Title: Tidy Characterizations of Model Performance
Description: Tidy tools for quantifying how well model fits to a data set such as confusion matrices, class probability curve summaries, and regression metrics (e.g., RMSE).
Author: Max Kuhn [aut],
Davis Vaughan [aut, cre],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between yardstick versions 0.0.3 dated 2019-03-08 and 0.0.4 dated 2019-08-26
DESCRIPTION | 19 MD5 | 208 +++++---- NAMESPACE | 8 NEWS.md | 34 + R/RcppExports.R | 4 R/class-accuracy.R | 1 R/class-bal_accuracy.R | 1 R/class-detection_prevalence.R | 1 R/class-f_meas.R | 5 R/class-j_index.R | 1 R/class-kap.R | 1 R/class-mcc.R | 14 R/class-npv.R | 1 R/class-ppv.R | 1 R/class-precision.R | 83 +++ R/class-recall.R | 93 +++- R/class-sens.R | 121 +++++ R/class-spec.R | 88 +++- R/conditions.R |only R/data.R | 22 - R/metrics.R | 214 +++++----- R/num-ccc.R | 1 R/num-huber_loss.R | 1 R/num-iic.R |only R/num-mae.R | 1 R/num-mape.R | 1 R/num-mase.R | 1 R/num-pseudo_huber_loss.R | 1 R/num-rmse.R | 1 R/num-rpd.R | 1 R/num-rpiq.R | 1 R/num-rsq.R | 3 R/num-rsq_trad.R | 1 R/num-smape.R | 1 R/prob-average_precision.R |only R/prob-gain_capture.R | 7 R/prob-gain_curve.R | 8 R/prob-lift_curve.R | 8 R/prob-mn_log_loss.R | 26 - R/prob-pr_auc.R | 8 R/prob-pr_curve.R | 27 - R/prob-roc_auc.R | 36 + R/prob-roc_curve.R | 25 - R/selectors.R | 11 README.md | 6 build/vignette.rds |binary inst/doc/custom-metrics.html | 78 +-- inst/doc/metric-types.html | 31 + inst/doc/multiclass.html | 9 man/average_precision.Rd |only man/bal_accuracy.Rd | 7 man/ccc.Rd | 18 man/conf_mat.Rd | 2 man/detection_prevalence.Rd | 7 man/f_meas.Rd | 7 man/gain_capture.Rd | 46 +- man/gain_curve.Rd | 29 + man/hpc_cv.Rd | 10 man/huber_loss.Rd | 18 man/huber_loss_pseudo.Rd | 18 man/iic.Rd |only man/j_index.Rd | 7 man/lift_curve.Rd | 29 + man/mae.Rd | 16 man/mape.Rd | 16 man/mase.Rd | 16 man/mcc.Rd | 7 man/metric_set.Rd | 8 man/metrics.Rd | 2 man/mn_log_loss.Rd | 5 man/npv.Rd | 7 man/ppv.Rd | 7 man/pr_auc.Rd | 43 +- man/pr_curve.Rd | 28 - man/precision.Rd | 14 man/recall.Rd | 14 man/rmse.Rd | 16 man/roc_auc.Rd | 67 ++- man/roc_curve.Rd | 30 + man/rpd.Rd | 10 man/rpiq.Rd | 10 man/rsq.Rd | 10 man/rsq_trad.Rd | 8 man/sens.Rd | 17 man/smape.Rd | 16 man/spec.Rd | 17 man/summary.conf_mat.Rd | 7 man/two_class_example.Rd | 6 src/RcppExports.cpp | 9 src/pr-curve.cpp | 136 +++--- tests/testthat/test-class-f_meas-precision-warning-binary.txt |only tests/testthat/test-class-f_meas-precision-warning-multiclass.txt |only tests/testthat/test-class-f_meas-recall-warning-binary.txt |only tests/testthat/test-class-f_meas-recall-warning-multiclass.txt |only tests/testthat/test-class-f_meas.R | 92 ++-- tests/testthat/test-class-mcc.R | 8 tests/testthat/test-class-precision-warning-binary.txt |only tests/testthat/test-class-precision-warning-multiclass.txt |only tests/testthat/test-class-precision.R | 50 ++ tests/testthat/test-class-recall-warning-binary.txt |only tests/testthat/test-class-recall-warning-multiclass.txt |only tests/testthat/test-class-recall.R | 43 +- tests/testthat/test-class-sens-warning-binary.txt |only tests/testthat/test-class-sens-warning-multiclass.txt |only tests/testthat/test-class-sens.R | 43 ++ tests/testthat/test-class-spec-warning-binary.txt |only tests/testthat/test-class-spec-warning-multiclass.txt |only tests/testthat/test-class-spec.R | 43 ++ tests/testthat/test-numeric.R | 35 + tests/testthat/test-prob-average_precision.R |only tests/testthat/test-prob-mn_log_loss.R | 26 + tests/testthat/test-prob-pr.R | 157 +++++++ tests/testthat/test-prob-roc.R | 74 +++ tests/testthat/test_metrics.R | 56 ++ 114 files changed, 1921 insertions(+), 660 deletions(-)
Title: Nonparametric Variable Importance
Description: Calculate point estimates of and valid confidence intervals for
nonparametric variable importance measures in high and low dimensions,
using flexible estimators of the underlying regression functions. For more information
about the methods, please see Williamson et al. (2017) <https://biostats.bepress.com/uwbiostat/paper422/>.
Author: Brian D. Williamson [aut, cre],
Noah Simon [aut],
Marco Carone [aut]
Maintainer: Brian D. Williamson <brianw26@uw.edu>
Diff between vimp versions 1.1.5 dated 2019-08-09 and 1.1.6 dated 2019-08-26
DESCRIPTION | 9 +- MD5 | 12 +-- inst/doc/introduction_to_vimp.html | 42 ++++++------ tests/testthat/test_average_vimp_regression.R | 24 ++++--- tests/testthat/test_cv_vim.R | 88 ++++++++++++++------------ tests/testthat/test_merge_vimp_regression.R | 18 +++-- tests/testthat/test_vimp_regression.R | 30 ++++---- 7 files changed, 122 insertions(+), 101 deletions(-)
Title: Provenance Visualizer
Description: Displays provenance graphically for provenance collected by the 'rdt' or
'rdtLite' packages, or other tools providing compatible PROV JSON output. The exact
format of the JSON created by 'rdt' and 'rdtLite' is described in
<https://github.com/End-to-end-provenance/ExtendedProvJson>. More information about
rdtLite and associated tools is available at <https://github.com/End-to-end-provenance/>
and Barbara Lerner, Emery Boose, and Luis Perez (2018), Using Introspection to Collect
Provenance in R, Informatics, <doi: 10.3390/informatics5010012>.
Author: Emery Boose [ctb],
Barbara Lerner [aut, cre],
Sofiya Taskova [aut],
Miruna Oprescu [aut],
Nikki Hoffler [aut],
Marios Dardas [aut],
Elizabeth Fong [ctb],
Thomas Pasquier [ctb],
Matthew Lau [ctb],
Aaron Ellison [res],
Margo Seltzer [res]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Diff between provViz versions 1.0.5 dated 2019-06-10 and 1.0.6 dated 2019-08-26
provViz-1.0.5/provViz/inst/testdata/script.R |only provViz-1.0.6/provViz/DESCRIPTION | 8 +- provViz-1.0.6/provViz/MD5 | 10 +- provViz-1.0.6/provViz/NEWS | 8 +- provViz-1.0.6/provViz/inst/java/DDGExplorer.jar |binary provViz-1.0.6/provViz/inst/testdata/prov.json | 93 +++++++++++------------- provViz-1.0.6/provViz/inst/testscripts |only 7 files changed, 60 insertions(+), 59 deletions(-)
Title: Meta-Feature Extractor
Description: Extracts meta-features from datasets to support the design of
recommendation systems based on Meta-Learning. The meta-features, also called
characterization measures, are able to characterize the complexity of datasets
and to provide estimates of algorithm performance. The package contains not
only the standard characterization measures, but also more recent
characterization measures. By making available a large set of meta-feature
extraction functions, tasks like comprehensive data characterization, deep
data exploration and large number of Meta-Learning based data analysis can be
performed. These concepts are described in the paper: Adriano Rivolli, Luis
Garcia, Carlos Soares, Joaquin Vanschoren, and Andre de Carvalho. Towards
Reproducible Empirical Research in Meta-Learning.
Author: Adriano Rivolli [aut, cre],
Luis P. F. Garcia [aut],
Andre C. P. L. F. de Carvalho [ths]
Maintainer: Adriano Rivolli <rivolli@utfpr.edu.br>
Diff between mfe versions 0.1.2 dated 2019-04-10 and 0.1.3 dated 2019-08-26
DESCRIPTION | 20 ++--- MD5 | 65 ++++++++++-------- NAMESPACE | 8 ++ NEWS.md | 11 ++- R/clustering.R |only R/general.R | 2 R/infotheo.R | 3 R/internal.R | 92 +++++++++++++++++-------- R/landmarking.R | 55 ++++++++++----- R/metafeatures.R | 7 + R/model.based.R | 54 +++++++-------- R/relative.R |only R/statistical.R | 4 - README.md | 7 + build/vignette.rds |binary inst/doc/mfe-vignette.R | 23 ++++++ inst/doc/mfe-vignette.Rmd | 44 +++++++++++- inst/doc/mfe-vignette.html | 121 ++++++++++++++++++++++++++-------- man/clustering.Rd |only man/general.Rd | 5 - man/infotheo.Rd | 5 - man/landmarking.Rd | 19 +++-- man/ls.clustering.Rd |only man/ls.relative.Rd |only man/metafeatures.Rd | 2 man/model.based.Rd | 5 - man/relative.Rd |only man/statistical.Rd | 7 + tests/testthat/test_clustering.R |only tests/testthat/test_general.R | 16 +--- tests/testthat/test_infotheo.R | 32 ++++++-- tests/testthat/test_landmarking.R | 40 ++++++++--- tests/testthat/test_metafeatures.R | 60 +++++++++++----- tests/testthat/test_model.based.R | 15 +--- tests/testthat/test_post.processing.R |only tests/testthat/test_relative.R |only tests/testthat/test_statistical.R | 24 ++++-- vignettes/mfe-vignette.Rmd | 44 +++++++++++- 38 files changed, 557 insertions(+), 233 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov
chains more easily. In addition functions to perform statistical (fitting
and drawing random variates) and probabilistic (analysis of their structural
proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut, cre]
(<https://orcid.org/0000-0002-0315-8888>),
Tae Seung Kang [aut],
Sai Bhargav Yalamanchi [aut],
Mildenberger Thoralf [ctb] (<https://orcid.org/0000-0001-7242-1873>),
Deepak Yadav [aut],
Ignacio Cordón [aut] (<https://orcid.org/0000-0002-3152-0231>),
Vandit Jain [ctb],
Toni Giorgino [ctb] (<https://orcid.org/0000-0001-6449-0596>)
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.6.9.16 dated 2019-07-22 and 0.7.0 dated 2019-08-26
