Wed, 14 Jul 2021

Package hardhat updated to version 0.1.6 with previous version 0.1.5 dated 2020-11-09

Title: Construct Modeling Packages
Description: Building modeling packages is hard. A large amount of effort generally goes into providing an implementation for a new method that is efficient, fast, and correct, but often less emphasis is put on the user interface. A good interface requires specialized knowledge about S3 methods and formulas, which the average package developer might not have. The goal of 'hardhat' is to reduce the burden around building new modeling packages by providing functionality for preprocessing, predicting, and validating input.
Author: Davis Vaughan [aut, cre], Max Kuhn [aut], RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>

Diff between hardhat versions 0.1.5 dated 2020-11-09 and 0.1.6 dated 2021-07-14

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 16 files changed, 99 insertions(+), 802 deletions(-)

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Package albatross updated to version 0.3-2 with previous version 0.3-1 dated 2021-04-03

Title: PARAFAC Analysis of Fluorescence Excitation-Emission Matrices
Description: Perform parallel factor analysis (PARAFAC: Hitchcock, 1927) <doi:10.1002/sapm192761164> on fluorescence excitation-emission matrices (FEEMs): handle scattering signal and inner filter effect, scale the dataset, fit the model; perform split-half validation or jack-knifing. A modified approach called "randomised split-half" is also available. The package has a low dependency footprint (only two direct dependencies not in core or recommended; four total non-core/recommended dependencies) and has been tested on a wide range of R versions (including R as old as 3.3.3 from Debian Stretch).
Author: Ivan Krylov [aut, cre], Timur Labutin [ths]
Maintainer: Ivan Krylov <ikrylov@laser.chem.msu.ru>

Diff between albatross versions 0.3-1 dated 2021-04-03 and 0.3-2 dated 2021-07-14

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Package sever updated to version 0.0.7 with previous version 0.0.6 dated 2020-10-19

Title: Customise 'Shiny' Disconnected Screens and Error Messages
Description: Customise 'Shiny' disconnected screens as well as sanitize error messages to make them clearer and friendlier to the user.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>

Diff between sever versions 0.0.6 dated 2020-10-19 and 0.0.7 dated 2021-07-14

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More information about sever at CRAN
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Package echarts4r updated to version 0.4.1 with previous version 0.4.0 dated 2021-03-07

Title: Create Interactive Graphs with 'Echarts JavaScript' Version 5
Description: Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.
Author: John Coene [aut, cre, cph], Wei Su [ctb], Helgasoft [ctb], Xianying Tan [ctb] (<https://orcid.org/0000-0002-6072-3521>), Robin Cura [ctb] (<https://orcid.org/0000-0001-5926-1828>)
Maintainer: John Coene <jcoenep@gmail.com>

Diff between echarts4r versions 0.4.0 dated 2021-03-07 and 0.4.1 dated 2021-07-14

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More information about echarts4r at CRAN
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Package packer updated to version 0.1.0 with previous version 0.0.6 dated 2020-10-20

Title: An Opinionated Framework for Using 'JavaScript'
Description: Enforces good practice and provides convenience functions to make work with 'JavaScript' not just easier but also scalable. It is a robust wrapper to 'NPM' and 'webpack' that enables to compartmentalize 'JavaScript' code, leverage 'NPM' packages, and much more.
Author: John Coene [aut, cre] (<https://orcid.org/0000-0002-6637-4107>)
Maintainer: John Coene <jcoenep@gmail.com>

Diff between packer versions 0.0.6 dated 2020-10-20 and 0.1.0 dated 2021-07-14

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Package mvdalab updated to version 1.6 with previous version 1.5 dated 2021-05-14

Title: Multivariate Data Analysis Laboratory
Description: An open-source implementation of latent variable methods and multivariate modeling tools. The focus is on exploratory analyses using dimensionality reduction methods including low dimensional embedding, classical multivariate statistical tools, and tools for enhanced interpretation of machine learning methods (i.e. intelligible models to provide important information for end-users). Target domains include extension to dedicated applications e.g. for manufacturing process modeling, spectroscopic analyses, and data mining.
Author: Nelson Lee Afanador, Thanh Tran, Lionel Blanchet, and Richard Baumgartner
Maintainer: Nelson Lee Afanador <nelson.afanador@gmail.com>

Diff between mvdalab versions 1.5 dated 2021-05-14 and 1.6 dated 2021-07-14

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Package volesti updated to version 1.1.2-2 with previous version 1.1.2 dated 2020-10-19

Title: Volume Approximation and Sampling of Convex Polytopes
Description: Provides an R interface for 'volesti' C++ package. 'volesti' computes estimations of volume of polytopes given by (i) a set of points, (ii) linear inequalities or (iii) Minkowski sum of segments (a.k.a. zonotopes). There are three algorithms for volume estimation as well as algorithms for sampling, rounding and rotating polytopes. Moreover, 'volesti' provides algorithms for estimating copulas useful in computational finance.
Author: Vissarion Fisikopoulos <vissarion.fisikopoulos@gmail.com> [aut, cph, cre], Apostolos Chalkis <tolis.chal@gmail.com> [cph, aut], contributors in file inst/AUTHORS
Maintainer: Vissarion Fisikopoulos <vissarion.fisikopoulos@gmail.com>

Diff between volesti versions 1.1.2 dated 2020-10-19 and 1.1.2-2 dated 2021-07-14

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 volesti-1.1.2-2/volesti/NEWS.md                        |   11 +++
 volesti-1.1.2-2/volesti/R/RcppExports.R                |   25 +--------
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Package postGGIR updated to version 2.4.0 with previous version 2.0.0 dated 2021-05-06

Title: Data Processing after Running 'GGIR' for Accelerometer Data
Description: Generate all necessary R/Rmd/shell files for data processing after running 'GGIR' (v2.4.0) for accelerometer data. In part 1, all csv files in the GGIR output directory were read, transformed and then merged. In part 2, the GGIR output files were checked and summarized in one excel sheet. In part 3, the merged data was cleaned according to the number of valid hours on each night and the number of valid days for each subject. In part 4, the cleaned activity data was imputed by the average Euclidean norm minus one (ENMO) over all the valid days for each subject. Finally, a comprehensive report of data processing was created using Rmarkdown, and the report includes few exploratory plots and multiple commonly used features extracted from minute level actigraphy data.
Author: Wei Guo [aut, cre], Vadim Zipunnikov [aut], Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>

Diff between postGGIR versions 2.0.0 dated 2021-05-06 and 2.4.0 dated 2021-07-14

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 MD5                                               |   22 ++++++++++-----------
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Package modeldata updated to version 0.1.1 with previous version 0.1.0 dated 2020-10-22

