Title: Wizardry Code Offensive Programming R Documentation
Description: Allows to generate automatically R documentation files from offensive
programming test cases. It populates most of the section of the documentation
content from the offensive programming instrumentation. This reduces greatly the
package producer effort and time to get to a fully documented manual page for
any instrumented function. Following documentation sections are now automatically
filled from instrumentation data: title, description, usage, arguments, value,
author, examples. Sections references, notes and keyword are instrumented to
industrialize their production. Produced manual pages are ready for completion
(e.g note section if needed), language and phrasal adjustments. Main task for
the package producer is now review, no more content production. Refer to
chapter 11 of Offensive Programming Book, Fabien GELINEAU (2019,
ISBN:979-10-699-4075-8), to learn about details and get value from this
package.
Author: Fabien Gelineau <neonira@gmail.com>
Maintainer: Fabien Gelineau <neonira@gmail.com>
Diff between wyz.code.rdoc versions 1.1.7 dated 2019-10-08 and 1.1.15 dated 2020-02-13
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Title: Analysis of Subjective Perspectives Using Q Methodology
Description: Analysis of Q methodology, used to identify distinct perspectives existing within a group.
This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see <http://qmethod.org>).
A single function runs the full analysis. Each step can be run separately using the corresponding functions: for automatic flagging of Q-sorts (manual flagging is optional), for statement scores, for distinguishing and consensus statements, and for general characteristics of the factors.
Additional functions are available to import and export data, to print and plot, to import raw data from individual *.CSV files, and to make printable cards.
The package also offers functions to print Q cards and to generate Q distributions for study administration.
The package uses principal components and it allows manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix.
See further details in the package documentation, and in the web pages below, which include a cookbook, guidelines for more advanced analysis (how to perform manual flagging or change the sign of factors), data management, and a beta graphical user interface for online and offline use.
Author: Aiora Zabala [aut, cre] (Main author,
<https://orcid.org/0000-0001-8534-3325>),
Maximilian Held [aut] (Author of additional data management functions)
Maintainer: Aiora Zabala <aiora.zabala@gmail.com>
Diff between qmethod versions 1.5.4 dated 2018-05-22 and 1.5.5 dated 2020-02-13
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/make.cards.R | 4 ++-- R/qdc.R | 12 ++++++------ R/qmethod.R | 6 ++++-- man/export.pqmethod.Rd | 19 +++++++++---------- man/make.cards.Rd | 6 ++++-- man/qdc.Rd | 12 ++++++++++-- man/qmethod.Rd | 44 ++++++++++++++++++++++++++++++++++++-------- 9 files changed, 84 insertions(+), 45 deletions(-)
Title: The Pareto and the Piecewise Pareto Distribution
Description: Utilities for the Pareto and piecewise Pareto distribution
that are useful for reinsurance pricing. In particular, the package provides
a non-trivial algorithm that can be used to match the expected losses of a
tower of reinsurance layers with a layer-independent collective risk model.
The theoretical background of the matching algorithm and most other methods
are described in Ulrich Riegel (2018) <doi:10.1007/s13385-018-0177-3>.
Author: Ulrich Riegel [aut, cre]
Maintainer: Ulrich Riegel <ulrich.riegel@gmx.de>
Diff between Pareto versions 1.1.0 dated 2019-12-17 and 1.1.3 dated 2020-02-13
DESCRIPTION | 8 MD5 | 31 +-- NAMESPACE | 1 NEWS.md | 7 R/Functions.R | 210 +++++++++++++++++++++--- README.md | 2 build/vignette.rds |binary inst/doc/Pareto.R | 8 inst/doc/Pareto.Rmd | 25 ++ inst/doc/Pareto.html | 73 +++++--- man/Pareto_ML_Estimator_Alpha.Rd | 22 +- man/PiecewisePareto_ML_Estimator_Alpha.Rd |only man/PiecewisePareto_Match_Layer_Losses.Rd | 3 man/rPareto.Rd | 7 tests/testthat/test_functions_Pareto.R | 47 +---- tests/testthat/test_functions_PiecewisePareto.R | 27 +++ vignettes/Pareto.Rmd | 25 ++ 17 files changed, 392 insertions(+), 104 deletions(-)
Title: Smoothed Bootstrap and Random Generation from Kernel Densities
Description: Smoothed bootstrap and functions for random generation from
univariate and multivariate kernel densities. It does not
estimate kernel densities.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+kernelboot@gmail.com>
Diff between kernelboot versions 0.1.6 dated 2019-11-07 and 0.1.7 dated 2020-02-13
DESCRIPTION | 10 ++-- MD5 | 44 ++++++++++---------- NAMESPACE | 1 R/RcppExports.R | 1 R/bandwidth.R | 1 R/kernelboot-methods.R | 1 R/kernelboot-package.R | 2 R/kernelboot.R | 65 ++++++++++++++++++------------- R/multivar-gaussian-kd.R | 1 R/multivar-kd.R | 1 R/univar-kd.R | 1 README.md | 2 man/kernelboot.Rd | 23 +++++++--- man/rmvk.Rd | 13 ++++-- man/ruvk.Rd | 13 ++++-- man/summary.kernelboot.Rd | 3 - tests/test_parallel.R | 7 +-- tests/testthat/test_bandwidth.R | 2 tests/testthat/test_kernelboot.R | 35 +++------------- tests/testthat/test_misc.R | 1 tests/testthat/test_multivar-gaussian.R | 3 - tests/testthat/test_univar-kd.R | 1 tests/testthat/test_univar_vs_multivar.R | 5 -- 23 files changed, 112 insertions(+), 124 deletions(-)
Title: Interface to 'ECMWF' and 'CDS' Data Web Services
Description: Programmatic interface to the European Centre for Medium-Range
Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>)
and Copernicus's Climate Data Store (CDS;
<https://cds.climate.copernicus.eu>). Allows for easy downloads of weather
forecasts and climate reanalysis data in R.
Author: Koen Hufkens [aut, cre] (<https://orcid.org/0000-0002-5070-8109>),
Reto Stauffer [ctb] (<https://orcid.org/0000-0002-3798-5507>),
Elio Campitelli [ctb] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between ecmwfr versions 1.2.1 dated 2019-04-23 and 1.2.2 dated 2020-02-13
DESCRIPTION | 14 MD5 | 68 ++-- R/addin.R | 3 R/wf_archetype.R | 6 R/wf_check_request.R | 1 R/wf_datasets.R | 1 R/wf_delete.R | 1 R/wf_get_key.R | 1 R/wf_product_info.R | 1 R/wf_request.R | 79 ++++- R/wf_services.R | 1 R/wf_set_key.R | 4 R/wf_transfer.R | 64 +++- R/wf_user_info.R | 1 R/zzz.R | 28 + build/vignette.rds |binary inst/doc/advanced_vignette.R | 8 inst/doc/advanced_vignette.html | 372 ++++++++++++++++++++------ inst/doc/cds_vignette.R | 8 inst/doc/cds_vignette.html | 350 ++++++++++++++++++++---- inst/doc/webapi_vignette.R | 16 - inst/doc/webapi_vignette.html | 464 ++++++++++++++++++++++++--------- man/wf_check_request.Rd | 4 man/wf_datasets.Rd | 4 man/wf_delete.Rd | 4 man/wf_get_key.Rd | 2 man/wf_product_info.Rd | 4 man/wf_request.Rd | 25 + man/wf_services.Rd | 4 man/wf_set_key.Rd | 2 man/wf_transfer.Rd | 16 - man/wf_user_info.Rd | 4 tests/testthat/test_cds.R | 3 tests/testthat/test_ecmwf.r | 156 ++++++----- tests/testthat/test_helper_functions.R | 1 35 files changed, 1243 insertions(+), 477 deletions(-)
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application 'wallace' is a modular platform for reproducible modeling of species niches and distributions. 'wallace' guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
Author: Jamie M. Kass [aut],
Gonzalo E. Pinilla-Buitrago [aut, cre],
Bruno Vilela [aut],
Matthew E. Aiello-Lammens [aut],
Robert Muscarella [aut],
Cory Merow [aut],
Robert P. Anderson [aut]
Maintainer: Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@gradcenter.cuny.edu>
Diff between wallace versions 1.0.6 dated 2018-10-07 and 1.0.6.2 dated 2020-02-13
DESCRIPTION | 22 +++---- MD5 | 24 ++++---- NAMESPACE | 2 NEWS.md | 11 ++- R/run_wallace.R | 15 +++-- R/wallace-package.R | 11 +-- README.md | 16 ++--- inst/shiny/Rmd/text_intro.Rmd | 2 inst/shiny/Rmd/text_intro_tab.Rmd | 2 inst/shiny/Rmd/userReport.Rmd | 8 +- inst/shiny/modules/mod_c4_bgExtent.R | 2 man/run_wallace.Rd | 55 +++++++++++-------- man/wallace-package.Rd | 101 ++++++++++++++++++----------------- 13 files changed, 147 insertions(+), 124 deletions(-)
Title: Interactive Tutorials for R
Description: Create interactive tutorials using R Markdown. Use a combination
of narrative, figures, videos, exercises, and quizzes to create self-paced
tutorials for learning about R and R packages.
Author: Barret Schloerke [aut, cre] (<https://orcid.org/0000-0001-9986-114X>),
JJ Allaire [aut],
Barbara Borges [aut],
Angela Li [ctb] (vignette),
RStudio [cph, fnd],
Ajax.org B.V. [ctb, cph] (Ace library),
Zeno Rocha [ctb, cph] (clipboard.js library),
Nick Payne [ctb, cph] (Bootbox library),
Jake Archibald [ctb, cph] (idb-keyval library)
Maintainer: Barret Schloerke <barret@rstudio.com>
Diff between learnr versions 0.10.0 dated 2019-11-09 and 0.10.1 dated 2020-02-13
learnr-0.10.0/learnr/R/install_tutorial_dependencies.R |only learnr-0.10.1/learnr/DESCRIPTION | 18 +- learnr-0.10.1/learnr/MD5 | 76 +++++----- learnr-0.10.1/learnr/NAMESPACE | 1 learnr-0.10.1/learnr/NEWS.md | 30 +++ learnr-0.10.1/learnr/R/available_tutorials.R | 50 +++++- learnr-0.10.1/learnr/R/evaluators.R | 4 learnr-0.10.1/learnr/R/events.R | 10 + learnr-0.10.1/learnr/R/http-handlers.R | 3 learnr-0.10.1/learnr/R/initialize.R | 9 + learnr-0.10.1/learnr/R/question_methods.R | 1 learnr-0.10.1/learnr/R/tutorial_package_dependencies.R |only learnr-0.10.1/learnr/build |only learnr-0.10.1/learnr/inst/doc |only learnr-0.10.1/learnr/inst/lib/tutorial/tutorial.js | 2 learnr-0.10.1/learnr/inst/rmarkdown/templates/tutorial/resources/tutorial-format.js | 5 learnr-0.10.1/learnr/inst/tutorials/ex-data-basics/ex-data-basics.Rmd | 3 learnr-0.10.1/learnr/inst/tutorials/ex-data-filter/ex-data-filter.Rmd | 4 learnr-0.10.1/learnr/inst/tutorials/ex-data-mutate/ex-data-mutate.Rmd | 2 learnr-0.10.1/learnr/inst/tutorials/ex-data-summarise/ex-data-manip-summarise.Rmd | 5 learnr-0.10.1/learnr/inst/tutorials/ex-setup-r/ex-setup-r.Rmd | 3 learnr-0.10.1/learnr/inst/tutorials/hello/hello.Rmd | 9 - learnr-0.10.1/learnr/inst/tutorials/quiz_question/quiz_question.Rmd | 3 learnr-0.10.1/learnr/inst/tutorials/slidy/slidy.Rmd | 3 learnr-0.10.1/learnr/man/available_tutorials.Rd | 2 learnr-0.10.1/learnr/man/format_quiz.Rd | 2 learnr-0.10.1/learnr/man/mark_as_correct_incorrect.Rd | 2 learnr-0.10.1/learnr/man/question_checkbox.Rd | 12 + learnr-0.10.1/learnr/man/question_methods.Rd | 2 learnr-0.10.1/learnr/man/question_radio.Rd | 12 + learnr-0.10.1/learnr/man/question_text.Rd | 16 +- learnr-0.10.1/learnr/man/quiz.Rd | 22 ++ learnr-0.10.1/learnr/man/tutorial.Rd | 44 +++-- learnr-0.10.1/learnr/man/tutorial_options.Rd | 14 + learnr-0.10.1/learnr/man/tutorial_package_dependencies.Rd |only learnr-0.10.1/learnr/tests/testthat.R | 9 - learnr-0.10.1/learnr/tests/testthat/test-dependency.R | 8 + learnr-0.10.1/learnr/tests/testthat/test-install-dependencies.R | 1 learnr-0.10.1/learnr/vignettes |only 39 files changed, 286 insertions(+), 101 deletions(-)
Title: Statistical Modelling for Plant Size Distributions
Description: Developed for the following tasks. I) Computing the probability density function, cumulative distribution function, random generation, and estimating the parameters of the eleven mixture models including mixture of Birnbaum-Saunders, BurrXII, Chen, F, Frechet, gamma, Gompertz, log-logistic, log-normal, Lomax, and Weibull. II) Point estimation of the parameters of two- and three-parameter Weibull distributions. In the case of two-parameter, twelve methods consist of generalized least square type 1, generalized least square type 2, L-moment, maximum likelihood, logarithmic moment, moment, percentile, rank correlation, least square, weighted maximum likelihood, U-statistic, weighted least square are used and investigated methods for the three-parameter case are: maximum likelihood, modified moment type 1, modified moment type 2, modified moment type 3, modified maximum likelihood type 1, modified maximum likelihood type 2, modified maximum likelihood type 3, modified maximum likelihood type 4, moment, maximum product spacing, T-L moment, and weighted maximum likelihood. III) The Bayesian estimators of the three-parameter Weibull distribution developed by Green et al. (1994) <doi:10.2307/2533217>. IV) Estimating parameters of the three-parameter Birnbaum-Saunders, generalized exponential, and Weibull distributions fitted to grouped data using three methods including approximated maximum likelihood, expectation maximization, and maximum likelihood. V) Estimating the parameters of the gamma, log-normal, and Weibull mixture models fitted to the grouped data through the EM algorithm, VI) Estimating parameters of the nonlinear height curve fitted to the height-diameter observation, and VII) estimating parameters, computing probability density function, cumulative distribution function, and generating realizations from gamma shape mixture model introduced by Venturini et al. (2008) <doi:10.1214/07-AOAS156>.
