Sat, 04 Dec 2021

Package apsimx updated to version 2.2 with previous version 2.0 dated 2021-08-20

Title: Inspect, Read, Edit and Run 'APSIM' "Next Generation" and 'APSIM' Classic
Description: The functions in this package inspect, read, edit and run files for 'APSIM' "Next Generation" ('JSON') and 'APSIM' "Classic" ('XML'). The files with an 'apsim' extension correspond to 'APSIM' Classic (7.x) - Windows only - and the ones with an 'apsimx' extension correspond to 'APSIM' "Next Generation". For more information about 'APSIM' see (<https://www.apsim.info/>) and for 'APSIM' next generation (<https://apsimnextgeneration.netlify.app/>).
Author: Fernando Miguez [aut, cre] (<https://orcid.org/0000-0002-4627-8329>)
Maintainer: Fernando Miguez <femiguez@iastate.edu>

Diff between apsimx versions 2.0 dated 2021-08-20 and 2.2 dated 2021-12-04

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Package rbibutils updated to version 2.2.5 with previous version 2.2.4 dated 2021-10-11

Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam <https://sourceforge.net/projects/bibutils/>. Supports all bibliography formats and character encodings implemented in 'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)), Chris Putman [aut] (src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/), Richard Mathar [ctb] (src/addsout.c), Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c)
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package LCCR updated to version 1.3 with previous version 1.2 dated 2021-10-03

Title: Latent Class Capture-Recapture Models
Description: Estimation of latent class models with individual covariates for capture-recapture data. See Forcina and Bartolucci (2021)<arxiv:2106.03811>.
Author: Francesco Bartolucci [aut, cre], Antonio Forcina [aut]
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>

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Package SSDforR updated to version 1.5.23 with previous version 1.5.22 dated 2021-08-02

Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre], Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>

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Package bhm updated to version 1.17 with previous version 1.16 dated 2020-04-13

Title: Biomarker Threshold Models
Description: Contains tools to fit both predictive and prognostic biomarker effects using biomarker threshold models and continuous threshold models. Evaluate the treatment effect, biomarker effect and treatment-biomarker interaction using probability index measurement. Test for treatment-biomarker interaction using residual bootstrap method.
Author: Bingshu E. Chen
Maintainer: Bingshu E. Chen <bingshu.chen@queensu.ca>

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Package targets updated to version 0.9.0 with previous version 0.8.1 dated 2021-10-26

Title: Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Description: As a pipeline toolkit for Statistics and data science in R, the 'targets' package brings together function-oriented programming and 'Make'-like declarative workflows. It analyzes the dependency relationships among the tasks of a workflow, skips steps that are already up to date, runs the necessary computation with optional parallel workers, abstracts files as R objects, and provides tangible evidence that the results match the underlying code and data. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Matthew T. Warkentin [ctb], Samantha Oliver [rev] (<https://orcid.org/0000-0001-5668-1165>), Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>), Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package RcppAPT updated to version 0.0.8 with previous version 0.0.7 dated 2021-04-16

Title: 'Rcpp' Interface to the APT Package Manager
Description: The 'APT Package Management System' provides Debian and Debian-derived Linux systems with a powerful system to resolve package dependencies. This package offers access directly from R. This can only work on a system with a suitable 'libapt-pkg-dev' installation so functionality is curtailed if such a library is not found.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package AsyK updated to version 1.5.5 with previous version 1.5.4 dated 2020-02-13

Title: Kernel Density Estimation
Description: A collection of functions related to density estimation by using Chen's (2000) idea. Mean Squared Errors (MSE) are calculated for estimated curves. For this purpose, R functions allow the distribution to be Gamma, Exponential or Weibull. For details see Chen (2000), Scaillet (2004) <doi:10.1080/10485250310001624819> and Khan and Akbar.
Author: Javaria Ahmad Khan, Atif Akbar.
Maintainer: Javaria Ahmad Khan <jakhan0@yahoo.com>

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Package keyholder updated to version 0.1.6 with previous version 0.1.5 dated 2020-05-09

Title: Store Data About Rows
Description: Tools for keeping track of information, named "keys", about rows of data frame like objects. This is done by creating special attribute "keys" which is updated after every change in rows (subsetting, ordering, etc.). This package is designed to work tightly with 'dplyr' package.
Author: Evgeni Chasnovski [aut, cre] (<https://orcid.org/0000-0002-1617-4019>)
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>

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Package Rsagacmd updated to version 0.1.2 with previous version 0.1.1 dated 2021-07-08

Title: Linking R with the Open-Source 'SAGA-GIS' Software
Description: Provides an R scripting interface to the open-source 'SAGA-GIS' (System for Automated Geoscientific Analyses Geographical Information System) software. 'Rsagacmd' dynamically generates R functions for every 'SAGA-GIS' geoprocessing tool based on the user's currently installed 'SAGA-GIS' version. These functions are contained within an S3 object and are accessed as a named list of libraries and tools. This structure facilitates an easier scripting experience by organizing the large number of 'SAGA-GIS' geoprocessing tools (>700) by their respective library. Interactive scripting can fully take advantage of code autocompletion tools (e.g. in 'Rstudio'), allowing for each tools syntax to be quickly recognized. Furthermore, the most common types of spatial data (via the 'raster', 'terra', 'sp', and 'sf' packages) along with non-spatial data are automatically passed from R to the 'SAGA-GIS' command line tool for geoprocessing operations, and the results are loaded as the appropriate R object. Outputs from individual 'SAGA-GIS' tools can also be chained using pipes from the 'magrittr' and 'dplyr' packages to combine complex geoprocessing operations together in a single statement. 'SAGA-GIS' is available under a GPLv2 / LGPLv2 licence from <https://sourceforge.net/projects/saga-gis/> including Windows x86/x64 binaries. SAGA-GIS is also included in Debian/Ubuntu default software repositories and is available for macOS using homebrew (<https://brew.sh/>) from the osgeo/osgeo4mac (<https://github.com/OSGeo/homebrew-osgeo4mac>) formula tap, as well as being bundled within the 'QGIS' application bundle for macOS. Rsagacmd has currently been tested on 'SAGA-GIS' versions from 2.3.1 to 8.0.1 on Windows, Linux and macOS.
Author: Steven Pawley [aut, cre]
Maintainer: Steven Pawley <dr.stevenpawley@gmail.com>

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Package paws.common updated to version 0.3.15 with previous version 0.3.14 dated 2021-10-24

Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.common versions 0.3.14 dated 2021-10-24 and 0.3.15 dated 2021-12-04

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Package leidenAlg updated to version 1.0.1 with previous version 1.0.0 dated 2021-11-19

Title: Implements the Leiden Algorithm via an R Interface
Description: An R interface to the Leiden algorithm, an iterative community detection algorithm on networks. The algorithm is designed to converge to a partition in which all subsets of all communities are locally optimally assigned, yielding communities guaranteed to be connected. The implementation proves to be fast, scales well, and can be run on graphs of millions of nodes (as long as they can fit in memory). The original implementation was constructed as a python interface "leidenalg" found here: <https://github.com/vtraag/leidenalg>. The algorithm was originally described in Traag, V.A., Waltman, L. & van Eck, N.J. "From Louvain to Leiden: guaranteeing well-connected communities". Sci Rep 9, 5233 (2019) <doi:10.1038/s41598-019-41695-z>.
Author: Peter Kharchenko [aut], Viktor Petukhov [aut], V.A. Traag [ctb], Gábor Csárdi [ctb], Tamás Nepusz [ctb], Minh Van Nguyen [ctb], Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

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Package healthyR.ts updated to version 0.1.6 with previous version 0.1.5 dated 2021-11-10

Title: The Time Series Modeling Companion to 'healthyR'
Description: Hospital time series data analysis workflow tools, modeling, and automations. This library provides many useful tools to review common administrative time series hospital data. Some of these include average length of stay, and readmission rates. The aim is to provide a simple and consistent verb framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre], Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>

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Package fasstr updated to version 0.4.0 with previous version 0.3.3 dated 2021-10-21

Title: Analyze, Summarize, and Visualize Daily Streamflow Data
Description: The Flow Analysis Summary Statistics Tool for R, 'fasstr', provides various functions to tidy and screen daily stream discharge data, calculate and visualize various summary statistics and metrics, and compute annual trending and volume frequency analyses. It features useful function arguments for filtering of and handling dates, customizing data and metrics, and the ability to pull daily data directly from the Water Survey of Canada hydrometric database (<https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>).
Author: Jon Goetz [aut, cre] (<https://orcid.org/0000-0002-4993-1119>), Carl James Schwarz [aut], Robin Pike [ctb], Province of British Columbia [cph]
Maintainer: Jon Goetz <jon.goetz@gov.bc.ca>

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Package bytescircle updated to version 1.1.2 with previous version 1.1.1 dated 2021-11-21

Title: Statistics About Bytes Contained in a File as a Circle Plot
Description: Shows statistics about bytes contained in a file as a circle graph of deviations from mean in sigma increments. The function can be useful for statistically analyze the content of files in a glimpse: text files are shown as a green centered crown, compressed and encrypted files should be shown as equally distributed variations with a very low CV (sigma/mean), and other types of files can be classified between these two categories depending on their text vs binary content, which can be useful to quickly determine how information is stored inside them (databases, multimedia files, etc).
Author: Roberto S. Galende [aut, cre]
Maintainer: Roberto S. Galende <roberto.s.galende@gmail.com>

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Package APCI updated to version 1.0.4 with previous version 1.0.3 dated 2021-10-21

Title: A New Age-Period-Cohort Model for Describing and Investigating Inter-Cohort Differences and Life Course Dynamics
Description: It implemented Age-Period-Interaction Model (APC-I Model) proposed in the paper of Liying Luo and James S. Hodges in 2019. A new age-period-cohort model for describing and investigating inter-cohort differences and life course dynamics.
Author: Jiahui Xu [aut, cre], Liying Luo [aut]
Maintainer: Jiahui Xu <jpx5053@psu.edu>

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Fri, 03 Dec 2021

Package testthat updated to version 3.1.1 with previous version 3.1.0 dated 2021-10-04

Title: Unit Testing for R
Description: Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy to learn and use, and integrates with your existing 'workflow'.
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd], R Core team [ctb] (Implementation of utils::recover())
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package tesseract updated to version 4.2.0 with previous version 4.1.2 dated 2021-09-18

Title: Open Source OCR Engine
Description: Bindings to 'Tesseract' <https://opensource.google/projects/tesseract>: a powerful optical character recognition (OCR) engine that supports over 100 languages. The engine is highly configurable in order to tune the detection algorithms and obtain the best possible results.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package sregsurvey updated to version 0.1.1 with previous version 0.1.0 dated 2021-09-15

Title: Semiparametric Model-Assisted Estimation in Finite Population
Description: It is a framework to fit semiparametric regression estimators for the total parameter of a finite population when the interest variable is asymmetric distributed. The main references for this package are: Sarndal C.E., Swensson B., and Wretman J. (2003,ISBN: 978-0-387-40620-6, "Model Assisted Survey Sampling." Springer-Verlag) and Cardozo C.A and Alonso-Malaver C.E. (2021). "Semi-parametric model assisted estimation in finite populations." In preparation.
Author: Carlos Alberto Cardozo Delgado [aut, cre, cph], Carlos E. Alonso-Malaver [aut]
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>

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Package soilDB updated to version 2.6.9 with previous version 2.6.5 dated 2021-08-21

Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: Dylan Beaudette [aut], Jay Skovlin [aut], Stephen Roecker [aut], Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>

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Package mpath updated to version 0.4-2.20 with previous version 0.4-2.19 dated 2021-04-05

Title: Regularized Linear Models
Description: Algorithms compute concave convex (CC) estimators including robust (penalized) generalized linear models and robust support vector machines via the COCO - composite optimization by conjugation operator. The package also contains penalized Poisson, negative binomial, zero-inflated Poisson, zero-inflated negative binomial regression models and robust models with non-convex loss functions. Wang et al. (2014) <doi:10.1002/sim.6314>, Wang et al. (2015) <doi:10.1002/bimj.201400143>, Wang et al. (2016) <doi:10.1177/0962280214530608>, Wang (2021) <doi:10.1007/s11749-021-00770-2>, Wang (2020) <arXiv:2010.02848>.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, and Patrick Breheny
Maintainer: Zhu Wang <wangz1@uthscsa.edu>

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Package mapsPERU updated to version 1.0.2 with previous version 0.1.3 dated 2021-10-30

Title: Maps of Peru
Description: Information of the centroids and geographical limits of the regions, departments, provinces and districts of Peru.
Author: Jorge L. C. Musaja [aut, cre]
Maintainer: Jorge L. C. Musaja <musajajorge@gmail.com>

Diff between mapsPERU versions 0.1.3 dated 2021-10-30 and 1.0.2 dated 2021-12-03

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New package mispitools with initial version 0.1.0
Package: mispitools
Title: Missing Person Identification Tools
Version: 0.1.0
Description: Open-source software for computing Likelihood ratios thresholds and error rates in DNA kinship testingi. Marsico FL. et al (2021) <doi:10.1016/j.fsigen.2021.102519>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: forrel, pedtools, plotly, dplyr, highcharter
URL: https://github.com/MarsicoFL/mispitools
BugReports: https://github.com/MarsicoFL/mispitools/issues
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-12-03 18:01:39 UTC; franco
Author: Franco Marsico [aut, cre] (<https://orcid.org/0000-0002-0740-5516>)
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-03 22:50:12 UTC

More information about mispitools at CRAN
Permanent link

Package mailR updated to version 0.8 with previous version 0.4.1 dated 2015-01-13

Title: A Utility to Send Emails from R
Description: Interface to Apache Commons Email to send emails from R.
Author: Rahul Premraj
Maintainer: Rahul Premraj <r.premraj+mailR@gmail.com>

Diff between mailR versions 0.4.1 dated 2015-01-13 and 0.8 dated 2021-12-03

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Package easyDifferentialGeneCoexpression updated to version 0.8 with previous version 0.7 dated 2021-12-02

Title: Easily Computes the Differential Coexpression Analysis
Description: A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression. If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found. Platforms available: GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.
Author: Davide Chicco [aut, cre] (<https://orcid.org/0000-0001-9655-7142>)
Maintainer: Davide Chicco <davidechicco@davidechicco.it>

Diff between easyDifferentialGeneCoexpression versions 0.7 dated 2021-12-02 and 0.8 dated 2021-12-03

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Package BayesMallows updated to version 1.1.0 with previous version 1.0.4 dated 2021-11-17

Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen [aut, cre] (<https://orcid.org/0000-0003-0724-3542>), Valeria Vitelli [aut] (<https://orcid.org/0000-0002-6746-0453>), Marta Crispino [aut], Qinghua Liu [aut], Cristina Mollica [aut], Luca Tardella [aut], Anja Stein [aut], Waldir Leoncio [ctr]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>

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Package tsibble updated to version 1.1.1 with previous version 1.1.0 dated 2021-10-22

Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') for temporal data in an data- and model-oriented format. The 'tsibble' provides tools to easily manipulate and analyse temporal data, such as filling in time gaps and aggregating over calendar periods.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>), Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>), Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>), Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>), Tyler Smith [ctb], Wil Davis [ctb]
Maintainer: Earo Wang <earo.wang@gmail.com>

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Package lares updated to version 5.0.4 with previous version 5.0.3 dated 2021-11-16

Title: Analytics, Data Mining & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Exploratory, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or extensive programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>

Diff between lares versions 5.0.3 dated 2021-11-16 and 5.0.4 dated 2021-12-03

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Package excluder updated to version 0.3.3 with previous version 0.3.2 dated 2021-11-18

Title: Checks for Exclusion Criteria in Online Data
Description: Data that are collected through online sources such as Mechanical Turk may require excluding rows because of IP address duplication, geolocation, or completion duration. This package facilitates exclusion of these data for Qualtrics datasets.
Author: Jeffrey R. Stevens [aut, cre, cph] (<https://orcid.org/0000-0003-2375-1360>), Joseph O'Brien [rev] (<https://orcid.org/0000-0001-9851-5077>), Julia Silge [rev] (<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@gmail.com>

Diff between excluder versions 0.3.2 dated 2021-11-18 and 0.3.3 dated 2021-12-03

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New package fastshap with initial version 0.0.6
Package: fastshap
Title: Fast Approximate Shapley Values
Version: 0.0.6
Description: Computes fast (relative to other implementations) approximate Shapley values for any supervised learning model. Shapley values help to explain the predictions from any black box model using ideas from game theory; see Strumbel and Kononenko (2014) <doi:10.1007/s10115-013-0679-x> for details.
License: GPL (>= 2)
URL: https://github.com/bgreenwell/fastshap
BugReports: https://github.com/bgreenwell/fastshap/issues
Imports: abind, ggplot2 (>= 3.3.4), gridExtra, matrixStats, plyr, Rcpp (>= 1.0.1), tibble
Suggests: AmesHousing, covr, earth, htmltools, knitr, lightgbm, ranger, reticulate (>= 1.14), rmarkdown, rstudioapi, tinytest, titanic, xgboost
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2021-12-03 17:15:33 UTC; bgreenwell
Author: Brandon Greenwell [aut, cre] (<https://orcid.org/0000-0002-8120-0084>)
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-03 19:20:02 UTC

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New package crestr with initial version 1.0.0
Package: crestr
Title: A Probabilistic Approach to Reconstruct Past Climates Using Biological Climate Proxies
Version: 1.0.0
Description: Applies the CREST climate reconstruction method. It can be used using the calibration data that can be obtained through the package or by importing private data. An ensemble of graphical outputs were designed to facilitate the use of the package and the interpretation of the results. More information can be found form Chevalier (2021) <doi:10.5194/cp-2021-153>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: clipr, DBI, methods, plyr, raster, rgdal, rgeos, RPostgres, scales, sp, stringr, viridis
Suggests: knitr, openxlsx, plot3D, rmarkdown, pals
Depends: R (>= 2.10)
Language: en-us
VignetteBuilder: knitr
URL: https://github.com/mchevalier2/crestr, https://mchevalier2.github.io/crestr/index.html
BugReports: https://github.com/mchevalier2/crestr/issues
NeedsCompilation: no
Packaged: 2021-12-03 13:58:44 UTC; mchevali1
Author: Manuel Chevalier [aut, cre] (<https://orcid.org/0000-0002-8183-9881>)
Maintainer: Manuel Chevalier <chevalier.manuel@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-03 19:20:04 UTC

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New package spectator with initial version 0.1.0
Package: spectator
Title: Interface to the 'Spectator Earth' API
Version: 0.1.0
Description: Provides interface to the 'Spectator Earth' API <https://api.spectator.earth/>, mainly for obtaining the acquisition plans and satellite overpasses for Sentinel-1, Sentinel-2 and Landsat-8 satellites. Current position and trajectory can also be obtained for a much larger set of satellites. It is also possible to search the archive for available images over the area of interest for a given (past) period, get the URL links to download the whole image tiles, or alternatively to download the image for just the area of interest based on selected spectral bands.
License: GPL-3
Depends: R (>= 3.5.0)
Imports: geojsonsf, httr, sf
Suggests: calendar, calendR, httptest, knitr, lubridate, lutz, maps, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2021-12-03 12:01:45 UTC; zivan
Author: Zivan Karaman [aut, cre, cph] (<https://orcid.org/0000-0002-8933-4589>)
Maintainer: Zivan Karaman <zivan.karaman@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-03 19:00:02 UTC

