Tue, 26 May 2020

New package UniprotR with initial version 1.3.0
Package: UniprotR
Title: Retrieving Information of Proteins from Uniprot
Version: 1.3.0
Authors@R: c(person("Mohamed", "Soudy", email = "MohmedSoudy2009@gmail.com", role=c("aut", "cre")), person("Ali", "Mostafa", email = "ali.mo.anwar@std.agr.cu.edu.eg", role = "aut"))
Author: Mohamed Soudy [aut, cre], Ali Mostafa [aut]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: utils , grDevices , graphics, httr , plyr , dplyr , scales , stats , magrittr , magick , data.tree , ggplot2 , tidyverse , grid , gridExtra , ggpubr , alakazam, curl
URL: https://github.com/Proteomicslab57357/UniprotR
BugReports: https://github.com/Proteomicslab57357/UniprotR/issues
NeedsCompilation: no
Packaged: 2020-05-26 16:51:55 UTC; RSH
Repository: CRAN
Date/Publication: 2020-05-26 22:40:08 UTC

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New package treeman with initial version 1.1.4
Package: treeman
Type: Package
Title: Phylogenetic Tree Manipulation Class and Methods
Version: 1.1.4
Author: D.J. Bennett
Maintainer: D.J. Bennett <dominic.john.bennett@gmail.com>
Description: S4 class and methods for intuitive and efficient phylogenetic tree manipulation.
License: GPL-2
Depends: R (>= 3.2.4), methods
Imports: plyr, ape, RJSONIO, stringr, bigmemory
Suggests: testthat
RoxygenNote: 7.0.2
Collate: 'calc-methods.R' 'check_methods.R' 'cnvrt-methods.R' 'gen-methods.R' 'get-nd-methods.R' 'get-nds-methods.R' 'get-spcl-methods.R' 'manip-methods.R' 'ndlst-methods.R' 'ndmtrx-methods.R' 'node-declaration.R' 'read-write-methods.R' 'server-methods.R' 'set-methods.R' 'treeman-declaration.R' 'treemen-declaration.R' 'update-methods.R' 'viz-methods.R' 'zzz.R'
NeedsCompilation: yes
Packaged: 2020-05-26 17:31:36 UTC; domben
Repository: CRAN
Date/Publication: 2020-05-26 22:40:02 UTC

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Package RobMixReg updated to version 0.2.1 with previous version 0.2.0 dated 2020-05-11

Title: Robust Mixture Regression
Description: Finite mixture models are a popular technique for modelling unobserved heterogeneity or to approximate general distribution functions in a semi-parametric way. They are used in a lot of different areas such as astronomy, biology, economics, marketing or medicine. This package is the implementation of popular robust mixture regression methods based on different algorithms including: fleximix, finite mixture models and latent class regression; CTLERob, component-wise adaptive trimming likelihood estimation; mixbi, bi-square estimation; mixL, Laplacian distribution; mixt, t-distribution; TLE, trimmed likelihood estimation. The implemented algorithms includes: CTLERob stands for Component-wise adaptive Trimming Likelihood Estimation based mixture regression; mixbi stands for mixture regression based on bi-square estimation; mixLstands for mixture regression based on Laplacian distribution; TLE stands for Trimmed Likelihood Estimation based mixture regression. For more detail of the algorithms, please refer to below references. Reference: Chun Yu, Weixin Yao, Kun Chen (2017) <doi:10.1002/cjs.11310>. NeyKov N, Filzmoser P, Dimova R et al. (2007) <doi:10.1016/j.csda.2006.12.024>. Bai X, Yao W. Boyer JE (2012) <doi:10.1016/j.csda.2012.01.016>. Wennan Chang, Xinyu Zhou, Yong Zang, Chi Zhang, Sha Cao (2020) <arXiv:2005.11599>.
Author: Sha Cao [aut, cph, ths], Wennan Chang [aut, cre], Chi Zhang [aut, ctb, ths]
Maintainer: Wennan Chang <wnchang@iu.edu>

Diff between RobMixReg versions 0.2.0 dated 2020-05-11 and 0.2.1 dated 2020-05-26

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Package PRIMME updated to version 3.1-1 with previous version 3.0-0 dated 2019-07-25

Title: Eigenvalues and Singular Values and Vectors from Large Matrices
Description: R interface to 'PRIMME' <http://www.cs.wm.edu/~andreas/software>, a C library for computing a few eigenvalues and their corresponding eigenvectors of a real symmetric or complex Hermitian matrix, or generalized Hermitian eigenproblem. It can also compute singular values and vectors of a square or rectangular matrix. 'PRIMME' finds largest, smallest, or interior singular/eigenvalues and can use preconditioning to accelerate convergence. General description of the methods are provided in the papers Stathopoulos (2010, <doi:10.1145/1731022.1731031>) and Wu (2017, <doi:10.1137/16M1082214>). See 'citation("PRIMME")' for details.
Author: Eloy Romero [aut, cre], Andreas Stathopoulos [aut], College of William & Mary [cph]
Maintainer: Eloy Romero <eloy@cs.wm.edu>

Diff between PRIMME versions 3.0-0 dated 2019-07-25 and 3.1-1 dated 2020-05-26

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Package poismf updated to version 0.2.0 with previous version 0.1.3 dated 2019-09-04

Title: Factorization of Sparse Counts Matrices Through Poisson Likelihood
Description: Creates a low-rank factorization of a sparse counts matrix by maximizing Poisson likelihood with l1/l2 regularization with all non-negative latent factors (e.g. for recommender systems or topic modeling) (Cortes, (2018) <arXiv:1811.01908>). Similar to hierarchical Poisson factorization, but follows an optimization-based approach with regularization instead of a hierarchical structure, and is fit through either proximal gradient or conjugate gradient instead of variational inference.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

Diff between poismf versions 0.1.3 dated 2019-09-04 and 0.2.0 dated 2020-05-26

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Package outsider.base updated to version 0.1.2 with previous version 0.1.1 dated 2020-05-22