Author: Mahdi Teimouri
Maintainer: Mahdi Teimouri <teimouri@aut.ac.ir>
Diff between ForestFit versions 0.4.7 dated 2020-01-22 and 0.5.7 dated 2020-02-13
ForestFit-0.4.7/ForestFit/R/zzz.R |only ForestFit-0.5.7/ForestFit/DESCRIPTION | 8 ++++---- ForestFit-0.5.7/ForestFit/MD5 | 14 +++++++++----- ForestFit-0.5.7/ForestFit/R/welcome.R |only ForestFit-0.5.7/ForestFit/data/HW.txt |only ForestFit-0.5.7/ForestFit/data/SW.txt |only ForestFit-0.5.7/ForestFit/man/DBH.Rd | 15 +++++++-------- ForestFit-0.5.7/ForestFit/man/HW.Rd |only ForestFit-0.5.7/ForestFit/man/SW.Rd |only ForestFit-0.5.7/ForestFit/man/fitbayesJSB.Rd | 16 ++++++++-------- ForestFit-0.5.7/ForestFit/man/fitmixture.Rd | 14 ++++++-------- 11 files changed, 34 insertions(+), 33 deletions(-)
Title: Heatmap-Related Plots and Smooth Multiband Color Interpolation
Description: Supports combined contour-heat plots and 3D bar/surface plots, for plotting scalar fields, either discretely-spaced or continuously-spaced. Also, supports matrix visualization (per se), isosurfaces (for scalar fields over three variables), triangular plots and vector fields. All plots use static vector graphics (suitable for Sweave documents), but high resolution heatmaps can produce smooth raster-like visual effects. Contains a flexible system for smooth multiband color interpolation in RGB, HSV and HCL color spaces.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Diff between barsurf versions 0.3.1 dated 2019-05-23 and 0.4.0 dated 2020-02-13
barsurf-0.3.1/barsurf/R/transform.r |only barsurf-0.3.1/barsurf/man/rd_1_plots_discrete.Rd |only barsurf-0.3.1/barsurf/man/rd_2_plots_continuous.Rd |only barsurf-0.3.1/barsurf/man/rd_3_plots_triangular.Rd |only barsurf-0.3.1/barsurf/man/rd_4_color_conversion.Rd |only barsurf-0.3.1/barsurf/man/rd_5_color_themes.Rd |only barsurf-0.4.0/barsurf/DESCRIPTION | 18 barsurf-0.4.0/barsurf/MD5 | 48 barsurf-0.4.0/barsurf/NAMESPACE | 15 barsurf-0.4.0/barsurf/R/color.r | 161 +- barsurf-0.4.0/barsurf/R/init.r | 20 barsurf-0.4.0/barsurf/R/litmus.r |only barsurf-0.4.0/barsurf/R/other.r |only barsurf-0.4.0/barsurf/R/plot2d.r | 654 ++++++---- barsurf-0.4.0/barsurf/R/plot3d.r | 479 +++---- barsurf-0.4.0/barsurf/R/plot3v.r |only barsurf-0.4.0/barsurf/R/projection.r | 82 + barsurf-0.4.0/barsurf/build/vignette.rds |binary barsurf-0.4.0/barsurf/inst/doc/barsurf.R | 351 ++++- barsurf-0.4.0/barsurf/inst/doc/barsurf.Rnw | 612 +++++++-- barsurf-0.4.0/barsurf/inst/doc/barsurf.pdf |binary barsurf-0.4.0/barsurf/man/01_scalar_fields_discretely-spaced.Rd |only barsurf-0.4.0/barsurf/man/02_scalar_fields_continuously-spaced_.Rd |only barsurf-0.4.0/barsurf/man/03_plot_contour_3d.Rd |only barsurf-0.4.0/barsurf/man/04_plot_cfield_3d.Rd |only barsurf-0.4.0/barsurf/man/05_vector_fields.Rd |only barsurf-0.4.0/barsurf/man/06_color_themes.Rd |only barsurf-0.4.0/barsurf/man/07_barface_objects.Rd |only barsurf-0.4.0/barsurf/man/08_litmus_objects.Rd |only barsurf-0.4.0/barsurf/man/09_multi-litmus_objects.Rd |only barsurf-0.4.0/barsurf/man/10_supporting_methods.Rd |only barsurf-0.4.0/barsurf/man/11_other_supporting_functions_1.Rd |only barsurf-0.4.0/barsurf/man/12_other_supporting_functions_2.Rd |only barsurf-0.4.0/barsurf/man/13_sample_functions.Rd |only barsurf-0.4.0/barsurf/man/14_fitting_litmus_objects_to_data.Rd |only barsurf-0.4.0/barsurf/man/15_deprecated.Rd |only barsurf-0.4.0/barsurf/vignettes/barsurf.Rnw | 612 +++++++-- 37 files changed, 2218 insertions(+), 834 deletions(-)
Title: R Functions for Working with Spatial Data
Description: Spatial functions meant to enhance the core functionality of the
package "raster", including a parallel processing engine for use with
rasters.
Author: Jonathan Asher Greenberg
Maintainer: Jonathan Asher Greenberg <spatial-tools@estarcion.net>
Diff between spatial.tools versions 1.6.0 dated 2018-04-22 and 1.6.2 dated 2020-02-13
DESCRIPTION | 10 ++++----- MD5 | 43 ++++++++++++++++++++--------------------- R/bbox_to_SpatialPolygons.R | 8 +++---- R/binary_image_write.R | 4 +-- R/fix_extent.R | 2 - R/focal_hpc.R | 10 ++++----- R/getValuesBlock_stackfix.R | 4 +-- R/is.Raster.R | 2 - R/list.raster.files.R | 2 - R/predict_rasterEngine.R | 40 ++++++++++++++++++++++++++++++-------- R/projectRaster_rigorous.R | 4 +-- README.md |only man/binary_image_write.Rd | 10 +++++++-- man/build_raster_header.Rd | 14 ++++++++++--- man/create_blank_raster.Rd | 20 ++++++++++++++----- man/focal_hpc.Rd | 30 +++++++++++++++++++++------- man/getValuesBlock_enhanced.Rd | 12 +++++++++-- man/getValuesBlock_stackfix.Rd | 10 +++++++-- man/list.raster.files.Rd | 11 +++++++--- man/predict_rasterEngine.Rd | 17 ++++++++++++++-- man/projectRaster_rigorous.Rd | 10 +++++++-- man/rasterEngine.Rd | 31 ++++++++++++++++++++++------- man/spatial_sync_raster.Rd | 11 ++++++++-- 23 files changed, 216 insertions(+), 89 deletions(-)
Title: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities
Description: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities.
Author: Jonathan Asher Greenberg and Matteo Mattiuzzi
Maintainer: Jonathan Asher Greenberg <gdalUtils@estarcion.net>
Diff between gdalUtils versions 2.0.3 dated 2020-01-16 and 2.0.3.2 dated 2020-02-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/gdal_translate.R | 17 ++++++++++++++++- R/mosaic_rasters.R | 5 ++++- man/gdal_translate.Rd | 2 +- 5 files changed, 28 insertions(+), 10 deletions(-)
Title: Extract Features from Images
Description: Synthesize images into characteristic features for time-series analysis or machine learning applications. The package was originally intended for monitoring volcanic eruptions in video data by highlighting and extracting regions above the vent associated with plume activity. However, the functions within are general and have wide applications for image processing, analyzing, filtering, and plotting.
Author: Alex J.C. Witsil
Maintainer: Alex J.C. Witsil <alexjcwitsil@gmail.com>
Diff between imagefx versions 0.3.0 dated 2019-11-12 and 0.4.1 dated 2020-02-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++++----- NAMESPACE | 1 + R/build.lap.r |only R/fftshift.r | 5 ++--- R/points2.r |only build/vignette.rds |binary man/build.lap.Rd |only man/fftshift.Rd | 2 +- man/points2.Rd |only 10 files changed, 16 insertions(+), 12 deletions(-)
Title: Multiple Fill and Colour Scales in 'ggplot2'
Description: Use multiple fill and colour scales in 'ggplot2'.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between ggnewscale versions 0.4.0 dated 2019-10-06 and 0.4.1 dated 2020-02-13
DESCRIPTION | 16 +++++++++------- MD5 | 16 +++++++++------- NAMESPACE | 3 +++ NEWS.md | 6 ++++++ R/new-scale.R | 9 ++++++--- README.md | 2 +- man/figures/README-unnamed-chunk-1-1.png |binary man/ggnewscale-package.Rd | 8 ++++---- tests |only 9 files changed, 38 insertions(+), 22 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the only parameter is a specified cut-off P-value which can be interpreted as the probability of a false positive being included in the final selection. For more information see the website below and the accompanying papers: L. Davies and L. Duembgen, "A Model-free Approach to Linear Least Squares Regression with Exact Probabilities and Applications to Covariate Selection", 2019, <arXiv:1906.01990>. L. Davies, "Lasso, Knockoff and Gaussian covariates: A comparison", 2018, <arXiv:1807.09633>.
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <laurie.davies@uni-due.de>
Diff between gausscov versions 0.0.2 dated 2019-09-11 and 0.0.3 dated 2020-02-13
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Title: A Model Comparison Perspective
Description: Accompanies "Designing experiments and
analyzing data: A model comparison perspective" (3rd ed.) by
Maxwell, Delaney, & Kelley (2018; Routledge).
Contains all of the data sets in the book's chapters and
end-of-chapter exercises. Information about the book is available at
<http://www.DesigningExperiments.com>.
Author: Scott Maxwell [aut],
Harold Delaney [aut],
Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between AMCP versions 0.0.4 dated 2017-02-18 and 1.0.0 dated 2020-02-13
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-22 1.0
Title: Non-Invasive Pretty Printing of R Code
Description: Pretty-prints R code without changing the user's
formatting intent.
Author: Kirill Müller [aut],
Lorenz Walthert [cre, aut]
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between styler versions 1.3.0 dated 2020-02-10 and 1.3.1 dated 2020-02-13
DESCRIPTION | 6 +- MD5 | 24 ++++----- NEWS.md | 38 ++++++++++++++- R/nest.R | 10 ++-- R/token-create.R | 2 R/transform-block.R | 2 R/visit.R | 2 inst/doc/customizing_styler.html | 8 +-- inst/doc/introducing_styler.html | 4 - man/create_tokens.Rd | 2 man/drop_cached_children.Rd | 7 +- tests/testthat/test-cache-high-level-api.R | 72 +++++++++++++++++++++++++---- tests/testthat/test-cache-low-level-api.R | 42 ++++++++++++++++ 13 files changed, 178 insertions(+), 41 deletions(-)
Title: Routines for Exponential Power Distribution
Description: A collection of utilities referred to Exponential Power distribution, also known as General Error Distribution (see Mineo, A.M. and Ruggieri, M. (2005), A software Tool for the Exponential Power Distribution: The normalp package. In Journal of Statistical Software, Vol. 12, Issue 4).
Author: Angelo M. Mineo <angelo.mineo@unipa.it>
Maintainer: Angelo M. Mineo <angelo.mineo@unipa.it>
Diff between normalp versions 0.7.0.1 dated 2018-08-31 and 0.7.1 dated 2020-02-13
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NAMESPACE | 3 --- R/lmp.R | 2 +- man/normalp-package.Rd | 4 ++-- man/paramp.Rd | 1 - 6 files changed, 15 insertions(+), 19 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.0-4 dated 2020-01-13 and 1.0-5 dated 2020-02-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/NEWS.Rd | 7 +++++++ inst/doc/mlt.Rnw | 6 +++--- inst/doc/mlt.pdf |binary vignettes/mlt.Rnw | 6 +++--- 6 files changed, 22 insertions(+), 15 deletions(-)
Title: Visualizations of High-Dimensional Data
Description: Gives access to data visualisation methods that are relevant from the data scientist's point of view. The flagship idea of 'DataVisualizations' is the mirrored density plot (MD-plot) for either classified or non-classified multivariate data presented in Thrun et al. (2019) <arXiv:1908.06081>. The MD-plot outperforms the box-and-whisker diagram (box plot), violin plot and bean plot. Furthermore, a collection of various visualization methods for univariate data is provided. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through a combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). Additionally, visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for two variables as well as the Shepard density plot and the Bland-Altman plot are presented here. Pertaining to classified high-dimensional data, a number of visualizations are described, such as f.ex. the heat map and silhouette plot. A political map of the world or Germany can be visualized with the additional information defined by a classification of countries or regions. By extending the political map further, an uncomplicated function for a Choropleth map can be used which is useful for measurements across a geographic area. For categorical features, the Pie charts, slope charts and fan plots, improved by the ABC analysis, become usable. More detailed explanations are found in the book by Thrun, M.C.: "Projection-Based Clustering through Self-Organization and Swarm Intelligence" (2018) <doi:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph] (<https://orcid.org/0000-0001-9542-5543>),
Felix Pape [aut, rev],
Onno Hansen-Goos [ctr, ctb],
Dirk Eddelbuettel [ctr],
Craig Varrichio [ctr],
Alfred Ultsch [dtc, ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between DataVisualizations versions 1.1.10 dated 2020-02-02 and 1.1.11 dated 2020-02-13
DESCRIPTION | 8 +++--- MD5 | 20 +++++++++------- NAMESPACE | 1 R/CombineCols.R |only R/MDplot.R | 2 - R/MDplot4multiplevectors.R | 4 +-- R/Plot3D.R | 46 ++++++++++++++++++++++++++++++++------- build/partial.rdb |binary inst/NEWS | 4 +++ inst/doc/DataVisualizations.html | 18 +++++++-------- man/CombineCols.Rd |only man/Plot3D.Rd | 19 +++++++++++----- 12 files changed, 84 insertions(+), 38 deletions(-)
More information about DataVisualizations at CRAN
Permanent link
Title: An Implementation of Crime Analysis Methods
Description: An implementation of functions for the analysis of crime incident or records
management system data. The package implements analysis algorithms scaled for city
or regional crime analysis units. The package provides functions for kernel density
estimation for crime heat maps, geocoding using the 'Google Maps' API, spatio-temporal
map comparison across time intervals, time series analysis (forecasting and decomposition),
and near repeat analysis (with crime network linkage).
Author: Jamie Spaulding and Keith Morris
Maintainer: Jamie Spaulding <jspauldi@mix.wvu.edu>
Diff between rcrimeanalysis versions 0.2.0 dated 2020-02-09 and 0.3.1 dated 2020-02-13
DESCRIPTION | 11 ++---- MD5 | 28 ++++++++-------- NAMESPACE | 16 ++++++--- R/geocode_address.R | 1 R/id_repeat.R |only R/kde_int_comp.R | 45 ++++++++++++++++++++++++-- R/kde_map.R | 22 ++++++------- R/near_repeat_analysis.R | 7 +--- R/ts_daily_decomp.R | 30 +++++------------ R/ts_forecast.R | 74 +++++++++++++++++--------------------------- data/crimes.rda |binary man/id_repeat.Rd |only man/kde_int_comp.Rd | 2 - man/near_repeat_analysis.Rd | 7 +--- man/ts_daily_decomp.Rd | 30 +++++------------ man/ts_forecast.Rd | 34 ++++++++++---------- 16 files changed, 152 insertions(+), 155 deletions(-)
More information about rcrimeanalysis at CRAN
Permanent link
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.4.8 dated 2020-01-08 and 0.4.9 dated 2020-02-13
DESCRIPTION | 8 MD5 | 92 ++-- R/ANOVA.R | 19 - R/ARMA.R | 2 R/ARMA_optim.R | 23 - R/Binary_ANOVA.R | 31 + R/Boost.R | 30 + R/Causation.R | 125 +++--- R/Dependence.R | 34 + R/Dependence_base.R | 78 ++-- R/Dependence_matrix.R | 69 ++- R/Internal_Functions.R | 66 ++- R/Multivariate_Regression.R | 28 + R/NNS_Distance.R | 6 R/NNS_VAR.R | 143 +++++-- R/Numerical_Differentiation.R | 6 R/Partition_Map.R | 138 +++++-- R/Regression.R | 359 ++++++++----------- R/Seasonality_Test.R | 14 R/Stack.R | 350 +++++++++--------- R/Uni_Causation.R | 7 R/dy_d_wrt.R | 90 ++-- inst/doc/NNSvignette_Classification.R | 2 inst/doc/NNSvignette_Classification.Rmd | 2 inst/doc/NNSvignette_Classification.html | 114 ++---- inst/doc/NNSvignette_Clustering_and_Regression.R | 12 inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 19 - inst/doc/NNSvignette_Clustering_and_Regression.html | 234 ++++++------ inst/doc/NNSvignette_Correlation_and_Dependence.R | 6 inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 6 inst/doc/NNSvignette_Correlation_and_Dependence.html | 190 ++++------ inst/doc/NNSvignette_Forecasting.R | 44 +- inst/doc/NNSvignette_Forecasting.Rmd | 46 ++ inst/doc/NNSvignette_Forecasting.html | 149 ++++--- inst/doc/NNSvignette_Partial_Moments.html | 100 ++--- man/NNS.VAR.Rd | 25 + man/NNS.boost.Rd | 4 man/NNS.caus.Rd | 3 man/NNS.dep.Rd | 6 man/NNS.dep.base.Rd | 8 man/NNS.part.Rd | 4 man/NNS.reg.Rd | 6 man/dy.d_.Rd | 11 vignettes/NNSvignette_Classification.Rmd | 2 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 19 - vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 6 vignettes/NNSvignette_Forecasting.Rmd | 46 ++ 47 files changed, 1610 insertions(+), 1172 deletions(-)
Title: Text to Speech
Description: Unifies different text to speech engines, such as
Google, Microsoft, and Amazon. Text synthesis can be done
in any engine with a simple switch of an argument denoting
the service requested. The 'aws.polly' package has been
orphaned and can be found from the CRAN archives.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between text2speech versions 0.2.9 dated 2020-01-13 and 0.2.10 dated 2020-02-13
DESCRIPTION | 9 ++++--- MD5 | 18 +++++++-------- NEWS.md | 4 +++ R/pcm_to_wav.R | 3 +- R/tts_backend.R | 2 - R/tts_synthesize.R | 2 - build/vignette.rds |binary inst/doc/listing_voices.html | 50 ++++++++++++++----------------------------- man/pcm_to_wav.Rd | 3 +- man/tts.Rd | 6 +---- 10 files changed, 43 insertions(+), 54 deletions(-)
Title: Generalized Tensor Regression with Covariates on Multiple Modes
Description: Implement the generalized tensor regression in Xu, Hu and Wang (2019) <arXiv:1910.09499>. Solve tensor-response regression given covariates on multiple modes with alternating updating algorithm.
