- man/Sim-Functions.Rd | 22 ++-- man/cournot_tariff.Rd | 2 8 files changed, 150 insertions(+), 171 deletions(-)
Title: Functions for Tidy Analysis and Generation of Random Data
Description: To make it easy to generate random numbers based upon the underlying stats
distribution functions. All data is returned in a tidy and structured
format making working with the data simple and straight forward. Given that the
data is returned in a tidy 'tibble' it lends itself to working with the rest of the
'tidyverse'.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between TidyDensity versions 1.5.1 dated 2025-07-23 and 1.5.2 dated 2025-09-06
DESCRIPTION | 6 MD5 | 74 +-- NEWS.md | 14 R/autoplot-triangular.R | 288 ++++++------- R/est-param-triangular.R | 226 +++++----- R/helper-dist-type-extract.R | 84 ++-- R/random-tidy-geom.R | 274 ++++++------- R/random-tidy-mixture.R | 414 ++++++++++++-------- R/stats-triangular-tbl.R | 190 ++++----- R/tidy_distribution_summary_tbl.R | 170 ++++---- R/utils-convert-to-ts.R | 224 +++++----- R/utils-quantile-normalize.R | 170 +++----- README.md | 26 - build/vignette.rds |binary inst/doc/getting-started.html | 45 +- man/bootstrap_p_vec.Rd | 110 ++--- man/bootstrap_q_vec.Rd | 112 ++--- man/cgmean.Rd | 92 ++-- man/chmean.Rd | 92 ++-- man/ckurtosis.Rd | 90 ++-- man/cmean.Rd | 92 ++-- man/cmedian.Rd | 90 ++-- man/csd.Rd | 92 ++-- man/cskewness.Rd | 90 ++-- man/cvar.Rd | 94 ++-- man/dist_type_extractor.Rd | 72 +-- man/figures/README-more_than_nine_simulations-1.png |binary man/figures/README-more_than_nine_simulations-2.png |binary man/figures/README-more_than_nine_simulations-3.png |binary man/figures/README-more_than_nine_simulations-4.png |binary man/figures/README-plot_density-1.png |binary man/figures/README-plot_density-2.png |binary man/figures/README-plot_density-3.png |binary man/figures/README-plot_density-4.png |binary man/quantile_normalize.Rd | 12 man/tidy_mixture_density.Rd | 35 + man/tidy_stat_tbl.Rd | 182 ++++---- man/triangle_plot.Rd | 70 +-- 38 files changed, 1839 insertions(+), 1691 deletions(-)
Title: Applies Display Metadata to Analysis Results Datasets
Description: Creates a framework to store and apply display metadata to
Analysis Results Datasets (ARDs). The use of 'tfrmt' allows users to
define table format and styling without the data, and later apply the
format to the data.
Author: Becca Krouse [aut, cre],
Christina Fillmore [aut] ,
Ellis Hughes [aut] ,
Karima Ahmad [aut] ,
Shannon Haughton [aut],
Dragoș Moldovan-Gruenfeld [aut],
GlaxoSmithKline Research & Development Limited [cph, fnd],
Atorus Research LLC [cph, fnd]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Diff between tfrmt versions 0.1.3 dated 2024-10-15 and 0.2.0 dated 2025-09-06
tfrmt-0.1.3/tfrmt/R/display_row_frmts.R |only tfrmt-0.1.3/tfrmt/tests/testthat/test-display_row_frmts.R |only tfrmt-0.2.0/tfrmt/DESCRIPTION | 87 +--- tfrmt-0.2.0/tfrmt/MD5 | 55 +- tfrmt-0.2.0/tfrmt/NAMESPACE | 5 tfrmt-0.2.0/tfrmt/NEWS.md | 51 ++ tfrmt-0.2.0/tfrmt/R/apply_col_plan.R | 3 tfrmt-0.2.0/tfrmt/R/apply_row_grp_plan.R | 2 tfrmt-0.2.0/tfrmt/R/apply_tfrmt.R | 11 tfrmt-0.2.0/tfrmt/R/big_n.R | 55 ++ tfrmt-0.2.0/tfrmt/R/prep_card.R |only tfrmt-0.2.0/tfrmt/R/print_to_ggplot.R | 2 tfrmt-0.2.0/tfrmt/R/print_to_gt.R | 1 tfrmt-0.2.0/tfrmt/R/shuffle_card.R |only tfrmt-0.2.0/tfrmt/R/struct_utils.R | 6 tfrmt-0.2.0/tfrmt/R/tfrmt_checks.R | 4 tfrmt-0.2.0/tfrmt/README.md | 16 tfrmt-0.2.0/tfrmt/man/display_row_frmts.Rd | 34 - tfrmt-0.2.0/tfrmt/man/prep_big_n.Rd |only tfrmt-0.2.0/tfrmt/man/prep_combine_vars.Rd |only tfrmt-0.2.0/tfrmt/man/prep_hierarchical_fill.Rd |only tfrmt-0.2.0/tfrmt/man/prep_label.Rd |only tfrmt-0.2.0/tfrmt/man/print_to_ggplot.Rd | 2 tfrmt-0.2.0/tfrmt/man/shuffle_card.Rd |only tfrmt-0.2.0/tfrmt/tests/testthat/_snaps/prep_card.md |only tfrmt-0.2.0/tfrmt/tests/testthat/_snaps/shuffle_card.md |only tfrmt-0.2.0/tfrmt/tests/testthat/helper_transform_gt_html.R |only tfrmt-0.2.0/tfrmt/tests/testthat/test-apply_page_plan.R | 49 ++ tfrmt-0.2.0/tfrmt/tests/testthat/test-big_ns.R | 255 ++++++++++++ tfrmt-0.2.0/tfrmt/tests/testthat/test-col_style_structure.R | 26 - tfrmt-0.2.0/tfrmt/tests/testthat/test-display_insights.R |only tfrmt-0.2.0/tfrmt/tests/testthat/test-expr_to_filter.R | 28 + tfrmt-0.2.0/tfrmt/tests/testthat/test-make_mock_data.R | 24 - tfrmt-0.2.0/tfrmt/tests/testthat/test-prep_card.R |only tfrmt-0.2.0/tfrmt/tests/testthat/test-shuffle_card.R |only tfrmt-0.2.0/tfrmt/tests/testthat/test-utils_tfrmt.R | 54 ++ 36 files changed, 603 insertions(+), 167 deletions(-)
Title: Spatial Predictive Modeling
Description: Introduction to some novel accurate hybrid methods of geostatistical and machine learning methods for spatial predictive modelling. It contains two commonly used geostatistical methods, two machine learning methods, four hybrid methods and two averaging methods. For each method, two functions are provided. One function is for assessing the predictive errors and accuracy of the method based on cross-validation. The other one is for generating spatial predictions using the method. For details please see: Li, J., Potter, A., Huang, Z., Daniell, J. J. and Heap, A. (2010) <https://ecat.ga.gov.au/geonetwork/srv/eng/catalog.search#/metadata/71407>
Li, J., Heap, A. D., Potter, A., Huang, Z. and Daniell, J. (2011) <doi:10.1016/j.csr.2011.05.015>
Li, J., Heap, A. D., Potter, A. and Daniell, J. (2011) <doi:10.1016/j.envsoft.2011.07.004>
Li, J., Potter, A., Huang, Z. and Heap, A. (2012) <https://ecat.ga.gov.au/geonetwork/srv/eng/catalog.search#/metadata/74030>.
Author: Jin Li [aut, cre]
Maintainer: Jin Li <jinli68@gmail.com>
Diff between spm versions 1.2.2 dated 2022-05-06 and 1.2.3 dated 2025-09-06
DESCRIPTION | 17 - MD5 | 22 +- R/gbmcv.R | 6 R/gbmidwcv.R | 4 R/gbmokgbmidwcv.R | 4 build/vignette.rds |binary inst/doc/spm.R | 176 ++++++++--------- inst/doc/spm.Rmd | 2 inst/doc/spm.html | 527 +++++++++++++++++++++++++++++++-------------------- man/gbmidwcv.Rd | 4 man/gbmokgbmidwcv.Rd | 4 vignettes/spm.Rmd | 2 12 files changed, 446 insertions(+), 322 deletions(-)
Title: Spatial Regression Analysis
Description: A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep'. These model fitting functions include maximum likelihood methods for cross-sectional models proposed by 'Cliff' and 'Ord' (1973, ISBN:0850860369) and (1981, ISBN:0850860814), fitting methods initially described by 'Ord' (1975) <doi:10.1080/01621459.1975.10480272>. The models are further described by 'Anselin' (1988) <doi:10.1007/978-94-015-7799-1>. Spatial two stage least squares and spatial general method of moment models initially proposed by 'Kelejian' and 'Prucha' (1998) <doi:10.1023/A:1007707430416> and (1999) <doi:10.1111/1468-2354.00027> are provided. Impact methods and MCMC fitting methods proposed by 'LeSage' and 'Pace' (2009) <doi:10.1201/9781420064254> are implemented for the family of cross-sectional spatial regression models. Methods for fitting the log determinant term in maximu [...truncated...]
