Title: Method Comparison Regression
Description: Regression methods to quantify the relation between two measurement
methods are provided by this package. In particular it addresses regression
problems with errors in both variables and without repeated measurements. It
implements the CLSI recommendations (see J. A. Budd et al.
(2018, <https://clsi.org/standards/products/method-evaluation/documents/ep09/>)
for analytical method comparison and bias estimation using patient samples.
Furthermore, algorithms for Theil-Sen and equivariant Passing-Bablok estimators
are implemented, see F. Dufey (2020, <doi:10.1515/ijb-2019-0157>) and
J. Raymaekers and F. Dufey (2022, <arXiv:2202:08060>).
A comprehensive overview over the implemented methods and references can be found
in the manual pages "mcr-package" and "mcreg".
Author: Sergej Potapov [aut, cre],
Fabian Model [aut],
Andre Schuetzenmeister [aut] ,
Ekaterina Manuilova [aut],
Florian Dufey [aut] ,
Jakob Raymaekers [aut] ,
Roche [cph, fnd]
Maintainer: Sergej Potapov <sergej.potapov@roche.com>
Diff between mcr versions 1.2.2 dated 2021-04-23 and 1.3.0 dated 2022-10-23
DESCRIPTION | 57 - MD5 | 229 ++-- NAMESPACE | 25 R/MCResult.r | 17 R/MCResultAnalytical.r | 5 R/MCResultAnalyticalMethods.r | 6 R/MCResultBCa.r | 5 R/MCResultBCaMethods.r | 8 R/MCResultJackknife.r | 4 R/MCResultJackknifeMethods.r | 10 R/MCResultMethods.r | 608 ++++++----- R/MCResultResampling.r | 4 R/MCResultResamplingMethods.r | 6 R/mcBootstrap.r | 404 +++---- R/mcCalcTstar.r | 6 R/mcDeming.r | 69 - R/mcLinReg.r | 85 - R/mcPBequi.r |only R/mcPaBa.r | 192 +-- R/mcPaBaLarge.r | 8 R/mcWDeming.r | 100 - R/mcrIncludeLegend.r | 4 R/mcrInterface.r | 313 +++-- R/zzz.r | 2 inst/ChangeLog.txt |only inst/RunRoxy.R |only inst/unitTests/TestCaseCollection/MC_TestCase_AnaIT_TD13.xml | 58 + inst/unitTests/TestCaseCollection/MC_TestCase_AnaIT_TD15.xml | 57 + inst/unitTests/TestCaseCollection/MC_TestCase_AnaIT_TD20.xml | 59 + inst/unitTests/TestCaseCollection/MC_TestCase_AnaIT_TD41.xml | 61 + inst/unitTests/TestCaseCollection/MC_TestCase_AnaIT_TD75.xml | 58 + inst/unitTests/TestCaseCollection/MC_TestCase_AnaIT_TD9.xml | 56 + inst/unitTests/runalltests.R | 2 inst/unitTests/runit.MCResultMethods.R | 4 inst/unitTests/runit.mcBootstrap.R | 40 inst/unitTests/runit.mcPBequi.R |only inst/unitTests/runit.mcPaBa.R | 4 inst/unitTests/runit.mcPaBaLarge.R | 32 inst/unitTests/runitMCReg.R | 12 inst/unitTests/testProtocol.html |only man/MCResult-class.Rd | 5 man/MCResult.calcBias.Rd | 45 man/MCResult.calcCUSUM.Rd | 29 man/MCResult.calcResponse.Rd | 22 man/MCResult.getCoefficients.Rd | 9 man/MCResult.getData.Rd | 9 man/MCResult.getErrorRatio.Rd | 5 man/MCResult.getFitted.Rd | 14 man/MCResult.getRegmethod.Rd | 8 man/MCResult.getResiduals.Rd | 25 man/MCResult.getWeights.Rd | 5 man/MCResult.initialize.Rd | 44 man/MCResult.plot.Rd | 170 +-- man/MCResult.plotBias.Rd | 140 +- man/MCResult.plotDifference.Rd | 132 +- man/MCResult.plotResiduals.Rd | 68 - man/MCResult.printSummary.Rd | 6 man/MCResultAnalytical-class.Rd | 5 man/MCResultAnalytical.calcResponse.Rd | 13 man/MCResultAnalytical.initialize.Rd | 41 man/MCResultAnalytical.printSummary.Rd | 8 man/MCResultBCa-class.Rd | 5 man/MCResultBCa.bootstrapSummary.Rd | 8 man/MCResultBCa.calcResponse.Rd | 24 man/MCResultBCa.initialize.Rd | 93 - man/MCResultBCa.plotBootstrapCoefficients.Rd | 12 man/MCResultBCa.plotBootstrapT.Rd | 13 man/MCResultBCa.printSummary.Rd | 8 man/MCResultJackknife-class.Rd | 5 man/MCResultJackknife.calcResponse.Rd | 13 man/MCResultJackknife.getJackknifeIntercept.Rd | 8 man/MCResultJackknife.getJackknifeSlope.Rd | 8 man/MCResultJackknife.getJackknifeStatistics.Rd | 9 man/MCResultJackknife.getRJIF.Rd | 21 man/MCResultJackknife.initialize.Rd | 51 man/MCResultJackknife.plotwithRJIF.Rd | 20 man/MCResultJackknife.printSummary.Rd | 8 man/MCResultResampling-class.Rd | 5 man/MCResultResampling.bootstrapSummary.Rd | 8 man/MCResultResampling.calcResponse.Rd | 24 man/MCResultResampling.initialize.Rd | 88 - man/MCResultResampling.plotBootstrapCoefficients.Rd | 12 man/MCResultResampling.plotBootstrapT.Rd | 13 man/MCResultResampling.printSummary.Rd | 8 man/calcDiff.Rd | 13 man/compareFit.Rd | 14 man/creatinine.Rd | 2 man/includeLegend.Rd | 83 - man/mc.PBequi.Rd |only man/mc.analytical.ci.Rd | 20 man/mc.bootstrap.Rd | 152 +- man/mc.calc.Student.Rd | 37 man/mc.calc.bca.Rd | 37 man/mc.calc.quant.Rd | 10 man/mc.calc.quantile.Rd | 28 man/mc.calc.tboot.Rd | 43 man/mc.calcAngleMat.R.Rd | 16 man/mc.calcAngleMat.Rd | 16 man/mc.calcLinnetCI.Rd | 34 man/mc.calcTstar.Rd | 24 man/mc.deming.Rd | 34 man/mc.linreg.Rd | 26 man/mc.make.CIframe.Rd | 20 man/mc.paba.LargeData.Rd | 65 - man/mc.paba.Rd | 42 man/mc.wdemingConstCV.Rd | 43 man/mc.wlinreg.Rd | 28 man/mcr-package.Rd | 51 man/mcreg.Rd | 451 +++----- man/newMCResult.Rd | 48 man/newMCResultAnalytical.Rd | 51 man/newMCResultBCa.Rd | 110 - man/newMCResultJackknife.Rd | 57 - man/newMCResultResampling.Rd | 102 - src/PaBaAlgorithm.c | 45 src/calcRegression.c |only src/calcRegression.h |only src/init.c | 22 src/utils.functions.c |only src/utils.functions.h |only src/vartau.f |only 121 files changed, 3137 insertions(+), 2464 deletions(-)
Title: Generalized UniFrac Distances, Distance-Based Multivariate
Methods and Feature-Based Univariate Methods for Microbiome
Data Analysis
Description: A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.
