Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Josh O'Brien [ctb],
Joseph O'Rourke [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.4-0 dated 2020-02-21 and 1.4-1 dated 2020-02-28
DESCRIPTION | 6 ++--- MD5 | 16 +++++++-------- R/CRS-methods.R | 53 ++++++++++++++++++++++++++------------------------ inst/NEWS.Rd | 10 +++++++++ inst/doc/csdacm.pdf |binary inst/doc/intro_sp.pdf |binary inst/doc/over.pdf |binary inst/include/sp.h | 2 - src/sp.h | 2 - 9 files changed, 51 insertions(+), 38 deletions(-)
Title: Selection Response Analysis
Description: Artificial selection through selective breeding is an efficient way to induce changes in traits of interest in experimental populations. This package (sra) provides a set of tools to analyse artificial-selection response datasets. The data typically feature for several generations the average value of a trait in a population, the variance of the trait, the population size and the average value of the parents that were chosen to breed. Sra implements two families of models aiming at describing the dynamics of the genetic architecture of the trait during the selection response. The first family relies on purely descriptive (phenomenological) models, based on an autoregressive framework. The second family provides different mechanistic models, accounting e.g. for inbreeding, mutations, genetic and environmental canalization, or epistasis. The parameters underlying the dynamics of the time series are estimated by maximum likelihood. The sra package thus provides (i) a wrapper for the R functions mle() and optim() aiming at fitting in a convenient way a predetermined set of models, and (ii) some functions to plot and analyze the output of the models.
Author: Arnaud Le Rouzic
Maintainer: Arnaud Le Rouzic <lerouzic@egce.cnrs-gif.fr>
Diff between sra versions 0.1.1 dated 2015-01-08 and 0.1.3 dated 2020-02-28
DESCRIPTION | 16 ++++++++-------- MD5 | 26 +++++++++++++------------- NAMESPACE | 5 ++++- R/logLik.srafit.R | 2 +- R/sraCanalization.R | 4 +++- R/sraCanalizationOpt.R | 2 +- R/sraCstvar.R | 4 +++- R/sraDirepistasis.R | 12 ++++++------ R/sraDrift.R | 4 +++- R/sraEpiTimeseries.R | 4 +++- R/sraMakeObject.R | 7 +++---- R/sraMutation.R | 4 +++- R/vcov.srafit.R | 2 +- man/sraAutoregTimeseries.Rd | 2 +- 14 files changed, 53 insertions(+), 41 deletions(-)
Title: Linear Models for Panel Data
Description: A set of estimators and tests for panel data
econometrics, as described in Baltagi (2013) Econometric Analysis of Panel Data, ISBN-13:978-1-118-67232-7,
Hsiao (2014) Analysis of Panel Data <doi:10.1017/CBO9781139839327> and
Croissant and Millo (2018), Panel Data Econometrics with R, ISBN:978-1-118-94918-4.
Author: Yves Croissant [aut, cre],
Giovanni Millo [aut],
Kevin Tappe [aut],
Ott Toomet [ctb],
Christian Kleiber [ctb],
Achim Zeileis [ctb],
Arne Henningsen [ctb],
Liviu Andronic [ctb],
Nina Schoenfelder [ctb]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between plm versions 2.2-2 dated 2020-02-21 and 2.2-3 dated 2020-02-28
DESCRIPTION | 13 MD5 | 148 + NEWS.md | 60 R/est_cce.R | 4 R/test_uroot.R | 6 R/tool_vcovG.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/Cigar.rda |binary data/Crime.rda |binary data/EmplUK.rda |binary data/Gasoline.rda |binary data/Grunfeld.rda |binary data/Hedonic.rda |binary data/LaborSupply.rda |binary data/Males.rda |binary data/Parity.rda |binary data/Produc.rda |binary data/RiceFarms.rda |binary data/Snmesp.rda |binary data/SumHes.rda |binary data/Wages.rda |binary inst/doc/plmFunction.html | 465 +---- inst/doc/plmModelComponents.html | 343 ---- inst/doc/plmPackage.html | 853 +++------- man/pcce.Rd | 4 man/vcovHC.plm.Rd | 2 tests/Examples/plm-Ex.Rout.save | 8 tests/test_Chow.Rout.save | 2 tests/test_Errors.Rout.save | 2 tests/test_Estimators.R | 8 tests/test_Estimators.Rout.save | 10 tests/test_Evaluation.Rout.save | 2 tests/test_FD_models.Rout.save | 2 tests/test_IV.Rout.save | 2 tests/test_R2_adj_R2.Rout.save |only tests/test_as.data.frame_as.matrix.R | 2 tests/test_as.data.frame_as.matrix.Rout.save |only tests/test_as.list.pdata.frame.Rout.save |only tests/test_clubSandwich_interoperability.Rout.save | 2 tests/test_detect_lin_dep_alias.Rout.save |only tests/test_fitted.plm.Rout.save |only tests/test_fixef.Rout.save |only tests/test_fixef_comp_lm_plm.Rout.save |only tests/test_is.pconsecutive.Rout.save |only tests/test_lag_lead.Rout.save | 2 tests/test_lagt_leadt.Rout.save | 2 tests/test_make.pconsecutive_pbalanced.Rout.save |only tests/test_misc.Rout.save |only tests/test_model.frame.Rout.save |only tests/test_model.matrix_effects.Rout.save |only tests/test_model.matrix_pmodel.response.Rout.save |only tests/test_nested.Rout.save | 2 tests/test_pFtest.Rout.save | 2 tests/test_pbgtest.Rout.save |only tests/test_pbnftest.Rout.save | 2 tests/test_pbsytest_unbalanced.Rout.save | 2 tests/test_pcdtest.Rout.save |only tests/test_pdata.frame_const_allNA_nonfinite.Rout.save |only tests/test_pdata.frame_extract_class_est_mod.Rout.save |only tests/test_pdata.frame_id_index_more.Rout.save | 2 tests/test_pdata.frame_print_duplicated_rownames.Rout.save |only tests/test_pdata.frame_subsetting.Rout.save | 2 tests/test_pdata.frame_unused_levels.Rout.save |only tests/test_pdiff_fd.Rout.save |only tests/test_pdwtest.Rout.save |only tests/test_pggls.Rout.save |only tests/test_pgmm.Rout.save | 2 tests/test_pgrangertest.Rout.save | 2 tests/test_pht.Rout.save | 2 tests/test_phtest_Hausman_regression.Rout.save | 2 tests/test_plm.data.Rout.save |only tests/test_plm_na.action.Rout.save |only tests/test_plmtest_unbalanced.Rout.save | 2 tests/test_preserve_rownames.Rout.save |only tests/test_pseries_subsetting.Rout.save |only tests/test_punbalancedness.Rout.save |only tests/test_purtest.R | 4 tests/test_purtest.Rout.save | 6 tests/test_pvar.Rout.save |only tests/test_pvcm.R | 4 tests/test_pvcm.Rout.save | 6 tests/test_pwaldtest.Rout.save | 2 tests/test_pwaldtest_vcovG_attr_cluster.Rout.save | 2 tests/test_pwfdtest_pwartest.Rout.save |only tests/test_pwtest.Rout.save |only tests/test_ranef.Rout.save | 2 tests/test_residuals_overall_fitted_exp.Rout.save |only tests/test_summary.plm_vcov.Rout.save |only tests/test_summary.pseries_character_logical_factor.Rout.save |only tests/test_vcovG_lin_dep.Rout.save |only tests/test_within_intercept.Rout.save | 2 92 files changed, 727 insertions(+), 1267 deletions(-)
Title: Time Series Forecasting with Machine Learning Methods
Description: The purpose of 'forecastML' is to simplify the process of multi-step-ahead forecasting with standard machine learning algorithms. 'forecastML' supports lagged, dynamic, static, and grouping features for modeling single and grouped numeric or factor/sequence time series. In addition, simple wrapper functions are used to support model-building with most R packages. This approach to forecasting is inspired by Bergmeir, Hyndman, and Koo's (2018) paper "A note on the validity of cross-validation for evaluating autoregressive time series prediction" <doi:10.1016/j.csda.2017.11.003>.
Author: Nickalus Redell
Maintainer: Nickalus Redell <nickalusredell@gmail.com>
Diff between forecastML versions 0.7.0 dated 2020-01-07 and 0.8.0 dated 2020-02-28
forecastML-0.7.0/forecastML/tools/forecastML_cheat_sheet.png |only forecastML-0.7.0/forecastML/tools/forecastML_cheat_sheet_data.png |only forecastML-0.7.0/forecastML/tools/forecastML_cheat_sheet_model.png |only forecastML-0.8.0/forecastML/DESCRIPTION | 14 forecastML-0.8.0/forecastML/MD5 | 121 forecastML-0.8.0/forecastML/NAMESPACE | 2 forecastML-0.8.0/forecastML/R/combine_forecasts.R | 352 +- forecastML-0.8.0/forecastML/R/create_windows.R | 71 forecastML-0.8.0/forecastML/R/lagged_df.R | 522 ++- forecastML-0.8.0/forecastML/R/return_error.R | 324 +- forecastML-0.8.0/forecastML/R/return_hyper.R | 24 forecastML-0.8.0/forecastML/R/train_model.R | 997 ++++--- forecastML-0.8.0/forecastML/R/zzz.R | 156 + forecastML-0.8.0/forecastML/README.md | 195 + forecastML-0.8.0/forecastML/build/vignette.rds |binary forecastML-0.8.0/forecastML/inst/doc/custom_functions.R | 24 forecastML-0.8.0/forecastML/inst/doc/custom_functions.Rmd | 4 forecastML-0.8.0/forecastML/inst/doc/custom_functions.html | 818 +++--- forecastML-0.8.0/forecastML/inst/doc/grouped_forecast.R | 99 forecastML-0.8.0/forecastML/inst/doc/grouped_forecast.Rmd | 141 - forecastML-0.8.0/forecastML/inst/doc/grouped_forecast.html | 1109 ++++---- forecastML-0.8.0/forecastML/inst/doc/grouped_forecast_sequences.R |only forecastML-0.8.0/forecastML/inst/doc/grouped_forecast_sequences.Rmd |only forecastML-0.8.0/forecastML/inst/doc/grouped_forecast_sequences.html |only forecastML-0.8.0/forecastML/inst/doc/lagged_features.R | 18 forecastML-0.8.0/forecastML/inst/doc/lagged_features.Rmd | 2 forecastML-0.8.0/forecastML/inst/doc/lagged_features.html | 783 +++-- forecastML-0.8.0/forecastML/inst/doc/package_overview.R | 100 forecastML-0.8.0/forecastML/inst/doc/package_overview.Rmd | 168 - forecastML-0.8.0/forecastML/inst/doc/package_overview.html | 1341 +++++----- forecastML-0.8.0/forecastML/man/combine_forecasts.Rd | 200 - forecastML-0.8.0/forecastML/man/create_lagged_df.Rd | 326 +- forecastML-0.8.0/forecastML/man/create_windows.Rd | 154 - forecastML-0.8.0/forecastML/man/data_buoy.Rd | 58 forecastML-0.8.0/forecastML/man/data_buoy_gaps.Rd | 64 forecastML-0.8.0/forecastML/man/data_seatbelts.Rd | 42 forecastML-0.8.0/forecastML/man/fill_gaps.Rd | 153 - forecastML-0.8.0/forecastML/man/plot.forecastML.Rd | 81 forecastML-0.8.0/forecastML/man/plot.forecast_model_hyper.Rd | 218 - forecastML-0.8.0/forecastML/man/plot.forecast_results.Rd | 90 forecastML-0.8.0/forecastML/man/plot.lagged_df.Rd | 80 forecastML-0.8.0/forecastML/man/plot.training_results.Rd | 85 forecastML-0.8.0/forecastML/man/plot.validation_error.Rd | 81 forecastML-0.8.0/forecastML/man/plot.windows.Rd | 91 forecastML-0.8.0/forecastML/man/predict.forecast_model.Rd | 261 - forecastML-0.8.0/forecastML/man/return_error.Rd | 261 - forecastML-0.8.0/forecastML/man/return_hyper.Rd | 208 - forecastML-0.8.0/forecastML/man/summary.lagged_df.Rd | 36 forecastML-0.8.0/forecastML/man/train_model.Rd | 202 - forecastML-0.8.0/forecastML/tests/testthat/test_create_lagged_df_grouped.R | 6 forecastML-0.8.0/forecastML/tests/testthat/test_create_lagged_df_grouped_multi_output.R |only forecastML-0.8.0/forecastML/tests/testthat/test_create_lagged_df_horizons.R | 4 forecastML-0.8.0/forecastML/tests/testthat/test_create_lagged_df_horizons_multi_output.R |only forecastML-0.8.0/forecastML/tests/testthat/test_create_lagged_df_lookback_multi_output.R |only forecastML-0.8.0/forecastML/tools/direct_forecast_illustration.PNG |only forecastML-0.8.0/forecastML/tools/features_table.png |only forecastML-0.8.0/forecastML/tools/forecastML_cheat_sheet.PNG |only forecastML-0.8.0/forecastML/tools/forecastML_cheat_sheet_data.PNG |only forecastML-0.8.0/forecastML/tools/forecastML_cheat_sheet_model.PNG |only forecastML-0.8.0/forecastML/tools/forecasts.png |binary forecastML-0.8.0/forecastML/tools/lightning_example.png |only forecastML-0.8.0/forecastML/tools/multi_outcome_forecast_plot.png |only forecastML-0.8.0/forecastML/tools/multi_outcome_train_plot.png |only forecastML-0.8.0/forecastML/tools/validation_data_forecasts.png |binary forecastML-0.8.0/forecastML/vignettes/custom_functions.Rmd | 4 forecastML-0.8.0/forecastML/vignettes/direct_forecast.png |only forecastML-0.8.0/forecastML/vignettes/features_table.png |only forecastML-0.8.0/forecastML/vignettes/grouped_forecast.Rmd | 141 - forecastML-0.8.0/forecastML/vignettes/grouped_forecast_sequences.Rmd |only forecastML-0.8.0/forecastML/vignettes/lagged_features.Rmd | 2 forecastML-0.8.0/forecastML/vignettes/multi_output_forecast.png |only forecastML-0.8.0/forecastML/vignettes/package_overview.Rmd | 168 - 72 files changed, 6004 insertions(+), 4397 deletions(-)
Title: Extending 'dendrogram' Functionality in R
Description: Offers a set of functions for extending
'dendrogram' objects in R, letting you visualize and compare trees of
'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different 'dendrograms' to one another.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Yoav Benjamini [ths],
Gavin Simpson [ctb],
Gregory Jefferis [aut, ctb] (imported code from his dendroextras
package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Cath [ctb] (https://github.com/CathG),
John Ma [ctb] (https://github.com/JohnMCMa),
Krzysiek G [ctb] (https://github.com/storaged),
Manuela Hummel [ctb] (https://github.com/hummelma),
Chase Clark [ctb] (https://github.com/chasemc),
Lucas Graybuck [ctb] (https://github.com/hypercompetent),
jdetribol [ctb] (https://github.com/jdetribol),
Ben Ho [ctb] (https://github.com/SplitInf),
Samuel Perreault [ctb] (https://github.com/samperochkin),
Christian Hennig [ctb] (http://www.homepages.ucl.ac.uk/~ucakche/),
David Bradley [ctb] (https://github.com/DBradley27)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.13.3 dated 2020-02-08 and 1.13.4 dated 2020-02-28
dendextend-1.13.3/dendextend/man/FM_index_profdpm.Rd |only dendextend-1.13.3/dendextend/vignettes/disabled |only dendextend-1.13.4/dendextend/ChangeLog | 400 ++ dendextend-1.13.4/dendextend/DESCRIPTION | 14 dendextend-1.13.4/dendextend/MD5 | 60 dendextend-1.13.4/dendextend/NAMESPACE | 1 dendextend-1.13.4/dendextend/NEWS | 8 dendextend-1.13.4/dendextend/NEWS.md | 15 dendextend-1.13.4/dendextend/R/bk_method.R | 183 - dendextend-1.13.4/dendextend/R/dist_long.R | 2 dendextend-1.13.4/dendextend/R/find_dend.R | 2 dendextend-1.13.4/dendextend/R/ggdend.R | 3 dendextend-1.13.4/dendextend/R/ggdendro.R | 4 dendextend-1.13.4/dendextend/R/pvclust.R | 2 dendextend-1.13.4/dendextend/build/vignette.rds |binary dendextend-1.13.4/dendextend/inst/doc/Cluster_Analysis.R | 86 dendextend-1.13.4/dendextend/inst/doc/Cluster_Analysis.html | 989 ++--- dendextend-1.13.4/dendextend/inst/doc/FAQ.R | 32 dendextend-1.13.4/dendextend/inst/doc/FAQ.html | 831 +--- dendextend-1.13.4/dendextend/inst/doc/Quick_Introduction.R | 24 dendextend-1.13.4/dendextend/inst/doc/Quick_Introduction.html | 351 -- dendextend-1.13.4/dendextend/inst/doc/dendextend.R | 160 dendextend-1.13.4/dendextend/inst/doc/dendextend.Rmd | 2 dendextend-1.13.4/dendextend/inst/doc/dendextend.html | 1682 ++++------ dendextend-1.13.4/dendextend/man/Bk.Rd | 9 dendextend-1.13.4/dendextend/man/Bk_permutations.Rd | 2 dendextend-1.13.4/dendextend/man/FM_index.Rd | 21 dendextend-1.13.4/dendextend/man/FM_index_R.Rd | 4 dendextend-1.13.4/dendextend/man/FM_index_permutation.Rd | 4 dendextend-1.13.4/dendextend/man/sort_2_clusters_vectors.Rd | 3 dendextend-1.13.4/dendextend/tests/testthat/test-bk_method.R | 74 dendextend-1.13.4/dendextend/vignettes/dendextend.Rmd | 2 32 files changed, 2147 insertions(+), 2823 deletions(-)
Title: Bayesian Optimization and Model-Based Optimization of Expensive
Black-Box Functions
Description: Flexible and comprehensive R toolbox for model-based optimization
('MBO'), also known as Bayesian optimization. It implements the Efficient
Global Optimization Algorithm and is designed for both single- and multi-
objective optimization with mixed continuous, categorical and conditional
parameters. The machine learning toolbox 'mlr' provide dozens of regression
learners to model the performance of the target algorithm with respect to
the parameter settings. It provides many different infill criteria to guide
the search process. Additional features include multi-point batch proposal,
parallel execution as well as visualization and sophisticated logging
mechanisms, which is especially useful for teaching and understanding of
algorithm behavior. 'mlrMBO' is implemented in a modular fashion, such that
single components can be easily replaced or adapted by the user for specific
use cases.
Author: Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Jakob Richter [aut, cre] (<https://orcid.org/0000-0003-4481-5554>),
Jakob Bossek [aut] (<https://orcid.org/0000-0002-4121-4668>),
Daniel Horn [aut],
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Janek Thomas [aut] (<https://orcid.org/0000-0003-4511-6245>)
Maintainer: Jakob Richter <code@jakob-r.de>
Diff between mlrMBO versions 1.1.3 dated 2019-12-02 and 1.1.4 dated 2020-02-28
mlrMBO-1.1.3/mlrMBO/tests/testthat/Rplots.pdf |only mlrMBO-1.1.4/mlrMBO/DESCRIPTION | 16 mlrMBO-1.1.4/mlrMBO/MD5 | 71 - mlrMBO-1.1.4/mlrMBO/NEWS.md | 8 mlrMBO-1.1.4/mlrMBO/R/SMBO.R | 2 mlrMBO-1.1.4/mlrMBO/R/checkStuff.R | 2 mlrMBO-1.1.4/mlrMBO/R/convertToDesign.R | 2 mlrMBO-1.1.4/mlrMBO/R/exampleRunMultiObj.R | 4 mlrMBO-1.1.4/mlrMBO/R/infillOptNSGA2.R | 2 mlrMBO-1.1.4/mlrMBO/R/infill_crits.R | 13 mlrMBO-1.1.4/mlrMBO/R/initOptProblem.R | 10 mlrMBO-1.1.4/mlrMBO/R/mbo.R | 2 mlrMBO-1.1.4/mlrMBO/R/plot_OptState.R | 107 + mlrMBO-1.1.4/mlrMBO/R/proposePointsMOIMBO.R | 4 mlrMBO-1.1.4/mlrMBO/R/renderExampleRunPlotSingleCrit1d.R | 3 mlrMBO-1.1.4/mlrMBO/R/renderExampleRunPlotSingleCrit2d.R | 5 mlrMBO-1.1.4/mlrMBO/R/renderExampleRunPlot_helpers.R | 3 mlrMBO-1.1.4/mlrMBO/R/setMBOControlInfill.R | 6 mlrMBO-1.1.4/mlrMBO/R/setMBOControlMultiPoint.R | 2 mlrMBO-1.1.4/mlrMBO/R/setMBOControlTermination.R | 4 mlrMBO-1.1.4/mlrMBO/R/utils.R | 13 mlrMBO-1.1.4/mlrMBO/R/zzz.R | 2 mlrMBO-1.1.4/mlrMBO/build/vignette.rds |binary mlrMBO-1.1.4/mlrMBO/inst/doc/mlrMBO.html | 701 ++++++---- mlrMBO-1.1.4/mlrMBO/man/mbo.Rd | 2 mlrMBO-1.1.4/mlrMBO/man/plot.OptState.Rd | 7 mlrMBO-1.1.4/mlrMBO/man/setMBOControlInfill.Rd | 6 mlrMBO-1.1.4/mlrMBO/man/setMBOControlMultiPoint.Rd | 2 mlrMBO-1.1.4/mlrMBO/man/setMBOControlTermination.Rd | 4 mlrMBO-1.1.4/mlrMBO/tests/testthat.R | 2 mlrMBO-1.1.4/mlrMBO/tests/testthat/helper_objects.R | 18 mlrMBO-1.1.4/mlrMBO/tests/testthat/test_infillcrits.R | 31 mlrMBO-1.1.4/mlrMBO/tests/testthat/test_initCrit.R | 22 mlrMBO-1.1.4/mlrMBO/tests/testthat/test_multiobj_dib.R | 4 mlrMBO-1.1.4/mlrMBO/tests/testthat/test_smbo.R | 18 mlrMBO-1.1.4/mlrMBO/vignettes/supplementary/parallelization.Rmd | 3 mlrMBO-1.1.4/mlrMBO/vignettes/supplementary/warmstart.Rmd | 11 37 files changed, 724 insertions(+), 388 deletions(-)
Title: Clustering with Matrix Gaussian and Matrix Transformation
Mixture Models
Description: Provides matrix Gaussian mixture models, matrix transformation mixture models and their model-based clustering results. The parsimonious models of the mean matrices and variance covariance matrices are implemented with a total of 196 variations.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Shuchismita Sarkar [ctb],
Michael Hutt [ctb, cph],
Stephen Moshier [ctb, cph],
Rouben Rostamian [ctb, cph],
Carl Edward Rasmussen [ctb, cph],
Dianne Cook [ctb, cph]
Maintainer: Xuwen Zhu <xzhu20@cba.ua.edu>
Diff between MatTransMix versions 0.1.6 dated 2019-11-08 and 0.1.7 dated 2020-02-28
DESCRIPTION | 8 +- MD5 | 44 ++++++------- NEWS | 4 + R/libMatTransFull.R | 100 ++++++++++++++++++++++++------- man/IMDb.Rd | 2 man/MatTrans.EM.Rd | 18 ----- man/MatTrans.init.Rd | 17 ----- man/crime.Rd | 2 src/Makevars | 2 src/MatTransMix.h | 13 +--- src/array.h | 137 ++----------------------------------------- src/crosen1.c | 140 ++++++++++---------------------------------- src/crosen2.c | 140 +++++++++++--------------------------------- src/libEVD.c | 19 ----- src/libEVD_LAPACK.c | 7 -- src/libFull.c | 90 +++++++++------------------- src/libMatrix.c | 42 ++----------- src/libPsi.c | 55 +++++------------ src/libSigma_1.c | 14 +--- src/libSigma_2.c | 85 +++++++------------------- src/registerDynamicSymbol.c | 1 src/runFull.c | 3 src/svd.c | 10 --- 23 files changed, 277 insertions(+), 676 deletions(-)
Title: A Swift, Versatile Phylogenomic and High-Throughput Sequencing
Simulator
Description: Simply and efficiently
simulates (i) variants from reference genomes and (ii) reads from both Illumina
<https://www.illumina.com/>
and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms.