Author: Zhuoyan Xu [aut, cre, cph],
Jiaxin Hu [aut, cph],
Miaoyan Wang [aut, cph]
Maintainer: Zhuoyan Xu <zxu444@stat.wisc.edu>
Diff between tensorregress versions 1.0 dated 2019-11-04 and 1.1 dated 2020-02-13
DESCRIPTION | 10 +-- MD5 | 10 +-- R/sele_rank.R | 2 man/sele_rank.Rd | 138 ++++++++++++++++++++++++--------------------- man/sim_data.Rd | 130 ++++++++++++++++++++++-------------------- man/tensor_regress.Rd | 153 ++++++++++++++++++++++++++------------------------ 6 files changed, 235 insertions(+), 208 deletions(-)
Title: A Shiny GUI for some Parameter Estimation Examples
Description: Allows specification and fitting of some parameter
estimation examples inspired by time-resolved spectroscopy via
a Shiny GUI.
Author: Joris Snellenburg [cre, aut],
Katharine Mullen [aut],
Ivo van Stokkum [aut]
Maintainer: Joris Snellenburg <j.snellenburg@vu.nl>
Diff between paramGUI versions 2.1.3 dated 2018-03-15 and 2.1.4 dated 2020-02-13
DESCRIPTION | 8 - MD5 | 34 +++--- NAMESPACE | 2 R/runApp.R | 6 - R/utility.R | 2 inst/shinyApps/paramGUI/app.R | 2 man/calcE.Rd | 40 ++++---- man/example_dataset.Rd | 42 ++++---- man/is_compressed.Rd | 38 +++---- man/is_rdata.Rd | 32 +++--- man/kroneckercol.Rd | 36 +++---- man/linlogtics.Rd | 42 ++++---- man/paramGUI.Rd | 17 +-- man/plotterforGUI.Rd | 79 ++++++++------- man/runGUI.Rd | 38 +++---- man/simndecay_gen_paramGUI.Rd | 208 +++++++++++++++++++++++------------------- man/spectemp.Rd | 52 +++++----- man/startGUI.Rd | 20 ++-- 18 files changed, 366 insertions(+), 332 deletions(-)
Title: Movement Data Visualization
Description: Tools to visualize movement data (e.g. from GPS tracking) and temporal changes of environmental data (e.g. from remote sensing) by creating video animations.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <movevis@schwalb-willmann.de>
Diff between moveVis versions 0.10.4 dated 2020-02-07 and 0.10.4-1 dated 2020-02-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 14 +++++++++++++- R/moveVis-internal.R | 29 ++++++++++++++++++++--------- README.md | 2 ++ 5 files changed, 43 insertions(+), 18 deletions(-)
Title: Inferring Longitudinal Dominance Hierarchies
Description: Provides functions for inferring longitudinal dominance hierarchies, which describe dominance relationships and their dynamics in a single latent hierarchy over time. Strauss & Holekamp (in press).
Author: Eli D. Strauss
Maintainer: Eli D. Strauss <straussed@gmail.com>
Diff between DynaRankR versions 1.0.0 dated 2019-01-18 and 1.1.0 dated 2020-02-13
DESCRIPTION | 9 +++++---- MD5 | 20 ++++++++++---------- NEWS.md | 6 +++++- R/add_new_ids.R | 12 ++++++++++++ R/add_new_ids_elo.R | 12 ++++++++++++ R/dyadic_similarity.R | 4 ++-- R/identify_inconsistencies.R | 3 +++ R/informed_matreorder.R | 33 +++++++++++++++++++++++---------- R/matrix_functions.R | 3 +++ man/informed_elo.Rd | 10 ++++++++-- man/informed_matreorder.Rd | 11 +++++++++-- 11 files changed, 92 insertions(+), 31 deletions(-)
Title: BioConductor Package Downloads Stats
Description: Download stats reports from the BioConductor.org stats website.
Author: Marcelo Ponce [aut, cre]
Maintainer: Marcelo Ponce <mponce@scinet.utoronto.ca>
Diff between bioC.logs versions 1.0 dated 2020-02-09 and 1.1 dated 2020-02-13
DESCRIPTION | 8 +- MD5 | 25 +++++-- NAMESPACE | 1 NEWS |only R/auxs-utils.R |only R/bioC_logs.R | 169 ++++++++++++++++++++++++++++++++++++++++++------ README.md | 47 ++++++++++++- inst/doc/bioC.logs.html | 64 +++++++++++++++--- man/Xyear.from.now.Rd |only man/bioC_downloads.Rd | 26 +++++-- man/checkDate.Rd |only man/checkDates.Rd |only man/checkValidDates.Rd |only man/daysInMonth.Rd |only man/last.day.month.Rd |only man/lst.year.Rd |only man/origin.of.times.Rd |only man/today.Rd |only man/year.from.now.Rd |only man/year.to.date.Rd |only 20 files changed, 291 insertions(+), 49 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-29 0.1.7
2017-12-06 0.1.5
2017-11-02 0.1.4
Title: Joint Sentiment Topic Modelling
Description: Estimates the Joint Sentiment Topic model and its reversed variety,
as described by Lin and He, 2009 <DOI:10.1145/1645953.1646003> and Lin, He, Everson and Ruger
(2012) <DOI:10.1109/TKDE.2011.48>.
Author: Max Boiten [cre, aut],
Chenghua Lin [cph],
Yulan He [cph]
Maintainer: Max Boiten <max_boiten@live.nl>
Diff between rJST versions 1.1 dated 2019-12-09 and 1.3 dated 2020-02-13
DESCRIPTION | 8 +-- MD5 | 22 ++++----- R/get_parameter.R | 8 +-- R/jst.R | 5 +- R/jst_reversed.R | 3 - R/topNwords.R | 28 ++++++------ inst/doc/rJST.html | 12 ++--- man/jst.Rd | 2 man/top20words-method.Rd | 2 man/topNwords-method.Rd | 2 tests/testthat/test-jst.R | 75 +++++++++++++++++++++++++++++++-- tests/testthat/test-jst_reversed.R | 83 ++++++++++++++++++++++++++++++++++--- 12 files changed, 194 insertions(+), 56 deletions(-)
Title: Handling Linear Gaussian Bayesian Networks
Description: Creation, manipulation, simulation of linear Gaussian Bayesian
networks from text files and more...
Author: Jean-Baptiste Denis [aut, cre], Marco Scutari [ctb]
Maintainer: Marco Scutari <marco.scutari@gmail.com>
Diff between rbmn versions 0.9-2 dated 2013-08-01 and 0.9-3 dated 2020-02-13
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- NAMESPACE | 5 +++++ R/f11.interface.code.r | 13 +++++++------ 4 files changed, 22 insertions(+), 16 deletions(-)
Title: Tools for Identifying Important Nodes in Networks
Description: Includes assorted tools for network analysis. Bridge centrality; goldbricker; MDS, PCA, & eigenmodel network plotting.
Author: Payton Jones [aut, cre]
Maintainer: Payton Jones <payton_jones@g.harvard.edu>
Diff between networktools versions 1.2.1 dated 2019-05-20 and 1.2.2 dated 2020-02-13
networktools-1.2.1/networktools/R/edge_impact.R |only networktools-1.2.1/networktools/R/global_impact.R |only networktools-1.2.1/networktools/R/structure_impact.R |only networktools-1.2.1/networktools/build |only networktools-1.2.1/networktools/inst |only networktools-1.2.1/networktools/man/edge.impact.Rd |only networktools-1.2.1/networktools/man/global.impact.Rd |only networktools-1.2.1/networktools/man/structure.impact.Rd |only networktools-1.2.1/networktools/vignettes |only networktools-1.2.2/networktools/DESCRIPTION | 12 - networktools-1.2.2/networktools/MD5 | 53 ++---- networktools-1.2.2/networktools/NAMESPACE | 4 networktools-1.2.2/networktools/NEWS.md | 13 + networktools-1.2.2/networktools/R/EIGENnet.R | 2 networktools-1.2.2/networktools/R/MDSnet.R | 87 ++++++++++- networktools-1.2.2/networktools/R/PCAnet.R | 2 networktools-1.2.2/networktools/R/hidden_functions.R | 4 networktools-1.2.2/networktools/R/impact.R | 13 - networktools-1.2.2/networktools/R/impact_NCT.R | 3 networktools-1.2.2/networktools/R/impact_boot.R | 2 networktools-1.2.2/networktools/R/summary_print_plot.R | 46 ++--- networktools-1.2.2/networktools/man/EIGENnet.Rd | 2 networktools-1.2.2/networktools/man/MDSnet.Rd | 2 networktools-1.2.2/networktools/man/PCAnet.Rd | 2 networktools-1.2.2/networktools/man/PROCRUSTESnet.Rd |only networktools-1.2.2/networktools/man/impact.NCT.Rd | 6 networktools-1.2.2/networktools/man/impact.Rd | 8 - networktools-1.2.2/networktools/man/impact.boot.Rd | 2 networktools-1.2.2/networktools/man/plot.bridge.Rd | 5 networktools-1.2.2/networktools/man/plot.edge.impact.Rd | 13 - networktools-1.2.2/networktools/man/plot.global.impact.Rd | 11 - networktools-1.2.2/networktools/man/plot.structure.impact.Rd | 11 - 32 files changed, 168 insertions(+), 135 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Fits regularization paths for linear regression, GLM, and Cox
regression models using lasso or nonconvex penalties, in particular the
minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD)
penalty, with options for additional L2 penalties (the "elastic net" idea).
Utilities for carrying out cross-validation as well as post-fitting
visualization, summarization, inference, and prediction are also provided.
Author: Patrick Breheny [aut, cre] (<https://orcid.org/0000-0002-0650-1119>)
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.11-1 dated 2019-02-26 and 3.11.2 dated 2020-02-13
ncvreg-3.11-1/ncvreg/R/cv.ncvreg.R |only ncvreg-3.11-1/ncvreg/R/cv.ncvsurv.R |only ncvreg-3.11-1/ncvreg/R/perm.ncvreg.R |only ncvreg-3.11-1/ncvreg/R/permres.ncvreg.R |only ncvreg-3.11-1/ncvreg/R/plot.cv.ncvreg.R |only ncvreg-3.11-1/ncvreg/R/plot.mfdr.R |only ncvreg-3.11-1/ncvreg/R/plot.ncvreg.R |only ncvreg-3.11-1/ncvreg/R/plot.ncvsurv.func.R |only ncvreg-3.11-1/ncvreg/R/predict.cv.R |only ncvreg-3.11-1/ncvreg/R/predict.surv.R |only ncvreg-3.11.2/ncvreg/DESCRIPTION | 17 +- ncvreg-3.11.2/ncvreg/MD5 | 109 ++++++++------ ncvreg-3.11.2/ncvreg/NAMESPACE | 2 ncvreg-3.11.2/ncvreg/NEWS.md | 5 ncvreg-3.11.2/ncvreg/R/auc.R | 2 ncvreg-3.11.2/ncvreg/R/convexMin.R | 12 - ncvreg-3.11.2/ncvreg/R/cv-ncvreg.R |only ncvreg-3.11.2/ncvreg/R/cv-ncvsurv.R |only ncvreg-3.11.2/ncvreg/R/local-mfdr.R | 145 ++++++++++++------- ncvreg-3.11.2/ncvreg/R/logLik.R | 20 -- ncvreg-3.11.2/ncvreg/R/loss.R | 4 ncvreg-3.11.2/ncvreg/R/mfdr.R | 12 - ncvreg-3.11.2/ncvreg/R/ncvreg.R | 51 +++--- ncvreg-3.11.2/ncvreg/R/ncvsurv.R | 38 ++-- ncvreg-3.11.2/ncvreg/R/perm-ncvreg.R |only ncvreg-3.11.2/ncvreg/R/permres-ncvreg.R |only ncvreg-3.11.2/ncvreg/R/plot-cv-ncvreg.R |only ncvreg-3.11.2/ncvreg/R/plot-mfdr.R |only ncvreg-3.11.2/ncvreg/R/plot-ncvreg.R |only ncvreg-3.11.2/ncvreg/R/plot-ncvsurv-func.R |only ncvreg-3.11.2/ncvreg/R/predict-cv.R |only ncvreg-3.11.2/ncvreg/R/predict-surv.R |only ncvreg-3.11.2/ncvreg/R/predict.R | 14 - ncvreg-3.11.2/ncvreg/R/setupLambda.R | 4 ncvreg-3.11.2/ncvreg/R/setupLambdaCox.R | 4 ncvreg-3.11.2/ncvreg/R/std.R | 36 ++++ ncvreg-3.11.2/ncvreg/R/summary-cv-ncvreg.R | 8 - ncvreg-3.11.2/ncvreg/R/summary-ncvreg.R | 44 ++++- ncvreg-3.11.2/ncvreg/README.md | 99 ++---------- ncvreg-3.11.2/ncvreg/build/vignette.rds |binary ncvreg-3.11.2/ncvreg/inst/doc/getting-started.R | 18 +- ncvreg-3.11.2/ncvreg/inst/doc/getting-started.html | 56 ++++--- ncvreg-3.11.2/ncvreg/inst/doc/getting-started.rmd | 4 ncvreg-3.11.2/ncvreg/inst/testing-functions.R |only ncvreg-3.11.2/ncvreg/inst/tests/gaussian.R | 15 - ncvreg-3.11.2/ncvreg/inst/tests/mfdr.R | 11 + ncvreg-3.11.2/ncvreg/inst/tests/ncvsurv.R | 4 ncvreg-3.11.2/ncvreg/inst/tests/standardize.R | 21 ++ ncvreg-3.11.2/ncvreg/man/figures |only ncvreg-3.11.2/ncvreg/man/local_mfdr.Rd |only ncvreg-3.11.2/ncvreg/man/ncvsurv.Rd | 2 ncvreg-3.11.2/ncvreg/man/plot-mfdr.Rd | 4 ncvreg-3.11.2/ncvreg/man/plot-ncvreg.Rd | 4 ncvreg-3.11.2/ncvreg/man/std.Rd | 42 ++--- ncvreg-3.11.2/ncvreg/man/summary-ncvreg.Rd | 3 ncvreg-3.11.2/ncvreg/src/binomial.c | 156 ++++++++++---------- ncvreg-3.11.2/ncvreg/src/gaussian.c | 136 ++++++++--------- ncvreg-3.11.2/ncvreg/src/poisson.c | 160 ++++++++++----------- ncvreg-3.11.2/ncvreg/tests |only ncvreg-3.11.2/ncvreg/vignettes/getting-started.rmd | 4 60 files changed, 683 insertions(+), 583 deletions(-)
Title: Explore and Map County-Level Hurricane Exposure in the United
States
Description: Allows users to create time series of tropical storm
exposure histories for chosen counties for a number of hazard metrics
(wind, rain, distance from the storm, etc.). This package interacts
with data available through the 'hurricaneexposuredata' package, which
is available in a 'drat' repository. To access this data package, see the
instructions at <https://github.com/geanders/hurricaneexposure>.
The size of the 'hurricaneexposuredata' package is
approximately 20 MB. This work was supported in part by grants from the National
Institute of Environmental Health Sciences (R00ES022631), the National Science
Foundation (1331399), and a NASA Applied Sciences Program/Public Health Program
Grant (NNX09AV81G).