Author: Roger Bivand [cre, aut] ,
Gianfranco Piras [aut],
Luc Anselin [ctb],
Andrew Bernat [ctb],
Eric Blankmeyer [ctb],
Yongwan Chun [ctb],
Virgilio Gomez-Rubio [ctb],
Daniel Griffith [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
James LeSage [ctb],
Ange [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spatialreg versions 1.4-1 dated 2025-09-04 and 1.4-2 dated 2025-09-06
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 6 +++++- R/sarlm_tests.R | 2 +- inst/tinytest/test_Durbin_factor.R | 16 ---------------- 5 files changed, 15 insertions(+), 27 deletions(-)
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon timescales (C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package uses the calibration curves from the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 1.3.0 dated 2025-07-24 and 1.4.0 dated 2025-09-06
rice-1.3.0/rice/R/realms.R |only rice-1.3.0/rice/man/BCADtoD14C.Rd |only rice-1.3.0/rice/man/C14toD14C.Rd |only rice-1.3.0/rice/man/D14CtoC14.Rd |only rice-1.3.0/rice/man/D14CtoF14C.Rd |only rice-1.3.0/rice/man/D14CtopMC.Rd |only rice-1.3.0/rice/man/F14CtoD14C.Rd |only rice-1.3.0/rice/man/b2ktoD14C.Rd |only rice-1.3.0/rice/man/calBPtoD14C.Rd |only rice-1.3.0/rice/man/draw.D14C.Rd |only rice-1.3.0/rice/man/pMCtoD14C.Rd |only rice-1.3.0/rice/tests/testthat/test-realms.R |only rice-1.4.0/rice/DESCRIPTION | 10 - rice-1.4.0/rice/MD5 | 176 +++++++++++------------ rice-1.4.0/rice/NAMESPACE | 20 +- rice-1.4.0/rice/NEWS.md | 22 +- rice-1.4.0/rice/R/calibrate.R | 36 ++-- rice-1.4.0/rice/R/marine.R | 21 ++ rice-1.4.0/rice/R/plots.R | 149 +++++++++---------- rice-1.4.0/rice/R/rice-package.R | 2 rice-1.4.0/rice/R/rice.R | 34 ++-- rice-1.4.0/rice/R/sets.R | 24 +-- rice-1.4.0/rice/R/shroud.R | 2 rice-1.4.0/rice/R/sources.R | 50 +++--- rice-1.4.0/rice/R/timescales.R |only rice-1.4.0/rice/README.md | 2 rice-1.4.0/rice/inst/CITATION | 74 ++------- rice-1.4.0/rice/inst/doc/rice.R | 14 - rice-1.4.0/rice/inst/doc/rice.Rmd | 46 +++--- rice-1.4.0/rice/inst/doc/rice.html | 157 ++++++++++---------- rice-1.4.0/rice/man/BCADtoC14.Rd | 6 rice-1.4.0/rice/man/BCADtoDelta14C.Rd |only rice-1.4.0/rice/man/BCADtoF14C.Rd | 6 rice-1.4.0/rice/man/BCADtob2k.Rd | 8 - rice-1.4.0/rice/man/BCADtocalBP.Rd | 10 - rice-1.4.0/rice/man/BCADtopMC.Rd | 8 - rice-1.4.0/rice/man/C14toBCAD.Rd | 8 - rice-1.4.0/rice/man/C14toDelta14C.Rd |only rice-1.4.0/rice/man/C14toF14C.Rd | 2 rice-1.4.0/rice/man/C14tob2k.Rd | 2 rice-1.4.0/rice/man/C14tocalBP.Rd | 2 rice-1.4.0/rice/man/C14topMC.Rd | 2 rice-1.4.0/rice/man/CtoF.Rd | 2 rice-1.4.0/rice/man/Delta14CtoC14.Rd |only rice-1.4.0/rice/man/Delta14CtoF14C.Rd |only rice-1.4.0/rice/man/Delta14CtopMC.Rd |only rice-1.4.0/rice/man/F14C.age.Rd | 2 rice-1.4.0/rice/man/F14CtoC14.Rd | 2 rice-1.4.0/rice/man/F14CtoDelta14C.Rd |only rice-1.4.0/rice/man/F14CtopMC.Rd | 2 rice-1.4.0/rice/man/FtoC.Rd | 2 rice-1.4.0/rice/man/adjust.background.Rd | 8 - rice-1.4.0/rice/man/adjust.fractionation.Rd | 4 rice-1.4.0/rice/man/age.F14C.Rd | 2 rice-1.4.0/rice/man/age.pMC.Rd | 2 rice-1.4.0/rice/man/as.bin.Rd | 4 rice-1.4.0/rice/man/as.one.Rd | 8 - rice-1.4.0/rice/man/b2ktoBCAD.Rd | 12 - rice-1.4.0/rice/man/b2ktoC14.Rd | 2 rice-1.4.0/rice/man/b2ktoDelta14C.Rd |only rice-1.4.0/rice/man/b2ktoF14C.Rd | 2 rice-1.4.0/rice/man/b2ktocalBP.Rd | 2 rice-1.4.0/rice/man/b2ktopMC.Rd | 2 rice-1.4.0/rice/man/calBPtoBCAD.Rd | 12 - rice-1.4.0/rice/man/calBPtoC14.Rd | 2 rice-1.4.0/rice/man/calBPtoDelta14C.Rd |only rice-1.4.0/rice/man/calBPtoF14C.Rd | 2 rice-1.4.0/rice/man/calBPtob2k.Rd | 2 rice-1.4.0/rice/man/calBPtopMC.Rd | 2 rice-1.4.0/rice/man/caldist.Rd | 6 rice-1.4.0/rice/man/calib.t.Rd | 4 rice-1.4.0/rice/man/calibrate.Rd | 4 rice-1.4.0/rice/man/clean.Rd | 2 rice-1.4.0/rice/man/contaminate.Rd | 2 rice-1.4.0/rice/man/draw.Delta14C.Rd |only rice-1.4.0/rice/man/draw.ccurve.Rd | 16 +- rice-1.4.0/rice/man/draw.dates.Rd | 6 rice-1.4.0/rice/man/find.shells.Rd | 3 rice-1.4.0/rice/man/fromto.Rd | 18 +- rice-1.4.0/rice/man/l.calib.Rd | 4 rice-1.4.0/rice/man/map.shells.Rd | 3 