Title: OECD PISA Datasets from 2000-2022 in an Easy-to-Use Format
Description: The Programme for International Student Assessment (PISA) is a global study conducted by the Organization for Economic Cooperation and Development (OECD) in member and non-member countries to assess educational systems by assessing 15-year-old school students academic performance in mathematics, science, and reading. This datasets contains information on their scores and other socioeconomic characteristics, information about their school and its infrastructure, as well as the countries that are taking part in the program.
Author: Kevin Wang [aut, cre],
Paul Yacobellis [aut],
Erika Siregar [aut],
Sarah Romanes [aut],
Kim Fitter [aut],
Giulio Valentino Dalla Riva [aut],
Dianne Cook [aut],
Nick Tierney [aut],
Priya Dingorkar [aut],
Shabarish Sai Subramanian [aut],
Guan Ru Chen [ [...truncated...]
Maintainer: Kevin Wang <kevinwangstats@gmail.com>
Diff between learningtower versions 1.0.1 dated 2023-02-18 and 1.1.0 dated 2024-12-21
learningtower-1.0.1/learningtower/data/datalist |only learningtower-1.1.0/learningtower/DESCRIPTION | 22 - learningtower-1.1.0/learningtower/LICENSE | 2 learningtower-1.1.0/learningtower/MD5 | 65 +-- learningtower-1.1.0/learningtower/NEWS.md |only learningtower-1.1.0/learningtower/R/data.R | 47 +- learningtower-1.1.0/learningtower/R/load_student.R | 11 learningtower-1.1.0/learningtower/R/zzz.R | 11 learningtower-1.1.0/learningtower/README.md | 181 ++++----- learningtower-1.1.0/learningtower/build/vignette.rds |binary learningtower-1.1.0/learningtower/data/countrycode.rda |binary learningtower-1.1.0/learningtower/data/school.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2000.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2003.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2006.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2009.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2012.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2015.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2018.rda |binary learningtower-1.1.0/learningtower/data/student_subset_2022.rda |only learningtower-1.1.0/learningtower/inst/CITATION |only learningtower-1.1.0/learningtower/inst/doc/learningtower_school.R | 47 +- learningtower-1.1.0/learningtower/inst/doc/learningtower_school.Rmd | 63 +-- learningtower-1.1.0/learningtower/inst/doc/learningtower_school.html | 118 +++--- learningtower-1.1.0/learningtower/inst/doc/learningtower_student.R | 52 -- learningtower-1.1.0/learningtower/inst/doc/learningtower_student.Rmd | 62 +-- learningtower-1.1.0/learningtower/inst/doc/learningtower_student.html | 194 +++++----- learningtower-1.1.0/learningtower/man/figures/readme.png |only learningtower-1.1.0/learningtower/man/load_student.Rd | 6 learningtower-1.1.0/learningtower/man/school.Rd | 12 learningtower-1.1.0/learningtower/man/student.Rd | 31 - learningtower-1.1.0/learningtower/tests/testthat/test-countrycode-col-types.R |only learningtower-1.1.0/learningtower/tests/testthat/test-merge.R |only learningtower-1.1.0/learningtower/tests/testthat/test-school-col-types.R |only learningtower-1.1.0/learningtower/tests/testthat/test-student-col-types.R |only learningtower-1.1.0/learningtower/tests/testthat/test-test-load.R | 10 learningtower-1.1.0/learningtower/vignettes/learningtower_school.Rmd | 63 +-- learningtower-1.1.0/learningtower/vignettes/learningtower_student.Rmd | 62 +-- 38 files changed, 549 insertions(+), 510 deletions(-)
Title: Self-Validated Ensemble Models with Elastic Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM, Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using Elastic Net regression via 'glmnet' (Friedman et al. <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). \\Code for the whole model test was taken from the supplementary material of Karl (2024). Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 1.2.1 dated 2024-12-07 and 1.3.0 dated 2024-12-21
