Thu, 15 Apr 2021

Package wrProteo updated to version 1.4.1 with previous version 1.4.0 dated 2021-03-10

Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data. Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted. Quantitative proteomics measurements frequently contain multiple NA values, due to physical absence of given peptides in some samples, limitations in sensitivity or other reasons. The functions provided here help to inspect graphically the data to investigate the nature of NA-values via their respective replicate measurements and to help/confirm the choice of NA-replacement by low random values. Dedicated filtering and statistical testing using the framework of package 'limma' <doi:10.18129/B9.bioc.limma> can be run, enhanced by multiple rounds of NA-replacements to provide robustness towards rare stochastic events. Multi-species samples, as frequently used in benchmark-tests (eg Navarro et al 2016 <doi:10.1038/nbt.3685>, Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>), can be run with special options separating the data into sub-groups during normalization and testing. As example the data-set from Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>) is provided quantified by MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), ProteomeDiscoverer, OpenMS (<doi:10.1038/nmeth.3959>) and Proline (Bouyssie et al 2020 <doi:10.1093/bioinformatics/btaa118>). Subsequently, ROC curves (Hand and Till 2001 <doi:10.1023/A:1010920819831>) can be constructed to compare multiple analysis approaches.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>

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Package fairml updated to version 0.4 with previous version 0.3 dated 2020-09-09

Title: Fair Models in Machine Learning
Description: Fair machine learning regression models which take sensitive attributes into account in model estimation. Currently implementing Komiyama et al. (2018) <http://proceedings.mlr.press/v80/komiyama18a/komiyama18a.pdf> and an improvement over the former that uses ridge regression to enforce fairness.
Author: Marco Scutari [aut, cre]
Maintainer: Marco Scutari <marco.scutari@gmail.com>

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Package YuGene (with last version 1.1.6) was removed from CRAN

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

2018-05-16 1.1.6
2015-11-19 1.1.5
2015-07-30 1.1.4
2014-07-13 1.1.2
2014-04-14 1.1.1
2014-02-20 1.1

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Package SPreFuGED (with last version 1.0) was removed from CRAN

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

2016-07-29 1.0

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Package duawranglr updated to version 0.6.7 with previous version 0.6.5 dated 2019-11-19

Title: Securely Wrangle Dataset According to Data Usage Agreement
Description: Create shareable data sets from raw data files that contain protected elements. Relying on master crosswalk files that list restricted variables, package functions warn users about possible violations of data usage agreement and prevent writing protected elements.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@coe.ufl.edu>

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Package violinplotter updated to version 2.0.1 with previous version 2.0.0 dated 2021-03-29

Title: Plotting and Comparing Means with Violin Plots
Description: Produces violin plots with optional mean comparison with Tukey's honest significant difference and linear regression. This package aims to be a simple and quick visualization tool for comparing means and assessing trends of categorical factors.
Author: Jefferson Paril <jeffersonparil@gmail.com>
Maintainer: Jefferson Paril <jeffersonparil@gmail.com>

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Package tidyverse updated to version 1.3.1 with previous version 1.3.0 dated 2019-11-21

Title: Easily Install and Load the 'Tidyverse'
Description: The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. Learn more about the 'tidyverse' at <https://www.tidyverse.org>.
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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New package LA with initial version 0.1.0
Package: LA
Title: Lioness Algorithm (LA)
Version: 0.1.0
Authors@R: c( person("Hongzhi", "Wang", email="hw34508@uga.edu", role=c("aut","cre")), person("Qian", "Xiao", role="aut"), person("Abhyuday", "Mandal", role="aut"))
Description: Contains Lioness Algorithm (LA) for finding optimal designs over continuous design space, optimal latin Hypercube Designs, and optimal order-of-addition designs. LA is a brand new nature-inspired meta-heuristic optimization algorithm. Detailed methodologies of LA and its implementation on numerical simulations can be found at Hongzhi Wang, Qian Xiao and Abhyuday Mandal (2021) <arXiv:2010.09154>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, devtools
Imports: stats, LHD, utils
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-04-14 21:09:47 UTC; wangh
Author: Hongzhi Wang [aut, cre], Qian Xiao [aut], Abhyuday Mandal [aut]
Maintainer: Hongzhi Wang <hw34508@uga.edu>
Repository: CRAN
Date/Publication: 2021-04-15 12:10:06 UTC

