Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible
outcome to evaluate the effectiveness of a new therapy (the true endpoint) is
difficult to measure. In such a situation, it can be an effective strategy to
replace the true endpoint by a (bio)marker that is easier to measure and that
allows for a prediction of the treatment effect on the true endpoint (a
surrogate endpoint). The package 'Surrogate' allows for an evaluation of the
appropriateness of a candidate surrogate endpoint based on the meta-analytic,
information-theoretic, and causal-inference frameworks. Part of this software
has been developed using funding provided from the European Union's Seventh
Framework Programme for research, technological development and demonstration
(Grant Agreement no 602552), the Special Research Fund (BOF) of Hasselt
University (BOF-number: BOF2OCPO3), GlaxoSmithKline Biologicals, Baekeland
Mandaat (HBC.2022.0145), and Johnson & Johnson Innovative Medicine.
Author: Wim Van Der Elst [cre, aut],
Florian Stijven [aut],
Fenny Ong [aut],
Dries De Witte [aut],
Paul Meyvisch [aut],
Alvaro Poveda [aut],
Ariel Alonso [aut],
Hannah Ensor [aut],
Christoper Weir [aut],
Geert Molenberghs [aut]
Maintainer: Wim Van Der Elst <wim.vanderelst@gmail.com>
Diff between Surrogate versions 3.3.0 dated 2024-06-12 and 3.3.1 dated 2025-01-23
Surrogate-3.3.0/Surrogate/tests/testthat/fixtures/sens-results-ovarian-guassian-comp.rds |only Surrogate-3.3.0/Surrogate/tests/testthat/test-ICABinCont_copula.R |only Surrogate-3.3.1/Surrogate/DESCRIPTION | 14 Surrogate-3.3.1/Surrogate/MD5 | 287 +- Surrogate-3.3.1/Surrogate/NAMESPACE | 453 ++-- Surrogate-3.3.1/Surrogate/NEWS.md | 6 Surrogate-3.3.1/Surrogate/R/AA.MultS.R | 34 Surrogate-3.3.1/Surrogate/R/Bootstrap.MEP.BinBin.R | 112 - Surrogate-3.3.1/Surrogate/R/CbC.R | 61 Surrogate-3.3.1/Surrogate/R/ECT.R | 10 Surrogate-3.3.1/Surrogate/R/ICA.Cont.Cont.MultS.R | 4 Surrogate-3.3.1/Surrogate/R/ICAContCont.R | 4 Surrogate-3.3.1/Surrogate/R/ICA_ContCont_copula.R |only Surrogate-3.3.1/Surrogate/R/ICA_OrdCont_copula.R |only Surrogate-3.3.1/Surrogate/R/ICA_OrdOrd_copula.R |only Surrogate-3.3.1/Surrogate/R/ICA_SurvSurv_copula.R | 298 +- Surrogate-3.3.1/Surrogate/R/ISTE.ContCont.R | 204 - Surrogate-3.3.1/Surrogate/R/ITCI-Dvine-inference-utils.R | 904 +++++--- Surrogate-3.3.1/Surrogate/R/MICAContCont.R | 4 Surrogate-3.3.1/Surrogate/R/MinSurrContCont.R | 4 Surrogate-3.3.1/Surrogate/R/Plot.FixedDiscrDiscrIT.R | 1 Surrogate-3.3.1/Surrogate/R/Pred.TrialT.ContCont.R | 80 Surrogate-3.3.1/Surrogate/R/Prentice.R | 40 Surrogate-3.3.1/Surrogate/R/Single.Trial.RE.AA.R | 318 +- Surrogate-3.3.1/Surrogate/R/SummaryITContCont.R | 29 Surrogate-3.3.1/Surrogate/R/SummaryMaxEntSPFBinBin.R | 19 Surrogate-3.3.1/Surrogate/R/SummaryMetaAnalyticMTSContCont.R | 64 Surrogate-3.3.1/Surrogate/R/SummaryMetaAnalyticSTSContCont.R | 19 Surrogate-3.3.1/Surrogate/R/SummarySPPBinBin.R | 81 Surrogate-3.3.1/Surrogate/R/SummaryTrialLevelMA.R | 5 Surrogate-3.3.1/Surrogate/R/Surrogate-package.R |only Surrogate-3.3.1/Surrogate/R/copula_utils.R | 302 ++ Surrogate-3.3.1/Surrogate/R/fit_model_BinCont_copula.R | 999 ++++----- Surrogate-3.3.1/Surrogate/R/fit_model_ContCont_copula.R |only Surrogate-3.3.1/Surrogate/R/fit_model_OrdCont_copula.R |only Surrogate-3.3.1/Surrogate/R/fit_model_OrdOrd_copula.R |only Surrogate-3.3.1/Surrogate/R/fit_model_SurvSurv.R | 1092 +++++----- Surrogate-3.3.1/Surrogate/R/goodness_of_fit_copula_models.R |only Surrogate-3.3.1/Surrogate/R/likelihood_copula_models.R | 14 Surrogate-3.3.1/Surrogate/R/plot.BinContCombnIT.R | 1 Surrogate-3.3.1/Surrogate/R/plot.Fano.BinBin.R | 1 Surrogate-3.3.1/Surrogate/R/plot.InfoTheoretic.R | 1 Surrogate-3.3.1/Surrogate/R/plot.MaxEntContCont.R | 1 Surrogate-3.3.1/Surrogate/R/plot.MaxEntSPF.BinBin.R | 98 Surrogate-3.3.1/Surrogate/R/plot.MetaAnalyticMTS.R | 3 Surrogate-3.3.1/Surrogate/R/plot.MetaAnalyticSTS.R | 1 Surrogate-3.3.1/Surrogate/R/plot.PPE.BinBin.R | 1 Surrogate-3.3.1/Surrogate/R/plot.SurvSurv.R | 1 Surrogate-3.3.1/Surrogate/R/plot.TrialLevelIT.R | 1 Surrogate-3.3.1/Surrogate/R/plot.TrialLevelMA.R | 1 Surrogate-3.3.1/Surrogate/R/plot.TwoStageSurvSurv.R | 1 Surrogate-3.3.1/Surrogate/R/plot.comb27.BinBin.R | 13 Surrogate-3.3.1/Surrogate/R/plot_ICABinBin.R | 1 Surrogate-3.3.1/Surrogate/R/plot_ICABinCont.R | 1 Surrogate-3.3.1/Surrogate/R/plot_MaxEntICABinBin.R | 15 Surrogate-3.3.1/Surrogate/R/plot_SPF.BinCont.R | 38 Surrogate-3.3.1/Surrogate/R/plot_SPPBinBin.R | 602 ++--- Surrogate-3.3.1/Surrogate/R/sensitivity_analysis_SurvSurv.R | 876 ++++---- Surrogate-3.3.1/Surrogate/R/sensitivity_analysis_copula.R |only Surrogate-3.3.1/Surrogate/R/sensitivity_intervals.R | 435 ++- Surrogate-3.3.1/Surrogate/R/summary.Fano.BinBin.R | 53 Surrogate-3.3.1/Surrogate/R/summary.FixedDIscrDiscrIT.R | 19 Surrogate-3.3.1/Surrogate/R/summary.MuContCont.MultS.R | 36 Surrogate-3.3.1/Surrogate/R/summary.PPE.BinBin.R | 26 Surrogate-3.3.1/Surrogate/R/summary.SurvSurv.R | 17 Surrogate-3.3.1/Surrogate/R/summary.TrialLevelIT.R | 9 Surrogate-3.3.1/Surrogate/R/summary.TwoStageSurvSurv.R | 10 Surrogate-3.3.1/Surrogate/R/summaryBinContCombnIT.R | 29 Surrogate-3.3.1/Surrogate/R/summary_ICABinBin.R | 95 Surrogate-3.3.1/Surrogate/R/summary_ICABinCont.R | 19 Surrogate-3.3.1/Surrogate/R/summary_MaxEntContCont.R | 15 Surrogate-3.3.1/Surrogate/R/summary_MaxEntICABinBin.R | 15 Surrogate-3.3.1/Surrogate/R/summary_SPFBinCont.R | 37 Surrogate-3.3.1/Surrogate/man/Dvine_ICA_confint.Rd | 3 Surrogate-3.3.1/Surrogate/man/FederatedApproachStage1.Rd | 2 Surrogate-3.3.1/Surrogate/man/FederatedApproachStage2.Rd | 2 Surrogate-3.3.1/Surrogate/man/FixedDiscrDiscrIT.Rd | 244 +- Surrogate-3.3.1/Surrogate/man/ICA_given_model_constructor.Rd | 27 Surrogate-3.3.1/Surrogate/man/ICA_given_model_constructor_SurvSurv.Rd |only Surrogate-3.3.1/Surrogate/man/Schizo.Rd | 4 Surrogate-3.3.1/Surrogate/man/Surrogate-package.Rd |only Surrogate-3.3.1/Surrogate/man/association_gof_copula.Rd |only Surrogate-3.3.1/Surrogate/man/clayton_loglik_copula_scale.Rd | 5 Surrogate-3.3.1/Surrogate/man/compute_ICA.Rd |only Surrogate-3.3.1/Surrogate/man/compute_ICA_ContCont.Rd |only Surrogate-3.3.1/Surrogate/man/compute_ICA_OrdCont.Rd |only Surrogate-3.3.1/Surrogate/man/compute_ICA_OrdOrd.Rd |only Surrogate-3.3.1/Surrogate/man/compute_ICA_SurvSurv.Rd | 6 Surrogate-3.3.1/Surrogate/man/constructor_ICA_estimator.Rd |only Surrogate-3.3.1/Surrogate/man/continuous_continuous_loglik.Rd |only Surrogate-3.3.1/Surrogate/man/delta_method_log_mutinfo.Rd | 3 Surrogate-3.3.1/Surrogate/man/estimate_ICA_ContCont.Rd |only Surrogate-3.3.1/Surrogate/man/estimate_ICA_OrdCont.Rd |only Surrogate-3.3.1/Surrogate/man/estimate_ICA_OrdOrd.Rd |only Surrogate-3.3.1/Surrogate/man/estimate_marginal.Rd |only Surrogate-3.3.1/Surrogate/man/figures |only Surrogate-3.3.1/Surrogate/man/fit_copula_ContCont.Rd |only Surrogate-3.3.1/Surrogate/man/fit_copula_OrdCont.Rd |only Surrogate-3.3.1/Surrogate/man/fit_copula_OrdOrd.Rd |only Surrogate-3.3.1/Surrogate/man/fit_copula_model_BinCont.Rd | 13 Surrogate-3.3.1/Surrogate/man/fit_copula_submodel_ContCont.Rd |only Surrogate-3.3.1/Surrogate/man/fit_copula_submodel_OrdCont.Rd |only Surrogate-3.3.1/Surrogate/man/fit_copula_submodel_OrdOrd.Rd |only Surrogate-3.3.1/Surrogate/man/fit_model_SurvSurv.Rd | 2 Surrogate-3.3.1/Surrogate/man/frank_loglik_copula_scale.Rd | 5 Surrogate-3.3.1/Surrogate/man/gaussian_loglik_copula_scale.Rd | 5 Surrogate-3.3.1/Surrogate/man/gumbel_loglik_copula_scale.Rd | 5 Surrogate-3.3.1/Surrogate/man/log_likelihood_copula_model.Rd | 6 Surrogate-3.3.1/Surrogate/man/loglik_copula_scale.Rd | 14 Surrogate-3.3.1/Surrogate/man/marginal_gof_copula.Rd |only Surrogate-3.3.1/Surrogate/man/new_vine_copula_fit.Rd |only Surrogate-3.3.1/Surrogate/man/ordinal_continuous_loglik.Rd |only Surrogate-3.3.1/Surrogate/man/ordinal_ordinal_loglik.Rd |only Surrogate-3.3.1/Surrogate/man/ordinal_to_cutpoints.Rd |only Surrogate-3.3.1/Surrogate/man/plot.vine_copula_fit.Rd |only Surrogate-3.3.1/Surrogate/man/print.vine_copula_fit.Rd |only Surrogate-3.3.1/Surrogate/man/sensitivity_analysis_SurvSurv_copula.Rd | 5 Surrogate-3.3.1/Surrogate/man/sensitivity_analysis_copula.Rd |only Surrogate-3.3.1/Surrogate/man/sensitivity_intervals_Dvine.Rd | 10 Surrogate-3.3.1/Surrogate/man/summary_level_bootstrap_ICA.Rd | 16 Surrogate-3.3.1/Surrogate/man/twostep_SurvSurv.Rd | 2 Surrogate-3.3.1/Surrogate/tests/testthat/_snaps/goodness_of_fit_copula_models |only Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/fit-and-save-models.R | 89 Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/ovarian-data-scr.rds |binary Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/ovarian-dvine-clayton.rds |binary Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/ovarian-dvine-gaussian-scr.rds |binary Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/ovarian-dvine-variable.rds |binary Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/schizo-dvine-clayton-ContCont.rds |only Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/schizo-dvine-clayton-OrdCont.rds |only Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/schizo-dvine-clayton.rds |binary Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/schizo-dvine-gaussian-OrdOrd.rds |only Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/sens-results-ovarian-clayton.rds |binary Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/sens-results-ovarian-gaussian-comp-sprho-restr.rds |binary Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/sens-results-ovarian-gaussian-comp.rds |binary Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/sens-results-schizo-clayton-ContCont.rds |only Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/sens-results-schizo-clayton-OrdCont.rds |only Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/sens-results-schizo-gaussian-OrdOrd.rds |only Surrogate-3.3.1/Surrogate/tests/testthat/fixtures/sensitivity-analysis-results.R | 143 - Surrogate-3.3.1/Surrogate/tests/testthat/test-FederatedApproachStage1.R |only Surrogate-3.3.1/Surrogate/tests/testthat/test-FederatedApproachStage2.R |only Surrogate-3.3.1/Surrogate/tests/testthat/test-ICA_BinCont_copula.R | 202 - Surrogate-3.3.1/Surrogate/tests/testthat/test-ICA_ContCont_copula.R |only Surrogate-3.3.1/Surrogate/tests/testthat/test-ICA_OrdCont_copula.R |only Surrogate-3.3.1/Surrogate/tests/testthat/test-ICA_OrdOrd_copula.R |only Surrogate-3.3.1/Surrogate/tests/testthat/test-ICA_SurvSurv_copula.R | 4 Surrogate-3.3.1/Surrogate/tests/testthat/test-ITCI-Dvine-inference-utils.R | 117 - Surrogate-3.3.1/Surrogate/tests/testthat/test-MetaAnalyticSurvBin.R | 33 Surrogate-3.3.1/Surrogate/tests/testthat/test-MetaAnalyticSurvCat.R | 33 Surrogate-3.3.1/Surrogate/tests/testthat/test-MetaAnalyticSurvCont.R | 34 Surrogate-3.3.1/Surrogate/tests/testthat/test-MetaAnalyticSurvSurv.R | 46 Surrogate-3.3.1/Surrogate/tests/testthat/test-copula_utils.R | 11 Surrogate-3.3.1/Surrogate/tests/testthat/test-fit_model_ContCont_copula.R |only Surrogate-3.3.1/Surrogate/tests/testthat/test-fit_model_OrdCont_copula.R |only Surrogate-3.3.1/Surrogate/tests/testthat/test-fit_model_OrdOrd_copula.R |only Surrogate-3.3.1/Surrogate/tests/testthat/test-goodness_of_fit_copula_models.R |only Surrogate-3.3.1/Surrogate/tests/testthat/test-likelihood_copula_models.R | 28 Surrogate-3.3.1/Surrogate/tests/testthat/test-sensitivity_analysis_BinCont_copula.R | 84 Surrogate-3.3.1/Surrogate/tests/testthat/test-sensitivity_analysis_SurvSurv.R | 311 +- Surrogate-3.3.1/Surrogate/tests/testthat/test-sensitivity_analysis_copula.R |only Surrogate-3.3.1/Surrogate/tests/testthat/test-sensitivity_intervals.R | 363 ++- 160 files changed, 5454 insertions(+), 4357 deletions(-)
Title: Diet Estimated Trophic Levels
Description: Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Borstein (2020) <doi:10.1007/s10750-020-04417-5>.
Author: Samuel R. Borstein [aut, cre]
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between dietr versions 1.1.6 dated 2025-01-13 and 1.1.6-1 dated 2025-01-23
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 2 +- R/ConvertFishbaseDiet.R | 9 +++++---- R/ConvertFishbaseFood.R | 7 +++++-- R/DietTroph.R | 2 +- R/FoodTroph.R | 2 +- inst/doc/dietr-vignette.html | 2 +- man/ConvertFishbaseDiet.Rd | 9 ++++++--- man/ConvertFishbaseFood.Rd | 7 ++++++- man/DietTroph.Rd | 2 ++ man/FoodTroph.Rd | 2 ++ tests/testthat/test_ConvertFishbaseDiet.R | 20 +++++++++++--------- tests/testthat/test_ConvertFishbaseFood.R | 18 +++++++++--------- tests/testthat/test_FoodTroph.R | 1 + 15 files changed, 69 insertions(+), 50 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to several United States Census Bureau
APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's
geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping
and spatial analysis.
Author: Kyle Walker [aut, cre],
Matt Herman [aut],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tidycensus versions 1.6.7 dated 2024-10-17 and 1.7.0 dated 2025-01-23
tidycensus-1.6.7/tidycensus/man/tidycensus.Rd |only tidycensus-1.7.0/tidycensus/DESCRIPTION | 10 ++--- tidycensus-1.7.0/tidycensus/MD5 | 20 +++++----- tidycensus-1.7.0/tidycensus/NEWS.md | 4 ++ tidycensus-1.7.0/tidycensus/R/acs.R | 33 +++++++++++++----- tidycensus-1.7.0/tidycensus/R/pums.R | 26 ++++++++++---- tidycensus-1.7.0/tidycensus/R/tidycensus-package.R | 12 ++---- tidycensus-1.7.0/tidycensus/data/acs5_geography.rda |binary tidycensus-1.7.0/tidycensus/man/acs5_geography.Rd | 2 - tidycensus-1.7.0/tidycensus/man/get_acs.Rd | 6 +-- tidycensus-1.7.0/tidycensus/man/get_pums.Rd | 4 +- tidycensus-1.7.0/tidycensus/man/tidycensus-package.Rd |only 12 files changed, 74 insertions(+), 43 deletions(-)
Title: Structural Equation Modeling with Deep Neural Network and
Machine Learning
Description: Training and validation of a custom (or data-driven) Structural
Equation Models using layer-wise Deep Neural Networks or node-wise
Machine Learning algorithms, which extend the fitting procedures of
the 'SEMgraph' R package <doi:10.32614/CRAN.package.SEMgraph>.
