Fri, 23 Apr 2021

Package tsxtreme updated to version 0.3.3 with previous version 0.3.2 dated 2018-12-21

Title: Bayesian Modelling of Extremal Dependence in Time Series
Description: Characterisation of the extremal dependence structure of time series, avoiding pre-processing and filtering as done typically with peaks-over-threshold methods. It uses the conditional approach of Heffernan and Tawn (2004) <DOI:10.1111/j.1467-9868.2004.02050.x> which is very flexible in terms of extremal and asymptotic dependence structures, and Bayesian methods improve efficiency and allow for deriving measures of uncertainty. For example, the extremal index, related to the size of clusters in time, can be estimated and samples from its posterior distribution obtained.
Author: Thomas Lugrin
Maintainer: Thomas Lugrin <thomas.lugrin@alumni.epfl.ch>

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Package maczic updated to version 0.2.0 with previous version 0.1.0 dated 2020-11-09

Title: Mediation Analysis for Count and Zero-Inflated Count Data
Description: Performs causal mediation analysis for count and zero-inflated count data without or with a post-treatment confounder; calculates power to detect prespecified causal mediation effects, direct effects, and total effects; performs sensitivity analysis when there is a treatment- induced mediator-outcome confounder as described by Cheng, J., Cheng, N.F., Guo, Z., Gregorich, S., Ismail, A.I., Gansky, S.A. (2018) <doi:10.1177/0962280216686131>. Implements Instrumental Variable (IV) method to estimate the controlled (natural) direct and mediation effects, and compute the bootstrap Confidence Intervals as described by Guo, Z., Small, D.S., Gansky, S.A., Cheng, J. (2018) <doi:10.1111/rssc.12233>. This software was made possible by Grant R03DE028410 from the The National Institute of Dental and Craniofacial Research, a component of the National Institutes of Health.
Author: Nancy Cheng, Zijian Guo, Jing Cheng
Maintainer: Nancy Cheng <Nancy.Cheng@ucsf.edu>

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Package websocket updated to version 1.4.0 with previous version 1.3.2 dated 2021-02-10

Title: 'WebSocket' Client Library
Description: Provides a 'WebSocket' client interface for R. 'WebSocket' is a protocol for low-overhead real-time communication: <https://en.wikipedia.org/wiki/WebSocket>.
Author: Winston Chang [aut, cre], Joe Cheng [aut], Alan Dipert [aut], Barbara Borges [aut], RStudio [cph], Peter Thorson [ctb, cph] (WebSocket++ library), René Nyffenegger [ctb, cph] (Base 64 library), Micael Hildenborg [ctb, cph] (SHA1 library), Aladdin Enterprises [cph] (MD5 library), Bjoern Hoehrmann [ctb, cph] (UTF8 Validation library)
Maintainer: Winston Chang <winston@rstudio.com>

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Package tsna updated to version 0.3.3 with previous version 0.3.1 dated 2020-01-20

Title: Tools for Temporal Social Network Analysis
Description: Temporal SNA tools for continuous- and discrete-time longitudinal networks having vertex, edge, and attribute dynamics stored in the 'networkDynamic' format. This work was supported by grant R01HD68395 from the National Institute of Health.
Author: Skye Bender-deMoll [aut, cre], Martina Morris [aut], James Moody [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>

Diff between tsna versions 0.3.1 dated 2020-01-20 and 0.3.3 dated 2021-04-23

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Package predictrace updated to version 2.0.0 with previous version 1.2.1 dated 2020-09-16

Title: Predict the Race and Gender of a Given Name Using Census and Social Security Administration Data
Description: Predicts the most common race of a surname and based on U.S. Census data, and the most common first named based on U.S. Social Security Administration data.
Author: Jacob Kaplan [aut, cre] (<https://orcid.org/0000-0002-0601-0387>)
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>

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Package haven updated to version 2.4.1 with previous version 2.4.0 dated 2021-04-14

Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the embedded 'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package httpuv updated to version 1.6.0 with previous version 1.5.5 dated 2021-01-13

Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
Author: Joe Cheng [aut], Winston Chang [aut, cre], RStudio, PBC [cph], Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Andrzej Krzemienski [cph] (optional.hpp)
Maintainer: Winston Chang <winston@rstudio.com>

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Package mdatools updated to version 0.11.4 with previous version 0.11.3 dated 2021-01-22

Title: Multivariate Data Analysis for Chemometrics
Description: Projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics. S. Kucheryavskiy (2020) <doi: 10.1016/j.chemolab.2020.103937>.
Author: Sergey Kucheryavskiy (<https://orcid.org/0000-0002-3145-7244>)
Maintainer: Sergey Kucheryavskiy <svkucheryavski@gmail.com>

Diff between mdatools versions 0.11.3 dated 2021-01-22 and 0.11.4 dated 2021-04-23

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Package ecm updated to version 6.1.0 with previous version 5.1.0 dated 2021-02-10

Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>

Diff between ecm versions 5.1.0 dated 2021-02-10 and 6.1.0 dated 2021-04-23

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Package selection.index updated to version 1.1.0 with previous version 1.0.0 dated 2021-04-06