markovchain-0.6.9.16/markovchain/R/0_classesAndMethods.R |only markovchain-0.6.9.16/markovchain/R/0_ctmcClassesAndMethodsSAI.R |only markovchain-0.6.9.16/markovchain/R/0_higherOrder.R |only markovchain-0.6.9.16/markovchain/R/0_hommc.R |only markovchain-0.6.9.16/markovchain/R/1_ctmcProbabilisticSAI.R |only markovchain-0.6.9.16/markovchain/R/1_functions4Fitting.R |only markovchain-0.6.9.16/markovchain/R/1_supplementaryPlot.R |only markovchain-0.6.9.16/markovchain/R/2_probabilistic.R |only markovchain-0.6.9.16/markovchain/R/5_statisticalTests.R |only markovchain-0.6.9.16/markovchain/inst/doc/complicate_steady_states_analysis.R |only markovchain-0.6.9.16/markovchain/inst/doc/complicate_steady_states_analysis.Rmd |only markovchain-0.6.9.16/markovchain/inst/doc/complicate_steady_states_analysis.pdf |only markovchain-0.6.9.16/markovchain/man/absorbingStates.Rd |only markovchain-0.6.9.16/markovchain/man/fitHigherOrderMarkovChain.Rd |only markovchain-0.6.9.16/markovchain/man/markovchain-package.Rd |only markovchain-0.6.9.16/markovchain/src/ctmcClassesAndMethodsSAI.cpp |only markovchain-0.6.9.16/markovchain/src/ctmcFittingsFunctions.cpp |only markovchain-0.6.9.16/markovchain/src/mapFitFunctionsSAI.h |only markovchain-0.6.9.16/markovchain/src/sampler.cpp |only markovchain-0.6.9.16/markovchain/src/sampler.h |only markovchain-0.6.9.16/markovchain/tests/testthat/setup-data.R |only markovchain-0.6.9.16/markovchain/tests/testthat/testBasic1.R |only markovchain-0.6.9.16/markovchain/tests/testthat/testMeanFirstPassageTimes.R |only markovchain-0.6.9.16/markovchain/tests/testthat/testRecurrentClasses.R |only markovchain-0.6.9.16/markovchain/vignettes/complicate_steady_states_analysis.Rmd |only markovchain-0.7.0/markovchain/ChangeLog | 10 markovchain-0.7.0/markovchain/DESCRIPTION | 18 markovchain-0.7.0/markovchain/MD5 | 196 - markovchain-0.7.0/markovchain/NAMESPACE | 149 - markovchain-0.7.0/markovchain/NEWS | 18 markovchain-0.7.0/markovchain/R/RcppExports.R | 320 ++ markovchain-0.7.0/markovchain/R/classesAndMethods.R |only markovchain-0.7.0/markovchain/R/ctmcClassesAndMethods.R |only markovchain-0.7.0/markovchain/R/ctmcProbabilistic.R |only markovchain-0.7.0/markovchain/R/fitHigherOrder.R |only markovchain-0.7.0/markovchain/R/fittingFunctions.R |only markovchain-0.7.0/markovchain/R/hommc.R |only markovchain-0.7.0/markovchain/R/markovchain.R |only markovchain-0.7.0/markovchain/R/probabilistic.R |only markovchain-0.7.0/markovchain/R/random.R | 9 markovchain-0.7.0/markovchain/R/statisticalTests.R |only markovchain-0.7.0/markovchain/R/supplementaryPlot.R |only markovchain-0.7.0/markovchain/R/sysdata.rda |binary markovchain-0.7.0/markovchain/R/utils.R |only markovchain-0.7.0/markovchain/R/zzz.R | 2 markovchain-0.7.0/markovchain/build/vignette.rds |binary markovchain-0.7.0/markovchain/inst/doc/an_introduction_to_markovchain_package.R | 58 markovchain-0.7.0/markovchain/inst/doc/an_introduction_to_markovchain_package.Rmd | 214 + markovchain-0.7.0/markovchain/inst/doc/an_introduction_to_markovchain_package.pdf |binary markovchain-0.7.0/markovchain/inst/doc/gsoc_2017_additions.pdf |binary markovchain-0.7.0/markovchain/inst/doc/higher_order_markov_chains.pdf |binary markovchain-0.7.0/markovchain/inst/doc/markvochain_crash_intro.pdf |binary markovchain-0.7.0/markovchain/man/ExpectedTime.Rd | 2 markovchain-0.7.0/markovchain/man/HigherOrderMarkovChain-class.Rd | 8 markovchain-0.7.0/markovchain/man/absorptionProbabilities.Rd |only markovchain-0.7.0/markovchain/man/committorAB.Rd | 2 markovchain-0.7.0/markovchain/man/conditionalDistribution.Rd | 2 markovchain-0.7.0/markovchain/man/ctmc-class.Rd | 83 markovchain-0.7.0/markovchain/man/ctmcFit.Rd | 58 markovchain-0.7.0/markovchain/man/expectedRewards.Rd | 2 markovchain-0.7.0/markovchain/man/expectedRewardsBeforeHittingA.Rd | 2 markovchain-0.7.0/markovchain/man/firstPassage.Rd | 2 markovchain-0.7.0/markovchain/man/firstPassageMultiple.Rd | 2 markovchain-0.7.0/markovchain/man/fitHighOrderMultivarMC.Rd | 2 markovchain-0.7.0/markovchain/man/fitHigherOrder.Rd |only markovchain-0.7.0/markovchain/man/freq2Generator.Rd | 2 markovchain-0.7.0/markovchain/man/generatorToTransitionMatrix.Rd | 47 markovchain-0.7.0/markovchain/man/getName.Rd | 2 markovchain-0.7.0/markovchain/man/hittingProbabilities.Rd | 11 markovchain-0.7.0/markovchain/man/hommc-class.Rd | 3 markovchain-0.7.0/markovchain/man/hommc-show.Rd | 2 markovchain-0.7.0/markovchain/man/ictmc-class.Rd | 2 markovchain-0.7.0/markovchain/man/impreciseProbabilityatT.Rd | 3 markovchain-0.7.0/markovchain/man/is.CTMCirreducible.Rd | 2 markovchain-0.7.0/markovchain/man/is.TimeReversible.Rd | 2 markovchain-0.7.0/markovchain/man/is.accessible.Rd | 7 markovchain-0.7.0/markovchain/man/is.irreducible.Rd | 5 markovchain-0.7.0/markovchain/man/is.regular.Rd |only markovchain-0.7.0/markovchain/man/markovchain-class.Rd | 168 - markovchain-0.7.0/markovchain/man/markovchain.Rd |only markovchain-0.7.0/markovchain/man/markovchainList-class.Rd | 99 markovchain-0.7.0/markovchain/man/markovchainListFit.Rd | 2 markovchain-0.7.0/markovchain/man/markovchainSequence.Rd | 2 markovchain-0.7.0/markovchain/man/meanAbsorptionTime.Rd |only markovchain-0.7.0/markovchain/man/meanFirstPassageTime.Rd | 55 markovchain-0.7.0/markovchain/man/meanNumVisits.Rd |only markovchain-0.7.0/markovchain/man/meanRecurrenceTime.Rd |only markovchain-0.7.0/markovchain/man/multinomialConfidenceIntervals.Rd | 4 markovchain-0.7.0/markovchain/man/names.Rd | 2 markovchain-0.7.0/markovchain/man/noofVisitsDist.Rd | 2 markovchain-0.7.0/markovchain/man/predictHommc.Rd | 2 markovchain-0.7.0/markovchain/man/predictiveDistribution.Rd | 71 markovchain-0.7.0/markovchain/man/priorDistribution.Rd | 71 markovchain-0.7.0/markovchain/man/probabilityatT.Rd | 2 markovchain-0.7.0/markovchain/man/rctmc.Rd | 83 markovchain-0.7.0/markovchain/man/rmarkovchain.Rd | 2 markovchain-0.7.0/markovchain/man/setName.Rd | 2 markovchain-0.7.0/markovchain/man/states.Rd | 2 markovchain-0.7.0/markovchain/man/statisticalTests.Rd | 2 markovchain-0.7.0/markovchain/man/steadyStates.Rd | 6 markovchain-0.7.0/markovchain/man/structuralAnalysis.Rd |only markovchain-0.7.0/markovchain/man/transition2Generator.Rd | 2 markovchain-0.7.0/markovchain/man/transitionProbability.Rd | 2 markovchain-0.7.0/markovchain/src/Makevars | 1 markovchain-0.7.0/markovchain/src/Makevars.win | 1 markovchain-0.7.0/markovchain/src/RcppExports.cpp | 373 +++ markovchain-0.7.0/markovchain/src/classesAndMethods.cpp | 96 markovchain-0.7.0/markovchain/src/ctmcClassesAndMethods.cpp |only markovchain-0.7.0/markovchain/src/ctmcFittingFunctions.cpp |only markovchain-0.7.0/markovchain/src/fitHigherOrder.cpp | 4 markovchain-0.7.0/markovchain/src/fittingFunctions.cpp | 15 markovchain-0.7.0/markovchain/src/mapFitFunctions.h |only markovchain-0.7.0/markovchain/src/probabilistic.cpp | 1076 ++++++++-- markovchain-0.7.0/markovchain/src/utils.cpp |only markovchain-0.7.0/markovchain/tests/testthat/setupData.R |only markovchain-0.7.0/markovchain/tests/testthat/testBasic.R |only markovchain-0.7.0/markovchain/tests/testthat/testCommClasses.R | 55 markovchain-0.7.0/markovchain/tests/testthat/testHittingProbabilities.R | 87 markovchain-0.7.0/markovchain/tests/testthat/testMarkovChainsClassification.R |only markovchain-0.7.0/markovchain/tests/testthat/testMeanMeasures.R |only markovchain-0.7.0/markovchain/tests/testthat/testOptimization.R | 7 markovchain-0.7.0/markovchain/tests/testthat/testPlot.R | 50 markovchain-0.7.0/markovchain/tests/testthat/testStatesClassification.R | 244 +- markovchain-0.7.0/markovchain/tests/testthat/testSteadyStates.R | 96 markovchain-0.7.0/markovchain/vignettes/an_introduction_to_markovchain_package.Rmd | 214 + 125 files changed, 2951 insertions(+), 1196 deletions(-)
Title: Effects and Importances of Model Ingredients
Description: Collection of tools for assessment of feature importance and feature effects.
Key functions are:
feature_importance() for assessment of global level feature importance,
ceteris_paribus() for calculation of the what-if plots,
partial_dependency() for partial dependency plots,
conditional_dependency() for conditional dependency plots,
accumulated_dependency() for accumulated local effects plots,
aggregate_profiles() and cluster_profiles() for aggregation of ceteris paribus profiles,
generic print() and plot() for better usability of selected explainers,
generic plotD3() for interactive, D3 based explanations, and
generic describe() for explanations in natural language.
The package 'ingredients' is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Hubert Baniecki [aut],
Adam Izdebski [aut],
Katarzyna Pekala [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between ingredients versions 0.3.3 dated 2019-05-01 and 0.3.9 dated 2019-08-26
ingredients-0.3.3/ingredients/R/aggreagate_profiles.R |only ingredients-0.3.3/ingredients/R/describe.R |only ingredients-0.3.3/ingredients/R/plotD3_feature_importance_explainer.R |only ingredients-0.3.3/ingredients/R/plot_aggregated_ceteris_paribus_explainer.R |only ingredients-0.3.3/ingredients/R/plot_ceteris_paribus_2d_explainer.R |only ingredients-0.3.3/ingredients/R/plot_ceteris_paribus_explainer.R |only ingredients-0.3.3/ingredients/R/plot_feature_importance_explainer.R |only ingredients-0.3.3/ingredients/R/print_aggregated_ceteris_paribus_explainer.R |only ingredients-0.3.3/ingredients/R/print_ceteris_paribus_descriptions.R |only ingredients-0.3.3/ingredients/R/print_ceteris_paribus_explainer.R |only ingredients-0.3.3/ingredients/R/select_samples.R |only ingredients-0.3.3/ingredients/R/theme_drwhy.R |only ingredients-0.3.3/ingredients/man/plotD3.Rd |only ingredients-0.3.3/ingredients/man/print.aggregated_ceteris_paribus_explainer.Rd |only ingredients-0.3.3/ingredients/man/print.ceteris_paribus_descriptions.Rd |only ingredients-0.3.3/ingredients/man/theme_drwhy.Rd |only ingredients-0.3.9/ingredients/DESCRIPTION | 35 ingredients-0.3.9/ingredients/MD5 | 174 ++-- ingredients-0.3.9/ingredients/NAMESPACE | 156 ++- ingredients-0.3.9/ingredients/NEWS.md | 31 ingredients-0.3.9/ingredients/R/accumulated_dependency.R | 127 +-- ingredients-0.3.9/ingredients/R/aggregate_profiles.R |only ingredients-0.3.9/ingredients/R/aspect_importance.R |only ingredients-0.3.9/ingredients/R/calculate_oscillations.R | 51 - ingredients-0.3.9/ingredients/R/calculate_variable_profile.R | 65 - ingredients-0.3.9/ingredients/R/ceteris_paribus.R | 111 +- ingredients-0.3.9/ingredients/R/ceteris_paribus_2d.R | 25 ingredients-0.3.9/ingredients/R/cluster_profiles.R | 24 ingredients-0.3.9/ingredients/R/conditional_dependency.R | 123 +- ingredients-0.3.9/ingredients/R/describe_aggregated_profiles.R |only ingredients-0.3.9/ingredients/R/describe_ceteris_paribus.R |only ingredients-0.3.9/ingredients/R/describe_feature_importance.R |only ingredients-0.3.9/ingredients/R/feature_importance.R | 419 ++++++---- ingredients-0.3.9/ingredients/R/partial_dependency.R | 128 +-- ingredients-0.3.9/ingredients/R/plotD3_aggregated_profiles.R |only ingredients-0.3.9/ingredients/R/plotD3_ceteris_paribus.R |only ingredients-0.3.9/ingredients/R/plotD3_feature_importance.R |only ingredients-0.3.9/ingredients/R/plot_aggregated_profiles.R |only ingredients-0.3.9/ingredients/R/plot_ceteris_paribus.R |only ingredients-0.3.9/ingredients/R/plot_ceteris_paribus_2d.R |only ingredients-0.3.9/ingredients/R/plot_ceteris_paribus_oscillations.R | 21 ingredients-0.3.9/ingredients/R/plot_feature_importance.R |only ingredients-0.3.9/ingredients/R/print_aggregated_profiles.R |only ingredients-0.3.9/ingredients/R/print_ceteris_paribus.R |only ingredients-0.3.9/ingredients/R/select_neighbours.R | 25 ingredients-0.3.9/ingredients/R/select_sample.R |only ingredients-0.3.9/ingredients/R/show_aggregated_profiles.R | 54 - 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Title: Model Agnostic Instance Level Variable Attributions
Description: Model agnostic tool for decomposition of predictions from black boxes.