Author: Mario Grassi [aut],
Barbara Tarantino [cre]
Maintainer: Barbara Tarantino <barbara.tarantino01@universitadipavia.it>
Diff between SEMdeep versions 0.1.0 dated 2024-09-16 and 1.0.0 dated 2025-01-23
SEMdeep-0.1.0/SEMdeep/man/benchmark.Rd |only SEMdeep-0.1.0/SEMdeep/man/getInputPvalue.Rd |only SEMdeep-1.0.0/SEMdeep/DESCRIPTION | 18 SEMdeep-1.0.0/SEMdeep/MD5 | 38 SEMdeep-1.0.0/SEMdeep/NAMESPACE | 26 SEMdeep-1.0.0/SEMdeep/NEWS.md | 33 SEMdeep-1.0.0/SEMdeep/R/SEMdnn.R | 1156 ++++++++++++--------- SEMdeep-1.0.0/SEMdeep/R/SEMhelp.R | 953 +++++++++++------ SEMdeep-1.0.0/SEMdeep/R/SEMml.R | 1121 ++++++++++++-------- SEMdeep-1.0.0/SEMdeep/man/SEMdnn.Rd | 175 +-- SEMdeep-1.0.0/SEMdeep/man/SEMml.Rd | 190 +-- SEMdeep-1.0.0/SEMdeep/man/classificationReport.Rd |only SEMdeep-1.0.0/SEMdeep/man/crossValidation.Rd |only SEMdeep-1.0.0/SEMdeep/man/getConnectionWeight.Rd | 35 SEMdeep-1.0.0/SEMdeep/man/getGradientWeight.Rd | 34 SEMdeep-1.0.0/SEMdeep/man/getShapleyR2.Rd | 93 - SEMdeep-1.0.0/SEMdeep/man/getSignificanceTest.Rd |only SEMdeep-1.0.0/SEMdeep/man/getVariableImportance.Rd |only SEMdeep-1.0.0/SEMdeep/man/mapGraph.Rd | 39 SEMdeep-1.0.0/SEMdeep/man/nplot.Rd | 17 SEMdeep-1.0.0/SEMdeep/man/predict.DNN.Rd | 59 - SEMdeep-1.0.0/SEMdeep/man/predict.ML.Rd | 57 - SEMdeep-1.0.0/SEMdeep/man/predict.SEM.Rd | 73 - 23 files changed, 2501 insertions(+), 1616 deletions(-)
Title: Assessing and Visualizing Fragility of Clinical Results with
Binary Outcomes
Description: A collection of user-friendly functions for assessing and visualizing fragility of individual studies (Walsh et al., 2014 <doi:10.1016/j.jclinepi.2013.10.019>; Lin, 2021 <doi:10.1111/jep.13428>), conventional pairwise meta-analyses (Atal et al., 2019 <doi:10.1016/j.jclinepi.2019.03.012>), and network meta-analyses of multiple treatments with binary outcomes (Xing et al., 2020 <doi:10.1016/j.jclinepi.2020.07.003>). The included functions are designed to: 1) calculate the fragility index (i.e., the minimal event status modifications that can alter the significance or non-significance of the original result) and fragility quotient (i.e., fragility index divided by sample size) at a specific significance level; 2) give the cases of event status modifications for altering the result's significance or non-significance and visualize these cases; 3) visualize the trend of statistical significance as event status is modified; 4) efficiently derive fragility indexes and f [...truncated...]
Author: Lifeng Lin [aut, cre] ,
Haitao Chu [aut]
Maintainer: Lifeng Lin <lifenglin@arizona.edu>
Diff between fragility versions 1.6 dated 2024-11-21 and 1.6.1 dated 2025-01-23
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- man/frag.ma.Rd | 6 ++++-- man/frag.ma.alpha.Rd | 4 ++-- man/frag.mas.Rd | 4 ++-- man/frag.nma.Rd | 10 +++++----- man/frag.nma.alpha.Rd | 12 ++++++------ man/frag.studies.Rd | 6 +++--- man/frag.study.Rd | 6 +++--- man/frag.study.alpha.Rd | 6 +++--- man/plot.frag.alpha.Rd | 8 ++++---- man/plot.frag.ma.Rd | 12 ++++++------ man/plot.frag.multi.Rd | 12 ++++++------ man/plot.frag.nma.Rd | 12 ++++++------ man/plot.frag.study.all.Rd | 8 ++++---- 15 files changed, 72 insertions(+), 70 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully
configurable HTTP/FTP requests where responses can be processed in memory, on
disk, or streaming via the callback or connection interfaces. Some knowledge
of 'libcurl' is recommended; for a more-user-friendly web client see the
'httr2' package which builds on this package with http specific tools and logic.
Author: Jeroen Ooms [aut, cre] ,
Hadley Wickham [ctb],
Posit Software, PBC [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between curl versions 6.1.0 dated 2025-01-06 and 6.2.0 dated 2025-01-23
DESCRIPTION | 6 +- MD5 | 26 +++++----- NEWS | 6 ++ R/multi.R | 4 - R/options.R | 2 R/parser.R | 8 ++- cleanup | 1 configure | 14 +++++ inst/doc/intro.R | 20 ++++---- inst/doc/intro.html | 102 +++++++++++++++++++++---------------------- man/multi.Rd | 2 src/init.c | 2 src/urlparser.c | 12 +++-- tests/testthat/test-parser.R | 5 +- 14 files changed, 121 insertions(+), 89 deletions(-)
Title: Run Any CLI Tool on a 'Conda' Environment
Description: Simplifies the execution of command line interface (CLI)
tools within isolated and reproducible environments. It enables users
to effortlessly manage 'Conda' environments, execute command line
tools, handle dependencies, and ensure reproducibility in their data
analysis workflows.
Author: Lucio Queiroz [aut, cre, cph] ,
Claudio Zanettini [aut, ctb]
Maintainer: Lucio Queiroz <luciorqueiroz@gmail.com>
Diff between condathis versions 0.1.0 dated 2024-12-11 and 0.1.1 dated 2025-01-23
DESCRIPTION | 6 +-- MD5 | 14 ++++----- NEWS.md | 12 +++++++ R/install_micromamba.R | 2 - R/rethrow_error_run.R | 31 +++++++++++++++++++- README.md | 8 +++-- man/install_micromamba.Rd | 2 - tests/testthat/test-run_bin.R | 64 ++++++++++++++++++++++++++++++++++++++++++ 8 files changed, 121 insertions(+), 18 deletions(-)
More information about AntibodyForests at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-19 1.2.0
2019-11-29 1.1.0
2019-05-09 1.0.0
Title: Connect to Your 'Zendesk' Data
Description: Facilitates making a connection to the
'Zendesk' API and executing various queries. You can use it to
get ticket, ticket metrics, and user data. The 'Zendesk' documentation is
available at <https://developer.zendesk.com/rest_api
/docs/support/introduction>. This package is not supported by
'Zendesk' (owner of the software).
Author: Chris Umphlett [aut, cre],
Avinash Panigrahi [aut]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>
Diff between zdeskR versions 0.4.1 dated 2024-03-25 and 0.4.2 dated 2025-01-23
DESCRIPTION | 8 +- MD5 | 12 +-- R/get_tickets.R | 2 R/get_users.R | 2 man/get_tickets.Rd | 2 man/get_tickets_comments.Rd | 136 ++++++++++++++++++++++---------------------- man/get_users.Rd | 2 7 files changed, 82 insertions(+), 82 deletions(-)
More information about pattern.checks at CRAN
Permanent link
More information about ncaavolleyballr at CRAN
Permanent link
Title: Datasets from the Datasaurus Dozen
Description: The Datasaurus Dozen is a set of datasets with the same
summary statistics. They retain the same summary statistics despite
having radically different distributions. The datasets represent a
larger and quirkier object lesson that is typically taught via
Anscombe's Quartet (available in the 'datasets' package). Anscombe's
Quartet contains four very different distributions with the same
summary statistics and as such highlights the value of visualisation
in understanding data, over and above summary statistics. As well as
being an engaging variant on the Quartet, the data is generated in a
novel way. The simulated annealing process used to derive datasets
from the original Datasaurus is detailed in "Same Stats, Different
Graphs: Generating Datasets with Varied Appearance and Identical
Statistics through Simulated Annealing" <doi:10.1145/3025453.3025912>.
Author: Colin Gillespie [cre, aut],
Steph Locke [aut],
Alberto Cairo [dtc],
Rhian Davies [aut],
Justin Matejka [dtc],
George Fitzmaurice [dtc],
Lucy D'Agostino McGowan [aut],
Richard Cotton [ctb],
Tim Book [ctb],
Jumping Rivers [fnd]
Maintainer: Colin Gillespie <colin@jumpingrivers.com>
Diff between datasauRus versions 0.1.8 dated 2024-02-26 and 0.1.9 dated 2025-01-23
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 3 +++ build/vignette.rds |binary inst/doc/Datasaurus.R | 16 ++++++++-------- inst/doc/Datasaurus.Rmd | 16 ++++++++-------- inst/doc/Datasaurus.html | 26 +++++++++++++------------- tests/testthat/test-datasets.R | 6 +++--- vignettes/Datasaurus.Rmd | 16 ++++++++-------- 9 files changed, 57 insertions(+), 54 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.3-0 dated 2024-11-19 and 3.3-1 dated 2025-01-23
DESCRIPTION | 16 +++++------ MD5 | 34 ++++++++++++------------ NEWS | 9 ++++++ inst/doc/bugfixes.Rnw | 7 +++++ inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 1 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.Rnw | 63 +++++++++++++++++++++++++++++++++++++++++---- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 1 man/latest.changes.Rd | 24 +++++++++++++++++ man/spatstat-package.Rd | 9 ++++-- vignettes/bugfixes.Rnw | 7 +++++ vignettes/updates.Rnw | 63 +++++++++++++++++++++++++++++++++++++++++---- 18 files changed, 196 insertions(+), 38 deletions(-)
Title: Test, Document, Containerise, and Deploy R Packages
Description: Reproducibility is essential to the progress of research,
yet achieving it remains elusive even in computational fields.
