Title: Identify Script Name
Description: Identifies the name of the current script
in a variety of contexts, e.g. interactively or
when sourced. Attempts to support RStudio environment.
Based on <https://stackoverflow.com/a/32016824/2292993>
and <https://stackoverflow.com/a/35842176/2292993>.
Author: Tim Bergsma [aut, cre]
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between script versions 0.1.1 dated 2023-06-28 and 0.1.3 dated 2024-11-27
DESCRIPTION | 16 ++++++++++------ MD5 | 6 +++--- NAMESPACE | 1 + R/script.R | 9 +++++++++ 4 files changed, 23 insertions(+), 9 deletions(-)
Title: Unified Framework for Numerical Optimizers
Description: Provides a unified object-oriented framework for numerical
optimizers in R. Allows for both minimization and maximization with any
optimizer, optimization over more than one function argument, measuring of
computation time, setting a time limit for long optimization tasks.
Author: Lennart Oelschlaeger [aut, cre]
,
Marius Oetting [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between optimizeR versions 1.1.1 dated 2024-06-19 and 1.1.2 dated 2024-11-27
DESCRIPTION | 10 +++++----- MD5 | 10 +++++++--- NAMESPACE | 1 + NEWS.md | 6 +++++- R/parameter_spaces.R |only man/ParameterSpaces.Rd |only tests/testthat/_snaps/parameter_spaces.md |only tests/testthat/test-parameter_spaces.R |only 8 files changed, 18 insertions(+), 9 deletions(-)
Title: Utilities for Developing Data Science Software
Description: Some general helper functions that I (and maybe others) find useful
when developing data science software.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between oeli versions 0.7.0 dated 2024-10-16 and 0.7.1 dated 2024-11-27
oeli-0.7.0/oeli/R/renv_development_packages.R |only oeli-0.7.0/oeli/man/renv_development_packages.Rd |only oeli-0.7.1/oeli/DESCRIPTION | 10 - oeli-0.7.1/oeli/MD5 | 69 +++++----- oeli-0.7.1/oeli/NAMESPACE | 4 oeli-0.7.1/oeli/NEWS.md | 12 + oeli-0.7.1/oeli/R/cholesky_root.R | 8 + oeli-0.7.1/oeli/R/covariance_differencing.R | 36 ++++- oeli-0.7.1/oeli/R/input_check_response.R | 63 +++++++-- oeli-0.7.1/oeli/R/map_indices.R |only oeli-0.7.1/oeli/R/oeli-package.R | 1 oeli-0.7.1/oeli/R/package_logo.R | 35 ++--- oeli-0.7.1/oeli/man/Dictionary.Rd | 1 oeli-0.7.1/oeli/man/Storage.Rd | 1 oeli-0.7.1/oeli/man/check_numeric_vector.Rd | 1 oeli-0.7.1/oeli/man/check_probability_vector.Rd | 1 oeli-0.7.1/oeli/man/chunk_vector.Rd | 1 oeli-0.7.1/oeli/man/diff_cov.Rd | 16 ++ oeli-0.7.1/oeli/man/identical_structure.Rd | 1 oeli-0.7.1/oeli/man/input_check_response.Rd | 40 ++++- oeli-0.7.1/oeli/man/insert_vector_entry.Rd | 1 oeli-0.7.1/oeli/man/map_indices.Rd |only oeli-0.7.1/oeli/man/match_arg.Rd | 1 oeli-0.7.1/oeli/man/match_numerics.Rd | 1 oeli-0.7.1/oeli/man/package_logo.Rd | 18 +- oeli-0.7.1/oeli/man/permutations.Rd | 1 oeli-0.7.1/oeli/man/print_data.frame.Rd | 1 oeli-0.7.1/oeli/man/print_matrix.Rd | 1 oeli-0.7.1/oeli/man/split_vector_at.Rd | 1 oeli-0.7.1/oeli/man/subsets.Rd | 1 oeli-0.7.1/oeli/man/system_information.Rd | 1 oeli-0.7.1/oeli/man/unexpected_error.Rd | 1 oeli-0.7.1/oeli/man/user_confirm.Rd | 1 oeli-0.7.1/oeli/man/vector_occurrence.Rd | 1 oeli-0.7.1/oeli/tests/testthat/test-cholesky_root.R | 5 oeli-0.7.1/oeli/tests/testthat/test-covariance_differencing.R | 9 + oeli-0.7.1/oeli/tests/testthat/test-input_check_response.R | 11 + oeli-0.7.1/oeli/tests/testthat/test-map_indices.R |only 38 files changed, 249 insertions(+), 106 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.4.0 dated 2024-11-26 and 1.4.1 dated 2024-11-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/OptimizerBatchIrace.R | 21 +++++++++++++-------- tests/testthat/helper.R | 17 +++++++++++------ tests/testthat/test_OptimizerIrace.R | 4 ++-- 6 files changed, 39 insertions(+), 25 deletions(-)
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS)
implemented by the MICE algorithm as described in Van Buuren and
Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has
its own imputation model. Built-in imputation models are provided for
continuous data (predictive mean matching, normal), binary data (logistic
regression), unordered categorical data (polytomous logistic regression)
and ordered categorical data (proportional odds). MICE can also impute
continuous two-level data (normal model, pan, second-level variables).
Passive imputation can be used to maintain consistency between variables.
Various diagnostic plots are available to inspect the quality of the
imputations.
Author: Stef van Buuren [aut, cre],
Karin Groothuis-Oudshoorn [aut],
Gerko Vink [ctb],
Rianne Schouten [ctb],
Alexander Robitzsch [ctb],
Patrick Rockenschaub [ctb],
Lisa Doove [ctb],
Shahab Jolani [ctb],
Margarita Moreno-Betancur [ctb],
Ian White [ctb],
Phil [...truncated...]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between mice versions 3.16.0 dated 2023-06-05 and 3.17.0 dated 2024-11-27
mice-3.16.0/mice/R/bwplot.R |only mice-3.16.0/mice/R/densityplot.R |only mice-3.16.0/mice/R/plot.R |only mice-3.16.0/mice/R/stripplot.R |only mice-3.16.0/mice/R/xyplot.R |only mice-3.16.0/mice/man/mads-class.Rd |only mice-3.16.0/mice/man/mids-class.Rd |only mice-3.16.0/mice/man/mira-class.Rd |only mice-3.16.0/mice/man/plot.mids.Rd |only mice-3.16.0/mice/man/print.mads.Rd |only mice-3.16.0/mice/src/Makevars |only mice-3.16.0/mice/src/Makevars.win |only mice-3.17.0/mice/DESCRIPTION | 25 mice-3.17.0/mice/MD5 | 270 ++++---- mice-3.17.0/mice/NAMESPACE | 25 mice-3.17.0/mice/NEWS.md | 285 ++++++--- mice-3.17.0/mice/R/D1.R | 3 mice-3.17.0/mice/R/D3.R | 3 mice-3.17.0/mice/R/ampute.R | 50 - mice-3.17.0/mice/R/ampute.continuous.R | 3 mice-3.17.0/mice/R/ampute.default.R | 1 mice-3.17.0/mice/R/ampute.discrete.R | 1 mice-3.17.0/mice/R/ampute.mcar.R | 1 mice-3.17.0/mice/R/anova.R | 5 mice-3.17.0/mice/R/as.R | 51 - mice-3.17.0/mice/R/auxiliary.R | 13 mice-3.17.0/mice/R/blocks.R | 14 mice-3.17.0/mice/R/bwplot.mads.R | 10 mice-3.17.0/mice/R/bwplot.mids.R |only mice-3.17.0/mice/R/cbind.R | 93 +- mice-3.17.0/mice/R/complete.R | 37 - mice-3.17.0/mice/R/convergence.R | 1 mice-3.17.0/mice/R/densityplot.mids.R |only mice-3.17.0/mice/R/df.residual.R | 5 mice-3.17.0/mice/R/edit.setup.R | 4 mice-3.17.0/mice/R/filter.R | 24 mice-3.17.0/mice/R/formula.R | 12 mice-3.17.0/mice/R/futuremice.R | 4 mice-3.17.0/mice/R/get.df.R | 37 - mice-3.17.0/mice/R/getfit.R | 4 mice-3.17.0/mice/R/ibind.R | 31 mice-3.17.0/mice/R/imports.R | 12 mice-3.17.0/mice/R/initialize.chain.R | 7 mice-3.17.0/mice/R/initialize.imp.R | 2 mice-3.17.0/mice/R/internal.R | 4 mice-3.17.0/mice/R/lm.R | 12 mice-3.17.0/mice/R/mads.R | 135 +++- mice-3.17.0/mice/R/mcar.R | 3 mice-3.17.0/mice/R/mdc.R | 6 mice-3.17.0/mice/R/method.R | 29 mice-3.17.0/mice/R/mice-package.R | 14 mice-3.17.0/mice/R/mice.R | 25 mice-3.17.0/mice/R/mice.impute.cart.R | 8 mice-3.17.0/mice/R/mice.impute.lda.R | 2 mice-3.17.0/mice/R/mice.impute.midastouch.R | 5 mice-3.17.0/mice/R/mice.impute.pmm.R | 103 ++- mice-3.17.0/mice/R/mice.impute.rf.R | 46 + mice-3.17.0/mice/R/mice.mids.R | 65 +- mice-3.17.0/mice/R/mids.R | 345 +++++++++-- mice-3.17.0/mice/R/mipo.R | 65 +- mice-3.17.0/mice/R/mira.R | 66 +- mice-3.17.0/mice/R/parlmice.R | 2 mice-3.17.0/mice/R/pool.R | 71 -- mice-3.17.0/mice/R/pool.table.R |only mice-3.17.0/mice/R/pool.vector.R |only mice-3.17.0/mice/R/predictorMatrix.R | 7 mice-3.17.0/mice/R/print.R | 63 -- mice-3.17.0/mice/R/quickpred.R | 8 mice-3.17.0/mice/R/rbind.R | 40 - mice-3.17.0/mice/R/sampler.R | 36 - mice-3.17.0/mice/R/stripplot.mids.R |only mice-3.17.0/mice/R/summary.R | 38 - mice-3.17.0/mice/R/tidiers.R | 6 mice-3.17.0/mice/R/walking.R | 2 mice-3.17.0/mice/R/windspeed.R | 4 mice-3.17.0/mice/R/with.R | 11 mice-3.17.0/mice/R/xyplot.mads.R | 13 mice-3.17.0/mice/R/xyplot.mids.R |only mice-3.17.0/mice/README.md | 20 mice-3.17.0/mice/build/partial.rdb |binary mice-3.17.0/mice/man/ampute.Rd | 27 mice-3.17.0/mice/man/ampute.continuous.Rd | 2 mice-3.17.0/mice/man/as.mids.Rd | 13 mice-3.17.0/mice/man/as.mira.Rd | 2 mice-3.17.0/mice/man/bwplot.mads.Rd | 7 mice-3.17.0/mice/man/bwplot.mids.Rd | 37 - mice-3.17.0/mice/man/complete.mids.Rd | 14 mice-3.17.0/mice/man/construct.blocks.Rd | 2 mice-3.17.0/mice/man/densityplot.mids.Rd | 32 - mice-3.17.0/mice/man/futuremice.Rd | 2 mice-3.17.0/mice/man/getfit.Rd | 2 mice-3.17.0/mice/man/glm.mids.Rd | 2 mice-3.17.0/mice/man/lm.mids.Rd | 2 mice-3.17.0/mice/man/mads.Rd |only mice-3.17.0/mice/man/make.blocks.Rd | 6 mice-3.17.0/mice/man/mdc.Rd | 6 mice-3.17.0/mice/man/mice.Rd | 48 + mice-3.17.0/mice/man/mice.impute.cart.Rd | 10 mice-3.17.0/mice/man/mice.impute.lasso.logreg.Rd | 4 mice-3.17.0/mice/man/mice.impute.lasso.norm.Rd | 4 mice-3.17.0/mice/man/mice.impute.lasso.select.logreg.Rd | 4 mice-3.17.0/mice/man/mice.impute.lasso.select.norm.Rd | 4 mice-3.17.0/mice/man/mice.impute.lda.Rd | 6 mice-3.17.0/mice/man/mice.impute.logreg.Rd | 2 mice-3.17.0/mice/man/mice.impute.logreg.boot.Rd | 2 mice-3.17.0/mice/man/mice.impute.mean.Rd | 4 mice-3.17.0/mice/man/mice.impute.midastouch.Rd | 9 mice-3.17.0/mice/man/mice.impute.mnar.Rd | 4 mice-3.17.0/mice/man/mice.impute.mpmm.Rd | 4 mice-3.17.0/mice/man/mice.impute.norm.Rd | 2 mice-3.17.0/mice/man/mice.impute.norm.boot.Rd | 4 mice-3.17.0/mice/man/mice.impute.norm.nob.Rd | 4 mice-3.17.0/mice/man/mice.impute.norm.predict.Rd | 4 mice-3.17.0/mice/man/mice.impute.pmm.Rd | 46 + mice-3.17.0/mice/man/mice.impute.polr.Rd | 4 mice-3.17.0/mice/man/mice.impute.polyreg.Rd | 4 mice-3.17.0/mice/man/mice.impute.quadratic.Rd | 4 mice-3.17.0/mice/man/mice.impute.rf.Rd | 24 mice-3.17.0/mice/man/mice.impute.ri.Rd | 4 mice-3.17.0/mice/man/mice.mids.Rd | 43 - mice-3.17.0/mice/man/mids.Rd |only mice-3.17.0/mice/man/mipo.Rd | 4 mice-3.17.0/mice/man/mira.Rd |only mice-3.17.0/mice/man/parlmice.Rd | 2 mice-3.17.0/mice/man/pool.table.Rd |only mice-3.17.0/mice/man/print.Rd | 19 mice-3.17.0/mice/man/reexports.Rd | 4 mice-3.17.0/mice/man/stripplot.mids.Rd | 36 - mice-3.17.0/mice/man/summary.Rd | 20 mice-3.17.0/mice/man/walking.Rd | 2 mice-3.17.0/mice/man/windspeed.Rd | 4 mice-3.17.0/mice/man/with.mids.Rd | 5 mice-3.17.0/mice/man/xyplot.mads.Rd | 10 mice-3.17.0/mice/man/xyplot.mids.Rd | 28 mice-3.17.0/mice/tests/testthat/test-ampute.R | 4 mice-3.17.0/mice/tests/testthat/test-as.mids.R | 40 - mice-3.17.0/mice/tests/testthat/test-complete.R | 15 mice-3.17.0/mice/tests/testthat/test-mice-initialize.R | 2 mice-3.17.0/mice/tests/testthat/test-mice.impute.2l.bin.R | 8 mice-3.17.0/mice/tests/testthat/test-mice.impute.durr.norm.R | 38 + mice-3.17.0/mice/tests/testthat/test-mice.impute.pmm.R | 83 ++ mice-3.17.0/mice/tests/testthat/test-mice.impute.rf.R | 1 mice-3.17.0/mice/tests/testthat/test-parlmice.R | 11 mice-3.17.0/mice/tests/testthat/test-pool.R | 4 mice-3.17.0/mice/tests/testthat/test-pool.vector.R |only mice-3.17.0/mice/tests/testthat/test-quickpred.R |only mice-3.17.0/mice/tests/testthat/test-rbind.R | 3 mice-3.17.0/mice/tests/testthat/test-tidiers.R | 10 148 files changed, 1832 insertions(+), 1212 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel Sjoberg [aut, cre],
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.2.1 dated 2024-09-03 and 0.2.2 dated 2024-11-27
DESCRIPTION | 10 MD5 | 293 +++++++------- NAMESPACE | 2 NEWS.md | 10 R/add_total_n.survey.design.R | 2 R/ard_aod_wald_test.R | 5 R/ard_attributes.survey.design.R | 2 R/ard_car_anova.R | 4 R/ard_car_vif.R | 4 R/ard_categorical.survey.design.R | 7 R/ard_categorical_ci.R | 6 R/ard_categorical_ci.survey.design.R | 7 R/ard_continuous.survey.design.R | 114 +++++ R/ard_continuous_ci.R | 2 R/ard_continuous_ci.survey.design.R | 5 R/ard_dichotomous.survey.design.R | 4 R/ard_effectsize_cohens_d.R | 8 R/ard_effectsize_hedges_g.R | 8 R/ard_emmeans_mean_difference.R | 4 R/ard_missing.survey.design.R | 4 R/ard_regression.R | 4 R/ard_regression_basic.R | 4 R/ard_smd_smd.R | 4 R/ard_stats_anova.R | 6 R/ard_stats_aov.R | 4 R/ard_stats_chisq_test.R | 4 R/ard_stats_fisher_test.R | 4 R/ard_stats_kruskal_test.R | 4 R/ard_stats_mcnemar_test.R | 8 R/ard_stats_mood_test.R | 6 R/ard_stats_oneway_test.R | 4 R/ard_stats_poisson_test.R | 6 R/ard_stats_prop_test.R | 4 R/ard_stats_t_test.R | 8 R/ard_stats_t_test_onesample.R | 4 R/ard_stats_wilcox_test.R | 8 R/ard_stats_wilcox_test_onesample.R | 4 R/ard_survey_svychisq.R | 4 R/ard_survey_svyranktest.R | 4 R/ard_survey_svyttest.R | 4 R/ard_survival_survdiff.R | 4 R/ard_survival_survfit.R | 109 ++++- R/ard_survival_survfit_diff.R | 4 R/construction_helpers.R | 6 R/import-standalone-check_pkg_installed.R | 78 +-- R/import-standalone-checks.R | 145 ++++++ R/import-standalone-cli_call_env.R | 4 R/import-standalone-forcats.R | 3 R/import-standalone-stringr.R | 17 R/import-standalone-tibble.R | 3 R/proportion_ci.R | 6 man/ard_aod_wald_test.Rd | 2 man/ard_attributes.Rd | 2 man/ard_car_anova.Rd | 2 man/ard_car_vif.Rd | 2 man/ard_categorical.survey.design.Rd | 4 man/ard_categorical_ci.Rd | 2 man/ard_categorical_ci.survey.design.Rd | 2 man/ard_continuous.survey.design.Rd | 2 man/ard_continuous_ci.Rd | 2 man/ard_continuous_ci.survey.design.Rd | 2 man/ard_dichotomous.survey.design.Rd | 4 man/ard_effectsize_cohens_d.Rd | 2 man/ard_effectsize_hedges_g.Rd | 2 man/ard_emmeans_mean_difference.Rd | 2 man/ard_missing.survey.design.Rd | 4 man/ard_regression.Rd | 2 man/ard_regression_basic.Rd | 2 man/ard_smd_smd.Rd | 2 man/ard_stats_anova.Rd | 2 man/ard_stats_aov.Rd | 2 man/ard_stats_chisq_test.Rd | 2 man/ard_stats_fisher_test.Rd | 2 man/ard_stats_kruskal_test.Rd | 2 man/ard_stats_mcnemar_test.Rd | 2 man/ard_stats_mood_test.Rd | 2 man/ard_stats_oneway_test.Rd | 2 man/ard_stats_poisson_test.Rd | 2 man/ard_stats_prop_test.Rd | 2 man/ard_stats_t_test.Rd | 2 man/ard_stats_t_test_onesample.Rd | 2 man/ard_stats_wilcox_test.Rd | 2 man/ard_stats_wilcox_test_onesample.Rd | 2 man/ard_survey_svychisq.Rd | 2 man/ard_survey_svyranktest.Rd | 2 man/ard_survey_svyttest.Rd | 2 man/ard_survival_survdiff.Rd | 2 man/ard_survival_survfit.Rd | 73 +++ man/ard_survival_survfit_diff.Rd | 2 man/ard_total_n.survey.design.Rd | 2 man/construction_helpers.Rd | 2 man/dot-format_cohens_d_results.Rd | 2 man/dot-format_hedges_g_results.Rd | 2 man/dot-format_mcnemartest_results.Rd | 2 man/dot-format_moodtest_results.Rd | 2 man/dot-format_poissontest_results.Rd | 2 man/dot-format_survfit_results.Rd | 2 man/dot-format_ttest_results.Rd | 2 man/dot-format_wilcoxtest_results.Rd | 2 man/dot-process_survfit_probs.Rd | 6 man/dot-process_survfit_time.Rd | 6 man/proportion_ci.Rd | 2 tests/testthat/_snaps/ard_attributes.survey.design.md | 13 tests/testthat/_snaps/ard_categorical_ci.survey.design.md | 48 +- tests/testthat/_snaps/ard_regression.md | 12 tests/testthat/_snaps/ard_survival_survfit.md | 89 ++++ tests/testthat/test-ard_aod_wald_test.R | 2 tests/testthat/test-ard_attributes.survey.design.R | 3 tests/testthat/test-ard_car_anova.R | 2 tests/testthat/test-ard_car_vif.R | 2 tests/testthat/test-ard_categorical.survey.design.R | 48 ++ tests/testthat/test-ard_categorical_ci.data.frame.R |only tests/testthat/test-ard_categorical_ci.survey.design.R | 33 + tests/testthat/test-ard_continuous.survey.design.R | 29 + tests/testthat/test-ard_continuous_ci.data.frame.R | 6 tests/testthat/test-ard_continuous_ci.survey.design.R | 13 tests/testthat/test-ard_dichotomous.survey.design.R | 2 tests/testthat/test-ard_effectsize_cohens_d.R | 2 tests/testthat/test-ard_effectsize_hedges_g.R | 2 tests/testthat/test-ard_emmeans_mean_difference.R | 2 tests/testthat/test-ard_missing.survey.design.R | 2 tests/testthat/test-ard_proportion_ci.R | 2 tests/testthat/test-ard_regression.R | 17 tests/testthat/test-ard_regression_basic.R | 2 tests/testthat/test-ard_smd_smd.R | 4 tests/testthat/test-ard_stats_anova.R | 2 tests/testthat/test-ard_stats_aov.R | 2 tests/testthat/test-ard_stats_chisq_test.R | 2 tests/testthat/test-ard_stats_fisher_test.R | 2 tests/testthat/test-ard_stats_kruskal_test.R | 2 tests/testthat/test-ard_stats_mcnemar_test.R | 2 tests/testthat/test-ard_stats_mood_test.R | 2 tests/testthat/test-ard_stats_oneway_test.R | 2 tests/testthat/test-ard_stats_poisson_test.R | 2 tests/testthat/test-ard_stats_prop_test.R | 2 tests/testthat/test-ard_stats_t_test.R | 2 tests/testthat/test-ard_stats_t_test_onesample.R | 2 tests/testthat/test-ard_stats_wilcox_test.R | 2 tests/testthat/test-ard_stats_wilcox_test_onesample.R | 2 tests/testthat/test-ard_survey_svychisq.R | 2 tests/testthat/test-ard_survey_svyranktest.R | 2 tests/testthat/test-ard_survey_svyttest.R | 2 tests/testthat/test-ard_survival_survdiff.R | 2 tests/testthat/test-ard_survival_survfit.R | 83 +++ tests/testthat/test-ard_survival_survfit_diff.R | 2 tests/testthat/test-ard_total_n.survey.design.R | 2 tests/testthat/test-construction_helpers.R | 2 tests/testthat/test-proportion_ci.R | 2 148 files changed, 1145 insertions(+), 482 deletions(-)
Title: Nested Cross-Validation with 'glmnet' and 'caret'
Description: Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package <doi:10.1093/bioadv/vbad048>. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.
Author: Myles Lewis [aut, cre] ,
Athina Spiliopoulou [aut] ,
Cankut Cubuk [ctb] ,
Katriona Goldmann [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between nestedcv versions 0.7.10 dated 2024-08-16 and 0.7.12 dated 2024-11-27
DESCRIPTION | 8 MD5 | 51 - NAMESPACE | 14 NEWS.md | 13 R/directionality.R | 1 R/predSummary.R | 12 R/repeatcv.R | 82 +- R/shap.R | 3 R/slim.R |only R/varImp.R | 197 ++++++- inst/doc/nestedcv.R | 1 inst/doc/nestedcv.Rmd | 1 inst/doc/nestedcv.html | 128 ++-- inst/doc/nestedcv_hsstan.Rmd | 5 inst/doc/nestedcv_hsstan.html | 1166 ------------------------------------------ inst/doc/nestedcv_shap.R | 10 inst/doc/nestedcv_shap.Rmd | 21 inst/doc/nestedcv_shap.html | 30 - man/plot_shap_beeswarm.Rd | 3 man/plot_var_ranks.Rd |only man/plot_var_stability.Rd | 3 man/predSummary.Rd | 6 man/repeatcv.Rd | 13 man/slim.Rd |only man/var_stability.Rd | 31 - vignettes/nestedcv.Rmd | 1 vignettes/nestedcv_hsstan.Rmd | 5 vignettes/nestedcv_shap.Rmd | 21 28 files changed, 465 insertions(+), 1361 deletions(-)
Title: Test and Item Analysis via Shiny
Description: Package including functions and interactive shiny application
for the psychometric analysis of educational tests, psychological
assessments, health-related and other types of multi-item
measurements, or ratings from multiple raters.
Author: Patricia Martinkova [aut, cre],
Adela Hladka [aut],
Jan Netik [aut],
Ondrej Leder [ctb],
Jakub Houdek [ctb],
Lubomir Stepanek [ctb],
Tomas Jurica [ctb],
Jana Vorlickova [ctb]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between ShinyItemAnalysis versions 1.5.1 dated 2024-04-24 and 1.5.2 dated 2024-11-27
ShinyItemAnalysis-1.5.1/ShinyItemAnalysis/inst/ShinyItemAnalysis/hexbin_alpha.png |only ShinyItemAnalysis-1.5.1/ShinyItemAnalysis/inst/ShinyItemAnalysis/www/math_in_tables.js |only ShinyItemAnalysis-1.5.1/ShinyItemAnalysis/inst/ShinyItemAnalysis/www/style.css |only ShinyItemAnalysis-1.5.1/ShinyItemAnalysis/inst/ShinyItemAnalysis/www/test.js |only ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/DESCRIPTION | 12 +- ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/MD5 | 32 ++---- ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/NEWS.md | 10 +- ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/R/blis.R | 47 +++++----- ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/R/plot_corr.R | 2 ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/README.md | 10 +- ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/build/partial.rdb |binary ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/inst/ShinyItemAnalysis/reporthtml.Rmd | 8 + ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/inst/ShinyItemAnalysis/reportpdf.Rmd | 6 + ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/inst/ShinyItemAnalysis/server/DIF.R | 8 - ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/inst/ShinyItemAnalysis/ui.R | 2 ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/inst/ShinyItemAnalysis/ui/uiAbout.R | 6 - ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/man/coef-BlisClass-method.Rd | 2 ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/man/fit_blis.Rd | 14 ++ ShinyItemAnalysis-1.5.2/ShinyItemAnalysis/man/plot_corr.Rd | 2 19 files changed, 99 insertions(+), 62 deletions(-)
More information about ShinyItemAnalysis at CRAN
Permanent link
Title: Some Useful Functions for Statistics and Visualization
Description: Offers a range of utilities and functions for everyday programming tasks. 1.Data Manipulation. Such as grouping
and merging, column splitting, and character expansion. 2.File Handling. Read and convert files in popular
formats. 3.Plotting Assistance. Helpful utilities for generating color palettes, validating color formats, and
adding transparency. 4.Statistical Analysis. Includes functions for pairwise comparisons and multiple testing
corrections, enabling perform statistical analyses with ease. 5.Graph Plotting, Provides efficient tools for
creating doughnut plot and multi-layered doughnut plot; Venn diagrams, including traditional Venn diagrams,
upset plots, and flower plots; Simplified functions for creating stacked bar plots, or a box plot with
alphabets group for multiple comparison group.
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <pengchen2001@zju.edu.cn>
Diff between pcutils versions 0.2.6 dated 2024-06-25 and 0.2.7 dated 2024-11-27
DESCRIPTION | 37 +++--- MD5 | 31 +++-- NAMESPACE | 5 NEWS.md | 11 + R/l_tools.R | 50 +++++++- R/plots.R | 99 ++++++++++++++-- R/project.R | 72 ++++++++++++ R/statistics.R | 282 ++++++++++++++++++++++++++++++++++++++--------- man/distance2df.Rd |only man/download2.Rd | 4 man/group_test.Rd | 11 + man/guolv.Rd | 4 man/hebing2.Rd |only man/igraph_translator.Rd |only man/list_to_dataframe.Rd |only man/make_py_pkg.Rd |only man/my_lm.Rd | 12 +- man/read.file.Rd | 2 man/venn.Rd | 3 19 files changed, 516 insertions(+), 107 deletions(-)
Title: Core Functions for Data Quality Assessment
Description: Perform data quality assessment ('DQA') of electronic health
records ('EHR'). Publication: Kapsner et al. (2021)
<doi:10.1055/s-0041-1733847>.