Title: Analysis of Selection Index in Plant Breeding
Description: The aim of most plant breeding programmes is simultaneous improvement of several characters. An objective method involving simultaneous selection for several attributes then becomes necessary. It has been recognised that most rapid improvements in the economic value is expected from selection applied simultaneously to all the characters which determine the economic value of a plant, and appropriate assigned weights to each character according to their economic importance, heritability and correlations between characters. So the selection for economic value is a complex matter. If the component characters are combined together into an index in such a way that when selection is applied to the index, as if index is the character to be improved, most rapid improvement of economic value is expected. Such an index was first proposed by Smith (1937 <doi:10.1111/j.1469-1809.1936.tb02143.x>) based on the Fisher's (1936 <doi:10.1111/j.1469-1809.1936.tb02137.x>) "discriminant function" Dabholkar (1999 <https://books.google.co.in/books?id=mlFtumAXQ0oC&lpg=PA4&ots=Xgxp1qLuxS&dq=elements%20of%20biometrical%20genetics&lr&pg=PP1#v=onepage&q&f=false>). In this package selection index is calculated based on the Smith (1937) selection index method.
Author: Zankrut Goyani [aut, cre, cph], Alok Shrivastva [aut], Yogesh Garde [aut], Arvind Chaudhary [aut]
Maintainer: Zankrut Goyani <zankrut20@gmail.com>

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Package BuyseTest updated to version 2.3.0 with previous version 2.2.6 dated 2021-03-16

Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring. GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints to estimate the probability that a random observation drawn from one group performs better than a random observation drawn from the other group (Mann-Whitney parameter). The net benefit and win ratio statistics, i.e. the difference and ratio between the probabilities relative to the intervention and control groups, can then also be estimated. Confidence intervals and p-values are obtained using permutations, a non-parametric bootstrap, or the asymptotic theory. The software enables the use of thresholds of minimal importance difference, stratification, non-prioritized endpoints (O'Brien test), and can handle right-censoring and competing-risks.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>), Julien Peron [ctb], Eva Cantagallo [aut]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>

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Package taxonomizr updated to version 0.7.1 with previous version 0.6.0 dated 2021-02-08

Title: Functions to Work with NCBI Accessions and Taxonomy
Description: Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to downloads NCBI data dumps and create a local database for fast and local taxonomic assignment.
Author: Scott Sherrill-Mix [aut, cre]
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>

Diff between taxonomizr versions 0.6.0 dated 2021-02-08 and 0.7.1 dated 2021-04-23

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New package rENA with initial version 0.2.3
Package: rENA
Title: Epistemic Network Analysis
Author: Cody L Marquart [aut, cre] (<https://orcid.org/0000-0002-3387-6792>), Zachari Swiecki [aut], Wesley Collier [aut], Brendan Eagan [aut], Roman Woodward [aut], David Williamson Shaffer [aut]
Authors@R: c(person("Cody L", "Marquart", role = c("aut", "cre"), email="cody.marquart@wisc.edu", comment = c(ORCID = "0000-0002-3387-6792")), person("Zachari","Swiecki", role = c("aut"), email="swiecki@wisc.edu"), person("Wesley","Collier", role = c("aut"), email="wcollier@wisc.edu"), person("Brendan","Eagan", role = c("aut"), email="beagan@wisc.edu"), person("Roman", "Woodward", role = c("aut"), email="rwoodward3@wisc.edu"), person("David Williamson", "Shaffer", role = c("aut"), email = "dws@education.wisc.edu"))
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Version: 0.2.3
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016).
LazyData: TRUE
Depends: R (>= 3.0.0)
License: GPL-3 | file LICENSE
LinkingTo: Rcpp, RcppArmadillo
Imports: data.table, Rcpp, R6, methods, foreach, stats, plotly, doParallel, parallel, scales, magrittr, concatenate
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, webshot
NeedsCompilation: yes
Packaged: 2021-04-22 11:15:39 UTC; clmarquart
Repository: CRAN
Date/Publication: 2021-04-23 15:10:06 UTC

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Package later updated to version 1.2.0 with previous version 1.1.0.1 dated 2020-06-05

Title: Utilities for Scheduling Functions to Execute Later with Event Loops
Description: Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The functions are scheduled in an event loop.
Author: Winston Chang [aut, cre], Joe Cheng [aut], RStudio [cph], Marcus Geelnard [ctb, cph] (TinyCThread library, https://tinycthread.github.io/), Evan Nemerson [ctb, cph] (TinyCThread library, https://tinycthread.github.io/)
Maintainer: Winston Chang <winston@rstudio.com>

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Package fontawesome updated to version 0.2.1 with previous version 0.2.0 dated 2021-03-28

Title: Easily Work with 'Font Awesome' Icons
Description: Easily and flexibly insert 'Font Awesome' icons into 'R Markdown' documents and 'Shiny' apps. These icons can be inserted into HTML content through inline 'SVG' tags or 'i' tags. There is also a utility function for exporting 'Font Awesome' icons as 'PNG' images for those situations where raster graphics are needed.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Winston Chang [ctb], Dave Gandy [ctb, cph] (Font-Awesome font), RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>

