Title: Provides Easy Access to Complex Systems Datasets
Description: Provides easy-to-use and easy-to-access datasets from the
Index of COmplex Networks (ICON) database available on the University
of Colorado website. All datasets can be loaded with a single function
call and new datasets are being slowly added from ICON at
<https://icon.colorado.edu>. Specific ICON datasets of interest can
be requested at the BugReports URL <https://github.com/rrrlw/ICON/issues>.
Author: Raoul Wadhwa [aut, cre] (<https://orcid.org/0000-0003-0503-9580>),
Jacob Scott [aut] (<https://orcid.org/0000-0003-2971-7673>)
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Diff between ICON versions 0.3.0 dated 2020-08-29 and 0.4.0 dated 2020-10-23
DESCRIPTION | 32 +++++++++++++++++++++----------- MD5 | 25 ++++++++++++++++++------- NAMESPACE | 2 ++ R/acquire.R | 16 +++++++++++++--- R/data.R | 1 + R/s3.R |only build |only data/ICON_data.rda |binary inst |only man/ICON_data.Rd | 1 + man/as.network.ICON.Rd |only man/get_data.Rd | 4 +++- tests |only vignettes |only 14 files changed, 59 insertions(+), 22 deletions(-)
Title: Extend the 'copula' Package with Families and Models from
'VineCopula'
Description: Provides new classes for (rotated) BB1, BB6, BB7, BB8, and
Tawn copulas, extends the existing Gumbel and Clayton families with
rotations, and allows to set up a vine copula model using the 'copula' API.
Corresponding objects from the 'VineCopula' API can easily be converted.
Author: Thomas Nagler [aut, cre],
Benedikt Graeler [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between VC2copula versions 0.1.0 dated 2019-12-15 and 0.1.1 dated 2020-10-23
VC2copula-0.1.0/VC2copula/R/tawnCopula.R |only VC2copula-0.1.1/VC2copula/DESCRIPTION | 11 +-- VC2copula-0.1.1/VC2copula/MD5 | 36 +++++----- VC2copula-0.1.1/VC2copula/NAMESPACE | 31 ++++++++ VC2copula-0.1.1/VC2copula/NEWS.md | 7 + VC2copula-0.1.1/VC2copula/R/0_wrappers.R | 5 + VC2copula-0.1.1/VC2copula/R/BB6copula.R | 2 VC2copula-0.1.1/VC2copula/R/BB7copula.R | 2 VC2copula-0.1.1/VC2copula/R/BB8copula.R | 2 VC2copula-0.1.1/VC2copula/R/VC2copula-package.R | 1 VC2copula-0.1.1/VC2copula/R/joeBiCopula.R | 7 + VC2copula-0.1.1/VC2copula/R/surClaytonCopula.R | 7 + VC2copula-0.1.1/VC2copula/R/surGumbelCopula.R | 8 ++ VC2copula-0.1.1/VC2copula/R/tawnT1Copula.R | 25 ++++++ VC2copula-0.1.1/VC2copula/R/tawnT2Copula.R | 2 VC2copula-0.1.1/VC2copula/README.md | 7 - VC2copula-0.1.1/VC2copula/man/tawnT1Copula-class.Rd | 16 ---- VC2copula-0.1.1/VC2copula/man/tawnT1Copula.Rd | 29 -------- VC2copula-0.1.1/VC2copula/src |only VC2copula-0.1.1/VC2copula/tests/testthat/test-bivariate-models.R | 26 ++++++- 20 files changed, 153 insertions(+), 71 deletions(-)
Title: Data Language Engine for 'knitr' / 'rmarkdown'
Description: Implements a data language engine for incorporating data directly in
'rmarkdown' documents so that they can be made completely standalone.
Author: David M. Kaplan [aut, cre, cph]
(<https://orcid.org/0000-0001-6087-359X>, dmkaplan2000)
Maintainer: David M. Kaplan <dmkaplan2000@gmail.com>
Diff between knitrdata versions 0.5.1 dated 2020-10-22 and 0.5.2 dated 2020-10-23
knitrdata-0.5.1/knitrdata/R/is.file.binary.R |only knitrdata-0.5.2/knitrdata/DESCRIPTION | 9 +- knitrdata-0.5.2/knitrdata/MD5 | 36 +++++----- knitrdata-0.5.2/knitrdata/NAMESPACE | 2 knitrdata-0.5.2/knitrdata/NEWS.md | 5 + knitrdata-0.5.2/knitrdata/R/create_chunks.R | 9 +- knitrdata-0.5.2/knitrdata/R/data_engine.R | 27 +++---- knitrdata-0.5.2/knitrdata/R/rstudio_addins.R | 8 +- knitrdata-0.5.2/knitrdata/R/utils.R |only knitrdata-0.5.2/knitrdata/inst/doc/data_language_engine_vignette.Rmd | 14 +++ knitrdata-0.5.2/knitrdata/inst/doc/data_language_engine_vignette.html | 17 +++- knitrdata-0.5.2/knitrdata/man/create_chunk.Rd | 4 - knitrdata-0.5.2/knitrdata/man/data_decode.Rd | 17 ++-- knitrdata-0.5.2/knitrdata/man/is.file.binary.Rd | 2 knitrdata-0.5.2/knitrdata/man/list_rmd_chunks.Rd | 4 - knitrdata-0.5.2/knitrdata/man/platform.newline.Rd |only knitrdata-0.5.2/knitrdata/tests/test.create_chunks.R | 2 knitrdata-0.5.2/knitrdata/tests/test.data_encode_decode.R | 2 knitrdata-0.5.2/knitrdata/tests/test.large_data_chunk.R | 2 knitrdata-0.5.2/knitrdata/tests/test.md5sum_chunks.R |only knitrdata-0.5.2/knitrdata/vignettes/data_language_engine_vignette.Rmd | 14 +++ 21 files changed, 109 insertions(+), 65 deletions(-)
Title: 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' provides many desirable
features. This package bundles these header files for easy use by R packages via a simple
'LinkingTo:' inclusion.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSpdlog versions 0.0.2 dated 2020-09-20 and 0.0.3 dated 2020-10-23
ChangeLog | 47 ++++++++++++++ DESCRIPTION | 20 ++---- MD5 | 71 +++++++++++----------- R/RcppExports.R | 14 ++++ README.md | 32 +++++---- build/partial.rdb |binary build/vignette.rds |only cleanup | 2 inst/NEWS.Rd | 13 ++++ inst/doc |only inst/examples/exampleThree.cpp | 5 + inst/examples/exampleTwo.cpp | 6 + inst/include/RcppSpdlog | 19 ++++- inst/include/spdlog/async.h | 6 - inst/include/spdlog/cfg/argv.h | 3 inst/include/spdlog/cfg/env.h | 8 +- inst/include/spdlog/cfg/helpers-inl.h | 28 ++++++-- inst/include/spdlog/cfg/helpers.h | 5 - inst/include/spdlog/common.h | 2 inst/include/spdlog/details/registry-inl.h | 30 ++++++--- inst/include/spdlog/details/registry.h | 9 +- inst/include/spdlog/details/synchronous_factory.h | 2 inst/include/spdlog/fmt/bin_to_hex.h | 2 inst/include/spdlog/logger-inl.h | 7 +- inst/include/spdlog/logger.h | 22 +++--- inst/include/spdlog/pattern_formatter-inl.h | 10 +-- inst/include/spdlog/pattern_formatter.h | 6 - inst/include/spdlog/sinks/msvc_sink.h | 10 +-- inst/include/spdlog/sinks/stdout_sinks-inl.h | 35 +++++++++- inst/include/spdlog/sinks/stdout_sinks.h | 7 ++ inst/include/spdlog/sinks/wincolor_sink-inl.h | 18 +---- inst/include/spdlog/spdlog.h | 18 ++--- inst/include/spdlog/stopwatch.h | 4 - inst/include/spdlog/version.h | 2 man/setLogLevel.Rd |only src/RcppExports.cpp | 11 +++ src/exampleRsink.cpp | 41 ++++++++---- vignettes |only 38 files changed, 353 insertions(+), 162 deletions(-)
Title: NASA's Global Ecosystem Dynamics Investigation (GEDI) Data
Visualization and Processing
Description: Set of tools for downloading, reading, visualizing and processing GEDI Level1B, Level2A and Level2B data.