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New package skater with initial version 0.1.0
Package: skater
Title: Utilities for SNP-Based Kinship Analysis
Description: Utilities for single nucleotide polymorphism (SNP) based kinship analysis testing and evaluation. The 'skater' package contains functions for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing identity by descent (IBD) segment data. Package functions and methods are described in Turner et al. (2021) "skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation" <doi:10.1101/2021.07.21.453083>.
Version: 0.1.0
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.0.0)
Imports: magrittr, dplyr, tidyr, readr, purrr, kinship2, corrr, grDevices, tibble, rlang
Suggests: rmarkdown, markdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-03 09:37:01 UTC; turner
Author: Stephen Turner [aut, cre] (<https://orcid.org/0000-0001-9140-9028>), Matthew Scholz [aut] (<https://orcid.org/0000-0003-3686-1227>), VP Nagraj [aut] (<https://orcid.org/0000-0003-0060-566X>), Signature Science, LLC. [cph]
Maintainer: Stephen Turner <vustephen@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-03 18:50:02 UTC

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New package MulvariateRandomForestVarImp with initial version 0.0.1
Package: MulvariateRandomForestVarImp
Title: Variable Importance Measures for Multivariate Random Forests
Version: 0.0.1
Description: Calculates post-hoc variable importance measures for multivariate random forests. These are given by split improvement for splits defined by feature j as measured using user-defined (i.e. training or test) examples. Importance measures can also be calculated on a per-outcome variable basis using the change in predictions for each split. Both measures can be optionally thresholded to include only splits that produce statistically significant changes as measured by an F-test.
License: GPL (>= 3)
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
Imports: MultivariateRandomForest (>= 1.1.5), MASS (>= 7.3.0)
URL: https://github.com/Megatvini/VIM/
BugReports: https://github.com/Megatvini/VIM/issues
NeedsCompilation: no
Packaged: 2021-12-03 07:45:57 UTC; Nika
Author: Sikdar Sharmistha [aut], Hooker Giles [aut], Kadiyali Vrinda [ctb], Dogonadze Nika [cre]
Maintainer: Dogonadze Nika <nika.dogonadze@toptal.com>
Repository: CRAN
Date/Publication: 2021-12-03 18:50:07 UTC

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New package cata with initial version 0.0.10.3
Package: cata
Title: Analysis of Check-All-that-Apply (CATA) Data
Version: 0.0.10.3
Date: 2021-11-30
Author: J.C. Castura [aut, cre, ctb] (<https://orcid.org/0000-0002-1640-833X>)
Maintainer: J.C. Castura <jcastura@compusense.com>
Description: Functions for analyzing check-all-that-apply (CATA) data from consumer and sensory tests. Cochran's Q test, McNemar's test, and Penalty-Lift analysis provided, as described in for CATA data analysis by Meyners, Castura & Carr (2013) <doi:10.1016/j.foodqual.2013.06.010>. Cluster analysis can be performed using b-cluster analysis. The quality of cluster analysis solutions can be evaluated using various measures. The methods related to b-cluster analysis are described in a pre-print manuscript by Castura, Meyners, Varela & Naes (2021) <https://secure.compusense.com/research/wp-content/uploads/2021/12/Castura_bcluster_submitted_20211130.pdf>.
Depends: R (>= 4.1.0)
Imports: grDevices, stats, utils, graphics
License: GPL (>= 2)
LazyData: TRUE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-12-02 22:49:36 UTC; jcastura
Repository: CRAN
Date/Publication: 2021-12-03 18:10:01 UTC

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New package DeductiveR with initial version 1.0.0
Package: DeductiveR
Title: Deductive Rational Method
Version: 1.0.0
Date: 2021-11-22
Description: Apply the Deductive Rational Method to a monthly series of flow or precipitation data to fill in missing data. The method is as described in: Campos, D.F., (1984, ISBN:9686194444).
License: GPL-3
Encoding: UTF-8
Imports: dplyr, reshape2, ggplot2, moments
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-02 20:09:06 UTC; CLAA300697
Author: Alonso Arriagada [aut, cre]
Maintainer: Alonso Arriagada <alonso.arriagada@usach.cl>
Repository: CRAN
Date/Publication: 2021-12-03 17:50:02 UTC

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New package amt with initial version 0.1.5
Package: amt
Title: Animal Movement Tools
Version: 0.1.5
Description: Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate home ranges, track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses, and simulation of space-use from fitted step-selection functions.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/jmsigner/amt
Depends: R (>= 3.5),
Imports: checkmate, circular, ctmm, dplyr (>= 0.7.0), fitdistrplus, lubridate, magrittr, methods, purrr, raster, Rdpack, Rcpp (>= 0.12.7), rgeos, rlang, sf, sp, survival, tibble, tidyr (>= 1.0.0)
Suggests: adehabitatLT, adehabitatMA, broom, ggplot2, ggraph, geosphere, KernSmooth, FNN, leaflet, moveHMM, move, sessioninfo, spacetime, trajectories, knitr, rmarkdown, tinytest, tidygraph, maptools
LinkingTo: Rcpp
RdMacros: Rdpack
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-12-02 22:02:23 UTC; jsigner
Author: Johannes Signer [aut, cre], Brian Smith [ctb], Bjoern Reineking [ctb], Ulrike Schlaegel [ctb], John Fieberg [ctb], Josh O'Brien [ctb], Bernardo Niebuhr [ctb], Scott LaPoint [dtc]
Maintainer: Johannes Signer <jsigner@gwdg.de>
Repository: CRAN
Date/Publication: 2021-12-03 18:00:02 UTC

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New package AeroSampleR with initial version 0.1.12
Package: AeroSampleR
Title: Estimate Aerosol Particle Collection Through Sample Lines
Version: 0.1.12
Author: Mark Hogue
Maintainer: Mark Hogue <mark.hogue@srs.gov>
Description: Estimate ideal efficiencies of aerosol sampling through sample lines. Functions were developed consistent with the approach described in Hogue, Mark; Thompson, Martha; Farfan, Eduardo; Hadlock, Dennis, (2014), "Hand Calculations for Transport of Radioactive Aerosols through Sampling Systems" Health Phys 106, 5, S78-S87, <doi:10.1097/HP.0000000000000092>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: dplyr, purrr, magrittr, tidyr, ggplot2, ggthemes, stringr, tidyselect
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-12-02 21:44:06 UTC; markh
Repository: CRAN
Date/Publication: 2021-12-03 18:00:07 UTC

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Package Ternary updated to version 1.2.4 with previous version 1.2.3 dated 2021-10-08

Title: Create Ternary Plots
Description: Plots ternary diagrams (simplex plots / Gibbs triangles) using the standard graphics functions. An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions. Includes a 'Shiny' user interface for point-and-click plotting.
Author: Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Lilian Sanselme [ctb]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

Diff between Ternary versions 1.2.3 dated 2021-10-08 and 1.2.4 dated 2021-12-03

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Package tLagPropOdds updated to version 1.5 with previous version 1.2 dated 2021-10-21

Title: Proportional Odds Model with Censored, Time-Lagged Categorical Outcome
Description: Implements a semiparametric estimator for the odds ratio model with censored, time-lagged, ordered categorical outcome in a randomized clinical trial that incorporates baseline and time-dependent information. Tsiatis, A. A. and Davidian, M. (2021) <arXiv:2106.15559>.
Author: Marie Davidian [aut], A. A. Tsiatis [aut], Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>

Diff between tLagPropOdds versions 1.2 dated 2021-10-21 and 1.5 dated 2021-12-03

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Package sdmpredictors updated to version 0.2.11 with previous version 0.2.10 dated 2021-09-20

Title: Species Distribution Modelling Predictor Datasets
Description: Terrestrial and marine predictors for species distribution modelling from multiple sources, including WorldClim <https://www.worldclim.org/>,, ENVIREM <https://envirem.github.io/>, Bio-ORACLE <https://bio-oracle.org/> and MARSPEC <http://www.marspec.org/>.
Author: Samuel Bosch [aut], Lennert Tyberghein [ctb], Olivier De Clerck [ctb], Salvador Fernandez [aut, cre], Lennert Schepers [ctb]
Maintainer: Salvador Fernandez <salvador.fernandez@vliz.be>

Diff between sdmpredictors versions 0.2.10 dated 2021-09-20 and 0.2.11 dated 2021-12-03

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Package coro updated to version 1.0.2 with previous version 1.0.1 dated 2020-12-17

Title: 'Coroutines' for R
Description: Provides 'coroutines' for R, a family of functions that can be suspended and resumed later on. This includes 'async' functions (which await) and generators (which yield). 'Async' functions are based on the concurrency framework of the 'promises' package. Generators are based on a dependency free iteration protocol defined in 'coro' and are compatible with iterators from the 'reticulate' package.
Author: Lionel Henry [aut, cre], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

Diff between coro versions 1.0.1 dated 2020-12-17 and 1.0.2 dated 2021-12-03

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Package threeBrain updated to version 0.2.4 with previous version 0.2.3 dated 2021-10-13

Title: 3D Brain Visualization
Description: A fast, interactive cross-platform, and easy to share 'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or 'AFNI/SUMA' surfaces. The viewer widget can be either standalone or embedded into 'R-shiny' applications. The standalone version only require a web browser with 'WebGL2' support (for example, 'Chrome'). It can be inserted into any websites; see <https://dipterix.org/project/threebrain/>). as an example. The 'R-shiny' support allows the 3D viewer to be dynamically generated from reactive user inputs. This feature has been fully adopted by 'RAVE' <https://openwetware.org/wiki/RAVE>, an interactive toolbox to analyze 'iEEG/eCoG' data. Documentation about 'threeBrain' is provided by <https://dipterix.org/threeBrain/> and several vignettes included in this package. To cite the package, please check our 'NeuroImage' paper by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>), or see 'citation("threeBrain")' for details.
Author: Zhengjia Wang [aut, cre, cph], John Magnotti [aut], Xiang Zhang [ctb, res], Brian Metzger [res], Elizabeth Nesbitt [res], Meng Li [ths], Michael Beauchamp [aut, dtc]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>

Diff between threeBrain versions 0.2.3 dated 2021-10-13 and 0.2.4 dated 2021-12-03

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Package QWDAP updated to version 1.1.8 with previous version 1.1.7 dated 2021-11-25

Title: Quantum Walk-Based Data Analysis and Prediction
Description: Modeling and predicting time series based on continuous time quantum.This package can be divided into three parts: Basis Generation, Data Modeling and Prediction, and Model Evaluation according to the analysis process of time series. 'Basis Generation' has realized the continuous time quantum walk simulation for generating modes as the basis. Some regression methods are used to model the observed time series and predict in 'Data Modeling and Prediction', and 'Model Evaluation' can be used to evaluate the data correspondence between two series.
Author: Binghuang Pan [aut, cre], Zhaoyuan Yu [aut], Xu Hu [ctb], Dongshuang Li [ctb], Yuhao Teng [ctb], Xinxin Zhou [ctb]
Maintainer: Binghuang Pan <bright1up@163.com>

Diff between QWDAP versions 1.1.7 dated 2021-11-25 and 1.1.8 dated 2021-12-03

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Package littler updated to version 0.3.15 with previous version 0.3.14 dated 2021-10-05

Title: R at the Command-Line via 'r'
Description: A scripting and command-line front-end is provided by 'r' (aka 'littler') as a lightweight binary wrapper around the GNU R language and environment for statistical computing and graphics. While R can be used in batch mode, the r binary adds full support for both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path expression as the first line in scripts) as well as command-line use in standard Unix pipelines. In other words, r provides the R language without the environment.
Author: Dirk Eddelbuettel and Jeff Horner
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between littler versions 0.3.14 dated 2021-10-05 and 0.3.15 dated 2021-12-03

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Package irlba updated to version 2.3.4 with previous version 2.3.3 dated 2019-02-05

Title: Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices
Description: Fast and memory efficient methods for truncated singular value decomposition and principal components analysis of large sparse and dense matrices.
Author: Jim Baglama [aut, cph], Lothar Reichel [aut, cph], B. W. Lewis [aut, cre, cph]
Maintainer: B. W. Lewis <blewis@illposed.net>

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Package pollen updated to version 0.82.0 with previous version 0.72.0 dated 2020-03-15

Title: Analysis of Aerobiological Data
Description: Supports analysis of aerobiological data. Available features include determination of pollen season limits, replacement of outliers (Kasprzyk and Walanus (2014) <doi:10.1007/s10453-014-9332-8>), calculation of growing degree days (Baskerville and Emin (1969) <doi:10.2307/1933912>), and determination of the base temperature for growing degree days (Yang et al. (1995) <doi:10.1016/0168-1923(94)02185-M).
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

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Package geodata updated to version 0.3-5 with previous version 0.3-2 dated 2021-09-29

Title: Download Geographic Data
Description: Functions for downloading of geographic data for use in spatial data analysis and mapping. The package facilitates access to climate, elevation, soil, species occurrence, and administrative boundary data.
Author: Robert J. Hijmans [cre, aut], Aniruddha Ghosh [ctb], Alex Mandel [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

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Package conleyreg updated to version 0.1.5 with previous version 0.1.4 dated 2021-06-28

Title: Estimations using Conley Standard Errors
Description: Functions calculating Conley (1999) <doi:10.1016/S0304-4076(98)00084-0> standard errors. The package started by merging and extending multiple packages and other published scripts on this econometric technique. It strongly emphasizes computational optimization. Details are available in the function documentation and in the vignette.
Author: Christian Düben [aut, cre], Richard Bluhm [cph], Luis Calderon [cph], Darin Christensen [cph], Timothy Conley [cph], Thiemo Fetzer [cph], Leander Heldring [cph]
Maintainer: Christian Düben <christian.dueben@uni-hamburg.de>

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New package ActivePathways with initial version 1.0.3
Package: ActivePathways
Title: Integrative Pathway Enrichment Analysis of Multivariate Omics Data
Version: 1.0.3
Description: Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The package is part of the following publication: Integrative Pathway Enrichment Analysis of Multivariate Omics Data. Paczkowska M^, Barenboim J^, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group; Reimand J, PCAWG Consortium. Nature Communications (2020) <doi:10.1038/s41467-019-13983-9>.
Depends: R (>= 3.6)
Imports: data.table, ggplot2
License: GPL-3
URL:
BugReports: https://github.com/reimandlab/ActivePathways/issues
Encoding: UTF-8
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-11-30 19:48:25 UTC; jreimand
Author: Juri Reimand [aut, cre], Jonathan Barenboim [aut]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>
Repository: CRAN
Date/Publication: 2021-12-03 12:50:05 UTC

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Package RWsearch updated to version 4.9.8 with previous version 4.9.3 dated 2021-06-05

Title: Lazy Search in R Packages, Task Views, CRAN, the Web. All-in-One Download
Description: Search by keywords in R packages, task views, CRAN, the web and display the results in the console or in txt, html or pdf files. Download the package documentation (html index, README, NEWS, pdf manual, vignettes, source code, binaries) with a single instruction. Visualize the package dependencies and CRAN checks. Compare the package versions, unload and install the packages and their dependencies in a safe order. Explore CRAN archives. Use the above functions for task view maintenance. Access web search engines from the console thanks to 80+ bookmarks. All functions accept standard and non-standard evaluation.
Author: Patrice Kiener [aut, cre] (<https://orcid.org/0000-0002-0505-9920>)
Maintainer: Patrice Kiener <rpackages@inmodelia.com>

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Package Rfast updated to version 2.0.4 with previous version 2.0.3 dated 2021-05-17

Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>

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Package admisc updated to version 0.21 with previous version 0.20 dated 2021-11-14

Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'declared', 'DDIwR', 'mixed', 'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum of Products expressions, for both binary and multi-value crisp sets, and extracts information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly flexible recoding routine.
Author: Adrian Dusa [aut, cre, cph] (<https://orcid.org/0000-0002-3525-9253>)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

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Package sjmisc updated to version 2.8.9 with previous version 2.8.7 dated 2021-05-12

Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data, and all integrate seamlessly into a 'tidyverse'-workflow.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Iago Giné-Vázquez [ctb], Alexander Bartel [ctb] (<https://orcid.org/0000-0002-1280-6138>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package sdcTable updated to version 0.32.2 with previous version 0.32.1 dated 2021-09-30

Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in tabular data such as primary and secondary cell suppression as described for example in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@gmail.com>

Diff between sdcTable versions 0.32.1 dated 2021-09-30 and 0.32.2 dated 2021-12-03

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 sdcTable-0.32.2/sdcTable/DESCRIPTION                                                                           |   10 +--
 sdcTable-0.32.2/sdcTable/MD5                                                                                   |   30 ++++-----
 sdcTable-0.32.2/sdcTable/R/change_cellstatus.R                                                                 |    2 
 sdcTable-0.32.2/sdcTable/R/methods_class_sdcProblem.r                                                          |   23 ++++---
 sdcTable-0.32.2/sdcTable/R/primarySuppression.R                                                                |    7 +-
 sdcTable-0.32.2/sdcTable/R/protect_linked_tables.R                                                             |   10 +--
 sdcTable-0.32.2/sdcTable/R/utils.R                                                                             |   31 +++-------
 sdcTable-0.32.2/sdcTable/R/utils_simpleheuristic.R                                                             |   10 ++-
 sdcTable-0.32.2/sdcTable/build/vignette.rds                                                                    |binary
 sdcTable-0.32.2/sdcTable/inst/doc/sdcTable.html                                                                |   15 +---
 sdcTable-0.32.2/sdcTable/man/change_cellstatus.Rd                                                              |    2 
 sdcTable-0.32.2/sdcTable/man/primarySuppression.Rd                                                             |    7 +-
 sdcTable-0.32.2/sdcTable/man/protect_linked_tables.Rd                                                          |   10 +--
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Package meta updated to version 5.1-1 with previous version 5.1-0 dated 2021-11-17

Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from 'RevMan 5'; - prediction interval, Hartung-Knapp method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression; - generalised linear mixed models; - produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>

Diff between meta versions 5.1-0 dated 2021-11-17 and 5.1-1 dated 2021-12-03

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Package AgroR updated to version 1.2.5 with previous version 1.2.4 dated 2021-11-30

Title: Experimental Statistics and Graphics for Agricultural Sciences
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4), ANOVA of aligned ranks (Wobbrock, J.O., Findlater, L., Gergle, D., Higgins, JJ (2011), <doi:10.1145/1978942.1978963>) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).
Author: Gabriel Danilo Shimizu [aut, cre] (<https://orcid.org/0000-0001-8524-508X>), Rodrigo Yudi Palhaci Marubayashi [aut, ctb] (<https://orcid.org/0000-0003-2778-8654>), Leandro Simoes Azeredo Goncalves [aut, ctb] (<https://orcid.org/0000-0001-9700-9375>)
Maintainer: Gabriel Danilo Shimizu <shimizu@uel.br>

Diff between AgroR versions 1.2.4 dated 2021-11-30 and 1.2.5 dated 2021-12-03

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Package pkgdown updated to version 2.0.1 with previous version 2.0.0 dated 2021-11-30

Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Jay Hesselberth [aut] (<https://orcid.org/0000-0002-6299-179X>), Maëlle Salmon [aut] (<https://orcid.org/0000-0002-2815-0399>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between pkgdown versions 2.0.0 dated 2021-11-30 and 2.0.1 dated 2021-12-03

