Title: A 'ggplot2' Implement of Venn Diagram
Description: Easy-to-use functions to generate 2-7 sets Venn plot in publication quality.
'ggVennDiagram' plot Venn using well-defined geometry dataset and 'ggplot2'. The shapes of 2-4 sets
Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which
are developed and imported from another package 'venn', authored by Adrian Dusa. We provided internal functions to
integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections
of them, then separately plot Venn in three components: set edges, set labels, and regions.
From version 1.0, it is possible to customize these components as you demand in ordinary 'ggplot2' grammar.
Author: Chun-Hui Gao [aut, cre] (<https://orcid.org/0000-0002-1445-7939>),
Guangchuang Yu [ctb] (<https://orcid.org/0000-0002-6485-8781>),
Adrian Dusa [ctb]
Maintainer: Chun-Hui Gao <gaospecial@gmail.com>
Diff between ggVennDiagram versions 1.0.7 dated 2021-04-28 and 1.1.0 dated 2021-05-07
DESCRIPTION | 20 +++- MD5 | 43 +++++---- NAMESPACE | 66 +++++++-------- NEWS.md | 13 ++- R/Construct.R | 4 R/ggVennDiagram.R | 130 ++++++++++++++++++++++++------ R/plot_shapes.R | 32 +++++-- R/process_data.R | 3 R/shape_generator.R | 6 + README.md | 17 +++ man/Venn-class.Rd | 4 man/ellipse.Rd | 4 man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/get_shape_data.Rd | 3 man/ggVennDiagram.Rd | 32 ++++++- man/plot_shapes.Rd | 10 ++ man/plot_venn.Rd | 43 +++++++-- man/vennplot-shapes.Rd |only 23 files changed, 311 insertions(+), 119 deletions(-)
Title: Apply Sojourn Methods for Processing ActiGraph Accelerometer
Data
Description: Provides a simple way for utilizing Sojourn methods for
accelerometer processing, as detailed in Lyden K, Keadle S,
Staudenmayer J, & Freedson P (2014) <doi:10.1249/MSS.0b013e3182a42a2d>,
Ellingson LD, Schwabacher IJ, Kim Y, Welk GJ, & Cook DB (2016)
<doi:10.1249/MSS.0000000000000915>, and Hibbing PR, Ellingson LD,
Dixon PM, & Welk GJ (2018) <doi:10.1249/MSS.0000000000001486>.
Author: Paul R. Hibbing [aut, cre],
Kate Lyden [aut],
Isaac J. Schwabacher [aut]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
Diff between Sojourn versions 1.0.2 dated 2021-04-12 and 1.1.0 dated 2021-05-07
Sojourn-1.0.2/Sojourn/R/RcppExports.R |only Sojourn-1.0.2/Sojourn/man/combine.sojourns.Rd |only Sojourn-1.1.0/Sojourn/DESCRIPTION | 14 Sojourn-1.1.0/Sojourn/MD5 | 46 - Sojourn-1.1.0/Sojourn/NAMESPACE | 2 Sojourn-1.1.0/Sojourn/NEWS.md | 5 Sojourn-1.1.0/Sojourn/R/SIP_Functions.R | 77 -- Sojourn-1.1.0/Sojourn/R/SIP_Soj_3x.R | 24 Sojourn-1.1.0/Sojourn/R/Sojourn.R | 6 Sojourn-1.1.0/Sojourn/R/Utils.R | 61 + Sojourn-1.1.0/Sojourn/R/combine_sojourns.R |only Sojourn-1.1.0/Sojourn/R/compute_bouts_info.R | 16 Sojourn-1.1.0/Sojourn/R/soj_1x_original.R | 20 Sojourn-1.1.0/Sojourn/R/soj_3x_original.R | 653 +++--------------- Sojourn-1.1.0/Sojourn/R/sysdata.rda |only Sojourn-1.1.0/Sojourn/R/youth_apply_sojourn.R | 31 Sojourn-1.1.0/Sojourn/R/youth_get_sojourns.R | 14 Sojourn-1.1.0/Sojourn/README.md | 3 Sojourn-1.1.0/Sojourn/man/apply_youth_sojourn.Rd | 21 Sojourn-1.1.0/Sojourn/man/combine_sojourns.Rd |only Sojourn-1.1.0/Sojourn/man/compute.bouts.info.Rd | 16 Sojourn-1.1.0/Sojourn/man/get_youth_sojourns.Rd | 2 Sojourn-1.1.0/Sojourn/man/prep_nnet_soj3x_original.Rd |only Sojourn-1.1.0/Sojourn/man/soj_1x_original.Rd | 6 Sojourn-1.1.0/Sojourn/man/soj_3x_original.Rd | 13 Sojourn-1.1.0/Sojourn/man/sojourn_3x_SIP.Rd | 4 Sojourn-1.1.0/Sojourn/tests/testthat/test_sojOutput.R | 7 27 files changed, 305 insertions(+), 736 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph] (R/stanmodels.R, configure,
configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.6-5 dated 2020-05-07 and 0.7-0 dated 2021-05-07
DESCRIPTION | 15 MD5 | 70 + NAMESPACE | 14 R/OncoBayes2-package.R | 8 R/blrm_exnex.R | 16 R/blrm_formula_linear.R | 76 +- R/blrm_formula_saturating.R | 72 +- R/blrm_trial.R | 291 ++++++-- R/log_sum_exp.R |only R/plot_blrm.R |only R/predictive_interval.R | 8 R/summary.R | 256 ++++++- R/sysdata.rda |binary inst/NEWS | 12 inst/doc/OncoBayes2.pdf |binary inst/doc/introduction.R | 333 ++------- inst/doc/introduction.Rmd | 515 ++++++-------- inst/doc/introduction.html | 1058 ++++++++++++++++-------------- inst/sbc/calibration.md5 | 6 inst/sbc/make_reference_rankhist.R | 10 inst/sbc/sbc_example_models.R | 9 inst/sbc/sbc_report.R | 232 +----- inst/sbc/sbc_report.html |only inst/sbc/sbc_report_plots.R |only inst/sbc/sbc_tools.R | 13 man/blrm_formula_linear.Rd | 8 man/blrm_formula_saturating.Rd | 8 man/blrm_trial.Rd | 2 man/dot-marginSums.Rd |only man/dot-proportions.Rd |only man/dot-validate_group_stratum_nesting.Rd |only man/log_mean_exp.Rd |only man/log_sum_exp.Rd |only man/plot_blrm.Rd |only man/summary.blrm_trial.Rd | 14 man/summary.blrmfit.Rd | 29 tests/testthat/helper-plots.R |only tests/testthat/test-blrm_exnex.R | 94 ++ tests/testthat/test-blrm_trial.R | 350 +++++++++ tests/testthat/test-plots.R |only tools/build_ref_pdf.sh | 1 vignettes/introduction.Rmd | 515 ++++++-------- 42 files changed, 2318 insertions(+), 1717 deletions(-)
Title: Geospatial Queries Using 'PyMongo'
Description: Utilizes methods of the 'PyMongo' 'Python' library to initialize, insert and query 'GeoJson' data (see <https://github.com/mongodb/mongo-python-driver> for more information on 'PyMongo'). Furthermore, it allows the user to validate 'GeoJson' objects and to use the console for 'MongoDB' (bulk) commands. The 'reticulate' package provides the 'R' interface to 'Python' modules, classes and functions.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between GeoMongo versions 1.0.1 dated 2017-09-09 and 1.0.2 dated 2021-05-07
DESCRIPTION | 18 MD5 | 40 - NAMESPACE | 5 NEWS.md | 6 R/package.R | 35 - R/utils.R | 45 - README.md | 10 build/vignette.rds |binary inst/CITATION |only inst/doc/the_GeoMongo_package.R | 82 +- inst/doc/the_GeoMongo_package.Rmd | 4 inst/doc/the_GeoMongo_package.html | 1141 ++++++++++++++++++++++--------------- man/geomongo.Rd | 191 ++++-- man/json_schema_validator.Rd | 34 - man/mongodb_console.Rd | 4 tests |only vignettes/the_GeoMongo_package.Rmd | 4 17 files changed, 1011 insertions(+), 608 deletions(-)
Title: Generate Standardized Data
Description: Creates simulated data from structural equation models with standardized loading. Data generation methods are described in Schneider (2013) <doi:10.1177/0734282913478046>.
Author: W. Joel Schneider [aut, cre] (<https://orcid.org/0000-0002-8393-5316>)
Maintainer: W. Joel Schneider <w.joel.schneider@gmail.com>
Diff between simstandard versions 0.6.2 dated 2021-01-21 and 0.6.3 dated 2021-05-07
DESCRIPTION | 8 - MD5 | 28 ++--- NAMESPACE | 4 NEWS.md | 11 ++ R/main.R | 185 ++++++++++++++++++++++++++++++++-- README.md | 12 +- build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/simstandard_tutorial.html | 39 ++----- man/add_composite_scores.Rd | 12 ++ man/add_factor_scores.Rd | 3 man/get_factor_score_coefficients.Rd |only man/get_factor_score_validity.Rd |only man/get_factor_score_validity_se.Rd |only man/get_model_implied_correlations.Rd | 2 man/get_model_names.Rd |only tests/testthat/testthat.R | 20 +++ 17 files changed, 266 insertions(+), 59 deletions(-)
Title: Download, Compile and Link 'OpenBLAS' Library with R
Description: The 'ropenblas' package (<https://prdm0.github.io/ropenblas/>) is useful for users of any 'GNU/Linux' distribution. It will be possible to download, compile and link the 'OpenBLAS' library (<https://www.openblas.net/>) with the R language, always by the same procedure, regardless of the 'GNU/Linux' distribution used. With the 'ropenblas' package it is possible to download, compile and link the latest version of the 'OpenBLAS' library even the repositories of the 'GNU/Linux' distribution used do not include the latest versions of 'OpenBLAS'. If of interest, older versions of the 'OpenBLAS' library may be considered. Linking R with an optimized version of 'BLAS' (<http://www.netlib.org/blas/>) may improve the computational performance of R code. The 'OpenBLAS' library is an optimized implementation of 'BLAS' that can be easily linked to R with the 'ropenblas' package.