SVEMnet-1.2.1/SVEMnet/inst/scripts |only SVEMnet-1.3.0/SVEMnet/DESCRIPTION | 10 SVEMnet-1.3.0/SVEMnet/MD5 | 36 SVEMnet-1.3.0/SVEMnet/NAMESPACE | 7 SVEMnet-1.3.0/SVEMnet/NEWS | 4 SVEMnet-1.3.0/SVEMnet/R/SVEMnet-package.R | 1 SVEMnet-1.3.0/SVEMnet/R/glmnet_with_cv.R |only SVEMnet-1.3.0/SVEMnet/R/svem_significance_test.R | 2 SVEMnet-1.3.0/SVEMnet/R/svem_significance_test_parallel.R | 27 SVEMnet-1.3.0/SVEMnet/R/svemnet_sim_mixture.R |only SVEMnet-1.3.0/SVEMnet/inst/doc/SVEMnet_vignette.R | 21 SVEMnet-1.3.0/SVEMnet/inst/doc/SVEMnet_vignette.Rmd | 37 SVEMnet-1.3.0/SVEMnet/inst/doc/SVEMnet_vignette.html | 847 ++++++++++- SVEMnet-1.3.0/SVEMnet/man/SVEMnet-package.Rd | 1 SVEMnet-1.3.0/SVEMnet/man/glmnet_with_cv.Rd |only SVEMnet-1.3.0/SVEMnet/man/predict_cv.Rd |only SVEMnet-1.3.0/SVEMnet/man/svem_significance_test.Rd | 2 SVEMnet-1.3.0/SVEMnet/man/svem_significance_test_parallel.Rd | 7 SVEMnet-1.3.0/SVEMnet/vignettes/SVEMnet_vignette.Rmd | 37 SVEMnet-1.3.0/SVEMnet/vignettes/figures/mixture_v2.png |only SVEMnet-1.3.0/SVEMnet/vignettes/svemnet_sim.R |only SVEMnet-1.3.0/SVEMnet/vignettes/svemnet_sim_identity.R |only SVEMnet-1.3.0/SVEMnet/vignettes/svemnet_sim_mixture_v2.R |only 23 files changed, 964 insertions(+), 75 deletions(-)
Title: Variable Table for Variable Documentation
Description: Automatically generates HTML variable documentation including variable names, labels, classes, value labels (if applicable), value ranges, and summary statistics. See the vignette "vtable" for a package overview.
Author: Nick Huntington-Klein [aut, cre]
Maintainer: Nick Huntington-Klein <nhuntington-klein@seattleu.edu>
Diff between vtable versions 1.4.7 dated 2024-10-17 and 1.4.8 dated 2024-12-21
DESCRIPTION | 6 +- MD5 | 44 +++++++------- NEWS.md | 4 + R/dftotable.R | 2 R/helpers.R | 6 +- R/sumtable.R | 26 +++++++- R/vtable.R | 63 ++++++++++++++++----- build/vignette.rds |binary inst/doc/dftotable.R | 98 ++++++++++++++++---------------- inst/doc/dftotable.html | 4 - inst/doc/labeltable.R | 28 ++++----- inst/doc/labeltable.html | 4 - inst/doc/sumtable.R | 98 ++++++++++++++++---------------- inst/doc/sumtable.html | 4 - inst/doc/vtable.html | 4 - inst/doc/vtablefunction.R | 128 +++++++++++++++++++++---------------------- inst/doc/vtablefunction.html | 4 - inst/doc/vtablehelpers.R | 18 +++--- inst/doc/vtablehelpers.html | 10 +-- man/dftoLaTeX.Rd | 2 man/sumtable.Rd | 2 man/vtable.Rd | 6 +- man/weighted.sd.Rd | 2 23 files changed, 312 insertions(+), 251 deletions(-)
Title: Smooth Survival Models, Including Generalized Survival Models
Description: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth <doi:10.1177/0962280216664760>. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects <doi:10.1002/sim.7451>, and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0 [...truncated...]
Author: Mark Clements [aut, cre],
Xing-Rong Liu [aut],
Benjamin Christoffersen [aut],
Paul Lambert [ctb],
Lasse Hjort Jakobsen [ctb],
Alessandro Gasparini [ctb],
Gordon Smyth [cph],
Patrick Alken [cph],
Simon Wood [cph],
Rhys Ulerich [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between rstpm2 versions 1.6.6 dated 2024-10-29 and 1.6.6.1 dated 2024-12-21
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ data/brcancer.rda |binary data/colon.rda |binary data/legendre.quadrature.rule.200.rda |binary data/popmort.rda |binary src/test-nmmin.cpp | 16 ++++++++-------- 7 files changed, 17 insertions(+), 17 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column and row wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>. c) Chatzipantsiou C., Dimitriadis M., Papadakis M. and Tsagris M. (2020). Extremely Efficient Permutation and Bootstrap Hypothesis Tests Using Hypothesis Tests Using R. Journal of Modern Applied Statistical Methods, 18(2), eP2898. <doi:10.48550/arXiv.1806.10947>.