Author: Jun Chen, Xianyang Zhang, Lu Yang
Maintainer: Jun Chen <chen.jun2@mayo.edu>
Diff between GUniFrac versions 1.6 dated 2022-05-17 and 1.7 dated 2022-10-23
DESCRIPTION | 8 MD5 | 29 - NAMESPACE | 1 R/SimMSeq.R | 189 ++++++++ R/ZicoSeq.R | 23 - build/vignette.rds |binary data/stool.otu.tab.rda |binary data/throat.meta.rda |binary data/throat.otu.tab.rda |binary data/throat.tree.rda |binary data/vaginal.otu.tab.rda |binary inst/doc/ZicoSeq.html | 1019 +++++++++++++++++++++++++++-------------------- man/SimulateMSeq.Rd | 8 man/SimulateMSeqC.Rd |only man/ZicoSeq.Rd | 5 man/ZicoSeq.plot.Rd | 2 16 files changed, 825 insertions(+), 459 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]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between ggeffects versions 1.1.3 dated 2022-08-07 and 1.1.4 dated 2022-10-23
ggeffects-1.1.3/ggeffects/build/partial.rdb |only ggeffects-1.1.4/ggeffects/DESCRIPTION | 17 ggeffects-1.1.4/ggeffects/MD5 | 286 ++--- ggeffects-1.1.4/ggeffects/NEWS.md | 22 ggeffects-1.1.4/ggeffects/R/collapse_re_data.R | 19 ggeffects-1.1.4/ggeffects/R/emmeans_prediction_data.R | 78 - ggeffects-1.1.4/ggeffects/R/get_predictions_MixMod.R | 14 ggeffects-1.1.4/ggeffects/R/get_predictions_cgam.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_clm.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_clm2.R | 3 ggeffects-1.1.4/ggeffects/R/get_predictions_clmm.R | 13 ggeffects-1.1.4/ggeffects/R/get_predictions_coxph.R | 15 ggeffects-1.1.4/ggeffects/R/get_predictions_gam.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_gam2.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_gamlss.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_geeglm.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_generic.R | 5 ggeffects-1.1.4/ggeffects/R/get_predictions_generic2.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_glimML.R | 6 ggeffects-1.1.4/ggeffects/R/get_predictions_glm.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_glmmTMB.R | 14 ggeffects-1.1.4/ggeffects/R/get_predictions_glmrob_base.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_lm.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_lme.R | 10 ggeffects-1.1.4/ggeffects/R/get_predictions_logitr.R |only ggeffects-1.1.4/ggeffects/R/get_predictions_lrm.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_mclogit.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_merMod.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_mixor.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_mlogit.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_multinom.R | 4 ggeffects-1.1.4/ggeffects/R/get_predictions_ols.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_polr.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_stan.R | 10 ggeffects-1.1.4/ggeffects/R/get_predictions_survival.R | 12 ggeffects-1.1.4/ggeffects/R/get_predictions_svyglm.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_tobit.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_vglm.R | 7 ggeffects-1.1.4/ggeffects/R/get_predictions_wbm.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_zelig.R | 2 ggeffects-1.1.4/ggeffects/R/get_predictions_zeroinfl.R | 2 ggeffects-1.1.4/ggeffects/R/getter.R | 117 +- ggeffects-1.1.4/ggeffects/R/ggeffect.R | 12 ggeffects-1.1.4/ggeffects/R/ggemmeans.R | 18 ggeffects-1.1.4/ggeffects/R/ggemmeans_add_confint.R | 2 ggeffects-1.1.4/ggeffects/R/ggemmeans_zi_predictions.R | 6 ggeffects-1.1.4/ggeffects/R/ggpredict.R | 571 +++++----- ggeffects-1.1.4/ggeffects/R/moderator_pattern.R | 65 - ggeffects-1.1.4/ggeffects/R/new_data.R | 6 ggeffects-1.1.4/ggeffects/R/plot.R | 183 +-- ggeffects-1.1.4/ggeffects/R/pool_predictions.R | 19 ggeffects-1.1.4/ggeffects/R/post_processing_predictions.R | 2 ggeffects-1.1.4/ggeffects/R/predict_zero_inflation.R | 82 - ggeffects-1.1.4/ggeffects/R/predictions.R | 4 ggeffects-1.1.4/ggeffects/R/pretty_range.R | 14 ggeffects-1.1.4/ggeffects/R/print.R | 8 ggeffects-1.1.4/ggeffects/R/residualize_over_grid.R | 46 ggeffects-1.1.4/ggeffects/R/simulate_predictions.R | 11 ggeffects-1.1.4/ggeffects/R/standard_error_predictions.R | 15 ggeffects-1.1.4/ggeffects/R/themes.R | 19 ggeffects-1.1.4/ggeffects/R/utils.R | 101 - ggeffects-1.1.4/ggeffects/R/utils_check_transformations.R | 4 ggeffects-1.1.4/ggeffects/R/utils_colors.R | 2 ggeffects-1.1.4/ggeffects/R/utils_get_cleaned_terms.R | 2 ggeffects-1.1.4/ggeffects/R/utils_get_data_grid.R | 78 - ggeffects-1.1.4/ggeffects/R/utils_get_representative_values.R | 7 ggeffects-1.1.4/ggeffects/R/utils_ggpredict.R | 6 ggeffects-1.1.4/ggeffects/R/utils_handle_labels.R | 41 ggeffects-1.1.4/ggeffects/R/utils_model_function.R | 1 ggeffects-1.1.4/ggeffects/R/utils_select.R | 2 ggeffects-1.1.4/ggeffects/R/vcov.R | 57 ggeffects-1.1.4/ggeffects/README.md | 52 ggeffects-1.1.4/ggeffects/inst/doc/content.html | 252 ++++ ggeffects-1.1.4/ggeffects/man/collapse_by_group.Rd | 16 ggeffects-1.1.4/ggeffects/man/figures/unnamed-chunk-4-1.png |binary ggeffects-1.1.4/ggeffects/man/figures/unnamed-chunk-5-1.png |binary ggeffects-1.1.4/ggeffects/man/figures/unnamed-chunk-6-1.png |binary ggeffects-1.1.4/ggeffects/man/get_title.Rd | 21 ggeffects-1.1.4/ggeffects/man/ggpredict.Rd | 529 ++++----- ggeffects-1.1.4/ggeffects/man/new_data.Rd | 8 ggeffects-1.1.4/ggeffects/man/plot.Rd | 49 ggeffects-1.1.4/ggeffects/man/pool_predictions.Rd | 10 ggeffects-1.1.4/ggeffects/man/pretty_range.Rd | 6 ggeffects-1.1.4/ggeffects/man/residualize_over_grid.Rd | 28 ggeffects-1.1.4/ggeffects/man/values_at.Rd | 44 ggeffects-1.1.4/ggeffects/man/vcov.Rd | 16 ggeffects-1.1.4/ggeffects/tests/testthat/helper-requiet.R |only ggeffects-1.1.4/ggeffects/tests/testthat/test-Gam2.