It can either read reference genomes from FASTA files or simulate new ones.
Genomic variants can be simulated using summary statistics, phylogenies,
Variant Call Format (VCF) files, and coalescent simulations—the latter of which
can include selection, recombination, and demographic fluctuations.
'jackalope' can simulate single, paired-end, or mate-pair Illumina reads,
as well as PacBio reads.
These simulations include sequencing errors, mapping qualities, multiplexing,
and optical/polymerase chain reaction (PCR) duplicates.
Simulating Illumina sequencing is based on ART
by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>.
PacBio sequencing simulation is based on
SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>.
All outputs can be written to standard file formats.
Author: Lucas A. Nell [cph, aut, cre] (<https://orcid.org/0000-0003-3209-0517>)
Maintainer: Lucas A. Nell <lucas@lucasnell.com>
Diff between jackalope versions 1.0.0 dated 2019-11-22 and 1.1.0 dated 2020-02-28
jackalope-1.0.0/jackalope/R/create_variants.R |only jackalope-1.0.0/jackalope/R/vars_functions.R |only jackalope-1.0.0/jackalope/R/vars_functions_classes.R |only jackalope-1.0.0/jackalope/man/create_variants.Rd |only jackalope-1.0.0/jackalope/man/variants.Rd |only jackalope-1.0.0/jackalope/man/vars_functions.Rd |only jackalope-1.0.0/jackalope/man/vars_gtrees.Rd |only jackalope-1.0.0/jackalope/man/vars_phylo.Rd |only jackalope-1.0.0/jackalope/man/vars_ssites.Rd |only jackalope-1.0.0/jackalope/man/vars_theta.Rd |only jackalope-1.0.0/jackalope/man/vars_vcf.Rd |only jackalope-1.0.0/jackalope/src/ref_var_access.cpp |only jackalope-1.0.0/jackalope/src/var_classes.cpp |only jackalope-1.0.0/jackalope/src/var_classes.h |only jackalope-1.0.0/jackalope/src/vars_ssites.cpp |only jackalope-1.1.0/jackalope/DESCRIPTION | 8 jackalope-1.1.0/jackalope/MD5 | 148 +- jackalope-1.1.0/jackalope/NAMESPACE | 14 jackalope-1.1.0/jackalope/NEWS.md | 9 jackalope-1.1.0/jackalope/R/RcppExports.R | 260 +-- jackalope-1.1.0/jackalope/R/aaa-classes.R | 693 ++++++---- jackalope-1.1.0/jackalope/R/create_haplotypes.R |only jackalope-1.1.0/jackalope/R/haps_functions.R |only jackalope-1.1.0/jackalope/R/haps_functions_classes.R |only jackalope-1.1.0/jackalope/R/hts_illumina.R | 86 - jackalope-1.1.0/jackalope/R/hts_pacbio.R | 60 jackalope-1.1.0/jackalope/R/jackalope.R | 4 jackalope-1.1.0/jackalope/R/mevo.R | 93 - jackalope-1.1.0/jackalope/R/read_write.R | 62 jackalope-1.1.0/jackalope/README.md | 37 jackalope-1.1.0/jackalope/build/vignette.rds |binary jackalope-1.1.0/jackalope/inst/doc/jackalope-intro.R | 156 +- jackalope-1.1.0/jackalope/inst/doc/jackalope-intro.Rmd | 380 ++++- jackalope-1.1.0/jackalope/inst/doc/jackalope-intro.html | 344 ++-- jackalope-1.1.0/jackalope/inst/doc/sub-models.Rmd | 3 jackalope-1.1.0/jackalope/inst/doc/sub-models.html | 12 jackalope-1.1.0/jackalope/man/create_genome.Rd | 9 jackalope-1.1.0/jackalope/man/create_haplotypes.Rd |only jackalope-1.1.0/jackalope/man/haplotypes.Rd |only jackalope-1.1.0/jackalope/man/haps_functions.Rd |only jackalope-1.1.0/jackalope/man/haps_gtrees.Rd |only jackalope-1.1.0/jackalope/man/haps_phylo.Rd |only jackalope-1.1.0/jackalope/man/haps_ssites.Rd |only jackalope-1.1.0/jackalope/man/haps_theta.Rd |only jackalope-1.1.0/jackalope/man/haps_vcf.Rd |only jackalope-1.1.0/jackalope/man/illumina.Rd | 24 jackalope-1.1.0/jackalope/man/indels.Rd | 4 jackalope-1.1.0/jackalope/man/jackalope.Rd | 5 jackalope-1.1.0/jackalope/man/pacbio.Rd | 20 jackalope-1.1.0/jackalope/man/ref_genome.Rd | 492 ++++++- jackalope-1.1.0/jackalope/man/sub_models.Rd | 69 jackalope-1.1.0/jackalope/man/write_fasta.Rd | 25 jackalope-1.1.0/jackalope/man/write_vcf.Rd | 26 jackalope-1.1.0/jackalope/src/Makevars | 6 jackalope-1.1.0/jackalope/src/Makevars.win | 7 jackalope-1.1.0/jackalope/src/RcppExports.cpp | 367 ++--- jackalope-1.1.0/jackalope/src/alter_reference.cpp | 61 jackalope-1.1.0/jackalope/src/hap_classes.cpp |only jackalope-1.1.0/jackalope/src/hap_classes.h |only jackalope-1.1.0/jackalope/src/haps_ssites.cpp |only jackalope-1.1.0/jackalope/src/hts.h | 34 jackalope-1.1.0/jackalope/src/hts_illumina.cpp | 64 jackalope-1.1.0/jackalope/src/hts_illumina.h | 104 - jackalope-1.1.0/jackalope/src/hts_pacbio.cpp | 64 jackalope-1.1.0/jackalope/src/hts_pacbio.h | 100 - jackalope-1.1.0/jackalope/src/io.h | 2 jackalope-1.1.0/jackalope/src/io_fasta.cpp | 42 jackalope-1.1.0/jackalope/src/io_ms.cpp | 2 jackalope-1.1.0/jackalope/src/io_vcf.cpp | 124 - jackalope-1.1.0/jackalope/src/io_vcf.h | 114 - jackalope-1.1.0/jackalope/src/mutator.cpp | 8 jackalope-1.1.0/jackalope/src/mutator.h | 4 jackalope-1.1.0/jackalope/src/mutator_indels.cpp | 142 +- jackalope-1.1.0/jackalope/src/mutator_indels.h | 52 jackalope-1.1.0/jackalope/src/mutator_subs.cpp | 68 jackalope-1.1.0/jackalope/src/mutator_subs.h | 12 jackalope-1.1.0/jackalope/src/mutator_type.h | 2 jackalope-1.1.0/jackalope/src/phylogenomics.cpp | 38 jackalope-1.1.0/jackalope/src/phylogenomics.h | 26 jackalope-1.1.0/jackalope/src/ref_hap_access.cpp |only jackalope-1.1.0/jackalope/src/sub_models.cpp | 114 - jackalope-1.1.0/jackalope/tests/testthat/test-R_classes.R | 176 +- jackalope-1.1.0/jackalope/tests/testthat/test-create_mevo.R | 31 jackalope-1.1.0/jackalope/tests/testthat/test-fasta_IO.R | 24 jackalope-1.1.0/jackalope/tests/testthat/test-sequencer.R | 26 jackalope-1.1.0/jackalope/tests/testthat/test-variants_coal.R | 141 +- jackalope-1.1.0/jackalope/tests/testthat/test-variants_other.R | 98 - jackalope-1.1.0/jackalope/tests/testthat/test-vcf_IO.R | 180 +- jackalope-1.1.0/jackalope/vignettes/jackalope-intro.Rmd | 380 ++++- jackalope-1.1.0/jackalope/vignettes/sub-models.Rmd | 3 90 files changed, 3506 insertions(+), 2153 deletions(-)
Title: Computes the Scores for Different Implicit Measures
Description: A tool for computing the scores for the Implicit Association Test
(IAT; Greenwald, McGhee & Schwartz (1998) <doi:10.1037/0022-3514.74.6.1464>)
and the Single Category-IAT (SC-IAT: Karpinski & Steinman
(2006) <doi:10.1037/0022-3514.91.1.16>). Functions for preparing the data
(both for the IAT and the SC-IAT), plotting the results, and obtaining a
table with the scores of implicit measures descriptive statistics are
provided.
Author: Ottavia M. Epifania [aut, cre],
Pasquale Anselmi [ctb],
Egidio Robusto [ctb]
Maintainer: Ottavia M. Epifania <otta.epifania@gmail.com>
Diff between implicitMeasures versions 0.1.0 dated 2019-08-20 and 0.1.1 dated 2020-02-28
DESCRIPTION | 10 +- MD5 | 55 +++++------ NAMESPACE | 3 NEWS.md |only R/Dsciat.R | 2 R/clean_iat.R | 15 ++- R/clean_sciat.R | 15 ++- R/multi_dscore.R | 2 README.md | 15 ++- build/vignette.rds |binary inst/doc/IAT-example.R | 30 +++--- inst/doc/IAT-example.html | 21 +--- inst/doc/SC-IAT-example.R | 24 ++-- inst/doc/SC-IAT-example.html | 70 ++++++-------- inst/doc/implicitMeasures.R | 14 +- inst/doc/implicitMeasures.Rmd | 8 + inst/doc/implicitMeasures.html | 29 +++--- man/Dsciat.Rd | 175 ++++++++++++++++++------------------ man/IATrel.Rd | 86 ++++++++--------- man/clean_iat.Rd | 198 +++++++++++++++++++++-------------------- man/clean_sciat.Rd | 181 +++++++++++++++++++------------------ man/computeD.Rd | 168 +++++++++++++++++----------------- man/d_distr.Rd | 176 ++++++++++++++++++------------------ man/d_plot.Rd | 178 +++++++++++++++++++----------------- man/descript_d.Rd | 134 +++++++++++++-------------- man/multi_dsciat.Rd | 153 ++++++++++++++++--------------- man/multi_dscore.Rd | 106 ++++++++++----------- man/raw_data.Rd | 116 ++++++++++++------------ vignettes/implicitMeasures.Rmd | 8 + 29 files changed, 1027 insertions(+), 965 deletions(-)
More information about implicitMeasures at CRAN
Permanent link
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.68 dated 2019-05-23 and 1.69 dated 2020-02-28
Changelog | 83 +++ DESCRIPTION | 10 MD5 | 39 - NAMESPACE | 1 R/Functions.R | 905 ++++++++---------------------------- R/blockwiseModulesC.R | 9 R/empiricalBayesLM.R | 13 R/heatmapWithLegend.R | 96 +++ R/hierarchicalConsensusModules.R | 65 +- R/labeledHeatmap.R |only R/matchLabels.R | 12 R/userListEnrichment.R | 2 man/binarizeCategoricalColumns.Rd | 3 man/chooseTopHubInEachModule.Rd | 3 man/empiricalBayesLM.Rd | 9 man/hierarchicalConsensusModules.Rd | 5 man/kMEcomparisonScatterplot.Rd | 3 man/labeledHeatmap.Rd | 9 man/plotColorUnderTree.Rd | 12 man/userListEnrichment.Rd | 25 src/corFunctions.c | 2 21 files changed, 511 insertions(+), 795 deletions(-)
Title: Approximation of First-Passage-Time Densities for Diffusion
Processes
Description: Efficient approximation of first-passage-time densities for diffusion processes based on the First-Passage-Time Location (FPTL) function.
Author: Patricia Rom<e1>n-Rom<e1>n, Juan J. Serrano-P<e9>rez and Francisco Torres-Ruiz.
Maintainer: Juan J. Serrano-P<e9>rez <jjserra@ugr.es>
Diff between fptdApprox versions 2.1 dated 2015-08-25 and 2.2 dated 2020-02-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/Approx.fpt.density.R | 1 + R/plot.fpt.density.R | 14 ++++++++++---- R/report.fpt.density.R | 8 +++----- man/fptdApprox-package.Rd | 4 ++-- 6 files changed, 25 insertions(+), 20 deletions(-)
Title: Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files
Description: Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.
Author: Adrian Dragulescu [aut],
Cole Arendt [aut, cre]
Maintainer: Cole Arendt <cole.arendt@outlook.com>
Diff between xlsx versions 0.6.2 dated 2020-02-12 and 0.6.3 dated 2020-02-28
DESCRIPTION | 6 - MD5 | 29 +++--- NAMESPACE | 2 NEWS | 8 + R/CellBlock.R | 3 R/utilities.R | 38 ++++++++ build/vignette.rds |binary inst/doc/excel_report.R | 8 - inst/doc/excel_report.html | 189 ++++++++++++++++++++++---------------------- inst/doc/xlsx.R | 4 inst/doc/xlsx.html | 11 +- man/CellBlock.Rd | 3 man/addDataFrame.Rd | 4 man/set_java_tmp_dir.Rd |only man/xlsx-package.Rd | 11 -- tests/testthat/test-utils.R | 15 +++ 16 files changed, 195 insertions(+), 136 deletions(-)
Title: Time Series with Matrix Profile
Description: A toolkit implementing the Matrix Profile concept
that was created by CS-UCR
<http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.