Author: Brooke Anderson [aut, cre],
Meilin Yan [aut],
Joshua Ferreri [aut],
William Crosson [ctb],
Mohammad Al-Hamdan [ctb],
Andrea Schumacher [ctb],
Dirk Eddelbuettel [ctb]
Maintainer: Brooke Anderson <brooke.anderson@colostate.edu>
Diff between hurricaneexposure versions 0.1.0 dated 2019-04-01 and 0.1.1 dated 2020-02-13
DESCRIPTION | 28 +- MD5 | 56 ++--- NEWS.md | 8 R/event_exposure.R | 14 - R/map_exposure.R | 52 ++--- R/wind_exposure.R | 14 + build/vignette.rds |binary inst/doc/hurricaneexposure.R | 71 +++--- inst/doc/hurricaneexposure.Rmd | 47 ++-- inst/doc/hurricaneexposure.html | 414 +++++++++++++++++++++------------------- man/county_events.Rd | 45 ++-- man/county_rain.Rd | 10 man/county_wind.Rd | 24 ++ man/distance_exposure.Rd | 10 man/events_exposure.Rd | 12 - man/filter_storm_data.Rd | 15 + man/filter_wind_data.Rd | 12 - man/hurr_choropleth.Rd | 8 man/interp_track.Rd | 17 - man/map_counties.Rd | 15 + man/map_event_exposure.Rd | 8 man/map_rain_exposure.Rd | 9 man/map_tracks.Rd | 10 man/map_wind_exposure.Rd | 9 man/multi_county_events.Rd | 2 man/multi_county_rain.Rd | 10 man/rain_exposure.Rd | 12 - man/wind_exposure.Rd | 11 - vignettes/hurricaneexposure.Rmd | 47 ++-- 29 files changed, 587 insertions(+), 403 deletions(-)
More information about hurricaneexposure at CRAN
Permanent link
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers. The package is enhanced when the 'gt' package is installed.
Use this code to install: 'remotes::install_github("rstudio/gt", ref =
gtsummary::gt_sha)'.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Stephanie Lobaugh [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.2.5 dated 2020-02-11 and 1.2.6 dated 2020-02-13
DESCRIPTION | 17 MD5 | 24 NEWS.md | 4 R/tidy_vetted.R | 6 R/utils-tbl_regression.R | 4 build/gtsummary.pdf | 4684 +++++++++++++++++------------------ inst/doc/gallery.html | 680 ++--- inst/doc/global_options.html | 68 inst/doc/inline_text.html | 136 - inst/doc/tbl_regression.html | 272 +- inst/doc/tbl_summary.html | 340 +- man/tidy_vetted.Rd | 6 tests/testthat/test-tbl_regression.R | 18 13 files changed, 3142 insertions(+), 3117 deletions(-)
Title: Methods for Calculating Gradient Surface Metrics
Description: Methods for calculating gradient surface metrics for
continuous analysis of landscape features.
Author: Annie C. Smith, Phoebe Zarnetske, Kyla Dahlin, Adam Wilson, Andrew Latimer
Maintainer: Annie C. Smith <annie.smith@dnr.wa.gov>
Diff between geodiv versions 0.1.0 dated 2020-01-31 and 0.1.1 dated 2020-02-13
DESCRIPTION | 14 +++++++------- MD5 | 7 ++++--- NEWS.md |only R/movingwindow.R | 6 +++--- src/sfd.cpp | 5 ++--- 5 files changed, 16 insertions(+), 16 deletions(-)
Title: Creates Safety Results Summary in XML to Upload to EudraCT
Description: The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ) is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by EudraCT and formats them into the precise requirements to directly upload an XML file into the web portal, with no further data entry by hand.
Author: Simon Bond [cre],
Beatrice Pantaleo [aut]
Maintainer: Simon Bond <simon.bond@addenbrookes.nhs.uk>
Diff between eudract versions 0.9.0 dated 2019-11-07 and 0.9.1 dated 2020-02-13
DESCRIPTION | 8 MD5 | 19 NEWS.md | 4 inst/doc/eudract.R | 10 inst/doc/eudract.html | 85 inst/extdata/safety__upload.xml | 3676 ++++++++++----------- inst/extdata/simpleToEudraCT.xslt | 9 tests/testthat/data/all_soc_v2.csv |only tests/testthat/eudract.xml |only tests/testthat/reference/table_eudract.xml | 4972 ++++++++++++++--------------- tests/testthat/simple.xml |only tests/testthat/test_basic.R | 5 12 files changed, 4403 insertions(+), 4385 deletions(-)
Title: Integrated Stratigraphy
Description: Includes bases for litholog generation: graphical functions
based on R base graphics, interval management functions and svg importation
functions among others. Also include stereographic projection functions,
and other functions made to deal with large datasets while keeping options
to get into the details of the data.
When using for publication please cite Wouters, S., Da Silva, A.C. Crucifix,
M., Sinnesael, M., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2019,
Litholog generation with the StratigrapheR package and signal decomposition
for cyclostratigraphic purposes. Geophysical Research Abstracts Vol. 21,
EGU2019-5520, 2019, EGU General Assembly 2019.
<http://hdl.handle.net/2268/234402>
The palaeomagnetism functions are based on:
Tauxe, L., 2010. Essentials of Paleomagnetism. University of California
Press. <https://earthref.org/MagIC/books/Tauxe/Essentials/>;
Allmendinger, R. W., Cardozo, N. C., and Fisher, D., 2013, Structural
Geology Algorithms: Vectors & Tensors: Cambridge, England, Cambridge
University Press, 289 pp.;
Cardozo, N., and Allmendinger, R. W., 2013, Spherical projections
with OSXStereonet: Computers & Geosciences, v. 51, no. 0, p. 193 - 205,
<doi: 10.1016/j.cageo.2012.07.021>.
Author: Sebastien Wouters [aut, cre], Adam D. Smith [ctb]
Maintainer: Sebastien Wouters <sebastien.wouters@doct.uliege.be>
Diff between StratigrapheR versions 0.0.7 dated 2019-12-05 and 0.0.8 dated 2020-02-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/StratigrapheR.R | 2 +- R/earnet.R | 1 - man/StratigrapheR.Rd | 2 +- man/earnet.Rd | 2 -- 6 files changed, 10 insertions(+), 13 deletions(-)
Title: Import Financial Data from the 'SimFin' Project
Description: Uses the 'SimFin' (SIMmplifying FINnance) api at <https://simfin.com/data/access/api> to download financial data straight into your R session.
It includes financial statements -- balance sheet, cash flow and income statement -- and adjusted daily price of stocks.
The available data is comprehensive, going back to 2005 and available for quarters (Q1, Q2, Q3, Q4) and years (FY).
Author: Marcelo S. Perlin
Maintainer: Marcelo S. Perlin <marceloperlin@gmail.com>
Diff between simfinR versions 0.1.0 dated 2019-12-04 and 0.2.0 dated 2020-02-13
DESCRIPTION | 12 ++++++------ MD5 | 4 +++- NEWS.md |only R/onAttach.R |only 4 files changed, 9 insertions(+), 7 deletions(-)
Title: R Interface to C API of GLPK
Description: R Interface to C API of GLPK, depends on GLPK Version >= 4.42.
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut],
Louis Luangkesorn [ctb]
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
Diff between glpkAPI versions 1.3.1 dated 2018-09-14 and 1.3.2 dated 2020-02-13
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------ build/vignette.rds |binary configure | 55 +++++++++++++++++++++++++------------------ configure.ac | 3 -- inst/NEWS.Rd | 7 +++++ inst/doc/glpk-gmpl-intro.pdf |binary inst/doc/glpkAPI.R | 1 inst/doc/glpkAPI.pdf |binary 9 files changed, 53 insertions(+), 37 deletions(-)
Title: R Interface to C API of COIN-or Clp
Description: R Interface to C API of COIN-OR Clp, depends on COIN-OR Clp Version >= 1.12.0.
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut],
C. Jonathan Fritzemeier [ctb]
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
Diff between clpAPI versions 1.2.11 dated 2019-06-14 and 1.2.13 dated 2020-02-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- build/vignette.rds |binary configure | 19 +++++++++---------- configure.ac | 3 +-- inst/NEWS.Rd | 7 +++++++ inst/doc/clpAPI.R | 1 - inst/doc/clpAPI.pdf |binary src/config.h | 4 ++-- 9 files changed, 31 insertions(+), 27 deletions(-)
Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download a large number of trade data from Yahoo Finance <https://finance.yahoo.com/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between BatchGetSymbols versions 2.5.4 dated 2019-10-12 and 2.5.5 dated 2020-02-13
DESCRIPTION | 12 +- MD5 | 18 ++-- NEWS.md | 5 + R/Utils.R | 13 ++- build/vignette.rds |binary inst/doc/BatchGetSymbols-vignette.R | 8 - inst/doc/BatchGetSymbols-vignette.html | 137 ++++++++++++++++----------------- man/BatchGetSymbols.Rd | 21 +++-- man/GetIbovStocks.Rd | 3 man/myGetSymbols.Rd | 16 +++ 10 files changed, 131 insertions(+), 102 deletions(-)
More information about BatchGetSymbols at CRAN
Permanent link
Title: (Robust) Mediation Analysis
Description: Perform mediation analysis via a (fast and robust) bootstrap test.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robmed versions 0.5.0 dated 2019-10-22 and 0.6.0 dated 2020-02-13
robmed-0.5.0/robmed/R/fortify.R |only robmed-0.5.0/robmed/man/fortify.test_mediation.Rd |only robmed-0.5.0/robmed/man/plot_mediation.Rd |only robmed-0.6.0/robmed/DESCRIPTION | 8 robmed-0.6.0/robmed/MD5 | 163 + robmed-0.6.0/robmed/NAMESPACE | 35 robmed-0.6.0/robmed/NEWS | 39 robmed-0.6.0/robmed/R/boot.R | 4 robmed-0.6.0/robmed/R/ci_plot.R |only robmed-0.6.0/robmed/R/coef.R | 4 robmed-0.6.0/robmed/R/confint.R | 42 robmed-0.6.0/robmed/R/control.R | 16 robmed-0.6.0/robmed/R/cov_Huber.R | 6 robmed-0.6.0/robmed/R/cov_ML.R | 2 robmed-0.6.0/robmed/R/density_plot.R |only robmed-0.6.0/robmed/R/ellipse_plot.R |only robmed-0.6.0/robmed/R/fit_mediation.R | 661 ++++++- robmed-0.6.0/robmed/R/formula.R |only robmed-0.6.0/robmed/R/p_value.R | 11 robmed-0.6.0/robmed/R/plot.R | 190 -- robmed-0.6.0/robmed/R/print.R | 17 robmed-0.6.0/robmed/R/retest.R | 4 robmed-0.6.0/robmed/R/rob_F_test.R | 2 robmed-0.6.0/robmed/R/robmed-deprecated.R |only robmed-0.6.0/robmed/R/setup_ci_plot.R |only robmed-0.6.0/robmed/R/setup_density_plot.R |only robmed-0.6.0/robmed/R/setup_ellipse_plot.R |only robmed-0.6.0/robmed/R/summary.R | 49 robmed-0.6.0/robmed/R/test_mediation.R | 880 +++++++--- robmed-0.6.0/robmed/R/utils.R |only robmed-0.6.0/robmed/R/weights.R | 2 robmed-0.6.0/robmed/build/partial.rdb |binary robmed-0.6.0/robmed/data/BSG2014.RData |binary robmed-0.6.0/robmed/demo/case1.R | 2 robmed-0.6.0/robmed/demo/case2.R | 67 robmed-0.6.0/robmed/demo/case3.R | 67 robmed-0.6.0/robmed/demo/descriptives.R | 2 robmed-0.6.0/robmed/inst/shiny-examples/simulation/server.R | 22 robmed-0.6.0/robmed/man/boot_samples.Rd | 4 robmed-0.6.0/robmed/man/ci_plot.Rd |only robmed-0.6.0/robmed/man/coef.test_mediation.Rd | 4 robmed-0.6.0/robmed/man/confint.test_mediation.Rd | 22 robmed-0.6.0/robmed/man/cov_Huber.Rd | 6 robmed-0.6.0/robmed/man/cov_ML.Rd | 2 robmed-0.6.0/robmed/man/cov_control.Rd | 4 robmed-0.6.0/robmed/man/density_plot.Rd |only robmed-0.6.0/robmed/man/ellipse_plot.Rd |only robmed-0.6.0/robmed/man/fit_mediation.Rd | 146 + robmed-0.6.0/robmed/man/m.Rd |only robmed-0.6.0/robmed/man/p_value.Rd | 11 robmed-0.6.0/robmed/man/plot-methods.Rd |only robmed-0.6.0/robmed/man/reg_control.Rd | 12 robmed-0.6.0/robmed/man/retest.Rd | 4 robmed-0.6.0/robmed/man/robmed-deprecated.Rd |only robmed-0.6.0/robmed/man/setup_ci_plot.Rd |only robmed-0.6.0/robmed/man/setup_density_plot.Rd |only robmed-0.6.0/robmed/man/setup_ellipse_plot.Rd |only robmed-0.6.0/robmed/man/summary.test_mediation.Rd | 16 robmed-0.6.0/robmed/man/test_mediation.Rd | 158 + robmed-0.6.0/robmed/man/weights.cov_Huber.Rd | 2 robmed-0.6.0/robmed/tests/testthat/test-median_bootstrap-regression-multiple-covariates.R | 225 +- robmed-0.6.0/robmed/tests/testthat/test-median_bootstrap-regression-multiple-no_covariates.R | 223 +- robmed-0.6.0/robmed/tests/testthat/test-median_bootstrap-regression-simple-covariates.R | 215 +- robmed-0.6.0/robmed/tests/testthat/test-median_bootstrap-regression-simple-no_covariates.R | 217 +- robmed-0.6.0/robmed/tests/testthat/test-median_fit-regression-multiple-covariates.R | 36 robmed-0.6.0/robmed/tests/testthat/test-median_fit-regression-multiple-no_covariates.R | 35 robmed-0.6.0/robmed/tests/testthat/test-median_fit-regression-simple-covariates.R | 35 robmed-0.6.0/robmed/tests/testthat/test-median_fit-regression-simple-no_covariates.R | 35 robmed-0.6.0/robmed/tests/testthat/test-median_sobel-regression.R | 131 + robmed-0.6.0/robmed/tests/testthat/test-robust_bootstrap-covariance.R | 226 +- robmed-0.6.0/robmed/tests/testthat/test-robust_bootstrap-regression-multiple-covariates.R | 238 +- robmed-0.6.0/robmed/tests/testthat/test-robust_bootstrap-regression-multiple-no_covariates.R | 237 +- robmed-0.6.0/robmed/tests/testthat/test-robust_bootstrap-regression-simple-covariates.R | 228 +- robmed-0.6.0/robmed/tests/testthat/test-robust_bootstrap-regression-simple-no_covariates.R | 230 +- robmed-0.6.0/robmed/tests/testthat/test-robust_fit-covariance.R | 102 + robmed-0.6.0/robmed/tests/testthat/test-robust_fit-regression-multiple-covariates.R | 97 + robmed-0.6.0/robmed/tests/testthat/test-robust_fit-regression-multiple-no_covariates.R | 114 + robmed-0.6.0/robmed/tests/testthat/test-robust_fit-regression-simple-covariates.R | 97 + robmed-0.6.0/robmed/tests/testthat/test-robust_fit-regression-simple-no_covariates.R | 113 + robmed-0.6.0/robmed/tests/testthat/test-robust_sobel-covariance.R | 126 + robmed-0.6.0/robmed/tests/testthat/test-robust_sobel-regression.R | 140 + robmed-0.6.0/robmed/tests/testthat/test-standard_bootstrap-covariance.R | 218 +- robmed-0.6.0/robmed/tests/testthat/test-standard_bootstrap-regression-multiple-covariates.R | 232 +- robmed-0.6.0/robmed/tests/testthat/test-standard_bootstrap-regression-multiple-no_covariates.R | 230 +- robmed-0.6.0/robmed/tests/testthat/test-standard_bootstrap-regression-simple-covariates.R | 224 +- robmed-0.6.0/robmed/tests/testthat/test-standard_bootstrap-regression-simple-no_covariates.R | 226 +- robmed-0.6.0/robmed/tests/testthat/test-standard_fit-covariance.R | 102 + robmed-0.6.0/robmed/tests/testthat/test-standard_fit-regression-multiple-covariates.R | 87 robmed-0.6.0/robmed/tests/testthat/test-standard_fit-regression-multiple-no_covariates.R | 102 + robmed-0.6.0/robmed/tests/testthat/test-standard_fit-regression-simple-covariates.R | 86 robmed-0.6.0/robmed/tests/testthat/test-standard_fit-regression-simple-no_covariates.R | 102 + robmed-0.6.0/robmed/tests/testthat/test-standard_sobel-covariance.R | 126 + robmed-0.6.0/robmed/tests/testthat/test-standard_sobel-regression.R | 126 + 93 files changed, 5533 insertions(+), 2114 deletions(-)
Title: Doubly Truncated Data Analysis, Cumulative Incidence Functions
Description: Nonparametric estimator of the cumulative incidences of competing risks under double truncation. The estimator generalizes the Efron-Petrosian NPMLE (Non-Parametric Maximun Likelihood Estimator) to the competing risks setting. Efron, B. and Petrosian, V. (1999) <doi:10.2307/2669997>.
