Sun, 17 Oct 2021

Package JBrowseR updated to version 0.9.0 with previous version 0.8.1 dated 2021-07-07

Title: An R Interface to the JBrowse 2 Genome Browser
Description: Provides an R interface to the JBrowse 2 genome browser. Enables embedding a JB2 genome browser in a Shiny app or R Markdown document. The browser can also be launched from an interactive R console. The browser can be loaded with a variety of common genomics data types, and can be used with a custom theme.
Author: Elliot Hershberg [aut, cre] (<https://orcid.org/0000-0003-2068-3366>), the JBrowse 2 Team [aut]
Maintainer: Elliot Hershberg <eahershberg@gmail.com>

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Package tidygeocoder updated to version 1.0.4 with previous version 1.0.3 dated 2021-04-19

Title: Geocoding Made Easy
Description: An intuitive interface for getting data from geocoding services.
Author: Jesse Cambon [aut, cre] (<https://orcid.org/0000-0001-6854-1514>), Diego Hernangómez [aut] (<https://orcid.org/0000-0001-8457-4658>), Christopher Belanger [aut] (<https://orcid.org/0000-0003-2070-5721>), Daniel Possenriede [aut] (<https://orcid.org/0000-0002-6738-9845>)
Maintainer: Jesse Cambon <jesse.cambon@gmail.com>

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Package Seurat updated to version 4.0.5 with previous version 4.0.4 dated 2021-08-20

Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]
Maintainer: Paul Hoffman <seurat@nygenome.org>

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Package rcdk updated to version 3.6.0 with previous version 3.5.0 dated 2020-03-11

Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph], Zachary Charlop-Powers [cre], Emma Schymanski [ctb]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>

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Package qtl2 updated to version 0.28 with previous version 0.24 dated 2020-12-18

Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>), R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>

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More information about qtl2 at CRAN
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Package FKF updated to version 0.2.2 with previous version 0.2.1 dated 2021-09-28

Title: Fast Kalman Filter
Description: This is a fast and flexible implementation of the Kalman filter and smoother, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in BLAS and LAPACK. Due to the speed of the filter, the fitting of high-dimensional linear state space models to large datasets becomes possible. This package also contains a plot function for the visualization of the state vector and graphical diagnostics of the residuals.
Author: David Luethi [aut], Philipp Erb [aut], Simon Otziger [aut], Daniel McDonald [aut], Paul Smith [aut, cre] (<https://orcid.org/0000-0002-0034-3412>)
Maintainer: Paul Smith <paul@waternumbers.co.uk>

Diff between FKF versions 0.2.1 dated 2021-09-28 and 0.2.2 dated 2021-10-17

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New package RSC with initial version 2.0
Package: RSC
Title: Robust and Sparse Correlation Matrix
Description: Performs robust and sparse correlation matrix estimation. Robustness is achieved based on a simple robust pairwise correlation estimator, while sparsity is obtained based on thresholding. The optimal thresholding is tuned via cross-validation. See Serra, Coretto, Fratello and Tagliaferri (2018) <doi:10.1093/bioinformatics/btx642>.
Author: Luca Coraggio [cre, aut], Pietro Coretto [aut], Angela Serra [aut], Roberto Tagliaferri [ctb]
Maintainer: Luca Coraggio <luca.coraggio@unina.it>
NeedsCompilation: yes
Imports: stats, graphics, Matrix, methods, parallel, foreach, doParallel, utils
License: GPL (>= 2)
Version: 2.0
Date: 2021-10-14
Packaged: 2021-10-14 14:44:39 UTC; luco
Repository: CRAN
Date/Publication: 2021-10-17 20:00:08 UTC