Supports additive attributions and attributions with interactions.
The Break Down Table shows contributions of every variable to a final prediction.
The Break Down Plot presents variable contributions in a concise graphical way.
This package works for classification and regression models.
It is an extension of the 'breakDown' package (Staniak and Biecek 2018) <doi:10.32614/RJ-2018-072>,
with new and faster strategies for orderings.
It supports interactions in explanations and has interactive visuals (implemented with 'D3.js' library).
The methodology behind is described in the 'iBreakDown' article (Gosiewska and Biecek 2019) <arXiv:1903.11420>
This package is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre],
Alicja Gosiewska [aut],
Hubert Baniecki [aut],
Adam Izdebski [aut],
Dariusz Komosinski [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between iBreakDown versions 0.9.6 dated 2019-04-30 and 0.9.9 dated 2019-08-26
iBreakDown-0.9.6/iBreakDown/inst/breakDownD3.css |only iBreakDown-0.9.6/iBreakDown/inst/breakDownD3.js |only iBreakDown-0.9.6/iBreakDown/inst/tooltipD3.js |only iBreakDown-0.9.6/iBreakDown/man/plotD3.Rd |only iBreakDown-0.9.9/iBreakDown/DESCRIPTION | 22 iBreakDown-0.9.9/iBreakDown/MD5 | 96 iBreakDown-0.9.9/iBreakDown/NAMESPACE | 70 iBreakDown-0.9.9/iBreakDown/NEWS.md | 13 iBreakDown-0.9.9/iBreakDown/R/break_down.R | 4 iBreakDown-0.9.9/iBreakDown/R/break_down_uncertainty.R | 65 iBreakDown-0.9.9/iBreakDown/R/describe_breakdown.R |only iBreakDown-0.9.9/iBreakDown/R/describe_shap.R |only iBreakDown-0.9.9/iBreakDown/R/local_attributions.R | 55 iBreakDown-0.9.9/iBreakDown/R/local_interactions.R | 6 iBreakDown-0.9.9/iBreakDown/R/plotD3_break_down.R | 254 iBreakDown-0.9.9/iBreakDown/R/plotD3_shap.R |only iBreakDown-0.9.9/iBreakDown/R/plot_break_down.R | 20 iBreakDown-0.9.9/iBreakDown/R/plot_break_down_uncertainty.R | 4 iBreakDown-0.9.9/iBreakDown/R/print_break_down.R | 7 iBreakDown-0.9.9/iBreakDown/R/print_break_down_descriptions.R |only iBreakDown-0.9.9/iBreakDown/R/print_break_down_uncertainty.R | 14 iBreakDown-0.9.9/iBreakDown/build/vignette.rds |binary iBreakDown-0.9.9/iBreakDown/inst/d3js |only iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_classification.R | 184 iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_classification.Rmd | 6 iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_classification.html | 2775 +++++- iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_description.R |only iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_description.Rmd |only iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_description.html |only iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_regression.R | 182 iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_regression.Rmd | 2 iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_regression.html | 1020 +- iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_titanic.R | 124 iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_titanic.Rmd | 230 iBreakDown-0.9.9/iBreakDown/inst/doc/vignette_iBreakDown_titanic.html | 4384 ++++------ iBreakDown-0.9.9/iBreakDown/man/break_down.Rd | 170 iBreakDown-0.9.9/iBreakDown/man/break_down_uncertainty.Rd | 226 iBreakDown-0.9.9/iBreakDown/man/describe.Rd |only iBreakDown-0.9.9/iBreakDown/man/local_attributions.Rd | 206 iBreakDown-0.9.9/iBreakDown/man/local_interactions.Rd | 210 iBreakDown-0.9.9/iBreakDown/man/plot.break_down.Rd | 248 iBreakDown-0.9.9/iBreakDown/man/plot.break_down_uncertainty.Rd | 165 iBreakDown-0.9.9/iBreakDown/man/plotD3_break_down.Rd |only iBreakDown-0.9.9/iBreakDown/man/plotD3_shap.Rd |only iBreakDown-0.9.9/iBreakDown/man/print.break_down.Rd | 59 iBreakDown-0.9.9/iBreakDown/man/print.break_down_description.Rd |only iBreakDown-0.9.9/iBreakDown/man/print.break_down_uncertainty.Rd | 128 iBreakDown-0.9.9/iBreakDown/tests/testthat/test_break_down.R | 2 iBreakDown-0.9.9/iBreakDown/tests/testthat/test_break_down_uncertainty.R | 6 iBreakDown-0.9.9/iBreakDown/tests/testthat/test_describe.R |only iBreakDown-0.9.9/iBreakDown/tests/testthat/test_plot.R | 10 iBreakDown-0.9.9/iBreakDown/vignettes/vignette_iBreakDown_classification.Rmd | 6 iBreakDown-0.9.9/iBreakDown/vignettes/vignette_iBreakDown_description.Rmd |only iBreakDown-0.9.9/iBreakDown/vignettes/vignette_iBreakDown_regression.Rmd | 2 iBreakDown-0.9.9/iBreakDown/vignettes/vignette_iBreakDown_titanic.Rmd | 230 55 files changed, 6430 insertions(+), 4775 deletions(-)
Title: Generalized Linear Mixed Model Association Tests
Description: Perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. First, GMMAT fits a GLMM with covariate adjustment and random effects to account for population structure and familial or cryptic relatedness. For GWAS, GMMAT performs score tests for each genetic variant as proposed in Chen et al. (2016) <DOI:10.1016/j.ajhg.2016.02.012>. For candidate gene studies, GMMAT can also perform Wald tests to get the effect size estimate for each genetic variant. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT) as proposed in Chen et al. (2019) <DOI:10.1016/j.ajhg.2018.12.012>, including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.
Author: Han Chen, Matthew P. Conomos
Maintainer: Han Chen <Han.Chen.2@uth.tmc.edu>
Diff between GMMAT versions 1.1.0 dated 2019-05-22 and 1.1.1 dated 2019-08-26
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + R/glmm.wald.R | 8 ++++---- R/glmmkin.R | 4 ++-- inst/doc/GMMAT.R | 6 +++--- inst/doc/GMMAT.Rnw | 18 ++++++++++++------ inst/doc/GMMAT.pdf |binary man/GMMAT-package.Rd | 4 ++-- man/glmm.score.meta.Rd | 2 ++ vignettes/GMMAT.Rnw | 18 ++++++++++++------ 11 files changed, 53 insertions(+), 38 deletions(-)
Title: Hypothesis Testing and Power Calculations for Comparing
Metagenomic Samples from HMP
Description: Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.
Author: Patricio S. La Rosa, Elena Deych, Sharina Carter, Berkley Shands, Dake Yang, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between HMP versions 1.6 dated 2018-10-31 and 2.0 dated 2019-08-26
DESCRIPTION | 8 ++-- MD5 | 66 ++++++++++++++++++++--------------- NEWS | 24 ++++++++++++ R/DM.Rpart.Base.Old.R |only R/DM.Rpart.CV.Consensus.R | 30 +++++++++------- R/DM.Rpart.CV.R | 31 +++++++++++++--- R/DM.Rpart.R | 6 +-- R/Data.filter.R | 34 +++++++----------- R/MC.Xdc.statistics.R | 14 ------- R/MC.Xmc.statistics.R | 14 ------- R/MC.Xmcupo.statistics.R | 14 ------- R/MC.Xoc.statistics.R | 14 ------- R/MC.Xsc.statistics.R | 8 ---- R/MC.ZT.statistics.R | 8 ---- R/Plot.PI.R | 4 +- R/formatDataSets.R | 8 +--- R/rpartCV.R | 82 +++++++++++++++----------------------------- R/rpartCVSingle.R |only R/rpartSplit.R | 19 ++++++---- R/rpartSplitOld.R |only build |only data/dmrp_covars.rda |only data/dmrp_data.rda |only inst |only man/DM.Rpart.Rd | 23 +++++++++--- man/Data.filter.Rd | 6 +-- man/HMP-internal.Rd | 5 ++ man/HMP-package.Rd | 2 + man/MC.Xdc.statistics.Rd | 6 +-- man/MC.Xmc.statistics.Rd | 6 +-- man/MC.Xmcupo.statistics.Rd | 5 -- man/MC.Xoc.statistics.Rd | 5 -- man/MC.Xsc.statistics.Rd | 3 - man/MC.ZT.statistics.Rd | 3 - man/dmrp_covars.Rd |only man/dmrp_data.Rd |only man/formatDataSets.Rd | 3 - vignettes |only 38 files changed, 214 insertions(+), 237 deletions(-)
Title: Bayesian Methods to Estimate the Proportion of Liars in Coin
Flip Experiments
Description: Implements Bayesian methods, described in
Hugh-Jones (2019) <doi:10.1007/s40881-019-00069-x>, for estimating the
proportion of liars in coin flip-style experiments, where subjects
report a random outcome and are paid for reporting a "good" outcome.
Author: David Hugh-Jones <davidhughjones@gmail.com>
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between truelies versions 0.1.0 dated 2019-06-28 and 0.2.0 dated 2019-08-26
truelies-0.1.0/truelies/R/bayesian-heads-cts.R |only truelies-0.2.0/truelies/DESCRIPTION | 22 +++++---- truelies-0.2.0/truelies/MD5 | 35 +++++++-------- truelies-0.2.0/truelies/NAMESPACE | 3 + truelies-0.2.0/truelies/NEWS.md | 5 ++ truelies-0.2.0/truelies/R/functions.R |only truelies-0.2.0/truelies/R/truelies-package.R | 9 +++ truelies-0.2.0/truelies/README.md | 12 +++-- truelies-0.2.0/truelies/man/compare_dists.Rd | 2 truelies-0.2.0/truelies/man/difference_dist.Rd | 2 truelies-0.2.0/truelies/man/dist_hdr.Rd | 2 truelies-0.2.0/truelies/man/dist_mean.Rd | 2 truelies-0.2.0/truelies/man/dist_quantile.Rd | 2 truelies-0.2.0/truelies/man/empirical_bayes.Rd |only truelies-0.2.0/truelies/man/figures/README-example-1.png |binary truelies-0.2.0/truelies/man/power_calc.Rd | 5 +- truelies-0.2.0/truelies/man/power_calc_difference.Rd | 5 +- truelies-0.2.0/truelies/man/print.densityFunction.Rd | 2 truelies-0.2.0/truelies/man/truelies-package.Rd | 24 ++++++++-- truelies-0.2.0/truelies/man/update_prior.Rd | 7 +-- 20 files changed, 92 insertions(+), 47 deletions(-)
Title: Portfolio Management with R
Description: Functions and examples for 'Portfolio
Management with R': backtesting investment and
trading strategies, computing profit/loss and
returns, analysing trades, handling lists of
transactions, reporting, and more.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between PMwR versions 0.11-1 dated 2019-06-03 and 0.12-0 dated 2019-08-26
ChangeLog | 84 +++++++++++++++++++++++++++++++++--- DESCRIPTION | 8 +-- MD5 | 50 ++++++++++----------- NAMESPACE | 1 NEWS | 46 +++++++++++++++++++ R/btest.R | 54 +++++++++++++++-------- R/pl.R | 34 +++++++++----- R/position.R | 19 +++++++- R/pricetable.R | 27 +++++++++-- R/returns.R | 57 ++++++++++++------------ R/valuation.R | 11 +++- build/vignette.rds |binary inst/doc/An_overview_of_PMwR.pdf |binary inst/doc/Computing_returns.pdf |binary inst/doc/Drawdowns_streaks.pdf |binary inst/doc/FinTeX.pdf |binary inst/doc/pl_open_positions.pdf |binary inst/doc/q32.pdf |binary inst/unitTests/test_results.txt | 31 +++++++------ inst/unitTests/ut_PMwR.R | 90 +++++++++++++++++++++++++++++++++++++++ man/btest.Rd | 6 ++ man/pl.Rd | 16 ++++-- man/pricetable.Rd | 10 +++- man/quote32.Rd | 9 +-- man/rc.Rd | 18 ++++++- man/valuation.Rd | 7 ++- 26 files changed, 444 insertions(+), 134 deletions(-)
Title: Length-Based Spawning Potential Ratio
Description: Simulate expected equilibrium length composition, yield-per-recruit, and
the spawning potential ratio (SPR) using the length-based SPR (LBSPR) model. Fit the LBSPR
model to length data to estimate selectivity, relative apical fishing mortality, and
the spawning potential ratio for data-limited fisheries.