Author: Francisco Bischoff [aut, cre] (<https://orcid.org/0000-0002-5301-8672>),
Michael Yeh [res, ccp, ctb] (<https://orcid.org/0000-0002-9807-2963>),
Diego Silva [res, ccp, ctb] (<https://orcid.org/0000-0002-5184-9413>),
Yan Zhu [res, ccp, ctb] (<https://orcid.org/0000-0002-5952-2108>),
Hoang Dau [res, ccp, ctb] (<https://orcid.org/0000-0003-2439-5185>),
Michele Linardi [res, ccp, ctb]
(<https://orcid.org/0000-0002-3249-2068>)
Maintainer: Francisco Bischoff <fbischoff@med.up.pt>
Diff between tsmp versions 0.3.5 dated 2019-06-05 and 0.4.8 dated 2020-02-28
tsmp-0.3.5/tsmp/NEWS.md |only tsmp-0.3.5/tsmp/tests/update-version.R |only tsmp-0.4.8/tsmp/DESCRIPTION | 78 +- tsmp-0.4.8/tsmp/MD5 | 292 ++++++---- tsmp-0.4.8/tsmp/NAMESPACE | 225 ++++---- tsmp-0.4.8/tsmp/NEWS | 12 tsmp-0.4.8/tsmp/R/RcppExports.R |only tsmp-0.4.8/tsmp/R/analyze.R |only tsmp-0.4.8/tsmp/R/annotations.R | 66 +- tsmp-0.4.8/tsmp/R/compute.R |only tsmp-0.4.8/tsmp/R/discords.R |only tsmp-0.4.8/tsmp/R/dist_profile.R | 20 tsmp-0.4.8/tsmp/R/find-chains.R | 6 tsmp-0.4.8/tsmp/R/find-discord.R | 133 ++++ tsmp-0.4.8/tsmp/R/find-motifs.R | 157 +++++ tsmp-0.4.8/tsmp/R/find-snippet.R |only tsmp-0.4.8/tsmp/R/fluss.R | 22 tsmp-0.4.8/tsmp/R/mass-pre-w.R | 6 tsmp-0.4.8/tsmp/R/mass-pre.R | 2 tsmp-0.4.8/tsmp/R/mass.R | 8 tsmp-0.4.8/tsmp/R/mass_v2.R | 10 tsmp-0.4.8/tsmp/R/mass_v3.R | 25 tsmp-0.4.8/tsmp/R/mass_weighted.R | 8 tsmp-0.4.8/tsmp/R/misc.R | 389 +++++++++++--- tsmp-0.4.8/tsmp/R/motifs-discords-small.R |only tsmp-0.4.8/tsmp/R/motifs.R |only tsmp-0.4.8/tsmp/R/mp-fluss-data.R | 52 - tsmp-0.4.8/tsmp/R/mp-gait-data.R | 20 tsmp-0.4.8/tsmp/R/mp-meat-data.R | 66 +- tsmp-0.4.8/tsmp/R/mp-test-data.R | 46 - tsmp-0.4.8/tsmp/R/mpdist.R |only tsmp-0.4.8/tsmp/R/mpx.R |only tsmp-0.4.8/tsmp/R/mstomp-par.R | 5 tsmp-0.4.8/tsmp/R/mstomp.R | 13 tsmp-0.4.8/tsmp/R/plot.R | 367 ++++++++++++- tsmp-0.4.8/tsmp/R/pmp.R |only tsmp-0.4.8/tsmp/R/print.R | 81 ++ tsmp-0.4.8/tsmp/R/salient.R | 41 - tsmp-0.4.8/tsmp/R/scrimp.R | 24 tsmp-0.4.8/tsmp/R/sdts-predict.R | 8 tsmp-0.4.8/tsmp/R/sdts-train.R | 8 tsmp-0.4.8/tsmp/R/serialize.R |only tsmp-0.4.8/tsmp/R/simple.R | 9 tsmp-0.4.8/tsmp/R/stamp-par.R | 9 tsmp-0.4.8/tsmp/R/stamp.R | 19 tsmp-0.4.8/tsmp/R/stomp-par.R | 8 tsmp-0.4.8/tsmp/R/stomp.R | 21 tsmp-0.4.8/tsmp/R/stompi.R | 3 tsmp-0.4.8/tsmp/R/subset.R | 86 +++ tsmp-0.4.8/tsmp/R/tsmp-package.R |only tsmp-0.4.8/tsmp/R/tsmp.R | 32 - tsmp-0.4.8/tsmp/R/utils-pipe.R | 46 - tsmp-0.4.8/tsmp/R/valmod.R | 27 tsmp-0.4.8/tsmp/R/visualize.R |only tsmp-0.4.8/tsmp/R/zzz.R |only tsmp-0.4.8/tsmp/README.md | 67 +- tsmp-0.4.8/tsmp/build/vignette.rds |binary tsmp-0.4.8/tsmp/data/motifs_discords_small.rda |only tsmp-0.4.8/tsmp/inst/WORDLIST | 21 tsmp-0.4.8/tsmp/inst/doc/press.R | 6 tsmp-0.4.8/tsmp/inst/doc/press.html | 21 tsmp-0.4.8/tsmp/man/analyze.Rd |only tsmp-0.4.8/tsmp/man/as.matrixprofile.Rd | 169 +++--- tsmp-0.4.8/tsmp/man/av_apply.Rd | 80 +- tsmp-0.4.8/tsmp/man/av_complexity.Rd | 92 +-- tsmp-0.4.8/tsmp/man/av_hardlimit_artifact.Rd | 88 +-- tsmp-0.4.8/tsmp/man/av_motion_artifact.Rd | 88 +-- tsmp-0.4.8/tsmp/man/av_stop_word.Rd | 119 ++-- tsmp-0.4.8/tsmp/man/av_zerocrossing.Rd | 89 +-- tsmp-0.4.8/tsmp/man/compute.Rd |only tsmp-0.4.8/tsmp/man/discords.Rd |only tsmp-0.4.8/tsmp/man/dist_profile.Rd | 185 +++--- tsmp-0.4.8/tsmp/man/fast_avg_sd.Rd |only tsmp-0.4.8/tsmp/man/fast_movavg.Rd | 44 - tsmp-0.4.8/tsmp/man/fast_movsd.Rd | 46 - tsmp-0.4.8/tsmp/man/find_chains.Rd | 64 +- tsmp-0.4.8/tsmp/man/find_discord.Rd | 107 ++- tsmp-0.4.8/tsmp/man/find_motif.Rd | 154 +++-- tsmp-0.4.8/tsmp/man/find_snippet.Rd |only tsmp-0.4.8/tsmp/man/floss.Rd | 138 ++-- tsmp-0.4.8/tsmp/man/floss_cac.Rd | 107 +-- tsmp-0.4.8/tsmp/man/floss_extract.Rd | 99 +-- tsmp-0.4.8/tsmp/man/fluss.Rd | 99 +-- tsmp-0.4.8/tsmp/man/fluss_cac.Rd | 95 +-- tsmp-0.4.8/tsmp/man/fluss_extract.Rd | 95 +-- tsmp-0.4.8/tsmp/man/fluss_score.Rd | 97 +-- tsmp-0.4.8/tsmp/man/get_data.Rd | 42 - tsmp-0.4.8/tsmp/man/mass-deprecated.Rd | 98 +-- tsmp-0.4.8/tsmp/man/mass_pre.Rd | 98 +-- tsmp-0.4.8/tsmp/man/mass_pre_w.Rd | 108 +-- tsmp-0.4.8/tsmp/man/mass_v2.Rd | 143 ++--- tsmp-0.4.8/tsmp/man/mass_v3.Rd | 155 ++--- tsmp-0.4.8/tsmp/man/mass_weighted.Rd | 143 ++--- tsmp-0.4.8/tsmp/man/min_mp_idx.Rd | 54 - tsmp-0.4.8/tsmp/man/motifs.Rd |only tsmp-0.4.8/tsmp/man/motifs_discords_small.Rd |only tsmp-0.4.8/tsmp/man/mp_fluss_data.Rd | 88 +-- tsmp-0.4.8/tsmp/man/mp_gait_data.Rd | 46 - tsmp-0.4.8/tsmp/man/mp_meat_data.Rd | 94 +-- tsmp-0.4.8/tsmp/man/mp_test_data.Rd | 76 +- tsmp-0.4.8/tsmp/man/mp_toy_data.Rd | 58 +- tsmp-0.4.8/tsmp/man/mpdist.Rd |only tsmp-0.4.8/tsmp/man/mpx.Rd |only tsmp-0.4.8/tsmp/man/mstomp.Rd | 206 +++---- tsmp-0.4.8/tsmp/man/pipe.Rd | 34 - tsmp-0.4.8/tsmp/man/plot.Rd | 281 ++++++---- tsmp-0.4.8/tsmp/man/plot_arcs.Rd | 132 ++-- tsmp-0.4.8/tsmp/man/pmp.Rd |only tsmp-0.4.8/tsmp/man/pmp_upper_bound.Rd |only tsmp-0.4.8/tsmp/man/read.Rd |only tsmp-0.4.8/tsmp/man/remove_class.Rd | 54 - tsmp-0.4.8/tsmp/man/salient_mds.Rd | 90 +-- tsmp-0.4.8/tsmp/man/salient_score.Rd | 90 +-- tsmp-0.4.8/tsmp/man/salient_subsequences.Rd | 136 ++-- tsmp-0.4.8/tsmp/man/scrimp.Rd | 146 ++--- tsmp-0.4.8/tsmp/man/sdts_predict.Rd | 117 ++-- tsmp-0.4.8/tsmp/man/sdts_score.Rd | 115 ++-- tsmp-0.4.8/tsmp/man/sdts_train.Rd | 152 ++--- tsmp-0.4.8/tsmp/man/set_data.Rd | 46 - tsmp-0.4.8/tsmp/man/simple_fast.Rd | 105 +-- tsmp-0.4.8/tsmp/man/stamp.Rd | 203 +++---- tsmp-0.4.8/tsmp/man/stomp.Rd | 169 +++--- tsmp-0.4.8/tsmp/man/stompi_update.Rd | 60 +- tsmp-0.4.8/tsmp/man/tsmp-deprecated.Rd | 52 + tsmp-0.4.8/tsmp/man/tsmp.Rd | 334 ++++++------ tsmp-0.4.8/tsmp/man/valmod.Rd | 153 ++--- tsmp-0.4.8/tsmp/man/visualize.Rd |only tsmp-0.4.8/tsmp/man/write.Rd |only tsmp-0.4.8/tsmp/src |only tsmp-0.4.8/tsmp/tests/figs/deps.txt | 6 tsmp-0.4.8/tsmp/tests/figs/testing-api-visualize |only tsmp-0.4.8/tsmp/tests/figs/testing-plots/plot-snippet.svg |only tsmp-0.4.8/tsmp/tests/prints/chain-print | 24 tsmp-0.4.8/tsmp/tests/prints/discord-print | 2 tsmp-0.4.8/tsmp/tests/prints/mmotif-print | 2 tsmp-0.4.8/tsmp/tests/prints/motif-print | 24 tsmp-0.4.8/tsmp/tests/prints/motif_valmod-print | 2 tsmp-0.4.8/tsmp/tests/prints/salient-print | 22 tsmp-0.4.8/tsmp/tests/prints/snippet-print |only tsmp-0.4.8/tsmp/tests/prints/valmod-print | 12 tsmp-0.4.8/tsmp/tests/spelling.R | 10 tsmp-0.4.8/tsmp/tests/testthat/test-analyze.R |only tsmp-0.4.8/tsmp/tests/testthat/test-annotation.R | 88 +-- tsmp-0.4.8/tsmp/tests/testthat/test-basics.R | 19 tsmp-0.4.8/tsmp/tests/testthat/test-compute.R |only tsmp-0.4.8/tsmp/tests/testthat/test-discords.R |only tsmp-0.4.8/tsmp/tests/testthat/test-find-chains.R | 32 - tsmp-0.4.8/tsmp/tests/testthat/test-find-discord.R | 4 tsmp-0.4.8/tsmp/tests/testthat/test-fluss.R | 2 tsmp-0.4.8/tsmp/tests/testthat/test-mass-agressive.R |only tsmp-0.4.8/tsmp/tests/testthat/test-misc.R | 84 +-- tsmp-0.4.8/tsmp/tests/testthat/test-motifs.R |only tsmp-0.4.8/tsmp/tests/testthat/test-mpdist.R |only tsmp-0.4.8/tsmp/tests/testthat/test-mstomp-search.R | 2 tsmp-0.4.8/tsmp/tests/testthat/test-plot-print.R | 6 tsmp-0.4.8/tsmp/tests/testthat/test-salient.R | 6 tsmp-0.4.8/tsmp/tests/testthat/test-sdts.R | 96 +-- tsmp-0.4.8/tsmp/tests/testthat/test-serialize.R |only tsmp-0.4.8/tsmp/tests/testthat/test-simple.R | 102 +-- tsmp-0.4.8/tsmp/tests/testthat/test-stamps.R | 119 ++-- tsmp-0.4.8/tsmp/tests/testthat/test-stomp-search.R | 66 +- tsmp-0.4.8/tsmp/tests/testthat/test-subset.R | 87 ++- tsmp-0.4.8/tsmp/tests/testthat/test-valmod.R | 54 - tsmp-0.4.8/tsmp/tests/testthat/test-visualize.R |only 164 files changed, 5520 insertions(+), 3849 deletions(-)
Title: 'TRFLP' Analysis and Matching Package for R
Description: Matching terminal restriction fragment length
polymorphism ('TRFLP') profiles between unknown samples and a
database of known samples. 'TRAMPR' facilitates analysis of
many unknown profiles at once, and provides tools for working
directly with electrophoresis output through to generating
summaries suitable for community analyses with R's rich set of
statistical functions. 'TRAMPR' also resolves the issues of
multiple 'TRFLP' profiles within a species, and shared 'TRFLP'
profiles across species.
Author: Rich FitzJohn & Ian Dickie
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between TRAMPR versions 1.0-8 dated 2016-06-13 and 1.0-9 dated 2020-02-28
ChangeLog | 4 ++++ DESCRIPTION | 12 ++++++------ MD5 | 15 ++++++++------- README.md |only build/vignette.rds |binary inst/doc/TRAMPRdemo.R | 2 +- inst/doc/TRAMPRdemo.Rnw | 2 +- inst/doc/TRAMPRdemo.pdf |binary vignettes/TRAMPRdemo.Rnw | 2 +- 9 files changed, 21 insertions(+), 16 deletions(-)
Title: Multivariate Data Handling with S4 Classes and Sparse Matrices
Description: An S4 update of the 'mefa' package
using sparse matrices for enhanced efficiency.
Sparse array-like objects are supported via
lists of sparse matrices.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between mefa4 versions 0.3-6 dated 2019-06-21 and 0.3-7 dated 2020-02-28
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/redistribute.R | 9 ++++++--- man/Mefa.Rd | 17 ++++++++++------- man/Melt.Rd | 5 +++-- man/Xtab.Rd | 6 ++++-- man/groupSums.Rd | 31 +++++++++++++++++-------------- man/mbind.Rd | 9 ++++++--- man/nameAlnum.Rd | 9 ++++++--- man/samp.Rd | 9 ++++++--- tests/mefa4examples.R | 18 ++++++++++++------ 11 files changed, 84 insertions(+), 57 deletions(-)
Title: Tools for Healthcare Machine Learning
Description: A machine learning toolbox tailored to healthcare data.
Author: Levi Thatcher [aut],
Michael Levy [aut],
Mike Mastanduno [aut, cre],
Taylor Larsen [aut],
Taylor Miller [aut],
Rex Sumsion [aut]
Maintainer: Mike Mastanduno <michael.mastanduno@healthcatalyst.com>
Diff between healthcareai versions 2.3.0 dated 2018-12-12 and 2.4.0 dated 2020-02-28
DESCRIPTION | 22 - MD5 | 150 +++++----- NAMESPACE | 1 R/control_chart.R | 4 R/db_connections.R | 2 R/explore.R | 4 R/get_thresholds.R | 4 R/globals.R | 3 R/hcai-impute.R | 3 R/interpret.R | 2 R/list_variables.R | 2 R/missingness.R | 4 R/plot_predictions.R | 12 R/predict.R | 5 R/prep_data.R | 29 + R/prep_data_utils.R | 2 R/step_dummy_hcai.R | 2 R/step_hcai_missing.R | 2 R/training_setup.R | 6 R/utilities.R | 2 R/variable_importance.R | 2 README.md | 2 man/add_best_levels.Rd | 31 +- man/as.model_list.Rd | 16 - man/build_connection_string.Rd | 10 man/control_chart.Rd | 18 - man/db_read.Rd | 1 man/explore.Rd | 9 man/flash_models.Rd | 13 man/get_hyperparameter_defaults.Rd | 17 - man/get_thresholds.Rd | 3 man/hcai_impute.Rd | 10 man/healthcareai.Rd | 1 man/impute.Rd | 13 man/machine_learn.Rd | 17 - man/missingness.Rd | 7 man/pip.Rd | 15 - man/plot.explore_df.Rd | 25 + man/plot.interpret.Rd | 13 man/plot.missingness.Rd | 12 man/plot.model_list.Rd | 3 man/plot.predicted_df.Rd | 36 +- man/plot.thresholds_df.Rd | 14 man/plot.variable_importance.Rd | 13 man/predict.model_list.Rd | 11 man/prep_data.Rd | 24 + man/step_add_levels.Rd | 13 man/step_date_hcai.Rd | 13 man/step_dummy_hcai.Rd | 19 - man/step_locfimpute.Rd | 10 man/step_missing.Rd | 11 man/tune_models.Rd | 16 - tests/testthat/Rplots.pdf |binary tests/testthat/rmodel_info_LMM.rda |only tests/testthat/rmodel_info_RF.rda |only tests/testthat/rmodel_info_XGB.rda |only tests/testthat/rmodel_info_lasso.rda |only tests/testthat/rmodel_info_non-deterministic-tree-ensemble_RF.rda |only tests/testthat/rmodel_probability_LMM.rda |only tests/testthat/rmodel_probability_RF.rda |only tests/testthat/rmodel_probability_XGB.rda |only tests/testthat/rmodel_probability_lasso.rda |only tests/testthat/rmodel_probability_non-deterministic-tree-ensemble_RF.rda |only tests/testthat/test-db-connections.R | 6 tests/testthat/test-explore.R | 10 tests/testthat/test-get_best_levels.R | 4 tests/testthat/test-hcai-impute.R | 28 - tests/testthat/test-impute.r | 34 +- tests/testthat/test-interpret.R | 2 tests/testthat/test-missingness.R | 14 tests/testthat/test-model_list.R | 23 - tests/testthat/test-pip.R | 12 tests/testthat/test-predict.R | 29 - tests/testthat/test-prep_data.R | 11 tests/testthat/test-split_train_test.R | 5 tests/testthat/test-step-hcai-missing.R | 24 - tests/testthat/test-step_add_levels.R | 2 tests/testthat/test-step_locfimpute.R | 4 tests/testthat/test-tune_models.R | 2 tests/testthat/test-variable_importance.R | 4 tests/testthat/test-zlint.R | 17 - 81 files changed, 590 insertions(+), 320 deletions(-)
Title: General Polygon Clipping Library for R
Description: General polygon clipping routines for R based on Alan Murta's C library.
Author: Roger D. Peng <rpeng@jhsph.edu> with contributions from Duncan Murdoch and Barry Rowlingson; GPC library by Alan Murta
Maintainer: Roger D. Peng <rpeng@jhsph.edu>
Diff between gpclib versions 1.5-5 dated 2013-04-01 and 1.5-6 dated 2020-02-28
gpclib-1.5-5/gpclib/tests/bug1.R |only gpclib-1.5-5/gpclib/tests/bug1.Rout.save |only gpclib-1.5-5/gpclib/tests/bug1_data.RData |only gpclib-1.5-6/gpclib/DESCRIPTION | 18 +-- gpclib-1.5-6/gpclib/MD5 | 15 +- gpclib-1.5-6/gpclib/NAMESPACE | 4 gpclib-1.5-6/gpclib/R/Rgpc.R | 11 - gpclib-1.5-6/gpclib/src/Rgpc.c | 145 +++----------------------- gpclib-1.5-6/gpclib/src/gpc.c | 46 -------- gpclib-1.5-6/gpclib/tests/reg-tests.Rout.save | 16 +- 10 files changed, 50 insertions(+), 205 deletions(-)
Title: Visualization and Estimation of Effect Sizes
Description: A variety of methods are provided to estimate and visualize
distributional differences in terms of effect sizes. Particular emphasis
is upon evaluating differences between two or more distributions across
the entire scale, rather than at a single point (e.g., differences in
means). For example, Probability-Probability (PP) plots display the
difference between two or more distributions, matched by their empirical
CDFs (see Ho and Reardon, 2012; <doi:10.3102/1076998611411918>), allowing
for examinations of where on the scale distributional differences are
largest or smallest. The area under the PP curve (AUC) is an effect-size
metric, corresponding to the probability that a randomly selected
observation from the x-axis distribution will have a higher value
than a randomly selected observation from the y-axis distribution.
Binned effect size plots are also available, in which the distributions
are split into bins (set by the user) and separate effect sizes (Cohen's
d) are produced for each bin - again providing a means to evaluate the
consistency (or lack thereof) of the difference between two or more
distributions at different points on the scale. Evaluation of empirical
CDFs is also provided, with built-in arguments for providing annotations
to help evaluate distributional differences at specific points (e.g.,
semi-transparent shading). All function take a consistent argument
structure. Calculation of specific effect sizes is also possible. The
following effect sizes are estimable: (a) Cohen's d, (b) Hedges' g,
(c) percentage above a cut, (d) transformed (normalized) percentage above
a cut, (e) area under the PP curve, and (f) the V statistic (see Ho,
2009; <doi:10.3102/1076998609332755>), which essentially transforms the
area under the curve to standard deviation units. By default, effect sizes
are calculated for all possible pairwise comparisons, but a reference
group (distribution) can be specified.
Author: Daniel Anderson [aut, cre]
Maintainer: Daniel Anderson <daniela@uoregon.edu>
Diff between esvis versions 0.2.0 dated 2018-04-09 and 0.3.0 dated 2020-02-28
esvis-0.2.0/esvis/R/binned_utils.R |only esvis-0.2.0/esvis/R/helper_funs.R |only esvis-0.2.0/esvis/R/pp_utils.R |only esvis-0.2.0/esvis/man/cdfs.Rd |only esvis-0.2.0/esvis/man/col_hue.Rd |only esvis-0.2.0/esvis/man/col_scheme.Rd |only esvis-0.2.0/esvis/man/create_base_legend.Rd |only esvis-0.2.0/esvis/man/create_cut_refs.Rd |only esvis-0.2.0/esvis/man/create_legend.Rd |only esvis-0.2.0/esvis/man/create_vec.Rd |only esvis-0.2.0/esvis/man/empty_plot.Rd |only esvis-0.2.0/esvis/man/parse_form.Rd |only esvis-0.2.0/esvis/man/pooled_sd.Rd |only esvis-0.2.0/esvis/man/pp_annotate.Rd |only esvis-0.2.0/esvis/man/pp_calcs.Rd |only esvis-0.2.0/esvis/man/probs.Rd |only esvis-0.2.0/esvis/man/qtile_es.Rd |only esvis-0.2.0/esvis/man/qtile_mean_diffs.Rd |only esvis-0.2.0/esvis/man/qtile_n.Rd |only esvis-0.2.0/esvis/man/seg_match.Rd |only esvis-0.2.0/esvis/man/themes.Rd |only esvis-0.2.0/esvis/tests/testthat/test-binned_es_plot.R |only esvis-0.2.0/esvis/tests/testthat/test-cdfs.R |only esvis-0.2.0/esvis/tests/testthat/test-pac.R |only esvis-0.2.0/esvis/tests/testthat/test-parse_form.R |only esvis-0.2.0/esvis/tests/testthat/test-probs.R |only esvis-0.2.0/esvis/tests/testthat/test-tpac.R |only esvis-0.3.0/esvis/DESCRIPTION | 15 esvis-0.3.0/esvis/MD5 | 89 - esvis-0.3.0/esvis/NAMESPACE | 94 + esvis-0.3.0/esvis/NEWS.md | 14 esvis-0.3.0/esvis/R/binned_es_plot.R | 367 ++---- esvis-0.3.0/esvis/R/ecdf_plot.R | 277 +--- esvis-0.3.0/esvis/R/es_calcs.R | 1019 ++++++++--------- esvis-0.3.0/esvis/R/esvis-package.R |only esvis-0.3.0/esvis/R/pp_plot.R | 430 ++----- esvis-0.3.0/esvis/R/seda.R | 4 esvis-0.3.0/esvis/R/utils.R |only esvis-0.3.0/esvis/README.md | 233 ++- esvis-0.3.0/esvis/man/auc.Rd | 98 - esvis-0.3.0/esvis/man/binned_es.Rd |only esvis-0.3.0/esvis/man/binned_plot.Rd | 200 +-- esvis-0.3.0/esvis/man/coh.Rd |only esvis-0.3.0/esvis/man/coh_d.Rd | 62 - esvis-0.3.0/esvis/man/descrip_stats.Rd |only esvis-0.3.0/esvis/man/ecdf_fun.Rd |only esvis-0.3.0/esvis/man/ecdf_plot.Rd | 154 +- esvis-0.3.0/esvis/man/esvis-package.Rd |only esvis-0.3.0/esvis/man/hedg.Rd |only esvis-0.3.0/esvis/man/hedg_g.Rd | 59 esvis-0.3.0/esvis/man/pac.Rd | 87 - esvis-0.3.0/esvis/man/pac_compare.Rd |only esvis-0.3.0/esvis/man/paired_ecdf.Rd |only esvis-0.3.0/esvis/man/pp_plot.Rd | 210 +-- esvis-0.3.0/esvis/man/psd.Rd |only esvis-0.3.0/esvis/man/seda.Rd | 4 esvis-0.3.0/esvis/man/tpac.Rd | 88 - esvis-0.3.0/esvis/man/tpac_compare.Rd |only esvis-0.3.0/esvis/man/v.Rd | 76 - esvis-0.3.0/esvis/tests/testthat/test-auc.R | 51 esvis-0.3.0/esvis/tests/testthat/test-coh_d.R | 54 esvis-0.3.0/esvis/tests/testthat/test-ecdf_plot.R | 82 - esvis-0.3.0/esvis/tests/testthat/test-hedge_g.R | 55 esvis-0.3.0/esvis/tests/testthat/test-pp_plot.R | 149 -- esvis-0.3.0/esvis/tests/testthat/test-v.R | 54 65 files changed, 1955 insertions(+), 2070 deletions(-)
Title: Animation of Observed Trajectories Using Spline-Based
Interpolation
Description: Animation of observed trajectories using spline-based interpolation (see for example, Buderman, F. E., Hooten, M. B., Ivan, J. S. and Shenk, T. M. (2016), <doi:10.1111/2041-210X.12465> "A functional model for characterizing long-distance movement behaviour". Methods Ecol Evol). Intended to be used exploratory data analysis, and perhaps for preparation of presentations.
Author: Henry Scharf
Maintainer: Henry Scharf <hscharf@sdsu.edu>
Diff between anipaths versions 0.9.7 dated 2019-02-26 and 0.9.8 dated 2020-02-28
DESCRIPTION | 18 +- MD5 | 23 +-- NAMESPACE | 2 NEWS | 11 + R/animate_paths.R | 56 ++++--- build/vignette.rds |binary inst/doc/anipaths.R | 2 inst/doc/anipaths.Rmd | 6 inst/doc/anipaths.html | 357 +++++++++++++++++++++++++++---------------------- man/animate_paths.Rd | 77 ++++++++-- man/plot.Rd | 3 vignettes/anipaths.Rmd | 6 vignettes/anipaths.md |only 13 files changed, 332 insertions(+), 229 deletions(-)
Title: Audit and Research Functions for Transplantation
Description: A set of vectorised functions to calculate medical equations used in transplantation,
focused mainly on transplantation of abdominal organs. These functions include donor and recipient
risk indices as used by NHS Blood & Transplant, OPTN/UNOS and Eurotransplant, tools for
quantifying HLA mismatches, functions for calculating estimated glomerular filtration rate (eGFR),
a function to calculate the APRI (AST to platelet ratio) score used in initial screening of suitability to receive a
transplant from a hepatitis C seropositive donor and some biochemical unit converter functions.