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New package qra with initial version 0.2.6
Package: qra
Title: Quantal Response Analysis for Dose-Mortality Data
Date: 2021-10-10
Version: 0.2.6
Maintainer: John Maindonald <john@statsresearch.co.nz>
Description: Functions are provided that implement the use of the Fieller's formula methodology, for calculating a confidence interval for a ratio of (possibly, correlated) means. See Fieller (1954) <doi:10.1111/j.2517-6161.1954.tb00159.x>. Here, the application of primary interest is to studies of insect mortality response to increasing doses of a fumigant, or, e.g., to time in coolstorage. The formula is used to calculate a confidence interval for the dose or time required to achieve a specified mortality proportion, commonly 0.5 or 0.99. Vignettes demonstrate link functions that may be considered, checks on fitted models, and alternative choices of error family. Note in particular the betabinomial error family. See also Maindonald, Waddell, and Petry (2001) <doi:10.1016/S0925-5214(01)00082-5>.
Encoding: UTF-8
License: GPL-3
Depends: R (>= 4.1.0), lattice, latticeExtra, knitr, rmarkdown
Imports: lme4, splines, ggplot2
Suggests: robustlmm, MASS, fitODBOD, VGAM, glmmTMB (>= 1.1.2), gamlss, prettydoc, DHARMa, kableExtra (>= 1.2), plotrix, dfoptim, optimx, bookdown
VignetteBuilder: knitr, rmarkdown, bookdown, prettydoc
LazyData: TRUE
NeedsCompilation: no
Packaged: 2021-10-10 07:36:57 UTC; johnm1
Author: John Maindonald [aut, cre] (<https://orcid.org/0000-0002-0106-9224>)
Repository: CRAN
Date/Publication: 2021-10-17 20:00:02 UTC

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Package portfolioBacktest updated to version 0.3.1 with previous version 0.3.0 dated 2021-09-21

Title: Automated Backtesting of Portfolios over Multiple Datasets
Description: Automated backtesting of multiple portfolios over multiple datasets of stock prices in a rolling-window fashion. Intended for researchers and practitioners to backtest a set of different portfolios, as well as by a course instructor to assess the students in their portfolio design in a fully automated and convenient manner, with results conveniently formatted in tables and plots. Each portfolio design is easily defined as a function that takes as input a window of the stock prices and outputs the portfolio weights. Multiple portfolios can be easily specified as a list of functions or as files in a folder. Multiple datasets can be conveniently extracted randomly from different markets, different time periods, and different subsets of the stock universe. The results can be later assessed and ranked with tables based on a number of performance criteria (e.g., expected return, volatility, Sharpe ratio, drawdown, turnover rate, return on investment, computational time, etc.), as well as plotted in a number of ways with nice barplots and boxplots.
Author: Daniel P. Palomar [cre, aut], Rui Zhou [aut]
Maintainer: Daniel P. Palomar <daniel.p.palomar@gmail.com>

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Package LMMstar updated to version 0.3.3 with previous version 0.3.2 dated 2021-10-05

Title: Repeated Measurement Models for Discrete Times
Description: Companion R package for the course "Statistical analysis of correlated and repeated measurements for health science researchers" taught by the section of Biostatistics of the University of Copenhagen. It provides functions for computing summary statistics and obtaining graphical displays of longitudinal data, as well as for statistical modeling and statistical inference using linear mixed model.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>), Julie Forman [aut] (<https://orcid.org/0000-0001-7368-0869>)
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>

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Package NMproject updated to version 0.6.7 with previous version 0.6.5 dated 2021-09-02

Title: Script Based 'NONMEM' Model Development
Description: Industrialisation of 'NONMEM' <https://www.iconplc.com/innovation/nonmem/> via fully and rapidly reusable model development 'workflows' entirely within 'RStudio'. Quickly get started with new models by importing 'NONMEM' templates from the built-in code library. Manipulate 'NONMEM' code from within R either via the tracked 'manual edit' interface or 'programmatically' via convenience functions. Script 'workflows' by piping sequences of model building steps from control file creation, to execution, to post-processing and evaluation. Run caching makes 'workflows' R markdown friendly for easy documentation of thoughts and modelling decisions alongside executable code. Share, reuse and recycle 'workflows' for new problems.
Author: Tarj Sahota [aut, cre, cph], AstraZeneca [cph], Nuria Buil Bruna [ctb], Stein Schalkwijk [ctb]
Maintainer: Tarj Sahota <t.sahota0@gmail.com>