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New package abn with initial version 2.5-0
Package: abn
Version: 2.5-0
Date: 2021-04-21
Title: Modelling Multivariate Data with Additive Bayesian Networks
Authors@R: c(person(given = "Gilles", family = "Kratzer", role = c("aut", "cre"), email = "gilles.kratzer@gmail.com", comment = c(ORCID = "0000-0002-5929-8935")), person(given = "Fraser Iain", family = "Lewis", role = "aut", email = "fraser.iain.lewis@gmail.com", comment = c(ORCID = "0000-0003-4580-2712")), person(given = "Reinhard", family = "Furrer", role = "ctb", email = "reinhard.furrer@math.uzh.ch", comment = c(ORCID = "0000-0002-6319-2332")), person(given = "Marta", family = "Pittavino", role = "ctb", email = "marta.pittavino@math.uzh.ch", comment = c(ORCID = "0000-0002-1232-1034")))
Author: Gilles Kratzer [aut, cre] (<https://orcid.org/0000-0002-5929-8935>), Fraser Iain Lewis [aut] (<https://orcid.org/0000-0003-4580-2712>), Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>), Marta Pittavino [ctb] (<https://orcid.org/0000-0002-1232-1034>)
Maintainer: Gilles Kratzer <gilles.kratzer@gmail.com>
Imports: methods, rjags
LinkingTo: Rcpp, RcppArmadillo
Depends: nnet, lme4, Rgraphviz, R (>= 4.0.0)
Suggests: INLA, knitr, R.rsp, testthat, entropy, moments, boot, brglm
VignetteBuilder: R.rsp
Additional_repositories: https://inla.r-inla-download.org/R/stable/
SystemRequirements: Gnu Scientific Library version >= 1.12
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from <https://www.r-inla.org>. The computing library JAGS <https://mcmc-jags.sourceforge.io> is used to simulate 'abn'-like data. A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the 'abn' website <http://r-bayesian-networks.org>.
License: GPL (>= 2)
LazyData: true
URL: http://r-bayesian-networks.org
BugReports: https://git.math.uzh.ch/reinhard.furrer/abn/-/issues
NeedsCompilation: yes
Packaged: 2021-04-21 07:14:53 UTC; furrer
Repository: CRAN
Date/Publication: 2021-04-23 15:10:10 UTC

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New package wordpressr with initial version 0.2.2
Package: wordpressr
Title: An API Wrapper for WordPress Site APIs
Version: 0.2.2
Authors@R: c(person("Simit", "Patel", email = "simit@sixjupiter.com", role = c("aut", "cre")), person(given = 'SixJupiter',role = c('cph','fnd')))
URL: https://sixjupiter.com/wordpressr/
BugReports: https://github.com/simitpatel/wordpressr/issues
Description: An API wrapper that helps R developers retrieve data from a WordPress site's API in tidy format, in addition to publishing content on the WordPress site (WordPress API documentation: <https://developer.wordpress.org/rest-api/>).
Imports: httr, tibble, dplyr, tidyr, magrittr, glue, purrr
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat, stringi
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-04-14 02:09:09 UTC; simit.patel
Author: Simit Patel [aut, cre], SixJupiter [cph, fnd]
Maintainer: Simit Patel <simit@sixjupiter.com>
Repository: CRAN
Date/Publication: 2021-04-23 15:00:03 UTC

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Package RUVIIIC updated to version 1.0.19 with previous version 1.0.18 dated 2021-04-10

Title: RUV-III-C
Description: Variations of Remove Unwanted Variation-III (RUV-III) known as RUV-III-C (RUV-III Complete). RUV-III performs normalisation using negative control variables and replication. RUV-III-C extends this method to cases where the data contains missing values, by applying RUV-III to complete subsets of the data. Originally designed for SWATH-MS proteomics datasets. Poulos et al. (2020) <doi:10.1038/s41467-020-17641-3>.
Author: Rohan Shah [aut, cre], Sean Peters [ctb], Qing Zhong [ctb], Children's Medical Research Institute [cph]
Maintainer: Rohan Shah <rshah@cmri.org.au>

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Package qqplotr updated to version 0.0.5 with previous version 0.0.4 dated 2020-02-04

Title: Quantile-Quantile Plot Extensions for 'ggplot2'
Description: Extensions of 'ggplot2' Q-Q plot functionalities.
Author: Alexandre Almeida [aut], Adam Loy [aut, cre], Heike Hofmann [aut]
Maintainer: Adam Loy <loyad01@gmail.com>

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Package midasml updated to version 0.1.4 with previous version 0.1.3 dated 2021-04-22

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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Package Markovchart updated to version 2.0.0 with previous version 1.1.1 dated 2020-12-16