See Hordyk et al (2016) <doi:10.1139/cjfas-2015-0422> for more information about the
LBSPR assessment method.
Author: Adrian Hordyk [aut, cre]
Maintainer: Adrian Hordyk <ar.hordyk@gmail.com>
Diff between LBSPR versions 0.1.3 dated 2019-03-12 and 0.1.4 dated 2019-08-26
DESCRIPTION | 6 MD5 | 10 R/plotSize.r | 30 - build/vignette.rds |binary inst/doc/LBSPR.html | 1415 +++++++++++++++++++++++++++++++++++++++++++++++++--- man/plotSize.Rd | 4 6 files changed, 1367 insertions(+), 98 deletions(-)
Title: Tests for Rotational Symmetry on the Hypersphere
Description: Implementation of the tests for rotational symmetry on the
hypersphere proposed in García-Portugués, Paindaveine and Verdebout
(2019) <arXiv:1706.05030>. The package also implements the proposed
distributions on the hypersphere, based on the tangent-normal
decomposition, and allows for the replication of the data
application considered in the paper.
Author: Eduardo García-Portugués [aut, cre],
Davy Paindaveine [aut],
Thomas Verdebout [aut]
Maintainer: Eduardo García-Portugués <edgarcia@est-econ.uc3m.es>
Diff between rotasym versions 1.0-5 dated 2019-05-15 and 1.0-6 dated 2019-08-26
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 1 - NEWS.md | 5 +++++ R/ACG.R | 2 +- R/auxiliary.R | 4 ++-- R/rotasym-package.R | 2 +- R/unif.R | 2 +- inst/CITATION | 2 +- 9 files changed, 24 insertions(+), 20 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <http://glottolog.org> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <http://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://ropensci.github.io/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.0.13 dated 2018-06-14 and 1.0.14 dated 2019-08-26
lingtypology-1.0.13/lingtypology/inst/doc/manual |only lingtypology-1.0.13/lingtypology/tests/testthat/test-phoible-features.R |only lingtypology-1.0.14/lingtypology/DESCRIPTION | 17 lingtypology-1.0.14/lingtypology/MD5 | 107 - lingtypology-1.0.14/lingtypology/NAMESPACE | 12 lingtypology-1.0.14/lingtypology/NEWS | 10 lingtypology-1.0.14/lingtypology/R/afbo.feature.R | 2 lingtypology-1.0.14/lingtypology/R/amap.R |only lingtypology-1.0.14/lingtypology/R/autotyp.feature.R | 8 lingtypology-1.0.14/lingtypology/R/ggmap.feature.R |only lingtypology-1.0.14/lingtypology/R/gltc.iso.R | 5 lingtypology-1.0.14/lingtypology/R/is.glottolog.R | 5 lingtypology-1.0.14/lingtypology/R/iso.gltc.R | 5 lingtypology-1.0.14/lingtypology/R/lang.gltc.R | 5 lingtypology-1.0.14/lingtypology/R/lang.iso.R | 5 lingtypology-1.0.14/lingtypology/R/map.feature.R | 21 lingtypology-1.0.14/lingtypology/R/oto_mangueanIC.feature.R | 2 lingtypology-1.0.14/lingtypology/R/phoible.R |only lingtypology-1.0.14/lingtypology/R/phoible.feature.R | 33 lingtypology-1.0.14/lingtypology/R/polygon.points_fd.R | 11 lingtypology-1.0.14/lingtypology/R/polygon.points_kde.R | 11 lingtypology-1.0.14/lingtypology/R/sails.feature.R | 2 lingtypology-1.0.14/lingtypology/R/uralex.R |only lingtypology-1.0.14/lingtypology/R/uralex.feature.R |only lingtypology-1.0.14/lingtypology/R/valpal.feature.R | 2 lingtypology-1.0.14/lingtypology/R/wals.feature.R | 2 lingtypology-1.0.14/lingtypology/build/vignette.rds |binary lingtypology-1.0.14/lingtypology/data/amap.RData |only lingtypology-1.0.14/lingtypology/data/datalist | 3 lingtypology-1.0.14/lingtypology/data/glottolog.modified.RData |binary lingtypology-1.0.14/lingtypology/data/glottolog.original.RData |binary lingtypology-1.0.14/lingtypology/data/phoible.RData |only lingtypology-1.0.14/lingtypology/data/uralex.RData |only lingtypology-1.0.14/lingtypology/inst/doc/lingtypology_creating_maps.Rmd | 4 lingtypology-1.0.14/lingtypology/inst/doc/lingtypology_creating_maps.html | 845 ++++++---- lingtypology-1.0.14/lingtypology/inst/doc/lingtypology_db_API.R | 8 lingtypology-1.0.14/lingtypology/inst/doc/lingtypology_db_API.Rmd | 14 lingtypology-1.0.14/lingtypology/inst/doc/lingtypology_db_API.html | 409 +++- lingtypology-1.0.14/lingtypology/inst/doc/lingtypology_dplyr.html | 484 ++++- lingtypology-1.0.14/lingtypology/inst/doc/lingtypology_glottolog_functions.html | 359 +++- lingtypology-1.0.14/lingtypology/inst/doc/lingtypology_intro.R | 2 lingtypology-1.0.14/lingtypology/inst/doc/lingtypology_intro.Rmd | 2 lingtypology-1.0.14/lingtypology/inst/doc/lingtypology_intro.html | 329 +++ lingtypology-1.0.14/lingtypology/man/afbo.feature.Rd | 2 lingtypology-1.0.14/lingtypology/man/amap.Rd |only lingtypology-1.0.14/lingtypology/man/autotyp.feature.Rd | 2 lingtypology-1.0.14/lingtypology/man/ggmap.feature.Rd |only lingtypology-1.0.14/lingtypology/man/long.lang.Rd | 3 lingtypology-1.0.14/lingtypology/man/map.feature.Rd | 37 lingtypology-1.0.14/lingtypology/man/oto_mangueanIC.feature.Rd | 2 lingtypology-1.0.14/lingtypology/man/phoible.Rd |only lingtypology-1.0.14/lingtypology/man/phoible.feature.Rd | 6 lingtypology-1.0.14/lingtypology/man/sails.feature.Rd | 2 lingtypology-1.0.14/lingtypology/man/uralex.Rd |only lingtypology-1.0.14/lingtypology/man/uralex.feature.Rd |only lingtypology-1.0.14/lingtypology/man/valpal.feature.Rd | 2 lingtypology-1.0.14/lingtypology/man/wals.feature.Rd | 2 lingtypology-1.0.14/lingtypology/tests/testthat/test-lang-aff.R | 8 lingtypology-1.0.14/lingtypology/tests/testthat/test-lang-country.R | 6 lingtypology-1.0.14/lingtypology/vignettes/lingtypology_creating_maps.Rmd | 4 lingtypology-1.0.14/lingtypology/vignettes/lingtypology_db_API.Rmd | 14 lingtypology-1.0.14/lingtypology/vignettes/lingtypology_intro.Rmd | 2 62 files changed, 2041 insertions(+), 775 deletions(-)
Title: Inspection, Comparison and Visualisation of Data Frames
Description: A collection of utilities for columnwise summary, comparison and visualisation of data frames. Functions report missingness, categorical levels, numeric distribution, correlation, column types and memory usage.
Author: Alastair Rushworth [aut, cre],
David Wilkins [ctb]
Maintainer: Alastair Rushworth <alastairmrushworth@gmail.com>
Diff between inspectdf versions 0.0.4 dated 2019-07-27 and 0.0.5 dated 2019-08-26
DESCRIPTION | 8 +-- MD5 | 50 +++++++++++----------- NAMESPACE | 3 - NEWS.md | 45 ++++++++++++++------ R/cor_test.R | 80 +++++++++++++++-------------------- R/inspect_cat.R | 33 +++++++------- R/inspect_cor.R | 50 ++++++++++++---------- R/inspect_imb.R | 45 ++++++++++---------- R/inspect_mem.R | 19 ++++---- R/inspect_na.R | 19 ++++---- R/inspect_num.R | 114 +++++++++++++++++++++++++++++---------------------- R/inspect_types.R | 4 - R/plot_cor.R | 12 +++-- R/plot_grouped.R | 10 +++- R/plot_imb.R | 14 ++++++ R/plot_na.R | 8 ++- R/plot_num.R | 27 +++++++----- R/show_plot.R | 11 ++++ R/zzz.R | 2 man/inspect_cat.Rd | 35 ++++++++------- man/inspect_cor.Rd | 45 +++++++++++--------- man/inspect_imb.Rd | 23 ++++------ man/inspect_mem.Rd | 19 ++++---- man/inspect_na.Rd | 16 +++---- man/inspect_num.Rd | 25 +++++------ man/inspect_types.Rd | 4 - 26 files changed, 401 insertions(+), 320 deletions(-)
Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates compilers
needed to build R packages on various platforms and ensures the PATH is
configured appropriately so R can use them.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
RStudio [cph]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between pkgbuild versions 1.0.4 dated 2019-08-05 and 1.0.5 dated 2019-08-26
DESCRIPTION | 6 +- MD5 | 42 ++++++++-------- NAMESPACE | 78 +++++++++++++++--------------- NEWS.md | 6 ++ R/build-tools.R | 9 +-- R/build.R | 4 - R/compile-dll.R | 2 man/build.Rd | 120 +++++++++++++++++++++++------------------------ man/clean_dll.Rd | 34 ++++++------- man/compile_dll.Rd | 90 +++++++++++++++++------------------ man/compiler_flags.Rd | 60 +++++++++++------------ man/has_build_tools.Rd | 116 +++++++++++++++++++++++---------------------- man/has_compiler.Rd | 64 ++++++++++++------------- man/has_latex.Rd | 28 +++++----- man/has_rtools.Rd | 90 +++++++++++++++++------------------ man/needs_compile.Rd | 34 ++++++------- man/pkg_has_src.Rd | 28 +++++----- man/pkg_links_to_rcpp.Rd | 30 +++++------ man/pkgbuild_process.Rd | 92 ++++++++++++++++++------------------ man/rcmd_build_tools.Rd | 70 +++++++++++++-------------- man/with_debug.Rd | 78 +++++++++++++++--------------- man/without_compiler.Rd | 38 +++++++------- 22 files changed, 564 insertions(+), 555 deletions(-)
Title: Interactively Explore Dimension-Reduced Embeddings
Description: A tool to interactively explore the
embeddings created by dimension reduction methods such as
Principal Components Analysis (PCA), Multidimensional Scaling (MDS),
T-distributed Stochastic Neighbour Embedding (t-SNE),
Uniform Manifold Approximation and Projection (UMAP) or any other.