Author: Manos Papadakis [aut, cre, cph],
Michail Tsagris [aut],
Marios Dimitriadis [ctb],
Stefanos Fafalios [aut],
Ioannis Tsamardinos [ctb],
Matteo Fasiolo [ctb],
Giorgos Borboudakis [ctb],
John Burkardt [ctb],
Changliang Zou [ctb],
Kleanthi Lakiotaki [ctb] [...truncated...]
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 2.1.0 dated 2023-11-09 and 2.1.2 dated 2024-12-21
Rfast-2.1.0/Rfast/R/F-tests.R |only Rfast-2.1.0/Rfast/src/calc_qpois_regs.cpp |only Rfast-2.1.0/Rfast/src/calc_qpois_regs.h |only Rfast-2.1.0/Rfast/src/total_dista.cpp |only Rfast-2.1.0/Rfast/src/total_dists.cpp |only Rfast-2.1.2/Rfast/DESCRIPTION | 10 Rfast-2.1.2/Rfast/MD5 | 160 - Rfast-2.1.2/Rfast/NAMESPACE | 2 Rfast-2.1.2/Rfast/NEWS.md | 45 Rfast-2.1.2/Rfast/R/Dist.R | 28 Rfast-2.1.2/Rfast/R/anova_related.R | 70 Rfast-2.1.2/Rfast/R/as_integer.R | 4 Rfast-2.1.2/Rfast/R/dista.R | 21 Rfast-2.1.2/Rfast/R/distance_cov_cor.R | 2 Rfast-2.1.2/Rfast/R/group.R | 13 Rfast-2.1.2/Rfast/R/mad2.R | 7 Rfast-2.1.2/Rfast/R/random_values_simulation.R | 6 Rfast-2.1.2/Rfast/R/real_mle.R | 6 Rfast-2.1.2/Rfast/R/regression_models.R | 69 Rfast-2.1.2/Rfast/R/sort_unique.R | 5 Rfast-2.1.2/Rfast/R/system_and_package.R | 60 Rfast-2.1.2/Rfast/R/ttest_related_functions.R | 34 Rfast-2.1.2/Rfast/README.md | 12 Rfast-2.1.2/Rfast/build/partial.rdb |binary Rfast-2.1.2/Rfast/inst/include/Rfast/Set.h |only Rfast-2.1.2/Rfast/inst/include/Rfast/matrix.hpp | 50 Rfast-2.1.2/Rfast/inst/include/Rfast/parallel.h | 2 Rfast-2.1.2/Rfast/inst/include/Rfast/templates.h | 21 Rfast-2.1.2/Rfast/inst/include/Rfast/types.hpp | 75 Rfast-2.1.2/Rfast/inst/include/Rfast/vector.hpp | 25 Rfast-2.1.2/Rfast/man/AddToNamespace.Rd | 7 Rfast-2.1.2/Rfast/man/Dist.Rd | 58 Rfast-2.1.2/Rfast/man/Lgamma.Rd | 2 Rfast-2.1.2/Rfast/man/Median.Rd | 2 Rfast-2.1.2/Rfast/man/Order.Rd | 2 Rfast-2.1.2/Rfast/man/Stack.Rd | 2 Rfast-2.1.2/Rfast/man/Table.Rd | 2 Rfast-2.1.2/Rfast/man/checkNamespace.Rd | 16 Rfast-2.1.2/Rfast/man/coeff.Rd | 2 Rfast-2.1.2/Rfast/man/colnormal.mle.Rd | 2 Rfast-2.1.2/Rfast/man/colrange.Rd | 2 Rfast-2.1.2/Rfast/man/cor.fsreg.Rd | 2 Rfast-2.1.2/Rfast/man/dista.Rd | 39 Rfast-2.1.2/Rfast/man/env.copy.Rd | 2 Rfast-2.1.2/Rfast/man/ftest.Rd | 2 