Title: Data Sets Used Useful for Modeling Packages
Description: Data sets used for demonstrating or testing model-related packages are contained in this package.
Author: Max Kuhn [aut, cre], RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>

Diff between modeldata versions 0.1.0 dated 2020-10-22 and 0.1.1 dated 2021-07-14

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Package incidence2 updated to version 1.2.1 with previous version 1.2.0 dated 2021-07-07

Title: Compute, Handle and Plot Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence2' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis (<https://www.reconverse.org>).
Author: Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>), Thibaut Jombart [ctb], Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>

Diff between incidence2 versions 1.2.0 dated 2021-07-07 and 1.2.1 dated 2021-07-14

 DESCRIPTION                              |    6 +++---
 MD5                                      |   14 +++++++-------
 NEWS.md                                  |    6 ++++++
 R/build_incidence.R                      |   12 ++++++------
 R/incidence.R                            |    4 ----
 R/make_grate.R                           |    7 +++++++
 inst/doc/handling_incidence_objects.html |   24 ++++++++++++------------
 tests/testthat/test-incidence.R          |    6 ++++--
 8 files changed, 45 insertions(+), 34 deletions(-)

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Package EpiCurve updated to version 2.4-2 with previous version 2.4-1 dated 2020-08-26

Title: Plot an Epidemic Curve
Description: Creates simple or stacked epidemic curves for hourly, daily, weekly or monthly outcome data.
Author: Jean Pierre Decorps [aut, cre]
Maintainer: Jean Pierre Decorps <jean.pierre.decorps@gmail.com>

Diff between EpiCurve versions 2.4-1 dated 2020-08-26 and 2.4-2 dated 2021-07-14

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 MD5                   |   10 ++++----
 R/EpiCurve..R         |   27 +++++++++--------------
 README.md             |    2 +
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 inst/doc/EpiCurve.pdf |binary
 6 files changed, 51 insertions(+), 55 deletions(-)

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Package baguette updated to version 0.1.1 with previous version 0.1.0 dated 2020-10-28

Title: Efficient Model Functions for Bagging
Description: Tree- and rule-based models can be bagged using this package and their predictions equations are stored in an efficient format to reduce the model objects size and speed.
Author: Max Kuhn [aut, cre] (<https://orcid.org/0000-0003-2402-136X>), RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>

Diff between baguette versions 0.1.0 dated 2020-10-28 and 0.1.1 dated 2021-07-14

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 MD5                        |   26 +++++++++++++-----------
 NEWS.md                    |    6 +++++
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Package stringi updated to version 1.7.2 with previous version 1.6.2 dated 2021-05-17

Title: Character String Processing Facilities
Description: A multitude of character string/text/natural language processing tools: pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date-time formatting and parsing, and many more. They are fast, consistent, convenient, and - thanks to 'ICU' (International Components for Unicode) - portable across all locales and platforms.
Author: Marek Gagolewski [aut, cre, cph] (<https://orcid.org/0000-0003-0637-6028>), Bartek Tartanus [ctb], and others (stringi source code); IBM, Unicode, Inc. and others (ICU4C source code, Unicode Character Database)
Maintainer: Marek Gagolewski <marek@gagolewski.com>

Diff between stringi versions 1.6.2 dated 2021-05-17 and 1.7.2 dated 2021-07-14

 DESCRIPTION                              |    8 
 MD5                                      |  301 ++++----
 NAMESPACE                                |    4 
 NEWS                                     |   89 ++
 R/encoding_management.R                  |    2 
 R/internal_prepare_arg.R                 |   56 -
 R/length.R                               |    6 
 R/pad.R                                  |    8 
 R/search.R                               |   34 
 R/search_count_4.R                       |    2 
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 R/search_extract_4.R                     |    2 
 R/search_locate_4.R                      |  276 ++++---
 R/search_locate_bound.R                  |  125 ++-
 R/search_match_4.R                       |   13 
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 R/search_subset_4.R                      |   51 -
 R/sprintf.R                              |  213 +++++-
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 R/time_calendar.R                        |    8 
 R/time_format.R                          |  157 +---
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 R/trans_transliterate.R                  |   47 +
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 src/stri_container_regex.cpp             |  237 ++++++
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 src/stri_encoding_management.cpp         |    2 
 src/stri_escape.cpp                      |   17 
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 src/stri_pad.cpp                         |   14 
 src/stri_prepare_arg.cpp                 | 1078 +++++++++++++++++++++----------
 src/stri_random.cpp                      |   13 
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 src/stri_search_coll_extract.cpp         |   10 
 src/stri_search_coll_locate.cpp          |   69 +
 src/stri_search_coll_replace.cpp         |   12 
 src/stri_search_coll_split.cpp           |   12 
 src/stri_search_coll_startsendswith.cpp  |   12 
 src/stri_search_coll_subset.cpp          |   99 +-
 src/stri_search_common.cpp               |   24 
 src/stri_search_fixed_count.cpp          |    4 
 src/stri_search_fixed_detect.cpp         |    6 
 src/stri_search_fixed_extract.cpp        |   10 
 src/stri_search_fixed_locate.cpp         |   71 +-
 src/stri_search_fixed_replace.cpp        |   28 
 src/stri_search_fixed_split.cpp          |   12 
 src/stri_search_fixed_startsendswith.cpp |   12 
 src/stri_search_fixed_subset.cpp         |   95 +-
 src/stri_search_in.cpp                   |   18 
 src/stri_search_other_split.cpp          |    8 
 src/stri_search_regex_count.cpp          |    4 
 src/stri_search_regex_detect.cpp         |    4 
 src/stri_search_regex_extract.cpp        |   10 
 src/stri_search_regex_locate.cpp         |  380 ++++++++--
 src/stri_search_regex_match.cpp          |   59 +
 src/stri_search_regex_replace.cpp        |  120 +++
 src/stri_search_regex_split.cpp          |   12 
 src/stri_search_regex_subset.cpp         |   91 +-
 src/stri_sort.cpp                        |   12 
 src/stri_sprintf.cpp                     |only
 src/stri_stats.cpp                       |    4 
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 src/stri_string8buf.h                    |   21 
 src/stri_stringi.cpp                     |   69 -
 src/stri_stringi.h                       |   85 +-
 src/stri_sub.cpp                         |  231 ++++--
 src/stri_test.cpp                        |    8 
 src/stri_time_calendar.cpp               |   90 +-
 src/stri_time_format.cpp                 |  422 ++++++++----
 src/stri_time_zone.cpp                   |    4 
 src/stri_trans_casemap.cpp               |    4 
 src/stri_trans_normalization.cpp         |    4 
 src/stri_trans_other.cpp                 |   10 
 src/stri_trans_transliterate.cpp         |   50 +
 src/stri_ucnv.h                          |    3 
 src/stri_utils.cpp                       |   13 
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 153 files changed, 5002 insertions(+), 2439 deletions(-)