All functions are designed to work with either US or international units.
References for the equations are provided in the vignettes and function documentation.
Author: John Asher [aut, cre] (<https://orcid.org/0000-0001-8735-6453>)
Maintainer: John Asher <john.asher@outlook.com>
Diff between transplantr versions 0.1.0 dated 2020-01-07 and 0.2.0 dated 2020-02-28
DESCRIPTION | 8 +- MD5 | 60 ++++++++++------ NAMESPACE | 16 ++++ NEWS.md | 16 ++++ R/liver_scores.R |only R/nankivell_walser.R |only R/ukkri.R | 3 README.md | 5 + build/vignette.rds |binary inst/doc/egfr.R | 18 ++-- inst/doc/egfr.Rmd | 10 ++ inst/doc/egfr.html | 16 ++-- inst/doc/hla_mismatch_grade.R | 8 +- inst/doc/hla_mismatch_grade.html | 11 +-- inst/doc/kidney_risk_scores.R | 24 +++--- inst/doc/kidney_risk_scores.html | 21 ++--- inst/doc/liver_recipient_scoring.R | 55 +++++++++++++-- inst/doc/liver_recipient_scoring.Rmd | 105 +++++++++++++++++++++++++++- inst/doc/liver_recipient_scoring.html | 124 +++++++++++++++++++++++++--------- man/bar_score.Rd |only man/et_dri.Rd |only man/liver_dri.Rd |only man/nankivell.Rd |only man/nankivell_US.Rd |only man/nankivell_spk.Rd |only man/nankivell_spk_US.Rd |only man/p_soft.Rd |only man/p_soft_US.Rd |only man/pedi_soft.Rd |only man/soft.Rd |only man/soft2.Rd |only man/soft2_US.Rd |only man/soft_US.Rd |only man/walser.Rd |only man/walser_US.Rd |only tests/testthat/test_egfr.R | 18 ++++ tests/testthat/test_kri.R | 2 tests/testthat/test_liver.R | 34 +++++++++ vignettes/egfr.Rmd | 10 ++ vignettes/liver_recipient_scoring.Rmd | 105 +++++++++++++++++++++++++++- 40 files changed, 544 insertions(+), 125 deletions(-)
Title: Tidy Verbs for Fast Data Manipulation
Description: A toolkit of tidy data manipulation verbs with 'data.table' as the backend.
Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table',
'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain.
This package is inspired by 'maditr', but follows a different philosophy of design,
such as prohibiting in place replacement and used a "_dt" suffix API.
Also, 'tidyfst' would introduce more tidy data verbs from (and for) other packages,
including but not limited to 'fst','tidyverse' and 'data.table'.
Author: Tian-Yuan Huang [aut, cre] (<https://orcid.org/0000-0002-3591-4203>)
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between tidyfst versions 0.6.6 dated 2020-02-24 and 0.6.9 dated 2020-02-28
tidyfst-0.6.6/tidyfst/R/show_tibble.R |only tidyfst-0.6.6/tidyfst/inst/doc/example5_tibble.R |only tidyfst-0.6.6/tidyfst/inst/doc/example5_tibble.Rmd |only tidyfst-0.6.6/tidyfst/inst/doc/example5_tibble.html |only tidyfst-0.6.6/tidyfst/man/select_dt.Rd |only tidyfst-0.6.6/tidyfst/man/show_tibble.Rd |only tidyfst-0.6.6/tidyfst/vignettes/example5_tibble.Rmd |only tidyfst-0.6.9/tidyfst/DESCRIPTION | 10 tidyfst-0.6.9/tidyfst/MD5 | 50 - tidyfst-0.6.9/tidyfst/NAMESPACE | 3 tidyfst-0.6.9/tidyfst/R/all_at_if.R | 30 tidyfst-0.6.9/tidyfst/R/group_dt.R | 21 tidyfst-0.6.9/tidyfst/R/mutate_when.R | 3 tidyfst-0.6.9/tidyfst/R/on_attach.R | 1 tidyfst-0.6.9/tidyfst/R/select_dt.R | 43 + tidyfst-0.6.9/tidyfst/build/vignette.rds |binary tidyfst-0.6.9/tidyfst/inst/doc/example1_intro.R | 267 ++++++- tidyfst-0.6.9/tidyfst/inst/doc/example1_intro.Rmd | 183 +++++ tidyfst-0.6.9/tidyfst/inst/doc/example1_intro.html | 644 +++++-------------- tidyfst-0.6.9/tidyfst/inst/doc/example2_join.html | 370 ++++++---- tidyfst-0.6.9/tidyfst/inst/doc/example3_reshape.html | 147 ++-- tidyfst-0.6.9/tidyfst/inst/doc/example4_nest.Rmd | 2 tidyfst-0.6.9/tidyfst/inst/doc/example4_nest.html | 91 +- tidyfst-0.6.9/tidyfst/inst/doc/example5_fst.R |only tidyfst-0.6.9/tidyfst/inst/doc/example5_fst.Rmd |only tidyfst-0.6.9/tidyfst/inst/doc/example5_fst.html |only tidyfst-0.6.9/tidyfst/man/all_at_if.Rd | 20 tidyfst-0.6.9/tidyfst/man/group_dt.Rd | 12 tidyfst-0.6.9/tidyfst/man/select.Rd |only tidyfst-0.6.9/tidyfst/vignettes/example1_intro.Rmd | 183 +++++ tidyfst-0.6.9/tidyfst/vignettes/example4_nest.Rmd | 2 tidyfst-0.6.9/tidyfst/vignettes/example5_fst.Rmd |only 32 files changed, 1237 insertions(+), 845 deletions(-)
Title: Generalized Label Formatting
Description: The 'spork' syntax describes
label formatting concisely, supporting
mixed nesting of subscripts and superscripts
to arbitrary depth. It intends to be easy
to read and write in plain text, and easy
to convert to equivalent presentations
in 'plotmath' and 'latex'. Greek symbols
and a multiplication symbol are explicitly
supported. See ?as_spork and ?as_previews.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between spork versions 0.1.1 dated 2020-02-27 and 0.1.6 dated 2020-02-28
spork-0.1.1/spork/R/spork-to-latex.R |only spork-0.1.1/spork/R/spork-to-plotmath.R |only spork-0.1.1/spork/R/sporklet.R |only spork-0.1.1/spork/man/spork_to_latex.Rd |only spork-0.1.1/spork/man/spork_to_plotmath.Rd |only spork-0.1.1/spork/man/sporklet.Rd |only spork-0.1.6/spork/DESCRIPTION | 8 spork-0.1.6/spork/MD5 | 88 ++++--- spork-0.1.6/spork/NAMESPACE | 16 + spork-0.1.6/spork/R/concatenate.R |only spork-0.1.6/spork/R/expression.R |only spork-0.1.6/spork/R/latex.R |only spork-0.1.6/spork/R/plotmath.R |only spork-0.1.6/spork/R/preview.R | 16 + spork-0.1.6/spork/R/spar.R |only spork-0.1.6/spork/R/spork.R | 267 ++++-------------------- spork-0.1.6/spork/man/as.expression.plotmath.Rd | 114 +++++----- spork-0.1.6/spork/man/as.list.spork.Rd |only spork-0.1.6/spork/man/as.png.plotmath.Rd | 116 +++++----- spork-0.1.6/spork/man/as.png.spork.Rd | 117 +++++----- spork-0.1.6/spork/man/as_latex.Rd | 62 ++--- spork-0.1.6/spork/man/as_latex.spar.Rd |only spork-0.1.6/spork/man/as_latex.spork.Rd | 95 +++++--- spork-0.1.6/spork/man/as_plotmath.Rd | 68 +++--- spork-0.1.6/spork/man/as_plotmath.spar.Rd |only spork-0.1.6/spork/man/as_plotmath.spork.Rd | 96 +++++--- spork-0.1.6/spork/man/as_preview.Rd | 87 +++---- spork-0.1.6/spork/man/as_preview.latex.Rd | 121 +++++----- spork-0.1.6/spork/man/as_preview.plotmath.Rd | 88 +++---- spork-0.1.6/spork/man/as_previews.Rd | 70 +++--- spork-0.1.6/spork/man/as_previews.spork.Rd | 138 +++++++----- spork-0.1.6/spork/man/as_spar.Rd |only spork-0.1.6/spork/man/as_spar.spork.Rd |only spork-0.1.6/spork/man/as_spork.Rd | 111 +++++---- spork-0.1.6/spork/man/as_spork.character.Rd | 77 ++++-- spork-0.1.6/spork/man/as_spork.factor.Rd | 70 +++--- spork-0.1.6/spork/man/as_spork.spork.Rd |only spork-0.1.6/spork/man/concatenate.NULL.Rd |only spork-0.1.6/spork/man/concatenate.Rd |only spork-0.1.6/spork/man/concatenate.character.Rd |only spork-0.1.6/spork/man/concatenate.latex.Rd |only spork-0.1.6/spork/man/concatenate.plotmath.Rd |only spork-0.1.6/spork/man/ggplot.plotmath.Rd | 97 ++++---- spork-0.1.6/spork/man/ggplot.spork.Rd | 97 ++++---- spork-0.1.6/spork/man/goodToken.Rd | 71 +++--- spork-0.1.6/spork/man/latexToken.Rd | 100 +++++--- spork-0.1.6/spork/man/plotmathToken.Rd | 97 ++++---- spork-0.1.6/spork/man/reexports.Rd | 32 +- spork-0.1.6/spork/man/sub-.latex.Rd | 78 +++---- spork-0.1.6/spork/man/sub-.plotmath.Rd | 83 +++---- spork-0.1.6/spork/man/sub-.spork.Rd | 84 +++---- spork-0.1.6/spork/man/sub-sub-.latex.Rd | 78 +++---- spork-0.1.6/spork/man/sub-sub-.plotmath.Rd | 83 +++---- spork-0.1.6/spork/man/sub-sub-.spork.Rd | 84 +++---- spork-0.1.6/spork/tests/testthat/Rplots.pdf |binary spork-0.1.6/spork/tests/testthat/test-spork.R | 164 +++++++++++++- 56 files changed, 1571 insertions(+), 1402 deletions(-)
Title: Detecting Politeness Features in Text
Description: Detecting markers of politeness in English natural language. This package allows researchers to easily visualize and quantify politeness between groups of documents. This package combines prior research on the linguistic markers of politeness (Brown & Levinson, 1987 <http://psycnet.apa.org/record/1987-97641-000>; Danescu-Niculescu-Mizil et al., 2013 <arXiv:1306.6078>; Voigt et al., 2017 <doi:10.1073/pnas.1702413114>). We thank the Spencer Foundation, the Hewlett Foundation, and Harvard's Institute for Quantitative Social Science for support.
Author: Mike Yeomans, Alejandro Kantor, Dustin Tingley
Maintainer: Mike Yeomans <mk.yeomans@gmail.com>
Diff between politeness versions 0.5.0 dated 2020-02-26 and 0.5.1 dated 2020-02-28
DESCRIPTION | 10 +++++----- MD5 | 7 ++++--- data/receptTrain.rdata |binary inst/doc/politeness.html | 6 +++--- tests/testthat/test-receptiveness.R |only 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Perform Pharmacokinetic Non-Compartmental Analysis
Description: Compute standard Non-Compartmental Analysis (NCA) parameters for
typical pharmacokinetic analyses and summarize them.
Author: Bill Denney [aut, cre] (<https://orcid.org/0000-0002-5759-428X>),
Clare Buckeridge [aut],
Sridhar Duvvuri [ctb]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between PKNCA versions 0.9.1 dated 2019-07-29 and 0.9.2 dated 2020-02-28
PKNCA-0.9.1/PKNCA/R/actual_time_calc.R |only PKNCA-0.9.2/PKNCA/DESCRIPTION | 18 PKNCA-0.9.2/PKNCA/MD5 | 340 +- PKNCA-0.9.2/PKNCA/NAMESPACE | 9 PKNCA-0.9.2/PKNCA/NEWS.md | 27 PKNCA-0.9.2/PKNCA/R/001-add.interval.col.R | 19 PKNCA-0.9.2/PKNCA/R/002-pk.business.rules.R | 108 PKNCA-0.9.2/PKNCA/R/AIC.list.R | 2 PKNCA-0.9.2/PKNCA/R/PKNCA.R | 14 PKNCA-0.9.2/PKNCA/R/PKNCA.options.R | 2 PKNCA-0.9.2/PKNCA/R/auc.R | 140 PKNCA-0.9.2/PKNCA/R/aucint.R | 19 PKNCA-0.9.2/PKNCA/R/check.intervals.R | 206 - PKNCA-0.9.2/PKNCA/R/choose.intervals.R | 100 PKNCA-0.9.2/PKNCA/R/class-PKNCAconc.R | 23 PKNCA-0.9.2/PKNCA/R/class-PKNCAdose.R | 4 PKNCA-0.9.2/PKNCA/R/class-PKNCAresults.R | 123 PKNCA-0.9.2/PKNCA/R/cleaners.R | 2 PKNCA-0.9.2/PKNCA/R/general.functions.R | 38 PKNCA-0.9.2/PKNCA/R/half.life.R | 68 PKNCA-0.9.2/PKNCA/R/interpolate.conc.R | 227 - PKNCA-0.9.2/PKNCA/R/parseFormula.R | 3 PKNCA-0.9.2/PKNCA/R/pk.calc.all.R | 67 PKNCA-0.9.2/PKNCA/R/pk.calc.simple.R | 9 PKNCA-0.9.2/PKNCA/R/provenance.R | 2 PKNCA-0.9.2/PKNCA/R/superposition.R | 1 PKNCA-0.9.2/PKNCA/R/time_calc.R |only PKNCA-0.9.2/PKNCA/R/tss.R | 14 PKNCA-0.9.2/PKNCA/R/tss.monoexponential.R | 114 PKNCA-0.9.2/PKNCA/R/tss.stepwise.linear.R | 7 PKNCA-0.9.2/PKNCA/README.md | 4 PKNCA-0.9.2/PKNCA/build/vignette.rds |binary PKNCA-0.9.2/PKNCA/inst/doc/AUC-Calculation-with-PKNCA.R | 24 PKNCA-0.9.2/PKNCA/inst/doc/AUC-Calculation-with-PKNCA.html | 11 PKNCA-0.9.2/PKNCA/inst/doc/Data-Cleaning-in-PKNCA.html | 7 PKNCA-0.9.2/PKNCA/inst/doc/Example-theophylline.R | 30 PKNCA-0.9.2/PKNCA/inst/doc/Example-theophylline.html | 175 - PKNCA-0.9.2/PKNCA/inst/doc/Introduction-and-Usage.R | 28 PKNCA-0.9.2/PKNCA/inst/doc/Introduction-and-Usage.html | 101 PKNCA-0.9.2/PKNCA/inst/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.R | 8 PKNCA-0.9.2/PKNCA/inst/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.html | 11 PKNCA-0.9.2/PKNCA/inst/doc/Options-for-Controlling-PKNCA.R | 4 PKNCA-0.9.2/PKNCA/inst/doc/Options-for-Controlling-PKNCA.html | 13 PKNCA-0.9.2/PKNCA/inst/doc/PKNCA-validation.R | 14 PKNCA-0.9.2/PKNCA/inst/doc/PKNCA-validation.Rmd | 10 PKNCA-0.9.2/PKNCA/inst/doc/PKNCA-validation.html | 44 PKNCA-0.9.2/PKNCA/inst/doc/Selection-of-Calculation-Intervals.R | 28 PKNCA-0.9.2/PKNCA/inst/doc/Selection-of-Calculation-Intervals.html | 11 PKNCA-0.9.2/PKNCA/inst/doc/Superposition.R | 26 PKNCA-0.9.2/PKNCA/inst/doc/Superposition.html | 21 PKNCA-0.9.2/PKNCA/inst/doc/Writing-Parameter-Functions.R | 2 PKNCA-0.9.2/PKNCA/inst/doc/Writing-Parameter-Functions.Rmd | 4 PKNCA-0.9.2/PKNCA/inst/doc/Writing-Parameter-Functions.html | 14 PKNCA-0.9.2/PKNCA/man/AIC.list.Rd | 58 PKNCA-0.9.2/PKNCA/man/PKNCA.Rd | 72 PKNCA-0.9.2/PKNCA/man/PKNCA.choose.option.Rd | 61 PKNCA-0.9.2/PKNCA/man/PKNCA.options.Rd | 125 PKNCA-0.9.2/PKNCA/man/PKNCA.options.describe.Rd | 38 PKNCA-0.9.2/PKNCA/man/PKNCA.set.summary.Rd | 125 PKNCA-0.9.2/PKNCA/man/PKNCAconc.Rd | 160 - PKNCA-0.9.2/PKNCA/man/PKNCAdata.Rd | 141 PKNCA-0.9.2/PKNCA/man/PKNCAdose.Rd | 163 - PKNCA-0.9.2/PKNCA/man/PKNCAresults.Rd | 66 PKNCA-0.9.2/PKNCA/man/add.interval.col.Rd | 199 - PKNCA-0.9.2/PKNCA/man/addProvenance.Rd | 52 PKNCA-0.9.2/PKNCA/man/adj.r.squared.Rd | 36 PKNCA-0.9.2/PKNCA/man/as.data.frame.PKNCAresults.Rd | 49 PKNCA-0.9.2/PKNCA/man/business.mean.Rd | 138 PKNCA-0.9.2/PKNCA/man/check.conc.time.Rd | 74 PKNCA-0.9.2/PKNCA/man/check.conversion.Rd | 46 PKNCA-0.9.2/PKNCA/man/check.interval.deps.Rd | 61 PKNCA-0.9.2/PKNCA/man/check.interval.specification.Rd | 77 PKNCA-0.9.2/PKNCA/man/checkProvenance.Rd | 44 PKNCA-0.9.2/PKNCA/man/choose.auc.intervals.Rd | 114 PKNCA-0.9.2/PKNCA/man/clean.conc.blq.Rd | 142 PKNCA-0.9.2/PKNCA/man/clean.conc.na.Rd | 74 PKNCA-0.9.2/PKNCA/man/exclude.Rd | 123 PKNCA-0.9.2/PKNCA/man/exclude_nca.Rd | 117 PKNCA-0.9.2/PKNCA/man/find.tau.Rd | 84 PKNCA-0.9.2/PKNCA/man/findOperator.Rd | 65 PKNCA-0.9.2/PKNCA/man/fit_half_life.Rd | 60 PKNCA-0.9.2/PKNCA/man/formula.PKNCAconc.Rd | 44 PKNCA-0.9.2/PKNCA/man/formula.parseFormula.Rd | 62 PKNCA-0.9.2/PKNCA/man/geomean.Rd | 82 PKNCA-0.9.2/PKNCA/man/get.best.model.Rd | 46 PKNCA-0.9.2/PKNCA/man/get.first.model.Rd | 38 PKNCA-0.9.2/PKNCA/man/get.interval.cols.Rd | 59 PKNCA-0.9.2/PKNCA/man/get.parameter.deps.Rd | 55 PKNCA-0.9.2/PKNCA/man/getAttributeColumn.Rd | 48 PKNCA-0.9.2/PKNCA/man/getColumnValueOrNot.Rd | 62 PKNCA-0.9.2/PKNCA/man/getData.PKNCAconc.Rd | 32 PKNCA-0.9.2/PKNCA/man/getData.PKNCAdata.Rd | 26 PKNCA-0.9.2/PKNCA/man/getData.PKNCAresults.Rd | 26 PKNCA-0.9.2/PKNCA/man/getDataName.Rd | 93 PKNCA-0.9.2/PKNCA/man/getDepVar.Rd | 53 PKNCA-0.9.2/PKNCA/man/getGroups.PKNCAconc.Rd | 92 PKNCA-0.9.2/PKNCA/man/getIndepVar.Rd | 53 PKNCA-0.9.2/PKNCA/man/interp.extrap.conc.Rd | 320 +- PKNCA-0.9.2/PKNCA/man/merge.splitlist.Rd | 58 PKNCA-0.9.2/PKNCA/man/model.frame.PKNCAconc.Rd | 52 PKNCA-0.9.2/PKNCA/man/normalize_exclude.Rd | 34 PKNCA-0.9.2/PKNCA/man/parseFormula.Rd | 101 PKNCA-0.9.2/PKNCA/man/pk.business.Rd | 67 PKNCA-0.9.2/PKNCA/man/pk.calc.ae.Rd | 60 PKNCA-0.9.2/PKNCA/man/pk.calc.aucint.Rd | 253 + PKNCA-0.9.2/PKNCA/man/pk.calc.aucpext.Rd | 52 PKNCA-0.9.2/PKNCA/man/pk.calc.auxc.Rd | 342 +- PKNCA-0.9.2/PKNCA/man/pk.calc.c0.Rd | 147 PKNCA-0.9.2/PKNCA/man/pk.calc.cav.Rd | 48 PKNCA-0.9.2/PKNCA/man/pk.calc.ceoi.Rd | 50 PKNCA-0.9.2/PKNCA/man/pk.calc.cl.Rd | 68 PKNCA-0.9.2/PKNCA/man/pk.calc.clast.obs.Rd | 46 PKNCA-0.9.2/PKNCA/man/pk.calc.clr.Rd | 58 PKNCA-0.9.2/PKNCA/man/pk.calc.cmax.Rd | 58 PKNCA-0.9.2/PKNCA/man/pk.calc.ctrough.Rd | 44 PKNCA-0.9.2/PKNCA/man/pk.calc.deg.fluc.Rd | 48 PKNCA-0.9.2/PKNCA/man/pk.calc.dn.Rd | 42 PKNCA-0.9.2/PKNCA/man/pk.calc.f.Rd | 50 PKNCA-0.9.2/PKNCA/man/pk.calc.fe.Rd | 56 PKNCA-0.9.2/PKNCA/man/pk.calc.half.life.Rd | 212 - PKNCA-0.9.2/PKNCA/man/pk.calc.kel.Rd | 36 PKNCA-0.9.2/PKNCA/man/pk.calc.mrt.Rd | 78 PKNCA-0.9.2/PKNCA/man/pk.calc.mrt.md.Rd | 72 PKNCA-0.9.2/PKNCA/man/pk.calc.ptr.Rd | 42 PKNCA-0.9.2/PKNCA/man/pk.calc.swing.Rd | 46 PKNCA-0.9.2/PKNCA/man/pk.calc.thalf.eff.Rd | 38 PKNCA-0.9.2/PKNCA/man/pk.calc.tlag.Rd | 46 PKNCA-0.9.2/PKNCA/man/pk.calc.tlast.Rd | 62 PKNCA-0.9.2/PKNCA/man/pk.calc.tmax.Rd | 75 PKNCA-0.9.2/PKNCA/man/pk.calc.vd.Rd | 70 PKNCA-0.9.2/PKNCA/man/pk.calc.vss.Rd | 42 PKNCA-0.9.2/PKNCA/man/pk.calc.vz.Rd | 36 PKNCA-0.9.2/PKNCA/man/pk.nca.Rd | 67 PKNCA-0.9.2/PKNCA/man/pk.nca.interval.Rd | 158 - PKNCA-0.9.2/PKNCA/man/pk.tss.Rd | 60 PKNCA-0.9.2/PKNCA/man/pk.tss.data.prep.Rd | 102 PKNCA-0.9.2/PKNCA/man/pk.tss.monoexponential.Rd | 109 PKNCA-0.9.2/PKNCA/man/pk.tss.monoexponential.individual.Rd | 75 PKNCA-0.9.2/PKNCA/man/pk.tss.monoexponential.population.Rd | 79 PKNCA-0.9.2/PKNCA/man/pk.tss.stepwise.linear.Rd | 106 PKNCA-0.9.2/PKNCA/man/print.PKNCAconc.Rd | 66 PKNCA-0.9.2/PKNCA/man/print.PKNCAdata.Rd | 32 PKNCA-0.9.2/PKNCA/man/print.provenance.Rd | 36 PKNCA-0.9.2/PKNCA/man/print.summary_PKNCAresults.Rd | 46 PKNCA-0.9.2/PKNCA/man/reexports.Rd | 30 PKNCA-0.9.2/PKNCA/man/roundString.Rd | 74 PKNCA-0.9.2/PKNCA/man/roundingSummarize.Rd | 44 PKNCA-0.9.2/PKNCA/man/setAttributeColumn.Rd | 92 PKNCA-0.9.2/PKNCA/man/setDuration.Rd | 58 PKNCA-0.9.2/PKNCA/man/setExcludeColumn.Rd | 46 PKNCA-0.9.2/PKNCA/man/setRoute.Rd | 56 PKNCA-0.9.2/PKNCA/man/signifString.Rd | 95 PKNCA-0.9.2/PKNCA/man/sort.interval.cols.Rd | 20 PKNCA-0.9.2/PKNCA/man/split.PKNCAconc.Rd | 76 PKNCA-0.9.2/PKNCA/man/summary.PKNCAdata.Rd | 36 PKNCA-0.9.2/PKNCA/man/summary.PKNCAresults.Rd | 135 PKNCA-0.9.2/PKNCA/man/superposition.Rd | 190 - PKNCA-0.9.2/PKNCA/man/time_calc.Rd |only PKNCA-0.9.2/PKNCA/man/tss.monoexponential.generate.formula.Rd | 38 PKNCA-0.9.2/PKNCA/tests/testthat/generate.data.R | 41 PKNCA-0.9.2/PKNCA/tests/testthat/test-auc.R | 24 PKNCA-0.9.2/PKNCA/tests/testthat/test-check.intervals.R | 41 PKNCA-0.9.2/PKNCA/tests/testthat/test-class-PKNCAresults.R | 60 PKNCA-0.9.2/PKNCA/tests/testthat/test-cleaners.R | 44 PKNCA-0.9.2/PKNCA/tests/testthat/test-general.functions.R | 25 PKNCA-0.9.2/PKNCA/tests/testthat/test-half.life.R | 63 PKNCA-0.9.2/PKNCA/tests/testthat/test-interpolate.conc.R | 1475 ++++++---- PKNCA-0.9.2/PKNCA/tests/testthat/test-pk.calc.simple.R | 9 PKNCA-0.9.2/PKNCA/tests/testthat/test-superpostion.R | 56 PKNCA-0.9.2/PKNCA/tests/testthat/test-time.to.steady.state.R | 123 PKNCA-0.9.2/PKNCA/tests/testthat/test-time_calc.R |only PKNCA-0.9.2/PKNCA/vignettes/PKNCA-validation.Rmd | 10 PKNCA-0.9.2/PKNCA/vignettes/Writing-Parameter-Functions.Rmd | 4 173 files changed, 6779 insertions(+), 5762 deletions(-)
Title: Plot and Manipulate Multigraphs
Description: Functions to plot and manipulate multigraphs, signed and valued graphs, bipartite graphs, multilevel graphs, and Cayley graphs with different layout options. Please note that this package still under a devel version.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multigraph versions 0.92 dated 2019-12-02 and 0.93 dated 2020-02-28
DESCRIPTION | 10 +++--- MD5 | 23 +++++++------- R/multigraph.R | 73 ++++++++++++++++++++++++++++++---------------- inst |only man/bmgraph.Rd | 13 +++----- man/ccgraph.Rd | 11 +++--- man/conc.Rd | 2 - man/frcd.Rd | 6 +-- man/mbnd.Rd | 2 - man/mlgraph.Rd | 12 +++---- man/multigraph-package.Rd | 20 ++++++++---- man/multigraph.Rd | 58 ++++++++++++++++++++++-------------- man/stsm.Rd | 8 ++--- 13 files changed, 141 insertions(+), 97 deletions(-)
Title: Matching and Weighting Multiply Imputed Datasets
Description: Provides the necessary tools for the pre-processing techniques of matching and weighting multiply imputed datasets to control for effects of confounders and to reduce the degree of dependence on certain modeling assumptions in studying the causal associations between an exposure and an outcome. This package includes functions to perform matching within and across the multiply imputed datasets using several matching methods, to estimate weights of units in the imputed datasets using several weighting methods, to calculate the causal effect estimate in each matched or weighted dataset using parametric or non-parametric statistical models, and to pool the obtained estimates from these models according to Rubin's rules (please see <https://github.com/FarhadPishgar/MatchThem> for details).