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New package childdevdata with initial version 1.1.0
Package: childdevdata
Title: Child Development Data
Version: 1.1.0
Authors@R: c( person("Stef", "van Buuren", email = "stef.vanbuuren@tno.nl", role = c("cre", "aut")), person("Iris", "Eekhout", email = "iris.eekhout@tno.nl", role = "aut"), person("Marta", "Rubio Codina", email = "martarubio@iadb.org", role = "aut"), person("Orazio", "Attanasio", email = "orazio.attanasio@yale.edu", role = "aut"), person("Costas", "Meghir", email = "c.meghir@yale.edu", role = "aut"), person("Emla", "Fitzsimons", email = "e.fitzsimons@ucl.ac.uk", role = "aut"), person("Sally", "Grantham-McGregor", email = "sallymcgregor@yahoo.com", role = "aut"), person("Maria Caridad", "Araujo", email = "mcaraujo@iadb.org", role = "aut"), person("Susan", "Walker", email = "susan.walker@uwimona.edu.jm", role = "aut"), person("Susan", "Chang", role = "aut"), person("Christine", "Powell", role = "aut"), person("Ann", "Weber", email = "annweber@unr.edu", role = "aut"), person("Lia", "Fernald", email = "fernald@berkeley.edu", role = "aut"), person("Paul", "Verkerk", email = "paul.verkerk@tno.nl", role = "aut"), person("Linda", "Richter", email = "linda.richter@wits.ac.za", role = "aut"), person("Betsy", "Lozoff", email = "blozoff@umich.edu", role = "aut"))
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Description: Measuring child development starts by collecting responses to developmental milestones, such as "able to sit" or "says two words". There are many ways to combine such responses into summaries. The package bundles publicly available datasets with individual milestone data for children aged 0-5 years, with the aim of supporting the construction, evaluation, validation and interpretation of methodologies that aggregate milestone data into informative measures of child development.
License: CC BY 4.0
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
URL: https://github.com/d-score/childdevdata, https://d-score.org/childdevdata/
Suggests: spelling
Language: en-GB
NeedsCompilation: no
Packaged: 2021-04-14 21:31:02 UTC; buurensv
Author: Stef van Buuren [cre, aut], Iris Eekhout [aut], Marta Rubio Codina [aut], Orazio Attanasio [aut], Costas Meghir [aut], Emla Fitzsimons [aut], Sally Grantham-McGregor [aut], Maria Caridad Araujo [aut], Susan Walker [aut], Susan Chang [aut], Christine Powell [aut], Ann Weber [aut], Lia Fernald [aut], Paul Verkerk [aut], Linda Richter [aut], Betsy Lozoff [aut]
Repository: CRAN
Date/Publication: 2021-04-15 12:10:02 UTC

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New package QPmin with initial version 0.5-1
Package: QPmin
Version: 0.5-1
Date: 2021-03-29
Title: Linearly Constrained Indefinite Quadratic Program Solver
Author: Andrea Giusto
Maintainer: Andrea Giusto <andrea.giusto@gmail.com>
Depends: R (>= 3.1.0), Matrix, methods
Description: Active set method solver for the solution of indefinite quadratic programs, subject to lower bounds on linear functions of the variables and simple bounds on the variables themselves. The function QPmin() implements an algorithm similar to the one described in Gould (1991) <doi:10.1093/imanum/11.3.299> with the exception that an efficient sparse internal representation of the basis matrix is maintained thus allowing the solution of somewhat large problems.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2021-04-01 16:47:34 UTC; andrea
Repository: CRAN
Date/Publication: 2021-04-15 11:30:05 UTC

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Package jlctree updated to version 0.0.2 with previous version 0.0.1 dated 2018-12-27

Title: Joint Latent Class Trees for Joint Modeling of Time-to-Event and Longitudinal Data
Description: Implements the tree-based approach to joint modeling of time-to-event and longitudinal data. This approach looks for a tree-based partitioning such that within each estimated latent class defined by a terminal node, the time-to-event and longitudinal responses display a lack of association. See Zhang and Simonoff (2018) <arXiv:1812.01774>.
Author: Ningshan Zhang and Jeffrey S. Simonoff
Maintainer: Ningshan Zhang <nzhang@stern.nyu.edu>

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New package iAR with initial version 0.1.0
Package: iAR
Title: Irregularly Observed Autoregressive Models
Version: 0.1.0
Authors@R: c( person("Elorrieta", "Felipe", email = "felipe.elorrieta@usach.cl", role = c("aut","cre")), person("Ojeda", "Cesar", email = "cesar.ojeda@correounivalle.edu.co", role = "aut"), person("Eyheramendy", "Susana", email = "susana.eyheramendy@gmail.com", role = "aut"), person("Palma", "Wilfredo", email = "wilfredo.palma@gmail.com", role = "aut"))
Description: Data sets, functions and scripts with examples to implement autoregressive models for irregularly observed time series. The models available in this package are the irregular autoregressive model (Eyheramendy et al.(2018) <doi:10.1093/mnras/sty2487>), the complex irregular autoregressive model (Elorrieta et al.(2019) <doi:10.1051/0004-6361/201935560>) and the bivariate irregular autoregressive model.
Encoding: UTF-8
License: GPL-2
Imports: ggplot2,stats,Rdpack
Suggests: arfima
Depends: R (>= 3.5.0)
URL: https://github.com/felipeelorrieta
LazyData: true
RdMacros: Rdpack
NeedsCompilation: no
Packaged: 2021-04-14 13:15:44 UTC; felo
Author: Elorrieta Felipe [aut, cre], Ojeda Cesar [aut], Eyheramendy Susana [aut], Palma Wilfredo [aut]
Maintainer: Elorrieta Felipe <felipe.elorrieta@usach.cl>
Repository: CRAN
Date/Publication: 2021-04-15 11:30:02 UTC