Author: Jacobo de Uña Álvarez [aut],
José Carlos Soage González [cre]
Maintainer: José Carlos Soage González <jsoage@uvigo.es>
Diff between DTDA.cif versions 1.0.1 dated 2019-10-18 and 1.0.2 dated 2020-02-13
DESCRIPTION | 6 ++-- MD5 | 14 ++++----- R/DTDAcif-package.R | 2 - R/DTDAcif.R | 71 +++++++++++++++++++++++++++++++----------------- R/plot.DTDAcif.R | 70 +++++++++++++++++++++++++++++++++++------------ R/shen.R | 4 ++ man/DTDA.cif-package.Rd | 2 - man/plot.DTDAcif.Rd | 4 ++ 8 files changed, 118 insertions(+), 55 deletions(-)
Title: Processes Calcium Imaging Data
Description: Identifies the locations of neurons, and estimates their calcium concentrations over time using the SCALPEL method proposed in Petersen, Ashley; Simon, Noah; Witten, Daniela. SCALPEL: Extracting neurons from calcium imaging data. Ann. Appl. Stat. 12 (2018), no. 4, 2430--2456. doi:10.1214/18-AOAS1159. <https://projecteuclid.org/euclid.aoas/1542078051>.
Author: Ashley Petersen
Maintainer: Ashley Petersen <ashleyjpete@gmail.com>
Diff between scalpel versions 1.0.1 dated 2018-09-28 and 1.0.2 dated 2020-02-13
DESCRIPTION | 15 +++++++------ MD5 | 48 ++++++++++++++++++++++---------------------- NAMESPACE | 1 R/SCALPEL_step1.R | 10 +++++++-- R/scalpel-package.R | 6 +++-- man/getScalpel.Rd | 15 +++++++++++-- man/getScalpelStep3.Rd | 15 +++++++++++-- man/plotBrightest.Rd | 14 ++++++++++-- man/plotCandidateFrame.Rd | 14 ++++++++++-- man/plotCluster.Rd | 8 +++++-- man/plotFrame.Rd | 15 ++++++++++--- man/plotResults.Rd | 15 +++++++++++-- man/plotResultsAllLambda.Rd | 14 ++++++++++-- man/plotSpatial.Rd | 19 +++++++++++++---- man/plotTemporal.Rd | 11 ++++++++-- man/plotThresholdedFrame.Rd | 12 +++++++++-- man/plotVideoVariance.Rd | 13 +++++++++-- man/reviewNeurons.Rd | 8 +++++-- man/scalpel-package.Rd | 5 ++-- man/scalpel.Rd | 25 ++++++++++++++++++---- man/scalpelStep0.Rd | 9 ++++++-- man/scalpelStep1.Rd | 10 +++++++-- man/scalpelStep2.Rd | 3 -- man/scalpelStep3.Rd | 12 ++++++++--- src |only 25 files changed, 230 insertions(+), 87 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on 'Windows',
'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gábor Csárdi [aut, cre],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between ps versions 1.3.1 dated 2020-02-12 and 1.3.2 dated 2020-02-13
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/dummy.c | 4 ++-- 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Longitudinal Concordance Correlation
Description: Estimates the longitudinal concordance correlation to access the longitudinal agreement profile. The estimation approach implemented is variance components approach based on polynomial mixed effects regression model, as proposed by Oliveira, Hinde and Zocchi (2018) <doi:10.1007/s13253-018-0321-1>. In addition, non-parametric confidence intervals were implemented using percentile method or normal-approximation based on Fisher Z-transformation.
Author: Thiago de Paula Oliveira [aut, cre],
Rafael de Andrade Moral [aut],
Silvio Sandoval Zocchi [ctb],
Clarice Garcia Borges Demetrio [ctb],
John Hinde [aut]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@usp.br>
Diff between lcc versions 1.0.3 dated 2019-11-25 and 1.0.4 dated 2020-02-13
lcc-1.0.3/lcc/man/predict.lcc.Rd |only lcc-1.0.4/lcc/DESCRIPTION | 10 ++-- lcc-1.0.4/lcc/MD5 | 48 ++++++++++---------- lcc-1.0.4/lcc/NAMESPACE | 1 lcc-1.0.4/lcc/R/lcc.R | 22 ++++----- lcc-1.0.4/lcc/R/methods.R | 77 ++++++--------------------------- lcc-1.0.4/lcc/R/plotmethod_lcc.R | 4 - lcc-1.0.4/lcc/README.md |only lcc-1.0.4/lcc/man/AIC.lcc.Rd | 2 lcc-1.0.4/lcc/man/anova.lcc.Rd | 2 lcc-1.0.4/lcc/man/coef.lcc.Rd | 2 lcc-1.0.4/lcc/man/fitted.lcc.Rd | 2 lcc-1.0.4/lcc/man/getVarCov.lcc.Rd | 2 lcc-1.0.4/lcc/man/hue.Rd | 2 lcc-1.0.4/lcc/man/lcc.Rd | 12 ++--- lcc-1.0.4/lcc/man/lccPlot.Rd | 4 - lcc-1.0.4/lcc/man/logLik.lcc.Rd | 2 lcc-1.0.4/lcc/man/plot.lcc.Rd | 2 lcc-1.0.4/lcc/man/plotControl.Rd | 13 ++++- lcc-1.0.4/lcc/man/print.anova.lcc.Rd | 2 lcc-1.0.4/lcc/man/print.lcc.Rd | 2 lcc-1.0.4/lcc/man/print.summary.lcc.Rd | 2 lcc-1.0.4/lcc/man/ranef.lcc.Rd | 2 lcc-1.0.4/lcc/man/residuals.lcc.Rd | 2 lcc-1.0.4/lcc/man/summary.lcc.Rd | 2 lcc-1.0.4/lcc/man/vcov.lcc.Rd | 2 26 files changed, 91 insertions(+), 130 deletions(-)
Title: Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-13 dated 2018-08-31 and 1.7-15 dated 2020-02-13
ade4-1.7-13/ade4/R/EH.R |only ade4-1.7-13/ade4/R/dist.genet.R |only ade4-1.7-13/ade4/R/fuzzygenet.R |only ade4-1.7-13/ade4/R/genet.R |only ade4-1.7-13/ade4/R/optimEH.R |only ade4-1.7-13/ade4/R/orisaved.R |only ade4-1.7-13/ade4/R/randEH.R |only ade4-1.7-13/ade4/man/EH.Rd |only ade4-1.7-13/ade4/man/dist.genet.Rd |only ade4-1.7-13/ade4/man/fuzzygenet.Rd |only ade4-1.7-13/ade4/man/genet.Rd |only ade4-1.7-13/ade4/man/optimEH.Rd |only ade4-1.7-13/ade4/man/orisaved.Rd |only ade4-1.7-13/ade4/man/randEH.Rd |only ade4-1.7-15/ade4/ChangeLog | 83 +++ ade4-1.7-15/ade4/DESCRIPTION | 15 ade4-1.7-15/ade4/MD5 | 64 +- ade4-1.7-15/ade4/NAMESPACE | 17 ade4-1.7-15/ade4/R/ade4-deprecated.R | 767 ++++++++++++++++++++++++++++++++ ade4-1.7-15/ade4/R/dist.binary.R | 6 ade4-1.7-15/ade4/R/dist.ktab.R | 24 - ade4-1.7-15/ade4/R/krandtest.R | 47 + ade4-1.7-15/ade4/R/multispati.R | 302 ++++++------ ade4-1.7-15/ade4/R/randtest.dpcoa.R | 4 ade4-1.7-15/ade4/R/suprow.pta.R |only ade4-1.7-15/ade4/man/ade4-deprecated.Rd | 9 ade4-1.7-15/ade4/man/apis108.Rd | 5 ade4-1.7-15/ade4/man/bacteria.Rd | 2 ade4-1.7-15/ade4/man/cailliez.Rd | 2 ade4-1.7-15/ade4/man/casitas.Rd | 7 ade4-1.7-15/ade4/man/chevaine.Rd | 37 - ade4-1.7-15/ade4/man/hdpg.Rd | 17 ade4-1.7-15/ade4/man/kdist.Rd | 2 ade4-1.7-15/ade4/man/kdisteuclid.Rd | 3 ade4-1.7-15/ade4/man/krandtest.Rd | 59 +- ade4-1.7-15/ade4/man/multispati.Rd | 2 ade4-1.7-15/ade4/man/oribatid.Rd | 4 ade4-1.7-15/ade4/man/randtest.Rd | 58 +- ade4-1.7-15/ade4/man/randtest.dpcoa.Rd | 4 ade4-1.7-15/ade4/man/s.kde2d.Rd | 11 ade4-1.7-15/ade4/man/suprow.pta.Rd |only 41 files changed, 1211 insertions(+), 340 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 0.2.6 dated 2019-06-14 and 0.2.7 dated 2020-02-13
DESCRIPTION | 34 ++- MD5 | 82 +++++---- NAMESPACE | 26 ++- NEWS.md | 18 ++ R/Ensemble.SDM.R | 13 + R/SDM.R | 1 R/Stacked.SDM.R | 10 - R/accuracy.R |only R/checkargs.R | 10 - R/ensemble.R | 67 ++++--- R/ensemble_modelling.R | 17 - R/evaluate.R | 38 ++-- R/load_model.R | 26 +-- R/mapDiversity.R | 118 ++++++++----- R/modelling.R | 3 R/optim.thresh.R |only R/plot.model.R | 213 +++++++++++++----------- R/project.R | 114 ++++++++++++- R/save.model.R | 40 ++-- R/stack_modelling.R | 94 +++++----- R/stacking.R | 118 ++++++------- R/update.stack.R | 33 +-- README.md | 4 inst/doc/GUI.html | 4 inst/doc/SSDM.R | 5 inst/doc/SSDM.Rmd | 38 +++- inst/doc/SSDM.html | 107 ++++++------ inst/shiny/gui/server.R | 319 ++++++++++++++++++++++++------------- inst/shiny/gui/ui.R | 51 ++++- man/Ensemble.SDM-class.Rd | 4 man/Stacked.SDM-class.Rd | 2 man/ensemble.Rd | 5 man/ensemble_modelling.Rd | 3 man/evaluate.Rd | 5 man/load.model.Rd | 4 man/modelling.Rd | 3 man/project.Rd |only man/save.model.Rd | 10 - man/stack_modelling.Rd | 8 man/stacking.Rd | 6 man/update-Stacked.SDM-method.Rd | 3 tests/testthat/test_project_ESDM.R |only tests/testthat/test_project_SDM.R |only tests/testthat/test_project_SSDM.R |only vignettes/SSDM.Rmd | 38 +++- 45 files changed, 1029 insertions(+), 665 deletions(-)
Title: Functions for Spatial Point Pattern Analysis
Description: Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on 'spatstat'), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones" and in the papers by De la Cruz et al. (2008) <doi:10.1111/j.0906-7590.2008.05299.x> and Olano et al. (2009) <doi:10.1051/forest:2008074>.
Author: Marcelino de la Cruz Rot, with contributions of Philip M. Dixon and Jose M. Blanco-Moreno
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@urjc.es>
Diff between ecespa versions 1.1-10 dated 2018-02-06 and 1.1-11 dated 2020-02-13
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- man/00ecespa.Rd | 43 +++++++++++++++++++++++++------------------ man/Helianthemum.Rd | 10 +++------- man/K012.Rd | 9 +++++---- man/K1K2.rd | 10 +++------- man/Kci.Rd | 2 +- man/Kinhom.log.rd | 6 +++--- man/Kmulti.ls.Rd | 7 +++++-- man/LF.gof.Rd | 2 +- man/dixon2002.Rd | 11 +++++++---- man/getis.rd | 3 ++- man/gypsophylous.rd | 6 +++--- man/ipc.estK.Rd | 4 +++- man/rIPCP.Rd | 5 ++++- man/seedlings.Rd | 8 ++++---- man/swamp.Rd | 8 ++++---- man/syrjala.Rd | 8 ++++---- src/init.c | 2 +- src/syrjalala.f | 28 +++++++++++++++++----------- src/wrp.c | 3 +-- 21 files changed, 120 insertions(+), 103 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-03 0.1.0
Title: Integrating Phylogenies and Ecology
Description: Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.
Author: Steven W. Kembel <steve.kembel@gmail.com>, David D. Ackerly <dackerly@berkeley.edu>, Simon P. Blomberg <s.blomberg1@uq.edu.au>, Will K. Cornwell <cornwell@zoology.ubc.ca>, Peter D. Cowan <pdc@berkeley.edu>, Matthew R. Helmus <mrhelmus@wisc.edu>, Helene Morlon <morlon.helene@gmail.com>, Campbell O. Webb <cwebb@oeb.harvard.edu>
Maintainer: Steven W. Kembel <steve.kembel@gmail.com>
Diff between picante versions 1.8 dated 2019-03-21 and 1.8.1 dated 2020-02-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/data.checking.R | 6 +++--- README.md | 6 ++---- build/vignette.rds |binary inst/doc/picante-intro.pdf |binary man/picante-package.Rd | 4 ++-- man/utility.Rd | 1 - 8 files changed, 18 insertions(+), 21 deletions(-)
Title: Convert Data from and to 'GeoJSON' or 'TopoJSON'
Description: Convert data to 'GeoJSON' or 'TopoJSON' from various R classes,
including vectors, lists, data frames, shape files, and spatial classes.
'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos',
but rather aims to be a high level client to simplify conversions of data
from and to 'GeoJSON' and 'TopoJSON'.