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Package gplsim updated to version 0.9.1 with previous version 0.9.0 dated 2021-12-02

Title: Penalized Spline Estimation for GPLSIM
Description: We provides functions that employ penalized spline (P-spline) to estimate generalized partially linear single index models (GPLSIM), which extend the generalized linear models to include nonlinear effect for some predictors. Please see Y. (2017) at <doi:10.1007/s11222-016-9639-0> and Y., and R. (2002) at <doi:10.1198/016214502388618861> for more details.
Author: Tianhai Zu [aut, trl, cre], Yan Yu [aut]
Maintainer: Tianhai Zu <zuti@mail.uc.edu>

Diff between gplsim versions 0.9.0 dated 2021-12-02 and 0.9.1 dated 2021-12-03

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Package gdalcubes updated to version 0.5.1 with previous version 0.5.0 dated 2021-10-28

Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, and plotting. The package implements lazy evaluation and multithreading. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] (<https://orcid.org/0000-0001-5281-3896>), Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>), Roger Bivand [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Lewis Van Winkle [cph], Ole Christian Eidheim [cph], Howard Hinnant [cph], Adrian Colomitchi [cph], Florian Dang [cph], Paul Thompson [cph], Tomasz Kamiński [cph], Dropbox, Inc. [cph]
Maintainer: Marius Appel <marius.appel@uni-muenster.de>

Diff between gdalcubes versions 0.5.0 dated 2021-10-28 and 0.5.1 dated 2021-12-03

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New package SNPassoc with initial version 2.0-11
Package: SNPassoc
Version: 2.0-11
Date: 2021-11-15
Depends: R (>= 4.0.0)
Imports: haplo.stats, mvtnorm, parallel, survival, tidyr, plyr, ggplot2, BiocStyle, poisbinom, Biostrings, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, GenomicRanges, IRanges, S4Vectors, org.Hs.eg.db
Suggests: testthat, knitr, rmarkdown, biomaRt, SNPlocs.Hsapiens.dbSNP144.GRCh38, MafDb.1Kgenomes.phase3.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, GenomicScores, BSgenome
Title: SNPs-Based Whole Genome Association Studies
Description: Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.
URL: https://github.com/isglobal-brge/SNPassoc
License: GPL (>= 2)
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-02 14:45:01 UTC; mailos
Author: Victor Moreno [aut], Juan R Gonzalez [aut, cre]
Maintainer: Juan R Gonzalez <juanr.gonzalez@isglobal.org>
Repository: CRAN
Date/Publication: 2021-12-03 08:40:02 UTC

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New package RCzechia with initial version 1.9.1
Package: RCzechia
Title: Spatial Objects of the Czech Republic
Version: 1.9.1
Date: 2021-12-02
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Description: Administrative regions and other spatial objects of the Czech Republic.
URL: https://github.com/jlacko/RCzechia
BugReports: https://github.com/jlacko/RCzechia/issues
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.3.0), sf
Imports: curl, httr, jsonlite, magrittr
Suggests: raster, readxl, units, ggplot2, stringr, rvest, xml2, scales, knitr, testthat, roxygen2, devtools, rmarkdown, dplyr, lwgeom, s2, covr
SystemRequirements: GDAL (>= 2.2.3), GEOS (>= 3.6.2), PROJ (>= 4.9.3)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-02 15:25:57 UTC; jindra
Repository: CRAN
Date/Publication: 2021-12-03 08:40:06 UTC

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New package litRiddle with initial version 0.4.1
Package: litRiddle
Title: Dataset and Tools to Research the Riddle of Literary Quality
Version: 0.4.1
Date: 2021-12-2
Author: Maciej Eder [aut, cre], Karina van Dalen-Oskam [aut], Joris van Zundert [aut], Saskia Lensink [aut]
Maintainer: Maciej Eder <maciejeder@gmail.com>
URL: https://literaryquality.huygens.knaw.nl/
Depends: R (>= 3.5.0)
Imports: dplyr, ggplot2
Suggests: stylo, knitr, rmarkdown
Description: Dataset and functions to explore quality of literary novels. The package is a part of the Riddle of Literary Quality project, and it contains the data of a reader survey about fiction in Dutch, a description of the novels the readers rated, and the results of stylistic measurements of the novels. The package also contains functions to combine, analyze, and visualize these data.
License: GPL (>= 3)
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-02 17:46:25 UTC; m
Repository: CRAN
Date/Publication: 2021-12-03 09:00:02 UTC

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New package lactater with initial version 0.1.0
Package: lactater
Title: Tools for Analyzing Lactate Thresholds
Version: 0.1.0
Description: Set of tools for analyzing lactate thresholds from a step incremental test to exhaustion. Easily analyze the methods Log-log, Onset of Blood Lactate Accumulation (OBLA), Baseline plus (Bsln+), Dmax, Lactate Turning Point (LTP), and Lactate / Intensity ratio (LTratio) in cycling, running, or swimming. Beaver WL, Wasserman K, Whipp BJ (1985) <doi:10.1152/jappl.1985.59.6.1936>. Heck H, Mader A, Hess G, Mücke S, Müller R, Hollmann W (1985) <doi:10.1055/s-2008-1025824>. Kindermann W, Simon G, Keul J (1979) <doi:10.1007/BF00421101>. Skinner JS, Mclellan TH (1980) <doi:10.1080/02701367.1980.10609285>. Berg A, Jakob E, Lehmann M, Dickhuth HH, Huber G, Keul J (1990) <PMID:2408033>. Zoladz JA, Rademaker AC, Sargeant AJ (1995) <doi:10.1113/jphysiol.1995.sp020959>. Cheng B, Kuipers H, Snyder A, Keizer H, Jeukendrup A, Hesselink M (1992) <doi:10.1055/s-2007-1021309>. Bishop D, Jenkins DG, Mackinnon LT (1998) <doi:10.1097/00005768-199808000-00014>. Hughson RL, Weisiger KH, Swanson GD (1987) <doi:10.1152/jappl.1987.62.5.1975>. Jamnick NA, Botella J, Pyne DB, Bishop DJ (2018) <doi:10.1371/journal.pone.0199794>. Hofmann P, Tschakert G (2017) <doi:10.3389/fphys.2017.00337>. Hofmann P, Pokan R, von Duvillard SP, Seibert FJ, Zweiker R, Schmid P (1997) <doi:10.1097/00005768-199706000-00005>. Pokan R, Hofmann P, Von Duvillard SP, et al. (1997) <doi:10.1097/00005768-199708000-00009>. Dickhuth H-H, Yin L, Niess A, et al. (1999) <doi:10.1055/s-2007-971105>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: bsplus, covr, datapasta, glue, knitr, miniUI, rhandsontable, rmarkdown, shiny, shinyjs, shinyWidgets, spelling, testthat (>= 3.0.0)
Imports: magrittr, broom, dplyr, ggplot2, ggtext, patchwork, lubridate, minpack.lm, pracma, rlang, segmented, stringr, tidyr, forcats
Depends: R (>= 2.10)
Language: en-US
NeedsCompilation: no
Packaged: 2021-12-02 14:40:49 UTC; fmattioni
Author: Felipe Mattioni Maturana [aut, cre] (<https://orcid.org/0000-0002-4221-6104>)
Maintainer: Felipe Mattioni Maturana <felipe.mattioni@med.uni-tuebingen.de>
Repository: CRAN
Date/Publication: 2021-12-03 08:30:02 UTC

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New package kfa with initial version 0.1.0
Package: kfa
Title: K-Fold Cross Validation for Factor Analysis
Version: 0.1.0
Author: Kyle Nickodem [aut, cre] and Peter Halpin [aut]
Maintainer: Kyle Nickodem <kyle.nickodem@gmail.com>
Description: Provides functions to explore possible factor structures for a set of variables and helps identify plausible and replicable structures via *k*-fold cross validation. The process combines the exploratory and confirmatory factor analytic approach to scale development (Flora & Flake, 2017) <doi:10.1037/cbs0000069> with a cross validation technique that maximizes the available data. Also available are functions to determine *k* by drawing on power analytic techniques for covariance structures (MacCallum, Browne, & Sugawara, 1996) <doi:10.1037/1082-989X.1.2.130>, generate model syntax, and summarize results in a report.
Depends: R (>= 3.6)
Imports: caret, doParallel, flextable (>= 0.6.3), foreach, GPArotation, knitr, lavaan (>= 0.6.9), officer, parallel, rmarkdown, semPlot, semTools (>= 0.5.5), simstandard
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: <https://github.com/knickodem/kfa>
BugReports: https://github.com/knickodem/kfa/issues
NeedsCompilation: no
Packaged: 2021-12-01 19:15:24 UTC; kylenick
Repository: CRAN
Date/Publication: 2021-12-03 08:20:02 UTC

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New package jagstargets with initial version 1.0.1
Package: jagstargets
Title: Targets for JAGS Workflows
Description: Bayesian data analysis usually incurs long runtimes and cumbersome custom code. A pipeline toolkit tailored to Bayesian statisticians, the 'jagstargets' R package is leverages 'targets' and 'R2jags' to ease this burden. 'jagstargets' makes it super easy to set up scalable JAGS pipelines that automatically parallelize the computation and skip expensive steps when the results are already up to date. Minimal custom code is required, and there is no need to manually configure branching, so usage is much easier than 'targets' alone. For the underlying methodology, please refer to the documentation of 'targets' <doi:10.21105/joss.02959> and 'JAGS' (Plummer 2003) <https://www.r-project.org/conferences/DSC-2003/Proceedings/Plummer.pdf>.
Version: 1.0.1
License: MIT + file LICENSE
URL: https://docs.ropensci.org/jagstargets/, https://github.com/ropensci/jagstargets
BugReports: https://github.com/ropensci/jagstargets/issues
Depends: R (>= 3.5.0)
Imports: coda (>= 0.19.4), digest (>= 0.6.25), fst (>= 0.9.2), posterior (>= 1.0.1), purrr (>= 0.3.4), qs (>= 0.23.2), R2jags (>= 0.6.1), rjags (>= 4.10), rlang (>= 0.4.10), stats, targets (>= 0.6.0), tarchetypes (>= 0.0.1), tibble (>= 3.0.1), tools, utils, withr (>= 2.1.2),
Suggests: dplyr (>= 1.0.2), fs (>= 1.5.0), knitr (>= 1.30), R.utils (>= 2.10.1), rmarkdown (>= 2.3), testthat (>= 3.0.0), tidyr (>= 1.1.2), visNetwork (>= 2.0.9)
SystemRequirements: JAGS 4.x.y (https://mcmc-jags.sourceforge.net)
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-01 12:13:40 UTC; c240390
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), David Lawrence Miller [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-03 08:10:02 UTC

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New package index0 with initial version 0.0.1
Package: index0
Title: Zero-Based Indexing in R
Version: 0.0.1
Description: Extract and replace elements using indices that start from zero (rather than one), as is common in mathematical notation and other programming languages.
License: MIT + file LICENSE
Language: en-GB
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-12-02 10:49:54 UTC; David
Author: David Antony Selby [aut, cre] (<https://orcid.org/0000-0001-8026-5663>)
Maintainer: David Antony Selby <david.selby@manchester.ac.uk>
Repository: CRAN
Date/Publication: 2021-12-03 08:20:05 UTC

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New package FPLdata with initial version 0.1.0
Package: FPLdata
Title: Read in Fantasy Premier League Data
Version: 0.1.0
Maintainer: Andrew Little <andrewlittlebristol@gmail.com>
Description: This data contains a large variety of information on players and their current attributes on Fantasy Premier League <https://fantasy.premierleague.com/>. In particular, it contains a `next_gw_points` (next gameweek points) value for each player given their attributes in the current week. Rows represent player-gameweeks, i.e. for each player there is a row for each gameweek. This makes the data suitable for modelling a player's next gameweek points, given attributes such as form, total points, and cost at the current gameweek. This data can therefore be used to create Fantasy Premier League bots that may use a machine learning algorithm and a linear programming solver (for example) to return the best possible transfers and team to pick for each gameweek, thereby fully automating the decision making process in Fantasy Premier League. This function simply supplies the required data for such a task.
Imports: readr, dplyr
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-12-02 14:08:50 UTC; andrew.little
Author: Andrew Little [aut, cre]
Repository: CRAN
Date/Publication: 2021-12-03 08:30:05 UTC

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Package portalr updated to version 0.3.9 with previous version 0.3.8 dated 2021-05-23

Title: Create Useful Summaries of the Portal Data
Description: Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Project. Portal is a long-term (and ongoing) experimental monitoring site in the Chihuahua desert. The raw data files can be found at <https://github.com/weecology/portaldata>.
Author: Glenda M. Yenni [aut, cre] (<https://orcid.org/0000-0001-6969-1848>), Hao Ye [aut] (<https://orcid.org/0000-0002-8630-1458>), Erica M. Christensen [aut] (<https://orcid.org/0000-0002-5635-2502>), Juniper L. Simonis [aut] (<https://orcid.org/0000-0001-9798-0460>), Ellen K. Bledsoe [aut] (<https://orcid.org/0000-0002-3629-7235>), Renata M. Diaz [aut] (<https://orcid.org/0000-0003-0803-4734>), Shawn D. Taylor [aut] (<https://orcid.org/0000-0002-6178-6903>), Ethan P, White [aut] (<https://orcid.org/0000-0001-6728-7745>), S.K. Morgan Ernest [aut] (<https://orcid.org/0000-0002-6026-8530>), Weecology [cph]
Maintainer: Glenda M. Yenni <glenda@weecology.org>

Diff between portalr versions 0.3.8 dated 2021-05-23 and 0.3.9 dated 2021-12-03

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Package GPBayes updated to version 0.1.0-3 with previous version 0.1.0-2.1 dated 2021-10-08

Title: Tools for Gaussian Process Modeling in Uncertainty Quantification
Description: Gaussian processes (GPs) have been widely used to model spatial data, spatio-temporal data, and computer experiments in diverse areas of statistics including spatial statistics, spatio-temporal statistics, uncertainty quantification, and machine learning. This package creates basic tools for fitting and prediction based on GPs with spatial data, spatio-temporal data, and computer experiments. Key characteristics for this GP tool include: (1) the comprehensive implementation of various covariance functions including the Matérn family and the Confluent Hypergeometric family with isotropic form, tensor form, and automatic relevance determination form, where the isotropic form is widely used in spatial statistics, the tensor form is widely used in design and analysis of computer experiments and uncertainty quantification, and the automatic relevance determination form is widely used in machine learning; (2) implementations via Markov chain Monte Carlo (MCMC) algorithms and optimization algorithms for GP models with all the implemented covariance functions. The methods for fitting and prediction are mainly implemented in a Bayesian framework; (3) model evaluation via Fisher information and predictive metrics such as predictive scores; (4) built-in functionality for simulating GPs with all the implemented covariance functions; (5) unified implementation to allow easy specification of various GPs.
Author: Pulong Ma [aut, cre]
Maintainer: Pulong Ma <mpulong@gmail.com>

Diff between GPBayes versions 0.1.0-2.1 dated 2021-10-08 and 0.1.0-3 dated 2021-12-03

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Package ggstar updated to version 1.0.3 with previous version 1.0.2 dated 2021-04-07

Title: Multiple Geometric Shape Point Layer for 'ggplot2'
Description: To create the multiple polygonal point layer for easily discernible shapes, we developed the package, it is like the 'geom_point' of 'ggplot2'. It can be used to draw the scatter plot.
Author: Shuangbin Xu [aut, cre] (<https://orcid.org/0000-0003-3513-5362>)
Maintainer: Shuangbin Xu <xshuangbin@163.com>

Diff between ggstar versions 1.0.2 dated 2021-04-07 and 1.0.3 dated 2021-12-03

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Thu, 02 Dec 2021

Package VennDiagram updated to version 1.7.1 with previous version 1.7.0 dated 2021-10-30

Title: Generate High-Resolution Venn and Euler Plots
Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Author: Hanbo Chen
Maintainer: Paul Boutros <pboutros@mednet.ucla.edu>

Diff between VennDiagram versions 1.7.0 dated 2021-10-30 and 1.7.1 dated 2021-12-02

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Package ARCokrig updated to version 0.1.2 with previous version 0.1.1 dated 2020-07-08

Title: Autoregressive Cokriging Models for Multifidelity Codes
Description: For emulating multifidelity computer models. The major methods include univariate autoregressive cokriging and multivariate autoregressive cokriging. The autoregressive cokriging methods are implemented for both hierarchically nested design and non-nested design. For hierarchically nested design, the model parameters are estimated via standard optimization algorithms; For non-nested design, the model parameters are estimated via Monte Carlo expectation-maximization (MCEM) algorithms. In both cases, the priors are chosen such that the posterior distributions are proper. Notice that the uniform priors on range parameters in the correlation function lead to improper posteriors. This should be avoided when Bayesian analysis is adopted. The development of objective priors for autoregressive cokriging models can be found in Pulong Ma (2020) <DOI:10.1137/19M1289893>. The development of the multivariate autoregressive cokriging models with possibly non-nested design can be found in Pulong Ma, Georgios Karagiannis, Bledar A Konomi, Taylor G Asher, Gabriel R Toro, and Andrew T Cox (2019) <arXiv:1909.01836>.
Author: Pulong Ma [aut, cre]
Maintainer: Pulong Ma <mpulong@gmail.com>

Diff between ARCokrig versions 0.1.1 dated 2020-07-08 and 0.1.2 dated 2021-12-02

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Package tidyquery updated to version 0.2.3 with previous version 0.2.2 dated 2021-02-06

Title: Query 'R' Data Frames with 'SQL'
Description: Use 'SQL' 'SELECT' statements to query 'R' data frames.
Author: Ian Cook [aut, cre], Cloudera [cph]
Maintainer: Ian Cook <ianmcook@gmail.com>

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Package RawHummus updated to version 0.2.1 with previous version 0.2.0 dated 2021-10-11

Title: Raw Data Quality Control Tool for LC-MS System
Description: Assess LC–MS system performance by visualizing instrument log files and monitoring raw quality control samples within a project.
Author: Yonghui Dong
Maintainer: Yonghui Dong <yonghui.dong@gmail.com>

Diff between RawHummus versions 0.2.0 dated 2021-10-11 and 0.2.1 dated 2021-12-02

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Package mfp updated to version 1.5.2.1 with previous version 1.5.2 dated 2015-09-09

Title: Multivariable Fractional Polynomials
Description: Fractional polynomials are used to represent curvature in regression models. A key reference is Royston and Altman, 1994.
Author: original by Gareth Ambler <gareth@stats.ucl.ac.uk>, modified by Axel Benner <benner@dkfz.de>
Maintainer: ORPHANED

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Package udpipe updated to version 0.8.8 with previous version 0.8.6 dated 2021-06-01

Title: Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <https://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>. The toolkit also contains functionalities for commonly used data manipulations on texts which are enriched with the output of the parser. Namely functionalities and algorithms for collocations, token co-occurrence, document term matrix handling, term frequency inverse document frequency calculations, information retrieval metrics (Okapi BM25), handling of multi-word expressions, keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntactical patterns) sentiment scoring and semantic similarity analysis.
Author: Jan Wijffels [aut, cre, cph], BNOSAC [cph], Institute of Formal and Applied Linguistics, Faculty of Mathematics and Physics, Charles University in Prague, Czech Republic [cph], Milan Straka [ctb, cph], Jana Straková [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>