Author: Svetlana Ovchinnikova [aut, cre],
Simon Anders [aut]
Maintainer: Svetlana Ovchinnikova <s.ovchinnikova@zmbh.uni-heidelberg.de>
Diff between sleepwalk versions 0.1.0 dated 2019-04-04 and 0.2.0 dated 2019-08-26
sleepwalk-0.1.0/sleepwalk/inst/sleepwalk.html |only sleepwalk-0.2.0/sleepwalk/DESCRIPTION | 8 +++--- sleepwalk-0.2.0/sleepwalk/MD5 | 11 +++++--- sleepwalk-0.2.0/sleepwalk/NEWS.md |only sleepwalk-0.2.0/sleepwalk/R/sleepwalk.R | 25 ++++++++++++------- sleepwalk-0.2.0/sleepwalk/inst/lasso.js |only sleepwalk-0.2.0/sleepwalk/inst/sleepwalk_canvas.html |only sleepwalk-0.2.0/sleepwalk/inst/sleepwalk_svg.html |only sleepwalk-0.2.0/sleepwalk/man/sleepwalk.Rd | 9 ++++++ 9 files changed, 35 insertions(+), 18 deletions(-)
Title: Simultaneous Comparisons for Multiple Endpoints
Description: Simultaneous tests and confidence intervals are provided for one-way experimental designs with one or many normally distributed, primary response variables (endpoints). Differences (Hasler and Hothorn, 2011 <doi:10.2202/1557-4679.1258>) or ratios (Hasler and Hothorn, 2012 <doi:10.1080/19466315.2011.633868>) of means can be considered. Various contrasts can be chosen, unbalanced sample sizes are allowed as well as heterogeneous variances (Hasler and Hothorn, 2008 <doi:10.1002/bimj.200710466>) or covariance matrices (Hasler, 2014 <doi:10.1515/ijb-2012-0015>).
Author: Mario Hasler, Christof Kluss
Maintainer: Mario Hasler <hasler@email.uni-kiel.de>
Diff between SimComp versions 3.2 dated 2017-07-31 and 3.3 dated 2019-08-26
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/rcm.R | 2 +- build/partial.rdb |binary man/DfSattDiff.Rd | 13 +++++++------ man/DfSattRat.Rd | 15 ++++++++------- man/SimCiDiff.Rd | 34 ++++++++++++++++++---------------- man/SimCiRat.Rd | 39 +++++++++++++++++++++------------------ man/SimComp-package.Rd | 13 ++++++++----- man/SimTestDiff.Rd | 46 ++++++++++++++++++++++++++-------------------- man/SimTestRat.Rd | 37 +++++++++++++++++++------------------ man/coagulation.Rd | 2 +- 12 files changed, 125 insertions(+), 108 deletions(-)
Title: Exploratory Data Analysis and Data Preparation Tool-Box Book
Description: Around 10% of almost any predictive modeling project is spent in predictive modeling, 'funModeling' and the book Data Science Live Book (<https://livebook.datascienceheroes.com/>) are intended to cover remaining 90%: data preparation, profiling, selecting best variables 'dataViz', assessing model performance and other functions.
Author: Pablo Casas [aut, cre]
Maintainer: Pablo Casas <pcasas.biz@gmail.com>
Diff between funModeling versions 1.8 dated 2019-08-01 and 1.9 dated 2019-08-26
funModeling-1.8/funModeling/R/lares_model_plots.R |only funModeling-1.8/funModeling/man/ROC.Rd |only funModeling-1.8/funModeling/man/dist2d.Rd |only funModeling-1.8/funModeling/man/errors.Rd |only funModeling-1.8/funModeling/man/gg_colour_customs.Rd |only funModeling-1.8/funModeling/man/gg_fill_customs.Rd |only funModeling-1.8/funModeling/man/gg_text_customs.Rd |only funModeling-1.8/funModeling/man/lares_pal.Rd |only funModeling-1.8/funModeling/man/mae.Rd |only funModeling-1.8/funModeling/man/mape.Rd |only funModeling-1.8/funModeling/man/mplot_cuts.Rd |only funModeling-1.8/funModeling/man/mplot_cuts_error.Rd |only funModeling-1.8/funModeling/man/mplot_density.Rd |only funModeling-1.8/funModeling/man/mplot_full.Rd |only funModeling-1.8/funModeling/man/mplot_lineal.Rd |only funModeling-1.8/funModeling/man/mplot_metrics.Rd |only funModeling-1.8/funModeling/man/mplot_roc.Rd |only funModeling-1.8/funModeling/man/mplot_splits.Rd |only funModeling-1.8/funModeling/man/mse.Rd |only funModeling-1.8/funModeling/man/plot_palette.Rd |only funModeling-1.8/funModeling/man/rmse.Rd |only funModeling-1.8/funModeling/man/rsq.Rd |only funModeling-1.8/funModeling/man/rsqa.Rd |only funModeling-1.8/funModeling/man/scale_x_comma.Rd |only funModeling-1.8/funModeling/man/theme_lares.Rd |only funModeling-1.8/funModeling/man/theme_lares2.Rd |only funModeling-1.9/funModeling/DESCRIPTION | 12 ++--- funModeling-1.9/funModeling/MD5 | 41 ++++--------------- funModeling-1.9/funModeling/NAMESPACE | 36 +--------------- funModeling-1.9/funModeling/R/attach.R | 3 - funModeling-1.9/funModeling/R/data.R | 8 +++ funModeling-1.9/funModeling/R/data_integrity.R |only funModeling-1.9/funModeling/R/funModeling.R | 10 +--- funModeling-1.9/funModeling/data/metadata_models.rda |only funModeling-1.9/funModeling/man/data_integrity.Rd |only funModeling-1.9/funModeling/man/metadata_models.Rd |only funModeling-1.9/funModeling/man/status.Rd |only 37 files changed, 32 insertions(+), 78 deletions(-)
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsaf' R-package provides a collection of R-operators for the analysis and
manipulation of CM SAF NetCDF formatted data. The 'cmsaf' R-package is tested
for CM SAF NetCDF data. Other CF conform NetCDF data should be applicable, but there
is no guarantee for an error-free application.
The 'cmsaf' R-package includes a 'shiny' based interface for an easy application of
the 'cmsaf' package operators and the preparation and visualization of CM SAF NetCDF
data. CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.9.5 dated 2019-02-06 and 2.0.1 dated 2019-08-26
cmsaf-1.9.5/cmsaf/R/checkfile.R |only cmsaf-1.9.5/cmsaf/R/remapbil.R |only cmsaf-1.9.5/cmsaf/man/checkfile.Rd |only cmsaf-1.9.5/cmsaf/man/cmsaf-package.Rd |only cmsaf-1.9.5/cmsaf/man/remapbil.Rd |only cmsaf-2.0.1/cmsaf/DESCRIPTION | 56 - cmsaf-2.0.1/cmsaf/MD5 | 524 ++++++++--- cmsaf-2.0.1/cmsaf/NAMESPACE | 99 +- cmsaf-2.0.1/cmsaf/NEWS.md |only cmsaf-2.0.1/cmsaf/R/add_grid_info.R |only cmsaf-2.0.1/cmsaf/R/arith_wrapper.R |only cmsaf-2.0.1/cmsaf/R/arithc_wrapper.R |only cmsaf-2.0.1/cmsaf/R/box_mergetime.R | 593 ++++++------- cmsaf-2.0.1/cmsaf/R/calc_field.R |only cmsaf-2.0.1/cmsaf/R/calc_timx_result.R |only cmsaf-2.0.1/cmsaf/R/calc_trend.R |only cmsaf-2.0.1/cmsaf/R/change_att.R | 158 ++- cmsaf-2.0.1/cmsaf/R/check_constant.R |only cmsaf-2.0.1/cmsaf/R/check_dims.R |only cmsaf-2.0.1/cmsaf/R/check_format.R |only cmsaf-2.0.1/cmsaf/R/check_infile.R |only cmsaf-2.0.1/cmsaf/R/check_infiles.R |only cmsaf-2.0.1/cmsaf/R/check_nc_version.R |only cmsaf-2.0.1/cmsaf/R/check_outfile.R |only cmsaf-2.0.1/cmsaf/R/check_overwrite.R |only cmsaf-2.0.1/cmsaf/R/check_variable.R |only cmsaf-2.0.1/cmsaf/R/cmsaf.R |only cmsaf-2.0.1/cmsaf/R/cmsaf.add.R | 420 +-------- cmsaf-2.0.1/cmsaf/R/cmsaf.addc.R | 334 +------ cmsaf-2.0.1/cmsaf/R/cmsaf.cat.R | 511 ++++------- cmsaf-2.0.1/cmsaf/R/cmsaf.div.R | 455 +--------- cmsaf-2.0.1/cmsaf/R/cmsaf.divc.R | 364 +------- cmsaf-2.0.1/cmsaf/R/cmsaf.mul.R | 445 +-------- cmsaf-2.0.1/cmsaf/R/cmsaf.mulc.R | 362 +------- cmsaf-2.0.1/cmsaf/R/cmsaf.sub.R | 474 +--------- cmsaf-2.0.1/cmsaf/R/cmsaf.subc.R | 362 +------- cmsaf-2.0.1/cmsaf/R/constants.R |only cmsaf-2.0.1/cmsaf/R/correct_filename.R |only cmsaf-2.0.1/cmsaf/R/dayrange.R | 453 +++------- cmsaf-2.0.1/cmsaf/R/define_dims.R |only cmsaf-2.0.1/cmsaf/R/define_vars.R |only cmsaf-2.0.1/cmsaf/R/define_vars_trend.R |only cmsaf-2.0.1/cmsaf/R/divdpm.R | 353 +------ cmsaf-2.0.1/cmsaf/R/extract.level.R | 480 ++++------ cmsaf-2.0.1/cmsaf/R/extract.period.R | 433 +++------ cmsaf-2.0.1/cmsaf/R/fldmax.R | 329 +------ cmsaf-2.0.1/cmsaf/R/fldmean.R | 319 +------ cmsaf-2.0.1/cmsaf/R/fldmin.R | 329 +------ cmsaf-2.0.1/cmsaf/R/fldx_wrapper.R |only cmsaf-2.0.1/cmsaf/R/get_climatology.R |only cmsaf-2.0.1/cmsaf/R/get_date_time.R |only cmsaf-2.0.1/cmsaf/R/get_dimensions.R |only cmsaf-2.0.1/cmsaf/R/get_grid.R |only cmsaf-2.0.1/cmsaf/R/get_nc_version.R |only cmsaf-2.0.1/cmsaf/R/get_processing_time_string.R |only cmsaf-2.0.1/cmsaf/R/get_time.R | 146 +-- cmsaf-2.0.1/cmsaf/R/get_time_bnds_1.R |only cmsaf-2.0.1/cmsaf/R/get_time_bnds_from_file.R |only cmsaf-2.0.1/cmsaf/R/get_time_bnds_mul.R |only cmsaf-2.0.1/cmsaf/R/get_time_bounds.R |only cmsaf-2.0.1/cmsaf/R/get_time_bounds_doy.R |only cmsaf-2.0.1/cmsaf/R/get_time_bounds_year.R |only cmsaf-2.0.1/cmsaf/R/get_time_info.R |only cmsaf-2.0.1/cmsaf/R/get_var_atts.R |only cmsaf-2.0.1/cmsaf/R/get_var_from_vars.R |only cmsaf-2.0.1/cmsaf/R/get_var_prec.R |only cmsaf-2.0.1/cmsaf/R/is_leap_year.R |only cmsaf-2.0.1/cmsaf/R/levbox_mergetime.R | 450 ++-------- cmsaf-2.0.1/cmsaf/R/mon.anomaly.R | 466 +++------- cmsaf-2.0.1/cmsaf/R/monmax.R | 337 +------ cmsaf-2.0.1/cmsaf/R/monmean.R | 327 +------ cmsaf-2.0.1/cmsaf/R/monmin.R | 337 +------ cmsaf-2.0.1/cmsaf/R/monsd.R | 328 +------ cmsaf-2.0.1/cmsaf/R/monsum.R | 327 +------ cmsaf-2.0.1/cmsaf/R/monx_wrapper.R |only cmsaf-2.0.1/cmsaf/R/muldpm.R | 351 +------ cmsaf-2.0.1/cmsaf/R/multimonmean.R | 426 +++------ cmsaf-2.0.1/cmsaf/R/multimonsum.R | 447 +++------- cmsaf-2.0.1/cmsaf/R/ncinfo.R | 174 ++- cmsaf-2.0.1/cmsaf/R/read_file.R |only cmsaf-2.0.1/cmsaf/R/read_gridfile.R |only cmsaf-2.0.1/cmsaf/R/read_ncvar.R | 224 +---- cmsaf-2.0.1/cmsaf/R/redefine_grid_vars.R |only cmsaf-2.0.1/cmsaf/R/remap.R |only cmsaf-2.0.1/cmsaf/R/run_toolbox.R |only cmsaf-2.0.1/cmsaf/R/seas.anomaly.R | 545 ++++-------- cmsaf-2.0.1/cmsaf/R/seasmean.R | 326 +------ cmsaf-2.0.1/cmsaf/R/seassum.R | 326 +------ cmsaf-2.0.1/cmsaf/R/seasx_wrapper.R |only cmsaf-2.0.1/cmsaf/R/sellonlatbox.R | 488 ++++------ cmsaf-2.0.1/cmsaf/R/selmon.R | 438 +++------ cmsaf-2.0.1/cmsaf/R/selperiod.R | 432 +++------ cmsaf-2.0.1/cmsaf/R/selpoint.R | 567 +++++------- cmsaf-2.0.1/cmsaf/R/selpoint.multi.R | 1026 ++++++++--------------- cmsaf-2.0.1/cmsaf/R/seltime.R | 436 +++------ cmsaf-2.0.1/cmsaf/R/selyear.R | 440 +++------ cmsaf-2.0.1/cmsaf/R/set_seasons.R |only cmsaf-2.0.1/cmsaf/R/simplelm.R |only cmsaf-2.0.1/cmsaf/R/simplelm2.R |only cmsaf-2.0.1/cmsaf/R/timmax.R | 283 +----- cmsaf-2.0.1/cmsaf/R/timmean.R | 304 +----- cmsaf-2.0.1/cmsaf/R/timmin.R | 283 +----- cmsaf-2.0.1/cmsaf/R/timpctl.R | 284 +----- cmsaf-2.0.1/cmsaf/R/timsd.R | 274 +----- cmsaf-2.0.1/cmsaf/R/timsum.R | 302 +----- cmsaf-2.0.1/cmsaf/R/timx_wrapper.R |only cmsaf-2.0.1/cmsaf/R/trend.R | 512 +++-------- cmsaf-2.0.1/cmsaf/R/wfldmean.R | 325 +------ cmsaf-2.0.1/cmsaf/R/write_output_file.R |only cmsaf-2.0.1/cmsaf/R/write_output_file_trend.R |only cmsaf-2.0.1/cmsaf/R/xdpm_wrapper.R |only cmsaf-2.0.1/cmsaf/R/ydaymean.R | 398 +++----- cmsaf-2.0.1/cmsaf/R/year.anomaly.R | 479 +++------- cmsaf-2.0.1/cmsaf/R/yearmean.R | 394 +++----- cmsaf-2.0.1/cmsaf/R/yearsum.R | 395 +++----- cmsaf-2.0.1/cmsaf/R/ymonmax.R | 317 +------ cmsaf-2.0.1/cmsaf/R/ymonmean.R | 307 +----- cmsaf-2.0.1/cmsaf/R/ymonmin.R | 317 +------ cmsaf-2.0.1/cmsaf/R/ymonsd.R | 307 +----- cmsaf-2.0.1/cmsaf/R/ymonsum.R | 306 +----- cmsaf-2.0.1/cmsaf/R/ymonx_wrapper.R |only cmsaf-2.0.1/cmsaf/R/yseasmax.R | 337 +------ cmsaf-2.0.1/cmsaf/R/yseasmean.R | 332 +------ cmsaf-2.0.1/cmsaf/R/yseasmin.R | 339 +------ cmsaf-2.0.1/cmsaf/R/yseassd.R | 329 +------ cmsaf-2.0.1/cmsaf/R/yseasx_wrapper.R |only cmsaf-2.0.1/cmsaf/inst |only cmsaf-2.0.1/cmsaf/man/add_grid_info.Rd |only cmsaf-2.0.1/cmsaf/man/box_mergetime.Rd | 166 +-- cmsaf-2.0.1/cmsaf/man/change_att.Rd | 129 +- cmsaf-2.0.1/cmsaf/man/cmsaf.Rd |only cmsaf-2.0.1/cmsaf/man/cmsaf.add.Rd | 143 +-- cmsaf-2.0.1/cmsaf/man/cmsaf.addc.Rd | 109 +- cmsaf-2.0.1/cmsaf/man/cmsaf.cat.Rd | 125 +- cmsaf-2.0.1/cmsaf/man/cmsaf.div.Rd | 143 +-- cmsaf-2.0.1/cmsaf/man/cmsaf.divc.Rd | 114 +- cmsaf-2.0.1/cmsaf/man/cmsaf.mul.Rd | 139 +-- cmsaf-2.0.1/cmsaf/man/cmsaf.mulc.Rd | 116 +- cmsaf-2.0.1/cmsaf/man/cmsaf.sub.Rd | 140 +-- cmsaf-2.0.1/cmsaf/man/cmsaf.subc.Rd | 115 +- cmsaf-2.0.1/cmsaf/man/dayrange.Rd | 106 +- cmsaf-2.0.1/cmsaf/man/divdpm.Rd | 111 +- cmsaf-2.0.1/cmsaf/man/extract.level.Rd | 132 +- cmsaf-2.0.1/cmsaf/man/extract.period.Rd | 113 +- cmsaf-2.0.1/cmsaf/man/fldmax.Rd | 100 +- cmsaf-2.0.1/cmsaf/man/fldmean.Rd | 100 +- cmsaf-2.0.1/cmsaf/man/fldmin.Rd | 100 +- cmsaf-2.0.1/cmsaf/man/get_time.Rd | 35 cmsaf-2.0.1/cmsaf/man/levbox_mergetime.Rd | 180 ++-- cmsaf-2.0.1/cmsaf/man/mon.anomaly.Rd | 114 +- cmsaf-2.0.1/cmsaf/man/monmax.Rd | 107 +- cmsaf-2.0.1/cmsaf/man/monmean.Rd | 106 +- cmsaf-2.0.1/cmsaf/man/monmin.Rd | 107 +- cmsaf-2.0.1/cmsaf/man/monsd.Rd | 107 +- cmsaf-2.0.1/cmsaf/man/monsum.Rd | 110 +- cmsaf-2.0.1/cmsaf/man/muldpm.Rd | 109 +- cmsaf-2.0.1/cmsaf/man/multimonmean.Rd | 122 +- cmsaf-2.0.1/cmsaf/man/multimonsum.Rd | 121 +- cmsaf-2.0.1/cmsaf/man/ncinfo.Rd | 84 - cmsaf-2.0.1/cmsaf/man/read_ncvar.Rd | 84 - cmsaf-2.0.1/cmsaf/man/remap.Rd |only cmsaf-2.0.1/cmsaf/man/run_toolbox.Rd |only cmsaf-2.0.1/cmsaf/man/seas.anomaly.Rd | 105 +- cmsaf-2.0.1/cmsaf/man/seasmean.Rd | 106 +- cmsaf-2.0.1/cmsaf/man/seassum.Rd | 106 +- cmsaf-2.0.1/cmsaf/man/sellonlatbox.Rd | 126 +- cmsaf-2.0.1/cmsaf/man/selmon.Rd | 109 +- cmsaf-2.0.1/cmsaf/man/selperiod.Rd | 111 +- cmsaf-2.0.1/cmsaf/man/selpoint.Rd | 130 +- cmsaf-2.0.1/cmsaf/man/selpoint.multi.Rd | 172 +-- cmsaf-2.0.1/cmsaf/man/seltime.Rd | 112 +- cmsaf-2.0.1/cmsaf/man/selyear.Rd | 104 +- cmsaf-2.0.1/cmsaf/man/timmax.Rd | 104 +- cmsaf-2.0.1/cmsaf/man/timmean.Rd | 104 +- cmsaf-2.0.1/cmsaf/man/timmin.Rd | 104 +- cmsaf-2.0.1/cmsaf/man/timpctl.Rd | 115 +- cmsaf-2.0.1/cmsaf/man/timsd.Rd | 106 +- cmsaf-2.0.1/cmsaf/man/timsum.Rd | 108 +- cmsaf-2.0.1/cmsaf/man/trend.Rd | 137 +-- cmsaf-2.0.1/cmsaf/man/wfldmean.Rd | 101 +- cmsaf-2.0.1/cmsaf/man/ydaymean.Rd | 104 +- cmsaf-2.0.1/cmsaf/man/year.anomaly.Rd | 106 +- cmsaf-2.0.1/cmsaf/man/yearmean.Rd | 100 +- cmsaf-2.0.1/cmsaf/man/yearsum.Rd | 102 +- cmsaf-2.0.1/cmsaf/man/ymonmax.Rd | 107 +- cmsaf-2.0.1/cmsaf/man/ymonmean.Rd | 108 +- cmsaf-2.0.1/cmsaf/man/ymonmin.Rd | 107 +- cmsaf-2.0.1/cmsaf/man/ymonsd.Rd | 111 +- cmsaf-2.0.1/cmsaf/man/ymonsum.Rd | 107 +- cmsaf-2.0.1/cmsaf/man/yseasmax.Rd | 104 +- cmsaf-2.0.1/cmsaf/man/yseasmean.Rd | 111 +- cmsaf-2.0.1/cmsaf/man/yseasmin.Rd | 105 +- cmsaf-2.0.1/cmsaf/man/yseassd.Rd | 105 +- cmsaf-2.0.1/cmsaf/tests |only 194 files changed, 10804 insertions(+), 20561 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3'
with interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Quay Au [aut] (<https://orcid.org/0000-0002-5252-8902>),
Stefan Coors [aut] (<https://orcid.org/0000-0002-7465-2146>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3learners versions 0.1.1 dated 2019-08-05 and 0.1.2 dated 2019-08-26
mlr3learners-0.1.1/mlr3learners/inst |only mlr3learners-0.1.2/mlr3learners/DESCRIPTION | 20 - mlr3learners-0.1.2/mlr3learners/MD5 | 111 ++++------ mlr3learners-0.1.2/mlr3learners/NEWS.md | 4 mlr3learners-0.1.2/mlr3learners/R/LearnerClassifGlmnet.R | 17 + mlr3learners-0.1.2/mlr3learners/R/LearnerClassifKKNN.R | 15 + mlr3learners-0.1.2/mlr3learners/R/LearnerClassifLDA.R | 19 + mlr3learners-0.1.2/mlr3learners/R/LearnerClassifLogReg.R | 15 + mlr3learners-0.1.2/mlr3learners/R/LearnerClassifNaiveBayes.R | 15 + mlr3learners-0.1.2/mlr3learners/R/LearnerClassifQDA.R | 17 + mlr3learners-0.1.2/mlr3learners/R/LearnerClassifRanger.R | 22 + mlr3learners-0.1.2/mlr3learners/R/LearnerClassifSVM.R | 13 - mlr3learners-0.1.2/mlr3learners/R/LearnerClassifXgboost.R | 19 + mlr3learners-0.1.2/mlr3learners/R/LearnerRegrGlmnet.R | 18 + mlr3learners-0.1.2/mlr3learners/R/LearnerRegrKKNN.R | 15 + mlr3learners-0.1.2/mlr3learners/R/LearnerRegrKM.R | 19 + mlr3learners-0.1.2/mlr3learners/R/LearnerRegrLM.R | 15 + mlr3learners-0.1.2/mlr3learners/R/LearnerRegrRanger.R | 22 + mlr3learners-0.1.2/mlr3learners/R/LearnerRegrSVM.R | 13 - mlr3learners-0.1.2/mlr3learners/R/LearnerRegrXgboost.R | 18 + mlr3learners-0.1.2/mlr3learners/README.md | 7 mlr3learners-0.1.2/mlr3learners/build/partial.rdb |binary mlr3learners-0.1.2/mlr3learners/man/LearnerClassifGlmnet.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerClassifKKNN.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerClassifLDA.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerClassifLogReg.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerClassifNaiveBayes.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerClassifQDA.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerClassifRanger.Rd | 20 + mlr3learners-0.1.2/mlr3learners/man/LearnerClassifSVM.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerClassifXgboost.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerRegrGlmnet.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerRegrKKNN.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerRegrKM.Rd | 17 + mlr3learners-0.1.2/mlr3learners/man/LearnerRegrLM.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerRegrRanger.Rd | 20 + mlr3learners-0.1.2/mlr3learners/man/LearnerRegrSVM.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/LearnerRegrXgboost.Rd | 15 - mlr3learners-0.1.2/mlr3learners/man/mlr3learners-package.Rd | 10 mlr3learners-0.1.2/mlr3learners/tests/testthat.R | 9 mlr3learners-0.1.2/mlr3learners/tests/testthat/helper.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_classif_glmnet.R | 4 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_classif_kknn.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_classif_lda.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_classif_log_reg.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_classif_naive_bayes.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_classif_qda.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_classif_ranger.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_classif_svm.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_classif_xgboost.R | 6 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_regr_glmnet.R | 4 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_regr_kknn.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_regr_km.R | 17 - mlr3learners-0.1.2/mlr3learners/tests/testthat/test_regr_lm.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_regr_ranger.R | 3 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_regr_svm.R | 2 mlr3learners-0.1.2/mlr3learners/tests/testthat/test_regr_xgboost.R | 3 57 files changed, 504 insertions(+), 240 deletions(-)
Title: Data Base Backend for 'mlr3'
Description: Extends the 'mlr3' package with a backend to
transparently work with data bases. Internally relies on the
abstraction of package 'dbplyr' to interact with one of the many
supported data base management systems (DBMS).