Title: Base Package for 'Outsider'
Description: Base package for 'outsider' <https://github.com/ropensci/outsider>. The 'outsider' package and its sister packages enable the installation and running of external, command-line software within R. This base package is a key dependency of the user-facing 'outsider' package as it provides the utilities for interfacing between 'Docker' <https://www.docker.com> and R. It is intended that end-users of 'outsider' do not directly work with this base package.
Author: Dom Bennett [aut, cre] (<https://orcid.org/0000-0003-2722-1359>), Hannes Hettling [ctb] (<https://orcid.org/0000-0003-4144-2238>), Daniele Silvestro [ctb] (<https://orcid.org/0000-0003-0100-0961>), Rutger Vos [ctb] (<https://orcid.org/0000-0001-9254-7318>), Alexandre Antonelli [ctb] (<https://orcid.org/0000-0003-1842-9297>), Anna Krystalli [rev]
Maintainer: Dom Bennett <dominic.john.bennett@gmail.com>

Diff between outsider.base versions 0.1.1 dated 2020-05-22 and 0.1.2 dated 2020-05-26

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Package netCoin updated to version 1.1.25 with previous version 1.1.24 dated 2020-02-03

Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package. The methods are described in Escobar and Martinez-Uribe (2020) <doi:10.18637/jss.v093.i11>.
Author: Modesto Escobar <modesto@usal.es>, David Barrios <metal@usal.es>, Carlos Prieto <cprietos@usal.es>, Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>

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Package NACHO updated to version 1.0.1 with previous version 1.0.0 dated 2020-01-09

Title: NanoString Quality Control Dashboard
Description: NanoString nCounter data are gene expression assays where there is no need for the use of enzymes or amplification protocols and work with fluorescent barcodes (Geiss et al. (2018) <doi:10.1038/nbt1385>). Each barcode is assigned a messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its target can be counted. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA. 'NACHO' (NAnoString quality Control dasHbOard) is able to analyse the exported NanoString nCounter data and facilitates the user in performing a quality control. 'NACHO' does this by visualising quality control metrics, expression of control genes, principal components and sample specific size factors in an interactive web application.
Author: Mickaël Canouil [aut, cre] (<https://orcid.org/0000-0002-3396-4549>), Roderick Slieker [aut] (<https://orcid.org/0000-0003-0961-9152>), Gerard Bouland [aut]
Maintainer: Mickaël Canouil <mickael.canouil@cnrs.fr>

Diff between NACHO versions 1.0.0 dated 2020-01-09 and 1.0.1 dated 2020-05-26

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New package mediationsens with initial version 0.0.1
Package: mediationsens
Version: 0.0.1
Date: 2020-05-18
Title: Simulation-Based Sensitivity Analysis for Causal Mediation Studies
Author: Xu Qin and Fan Yang
Maintainer: Xu Qin <xuqin@pitt.edu>
Depends: mediation, distr
Description: We implement the simulation-based sensitivity analysis for causal mediation studies using the methods proposed by Qin and Yang (2020). It numerically and graphically evaluates the sensitivity of causal mediation analysis results to the presence of unmeasured pretreatment confounding. The proposed method has primary advantages over existing methods. First, using an unmeasured pretreatment confounder conditional associations with the treatment, mediator, and outcome as sensitivity parameters, the method enables users to intuitively assess sensitivity in reference to prior knowledge about the strength of a potential unmeasured pretreatment confounder. Second, the method accurately reflects the influence of unmeasured pretreatment confounding on the efficiency of estimation of the causal effects. Third, the method can be implemented in different causal mediation analysis approaches, including regression-based, simulation-based, and propensity score-based methods. It is applicable to both randomized experiments and observational studies.
License: GPL-2
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-05-19 01:06:45 UTC; Xu Qin
Repository: CRAN
Date/Publication: 2020-05-26 22:20:10 UTC

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Package iq updated to version 1.7 with previous version 1.5 dated 2020-05-18

Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the maximal peptide ratio extraction module of the MaxLFQ algorithm by Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a complete pipeline for processing proteomics data in data-independent acquisition mode (Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>). It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
Author: Thang Pham [aut, cre, cph, ctb] (<https://orcid.org/0000-0003-0333-2492>), Alex Henneman [ctb] (<https://orcid.org/0000-0002-3746-4410>)
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>

Diff between iq versions 1.5 dated 2020-05-18 and 1.7 dated 2020-05-26

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Package collapse updated to version 1.2.1 with previous version 1.2.0 dated 2020-05-19

Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation in R that is extremely fast, flexible and parsimonious to code with and programmer friendly. It is well integrated with 'dplyr', 'plm' and 'data.table'. --- Key Features: --- (1) Advanced data programming: A full set of fast statistical functions supporting grouped and weighted computations on vectors, matrices and data frames. Fast (ordered) and programmable grouping, factor generation, manipulation of data frames and data object conversions. (2) Advanced aggregation: Fast and easy multi-data-type, multi-function, weighted, parallelized and fully customized data aggregation. (3) Advanced transformations: Fast (grouped, weighted) replacing and sweeping out of statistics, scaling / standardizing, centering (i.e. between and within transformations), higher-dimensional centering (i.e. multiple fixed effects transformations), linear prediction and partialling-out. (4) Advanced time-computations: Fast (sequences of) lags / leads, and (lagged / leaded, iterated, quasi-, log-) differences and growth rates on (unordered) time-series and panel data. Multivariate auto, partial and cross-correlation functions for panel data. Panel data to (ts-)array conversions. (5) List processing: (Recursive) list search / identification, extraction / subsetting, data-apply, and generalized row-binding / unlisting in 2D. (6) Advanced data exploration: Fast (grouped, weighted, panel-decomposed) summary statistics for complex multilevel / panel data.
Author: Sebastian Krantz [aut, cre], Matt Dowle [ctb], Arun Srinivasan [ctb], Simen Gaure [ctb], Dirk Eddelbuettel [ctb], R Core Team and contributors worldwide [ctb], Martyn Plummer [cph], 1999-2016 The R Core Team [cph]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>