Author: Pedro Rafael D. Marinho [aut, cre]
(<https://orcid.org/0000-0003-1591-8300>)
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between ropenblas versions 0.2.9 dated 2021-02-16 and 0.2.10 dated 2021-05-07
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NAMESPACE | 3 +++ NEWS.md | 8 +++++++- R/ropenblas.R | 30 ++++++++++++------------------ 5 files changed, 33 insertions(+), 29 deletions(-)
Title: Collecting Counter Strike Global Offensive Data
Description: An implementation of calls designed to collect and organize in an easy way the data from the Steam API specifically for the Counter-Strike Global Offensive Game (CS Go) <https://developer.valvesoftware.com/wiki/Steam_Web_API>.
Author: Adson Costanzi [aut, cre] (<https://orcid.org/0000-0002-5210-2952>),
Rodrigo Fontoura [aut] (<https://orcid.org/0000-0002-8156-3424>)
Maintainer: Adson Costanzi <adsoncostanzi32@gmail.com>
Diff between CSGo versions 0.5.2 dated 2021-03-27 and 0.6.7 dated 2021-05-07
CSGo-0.5.2/CSGo/data/suport.rda |only CSGo-0.5.2/CSGo/man/suport.Rd |only CSGo-0.6.7/CSGo/DESCRIPTION | 8 +-- CSGo-0.6.7/CSGo/MD5 | 43 +++++++++-------- CSGo-0.6.7/CSGo/R/csgo_api_profile.R | 23 +++++++-- CSGo-0.6.7/CSGo/R/data.R | 31 ++++++++++++ CSGo-0.6.7/CSGo/R/get_stats_friends.R | 75 +++++++++++++++---------------- CSGo-0.6.7/CSGo/R/get_stats_user.R | 14 +++-- CSGo-0.6.7/CSGo/R/globals.R | 2 CSGo-0.6.7/CSGo/README.md | 2 CSGo-0.6.7/CSGo/build/vignette.rds |binary CSGo-0.6.7/CSGo/data/map_pictures.rda |only CSGo-0.6.7/CSGo/data/support.rda |only CSGo-0.6.7/CSGo/data/weapon_pictures.rda |only CSGo-0.6.7/CSGo/inst/doc/auth.R | 6 +- CSGo-0.6.7/CSGo/inst/doc/auth.Rmd | 8 +-- CSGo-0.6.7/CSGo/inst/doc/auth.html | 18 +++++-- CSGo-0.6.7/CSGo/inst/doc/usecase.Rmd | 8 +-- CSGo-0.6.7/CSGo/inst/doc/usecase.html | 20 +++++--- CSGo-0.6.7/CSGo/man/csgo_api_profile.Rd | 13 ++++- CSGo-0.6.7/CSGo/man/get_stats_friends.Rd | 7 ++ CSGo-0.6.7/CSGo/man/map_pictures.Rd |only CSGo-0.6.7/CSGo/man/support.Rd |only CSGo-0.6.7/CSGo/man/weapon_pictures.Rd |only CSGo-0.6.7/CSGo/vignettes/auth.Rmd | 8 +-- CSGo-0.6.7/CSGo/vignettes/img/logo.png |only CSGo-0.6.7/CSGo/vignettes/usecase.Rmd | 8 +-- 27 files changed, 188 insertions(+), 106 deletions(-)
Title: Regularized Greedy Forest
Description: Regularized Greedy Forest wrapper of the 'Regularized Greedy Forest' <https://github.com/RGF-team/rgf/tree/master/python-package> 'python' package, which also includes a Multi-core implementation (FastRGF) <https://github.com/RGF-team/rgf/tree/master/FastRGF>.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
Ryosuke Fukatani [cph] (Author of the python wrapper of the
'Regularized Greedy Forest' machine learning algorithm),
Nikita Titov [cph] (Author of the python wrapper of the 'Regularized
Greedy Forest' machine learning algorithm),
Tong Zhang [cph] (Author of the 'Regularized Greedy Forest' and of the
Multi-core implementation of Regularized Greedy Forest machine
learning algorithm),
Rie Johnson [cph] (Author of the 'Regularized Greedy Forest' machine
learning algorithm)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between RGF versions 1.0.7 dated 2021-03-16 and 1.0.8 dated 2021-05-07
DESCRIPTION | 15 ++++----- MD5 | 39 ++++++++++++----------- NEWS.md | 9 +++++ R/FastRGF_Classifier.R | 8 ++-- R/FastRGF_Regressor.R | 4 +- R/RGF_Classifier.R | 4 +- R/RGF_Regressor.R | 4 +- R/TO_scipy_sparse.R | 4 +- R/mat_2scipy_sparse.R | 4 +- R/package.R | 62 +++++++------------------------------- inst/CITATION |only inst/doc/the_RGF_package.html | 4 +- man/FastRGF_Classifier.Rd | 8 ++-- man/FastRGF_Regressor.Rd | 4 +- man/RGF_Classifier.Rd | 4 +- man/RGF_Regressor.Rd | 4 +- man/TO_scipy_sparse.Rd | 4 +- man/mat_2scipy_sparse.Rd | 4 +- tests/testthat/helper-skip.R | 4 +- tests/testthat/setup.R | 4 +- tests/testthat/test-RGF_package.R | 19 ----------- 21 files changed, 83 insertions(+), 129 deletions(-)
Title: Probabilistic Sex Estimate using Logistic Regression, Based on
VISual Traits of the Human Os Coxae
Description: An R-Shiny application implementing a method of sexing the human os coxae based on logistic regressions and Bruzek's nonmetric traits <doi:10.1002/ajpa.23855>.
Author: Frédéric Santos [aut, cre] (<https://orcid.org/0000-0003-1445-3871>),
Élodie Bernardeau [ctb]
Maintainer: Frédéric Santos <frederic.santos@u-bordeaux.fr>
Diff between PELVIS versions 2.0.2 dated 2020-06-25 and 2.0.3 dated 2021-05-07
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 3 ++- NEWS.md | 5 +++++ build |only man/dataframe_sexing.Rd | 14 +++++++------- man/start_pelvis.Rd | 2 +- 7 files changed, 26 insertions(+), 19 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <arXiv:1103.3817> and
Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework
allows for elastic analysis of functional data through phase and
amplitude separation.
Author: J. Derek Tucker <jdtuck@sandia.gov>
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 1.9.4 dated 2020-10-09 and 1.9.6 dated 2021-05-07
fdasrvf-1.9.4/fdasrvf/R/srsf_to_f.R |only fdasrvf-1.9.4/fdasrvf/man/srsf_to_f.Rd |only fdasrvf-1.9.6/fdasrvf/DESCRIPTION | 11 fdasrvf-1.9.6/fdasrvf/MD5 | 202 - fdasrvf-1.9.6/fdasrvf/NAMESPACE | 205 - fdasrvf-1.9.6/fdasrvf/NEWS | 206 - fdasrvf-1.9.6/fdasrvf/R/AmplitudeBoxplot.R | 340 +- fdasrvf-1.9.6/fdasrvf/R/PhaseBoxplot.R | 360 +- fdasrvf-1.9.6/fdasrvf/R/SqrtMean.R | 130 fdasrvf-1.9.6/fdasrvf/R/SqrtMedian.R | 158 fdasrvf-1.9.6/fdasrvf/R/align_fPCA.R | 580 +-- fdasrvf-1.9.6/fdasrvf/R/bayesian_functions.R | 98 fdasrvf-1.9.6/fdasrvf/R/calc_shape_dist.R | 71 fdasrvf-1.9.6/fdasrvf/R/curve_functions.R | 1127 +++--- fdasrvf-1.9.6/fdasrvf/R/curve_geodesic.R | 96 fdasrvf-1.9.6/fdasrvf/R/curve_karcher_cov.R | 93 fdasrvf-1.9.6/fdasrvf/R/curve_karcher_mean.R | 284 + fdasrvf-1.9.6/fdasrvf/R/curve_pair_align.R | 73 fdasrvf-1.9.6/fdasrvf/R/curve_principal_directions.R | 191 - fdasrvf-1.9.6/fdasrvf/R/curve_srvf_align.R | 129 fdasrvf-1.9.6/fdasrvf/R/curve_to_q.R | 66 fdasrvf-1.9.6/fdasrvf/R/elastic.depth.R | 130 fdasrvf-1.9.6/fdasrvf/R/elastic.distance.R | 78 fdasrvf-1.9.6/fdasrvf/R/elastic_logistic.R | 238 - fdasrvf-1.9.6/fdasrvf/R/elastic_lpcr_regression.R | 152 fdasrvf-1.9.6/fdasrvf/R/elastic_mlogistic.R | 260 - fdasrvf-1.9.6/fdasrvf/R/elastic_mlpcr_regression.R | 170 - fdasrvf-1.9.6/fdasrvf/R/elastic_pcr_regression.R | 162 fdasrvf-1.9.6/fdasrvf/R/elastic_prediction.R | 228 - fdasrvf-1.9.6/fdasrvf/R/elastic_regression.R | 304 - fdasrvf-1.9.6/fdasrvf/R/f_to_srvf.R | 52 fdasrvf-1.9.6/fdasrvf/R/fdasrvf-package.r | 309 - fdasrvf-1.9.6/fdasrvf/R/function_group_warp_bayes.R | 302 - fdasrvf-1.9.6/fdasrvf/R/function_mean_bayes.R | 226 - fdasrvf-1.9.6/fdasrvf/R/gauss_model.R | 224 - fdasrvf-1.9.6/fdasrvf/R/geometry.R | 276 - fdasrvf-1.9.6/fdasrvf/R/gradient.R | 84 fdasrvf-1.9.6/fdasrvf/R/horizFPCA.R | 166 - fdasrvf-1.9.6/fdasrvf/R/image_funcs.R | 842 ++--- fdasrvf-1.9.6/fdasrvf/R/invertGamma.R | 50 fdasrvf-1.9.6/fdasrvf/R/joint_gauss_model.R | 142 fdasrvf-1.9.6/fdasrvf/R/jointfPCA.R | 306 - fdasrvf-1.9.6/fdasrvf/R/kmeans.R | 423 +- fdasrvf-1.9.6/fdasrvf/R/multiple_align_functions.R | 318 - fdasrvf-1.9.6/fdasrvf/R/optimum.reparam.R | 208 - fdasrvf-1.9.6/fdasrvf/R/outlier.detection.R | 80 