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Package qqconf updated to version 1.1.0 with previous version 1.0.0 dated 2021-08-17

Title: Creates Simultaneous Testing Bands for QQ-Plots
Description: Provides functionality for creating Quantile-Quantile (QQ) and Probability-Probability (PP) plots with simultaneous testing bands to asses significance of sample deviation from a reference distribution.
Author: Eric Weine [aut, cre], Mary Sara McPeek [aut], Abney Mark [aut]
Maintainer: Eric Weine <ericweine15@gmail.com>

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Package DescrTab2 updated to version 2.1.7 with previous version 2.0.7 dated 2021-03-15

Title: Publication Quality Descriptive Statistics Tables
Description: Provides functions to create descriptive statistics tables for continuous and categorical variables. By default, summary statistics such as mean, standard deviation, quantiles, minimum and maximum for continuous variables and relative and absolute frequencies for categorical variables are calculated. 'DescrTab2' features a sophisticated algorithm to choose appropriate test statistics for your data and provides p-values. On top of this, confidence intervals for group differences of appropriated summary measures are automatically produces for two-group comparison. Tables generated by 'DescrTab2' can be integrated in a variety of document formats, including .html, .tex and .docx documents. 'DescrTab2' also allows printing tables to console and saving table objects for later use.
Author: Jan Meis [aut, cre] (<https://orcid.org/0000-0001-5407-7220>), Lukas Baumann [aut] (<https://orcid.org/0000-0001-7931-7470>), Maximilian Pilz [aut] (<https://orcid.org/0000-0002-9685-1613>), Lukas Sauer [aut] (<https://orcid.org/0000-0002-1340-9994>), Lorenz Uhlmann [ctb], Csilla van Lunteren [ctb], Kevin Kunzmann [ctb], Hao Zhu [ctb] (<https://orcid.org/0000-0002-3386-6076>)
Maintainer: Jan Meis <meis@imbi.uni-heidelberg.de>

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Package preferably updated to version 0.4 with previous version 0.3.1 dated 2021-05-02

Title: A 'pkgdown' Template
Description: This is an accessible template for 'pkgdown'. It uses two bootstrap themes, Flatly and Darkly and utilizes the 'prefers-color-scheme' CSS variable to automatically serve either of the two based on user’s operating system setting, or allowing them to manually toggle between them.
Author: Amir Masoud Abdol [aut, cre]
Maintainer: Amir Masoud Abdol <i@amirmasoudabdol.name>

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Permanent link

Package clock updated to version 0.6.0 with previous version 0.5.0 dated 2021-10-29

Title: Date-Time Types and Tools
Description: Provides a comprehensive library for date-time manipulations using a new family of orthogonal date-time classes (durations, time points, zoned-times, and calendars) that partition responsibilities so that the complexities of time zones are only considered when they are really needed. Capabilities include: date-time parsing, formatting, arithmetic, extraction and updating of components, and rounding.
Author: Davis Vaughan [aut, cre], RStudio [cph, fnd]
Maintainer: Davis Vaughan <davis@rstudio.com>

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Permanent link

New package RAT with initial version 0.1.0
Package: RAT
Title: Research Assessment Tools
Version: 0.1.0
Date: 2021-12-01
Description: Includes algorithms to assess research productivity and patterns, such as the h-index and i-index. Cardoso et al. (subm.) Quantifying the international collaboration of researchers and research institutions.
Depends: R (>= 3.5.0)
Imports: ggplot2, graphics, mapproj, stats, utils, wosr
Encoding: UTF-8
License: GPL-3
LazyData: true
NeedsCompilation: no
Packaged: 2021-12-02 11:23:45 UTC; ungol
Author: Pedro Cardoso [aut, cre], Stefano Mammola [aut]
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Repository: CRAN
Date/Publication: 2021-12-02 14:10:02 UTC

More information about RAT at CRAN
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Package qad updated to version 1.0.1 with previous version 1.0.0 dated 2021-02-27

Title: Quantification of Asymmetric Dependence
Description: A copula-based measure for quantifying asymmetry in dependence and associations. Documentation and theory about 'qad' is provided by the paper by Junker, Griessenberger & Trutschnig (2021, <doi:10.1016/j.csda.2020.107058>), and the paper by Trutschnig (2011, <doi:10.1016/j.jmaa.2011.06.013>).
Author: Florian Griessenberger [aut, cre], Robert R. Junker [aut], Valentin Petzel [aut], Wolfgang Trutschnig [aut]
Maintainer: Florian Griessenberger <florian.griessenberger@sbg.ac.at>

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New package rsat with initial version 0.1.16
Package: rsat
Title: Dealing with Multiplatform Satellite Images
Version: 0.1.16
Maintainer: Unai Pérez - Goya <unai.perez@unavarra.es>
Description: Downloading, customizing, and processing time series of satellite images for a region of interest. 'rsat' functions allow a unified access to multispectral images from Landsat, MODIS and Sentinel repositories. 'rsat' also offers capabilities for customizing satellite images, such as tile mosaicking, image cropping and new variables computation. Finally, 'rsat' covers the processing, including cloud masking, compositing and gap-filling/smoothing time series of images (Militino et al., 2018 <doi:10.3390/rs10030398> and Militino et al., 2019 <doi:10.1109/TGRS.2019.2904193>).
Depends: R (>= 4.0.0)
Imports: XML, curl, httr, leafem, leaflet, rjson, rvest, tmap, xml2, zip, methods, sp, Rdpack, fields, calendR, raster, sf, stars, terra
URL: https://github.com/ropensci/rsat
BugReports: https://github.com/ropensci/rsat/issues
RdMacros: Rdpack
Suggests: rgdal, knitr, rmarkdown, covr, testthat
License: GPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-02 08:10:44 UTC; unai.perez
Author: Unai Pérez - Goya [aut, cre] (<https://orcid.org/0000-0002-2796-9079>), Manuel Montesino - SanMartin [aut] (<https://orcid.org/0000-0002-0822-600X>), Ana F Militino [aut] (<https://orcid.org/0000-0002-0631-3919>), Maria Dolores Ugarte [aut] (<https://orcid.org/0000-0002-3505-8400>), Marc Weber [rev] (Marc reviewed rsat (v. 0.1.14) for rOpenSci, see <https://github.com/ropensci/software-review/issues/437>), Kelly Hondula [rev] (Kelly reviewed rsat (v. 0.1.14) for rOpenSci, see <https://github.com/ropensci/software-review/issues/437>)
Repository: CRAN
Date/Publication: 2021-12-02 13:40:02 UTC

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New package renz with initial version 0.1.1
Package: renz
Title: R-Enzymology
Version: 0.1.1
Author: Juan Carlos Aledo
Maintainer: Juan Carlos Aledo <caledo@uma.es>
Description: Contains utilities for the analysis of Michaelian kinetic data. Beside the classical linearization methods (Lineweaver-Burk, Eadie-Hofstee, Hanes-Woolf and Eisenthal-Cornish-Bowden), features include the ability to carry out weighted regression analysis that, in most cases, substantially improves the estimation of kinetic parameters (Aledo (2021) <doi:10.1002/bmb.21522>). To avoid data transformation and the potential biases introduced by them, the package also offers functions to directly fitting data to the Michaelis-Menten equation, either using ([S], v) or (time, [S]) data. Utilities to simulate substrate progress-curves (making use of the Lambert W function) are also provided. The package is accompanied of vignettes that aim to orientate the user in the choice of the most suitable method to estimate the kinetic parameter of an Michaelian enzyme.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0)
Imports: graphics, stats, VGAM
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-02 10:39:34 UTC; JCA
Repository: CRAN
Date/Publication: 2021-12-02 13:50:02 UTC

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Package R2BEAT updated to version 1.0.4 with previous version 1.0.3 dated 2021-06-24

Title: Multistage Sampling Allocation and Sample Selection
Description: Multivariate optimal allocation for different domains in one and two stages stratified sample design. R2BEAT extends the Neyman (1934) – Tschuprow (1923) allocation method to the case of several variables, adopting a generalization of the Bethel’s proposal (1989).R2BEAT develops this methodology but, moreover, it allows to determine the sample allocation in the multivariate and multi-domains case of estimates for two-stage stratified samples. It also allows to perform both Primary Stage Units and Secondary Stage Units selection. This package requires the availability of ReGenesees, that can be installed from <https://github.com/DiegoZardetto/ReGenesees>.
Author: Andrea Fasulo,Giulio Barcaroli,Stefano Falorsi,Alessio Guandalini,Daniela Pagliuca,Marco Dionisio Terribili
Maintainer: Andrea Fasulo <fasulo@istat.it>

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New package quiltr with initial version 0.1.0
Package: quiltr
Title: Qualtrics for Labelling Text using R
Version: 0.1.0
Description: Functions to convert text data for labelling into format appropriate for importing into Qualtrics. Supports multiple language, including right-to-left scripts as well as different response types. Outputs an Advance Format .txt file that read into Qualtrics.
License: MIT + file LICENSE
Language: en-US
Encoding: UTF-8
LazyData: true
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 2.10)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-02 10:24:57 UTC; cbarrie6
Author: Christopher Barrie [aut, cre] (<https://orcid.org/0000-0002-9156-990X>)
Maintainer: Christopher Barrie <christopher.barrie@ed.ac.uk>
Repository: CRAN
Date/Publication: 2021-12-02 13:40:07 UTC

More information about quiltr at CRAN
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Package MorphoTools2 updated to version 0.9.1 with previous version 0.9.0 dated 2021-11-22

Title: Multivariate Morphometric Analysis
Description: Tools for multivariate analyses of morphological data, wrapped in one package, to make the workflow convenient and fast. Statistical and graphical tools provide a comprehensive framework for checking and manipulating input data, statistical analyses, and visualization of results. Several methods are provided for the analysis of raw data, to make the dataset ready for downstream analyses. Integrated statistical methods include hierarchical classification, principal component analysis, principal coordinates analysis, non-metric multidimensional scaling, and multiple discriminant analyses: canonical, stepwise, and classificatory (linear, quadratic, and the non-parametric k nearest neighbours). The philosophy of the package will be described in Šlenker et al. (in prep).
Author: Marek Šlenker [aut, cre] (https://orcid.org/0000-0002-5919-890X) Petr Koutecký [ctb] (https://orcid.org/0000-0002-3455-850X) Karol Marhold [ctb] (https://orcid.org/0000-0002-7658-0844)
Maintainer: Marek Šlenker <marek.slenker@savba.sk>

Diff between MorphoTools2 versions 0.9.0 dated 2021-11-22 and 0.9.1 dated 2021-12-02

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Package MNARclust updated to version 1.1.0 with previous version 1.0.0 dated 2021-07-16

Title: Clustering Data with Non-Ignorable Missingness using Semi-Parametric Mixture Models
Description: Clustering of data under a non-ignorable missingness mechanism. Clustering is achieved by a semi-parametric mixture model and missingness is managed by using the pattern-mixture approach. More details of the approach are available in Du Roy de Chaumaray et al. (2020) <arXiv:2009.07662>.
Author: Marie Du Roy de Chaumaray [aut], Matthieu Marbac [aut, cre, cph]
Maintainer: Matthieu Marbac <matthieu.marbac-lourdelle@ensai.fr>

Diff between MNARclust versions 1.0.0 dated 2021-07-16 and 1.1.0 dated 2021-12-02

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Package cmsafvis updated to version 1.1.9 with previous version 1.1.8 dated 2021-11-02

Title: Tools to Visualize CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF) is a ground segment of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application Facilities. The CM SAF contributes to the sustainable monitoring of the climate system by providing essential climate variables related to the energy and water cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight National Meteorological and Hydrological Services. The 'cmsafvis' R-package provides a collection of R-operators for the analysis and visualization of CM SAF NetCDF data. CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>). Detailed information and test data are provided on the CM SAF webpage (<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre], Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>

Diff between cmsafvis versions 1.1.8 dated 2021-11-02 and 1.1.9 dated 2021-12-02

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More information about cmsafvis at CRAN
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Package cmsafops updated to version 1.2.2 with previous version 1.2.1 dated 2021-10-14

Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF) is a ground segment of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application Facilities. The CM SAF contributes to the sustainable monitoring of the climate system by providing essential climate variables related to the energy and water cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight National Meteorological and Hydrological Services. The 'cmsafops' R-package provides a collection of R-operators for the analysis and manipulation of CM SAF NetCDF formatted data. Other CF conform NetCDF data with time, longitude and latitude dimension should be applicable, but there is no guarantee for an error-free application. CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>). Detailed information and test data are provided on the CM SAF webpage (<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre], Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>

Diff between cmsafops versions 1.2.1 dated 2021-10-14 and 1.2.2 dated 2021-12-02

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More information about cmsafops at CRAN
Permanent link

Package cmsaf updated to version 3.3.1 with previous version 3.3.0 dated 2021-10-14

Title: A Toolbox for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF) is a ground segment of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application Facilities. The CM SAF contributes to the sustainable monitoring of the climate system by providing essential climate variables related to the energy and water cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight National Meteorological and Hydrological Services. The 'cmsaf' R-package includes a 'shiny' based interface for an easy application of the 'cmsafops' and 'cmsafvis' packages - the CM SAF R Toolbox. The Toolbox offers an easy way to prepare, manipulate, analyse and visualize CM SAF NetCDF formatted data. Other CF conform NetCDF data with time, longitude and latitude dimension should be applicable, but there is no guarantee for an error-free application. CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>). Detailed information and test data are provided on the CM SAF webpage (<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre], Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>

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Package ClusPred updated to version 1.1.0 with previous version 1.0.0 dated 2021-06-18

Title: Simultaneous Semi-Parametric Estimation of Clustering and Regression
Description: Parameter estimation of regression models with fixed group effects, when the group variable is missing while group-related variables are available. Parametric and semi-parametric approaches described in Marbac et al. (2020) <arXiv:2012.14159> are implemented.
Author: Matthieu Marbac [aut, cre, cph], Mohammed Sedki [aut], Christophe Biernacki [aut], Vincent Vandewalle [aut]
Maintainer: Matthieu Marbac <matthieu.marbac-lourdelle@ensai.fr>

Diff between ClusPred versions 1.0.0 dated 2021-06-18 and 1.1.0 dated 2021-12-02

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Package NetSci updated to version 0.1.2 with previous version 0.1.1 dated 2021-08-03

Title: Calculates Basic Network Measures Commonly Used in Network Medicine
Description: Calculates network measures such as Largest Connected Component (LCC), Proximity, Separation, Jaccard Index, along with permutation, when needed.
Author: Deisy Gysi
Maintainer: Deisy Morselli Gysi <deisy.ccnr@gmail.com>

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Package dialrjars updated to version 8.12.38 with previous version 8.12.29 dated 2021-08-23

Title: Required 'libphonenumber' jars for the 'dialr' Package
Description: Collects 'libphonenumber' jars required for the 'dialr' package.
Author: Danny Smith [aut, cre], Google Inc. [ctb, cph] (libphonenumber), Vonage Holdings Corp. [ctb, cph] (libphonenumber), Ian Galpin [ctb, cph] (libphonenumber), Ben Gertzfield [ctb, cph] (libphonenumber)
Maintainer: Danny Smith <danny@gorcha.org>

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Package elasdics updated to version 0.1.4 with previous version 0.1.3 dated 2021-10-28

Title: Elastic Analysis of Sparse, Dense and Irregular Curves
Description: Provides functions to align curves and to compute mean curves based on the elastic distance defined in the square-root-velocity framework. For more details on this framework see Srivastava and Klassen (2016, <doi:10.1007/978-1-4939-4020-2>). For more theoretical details on our methods and algorithms see Steyer et al. (2021, <arXiv:2104.11039>).
Author: Lisa Steyer <lisa.steyer@hu-berlin.de>
Maintainer: Lisa Steyer <lisa.steyer@hu-berlin.de>

Diff between elasdics versions 0.1.3 dated 2021-10-28 and 0.1.4 dated 2021-12-02

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Package PSweight updated to version 1.1.6 with previous version 1.1.5 dated 2021-10-28

Title: Propensity Score Weighting for Causal Inference with Observational Studies and Randomized Trials
Description: Supports propensity score weighting analysis of observational studies and randomized trials. Enables the estimation and inference of average causal effects with binary and multiple treatments using overlap weights (ATO), inverse probability of treatment weights (ATE), average treatment effect among the treated weights (ATT), matching weights (ATM) and entropy weights (ATEN), with and without propensity score trimming. These weights are members of the family of balancing weights introduced in Li, Morgan and Zaslavsky (2018) <doi:10.1080/01621459.2016.1260466> and Li and Li (2019) <doi:10.1214/19-AOAS1282>.
Author: Tianhui Zhou [aut, cre], Guangyu Tong [aut], Fan Li [aut], Laine Thomas [aut], Fan Li [aut]
Maintainer: Tianhui Zhou <tianhui.zhou@duke.edu>

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Package japanmesh updated to version 0.1.1 with previous version 0.1.0 dated 2021-11-19

Title: Functions for the Japanese Regional Mesh Codes ('JIS X 0410')
Description: Functions for the Japanese regional mesh codes defined in 'JIS X 0410' (<https://www.jisc.go.jp/app/jis/general/GnrJISNumberNameSearchList?show&jisStdNo=X0410>). Conversion between regional mesh codes and longitude/latitude, and between mesh codes of different scales.
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>

Diff between japanmesh versions 0.1.0 dated 2021-11-19 and 0.1.1 dated 2021-12-02

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New package hacksig with initial version 0.1.1
Package: hacksig
Title: A Tidy Framework to Hack Gene Expression Signatures
Version: 0.1.1
Description: A collection of cancer transcriptomics gene signatures as well as a simple and tidy interface to compute single sample enrichment scores either with the original procedure or with three alternatives: the "combined z-score" of Lee et al. (2008) <doi:10.1371/journal.pcbi.1000217>, the "single sample GSEA" of Barbie et al. (2009) <doi:10.1038/nature08460> and the "singscore" of Foroutan et al. (2018) <doi:10.1186/s12859-018-2435-4>. The 'get_sig_info()' function can be used to retrieve information about each signature implemented.
License: MIT + file LICENSE
URL: https://github.com/Acare/hacksig
BugReports: https://github.com/Acare/hacksig/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0)
Imports: dplyr (>= 1.0.7), future.apply (>= 1.8.1), rlang (>= 0.4.11), stats (>= 4.0.5), tibble (>= 3.1.5), tidyr (>= 1.1.4)
Suggests: covr, future (>= 1.22.1), ggplot2 (>= 3.3.5), knitr (>= 1.36), msigdbr (>= 7.4.1), purrr (>= 0.3.4), rmarkdown (>= 2.11)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-01 15:54:03 UTC; andrea
Author: Andrea Carenzo [aut, cre] (<https://orcid.org/0000-0001-6804-9984>), Loris De Cecco [aut] (<https://orcid.org/0000-0002-7066-473X>), Federico Pistore [aut]
Maintainer: Andrea Carenzo <andrea.carenzo@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-02 08:50:05 UTC