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New package distribglm with initial version 0.4.1
Package: distribglm
Title: Distributed Generalized Linear Models
Version: 0.4.1
Authors@R: c(person(given = "John", family = "Muschelli", email = "muschellij2@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6469-1750")) )
Description: Distributed generalized linear models (GLM) fitting using Fisher scoring from McCullagh and Nelder (1989) <ISBN:0412317605>. Models are to be fit using a primary-secondary relationship, where the results are written to a synced folder, but data can be elsewhere though it is loaded in memory. Additional functions are available for deploying a plumber 'API'.
License: GPL-3
Encoding: UTF-8
Imports: readr, stats
URL: https://github.com/muschellij2/distribglm
BugReports: https://github.com/muschellij2/distribglm/issues
Suggests: testthat (>= 2.1.0), httr, jsonlite, plumberDeploy, analogsea (>= 0.9.0)
NeedsCompilation: no
Packaged: 2021-04-14 13:27:56 UTC; johnmuschelli
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Repository: CRAN
Date/Publication: 2021-04-15 11:50:02 UTC

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Package viridis updated to version 0.6.0 with previous version 0.5.1 dated 2018-03-29

Title: Default Color Maps from 'matplotlib'
Description: Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This package also contains 'ggplot2' bindings for discrete and continuous color and fill scales. A lean version of the package called 'viridisLite' that does not include the 'ggplot2' bindings can be found at <https://cran.r-project.org/package=viridisLite>.
Author: Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>

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Package Superpower updated to version 0.1.1 with previous version 0.1.0 dated 2020-09-03

Title: Simulation-Based Power Analysis for Factorial Designs
Description: Functions to perform simulations of ANOVA designs of up to three factors. Calculates the observed power and average observed effect size for all main effects and interactions in the ANOVA, and all simple comparisons between conditions. Includes functions for analytic power calculations and additional helper functions that compute effect sizes for ANOVA designs, observed error rates in the simulations, and functions to plot power curves. Please see Lakens, D., & Caldwell, A. R. (2021). "Simulation-Based Power Analysis for Factorial Analysis of Variance Designs". <doi:10.1177/2515245920951503>.
Author: Aaron Caldwell [aut, cre], Daniel Lakens [aut], Lisa DeBruine [ctb], Jonathon Love [ctb], Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>

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Package spatstat.geom updated to version 2.1-0 with previous version 2.0-1 dated 2021-03-22

Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines types of spatial data such as point patterns, mainly in two dimensions, but also in higher dimensions. Provides class support, and functions for geometrical operations on spatial data, used in the 'spatstat' family of packages. Excludes spatial data on a linear network, which are covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre], Rolf Turner [aut], Ege Rubak [aut], Tilman Davies [ctb], Ute Hahn [ctb], Abdollah Jalilian [ctb], Sebastian Meyer [ctb], Suman Rakshit [ctb], Dominic Schuhmacher [ctb], Rasmus Waagepetersen [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.geom versions 2.0-1 dated 2021-03-22 and 2.1-0 dated 2021-04-15

 DESCRIPTION               |   31 ++++-------
 MD5                       |   30 +++++------
 NEWS                      |   45 +++++++++++++++++
 R/images.R                |   66 ++++++++++++++++---------
 R/nncross.R               |   43 ++++++++++------
 R/summary.im.R            |   80 ++++++++++++++++--------------
 R/window.R                |   41 +++++++++++----
 inst/doc/packagesizes.txt |    1 
 man/Extract.im.Rd         |  121 +++++++++++++++++++++++++---------------------
 man/discretise.Rd         |   38 ++++++++------
 src/knn3DdistX.h          |   10 ++-
 src/knnXdist.h            |   10 ++-
 src/nn3DdistX.h           |   10 ++-
 src/nndistX.h             |   15 +++--
 tests/testsGtoJ.R         |    2 
 tests/testsNtoO.R         |   25 +++++++++
 16 files changed, 360 insertions(+), 208 deletions(-)

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New package selfmade with initial version 0.1
Package: selfmade
Title: Selective Inference for Mixed and Additive Model Estimators
Version: 0.1
Authors@R: person("David", "Ruegamer", email = "david.ruegamer@gmail.com", role = c("aut", "cre"))
Description: Calculates Monte Carlo approximations to conduct selective inference for mixed and additive regression models after model selection as proposed by Ruegamer, Baumann and Greven (2020) <arXiv:2007.07930>.
Depends: R (>= 3.5)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: false
Imports: Matrix, lme4, mgcv
Suggests: knitr, rmarkdown, gamm4, lmerTest
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-04-13 21:45:55 UTC; david
Author: David Ruegamer [aut, cre]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Repository: CRAN
Date/Publication: 2021-04-15 08:30:02 UTC