fdasrvf-1.9.6/fdasrvf/R/pair_align_functions.R | 98 fdasrvf-1.9.6/fdasrvf/R/pair_align_functions_bayes.R | 342 +- fdasrvf-1.9.6/fdasrvf/R/pair_align_functions_expomap.R | 1610 ++++----- fdasrvf-1.9.6/fdasrvf/R/pair_align_image.R | 194 - fdasrvf-1.9.6/fdasrvf/R/plot.ampbox.R | 142 fdasrvf-1.9.6/fdasrvf/R/plot.fdakma.R | 58 fdasrvf-1.9.6/fdasrvf/R/plot.fdawarp.R | 68 fdasrvf-1.9.6/fdasrvf/R/plot.hfpca.R | 64 fdasrvf-1.9.6/fdasrvf/R/plot.jfpca.R | 90 fdasrvf-1.9.6/fdasrvf/R/plot.phbox.R | 138 fdasrvf-1.9.6/fdasrvf/R/plot.vfpca.R | 90 fdasrvf-1.9.6/fdasrvf/R/predict.lpcr.R | 292 - fdasrvf-1.9.6/fdasrvf/R/predict.mlpcr.R | 340 +- fdasrvf-1.9.6/fdasrvf/R/predict.pcr.R | 260 - fdasrvf-1.9.6/fdasrvf/R/q_to_curve.R | 55 fdasrvf-1.9.6/fdasrvf/R/regression_functions.R | 252 - fdasrvf-1.9.6/fdasrvf/R/reparam_curve.R | 284 - fdasrvf-1.9.6/fdasrvf/R/reparam_image.R | 180 - fdasrvf-1.9.6/fdasrvf/R/resamplecurve.R | 80 fdasrvf-1.9.6/fdasrvf/R/rgam.R | 116 fdasrvf-1.9.6/fdasrvf/R/sample_shapes.R | 136 fdasrvf-1.9.6/fdasrvf/R/smooth.data.R | 56 fdasrvf-1.9.6/fdasrvf/R/srvf_to_f.R |only fdasrvf-1.9.6/fdasrvf/R/summary.fdawarp.R | 28 fdasrvf-1.9.6/fdasrvf/R/time_warping.R | 544 +-- fdasrvf-1.9.6/fdasrvf/R/tolerance.R | 260 - fdasrvf-1.9.6/fdasrvf/R/utility_functions.R | 1644 +++++----- fdasrvf-1.9.6/fdasrvf/R/vertFPCA.R | 194 - fdasrvf-1.9.6/fdasrvf/R/warp_f_gamma.R | 58 fdasrvf-1.9.6/fdasrvf/R/warp_q_gamma.R | 68 fdasrvf-1.9.6/fdasrvf/README.md | 170 - fdasrvf-1.9.6/fdasrvf/man/beta.Rd | 34 fdasrvf-1.9.6/fdasrvf/man/calc_shape_dist.Rd | 12 fdasrvf-1.9.6/fdasrvf/man/curve_karcher_cov.Rd | 12 fdasrvf-1.9.6/fdasrvf/man/curve_karcher_mean.Rd | 95 fdasrvf-1.9.6/fdasrvf/man/curve_principal_directions.Rd | 23 fdasrvf-1.9.6/fdasrvf/man/curve_srvf_align.Rd | 14 fdasrvf-1.9.6/fdasrvf/man/curve_to_q.Rd | 2 fdasrvf-1.9.6/fdasrvf/man/elastic.depth.Rd | 66 fdasrvf-1.9.6/fdasrvf/man/f_to_srvf.Rd | 4 fdasrvf-1.9.6/fdasrvf/man/fdasrvf.Rd | 100 fdasrvf-1.9.6/fdasrvf/man/growth_vel.Rd | 32 fdasrvf-1.9.6/fdasrvf/man/im.Rd | 32 fdasrvf-1.9.6/fdasrvf/man/jointFPCA.Rd | 124 fdasrvf-1.9.6/fdasrvf/man/kmeans_align.Rd | 5 fdasrvf-1.9.6/fdasrvf/man/q_to_curve.Rd | 6 fdasrvf-1.9.6/fdasrvf/man/sample_shapes.Rd | 6 fdasrvf-1.9.6/fdasrvf/man/simu_data.Rd | 44 fdasrvf-1.9.6/fdasrvf/man/simu_warp.Rd | 44 fdasrvf-1.9.6/fdasrvf/man/simu_warp_median.Rd | 44 fdasrvf-1.9.6/fdasrvf/man/srvf_to_f.Rd |only fdasrvf-1.9.6/fdasrvf/man/toy_data.Rd | 38 fdasrvf-1.9.6/fdasrvf/man/toy_warp.Rd | 38 fdasrvf-1.9.6/fdasrvf/src/gropt/incl/DriverCpp.h | 2 fdasrvf-1.9.6/fdasrvf/src/gropt/incl/SphereTx.h | 2 fdasrvf-1.9.6/fdasrvf/tests/testthat.R | 16 fdasrvf-1.9.6/fdasrvf/tests/testthat/test_pair_align_functions_bayes.R | 40 fdasrvf-1.9.6/fdasrvf/tests/testthat/test_pair_align_functions_expomap.R | 226 - 104 files changed, 9684 insertions(+), 9438 deletions(-)
Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>
Diff between ecm versions 6.1.0 dated 2021-04-23 and 6.2.0 dated 2021-05-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/ecmave.R | 53 ++++++++++++++++++++++++++++++++++++++--------------- R/ecmaveback.r | 53 ++++++++++++++++++++++++++++++++++++++--------------- README.md | 4 ++-- 5 files changed, 85 insertions(+), 39 deletions(-)
Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 2.10.1 dated 2021-03-10 and 2.11.0 dated 2021-05-07
DESCRIPTION | 8 +++--- MD5 | 19 ++++++++------- NEWS.md | 7 +++++ R/dataset.R | 17 ++++++-------- R/object.R | 8 +++--- R/utils.R | 53 ++++++++++++++++++++++++++++++++++++-------- README.md | 2 - man/Dataset.data.Rd | 4 --- man/Dataset.query.Rd | 10 +++++++- man/Object.data.Rd | 4 +-- tests/testthat/test_query.R |only 11 files changed, 90 insertions(+), 42 deletions(-)
Title: Software Option Settings Manager for R
Description: Provides option settings management that goes
beyond R's default 'options' function. With this package, users can define
their own option settings manager holding option names, default values and
(if so desired) ranges or sets of allowed option values that will be
automatically checked. Settings can then be retrieved, altered and reset
to defaults with ease. For R programmers and package developers it offers
cloning and merging functionality which allows for conveniently defining
global and local options, possibly in a multilevel options hierarchy. See
the package vignette for some examples concerning functions, S4 classes,
and reference classes. There are convenience functions to reset par()
and options() to their 'factory defaults'.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between settings versions 0.2.4 dated 2015-10-27 and 0.2.7 dated 2021-05-07
settings-0.2.4/settings/inst/doc/settings.R |only settings-0.2.4/settings/inst/doc/settings.Rmd |only settings-0.2.4/settings/inst/doc/settings.html |only settings-0.2.4/settings/tests/testthat |only settings-0.2.4/settings/tests/testthat.R |only settings-0.2.4/settings/vignettes/settings.Rmd |only settings-0.2.7/settings/DESCRIPTION | 10 +- settings-0.2.7/settings/MD5 | 47 +++++----- settings-0.2.7/settings/NAMESPACE | 2 settings-0.2.7/settings/NEWS | 6 + settings-0.2.7/settings/R/options.R | 40 ++++++-- settings-0.2.7/settings/build/vignette.rds |binary settings-0.2.7/settings/inst/doc/Introduction_to_settings.R |only settings-0.2.7/settings/inst/doc/Introduction_to_settings.Rmd |only settings-0.2.7/settings/inst/doc/Introduction_to_settings.html |only settings-0.2.7/settings/inst/doc/Validating_and_manipulating_option_values.R |only settings-0.2.7/settings/inst/doc/Validating_and_manipulating_option_values.Rmd |only settings-0.2.7/settings/inst/doc/Validating_and_manipulating_option_values.html |only settings-0.2.7/settings/inst/tinytest |only settings-0.2.7/settings/man/clone_and_merge.Rd | 6 - settings-0.2.7/settings/man/defaults.Rd | 3 settings-0.2.7/settings/man/inlist.Rd | 3 settings-0.2.7/settings/man/is_setting.Rd | 3 settings-0.2.7/settings/man/options_manager.Rd | 12 +- settings-0.2.7/settings/man/reset.Rd | 3 settings-0.2.7/settings/man/reset_options.Rd | 3 settings-0.2.7/settings/man/reset_par.Rd | 5 - settings-0.2.7/settings/man/settings.Rd | 8 - settings-0.2.7/settings/man/stop_if_reserved.Rd | 6 - settings-0.2.7/settings/tests/tinytest.R |only settings-0.2.7/settings/vignettes/Introduction_to_settings.Rmd |only settings-0.2.7/settings/vignettes/Validating_and_manipulating_option_values.Rmd |only 32 files changed, 93 insertions(+), 64 deletions(-)
Title: Non Metric Space (Approximate) Library
Description: A Non-Metric Space Library ('NMSLIB' <https://github.com/nmslib/nmslib>) wrapper, which according to the authors "is an efficient cross-platform similarity search library and a toolkit for evaluation of similarity search methods. The goal of the 'NMSLIB' <https://github.com/nmslib/nmslib> Library is to create an effective and comprehensive toolkit for searching in generic non-metric spaces. Being comprehensive is important, because no single method is likely to be sufficient in all cases. Also note that exact solutions are hardly efficient in high dimensions and/or non-metric spaces. Hence, the main focus is on approximate methods". The wrapper also includes Approximate Kernel k-Nearest-Neighbor functions based on the 'NMSLIB' <https://github.com/nmslib/nmslib> 'Python' Library.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