Author: Carlos Alberto Silva [aut, cre, cph],
Caio Hamamura [aut, cph],
Ruben Valbuena [aut, ctb],
Steven Hancock [aut, ctb],
Adrian Cardil [aut, ctb],
Eben North Broadbent [aut, ctb],
Danilo Roberti Alves de Almeida [aut, ctb],
Celso H. L. Silva Junior [aut, ctb],
Carine Klauberg [aut, ctb],
Burton Garbow [cph] (Is the author of the MINPACK-1 Least Squares
Fitting Library),
Kenneth Hillstrom [cph] (Is the author of the MINPACK-1 Least Squares
Fitting Library),
Jorge More [cph] (Is the author of the MINPACK-1 Least Squares Fitting
Library),
Craig Markwardt [cph] (Is the author of the enhanced MINPACK-1 Least
Squares Fitting Library)
Maintainer: Carlos Alberto Silva <carlos_engflorestal@outlook.com>
Diff between rGEDI versions 0.1.8 dated 2020-07-15 and 0.1.9 dated 2020-10-23
DESCRIPTION | 14 MD5 | 18 R/getLevel2BVPM.R | 56 + README.md | 4 configure.ac | 7 inst/doc/tutorial.R | 89 ++ inst/doc/tutorial.Rmd | 1490 +++++++++++++++++++++++++------------------------ inst/doc/tutorial.html | 880 +++++++++++++++------------- man/gediWFMetrics.Rd | 2 vignettes/tutorial.Rmd | 1490 +++++++++++++++++++++++++------------------------ 10 files changed, 2153 insertions(+), 1897 deletions(-)
Title: Easily Visualize Data from 'ERDDAP' Servers via the 'rerddap'
Package
Description: Easily visualize and animate 'tabledap' and 'griddap' objects obtained via the 'rerddap' package in a simple one-line command, using either base graphics or 'ggplot2' graphics. 'plotdap' handles extracting and reshaping the data, map projections and continental outlines. Optionally the data can be animated through time using the 'gganmiate' package.
Author: Carson Sievert [aut],
Roy Mendelssohn [aut, ctb, cre]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between plotdap versions 0.0.7 dated 2020-03-20 and 0.0.8 dated 2020-10-23
DESCRIPTION | 12 MD5 | 16 - NEWS.md | 5 R/add_griddap.R | 2 build/vignette.rds |binary inst/doc/using_plotdap.Rmd | 16 - inst/doc/using_plotdap.html | 661 +++++++++++++++++++++++--------------------- man/reexports.Rd | 2 vignettes/using_plotdap.Rmd | 16 - 9 files changed, 397 insertions(+), 333 deletions(-)
Title: Graphical VAR for Experience Sampling Data
Description: Estimates within and between time point interactions in experience sampling data, using the Graphical vector autoregression model in combination with regularization. See also Epskamp, Waldorp, Mottus & Borsboom (2018) <doi:10.1080/00273171.2018.1454823>.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between graphicalVAR versions 0.2.3 dated 2020-04-09 and 0.2.4 dated 2020-10-23
DESCRIPTION | 6 MD5 | 46 ++-- NAMESPACE | 66 +++--- NEWS | 74 +++--- R/Kappa.R | 20 - R/RcppExports.R | 38 +-- R/Rothmana.R | 204 +++++++++--------- R/dataPrep.R | 244 +++++++++++----------- R/gVARsimulator.R | 350 ++++++++++++++++---------------- R/graphicalVAR.R | 534 ++++++++++++++++++++++++------------------------- R/lambdas.R | 242 +++++++++++----------- R/methods.R | 182 ++++++++-------- R/mlGraphicalVAR.R | 188 ++++++++--------- R/simMLgvar.R | 332 +++++++++++++++--------------- R/varGLM.R | 128 +++++------ man/S3.Rd | 52 ++-- man/graphicalVAR.Rd | 314 ++++++++++++++-------------- man/graphicalVARsim.Rd | 96 ++++---- man/mlGraphicalVAR.Rd | 212 +++++++++---------- man/plot.Rd | 82 +++---- man/randomGVARmodel.Rd | 106 ++++----- man/simMLgvar.Rd | 132 ++++++------ src/Makevars | 4 src/Makevars.win | 3 24 files changed, 1828 insertions(+), 1827 deletions(-)
Title: Use R for Fun
Description: This is a collection of R games and other funny stuff, such as the
classic Mine sweeper and sliding puzzles.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Yixuan Qiu [aut],
Taiyun Wei [aut]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between fun versions 0.2 dated 2018-12-05 and 0.3 dated 2020-10-23
DESCRIPTION | 8 ++--- MD5 | 66 +++++++++++++++++++++--------------------- NEWS | 6 +++ R/alzheimer_test.R | 2 - R/fun-package.R | 2 - R/gomoku.R | 6 +-- R/htmlspecialchars.R | 8 ++--- R/lights_out.R | 2 - R/mine_sweeper.R | 2 - R/random_password.R | 2 - R/shutdown.R | 2 - R/sliding_puzzle.R | 2 - R/tag_cloud.R | 13 +++----- R/tower_of_hanoi.R | 4 +- README.md | 4 +- demo/ChinaHeart2D.R | 2 - demo/ChinaHeart3D.R | 4 +- demo/GameOfLife.R | 4 +- demo/HappyNewYear2009Music.R | 2 - demo/HappyNewYear2009Taiyun.R | 2 - demo/HappyNewYear2009Yixuan.R | 2 - demo/RealTurtle.R | 2 - demo/TurtleGraphics.R | 2 - man/alzheimer_test.Rd | 12 +++++-- man/gomoku.Rd | 6 +-- man/htmlspecialchars.Rd | 8 ++--- man/lights_out.Rd | 14 +++++++- man/mine_sweeper.Rd | 2 - man/random_password.Rd | 2 - man/shutdown.Rd | 2 - man/sliding_puzzle.Rd | 2 - man/tagData.Rd | 8 +++-- man/tag_cloud.Rd | 39 +++++++++++++++++------- man/tower_of_hanoi.Rd | 4 +- 34 files changed, 141 insertions(+), 107 deletions(-)
Title: Bayesian Optimization and Model-Based Optimization of Expensive
Black-Box Functions
Description: Flexible and comprehensive R toolbox for model-based optimization
('MBO'), also known as Bayesian optimization. It implements the Efficient
Global Optimization Algorithm and is designed for both single- and multi-
objective optimization with mixed continuous, categorical and conditional
parameters. The machine learning toolbox 'mlr' provide dozens of regression
learners to model the performance of the target algorithm with respect to
the parameter settings. It provides many different infill criteria to guide
the search process. Additional features include multi-point batch proposal,
parallel execution as well as visualization and sophisticated logging
mechanisms, which is especially useful for teaching and understanding of
algorithm behavior. 'mlrMBO' is implemented in a modular fashion, such that
single components can be easily replaced or adapted by the user for specific
use cases.
Author: Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Jakob Richter [aut, cre] (<https://orcid.org/0000-0003-4481-5554>),
Jakob Bossek [aut] (<https://orcid.org/0000-0002-4121-4668>),
Daniel Horn [aut],
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Janek Thomas [aut] (<https://orcid.org/0000-0003-4511-6245>)
Maintainer: Jakob Richter <code@jakob-r.de>
Diff between mlrMBO versions 1.1.4 dated 2020-02-28 and 1.1.5 dated 2020-10-23
DESCRIPTION | 14 MD5 | 39 - NAMESPACE | 1 NEWS.md | 7 R/OptState.R | 3 R/SMBO.R | 4 R/exampleRunMultiObj.R | 2 R/infill_crits.R | 2 R/term_conds.R | 2 README.md | 45 + build/vignette.rds |binary inst/CITATION | 2 inst/doc/mlrMBO.Rmd | 2 inst/doc/mlrMBO.html | 681 ++++++++++------------------ man/infillcrits.Rd | 6 man/trafos.Rd | 4 tests/testthat/Rplots.pdf |only tests/testthat/test_check_design.R | 4 tests/testthat/test_smbo.R | 12 vignettes/mlrMBO.Rmd | 2 vignettes/supplementary/parallelization.Rmd | 2 21 files changed, 345 insertions(+), 489 deletions(-)
Title: Find Pattern in Files
Description: Creates a HTML widget which displays the results of searching for a pattern in files in a given folder. The results can be viewed in the 'RStudio' viewer pane, included in a 'R Markdown' document or in a 'Shiny' app.