Title: Markov Chain-Based Cost-Optimal Control Charts
Description: Functions for cost-optimal control charts with a focus on health care applications. Compared to assumptions in traditional control chart theory, here, we allow random shift sizes, random repair and random sampling times. The package focuses on X-bar charts with a sample size of 1 (representing the monitoring of a single patient at a time). The methods are described in Zempleni et al. (2004) <doi:10.1002/asmb.521>, Dobi and Zempleni (2019) <doi:10.1002/qre.2518> and Dobi and Zempleni (2019) <http://ac.inf.elte.hu/Vol_049_2019/129_49.pdf>.
Author: Balazs Dobi & Andras Zempleni
Maintainer: Balazs Dobi <dobibalazs@inf.elte.hu>

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Package KMunicate updated to version 0.2.1 with previous version 0.2.0 dated 2020-11-16

Title: KMunicate-Style Kaplan–Meier Plots
Description: Produce Kaplan–Meier plots in the style recommended following the KMunicate study by Morris et al. (2019) <doi:10.1136/bmjopen-2019-030215>. The KMunicate style consists of Kaplan-Meier curves with confidence intervals to quantify uncertainty and an extended risk table (per treatment arm) depicting the number of study subjects at risk, events, and censored observations over time. The resulting plots are built using 'ggplot2' and can be further customised to a certain extent, including themes, fonts, and colour scales.
Author: Alessandro Gasparini [aut, cre, cph] (<https://orcid.org/0000-0002-8319-7624>), Ary Serpa Neto [ctb]
Maintainer: Alessandro Gasparini <alessandro.gasparini@ki.se>

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Package IPLGP updated to version 1.2.0 with previous version 1.1.0 dated 2021-04-20

Title: Identification of Parental Lines via Genomic Prediction
Description: Combining genomic prediction with Monte Carlo simulation, three different strategies are implemented to select parental lines for multiple traits in plant breeding. The selection strategies include (i) GEBV-O considers only genomic estimated breeding values (GEBVs) of the candidate individuals; (ii) GD-O considers only genomic diversity (GD) of the candidate individuals; and (iii) GEBV-GD considers both GEBV and GD. The above method can be seen in Chung PY, Liao CT (2020) <doi:10.1371/journal.pone.0243159>. Multi-trait genomic best linear unbiased prediction (MT-GBLUP) model is used to simultaneously estimate GEBVs of the target traits, and then a selection index is adopted to evaluate the composite performance of an individual.
Author: Ping-Yuan Chung [cre], Chen-Tuo Liao [aut]
Maintainer: Ping-Yuan Chung <r06621204@ntu.edu.tw>

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Package GADMTools updated to version 3.8-2 with previous version 3.8-1 dated 2020-03-05

Title: Easy Use of 'GADM' Maps
Description: Manipulate, assemble, export <https://gadm.org/> maps. Create 'choropleth', 'isopleth', dots plot, proportional dots, dot-density and more.
Author: Jean Pierre Decorps [aut, cre]
Maintainer: Jean Pierre Decorps <jean.pierre.decorps@gmail.com>

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Package BDEsize updated to version 1.5 with previous version 1.2 dated 2019-11-01

Title: Efficient Determination of Sample Size in Balanced Design of Experiments
Description: For a balanced design of experiments, this package calculates the sample size required to detect a certain standardized effect size, under a significance level. This package also provides three graphs; detectable standardized effect size vs power, sample size vs detectable standardized effect size, and sample size vs power, which show the mutual relationship between the sample size, power and the detectable standardized effect size. The detailed procedure is described in R. V. Lenth (2006-9) <https://homepage.divms.uiowa.edu/~rlenth/Power/>, Y. B. Lim (1998), M. A. Kastenbaum, D. G. Hoel and K. O. Bowman (1970) <doi:10.2307/2334851>, and Douglas C. Montgomery (2013, ISBN: 0849323312).
Author: Jong Hee Chung [aut, cre], Yong Bin Lim [aut], Donghoh Kim [ctb]
Maintainer: Jong Hee Chung <jochung947@gmail.com>

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Package brio updated to version 1.1.2 with previous version 1.1.1 dated 2021-01-20

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, cre] (<https://orcid.org/0000-0002-2739-7082>), RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>

Diff between brio versions 1.1.1 dated 2021-01-20 and 1.1.2 dated 2021-04-23

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New package materialmodifier with initial version 1.0.0
Package: materialmodifier
Title: Apply Material Editing Effects
Version: 1.0.0
Authors@R: person(given = "Hiroyuki", family = "Tsuda", role = c("aut", "cre"), email = "tsuda16k@gmail.com", comment = c(ORCID = "0000-0001-9396-5327"))
Description: You can apply image processing effects that modifies the perceived material properties such as gloss, smoothness, and blemishes. This is an implementation of the algorithm proposed by Boyadzhiev et al. (2015) "Band-Sifting Decomposition for Image Based Material Editing". Documentation and practical tips of the package is available at <https://github.com/tsuda16k/materialmodifier>.
URL: https://github.com/tsuda16k/materialmodifier
BugReports: https://github.com/tsuda16k/materialmodifier/issues/
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: jpeg, magrittr, methods, png, readbitmap, stringr, downloader, imager, moments
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-04-22 15:39:17 UTC; tsuda
Author: Hiroyuki Tsuda [aut, cre] (<https://orcid.org/0000-0001-9396-5327>)
Maintainer: Hiroyuki Tsuda <tsuda16k@gmail.com>
Repository: CRAN
Date/Publication: 2021-04-23 12:20:02 UTC