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Package covid19br updated to version 0.1.3 with previous version 0.1.2 dated 2021-10-08

Title: Brazilian COVID-19 Pandemic Data
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at country, region, state, and city-levels. The package also downloads the world-level COVID-19 data from the John Hopkins University's repository.
Author: Fabio Demarqui [aut, cre], Cristiano Santos [aut], Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>

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Package MFPCA updated to version 1.3-9 with previous version 1.3-8 dated 2021-08-09

Title: Multivariate Functional Principal Component Analysis for Data Observed on Different Dimensional Domains
Description: Calculate a multivariate functional principal component analysis for data observed on different dimensional domains. The estimation algorithm relies on univariate basis expansions for each element of the multivariate functional data (Happ & Greven, 2018) <doi:10.1080/01621459.2016.1273115>. Multivariate and univariate functional data objects are represented by S4 classes for this type of data implemented in the package 'funData'. For more details on the general concepts of both packages and a case study, see Happ-Kurz (2020) <doi:10.18637/jss.v093.i05>.
Author: Clara Happ-Kurz [aut, cre] (<https://orcid.org/0000-0003-4737-3835>)
Maintainer: Clara Happ-Kurz <chk_R@gmx.de>

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Package funData updated to version 1.3-8 with previous version 1.3-7 dated 2021-08-03

Title: An S4 Class for Functional Data
Description: S4 classes for univariate and multivariate functional data with utility functions. See <doi:10.18637/jss.v093.i05> for a detailed description of the package functionalities and its interplay with the MFPCA package for multivariate functional principal component analysis <https://CRAN.R-project.org/package=MFPCA>.
Author: Clara Happ-Kurz [aut, cre]
Maintainer: Clara Happ-Kurz <chk_R@gmx.de>

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Package treebalance updated to version 1.1.0 with previous version 1.0.0 dated 2021-09-22

Title: Computation of Tree (Im)Balance Indices
Description: The aim of the 'R' package 'treebalance' is to provide functions for the computation of a large variety of (im)balance indices for rooted trees. The package accompanies the manuscript ''Tree balance indices: a comprehensive survey'' by M. Fischer, L. Herbst, S. Kersting, L. Kuehn and K. Wicke (2021) <arXiv:2109.12281>, which gives a precise definition for the terms 'balance index' and 'imbalance index' (Section 3) and provides an overview of the terminology in this manual (Section 2). For further information on (im)balance indices, see also Fischer et al. (2021) <https://treebalance.wordpress.com>. Considering both established and new (im)balance indices, 'treebalance' provides (among others) functions for calculating the following 18 established indices: the average leaf depth, the B1 and B2 index, the Colijn-Plazzotta rank, the normal, corrected, quadratic and equal weights Colless index, the family of Colless-like indices, the family of I-based indices, the Rogers J index, the Furnas rank, the rooted quartet index, the s-shape statistic, the Sackin index, the symmetry nodes index, the total cophenetic index and the variance of leaf depths. Additionally, we include 5 tree shape statistics that satisfy the definition of an (im)balance index but have not been thoroughly analyzed in terms of tree balance in the literature yet. These are: the maximum width, the maximum difference in widths, the maximal depth, the stairs1 and the stairs2 index. As input, most functions of 'treebalance' require a rooted (phylogenetic) tree in 'phylo' format (as introduced in 'ape' 1.9 in November 2006). 'phylo' is used to store (phylogenetic) trees with no vertices of out-degree one. For further information on the format we kindly refer the reader to E. Paradis (2012) <http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf>.
Author: Mareike Fischer [aut], Lina Herbst [aut], Sophie Kersting [aut], Luise Kuehn [aut, cre], Kristina Wicke [aut]
Maintainer: Luise Kuehn <treebalanceindices@gmail.com>

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Package dang updated to version 0.0.14 with previous version 0.0.13 dated 2021-02-17