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-MCMCglmm.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-MixMod.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-backtransform_response.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-betareg.R | 12 ggeffects-1.1.4/ggeffects/tests/testthat/test-brms-categ-cum.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-brms-ppd.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-brms-trial.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-clean_vars.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-clm.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-clm2.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-clmm.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-condition.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-contrasts.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-contrasts2.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-contrasts3.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-correct_se_sorting.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-coxph.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-decimals.R | 10 ggeffects-1.1.4/ggeffects/tests/testthat/test-emmeans_factor_char.R |only ggeffects-1.1.4/ggeffects/tests/testthat/test-extract_values.R | 13 ggeffects-1.1.4/ggeffects/tests/testthat/test-gamlss.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-gamm.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-gamm4.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-gee.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-geeglm.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-get_titles.R | 10 ggeffects-1.1.4/ggeffects/tests/testthat/test-glm.R | 10 ggeffects-1.1.4/ggeffects/tests/testthat/test-glmer.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-glmmTMB.R | 4 ggeffects-1.1.4/ggeffects/tests/testthat/test-glmrob_base.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-gls.R | 10 ggeffects-1.1.4/ggeffects/tests/testthat/test-ivreg.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-linear-models.R | 14 ggeffects-1.1.4/ggeffects/tests/testthat/test-lmer.R | 10 ggeffects-1.1.4/ggeffects/tests/testthat/test-lmrob_base.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-logistf.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-lrm.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-negbin.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-nlme.R | 46 ggeffects-1.1.4/ggeffects/tests/testthat/test-offset_zeroinfl.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-on-the-fly-factor.R | 20 ggeffects-1.1.4/ggeffects/tests/testthat/test-orm.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-plot.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-poisson.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-polr.R | 10 ggeffects-1.1.4/ggeffects/tests/testthat/test-poly-zeroinf.R | 9 ggeffects-1.1.4/ggeffects/tests/testthat/test-print.R | 10 ggeffects-1.1.4/ggeffects/tests/testthat/test-rq.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-rstanarm-ppd.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-rstanarm.R | 10 ggeffects-1.1.4/ggeffects/tests/testthat/test-survey.R | 12 ggeffects-1.1.4/ggeffects/tests/testthat/test-survreg.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-svyglmnb.R | 12 ggeffects-1.1.4/ggeffects/tests/testthat/test-tobit.R | 6 ggeffects-1.1.4/ggeffects/tests/testthat/test-vgam.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-vglm.R | 2 ggeffects-1.1.4/ggeffects/tests/testthat/test-zeroinfl.R | 8 ggeffects-1.1.4/ggeffects/tests/testthat/test-zi_prob.R | 2 146 files changed, 2019 insertions(+), 1548 deletions(-)
Title: Access Finnish Geospatial Data
Description: Tools for reading Finnish open geospatial data in R.
Author: Markus Kainu [aut, cre] ,
Joona Lehtomaki [aut] ,
Juuso Parkkinen [ctb] ,
Jani Miettinen [ctb],
Pyry Kantanen [ctb],
Sampo Vesanen [ctb],
Leo Lahti [aut]
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>
Diff between geofi versions 1.0.6 dated 2022-01-30 and 1.0.7 dated 2022-10-23
DESCRIPTION | 8 MD5 | 44 NEWS.md | 4 README.md | 6 build/vignette.rds |binary inst/CITATION | 2 inst/doc/geofi_datasets.R | 2 inst/doc/geofi_datasets.Rmd | 2 inst/doc/geofi_datasets.html | 322 + inst/doc/geofi_joining_attribute_data.R | 4 inst/doc/geofi_joining_attribute_data.Rmd | 10 inst/doc/geofi_joining_attribute_data.html | 313 + inst/doc/geofi_making_maps.R | 6 inst/doc/geofi_making_maps.Rmd | 6 inst/doc/geofi_making_maps.html | 5394 ++++++++++++++++++++++++++++- inst/doc/geofi_spatial_analysis.R | 99 inst/doc/geofi_spatial_analysis.Rmd | 135 inst/doc/geofi_spatial_analysis.html | 516 ++ man/figures/readme_map-1.png |binary vignettes/geofi_datasets.Rmd | 2 vignettes/geofi_joining_attribute_data.Rmd | 10 vignettes/geofi_making_maps.Rmd | 6 vignettes/geofi_spatial_analysis.Rmd | 135 23 files changed, 6785 insertions(+), 241 deletions(-)
Title: Tipping Point Analysis for Bayesian Dynamic Borrowing
Description: Tipping point analysis for clinical trials that employ Bayesian dynamic borrowing via robust meta-analytic predictive (MAP) priors. Mainly an implementation of an approach proposed by Best and colleagues (2021) is provided <doi:10.1002/pst.2093>. Further functions facilitate the specification of the robust MAP prior via expert elicitation (using the roulette method) and computation of the posterior distribution of the treatment effect with either fixed or stochastic expert-elicited weights. Intended use is the planning, analysis and interpretation of extrapolation studies in pediatric drug development, but applicability is generally wider.