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3db versions 0.1.1 dated 2019-08-01 and 0.1.2 dated 2019-08-26
mlr3db-0.1.1/mlr3db/R/as_sqlite.R |only mlr3db-0.1.1/mlr3db/inst |only mlr3db-0.1.1/mlr3db/man/as_sqlite.Rd |only mlr3db-0.1.1/mlr3db/tests/testthat/test_as_sqlite.R |only mlr3db-0.1.2/mlr3db/DESCRIPTION | 10 ++-- mlr3db-0.1.2/mlr3db/MD5 | 27 +++++------- mlr3db-0.1.2/mlr3db/NAMESPACE | 8 +-- mlr3db-0.1.2/mlr3db/NEWS.md | 8 +++ mlr3db-0.1.2/mlr3db/R/DataBackendDplyr.R | 12 ++++- mlr3db-0.1.2/mlr3db/R/as_sqlite_backend.R |only mlr3db-0.1.2/mlr3db/README.md | 3 + mlr3db-0.1.2/mlr3db/man/DataBackendDplyr.Rd | 20 +++++--- mlr3db-0.1.2/mlr3db/man/as_sqlite_backend.Rd |only mlr3db-0.1.2/mlr3db/man/mlr3db-package.Rd | 1 mlr3db-0.1.2/mlr3db/tests/testthat.R | 9 ++-- mlr3db-0.1.2/mlr3db/tests/testthat/test_as_sqlite_backend.R |only mlr3db-0.1.2/mlr3db/tests/testthat/test_basic_ops.R | 4 - mlr3db-0.1.2/mlr3db/tests/testthat/test_train_predict.R | 2 18 files changed, 62 insertions(+), 42 deletions(-)
Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>
Diff between gprofiler2 versions 0.1.5 dated 2019-07-04 and 0.1.6 dated 2019-08-26
DESCRIPTION | 6 +- MD5 | 7 +-- NAMESPACE | 1 R/gprofiler2.R | 102 +++++++++++++++++++++++++++++++++++++++++++++++++ man/upload_GMT_file.Rd |only 5 files changed, 110 insertions(+), 6 deletions(-)
Title: A Graphical User Interface for Dexter
Description: Classical Test and Item analysis,
Item Response analysis and data management for educational and psychological tests.
Author: jesse koops [aut, cre],
Eva de Schipper [aut],
Ivailo Partchev [aut, ctb],
Gunter Maris [aut, ctb],
Timo Bechger [aut, ctb],
Gareth Watts [aut, cph] (author of jquery.sparkline),
Hakim El Hattab [aut, cph] (author of zoom.js)
Maintainer: jesse koops <jesse.koops@cito.nl>
Diff between dextergui versions 0.1.6 dated 2019-03-06 and 0.2.0 dated 2019-08-26
dextergui-0.1.6/dextergui/R/color.R |only dextergui-0.2.0/dextergui/DESCRIPTION | 23 +- dextergui-0.2.0/dextergui/MD5 | 39 +-- dextergui-0.2.0/dextergui/NAMESPACE | 7 dextergui-0.2.0/dextergui/NEWS.md | 6 dextergui-0.2.0/dextergui/R/example.R | 56 +++-- dextergui-0.2.0/dextergui/R/gui.R | 18 - dextergui-0.2.0/dextergui/R/misc.R | 29 ++ dextergui-0.2.0/dextergui/R/serve.R | 215 +++++++++++--------- dextergui-0.2.0/dextergui/R/spark.R | 1 dextergui-0.2.0/dextergui/R/tags.R | 32 +- dextergui-0.2.0/dextergui/build/vignette.rds |binary dextergui-0.2.0/dextergui/inst/doc/dextergui.Rmd | 2 dextergui-0.2.0/dextergui/inst/doc/dextergui.html | 63 +++-- dextergui-0.2.0/dextergui/inst/extdata/manual.html | 85 ++----- dextergui-0.2.0/dextergui/inst/www/dt_extensions.js | 2 dextergui-0.2.0/dextergui/inst/www/img-select.js | 3 dextergui-0.2.0/dextergui/inst/www/pr_helper.js | 2 dextergui-0.2.0/dextergui/inst/www/shinydexter.css | 18 + dextergui-0.2.0/dextergui/man/dextergui.Rd | 8 dextergui-0.2.0/dextergui/vignettes/dextergui.Rmd | 2 21 files changed, 343 insertions(+), 268 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-05 1.1.5
Title: A Plotting Toolbox for 2D Oceanographic Data
Description: Plotting toolbox for 2D oceanographic data (satellite data, sst, chla, ocean fronts & bathymetry). Recognized classes and formats include ncdf4, Raster, '.nc' and '.gz' files.
Author: Robert K. Bauer
Maintainer: Robert K. Bauer <r.bauer@profish-technology.de>
Diff between oceanmap versions 0.1.0 dated 2018-05-26 and 0.1.0.1 dated 2019-08-26
oceanmap-0.1.0.1/oceanmap/DESCRIPTION | 6 ++--- oceanmap-0.1.0.1/oceanmap/MD5 | 15 ++++++-------- oceanmap-0.1.0.1/oceanmap/R/sysdata.rda |binary oceanmap-0.1.0.1/oceanmap/data/cmap.rda |binary oceanmap-0.1.0.1/oceanmap/data/cmap_topo.rda |binary oceanmap-0.1.0.1/oceanmap/data/parameter_definitions.rda |binary oceanmap-0.1.0.1/oceanmap/data/region_definitions.bkp.rda |binary oceanmap-0.1.0.1/oceanmap/data/region_definitions.rda |binary oceanmap-0.1.0/oceanmap/data/datalist |only 9 files changed, 10 insertions(+), 11 deletions(-)
Title: Advanced Graphics and Image-Processing in R
Description: Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg, tiff,
pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc).
All operations are vectorized via the Magick++ STL meaning they operate either
on a single frame or a series of frames for working with layers, collages,
or animation. In RStudio images are automatically previewed when printed to
the console, resulting in an interactive editing environment. The latest
version of the package includes a native graphics device for creating
in-memory graphics or drawing onto images using pixel coordinates.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between magick versions 2.1 dated 2019-07-25 and 2.2 dated 2019-08-26
DESCRIPTION | 12 +++---- MD5 | 58 ++++++++++++++++++------------------ NAMESPACE | 4 ++ NEWS | 10 ++++++ R/RcppExports.R | 16 +++++++-- R/autoview.R | 2 - R/base.R | 51 ++++++++++++++++++++++--------- R/color.R | 14 ++++++++ R/composite.R | 9 +++-- R/edit.R | 12 +++++++ R/init.R | 8 ++++ R/options.R | 6 +++ R/paint.R | 12 +++++-- R/video.R | 8 +++- inst/WORDLIST | 3 + inst/doc/intro.Rmd | 2 - inst/doc/intro.html | 77 +++++++++++++++++++++++------------------------- man/autoviewer.Rd | 2 - man/color.Rd | 6 +++ man/composite.Rd | 8 +++- man/editing.Rd | 8 ++++ man/options.Rd | 3 + man/painting.Rd | 7 +++- man/video.Rd | 6 ++- src/RcppExports.cpp | 46 +++++++++++++++++++++++----- src/composite.cpp | 38 +++++++++++++++-------- src/edit.cpp | 27 ++++++++++++++++ src/options.cpp | 3 + src/transformations.cpp | 17 +++++++++- vignettes/intro.Rmd | 2 - 30 files changed, 342 insertions(+), 135 deletions(-)
Title: Kinetic Analysis and Visualization of DCE-MRI Data
Description: Provides kinetic analysis of Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCE-MRI) data. Includes tools for fitting the Tofts (described in Tofts, Kermode (1991) <DOI:10.1002/mrm.1910170208>) and extended Tofts (described in Tofts et al. (1999) <https://www.ncbi.nlm.nih.gov/pubmed/10508281>) mathematical models to dynamic (signal vs. time) data associated with each voxel of an image and a Graphical User Inferface (GUI) for visualization and exploration of fitted model parameters over the volume of the image.
Author: Gregory Z. Ferl [aut, cre],
Georges Hankov [aut]
Maintainer: Gregory Z. Ferl <ferl.gregory@gene.com>
Diff between KATforDCEMRI versions 1.0 dated 2019-03-05 and 1.0.1 dated 2019-08-26
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/partial.rdb |binary data/datalist | 1 - data/dcemri.data.RData |binary 5 files changed, 7 insertions(+), 8 deletions(-)
Title: Endogenous Perturbation Analysis of Cancer
Description: Estimates sparse matrices A or G using fast lasso regression from mRNA transcript levels Y and CNA profiles U. Two models are provided, EPoC A where
AY + U + R = 0
and EPoC G where
Y = GU + E,
the matrices R and E are so far treated as noise. For
details see the manual page of 'lassoshooting' and the
article Rebecka Jörnsten, Tobias Abenius, Teresia Kling,
Linnéa Schmidt, Erik Johansson, Torbjörn E M Nordling,
Bodil Nordlander, Chris Sander, Peter Gennemark,
Keiko Funa, Björn Nilsson, Linda Lindahl, Sven Nelander
(2011) <doi:10.1038/msb.2011.17>.