Rfast-2.1.2/Rfast/man/gchi2Test.Rd | 4 Rfast-2.1.2/Rfast/man/geom.regs.Rd | 2 Rfast-2.1.2/Rfast/man/group.Rd | 10 Rfast-2.1.2/Rfast/man/is_integer.Rd | 7 Rfast-2.1.2/Rfast/man/iterator.Rd | 2 Rfast-2.1.2/Rfast/man/knn.cv.Rd | 5 Rfast-2.1.2/Rfast/man/macros/system.Rd | 54 Rfast-2.1.2/Rfast/man/mat.mult.Rd | 2 Rfast-2.1.2/Rfast/man/multinom.regs.Rd | 2 Rfast-2.1.2/Rfast/man/read.directory.Rd | 23 Rfast-2.1.2/Rfast/man/rowMins.Rd | 2 Rfast-2.1.2/Rfast/man/rvmf.Rd | 5 Rfast-2.1.2/Rfast/man/sort_unique.Rd | 7 Rfast-2.1.2/Rfast/man/sourceR.Rd | 11 Rfast-2.1.2/Rfast/man/ttests.Rd | 3 Rfast-2.1.2/Rfast/src/Coeff.cpp | 12 Rfast-2.1.2/Rfast/src/Coeff.h | 5 Rfast-2.1.2/Rfast/src/Dist.h | 83 Rfast-2.1.2/Rfast/src/add_to_namespace.cpp | 12 Rfast-2.1.2/Rfast/src/as_integer.cpp | 51 Rfast-2.1.2/Rfast/src/check.cpp | 110 - Rfast-2.1.2/Rfast/src/col_row_utilities.cpp | 9 Rfast-2.1.2/Rfast/src/col_row_utilities_p.cpp | 676 +++--- Rfast-2.1.2/Rfast/src/dista.cpp | 1171 ++++++++++-- Rfast-2.1.2/Rfast/src/dists.cpp | 2228 ++++++++++------------- Rfast-2.1.2/Rfast/src/each.cpp | 742 +++---- Rfast-2.1.2/Rfast/src/energy.cpp | 16 Rfast-2.1.2/Rfast/src/group.cpp | 1065 ++++++---- Rfast-2.1.2/Rfast/src/init.c | 66 Rfast-2.1.2/Rfast/src/maha_ex.cpp | 3 Rfast-2.1.2/Rfast/src/mn.cpp | 6 Rfast-2.1.2/Rfast/src/mn.h | 2 Rfast-2.1.2/Rfast/src/qpois.cpp | 37 Rfast-2.1.2/Rfast/src/read.cpp | 120 - Rfast-2.1.2/Rfast/src/rvmf.cpp | 450 ++-- Rfast-2.1.2/Rfast/src/sort_unique.cpp | 285 +- Rfast-2.1.2/Rfast/src/system_files.cpp | 79 Rfast-2.1.2/Rfast/src/system_files.h | 27 Rfast-2.1.2/Rfast/src/utilities.cpp | 518 ++--- 84 files changed, 4974 insertions(+), 3807 deletions(-)
Title: Estimation Statistics with Confidence Intervals
Description: A collection of functions and 'jamovi' module for the estimation approach to inferential statistics, the approach which emphasizes effect sizes, interval estimates, and meta-analysis. Nearly all functions are based on 'statpsych' and 'metafor'. This package is still under active development, and breaking changes are likely, especially with the plot and hypothesis test functions. Data sets are included for all examples from Cumming & Calin-Jageman (2024) <ISBN:9780367531508>.