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Package ncdfgeom updated to version 1.1.1 with previous version 1.1.0 dated 2019-08-28

Title: 'NetCDF' Geometry and Time Series
Description: Tools to create time series and geometry 'NetCDF' files.
Author: David Blodgett [aut, cre], Luke Winslow [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>

Diff between ncdfgeom versions 1.1.0 dated 2019-08-28 and 1.1.1 dated 2021-04-23

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Package shadowtext updated to version 0.0.8 with previous version 0.0.7 dated 2019-11-06

Title: Shadow Text Grob and Layer
Description: Implement shadowtextGrob() for 'grid' and geom_shadowtext() layer for 'ggplot2'. These functions create/draw text grob with background shadow.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between shadowtext versions 0.0.7 dated 2019-11-06 and 0.0.8 dated 2021-04-23

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

Title: Scatter Pie Plot
Description: Creates scatterpie plots, especially useful for plotting pies on a map.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between scatterpie versions 0.1.5 dated 2020-09-09 and 0.1.6 dated 2021-04-23

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New package rcolors with initial version 0.1.0
Package: rcolors
Title: 270 'NCL' Color Tables in R Language
Description: 'NCL' (NCAR Command Language) is one of the most popular spatial data mapping tools in meteorology studies, due to its beautiful output figures with plenty of color palettes designed by experts <https://www.ncl.ucar.edu/index.shtml>. Here we translate all 'NCL' color palettes into R hexadecimal RGB colors and provide color selection function, which will help users make a beautiful figure.
Version: 0.1.0
Authors@R: c( person("Dongdong", "Kong", role = c("aut", "cre"), email = "kongdd.sysu@gmail.com", comment = c(ORCID = "0000-0003-1836-8172")))
Depends: R (>= 3.1)
Imports: magrittr
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: testthat, covr
NeedsCompilation: no
Packaged: 2021-04-22 12:13:18 UTC; kongdd
Author: Dongdong Kong [aut, cre] (<https://orcid.org/0000-0003-1836-8172>)
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>
Repository: CRAN
Date/Publication: 2021-04-23 10:40:02 UTC

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Package GerminaR updated to version 2.1.1 with previous version 2.0.1 dated 2020-10-25

Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano-Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>), Omar Benites Alfaro [aut] (<https://orcid.org/0000-0002-6852-9598>), Denise Garcia de Santana [aut], Marli A. Ranal [aut], Marcelo F. Pompelli [aut, ths] (<https://orcid.org/0000-0002-4408-6374>), Federal University of Pernambuco [cph] (Register of application), Federal Rural University of Pernambuco [cph] (Post Graduate Program)
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>

Diff between GerminaR versions 2.0.1 dated 2020-10-25 and 2.1.1 dated 2021-04-23

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Package terrainr updated to version 0.4.0 with previous version 0.3.1 dated 2021-02-23

Title: Landscape Visualizations in R and 'Unity'
Description: Functions for the retrieval, manipulation, and visualization of 'geospatial' data, with an aim towards producing '3D' landscape visualizations in the 'Unity' '3D' rendering engine. Functions are also provided for retrieving elevation data and base map tiles from the 'USGS' National Map ('<https://apps.nationalmap.gov/services/>').
Author: Michael Mahoney [aut, cre] (<https://orcid.org/0000-0003-2402-304X>), Mike Johnson [rev] (Mike reviewed the package (v. 0.2.1) for rOpenSci, see <https://github.com/ropensci/software-review/issues/416>), Sydney Foks [rev] (Sydney reviewed the package (v. 0.2.1) for rOpenSci, see <https://github.com/ropensci/software-review/issues/416>)
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>

Diff between terrainr versions 0.3.1 dated 2021-02-23 and 0.4.0 dated 2021-04-23

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Package rPanglaoDB updated to version 0.2.0 with previous version 0.1.0 dated 2021-04-15

Title: Download and Merge Single-Cell RNA-Seq Data from the PanglaoDB Database
Description: Download and merge labeled single-cell RNA-seq data from the PanglaoDB <https://panglaodb.se/> into a Seurat object.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>), Marieke Kuijjer [aut] (<https://orcid.org/0000-0001-6280-3130>), James J. Cai [aut] (<https://orcid.org/0000-0002-8081-6725>)
Maintainer: Daniel Osorio <daniecos@uio.no>

Diff between rPanglaoDB versions 0.1.0 dated 2021-04-15 and 0.2.0 dated 2021-04-23

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Package rgl updated to version 0.106.8 with previous version 0.106.6 dated 2021-04-17

Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre], Daniel Adler [aut], Oleg Nenadic [ctb], Simon Urbanek [ctb], Ming Chen [ctb], Albrecht Gebhardt [ctb], Ben Bolker [ctb], Gabor Csardi [ctb], Adam Strzelecki [ctb], Alexander Senger [ctb], The R Core Team [ctb, cph], Dirk Eddelbuettel [ctb], The authors of Shiny [cph], The authors of knitr [cph], Jeroen Ooms [ctb], Yohann Demont [ctb], Joshua Ulrich [ctb], Xavier Fernandez i Marin [ctb], George Helffrich [ctb], Ivan Krylov [ctb]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>