rice-1.4.0/rice/man/muck.Rd | 2 rice-1.4.0/rice/man/older.Rd | 4 rice-1.4.0/rice/man/overlap.Rd | 2 rice-1.4.0/rice/man/p.range.Rd | 4 rice-1.4.0/rice/man/pMC.age.Rd | 2 rice-1.4.0/rice/man/pMCtoC14.Rd | 2 rice-1.4.0/rice/man/pMCtoDelta14C.Rd |only rice-1.4.0/rice/man/pMCtoF14C.Rd | 2 rice-1.4.0/rice/man/push.gamma.Rd | 7 rice-1.4.0/rice/man/push.normal.Rd | 5 rice-1.4.0/rice/man/r.calib.Rd | 4 rice-1.4.0/rice/man/rice-package.Rd | 2 rice-1.4.0/rice/man/rice.Rd | 4 rice-1.4.0/rice/man/shroud.Rd | 2 rice-1.4.0/rice/man/span.Rd | 2 rice-1.4.0/rice/man/spread.Rd | 2 rice-1.4.0/rice/man/younger.Rd | 4 rice-1.4.0/rice/tests/testthat/test-rice.R | 2 rice-1.4.0/rice/tests/testthat/test-timescales.R |only rice-1.4.0/rice/vignettes/rice.Rmd | 46 +++--- 101 files changed, 568 insertions(+), 569 deletions(-)
Title: Record Linkage Toolkit
Description: Functions to assist in performing probabilistic record linkage and
deduplication: generating pairs, comparing records, em-algorithm for
estimating m- and u-probabilities
(I. Fellegi & A. Sunter (1969) <doi:10.1080/01621459.1969.10501049>,
T.N. Herzog, F.J. Scheuren, & W.E. Winkler (2007),
"Data Quality and Record Linkage Techniques", ISBN:978-0-387-69502-0),
forcing one-to-one matching. Can also be
used for pre- and post-processing for machine learning methods for record
linkage. Focus is on memory, CPU performance and flexibility.
Author: Jan van der Laan [aut, cre]
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between reclin2 versions 0.5.0 dated 2024-02-09 and 0.6.0 dated 2025-09-06
DESCRIPTION | 15 +- MD5 | 120 +++++++++--------- NAMESPACE | 2 NEWS | 15 ++ R/RcppExports.R | 8 + R/add_from_x.R | 2 R/comparators.R | 2 R/compare_pairs.R | 2 R/compare_vars.R | 2 R/get_comparators.R | 1 R/get_inspect_pairs.R | 2 R/greedy.R | 18 ++ R/pair.R | 4 R/pair_blocking.R | 4 R/pair_minsim.R | 4 R/problink_em.R | 2 R/select_greedy.R | 5 R/select_n_to_m.R | 9 + R/select_preprocess.R | 4 R/utils.R |only README.md | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/deduplication.R | 1 inst/doc/deduplication.html | 23 +-- inst/doc/deduplication.md | 1 inst/doc/record_linkage_using_machine_learning.R | 1 inst/doc/record_linkage_using_machine_learning.html | 91 +++++++------- inst/doc/record_linkage_using_machine_learning.md | 1 inst/doc/using_a_cluster_for_record_linkage.html | 128 ++++++++++---------- man/add_from_x.Rd | 2 man/comparators.Rd | 2 man/compare_pairs.Rd | 2 man/compare_vars.Rd | 2 man/get_inspect_pairs.Rd | 2 man/greedy.Rd | 13 +- man/pair.Rd | 4 man/pair_blocking.Rd | 4 man/pair_minsim.Rd | 4 man/select_n_to_m.Rd | 7 + man/val_or.Rd |only src/RcppExports.cpp | 30 ++++ src/greedy.cpp | 54 ++++++++ tests/test_cluster_compare_vars.R | 1 tests/test_cluster_pair.R | 1 tests/test_cluster_pair_blocking.R | 1 tests/test_cluster_pair_minsim.R | 1 tests/test_compare_vars.R | 1 tests/test_distribute_over_cluster.R | 1 tests/test_greedy.R | 58 +++++++++ tests/test_merge_pairs.R | 1 tests/test_pair.R | 1 tests/test_pair_blocking.R | 1 tests/test_pair_minsim.R | 1 tests/test_problink_em.R | 1 tests/test_score_simple.R | 1 tests/test_select_greedy.R | 18 ++ tests/test_select_preprocess.R | 1 tests/test_select_unique.R | 1 tests/test_set_seed.R | 1 vignettes/deduplication.md | 1 vignettes/record_linkage_using_machine_learning.md | 1 62 files changed, 471 insertions(+), 220 deletions(-)
Title: Prediction Rule Ensembles
Description: Derives prediction rule ensembles (PREs). Largely follows the
procedure for deriving PREs as described in Friedman & Popescu (2008;
<DOI:10.1214/07-AOAS148>), with adjustments and improvements described in
Fokkema (2020; <DOI:10.18637/jss.v092.i12>) and Fokkema & Strobl
(2020; <DOI:10.1037/met0000256>). The main function pre() derives
prediction rule ensembles consisting of rules and/or linear terms for
continuous, binary, count, multinomial, survival and multivariate
continuous responses. Function gpe() derives generalized prediction
ensembles, consisting of rules, hinge and linear functions of the
predictor variables.
