Mon, 08 Jul 2019

Package qs updated to version 0.17.3 with previous version 0.17.1 dated 2019-06-25

Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd and lz4 code), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd bundled code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled code), Romain Francois [ctb, cph] (Derived example/tutorials for Alt-Rep structures), Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc library)
Maintainer: Travers Ching <traversc@gmail.com>

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Package AWR.Athena updated to version 2.0.7-0 with previous version 2.0.6-1 dated 2019-02-05

Title: 'AWS' Athena 'DBI' Wrapper
Description: 'RJDBC' based 'DBI' driver to Amazon Athena, which is an interactive query service to analyze data in Amazon 'S3' using standard 'SQL'.
Author: Neal Fultz <nfultz@gmail.com>, Gergely Daróczi <gergely@system1.com>
Maintainer: Neal Fultz <nfultz@gmail.com>

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Package wand updated to version 0.5.0 with previous version 0.2.0 dated 2016-08-15

Title: Retrieve 'Magic' Attributes from Files and Directories
Description: 'MIME' types are shorthand descriptors for file contents and can be determined from "magic" bytes in file headers, file contents or intuited from file extensions. Tools are provided to perform curated "magic" tests as well as mapping 'MIME' types from a database of over 1,500 extension mappings.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>)
Maintainer: Bob Rudis <bob@rud.is>

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Package rgl updated to version 0.100.26 with previous version 0.100.24 dated 2019-06-26

Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>

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Package randomForestSRC updated to version 2.9.1 with previous version 2.9.0 dated 2019-04-22

Title: Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for survival, competing risks, regression and classification based on Ishwaran and Kogalur's popular random survival forests (RSF) package. Handles missing data and now includes multivariate, unsupervised forests, quantile regression and solutions for class imbalanced data. New fast interface using subsampling and confidence regions for variable importance.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>

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Package mclust updated to version 5.4.5 with previous version 5.4.4 dated 2019-06-27

Title: Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.
Author: Chris Fraley [aut], Adrian E. Raftery [aut] (<https://orcid.org/0000-0002-6589-301X>), Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>), Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>), Michael Fop [ctb] (<https://orcid.org/0000-0003-3936-2757>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>

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Package googleAuthR updated to version 0.8.1 with previous version 0.8.0 dated 2019-06-30

Title: Authenticate and Create Google APIs
Description: Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>), Jennifer Bryan [ctb], Johann deBoer [ctb], Neal Richardson [ctb], David Kulp [ctb], Joe Cheng [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>

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Package contextual updated to version 0.9.8.2 with previous version 0.9.8.1 dated 2019-03-17

Title: Simulation and Analysis of Contextual Multi-Armed Bandit Policies
Description: Facilitates the simulation and evaluation of context-free and contextual multi-Armed Bandit policies or algorithms to ease the implementation, evaluation, and dissemination of both existing and new bandit algorithms and policies.
Author: Robin van Emden [aut, cre] (<https://orcid.org/0000-0001-5820-8638>), Maurits Kaptein [ctb] (<https://orcid.org/0000-0002-6316-7524>)
Maintainer: Robin van Emden <robinvanemden@gmail.com>

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Package genBaRcode updated to version 1.2.0 with previous version 1.1.0 dated 2018-08-10

Title: Analysis and Visualization Tools for Genetic Barcode Data
Description: Provides the necessary functions to identify and extract a selection of already available barcode constructs (Cornils, K. et al. (2014) <doi:10.1093/nar/gku081>) and freely choosable barcode designs from next generation sequence (NGS) data. Furthermore, it offers the possibility to account for sequence errors, the calculation of barcode similarities and provides a variety of visualisation tools (Thielecke, L. et al. (2017) <doi:10.1038/srep43249>).
Author: Lars Thielecke <lars.thielecke@tu-dresden.de>
Maintainer: Lars Thielecke <lars.thielecke@tu-dresden.de>

Diff between genBaRcode versions 1.1.0 dated 2018-08-10 and 1.2.0 dated 2019-07-08

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Package EpiEstim updated to version 2.2-1 with previous version 1.1-2 dated 2013-03-08