Author: Morten Dreher [aut],
Christian Stock [aut, cre] ,
Emma Torrini [ctb]
Maintainer: Christian Stock <christian.stock@boehringer-ingelheim.com>
Diff between tipmap versions 0.3.5 dated 2022-09-02 and 0.3.7 dated 2022-10-23
tipmap-0.3.5/tipmap/R/get_tipping_point.R |only tipmap-0.3.5/tipmap/man/get_tipping_point.Rd |only tipmap-0.3.5/tipmap/tests/testthat/test-get_tipping_point.R |only tipmap-0.3.7/tipmap/DESCRIPTION | 11 - tipmap-0.3.7/tipmap/MD5 | 34 +++- tipmap-0.3.7/tipmap/NAMESPACE | 1 tipmap-0.3.7/tipmap/NEWS.md | 7 tipmap-0.3.7/tipmap/R/create_tipmap_data.R | 2 tipmap-0.3.7/tipmap/R/get_tipping_points.R |only tipmap-0.3.7/tipmap/R/tipmap-package.R |only tipmap-0.3.7/tipmap/R/tipmap_plot.R | 26 +-- tipmap-0.3.7/tipmap/README.md | 79 ++++++----- tipmap-0.3.7/tipmap/build |only tipmap-0.3.7/tipmap/inst/doc |only tipmap-0.3.7/tipmap/man/create_tipmap_data.Rd | 2 tipmap-0.3.7/tipmap/man/get_tipping_points.Rd |only tipmap-0.3.7/tipmap/man/tipmap-package.Rd |only tipmap-0.3.7/tipmap/man/tipmap_plot.Rd | 10 - tipmap-0.3.7/tipmap/tests/testthat.R | 16 +- tipmap-0.3.7/tipmap/tests/testthat/test-get_tipping_points.R |only tipmap-0.3.7/tipmap/vignettes |only 21 files changed, 116 insertions(+), 72 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-10 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-13 1.1-5
2014-09-16 1.1-4
2013-03-26 1.1-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-23 0.1.1
2021-03-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-06 1.1.2
2020-08-05 1.1.1
2019-12-18 1.1.0
2019-08-30 1.0.1
2018-12-09 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-24 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-20 0.1.2
2021-06-18 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-04 1.0.6
2017-06-12 1.0.4
2017-06-06 1.0.3
2016-09-08 1.0.2
2015-08-13 1.0.0
2014-12-26 0.9.1
2014-10-28 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-29 0.5
2013-03-26 0.4
2006-04-27 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-14 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-02 2.2
2020-10-19 2.1
2020-06-17 2.0
2020-01-19 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-21 0.9.2
2015-09-07 0.9.1
2014-10-11 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-14 0.2
2013-12-19 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-06 1.4.0
2022-07-18 1.3.0
2022-03-25 1.2.3
2022-03-23 1.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-19 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-31 1.2
2017-09-24 1.1
2015-11-28 1.0
Title: Symbols for 'Markdown' and 'Shiny' Application
Description: Direct insertion of symbols (e.g. currencies, letters, arrows, mathematical symbols and so on) into 'Rmarkdown' documents and 'Shiny' applications by incorporating 'HTML' hex codes.
Author: Obinna Obianom
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between r2symbols versions 1.1 dated 2022-08-15 and 1.2 dated 2022-10-23
DESCRIPTION | 10 ++--- MD5 | 24 ++++++------ NEWS.md | 8 ++-- R/symbol.R | 13 ++++--- R/symbolSetting.R | 8 ++-- README.md | 65 +++++++++++++++++++++++++++++------ inst/doc/introduction_r_symbols.R | 6 +-- inst/doc/introduction_r_symbols.Rmd | 16 ++++---- inst/doc/introduction_r_symbols.html | 24 ++++++------ inst/doc/newversion_r_symbols.html | 6 +-- man/sym.setting.Rd | 4 +- man/symbol.setting.Rd | 4 +- vignettes/introduction_r_symbols.Rmd | 16 ++++---- 13 files changed, 127 insertions(+), 77 deletions(-)
Title: 'Neuroconductor' Base Package with Helper Functions for 'nifti'
Objects
Description: Base package for 'Neuroconductor', which includes many helper
functions that interact with objects of class 'nifti', implemented by
package 'oro.nifti', for reading/writing and also other manipulation
functions.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurobase versions 1.32.2 dated 2022-08-24 and 1.32.3 dated 2022-10-23
DESCRIPTION | 7 MD5 | 30 - NEWS.md | 4 R/getEmptyImageDimensions.R | 5 R/images2matrix.R | 2 R/mask_vals.R | 8 R/ortho_diff.R | 18 - R/randomize_mask.R | 2 R/replace_outside_hull.R | 2 R/rescale_img.R | 2 build/vignette.rds |binary inst/doc/neurobase.html | 346 +++----------------- inst/doc/nifti_basics.html | 705 ++++++----------------------------------- inst/doc/simple_io.html | 70 ---- man/getEmptyImageDimensions.Rd | 6 man/mask_vals-methods.Rd | 2 16 files changed, 255 insertions(+), 954 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. 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] ,
Katriona Goldmann [aut]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between nestedcv versions 0.3.0 dated 2022-09-10 and 0.4.0 dated 2022-10-23
DESCRIPTION | 15 ++-- MD5 | 48 ++++++++------ NAMESPACE | 16 ++++ NEWS.md | 21 ++++++ R/checkxy.R | 6 + R/class_balance.R | 19 +++-- R/complex_filters.R | 69 ++++++++++++++++++++ R/filters.R | 2 R/innercv_roc.R | 8 ++ R/nest_filter_balance.R | 60 ++++++++++++++--- R/nestcv.train.R | 126 +++++++++++++++++++++++++++++-------- R/nestcv_SuperLearner.R |only R/nestedcv.R | 75 ++++++++++++++-------- R/outercv.R | 91 +++++++++++++++++++-------- R/utils.R |only README.md | 6 + inst/doc/nestedcv.R | 11 ++- inst/doc/nestedcv.Rmd | 44 +++++++++++-- inst/doc/nestedcv.html | 151 +++++++++++++++++++++++++-------------------- man/class_balance.Rd | 7 -- man/layer_filter.Rd |only man/nestcv.SuperLearner.Rd |only man/nestcv.glmnet.Rd | 12 +++ man/nestcv.train.Rd | 33 ++++++++- man/outercv.Rd | 13 +++ man/supervisedPCA.Rd |only man/weight.Rd |only vignettes/nestedcv.Rmd | 44 +++++++++++-- 28 files changed, 657 insertions(+), 220 deletions(-)
Title: Reverse Engineers Regular Expression Patterns for R Objects
Description: Reverse engineer a regular expression pattern for the characters
contained in an R object. Individual characters can be categorised into
digits, letters, punctuation or spaces and encoded into run-lengths. This
can be used to summarise the structure of a dataset or identify non-standard
entries. Many non-character inputs such as numeric vectors and data frames
are supported.