Author: Scott Chamberlain [aut, cre],
Andy Teucher [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojsonio versions 0.8.0 dated 2019-10-29 and 0.9.0 dated 2020-02-13
geojsonio-0.8.0/geojsonio/inst/img |only geojsonio-0.9.0/geojsonio/DESCRIPTION | 14 - geojsonio-0.9.0/geojsonio/LICENSE | 2 geojsonio-0.9.0/geojsonio/MD5 | 115 ++++---- geojsonio-0.9.0/geojsonio/NAMESPACE | 13 - geojsonio-0.9.0/geojsonio/NEWS.md | 14 + geojsonio-0.9.0/geojsonio/R/as_spatial_methods.R | 19 - geojsonio-0.9.0/geojsonio/R/crs_convert.R | 2 geojsonio-0.9.0/geojsonio/R/file_to_geojson.r | 71 ++--- geojsonio-0.9.0/geojsonio/R/geojson_json.R | 7 geojsonio-0.9.0/geojsonio/R/geojson_list.R | 5 geojsonio-0.9.0/geojsonio/R/geojson_sf.R | 14 - geojsonio-0.9.0/geojsonio/R/geojson_sp.R | 11 geojsonio-0.9.0/geojsonio/R/geojson_write.r | 2 geojsonio-0.9.0/geojsonio/R/geojsonio-package.r | 5 geojsonio-0.9.0/geojsonio/R/mapgist.R | 6 geojsonio-0.9.0/geojsonio/R/postgis.R | 5 geojsonio-0.9.0/geojsonio/R/topojson_json.R | 12 geojsonio-0.9.0/geojsonio/R/topojson_list.R | 10 geojsonio-0.9.0/geojsonio/R/zzz.r | 46 ++- geojsonio-0.9.0/geojsonio/README.md | 20 - geojsonio-0.9.0/geojsonio/build/vignette.rds |binary geojsonio-0.9.0/geojsonio/inst/doc/geojson_spec.R | 2 geojsonio-0.9.0/geojsonio/inst/doc/geojson_spec.html | 15 - geojsonio-0.9.0/geojsonio/inst/doc/geojsonio.R | 2 geojsonio-0.9.0/geojsonio/inst/doc/geojsonio.html | 130 ++++------ geojsonio-0.9.0/geojsonio/inst/doc/maps.R | 2 geojsonio-0.9.0/geojsonio/inst/doc/maps.html | 120 ++++----- geojsonio-0.9.0/geojsonio/man/figures |only geojsonio-0.9.0/geojsonio/man/file_to_geojson.Rd | 37 +- geojsonio-0.9.0/geojsonio/man/geojson_json.Rd | 25 + geojsonio-0.9.0/geojsonio/man/geojson_list.Rd | 24 + geojsonio-0.9.0/geojsonio/man/geojson_read.Rd | 10 geojsonio-0.9.0/geojsonio/man/geojson_sf.Rd | 10 geojsonio-0.9.0/geojsonio/man/geojson_sp.Rd | 10 geojsonio-0.9.0/geojsonio/man/geojson_style.Rd | 26 +- geojsonio-0.9.0/geojsonio/man/geojson_write.Rd | 18 + geojsonio-0.9.0/geojsonio/man/geojsonio.Rd | 3 geojsonio-0.9.0/geojsonio/man/map_gist.Rd | 22 + geojsonio-0.9.0/geojsonio/man/map_leaf.Rd | 3 geojsonio-0.9.0/geojsonio/man/postgis.Rd | 5 geojsonio-0.9.0/geojsonio/man/projections.Rd | 25 + geojsonio-0.9.0/geojsonio/man/topojson_json.Rd | 33 +- geojsonio-0.9.0/geojsonio/man/topojson_list.Rd | 28 +- geojsonio-0.9.0/geojsonio/man/topojson_write.Rd | 21 + geojsonio-0.9.0/geojsonio/tests/testthat/test-as.json.R | 28 +- geojsonio-0.9.0/geojsonio/tests/testthat/test-crs_convert.R | 115 ++++---- geojsonio-0.9.0/geojsonio/tests/testthat/test-file_to_geojson.R | 4 geojsonio-0.9.0/geojsonio/tests/testthat/test-geojson_list.R | 62 ++-- geojsonio-0.9.0/geojsonio/tests/testthat/test-geojson_read.R | 8 geojsonio-0.9.0/geojsonio/tests/testthat/test-geojson_sf.R | 6 geojsonio-0.9.0/geojsonio/tests/testthat/test-geojson_sp.R | 6 geojsonio-0.9.0/geojsonio/tests/testthat/test-geojson_write.R | 54 ++-- geojsonio-0.9.0/geojsonio/tests/testthat/test-map_gist.R | 2 geojsonio-0.9.0/geojsonio/tests/testthat/test-topojson_json.R | 9 geojsonio-0.9.0/geojsonio/tests/testthat/test-topojson_list.R |only geojsonio-0.9.0/geojsonio/tests/testthat/test-topojson_write.R | 50 ++- geojsonio-0.9.0/geojsonio/tests/testthat/us_citites_two_row.rds |binary 58 files changed, 756 insertions(+), 552 deletions(-)
Title: Dynamic Models in Epidemiology
Description: Mathematical models of infectious diseases in humans and animals.
Both, deterministic and stochastic models can be simulated and plotted.
Author: Oswaldo Santos Baquero [aut, cre],
Fernando Silveira Marques [aut]
Maintainer: Oswaldo Santos Baquero <baquero@usp.br>
Diff between EpiDynamics versions 0.3.0 dated 2015-12-03 and 0.3.1 dated 2020-02-13
DESCRIPTION | 16 ++--- MD5 | 118 +++++++++++++++++++------------------- NEWS | 7 ++ R/EpiDynamics-package.R | 8 +- R/MultiStrainPartialImmunity.R | 1 R/SEIR.R | 1 R/SEIR4AgeClasses.R | 1 R/SEIRnStages.R | 1 R/SIR.R | 1 R/SIR2AgeClasses.R | 1 R/SIR2Stages.R | 1 R/SIR2TypesImports.R | 1 R/SIRAdditiveNoise.R | 1 R/SIRBirthDeath.R | 1 R/SIRCarrierState.R | 1 R/SIRDemogStoch.R | 1 R/SIRInducedMortality.R | 3 R/SIRInducedMortality2.R | 3 R/SIRPartialImmunity.R | 1 R/SIRScaledAdditiveNoise.R | 1 R/SIRSinusoidalBirth.R | 3 R/SIRSinusoidalForcing.R | 1 R/SIRTauLeap.R | 1 R/SIRTermTimeForcing.R | 9 +- R/SIRVector.R | 1 R/SIS.R | 1 R/SIS2RiskGroups.R | 1 R/SISDemogStoch.R | 1 R/SISPairwiseApprox.R | 1 R/SISinusoidalTransmBrith.R | 1 R/SISnRiskGroups.R | 1 man/EpiDynamics-package.Rd | 9 +- man/MultiStrainPartialImmunity.Rd | 2 man/PlotMods.Rd | 15 +++- man/SEIR.Rd | 2 man/SEIR4AgeClasses.Rd | 2 man/SEIRnStages.Rd | 2 man/SIR.Rd | 2 man/SIR2Stages.Rd | 2 man/SIR2TypesImports.Rd | 2 man/SIRAdditiveNoise.Rd | 2 man/SIRBirthDeath.Rd | 2 man/SIRCarrierState.Rd | 2 man/SIRDemogStoch.Rd | 2 man/SIRInducedMortality.Rd | 4 - man/SIRInducedMortality2.Rd | 4 - man/SIRPartialImmunity.Rd | 2 man/SIRScaledAdditiveNoise.Rd | 2 man/SIRSinusoidalBirth.Rd | 4 - man/SIRSinusoidalForcing.Rd | 2 man/SIRTauLeap.Rd | 2 man/SIRTermTimeForcing.Rd | 12 ++- man/SIRVector.Rd | 2 man/SIS.Rd | 2 man/SIS2RiskGroups.Rd | 2 man/SISDemogStoch.Rd | 2 man/SISPairwiseApprox.Rd | 2 man/SISinusoidalTransmBrith.Rd | 2 man/SISnRiskGroups.Rd | 2 man/sir2AgeClasses.Rd | 2 60 files changed, 111 insertions(+), 173 deletions(-)
Title: A Deep Learning for Statistical Classification and Regression
Analysis with Random Effects
Description: Statistical classification and regression have been popular among various fields and stayed in the limelight of scientists of those fields. Examples of the fields include clinical trials where the statistical classification of patients is indispensable to predict the clinical courses of diseases. Considering the negative impact of diseases on performing daily tasks, correctly classifying patients based on the clinical information is vital in that we need to identify patients of the high-risk group to develop a severe state and arrange medical treatment for them at an opportune moment. Deep learning - a part of artificial intelligence - has gained much attention, and research on it burgeons during past decades: see, e.g, Kazemi and Mirroshandel (2018) <DOI:10.1016/j.artmed.2017.12.001>. It is a veritable technique which was originally designed for the classification, and hence, the Buddle package can provide sublime solutions to various challenging classification and regression problems encountered in the clinical trials. The Buddle package is based on the back-propagation algorithm - together with various powerful techniques such as batch normalization and dropout - which performs a multi-layer feed-forward neural network: see Krizhevsky et. al (2017) <DOI:10.1145/3065386>, Schmidhuber (2015) <DOI:10.1016/j.neunet.2014.09.003> and LeCun et al. (1998) <DOI:10.1109/5.726791> for more details. This package contains two main functions: TrainBuddle() and FetchBuddle(). TrainBuddle() builds a feed-forward neural network model and trains the model. FetchBuddle() recalls the trained model which is the output of TrainBuddle(), classifies or regresses given data, and make a final prediction for the data.
Author: Jiwoong Kim <jwboys26 at gmail.com>
Maintainer: Jiwoong Kim <jwboys26@gmail.com>
Diff between Buddle versions 2.0 dated 2020-02-06 and 2.0.1 dated 2020-02-13
Buddle-2.0.1/Buddle/DESCRIPTION | 10 - Buddle-2.0.1/Buddle/MD5 | 82 +++++------- Buddle-2.0.1/Buddle/R/BuddleMain.R | 118 +++++++++++++++-- Buddle-2.0.1/Buddle/R/Img_data.R | 6 Buddle-2.0.1/Buddle/data/mnist_data.rda |binary Buddle-2.0.1/Buddle/man/CheckNonNumeric.Rd | 1 Buddle-2.0.1/Buddle/man/FetchBuddle.Rd | 17 +- Buddle-2.0.1/Buddle/man/GetPrecision.Rd | 4 Buddle-2.0.1/Buddle/man/MakeConfusionMatrix.Rd | 7 + Buddle-2.0.1/Buddle/man/Split2TrainTest.Rd | 19 ++ Buddle-2.0.1/Buddle/man/TrainBuddle.Rd | 34 ++++- Buddle-2.0.1/Buddle/man/mnist_data.Rd | 6 Buddle-2.0.1/Buddle/src/ActName.h | 4 Buddle-2.0.1/Buddle/src/Affine.h | 88 ++++++------ Buddle-2.0.1/Buddle/src/ArcSinH.h | 25 ++- Buddle-2.0.1/Buddle/src/ArcTan.h | 20 +- Buddle-2.0.1/Buddle/src/Batchnorm.h | 18 +- Buddle-2.0.1/Buddle/src/BentIdentity.h | 24 +-- Buddle-2.0.1/Buddle/src/Buddle.h | 68 +++++----- Buddle-2.0.1/Buddle/src/Common.h | 24 +-- Buddle-2.0.1/Buddle/src/Dropout.h | 22 +-- Buddle-2.0.1/Buddle/src/ElliotSig.h | 20 +- Buddle-2.0.1/Buddle/src/FInv.h | 20 +- Buddle-2.0.1/Buddle/src/Gaussian.h | 27 ++- Buddle-2.0.1/Buddle/src/Identity.h | 20 +- Buddle-2.0.1/Buddle/src/L2loss.h | 24 +-- Buddle-2.0.1/Buddle/src/Layer.h | 170 ++++++++++++------------- Buddle-2.0.1/Buddle/src/LeakyRelu.h | 18 +- Buddle-2.0.1/Buddle/src/Link.h | 36 ++--- Buddle-2.0.1/Buddle/src/Momentum.h | 8 - Buddle-2.0.1/Buddle/src/Optimization.h | 76 ++++++----- Buddle-2.0.1/Buddle/src/Relu.h | 20 +- Buddle-2.0.1/Buddle/src/Sigmoid.h | 22 +-- Buddle-2.0.1/Buddle/src/Sinc.h | 20 +- Buddle-2.0.1/Buddle/src/Sinusoid.h | 20 +- Buddle-2.0.1/Buddle/src/SoftPlus.h | 20 +- Buddle-2.0.1/Buddle/src/SoftmaxLoss.h | 24 +-- Buddle-2.0.1/Buddle/src/TanH.h | 20 +- Buddle-2.0.1/Buddle/src/cppMain.cpp | 6 Buddle-2.0/Buddle/data/datalist |only Buddle-2.0/Buddle/src/AdaGrad.h |only Buddle-2.0/Buddle/src/SGD.h |only Buddle-2.0/Buddle/src/SinH.h |only Buddle-2.0/Buddle/src/gBuddle.h |only Buddle-2.0/Buddle/src/gLayer.h |only 45 files changed, 662 insertions(+), 506 deletions(-)
Title: Birnbaum-Saunders Model
Description: It provides the density, distribution function, quantile function, random number generator, reliability function, failure rate, likelihood function, moments and EM algorithm for Maximum Likelihood estimators, also empirical quantile and generated envelope for a given sample, all this for the three parameter Birnbaum-Saunders model based on Skew-Normal Distribution. Also, it provides the random number generator for the mixture of Birnbaum-Saunders model based on Skew-Normal distribution. Additionally, we incorporate the EM algorithm based on the assumption that the error term follows a finite mixture of Sinh-normal distributions.
Author: Luis Benites Sanchez[cre, aut] <lbenitess@pucp.edu.pe>, Rocio Paola Maehara[cre, aut] <rp.maeharaa@up.edu.pe> and Paulo Jos<c3><a9> Alejandro Aybar Flores[ctb] <a.aybarf@alum.up.edu.pe>
Maintainer: Rocio Paola Maehara <rp.maeharaa@up.edu.pe>
Diff between bssn versions 0.7 dated 2016-03-17 and 1.0 dated 2020-02-13
bssn-0.7/bssn/R/functions.R |only bssn-0.7/bssn/data/ozone.txt.gz |only bssn-1.0/bssn/DESCRIPTION | 21 -- bssn-1.0/bssn/MD5 | 27 +- bssn-1.0/bssn/NAMESPACE | 32 +-- bssn-1.0/bssn/R/EMbssn.R | 101 +++++----- bssn-1.0/bssn/R/FMshnReg.R |only bssn-1.0/bssn/R/algEM.mix.log.bs.R |only bssn-1.0/bssn/R/algEMbssn.R | 236 +++++++++++------------ bssn-1.0/bssn/R/functions.mix.logbs.R |only bssn-1.0/bssn/R/functionsbs.R |only bssn-1.0/bssn/R/functionsbssn.R |only bssn-1.0/bssn/data/enzyme.txt |only bssn-1.0/bssn/data/ozone.txt |only bssn-1.0/bssn/man/EMbssn.Rd | 256 ++++++++++++------------- bssn-1.0/bssn/man/FMshnReg.Rd |only bssn-1.0/bssn/man/bssn-package.Rd | 10 - bssn-1.0/bssn/man/bssn.Rd | 338 +++++++++++++++++----------------- bssn-1.0/bssn/man/enzyme.Rd |only bssn-1.0/bssn/man/momentsbssn.Rd | 128 ++++++------ 20 files changed, 580 insertions(+), 569 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-18 0.2.5
2016-09-20 0.2.4
2016-05-30 0.2.3
2016-05-02 0.2.2
2016-04-05 0.2.1
2016-02-21 0.1.3
2015-12-31 0.1.2
2015-12-29 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-10 0.16.0.1
Title: Pipe-Friendly Framework for Basic Statistical Tests
Description: Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy,
for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses.
The output of each test is automatically transformed into a tidy data frame to facilitate visualization.
Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.
Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs
(repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs.
It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and
'Cramer V' for the association between categorical variables.
The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between rstatix versions 0.3.1 dated 2019-12-16 and 0.4.0 dated 2020-02-13
DESCRIPTION | 6 +- MD5 | 18 +++---- NEWS.md | 15 ++++++ R/cohens_d.R | 115 +++++++++++++++++++++++++++++------------------- R/cor_plot.R | 1 R/factorial_design.R | 1 R/tukey_hsd.R | 29 +++++++++++- man/cohens_d.Rd | 50 ++++++++++++-------- man/cor_plot.Rd | 2 man/factorial_design.Rd | 2 10 files changed, 155 insertions(+), 84 deletions(-)
Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.3. All
models return 'coda' mcmc objects that can then be summarized
using the 'coda' package. Some useful
utility functions such as density functions,
pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization are provided.
Author: Andrew D. Martin [aut], Kevin M. Quinn [aut], Jong Hee Park [aut,cre], Ghislain Vieilledent [ctb], Michael Malecki[ctb], Matthew Blackwell [ctb], Keith Poole [ctb], Craig Reed [ctb], Ben Goodrich [ctb], Ross Ihaka [cph], The R Development Core Team [cph], The R Foundation [cph], Pierre L'Ecuyer [cph], Makoto Matsumoto [cph], Takuji Nishimura [cph]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between MCMCpack versions 1.4-5 dated 2019-12-01 and 1.4-6 dated 2020-02-13
MCMCpack-1.4-5/MCMCpack/inst/HISTORY |only MCMCpack-1.4-6/MCMCpack/DESCRIPTION | 9 +++++---- MCMCpack-1.4-6/MCMCpack/MD5 | 8 ++++---- MCMCpack-1.4-6/MCMCpack/R/testpanelSubjectBreak.R | 2 +- MCMCpack-1.4-6/MCMCpack/inst/HISTORY.txt |only MCMCpack-1.4-6/MCMCpack/man/testpanelSubjectBreak.Rd | 2 +- 6 files changed, 11 insertions(+), 10 deletions(-)
Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data
visualization in R. However the default generated plots requires some formatting
before we can send them for publication. Furthermore, to customize a 'ggplot',
the syntax is opaque and this raises the level of difficulty for researchers
with no advanced R programming skills. 'ggpubr' provides some easy-to-use
functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggpubr versions 0.2.4 dated 2019-11-14 and 0.2.5 dated 2020-02-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 9 +++++++++ R/compare_means.R | 2 +- R/ggparagraph.R | 1 - R/stat_cor.R | 45 +++++++++++++++++++++++++++++---------------- R/stat_pvalue_manual.R | 2 -- man/ggparagraph.Rd | 2 -- man/stat_cor.Rd | 17 +++++++++++++---- 9 files changed, 64 insertions(+), 38 deletions(-)
Title: Ecological Inference and Higher-Dimension Data Management
Description: Provides methods for analyzing R by C ecological contingency
tables using the extreme case analysis, ecological regression,
and Multinomial-Dirichlet ecological inference models. Also
provides tools for manipulating higher-dimension data objects.