Author: Lorenz A. Kapsner [cre, aut] ,
Jonathan M. Mang [aut] ,
Helene Koester [ctb],
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen [cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between DQAstats versions 0.3.5 dated 2024-06-05 and 0.3.6 dated 2024-11-27
DQAstats-0.3.5/DQAstats/man/create_markdown.Rd |only DQAstats-0.3.6/DQAstats/DESCRIPTION | 10 DQAstats-0.3.6/DQAstats/MD5 | 117 DQAstats-0.3.6/DQAstats/NAMESPACE | 1 DQAstats-0.3.6/DQAstats/R/DQA.R | 1078 ++--- DQAstats-0.3.6/DQAstats/R/calc_cat_stats.R | 2 DQAstats-0.3.6/DQAstats/R/calc_counts.R | 316 - DQAstats-0.3.6/DQAstats/R/calc_description.R | 2 DQAstats-0.3.6/DQAstats/R/calc_stats.R | 2 DQAstats-0.3.6/DQAstats/R/categorical_analysis.R | 104 DQAstats-0.3.6/DQAstats/R/completeness.R | 358 - DQAstats-0.3.6/DQAstats/R/conformance.R | 1528 +++---- DQAstats-0.3.6/DQAstats/R/count_uniques.R | 160 DQAstats-0.3.6/DQAstats/R/create_pdf_report.R | 146 DQAstats-0.3.6/DQAstats/R/dataloading.R | 1961 +++++----- DQAstats-0.3.6/DQAstats/R/datamap.R | 392 - DQAstats-0.3.6/DQAstats/R/datetime_restrictions.R | 1242 +++--- DQAstats-0.3.6/DQAstats/R/descriptive_results.R | 580 +- DQAstats-0.3.6/DQAstats/R/difference_check.R | 420 +- DQAstats-0.3.6/DQAstats/R/etl.R | 2 DQAstats-0.3.6/DQAstats/R/export_results.R | 568 +- DQAstats-0.3.6/DQAstats/R/extensive_summary.R | 112 DQAstats-0.3.6/DQAstats/R/format_value_conformance_results.R | 2 DQAstats-0.3.6/DQAstats/R/get_key_col.R | 6 DQAstats-0.3.6/DQAstats/R/mdr.R | 782 +-- DQAstats-0.3.6/DQAstats/R/plausibilities.R | 2 DQAstats-0.3.6/DQAstats/R/plausibility_results.R | 1434 +++---- DQAstats-0.3.6/DQAstats/R/reduce_cat.R | 328 - DQAstats-0.3.6/DQAstats/R/report.R | 2 DQAstats-0.3.6/DQAstats/R/simple_summary.R | 48 DQAstats-0.3.6/DQAstats/R/test_csv.R | 280 - DQAstats-0.3.6/DQAstats/R/time_compare.R | 566 +- DQAstats-0.3.6/DQAstats/R/utils.R | 434 +- DQAstats-0.3.6/DQAstats/build/vignette.rds |binary DQAstats-0.3.6/DQAstats/inst/demo_data/utilities/RMD/DQA_report.qmd | 478 +- DQAstats-0.3.6/DQAstats/inst/demo_data/utilities/RMD/_header/header.tex | 20 DQAstats-0.3.6/DQAstats/inst/doc/DQAstats2SHIPdataset.R | 64 DQAstats-0.3.6/DQAstats/inst/doc/DQAstats2SHIPdataset.html | 12 DQAstats-0.3.6/DQAstats/inst/doc/DQAstats2SHIPdataset.qmd | 1 DQAstats-0.3.6/DQAstats/tests/testthat/test-DQA.R | 2 DQAstats-0.3.6/DQAstats/tests/testthat/test-MDR.R | 190 DQAstats-0.3.6/DQAstats/tests/testthat/test-check_date_restriction_requirements.R | 106 DQAstats-0.3.6/DQAstats/tests/testthat/test-completeness.R | 258 - DQAstats-0.3.6/DQAstats/tests/testthat/test-conformance.R | 310 - DQAstats-0.3.6/DQAstats/tests/testthat/test-dataloading.R | 324 - DQAstats-0.3.6/DQAstats/tests/testthat/test-datamap.R | 264 - DQAstats-0.3.6/DQAstats/tests/testthat/test-datetime_restrictions.R | 224 - DQAstats-0.3.6/DQAstats/tests/testthat/test-descriptive_results.R | 636 +-- DQAstats-0.3.6/DQAstats/tests/testthat/test-etl_and_differences_checks.R | 264 - DQAstats-0.3.6/DQAstats/tests/testthat/test-export.R | 302 - DQAstats-0.3.6/DQAstats/tests/testthat/test-helper_vars.R | 292 - DQAstats-0.3.6/DQAstats/tests/testthat/test-import.R | 210 - DQAstats-0.3.6/DQAstats/tests/testthat/test-lints.R | 64 DQAstats-0.3.6/DQAstats/tests/testthat/test-plausibilities.R | 292 - DQAstats-0.3.6/DQAstats/tests/testthat/test-readme.R | 162 DQAstats-0.3.6/DQAstats/tests/testthat/test-reduce_cat.R | 258 - DQAstats-0.3.6/DQAstats/tests/testthat/test-render_conformance.R | 328 - DQAstats-0.3.6/DQAstats/tests/testthat/test-stats.R | 108 DQAstats-0.3.6/DQAstats/tests/testthat/test-time_compare.R | 212 - DQAstats-0.3.6/DQAstats/vignettes/DQAstats2SHIPdataset.qmd | 1 60 files changed, 9151 insertions(+), 9216 deletions(-)
Title: Collection of Functions for Working with Age Intervals
Description: Provides a collection of efficient functions for working with
individual ages and corresponding intervals. These include functions for
conversion from an age to an interval, aggregation of ages with associated
counts in to intervals and the splitting of interval counts based on
specified age distributions.
Author: Tim Taylor [aut, cre, cph] ,
Edwin van Leeuwen [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ageutils versions 0.0.5 dated 2024-09-09 and 0.0.6 dated 2024-11-27
ageutils-0.0.5/ageutils/src/cut_ages.c |only ageutils-0.0.6/ageutils/DESCRIPTION | 6 - ageutils-0.0.6/ageutils/MD5 | 17 +- ageutils-0.0.6/ageutils/NEWS.md | 8 + ageutils-0.0.6/ageutils/R/cut_ages.R | 82 +++++++++++++- ageutils-0.0.6/ageutils/README.md | 14 +- ageutils-0.0.6/ageutils/man/cut_ages.Rd | 7 + ageutils-0.0.6/ageutils/src/init.c | 2 ageutils-0.0.6/ageutils/tests/testthat/_snaps/cut_ages.md | 12 +- ageutils-0.0.6/ageutils/tests/testthat/test-cut_ages.R | 2 10 files changed, 122 insertions(+), 28 deletions(-)
Title: Markdown-Based Surveys Using 'Quarto' and 'shiny'
Description: Generate surveys using markdown and R code chunks. Surveys are composed of two files: a survey.qmd 'Quarto' file defining the survey content (pages, questions, etc), and an app.R file defining a 'shiny' app with global settings (libraries, database configuration, etc.) and server configuration options (e.g., conditional skipping / display, etc.). Survey data collected from respondents is stored in a 'PostgreSQL' database. Features include controls for conditional skip logic (skip to a page based on an answer to a question), conditional display logic (display a question based on an answer to a question), a customizable progress bar, and a wide variety of question types, including multiple choice (single choice and multiple choices), select, text, numeric, multiple choice buttons, text area, and dates. Because the surveys render into a 'shiny' app, designers can also leverage the reactive capabilities of 'shiny' to create dynamic and interactive surveys.
Author: John Paul Helveston [aut, cre, cph]
,
Pingfan Hu [aut, cph] ,
Bogdan Bunea [aut, cph] ,
Stefan Munnes [ctb]
Maintainer: John Paul Helveston <john.helveston@gmail.com>
Diff between surveydown versions 0.5.0 dated 2024-11-25 and 0.5.1 dated 2024-11-27
DESCRIPTION | 6 MD5 | 24 - NEWS.md | 9 R/config.R | 29 - R/db.R | 27 - R/server.R | 1092 +++++++++++++++++++---------------------------- R/ui.R | 1 R/util.R | 8 README.md | 4 inst/doc/surveydown.Rmd | 2 inst/doc/surveydown.html | 2 man/sd_server.Rd | 12 vignettes/surveydown.Rmd | 2 13 files changed, 517 insertions(+), 701 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 0.22.0 dated 2024-11-24 and 0.22.1 dated 2024-11-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/Measure.R | 4 ++-- R/assertions.R | 23 +++++++++++++++-------- 5 files changed, 28 insertions(+), 17 deletions(-)
Title: Regression Modelling with 'GLM.jl' and 'MixedModels.jl' in
'Julia'
Description: Bindings to 'Julia' packages 'GLM.jl'
<doi:10.5281/zenodo.3376013> and 'MixedModels.jl'
<doi:10.5281/zenodo.12575371>, powered by 'JuliaConnectoR'. Fits
(generalized) linear (mixed-effects) regression models in 'Julia'
using familiar model fitting syntax from R. Offers 'broom'-style data
frame summary functionalities for 'Julia' regression models.
Author: June Choe [aut, cre]
Maintainer: June Choe <jchoe001@gmail.com>
Diff between jlme versions 0.4.0 dated 2024-10-09 and 0.4.1 dated 2024-11-27
DESCRIPTION | 9 MD5 | 12 - NEWS.md | 6 R/jl_-model.R | 221 +++++++++++----------- README.md | 16 + tests/testthat/test-jl.R | 64 +++--- tests/testthat/test-model.R | 424 ++++++++++++++++++++++---------------------- 7 files changed, 387 insertions(+), 365 deletions(-)
Title: Tools for Processing and Analyzing Files from the Hydrological
Catchment Model HYPE
Description: Work with model files (setup, input, output) from
the hydrological catchment model HYPE: Streamlined file import and export, standard
evaluation plot routines, diverse post-processing and aggregation routines
for hydrological model analysis. The HYPEtools package is also archived at <doi:10.5281/zenodo.7627955>
and can be cited in publications with Brendel et al. (2024) <doi:10.1016/j.envsoft.2024.106094>.
Author: Rene Capell [aut, cre] ,
Conrad Brendel [aut] ,
Jafet Andersson [ctb],
David Gustafsson [ctb],
Jude Musuuza [ctb],
Jude Lubega [ctb]
Maintainer: Rene Capell <hypetools.rene@smhi.se>
Diff between HYPEtools versions 1.6.3 dated 2024-09-05 and 1.6.4 dated 2024-11-27
DESCRIPTION | 6 +-- MD5 | 32 +++++++++--------- NEWS.md | 11 +++++- R/function_PlotBasinSummary.R | 2 - R/functioncollection_export.R | 10 +++++ R/functioncollection_import.R | 63 +++++++++++++++++++++++++----------- R/sysdata.rda |binary inst/doc/analyze_hype_ts.html | 4 +- inst/doc/basin_characteristics.html | 6 +-- inst/doc/basin_network.html | 4 +- inst/doc/import_files.html | 2 - inst/doc/modify_par.html | 2 - inst/doc/plot_map_statistics.html | 12 +++--- man/PlotBasinSummary.Rd | 1 man/ReadDescription.Rd | 36 ++++++++++++++------ man/ReadXobs.Rd | 2 - man/WriteObs.Rd | 8 +++- 17 files changed, 132 insertions(+), 69 deletions(-)
More information about antaresProcessing at CRAN
Permanent link
More information about autoslider.core at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-23 1.1
2024-01-09 1.0
2023-07-16 0.7.4
2023-05-21 0.7.3
2023-02-17 0.7.2
2022-09-18 0.7.1
2022-08-08 0.7.0
Title: Collection of Helper Functions
Description: Provides a collection of lightweight helper functions (imps) both
for interactive use and for inclusion within other packages. These include
functions for minimal input assertions, visualising colour palettes,
quoting user input, searching rows of a data frame and capturing string
tokens.