Author: Farhad Pishgar [aut, cre],
Noah Greifer [aut],
Clémence Leyrat [ctb],
Elizabeth Stuart [ctb]
Maintainer: Farhad Pishgar <Farhad.Pishgar@Gmail.com>
Diff between MatchThem versions 0.9.1 dated 2019-12-13 and 0.9.2 dated 2020-02-28
DESCRIPTION | 8 +- MD5 | 48 ++++++++-------- NAMESPACE | 3 - NEWS.md | 10 ++- R/class.functions.R | 30 +++++++--- R/complete.R | 74 +++++++------------------ R/matchthem.R | 8 +- R/pool.R | 3 - R/weightthem.R | 8 +- R/with.R | 8 +- README.md | 6 +- man/complete.Rd | 121 +++++++++++++++++++++--------------------- man/is.mimids.Rd | 90 +++++++++++++++---------------- man/is.mimipo.Rd | 104 ++++++++++++++++++------------------ man/is.mimira.Rd | 98 +++++++++++++++++----------------- man/is.wimids.Rd | 90 +++++++++++++++---------------- man/matchthem.Rd | 144 ++++++++++++++++++++++++++------------------------ man/mimids.Rd | 50 ++++++++--------- man/mimipo.Rd | 50 ++++++++--------- man/mimira.Rd | 50 ++++++++--------- man/osteoarthritis.Rd | 52 +++++++++--------- man/pool.Rd | 116 ++++++++++++++++++++-------------------- man/weightthem.Rd | 120 +++++++++++++++++++++-------------------- man/wimids.Rd | 50 ++++++++--------- man/with.Rd | 126 +++++++++++++++++++++---------------------- 25 files changed, 738 insertions(+), 729 deletions(-)
Title: Global Charcoal Database
Description: Contains the Global Charcoal database data. Data include charcoal
series (age, depth, charcoal quantity, associated units and methods) and
information on sedimentary sites (localisation, depositional environment, biome,
etc.) as well as publications informations. Since 4.0.0 the GCD mirrors the online SQL database at <http://paleofire.org>.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between GCD versions 4.0.5 dated 2019-12-11 and 4.0.6 dated 2020-02-28
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- NEWS | 6 ++++++ 3 files changed, 13 insertions(+), 6 deletions(-)
Title: Detect Differentiation Problems
Description: An algorithm based on graph theory tools to detect differentiation
problems. A differentiation problem occurs when aggregated
data are disseminated according to two different nomenclatures. By making the
difference for an additive variable X between an aggregate composed of categories
of the first nomenclature and an other aggregate, included in that first
aggregate, composed of categories of the second nomenclature,
it is sometimes possible to derive X on a small aggregate of records
which could then lead to a break of confidentiality.
The purpose of this package is to detect the set of aggregates composed of
categories of the first nomenclature which lead to a differentiation problem,
when given a confidentiality threshold. Reference: Vianney Costemalle (2019) <doi: 10.3233/SJI-190564>.
Author: Vianney Costemalle [aut, cre],
Arlindo Dos Santos [aut],
Francois Semecurbe [aut]
Maintainer: Vianney Costemalle <vianney.costemalle@insee.fr>
Diff between diffman versions 0.1.0 dated 2019-08-08 and 0.1.1 dated 2020-02-28
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/fct_merging.R | 2 +- R/fct_merging_test.R | 6 +++--- R/fct_search_diff.R | 12 ++++++------ man/agregate.Rd | 10 ++++++++-- man/differencierRcpp.Rd | 10 ++++++++-- man/diffman.Rd | 1 - man/find_pbm_diff.Rd | 10 ++++++++-- 9 files changed, 48 insertions(+), 31 deletions(-)
Title: Tests on Properties of Space-Time Covariance Functions
Description: Tests on properties of space-time covariance functions.
Tests on symmetry, separability and for assessing
different forms of non-separability are available. Moreover tests on
some classes of covariance functions, such that the classes of
product-sum models, Gneiting models and integrated product models have
been provided. It is the companion R package to the paper of
Cappello C., De Iaco S. and Posa D. <doi:10.1007/s00477-017-1472-2>.
Author: Sandra De Iaco [aut, cre],
Claudia Cappello [aut],
Donato Posa [aut],
Sabrina Maggio [ctb]
Maintainer: Sandra De Iaco <sandra.deiaco@unisalento.it>
Diff between covatest versions 1.1.1 dated 2018-12-02 and 1.1.2 dated 2020-02-28
DESCRIPTION | 11 MD5 | 36 R/blocks.R | 10 R/couples.R | 3 R/covablocks.R | 2 R/covaprop.R | 2 R/covastat.R | 2 R/covastatM.R | 2 R/read.STdata.R | 1867 ++++++++++++++++++++++++------------------------ R/sepindex.R | 7 R/vv_13.R | 2 man/blocks-class.Rd | 2 man/couples-class.Rd | 13 man/covablocks-class.Rd | 1 man/covaprop-class.Rd | 1 man/covastat-class.Rd | 1 man/covastatM-class.Rd | 11 man/read.STdata.Rd | 27 man/vv_13.Rd | 2 19 files changed, 1006 insertions(+), 996 deletions(-)
Title: Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Description: Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>),
Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>),
Guillaume Thirel [aut] (<https://orcid.org/0000-0002-1444-1830>),
Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>),
Claude Michel [aut, ths],
Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>),
François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>,
'Parameter estimation' vignettes),
Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>),
Nicolas Le Moine [ctb],
Thibaut Mathevet [ctb] (<https://orcid.org/0000-0002-4142-4454>),
Safouane Mouelhi [ctb],
Ludovic Oudin [ctb] (<https://orcid.org/0000-0002-3712-0933>),
Raji Pushpalatha [ctb],
Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGR versions 1.4.3.60 dated 2020-01-29 and 1.4.3.65 dated 2020-02-28
DESCRIPTION | 10 +-- MD5 | 26 ++++---- NEWS.md | 102 +++++++++++++++++++-------------- inst/doc/V01_get_started.html | 7 -- inst/doc/V02.1_param_optim.R | 2 inst/doc/V02.1_param_optim.Rmd | 2 inst/doc/V02.1_param_optim.html | 7 -- inst/doc/V02.2_param_mcmc.html | 7 -- inst/doc/V03_param_sets_GR4J.html | 7 -- inst/doc/V04_cemaneige_hysteresis.html | 7 -- man/Calibration_Michel.Rd | 2 man/Imax.Rd | 2 man/RunModel_GR5H.Rd | 2 vignettes/V02.1_param_optim.Rmd | 2 14 files changed, 99 insertions(+), 86 deletions(-)
Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, and functions for hierarchical computations are included. The hierarchy specification functions are useful within statistical disclosure control.
Author: Øyvind Langsrud [aut, cre],
Bjørn-Helge Mevik [cph]
Maintainer: Øyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 0.5.0 dated 2019-11-26 and 0.6.0 dated 2020-02-28
SSBtools-0.5.0/SSBtools/man/AutoLevel.Rd |only SSBtools-0.5.0/SSBtools/man/FixHierarchy.Rd |only SSBtools-0.6.0/SSBtools/DESCRIPTION | 10 SSBtools-0.6.0/SSBtools/MD5 | 68 - SSBtools-0.6.0/SSBtools/NAMESPACE | 4 SSBtools-0.6.0/SSBtools/R/FormulaSums.R | 291 ++---- SSBtools-0.6.0/SSBtools/R/Hierarchies2ModelMatrix.R | 44 SSBtools-0.6.0/SSBtools/R/HierarchiesAndFormula2ModelMatrix.R |only SSBtools-0.6.0/SSBtools/R/HierarchyCompute.R | 444 +++++++--- SSBtools-0.6.0/SSBtools/R/HierarchyCompute2.R |only SSBtools-0.6.0/SSBtools/R/MakeHierFormula.R | 95 +- SSBtools-0.6.0/SSBtools/R/RbindAllCbindIdMatch.r | 138 +-- SSBtools-0.6.0/SSBtools/R/SSBtoolsData.R | 2 SSBtools-0.6.0/SSBtools/R/forEasySdcTable.R | 1 SSBtools-0.6.0/SSBtools/man/AddLeadingZeros.Rd | 2 SSBtools-0.6.0/SSBtools/man/AutoHierarchies.Rd | 8 SSBtools-0.6.0/SSBtools/man/AutoSplit.Rd | 6 SSBtools-0.6.0/SSBtools/man/CbindIdMatch.Rd | 38 SSBtools-0.6.0/SSBtools/man/CrossDataDummyHierarchies.Rd | 2 SSBtools-0.6.0/SSBtools/man/DummyHierarchy.Rd | 6 SSBtools-0.6.0/SSBtools/man/FindDimLists.Rd | 2 SSBtools-0.6.0/SSBtools/man/FindTableGroup.Rd | 4 SSBtools-0.6.0/SSBtools/man/FormulaSums.Rd | 7 SSBtools-0.6.0/SSBtools/man/HierarchicalWildcardGlobbing.Rd | 10 SSBtools-0.6.0/SSBtools/man/Hierarchies2ModelMatrix.Rd | 39 SSBtools-0.6.0/SSBtools/man/HierarchiesAndFormula2ModelMatrix.Rd |only SSBtools-0.6.0/SSBtools/man/HierarchyCompute.Rd | 52 - SSBtools-0.6.0/SSBtools/man/HierarchyCompute2.Rd |only SSBtools-0.6.0/SSBtools/man/HierarchyComputeDummy.Rd | 2 SSBtools-0.6.0/SSBtools/man/Match.Rd | 4 SSBtools-0.6.0/SSBtools/man/RbindAll.Rd | 20 SSBtools-0.6.0/SSBtools/man/RowGroups.Rd | 4 SSBtools-0.6.0/SSBtools/man/SSBtoolsData.Rd | 4 SSBtools-0.6.0/SSBtools/man/Stack.Rd | 2 SSBtools-0.6.0/SSBtools/man/Unstack.Rd | 4 SSBtools-0.6.0/SSBtools/man/WildcardGlobbing.Rd | 2 SSBtools-0.6.0/SSBtools/man/matlabColon.Rd | 2 SSBtools-0.6.0/SSBtools/tests/testthat/test-HierarchyCompute.R | 310 ++++++ 38 files changed, 1070 insertions(+), 557 deletions(-)
Title: Scientific Graphing Functions for Factorial Designs
Description: A collection of functions that creates graphs with error
bars for data collected from one-way or higher factorial
designs.
Author: Manuel Morales <mmorales@williams.edu>, with code developed by
the R Development Core Team and with general advice from the R-help
listserv community, especially Duncan Murdoch.
Maintainer: Manuel Morales <Manuel.A.Morales@williams.edu>
Diff between sciplot versions 1.1-1 dated 2017-06-19 and 1.2-0 dated 2020-02-28
CHANGELOG | 3 DESCRIPTION | 6 MD5 | 12 - R/bargraphCI.R | 230 ++++++++++++------------- R/lineplotCI.R | 476 ++++++++++++++++++++++++++--------------------------- man/bargraph.CI.Rd | 6 man/lineplot.CI.Rd | 11 - 7 files changed, 380 insertions(+), 364 deletions(-)
Title: A Collection of Methods for Singular Spectrum Analysis
Description: Methods and tools for Singular Spectrum Analysis including decomposition, forecasting and gap-filling for univariate and multivariate time series.
Author: Anton Korobeynikov, Alex Shlemov, Konstantin Usevich, Nina Golyandina
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between Rssa versions 1.0 dated 2017-10-04 and 1.0.2 dated 2020-02-28
DESCRIPTION | 8 MD5 | 110 +++++------ R/chankel.R | 35 +++ R/eossa.R | 12 - R/hankel.R | 15 + R/pssa.R | 17 + R/ssa.R | 2 R/toeplitz.R | 17 + R/wossa.R | 16 + configure | 206 ++++++++++----------- configure.ac | 3 inst/CITATION | 51 +++-- man/AustralianWine.Rd | 30 +-- man/Barbara.rd | 38 +-- man/Mars.Rd | 38 +-- man/MotorVehicle.Rd | 30 +-- man/Rssa-package.Rd | 217 +++++++++++----------- man/USUnemployment.Rd | 36 +-- man/autossa.Rd | 234 ++++++++++++----------- man/bforecast.Rd | 178 +++++++++--------- man/cadzow.Rd | 204 ++++++++++---------- man/calcv.Rd | 112 +++++------ man/cleanup.Rd | 62 +++--- man/clone.Rd | 92 ++++----- man/clplot.Rd | 68 +++--- man/clusterify.Rd | 104 +++++----- man/decompose.Rd | 124 ++++++------ man/forecast.Rd | 208 ++++++++++----------- man/fossa.Rd | 404 +++++++++++++++++++++-------------------- man/frobenius.cor.Rd | 226 +++++++++++------------ man/gapfill.Rd | 216 +++++++++++----------- man/grouping.auto.Rd | 64 +++--- man/hankel.Rd | 132 ++++++------- man/hbhankel.Rd | 104 +++++----- man/hmatr.Rd | 168 ++++++++--------- man/igapfill.Rd | 213 +++++++++++---------- man/iossa.Rd | 469 ++++++++++++++++++++++++------------------------ man/iossa.result.Rd | 144 +++++++------- man/lrr.Rd | 205 ++++++++++---------- man/owcor.Rd | 178 +++++++++--------- man/parest.Rd | 21 +- man/plot.Rd | 268 +++++++++++++-------------- man/plot.reconstruct.Rd | 328 ++++++++++++++++----------------- man/precache.Rd | 76 +++---- man/reconstruct.Rd | 184 ++++++++++-------- man/residuals.Rd | 102 +++++----- man/rforecast.Rd | 272 ++++++++++++++------------- man/ssa-data.Rd | 216 +++++++++++----------- man/ssa-routines.Rd | 363 ++++++++++++++++++------------------- man/ssa.Rd | 60 +++--- man/ssa.capabilities.Rd | 60 +++--- man/summarize.gaps.Rd | 104 +++++----- man/toeplitz.Rd | 112 +++++------ man/vforecast.Rd | 237 ++++++++++++------------ man/wcor.Rd | 236 ++++++++++++------------ man/wnorm.Rd | 142 +++++++------- 56 files changed, 3925 insertions(+), 3646 deletions(-)
Title: Do a Git Style Diff of the Rows Between Two Dataframes with
Similar Structure
Description: Compares two dataframes which have the same column
structure to show the rows that have changed. Also gives a git style diff format
to quickly see what has changed in addition to summary statistics.
Author: Alex Joseph [aut, cre]
Maintainer: Alex Joseph <alexsanjoseph@gmail.com>
Diff between compareDF versions 2.0.0 dated 2020-01-08 and 2.0.1 dated 2020-02-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ R/fnsOutputs.R | 10 +++++++++- README.md | 1 + 5 files changed, 21 insertions(+), 9 deletions(-)
Title: Authentication Management for 'Shiny' Applications
Description: Simple and secure authentification mechanism for single 'Shiny' applications.
Credentials are stored in an encrypted 'SQLite' database. Source code of main application
is protected until authentication is successful.