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New package report with initial version 0.3.0
Package: report
Title: Automated Reporting of Results and Statistical Models
Version: 0.3.0
Authors@R: c(person(given = "Dominique", family = "Makowski", role = c("aut", "cre"), email = "dom.makowski@gmail.com", comment = c(ORCID = "0000-0001-5375-9967", Twitter = "@Dom_Makowski")), person(given = "Daniel", family = "Lüdecke", role = "aut", email = "d.luedecke@uke.de", comment = c(ORCID = "0000-0002-8895-3206")), person(given = "Mattan S.", family = "Ben-Shachar", role = "aut", email = "matanshm@post.bgu.ac.il", comment = c(ORCID = "0000-0002-4287-4801")), person(given = "Indrajeet", family = "Patil", role = "aut", email = "patilindrajeet.science@gmail.com", comment = c(ORCID = "0000-0003-1995-6531", Twitter = "@patilindrajeets")), person(given = "Rudolf", family = "Siegel", role = "ctb", email = "mutlusun@users.noreply.github.com", comment = c(ORCID = "0000-0002-6021-804X")))
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Description: The aim of the 'report' package is to bridge the gap between R’s output and the formatted results contained in your manuscript. This package converts statistical models and data frames into textual reports suited for publication, ensuring standardization and quality in results reporting.
License: GPL-3
URL: https://easystats.github.io/report/
BugReports: https://github.com/easystats/report/issues
Imports: bayestestR (>= 0.9.0), effectsize (>= 0.4.4), insight (>= 0.13.2), parameters (>= 0.13.0), performance (>= 0.7.1), stats, tools, utils
Suggests: BayesFactor, brms, dplyr, httr, knitr, lavaan, lme4, logspline, rmarkdown, rstanarm, spelling, testthat
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
Collate: 'cite_easystats.R' 'format_algorithm.R' 'format_citation.R' 'format_formula.R' 'format_model.R' 'format_text.R' 'utils_combine_tables.R' 'report.lm.R' 'report.MixMod.R' 'report_text.R' 'report.R' 'report.htest.R' 'report.aov.R' 'report.bayesfactor_models.R' 'report.lme4.R' 'report.stanreg.R' 'report.brmsfit.R' 'report.character.R' 'report.compare_performance.R' 'report.data.frame.R' 'report.default.R' 'report.factor.R' 'report.glm.R' 'report.glmmTMB.R' 'report.lavaan.R' 'report.lme.R' 'report.numeric.R' 'report.sessionInfo.R' 'report.survreg.R' 'report.test_performance.R' 'report.zeroinfl.R' 'report_effectsize.R' 'report_info.R' 'report_intecept.R' 'report_misc.R' 'report_model.R' 'report_parameters.R' 'report_participants.R' 'report_performance.R' 'report_priors.R' 'report_random.R' 'report_sample.R' 'report_statistics.R' 'report_table.R' 'startup_message.R' 'utils_data.R' 'utils_error_message.R' 'utils_grouped_df.R'
NeedsCompilation: no
Packaged: 2021-04-14 03:44:51 UTC; user
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>, @Dom_Makowski), Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>), Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>), Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets), Rudolf Siegel [ctb] (<https://orcid.org/0000-0002-6021-804X>)
Repository: CRAN
Date/Publication: 2021-04-15 08:50:22 UTC

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New package migraph with initial version 0.6.2
Package: migraph
Title: Multimodal and Multilevel Network Analysis
Version: 0.6.2
Date: 2021-04-13
Description: A set of tools that extend common social network analysis packages for analysing multimodal and multilevel networks. It includes functions for one- and two-mode (and sometimes three-mode) centrality, centralization, clustering, and constraint, as well as for one- and two-mode network regression and block-modelling. All functions operate with matrices, edge lists, and 'igraph', 'network'/'sna', and 'tidygraph' objects. The package is released as a complement to 'Multimodal Political Networks' (2021, ISBN:9781108985000), and includes various datasets used in the book.
URL: https://github.com/snlab-ch/migraph
BugReports: https://github.com/snlab-ch/migraph/issues
Depends: R (>= 4.0.0)
License: MIT + file LICENSE
Language: en-GB
Encoding: UTF-8
LazyData: true
Imports: igraph, tidygraph, ggplot2, ggraph, R6, magrittr, rlang, dplyr, purrr, tibble, tidyr, network
Suggests: testthat, roxygen2, covr, knitr, rmarkdown
Authors@R: c(person(given = "James", family = "Hollway", role = c("cph", "cre", "aut", "ctb"), email = "james.hollway@graduateinstitute.ch", comment = c("IHEID", ORCID = "0000-0002-8361-9647")))
NeedsCompilation: no
Packaged: 2021-04-13 18:37:05 UTC; hollway
Author: James Hollway [cph, cre, aut, ctb] (IHEID, <https://orcid.org/0000-0002-8361-9647>)
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Repository: CRAN
Date/Publication: 2021-04-15 08:20:02 UTC

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New package m61r with initial version 0.0.2
Package: m61r
Version: 0.0.2
Authors@R: c(person("Jean-Marie","Lepioufle", , "pv71u98h1@gmail.com", c("aut","cre")))
Title: Package About Data Manipulation in Pure Base R
Description: Data manipulation in one package and in base R. Minimal. No dependencies. 'dplyr' and 'tidyr'-like in one place. Nothing else than base R to build the package.
Depends: R (>= 3.4.4)
License: MIT + file LICENSE
URL: https://github.com/pv71u98h1/m61r/
BugReports: https://github.com/pv71u98h1/m61r/issues/
Encoding: UTF-8
LazyData: false
NeedsCompilation: no
Packaged: 2021-04-13 19:04:45 UTC; jean-marie
Author: Jean-Marie Lepioufle [aut, cre]
Maintainer: Jean-Marie Lepioufle <pv71u98h1@gmail.com>
Repository: CRAN
Date/Publication: 2021-04-15 08:20:05 UTC