Author: Jasper Watson [aut, cre]
Maintainer: Jasper Watson <jasper.g.watson@gmail.com>
Diff between inverseRegex versions 0.1.0 dated 2019-09-23 and 0.1.1 dated 2022-10-23
DESCRIPTION | 9 MD5 | 16 NEWS.md | 4 README.md | 26 - build/vignette.rds |binary inst/doc/overview.R | 16 inst/doc/overview.html | 645 +++++++++++++++++++++---------------- man/inverseRegex.Rd | 15 tests/testthat/test.inverseRegex.R | 22 - 9 files changed, 442 insertions(+), 311 deletions(-)
Title: R Interface to the 'DieHarder' RNG Test Suite
Description: The 'RDieHarder' package provides an R interface to
the 'DieHarder' suite of random number generators and tests that
was developed by Robert G. Brown and David Bauer, extending
earlier work by George Marsaglia and others. The 'DieHarder'
library code is included.
Author: Dirk Eddelbuettel, Robert G Brown, David Bauer
plus contributors to DieHarder
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RDieHarder versions 0.2.3 dated 2021-12-14 and 0.2.4 dated 2022-10-23
ChangeLog | 14 DESCRIPTION | 8 MD5 | 180 - README.md | 1 build/vignette.rds |binary configure | 1975 ++++++++++++------- configure.ac | 4 inst/doc/RDieHarder.pdf |binary src/Makevars.in | 6 src/add_ui_rngs.c | 2 src/choose_rng.c | 18 src/dieharder.c | 8 src/dieharder.h | 16 src/globals.c | 4 src/help.c | 30 src/init.c | 4 src/libdieharder/Makefile.in | 1 src/libdieharder/Makefile.win | 5 src/libdieharder/bits.c | 2 src/libdieharder/dab_dct.c | 4 src/libdieharder/diehard_craps.c | 2 src/libdieharder/dieharder/Dtest.h | 5 src/libdieharder/dieharder/Vtest.h | 2 src/libdieharder/dieharder/Xtest.h | 2 src/libdieharder/dieharder/dab_birthdays1.h | 2 src/libdieharder/dieharder/dab_bytedistrib.h | 2 src/libdieharder/dieharder/dab_dct.h | 2 src/libdieharder/dieharder/dab_filltree.h | 2 src/libdieharder/dieharder/dab_filltree2.h | 2 src/libdieharder/dieharder/dab_monobit2.h | 2 src/libdieharder/dieharder/dab_opso2.h | 2 src/libdieharder/dieharder/diehard_2dsphere.h | 2 src/libdieharder/dieharder/diehard_3dsphere.h | 2 src/libdieharder/dieharder/diehard_birthdays.h | 2 src/libdieharder/dieharder/diehard_bitstream.h | 2 src/libdieharder/dieharder/diehard_count_1s_byte.h | 2 src/libdieharder/dieharder/diehard_count_1s_stream.h | 2 src/libdieharder/dieharder/diehard_craps.h | 2 src/libdieharder/dieharder/diehard_dna.h | 2 src/libdieharder/dieharder/diehard_operm5.h | 2 src/libdieharder/dieharder/diehard_opso.h | 2 src/libdieharder/dieharder/diehard_oqso.h | 2 src/libdieharder/dieharder/diehard_parking_lot.h | 2 src/libdieharder/dieharder/diehard_rank_32x32.h | 2 src/libdieharder/dieharder/diehard_rank_6x8.h | 2 src/libdieharder/dieharder/diehard_runs.h | 2 src/libdieharder/dieharder/diehard_squeeze.h | 2 src/libdieharder/dieharder/diehard_sums.h | 2 src/libdieharder/dieharder/dieharder_rng_types.h | 2 src/libdieharder/dieharder/dieharder_test_types.h | 2 src/libdieharder/dieharder/libdieharder.h | 28 src/libdieharder/dieharder/marsaglia_tsang_gcd.h | 2 src/libdieharder/dieharder/rgb_bitdist.h | 2 src/libdieharder/dieharder/rgb_kstest_test.h | 2 src/libdieharder/dieharder/rgb_lagged_sums.h | 2 src/libdieharder/dieharder/rgb_minimum_distance.h | 2 src/libdieharder/dieharder/rgb_operm.h | 2 src/libdieharder/dieharder/rgb_permutations.h | 2 src/libdieharder/dieharder/rgb_persist.h | 3 src/libdieharder/dieharder/rgb_timing.h | 3 src/libdieharder/dieharder/std_test.h | 4 src/libdieharder/dieharder/sts_monobit.h | 2 src/libdieharder/dieharder/sts_runs.h | 2 src/libdieharder/dieharder/sts_serial.h | 3 src/libdieharder/dieharder/tests.h | 9 src/libdieharder/dieharder/verbose.h | 1 src/libdieharder/dieharder_rng_types.c | 2 src/libdieharder/dieharder_test_types.c | 2 src/libdieharder/random_seed.c | 2 src/libdieharder/rgb_lagged_sums.c | 2 src/libdieharder/rgb_operm.c | 43 src/libdieharder/rgb_permutations.c | 2 src/libdieharder/rgb_persist.c | 5 src/libdieharder/rgb_timing.c | 3 src/libdieharder/rngav.c | 2 src/libdieharder/rngs_gnu_r.c | 2 src/libdieharder/sample.c | 2 src/libdieharder/timing.c | 8 src/libdieharder/version.c | 4 src/list_rand.c | 2 src/list_rngs.c | 2 src/list_tests.c | 4 src/output.c | 6 src/output_rnds.c | 2 src/parsecl.c | 2 src/run_all_tests.c | 2 src/run_test.c | 2 src/startup.c | 2 src/time_rng.c | 6 src/user_template.c | 1 tests/RDieHarder.Rout.save | 2 91 files changed, 1597 insertions(+), 929 deletions(-)
Title: Interface to the 'SymEngine' Library
Description: Provides an R interface to 'SymEngine' <https://github.com/symengine/>,
a standalone 'C++' library for fast symbolic manipulation. The package has functionalities
for symbolic computation like calculating exact mathematical expressions, solving
systems of linear equations and code generation.