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New package gplsim with initial version 0.9.0
Package: gplsim
Title: Penalized Spline Estimation for GPLSIM
Version: 0.9.0
Date: 2021-11-24
Description: We provides functions that employ penalized spline (P-spline) to estimate generalized partially linear single index models (GPLSIM), which extend the generalized linear models to include nonlinear effect for some predictors. Please see Y. (2017) at <doi:10.1007/s11222-016-9639-0> and Y., and R. (2002) at <doi:10.1198/016214502388618861> for more details.
License: GPL-2
Encoding: UTF-8
Depends: R (>= 3.6.0)
Imports: mgcv, stats, minpack.lm
LazyData: true
NeedsCompilation: no
Packaged: 2021-12-01 14:40:06 UTC; tianhaizu
Author: Tianhai Zu [aut, trl, cre], Yan Yu [aut]
Maintainer: Tianhai Zu <zuti@mail.uc.edu>
Repository: CRAN
Date/Publication: 2021-12-02 08:30:02 UTC

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New package easyDifferentialGeneCoexpression with initial version 0.7
Encoding: UTF-8
Package: easyDifferentialGeneCoexpression
Title: Easily Computes the Differential Coexpression Analysis
Version: 0.7
Description: A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression. If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found. Platforms available: GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.
BugReports: https://github.com/davidechicco/easyDifferentialGeneCoexpression/issues
Depends: R (>= 4.0.0)
License: GPL-3
URL: https://github.com/davidechicco/easyDifferentialGeneCoexpression
Imports: WGCNA, Matrix, Biobase, GEOquery, diffcoexp, annotate, easypackages, geneExpressionFromGEO, dplyr, jetset, markdown, R.utils, magrittr, xml2
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-12-01 14:34:42 UTC; dave
Author: Davide Chicco [aut, cre] (<https://orcid.org/0000-0001-9655-7142>)
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Repository: CRAN
Date/Publication: 2021-12-02 08:30:05 UTC

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Package autostsm updated to version 2.1 with previous version 2.0 dated 2021-11-08

Title: Automatic Structural Time Series Models
Description: Automatic model selection for structural time series decomposition into trend, cycle, and seasonal components, plus optionality for structural interpolation, using the Kalman filter. Koopman, Siem Jan and Marius Ooms (2012) "Forecasting Economic Time Series Using Unobserved Components Time Series Models" <doi:10.1093/oxfordhb/9780195398649.013.0006>. Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>

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Package asteRisk updated to version 1.2.0 with previous version 1.1.0 dated 2021-07-05

Title: Computation of Satellite Position
Description: Provides basic functionalities to calculate the position of satellites given a known state vector. The package includes implementations of the SGP4 and SDP4 simplified perturbation models to propagate orbital state vectors, as well as utilities to read TLE files and convert coordinates between different frames of reference. Several of the functionalities of the package (including the high-precision numerical orbit propagator) require the coefficients and data included in the 'asteRiskData' package, available in a 'drat' repository. To install this data package, run 'install.packages("asteRiskData", repos="https://rafael-ayala.github.io/drat/")'. Felix R. Hoots, Ronald L. Roehrich and T.S. Kelso (1988) <https://celestrak.com/NORAD/documentation/spacetrk.pdf>. David Vallado, Paul Crawford, Richard Hujsak and T.S. Kelso (2012) <doi:10.2514/6.2006-6753>. Felix R. Hoots, Paul W. Schumacher Jr. and Robert A. Glover (2014) <doi:10.2514/1.9161>.
Author: Rafael Ayala [aut, cre] (<https://orcid.org/0000-0002-9332-4623>), Daniel Ayala [aut] (<https://orcid.org/0000-0003-2095-1009>), David Ruiz [aut] (<https://orcid.org/0000-0003-4460-5493>), Lara Selles Vidal [aut] (<https://orcid.org/0000-0003-2537-6824>)
Maintainer: Rafael Ayala <rafael.ayala@oist.jp>

Diff between asteRisk versions 1.1.0 dated 2021-07-05 and 1.2.0 dated 2021-12-02

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Package uwot updated to version 0.1.11 with previous version 0.1.10 dated 2020-12-15

Title: The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction
Description: An implementation of the Uniform Manifold Approximation and Projection dimensionality reduction by McInnes et al. (2018) <arXiv:1802.03426>. It also provides means to transform new data and to carry out supervised dimensionality reduction. An implementation of the related LargeVis method of Tang et al. (2016) <arXiv:1602.00370> is also provided. This is a complete re-implementation in R (and C++, via the 'Rcpp' package): no Python installation is required. See the uwot website (<https://github.com/jlmelville/uwot>) for more documentation and examples.
Author: James Melville [aut, cre], Aaron Lun [ctb], Mohamed Nadhir Djekidel [ctb], Yuhan Hao [ctb]
Maintainer: James Melville <jlmelville@gmail.com>

Diff between uwot versions 0.1.10 dated 2020-12-15 and 0.1.11 dated 2021-12-02

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Package GUTS updated to version 1.2 with previous version 1.1.1 dated 2019-07-05

Title: Fast Calculation of the Likelihood of a Stochastic Survival Model
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the fast calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert <carlo.albert@eawag.ch>, Sören Vogel <soeren.vogel@posteo.ch>, Oliver Jakoby <oliver.jakoby@rifcon.de>, Alexander Singer <alexander.singer@rifcon.de> and Dirk Nickisch <dirk.nickisch@rifcon.de>
Maintainer: Oliver Jakoby <oliver.jakoby@rifcon.de>

Diff between GUTS versions 1.1.1 dated 2019-07-05 and 1.2 dated 2021-12-02

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Package gridpattern updated to version 0.3.1 with previous version 0.2.1 dated 2021-07-17

Title: 'grid' Pattern Grobs
Description: Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.
Author: Mike FC [aut] (Code/docs adapted from ggpattern), Trevor L Davis [aut, cre], Thomas Lin Pedersen [ctb] (new_data_frame() copied from ggplot2)
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>

Diff between gridpattern versions 0.2.1 dated 2021-07-17 and 0.3.1 dated 2021-12-02

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Package rdrobust updated to version 1.0.8 with previous version 1.0.7 dated 2021-11-05

Title: Robust Data-Driven Statistical Inference in Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <sebastian.calonico@columbia.edu>, Matias D. Cattaneo <cattaneo@princeton.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@princeton.edu>
Maintainer: Sebastian Calonico <sebastian.calonico@columbia.edu>

Diff between rdrobust versions 1.0.7 dated 2021-11-05 and 1.0.8 dated 2021-12-02

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Package migest updated to version 2.0.2 with previous version 2.0.1 dated 2021-10-30

Title: Methods for the Indirect Estimation of Bilateral Migration
Description: Tools for estimating, measuring and working with migration data.
Author: Guy J. Abel [aut, cre] (<https://orcid.org/0000-0002-4893-5687>)
Maintainer: Guy J. Abel <g.j.abel@gmail.com>

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Package imputeMulti updated to version 0.8.3 with previous version 0.6.4 dated 2017-02-12

Title: Imputation Methods for Multivariate Multinomial Data
Description: Implements imputation methods using EM and Data Augmentation for multinomial data following the work of Schafer 1997 <ISBN: 978-0-412-04061-0>.
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>

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Package drat updated to version 0.2.2 with previous version 0.2.1 dated 2021-07-10

Title: 'Drat' R Archive Template
Description: Creation and use of R Repositories via helper functions to insert packages into a repository, and to add repository information to the current R session. Two primary types of repositories are support: gh-pages at GitHub, as well as local repositories on either the same machine or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel with contributions by Carl Boettiger, Neal Fultz, Sebastian Gibb, Colin Gillespie, Jan Górecki, Matt Jones, Thomas Leeper, Steven Pav, Jan Schulz, Christoph Stepper, Felix G.M. Ernst and Patrick Schratz.
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Wed, 01 Dec 2021

Package multidplyr updated to version 0.1.1 with previous version 0.1.0 dated 2021-02-08

Title: A Multi-Process 'dplyr' Backend
Description: Partition a data frame across multiple worker processes to provide simple multicore parallelism.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package mecor updated to version 1.0.0 with previous version 0.9.0 dated 2021-01-14

Title: Measurement Error Correction in Linear Models with a Continuous Outcome
Description: Covariate measurement error correction is implemented by means of regression calibration by Carroll RJ, Ruppert D, Stefanski LA & Crainiceanu CM (2006, ISBN:1584886331), efficient regression calibration by Spiegelman D, Carroll RJ & Kipnis V (2001) <doi:10.1002/1097-0258(20010115)20:1%3C139::AID-SIM644%3E3.0.CO;2-K> and maximum likelihood estimation by Bartlett JW, Stavola DBL & Frost C (2009) <doi:10.1002/sim.3713>. Outcome measurement error correction is implemented by means of the method of moments by Buonaccorsi JP (2010, ISBN:1420066560) and efficient method of moments by Keogh RH, Carroll RJ, Tooze JA, Kirkpatrick SI & Freedman LS (2014) <doi:10.1002/sim.7011>. Standard error estimation of the corrected estimators is implemented by means of the Delta method by Rosner B, Spiegelman D & Willett WC (1990) <doi:10.1093/oxfordjournals.aje.a115715> and Rosner B, Spiegelman D & Willett WC (1992) <doi:10.1093/oxfordjournals.aje.a116453>, the Fieller method described by Buonaccorsi JP (2010, ISBN:1420066560), and the Bootstrap by Carroll RJ, Ruppert D, Stefanski LA & Crainiceanu CM (2006, ISBN:1584886331).
Author: Linda Nab
Maintainer: Linda Nab <lindanab4@gmail.com>

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Package rmcorr updated to version 0.4.5 with previous version 0.4.4 dated 2021-08-10

Title: Repeated Measures Correlation
Description: Compute the repeated measures correlation, a statistical technique for determining the overall within-individual relationship among paired measures assessed on two or more occasions, first introduced by Bland and Altman (1995). Includes functions for diagnostics, p-value, effect size with confidence interval including optional bootstrapping, as well as graphing. Also includes several example datasets. For more details, see Bakdash and Marusich (2017) <doi:10.3389/fpsyg.2017.00456>.
Author: Jonathan Z. Bakdash, Laura R. Marusich
Maintainer: Laura R. Marusich <lmarusich@gmail.com>

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Package causaldata updated to version 0.1.3 with previous version 0.1.1 dated 2021-05-20

Title: Example Data Sets for Causal Inference Textbooks
Description: Example data sets to run the example problems from causal inference textbooks. Currently, contains data sets for Huntington-Klein, Nick (2021) "The Effect" <https://theeffectbook.net>, Cunningham, Scott (2021, ISBN-13: 978-0-300-25168-5) "Causal Inference: The Mixtape", and Hernán, Miguel and James Robins (2020) "Causal Inference: What If" <https://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/>.
Author: Nick Huntington-Klein [aut, cre] (<https://orcid.org/0000-0002-7352-3991>), Malcolm Barrett [aut] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Nick Huntington-Klein <nhuntington-klein@seattleu.edu>

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Package OECD updated to version 0.2.5 with previous version 0.2.4 dated 2019-10-15

Title: Search and Extract Data from the OECD
Description: Search and extract data from the Organization for Economic Cooperation and Development (OECD).
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>

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Package ConfusionTableR updated to version 1.0.4 with previous version 1.0.3 dated 2021-11-01

Title: Confusion Matrix Toolset
Description: Takes the outputs of a 'caret' confusion matrix and allows for the quick conversion of these list items to lists. The intended usage is to allow the tool to work with the outputs of machine learning classification models. This tool works with classification problems for binary and multi-classification problems and allows for the record level conversion of the confusion matrix outputs. This is useful, as it allows quick conversion of these objects for storage in database systems and to track ML model performance over time. Traditionally, this approach has been used for highlighting model representation and feature slippage.
Author: Gary Hutson [aut, cre] (<https://orcid.org/0000-0003-3534-6143>)
Maintainer: Gary Hutson <hutsons-hacks@outlook.com>

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Package ptmixed updated to version 1.1.1 with previous version 1.1.0 dated 2021-11-05

Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits the Poisson-Tweedie generalized linear mixed model described in Signorelli et al. (2021, <doi:10.1177/1471082X20936017>). Likelihood approximation based on adaptive Gauss Hermite quadrature rule.
Author: Mirko Signorelli [aut, cre, cph] (<https://orcid.org/0000-0002-8102-3356>), Pietro Spitali [ctb], Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>

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Package pencal updated to version 1.0.1 with previous version 1.0.0 dated 2021-09-03

Title: Penalized Regression Calibration (PRC)
Description: Computes penalized regression calibration (PRC), a statistical method that allows to predict survival from high-dimensional longitudinal predictors. PRC is described in Signorelli et al. (2021, <doi:10.1002/sim.9178>)).
Author: Mirko Signorelli [aut, cre, cph] (<https://orcid.org/0000-0002-8102-3356>), Pietro Spitali [ctb], Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>

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Package pak updated to version 0.2.0 with previous version 0.1.2.1 dated 2020-11-19

Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and more reliable. In particular, it performs all HTTP operations in parallel, so metadata resolution and package downloads are fast. Metadata and package files are cached on the local disk as well. 'pak' has a dependency solver, so it finds version conflicts before performing the installation. This version of 'pak' supports CRAN, 'Bioconductor' and 'GitHub' packages as well.
Author: Gábor Csárdi [aut, cre], Jim Hester [aut], RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package REddyProc updated to version 1.3.1 with previous version 1.3.0 dated 2021-10-14

Title: Post Processing of (Half-)Hourly Eddy-Covariance Measurements
Description: Standard and extensible Eddy-Covariance data post-processing (Wutzler et al. (2018) <doi:10.5194/bg-15-5015-2018>) includes uStar-filtering, gap-filling, and flux-partitioning. The Eddy-Covariance (EC) micrometeorological technique quantifies continuous exchange fluxes of gases, energy, and momentum between an ecosystem and the atmosphere. It is important for understanding ecosystem dynamics and upscaling exchange fluxes. (Aubinet et al. (2012) <doi:10.1007/978-94-007-2351-1>). This package inputs pre-processed (half-)hourly data and supports further processing. First, a quality-check and filtering is performed based on the relationship between measured flux and friction velocity (uStar) to discard biased data (Papale et al. (2006) <doi:10.5194/bg-3-571-2006>). Second, gaps in the data are filled based on information from environmental conditions (Reichstein et al. (2005) <doi:10.1111/j.1365-2486.2005.001002.x>). Third, the net flux of carbon dioxide is partitioned into its gross fluxes in and out of the ecosystem by night-time based and day-time based approaches (Lasslop et al. (2010) <doi:10.1111/j.1365-2486.2009.02041.x>).
Author: Department for Biogeochemical Integration at MPI-BGC, Jena, Germany [cph], Thomas Wutzler [aut, cre], Markus Reichstein [aut], Antje Maria Moffat [aut, trl], Olaf Menzer [ctb], Mirco Migliavacca [aut], Kerstin Sickel [ctb, trl], Ladislav <U+0160>igut [ctb]
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>

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Package likelihoodR updated to version 1.0.7 with previous version 1.0.6 dated 2021-10-29

Title: Likelihood Analyses for Common Statistical Tests
Description: A collection of functions that calculate the log likelihood (support) for a range of statistical tests. Where possible the likelihood function and likelihood interval for the observed data are displayed. The evidential approach used here is based on the book "Likelihood" by A.W.F. Edwards (1992, ISBN-13 : 978-0801844430), "Statistical Evidence" by R. Royall (1997, ISBN-13 : 978-0412044113), S.N. Goodman & R. Royall (2011) <doi:10.2105/AJPH.78.12.1568>, "Understanding Psychology as a Science" by Z. Dienes (2008, ISBN-13 : 978-0230542310), S. Glover & P. Dixon <https://link.springer.com/article/10.3758/BF03196706> and others. This package accompanies "Evidence-Based Statistics" by P. Cahusac (2020, ISBN-13 : 978-1119549802).
Author: Peter Cahusac [aut, cre] (<https://orcid.org/0000-0003-4976-2834>)
Maintainer: Peter Cahusac <peteqsac@gmail.com>

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Package radix (with last version 0.6) was removed from CRAN

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

2018-12-09 0.6
2018-09-17 0.5

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Package dfphase1 updated to version 1.1.4 with previous version 1.1.3 dated 2021-02-17

Title: Phase I Control Charts (with Emphasis on Distribution-Free Methods)
Description: Statistical methods for retrospectively detecting changes in location and/or dispersion of univariate and multivariate variables. Data values are assumed to be independent, can be individual (one observation at each instant of time) or subgrouped (more than one observation at each instant of time). Control limits are computed, often using a permutation approach, so that a prescribed false alarm probability is guaranteed without making any parametric assumptions on the stable (in-control) distribution. See G. Capizzi and G. Masarotto (2018) <doi:10.1007/978-3-319-75295-2_1> for an introduction to the package.
Author: Giovanna Capizzi and Guido Masarotto
Maintainer: Giovanna Capizzi <giovanna.capizzi@unipd.it>

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Package alookr updated to version 0.3.5 with previous version 0.3.4 dated 2021-02-22

Title: Model Classifier for Binary Classification
Description: A collection of tools that support data splitting, predictive modeling, and model evaluation. A typical function is to split a dataset into a training dataset and a test dataset. Then compare the data distribution of the two datasets. Another feature is to support the development of predictive models and to compare the performance of several predictive models, helping to select the best model.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>

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Package stringfish updated to version 0.15.5 with previous version 0.15.4 dated 2021-10-15

Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph], Phillip Hazel [ctb] (Bundled PCRE2 code), Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code), University of Cambridge [cph] (Bundled PCRE2 code), Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with PCRE2), Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash code)
Maintainer: Travers Ching <traversc@gmail.com>

Diff between stringfish versions 0.15.4 dated 2021-10-15 and 0.15.5 dated 2021-12-01

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Package relsurv updated to version 2.2-6 with previous version 2.2-5 dated 2021-07-05

Title: Relative Survival
Description: Contains functions for analysing relative survival data, including nonparametric estimators of net (marginal relative) survival, relative survival ratio, crude mortality, methods for fitting and checking additive and multiplicative regression models, transformation approach, methods for dealing with population mortality tables. Work has been described in Pohar Perme, Pavlic (2018) <doi:10.18637/jss.v087.i08>.
Author: Maja Pohar Perme [aut], Damjan Manevski [aut, cre]
Maintainer: Damjan Manevski <damjan.manevski@mf.uni-lj.si>

Diff between relsurv versions 2.2-5 dated 2021-07-05 and 2.2-6 dated 2021-12-01

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New package pedalfast.data with initial version 1.0.0
Package: pedalfast.data
Title: PEDALFAST Data
Version: 1.0.0
Description: Data files and documentation for PEDiatric vALidation oF vAriableS in TBI (PEDALFAST). The data was used in "Functional Status Scale in Children With Traumatic Brain Injury: A Prospective Cohort Study" by Bennett, Dixon, et al (2016) <doi:10.1097/PCC.0000000000000934>.
Language: en-US
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports:
Suggests: car, data.table, digest, dplyr, ggplot2, htmltools, knitr, lubridate, qwraps2 (>= 0.5.0), scales, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-11-30 23:11:23 UTC; peterdewitt
Author: Peter DeWitt [aut, cre] (<https://orcid.org/0000-0002-6391-0795>), Tell Bennet [aut] (<https://orcid.org/0000-0003-1483-4236>)
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Repository: CRAN
Date/Publication: 2021-12-01 11:10:02 UTC

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Package opencpu updated to version 2.2.6 with previous version 2.2.5 dated 2021-08-17

Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R. The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange with R. This provides a reliable and scalable foundation for statistical services or building R web applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user Linux stack based on Apache2. The entire system is fully open source and permissively licensed. The OpenCPU website has detailed documentation and example apps.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between opencpu versions 2.2.5 dated 2021-08-17 and 2.2.6 dated 2021-12-01