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New package segregatr with initial version 0.2.0
Package: segregatr
Title: Segregation Analysis for Variant Interpretation
Version: 0.2.0
Authors@R: person(given = "Magnus Dehli", family = "Vigeland", role = c("aut", "cre"), email = "m.d.vigeland@medisin.uio.no", comment = c(ORCID = "0000-0002-9134-4962"))
Description: An implementation of the full-likelihood Bayes factor (FLB) for evaluating segregation evidence in clinical medical genetics. The method was introduced by Thompson et al. (2003) <doi:10.1086/378100>, and further popularised by Bayrak-Toydemir et al. (2008) <doi:10.1016/j.yexmp.2008.03.006>. This implementation allows custom penetrance values and liability classes, and includes specialised pedigree visualisations.
License: GPL-3
URL: https://github.com/magnusdv/segregatr
BugReports: https://github.com/magnusdv/segregatr/issues
Encoding: UTF-8
Language: en-GB
Depends: pedtools
Imports: pedprobr
Suggests: testthat (>= 2.1.0)
NeedsCompilation: no
Packaged: 2021-04-13 08:57:36 UTC; magnusdv
Author: Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Repository: CRAN
Date/Publication: 2021-04-15 07:40:03 UTC

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New package rPanglaoDB with initial version 0.1.0
Package: rPanglaoDB
Title: Download and Merge Single-Cell RNA-Seq Data from the PanglaoDB Database
Version: 0.1.0
Authors@R: c(person("Daniel","Osorio", email = "daniecos@uio.no", role = c("aut","cre"), comment = c(ORCID = "0000-0003-4424-8422")), person("Marieke","Kuijjer", role = c("aut"), comment = c(ORCID = "0000-0001-6280-3130")), person("James J.","Cai", role = c("aut"), comment = c(ORCID = "0000-0002-8081-6725")))
Description: Download and merge labeled single-cell RNA-seq data from the PanglaoDB <https://panglaodb.se/> into a Seurat object.
License: GPL-3
Encoding: UTF-8
LazyData: false
Imports: methods, XML, xml2, Seurat, pbapply, Matrix
NeedsCompilation: no
Packaged: 2021-04-13 05:59:56 UTC; danie
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>
Repository: CRAN
Date/Publication: 2021-04-15 07:20:02 UTC

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New package RegKink with initial version 0.1.0
Package: RegKink
Version: 0.1.0
Title: Regression Kink with a Time-Varying Threshold
Authors@R: c( person("Lixiong", "Yang", email = "ylx@lzu.edu.cn", role = c("aut", "cre")))
Description: An algorithm is proposed to estimate regression kink model proposed by the paper, Lixiong Yang and Jen-Je Su (2018) <doi:10.1016/j.jimonfin.2018.06.002>.
Imports: MASS
Depends: R (>= 3.5.0)
License: GPL
Encoding: UTF-8
Author: Lixiong Yang [aut, cre]
Maintainer: Lixiong Yang <ylx@lzu.edu.cn>
NeedsCompilation: no
Packaged: 2021-04-13 07:58:25 UTC; ylx
Repository: CRAN
Date/Publication: 2021-04-15 07:30:06 UTC

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Package RcppParallel updated to version 5.1.2 with previous version 5.1.1 dated 2021-04-11

Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'. For example, the 'parallelFor()' function can be used to convert the work of a standard serial "for" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut], Romain Francois [aut, cph], Kevin Ushey [aut, cre], Gregory Vandenbrouck [aut], Marcus Geelnard [aut, cph] (TinyThread library, https://tinythreadpp.bitsnbites.eu/), Hamada S. Badr [ctb] (<https://orcid.org/0000-0002-9808-2344>), RStudio [cph], Intel [aut, cph] (Intel TBB library, https://www.threadingbuildingblocks.org/), Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>

Diff between RcppParallel versions 5.1.1 dated 2021-04-11 and 5.1.2 dated 2021-04-15