Author: Olivia Lau <olivia.lau@post.harvard.edu>, Ryan T. Moore
<rtm@american.edu>, Michael Kellermann <mrkellermann@gmail.com>
Maintainer: Michael Kellermann <mrkellermann@gmail.com>
Diff between eiPack versions 0.1-9 dated 2019-03-13 and 0.2-1 dated 2020-02-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- man/senc.Rd | 3 ++- src/eiutil.c | 3 ++- src/rbycei.c | 5 +---- src/rbycei2.c | 5 +---- src/rbyceicov2.c | 5 +---- src/rbyceicov4.c | 5 +---- 8 files changed, 19 insertions(+), 29 deletions(-)
Title: Comparison of Trees using a Tree Defining Polynomial
Description: Provides functionality for creation and comparison of polynomials that uniquely
describe trees as introduced in Liu (2019, <arXiv:1904.03332>). The core method
converts rooted unlabeled phylo objects from 'ape' to the tree defining polynomials
described with coefficient matrices. Additionally, a conversion for rooted binary trees
with binary trait labels is also provided. Once the polynomials of trees are calculated
there are functions to calculate distances, distance matrices and plot different distance
trees from a target tree. Manipulation and conversion to the tree defining polynomials is
implemented in C++ with 'Rcpp' and 'RcppArmadillo'. Furthermore, parallel programming with
'RcppThread' is used to improve performance converting to polynomials and calculating distances.
Author: Matthew Gould [aut, cre],
Pengyu Liu [ctb],
Caroline Colijn [ctb]
Maintainer: Matthew Gould <mgould@sfu.ca>
Diff between treenomial versions 1.0.1 dated 2019-12-06 and 1.1.2 dated 2020-02-13
DESCRIPTION | 8 - MD5 | 57 +++---- NAMESPACE | 1 NEWS.md | 14 + R/RcppExports.R | 12 - R/allTrees.R | 23 +- R/distFunctions.R | 225 +++++++++++++--------------- R/treeJuliaSet.R | 9 - R/treeToPoly.R | 237 +++++++++++++++--------------- R/wedge.R | 22 +- README.md | 32 +++- man/alignPoly.Rd | 4 man/allTrees.Rd | 10 - man/figures/README-plotExtremeTrees-1.png |only man/plotExtremeTrees.Rd | 18 +- man/polyDist.Rd | 10 - man/polyToDistMat.Rd | 12 - man/treeDist.Rd | 23 +- man/treeJuliaSet.Rd | 9 - man/treeToDistMat.Rd | 20 +- man/treeToPoly.Rd | 24 ++- man/wedge.Rd | 15 + src/RcppExports.cpp | 27 +-- src/allBinTreeShape.cpp | 6 src/coeffMatrix.cpp | 20 +- src/coeffMatrix.h | 15 - tests/testthat/Rplots.pdf |binary tests/testthat/test-coeff-building.R | 8 - tests/testthat/test-coeff-distances.R | 19 ++ tests/testthat/test-wedge.R | 6 30 files changed, 494 insertions(+), 392 deletions(-)
Title: Significant Zero Crossings
Description: Calculates and plots the SiZer map for scatterplot data. A
SiZer map is a way of examining when the p-th derivative of a
scatterplot-smoother is significantly negative, possibly zero or
significantly positive across a range of smoothing bandwidths.
Author: Derek Sonderegger [aut, cre]
Maintainer: Derek Sonderegger <derek.sonderegger@gmail.com>
Diff between SiZer versions 0.1-5 dated 2018-05-29 and 0.1-7 dated 2020-02-13
DESCRIPTION | 10 +++---- MD5 | 17 ++++++------ R/Arkansas.R | 2 + R/locally.weighted.polynomial.R | 46 +++++++++++++++++++--------------- README.md |only man/Arkansas.Rd | 2 - man/locally.weighted.polynomial.Rd | 10 +++++-- man/piecewise.linear.Rd | 10 +++++-- man/plot.LocallyWeightedPolynomial.Rd | 11 ++++++-- man/plot.SiZer.Rd | 8 ++++- 10 files changed, 75 insertions(+), 41 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility API
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF';
<https://www.gbif.org/developer/summary>). 'GBIF' is a database
of species occurrence records from sources all over the globe.
'rgbif' includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the 'GBIF'
tile map service to make 'rasters' summarizing huge amounts of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Damiano Oldoni [aut] (<https://orcid.org/0000-0003-3445-7562>),
Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>),
Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>),
Laurens Geffert [ctb],
Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>),
Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 2.0.0 dated 2020-01-31 and 2.1.0 dated 2020-02-13
rgbif-2.0.0/rgbif/man/occ_spellcheck.Rd |only rgbif-2.0.0/rgbif/tests/fixtures/occ_data_spellcheck.yml |only rgbif-2.0.0/rgbif/tests/fixtures/occ_search_spell_check.yml |only rgbif-2.0.0/rgbif/tests/fixtures/occ_spellcheck.yml |only rgbif-2.0.0/rgbif/tests/testthat/test-occ_spellcheck.R |only rgbif-2.1.0/rgbif/DESCRIPTION | 6 rgbif-2.1.0/rgbif/MD5 | 262 +++---- rgbif-2.1.0/rgbif/NEWS.md | 16 rgbif-2.1.0/rgbif/R/download_predicate_dsl.R | 94 +- rgbif-2.1.0/rgbif/R/download_queue.R | 7 rgbif-2.1.0/rgbif/R/elevation.r | 8 rgbif-2.1.0/rgbif/R/installations.r | 2 rgbif-2.1.0/rgbif/R/nodes.r | 2 rgbif-2.1.0/rgbif/R/occ_count.r | 1 rgbif-2.1.0/rgbif/R/occ_data.R | 4 rgbif-2.1.0/rgbif/R/occ_download.R | 2 rgbif-2.1.0/rgbif/R/occ_download_queue.R | 11 rgbif-2.1.0/rgbif/R/occ_search.r | 19 rgbif-2.1.0/rgbif/R/occ_spellcheck.R | 54 - rgbif-2.1.0/rgbif/R/organizations.r | 2 rgbif-2.1.0/rgbif/R/rgbif-package.r | 16 rgbif-2.1.0/rgbif/R/zzz.r | 24 rgbif-2.1.0/rgbif/inst/doc/downloads.html | 4 rgbif-2.1.0/rgbif/inst/doc/issues.html | 4 rgbif-2.1.0/rgbif/inst/doc/rgbif.html | 4 rgbif-2.1.0/rgbif/inst/doc/taxonomic_names.html | 4 rgbif-2.1.0/rgbif/man/GbifQueue.Rd | 7 rgbif-2.1.0/rgbif/man/download_predicates.Rd | 40 - rgbif-2.1.0/rgbif/man/elevation.Rd | 8 rgbif-2.1.0/rgbif/man/occ_count.Rd | 1 rgbif-2.1.0/rgbif/man/occ_data.Rd | 17 rgbif-2.1.0/rgbif/man/occ_download.Rd | 2 rgbif-2.1.0/rgbif/man/occ_download_queue.Rd | 11 rgbif-2.1.0/rgbif/man/occ_search.Rd | 19 rgbif-2.1.0/rgbif/man/occ_spellcheck-defunct.Rd |only rgbif-2.1.0/rgbif/tests/fixtures/dataset_metrics.yml | 70 +- rgbif-2.1.0/rgbif/tests/fixtures/dataset_metrics_error.yml | 60 - rgbif-2.1.0/rgbif/tests/fixtures/dataset_search.yml | 19 rgbif-2.1.0/rgbif/tests/fixtures/dataset_search_keyword.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/dataset_search_limit.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/dataset_search_query.yml | 19 rgbif-2.1.0/rgbif/tests/fixtures/dataset_search_repeated_params.yml | 36 - rgbif-2.1.0/rgbif/tests/fixtures/dataset_search_return.yml | 19 rgbif-2.1.0/rgbif/tests/fixtures/dataset_suggest.yml | 19 rgbif-2.1.0/rgbif/tests/fixtures/dataset_suggest_description.yml | 19 rgbif-2.1.0/rgbif/tests/fixtures/dataset_suggest_limit.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/dataset_suggest_query.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/dataset_suggest_repeated.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/datasets_contact.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/datasets_fails_well.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/datasets_metadata.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/datasets_single.yml | 15 rgbif-2.1.0/rgbif/tests/fixtures/elevation.yml | 52 - rgbif-2.1.0/rgbif/tests/fixtures/elevation_geonames_conn.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/elevation_geonames_conn_unauthorized.yml | 26 rgbif-2.1.0/rgbif/tests/fixtures/elevation_models.yml | 104 +- rgbif-2.1.0/rgbif/tests/fixtures/elevation_unauthorized.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/elevation_warning_zero_zero.yml | 21 rgbif-2.1.0/rgbif/tests/fixtures/enumeration.yml | 75 +- rgbif-2.1.0/rgbif/tests/fixtures/gbif_citation.yml | 34 rgbif-2.1.0/rgbif/tests/fixtures/gbif_citation_error.yml | 19 rgbif-2.1.0/rgbif/tests/fixtures/gbif_citation_occ_data.yml | 30 rgbif-2.1.0/rgbif/tests/fixtures/gbif_oai_get_records.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/gbif_oai_identify.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/gbif_oai_list_identifiers.yml | 15 rgbif-2.1.0/rgbif/tests/fixtures/gbif_oai_list_metadataformats.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/gbif_oai_list_sets.yml | 15 rgbif-2.1.0/rgbif/tests/fixtures/installations.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/installations_deleted.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/installations_uuid.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/installations_uuid_data.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/name_backbone.yml | 30 rgbif-2.1.0/rgbif/tests/fixtures/name_issues.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/name_lookup_habitat.yml | 95 +- rgbif-2.1.0/rgbif/tests/fixtures/name_suggest.yml | 99 +- rgbif-2.1.0/rgbif/tests/fixtures/name_suggest_many_args.yml | 21 rgbif-2.1.0/rgbif/tests/fixtures/name_usage.yml | 34 rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_children.yml | 36 - rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_descriptions.yml | 34 rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_distributions.yml | 59 - rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_media.yml | 347 +++++++++- rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_name.yml | 30 rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_parents.yml | 34 rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_references.yml | 57 - rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_related.yml | 36 - rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_speciesProfiles.yml | 74 +- rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_synonyms.yml | 38 - rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_typeSpecimens.yml | 30 rgbif-2.1.0/rgbif/tests/fixtures/name_usage_data_vernacularNames.yml | 38 - rgbif-2.1.0/rgbif/tests/fixtures/name_usage_fails_well.yml | 15 rgbif-2.1.0/rgbif/tests/fixtures/name_usage_return_data.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/networks.yml | 35 - rgbif-2.1.0/rgbif/tests/fixtures/nodes.yml | 41 - rgbif-2.1.0/rgbif/tests/fixtures/occ_count.yml | 88 +- rgbif-2.1.0/rgbif/tests/fixtures/occ_count_fails_well.yml | 66 - rgbif-2.1.0/rgbif/tests/fixtures/occ_data_args_with_many_inputs.yml | 51 - rgbif-2.1.0/rgbif/tests/fixtures/occ_data_catalog_number.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/occ_data_depth.yml | 54 - rgbif-2.1.0/rgbif/tests/fixtures/occ_data_elevation.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/occ_data_fails_well.yml | 28 rgbif-2.1.0/rgbif/tests/fixtures/occ_data_key_gbifid_character_class.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/occ_data_scientificname.yml | 85 +- rgbif-2.1.0/rgbif/tests/fixtures/occ_download_dataset_activity.yml | 55 - rgbif-2.1.0/rgbif/tests/fixtures/occ_download_dataset_activity_error.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/occ_download_datasets.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/occ_download_datasets_error.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/occ_download_list.yml | 19 rgbif-2.1.0/rgbif/tests/fixtures/occ_download_list_unauthorized.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/occ_download_queue.yml | 312 +++----- rgbif-2.1.0/rgbif/tests/fixtures/occ_facet.yml | 38 - rgbif-2.1.0/rgbif/tests/fixtures/occ_facet_paging.yml | 19 rgbif-2.1.0/rgbif/tests/fixtures/occ_facet_unknown_facet_var.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/occ_get.yml | 241 +++--- rgbif-2.1.0/rgbif/tests/fixtures/occ_get_other.yml | 68 + rgbif-2.1.0/rgbif/tests/fixtures/occ_metadata.yml | 171 ++-- rgbif-2.1.0/rgbif/tests/fixtures/occ_search_catalognumber.yml | 13 rgbif-2.1.0/rgbif/tests/fixtures/occ_search_depth.yml | 73 +- rgbif-2.1.0/rgbif/tests/fixtures/occ_search_elevation.yml | 32 rgbif-2.1.0/rgbif/tests/fixtures/occ_search_fails_well.yml | 26 rgbif-2.1.0/rgbif/tests/fixtures/occ_search_hierarchy_data.yml | 19 rgbif-2.1.0/rgbif/tests/fixtures/occ_search_key_gbifid_character_class.yml | 17 rgbif-2.1.0/rgbif/tests/fixtures/occ_search_many_inputs.yml | 51 - rgbif-2.1.0/rgbif/tests/fixtures/occ_search_scientificname.yml | 85 +- rgbif-2.1.0/rgbif/tests/fixtures/parsenames.yml | 45 - rgbif-2.1.0/rgbif/tests/fixtures/wkt_large_occ_data.yml | 19 rgbif-2.1.0/rgbif/tests/fixtures/wkt_large_occ_search.yml | 19 rgbif-2.1.0/rgbif/tests/testthat/test-download_parsing.R | 42 - rgbif-2.1.0/rgbif/tests/testthat/test-downloads.R | 4 rgbif-2.1.0/rgbif/tests/testthat/test-installations.r | 2 rgbif-2.1.0/rgbif/tests/testthat/test-occ_count.r | 26 rgbif-2.1.0/rgbif/tests/testthat/test-occ_data.R | 25 rgbif-2.1.0/rgbif/tests/testthat/test-occ_facet.R | 2 rgbif-2.1.0/rgbif/tests/testthat/test-occ_get.r | 10 rgbif-2.1.0/rgbif/tests/testthat/test-occ_metadata.r | 8 rgbif-2.1.0/rgbif/tests/testthat/test-occ_search.r | 25 135 files changed, 2573 insertions(+), 2169 deletions(-)