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New package bvpSolve with initial version 1.4
Package: bvpSolve
Version: 1.4
Title: Solvers for Boundary Value Problems of Differential Equations
Authors@R: c(person("Karline","Soetaert", role = c("aut","cre"), email = "karline.soetaert@nioz.nl"), person("Jeff","Cash", role = "aut", email = "j.cash@imperial.ac.uk"), person("Francesca","Mazzia", role = "aut", email = "mazzia@dm.uniba.it"), person("Uri M.","Ascher", role = "ctb", comment = "files colsysR.f, colnewR.f, coldaeR.f"), person("G.","Bader", role = "ctb", comment = "file colnewR.f"), person("J.","Christiansen", role = "ctb", comment = "file colsysR.f"), person("Robert R.","Russell", role = "ctb", comment = "file colsysR.f"))
Author: Karline Soetaert [aut, cre], Jeff Cash [aut], Francesca Mazzia [aut], Uri M. Ascher [ctb] (files colsysR.f, colnewR.f, coldaeR.f), G. Bader [ctb] (file colnewR.f), J. Christiansen [ctb] (file colsysR.f), Robert R. Russell [ctb] (file colsysR.f)
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Depends: R (>= 2.01), deSolve
Imports: rootSolve, stats, graphics, grDevices
Description: Functions that solve boundary value problems ('BVP') of systems of ordinary differential equations ('ODE') and differential algebraic equations ('DAE'). The functions provide an interface to the FORTRAN functions 'twpbvpC', 'colnew/colsys', and an R-implementation of the shooting method. 'Mazzia, F., J.R. Cash and K. Soetaert, 2014. <DOI:10.7494/OpMath.2014.34.2.387>.
License: GPL (>= 2)
LazyData: yes
NeedsCompilation: yes
Packaged: 2020-05-26 06:37:30 UTC; karlines
Repository: CRAN
Date/Publication: 2020-05-26 22:10:18 UTC

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New package BMTME with initial version 1.0.15
Package: BMTME
Title: Bayesian Multi-Trait Multi-Environment for Genomic Selection Analysis
Version: 1.0.15
Date: 2020-5-23
Language: en-US
Authors@R: c(person("Francisco Javier", "Luna-Vazquez", email = "frahik@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5370-7152")), person("Fernando H.", "Toledo", role = "aut"), person("Osval Antonio", "Montesinos-Lopez", email= "oamontes1@ucol.mx", role = "aut", comment = c(ORCID = "0000-0002-3973-6547")), person("Abelardo", "Montesinos-Lopez", role = "aut"), person("Jose", "Crossa", role = "aut", comment = c(ORCID = "0000-0001-9429-5855")))
Maintainer: Francisco Javier Luna-Vazquez <frahik@gmail.com>
Description: Genomic selection and prediction models with the capacity to use multiple traits and environments, through ready-to-use Bayesian models. It consists a group of functions that help to create regression models for some genomic models proposed by Montesinos-López, et al. (2016) <doi:10.1534/g3.116.032359> also in Montesinos-López et al. (2018) <doi:10.1534/g3.118.200728> and Montesinos-López et al. (2018) <doi:10.2134/agronj2018.06.0362>.
Depends: R (>= 3.5)
License: LGPL-3
Encoding: UTF-8
LazyData: true
Type: Package
RoxygenNote: 7.1.0
URL: https://github.com/frahik/BMTME
BugReports: https://github.com/frahik/BMTME/issues/new
NeedsCompilation: yes
Collate: BME.R BMTME.R BMTME_Package.R BMORS.R BMORSEnv.R cholesky.R datasets.R detectCore.R RandomPartition.R RcppExports.R utils.R
Imports: BGLR, doSNOW, dplyr, foreach, matrixcalc, mvtnorm, progress, snow, tidyr
LinkingTo: Rcpp, RcppArmadillo
SystemRequirements: C++11, GNU
Suggests: covr, testthat,
Packaged: 2020-05-26 21:39:45 UTC; frahik
Author: Francisco Javier Luna-Vazquez [aut, cre] (<https://orcid.org/0000-0002-5370-7152>), Fernando H. Toledo [aut], Osval Antonio Montesinos-Lopez [aut] (<https://orcid.org/0000-0002-3973-6547>), Abelardo Montesinos-Lopez [aut], Jose Crossa [aut] (<https://orcid.org/0000-0001-9429-5855>)
Repository: CRAN
Date/Publication: 2020-05-26 22:40:12 UTC

More information about BMTME at CRAN
Permanent link

Package tibbletime updated to version 0.1.4 with previous version 0.1.3 dated 2019-09-20

Title: Time Aware Tibbles
Description: Built on top of the 'tibble' package, 'tibbletime' is an extension that allows for the creation of time aware tibbles. Some immediate advantages of this include: the ability to perform time-based subsetting on tibbles, quickly summarising and aggregating results by time periods, and creating columns that can be used as 'dplyr' time-based groups.
Author: Davis Vaughan [aut, cre], Matt Dancho [aut]
Maintainer: Davis Vaughan <davis@rstudio.com>

Diff between tibbletime versions 0.1.3 dated 2019-09-20 and 0.1.4 dated 2020-05-26

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Package sperrorest updated to version 3.0.1 with previous version 3.0.0 dated 2020-04-13

Title: Perform Spatial Error Estimation and Variable Importance in Parallel
Description: Implements spatial error estimation and permutation-based variable importance measures for predictive models using spatial cross-validation and spatial block bootstrap.
Author: Alexander Brenning [aut, cre] (<https://orcid.org/0000-0001-6640-679X>), Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>), Tobias Herrmann [aut] (<https://orcid.org/0000-0001-9768-0708>)
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>

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Package servr updated to version 0.17 with previous version 0.16 dated 2020-03-02

Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Description: Start an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Carson Sievert [ctb], Jesse Anderson [ctb], Ramnath Vaidyanathan [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package rbokeh updated to version 0.5.1 with previous version 0.5.0 dated 2016-10-11

Title: R Interface for Bokeh
Description: A native R plotting library that provides a flexible declarative interface for creating interactive web-based graphics, backed by the Bokeh visualization library <https://bokeh.pydata.org/>.
Author: Ryan Hafen [aut, cre], Kenton Russell [ctb], Jonathan Owen [ctb], Barret Schloerke [ctb], Saptasrhi Guha [ctb], Continuum Analytics, Inc. [aut, cph] (Bokeh library in htmlwidgets/lib, https://bokeh.pydata.org)
Maintainer: Ryan Hafen <rhafen@gmail.com>

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Package nomnoml updated to version 0.2.0 with previous version 0.1.0 dated 2019-06-13

Title: Sassy 'UML' Diagrams
Description: A tool for drawing sassy 'UML' diagrams based on a simple syntax, see <http://www.nomnoml.com>. Supports styling, R Markdown and exporting diagrams in the PNG format.
Author: Javier Luraschi [aut, cre], Andrie de Vries [aut], Daniel Kallin [aut] (nomnoml.js library, http://nomnoml.com), RStudio [cph]
Maintainer: Javier Luraschi <javier@rstudio.com>