B. Naidan [cph] (Author of the Non-Metric Space Library (NMSLIB)),
L. Boytsov [cph] (Author of the Non-Metric Space Library (NMSLIB)),
Yu. Malkov [cph] (Author of the Non-Metric Space Library (NMSLIB)),
B. Frederickson [cph] (Author of the Non-Metric Space Library (NMSLIB)),
D. Novak [cph] (Author of the Non-Metric Space Library (NMSLIB))
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between nmslibR versions 1.0.4 dated 2020-03-08 and 1.0.5 dated 2021-05-07
nmslibR-1.0.4/nmslibR/R/zzz.R |only nmslibR-1.0.4/nmslibR/inst/COPYRIGHTS |only nmslibR-1.0.5/nmslibR/DESCRIPTION | 22 +- nmslibR-1.0.5/nmslibR/MD5 | 32 ++- nmslibR-1.0.5/nmslibR/NAMESPACE | 1 nmslibR-1.0.5/nmslibR/NEWS.md | 8 nmslibR-1.0.5/nmslibR/R/nmslib.R | 113 ++++++++----- nmslibR-1.0.5/nmslibR/R/package.R | 20 +- nmslibR-1.0.5/nmslibR/build/vignette.rds |binary nmslibR-1.0.5/nmslibR/inst/CITATION |only nmslibR-1.0.5/nmslibR/inst/doc/the_nmslibR_package.html | 30 +++ nmslibR-1.0.5/nmslibR/man/KernelKnnCV_nmslib.Rd | 2 nmslibR-1.0.5/nmslibR/man/KernelKnn_nmslib.Rd | 16 + nmslibR-1.0.5/nmslibR/man/NMSlib.Rd | 34 ++-- nmslibR-1.0.5/nmslibR/man/TO_scipy_sparse.Rd | 42 ++--- nmslibR-1.0.5/nmslibR/man/mat_2scipy_sparse.Rd | 20 +- nmslibR-1.0.5/nmslibR/tests/testthat/helper-init.R |only nmslibR-1.0.5/nmslibR/tests/testthat/helper-skip.R |only nmslibR-1.0.5/nmslibR/tests/testthat/setup.R |only nmslibR-1.0.5/nmslibR/tests/testthat/test-nmslibR_pkg.R | 130 ++-------------- 20 files changed, 225 insertions(+), 245 deletions(-)
Title: Subnational Data for the COVID-19 Outbreak
Description: An interface to subnational and national level COVID-19 data.
For all countries supported, this includes a daily time-series of
cases. Wherever available we also provide data on deaths,
hospitalisations, and tests. National level data is also supported
using a range of data sources as well as line list data and links to
intervention data sets.
Author: Sam Abbott [aut, cre] (<https://orcid.org/0000-0001-8057-8037>),
Katharine Sherratt [aut] (<https://orcid.org/0000-0003-2049-3423>),
Joe Palmer [aut],
Richard Martin-Nielsen [aut] (https://github.com/RichardMN),
Jonnie Bevan [aut],
Hamish Gibbs [aut] (<https://orcid.org/0000-0003-4413-453X>),
Sophie Meakin [ctb],
Joel Hellewell [ctb] (<https://orcid.org/0000-0003-2683-0849>),
Patrick Barks [ctb],
Paul Campbell [ctb],
Flavio Finger [ctb] (<https://orcid.org/0000-0002-8613-5170>),
Richard Boyes [ctb] (https://github.com/rboyes),
Hugo Gruson [ctb] (<https://orcid.org/0000-0002-4094-1476>),
Sebastian Funk [aut]
Maintainer: Sam Abbott <sam.abbott@lshtm.ac.uk>
Diff between covidregionaldata versions 0.9.0 dated 2021-04-24 and 0.9.1 dated 2021-05-07
DESCRIPTION | 14 MD5 | 173 ++++--- NAMESPACE | 6 NEWS.md | 23 R/Belgium.R | 1 R/Brazil.R | 1 R/Canada.R | 1 R/Colombia.R | 1 R/Cuba.R | 1 R/ECDC.R | 4 R/France.R | 1 R/Germany.R | 1 R/Google.R |only R/India.R | 1 R/Italy.R | 1 R/JHU.R |only R/Lithuania.R | 1 R/Mexico.R | 1 R/SouthAfrica.R | 1 R/UK.R | 87 +++ R/USA.R | 1 R/WHO.R | 8 R/datasets.R | 7 R/get_available_datasets.R | 15 R/get_national_data.R | 49 +- R/get_regional_data.R | 32 + R/processing.R | 66 ++ R/shared-methods.R | 251 ++++++++-- R/utils.R | 62 ++ README.md | 32 - build/vignette.rds |binary data/JHU_codes.rda |only inst/WORDLIST | 16 inst/doc/dataset-status.Rmd | 2 inst/doc/dataset-status.html | 215 +++++++++ inst/doc/quickstart.Rmd | 2 inst/doc/quickstart.html | 466 ++++++++++++++------ inst/doc/slowstart.Rmd | 4 inst/doc/slowstart.html | 301 ++++++++++-- man/Belgium.Rd | 20 man/Brazil.Rd | 20 man/Canada.Rd | 20 man/Colombia.Rd | 20 man/CountryDataClass.Rd | 39 + man/Cuba.Rd | 20 man/DataClass.Rd | 95 +++- man/ECDC.Rd | 11 man/France.Rd | 20 man/Germany.Rd | 20 man/Google.Rd |only man/India.Rd | 20 man/Italy.Rd | 20 man/JHU.Rd |only man/JHU_codes.Rd |only man/Lithuania.Rd | 20 man/Mexico.Rd | 20 man/SouthAfrica.Rd | 20 man/UK.Rd | 52 ++ man/USA.Rd | 20 man/WHO.Rd | 15 man/add_extra_na_cols.Rd | 8 man/calculate_columns_from_existing_data.Rd | 8 man/check_level.Rd |only man/complete_cumulative_columns.Rd | 8 man/download_excel.Rd |only man/fill_empty_dates_with_na.Rd | 8 man/get_available_datasets.Rd | 21 man/get_national_data.Rd | 57 ++ man/get_regional_data.Rd | 40 + man/glue_level.Rd |only man/initialise_dataclass.Rd | 62 ++ man/process_internal.Rd | 12 man/region_dispatch.Rd | 2 man/roxygen |only man/run_default_processing_fns.Rd |only man/run_optional_processing_fns.Rd |only man/set_negative_values_to_zero.Rd | 6 man/totalise_data.Rd | 6 tests/testthat/custom_data/Google_level_1.rds |only tests/testthat/custom_data/Google_level_2.rds |only tests/testthat/custom_data/Google_level_3.rds |only tests/testthat/custom_data/JHU_level_1.rds |only tests/testthat/custom_data/JHU_level_2.rds |only tests/testthat/custom_data/Mexico_level_1.rds |binary tests/testthat/custom_data/Mexico_level_2.rds |binary tests/testthat/custom_data/UK_level_1.rds |binary tests/testthat/custom_data/UK_level_2.rds |binary tests/testthat/custom_tests/test-regional-dataset.R | 10 tests/testthat/test-CountryDataClass.R | 1 tests/testthat/test-DataClass.R | 42 + tests/testthat/test-get_available_datasets.R | 4 tests/testthat/test-processing.R | 36 + tests/testthat/test-regional-datasets.R | 5 vignettes/dataset-status.Rmd | 2 vignettes/quickstart.Rmd | 2 vignettes/slowstart.Rmd | 4 96 files changed, 2176 insertions(+), 488 deletions(-)
More information about covidregionaldata at CRAN
Permanent link
Title: Multiple Testing Methods for Exploratory Research
Description: Provides an alternative approach to multiple testing
by calculating a simultaneous upper confidence bounds for the
number of true null hypotheses among any subset of the hypotheses of interest,
using the methods of Goeman and Solari (2011) <doi:10.1214/11-STS356>.
Author: Jelle Goeman, Aldo Solari, Rosa Meijer
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between cherry versions 0.6-13 dated 2019-09-20 and 0.6-14 dated 2021-05-07
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 17 ++++++++--------- build/vignette.rds |binary inst/doc/cherry.pdf |binary 5 files changed, 17 insertions(+), 18 deletions(-)
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>),
Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.12 dated 2021-03-28 and 1.30.13 dated 2021-05-07
DESCRIPTION | 6 +- MD5 | 34 +++++++-------- NEWS | 22 +++++++++ R/available.R | 6 ++ R/inet.R | 7 +++ R/install.R | 64 ++++++++++++++++++++++------ R/repositories.R | 2 R/valid.R | 60 +++++++++++++++----------- R/version.R | 28 +++++++----- build/vignette.rds |binary inst/doc/BiocManager.Rmd | 8 +-- inst/doc/BiocManager.html | 83 +++++++++++++++++++++---------------- man/available.Rd | 6 ++ man/install.Rd | 9 +++- tests/testthat/test_install.R | 36 +++++++++++++++- tests/testthat/test_repositories.R | 2 tests/testthat/test_version.R | 8 ++- vignettes/BiocManager.Rmd | 8 +-- 18 files changed, 268 insertions(+), 121 deletions(-)
Title: Model Agnostic Instance Level Variable Attributions
Description: Model agnostic tool for decomposition of predictions from black boxes.