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Package mlflow updated to version 1.19.0 with previous version 1.18.0 dated 2021-06-18

Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for the complete machine learning life cycle, see <https://mlflow.org/>. This package supports installing 'MLflow', tracking experiments, creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre], Javier Luraschi [aut], Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>), RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>

Diff between mlflow versions 1.18.0 dated 2021-06-18 and 1.19.0 dated 2021-07-14

 DESCRIPTION                           |   12 ++++++------
 MD5                                   |   10 +++++++---
 NAMESPACE                             |    2 ++
 R/model-registry.R                    |only
 R/tracking-rest.R                     |    9 +++++++++
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 man/mlflow_delete_registered_model.Rd |only
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 8 files changed, 24 insertions(+), 9 deletions(-)

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Package grf updated to version 2.0.2 with previous version 2.0.1 dated 2021-07-06

Title: Generalized Random Forests
Description: A pluggable package for forest-based statistical estimation and inference. GRF currently provides methods for non-parametric least-squares regression, quantile regression, survival regression and treatment effect estimation (optionally using instrumental variables), with support for missing values.
Author: Julie Tibshirani [aut, cre], Susan Athey [aut], Rina Friedberg [ctb], Vitor Hadad [ctb], David Hirshberg [ctb], Luke Miner [ctb], Erik Sverdrup [aut], Stefan Wager [aut], Marvin Wright [ctb]
Maintainer: Julie Tibshirani <jtibs@cs.stanford.edu>

Diff between grf versions 2.0.1 dated 2021-07-06 and 2.0.2 dated 2021-07-14

 DESCRIPTION                           |    6 +++---
 MD5                                   |    4 ++--
 tests/testthat/test_cran_smoke_test.R |   31 +------------------------------
 3 files changed, 6 insertions(+), 35 deletions(-)

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New package covglasso with initial version 1.0.3
Package: covglasso
Version: 1.0.3
Date: 2021-07-14
Title: Sparse Covariance Matrix Estimation
Description: Direct sparse covariance matrix estimation via the covariance graphical lasso by Bien, Tibshirani (2011) <doi:10.1093/biomet/asr054> using the fast coordinate descent algorithm of Wang (2014) <doi:10.1007/s11222-013-9385-5>.
Authors@R: c(person("Michael", "Fop", role = c("aut", "cre"), email = "michael.fop@ucd.ie", comment = c(ORCID = "0000-0003-3936-2757")), person("Hao", "Wang", role = "ctb"))
Maintainer: Michael Fop <michael.fop@ucd.ie>
Depends: R (>= 3.4)
Imports: Rcpp (>= 1.0)
Suggests: MASS
LinkingTo: Rcpp, RcppArmadillo
License: GPL-3
Repository: CRAN
ByteCompile: true
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2021-07-14 13:51:28 UTC; michael
Author: Michael Fop [aut, cre] (<https://orcid.org/0000-0003-3936-2757>), Hao Wang [ctb]
Date/Publication: 2021-07-14 15:10:16 UTC

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New package rock with initial version 0.4.1
Package: rock
Title: Reproducible Open Coding Kit
Version: 0.4.1
Authors@R: c(person(given = "Gjalt-Jorn Ygram", family = "Peters", role = c("aut", "cre"), email = "gjalt-jorn@behaviorchange.eu", comment = c(ORCID = "0000-0002-0336-9589")), person(given = "Szilvia", family = "Zorgo", role = c("ctb"), comment = c(ORCID = "0000-0002-6916-2097")))
Maintainer: Gjalt-Jorn Ygram Peters <gjalt-jorn@behaviorchange.eu>
Description: The Reproducible Open Coding Kit ('ROCK', and this package, 'rock') was developed to facilitate reproducible and open coding, specifically geared towards qualitative research methods. Although it is a general-purpose toolkit, three specific applications have been implemented, specifically an interface to the 'rENA' package that implements Epistemic Network Analysis ('ENA'), means to process notes from Cognitive Interviews ('CIs'), and means to work with decentralized construct taxonomies ('DCTs').
BugReports: https://gitlab.com/r-packages/rock/-/issues
URL: https://r-packages.gitlab.io/rock
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.0.0)
Imports: data.tree (>= 0.7.8), dplyr (>= 0.7.8), DiagrammeR (>= 1.0.0), DiagrammeRsvg (>= 0.1), ggplot2 (>= 3.2.0), glue (>= 1.3.0), graphics (>= 3.0.0), htmltools (>= 0.5.0), markdown (>= 1.1), purrr (>= 0.2.5), stats (>= 3.0.0), utils (>= 3.5.0), yum (>= 0.0.1)
Suggests: covr, justifier (>= 0.2.0), knitr, rENA (>= 0.1.6), rmarkdown, rstudioapi, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-07-13 12:30:45 UTC; micro
Author: Gjalt-Jorn Ygram Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>), Szilvia Zorgo [ctb] (<https://orcid.org/0000-0002-6916-2097>)
Repository: CRAN
Date/Publication: 2021-07-14 14:30:02 UTC

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Package readtext updated to version 0.81 with previous version 0.80 dated 2020-09-22

Title: Import and Handling for Plain and Formatted Text Files
Description: Functions for importing and handling text files and formatted text files with additional meta-data, such including '.csv', '.tab', '.json', '.xml', '.html', '.pdf', '.doc', '.docx', '.rtf', '.xls', '.xlsx', and others.
Author: Kenneth Benoit [aut, cre, cph], Adam Obeng [aut], Kohei Watanabe [ctb], Akitaka Matsuo [ctb], Paul Nulty [ctb], Stefan Müller [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

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New package moreparty with initial version 0.2.1
Package: moreparty
Title: A Toolbox for Conditional Inference Random Forests
Version: 0.2.1
Depends: R (>= 3.5.0), party
Imports: partykit, varImp, plyr, foreach, measures, methods, MASS, iml, pdp, vip, ggplot2, rlang
Suggests: doParallel, knitr, rmarkdown, rmdformats, GDAtools, RColorBrewer, caret, pROC, tidyverse, e1071
VignetteBuilder: knitr
Author: Nicolas Robette
Maintainer: Nicolas Robette <nicolas.robette@uvsq.fr>
Description: Additions to 'party' package : tools for the interpretation of forests (surrogate trees, prototypes, etc.), feature selection (see Gregorutti et al (2017) <arXiv:1310.5726>, Hapfelmeier and Ulm (2013) <doi:10.1016/j.csda.2012.09.020>, Altmann et al (2010) <doi:10.1093/bioinformatics/btq134>) and parallelized versions of conditional forest and variable importance functions.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-07-14 12:45:13 UTC; nrobette
Repository: CRAN
Date/Publication: 2021-07-14 14:50:02 UTC