Continuous Integration (CI) platforms offer a powerful way to launch automated workflows
to check and document code, but often require considerable time, effort,
and technical expertise to setup. We therefore developed the rworkflows suite
to make robust CI workflows easy and freely accessible to all R package developers.
rworkflows consists of 1) a CRAN/Bioconductor-compatible R package template,
2) an R package to quickly implement a standardised workflow, and
3) a centrally maintained GitHub Action.
Author: Brian Schilder [aut, cre] ,
Alan Murphy [aut, ctb] ,
Nathan Skene [aut]
Maintainer: Brian Schilder <brian_schilder@alumni.brown.edu>
Diff between rworkflows versions 1.0.2 dated 2024-09-22 and 1.0.6 dated 2025-01-23
DESCRIPTION | 6 +- MD5 | 35 ++++++++-------- NEWS.md | 32 ++++++++++++++ R/use_issue_template.R | 5 +- README.md | 44 ++++++++++---------- build/vignette.rds |binary inst/doc/bioconductor.html | 43 ++++++++++--------- inst/doc/depgraph.html | 39 +++++++++--------- inst/doc/docker.html | 39 +++++++++--------- inst/doc/repos.html | 39 +++++++++--------- inst/doc/rworkflows.html | 67 +++++++++++++++---------------- inst/templates/Dockerfile | 1 inst/templates/bug_report.yml |only inst/templates/config.yml |only inst/templates/feature_request.yml |only man/get_description.Rd | 9 +--- man/get_description_repo.Rd | 9 +--- man/infer_docker_org.Rd | 9 +--- man/use_issue_template.Rd | 2 tests/testthat/test-use_issue_template.R | 2 20 files changed, 208 insertions(+), 173 deletions(-)
Title: Names Your 'R Markdown' Chunks
Description: It names the 'R Markdown' chunks of files based on the
filename.
Author: Colin Gillespie [aut, cre],
Steph Locke [aut],
Maelle Salmon [aut] ,
Ellis Valentiner [ctb],
Charlie Hadley [ctb] ,
Jumping Rivers [fnd] ,
Han Oostdijk [ctb] ,
Patrick Schratz [ctb]
Maintainer: Colin Gillespie <colin@jumpingrivers.com>
Diff between namer versions 0.1.8 dated 2024-02-29 and 0.1.9 dated 2025-01-23
DESCRIPTION | 60 ++++++++++--------------------- LICENSE | 2 - MD5 | 36 +++++++++--------- NEWS.md | 16 +++++++- R/name_chunks.R | 35 +++++++++--------- R/name_chunks_addin.R | 16 +++++++- R/unname_chunks.R | 14 +++---- R/utils.R | 32 +++++++--------- build/vignette.rds |binary inst/doc/namer.html | 10 ++--- inst/examples/example6.Rmd | 4 +- inst/rstudio/addins.dcf | 12 +++++- man/name_chunks.Rd | 7 ++- tests/testthat/helper.R | 1 tests/testthat/test-get_chunk_info.R | 12 +++--- tests/testthat/test-name_chunks.R | 12 ++++++ tests/testthat/test-parse_chunk_header.R | 11 +++-- tests/testthat/test-unname_chunks.R | 24 ++++++------ tests/testthat/test-unname_dir_chunks.R | 15 +++---- 19 files changed, 178 insertions(+), 141 deletions(-)
Title: Manipulate MCMC Samples
Description: Functions and classes to store, manipulate and summarise
Monte Carlo Markov Chain (MCMC) samples. For more information see
Brooks et al. (2011) <isbn:978-1-4200-7941-8>.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [ctb] ,
Nadine Hussein [ctb] ,
Ayla Pearson [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between mcmcr versions 0.6.1 dated 2021-09-06 and 0.6.2 dated 2025-01-23
mcmcr-0.6.1/mcmcr/build |only mcmcr-0.6.1/mcmcr/man/figures/README-unnamed-chunk-4-1.png |only mcmcr-0.6.1/mcmcr/man/figures/README-unnamed-chunk-5-1.png |only mcmcr-0.6.2/mcmcr/DESCRIPTION | 42 +- mcmcr-0.6.2/mcmcr/MD5 | 165 +++++----- mcmcr-0.6.2/mcmcr/NAMESPACE | 38 ++ mcmcr-0.6.2/mcmcr/NEWS.md | 9 mcmcr-0.6.2/mcmcr/R/as-mcmc.R | 2 mcmcr-0.6.2/mcmcr/R/as-mcmc.list.R | 5 mcmcr-0.6.2/mcmcr/R/as-mcmcarray.R | 2 mcmcr-0.6.2/mcmcr/R/as-mcmcrs.R | 3 mcmcr-0.6.2/mcmcr/R/bind-chains.R | 2 mcmcr-0.6.2/mcmcr/R/check.R | 6 mcmcr-0.6.2/mcmcr/R/coef.R | 14 mcmcr-0.6.2/mcmcr/R/export.R | 1 mcmcr-0.6.2/mcmcr/R/internal.R | 12 mcmcr-0.6.2/mcmcr/R/mcmcr-package.R | 2 mcmcr-0.6.2/mcmcr/R/nchains.R | 2 mcmcr-0.6.2/mcmcr/R/niters.R | 2 mcmcr-0.6.2/mcmcr/R/pars.R | 2 mcmcr-0.6.2/mcmcr/R/rhat.R | 31 + mcmcr-0.6.2/mcmcr/R/test-helpers.R | 14 mcmcr-0.6.2/mcmcr/README.md | 151 +++++---- mcmcr-0.6.2/mcmcr/man/as.mcarray.Rd | 6 mcmcr-0.6.2/mcmcr/man/as.mcmc.mcarray.Rd | 6 mcmcr-0.6.2/mcmcr/man/as.mcmc.mcmc.Rd | 6 mcmcr-0.6.2/mcmcr/man/as.mcmc.mcmcarray.Rd | 6 mcmcr-0.6.2/mcmcr/man/as.mcmc.mcmcr.Rd | 6 mcmcr-0.6.2/mcmcr/man/as.mcmc.nlists.Rd |only mcmcr-0.6.2/mcmcr/man/as.mcmcr.Rd | 16 mcmcr-0.6.2/mcmcr/man/as.mcmcrs.Rd | 6 mcmcr-0.6.2/mcmcr/man/as_nlist.mcmcr.Rd | 13 mcmcr-0.6.2/mcmcr/man/as_nlists.mcmcr.Rd | 11 mcmcr-0.6.2/mcmcr/man/bind_parameters.Rd | 4 mcmcr-0.6.2/mcmcr/man/check_mcmcarray.Rd | 6 mcmcr-0.6.2/mcmcr/man/check_mcmcr.Rd | 6 mcmcr-0.6.2/mcmcr/man/chk_mcmcr.Rd | 8 mcmcr-0.6.2/mcmcr/man/coef.Rd | 4 mcmcr-0.6.2/mcmcr/man/combine_dimensions.Rd | 4 mcmcr-0.6.2/mcmcr/man/converged.default.Rd | 6 mcmcr-0.6.2/mcmcr/man/converged.mcmcrs.Rd | 6 mcmcr-0.6.2/mcmcr/man/esr.mcarray.Rd | 6 mcmcr-0.6.2/mcmcr/man/esr.mcmc.Rd | 6 mcmcr-0.6.2/mcmcr/man/esr.mcmc.list.Rd | 6 mcmcr-0.6.2/mcmcr/man/esr.mcmcarray.Rd | 6 mcmcr-0.6.2/mcmcr/man/esr.mcmcr.Rd | 6 mcmcr-0.6.2/mcmcr/man/esr.mcmcrs.Rd | 6 mcmcr-0.6.2/mcmcr/man/figures/README-unnamed-chunk-2-1.png |binary mcmcr-0.6.2/mcmcr/man/figures/lifecycle-deprecated.svg | 22 + mcmcr-0.6.2/mcmcr/man/figures/lifecycle-experimental.svg | 22 + mcmcr-0.6.2/mcmcr/man/figures/lifecycle-stable.svg | 30 + mcmcr-0.6.2/mcmcr/man/figures/lifecycle-superseded.svg | 22 + mcmcr-0.6.2/mcmcr/man/figures/logo.png |only mcmcr-0.6.2/mcmcr/man/fill_all.mcarray.Rd | 9 mcmcr-0.6.2/mcmcr/man/fill_all.mcmcarray.Rd | 9 mcmcr-0.6.2/mcmcr/man/fill_all.mcmcr.Rd | 9 mcmcr-0.6.2/mcmcr/man/fill_na.mcarray.Rd | 9 mcmcr-0.6.2/mcmcr/man/fill_na.mcmcarray.Rd | 9 mcmcr-0.6.2/mcmcr/man/fill_na.mcmcr.Rd | 9 mcmcr-0.6.2/mcmcr/man/is.mcarray.Rd | 4 mcmcr-0.6.2/mcmcr/man/is.mcmcarray.Rd | 4 mcmcr-0.6.2/mcmcr/man/mcmcr-package.Rd | 10 mcmcr-0.6.2/mcmcr/man/nchains.matrix.Rd |only mcmcr-0.6.2/mcmcr/man/niters.matrix.Rd |only mcmcr-0.6.2/mcmcr/man/reexports.Rd | 13 mcmcr-0.6.2/mcmcr/man/rhat.mcarray.Rd | 4 mcmcr-0.6.2/mcmcr/man/rhat.mcmc.Rd | 4 mcmcr-0.6.2/mcmcr/man/rhat.mcmc.list.Rd | 4 mcmcr-0.6.2/mcmcr/man/rhat.mcmcarray.Rd | 4 mcmcr-0.6.2/mcmcr/man/rhat.mcmcr.Rd | 4 mcmcr-0.6.2/mcmcr/man/rhat.mcmcrs.Rd | 4 mcmcr-0.6.2/mcmcr/man/subset.Rd | 8 mcmcr-0.6.2/mcmcr/man/vld_mcmcr.Rd | 8 mcmcr-0.6.2/mcmcr/man/zero.Rd | 8 mcmcr-0.6.2/mcmcr/tests/testthat/_snaps/estimates/estimates.csv | 4 mcmcr-0.6.2/mcmcr/tests/testthat/test-aaa-deprecated.R | 8 mcmcr-0.6.2/mcmcr/tests/testthat/test-aaa-zero.R | 10 mcmcr-0.6.2/mcmcr/tests/testthat/test-anyNA.R | 2 mcmcr-0.6.2/mcmcr/tests/testthat/test-as-term.R | 2 mcmcr-0.6.2/mcmcr/tests/testthat/test-bind-chains.R | 39 +- mcmcr-0.6.2/mcmcr/tests/testthat/test-coef.R | 4 mcmcr-0.6.2/mcmcr/tests/testthat/test-converged.R | 6 mcmcr-0.6.2/mcmcr/tests/testthat/test-esr.R | 24 + mcmcr-0.6.2/mcmcr/tests/testthat/test-ess.R | 21 + mcmcr-0.6.2/mcmcr/tests/testthat/test-estimates.R | 15 mcmcr-0.6.2/mcmcr/tests/testthat/test-parameters.R | 4 mcmcr-0.6.2/mcmcr/tests/testthat/test-rhat.R | 85 ++++- 87 files changed, 731 insertions(+), 383 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of sparse and dense matrix classes,
including general, symmetric, triangular, and diagonal matrices
with numeric, logical, or pattern entries. Efficient methods for
operating on such matrices, often wrapping the 'BLAS', 'LAPACK',
and 'SuiteSparse' libraries.