Author: Benoit Thieurmel [aut, cre],
Victor Perrier [aut]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between shinymanager versions 1.0.100 dated 2019-12-11 and 1.0.200 dated 2020-02-28
DESCRIPTION | 6 +- MD5 | 28 +++++------ NEWS.md | 8 +++ R/language.R | 107 +++++++++++++++++++++++++++++++++++++------ R/module-admin.R | 7 +- R/module-auth.R | 32 ++++++++++-- R/module-edit_user.R | 49 ++++++++++++++++++- R/secure-app.R | 56 +++++++++++++++++++--- README.md | 57 +++++++++++----------- inst/assets/timeout.js | 35 +++++++++++++- inst/doc/SQLite_Admin.Rmd | 34 +++++++++++-- inst/doc/SQLite_Admin.html | 90 +++++++++++++++++++++++++++++++++--- man/module-authentication.Rd | 69 ++++++++++++++++++--------- man/secure-app.Rd | 28 ++++++++++- vignettes/SQLite_Admin.Rmd | 34 +++++++++++-- 15 files changed, 516 insertions(+), 124 deletions(-)
Title: Wiener Process Distribution Functions
Description: Provides Wiener process distribution functions,
namely the Wiener first passage time density, CDF, quantile and random
functions. Additionally supplies a modelling function (wdm) and further
methods for the resulting object.
Author: Dominik Wabersich [aut, cre]
Maintainer: Dominik Wabersich <dominik.wabersich@gmail.com>
Diff between RWiener versions 1.3-1 dated 2017-02-22 and 1.3-2 dated 2020-02-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/tests.Rd | 4 ++-- man/wdm.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Neat and Painless Statistical Reporting
Description: User-friendly, clear and simple statistics, primarily for
publication in psychological science. The main functions are wrappers for
other packages, but there are various additions as well. Every relevant step
from data aggregation to reportable printed statistics is covered for basic
experimental designs.
Author: Gáspár Lukács [aut, cre] (<https://orcid.org/0000-0001-9401-4830>),
Bennett Kleinberg [ctb] (<https://orcid.org/0000-0003-1658-9086>)
Maintainer: Gáspár Lukács <lkcsgaspar@gmail.com>
Diff between neatStats versions 1.0.3 dated 2020-02-20 and 1.0.4 dated 2020-02-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/dems_neat.R | 6 ++++-- README.md | 4 +--- build/partial.rdb |binary man/dems_neat.Rd | 6 ++++-- 6 files changed, 18 insertions(+), 16 deletions(-)
Title: Manipulating DNA Sequences and Estimating Unambiguous Haplotype
Network with Statistical Parsimony
Description: Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel coding methods (only simple indel coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and collapses identical DNA sequences into haplotypes or inferring haplotypes using user provided absolute pairwise character difference matrix. This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.
Author: Caner Aktas
Maintainer: Caner Aktas <caktas.aca@gmail.com>
Diff between haplotypes versions 1.1.1 dated 2020-02-20 and 1.1.2 dated 2020-02-28
DESCRIPTION | 11 -- MD5 | 10 - NAMESPACE | 1 R/classdna.r | 235 ++++++++++++++++++++++++++++++++++++++++++++- man/haplotypes-internal.Rd | 1 man/pairPhiST-methods.Rd | 2 6 files changed, 244 insertions(+), 16 deletions(-)
Title: Stacked Species Distribution Modelling
Description: Allows to map species richness and endemism based on stacked
species distribution models (SSDM). Individuals SDMs can be created using a
single or multiple algorithms (ensemble SDMs). For each species, an SDM can
yield a habitat suitability map, a binary map, a between-algorithm variance
map, and can assess variable importance, algorithm accuracy, and between-
algorithm correlation. Methods to stack individual SDMs include summing
individual probabilities and thresholding then summing. Thresholding can be
based on a specific evaluation metric or by drawing repeatedly from a Bernoulli
distribution. The SSDM package also provides a user-friendly interface.
Author: Sylvain Schmitt, Robin Pouteau, Dimitri Justeau, Florian de Boissieu, Lukas Baumbach, Philippe Birnbaum
Maintainer: Sylvain Schmitt <sylvain.m.schmitt@gmail.com>
Diff between SSDM versions 0.2.7 dated 2020-02-13 and 0.2.8 dated 2020-02-28
DESCRIPTION | 6 ++-- MD5 | 10 +++---- NEWS.md | 5 +++ R/load_occ.R | 2 - inst/doc/GUI.html | 4 +-- inst/doc/SSDM.html | 70 ++++++++++++++++++++++++++--------------------------- 6 files changed, 51 insertions(+), 46 deletions(-)
Title: Programming with Big Data -- Scalable Linear Algebra Packages
Description: Utilizing scalable linear algebra packages mainly
including 'BLACS', 'PBLAS', and 'ScaLAPACK' in double precision via
'pbdMPI' based on 'ScaLAPACK' version 2.0.2.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Brian Ripley [ctb] (Solaris & Mac)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdSLAP versions 0.2-9 dated 2020-02-01 and 0.3-0 dated 2020-02-28
ChangeLog | 6 ++++ DESCRIPTION | 8 +++--- MD5 | 22 ++++++++-------- src/Makevars.in | 2 - src/ScaLAPACK/pdhseqr.f | 38 ++++++++++++++++++++++------ src/ScaLAPACK/pdlacon.f | 48 ++++++++++++++++++++++++++++++------ src/ScaLAPACK/pdlarf.f | 32 ++++++++++++++++++------ src/ScaLAPACK/pdlarz.f | 32 ++++++++++++++++++------ src/ScaLAPACK/pdlawil.f | 22 +++++++++++++--- src/ScaLAPACK/pdstebz.f | 8 +++++- src/ScaLAPACK/pdtrord.f | 64 +++++++++++++++++++++++++++++++++++++++--------- src/ScaLAPACK/pdtrsen.f | 32 ++++++++++++++++++++---- 12 files changed, 246 insertions(+), 68 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with this
package as described in Ostoic (2020) <DOI:10.18637/jss.v092.i11>. Among other things, it
makes it possible to create and manipulate multiplex, multimode, and multilevel network data
with different formats. There are effective ways available to treat multiple networks with
routines that combine algebraic systems like the partially ordered semigroup or the semiring
structure with the relational bundles occurring in different types of multivariate network
data sets. It also provides an algebraic approach for affiliation networks through Galois
derivations between families of the pairs of subsets in the two domains.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 2.9.2 dated 2019-12-02 and 2.9.4 dated 2020-02-28
DESCRIPTION | 23 +++---- MD5 | 77 ++++++++++++------------- R/diagram.R | 13 ++-- R/perm.R | 61 +++++++++++++------- R/ti.R | 22 ++++--- build/vignette.rds |binary inst/CHANGELOG | 15 +++- inst/CITATION |only inst/doc/TwoModeNetworks.R | 71 +++++++++++------------ inst/doc/TwoModeNetworks.Rnw | 127 ++++++++++++++++++------------------------ inst/doc/TwoModeNetworks.pdf |binary man/bundle.census.Rd | 15 ++-- man/bundles.Rd | 11 +-- man/cngr.Rd | 2 man/comps.Rd | 6 - man/cph.Rd | 4 - man/decomp.Rd | 4 - man/diagram.Rd | 9 +- man/diagram.levels.Rd | 2 man/expos.Rd | 7 +- man/fact.Rd | 17 +++-- man/fltr.Rd | 2 man/galois.Rd | 2 man/hierar.Rd | 5 - man/mlvl.Rd | 2 man/mnplx.Rd | 2 man/multiplex-package.Rd | 28 +++++---- man/neighb.Rd | 4 - man/perm.Rd | 8 +- man/pfvn.Rd | 2 man/read.gml.Rd | 12 ++- man/read.srt.Rd | 12 +-- man/semigroup.Rd | 2 man/signed.Rd | 2 man/strings.Rd | 2 man/summaryBundles.Rd | 11 ++- man/transf.Rd | 6 - man/wordT.Rd | 9 -- man/write.gml.Rd | 2 vignettes/TwoModeNetworks.Rnw | 127 ++++++++++++++++++------------------------ 40 files changed, 374 insertions(+), 352 deletions(-)
Title: Grouped Statistical Analyses in a Tidy Way
Description: Collection of functions to run statistical tests
across all combinations of multiple grouping variables.
Author: Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between groupedstats versions 0.1.1 dated 2020-01-14 and 0.2.0 dated 2020-02-28
groupedstats-0.1.1/groupedstats/R/set_cwd.R |only groupedstats-0.1.1/groupedstats/R/utils_formatting.R |only groupedstats-0.1.1/groupedstats/man/set_cwd.Rd |only groupedstats-0.1.1/groupedstats/man/signif_column.Rd |only groupedstats-0.1.1/groupedstats/man/specify_decimal_p.Rd |only groupedstats-0.1.1/groupedstats/tests/testthat/test-signif_column.R |only groupedstats-0.1.1/groupedstats/tests/testthat/test-specify_decimal_p.R |only groupedstats-0.2.0/groupedstats/DESCRIPTION | 16 +- groupedstats-0.2.0/groupedstats/MD5 | 34 ++--- groupedstats-0.2.0/groupedstats/NAMESPACE | 25 ++-- groupedstats-0.2.0/groupedstats/NEWS.md | 7 - groupedstats-0.2.0/groupedstats/R/grouped_summary.R | 2 groupedstats-0.2.0/groupedstats/R/reexports.R | 47 ++++++- groupedstats-0.2.0/groupedstats/README.md | 8 - groupedstats-0.2.0/groupedstats/build |only groupedstats-0.2.0/groupedstats/inst/WORDLIST | 17 +- groupedstats-0.2.0/groupedstats/inst/doc |only groupedstats-0.2.0/groupedstats/man/figures/README-grouped_summary3-1.png |binary groupedstats-0.2.0/groupedstats/man/groupedstats-package.Rd | 26 ++-- groupedstats-0.2.0/groupedstats/man/reexports.Rd | 13 +- groupedstats-0.2.0/groupedstats/tests/README.md | 62 ++++------ groupedstats-0.2.0/groupedstats/vignettes |only 22 files changed, 153 insertions(+), 104 deletions(-)
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also contains a
number of lower level 'CLI' elements: rules, boxes, trees, and
'Unicode' symbols with 'ASCII' alternatives. It integrates with the
'crayon' package to support 'ANSI' terminal colors.
Author: Gábor Csárdi [aut, cre],
Hadley Wickham [ctb],
Kirill Müller [ctb]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cli versions 2.0.1 dated 2020-01-08 and 2.0.2 dated 2020-02-28
DESCRIPTION | 6 +- MD5 | 39 ++++++++-------- NAMESPACE | 2 NEWS.md | 14 +++++ R/cliapp-docs.R | 4 - R/cliapp.R | 6 -- R/inline.R | 6 ++ R/internals.R | 18 ++++--- R/status-bar.R | 62 ++++++++++++-------------- R/sysdata.rda |binary R/themes.R | 22 ++++----- R/tty.R | 9 +++ R/unicode.R |only build/vignette.rds |binary man/cli_process_start.Rd | 6 +- man/cli_status.Rd | 2 man/containers.Rd | 4 - man/unicode-width-workaround.Rd |only tests/testthat/test-collapsing.R | 12 +++-- tests/testthat/test-pluralization.R | 4 - tests/testthat/test-status-bar.R | 85 ++++++++++++++++++++++++++++-------- tests/testthat/test-unicode.R |only 22 files changed, 191 insertions(+), 110 deletions(-)
Title: A Monte Carlo Valuation Framework for Variable Annuities
Description: Implementation of a Monte Carlo simulation engine for valuing synthetic portfolios of
variable annuities, which reflect realistic features of common annuity contracts in practice.
It aims to facilitate the development and dissemination of research related to the efficient
valuation of a portfolio of large variable annuities. The main valuation methodology was
proposed by Gan (2017) <doi:10.1515/demo-2017-0021>.
Author: Hengxin Li [aut, cph],
Ben Feng [aut, cph],
Mingyi Jiang [aut, cph, cre],
GuoJun Gan [ctb]
Maintainer: Mingyi Jiang <m64jiang@uwaterloo.ca>
Diff between vamc versions 0.2.0 dated 2020-02-03 and 0.2.1 dated 2020-02-28
DESCRIPTION | 6 MD5 | 30 ++-- NEWS.md | 11 + R/Step2_ScenarioGeneration.R | 6 R/Step3_PolicyGeneration.R | 3 R/Step4_MonteCarloValuation.R | 4 build/partial.rdb |binary inst/doc/my-vignette.R | 22 +-- inst/doc/my-vignette.Rmd | 36 ++--- inst/doc/my-vignette.html | 284 +++++++++++------------------------------- man/genFundScen.Rd | 2 man/genIndexScen.Rd | 12 + man/genPortInception.Rd | 1 man/valuateOnePolicy.Rd | 2 man/valuatePortfolio.Rd | 2 vignettes/my-vignette.Rmd | 36 ++--- 16 files changed, 169 insertions(+), 288 deletions(-)
Title: Radiation Safety
Description: Provides functions for radiation safety, also known as "radiation protection" and "radiological control". The science of radiation protection is called "health physics" and its engineering functions are called "radiological engineering". Functions in this package cover many of the computations needed by radiation safety professionals. Examples include: obtaining updated calibration and source check values for radiation monitors to account for radioactive decay in a reference source, simulating instrument readings to better understand measurement uncertainty, correcting instrument readings for geometry and ambient atmospheric conditions. Many of these functions are described in Johnson and Kirby (2011, ISBN-13: 978-1609134198). Utilities are also included for developing inputs and processing outputs with radiation transport codes, such as MCNP, a general-purpose Monte Carlo N-Particle code that can be used for neutron, photon, electron, or coupled neutron/photon/electron transport (Werner et. al. (2018) <doi:10.2172/1419730>).
Author: Mark Hogue <mark.hogue.chp@gmail.com>
Maintainer: Mark Hogue <mark.hogue.chp@gmail.com>
Diff between radsafer versions 2.1.0 dated 2019-12-18 and 2.2.0 dated 2020-02-28
radsafer-2.1.0/radsafer/R/RN_plt.R |only radsafer-2.1.0/radsafer/R/bin_screen_phot.R |only radsafer-2.1.0/radsafer/R/dk_activity.R |only radsafer-2.1.0/radsafer/R/dk_cf.R |only radsafer-2.1.0/radsafer/R/dk_reverse.R |only radsafer-2.1.0/radsafer/R/spec_0.1_0.3.R |only radsafer-2.1.0/radsafer/data/spec_0.1_0.3.rda |only radsafer-2.1.0/radsafer/man/RN_plt.Rd |only radsafer-2.1.0/radsafer/man/dk_activity.Rd |only radsafer-2.1.0/radsafer/man/dk_cf.Rd |only radsafer-2.1.0/radsafer/man/dk_reverse.Rd |only radsafer-2.1.0/radsafer/man/scan2spec.df.Rd |only radsafer-2.1.0/radsafer/man/spec_0.1_0.3.Rd |only radsafer-2.2.0/radsafer/DESCRIPTION | 8 radsafer-2.2.0/radsafer/MD5 | 102 ++--- radsafer-2.2.0/radsafer/NAMESPACE | 13 radsafer-2.2.0/radsafer/R/RN_bin_screen_phot.R |only radsafer-2.2.0/radsafer/R/RN_find_parent.R | 8 radsafer-2.2.0/radsafer/R/RN_index_screen.R | 8 radsafer-2.2.0/radsafer/R/RN_plot_search_results.R |only radsafer-2.2.0/radsafer/R/RN_plot_spectrum.R |only radsafer-2.2.0/radsafer/R/RN_save_spectrum.R |only radsafer-2.2.0/radsafer/R/RN_search_alpha_by_E.R |only radsafer-2.2.0/radsafer/R/RN_search_beta_by_E.R |only radsafer-2.2.0/radsafer/R/RN_search_phot_by_E.R |only radsafer-2.2.0/radsafer/R/mcnp_cone_angle.R | 41 -- radsafer-2.2.0/radsafer/R/mcnp_plot_out_spec.R | 49 +- radsafer-2.2.0/radsafer/R/mcnp_scan2plot.R |only radsafer-2.2.0/radsafer/R/mcnp_scan2spec.R | 37 + radsafer-2.2.0/radsafer/R/mcnp_scan_save.R |only radsafer-2.2.0/radsafer/R/mcnp_si_sp_RD.R | 9 radsafer-2.2.0/radsafer/R/mcnp_si_sp_hist.R | 4 radsafer-2.2.0/radsafer/R/search_alpha_by_E.R | 6 radsafer-2.2.0/radsafer/R/search_beta_by_E.R | 3 radsafer-2.2.0/radsafer/R/search_phot_by_E.R | 3 radsafer-2.2.0/radsafer/data/photons_cs137_hist.rda |binary radsafer-2.2.0/radsafer/inst/doc/Introduction_to_radsafer.R | 57 +-- radsafer-2.2.0/radsafer/inst/doc/Introduction_to_radsafer.Rmd | 140 ++++--- radsafer-2.2.0/radsafer/inst/doc/Introduction_to_radsafer.html | 188 +++++----- radsafer-2.2.0/radsafer/man/RN_Spec_Act.Rd | 8 radsafer-2.2.0/radsafer/man/RN_find_parent.Rd | 5 radsafer-2.2.0/radsafer/man/RN_index_screen.Rd | 14 radsafer-2.2.0/radsafer/man/RN_info.Rd | 8 radsafer-2.2.0/radsafer/man/RN_plot_search_results.Rd |only radsafer-2.2.0/radsafer/man/RN_plot_spectrum.Rd |only radsafer-2.2.0/radsafer/man/RN_save_spectrum.Rd |only radsafer-2.2.0/radsafer/man/RN_search_alpha_by_E.Rd |only radsafer-2.2.0/radsafer/man/RN_search_beta_by_E.Rd |only radsafer-2.2.0/radsafer/man/RN_search_phot_by_E.Rd |only radsafer-2.2.0/radsafer/man/bin_screen_phot.Rd | 38 +- radsafer-2.2.0/radsafer/man/dk_correct.Rd | 6 radsafer-2.2.0/radsafer/man/dk_pct_to_num_half_life.Rd | 5 radsafer-2.2.0/radsafer/man/dk_time.Rd | 6 radsafer-2.2.0/radsafer/man/mcnp_cone_angle.Rd | 4 radsafer-2.2.0/radsafer/man/mcnp_est_nps.Rd | 2 radsafer-2.2.0/radsafer/man/mcnp_matrix_rotations.Rd | 2 radsafer-2.2.0/radsafer/man/mcnp_plot_out_spec.Rd | 23 - radsafer-2.2.0/radsafer/man/mcnp_scan2plot.Rd |only radsafer-2.2.0/radsafer/man/mcnp_scan2spec.Rd | 15 radsafer-2.2.0/radsafer/man/mcnp_scan_save.Rd |only radsafer-2.2.0/radsafer/man/mcnp_si_sp_RD.Rd | 7 radsafer-2.2.0/radsafer/man/mcnp_si_sp_hist.Rd | 6 radsafer-2.2.0/radsafer/man/mcnp_si_sp_hist_scan.Rd | 2 radsafer-2.2.0/radsafer/man/search_alpha_by_E.Rd | 15 radsafer-2.2.0/radsafer/man/search_beta_by_E.Rd | 10 radsafer-2.2.0/radsafer/man/search_phot_by_E.Rd | 10 radsafer-2.2.0/radsafer/vignettes/Introduction_to_radsafer.Rmd | 140 ++++--- 67 files changed, 561 insertions(+), 441 deletions(-)
Title: Tidy Up Date/Time Ranges
Description: Collapse, partition, combine, fill gaps in and expand date/time ranges.
Author: Aljaz Jelenko [aut, cre]
Maintainer: Aljaz Jelenko <aljaz.jelenko@amis.net>
Diff between neatRanges versions 0.1.1 dated 2020-02-26 and 0.1.2 dated 2020-02-28
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- tests/testthat/testneatRanges_collapse.R | 34 +++++++++++++++--------------- tests/testthat/testneatRanges_combine.R | 12 +++++----- tests/testthat/testneatRanges_expand.R | 4 +-- tests/testthat/testneatRanges_fill.R | 8 +++---- tests/testthat/testneatRanges_partition.R | 8 +++---- 7 files changed, 42 insertions(+), 42 deletions(-)
Title: Pedigree and Genetic Groups
Description: Calculates additive and dominance genetic relationship matrices and their inverses, in matrix and tabular-sparse formats. It includes functions for checking and processing pedigree, as well as functions to calculate the matrix of genetic group contributions (Q), and adding those contributions to the genetic merit of animals (Quaas (1988) <doi:10.3168/jds.S0022-0302(88)79691-5>). Calculation of Q is computationally extensive. There are computationally optimized functions to calculate Q.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between ggroups versions 2.0.1 dated 2020-02-18 and 2.0.2 dated 2020-02-28
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- NAMESPACE | 1 + NEWS.md | 7 ++++++- R/smgsped.R |only man/smgsped.Rd |only 6 files changed, 16 insertions(+), 8 deletions(-)
Title: Bayesian Aggregate Treatment Effects
Description: Running and comparing meta-analyses of data with hierarchical
Bayesian models in Stan, including convenience functions for formatting
data, plotting and pooling measures specific to meta-analysis.