Author: Marjolein Fokkema [aut, cre],
Benjamin Christoffersen [aut]
Maintainer: Marjolein Fokkema <m.fokkema@fsw.leidenuniv.nl>
Diff between pre versions 1.0.7 dated 2024-01-12 and 1.0.8 dated 2025-09-06
pre-1.0.7/pre/NEWS |only pre-1.0.7/pre/inst/doc/missingness.R |only pre-1.0.7/pre/inst/doc/missingness.Rmd |only pre-1.0.7/pre/inst/doc/missingness.html |only pre-1.0.7/pre/inst/doc/tuning.R |only pre-1.0.7/pre/inst/doc/tuning.Rmd |only pre-1.0.7/pre/inst/doc/tuning.html |only pre-1.0.7/pre/vignettes/missingness.Rmd |only pre-1.0.7/pre/vignettes/tuning.Rmd |only pre-1.0.8/pre/DESCRIPTION | 26 pre-1.0.8/pre/MD5 | 65 pre-1.0.8/pre/NEWS.md |only pre-1.0.8/pre/R/gpe.R | 22 pre-1.0.8/pre/R/mi_pre.R | 2 pre-1.0.8/pre/R/pre.R | 801 ++++++---- pre-1.0.8/pre/build/partial.rdb |binary pre-1.0.8/pre/build/vignette.rds |binary pre-1.0.8/pre/inst/doc/Missingness.R |only pre-1.0.8/pre/inst/doc/Missingness.Rmd |only pre-1.0.8/pre/inst/doc/Missingness.html |only pre-1.0.8/pre/inst/doc/Tuning.R |only pre-1.0.8/pre/inst/doc/Tuning.Rmd |only pre-1.0.8/pre/inst/doc/Tuning.html |only pre-1.0.8/pre/inst/doc/relaxed.Rmd | 40 pre-1.0.8/pre/inst/doc/relaxed.html | 221 +- pre-1.0.8/pre/inst/doc/speed.R | 20 pre-1.0.8/pre/inst/doc/speed.Rmd | 40 pre-1.0.8/pre/inst/doc/speed.html | 82 - pre-1.0.8/pre/man/gpe.Rd | 2 pre-1.0.8/pre/man/gpe_cv.glmnet.Rd | 4 pre-1.0.8/pre/man/gpe_rules_pre.Rd | 8 pre-1.0.8/pre/man/gpe_trees.Rd | 14 pre-1.0.8/pre/man/pairplot.Rd | 10 pre-1.0.8/pre/man/pre.Rd | 39 pre-1.0.8/pre/man/rTerm.Rd | 2 pre-1.0.8/pre/man/singleplot.Rd | 9 pre-1.0.8/pre/tests/testthat/previous_results/airquality_w_pre_with_glmtree_w_offset.RDS |only pre-1.0.8/pre/tests/testthat/tests_pre.R | 14 pre-1.0.8/pre/vignettes/Missingness.Rmd |only pre-1.0.8/pre/vignettes/Tuning.Rmd |only pre-1.0.8/pre/vignettes/bib.bib | 190 ++ pre-1.0.8/pre/vignettes/relaxed.Rmd | 40 pre-1.0.8/pre/vignettes/speed.Rmd | 40 43 files changed, 1104 insertions(+), 587 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter@zoology.ubc.ca>
Diff between phylopath versions 1.3.0 dated 2024-06-11 and 1.3.1 dated 2025-09-06
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS.md | 5 +++++ R/internal.R | 3 --- R/print_and_plot.R | 4 ++-- build/vignette.rds |binary inst/doc/binary_models.html | 14 +++++++------- inst/doc/intro_to_phylopath.R | 12 ++++++------ inst/doc/intro_to_phylopath.html | 18 +++++++++--------- man/plot.DAG.Rd | 2 +- tests/testthat/test-check_models_data_tree.R |only 11 files changed, 44 insertions(+), 41 deletions(-)
Title: ADaM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Analysis Data Model (ADaM) datasets constructed
using the Study Data Tabulation Model (SDTM) datasets contained in the
'pharmaversesdtm' package and the template scripts from the 'admiral'
family of packages. ADaM dataset specifications are described in the
CDISC ADaM implementation guide, accessible by creating a free account
on <https://www.cdisc.org/>.