Author: Stéphane Laurent [aut, cre],
Rob Burns [ctb, cph] ('ansi-to-html' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between findInFiles versions 0.1.0 dated 2020-10-22 and 0.1.1 dated 2020-10-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/findInFiles.R | 5 +++++ 4 files changed, 16 insertions(+), 6 deletions(-)
Title: Early Detection of Public Health Threats from Twitter Data
Description: It allows you to automatically monitor trends of tweets by time, place and topic aiming at detecting public health threats early through the detection of signals (e.g. an unusual increase in the number of tweets). It was designed to focus on infectious diseases, and it can be extended to all hazards or other fields of study by modifying the topics and keywords.
Author: Francisco Orchard [aut, ctr] (<https://orcid.org/0000-0001-5793-3301>,
Author of the package and original code),
Laura Espinosa [aut, cre, fnd]
(<https://orcid.org/0000-0003-0748-9657>, Project manager, author
of the design and concept of the package, and package maintainer),
Ariana Wijermans [ctb] (Contributor to the design and concept of the
package),
Thomas Mollet [ctb, fnd] (Business owner of the project, and
contributor to the design and concept of the package),
Adrian Prodan [ctb],
Thomas Czernichow [ctb],
Maria Prieto Gonzalez [ctb],
Esther Kissling [ctb],
Michael Höhle [ctb]
Maintainer: Laura Espinosa <laura.espinosa@ecdc.europa.eu>
Diff between epitweetr versions 0.1.20 dated 2020-10-01 and 0.1.24 dated 2020-10-23
epitweetr-0.1.20/epitweetr/R/shiny_app.R |only epitweetr-0.1.24/epitweetr/DESCRIPTION | 15 epitweetr-0.1.24/epitweetr/MD5 | 80 epitweetr-0.1.24/epitweetr/R/aggregate.R | 1000 ++- epitweetr-0.1.24/epitweetr/R/alert.R | 1762 +++--- epitweetr-0.1.24/epitweetr/R/check.R | 914 +-- epitweetr-0.1.24/epitweetr/R/config.R | 1240 ++-- epitweetr-0.1.24/epitweetr/R/dataviz.R | 1627 +++--- epitweetr-0.1.24/epitweetr/R/geo-tagging.R | 1264 ++-- epitweetr-0.1.24/epitweetr/R/globals.R | 4 epitweetr-0.1.24/epitweetr/R/paths.R | 223 epitweetr-0.1.24/epitweetr/R/scheduler.R | 1318 ++--- epitweetr-0.1.24/epitweetr/R/search.R | 858 +-- epitweetr-0.1.24/epitweetr/R/shiny-app.R |only epitweetr-0.1.24/epitweetr/R/spark-bridge.R | 541 +- epitweetr-0.1.24/epitweetr/R/text-mining.R | 123 epitweetr-0.1.24/epitweetr/R/twitter-api.R | 273 - epitweetr-0.1.24/epitweetr/build/vignette.rds |binary epitweetr-0.1.24/epitweetr/inst/doc/epitweetr-vignette.R | 398 - epitweetr-0.1.24/epitweetr/inst/doc/epitweetr-vignette.Rmd | 2585 +++++----- epitweetr-0.1.24/epitweetr/inst/doc/epitweetr-vignette.html | 2376 +++++---- epitweetr-0.1.24/epitweetr/inst/extdata/detect.R | 26 epitweetr-0.1.24/epitweetr/inst/extdata/mail.html | 38 epitweetr-0.1.24/epitweetr/inst/extdata/sbt-deps.txt | 432 - epitweetr-0.1.24/epitweetr/inst/extdata/search.R | 24 epitweetr-0.1.24/epitweetr/inst/extdata/topics.xlsx |binary epitweetr-0.1.24/epitweetr/inst/java/README | 2 epitweetr-0.1.24/epitweetr/inst/java/ecdc-twitter-bundle_2.12-1.0.jar |binary epitweetr-0.1.24/epitweetr/inst/rmarkdown/dashboard.Rmd | 170 epitweetr-0.1.24/epitweetr/java/README | 36 epitweetr-0.1.24/epitweetr/java/ecdc-twitter-bundle_2.12-1.0-source.zip |binary epitweetr-0.1.24/epitweetr/man/aggregate_tweets.Rd | 4 epitweetr-0.1.24/epitweetr/man/check_all.Rd | 2 epitweetr-0.1.24/epitweetr/man/create_map.Rd | 2 epitweetr-0.1.24/epitweetr/man/epitweetr_app.Rd | 2 epitweetr-0.1.24/epitweetr/man/generate_alerts.Rd | 2 epitweetr-0.1.24/epitweetr/man/geotag_tweets.Rd | 2 epitweetr-0.1.24/epitweetr/man/get_aggregates.Rd | 4 epitweetr-0.1.24/epitweetr/man/search_loop.Rd | 2 epitweetr-0.1.24/epitweetr/man/setup_config.Rd | 4 epitweetr-0.1.24/epitweetr/vignettes/epitweetr-vignette.Rmd | 2585 +++++----- epitweetr-0.1.24/epitweetr/vignettes/epitweetr_refs.bib | 186 42 files changed, 10402 insertions(+), 9722 deletions(-)
Title: Inference of Gene Regulatory Networks
Description: We present 'corto' (Correlation Tool), a simple package to infer
gene regulatory networks and visualize master regulators from gene expression
data using DPI (Data Processing Inequality) and bootstrapping to recover edges.
An initial step is performed to calculate all significant
edges between a list of source nodes (centroids) and target genes.
Then all triplets containing two centroids and one target are tested
in a DPI step which removes edges. A bootstrapping process then calculates
the robustness of the network, eventually re-adding edges previously removed by DPI.
The algorithm has been optimized to run outside a computing cluster, using a fast correlation
implementation. The package finally provides functions to calculate network enrichment
analysis from RNA-Seq and ATAC-Seq signatures as described in the article by
Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.
Author: Federico M. Giorgi [aut, cre],
Daniele Mercatelli [ctb],
Gonzalo Lopez-Garcia [ctb]
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>
Diff between corto versions 1.1.2 dated 2020-10-13 and 1.1.3 dated 2020-10-23
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/functions.R | 7 +++++-- R/mra.R | 3 ++- inst/doc/corto_vignette.html | 2 +- man/scatter.Rd | 3 +++ 6 files changed, 19 insertions(+), 12 deletions(-)
Title: Miscellaneous Functions for Processing and Sample Selection of
Spectroscopic Data
Description: Functions to preprocess spectroscopic data
and conduct (representative) sample selection/calibration sampling.