Author: Douglas Bates [aut] ,
Martin Maechler [aut, cre] ,
Mikael Jagan [aut] ,
Timothy A. Davis [ctb] ,
pattern="License", full.names=TRUE, recursive=TRUE)),
George Karypis [ctb] ,
Jason Riedy [ctb] and onenormest, Copyright: Regents of the
University of C [...truncated...]
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.7-1 dated 2024-10-18 and 1.7-2 dated 2025-01-23
DESCRIPTION | 14 MD5 | 40 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 3314 +++++++++++++++++----------- inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/include/Matrix/version.h | 4 inst/scripts/SuiteSparse.patch | 14 src/SuiteSparse/AMD/Makefile | 2 src/SuiteSparse/CAMD/Makefile | 2 src/SuiteSparse/CCOLAMD/Makefile | 2 src/SuiteSparse/CHOLMOD/Makefile | 2 src/SuiteSparse/COLAMD/Makefile | 2 src/SuiteSparse/CXSparse/Makefile | 2 src/SuiteSparse/SuiteSparse_config/Makefile | 2 src/version.h | 4 tests/matprod.R | 8 21 files changed, 2120 insertions(+), 1292 deletions(-)
Title: The Lorentz Transform in Relativistic Physics
Description: The Lorentz transform in special relativity; also the
gyrogroup structure of three-velocities. Performs active and
passive transforms and has the ability to use units in which the
speed of light is not unity. Includes some experimental
functionality for celerity and rapidity. For general relativity,
see the 'schwarzschild' package.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between lorentz versions 1.1-1 dated 2024-04-02 and 1.1-2 dated 2025-01-23
DESCRIPTION | 9 +++++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- R/gyrogroup.R | 10 +++++----- R/stress_energy_tensor.R | 4 ++-- README.md | 22 +++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/JOSE/paper.md | 2 +- inst/doc/lorentz.Rnw | 6 +++--- inst/doc/lorentz.pdf |binary man/sol.Rd | 15 +++++++++++++++ vignettes/lorentz.Rnw | 6 +++--- 13 files changed, 58 insertions(+), 42 deletions(-)
Title: Additional Layout Algorithms for Network Visualizations
Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'.
Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>.
Some more specific algorithms allow the user to emphasize hidden group structures in networks or focus on specific nodes.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between graphlayouts versions 1.2.1 dated 2024-11-18 and 1.2.2 dated 2025-01-23
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- NEWS.md | 4 ++++ R/layout_backbone.R | 4 ++-- R/layout_multilevel.R | 7 ++++--- README.md | 7 +++---- man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example_un-1.png |binary man/figures/README-example_un-2.png |binary man/figures/README-flex_cent-1.png |binary man/layout_backbone.Rd | 4 ++-- man/layout_multilevel.Rd | 4 ++-- tests/testthat/test-layout_backbone.R | 1 + tests/testthat/test-layout_multilevel.R | 1 + tests/testthat/test-layouts.R | 1 + 16 files changed, 38 insertions(+), 31 deletions(-)
Title: Package Documentation Websites with 'Quarto', 'Docsify',
'Docute', or 'MkDocs'
Description: This is a simple and powerful package to create, render, preview,
and deploy documentation websites for 'R' packages. It is a lightweight and
flexible alternative to 'pkgdown', with support for many documentation
generators, including 'Quarto', 'Docute', 'Docsify', and 'MkDocs'.
Author: Etienne Bacher [aut, cre, cph],
Vincent Arel-Bundock [aut]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between altdoc versions 0.4.0 dated 2024-07-23 and 0.5.0 dated 2025-01-23
DESCRIPTION | 6 +- MD5 | 26 ++++----- NEWS.md | 15 +++++ R/import_misc.R | 65 +++++++++++++++--------- R/import_readme.R | 68 ++++++------------------- R/settings_quarto_website.R | 6 -- R/setup_docs.R | 6 -- build/vignette.rds |binary inst/doc/get-started.html | 2 inst/quarto_website/quarto_website.yml | 2 tests/testthat/_snaps/docsify/render_docs.md | 71 +++++++++++++-------------- tests/testthat/_snaps/docute/render_docs.md | 71 +++++++++++++-------------- tests/testthat/helper.R | 2 tests/testthat/test-setup_docs.R | 3 - 14 files changed, 165 insertions(+), 178 deletions(-)
Title: Spatial Visualisation of Admixture on a Projected Map
Description: Visualise admixture as pie charts on a projected map, admixture as traditional structure barplots or facet barplots, and scatter plots from genotype principal components analysis. A 'shiny' app allows users to create admixture maps interactively. Jenkins TL (2024) <doi:10.1111/1755-0998.13943>.
Author: Tom Jenkins [aut, cre, cph]
Maintainer: Tom Jenkins <tom.l.jenkins@outlook.com>
Diff between mapmixture versions 1.1.4 dated 2024-09-25 and 1.2.0 dated 2025-01-23
DESCRIPTION | 15 - MD5 | 40 +- NAMESPACE | 42 -- NEWS.md | 10 R/app_launch.R | 96 ++++-- R/app_ui.R | 254 ++++++++--------- R/func_data_transformation.R | 318 +++++++++++----------- R/func_mapmixture.R | 42 +- R/func_pie_charts.R | 382 +++++++++++++------------- R/func_process_input_data.R | 8 R/func_structure_plot.R | 4 R/mod_bar_plot.R | 92 +++--- R/mod_barplot_params.R | 122 ++++---- R/mod_file_upload.R | 109 +++---- R/mod_info_models.R | 104 +++---- R/mod_main_plot.R | 612 +++++++++++++++++++++---------------------- R/mod_map_params.R | 148 +++++----- R/mod_plot_bttn.R | 41 +- README.md | 1 man/add_pie_charts.Rd | 2 man/mapmixture.Rd | 2 21 files changed, 1223 insertions(+), 1221 deletions(-)
Title: Obtain, Organize, and Visualize NCEP Weather Data
Description: Contains functions to retrieve, organize, and visualize weather data from the NCEP/NCAR Reanalysis (<https://psl.noaa.gov/data/gridded/data.ncep.reanalysis.html>) and NCEP/DOE Reanalysis II (<https://psl.noaa.gov/data/gridded/data.ncep.reanalysis2.html>) datasets. Data are queried via the Internet and may be obtained for a specified spatial and temporal extent or interpolated to a point in space and time. We also provide functions to visualize these weather data on a map. There are also functions to simulate flight trajectories according to specified behavior using either NCEP wind data or data specified by the user.