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Package fritools updated to version 2.1.0 with previous version 2.0.0 dated 2021-05-31

Title: Utilities for the Forest Research Institute of the State Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper functions for finding and searching files on disk, searching for and removing R objects from the workspace. These are utilities for packages <https://CRAN.R-project.org/package=cleanr>, <https://CRAN.R-project.org/package=document>, <https://CRAN.R-project.org/package=fakemake>, <https://CRAN.R-project.org/package=packager> and <https://CRAN.R-project.org/package=rasciidoc>. Does not import or depend on any third party package, but on core R only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

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Package compositions updated to version 2.0-2 with previous version 2.0-1 dated 2021-01-08

Title: Compositional Data Analysis
Description: Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.
Author: K. Gerald van den Boogaart <boogaart@hzdr.de>, Raimon Tolosana-Delgado, Matevz Bren
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>

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Package cmna updated to version 1.0.5 with previous version 1.0.3 dated 2020-07-07

Title: Computational Methods for Numerical Analysis
Description: Provides the source and examples for James P. Howard, II, "Computational Methods for Numerical Analysis with R," <https://jameshoward.us/cmna/>, a book on numerical methods in R.
Author: James Howard [aut, cre] (<https://orcid.org/0000-0003-4530-1547>)
Maintainer: James Howard <jh@jameshoward.us>

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Package clinUtils updated to version 0.0.2 with previous version 0.0.1 dated 2021-06-08

Title: General Utility Functions for Analysis of Clinical Data
Description: Utility functions to facilitate the import, the reporting and analysis of clinical data. Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate the package functionalities.
Author: Laure Cougnaud [aut], Michela Pasetto [aut, cre], Open Analytics [cph]
Maintainer: Michela Pasetto <michela.pasetto@openanalytics.eu>

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Package statswalesr updated to version 0.1.4 with previous version 0.1.3 dated 2021-05-12

Title: Easily Extract Data from 'StatsWales'
Description: Download data from 'StatsWales' into R. Removes the need for the user to write their own loops when parsing data from the 'StatsWales' API. Provides functions for datasets (<http://open.statswales.gov.wales/en-gb/dataset>) and metadata (<http://open.statswales.gov.wales/en-gb/discover/metadata>) endpoints.
Author: Jamie Ralph [aut, cre]
Maintainer: Jamie Ralph <jamesryanralph@outlook.com>

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Package seewave updated to version 2.1.8 with previous version 2.1.6 dated 2020-05-28

Title: Sound Analysis and Synthesis
Description: Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses. See Sueur et al. (2008) <doi:10.1080/09524622.2008.9753600> and Sueur (2018) <doi:10.1007/978-3-319-77647-7>.
Author: Jerome Sueur <sueur@mnhn.fr> [cre, au], Thierry Aubin [au], Caroline Simonis [au], Laurent Lellouch [main ctrb], Pierre Aumond [ctrb], Ethan C. Brown [ctrb], Guillaume Corbeau [ctrb], Marion Depraetere [ctrb], Camille Desjonqueres [ctrb], Francois Fabianek [ctrb], Amandine Gasc [ctrb], Eric Kasten [ctrb], Stefanie LaZerte [ctrb], Jonathan Lees [ctrb], Jean Marchal [ctrb], Andre Mikulec [ctrb], Sandrine Pavoine [ctrb], David Pinaud [ctrb], Alicia Stotz [ctrb], Luis J. Villanueva-Rivera [ctrb], Zev Ross [ctrb], Carl G. Witthoft [ctrb], Hristo Zhivomirov [ctrb].
Maintainer: Jerome Sueur <sueur@mnhn.fr>

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Package rebmix updated to version 2.13.0 with previous version 2.12.0 dated 2020-06-08

Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] (<https://orcid.org/0000-0003-0637-3812>), Branislav Panic [ctb] (<https://orcid.org/0000-0001-8349-8550>), Jernej Klemenc [ctb] (<https://orcid.org/0000-0002-6778-6728>), Simon Oman [ctb] (<https://orcid.org/0000-0001-8213-0818>)
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>

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Package posterior updated to version 1.0.1 with previous version 1.0.0 dated 2021-07-13

Title: Tools for Working with Posterior Distributions
Description: Provides useful tools for both users and developers of packages for fitting Bayesian models or working with output from Bayesian models. The primary goals of the package are to: (a) Efficiently convert between many different useful formats of draws (samples) from posterior or prior distributions. (b) Provide consistent methods for operations commonly performed on draws, for example, subsetting, binding, or mutating draws. (c) Provide various summaries of draws in convenient formats. (d) Provide lightweight implementations of state of the art posterior inference diagnostics. References: Vehtari et al. (2021) <doi:10.1214/20-BA1221>.
Author: Paul-Christian Bürkner [aut, cre], Jonah Gabry [aut], Matthew Kay [aut], Aki Vehtari [aut], Måns Magnusson [ctb], Rok Češnovar [ctb], Ben Lambert [ctb], Ozan Adıgüzel [ctb], Jacob Socolar [ctb]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>

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Package odin updated to version 1.2.1 with previous version 1.2.0 dated 2021-07-07

Title: ODE Generation and Integration
Description: Generate systems of ordinary differential equations (ODE) and integrate them, using a domain specific language (DSL). The DSL uses R's syntax, but compiles to C in order to efficiently solve the system. A solver is not provided, but instead interfaces to the packages 'deSolve' and 'dde' are generated. With these, while solving the differential equations, no allocations are done and the calculations remain entirely in compiled code. Alternatively, a model can be transpiled to R for use in contexts where a C compiler is not present. After compilation, models can be inspected to return information about parameters and outputs, or intermediate values after calculations. 'odin' is not targeted at any particular domain and is suitable for any system that can be expressed primarily as mathematical expressions. Additional support is provided for working with delays (delay differential equations, DDE), using interpolated functions during interpolation, and for integrating quantities that represent arrays.
Author: Rich FitzJohn [aut, cre], Thibaut Jombart [ctb], Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>

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Package distr6 updated to version 1.5.4 with previous version 1.5.2 dated 2021-04-17