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Package httpuv updated to version 1.5.3.1 with previous version 1.5.2 dated 2019-09-11

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, Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Winston Chang [ctb]
Maintainer: Joe Cheng <joe@rstudio.com>

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 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/cygwin.c                             |    5 
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More information about httpuv at CRAN
Permanent link

Package pollster updated to version 0.1.2 with previous version 0.1.1 dated 2020-04-08

Title: Calculate Crosstab and Topline Tables of Weighted Survey Data
Description: Calculate common types of tables for weighted survey data. Options include topline and (2-way and 3-way) crosstab tables of categorical or ordinal data as well as summary tables of weighted numeric variables. Optionally, include the margin of error at selected confidence intervals including the design effect. The design effect is calculated as described by Kish (1965) <doi:10.1002/bimj.19680100122> beginning on page 257. Output takes the form of tibbles (simple data frames). This package conveniently handles labelled data, such as that commonly used by 'Stata' and 'SPSS.' Complex survey design is not supported at this time.
Author: John D. Johnson [aut, cre]
Maintainer: John D. Johnson <john.d.johnson@marquette.edu>

Diff between pollster versions 0.1.1 dated 2020-04-08 and 0.1.2 dated 2020-05-26

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More information about pollster at CRAN
Permanent link

Package bmixture updated to version 1.6 with previous version 1.5 dated 2020-05-13

Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation of finite mixture of distributions, mainly mixture of Gamma, Normal and t-distributions. The package is implemented the Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
Author: Reza Mohammadi [aut, cre] (<https://orcid.org/0000-0001-9538-0648>)
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>

Diff between bmixture versions 1.5 dated 2020-05-13 and 1.6 dated 2020-05-26

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More information about bmixture at CRAN
Permanent link

Package smerc updated to version 1.2 with previous version 1.1 dated 2019-09-19

Title: Statistical Methods for Regional Counts
Description: Implements statistical methods for analyzing the counts of areal data, with a focus on the detection of spatial clusters and clustering. The package has a heavy emphasis on spatial scan methods, which were first introduced by Kulldorff and Nagarwalla (1995) <doi:10.1002/sim.4780140809> and Kulldorff (1997) <doi:10.1080/03610929708831995>.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>

Diff between smerc versions 1.1 dated 2019-09-19 and 1.2 dated 2020-05-26

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 smerc-1.2/smerc/R/elliptic.nn.R                         |   15 
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 smerc-1.2/smerc/R/elliptic.test2.R                      |only
 smerc-1.2/smerc/R/fast.sim.R                            |   93 +--
 smerc-1.2/smerc/R/fast.test2.R                          |only
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Package modelsummary updated to version 0.3.0 with previous version 0.2.1 dated 2020-04-30

Title: Summary Tables for Statistical Models: Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable summary tables for statistical models. 'modelsummary' leverages the power of the 'gt', 'kableExtra' and 'broom' packages. It supports dozens of model types, and can produce tables in HTML, LaTeX, RTF, Text/Markdown, JPG, PNG, and LaTeX formats. The tables can also be integrated in 'Rmarkdown', 'knitr', or 'Sweave' dynamic documents.
Author: Vincent Arel-Bundock [aut, cre] (<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

Diff between modelsummary versions 0.2.1 dated 2020-04-30 and 0.3.0 dated 2020-05-26

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New package ot with initial version 0.2.0
Package: ot
Type: Package
Title: 'Open Tracing'
Version: 0.2.0
Author: Neal Fultz <nfultz@gmail.com>
Maintainer: Neal Fultz <nfultz@gmail.com>
Description: 'Open Tracing' <https://opentracing.io> allows developers to add instrumentation to their application code using interfaces that are vendor-agnostic. This is used to monitor services, triage failures and find performance bottlenecks, among other things. The 'ot' package has generic methods to be extended when implementing the specification for a specific vendor.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-05-18 16:15:43.31 UTC; nfultz
Repository: CRAN
Date/Publication: 2020-05-26 16:10:02 UTC

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Package tables updated to version 0.9.3 with previous version 0.8.8 dated 2019-05-13

Title: Formula-Driven Table Generation
Description: Computes and displays complex tables of summary statistics. Output may be in LaTeX, HTML, plain text, or an R matrix for further processing.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>

Diff between tables versions 0.8.8 dated 2019-05-13 and 0.9.3 dated 2020-05-26

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Package rRofex updated to version 1.6.11 with previous version 1.6.9 dated 2020-05-20

Title: Interface to 'Matba Rofex' Trading API
Description: Execute API calls to the 'Matba Rofex' <https://apihub.primary.com.ar> trading platform. Functionality includes accessing account data and current holdings, retrieving investment quotes, placing and canceling orders, and getting reference data for instruments.
Author: Augusto Hassel [aut, cre], Juan Francisco Gomez [ctb], Matba Rofex [cph]
Maintainer: Augusto Hassel <ahassel@primary.com.ar>

Diff between rRofex versions 1.6.9 dated 2020-05-20 and 1.6.11 dated 2020-05-26

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Package riskclustr updated to version 0.3 with previous version 0.2 dated 2019-09-07

Title: Functions to Study Etiologic Heterogeneity
Description: A collection of functions related to the study of etiologic heterogeneity both across disease subtypes and across individual disease markers. The included functions allow one to quantify the extent of etiologic heterogeneity in the context of a case-control study, and provide p-values to test for etiologic heterogeneity across individual risk factors. Begg CB, Zabor EC, Bernstein JL, Bernstein L, Press MF, Seshan VE (2013) <doi: 10.1002/sim.5902>.
Author: Emily C. Zabor [aut, cre]
Maintainer: Emily C. Zabor <zabore2@ccf.org>

Diff between riskclustr versions 0.2 dated 2019-09-07 and 0.3 dated 2020-05-26

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Package orientlib updated to version 0.10.4 with previous version 0.10.3 dated 2013-03-22

Title: Support for Orientation Data
Description: Representations, conversions and display of orientation SO(3) data. See the orientlib help topic for details.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>

Diff between orientlib versions 0.10.3 dated 2013-03-22 and 0.10.4 dated 2020-05-26