Author: Antoine Stevens [aut, cre] (<https://orcid.org/0000-0002-1588-7519>),
Leonardo Ramirez-Lopez [aut, cre] (<https://orcid.org/0000-0002-5369-5120>),
Guillaume Hans [ctb] (<https://orcid.org/0000-0002-6503-5760>)
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between prospectr versions 0.2.0 dated 2020-03-14 and 0.2.1 dated 2020-10-23
prospectr-0.2.0/prospectr/R/mTransformation.R |only prospectr-0.2.0/prospectr/man/ResampleCppM.Rd |only prospectr-0.2.0/prospectr/man/dot-get_nircal_comments.Rd |only prospectr-0.2.0/prospectr/man/dot-get_nircal_description.Rd |only prospectr-0.2.0/prospectr/man/dot-get_nircal_indices.Rd |only prospectr-0.2.0/prospectr/man/dot-get_nircal_lengthspc.Rd |only prospectr-0.2.0/prospectr/man/dot-get_nircal_metadata.Rd |only prospectr-0.2.0/prospectr/man/dot-get_nircal_response.Rd |only prospectr-0.2.0/prospectr/man/dot-get_nircal_spectra.Rd |only prospectr-0.2.0/prospectr/src/Resample.cpp |only prospectr-0.2.0/prospectr/src/bitwise.cpp |only prospectr-0.2.0/prospectr/src/conv.cpp |only prospectr-0.2.0/prospectr/src/fastDist.cpp |only prospectr-0.2.0/prospectr/src/residLm.cpp |only prospectr-0.2.0/prospectr/vignettes/one.bib |only prospectr-0.2.1/prospectr/DESCRIPTION | 24 prospectr-0.2.1/prospectr/LICENSE |only prospectr-0.2.1/prospectr/MD5 | 182 - prospectr-0.2.1/prospectr/NAMESPACE | 5 prospectr-0.2.1/prospectr/NEWS | 14 prospectr-0.2.1/prospectr/R/AAA.R | 15 prospectr-0.2.1/prospectr/R/Cul.R | 10 prospectr-0.2.1/prospectr/R/NIRsoil.R | 36 prospectr-0.2.1/prospectr/R/RcppExports.R | 45 prospectr-0.2.1/prospectr/R/binning.R | 136 prospectr-0.2.1/prospectr/R/blockNorm.R | 112 prospectr-0.2.1/prospectr/R/blockScale.R | 60 prospectr-0.2.1/prospectr/R/cochranTest.R | 181 - prospectr-0.2.1/prospectr/R/continuumRemoval.R | 180 - prospectr-0.2.1/prospectr/R/detrend.R | 146 - prospectr-0.2.1/prospectr/R/duplex.R | 367 +- prospectr-0.2.1/prospectr/R/e2m.R |only prospectr-0.2.1/prospectr/R/gapDer.R | 181 - prospectr-0.2.1/prospectr/R/honigs.R | 206 - prospectr-0.2.1/prospectr/R/kenstone.R | 299 +- prospectr-0.2.1/prospectr/R/movav.R | 98 prospectr-0.2.1/prospectr/R/msc.R |only prospectr-0.2.1/prospectr/R/naes.R | 239 - prospectr-0.2.1/prospectr/R/prospectr.R | 111 prospectr-0.2.1/prospectr/R/puchwein.R | 276 + prospectr-0.2.1/prospectr/R/readASD.R | 1059 +++---- prospectr-0.2.1/prospectr/R/read_nircal.R | 1018 ++++--- prospectr-0.2.1/prospectr/R/resample.R | 98 prospectr-0.2.1/prospectr/R/resample2.R | 108 prospectr-0.2.1/prospectr/R/savitzkyGolay.R | 163 - prospectr-0.2.1/prospectr/R/shenkWest.R | 169 - prospectr-0.2.1/prospectr/R/spliceCorrection.R | 117 prospectr-0.2.1/prospectr/R/standardNormalVariate.R | 59 prospectr-0.2.1/prospectr/README.md |only prospectr-0.2.1/prospectr/build/prospectr.pdf |only prospectr-0.2.1/prospectr/build/vignette.rds |binary prospectr-0.2.1/prospectr/inst/doc/prospectr.R | 147 - prospectr-0.2.1/prospectr/inst/doc/prospectr.Rmd | 467 ++- prospectr-0.2.1/prospectr/inst/doc/prospectr.html | 1661 +++++++----- prospectr-0.2.1/prospectr/man/NIRsoil.Rd | 32 prospectr-0.2.1/prospectr/man/binning.Rd | 57 prospectr-0.2.1/prospectr/man/blockNorm.Rd | 28 prospectr-0.2.1/prospectr/man/blockScale.Rd | 30 prospectr-0.2.1/prospectr/man/cochranTest.Rd | 61 prospectr-0.2.1/prospectr/man/continuumRemoval.Rd | 63 prospectr-0.2.1/prospectr/man/detrend.Rd | 74 prospectr-0.2.1/prospectr/man/duplex.Rd | 114 prospectr-0.2.1/prospectr/man/e2m.Rd | 30 prospectr-0.2.1/prospectr/man/figures |only prospectr-0.2.1/prospectr/man/gapDer.Rd | 71 prospectr-0.2.1/prospectr/man/get_msc_coeff.Rd |only prospectr-0.2.1/prospectr/man/get_nircal_comments.Rd |only prospectr-0.2.1/prospectr/man/get_nircal_description.Rd |only prospectr-0.2.1/prospectr/man/get_nircal_indices.Rd |only prospectr-0.2.1/prospectr/man/get_nircal_lengthspc.Rd |only prospectr-0.2.1/prospectr/man/get_nircal_metadata.Rd |only prospectr-0.2.1/prospectr/man/get_nircal_response.Rd |only prospectr-0.2.1/prospectr/man/get_nircal_spectra.Rd |only prospectr-0.2.1/prospectr/man/honigs.Rd | 99 prospectr-0.2.1/prospectr/man/kenStone.Rd | 125 prospectr-0.2.1/prospectr/man/movav.Rd | 35 prospectr-0.2.1/prospectr/man/msc.Rd |only prospectr-0.2.1/prospectr/man/naes.Rd | 110 prospectr-0.2.1/prospectr/man/prospectr-package.Rd | 92 prospectr-0.2.1/prospectr/man/puchwein.Rd | 136 prospectr-0.2.1/prospectr/man/readASD.Rd | 45 prospectr-0.2.1/prospectr/man/read_nircal.Rd | 35 prospectr-0.2.1/prospectr/man/resample.Rd | 27 prospectr-0.2.1/prospectr/man/resample2.Rd | 43 prospectr-0.2.1/prospectr/man/resample_fwhm.Rd |only prospectr-0.2.1/prospectr/man/savitzkyGolay.Rd | 81 prospectr-0.2.1/prospectr/man/shenkWest.Rd | 78 prospectr-0.2.1/prospectr/man/spliceCorrection.Rd | 16 prospectr-0.2.1/prospectr/man/sqrtSm.Rd | 2 prospectr-0.2.1/prospectr/man/standardNormalVariate.Rd | 44 prospectr-0.2.1/prospectr/src/Makevars | 7 prospectr-0.2.1/prospectr/src/RcppExports.cpp | 73 prospectr-0.2.1/prospectr/src/processing_helpers.cpp |only prospectr-0.2.1/prospectr/tests |only prospectr-0.2.1/prospectr/vignettes/logo.jpg |only prospectr-0.2.1/prospectr/vignettes/prospectr.Rmd | 467 ++- prospectr-0.2.1/prospectr/vignettes/prospectr.bib |only 97 files changed, 6160 insertions(+), 3904 deletions(-)
Title: Setup and connect to 'OpenTripPlanner'
Description: Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>.
OTP is an open source platform for multi-modal and multi-agency
journey planning written in 'Java'. The package allows you to manage a local version or
connect to remote OTP server.
This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).