Title: The Complete R6 Probability Distributions Interface
Description: An R6 object oriented distributions package. Unified interface for 42 probability distributions and 11 kernels including functionality for multiple scientific types. Additionally functionality for composite distributions and numerical imputation. Design patterns including wrappers and decorators are described in Gamma et al. (1994, ISBN:0-201-63361-2). For quick reference of probability distributions including d/p/q/r functions and results we refer to McLaughlin, M. P. (2001). Additionally Devroye (1986, ISBN:0-387-96305-7) for sampling the Dirichlet distribution, Gentle (2009) <doi:10.1007/978-0-387-98144-4> for sampling the Multivariate Normal distribution and Michael et al. (1976) <doi:10.2307/2683801> for sampling the Wald distribution.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>), Franz Kiraly [aut], Peter Ruckdeschel [ctb] (Author of distr), Matthias Kohl [ctb] (Author of distr), Nurul Ain Toha [ctb], Shen Chen [ctb], Jordan Deenichin [ctb], Chengyang Gao [ctb], Chloe Zhaoyuan Gu [ctb], Yunjie He [ctb], Xiaowen Huang [ctb], Shuhan Liu [ctb], Runlong Yu [ctb], Chijing Zeng [ctb], Qian Zhou [ctb]
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>

Diff between distr6 versions 1.5.2 dated 2021-04-17 and 1.5.4 dated 2021-07-14

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Package clustMixType updated to version 0.2-14 with previous version 0.2-11 dated 2021-03-10

Title: k-Prototypes Clustering for Mixed Variable-Type Data
Description: Functions to perform k-prototypes partitioning clustering for mixed variable-type data according to Z.Huang (1998): Extensions to the k-Means Algorithm for Clustering Large Data Sets with Categorical Variables, Data Mining and Knowledge Discovery 2, 283-304, <DOI:10.1023/A:1009769707641>.
Author: Gero Szepannek [aut, cre], Rabea Aschenbruck [aut]
Maintainer: Gero Szepannek <gero.szepannek@web.de>

Diff between clustMixType versions 0.2-11 dated 2021-03-10 and 0.2-14 dated 2021-07-14

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Package clinDataReview updated to version 1.1.0 with previous version 1.0.0 dated 2021-06-30

Title: Clinical Data Review Tool
Description: Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.
Author: Laure Cougnaud [aut, cre], Michela Pasetto [aut], Lennart Tuijnder [aut], Arne De Roeck [ctb], Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>

Diff between clinDataReview versions 1.0.0 dated 2021-06-30 and 1.1.0 dated 2021-07-14

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Package ranger updated to version 0.13.1 with previous version 0.12.1 dated 2020-01-10

Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently. In addition to data frames, datasets of class 'gwaa.data' (R package 'GenABEL') and 'dgCMatrix' (R package 'Matrix') can be directly analyzed.
Author: Marvin N. Wright [aut, cre], Stefan Wager [ctb], Philipp Probst [ctb]
Maintainer: Marvin N. Wright <cran@wrig.de>

Diff between ranger versions 0.12.1 dated 2020-01-10 and 0.13.1 dated 2021-07-14

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Package ggpp updated to version 0.4.1 with previous version 0.4.0 dated 2021-05-28

Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Geomas: geom_table(), geom_plot() and geom_grob() add insets to plots using native data coordinates, while geom_table_npc(), geom_plot_npc() and geom_grob_npc() do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: select observations based on 2D density. Positions: radial nudging away from a center point and nudging away from a line or curve.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package scoringutils updated to version 0.1.7 with previous version 0.1.4 dated 2020-11-17

Title: Utilities for Scoring and Assessing Predictions
Description: Combines a collection of metrics and proper scoring rules (Tilmann Gneiting & Adrian E Raftery (2007) <doi:10.1198/016214506000001437>) with an easy to use wrapper that can be used to automatically evaluate predictions. Apart from proper scoring rules functions are provided to assess bias, sharpness and calibration (Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe, Rosalind M. Eggo, W. John Edmunds (2019) <doi:10.1371/journal.pcbi.1006785>) of forecasts. Several types of predictions can be evaluated: probabilistic forecasts (generally predictive samples generated by Markov Chain Monte Carlo procedures), quantile forecasts or point forecasts. Observed values and predictions can be either continuous, integer, or binary. Users can either choose to apply these rules separately in a vector / matrix format that can be flexibly used within other packages, or they can choose to do an automatic evaluation of their forecasts. This is implemented with 'data.table' and provides a consistent and very efficient framework for evaluating various types of predictions.
Author: Nikos Bosse [aut, cre] (<https://orcid.org/0000-0002-7750-5280>), Sam Abbott [aut] (<https://orcid.org/0000-0001-8057-8037>), Johannes Bracher [ctb] (<https://orcid.org/0000-0002-3777-1410>), Joel Hellewell [ctb] (<https://orcid.org/0000-0003-2683-0849>), Sophie Meakins [ctb], James Munday [ctb], Katharine Sherratt [ctb], Sebastian Funk [aut]
Maintainer: Nikos Bosse <nikosbosse@gmail.com>

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Package implied updated to version 0.4.0 with previous version 0.3.1 dated 2020-08-02

Title: Convert Between Bookmaker Odds and Probabilities
Description: Convert between bookmaker odds and probabilities. Eight different algorithms are available, including basic normalization, Shin's method (Hyun Song Shin, (1992) <doi:10.2307/2234526>), and others.
Author: Jonas Christoffer Lindstrøm
Maintainer: Jonas Christoffer Lindstrøm <jonaslindstrom88@gmail.com>

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New package tosr with initial version 0.1.0
Package: tosr
Title: Create the Tree of Science from WoS and Scopus
Version: 0.1.0
Authors@R: c(person(given = "Sebastian", family = "Robledo", role = c("aut", "cre"), email = "sebastian.robledogi@amigo.edu.co", comment = c(ORCID = "0000-0003-4357-4402")), person(given = "Martha", family = "Zuluaga", role = c("aut"), email = "martha.zuluaga@unad.edu.co", comment = c(ORCID = "0000-0003-1720-8476")), person(given = "Oscar", family = "Arbelaez Echeverry", role = c("aut"), email = "oscar@coreofscience.com", comment = c(ORCID = "0000-0002-3097-9438")), person(given = "Luis Alexander", family = "Valencia Hernandez", role = c("aut"), email = "lavalenciah@unal.edu.co"), person(given = "Centro de Bioinformática y Biología computacional de Colombia - BIOS", role = c("cph", "fnd")))
Description: The goal of 'tosr' is to create the Tree of Science from Web of Science (WoS) and Scopus data. It can read files from both sources at the same time. More information can be found in Valencia-Hernández (2020) <https://revistas.unal.edu.co/index.php/ingeinv/article/view/77718>.
License: MIT + file LICENSE
URL: https://github.com/coreofscience/tosr, https://coreofscience.github.io/tosr/
BugReports: https://github.com/coreofscience/tosr/issues
Encoding: UTF-8
LazyData: true
Imports: bibliometrix, igraph, CINNA, dplyr, rebus, magrittr, stringr, tidyr, stats, rlang, tibble
Depends: R (>= 2.10)
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-07-13 23:59:11 UTC; sebastianrobledo
Author: Sebastian Robledo [aut, cre] (<https://orcid.org/0000-0003-4357-4402>), Martha Zuluaga [aut] (<https://orcid.org/0000-0003-1720-8476>), Oscar Arbelaez Echeverry [aut] (<https://orcid.org/0000-0002-3097-9438>), Luis Alexander Valencia Hernandez [aut], Centro de Bioinformática y Biología computacional de Colombia - BIOS [cph, fnd]
Maintainer: Sebastian Robledo <sebastian.robledogi@amigo.edu.co>
Repository: CRAN
Date/Publication: 2021-07-14 09:30:02 UTC