Author: Tim Taylor [aut, cre, cph] ,
R Core Team [cph] ,
Toby Hocking [cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ympes versions 1.6.0 dated 2024-10-31 and 1.7.0 dated 2024-11-27
ympes-1.6.0/ympes/R/new_package.R |only ympes-1.6.0/ympes/inst/skeletons |only ympes-1.6.0/ympes/man/new_package.Rd |only ympes-1.7.0/ympes/DESCRIPTION | 9 - ympes-1.7.0/ympes/MD5 | 24 +---- ympes-1.7.0/ympes/NAMESPACE | 2 ympes-1.7.0/ympes/NEWS.md | 19 ++++ ympes-1.7.0/ympes/R/assert.R | 39 +++++++- ympes-1.7.0/ympes/R/cc.R | 28 ++++-- ympes-1.7.0/ympes/inst/doc/ympes.html | 28 +++--- ympes-1.7.0/ympes/inst/tinytest/test_assertions.R | 100 +++++++++++----------- ympes-1.7.0/ympes/man/assertions.Rd | 4 ympes-1.7.0/ympes/man/cc.Rd | 10 +- 13 files changed, 162 insertions(+), 101 deletions(-)
Title: Analyzes Real-World Treatment Patterns of a Study Population of
Interest
Description: Computes treatment patterns within a given cohort using the Observational
Medical Outcomes Partnership (OMOP) common data model (CDM). As described
in Markus, Verhamme, Kors, and Rijnbeek (2022) <doi:10.1016/j.cmpb.2022.107081>.
Author: Aniek Markus [aut] ,
Maarten van Kessel [cre]
Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
Diff between TreatmentPatterns versions 2.6.9 dated 2024-09-02 and 2.7.0 dated 2024-11-27
TreatmentPatterns-2.6.9/TreatmentPatterns/inst/DummyOutput/summaryStatsTherapyDuration.csv |only TreatmentPatterns-2.6.9/TreatmentPatterns/man/createSankeyDiagram2.Rd |only TreatmentPatterns-2.6.9/TreatmentPatterns/man/createSunburstPlot2.Rd |only TreatmentPatterns-2.7.0/TreatmentPatterns/DESCRIPTION | 17 TreatmentPatterns-2.7.0/TreatmentPatterns/MD5 | 97 TreatmentPatterns-2.7.0/TreatmentPatterns/NAMESPACE | 5 TreatmentPatterns-2.7.0/TreatmentPatterns/NEWS.md | 12 TreatmentPatterns-2.7.0/TreatmentPatterns/R/CDMInterface.R | 123 TreatmentPatterns-2.7.0/TreatmentPatterns/R/CharacterizationPlots.R | 16 TreatmentPatterns-2.7.0/TreatmentPatterns/R/InputHandler.R | 24 TreatmentPatterns-2.7.0/TreatmentPatterns/R/InteractivePlots.R | 18 TreatmentPatterns-2.7.0/TreatmentPatterns/R/SankeyDiagram.R | 16 TreatmentPatterns-2.7.0/TreatmentPatterns/R/ShinyApp.R | 15 TreatmentPatterns-2.7.0/TreatmentPatterns/R/ShinyModule.R | 16 TreatmentPatterns-2.7.0/TreatmentPatterns/R/SunburstPlot.R | 16 TreatmentPatterns-2.7.0/TreatmentPatterns/R/TreatmentPatterns-package.R | 25 TreatmentPatterns-2.7.0/TreatmentPatterns/R/attrition.R |only TreatmentPatterns-2.7.0/TreatmentPatterns/R/computePathways.R | 48 TreatmentPatterns-2.7.0/TreatmentPatterns/R/constructPathways.R | 218 TreatmentPatterns-2.7.0/TreatmentPatterns/R/createSankeyDiagram.R | 45 TreatmentPatterns-2.7.0/TreatmentPatterns/R/createSunburstPlot.R | 48 TreatmentPatterns-2.7.0/TreatmentPatterns/R/executeTreatmentPatterns.R | 18 TreatmentPatterns-2.7.0/TreatmentPatterns/R/export.R | 114 TreatmentPatterns-2.7.0/TreatmentPatterns/R/plotEventDuration.R |only TreatmentPatterns-2.7.0/TreatmentPatterns/README.md | 2 TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/countsAge.csv | 86 TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/countsSex.csv | 4 TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/countsYear.csv | 97 TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/metadata.csv | 2 TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/output.zip |binary TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/summaryEventDuration.csv |only TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/treatmentPathways.csv | 9469 +++++++++- TreatmentPatterns-2.7.0/TreatmentPatterns/inst/doc/DefiningCohorts.R | 38 TreatmentPatterns-2.7.0/TreatmentPatterns/inst/doc/DefiningCohorts.html | 16 TreatmentPatterns-2.7.0/TreatmentPatterns/inst/sql/selectData.sql | 14 TreatmentPatterns-2.7.0/TreatmentPatterns/man/CharacterizationPlots.Rd | 2 TreatmentPatterns-2.7.0/TreatmentPatterns/man/InputHandler.Rd | 2 TreatmentPatterns-2.7.0/TreatmentPatterns/man/SankeyDiagram.Rd | 2 TreatmentPatterns-2.7.0/TreatmentPatterns/man/SunburstPlot.Rd | 2 TreatmentPatterns-2.7.0/TreatmentPatterns/man/computePathways.Rd | 7 TreatmentPatterns-2.7.0/TreatmentPatterns/man/plotEventDuration.Rd |only TreatmentPatterns-2.7.0/TreatmentPatterns/tests/testthat/helper-ableToRun.R | 8 TreatmentPatterns-2.7.0/TreatmentPatterns/tests/testthat/test-CDMInterface.R | 20 TreatmentPatterns-2.7.0/TreatmentPatterns/tests/testthat/test-CDMInterfaceCDMC.R | 4 TreatmentPatterns-2.7.0/TreatmentPatterns/tests/testthat/test-InputHandler.R | 2 TreatmentPatterns-2.7.0/TreatmentPatterns/tests/testthat/test-ShinyApp.R | 2 TreatmentPatterns-2.7.0/TreatmentPatterns/tests/testthat/test-computePathways.R | 154 TreatmentPatterns-2.7.0/TreatmentPatterns/tests/testthat/test-executeTreatmentPatterns.R | 4 TreatmentPatterns-2.7.0/TreatmentPatterns/tests/testthat/test-export.R | 36 TreatmentPatterns-2.7.0/TreatmentPatterns/tests/testthat/test-pathwaysLogical.R | 52 TreatmentPatterns-2.7.0/TreatmentPatterns/tests/testthat/test-plotEventDuration.R |only TreatmentPatterns-2.7.0/TreatmentPatterns/vignettes/articles/ComputingTreatmentPathways.Rmd | 16 TreatmentPatterns-2.7.0/TreatmentPatterns/vignettes/articles/PareReport.Rmd | 6 TreatmentPatterns-2.7.0/TreatmentPatterns/vignettes/articles/latestChanges.Rmd |only 54 files changed, 10380 insertions(+), 558 deletions(-)
More information about TreatmentPatterns at CRAN
Permanent link
Title: Tree Ring Analysis of Disturbance Events in R
Description: Tree Ring Analysis of Disturbance Events in R (TRADER) package provides functions for disturbance reconstruction from tree-ring data, e.g. boundary line, absolute increase, growth averaging methods.