Author: Malcolm Morgan [aut, cre] (<https://orcid.org/0000-0002-9488-9183>),
Marcus Young [aut] (<https://orcid.org/0000-0003-4627-1116>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Layik Hama [ctb] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Malcolm Morgan <m.morgan1@leeds.ac.uk>
Diff between opentripplanner versions 0.2.3.0 dated 2020-06-09 and 0.3.0 dated 2020-10-23
DESCRIPTION | 11 - MD5 | 70 +++---- NEWS.md | 24 ++ R/data.R | 11 - R/otp-config.R | 34 ++- R/otp-connect.R | 30 ++- R/otp-download.R | 52 ++++- R/otp-geocode.R | 13 - R/otp-isochrone-batch.R | 113 +++++------ R/otp-plan.R | 307 ++++++++++---------------------- R/otp-routing-options.R | 301 +++++++++++++++---------------- R/otp-setup.R | 9 R/utility-functions.R |only README.md | 7 data/json_example_drive.rda |binary data/json_example_long_drive.rda |only data/json_example_transit.rda |binary inst/doc/advanced_features.R | 1 inst/doc/advanced_features.Rmd | 14 + inst/doc/advanced_features.html | 17 + inst/doc/known_issues.html | 4 inst/doc/opentripplanner.R | 9 inst/doc/opentripplanner.Rmd | 58 +++--- inst/doc/opentripplanner.html | 124 ++++++------ inst/doc/prerequisites.Rmd | 4 inst/doc/prerequisites.html | 8 man/json_example_drive.Rd | 2 man/json_example_long_drive.Rd |only man/json_example_transit.Rd | 2 man/otp_dl_jar.Rd | 14 + man/otp_plan.Rd | 11 - tests/testthat/test_01_internal_funcs.R | 55 +++-- tests/testthat/test_02_without_OTP.R | 23 +- tests/testthat/test_03_with_OTP.R | 101 +++++++--- vignettes/advanced_features.Rmd | 14 + vignettes/images/msoa.JPG |only vignettes/opentripplanner.Rmd | 58 +++--- vignettes/prerequisites.Rmd | 4 38 files changed, 794 insertions(+), 711 deletions(-)
More information about opentripplanner at CRAN
Permanent link
Title: Tests in Linear Mixed Effects Models
Description: Provides p-values in type I, II or III anova and summary tables
for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A
Kenward-Roger method is also available via the pbkrtest package. Model selection
methods include step, drop1 and anova-like tables for random effects (ranova).
Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed
effects are also available.
Author: Alexandra Kuznetsova [aut],
Per Bruun Brockhoff [aut, ths],
Rune Haubo Bojesen Christensen [aut, cre],
Sofie Pødenphant Jensen [ctb]
Maintainer: Rune Haubo Bojesen Christensen <Rune.Haubo@gmail.com>
Diff between lmerTest versions 3.1-2 dated 2020-04-08 and 3.1-3 dated 2020-10-23
DESCRIPTION | 20 ++++++++++---------- MD5 | 23 ++++++++++++----------- NEWS.md | 7 +++++++ R/contrast_utils.R | 4 ++-- R/drop1.R | 2 +- R/lmerTest.R | 2 +- R/ranova.R | 14 +++++++------- R/step.R | 7 ++++--- R/terms_utils.R | 1 - R/utils.R | 4 +++- man/lmerTest-package.Rd | 2 +- tests/test_contrast_utils.R |only tests/test_ranova_step.R | 19 ++++++++++++++++++- 13 files changed, 66 insertions(+), 39 deletions(-)
Title: Computation and Plots of Influence Functions for Risk and
Performance Measures
Description: Computes the influence functions time series of the returns for the risk and
performance measures as mentioned in Chen and Martin (2018)
<https://www.ssrn.com/abstract=3085672>, as well as in Zhang et al. (2019)
<https://www.ssrn.com/abstract=3415903>. Also evaluates estimators influence
functions at a set of parameter values and plots them to display the shapes of
the influence functions.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Shengyu Zhang <syzhang@uw.edu>,
Douglas Martin <doug@amath.washington.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPEIF versions 1.0.8 dated 2020-04-23 and 1.1.0 dated 2020-10-23
RPEIF-1.0.8/RPEIF/R/IF_Omega.R |only RPEIF-1.0.8/RPEIF/R/IF_Rachev.R |only RPEIF-1.0.8/RPEIF/R/InfluenceFunctions_R.R |only RPEIF-1.0.8/RPEIF/R/RiskPerformanceMeasure_Functions_R.R |only RPEIF-1.0.8/RPEIF/R/RobustFilter_R.R |only RPEIF-1.0.8/RPEIF/man/IF.Omega.Rd |only RPEIF-1.0.8/RPEIF/man/IF.RachR.Rd |only RPEIF-1.1.0/RPEIF/DESCRIPTION | 18 RPEIF-1.1.0/RPEIF/MD5 | 75 +- RPEIF-1.1.0/RPEIF/NAMESPACE | 5 RPEIF-1.1.0/RPEIF/NEWS.md | 12 RPEIF-1.1.0/RPEIF/R/DataCheck.R |only RPEIF-1.1.0/RPEIF/R/EvaluateShape.R |only RPEIF-1.1.0/RPEIF/R/IF_DSR.R |only RPEIF-1.1.0/RPEIF/R/IF_ES.R | 173 +----- RPEIF-1.1.0/RPEIF/R/IF_ESRatio.R | 181 +----- RPEIF-1.1.0/RPEIF/R/IF_LPM.R | 269 ++------- RPEIF-1.1.0/RPEIF/R/IF_OmegaRatio.R |only RPEIF-1.1.0/RPEIF/R/IF_RachevRatio.R |only RPEIF-1.1.0/RPEIF/R/IF_SD.R | 157 +---- RPEIF-1.1.0/RPEIF/R/IF_SR.R | 171 +----- RPEIF-1.1.0/RPEIF/R/IF_SemiSD.R | 183 +----- RPEIF-1.1.0/RPEIF/R/IF_SoR.R | 419 +++++---------- RPEIF-1.1.0/RPEIF/R/IF_VaR.R | 167 +---- RPEIF-1.1.0/RPEIF/R/IF_VaRratio.R | 179 +----- RPEIF-1.1.0/RPEIF/R/IF_mean.R | 163 +---- RPEIF-1.1.0/RPEIF/R/InfluenceFunctions.R |only RPEIF-1.1.0/RPEIF/R/NuisanceData.R |only RPEIF-1.1.0/RPEIF/R/Nuisance_Parameters.R | 74 +- RPEIF-1.1.0/RPEIF/R/RiskPerformanceMeasure_Functions.R |only RPEIF-1.1.0/RPEIF/R/RobustFilter.R |only RPEIF-1.1.0/RPEIF/README.md | 12 RPEIF-1.1.0/RPEIF/data |only RPEIF-1.1.0/RPEIF/inst/doc/RPEIFVignette.pdf |binary RPEIF-1.1.0/RPEIF/man/IF.DSR.Rd |only RPEIF-1.1.0/RPEIF/man/IF.ES.Rd | 29 - RPEIF-1.1.0/RPEIF/man/IF.ESratio.Rd | 29 - RPEIF-1.1.0/RPEIF/man/IF.LPM.Rd | 29 - RPEIF-1.1.0/RPEIF/man/IF.OmegaRatio.Rd |only RPEIF-1.1.0/RPEIF/man/IF.RachevRatio.Rd |only RPEIF-1.1.0/RPEIF/man/IF.Rd | 33 - RPEIF-1.1.0/RPEIF/man/IF.SD.Rd | 27 RPEIF-1.1.0/RPEIF/man/IF.SR.Rd | 29 - RPEIF-1.1.0/RPEIF/man/IF.SemiSD.Rd | 32 - RPEIF-1.1.0/RPEIF/man/IF.SoR.Rd | 35 - RPEIF-1.1.0/RPEIF/man/IF.VaR.Rd | 29 - RPEIF-1.1.0/RPEIF/man/IF.VaRratio.Rd | 29 - RPEIF-1.1.0/RPEIF/man/IF.mean.Rd | 29 - RPEIF-1.1.0/RPEIF/man/edhec.Rd |only 49 files changed, 797 insertions(+), 1791 deletions(-)
Title: Power and Sample Size for (Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used in bioequivalence studies. Use known.designs() to
see the designs supported. Power and sample size can be obtained based on
different methods, amongst them prominently the TOST procedure (two one-sided t-tests).
See README and NEWS for further information.