Author: Fanny Gautier [aut, cre] ,
Stefan Bundfuss [aut] ,
Edoardo Mancini [aut] ,
Lina Patil [aut],
Vladyslav Shuliar [aut] ,
Cytel Inc. [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline LLC [cph, fnd]
Maintainer: Fanny Gautier <fanny.gautier@cytel.com>
Diff between pharmaverseadam versions 1.1.0 dated 2024-10-25 and 1.2.0 dated 2025-09-06
DESCRIPTION | 68 ++++--- MD5 | 167 +++++++++--------- NAMESPACE | 1 NEWS.md | 58 +++++- R/adae.R | 21 +- R/adbcva_ophtha.R | 82 ++------ R/adce_vaccine.R | 7 R/adcm.R | 19 +- R/adcoeq_metabolic.R |only R/adeg.R | 29 ++- R/adex.R | 40 +++- R/adface_vaccine.R | 43 ++++ R/adis_vaccine.R | 37 +++- R/adlb.R | 68 ++++++- R/adlb_metabolic.R |only R/adlbhy.R | 17 + R/admh.R | 17 - R/adoe_ophtha.R | 32 ++- R/adpc.R | 25 +- R/adpp.R | 17 - R/adppk.R | 13 + R/adrs_onco.R | 26 ++ R/adsl.R | 15 - R/adsl_vaccine.R | 7 R/adtr_onco.R | 24 ++ R/adtte_onco.R | 14 + R/advfq_ophtha.R | 32 ++- R/advs.R | 30 ++- R/advs_metabolic.R |only R/advs_peds.R | 25 ++ R/pharmaverseadam-package.R | 1 README.md | 101 +++++++---- data/adae.rda |binary data/adbcva_ophtha.rda |binary data/adce_vaccine.rda |binary data/adcm.rda |binary data/adcoeq_metabolic.rda |only data/adeg.rda |binary data/adex.rda |binary data/adface_vaccine.rda |binary data/adis_vaccine.rda |binary data/adlb.rda |binary data/adlb_metabolic.rda |only data/adlbhy.rda |binary data/admh.rda |binary data/adoe_ophtha.rda |binary data/adpc.rda |binary data/adpp.rda |binary data/adppk.rda |binary data/adrs_onco.rda |binary data/adsl.rda |binary data/adsl_vaccine.rda |binary data/adtr_onco.rda |binary data/adtte_onco.rda |binary data/advfq_ophtha.rda |binary data/advs.rda |binary data/advs_metabolic.rda |only data/advs_peds.rda |binary inst/WORDLIST | 374 +++++++++++++++++++++++++---------------- inst/extdata/adams-specs.json |only inst/extdata/adams-specs.xlsx |binary man/adae.Rd | 16 - man/adbcva_ophtha.Rd | 78 ++------ man/adce_vaccine.Rd | 2 man/adcm.Rd | 14 - man/adcoeq_metabolic.Rd |only man/adeg.Rd | 25 ++ man/adex.Rd | 36 +++ man/adface_vaccine.Rd | 39 ++++ man/adis_vaccine.Rd | 33 +++ man/adlb.Rd | 64 ++++++- man/adlb_metabolic.Rd |only man/adlbhy.Rd | 13 + man/admh.Rd | 12 - man/adoe_ophtha.Rd | 28 ++- man/adpc.Rd | 21 +- man/adpp.Rd | 12 - man/adppk.Rd | 9 man/adrs_onco.Rd | 22 ++ man/adsl.Rd | 10 - man/adsl_vaccine.Rd | 2 man/adtr_onco.Rd | 20 +- man/adtte_onco.Rd | 10 - man/advfq_ophtha.Rd | 28 ++- man/advs.Rd | 26 ++ man/advs_metabolic.Rd |only man/advs_peds.Rd | 21 ++ man/figures/cytel_logo.png |only man/figures/gsk_logo.png |only man/figures/roche_logo.png |only man/pharmaverseadam-package.Rd | 17 + 91 files changed, 1323 insertions(+), 645 deletions(-)
More information about pharmaverseadam at CRAN
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Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for (1) data handling (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and cluster scores, reading and writing Excel and SPSS files), (2) descriptive statistics (e.g., frequency table, cross tabulation, effect size measures), (3) missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), (4) multilevel data (e.g., multilevel descriptive statistics, within-group and between-group correlation matrix, multilevel confirmatory factor analysis, level-specific fit indices, cross-level measurement equivalence evaluation, multilevel composite reliability, and multilevel R-squared measures), (5) item analysis (e.g., confirmatory factor analysis, coefficient alpha and omega, between-group and longitudinal measurement equivalence evaluation), (6) statistical analysis (e.g., bootstrap confidence intervals, collinearity and resid [...truncated...]