 RcppParallel-5.1.1/RcppParallel/inst/NEWS                     |only
 RcppParallel-5.1.1/RcppParallel/inst/include/RcppParallel/tbb |only
 RcppParallel-5.1.1/RcppParallel/inst/include/serial           |only
 RcppParallel-5.1.1/RcppParallel/inst/include/tbb              |only
 RcppParallel-5.1.2/RcppParallel/DESCRIPTION                   |    6 
 RcppParallel-5.1.2/RcppParallel/MD5                           |  167 -------
 RcppParallel-5.1.2/RcppParallel/NAMESPACE                     |    1 
 RcppParallel-5.1.2/RcppParallel/NEWS.md                       |only
 RcppParallel-5.1.2/RcppParallel/R/RcppParallel-package.R      |    3 
 RcppParallel-5.1.2/RcppParallel/R/flags.R                     |  126 -----
 RcppParallel-5.1.2/RcppParallel/R/hooks.R                     |   79 +--
 RcppParallel-5.1.2/RcppParallel/R/plugin.R                    |only
 RcppParallel-5.1.2/RcppParallel/R/tbb.R                       |only
 RcppParallel-5.1.2/RcppParallel/R/utils.R                     |only
 RcppParallel-5.1.2/RcppParallel/man/RcppParallel-package.Rd   |    2 
 RcppParallel-5.1.2/RcppParallel/man/flags.Rd                  |   17 
 RcppParallel-5.1.2/RcppParallel/man/tbbLibraryPath.Rd         |only
 RcppParallel-5.1.2/RcppParallel/src/Makevars.in               |  230 +++++-----
 RcppParallel-5.1.2/RcppParallel/src/install.libs.R            |only
 RcppParallel-5.1.2/RcppParallel/tools/config/configure.R      |   21 
 20 files changed, 226 insertions(+), 426 deletions(-)

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New package onsr with initial version 1.0.0
Package: onsr
Title: Client for the 'ONS' API
Version: 1.0.0
Authors@R: person(given = "Kostas", family = "Vasilopoulos", role = c("aut", "cre"), email = "k.vasilopoulo@gmail.com")
Description: Client for the 'Office of National Statistics' ('ONS') API <https://api.beta.ons.gov.uk/v1>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: httr, jsonlite, readr, tibble
URL: https://kvasilopoulos.github.io/onsr/
BugReports: https://github.com/kvasilopoulos/onsr/issues
Suggests: testthat (>= 3.0.0), data.table, vroom, curl
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-04-13 15:16:21 UTC; T460p
Author: Kostas Vasilopoulos [aut, cre]
Maintainer: Kostas Vasilopoulos <k.vasilopoulo@gmail.com>
Repository: CRAN
Date/Publication: 2021-04-15 08:00:02 UTC

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New package measurementProtocol with initial version 0.1.0
Package: measurementProtocol
Version: 0.1.0
Title: Send Data from R to the Measurement Protocol
Description: Send server-side tracking data from R. The Measurement Protocol version 2 <https://developers.google.com/analytics/devguides/collection/protocol/ga4> allows sending HTTP tracking events from R code.
Authors@R: c(person("Mark", "Edmondson", email = "r@sunholo.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8434-3881")), person("Sunholo Ltd", role = "cph"))
URL: https://code.markedmondson.me/measurementProtocol/
BugReports: https://github.com/MarkEdmondson1234/measurementProtocol
Depends: R (>= 3.3.0)
Imports: assertthat (>= 0.2.0), cli, httr (>= 1.3.1), jsonlite (>= 1.5), rappdirs (>= 0.3.3), stats, utils
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-04-13 08:18:41 UTC; mark
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>), Sunholo Ltd [cph]
Maintainer: Mark Edmondson <r@sunholo.com>
Repository: CRAN
Date/Publication: 2021-04-15 07:40:06 UTC

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New package longit with initial version 0.1.0
Title: High Dimensional Longitudinal Data Analysis Using MCMC
Package: longit
Version: 0.1.0
Date: 2021-04-06
Depends: R (>= 2.10)
Imports: AICcmodavg, missForest,R2jags,rjags,utils
LazyData: Yes
LazyDataCompression: xz
ByteCompile: Yes
Authors@R: c(person(("Atanu"), "Bhattacharjee", email="atanustat@gmail.com", role=c("aut", "cre","ctb")),person(("Akash"), "Pawar", role=c("aut","ctb")),person(("Bhrigu Kumar"),"Rajbongshi", role=c("aut","ctb")))
Description: High dimensional longitudinal data analysis with Markov Chain Monte Carlo(MCMC). Currently support mixed effect regression with or without missing observations by considering covariance structures. It provides estimates by missing at random and missing not at random assumptions. In this R package, we present Bayesian approaches that statisticians and clinical researchers can easily use. The functions' methodology is based on the book "Bayesian Approaches in Oncology Using R and OpenBUGS" by Bhattacharjee A (2020) <doi:10.1201/9780429329449-14>.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Maintainer: Atanu Bhattacharjee <atanustat@gmail.com>
Packaged: 2021-04-13 17:02:31 UTC; atanu
Author: Atanu Bhattacharjee [aut, cre, ctb], Akash Pawar [aut, ctb], Bhrigu Kumar Rajbongshi [aut, ctb]
Repository: CRAN
Date/Publication: 2021-04-15 08:00:05 UTC