Diff between rgl versions 0.106.6 dated 2021-04-17 and 0.106.8 dated 2021-04-23

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Package meme updated to version 0.2.3 with previous version 0.2.2 dated 2019-08-05

Title: Create Meme
Description: The word 'Meme' was originated from the book, 'The Selfish Gene', authored by Richard Dawkins (1976). It is a unit of culture that is passed from one generation to another and correlates to the gene, the unit of physical heredity. The internet memes are captioned photos that are intended to be funny, ridiculous. Memes behave like infectious viruses and travel from person to person quickly through social media. The 'meme' package allows users to make custom memes.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between meme versions 0.2.2 dated 2019-08-05 and 0.2.3 dated 2021-04-23

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Package dlstats updated to version 0.1.4 with previous version 0.1.3 dated 2019-11-14

Title: Download Stats of R Packages
Description: Monthly download stats of 'CRAN' and 'Bioconductor' packages. Download stats of 'CRAN' packages is from the 'RStudio' 'CRAN mirror', see <https://cranlogs.r-pkg.org:443>. 'Bioconductor' package download stats is at <https://bioconductor.org/packages/stats/>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between dlstats versions 0.1.3 dated 2019-11-14 and 0.1.4 dated 2021-04-23

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Package V8 updated to version 3.4.1 with previous version 3.4.0 dated 2020-11-04

Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8: Google's open source JavaScript and WebAssembly engine. This package can be compiled either with V8 version 6 and up, a NodeJS shared library, or the legacy 3.14/3.15 branch of V8.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between V8 versions 3.4.0 dated 2020-11-04 and 3.4.1 dated 2021-04-23

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Package rrcovHD updated to version 0.2-7 with previous version 0.2-6 dated 2019-11-29

Title: Robust Multivariate Methods for High Dimensional Data
Description: Robust multivariate methods for high dimensional data including outlier detection (Filzmoser and Todorov (2013) <doi:10.1016/j.ins.2012.10.017>), robust sparse PCA (Croux et al. (2013) <doi:10.1080/00401706.2012.727746>, Todorov and Filzmoser (2013) <doi:10.1007/978-3-642-33042-1_31>), robust PLS (Todorov and Filzmoser (2014) <doi:10.17713/ajs.v43i4.44>), and robust sparse classification (Ortner et al. (2020) <doi:10.1007/s10618-019-00666-8>).
Author: Valentin Todorov [aut, cre] (<https://orcid.org/0000-0003-4215-0245>)
Maintainer: Valentin Todorov <valentin.todorov@chello.at>

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More information about rrcovHD at CRAN
Permanent link

Package paleopop updated to version 2.1.1 with previous version 2.1.0 dated 2021-04-22

Title: Pattern-Oriented Modeling Framework for Coupled Niche-Population Paleo-Climatic Models
Description: This extension of the poems pattern-oriented modeling (POM) framework provides a collection of modules and functions customized for paleontological time-scales, and optimized for single-generation transitions and large populations, across multiple generations.
Author: Sean Haythorne [aut], Julia Pilowsky [aut, cre] (<https://orcid.org/0000-0002-6376-2585>)
Maintainer: Julia Pilowsky <julia.pilowsky@adelaide.edu.au>

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Permanent link

Package npreg updated to version 1.0-6 with previous version 1.0-5 dated 2020-11-30

Title: Nonparametric Regression via Smoothing Splines
Description: Multiple and generalized nonparametric regression using smoothing spline ANOVA models and generalized additive models, as described in Helwig (2020) <doi:10.4135/9781526421036885885>. Includes support for Gaussian and non-Gaussian responses, smoothers for multiple types of predictors, interactions between smoothers of mixed types, and eight different methods for smoothing parameter selection.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>

Diff between npreg versions 1.0-5 dated 2020-11-30 and 1.0-6 dated 2021-04-23

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Package mockthat updated to version 0.2.6 with previous version 0.2.4 dated 2020-12-09

Title: Function Mocking for Unit Testing in R
Description: With the deprecation of mocking capabilities shipped with 'testthat' as of 'edition 3' it is left to third-party packages to replace this functionality, which in some test-scenarios is essential in order to run unit tests in limited environments (such as no Internet connection). Mocking in this setting means temporarily substituting a function with a stub that acts in some sense like the original function (for example by serving a HTTP response that has been cached as a file). The only exported function 'with_mock()' is modeled after the eponymous 'testthat' function with the intention of providing a drop-in replacement.
Author: Nicolas Bennett [aut, cre]
Maintainer: Nicolas Bennett <nicolas.bennett@stat.math.ethz.ch>

Diff between mockthat versions 0.2.4 dated 2020-12-09 and 0.2.6 dated 2021-04-23

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Package mcr updated to version 1.2.2 with previous version 1.2.1 dated 2014-02-12