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New package SocEpi with initial version 1.0.0
Package: SocEpi
Type: Package
Title: Health Inequality Analysis
Version: 1.0.0
Authors@R: person("Mirjam", "Allik", email="mirjam.allik@gmail.com", role=c("aut", "cre"))
Description: Tools for calculating deprivation measures and analysing health outcomes and mortality by deprivation. Included are the functions: zscore() and w_pcntile() for developing deprivation measures and the functions smr(), st_rate() and rii() for calculating standardized mortality ratios, direct standardized rates and Slope and Relative indices of Inequality (SII and RII). Test data is included (dep_data and health_data). The RII/SII are calculated following Pamuk ER (1985) <doi:10.1080/0032472031000141256>. The confidence intervals for SII/RII are calculated using a multinomial distribution as described in Lumme et al (2015) <doi:10.1007/s10742-015-0137-1>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Depends: R (>= 3.2.0)
Imports: tidyr, dplyr, Rcpp
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2020-05-18 08:15:04 UTC; ma166k
Author: Mirjam Allik [aut, cre]
Maintainer: Mirjam Allik <mirjam.allik@gmail.com>
Repository: CRAN
Date/Publication: 2020-05-26 14:20:06 UTC

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New package rbiom with initial version 1.0.0
Package: rbiom
Type: Package
Title: Read/Write, Transform, and Summarize 'BIOM' Data
Version: 1.0.0
Authors@R: person("Daniel P.", "Smith", email = "dansmith@orst.edu", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-2479-2044"))
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files. Features include reading/writing all 'BIOM' formats, rarefaction, alpha diversity, beta diversity (including 'UniFrac'), summarizing counts by taxonomic level, and sample subsetting. Standalone functions for reading, writing, and subsetting phylogenetic trees are also provided. All CPU intensive operations are encoded in C with multi-thread support.
URL: https://cmmr.github.io/rbiom/index.html
BugReports: https://github.com/cmmr/rbiom/issues
License: AGPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
LinkingTo: Rcpp, RcppParallel
Imports: magrittr, methods, plyr, Rcpp, RcppParallel, R.utils, rhdf5, rjson, slam, openxlsx
Suggests: ape, reshape2, testthat
RoxygenNote: 7.1.0
NeedsCompilation: yes
Packaged: 2020-05-18 06:12:09 UTC; Daniel
Author: Daniel P. Smith [aut, cre, cph] (<https://orcid.org/0000-0002-2479-2044>)
Maintainer: Daniel P. Smith <dansmith@orst.edu>
Repository: CRAN
Date/Publication: 2020-05-26 14:20:02 UTC

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Package lcmm updated to version 1.8.1.1 with previous version 1.8.1 dated 2019-06-26

Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>

Diff between lcmm versions 1.8.1 dated 2019-06-26 and 1.8.1.1 dated 2020-05-26

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New package eventr with initial version 1.0.0
Package: eventr
Title: Create Event Based Data Architectures
Version: 1.0.0
Authors@R: c( person(given = "Alvaro", family = "Franquet", role = c("aut", "cre"), email = "afranquet@salutemporda.cat"), person(given = "Maria Antonia", family = "Barceló", role = c("aut"), email = "antonia.barcelo@udg.edu", comment = c(ORCID = "0000-0001-9720-690X")), person(given = "Marc", family = "Saez", role = c("aut"), email = "marc.saez@udg.edu", comment = c(ORCID = "0000-0003-1882-0157")), person(given = "Pere", family = "Plaja", role = c("aut"), email = "pplaja@salutemporda.cat") )
Description: Event-driven programming is a programming paradigm where the flow of execution is defined by event. In this paradigm an event can be defined as "a change in the state" of an object. This package offers a set of functions for creating event-based architectures using three basic functions: events, dispatchers, and handlers. The handlers manage the events, the dispatchers are in charge of redirecting the events to each of the handlers, finally the events are the objects that carry the information about the change of state.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Imports: purrr, dplyr, magrittr
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2020-05-18 14:12:01 UTC; afranquet
Author: Alvaro Franquet [aut, cre], Maria Antonia Barceló [aut] (<https://orcid.org/0000-0001-9720-690X>), Marc Saez [aut] (<https://orcid.org/0000-0003-1882-0157>), Pere Plaja [aut]
Maintainer: Alvaro Franquet <afranquet@salutemporda.cat>
Repository: CRAN
Date/Publication: 2020-05-26 14:40:02 UTC

More information about eventr at CRAN
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Package SP2000 updated to version 0.0.8 with previous version 0.0.7 dated 2020-05-22

Title: Catalogue of Life Toolkit
Description: A programmatic interface to <http://sp2000.org.cn>, re-written based on an accompanying 'Species 2000' API. Access tables describing catalogue of the Chinese known species of animals, plants, fungi, micro-organisms, and more. This package also supports access to catalogue of life global <http://catalogueoflife.org> and catalogue of life Taiwan <http://taibnet.sinica.edu.tw/home_eng.php?>. The development of 'SP2000' package were supported by Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China <No.2019HJ2096001006> and Yunnan University's Research Innovation Fund for Graduate Students <No.2019227>.
Author: Liuyong Ding [aut, cre], Minrui Huang [ctb], Ke Yang [ctb], Jun Wang [ctb], Juan Tao [ctb], Chengzhi Ding [ctb], Daming He [ctb]
Maintainer: Liuyong Ding <ly_ding@126.com>

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Package wilson updated to version 2.4.0 with previous version 2.3.1 dated 2019-11-18

Title: Web-Based Interactive Omics Visualization
Description: Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data. This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
Author: Hendrik Schultheis [aut, cre], Jens Preussner [aut], Looso Mario [aut]
Maintainer: Hendrik Schultheis <hendrik.schultheis@mpi-bn.mpg.de>

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Package srvyr updated to version 0.3.10 with previous version 0.3.9 dated 2020-05-04

Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre], Thomas Lumley [ctb], Tomasz Żółtak [ctb], Ben Schneider [ctb]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>

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Package rrscale updated to version 1.0 with previous version 0.1.3 dated 2019-03-13

Title: Robust Re-Scaling to Better Recover Latent Effects in Data
Description: Non-linear transformations of data to better discover latent effects. Applies a sequence of three transformations (1) a Gaussianizing transformation, (2) a Z-score transformation, and (3) an outlier removal transformation. A publication describing the method has the following citation: Gregory J. Hunt, Mark A. Dane, James E. Korkola, Laura M. Heiser & Johann A. Gagnon-Bartsch (2020) "Automatic Transformation and Integration to Improve Visualization and Discovery of Latent Effects in Imaging Data", Journal of Computational and Graphical Statistics, <doi:10.1080/10618600.2020.1741379>.
Author: Gregory Hunt [aut, cre], Johann Gagnon-Bartsch [aut]
Maintainer: Gregory Hunt <ghunt@wm.edu>