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New package nphPower with initial version 1.0.0
Package: nphPower
Title: Sample Size Calculation under Non-Proportional Hazards
Version: 1.0.0
Description: Performs combination tests and sample size calculation for fixed design with survival endpoints using combination tests under either proportional hazards or non-proportional hazards. The combination tests include maximum weighted log-rank test and projection test. The sample size calculation procedure is very flexible, allowing for user-defined hazard ratio function and considering various trial conditions like staggered entry, drop-out etc. Trial simulation function is also provided to facilitate the empirical power calculation. The references for projection test and maximum weighted logrank test include Brendel et al. (2014) <doi:10.1111/sjos.12059> and Cheng and He (2021) <arXiv:2110.03833>. The references for sample size calculation under proportional hazard include Schoenfeld (1981) <doi:10.1093/biomet/68.1.316> and Freedman (1982) <doi:10.1002/sim.4780010204>. The references for calculation under non-proportional hazards include Lakatos (1988) <doi:10.2307/2531910> and Cheng and He (2021) (under review).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: survival, stats, mvtnorm, MASS, zoo
Suggests: rmarkdown, knitr
URL: https://github.com/hcheng99/nphPower
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-12-01 03:04:02 UTC; hcheng
Author: Huan Cheng [aut, cre] (<https://orcid.org/0000-0002-2552-7656>)
Maintainer: Huan Cheng <hcheng1118@hotmail.com>
Repository: CRAN
Date/Publication: 2021-12-01 11:20:06 UTC

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Package hhsmm updated to version 0.2.3 with previous version 0.2.2 dated 2021-11-23

Title: Hidden Hybrid Markov/Semi-Markov Model Fitting
Description: Develops algorithms for fitting, prediction, simulation and initialization of the hidden hybrid Markov/semi-Markov model, introduced by Guedon (2005) <doi:10.1016/j.csda.2004.05.033>, which also includes several tools for handling missing data, fitting regime sweaching regression and auto-regressive hidden hybrid Markov/semi-Markov model, and many other useful tools.
Author: Morteza Amini [aut, cre, cph], Afarin Bayat [aut]
Maintainer: Morteza Amini <morteza.amini@ut.ac.ir>

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Package blockmodels updated to version 1.1.5 with previous version 1.1.4 dated 2020-11-23

Title: Latent and Stochastic Block Model Estimation by a 'V-EM' Algorithm
Description: Latent and Stochastic Block Model estimation by a Variational EM algorithm. Various probability distribution are provided (Bernoulli, Poisson...), with or without covariates.
Author: Jean-Benoist Leger <jbleger@hds.utc.fr>, Pierre Barbillon <pierre.barbillon@agroparistech.fr>, Julien Chiquet <julien.chiquet@inrae.fr>
Maintainer: Jean-Benoist Leger <jbleger@hds.utc.fr>

Diff between blockmodels versions 1.1.4 dated 2020-11-23 and 1.1.5 dated 2021-12-01

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New package siqr with initial version 0.8.0
Package: siqr
Title: An R Package for Single-Index Quantile Regression
Version: 0.8.0
Language: en-US
Description: Single-Index Quantile Regression is effective in some scenarios. We provides functions that allow users to fit Single-Index Quantile Regression model. It also provides functions to do prediction, estimate standard errors of the single-index coefficients via bootstrap, and visualize the estimated univariate function. Please see W., Y., Y. (2010) <doi:10.1016/j.jmva.2010.02.003> for details.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.6.0)
Imports: MASS, stats, quantreg, KernSmooth
NeedsCompilation: no
Packaged: 2021-11-30 15:56:13 UTC; tianhaizu
Author: Tianhai Zu [cre], Yan Yu [aut]
Maintainer: Tianhai Zu <zuti@mail.uc.edu>
Repository: CRAN
Date/Publication: 2021-12-01 10:30:02 UTC

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New package regweight with initial version 1.0.1
Package: regweight
Title: Convenience Functions for Implicit Regression Weights
Version: 1.0.1
Description: A simple wrapper for calculating regression weights as defined by Aronow and Samii (2015) <doi:10.1111/ajps.12185>. Given a model object and a term of interest, 'regweight' will calculate implicit regression weights and provide a variety of useful visualizations and summary statistics.
URL: https://github.com/ddimmery/regweight https://ddimmery.github.io/regweight/
BugReports: https://github.com/ddimmery/regweight/issues
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: covr, CBPS, devtools, estimatr, knitr, rmarkdown, sf, testthat (>= 3.0.0), USAboundaries
Imports: checkmate, dplyr, ggplot2, glue, gt, lpdensity, rlang, scales, tidyr, tidyselect
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-11-30 15:04:59 UTC; drewd
Author: Drew Dimmery [aut, cre] (<https://orcid.org/0000-0001-9602-6325>)
Maintainer: Drew Dimmery <drew.dimmery@univie.ac.at>
Repository: CRAN
Date/Publication: 2021-12-01 10:30:05 UTC

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Package precommit updated to version 0.2.0 with previous version 0.1.3 dated 2020-10-10

Title: Pre-Commit Hooks
Description: Useful git hooks for R building on top of the multi-language framework 'pre-commit' for hook management. This package provides git hooks for common tasks like formatting files with 'styler' or spell checking as well as wrapper functions to access the 'pre-commit' executable.
Author: Lorenz Walthert
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>

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New package optedr with initial version 1.0.0
Package: optedr
Title: Calculating Optimal and D-Augmented Designs
Version: 1.0.0
Description: Calculates D-, Ds-, A- and I-optimal designs for non-linear models, via an implementation of the cocktail algorithm (Yu, 2011, <doi:10.1007/s11222-010-9183-2>). Compares designs via their efficiency, and D-augments any design with a controlled efficiency. An efficient rounding function has been provided to transform approximate designs to exact designs.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/kezrael/optedr
BugReports: https://github.com/kezrael/optedr/issues
Suggests: testthat (>= 3.0.0), mockery, markdown, tidyverse
Imports: ggplot2, purrr, rlang, crayon, cli, magrittr, dplyr, nleqslv, shiny, DT, shinydashboard, shinyalert, plotly, hrbrthemes, shinyjs, nloptr, orthopolynom
NeedsCompilation: no
Packaged: 2021-11-30 09:11:59 UTC; Carlos.CalleArroyo
Author: Carlos de la Calle-Arroyo [aut, cre] (<https://orcid.org/0000-0002-5099-888X>), Jesús López-Fidalgo [aut] (<https://orcid.org/0000-0001-7502-8188>), Licesio J. Rodríguez-Aragón [aut] (<https://orcid.org/0000-0003-4970-3877>)
Maintainer: Carlos de la Calle-Arroyo <carlos.calle.arroyo@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-01 10:10:05 UTC

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Package nodbi updated to version 0.6.0 with previous version 0.5.1 dated 2021-11-26

Title: 'NoSQL' Database Connector
Description: Simplified document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1' and 'PostgreSQL'.
Author: Ralf Herold [aut, cre] (<https://orcid.org/0000-0002-8148-6748>), Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Rich FitzJohn [aut], Jeroen Ooms [aut]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>

Diff between nodbi versions 0.5.1 dated 2021-11-26 and 0.6.0 dated 2021-12-01

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New package huito with initial version 0.1.0
Package: huito
Version: 0.1.0
Title: Flexible and Reproducible Label Designs
Description: An open-source R package to deploys flexible and reproducible labels using layers. The 'huito' package is part of the 'inkaverse' project for developing different procedures and tools used in plant science and experimental designs. Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Date: 2021-11-30
URL: https://huito.inkaverse.com/, https://github.com/flavjack/huito
BugReports: https://github.com/flavjack/huito/issues/
Depends: magick, cowplot, ggplot2, dplyr
Imports: tidyr, tibble, purrr, sysfonts, showtext, qrcode, pdftools
Suggests: knitr, rmarkdown, gsheet, inti
VignetteBuilder: knitr
License: GPL-3 | file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-11-30 09:34:53 UTC; flavjack
Author: Flavio Lozano-Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>)
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Repository: CRAN
Date/Publication: 2021-12-01 10:10:09 UTC

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New package CAMML with initial version 0.1.0
Package: CAMML
Title: Cell-Typing using Variance Adjusted Mahalanobis Distances with Multi-Labeling
Version: 0.1.0
Maintainer: Courtney Schiebout <courtney.t.schiebout.gr@dartmouth.edu>
Description: Creates multi-label cell-types for single-cell RNA-sequencing data based on weighted VAM scoring of cell-type specific gene sets. Schiebout, Frost (2022) <https://psb.stanford.edu/psb-online/proceedings/psb22/schiebout.pdf>.
License: GPL (>= 2)
Copyright: Dartmouth College
Depends: R (>= 3.6.0)
Imports: VAM, Seurat (>= 4.0.0), MASS, Matrix, dplyr, utils, edgeR, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, SeuratObject (>= 4.0.0)
Suggests: sctransform (>= 0.3.2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-11-30 14:07:14 UTC; ctschiebout
Author: H. Robert Frost [aut], Courtney Schiebout [aut, cre] (<https://orcid.org/0000-0002-4830-8237>)
Repository: CRAN
Date/Publication: 2021-12-01 10:20:05 UTC

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Package anticlust updated to version 0.6.0 with previous version 0.5.6 dated 2020-11-24

Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements into groups (i.e., anticlusters) with the goal of maximizing between-group similarity or within-group heterogeneity. The anticlustering approach thereby reverses the logic of cluster analysis that strives for high within-group homogeneity and low similarity of the different groups. Computationally, anticlustering is accomplished by maximizing instead of minimizing a clustering objective function, such as the intra-cluster variance (used in k-means clustering) or the sum of pairwise distances within clusters. The function anticlustering() implements exact and heuristic anticlustering algorithms as described in Papenberg and Klau (2021; <doi:10.1037/met0000301>). The exact algorithms require that the GNU linear programming kit (<https://www.gnu.org/software/glpk/glpk.html>) is available and the R package 'Rglpk' (<https://cran.R-project.org/package=Rglpk>) is installed. A bicriterion anticlustering method proposed by Brusco et al. (2020; <doi:10.1111/bmsp.12186>) is available through the function bicriterion_anticlustering(). Some other functions are available to solve classical clustering problems. The function balanced_clustering() applies a cluster analysis under size constraints, i.e., creates equal-sized clusters. The function matching() can be used for (unrestricted, bipartite, or K-partite) matching. The function wce() can be used optimally solve the (weighted) cluster editing problem, also known as correlation clustering, clique partitioning problem or transitivity clustering.
Author: Martin Papenberg [aut, cre] (<https://orcid.org/0000-0002-9900-4268>), Meik Michalke [ctb] (centroid based clustering algorithm), Gunnar W. Klau [ths], Juliane V. Tkotz [ctb] (package logo), Martin Breuer [ctb] (Bicriterion algorithm by Brusco et al.)
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>

Diff between anticlust versions 0.5.6 dated 2020-11-24 and 0.6.0 dated 2021-12-01

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Package smooth updated to version 3.1.4 with previous version 3.1.3 dated 2021-09-22

Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting. The package includes ADAM (Svetunkov, 2021, <https://openforecast.org/adam/>), Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>), SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>), Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>), Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>) and several simulation functions. It also allows dealing with intermittent demand based on the iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>

Diff between smooth versions 3.1.3 dated 2021-09-22 and 3.1.4 dated 2021-12-01

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Package rcosmo updated to version 1.1.3 with previous version 1.1.2 dated 2020-02-14

Title: Cosmic Microwave Background Data Analysis
Description: Handling and Analysing Spherical, HEALPix and Cosmic Microwave Background data on a HEALPix grid.
Author: Daniel Fryer [aut, cre] (<https://orcid.org/0000-0001-6032-0522>), Andriy Olenko [aut] (<https://orcid.org/0000-0002-0917-7000>), Ming Li [aut] (<https://orcid.org/0000-0002-1218-2804>), Yuguang Wang [aut]
Maintainer: Daniel Fryer <d.fryer@latrobe.edu.au>

Diff between rcosmo versions 1.1.2 dated 2020-02-14 and 1.1.3 dated 2021-12-01

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New package onemap with initial version 2.8.0
Package: onemap
Title: Construction of Genetic Maps in Experimental Crosses
Version: 2.8.0
Description: Analysis of molecular marker data from model (backcrosses, F2 and recombinant inbred lines) and non-model systems (i. e. outcrossing species). For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu et al. (2002) <doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint approaches using hidden Markov models.
Date: 2021-11-30
Author: Gabriel Margarido [aut], Marcelo Mollinari [aut], Cristiane Taniguti [ctb, cre], Getulio Ferreira [ctb], Rodrigo Amadeu [ctb], Karl Broman [ctb], Katharine Preedy [ctb, cph] (MDS ordering algorithm), Bastian Schiffthaler [ctb, cph] (HMM parallelization), Augusto Garcia [aut, ctb]
LinkingTo: Rcpp (>= 0.10.5)
Depends: R (>= 3.6.0)
Imports: ggplot2 (>= 2.2.1), plotly (>= 4.7.1), reshape2 (>= 1.4.1), Rcpp (>= 0.10.5), graphics, methods, stats, utils, grDevices, smacof, princurve, parallel, dplyr, tidyr, htmlwidgets, ggpubr, RColorBrewer, dendextend, rebus, vcfR (>= 1.6.0)
Suggests: knitr (>= 1.10), rmarkdown, testthat, stringr
VignetteBuilder: knitr
Encoding: UTF-8
License: GPL-3
URL: https://github.com/augusto-garcia/onemap
BugReports: https://github.com/augusto-garcia/onemap/wiki
Maintainer: Cristiane Taniguti <chtaniguti@tamu.edu>
Repository: CRAN
Packaged: 2021-11-30 21:25:58 UTC; chtan
NeedsCompilation: yes
Date/Publication: 2021-12-01 10:00:02 UTC
biocViews:

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New package nowcastDFM with initial version 1.0.0
Package: nowcastDFM
Title: DFMs for Nowcasting
Version: 1.0.0
Description: Run dynamic factor models (DFM) in R. Adapted from Bok et al. (2017) <https://www.newyorkfed.org/medialibrary/media/research/staff_reports/sr830.pdf>. The package provides the ability to estimate a DFM model, obtain predictions from estimated models, and obtain the impact of new data releases on model predictions.
Depends: R (>= 3.3.0), dplyr (>= 0.8.0.1), matlab (>= 1.0.2), pracma (>= 2.3.3), signal (>= 0.7-7)
License: GPL-3
Encoding: UTF-8
URL: https://github.com/dhopp1/nowcastDFM/, https://www.newyorkfed.org/medialibrary/media/research/staff_reports/sr830.pdf, https://github.com/FRBNY-TimeSeriesAnalysis/Nowcasting
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-11-30 09:00:54 UTC; Daniel.Hopp
Author: Daniel Hopp [aut, cre], Fernando Cantu [aut]
Maintainer: Daniel Hopp <daniel.hopp@un.org>
Repository: CRAN
Date/Publication: 2021-12-01 10:00:07 UTC

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Package bigstatsr updated to version 1.5.5 with previous version 1.5.1 dated 2021-04-05

Title: Statistical Tools for Filebacked Big Matrices
Description: Easy-to-use, efficient, flexible and scalable statistical tools. Package bigstatsr provides and uses Filebacked Big Matrices via memory-mapping. It provides for instance matrix operations, Principal Component Analysis, sparse linear supervised models, utility functions and more <doi:10.1093/bioinformatics/bty185>.
Author: Florian Privé [aut, cre], Michael Blum [ths], Hugues Aschard [ths]
Maintainer: Florian Privé <florian.prive.21@gmail.com>

Diff between bigstatsr versions 1.5.1 dated 2021-04-05 and 1.5.5 dated 2021-12-01

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Package RJSplot updated to version 2.7 with previous version 2.5 dated 2017-11-02

Title: Interactive Graphs with R
Description: Creates interactive graphs with 'R'. It joins the data analysis power of R and the visualization libraries of JavaScript in one package.
Author: Carlos Prieto <cprietos@usal.es>, David Barrios <metal@usal.es>
Maintainer: Carlos Prieto <cprietos@usal.es>

Diff between RJSplot versions 2.5 dated 2017-11-02 and 2.7 dated 2021-12-01

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New package weathercan with initial version 0.6.2
Package: weathercan
Title: Download Weather Data from Environment and Climate Change Canada
Version: 0.6.2
Description: Provides means for downloading historical weather data from the Environment and Climate Change Canada website (<https://climate.weather.gc.ca/historical_data/search_historic_data_e.html>). Data can be downloaded from multiple stations and over large date ranges and automatically processed into a single dataset. Tools are also provided to identify stations either by name or proximity to a location.
License: GPL-3
Language: en-CA
BugReports: https://github.com/ropensci/weathercan/issues/
LazyData: TRUE
URL: https://docs.ropensci.org/weathercan/, https://github.com/ropensci/weathercan/
Depends: R (>= 3.3.0)
Imports: dplyr (>= 1.0.0), httr (>= 1.4.2), lubridate (>= 1.7.1), memoise (>= 2.0.0), methods (>= 3.2.2), purrr (>= 0.3.4), rlang (>= 0.1.4), readr (>= 2.0.0), rvest (>= 0.3.4), stringi (>= 1.1.2), stringr (>= 1.4.0), tidyr (>= 1.1.3), tidyselect (>= 1.0.0), xml2 (>= 0.1.2), rappdirs (>= 0.3.3)
Suggests: devtools, ggplot2, htmltools, knitr, leaflet, lutz, mockery, naniar, rmarkdown, sf, sp, testthat, vcr (>= 1.0.2)
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-11-30 18:33:58 UTC; steffi
Author: Steffi LaZerte [aut, cre] (<https://orcid.org/0000-0002-7690-8360>), Sam Albers [ctb] (<https://orcid.org/0000-0002-9270-7884>), Nick Brown [ctb] (<https://orcid.org/0000-0002-2719-0671>), Kevin Cazelles [ctb] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Steffi LaZerte <steffi@steffi.ca>
Repository: CRAN
Date/Publication: 2021-12-01 08:00:02 UTC

More information about weathercan at CRAN
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Package lsr updated to version 0.5.2 with previous version 0.5.1 dated 2021-09-20

Title: Companion to "Learning Statistics with R"
Description: A collection of tools intended to make introductory statistics easier to teach, including wrappers for common hypothesis tests and basic data manipulation. It accompanies Navarro, D. J. (2015). Learning Statistics with R: A Tutorial for Psychology Students and Other Beginners, Version 0.6.
Author: Danielle Navarro [aut, cre] (<https://orcid.org/0000-0001-7648-6578>)
Maintainer: Danielle Navarro <djnavarro@protonmail.com>

Diff between lsr versions 0.5.1 dated 2021-09-20 and 0.5.2 dated 2021-12-01

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Package greybox updated to version 1.0.2 with previous version 1.0.1 dated 2021-09-22

Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its application to forecasting. The main scope of the package is in variables selection and models specification for cases of time series data. This includes promotional modelling, selection between different dynamic regressions with non-standard distributions of errors, selection based on cross validation, solutions to the fat regression model problem and more. Models developed in the package are tailored specifically for forecasting purposes. So as a results there are several methods that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics and Forecasting, Lancaster University, UK), Yves R. Sagaert [ctb] (Visiting Research at Centre for Marketing Analytics and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>