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New package libbib with initial version 1.0
Package: libbib
Title: Various Utilities for Library Science/Assessment and Cataloging
Version: 1.0
Authors@R: person("Tony", "Fischetti", email="tony.fischetti@gmail.com", role=c("aut", "cre"))
Maintainer: Tony Fischetti <tony.fischetti@gmail.com>
Description: Provides functions for validating and normalizing bibliographic codes such as ISBN, ISSN, and LCCN. Also provides functions to translate LC Call numbers to their subject classifications or subclassifications.
License: GPL-3
Depends: R (>= 3.5.0), data.table, utils
Imports: stringr
Suggests: assertr, testthat, knitr, magrittr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-04-13 15:02:26 UTC; tonyfischetti
Author: Tony Fischetti [aut, cre]
Repository: CRAN
Date/Publication: 2021-04-15 07:50:03 UTC

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New package iSubGen with initial version 1.0.0
Package: iSubGen
Title: Integrative Subtype Generation
Version: 1.0.0
Date: 2021-04-07
Author: Natalie Fox
Maintainer: Natalie Fox <nfox@mednet.ucla.edu>
Description: Multi-data type subtyping, which is data type agnostic and accepts missing data. Subtyping is performed using intermediary assessments created with autoencoders and similarity calculations.
Depends: R (>= 3.2.3)
Imports: ConsensusClusterPlus, cluster (>= 1.14.4), keras, tensorflow, philentropy
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
License: GPL-2
NeedsCompilation: no
Packaged: 2021-04-13 03:51:51 UTC; nfox
Repository: CRAN
Date/Publication: 2021-04-15 07:20:05 UTC

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New package himach with initial version 0.1.0
Package: himach
Title: High Mach Finds Routes for Supersonic Aircraft
Version: 0.1.0
Authors@R: c(person(given = "David", family = "Marsh", role = c("aut", "cre"), email = "david.marsh@eurocontrol.int"), person(family = "EUROCONTROL", role = c("fnd", "cph")))
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!
License: MIT + file LICENSE
URL: https://github.com/david6marsh/himach
BugReports: https://github.com/david6marsh/himach/issues
Depends: R (>= 3.5.0)
Imports: cppRouting, dplyr (>= 1.0.0), ggplot2, s2, sf (>= 0.9-7), sp, tidyr
Suggests: airportr, cowplot, data.table, geosphere, knitr, methods, purrr, progress, rmarkdown, rnaturalearthdata, scales, stringr, testthat, units, utils, viridis, covr
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
Language: en-GB
NeedsCompilation: no
Packaged: 2021-04-13 07:34:34 UTC; david
Author: David Marsh [aut, cre], EUROCONTROL [fnd, cph]
Maintainer: David Marsh <david.marsh@eurocontrol.int>
Repository: CRAN
Date/Publication: 2021-04-15 07:30:02 UTC

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Package geeCRT updated to version 0.1.0 with previous version 0.0.1 dated 2020-11-11

Title: Bias-Corrected GEE for Cluster Randomized Trials
Description: Population-averaged models have been increasingly used in the design and analysis of cluster randomized trials (CRTs). To facilitate the applications of population-averaged models in CRTs, the package implements the generalized estimating equations (GEE) and matrix-adjusted estimating equations (MAEE) approaches to jointly estimate the marginal mean models correlation models both for general CRTs and stepped wedge CRTs. Despite the general GEE/MAEE approach, the package also implements a fast cluster-period GEE method by Li et al. (2021) <doi:10.1093/biostatistics/kxaa056> specifically for stepped wedge CRTs with large and variable cluster-period sizes and gives a simple and efficient estimating equations approach based on the cluster-period means to estimate the intervention effects as well as correlation parameters. In addition, the package also provides functions for generating correlated binary data with specific mean vector and correlation matrix based on the multivariate probit method in Emrich and Piedmonte (1991) <doi:10.1080/00031305.1991.10475828> or the conditional linear family method in Qaqish (2003) <doi:10.1093/biomet/90.2.455>.
Author: Hengshi Yu [aut, cre], Fan Li [aut], Paul Rathouz [aut], Elizabeth L. Turner [aut], John Preisser [aut]
Maintainer: Hengshi Yu <hengshi@umich.edu>

Diff between geeCRT versions 0.0.1 dated 2020-11-11 and 0.1.0 dated 2021-04-15

 DESCRIPTION             |   15 
 MD5                     |   42 -
 R/binMAEE.R             | 1538 +++++++++++++++++++++----------------------
 R/contMAEE.R            | 1556 +++++++++++++++++++++----------------------
 R/cpgeeSWD.R            |  108 +--
 R/cpgee_ed.R            | 1691 +++++++++++++++++++++++------------------------
 R/cpgee_exc.R           | 1700 ++++++++++++++++++++++--------------------------
 R/cpgee_nex.R           | 1620 ++++++++++++++++++++++-----------------------
 R/geemaee.R             |   97 +-
 R/print_cpgeeSWD.R      |   10 
 R/print_geemaee.R       |    8 
 R/sampleSWCRTLarge.R    |    2 
 R/sampleSWCRTSmall.R    |    2 
 R/simbinCLF.R           |  269 +++----
 R/simbinPROBIT.R        |  217 +++---
 build                   |only
 inst                    |only
 man/cpgeeSWD.Rd         |   60 -
 man/geemaee.Rd          |   77 +-
 man/sampleSWCRTLarge.Rd |    2 
 man/sampleSWCRTSmall.Rd |    2 
 vignettes               |only
 22 files changed, 4432 insertions(+), 4584 deletions(-)