Author: Witold Wiecek [cre, aut],
Rachael Meager [aut],
Brice Green [ctb] (predict(), loo_compare, many visuals),
Trustees of Columbia University [cph] (tools/make_cc.R)
Maintainer: Witold Wiecek <witold.wiecek@gmail.com>
Diff between baggr versions 0.3.0 dated 2020-01-08 and 0.4.0 dated 2020-02-28
baggr-0.3.0/baggr/inst/models |only baggr-0.4.0/baggr/DESCRIPTION | 12 baggr-0.4.0/baggr/MD5 | 134 ++-- baggr-0.4.0/baggr/NAMESPACE | 6 baggr-0.4.0/baggr/NEWS.md | 31 + baggr-0.4.0/baggr/R/auto_prior.R | 124 ++-- baggr-0.4.0/baggr/R/baggr-package.R | 15 baggr-0.4.0/baggr/R/baggr.R | 109 ++- baggr-0.4.0/baggr/R/baggr_compare.R | 326 ++++++++-- baggr-0.4.0/baggr/R/convert_inputs.R | 115 ++- baggr-0.4.0/baggr/R/fixed_effects.R |only baggr-0.4.0/baggr/R/forest_plot.R | 60 + baggr-0.4.0/baggr/R/group_effects.R | 6 baggr-0.4.0/baggr/R/loocv.R | 4 baggr-0.4.0/baggr/R/mint.R | 16 baggr-0.4.0/baggr/R/pooling_metrics.R | 8 baggr-0.4.0/baggr/R/predict.R |only baggr-0.4.0/baggr/R/print_baggr.R | 29 baggr-0.4.0/baggr/R/prior_dist.R | 27 baggr-0.4.0/baggr/R/trt_effects.R | 26 baggr-0.4.0/baggr/build/vignette.rds |binary baggr-0.4.0/baggr/inst/doc/baggr.R | 55 - baggr-0.4.0/baggr/inst/doc/baggr.Rmd | 14 baggr-0.4.0/baggr/inst/doc/baggr.html | 269 ++++---- baggr-0.4.0/baggr/inst/doc/baggr_binary.R | 110 ++- baggr-0.4.0/baggr/inst/doc/baggr_binary.Rmd | 131 +++- baggr-0.4.0/baggr/inst/doc/baggr_binary.html | 583 +++++++++++-------- baggr-0.4.0/baggr/man/baggr-package.Rd | 14 baggr-0.4.0/baggr/man/baggr.Rd | 108 ++- baggr-0.4.0/baggr/man/baggr_compare.Rd | 69 +- baggr-0.4.0/baggr/man/baggr_plot.Rd | 13 baggr-0.4.0/baggr/man/convert_inputs.Rd | 27 baggr-0.4.0/baggr/man/fixed_effects.Rd |only baggr-0.4.0/baggr/man/forest_plot.Rd | 20 baggr-0.4.0/baggr/man/get_n_samples.Rd |only baggr-0.4.0/baggr/man/microcredit.Rd | 72 +- baggr-0.4.0/baggr/man/microcredit_simplified.Rd | 70 +- baggr-0.4.0/baggr/man/mint.Rd | 2 baggr-0.4.0/baggr/man/plot.baggr.Rd | 46 - baggr-0.4.0/baggr/man/plot.baggr_compare.Rd |only baggr-0.4.0/baggr/man/pooling.Rd | 10 baggr-0.4.0/baggr/man/pp_check.baggr.Rd |only baggr-0.4.0/baggr/man/predict.baggr.Rd |only baggr-0.4.0/baggr/man/predict_mutau.Rd |only baggr-0.4.0/baggr/man/predict_quantiles.Rd |only baggr-0.4.0/baggr/man/predict_rubin.Rd |only baggr-0.4.0/baggr/man/predict_unknown.Rd |only baggr-0.4.0/baggr/man/prepare_ma.Rd | 16 baggr-0.4.0/baggr/man/prepare_prior.Rd | 21 baggr-0.4.0/baggr/man/print.baggr.Rd | 6 baggr-0.4.0/baggr/man/print.baggr_compare.Rd |only baggr-0.4.0/baggr/man/print.plot_list.Rd |only baggr-0.4.0/baggr/man/rubin_data.Rd |only baggr-0.4.0/baggr/man/schools.Rd | 46 - baggr-0.4.0/baggr/man/set_prior_val.Rd |only baggr-0.4.0/baggr/man/show_model.Rd | 38 - baggr-0.4.0/baggr/man/stop_not_implemented.Rd |only baggr-0.4.0/baggr/man/treatment_effect.Rd | 3 baggr-0.4.0/baggr/src/stan_files/chunks/license.stan | 28 baggr-0.4.0/baggr/src/stan_files/full.stan | 173 ++--- baggr-0.4.0/baggr/src/stan_files/functions |only baggr-0.4.0/baggr/src/stan_files/logit.stan | 99 +-- baggr-0.4.0/baggr/src/stan_files/mutau.stan | 54 - baggr-0.4.0/baggr/src/stan_files/rubin.stan | 122 ++- baggr-0.4.0/baggr/tests/testthat/Rplots.pdf |binary baggr-0.4.0/baggr/tests/testthat/test_8schools.R | 2 baggr-0.4.0/baggr/tests/testthat/test_binary.R | 91 ++ baggr-0.4.0/baggr/tests/testthat/test_full.R | 92 ++ baggr-0.4.0/baggr/tests/testthat/test_helpers.R | 14 baggr-0.4.0/baggr/tests/testthat/test_mutau.R | 25 baggr-0.4.0/baggr/tests/testthat/test_ordering.R |only baggr-0.4.0/baggr/tests/testthat/test_prior.R | 9 baggr-0.4.0/baggr/tests/testthat/test_rubin.R | 95 ++- baggr-0.4.0/baggr/vignettes/baggr.Rmd | 14 baggr-0.4.0/baggr/vignettes/baggr.bib | 17 baggr-0.4.0/baggr/vignettes/baggr_binary.Rmd | 131 +++- 76 files changed, 2516 insertions(+), 1241 deletions(-)
Title: Programming with Big Data -- Base Wrappers for Distributed
Matrices
Description: An interface to and extensions for the 'PBLAS' and 'ScaLAPACK'
numerical libraries. This enables R to utilize distributed linear algebra
for codes written in the 'SPMD' fashion. This interface is deliberately
low-level and mimics the style of the native libraries it wraps. For a much
higher level way of managing distributed matrices, see the 'pbdDMAT'
package.
Author: Drew Schmidt [aut],
Wei-Chen Chen [aut, cre],
Sebastien Lamy de la Chapelle [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Ewan Higgs [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdBASE versions 0.5-2 dated 2020-02-02 and 0.5-3 dated 2020-02-28
ChangeLog | 5 +++++ DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- README.md | 1 - inst/doc/pbdBASE-guide.Rnw | 2 +- inst/doc/pbdBASE-guide.pdf |binary src/base/linalg/norms.f90 | 12 +++++++++--- src/base/linalg/pinverse.f90 | 13 ++++++++++--- vignettes/pbdBASE-guide.Rnw | 2 +- 9 files changed, 37 insertions(+), 20 deletions(-)
More information about IOHexperimenter at CRAN
Permanent link
Title: Detecting Anomalies in Data
Description: Implements Collective And Point Anomaly (CAPA) <arXiv:1806.01947>, Multi-Variate Collective And Point Anomaly (MVCAPA) <arXiv:1909.01691>, and Proportion Adaptive Segment Selection (PASS) <doi:10.1093/biomet/ass059> methods for the detection of anomalies in time series data.
Author: Alex Fisch [aut],
Daniel Grose [aut, cre],
Lawrence Bardwell [ctb],
Idris Eckley [ths],
Paul Fearnhead [ths]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between anomaly versions 2.0.2 dated 2019-09-19 and 2.0.4 dated 2020-02-28
DESCRIPTION | 12 ++++++------ MD5 | 30 +++++++++++++++--------------- NAMESPACE | 2 +- R/ac_corrected.R | 6 +++--- R/anomaly_series.R | 4 ++-- R/capa.R | 13 +++++++------ R/pass.class.R | 4 ++-- build/partial.rdb |binary man/anomaly_series.Rd | 10 ++++++++-- man/capa.Rd | 13 ++++++++++--- man/capa.mv.Rd | 13 ++++++++++--- man/capa.uv.Rd | 11 +++++++++-- man/pass.Rd | 3 +-- man/plot-methods.Rd | 20 ++++++++++---------- man/simulate.Rd | 10 ++++++++-- man/summary-methods.Rd | 12 ++++++------ 16 files changed, 98 insertions(+), 65 deletions(-)
Title: Hypothesis Matrix Translation
Description: Translation between experimental null hypotheses, hypothesis matrices, and contrast matrices as used in linear regression models. The package is based on the method described in Schad, Vasishth, Hohenstein, and Kliegl (2019) <doi:10.1016/j.jml.2019.104038>.
Author: Maximilian M. Rabe [aut, cre],
Shravan Vasishth [aut],
Sven Hohenstein [aut],
Reinhold Kliegl [aut],
Daniel J. Schad [aut]
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>
Diff between hypr versions 0.1.5 dated 2019-12-04 and 0.1.6 dated 2020-02-28
hypr-0.1.5/hypr/man/plus-hypr-hypr-method.Rd |only hypr-0.1.6/hypr/DESCRIPTION | 8 - hypr-0.1.6/hypr/MD5 | 30 +++--- hypr-0.1.6/hypr/NAMESPACE | 3 hypr-0.1.6/hypr/R/hypr.R | 126 +++++++++++++++++++++----- hypr-0.1.6/hypr/inst/doc/hypr-contrasts.R | 12 +- hypr-0.1.6/hypr/inst/doc/hypr-contrasts.html | 7 - hypr-0.1.6/hypr/inst/doc/hypr-intro.R | 28 ++--- hypr-0.1.6/hypr/inst/doc/hypr-intro.html | 7 - hypr-0.1.6/hypr/inst/doc/hypr-regression.R | 25 ++--- hypr-0.1.6/hypr/inst/doc/hypr-regression.Rmd | 3 hypr-0.1.6/hypr/inst/doc/hypr-regression.html | 82 ++++++++-------- hypr-0.1.6/hypr/man/cmat.Rd | 11 +- hypr-0.1.6/hypr/man/combination.Rd |only hypr-0.1.6/hypr/man/conversions.Rd | 8 + hypr-0.1.6/hypr/man/hypr.Rd | 9 + hypr-0.1.6/hypr/vignettes/hypr-regression.Rmd | 3 17 files changed, 229 insertions(+), 133 deletions(-)
More information about CompoundEvents at CRAN
Permanent link
Title: Granier's Sap Flow Sensors (TDP) Analysis
Description: Set of functions designed to help in the
analysis of TDP sensors. Features includes dates and time conversion, weather
data interpolation, daily maximum of tension analysis and calculations required
to convert sap flow density data to sap flow rates at the tree and plot scale (For more information see : Granier (1985) <DOI:10.1051/forest:19850204> & Granier (1987) <DOI:10.1093/treephys/3.4.309>).
Author: Maxime Durand
Maintainer: Maxime Durand <duran1211@gmail.com>
Diff between TDPanalysis versions 0.99 dated 2016-10-18 and 1.0 dated 2020-02-28
DESCRIPTION | 10 ++++---- MD5 | 28 +++++++++++----------- NAMESPACE | 2 - R/Tmax.R | 12 ++++----- man/SpFl.Rd | 33 ++++++++++++-------------- man/SpWd_Area_calc.Rd | 57 ++++++++++++++++++++++----------------------- man/Tmax.find.Rd | 55 +++++++++++++++++++++----------------------- man/Tmax.mean.Rd | 55 +++++++++++++++++++++----------------------- man/Tmaxplot.Rd | 55 +++++++++++++++++++++----------------------- man/Wat.transp.Rd | 61 ++++++++++++++++++++++++------------------------- man/date.to.DOY.Rd | 47 ++++++++++++++++++------------------- man/datetime.Rd | 55 +++++++++++++++++++++----------------------- man/remove.fun.Rd | 61 ++++++++++++++++++++++++------------------------- man/tens.to.sapflow.Rd | 59 +++++++++++++++++++++++------------------------ man/timecont.Rd | 53 ++++++++++++++++++++---------------------- 15 files changed, 316 insertions(+), 327 deletions(-)
Title: Summaries and Population Structure Analyses of Genetic Data
Description: A toolkit for analyzing stratified population genetic data.
Functions are provided for summarizing and checking loci
(haploid, diploid, and polyploid), single stranded DNA sequences,
calculating most population subdivision metrics, and running external programs
such as structure and fastsimcoal. The package is further described in
Archer et al (2016) <doi:10.1111/1755-0998.12559>.
Author: Eric Archer [aut, cre],
Paula Adams [aut],
Brita Schneiders [aut],
Sarina Fernandez [aut],
Warren Asfazadour [aut]
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between strataG versions 2.0.2 dated 2017-04-11 and 2.4.905 dated 2020-02-28
strataG-2.0.2/strataG/R/alleleFreqFormat.R |only strataG-2.0.2/strataG/R/as.array.gtypes.R |only strataG-2.0.2/strataG/R/as.matrix.gtypes.R |only strataG-2.0.2/strataG/R/fastsimcoal.R |only strataG-2.0.2/strataG/R/fastsimcoal.input.R |only strataG-2.0.2/strataG/R/initialize.gtypes.R |only strataG-2.0.2/strataG/R/iupacCode.R |only strataG-2.0.2/strataG/R/numericSNPmat.R |only strataG-2.0.2/strataG/R/qaqc.R |only strataG-2.0.2/strataG/R/show.gtypes.R |only strataG-2.0.2/strataG/R/strataGUI.R |only strataG-2.0.2/strataG/R/summarizeSamples.R |only strataG-2.0.2/strataG/R/summary.gtypes.R |only strataG-2.0.2/strataG/R/validIupacCodes.R |only strataG-2.0.2/strataG/R/write.gtypes.R |only strataG-2.0.2/strataG/inst/doc/qaqc.R |only strataG-2.0.2/strataG/inst/doc/qaqc.Rmd |only strataG-2.0.2/strataG/inst/doc/qaqc.html |only strataG-2.0.2/strataG/inst/shiny |only strataG-2.0.2/strataG/man/alleleFreqFormat.Rd |only strataG-2.0.2/strataG/man/as.array.gtypes.Rd |only strataG-2.0.2/strataG/man/as.matrix-gtypes-method.Rd |only strataG-2.0.2/strataG/man/fastsimcoal.Rd |only strataG-2.0.2/strataG/man/fastsimcoal.input.Rd |only strataG-2.0.2/strataG/man/iupacCode.Rd |only strataG-2.0.2/strataG/man/numericSNPmat.Rd |only strataG-2.0.2/strataG/man/qaqc.Rd |only strataG-2.0.2/strataG/man/show-gtypes-method.Rd |only strataG-2.0.2/strataG/man/strataG-internal.Rd |only strataG-2.0.2/strataG/man/strataGUI.Rd |only strataG-2.0.2/strataG/man/summarizeSamples.Rd |only strataG-2.0.2/strataG/man/validIupacCodes.Rd |only strataG-2.0.2/strataG/man/write.gtypes.Rd |only strataG-2.0.2/strataG/vignettes/qaqc.Rmd |only strataG-2.4.905/strataG/DESCRIPTION | 66 strataG-2.4.905/strataG/MD5 | 432 +-- strataG-2.4.905/strataG/NAMESPACE | 187 - strataG-2.4.905/strataG/R/LDgenepop.R | 71 strataG-2.4.905/strataG/R/RcppExports.R | 48 strataG-2.4.905/strataG/R/TiTvRatio.R | 29 strataG-2.4.905/strataG/R/alleleFreqs.R | 65 strataG-2.4.905/strataG/R/alleleSplit.R | 7 strataG-2.4.905/strataG/R/allelicRichness.R | 23 strataG-2.4.905/strataG/R/arlequin.R | 672 ++++- strataG-2.4.905/strataG/R/as.data.frame.gtypes.R | 150 + strataG-2.4.905/strataG/R/as.multidna.R | 13 strataG-2.4.905/strataG/R/baseFreqs.R | 79 strataG-2.4.905/strataG/R/clumpp.R | 30 strataG-2.4.905/strataG/R/createConsensus.R | 25 strataG-2.4.905/strataG/R/df2gtypes.R | 36 strataG-2.4.905/strataG/R/dupGenotypes.R | 70 strataG-2.4.905/strataG/R/evanno.R | 72 strataG-2.4.905/strataG/R/expandHaplotypes.R | 28 strataG-2.4.905/strataG/R/fasta.R | 51 strataG-2.4.905/strataG/R/fixedDifferences.R | 27 strataG-2.4.905/strataG/R/fixedSites.R | 44 strataG-2.4.905/strataG/R/freq2GenData.R | 15 strataG-2.4.905/strataG/R/fsc.input.R |only strataG-2.4.905/strataG/R/fscRead.R |only strataG-2.4.905/strataG/R/fscRun.R |only strataG-2.4.905/strataG/R/fscWrite.R |only strataG-2.4.905/strataG/R/fusFs.R | 61 strataG-2.4.905/strataG/R/gelato.R | 142 - strataG-2.4.905/strataG/R/genepop.R | 124 - strataG-2.4.905/strataG/R/gtypes.accessors.R | 425 ++- strataG-2.4.905/strataG/R/gtypes.class.R | 79 strataG-2.4.905/strataG/R/gtypes.initialize.R |only strataG-2.4.905/strataG/R/gtypes.show.R |only strataG-2.4.905/strataG/R/gtypes.summary.R |only strataG-2.4.905/strataG/R/gtypes2genind.R | 24 strataG-2.4.905/strataG/R/gtypes2loci.R | 36 strataG-2.4.905/strataG/R/gtypes2phyDat.R | 17 strataG-2.4.905/strataG/R/heterozygosity.R | 69 strataG-2.4.905/strataG/R/hweTest.R | 61 strataG-2.4.905/strataG/R/is.gtypes.R | 3 strataG-2.4.905/strataG/R/iupac.R |only strataG-2.4.905/strataG/R/jackHWE.R | 145 - strataG-2.4.905/strataG/R/labelHaplotypes.R | 174 - strataG-2.4.905/strataG/R/landscape2gtypes.R |only strataG-2.4.905/strataG/R/ldNe.R | 214 + strataG-2.4.905/strataG/R/lowFreqSubs.R | 76 strataG-2.4.905/strataG/R/mRatio.R | 139 - strataG-2.4.905/strataG/R/maf.R | 61 strataG-2.4.905/strataG/R/mafft.R | 51 strataG-2.4.905/strataG/R/maverickRun.R | 18 strataG-2.4.905/strataG/R/mega.R | 35 strataG-2.4.905/strataG/R/mostDistantSequences.R | 141 - strataG-2.4.905/strataG/R/mostRepresentativeSequences.R | 96 strataG-2.4.905/strataG/R/neiDa.R | 30 strataG-2.4.905/strataG/R/nucleotideDivergence.R | 113 strataG-2.4.905/strataG/R/nucleotideDiversity.R | 42 strataG-2.4.905/strataG/R/numAlleles.R | 18 strataG-2.4.905/strataG/R/numGenotyped.R | 19 strataG-2.4.905/strataG/R/numMissing.R | 23 strataG-2.4.905/strataG/R/permuteStrata.R | 8 strataG-2.4.905/strataG/R/phase.R | 100 strataG-2.4.905/strataG/R/popGenEqns.R | 4 strataG-2.4.905/strataG/R/popStructStat.R | 401 ++- strataG-2.4.905/strataG/R/popStructTest.R | 221 - strataG-2.4.905/strataG/R/privateAlleles.R | 28 strataG-2.4.905/strataG/R/propUniqueAlleles.R | 36 strataG-2.4.905/strataG/R/readGenData.R | 26 strataG-2.4.905/strataG/R/removeSequences.R | 18 strataG-2.4.905/strataG/R/sequence2gtypes.R | 36 strataG-2.4.905/strataG/R/sequenceLikelihoods.R | 116 strataG-2.4.905/strataG/R/sfs.R |only strataG-2.4.905/strataG/R/sharedLoci.R | 148 - strataG-2.4.905/strataG/R/simGammaHaps.R | 21 strataG-2.4.905/strataG/R/strataG-internal.R | 199 + strataG-2.4.905/strataG/R/strataG-package.R | 7 strataG-2.4.905/strataG/R/strataSplit.R | 10 strataG-2.4.905/strataG/R/stratify.R | 54 strataG-2.4.905/strataG/R/structure.R | 178 - strataG-2.4.905/strataG/R/structurePlot.R | 105 strataG-2.4.905/strataG/R/summarizeAll.R |only strataG-2.4.905/strataG/R/summarizeInds.R |only strataG-2.4.905/strataG/R/summarizeLoci.R | 36 strataG-2.4.905/strataG/R/summarizeSeqs.R | 9 strataG-2.4.905/strataG/R/tajimasD.R | 81 strataG-2.4.905/strataG/R/theta.R | 13 strataG-2.4.905/strataG/R/trimNs.R | 6 strataG-2.4.905/strataG/R/variableSites.R | 44 strataG-2.4.905/strataG/R/write.nexus.snapp.R | 12 strataG-2.4.905/strataG/R/writeGtypes.R |only strataG-2.4.905/strataG/README.md | 45 strataG-2.4.905/strataG/build/vignette.rds |binary strataG-2.4.905/strataG/data/dloop.g.rda |binary strataG-2.4.905/strataG/data/dolph.haps.rda |binary strataG-2.4.905/strataG/data/dolph.msats.rda |binary strataG-2.4.905/strataG/data/dolph.seqs.rda |binary strataG-2.4.905/strataG/data/dolph.strata.rda |binary strataG-2.4.905/strataG/data/msats.g.rda |binary strataG-2.4.905/strataG/inst/doc/external.programs.Rmd | 2 strataG-2.4.905/strataG/inst/doc/external.programs.html | 202 + strataG-2.4.905/strataG/inst/doc/gtypes.R | 97 strataG-2.4.905/strataG/inst/doc/gtypes.Rmd | 135 - strataG-2.4.905/strataG/inst/doc/gtypes.html | 1172 ++++++---- strataG-2.4.905/strataG/inst/doc/population.structure.R | 22 strataG-2.4.905/strataG/inst/doc/population.structure.Rmd | 18 strataG-2.4.905/strataG/inst/doc/population.structure.html | 436 ++- strataG-2.4.905/strataG/inst/doc/sequences.R | 32 strataG-2.4.905/strataG/inst/doc/sequences.Rmd | 8 strataG-2.4.905/strataG/inst/doc/sequences.html | 755 +++--- strataG-2.4.905/strataG/inst/doc/summaries.R | 57 strataG-2.4.905/strataG/inst/doc/summaries.Rmd | 51 strataG-2.4.905/strataG/inst/doc/summaries.html | 1044 ++++++-- strataG-2.4.905/strataG/inst/fastsimcoal2.html |only strataG-2.4.905/strataG/man/LDgenepop.Rd | 17 strataG-2.4.905/strataG/man/alleleFreqs.Rd | 28 strataG-2.4.905/strataG/man/alleleSplit.Rd | 1 strataG-2.4.905/strataG/man/allelicRichness.Rd | 10 strataG-2.4.905/strataG/man/arlequin.Rd | 78 strataG-2.4.905/strataG/man/as.data.frame.gtypes.Rd | 59 strataG-2.4.905/strataG/man/as.multidna.Rd | 2 strataG-2.4.905/strataG/man/baseFreqs.Rd | 23 strataG-2.4.905/strataG/man/clumpp.Rd | 14 strataG-2.4.905/strataG/man/createConsensus.Rd | 5 strataG-2.4.905/strataG/man/df2gtypes.Rd | 23 strataG-2.4.905/strataG/man/dupGenotypes.Rd | 12 strataG-2.4.905/strataG/man/evanno.Rd | 8 strataG-2.4.905/strataG/man/expandHaplotypes.Rd | 10 strataG-2.4.905/strataG/man/fasta.Rd | 2 strataG-2.4.905/strataG/man/fixedDifferences.Rd | 20 strataG-2.4.905/strataG/man/fixedSites.Rd | 5 strataG-2.4.905/strataG/man/freq2GenData.Rd | 13 strataG-2.4.905/strataG/man/fsc.input.Rd |only strataG-2.4.905/strataG/man/fscRead.Rd |only strataG-2.4.905/strataG/man/fscRun.Rd |only strataG-2.4.905/strataG/man/fscWrite.Rd |only strataG-2.4.905/strataG/man/fusFs.Rd | 7 strataG-2.4.905/strataG/man/gelato.Rd | 19 strataG-2.4.905/strataG/man/genepop.Rd | 23 strataG-2.4.905/strataG/man/gtypes-class.Rd | 6 strataG-2.4.905/strataG/man/gtypes.accessors.Rd | 257 +- strataG-2.4.905/strataG/man/gtypes.show.Rd |only strataG-2.4.905/strataG/man/gtypes2phyDat.Rd | 6 strataG-2.4.905/strataG/man/heterozygosity.Rd | 26 strataG-2.4.905/strataG/man/hweTest.Rd | 30 strataG-2.4.905/strataG/man/initialize-gtypes-method.Rd | 36 strataG-2.4.905/strataG/man/iupac.Rd |only strataG-2.4.905/strataG/man/jackHWE.Rd | 22 strataG-2.4.905/strataG/man/labelHaplotypes.Rd | 12 strataG-2.4.905/strataG/man/landscape2gtypes.Rd |only strataG-2.4.905/strataG/man/ldNe.Rd | 39 strataG-2.4.905/strataG/man/lowFreqSubs.Rd | 8 strataG-2.4.905/strataG/man/mRatio.Rd | 33 strataG-2.4.905/strataG/man/maf.Rd | 22 strataG-2.4.905/strataG/man/mafft.Rd | 26 strataG-2.4.905/strataG/man/maverickRun.Rd | 14 strataG-2.4.905/strataG/man/mega.Rd | 13 strataG-2.4.905/strataG/man/mostDistantSequences.Rd | 36 strataG-2.4.905/strataG/man/mostRepresentativeSequences.Rd | 25 strataG-2.4.905/strataG/man/nucleotideDivergence.Rd | 15 strataG-2.4.905/strataG/man/nucleotideDiversity.Rd | 11 strataG-2.4.905/strataG/man/numAlleles.Rd | 9 strataG-2.4.905/strataG/man/numGenotyped.Rd | 6 strataG-2.4.905/strataG/man/numMissing.Rd | 4 strataG-2.4.905/strataG/man/phase.Rd | 75 strataG-2.4.905/strataG/man/popStructStat.Rd | 65 strataG-2.4.905/strataG/man/popStructTest.Rd | 67 strataG-2.4.905/strataG/man/propUniqueAlleles.Rd | 9 strataG-2.4.905/strataG/man/readGenData.Rd | 8 strataG-2.4.905/strataG/man/removeSequences.Rd | 2 strataG-2.4.905/strataG/man/sequence2gtypes.Rd | 18 strataG-2.4.905/strataG/man/sequenceLikelihoods.Rd | 19 strataG-2.4.905/strataG/man/sfs.Rd |only strataG-2.4.905/strataG/man/sharedLoci.Rd | 22 strataG-2.4.905/strataG/man/simGammaHaps.Rd | 3 strataG-2.4.905/strataG/man/strataSplit.Rd | 2 strataG-2.4.905/strataG/man/stratify.Rd | 7 strataG-2.4.905/strataG/man/structure.Rd | 50 strataG-2.4.905/strataG/man/structurePlot.Rd | 30 strataG-2.4.905/strataG/man/summarizeAll.Rd |only strataG-2.4.905/strataG/man/summarizeInds.Rd |only strataG-2.4.905/strataG/man/summarizeLoci.Rd | 4 strataG-2.4.905/strataG/man/summary-gtypes-method.Rd | 9 strataG-2.4.905/strataG/man/tajimasD.Rd | 4 strataG-2.4.905/strataG/man/theta.Rd | 6 strataG-2.4.905/strataG/man/variableSites.Rd | 5 strataG-2.4.905/strataG/man/writeGtypes.Rd |only strataG-2.4.905/strataG/src/Hstats_C.cpp | 10 strataG-2.4.905/strataG/src/RcppExports.cpp | 60 strataG-2.4.905/strataG/src/init.c | 92 strataG-2.4.905/strataG/src/statFis_C.cpp | 2 strataG-2.4.905/strataG/tests/testthat/test-gtypes.accessors.R |only strataG-2.4.905/strataG/tests/testthat/test-gtypes.conversions.R |only strataG-2.4.905/strataG/tests/testthat/test-gtypes.creation.R |only strataG-2.4.905/strataG/tests/testthat/test-locus.summaries.R |only strataG-2.4.905/strataG/tests/testthat/test-popStructStats.R | 35 strataG-2.4.905/strataG/tests/testthat/test-private.alleles.R |only strataG-2.4.905/strataG/tests/testthat/test-sequence.summaries.R |only strataG-2.4.905/strataG/tests/testthat/test-shared.loci.R |only strataG-2.4.905/strataG/vignettes/external.programs.Rmd | 2 strataG-2.4.905/strataG/vignettes/gtypes.Rmd | 135 - strataG-2.4.905/strataG/vignettes/population.structure.Rmd | 18 strataG-2.4.905/strataG/vignettes/sequences.Rmd | 8 strataG-2.4.905/strataG/vignettes/summaries.Rmd | 51 237 files changed, 7873 insertions(+), 4649 deletions(-)
Title: Quantile Regression Coefficients Modeling
Description: Parametric modeling of quantile regression coefficient functions.