Author: Jialin Ma [cre, aut],
Isuru Fernando [aut],
Xin Chen [aut]
Maintainer: Jialin Ma <marlin@inventati.org>
Diff between symengine versions 0.2.1 dated 2022-04-28 and 0.2.2 dated 2022-10-23
DESCRIPTION | 6 MD5 | 16 +- build/vignette.rds |binary configure | 44 ++----- configure.win | 44 ++----- inst/doc/odesystem.html | 176 ++++++++++++++++------------- inst/doc/quick_start.html | 176 ++++++++++++++++------------- src/upstream.tar |binary tools/cran_comments/cran-comments_0.2.2.md |only tools/translate_to_cmake_flags.R |only 10 files changed, 245 insertions(+), 217 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle,
and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
Author: Manuel Lopez-Ibanez [aut, cre]
,
Jeremie Dubois-Lacoste [aut],
Leslie Perez Caceres [aut],
Thomas Stuetzle [aut],
Mauro Birattari [aut],
Eric Yuan [ctb],
Prasanna Balaprakash [ctb],
Nguyen Dang [ctb]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 3.4.1 dated 2020-03-31 and 3.5 dated 2022-10-23
irace-3.4.1/irace/R/irace2pyimp.R |only irace-3.4.1/irace/inst/examples/irace2pyimp |only irace-3.4.1/irace/inst/examples/matlab/RUN.m |only irace-3.4.1/irace/inst/examples/matlab/scenario2.txt |only irace-3.4.1/irace/inst/examples/matlab/target-runner |only irace-3.4.1/irace/man/configurationsBoxplot.Rd |only irace-3.4.1/irace/man/irace.usage.Rd |only irace-3.4.1/irace/man/irace2pyimp.Rd |only irace-3.4.1/irace/man/irace2pyimp_cmdline.Rd |only irace-3.4.1/irace/man/parallelCoordinatesPlot.Rd |only irace-3.4.1/irace/man/parameterFrequency.Rd |only irace-3.4.1/irace/man/scenario.update.paths.Rd |only irace-3.4.1/irace/man/testing.main.Rd |only irace-3.4.1/irace/src/iracebin/irace2pyimp.c |only irace-3.4.1/irace/tests/testthat/irace2pyimp |only irace-3.4.1/irace/tests/testthat/test-irace2pyimp.R |only irace-3.4.1/irace/vignettes/log-ablation.Rdata |only irace-3.5/irace/.Rinstignore | 2 irace-3.5/irace/BUGS | 108 - irace-3.5/irace/DESCRIPTION | 13 irace-3.5/irace/MD5 | 256 ++-- irace-3.5/irace/NAMESPACE | 20 irace-3.5/irace/NEWS.md | 245 +++- irace-3.5/irace/R/ablation.R | 446 ++++--- irace-3.5/irace/R/argparser.R | 82 + irace-3.5/irace/R/cluster.R | 55 irace-3.5/irace/R/generation.R | 122 +- irace-3.5/irace/R/irace-options.R | 206 +-- irace-3.5/irace/R/irace-package.R | 48 irace-3.5/irace/R/irace.R | 254 ++-- irace-3.5/irace/R/main.R | 373 +++--- irace-3.5/irace/R/model.R | 28 irace-3.5/irace/R/parameterAnalysis.R | 479 -------- irace-3.5/irace/R/parameterExploration.R | 14 irace-3.5/irace/R/path_rel2abs.R |only irace-3.5/irace/R/race-wrapper.R | 149 +- irace-3.5/irace/R/race.R | 368 +++--- irace-3.5/irace/R/readConfiguration.R | 503 ++++---- irace-3.5/irace/R/readParameters.R | 234 +++- irace-3.5/irace/R/testing.R | 16 irace-3.5/irace/R/timer.R |only irace-3.5/irace/R/tnorm.R | 10 irace-3.5/irace/R/utils.R | 310 ++--- irace-3.5/irace/R/version.R | 5 irace-3.5/irace/R/zzz.R |only irace-3.5/irace/README.md | 163 +- irace-3.5/irace/build/partial.rdb |binary irace-3.5/irace/build/vignette.rds |binary irace-3.5/irace/cleanup | 4 irace-3.5/irace/inst/bin/parallel-irace-mpi | 5 irace-3.5/irace/inst/bin/parallel-irace-qsub | 5 irace-3.5/irace/inst/bin/parallel-irace-slurm |only irace-3.5/irace/inst/doc/irace-package.R | 59 - 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Title: Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution,
provides a wide variety of shapes with one functional form.
This package provides random numbers, quantiles, probabilities,
densities and density quantiles for four different types of the distribution,
the FKML (Freimer et al 1988), RS (Ramberg and Schmeiser 1974), GPD (van Staden
and Loots 2009) and FM5 - see documentation for details.
It provides the density function, distribution function, and Quantile-Quantile
plots.
It implements a variety of estimation methods for the distribution,
including diagnostic plots.
Estimation methods include the starship (all 4 types),
method of L-Moments for the GPD and FKML types, and a
number of methods for only the FKML type.
These include maximum likelihood, maximum product of spacings,
Titterington's method, Moments, Trimmed L-Moments and
Distributional Least Absolutes.
Author: Robert King [aut, cre] ,
Benjamin Dean [aut],
Sigbert Klinke [aut],
Paul van Staden [aut]
Maintainer: Robert King <Robert.King.Newcastle@gmail.com>
Diff between gld versions 2.6.5 dated 2022-06-29 and 2.6.6 dated 2022-10-23
Changelog | 3 + DESCRIPTION | 8 +-- MD5 | 14 +++--- NEWS | 99 +++++++++++++++++++++++------------------------- build/partial.rdb |binary man/fit.fkml.moments.Rd | 1 man/gld.moments.Rd | 1 src/gld.rs.fx.c | 7 +-- 8 files changed, 67 insertions(+), 66 deletions(-)
Title: Interactive Sketches
Description: Creates static / animated / interactive visualisations embeddable
in R Markdown documents. It implements an R-to-JavaScript transpiler and
enables users to write JavaScript applications using the syntax of R.