Author: Robert Calin-Jageman [aut, cre, cph]
Maintainer: Robert Calin-Jageman <rcalinjageman@dom.edu>
Diff between esci versions 1.0.5 dated 2024-09-23 and 1.0.6 dated 2024-12-21
DESCRIPTION | 10 MD5 | 200 +++++---- NAMESPACE | 1 NEWS.md | 13 R/data.R | 5 R/esci-package.R | 1 R/estimate_mdiff_2x2_mixed.R | 455 ++++++++++++++++++++-- R/jamovimdiff2x2.b.R | 7 R/jamovimdiff2x2.h.R | 8 R/plot_meta.R | 8 R/tools_jamovi.R | 4 README.md | 2 build/stage23.rdb |binary data/data_effronraj_fakenews.rda |binary man/data_altruism_happiness.Rd | 76 +-- man/data_anchor_estimate_ma.Rd | 86 ++-- man/data_basol_badnews.Rd | 96 ++-- man/data_bem_psychic.Rd | 96 ++-- man/data_bodywellf.Rd | 48 +- man/data_bodywellfm.Rd | 48 +- man/data_bodywellm.Rd | 48 +- man/data_campus_involvement.Rd | 66 +-- man/data_chap_8_paired_ex_8.18.Rd | 54 +- man/data_clean_moral.Rd | 78 +-- man/data_college_survey_1.Rd | 90 ++-- man/data_college_survey_2.Rd | 76 +-- man/data_damischrcj.Rd | 52 +- man/data_effronraj_fakenews.Rd | 6 man/data_emotion_heartrate.Rd | 64 +-- man/data_exam_scores.Rd | 58 +- man/data_flag_priming_ma.Rd | 76 +-- man/data_gender_math_iat.Rd | 78 +-- man/data_gender_math_iat_ma.Rd | 84 ++-- man/data_halagappa.Rd | 82 +-- man/data_home_prices.Rd | 66 +-- man/data_kardas_expt_3.Rd | 86 ++-- man/data_kardas_expt_4.Rd | 94 ++-- man/data_labels_flavor.Rd | 78 +-- man/data_latimier_3groups.Rd | 84 ++-- man/data_latimier_prequiz.Rd | 56 +- man/data_latimier_quiz.Rd | 56 +- man/data_latimier_quiz_prequiz.Rd | 56 +- man/data_latimier_reread.Rd | 56 +- man/data_latimier_reread_prequiz.Rd | 56 +- man/data_latimier_reread_quiz.Rd | 56 +- man/data_macnamara_r_ma.Rd | 86 ++-- man/data_mccabemichael_brain.Rd | 130 +++--- man/data_mccabemichael_brain2.Rd | 68 +-- man/data_meditationbrain.Rd | 92 ++-- man/data_organicmoral.Rd | 92 ++-- man/data_penlaptop1.Rd | 52 +- man/data_powerperformance_ma.Rd | 94 ++-- man/data_rattanmotivation.Rd | 82 +-- man/data_religionsharing.Rd | 72 +-- man/data_religious_belief.Rd | 54 +- man/data_selfexplain.Rd | 78 +-- man/data_simmonscredibility.Rd | 120 ++--- man/data_sleep_beauty.Rd | 58 +- man/data_smithrecall.Rd | 54 +- man/data_stickgold.Rd | 74 +-- man/data_studystrategies.Rd | 82 +-- man/data_thomason_1.Rd | 60 +- man/data_videogameaggression.Rd | 74 +-- man/estimate_mdiff_2x2_mixed.Rd | 5 man/estimate_r.Rd | 312 +++++++-------- tests/testthat/_snaps |only tests/testthat/test_CI_diamond_ratio.R | 1 tests/testthat/test_CI_smd_ind_contrast.R | 1 tests/testthat/test_estimate_magnitude.R | 22 - tests/testthat/test_estimate_mdiff_2x2between.R | 58 -- tests/testthat/test_estimate_mdiff_2x2mixed.R | 240 +++++++++-- tests/testthat/test_estimate_mdiff_ind_contrast.R | 39 - tests/testthat/test_estimate_mdiff_one.R | 6 tests/testthat/test_estimate_mdiff_paired.R | 40 - tests/testthat/test_estimate_mdiff_two.R | 38 - tests/testthat/test_estimate_meta_d1.R | 9 tests/testthat/test_estimate_meta_d2.R | 15 tests/testthat/test_estimate_meta_mdiff_two.R | 62 -- tests/testthat/test_estimate_meta_mean.R | 35 - tests/testthat/test_estimate_meta_pdiff_two.R | 3 tests/testthat/test_estimate_meta_r.R | 1 tests/testthat/test_estimate_pdiff_ind_contrast.R | 10 tests/testthat/test_estimate_pdiff_one.R | 8 tests/testthat/test_estimate_pdiff_paired.R | 8 tests/testthat/test_estimate_pdiff_two.R | 8 tests/testthat/test_estimate_proportion.R | 6 tests/testthat/test_estimate_r.R | 7 tests/testthat/test_estimate_rdiff_two.R | 9 tests/testthat/test_overview.R | 2 tests/testthat/test_overview_nominal.R | 2 90 files changed, 2887 insertions(+), 2302 deletions(-)
Title: Analyzing and Visualizing Multidimensional Plant Traits
Description: Implements analytical methods for multidimensional plant traits, including Competitors-Stress tolerators-Ruderals strategy analysis using leaf traits, Leaf-Height-Seed strategy analysis, Niche Periodicity Table analysis, and Trait Network analysis. Provides functions for data analysis, visualization, and network metrics calculation. Methods are based on Grime (1974) <doi:10.1038/250026a0>, Pierce et al. (2017) <doi:10.1111/1365-2435.12882>, Westoby (1998) <doi:10.1023/A:1004327224729>, Yang et al. (2022) <doi:10.1016/j.foreco.2022.120540>, Winemiller et al. (2015) <doi:10.1111/ele.12462>, He et al. (2020) <doi:10.1016/j.tree.2020.06.003>.