Can be used with censored and truncated data.
Author: Paolo Frumento <paolo.frumento@unipi.it>
Maintainer: Paolo Frumento <paolo.frumento@unipi.it>
Diff between qrcm versions 2.1 dated 2017-03-27 and 2.2 dated 2020-02-28
DESCRIPTION | 16 ++++++++-------- MD5 | 24 ++++++++++++------------ NAMESPACE | 3 ++- NEWS.md | 10 +++++++--- R/qrcm.R | 24 ++++++++++++++---------- man/iqr.Rd | 7 +++---- man/plf.Rd | 2 +- man/plot.iqr.Rd | 2 +- man/predict.iqr.Rd | 2 +- man/qrcm-package.Rd | 8 ++++---- man/slp.Rd | 2 +- man/summary.iqr.Rd | 2 +- man/test.fit.Rd | 8 ++++---- 13 files changed, 59 insertions(+), 51 deletions(-)
Title: Optimal Scaling
Description: Optimal scaling of a data vector is obtained through a least-squares transformation subject to appropriate measurement constraints. Further information about this methodology is provided by Young (1981)<doi:10.1007/BF02293796> and Jacoby (1999)< doi:10.2307/2991794>.
Author: William G. Jacoby
Maintainer: William G. Jacoby <wm.g.jacoby@gmail.com>
Diff between optiscale versions 1.1 dated 2014-08-01 and 1.2 dated 2020-02-28
DESCRIPTION | 15 +++++++-------- MD5 | 10 +++++----- NAMESPACE | 1 + man/elec92.Rd | 2 +- man/opscale.Rd | 3 --- man/optiscale-package.Rd | 4 ++-- 6 files changed, 16 insertions(+), 19 deletions(-)
Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. 'naniar' provides data structures
and functions that facilitate the plotting of missing values and examination
of imputations. This allows missing data dependencies to be explored with
minimal deviation from the common work patterns of 'ggplot2' and tidy data.
The work is fully discussed at Tierney & Cook (2018) <arXiv:1809.02264>.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>),
Di Cook [aut] (<https://orcid.org/0000-0002-3813-7155>),
Miles McBain [aut] (<https://orcid.org/0000-0003-2865-2548>),
Colin Fay [aut] (<https://orcid.org/0000-0001-7343-1846>),
Mitchell O'Hara-Wild [ctb],
Jim Hester [ctb],
Luke Smith [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between naniar versions 0.4.2 dated 2019-02-15 and 0.5.0 dated 2020-02-28
naniar-0.4.2/naniar/man/all_row_complete.Rd |only naniar-0.4.2/naniar/man/all_row_miss.Rd |only naniar-0.4.2/naniar/man/miss-complete-case-pct.Rd |only naniar-0.4.2/naniar/man/miss-complete-case-prop.Rd |only naniar-0.4.2/naniar/man/miss-complete-var-pct.Rd |only naniar-0.4.2/naniar/man/miss-complete-var-prop.Rd |only naniar-0.4.2/naniar/man/test_if_shadow.Rd |only naniar-0.4.2/naniar/tests/figs/naniar-plots |only naniar-0.4.2/naniar/tests/figs/test-gg-miss-upset-r |only naniar-0.5.0/naniar/DESCRIPTION | 15 naniar-0.5.0/naniar/MD5 | 281 +-- naniar-0.5.0/naniar/NAMESPACE | 7 naniar-0.5.0/naniar/NEWS.md | 41 naniar-0.5.0/naniar/R/add-cols.R | 4 naniar-0.5.0/naniar/R/add-n-prop-miss.R | 4 naniar-0.5.0/naniar/R/data-riskfactors.R | 2 naniar-0.5.0/naniar/R/gg-miss-fct.R | 14 naniar-0.5.0/naniar/R/gg-miss-upset.R | 24 naniar-0.5.0/naniar/R/gg-miss-which.R | 4 naniar-0.5.0/naniar/R/impute_below.R | 16 naniar-0.5.0/naniar/R/miss-complete-x-pct-prop.R | 146 - naniar-0.5.0/naniar/R/miss-scan-count.R | 4 naniar-0.5.0/naniar/R/miss-x-cumsum.R | 12 naniar-0.5.0/naniar/R/miss-x-run.R | 2 naniar-0.5.0/naniar/R/miss-x-span.R | 2 naniar-0.5.0/naniar/R/miss-x-summary.R | 5 naniar-0.5.0/naniar/R/miss-x-table.R | 2 naniar-0.5.0/naniar/R/n-var-miss.R | 3 naniar-0.5.0/naniar/R/prop-pct-var-case-miss-complete.R | 25 naniar-0.5.0/naniar/R/replace-to-na.R | 20 naniar-0.5.0/naniar/R/scoped-replace-with-na.R | 2 naniar-0.5.0/naniar/R/shadow-recode.R | 5 naniar-0.5.0/naniar/R/shadows.R | 33 naniar-0.5.0/naniar/R/utils.R | 69 naniar-0.5.0/naniar/README.md | 79 - 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naniar-0.5.0/naniar/tests/testthat/test-miss-case-summary.R | 2 naniar-0.5.0/naniar/tests/testthat/test-miss-case-table.R | 2 naniar-0.5.0/naniar/tests/testthat/test-miss-scan-count.R | 30 naniar-0.5.0/naniar/tests/testthat/test-miss-summary.R | 11 naniar-0.5.0/naniar/tests/testthat/test-miss-var-run.R |only naniar-0.5.0/naniar/tests/testthat/test-miss-var-span.R |only naniar-0.5.0/naniar/tests/testthat/test-miss-var-summary.R | 2 naniar-0.5.0/naniar/tests/testthat/test-miss-var-table.R | 2 naniar-0.5.0/naniar/tests/testthat/test-prop-cases-not-zero.R |only naniar-0.5.0/naniar/tests/testthat/test-prop_row.R |only naniar-0.5.0/naniar/tests/testthat/test-replace-with-na.R | 9 naniar-0.5.0/naniar/tests/testthat/test-unbind.R |only naniar-0.5.0/naniar/vignettes/getting-started-w-naniar.Rmd | 20 naniar-0.5.0/naniar/vignettes/naniar-visualisation.Rmd | 16 naniar-0.5.0/naniar/vignettes/replace-with-na.Rmd | 10 146 files changed, 5751 insertions(+), 5580 deletions(-)
Title: Organizing Data in Hypercubes
Description: Provides functions and methods for organizing data in hypercubes
(i.e., a multi-dimensional cube). Cubes are generated from molten data frames.
Each cube can be manipulated with five operations: rotation (change.dimensionOrder()),
dicing and slicing (add.selection(), remove.selection()), drilling down (add.aggregation()),
and rolling up (remove.aggregation()).
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@th-deg.de>
Diff between hypercube versions 0.2.0 dated 2019-09-18 and 0.2.1 dated 2020-02-28
DESCRIPTION | 14 ++-- MD5 | 47 +++++++------- NAMESPACE | 3 NEWS | 36 ++++++---- R/cube.R | 143 ++++++++++++++++++++++++++++++++++++------- R/dimension.R | 4 - R/hypercube-package.R | 8 +- man/Cube-class.Rd | 74 +++++++++++----------- man/Dimension-class.Rd | 70 ++++++++++----------- man/add.aggregation.Rd | 89 +++++++++++++------------- man/add.selection.Rd | 86 ++++++++++++------------- man/as.data.frame.Cube.Rd | 83 ++++++++++++------------ man/change.dimensionOrder.Rd | 74 +++++++++++----------- man/generateCube.Rd | 84 +++++++++++++------------ man/hypercube-package.Rd | 82 ++++++++++++------------ man/importance.Rd | 72 ++++++++++----------- man/plot-Cube-method.Rd | 74 +++++++++++----------- man/print.Importances.Rd | 68 ++++++++++---------- man/remove.aggregation.Rd | 90 +++++++++++++-------------- man/remove.selection.Rd | 84 ++++++++++++------------- man/sales.Rd | 52 +++++++-------- man/show-Cube-method.Rd | 61 +++++++++--------- man/show-Dimension-method.Rd | 57 ++++++++--------- man/sparsity.Rd | 72 ++++++++++----------- man/summary.Rd |only 25 files changed, 824 insertions(+), 703 deletions(-)
Title: Construct Modeling Packages
Description: Building modeling packages is hard. A large amount of effort
generally goes into providing an implementation for a new method that is
efficient, fast, and correct, but often less emphasis is put on the user
interface. A good interface requires specialized knowledge about S3 methods
and formulas, which the average package developer might not have.
The goal of 'hardhat' is to reduce the burden around building new modeling
packages by providing functionality for preprocessing, predicting, and
validating input.
Author: Davis Vaughan [aut, cre],
Max Kuhn [aut],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between hardhat versions 0.1.1 dated 2020-01-08 and 0.1.2 dated 2020-02-28
DESCRIPTION | 8 ++++---- MD5 | 33 +++++++++++++++++---------------- NEWS.md | 9 +++++++++ R/blueprint-recipe-default.R | 4 ++-- R/blueprint-recipe.R | 2 +- R/model-matrix.R | 11 +++++++++-- README.md | 2 -- build/hardhat.pdf |binary inst/doc/forge.html | 14 ++++++-------- inst/doc/mold.html | 11 ++++------- inst/doc/package.html | 13 +++++-------- man/default_recipe_blueprint.Rd | 2 +- man/new-blueprint.Rd | 2 +- man/new-default-blueprint.Rd | 2 +- tests/testthat/test-forge-recipe.R | 2 +- tests/testthat/test-model-matrix.R |only tests/testthat/test-mold-recipe.R | 18 ++++++++++++++++++ tests/testthat/test-validation.R | 4 ++-- 18 files changed, 81 insertions(+), 56 deletions(-)
Title: Genealogical Data Analysis
Description: Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations.
Author: Louis Houde [aut],
Jean-Francois Lefebvre [aut],
Valery Roy-Lagace [aut],
Sebastien Lemieux [aut],
Michael J. Fromberger [ctb],
Marie-Helene Roy-Gagnon [cre]
Maintainer: Marie-Helene Roy-Gagnon <mroygagn@uottawa.ca>
Diff between GENLIB versions 1.0.6 dated 2018-05-30 and 1.0.7 dated 2020-02-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/fonctionsBase.R | 6 ++++-- man/genea140.Rd | 2 +- man/geneaJi.Rd | 2 +- man/pop140.Rd | 2 +- 6 files changed, 16 insertions(+), 14 deletions(-)
Title: Analysis and Visualization of Droplet Digital PCR in R and on
the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR
(ddPCR) data in R. This is the first non-proprietary software for analyzing
two-channel ddPCR data. An interactive tool was also created and is available
online to facilitate this analysis for anyone who is not comfortable with
using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ddpcr versions 1.12 dated 2020-01-13 and 1.13 dated 2020-02-28
DESCRIPTION | 6 MD5 | 34 ++--- NEWS.md | 4 R/failures.R | 64 ++++----- R/type-custom_thresholds.R | 75 +++++------ R/utils.R | 86 ++++++------- build/vignette.rds |binary inst/doc/algorithm.html | 15 -- inst/doc/extend.html | 262 +++++++++++++++++++--------------------- inst/doc/overview.html | 230 +++++++++++++++++------------------ inst/doc/technical_details.html | 15 -- inst/shiny/server/tab-results.R | 72 +++++----- man/custom_thresholds.Rd | 2 man/move_back.Rd | 2 man/move_front.Rd | 2 man/remove_failures.Rd | 2 man/wells_success.Rd | 2 tests/testthat/test-utils.R | 22 +-- 18 files changed, 443 insertions(+), 452 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-31 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-27 3.0
Title: Testing for Symmetry of Data and Model Residuals
Description: Implementations of a large number of tests for symmetry and their
bootstrap variants, which can be used for testing the symmetry of random
samples around a known or unknown mean. Functions are also there for testing
the symmetry of model residuals around zero. Currently, the supported models
are linear models and generalized autoregressive conditional
heteroskedasticity (GARCH) models (fitted with the 'fGarch' package). All
tests are implemented using the 'Rcpp' package which ensures great
performance of the code.
Author: Blagoje Ivanović [aut, cre]
Bojana Milošević [aut]
Marko Obradović [aut]
Maintainer: Blagoje Ivanović <blagoje_ivanovic@matf.bg.ac.rs>
Diff between symmetry versions 0.1.1 dated 2019-08-29 and 0.2.1 dated 2020-02-28
symmetry-0.1.1/symmetry/R/CHstatistic.R |only symmetry-0.1.1/symmetry/R/Mstatistic.R |only symmetry-0.1.1/symmetry/R/S1statistic.R |only symmetry-0.1.1/symmetry/R/S2statistic.R |only symmetry-0.1.1/symmetry/R/T1statistic.R |only symmetry-0.1.1/symmetry/R/T2statistic.R |only symmetry-0.1.1/symmetry/src/CH.cpp |only symmetry-0.1.1/symmetry/src/M.cpp |only symmetry-0.1.1/symmetry/src/S1.cpp |only symmetry-0.1.1/symmetry/src/S2.cpp |only symmetry-0.1.1/symmetry/src/T1.cpp |only symmetry-0.1.1/symmetry/src/T2.cpp |only symmetry-0.2.1/symmetry/DESCRIPTION | 8 - symmetry-0.2.1/symmetry/MD5 | 55 ++++--- symmetry-0.2.1/symmetry/NAMESPACE | 15 +- symmetry-0.2.1/symmetry/NEWS.md |only symmetry-0.2.1/symmetry/R/AAA_statistics_docs.R | 11 - symmetry-0.2.1/symmetry/R/BH2statistic.R |only symmetry-0.2.1/symmetry/R/BHC1statistic.R |only symmetry-0.2.1/symmetry/R/BHC2statistic.R |only symmetry-0.2.1/symmetry/R/FMstatistic.R |only symmetry-0.2.1/symmetry/R/HMstatistic.R |only symmetry-0.2.1/symmetry/R/MIstatistic.R |only symmetry-0.2.1/symmetry/R/NAC1statistic.R |only symmetry-0.2.1/symmetry/R/NAC2statistic.R |only symmetry-0.2.1/symmetry/R/RWstatistic.R |only symmetry-0.2.1/symmetry/R/RcppExports.R | 56 ++++--- symmetry-0.2.1/symmetry/R/symmetry_test.R | 4 symmetry-0.2.1/symmetry/build/partial.rdb |binary symmetry-0.2.1/symmetry/inst/REFERENCES.bib | 10 + symmetry-0.2.1/symmetry/inst/include/test_stats.h | 15 +- symmetry-0.2.1/symmetry/man/TestStatistics.Rd | 59 ++++---- symmetry-0.2.1/symmetry/man/symmetry_test.Rd | 2 symmetry-0.2.1/symmetry/src/BH2.cpp |only symmetry-0.2.1/symmetry/src/BHC1.cpp |only symmetry-0.2.1/symmetry/src/BHC2.cpp |only symmetry-0.2.1/symmetry/src/FM.cpp |only symmetry-0.2.1/symmetry/src/HM.cpp |only symmetry-0.2.1/symmetry/src/MI.cpp |only symmetry-0.2.1/symmetry/src/NAC1.cpp |only symmetry-0.2.1/symmetry/src/NAC2.cpp |only symmetry-0.2.1/symmetry/src/RW.cpp |only symmetry-0.2.1/symmetry/src/RcppExports.cpp | 161 +++++++++++++--------- symmetry-0.2.1/symmetry/src/bootstrap.cpp | 33 ++-- 44 files changed, 261 insertions(+), 168 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-08 0.0.2
2013-04-01 0.0.1