Title: Estimate Time Varying Reproduction Numbers from Epidemic Curves
Description: Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.
Author: Anne Cori [aut, cre] (<https://orcid.org/0000-0002-8443-9162>), Simon Cauchemez [ctb], Neil M. Ferguson [ctb] (<https://orcid.org/0000-0002-1154-8093>), Christophe Fraser [ctb] (<https://orcid.org/0000-0003-2399-9657>), Elisabeth Dahlqwist [ctb] (<https://orcid.org/0000-0001-5797-6803>), P. Alex Demarsh [ctb], Thibaut Jombart [ctb] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>), Justin Lessler [ctb] (<https://orcid.org/0000-0002-9741-8109>), Shikun Li [ctb], Jonathan A. Polonsky [ctb] (<https://orcid.org/0000-0002-8634-4255>), Jake Stockwin [ctb], Robin Thompson [ctb] (<https://orcid.org/0000-0001-8545-5212>), Rolina van Gaalen [ctb]
Maintainer: Anne Cori <a.cori@imperial.ac.uk>

Diff between EpiEstim versions 1.1-2 dated 2013-03-08 and 2.2-1 dated 2019-07-08

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Package detrendr updated to version 0.6.4 with previous version 0.6.3 dated 2019-06-29

Title: Detrend Images
Description: Detrend fluorescence microscopy image series for fluorescence fluctuation and correlation spectroscopy ('FCS' and 'FFS') analysis. This package contains functionality published in a 2016 paper <doi:10.1093/bioinformatics/btx434> but it has been extended since then with the Robin Hood algorithm and thus contains unpublished work.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>), Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>), Sergi Padilla-Parra [ctb, ths, cph] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between detrendr versions 0.6.3 dated 2019-06-29 and 0.6.4 dated 2019-07-08

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Package dbparser updated to version 1.0.2 with previous version 1.0.1 dated 2019-04-16

Title: 'DrugBank' Database XML Parser
Description: This tool is for parsing the 'DrugBank' XML database <http://drugbank.ca/>. The parsed data are then returned in a proper 'R' dataframe with the ability to save them in a given database.
Author: Mohammed Ali [aut, cre], Ali Ezzat [aut]
Maintainer: Mohammed Ali <moh_fcis@yahoo.com>

Diff between dbparser versions 1.0.1 dated 2019-04-16 and 1.0.2 dated 2019-07-08

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Package GWmodel updated to version 2.1-2 with previous version 2.1-1 dated 2019-07-03

Title: Geographically-Weighted Models
Description: In GWmodel, we introduce techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. GWmodel includes functions to calibrate: GW summary statistics, GW principal components analysis, GW discriminant analysis and various forms of GW regression; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Daisuke Murakami[aut],Isabella Gollini[ctb]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>

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Package EmpiricalCalibration updated to version 2.0.0 with previous version 1.4.0 dated 2018-11-24

Title: Routines for Performing Empirical Calibration of Observational Study Estimates
Description: Routines for performing empirical calibration of observational study estimates. By using a set of negative control hypotheses we can estimate the empirical null distribution of a particular observational study setup. This empirical null distribution can be used to compute a calibrated p-value, which reflects the probability of observing an estimated effect size when the null hypothesis is true taking both random and systematic error into account. A similar approach can be used to calibrate confidence intervals, using both negative and positive controls.
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

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Package fastICA updated to version 1.2-2 with previous version 1.2-1 dated 2017-06-12

Title: FastICA Algorithms to Perform ICA and Projection Pursuit
Description: Implementation of FastICA algorithm to perform Independent Component Analysis (ICA) and Projection Pursuit.
Author: J L Marchini, C Heaton and B D Ripley <ripley@stats.ox.ac.uk>
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package econetwork updated to version 0.2 with previous version 0.1 dated 2019-01-11

Title: Analyzing Ecological Networks
Description: A collection of advanced tools, methods and models specifically designed for analyzing different types of ecological networks - especially antagonistic (food webs, host-parasite), mutualistic (plant-pollinator, plant-fungus, etc) and competitive networks, as well as their variability in time and space. Statistical models are developed to describe and understand the mechanisms that determine species interactions, and to decipher the organization of these (multi-layer) ecological networks.
Author: Stephane Dray [ctb], Catherine Matias [ctb], Vincent Miele [aut, cre], Marc Ohlmann [aut], Wilfried Thuiller [ctb]
Maintainer: Vincent Miele <vincent.miele@univ-lyon1.fr>