Author: Rebecka Jornsten, Tobias Abenius, Sven Nelander
Maintainer: Tobias Abenius <Tobias.Abenius@Chalmers.se>
Diff between epoc versions 0.2.6-1 dated 2018-11-29 and 0.2.6-1.1 dated 2019-08-26
epoc-0.2.6-1.1/epoc/DESCRIPTION | 6 +++--- epoc-0.2.6-1.1/epoc/MD5 | 7 +++---- epoc-0.2.6-1.1/epoc/data/synth.rda |binary epoc-0.2.6-1.1/epoc/man/synth.Rd | 2 +- epoc-0.2.6-1/epoc/data/datalist |only 5 files changed, 7 insertions(+), 8 deletions(-)
Title: Measuring Disparity
Description: A modular package for measuring disparity from multidimensional matrices. Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics (Guillerme (2018) <doi:10.1111/2041-210X.13022>). The package also provides functions for looking at disparity in a serial way (e.g. disparity through time - Guillerme and Cooper (2018) <doi:10.1111/pala.12364>) or per groups as well as visualising the results. Finally, this package provides several basic statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph],
Mark N Puttick [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>
Diff between dispRity versions 1.2.3 dated 2019-03-13 and 1.3 dated 2019-08-26
dispRity-1.2.3/dispRity/inst/vignettes/model_test_vignette.html |only dispRity-1.3/dispRity/DESCRIPTION | 12 dispRity-1.3/dispRity/MD5 | 137 +- dispRity-1.3/dispRity/NAMESPACE | 11 dispRity-1.3/dispRity/NEWS.md | 36 dispRity-1.3/dispRity/R/Claddis.ordination.R | 57 + dispRity-1.3/dispRity/R/Claddis.ordination_fun.R |only dispRity-1.3/dispRity/R/adonis.dispRity.R | 2 dispRity-1.3/dispRity/R/bhatt.coeff.R | 2 dispRity-1.3/dispRity/R/boot.matrix.R | 80 + dispRity-1.3/dispRity/R/boot.matrix_fun.R | 59 - dispRity-1.3/dispRity/R/char.diff.R | 2 dispRity-1.3/dispRity/R/check.morpho.R | 6 dispRity-1.3/dispRity/R/chrono.subsets.R | 226 +++- dispRity-1.3/dispRity/R/chrono.subsets_fun.R | 126 ++ dispRity-1.3/dispRity/R/clean.data.R | 25 dispRity-1.3/dispRity/R/crown.stem.R | 2 dispRity-1.3/dispRity/R/dispRity-package.R | 32 dispRity-1.3/dispRity/R/dispRity.R | 28 dispRity-1.3/dispRity/R/dispRity.metric.R | 459 ++++++---- dispRity-1.3/dispRity/R/dispRity.utilities.R | 21 dispRity-1.3/dispRity/R/dispRity_fun.R | 112 -- dispRity-1.3/dispRity/R/dtt.dispRity.R | 49 - dispRity-1.3/dispRity/R/get.bin.ages.R | 4 dispRity-1.3/dispRity/R/make.metric.R | 2 dispRity-1.3/dispRity/R/model.test.R | 30 dispRity-1.3/dispRity/R/model.test.sim.R | 61 - dispRity-1.3/dispRity/R/model.test.wrapper.R | 2 dispRity-1.3/dispRity/R/model.test_fun.R | 144 +-- dispRity-1.3/dispRity/R/null.test.R | 2 dispRity-1.3/dispRity/R/pair.plot.R | 2 dispRity-1.3/dispRity/R/plot.dispRity.R | 56 - dispRity-1.3/dispRity/R/plot.dispRity_fun.R | 84 + dispRity-1.3/dispRity/R/print.dispRity.R | 2 dispRity-1.3/dispRity/R/reduce.matrix.R |only dispRity-1.3/dispRity/R/remove.zero.brlen.R |only dispRity-1.3/dispRity/R/sanitizing.R | 29 dispRity-1.3/dispRity/R/sequential.test.R | 2 dispRity-1.3/dispRity/R/sim.morpho.R | 2 dispRity-1.3/dispRity/R/slice.tree.R | 84 + dispRity-1.3/dispRity/R/slice.tree_fun.R | 121 ++ dispRity-1.3/dispRity/R/slide.nodes.R |only dispRity-1.3/dispRity/R/slide.nodes_fun.R |only dispRity-1.3/dispRity/R/space.maker.R | 35 dispRity-1.3/dispRity/R/summary.dispRity.R | 15 dispRity-1.3/dispRity/R/summary.dispRity_fun.R | 2 dispRity-1.3/dispRity/R/test.dispRity.R | 8 dispRity-1.3/dispRity/R/test.dispRity_fun.R | 55 - dispRity-1.3/dispRity/R/zzz.R | 2 dispRity-1.3/dispRity/data/disparity.rda |binary dispRity-1.3/dispRity/inst/vignettes/generating_inapplicable_characters.Rmd |only dispRity-1.3/dispRity/man/Claddis.ordination.Rd | 35 dispRity-1.3/dispRity/man/adonis.dispRity.Rd | 4 dispRity-1.3/dispRity/man/boot.matrix.Rd | 8 dispRity-1.3/dispRity/man/chrono.subsets.Rd | 2 dispRity-1.3/dispRity/man/dispRity-package.Rd | 6 dispRity-1.3/dispRity/man/dispRity.metric.Rd | 198 ++-- dispRity-1.3/dispRity/man/dispRity.through.time.Rd | 3 dispRity-1.3/dispRity/man/get.ancestors.Rd |only dispRity-1.3/dispRity/man/model.test.Rd | 3 dispRity-1.3/dispRity/man/model.test.sim.Rd | 7 dispRity-1.3/dispRity/man/model.test.wrapper.Rd | 9 dispRity-1.3/dispRity/man/nodes.coordinates.Rd | 2 dispRity-1.3/dispRity/man/pair.plot.Rd | 4 dispRity-1.3/dispRity/man/plot.char.diff.Rd | 4 dispRity-1.3/dispRity/man/plot.dispRity.Rd | 16 dispRity-1.3/dispRity/man/reduce.matrix.Rd |only dispRity-1.3/dispRity/man/remove.zero.brlen.Rd |only dispRity-1.3/dispRity/man/rescale.dispRity.Rd | 9 dispRity-1.3/dispRity/man/sim.morpho.Rd | 5 dispRity-1.3/dispRity/man/slice.tree.Rd | 2 dispRity-1.3/dispRity/man/slide.nodes.Rd |only dispRity-1.3/dispRity/man/space.maker.Rd | 2 dispRity-1.3/dispRity/man/summary.dispRity.Rd | 5 dispRity-1.3/dispRity/man/test.dispRity.Rd | 4 75 files changed, 1640 insertions(+), 916 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Description: Produces an economic evaluation of a Bayesian model in the form of MCMC simulations. Given suitable variables of cost and effectiveness / utility for two or more interventions, This package computes the most cost-effective alternative and produces graphical summaries and probabilistic sensitivity analysis.
Author: Gianluca Baio, Andrea Berardi, Anna Heath
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>
Diff between BCEA versions 2.3-1 dated 2019-08-05 and 2.3-1.1 dated 2019-08-26
BCEA-2.3-1.1/BCEA/DESCRIPTION | 6 +++--- BCEA-2.3-1.1/BCEA/MD5 | 7 +++---- BCEA-2.3-1.1/BCEA/data/Smoking.RData |binary BCEA-2.3-1.1/BCEA/data/Vaccine.RData |binary BCEA-2.3-1/BCEA/data/datalist |only 5 files changed, 6 insertions(+), 7 deletions(-)
Title: Chronological Objects which can Handle Dates and Times
Description: Provides chronological objects which can handle dates and times.
Author: David James [aut] (S original),
Kurt Hornik [aut, trl, cre] (<https://orcid.org/0000-0003-4198-9911>),
Gabor Grothendieck [ctb],
R Core Team [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between chron versions 2.3-53 dated 2018-09-09 and 2.3-54 dated 2019-08-26
ChangeLog | 15 +++++++++++++++ DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 4 +++- R/dates.R | 5 +++++ R/times.R | 5 +++++ man/dates.Rd | 2 ++ 7 files changed, 39 insertions(+), 10 deletions(-)
Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions
and Diversity
Description: Analysis of plant pathogen pathotype survey data. Functions
provided calculate distribution of susceptibilities, distribution of
complexities with statistics, pathotype frequency distribution, as well as
diversity indices for pathotypes. This package is meant to be a direct
replacement for Herrmann, Löwer, Schachtel's (1999)
<doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS',
previously used for pathotype analysis.
Author: Austin G. McCoy [aut, ccp] (<https://orcid.org/0000-0003-2483-4184>),
Zachary Noel [aut, ccp] (<https://orcid.org/0000-0001-6375-8300>),
Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Martin Chilvers [aut] (<https://orcid.org/0000-0001-8832-1666>),
Zhian N. Kamvar [ctb, rev] (<https://orcid.org/0000-0003-1458-7108>),
Michigan Soybean Promotion Committee [fnd],
Project GREEEN [fnd],
North Central Soybean Research Program [fnd],
GRDC Project DAQ00186 [fnd]
Maintainer: Adam H. Sparks <adam.sparks@usq.edu.au>
Diff between hagis versions 2.0.0 dated 2019-06-24 and 3.0.0 dated 2019-08-26
hagis-2.0.0/hagis/inst/extdata |only hagis-2.0.0/hagis/tests/figs/autoplot-hagis-complexities |only hagis-2.0.0/hagis/tests/figs/autoplot-hagis-rps-summary |only hagis-2.0.0/hagis/tests/testthat/test-plot_hagis_complexities.R |only hagis-2.0.0/hagis/tests/testthat/test-plot_rps_summary.R |only hagis-3.0.0/hagis/DESCRIPTION | 25 hagis-3.0.0/hagis/MD5 | 86 hagis-3.0.0/hagis/NAMESPACE | 5 hagis-3.0.0/hagis/NEWS.md | 39 hagis-3.0.0/hagis/R/calculate_complexities.R | 246 +- hagis-3.0.0/hagis/R/calculate_diversities.R | 171 - hagis-3.0.0/hagis/R/data.R |only hagis-3.0.0/hagis/R/defunct.R |only hagis-3.0.0/hagis/R/hagis-package.R | 4 hagis-3.0.0/hagis/R/internal_functions.R | 37 hagis-3.0.0/hagis/R/summarize_gene.R | 169 - hagis-3.0.0/hagis/README.md | 15 hagis-3.0.0/hagis/build/vignette.rds |binary hagis-3.0.0/hagis/data |only hagis-3.0.0/hagis/inst/CITATION | 33 hagis-3.0.0/hagis/inst/doc/hagis.R | 75 hagis-3.0.0/hagis/inst/doc/hagis.Rmd | 145 - hagis-3.0.0/hagis/inst/doc/hagis.html | 1084 +++++----- hagis-3.0.0/hagis/inst/paper/paper.Rmd | 24 hagis-3.0.0/hagis/inst/paper/paper.docx |binary hagis-3.0.0/hagis/man/P_sojae_survey.Rd |only hagis-3.0.0/hagis/man/autoplot.hagis.complexities.Rd |only hagis-3.0.0/hagis/man/autoplot.hagis.gene.summary.Rd |only hagis-3.0.0/hagis/man/calculate_complexities.Rd | 33 hagis-3.0.0/hagis/man/calculate_diversities.Rd | 63 hagis-3.0.0/hagis/man/diversities_table.Rd | 12 hagis-3.0.0/hagis/man/hagis.Rd | 4 hagis-3.0.0/hagis/man/individual_pathotypes.Rd | 12 hagis-3.0.0/hagis/man/summarize_gene.Rd | 40 hagis-3.0.0/hagis/tests/figs/deps.txt | 2 hagis-3.0.0/hagis/tests/figs/plot-hagis-complexities |only hagis-3.0.0/hagis/tests/figs/plot-hagis-gene-summary |only hagis-3.0.0/hagis/tests/testthat/test-autoplot_hagis_complexities.R |only hagis-3.0.0/hagis/tests/testthat/test-autoplot_rps_summary.R |only hagis-3.0.0/hagis/tests/testthat/test-calculate_complexities.R | 163 - hagis-3.0.0/hagis/tests/testthat/test-calculate_diversities.R | 200 + hagis-3.0.0/hagis/tests/testthat/test-defunct.R |only hagis-3.0.0/hagis/tests/testthat/test-diversities_table.R | 45 hagis-3.0.0/hagis/tests/testthat/test-individual_pathotypes.R | 5 hagis-3.0.0/hagis/vignettes/hagis.Rmd | 145 - 45 files changed, 1665 insertions(+), 1217 deletions(-)
Title: Functions and Data for "Epidemics: Models and Data in R"
Description: Functions, data sets and shiny apps for "Epidemics: Models and Data in R" by Ottar N. Bjornstad (ISBN 978-3-319-97487-3) <https://www.springer.com/gp/book/9783319974866>. The package contains functions to study the S(E)IR model, spatial and age-structured SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the coursera Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.
Author: Ottar N. Bjornstad [aut, cre]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>
Diff between epimdr versions 0.6-3 dated 2019-05-03 and 0.6-4 dated 2019-08-26
CHANGES | 2 ++ DESCRIPTION | 12 ++++++------ MD5 | 10 ++++++---- NAMESPACE | 2 +- R/flowField.R |only R/shiny.r | 1 - man/flowField.Rd |only 7 files changed, 15 insertions(+), 12 deletions(-)
Title: Accessing Statistics Canada Data Table and Vectors
Description: Searches for, accesses, and retrieves new-format and old-format Statistics Canada data
tables, as well as individual vectors, as tidy data frames. This package deals with encoding issues, allows for
bilingual English or French language data retrieval, and bundles convenience functions
to make it easier to work with retrieved table data. Optional caching features are provided.
Author: Jens von Bergmann [cre],
Dmitry Shkolnik [aut]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cansim versions 0.3.1 dated 2019-08-19 and 0.3.2 dated 2019-08-26
DESCRIPTION | 6 ++--- MD5 | 10 ++++----- NEWS.md | 5 ++++ R/cansim.R | 12 ++++++++--- R/sysdata.rda |binary inst/doc/cansim.html | 54 +++++++++++++++++++++++---------------------------- 6 files changed, 47 insertions(+), 40 deletions(-)