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Package questionr updated to version 0.7.1 with previous version 0.7.0 dated 2018-11-26

Title: Functions to Make Surveys Processing Easier
Description: Set of functions to make the processing and analysis of surveys easier : interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.
Author: Julien Barnier [aut, cre], François Briatte [aut], Joseph Larmarange [aut]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

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New package nodiv with initial version 1.4.0
Package: nodiv
Type: Package
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Version: 1.4.0
Date: 2020-05-26
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@sund.ku.dk>
Description: An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Depends: R (>= 3.0)
Imports: picante, raster, ape, sp, vegan, utils
Suggests: RColorBrewer, parallel, testthat, colorspace
License: MIT + file LICENSE
URL: https://github.com/mkborregaard/nodiv
NeedsCompilation: no
Packaged: 2020-05-26 11:11:33 UTC; michael
Repository: CRAN
Date/Publication: 2020-05-26 11:30:09 UTC

More information about nodiv at CRAN
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Package geohashTools updated to version 0.3.1 with previous version 0.3.0 dated 2019-10-03

Title: Tools for Working with Geohashes
Description: Tools for working with Gustavo Niemeyer's geohash coordinate system, including API for interacting with other common R GIS libraries.
Author: Michael Chirico [aut, cre], Dmitry Shkolnik [ctb]
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>

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Package strand updated to version 0.1.3 with previous version 0.1.2 dated 2020-05-23

Title: A Framework for Investment Strategy Simulation
Description: Provides a framework for performing discrete (share-level) simulations of investment strategies. Simulated portfolios optimize exposure to an input signal subject to constraints such as position size and factor exposure.
Author: Jeff Enos [cre, aut], David Kane [aut], Strand Technologies, Inc. [cph]
Maintainer: Jeff Enos <jeff@strand.tech>

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Package sn updated to version 1.6-2 with previous version 1.6-1 dated 2020-04-01

Title: The Skew-Normal and Related Distributions Such as the Skew-t
Description: Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provide related statistical methods for data fitting and model diagnostics, in the univariate and the multivariate case.
Author: Adelchi Azzalini [aut, cre] (<https://orcid.org/0000-0002-7583-1269>)
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>

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Package holodeck updated to version 0.2.1 with previous version 0.2.0 dated 2019-04-16

Title: A Tidy Interface for Simulating Multivariate Data
Description: Provides pipe-friendly (%>%) wrapper functions for MASS::mvrnorm() to create simulated multivariate data sets with groups of variables with different degrees of variance, covariance, and effect size.
Author: Eric Scott [aut, cre] (<https://orcid.org/0000-0002-7430-7879>)
Maintainer: Eric Scott <scottericr@gmail.com>

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Package glmulti updated to version 1.0.8 with previous version 1.0.7.1 dated 2019-04-14

Title: Model Selection and Multimodel Inference Made Easy
Description: Automated model selection and model-averaging. Provides a wrapper for glm and other functions, automatically generating all possible models (under constraints set by the user) with the specified response and explanatory variables, and finding the best models in terms of some Information Criterion (AIC, AICc or BIC). Can handle very large numbers of candidate models. Features a Genetic Algorithm to find the best models when an exhaustive screening of the candidates is not feasible.
Author: Vincent Calcagno [aut, cre]
Maintainer: Vincent Calcagno <vincent.calcagno@inrae.fr>

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Package ggspatial updated to version 1.1.2 with previous version 1.1.1 dated 2020-04-27

Title: Spatial Data Framework for ggplot2
Description: Spatial data plus the power of the ggplot2 framework means easier mapping when input data are already in the form of spatial objects.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>), Brent Thorne [ctb] (<https://orcid.org/0000-0002-1099-3857>)
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>

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Package geofacet updated to version 0.2.0 with previous version 0.1.10 dated 2019-03-13

Title: 'ggplot2' Faceting Utilities for Geographical Data
Description: Provides geofaceting functionality for 'ggplot2'. Geofaceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.
Author: Ryan Hafen [aut, cre], Barret Schloerke [ctb]
Maintainer: Ryan Hafen <rhafen@gmail.com>

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Package ebreg updated to version 0.1.2 with previous version 0.1.1 dated 2020-05-21

Title: Implementation of the Empirical Bayes Method
Description: Implements a Bayesian-like approach to the high-dimensional sparse linear regression problem based on an empirical or data-dependent prior distribution, which can be used for estimation/inference on the model parameters, variable selection, and prediction of a future response. The method was first presented in Martin, Ryan and Mess, Raymond and Walker, Stephen G (2017) <doi:10.3150/15-BEJ797>. More details focused on the prediction problem are given in Martin, Ryan and Tang, Yiqi (2019) <arXiv:1903.00961>.
Author: Yiqi Tang, Ryan Martin
Maintainer: Yiqi Tang <ytang22@ncsu.edu>

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Package CB2 updated to version 1.3.3 with previous version 1.3.2 dated 2020-05-12

Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyun-hwan.jeong@bcm.edu>

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Package XICOR updated to version 0.3.3 with previous version 0.3.2 dated 2020-04-28

Title: Association Measurement Through Cross Rank Increments
Description: Computes robust association measures that do not presuppose linearity. The xi correlation (xicor) is based on cross correlation between ranked increments. The reference for the methods implemented here is Chatterjee, Sourav (2020) <arXiv:1909.10140> This package includes the Galton peas example.
Author: Susan Holmes [aut,cre], Sourav Chatterjee [aut]
Maintainer: Susan Holmes <sp.holmes@gmail.com>

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New package SoupX with initial version 1.4.5
Package: SoupX
Title: Single Cell mRNA Soup eXterminator
Version: 1.4.5
Date: 2020-05-15
Author: Matthew Daniel Young
Maintainer: Matthew Daniel Young <my4@sanger.ac.uk>
Description: Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.
URL: https://github.com/constantAmateur/SoupX
Suggests: knitr, rstan, DropletUtils, rmarkdown
VignetteBuilder: knitr
Imports: ggplot2, Matrix, methods, Seurat
Depends: R (>= 3.5.0)
LazyData: true
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.0.2
NeedsCompilation: no
Packaged: 2020-05-15 16:36:15 UTC; my4
Repository: CRAN
Date/Publication: 2020-05-26 10:00:06 UTC