Supports additive attributions and attributions with interactions.
The Break Down Table shows contributions of every variable to a final prediction.
The Break Down Plot presents variable contributions in a concise graphical way.
This package works for classification and regression models.
It is an extension of the 'breakDown' package (Staniak and Biecek 2018) <doi:10.32614/RJ-2018-072>,
with new and faster strategies for orderings.
It supports interactions in explanations and has interactive visuals (implemented with 'D3.js' library).
The methodology behind is described in the 'iBreakDown' article (Gosiewska and Biecek 2019) <arXiv:1903.11420>
This package is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Alicja Gosiewska [aut] (<https://orcid.org/0000-0001-6563-5742>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>),
Adam Izdebski [aut],
Dariusz Komosinski [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between iBreakDown versions 1.3.1 dated 2020-07-29 and 2.0.1 dated 2021-05-07
iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_classification.R |only iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_classification.Rmd |only iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_classification.html |only iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_regression.R |only iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_regression.Rmd |only iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_regression.html |only iBreakDown-1.3.1/iBreakDown/vignettes/vignette_iBreakDown_classification.Rmd |only iBreakDown-1.3.1/iBreakDown/vignettes/vignette_iBreakDown_regression.Rmd |only iBreakDown-2.0.1/iBreakDown/DESCRIPTION | 7 iBreakDown-2.0.1/iBreakDown/MD5 | 70 ++--- iBreakDown-2.0.1/iBreakDown/NEWS.md | 5 iBreakDown-2.0.1/iBreakDown/R/break_down.R | 2 iBreakDown-2.0.1/iBreakDown/R/break_down_uncertainty.R | 10 iBreakDown-2.0.1/iBreakDown/R/describe_breakdown.R | 2 iBreakDown-2.0.1/iBreakDown/R/local_attributions.R | 2 iBreakDown-2.0.1/iBreakDown/R/local_interactions.R | 2 iBreakDown-2.0.1/iBreakDown/R/plotD3_break_down.R | 9 iBreakDown-2.0.1/iBreakDown/R/plotD3_shap.R | 9 iBreakDown-2.0.1/iBreakDown/R/plot_break_down.R | 9 iBreakDown-2.0.1/iBreakDown/R/plot_break_down_uncertainty.R | 2 iBreakDown-2.0.1/iBreakDown/R/print_break_down.R | 2 iBreakDown-2.0.1/iBreakDown/R/print_break_down_descriptions.R | 2 iBreakDown-2.0.1/iBreakDown/R/print_break_down_uncertainty.R | 2 iBreakDown-2.0.1/iBreakDown/build/vignette.rds |binary iBreakDown-2.0.1/iBreakDown/inst/d3js/breakDownD3.js | 8 iBreakDown-2.0.1/iBreakDown/inst/d3js/shapD3.js | 8 iBreakDown-2.0.1/iBreakDown/inst/doc/vignette_iBreakDown_description.html | 136 +++++++--- iBreakDown-2.0.1/iBreakDown/inst/doc/vignette_iBreakDown_titanic.html | 120 +++++++- iBreakDown-2.0.1/iBreakDown/man/break_down.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/break_down_uncertainty.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/describe.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/local_attributions.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/local_interactions.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/plot.break_down.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/plot.break_down_uncertainty.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/plotD3_break_down.Rd | 7 iBreakDown-2.0.1/iBreakDown/man/plotD3_shap.Rd | 7 iBreakDown-2.0.1/iBreakDown/man/print.break_down.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/print.break_down_description.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/print.break_down_uncertainty.Rd | 2 40 files changed, 305 insertions(+), 136 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-29 0.1.2
2020-08-14 0.1.1
2020-07-16 0.1.0
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Mattan S. Ben-Shachar [aut, ctb]
(<https://orcid.org/0000-0002-4287-4801>),
Brenton M. Wiernik [aut] (<https://orcid.org/0000-0001-9560-6336>,
@bmwiernik)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.13.2 dated 2021-04-01 and 0.14.0 dated 2021-05-07
DESCRIPTION | 17 MD5 | 253 ++- NAMESPACE | 111 - NEWS.md | 80 + R/check_if_installed.R |only R/clean_names.R | 2 R/clean_parameters.R | 13 R/compute_variances.R | 49 R/ellipsis_info.R | 41 R/export_table.R | 47 R/find_formula.R | 382 ++++-- R/find_interactions.R | 1 R/find_parameter_zi.R | 1 R/find_parameters.R | 51 R/find_parameters_bayesian.R | 139 +- R/find_parameters_emmeans.R | 3 R/find_parameters_gam.R | 21 R/find_parameters_mfx.R | 23 R/find_parameters_mixed.R | 13 R/find_predictors.R | 17 R/find_random.R | 2 R/find_random_slopes.R | 2 R/find_response.R | 60 R/find_smooth.R | 2 R/find_statistic.R | 243 --- R/find_terms.R | 26 R/find_variables.R | 15 R/find_weights.R | 2 R/format_message.R |only R/format_string.R |only R/format_table.R | 31 R/format_value.R | 36 R/get_auxiliary.R | 42 R/get_call.R | 12 R/get_data.R | 91 - R/get_deviance.R | 37 R/get_df.R | 118 + R/get_family.R | 2 R/get_loglikelihood.R | 23 R/get_modelmatrix.R |only R/get_parameters.R | 38 R/get_parameters_bayesian.R | 15 R/get_parameters_censored.R | 2 R/get_parameters_gam.R | 22 R/get_parameters_mfx.R | 1 R/get_parameters_mixed.R | 4 R/get_parameters_others.R | 53 R/get_parameters_zi.R | 1 R/get_predicted.R | 411 +++++- R/get_predicted_ci.R | 45 R/get_predicted_methods.R | 1 R/get_predictors.R | 2 R/get_priors.R | 67 - R/get_residuals.R | 16 R/get_response.R | 6 R/get_sigma.R | 169 ++ R/get_statistic.R | 204 ++- R/get_varcov.R | 44 R/get_weights.R | 9 R/helper_functions.R | 113 - R/is_model.R | 16 R/is_model_supported.R | 145 -- R/is_multivariate.R | 2 R/link_function.R | 12 R/link_inverse.R | 32 R/model_info.R | 67 - R/model_name.R | 2 R/n_obs.R | 39 R/n_parameters.R | 21 R/null_model.R | 3 R/print_parameters.R | 3 R/reshape_ci.R | 1 R/utils_get_data.R | 148 +- R/utils_model_info.R | 41 README.md | 35 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/WORDLIST | 48 inst/doc/display.html | 144 +- man/check_if_installed.Rd |only man/find_formula.Rd | 11 man/find_interactions.Rd | 8 man/find_parameters.BGGM.Rd | 268 ++-- man/find_parameters.averaging.Rd | 22 man/find_parameters.betamfx.Rd | 126 + man/find_parameters.gamlss.Rd | 112 - man/find_parameters.glmmTMB.Rd | 123 - man/find_parameters.zeroinfl.Rd | 22 man/find_predictors.Rd | 119 - man/find_terms.Rd | 4 man/find_variables.Rd | 169 +- man/format_message.Rd |only man/format_string.Rd |only man/get_auxiliary.Rd | 142 +- man/get_data.Rd | 248 +-- man/get_deviance.Rd | 9 man/get_df.Rd | 65 - man/get_loglikelihood.Rd | 4 man/get_modelmatrix.Rd |only man/get_parameters.BGGM.Rd | 349 ++--- man/get_parameters.betamfx.Rd | 80 - man/get_parameters.betareg.Rd | 15 man/get_parameters.gamm.Rd | 96 - man/get_parameters.glmm.Rd | 21 man/get_parameters.zeroinfl.Rd | 8 man/get_predicted.Rd | 93 + man/get_predicted_ci.Rd | 13 man/get_response.Rd | 4 man/get_sigma.Rd | 9 man/get_statistic.Rd | 14 man/get_varcov.Rd | 208 +-- man/model_info.Rd | 1 man/n_parameters.Rd | 8 tests/testthat.R | 41 tests/testthat/_snaps |only tests/testthat/test-GLMMadaptive.R | 6 tests/testthat/test-bigglm.R | 2 tests/testthat/test-brms.R | 6 tests/testthat/test-check_if_installed.R |only tests/testthat/test-coxme.R | 3 tests/testthat/test-coxph.R | 1 tests/testthat/test-export_table.R | 70 - tests/testthat/test-find_formula-data.R |only tests/testthat/test-formatting.R |only tests/testthat/test-gam.R | 2 tests/testthat/test-get_predicted.R | 37 tests/testthat/test-get_residuals.R | 3 tests/testthat/test-glmmTMB.R | 6 tests/testthat/test-mixed.R | 2 tests/testthat/test-mvrstanarm.R | 1965 +++++++++++++++---------------- tests/testthat/test-r3_4.R |only tests/testthat/test-survfit.R | 1 tests/testthat/test-survreg.R | 2 134 files changed, 4940 insertions(+), 3570 deletions(-)
Title: Plots of the Empirical Attainment Function
Description: Computation and visualization of the empirical attainment function (EAF) for the analysis of random sets in multi-criterion optimization. M. López-Ibáñez, L. Paquete, and T. Stützle (2010) <doi:10.1007/978-3-642-02538-9_9>.