Author: Michael U. Kemp [aut, cre],
E. Emiel van Loon [ths],
Judy Shamoun-Baranes [ths],
Willem Bouten [ths]
Maintainer: Michael U. Kemp <mukemp+RNCEP@gmail.com>
Diff between RNCEP versions 1.0.10 dated 2020-05-27 and 1.0.11 dated 2025-01-23
DESCRIPTION | 34 +++++++++++++++++++++++++++------- MD5 | 24 ++++++++++++------------ R/NCEP.interp.R | 2 +- R/robust.NCEP.interp.gaussian.R | 4 ++-- R/robust.NCEP.interp.pressure.R | 4 ++-- R/robust.NCEP.interp.surface.R | 4 ++-- inst/CITATION | 12 ++++++------ man/NCEP.bind.Rd | 2 +- man/NCEP.gather.Rd | 2 +- man/NCEP.interp.Rd | 2 +- man/NCEP.loxodrome.Rd | 2 +- man/NCEP.track2kml.Rd | 2 +- man/RNCEP-package.Rd | 6 +++--- 13 files changed, 60 insertions(+), 40 deletions(-)
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel [aut, cre] ,
QuantLib Authors [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.0.13 dated 2024-10-15 and 0.0.14 dated 2025-01-23
qlcal-0.0.13/qlcal/demo |only qlcal-0.0.14/qlcal/ChangeLog | 17 +++ qlcal-0.0.14/qlcal/DESCRIPTION | 8 - qlcal-0.0.14/qlcal/MD5 | 19 ++-- qlcal-0.0.14/qlcal/build/partial.rdb |binary qlcal-0.0.14/qlcal/inst/NEWS.Rd | 8 + qlcal-0.0.14/qlcal/inst/examples |only qlcal-0.0.14/qlcal/src/calendars.cpp | 7 + qlcal-0.0.14/qlcal/src/ql/time/calendars/newzealand.cpp | 61 +++++++++++--- qlcal-0.0.14/qlcal/src/ql/time/calendars/newzealand.hpp | 44 +++++++--- qlcal-0.0.14/qlcal/src/ql/time/calendars/unitedstates.cpp | 7 + 11 files changed, 128 insertions(+), 43 deletions(-)
Title: Laplace Factor Model Analysis and Evaluation
Description: Enables the generation of Laplace factor models across diverse Laplace distributions and facilitates the application of Sparse Online Principal Component (SOPC), Incremental Principal Component (IPC), Projected Principal Component (PPC), Perturbation Principal Component (PPC), Stochastic Approximation Principal Component (SAPC), Sparse Principal Component (SPC) and other PC methods and Farm Test methods to these models. Evaluates the efficacy of these methods within the context of Laplace factor models by scrutinizing parameter estimation accuracy, mean square error, and the degree of sparsity.
Author: Guangbao Guo [aut, cre],
Siqi Liu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between LFM versions 0.1.0 dated 2024-11-19 and 0.2.0 dated 2025-01-23
LFM-0.1.0/LFM/R/PPC_LFM.R |only LFM-0.1.0/LFM/man/PPC_LFM.Rd |only LFM-0.2.0/LFM/DESCRIPTION | 10 +++--- LFM-0.2.0/LFM/MD5 | 20 ++++++++++--- LFM-0.2.0/LFM/NAMESPACE | 63 +++++++++++++++++++++++------------------ LFM-0.2.0/LFM/R/FanPC_LFM.R |only LFM-0.2.0/LFM/R/GulPC_LFM.R |only LFM-0.2.0/LFM/R/OPC_LFM.R |only LFM-0.2.0/LFM/R/PC1_LFM.R |only LFM-0.2.0/LFM/R/PC2_LFM.R |only LFM-0.2.0/LFM/R/PPC1_LFM.R |only LFM-0.2.0/LFM/R/PPC2_LFM.R |only LFM-0.2.0/LFM/man/FanPC_LFM.Rd |only LFM-0.2.0/LFM/man/GulPC_LFM.Rd |only LFM-0.2.0/LFM/man/OPC_LFM.Rd |only LFM-0.2.0/LFM/man/PC1_LFM.Rd |only LFM-0.2.0/LFM/man/PC2_LFM.Rd |only LFM-0.2.0/LFM/man/PPC1_LFM.Rd |only LFM-0.2.0/LFM/man/PPC2_LFM.Rd |only 19 files changed, 57 insertions(+), 36 deletions(-)
Title: Bayesian Mixtures with an Unknown Number of Components
Description: Fits Bayesian finite mixtures with an unknown number of components using the telescoping sampler and different component distributions. For more details see Frühwirth-Schnatter et al. (2021) <doi:10.1214/21-BA1294>.
Author: Gertraud Malsiner-Walli [aut, cre]
,
Bettina Gruen [aut] ,
Sylvia Fruehwirth-Schnatter [aut]
Maintainer: Gertraud Malsiner-Walli <Gertraud.Malsiner-Walli@wu.ac.at>
Diff between telescope versions 0.1-0 dated 2024-06-15 and 0.2-0 dated 2025-01-23
DESCRIPTION | 10 +-- MD5 | 71 +++++++++++++++----------- NAMESPACE | 4 + R/SimData.R |only R/identifyLCAMixture.R |only R/identifyMixture.R | 2 R/sampleLCA.R | 34 ++++-------- R/sampleLCAMixture.R |only R/sampleMultNormMixture.R | 44 +++++----------- R/samplePoisMixture.R | 41 +++++---------- R/sampleUniNormMixture.R | 44 ++++++---------- build/vignette.rds |binary data |only inst/CITATION |only inst/NEWS.Rd |only inst/doc/Bayesian_LCA.R | 4 - inst/doc/Bayesian_LCA.Rmd | 6 +- inst/doc/Bayesian_LCA.html | 47 ++++++++--------- inst/doc/Bayesian_LCA_mixtures.R |only inst/doc/Bayesian_LCA_mixtures.Rmd |only inst/doc/Bayesian_LCA_mixtures.html |only inst/doc/Bayesian_Poisson_mixtures.R | 4 - inst/doc/Bayesian_Poisson_mixtures.Rmd | 6 +- inst/doc/Bayesian_Poisson_mixtures.html | 40 +++++++------- inst/doc/Bayesian_mult_Gaussian_mixtures.R | 4 - inst/doc/Bayesian_mult_Gaussian_mixtures.Rmd | 6 +- inst/doc/Bayesian_mult_Gaussian_mixtures.html | 49 ++++++++--------- inst/doc/Bayesian_univ_Gaussian_mixtures.R | 4 - inst/doc/Bayesian_univ_Gaussian_mixtures.Rmd | 6 +- inst/doc/Bayesian_univ_Gaussian_mixtures.html | 27 +++++---- man/SimData.Rd |only man/identifyLCAMixture.Rd |only man/sampleLCA.Rd | 7 +- man/sampleLCAMixture.Rd |only man/sampleMultNormMixture.Rd | 7 +- man/samplePoisMixture.Rd | 7 +- man/sampleUniNormMixture.Rd | 8 +- vignettes/Bayesian_LCA.Rmd | 6 +- vignettes/Bayesian_LCA_mixtures.Rmd |only vignettes/Bayesian_Poisson_mixtures.Rmd | 6 +- vignettes/Bayesian_mult_Gaussian_mixtures.Rmd | 6 +- vignettes/Bayesian_univ_Gaussian_mixtures.Rmd | 6 +- vignettes/telescope.bib | 47 +++++++++++------ 43 files changed, 269 insertions(+), 284 deletions(-)
Title: Create Simple Predictive Models on Bayesian Belief Networks
Description: A system to build, visualise and evaluate Bayesian belief networks. The methods are described in Stafford et al. (2015) <doi:10.12688/f1000research.5981.1>.
Author: Victoria Dominguez Almela [cre, aut]
,
Richard Stafford [cph, aut]
Maintainer: Victoria Dominguez Almela <vda1r22@soton.ac.uk>
Diff between bbnet versions 1.0.1 dated 2024-05-18 and 1.1.0 dated 2025-01-23
DESCRIPTION | 6 MD5 | 26 ++-- NEWS.md | 11 + R/bbn.predict.R | 8 + R/bbn.sensitivity.R | 2 R/bbn.timeseries.R | 12 + R/bbn.visualise.R | 12 + README.md | 61 ++++++---- inst/doc/bbnet.html | 182 ++++++++++++++++-------------- man/figures/README-unnamed-chunk-10-3.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-6-4.png |binary man/figures/README-unnamed-chunk-8-1.png |binary 14 files changed, 202 insertions(+), 118 deletions(-)
Title: SDTM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Study Data Tabulation Model (SDTM) datasets from the Clinical
Data Interchange Standards Consortium (CDISC) pilot project used for testing
and developing Analysis Data Model (ADaM) datasets inside the pharmaverse
family of packages. SDTM dataset specifications are described in the CDISC SDTM implementation guide,
accessible by creating a free account on <https://www.cdisc.org/>.