Author: Yan He [aut, cre]
Maintainer: Yan He <heyan@njfu.edu.cn>
Diff between MultiTraits versions 0.1.0 dated 2024-11-26 and 0.2.0 dated 2024-12-21
MultiTraits-0.1.0/MultiTraits/data/WH.rda |only MultiTraits-0.1.0/MultiTraits/man/WH.Rd |only MultiTraits-0.1.0/MultiTraits/man/figures/1.png |only MultiTraits-0.1.0/MultiTraits/man/figures/2.png |only MultiTraits-0.1.0/MultiTraits/man/figures/3.png |only MultiTraits-0.1.0/MultiTraits/man/figures/4.png |only MultiTraits-0.1.0/MultiTraits/man/figures/5.png |only MultiTraits-0.2.0/MultiTraits/DESCRIPTION | 8 MultiTraits-0.2.0/MultiTraits/MD5 | 51 MultiTraits-0.2.0/MultiTraits/NAMESPACE | 8 MultiTraits-0.2.0/MultiTraits/NEWS.md |only MultiTraits-0.2.0/MultiTraits/R/CSR.R | 105 - MultiTraits-0.2.0/MultiTraits/R/LHS.R | 40 MultiTraits-0.2.0/MultiTraits/R/NPT.R | 40 MultiTraits-0.2.0/MultiTraits/R/TN.R | 77 MultiTraits-0.2.0/MultiTraits/R/data.R | 63 MultiTraits-0.2.0/MultiTraits/README.md | 173 + MultiTraits-0.2.0/MultiTraits/build/vignette.rds |binary MultiTraits-0.2.0/MultiTraits/inst/doc/MultiTraits_tutorial.R | 76 MultiTraits-0.2.0/MultiTraits/inst/doc/MultiTraits_tutorial.Rmd | 167 + MultiTraits-0.2.0/MultiTraits/inst/doc/MultiTraits_tutorial.html | 1005 +++++----- MultiTraits-0.2.0/MultiTraits/man/CSR_plot.Rd | 42 MultiTraits-0.2.0/MultiTraits/man/PFF.Rd | 8 MultiTraits-0.2.0/MultiTraits/man/TN.Rd | 15 MultiTraits-0.2.0/MultiTraits/man/TN_corr.Rd | 15 MultiTraits-0.2.0/MultiTraits/man/TN_metrics.Rd | 10 MultiTraits-0.2.0/MultiTraits/man/TN_plot.Rd | 21 MultiTraits-0.2.0/MultiTraits/man/figures/1.jpg |only MultiTraits-0.2.0/MultiTraits/man/figures/2.jpg |only MultiTraits-0.2.0/MultiTraits/man/figures/3.jpg |only MultiTraits-0.2.0/MultiTraits/man/figures/4.jpg |only MultiTraits-0.2.0/MultiTraits/man/figures/5.jpg |only MultiTraits-0.2.0/MultiTraits/vignettes/MultiTraits_tutorial.Rmd | 167 + 33 files changed, 1278 insertions(+), 813 deletions(-)
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.6.0 dated 2024-09-29 and 0.7.0 dated 2024-12-21
vcfppR-0.6.0/vcfppR/src/htslib-1.18 |only vcfppR-0.6.0/vcfppR/src/htslib-1.19.1 |only vcfppR-0.7.0/vcfppR/DESCRIPTION | 6 vcfppR-0.7.0/vcfppR/MD5 | 659 +++------- vcfppR-0.7.0/vcfppR/NEWS.md | 6 vcfppR-0.7.0/vcfppR/R/common.R | 10 vcfppR-0.7.0/vcfppR/R/vcf-compare.R | 9 vcfppR-0.7.0/vcfppR/R/vcf-tables.R | 1 vcfppR-0.7.0/vcfppR/README.md | 12 vcfppR-0.7.0/vcfppR/build/vignette.rds |binary vcfppR-0.7.0/vcfppR/cleanup | 4 vcfppR-0.7.0/vcfppR/cleanup.win | 4 vcfppR-0.7.0/vcfppR/configure |only vcfppR-0.7.0/vcfppR/configure.win |only vcfppR-0.7.0/vcfppR/inst/doc/concordance-of-two-vcf-files.html | 209 +-- vcfppR-0.7.0/vcfppR/inst/include/vcfpp.h | 13 vcfppR-0.7.0/vcfppR/man/vcfcomp.Rd | 8 vcfppR-0.7.0/vcfppR/src/Makevars | 18 vcfppR-0.7.0/vcfppR/src/Makevars.win | 15 vcfppR-0.7.0/vcfppR/src/htslib-1.21 |only vcfppR-0.7.0/vcfppR/src/vcf-reader.cpp | 4 21 files changed, 370 insertions(+), 608 deletions(-)
Title: 'calendR' Fork with Additional Features (Backwards Compatible)
Description: Fork of 'calendR' R package to generate ready to print
calendars with 'ggplot2' (see <https://r-coder.com/calendar-plot-r/>)
with additional features (backwards compatible).