Author: Chun Fung Kwok [aut, cre] ,
Kate Saunders [ctb]
Maintainer: Chun Fung Kwok <jkwok@svi.edu.au>
Diff between sketch versions 1.1.17 dated 2021-10-06 and 1.1.19 dated 2022-10-23
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Title: Easy Graphs for Data Visualisation and Linear Models for ANOVA
Description: Easily explore data by plotting graphs with a few lines of code. Use these ggplot() wrappers to quickly draw graphs of scatter/dots with box-whiskers, violins or SD error bars, data distributions, before-after graphs, factorial ANOVA and more. Customise graphs in many ways, for example, by choosing from colour blind-friendly palettes (12 discreet, 3 continuous and 2 divergent palettes). Use the simple code for ANOVA as ordinary (lm()) or mixed-effects linear models (lmer()), including randomised-block or repeated-measures designs, and fit non-linear outcomes as a generalised additive model (gam) using mgcv(). Obtain estimated marginal means and perform post-hoc comparisons on fitted models (via emmeans()). Also includes small datasets for practicing code and teaching basics before users move on to more complex designs. See vignettes for details on usage <https://grafify-vignettes.netlify.app/>. Citation: <doi:10.5281/zenodo.5136508>.
Author: Avinash R Shenoy [cre, aut]
Maintainer: Avinash R Shenoy <a.shenoy@imperial.ac.uk>
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grafify-3.0.0/grafify/man/plot_dotbar_sd.Rd | 71 +- grafify-3.0.0/grafify/man/plot_dotbox.Rd | 67 +- grafify-3.0.0/grafify/man/plot_dotviolin.Rd | 85 ++- grafify-3.0.0/grafify/man/plot_gam_predict.Rd |only grafify-3.0.0/grafify/man/plot_grafify_palette.Rd | 7 grafify-3.0.0/grafify/man/plot_histogram.Rd | 32 - grafify-3.0.0/grafify/man/plot_lm_predict.Rd |only grafify-3.0.0/grafify/man/plot_logscale.Rd |only grafify-3.0.0/grafify/man/plot_point_sd.Rd | 47 + grafify-3.0.0/grafify/man/plot_qq_gam.Rd |only grafify-3.0.0/grafify/man/plot_qqline.Rd | 35 - grafify-3.0.0/grafify/man/plot_qqmodel.Rd | 24 grafify-3.0.0/grafify/man/plot_scatterbar_sd.Rd | 77 ++- grafify-3.0.0/grafify/man/plot_scatterbox.Rd | 193 ++++--- grafify-3.0.0/grafify/man/plot_scatterviolin.Rd | 245 +++++----- grafify-3.0.0/grafify/man/plot_xy_CatGroup.Rd | 90 +++ grafify-3.0.0/grafify/man/plot_xy_NumGroup.Rd | 68 ++ grafify-3.0.0/grafify/man/scale_colour_grafify.Rd | 35 - grafify-3.0.0/grafify/man/scale_fill_grafify.Rd | 28 - grafify-3.0.0/grafify/man/table_summary.Rd |only grafify-3.0.0/grafify/man/table_x_reorder.Rd |only grafify-3.0.0/grafify/man/theme_grafify.Rd |only grafify-3.0.0/grafify/tests/testthat/test-plot_bar_sd.R | 21 grafify-3.0.0/grafify/tests/testthat/test-plot_dotbar_sd.R | 21 grafify-3.0.0/grafify/tests/testthat/test-plot_dotbox.R | 21 grafify-3.0.0/grafify/tests/testthat/test-plot_dotviolin.R | 22 grafify-3.0.0/grafify/tests/testthat/test-plot_point_sd.R | 20 grafify-3.0.0/grafify/tests/testthat/test-plot_scatterbar_sd.R | 21 grafify-3.0.0/grafify/tests/testthat/test-plot_scatterbox.R | 21 grafify-3.0.0/grafify/tests/testthat/test-plot_scatterviolin.R | 21 grafify-3.0.0/grafify/tests/testthat/test-scale_colour_grafify.R | 88 --- 118 files changed, 3358 insertions(+), 1943 deletions(-)
Title: In-Text Resizing for Containers, Images and Data Tables in
'Shiny', 'Markdown' and 'Quarto' Documents
Description: Automatic resizing toolbar for containers, images and tables. Most suitable to include resize functionality in 'Markdown', 'Rmarkdown' and 'Quarto' documents.
Author: Obinna Obianom
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between r2resize versions 1.2 dated 2022-09-12 and 1.3 dated 2022-10-23
r2resize-1.2/r2resize/R/setResizer.R |only r2resize-1.3/r2resize/DESCRIPTION | 14 r2resize-1.3/r2resize/MD5 | 48 r2resize-1.3/r2resize/NAMESPACE | 4 r2resize-1.3/r2resize/NEWS.md | 13 r2resize-1.3/r2resize/R/containerResizer.R |only r2resize-1.3/r2resize/R/markdownResizer.R |only r2resize-1.3/r2resize/README.md | 37 r2resize-1.3/r2resize/build/vignette.rds |binary r2resize-1.3/r2resize/inst/doc/introduction_r2resize.R | 37 r2resize-1.3/r2resize/inst/doc/introduction_r2resize.Rmd | 58 r2resize-1.3/r2resize/inst/doc/introduction_r2resize.html | 2757 ---------- r2resize-1.3/r2resize/inst/doc/resizable_containers_split_screen_r2resize.R |only r2resize-1.3/r2resize/inst/doc/resizable_containers_split_screen_r2resize.Rmd |only r2resize-1.3/r2resize/inst/doc/resizable_containers_split_screen_r2resize.html |only r2resize-1.3/r2resize/inst/examples/sample1.Rmd | 103 r2resize-1.3/r2resize/inst/examples/sample1.html | 1337 ---- r2resize-1.3/r2resize/inst/themes/default.css | 180 r2resize-1.3/r2resize/inst/themes/default_top.js | 2 r2resize-1.3/r2resize/inst/themes/divsplitter.js |only r2resize-1.3/r2resize/inst/themes/empahsisCard.css |only r2resize-1.3/r2resize/inst/themes/rezcontCard.css |only r2resize-1.3/r2resize/inst/themes/rezcontCard.js |only r2resize-1.3/r2resize/inst/themes/splitCard.css |only r2resize-1.3/r2resize/inst/themes/windowCard.css |only r2resize-1.3/r2resize/inst/themes/windowCard.js |only r2resize-1.3/r2resize/man/add.resizer.Rd | 2 r2resize-1.3/r2resize/man/empahsisCard.Rd |only r2resize-1.3/r2resize/man/r2resize-package.Rd | 4 r2resize-1.3/r2resize/man/sizeableCard.Rd |only r2resize-1.3/r2resize/man/splitCard.Rd |only r2resize-1.3/r2resize/man/windowCard.Rd |only r2resize-1.3/r2resize/vignettes/introduction_r2resize.Rmd | 58 r2resize-1.3/r2resize/vignettes/resizable_containers_split_screen_r2resize.Rmd |only 34 files changed, 374 insertions(+), 4280 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is provided. Wrapper routines for blackbox optimization under mixed equality and inequality constraints via an augmented Lagrangian scheme, and for large scale computer model calibration, are also provided. For details and tutorial, see Gramacy (2016 <doi:10.18637/jss.v072.i01>.