Title: 'Dang' Associated New Goodies
Description: A collection of utility functions.
Author: Dirk Eddelbuettel with contributions by Brodie Gaslam, Kevin Denny, Kabira Namit, Colin Gillespie, R Core, Josh Ulrich, Jordan Mark Barbone, and others.
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package osmdata updated to version 0.1.8 with previous version 0.1.7 dated 2021-10-07

Title: Import 'OpenStreetMap' Data as Simple Features or Spatial Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server (<https://overpass-api.de/>) and processed with very fast 'C++' routines for return to 'R'.
Author: Mark Padgham [aut, cre], Bob Rudis [aut], Robin Lovelace [aut], Maëlle Salmon [aut], Andrew Smith [ctb], James Smith [ctb], Andrea Gilardi [ctb], Enrico Spinielli [ctb], Anthony North [ctb], Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Finkelstein Noam [ctb, cph] (Author of included stub.R code), Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>

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Package conjurer updated to version 1.3.0 with previous version 1.2.0 dated 2020-09-08

Title: A Parametric Method for Generating Synthetic Data
Description: Builds synthetic data applicable across multiple domains. This package also provides flexibility to control data distribution to make it relevant to many industry examples.
Author: Sidharth Macherla [aut, cre] (<https://orcid.org/0000-0002-4825-2026>)
Maintainer: Sidharth Macherla <msidharthrasik@gmail.com>

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Package expands (with last version 2.1.3) was removed from CRAN

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2021-09-03 2.1.3

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Package libproj (with last version 8.1.0-1) was removed from CRAN

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

2021-10-05 8.1.0-1

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Package bayesnec updated to version 2.0.2 with previous version 2.0.1 dated 2021-09-20

Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECX' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>. This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020)<doi:10.5281/ZENODO.3966864>.
Author: Rebecca Fisher [aut, cre], Diego Barneche [aut], Gerard Ricardo [aut], David Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>

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Package prismatic updated to version 1.1.0 with previous version 1.0.0 dated 2021-01-05

Title: Color Manipulation Tools
Description: Manipulate and visualize colors in a intuitive, low-dependency and functional way.
Author: Emil Hvitfeldt [aut, cre] (<https://orcid.org/0000-0002-0679-1945>)
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>

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 prismatic-1.1.0/prismatic/tests/testthat/test-greyscale.R       |   34 +-
 prismatic-1.1.0/prismatic/tests/testthat/test-lightness.R       |  150 ++++++----
 prismatic-1.1.0/prismatic/tests/testthat/test-mix.R             |   43 ++
 prismatic-1.1.0/prismatic/tests/testthat/test-negate.R          |   17 -
 prismatic-1.1.0/prismatic/tests/testthat/test-rotate.R          |   43 ++
 prismatic-1.1.0/prismatic/tests/testthat/test-saturate.R        |   81 ++++-
 28 files changed, 457 insertions(+), 276 deletions(-)

More information about prismatic at CRAN
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Package pedSimulate updated to version 1.2.1 with previous version 1.2.0 dated 2021-09-06

Title: Pedigree, Genetic Merit, Phenotype, and Genotype Simulation
Description: Simulate pedigree, genetic merits and phenotypes with random/non-random matings followed by random/non-random selection with different intensities and patterns in males and females. Genotypes can be simulated for a given pedigree. Bijma, P. & Rutten, M. (2002) <https://www.wur.nl/en/Research-Results/Chair-groups/Animal-Sciences/Animal-Breeding-and-Genomics-Group/Research/Software.htm>.
Author: Mohammad Ali Nilforooshan [aut, cre] (<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>

Diff between pedSimulate versions 1.2.0 dated 2021-09-06 and 1.2.1 dated 2021-10-17

 DESCRIPTION        |    6 +++---
 MD5                |    8 ++++----
 NEWS.md            |    4 ++++
 R/hs_mate_finder.R |    2 +-
 R/simulateGen.R    |    1 +
 5 files changed, 13 insertions(+), 8 deletions(-)

More information about pedSimulate at CRAN
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