Author: Edoardo Mancini [aut, cre] ,
Gayatri G [aut],
Kangjie Zhang [aut],
Pooja Kumari [aut],
Stefan Bundfuss [aut] ,
Zelos Zhu [aut],
Sadchla Mascary [aut],
Vladyslav Shuliar [aut] ,
Vinh Nguyen [aut]
Maintainer: Edoardo Mancini <edoardo.mancini@roche.com>
Diff between pharmaversesdtm versions 1.1.0 dated 2024-10-25 and 1.2.0 dated 2025-01-23
pharmaversesdtm-1.1.0/pharmaversesdtm/R/data.R |only pharmaversesdtm-1.1.0/pharmaversesdtm/man/figures |only pharmaversesdtm-1.1.0/pharmaversesdtm/man/roxygen |only pharmaversesdtm-1.2.0/pharmaversesdtm/DESCRIPTION | 12 pharmaversesdtm-1.2.0/pharmaversesdtm/MD5 | 158 ++++++---- pharmaversesdtm-1.2.0/pharmaversesdtm/NEWS.md | 18 + pharmaversesdtm-1.2.0/pharmaversesdtm/R/ae.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/ae_ophtha.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/ce_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/cm.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/dm.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/dm_peds.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/dm_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/ds.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/eg.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/ex.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/ex_ophtha.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/ex_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/face_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/is_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/lb.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/mh.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/oe_ophtha.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/pc.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/pp.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/qs_ophtha.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/rs_onco.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/rs_onco_ca125.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/rs_onco_imwg.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/rs_onco_irecist.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/rs_onco_recist.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/sc_ophtha.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/sdg_db.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/smq_db.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/suppae.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/suppce_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/suppdm.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/suppdm_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/suppds.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/suppex_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/suppface_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/suppis_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/supprs_onco_ca125.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/supprs_onco_imwg.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/supptr_onco.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/sv.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/tr_onco.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/tr_onco_recist.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/ts.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/tu_onco.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/tu_onco_recist.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/vs.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/vs_peds.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/R/vs_vaccine.R |only pharmaversesdtm-1.2.0/pharmaversesdtm/README.md | 94 +++-- pharmaversesdtm-1.2.0/pharmaversesdtm/data/rs_onco_ca125.rda |only pharmaversesdtm-1.2.0/pharmaversesdtm/data/supprs_onco_ca125.rda |only pharmaversesdtm-1.2.0/pharmaversesdtm/inst/WORDLIST | 17 - pharmaversesdtm-1.2.0/pharmaversesdtm/inst/extdata |only pharmaversesdtm-1.2.0/pharmaversesdtm/man/ae.Rd | 53 +++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/ae_ophtha.Rd | 52 +++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/ce_vaccine.Rd | 44 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/cm.Rd | 37 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/dm.Rd | 40 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/dm_peds.Rd | 41 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/dm_vaccine.Rd | 43 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/ds.Rd | 28 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/eg.Rd | 39 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/ex.Rd | 32 +- pharmaversesdtm-1.2.0/pharmaversesdtm/man/ex_ophtha.Rd | 34 +- pharmaversesdtm-1.2.0/pharmaversesdtm/man/ex_vaccine.Rd | 36 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/face_vaccine.Rd | 45 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/is_vaccine.Rd | 39 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/lb.Rd | 38 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/mh.Rd | 43 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/oe_ophtha.Rd | 41 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/pc.Rd | 35 +- pharmaversesdtm-1.2.0/pharmaversesdtm/man/pharmaversesdtm-package.Rd | 3 pharmaversesdtm-1.2.0/pharmaversesdtm/man/pp.Rd | 29 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/qs_ophtha.Rd | 35 +- pharmaversesdtm-1.2.0/pharmaversesdtm/man/rs_onco.Rd | 35 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/rs_onco_ca125.Rd |only pharmaversesdtm-1.2.0/pharmaversesdtm/man/rs_onco_imwg.Rd | 36 +- pharmaversesdtm-1.2.0/pharmaversesdtm/man/rs_onco_irecist.Rd | 38 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/rs_onco_recist.Rd | 32 +- pharmaversesdtm-1.2.0/pharmaversesdtm/man/sc_ophtha.Rd | 28 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/sdg_db.Rd | 21 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/smq_db.Rd | 22 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/suppae.Rd | 25 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/suppce_vaccine.Rd | 24 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/suppdm.Rd | 25 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/suppdm_vaccine.Rd | 24 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/suppds.Rd | 24 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/suppex_vaccine.Rd | 24 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/suppface_vaccine.Rd | 24 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/suppis_vaccine.Rd | 25 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/supprs_onco_ca125.Rd |only pharmaversesdtm-1.2.0/pharmaversesdtm/man/supprs_onco_imwg.Rd | 28 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/supptr_onco.Rd | 25 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/sv.Rd | 26 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/tr_onco.Rd | 40 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/tr_onco_recist.Rd | 38 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/ts.Rd | 21 + pharmaversesdtm-1.2.0/pharmaversesdtm/man/tu_onco.Rd | 34 +- pharmaversesdtm-1.2.0/pharmaversesdtm/man/tu_onco_recist.Rd | 35 +- pharmaversesdtm-1.2.0/pharmaversesdtm/man/vs.Rd | 39 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/vs_peds.Rd | 41 ++ pharmaversesdtm-1.2.0/pharmaversesdtm/man/vs_vaccine.Rd | 38 ++ 108 files changed, 1569 insertions(+), 289 deletions(-)
More information about pharmaversesdtm at CRAN
Permanent link
Title: Exploring Water Quality Monitoring Data
Description: Functions to assist in the processing and
exploration of data from environmental monitoring programs.
The package name stands for "water quality" and reflects the
original focus on time series data for physical and chemical
properties of water, as well as the biota. Intended for
programs that sample approximately monthly, quarterly or
annually at discrete stations, a feature of many legacy data
sets. Most of the functions should be useful for analysis of
similar-frequency time series regardless of the subject
matter.
Author: Alan Jassby [aut],
James Cloern [ctb],
Jemma Stachelek [ctb, cre]
Maintainer: Jemma Stachelek <jemma.stachelek@gmail.com>
Diff between wql versions 1.0.1 dated 2024-05-28 and 1.0.2 dated 2025-01-23
DESCRIPTION | 8 +++---- MD5 | 22 ++++++++++----------- NEWS.md | 31 ++++++++++++++++++++++++++++- R/wql-package.R | 3 -- README.md | 48 +++++++++++++++++++++++----------------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 29 ++++++++++++++------------- inst/doc/wql-package.Rmd | 2 - inst/doc/wql-package.html | 48 +++++++++++++++++++++++----------------------- man/wql-package.Rd | 1 vignettes/wql-package.Rmd | 2 - 12 files changed, 112 insertions(+), 82 deletions(-)
Title: Fitting (Exponential/Diffusion) RT-MPT Models
Description: Fit (exponential or diffusion) response-time extended multinomial processing tree (RT-MPT) models
by Klauer and Kellen (2018) <doi:10.1016/j.jmp.2017.12.003> and Klauer, Hartmann, and Meyer-Grant (submitted).
The RT-MPT class not only incorporate frequencies like traditional multinomial processing tree (MPT) models,
but also latencies. This enables it to estimate process completion times and encoding plus motor execution times
next to the process probabilities of traditional MPTs. 'rtmpt' is a hierarchical Bayesian framework and posterior
samples are sampled using a Metropolis-within-Gibbs sampler (for exponential RT-MPTs) or Hamiltonian-within-Gibbs
sampler (for diffusion RT-MPTs).
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Constantin G. Meyer-Grant [aut, ctb],
Henrik Singmann [ctb, aut],
Jean Marie Linhart [ctb],
Frederick Novomestky [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between rtmpt versions 2.0-1 dated 2024-04-04 and 2.0-2 dated 2025-01-23
DESCRIPTION | 8 +-- MD5 | 28 +++++----- NAMESPACE | 10 +++ R/make_mcmc.R | 4 - R/print_rtmpt.R | 2 R/set_params.R | 110 +++++++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/rtmpt_guideline.html | 4 - man/a2a.Rd | 2 man/a2const.Rd | 2 man/nu2const.Rd | 16 +++++- man/nu2nu.Rd | 16 +++++- man/omega2const.Rd | 16 +++++- man/omega2omega.Rd | 16 +++++- man/tau2tau.Rd | 14 +++++ 15 files changed, 207 insertions(+), 41 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and
much more.
Author: Gabor Csardi [aut] ,
Tamas Nepusz [aut] ,
Vincent Traag [aut] ,
Szabolcs Horvat [aut] ,
Fabio Zanini [aut] ,
Daniel Noom [aut],
Kirill Mueller [aut, cre] ,
Maelle Salmon [ctb],
Michael Antonov [ctb],
Chan Zuckerberg Initiative [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between igraph versions 2.1.3 dated 2025-01-07 and 2.1.4 dated 2025-01-23
DESCRIPTION | 6 +- MD5 | 10 ++-- NEWS.md | 7 +++ inst/doc/igraph.html | 55 +++++++++++++-------------- inst/doc/igraph_ES.html | 83 ++++++++++++++++++++--------------------- tests/testthat/test-graphNEL.R | 4 - 6 files changed, 86 insertions(+), 79 deletions(-)
Title: Advanced Toolset for Efficient Time Series Dissimilarity
Analysis
Description: Fast C++ implementation of Dynamic Time Warping for time series dissimilarity analysis, with applications in environmental monitoring and sensor data analysis, climate science, signal processing and pattern recognition, and financial data analysis. Built upon the ideas presented in Benito and Birks (2020) <doi:10.1111/ecog.04895>, provides tools for analyzing time series of varying lengths and structures, including irregular multivariate time series. Key features include individual variable contribution analysis, restricted permutation tests for statistical significance, and imputation of missing data via GAMs. Additionally, the package provides an ample set of tools to prepare and manage time series data.