Author: Robert B. Gramacy <rbg@vt.edu>, Furong Sun <furongs@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between laGP versions 1.5-7 dated 2022-06-27 and 1.5-8 dated 2022-10-23
ChangeLog | 6 ++++ DESCRIPTION | 8 +++--- MD5 | 12 ++++----- inst/doc/laGP.pdf |binary src/init.c | 4 +-- src/linalg.c | 65 ++++++++++++++---------------------------------------- src/rhelp.h | 13 +++++----- 7 files changed, 43 insertions(+), 65 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) simulation and inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associ [...truncated...]
Author: Moreno Bevilacqua [aut, cre] ,
Victor Morales-Onate [aut] ,
Christian Caamano-Carrillo [aut]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 1.0.2 dated 2022-09-04 and 1.0.3 dated 2022-10-23
DESCRIPTION | 10 - MD5 | 32 +++--- R/GeoCorrFct_Cop.R | 17 ++- R/GeoScatterplot.R | 10 - R/GeoSim.r | 1 R/GeoSimCopula.R | 209 ++++++++++++++++++++++++++++++++++++++++- R/Utility.r | 6 - man/GeoCovariogram.Rd | 4 man/GeoFit.Rd | 40 ------- man/GeoKrig.Rd | 67 ------------- man/GeoKrigloc.Rd | 71 ------------- man/GeoScatterplot.Rd | 3 man/GeoTests.Rd | 2 src/CompositeLikelihoodCond2.c | 8 - src/Distributions.c | 22 ---- src/GeoModels_init.c | 4 src/Utility.c | 4 17 files changed, 265 insertions(+), 245 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut] ,
Vincent Arel-Bundock [aut, ctb]
,
Alex Hayes [rev] ,
Grant McDermott [ [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 0.18.5 dated 2022-10-12 and 0.18.6 dated 2022-10-23
DESCRIPTION | 25 + MD5 | 71 ++-- NAMESPACE | 9 NEWS.md | 18 + R/find_formula.R | 17 + R/find_predictors.R | 17 + R/find_response.R | 5 R/find_statistic.R | 2 R/format_table.R | 3 R/get_datagrid.R | 7 R/get_predicted.R | 22 + R/get_predicted_bayesian.R | 1 R/insight-package.R | 2 R/is_model.R | 2 R/is_model_supported.R | 4 R/link_function.R | 3 R/link_inverse.R | 12 R/model_info.R | 3 R/n_obs.R | 6 R/n_parameters.R | 12 README.md | 140 ++++----- inst/doc/display.R | 4 inst/doc/display.Rmd | 4 inst/doc/display.html | 184 +++++------ man/insight-package.Rd | 111 +++---- tests/testthat/test-cgam.R | 2 tests/testthat/test-coxph.R | 1 tests/testthat/test-gam.R | 2 tests/testthat/test-get_datagrid.R | 6 tests/testthat/test-get_predicted.R | 15 tests/testthat/test-glmmTMB.R | 3 tests/testthat/test-is_converged.R | 2 tests/testthat/test-logitr.R |only tests/testthat/test-model_data.R | 3 tests/testthat/test-null_model.R | 3 tests/testthat/test-rlmer.R | 556 +++++++++++++++++------------------- vignettes/display.Rmd | 4 37 files changed, 707 insertions(+), 574 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'rxode2' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [ctb],
Rik Schoemaker [ctb] ,
Justin Wilkins [ctb] ,
Wenping Wang [ctb],
Mirjam Trame [ctb],
Huijuan Xu [ctb],
John Harrold [ctb],
Bill Denney [ctb] ,
Theodoros Papathanasiou [ctb],
Teun Post [ctb],
Richard Hooi [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2 versions 2.0.7 dated 2022-06-27 and 2.0.8 dated 2022-10-23
nlmixr2-2.0.7/nlmixr2/build |only nlmixr2-2.0.7/nlmixr2/inst/doc |only nlmixr2-2.0.7/nlmixr2/vignettes |only nlmixr2-2.0.8/nlmixr2/DESCRIPTION | 12 nlmixr2-2.0.8/nlmixr2/MD5 | 101 ++-- nlmixr2-2.0.8/nlmixr2/NAMESPACE | 4 nlmixr2-2.0.8/nlmixr2/NEWS.md | 8 nlmixr2-2.0.8/nlmixr2/R/hardReexports.R | 109 +++- nlmixr2-2.0.8/nlmixr2/R/reexports.R | 4 nlmixr2-2.0.8/nlmixr2/R/utils.R | 61 +- nlmixr2-2.0.8/nlmixr2/README.md | 228 +++------- nlmixr2-2.0.8/nlmixr2/man/bootplot.Rd | 9 nlmixr2-2.0.8/nlmixr2/man/bootstrapFit.Rd | 60 ++ nlmixr2-2.0.8/nlmixr2/man/covarSearchAuto.Rd | 22 nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-1.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-10.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-11.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-12.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-13.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-14.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-15.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-16.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-17.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-18.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-19.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-2.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-20.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-21.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-22.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-23.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-24.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-25.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-26.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-27.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-28.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-3.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-4.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-5.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-6.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-7.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-8.png |binary nlmixr2-2.0.8/nlmixr2/man/figures/README-unnamed-chunk-2-9.png |binary nlmixr2-2.0.8/nlmixr2/man/foceiControl.Rd | 109 ++++ nlmixr2-2.0.8/nlmixr2/man/nlmeControl.Rd | 2 nlmixr2-2.0.8/nlmixr2/man/reexports.Rd | 4 nlmixr2-2.0.8/nlmixr2/man/saemControl.Rd | 12 nlmixr2-2.0.8/nlmixr2/man/vpcCens.Rd |only nlmixr2-2.0.8/nlmixr2/man/vpcCensTad.Rd |only nlmixr2-2.0.8/nlmixr2/man/vpcPlot.Rd | 17 nlmixr2-2.0.8/nlmixr2/man/vpcPlotTad.Rd |only nlmixr2-2.0.8/nlmixr2/man/vpcSim.Rd | 6 nlmixr2-2.0.8/nlmixr2/tests/testthat/test-basic-nlmixr2.R | 22 nlmixr2-2.0.8/nlmixr2/tests/testthat/test-ini-pipe.R |only 53 files changed, 473 insertions(+), 317 deletions(-)