Author: Manuel López-Ibáñez [aut, cre]
(<https://orcid.org/0000-0001-9974-1295>),
Marco Chiarandini [aut],
Carlos Fonseca [aut],
Luís Paquete [aut],
Thomas Stützle [aut],
Mickaël Binois [ctb]
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between eaf versions 2.0 dated 2021-02-08 and 2.1 dated 2021-05-07
DESCRIPTION | 6 +- MD5 | 43 +++++++++---------- NEWS.md | 23 +++++----- R/eaf.R | 82 ++++++++++++++++++++----------------- R/epsilon.R | 67 +++++++++++++++++++++--------- R/igd.R | 76 +++++++++++++++++++++++++--------- R/vorob.R | 4 - README.md | 14 +++--- build/partial.rdb |binary man/eafdiffplot.Rd | 2 man/eafplot.Rd | 12 ++--- man/eafs.Rd | 2 man/epsilon.Rd | 60 +++++++++++++++++++-------- man/igd.Rd | 75 +++++++++++++++++++++++++-------- src/Makevars.win | 4 - src/eaf/bit_array.h | 5 -- src/eaf/svn_version | 2 src/mo-tools/igd.c | 9 ---- src/mo-tools/igd.h | 67 +++++++++++++----------------- src/mo-tools/nondominated.c | 14 +++--- src/mo-tools/svn_version | 2 src/mo-tools/whv.c | 10 ++-- tests/testthat/test-eafplot-list.R |only 23 files changed, 354 insertions(+), 225 deletions(-)
Title: Create, Survey and Analyse Discrete Choice Experiments
Description: This app is intended to be a complete package for creating, surveying, and analysing discrete choice experiments. Although all these functionalities are available, the app can also be used only to obtain the design of a discrete choice experiment. Reference: Perez-Troncoso, D. (2021) <https://github.com/danielpereztr/DCEtool>.
Author: Daniel Perez Troncoso [aut, cre]
(<https://orcid.org/0000-0003-0091-8148>)
Maintainer: Daniel Perez Troncoso <danielperez@ugr.es>
Diff between DCEtool versions 0.0.1 dated 2021-04-21 and 0.1.1 dated 2021-05-07
DESCRIPTION | 8 ++-- MD5 | 13 +++---- NAMESPACE | 98 +++++++++++++++++++++++++++--------------------------- NEWS.md | 2 + R/app.r | 22 +++++++----- R/helpfiles |only build/partial.rdb |binary man/DCEtool.Rd | 2 + 8 files changed, 77 insertions(+), 68 deletions(-)
Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery
and replicability rates on the bases of test-statistics of published studies. The package
provides functions for fitting the new density and EM version
(Bartoš & Schimmack, 2020, <doi:10.31234/osf.io/urgtn>) as well as the original density
z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>). Furthermore, the package
provides summarizing and plotting functions for the fitted z-curve objects. See the
aforementioned articles for more information about the z-curves, expected discovery
and replicability rates, validation studies, and limitations.
Author: František Bartoš [aut, cre],
Ulrich Schimmack [aut]
Maintainer: František Bartoš <f.bartos96@gmail.com>
Diff between zcurve versions 1.0.8 dated 2021-01-17 and 1.0.9 dated 2021-05-07
DESCRIPTION | 8 +-- MD5 | 21 +++++----- R/main.R | 3 - R/tools.R | 31 +++++++++------ R/zzz.R |only README.md | 63 +++++++++++++++++-------------- build/partial.rdb |binary inst/REFERENCES.bib | 6 +- man/figures/README-unnamed-chunk-6-1.png |binary man/power_to_z.Rd | 3 + man/z_to_power.Rd | 9 +++- man/zcurve-package.Rd | 2 12 files changed, 85 insertions(+), 61 deletions(-)
Title: Generate Treasury Total Returns from Yield Data
Description: Generate Total Returns (TR) from bond yield data with fixed maturity, e.g.
reported treasury yields. The generated TR series are very close to alternative series
that can be purchased (e.g. CRSP, Bloomberg), suggesting they are a high-quality
alternative for those, see Swinkels (2019) <doi:10.3390/data4030091>.
Author: Martin Geissmann [aut, cre]
Maintainer: Martin Geissmann <mg@econovo.ch>
Diff between treasuryTR versions 0.1.2 dated 2021-04-14 and 0.1.3 dated 2021-05-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/xts_to_tibble.R | 3 +++ inst/doc/treasuryTR.html | 40 ++++++++++++++++++++-------------------- man/xts_to_tibble.Rd | 3 +++ 5 files changed, 33 insertions(+), 27 deletions(-)
Title: Blind Source Separation for Multivariate Spatial Data
Description: Blind source separation for multivariate spatial data based on simultaneous/joint diagonalization of local covariance matrices. This package is an implementation of the methods described in Bachoc, Genton, Nordhausen, Ruiz-Gazen and Virta (2020) <doi:10.1093/biomet/asz079>.
Author: Christoph Muehlmann [aut, cre]
(<https://orcid.org/0000-0001-7330-8434>),
Klaus Nordhausen [aut] (<https://orcid.org/0000-0002-3758-8501>),
Joni Virta [aut] (<https://orcid.org/0000-0002-2150-2769>)
Maintainer: Christoph Muehlmann <christoph.muehlmann@tuwien.ac.at>
Diff between SpatialBSS versions 0.9-0 dated 2020-11-04 and 0.10-0 dated 2021-05-07
DESCRIPTION | 8 ++++---- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 2 +- R/sbss.R | 10 +++++++--- R/utils.R | 19 ++++++++++++------- build/partial.rdb |only build/vignette.rds |binary inst/ChangeLog.txt | 6 ++++++ inst/doc/SBSS.R | 11 ++++++++--- inst/doc/SBSS.Rmd | 27 ++++++++++++++++++++------- inst/doc/SBSS.html | 31 ++++++++++++++++++++++--------- man/SpatialBSS-package.Rd | 10 ++++++---- man/local_covariance_matrix.Rd | 15 +++++++++------ man/sbss.Rd | 20 ++++++++++++++------ man/spatial_kernel_matrix.Rd | 9 ++++++--- man/white_data.Rd |only vignettes/SBSS.Rmd | 27 ++++++++++++++++++++------- 17 files changed, 151 insertions(+), 74 deletions(-)
Title: Build Panel Data Sets from PSID Raw Data
Description: Makes it easy to build panel data in wide format from Panel Survey
of Income Dynamics ('PSID') delivered raw data. Downloads data directly from
the PSID server using the 'SAScii' package. 'psidR' takes care of merging
data from each wave onto a cross-period index file, so that individuals can be
followed over time. The user must specify which years they are interested in,
and the 'PSID' variable names (e.g. ER21003) for each year (they differ in each
year). The package offers helper functions to retrieve variable names from different
waves. There are different panel data designs and sample subsetting criteria
implemented ("SRC", "SEO", "immigrant" and "latino" samples).
Author: Florian Oswald
Maintainer: Florian Oswald <florian.oswald@gmail.com>
Diff between psidR versions 2.0 dated 2020-02-26 and 2.1 dated 2021-05-07
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 7 +++++++ R/build.panel.r | 32 +++++++++++++++++--------------- R/makeids.r | 20 ++++++++++---------- man/build.panel.Rd | 39 ++++++++++++++++++++++++++------------- man/get.psid.Rd | 2 +- man/getNamesPSID.Rd | 2 +- man/psidR.Rd | 1 - tests/testthat/test_testPSID.R | 4 ++-- 10 files changed, 78 insertions(+), 57 deletions(-)
Title: Miscellaneous Functions for Data Cleaning and Analysis
Description: Provides functions needed for data cleaning and
formatting and forms data cleaning and wrangling backend for the
following packages: 'ggstatsplot', 'pairwiseComparisons', and
'statsExpressions'.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ipmisc versions 6.0.0 dated 2021-02-13 and 6.0.2 dated 2021-05-07
ipmisc-6.0.0/ipmisc/build |only ipmisc-6.0.0/ipmisc/man/figures |only ipmisc-6.0.2/ipmisc/DESCRIPTION | 12 ipmisc-6.0.2/ipmisc/LICENSE | 1348 +++++----- ipmisc-6.0.2/ipmisc/MD5 | 53 ipmisc-6.0.2/ipmisc/NAMESPACE | 80 ipmisc-6.0.2/ipmisc/NEWS.md | 204 - ipmisc-6.0.2/ipmisc/R/data.R | 126 ipmisc-6.0.2/ipmisc/R/format_num.R | 88 ipmisc-6.0.2/ipmisc/R/global_vars.R | 14 ipmisc-6.0.2/ipmisc/R/long_to_wide_converter.R | 218 - ipmisc-6.0.2/ipmisc/R/reexports.R | 98 ipmisc-6.0.2/ipmisc/R/stats_type_switch.R | 66 ipmisc-6.0.2/ipmisc/README.md | 154 - ipmisc-6.0.2/ipmisc/inst/WORDLIST | 49 ipmisc-6.0.2/ipmisc/man/format_num.Rd | 2 ipmisc-6.0.2/ipmisc/man/long_to_wide_converter.Rd | 163 - ipmisc-6.0.2/ipmisc/man/reexports.Rd | 65 ipmisc-6.0.2/ipmisc/man/stats_type_switch.Rd | 20 ipmisc-6.0.2/ipmisc/tests/spelling.R | 12 ipmisc-6.0.2/ipmisc/tests/testthat.R | 8 ipmisc-6.0.2/ipmisc/tests/testthat/_snaps/long_to_wide_converter.md | 280 +- ipmisc-6.0.2/ipmisc/tests/testthat/test-format_num.R | 64 ipmisc-6.0.2/ipmisc/tests/testthat/test-long_to_wide_converter.R | 338 +- ipmisc-6.0.2/ipmisc/tests/testthat/test-stats_type_switch.R | 34 25 files changed, 1768 insertions(+), 1728 deletions(-)
Title: Fuzzy String Matching
Description: Fuzzy string matching implementation of the 'fuzzywuzzy' <https://github.com/seatgeek/fuzzywuzzy> 'python' package. It uses the Levenshtein Distance <https://en.wikipedia.org/wiki/Levenshtein_distance> to calculate the differences between sequences.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
SeatGeek Inc [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between fuzzywuzzyR versions 1.0.3 dated 2018-02-26 and 1.0.4 dated 2021-05-07
DESCRIPTION | 17 MD5 | 32 NEWS.md | 5 R/fuzzy_w.R | 595 +++++++----- R/package.R | 39 README.md | 9 build/vignette.rds |binary inst/CITATION |only inst/doc/functionality_of_fuzzywuzzyR_package.R | 60 - inst/doc/functionality_of_fuzzywuzzyR_package.html | 804 +++++++++++------ man/FuzzExtract.Rd | 271 ++++- man/FuzzMatcher.Rd | 328 ++++++ man/FuzzUtils.Rd | 203 +++- man/GetCloseMatches.Rd | 20 man/SequenceMatcher.Rd | 129 ++ tests/testthat/helper-init.R |only tests/testthat/helper-skip.R |only tests/testthat/setup.R |only tests/testthat/test_package.R | 991 +++++++++++---------- 19 files changed, 2348 insertions(+), 1155 deletions(-)
Title: Co-Correspondence Analysis Methods
Description: Fits predictive and symmetric co-correspondence analysis (CoCA) models to relate one data matrix to another data matrix. More specifically, CoCA maximises the weighted covariance between the weighted averaged species scores of one community and the weighted averaged species scores of another community. CoCA attempts to find patterns that are common to both communities.