Author: Pavel Fibich [aut, cre],
Jan Altman [aut],
Tuomas Aakala [aut],
Jiri Dolezal [aut]
Maintainer: Pavel Fibich <pavel.fibich@prf.jcu.cz>
Diff between TRADER versions 1.2-4 dated 2024-02-06 and 1.2-5 dated 2024-11-27
DESCRIPTION | 8 +- MD5 | 6 - R/trader.R | 177 +++++++++++++++++++++------------------------------------- inst/CITATION | 5 - 4 files changed, 76 insertions(+), 120 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between parameters versions 0.23.0 dated 2024-10-18 and 0.24.0 dated 2024-11-27
parameters-0.23.0/parameters/man/model_parameters.averaging.Rd |only parameters-0.23.0/parameters/man/model_parameters.kmeans.Rd |only parameters-0.23.0/parameters/man/model_parameters.merMod.Rd |only parameters-0.23.0/parameters/man/model_parameters.stanreg.Rd |only parameters-0.23.0/parameters/man/p_value.BFBayesFactor.Rd |only parameters-0.23.0/parameters/man/p_value.DirichletRegModel.Rd |only parameters-0.23.0/parameters/man/p_value.poissonmfx.Rd |only parameters-0.23.0/parameters/man/p_value.zcpglm.Rd |only parameters-0.23.0/parameters/tests/testthat/test-pretty_namesR.R |only parameters-0.24.0/parameters/DESCRIPTION | 12 parameters-0.24.0/parameters/MD5 | 287 +++++----- parameters-0.24.0/parameters/NAMESPACE | 2 parameters-0.24.0/parameters/NEWS.md | 26 parameters-0.24.0/parameters/R/1_model_parameters.R | 98 +-- parameters-0.24.0/parameters/R/2_ci.R | 60 +- parameters-0.24.0/parameters/R/3_p_value.R | 27 parameters-0.24.0/parameters/R/4_standard_error.R | 42 - parameters-0.24.0/parameters/R/5_simulate_model.R | 12 parameters-0.24.0/parameters/R/bootstrap_model.R | 26 parameters-0.24.0/parameters/R/ci_generic.R | 37 - parameters-0.24.0/parameters/R/cluster_performance.R | 37 - parameters-0.24.0/parameters/R/compare_parameters.R | 2 parameters-0.24.0/parameters/R/equivalence_test.R | 12 parameters-0.24.0/parameters/R/extract_parameters.R | 14 parameters-0.24.0/parameters/R/extract_parameters_anova.R | 21 parameters-0.24.0/parameters/R/extract_random_variances.R | 9 parameters-0.24.0/parameters/R/format.R | 15 parameters-0.24.0/parameters/R/format_parameters.R | 3 parameters-0.24.0/parameters/R/methods_BayesFactor.R | 18 parameters-0.24.0/parameters/R/methods_DirichletReg.R | 62 -- parameters-0.24.0/parameters/R/methods_FactoMineR.R | 2 parameters-0.24.0/parameters/R/methods_MCMCglmm.R | 1 parameters-0.24.0/parameters/R/methods_aod.R | 43 + parameters-0.24.0/parameters/R/methods_aov.R | 10 parameters-0.24.0/parameters/R/methods_averaging.R | 67 -- parameters-0.24.0/parameters/R/methods_bamlss.R | 1 parameters-0.24.0/parameters/R/methods_base.R | 2 parameters-0.24.0/parameters/R/methods_betareg.R | 37 - parameters-0.24.0/parameters/R/methods_bife.R | 3 parameters-0.24.0/parameters/R/methods_brglm2.R | 1 parameters-0.24.0/parameters/R/methods_brms.R | 80 ++ parameters-0.24.0/parameters/R/methods_censReg.R | 1 parameters-0.24.0/parameters/R/methods_cgam.R | 9 parameters-0.24.0/parameters/R/methods_cplm.R | 117 ++-- parameters-0.24.0/parameters/R/methods_dbscan.R | 27 parameters-0.24.0/parameters/R/methods_emmeans.R | 1 parameters-0.24.0/parameters/R/methods_fixest.R | 4 parameters-0.24.0/parameters/R/methods_glmmTMB.R | 200 ++++++ parameters-0.24.0/parameters/R/methods_glmx.R | 12 parameters-0.24.0/parameters/R/methods_hclust.R | 107 ++- parameters-0.24.0/parameters/R/methods_hglm.R | 4 parameters-0.24.0/parameters/R/methods_kmeans.R | 54 - parameters-0.24.0/parameters/R/methods_lavaan.R | 1 parameters-0.24.0/parameters/R/methods_lme4.R | 165 ----- parameters-0.24.0/parameters/R/methods_marginaleffects.R | 1 parameters-0.24.0/parameters/R/methods_mass.R | 1 parameters-0.24.0/parameters/R/methods_mclust.R | 7 parameters-0.24.0/parameters/R/methods_metafor.R | 4 parameters-0.24.0/parameters/R/methods_metaplus.R | 5 parameters-0.24.0/parameters/R/methods_mfx.R | 154 ++--- parameters-0.24.0/parameters/R/methods_mgcv.R | 1 parameters-0.24.0/parameters/R/methods_mhurdle.R | 8 parameters-0.24.0/parameters/R/methods_mice.R | 1 parameters-0.24.0/parameters/R/methods_mixed.R | 1 parameters-0.24.0/parameters/R/methods_mixmod.R | 1 parameters-0.24.0/parameters/R/methods_mjoint.R | 7 parameters-0.24.0/parameters/R/methods_mlm.R | 2 parameters-0.24.0/parameters/R/methods_mvord.R | 5 parameters-0.24.0/parameters/R/methods_nestedLogit.R | 4 parameters-0.24.0/parameters/R/methods_nlme.R | 1 parameters-0.24.0/parameters/R/methods_ordinal.R | 26 parameters-0.24.0/parameters/R/methods_other.R | 1 parameters-0.24.0/parameters/R/methods_pam.R | 15 parameters-0.24.0/parameters/R/methods_panelr.R | 34 + parameters-0.24.0/parameters/R/methods_posterior.R | 1 parameters-0.24.0/parameters/R/methods_pscl.R | 35 - parameters-0.24.0/parameters/R/methods_rstanarm.R | 60 -- parameters-0.24.0/parameters/R/methods_scam.R | 1 parameters-0.24.0/parameters/R/methods_selection.R | 8 parameters-0.24.0/parameters/R/methods_systemfit.R | 4 parameters-0.24.0/parameters/R/n_clusters.R | 2 parameters-0.24.0/parameters/R/p_value_kenward.R | 4 parameters-0.24.0/parameters/R/pool_parameters.R | 4 parameters-0.24.0/parameters/R/print.parameters_model.R | 37 - parameters-0.24.0/parameters/R/simulate_parameters.R | 2 parameters-0.24.0/parameters/R/standardize_info.R | 6 parameters-0.24.0/parameters/R/utils.R | 7 parameters-0.24.0/parameters/R/utils_format.R | 4 parameters-0.24.0/parameters/R/utils_model_parameters.R | 8 parameters-0.24.0/parameters/build/partial.rdb |binary parameters-0.24.0/parameters/build/vignette.rds |binary parameters-0.24.0/parameters/inst/WORDLIST | 4 parameters-0.24.0/parameters/man/bootstrap_model.Rd | 17 parameters-0.24.0/parameters/man/ci.default.Rd | 128 +++- parameters-0.24.0/parameters/man/cluster_performance.Rd | 25 parameters-0.24.0/parameters/man/compare_parameters.Rd | 59 +- parameters-0.24.0/parameters/man/display.parameters_model.Rd | 41 - parameters-0.24.0/parameters/man/equivalence_test.lm.Rd | 56 - parameters-0.24.0/parameters/man/model_parameters.Rd | 53 + parameters-0.24.0/parameters/man/model_parameters.aov.Rd | 12 parameters-0.24.0/parameters/man/model_parameters.brmsfit.Rd |only parameters-0.24.0/parameters/man/model_parameters.cgam.Rd | 110 +-- parameters-0.24.0/parameters/man/model_parameters.default.Rd | 131 +--- parameters-0.24.0/parameters/man/model_parameters.glht.Rd | 47 - parameters-0.24.0/parameters/man/model_parameters.glimML.Rd |only parameters-0.24.0/parameters/man/model_parameters.glmmTMB.Rd |only parameters-0.24.0/parameters/man/model_parameters.hclust.Rd |only parameters-0.24.0/parameters/man/model_parameters.htest.Rd | 29 - parameters-0.24.0/parameters/man/model_parameters.mira.Rd | 32 - parameters-0.24.0/parameters/man/model_parameters.mlm.Rd | 219 +++---- parameters-0.24.0/parameters/man/model_parameters.principal.Rd | 45 - parameters-0.24.0/parameters/man/model_parameters.rma.Rd | 57 + parameters-0.24.0/parameters/man/model_parameters.zcpglm.Rd | 132 +++- parameters-0.24.0/parameters/man/n_clusters.Rd | 29 - parameters-0.24.0/parameters/man/p_direction.lm.Rd | 32 - parameters-0.24.0/parameters/man/p_function.Rd | 94 +-- parameters-0.24.0/parameters/man/p_significance.lm.Rd | 32 - parameters-0.24.0/parameters/man/p_value.Rd | 125 +++- parameters-0.24.0/parameters/man/parameters-package.Rd | 2 parameters-0.24.0/parameters/man/pool_parameters.Rd | 36 - parameters-0.24.0/parameters/man/print.compare_parameters.Rd | 47 - parameters-0.24.0/parameters/man/print.parameters_model.Rd | 47 - parameters-0.24.0/parameters/man/simulate_model.Rd | 61 +- parameters-0.24.0/parameters/man/simulate_parameters.Rd | 21 parameters-0.24.0/parameters/man/standard_error.Rd | 76 -- parameters-0.24.0/parameters/tests/testthat/_snaps/averaging.md |only parameters-0.24.0/parameters/tests/testthat/_snaps/complete_separation.md | 124 ++-- parameters-0.24.0/parameters/tests/testthat/_snaps/coxph.md |only parameters-0.24.0/parameters/tests/testthat/_snaps/model_parameters.anova.md | 86 ++ parameters-0.24.0/parameters/tests/testthat/_snaps/model_parameters.ggeffects.md | 70 +- parameters-0.24.0/parameters/tests/testthat/_snaps/panelr.md |only parameters-0.24.0/parameters/tests/testthat/_snaps/pca.md | 64 +- parameters-0.24.0/parameters/tests/testthat/_snaps/pretty_names.md |only parameters-0.24.0/parameters/tests/testthat/_snaps/printing.md | 8 parameters-0.24.0/parameters/tests/testthat/_snaps/printing2.md | 34 + parameters-0.24.0/parameters/tests/testthat/_snaps/serp.md | 48 - parameters-0.24.0/parameters/tests/testthat/test-averaging.R |only parameters-0.24.0/parameters/tests/testthat/test-compare_parameters.R | 2 parameters-0.24.0/parameters/tests/testthat/test-complete_separation.R | 52 - parameters-0.24.0/parameters/tests/testthat/test-coxph.R | 17 parameters-0.24.0/parameters/tests/testthat/test-equivalence_test.R | 1 parameters-0.24.0/parameters/tests/testthat/test-format_parameters.R | 2 parameters-0.24.0/parameters/tests/testthat/test-marginaleffects.R | 3 parameters-0.24.0/parameters/tests/testthat/test-model_parameters.anova.R | 22 parameters-0.24.0/parameters/tests/testthat/test-model_parameters.fixest.R | 18 parameters-0.24.0/parameters/tests/testthat/test-model_parameters_robust.R | 4 parameters-0.24.0/parameters/tests/testthat/test-model_parameters_std_mixed.R | 1 parameters-0.24.0/parameters/tests/testthat/test-panelr.R | 10 parameters-0.24.0/parameters/tests/testthat/test-pipe.R | 27 parameters-0.24.0/parameters/tests/testthat/test-pretty_names.R |only parameters-0.24.0/parameters/tests/testthat/test-print_AER_labels.R | 16 parameters-0.24.0/parameters/tests/testthat/test-printing.R | 16 parameters-0.24.0/parameters/tests/testthat/test-printing2.R | 34 + parameters-0.24.0/parameters/tests/testthat/test-serp.R | 1 154 files changed, 2510 insertions(+), 2182 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical
models and returns the result as tidy data frames. These data frames are
ready to use with the 'ggplot2'-package. Effects and predictions can be
calculated for many different models. Interaction terms, splines and
polynomial terms are also supported. The main functions are ggpredict(),
ggemmeans() and ggeffect(). There is a generic plot()-method to plot the
results using 'ggplot2'.