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Package digest updated to version 0.6.29 with previous version 0.6.28 dated 2021-09-23

Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash' and 'blake3' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek, Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen, Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx, Michel Lang, Viliam Simko, Kurt Hornik, Radford Neal, Kendon Bell, Matthew de Queljoe, Ion Suruceanu, Bill Denney, Dirk Schumacher, and Winston Chang.
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between digest versions 0.6.28 dated 2021-09-23 and 0.6.29 dated 2021-12-01

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Package bcTSNE updated to version 0.11.1 with previous version 0.10.0 dated 2020-04-28

Title: Projected t-SNE for Batch Correction
Description: Implements the projected t-SNE method for batch correction of high-dimensional data. Please see Aliverti et al. (2020) <doi:10.1093/bioinformatics/btaa189> for more information.
Author: Dayne L Filer [aut, cre], Emanuele Aliverti [aut], Jeff Tilson [aut], Kirk C Wilhelmsen [aut], David B Dunson [aut]
Maintainer: Dayne L Filer <dayne.filer@gmail.com>

Diff between bcTSNE versions 0.10.0 dated 2020-04-28 and 0.11.1 dated 2021-12-01

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Package bRacatus (with last version 1.0.6) was removed from CRAN

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

2021-11-09 1.0.6

Permanent link
Package litRiddle (with last version 0.4.0) was removed from CRAN

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

2021-11-10 0.4.0

Permanent link
Package occCite (with last version 0.5.1) was removed from CRAN

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

2021-11-01 0.5.1

Permanent link
Package himach updated to version 0.2.3 with previous version 0.2.2 dated 2021-11-21

Title: High Mach Finds Routes for Supersonic Aircraft
Description: For supersonic aircraft, flying subsonic over land, High Mach finds the best route between airports. Allows for coastal buffer and potentially closed regions. Uses a minimal model of aircraft performance: the focus is on time saved versus subsonic flight, rather than on vertical flight profile. For modelling and forecasting, not for planning your flight!
Author: David Marsh [aut, cre], EUROCONTROL [fnd, cph]
Maintainer: David Marsh <david.marsh@eurocontrol.int>

Diff between himach versions 0.2.2 dated 2021-11-21 and 0.2.3 dated 2021-12-01

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Package rnoaa updated to version 1.3.8 with previous version 1.3.7 dated 2021-11-18

Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate 'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for each of the 'API' 'endpoints': data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS', tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Daniel Hocking [ctb, cre] (<https://orcid.org/0000-0003-1889-9184>), Brooke Anderson [ctb], Maëlle Salmon [ctb], Adam Erickson [ctb], Nicholas Potter [ctb], Joseph Stachelek [ctb], Alex Simmons [ctb], Karthik Ram [ctb], Hart Edmund [ctb], rOpenSci [fnd] (https://ropensci.org)
Maintainer: Daniel Hocking <djhocking@gmail.com>

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Package polycor updated to version 0.8-0 with previous version 0.7-10 dated 2019-08-05

Title: Polychoric and Polyserial Correlations
Description: Computes polychoric and polyserial correlations by quick "two-step" methods or ML, optionally with standard errors; tetrachoric and biserial correlations are special cases.
Author: John Fox [aut, cre]
Maintainer: John Fox <jfox@mcmaster.ca>

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Package OmicNavigator updated to version 1.8.0 with previous version 1.4.3 dated 2021-08-05

Title: Open-Source Software for 'Omic' Data Analysis and Visualization
Description: A tool for interactive exploration of the results from 'omics' experiments to facilitate novel discoveries from high-throughput biology. The software includes R functions for the 'bioinformatician' to deposit study metadata and the outputs from statistical analyses (e.g. differential expression, enrichment). These results are then exported to an interactive JavaScript dashboard that can be interrogated on the user’s local machine or deployed online to be explored by collaborators. The dashboard includes 'sortable' tables, interactive plots including network visualization, and fine-grained filtering based on statistical significance.
Author: Terrence Ernst [aut] (Web application), John Blischak [aut, cre] (<https://orcid.org/0000-0003-2634-9879>), Paul Nordlund [aut] (Web application), Justin Moore [aut] (UpSet-related functions and web application), Joe Dalen [aut] (Barcode functionality and web application), Akshay Bhamidipati [aut] (Web application), Brett Engelmann [aut], Marco Curado [aut] (Improved plotting capabilities), AbbVie Inc. [cph, fnd]
Maintainer: John Blischak <jdblischak@gmail.com>

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Tue, 30 Nov 2021

Package table.express updated to version 0.3.2 with previous version 0.3.1 dated 2019-09-07

Title: Build 'data.table' Expressions with Data Manipulation Verbs
Description: A specialization of 'dplyr' data manipulation verbs that parse and build expressions which are ultimately evaluated by 'data.table', letting it handle all optimizations. A set of additional verbs is also provided to facilitate some common operations on a subset of the data.
Author: Alexis Sarda-Espinosa [cre, aut]
Maintainer: Alexis Sarda-Espinosa <alexis.sarda@gmail.com>

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Package pvaluefunctions updated to version 1.6.2 with previous version 1.6.1 dated 2020-12-09

Title: Creates and Plots P-Value Functions, S-Value Functions, Confidence Distributions and Confidence Densities
Description: Contains functions to compute and plot confidence distributions, confidence densities, p-value functions and s-value (surprisal) functions for several commonly used estimates. Instead of just calculating one p-value and one confidence interval, p-value functions display p-values and confidence intervals for many levels thereby allowing to gauge the compatibility of several parameter values with the data. These methods are discussed by Infanger D, Schmidt-Trucksäss A. (2019) <doi:10.1002/sim.8293>; Poole C. (1987) <doi:10.2105/AJPH.77.2.195>; Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>; Bender R, Berg G, Zeeb H. (2005) <doi:10.1002/bimj.200410104> ; Singh K, Xie M, Strawderman WE. (2007) <doi:10.1214/074921707000000102>; Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052); Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>; Greenland S. (2019) <doi:10.1080/00031305.2018.1529625> and Rafi Z, Greenland S. (2020) <doi:10.1186/s12874-020-01105-9>.
Author: Denis Infanger [aut, cre] (<https://orcid.org/0000-0001-9028-7110>)
Maintainer: Denis Infanger <denis.infanger@unibas.ch>

Diff between pvaluefunctions versions 1.6.1 dated 2020-12-09 and 1.6.2 dated 2021-11-30

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Package PostcodesioR updated to version 0.3.1 with previous version 0.3.0 dated 2021-01-07

Title: API Wrapper Around 'Postcodes.io'
Description: Free UK geocoding using data from Office for National Statistics. It is using several functions to get information about post codes, outward codes, reverse geocoding, nearest post codes/outward codes, validation, or randomly generate a post code. API wrapper around <https://postcodes.io>.
Author: Eryk Walczak [aut, cre] (<https://orcid.org/0000-0001-8724-462X>), Claudia Vitolo [rev] (<https://orcid.org/0000-0002-4252-1176>), Robin Lovelace [rev] (<https://orcid.org/0000-0001-5679-6536>)
Maintainer: Eryk Walczak <erykjwalczak@gmail.com>

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Package activegp updated to version 1.0.6 with previous version 1.0.5 dated 2020-10-27

Title: Gaussian Process Based Design and Analysis for the Active Subspace Method
Description: The active subspace method is a sensitivity analysis technique that finds important linear combinations of input variables for a simulator. This package provides functions allowing estimation of the active subspace without gradient information using Gaussian processes as well as sequential experimental design tools to minimize the amount of data required to do so. Implements Wycoff et al. (2019) <arXiv:1907.11572>.
Author: Nathan Wycoff, Mickael Binois
Maintainer: Nathan Wycoff <nathan.wycoff@georgetown.edu>

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Package datefixR updated to version 0.1.2 with previous version 0.1.1 dated 2021-11-05

Title: Fix Really Messy Dates
Description: Fixes messy dates in data frames such as those entered via text boxes. Standardizes / - and whitespace separation, month abbreviations, and year first or day first by converting to R's built-in Date class. Imputes missing date or month using user-provided values.
Author: Nathan Constantine-Cooke [aut, cre] (<https://orcid.org/0000-0002-4437-8713>)
Maintainer: Nathan Constantine-Cooke <nathan.constantine-cooke@ed.ac.uk>

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New package Wcompo with initial version 1.0
Package: Wcompo
Title: Semiparametric Proportional Means Regression of Weighted Composite Endpoint
Version: 1.0
Author: Lu Mao
Maintainer: Lu Mao <lmao@biostat.wisc.edu>
URL: https://sites.google.com/view/lmaowisc/
Description: Implements inferential and graphic procedures for the semiparametric proportional means regression of weighted composite endpoint of recurrent event and death (Mao and Lin, 2016, <doi:10.1093/biostatistics/kxv050>).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Imports: survival
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2021-11-29 21:30:23 UTC; lmao
Repository: CRAN
Date/Publication: 2021-11-30 21:30:02 UTC

More information about Wcompo at CRAN
Permanent link

Package RobStatTM updated to version 1.0.3 with previous version 1.0.2 dated 2020-03-02

Title: Robust Statistics: Theory and Methods
Description: Companion package for the book: "Robust Statistics: Theory and Methods, second edition", <http://www.wiley.com/go/maronna/robust>. This package contains code that implements the robust estimators discussed in the recent second edition of the book above, as well as the scripts reproducing all the examples in the book.
Author: Matias Salibian-Barrera [cre], Victor Yohai [aut], Ricardo Maronna [aut], Doug Martin [aut], Gregory Brownson [aut] (ShinyUI), Kjell Konis [aut], Kjell Konis [cph] (erfi), Christophe Croux [ctb] (WBYlogreg, BYlogreg), Gentiane Haesbroeck [ctb] (WBYlogreg, BYlogreg), Martin Maechler [cph] (lmrob.fit, lmrob..M..fit, lmrob.S), Manuel Koller [cph] (lmrob.fit, .vcov.avar1, lmrob.S, lmrob.lar), Matias Salibian-Barrera [aut]
Maintainer: Matias Salibian-Barrera <matias@stat.ubc.ca>

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Package pkgdown updated to version 2.0.0 with previous version 1.6.1 dated 2020-09-12

Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>), Jay Hesselberth [aut] (<https://orcid.org/0000-0002-6299-179X>), Maëlle Salmon [aut] (<https://orcid.org/0000-0002-2815-0399>), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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New package FourWayHMM with initial version 1.0.0
Package: FourWayHMM
Title: Parsimonious Hidden Markov Models for Four-Way Data
Version: 1.0.0
Description: Implements parsimonious hidden Markov models for four-way data via expectation- conditional maximization algorithm, as described in Tomarchio et al. (2020) <arXiv:2107.04330>. The matrix-variate normal distribution is used as emission distribution. For each hidden state, parsimony is reached via the eigen-decomposition of the covariance matrices of the emission distribution. This produces a family of 98 parsimonious hidden Markov models.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: withr, snow, doSNOW, foreach, mclust, tensor, tidyr, data.table, LaplacesDemon
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-11-29 17:24:17 UTC; Daniele
Author: Salvatore D. Tomarchio [aut, cre], Antonio Punzo [aut], Antonello Maruotti [aut]
Maintainer: Salvatore D. Tomarchio <daniele.tomarchio@unict.it>
Repository: CRAN
Date/Publication: 2021-11-30 21:20:02 UTC

More information about FourWayHMM at CRAN
Permanent link

Package diyar updated to version 0.4.0 with previous version 0.3.1 dated 2021-08-09

Title: Record Linkage and Epidemiological Case Definitions in R
Description: An R package for record linkage and implementing epidemiological case definitions in R. Record linkage is implemented either through a multistage deterministic approach or a probabilistic approach. Matching records are assigned to unique groups. There are mechanisms to address missing data and conflicting matches across linkage stages. Track and assign events (e.g. sample collection) and periods (e.g. hospital admission) to unique groups based on a case definition. The tracking process permits several options such as episode lengths and recurrence. Duplicate events or records can then be identified for removal or further analyses.
Author: Olisaeloka Nsonwu
Maintainer: Olisaeloka Nsonwu <olisa.nsonwu@gmail.com>

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New package AustralianPoliticians with initial version 0.1.0
Package: AustralianPoliticians
Title: Provides Datasets About Australian Politicians
Version: 0.1.0
Description: Provides access to biographical and political data about Australian federal politicians who served between 1901 and 2021. This enhances how reproducible research is that uses this data.
Depends: R (>= 2.10)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
URL: https://github.com/RohanAlexander/AustralianPoliticians
BugReports: https://github.com/RohanAlexander/AustralianPoliticians/issues
Imports: dplyr, readr, purrr, utils, tibble
Suggests: rmarkdown, knitr, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-11-29 20:57:22 UTC; rohanalexander
Author: Rohan Alexander [aut, cre] (<https://orcid.org/0000-0001-6759-7276>), Paul A. Hodgetts [aut]
Maintainer: Rohan Alexander <rohan.alexander@utoronto.ca>
Repository: CRAN
Date/Publication: 2021-11-30 21:30:04 UTC

More information about AustralianPoliticians at CRAN
Permanent link

Package ActiveDriverWGS updated to version 1.1.2 with previous version 1.1.1 dated 2020-09-17

Title: A Driver Discovery Tool for Cancer Whole Genomes
Description: A method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. 'ActiveDriverWGS' detects coding and noncoding driver elements using whole genome sequencing data. The method is part of the following publication: Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. Molecular Cell (2020) <doi:10.1016/j.molcel.2019.12.027>.
Author: Juri Reimand [aut, cre], Helen Zhu [aut]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>

Diff between ActiveDriverWGS versions 1.1.1 dated 2020-09-17 and 1.1.2 dated 2021-11-30

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Permanent link

Package text2sdg updated to version 0.1.2 with previous version 0.1.1 dated 2021-11-07

Title: Detecting UN Sustainable Development Goals in Text
Description: The United Nations’ Sustainable Development Goals (SDGs) have become an important guideline for organisations to monitor and plan their contributions to social, economic, and environmental transformations. The 'text2sdg' package is an open-source analysis package that identifies SDGs in text using scientifically developed query systems, opening up the opportunity to monitor any type of text-based data, such as scientific output or corporate publications.
Author: Dirk U. Wulff [aut] (<https://orcid.org/0000-0002-4008-8022>), Dominik S. Meier [aut, cre] (<https://orcid.org/0000-0002-3999-1388>), Rui Mata [ctb] (<https://orcid.org/0000-0002-1679-906X>)
Maintainer: Dominik S. Meier <dominikmeier@outlook.com>

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Package readr updated to version 2.1.1 with previous version 2.1.0 dated 2021-11-11

Title: Read Rectangular Text Data
Description: The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.
Author: Hadley Wickham [aut], Jim Hester [aut], Romain Francois [ctb], Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), RStudio [cph, fnd], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)
Maintainer: Jennifer Bryan <jenny@rstudio.com>

Diff between readr versions 2.1.0 dated 2021-11-11 and 2.1.1 dated 2021-11-30

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Package LWFBrook90R updated to version 0.4.5 with previous version 0.4.4 dated 2021-02-24

Title: Simulate Evapotranspiration and Soil Moisture with the SVAT Model LWF-Brook90
Description: Provides a flexible and easy-to use interface for the soil vegetation atmosphere transport (SVAT) model LWF-BROOK90, written in Fortran. The model simulates daily transpiration, interception, soil and snow evaporation, streamflow and soil water fluxes through a soil profile covered with vegetation, as described in Hammel & Kennel (2001, ISBN:978-3-933506-16-0) and Federer et al. (2003) <doi:10.1175/1525-7541(2003)004%3C1276:SOAETS%3E2.0.CO;2>. A set of high-level functions for model set up, execution and parallelization provides easy access to plot-level SVAT simulations, as well as multi-run and large-scale applications.
Author: Paul Schmidt-Walter [aut, cre] (<https://orcid.org/0000-0003-2699-0893>), Volodymyr Trotsiuk [aut] (<https://orcid.org/0000-0002-8363-656X>), Klaus Hammel [aut], Martin Kennel [aut], Anthony Federer [aut], Robert Nuske [ctb] (<https://orcid.org/0000-0001-9773-2061>), Bavarian State Institute of Forestry (LWF) [cph, fnd], Northwest German Forest Research Institute (NW-FVA) [cph, fnd]
Maintainer: Paul Schmidt-Walter <paulsw@posteo.de>

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Package xml2 updated to version 1.3.3 with previous version 1.3.2 dated 2020-04-23

Title: Parse XML
Description: Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.
Author: Hadley Wickham [aut, cre], Jim Hester [aut], Jeroen Ooms [aut], RStudio [cph], R Foundation [ctb] (Copy of R-project homepage cached as example)
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package withr updated to version 2.4.3 with previous version 2.4.2 dated 2021-04-18

Title: Run Code 'With' Temporarily Modified Global State
Description: A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.
Author: Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package vroom updated to version 1.5.7 with previous version 1.5.6 dated 2021-11-10

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] (<https://orcid.org/0000-0002-2739-7082>), Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

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Package SIPDIBGE updated to version 0.1.6 with previous version 0.1.5 dated 2021-10-05

Title: Collection of Household Survey Packages Conducted by IBGE
Description: Provides access to packages developed for downloading, reading and analyzing microdata from household surveys conducted by Brazilian Institute of Geography and Statistics - IBGE. More information can be obtained from the official website <https://www.ibge.gov.br/>.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package quanteda updated to version 3.2.0 with previous version 3.1.0 dated 2021-08-17

Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for quantitative text analysis in R. Provides functionality for corpus management, creating and manipulating tokens and ngrams, exploring keywords in context, forming and manipulating sparse matrices of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and distances, applying content dictionaries, applying supervised and unsupervised machine learning, visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph] (<https://orcid.org/0000-0002-0797-564X>), Kohei Watanabe [aut] (<https://orcid.org/0000-0001-6519-5265>), Haiyan Wang [aut] (<https://orcid.org/0000-0003-4992-4311>), Paul Nulty [aut] (<https://orcid.org/0000-0002-7214-4666>), Adam Obeng [aut] (<https://orcid.org/0000-0002-2906-4775>), Stefan Müller [aut] (<https://orcid.org/0000-0002-6315-4125>), Akitaka Matsuo [aut] (<https://orcid.org/0000-0002-3323-6330>), William Lowe [aut] (<https://orcid.org/0000-0002-1549-6163>), Christian Müller [ctb], European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

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Package POFIBGE updated to version 0.1.5 with previous version 0.1.4 dated 2021-10-15

Title: Downloading, Reading and Analyzing POF Microdata
Description: Provides tools for downloading, reading and analyzing the POF, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package PNSIBGE updated to version 0.1.6 with previous version 0.1.5 dated 2021-10-15

Title: Downloading, Reading and Analyzing PNS Microdata
Description: Provides tools for downloading, reading and analyzing the PNS, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package PNADcIBGE updated to version 0.7.0 with previous version 0.6.5 dated 2021-06-24

Title: Downloading, Reading and Analyzing PNADC Microdata
Description: Provides tools for downloading, reading and analyzing the PNADC, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Douglas Braga [aut], Gabriel Assuncao [aut, cre], Luna Hidalgo [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package pkgload updated to version 1.2.4 with previous version 1.2.3 dated 2021-10-13

Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then attaching it. This is a key part of the 'devtools' package as it allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut], Winston Chang [aut], Jim Hester [aut], Lionel Henry [aut, cre], RStudio [cph], R Core team [ctb] (Some namespace and vignette code extracted from base R)
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package midasml updated to version 0.1.6 with previous version 0.1.5-1 dated 2021-05-20

Title: Estimation and Prediction Methods for High-Dimensional Mixed Frequency Time Series Data
Description: The 'midasml' package implements estimation and prediction methods for high-dimensional mixed-frequency (MIDAS) time-series and panel data regression models. The regularized MIDAS models are estimated using orthogonal (e.g. Legendre) polynomials and sparse-group LASSO (sg-LASSO) estimator. For more information on the 'midasml' approach see Babii, Ghysels, and Striaukas (2021, JBES forthcoming) <doi:10.1080/07350015.2021.1899933>. The package is equipped with the fast implementation of the sg-LASSO estimator by means of proximal block coordinate descent. High-dimensional mixed frequency time-series data can also be easily manipulated with functions provided in the package.
Author: Jonas Striaukas [cre, aut], Andrii Babii [aut], Eric Ghysels [aut], Alex Kostrov [ctb] (Contributions to analytical gradients for non-linear low-dimensional MIDAS estimation code)
Maintainer: Jonas Striaukas <jonas.striaukas@gmail.com>

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New package EpiSignalDetection with initial version 0.1.2
Package: EpiSignalDetection
Title: Signal Detection Analysis
Version: 0.1.2
Date: 2021-10-27
Description: Exploring time series for signal detection. It is specifically designed to detect possible outbreaks using infectious disease surveillance data at the European Union / European Economic Area or country level. Automatic detection tools used are presented in the paper "Monitoring count time series in R: aberration detection in public health surveillance", by Salmon (2016) <doi:10.18637/jss.v070.i10>. The package includes: - Signal Detection tool, an interactive 'shiny' application in which the user can import external data and perform basic signal detection analyses; - An automated report in HTML format, presenting the results of the time series analysis in tables and graphs. This report can also be stratified by population characteristics (see 'Population' variable). This project was funded by the European Centre for Disease Prevention and Control.
Depends: R (>= 3.4.0)
License: EUPL
Encoding: UTF-8
LazyData: true
Imports: dplyr, graphics, ISOweek, rmarkdown, shiny, surveillance, utils
Suggests: DT, ggplot2, knitr (>= 1.20), pander
VignetteBuilder: knitr
SystemRequirements: pandoc (>= 1.12.3)
URL: https://github.com/EU-ECDC/EpiSignalDetection
NeedsCompilation: no
Packaged: 2021-10-27 16:20:04 UTC; LMC
Author: Lore Merdrignac [aut, ctr, cre] (Author of the package and original code), Joana Gomes Dias [aut, fnd] (Project manager), Esther Kissling [aut, ctr], Tommi Karki [aut, fnd], Margot Einoder-Moreno [ctb, fnd]
Maintainer: Lore Merdrignac <l.merdrignac@epiconcept.fr>
Repository: CRAN
Date/Publication: 2021-11-30 15:00:02 UTC

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Package COVIDIBGE updated to version 0.1.8 with previous version 0.1.7 dated 2021-11-03

Title: Downloading, Reading and Analyzing PNAD COVID19 Microdata
Description: Provides tools for downloading, reading and analyzing the PNAD COVID19, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

Diff between COVIDIBGE versions 0.1.7 dated 2021-11-03 and 0.1.8 dated 2021-11-30

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More information about COVIDIBGE at CRAN
Permanent link

New package AgroR with initial version 1.2.4
Package: AgroR
Title: Experimental Statistics and Graphics for Agricultural Sciences
Version: 1.2.4
Date: 2021-10-13
Maintainer: Gabriel Danilo Shimizu <shimizu@uel.br>
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4), ANOVA of aligned ranks (Wobbrock, J.O., Findlater, L., Gergle, D., Higgins, JJ (2011), <doi:10.1145/1978942.1978963>) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).
Encoding: UTF-8
Imports: ggplot2, nortest, ScottKnott, lme4, crayon, lmtest, stringr, Hmisc, emmeans, ARTool, multcomp, ggrepel, reshape2, MASS, cowplot, multcompView, RColorBrewer, drc, dunn.test
Suggests: DT, knitr, rmarkdown, roxygen2
Depends: R (>= 3.6.0)
License: GPL (>= 2)
URL: https://agronomiar.github.io/AgroR_package/index.html
NeedsCompilation: no
Packaged: 2021-10-13 14:34:58 UTC; Gabriel
Author: Gabriel Danilo Shimizu [aut, cre] (<https://orcid.org/0000-0001-8524-508X>), Rodrigo Yudi Palhaci Marubayashi [aut, ctb] (<https://orcid.org/0000-0003-2778-8654>), Leandro Simoes Azeredo Goncalves [aut, ctb] (<https://orcid.org/0000-0001-9700-9375>)
Repository: CRAN
Date/Publication: 2021-11-30 15:00:06 UTC

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Package urlchecker updated to version 1.0.1 with previous version 1.0.0 dated 2021-03-04

Title: Run CRAN URL Checks from Older R Versions
Description: Provide the URL checking tools available in R 4.1+ as a package for earlier versions of R. Also uses concurrent requests so can be much faster than the serial versions.
Author: R Core team [aut] (The code in urltools.R adapted from the tools package), Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Gábor Csárdi [aut, cre], RStudio [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between urlchecker versions 1.0.0 dated 2021-03-04 and 1.0.1 dated 2021-11-30

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Package remotes updated to version 2.4.2 with previous version 2.4.1 dated 2021-09-29

Title: R Package Installation from Remote Repositories, Including 'GitHub'
Description: Download and install R packages stored in 'GitHub', 'GitLab', 'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Author: Gábor Csárdi [aut, cre], Jim Hester [aut], Hadley Wickham [aut], Winston Chang [aut], RStudio [cph], Martin Morgan [aut], Dan Tenenbaum [aut], Mango Solutions [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package pkgbuild updated to version 1.2.1 with previous version 1.2.0 dated 2020-12-15

Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.
Author: Hadley Wickham [aut], Jim Hester [aut], Gábor Csárdi [aut, cre], RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package fs updated to version 1.5.1 with previous version 1.5.0 dated 2020-07-31

Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built on top of the 'libuv' C library.
Author: Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut, cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), RStudio [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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More information about fs at CRAN
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Package brio updated to version 1.1.3 with previous version 1.1.2 dated 2021-04-23

Title: Basic R Input Output
Description: Functions to handle basic input output, these functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.
Author: Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Gábor Csárdi [aut, cre], RStudio [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package bpp updated to version 1.0.3 with previous version 1.0.2 dated 2021-05-20

Title: Computations Around Bayesian Predictive Power
Description: Implements functions to update Bayesian Predictive Power Computations after not stopping a clinical trial at an interim analysis. Such an interim analysis can either be blinded or unblinded. Code is provided for Normally distributed endpoints with known variance, with a prominent example being the hazard ratio.
Author: Kaspar Rufibach, Paul Jordan, Markus Abt
Maintainer: Kaspar Rufibach <kaspar.rufibach@roche.com>

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More information about bpp at CRAN
Permanent link

Package available updated to version 1.0.5 with previous version 1.0.4 dated 2019-07-19

Title: Check if the Title of a Package is Available, Appropriate and Interesting
Description: Check if a given package name is available to use. It checks the name's validity. Checks if it is used on 'GitHub', 'CRAN' and 'Bioconductor'. Checks for unintended meanings by querying Urban Dictionary, 'Wiktionary' and Wikipedia.
Author: Carl Ganz [aut], Gábor Csárdi [aut, cre], Jim Hester [aut], Molly Lewis [aut], Rachael Tatman [aut]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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More information about available at CRAN
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Package archive updated to version 1.1.3 with previous version 1.1.2 dated 2021-10-25

Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the Multi-format archive and compression library. Offers R connections and direct extraction for many archive formats including 'tar', 'ZIP', '7-zip', 'RAR', 'CAB' and compression formats including 'gzip', 'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>), Gábor Csárdi [aut, cre], Ondrej Holy [cph] (archive_write_add_filter implementation), RStudio [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

Diff between archive versions 1.1.2 dated 2021-10-25 and 1.1.3 dated 2021-11-30

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Package sparklyr updated to version 1.7.3 with previous version 1.7.2 dated 2021-09-16

Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data processing, see <http://spark.apache.org>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut], Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>), Kevin Ushey [aut], JJ Allaire [aut], Samuel Macedo [ctb], Hossein Falaki [aut], Lu Wang [aut], Andy Zhang [aut], Yitao Li [aut, cre] (<https://orcid.org/0000-0002-1261-905X>), Jozef Hajnala [ctb], Maciej Szymkiewicz [ctb] (<https://orcid.org/0000-0003-1469-9396>), Wil Davis [ctb], RStudio [cph], The Apache Software Foundation [aut, cph]
Maintainer: Yitao Li <yitao@rstudio.com>

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Package GeoFIS updated to version 1.0.2 with previous version 1.0.1 dated 2021-07-22

Title: Spatial Data Processing for Decision Making
Description: Methods for processing spatial data for decision-making. This package is an R implementation of methods provided by the open source software GeoFIS <https://www.geofis.org> (Leroux et al. 2018) <doi:10.3390/agriculture8060073>. The main functionalities are the management zone delineation (Pedroso et al. 2010) <doi:10.1016/j.compag.2009.10.007> and data aggregation (Mora-Herrera et al. 2020) <doi:10.1016/j.compag.2020.105624>.
Author: Serge Guillaume [aut], Jean-Luc Lablée [aut, cre], INRAE [cph] (National Research Institute for Agriculture, Food and Environment, France)
Maintainer: Jean-Luc Lablée <jean-luc.lablee@inrae.fr>

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New package tsentiment with initial version 1.0.4
Package: tsentiment
Title: Fetching Tweet Data for Sentiment Analysis
Version: 1.0.4
Author: Hakki Sabah <hakkisabah@hotmail.com>
Maintainer: Hakki Sabah <hakkisabah@hotmail.com>
Description: Which uses Twitter APIs for the necessary data in sentiment analysis, acts as a middleware with the approved Twitter Application. A special access key is given to users who subscribe to the application with their Twitter account. With this special access key, the user defined keyword for sentiment analysis can be searched in twitter recent searches and results can be obtained( more information <https://github.com/hakkisabah/tsentiment> ). In addition, a service named tsentiment-services has been developed to provide all these operations ( for more information <https://github.com/hakkisabah/tsentiment-services> ). After the successful results obtained and in line with the permissions given by the user, the results of the analysis of the word cloud and bar graph saved in the user folder directory can be seen. In each analysis performed, the previous analysis visual result is deleted and this is the basic information you need to know as a practice rule. 'tsentiment' package provides a free service that acts as a middleware for easy data extraction from Twitter, and in return, the user rate limit is reduced by 30 requests from the total limit and the remaining requests are used. These 30 requests are reserved for use in application analytics. For information about endpoints, you can refer to the limit information in the "GET search/tweets" row in the Endpoints column in the list at <https://developer.twitter.com/en/docs/twitter-api/v1/rate-limits>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/hakkisabah/tsentiment, https://www.tsentiment.com
BugReports: https://github.com/hakkisabah/tsentiment/issues
Depends: R (>= 4.0)
Imports: reshape2,wordcloud,wordcloud2,ggplot2,httr,syuzhet,tidytext,dplyr,tibble,progress,stringi
NeedsCompilation: no
Packaged: 2021-11-27 18:13:35 UTC; hakki
Repository: CRAN
Date/Publication: 2021-11-30 11:30:02 UTC

More information about tsentiment at CRAN
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Package BayesCTDesign updated to version 0.6.1 with previous version 0.6.0 dated 2019-08-02

Title: Two Arm Bayesian Clinical Trial Design with and Without Historical Control Data
Description: A set of functions to help clinical trial researchers calculate power and sample size for two-arm Bayesian randomized clinical trials that do or do not incorporate historical control data. At some point during the design process, a clinical trial researcher who is designing a basic two-arm Bayesian randomized clinical trial needs to make decisions about power and sample size within the context of hypothesized treatment effects. Through simulation, the simple_sim() function will estimate power and other user specified clinical trial characteristics at user specified sample sizes given user defined scenarios about treatment effect,control group characteristics, and outcome. If the clinical trial researcher has access to historical control data, then the researcher can design a two-arm Bayesian randomized clinical trial that incorporates the historical data. In such a case, the researcher needs to work through the potential consequences of historical and randomized control differences on trial characteristics, in addition to working through issues regarding power in the context of sample size, treatment effect size, and outcome. If a researcher designs a clinical trial that will incorporate historical control data, the researcher needs the randomized controls to be from the same population as the historical controls. What if this is not the case when the designed trial is implemented? During the design phase, the researcher needs to investigate the negative effects of possible historic/randomized control differences on power, type one error, and other trial characteristics. Using this information, the researcher should design the trial to mitigate these negative effects. Through simulation, the historic_sim() function will estimate power and other user specified clinical trial characteristics at user specified sample sizes given user defined scenarios about historical and randomized control differences as well as treatment effects and outcomes. The results from historic_sim() and simple_sim() can be printed with print_table() and graphed with plot_table() methods. Outcomes considered are Gaussian, Poisson, Bernoulli, Lognormal, Weibull, and Piecewise Exponential. The methods are described in Eggleston et al. (2021) <doi:10.18637/jss.v100.i21>.
Author: Barry Eggleston [cre, aut], Doug Wilson [aut], Becky McNeil [aut], Joseph Ibrahim [aut], Diane Catellier [fnd, rth, aut]
Maintainer: Barry Eggleston <beggleston@rti.org>

Diff between BayesCTDesign versions 0.6.0 dated 2019-08-02 and 0.6.1 dated 2021-11-30

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 BayesCTDesign-0.6.1/BayesCTDesign/DESCRIPTION                        |   17 
 BayesCTDesign-0.6.1/BayesCTDesign/MD5                                |   59 
 BayesCTDesign-0.6.1/BayesCTDesign/NAMESPACE                          |   28 
 BayesCTDesign-0.6.1/BayesCTDesign/NEWS.md                            |   26 
 BayesCTDesign-0.6.1/BayesCTDesign/R/BayesCTDesigncode.R              | 5620 ++--------
 BayesCTDesign-0.6.1/BayesCTDesign/R/BernoulliCode.R                  | 2344 ++--
 BayesCTDesign-0.6.1/BayesCTDesign/R/BernoulliErrorChecks.R           |  250 
 BayesCTDesign-0.6.1/BayesCTDesign/R/GaussianCode.R                   | 2376 ++--
 BayesCTDesign-0.6.1/BayesCTDesign/R/GaussianErrorChecks.R            |  234 
 BayesCTDesign-0.6.1/BayesCTDesign/R/GlobalErrorChecks.R              |  381 
 BayesCTDesign-0.6.1/BayesCTDesign/R/LogNormalCode.R                  | 2626 ++--
 BayesCTDesign-0.6.1/BayesCTDesign/R/LogNormalErrorChecks.R           |  306 
 BayesCTDesign-0.6.1/BayesCTDesign/R/PWECode.R                        |    9 
 BayesCTDesign-0.6.1/BayesCTDesign/R/PWEErrorChecks.R                 |  386 
 BayesCTDesign-0.6.1/BayesCTDesign/R/PoissonCode.R                    | 2330 ++--
 BayesCTDesign-0.6.1/BayesCTDesign/R/PoissonErrorChecks.R             |  248 
 BayesCTDesign-0.6.1/BayesCTDesign/R/WeibullCode.R                    | 2712 ++--
 BayesCTDesign-0.6.1/BayesCTDesign/R/WeibullErrorChecks.R             |  308 
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 33 files changed, 9607 insertions(+), 13254 deletions(-)

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Package meta4diag updated to version 2.1.1 with previous version 2.0.8 dated 2018-07-23

Title: Meta-Analysis for Diagnostic Test Studies
Description: Bayesian inference analysis for bivariate meta-analysis of diagnostic test studies using integrated nested Laplace approximation with INLA. A purpose built graphic user interface is available. The installation of R package INLA is compulsory for successful usage. The INLA package can be obtained from <https://www.r-inla.org>. We recommend the testing version, which can be downloaded by running: install.packages("INLA", repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/testing"), dep=TRUE).
Author: Jingyi Guo <jingyi.guo@ntnu.no> and Andrea Riebler <andrea.riebler@ntnu.no>
Maintainer: Jingyi Guo <jingyi.guo@ntnu.no>

Diff between meta4diag versions 2.0.8 dated 2018-07-23 and 2.1.1 dated 2021-11-30

 DESCRIPTION         |   18 +++++++++---------
 MD5                 |   18 +++++++++---------
 R/makeObject.R      |   17 ++++++++++++-----
 R/runModel.R        |    4 ++--
 R/uuu.R             |    2 ++
 data/Catheter.rda   |binary
 data/Scheidler.rda  |binary
 data/Telomerase.rda |binary
 data/table_cor.rda  |binary
 data/table_var.rda  |binary
 10 files changed, 34 insertions(+), 25 deletions(-)

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Package DDIwR updated to version 0.9 with previous version 0.8 dated 2021-09-02

Title: DDI with R
Description: Useful functions for various DDI (Data Documentation Initiative) related inputs and outputs. Converts data files to and from SPSS, Stata, SAS, R and Excel, including user declared missing values.
Author: Adrian Dusa [aut, cre, cph] (<https://orcid.org/0000-0002-3525-9253>)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

Diff between DDIwR versions 0.8 dated 2021-09-02 and 0.9 dated 2021-11-30

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 DDIwR-0.9/DDIwR/R/checkType.R          |    5 
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 DDIwR-0.9/DDIwR/R/getFiles.R           |    6 
 DDIwR-0.9/DDIwR/R/getMetadata.R        |   53 ++++++-
 DDIwR-0.9/DDIwR/R/make_labelled.R      |    2 
 DDIwR-0.9/DDIwR/R/recodeValues.R       |only
 DDIwR-0.9/DDIwR/R/setupfile.R          |  222 +++++++++++++++++++++------------
 DDIwR-0.9/DDIwR/R/treatPath.R          |   11 +
 DDIwR-0.9/DDIwR/inst/ChangeLog         |   13 +
 DDIwR-0.9/DDIwR/man/DDIwR-internal.Rd  |    1 
 DDIwR-0.9/DDIwR/man/DDIwR.package.Rd   |    4 
 DDIwR-0.9/DDIwR/man/convert.Rd         |   21 ++-
 DDIwR-0.9/DDIwR/man/exportDDI.Rd       |   28 ++--
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 24 files changed, 416 insertions(+), 175 deletions(-)

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New package soilphysics with initial version 4.1
Package: soilphysics
Title: Soil Physical Analysis
Version: 4.1
Date: 2021-11-21
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva [aut, cre] (<https://orcid.org/0000-0003-2518-542X>), Renato Paiva de Lima [aut] (<https://orcid.org/0000-0003-0524-439X>)
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
URL: https://arsilva87.github.io/soilphysics/
Imports: utils, stats, graphics, boot, grDevices, datasets, MASS, shiny, shinydashboard, fields
Suggests: knitr, rmarkdown, rpanel, tcltk
VignetteBuilder: knitr
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2021-11-21 11:41:00 UTC; User
Repository: CRAN
Date/Publication: 2021-11-30 09:50:02 UTC

More information about soilphysics at CRAN
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