Author: Detlew Labes [aut, cre] (<https://orcid.org/0000-0003-2169-426X>),
Helmut Schütz [aut] (<https://orcid.org/0000-0002-1167-7880>),
Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.5-0 dated 2020-08-05 and 1.5-1 dated 2020-10-23
DESCRIPTION | 18 MD5 | 150 +-- NEWS.md | 32 R/SampleSize.R | 28 R/SampleSize_HVNTID.R | 8 R/expSampleSize.R | 20 R/exppower.R | 14 R/power.R | 11 R/power_TOST_sim.R | 14 R/power_scABEL2.R | 2 R/sampleN.RSABE2L.sdsims.R | 8 R/sampleN.scABEL.ad.R | 1 R/sampleN.scABEL.sdsims.R | 9 R/sampleN_2TOST_sim.R | 1 R/samplesize_RSABE.R | 11 R/samplesize_RSABE_NTID.R | 4 R/samplesize_scABEL.R | 8 R/samplesize_scABEL2.R | 2 R/scABEL.ad.R | 1 README.md | 462 ++++++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ABE.R | 189 ++-- inst/doc/ABE.Rmd | 389 +++++---- inst/doc/ABE.html | 659 +++++++++------ inst/doc/DP.R | 20 inst/doc/DP.Rmd | 54 - inst/doc/DP.html | 139 ++- inst/doc/Expected_Power_for_TOST.pdf |binary inst/doc/NI.R | 18 inst/doc/NI.Rmd | 78 - inst/doc/NI.html | 133 ++- inst/doc/PA.R | 12 inst/doc/PA.Rmd | 91 +- inst/doc/PA.html | 151 ++- inst/doc/RSABE.Rmd | 88 -- inst/doc/RSABE.html | 1508 +++++++++++++++-------------------- inst/doc/vignette.R | 64 + inst/doc/vignette.Rmd | 174 ++-- inst/doc/vignette.html | 324 ++++--- man/CI.RatioF.Rd | 2 man/CVfromCI.Rd | 2 man/CVpooled.Rd | 2 man/CVwRfromU.Rd | 2 man/expsampleN.TOST.Rd | 2 man/expsampleN.noninf.Rd | 4 man/pa.NTIDFDA.Rd | 2 man/power.HVNTID.Rd | 2 man/power.NTIDFDA.Rd | 2 man/power.RSABE.Rd | 2 man/power.RSABE2L.sdsims.Rd | 2 man/power.RatioF.Rd | 8 man/power.TOST.sds.Rd | 2 man/power.TOST.sim.Rd | 2 man/power.dp.Rd | 2 man/power.scABEL.Rd | 2 man/power.scABEL.sdsims.Rd | 2 man/pvalue.TOST.Rd | 2 man/sampleN.2TOST.Rd | 6 man/sampleN.NTIDFDA.Rd | 2 man/sampleN.RSABE.Rd | 4 man/sampleN.RSABE2L.sdsims.Rd | 2 man/sampleN.RatioF.Rd | 10 man/sampleN.TOST.Rd | 4 man/sampleN.dp.Rd | 2 man/sampleN.noninf.Rd | 2 man/sampleN.scABEL.Rd | 4 man/sampleN.scABEL.ad.Rd | 2 man/sampleN.scABEL.sdsims.Rd | 4 man/scABEL.ad.Rd | 2 vignettes/ABE.Rmd | 389 +++++---- vignettes/DP.Rmd | 54 - vignettes/NI.Rmd | 78 - vignettes/PA.Rmd | 91 +- vignettes/RSABE.Rmd | 88 -- vignettes/vignette.Rmd | 174 ++-- 76 files changed, 3426 insertions(+), 2431 deletions(-)
Title: An R Package for Estimating a Group-Effect in Latent Class
Analysis
Description: Fits latent class analysis (LCA) including group variable and covariates.
The group variable can be handled either by multilevel LCA described in Vermunt (2003) <DOI:10.1111/j.0081-1750.2003.t01-1-00131.x> or standard LCA at each level of group variable.
The covariates can be incorporated in the form of logistic regression (Bandeen-Roche et al. (1997) <DOI:10.1080/01621459.1997.10473658>).
Author: Youngsun Kim [aut, cre],
Hwan Chung [aut]
Maintainer: Youngsun Kim <kim0sun@korea.ac.kr>
Diff between glca versions 1.0.2 dated 2020-10-20 and 1.1.0 dated 2020-10-23
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 3 --- R/coef.glca.R | 10 +++++----- R/glca.R | 49 +++++++++++++++++++++++++------------------------ R/glca.gof.R | 16 ++++++++-------- R/item.R | 4 ++-- R/plot.glca.R | 6 +++--- build/partial.rdb |binary man/coef.glca.Rd | 10 +++++----- man/glca.Rd | 49 +++++++++++++++++++++++++------------------------ man/glca.gof.Rd | 16 ++++++++-------- man/item.Rd | 4 ++-- man/plot.glca.Rd | 6 +++--- 14 files changed, 103 insertions(+), 104 deletions(-)
Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor
(Pya and Wood, 2015) <doi:10.1007/s11222-013-9448-7>.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of gam()
in package 'mgcv' are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-7 dated 2020-09-24 and 1.2-8 dated 2020-10-23
ChangeLog | 5 ++++- DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/predict.scam.R | 2 +- build/partial.rdb |binary man/predict.scam.Rd | 2 +- 6 files changed, 15 insertions(+), 12 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] (<https://orcid.org/0000-0001-8316-9503>),
Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>),
Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>),
Steven Walker [aut] (<https://orcid.org/0000-0002-4394-9078>),
Rune Haubo Bojesen Christensen [ctb]
(<https://orcid.org/0000-0002-4494-3399>),
Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>),
Bin Dai [ctb],
Fabian Scheipl [ctb] (<https://orcid.org/0000-0001-8172-3603>),
Gabor Grothendieck [ctb],
Peter Green [ctb] (<https://orcid.org/0000-0002-0238-9852>),
John Fox [ctb],
Alexander Bauer [ctb],
Pavel N. Krivitsky [ctb, cph] (<https://orcid.org/0000-0002-9101-3362>,
shared copyright on simulate.formula)
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-23 dated 2020-04-07 and 1.1-25 dated 2020-10-23