Author: Blas M. Benito [aut, cre, cph]
Maintainer: Blas M. Benito <blasbenito@gmail.com>
Diff between distantia versions 2.0.0 dated 2025-01-08 and 2.0.1 dated 2025-01-23
DESCRIPTION | 6 ++--- MD5 | 40 ++++++++++++++++++------------------ NEWS.md | 8 +++++++ R/RcppExports.R | 22 +++++++++---------- R/data.R | 2 - R/psi_cost_matrix.R | 10 ++++----- R/psi_cost_path_sum.R | 4 ++- README.md | 20 ++++++++---------- man/cost_path_cpp.Rd | 6 ++--- man/covid_counties.Rd | 2 - man/importance_dtw_cpp.Rd | 4 +-- man/importance_dtw_legacy_cpp.Rd | 6 ++--- man/psi_dtw_cpp.Rd | 6 ++--- src/auto_sum.cpp | 19 ++++++++++++----- src/cost_matrix.cpp | 14 ++++++++---- src/cost_path.cpp | 17 +++++++++------ src/distance_methods.cpp | 6 ++--- src/importance.cpp | 12 +++++----- src/psi.cpp | 15 ++++++++----- tests/testthat/test-distantia.R | 16 ++++++++++++++ tests/testthat/test-tsl_transform.R | 3 +- 21 files changed, 142 insertions(+), 96 deletions(-)
Title: Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Description: Provides functions for forest objects detection, structure metrics
computation, model calibration and mapping with airborne laser scanning:
co-registration of field plots (Monnet and Mermin (2014)
<doi:10.3390/f5092307>); tree detection (method 1 in Eysn et al. (2015)
<doi:10.3390/f6051721>) and segmentation; forest parameters estimation with
the area-based approach: model calibration with ground reference, and maps
export (Aussenac et al. (2023) <doi:10.12688/openreseurope.15373.2>);
extraction of both physical (gaps, edges, trees) and statistical
features useful for e.g. habitat suitability modeling (Glad et al. (2020)
<doi:10.1002/rse2.117>) and forest maturity mapping (Fuhr et al. (2022)
<doi:10.1002/rse2.274>).
Author: Jean-Matthieu Monnet [aut, cre]
,
Pascal Obstetar [ctb]
Maintainer: Jean-Matthieu Monnet <jean-matthieu.monnet@inrae.fr>
Diff between lidaRtRee versions 4.0.5 dated 2023-04-07 and 4.0.8 dated 2025-01-23
DESCRIPTION | 37 ++++++++------- MD5 | 61 +++++++++++++------------ NEWS.md |only R/aba.R | 58 ++++++++++++++---------- R/common.R | 31 ++----------- R/extdata.R | 2 R/gap_detection.R | 2 R/metrics.R | 97 ++++++++++++++++++++++++++++------------- R/optical_metrics.R | 2 R/quatre_montagnes-data.R | 2 R/raster_metrics.R | 8 ++- R/tree_detection.R | 2 README.md |only build/partial.rdb |binary inst/CITATION |only inst/extdata/las_chablais3.laz |binary man/aba_build_model.Rd | 11 +++- man/aba_metrics.Rd | 2 man/aba_plot.Rd | 7 +- man/aba_predict.Rd | 5 +- man/add_vegetation_indices.Rd | 2 man/boxcox_tr.Rd | 2 man/clouds_metrics.Rd | 4 - man/clouds_tree_metrics.Rd | 31 +++++++++++-- man/convert_raster.Rd | 11 ---- man/figures |only man/las_chablais3.Rd | 2 man/points2DSM.Rd | 4 - man/points2DTM.Rd | 4 - man/quatre_montagnes.Rd | 2 man/raster2Cimg.Rd | 2 man/raster_metrics.Rd | 5 ++ man/terrain_points_metrics.Rd | 2 33 files changed, 236 insertions(+), 162 deletions(-)
Title: GWAS with Trio and Duo Data using Knockoff Statistics for FDR
Control
Description: Identification of putative causal variants in genome-wide association studies with trio and duo families. The package calculates the W feature statistics from KnockoffTrio and p-values from the family-based association test (FBAT) using trio and/or duo data. Compared to previous versions, a significant improvement has been made in Version 1.1.0 to allow the package to be applied not only to trio families but also to duo families. The package implements the methods in the paper: "Yang, Y., Wang, C., Liu, L., Buxbaum, J., He, Z., & Ionita-Laza, I. (2022). KnockoffTrio: A knockoff framework for the identification of putative causal variants in genome-wide association studies with trio design. The American Journal of Human Genetics, 109(10), 1761-1776."
Author: Yi Yang [aut, cre]
Maintainer: Yi Yang <yi.yang@cityu.edu.hk>
Diff between KnockoffTrio versions 1.0.2 dated 2023-12-08 and 1.1.0 dated 2025-01-23
KnockoffTrio-1.0.2/KnockoffTrio/README.md |only KnockoffTrio-1.1.0/KnockoffTrio/DESCRIPTION | 13 KnockoffTrio-1.1.0/KnockoffTrio/MD5 | 25 - KnockoffTrio-1.1.0/KnockoffTrio/R/KnockoffTrio.R | 128 +++-- KnockoffTrio-1.1.0/KnockoffTrio/R/causal_loci.R | 38 + KnockoffTrio-1.1.0/KnockoffTrio/R/create_knockoff.R | 235 ++++++---- KnockoffTrio-1.1.0/KnockoffTrio/R/data.R | 7 KnockoffTrio-1.1.0/KnockoffTrio/R/meta_analysis.R | 15 KnockoffTrio-1.1.0/KnockoffTrio/data/KnockoffTrio.example.rda |binary KnockoffTrio-1.1.0/KnockoffTrio/man/KnockoffTrio.Rd | 66 ++ KnockoffTrio-1.1.0/KnockoffTrio/man/KnockoffTrio.example.Rd | 7 KnockoffTrio-1.1.0/KnockoffTrio/man/causal_loci.Rd | 38 + KnockoffTrio-1.1.0/KnockoffTrio/man/create_knockoff.Rd | 28 - KnockoffTrio-1.1.0/KnockoffTrio/man/meta_analysis.Rd | 10 14 files changed, 419 insertions(+), 191 deletions(-)
Title: Selective Editing via Mixture Models
Description: Detection of outliers and influential errors using a latent variable model.
Author: Ugo Guarnera [aut],
Teresa Buglielli [aut, cre]
Maintainer: Teresa Buglielli <teresa.buglielli@gmail.com>
Diff between SeleMix versions 1.0.2 dated 2020-11-28 and 1.0.3 dated 2025-01-23
DESCRIPTION | 25 +++++++++----- MD5 | 19 +++++------ NAMESPACE | 2 - NEWS | 30 +++++++++-------- R/check.vars.r | 27 +++++++-------- R/ml.est.R | 95 ++++++++++++++++++++++++++++++-------------------------- R/pred.y.r | 6 +-- R/sel.edit.r | 15 ++++---- build |only man/ml.est.Rd | 2 - man/sel.edit.Rd | 2 - 11 files changed, 118 insertions(+), 105 deletions(-)
Title: Creation of Mock Observational Medical Outcomes Partnership
Common Data Model
Description: Creates mock data for testing and package development for the
Observational Medical Outcomes Partnership common data model. The
package offers functions crafted with pipeline-friendly
implementation, enabling users to effortlessly include only the
necessary tables for their testing needs.
Author: Mike Du [aut, cre] ,
Marti Catala [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Mike Du <mike.du@ndorms.ox.ac.uk>
Diff between omock versions 0.3.1 dated 2024-10-15 and 0.3.2 dated 2025-01-23
DESCRIPTION | 8 +-- MD5 | 45 +++++++++---------- NEWS.md | 2 R/checkInputs.R | 2 R/mockCdmFromTables.R | 15 +++++- R/mockConditionOccurrence.R | 3 - R/mockDrugExposure.R | 3 - R/mockMeasurement.R | 3 - R/mockObservation.R | 3 - R/mockProcedureOccurrence.R | 3 - R/mockVisitOccurrence.R | 3 - R/mockVocabulary.R | 6 ++ README.md | 12 ++--- inst/CITATION |only inst/doc/a01_Creating_synthetic_clinical_tables.html | 18 +++---- inst/doc/a02_Creating_synthetic_cohorts.html | 4 - inst/doc/a03_Creating_a_synthetic_vocabulary.html | 4 - inst/doc/a04_Building_a_bespoke_mock_cdm.html | 4 - tests/testthat/test-mockCdmFromTables.R | 4 + tests/testthat/test-mockCondtitionOccurrence.R | 3 - tests/testthat/test-mockDrugExposure.R | 3 - tests/testthat/test-mockMeasurement.R | 3 - tests/testthat/test-mockObservation.R | 3 - tests/testthat/test-mockVocabularyTables.R | 3 - 24 files changed, 94 insertions(+), 63 deletions(-)
Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 <doi:10.1002/sim.2897> or Baker and Jackson, 2008 <doi:10.1007/s10729-007-9041-8>) or mixtures of normals (Beath, 2014 <doi:10.1002/jrsm.1114>).
Author: Ken Beath [aut, cre],
Ben Bolker [aut],
R Development Core Team [aut]
Maintainer: Ken Beath <ken@kjbeath.id.au>
Diff between metaplus versions 1.0-5 dated 2024-07-04 and 1.0-6 dated 2025-01-23
DESCRIPTION | 11 - MD5 | 10 - NAMESPACE | 2 R/makestart.profilemix.metaplus.R | 302 +++++++++++++++++++++----------------- build/vignette.rds |binary inst/NEWS | 4 6 files changed, 183 insertions(+), 146 deletions(-)