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.7.4 dated 2025-08-18 and 0.7.5 dated 2025-09-06
DESCRIPTION | 12 MD5 | 198 ++++++------ NAMESPACE | 1 NEWS.md | 28 + R/aov.b.R | 7 R/aov.w.R | 7 R/blimp.R | 10 R/blimp.bayes.R | 7 R/blimp.plot.R | 7 R/blimp.print.R | 7 R/blimp.update.R | 10 R/center.R | 7 R/check.collin.R | 7 R/check.outlier.R | 7 R/check.resid.R | 9 R/chr.color.R | 7 R/chr.grep.R | 14 R/chr.gsub.R | 12 R/chr.omit.R | 10 R/chr.trim.R | 7 R/chr.trunc.R | 17 - R/ci.cor.R | 7 R/ci.mean.R | 7 R/ci.mean.diff.R | 7 R/ci.mean.w.R | 7 R/ci.prop.R | 7 R/ci.prop.diff.R | 7 R/ci.var.R | 7 R/cluster.rwg.R | 10 R/cluster.scores.R | 10 R/coding.R | 5 R/coeff.robust.R | 326 ++++++++++++++++---- R/coeff.std.R | 9 R/cohens.d.R | 16 R/cor.matrix.R | 7 R/crosstab.R | 7 R/descript.R | 138 ++++---- R/df.check.R | 7 R/df.duplicated.R | 7 R/df.head.R | 7 R/df.long.R | 14 R/df.move.R | 12 R/df.rbind.R | 5 R/df.rename.R | 4 R/df.subset.R | 5 R/dominance.R | 7 R/dominance.manual.R | 7 R/effsize.R | 5 R/freq.R | 309 ++++++++---------- R/item.alpha.R | 7 R/item.cfa.R | 7 R/item.invar.R | 7 R/item.omega.R | 7 R/item.reverse.R | 7 R/item.scores.R | 7 R/lagged.R | 7 R/mplus.R | 10 R/mplus.bayes.R | 7 R/mplus.lca.R | 7 R/mplus.plot.R | 7 R/mplus.print.R | 7 R/mplus.update.R | 10 R/multilevel.cfa.R | 12 R/multilevel.cor.R | 12 R/multilevel.descript.R | 12 R/multilevel.fit.R | 5 R/multilevel.icc.R | 12 R/multilevel.invar.R | 10 R/multilevel.omega.R | 12 R/multilevel.r2.manual.R | 21 - R/na.as.R | 14 R/na.auxiliary.R | 7 R/na.coverage.R | 7 R/na.descript.R | 7 R/na.indicator.R | 7 R/na.pattern.R | 7 R/na.prop.R | 7 R/na.test.R | 7 R/plot.misty.object.R | 7 R/print.misty.object.R | 766 ++++++++++++++++++++++++++++++++++++++++------- R/rec.R | 12 R/robust.lmer.R |only R/script.open.R | 7 R/setsource.R | 5 R/skewness.R | 14 R/summa.R | 294 +++++++++++++----- R/test.levene.R | 7 R/test.t.R | 14 R/test.welch.R | 7 R/test.z.R | 16 R/uniq.R | 14 R/utils.R | 6 R/write.result.R | 254 ++++++++++++--- R/write.sav.R | 7 R/write.xlsx.R | 5 man/check.resid.Rd | 2 man/coeff.robust.Rd | 225 ++++++++++--- man/descript.Rd | 9 man/freq.Rd | 23 - man/robust.lmer.Rd |only man/summa.Rd | 97 ++++- 101 files changed, 2169 insertions(+), 1235 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of discrete response data using
unidimensional and multidimensional item analysis models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory item factor analysis models
are estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier models are available for modeling item testlets using
dimension reduction EM algorithms, while multiple group analyses and
mixed effects designs are included for detecting differential item, bundle,
and test functioning, and for modeling item and person covariates.
Finally, latent class models such as the DINA, DINO, multidimensional latent class,
mixture IRT models, and zero-inflated response models are supported, as well
as a wide family of probabilistic unfolding models.
Author: Phil Chalmers [aut, cre] ,
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.44.0 dated 2025-01-28 and 1.45.1 dated 2025-09-06
DESCRIPTION | 9 - MD5 | 288 ++++++++++++++++++------------------ NEWS.md | 15 + R/03-estimation.R | 40 +++-- R/04-PrepData.R | 5 R/05-model.elements.R | 2 R/DIF.R | 2 R/DRF.R | 6 R/DTF.R | 2 R/DeltaMethod.R | 8 - R/EMstep.group.R | 11 + R/M2.R | 2 R/MDIFF.R | 2 R/MDISC.R | 2 R/MHRM.utils.R | 2 R/PLCI.mirt.R | 14 - R/RCI.R | 135 ++++++++++++---- R/RMSD_DIF.R | 26 ++- R/SIBTEST.R | 13 + R/SingleGroup-methods.R | 20 +- R/areainfo.R | 2 R/averageMI.R | 2 R/bfactor.R | 2 R/boot.LR.R | 2 R/boot.mirt.R | 4 R/createItem.R | 2 R/empirical_ES.R | 2 R/empirical_plot.R | 2 R/empirical_rxx.R | 2 R/estfun.R | 2 R/expand.table.R | 2 R/expected.test.R | 2 R/extract.group.R | 17 +- R/extract.item.R | 13 - R/extract.mirt.R | 2 R/fixedCalib.R | 2 R/fixef.R | 2 R/fscores.R | 18 +- R/fscores.internal.R | 4 R/gen.difficulty.R | 2 R/imputeMissing.R | 2 R/itemGAM.R | 6 R/itemfit.R | 2 R/iteminfo.R | 2 R/itemplot.R | 2 R/itemstats.R | 47 +++-- R/lagrange.R | 2 R/likert2int.R | 2 R/marginal_rxx.R | 32 +++- R/mdirt.R | 2 R/mirt-package.R | 18 +- R/mirt.R | 4 R/mirt.model.R | 2 R/mixedmirt.R | 4 R/mod2values.R | 2 R/multipleGroup.R | 5 R/numerical_deriv.R | 2 R/personfit.R | 2 R/poly2dich.R | 2 R/randef.R | 17 +- R/read.mirt.R | 2 R/reverse.score.R | 4 R/simdata.R | 4 R/testinfo.R | 2 R/utils.R | 11 + R/wald.R | 2 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/mirt-vignettes.html | 124 +++++++++------ man/Attitude.Rd | 2 man/Bock1997.Rd | 2 man/DIF.Rd | 2 man/DRF.Rd | 4 man/DTF.Rd | 2 man/DeltaMethod.Rd | 8 - man/LSAT6.Rd | 2 man/LSAT7.Rd | 4 man/M2.Rd | 2 man/MDIFF.Rd | 2 man/MDISC.Rd | 2 man/PLCI.mirt.Rd | 8 - man/RCI.Rd | 77 +++++++++ man/RMSD_DIF.Rd | 22 ++ man/SAT12.Rd | 2 man/SIBTEST.Rd | 8 - man/SLF.Rd | 2 man/Science.Rd | 2 man/anova-method.Rd | 2 man/areainfo.Rd | 2 man/averageMI.Rd | 2 man/bfactor.Rd | 2 man/boot.LR.Rd | 2 man/boot.mirt.Rd | 4 man/coef-method.Rd | 2 man/createItem.Rd | 2 man/deAyala.Rd | 2 man/draw_parameters.Rd | 2 man/empirical_ES.Rd | 2 man/empirical_plot.Rd | 2 man/empirical_rxx.Rd | 2 man/estfun.AllModelClass.Rd | 2 man/expand.table.Rd | 2 man/expected.test.Rd | 2 man/extract.group.Rd | 7 man/extract.item.Rd | 11 - man/extract.mirt.Rd | 2 man/fixedCalib.Rd | 2 man/fixef.Rd | 2 man/fscores.Rd | 11 + man/gen.difficulty.Rd | 2 man/imputeMissing.Rd | 2 man/itemGAM.Rd | 6 man/itemfit.Rd | 2 man/iteminfo.Rd | 2 man/itemplot.Rd | 2 man/itemstats.Rd | 16 +- man/lagrange.Rd | 2 man/likert2int.Rd | 2 man/logLik-method.Rd | 2 man/marginal_rxx.Rd | 32 +++- man/mdirt.Rd | 2 man/mirt.Rd | 4 man/mirt.model.Rd | 2 man/mixedmirt.Rd | 4 man/mod2values.Rd | 2 man/multipleGroup.Rd | 5 man/numerical_deriv.Rd | 2 man/personfit.Rd | 2 man/plot-method.Rd | 2 man/poly2dich.Rd | 2 man/print-method.Rd | 2 man/randef.Rd | 10 + man/read.mirt.Rd | 2 man/residuals-method.Rd | 2 man/reverse.score.Rd | 4 man/secondOrderTest.Rd | 2 man/show-method.Rd | 2 man/simdata.Rd | 2 man/summary-method.Rd | 2 man/testinfo.Rd | 2 man/vcov-method.Rd | 2 man/wald.Rd | 2 src/Makevars | 2 tests/testthat/test-09-mirt.model.R | 9 + 145 files changed, 885 insertions(+), 481 deletions(-)
Title: Miscellaneous Utilities and Functions
Description: Miscellaneous tools and functions,
including: generate descriptive statistics tables,
format output, visualize relations among variables or check
distributions, and generic functions for residual and
model diagnostics.
Author: Joshua F. Wiley [aut, cre]
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between JWileymisc versions 1.4.3 dated 2025-04-13 and 1.4.4 dated 2025-09-06
DESCRIPTION | 9 MD5 | 57 NAMESPACE | 502 +++---- NEWS.md | 14 R/data.R | 2 R/descriptives.R | 2 R/descriptives_helpers.R | 505 +++---- R/diagnostics.R | 2 R/geoms_themes.R | 130 - R/plotting.R | 1866 +++++++++++++-------------- R/scoring.R | 2 R/styler.R | 1654 ++++++++++++------------ R/utils.R | 1147 ++++++++-------- R/visual_acuity.R | 9 build/partial.rdb |binary build/vignette.rds |binary inst/doc/diagnostics-vignette.R | 240 +-- inst/doc/diagnostics-vignette.html | 1322 +++++++++---------- inst/doc/exploratory-vignette.R | 476 +++--- inst/doc/exploratory-vignette.html | 1996 ++++++++++++++--------------- inst/doc/model-test-vignette.R | 84 - inst/doc/model-test-vignette.html | 1004 +++++++------- man/VAObject-class.Rd | 10 man/aces_daily.Rd | 2 man/density_inversion.Rd |only man/styletests.Rd | 4 man/testDistribution.Rd | 338 ++-- tests/testthat/test-SEMSummary.R | 1 tests/testthat/test-descriptives-helpers.R | 170 +- tests/testthat/test-descriptives.R | 16 30 files changed, 5841 insertions(+), 5723 deletions(-)
Title: Fitting Deep Distributional Regression
Description: Allows for the specification of semi-structured deep distributional regression models which are fitted in a neural network as
proposed by Ruegamer et al. (2023) <doi:10.18637/jss.v105.i02>.
Predictors can be modeled using structured (penalized) linear effects, structured non-linear effects or using an unstructured deep network model.
Author: David Ruegamer [aut, cre],
Christopher Marquardt [ctb],
Laetitia Frost [ctb],
Florian Pfisterer [ctb],
Philipp Baumann [ctb],
Chris Kolb [ctb],
Lucas Kook [ctb]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between deepregression versions 2.3.1 dated 2025-09-01 and 2.3.2 dated 2025-09-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/python/utils/types.py | 7 ++++++- 3 files changed, 11 insertions(+), 6 deletions(-)
More information about deepregression at CRAN
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