Title: Method Comparison Regression
Description: Regression methods to quantify the relation between two measurement methods. In particular it addresses regression problems with errors in both variables and without repeated measurements. The package provides implementations of Deming regression, weighted Deming regression, and Passing-Bablok regression following the CLSI EP09-A3 recommendations for analytical method comparison and bias estimation using patient samples.
Author: Ekaterina Manuilova <ekaterina.manuilova@roche.com> Andre Schuetzenmeister <andre.schuetzenmeister@roche.com> Fabian Model <fabian.model@roche.com>
Maintainer: Sergej Potapov <sergej.potapov@roche.com>

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Package iNZightTools updated to version 1.11.0 with previous version 1.10 dated 2020-12-14

Title: Tools for 'iNZight'
Description: Provides a collection of wrapper functions for common variable and dataset manipulation workflows primarily used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Additionally, many of the functions return the 'tidyverse' code used to obtain the result in an effort to bridge the gap between GUI and coding.
Author: Tom Elliott [aut, cre] (<https://orcid.org/0000-0002-7815-6318>), Christoph Knopf [ctb], Akshay Gupta [ctb], Owen Jin [aut] (Tidyverse variable/data manipulation functions), Lushi Cai [ctb], Yiwen He [aut] (Dates/times and dataset manipulation), Daniel Barnett [aut] (Data validation)
Maintainer: Tom Elliott <tom.elliott@auckland.ac.nz>

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Package himach updated to version 0.1.1 with previous version 0.1.0 dated 2021-04-15

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 minimal model of aircraft performance: focus is on time saved versus subsonic flight, rather than 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 0.1.0 dated 2021-04-15 and 0.1.1 dated 2021-04-23

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Permanent link

Package BAwiR updated to version 1.2.6 with previous version 1.2.5 dated 2021-02-12

Title: Analysis of Basketball Data
Description: Collection of tools to work with basketball data. Functions available are related to friendly web scraping and visualization. Data were obtained from <https://www.euroleague.net/>, <https://www.eurocupbasketball.com/> and <http://www.acb.com>, following the instructions of their respectives robots.txt files, when available. Tools for visualization include a population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats, team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games and maps of nationalities. Please see Vinue (2020) <doi:10.1089/big.2018.0124>.
Author: Guillermo Vinue
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>

Diff between BAwiR versions 1.2.5 dated 2021-02-12 and 1.2.6 dated 2021-04-23

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New package ra4bayesmeta with initial version 1.0-7
Package: ra4bayesmeta
Title: Reference Analysis for Bayesian Meta-Analysis
Version: 1.0-7
Date: 2021-04-21
Authors@R: c(person("Manuela", "Ott", role = c("aut", "cre"), email = "manuela.c.ott@gmail.com"), person("Malgorzata", "Roos", role = "aut") )
Author: Manuela Ott [aut, cre], Malgorzata Roos [aut]
Maintainer: Manuela Ott <manuela.c.ott@gmail.com>
Description: Functionality for performing a principled reference analysis in the Bayesian normal-normal hierarchical model used for Bayesian meta-analysis, as described in Ott, Plummer and Roos (2021, "How vague is vague? How informative is informative? Reference analysis for Bayesian meta-analysis", under minor revision for Statistics in Medicine). Computes a reference posterior, induced by a minimally informative improper reference prior for the between-study (heterogeneity) standard deviation. Determines additional proper anti-conservative (and conservative) prior benchmarks. Includes functions for reference analyses at both the posterior and the prior level, which, given the data, quantify the informativeness of a heterogeneity prior of interest relative to the minimally informative reference prior and the proper prior benchmarks. The functions operate on data sets which are compatible with the 'bayesmeta' package.
Depends: bayesmeta, R (>= 3.5.0)
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2021-04-21 06:18:15 UTC; manuela
Repository: CRAN
Date/Publication: 2021-04-23 07:50:03 UTC

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New package protti with initial version 0.1.0
Package: protti
Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
Version: 0.1.0
Authors@R: c(person(given = "Jan-Philipp", family = "Quast", role = c("aut", "cre"), email = "quast@imsb.biol.ethz.ch"), person(given = "Dina", family = "Schuster", role = c("aut"), email = "dschuster@ethz.ch"), person(given = "ETH Zurich", role = c("cph", "fnd")))
Description: Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Schopper et al. (2017) <doi:10.1038/nprot.2017.100>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
biocViews:
Imports: rlang, dplyr, stringr, magrittr, data.table, janitor, progress, purrr, tidyr, ggplot2, forcats, tibble, plotly, ggrepel, methods, utils, grDevices
Suggests: testthat, covr, knitr, rmarkdown, proDA, limma, dendextend, pheatmap, heatmaply, viridis, iq, furrr, future, parallel, seriation, drc, naniar, httr, igraph, stringi, STRINGdb
Depends: R (>= 4.0)
URL: https://github.com/jpquast/protti, https://jpquast.github.io/protti/
BugReports: https://github.com/jpquast/protti/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-04-21 17:16:14 UTC; jan-philippquast
Author: Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]
Maintainer: Jan-Philipp Quast <quast@imsb.biol.ethz.ch>
Repository: CRAN
Date/Publication: 2021-04-23 08:00:02 UTC