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Package ClustBlock updated to version 2.0.0 with previous version 1.0.0 dated 2019-03-06

Title: Clustering of Datasets
Description: Hierarchical and partitioning algorithms of blocks of variables. The partitioning algorithm includes an option called noise cluster to set aside atypical blocks of variables. The CLUSTATIS method (for quantitative blocks) (Llobell, Cariou, Vigneau, Labenne & Qannari (2018) <doi:10.1016/j.foodqual.2018.05.013>) and the CLUSCATA method (for Check-All-That-Apply data) (Llobell, Cariou, Vigneau, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2018.09.006>) are the core of this package.
Author: Fabien Llobell [aut, cre] (Oniris/XLSTAT), Evelyne Vigneau [ctb] (Oniris), Veronique Cariou [ctb] (Oniris), El Mostafa Qannari [ctb] (Oniris)
Maintainer: Fabien Llobell <fabien.llobell@oniris-nantes.fr>

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Package nandb updated to version 2.0.4 with previous version 2.0.3 dated 2019-06-28

Title: Number and Brightness Image Analysis
Description: Calculation of molecular number and brightness from fluorescence microscopy image series. The software was published in a 2016 paper <doi:10.1093/bioinformatics/btx434>. The seminal paper for the technique is Digman et al. 2008 <doi:10.1529/biophysj.107.114645>. A review of the technique was published in 2017 <doi:10.1016/j.ymeth.2017.12.001>.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>), Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>), Sergi Padilla-Parra [ctb, ths, cph] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package autothresholdr updated to version 1.3.5 with previous version 1.3.4 dated 2019-06-28

Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Algorithms for automatically finding appropriate thresholds for numerical data, with special functions for thresholding images. Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R users. See <http://imagej.net/Auto_Threshold> and Landini et al. (2017) <DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl] (<https://orcid.org/0000-0002-5239-4043>), Luis Alvarez [ctb] (<https://orcid.org/0000-0003-1316-1906>), Sergi Padilla-Parra [ctb, ths] (<https://orcid.org/0000-0002-8010-9481>), Gabriel Landini [ctb, cph] (<https://orcid.org/0000-0002-9689-0989>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Package AnalyzeFMRI updated to version 1.1-20 with previous version 1.1-19 dated 2019-06-26

Title: Functions for Analysis of fMRI Datasets Stored in the ANALYZE or NIFTI Format
Description: Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format. Note that the latest version of XQuartz seems to be necessary under MacOS.
Author: Pierre Lafaye De Micheaux [aut, cre], Jonathan L Marchini [aut]
Maintainer: Pierre Lafaye De Micheaux <lafaye@unsw.edu.au>

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Package swephR updated to version 0.2.1 with previous version 0.2.0 dated 2019-07-05

Title: High Precision Swiss Ephemeris
Description: The Swiss Ephemeris (version 2.08) is a high precision ephemeris based upon the DE431 ephemerides from NASA's JPL. It covers the time range 13201 BCE to 17191 CE. This package uses the semi-analytic theory by Steve Moshier. For faster and more accurate calculations, the compressed Swiss Ephemeris data is available in the 'swephRdata' package. To access this data package, run 'install.packages("swephRdata", repos = "https://rstub.github.io/drat/", type = "source")'. The size of the 'swephRdata' package is approximately 115 MB. The user can also use the original JPL DE431 data.
Author: Ralf Stubner [aut, cre], Victor Reijs [aut], Authors and copyright holder of the Swiss Ephemeris [aut, cph] (see LICENSE for details)
Maintainer: Ralf Stubner <ralf.stubner@gmail.com>

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Package ppgmmga updated to version 1.2 with previous version 1.1 dated 2019-06-03