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Package rmweather updated to version 0.1.4 with previous version 0.1.3 dated 2018-11-12

Title: Tools to Conduct Meteorological Normalisation on Air Quality Data
Description: An integrated set of tools to allow data users to conduct meteorological normalisation on air quality data. This meteorological normalisation technique uses predictive random forest models to remove variation of pollutant concentrations so trends and interventions can be explored in a robust way. For examples, see Grange et al. (2018) <doi:10.5194/acp-18-6223-2018> and Grange and Carslaw (2019) <doi:10.1016/j.scitotenv.2018.10.344>.
Author: Stuart K. Grange [cre, aut] (<https://orcid.org/0000-0003-4093-3596>)
Maintainer: Stuart K. Grange <stuart.grange@york.ac.uk>

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Package mlogit updated to version 1.1-0 with previous version 1.0-3.1 dated 2020-03-12

Title: Multinomial Logit Models
Description: Maximum Likelihood estimation of random utility discrete choice models, as described in Kenneth Train (2009) Discrete Choice Methods with Simulations <doi:10.1017/CBO9780511805271>.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>

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New package crispRdesignR with initial version 1.1.5
Package: crispRdesignR
Type: Package
Title: Guide Sequence Design for CRISPR/Cas9
Version: 1.1.5
Encoding: UTF-8
Authors@R: c( person("Dylan", "Beeber", email = "dylan.beeber@gmail.com", role = c("aut", "cre")), person("Frederic", "Chain", role = "aut"))
Description: Designs guide sequences for CRISPR/Cas9 genome editing and provides information on sequence features pertinent to guide efficiency. Sequence features include annotated off-target predictions in a user-selected genome and a predicted efficiency score based on the model described in Doench et al. (2016) <doi:10.1038/nbt.3437>. Users are able to import additional genomes and genome annotation files to use when searching and annotating off-target hits. All guide sequences and off-target data can be generated through the 'R' console with sgRNA_Design() or through 'crispRdesignR's' user interface with crispRdesignRUI(). CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and the associated protein Cas9 refer to a technique used in genome editing.
URL: <https://github.com/dylanbeeber/crispRdesignR>
License: GPL-3
Depends: R (>= 2.10)
Imports: Biostrings, gbm, GenomicRanges, BiocGenerics, IRanges, GenomeInfoDb, S4Vectors, rtracklayer, stringr, vtreat, shiny, DT
Suggests: BSgenome.Scerevisiae.UCSC.sacCer2
LazyData: true
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-05-16 22:56:21 UTC; Dylan
Author: Dylan Beeber [aut, cre], Frederic Chain [aut]
Maintainer: Dylan Beeber <dylan.beeber@gmail.com>
Repository: CRAN
Date/Publication: 2020-05-26 10:00:03 UTC

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New package climwin with initial version 1.2.3
Package: climwin
Type: Package
Title: Climate Window Analysis
Version: 1.2.3
Author: Liam D. Bailey and Martijn van de Pol
Maintainer: Liam D. Bailey <liam.bailey@liamdbailey.com>
URL: https://github.com/LiamDBailey/climwin
BugReports: https://github.com/LiamDBailey/climwin/issues
Description: Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a given biological response. Please see van de Pol et al. (2016) <doi:10.1111/2041-210X.12590> and Bailey and van de Pol (2016) <doi:10.1371/journal.pone.0167980> for details.
Depends: R (>= 2.10), ggplot2, gridExtra, Matrix
Imports: evd, lubridate, lme4, MuMIn, reshape, numDeriv, RcppRoll, nlme
Suggests: testthat, knitr, rmarkdown
License: GPL-2
Repository: CRAN
LazyData: True
VignetteBuilder: knitr
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2020-05-26 07:54:24 UTC; Liam
Date/Publication: 2020-05-26 09:50:06 UTC

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New package BayesSenMC with initial version 0.1.2
Package: BayesSenMC
Title: Different Models of Posterior Distributions of Adjusted Odds Ratio
Version: 0.1.2
Author: Jinhui Yang, Haitao Chu, and Lifeng Lin
Maintainer: Jinhui Yang <james.yangjinhui@gmail.com>
Description: Generates different posterior distributions of adjusted odds ratio under different priors of sensitivity and specificity, and plots the models for comparison. It also provides estimations for the specifications of the models using diagnostics of exposure status with a non-linear mixed effects model. It implements the methods that are first proposed in <doi:10.1016/j.annepidem.2006.04.001> and <doi:10.1177/0272989X09353452>.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: dplyr, ggplot2, rstan (>= 2.16.2), lme4,
Depends: Rcpp (>= 0.12.19)
Suggests: gridExtra
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2020-05-26 04:38:18 UTC; james
Repository: CRAN
Date/Publication: 2020-05-26 09:50:11 UTC

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Package antaresViz updated to version 0.15.2 with previous version 0.15.1 dated 2020-02-24

Title: Antares Visualizations
Description: Visualize results generated by Antares, a powerful open source software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). This package provides functions that create interactive charts to help Antares users visually explore the results of their simulations.
Author: Veronique Bachelier [aut, cre], Jalal-Edine Zawam [aut], Francois Guillem [aut], Benoit Thieurmel [aut], Titouan Robert [aut], Baptiste Seguinot [ctb], RTE [cph]
Maintainer: Veronique Bachelier <veronique.bachelier@rte-france.com>

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Package flippant (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:

2017-02-04 1.1.0
2016-12-21 1.0.2

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Package ArfimaMLM (with last version 1.3) was removed from CRAN

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

2015-01-21 1.3

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Package ifultools updated to version 2.0-5.1 with previous version 2.0-5 dated 2019-03-04

Title: Insightful Research Tools
Description: Insightful Research Tools.
Author: William Constantine [cre, aut]
Maintainer: ORPHANED

Diff between ifultools versions 2.0-5 dated 2019-03-04 and 2.0-5.1 dated 2020-05-26

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Package biglmm updated to version 0.9-2 with previous version 0.9-1 dated 2018-07-31