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New package rbedrock with initial version 0.1.0
Package: rbedrock
Title: Analysis and Manipulation of Data from Minecraft Bedrock Edition
Version: 0.1.0
Authors@R: c( person("Reed", "Cartwright", role = c("aut", "cre"), email = "racartwright@gmail.com", comment = c(ORCID = "0000-0002-0837-9380")), person("Rich", "FitzJohn", role = "ctb", email = "rich.fitzjohn@gmail.com"), person(c("Christian", "Stigen"), "Larsen", role = "ctb"), person("The LevelDB Authors", "", role="cph") )
Description: Implements an interface to Minecraft (Bedrock Edition) worlds. Supports the analysis and management of these worlds and game saves.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
SystemRequirements: C++11, cmake, zlib, GNU make
NeedsCompilation: yes
Depends: R (>= 3.6.0)
Imports: tibble, R6, stringr, bit64, bitops, rappdirs, rlang, dplyr, purrr, magrittr, readr, utils, digest, vctrs, tidyr, fs
Suggests: zip, testthat, jsonlite,
URL: https://github.com/reedacartwright/rbedrock
BugReports: https://github.com/reedacartwright/rbedrock/issues
Packaged: 2021-07-13 21:23:51 UTC; reed
Author: Reed Cartwright [aut, cre] (<https://orcid.org/0000-0002-0837-9380>), Rich FitzJohn [ctb], Christian Stigen Larsen [ctb], The LevelDB Authors [cph]
Maintainer: Reed Cartwright <racartwright@gmail.com>
Repository: CRAN
Date/Publication: 2021-07-14 09:20:02 UTC

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Package moult updated to version 2.2.0 with previous version 2.1.0 dated 2018-01-12

Title: Models for Analysing Moult in Birds
Description: Functions to estimate start and duration of moult from moult data, based on models developed in Underhill and Zucchini (1988, 1990).
Author: Birgit Erni <birgit.erni@uct.ac.za>. Based on models developed by Underhill and Zucchini (1988, 1990).
Maintainer: Birgit Erni <birgit.erni@uct.ac.za>

Diff between moult versions 2.1.0 dated 2018-01-12 and 2.2.0 dated 2021-07-14

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 R/ms2pfmg.R                 |   42 ++++++++++--------
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Package mlr3misc updated to version 0.9.3 with previous version 0.9.2 dated 2021-06-29

Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions used in 'mlr3' and its companion packages. Comes with helper functions for functional programming, for printing, to work with 'data.table', as well as some generally useful 'R6' classes. This package also supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3misc versions 0.9.2 dated 2021-06-29 and 0.9.3 dated 2021-07-14

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Package GFDsurv updated to version 0.1.0 with previous version 0.0.2 dated 2021-04-20

Title: Tests for Survival Data in General Factorial Designs
Description: Implemented are three Wald-type statistic and respective permuted versions for null hypotheses formulated in terms of cumulative hazard rate functions, medians and the concordance measure, respectively, in the general framework of survival factorial designs with possibly heterogeneous survival and/or censoring distributions, for crossed designs with an arbitrary number of factors and nested designs with up to three factors. Ditzhaus, Dobler and Pauly (2020) <doi:10.1177/0962280220980784> Ditzhaus, Janssen, Pauly (2020) <arXiv: 2004.10818v2> Dobler and Pauly (2019) <doi:10.1177/0962280219831316>.
Author: Marc Ditzhaus [aut], Dennis Dobler [aut], Markus Pauly [aut], Philipp Steinhauer [aut, cre]
Maintainer: Philipp Steinhauer <philipp.steinhauer@tu-dortmund.de>

Diff between GFDsurv versions 0.0.2 dated 2021-04-20 and 0.1.0 dated 2021-07-14

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 4 files changed, 13 insertions(+), 19 deletions(-)

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New package ffp with initial version 0.1.0
Package: ffp
Title: Stress Test Historical Scenarios with Fully Flexible Probabilities
Version: 0.1.0
Authors@R: person(given = "Bernardo", family = "Reckziegel", role = c("aut", "cre", "cph"), email = "bernardo_cse@hotmail.com")
Description: Implements numerical entropy-pooling for scenario analysis as described in Meucci, Attilio (2010) <doi:10.2139/ssrn.1696802>.
License: MIT + file LICENSE
URL: https://github.com/Reckziegel/FFP
BugReports: https://github.com/Reckziegel/FFP/issues
Depends: R (>= 2.10)
Imports: assertthat (>= 0.2.1), dplyr (>= 1.0.6), forcats (>= 0.5.1), ggdist (>= 2.4.0), ggplot2 (>= 3.3.3), lubridate (>= 1.7.10), magrittr (>= 2.0.1), methods, mvtnorm (>= 1.1-1), NlcOptim (>= 0.6), pracma (>= 2.3.3), purrr (>= 0.3.4), rlang (>= 0.1.2), scales (>= 1.1.1), stats, tibble (>= 3.1.1), tidyr (>= 1.1.3), usethis (>= 0.2.1), vctrs (>= 0.3.7), xts (>= 0.12.1)
Suggests: covr, knitr (>= 1.33), markdown, roxygen2, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2021-07-13 18:55:47 UTC; bernardo.reckziegel
Author: Bernardo Reckziegel [aut, cre, cph]
Maintainer: Bernardo Reckziegel <bernardo_cse@hotmail.com>
Repository: CRAN
Date/Publication: 2021-07-14 09:10:08 UTC