Author: Original Matlab routines by C.J.F. ter Braak and A.P. Schaffers. R port by Gavin L. Simpson.
Function simpls based on simpls.fit (package pls) by Ron Wehrens and Bjorn-Helge Mevik.
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between cocorresp versions 0.4-1 dated 2019-12-19 and 0.4-3 dated 2021-05-07
DESCRIPTION | 12 MD5 | 34 +- R/eigenvals.R | 3 R/print.crossval.R | 6 R/print.predcoca.R | 5 R/print.summary.crossval.R | 6 README.md | 24 - build/vignette.rds |binary data/beetles.rda |binary data/bryophyte.rda |binary data/plants.rda |binary data/vascular.rda |binary inst/ChangeLog | 16 inst/doc/cocorresp-intro.Rmd | 19 - inst/doc/cocorresp-intro.html | 578 ++++++++++++++++++++-------------- tests/Examples/cocorresp-Ex.Rout.save | 28 - tests/testthat/test-eigenvals.R | 9 vignettes/cocorresp-intro.Rmd | 19 - 18 files changed, 451 insertions(+), 308 deletions(-)
Title: Make 'ggplot2' and 'leaflet' Visualisation Easier
Description: Wrapper functions to make 'ggplot2' and 'leaflet' visualisation easier and prettier.
Author: David Hodge [aut, cre] (<https://orcid.org/0000-0002-3868-7501>),
Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between simplevis versions 3.0.0 dated 2021-04-30 and 3.1.0 dated 2021-05-07
simplevis-3.0.0/simplevis/R/plotly.R |only simplevis-3.0.0/simplevis/data/datalist |only simplevis-3.0.0/simplevis/data/example_stars.rda |only simplevis-3.0.0/simplevis/data/example_stars_2.rda |only simplevis-3.0.0/simplevis/man/example_stars.Rd |only simplevis-3.0.0/simplevis/man/example_stars_2.Rd |only simplevis-3.0.0/simplevis/man/plotly_legend_order.Rd |only simplevis-3.0.0/simplevis/man/plotly_legend_rev.Rd |only simplevis-3.1.0/simplevis/DESCRIPTION | 18 - simplevis-3.1.0/simplevis/MD5 | 92 ++++------ simplevis-3.1.0/simplevis/NAMESPACE | 12 - simplevis-3.1.0/simplevis/NEWS.md | 16 + simplevis-3.1.0/simplevis/R/data.R | 16 - simplevis-3.1.0/simplevis/R/ggplot_boxplot.R | 37 +--- simplevis-3.1.0/simplevis/R/ggplot_hbar.R | 81 +++----- simplevis-3.1.0/simplevis/R/ggplot_line.R | 24 +- simplevis-3.1.0/simplevis/R/ggplot_point.R | 24 +- simplevis-3.1.0/simplevis/R/ggplot_sf.R | 30 +-- simplevis-3.1.0/simplevis/R/ggplot_vbar.R | 34 +-- simplevis-3.1.0/simplevis/R/ggplotly.R |only simplevis-3.1.0/simplevis/R/imports.R | 16 - simplevis-3.1.0/simplevis/R/leaflet_basemap.R | 7 simplevis-3.1.0/simplevis/R/leaflet_sf.R | 59 +++--- simplevis-3.1.0/simplevis/R/other.R | 33 ++- simplevis-3.1.0/simplevis/inst/doc/simplevis.R | 18 - simplevis-3.1.0/simplevis/inst/doc/simplevis.Rmd | 20 +- simplevis-3.1.0/simplevis/inst/doc/simplevis.html | 76 ++++---- simplevis-3.1.0/simplevis/inst/shiny/template1/data/template1.zip |binary simplevis-3.1.0/simplevis/inst/shiny/template1/server.R | 1 simplevis-3.1.0/simplevis/inst/shiny/template2/data/template2.zip |binary simplevis-3.1.0/simplevis/inst/shiny/template2/server.R | 1 simplevis-3.1.0/simplevis/man/ggplot_boxplot.Rd | 7 simplevis-3.1.0/simplevis/man/ggplot_boxplot_col.Rd | 6 simplevis-3.1.0/simplevis/man/ggplot_boxplot_col_facet.Rd | 6 simplevis-3.1.0/simplevis/man/ggplot_hbar_col.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_hbar_col_facet.Rd | 6 simplevis-3.1.0/simplevis/man/ggplot_line_col.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_line_col_facet.Rd | 6 simplevis-3.1.0/simplevis/man/ggplot_point_col.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_point_col_facet.Rd | 6 simplevis-3.1.0/simplevis/man/ggplot_sf.Rd | 4 simplevis-3.1.0/simplevis/man/ggplot_sf_col.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_sf_col_facet.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_vbar_col.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_vbar_col_facet.Rd | 6 simplevis-3.1.0/simplevis/man/leaflet_basemap.Rd | 7 simplevis-3.1.0/simplevis/man/leaflet_sf.Rd | 4 simplevis-3.1.0/simplevis/man/leaflet_sf_col.Rd | 4 simplevis-3.1.0/simplevis/man/mutate_text.Rd | 4 simplevis-3.1.0/simplevis/man/plotly_camera.Rd | 9 simplevis-3.1.0/simplevis/man/plotly_col_legend.Rd |only simplevis-3.1.0/simplevis/vignettes/simplevis.Rmd | 20 +- 52 files changed, 349 insertions(+), 409 deletions(-)
Title: Gamma Lasso Regression
Description: The gamma lasso algorithm provides regularization paths corresponding to a range of non-convex cost functions between L0 and L1 norms. As much as possible, usage for this package is analogous to that for the glmnet package (which does the same thing for penalization between L1 and L2 norms). For details see: Taddy (2017 JCGS), 'One-Step Estimator Paths for Concave Regularization', <arXiv:1308.5623>.