lme4-1.1-23/lme4/inst/doc/lme4 |only lme4-1.1-23/lme4/inst/testdata/Rplots.pdf |only lme4-1.1-23/lme4/inst/testdata/badhess.RData |only lme4-1.1-23/lme4/inst/testdata/lme-tst-fits.Rout |only lme4-1.1-23/lme4/inst/testdata/tmp.txt |only lme4-1.1-23/lme4/inst/vignettedata |only lme4-1.1-23/lme4/tests/Rplots.pdf |only lme4-1.1-23/lme4/tests/devfunQ.R |only lme4-1.1-23/lme4/tests/lme-tst-fits.rda |only lme4-1.1-23/lme4/tests/mkRout |only lme4-1.1-23/lme4/tests/refit_allequal.RData |only lme4-1.1-23/lme4/tests/savecopy.rda |only lme4-1.1-23/lme4/tests/test_times.R |only lme4-1.1-23/lme4/tests/test_timings.RData |only lme4-1.1-23/lme4/tests/testthat/test-methods.Rout |only lme4-1.1-23/lme4/tests/utils.R |only lme4-1.1-23/lme4/vignettes/lmerperf.md |only lme4-1.1-25/lme4/DESCRIPTION | 20 lme4-1.1-25/lme4/LICENSE.note |only lme4-1.1-25/lme4/MD5 | 138 +++--- lme4-1.1-25/lme4/NAMESPACE | 8 lme4-1.1-25/lme4/R/lmer.R | 69 +-- lme4-1.1-25/lme4/R/modular.R | 1 lme4-1.1-25/lme4/R/nbinom.R | 18 lme4-1.1-25/lme4/R/predict.R | 75 ++- lme4-1.1-25/lme4/R/profile.R | 2 lme4-1.1-25/lme4/R/simulate.formula.R |only lme4-1.1-25/lme4/R/sparsegrid.R | 23 - lme4-1.1-25/lme4/R/utilities.R | 58 -- lme4-1.1-25/lme4/build/partial.rdb |binary lme4-1.1-25/lme4/build/vignette.rds |binary lme4-1.1-25/lme4/inst/NEWS.Rd | 59 ++ lme4-1.1-25/lme4/inst/doc/PLSvGLS.R |only lme4-1.1-25/lme4/inst/doc/PLSvGLS.Rnw |only lme4-1.1-25/lme4/inst/doc/PLSvGLS.pdf |binary lme4-1.1-25/lme4/inst/doc/Theory.R |only lme4-1.1-25/lme4/inst/doc/Theory.Rnw |only lme4-1.1-25/lme4/inst/doc/Theory.pdf |binary lme4-1.1-25/lme4/inst/doc/lmer.R |only lme4-1.1-25/lme4/inst/doc/lmer.Rnw |only lme4-1.1-25/lme4/inst/doc/lmer.pdf |binary lme4-1.1-25/lme4/inst/doc/lmerperf.R |only lme4-1.1-25/lme4/inst/doc/lmerperf.Rmd |only lme4-1.1-25/lme4/inst/doc/lmerperf.html | 326 ++++++++++++++-- lme4-1.1-25/lme4/man/allFit.Rd | 46 +- lme4-1.1-25/lme4/man/bootMer.Rd | 6 lme4-1.1-25/lme4/man/confint.merMod.Rd | 5 lme4-1.1-25/lme4/man/convergence.Rd | 7 lme4-1.1-25/lme4/man/glmer.Rd | 2 lme4-1.1-25/lme4/man/glmer.nb.Rd | 8 lme4-1.1-25/lme4/man/grouseticks.Rd | 2 lme4-1.1-25/lme4/man/influence.merMod.Rd | 35 - lme4-1.1-25/lme4/man/lme4_testlevel.Rd |only lme4-1.1-25/lme4/man/profile-methods.Rd | 8 lme4-1.1-25/lme4/man/pvalues.Rd | 3 lme4-1.1-25/lme4/man/simulate.formula.Rd |only lme4-1.1-25/lme4/man/simulate.merMod.Rd | 12 lme4-1.1-25/lme4/src/external.cpp | 10 lme4-1.1-25/lme4/src/optimizer.h | 6 lme4-1.1-25/lme4/tests/fewlevels.R | 3 lme4-1.1-25/lme4/tests/lmer-1.R | 11 lme4-1.1-25/lme4/tests/lmer-1.Rout.save | 35 - lme4-1.1-25/lme4/tests/nlmer.R | 9 lme4-1.1-25/lme4/tests/nlmer.Rout.save | 25 - lme4-1.1-25/lme4/tests/polytomous.R | 2 lme4-1.1-25/lme4/tests/profile-tst.R | 3 lme4-1.1-25/lme4/tests/refit.R | 3 lme4-1.1-25/lme4/tests/simulate.R | 3 lme4-1.1-25/lme4/tests/testthat/test-allFit.R | 3 lme4-1.1-25/lme4/tests/testthat/test-formulaEval.R | 46 +- lme4-1.1-25/lme4/tests/testthat/test-glmer.R | 4 lme4-1.1-25/lme4/tests/testthat/test-glmernb.R | 4 lme4-1.1-25/lme4/tests/testthat/test-lmer.R | 64 +++ lme4-1.1-25/lme4/tests/testthat/test-methods.R | 15 lme4-1.1-25/lme4/tests/testthat/test-nbinom.R | 15 lme4-1.1-25/lme4/tests/testthat/test-nlmer.R | 4 lme4-1.1-25/lme4/tests/testthat/test-predict.R | 31 + lme4-1.1-25/lme4/tests/testthat/test-simulate_formula.R |only lme4-1.1-25/lme4/vignettes/Theory.Rnw | 29 - lme4-1.1-25/lme4/vignettes/lmer.Rnw | 2 80 files changed, 887 insertions(+), 371 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-18 1.0.5
2017-08-14 1.0.4
2017-05-11 1.0.3
2017-02-20 1.0.2
2017-02-06 1.0.1
2017-01-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-07 2.7-1
2019-03-25 2.7-0
2018-03-19 2.6-3
2017-11-28 2.5-1
2017-03-26 2.4-0
2016-09-18 2.3-0
2016-06-30 2.2-5
2015-12-10 2.2-4
2015-10-01 2.2.3
2015-09-17 2.2.2
2015-07-14 2.2.1
2015-03-11 2.2.0
2014-11-01 2.1.2
2014-05-13 2.1.1
2014-03-19 2.1.0
2013-11-19 2.0.5
2013-05-29 2.0.3
2012-12-17 1.2.4
2012-11-15 1.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-14 1.5.1
2017-02-20 1.5
2016-07-07 1.4
2016-06-15 1.3
2016-06-14 1.2
2016-06-13 1.1
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. The central algorithm is
Fisher scoring and iterative reweighted least squares.
At the heart of this package are the vector generalized linear
and additive model (VGLM/VGAM) classes. VGLMs can be loosely
thought of as multivariate GLMs. VGAMs are data-driven
VGLMs that use smoothing. The book "Vector Generalized
Linear and Additive Models: With an Implementation in R"
(Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of
the statistical framework and the package. Currently only
fixed-effects models are implemented. Many (150+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE. The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CAO). Hauck-Donner effect detection is implemented.
Note that these functions are subject to change;
see the NEWS and ChangeLog files for latest changes.
Author: Thomas Yee [aut, cre],
Cleve Moler [ctb] (author of several LINPACK routines)
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 1.1-3 dated 2020-04-28 and 1.1-4 dated 2020-10-23