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New package tcplfit2 with initial version 0.1.1
Package: tcplfit2
Title: Concentration-Response Modeling of HTS or Transcriptomics Data
Version: 0.1.1
Authors@R: c(person("Thomas", "Sheffield", email = "tysheff@gmail.com", role = c("aut")), person("Richard", "Judson", role = c("ctb"),email = "Judson.Richard@epa.gov"), person("Jason", "Brown", role = c("ctb", "cre"),email = "brown.jason@epa.gov") )
Description: Performs the basic concentration response curve fitting used in the 'tcpl' package. It is a substitute for the original tcplFit() function (and sub-functions) and allows a wider variety of concentration-response models. All of the models included in the 'BMDExpress' package are now part of this package, and the output includes a calculation of the bmd (Benchmark Dose or concentration) value.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: stats, future, methods, numDeriv, RColorBrewer, future.apply, stringr, stringi
NeedsCompilation: no
Packaged: 2021-07-13 15:44:15 UTC; jbrown20
Author: Thomas Sheffield [aut], Richard Judson [ctb], Jason Brown [ctb, cre]
Maintainer: Jason Brown <brown.jason@epa.gov>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2021-07-14 08:30:02 UTC

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New package SOP with initial version 1.0
Package: SOP
Title: Generalised Additive P-Spline Regression Models Estimation
Version: 1.0
Date: 2021-07-03
Authors@R: c( person(given = "Maria Xose", family = "Rodriguez-Alvarez", email = "mxrodriguez@bcamath.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1329-9238")), person(given = "Manuel", family = "Oviedo de la Fuente", email = "manuel.ovideo@usc.es", role = c("aut")), person(given = "Maria", family = "Durban", email = "mdurban@est-econ.uc3m.es", role = c("ctb")), person(given = "Paul H.C.", family = "Eilers", email = "p.eilers@erasmusmc.nl", role = c("ctb")), person(given = "Dae-Jin", family = "Lee", email = "dlee@bcamath.org", role = c("ctb")), person(given = "Mikis", family = "Stasinopoulos", email = "d.stasinopoulos@londonmet.ac.uk", role = c("ctb")))
Imports: stats, MASS
Suggests: SpATS
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@bcamath.org>
Description: Generalised additive P-spline regression models estimation using the separation of overlapping precision matrices (SOP) method. Estimation is based on the equivalence between P-splines and linear mixed models, and variance/smoothing parameters are estimated based on restricted maximum likelihood (REML). The package enables users to estimate P-spline models with overlapping penalties. Based on the work described in Rodriguez-Alvarez et al. (2015) <doi:10.1007/s11222-014-9464-2>; Rodriguez-Alvarez et al. (2019) <doi:10.1007/s11222-018-9818-2>, and Eilers and Marx (1996) <doi:10.1214/ss/1038425655>.
License: GPL-2
NeedsCompilation: no
Packaged: 2021-07-13 15:59:21 UTC; mrodriguez
Author: Maria Xose Rodriguez-Alvarez [aut, cre] (<https://orcid.org/0000-0002-1329-9238>), Manuel Oviedo de la Fuente [aut], Maria Durban [ctb], Paul H.C. Eilers [ctb], Dae-Jin Lee [ctb], Mikis Stasinopoulos [ctb]
Repository: CRAN
Date/Publication: 2021-07-14 08:40:02 UTC

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New package shiny.reglog with initial version 0.2.0.2
Package: shiny.reglog
Title: Optional Login and Registration Module System for ShinyApps
Version: 0.2.0.2
Authors@R: person(given = "Michal", family = "Kosinski", role = c("aut", "cre"), email = "kosinski.mich@gmail.com", comment = c(ORCID = "https://orcid.org/0000-0002-8426-3654"))
Description: Package creates UI modules for Login, Register and Password Reset boxes and server module for reading and writing user database contained within googlesheet or sqlite file. Creates automatic e-mail messages after registration and for resetting password procedure. Currently supports English language (default) and Polish. The authentication system created with shiny.reglog is designed to be optional: user don't need to be logged-in to access your application, but when logged-in the user data can be used to read from and write to relational databases.
Imports: shiny, dplyr, dbplyr, scrypt, R6, DBI, googlesheets4, RSQLite, lubridate
Suggests: shinydashboard, googledrive, gmailr, emayili
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-07-13 18:48:00 UTC; micha
Author: Michal Kosinski [aut, cre] (<https://orcid.org/0000-0002-8426-3654>)
Maintainer: Michal Kosinski <kosinski.mich@gmail.com>
Repository: CRAN
Date/Publication: 2021-07-14 09:00:02 UTC

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New package PhageCocktail with initial version 1.0.0
Package: PhageCocktail
Title: Design of the Best Phage Cocktail
Version: 1.0.0
Authors@R: c(person(given = "Maria Victoria", family = "Diaz-Galian", role = c("aut", "cre"), email = "mvdiazgalian@unex.es", comment = c(ORCID = "0000-0003-2543-6081")), person(given = "Miguel A.", family = "Vega-Rodriguez", role = "aut", email = "mavega@unex.es", comment = c(ORCID = "0000-0002-3003-758X")), person(given = "Felipe", family = "Molina", role = "aut", email = "fmolina@unex.es", comment = c(ORCID = "0000-0002-9167-7097")))
Description: There are 4 possible methods: "ExhaustiveSearch"; "ExhaustivePhi"; "ClusteringSearch"; and "ClusteringPhi". "ExhaustiveSearch"--> gives you the best phage cocktail from a phage-bacteria infection network. It checks different phage cocktail sizes from 1 to 7 and only stops before if it lyses all bacteria. Other option is when users have decided not to obtain a phage cocktail size higher than a limit value. "ExhaustivePhi"--> firstly, it finds Phi out. Phi is a formula indicating the necessary phage cocktail size. Phi needs nestedness temperature and fill, which are internally calculated. This function will only look for the best combination (phage cocktail) with a Phi size. "ClusteringSearch"--> firstly, an agglomerative hierarchical clustering using Ward's algorithm is calculated for phages. They will be clustered according to bacteria lysed by them. PhageCocktail() chooses how many clusters are needed in order to select 1 phage per cluster. Using the phages selected during the clustering, it checks different phage cocktail sizes from 1 to 7 and only stops before if it lyses all bacteria. Other option is when users have decided not to obtain a phage cocktail size higher than a limit value. "ClusteringPhi"--> firstly, an agglomerative hierarchical clustering using Ward's algorithm is calculated for phages. They will be clustered according to bacteria lysed by them. PhageCocktail() chooses how many clusters are needed in order to select 1 phage per cluster. Once the function has one phage per cluster, it calculates Phi. If the number of clusters is less than Phi number, it will be changed to obtain, as minimum, this quantity of candidates (phages). Then, it calculates the best combination of Phi phages using those selected during the clustering with Ward algorithm.
Imports: readxl, stringr, factoextra, bipartite, smerc, RJSONIO
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-07-13 15:52:48 UTC; MVDia
Author: Maria Victoria Diaz-Galian [aut, cre] (<https://orcid.org/0000-0003-2543-6081>), Miguel A. Vega-Rodriguez [aut] (<https://orcid.org/0000-0002-3003-758X>), Felipe Molina [aut] (<https://orcid.org/0000-0002-9167-7097>)
Maintainer: Maria Victoria Diaz-Galian <mvdiazgalian@unex.es>
Repository: CRAN
Date/Publication: 2021-07-14 08:30:05 UTC