Author: Matt Taddy <mataddy@gmail.com>
Maintainer: Matt Taddy <mataddy@gmail.com>
Diff between gamlr versions 1.13-6 dated 2020-06-08 and 1.13-7 dated 2021-05-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- NAMESPACE | 4 ++-- R/cv.gamlr.R | 15 ++++++++++----- R/doubleML.R |only R/gamlr.R | 3 +-- R/naref.R |only man/doubleML.Rd |only man/naref.Rd |only 9 files changed, 25 insertions(+), 17 deletions(-)
Title: Analysis of Niche Evolution using Niche and Distribution Models
Description: Description: Tools for constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Author: Dan Warren [aut, cre] (<https://orcid.org/0000-0002-8747-2451>),
Nick Matzke [ctb],
Marcel Cardillo [ctb],
John Baumgartner [ctb],
Linda Beaumont [ctb],
Nicholas Huron [ctb],
Marianna Simoes [ctb],
Teresa Iglesias [ctb],
Russell Dinnage [aut] (<https://orcid.org/0000-0003-0846-2819>)
Maintainer: Dan Warren <dan.l.warren@gmail.com>
Diff between ENMTools versions 1.0.3 dated 2021-04-02 and 1.0.4 dated 2021-05-07
DESCRIPTION | 8 ++-- MD5 | 70 ++++++++++++++++++++-------------------- NAMESPACE | 7 ++-- NEWS.md | 22 ++++++++++++ R/background.points.buffer.R | 14 ++------ R/background.raster.buffer.R | 17 ++------- R/background.shape.buffer.R | 9 ++--- R/check.bg.R | 61 +++++++++++++++++++++++++++++++--- R/check.env.R |only R/enmtools.bc.R | 30 ++++++++++------- R/enmtools.dm.R | 26 +++++++++----- R/enmtools.ecospat.bg.R | 1 R/enmtools.ecospat.id.R | 1 R/enmtools.gam.R | 30 ++++++++++------- R/enmtools.glm.R | 30 ++++++++++------- R/enmtools.maxent.R | 54 ++++++++++++++++++------------ R/enmtools.rf.R | 30 ++++++++++------- R/enmtools.rf.ranger.R | 32 ++++++++++-------- R/multistack.pca.R | 9 +---- R/package.depends.R | 4 +- R/zzz.R | 2 - man/background.points.buffer.Rd | 4 -- man/background.raster.buffer.Rd | 4 -- man/background.shape.buffer.Rd | 4 -- man/check.bg.Rd | 5 ++ man/check.env.Rd |only man/enmtools.bc.Rd | 6 +++ man/enmtools.dm.Rd | 6 +++ man/enmtools.ecospat.bg.Rd | 1 man/enmtools.ecospat.id.Rd | 1 man/enmtools.gam.Rd | 6 +++ man/enmtools.glm.Rd | 6 +++ man/enmtools.maxent.Rd | 6 +++ man/enmtools.rf.Rd | 6 +++ man/enmtools.rf.ranger.Rd | 6 +++ man/install.extras.Rd | 2 - man/multistack.pca.Rd | 9 +---- 37 files changed, 335 insertions(+), 194 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>),
Andrew Dunning [ctb] (<https://orcid.org/0000-0003-0464-5036>),
Atsushi Yasumoto [ctb, cph] (<https://orcid.org/0000-0002-8335-495X>,
Number sections Lua filter),
Barret Schloerke [ctb],
Carson Sievert [ctb] (<https://orcid.org/0000-0002-4958-2844>),
Christophe Dervieux [ctb],
Devon Ryan [ctb] (<https://orcid.org/0000-0002-8549-0971>),
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Jeff Allen [ctb],
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>),
Malcolm Barrett [ctb],
Rob Hyndman [ctb],
Romain Lesur [ctb],
Roy Storey [ctb],
Ruben Arslan [ctb],
Sergio Oller [ctb],
RStudio, PBC [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs),
Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter),
Albert Krewinkel [ctb, cph] (pagebreak Lua filter)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.7 dated 2021-02-19 and 2.8 dated 2021-05-07
DESCRIPTION | 18 ++--- MD5 | 108 ++++++++++++++++--------------- NEWS.md | 39 ++++++++++- R/beamer_presentation.R | 4 - R/context_document.R | 2 R/html_document.R | 30 ++------ R/html_document_base.R | 64 +++++++++++++++++- R/html_vignette.R | 1 R/ioslides_presentation.R | 3 R/output_format.R | 39 ++++++++--- R/pandoc.R | 2 R/pdf_document.R | 6 - R/render.R | 54 ++++++++------- R/render_site.R | 16 ++-- R/shiny.R | 23 ++++-- R/shiny_prerendered.R | 44 +++++++++--- R/slidy_presentation.R | 1 R/tufte_handout.R | 24 ++---- R/util.R | 6 - README.md | 24 ++++-- build/vignette.rds |binary inst/doc/lua-filters.Rmd | 40 ++++++++++- inst/doc/lua-filters.html | 85 +++++++++++++++--------- inst/doc/rmarkdown.R | 13 +++ inst/doc/rmarkdown.Rmd | 66 ++++++++++++++---- inst/doc/rmarkdown.html | 46 +++++++++---- inst/rmarkdown/lua/latex-div.lua | 20 ++++- inst/rmarkdown/lua/number-sections.lua | 17 ++++ inst/rmarkdown/lua/pagebreak.lua | 17 ++++ inst/rmarkdown/lua/shared.lua |only inst/rmd/h/default.html | 11 ++- inst/rmd/h/navigation-1.1/codefolding.js | 17 ++++ inst/rmd/ioslides/default.html | 3 inst/rmd/slidy/default.html | 3 man/beamer_presentation.Rd | 4 - man/context_document.Rd | 2 man/figures |only man/html_document.Rd | 9 +- man/html_document_base.Rd | 6 + man/html_notebook.Rd | 5 + man/html_vignette.Rd | 2 man/ioslides_presentation.Rd | 2 man/pandoc_args.Rd | 2 man/pandoc_options.Rd | 2 man/pdf_document.Rd | 4 - man/render.Rd | 5 + man/render_site.Rd | 16 ++-- man/slidy_presentation.Rd | 2 man/tufte_handout.Rd | 19 ----- tests/testthat/_snaps/lua-filters.md |only tests/testthat/helpers.R | 30 +++++++- tests/testthat/test-lua-filters.R | 49 ++++++++++++-- tests/testthat/test-output_format.R | 8 ++ tests/testthat/test-shiny.R | 15 +++- tests/testthat/test-shiny_prerendered.R |only vignettes/lua-filters.Rmd | 40 ++++++++++- vignettes/rmarkdown.Rmd | 66 ++++++++++++++---- 57 files changed, 817 insertions(+), 317 deletions(-)
Title: Estimates of Standard Errors for Risk and Performance Measures
Description: Estimates of standard errors of popular risk and performance
measures for asset or portfolio returns using methods as described in
Chen and Martin (2018) <https://www.ssrn.com/abstract=3085672>.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Xin Chen <chenx26@uw.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPESE versions 1.2.0 dated 2021-03-10 and 1.2.1 dated 2021-05-07
RPESE-1.2.0/RPESE/R/robLoc_SE.R |only RPESE-1.2.0/RPESE/man/robLoc.SE.Rd |only RPESE-1.2.1/RPESE/DESCRIPTION | 8 ++-- RPESE-1.2.1/RPESE/MD5 | 50 +++++++++++++-------------- RPESE-1.2.1/RPESE/NAMESPACE | 2 - RPESE-1.2.1/RPESE/NEWS.md | 4 ++ RPESE-1.2.1/RPESE/R/DSR_SE.R | 2 - RPESE-1.2.1/RPESE/R/ESratio_SE.R | 2 - RPESE-1.2.1/RPESE/R/EstimatorSE.R | 8 ++-- RPESE-1.2.1/RPESE/R/Mean_SE.R | 2 - RPESE-1.2.1/RPESE/R/Measures.R | 6 +-- RPESE-1.2.1/RPESE/R/OmegaRatio_SE.R | 2 - RPESE-1.2.1/RPESE/R/RachevRatio_SE.R | 2 - RPESE-1.2.1/RPESE/R/SR_SE.R | 2 - RPESE-1.2.1/RPESE/R/SoR_SE.R | 2 - RPESE-1.2.1/RPESE/R/VaRratio_SE.R | 2 - RPESE-1.2.1/RPESE/R/robMean_SE.R |only RPESE-1.2.1/RPESE/inst/doc/RPESEVignette.pdf |binary RPESE-1.2.1/RPESE/man/DSR.SE.Rd | 2 - RPESE-1.2.1/RPESE/man/ESratio.SE.Rd | 2 - RPESE-1.2.1/RPESE/man/EstimatorSE.Rd | 2 - RPESE-1.2.1/RPESE/man/Mean.SE.Rd | 2 - RPESE-1.2.1/RPESE/man/OmegaRatio.SE.Rd | 2 - RPESE-1.2.1/RPESE/man/RachevRatio.SE.Rd | 2 - RPESE-1.2.1/RPESE/man/SR.SE.Rd | 2 - RPESE-1.2.1/RPESE/man/SoR.SE.Rd | 2 - RPESE-1.2.1/RPESE/man/VaRratio.SE.Rd | 2 - RPESE-1.2.1/RPESE/man/robMean.SE.Rd |only 28 files changed, 58 insertions(+), 54 deletions(-)
Title: Assessing the Partial Association Between Ordinal Variables
Description: An implementation of the unified framework for assessing partial association
between ordinal variables after adjusting for a set of covariates (Dungang Liu, Shaobo
Li, Yan Yu and Irini Moustaki (2020), accepted by the Journal of the American
Statistical Association). This package provides a set of tools to quantify, visualize,
and test partial associations between multiple ordinal variables. It can produce a number
of $phi$ measures, partial regression plots, 3-D plots, and $p$-values for testing
$H_0: phi=0$ or $H_0: phi <= delta$.
Author: Xiaorui (Jeremy) Zhu [aut, cre],
Shaobo Li [aut],
Dungang Liu [ctb, aut],
Yuejie Chen [ctb]
Maintainer: Xiaorui (Jeremy) Zhu <zhuxiaorui1989@gmail.com>
Diff between PAsso versions 0.1.8 dated 2020-07-13 and 0.1.9 dated 2021-05-07
DESCRIPTION | 43 ++++---- MD5 | 56 +++++------ NAMESPACE | 3 NEWS.md | 14 ++ R/PAsso.R | 11 +- R/autoplot.R | 3 R/diagnostic.plot.R | 18 ++- R/residuals.R | 189 +++++++++++++++++++++++++++++++++++---- R/surrogate.R | 4 R/utils.R | 56 +++++++---- README.md | 107 +++++++++++----------- build |only man/PAsso.Rd | 11 +- man/autoplot.Rd | 3 man/residuals.Rd | 33 ++++-- man/residualsVGAM.Rd |only man/surrogate.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-PAsso.R | 9 + tests/testthat/test-autoplot.R | 10 -- tests/testthat/test-data.R | 2 tests/testthat/test-diagnostic.R | 41 +++++++- tests/testthat/test-gumbel.R | 2 tests/testthat/test-plot.R | 2 tests/testthat/test-plot3D.R | 2 tests/testthat/test-residuals.R | 69 ++++++++++++++ tests/testthat/test-surrogate.R | 2 tests/testthat/test-test.R | 2 tests/testthat/test-truncated.R | 2 tests/testthat/test-utils.R | 2 30 files changed, 502 insertions(+), 198 deletions(-)
Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
Author: Joe Cheng [aut],
Winston Chang [aut, cre],
RStudio, PBC [cph],
Hector Corrada Bravo [ctb],
Jeroen Ooms [ctb],
Andrzej Krzemienski [cph] (optional.hpp)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between httpuv versions 1.6.0 dated 2021-04-23 and 1.6.1 dated 2021-05-07
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 9 +++++++-- src/timegm.cpp | 27 +++++++++++++++++++++++++-- src/timegm.h | 4 +--- src/utils.cpp | 2 +- 6 files changed, 42 insertions(+), 16 deletions(-)
Title: System for Building and Debugging C/C++ Dynamic Libraries
Description: A build system based on 'GNU make' that creates and
maintains (simply) make files in an R session and provides
GUI debugging support through 'Microsoft Visual Code'.
Author: Paavo Jumppanen [aut, cre]
Maintainer: Paavo Jumppanen <paavo.jumppanen@csiro.au>
Diff between BuildSys versions 1.0.9 dated 2021-04-30 and 1.1.0 dated 2021-05-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/BuildSys.R | 10 ++++++---- build/partial.rdb |binary 4 files changed, 13 insertions(+), 11 deletions(-)