Title: Fit Poolwise Regression Models
Description: Functions for calculating power and fitting regression models in studies where a biomarker is measured in "pooled" samples rather than for each individual. Approaches for handling measurement error follow the framework of Schisterman et al. (2010) <doi:10.1002/sim.3823>.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen <vandomed@gmail.com>
Diff between pooling versions 1.1.1 dated 2018-04-26 and 1.1.2 dated 2020-02-13
pooling-1.1.1/pooling/R/dfa_xerrors.R |only pooling-1.1.1/pooling/R/gamma_constantscale.R |only pooling-1.1.1/pooling/R/lognormal.R |only pooling-1.1.1/pooling/R/logreg_xerrors.R |only pooling-1.1.1/pooling/data/dat1.rda |only pooling-1.1.1/pooling/data/dat1_xtilde.rda |only pooling-1.1.1/pooling/data/pdat2_c.rda |only pooling-1.1.1/pooling/man/dat1.Rd |only pooling-1.1.1/pooling/man/dat1_xtilde.Rd |only pooling-1.1.1/pooling/man/dfa_xerrors.Rd |only pooling-1.1.1/pooling/man/gamma_constantscale.Rd |only pooling-1.1.1/pooling/man/lognormal.Rd |only pooling-1.1.1/pooling/man/logreg_xerrors.Rd |only pooling-1.1.1/pooling/man/pdat2_c.Rd |only pooling-1.1.2/pooling/DESCRIPTION | 15 pooling-1.1.2/pooling/MD5 | 108 ++-- pooling-1.1.2/pooling/NAMESPACE | 26 - pooling-1.1.2/pooling/R/cond_logreg.R |only pooling-1.1.2/pooling/R/form_pools.R |only pooling-1.1.2/pooling/R/p_dfa_xerrors.R | 55 +- pooling-1.1.2/pooling/R/p_dfa_xerrors2.R | 158 ++++-- pooling-1.1.2/pooling/R/p_gdfa.R |only pooling-1.1.2/pooling/R/p_gdfa_constant.R |only pooling-1.1.2/pooling/R/p_gdfa_nonconstant.R |only pooling-1.1.2/pooling/R/p_linreg_yerrors.R |only pooling-1.1.2/pooling/R/p_logreg.R | 74 +- pooling-1.1.2/pooling/R/p_logreg_xerrors.R | 484 ++++++++++--------- pooling-1.1.2/pooling/R/p_logreg_xerrors2.R | 478 +++++++++++------- pooling-1.1.2/pooling/R/p_ndfa.R |only pooling-1.1.2/pooling/R/p_ndfa_constant.R |only pooling-1.1.2/pooling/R/p_ndfa_nonconstant.R |only pooling-1.1.2/pooling/R/plot_dfa.R | 307 +----------- pooling-1.1.2/pooling/R/plot_dfa2.R | 90 +-- pooling-1.1.2/pooling/R/plot_gdfa.R |only pooling-1.1.2/pooling/R/plot_ndfa.R |only pooling-1.1.2/pooling/R/poolcost_t.R | 128 +++-- pooling-1.1.2/pooling/R/poolcushion_t.R |only pooling-1.1.2/pooling/R/pooling-data.R | 78 +-- pooling-1.1.2/pooling/R/pooling.R | 11 pooling-1.1.2/pooling/R/poolpower_t.R | 199 +++++-- pooling-1.1.2/pooling/R/poolvar_t.R | 107 ++-- pooling-1.1.2/pooling/data/dat_cond_logreg.rda |only pooling-1.1.2/pooling/data/dat_p_gdfa.rda |only pooling-1.1.2/pooling/data/dat_p_linreg_yerrors.rda |only pooling-1.1.2/pooling/data/dat_p_ndfa.rda |only pooling-1.1.2/pooling/data/pdat1.rda |binary pooling-1.1.2/pooling/data/pdat2.rda |binary pooling-1.1.2/pooling/data/simdata_biostatistics.rda |only pooling-1.1.2/pooling/man/cond_logreg.Rd |only pooling-1.1.2/pooling/man/dat_cond_logreg.Rd |only pooling-1.1.2/pooling/man/dat_p_gdfa.Rd |only pooling-1.1.2/pooling/man/dat_p_linreg_yerrors.Rd |only pooling-1.1.2/pooling/man/dat_p_ndfa.Rd |only pooling-1.1.2/pooling/man/form_pools.Rd |only pooling-1.1.2/pooling/man/p_dfa_xerrors.Rd | 20 pooling-1.1.2/pooling/man/p_dfa_xerrors2.Rd | 66 +- pooling-1.1.2/pooling/man/p_gdfa.Rd |only pooling-1.1.2/pooling/man/p_gdfa_constant.Rd |only pooling-1.1.2/pooling/man/p_gdfa_nonconstant.Rd |only pooling-1.1.2/pooling/man/p_linreg_yerrors.Rd |only pooling-1.1.2/pooling/man/p_logreg.Rd | 20 pooling-1.1.2/pooling/man/p_logreg_xerrors.Rd | 92 ++- pooling-1.1.2/pooling/man/p_logreg_xerrors2.Rd | 102 ++-- pooling-1.1.2/pooling/man/p_ndfa.Rd |only pooling-1.1.2/pooling/man/p_ndfa_constant.Rd |only pooling-1.1.2/pooling/man/p_ndfa_nonconstant.Rd |only pooling-1.1.2/pooling/man/pdat1.Rd | 8 pooling-1.1.2/pooling/man/pdat2.Rd | 10 pooling-1.1.2/pooling/man/plot_dfa.Rd | 8 pooling-1.1.2/pooling/man/plot_dfa2.Rd | 37 - pooling-1.1.2/pooling/man/plot_gdfa.Rd |only pooling-1.1.2/pooling/man/plot_ndfa.Rd |only pooling-1.1.2/pooling/man/poolcost_t.Rd | 33 - pooling-1.1.2/pooling/man/poolcushion_t.Rd |only pooling-1.1.2/pooling/man/pooling.Rd | 4 pooling-1.1.2/pooling/man/poolpower_t.Rd | 47 - pooling-1.1.2/pooling/man/poolvar_t.Rd | 23 pooling-1.1.2/pooling/man/simdata.Rd |only pooling-1.1.2/pooling/man/test_pe.Rd | 4 79 files changed, 1568 insertions(+), 1224 deletions(-)
Title: Implementing Dispersal into Species Distribution Models
Description: Functions for implementing species dispersal into projections
of species distribution models (e.g. under climate change scenarios).
Author: Robin Engler <robin.engler@gmail.com> and
Wim Hordijk <wim@WorldWideWanderings.net> and
Loic Pellissier <loic.pellissier@unil.ch>
Maintainer: ORPHANED
Diff between MigClim versions 1.6.1 dated 2020-01-18 and 1.6.2 dated 2020-02-13
MigClim-1.6.1/MigClim/R/MigClim.migrate.R |only MigClim-1.6.1/MigClim/man/MigClim.migrate.Rd |only MigClim-1.6.2/MigClim/DESCRIPTION | 7 +++---- MigClim-1.6.2/MigClim/MD5 | 12 +++++------- MigClim-1.6.2/MigClim/NAMESPACE | 4 ++-- MigClim-1.6.2/MigClim/src/genclust.c | 2 +- MigClim-1.6.2/MigClim/src/migrate.c | 4 ++-- MigClim-1.6.2/MigClim/src/validate.c | 4 ++-- 8 files changed, 15 insertions(+), 18 deletions(-)
Title: Tools for Validating 'GeoJSON'
Description: Tools for linting 'GeoJSON'. Includes tools for interacting with the
online tool <http://geojsonlint.com>, the 'Javascript' library 'geojsonhint'
(<https://www.npmjs.com/package/geojsonhint>), and validating against a
'GeoJSON' schema via the 'Javascript' library
(<https://www.npmjs.com/package/is-my-json-valid>). Some tools work locally
while others require an internet connection.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Andy Teucher [aut],
Tom MacWright [cph] (geojsonhint Javascript library),
Mads Kristensen [cph] (geojson schema)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojsonlint versions 0.3.0 dated 2019-02-08 and 0.4.0 dated 2020-02-13
geojsonlint-0.3.0/geojsonlint/inst/doc/geojsonlint_vignette.R |only geojsonlint-0.3.0/geojsonlint/inst/doc/geojsonlint_vignette.Rmd |only geojsonlint-0.3.0/geojsonlint/inst/doc/geojsonlint_vignette.html |only geojsonlint-0.3.0/geojsonlint/man/geojson_lint.Rd |only geojsonlint-0.3.0/geojsonlint/tests/testthat/test-geojson_lint.R |only geojsonlint-0.3.0/geojsonlint/vignettes/geojsonlint_vignette.Rmd |only geojsonlint-0.4.0/geojsonlint/DESCRIPTION | 13 - geojsonlint-0.4.0/geojsonlint/LICENSE | 2 geojsonlint-0.4.0/geojsonlint/MD5 | 39 +-- geojsonlint-0.4.0/geojsonlint/NAMESPACE | 6 geojsonlint-0.4.0/geojsonlint/NEWS.md | 12 + geojsonlint-0.4.0/geojsonlint/R/geojson_validate.R | 4 geojsonlint-0.4.0/geojsonlint/R/geojsonhint.R | 4 geojsonlint-0.4.0/geojsonlint/R/geojsonlint-package.r | 4 geojsonlint-0.4.0/geojsonlint/R/geojsonlint.R | 117 ---------- geojsonlint-0.4.0/geojsonlint/R/zzz.R | 7 geojsonlint-0.4.0/geojsonlint/README.md | 52 ---- geojsonlint-0.4.0/geojsonlint/build/vignette.rds |binary geojsonlint-0.4.0/geojsonlint/inst/doc/geojsonlint.R |only geojsonlint-0.4.0/geojsonlint/inst/doc/geojsonlint.Rmd |only geojsonlint-0.4.0/geojsonlint/inst/doc/geojsonlint.html |only geojsonlint-0.4.0/geojsonlint/man/geojson_hint.Rd | 4 geojsonlint-0.4.0/geojsonlint/man/geojson_lint-defunct.Rd |only geojsonlint-0.4.0/geojsonlint/man/geojson_validate.Rd | 6 geojsonlint-0.4.0/geojsonlint/man/geojsonlint-package.Rd | 2 geojsonlint-0.4.0/geojsonlint/vignettes/geojsonlint.Rmd |only 26 files changed, 65 insertions(+), 207 deletions(-)
Title: Kernel Density Estimation and Selection of Optimum Bandwidth
Description: A collection of functions related to density estimation by using Chen's (2000) idea. Mean Squared Errors (MSE) are calculated for estimated curves. For this purpose, R functions allow the distribution to be Gamma, Exponential or Weibull. For details see Chen (2000), Scaillet (2004) <doi:10.1080/10485250310001624819> and Khan and Akbar.
Author: Javaria Ahmad Khan, Atif Akbar.
Maintainer: Javaria Ahmad Khan <jakhan0@yahoo.com>
Diff between AsyK versions 1.5.3 dated 2020-01-21 and 1.5.4 dated 2020-02-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/AsyK.R | 54 +++++++++++++++--------------------------------------- man/Laplace.Rd | 2 +- man/compLR.Rd | 8 +++++--- man/laphcomp.Rd | 6 +++--- man/mseLap.Rd | 4 ++-- man/mseRIG.Rd | 2 +- man/righcomp.Rd | 6 +++--- 9 files changed, 42 insertions(+), 64 deletions(-)
Title: Studio Ghibli Colour Palettes
Description: Colour palettes inspired by Studio Ghibli <https://en.wikipedia.org/wiki/Studio_Ghibli>
films, ported to R for your enjoyment.
Author: Ewen Henderson [aut, cre] (<https://orcid.org/0000-0002-4748-4693>),
Danielle Desrosiers [ctb],
Michael Chirico [ctb]
Maintainer: Ewen Henderson <ewenhenderson@gmail.com>
Diff between ghibli versions 0.3.0 dated 2019-09-02 and 0.3.1 dated 2020-02-13
DESCRIPTION | 12 +++++++----- MD5 | 13 +++++++------ NEWS.md | 4 ++++ R/onLoad.R |only inst/doc/ghibli-guide.html | 4 ++-- man/figures/README-ggplot2-eg-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/ghibli-package.Rd | 1 + 8 files changed, 21 insertions(+), 13 deletions(-)
Title: Analyze and Create Elegant Directed Acyclic Graphs
Description: Tidy, analyze, and plot directed acyclic graphs
(DAGs). 'ggdag' is built on top of 'dagitty', an R package that uses
the 'DAGitty' web tool (<http://dagitty.net>) for creating and
analyzing DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty'
objects using 'ggplot2' and 'ggraph', as well as common analytic and
graphical functions, such as determining adjustment sets and node
relationships.
Author: Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Diff between ggdag versions 0.2.1 dated 2019-12-06 and 0.2.2 dated 2020-02-13
ggdag-0.2.1/ggdag/man/expand_scale.Rd |only ggdag-0.2.1/ggdag/tests/testthat/test_tidy_dagitty.R |only ggdag-0.2.2/ggdag/DESCRIPTION | 16 ggdag-0.2.2/ggdag/MD5 | 124 ++++-- ggdag-0.2.2/ggdag/NAMESPACE | 5 ggdag-0.2.2/ggdag/NEWS.md | 7 ggdag-0.2.2/ggdag/R/StatsandGeoms.R | 28 - ggdag-0.2.2/ggdag/R/adjustment_sets.R | 6 ggdag-0.2.2/ggdag/R/colliders.R | 21 - ggdag-0.2.2/ggdag/R/dagify.R | 3 ggdag-0.2.2/ggdag/R/drelationship.R | 2 ggdag-0.2.2/ggdag/R/equivalence.R | 10 ggdag-0.2.2/ggdag/R/geom_dag.R | 11 ggdag-0.2.2/ggdag/R/paths.R | 38 + ggdag-0.2.2/ggdag/R/simulate_data.R | 2 ggdag-0.2.2/ggdag/R/themes.R | 6 ggdag-0.2.2/ggdag/R/tidy_dag.R | 10 ggdag-0.2.2/ggdag/R/utils.R | 74 +-- ggdag-0.2.2/ggdag/README.md | 36 - ggdag-0.2.2/ggdag/inst/WORDLIST | 2 ggdag-0.2.2/ggdag/inst/doc/bias-structures.html | 303 +++++++-------- ggdag-0.2.2/ggdag/inst/doc/intro-to-dags.html | 139 +++---- ggdag-0.2.2/ggdag/inst/doc/intro-to-ggdag.html | 311 +++++++--------- ggdag-0.2.2/ggdag/man/adjustment_sets.Rd | 8 ggdag-0.2.2/ggdag/man/as.tbl.tidy_daggity.Rd | 5 ggdag-0.2.2/ggdag/man/equivalent.Rd | 8 ggdag-0.2.2/ggdag/man/expand_plot.Rd | 6 ggdag-0.2.2/ggdag/man/figures/ggdag-2.png |binary ggdag-0.2.2/ggdag/man/geom_dag_collider_edges.Rd | 12 ggdag-0.2.2/ggdag/man/geom_dag_edge_functions.Rd | 1 ggdag-0.2.2/ggdag/man/geom_dag_text.Rd | 12 ggdag-0.2.2/ggdag/man/ggplot.tidy_dagitty.Rd | 2 ggdag-0.2.2/ggdag/man/node_point.Rd | 12 ggdag-0.2.2/ggdag/man/paths.Rd | 6 ggdag-0.2.2/ggdag/tests/figs |only ggdag-0.2.2/ggdag/tests/testthat/helper-load_dag.R |only ggdag-0.2.2/ggdag/tests/testthat/test-StatsandGeoms.R |only ggdag-0.2.2/ggdag/tests/testthat/test-adjustment_sets.R |only ggdag-0.2.2/ggdag/tests/testthat/test-as_tbl_graph.R |only ggdag-0.2.2/ggdag/tests/testthat/test-canonical.R |only ggdag-0.2.2/ggdag/tests/testthat/test-colliders.R |only ggdag-0.2.2/ggdag/tests/testthat/test-dag_labels.R |only ggdag-0.2.2/ggdag/tests/testthat/test-dagify.R |only ggdag-0.2.2/ggdag/tests/testthat/test-dplyr_methods.R |only ggdag-0.2.2/ggdag/tests/testthat/test-drelationship.R |only ggdag-0.2.2/ggdag/tests/testthat/test-equivalence.R |only ggdag-0.2.2/ggdag/tests/testthat/test-exogenous.R |only ggdag-0.2.2/ggdag/tests/testthat/test-geom_dag.R |only ggdag-0.2.2/ggdag/tests/testthat/test-ggdag.R |only ggdag-0.2.2/ggdag/tests/testthat/test-instrumental.R |only ggdag-0.2.2/ggdag/tests/testthat/test-paths.R |only ggdag-0.2.2/ggdag/tests/testthat/test-quick_plots.R |only ggdag-0.2.2/ggdag/tests/testthat/test-relations.R |only ggdag-0.2.2/ggdag/tests/testthat/test-simulate_data.R |only ggdag-0.2.2/ggdag/tests/testthat/test-status.R |only ggdag-0.2.2/ggdag/tests/testthat/test-themes.R |only ggdag-0.2.2/ggdag/tests/testthat/test-tidy_dag.R |only 57 files changed, 645 insertions(+), 581 deletions(-)