Author: Daniel Luedecke [aut, cre] ,
Frederik Aust [ctb] ,
Sam Crawley [ctb] ,
Mattan S. Ben-Shachar [ctb] ,
Sean C. Anderson [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between ggeffects versions 1.7.2 dated 2024-10-13 and 2.0.0 dated 2024-11-27
ggeffects-1.7.2/ggeffects/R/get_predictions_coxph.R |only ggeffects-1.7.2/ggeffects/R/get_predictions_generic.R |only ggeffects-1.7.2/ggeffects/R/get_predictions_generic2.R |only ggeffects-1.7.2/ggeffects/R/get_predictions_mblogit.r |only ggeffects-1.7.2/ggeffects/R/get_predictions_mclogit.R |only ggeffects-1.7.2/ggeffects/R/get_predictions_vgam.R |only ggeffects-1.7.2/ggeffects/R/get_predictions_zelig.R |only ggeffects-1.7.2/ggeffects/R/predictions.R |only ggeffects-1.7.2/ggeffects/R/utils_model_function.R |only ggeffects-2.0.0/ggeffects/DESCRIPTION | 33 ggeffects-2.0.0/ggeffects/MD5 | 356 +-- ggeffects-2.0.0/ggeffects/NAMESPACE | 90 ggeffects-2.0.0/ggeffects/NEWS.md | 53 ggeffects-2.0.0/ggeffects/R/emmeans_prediction_data.R | 85 ggeffects-2.0.0/ggeffects/R/format.R | 5 ggeffects-2.0.0/ggeffects/R/get_predictions.R |only ggeffects-2.0.0/ggeffects/R/get_predictions_MCMCglmm.R | 31 ggeffects-2.0.0/ggeffects/R/get_predictions_MixMod.R | 52 ggeffects-2.0.0/ggeffects/R/get_predictions_averaging.R |only ggeffects-2.0.0/ggeffects/R/get_predictions_bamlss.R | 19 ggeffects-2.0.0/ggeffects/R/get_predictions_bayesglm.R |only ggeffects-2.0.0/ggeffects/R/get_predictions_bayesx.R | 17 ggeffects-2.0.0/ggeffects/R/get_predictions_betareg.R |only ggeffects-2.0.0/ggeffects/R/get_predictions_cgam.R | 37 ggeffects-2.0.0/ggeffects/R/get_predictions_clm.R | 23 ggeffects-2.0.0/ggeffects/R/get_predictions_clm2.R | 19 ggeffects-2.0.0/ggeffects/R/get_predictions_clmm.R | 25 ggeffects-2.0.0/ggeffects/R/get_predictions_gam.R | 45 ggeffects-2.0.0/ggeffects/R/get_predictions_gam2.R | 50 ggeffects-2.0.0/ggeffects/R/get_predictions_gamlss.R | 56 ggeffects-2.0.0/ggeffects/R/get_predictions_gee.R | 17 ggeffects-2.0.0/ggeffects/R/get_predictions_geeglm.R | 65 ggeffects-2.0.0/ggeffects/R/get_predictions_glimML.R | 44 ggeffects-2.0.0/ggeffects/R/get_predictions_glm.R | 85 ggeffects-2.0.0/ggeffects/R/get_predictions_glmRob.R | 43 ggeffects-2.0.0/ggeffects/R/get_predictions_glmgee.R | 51 ggeffects-2.0.0/ggeffects/R/get_predictions_glmmTMB.R | 78 ggeffects-2.0.0/ggeffects/R/get_predictions_glmrob_base.R | 32 ggeffects-2.0.0/ggeffects/R/get_predictions_lm.R | 54 ggeffects-2.0.0/ggeffects/R/get_predictions_lme.R | 96 ggeffects-2.0.0/ggeffects/R/get_predictions_lmrob_base.R | 39 ggeffects-2.0.0/ggeffects/R/get_predictions_logistf.R | 37 ggeffects-2.0.0/ggeffects/R/get_predictions_logitr.R | 25 ggeffects-2.0.0/ggeffects/R/get_predictions_lrm.R | 56 ggeffects-2.0.0/ggeffects/R/get_predictions_merMod.R | 56 ggeffects-2.0.0/ggeffects/R/get_predictions_mixor.R | 51 ggeffects-2.0.0/ggeffects/R/get_predictions_mlogit.R | 199 + ggeffects-2.0.0/ggeffects/R/get_predictions_multinom.R | 62 ggeffects-2.0.0/ggeffects/R/get_predictions_nestedLogit.R | 31 ggeffects-2.0.0/ggeffects/R/get_predictions_ols.R | 41 ggeffects-2.0.0/ggeffects/R/get_predictions_polr.R | 61 ggeffects-2.0.0/ggeffects/R/get_predictions_rq.R | 39 ggeffects-2.0.0/ggeffects/R/get_predictions_rqs.R | 29 ggeffects-2.0.0/ggeffects/R/get_predictions_sdmTMB.R | 28 ggeffects-2.0.0/ggeffects/R/get_predictions_speedglm.R |only ggeffects-2.0.0/ggeffects/R/get_predictions_stan.R | 39 ggeffects-2.0.0/ggeffects/R/get_predictions_survival.R | 133 + ggeffects-2.0.0/ggeffects/R/get_predictions_svyglm.R | 49 ggeffects-2.0.0/ggeffects/R/get_predictions_svyglmnb.R | 36 ggeffects-2.0.0/ggeffects/R/get_predictions_tobit.R | 96 ggeffects-2.0.0/ggeffects/R/get_predictions_vglm.R | 67 ggeffects-2.0.0/ggeffects/R/get_predictions_wbm.R | 39 ggeffects-2.0.0/ggeffects/R/get_predictions_zeroinfl.R | 73 ggeffects-2.0.0/ggeffects/R/ggaverage.R | 62 ggeffects-2.0.0/ggeffects/R/ggeffect.R | 67 ggeffects-2.0.0/ggeffects/R/ggemmeans.R | 122 - ggeffects-2.0.0/ggeffects/R/ggemmeans_add_confint.R | 10 ggeffects-2.0.0/ggeffects/R/ggemmeans_zi_predictions.R | 22 ggeffects-2.0.0/ggeffects/R/ggpredict.R | 198 - ggeffects-2.0.0/ggeffects/R/johnson_neyman.R | 13 ggeffects-2.0.0/ggeffects/R/new_data.R | 4 ggeffects-2.0.0/ggeffects/R/plot.R | 1053 +++------- ggeffects-2.0.0/ggeffects/R/pool_predictions.R | 10 ggeffects-2.0.0/ggeffects/R/post_processing_labels.R | 66 ggeffects-2.0.0/ggeffects/R/predict_response.R | 299 +- ggeffects-2.0.0/ggeffects/R/predict_zero_inflation.R | 32 ggeffects-2.0.0/ggeffects/R/print.R | 22 ggeffects-2.0.0/ggeffects/R/sanitize_type_arg.R | 80 ggeffects-2.0.0/ggeffects/R/simulate_predictions.R | 75 ggeffects-2.0.0/ggeffects/R/standard_error_predictions.R | 66 ggeffects-2.0.0/ggeffects/R/test_predictions.R | 743 +------ ggeffects-2.0.0/ggeffects/R/test_predictions_emmeans.R | 34 ggeffects-2.0.0/ggeffects/R/test_predictions_ggeffects.R | 14 ggeffects-2.0.0/ggeffects/R/themes.R | 88 ggeffects-2.0.0/ggeffects/R/tp_label_hypothesis_categorical.R |only ggeffects-2.0.0/ggeffects/R/tp_label_hypothesis_slopes.R |only ggeffects-2.0.0/ggeffects/R/tp_label_pairwise_categorical.R |only 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ggeffects-2.0.0/ggeffects/tests/testthat/test-backtransform_response.R | 25 ggeffects-2.0.0/ggeffects/tests/testthat/test-betareg.R | 5 ggeffects-2.0.0/ggeffects/tests/testthat/test-bias_correction.R | 35 ggeffects-2.0.0/ggeffects/tests/testthat/test-brglm.R |only ggeffects-2.0.0/ggeffects/tests/testthat/test-brms-ppd.R | 16 ggeffects-2.0.0/ggeffects/tests/testthat/test-brms-trial.R | 7 ggeffects-2.0.0/ggeffects/tests/testthat/test-check_vars.R | 2 ggeffects-2.0.0/ggeffects/tests/testthat/test-ci_backticks-names.R | 13 ggeffects-2.0.0/ggeffects/tests/testthat/test-clm.R | 4 ggeffects-2.0.0/ggeffects/tests/testthat/test-clmm.R | 6 ggeffects-2.0.0/ggeffects/tests/testthat/test-condition.R | 37 ggeffects-2.0.0/ggeffects/tests/testthat/test-emmeans-weights.R | 16 ggeffects-2.0.0/ggeffects/tests/testthat/test-fixest.R | 40 ggeffects-2.0.0/ggeffects/tests/testthat/test-focal_character.R | 2 ggeffects-2.0.0/ggeffects/tests/testthat/test-focal_only_random.R | 8 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ggeffects-2.0.0/ggeffects/tests/testthat/test-zeroinfl.R | 6 ggeffects-2.0.0/ggeffects/tests/testthat/test-zi_prob.R | 29 ggeffects-2.0.0/ggeffects/vignettes/content.Rmd | 1 193 files changed, 5923 insertions(+), 5151 deletions(-)
Title: Visualizing the Elements Within Bio-Sequences
Description: Visualizing the types and distribution of elements within
bio-sequences. At the same time, We have developed a geom layer,
geom_rrect(), that can generate rounded rectangles. No external references
are used in the development of this package.