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Package BayesRGMM (with last version 1.0) was removed from CRAN

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

2021-03-31 1.0

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Package deepdep (with last version 0.2.2) was removed from CRAN

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

2021-03-31 0.2.2
2020-05-06 0.2.1
2020-03-06 0.2.0

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Package tidysq (with last version 1.1.0) was removed from CRAN

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

2021-03-12 1.1.0

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Package zipcodeR updated to version 0.3.0 with previous version 0.2.0 dated 2020-12-12

Title: Data & Functions for Working with US ZIP Codes
Description: Make working with ZIP codes in R painless with an integrated dataset of U.S. ZIP codes and functions for working with them. Search ZIP codes by multiple geographies, including state, county, city & across time zones. Also included are functions for relating ZIP codes to Census data.
Author: Gavin Rozzi [aut, cre] (<https://orcid.org/0000-0002-9969-8175>)
Maintainer: Gavin Rozzi <gr@gavinrozzi.com>

Diff between zipcodeR versions 0.2.0 dated 2020-12-12 and 0.3.0 dated 2021-04-15

 DESCRIPTION              |   13 
 MD5                      |   61 +-
 NAMESPACE                |   44 +-
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Package kubik updated to version 0.3.0 with previous version 0.2.0 dated 2020-03-23

Title: Cubic Hermite Splines and Related Root Finding Methods
Description: Supports cubic Hermite splines (Fritsch & Carlson, 1980 <doi:10.1137/0717021>), along with their derivatives/integrals. Also, supports monotonically increasing/decreasing splines, and computes their roots and minimum/maximum points.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>

Diff between kubik versions 0.2.0 dated 2020-03-23 and 0.3.0 dated 2021-04-15

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Package H2x2Factorial updated to version 1.1.0 with previous version 1.0.3 dated 2021-02-06

Title: Sample Size Calculation in Hierarchical 2x2 Factorial Trials
Description: Implements the sample size methods for hierarchical 2x2 factorial trials under a series of hypothesis tests proposed in "Sample size calculation in hierarchical 2x2 factorial trials with unequal cluster sizes" (under review), and provides the table and plot generators for the sample size estimations.
Author: Zizhong Tian [aut, cre], Denise Esserman [aut], Guangyu Tong [aut], Fan Li [aut]
Maintainer: Zizhong Tian <zizhong.tian@yale.edu>

Diff between H2x2Factorial versions 1.0.3 dated 2021-02-06 and 1.1.0 dated 2021-04-15

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Package DatabaseConnector updated to version 4.0.2 with previous version 4.0.0 dated 2021-03-02

Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server', 'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', and 'SQLite'). Also includes support for fetching data as 'Andromeda' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases (except SQLite).
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut], Observational Health Data Science and Informatics [cph], Microsoft Inc. [cph] (SQL Server JDBC driver), PostgreSQL Global Development Group [cph] (PostgreSQL JDBC driver), Oracle Inc. [cph] (Oracle JDBC driver), Amazon Inc. [cph] (RedShift JDBC driver)
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

Diff between DatabaseConnector versions 4.0.0 dated 2021-03-02 and 4.0.2 dated 2021-04-15

 DESCRIPTION                                                       |   10 
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 R/CtasHack.R                                                      |    6 
 R/DBI.R                                                           |   16 
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 R/Drivers.R                                                       |   18 
 R/InsertTable.R                                                   |    7 
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 21 files changed, 3779 insertions(+), 3746 deletions(-)

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Package CBCgrps updated to version 2.8.2 with previous version 2.8.1 dated 2020-08-26

Title: Compare Baseline Characteristics Between Groups
Description: Compare baseline characteristics between two or more groups. The variables being compared can be factor and numeric variables. The function will automatically judge the type and distribution of the variables, and make statistical description and bivariate analysis.
Author: Zhongheng Zhang, Sir Run Run Shaw hospital, Zhejiang university school of medicine
Maintainer: Zhongheng Zhang <zh_zhang1984@zju.edu.cn>

Diff between CBCgrps versions 2.8.1 dated 2020-08-26 and 2.8.2 dated 2021-04-15

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Package arctools updated to version 1.1.2 with previous version 1.1.0 dated 2021-01-09

Title: Processing and Physical Activity Summaries of Minute Level Activity Data
Description: Provides functions to process minute level actigraphy-measured activity counts data and extract commonly used physical activity volume and fragmentation metrics.
Author: Marta Karas [aut, cre] (<https://orcid.org/0000-0001-5889-3970>), Jacek Urbanek [aut] (<https://orcid.org/0000-0002-1890-8899>), Jennifer Schrack [aut] (<https://orcid.org/0000-0001-9244-9267>)
Maintainer: Marta Karas <marta.karass@gmail.com>

Diff between arctools versions 1.1.0 dated 2021-01-09 and 1.1.2 dated 2021-04-15

 DESCRIPTION                  |    6 +++---
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Package BaMORC (with last version 1.0.1) was removed from CRAN

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

2019-01-02 1.0.1
2018-11-14 1.0

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