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New package braggR with initial version 0.1.0
Package: braggR
Title: Calculate the Revealed Aggregator of Probability Predictions
Version: 0.1.0
Authors@R: c(person(given = "Ville", family = "Satopää", email = "ville.satopaa@gmail.com", role = c("aut", "cre", "cph")))
Description: Forecasters predicting the chances of a future event may disagree due to differing evidence or noise. To harness the collective evidence of the crowd, Ville Satopää (2021) "Regularized Aggregation of One-off Probability Predictions" <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3769945> proposes a Bayesian aggregator that is regularized by analyzing the forecasters' disagreement and ascribing over-dispersion to noise. This aggregator requires no user intervention and can be computed efficiently even for a large numbers of predictions. The author evaluates the aggregator on subjective probability predictions collected during a four-year forecasting tournament sponsored by the US intelligence community. The aggregator improves the accuracy of simple averaging by around 20% and other state-of-the-art aggregators by 10-25%. The advantage stems almost exclusively from improved calibration. This aggregator -- know as "the revealed aggregator" -- inputs a) forecasters' probability predictions (p) of a future binary event and b) the forecasters' base rate (p0) of the future event. In this R-package, the function sample_aggregator(p,p0,...) allows the user to calculate the revealed aggregator. Its use is illustrated with a simple stylized example.
License: GPL-2
Copyright: (c) Ville Satopaa
Encoding: UTF-8
LinkingTo: Rcpp
Imports: Rcpp
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2021-04-16 12:33:30 UTC; ville.satopaa
Author: Ville Satopää [aut, cre, cph]
Maintainer: Ville Satopää <ville.satopaa@gmail.com>
Repository: CRAN
Date/Publication: 2021-04-23 07:50:06 UTC

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Package NPP updated to version 0.4.0 with previous version 0.3.0 dated 2021-01-14

Title: Normalized Power Prior Bayesian Analysis
Description: Posterior sampling in several commonly used distributions using normalized power prior as described in Duan, Ye and Smith (2006) <doi:10.1002/env.752> and Ibrahim et.al. (2015) <doi:10.1002/sim.6728>. Sampling of the power parameter is achieved via either independence Metropolis-Hastings or random walk Metropolis-Hastings based on transformation.
Author: Zifei Han, Tianyu Bai and Keying Ye
Maintainer: Zifei Han <hanzifei1@gmail.com>

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Package swissdd (with last version 1.1.1) was removed from CRAN

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

2021-02-15 1.1.1
2021-02-03 1.1.0
2020-10-25 1.0.4

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Package tune updated to version 0.1.5 with previous version 0.1.4 dated 2021-04-20

Title: Tidy Tuning Tools
Description: The ability to tune models is important. 'tune' contains functions and classes to be used in conjunction with other 'tidymodels' packages for finding reasonable values of hyper-parameters in models, pre-processing methods, and post-processing steps.
Author: Max Kuhn [aut, cre] (<https://orcid.org/0000-0003-2402-136X>), RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>

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Package SSBtools updated to version 1.1.0 with previous version 1.0.0 dated 2021-03-04

Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, and functions for hierarchical computations are included (Langsrud, 2020) <doi:10.13140/RG.2.2.27313.61283>. The hierarchy specification functions are useful within statistical disclosure control.
Author: Øyvind Langsrud [aut, cre], Bjørn-Helge Mevik [cph]
Maintainer: Øyvind Langsrud <oyl@ssb.no>

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Package pcaPP updated to version 1.9-74 with previous version 1.9-73 dated 2018-01-14

Title: Robust PCA by Projection Pursuit
Description: Provides functions for robust PCA by projection pursuit. The methods are described in Croux et al. (2006) <doi:10.2139/ssrn.968376>, Croux et al. (2013) <doi:10.1080/00401706.2012.727746>, Todorov and Filzmoser (2013) <doi:10.1007/978-3-642-33042-1_31>.
Author: Peter Filzmoser, Heinrich Fritz, Klaudius Kalcher
Maintainer: Valentin Todorov <valentin.todorov@chello.at>

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Package NatureSounds updated to version 1.0.4 with previous version 1.0.3 dated 2020-03-13

Title: Animal Sounds for Bioacustic Analysis
Description: Collection of example animal sounds for bioacoustic analysis.
Author: Marcelo Araya-Salas [aut, cre]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>

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Package khroma updated to version 1.5.0 with previous version 1.4.1 dated 2021-03-17

Title: Colour Schemes for Scientific Data Visualization
Description: Colour schemes ready for each type of data (qualitative, diverging or sequential), with colours that are distinct for all people, including colour-blind readers. This package provides an implementation of Paul Tol (2018) and Fabio Crameri (2018) <doi: 10.5194/gmd-11-2541-2018> colour schemes for use with 'graphics' or 'ggplot2'. It provides tools to simulate colour-blindness and to test how well the colours of any palette are identifiable. Several scientific thematic schemes (geologic timescale, land cover, FAO soils, etc.) are also implemented.
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>), Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>), Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>

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