Author: Shiqi Zhao [aut, cre, cph]
Maintainer: Shiqi Zhao <zhaosq89@163.com>
Diff between BioVizSeq versions 0.1.0 dated 2024-11-20 and 0.1.1 dated 2024-11-27
DESCRIPTION | 6 MD5 | 11 NEWS.md | 9 R/gff_plot.R | 19 + R/smart_plot.R | 2 inst/extdata/idpro.gff3 |only inst/extdata/iprscan.tsv | 703 +++-------------------------------------------- 7 files changed, 85 insertions(+), 665 deletions(-)
Title: Get Data from the Swiss Federal Statistical Office
Description: Search and download data from the Swiss Federal Statistical Office (BFS) APIs <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre, cph]
,
Janosch Brenzel-Weiss [ctb],
Joao Martins [ctb],
Philipp Baumann [ctb]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between BFS versions 0.5.10 dated 2024-09-27 and 0.5.11 dated 2024-11-27
DESCRIPTION | 6 MD5 | 22 +- NAMESPACE | 1 NEWS.md | 10 + R/bfs_get_base_maps.R | 6 R/bfs_get_catalog_data.R | 35 ++-- R/bfs_get_catalog_tables.R | 15 - R/globals.R | 5 README.md | 356 ++++++++++++++++++++++++++++++------------ man/bfs_get_base_maps.Rd | 6 man/bfs_get_catalog_data.Rd | 11 + man/bfs_get_catalog_tables.Rd | 5 12 files changed, 332 insertions(+), 146 deletions(-)
Title: Plots for Visualizing the Data Produced by the 'irace' Package
Description: Graphical visualization tools for analyzing the data produced by 'irace'. The 'iraceplot' package enables users to analyze the performance and the parameter space data sampled by the configuration during the search process. It provides a set of functions that generate different plots to visualize the configurations sampled during the execution of 'irace' and their performance. The functions just require the log file generated by 'irace' and, in some cases, they can be used with user-provided data.
Author: Manuel Lopez-Ibanez [aut, cre]
,
Pablo Onate Marin [aut],
Leslie Perez Caceres [aut]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between iraceplot versions 1.3 dated 2024-05-15 and 2.0.0 dated 2024-11-27
iraceplot-1.3/iraceplot/R/irace_summarise.R |only iraceplot-1.3/iraceplot/man/has_testing_data.Rd |only iraceplot-1.3/iraceplot/man/irace_summarise.Rd |only iraceplot-1.3/iraceplot/man/read_ablogfile.Rd |only iraceplot-2.0.0/iraceplot/DESCRIPTION | 18 +- iraceplot-2.0.0/iraceplot/MD5 | 94 ++++++------ iraceplot-2.0.0/iraceplot/NAMESPACE | 5 iraceplot-2.0.0/iraceplot/NEWS.md | 20 ++ iraceplot-2.0.0/iraceplot/R/boxplot_performance.R | 53 +++---- iraceplot-2.0.0/iraceplot/R/common.R | 50 ++---- iraceplot-2.0.0/iraceplot/R/configurations_display.R | 90 ++++++------ iraceplot-2.0.0/iraceplot/R/distance_config.R | 15 +- iraceplot-2.0.0/iraceplot/R/iraceplot-package.R | 2 iraceplot-2.0.0/iraceplot/R/parallel_cat.R | 81 +++++----- iraceplot-2.0.0/iraceplot/R/parallel_coord.R | 96 ++++++------- iraceplot-2.0.0/iraceplot/R/parameters_summarise.R | 21 +- iraceplot-2.0.0/iraceplot/R/parameters_tree.R | 19 +- iraceplot-2.0.0/iraceplot/R/plot_experiments_matrix.R | 39 ++--- iraceplot-2.0.0/iraceplot/R/plot_model.R | 67 ++++----- iraceplot-2.0.0/iraceplot/R/reexport.R | 32 +--- iraceplot-2.0.0/iraceplot/R/sampling_distance.R | 7 iraceplot-2.0.0/iraceplot/R/sampling_frequency.R | 45 ++---- iraceplot-2.0.0/iraceplot/R/sampling_frequency_iteration.R | 76 +++------- iraceplot-2.0.0/iraceplot/R/sampling_heatmap.R | 58 ++++--- iraceplot-2.0.0/iraceplot/R/sampling_pie.R | 39 ++--- iraceplot-2.0.0/iraceplot/R/scatter_performance.R | 2 iraceplot-2.0.0/iraceplot/R/summarise_by_configuration.R | 25 ++- iraceplot-2.0.0/iraceplot/R/summarise_by_instance.R | 21 +- iraceplot-2.0.0/iraceplot/R/summarise_by_iteration.R | 4 iraceplot-2.0.0/iraceplot/README.md | 15 +- iraceplot-2.0.0/iraceplot/build/partial.rdb |binary iraceplot-2.0.0/iraceplot/inst/doc/iraceplot_package.R | 6 iraceplot-2.0.0/iraceplot/inst/doc/iraceplot_package.Rmd | 6 iraceplot-2.0.0/iraceplot/inst/doc/iraceplot_package.html | 6 iraceplot-2.0.0/iraceplot/inst/exdata/guide-example.Rdata |binary iraceplot-2.0.0/iraceplot/inst/template/report_html.Rmd | 15 -- iraceplot-2.0.0/iraceplot/man/boxplot_performance.Rd | 6 iraceplot-2.0.0/iraceplot/man/configurations_display.Rd | 4 iraceplot-2.0.0/iraceplot/man/parallel_coord.Rd | 7 iraceplot-2.0.0/iraceplot/man/parameters_summarise.Rd | 18 +- iraceplot-2.0.0/iraceplot/man/parameters_tree.Rd | 17 +- iraceplot-2.0.0/iraceplot/man/plot_configurations.Rd | 14 + iraceplot-2.0.0/iraceplot/man/plot_experiments_matrix.Rd | 11 + iraceplot-2.0.0/iraceplot/man/reexports.Rd | 5 iraceplot-2.0.0/iraceplot/man/sampling_frequency.Rd | 11 - iraceplot-2.0.0/iraceplot/man/sampling_heatmap2.Rd | 2 iraceplot-2.0.0/iraceplot/tests/testthat/bug32.Rdata |binary iraceplot-2.0.0/iraceplot/tests/testthat/test-bug-32.R | 21 +- iraceplot-2.0.0/iraceplot/vignettes/iraceplot_package.Rmd | 6 iraceplot-2.0.0/iraceplot/vignettes/user_guide/guide.Rmd | 6 50 files changed, 587 insertions(+), 568 deletions(-)
Title: Automatic Short Form Creation
Description: Performs automatic creation of short forms of scales with an
ant colony optimization algorithm and a Tabu search. As implemented in the
package, the ant colony algorithm randomly selects items to build a model of
a specified length, then updates the probability of item selection according
to the fit of the best model within each set of searches. The algorithm
continues until the same items are selected by multiple ants a given number
of times in a row. On the other hand, the Tabu search changes one parameter at
a time to be either free, constrained, or fixed while keeping track of the
changes made and putting changes that result in worse fit in a "tabu" list
so that the algorithm does not revisit them for some number of searches.
See Leite, Huang, & Marcoulides (2008) <doi:10.1080/00273170802285743> for
an applied example of the ant colony algorithm, and Marcoulides & Falk (2018)
<doi:10.1080/10705511.2017.1409074> for an applied example of the Tabu search.
Author: Anthony Raborn [aut, cre] ,
Walter Leite [aut]
Maintainer: Anthony Raborn <anthony.w.raborn@gmail.com>
Diff between ShortForm versions 0.5.5 dated 2024-06-05 and 0.5.6 dated 2024-11-27
DESCRIPTION | 8 +++--- MD5 | 10 ++++---- NEWS.md | 6 +++++ R/ACO_lavaan.R | 57 ++++++++++++++++++++++++++++++++---------------- build/partial.rdb |binary man/antcolony.lavaan.Rd | 7 +++++ 6 files changed, 59 insertions(+), 29 deletions(-)
Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards
Consortium) compliant Analysis Results Data objects. These objects are
used and re-used to construct summary tables, visualizations, and
written reports. The package also exports utilities for working with
these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] ,
Becca Krouse [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cards versions 0.3.0 dated 2024-10-03 and 0.4.0 dated 2024-11-27
cards-0.3.0/cards/man/check_pkg_installed.Rd |only cards-0.3.0/cards/tests/testthat/_snaps/check_pkg_installed.md |only cards-0.3.0/cards/tests/testthat/test-check_pkg_installed.R |only cards-0.4.0/cards/DESCRIPTION | 6 cards-0.4.0/cards/MD5 | 59 +++--- cards-0.4.0/cards/NAMESPACE | 8 cards-0.4.0/cards/NEWS.md | 24 ++ cards-0.4.0/cards/R/ard_categorical.R | 2 cards-0.4.0/cards/R/ard_continuous.R | 15 + cards-0.4.0/cards/R/ard_pairwise.R |only cards-0.4.0/cards/R/ard_strata.R | 4 cards-0.4.0/cards/R/as_card_fn.R |only cards-0.4.0/cards/R/import-standalone-check_pkg_installed.R | 89 +++++----- cards-0.4.0/cards/R/import-standalone-checks.R | 4 cards-0.4.0/cards/R/import-standalone-cli_call_env.R | 5 cards-0.4.0/cards/R/import-standalone-forcats.R | 39 ++++ cards-0.4.0/cards/R/import-standalone-stringr.R | 17 + cards-0.4.0/cards/R/import-standalone-tibble.R | 3 cards-0.4.0/cards/R/print.R | 9 + cards-0.4.0/cards/R/print_ard_conditions.R | 2 cards-0.4.0/cards/R/tidy_ard_order.R | 1 cards-0.4.0/cards/man/ard_categorical.Rd | 2 cards-0.4.0/cards/man/ard_dichotomous.Rd | 2 cards-0.4.0/cards/man/ard_pairwise.Rd |only cards-0.4.0/cards/man/ard_strata.Rd | 2 cards-0.4.0/cards/man/as_cards_fn.Rd |only cards-0.4.0/cards/man/dot-calculate_tabulation_statistics.Rd | 2 cards-0.4.0/cards/man/dot-lst_results_as_df.Rd | 2 cards-0.4.0/cards/man/dot-process_denominator.Rd | 2 cards-0.4.0/cards/tests/testthat/_snaps/ard_pairwise.md |only cards-0.4.0/cards/tests/testthat/test-ard_complex.R | 30 +++ cards-0.4.0/cards/tests/testthat/test-ard_continuous.R | 31 +++ cards-0.4.0/cards/tests/testthat/test-ard_hierarchical.R | 34 +++ cards-0.4.0/cards/tests/testthat/test-ard_pairwise.R |only cards-0.4.0/cards/tests/testthat/test-as_cards_fn.R |only cards-0.4.0/cards/tests/testthat/test-tidy_ard_column_order.R |only 36 files changed, 290 insertions(+), 104 deletions(-)