Title: Projection Pursuit Based on Gaussian Mixtures and Evolutionary Algorithms
Description: Projection Pursuit (PP) algorithm for dimension reduction based on Gaussian Mixture Models (GMMs) for density estimation using Genetic Algorithms (GAs) to maximise an approximated negentropy index. For more details see Scrucca and Serafini (2019) <doi:10.1080/10618600.2019.1598871>.
Author: Alessio Serafini [aut, cre] (<https://orcid.org/0000-0002-8579-5695>), Luca Scrucca [aut] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Alessio Serafini <srf.alessio@gmail.com>

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Package manymodelr updated to version 0.2.2 with previous version 0.2.1 dated 2019-07-04

Title: Build and Tune Several Models
Description: Frequently one needs a convenient way to build and tune several models in one go.The goal is to provide a number of convenience functions useful in machine learning applications. It provides the ability to build, tune and obtain predictions of several models in one function. The models are built using 'caret' functions with easier to read syntax. Kuhn(2014) <arXiv:1405.6974v14>. Kuhn(2008) <doi10.18637/jss.v028.i05>. Chambers,J.M.(1992) <doi:10.1371/journal.pone.0053143>. Wilkinson,G.N. and Rogers, C. E. (1973) <doi:10.2307/2346786>.
Author: Nelson Gonzabato [aut, cre]
Maintainer: Nelson Gonzabato <gonzabato@hotmail.com>

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Package bzinb updated to version 1.0.3 with previous version 1.0.1 dated 2019-04-18

Title: Bivariate Zero-Inflated Negative Binomial Model Estimator
Description: Provides a maximum likelihood estimation of Bivariate Zero-Inflated Negative Binomial (BZINB) model or the nested model parameters. Also estimates the underlying correlation of the a pair of count data. See Cho, H., Liu, C., Preisser, J., and Wu, D. (In preparation) for details.
Author: Hunyong Cho, Chuwen Liu, Jinyoung Park, Di Wu
Maintainer: Hunyong Cho <hunycho@live.unc.edu>

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Package eplusr updated to version 0.10.3 with previous version 0.10.2 dated 2019-05-13

Title: A Toolkit for Using Whole Building Simulation Program 'EnergyPlus'
Description: A rich toolkit of using the whole building simulation program 'EnergyPlus'(<https://energyplus.net>), which enables programmatic navigation, modification of 'EnergyPlus' models and makes it less painful to do parametric simulations and analysis.
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>)
Maintainer: Hongyuan Jia <hongyuan.jia@bears-berkeley.sg>

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Package CeRNASeek updated to version 2.0 with previous version 1.0 dated 2019-04-04

Title: Identification and Analysis of ceRNA Regulation
Description: Provides several functions to identify and analyse miRNA sponge, including popular methods for identifying miRNA sponge interactions, two types of global ceRNA regulation prediction methods and four types of context-specific prediction methods( Li Y et al.(2017) <doi:10.1093/bib/bbx137>), which are based on miRNA-messenger RNA regulation alone, or by integrating heterogeneous data, respectively. In addition, this package provides several network analysis modules for viewing the constructed ceRNA-ceRNA network and analysis of the topological features.
Author: Mengying Zhang,Yongsheng Li,Juan Xu*,Xia Li*
Maintainer: Mengying Zhang <zhangmengying@hrbmu.edu.cn>

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More information about CeRNASeek at CRAN
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Package metR updated to version 0.4.0 with previous version 0.3.0 dated 2019-03-12

Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing with meteorological data in the tidy data framework. Extends 'ggplot2' for better plotting of scalar and vector fields and provides commonly used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>

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Package DSAIRM updated to version 0.8.2 with previous version 0.8.0 dated 2019-04-04

Title: Dynamical Systems Approach to Immune Response Modeling
Description: A collection of 'shiny' apps that allow for the simulation and exploration of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models. The development of this package was partially supported by NIH grant U19AI117891.
Author: Andreas Handel [aut, cre] (<https://orcid.org/0000-0002-4622-1146>), Yang Ge [ctb], Spencer Hall [ctb], Sina Solaimanpour [ctb], Henok Woldu [ctb]
Maintainer: Andreas Handel <ahandel@uga.edu>

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More information about DSAIRM at CRAN
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