Title: Bounded Memory Linear and Generalized Linear Models
Description: Regression for data too large to fit in memory. This package functions exactly like the 'biglm' package, but works with later versions of R.
Author: Thomas Lumley [aut], Christophe Dutang [ctb], Alan Miller [ctb] (Algorithm AS 274), Morven Gentleman [ctb] (Algorithm AS 75), Mark Purver [cre]
Maintainer: Mark Purver <mark_purver@hotmail.com>

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Package biglm updated to version 0.9-2 with previous version 0.9-1 dated 2013-05-15

Title: bounded memory linear and generalized linear models
Description: Regression for data too large to fit in memory
Author: Thomas Lumley
Maintainer: Thomas Lumley <tlumley@u.washington.edu>

Diff between biglm versions 0.9-1 dated 2013-05-15 and 0.9-2 dated 2020-05-26

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Package Iso updated to version 0.0-18.1 with previous version 0.0-18 dated 2019-06-05

Title: Functions to Perform Isotonic Regression
Description: Linear order and unimodal order (univariate) isotonic regression; bivariate isotonic regression with linear order on both variables.
Author: Rolf Turner <r.turner@auckland.ac.nz>
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>

Diff between Iso versions 0.0-18 dated 2019-06-05 and 0.0-18.1 dated 2020-05-26

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Package IMaGES updated to version 0.1.1 with previous version 0.1 dated 2019-01-25

Title: Independent Multiple-Sample Greedy Equivalence Search Implementation
Description: Functions for the implementation of Independent Multiple-sample Greedy Equivalence Search (IMaGES), a causal inference algorithm for creating aggregate graphs and structural equation modeling data for one or more datasets. This package is useful for time series data with specific regions of interest. This implementation is inspired by the paper "Six problems for causal inference from fMRI" by Ramsey, Hanson, Hanson, Halchenko, Poldrack, and Glymour (2010) <DOI:10.1016/j.neuroimage.2009.08.065>. The IMaGES algorithm uses a modified BIC score to compute goodness of fit of edge additions, subtractions, and turns across all datasets and returns a representative graph, along with structural equation modeling data for the global graph and individual datasets, means, and standard errors. Functions for plotting the resulting graph(s) are provided. This package is built upon the 'pcalg' package.
Author: Noah Frazier-Logue [aut, cre], Stephen Jose Hanson [aut], Markus Kalisch [ctb], Alain Hauser [ctb], Martin Maechler [ctb], Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb], Antti Hyttinen [ctb], Jonas Peters [ctb], Nicoletta Andri [ctb], Emilija Perkovic [ctb], Preetam Nandy [ctb], Philipp Ruetimann [ctb], Daniel Stekhoven [ctb], Manuel Schuerch [ctb]
Maintainer: Noah Frazier-Logue <n.frazier.logue@nyu.edu>

Diff between IMaGES versions 0.1 dated 2019-01-25 and 0.1.1 dated 2020-05-26

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Package gss updated to version 2.2-2 with previous version 2.2-1 dated 2020-05-17

Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate function estimation using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>

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Package ContaminatedMixt updated to version 1.3.4.1 with previous version 1.3.4 dated 2019-08-27

Title: Clustering and Classification with the Contaminated Normal
Description: Fits mixtures of multivariate contaminated normal distributions (with eigen-decomposed scale matrices) via the expectation conditional- maximization algorithm under a clustering or classification paradigm Methods are described in Antonio Punzo, Angelo Mazza, and Paul D McNicholas (2018) <doi:10.18637/jss.v085.i10>.
Author: Antonio Punzo, Angelo Mazza, Paul D. McNicholas
Maintainer: Angelo Mazza <a.mazza@unict.it>

Diff between ContaminatedMixt versions 1.3.4 dated 2019-08-27 and 1.3.4.1 dated 2020-05-26

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Package C50 updated to version 0.1.3.1 with previous version 0.1.3 dated 2020-01-13

Title: C5.0 Decision Trees and Rule-Based Models
Description: C5.0 decision trees and rule-based models for pattern recognition that extend the work of Quinlan (1993, ISBN:1-55860-238-0).
Author: Max Kuhn [aut, cre], Steve Weston [ctb], Mark Culp [ctb], Nathan Coulter [ctb], Ross Quinlan [aut] (Author of imported C code), RuleQuest Research [cph] (Copyright holder of imported C code), Rulequest Research Pty Ltd. [cph] (Copyright holder of imported C code)
Maintainer: Max Kuhn <mxkuhn@gmail.com>

Diff between C50 versions 0.1.3 dated 2020-01-13 and 0.1.3.1 dated 2020-05-26

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Package btb updated to version 0.1.30.1 with previous version 0.1.30 dated 2018-05-23

Title: Beyond the Border - Kernel Density Estimation for Urban Geography
Description: The kernelSmoothing() function allows you to square and smooth geolocated data. It calculates a classical kernel smoothing (conservative) or a geographically weighted median. There are four major call modes of the function. The first call mode is kernelSmoothing(obs, epsg, cellsize, bandwith) for a classical kernel smoothing and automatic grid. The second call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, quantiles) for a geographically weighted median and automatic grid. The third call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, centroids) for a classical kernel smoothing and user grid. The fourth call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, quantiles, centroids) for a geographically weighted median and user grid. Geographically weighted summary statistics : a framework for localised exploratory data analysis, C.Brunsdon & al., in Computers, Environment and Urban Systems C.Brunsdon & al. (2002) <doi:10.1016/S0198-9715(01)00009-6>, Statistical Analysis of Spatial and Spatio-Temporal Point Patterns, Third Edition, Diggle, pp. 83-86, (2003) <doi:10.1080/13658816.2014.937718>.
Author: Arlindo Dos Santos [cre], Francois Semecurbe [drt, aut], Auriane Renaud [ctb], Cynthia Faivre [ctb], Thierry Cornely [ctb], Farida Marouchi [ctb], Farida Marouchi [ctb]
Maintainer: Arlindo Dos Santos <Arlindo.Dos-Santos@insee.fr>

Diff between btb versions 0.1.30 dated 2018-05-23 and 0.1.30.1 dated 2020-05-26

 DESCRIPTION |    6 +++---
 MD5         |    4 ++--
 src/init.c  |    2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

More information about btb at CRAN
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Package opart (with last version 2019.1.0) was removed from CRAN

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

2019-09-04 2019.1.0

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Package DCPO (with last version 0.5.2) was removed from CRAN

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

2020-04-28 0.5.2
2020-04-14 0.5.1

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