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New package FeatureTerminatoR with initial version 1.0.0
Package: FeatureTerminatoR
Title: Feature Selection Engine to Remove Features with Minimal Predictive Power
Version: 1.0.0
Authors@R: c( person("Gary", "Hutson", , "hutsons-hacks@outlook.com", c("aut", "cre"), comment = c(ORCID="0000-0003-3534-6143")))
Maintainer: Gary Hutson <hutsons-hacks@outlook.com>
Description: The aim is to take in data.frame inputs and utilises methods, such as recursive feature engineering, to enable the features to be removed. What this does differently from the other packages, is that it gives you the choice to remove the variables manually, or it automated this process. Feature selection is a concept in machine learning, and statistical pipelines, whereby unimportant, or less predictive variables are eliminated from the analysis, see Boughaci (2018) <doi:10.1007/s40595-018-0107-y>.
License: GPL-3
Encoding: UTF-8
Imports: ggplot2, caret, tibble, dplyr, stats, utils, lattice, e1071, randomForest
Suggests: knitr, markdown, rmarkdown
LazyData: FALSE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-07-13 18:50:19 UTC; garyh
Author: Gary Hutson [aut, cre] (<https://orcid.org/0000-0003-3534-6143>)
Repository: CRAN
Date/Publication: 2021-07-14 09:00:04 UTC

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Package robustMVMR updated to version 0.3.1 with previous version 0.1.0 dated 2020-05-02

Title: Perform the Robust Multivariable Mendelian Randomization Analysis
Description: Perform the robust multivariable Mendelian randomization 'robustMVMR' analysis in the two-sample Mendelian randomization setting. An example paper using the 'robustMVMR' package can be found in Yang et al. (2021) <doi:10.1080/15412555.2021.1955848>. In details, the 'robustMVMR' package produces both the robust estimators and the robust standard errors via the MM-estimates, which has been demonstrated to protect against heteroskedasticity, autocorrelation, and the presence of outliers in Yohai (1987) <doi:10.1214/aos/1176350366> and Croux (2003) <https://EconPapers.repec.org/RePEc:ete:ceswps:ces0316>.
Author: Zhao Yang
Maintainer: Zhao Yang <yangz98@connect.hku.hk>

Diff between robustMVMR versions 0.1.0 dated 2020-05-02 and 0.3.1 dated 2021-07-14

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Package peRspective updated to version 0.1.1 with previous version 0.1.0 dated 2019-05-20

Title: Interface to the 'Perspective' API
Description: Interface to the 'Perspective' API, which can be found at the following URL: <https://github.com/conversationai/perspectiveapi#perspective-comment-analyzer-api>. The 'Perspective' API uses machine learning models to score the perceived impact a comment might have on a conversation (i.e. TOXICITY, INFLAMMATORY, etc.). 'peRspective' provides access to the API and returns tidy data frames with results of the specified machine learning model(s).
Author: Fabio Votta [aut, cre]
Maintainer: Fabio Votta <fabio.votta@gmail.com>

Diff between peRspective versions 0.1.0 dated 2019-05-20 and 0.1.1 dated 2021-07-14

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 peRspective-0.1.1/peRspective/tests/testthat/test-prsp-stream.R         |   27 +++
 peRspective-0.1.1/peRspective/tests/testthat/test-sentence-comment.R    |    1 
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 33 files changed, 251 insertions(+), 96 deletions(-)

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Package gpboost updated to version 0.6.6 with previous version 0.6.3 dated 2021-06-18

Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2020) <arXiv:2004.02653> and Sigrist (2021) <arXiv:2105.08966> for more information on the methodology.
Author: Fabio Sigrist [aut, cre], Benoit Jacob [cph], Gael Guennebaud [cph], Nicolas Carre [cph], Pierre Zoppitelli [cph], Gauthier Brun [cph], Jean Ceccato [cph], Jitse Niesen [cph], Other authors of Eigen for the included version of Eigen [ctb, cph], Timothy A. Davis [cph], Guolin Ke [ctb], Damien Soukhavong [ctb], James Lamb [ctb], Other authors of LightGBM for the included version of LightGBM [ctb], Microsoft Corporation [cph], Dropbox, Inc. [cph], Jay Loden [cph], Dave Daeschler [cph], Giampaolo Rodola [cph], Alberto Ferreira [ctb], Daniel Lemire [ctb], Victor Zverovich [cph], IBM Corporation [ctb], Keith O'Hara [cph], Stephen L. Moshier [cph]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>

Diff between gpboost versions 0.6.3 dated 2021-06-18 and 0.6.6 dated 2021-07-14

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Package gjam updated to version 2.3.9 with previous version 2.3.8 dated 2021-07-06

Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>

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Package MisRepARMA updated to version 0.0.2 with previous version 0.0.1 dated 2021-06-30

Title: Misreported Time Series Analysis
Description: Provides a simple and trustworthy methodology for the analysis of misreported continuous time series. See Moriña, D, Fernández-Fontelo, A, Cabaña, A, Puig P. (2021) <arXiv:2003.09202v2>.
Author: David Moriña Soler [aut, cre] (<https://orcid.org/0000-0001-5949-7443>), Amanda Fernández-Fontelo [aut], Alejandra Cabaña [aut], Pedro Puig [aut]
Maintainer: David Moriña Soler <dmorina@ub.edu>

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Package BIRDS (with last version 0.2.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-06-26 0.2.0
2021-03-01 0.1.27.1
2020-10-08 0.1.2
2020-03-20 0.1

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Package vroom updated to version 1.5.3 with previous version 1.5.2 dated 2021-07-08

Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>), Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>

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Package tfautograph updated to version 0.3.0 with previous version 0.2.0 dated 2020-01-08

Title: Autograph R for 'Tensorflow'
Description: Translate R control flow expressions into 'Tensorflow' graphs.
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <kalinowskit@gmail.com>

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Package sasLM updated to version 0.6.1 with previous version 0.6.0 dated 2021-06-15

Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, and ANOVA. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that. Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

Diff between sasLM versions 0.6.0 dated 2021-06-15 and 0.6.1 dated 2021-07-14

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