'calendRio' provides a 'calendR()' function that serves as a drop-in
replacement for the upstream version but allows for additional
parameters unlocking extra functionality.
Author: Jose Carlos Soage Gonzalez [aut, cph],
Natalia Perez Veiga [aut, cph],
Marcel Schilling [aut, cph, cre]
Maintainer: Marcel Schilling <foss@mschilli.com>
Diff between calendRio versions 0.2.0 dated 2022-03-10 and 0.2.1 dated 2024-12-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/calendRio.R | 16 ++++++++++------ 3 files changed, 16 insertions(+), 12 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: The quantile varying coefficient model is robust to data heterogeneity,
outliers and heavy-tailed distributions in the response variable. In addition,
it can flexibly model dynamic patterns of regression coefficients through
nonparametric varying coefficient functions. In this package, we have implemented
the Gibbs samplers of the penalized Bayesian quantile varying coefficient model with
spike-and-slab priors [Zhou et al.(2023)]<doi:10.1016/j.csda.2023.107808> for efficient
Bayesian shrinkage estimation, variable selection and statistical inference. In particular,
valid Bayesian inferences on sparse quantile varying coefficient functions can be validated
on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms of the proposed
and alternative models can be efficiently performed by using the package.
Author: Cen Wu [aut, cre],
Kun Fan [aut],
Jie Ren [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.0.2 dated 2023-09-14 and 1.0.3 dated 2024-12-21
DESCRIPTION | 35 +++-- MD5 | 38 +++--- R/NonRobust.R |only R/RcppExports.R | 8 + R/Robust.R |only R/pqrBayes-package.R | 14 +- R/pqrBayes.R | 264 +++------------------------------------------ R/predict.pqrBayes.R | 219 ++++++++++++++++++------------------- R/select.VC.R | 160 +++++++++++++++------------ README.md | 38 ++++-- build/partial.rdb |binary man/data.Rd | 90 +++++++-------- man/pqrBayes-package.Rd | 121 ++++++++++---------- man/pqrBayes.Rd | 206 ++++++++++++++++++----------------- man/predict.pqrBayes.Rd | 108 +++++++++--------- man/print.VCselect.Rd | 48 ++++---- man/print.pqrBayes.Rd | 48 ++++---- man/print.pqrBayes.pred.Rd | 48 ++++---- man/select.VC.Rd | 99 ++++++++++------ src/BGL-SS0.cpp |only src/BGL.cpp |only src/RcppExports.cpp | 59 ++++++++++ 22 files changed, 762 insertions(+), 841 deletions(-)
Title: Lattice Options and Add-Ins
Description: Various plots and functions that make use of the lattice/trellis plotting framework.
The plots, which include loaPlot(), loaMapPlot() and trianglePlot(), and use panelPal(), a function that
extends 'lattice' and 'hexbin' package methods to automate plot subscript and panel-to-panel
and panel-to-key synchronization/management.
Author: Karl Ropkins [aut, cre]
Maintainer: Karl Ropkins <karl.ropkins@gmail.com>
Diff between loa versions 0.3.0.1 dated 2024-12-13 and 0.3.1.1 dated 2024-12-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 8 ++++++++ R/specialist.panels.01.R | 21 +++++++++++++-------- R/specialist.panels.03.zcase.glyphs.R | 4 ++-- man/2.1.specialist.panels.Rd | 2 +- man/loa-package.Rd | 4 ++-- 7 files changed, 36 insertions(+), 23 deletions(-)