VGAM-1.1-3/VGAM/build/vignette.rds |only VGAM-1.1-3/VGAM/inst/doc |only VGAM-1.1-3/VGAM/man/gabinomial.mlm.Rd |only VGAM-1.1-3/VGAM/man/gaitbinom.mlmUC.Rd |only VGAM-1.1-3/VGAM/man/gaitlog.mix.Rd |only VGAM-1.1-3/VGAM/man/gaitnbinom.mixUC.Rd |only VGAM-1.1-3/VGAM/man/gaitnbinom.mlmUC.Rd |only VGAM-1.1-3/VGAM/man/gaitpoisson.mix.Rd |only VGAM-1.1-3/VGAM/man/gaitpoisson.mlm.Rd |only VGAM-1.1-3/VGAM/man/gatnbinomial.mix.Rd |only VGAM-1.1-3/VGAM/man/gatnbinomial.mlm.Rd |only VGAM-1.1-3/VGAM/man/genpoisUC.Rd |only VGAM-1.1-3/VGAM/man/genpoisson.Rd |only VGAM-1.1-3/VGAM/man/gtbinomial.Rd |only VGAM-1.1-3/VGAM/man/oalog.Rd |only VGAM-1.1-3/VGAM/man/oalogUC.Rd |only VGAM-1.1-3/VGAM/man/oapospoisUC.Rd |only VGAM-1.1-3/VGAM/man/oapospoisson.Rd |only VGAM-1.1-3/VGAM/man/oazeta.Rd |only VGAM-1.1-3/VGAM/man/oazetaUC.Rd |only VGAM-1.1-3/VGAM/man/oilog.Rd |only VGAM-1.1-3/VGAM/man/oilogUC.Rd |only VGAM-1.1-3/VGAM/man/oiposbinomUC.Rd |only VGAM-1.1-3/VGAM/man/oiposbinomial.Rd |only VGAM-1.1-3/VGAM/man/oipospoisUC.Rd |only VGAM-1.1-3/VGAM/man/oipospoisson.Rd |only VGAM-1.1-3/VGAM/man/oizeta.Rd |only VGAM-1.1-3/VGAM/man/oizetaUC.Rd |only VGAM-1.1-3/VGAM/man/oizipf.Rd |only VGAM-1.1-3/VGAM/man/oizipfUC.Rd |only VGAM-1.1-3/VGAM/man/otlog.Rd |only VGAM-1.1-3/VGAM/man/otlogUC.Rd |only VGAM-1.1-3/VGAM/man/otpospoisUC.Rd |only VGAM-1.1-3/VGAM/man/otpospoisson.Rd |only VGAM-1.1-3/VGAM/man/otzeta.Rd |only VGAM-1.1-3/VGAM/man/otzetaUC.Rd |only VGAM-1.1-3/VGAM/man/posbinomUC.Rd |only VGAM-1.1-3/VGAM/man/posnegbinUC.Rd |only VGAM-1.1-3/VGAM/man/pospoisUC.Rd |only VGAM-1.1-3/VGAM/vignettes |only VGAM-1.1-4/VGAM/BUGS | 9 VGAM-1.1-4/VGAM/DESCRIPTION | 16 VGAM-1.1-4/VGAM/MD5 | 253 VGAM-1.1-4/VGAM/NAMESPACE | 86 VGAM-1.1-4/VGAM/NEWS | 42 VGAM-1.1-4/VGAM/R/effects.vglm.q | 90 VGAM-1.1-4/VGAM/R/family.actuary.R | 16 VGAM-1.1-4/VGAM/R/family.aunivariate.R | 1078 - VGAM-1.1-4/VGAM/R/family.basics.R | 85 VGAM-1.1-4/VGAM/R/family.categorical.R | 4 VGAM-1.1-4/VGAM/R/family.extremes.R | 84 VGAM-1.1-4/VGAM/R/family.gait.R |14588 ++++++++++++++------------- VGAM-1.1-4/VGAM/R/family.glmgam.R | 12 VGAM-1.1-4/VGAM/R/family.maths.R | 22 VGAM-1.1-4/VGAM/R/family.nbd.R | 7 VGAM-1.1-4/VGAM/R/family.oneinf.R | 3075 +---- VGAM-1.1-4/VGAM/R/family.others.R | 2 VGAM-1.1-4/VGAM/R/family.positive.R | 384 VGAM-1.1-4/VGAM/R/family.qreg.R | 51 VGAM-1.1-4/VGAM/R/family.univariate.R | 1549 ++ VGAM-1.1-4/VGAM/R/family.zeroinf.R | 954 - VGAM-1.1-4/VGAM/R/hdeff.R | 56 VGAM-1.1-4/VGAM/R/lrp.R | 6 VGAM-1.1-4/VGAM/R/plot.vgam.R | 135 VGAM-1.1-4/VGAM/R/predict.vlm.q | 10 VGAM-1.1-4/VGAM/R/rootogram4.vglm.R | 284 VGAM-1.1-4/VGAM/R/rootogramsubset.R | 6 VGAM-1.1-4/VGAM/R/s.vam.q | 16 VGAM-1.1-4/VGAM/R/summary.vgam.q | 2 VGAM-1.1-4/VGAM/R/summary.vglm.q | 11 VGAM-1.1-4/VGAM/R/summary.vlm.q | 3 VGAM-1.1-4/VGAM/R/wald0.R | 212 VGAM-1.1-4/VGAM/build/partial.rdb |binary VGAM-1.1-4/VGAM/inst/CITATION | 12 VGAM-1.1-4/VGAM/man/CommonVGAMffArguments.Rd | 18 VGAM-1.1-4/VGAM/man/Influence.Rd |only VGAM-1.1-4/VGAM/man/Trunc.Rd |only VGAM-1.1-4/VGAM/man/VGAM-package.Rd | 9 VGAM-1.1-4/VGAM/man/acat.Rd | 2 VGAM-1.1-4/VGAM/man/alteredvglm.Rd | 49 VGAM-1.1-4/VGAM/man/anovavglm.Rd | 24 VGAM-1.1-4/VGAM/man/backPain.Rd | 2 VGAM-1.1-4/VGAM/man/biclaytoncop.Rd | 21 VGAM-1.1-4/VGAM/man/biclaytoncopUC.Rd | 4 VGAM-1.1-4/VGAM/man/binomialff.Rd | 2 VGAM-1.1-4/VGAM/man/binormalcop.Rd | 18 VGAM-1.1-4/VGAM/man/bistudentt.Rd | 6 VGAM-1.1-4/VGAM/man/bistudenttUC.Rd | 17 VGAM-1.1-4/VGAM/man/cao.Rd | 3 VGAM-1.1-4/VGAM/man/cratio.Rd | 2 VGAM-1.1-4/VGAM/man/cumulative.Rd | 2 VGAM-1.1-4/VGAM/man/dgaitplot.Rd |only VGAM-1.1-4/VGAM/man/diffzetaUC.Rd | 2 VGAM-1.1-4/VGAM/man/gaitbinomUC.Rd |only VGAM-1.1-4/VGAM/man/gaitlog.Rd |only VGAM-1.1-4/VGAM/man/gaitlogUC.Rd | 114 VGAM-1.1-4/VGAM/man/gaitnbinomUC.Rd |only VGAM-1.1-4/VGAM/man/gaitpoisUC.Rd | 194 VGAM-1.1-4/VGAM/man/gaitpoisson.Rd |only VGAM-1.1-4/VGAM/man/gaitzeta.Rd |only VGAM-1.1-4/VGAM/man/gaitzetaUC.Rd | 112 VGAM-1.1-4/VGAM/man/gengammaUC.Rd | 2 VGAM-1.1-4/VGAM/man/genpois0UC.Rd |only VGAM-1.1-4/VGAM/man/genpois1UC.Rd |only VGAM-1.1-4/VGAM/man/genpoisson0.Rd |only VGAM-1.1-4/VGAM/man/genpoisson1.Rd |only VGAM-1.1-4/VGAM/man/genpoisson2.Rd |only VGAM-1.1-4/VGAM/man/gompertzUC.Rd | 2 VGAM-1.1-4/VGAM/man/hdeff.Rd | 51 VGAM-1.1-4/VGAM/man/inv.gaussianff.Rd | 4 VGAM-1.1-4/VGAM/man/logUC.Rd | 9 VGAM-1.1-4/VGAM/man/logff.Rd | 9 VGAM-1.1-4/VGAM/man/lrt.stat.Rd | 8 VGAM-1.1-4/VGAM/man/lrtest.Rd | 11 VGAM-1.1-4/VGAM/man/multilogitlink.Rd | 6 VGAM-1.1-4/VGAM/man/multinomial.Rd | 4 VGAM-1.1-4/VGAM/man/negbinomial.Rd | 12 VGAM-1.1-4/VGAM/man/notdocumentedyet.Rd | 22 VGAM-1.1-4/VGAM/man/plotdgait.Rd |only VGAM-1.1-4/VGAM/man/plotrcim0.Rd | 5 VGAM-1.1-4/VGAM/man/poissonff.Rd | 13 VGAM-1.1-4/VGAM/man/posbernoulli.t.Rd | 2 VGAM-1.1-4/VGAM/man/posbinomial.Rd | 5 VGAM-1.1-4/VGAM/man/posnegbinomial.Rd | 25 VGAM-1.1-4/VGAM/man/pospoisson.Rd | 18 VGAM-1.1-4/VGAM/man/propodds.Rd | 2 VGAM-1.1-4/VGAM/man/rayleighUC.Rd | 2 VGAM-1.1-4/VGAM/man/round2.Rd |only VGAM-1.1-4/VGAM/man/score.stat.Rd | 50 VGAM-1.1-4/VGAM/man/specialsvglm.Rd | 15 VGAM-1.1-4/VGAM/man/sratio.Rd | 2 VGAM-1.1-4/VGAM/man/step4vglm.Rd | 14 VGAM-1.1-4/VGAM/man/summarypvgam.Rd | 2 VGAM-1.1-4/VGAM/man/summaryvglm.Rd | 10 VGAM-1.1-4/VGAM/man/tobit.Rd | 6 VGAM-1.1-4/VGAM/man/undocumented-methods.Rd | 16 VGAM-1.1-4/VGAM/man/vgam.Rd | 9 VGAM-1.1-4/VGAM/man/vglm.Rd | 2 VGAM-1.1-4/VGAM/man/vglmff-class.Rd | 4 VGAM-1.1-4/VGAM/man/wald.stat.Rd | 96 VGAM-1.1-4/VGAM/man/zabinomUC.Rd | 4 VGAM-1.1-4/VGAM/man/zanegbinUC.Rd | 12 VGAM-1.1-4/VGAM/man/zanegbinomial.Rd | 9 VGAM-1.1-4/VGAM/man/zapoisson.Rd | 21 VGAM-1.1-4/VGAM/man/zeta.Rd | 6 VGAM-1.1-4/VGAM/man/zetaUC.Rd | 6 VGAM-1.1-4/VGAM/man/zetaff.Rd | 11 VGAM-1.1-4/VGAM/man/zibinomUC.Rd | 4 VGAM-1.1-4/VGAM/man/zibinomial.Rd | 5 VGAM-1.1-4/VGAM/man/zipoisUC.Rd | 6 VGAM-1.1-4/VGAM/man/zipoisson.Rd | 3 151 files changed, 11396 insertions(+), 12890 deletions(-)